Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2446
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: 94522
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:5741 original size:15 final size:14
Alignment explanation
Indices: 5720--5784 Score: 80
Period size: 14 Copynumber: 4.6 Consensus size: 14
5710 TTCTCTTCAA
5720 AAAAAAAAAAAGGAGC
1 AAAAAAAAAAA--AGC
5736 AAAAAAAAAAAAGC
1 AAAAAAAAAAAAGC
5750 AAAAAAAAAAAA-C
1 AAAAAAAAAAAAGC
*
5763 AAAAAAACAAAA-C
1 AAAAAAAAAAAAGC
5776 AAAGAAAAA
1 AAA-AAAAA
5785 GAGAGAAAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
13 16 0.35
14 19 0.41
16 11 0.24
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAGC
Found at i:6834 original size:55 final size:55
Alignment explanation
Indices: 6768--7555 Score: 1170
Period size: 55 Copynumber: 14.3 Consensus size: 55
6758 TCCGCTTTTT
*
6768 AGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
6823 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
6878 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
6933 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
6988 AGTCCTCAACGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
7043 AGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
7098 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA--TTGTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-T-C
*
7153 AGTCTTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
7208 AGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
7263 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
7318 AGTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
7373 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
7428 ATTCCCCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTGGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
7483 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
7538 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
7556 TACAATTTAT
Statistics
Matches: 687, Mismatches: 31, Indels: 30
0.92 0.04 0.04
Matches are distributed among these distances:
53 2 0.00
54 15 0.02
55 655 0.95
56 13 0.02
57 2 0.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:7094 original size:29 final size:29
Alignment explanation
Indices: 7006--7094 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
6996 ACGAGCAGGA
7006 CACCTCTTAAAGCCCACACAAGTTGGTGG
1 CACCTCTTAAAGCCCACACAAGTTGGTGG
* * **
7035 CACCT-TT-CAGTCCC-CA-AAG-AGCAGG
1 CACCTCTTAAAG-CCCACACAAGTTGGTGG
7060 ACACCTCTTAAAGCCCACACAAGTTGGTGG
1 -CACCTCTTAAAGCCCACACAAGTTGGTGG
7090 CACCT
1 CACCT
7095 TTCAGTCCTC
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 8 0.18
27 9 0.20
28 9 0.20
29 13 0.29
30 3 0.07
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (29 bp):
CACCTCTTAAAGCCCACACAAGTTGGTGG
Found at i:7120 original size:26 final size:26
Alignment explanation
Indices: 7035--7289 Score: 81
Period size: 26 Copynumber: 9.3 Consensus size: 26
7025 AAGTTGGTGG
*
7035 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
7061 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
7090 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * **
7116 CACCTTTCAAAGCCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCACA-AAG-AGCAGGA
**
7145 CA--TTGTCCAGTCTTCAAAGAGCAGGA
1 CACCTT-T-CAGTCCACAAAGAGCAGGA
* * * **
7171 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
7200 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
7226 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
7255 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
7281 CACCTTTCA
1 CACCTTTCA
7290 AAGCCCACAC
Statistics
Matches: 157, Mismatches: 49, Indels: 46
0.62 0.19 0.18
Matches are distributed among these distances:
25 12 0.08
26 41 0.26
27 29 0.18
28 32 0.20
29 31 0.20
30 12 0.08
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (26 bp):
CACCTTTCAGTCCACAAAGAGCAGGA
Found at i:8167 original size:13 final size:13
Alignment explanation
Indices: 8149--8186 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
8139 GATAAAGTGT
8149 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
8162 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
8175 ---AAAAAAAAAA
1 TTGAAAAAAAAAA
8185 TT
1 TT
8187 AAATGTATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.43
13 13 0.57
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (13 bp):
TTGAAAAAAAAAA
Found at i:8214 original size:21 final size:21
Alignment explanation
Indices: 8188--8244 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
8178 AAAAAAATTA
* *
8188 AATGTATCGATACATTTTTTG
1 AATGTATCGATACATTTGTGG
8209 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTGG
8230 AATGTATCGATACAT
1 AATGTATCGATACAT
8245 CCTACAAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.40
Consensus pattern (21 bp):
AATGTATCGATACATTTGTGG
Found at i:8324 original size:19 final size:19
Alignment explanation
Indices: 8300--8367 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
8290 AATTCAACAA
8300 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
8319 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
8334 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
8351 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
8368 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:8339 original size:13 final size:13
Alignment explanation
Indices: 8321--8345 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8311 ACATAAGTTT
8321 TGTATCGATACAA
1 TGTATCGATACAA
8334 TGTATCGATACA
1 TGTATCGATACA
8346 TAAGTATTGT
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:8343 original size:32 final size:32
Alignment explanation
Indices: 8302--8364 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
8292 TTCAACAATT
*
8302 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
8334 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
8365 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:8425 original size:13 final size:13
Alignment explanation
Indices: 8407--8432 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8397 CATTTTTCTG
8407 TGTATCGATACAT
1 TGTATCGATACAT
8420 TGTATCGATACAT
1 TGTATCGATACAT
8433 AGATCTTTGT
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:8429 original size:33 final size:33
Alignment explanation
Indices: 8387--8453 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
8377 GCCAAGGAAA
***
8387 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATAGATCTGTGTATCGATACAT
*
8420 TGTATCGATACATAGATCTTTGTATCGATACAT
1 TGTATCGATACATAGATCTGTGTATCGATACAT
8453 T
1 T
8454 TGGAAATTTT
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:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATAGATCTGTGTATCGATACAT
Found at i:10936 original size:28 final size:28
Alignment explanation
Indices: 10900--10981 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
10890 TTTTTTCACA
*
10900 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
10928 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
10956 --CGAAGGAACACTCCAACCTCGTTATT
1 ATCG--GGGATACTCCAACCTCGTTATT
10982 ATCTCCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 2 0.04
28 43 0.96
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:12133 original size:21 final size:22
Alignment explanation
Indices: 12109--12161 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
12099 AGTTAAACAC
12109 ATCAAAATAAAAA-AATAAAAA
1 ATCAAAATAAAAATAATAAAAA
*
12130 ATC-AAATAAAAATAATGAAAA
1 ATCAAAATAAAAATAATAAAAA
*
12151 A-CAAAGTAAAA
1 ATCAAAATAAAA
12162 TCTACGTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.15
Consensus pattern (22 bp):
ATCAAAATAAAAATAATAAAAA
Found at i:12138 original size:20 final size:20
Alignment explanation
Indices: 12113--12161 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
12103 AAACACATCA
12113 AAATAAAAA-AATAAAAAATC
1 AAATAAAAATAATAAAAAA-C
*
12133 AAATAAAAATAATGAAAAAC
1 AAATAAAAATAATAAAAAAC
12153 AAAGTAAAA
1 AAA-TAAAA
12162 TCTACGTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.14
Consensus pattern (20 bp):
AAATAAAAATAATAAAAAAC
Found at i:13441 original size:22 final size:21
Alignment explanation
Indices: 13410--13450 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
13400 ACATTATAAT
13410 CAAACAAT-AATGAGCTTTAAA
1 CAAACAATAAATGAG-TTTAAA
13431 CAAACTAATAAATGAGTTTA
1 CAAAC-AATAAATGAGTTTA
13451 TTTGTGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 7 0.39
23 6 0.33
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (21 bp):
CAAACAATAAATGAGTTTAAA
Found at i:15134 original size:130 final size:130
Alignment explanation
Indices: 14919--15229 Score: 341
Period size: 130 Copynumber: 2.4 Consensus size: 130
14909 AATATTTTGG
* * *
14919 AGATAATAACGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAA
1 AGATAATAACGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAAA
** *
14984 AATCGATGATTTAGAAATAAGGCAAGGGTTGAAGTGTCCTCGATTATAGAAAATAGATGTTTCAA
66 AATCGAACATTTAGAAATAAGGCAAGGGTTGAAGTATCCTCGATTATAGAAAATAGATGTTTCAA
*
15049 AGATAA-AATCGGGATTGGAGTATCCCCGT-GAAAATAATGGGGTTGGAGTATCCCCAATTATGA
1 AGATAATAA-CGGGATTGGAGTATCCCC-TCGAAAATAACGGGGTTGGAGTATCCCCAATTATGA
* ** * * *
15112 GAAATC-AACATTTTAGAAATAAGGCCGGGGTTGAAGTATCCTTGATTGT-GAGAAATCA-ATAT
64 AAAATCGAACA-TTTAGAAATAAGGCAAGGGTTGAAGTATCCTCGATTATAGA-AAAT-AGATGT
**
15174 TTGGGA
126 TT-CAA
* *
15180 A-ATAA-AGCCGGGGTTGGAGTATCCCCTC-AGAAATAACGGGGTTGGAGTAT
1 AGATAATA-ACGGGATTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTAT
15230 TCCCGATGAA
Statistics
Matches: 154, Mismatches: 18, Indels: 18
0.81 0.09 0.09
Matches are distributed among these distances:
129 8 0.05
130 142 0.92
131 4 0.03
ACGTcount: A:0.34, C:0.13, G:0.27, T:0.26
Consensus pattern (130 bp):
AGATAATAACGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAAA
AATCGAACATTTAGAAATAAGGCAAGGGTTGAAGTATCCTCGATTATAGAAAATAGATGTTTCAA
Found at i:15258 original size:28 final size:28
Alignment explanation
Indices: 15188--15264 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
15178 GAAATAAAGC
* *
15188 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATTCCC-GATGAAATAA
15216 CGGGGTTGGAGTATTCCCGATGAAATAA
1 CGGGGTTGGAGTATTCCCGATGAAATAA
*
15244 TGGGGTTGGAGTATTCCCGAT
1 CGGGGTTGGAGTATTCCCGAT
15265 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 1 0.02
28 44 0.98
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (28 bp):
CGGGGTTGGAGTATTCCCGATGAAATAA
Found at i:15314 original size:51 final size:51
Alignment explanation
Indices: 15246--15363 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 51
15236 TGAAATAATG
* *
15246 GGGTTGGAGTATTCCCGATTGTGAAAAATTAGAGTTTT-GAAAATAAAATC-
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTAGAGTTTTAG-AAATAAAACCA
* * * *
15296 GGAGTTGGAGTATCCCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAACCA
1 GG-GTTGGAGTATCCCCGATTGTGAAAAATTAGAGTTTTAGAAATAAAACCA
15348 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
15364 TCGAAAATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
50 2 0.03
51 54 0.92
52 3 0.05
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.30
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCGATTGTGAAAAATTAGAGTTTTAGAAATAAAACCA
Found at i:17709 original size:20 final size:19
Alignment explanation
Indices: 17684--17757 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 19
17674 AAAATGCCTG
*
17684 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATG-AA
*
17704 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-A
17724 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AA
17744 AATGTATCGATACA
1 AATGTATCGATACA
17758 TCTTGGTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (19 bp):
AATGTATCGATACAATGAA
Found at i:17794 original size:13 final size:13
Alignment explanation
Indices: 17776--17801 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17766 AATTTCCTAG
17776 ATGTATCGATACA
1 ATGTATCGATACA
17789 ATGTATCGATACA
1 ATGTATCGATACA
17802 TTTCCTTGGC
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:20021 original size:326 final size:326
Alignment explanation
Indices: 19428--20046 Score: 1193
Period size: 326 Copynumber: 1.9 Consensus size: 326
19418 TTATCTCCAT
*
19428 TGTCGTAACGTGCGCTCGACCCCGATAATAGGGCAAATGAGGCACGCTCGACTTAATATCCCTCG
1 TGTCGTAACGTGCGCTCGACCCCGACAATAGGGCAAATGAGGCACGCTCGACTTAATATCCCTCG
19493 TGATTGGGGATTTCTATGGCATGATGGGAAGTGTGCTGATTAAAGGGGGAAGATCAGTAGATGAA
66 TGATTGGGGATTTCTATGGCATGATGGGAAGTGTGCTGATTAAAGGGGGAAGATCAGTAGATGAA
19558 TCGCCCATCTAATTGATCTTCAATGGTCACTATGAAGTGACCGAAATTTTGGAGTCGCCACCGAT
131 TCGCCCATCTAATTGATCTTCAATGGTCACTATGAAGTGACCGAAATTTTGGAGTCGCCACCGAT
*
19623 TATTTCGAGCTAGGCATGATCGGATGCCTATTGAAACCTATGTCTTGAGTTACGAAACTCAAAAC
196 CATTTCGAGCTAGGCATGATCGGATGCCTATTGAAACCTATGTCTTGAGTTACGAAACTCAAAAC
*
19688 ATCGATCCTGTGGTCTGCGTACTTTAGAGATTCTCACACTTTATGTCCCCAGTGGAGTCGCCAAA
261 ATCGATCCCGTGGTCTGCGTACTTTAGAGATTCTCACACTTTATGTCCCCAGTGGAGTCGCCAAA
19753 C
326 C
* *
19754 TGTCGTAACGTGCGCTCGACCCCGGCGATAGGGCAAATGAGGCACGCTCGACTTAATATCCCTCG
1 TGTCGTAACGTGCGCTCGACCCCGACAATAGGGCAAATGAGGCACGCTCGACTTAATATCCCTCG
19819 TGATTGGGGATTTCTATGGCATGATGGGAAGTGTGCTGATTAAAGGGGGAAGATCAGTAGATGAA
66 TGATTGGGGATTTCTATGGCATGATGGGAAGTGTGCTGATTAAAGGGGGAAGATCAGTAGATGAA
19884 TCGCCCATCTAATTGATCTTCAATGGTCACTATGAAGTGACCGAAATTTTGGAGTCGCCACCGAT
131 TCGCCCATCTAATTGATCTTCAATGGTCACTATGAAGTGACCGAAATTTTGGAGTCGCCACCGAT
19949 CATTTCGAGCTAGGCATGATCGGATGCCTATTGAAACCTATGTCTTGAGTTACGAAACTCAAAAC
196 CATTTCGAGCTAGGCATGATCGGATGCCTATTGAAACCTATGTCTTGAGTTACGAAACTCAAAAC
20014 ATCGATCCCGTGGTCTGCGTACTTTAGAGATTC
261 ATCGATCCCGTGGTCTGCGTACTTTAGAGATTC
20047 GCCGGTTGGG
Statistics
Matches: 288, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
326 288 1.00
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.27
Consensus pattern (326 bp):
TGTCGTAACGTGCGCTCGACCCCGACAATAGGGCAAATGAGGCACGCTCGACTTAATATCCCTCG
TGATTGGGGATTTCTATGGCATGATGGGAAGTGTGCTGATTAAAGGGGGAAGATCAGTAGATGAA
TCGCCCATCTAATTGATCTTCAATGGTCACTATGAAGTGACCGAAATTTTGGAGTCGCCACCGAT
CATTTCGAGCTAGGCATGATCGGATGCCTATTGAAACCTATGTCTTGAGTTACGAAACTCAAAAC
ATCGATCCCGTGGTCTGCGTACTTTAGAGATTCTCACACTTTATGTCCCCAGTGGAGTCGCCAAA
C
Found at i:22876 original size:52 final size:52
Alignment explanation
Indices: 22806--22926 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
22796 GAAAATTTAT
*
22806 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
* *
22858 TTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
22910 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
22927 AAGATCGGTG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:22939 original size:52 final size:52
Alignment explanation
Indices: 22806--22946 Score: 187
Period size: 52 Copynumber: 2.7 Consensus size: 52
22796 GAAAATTTAT
*
22806 CTGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGC
* *** *
22858 TTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGC
*
22910 CTGCATGTATCGATACA-AAGATCGGTGTATCGATACA
1 CTGCATGTATCGATACATAAGAT-AGTGTATCGATACA
22947 ATGTATCGAT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 4 0.05
52 74 0.95
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
CTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:22953 original size:13 final size:13
Alignment explanation
Indices: 22935--22959 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22925 CAAAGATCGG
22935 TGTATCGATACAA
1 TGTATCGATACAA
22948 TGTATCGATACA
1 TGTATCGATACA
22960 TTTGAGTAAT
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:23047 original size:35 final size:35
Alignment explanation
Indices: 23001--23083 Score: 116
Period size: 33 Copynumber: 2.4 Consensus size: 35
22991 AGTAGCTTAA
23001 ATTGTATCGATACAAAAAAAAATATGTATCGATAT
1 ATTGTATCGATACAAAAAAAAATATGTATCGATAT
* ***
23036 ATTGTATCGATAC--AACATTTTATGTATCGATAT
1 ATTGTATCGATACAAAAAAAAATATGTATCGATAT
23069 ATTGTATCGATACAA
1 ATTGTATCGATACAA
23084 CATTTTATGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
33 29 0.69
35 13 0.31
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (35 bp):
ATTGTATCGATACAAAAAAAAATATGTATCGATAT
Found at i:23063 original size:20 final size:20
Alignment explanation
Indices: 23038--23103 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
23028 ATCGATATAT
23038 TGTATCGATACAACATTTTA
1 TGTATCGATACAACATTTTA
*
23058 TGTATCGAT-----A-TAT-
1 TGTATCGATACAACATTTTA
23071 TGTATCGATACAACATTTTA
1 TGTATCGATACAACATTTTA
23091 TGTATCGATACAA
1 TGTATCGATACAA
23104 ATCGTTGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 9 0.24
14 2 0.05
15 1 0.03
18 1 0.03
19 2 0.05
20 22 0.59
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (20 bp):
TGTATCGATACAACATTTTA
Found at i:23065 original size:33 final size:33
Alignment explanation
Indices: 23023--23100 Score: 156
Period size: 33 Copynumber: 2.4 Consensus size: 33
23013 CAAAAAAAAA
23023 TATGTATCGATATATTGTATCGATACAACATTT
1 TATGTATCGATATATTGTATCGATACAACATTT
23056 TATGTATCGATATATTGTATCGATACAACATTT
1 TATGTATCGATATATTGTATCGATACAACATTT
23089 TATGTATCGATA
1 TATGTATCGATA
23101 CAAATCGTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (33 bp):
TATGTATCGATATATTGTATCGATACAACATTT
Found at i:24019 original size:67 final size:68
Alignment explanation
Indices: 23893--24019 Score: 159
Period size: 67 Copynumber: 1.9 Consensus size: 68
23883 ATTGGGTTTT
* * *
23893 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
23958 AGA
66 AGA
* * * **
23961 AAAG-TGATAAAGATGCTAATATGTTGATTCACGGCCAATGATATTAGG-CTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATT-GGACTTAAAGATGA
24020 GAAAAAGGAT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
67 44 0.88
68 6 0.12
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.25
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:24241 original size:49 final size:49
Alignment explanation
Indices: 24032--24644 Score: 840
Period size: 49 Copynumber: 12.7 Consensus size: 49
24022 AAAAGGATGT
*
24032 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* *
24084 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
24127 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
24175 CAATGTGCTGGTTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
24224 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
24273 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
24322 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
24371 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
24420 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
24469 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-AT---GGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
24512 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
24560 CAATGTGCTGATTCATGACCAACTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
24609 CAATATGCTAATTCAAGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
24645 GAAGGGTTGC
Statistics
Matches: 496, Mismatches: 52, Indels: 29
0.86 0.09 0.05
Matches are distributed among these distances:
43 77 0.16
45 1 0.00
46 3 0.01
47 1 0.00
48 89 0.18
49 293 0.59
52 32 0.06
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:24765 original size:34 final size:35
Alignment explanation
Indices: 24721--24791 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
24711 TGCCACTAAC
* *
24721 TTGTGGGCTTA-AAAAGAAAAAGAGTGCTATAGAG
1 TTGTGAGCTTACAAAAGAAAAAGAGTGCCATAGAG
*
24755 TTGTGAGCTTACAAAAGAAAAAGAGTGCCATGGAG
1 TTGTGAGCTTACAAAAGAAAAAGAGTGCCATAGAG
24790 TT
1 TT
24792 ATGGACTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 10 0.30
35 23 0.70
ACGTcount: A:0.39, C:0.08, G:0.28, T:0.24
Consensus pattern (35 bp):
TTGTGAGCTTACAAAAGAAAAAGAGTGCCATAGAG
Found at i:24853 original size:30 final size:29
Alignment explanation
Indices: 24799--24885 Score: 99
Period size: 27 Copynumber: 3.1 Consensus size: 29
24789 GTTATGGACT
*
24799 TTGGAAAA-GATGCCACCGACTTGTGGGC
1 TTGGAAAAGGATGCCACTGACTTGTGGGC
* *
24827 TTCGGAAAAGGGTGCCACTGATTTGTGGGC
1 TT-GGAAAAGGATGCCACTGACTTGTGGGC
* *
24857 TTTG--AAGGTTGCCACTGACTTGTGGGC
1 TTGGAAAAGGATGCCACTGACTTGTGGGC
24884 TT
1 TT
24886 AAAAAGAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
27 23 0.45
28 2 0.04
29 7 0.14
30 19 0.37
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (29 bp):
TTGGAAAAGGATGCCACTGACTTGTGGGC
Found at i:24921 original size:34 final size:34
Alignment explanation
Indices: 24866--25416 Score: 406
Period size: 34 Copynumber: 17.5 Consensus size: 34
24856 CTTTGAAGGT
* * *
24866 TGCCACTGACTTGTGGGCTTAAAAAGAAAAAGAG
1 TGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAG
* *
24900 TGCCACGGAGTCGTGGACTT------AAAAAG-G
1 TGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAG
*
24927 TGCCACGGAGTTGTGGGCTT-----TAAAAAGAG
1 TGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAG
* * *
24956 TGCCACGGAGTCGTGGACTTAAAAGGAAAAAGGG
1 TGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAG
*
24990 TGCCACGGAGTTGTGGGCTTTAAAATG---AAG-G
1 TGCCACGGAGTTGTGGGC-TTAAAAGGAAAAAGAG
* *
25021 TGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGTG
1 TGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAG
25055 TGCCACGGAGTTGTGGGCTTAAAAGG-AAAAGAG
1 TGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAG
* * *
25088 TGCCACGTAGTTGT-GGCTTTAAAGGAAAAAAGGG
1 TGCCACGGAGTTGTGGGCTTAAAAGG-AAAAAGAG
* *
25122 TGCCACGGAGTCGTGGACTTAAAA-G-----G-G
1 TGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAG
*
25149 TGCCACGGAGTTGTGGGCTT-----TAAAAAGAG
1 TGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAG
* *
25178 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGG
1 TGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAG
** *
25212 TGCCACGGAGTTGTGGGCTTTGAA--AAGAAG-G
1 TGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAG
* * *
25243 TGCCACGCAGCTGTGGGCTTAGAAGGAAAAAGAG
1 TGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAG
*
25277 TGCCACGGAGTTGTGGGCTT-AAACG-----G-G
1 TGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAG
* *
25304 TGCCACGAAGTTGTGGGCTTAAAAGG-AAAAGCG
1 TGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAG
* *
25337 TGCCACGTAGTTATGGGCTTTGAAAAGG----AG-G
1 TGCCACGGAGTTGTGGGC-TT-AAAAGGAAAAAGAG
* *
25368 TGCCACGGAGTTGTGGACTTTGAAA-GAAAAAG-G
1 TGCCACGGAGTTGTGGGC-TTAAAAGGAAAAAGAG
* *
25401 TGCCACAGAGTCGTGG
1 TGCCACGGAGTTGTGG
25417 ACTTTGATGC
Statistics
Matches: 424, Mismatches: 52, Indels: 83
0.76 0.09 0.15
Matches are distributed among these distances:
27 58 0.14
28 19 0.04
29 40 0.09
30 9 0.02
31 60 0.14
32 21 0.05
33 64 0.15
34 133 0.31
35 20 0.05
ACGTcount: A:0.30, C:0.15, G:0.35, T:0.21
Consensus pattern (34 bp):
TGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAG
Found at i:25058 original size:65 final size:62
Alignment explanation
Indices: 24861--25416 Score: 368
Period size: 65 Copynumber: 8.8 Consensus size: 62
24851 GTGGGCTTTG
* * * *
24861 AAGGTTGCCACTGACTTGTGGGCTTAAAAAGAAAAAGAGTGCCACGGAGTCGTGGACTT-----A
1 AAGG-TGCCACGGAGTTGTGGGCTTAAAAAG---AAG-GTGCCACGGAGTTGTGGGCTTAAAGGA
24921 AA
61 AA
* *
24923 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAG-A-GTGCCACGGAGTCGTGGACTTAAAAGGAAA
1 AAGGTGCCACGGAGTTGTGGGC-TTAAAAAGAAGGTGCCACGGAGTTGTGGGCTT-AAAGGAAA
*
24985 AAGGGTGCCACGGAGTTGTGGGCTTTAAAATGAAGGTGCCACGGAGTTGTGGGCTTAGAAGGAAA
1 AA-GGTGCCACGGAGTTGTGGGC-TTAAAAAGAAGGTGCCACGGAGTTGTGGGCTTA-AAGGAAA
* *
25050 AAGTGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAGAGTGCCACGTAGTTGT-GGCTTTAAAGGA
1 AAG-GTGCCACGGAGTTGTGGGCTTAAAA--AGAAG-GTGCCACGGAGTTGTGGGC-TTAAAGG-
25114 AAA
60 AAA
* * *
25117 AAGGGTGCCACGGAGTCGTGGACTT-AAAAG--GGTGCCACGGAGTTGTGGGCTTTAA--AAA
1 AA-GGTGCCACGGAGTTGTGGGCTTAAAAAGAAGGTGCCACGGAGTTGTGGGCTTAAAGGAAA
* * * *
25175 GA-GTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTTTGAA--A
1 AAGGTGCCACGGAGTTGTGGGCTT-AAA--AAGAA-GGTGCCACGGAGTTGTGGGC-TTAAAGGA
*
25237 AG
61 AA
* * * *
25239 AAGGTGCCACGCAGCTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACG--
1 AAGGTGCCACGGAGTTGTGGGCTTA-AA--AAGAAG-GTGCCACGGAGTTGTGGGCTTAAAGGAA
25302 -
62 A
* * * * *
25302 --GGTGCCACGAAGTTGTGGGCTTAAAAGGAAAAGCGTGCCACGTAGTTATGGGCTT---TGAAA
1 AAGGTGCCACGGAGTTGTGGGCTTAAAA--AGAAG-GTGCCACGGAGTTGTGGGCTTAAAGGAAA
* * * *
25362 AGGAGGTGCCACGGAGTTGTGGACTTTGAAAGAAAAAGGTGCCACAGAGTCGTGG
1 A--AGGTGCCACGGAGTTGTGGGC-TT-AAA-AAGAAGGTGCCACGGAGTTGTGG
25417 ACTTTGATGC
Statistics
Matches: 415, Mismatches: 35, Indels: 86
0.77 0.07 0.16
Matches are distributed among these distances:
56 41 0.10
57 1 0.00
58 8 0.02
60 28 0.07
61 55 0.13
62 21 0.05
63 48 0.12
64 54 0.13
65 100 0.24
66 16 0.04
67 42 0.10
68 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.21
Consensus pattern (62 bp):
AAGGTGCCACGGAGTTGTGGGCTTAAAAAGAAGGTGCCACGGAGTTGTGGGCTTAAAGGAAA
Found at i:25153 original size:222 final size:216
Alignment explanation
Indices: 24832--25420 Score: 765
Period size: 222 Copynumber: 2.7 Consensus size: 216
24822 TGGGCTTCGG
* * * * * * *
24832 AAAAGGGTGCCACTGATTTGTGGGCTTTGAA-GGTTGCCACTG-ACTTGTGGGCTTAAAAAGAAA
1 AAAAGAGTGCCACGGAGTTGTGGGC-TTAAACGGGTGCCAC-GAAGTTGTGGGCTTAAAAGGAAA
*
24895 AAGAGTGCCACGGAGTCGTGGACTTAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCC
64 AAGAGTGCCACGGAGTCGTGGACTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCC
24960 ACGGAGTCGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTTT-AAAATGAAGGTGC
129 ACGGAGTCGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAA-GAAGGTGC
* *
25024 CACGGAGTTGTGGGCTTAGAAGGA
193 CACGCAGCTGTGGGCTTAGAAGGA
* * * *
25048 AAAAGTGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAGAGTGCCACGTAGTTGT-GGCTTTAAAG
1 AAAAGAGTGCCACGGAGTTGTGGGCTT-AAACG----G-GTGCCACGAAGTTGTGGGCTTAAAAG
*
25112 GAAAAAAGGGTGCCACGGAGTCGTGGACTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGA
60 G-AAAAAGAGTGCCACGGAGTCGTGGACTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGA
*
25177 GTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAG
124 GTGCCACGGAGTCGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAG
25242 GTGCCACGCAGCTGTGGGCTTAGAAGGA
189 GTGCCACGCAGCTGTGGGCTTAGAAGGA
25270 AAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGGTGCCACGAAGTTGTGGGCTTAAAAGG-AAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGGTGCCACGAAGTTGTGGGCTTAAAAGGAAAAA
* * ** * * *
25334 GCGTGCCACGTAGTTATGGGCTTTGAAAAGGAGGTGCCACGGAGTTGTGGACTTTGAAAGAAAAA
66 GAGTGCCACGGAGTCGTGGAC-TT-AAAA-G-GGTGCCACGGAGTTGTGGGCTTT--AA-AAAGA
*
25399 GGTGCCACAGAGTCGTGGACTT
124 -GTGCCACGGAGTCGTGGACTT
25421 TGATGCCACT
Statistics
Matches: 328, Mismatches: 26, Indels: 31
0.85 0.07 0.08
Matches are distributed among these distances:
215 22 0.07
216 40 0.12
217 16 0.05
218 1 0.00
219 22 0.07
221 17 0.05
222 187 0.57
223 23 0.07
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.21
Consensus pattern (216 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGGTGCCACGAAGTTGTGGGCTTAAAAGGAAAAA
GAGTGCCACGGAGTCGTGGACTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCAC
GGAGTCGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCAC
GCAGCTGTGGGCTTAGAAGGA
Found at i:25316 original size:155 final size:153
Alignment explanation
Indices: 24832--25327 Score: 541
Period size: 155 Copynumber: 3.2 Consensus size: 153
24822 TGGGCTTCGG
* * * * * *
24832 AAAAGGGTGCCACTGATTTGTGGGCTTT--GAAG-GTTGCCACTGACTTGTGGGCTTAAAAAGAA
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAG-TGCCACGGAGTTGTGGGCTTAAAAGGAA
* * * *
24894 AAAGAGTGCCACGGAGTCGTGGACTT-AAA-AAGGTGCCACGGAGTTGTGGGCTT----TAAAAA
65 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGAAGGTGCCACGCAGTTGTGGGCTTAAAGGAAAAA
24953 GAGTGCCACGGAGTCGTGGACTTAAAAGGA
130 GAGTGCCACGGAGTCGTGGACTT------A
* *
24983 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAATGAAGGTGCCACGGAGTTGTGGGCTTAGAAGGA
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAG-A-GTGCCACGGAGTTGTGGGCTTAAAAGGA
* *
25048 AAAAGTGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAGAGTGCCACGTAGTTGT-GGCTTTAAAG
64 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAA-G--AAG-GTGCCACGCAGTTGTGGGC-TTAAAG
*
25112 GAAAAAAGGGTGCCACGGAGTCGTGGACTT-
124 G-AAAAAGAGTGCCACGGAGTCGTGGACTTA
*
25142 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAAA
* *
25207 AAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGCAGCTGTGGGCTTAGAAGGAAA
66 AAGAGTGCCACGGAGTTGTGGGC-TT-AAAAGAAGGTGCCACGCAGTTGTGGGCTTA-AAGGAAA
* *
25272 AAGAGTGCCACGGAGTTGTGGGCTT-
128 AAGAGTGCCACGGAGTCGTGGACTTA
* *
25297 AAACGGGTGCCACGAAGTTGTGGGC-TTAAAA
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAA
25328 GGAAAAGCGT
Statistics
Matches: 299, Mismatches: 25, Indels: 39
0.82 0.07 0.11
Matches are distributed among these distances:
151 26 0.09
153 2 0.01
154 6 0.02
155 111 0.37
156 14 0.05
157 50 0.17
158 4 0.01
159 37 0.12
160 6 0.02
161 16 0.05
166 27 0.09
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.21
Consensus pattern (153 bp):
AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAAA
AAGAGTGCCACGGAGTTGTGGGCTTAAAAGAAGGTGCCACGCAGTTGTGGGCTTAAAGGAAAAAG
AGTGCCACGGAGTCGTGGACTTA
Found at i:25488 original size:31 final size:31
Alignment explanation
Indices: 25451--25846 Score: 286
Period size: 31 Copynumber: 12.7 Consensus size: 31
25441 CTTAAAAGGG
* * *
25451 ATGCCACTGAATTGTCGACTTTTAGGACAAA
1 ATGCCACTGAGTCGTGGACTTTTAGGACAAA
* * * * *
25482 ATGCCACTGAGTCGTGGGCTTTGAGAAGAGA
1 ATGCCACTGAGTCGTGGACTTTTAGGACAAA
* * * ** *
25513 TTGCCACTGAGTCGTGGACTTTAAGAAGGAG
1 ATGCCACTGAGTCGTGGACTTTTAGGACAAA
* * *
25544 ATGCCACTGAATTGTGAAC-TTTAGGACAAA
1 ATGCCACTGAGTCGTGGACTTTTAGGACAAA
* * *
25574 ATGCCATTGAGTCGTGGGCTTTGAGAAGA-AAA
1 ATGCCACTGAGTCGTGGACTTTTAG--GACAAA
*
25606 AGGTGCCACGGAGTCGTGGAC-TTTAGGACAAA
1 A--TGCCACTGAGTCGTGGACTTTTAGGACAAA
* * *
25638 ATGCCACTGAATTGTGAAC-TTTAGGACAAA
1 ATGCCACTGAGTCGTGGACTTTTAGGACAAA
* * *
25668 ATGCCATTGAGTCGTGGGCTTTGAGAAGA-AAA
1 ATGCCACTGAGTCGTGGACTTTTAG--GACAAA
*
25700 AGGTGCCACGGAGTCGTGGAC-TTTAGGACAAA
1 A--TGCCACTGAGTCGTGGACTTTTAGGACAAA
* * * *
25732 ATGCCACTGATTCGTGGGCTTTGAAGA-AAA
1 ATGCCACTGAGTCGTGGACTTTTAGGACAAA
* *
25762 GGATGCCACTAAGTCGTGGACTTTGA-GACAAA
1 --ATGCCACTGAGTCGTGGACTTTTAGGACAAA
* * * * *
25794 ATGCCATTGAGTCGTGGACTTTGAGAAGAGA
1 ATGCCACTGAGTCGTGGACTTTTAGGACAAA
*
25825 TTGCCACTGAGTCGTGGACTTT
1 ATGCCACTGAGTCGTGGACTTT
25847 AAAAAGGTAT
Statistics
Matches: 286, Mismatches: 62, Indels: 34
0.75 0.16 0.09
Matches are distributed among these distances:
30 99 0.35
31 105 0.37
32 40 0.14
33 12 0.04
34 30 0.10
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.25
Consensus pattern (31 bp):
ATGCCACTGAGTCGTGGACTTTTAGGACAAA
Found at i:25671 original size:94 final size:94
Alignment explanation
Indices: 25451--25741 Score: 457
Period size: 94 Copynumber: 3.1 Consensus size: 94
25441 CTTAAAAGGG
* *
25451 ATGCCACTGAATTGTCG-ACTTTTAGGACAAAATGCCACTGAGTCGTGGGCTTTGAGAAG--AGA
1 ATGCCACTGAATTGT-GAAC-TTTAGGACAAAATGCCATTGAGTCGTGGGCTTTGAGAAGAAAAA
* * * *
25513 -TTGCCACTGAGTCGTGGACTTTAAGA-AGGAG
64 GGTGCCACGGAGTCGTGGACTTTAGGACA--AA
25544 ATGCCACTGAATTGTGAACTTTAGGACAAAATGCCATTGAGTCGTGGGCTTTGAGAAGAAAAAGG
1 ATGCCACTGAATTGTGAACTTTAGGACAAAATGCCATTGAGTCGTGGGCTTTGAGAAGAAAAAGG
25609 TGCCACGGAGTCGTGGACTTTAGGACAAA
66 TGCCACGGAGTCGTGGACTTTAGGACAAA
25638 ATGCCACTGAATTGTGAACTTTAGGACAAAATGCCATTGAGTCGTGGGCTTTGAGAAGAAAAAGG
1 ATGCCACTGAATTGTGAACTTTAGGACAAAATGCCATTGAGTCGTGGGCTTTGAGAAGAAAAAGG
25703 TGCCACGGAGTCGTGGACTTTAGGACAAA
66 TGCCACGGAGTCGTGGACTTTAGGACAAA
25732 ATGCCACTGA
1 ATGCCACTGA
25742 TTCGTGGGCT
Statistics
Matches: 187, Mismatches: 6, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
92 39 0.21
93 17 0.09
94 107 0.57
95 23 0.12
96 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.24
Consensus pattern (94 bp):
ATGCCACTGAATTGTGAACTTTAGGACAAAATGCCATTGAGTCGTGGGCTTTGAGAAGAAAAAGG
TGCCACGGAGTCGTGGACTTTAGGACAAA
Found at i:25747 original size:30 final size:30
Alignment explanation
Indices: 25451--25847 Score: 309
Period size: 30 Copynumber: 12.8 Consensus size: 30
25441 CTTAAAAGGG
* * *
25451 ATGCCACTGAATTGTCGACTTTTAGGACAAA
1 ATGCCACTGAGTCGTGGAC-TTTAGGACAAA
* * * *
25482 ATGCCACTGAGTCGTGGGCTTTGAGAAGAGA
1 ATGCCACTGAGTCGTGGACTTT-AGGACAAA
* * *
25513 TTGCCACTGAGTCGTGGACTTTAAGA-AGGAG
1 ATGCCACTGAGTCGTGGACTTTAGGACA--AA
* * *
25544 ATGCCACTGAATTGTGAACTTTAGGACAAA
1 ATGCCACTGAGTCGTGGACTTTAGGACAAA
* *
25574 ATGCCATTGAGTCGTGGGCTTTGAGAAGA-AAA
1 ATGCCACTGAGTCGTGGACTTT-AG--GACAAA
*
25606 AGGTGCCACGGAGTCGTGGACTTTAGGACAAA
1 A--TGCCACTGAGTCGTGGACTTTAGGACAAA
* * *
25638 ATGCCACTGAATTGTGAACTTTAGGACAAA
1 ATGCCACTGAGTCGTGGACTTTAGGACAAA
* *
25668 ATGCCATTGAGTCGTGGGCTTTGAGAAGA-AAA
1 ATGCCACTGAGTCGTGGACTTT-AG--GACAAA
*
25700 AGGTGCCACGGAGTCGTGGACTTTAGGACAAA
1 A--TGCCACTGAGTCGTGGACTTTAGGACAAA
* * *
25732 ATGCCACTGATTCGTGGGCTTTGAAGA-AAA
1 ATGCCACTGAGTCGTGGACTTT-AGGACAAA
*
25762 GGATGCCACTAAGTCGTGGACTTT-GAGACAAA
1 --ATGCCACTGAGTCGTGGACTTTAG-GACAAA
* * * *
25794 ATGCCATTGAGTCGTGGACTTTGAGAAGAGA
1 ATGCCACTGAGTCGTGGACTTT-AGGACAAA
*
25825 TTGCCACTGAGTCGTGGACTTTA
1 ATGCCACTGAGTCGTGGACTTTA
25848 AAAAGGTATT
Statistics
Matches: 289, Mismatches: 54, Indels: 47
0.74 0.14 0.12
Matches are distributed among these distances:
29 1 0.00
30 107 0.37
31 97 0.34
32 40 0.14
33 8 0.03
34 36 0.12
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.25
Consensus pattern (30 bp):
ATGCCACTGAGTCGTGGACTTTAGGACAAA
Found at i:26823 original size:16 final size:16
Alignment explanation
Indices: 26799--26830 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
26789 TTTTTCCTCT
*
26799 TTTTTTTTCTTTTTTG
1 TTTTGTTTCTTTTTTG
26815 TTTTGTTTCTTTTTTG
1 TTTTGTTTCTTTTTTG
26831 GAAAAGAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.84
Consensus pattern (16 bp):
TTTTGTTTCTTTTTTG
Found at i:34027 original size:52 final size:52
Alignment explanation
Indices: 33957--34077 Score: 206
Period size: 52 Copynumber: 2.3 Consensus size: 52
33947 GAAAATTTTT
*
33957 TTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 TTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
34009 TTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 TTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
* *
34061 CTGCATATATCGATACA
1 TTGCATGTATCGATACA
34078 AAGATCGGTG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (52 bp):
TTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:34090 original size:52 final size:52
Alignment explanation
Indices: 33958--34097 Score: 167
Period size: 52 Copynumber: 2.7 Consensus size: 52
33948 AAAATTTTTT
* * *
33958 TGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGCT
1 TGCATATATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGCC
* *** *
34010 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATATATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCC
*
34062 TGCATATATCGATACA-AAGATCGGTGTATCGATACA
1 TGCATATATCGATACATAAGAT-AGTGTATCGATACA
34098 ATATATCAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 4 0.05
52 73 0.95
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (52 bp):
TGCATATATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCC
Found at i:35359 original size:49 final size:49
Alignment explanation
Indices: 35150--35760 Score: 804
Period size: 49 Copynumber: 12.7 Consensus size: 49
35140 AAAAGGATGT
*
35150 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* *
35202 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
35245 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
35293 CAATGTGCTGGTTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
35342 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
35391 CAATATGCTGATTCAAGGCCAGCT--ATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
35438 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
35487 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
35536 CAATGTGCTGAGTCAAGGCCAACTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
35585 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-AT---GGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
35628 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
35676 CAATGTGCTAATTCATGACCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * * *
35725 CAATATGCTAATTCAGGGCCAGGTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
35761 GAAGGGTTGC
Statistics
Matches: 493, Mismatches: 51, Indels: 33
0.85 0.09 0.06
Matches are distributed among these distances:
43 77 0.16
45 1 0.00
46 3 0.01
47 43 0.09
48 89 0.18
49 248 0.50
52 32 0.06
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:35833 original size:30 final size:30
Alignment explanation
Indices: 35797--36059 Score: 182
Period size: 30 Copynumber: 8.7 Consensus size: 30
35787 CTTTAGAGGT
35797 TGCCACTGACTTGTGGGCTTTTGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTTGAAAAGGG
* ** *
35827 TGCCACTAACTTGTGGGCTTAAAAAGAAAAAGAG
1 TGCCACTGACTTGTGGGCTT---TTG-AAAAGGG
* * * ** *
35861 TGCTA-TAGAGTTGTGAGCTTACAAAAGAAAAAGAG
1 TGCCACT-GACTTGTGGGCTT----TTG-AAAAGGG
* * * *
35896 TGCCA-TGGAGTTGTGGACTTTGGAAAA-GA
1 TGCCACT-GACTTGTGGGCTTTTGAAAAGGG
* **
35925 TGCCACCGACTTGTGGGCTTCGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTTGAAAAGGG
* *
35955 TGCCACTGATTTGTGGGC-TTTG--AAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAAAGGG
*
35982 TGCCACTGACTTGTGGGCTTTTG--AAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAAAGGG
36010 TGCCACTGACTTGTGGGCTTTTGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTTGAAAAGGG
*
36040 TGCCACTAACTTGTGGGCTT
1 TGCCACTGACTTGTGGGCTT
36060 AAAAAGAAAA
Statistics
Matches: 192, Mismatches: 30, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
27 21 0.11
28 32 0.17
29 24 0.12
30 63 0.33
31 1 0.01
33 2 0.01
34 20 0.10
35 29 0.15
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (30 bp):
TGCCACTGACTTGTGGGCTTTTGAAAAGGG
Found at i:35875 original size:34 final size:35
Alignment explanation
Indices: 35820--35911 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 35
35810 TGGGCTTTTG
* *
35820 AAAAGGGTGCCACTA-ACTTGTGGGCTTA-AAAAGA
1 AAAAGAGTGCCA-TAGAGTTGTGGGCTTACAAAAGA
* *
35854 AAAAGAGTGCTATAGAGTTGTGAGCTTACAAAAGA
1 AAAAGAGTGCCATAGAGTTGTGGGCTTACAAAAGA
*
35889 AAAAGAGTGCCATGGAGTTGTGG
1 AAAAGAGTGCCATAGAGTTGTGG
35912 ACTTTGGAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
33 2 0.04
34 21 0.43
35 26 0.53
ACGTcount: A:0.38, C:0.11, G:0.29, T:0.22
Consensus pattern (35 bp):
AAAAGAGTGCCATAGAGTTGTGGGCTTACAAAAGA
Found at i:38660 original size:19 final size:19
Alignment explanation
Indices: 38621--38657 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
38611 AATTGAACTT
38621 GAAGAAAAACAAAAAAGAA
1 GAAGAAAAACAAAAAAGAA
*
38640 GAAGAAGAA-AAAAAAGAA
1 GAAGAAAAACAAAAAAGAA
38658 AGACCTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (19 bp):
GAAGAAAAACAAAAAAGAA
Found at i:38741 original size:20 final size:20
Alignment explanation
Indices: 38716--38758 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
38706 AAGGTGTTTA
38716 AAATAGTTTGGCTAGAAAAG
1 AAATAGTTTGGCTAGAAAAG
38736 AAATAGTTTGGCTAGAAAAG
1 AAATAGTTTGGCTAGAAAAG
38756 AAA
1 AAA
38759 CTCTTTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.49, C:0.05, G:0.23, T:0.23
Consensus pattern (20 bp):
AAATAGTTTGGCTAGAAAAG
Found at i:40021 original size:22 final size:22
Alignment explanation
Indices: 39996--40043 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
39986 TCTCGTATCT
39996 CCTCCAAACCTCTACCAGAAAA
1 CCTCCAAACCTCTACCAGAAAA
40018 CCTCCAAACCTCTACCAGAAAA
1 CCTCCAAACCTCTACCAGAAAA
40040 CCTC
1 CCTC
40044 TAAAACTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.44, G:0.04, T:0.15
Consensus pattern (22 bp):
CCTCCAAACCTCTACCAGAAAA
Found at i:41230 original size:13 final size:13
Alignment explanation
Indices: 41212--41237 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41202 TACACCAAGT
41212 ATGTATCGATACA
1 ATGTATCGATACA
41225 ATGTATCGATACA
1 ATGTATCGATACA
41238 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:41235 original size:32 final size:33
Alignment explanation
Indices: 41194--41257 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
41184 TAGCCAAACT
* **
41194 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
41226 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
41258 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:42189 original size:34 final size:35
Alignment explanation
Indices: 42126--42192 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
42116 CTAAGTGATT
42126 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
42162 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
42193 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:45837 original size:19 final size:20
Alignment explanation
Indices: 45815--45864 Score: 57
Period size: 24 Copynumber: 2.4 Consensus size: 20
45805 TTATATGCAA
45815 ATAAATTT-TTGATATGTGT
1 ATAAATTTATTGATATGTGT
45834 ATAAATTACCTTATTGATATGTGT
1 ATAAA-T---TTATTGATATGTGT
45858 ATAAATT
1 ATAAATT
45865 ACCTTATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
19 5 0.19
20 2 0.08
23 3 0.12
24 16 0.62
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.48
Consensus pattern (20 bp):
ATAAATTTATTGATATGTGT
Found at i:45850 original size:24 final size:24
Alignment explanation
Indices: 45823--45872 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
45813 AAATAAATTT
45823 TTGATATGTGTATAAATTACCTTA
1 TTGATATGTGTATAAATTACCTTA
45847 TTGATATGTGTATAAATTACCTTA
1 TTGATATGTGTATAAATTACCTTA
45871 TT
1 TT
45873 AAGGGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (24 bp):
TTGATATGTGTATAAATTACCTTA
Found at i:46579 original size:13 final size:13
Alignment explanation
Indices: 46561--46586 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46551 TACACCAAGT
46561 ATGTATCGATACA
1 ATGTATCGATACA
46574 ATGTATCGATACA
1 ATGTATCGATACA
46587 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:46584 original size:32 final size:33
Alignment explanation
Indices: 46543--46606 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
46533 TAGCCAAACT
* **
46543 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
46575 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
46607 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:47107 original size:34 final size:35
Alignment explanation
Indices: 47044--47110 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
47034 CTAAGTGATT
47044 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
47080 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
47111 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:48578 original size:81 final size:81
Alignment explanation
Indices: 48484--48678 Score: 200
Period size: 82 Copynumber: 2.4 Consensus size: 81
48474 CTAATTAAGG
* ** * * *
48484 GGATACTCCAATCTTGTTTTTCT-TACAACTAATCTTTAATTTACATTTTTAAGGATAATTCAAC
1 GGATACTCCAATCTCGTTTTTCTATACAAAAAATCTTAAATTTACATTCTTAA-GATAATCCAAC
48548 CCCATCTCTCTAAAAAC
65 CCCATCTCTCTAAAAAC
* * *
48565 GGATACTCTAATCTCGTTTTTCTGATCCAAAAAATCTTAAATTTACATTCTTAAGATACTCCAAC
1 GGATACTCCAATCTCGTTTTTCT-ATACAAAAAATCTTAAATTTACATTCTTAAGATAATCCAAC
* *
48630 CCCA-CTTCTCCAAAGA-
65 CCCATC-TCTCTAAAAAC
* *
48646 GTGATACTCTAACCTCGATTTTT-TATACAAAAA
1 G-GATACTCCAATCTCG-TTTTTCTATACAAAAA
48679 GACTTGAATT
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
81 31 0.32
82 36 0.38
83 29 0.30
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.36
Consensus pattern (81 bp):
GGATACTCCAATCTCGTTTTTCTATACAAAAAATCTTAAATTTACATTCTTAAGATAATCCAACC
CCATCTCTCTAAAAAC
Found at i:54262 original size:26 final size:25
Alignment explanation
Indices: 54232--54289 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 25
54222 TAATAATATC
54232 AATAATACTAATTTTTAAAAATATTT
1 AATAATACTAATTTTTAAAAA-ATTT
* *
54258 AATAAAAATTAATTTTTAAAAAATTT
1 AAT-AATACTAATTTTTAAAAAATTT
54284 AA-AATA
1 AATAATA
54290 AAAAGAACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 3 0.11
26 9 0.32
27 16 0.57
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
AATAATACTAATTTTTAAAAAATTT
Found at i:54292 original size:27 final size:27
Alignment explanation
Indices: 54240--54292 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
54230 TCAATAATAC
*
54240 TAATTTTTAAAAATATTTAATAAAAAT
1 TAATTTTTAAAAATATTTAAAAAAAAT
54267 TAATTTTTAAAAA-ATTTAAAATAAAA
1 TAATTTTTAAAAATATTTAAAA-AAAA
54293 AGAACAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
TAATTTTTAAAAATATTTAAAAAAAAT
Found at i:55237 original size:15 final size:16
Alignment explanation
Indices: 55207--55239 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
55197 CTTAGATGAG
55207 TTATTAGTTTTATATT
1 TTATTAGTTTTATATT
*
55223 TTATTA-TTTTTTATT
1 TTATTAGTTTTATATT
55238 TT
1 TT
55240 TTAATATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (16 bp):
TTATTAGTTTTATATT
Found at i:55707 original size:20 final size:20
Alignment explanation
Indices: 55682--55722 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
55672 ACGTGGGTAG
*
55682 TTTTTT-AAGAAATTATTAAT
1 TTTTTTAAAAAAATTA-TAAT
55702 TTTTTTAAAAAAATTATAAT
1 TTTTTTAAAAAAATTATAAT
55722 T
1 T
55723 AAAAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTTTTAAAAAAATTATAAT
Found at i:55726 original size:15 final size:14
Alignment explanation
Indices: 55706--55737 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
55696 ATTAATTTTT
55706 TTAAAAAAATTATAA
1 TTAAAAAAATTA-AA
55721 TTAAAAAAATTAAA
1 TTAAAAAAATTAAA
55735 TTA
1 TTA
55738 CATTCATACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TTAAAAAAATTAAA
Found at i:56428 original size:16 final size:15
Alignment explanation
Indices: 56409--56456 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 15
56399 ATTTTAAAAA
56409 TAATAT-TTAATATTAT
1 TAATATGTT-ATATT-T
56425 TAATATGTTATATTT
1 TAATATGTTATATTT
56440 TAATA---TATATTT
1 TAATATGTTATATTT
56452 TAATA
1 TAATA
56457 ATATAATAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 12 0.39
15 6 0.19
16 11 0.35
17 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
TAATATGTTATATTT
Found at i:56450 original size:35 final size:34
Alignment explanation
Indices: 56388--56485 Score: 96
Period size: 35 Copynumber: 2.9 Consensus size: 34
56378 TAAAAACAAT
* *
56388 TATAATA--TATTATTTTAAAAATAATATTTAATAT
1 TATAATAGTTATTATTTT-AATAT-ATATTTAATAA
56422 TATTAATATGTTA-TATTTTAATATATATTTTAATAA
1 TA-TAATA-GTTATTATTTTAATATATA-TTTAATAA
*
56458 TATAATAGTTATTATTTT-ATATTTATTT
1 TATAATAGTTATTATTTTAATATATATTT
56486 GTAAAATTTA
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
33 3 0.05
34 12 0.22
35 19 0.35
36 13 0.24
37 6 0.11
38 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (34 bp):
TATAATAGTTATTATTTTAATATATATTTAATAA
Found at i:56485 original size:34 final size:36
Alignment explanation
Indices: 56407--56485 Score: 96
Period size: 34 Copynumber: 2.3 Consensus size: 36
56397 TTATTTTAAA
*
56407 AATA-ATA-TTTAATATTATTAATATGTTATATTTT
1 AATATATATTTTAATAATATTAATATGTTATATTTT
56441 AATATATATTTTAATAATA-TAATA-GTTATTATTTT
1 AATATATATTTTAATAATATTAATATGTTA-TATTTT
*
56476 -ATATTTATTT
1 AATATATATTT
56486 GTAAAATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
34 17 0.43
35 14 0.35
36 9 0.22
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (36 bp):
AATATATATTTTAATAATATTAATATGTTATATTTT
Found at i:67340 original size:2 final size:2
Alignment explanation
Indices: 67328--67361 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
67318 ATTAATTTCG
* *
67328 TA TA TA AA TA TA TA TA TA AA 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
67362 AAGATACAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:67345 original size:12 final size:12
Alignment explanation
Indices: 67328--67357 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
67318 ATTAATTTCG
67328 TATATAAATATA
1 TATATAAATATA
67340 TATATAAATATA
1 TATATAAATATA
67352 TATATA
1 TATATA
67358 TATAAAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAAATATA
Found at i:67949 original size:2 final size:2
Alignment explanation
Indices: 67942--67972 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
67932 GTAAACTGTT
67942 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
67973 GACTAACTCA
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:71503 original size:19 final size:19
Alignment explanation
Indices: 71454--71503 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
71444 TTTTAAGTAT
*
71454 TATTTTATATAACTAATAA
1 TATTTTATGTAACTAATAA
71473 TA-TTTATAGTAACTAATAA
1 TATTTTAT-GTAACTAATAA
71492 TATTTTATGTAA
1 TATTTTATGTAA
71504 TATTATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.18
19 18 0.64
20 5 0.18
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (19 bp):
TATTTTATGTAACTAATAA
Found at i:71738 original size:19 final size:19
Alignment explanation
Indices: 71683--71739 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
71673 ATTGTTATTA
71683 GGTAATATTTTATGTAATAT
1 GGTAATATTTTATGTAAT-T
*
71703 -GTAATTTTTTATGTAATT
1 GGTAATATTTTATGTAATT
* *
71721 GGTAATATTATATTTAATT
1 GGTAATATTTTATGTAATT
71740 ATGATAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 1 0.03
19 31 0.97
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (19 bp):
GGTAATATTTTATGTAATT
Found at i:71788 original size:21 final size:19
Alignment explanation
Indices: 71751--71797 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
71741 TGATAAAAAT
71751 TATAATTAAATAATTTTTA
1 TATAATTAAATAATTTTTA
*
71770 TATAACTTACAATATTTTTTA
1 TATAA-TTA-AATAATTTTTA
*
71791 TACAATT
1 TATAATT
71798 GATCATGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 5 0.21
21 14 0.58
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (19 bp):
TATAATTAAATAATTTTTA
Found at i:72020 original size:21 final size:21
Alignment explanation
Indices: 71956--72029 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
71946 TATTATTGAC
*
71956 TAATATTTTACATAATTCATAA
1 TAATATTTTATATAATT-ATAA
* * *
71978 T-AT-TTTTAATGTAA-TGTGA
1 TAATATTTT-ATATAATTATAA
71997 TAATATTTTATATAATTATAA
1 TAATATTTTATATAATTATAA
* *
72018 TAAAATTATATA
1 TAATATTTTATA
72030 ATAAAAATAT
Statistics
Matches: 39, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
19 3 0.08
20 12 0.31
21 23 0.59
22 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.49
Consensus pattern (21 bp):
TAATATTTTATATAATTATAA
Found at i:72058 original size:12 final size:13
Alignment explanation
Indices: 72010--72059 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
72000 TATTTTATAT
72010 AATTATA-AT-AA
1 AATTATATATAAA
72021 AATTATATAATAAA
1 AATTATAT-ATAAA
*
72035 AATATGTATATAAA
1 AAT-TATATATAAA
72049 AATT-TATATAA
1 AATTATATATAA
72060 CTTGTAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
11 7 0.21
12 7 0.21
13 3 0.09
14 13 0.38
15 4 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (13 bp):
AATTATATATAAA
Found at i:72486 original size:5 final size:5
Alignment explanation
Indices: 72476--72608 Score: 64
Period size: 5 Copynumber: 27.2 Consensus size: 5
72466 GATTAATAAA
* * **
72476 AATAT AATAT AATAT AATAT AATGT GATAT AATATT AATAT -ATAT TTTA-
1 AATAT AATAT AATAT AATAT AATAT AATAT AATA-T AATAT AATAT AATAT
* * * * *
72525 AATTT TATAT AATAT AA-AT TAT-T AATAT -ATTT AAATAT AA-AA AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT
* * * *
72572 AAAAT ATTTT AAATAT AATTAT AATGT AATA- AATAT A
1 AATAT AATAT -AATAT AA-TAT AATAT AATAT AATAT A
72609 TAAAAAATTT
Statistics
Matches: 92, Mismatches: 25, Indels: 22
0.66 0.18 0.16
Matches are distributed among these distances:
4 21 0.23
5 55 0.60
6 16 0.17
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (5 bp):
AATAT
Found at i:72533 original size:16 final size:17
Alignment explanation
Indices: 72509--72560 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
72499 GTGATATAAT
*
72509 ATTAATATATATTTTAA
1 ATTATTATATATTTTAA
* *
72526 ATT-TTATATAATATAA
1 ATTATTATATATTTTAA
72542 ATTATTA-ATATATTTAA
1 ATTATTATATAT-TTTAA
72559 AT
1 AT
72561 ATAAAAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 16 0.57
17 12 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTATTATATATTTTAA
Found at i:73539 original size:23 final size:24
Alignment explanation
Indices: 73493--73540 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
73483 TTTAGTTAAG
*
73493 ATTAAATAGATTTTTAAATATTTT
1 ATTAAATAGATTTTAAAATATTTT
*
73517 ATTAAATATATTTTAAAAT-TTTT
1 ATTAAATAGATTTTAAAATATTTT
73540 A
1 A
73541 AATATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTAAATAGATTTTAAAATATTTT
Found at i:73952 original size:16 final size:16
Alignment explanation
Indices: 73933--73994 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
73923 AGCCCGAATT
73933 CGAATAAACTCAAACC
1 CGAATAAACTCAAACC
**
73949 CGAA-AAAGCTTGAACC
1 CGAATAAA-CTCAAACC
* *
73965 CGAATAAGCTCAAACT
1 CGAATAAACTCAAACC
*
73981 CGAATAAACCCAAA
1 CGAATAAACTCAAA
73995 TTTAAAAGAG
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
15 3 0.08
16 31 0.86
17 2 0.06
ACGTcount: A:0.48, C:0.27, G:0.11, T:0.13
Consensus pattern (16 bp):
CGAATAAACTCAAACC
Found at i:73952 original size:32 final size:32
Alignment explanation
Indices: 73916--73996 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
73906 GAATCCGAAT
73916 CCGAATAAGCCCGAATTCGAATAAACTCAAAC
1 CCGAATAAGCCCGAATTCGAATAAACTCAAAC
* ** ** *
73948 CCGAAAAAGCTTGAACCCGAATAAGCTCAAAC
1 CCGAATAAGCCCGAATTCGAATAAACTCAAAC
* * *
73980 TCGAATAAACCCAAATT
1 CCGAATAAGCCCGAATT
73997 TAAAAGAGCC
Statistics
Matches: 35, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.44, C:0.27, G:0.12, T:0.16
Consensus pattern (32 bp):
CCGAATAAGCCCGAATTCGAATAAACTCAAAC
Found at i:74178 original size:14 final size:15
Alignment explanation
Indices: 74161--74192 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
74151 TATTTATTTT
74161 TTAAAT-TTAAAATA
1 TTAAATATTAAAATA
74175 TT-AATATTAAAATA
1 TTAAATATTAAAATA
74189 TTAA
1 TTAA
74193 TAGATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
13 3 0.19
14 12 0.75
15 1 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAAATATTAAAATA
Found at i:74193 original size:14 final size:14
Alignment explanation
Indices: 74167--74194 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
74157 TTTTTTAAAT
74167 TTAAAATATTAATA
1 TTAAAATATTAATA
74181 TTAAAATATTAATA
1 TTAAAATATTAATA
74195 GATATATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAATATTAATA
Found at i:74968 original size:16 final size:16
Alignment explanation
Indices: 74921--74968 Score: 78
Period size: 16 Copynumber: 3.0 Consensus size: 16
74911 AATTGAGTAA
* *
74921 TTTTATATTTAAATTA
1 TTTTAAATTTAAATTT
74937 TTTTAAATTTAAATTT
1 TTTTAAATTTAAATTT
74953 TTTTAAATTTAAATTT
1 TTTTAAATTTAAATTT
74969 ATTCAAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTAAATTTAAATTT
Found at i:74979 original size:16 final size:16
Alignment explanation
Indices: 74927--74979 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
74917 GTAATTTTAT
*
74927 ATTTAAA-TTATTTTAA
1 ATTTAAATTTA-TTCAA
* *
74943 ATTTAAATTTTTTTAA
1 ATTTAAATTTATTCAA
74959 ATTTAAATTTATTCAA
1 ATTTAAATTTATTCAA
*
74975 GTTTA
1 ATTTA
74980 GACTTATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 30 0.94
17 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (16 bp):
ATTTAAATTTATTCAA
Found at i:75138 original size:21 final size:20
Alignment explanation
Indices: 75089--75139 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
75079 TATTATTGAT
75089 TAATATTTT-ACGTAATTCA
1 TAATATTTTAACGTAATTCA
* *
75108 TAATATTTTTAATGTAATGTGA
1 TAATA-TTTTAACGTAAT-TCA
75130 TAATATTTTA
1 TAATATTTTA
75140 TATAATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 5 0.19
20 4 0.15
21 11 0.41
22 7 0.26
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (20 bp):
TAATATTTTAACGTAATTCA
Found at i:75607 original size:10 final size:10
Alignment explanation
Indices: 75592--75630 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
75582 GTTAATAAAA
75592 ATATAATATG
1 ATATAATATG
*
75602 ATATAATATA
1 ATATAATATG
* *
75612 ATGTAAAATG
1 ATATAATATG
75622 ATATAATAT
1 ATATAATAT
75631 TGATTATATT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (10 bp):
ATATAATATG
Found at i:75685 original size:25 final size:26
Alignment explanation
Indices: 75636--75689 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
75626 AATATTGATT
75636 ATATTTTAAAATTTATATAATATAAA
1 ATATTTTAAAATTTATATAATATAAA
*
75662 ATATTTT-AAATTTA-ATTATAATAAA
1 ATATTTTAAAATTTATATAAT-ATAAA
75687 ATA
1 ATA
75690 ATATATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 4 0.15
25 15 0.58
26 7 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATTTTAAAATTTATATAATATAAA
Found at i:76432 original size:24 final size:24
Alignment explanation
Indices: 76367--76437 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
76357 TATTATGTTT
**
76367 TAATAAATTTTATTTTAAT-TTAA
1 TAATAAATAATATTTTAATATTAA
* * * *
76390 TTATATA-AATATATAAATATTAA
1 TAATAAATAATATTTTAATATTAA
76413 TAATAAATAATATTTTAATATTAA
1 TAATAAATAATATTTTAATATTAA
76437 T
1 T
76438 TTAAACAGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
22 7 0.19
23 14 0.39
24 15 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TAATAAATAATATTTTAATATTAA
Found at i:79830 original size:20 final size:21
Alignment explanation
Indices: 79801--79843 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
79791 TATATAGATA
* *
79801 ATTTTTAATTT-AATAAATAT
1 ATTTTAAATTTAAATAAAAAT
79821 ATTTTAAATTTAAATAAAAAT
1 ATTTTAAATTTAAATAAAAAT
79842 AT
1 AT
79844 AGTAACTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTTTAAATTTAAATAAAAAT
Found at i:82350 original size:2 final size:2
Alignment explanation
Indices: 82343--82392 Score: 91
Period size: 2 Copynumber: 24.5 Consensus size: 2
82333 CGCATCAACG
82343 AT AT AT AT 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 AT AT AT AT
82385 AT GAT AT A
1 AT -AT AT A
82393 CTAAAAAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 45 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:82823 original size:15 final size:14
Alignment explanation
Indices: 82803--82833 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
82793 TTCGCTTGGT
82803 AAGATTTTCTCAGAA
1 AAGATTTTCTCA-AA
82818 AAGATTTTCTCAAA
1 AAGATTTTCTCAAA
82832 AA
1 AA
82834 TGTCGAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (14 bp):
AAGATTTTCTCAAA
Found at i:90586 original size:20 final size:20
Alignment explanation
Indices: 90550--90587 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
90540 AGGATCCAGA
*
90550 TTAATTAGGCTTAATTTTTT
1 TTAATTAGACTTAATTTTTT
90570 TTAATTTAGACTT-ATTTT
1 TTAA-TTAGACTTAATTTT
90588 AAAAAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.61
Consensus pattern (20 bp):
TTAATTAGACTTAATTTTTT
Found at i:91105 original size:30 final size:31
Alignment explanation
Indices: 91069--91135 Score: 109
Period size: 30 Copynumber: 2.2 Consensus size: 31
91059 TGAACAGTAC
*
91069 ATGTATCGATACATTCT-TTTTTTTATCCAG
1 ATGTATCGATACATTCTCTTTTTTTACCCAG
91099 ATGTATCGATACATTCTGCTTTTTTTACCCAG
1 ATGTATCGATACATTCT-CTTTTTTTACCCAG
91131 ATGTA
1 ATGTA
91136 ACAATATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 17 0.50
32 17 0.50
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (31 bp):
ATGTATCGATACATTCTCTTTTTTTACCCAG
Found at i:92809 original size:33 final size:32
Alignment explanation
Indices: 92765--92827 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
92755 CACACCCAGA
* * * *
92765 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCAATACATGAT-CATTGTATCAATACAT
92798 TGTATCAATACATGATCATTGTATCAATAC
1 TGTATCAATACATGATCATTGTATCAATAC
92828 CTGGACAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 12 0.46
33 14 0.54
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.40
Consensus pattern (32 bp):
TGTATCAATACATGATCATTGTATCAATACAT
Found at i:92819 original size:19 final size:18
Alignment explanation
Indices: 92794--92856 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 18
92784 TTGTATCGAT
92794 ACATTGTATCAATACATG
1 ACATTGTATCAATACATG
*
92812 ATCATTGTATCAATACCTGG
1 A-CATTGTATCAATACAT-G
92832 ACAATTGTATCAATACATG
1 AC-ATTGTATCAATACATG
*
92851 AAATTG
1 ACATTG
92857 GCAGTAGCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
18 5 0.13
19 18 0.46
20 16 0.41
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (18 bp):
ACATTGTATCAATACATG
Found at i:92903 original size:13 final size:13
Alignment explanation
Indices: 92885--92917 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
92875 CTCGATACAT
92885 GATACATTGTATC
1 GATACATTGTATC
*
92898 GATACAATGTATC
1 GATACATTGTATC
92911 GATACAT
1 GATACAT
92918 GATGAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
GATACATTGTATC
Done.