Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold150
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1854615
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 196055 characters in sequence are not A, C, G, or T
File 2 of 6
Found at i:2340 original size:21 final size:21
Alignment explanation
Indices: 2316--2424 Score: 148
Period size: 21 Copynumber: 5.2 Consensus size: 21
2306 TATTTTATTC
* *
2316 ATATGCAATAGTAATATCATT
1 ATATGCAGTAGTAACATCATT
*
2337 ATATGCAGTGGTAACATCATT
1 ATATGCAGTAGTAACATCATT
* *
2358 ACATGCAGTGGTAACATCATT
1 ATATGCAGTAGTAACATCATT
*
2379 ATATGCAGTACTAACATCATT
1 ATATGCAGTAGTAACATCATT
2400 ATATGCAGT-GCTAACATCATT
1 ATATGCAGTAG-TAACATCATT
2421 ATAT
1 ATAT
2425 ACTGTTATTT
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
21 79 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (21 bp):
ATATGCAGTAGTAACATCATT
Found at i:2377 original size:42 final size:42
Alignment explanation
Indices: 2326--2485 Score: 158
Period size: 42 Copynumber: 3.8 Consensus size: 42
2316 ATATGCAATA
*
2326 GTAATATCATTATATGCAGTGGTAACATCATTACATGCAGTG
1 GTAACATCATTATATGCAGTGGTAACATCATTACATGCAGTG
** *
2368 GTAACATCATTATATGCAGTACTAACATCATTATATGCAGTG
1 GTAACATCATTATATGCAGTGGTAACATCATTACATGCAGTG
* * * ** ** * * * *
2410 CTAACATCATTATATACTGTTATTTCACCATTATATTCAGGG
1 GTAACATCATTATATGCAGTGGTAACATCATTACATGCAGTG
* * *
2452 GTAAAATCTTTATATGAAGTGGTAACATCATTAC
1 GTAACATCATTATATGCAGTGGTAACATCATTAC
2486 GTTATGTCGT
Statistics
Matches: 92, Mismatches: 26, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
42 92 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (42 bp):
GTAACATCATTATATGCAGTGGTAACATCATTACATGCAGTG
Found at i:2442 original size:63 final size:63
Alignment explanation
Indices: 2316--2485 Score: 178
Period size: 63 Copynumber: 2.7 Consensus size: 63
2306 TATTTTATTC
* * * * *
2316 ATATGCAATAGTAATATCATTATATGCAGTGGTAACATCATTACATGCAGTGGTAACATCATT
1 ATATGCAGTAGTAAAATCATTATATGCAGTGGTAACATCATTACATACAGTGATAACACCATT
* * * * * * **
2379 ATATGCAGTACTAACATCATTATATGCAGTGCTAACATCATTATATACTGTTATTTCACCATT
1 ATATGCAGTAGTAAAATCATTATATGCAGTGGTAACATCATTACATACAGTGATAACACCATT
* ** * *
2442 ATATTCAGGGGTAAAATCTTTATATGAAGTGGTAACATCATTAC
1 ATATGCAGTAGTAAAATCATTATATGCAGTGGTAACATCATTAC
2486 GTTATGTCGT
Statistics
Matches: 86, Mismatches: 21, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
63 86 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Consensus pattern (63 bp):
ATATGCAGTAGTAAAATCATTATATGCAGTGGTAACATCATTACATACAGTGATAACACCATT
Found at i:2802 original size:21 final size:21
Alignment explanation
Indices: 2776--3545 Score: 984
Period size: 21 Copynumber: 36.7 Consensus size: 21
2766 TTAGATGATT
2776 TTATTATATGCTGTGGGTCTA
1 TTATTATATGCTGTGGGTCTA
*
2797 TTATTATATGCTGTGGTTCTA
1 TTATTATATGCTGTGGGTCTA
*
2818 TAATTATATGCTGTGGGTCTA
1 TTATTATATGCTGTGGGTCTA
2839 TTATTATATGCTGTGGGTCTA
1 TTATTATATGCTGTGGGTCTA
2860 TTATTATATGCTGTGGGTCTA
1 TTATTATATGCTGTGGGTCTA
2881 TTATTATATGCTGTGGGTCTA
1 TTATTATATGCTGTGGGTCTA
*
2902 TTATTATATGCTGTGGTTCTA
1 TTATTATATGCTGTGGGTCTA
2923 TTATTATATGCTGTGGGTCTA
1 TTATTATATGCTGTGGGTCTA
*
2944 TAATTATATGCTGTGGGTCTA
1 TTATTATATGCTGTGGGTCTA
*
2965 TTATTATATGCTGTGGTTCTA
1 TTATTATATGCTGTGGGTCTA
* *
2986 TAATTATATGCTGTGGTTCTA
1 TTATTATATGCTGTGGGTCTA
3007 TTATTATATGCTGTGGGTCTA
1 TTATTATATGCTGTGGGTCTA
*
3028 TAATTATATGCTGTGGGTCTA
1 TTATTATATGCTGTGGGTCTA
*
3049 TTATTATATGCTGTGGTTCTA
1 TTATTATATGCTGTGGGTCTA
* *
3070 TAATTATATGCTGTGGTTCTA
1 TTATTATATGCTGTGGGTCTA
*
3091 TTATTATATGCTGTGGTTCTA
1 TTATTATATGCTGTGGGTCTA
* *
3112 TTCTTATATGCTGTGGATCTA
1 TTATTATATGCTGTGGGTCTA
3133 TTATTATATGCTGTGGGT-TCA
1 TTATTATATGCTGTGGGTCT-A
3154 --ATTATATGCTGTGGGT-TCA
1 TTATTATATGCTGTGGGTCT-A
*
3173 TAATTATATGCTGTGGGTCTA
1 TTATTATATGCTGTGGGTCTA
*
3194 TTATTATATGTTGTGGGTCTA
1 TTATTATATGCTGTGGGTCTA
*
3215 TTGTTATATGCTGTGGGT-TCA
1 TTATTATATGCTGTGGGTCT-A
* *
3236 TAATTATATGCTGT-GGTTTCA
1 TTATTATATGCTGTGGGTCT-A
*
3257 TTATTATATGCTGT-GGTTTCA
1 TTATTATATGCTGTGGGTCT-A
*
3278 TAATTATATGCTGTGGGT-TCA
1 TTATTATATGCTGTGGGTCT-A
*
3299 TTATTATATGCTGT-GGTTTCA
1 TTATTATATGCTGTGGGTCT-A
3320 TTATTATATGCTGTGGGT-TCA
1 TTATTATATGCTGTGGGTCT-A
3341 TTATTATATGCTGTGGGT-TCA
1 TTATTATATGCTGTGGGTCT-A
* *
3362 TAATTATATGCTGT-GGTTTCA
1 TTATTATATGCTGTGGGTCT-A
*
3383 TTATTATATGCTGT-GGTTTCA
1 TTATTATATGCTGTGGGTCT-A
3404 TTATTATATGCTGTGGGT-TCA
1 TTATTATATGCTGTGGGTCT-A
*
3425 TTATTATATGCTGT-GGTTTCA
1 TTATTATATGCTGTGGGTCT-A
3446 TTATTATATGCTGTGGGT-TCA
1 TTATTATATGCTGTGGGTCT-A
*
3467 TAATTATATGCTGTGGGT-TCA
1 TTATTATATGCTGTGGGTCT-A
3488 TTATTATATGCTGTGGGT-TCA
1 TTATTATATGCTGTGGGTCT-A
*
3509 TAATTATATGCTGTGGGTTCATAA
1 TTATTATATGCTGTGGG-TC-T-A
3533 TTA-TATATGCTGT
1 TTATTATATGCTGT
3546 CGTTTATTCG
Statistics
Matches: 696, Mismatches: 37, Indels: 30
0.91 0.05 0.04
Matches are distributed among these distances:
19 19 0.03
20 14 0.02
21 635 0.91
22 14 0.02
23 10 0.01
24 4 0.01
ACGTcount: A:0.21, C:0.09, G:0.22, T:0.48
Consensus pattern (21 bp):
TTATTATATGCTGTGGGTCTA
Found at i:4571 original size:21 final size:20
Alignment explanation
Indices: 4545--5055 Score: 603
Period size: 21 Copynumber: 24.4 Consensus size: 20
4535 ACGACAGCAT
*
4545 ATATAATTATGTACCCACAGC
1 ATATAATAATG-ACCCACAGC
*
4566 ATATAATTATGAACCCACAGC
1 ATATAATAATG-ACCCACAGC
4587 ATATAATAATGAACCCACAGC
1 ATATAATAATG-ACCCACAGC
4608 ATATAATAATGAACCCACAGC
1 ATATAATAATG-ACCCACAGC
*
4629 ATATAATAATGAAACCACAGC
1 ATATAATAATG-ACCCACAGC
*
4650 ATATAATAATGAAACCACAGC
1 ATATAATAATG-ACCCACAGC
*
4671 ATATAATTATGAACCCACAGC
1 ATATAATAATG-ACCCACAGC
*
4692 ATATAATAATGAAACCACAGC
1 ATATAATAATG-ACCCACAGC
4713 ATATAATAATGAACCCACAGC
1 ATATAATAATG-ACCCACAGC
4734 ATATAATAATAGACCCACAGC
1 ATATAATAAT-GACCCACAGC
4755 ATATAATAATAGACCCACAGC
1 ATATAATAAT-GACCCACAGC
*
4776 ATATAATTATGAACCCACAGC
1 ATATAATAATG-ACCCACAGC
4797 ATATAAT--TGAACCCACAGC
1 ATATAATAATG-ACCCACAGC
4816 ATATAATAATAGACCCACAGC
1 ATATAATAAT-GACCCACAGC
* *
4837 ATATAATTATAGAACCACAGC
1 ATATAATAAT-GACCCACAGC
*
4858 ATATAATAATAGAACCACAGC
1 ATATAATAAT-GACCCACAGC
* *
4879 ATATAATTATAGAACCACAGC
1 ATATAATAAT-GACCCACAGC
* * *
4900 ATATAATTATAAAACCACAGC
1 ATATAATAAT-GACCCACAGC
4921 ATATAATAATAGACCCACAGC
1 ATATAATAAT-GACCCACAGC
* *
4942 ATATAATTATAGAACCACAGC
1 ATATAATAAT-GACCCACAGC
4963 ATATAATAATAGACCCACAGC
1 ATATAATAAT-GACCCACAGC
*
4984 ATATAATTATAGACCCACAGC
1 ATATAATAAT-GACCCACAGC
* *
5005 ATATAATTATAGAACCACAGC
1 ATATAATAAT-GACCCACAGC
*
5026 ATATAATAAAAGACCCACAGC
1 ATATAAT-AATGACCCACAGC
5047 ATATAATAA
1 ATATAATAA
5056 AATCATCTAA
Statistics
Matches: 458, Mismatches: 26, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.04
20 3 0.01
21 433 0.95
22 3 0.01
ACGTcount: A:0.48, C:0.22, G:0.09, T:0.21
Consensus pattern (20 bp):
ATATAATAATGACCCACAGC
Found at i:4627 original size:63 final size:62
Alignment explanation
Indices: 4545--5055 Score: 671
Period size: 63 Copynumber: 8.1 Consensus size: 62
4535 ACGACAGCAT
* * *
4545 ATATAATTATGTACCCACAGCATATAATTATGAACCCACAGCATATAATAATGAACCCACAGC
1 ATATAATAATGAACCCACAGCATATAATAATGAA-CCACAGCATATAATAATGAACCCACAGC
*
4608 ATATAATAATGAACCCACAGCATATAATAATGAAACCACAGCATATAATAATGAAACCACAGC
1 ATATAATAATGAACCCACAGCATATAATAATG-AACCACAGCATATAATAATGAACCCACAGC
*
4671 ATATAATTATGAACCCACAGCATATAATAATGAAACCACAGCATATAATAATGAACCCACAGC
1 ATATAATAATGAACCCACAGCATATAATAATG-AACCACAGCATATAATAATGAACCCACAGC
* *
4734 ATATAATAAT-AGACCCACAGCATATAATAATAGACCCACAGCATATAATTATGAACCCACAGC
1 ATATAATAATGA-ACCCACAGCATATAATAAT-GAACCACAGCATATAATAATGAACCCACAGC
* *
4797 ATATAAT--TGAACCCACAGCATATAATAATAGACCCACAGCATATAATTATAGAA-CCACAGC
1 ATATAATAATGAACCCACAGCATATAATAAT-GAACCACAGCATATAATAAT-GAACCCACAGC
* * * *
4858 ATATAATAATAGAA-CCACAGCATATAATTATAGAACCACAGCATATAATTATAAAACCACAGC
1 ATATAATAAT-GAACCCACAGCATATAATAAT-GAACCACAGCATATAATAATGAACCCACAGC
*
4921 ATATAATAAT-AGACCCACAGCATATAATTATAGAACCACAGCATATAATAAT-AGACCCACAGC
1 ATATAATAATGA-ACCCACAGCATATAATAAT-GAACCACAGCATATAATAATGA-ACCCACAGC
* * *
4984 ATATAATTAT-AGACCCACAGCATATAATTATAGAACCACAGCATATAATAA-AAGACCCACAGC
1 ATATAATAATGA-ACCCACAGCATATAATAAT-GAACCACAGCATATAATAATGA-ACCCACAGC
5047 ATATAATAA
1 ATATAATAA
5056 AATCATCTAA
Statistics
Matches: 419, Mismatches: 16, Indels: 26
0.91 0.03 0.06
Matches are distributed among these distances:
61 56 0.13
62 9 0.02
63 348 0.83
64 6 0.01
ACGTcount: A:0.48, C:0.22, G:0.09, T:0.21
Consensus pattern (62 bp):
ATATAATAATGAACCCACAGCATATAATAATGAACCACAGCATATAATAATGAACCCACAGC
Found at i:5330 original size:11 final size:11
Alignment explanation
Indices: 5310--5363 Score: 90
Period size: 11 Copynumber: 4.9 Consensus size: 11
5300 ATTTTTTTAA
5310 TGGCTTAAAGG
1 TGGCTTAAAGG
*
5321 TGGCTAAAAGG
1 TGGCTTAAAGG
*
5332 TAGCTTAAAGG
1 TGGCTTAAAGG
5343 TGGCTTAAAGG
1 TGGCTTAAAGG
5354 TGGCTTAAAG
1 TGGCTTAAAG
5364 AAGTTTGGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 39 1.00
ACGTcount: A:0.31, C:0.09, G:0.33, T:0.26
Consensus pattern (11 bp):
TGGCTTAAAGG
Found at i:5411 original size:11 final size:11
Alignment explanation
Indices: 5395--5423 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
5385 ATAAGTTGTC
5395 CTTAAAGGTGG
1 CTTAAAGGTGG
5406 CTTAAAGGTGG
1 CTTAAAGGTGG
5417 CTTAAAG
1 CTTAAAG
5424 ATAGTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:5454 original size:11 final size:11
Alignment explanation
Indices: 5440--5480 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
5430 TTTAAGCTGC
5440 CTTTAAGCCAT
1 CTTTAAGCCAT
* **
5451 CTTTACGCTTT
1 CTTTAAGCCAT
5462 CTTTAAGCCAT
1 CTTTAAGCCAT
5473 CTTTAAGC
1 CTTTAAGC
5481 AACACATATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.22, C:0.27, G:0.10, T:0.41
Consensus pattern (11 bp):
CTTTAAGCCAT
Found at i:5505 original size:11 final size:11
Alignment explanation
Indices: 5489--5520 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
5479 GCAACACATA
5489 TAGCTTAAAGG
1 TAGCTTAAAGG
5500 TAGCTTAAAGG
1 TAGCTTAAAGG
*
5511 TGGCTTAAAG
1 TAGCTTAAAG
5521 ATCGTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.28
Consensus pattern (11 bp):
TAGCTTAAAGG
Found at i:5551 original size:21 final size:21
Alignment explanation
Indices: 5525--5564 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5515 TTAAAGATCG
5525 TCTTTAAGCTACCTTTAAGCA
1 TCTTTAAGCTACCTTTAAGCA
*
5546 TCTTTAAGCTATCTTTAAG
1 TCTTTAAGCTACCTTTAAG
5565 GAGAACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (21 bp):
TCTTTAAGCTACCTTTAAGCA
Found at i:5552 original size:10 final size:11
Alignment explanation
Indices: 5525--5564 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
5515 TTAAAGATCG
5525 TCTTTAAGCTA
1 TCTTTAAGCTA
*
5536 CCTTTAAGC-A
1 TCTTTAAGCTA
5546 TCTTTAAGCTA
1 TCTTTAAGCTA
5557 TCTTTAAG
1 TCTTTAAG
5565 GAGAACTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (11 bp):
TCTTTAAGCTA
Found at i:8777 original size:4 final size:4
Alignment explanation
Indices: 8777--8823 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
8767 GTATATATAT
8777 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
8824 TATATATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:8828 original size:4 final size:4
Alignment explanation
Indices: 8821--8852 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
8811 AGATAGATAG
8821 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
8853 NNNNNNNNNN
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:8852 original size:8 final size:8
Alignment explanation
Indices: 8768--8851 Score: 87
Period size: 8 Copynumber: 10.5 Consensus size: 8
8758 TGTAAACGTG
*
8768 TATATATA
1 TATAGATA
8776 TATAGATA
1 TATAGATA
*
8784 GATAGATA
1 TATAGATA
*
8792 GATAGATA
1 TATAGATA
*
8800 GATAGATA
1 TATAGATA
*
8808 GATAGATA
1 TATAGATA
*
8816 GATAGATA
1 TATAGATA
*
8824 TATATATA
1 TATAGATA
*
8832 TATATATA
1 TATAGATA
*
8840 TATATATA
1 TATAGATA
8848 TATA
1 TATA
8852 TNNNNNNNNN
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (8 bp):
TATAGATA
Found at i:8852 original size:12 final size:12
Alignment explanation
Indices: 8773--8851 Score: 95
Period size: 12 Copynumber: 6.6 Consensus size: 12
8763 ACGTGTATAT
8773 ATATATAGATAG
1 ATATATAGATAG
*
8785 ATAGATAGATAG
1 ATATATAGATAG
*
8797 ATAGATAGATAG
1 ATATATAGATAG
*
8809 ATAGATAGATAG
1 ATATATAGATAG
* *
8821 ATATATATATAT
1 ATATATAGATAG
* *
8833 ATATATATATAT
1 ATATATAGATAG
8845 ATATATA
1 ATATATA
8852 TNNNNNNNNN
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.35
Consensus pattern (12 bp):
ATATATAGATAG
Found at i:10615 original size:2 final size:2
Alignment explanation
Indices: 10608--10639 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
10598 NNNNNNNNAC
*
10608 AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10640 TAGTGTGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:16136 original size:1 final size:1
Alignment explanation
Indices: 16130--16158 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
16120 CTTGGTCTTG
16130 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
16159 GGTTCTGGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:26089 original size:11 final size:11
Alignment explanation
Indices: 26073--26098 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
26063 TAATTAAGGT
26073 TTCAATAAACA
1 TTCAATAAACA
26084 TTCAATAAACA
1 TTCAATAAACA
26095 TTCA
1 TTCA
26099 CATCTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (11 bp):
TTCAATAAACA
Found at i:39407 original size:4 final size:4
Alignment explanation
Indices: 39398--41968 Score: 5101
Period size: 4 Copynumber: 643.0 Consensus size: 4
39388 AGATTCAATA
39398 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
*
39446 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG A-TCT A-TG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGT-G AGTG AGTG AGTG
39493 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
39541 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
39589 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
39637 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
39685 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
39733 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
39781 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
39829 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
39877 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
39925 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
39973 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40021 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40069 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40117 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40165 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40213 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40261 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40309 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40357 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40405 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40453 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40501 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40549 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40597 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40645 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40693 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40741 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40789 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40837 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40885 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40933 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
40981 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
41029 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
*
41077 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGGG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
41125 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
41173 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
41221 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
41269 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
41317 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
41365 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
41413 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
41461 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
41509 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
41557 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
41605 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
41653 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
41701 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
41749 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
41797 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
41845 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
41893 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG
41941 AGTG AGTG AGTG AGTG AGTG AGTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG
41969 CGCGATTAAT
Statistics
Matches: 2561, Mismatches: 4, Indels: 4
1.00 0.00 0.00
Matches are distributed among these distances:
3 2 0.00
4 2559 1.00
ACGTcount: A:0.25, C:0.00, G:0.50, T:0.25
Consensus pattern (4 bp):
AGTG
Found at i:42110 original size:17 final size:18
Alignment explanation
Indices: 42088--42124 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
42078 AGAATATAAA
42088 CAACAAAGAT-ACAAT-TG
1 CAACAAA-ATAACAATGTG
42105 CAACAAAATAACAATGTG
1 CAACAAAATAACAATGTG
42123 CA
1 CA
42125 TGTACATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.11
17 12 0.67
18 4 0.22
ACGTcount: A:0.54, C:0.19, G:0.11, T:0.16
Consensus pattern (18 bp):
CAACAAAATAACAATGTG
Found at i:45194 original size:3 final size:3
Alignment explanation
Indices: 45186--45306 Score: 217
Period size: 3 Copynumber: 40.7 Consensus size: 3
45176 TTAGTATTCT
45186 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
45234 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
45282 GAA GAA AAA GAA AAA G-A GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
45307 TACATTAACA
Statistics
Matches: 113, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
2 2 0.02
3 111 0.98
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:59004 original size:1 final size:1
Alignment explanation
Indices: 58998--59041 Score: 79
Period size: 1 Copynumber: 44.0 Consensus size: 1
58988 CATTGCTGCG
*
58998 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
59042 TCCTCCCGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.98, G:0.02, T:0.00
Consensus pattern (1 bp):
C
Found at i:59049 original size:18 final size:16
Alignment explanation
Indices: 59000--59053 Score: 81
Period size: 16 Copynumber: 3.2 Consensus size: 16
58990 TTGCTGCGCC
*
59000 CCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCG
59016 CCCCCCCCCCCCCCCG
1 CCCCCCCCCCCCCCCG
59032 CCCCCCCCCCTCCTCCCG
1 CCCCCCCCCC-CC-CCCG
59050 CCCC
1 CCCC
59054 GCTGACAGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
16 25 0.71
17 2 0.06
18 8 0.23
ACGTcount: A:0.00, C:0.93, G:0.04, T:0.04
Consensus pattern (16 bp):
CCCCCCCCCCCCCCCG
Found at i:61601 original size:23 final size:22
Alignment explanation
Indices: 61564--61625 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
61554 ATGGTTCTCG
*
61564 CACGCTTTG-CTCGAAACGATTTA
1 CACGCTTTGTC-CGAAACG-TCTA
* *
61587 CATGCTTTGTCCGAAAC-TCTG
1 CACGCTTTGTCCGAAACGTCTA
61608 CACGCTTTGTCCGAAACG
1 CACGCTTTGTCCGAAACG
61626 CTAAACGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
21 18 0.55
23 14 0.42
24 1 0.03
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (22 bp):
CACGCTTTGTCCGAAACGTCTA
Found at i:61643 original size:21 final size:21
Alignment explanation
Indices: 61619--61667 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
61609 ACGCTTTGTC
* *
61619 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGATTCACA
**
61640 CGAAACGCTTCACGATTCACA
1 CGAAACGCTAAACGATTCACA
61661 CGAAACG
1 CGAAACG
61668 GTTAACACGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.29, G:0.18, T:0.16
Consensus pattern (21 bp):
CGAAACGCTAAACGATTCACA
Found at i:67635 original size:2 final size:2
Alignment explanation
Indices: 67628--67680 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
67618 ATTGTTCCTT
67628 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
67670 GA GA GA GA GA G
1 GA GA GA GA GA G
67681 TAGTTGTTGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:79861 original size:58 final size:57
Alignment explanation
Indices: 79769--79885 Score: 216
Period size: 58 Copynumber: 2.0 Consensus size: 57
79759 CACGAATAGA
*
79769 CTTACATTTGTTTTTTGCAAAATATATGGAAAAATCTTTAACTTTTCGTTTTAAGAG
1 CTTACATTTGTTTTTTCCAAAATATATGGAAAAATCTTTAACTTTTCGTTTTAAGAG
79826 CTNTACATTTGTTTTTTCCAAAATATATGGAAAAATCTTTAACTTTTCGTTTTAAGAG
1 CT-TACATTTGTTTTTTCCAAAATATATGGAAAAATCTTTAACTTTTCGTTTTAAGAG
79884 CT
1 CT
79886 CCCATCTGTC
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
57 2 0.03
58 56 0.97
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.45
Consensus pattern (57 bp):
CTTACATTTGTTTTTTCCAAAATATATGGAAAAATCTTTAACTTTTCGTTTTAAGAG
Found at i:83505 original size:166 final size:166
Alignment explanation
Indices: 83231--84355 Score: 1563
Period size: 166 Copynumber: 6.8 Consensus size: 166
83221 GTGAATATGC
* * * * * * *
83231 AAAATAAGCAAAGTCGACATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCACG
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* * * *
83296 ATATGGCATGCCTTAACAAACACTGTGTAAAAATTTCAAGCATCTCCGATAAATAGCTGCTGAGA
66 ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
83361 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCAA
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCAA
* * * *
83397 AAAATAAACAAAGTCATTATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACA
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* * * * * *
83462 ATATGGCATGCCAAAACGAATAGTGTGTTAACATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
66 ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
*
83527 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCAA
* ** **
83563 AAAATAAACAAAGTCGTCATTTAACAGGAAGATGACACCCGATTGGTACCGAAATATATCCCACG
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* * * * *
83628 ATATGGCATGCCTATACAAATATTGTGTAAATATTTAAAGCATCT--GA-AAACAGTTGCTGAGA
66 ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
* *
83690 AATCTTTGAAGAAAATTTGTTTGAAAATTTTGGTTAA
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGG-CAA
* * * * *
83727 TAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGGCCGATTGATACAAAAATATATCCCACA
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* * * ** *
83792 ATATCGCATGCCTAAGCAAATAGTGTGTTTAAATTTCAAGCATCTGCGATAAATAGTTGTTGAGA
66 ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
* *
83857 ATTCTTTGGCGAAAATTTGTTTGAAAATTTTGGCAA
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCAA
* * ** * * *
83893 AAAATAAACAAAGTCGACATTTAACAGGACGTTGACGTCTAATTGGTACTAAAATACATCTCACG
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* * *
83958 ATATAGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAGA
66 ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
* * **
84023 ATTCTTTGACGGAAATTTGTTTGAAAATTTTGGCTT
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCAA
*
84059 AAATTAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* * *
84124 ATATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCAACTGCGATAAACAGTTGCTGAGA
66 ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
*
84189 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGG-CAA
* *
84226 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCATG
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* ** *
84291 ATATGGCATGCCTTAACAAGCACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
66 ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
84356 TAAATGCGAC
Statistics
Matches: 841, Mismatches: 113, Indels: 9
0.87 0.12 0.01
Matches are distributed among these distances:
163 45 0.05
164 96 0.11
166 537 0.64
167 163 0.19
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (166 bp):
AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCAA
Found at i:84216 original size:332 final size:330
Alignment explanation
Indices: 83231--84355 Score: 1587
Period size: 330 Copynumber: 3.4 Consensus size: 330
83221 GTGAATATGC
* * * *
83231 AAAATAAGCAAAGTCGACATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCACG
1 AAAATAAACAAAGTCGACATTTAACAGGAAGTTGACATCCGATTGGTACA-AAATATATCCCACG
* * *
83296 ATATGGCATGCCTTAACAAACACTGTGTAAAAATTTCAAGCATCTCCGATAAATAGCTGCTGAGA
65 ATATGGCATGCCTTAACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAGA
** * *
83361 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCAAAAAATAAACAAAGTCATTATTTAACAGGA
130 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTTAAAATAAACAAAGTCGTCATTTAACAGGA
* *
83426 AGTTGACGTCCGATTGATACAAAAATATATCCCACAATATGGCATGCCAAAACGAATAGTGTGTT
195 AGTTGACGTCCGATTGATACAAAAATATATCCCACAATATGGCATGCC-TAACAAATAGTGTGTT
* *
83491 AACATTTCAAGCATCTGCGATAAATAGCTGCTGAGAAATCTTTGACGAAAATTTGTTTGAAAATT
259 AAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAATCTTTGACGAAAATTTGTTTGAAAATT
*
83556 TTGGCTA
324 TTGGCAA
* * * *
83563 AAAATAAACAAAGTCGTCATTTAACAGGAAGATGACACCCGATTGGTACCGAAATATATCCCACG
1 AAAATAAACAAAGTCGACATTTAACAGGAAGTTGACATCCGATTGGTA-CAAAATATATCCCACG
* * * *
83628 ATATGGCATGCC-TATACAAATATTGTGTAAATATTTAAAGCATCT--GA-AAACAGTTGCTGAG
65 ATATGGCATGCCTTA-ACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAG
* *
83689 AAATCTTTGAAGAAAATTTGTTTGAAAATTTTGG-TTAATAAATAAGCAAAGTCGTCATTTAACA
129 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTT-A-AAATAAACAAAGTCGTCATTTAACA
* *
83753 GGAAGTTGACGGCCGATTGATACAAAAATATATCCCACAATATCGCATGCCTAAGCAAATAGTGT
192 GGAAGTTGACGTCCGATTGATACAAAAATATATCCCACAATATGGCATGCCTAA-CAAATAGTGT
* * * *
83818 GTTTAAATTTCAAGCATCTGCGATAAATAGTTGTTGAGAATTCTTTGGCGAAAATTTGTTTGAAA
256 GTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAATCTTTGACGAAAATTTGTTTGAAA
83883 ATTTTGGCAA
321 ATTTTGGCAA
* * ** * *
83893 AAAATAAACAAAGTCGACATTTAACAGGACGTTGACGTCTAATTGGTACTAAAATACATCTCACG
1 AAAATAAACAAAGTCGACATTTAACAGGAAGTTGACATCCGATTGGTAC-AAAATATATCCCACG
* *
83958 ATATAGCATGCC-TATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAG
65 ATATGGCATGCCTTA-ACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAG
* * *
84022 AATTCTTTGACGGAAATTTGTTTGAAAATTTTGGCTTAAATTAAACAAAGTCGTCATTTAACAGG
129 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTTAAAATAAACAAAGTCGTCATTTAACAGG
* * *
84087 AAGTTGACGTCCGATTGGTACAAAAATATATCCCACGATATGGCATGCCTATACAAATACTGTGT
194 AAGTTGACGTCCGATTGATACAAAAATATATCCCACAATATGGCATGCCTA-ACAAATAGTGTGT
* * *
84152 AAAAATTTCAAGCAACTGCGATAAACAGTTGCTGAGAAATCTTTGACGAAAATTTGTTTGAAAAT
258 TAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAATCTTTGACGAAAATTTGTTTGAAAAT
*
84217 TTTGGTTAA
323 TTTGG-CAA
* * * *
84226 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCATG
1 AAAATAAACAAAGTCGACATTTAACAGGAAGTTGACATCCGATTGGTAC-AAAATATATCCCACG
* * *
84291 ATATGGCATGCCTTAACAAGCACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
65 ATATGGCATGCCTTAACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAGA
84356 TAAATGCGAC
Statistics
Matches: 704, Mismatches: 76, Indels: 25
0.87 0.09 0.03
Matches are distributed among these distances:
329 49 0.07
330 244 0.35
331 2 0.00
332 242 0.34
333 163 0.23
334 4 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (330 bp):
AAAATAAACAAAGTCGACATTTAACAGGAAGTTGACATCCGATTGGTACAAAATATATCCCACGA
TATGGCATGCCTTAACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAGAA
ATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTTAAAATAAACAAAGTCGTCATTTAACAGGAA
GTTGACGTCCGATTGATACAAAAATATATCCCACAATATGGCATGCCTAACAAATAGTGTGTTAA
AATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAATCTTTGACGAAAATTTGTTTGAAAATTTT
GGCAA
Found at i:84407 original size:20 final size:20
Alignment explanation
Indices: 84382--84424 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
84372 TTTTGTTACG
84382 GACGGACAGACAGACAGACA
1 GACGGACAGACAGACAGACA
* *
84402 GACGGACGGACGGACAGACA
1 GACGGACAGACAGACAGACA
84422 GAC
1 GAC
84425 ACACAAGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.26, G:0.35, T:0.00
Consensus pattern (20 bp):
GACGGACAGACAGACAGACA
Found at i:84408 original size:24 final size:24
Alignment explanation
Indices: 84379--84425 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
84369 AATTTTTGTT
84379 ACGGACGGACAGACAGACAGACAG
1 ACGGACGGACAGACAGACAGACAG
*
84403 ACGGACGGACGGACAGACAGACA
1 ACGGACGGACAGACAGACAGACA
84426 CACAAGGGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.26, G:0.34, T:0.00
Consensus pattern (24 bp):
ACGGACGGACAGACAGACAGACAG
Found at i:84421 original size:4 final size:4
Alignment explanation
Indices: 84386--84425 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
84376 GTTACGGACG
* * *
84386 GACA GACA GACA GACA GACG GACG GACG GACA GACA GACA
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA
84426 CACAAGGGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.42, C:0.25, G:0.33, T:0.00
Consensus pattern (4 bp):
GACA
Found at i:88699 original size:168 final size:168
Alignment explanation
Indices: 88386--89321 Score: 1175
Period size: 168 Copynumber: 5.6 Consensus size: 168
88376 TTCATATCCA
* * * * *
88386 TGAAATCCATGATCCCTGGGTCAGGAGTTCAGGCTCTAGGGT-GAGGCCAACT-TGGCCATATAG
1 TGAAATTCATGACCCCTGAGTCAGGGGTTCAGGCTCTAGGGTAG-GGCCAA-TATGGCCACATAG
* *
88449 TAAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTTAAAAACTAAA
64 TAAAAACGAATTAAATCTTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTTAAAAACTAAA
* * * *
88514 TGCCTGGTTAAGATGTCCCTGAGGCCCTCTTCCAAAATTG
129 TGCCTGGTTATGATGTCCATGAAGCCCTCTACCAAAATTG
* * * *
88554 CGAAATTCATGACCCCTGAGTCAGGGGTTCAGGCACTAGGGTAGGGCCAATATGGGCACAGAGTA
1 TGAAATTCATGACCCCTGAGTCAGGGGTTCAGGCTCTAGGGTAGGGCCAATATGGCCACATAGTA
* * * * * *
88619 ACAACGAATTTAATCTTTGAAAATCTTCTTCTCTACTACCACATAGATTTGTTAAAAACTAAATG
66 AAAACGAATTAAATCTTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTTAAAAACTAAATG
* * * *
88684 CATGATTATGATGTCCATGAAGCCCTGTACCTAAATTG
131 CCTGGTTATGATGTCCATGAAGCCCTCTACCAAAATTG
*
88722 TGAAATTCATGA--CC----TC-TGGG-TCAGGCTCTAGGGTAGGGCCAATATGGCC-CAATAGT
1 TGAAATTCATGACCCCTGAGTCAGGGGTTCAGGCTCTAGGGTAGGGCCAATATGGCCAC-ATAGT
* * * * *
88778 TAAAATGTATTGAATCTAAGAAAATCTTCTTCTCTACTCCCATATATATTTGTTAAAAACTAAAT
65 AAAAACGAATTAAATCTTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTTAAAAACTAAAT
* *
88843 GCCTGGTTATGATGTCCATGAAGTCCTCTACTAAAATTG
130 GCCTGGTTATGATGTCCATGAAGCCCTCTACCAAAATTG
* * * * * * * * *
88882 GGAAATTCATGATCCCTGGGTCAGGAGTTCAGGCTCTAAGTTGGGGCTAACT-TGGCCATATAGT
1 TGAAATTCATGACCCCTGAGTCAGGGGTTCAGGCTCTAGGGTAGGGCCAA-TATGGCCACATAGT
* *
88946 AAAAA-TATATTAAATCTTAGAAAA---TCTTCTCTACTCCCATATATTTTTGTTAAAAACTAAA
65 AAAAACGA-ATTAAATCTTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTTAAAAACTAAA
*
89007 TGCCTGGTTATGATGTCCATGAAGCCCTCTACCAAAATAG
129 TGCCTGGTTATGATGTCCATGAAGCCCTCTACCAAAATTG
* * *
89047 TGAAATTCATGACCCCTGAGTAAGGGGTTCTGACTCTAGGGTAGGGCCAATATGGCCACATAGTA
1 TGAAATTCATGACCCCTGAGTCAGGGGTTCAGGCTCTAGGGTAGGGCCAATATGGCCACATAGTA
* * * *
89112 AAAACGAATTAAATCTTTGAAAATCTTCTTCTCTACTACCATATAGATTTGTTACAAACTAAATG
66 AAAACGAATTAAATCTTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTTAAAAACTAAATG
* * *
89177 CATGATTATGATGTCCATGAAGCCCTCTACCTAAATTG
131 CCTGGTTATGATGTCCATGAAGCCCTCTACCAAAATTG
* * *
89215 TGAAATTCATGACCCCTGAGTCACGGGGTTCATGCTCTAGGGTAGGGCCAATATGGCCCCATAGA
1 TGAAATTCATGACCCCTGAGTCA-GGGGTTCAGGCTCTAGGGTAGGGCCAATATGGCCACATAGT
*
89280 AAAAACGAATTAAATCTTTGAAAATCTTCTTCTCTACTCCCA
65 AAAAACGAATTAAATCTTAGAAAATCTTCTTCTCTACTCCCA
89322 CACATGTGGG
Statistics
Matches: 656, Mismatches: 92, Indels: 39
0.83 0.12 0.05
Matches are distributed among these distances:
159 1 0.00
160 130 0.20
161 3 0.00
162 4 0.01
164 1 0.00
165 143 0.22
166 5 0.01
167 3 0.00
168 287 0.44
169 79 0.12
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (168 bp):
TGAAATTCATGACCCCTGAGTCAGGGGTTCAGGCTCTAGGGTAGGGCCAATATGGCCACATAGTA
AAAACGAATTAAATCTTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTTAAAAACTAAATG
CCTGGTTATGATGTCCATGAAGCCCTCTACCAAAATTG
Found at i:89677 original size:46 final size:47
Alignment explanation
Indices: 89592--89682 Score: 166
Period size: 46 Copynumber: 1.9 Consensus size: 47
89582 TTGACTCTAG
89592 GGCAGGGCCAAAATGAATGAATATAGGTGTTAAAATGCATATAATTAT
1 GGCAGGGCCAAAATGAATG-ATATAGGTGTTAAAATGCATATAATTAT
89640 GGCAGGGCCAAAATGAATG-TATAGGTGTTAAAATGCATATAAT
1 GGCAGGGCCAAAATGAATGATATAGGTGTTAAAATGCATATAAT
89683 GTTAAAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 24 0.56
48 19 0.44
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (47 bp):
GGCAGGGCCAAAATGAATGATATAGGTGTTAAAATGCATATAATTAT
Found at i:90101 original size:22 final size:22
Alignment explanation
Indices: 90060--90101 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
90050 TTCCCTTGCA
*
90060 TTTTGTTGCTTATTTAAATTAT
1 TTTTGTTACTTATTTAAATTAT
* *
90082 TTTTGTTACTTGTTTTAATT
1 TTTTGTTACTTATTTAAATT
90102 CATTAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.05, G:0.10, T:0.67
Consensus pattern (22 bp):
TTTTGTTACTTATTTAAATTAT
Found at i:92603 original size:2 final size:2
Alignment explanation
Indices: 92596--92642 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
92586 AAGTTCTTAA
92596 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
92638 AG AG A
1 AG AG A
92643 ATACTAAACT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:93716 original size:249 final size:249
Alignment explanation
Indices: 93278--93774 Score: 976
Period size: 249 Copynumber: 2.0 Consensus size: 249
93268 AACTATTTAT
*
93278 GAGAGTCCATGGAATAACATACAGTCATGTCATTAACGAACCCAAAAGACCCCTGCATCTTGTGT
1 GAGAGTCCATGGAATAACATACAGTCATGTCATTAACGAACCCAAAAGACCCCTGCATCTTGCGT
93343 AAATAAGAAACTGGTAATTTAAAAACCATTCAGATTTTTTTTAACAATACAATACCAAGAATCCT
66 AAATAAGAAACTGGTAATTTAAAAACCATTCAGATTTTTTTTAACAATACAATACCAAGAATCCT
*
93408 CTGAAAGGAGGGCGTTCTAGTTATTTTTAAGTTCATGGTTAGATTACAGAGTAGCATAATTAAAA
131 CTGAAAGGAGGACGTTCTAGTTATTTTTAAGTTCATGGTTAGATTACAGAGTAGCATAATTAAAA
93473 AGATCTTCTCTTTAGAAAAAAATGACATTTTTTCTATGTAGATGCGTAGTGGGG
196 AGATCTTCTCTTTAGAAAAAAATGACATTTTTTCTATGTAGATGCGTAGTGGGG
93527 GAGAGTCCATGGAATAACATACAGTCATGTCATTAACGAACCCAAAAGACCCCTGCATCTTGCGT
1 GAGAGTCCATGGAATAACATACAGTCATGTCATTAACGAACCCAAAAGACCCCTGCATCTTGCGT
93592 AAATAAGAAACTGGTAATTTAAAAACCATTCAGATTTTTTTTAACAATACAATACCAAGAATCCT
66 AAATAAGAAACTGGTAATTTAAAAACCATTCAGATTTTTTTTAACAATACAATACCAAGAATCCT
93657 CTGAAAGGAGGACGTTCTAGTTATTTTTAAGTTCATGGTTAGATTACAGAGTAGCATAATTAAAA
131 CTGAAAGGAGGACGTTCTAGTTATTTTTAAGTTCATGGTTAGATTACAGAGTAGCATAATTAAAA
93722 AGATCTTCTCTTTAGAAAAAAATGACATTTTTTCTATGTAGATGCGTAGTGGG
196 AGATCTTCTCTTTAGAAAAAAATGACATTTTTTCTATGTAGATGCGTAGTGGG
93775 TTTTTTATGT
Statistics
Matches: 246, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
249 246 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (249 bp):
GAGAGTCCATGGAATAACATACAGTCATGTCATTAACGAACCCAAAAGACCCCTGCATCTTGCGT
AAATAAGAAACTGGTAATTTAAAAACCATTCAGATTTTTTTTAACAATACAATACCAAGAATCCT
CTGAAAGGAGGACGTTCTAGTTATTTTTAAGTTCATGGTTAGATTACAGAGTAGCATAATTAAAA
AGATCTTCTCTTTAGAAAAAAATGACATTTTTTCTATGTAGATGCGTAGTGGGG
Found at i:94303 original size:2 final size:2
Alignment explanation
Indices: 94296--94325 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
94286 TTCCTTAAAA
94296 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
94326 TATACTGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:98590 original size:18 final size:18
Alignment explanation
Indices: 98569--98616 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
98559 AGAGTTTGGA
98569 GCGGAGGAGACAGAGGAT
1 GCGGAGGAGACAGAGGAT
*
98587 GCGGGAGAAG-CAGAGGAT
1 GC-GGAGGAGACAGAGGAT
* *
98605 GAGCAGGAGACA
1 GCGGAGGAGACA
98617 CAGGGTAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 5 0.21
18 13 0.54
19 6 0.25
ACGTcount: A:0.35, C:0.12, G:0.48, T:0.04
Consensus pattern (18 bp):
GCGGAGGAGACAGAGGAT
Found at i:113293 original size:21 final size:21
Alignment explanation
Indices: 113264--113308 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
113254 GTAAAGTTCA
*
113264 AAACAAAATAGAAACGAAACG
1 AAACAAAATAAAAACGAAACG
*
113285 AAACGAAATAAAAACGAAACG
1 AAACAAAATAAAAACGAAACG
113306 AAA
1 AAA
113309 TCTACCGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.69, C:0.13, G:0.13, T:0.04
Consensus pattern (21 bp):
AAACAAAATAAAAACGAAACG
Found at i:115421 original size:2 final size:2
Alignment explanation
Indices: 115414--115443 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
115404 CAAATACAGA
115414 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
115444 ATATATATNG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:115582 original size:188 final size:187
Alignment explanation
Indices: 115265--115639 Score: 741
Period size: 188 Copynumber: 2.0 Consensus size: 187
115255 AATGGAGTTG
115265 GTTCGTTGTCCATATGTGGAAAGCGGGCTTTGAATTCTTTCACCTGCAAGCGAGAAAATAGATCA
1 GTTCGTTGTCCATATGTGGAAAGCGGGCTTTGAATTCTTTCACCTGCAAGCGAGAAAATAGATCA
115330 GCGGCTGTATTAGATATTCCTTGAATATGTTCAAACACTTGTTATATAAATAAAATTTGACACCG
66 GCGGCTGTATTAGATATTCCTTGAATATGTTCAAACACTTGTTATATAAATAAAATTTGACACCG
115395 ATAAAGGTGCAAATACAGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATATATAT
131 ATAAAGGTGCAAATACAGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATATATAT
115452 NGTTCGTTGTCCATATGTGGAAAGCGGGCTTTGAATTCTTTCACCTGCAAGCGAGAAAATAGATC
1 -GTTCGTTGTCCATATGTGGAAAGCGGGCTTTGAATTCTTTCACCTGCAAGCGAGAAAATAGATC
115517 AGCGGCTGTATTAGATATTCCTTGAATATGTTCAAACACTTGTTATATAAATAAAATTTGACACC
65 AGCGGCTGTATTAGATATTCCTTGAATATGTTCAAACACTTGTTATATAAATAAAATTTGACACC
115582 GATAAAGGTGCAAATACAGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATATATAT
130 GATAAAGGTGCAAATACAGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATATATAT
115640 NNNNNNNNNN
Statistics
Matches: 187, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
188 187 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (187 bp):
GTTCGTTGTCCATATGTGGAAAGCGGGCTTTGAATTCTTTCACCTGCAAGCGAGAAAATAGATCA
GCGGCTGTATTAGATATTCCTTGAATATGTTCAAACACTTGTTATATAAATAAAATTTGACACCG
ATAAAGGTGCAAATACAGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATATATAT
Found at i:115609 original size:2 final size:2
Alignment explanation
Indices: 115602--115631 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
115592 CAAATACAGA
115602 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
115632 ATATATATNN
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:125464 original size:2 final size:2
Alignment explanation
Indices: 125457--125502 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
125447 CAGTATAGGG
*
125457 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
125499 GA GA
1 GA GA
125503 AGAAGNNNNN
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:125969 original size:2 final size:2
Alignment explanation
Indices: 125962--126021 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
125952 NNNNNNNNNN
125962 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
126004 TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC
126022 CGTCCAATAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:130734 original size:1 final size:1
Alignment explanation
Indices: 130728--130765 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
130718 AAAGAATTTG
130728 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
130766 CTTAGCTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:134398 original size:2 final size:2
Alignment explanation
Indices: 134391--134438 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
134381 AAGTGACGTT
134391 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
134433 GA GA GA
1 GA GA GA
134439 ATGAATTATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:137662 original size:18 final size:18
Alignment explanation
Indices: 137639--137685 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
137629 AACAATATTT
137639 ATATTCAATAAACAGTAA
1 ATATTCAATAAACAGTAA
*
137657 ATATTCAATAAACAGTAT
1 ATATTCAATAAACAGTAA
137675 ATATTCAATAA
1 ATATTCAATAA
137686 GAACAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.32
Consensus pattern (18 bp):
ATATTCAATAAACAGTAA
Found at i:137763 original size:2 final size:2
Alignment explanation
Indices: 137756--137789 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
137746 ATTGACGAAC
137756 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
137790 TATTTCCTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:139112 original size:24 final size:24
Alignment explanation
Indices: 139085--139131 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
139075 ATAGGGAAAT
*
139085 AGGGATATATGGG-TATAGCGATAA
1 AGGGATATA-GGGACATAGCGATAA
139109 AGGGATATAGGGACATAGCGATA
1 AGGGATATAGGGACATAGCGATA
139132 CAATCTAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.38, C:0.06, G:0.34, T:0.21
Consensus pattern (24 bp):
AGGGATATAGGGACATAGCGATAA
Found at i:139897 original size:2 final size:2
Alignment explanation
Indices: 139890--139948 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
139880 AATAATAATA
*
139890 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
139932 AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG A
139949 ACATTATTAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:152625 original size:12 final size:11
Alignment explanation
Indices: 152608--152636 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
152598 CCCGTGCAGC
152608 AAAAAAAAAAT
1 AAAAAAAAAAT
152619 AAAAAAAAAAT
1 AAAAAAAAAAT
152630 AAAAAAA
1 AAAAAAA
152637 TTCTGCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (11 bp):
AAAAAAAAAAT
Found at i:153075 original size:41 final size:41
Alignment explanation
Indices: 153030--153127 Score: 160
Period size: 41 Copynumber: 2.4 Consensus size: 41
153020 TCTGTAAATT
* *
153030 TATCCTCAACAACAAATATATTATTCATCACTTACTACAAC
1 TATCCTCAACAACAAATATATCATTCATCACTTACCACAAC
*
153071 TATCCTCAACAGCAAATATATCATTCATCACTTACCACAAC
1 TATCCTCAACAACAAATATATCATTCATCACTTACCACAAC
*
153112 TATCCTAAACAACAAA
1 TATCCTCAACAACAAA
153128 AAATAATCAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.43, C:0.29, G:0.01, T:0.28
Consensus pattern (41 bp):
TATCCTCAACAACAAATATATCATTCATCACTTACCACAAC
Found at i:153239 original size:42 final size:42
Alignment explanation
Indices: 153193--153634 Score: 649
Period size: 42 Copynumber: 10.6 Consensus size: 42
153183 TTAAGAGGTT
* * *
153193 TATCCTAAACAACAAATAAAATGATTCATCAGTAAGTAAATC
1 TATCCTAAACAACAAATAAAATGATCCATCAGTTAGTAAAAC
*
153235 TATCCTAAACAAC--A-AAAATGATCCATCAGTTAGTAAATC
1 TATCCTAAACAACAAATAAAATGATCCATCAGTTAGTAAAAC
* *
153274 TATCCTAAACAACAAATAAAATGATTCATCAGTTAGTAAATC
1 TATCCTAAACAACAAATAAAATGATCCATCAGTTAGTAAAAC
*
153316 TATCCTAAACAACAAATAAAATGATCCATCAGTTAGTAAATC
1 TATCCTAAACAACAAATAAAATGATCCATCAGTTAGTAAAAC
*
153358 TAACCTAAACAACAAATAAAATGATCCATCAGTTAGTAAAAC
1 TATCCTAAACAACAAATAAAATGATCCATCAGTTAGTAAAAC
*
153400 TGTCCTAAACAACAAATAAAATGATCCATCAGTTAGTAAAAC
1 TATCCTAAACAACAAATAAAATGATCCATCAGTTAGTAAAAC
*
153442 TGTCCTAAACAACAAATAAAATGATCCATCAGTTAGTAAAAC
1 TATCCTAAACAACAAATAAAATGATCCATCAGTTAGTAAAAC
*
153484 TGTCCTAAACAACAAATAAAATGATCCATCAGTTAGTAAAAC
1 TATCCTAAACAACAAATAAAATGATCCATCAGTTAGTAAAAC
* *
153526 TGTCCTAAACAACAAATAAAATGATCAATCAGTTAGTAAAAC
1 TATCCTAAACAACAAATAAAATGATCCATCAGTTAGTAAAAC
* * ** * * *
153568 TATCCTGAACAGCAAATAAGTTCATCCATCAGTTCGTACATA-
1 TATCCTAAACAACAAATAAAATGATCCATCAGTTAGTA-AAAC
* *
153610 TATGCTATACAACAAATAAAATGAT
1 TATCCTAAACAACAAATAAAATGAT
153635 TTATTATCTA
Statistics
Matches: 371, Mismatches: 25, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
39 36 0.10
40 1 0.00
41 1 0.00
42 331 0.89
43 2 0.01
ACGTcount: A:0.48, C:0.19, G:0.09, T:0.25
Consensus pattern (42 bp):
TATCCTAAACAACAAATAAAATGATCCATCAGTTAGTAAAAC
Found at i:153991 original size:32 final size:32
Alignment explanation
Indices: 153945--154171 Score: 310
Period size: 32 Copynumber: 7.1 Consensus size: 32
153935 TGTATGGATC
*
153945 GTCATGTAAGTTGTTGATTGGTCAGATTATAA
1 GTCATGTAAGTTGTTGATTGGTCAGATTAAAA
* * * *
153977 GTCACGTAAGTTGTTGACTAGTCAGATTACAA
1 GTCATGTAAGTTGTTGATTGGTCAGATTAAAA
*
154009 GTCATGTAAGTTGTTGATTGATCAGATTAAAA
1 GTCATGTAAGTTGTTGATTGGTCAGATTAAAA
* ** *
154041 TTCACATAAGTTGTTGATTGATCAGATTAAAA
1 GTCATGTAAGTTGTTGATTGGTCAGATTAAAA
*
154073 GTCATGTAAGTTGTTGATTGGTCAGATAAAAA
1 GTCATGTAAGTTGTTGATTGGTCAGATTAAAA
*
154105 GTCATGTAAGTTGTTGATTGGTCAGATTACAA
1 GTCATGTAAGTTGTTGATTGGTCAGATTAAAA
* * * *
154137 GTCACGCAAGTTGTTGATTGGTCAGCTTACAA
1 GTCATGTAAGTTGTTGATTGGTCAGATTAAAA
154169 GTC
1 GTC
154172 TCACCAACGT
Statistics
Matches: 173, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 173 1.00
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.36
Consensus pattern (32 bp):
GTCATGTAAGTTGTTGATTGGTCAGATTAAAA
Found at i:157780 original size:2 final size:2
Alignment explanation
Indices: 157773--157809 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
157763 TGATTCTCAG
157773 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
157810 GTGTTAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:157874 original size:2 final size:2
Alignment explanation
Indices: 157867--157891 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
157857 ACAAGGGTTG
157867 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
157892 ACTTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:160484 original size:2 final size:2
Alignment explanation
Indices: 160477--160513 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
160467 TGATTCTCAG
160477 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
160514 GTGTTAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:160578 original size:2 final size:2
Alignment explanation
Indices: 160571--160595 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
160561 ACAAGGGTTG
160571 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
160596 ACTTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:175154 original size:33 final size:32
Alignment explanation
Indices: 175117--175208 Score: 114
Period size: 32 Copynumber: 2.8 Consensus size: 32
175107 GGAAAGCCCA
175117 CTATATA-CTCAGCTTTCCGTGGGGGAAAAACTG
1 CTATATAGC-CAGCTTTCCG-GGGGGAAAAACTG
** *
175150 CTATATAGCCATTTTTCCGGGGGGAAGAACTG
1 CTATATAGCCAGCTTTCCGGGGGGAAAAACTG
**
175182 CTATATAGCCATTTTTCCGGGGGGAAA
1 CTATATAGCCAGCTTTCCGGGGGGAAA
175209 GATGGCTAGG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
32 38 0.70
33 15 0.28
34 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (32 bp):
CTATATAGCCAGCTTTCCGGGGGGAAAAACTG
Found at i:175181 original size:32 final size:32
Alignment explanation
Indices: 175130--175208 Score: 140
Period size: 32 Copynumber: 2.4 Consensus size: 32
175120 TATACTCAGC
175130 TTTCCGTGGGGGAAAAACTGCTATATAGCCATT
1 TTTCCG-GGGGGAAAAACTGCTATATAGCCATT
*
175163 TTTCCGGGGGGAAGAACTGCTATATAGCCATT
1 TTTCCGGGGGGAAAAACTGCTATATAGCCATT
175195 TTTCCGGGGGGAAA
1 TTTCCGGGGGGAAA
175209 GATGGCTAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 38 0.86
33 6 0.14
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (32 bp):
TTTCCGGGGGGAAAAACTGCTATATAGCCATT
Found at i:179295 original size:52 final size:52
Alignment explanation
Indices: 179231--179335 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
179221 AAATAATAAT
* *
179231 AAAAAACATTACAATCTCTATAAGGTCTTCCGTTGGAAACGGAAGACCTTAA
1 AAAAAACATTACAATCACTATAAGGTCTTCCGTTGGAAACGGAAGACATTAA
*
179283 AAAAAACCTTACAATCACTATAAGGTCTTCCGTTGGAAACGGAAGACATTAA
1 AAAAAACATTACAATCACTATAAGGTCTTCCGTTGGAAACGGAAGACATTAA
179335 A
1 A
179336 TAGATCGGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (52 bp):
AAAAAACATTACAATCACTATAAGGTCTTCCGTTGGAAACGGAAGACATTAA
Found at i:181331 original size:12 final size:12
Alignment explanation
Indices: 181314--181339 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
181304 ATAAATGATG
181314 ATACTAATACCC
1 ATACTAATACCC
181326 ATACTAATACCC
1 ATACTAATACCC
181338 AT
1 AT
181340 CCCTTGTCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (12 bp):
ATACTAATACCC
Found at i:182049 original size:12 final size:12
Alignment explanation
Indices: 182032--182056 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
182022 TATTTTGTTC
182032 TCGACATCATGA
1 TCGACATCATGA
182044 TCGACATCATGA
1 TCGACATCATGA
182056 T
1 T
182057 ATATGTCAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (12 bp):
TCGACATCATGA
Found at i:183513 original size:2 final size:2
Alignment explanation
Indices: 183508--183553 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
183498 ACACATGCAC
*
183508 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AA AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
183549 AG AG A
1 AG AG A
183554 TTACCTGTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:190033 original size:2 final size:2
Alignment explanation
Indices: 190028--190088 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
190018 AGTGTGTTAT
190028 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
190070 GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA G
190089 TAGTTTCAGT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:191016 original size:2 final size:2
Alignment explanation
Indices: 191009--191072 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
190999 TGACTTGACT
191009 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
191051 GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA
191073 NNNNNNNNNN
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:192389 original size:2 final size:2
Alignment explanation
Indices: 192382--192430 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
192372 NNNNNNNNNN
192382 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
192424 CT CT CT C
1 CT CT CT C
192431 ATCACGTAGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:193631 original size:20 final size:21
Alignment explanation
Indices: 193588--193631 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
193578 ATACTATAGG
* *
193588 TACATTATGTCAAATTATCAT
1 TACATTATGTCAAAGTACCAT
193609 TACATTATGTCAAAGT-CCAT
1 TACATTATGTCAAAGTACCAT
193629 TAC
1 TAC
193632 GTGGTGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (21 bp):
TACATTATGTCAAAGTACCAT
Found at i:193861 original size:42 final size:41
Alignment explanation
Indices: 193815--193949 Score: 121
Period size: 42 Copynumber: 3.2 Consensus size: 41
193805 TTCGACACTG
* *
193815 TATTACATGGGACGAATGTATCCTTACATTATGTCAACATTT
1 TATTACATGCG-CGAATATATCCTTACATTATGTCAACATTT
* * * *
193857 TATTACATGCTTTC-AATATATCCTTACATTATATCAACACTG
1 TATTACATGC--GCGAATATATCCTTACATTATGTCAACATTT
* * * *
193899 CAGTACGTAT-CGCGATTCTATCCTTACATTATGTCAACATTT
1 TATTAC--ATGCGCGAATATATCCTTACATTATGTCAACATTT
193941 TATTACATG
1 TATTACATG
193950 ATATCAATGC
Statistics
Matches: 71, Mismatches: 16, Indels: 13
0.71 0.16 0.13
Matches are distributed among these distances:
40 2 0.03
41 1 0.01
42 64 0.90
43 2 0.03
44 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.39
Consensus pattern (41 bp):
TATTACATGCGCGAATATATCCTTACATTATGTCAACATTT
Found at i:194779 original size:21 final size:22
Alignment explanation
Indices: 194755--194800 Score: 85
Period size: 21 Copynumber: 2.1 Consensus size: 22
194745 ATTTAGTCTC
194755 AAAGTATTTAGTAGTTAAAA-T
1 AAAGTATTTAGTAGTTAAAAGT
194776 AAAGTATTTAGTAGTTAAAAGT
1 AAAGTATTTAGTAGTTAAAAGT
194798 AAA
1 AAA
194801 CGTTGCTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (22 bp):
AAAGTATTTAGTAGTTAAAAGT
Found at i:196103 original size:21 final size:21
Alignment explanation
Indices: 196077--196145 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
196067 TATTTACACC
*
196077 ATGTAATAAAGTGTTGATAAA
1 ATGTAATAAAGTGTTGATATA
*
196098 ATGTAA-AAA-TGCATTGATATC
1 ATGTAATAAAGTG--TTGATATA
*
196119 ATGTAATGAAAG-GTTGACATA
1 ATGTAAT-AAAGTGTTGATATA
196140 ATGTAA
1 ATGTAA
196146 GGATAGAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
19 2 0.05
20 3 0.08
21 30 0.77
23 4 0.10
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (21 bp):
ATGTAATAAAGTGTTGATATA
Found at i:196257 original size:84 final size:84
Alignment explanation
Indices: 196075--196269 Score: 201
Period size: 84 Copynumber: 2.3 Consensus size: 84
196065 TATATTTACA
* * * * * *
196075 CCATGTAATAAAGTGTTGATAAAATGTAAAAATGCATTGATATCATGTAATGAAAGGTTGACATA
1 CCATGTAATACAGTGTTGATATAATGTAAAAATACATTGAAAGCATGTAATAAAAGGTTGACATA
* * *
196140 ATGTAAGGATAGAATCGCG
66 ATATAAGGATACAATCGCC
** * * * ** * *
196159 ATACGTACTGCAGTGTTGATATAATGTAAGGATATATTGAAAGCATGTAATAAAATGTTGACATA
1 CCATGTAATACAGTGTTGATATAATGTAAAAATACATTGAAAGCATGTAATAAAAGGTTGACATA
*
196224 ATATAAGGATACATTCGCC
66 ATATAAGGATACAATCGCC
* *
196243 CCATGTAATACAGTGTCGAAATAATGT
1 CCATGTAATACAGTGTTGATATAATGT
196270 CATGATGTAT
Statistics
Matches: 85, Mismatches: 26, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (84 bp):
CCATGTAATACAGTGTTGATATAATGTAAAAATACATTGAAAGCATGTAATAAAAGGTTGACATA
ATATAAGGATACAATCGCC
Found at i:196461 original size:20 final size:21
Alignment explanation
Indices: 196436--196479 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
196426 TTCACACCAC
*
196436 GTAATGG-ACTTTGACATAAT
1 GTAATGGTAATTTGACATAAT
196456 GTAATGGTAATTTGACATAAT
1 GTAATGGTAATTTGACATAAT
196477 GTA
1 GTA
196480 CCTATAGTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.36
Consensus pattern (21 bp):
GTAATGGTAATTTGACATAAT
Found at i:197751 original size:21 final size:21
Alignment explanation
Indices: 197727--197769 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
197717 TAATTAGATA
197727 TTGAATCTCGAATTTCGAATC
1 TTGAATCTCGAATTTCGAATC
*
197748 TTGAATCTCGTATTTCGAATC
1 TTGAATCTCGAATTTCGAATC
197769 T
1 T
197770 CGTATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (21 bp):
TTGAATCTCGAATTTCGAATC
Found at i:197788 original size:14 final size:14
Alignment explanation
Indices: 197750--197776 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
197740 TTCGAATCTT
197750 GAATCTCGTATTTC
1 GAATCTCGTATTTC
197764 GAATCTCGTATTT
1 GAATCTCGTATTT
197777 TAAGTCTCGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (14 bp):
GAATCTCGTATTTC
Found at i:202299 original size:21 final size:21
Alignment explanation
Indices: 202275--202677 Score: 407
Period size: 21 Copynumber: 19.1 Consensus size: 21
202265 TCTACACTTT
202275 ACACTTTAATCTGTAAATTTC
1 ACACTTTAATCTGTAAATTTC
*
202296 ACACTTTAATCTGTAAAATTC
1 ACACTTTAATCTGTAAATTTC
* * ** *
202317 AAATTTTAAAGTGTAAAATTC
1 ACACTTTAATCTGTAAATTTC
*
202338 ACACTTTAATCTGTAAATTTT
1 ACACTTTAATCTGTAAATTTC
202359 ACACTTTAATCTGTAAATTTC
1 ACACTTTAATCTGTAAATTTC
* *
202380 ACACTTTAATGTTTGAAATTT-
1 ACACTTTAATCTGT-AAATTTC
202401 ACACTTTAATCTGTAAAATTT-
1 ACACTTTAATCTGT-AAATTTC
* * *
202422 ACACTTTAATCTATAACTTTT
1 ACACTTTAATCTGTAAATTTC
*
202443 ACCCTTTAATCTGTAAATTTC
1 ACACTTTAATCTGTAAATTTC
*
202464 ACACTTTAATCTGTAAATTTT
1 ACACTTTAATCTGTAAATTTC
* * *
202485 ACACTTCAATTTGTAAATTTA
1 ACACTTTAATCTGTAAATTTC
* *
202506 ACACTTTAATTTGTAAATTTT
1 ACACTTTAATCTGTAAATTTC
* * *
202527 ACAATTAAATCTGTAAATTTT
1 ACACTTTAATCTGTAAATTTC
* ** *
202548 ACACTTTACTCTAAAAAAATTC
1 ACACTTTAATCT-GTAAATTTC
* *
202570 ACACTTTGATCTGTAAATTTT
1 ACACTTTAATCTGTAAATTTC
* *
202591 ACACTTTAATATGTAAATTTT
1 ACACTTTAATCTGTAAATTTC
* ** *
202612 AAACTTTGTTCTGTAAATTTT
1 ACACTTTAATCTGTAAATTTC
*
202633 A-ACCTTTAATCTGTAAAATTC
1 ACA-CTTTAATCTGTAAATTTC
** *
202654 ACACTTTAAAATGTAAAATTC
1 ACACTTTAATCTGTAAATTTC
202675 ACA
1 ACA
202678 TTTTTTTATT
Statistics
Matches: 319, Mismatches: 58, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
20 6 0.02
21 291 0.91
22 22 0.07
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.43
Consensus pattern (21 bp):
ACACTTTAATCTGTAAATTTC
Found at i:203760 original size:21 final size:21
Alignment explanation
Indices: 203734--203777 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
203724 TATCAATTCT
203734 ATACTGTGTTACTGACTAGTG
1 ATACTGTGTTACTGACTAGTG
203755 ATACTGTGTTACTGACTAGTG
1 ATACTGTGTTACTGACTAGTG
203776 AT
1 AT
203778 TAAGAGGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.39
Consensus pattern (21 bp):
ATACTGTGTTACTGACTAGTG
Found at i:206276 original size:228 final size:228
Alignment explanation
Indices: 205879--206393 Score: 967
Period size: 228 Copynumber: 2.3 Consensus size: 228
205869 GATGATATCC
* *
205879 GATATGTTTTACTGTAAACAAACTACTGCAACTTATAAATACAGGTGAATCAATATTATATATAT
1 GATATGTTTTACTGTAAACAAACTACTGTAACTTATAAATACAGGTGAATCAATATAATATATAT
205944 GTATCACATGTACATATATCATATATATGTCATCAATTGATCATTCCGACAAAGATGGCAGGAAT
66 GTATCACATGTACATATATCATATATATGTCATCAATTGATCATTCCGACAAAGATGGCAGGAAT
* *
206009 TTTGAGATATAAAAATCTAGCATTGTTGAAATGTTTTGAGCCCATGTGTCATCTTTCAATATCCT
131 TTTGAGAAATAAAAATCTAACATTGTTGAAATGTTTTGAGCCCATGTGTCATCTTTCAATATCCT
206074 GACAATTTTCAAATCTACTAGAGTCCATATGAT
196 GACAATTTTCAAATCTACTAGAGTCCATATGAT
206107 GATATGTTTTACTGTAAACAAACTACTGTAACTTATAAATACAGGTGAATCAATATAATATATAT
1 GATATGTTTTACTGTAAACAAACTACTGTAACTTATAAATACAGGTGAATCAATATAATATATAT
* *
206172 GTATCACATGTATATATATCATGTATATGTCATCAATTGATCATTCCGACAAAGATGGCAGGAAT
66 GTATCACATGTACATATATCATATATATGTCATCAATTGATCATTCCGACAAAGATGGCAGGAAT
206237 TTTGAGAAATAAAAATCTAACATTGTTGAAATGTTTTGAGCCCATGTGTCATCTTTCAATATCCT
131 TTTGAGAAATAAAAATCTAACATTGTTGAAATGTTTTGAGCCCATGTGTCATCTTTCAATATCCT
206302 GACAATTTTCAAATCTACTAGAGTCCATATGAT
196 GACAATTTTCAAATCTACTAGAGTCCATATGAT
*
206335 GATATGTTTTACTGTAAACAAATTACTGTAACTTATAAATACAGGTGAATCAATATAAT
1 GATATGTTTTACTGTAAACAAACTACTGTAACTTATAAATACAGGTGAATCAATATAAT
206394 NNNNNNNNNN
Statistics
Matches: 280, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
228 280 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.35
Consensus pattern (228 bp):
GATATGTTTTACTGTAAACAAACTACTGTAACTTATAAATACAGGTGAATCAATATAATATATAT
GTATCACATGTACATATATCATATATATGTCATCAATTGATCATTCCGACAAAGATGGCAGGAAT
TTTGAGAAATAAAAATCTAACATTGTTGAAATGTTTTGAGCCCATGTGTCATCTTTCAATATCCT
GACAATTTTCAAATCTACTAGAGTCCATATGAT
Found at i:211242 original size:17 final size:16
Alignment explanation
Indices: 211217--211251 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
211207 CTGGCATGCG
211217 ACCAATTCTCGCCGAGT
1 ACCAATTCTCGCC-AGT
*
211234 ACCATTTCTCGCCAGT
1 ACCAATTCTCGCCAGT
211250 AC
1 AC
211252 ATTGTGACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.23, C:0.37, G:0.14, T:0.26
Consensus pattern (16 bp):
ACCAATTCTCGCCAGT
Found at i:219671 original size:2 final size:2
Alignment explanation
Indices: 219664--219743 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
219654 GTAAAATAAA
219664 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
219706 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
219744 GTTCTTTTAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:222382 original size:18 final size:19
Alignment explanation
Indices: 222349--222385 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
222339 ATGCTTTAAG
222349 TAGTATGCAATGTAAAATT
1 TAGTATGCAATGTAAAATT
*
222368 TAGTATGC-GTGTAAAATT
1 TAGTATGCAATGTAAAATT
222386 AGCATGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (19 bp):
TAGTATGCAATGTAAAATT
Found at i:225608 original size:21 final size:21
Alignment explanation
Indices: 225583--225642 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
225573 TGCGTCTTTT
225583 AACCCCAAGGAACCCCAAGGA
1 AACCCCAAGGAACCCCAAGGA
*
225604 AACCCCAAGGAACCTCAAGGA
1 AACCCCAAGGAACCCCAAGGA
*
225625 TACCCCAAGGAACCCCAA
1 AACCCCAAGGAACCCCAA
225643 TGACAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.42, C:0.38, G:0.17, T:0.03
Consensus pattern (21 bp):
AACCCCAAGGAACCCCAAGGA
Found at i:225609 original size:11 final size:10
Alignment explanation
Indices: 225583--225642 Score: 93
Period size: 10 Copynumber: 5.8 Consensus size: 10
225573 TGCGTCTTTT
225583 AACCCCAAGG
1 AACCCCAAGG
225593 AACCCCAAGG
1 AACCCCAAGG
225603 AAACCCCAAGG
1 -AACCCCAAGG
*
225614 AACCTCAAGG
1 AACCCCAAGG
225624 ATACCCCAAGG
1 A-ACCCCAAGG
225635 AACCCCAA
1 AACCCCAA
225643 TGACAAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
10 27 0.59
11 19 0.41
ACGTcount: A:0.42, C:0.38, G:0.17, T:0.03
Consensus pattern (10 bp):
AACCCCAAGG
Found at i:225722 original size:11 final size:11
Alignment explanation
Indices: 225706--225748 Score: 70
Period size: 11 Copynumber: 4.0 Consensus size: 11
225696 TCACCTCTTA
225706 GTACCCCAAGG
1 GTACCCCAAGG
225717 GTACCCCAAGG
1 GTACCCCAAGG
225728 GTACCCCAA-G
1 GTACCCCAAGG
*
225738 GAACCCCAAGG
1 GTACCCCAAGG
225749 AAACCCGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 9 0.30
11 21 0.70
ACGTcount: A:0.30, C:0.37, G:0.26, T:0.07
Consensus pattern (11 bp):
GTACCCCAAGG
Found at i:225731 original size:22 final size:21
Alignment explanation
Indices: 225706--225748 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
225696 TCACCTCTTA
*
225706 GTACCCCAAGGGTACCCCAAGG
1 GTACCCCAA-GGAACCCCAAGG
225728 GTACCCCAAGGAACCCCAAGG
1 GTACCCCAAGGAACCCCAAGG
225749 AAACCCGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.30, C:0.37, G:0.26, T:0.07
Consensus pattern (21 bp):
GTACCCCAAGGAACCCCAAGG
Found at i:225745 original size:10 final size:10
Alignment explanation
Indices: 225708--225774 Score: 55
Period size: 11 Copynumber: 6.4 Consensus size: 10
225698 ACCTCTTAGT
*
225708 ACCCCAAGGGT
1 ACCCCAA-GGA
*
225719 ACCCCAAGGGT
1 ACCCCAA-GGA
225730 ACCCCAAGGA
1 ACCCCAAGGA
225740 ACCCCAAGGAA
1 ACCCCAAGG-A
*
225751 ACCCGTAA-GA
1 ACCC-CAAGGA
*
225761 ACCCCATGGA
1 ACCCCAAGGA
225771 ACCC
1 ACCC
225775 AAATGATAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
9 1 0.02
10 22 0.45
11 24 0.49
12 2 0.04
ACGTcount: A:0.34, C:0.39, G:0.21, T:0.06
Consensus pattern (10 bp):
ACCCCAAGGA
Found at i:225753 original size:11 final size:11
Alignment explanation
Indices: 225708--225754 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
225698 ACCTCTTAGT
*
225708 ACCCCAAGGGT
1 ACCCCAAGGGA
*
225719 ACCCCAAGGGT
1 ACCCCAAGGGA
225730 ACCCCAA-GGA
1 ACCCCAAGGGA
*
225740 ACCCCAAGGAA
1 ACCCCAAGGGA
225751 ACCC
1 ACCC
225755 GTAAGAACCC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
10 9 0.27
11 24 0.73
ACGTcount: A:0.34, C:0.40, G:0.21, T:0.04
Consensus pattern (11 bp):
ACCCCAAGGGA
Found at i:225754 original size:21 final size:21
Alignment explanation
Indices: 225708--225771 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
225698 ACCTCTTAGT
* **
225708 ACCCCAAGGGTACCCCAAGGGT
1 ACCCCAA-GGAACCCCAAGGAA
225730 ACCCCAAGGAACCCCAAGGAA
1 ACCCCAAGGAACCCCAAGGAA
* *
225751 ACCCGTAA-GAACCCCATGGAA
1 ACCC-CAAGGAACCCCAAGGAA
225772 CCCAAATGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 27 0.75
22 9 0.25
ACGTcount: A:0.36, C:0.36, G:0.22, T:0.06
Consensus pattern (21 bp):
ACCCCAAGGAACCCCAAGGAA
Found at i:225940 original size:10 final size:11
Alignment explanation
Indices: 225913--225947 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
225903 CACCTCGTAG
225913 TACCCCAAGGA
1 TACCCCAAGGA
225924 TACCCCAAGGA
1 TACCCCAAGGA
*
225935 -ACCCCAAGTA
1 TACCCCAAGGA
225945 TAC
1 TAC
225948 TCATTAGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.37, C:0.37, G:0.14, T:0.11
Consensus pattern (11 bp):
TACCCCAAGGA
Found at i:231452 original size:173 final size:170
Alignment explanation
Indices: 231163--231856 Score: 1003
Period size: 173 Copynumber: 4.1 Consensus size: 170
231153 AGTTCCTTGA
* * * * *
231163 GGTATCCTTGGGGTTCTGTGGTGTAACAAGAGTTATGAATCTGTATTTTTAGGGTATTCTTGGAG
1 GGTATCCTTGGGGTTCTATGGAGTATCAAGAGTTATGATTCTGTATTATTAGGGTATTCTTGGAG
* * *
231228 TTCCTTGGGATATCCCTGGGGTTCCCTGGGATTCTTAGAAGCGTATCTGGAATACCAATGAGTCC
66 TTCCTTGGGATATCCCTGGGGTTCCCTGGGATTCCTAGAGGTGTATCTGGAATACCAATGAGTCC
* * *
231293 CCAGGGTTATCCAGAGTTTTAGATTTGTATTGCAGCGTATTAC
131 CCAGGGTTATCAAGAGTTTTAAATTTGTATT-CA--GTATTAG
* *
231336 GGTATCCTTGGGGTTCTATGGAGTATCAAGATTTATGATTCTGTATTATAAGGGTATTCTTGGAG
1 GGTATCCTTGGGGTTCTATGGAGTATCAAGAGTTATGATTCTGTATTATTAGGGTATTCTTGGAG
231401 TTCCTTGGGATATCCCTGGGGTTCCCTGGGATTCCTAGAGGTGTATCTGGAATACCAATGAGTCC
66 TTCCTTGGGATATCCCTGGGGTTCCCTGGGATTCCTAGAGGTGTATCTGGAATACCAATGAGTCC
* *
231466 CCAGGGTTATCAAAAGTTTTACATTTGTATTACAATGTATTAG
131 CCAGGGTTATCAAGAGTTTTAAATTTGTATT-C-A-GTATTAG
*
231509 GGTATCCTTGGGGTTCTATGGAGTATTAAGAGTTATGATTCTGTATTATTAGGGTATTCTTGGAG
1 GGTATCCTTGGGGTTCTATGGAGTATCAAGAGTTATGATTCTGTATTATTAGGGTATTCTTGGAG
*
231574 TTCCTTGGGATATCCATGGGGTTCCCTGGGATTCCTAGAGGTGTATCTGGAATACCAATGAGTCC
66 TTCCTTGGGATATCCCTGGGGTTCCCTGGGATTCCTAGAGGTGTATCTGGAATACCAATGAGTCC
*
231639 TCAGGGTTAAT-AAGAGTTTTAAATTTGTA-T---TATTAG
131 CCAGGGTT-ATCAAGAGTTTTAAATTTGTATTCAGTATTAG
231675 GGTATCCTTGGGGTTCTATGGAGTATCAAGAGTTATGATTCTGTATTATTAGGGTATTCTTGGAG
1 GGTATCCTTGGGGTTCTATGGAGTATCAAGAGTTATGATTCTGTATTATTAGGGTATTCTTGGAG
* * * *
231740 TTCCTTGGGATATCCCAGGGGTTCCCTGTGG-TTCTTAGAGGTGTGTCTGGAATACCAGTGAGTC
66 TTCCTTGGGATATCCCTGGGGTTCCCTG-GGATTCCTAGAGGTGTATCTGGAATACCAATGAGTC
* * * *
231804 CCCAGGGGTACCACGAGTTTAAAATTTGTA-TC---ATTAG
130 CCCAGGGTTATCAAGAGTTTTAAATTTGTATTCAGTATTAG
*
231841 GGTATCCTTGAGGTTC
1 GGTATCCTTGGGGTTC
231857 CTTGGGATTC
Statistics
Matches: 481, Mismatches: 35, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
165 1 0.00
166 170 0.35
167 2 0.00
172 1 0.00
173 304 0.63
174 3 0.01
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.36
Consensus pattern (170 bp):
GGTATCCTTGGGGTTCTATGGAGTATCAAGAGTTATGATTCTGTATTATTAGGGTATTCTTGGAG
TTCCTTGGGATATCCCTGGGGTTCCCTGGGATTCCTAGAGGTGTATCTGGAATACCAATGAGTCC
CCAGGGTTATCAAGAGTTTTAAATTTGTATTCAGTATTAG
Found at i:232043 original size:21 final size:21
Alignment explanation
Indices: 232019--232091 Score: 139
Period size: 21 Copynumber: 3.5 Consensus size: 21
232009 CATTGGAGTA
232019 TCCTTGGGGTTTCCTTGGGGT
1 TCCTTGGGGTTTCCTTGGGGT
232040 TCCTTGGGGTTTCCTTGGGGT
1 TCCTTGGGGTTTCCTTGGGGT
232061 TCCTTGGGG-TTCCTTGGGGT
1 TCCTTGGGGTTTCCTTGGGGT
232081 TCCTTGGGGTT
1 TCCTTGGGGTT
232092 AAAAGACGTG
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
20 20 0.39
21 31 0.61
ACGTcount: A:0.00, C:0.19, G:0.38, T:0.42
Consensus pattern (21 bp):
TCCTTGGGGTTTCCTTGGGGT
Found at i:232044 original size:10 final size:10
Alignment explanation
Indices: 232019--232091 Score: 128
Period size: 10 Copynumber: 7.1 Consensus size: 10
232009 CATTGGAGTA
232019 TCCTTGGGGTT
1 TCCTTGGGG-T
232030 TCCTTGGGGT
1 TCCTTGGGGT
232040 TCCTTGGGGTT
1 TCCTTGGGG-T
232051 TCCTTGGGGT
1 TCCTTGGGGT
232061 TCCTTGGGGT
1 TCCTTGGGGT
232071 TCCTTGGGGT
1 TCCTTGGGGT
232081 TCCTTGGGGT
1 TCCTTGGGGT
232091 T
1 T
232092 AAAAGACGTG
Statistics
Matches: 61, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
10 42 0.69
11 19 0.31
ACGTcount: A:0.00, C:0.19, G:0.38, T:0.42
Consensus pattern (10 bp):
TCCTTGGGGT
Found at i:235604 original size:1 final size:1
Alignment explanation
Indices: 235600--235783 Score: 359
Period size: 1 Copynumber: 184.0 Consensus size: 1
235590 GATTTTTTCT
235600 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
235665 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
235730 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
235784 TACCGTAACT
Statistics
Matches: 181, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
1 181 1.00
ACGTcount: A:0.99, C:0.00, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:240139 original size:16 final size:16
Alignment explanation
Indices: 240118--240149 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
240108 ATCCTTTAAT
240118 GTACATGTTGTAAAAC
1 GTACATGTTGTAAAAC
240134 GTACATGTTGTAAAAC
1 GTACATGTTGTAAAAC
240150 AGCTAATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (16 bp):
GTACATGTTGTAAAAC
Found at i:254874 original size:99 final size:99
Alignment explanation
Indices: 254704--254896 Score: 386
Period size: 99 Copynumber: 1.9 Consensus size: 99
254694 NNNNNNNNNN
254704 GGGGGGGGGGGTTCATTTAAAGAAAAACAAACTAAATTGTTATTGGTAACTATATATATTTAGGT
1 GGGGGGGGGGGTTCATTTAAAGAAAAACAAACTAAATTGTTATTGGTAACTATATATATTTAGGT
254769 AAATTTAAAATCATTAAAATGCATACATTTTTTG
66 AAATTTAAAATCATTAAAATGCATACATTTTTTG
254803 GGGGGGGGGGGTTCATTTAAAGAAAAACAAACTAAATTGTTATTGGTAACTATATATATTTAGGT
1 GGGGGGGGGGGTTCATTTAAAGAAAAACAAACTAAATTGTTATTGGTAACTATATATATTTAGGT
254868 AAATTTAAAATCATTAAAATGCATACATT
66 AAATTTAAAATCATTAAAATGCATACATT
254897 AAAATTACTG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 94 1.00
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.34
Consensus pattern (99 bp):
GGGGGGGGGGGTTCATTTAAAGAAAAACAAACTAAATTGTTATTGGTAACTATATATATTTAGGT
AAATTTAAAATCATTAAAATGCATACATTTTTTG
Found at i:257151 original size:16 final size:16
Alignment explanation
Indices: 257130--257160 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
257120 AGGACTTTTT
257130 GTTAACAAGCGTTACC
1 GTTAACAAGCGTTACC
257146 GTTAACAAGCGTTAC
1 GTTAACAAGCGTTAC
257161 TACTTAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (16 bp):
GTTAACAAGCGTTACC
Found at i:262792 original size:149 final size:149
Alignment explanation
Indices: 262521--262797 Score: 335
Period size: 149 Copynumber: 1.9 Consensus size: 149
262511 ACGCAGTTCA
* * * * * *
262521 TTGCAAATAAGCCCGAATCTCAAAAAGTAGAGATGATCTTTCCACTATATTTTCACAGTGGTAGT
1 TTGCAAATAAACCCGAATCTCAAAAACTAGAGATGACCCTTCCACCATATTTTCACAGTGGAAGT
* * * * * *
262586 GGTTTACTACTAGCAGATGGCTCTGAAAATTTCAGGCCCCAAATATGATTTAAAAATTTTGAACT
66 GGTATACTACTAGCAGATGACCCTGAAAATTTCAGGCACCAAATACGAATTAAAAATTTTGAACT
262651 GCAAACTGCGTTCTAGAAC
131 GCAAACTGCGTTCTAGAAC
262670 TTGCAAATAAACCCGAATCTCAAAAACTAGAGATGACCACTT-CACCAT-TTTCTCACAGTGGAA
1 TTGCAAATAAACCCGAATCTCAAAAACTAGAGATGACC-CTTCCACCATATTT-TCACAGTGGAA
* * * * * * *
262733 GTTGTATACCT-TTAGTAGATGACCCTGATAATTTCAGGTACCTAATACGAATTATAAATTTTGA
64 GTGGTATA-CTACTAGCAGATGACCCTGAAAATTTCAGGCACCAAATACGAATTAAAAATTTTGA
262797 A
128 A
262798 TTTATTAACT
Statistics
Matches: 106, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
148 3 0.03
149 99 0.93
150 4 0.04
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (149 bp):
TTGCAAATAAACCCGAATCTCAAAAACTAGAGATGACCCTTCCACCATATTTTCACAGTGGAAGT
GGTATACTACTAGCAGATGACCCTGAAAATTTCAGGCACCAAATACGAATTAAAAATTTTGAACT
GCAAACTGCGTTCTAGAAC
Found at i:273008 original size:2 final size:2
Alignment explanation
Indices: 272995--273054 Score: 68
Period size: 2 Copynumber: 30.0 Consensus size: 2
272985 AATATCTCAA
* * *
272995 TC TC TT TC TC TC TC TC TC TC TC TG TG TC TC TC AT- TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -TC TC TC TC TC
*
273037 TC TC TC TT TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC
273055 ATTCTTGGAC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.96
3 1 0.02
ACGTcount: A:0.02, C:0.42, G:0.03, T:0.53
Consensus pattern (2 bp):
TC
Found at i:274705 original size:15 final size:15
Alignment explanation
Indices: 274685--274715 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
274675 ACAACCTTAA
274685 AAAACAATAACCAAT
1 AAAACAATAACCAAT
274700 AAAACAATAACCAAT
1 AAAACAATAACCAAT
274715 A
1 A
274716 CAAAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.19, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAACAATAACCAAT
Found at i:275522 original size:25 final size:25
Alignment explanation
Indices: 275494--275564 Score: 68
Period size: 25 Copynumber: 3.2 Consensus size: 25
275484 GAATTTGCGA
275494 TATCAGTAACTGAATCATACAATAT
1 TATCAGTAACTGAATCATACAATAT
* *
275519 TATC--T-A-T-AAGCAT--GAT-T
1 TATCAGTAACTGAATCATACAATAT
275536 TATCAGTAACTGAATCATACAATAT
1 TATCAGTAACTGAATCATACAATAT
275561 TATC
1 TATC
275565 TATAAGCATG
Statistics
Matches: 34, Mismatches: 4, Indels: 16
0.63 0.07 0.30
Matches are distributed among these distances:
17 5 0.15
18 2 0.06
19 1 0.03
20 6 0.18
21 2 0.06
22 6 0.18
23 1 0.03
24 2 0.06
25 9 0.26
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.35
Consensus pattern (25 bp):
TATCAGTAACTGAATCATACAATAT
Found at i:275541 original size:42 final size:42
Alignment explanation
Indices: 275494--275590 Score: 176
Period size: 42 Copynumber: 2.3 Consensus size: 42
275484 GAATTTGCGA
275494 TATCAGTAACTGAATCATACAATATTATCTATAAGCATGATT
1 TATCAGTAACTGAATCATACAATATTATCTATAAGCATGATT
275536 TATCAGTAACTGAATCATACAATATTATCTATAAGCATGATT
1 TATCAGTAACTGAATCATACAATATTATCTATAAGCATGATT
* *
275578 TATCTGTATCTGA
1 TATCAGTAACTGA
275591 GATCGAGTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.37
Consensus pattern (42 bp):
TATCAGTAACTGAATCATACAATATTATCTATAAGCATGATT
Found at i:284059 original size:184 final size:184
Alignment explanation
Indices: 283750--284153 Score: 790
Period size: 184 Copynumber: 2.2 Consensus size: 184
283740 ACATAATGAT
283750 CACGACCAGTAAGAGGCTTAGCTAGCCTGGCGAAAAATGCGACATTTCGTATAATACAGTTATGA
1 CACGACCAGTAAGAGGCTTAGCTAGCCTGGCGAAAAATGCGACATTTCGTATAATACAGTTATGA
*
283815 TGGGATTTCTTTCAAAGGGCTGGGTAACAAACACCCTGTATCCCATATTTGGGCCTTCATATTTG
66 TGGGATTTCTTTCAAAGGGCTGGCTAACAAACACCCTGTATCCCATATTTGGGCCTTCATATTTG
283880 GTGGGGATGGGGCCCCGGGACAGCCCAGTCGACCCTCAAAAGGAATTGGGTTTA
131 GTGGGGATGGGGCCCCGGGACAGCCCAGTCGACCCTCAAAAGGAATTGGGTTTA
283934 CACGACCAGTAAGAGGCTTAGCTAGCCTGGCGAAAAATGCGACATTTCGTATAATACAGTTATGA
1 CACGACCAGTAAGAGGCTTAGCTAGCCTGGCGAAAAATGCGACATTTCGTATAATACAGTTATGA
*
283999 TGGGATTTCTTTCAAGGGGCTGGCTAACAAACACCCTGTATCCCATATTTGGGCCTTCATATTTG
66 TGGGATTTCTTTCAAAGGGCTGGCTAACAAACACCCTGTATCCCATATTTGGGCCTTCATATTTG
284064 GTGGGGATGGGGCCCCGGGACAGCCCAGTCGACCCTCAAAAGGAATTGGGTTTA
131 GTGGGGATGGGGCCCCGGGACAGCCCAGTCGACCCTCAAAAGGAATTGGGTTTA
284118 CACGACCAGTAAGAGGCTTAGCTAGCCTGGCGAAAA
1 CACGACCAGTAAGAGGCTTAGCTAGCCTGGCGAAAA
284154 NNNNNNNNNN
Statistics
Matches: 218, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
184 218 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (184 bp):
CACGACCAGTAAGAGGCTTAGCTAGCCTGGCGAAAAATGCGACATTTCGTATAATACAGTTATGA
TGGGATTTCTTTCAAAGGGCTGGCTAACAAACACCCTGTATCCCATATTTGGGCCTTCATATTTG
GTGGGGATGGGGCCCCGGGACAGCCCAGTCGACCCTCAAAAGGAATTGGGTTTA
Found at i:310444 original size:14 final size:15
Alignment explanation
Indices: 310400--310449 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 15
310390 TTTTAATGTC
310400 AACTAATATAGATACA
1 AACT-ATATAGATACA
310416 AACATTATAATAGATACA
1 AAC--TAT-ATAGATACA
310434 AAC-ATATAGATACA
1 AACTATATAGATACA
310448 AA
1 AA
310450 ATTCTATACT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
14 11 0.35
15 2 0.06
16 3 0.10
17 2 0.06
18 13 0.42
ACGTcount: A:0.58, C:0.12, G:0.06, T:0.24
Consensus pattern (15 bp):
AACTATATAGATACA
Found at i:316141 original size:26 final size:27
Alignment explanation
Indices: 316101--316157 Score: 107
Period size: 26 Copynumber: 2.1 Consensus size: 27
316091 ATTACTGACC
316101 AAAACACCCATCAGATAAACTATGTTT
1 AAAACACCCATCAGATAAACTATGTTT
316128 AAAACA-CCATCAGATAAACTATGTTT
1 AAAACACCCATCAGATAAACTATGTTT
316154 AAAA
1 AAAA
316158 AACACCTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 24 0.80
27 6 0.20
ACGTcount: A:0.49, C:0.19, G:0.07, T:0.25
Consensus pattern (27 bp):
AAAACACCCATCAGATAAACTATGTTT
Found at i:340625 original size:57 final size:57
Alignment explanation
Indices: 340536--340701 Score: 314
Period size: 57 Copynumber: 2.9 Consensus size: 57
340526 CACTTCAAGG
*
340536 ATGTTCGGTGCTTCAAAAAGTATGGATTTCTACATAGAAAAAATAGTATATTCGTACA
1 ATGTTAGGTGCTTC-AAAAGTATGGATTTCTACATAGAAAAAATAGTATATTCGTACA
340594 ATGTTAGGTGCTTCAAAAGTATGGATTTCTACATAGAAAAAATAGTATATTCGTACA
1 ATGTTAGGTGCTTCAAAAGTATGGATTTCTACATAGAAAAAATAGTATATTCGTACA
340651 ATGTTAGGTGCTTCAAAAGTATGGATTTCTACATAGAAAAAATAGTATATT
1 ATGTTAGGTGCTTCAAAAGTATGGATTTCTACATAGAAAAAATAGTATATT
340702 NNNNNNNNNN
Statistics
Matches: 107, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
57 94 0.88
58 13 0.12
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (57 bp):
ATGTTAGGTGCTTCAAAAGTATGGATTTCTACATAGAAAAAATAGTATATTCGTACA
Found at i:358549 original size:44 final size:45
Alignment explanation
Indices: 358481--358591 Score: 179
Period size: 44 Copynumber: 2.5 Consensus size: 45
358471 ATTGTATCAC
358481 AATCTGGCTCCATGCATCAGTTATCAGTTGCTACAAGTGTTTTTA
1 AATCTGGCTCCATGCATCAGTTATCAGTTGCTACAAGTGTTTTTA
* * * *
358526 AATTTGGCT-CATGCGTCAGTTATCAGTTGTTACACGTGTTTTTA
1 AATCTGGCTCCATGCATCAGTTATCAGTTGCTACAAGTGTTTTTA
358570 AATCTGGCTCCATGCATCAGTT
1 AATCTGGCTCCATGCATCAGTT
358592 TCTACATGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 40 0.68
45 19 0.32
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.39
Consensus pattern (45 bp):
AATCTGGCTCCATGCATCAGTTATCAGTTGCTACAAGTGTTTTTA
Found at i:358993 original size:2 final size:2
Alignment explanation
Indices: 358986--359054 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
358976 ACAGCTGTAC
358986 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
359028 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
359055 TTAAAATATC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:363738 original size:7 final size:7
Alignment explanation
Indices: 363726--363792 Score: 62
Period size: 7 Copynumber: 9.6 Consensus size: 7
363716 GAGAAGGGTC
363726 ATTCGAG
1 ATTCGAG
363733 ATTCGAG
1 ATTCGAG
* *
363740 ATTCCAA
1 ATTCGAG
*
363747 ATACGAG
1 ATTCGAG
*
363754 ATTCGAT
1 ATTCGAG
*
363761 ATACGAG
1 ATTCGAG
*
363768 ATTCAAG
1 ATTCGAG
*
363775 ATTCGAA
1 ATTCGAG
*
363782 ATTCAAG
1 ATTCGAG
363789 ATTC
1 ATTC
363793 AATATCTAAA
Statistics
Matches: 45, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.28
Consensus pattern (7 bp):
ATTCGAG
Found at i:364311 original size:2 final size:2
Alignment explanation
Indices: 364304--364347 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
364294 TTGTCGATAT
364304 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
364346 GA
1 GA
364348 TTGATTAAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:364983 original size:1 final size:1
Alignment explanation
Indices: 364977--365001 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
364967 GTGTGTGTGT
364977 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
365002 CTCGTGTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:370628 original size:4 final size:4
Alignment explanation
Indices: 370612--370648 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
370602 CTCTTCTATT
*
370612 ATCG ATTG ATCG ATCG ATCG ATCG ATCG ATCG ATCG A
1 ATCG ATCG ATCG ATCG ATCG ATCG ATCG ATCG ATCG A
370649 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (4 bp):
ATCG
Found at i:377056 original size:42 final size:42
Alignment explanation
Indices: 376992--377083 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
376982 CGTCATCTTC
* ** *
376992 ATAATCACAGCATAATTTAATAAGGCACCATCTTCACATGAA
1 ATAACCACAGCATAATAAAATAAAGCACCATCTTCACATGAA
**
377034 ATAACCACAGCATAATAAAATAAAGCACCATCTTCTTATGAA
1 ATAACCACAGCATAATAAAATAAAGCACCATCTTCACATGAA
*
377076 ATAGCCAC
1 ATAACCAC
377084 GTAAGGCAGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.45, C:0.23, G:0.09, T:0.24
Consensus pattern (42 bp):
ATAACCACAGCATAATAAAATAAAGCACCATCTTCACATGAA
Found at i:377698 original size:16 final size:16
Alignment explanation
Indices: 377673--377706 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
377663 TGTTACCATT
*
377673 AACTACTTACTTTAAA
1 AACTAATTACTTTAAA
377689 AACTAATTACTTTAAA
1 AACTAATTACTTTAAA
377705 AA
1 AA
377707 ATGACAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (16 bp):
AACTAATTACTTTAAA
Found at i:378705 original size:23 final size:23
Alignment explanation
Indices: 378677--378720 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
378667 CCGTGTGTAT
378677 ACTGCTGTGTAGC-GACGTGTGCA
1 ACTGCTGTGTAGCAG-CGTGTGCA
378700 ACTGCTGTGTAGCAGCGTGTG
1 ACTGCTGTGTAGCAGCGTGTG
378721 TATTTAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.16, C:0.20, G:0.36, T:0.27
Consensus pattern (23 bp):
ACTGCTGTGTAGCAGCGTGTGCA
Found at i:391199 original size:17 final size:17
Alignment explanation
Indices: 391173--391212 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
391163 TCTTTATCAA
*
391173 TTTACGCTTTGATTTTC
1 TTTACACTTTGATTTTC
*
391190 TTTACACTTTGATTTTG
1 TTTACACTTTGATTTTC
391207 TTTACA
1 TTTACA
391213 AAAAAAGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.17, C:0.15, G:0.10, T:0.57
Consensus pattern (17 bp):
TTTACACTTTGATTTTC
Found at i:393579 original size:2 final size:2
Alignment explanation
Indices: 393572--393604 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
393562 GATTATACAG
393572 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
393605 AGAGAGAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:393609 original size:2 final size:2
Alignment explanation
Indices: 393604--393641 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
393594 GTGTGTGTGT
393604 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
393642 TTTTGAAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:398127 original size:17 final size:17
Alignment explanation
Indices: 398101--398135 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
398091 TACTTCCCGT
*
398101 TGATATCTTCTGATAAC
1 TGATAACTTCTGATAAC
398118 TGATAACTTCTGATAAC
1 TGATAACTTCTGATAAC
398135 T
1 T
398136 TATCCAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.40
Consensus pattern (17 bp):
TGATAACTTCTGATAAC
Done.