Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold628
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: 76645
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:9895 original size:28 final size:28
Alignment explanation
Indices: 9814--9895 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
9804 TTTTGGAGAT
*
9814 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
9842 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
9870 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
9896 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:10032 original size:51 final size:51
Alignment explanation
Indices: 9878--10044 Score: 203
Period size: 51 Copynumber: 3.3 Consensus size: 51
9868 GAAATAACGA
* * *
9878 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * *
9930 AATTGGAGTATCCCCGA-TA-GAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
9979 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
10030 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
10045 TCAGAAATAA
Statistics
Matches: 95, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
49 30 0.32
50 12 0.13
51 39 0.41
52 14 0.15
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:10090 original size:27 final size:28
Alignment explanation
Indices: 10027--10102 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
10017 AAAATAAAGT
*
10027 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
10055 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
10082 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
10103 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:12587 original size:13 final size:13
Alignment explanation
Indices: 12569--12594 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12559 ACAAAGATCC
12569 ATGTATCGATACA
1 ATGTATCGATACA
12582 ATGTATCGATACA
1 ATGTATCGATACA
12595 CAGAAAAATG
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:12590 original size:33 final size:33
Alignment explanation
Indices: 12548--12614 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
12538 AAAATTTCCA
***
12548 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
12581 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
12614 A
1 A
12615 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:12658 original size:19 final size:19
Alignment explanation
Indices: 12634--12688 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
12624 CAGTAGCTAA
*
12634 TTATGTATCGATACAATAC
1 TTATGTATCGATACAAAAC
12653 TTATGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
12672 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
12689 TCGTTGAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:12754 original size:21 final size:21
Alignment explanation
Indices: 12724--12801 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
12714 GTTGGGACCC
12724 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGTAGAA
*
12745 TGTATTGATACATTTGT-GAA
1 TGTATCGATACATTTGTAGAA
* *
12765 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTA-GAA
12786 TGTATCGATACATTTG
1 TGTATCGATACATTTG
12802 GAATTTTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.06
20 14 0.29
21 30 0.61
22 2 0.04
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTTGTAGAA
Found at i:12788 original size:41 final size:40
Alignment explanation
Indices: 12724--12805 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 40
12714 GTTGGGACCC
* * *
12724 TGTATCGATACATTTGTAGAATGTATTGATACATTTGTGAA
1 TGTATCGATACATTTCTAAAATGTATCGATACATTTG-GAA
12765 TGTATCGATACA-TTCTACAAATGTATCGATACATTTGGAA
1 TGTATCGATACATTTCTA-AAATGTATCGATACATTTGGAA
12805 T
1 T
12806 TTTTTTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 8 0.22
41 29 0.78
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (40 bp):
TGTATCGATACATTTCTAAAATGTATCGATACATTTGGAA
Found at i:15925 original size:20 final size:19
Alignment explanation
Indices: 15871--15925 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
15861 AAAACCCTTA
* *
15871 AAAGTATCGATACACAATTC
1 AAAGTATCGATACA-TATTT
15891 AAAGTATCGATACATATTT
1 AAAGTATCGATACATATTT
15910 AAATGTATCGATACAT
1 AAA-GTATCGATACAT
15926 TTCTTGGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 6 0.19
20 26 0.81
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.31
Consensus pattern (19 bp):
AAAGTATCGATACATATTT
Found at i:18213 original size:21 final size:21
Alignment explanation
Indices: 18180--18224 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
18170 TTGCAAGTTG
*
18180 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
18202 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
18222 AAA
1 AAA
18225 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:20048 original size:15 final size:15
Alignment explanation
Indices: 20028--20058 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20018 TAAAAATGTC
*
20028 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
20043 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
20058 C
1 C
20059 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:22158 original size:13 final size:13
Alignment explanation
Indices: 22117--22165 Score: 75
Period size: 12 Copynumber: 3.9 Consensus size: 13
22107 GGAAATTCAA
22117 TGTATCGATACAT
1 TGTATCGATACAT
*
22130 T-TTTCGATAC-T
1 TGTATCGATACAT
22141 TGTATCGATACAT
1 TGTATCGATACAT
22154 TGTATCGATACA
1 TGTATCGATACA
22166 AGGTGATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 2 0.06
12 16 0.50
13 14 0.44
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:22329 original size:20 final size:20
Alignment explanation
Indices: 22286--22331 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
22276 AAATCTTTTG
22286 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
22307 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
22327 CAAAA
1 CAAAA
22332 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:24646 original size:20 final size:21
Alignment explanation
Indices: 24623--24675 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
24613 ACAATTCAAA
***
24623 GTATCGATACATGTTGAA-AT
1 GTATCGATACATGAAAAAGAT
24643 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGAAAAAGAT
24664 GTATCGATACAT
1 GTATCGATACAT
24676 TTCTTGGCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (21 bp):
GTATCGATACATGAAAAAGAT
Found at i:24732 original size:13 final size:13
Alignment explanation
Indices: 24714--24739 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24704 TACAGCAAGT
24714 ATGTATCGATACA
1 ATGTATCGATACA
24727 ATGTATCGATACA
1 ATGTATCGATACA
24740 CAAAAAATTG
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:26293 original size:20 final size:22
Alignment explanation
Indices: 26268--26312 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
26258 GATACTTTGG
26268 ATTATTTTT-TACTTG-AAAAC
1 ATTATTTTTATACTTGAAAAAC
*
26288 ATTATTTTTATGCTTGAAAAAC
1 ATTATTTTTATACTTGAAAAAC
26310 ATT
1 ATT
26313 TATACTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.41
21 5 0.23
22 8 0.36
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.49
Consensus pattern (22 bp):
ATTATTTTTATACTTGAAAAAC
Found at i:27661 original size:29 final size:29
Alignment explanation
Indices: 27576--27773 Score: 243
Period size: 29 Copynumber: 6.8 Consensus size: 29
27566 AGATATTCTG
* * **
27576 GTGTTTTAATTGACTTTTCATTTCTTTCA
1 GTGTTTTAGTTGACTTTTAATTTCTTTTT
* * *
27605 GTGTTGTGGTTGACTTTTTAATTACTTTTT
1 GTGTTTTAGTTGAC-TTTTAATTTCTTTTT
* * *
27635 GTGTTTTAGTTGGCTTTTAATTCCTTTTA
1 GTGTTTTAGTTGACTTTTAATTTCTTTTT
* * *
27664 GTGTTTTAATTTACTTTTAATTTATTTTT
1 GTGTTTTAGTTGACTTTTAATTTCTTTTT
*
27693 GTGTTTTAGTTCACTTTTAATTTCTTTTT
1 GTGTTTTAGTTGACTTTTAATTTCTTTTT
27722 GTGTTTTAGTTGACCTTTTAATTTCTTTTT
1 GTGTTTTAGTTGA-CTTTTAATTTCTTTTT
*
27752 GTGTTTTAGTTGACCTTTAATT
1 GTGTTTTAGTTGACTTTTAATT
27774 CCTTAGCTTT
Statistics
Matches: 144, Mismatches: 23, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
29 93 0.65
30 51 0.35
ACGTcount: A:0.16, C:0.09, G:0.14, T:0.62
Consensus pattern (29 bp):
GTGTTTTAGTTGACTTTTAATTTCTTTTT
Found at i:27668 original size:59 final size:58
Alignment explanation
Indices: 27576--27777 Score: 244
Period size: 59 Copynumber: 3.4 Consensus size: 58
27566 AGATATTCTG
* * * * * *
27576 GTGTTTTAATTGACTTTTCATTTCTTTCAGTGTTGTGGTTGACTTTTTAATTACTTTTT
1 GTGTTTTAGTTGACTTTTAATTCCTTTTAGTGTTTTAGTTGAC-TTTTAATTACTTTTT
* * *
27635 GTGTTTTAGTTGGCTTTTAATTCCTTTTAGTGTTTTAATTTACTTTTAATTTA-TTTTT
1 GTGTTTTAGTTGACTTTTAATTCCTTTTAGTGTTTTAGTTGACTTTTAA-TTACTTTTT
* * * *
27693 GTGTTTTAGTTCACTTTTAATTTCTTTTTGTGTTTTAGTTGACCTTTTAATTTCTTTTT
1 GTGTTTTAGTTGACTTTTAATTCCTTTTAGTGTTTTAGTTGA-CTTTTAATTACTTTTT
*
27752 GTGTTTTAGTTGACCTTTAATTCCTT
1 GTGTTTTAGTTGACTTTTAATTCCTT
27778 AGCTTTATAT
Statistics
Matches: 121, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
58 49 0.40
59 72 0.60
ACGTcount: A:0.15, C:0.10, G:0.13, T:0.61
Consensus pattern (58 bp):
GTGTTTTAGTTGACTTTTAATTCCTTTTAGTGTTTTAGTTGACTTTTAATTACTTTTT
Found at i:32862 original size:21 final size:20
Alignment explanation
Indices: 32838--32892 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
32828 TTGCTAAGTC
32838 TGTATTGATACAATGAGCCAA
1 TGTATTGATACAATG-GCCAA
* * **
32859 TGTATCGATACATTGGCCTT
1 TGTATTGATACAATGGCCAA
32879 TGGTATTGATACAA
1 T-GTATTGATACAA
32893 CCTCCCATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35
Consensus pattern (20 bp):
TGTATTGATACAATGGCCAA
Found at i:34294 original size:28 final size:28
Alignment explanation
Indices: 34246--34313 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
34236 CATAATTTTA
*
34246 ATAATTTTAAATTATTATTTAACATAAAT
1 ATAATTTT-AATTATAATTTAACATAAAT
* **
34275 ATAATTTTATTTATAATTTATTATAAAT
1 ATAATTTTAATTATAATTTAACATAAAT
34303 ATAATTTTAAT
1 ATAATTTTAAT
34314 AATTTTTCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 26 0.76
29 8 0.24
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (28 bp):
ATAATTTTAATTATAATTTAACATAAAT
Found at i:34309 original size:66 final size:68
Alignment explanation
Indices: 34187--34402 Score: 199
Period size: 70 Copynumber: 3.1 Consensus size: 68
34177 AATATATATT
* * * * *
34187 TTATTATT-AATATAAATATATATTTAATAAT-TTATTTTTGTAATATAAACATAATTTTAATAA
1 TTATTATTCAACATAAATATA-ATTTTATTATATTA-TATT-TAATATAAATATAATTTTAATAA
34250 TTTTAAA
63 TTTT-AA
* *
34257 TTATTATTTAACATAAATATAATTTTATT-TA-TA-ATTTATTATAAATATAATTTTAATAATTT
1 TTATTATTCAACATAAATATAATTTTATTATATTATATTTAATATAAATATAATTTTAATAA---
*
34319 TTCTTTTA
63 -T-TTTAA
* *
34327 TTATTATTCAACATAAATGTAATTTTATTATATTTATTATTTAATATAAATATAAGTTTAATAAA
1 TTATTATTCAACATAAATATAATTTTATTATA-TTA-TATTTAATATAAATATAATTTTAAT-AA
34392 TTTTAA
63 TTTTAA
34398 TTATT
1 TTATT
34403 TATTATATAT
Statistics
Matches: 121, Mismatches: 12, Indels: 25
0.77 0.08 0.16
Matches are distributed among these distances:
66 21 0.17
67 2 0.02
69 3 0.02
70 43 0.36
71 25 0.21
72 1 0.01
73 2 0.02
75 22 0.18
76 2 0.02
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (68 bp):
TTATTATTCAACATAAATATAATTTTATTATATTATATTTAATATAAATATAATTTTAATAATTT
TAA
Found at i:34316 original size:75 final size:75
Alignment explanation
Indices: 34237--34408 Score: 194
Period size: 75 Copynumber: 2.3 Consensus size: 75
34227 TAATATAAAC
* *
34237 ATAATTTTAATAATTTTAAATTATTATTTAACATAAATATAATTTTATT-TA-TA-ATTTATTAT
1 ATAATTTTAAT-ATTTT--ATTATTATTCAACATAAATATAATTTTATTATATTATATTTAATAT
*
34299 AAATATAATTTTA
63 AAATATAAGTTTA
* *
34312 ATAATTTT--TCTTTTATTATTATTCAACATAAATGTAATTTTATTATATTTATTATTTAATATA
1 ATAATTTTAATATTTTATTATTATTCAACATAAATATAATTTTATTATA-TTA-TATTTAATATA
34375 AATATAAGTTTA
64 AATATAAGTTTA
34387 ATAAATTTTAAT-TATTTATTAT
1 AT-AATTTTAATAT-TTTATTAT
34409 ATATAAATGC
Statistics
Matches: 83, Mismatches: 5, Indels: 15
0.81 0.05 0.15
Matches are distributed among these distances:
70 28 0.34
71 2 0.02
72 4 0.05
73 3 0.04
75 30 0.36
76 6 0.07
77 1 0.01
78 9 0.11
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (75 bp):
ATAATTTTAATATTTTATTATTATTCAACATAAATATAATTTTATTATATTATATTTAATATAAA
TATAAGTTTA
Found at i:34627 original size:65 final size:65
Alignment explanation
Indices: 34524--34654 Score: 174
Period size: 65 Copynumber: 2.0 Consensus size: 65
34514 TTTTAACCTC
* * * *
34524 ACTACTATAATATTCAATCTTACCATTACAATAATTAATCTT-ATTATCATCGTTGCTTTTATCT
1 ACTACTATAACATTCAATCTAACCATTACAATAATTAAT-TTCATTATCACCGTTGCTTTCATCT
34588 T
65 T
** * *
34589 ACTACTATAACATTCAATCTAATTATTATAATAATTAATTTCATTATTACCGTTGCTTTCATCTT
1 ACTACTATAACATTCAATCTAACCATTACAATAATTAATTTCATTATCACCGTTGCTTTCATCTT
34654 A
1 A
34655 ATAAAATCAA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
64 2 0.04
65 55 0.96
ACGTcount: A:0.34, C:0.18, G:0.03, T:0.46
Consensus pattern (65 bp):
ACTACTATAACATTCAATCTAACCATTACAATAATTAATTTCATTATCACCGTTGCTTTCATCTT
Found at i:37132 original size:2 final size:2
Alignment explanation
Indices: 37127--37157 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
37117 TAGTAGTGTG
37127 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
37158 CAGCAAGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37912 original size:16 final size:16
Alignment explanation
Indices: 37891--37938 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
37881 TCATTTATTC
*
37891 AAATTTAAAATAATTT
1 AAATTTAAAAAAATTT
37907 AAATTTAAAAAAATTT
1 AAATTTAAAAAAATTT
*
37923 AAAACTTAAAAAAATT
1 -AAATTTAAAAAAATT
37939 CAAACCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 15 0.52
17 14 0.48
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTTAAAAAAATTT
Found at i:37931 original size:17 final size:16
Alignment explanation
Indices: 37895--37943 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
37885 TTATTCAAAT
* *
37895 TTAAAATAATTTAAAT
1 TTAAAAAAATTTAAAC
37911 TTAAAAAAATTTAAAAC
1 TTAAAAAAATTT-AAAC
*
37928 TTAAAAAAATTCAAAC
1 TTAAAAAAATTTAAAC
37944 CAAAATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 15 0.52
17 14 0.48
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (16 bp):
TTAAAAAAATTTAAAC
Found at i:37943 original size:16 final size:16
Alignment explanation
Indices: 37887--37943 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
37877 CAACTCATTT
* *
37887 ATTCAAATTTAAAATA
1 ATTCAAACTTAAAAAA
* *
37903 ATTTAAATTTAAAAAA
1 ATTCAAACTTAAAAAA
*
37919 ATTTAAAACTTAAAAAA
1 A-TTCAAACTTAAAAAA
37936 ATTCAAAC
1 ATTCAAAC
37944 CAAAATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
16 21 0.60
17 14 0.40
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTCAAACTTAAAAAA
Found at i:40953 original size:25 final size:24
Alignment explanation
Indices: 40924--41004 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 24
40914 TGATACATTG
40924 AAAAATGTATCGATACATCTGGGTAAAA
1 AAAAATGTATCGATACAT-TGGGT---A
40952 AACAGAATGTATCGATACA-T---TA
1 AA-A-AATGTATCGATACATTGGGTA
40974 AAAAATGTATCGATACATTTGGGTA
1 AAAAATGTATCGATACA-TTGGGTA
40999 AAAAAT
1 AAAAAT
41005 AGAATGTATC
Statistics
Matches: 46, Mismatches: 0, Indels: 17
0.73 0.00 0.27
Matches are distributed among these distances:
20 14 0.30
21 1 0.02
22 4 0.09
25 9 0.20
28 3 0.07
29 1 0.02
30 14 0.30
ACGTcount: A:0.47, C:0.10, G:0.16, T:0.27
Consensus pattern (24 bp):
AAAAATGTATCGATACATTGGGTA
Found at i:40963 original size:30 final size:28
Alignment explanation
Indices: 40927--41021 Score: 98
Period size: 30 Copynumber: 3.5 Consensus size: 28
40917 TACATTGAAA
40927 AATGTATCGATACATCTGGGTAAAAAACAG
1 AATGTATCGATACAT-TGGGTAAAAAA-AG
40957 AATGTATCGATACA-T---T---AAAA-
1 AATGTATCGATACATTGGGTAAAAAAAG
40977 AATGTATCGATACATTTGGGTAAAAAATAG
1 AATGTATCGATACA-TTGGGTAAAAAA-AG
41007 AATGTATCGATACAT
1 AATGTATCGATACAT
41022 GTACTGTTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 21
0.72 0.00 0.28
Matches are distributed among these distances:
20 14 0.25
21 1 0.02
22 4 0.07
25 2 0.04
28 4 0.07
29 2 0.04
30 28 0.51
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (28 bp):
AATGTATCGATACATTGGGTAAAAAAAG
Found at i:40969 original size:50 final size:50
Alignment explanation
Indices: 40908--41021 Score: 192
Period size: 50 Copynumber: 2.3 Consensus size: 50
40898 AATTAACTAG
* *
40908 ATGTATTGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAACAGA
1 ATGTATCGATACATTAAAAAATGTATCGATACATCTGGGTAAAAAACAGA
* *
40958 ATGTATCGATACATTAAAAAATGTATCGATACATTTGGGTAAAAAATAGA
1 ATGTATCGATACATTAAAAAATGTATCGATACATCTGGGTAAAAAACAGA
41008 ATGTATCGATACAT
1 ATGTATCGATACAT
41022 GTACTGTTAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.30
Consensus pattern (50 bp):
ATGTATCGATACATTAAAAAATGTATCGATACATCTGGGTAAAAAACAGA
Found at i:43762 original size:28 final size:28
Alignment explanation
Indices: 43168--43763 Score: 779
Period size: 28 Copynumber: 21.1 Consensus size: 28
43158 CTTGTGTGGG
43168 AAAGGATGCCACTGACTTGTGGGCTTTG-
1 AAAGG-TGCCACTGACTTGTGGGCTTTGA
43196 AAAGGATGCCACTGACTTGTGGGCTTTG-
1 AAAGG-TGCCACTGACTTGTGGGCTTTGA
* *
43224 AAAGGATCCCACTGACTTGTGGACTTTGA
1 AAAGG-TGCCACTGACTTGTGGGCTTTGA
* * * *
43253 GAAGGTGCAACTAACTTGTGGGCTTTCA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
*
43281 AGAGGTGCCACTGACTTGTGGGCTTTGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
43309 AAAGGTGCCACTGACTTGTGGGCTTTGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
*
43337 AAAGGTGCCACTGACTTGTAGGCTTTGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
** *
43365 AAAGAAGCCACTGACTTGTGGGCTCTGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
*
43393 AAAGATGCCACTGACTTGTGGGCTTTGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
* * *
43421 AAAGATGCCACAGACTTGTAGGCTTTGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
43449 AAA-GTGCCACTGACTTGTGGGCTTTGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
** *
43476 AAACATGCCACTGACTTGTGAGCTTTGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
* * * *
43504 AAAGGCGCCATTGACTTGCGAGCTTTGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
* *
43532 AAAGGTGCCACTGACTAGTGGGATTTG-
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
* *
43559 AAAGGAAGCCACTAACTTGTGGGCTTTG-
1 AAAGG-TGCCACTGACTTGTGGGCTTTGA
*
43587 AAAGGATGCCACTGACTTGTAGGCTTTGA
1 AAAGG-TGCCACTGACTTGTGGGCTTTGA
*
43616 AAAGGTGCCACTGACTTGTGGCCTTTGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
**
43644 AAAGGGATGCCACTGACTTGCAGGCTTTGA
1 AAA-GG-TGCCACTGACTTGTGGGCTTTGA
*
43674 AAAGGTGCCACTAACTTGTGGGCTTTGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
* *
43702 AAAGGGTTACCACTAACTTGTGGGCTTTGA
1 AAA-GG-TGCCACTGACTTGTGGGCTTTGA
43732 AAAGGTGCCACTGACTTGTGGGCTTTGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
43760 AAAG
1 AAAG
43764 AGGTCGTATT
Statistics
Matches: 503, Mismatches: 57, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
27 29 0.06
28 409 0.81
29 17 0.03
30 48 0.10
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.27
Consensus pattern (28 bp):
AAAGGTGCCACTGACTTGTGGGCTTTGA
Found at i:45110 original size:18 final size:18
Alignment explanation
Indices: 45085--45123 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
45075 CTTTTTTGTG
*
45085 TTGTTTTTTTTTTTGGTTT
1 TTGTTTTTTTTCTT-GTTT
45104 TTGTTTTTTTTCTTGTTT
1 TTGTTTTTTTTCTTGTTT
45122 TT
1 TT
45124 AATTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.85
Consensus pattern (18 bp):
TTGTTTTTTTTCTTGTTT
Found at i:45129 original size:18 final size:19
Alignment explanation
Indices: 45089--45132 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
45079 TTTGTGTTGT
* **
45089 TTTTTTTTTTGGTTTTTGT
1 TTTTTTTCTTGGTTTTTAA
45108 TTTTTTTCTT-GTTTTTAA
1 TTTTTTTCTTGGTTTTTAA
45126 TTTTTTT
1 TTTTTTT
45133 AAAAAGGACG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.05, C:0.02, G:0.09, T:0.84
Consensus pattern (19 bp):
TTTTTTTCTTGGTTTTTAA
Found at i:45129 original size:19 final size:19
Alignment explanation
Indices: 45088--45132 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
45078 TTTTGTGTTG
* *
45088 TTTTTTTTTTTGGTTTTTG
1 TTTTTTTTCTTGGTTTTTA
45107 TTTTTTTTCTT-GTTTTTAA
1 TTTTTTTTCTTGGTTTTT-A
45126 TTTTTTT
1 TTTTTTT
45133 AAAAAGGACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.04, C:0.02, G:0.09, T:0.84
Consensus pattern (19 bp):
TTTTTTTTCTTGGTTTTTA
Found at i:51558 original size:20 final size:19
Alignment explanation
Indices: 51533--51571 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
51523 TATCGATACA
51533 ATGTATTGATACATTGTCTC
1 ATGTATTGATACATT-TCTC
51553 ATGTATTGATACATTTCTC
1 ATGTATTGATACATTTCTC
51572 TTAGGGTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (19 bp):
ATGTATTGATACATTTCTC
Found at i:51637 original size:19 final size:20
Alignment explanation
Indices: 51594--51646 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
51584 CTGCTAGTTT
51594 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAG
* *
51614 TATGTATTGATACAA-TGAG
1 CATGTATCGATACAATTGAG
51633 CATGTATCGATACA
1 CATGTATCGATACA
51647 TTGTATCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:54063 original size:10 final size:10
Alignment explanation
Indices: 54050--54077 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
54040 GAATTAATGC
54050 AAATTTGATG
1 AAATTTGATG
54060 AAATTTGATG
1 AAATTTGATG
54070 AAATTTGA
1 AAATTTGA
54078 AAAAGGAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.39
Consensus pattern (10 bp):
AAATTTGATG
Found at i:59622 original size:28 final size:28
Alignment explanation
Indices: 59582--59681 Score: 155
Period size: 28 Copynumber: 3.6 Consensus size: 28
59572 GGAATAAAGC
59582 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCTCGGAAGTAA
59610 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCTCGGAAGTAA
*** *
59638 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCTCGGAAGTAA
*
59666 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
59682 TCGATTGTGA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 67 1.00
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTCGGAAGTAA
Found at i:59739 original size:52 final size:52
Alignment explanation
Indices: 59670--60006 Score: 194
Period size: 52 Copynumber: 6.4 Consensus size: 52
59660 AAATAACGAG
*
59670 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
** * ** * *
59722 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
* * * *
59775 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATCGGA
** **** * * *
59826 GTTGGAGTATCCCC---TCAGAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTGAAA-AA-----TTGGTA-T-TTTTGGA-AATAAAATCGGA
*
59881 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
* * * * *
59935 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
*
59986 GTTGGAATATCCCCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
60007 GAGAATTGAT
Statistics
Matches: 214, Mismatches: 44, Indels: 54
0.69 0.14 0.17
Matches are distributed among these distances:
48 4 0.02
49 3 0.01
51 38 0.18
52 79 0.37
53 33 0.15
54 28 0.13
55 18 0.08
56 2 0.01
57 2 0.01
58 6 0.03
59 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:59866 original size:28 final size:27
Alignment explanation
Indices: 59826--59894 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 27
59816 TAAAACCGGA
59826 GTTGGAGTATCCCCTCA-GAAATAACGGG
1 GTTGGAGTATCCCC-CATG-AATAACGGG
* *
59854 GTTGGAGTATCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCCATGAATAACGGG
59881 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
59895 GATTGTGAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (27 bp):
GTTGGAGTATCCCCCATGAATAACGGG
Found at i:59868 original size:212 final size:212
Alignment explanation
Indices: 59614--60008 Score: 634
Period size: 212 Copynumber: 1.9 Consensus size: 212
59604 AAGTAACGGG
* *
59614 GTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTA
1 GTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATG-AATAACGAGGTTGGAGTA
* *
59679 TCCTCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAA
65 TCCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAA
* *
59742 AGGAAAATTGGCGTTTTGAAAATAAAACCAGGA-TTGGAGTATCCCCGATTGTGGAAAAATTAGT
130 A-GAAAATTAGCGTTTTGAAAATAAAACC-GGAGTTGGAATATCCCCGATTGTGGAAAAATTAGT
59806 GTTTTAGCGATAAAACCGGA
193 GTTTTAGCGATAAAACCGGA
* *
59826 GTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTAT
1 GTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAATAACGAGGTTGGAGTAT
* *
59891 CCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTATA
66 CCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAA
* *
59956 GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
131 GAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
60009 GAATTGATAA
Statistics
Matches: 168, Mismatches: 12, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
211 32 0.19
212 97 0.58
213 39 0.23
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (212 bp):
GTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAATAACGAGGTTGGAGTAT
CCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAA
GAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTT
TTAGCGATAAAACCGGA
Found at i:59981 original size:51 final size:53
Alignment explanation
Indices: 59885--60003 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 53
59875 AACGGGGTTG
* * *
59885 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
59939 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
*
59990 GAATATCCCCGATT
1 GAGTATCCCCGATT
60004 GTGGAGAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 34 0.58
52 2 0.03
53 8 0.14
54 15 0.25
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:62392 original size:13 final size:13
Alignment explanation
Indices: 62374--62399 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
62364 ACAAAGATCC
62374 ATGTATCGATACA
1 ATGTATCGATACA
62387 ATGTATCGATACA
1 ATGTATCGATACA
62400 CAGAAAAATG
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:62395 original size:33 final size:33
Alignment explanation
Indices: 62353--62419 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
62343 AAAATTTCCA
***
62353 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
62386 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
62419 A
1 A
62420 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:62463 original size:19 final size:18
Alignment explanation
Indices: 62439--62538 Score: 103
Period size: 19 Copynumber: 5.9 Consensus size: 18
62429 CAGTAGCTAA
62439 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
62458 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
62473 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
62490 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
62505 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
62522 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
62539 TTGTTGAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.32
14 2 0.03
16 4 0.06
18 5 0.07
19 36 0.52
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:62479 original size:13 final size:13
Alignment explanation
Indices: 62461--62517 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
62451 ACAATACTTA
62461 TGTATCGATACAT
1 TGTATCGATACAT
62474 TGTATCGATACAAAACTT
1 TGTATCGATAC---A--T
62492 ATGTATCGATACAT
1 -TGTATCGATACAT
62506 TGTATCGATACA
1 TGTATCGATACA
62518 AAACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:62483 original size:32 final size:32
Alignment explanation
Indices: 62442--62536 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
62432 TAGCTAATTA
*
62442 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
62474 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
62506 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
62537 AATTGTTGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:62621 original size:21 final size:21
Alignment explanation
Indices: 62595--62651 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
62585 ATTTTGTAGG
62595 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
62616 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
62637 ATGTATCGATACATT
1 ATGTATCGATACATT
62652 TGGATAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:62679 original size:11 final size:13
Alignment explanation
Indices: 62662--62694 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
62652 TGGATAATTT
*
62662 TTTTTTTTTA-AA
1 TTTTTTTTAATAA
62674 TTTTTTTTAATAA
1 TTTTTTTTAATAA
62687 TTTTTTTT
1 TTTTTTTT
62695 TTCAAACACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTTTAATAA
Found at i:62679 original size:13 final size:14
Alignment explanation
Indices: 62655--62696 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
62645 ATACATTTGG
62655 ATAATTTTTTTTTT
1 ATAATTTTTTTTTT
* * *
62669 TTAAATTTTTTTTA
1 ATAATTTTTTTTTT
62683 ATAATTTTTTTTTT
1 ATAATTTTTTTTTT
62697 CAAACACTCT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
ATAATTTTTTTTTT
Found at i:63496 original size:55 final size:56
Alignment explanation
Indices: 63383--64654 Score: 1392
Period size: 55 Copynumber: 22.5 Consensus size: 56
63373 ATAAAGTGTA
* * * * * *
63383 TCCTTCTCATTGAGGAGTAAAAAGTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAGAGGTG
*
63438 TCCTGCTCTTTGAAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAGAGGTG
* * **
63493 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG--AAG---AGGTG
** * *
63554 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTT-AAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAGAGGTG
* *
63609 TCCTGCTCTTTGAGGATTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAGAGGTG
* * * **
63664 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACCTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG--AAG---AGGTG
** * *
63725 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTT-AAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAGAGGTG
* *
63780 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAGAGGTG
* * **
63835 TCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG--AAG---AGGTG
* * *
63896 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTCGGGTGGCCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAGAGGTG
* *
63950 TCCTGCTCTCTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAGAGGTG
*
64005 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAGAGGTG
* **
64060 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG--AAG---AGGTG
* * *
64121 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTCGGGTGGCCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAGAGGTG
* *
64175 TCCTGCTCTCTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAGAGGTG
*
64230 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAGAGGTG
* **
64285 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG--AAG---AGGTG
* * *
64346 TCCTGCTCTTTGAGAACTG-AAGGTGCCACCAACTCGGGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAGAGGTG
* *
64400 TCCTGCTCTCTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAGAGGTG
**
64455 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAGAGGTG
* **
64510 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG--AAG---AGGTG
* * * * *
64571 TCCTGCTCTTTGAGAACTG-AAGGTGCCACCAACTCGGGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----GAAGAGGTG
*
64630 TCCCGCTCTTTGAGGACTG-AAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTG
64655 GAAGGAGAAG
Statistics
Matches: 1058, Mismatches: 100, Indels: 114
0.83 0.08 0.09
Matches are distributed among these distances:
54 78 0.07
55 630 0.60
56 24 0.02
57 19 0.02
58 7 0.01
59 26 0.02
60 98 0.09
61 173 0.16
62 2 0.00
64 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (56 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAGAGGTG
Found at i:63542 original size:29 final size:29
Alignment explanation
Indices: 63455--63543 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
63445 CTTTGAAGAC
63455 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
** *
63484 T-AAGAGGTGTCCTGC-TCTT-TG-GGGAC--
1 TGAA-AGGTG-CCACCAACTTGTGTGGG-CTT
63510 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
63539 TGAAA
1 TGAAA
63544 AGAAAAAGCA
Statistics
Matches: 45, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
25 3 0.07
26 9 0.20
27 8 0.18
28 8 0.18
29 14 0.31
30 3 0.07
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.28
Consensus pattern (29 bp):
TGAAAGGTGCCACCAACTTGTGTGGGCTT
Found at i:64024 original size:225 final size:225
Alignment explanation
Indices: 63383--64618 Score: 1881
Period size: 225 Copynumber: 5.5 Consensus size: 225
63373 ATAAAGTGTA
* * * * * *
63383 TCCTTCTCATTGAGGAGTAAAAAGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCGTCCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
* * * * *
63442 GCTCTTTGAAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGG
66 GCTCTTTGAGGACTG-AAGGTGCCACCAACTCGGGTGGGCTTTAAGAGGTGTCCTGCTCTCTGAG
* **
63507 GACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGAC
130 GACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCCTGCTCTTTGAGGAC
* * *
63571 TGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
188 TGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * **
63609 TCCTGCTCTTTGAGGATTGGAAA-ATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCC
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
* * * **
63667 TGCTCTTTGGGGACTGAAAGGTGCCACCAAC-CTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGC
65 TGCTCTTTGAGGACTG-AAGGTGCCACCAACTC-GGGTGGGCTTT---AAG---AGGTGTCCTGC
* * * *
63731 TCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGA
122 TCTCTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGA
*
63796 CTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
187 CTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
63835 TCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
*
63900 GCTCTTTGAGGACTGAAGGTGCCACCAACTCGGGTGGCCTTTAAGAGGTGTCCTGCTCTCTGAGG
66 GCTCTTTGAGGACTGAAGGTGCCACCAACTCGGGTGGGCTTTAAGAGGTGTCCTGCTCTCTGAGG
63965 ACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAAT
131 ACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAAT
64030 GCCACCAACTTGTGTGGGCTTTGAAAGGTG
196 GCCACCAACTTGTGTGGGCTTTGAAAGGTG
64060 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
*
64125 GCTCTTTGAGGACTGAAGGTGCCACCAACTCGGGTGGCCTTTAAGAGGTGTCCTGCTCTCTGAGG
66 GCTCTTTGAGGACTGAAGGTGCCACCAACTCGGGTGGGCTTTAAGAGGTGTCCTGCTCTCTGAGG
64190 ACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAAT
131 ACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAAT
64255 GCCACCAACTTGTGTGGGCTTTGAAAGGTG
196 GCCACCAACTTGTGTGGGCTTTGAAAGGTG
64285 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
*
64350 GCTCTTTGAGAACTGAAGGTGCCACCAACTCGGGTGGGCTTTAAGAGGTGTCCTGCTCTCTGAGG
66 GCTCTTTGAGGACTGAAGGTGCCACCAACTCGGGTGGGCTTTAAGAGGTGTCCTGCTCTCTGAGG
*
64415 ACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAAAT
131 ACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAAT
64480 GCCACCAACTTGTGTGGGCTTTGAAAGGTG
196 GCCACCAACTTGTGTGGGCTTTGAAAGGTG
64510 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
*
64575 GCTCTTTGAGAACTGAAGGTGCCACCAACTCGGGTGGGCTTTAA
66 GCTCTTTGAGGACTGAAGGTGCCACCAACTCGGGTGGGCTTTAA
64619 AAGAAAAGGC
Statistics
Matches: 950, Mismatches: 43, Indels: 35
0.92 0.04 0.03
Matches are distributed among these distances:
225 666 0.70
226 180 0.19
227 7 0.01
228 3 0.00
229 3 0.00
231 27 0.03
232 61 0.06
233 3 0.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (225 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
GCTCTTTGAGGACTGAAGGTGCCACCAACTCGGGTGGGCTTTAAGAGGTGTCCTGCTCTCTGAGG
ACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAAT
GCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:64475 original size:26 final size:26
Alignment explanation
Indices: 64446--64535 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
64436 GTGTGGGCTT
64446 TGAAAGGTGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGAGGAC
** ** * * *
64472 TGAAAAATG-CCACCAACTTGTGTGGGC
1 TGAAAGGTGTCCTGC-TCTT-TGAGGAC
64499 TTTGAAAGGTGTCCTGCTCTTTGAGGAC
1 --TGAAAGGTGTCCTGCTCTTTGAGGAC
64527 TGAAAGGTG
1 TGAAAGGTG
64536 CCACCAACTT
Statistics
Matches: 45, Mismatches: 14, Indels: 10
0.65 0.20 0.14
Matches are distributed among these distances:
25 3 0.07
26 19 0.42
27 5 0.11
28 5 0.11
29 10 0.22
30 3 0.07
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGAGGAC
Found at i:65634 original size:17 final size:18
Alignment explanation
Indices: 65614--65647 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
65604 CTTAAGTAGA
65614 TTTTT-CTTTTTTTTTTT
1 TTTTTGCTTTTTTTTTTT
65631 TTTTTGCTTTTTTTTTT
1 TTTTTGCTTTTTTTTTT
65648 AAGAGAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.91
Consensus pattern (18 bp):
TTTTTGCTTTTTTTTTTT
Done.