Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023262.1 Corchorus olitorius cultivar O-4 contig23295, whole genome shotgun sequence
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: 14446
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:2882 original size:21 final size:21
Alignment explanation
Indices: 2852--2891 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2842 CTAAAAACAG
*
2852 GACAAGTCCTGCCCAGGACTT
1 GACAACTCCTGCCCAGGACTT
2873 GACAACTCCTGCCCAGGAC
1 GACAACTCCTGCCCAGGAC
2892 CTGGTCTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.38, G:0.23, T:0.15
Consensus pattern (21 bp):
GACAACTCCTGCCCAGGACTT
Found at i:2953 original size:21 final size:21
Alignment explanation
Indices: 2928--2967 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2918 AAATCAGAAC
2928 AACTCCTGCCCAGGACTTGAG
1 AACTCCTGCCCAGGACTTGAG
*
2949 AACTCCTGCTCAGGACTTG
1 AACTCCTGCCCAGGACTTG
2968 GTCTGTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.23
Consensus pattern (21 bp):
AACTCCTGCCCAGGACTTGAG
Found at i:2977 original size:73 final size:71
Alignment explanation
Indices: 2844--3039 Score: 286
Period size: 73 Copynumber: 2.7 Consensus size: 71
2834 ATTGAAGCCT
* * *
2844 AAAAA-CAGGACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGTTGAAAGA
1 AAAAATCAGAACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAA
2908 CGGAAG
66 CGGAAG
* * *
2914 AAAAAAATCAGAACAACTCCTGCCCAGGACTTGAGAACTCCTGCTCAGGACTTGGTCTGTTGAAA
1 --AAAAATCAGAACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAA
2979 AACGGAAG
64 AACGGAAG
* *
2987 AAAATTCAGAACAAGTCCTGTCCAGGACTTGGACAACTCCTGCCCAGGACTTG
1 AAAAATCAGAACAAGTCCTGCCCAGGACTT-GACAACTCCTGCCCAGGACTTG
3040 TTGTGGAAAA
Statistics
Matches: 111, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
71 27 0.24
72 25 0.23
73 59 0.53
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (71 bp):
AAAAATCAGAACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAA
CGGAAG
Found at i:3027 original size:22 final size:22
Alignment explanation
Indices: 2997--3039 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2987 AAAATTCAGA
* *
2997 ACAAGTCCTGTCCAGGACTTGG
1 ACAACTCCTGCCCAGGACTTGG
3019 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
3040 TTGTGGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21
Consensus pattern (22 bp):
ACAACTCCTGCCCAGGACTTGG
Found at i:8752 original size:26 final size:23
Alignment explanation
Indices: 8722--8768 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
8712 CTTGAAAATT
8722 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAAC-TTGAT-GAT-AGATGGA
8748 TGAAAAACTTGATGATAGATG
1 TGAAAAACTTGATGATAGATG
8769 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (23 bp):
TGAAAAACTTGATGATAGATGGA
Found at i:11921 original size:154 final size:154
Alignment explanation
Indices: 11641--12549 Score: 1557
Period size: 154 Copynumber: 5.9 Consensus size: 154
11631 ATATTGCATT
* * *
11641 TTTTCTTTCCATTTTTTATGGACTAACTATAATCATTTTGGGGAGATTAGTCCACTGTGAAGTTT
1 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
** *
11706 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGT
66 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGT
11771 CTTCGATTTGGCAAACCTCAATGC
131 CTTCGATTTGGCAAACCTCAATGC
11795 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
1 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
*
11860 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGT
66 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGT
11925 CTTCGATTTGGCAAACCTCAATGC
131 CTTCGATTTGGCAAACCTCAATGC
11949 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
1 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
*
12014 TTAGCTCATTTGGAACACTTGTTATATTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGT
66 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGT
12079 CTTCGATTTGGCAAACCTCAATGC
131 CTTCGATTTGGCAAACCTCAATGC
* * *
12103 TTTTCTTTCTATTGTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAATTTT
1 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
* * * *
12168 TTAGCTCATTTAGAACACTTGCTATTTTGGTCCTATCGGGGCCCATTAGTTCTGTTTTGAATCGT
66 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGT
*
12233 CTTCGATTTGGCAAACCTCAATGA
131 CTTCGATTTGGCAAACCTCAATGC
* * *
12257 TTTTCTTACCATTGTTTAGGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTT
1 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
* * *
12322 TAAAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCTCATTTGTTCCGTTTTGAATCG
66 T-TAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCG
*
12387 TCTTCGATTTGTCAAACCTCAATGC
130 TCTTCGATTTGGCAAACCTCAATGC
* *
12412 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGCGAGATTAGTCCACTGTGAACTTT
1 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
* * *
12477 TTAGCTCATTTGGAACACTTGTTATTTTGGGACAATCGAGGCCCATTAGTTCCGTTTTGAATCGT
66 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGT
12542 CTTCGATT
131 CTTCGATT
12550 GTTAATGGCC
Statistics
Matches: 711, Mismatches: 43, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
154 571 0.80
155 140 0.20
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (154 bp):
TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGT
CTTCGATTTGGCAAACCTCAATGC
Found at i:12534 original size:463 final size:462
Alignment explanation
Indices: 11641--12549 Score: 1577
Period size: 463 Copynumber: 2.0 Consensus size: 462
11631 ATATTGCATT
* *
11641 TTTTCTTTCCATTTTTTATGGACTAACTATAATCATTTTGGGGAGATTAGTCCACTGTGAAGTTT
1 TTTTCTTTCCATTGTTTACGGACTAACTATAATCATTTTGGGGAGATTAGTCCACTGTGAAGTTT
* *
11706 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGT
66 TTAGCTCATTTAGAACACTTGCTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGT
* * *
11771 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
131 CTTCGATTTGGCAAACCTCAATGATTTTCTTACCATTGTTTAGGGCCTAACTATAATCATTTTGG
* *
11836 TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGG
196 TAAGATTAGTCCACTGTGAAGTTTTAAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGG
11901 CTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTT
261 CTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTT
* *
11966 ATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
326 ATGGCCTAACTATAATCATTTTGGCGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACA
* * *
12031 CTTGTTATATTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACC
391 CTTGTTATATTGGGACAATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACC
12096 TCAATGC
456 TCAATGC
* * * *
12103 TTTTCTTTCTATTGTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAATTTT
1 TTTTCTTTCCATTGTTTACGGACTAACTATAATCATTTTGGGGAGATTAGTCCACTGTGAAGTTT
* * *
12168 TTAGCTCATTTAGAACACTTGCTATTTTGGTCCTATCGGGGCCCATTAGT-TCTGTTTTGAATCG
66 TTAGCTCATTTAGAACACTTGCTATTTTGGGCCTATCGGGGCCCATTAGTGAC-GTATTGAATCG
12232 TCTTCGATTTGGCAAACCTCAATGATTTTCTTACCATTGTTTAGGGCCTAACTATAATCATTTTG
130 TCTTCGATTTGGCAAACCTCAATGATTTTCTTACCATTGTTTAGGGCCTAACTATAATCATTTTG
12297 GTAAGATTAGTCCACTGTGAAGTTTTAAAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGG
195 GTAAGATTAGTCCACTGTGAAGTTTT-AAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGG
* *
12362 GGCTCATTTGTTCCGTTTTGAATCGTCTTCGATTTGTCAAACCTCAATGCTTTTCTTTCCATTGT
259 GGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
12427 TTATGGCCTAACTATAATCATTTTGGCGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAA
324 TTATGGCCTAACTATAATCATTTTGGCGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAA
*
12492 CACTTGTTATTTTGGGACAATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATT
389 CACTTGTTATATTGGGACAATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATT
12550 GTTAATGGCC
Statistics
Matches: 421, Mismatches: 24, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
461 1 0.00
462 203 0.48
463 217 0.52
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (462 bp):
TTTTCTTTCCATTGTTTACGGACTAACTATAATCATTTTGGGGAGATTAGTCCACTGTGAAGTTT
TTAGCTCATTTAGAACACTTGCTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGT
CTTCGATTTGGCAAACCTCAATGATTTTCTTACCATTGTTTAGGGCCTAACTATAATCATTTTGG
TAAGATTAGTCCACTGTGAAGTTTTAAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGG
CTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTT
ATGGCCTAACTATAATCATTTTGGCGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACA
CTTGTTATATTGGGACAATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACC
TCAATGC
Found at i:12644 original size:125 final size:125
Alignment explanation
Indices: 12422--12673 Score: 423
Period size: 125 Copynumber: 2.0 Consensus size: 125
12412 TTTTCTTTCC
*
12422 ATTGTTTATGGCCTAACTATAATCATTTTGGCGAGATTAGTCCACTGTGAACTTTTTAGCTCATT
1 ATTGTTAATGGCCTAACTATAATCATTTTGGCGAGATTAGTCCACTGTGAACTTTTTAGCTCATT
12487 TGGAACACTTGTTATTTTGGGACAATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
66 TGGAACACTTGTTATTTTGGGACAATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
** *
12547 ATTGTTAATGGCCTAACTATAATCATTTTGTTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
1 ATTGTTAATGGCCTAACTATAATCATTTTGGCGAGATTAGTCCACTGTGAACTTTTTAGCTCATT
* * * * *
12612 TGGAACATTTGTTATTTTGGGCCTATTGAGGCCCATTAGTTCCGTTTTGAATTGTCTTCG
66 TGGAACACTTGTTATTTTGGGACAATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
12672 AT
1 AT
12674 GTGGCAAACC
Statistics
Matches: 118, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
125 118 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (125 bp):
ATTGTTAATGGCCTAACTATAATCATTTTGGCGAGATTAGTCCACTGTGAACTTTTTAGCTCATT
TGGAACACTTGTTATTTTGGGACAATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCG
Found at i:12777 original size:279 final size:280
Alignment explanation
Indices: 12267--12826 Score: 906
Period size: 279 Copynumber: 2.0 Consensus size: 280
12257 TTTTCTTACC
*
12267 ATTGTTTAGGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTAAAGCTCAT
1 ATTGTTAAGGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTAAAGCTCAT
* * * *
12332 TTGGAACACTTGTTATTTTGGGCCTATCGGGGCTCATTTGTTCCGTTTTGAATCGTCTTCGATTT
66 TTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATGT
* * *
12397 GTCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGCGAGATTAG
131 GGCAAACCTCAATGCTTTTCTTTCCAATGTTTAAGGCCTAACTATAATCATTTTGGCGAGATTAG
* **
12462 TCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGACAATCGAGGCCCATTAGT
196 TCCACTGTGAACTTTATAGCTCAGATGGAACACTTGTTATTTTGGGACAATCGAGGCCCATTAGT
*
12527 TCCGTTTTGAATCGTCTTCG
261 TCCGTTATGAATCGTCTTCG
* * * *
12547 ATTGTTAATGGCCTAACTATAATCATTTTGTTGAGATTAGTCCACTGTGAAGTTTT-TAGCTCAT
1 ATTGTTAAGGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTAAAGCTCAT
* * *
12611 TTGGAACATTTGTTATTTTGGGCCTATTGAGGCCCATTAGTTCCGTTTTGAATTGTCTTCGATGT
66 TTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATGT
*
12676 GGCAAACCTCAATGCTTTTCTTTCCAATGTTTAAGGCCTAACTATAATCATTTTGGTGAGATTAG
131 GGCAAACCTCAATGCTTTTCTTTCCAATGTTTAAGGCCTAACTATAATCATTTTGGCGAGATTAG
* * *
12741 TCCACTGTGAACTTTATAGCTCAGATGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTCGT
196 TCCACTGTGAACTTTATAGCTCAGATGGAACACTTGTTATTTTGGGACAATCGAGGCCCATTAGT
12806 TCCGTTATGAATCGTCTTCG
261 TCCGTTATGAATCGTCTTCG
12826 A
1 A
12827 CGTGGCAAAC
Statistics
Matches: 257, Mismatches: 23, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
279 205 0.80
280 52 0.20
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.40
Consensus pattern (280 bp):
ATTGTTAAGGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTAAAGCTCAT
TTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATGT
GGCAAACCTCAATGCTTTTCTTTCCAATGTTTAAGGCCTAACTATAATCATTTTGGCGAGATTAG
TCCACTGTGAACTTTATAGCTCAGATGGAACACTTGTTATTTTGGGACAATCGAGGCCCATTAGT
TCCGTTATGAATCGTCTTCG
Found at i:13346 original size:153 final size:154
Alignment explanation
Indices: 12547--14435 Score: 2731
Period size: 154 Copynumber: 12.3 Consensus size: 154
12537 ATCGTCTTCG
* *
12547 ATTGTTAATGGCCTAACTATAATCATTTTGTTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
1 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
* * * ** * *
12612 TGGAACATTTGTTATTTTGGGCCTATTGAGGCCCATTAGTTCCGTTTTGAATTGTCTTCGATGTG
66 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTG
12677 GCAAACCTCAATGCTTTTCTTTCC
131 GCAAACCTCAATGCTTTTCTTTCC
* * * * **
12701 AATGTTTAAGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTATAGCTCAGA
1 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
* * ** * **
12766 TGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTCGTTCCGTTATGAATCGTCTTCGACGTG
66 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTG
12831 GCAAACCTCAATGCTTTTCTTTCC
131 GCAAACCTCAATGCTTTTCTTTCC
*
12855 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTGTAGCTCATT
1 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
* * ** * *
12920 TGGAACACTTGTTATTTTGGGCCTATTGAGGCCCATTAGTTTCGTTTTGAATCATCTTCGATTAG
66 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTG
12985 GCAAACCTCAATGCTTTTCTTTCC
131 GCAAACCTCAATGCTTTTCTTTCC
13009 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
1 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
* * *
13074 TGGAACACTTGTTATTTTGGGCCTATTGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTA
66 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTG
*
13139 GCAAACCTCATTGCTTTTCTTTCC
131 GCAAACCTCAATGCTTTTCTTTCC
* * * * * *
13163 ATCGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCGCAGTGAAGGTATTAACTCATT
1 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
** * *
13228 TGGAACACTTGTTATTTTGGGCCTATC-GGGCCCATTAGTTCCGTTTTGAATCATCTTCGATTAG
66 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTG
13292 GCAAACCTCAATGCTTTTCTTTCC
131 GCAAACCTCAATGCTTTTCTTTCC
* * * *
13316 ATTGTTTATGGCCTAACCATAATCAGTTTGGTGAGAGTAGTCCACTGTGAACTTTTTAGCTCATT
1 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
* * *
13381 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAGTCTTCTTCGATTTG
66 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTG
13446 GCAAACCTCAATGCTTTTCTTTCC
131 GCAAACCTCAATGCTTTTCTTTCC
* * * * * * *
13470 ATTGTTTATGGCCTAACGATAATCATTTTGTTTAAATTAGTCCATTTTGAAGTTTTTTGCTCATT
1 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
* * *
13535 CT-GAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCTTCTTCGAATT
66 -TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTT
* *
13599 GTCAAGCCTCAATGCTTTTCTTTCC
130 GGCAAACCTCAATGCTTTTCTTTCC
* *
13624 ATT-TTTATGGCCTAACTATAATCATTTTGGTTAGATTAGTCCACTTTGAAGTTTTTAGCTCATT
1 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
* * **
13688 TTGAACACTTGTTATCTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
66 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTG
*
13753 GCAAACTTCAATGCTTTTCTTTCC
131 GCAAACCTCAATGCTTTTCTTTCC
* *
13777 ATTGTGTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTAG-GAAGTTTGTAGCTCAT
1 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT-GTGAAGTTTTTAGCTCAT
* * *
13841 TTGGAACACTAGTTATATTGGGCCTAT-GGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTT
65 TTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTT
*
13905 GGCAAACCTAAATGCTTTTCTTTCC
130 GGCAAACCTCAATGCTTTTCTTTCC
* * *
13930 ATTGTGTATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTATGAAGTTTTTAGCTCATT
1 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
* * ** *
13995 TGGAGCACTTGTTATATT--GCTCTATCGGGGCCCATTAGTTTCATTTTGAATCGTCTTCGATTT
66 TGGAACACTTGTTATTTTGGGC-CTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTT
*
14058 GG-AAACCTTCGATGCTTTTCTTTCC
130 GGCAAACC-TCAATGCTTTTCTTTCC
* *
14083 ATTGTTTATGGCCTAACTATAATCA-TTTGGTGATATTAGTCCATTGTGAAGTTTTTAGCTCATT
1 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
* * *
14147 TGGAAAACTTG-TATTTTGGGCATATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTG
66 TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTG
14211 GCAAACCTCAATGCTTTTCTTTCC
131 GCAAACCTCAATGCTTTTCTTTCC
* * *
14235 ATTGTGTATGGCCTAACTATAATCATTTTGGT-AAATTTAGTCTACTGTGAAGTTTTTAGCTCAT
1 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA-TTAGTCCACTGTGAAGTTTTTAGCTCAT
* * *
14299 TTGGAACAATTG-TATTTTGGGCCTTTCGGGGCCCATTAGTGACGTTTTGAAATCGTCTTCGATC
65 TTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTG-AATCGTCTTCGATT
* * *
14363 TAGCAAACCCCGATGCTTTTCTTTCC
129 TGGCAAACCTCAATGCTTTTCTTTCC
* *
14389 ATTGTTTATGGGCCTAACTGTAATAATTTTGGTGAGATTAGTCCACT
1 ATTGTTTAT-GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
14436 ATTTACCTAT
Statistics
Matches: 1568, Mismatches: 150, Indels: 33
0.90 0.09 0.02
Matches are distributed among these distances:
151 7 0.00
152 135 0.09
153 564 0.36
154 829 0.53
155 31 0.02
156 2 0.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (154 bp):
ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
TGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTG
GCAAACCTCAATGCTTTTCTTTCC
Found at i:13405 original size:307 final size:306
Alignment explanation
Indices: 12547--14435 Score: 2668
Period size: 307 Copynumber: 6.2 Consensus size: 306
12537 ATCGTCTTCG
* * *
12547 ATTGTTAATGGCCTAACTATAATCATTTTGTTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATT
1 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGGTTTTAGCTCATT
* * ** *
12612 TGGAACATTTGTTATTTTGGGCCTATTGAGGCCCATTAGTTCCGTTTTGAATTGTCTTCGATGTG
66 TGGAACACTTGTTATTTTGGGCCTATCG-GGCCCATTAGTGACGTTTTGAATCGTCTTCGAT-TG
* *
12677 GCAAACCTCAATGCTTTTCTTTCCAATGTTTAAGGCCTAACTATAATCATTTTGGTGAGATTAGT
129 GCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGT
* * ** * * *
12742 CCACTGTGAACTTTATAGCTCAGATGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTCGTT
194 CCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTG
* * **
12807 CCGTTATGAATCGTCTTCGACGTGGCAAACCTCAATGCTTTTCTTTCC
259 ACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
12855 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA-GTTTGTAGCTCAT
1 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGGTTT-TAGCTCAT
* ** *
12919 TTGGAACACTTGTTATTTTGGGCCTATTGAGGCCCATTAGTTTCGTTTTGAATCATCTTCGATTA
65 TTGGAACACTTGTTATTTTGGGCCTATCG-GGCCCATTAGTGACGTTTTGAATCGTCTTCGATT-
12984 GGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
128 GGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
*
13049 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATTGGGGCCCATTAGT
193 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT
* * *
13114 GACGTATTGAATCGTCTTCGATTTAGCAAACCTCATTGCTTTTCTTTCC
258 GACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
* * * * *
13163 ATCGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCGCAGTGAAGGTATTAACTCATT
1 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGGTTTTAGCTCATT
** *
13228 TGGAACACTTGTTATTTTGGGCCTATCGGGCCCATTAGTTCCGTTTTGAATCATCTTCGATTAGG
66 TGGAACACTTGTTATTTTGGGCCTATCGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATT-GG
* * *
13293 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACCATAATCAGTTTGGTGAGAGTAGTC
130 CAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
*
13358 CACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGA
195 CACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGA
* * *
13423 CGTATTGAGTCTTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
260 CGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
* * * * * * * *
13470 ATTGTTTATGGCCTAACGATAATCATTTTGTTTAAATTAGTCCATTTTGAAGTTTTTTGCTCATT
1 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGGTTTTAGCTCATT
* *
13535 CT-GAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCTTCTTCGAATT
66 -TGGAACACTTGTTATTTTGGGCCTATC-GGGCCCATTAGTGACGTTTTGAATCGTCTTCG-ATT
* * *
13599 GTCAAGCCTCAATGCTTTTCTTTCCATT-TTTATGGCCTAACTATAATCATTTTGGTTAGATTAG
128 GGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
* * *
13663 TCCACTTTGAAGTTTTTAGCTCATTTTGAACACTTGTTATCTTGGGCCTATCGGGGCCCATTAGT
193 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT
** *
13728 TCCGTTTTGAATCGTCTTCGATTTGGCAAACTTCAATGCTTTTCTTTCC
258 GACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
*
13777 ATTGTGTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTAG-GAA-GTTTGTAGCTCA
1 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT-GTGAAGGTTT-TAGCTCA
* * * *
13840 TTTGGAACACTAGTTATATTGGGCCTATGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTT
64 TTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCATTAGTGACGTTTTGAATCGTCTTCGA-TT
* * *
13905 GGCAAACCTAAATGCTTTTCTTTCCATTGTGTATGGCCTAACTATAATCATTTTAGTGAGATTAG
128 GGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
* * *
13970 TCCACTATGAAGTTTTTAGCTCATTTGGAGCACTTGTTATATT--GCTCTATCGGGGCCCATTAG
193 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGC-CTATCGGGGCCCATTAG
** * *
14033 TTTCATTTTGAATCGTCTTCGATTTGG-AAACCTTCGATGCTTTTCTTTCC
257 TGACGTTTTGAATCGTCTTCGATTTGGCAAACC-TCAATGCTTTTCTTTCC
* * *
14083 ATTGTTTATGGCCTAACTATAATCA-TTTGGTGATATTAGTCCATTGTGAAGTTTTTAGCTCATT
1 ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGGTTTTAGCTCATT
* * *
14147 TGGAAAACTTG-TATTTTGGGCATATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTG
66 TGGAACACTTGTTATTTTGGGCCTATC-GGGCCCATTAGTGACGTTTTGAATCGTCTTCGA-TTG
* *
14211 GCAAACCTCAATGCTTTTCTTTCCATTGTGTATGGCCTAACTATAATCATTTTGGT-AAATTTAG
129 GCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGA-TTAG
* * *
14275 TCTACTGTGAAGTTTTTAGCTCATTTGGAACAATTG-TATTTTGGGCCTTTCGGGGCCCATTAGT
193 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT
* * * *
14339 GACGTTTTGAAATCGTCTTCGATCTAGCAAACCCCGATGCTTTTCTTTCC
258 GACGTTTTG-AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
* *
14389 ATTGTTTATGGGCCTAACTGTAATAATTTTGGTGAGATTAGTCCACT
1 ATTGTTTAT-GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
14436 ATTTACCTAT
Statistics
Matches: 1428, Mismatches: 130, Indels: 46
0.89 0.08 0.03
Matches are distributed among these distances:
304 20 0.01
305 196 0.14
306 187 0.13
307 585 0.41
308 434 0.30
309 6 0.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (306 bp):
ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGGTTTTAGCTCATT
TGGAACACTTGTTATTTTGGGCCTATCGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTGGC
AAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCC
ACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGAC
GTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
Done.