Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold448
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: 1018568
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.28
Warning! 171214 characters in sequence are not A, C, G, or T
File 4 of 3
Found at i:881332 original size:3 final size:3
Alignment explanation
Indices: 881326--881377 Score: 95
Period size: 3 Copynumber: 17.0 Consensus size: 3
881316 AGGAAGAAGT
881326 AGG AGG AGG AGG AGG AGG AAGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG -AGG AGG AGG AGG AGG AGG AGG AGG AGG
881372 AGG AGG
1 AGG AGG
881378 CTTCAATCCT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:883788 original size:63 final size:63
Alignment explanation
Indices: 883699--884043 Score: 344
Period size: 63 Copynumber: 5.6 Consensus size: 63
883689 TTTTATTTTC
* * **
883699 TACACTTTAATCTGTAAATTTTACACTTTAATCTGTAAATTTTACACTTTAATCTGTAAAATT
1 TACACATTAATCTGTAAAATTTACACTTTAAAGTGTAAATTTTACACTTTAATCTGTAAAATT
* * * * *
883762 CACACATTAATGTGTAAAATTCACACTTTAAAGTGTAAAATTCACACTTTAATCTGTAAAATT
1 TACACATTAATCTGTAAAATTTACACTTTAAAGTGTAAATTTTACACTTTAATCTGTAAAATT
* * * ** * *
883825 CACACTTTAATCTGTAAATTTTACACTTTAATCTGTAAATTTTACATTTTAATCTGTAAATTT
1 TACACATTAATCTGTAAAATTTACACTTTAAAGTGTAAATTTTACACTTTAATCTGTAAAATT
* * * *
883888 TACACTTTAATCTGTAAAATTCACACTTTAAAGTGTAAA-ATT-CAC---AA-GTGTAAAATT
1 TACACATTAATCTGTAAAATTTACACTTTAAAGTGTAAATTTTACACTTTAATCTGTAAAATT
** ** * * * ** *
883945 TACGGATTAAAGTGTAAATTTTACACTTTCAAGTGTGAATTTTACA-GATAATGTGTAAAATT
1 TACACATTAATCTGTAAAATTTACACTTTAAAGTGTAAATTTTACACTTTAATCTGTAAAATT
* **
884007 TACAGATTAAAGTGTAAAATTTACACTTTAAAGTGTA
1 TACACATTAATCTGTAAAATTTACACTTTAAAGTGTA
884044 GAAAATAAAA
Statistics
Matches: 234, Mismatches: 42, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
57 38 0.16
58 4 0.02
59 2 0.01
61 4 0.02
62 45 0.19
63 141 0.60
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (63 bp):
TACACATTAATCTGTAAAATTTACACTTTAAAGTGTAAATTTTACACTTTAATCTGTAAAATT
Found at i:883930 original size:21 final size:21
Alignment explanation
Indices: 883699--884043 Score: 310
Period size: 21 Copynumber: 16.8 Consensus size: 21
883689 TTTTATTTTC
* *
883699 TACACTTTAATCTGTAAATTT
1 TACACTTTAATGTGTAAAATT
* *
883720 TACACTTTAATCTGTAAATTT
1 TACACTTTAATGTGTAAAATT
*
883741 TACACTTTAATCTGTAAAATT
1 TACACTTTAATGTGTAAAATT
* *
883762 CACACATTAATGTGTAAAATT
1 TACACTTTAATGTGTAAAATT
* *
883783 CACACTTTAAAGTGTAAAATT
1 TACACTTTAATGTGTAAAATT
* *
883804 CACACTTTAATCTGTAAAATT
1 TACACTTTAATGTGTAAAATT
* * *
883825 CACACTTTAATCTGTAAATTT
1 TACACTTTAATGTGTAAAATT
* *
883846 TACACTTTAATCTGTAAATTT
1 TACACTTTAATGTGTAAAATT
* * *
883867 TACATTTTAATCTGTAAATTT
1 TACACTTTAATGTGTAAAATT
*
883888 TACACTTTAATCTGTAAAATT
1 TACACTTTAATGTGTAAAATT
* *
883909 CACACTTTAAAGTGTAAAA-T
1 TACACTTTAATGTGTAAAATT
883929 T-CAC---AA-GTGTAAAATT
1 TACACTTTAATGTGTAAAATT
*** * *
883945 TACGGATTAAAGTGTAAATTT
1 TACACTTTAATGTGTAAAATT
* *
883966 TACACTTTCAA-GTGTGAATTT
1 TACACTTT-AATGTGTAAAATT
**
883987 TACA-GATAATGTGTAAAATT
1 TACACTTTAATGTGTAAAATT
** *
884007 TACAGATTAAAGTGTAAAATT
1 TACACTTTAATGTGTAAAATT
*
884028 TACACTTTAAAGTGTA
1 TACACTTTAATGTGTA
884044 GAAAATAAAA
Statistics
Matches: 282, Mismatches: 33, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
15 8 0.03
16 4 0.01
17 1 0.00
19 5 0.02
20 16 0.06
21 246 0.87
22 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (21 bp):
TACACTTTAATGTGTAAAATT
Found at i:886941 original size:39 final size:38
Alignment explanation
Indices: 886872--886947 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
886862 GATTTTTTCC
*
886872 GGGGGGGGGGGGGGGGCCCAAGGAAAAATTTTTTTTTG
1 GGGGGGGGGGGGGGGGCCCAAGGAAAAATTTTGTTTTG
* *
886910 GGGGGGGGGGGGGGGTGTCCAA-GAGATAATTTTGTTTT
1 GGGGGGGGGGGGGGG-GCCCAAGGA-AAAATTTTGTTTT
886948 CGGAGGTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 17 0.52
39 16 0.48
ACGTcount: A:0.17, C:0.07, G:0.50, T:0.26
Consensus pattern (38 bp):
GGGGGGGGGGGGGGGGCCCAAGGAAAAATTTTGTTTTG
Found at i:888928 original size:32 final size:32
Alignment explanation
Indices: 888880--889331 Score: 591
Period size: 32 Copynumber: 14.1 Consensus size: 32
888870 ATGATGAATA
* *
888880 AAGAGTTGCTCAATGCAGGCATTGGACGACTG
1 AAGAGTCGCTCAATGCAGGCATTGGAAGACTG
* * *
888912 AGGAGTCGCTCAATGCAGGCATTGGAAAAATG
1 AAGAGTCGCTCAATGCAGGCATTGGAAGACTG
* * * *
888944 AAGAGACGTTCAATGCAGGCATTGGACGA-TT
1 AAGAGTCGCTCAATGCAGGCATTGGAAGACTG
* *
888975 AAGGAGTCGCTCAATGCAGGCATTGGAACAACAG
1 AA-GAGTCGCTCAATGCAGGCATTGGAA-GACTG
* ** * * *
889009 AGGAGAAGCCCAATGCAGGCATTGGACGATTG
1 AAGAGTCGCTCAATGCAGGCATTGGAAGACTG
* *
889041 AGGAGTCGCTCAATGCAGGCATTGGAAAAACTG
1 AAGAGTCGCTCAATGCAGGCATTGG-AAGACTG
* *
889074 AAGAGTCGTTCAGTGCAGGCATTGGAAGACTG
1 AAGAGTCGCTCAATGCAGGCATTGGAAGACTG
889106 AAGAGTCGCTCAATGCAGGCATTGGAAGACTG
1 AAGAGTCGCTCAATGCAGGCATTGGAAGACTG
*
889138 AAGAGTCGCTCAATGTAGGCATTGGAAGACTG
1 AAGAGTCGCTCAATGCAGGCATTGGAAGACTG
** *
889170 AAGAGTCGCTCAATGCAGGCATTGGTCGATTG
1 AAGAGTCGCTCAATGCAGGCATTGGAAGACTG
* * *
889202 AGGAGTCGTTCAATGCAGGCATTGGACGACTG
1 AAGAGTCGCTCAATGCAGGCATTGGAAGACTG
889234 AAGAGTCGCTCAATGCAGGCATTGGAAGACTG
1 AAGAGTCGCTCAATGCAGGCATTGGAAGACTG
* *
889266 AAGAGCCACTCAATGCAGGCATTGGAAGACTG
1 AAGAGTCGCTCAATGCAGGCATTGGAAGACTG
*
889298 AAGAGACGCTCAATGCAGGCATTGGAAGACTG
1 AAGAGTCGCTCAATGCAGGCATTGGAAGACTG
889330 AA
1 AA
889332 TTATAGTGAT
Statistics
Matches: 363, Mismatches: 53, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
31 3 0.01
32 311 0.86
33 48 0.13
34 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.19
Consensus pattern (32 bp):
AAGAGTCGCTCAATGCAGGCATTGGAAGACTG
Found at i:895667 original size:12 final size:13
Alignment explanation
Indices: 895642--895674 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
895632 GGGGATTAAG
*
895642 TTTTTGTTGTGTT
1 TTTTTTTTGTGTT
895655 TTTTTTTTG-GTT
1 TTTTTTTTGTGTT
895667 TTTTTTTT
1 TTTTTTTT
895675 TTTGCTTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (13 bp):
TTTTTTTTGTGTT
Found at i:895867 original size:12 final size:13
Alignment explanation
Indices: 895842--895874 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
895832 GGGGATTAAG
*
895842 TTTTTGTTGTGTT
1 TTTTTTTTGTGTT
895855 TTTTTTTTG-GTT
1 TTTTTTTTGTGTT
895867 TTTTTTTT
1 TTTTTTTT
895875 TTTGCTTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (13 bp):
TTTTTTTTGTGTT
Found at i:895907 original size:200 final size:200
Alignment explanation
Indices: 895564--895963 Score: 800
Period size: 200 Copynumber: 2.0 Consensus size: 200
895554 AGGTAAGATT
895564 TTCTTTTTGAAGTTATAGGTATACTCCCCACCCCCACACCCCCACCCCATTATGATTTTCATGAT
1 TTCTTTTTGAAGTTATAGGTATACTCCCCACCCCCACACCCCCACCCCATTATGATTTTCATGAT
895629 TTTGGGGATTAAGTTTTTGTTGTGTTTTTTTTTTGGTTTTTTTTTTTTTGCTTGTCAAGATTTCT
66 TTTGGGGATTAAGTTTTTGTTGTGTTTTTTTTTTGGTTTTTTTTTTTTTGCTTGTCAAGATTTCT
895694 GACGATTAGTCTAGCCTTTCAATTTGCTTCCGACGCCTCTGCATTTGCACAGAGTTGCGAATTTC
131 GACGATTAGTCTAGCCTTTCAATTTGCTTCCGACGCCTCTGCATTTGCACAGAGTTGCGAATTTC
895759 TAATA
196 TAATA
895764 TTCTTTTTGAAGTTATAGGTATACTCCCCACCCCCACACCCCCACCCCATTATGATTTTCATGAT
1 TTCTTTTTGAAGTTATAGGTATACTCCCCACCCCCACACCCCCACCCCATTATGATTTTCATGAT
895829 TTTGGGGATTAAGTTTTTGTTGTGTTTTTTTTTTGGTTTTTTTTTTTTTGCTTGTCAAGATTTCT
66 TTTGGGGATTAAGTTTTTGTTGTGTTTTTTTTTTGGTTTTTTTTTTTTTGCTTGTCAAGATTTCT
895894 GACGATTAGTCTAGCCTTTCAATTTGCTTCCGACGCCTCTGCATTTGCACAGAGTTGCGAATTTC
131 GACGATTAGTCTAGCCTTTCAATTTGCTTCCGACGCCTCTGCATTTGCACAGAGTTGCGAATTTC
895959 TAATA
196 TAATA
895964 AAATGTAATT
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 200 1.00
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.45
Consensus pattern (200 bp):
TTCTTTTTGAAGTTATAGGTATACTCCCCACCCCCACACCCCCACCCCATTATGATTTTCATGAT
TTTGGGGATTAAGTTTTTGTTGTGTTTTTTTTTTGGTTTTTTTTTTTTTGCTTGTCAAGATTTCT
GACGATTAGTCTAGCCTTTCAATTTGCTTCCGACGCCTCTGCATTTGCACAGAGTTGCGAATTTC
TAATA
Found at i:904466 original size:2 final size:2
Alignment explanation
Indices: 904459--904503 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
904449 GTCTAATTCA
904459 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
904501 TC T
1 TC T
904504 GTGACTGTGC
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:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:908878 original size:11 final size:11
Alignment explanation
Indices: 908862--908887 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
908852 TCCCCTGGAA
908862 ATATTTTCTGG
1 ATATTTTCTGG
908873 ATATTTTCTGG
1 ATATTTTCTGG
908884 ATAT
1 ATAT
908888 GCCATGCACT
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:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (11 bp):
ATATTTTCTGG
Found at i:921712 original size:2 final size:2
Alignment explanation
Indices: 921705--921774 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
921695 CACATTATAA
921705 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
921747 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
921775 CTTAGATATG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:929266 original size:30 final size:30
Alignment explanation
Indices: 929232--929290 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
929222 AACAAGGGTT
929232 TGTGAGAAGCTATGCGGATCAGAAACCCTG
1 TGTGAGAAGCTATGCGGATCAGAAACCCTG
929262 TGTGAGAAGCTATGCGGATCAGAAACCCT
1 TGTGAGAAGCTATGCGGATCAGAAACCCT
929291 TGACTTGGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.20
Consensus pattern (30 bp):
TGTGAGAAGCTATGCGGATCAGAAACCCTG
Found at i:941783 original size:17 final size:16
Alignment explanation
Indices: 941743--941860 Score: 92
Period size: 16 Copynumber: 7.2 Consensus size: 16
941733 CAGACAGGTT
941743 GATAATACGGATAGATA
1 GATAA-ACGGATAGATA
*
941760 AATAAACGGATAGATA
1 GATAAACGGATAGATA
*
941776 GTTAAAACGGATAGATA
1 GAT-AAACGGATAGATA
* **
941793 GATAGATAGATAGATA
1 GATAAACGGATAGATA
* **
941809 GATAGATAGATAGATA
1 GATAAACGGATAGATA
* **
941825 GATAGATAGATAGATA
1 GATAAACGGATAGATA
* **
941841 GATAGATAGATAGATA
1 GATAAACGGATAGATA
941857 GATA
1 GATA
941861 GATAGATAGA
Statistics
Matches: 93, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
16 74 0.80
17 19 0.20
ACGTcount: A:0.50, C:0.03, G:0.24, T:0.24
Consensus pattern (16 bp):
GATAAACGGATAGATA
Found at i:941792 original size:4 final size:4
Alignment explanation
Indices: 941785--941872 Score: 176
Period size: 4 Copynumber: 22.0 Consensus size: 4
941775 AGTTAAAACG
941785 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
941833 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
941873 CATCGTCAAA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 84 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
GATA
Found at i:950541 original size:9 final size:9
Alignment explanation
Indices: 950526--950571 Score: 58
Period size: 9 Copynumber: 5.0 Consensus size: 9
950516 TCTTTGTTTG
950526 TTTCTTTTT
1 TTTCTTTTT
*
950535 CTTCTTTTT
1 TTTCTTTTT
950544 TTTCTTCTTT
1 TTTCTT-TTT
950554 TTTCTCTTTT
1 TTTCT-TTTT
950564 TTT-TTTTT
1 TTTCTTTTT
950572 AGGGGGGGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
8 4 0.12
9 14 0.42
10 14 0.42
11 1 0.03
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:950541 original size:21 final size:21
Alignment explanation
Indices: 950515--950565 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
950505 TTATGATAGT
950515 TTCTTTGTTTGT-TTCTTTTTC
1 TTCTTT-TTTGTCTTCTTTTTC
*
950536 TTCTTTTTTTTCTTCTTTTT-
1 TTCTTTTTTGTCTTCTTTTTC
950556 TCTCTTTTTT
1 T-TCTTTTTT
950566 TTTTTTAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (21 bp):
TTCTTTTTTGTCTTCTTTTTC
Found at i:950545 original size:12 final size:12
Alignment explanation
Indices: 950530--950569 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
950520 TGTTTGTTTC
950530 TTTTTCTTCTTT
1 TTTTTCTTCTTT
950542 TTTTTCTTCTTT
1 TTTTTCTTCTTT
*
950554 TTTCTCTT-TTT
1 TTTTTCTTCTTT
950565 TTTTT
1 TTTTT
950570 TTAGGGGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 7 0.27
12 19 0.73
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTCTTCTTT
Found at i:964614 original size:2 final size:2
Alignment explanation
Indices: 964607--964688 Score: 157
Period size: 2 Copynumber: 41.5 Consensus size: 2
964597 ACGAAGGTAG
964607 GA GA GA GA GA GA GA GA GA GA GA GA G- 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
964648 GA GA 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 GA GA G
964689 GGGGTAAAGA
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 78 0.99
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:966182 original size:21 final size:20
Alignment explanation
Indices: 966143--966181 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
966133 CACATGGTTT
*
966143 GTAAAAACAATTTATTTTTC
1 GTAAAAAAAATTTATTTTTC
966163 GTAAAAAAAGATTT-TTTTT
1 GTAAAAAAA-ATTTATTTTT
966182 TTACTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (20 bp):
GTAAAAAAAATTTATTTTTC
Found at i:970848 original size:2 final size:2
Alignment explanation
Indices: 970841--970913 Score: 128
Period size: 2 Copynumber: 36.5 Consensus size: 2
970831 ATAAGTAACA
* *
970841 TC TC TC TC TC TC TC TC TC TC TC TG TC TC TC TG 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
970883 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
970914 GATTCCAATG
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.51
Consensus pattern (2 bp):
TC
Found at i:983638 original size:8 final size:8
Alignment explanation
Indices: 983617--983658 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
983607 GATCACATTT
983617 TGTCCGTC
1 TGTCCGTC
983625 -GTCCGTC
1 TGTCCGTC
983632 TGTCCGTC
1 TGTCCGTC
* *
983640 CGTCTGTC
1 TGTCCGTC
983648 TGTCCGTC
1 TGTCCGTC
983656 TGT
1 TGT
983659 AAACTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 7 0.24
8 22 0.76
ACGTcount: A:0.00, C:0.36, G:0.26, T:0.38
Consensus pattern (8 bp):
TGTCCGTC
Found at i:983641 original size:12 final size:12
Alignment explanation
Indices: 983624--983658 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
983614 TTTTGTCCGT
983624 CGTCCGTCTGTC
1 CGTCCGTCTGTC
983636 CGTCCGTCTGTC
1 CGTCCGTCTGTC
*
983648 TGTCCGTCTGT
1 CGTCCGTCTGT
983659 AAACTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.37, G:0.26, T:0.37
Consensus pattern (12 bp):
CGTCCGTCTGTC
Found at i:991505 original size:2 final size:2
Alignment explanation
Indices: 991498--991537 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
991488 TCACAAGAAA
991498 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
991538 GATCGCGTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:991970 original size:12 final size:12
Alignment explanation
Indices: 991924--991987 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
991914 AGAAACATCC
991924 TAAGATATGTC-
1 TAAGATATGTCT
* *
991935 TCAGAT-TGGTCA
1 TAAGATAT-GTCT
991947 TAAGAT-TCGTCT
1 TAAGATAT-GTCT
991959 TAAGATATGTCT
1 TAAGATATGTCT
* *
991971 TAGGACATGTCT
1 TAAGATATGTCT
991983 TAAGA
1 TAAGA
991988 CGAATCTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
10 1 0.02
11 8 0.19
12 33 0.77
13 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.36
Consensus pattern (12 bp):
TAAGATATGTCT
Found at i:996777 original size:15 final size:15
Alignment explanation
Indices: 996757--996788 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
996747 TGAGGAGGAG
*
996757 CTAGAGGAGCTTGAA
1 CTAGAGGAACTTGAA
996772 CTAGAGGAACTTGAA
1 CTAGAGGAACTTGAA
996787 CT
1 CT
996789 TGAGCTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (15 bp):
CTAGAGGAACTTGAA
Found at i:1008941 original size:162 final size:161
Alignment explanation
Indices: 1008617--1008959 Score: 470
Period size: 162 Copynumber: 2.1 Consensus size: 161
1008607 AACATCCACA
* * * ** *
1008617 AAGAAAATGAACGTAAACTGCAAATAACTGGATTTTTTCTATGTCCAAGGGGTATAACTCTATTG
1 AAGAAAATGAACGGAAACTGCAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTATCG
* * * * * *
1008682 AAAAATGCTCTATCGTAGCCAATATCGAACTTGACCTAGTTATTATCATGATAAACCTGTATGCA
66 AAAAATGCTCGATCGTACCCAAAATCAAACTTGACCTAGATATTATCATGATAAACCTGTATACA
*
1008747 AAATTTCATTCCAATATAATGATCCTCTGCG
131 AAATTTCATTCCAATATAATCATCCTCTGCG
* *
1008778 AAGAAAATGAGCGGAAACTGCAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGTCG
1 AAGAAAATGAACGGAAACTGCAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTATCG
*
1008843 AAAATTGCTCGATCGTACCCAAAATTCAAACTTGACCTAGATATTATCATGATAAACCTGTATAC
66 AAAAATGCTCGATCGTACCCAAAA-TCAAACTTGACCTAGATATTATCATGATAAACCTGTATAC
* * ** *
1008908 CAAATTTCATTTCAATATGTTCATTCTCTGCG
130 AAAATTTCATTCCAATATAATCATCCTCTGCG
* *
1008940 AAGACAATGAATGGAAACTG
1 AAGAAAATGAACGGAAACTG
1008960 TTAGTGGACC
Statistics
Matches: 157, Mismatches: 24, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
161 77 0.49
162 80 0.51
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (161 bp):
AAGAAAATGAACGGAAACTGCAAATAACTGGAATTTTTCTACGTCCAAGGGCCATAACTCTATCG
AAAAATGCTCGATCGTACCCAAAATCAAACTTGACCTAGATATTATCATGATAAACCTGTATACA
AAATTTCATTCCAATATAATCATCCTCTGCG
Found at i:1008975 original size:4 final size:4
Alignment explanation
Indices: 1008966--1009000 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
1008956 ACTGTTAGTG
* *
1008966 GACC GACC GACC GACC GACA GTCC GACC GACC GAC
1 GACC GACC GACC GACC GACC GACC GACC GACC GAC
1009001 AGACAGCAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.46, G:0.26, T:0.03
Consensus pattern (4 bp):
GACC
Found at i:1008993 original size:16 final size:16
Alignment explanation
Indices: 1008972--1009002 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1008962 AGTGGACCGA
1008972 CCGACCGACCGACAGT
1 CCGACCGACCGACAGT
1008988 CCGACCGACCGACAG
1 CCGACCGACCGACAG
1009003 ACAGCAGCAA
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:0.26, C:0.45, G:0.26, T:0.03
Consensus pattern (16 bp):
CCGACCGACCGACAGT
Found at i:1008993 original size:20 final size:20
Alignment explanation
Indices: 1008968--1009006 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1008958 TGTTAGTGGA
*
1008968 CCGACCGACCGACCGACAGT
1 CCGACCGACCGACAGACAGT
1008988 CCGACCGACCGACAGACAG
1 CCGACCGACCGACAGACAG
1009007 CAGCAAAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.44, G:0.26, T:0.03
Consensus pattern (20 bp):
CCGACCGACCGACAGACAGT
Found at i:1009331 original size:10 final size:11
Alignment explanation
Indices: 1009316--1009344 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1009306 AGTGTGTACT
1009316 AGTAATTG-AA
1 AGTAATTGAAA
1009326 AGTAATTGAAA
1 AGTAATTGAAA
1009337 AGTAATTG
1 AGTAATTG
1009345 GAATAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.31
Consensus pattern (11 bp):
AGTAATTGAAA
Found at i:1010446 original size:32 final size:33
Alignment explanation
Indices: 1010400--1010461 Score: 117
Period size: 32 Copynumber: 1.9 Consensus size: 33
1010390 CTTCCAAACC
1010400 GGAATAATCTTATATTGTTTATTTGTACCACGT
1 GGAATAATCTTATATTGTTTATTTGTACCACGT
1010433 GGAA-AATCTTATATTGTTTATTTGTACCA
1 GGAATAATCTTATATTGTTTATTTGTACCA
1010462 ATTGGTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (33 bp):
GGAATAATCTTATATTGTTTATTTGTACCACGT
Found at i:1011979 original size:16 final size:16
Alignment explanation
Indices: 1011958--1012005 Score: 87
Period size: 16 Copynumber: 3.0 Consensus size: 16
1011948 AAAGAATGAT
1011958 GGAGAAAACGTACCCA
1 GGAGAAAACGTACCCA
*
1011974 GGAGAAAACATACCCA
1 GGAGAAAACGTACCCA
1011990 GGAGAAAACGTACCCA
1 GGAGAAAACGTACCCA
1012006 ATTTATAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.46, C:0.25, G:0.23, T:0.06
Consensus pattern (16 bp):
GGAGAAAACGTACCCA
Found at i:1013041 original size:31 final size:31
Alignment explanation
Indices: 1012989--1013050 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1012979 GATTTTCAAA
***
1012989 GGGTACGTTTTCTCTTGGAGAAAACATACCC
1 GGGTACGTTTTCTCCACGAGAAAACATACCC
*
1013020 GGGTACGTTTTCTCCACGAGAAAACGTACCC
1 GGGTACGTTTTCTCCACGAGAAAACATACCC
1013051 CAGAGATTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (31 bp):
GGGTACGTTTTCTCCACGAGAAAACATACCC
Found at i:1013077 original size:16 final size:16
Alignment explanation
Indices: 1013058--1013107 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
1013048 CCCCAGAGAT
1013058 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
*
1013074 TGGGTACGTTTTCTCT
1 TGGGTACGTTTTCTCC
*
1013090 TGGGTACGTTTTTTCC
1 TGGGTACGTTTTCTCC
1013106 TG
1 TG
1013108 ATACCAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.06, C:0.20, G:0.26, T:0.48
Consensus pattern (16 bp):
TGGGTACGTTTTCTCC
Found at i:1015024 original size:167 final size:166
Alignment explanation
Indices: 1014748--1015080 Score: 648
Period size: 167 Copynumber: 2.0 Consensus size: 166
1014738 GGAGTAGACT
1014748 GAAAGCTCTTAGCTAGCAAAGATGTAGATATATAACATTCTATTGTCATATATACAGGTGCCCTA
1 GAAAGCTCTTAGCTAGCAAAGATGTAGATATATAACATTCTATTGTCATATATACAGGTGCCCTA
1014813 TATACCATTAAGGGCTACGGCTAATATGCAGTTAAAAATCCCTGCCCCTTTTTAAATACTAATTA
66 TATACCATTAAGGGCTACGGCTAATATGCAGTTAAAAATCCCTGCCCCTTTTTAAATACTAATTA
1014878 AGGTATCCACTAGCCCTTTAATCGATTTTATATATA
131 AGGTATCCACTAGCCCTTTAATCGATTTTATATATA
1014914 NGAAAGCTCTTAGCTAGCAAAGATGTAGATATATAACATTCTATTGTCATATATACAGGTGCCCT
1 -GAAAGCTCTTAGCTAGCAAAGATGTAGATATATAACATTCTATTGTCATATATACAGGTGCCCT
*
1014979 ATATACCATTAAGGGCTACGGCTAATATGCAGTTAAAAATCCCTGCCCCTTTTTAAATTCTAATT
65 ATATACCATTAAGGGCTACGGCTAATATGCAGTTAAAAATCCCTGCCCCTTTTTAAATACTAATT
1015044 AAGGTATCCACTAGCCCTTTAATCGATTTTATATATA
130 AAGGTATCCACTAGCCCTTTAATCGATTTTATATATA
1015081 TATACCGTAT
Statistics
Matches: 165, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
167 165 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (166 bp):
GAAAGCTCTTAGCTAGCAAAGATGTAGATATATAACATTCTATTGTCATATATACAGGTGCCCTA
TATACCATTAAGGGCTACGGCTAATATGCAGTTAAAAATCCCTGCCCCTTTTTAAATACTAATTA
AGGTATCCACTAGCCCTTTAATCGATTTTATATATA
Found at i:1017997 original size:24 final size:26
Alignment explanation
Indices: 1017961--1018015 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 26
1017951 TGCTGCCTTC
1017961 TTGGGCTTTGCT-GCCTTCTTTG-CT
1 TTGGGCTTTGCTGGCCTTCTTTGCCT
1017985 TTGGG-TTTGGCTGGGGCCTTCTTTGCCT
1 TTGGGCTTT-GCT--GGCCTTCTTTGCCT
1018013 TTG
1 TTG
1018016 CTGGGGACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
23 3 0.12
24 8 0.31
27 10 0.38
28 5 0.19
ACGTcount: A:0.00, C:0.22, G:0.31, T:0.47
Consensus pattern (26 bp):
TTGGGCTTTGCTGGCCTTCTTTGCCT
Done.