Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3361
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 44329
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Found at i:3809 original size:79 final size:81
Alignment explanation
Indices: 3673--3857 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
3663 TTGAATGATG
*
3673 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
3737 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
3752 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
3814 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
3832 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
3858 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:3871 original size:40 final size:40
Alignment explanation
Indices: 3674--3857 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
3664 TGAATGATGT
* * * *
3674 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
3714 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
3754 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
3792 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
3833 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
3858 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:3879 original size:79 final size:79
Alignment explanation
Indices: 3674--3890 Score: 201
Period size: 79 Copynumber: 2.7 Consensus size: 79
3664 TGAATGATGT
** * * * **
3674 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAA-ATCCCGAAGGCATT
*
3737 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATA
** * *
3754 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
*
3819 GCGAGTTACT-ATAA
66 GCGAGATACTAAT-A
* * *
3833 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
3891 TACGTGATTT
Statistics
Matches: 116, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
78 3 0.03
79 71 0.61
80 42 0.36
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
GCGAGATACTAATA
Found at i:9944 original size:37 final size:37
Alignment explanation
Indices: 9903--10060 Score: 307
Period size: 37 Copynumber: 4.3 Consensus size: 37
9893 ATATGAAGTT
*
9903 ATCGGGTCTTACCCGGACAAAATCTCCACACGTAGTC
1 ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
9940 ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
1 ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
9977 ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
1 ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
10014 ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
1 ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
10051 ATCGGGTCTT
1 ATCGGGTCTT
10061 TAGAGCTCGG
Statistics
Matches: 120, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 120 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.25
Consensus pattern (37 bp):
ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
Found at i:10257 original size:47 final size:47
Alignment explanation
Indices: 10179--10536 Score: 590
Period size: 47 Copynumber: 7.6 Consensus size: 47
10169 CCCTTCGGGA
* * * * * *
10179 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
10226 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10273 CTTATCACATATATACACTTTCACATTCATCACCTCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10320 CTTATCACATATATACACTTTTACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10367 CTTATCACATATATATACACTTTCACATTCATCACCTCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10416 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10463 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10510 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
10537 TATTGAAATA
Statistics
Matches: 291, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
47 246 0.85
49 45 0.15
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:10435 original size:143 final size:141
Alignment explanation
Indices: 10179--10536 Score: 590
Period size: 143 Copynumber: 2.5 Consensus size: 141
10169 CCCTTCGGGA
* * * * * * * *
10179 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
10244 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACCTC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
10309 GGCCATTAGGC
131 GGCCATTAGGC
*
10320 CTTATCACATATATACACTTTTACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
*
10385 ACTTTCACATTCATCACCTCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
*
10450 TCGGCTATTAGGC
129 TCGGCCATTAGGC
10463 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
10528 TTTCACATT
66 TTTCACATT
10537 TATTGAAATA
Statistics
Matches: 202, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
141 65 0.32
143 137 0.68
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.33
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:15278 original size:47 final size:47
Alignment explanation
Indices: 15224--15417 Score: 280
Period size: 47 Copynumber: 4.1 Consensus size: 47
15214 TTAGGATTTT
* ** * *
15224 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCA
15271 ATGTGATGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
15318 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
15365 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGTCA
1 ATGTGATGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCA
15412 ATGTGA
1 ATGTGA
15418 AATATATATA
Statistics
Matches: 131, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 131 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:15373 original size:25 final size:25
Alignment explanation
Indices: 15298--15373 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
15288 ATGCATATAT
15298 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
15323 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
15345 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
15370 GTGA
1 GTGA
15374 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:15729 original size:37 final size:37
Alignment explanation
Indices: 15621--15729 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
15611 GGAAATATAT
*
15621 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
15658 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
15695 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
15730 CATCTGAGAT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:16804 original size:30 final size:30
Alignment explanation
Indices: 16768--16826 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
16758 AATAGACGTG
16768 ATTGCCTAAATTGACAAATCATCAAACATA
1 ATTGCCTAAATTGACAAATCATCAAACATA
* *
16798 ATTGCCTAAATTGACGAATCATCAGACAT
1 ATTGCCTAAATTGACAAATCATCAAACAT
16827 GACCCAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.27
Consensus pattern (30 bp):
ATTGCCTAAATTGACAAATCATCAAACATA
Found at i:18164 original size:11 final size:11
Alignment explanation
Indices: 18133--18168 Score: 56
Period size: 12 Copynumber: 3.3 Consensus size: 11
18123 GGCCCATACC
18133 AAAACCAAAAT
1 AAAACCAAAAT
18144 AAAACACAAAAT
1 AAAAC-CAAAAT
18156 AAAACC-AAAT
1 AAAACCAAAAT
18166 AAA
1 AAA
18169 TTAAACAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 7 0.29
11 6 0.25
12 11 0.46
ACGTcount: A:0.75, C:0.17, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAACCAAAAT
Found at i:18246 original size:22 final size:21
Alignment explanation
Indices: 18208--18249 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
18198 CCCAAAATAC
* *
18208 AAAAAAATAGAAGCCCAAACA
1 AAAAAAATAAAACCCCAAACA
18229 AAAAAAATTAAAACCCCAAAC
1 AAAAAAA-TAAAACCCCAAAC
18250 CCTAGCCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.67, C:0.21, G:0.05, T:0.07
Consensus pattern (21 bp):
AAAAAAATAAAACCCCAAACA
Found at i:19462 original size:20 final size:20
Alignment explanation
Indices: 19423--19482 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
19413 GTGATTCTTG
* * *
19423 ATTATTTTATTATCAAATTA
1 ATTAGTTTATTATTATATTA
19443 ATTAGTTTATTATTATATT-
1 ATTAGTTTATTATTATATTA
* *
19462 ATTTGTTTTGTTATTATATTA
1 ATTAG-TTTATTATTATATTA
19483 CTAAATTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.62
Consensus pattern (20 bp):
ATTAGTTTATTATTATATTA
Found at i:19791 original size:4 final size:4
Alignment explanation
Indices: 19782--19806 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
19772 CAATATGGTT
19782 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
19807 CTTTCCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:21570 original size:23 final size:23
Alignment explanation
Indices: 21518--21643 Score: 78
Period size: 23 Copynumber: 5.6 Consensus size: 23
21508 ATCACCCAAA
* * * *
21518 AAACATAACC-AAGTTACCCTCT
1 AAACACAACCAAAGGTACCTTCC
* *
21540 AAATACAACCATAGGTACCCTT-C
1 AAACACAACCAAAGGTA-CCTTCC
* *
21563 GAACACAACCAAATGTACCTTCC
1 AAACACAACCAAAGGTACCTTCC
** *
21586 AAACACAACCAAACATACCCTCC
1 AAACACAACCAAAGGTACCTTCC
* ** *
21609 AAGCACAACCAAATATACCCT-C
1 AAACACAACCAAAGGTACCTTCC
*
21631 TAACACAACCAAA
1 AAACACAACCAAA
21644 TTGATAGCAT
Statistics
Matches: 83, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
22 24 0.29
23 56 0.67
24 3 0.04
ACGTcount: A:0.44, C:0.35, G:0.05, T:0.16
Consensus pattern (23 bp):
AAACACAACCAAAGGTACCTTCC
Found at i:24506 original size:5 final size:6
Alignment explanation
Indices: 24489--24558 Score: 68
Period size: 6 Copynumber: 11.0 Consensus size: 6
24479 AGAAACAACC
* *
24489 ATAAAA ATAAAA ATAAAACA ACTAAAA ACAAAA ATAAAG ATAAAA ATAAAAA
1 ATAAAA ATAAAA AT-AAA-A A-TAAAA ATAAAA ATAAAA ATAAAA AT-AAAA
* *
24541 ATAAAA CTAAAA AGAAAA
1 ATAAAA ATAAAA ATAAAA
24559 CAAATAAACT
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
6 36 0.68
7 11 0.21
8 5 0.09
9 1 0.02
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.13
Consensus pattern (6 bp):
ATAAAA
Found at i:24540 original size:19 final size:19
Alignment explanation
Indices: 24508--24558 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
24498 AAAATAAAAC
*
24508 AACTAAAAA-CAAAAATAA
1 AACTAAAAAGAAAAAATAA
*
24526 AGA-TAAAAATAAAAAATAA
1 A-ACTAAAAAGAAAAAATAA
24545 AACTAAAAAGAAAA
1 AACTAAAAAGAAAA
24559 CAAATAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.78, C:0.06, G:0.04, T:0.12
Consensus pattern (19 bp):
AACTAAAAAGAAAAAATAA
Found at i:28249 original size:37 final size:37
Alignment explanation
Indices: 28199--28277 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
28189 TTATTACGAA
* * *
28199 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
28236 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
28273 GTCTT
1 GTCTT
28278 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:28474 original size:47 final size:47
Alignment explanation
Indices: 28396--28763 Score: 549
Period size: 47 Copynumber: 7.7 Consensus size: 47
28386 CCCTTCGGGA
* * * * * * *
28396 CTTATCACATTTATACACTTCCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28443 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28490 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28537 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28586 CTTATCACATATATACACTTTCACATTGATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28633 CTTATCACATAAATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28680 CTTATCATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATC--ACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
28729 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
28764 AGAATCCTAA
Statistics
Matches: 296, Mismatches: 20, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
46 1 0.00
47 203 0.69
49 92 0.31
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28665 original size:143 final size:143
Alignment explanation
Indices: 28396--28763 Score: 580
Period size: 143 Copynumber: 2.6 Consensus size: 143
28386 CCCTTCGGGA
* * * * * * * *
28396 CTTATCACAT-T-TATACACTTCCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
28459 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAAATACACTTTCACATTCATCACA
28524 TCGGCCATTAGGC
131 TCGGCCATTAGGC
28537 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
28602 ACTTTCACATTGATCACATCGGCCATTAGGCCTTATCACATAAATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAAATACACTTTCACATTCATCACA
28667 TCGGCCATTAGGC
131 TCGGCCATTAGGC
* * *
28680 CTTATCATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCTCATATATGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
28745 A-TGTTCACATCCATCACAT
66 ACT-TTCACATTCATCACAT
28764 AGAATCCTAA
Statistics
Matches: 209, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
141 10 0.05
142 2 0.01
143 197 0.94
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (143 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAAATACACTTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:28752 original size:96 final size:94
Alignment explanation
Indices: 28396--28763 Score: 549
Period size: 96 Copynumber: 3.9 Consensus size: 94
28386 CCCTTCGGGA
* * * * * * * * *
28396 CTTATCACATTTATACACTTCCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
28461 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
28490 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
28555 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
* *
28586 CTTATCACATATATACACTTTCACATTGATCACATCGGCCATTAGGCCTTATCACATAAATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
28651 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
* * *
28680 CTTATCATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCTCATATATGC
1 CTTATC--ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
28745 A-TGTTCACATCCATCACAT
64 ACT-TTCACATTCATCACAT
28764 AGAATCCTAA
Statistics
Matches: 252, Mismatches: 17, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
94 90 0.36
95 1 0.00
96 161 0.64
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:31677 original size:40 final size:40
Alignment explanation
Indices: 31645--32104 Score: 481
Period size: 40 Copynumber: 11.6 Consensus size: 40
31635 CCAGCATGAT
* * * *
31645 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** * *
31685 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
31725 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
31765 TGCTCTTCGGGACATAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
31805 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
31845 TGCTCTTCGGGACTTAG-CCGGAT-CATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
31883 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * * * *
31923 TGCTCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
1 TGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCACGAA
* ** * * *
31964 TGC-CTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCACGAA
* * * *
32004 TGC-CTTCGGG-CTTAGCCCGGAATTA-GTAACTCGCACAAA
1 TGCTCTTCGGGACTTAGCCCGG-A-TACATCACTAGCACGAA
* **
32043 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC-AA
1 TGCTCTTCGGGA-CTTAGCCCGGATA-CATCAC-TAGCACGAA
*
32083 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
32105 CATCATTCGA
Statistics
Matches: 367, Mismatches: 42, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
38 34 0.09
39 41 0.11
40 271 0.74
41 21 0.06
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:31935 original size:158 final size:161
Alignment explanation
Indices: 31645--31986 Score: 512
Period size: 158 Copynumber: 2.1 Consensus size: 161
31635 CCAGCATGAT
* * **
31645 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATA
1 TGCTCTTCGGGACTTAGCCCGGATACAACACCAGCACGAATGCTCTTCGGGACTTAGCACGGATA
*
31710 TATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGG
66 CATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGG
* *
31775 GACATAGCCCGGATACA-TCACTAGCACGAA
131 GACATAGCCCGGATACAGTAACTAGCACAAA
* * * *
31805 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGC-CGGAT-
1 TGCTCTTCGGGACTTAGCCCGGATACAACACCAGCACGAATGCTCTTCGGGACTTAGCACGGATA
31868 CATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGG
66 CATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGG
* * * *
31933 GACTTAGCCCGGTTATAGTAACTCGCACAAA
131 GACATAGCCCGGATACAGTAACTAGCACAAA
*
31964 TGC-CTTCGGGACTTAACCCGGAT
1 TGCTCTTCGGGACTTAGCCCGGAT
31987 TTAGTAACTC
Statistics
Matches: 164, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
158 96 0.59
159 18 0.11
160 50 0.30
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (161 bp):
TGCTCTTCGGGACTTAGCCCGGATACAACACCAGCACGAATGCTCTTCGGGACTTAGCACGGATA
CATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGG
GACATAGCCCGGATACAGTAACTAGCACAAA
Found at i:32011 original size:158 final size:157
Alignment explanation
Indices: 31645--32104 Score: 500
Period size: 158 Copynumber: 2.9 Consensus size: 157
31635 CCAGCATGAT
* * * * * *
31645 TGCTCTTCGGGACCTAGCCCGGATATA-ACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGAT
1 TGCTCTTCGGAACTTAACCCGGATACATA-ACTAGCACGAATGCTCTTC-GGGCTTAGC-CGGAT
31709 ATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCG
63 -TATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCG
* * *
31774 GGACATAGCCCGGATACATCACTAGCACGAA
127 GGACTTAGCCCGGATACATAACTAGCACAAA
* * * *
31805 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCGGATCA
1 TGCTCTTCGGAACTTAACCCGGATACATAACTAGCACGAATGCTCTTCGGG-CTTAGCCGGATTA
31870 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
65 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
* * *
31935 CTTAGCCCGGTTATAGTAACTCGCACAAA
130 CTTAGCCCGGATACA-TAACTAGCACAAA
* ** * *
31964 TGC-CTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGC-CTTCGGGCTTAGCCCGGAAT
1 TGCTCTTCGGAACTTAACCCGGATACA-TAACTAGCACGAATGCTCTTCGGGCTTAG-CCGG-AT
* * * * * ** * *
32027 TAGTAACTCGCACAAATGC-CTTCGGATCTTAGTCCGGATATGGTCACTTAGCA-CAAAGC-CTT
63 TA-TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATA-CATCAC-TAGCATGAATGCTCTT
32089 CGGGACTTAGCCCGGA
125 CGGGACTTAGCCCGGA
32105 CATCATTCGA
Statistics
Matches: 258, Mismatches: 33, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
157 5 0.02
158 108 0.42
159 73 0.28
160 67 0.26
161 5 0.02
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (157 bp):
TGCTCTTCGGAACTTAACCCGGATACATAACTAGCACGAATGCTCTTCGGGCTTAGCCGGATTAT
CACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGAC
TTAGCCCGGATACATAACTAGCACAAA
Found at i:34013 original size:33 final size:38
Alignment explanation
Indices: 33954--34029 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 38
33944 TTATTACGAA
*
33954 GTCTTAACCCGGACATAATCTCCACACG-AGTTATCGG
1 GTCTTAACCCGGACATAATCTCCACACGTAGTCATCGG
33991 GTCTT-ACCC-GACA-AATC-CCACACGTAGTCATCGG
1 GTCTTAACCCGGACATAATCTCCACACGTAGTCATCGG
34025 GTCTT
1 GTCTT
34030 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
33 7 0.19
34 17 0.46
35 4 0.11
36 4 0.11
37 5 0.14
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (38 bp):
GTCTTAACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:34322 original size:44 final size:47
Alignment explanation
Indices: 34153--34534 Score: 568
Period size: 44 Copynumber: 8.5 Consensus size: 47
34143 CTTATCATTT
* * * * * *
34153 TATACACTTTCACATCCATCACGTTGGCCACTCGGCC-TGTCACATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
34199 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
34246 -ATA-ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA-A-A
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
34289 TATACACTTTCACA-TCATCACATCGGCCATTAGGCCTTATCACATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
34335 TATACACTTT--CATT--TCACATCGGCCATTAGGCCTTATCACATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
34378 TATACACTTTCACATTCATCACATC-G--ATTAGGCCTTATCACATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
*
34422 TATATACTTTCACATTCATCACATCGGCCATTAGGCC-T-TCAC--A
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
34465 TATACAC-TTCACATTCATCACATC-GCCATTAGGCCTTATCACATA
1 TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
34510 TATACACTTTCACATTCATCACATC
1 TATACACTTTCACATTCATCACATC
34535 ATTAGGCCTT
Statistics
Matches: 310, Mismatches: 8, Indels: 36
0.88 0.02 0.10
Matches are distributed among these distances:
41 11 0.04
42 18 0.06
43 51 0.16
44 76 0.25
45 66 0.21
46 65 0.21
47 23 0.07
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
TATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
Found at i:34572 original size:42 final size:44
Alignment explanation
Indices: 34192--34575 Score: 440
Period size: 44 Copynumber: 8.7 Consensus size: 44
34182 ACTCGGCCTG
34192 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACAT---CCATTAGGCCTTA
34239 TCACATA-ATA-ACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACAT---CCATTAGGCCTTA
34284 TCA-A-ATATACACTTTCACA-TCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACAT---CCATTAGGCCTTA
* **
34328 TCACATATATACACTTTCA-TTTCA-CATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCA-CATCCATTAGGCCTTA
*
34371 TCACATATATACACTTTCACATTCATCACATCGATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCCATTAGGCCTTA
*
34415 TCACATATATATACTTTCACATTCATCACATCGGCCATTAGGCC-T-
1 TCACATATATACACTTTCACATTCATCACAT---CCATTAGGCCTTA
34460 TCAC--ATATACAC-TTCACATTCATCACATCGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACAT--CCATTAGGCCTTA
34503 TCACATATATACACTTTCACATTCATCACAT-CATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCCATTAGGCCTTA
* *
34546 T-ATC-TATATGCA-TGTTCACATCCATCACAT
1 TCA-CATATATACACT-TTCACATTCATCACAT
34576 AGAATCCTAA
Statistics
Matches: 306, Mismatches: 13, Indels: 41
0.85 0.04 0.11
Matches are distributed among these distances:
41 12 0.04
42 40 0.13
43 58 0.19
44 79 0.26
45 64 0.21
46 37 0.12
47 16 0.05
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (44 bp):
TCACATATATACACTTTCACATTCATCACATCCATTAGGCCTTA
Done.