Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 45 of 45
Found at i:7940308 original size:20 final size:20
Alignment explanation
Indices: 7940265--7940310 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
7940255 AAATCTTTTG
7940265 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
7940286 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
7940306 CAAAA
1 CAAAA
7940311 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:7942052 original size:38 final size:39
Alignment explanation
Indices: 7941987--7942072 Score: 95
Period size: 38 Copynumber: 2.3 Consensus size: 39
7941977 TTTTTAATAA
** *
7941987 AAGGGGAGAATGCGTGAATTTGCTAAAATTACCTT-ATT
1 AAGGGGAGAATGCACGAACTTGCTAAAATTACCTTGATT
* * **
7942025 AAGGGGAGAATGTACGAACTTGTTAAAATTATTTTGATT
1 AAGGGGAGAATGCACGAACTTGCTAAAATTACCTTGATT
7942064 AA-GGGAGAA
1 AAGGGGAGAA
7942073 ATAAAAGAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 35 0.88
39 5 0.12
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (39 bp):
AAGGGGAGAATGCACGAACTTGCTAAAATTACCTTGATT
Found at i:7942712 original size:13 final size:13
Alignment explanation
Indices: 7942694--7942719 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7942684 TACACCAAGT
7942694 ATGTATCGATACA
1 ATGTATCGATACA
7942707 ATGTATCGATACA
1 ATGTATCGATACA
7942720 TCAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:7958464 original size:23 final size:23
Alignment explanation
Indices: 7958438--7958481 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
7958428 TTTTTTTTGT
*
7958438 TTTACTTGGGCTTTTAGTTTAAG
1 TTTACATGGGCTTTTAGTTTAAG
* *
7958461 TTTAGATGGGTTTTTAGTTTA
1 TTTACATGGGCTTTTAGTTTA
7958482 GATTTAAATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.18, C:0.05, G:0.23, T:0.55
Consensus pattern (23 bp):
TTTACATGGGCTTTTAGTTTAAG
Found at i:7958487 original size:23 final size:23
Alignment explanation
Indices: 7958444--7958492 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
7958434 TTGTTTTACT
*
7958444 TGGGCTTTTAGTTTAAGTTTAGA
1 TGGGCTTTTAGTTTAAGTTTAAA
*
7958467 TGGGTTTTTAGTTT-AGATTTAAA
1 TGGGCTTTTAGTTTAAG-TTTAAA
7958490 TGG
1 TGG
7958493 ACTTAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.22, C:0.02, G:0.27, T:0.49
Consensus pattern (23 bp):
TGGGCTTTTAGTTTAAGTTTAAA
Found at i:7959149 original size:32 final size:31
Alignment explanation
Indices: 7959113--7959212 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 31
7959103 AATGATGGTT
*
7959113 AAATTTATAAATAATTATATCTAATATTTATC
1 AAATTTATAAATAATTATAT-TAATATTCATC
* * * *
7959145 AAATTTACAAGTAATTTTATTAATATTCATT
1 AAATTTATAAATAATTATATTAATATTCATC
* * * * *
7959176 AAATTTATGAGTAATCATATTTA-ATTCAGC
1 AAATTTATAAATAATTATATTAATATTCATC
7959206 AAATTTA
1 AAATTTA
7959213 AGATTAATAA
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
30 12 0.21
31 27 0.48
32 17 0.30
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (31 bp):
AAATTTATAAATAATTATATTAATATTCATC
Found at i:7959180 original size:31 final size:32
Alignment explanation
Indices: 7959111--7959182 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 32
7959101 TTAATGATGG
* *
7959111 TTAAATTTATAAATAATTATATCTAATATTTA
1 TTAAATTTACAAATAATTATATCTAATATTCA
* * *
7959143 TCAAATTTACAAGTAATTTTAT-TAATATTCA
1 TTAAATTTACAAATAATTATATCTAATATTCA
7959174 TTAAATTTA
1 TTAAATTTA
7959183 TGAGTAATCA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 16 0.47
32 18 0.53
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (32 bp):
TTAAATTTACAAATAATTATATCTAATATTCA
Found at i:7959189 original size:31 final size:32
Alignment explanation
Indices: 7959111--7959200 Score: 101
Period size: 31 Copynumber: 2.8 Consensus size: 32
7959101 TTAATGATGG
* *
7959111 TTAAATTTATAAATAATTATATCTAATATTTA
1 TTAAATTTATAAGTAATTATATCTAATATTCA
* * *
7959143 TCAAATTTACAAGTAATTTTAT-TAATATTCA
1 TTAAATTTATAAGTAATTATATCTAATATTCA
* * *
7959174 TTAAATTTATGAGTAATCATATTTAAT
1 TTAAATTTATAAGTAATTATATCTAAT
7959201 TCAGCAAATT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 25 0.53
32 22 0.47
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (32 bp):
TTAAATTTATAAGTAATTATATCTAATATTCA
Found at i:7961439 original size:18 final size:19
Alignment explanation
Indices: 7961413--7961450 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
7961403 CGATTAAAAC
*
7961413 AAAAGTAAAATAA-TTAAA
1 AAAAGTAAAAGAATTTAAA
*
7961431 AAAATTAAAAGAATTTAAA
1 AAAAGTAAAAGAATTTAAA
7961450 A
1 A
7961451 GAAAAACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (19 bp):
AAAAGTAAAAGAATTTAAA
Found at i:7962087 original size:20 final size:21
Alignment explanation
Indices: 7962062--7962101 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
7962052 CTTTCAATTT
7962062 TTTTAAT-TTTTTACTTTTGC
1 TTTTAATCTTTTTACTTTTGC
7962082 TTTTAATCTTTTTACTTTTG
1 TTTTAATCTTTTTACTTTTG
7962102 TAATTTGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTTAATCTTTTTACTTTTGC
Found at i:7964312 original size:21 final size:21
Alignment explanation
Indices: 7964288--7964329 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
7964278 ACATGTCATT
* *
7964288 TAATCAGTTTATTTTTAATAA
1 TAATCAATTTATTTTAAATAA
*
7964309 TAATTAATTTATTTTAAATAA
1 TAATCAATTTATTTTAAATAA
7964330 AAACAACATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TAATCAATTTATTTTAAATAA
Found at i:7964436 original size:22 final size:22
Alignment explanation
Indices: 7964403--7964450 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
7964393 TTTAACATAT
* *
7964403 ATTTGAACTAAAATATAATTTA
1 ATTTGAACTAAAATAAAATTAA
*
7964425 ATTTGATA-TAAATTAAAATTAA
1 ATTTGA-ACTAAAATAAAATTAA
7964447 ATTT
1 ATTT
7964451 TATGATTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (22 bp):
ATTTGAACTAAAATAAAATTAA
Found at i:7968481 original size:11 final size:11
Alignment explanation
Indices: 7968465--7968515 Score: 52
Period size: 10 Copynumber: 4.6 Consensus size: 11
7968455 AAAAAATTTG
7968465 AAAAAAAA-AA
1 AAAAAAAAGAA
*
7968475 AAGAAAAAG-A
1 AAAAAAAAGAA
*
7968485 AAAATAAAGAA
1 AAAAAAAAGAA
7968496 AAAATAAAAGAA
1 AAAA-AAAAGAA
7968508 AAATAAAA
1 AAA-AAAA
7968516 CTTTTTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 15 0.45
11 5 0.15
12 12 0.36
13 1 0.03
ACGTcount: A:0.86, C:0.00, G:0.08, T:0.06
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:7968487 original size:16 final size:16
Alignment explanation
Indices: 7968468--7968498 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7968458 AAATTTGAAA
7968468 AAAAAAAAAGAAAAAG
1 AAAAAAAAAGAAAAAG
*
7968484 AAAAATAAAGAAAAA
1 AAAAAAAAAGAAAAA
7968499 ATAAAAGAAA
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:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAG
Found at i:7968497 original size:22 final size:21
Alignment explanation
Indices: 7968464--7968515 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
7968454 AAAAAAATTT
*
7968464 GAAAAA-AAAAAAAGA-AAAA
1 GAAAAATAAAAAAAAATAAAA
7968483 GAAAAATAAAGAAAAAATAAAA
1 GAAAAATAAA-AAAAAATAAAA
7968505 GAAAAATAAAA
1 GAAAAATAAAA
7968516 CTTTTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 6 0.21
20 3 0.10
21 6 0.21
22 14 0.48
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.06
Consensus pattern (21 bp):
GAAAAATAAAAAAAAATAAAA
Found at i:7968504 original size:16 final size:14
Alignment explanation
Indices: 7968465--7968504 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
7968455 AAAAAATTTG
7968465 AAAAAAAAAAAAGA
1 AAAAAAAAAAAAGA
7968479 AAAAGAAAAATAAAGA
1 AAAA-AAAAA-AAAGA
*
7968495 AAAAATAAAA
1 AAAAAAAAAA
7968505 GAAAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 5 0.22
15 9 0.39
16 9 0.39
ACGTcount: A:0.88, C:0.00, G:0.07, T:0.05
Consensus pattern (14 bp):
AAAAAAAAAAAAGA
Found at i:7969445 original size:2 final size:2
Alignment explanation
Indices: 7969438--7969471 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
7969428 CATTTTAGAC
7969438 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7969472 TTTAGAGTCA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7970236 original size:151 final size:150
Alignment explanation
Indices: 7969978--7970263 Score: 491
Period size: 151 Copynumber: 1.9 Consensus size: 150
7969968 TTTTATCATT
*
7969978 GCCCAATTTGGCATTAGGTGTGGCATTCTATTTAAACACCTTCATGTAAAAATAATTTCATAAGG
1 GCCCAATTTGGCATTAGGTGTGGCATTCTATTTAAACACCTTCATGTAAAAATAAGTTCATAAGG
*
7970043 TCACCTTAGTAATTTTCACATTAAAACCAAGTACTCAGGATAATATTAACACTTTCATGTCAAGA
66 TCACCTTAGTAATTTTCACATTAAAACCAAGTACTCAAGATAATATTAACACTTTCATGTCAAGA
7970108 TATGTTCATCGCCCAATTTG
131 TATGTTCATCGCCCAATTTG
* * *
7970128 GCCCTAATTTGGCATTAGGTGTGGCGTTCTATTTAGACACTTTCATGTAAAAATAAGTTCATAAG
1 GCCC-AATTTGGCATTAGGTGTGGCATTCTATTTAAACACCTTCATGTAAAAATAAGTTCATAAG
* * *
7970193 GTCACCTTAGTAATTTTCACATTAAAATCAAGTACTTAAGATAATATTAACACTTTTATGTCAAG
65 GTCACCTTAGTAATTTTCACATTAAAACCAAGTACTCAAGATAATATTAACACTTTCATGTCAAG
7970258 ATATGT
130 ATATGT
7970264 CTATAAGTTC
Statistics
Matches: 127, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
150 4 0.03
151 123 0.97
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (150 bp):
GCCCAATTTGGCATTAGGTGTGGCATTCTATTTAAACACCTTCATGTAAAAATAAGTTCATAAGG
TCACCTTAGTAATTTTCACATTAAAACCAAGTACTCAAGATAATATTAACACTTTCATGTCAAGA
TATGTTCATCGCCCAATTTG
Found at i:7970296 original size:78 final size:77
Alignment explanation
Indices: 7970164--7970398 Score: 222
Period size: 78 Copynumber: 3.0 Consensus size: 77
7970154 TTCTATTTAG
* * * * * * *
7970164 ACACTTTCATGTAAAAATAAGTTCATAAGGTCACCT-TAGTAATTTTCACATTAAAATCAAGTAC
1 ACACTTTTATGTCAAGATATGTCCATAAGCTCA-CTATAGTAATTTTCATATTAAAATCAAGT-C
7970228 TTAAGATAATATTA
64 TTAAGATAATATTA
* * * * * *
7970242 ACACTTTTATGTCAAGATATGTCTATAAGTTCCCTCTAGTAATTTTCATGTTAAAACTC-AGTTT
1 ACACTTTTATGTCAAGATATGTCCATAAGCTCACTATAGTAATTTTCATATTAAAA-TCAAGTCT
*
7970306 TCATGATAATATTA
65 T-AAGATAATATTA
* * * *
7970320 GCACTTTTATGTTAAGATATTTCCATAAGCTCACTATAATAATTTTTCATATTAAAATCAAGTCC
1 ACACTTTTATGTCAAGATATGTCCATAAGCTCACTATAGTAA-TTTTCATATTAAAATCAAGT-C
* *
7970385 TTAGGATCATATTA
64 TTAAGATAATATTA
7970399 GCGTTTTCAT
Statistics
Matches: 127, Mismatches: 24, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
77 4 0.03
78 93 0.73
79 28 0.22
80 2 0.02
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (77 bp):
ACACTTTTATGTCAAGATATGTCCATAAGCTCACTATAGTAATTTTCATATTAAAATCAAGTCTT
AAGATAATATTA
Found at i:7971828 original size:2 final size:2
Alignment explanation
Indices: 7971775--7971814 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
7971765 GCTTTAACAG
7971775 TA TA 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 TA TA
7971815 ATAACATCAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7973740 original size:82 final size:82
Alignment explanation
Indices: 7973603--7973758 Score: 231
Period size: 82 Copynumber: 1.9 Consensus size: 82
7973593 ATTTATTCTT
* * * * *
7973603 AACTTAAAAATGCCCCTTTCAAACATTAAATCCAAGAAATACTTAACATTAAAGTTTTATGTTCT
1 AACTTAAAAATACACCTTTCAAACATTAAATCCAAGAAATACTTAACATAAAAGTTCTACGTTCT
7973668 ACTAAATTTCGGGGAGA
66 ACTAAATTTCGGGGAGA
* * * *
7973685 AACTTAAAAATACACCTTTCAAACATTAAATCTAAGAACTATTTAATATAAAAGTTCTACGTTCT
1 AACTTAAAAATACACCTTTCAAACATTAAATCCAAGAAATACTTAACATAAAAGTTCTACGTTCT
7973750 ACTAAATTT
66 ACTAAATTT
7973759 TAGGGAGCTT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
82 65 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (82 bp):
AACTTAAAAATACACCTTTCAAACATTAAATCCAAGAAATACTTAACATAAAAGTTCTACGTTCT
ACTAAATTTCGGGGAGA
Found at i:7975365 original size:3 final size:3
Alignment explanation
Indices: 7975357--7975395 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
7975347 ATATGCAACA
*
7975357 AAT AAT AAT AAT AAT TAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
7975396 GATGATGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:7978680 original size:24 final size:23
Alignment explanation
Indices: 7978630--7978680 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
7978620 TCACTAAATT
* * *
7978630 TTTAAATAATAATAATTAATTAG
1 TTTAAATAAAAATAATTAATAAA
*
7978653 TTTAAATAAAAATATTTTAATAAA
1 TTTAAATAAAAATA-ATTAATAAA
7978677 TTTA
1 TTTA
7978681 TTTCAAAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TTTAAATAAAAATAATTAATAAA
Found at i:7978958 original size:30 final size:29
Alignment explanation
Indices: 7978922--7979007 Score: 88
Period size: 29 Copynumber: 2.9 Consensus size: 29
7978912 GAATAATAAT
*
7978922 TTAAAGAAATAATTATATTTGTTATAAATC
1 TTAAAGAAATAAATATATTT-TTATAAATC
* *
7978952 TTAAAG-AATAAATAAATATTTT-TAAATT
1 TTAAAGAAATAAATATAT-TTTTATAAATC
7978980 TTAAA-ATAATAAATATATTTTTTATAAA
1 TTAAAGA-AATAAATATA-TTTTTATAAA
7979008 AATTGAGAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
28 10 0.21
29 24 0.51
30 13 0.28
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (29 bp):
TTAAAGAAATAAATATATTTTTATAAATC
Found at i:7980446 original size:15 final size:16
Alignment explanation
Indices: 7980426--7980464 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
7980416 TATTATGTTA
7980426 ATATAA-TTTAATATT
1 ATATAACTTTAATATT
7980441 ATATAACTTTTAATATT
1 ATATAAC-TTTAATATT
*
7980458 ATTTAAC
1 ATATAAC
7980465 ATTTCATCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.29
17 15 0.71
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATAACTTTAATATT
Found at i:7980454 original size:17 final size:17
Alignment explanation
Indices: 7980432--7980464 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
7980422 GTTAATATAA
7980432 TTTAATATTATATAACT
1 TTTAATATTATATAACT
*
7980449 TTTAATATTATTTAAC
1 TTTAATATTATATAAC
7980465 ATTTCATCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATATTATATAACT
Found at i:7982935 original size:22 final size:25
Alignment explanation
Indices: 7982889--7982941 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
7982879 TGAATGAAAA
*
7982889 ATTTTATTATCTTTAAATATCTAAAT
1 ATTTTATTATCTTTAAACA-CTAAAT
7982915 -TTTTATTAT-TTTAAACA-TAAAT
1 ATTTTATTATCTTTAAACACTAAAT
7982937 ATTTT
1 ATTTT
7982942 TATCGTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 5 0.20
23 4 0.16
24 7 0.28
25 9 0.36
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTTTATTATCTTTAAACACTAAAT
Found at i:7982940 original size:24 final size:25
Alignment explanation
Indices: 7982885--7982944 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
7982875 TTTTTGAATG
* *
7982885 AAAAATTTTATTATCTTTAAATATC
1 AAAATTTTTATTATCTTTAAACATC
*
7982910 TAAATTTTTATTAT-TTTAAACAT-
1 AAAATTTTTATTATCTTTAAACATC
7982933 AAATATTTTTAT
1 AAA-ATTTTTAT
7982945 CGTTTTAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 2 0.07
24 16 0.53
25 12 0.40
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (25 bp):
AAAATTTTTATTATCTTTAAACATC
Found at i:7989272 original size:23 final size:23
Alignment explanation
Indices: 7989236--7989291 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
7989226 CAAATTATAA
*
7989236 AAATATACAAATTT-TTAAATTTT
1 AAATATA-AAATTTATTAAATTTG
**
7989259 AAATATAAAGATTTATTGGATTTG
1 AAATATAAA-ATTTATTAAATTTG
7989283 AAATATAAA
1 AAATATAAA
7989292 TAAATACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.07
23 11 0.39
24 15 0.54
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (23 bp):
AAATATAAAATTTATTAAATTTG
Found at i:7989359 original size:2 final size:2
Alignment explanation
Indices: 7989352--7989383 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
7989342 TTTGTAGTTT
*
7989352 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7989384 AGGTTCGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7989649 original size:37 final size:37
Alignment explanation
Indices: 7989581--7989691 Score: 99
Period size: 37 Copynumber: 3.1 Consensus size: 37
7989571 AATTAGTTGA
* * *
7989581 TTTTAAAATTATTTTTAATATT-AT--TAAATTAATT
1 TTTTAAAATTATTTCTAATTTTAATAATATATTAATT
*
7989615 TTTTATTAAATTA-TTCTAA-TTTAGATAA-ATATTAAATA
1 TTTTA--AAATTATTTCTAATTTTA-ATAATATATT-AATT
*
7989653 TTTTAAATTTATTTCTAATTTTAATAATATATTAATT
1 TTTTAAAATTATTTCTAATTTTAATAATATATTAATT
7989690 TT
1 TT
7989692 GAAATAAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
34 7 0.11
35 5 0.08
36 13 0.21
37 19 0.31
38 17 0.28
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.57
Consensus pattern (37 bp):
TTTTAAAATTATTTCTAATTTTAATAATATATTAATT
Found at i:7989702 original size:16 final size:17
Alignment explanation
Indices: 7989668--7989705 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
7989658 AATTTATTTC
*
7989668 TAATTTTAATAATATAT
1 TAATTTTAATAATAAAT
*
7989685 TAATTTTGA-AATAAAT
1 TAATTTTAATAATAAAT
7989701 TAATT
1 TAATT
7989706 AATTCAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TAATTTTAATAATAAAT
Done.