Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold107
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: 1028272
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.29
Warning! 136574 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:354478 original size:15 final size:15
Alignment explanation
Indices: 354448--354480 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
354438 CGTTTCGCTG
354448 AAATTTGGTATCTTA
1 AAATTTGGTATCTTA
354463 AAATGTTGGTAT-TTA
1 AAAT-TTGGTATCTTA
354478 AAA
1 AAA
354481 CATTAACGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (15 bp):
AAATTTGGTATCTTA
Found at i:366301 original size:28 final size:28
Alignment explanation
Indices: 366269--366326 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
366259 AATAGATATT
366269 AATAAAGAAACTTTAAAATGCAGGTTTC
1 AATAAAGAAACTTTAAAATGCAGGTTTC
366297 AATAAAGAAACTTTAAAATGCAGGTTTC
1 AATAAAGAAACTTTAAAATGCAGGTTTC
366325 AA
1 AA
366327 GCTGTTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (28 bp):
AATAAAGAAACTTTAAAATGCAGGTTTC
Found at i:372684 original size:14 final size:14
Alignment explanation
Indices: 372667--372693 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
372657 ATTTAAGAGT
372667 TTATTTACAAGATA
1 TTATTTACAAGATA
372681 TTATTTACAAGAT
1 TTATTTACAAGAT
372694 GCAAAAAAAA
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:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (14 bp):
TTATTTACAAGATA
Found at i:375473 original size:30 final size:30
Alignment explanation
Indices: 375437--375498 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
375427 TAAAAGAGGG
375437 GCATGTAATACGGAAACTGGAGAAGTATAA
1 GCATGTAATACGGAAACTGGAGAAGTATAA
375467 GCATGTAATACGGAAACTGGAGAAGTATAA
1 GCATGTAATACGGAAACTGGAGAAGTATAA
375497 GC
1 GC
375499 CGCTGTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.42, C:0.11, G:0.27, T:0.19
Consensus pattern (30 bp):
GCATGTAATACGGAAACTGGAGAAGTATAA
Found at i:377343 original size:16 final size:16
Alignment explanation
Indices: 377322--377360 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
377312 TCCTCTAACC
*
377322 AAAAAAAGAAAAGAAA
1 AAAAAAAAAAAAGAAA
*
377338 AAAAAAAAAAAAGAAG
1 AAAAAAAAAAAAGAAA
377354 AAAAAAA
1 AAAAAAA
377361 CACCAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAGAAA
Found at i:377346 original size:21 final size:19
Alignment explanation
Indices: 377322--377360 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
377312 TCCTCTAACC
*
377322 AAAAAAAGAA-AAGAAAAA
1 AAAAAAAAAAGAAGAAAAA
377340 AAAAAAAAAAGAAGAAAAA
1 AAAAAAAAAAGAAGAAAAA
377359 AA
1 AA
377361 CACCAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAGAAGAAAAA
Found at i:378239 original size:2 final size:2
Alignment explanation
Indices: 378234--378268 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
378224 CAGCACAGCT
378234 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 G
378269 TGCGAGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:378625 original size:5 final size:5
Alignment explanation
Indices: 378615--378651 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
378605 GTTGTTGGTT
378615 TTTTG TTTTG TTTTG -TTT- TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
378652 TTTCTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 6 0.20
5 24 0.80
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (5 bp):
TTTTG
Found at i:378636 original size:13 final size:13
Alignment explanation
Indices: 378620--378663 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
378610 TGGTTTTTTG
378620 TTTTGTTTTGTTT
1 TTTTGTTTTGTTT
378633 TTTTGTTTTGTTT
1 TTTTGTTTTGTTT
*
378646 TGTTT-TTTTCTTT
1 T-TTTGTTTTGTTT
378659 TTTTG
1 TTTTG
378664 CTCCTTAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 3 0.11
13 22 0.79
14 3 0.11
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (13 bp):
TTTTGTTTTGTTT
Found at i:378636 original size:18 final size:18
Alignment explanation
Indices: 378601--378659 Score: 91
Period size: 18 Copynumber: 3.2 Consensus size: 18
378591 GTTTTTGGGT
*
378601 TTTTGTTGTTGGTTTTTTG
1 TTTTGTT-TTGTTTTTTTG
378620 TTTTGTTTTGTTTTTTTG
1 TTTTGTTTTGTTTTTTTG
*
378638 TTTTGTTTTGTTTTTTTC
1 TTTTGTTTTGTTTTTTTG
378656 TTTT
1 TTTT
378660 TTTGCTCCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
18 31 0.82
19 7 0.18
ACGTcount: A:0.00, C:0.02, G:0.17, T:0.81
Consensus pattern (18 bp):
TTTTGTTTTGTTTTTTTG
Found at i:378645 original size:23 final size:21
Alignment explanation
Indices: 378613--378663 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 21
378603 TTGTTGTTGG
*
378613 TTTTTTGTTTTGTTTTGTTTTT
1 TTTTTTGTTTTGTTTT-TTTCT
378635 TTGTTTTGTTTTGTTTTTTTCT
1 TT-TTTTGTTTTGTTTTTTTCT
378657 TTTTTTG
1 TTTTTTG
378664 CTCCTTAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 5 0.19
22 8 0.30
23 14 0.52
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (21 bp):
TTTTTTGTTTTGTTTTTTTCT
Found at i:391441 original size:16 final size:16
Alignment explanation
Indices: 391420--391458 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
391410 ATATTGAGAT
*
391420 TACGAGTCTGTTTGGG
1 TACGAGTCAGTTTGGG
391436 TACGAGTCAGTTTGGG
1 TACGAGTCAGTTTGGG
391452 TACGAGT
1 TACGAGT
391459 TGATGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.18, C:0.13, G:0.36, T:0.33
Consensus pattern (16 bp):
TACGAGTCAGTTTGGG
Found at i:400585 original size:16 final size:16
Alignment explanation
Indices: 400564--400594 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
400554 ATGGATTTAC
*
400564 TTCGTTATATCCGTAA
1 TTCGTTATATACGTAA
400580 TTCGTTATATACGTA
1 TTCGTTATATACGTA
400595 TAACGAATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (16 bp):
TTCGTTATATACGTAA
Found at i:403964 original size:46 final size:47
Alignment explanation
Indices: 403911--404007 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 47
403901 TGTCAACCAT
403911 ATATGCAATA-TTCAAAAGCTGGTA-TTTGTTTCATAAATTATCAGAA
1 ATATGCAA-AGTTCAAAAGCTGGTATTTTGTTTCATAAATTATCAGAA
*
403957 ATATGCAAAGTTCAAAAGCTGGTATTTTTTTTTTCATAAATTATCAGAA
1 ATATGCAAAGTTCAAAAGCTGGTA--TTTTGTTTCATAAATTATCAGAA
404006 AT
1 AT
404008 CAAAATCCTA
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
45 1 0.02
46 22 0.48
49 23 0.50
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.39
Consensus pattern (47 bp):
ATATGCAAAGTTCAAAAGCTGGTATTTTGTTTCATAAATTATCAGAA
Found at i:416485 original size:16 final size:16
Alignment explanation
Indices: 416464--416498 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
416454 GATTATGGGA
416464 AATTTAAGTATAGTTT
1 AATTTAAGTATAGTTT
416480 AATTTAAGTATAGTTT
1 AATTTAAGTATAGTTT
416496 AAT
1 AAT
416499 AGAATACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (16 bp):
AATTTAAGTATAGTTT
Found at i:417875 original size:2 final size:2
Alignment explanation
Indices: 417868--417901 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
417858 TCTAATTTTG
417868 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
417902 AAAGAAAAAA
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:418615 original size:182 final size:182
Alignment explanation
Indices: 418296--418631 Score: 546
Period size: 182 Copynumber: 1.8 Consensus size: 182
418286 AATATATAGT
* *
418296 TAAAAGAAACAGACTATAATGGTAAAACATGCAAGGATATTTATATGAATCGAACTATAACCGAA
1 TAAAAGAAACAGACTATAATGGTAAAACATGCAAGAATATTTATATGAATCAAACTATAACCGAA
* * * * * *
418361 AACATCGTAATTTGGATAGCCGAAACCGAAACTTTTATTCAAGGTAGTTTGTAGCAATGATGTGT
66 AACACCGTAATTTGGAAAGCCGAAACCGAAACTGTTATTCAAGGTAATTTATAGCAATAATGTGT
418426 AAATAATTTATTGGGTTTTATTATCATTTAAATTAGAGGGAAATATTGAAAA
131 AAATAATTTATTGGGTTTTATTATCATTTAAATTAGAGGGAAATATTGAAAA
* *
418478 TAAAAGAAACAGACTATAATGGTAAAACATGTAAGAATATTTATATGAATCAAATTATAACCGAA
1 TAAAAGAAACAGACTATAATGGTAAAACATGCAAGAATATTTATATGAATCAAACTATAACCGAA
* * *
418543 AACACCGTAATTTGGAAAGCCGAAACGGAAACTGTTATTCACGGTAATTTATAGTAATAATGTGT
66 AACACCGTAATTTGGAAAGCCGAAACCGAAACTGTTATTCAAGGTAATTTATAGCAATAATGTGT
*
418608 TAATAATTTATTGGGTTTTATTAT
131 AAATAATTTATTGGGTTTTATTAT
418632 TAATGAAGTT
Statistics
Matches: 140, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
182 140 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.32
Consensus pattern (182 bp):
TAAAAGAAACAGACTATAATGGTAAAACATGCAAGAATATTTATATGAATCAAACTATAACCGAA
AACACCGTAATTTGGAAAGCCGAAACCGAAACTGTTATTCAAGGTAATTTATAGCAATAATGTGT
AAATAATTTATTGGGTTTTATTATCATTTAAATTAGAGGGAAATATTGAAAA
Found at i:420142 original size:88 final size:88
Alignment explanation
Indices: 420028--420238 Score: 359
Period size: 88 Copynumber: 2.4 Consensus size: 88
420018 AAAATATAAA
* * * **
420028 AAGTTTCAGTAAGTTTCAGTTGCGGAAACCCTTTGTAAACAATATGTTTCCCAATTGTATATGGA
1 AAGTTTCAGTAAGTTTCCGTTGCGGAAACCATTTGTAAACAATATGTATCCCAAACGTATATGGA
*
420093 GGTTGAAACTATGCAGAAACTTC
66 GATTGAAACTATGCAGAAACTTC
*
420116 AAGTTTCAGTAAGTTTCCGTCGCGGAAACCATTTGTAAACAATATGTATCCCAAACGTATATGGA
1 AAGTTTCAGTAAGTTTCCGTTGCGGAAACCATTTGTAAACAATATGTATCCCAAACGTATATGGA
420181 GATTGAAACTATGCAGAAACTTC
66 GATTGAAACTATGCAGAAACTTC
420204 AAGTTTCAGTAAGTTTCCGTTGCGGAAACCATTTG
1 AAGTTTCAGTAAGTTTCCGTTGCGGAAACCATTTG
420239 GATTCATGGA
Statistics
Matches: 115, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 115 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (88 bp):
AAGTTTCAGTAAGTTTCCGTTGCGGAAACCATTTGTAAACAATATGTATCCCAAACGTATATGGA
GATTGAAACTATGCAGAAACTTC
Found at i:425135 original size:6 final size:6
Alignment explanation
Indices: 425110--425231 Score: 100
Period size: 6 Copynumber: 20.3 Consensus size: 6
425100 ACAACCACGT
* * * * * * *
425110 CTACTG CTACTT CTATTA CTACTA CTTCTA CTGCTA CTTCTA TTACTA
1 CTACTA CTACTA CTACTA CTACTA CTACTA CTACTA CTACTA CTACTA
* * * * * *
425158 CTACTA TTACTG CTACTA CTAGTA GTACTA CTACTA CTACTA ATACTG
1 CTACTA CTACTA CTACTA CTACTA CTACTA CTACTA CTACTA CTACTA
* * *
425206 GTATTA CTACTA CTATTA CTACTA CT
1 CTACTA CTACTA CTACTA CTACTA CT
425232 GACAACTTTT
Statistics
Matches: 89, Mismatches: 27, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 89 1.00
ACGTcount: A:0.28, C:0.26, G:0.06, T:0.40
Consensus pattern (6 bp):
CTACTA
Found at i:425147 original size:27 final size:27
Alignment explanation
Indices: 425109--425219 Score: 125
Period size: 27 Copynumber: 4.0 Consensus size: 27
425099 TACAACCACG
425109 TCTACTGCTACTTCTATTACTACTACT
1 TCTACTGCTACTTCTATTACTACTACT
425136 TCTACTGCTACTTCTATTACTACTACT
1 TCTACTGCTACTTCTATTACTACTACT
*
425163 AT-TACTGCTACTACTAGTAGTACTACTACT
1 -TCTACTGCTACTTCTA-T--TACTACTACT
* ** **
425193 ACTACTAATACTGGTATTACTACTACT
1 TCTACTGCTACTTCTATTACTACTACT
425220 ATTACTACTA
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
27 50 0.68
28 2 0.03
29 1 0.01
30 20 0.27
ACGTcount: A:0.27, C:0.26, G:0.06, T:0.41
Consensus pattern (27 bp):
TCTACTGCTACTTCTATTACTACTACT
Found at i:425220 original size:27 final size:27
Alignment explanation
Indices: 425123--425232 Score: 112
Period size: 27 Copynumber: 4.0 Consensus size: 27
425113 CTGCTACTTC
* * **
425123 TATTACTACTACTTCTACTGCTACTTC
1 TATTACTACTACTACTACTACTACTGG
* *
425150 TATTACTACTACTATTACTGCTACTACTAG
1 TATTACTACTAC---TACTACTACTACTGG
* *
425180 TAGTACTACTACTACTACTAATACTGG
1 TATTACTACTACTACTACTACTACTGG
*
425207 TATTACTACTACTATTACTACTACTG
1 TATTACTACTACTACTACTACTACTG
425233 ACAACTTTTA
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
27 47 0.69
30 21 0.31
ACGTcount: A:0.29, C:0.25, G:0.06, T:0.40
Consensus pattern (27 bp):
TATTACTACTACTACTACTACTACTGG
Found at i:425347 original size:21 final size:21
Alignment explanation
Indices: 425322--425378 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
425312 TGTACTAACA
* *
425322 ACTTTTACCACTACTACTAT-T
1 ACTTTAACCATTACTAC-ATGT
*
425343 ACTTTAACTATTACTACATGT
1 ACTTTAACCATTACTACATGT
425364 ACTTTAACCATTACT
1 ACTTTAACCATTACT
425379 CTTACTAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.32, C:0.25, G:0.02, T:0.42
Consensus pattern (21 bp):
ACTTTAACCATTACTACATGT
Found at i:429174 original size:42 final size:43
Alignment explanation
Indices: 429115--429199 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 43
429105 TCTTTTTGTT
* *
429115 TACATTGTTAGAATGTAATTTT-CTTTTTTTTACTTAATAATA
1 TACATTCTTAAAATGTAATTTTCCTTTTTTTTACTTAATAATA
*
429157 TACATTCTTAAAATGTAATTTTCCTTTTTTTTTCTTAATAATA
1 TACATTCTTAAAATGTAATTTTCCTTTTTTTTACTTAATAATA
429200 AAAATTTGCT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 20 0.51
43 19 0.49
ACGTcount: A:0.31, C:0.09, G:0.05, T:0.55
Consensus pattern (43 bp):
TACATTCTTAAAATGTAATTTTCCTTTTTTTTACTTAATAATA
Found at i:430736 original size:2 final size:2
Alignment explanation
Indices: 430731--430766 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
430721 TGTGTGTGTG
430731 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
430767 NNNNNNNNNN
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:432511 original size:58 final size:57
Alignment explanation
Indices: 432420--432595 Score: 271
Period size: 58 Copynumber: 3.0 Consensus size: 57
432410 CCACTTCTCG
* *
432420 CAACAAATATTTTCCGTAAATTTACATACACAAAATCTAATTTTGAGGGAGTTGCCCC
1 CAACAAATATTTTCCATAAATTTACATATACAAAAT-TAATTTTGAGGGAGTTGCCCC
*
432478 CAACAGATATTTTCCATAAATTTACATATACAAAATTCAATTTTGAGGGAGTTGCCCC
1 CAACAAATATTTTCCATAAATTTACATATACAAAATT-AATTTTGAGGGAGTTGCCCC
* * *
432536 CAACAAATATTTTCCATAAGTTTACATTTGCAAAATTTAATTTTGAGGGAGTTGCCCC
1 CAACAAATATTTTCCATAAATTTACATATACAAAA-TTAATTTTGAGGGAGTTGCCCC
432594 CA
1 CA
432596 CCTCCTTTTT
Statistics
Matches: 109, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
57 1 0.01
58 106 0.97
59 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (57 bp):
CAACAAATATTTTCCATAAATTTACATATACAAAATTAATTTTGAGGGAGTTGCCCC
Found at i:433556 original size:23 final size:22
Alignment explanation
Indices: 433524--433567 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
433514 CAAAGGTTCA
433524 ATATGATACAATCATACATATC
1 ATATGATACAATCATACATATC
433546 ATATGTATACAATCATACATAT
1 ATATG-ATACAATCATACATAT
433568 ACAATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (22 bp):
ATATGATACAATCATACATATC
Found at i:434223 original size:3 final size:3
Alignment explanation
Indices: 434217--434248 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
434207 GCAGCAAAAA
434217 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
434249 ATCCGTAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:435072 original size:4 final size:4
Alignment explanation
Indices: 435063--435134 Score: 53
Period size: 4 Copynumber: 18.2 Consensus size: 4
435053 CAAAGATTGC
*
435063 ATAA ATAA ATTAA CTATAA ATAA ATAA A-AA ATAA ACAA ATAA A-AA A-AA
1 ATAA ATAA A-TAA --ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* * *
435111 AT-A ATAT CTAA ATTA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
435135 CTCAATCAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
3 12 0.22
4 35 0.65
5 3 0.06
6 3 0.06
7 1 0.02
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:435096 original size:15 final size:15
Alignment explanation
Indices: 435063--435114 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
435053 CAAAGATTGC
* **
435063 ATAAATAAATTAACT
1 ATAAATAAATAAAAA
435078 ATAAATAAATAAAAA
1 ATAAATAAATAAAAA
*
435093 ATAAACAAATAAAAA
1 ATAAATAAATAAAAA
435108 A-AAATAA
1 ATAAATAA
435115 TATCTAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 5 0.16
15 27 0.84
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (15 bp):
ATAAATAAATAAAAA
Found at i:440500 original size:18 final size:18
Alignment explanation
Indices: 440477--440515 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
440467 AATTAATCGT
440477 ATGTATATTATCAAGATG
1 ATGTATATTATCAAGATG
*
440495 ATGTATATTATTAAGATG
1 ATGTATATTATCAAGATG
440513 ATG
1 ATG
440516 AACGTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (18 bp):
ATGTATATTATCAAGATG
Found at i:449835 original size:16 final size:17
Alignment explanation
Indices: 449810--449843 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
449800 ATTTGCTAGT
449810 TGTTGATTTTTTT-TTC
1 TGTTGATTTTTTTCTTC
*
449826 TGTTGTTTTTTTTCTTC
1 TGTTGATTTTTTTCTTC
449843 T
1 T
449844 TTCTTCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.03, C:0.09, G:0.12, T:0.76
Consensus pattern (17 bp):
TGTTGATTTTTTTCTTC
Found at i:455668 original size:29 final size:29
Alignment explanation
Indices: 455626--455715 Score: 171
Period size: 29 Copynumber: 3.1 Consensus size: 29
455616 TAAATGGGGC
*
455626 TTGATCATCTAGGGGACACCCGTTCTGTT
1 TTGATCATCTAGGGGACACCCGTCCTGTT
455655 TTGATCATCTAGGGGACACCCGTCCTGTT
1 TTGATCATCTAGGGGACACCCGTCCTGTT
455684 TTGATCATCTAGGGGACACCCGTCCTGTT
1 TTGATCATCTAGGGGACACCCGTCCTGTT
455713 TTG
1 TTG
455716 CAGCCTGCTA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (29 bp):
TTGATCATCTAGGGGACACCCGTCCTGTT
Found at i:457240 original size:20 final size:21
Alignment explanation
Indices: 457212--457250 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
457202 TTATCTCCAC
*
457212 AAATTAATCAAC-AACAAATA
1 AAATCAATCAACAAACAAATA
457232 AAATCAATCAACAAACAAA
1 AAATCAATCAACAAACAAA
457251 ACAAATAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.67, C:0.18, G:0.00, T:0.15
Consensus pattern (21 bp):
AAATCAATCAACAAACAAATA
Found at i:457245 original size:17 final size:16
Alignment explanation
Indices: 457217--457251 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
457207 TCCACAAATT
*
457217 AATCAACAACAAATAA
1 AATCAACAACAAACAA
457233 AATCAATCAACAAACAA
1 AATCAA-CAACAAACAA
457250 AA
1 AA
457252 CAAATAACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.69, C:0.20, G:0.00, T:0.11
Consensus pattern (16 bp):
AATCAACAACAAACAA
Found at i:458521 original size:5 final size:5
Alignment explanation
Indices: 458504--458533 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
458494 TATGATACAT
458504 AATTC ATATTC AATTC AATTC AATTC AATT
1 AATTC A-ATTC AATTC AATTC AATTC AATT
458534 TATTCTCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (5 bp):
AATTC
Found at i:460628 original size:2 final size:2
Alignment explanation
Indices: 460621--460669 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
460611 CTTCTGATAA
460621 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
460663 TC TC TC T
1 TC TC TC T
460670 ACTTACTGGA
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:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:464252 original size:1 final size:1
Alignment explanation
Indices: 464246--464276 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
464236 AGGCGTCGGA
464246 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
464277 CTTGGGGCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:464395 original size:2 final size:2
Alignment explanation
Indices: 464390--464414 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
464380 CCCCCCCCCC
464390 CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA C
464415 GAATTAGGAA
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:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:467625 original size:17 final size:17
Alignment explanation
Indices: 467603--467638 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
467593 TTTATTAATA
467603 AAATTAGTAAATTCATT
1 AAATTAGTAAATTCATT
467620 AAATTAGTAAATTCATT
1 AAATTAGTAAATTCATT
467637 AA
1 AA
467639 TGTAATCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (17 bp):
AAATTAGTAAATTCATT
Found at i:476037 original size:14 final size:14
Alignment explanation
Indices: 476018--476050 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
476008 CGTCTGTCTG
*
476018 TATTTTTTTTTACA
1 TATTTTTTTTTAAA
476032 TATTTTTTTTTAAA
1 TATTTTTTTTTAAA
476046 TATTT
1 TATTT
476051 GGCCAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTTTTTTTTAAA
Found at i:479743 original size:442 final size:437
Alignment explanation
Indices: 478474--479906 Score: 2465
Period size: 437 Copynumber: 3.3 Consensus size: 437
478464 CGTTTGATAA
* * *
478474 CAAGAAAAAGGGGCTGGTCCCTT-AAATAAGGGGCCAAAAGGGCTCTAAAGTCTTTCTCCCATAG
1 CAAGAAAAAGGGGCTGG-CCCTTCAATTTAGGGGCCAAAAGGGCTCTAAAGTCTTTCTTCCATAG
*
478538 CACTTTACTGAGAAATATTTTGTAATATGTTTAAGAAGCAAAAATGTTCATCTTTTACTCATTAA
65 CACTTTACTGAGAAATATTTTGTAATATGTTTAAGAAGCAAAAATGTTCATCTTTTACTAATTAA
*
478603 ACTATACATTATAAATTTTTTATTATGCGTTACGTAATTAGGGGTTTTAAGGGGCCAAAAATCCA
130 ACTATACATTATAAATTTTTTATTATGCGTTACGTAATTAGGGGTTTTAAGGGGCCAAAAGTCCA
478668 AAACTTCGATCGAATATATCTCAAAAAGGACAAATATTTTGAAAAGCAATATAGAATAAAAGATG
195 AAACTTCGATCGAATATATCTCAAAAAGGACAAATATTTTGAAAAGCAATATAGAATAAAAGATG
478733 CTTAGAATGATGTTTTAAACAATATTCAATCATAAAAGTTTCGTTATCTGGCCCCAATAAGGAGA
260 CTTAGAATGATGTTTTAAACAATATTCAATCATAAAAGTTTCGTTATCTGGCCCCAATAAGGAGA
* * **
478798 TTAGGGGTCGGCCCCTAAAATGTCCTTTCCCAGATAGCTCTTAAACGGCAAAGAATTTCTAAACA
325 TTAGGGGTCGGCCCCTAAAATGTCATATCCCAGATAGCTCAAAAACGGCAAAGAATTTCTAAACA
478863 CTTGTTGAACAAAATATGTTTAATATCAAAAGAACTTTCGTATGATGC
390 CTTGTTGAACAAAATATGTTTAATATCAAAAGAACTTTCGTATGATGC
*
478911 CAAGAAAAAGGGGCTGGCCCTTCAATTTAGGGGCCAAAAGGGCTCTAAAGTCTTTCTTCTATAGC
1 CAAGAAAAAGGGGCTGGCCCTTCAATTTAGGGGCCAAAAGGGCTCTAAAGTCTTTCTTCCATAGC
* * * *
478976 ACTTTACTGAGAAATGTTTTGTAATATGTTTAAGAAGCAAAAATGTTCATCTTTCATTAATAAAA
66 ACTTTACTGAGAAATATTTTGTAATATGTTTAAGAAGCAAAAATGTTCATCTTTTACTAATTAAA
* *
479041 CTATACATTATAAAATTTTTATTATGCGTTACGTAATAAGGGGTTTTAAGGGGCCAAAAGTCCAA
131 CTATACATTATAAATTTTTTATTATGCGTTACGTAATTAGGGGTTTTAAGGGGCCAAAAGTCCAA
* * * *
479106 AATTTCAATCGAATATATCTCAAAAAGAACAAATATTTTAAAAAGCAATATAGAATAAAAGATGC
196 AACTTCGATCGAATATATCTCAAAAAGGACAAATATTTTGAAAAGCAATATAGAATAAAAGATGC
479171 TTAGAATGATGTTTTAAACAATATTCAATCATAAAAGTTTCGTTATCTGGCCCCAATAAGGAGAT
261 TTAGAATGATGTTTTAAACAATATTCAATCATAAAAGTTTCGTTATCTGGCCCCAATAAGGAGAT
* *
479236 TAGGGGTCGGCCCCTTAAATATCATATCCCAGATAGCTCAAAAACGGCAAAGAATTTCTAAACAC
326 TAGGGGTCGGCCCCTAAAATGTCATATCCCAGATAGCTCAAAAACGGCAAAGAATTTCTAAACAC
*
479301 TTGTTGTACAAAATATGTTTAATATCAAAAGAACTTTCGTATGATGC
391 TTGTTGAACAAAATATGTTTAATATCAAAAGAACTTTCGTATGATGC
*
479348 CAAGAAAAAGGGGCTGGCCCTTCAATTTAGGGGCCAAAAGGGCTCTAAAGTCTGTCTTCCATAGC
1 CAAGAAAAAGGGGCTGGCCCTTCAATTTAGGGGCCAAAAGGGCTCTAAAGTCTTTCTTCCATAGC
*
479413 ACTTTACTGAGAAATATTTTGTCATATGTTTAAGAAGCAAAAATGTTCATCTTTTACTAATTAAA
66 ACTTTACTGAGAAATATTTTGTAATATGTTTAAGAAGCAAAAATGTTCATCTTTTACTAATTAAA
*
479478 CTATACATTATAAATTTTTTATTATGCGTTACGTACCGTAATTAGGGGTTTTAAGGGGTCAAAAG
131 CTATACATTATAAATTTTTTATTATGCG-T---TA-CGTAATTAGGGGTTTTAAGGGGCCAAAAG
*
479543 TCCAAAACTTCGATCGAATATATCTAAAAAAGGACAAATATTTTGAAAAGCAATATAGAATAAAA
191 TCCAAAACTTCGATCGAATATATCTCAAAAAGGACAAATATTTTGAAAAGCAATATAGAATAAAA
479608 GATGCTTAGAATGATGTTTTAAACAATATTCAATCATAAAAGTTTCGTTATCTGGCCCCAATAAG
256 GATGCTTAGAATGATGTTTTAAACAATATTCAATCATAAAAGTTTCGTTATCTGGCCCCAATAAG
* **
479673 GAGATTAGGGGTCGGCCCCTAAAACGTCATATCCCAGATAGCTCAAAAACATCAAAGAATTTCTA
321 GAGATTAGGGGTCGGCCCCTAAAATGTCATATCCCAGATAGCTCAAAAACGGCAAAGAATTTCTA
* *
479738 AACACTTGTTGAACAAAATATGTTAAATATCATAAGAACTTTCGTATGATGC
386 AACACTTGTTGAACAAAATATGTTTAATATCAAAAGAACTTTCGTATGATGC
*
479790 CAAGAAAAAGGGGCTGGCCCTTCAATTTAGGGACCAAAAGGGCTCTAAAGTCTTTCTTCCATAGC
1 CAAGAAAAAGGGGCTGGCCCTTCAATTTAGGGGCCAAAAGGGCTCTAAAGTCTTTCTTCCATAGC
* * *
479855 ACTTTACTGAAAAATGA-TTTGTTATATGTTTAGGAAGCAAAAATGTTCATCT
66 ACTTTACTGAGAAAT-ATTTTGTAATATGTTTAAGAAGCAAAAATGTTCATCT
479907 CACATTTATT
Statistics
Matches: 938, Mismatches: 51, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
436 5 0.01
437 558 0.59
438 1 0.00
441 2 0.00
442 371 0.40
443 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (437 bp):
CAAGAAAAAGGGGCTGGCCCTTCAATTTAGGGGCCAAAAGGGCTCTAAAGTCTTTCTTCCATAGC
ACTTTACTGAGAAATATTTTGTAATATGTTTAAGAAGCAAAAATGTTCATCTTTTACTAATTAAA
CTATACATTATAAATTTTTTATTATGCGTTACGTAATTAGGGGTTTTAAGGGGCCAAAAGTCCAA
AACTTCGATCGAATATATCTCAAAAAGGACAAATATTTTGAAAAGCAATATAGAATAAAAGATGC
TTAGAATGATGTTTTAAACAATATTCAATCATAAAAGTTTCGTTATCTGGCCCCAATAAGGAGAT
TAGGGGTCGGCCCCTAAAATGTCATATCCCAGATAGCTCAAAAACGGCAAAGAATTTCTAAACAC
TTGTTGAACAAAATATGTTTAATATCAAAAGAACTTTCGTATGATGC
Found at i:481013 original size:2 final size:2
Alignment explanation
Indices: 481006--481038 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
480996 ATTTAATTGA
481006 AG AG AG 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 AG AG AG A
481039 TCAACACTGA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:484834 original size:15 final size:15
Alignment explanation
Indices: 484814--484849 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
484804 CTGAACCCTT
484814 AAAGCTTAACATCCC
1 AAAGCTTAACATCCC
484829 AAAGCTTAACATCCC
1 AAAGCTTAACATCCC
484844 AAAGCT
1 AAAGCT
484850 AAACCTTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (15 bp):
AAAGCTTAACATCCC
Found at i:484945 original size:21 final size:21
Alignment explanation
Indices: 484919--484966 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
484909 TGACGCTACC
*
484919 CAAATTTAAACTCCCTAAA-TT
1 CAAATTCAAACTCCC-AAAGTT
*
484940 CAAATTCAAGCTCCCAAAGTT
1 CAAATTCAAACTCCCAAAGTT
484961 CAAATT
1 CAAATT
484967 ACCTAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.42, C:0.25, G:0.04, T:0.29
Consensus pattern (21 bp):
CAAATTCAAACTCCCAAAGTT
Found at i:488066 original size:115 final size:115
Alignment explanation
Indices: 487864--488093 Score: 388
Period size: 115 Copynumber: 2.0 Consensus size: 115
487854 TCTGTTATTT
* * * ** *
487864 TCAAGAACTAATTCTTGTCAGTGGTGATGATTTGTGATAAGGTCCGAACACTGTTGCACTTTTGG
1 TCAAGAACTAAGTCTTGTCAGCGGTGATGATTTGTGATAAGGGCAAAACACTGTTGCACTTTCGG
487929 TTTGCCAGAGAAACTGCATAGGTGAGTTGATTAAAATCAACTCCCAAAAA
66 TTTGCCAGAGAAACTGCATAGGTGAGTTGATTAAAATCAACTCCCAAAAA
*
487979 TCAAGAACTAAGTCTTGTCAGCGGTGATGATTTGTGATAAGGGCAAAACACTGTTTCACTTTCGG
1 TCAAGAACTAAGTCTTGTCAGCGGTGATGATTTGTGATAAGGGCAAAACACTGTTGCACTTTCGG
*
488044 TTTGCCAGAGAAACTGCATAGGTGAGTTGATTAAAATCTACTCCCAAAAA
66 TTTGCCAGAGAAACTGCATAGGTGAGTTGATTAAAATCAACTCCCAAAAA
488094 CTAGTGTCTT
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
115 107 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.30
Consensus pattern (115 bp):
TCAAGAACTAAGTCTTGTCAGCGGTGATGATTTGTGATAAGGGCAAAACACTGTTGCACTTTCGG
TTTGCCAGAGAAACTGCATAGGTGAGTTGATTAAAATCAACTCCCAAAAA
Found at i:488491 original size:2 final size:2
Alignment explanation
Indices: 488484--488533 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
488474 GATTCTTAGC
488484 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
488526 AG AG AG AG
1 AG AG AG AG
488534 TTTTGATAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:492897 original size:28 final size:29
Alignment explanation
Indices: 492811--492920 Score: 167
Period size: 28 Copynumber: 4.0 Consensus size: 29
492801 CGACTATCTC
*
492811 TGTCAATCATCCAGTATTTT-ATTGA---
1 TGTCAATCATCCAGTGTTTTCATTGAGGT
492836 TGTCAATCATCCAGTGTTTTCATTGAGGT
1 TGTCAATCATCCAGTGTTTTCATTGAGGT
492865 TGTCAATCATCCAGTGTTTT-ATTGAGGT
1 TGTCAATCATCCAGTGTTTTCATTGAGGT
*
492893 TGTCAATCATTCAGTGTTTTCATTGAGG
1 TGTCAATCATCCAGTGTTTTCATTGAGG
492921 ACACCTCTTG
Statistics
Matches: 78, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
25 19 0.24
26 5 0.06
28 27 0.35
29 27 0.35
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (29 bp):
TGTCAATCATCCAGTGTTTTCATTGAGGT
Found at i:492917 original size:57 final size:54
Alignment explanation
Indices: 492811--492920 Score: 175
Period size: 57 Copynumber: 2.0 Consensus size: 54
492801 CGACTATCTC
492811 TGTCAATCATCCAGTATTTTATTGATGTCAATCATCCAGTGTTTTCATTGAGGT
1 TGTCAATCATCCAGTATTTTATTGATGTCAATCATCCAGTGTTTTCATTGAGGT
* *
492865 TGTCAATCATCCAGTGTTTTATTGAGGTTGTCAATCATTCAGTGTTTTCATTGAGG
1 TGTCAATCATCCAGTATTTTATTGA---TGTCAATCATCCAGTGTTTTCATTGAGG
492921 ACACCTCTTG
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
54 24 0.47
57 27 0.53
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (54 bp):
TGTCAATCATCCAGTATTTTATTGATGTCAATCATCCAGTGTTTTCATTGAGGT
Found at i:496009 original size:81 final size:78
Alignment explanation
Indices: 495906--496141 Score: 223
Period size: 81 Copynumber: 2.9 Consensus size: 78
495896 AGAGACACTA
* * *
495906 ACACACTTGAAACAGCCACATTCAAATGTTGAAAATCGGAATGAGAACTTACAAAGTAAGGAAAA
1 ACACACATGAAACAGCCACATTCAAA-G-TGAAAATAGGACTGAGAACTTACAAAG-AAGGAAAA
*
495971 ATGTTTGGTGGACGAG
63 ATGTATGGTGGACGAG
*
495987 ACACACAT-AAATCAGCCACATTCCAAAGCTGAGAAA-AGGACTGA-ATA-TTCACAAAGAAAAG
1 ACACACATGAAA-CAGCCACATT-CAAAG-TGA-AAATAGGACTGAGA-ACTT-ACAAAG-AAGG
496048 AAAAATGTATGGTGGACGAG
59 AAAAATGTATGGTGGACGAG
* * * * *
496068 ACATACTTGAAAGAGCCACATTCCAA-TGAAAATTGGACTGAGAACTTACCAAA-AATGGAAAAA
1 ACACACATGAAACAGCCACATTCAAAGTGAAAATAGGACTGAGAACTTA-CAAAGAA-GGAAAAA
*
496131 AGTATGGTGGA
64 TGTATGGTGGA
496142 TGCCATACAA
Statistics
Matches: 130, Mismatches: 14, Indels: 25
0.77 0.08 0.15
Matches are distributed among these distances:
77 5 0.04
78 28 0.22
79 7 0.05
80 9 0.07
81 71 0.55
82 10 0.08
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (78 bp):
ACACACATGAAACAGCCACATTCAAAGTGAAAATAGGACTGAGAACTTACAAAGAAGGAAAAATG
TATGGTGGACGAG
Found at i:497121 original size:48 final size:48
Alignment explanation
Indices: 497069--497214 Score: 211
Period size: 48 Copynumber: 3.0 Consensus size: 48
497059 GTGGGTACCA
* *
497069 TTACAACTCTGAACATGTGTACCGTACACGCGATTCGTGAGGATGCAG
1 TTACAGCTCCGAACATGTGTACCGTACACGCGATTCGTGAGGATGCAG
* * * *
497117 TTACAGCTCCGAACATGTGTACCATACACGCGATTCATGAAGATGCAA
1 TTACAGCTCCGAACATGTGTACCGTACACGCGATTCGTGAGGATGCAG
* **
497165 ATACAGCTCCGAACATGTGTACCGTACACGCGATTCGAAAGGATGCAG
1 TTACAGCTCCGAACATGTGTACCGTACACGCGATTCGTGAGGATGCAG
497213 TT
1 TT
497215 GAAGATACCA
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 84 1.00
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (48 bp):
TTACAGCTCCGAACATGTGTACCGTACACGCGATTCGTGAGGATGCAG
Found at i:501582 original size:20 final size:20
Alignment explanation
Indices: 501559--501600 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
501549 ATAACATTGC
*
501559 ATCATATCATATGACACAAT
1 ATCATATCATATCACACAAT
*
501579 ATCATATCGTATCACACAAT
1 ATCATATCATATCACACAAT
501599 AT
1 AT
501601 TATACAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (20 bp):
ATCATATCATATCACACAAT
Found at i:502186 original size:19 final size:20
Alignment explanation
Indices: 502156--502193 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
502146 AAAAGCACCT
*
502156 GCTCCAAAAAACTTTAACCA
1 GCTCCAAAAAACCTTAACCA
502176 GCTCC-AAAAACCTTAACC
1 GCTCCAAAAAACCTTAACC
502194 TCATTCAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.42, C:0.34, G:0.05, T:0.18
Consensus pattern (20 bp):
GCTCCAAAAAACCTTAACCA
Found at i:502497 original size:19 final size:19
Alignment explanation
Indices: 502473--502520 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
502463 GTAGCAGGGC
502473 ACCTGCTCCAAAACCTTTA
1 ACCTGCTCCAAAACCTTTA
502492 ACCTGCTCCAAAACCTTTA
1 ACCTGCTCCAAAACCTTTA
*
502511 ACCTCCTCCA
1 ACCTGCTCCA
502521 GCATCTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.29, C:0.42, G:0.04, T:0.25
Consensus pattern (19 bp):
ACCTGCTCCAAAACCTTTA
Found at i:503308 original size:1 final size:1
Alignment explanation
Indices: 503302--503339 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
503292 AAGTTTGAAT
503302 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
503340 TCATCTAAGT
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:506126 original size:14 final size:14
Alignment explanation
Indices: 506107--506134 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
506097 GCTTATACTG
506107 CAAACAACGTAGTT
1 CAAACAACGTAGTT
506121 CAAACAACGTAGTT
1 CAAACAACGTAGTT
506135 TAAAACAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (14 bp):
CAAACAACGTAGTT
Found at i:510414 original size:2 final size:2
Alignment explanation
Indices: 510407--510460 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
510397 CTTCCATAAA
510407 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
510449 TC TC TC TC TC TC
1 TC TC TC TC TC TC
510461 ATGCAATAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:513910 original size:13 final size:13
Alignment explanation
Indices: 513892--513942 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
513882 NNNNNNNNNN
513892 ATATATATATTAT
1 ATATATATATTAT
513905 ATATATATA-TAT
1 ATATATATATTAT
*
513917 CATACATAT-TTAT
1 -ATATATATATTAT
513930 A-ATA-ATATTAT
1 ATATATATATTAT
513941 AT
1 AT
513943 TACATATAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
10 2 0.06
11 7 0.22
12 4 0.12
13 19 0.59
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (13 bp):
ATATATATATTAT
Found at i:513912 original size:15 final size:14
Alignment explanation
Indices: 513892--513950 Score: 52
Period size: 13 Copynumber: 4.4 Consensus size: 14
513882 NNNNNNNNNN
513892 ATATA-TATATTAT
1 ATATATTATATTAT
*
513905 ATATATATATATCAT
1 ATATAT-TATATTAT
* *
513920 ACATATT-TATAAT
1 ATATATTATATTAT
*
513933 A-ATATTATATTAC
1 ATATATTATATTAT
513946 ATATA
1 ATATA
513951 ACTATATCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
12 5 0.14
13 16 0.43
14 4 0.11
15 12 0.32
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (14 bp):
ATATATTATATTAT
Found at i:514281 original size:22 final size:22
Alignment explanation
Indices: 514253--514307 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
514243 CATCCACTCA
514253 GGGTTTACTTTAGGTCTACCTG
1 GGGTTTACTTTAGGTCTACCTG
*
514275 GGGTTTACTTTGGGTCTACCTG
1 GGGTTTACTTTAGGTCTACCTG
*
514297 GGGTTTGCTTT
1 GGGTTTACTTT
514308 TGGGGTCCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.09, C:0.16, G:0.31, T:0.44
Consensus pattern (22 bp):
GGGTTTACTTTAGGTCTACCTG
Found at i:514819 original size:23 final size:21
Alignment explanation
Indices: 514791--514844 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 21
514781 AAAGTTTTAT
514791 TAATATTAAAATATACTATTAAA
1 TAATATTAAAAT-TA-TATTAAA
*
514814 TAATATT-AAATTATATTATA
1 TAATATTAAAATTATATTAAA
*
514834 TTATATTAAAA
1 TAATATTAAAA
514845 GAGTGCTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 12 0.43
21 5 0.18
22 4 0.14
23 7 0.25
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATATTAAAATTATATTAAA
Found at i:514822 original size:10 final size:10
Alignment explanation
Indices: 514791--514843 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
514781 AAAGTTTTAT
514791 TAATATTAAAA
1 TAATATT-AAA
514802 TATACTATTAAA
1 TA-A-TATTAAA
514814 TAATATTAAA
1 TAATATTAAA
* *
514824 TTATATTATA
1 TAATATTAAA
*
514834 TTATATTAAA
1 TAATATTAAA
514844 AGAGTGCTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
10 24 0.65
11 3 0.08
12 6 0.16
13 4 0.11
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (10 bp):
TAATATTAAA
Found at i:516349 original size:13 final size:13
Alignment explanation
Indices: 516331--516359 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
516321 GCATGTTGGG
516331 CATGGATTAAGTA
1 CATGGATTAAGTA
516344 CATGGATTAAGTA
1 CATGGATTAAGTA
516357 CAT
1 CAT
516360 ATACGATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (13 bp):
CATGGATTAAGTA
Found at i:517673 original size:3 final size:3
Alignment explanation
Indices: 517665--517703 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
517655 AGAGGATGTA
517665 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
517704 TTCTTACAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:518360 original size:92 final size:92
Alignment explanation
Indices: 518203--518417 Score: 313
Period size: 92 Copynumber: 2.3 Consensus size: 92
518193 CTACACTCAC
* * *
518203 CACATTGACCAATAATATAGGATCCATAGCCAGAATGTGTGCTCAAACTCAGGTAAGTGACTCAA
1 CACATTGACAAATGATATAGGACCCATAGCCAGAATGTGTGCTCAAACTCAGGTAAGTGACTCAA
* ****
518268 CAATGAAAAACAGGTACTTAGGTGGGT
66 CAATGAAAAACAGCTACTTAGACAAGT
*
518295 CACATTGACAAATGATATAGGACCCACAGCCAGAATGTGTGCTCAAACTCAGGTAAGTGACTCAA
1 CACATTGACAAATGATATAGGACCCATAGCCAGAATGTGTGCTCAAACTCAGGTAAGTGACTCAA
*
518360 CAATGAAAAATAGCTACTTAGACAAGT
66 CAATGAAAAACAGCTACTTAGACAAGT
* * *
518387 CACATTGACTAGTGATATATGACCCATAGCC
1 CACATTGACAAATGATATAGGACCCATAGCC
518418 TGATGATTCC
Statistics
Matches: 109, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
92 109 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (92 bp):
CACATTGACAAATGATATAGGACCCATAGCCAGAATGTGTGCTCAAACTCAGGTAAGTGACTCAA
CAATGAAAAACAGCTACTTAGACAAGT
Found at i:519618 original size:16 final size:16
Alignment explanation
Indices: 519589--519619 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
519579 ACAGACAAAC
519589 GGACGGACGGACAGAT
1 GGACGGACGGACAGAT
*
519605 GGACGGGCGGACAGA
1 GGACGGACGGACAGA
519620 CAGACAGATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.19, G:0.48, T:0.03
Consensus pattern (16 bp):
GGACGGACGGACAGAT
Found at i:521775 original size:17 final size:17
Alignment explanation
Indices: 521753--521837 Score: 51
Period size: 17 Copynumber: 5.4 Consensus size: 17
521743 GTCTTACATA
521753 GTCTAATAGATGTCATT
1 GTCTAATAGATGTCATT
521770 GTCTAAT-GAATGT-A--
1 GTCTAATAG-ATGTCATT
* **
521784 GTATTCTAGATGTCATT
1 GTCTAATAGATGTCATT
*
521801 GTCTAATCA-ATG-CAGT
1 GTCTAAT-AGATGTCATT
*
521817 GT-T-ATAAATGTCATT
1 GTCTAATAGATGTCATT
521832 GTCTAA
1 GTCTAA
521838 ACAATGTCAT
Statistics
Matches: 50, Mismatches: 8, Indels: 20
0.64 0.10 0.26
Matches are distributed among these distances:
13 1 0.02
14 13 0.26
15 8 0.16
16 8 0.16
17 19 0.38
18 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.40
Consensus pattern (17 bp):
GTCTAATAGATGTCATT
Found at i:521794 original size:31 final size:31
Alignment explanation
Indices: 521751--521969 Score: 215
Period size: 31 Copynumber: 6.9 Consensus size: 31
521741 TAGTCTTACA
* *
521751 TAGTCTAATAGATGTCATTGTCTAATGAATG
1 TAGTCTTATAGATGTCATTGTCTAATCAATG
* *
521782 TAGTATTCTAGATGTCATTGTCTAATCAATG
1 TAGTCTTATAGATGTCATTGTCTAATCAATG
* * * *
521813 CAGTGTTATAAATGTCATTGTCTAAACAATG
1 TAGTCTTATAGATGTCATTGTCTAATCAATG
* * * *
521844 TCA-TCCTATTTTTATTGATGTCATGGTCTACTTAATG
1 T-AGT-C-----TTATAGATGTCATTGTCTAATCAATG
* *
521881 TAGTCTTGTAGATGTCATTGTTTAATCAATG
1 TAGTCTTATAGATGTCATTGTCTAATCAATG
* *
521912 TAATCTTATAAATGTCATTGTCTAATCAATG
1 TAGTCTTATAGATGTCATTGTCTAATCAATG
*
521943 TAGTCTTATAAATGTCATTGTCTAATC
1 TAGTCTTATAGATGTCATTGTCTAATC
521970 CATGCTAGAT
Statistics
Matches: 152, Mismatches: 28, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
31 127 0.84
32 1 0.01
36 2 0.01
37 22 0.14
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (31 bp):
TAGTCTTATAGATGTCATTGTCTAATCAATG
Found at i:521845 original size:17 final size:17
Alignment explanation
Indices: 521793--521847 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
521783 AGTATTCTAG
*
521793 ATGTCATTGTCTAATCA
1 ATGTCATTGTCTAAACA
* *
521810 ATG-CAGTGT-TATA-A
1 ATGTCATTGTCTAAACA
521824 ATGTCATTGTCTAAACA
1 ATGTCATTGTCTAAACA
521841 ATGTCAT
1 ATGTCAT
521848 CCTATTTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 4 0.13
15 7 0.23
16 8 0.27
17 11 0.37
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (17 bp):
ATGTCATTGTCTAAACA
Found at i:521932 original size:99 final size:99
Alignment explanation
Indices: 521761--521943 Score: 276
Period size: 99 Copynumber: 1.8 Consensus size: 99
521751 TAGTCTAATA
* * *
521761 GATGTCATTGTCTAATGAATGTAGTATTCTAGATGTCATTGTCTAATCAATGCAGTGTTATAAAT
1 GATGTCATGGTCTAATGAATGTAGTATTCTAGATGTCATTGTCTAATCAATGCAATCTTATAAAT
521826 GTCATTGTCTAAACAATGTCATCCTATTTTTATT
66 GTCATTGTCTAAACAATGTCATCCTATTTTTATT
* * * * * *
521860 GATGTCATGGTCTACTTAATGTAGTCTTGTAGATGTCATTGTTTAATCAATGTAATCTTATAAAT
1 GATGTCATGGTCTAATGAATGTAGTATTCTAGATGTCATTGTCTAATCAATGCAATCTTATAAAT
*
521925 GTCATTGTCTAATCAATGT
66 GTCATTGTCTAAACAATGT
521944 AGTCTTATAA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
99 74 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.43
Consensus pattern (99 bp):
GATGTCATGGTCTAATGAATGTAGTATTCTAGATGTCATTGTCTAATCAATGCAATCTTATAAAT
GTCATTGTCTAAACAATGTCATCCTATTTTTATT
Found at i:522886 original size:28 final size:28
Alignment explanation
Indices: 522856--523162 Score: 578
Period size: 28 Copynumber: 11.0 Consensus size: 28
522846 TCTTACACTA
*
522856 TCTGGTACTTGGTGTATGTACACAGCTA
1 TCTGGTACTTGGTGTATGTACACAGCTT
* *
522884 TCTGGTACTTGGTGTATGTACACATCTA
1 TCTGGTACTTGGTGTATGTACACAGCTT
*
522912 TCTAGTACTTGGTGTATGTACACAGCTT
1 TCTGGTACTTGGTGTATGTACACAGCTT
522940 TCTGGTACTTGGTGTATGTACACAGCTT
1 TCTGGTACTTGGTGTATGTACACAGCTT
522968 TCTGGTACTTGGTGTATGTACACAGCTT
1 TCTGGTACTTGGTGTATGTACACAGCTT
522996 TCTGGTACTTGGTGTATGTACACAGCTT
1 TCTGGTACTTGGTGTATGTACACAGCTT
523024 TCTGGTACTTGGTGTATGTACACAGCTT
1 TCTGGTACTTGGTGTATGTACACAGCTT
523052 TCTGGTACTTGGTGTATGTACACAGCTT
1 TCTGGTACTTGGTGTATGTACACAGCTT
523080 TCTGGTACTTGGTGTATGTACACAGCTT
1 TCTGGTACTTGGTGTATGTACACAGCTT
523108 TCTGGTACTTGGTGTATGTACACAGCTT
1 TCTGGTACTTGGTGTATGTACACAGCTT
523136 TCTGGTACTTGGTGTATGTACACAGCT
1 TCTGGTACTTGGTGTATGTACACAGCT
523163 NNNNNNNNNN
Statistics
Matches: 274, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 274 1.00
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (28 bp):
TCTGGTACTTGGTGTATGTACACAGCTT
Found at i:532184 original size:170 final size:170
Alignment explanation
Indices: 531902--532243 Score: 684
Period size: 170 Copynumber: 2.0 Consensus size: 170
531892 TATGACAAGA
531902 AACTTGTTAGGATAAAATCTGTAATCGAACAATGGAGCAAACGACACTTGACTCCAATTGGAAGG
1 AACTTGTTAGGATAAAATCTGTAATCGAACAATGGAGCAAACGACACTTGACTCCAATTGGAAGG
531967 ATAACACTGGTTAAGTCTCTTTTAATTTCACAATTAAACCACTTATTTATAGCCTTACCAAACCC
66 ATAACACTGGTTAAGTCTCTTTTAATTTCACAATTAAACCACTTATTTATAGCCTTACCAAACCC
532032 TCAGAGTAAAACATTAAAAGAATTAAACAATATTCTATTC
131 TCAGAGTAAAACATTAAAAGAATTAAACAATATTCTATTC
532072 AACTTGTTAGGATAAAATCTGTAATCGAACAATGGAGCAAACGACACTTGACTCCAATTGGAAGG
1 AACTTGTTAGGATAAAATCTGTAATCGAACAATGGAGCAAACGACACTTGACTCCAATTGGAAGG
532137 ATAACACTGGTTAAGTCTCTTTTAATTTCACAATTAAACCACTTATTTATAGCCTTACCAAACCC
66 ATAACACTGGTTAAGTCTCTTTTAATTTCACAATTAAACCACTTATTTATAGCCTTACCAAACCC
532202 TCAGAGTAAAACATTAAAAGAATTAAACAATATTCTATTC
131 TCAGAGTAAAACATTAAAAGAATTAAACAATATTCTATTC
532242 AA
1 AA
532244 TTTTATTTGG
Statistics
Matches: 172, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
170 172 1.00
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (170 bp):
AACTTGTTAGGATAAAATCTGTAATCGAACAATGGAGCAAACGACACTTGACTCCAATTGGAAGG
ATAACACTGGTTAAGTCTCTTTTAATTTCACAATTAAACCACTTATTTATAGCCTTACCAAACCC
TCAGAGTAAAACATTAAAAGAATTAAACAATATTCTATTC
Found at i:533473 original size:2 final size:2
Alignment explanation
Indices: 533466--533510 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
533456 ACTCTAAGTG
533466 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
533508 CT C
1 CT C
533511 AATAAAAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:533695 original size:1 final size:1
Alignment explanation
Indices: 533689--533734 Score: 92
Period size: 1 Copynumber: 46.0 Consensus size: 1
533679 ACACTTCATC
533689 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
533735 CAATACACGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:541742 original size:2 final size:2
Alignment explanation
Indices: 541735--541770 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
541725 TAGTTGTTTT
*
541735 TG TG TG TG TG TG TG TG TG TG TG ATA TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG -TG TG TG TG TG TG T
541771 TTTTTGTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.97
3 1 0.03
ACGTcount: A:0.06, C:0.00, G:0.44, T:0.50
Consensus pattern (2 bp):
TG
Found at i:553622 original size:15 final size:15
Alignment explanation
Indices: 553604--553635 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
553594 AGAAGGTGAG
553604 GATGATGATGATGAA
1 GATGATGATGATGAA
553619 GATGATGATGATGAA
1 GATGATGATGATGAA
553634 GA
1 GA
553636 GGAGGAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.34, T:0.25
Consensus pattern (15 bp):
GATGATGATGATGAA
Found at i:555680 original size:4 final size:4
Alignment explanation
Indices: 555649--555696 Score: 60
Period size: 4 Copynumber: 12.0 Consensus size: 4
555639 GGGACAGACA
* * * *
555649 GACG GACT GACG GACG GACA GACA GACG GACG GACG GACT GACG GACG
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
555697 CAGAGGAAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.29, C:0.25, G:0.42, T:0.04
Consensus pattern (4 bp):
GACG
Found at i:555696 original size:12 final size:12
Alignment explanation
Indices: 555640--555687 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
555630 AACTGAAGTG
*
555640 GGACAGACAGAC
1 GGACAGACGGAC
*
555652 GGACTGACGGAC
1 GGACAGACGGAC
*
555664 GGACAGACAGAC
1 GGACAGACGGAC
*
555676 GGACGGACGGAC
1 GGACAGACGGAC
555688 TGACGGACGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.33, C:0.25, G:0.40, T:0.02
Consensus pattern (12 bp):
GGACAGACGGAC
Found at i:558926 original size:18 final size:18
Alignment explanation
Indices: 558903--558937 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
558893 TTGAATTTTG
558903 TACATATGAAGATTTGGT
1 TACATATGAAGATTTGGT
558921 TACATATGAAGATTTGG
1 TACATATGAAGATTTGG
558938 GTTGCTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (18 bp):
TACATATGAAGATTTGGT
Found at i:563848 original size:1 final size:1
Alignment explanation
Indices: 563844--563872 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
563834 GTGTGTGTGT
563844 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
563873 AGTGAATTGA
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:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:568790 original size:1 final size:1
Alignment explanation
Indices: 568784--568812 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
568774 GATAGAAGGA
568784 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
568813 AAGAACTTGC
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:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:569132 original size:44 final size:44
Alignment explanation
Indices: 569069--569152 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
569059 TTAGCTAAGA
*
569069 TTACAGAGAACATTTGTGCTATTCTGTATCCATTTACTCGAAAT
1 TTACAGAGAACATTTGTGCTATTCCGTATCCATTTACTCGAAAT
569113 TTACAGAGAACATTTGTGCTATTCCGTATCCATTTACTCG
1 TTACAGAGAACATTTGTGCTATTCCGTATCCATTTACTCG
569153 TAATGATATG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.38
Consensus pattern (44 bp):
TTACAGAGAACATTTGTGCTATTCCGTATCCATTTACTCGAAAT
Found at i:569647 original size:2 final size:2
Alignment explanation
Indices: 569640--569676 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
569630 TATATGAAAA
569640 AG AG AG AG AG 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 AG AG AG AG AG A
569677 TCGGCCAATA
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:570895 original size:2 final size:2
Alignment explanation
Indices: 570890--570935 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
570880 ACTTTATCTC
570890 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
570932 AG AG
1 AG AG
570936 CAAGGGTTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:571318 original size:6 final size:6
Alignment explanation
Indices: 571307--571344 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
571297 TGCTATACCC
571307 TCGGCG TCGGCG TCGGCGG T-GGCG TCGGCG TCGGCG TC
1 TCGGCG TCGGCG TCGGC-G TCGGCG TCGGCG TCGGCG TC
571345 CGGACCTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 2 0.07
6 26 0.87
7 2 0.07
ACGTcount: A:0.00, C:0.32, G:0.50, T:0.18
Consensus pattern (6 bp):
TCGGCG
Found at i:571701 original size:177 final size:178
Alignment explanation
Indices: 571482--571830 Score: 463
Period size: 181 Copynumber: 1.9 Consensus size: 178
571472 GGGTCCTAAA
* ***
571482 TTTCAGATGCTGGAGGAGGTTAAGGTTGTTGGACCAGG-T-TAAAGTTTTTGTTGCAGGTGCCCT
1 TTTCAGATGCTGGAGGAGGTTAAGGTTGTTAGACCAGGTTATAAAGTTTTTGAAACAGGTGCCCT
* * *
571545 TTGAT-AGCAATATCTTAGTTACTGCTGGTCCGTACTTCACCAAACTTGCATGGATGGTGCGTCT
66 CTGATGAG--ATATCTTAGTTACTACTGGTCCGTACTTCACCAAACTTCCATGGATGGTGCGTCT
571609 TATGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGG
129 TATGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGG
* * *
571659 TTTCGGATGCTGGAGGAGGTTAAGGTT-TTAAGAGCTGGTTAAATAAAGTTTTTGAAACAGGTGC
1 TTTCAGATGCTGGAGGAGGTTAAGGTTGTT-AGACCAGGTT--ATAAAGTTTTTGAAACAGGTGC
* * * * *
571723 CCTCTGATGATGATATCTTAGTTATTACTTGTCCTTACTTCACCAGACTTCCATGGATGGTGTGT
63 CCTCTGATGA-GATATCTTAGTTACTACTGGTCCGTACTTCACCAAACTTCCATGGATGGTGCGT
* *
571788 CTTATGATACTGATGCACCTGACAGGCTTGAATGCTGAGTCTG
127 CTTATGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTG
571831 GTTTCGGATG
Statistics
Matches: 148, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
176 2 0.01
177 31 0.21
178 1 0.01
181 112 0.76
182 1 0.01
183 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.34
Consensus pattern (178 bp):
TTTCAGATGCTGGAGGAGGTTAAGGTTGTTAGACCAGGTTATAAAGTTTTTGAAACAGGTGCCCT
CTGATGAGATATCTTAGTTACTACTGGTCCGTACTTCACCAAACTTCCATGGATGGTGCGTCTTA
TGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGG
Found at i:572512 original size:20 final size:20
Alignment explanation
Indices: 572489--572531 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
572479 TATGATATAG
572489 TATTGTATGATATGAAACAA
1 TATTGTATGATATGAAACAA
* *
572509 TATTGTTTGATATGATACAA
1 TATTGTATGATATGAAACAA
572529 TAT
1 TAT
572532 GATATATTAT
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:0.05, G:0.14, T:0.42
Consensus pattern (20 bp):
TATTGTATGATATGAAACAA
Found at i:572641 original size:28 final size:28
Alignment explanation
Indices: 572592--572645 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
572582 ATCAATTTTT
572592 TGATATTTTATGATATGATATTGTATCA
1 TGATATTTTATGATATGATATTGTATCA
572620 TGATATTGTTATG-TAT-AGTATTGTAT
1 TGATATT-TTATGATATGA-TATTGTAT
572646 ATTATGATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 1 0.04
28 18 0.75
29 5 0.21
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.52
Consensus pattern (28 bp):
TGATATTTTATGATATGATATTGTATCA
Found at i:572806 original size:15 final size:15
Alignment explanation
Indices: 572773--572974 Score: 84
Period size: 15 Copynumber: 12.5 Consensus size: 15
572763 ATATTCTATA
* **
572773 ATATTGTATCATACA
1 ATATTGTATAATATG
572788 ATATTGTATAATATG
1 ATATTGTATAATATG
572803 ATATTGGTTTCAGTAATATAG
1 ATATT-G--T-A-TAATAT-G
* * *
572824 A-ATTATATCACATG
1 ATATTGTATAATATG
* *
572838 AAATTGTATTATATG
1 ATATTGTATAATATG
*
572853 ATATTGTAATATTATATA
1 ATATTGT-ATA--ATATG
* *
572871 ATATTGTATCATACG
1 ATATTGTATAATATG
*
572886 ATATTGTATGATATG
1 ATATTGTATAATATG
*
572901 ATATTGGT-TTATATG
1 ATATT-GTATAATATG
*
572916 ATATTGTAATATCATGTG
1 ATATTGT-ATA--ATATG
* *
572934 ATATTATCATATCACATG
1 ATATTGT-ATA--ATATG
* *
572952 AAATTGTATTATATG
1 ATATTGTATAATATG
572967 ATATTGTA
1 ATATTGTA
572975 ATATATATTA
Statistics
Matches: 143, Mismatches: 29, Indels: 30
0.71 0.14 0.15
Matches are distributed among these distances:
14 4 0.03
15 80 0.56
16 7 0.05
17 5 0.03
18 35 0.24
19 1 0.01
20 9 0.06
21 2 0.01
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (15 bp):
ATATTGTATAATATG
Found at i:577488 original size:14 final size:14
Alignment explanation
Indices: 577469--577495 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
577459 AATGAATGAC
577469 TACATTAAACAATG
1 TACATTAAACAATG
577483 TACATTAAACAAT
1 TACATTAAACAAT
577496 AAGCTTTATT
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:0.52, C:0.15, G:0.04, T:0.30
Consensus pattern (14 bp):
TACATTAAACAATG
Found at i:592357 original size:19 final size:19
Alignment explanation
Indices: 592333--592370 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
592323 GGTAATCATT
592333 ATTTATTTATCATCCATAC
1 ATTTATTTATCATCCATAC
*
592352 ATTTATTTATCCTCCATAC
1 ATTTATTTATCATCCATAC
592371 CCAAAGTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTATTTATCATCCATAC
Found at i:594340 original size:36 final size:36
Alignment explanation
Indices: 594291--594381 Score: 157
Period size: 36 Copynumber: 2.5 Consensus size: 36
594281 GTTGTGATAA
594291 ATATGACAC-TTGACCTTGTGATGTATCAGTACATGT
1 ATATGAC-CTTTGACCTTGTGATGTATCAGTACATGT
*
594327 ATATGACCTTTGACCTTGCGATGTATCAGTACATGT
1 ATATGACCTTTGACCTTGTGATGTATCAGTACATGT
594363 ATATGACCTTTGACCTTGT
1 ATATGACCTTTGACCTTGT
594382 AATAGTTGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
35 1 0.02
36 51 0.98
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (36 bp):
ATATGACCTTTGACCTTGTGATGTATCAGTACATGT
Found at i:602996 original size:2 final size:2
Alignment explanation
Indices: 602989--603048 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
602979 GTCTTTGTGC
602989 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
603031 AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG
603049 GGGGGGGTTT
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:603119 original size:2 final size:2
Alignment explanation
Indices: 603112--603141 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
603102 GGAGGGGGAA
603112 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
603142 GTGGTTTAGT
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:604623 original size:19 final size:19
Alignment explanation
Indices: 604599--604647 Score: 53
Period size: 23 Copynumber: 2.4 Consensus size: 19
604589 CAGTTTATGC
604599 TTTATAAGCCACGAAGCGG
1 TTTATAAGCCACGAAGCGG
*
604618 TTTATAAAAAAGCCGCGAAGCGG
1 TTTAT----AAGCCACGAAGCGG
604641 TTTATAA
1 TTTATAA
604648 AAAAGTGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
19 7 0.28
23 18 0.72
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.24
Consensus pattern (19 bp):
TTTATAAGCCACGAAGCGG
Found at i:604636 original size:23 final size:23
Alignment explanation
Indices: 604604--604652 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
604594 TATGCTTTAT
604604 AAGCCACGAAGCGGTTTATAAAA
1 AAGCCACGAAGCGGTTTATAAAA
*
604627 AAGCCGCGAAGCGGTTTATAAAA
1 AAGCCACGAAGCGGTTTATAAAA
604650 AAG
1 AAG
604653 TGTAAACTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.16
Consensus pattern (23 bp):
AAGCCACGAAGCGGTTTATAAAA
Found at i:631681 original size:2 final size:2
Alignment explanation
Indices: 631674--631739 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
631664 GACAGGCTAA
*
631674 TC TC TC TC TC TT 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
631716 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
631740 ACCAATAACC
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:634158 original size:2 final size:2
Alignment explanation
Indices: 634153--634188 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
634143 ACACCTAAAC
*
634153 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
634189 TGGTCAATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:642394 original size:16 final size:17
Alignment explanation
Indices: 642368--642408 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
642358 AACTTAAAAG
642368 TTGATTTGATTGGTTAA
1 TTGATTTGATTGGTTAA
642385 TTGA-TTGATTGGTTAA
1 TTGATTTGATTGGTTAA
*
642401 TTGGTTTG
1 TTGATTTG
642409 TAACCAATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.54
Consensus pattern (17 bp):
TTGATTTGATTGGTTAA
Found at i:653681 original size:2 final size:2
Alignment explanation
Indices: 653674--653702 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
653664 GAAAATCCCC
653674 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
653703 ACACACACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:653707 original size:2 final size:2
Alignment explanation
Indices: 653702--653743 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
653692 CTCTCTCTCT
653702 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
653744 TAAANNNNNN
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:657530 original size:27 final size:27
Alignment explanation
Indices: 657480--657532 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
657470 GTCTAAGGTA
**
657480 AGATTTGTAAAACCGCTTTTGTACGAT
1 AGATTTGTAAAACCGCTTCGGTACGAT
657507 AGATTTGTAAAACCGCTTCGGTACGA
1 AGATTTGTAAAACCGCTTCGGTACGA
657533 GATCGAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (27 bp):
AGATTTGTAAAACCGCTTCGGTACGAT
Found at i:674511 original size:18 final size:18
Alignment explanation
Indices: 674484--674525 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
674474 CCGTCGACAC
674484 GCGACCCCCAATATACAA
1 GCGACCCCCAATATACAA
*
674502 GCGACTCCCAATATACAA
1 GCGACCCCCAATATACAA
*
674520 GTGACC
1 GCGACC
674526 AGCTGCAGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.36, G:0.14, T:0.14
Consensus pattern (18 bp):
GCGACCCCCAATATACAA
Found at i:676732 original size:40 final size:40
Alignment explanation
Indices: 676677--676757 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
676667 TGTTAAGCTT
*
676677 CGAATTATAAGCAAGATACAGAGATTTGCTCACAATTGTA
1 CGAATTATAAGCAAGAGACAGAGATTTGCTCACAATTGTA
676717 CGAATTATAAGCAAGAGACAGAGATTTGCTCACAATTGTA
1 CGAATTATAAGCAAGAGACAGAGATTTGCTCACAATTGTA
676757 C
1 C
676758 ACAGATCTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (40 bp):
CGAATTATAAGCAAGAGACAGAGATTTGCTCACAATTGTA
Found at i:677192 original size:166 final size:166
Alignment explanation
Indices: 676900--678802 Score: 2588
Period size: 166 Copynumber: 11.5 Consensus size: 166
676890 CCTGAGGGTT
* ** * * **
676900 GGGCCACAATGTGGG-TAAAAGTTTAACAAATGAATATATAGAGTAAATCTTTAATGATCTTCTT
1 GGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTT
* * *
676964 CTCAGAAATTAATCGGCCAGGAAAGCTGAAACTTGTGTGGAACCATCCTCAGGTAGTGTAGATTC
66 CTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTC
*
677029 AAAGTTGTGAACATCATGACCCCCGGGGGTAGGATG
131 AAAGTTGTGAAAATCATGACCCCCGGGGGTAGGATG
* * * * * *
677065 GGGTCGCAATGGGGGATCGAAGTTTAACATATGAATACATAAAGTAAATCTTTAAAAATTTTCTT
1 GGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTT
* *
677130 CTCAGAAACTAATCGGCCAGGAAAGCTGACACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTC
66 CTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTC
*
677195 AAAGTTGTGAAAATCATGACACCC-GGGGTAGGATGG
131 AAAGTTGTGAAAATCATGACCCCCGGGGGTAGGAT-G
* * * *
677231 GGGCCACAGTGGTGGG-TTGAAGTTTTACATAGGAATATATACAGTAAATCTTTAAAAATCTTCT
1 GGGCCACAATGG-GGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCT
* *
677295 TCTCAGAAACAAATCAGCCAGGAAAGCTGAAACTTGTGT-GAAGGCATCCTCAGGTAGTGTAAAT
65 TCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAA-GCATCCTCAGGTAGTGTAGAT
* * * *
677359 TCAAAGTTGTGAAAATGATGATCCCCGGGGATAGGGTG
129 TCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGATG
*
677397 GGGCCACAATGGTGGG-TCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTC-
1 GGGCCACAATGG-GGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCT
* * * *
677460 T-T-AGAAACTAATCATCCAGGAAAGCTGACACTTGTGTGGATGCATCCTCAGGTAGTGTAAATT
65 TCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATT
* *
677523 TAAAGTTGTGAAAATCATGACCCCCGGGTGTAGGATG
130 CAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGATG
*
677560 GGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATGTTCTT
1 GGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTT
*
677625 CTCAGAAACTAATCAGCC-GGCAAAGCTGAAACTTGTGTGGAAGCATTCTCAGGTAGTGTAGATT
66 CTCAGAAACTAATCAGCCAGG-AAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATT
* * * * **
677689 CAAAATTGTGAAAATAATAACCCCTGTAGGTAGG-TGG
130 CAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGAT-G
* *
677726 GGGCCACAATGGGGGATCGAAGTTTAACATATGATTATATAGAGTAAATCTTTAAAAATCTTCTT
1 GGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTT
* * * *
677791 CTCAGAAACTAATAAGCCAGGAAAGCTGAAACTTGTGTGGAACCATCCCCAGGTAGTGTAGATGC
66 CTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTC
* *
677856 AAAGTTGTGAAAATCATGA-CACCAGGGGTAGGATGG
131 AAAGTTGTGAAAATCATGACCCCCGGGGGTAGGAT-G
* * *
677892 GGGCCACAATGGTGGG-TTGAAGTTTTACATAGGAATATATACAGTAAATCTTTAAAAATCTTCT
1 GGGCCACAATGG-GGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCT
* * * *
677956 TCTCAGAAACAAATCAGCCAGGAAAGCTGAAACTTGTGT-GAACCATCCCCAGGTAGTGTAAATT
65 TCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATT
* * * *
678020 CAAAGTTGTGAAAATGATGATCCCCGGGGATAGGGTG
130 CAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGATG
* *
678057 GGGCCACAATGGTGGG-TCGAAGTTTTACATAGGAATATATAGTGTAAATCTTTAAAAATCTTCT
1 GGGCCACAATGG-GGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCT
* * * *
678121 TCTCAGAAACTAATCAGCCAGGAAAGCTGACACCTGTGTGGATGCATCCTCAGGTAGTGTAAATT
65 TCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATT
* *
678186 TAAAGTTGTGAAAATCATGACCCCCGGGTGTAGGATG
130 CAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGATG
* *
678223 GGGCCACTATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATGTTCTT
1 GGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTT
*
678288 CTCAGAAACTAATCAGCC-GGCAAAGCTGAAACTTGTGTGGAAGCATTCTCAGGTAGTGTAGATT
66 CTCAGAAACTAATCAGCCAGG-AAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATT
* * * * **
678352 CAAAATTGTGAAAATAATAACCCCTGTAGGTAGG-TGG
130 CAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGAT-G
* *
678389 GGGCCACAATGGGGGATCGAAGTTTAACATATGATTATATAGAGTAAATCTTTAAAAATCTTCTT
1 GGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTT
* * *
678454 CTCAGAAACTAATAAGCCAGGAAAGCTGAAACTTGTGTGGAACCATCCCCAGGTAGTGTAGATTC
66 CTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTC
* * * * *
678519 AAATTTGTGAAAATCATGATCCCTGGGGGTAGGTTT
131 AAAGTTGTGAAAATCATGACCCCCGGGGGTAGGATG
* * * *
678555 GGGCCACAATGGGAGG-TCGATGTTTTACATAGGAATAAACAGAGTAAATCTTTAAAAATCTTCT
1 GGGCCACAATGGG-GGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCT
* * *
678619 TCTCAGAAACTAATTAGCCAGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTAGTGTAGACT
65 TCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATT
* * *
678684 CAAAGTTGTGAAAATCATGATCCCCAGGGGTAGGGTG
130 CAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGATG
* * * * *
678721 GGGTCACAAT-GGGGAGTCAAAGTTTATCAAAGGAATATATAGGGTAAATCTTTAAAAA---TCT
1 GGGCCACAATGGGGGA-TCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCT
678782 TCTCAGAAACTAATCAGCCAG
65 TCTCAGAAACTAATCAGCCAG
678803 ATGATTCTTC
Statistics
Matches: 1548, Mismatches: 165, Indels: 52
0.88 0.09 0.03
Matches are distributed among these distances:
162 3 0.00
163 165 0.11
164 6 0.00
165 186 0.12
166 1167 0.75
167 21 0.01
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.27
Consensus pattern (166 bp):
GGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTT
CTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTC
AAAGTTGTGAAAATCATGACCCCCGGGGGTAGGATG
Found at i:677916 original size:495 final size:494
Alignment explanation
Indices: 676900--678802 Score: 2618
Period size: 495 Copynumber: 3.8 Consensus size: 494
676890 CCTGAGGGTT
** * * **
676900 GGGCCACAAT-GTGGGTAAAAGTTTAACAAATGAATATATAGAGTAAATCTTTAATGATCTTCTT
1 GGGCCACAATGGTGGGTCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTT
* * * *
676964 CTCAGAAATTAATCGGCCAGGAAAGCTGAAACTTGTGTGGAACCATCCTCAGGTAGTGTAGATTC
66 CTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAACCATCCCCAGGTAGTGTAAATTC
* * *
677029 AAAGTTGTGAACATCATGACCCCCGGGGGTAGGATGGGGTCGCAATGGGGGATCGAAGTTTAACA
131 AAAGTTGTGAAAATCATGACCCCCGGGGGTAGGATGGGGCCACAATGGGGG-TCGAAGTTTAACA
* * * * *
677094 TATGAATACATAAAGTAAATCTTTAAAAATTTTCTTCTCAGAAACTAATCGGCCAGGAAAGCTGA
195 TAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGA
* *
677159 CACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACACCCGGGGT
260 AACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATAAC-CCCGGGGT
* * * *
677224 AGGATGGGGGCCACAGTGGTGGG-TTGAAGTTTTACATAGGAATATATACAGTAAATCTTTAAAA
324 AGGATGGGGGCCACAATGG-GGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAA
*
677288 ATCTTCTTCTCAGAAACAAATCAGCCAGGAAAGCTGAAACTTGTGT-GAAGGCATCCTCAGGTAG
388 ATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAA-GCATCCTCAGGTAG
* * *
677352 TGTAAATTCAAAGTTGTGAAAATGATGATCCCCGGGGATAGG-GTG
452 TGTAGATTCAAAGTTGTGAAAATAATGA-CCCAGGGG-TAGGTG-G
*
677397 GGGCCACAATGGTGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTC-T
1 GGGCCACAATGGTGGGTCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTT
* * ** * *
677461 -T-AGAAACTAATCATCCAGGAAAGCTGACACTTGTGTGGATGCATCCTCAGGTAGTGTAAATTT
66 CTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAACCATCCCCAGGTAGTGTAAATTC
*
677524 AAAGTTGTGAAAATCATGACCCCCGGGTGTAGGATGGGGCCACAATGGGGGATCGAAGTTTAACA
131 AAAGTTGTGAAAATCATGACCCCCGGGGGTAGGATGGGGCCACAATGGGGG-TCGAAGTTTAACA
*
677589 TAGGAATATATAGAGTAAATCTTTAAAAATGTTCTTCTCAGAAACTAATCAGCC-GGCAAAGCTG
195 TAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGG-AAAGCTG
* * * *
677653 AAACTTGTGTGGAAGCATTCTCAGGTAGTGTAGATTCAAAATTGTGAAAATAATAACCCCTGTAG
259 AAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATAACCCC-G-GG
* *
677718 GTAGG-TGGGGGCCACAATGGGGGATCGAAGTTTAACATATGATTATATAGAGTAAATCTTTAAA
322 GTAGGATGGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAA
* * *
677782 AATCTTCTTCTCAGAAACTAATAAGCCAGGAAAGCTGAAACTTGTGTGGAACCATCCCCAGGTAG
387 AATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAG
* *
677847 TGTAGATGCAAAGTTGTGAAAATCATGACACCAGGGGTAGGATGG
452 TGTAGATTCAAAGTTGTGAAAATAATGAC-CCAGGGGTAGG-TGG
* * *
677892 GGGCCACAATGGTGGGTTGAAGTTTTACATAGGAATATATACAGTAAATCTTTAAAAATCTTCTT
1 GGGCCACAATGGTGGGTCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTT
*
677957 CTCAGAAACAAATCAGCCAGGAAAGCTGAAACTTGTGT-GAACCATCCCCAGGTAGTGTAAATTC
66 CTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAACCATCCCCAGGTAGTGTAAATTC
* * * * *
678021 AAAGTTGTGAAAATGATGATCCCCGGGGATAGGGTGGGGCCACAATGGTGGGTCGAAGTTTTACA
131 AAAGTTGTGAAAATCATGACCCCCGGGGGTAGGATGGGGCCACAATGG-GGGTCGAAGTTTAACA
*
678086 TAGGAATATATAGTGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGA
195 TAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGA
* * * * * *
678151 CACCTGTGTGGATGCATCCTCAGGTAGTGTAAATTTAAAGTTGTGAAAATCATGACCCCCGGGTG
260 AACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCAT-AACCCCGGG-G
*
678216 TAGGAT-GGGGCCACTATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAA
323 TAGGATGGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAA
* *
678280 ATGTTCTTCTCAGAAACTAATCAGCC-GGCAAAGCTGAAACTTGTGTGGAAGCATTCTCAGGTAG
388 ATCTTCTTCTCAGAAACTAATCAGCCAGG-AAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAG
* * * *
678344 TGTAGATTCAAAATTGTGAAAATAATAACCCCTGTAGGTAGGTGG
452 TGTAGATTCAAAGTTGTGAAAATAATGA-CCCAG-GGGTAGGTGG
* *
678389 GGGCCACAATGG-GGGATCGAAGTTTAACATATGATTATATAGAGTAAATCTTTAAAAATCTTCT
1 GGGCCACAATGGTGGG-TCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCT
* *
678453 TCTCAGAAACTAATAAGCCAGGAAAGCTGAAACTTGTGTGGAACCATCCCCAGGTAGTGTAGATT
65 TCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAACCATCCCCAGGTAGTGTAAATT
* * * * * * *
678518 CAAATTTGTGAAAATCATGATCCCTGGGGGTAGGTTTGGGCCACAATGGGAGGTCGATGTTTTAC
130 CAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGATGGGGCCACAATGGG-GGTCGAAGTTTAAC
* * *
678583 ATAGGAATAAACAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATTAGCCAGGAAAGCTG
194 ATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTG
* * *
678648 AAACTTGTGTGAAAGCATCCTCAGGTAGTGTAGACTCAAAGTTGTGAAAATCATGATCCCCAGGG
259 AAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCAT-AACCCC-GGG
* * * * * *
678713 GTAGGGT-GGGGTCACAAT-GGGGAGTCAAAGTTTATCAAAGGAATATATAGGGTAAATCTTTAA
322 GTAGGATGGGGGCCACAATGGGGGA-TCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAA
678776 AAA---TCTTCTCAGAAACTAATCAGCCAG
386 AAATCTTCTTCTCAGAAACTAATCAGCCAG
678803 ATGATTCTTC
Statistics
Matches: 1261, Mismatches: 119, Indels: 53
0.88 0.08 0.04
Matches are distributed among these distances:
494 13 0.01
495 445 0.35
496 19 0.02
497 439 0.35
498 342 0.27
499 3 0.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.27
Consensus pattern (494 bp):
GGGCCACAATGGTGGGTCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTT
CTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAACCATCCCCAGGTAGTGTAAATTC
AAAGTTGTGAAAATCATGACCCCCGGGGGTAGGATGGGGCCACAATGGGGGTCGAAGTTTAACAT
AGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAA
ACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATAACCCCGGGGTAG
GATGGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATC
TTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTA
GATTCAAAGTTGTGAAAATAATGACCCAGGGGTAGGTGG
Found at i:679766 original size:10 final size:10
Alignment explanation
Indices: 679751--679775 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
679741 AGTCTCAAGC
679751 GAGAGAGAGG
1 GAGAGAGAGG
679761 GAGAGAGAGG
1 GAGAGAGAGG
679771 GAGAG
1 GAGAG
679776 GGGGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (10 bp):
GAGAGAGAGG
Found at i:689325 original size:21 final size:21
Alignment explanation
Indices: 689299--689342 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
689289 TAAATCAAAT
689299 TAGGCTAAAATTTGTATACTA
1 TAGGCTAAAATTTGTATACTA
689320 TAGGCTAAAATTTGTATACTA
1 TAGGCTAAAATTTGTATACTA
689341 TA
1 TA
689343 CGAAATTGAG
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:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
TAGGCTAAAATTTGTATACTA
Found at i:692136 original size:11 final size:11
Alignment explanation
Indices: 692122--692146 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
692112 GACATTCCAA
692122 TTCCATTATTT
1 TTCCATTATTT
692133 TTCCATTATTT
1 TTCCATTATTT
692144 TTC
1 TTC
692147 TGGACATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCCATTATTT
Found at i:693312 original size:2 final size:2
Alignment explanation
Indices: 693305--693335 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
693295 TAGCTCTGTG
*
693305 GA GA GA GA TA 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 G
693336 TATGAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.48, T:0.03
Consensus pattern (2 bp):
GA
Found at i:697484 original size:9 final size:9
Alignment explanation
Indices: 697470--697498 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
697460 TTCCATATCA
697470 TTAAGACTG
1 TTAAGACTG
697479 TTAAGACTG
1 TTAAGACTG
697488 TTAAGACTG
1 TTAAGACTG
697497 TT
1 TT
697499 GAACATGTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (9 bp):
TTAAGACTG
Found at i:704270 original size:435 final size:434
Alignment explanation
Indices: 703584--704389 Score: 1330
Period size: 435 Copynumber: 1.9 Consensus size: 434
703574 TAATGATTTC
703584 ATCATGTGTTACGTAATTAGGGGGTTTTAAGGGGCCAGAAGTCCAAAATTTCGATCAATAATATC
1 ATCATGTGTTACGTAATTAGGGGGTTTTAAGGGGCCAGAAGTCCAAAATTTCGATCAATAATATC
*
703649 TCAAAAAGGACAAATATTTCGAAAAGCAATATAGAATAAAAGATGCTTAGAATAATGTTTTAAAC
66 TCAAAAAGGACAAATATTTCGAAAAGCAATATAGAATAAAAGATGCTTAGAATAAGGTTTTAAAC
**
703714 AATATTCAATCATAAAAGTTTCACCATCTGGCCCCAAAAAGGAGATAAGGGGTCGGCCCCTAAAA
131 AATATTCAATCATAAAAAATTCACCATCTGGCCCCAAAAAGGAGATAAGGGGTCGGCCCCTAAAA
* * * *
703779 CGTCCTATCCCAGATAGCTCAAAGACGGCAAAAAATTTCTAAACGCTGTTGAACAAAATATGTTT
196 CGTCATATCCCAGATAGCTCAAAAACGGCAAAAAATTTCTAAACACTGTCGAACAAAATATGTTT
* *
703844 AATATCAAAAGACCTTTTATATGATGTCAAGAAAAAGGGACTGGCCCTTCAATTTAGGGGCCAAA
261 AATATCAAAAGACCTTTCATATGATCTCAAG--AAAGGGACTGGCCCTTCAATTTAGGGGCCAAA
*
703909 AGGGCCCCAAAATCTTTCTT-TAATAACACTTTACTGAGAAATATTTTGCAATATGTCTAAGAAG
324 AGGGCCCCAAAATCTTTCTTAT-ATAACACTTTACTGAGAAATACTTTGCAATATGTCTAAGAAG
703973 CATAAATGTTCATCTTTCACTTATAAACTATACATTATAAAATGTTT
388 CATAAATGTTCATCTTTCACTTATAAACTATACATTATAAAATGTTT
*
704020 ATCATGTGTTACGTAATTA-GGGGTTTTAAGGGGCCAGAAGTCGAAAATTTCGATCAATAATATC
1 ATCATGTGTTACGTAATTAGGGGGTTTTAAGGGGCCAGAAGTCCAAAATTTCGATCAATAATATC
* *
704084 TCAAAAAGGACAAATATTTTGAAAAGCAATATAGAATAAAAGATGCTTAGAATGAGGTTTTAAAC
66 TCAAAAAGGACAAATATTTCGAAAAGCAATATAGAATAAAAGATGCTTAGAATAAGGTTTTAAAC
***
704149 AATA-TCAATCATAAAAAATTCGTTATCTGGCCCCAAAAAGGAGATAAGGGGTCGGCCCCTAAAA
131 AATATTCAATCATAAAAAATTCACCATCTGGCCCCAAAAAGGAGATAAGGGGTCGGCCCCTAAAA
* *
704213 CGTCATATCCCAGATAGCTCAAAAACGGCAAAGATTTTCTAAACACTTGTCGAACAAAATATGTT
196 CGTCATATCCCAGATAGCTCAAAAACGGCAAAAAATTTCTAAACAC-TGTCGAACAAAATATGTT
* *
704278 TAATATCAAAAGACCTTTCATATGATCTCAAGAAAGGGGCTGGCCCTTCTATTTAGGGGCCAAAA
260 TAATATCAAAAGACCTTTCATATGATCTCAAGAAAGGGACTGGCCCTTCAATTTAGGGGCCAAAA
* ** * *
704343 GGGCTCCAATTTCTTTCTTATATAGCACTTTACTGAGATATACTTTG
325 GGGCCCCAAAATCTTTCTTATATAACACTTTACTGAGAAATACTTTG
704390 AAAAGCAATA
Statistics
Matches: 343, Mismatches: 25, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
433 70 0.20
434 97 0.28
435 157 0.46
436 19 0.06
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (434 bp):
ATCATGTGTTACGTAATTAGGGGGTTTTAAGGGGCCAGAAGTCCAAAATTTCGATCAATAATATC
TCAAAAAGGACAAATATTTCGAAAAGCAATATAGAATAAAAGATGCTTAGAATAAGGTTTTAAAC
AATATTCAATCATAAAAAATTCACCATCTGGCCCCAAAAAGGAGATAAGGGGTCGGCCCCTAAAA
CGTCATATCCCAGATAGCTCAAAAACGGCAAAAAATTTCTAAACACTGTCGAACAAAATATGTTT
AATATCAAAAGACCTTTCATATGATCTCAAGAAAGGGACTGGCCCTTCAATTTAGGGGCCAAAAG
GGCCCCAAAATCTTTCTTATATAACACTTTACTGAGAAATACTTTGCAATATGTCTAAGAAGCAT
AAATGTTCATCTTTCACTTATAAACTATACATTATAAAATGTTT
Found at i:709752 original size:22 final size:22
Alignment explanation
Indices: 709724--709769 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
709714 AACATATTTT
*
709724 GATCAGAGATGTAACTTGCCAA
1 GATCAGAGATGTAACTAGCCAA
709746 GATCAGAGATGTAACTAGCCAA
1 GATCAGAGATGTAACTAGCCAA
709768 GA
1 GA
709770 CTAATAACTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (22 bp):
GATCAGAGATGTAACTAGCCAA
Found at i:710680 original size:11 final size:11
Alignment explanation
Indices: 710664--710697 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
710654 AATGCAATTT
710664 CTAAGTAAACC
1 CTAAGTAAACC
710675 CTAAGTAAACC
1 CTAAGTAAACC
*
710686 CAAAGTAAACC
1 CTAAGTAAACC
710697 C
1 C
710698 CGAGTGGACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.47, C:0.29, G:0.09, T:0.15
Consensus pattern (11 bp):
CTAAGTAAACC
Found at i:711735 original size:11 final size:11
Alignment explanation
Indices: 711719--711761 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
711709 GTCCAAACTT
711719 CTTTAAGCCAC
1 CTTTAAGCCAC
*
711730 CTTTAAGTCAC
1 CTTTAAGCCAC
*
711741 CTATAAGCCAC
1 CTTTAAGCCAC
711752 CTTTAAGCCA
1 CTTTAAGCCA
711762 TAACAACCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.30, C:0.33, G:0.09, T:0.28
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:712667 original size:21 final size:21
Alignment explanation
Indices: 712638--712731 Score: 80
Period size: 21 Copynumber: 4.4 Consensus size: 21
712628 CAATCCTATC
* *
712638 CTATTGTGCGTTTATATTGTT
1 CTATCGTGCGTTTATACTGTT
* * * * *
712659 CTATCGTGCATTAATCCTATC
1 CTATCGTGCGTTTATACTGTT
*
712680 CTATCGTGCGTGTATACTGTT
1 CTATCGTGCGTTTATACTGTT
* * *
712701 CTATCGTGCGTTAATCCTATTT
1 CTATCGTGCGTTTATACT-GTT
712723 CTATCGTGC
1 CTATCGTGC
712732 ATGAATCCTA
Statistics
Matches: 55, Mismatches: 17, Indels: 1
0.75 0.23 0.01
Matches are distributed among these distances:
21 44 0.80
22 11 0.20
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (21 bp):
CTATCGTGCGTTTATACTGTT
Found at i:712678 original size:42 final size:42
Alignment explanation
Indices: 712619--712731 Score: 154
Period size: 42 Copynumber: 2.7 Consensus size: 42
712609 TCCTTTTTAA
* * * * *
712619 ATCGTGTATCAATCCTATCCTATTGTGCGTTTATATTGTTCT
1 ATCGTGCATTAATCCTATCCTATCGTGCGTGTATACTGTTCT
712661 ATCGTGCATTAATCCTATCCTATCGTGCGTGTATACTGTTCT
1 ATCGTGCATTAATCCTATCCTATCGTGCGTGTATACTGTTCT
* *
712703 ATCGTGCGTTAATCCTATTTCTATCGTGC
1 ATCGTGCATTAATCCTA-TCCTATCGTGC
712732 ATGAATCCTA
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
42 53 0.84
43 10 0.16
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (42 bp):
ATCGTGCATTAATCCTATCCTATCGTGCGTGTATACTGTTCT
Found at i:712749 original size:21 final size:21
Alignment explanation
Indices: 712659--712750 Score: 94
Period size: 21 Copynumber: 4.3 Consensus size: 21
712649 TTATATTGTT
*
712659 CTATCGTGCATTAATCCTATC
1 CTATCGTGCATGAATCCTATC
* * * * *
712680 CTATCGTGCGTGTATACTGTT
1 CTATCGTGCATGAATCCTATC
* * *
712701 CTATCGTGCGTTAATCCTATTT
1 CTATCGTGCATGAATCCTA-TC
712723 CTATCGTGCATGAATCCTATC
1 CTATCGTGCATGAATCCTATC
712744 CTATCGT
1 CTATCGT
712751 TTATCTTGTA
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
21 38 0.67
22 19 0.33
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (21 bp):
CTATCGTGCATGAATCCTATC
Found at i:735825 original size:20 final size:20
Alignment explanation
Indices: 735760--735825 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
735750 GTAAAAAATG
*
735760 TCAGTAATTTTCTAAGTTTA
1 TCAGTACTTTTCTAAGTTTA
* *
735780 TCAGTAC-TGTCTAAGTTTG
1 TCAGTACTTTTCTAAGTTTA
*
735799 TCAGTACTTTTCTAAGTTTC
1 TCAGTACTTTTCTAAGTTTA
735819 TCAGTAC
1 TCAGTAC
735826 CGTCAGTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 17 0.43
20 23 0.57
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (20 bp):
TCAGTACTTTTCTAAGTTTA
Found at i:735855 original size:41 final size:41
Alignment explanation
Indices: 735716--735874 Score: 178
Period size: 41 Copynumber: 3.9 Consensus size: 41
735706 TATCAGTACT
* * * *
735716 TGTCAGTACTTCTCTACGTTTTTCAATACCGTCAGTAAAAAA
1 TGTCAGTACTTTTCTAAGTTTATCAGTACCGTCAGT-AAAAA
* * ***
735758 TGTCAGTAATTTTCTAAGTTTATCAGTACTGTC--TAAGTT
1 TGTCAGTACTTTTCTAAGTTTATCAGTACCGTCAGTAAAAA
*
735797 TGTCAGTACTTTTCTAAGTTTCTCAGTACCGTCAGTAAAAA
1 TGTCAGTACTTTTCTAAGTTTATCAGTACCGTCAGTAAAAA
* **
735838 CGTCAGTACTTTTCTAAGTTTATCAGTAATGTCAGTA
1 TGTCAGTACTTTTCTAAGTTTATCAGTACCGTCAGTA
735875 CATTGTCAGT
Statistics
Matches: 96, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
39 32 0.33
40 1 0.01
41 36 0.38
42 27 0.28
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (41 bp):
TGTCAGTACTTTTCTAAGTTTATCAGTACCGTCAGTAAAAA
Found at i:735861 original size:80 final size:81
Alignment explanation
Indices: 735715--735870 Score: 242
Period size: 80 Copynumber: 1.9 Consensus size: 81
735705 TTATCAGTAC
* * *
735715 TTGTCAGTACTTCTCTACGTTTTTCAATACCGTCAGTAAAAAATGTCAGTAATTTTCTAAGTTTA
1 TTGTCAGTACTTCTCTAAGTTTCTCAATACCGTCAGTAAAAAACGTCAGTAATTTTCTAAGTTTA
*
735780 TCAGTACTGTCTAAGT
66 TCAGTAATGTCTAAGT
* * *
735796 TTGTCAGTACTTTTCTAAGTTTCTCAGTACCGTCAGT-AAAAACGTCAGTACTTTTCTAAGTTTA
1 TTGTCAGTACTTCTCTAAGTTTCTCAATACCGTCAGTAAAAAACGTCAGTAATTTTCTAAGTTTA
735860 TCAGTAATGTC
66 TCAGTAATGTC
735871 AGTACATTGT
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
80 35 0.51
81 33 0.49
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (81 bp):
TTGTCAGTACTTCTCTAAGTTTCTCAATACCGTCAGTAAAAAACGTCAGTAATTTTCTAAGTTTA
TCAGTAATGTCTAAGT
Done.