Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2286
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: 36661
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:531 original size:31 final size:32
Alignment explanation
Indices: 474--533 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
464 ATTGGGCTAG
474 AAGGGTGCCACCGACTTGTGTGGGCTTTGGAA
1 AAGGGTGCCACCGACTTGTGTGGGCTTTGGAA
* *
506 AAGGGTGCCACTGATTTG-GTGGGCTTTG
1 AAGGGTGCCACCGACTTGTGTGGGCTTTG
534 AAGATTGCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.17, C:0.17, G:0.38, T:0.28
Consensus pattern (32 bp):
AAGGGTGCCACCGACTTGTGTGGGCTTTGGAA
Found at i:661 original size:86 final size:85
Alignment explanation
Indices: 562--723 Score: 265
Period size: 86 Copynumber: 1.9 Consensus size: 85
552 TGTGGGCTAT
* *
562 TTTAAAGGTTGCCACTTGACTTGTGGGCTTTTG-AACATATGCC-CTGACTTGTGGGCTTTTAAC
1 TTTAAAGGTTGCCAC-TGACTTGTGGGC-TTTGAAAAATATGCCACTGACTTGTGGGCTTTTAAA
625 AGGGTGCCACTAACCTTGTGGGC
64 AGGG-GCCACTAACCTTGTGGGC
648 TTTAAAGGTTGCCACTGACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGGCTTTTAAAAG
1 TTTAAAGGTTGCCACTGACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGGCTTTTAAAAG
713 GGGCCACTAAC
66 GGGCCACTAAC
724 TGTGGGGCTG
Statistics
Matches: 72, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
84 4 0.06
85 30 0.42
86 38 0.53
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (85 bp):
TTTAAAGGTTGCCACTGACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGGCTTTTAAAAG
GGGCCACTAACCTTGTGGGC
Found at i:710 original size:57 final size:57
Alignment explanation
Indices: 479--706 Score: 210
Period size: 57 Copynumber: 3.9 Consensus size: 57
469 GCTAGAAGGG
* * *
479 TGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGGTGGGCTTTGAAGAT
1 TGCCACTGACTT-TGTGGGCTTT-GAAAAGGGTGCCACTGACTT-GTGGGCTTTAAAGAT
* ** * * *
539 TGCCACGGACCTTTGTGGGCTATTTTAAAGGTTGCCACTTGACTTGTGGGCTTTTGAACAT
1 TGCCACTGA-CTTTGTGGGCT-TTGAAAAGGGTGCCAC-TGACTTGTGGGC-TTTAAAGAT
* * * *
600 ATGCC-CTGAC-TTGTGGGCTTTTAACAGGGTGCCACTAACCTTGTGGGCTTTAAAGGT
1 -TGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCACTGA-CTTGTGGGCTTTAAAGAT
***
657 TGCCACTGAC-TTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGGCTTT
1 TGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTT
707 TAAAAGGGGC
Statistics
Matches: 141, Mismatches: 20, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
56 16 0.11
57 35 0.25
58 22 0.16
59 9 0.06
60 34 0.24
61 21 0.15
62 4 0.03
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (57 bp):
TGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTAAAGAT
Found at i:720 original size:28 final size:28
Alignment explanation
Indices: 477--729 Score: 174
Period size: 28 Copynumber: 8.7 Consensus size: 28
467 GGGCTAGAAG
* *
477 GGTGCCACCGACTTGTGTGGGCTTTGGAAAA
1 GGTGCCACTGAC-T-TGTGGGCTTT-TAAAA
* * *
508 GGGTGCCACTGATTTGGTGGGCTTTGAAGA
1 -GGTGCCACTGACTT-GTGGGCTTTTAAAA
* * *
538 -TTGCCACGGACCTTTGTGGGCTATTTTAAA
1 GGTGCCACTGA-C-TTGTGGGCT-TTTAAAA
*
568 GGTTGCCACTTGACTTGTGGGCTTTTGAACA
1 GG-TGCCAC-TGACTTGTGGGCTTTT-AAAA
** *
599 TATGCC-CTGACTTGTGGGCTTTTAACAG
1 GGTGCCACTGACTTGTGGGCTTTTAA-AA
*
627 GGTGCCACTAACCTTGTGGGC-TTT-AAA
1 GGTGCCACTGA-CTTGTGGGCTTTTAAAA
*
654 GGTTGCCACTGACTTGTGGGCTTTGAAAAA
1 GG-TGCCACTGACTTGTGGGCTTT-TAAAA
**
684 TATGCCACTGACTTGTGGGCTTTTAAAA
1 GGTGCCACTGACTTGTGGGCTTTTAAAA
* *
712 GGGGCCACTAAC-TGTGGG
1 GGTGCCACTGACTTGTGGG
730 GCTGAAAAGA
Statistics
Matches: 176, Mismatches: 30, Indels: 35
0.73 0.12 0.15
Matches are distributed among these distances:
27 20 0.11
28 51 0.29
29 35 0.20
30 30 0.17
31 21 0.12
32 17 0.10
33 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (28 bp):
GGTGCCACTGACTTGTGGGCTTTTAAAA
Found at i:2375 original size:1 final size:1
Alignment explanation
Indices: 2371--2498 Score: 94
Period size: 1 Copynumber: 128.0 Consensus size: 1
2361 TCGGACCCCC
* * * * * * * *
2371 TTTTTTTTTTGTTTGTTTTTATTGTTTTGTTTTTTTTTTTCTTTTGTTTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** ** * ** * * *
2436 TTTTTTTTTTTCATTCATTTTTTTTTGTTTTTTTTCATTTTTTTTTTTGTTTTGTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2499 GGAGGACGCC
Statistics
Matches: 94, Mismatches: 33, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 94 1.00
ACGTcount: A:0.03, C:0.03, G:0.08, T:0.86
Consensus pattern (1 bp):
T
Found at i:2407 original size:30 final size:29
Alignment explanation
Indices: 2371--2498 Score: 120
Period size: 30 Copynumber: 4.3 Consensus size: 29
2361 TCGGACCCCC
*
2371 TTTTTTTTTTGTTTGTTTTTATTGTTTTGT
1 TTTTTTTTTTCTTTGTTTTTATTGTTTT-T
2401 TTTTTTTTTTCTTTTGTTTTT-TTGTTTTT
1 TTTTTTTTTTC-TTTGTTTTTATTGTTTTT
*
2430 TTTTTTTTTT-TTTTTTTCATTCATT-TTTTT
1 TTTTTTTTTTCTTTGTTT--TT-ATTGTTTTT
* *
2460 TTGTTTTTTTTCATTT-TTTTTTTTGTTTTG
1 TT-TTTTTTTTC-TTTGTTTTTATTGTTTTT
*
2490 TTGTTTTTT
1 TTTTTTTTT
2499 GGAGGACGCC
Statistics
Matches: 84, Mismatches: 5, Indels: 19
0.78 0.05 0.18
Matches are distributed among these distances:
27 6 0.07
29 21 0.25
30 32 0.38
31 19 0.23
32 3 0.04
33 3 0.04
ACGTcount: A:0.03, C:0.03, G:0.08, T:0.86
Consensus pattern (29 bp):
TTTTTTTTTTCTTTGTTTTTATTGTTTTT
Found at i:2456 original size:24 final size:22
Alignment explanation
Indices: 2372--2488 Score: 114
Period size: 22 Copynumber: 5.2 Consensus size: 22
2362 CGGACCCCCT
** *
2372 TTTTTTTTTGTTTGTTTTTATTG
1 TTTTTTTTCATTT-TTTTTTTTG
2395 TTTTGTTTT--TTTTTTTCTTTTG
1 TTTT-TTTTCATTTTTTT-TTTTG
* *
2417 TTTTTTTGT-TTTTTTTTTTTTT
1 TTTTTTT-TCATTTTTTTTTTTG
2439 TTTTTTTTCATTCATTTTTTTTTG
1 TTTTTTTTCATT--TTTTTTTTTG
2463 TTTTTTTTCATTTTTTTTTTTG
1 TTTTTTTTCATTTTTTTTTTTG
2485 TTTT
1 TTTT
2489 GTTGTTTTTT
Statistics
Matches: 83, Mismatches: 4, Indels: 15
0.81 0.04 0.15
Matches are distributed among these distances:
21 8 0.10
22 39 0.47
23 11 0.13
24 25 0.30
ACGTcount: A:0.03, C:0.03, G:0.07, T:0.86
Consensus pattern (22 bp):
TTTTTTTTCATTTTTTTTTTTG
Found at i:5846 original size:33 final size:33
Alignment explanation
Indices: 5809--5875 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5799 TTCAACGATT
5809 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
5842 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
5875 T
1 T
5876 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:5847 original size:13 final size:13
Alignment explanation
Indices: 5829--5853 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5819 CATAAAATGT
5829 TGTATCGATACAA
1 TGTATCGATACAA
5842 TGTATCGATACA
1 TGTATCGATACA
5854 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5934 original size:13 final size:13
Alignment explanation
Indices: 5916--5940 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5906 ATTACTCAAA
5916 TGTATCGATACAT
1 TGTATCGATACAT
5929 TGTATCGATACA
1 TGTATCGATACA
5941 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6042 original size:52 final size:52
Alignment explanation
Indices: 5949--6072 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
5939 CACTGATCTT
*
5949 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
6000 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
6052 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
6073 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 19 0.28
52 50 0.72
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:11550 original size:13 final size:13
Alignment explanation
Indices: 11534--11558 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11524 ATGTTACACA
11534 GTATCGATACATT
1 GTATCGATACATT
11547 GTATCGATACAT
1 GTATCGATACAT
11559 GTTGCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:11553 original size:33 final size:33
Alignment explanation
Indices: 11511--11576 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
11501 TACACATTTA
11511 ATTGTATCGATACATGTTACACAGTATCGATAC
1 ATTGTATCGATACATGTTACACAGTATCGATAC
* **
11544 ATTGTATCGATACATGTTGCATTGTATCGATAC
1 ATTGTATCGATACATGTTACACAGTATCGATAC
11577 TTGAAAAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (33 bp):
ATTGTATCGATACATGTTACACAGTATCGATAC
Found at i:14450 original size:19 final size:19
Alignment explanation
Indices: 14426--14462 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
14416 CGAGTTATTC
14426 ATTTAAGTGTAAAAAATTA
1 ATTTAAGTGTAAAAAATTA
* *
14445 ATTTAATTTTAAAAAATT
1 ATTTAAGTGTAAAAAATT
14463 TGAATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
ATTTAAGTGTAAAAAATTA
Found at i:14480 original size:19 final size:19
Alignment explanation
Indices: 14458--14499 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
14448 TAATTTTAAA
*
14458 AAATTTGAATAA-AAATATT
1 AAATTTAAATAATAAAT-TT
14477 AAATTTAAATAATAAATTT
1 AAATTTAAATAATAAATTT
14496 AAAT
1 AAAT
14500 AAAAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AAATTTAAATAATAAATTT
Found at i:14486 original size:13 final size:13
Alignment explanation
Indices: 14470--14510 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
14460 ATTTGAATAA
*
14470 AAATATTAAATTT
1 AAATAATAAATTT
14483 AAATAATAAATTT
1 AAATAATAAATTT
14496 AAATAA-AAA-TT
1 AAATAATAAATTT
14507 AAAT
1 AAAT
14511 TTTTTTATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 6 0.22
12 3 0.11
13 18 0.67
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAATAATAAATTT
Found at i:15169 original size:61 final size:57
Alignment explanation
Indices: 15104--15235 Score: 151
Period size: 61 Copynumber: 2.2 Consensus size: 57
15094 TAAGAGGTGG
*
15104 ATTTTTTTAATTTTAGTAGT-TTTTTTTAAAAATATAAAAGTACTTACGTATCCTTAAAA-T
1 ATTTTTTTAATTTTAATAGTGTTTTTTT---AATATAAAAGTACTTA--TATCCTTAAAACT
*
15164 CATTTTTTTTAAATTTTAATAGTGTTTTTTTAATATAAAAGTACTTATATCCTTGAAACT
1 -A-TTTTTTT-AATTTTAATAGTGTTTTTTTAATATAAAAGTACTTATATCCTTAAAACT
*
15224 ATTATTTTAATT
1 ATTTTTTTAATT
15236 ACATTTTTGT
Statistics
Matches: 64, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
57 4 0.06
58 6 0.09
59 11 0.17
60 1 0.02
61 17 0.27
62 7 0.11
63 11 0.17
64 7 0.11
ACGTcount: A:0.35, C:0.07, G:0.06, T:0.52
Consensus pattern (57 bp):
ATTTTTTTAATTTTAATAGTGTTTTTTTAATATAAAAGTACTTATATCCTTAAAACT
Found at i:16459 original size:3 final size:3
Alignment explanation
Indices: 16451--16503 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
16441 GCTAGAGACT
16451 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16499 TTA TT
1 TTA TT
16504 CTAAAGGAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:19823 original size:86 final size:86
Alignment explanation
Indices: 19716--19916 Score: 334
Period size: 86 Copynumber: 2.3 Consensus size: 86
19706 AGATTGCACC
19716 GTATCGATACATGACCAAATGTATCGATACTTGAAAAGAATATATCGATACAGGTCATTGGCAAT
1 GTATCGATACATGACCAAATGTATCGATACTTGAAAAGAATATATCGATACAGGTCATTGGCAAT
* *
19781 AGCTTGGCAGTAGCCAAATTT
66 AGCTTGGCAATAACCAAATTT
*
19802 GTATCGATACATGACCAAATGTATCGATACTTGAAAAGAATATATCGATACAGGTCATTGGCAGT
1 GTATCGATACATGACCAAATGTATCGATACTTGAAAAGAATATATCGATACAGGTCATTGGCAAT
*
19867 AGCTTGGCAATAATCAAATTT
66 AGCTTGGCAATAACCAAATTT
*
19888 GTATCGATACA-CA-CAATATGTATCGATAC
1 GTATCGATACATGACCAA-ATGTATCGATAC
19917 ATTATATCGA
Statistics
Matches: 109, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
84 3 0.03
85 13 0.12
86 93 0.85
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.28
Consensus pattern (86 bp):
GTATCGATACATGACCAAATGTATCGATACTTGAAAAGAATATATCGATACAGGTCATTGGCAAT
AGCTTGGCAATAACCAAATTT
Found at i:19947 original size:33 final size:32
Alignment explanation
Indices: 19889--19952 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
19879 ATCAAATTTG
*
19889 TATCGATACACACAATATGTATCGATACATTA
1 TATCGATACACACAAAATGTATCGATACATTA
*
19921 TATCGATACATCCCAAAATGTATCGATACATT
1 TATCGATACA-CACAAAATGTATCGATACATT
19953 GGCTAGTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 10 0.34
33 19 0.66
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.31
Consensus pattern (32 bp):
TATCGATACACACAAAATGTATCGATACATTA
Found at i:24796 original size:13 final size:13
Alignment explanation
Indices: 24778--24803 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24768 CATTTTTTGG
24778 TGTATCGATACAT
1 TGTATCGATACAT
24791 TGTATCGATACAT
1 TGTATCGATACAT
24804 ACTTTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:24818 original size:32 final size:33
Alignment explanation
Indices: 24758--24821 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
24748 TACAAGCTAA
**
24758 TGTATCGATACATTTTTTGGTGTATCGATACAT
1 TGTATCGATACATACTTTGGTGTATCGATACAT
24791 TGTATCGATACATACTTT-GTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
24822 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:24898 original size:20 final size:20
Alignment explanation
Indices: 24851--24925 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 20
24841 AATCCCAATG
* *
24851 ACATGTATCGATACATCTTTT
1 ACATGTATCGATACAT-TGTA
*
24872 TCATGTATCGATACATTGTA
1 ACATGTATCGATACATTGTA
*
24892 ACATGTATCGATACTTTG-A
1 ACATGTATCGATACATTGTA
*
24911 ATTATGTATCGATAC
1 A-CATGTATCGATAC
24926 TTTTTAGGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.04
20 30 0.64
21 15 0.32
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (20 bp):
ACATGTATCGATACATTGTA
Found at i:27367 original size:13 final size:13
Alignment explanation
Indices: 27349--27387 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
27339 ATAAACCCCC
*
27349 TGTATCGATACAG
1 TGTATCGATACAA
27362 TGTATCGATACAA
1 TGTATCGATACAA
27375 TGTATCGATACAA
1 TGTATCGATACAA
27388 AGAAAGATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:27399 original size:20 final size:20
Alignment explanation
Indices: 27374--27452 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 20
27364 TATCGATACA
27374 ATGTATCGATACAAAGAAAG
1 ATGTATCGATACAAAGAAAG
**
27394 ATGTATCGATACATTGAATTTTCCAG
1 ATGTATCGATACAAAGAA------AG
* *
27420 ATGTATCGATACACAGAAAC
1 ATGTATCGATACAAAGAAAG
27440 ATGTATCGATACA
1 ATGTATCGATACA
27453 TTTTGGAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 30 0.62
26 18 0.38
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (20 bp):
ATGTATCGATACAAAGAAAG
Found at i:33581 original size:13 final size:13
Alignment explanation
Indices: 33563--33588 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33553 CATTTTTTGG
33563 TGTATCGATACAT
1 TGTATCGATACAT
33576 TGTATCGATACAT
1 TGTATCGATACAT
33589 ACTTTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:33603 original size:32 final size:33
Alignment explanation
Indices: 33543--33606 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
33533 TACAAGCTAA
**
33543 TGTATCGATACATTTTTTGGTGTATCGATACAT
1 TGTATCGATACATACTTTGGTGTATCGATACAT
33576 TGTATCGATACATACTTT-GTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
33607 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:35243 original size:8 final size:8
Alignment explanation
Indices: 35230--35263 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
35220 ATTTGATTAA
35230 ATTTTGTG
1 ATTTTGTG
35238 ATTTTGTG
1 ATTTTGTG
35246 ATTTTGTG
1 ATTTTGTG
35254 ATTTTGTG
1 ATTTTGTG
35262 AT
1 AT
35264 GAATGATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.15, C:0.00, G:0.24, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:35644 original size:20 final size:20
Alignment explanation
Indices: 35609--35649 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
35599 CAAATTTCTT
35609 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAAT-CATC
35631 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
35650 AACAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
GTTTTTCACTCAAAATCATC
Found at i:35943 original size:20 final size:21
Alignment explanation
Indices: 35911--35952 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
35901 CCTCTAGGCA
*
35911 GCACCCACCAGGTCGCGACCG
1 GCACCCACCAGGTCGCAACCG
35932 GCACCC-CCAGGTCGCAACCG
1 GCACCCACCAGGTCGCAACCG
35952 G
1 G
35953 GCAGCCCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.19, C:0.48, G:0.29, T:0.05
Consensus pattern (21 bp):
GCACCCACCAGGTCGCAACCG
Done.