Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022441.1 Corchorus olitorius cultivar O-4 contig22474, 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: 13061
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Found at i:7408 original size:121 final size:122
Alignment explanation
Indices: 7191--7431 Score: 333
Period size: 121 Copynumber: 2.0 Consensus size: 122
7181 CATTGCATTG
* * * * *
7191 ATTTGCTTGCTGTGATTTTCCTTTTTCTGCTACGATGGTTTCTTGATAGTGTTTCTTCTCGTCTG
1 ATTTGCTTGCTGTGAGTATCCTTTTTCTGCTACGATGGTTTCTAGATAATGTTTCTTCTCCTCTG
** **
7256 CAGTTGTATTCCCATTGGAGCTGAGTTTATCCCTGTGGCAGCTGGGATTGCCTTCAA
66 CAGTTGTATTCCCATTGGAGCTGAGCATATCCCTGTGGCAGCAAGGATTGCCTTCAA
* **
7313 ATTTGCTTGCTGTGAGTATCCTTTTTCTGTTTTGATGGTTTCTAGATAATG-TTCTTCTCCTCTG
1 ATTTGCTTGCTGTGAGTATCCTTTTTCTGCTACGATGGTTTCTAGATAATGTTTCTTCTCCTCTG
* *
7377 CAGTTGT-CTCTCCATTGGAGCTGAGCATATCCTTGTGGCAGCAAGGATTGCCTTC
66 CAGTTGTATTC-CCATTGGAGCTGAGCATATCCCTGTGGCAGCAAGGATTGCCTTC
7432 CTGTCTCGAG
Statistics
Matches: 104, Mismatches: 14, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
120 2 0.02
121 58 0.56
122 44 0.42
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.43
Consensus pattern (122 bp):
ATTTGCTTGCTGTGAGTATCCTTTTTCTGCTACGATGGTTTCTAGATAATGTTTCTTCTCCTCTG
CAGTTGTATTCCCATTGGAGCTGAGCATATCCCTGTGGCAGCAAGGATTGCCTTCAA
Found at i:7540 original size:20 final size:20
Alignment explanation
Indices: 7495--7828 Score: 251
Period size: 20 Copynumber: 16.5 Consensus size: 20
7485 CATTGAGGGC
*
7495 CAATGTGAATTAAGGCAAGTT
1 CAATGTGAATT-AGGAAAGTT
*
7516 CAATGTGAATTGGGAAAGTT
1 CAATGTGAATTAGGAAAGTT
* * *
7536 GAATGTGAATAAGGCAAGTT
1 CAATGTGAATTAGGAAAGTT
*
7556 CAATGTGAATTGGGAAAGTT
1 CAATGTGAATTAGGAAAGTT
* * *
7576 GAATGTGAATAAGGCAAGTT
1 CAATGTGAATTAGGAAAGTT
*
7596 CAATGTGAATTGGGAAAGTT
1 CAATGTGAATTAGGAAAGTT
* * *
7616 GAATGTGAATAAGGCAAGTT
1 CAATGTGAATTAGGAAAGTT
* *
7636 CAATGTGAATTGGGAAATTT
1 CAATGTGAATTAGGAAAGTT
* * *
7656 GAATGTGAATCAAGGCAAGTT
1 CAATGTGAAT-TAGGAAAGTT
* * *
7677 CAATGTCAATTGGGAATGTT
1 CAATGTGAATTAGGAAAGTT
* *
7697 GAATGTG-ATTAAGGCAAGTT
1 CAATGTGAATT-AGGAAAGTT
* *
7717 CAATGTCAATT-GGAAAATTT
1 CAATGTGAATTAGG-AAAGTT
* * *
7737 GAATGTGAATCAAGGCAAGTT
1 CAATGTGAAT-TAGGAAAGTT
* *
7758 CAATGTCAATT-GGAAAATTT
1 CAATGTGAATTAGG-AAAGTT
* * *
7778 GAATGTGAATCAAGGCAAGTT
1 CAATGTGAAT-TAGGAAAGTT
* *
7799 CAATGTCAATTGGGAAAGTT
1 CAATGTGAATTAGGAAAGTT
**
7819 TTATGTGAAT
1 CAATGTGAAT
7829 GCGCTGCGTA
Statistics
Matches: 234, Mismatches: 70, Indels: 19
0.72 0.22 0.06
Matches are distributed among these distances:
19 7 0.03
20 171 0.73
21 52 0.22
22 4 0.02
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (20 bp):
CAATGTGAATTAGGAAAGTT
Found at i:7553 original size:40 final size:40
Alignment explanation
Indices: 7496--7828 Score: 513
Period size: 40 Copynumber: 8.2 Consensus size: 40
7486 ATTGAGGGCC
*
7496 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
1 AATGTGAA-TAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
7537 AATGTGAATAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
7577 AATGTGAATAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
* *
7617 AATGTGAATAAGGCAAGTTCAATGTGAATTGGGAAATTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
7657 AATGTGAATCAAGGCAAGTTCAATGTCAATTGGGAATGTTG
1 AATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTTG
* * *
7698 AATGTGATTAAGGCAAGTTCAATGTCAATTGGAAAATTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
* *
7738 AATGTGAATCAAGGCAAGTTCAATGTCAATTGGAAAATTTG
1 AATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
7779 AATGTGAATCAAGGCAAGTTCAATGTCAATTGGGAAAGTTT
1 AATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
7820 TATGTGAAT
1 AATGTGAAT
7829 GCGCTGCGTA
Statistics
Matches: 277, Mismatches: 13, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
40 156 0.56
41 121 0.44
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (40 bp):
AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
Found at i:9095 original size:10 final size:10
Alignment explanation
Indices: 9080--9104 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9070 ACTTGTTTTA
9080 AAAGAAAAAG
1 AAAGAAAAAG
9090 AAAGAAAAAG
1 AAAGAAAAAG
9100 AAAGA
1 AAAGA
9105 GCTTTTAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:10226 original size:2 final size:2
Alignment explanation
Indices: 10219--10248 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10209 ACACGTTGAA
10219 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
10249 TCATCTAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11079 original size:333 final size:332
Alignment explanation
Indices: 10239--11080 Score: 1102
Period size: 332 Copynumber: 2.5 Consensus size: 332
10229 ATATATATAT
* * * * *
10239 ATATATATATTCATCTAACCAAATCTCAGTCGCATTGGATTTACGGATTTGTTTTTACGAACATC
1 ATATATATATTCATATAACCAAATCTCAGTCACAATGGATTTAAGGATTTGTTTTTACGAGCATC
* * *
10304 AGAATCTTGTTTCGTTTTTTACTAGAAATTAATTCAAAAAAATAGGAAAAATAATATTAGAAGCG
66 AGAATCTTGTTTCGTTTTTCATTAGAAATTAATTCAAAAAAATAGGAAAAACAATATTAGAAGCG
* * *
10369 TGAAAAGGCTTTTAATCTTTTTGGCATTGAATTATATACTTTTTACGACTATTATGTCAAAAAAT
131 TGAAAAGCCTTTTAATCTTTTTGGCATTGAATTATATACTTTTTACAAATATTATGTCAAAAAAT
* ** *
10434 TGAGGAAAAATTTTTCCGCTCAGTTTTTGCAAAAATTTTAGCTTAAATCGTGTACTATCCATCAC
196 TAAGGAAAAATTTTTCCGCTCAGTTTTTGCAAAAATTTTAGCCGAAATCGTGTACTAACCATCAC
*** * *** * **
10499 AATTTTTGGCTAAAAATGTGTTCCGGGCCCCGGTTCAGTTTTAGATTATTTTCGGTTCCAAGACT
261 AATTTTTGGCTAAAAACACGTTCCGGGCCCAGACACAGTTTTAGATAATTTTCGGCGCCAAGACT
10564 CCTTGAA
326 CCTTGAA
* * * ** * * *
10571 ATATCTATATTTATCA-AATCAAATCTCAACCACAATTGATTTATA-GACTTGTTTTTACGAGGA
1 ATATATATATTCAT-ATAACCAAATCTCAGTCACAATGGATTTA-AGGATTTGTTTTTACGAGCA
* * * *
10634 TCAGAATCTTGTTTCG-ATTTCTATTAGAAATTAATACAAAAAAATAGGAAAAACGATATTAAAA
64 TCAGAATCTTGTTTCGTTTTTC-ATTAGAAATTAATTCAAAAAAATAGGAAAAACAATATTAGAA
* * * *
10698 GCGTGAAAAGCCTTTTAATCTTTTTGGGATCGAATTATATAATTTTTACAAATATTGTGTCAAAA
128 GCGTGAAAAGCCTTTTAATCTTTTTGGCATTGAATTATATACTTTTTACAAATATTATGTCAAAA
* *
10763 AATTAAGTAAAAATTTTTCCGGCTCAGTTTTTGC-AAAATTTTAGCCGAAATCGTGTGCTAACCA
193 AATTAAGGAAAAATTTTTCC-GCTCAGTTTTTGCAAAAATTTTAGCCGAAATCGTGTACTAACCA
* * * *
10827 TCACAGTTTTTGGCTAAAAGCACGTTCCGGGCCCATACACAGTTTT-GCATAATTTTTGGCGCCA
257 TCACAATTTTTGGCTAAAAACACGTTCCGGGCCCAGACACAGTTTTAG-ATAATTTTCGGCGCCA
*
10891 AGACTCGTTGAA
321 AGACTCCTTGAA
* * *
10903 GTATATATGTTCATATAACCAAATCTCAGTCACAATGGATTTAAGGATTTCTTTTTTACGAGCAT
1 ATATATATATTCATATAACCAAATCTCAGTCACAATGGATTTAAGGATTT-GTTTTTACGAGCAT
*
10968 CAGAATCTTGTTTCGTTTTTCATTAGAAATTAATTCGAAAAAATAGGAAAAACAATATTAGAAGC
65 CAGAATCTTGTTTCGTTTTTCATTAGAAATTAATTCAAAAAAATAGGAAAAACAATATTAGAAGC
*
11033 GTGAAAAGCCTTTTAAT-TTTTATGACATTGAATTATATACTTTTTACA
130 GTGAAAAGCCTTTTAATCTTTT-TGGCATTGAATTATATACTTTTTACA
11081 GTATTTTTAC
Statistics
Matches: 432, Mismatches: 68, Indels: 19
0.83 0.13 0.04
Matches are distributed among these distances:
331 6 0.01
332 303 0.70
333 119 0.28
334 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (332 bp):
ATATATATATTCATATAACCAAATCTCAGTCACAATGGATTTAAGGATTTGTTTTTACGAGCATC
AGAATCTTGTTTCGTTTTTCATTAGAAATTAATTCAAAAAAATAGGAAAAACAATATTAGAAGCG
TGAAAAGCCTTTTAATCTTTTTGGCATTGAATTATATACTTTTTACAAATATTATGTCAAAAAAT
TAAGGAAAAATTTTTCCGCTCAGTTTTTGCAAAAATTTTAGCCGAAATCGTGTACTAACCATCAC
AATTTTTGGCTAAAAACACGTTCCGGGCCCAGACACAGTTTTAGATAATTTTCGGCGCCAAGACT
CCTTGAA
Found at i:11157 original size:794 final size:793
Alignment explanation
Indices: 10290--11831 Score: 2312
Period size: 794 Copynumber: 1.9 Consensus size: 793
10280 TACGGATTTG
* **
10290 TTTTTACGAACATCAGAATCTTGTTTCGTTTTTTACTAGAAATTAATTCAAAAAAATAGGAAAAA
1 TTTTTACGAACAACAGAATCTTGTTTCCATTTTTACTAGAAATTAATTCAAAAAAATAGGAAAAA
10355 TAATATTAGAAGCGTGAAAAGGCTTTTAATCTTTTTGGCATTGAATTATATACTTTTTACGACTA
66 TAATATTAGAAGCGTGAAAAGGCTTTTAATCTTTTTGGCATTGAATTATATACTTTTTACGACTA
* * *
10420 TTATGT-CAAAAAATTGAGGAAAAATTTTTCCGCTCAGTTTTTGCAAAAATTTTAGCTTAAATCG
131 TTATGTGAAAAAAATTGAGGAAAAATTTTTCCGCTCAATTTTTG-AAAAATTTTAGCTGAAATCG
* * * * *
10484 TGTACTATCCATCACAATTTTTGGCTAAAAATGTGTTCCGGGCCCCGGTTCAGTTTTAG-ATTAT
195 TGTACTATCCATCACAAGTTTTGGCCAAAAAGGTGTTCCGGGCCCCGGCTCAGTTTT-GCATGAT
** * *
10548 TTTCGGTTCCAAGACTCCTTGAAATATCTATATTTATCAAATCAAATCTCAACCACAATTGATTT
259 TTTCGGCGCCAAGACTCCTTGAAATATCTATATTTATCAAACCAAATCTCAACCACAATTAATTT
* * *
10613 ATAGACTTGTTTTTACGAGGATCAGAATCTTGTTTCGATTTCTATTAGAAATTA-ATACAAAAAA
324 AAAGACGTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTCTA-TAGAAATTATATA-AAAAAA
* *
10677 ATAGGAAAAACGATATTAAAAGCGTGAAAAGCCTTTTAATCTTTTTGGGATCGAATTATATAATT
387 ATAGGAAAAACCATATTAAAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATCGAATTATATAATT
* * *
10742 TTTACAAATATTGTGTCAAAAAATTAAGTAAAAATTTTTCCGGCTCAGTTTTTGCAAAATTTTAG
452 TTTACAAATATTGTGTCAAAAAATTAAGGAAAAAATTTT-CGACTCAGTTTTTGCAAAATTTTAG
* * * *
10807 CCGAAA-TCGTGTGCTAACCATCACAGTTTTTGGCTAAAAGCACGTTCCGGGCCC-ATACACAGT
516 CC-AAATTCGTGTACTAACCATCACAGTTTTTGACAAAAAACACGTTCCGGGCCCGATACA-A-T
* * * *
10870 TTTGCATAATTTTTGGCGCCAAGACTCGTTG-A-A-GTATATATGTTCATATAACCAAATCTCAG
578 TTTGCATAATTTATGGCGCCAAGACACGTTGAATATATATATATATTCATATAACCAAATCTCAG
* * *
10932 TCACAATGGATTTAAGGATTTCTTTTTTACGAGCATCAGAATCTTGTTTCGTTTTTCATTAGAAA
643 TCACAATGGATTTAAGGATTT-GTTTTTACGAACATCAGAATCTTGTTTCGTTTTTCACTAGAAA
10997 TTAATTCGAAA-AAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCTTTTAATTTTTATGACAT
707 TTAATTC-AAATAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCTTTTAATTTTTATGACAT
11061 TGAATTATATACTTTTTACAGTA
771 TGAATTATATACTTTTTACAGTA
* * *
11084 TTTTTACGAGCAACAGAATCTTGTTTCCATTTTTATTAGAAATTAATTTAAAAAAATAGGAAAAA
1 TTTTTACGAACAACAGAATCTTGTTTCCATTTTTACTAGAAATTAATTCAAAAAAATAGGAAAAA
* *
11149 -AGATATTAGAAGTGTGAAAAGGCTTTTAATCTTTTTGGCATTGAATTATATACTTTTTCCGACT
66 TA-ATATTAGAAGCGTGAAAAGGCTTTTAATCTTTTTGGCATTGAATTATATACTTTTTACGACT
* * *
11213 ATTGTGTGAAAAAAATTGAGGAAAAATTTTTCGGCTCAATTTTTGTAAAATTTTAGCTGAAATCG
130 ATTATGTGAAAAAAATTGAGGAAAAATTTTTCCGCTCAATTTTTGAAAAATTTTAGCTGAAATCG
** *
11278 TGTACTATCCATCACGGGTTTTGGCCAAAAAGGTGTTCCGGGGCCCGGCTCAGTTTTGCATGATT
195 TGTACTATCCATCACAAGTTTTGGCCAAAAAGGTGTTCCGGGCCCCGGCTCAGTTTTGCATGATT
* *
11343 TTTGGCGCCAAGACTCCTTGAAATATCTATATTTATCAAACCAAATCTCAGCCACAATTAATTTA
260 TTCGGCGCCAAGACTCCTTGAAATATCTATATTTATCAAACCAAATCTCAACCACAATTAATTTA
* *
11408 AAGACGTGTTTTTACGAGCATCGGAATCTTGTTTCGATTTCTATAGAAATTATTTAAAAAAAATA
325 AAGACGTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATAGAAATTATATAAAAAAAATA
* *
11473 GGAAAAACCATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATTGAATTATATAATTTTT
390 GGAAAAACCATATTAAAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATCGAATTATATAATTTTT
* * * * * *
11538 ACGACTATTGTGTGAAAAATTTGAGGAAAAAATTTTCGACTCAGTTTTTGCAAAATTTTAGTCAA
455 ACAAATATTGTGTCAAAAAATTAAGGAAAAAATTTTCGACTCAGTTTTTGCAAAATTTTAGCCAA
* *
11603 ATTCGTGTACTAACTATCACAGTTTTTGACAAAAAATACGTTCCGGGCCCTGATACAATTTTGCA
520 ATTCGTGTACTAACCATCACAGTTTTTGACAAAAAACACGTTCCGGGCCC-GATACAATTTTGCA
*
11668 TAATTTATGGCGCCAAGACACGTTGAAATATATATATATATTCATCTAACCAAATCTCAGTCACA
584 TAATTTATGGCGCCAAGACACGTTG-AATATATATATATATTCATATAACCAAATCTCAGTCACA
* * *
11733 TTGGATTTACGGATTTGTTTTTACGAACATCAGAATCTTGTTTCGTTTTTTACTAGAAATTAATT
648 ATGGATTTAAGGATTTGTTTTTACGAACATCAGAATCTTGTTTCGTTTTTCACTAGAAATTAATT
* *
11798 CAAATACATAGGAAAAATAATATTAGAAGCGTGA
713 CAAATAAATAGGAAAAACAATATTAGAAGCGTGA
11832 GAACTGAAAA
Statistics
Matches: 671, Mismatches: 65, Indels: 23
0.88 0.09 0.03
Matches are distributed among these distances:
791 3 0.00
792 97 0.14
793 111 0.17
794 307 0.46
795 108 0.16
796 45 0.07
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Consensus pattern (793 bp):
TTTTTACGAACAACAGAATCTTGTTTCCATTTTTACTAGAAATTAATTCAAAAAAATAGGAAAAA
TAATATTAGAAGCGTGAAAAGGCTTTTAATCTTTTTGGCATTGAATTATATACTTTTTACGACTA
TTATGTGAAAAAAATTGAGGAAAAATTTTTCCGCTCAATTTTTGAAAAATTTTAGCTGAAATCGT
GTACTATCCATCACAAGTTTTGGCCAAAAAGGTGTTCCGGGCCCCGGCTCAGTTTTGCATGATTT
TCGGCGCCAAGACTCCTTGAAATATCTATATTTATCAAACCAAATCTCAACCACAATTAATTTAA
AGACGTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATAGAAATTATATAAAAAAAATAG
GAAAAACCATATTAAAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATCGAATTATATAATTTTTA
CAAATATTGTGTCAAAAAATTAAGGAAAAAATTTTCGACTCAGTTTTTGCAAAATTTTAGCCAAA
TTCGTGTACTAACCATCACAGTTTTTGACAAAAAACACGTTCCGGGCCCGATACAATTTTGCATA
ATTTATGGCGCCAAGACACGTTGAATATATATATATATTCATATAACCAAATCTCAGTCACAATG
GATTTAAGGATTTGTTTTTACGAACATCAGAATCTTGTTTCGTTTTTCACTAGAAATTAATTCAA
ATAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCTTTTAATTTTTATGACATTGAATTATAT
ACTTTTTACAGTA
Found at i:11191 original size:129 final size:129
Alignment explanation
Indices: 10955--11206 Score: 393
Period size: 129 Copynumber: 2.0 Consensus size: 129
10945 AAGGATTTCT
* * *
10955 TTTTTACGAGCATCAGAATCTTGTTTCGTTTTTCATTAGAAATTAATTCGAAAAAATAGGAAAAA
1 TTTTTACGAGCAACAGAATCTTGTTTCATTTTTCATTAGAAATTAATTCAAAAAAATAGGAAAAA
11020 CAATATTAGAAGCGTGAAAAGCCTTTTAATTTTTATGACATTGAATTATATACTTTTTACAGTA
66 CAATATTAGAAGCGTGAAAAGCCTTTTAATTTTTATGACATTGAATTATATACTTTTTACAGTA
*
11084 TTTTTACGAGCAACAGAATCTTGTTTCCATTTTT-ATTAGAAATTAATTTAAAAAAATAGGAAAA
1 TTTTTACGAGCAACAGAATCTTGTTT-CATTTTTCATTAGAAATTAATTCAAAAAAATAGGAAAA
* * *
11148 A-AGATATTAGAAGTGTGAAAAGGCTTTTAATCTTTT-TGGCATTGAATTATATACTTTTT
65 ACA-ATATTAGAAGCGTGAAAAGCCTTTTAAT-TTTTATGACATTGAATTATATACTTTTT
11207 CCGACTATTG
Statistics
Matches: 113, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
128 1 0.01
129 102 0.90
130 10 0.09
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (129 bp):
TTTTTACGAGCAACAGAATCTTGTTTCATTTTTCATTAGAAATTAATTCAAAAAAATAGGAAAAA
CAATATTAGAAGCGTGAAAAGCCTTTTAATTTTTATGACATTGAATTATATACTTTTTACAGTA
Found at i:12322 original size:333 final size:332
Alignment explanation
Indices: 11084--12385 Score: 1695
Period size: 333 Copynumber: 3.9 Consensus size: 332
11074 TTTTACAGTA
* * * *
11084 TTTTTACGAGCAACAGAATCTTGTTTCCATTTTTATTAGAAATTAATTTAAAAAAATAGGAAAAA
1 TTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAAATTAATTAAAAAAAATAGGAAAAA
* * * *
11149 AGATATTAGAAGTGTGAAAAGGCTTTTAATCTTTTTGGCATTGAATTATATACTTTTTCCGACTA
66 CGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATTGAATTATATACTTTTTACGACTA
* *
11214 TTGTGTGAAAAAAATTGAGGAAAAATTTTTCGGCTCAATTTTTGTAAAATTTTAGCTGAAATCGT
131 TTGTGTG-AAAAAATTGAGGAAAAATTTTTCGACTCAATTTTTGCAAAATTTTAGCTGAAATCGT
* * *
11279 GTACTATCCATCACGGGTTTTGGCCAAAAAGGTGTTCCGGGG-CCCGGCTCAGTTTTGCATGATT
195 GTACTATCCATCACAGTTTTTGGCAAAAAAGGTGTTCCGGGGCCCCGGCTCAGTTTTGCATGATT
* *
11343 TTTGGCGCCAAGACTCCTTGAAATATCTATATTTATCAAACCAAATCTCAGCCACAATTAATTTA
260 TTTGGCGCCAAGACTCCTTGAAATATCTATATTTATTAAACCAAATCTCAGCCACAATTGATTTA
*
11408 AAGACGTG
325 AAGACTTG
* *
11416 TTTTTACGAGCATCGGAATCTTGTTTCGATTTCTA-TAGAAATTATTTAAAAAAAATAGGAAAAA
1 TTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAAATTAATTAAAAAAAATAGGAAAAA
* *
11480 CCATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATTGAATTATATAATTTTTACGACTA
66 CGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATTGAATTATATACTTTTTACGACTA
* * * *
11545 TTGTGTGAAAAATTTGAGGAAAAAATTTTCGACTCAGTTTTTGCAAAATTTTAG-TCAAATTCGT
131 TTGTGTGAAAAAATTGAGGAAAAATTTTTCGACTCAATTTTTGCAAAATTTTAGCTGAAA-TCGT
* * * *** * * * *
11609 GTACTAACTATCACAGTTTTTGACAAAAAATACGTTCC-GGG-CCCTGATACAATTTTGCATAAT
195 GTACTATCCATCACAGTTTTTGGCAAAAAAGGTGTTCCGGGGCCCCGGCT-CAGTTTTGCATGAT
* * * * * *
11672 TTATGGCGCCAAGACACGTTGAAATATATATATATATTCATCTAACCAAATCTCAGTCAC-ATTG
259 TTTTGGCGCCAAGACTCCTTGAAATATCTATATTTATT-A---AACCAAATCTCAGCCACAATT-
** *
11736 GATTTACGGATTTG
319 GATTTAAAGACTTG
* * * * * * *
11750 TTTTTACGAACATCAGAATCTTGTTTCGTTTTTTACTAGAAATTAATTCAAATACATAGGAAAAA
1 TTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAAATTAATTAAAAAAAATAGGAAAAA
** * *
11815 TAATATTAGAAGCGTGAGAACTGAAAAGGCTTTTAGTCTTTTTGGCATTGAATTATATACTTTTT
66 CGATATTAGAAGC----G---TGAAAAGCCTTTTAATCTTTTTGGCATTGAATTATATACTTTTT
* * * *
11880 ACGACTATTATGTCAAAAAATTGAGGAAAACTTTTTCCG-CTCAGTTTTTGCAAAAGTTTTAGCT
124 ACGACTATTGTGTGAAAAAATTGAGGAAAAATTTTT-CGACTCAATTTTTGCAAAA-TTTTAGCT
* * * * *
11944 TAAATCGTGTACTATCCATCACAATTTTTGGCTAAAAATGTGTTCCGGGGCCCCGGTTCAGTTTT
187 GAAATCGTGTACTATCCATCACAGTTTTTGGCAAAAAAGGTGTTCCGGGGCCCCGGCTCAGTTTT
* * * *
12009 AG-ATTATTTTCGGCGCCAAGACTCCTTGAAATATCTTTATTTATTAAACCAAATCTCAACCACA
252 -GCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTTATTAAACCAAATCTCAGCCACA
*
12073 ATTGATTTATAGACTTG
316 ATTGATTTAAAGACTTG
* *
12090 TTTTTACGAGGATCGGAATCTTGTTTCGATTTCTATTAGAAATTAATTAAAAAAAATAGGAAAAA
1 TTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAAATTAATTAAAAAAAATAGGAAAAA
*
12155 CGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATTGAATTATATACTTTTTCCGACTA
66 CGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATTGAATTATATACTTTTTACGACTA
12220 TTGTGTGAAAAAATTGAGGAAAAATTTTTCGACTCAATTTTTGCAAAATTATT-GCTGAAATCGT
131 TTGTGTGAAAAAATTGAGGAAAAATTTTTCGACTCAATTTTTGCAAAATT-TTAGCTGAAATCGT
*
12284 GTACTATCCATCACGGTTTTTGGCAAAAAAAGGTGTTCCGGGGCCCCGGCTCAGTTTTGCATGAT
195 GTACTATCCATCACAGTTTTTGGC-AAAAAAGGTGTTCCGGGGCCCCGGCTCAGTTTTGCATGAT
* *
12349 TTTTGGCCCCAAGACTCTTTGAAATATCTATATTTAT
259 TTTTGGCGCCAAGACTCCTTGAAATATCTATATTTAT
12386 CTATCACGGT
Statistics
Matches: 830, Mismatches: 114, Indels: 51
0.83 0.11 0.05
Matches are distributed among these distances:
329 12 0.01
330 119 0.14
331 94 0.11
332 68 0.08
333 161 0.19
334 56 0.07
335 36 0.04
336 1 0.00
339 1 0.00
340 93 0.11
341 3 0.00
342 88 0.11
343 44 0.05
344 48 0.06
345 6 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (332 bp):
TTTTTACGAGCATCAGAATCTTGTTTCGATTTCTATTAGAAATTAATTAAAAAAAATAGGAAAAA
CGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATTGAATTATATACTTTTTACGACTA
TTGTGTGAAAAAATTGAGGAAAAATTTTTCGACTCAATTTTTGCAAAATTTTAGCTGAAATCGTG
TACTATCCATCACAGTTTTTGGCAAAAAAGGTGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTT
TTGGCGCCAAGACTCCTTGAAATATCTATATTTATTAAACCAAATCTCAGCCACAATTGATTTAA
AGACTTG
Found at i:12423 original size:94 final size:95
Alignment explanation
Indices: 12288--12480 Score: 325
Period size: 94 Copynumber: 2.0 Consensus size: 95
12278 AATCGTGTAC
12288 TATCCATCACGGTTTTTGGCAAAAAAAGGTGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTT
1 TATCCATCACGGTTTTTGGCAAAAAAAGGTGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTT
**
12353 GGCCCCAAGACTCTTTGAAATATCTATATT
66 AACCCCAAGACTCTTTGAAATATCTATATT
* *
12383 TATCTATCACGGTTTTTGGC-AAAAAAGGTGTTCCGGGGCCCCGGTTCAGTTTTGCATGATTTTT
1 TATCCATCACGGTTTTTGGCAAAAAAAGGTGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTT
**
12447 AATGCCAAGACTCTTTGAAATATCTATATT
66 AACCCCAAGACTCTTTGAAATATCTATATT
12477 TATC
1 TATC
12481 AAACCAAATC
Statistics
Matches: 92, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
94 73 0.79
95 19 0.21
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (95 bp):
TATCCATCACGGTTTTTGGCAAAAAAAGGTGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTT
AACCCCAAGACTCTTTGAAATATCTATATT
Found at i:13029 original size:330 final size:332
Alignment explanation
Indices: 12383--13061 Score: 1218
Period size: 330 Copynumber: 2.1 Consensus size: 332
12373 TATCTATATT
* *
12383 TATCTATCACGGTTTTTGGCAAAAAAGGTGTTCCGGGGCCCCGGTTCAGTTTTGCATGATTTTTA
1 TATCCATCACGGTTTTTGGCAAAAAAGGTGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTA
**
12448 ATGCCAAGACTCTTTGAAATATCTATATTTATCAAACCAAATCTCAGCCACAATTGATTTAAAGA
66 ACCCCAAGACTCTTTGAAATATCTATATTTATCAAACCAAATCTCAGCCACAATTGATTTAAAGA
* *
12513 CGTGTTTTTACGAGCATCGGAATCTTGTTTCGATTTCTACTAGAAATTAATTTAAAAAAATAGGG
131 CGTGTTTTTACGAGCATCGGAATCTTGTTTCGATTTCTACTAGAAATTAATTAAAAAAAATAGGA
* *
12578 AAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATTGATTTATATACTTTTTCCG
196 AAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATTGAATTATATACTTTTCCCG
12643 ACTATTGTGTGAAAAAATTGAGGAAAAATTTTTCGGCTCAATTTTTGCAAAATTTTTGCCGAAAT
261 ACTATTGTGTGAAAAAATTGAGGAAAAATTTTTCGGCTCAATTTTTGCAAAATTTTTGCCGAAAT
12708 CGTGTAC
326 CGTGTAC
*
12715 TATCCATCACGGTTTTTGGCAAAAAAGGTGTTCCGGGG-CCC-GCTCAGTTTTGCATGATTTTTG
1 TATCCATCACGGTTTTTGGCAAAAAAGGTGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTA
* *
12778 GCCCCAAGACTCTTTGAAATTTCTATATTTATCAAACCAAATCTCAGCCACAATTGATTTAAAGA
66 ACCCCAAGACTCTTTGAAATATCTATATTTATCAAACCAAATCTCAGCCACAATTGATTTAAAGA
* * *
12843 CGTGTTTTTACGAGCATCGGAATCTTGTTTCGATTTCTATTAGATATTTATTAAAAAAAATAGGA
131 CGTGTTTTTACGAGCATCGGAATCTTGTTTCGATTTCTACTAGAAATTAATTAAAAAAAATAGGA
12908 AAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATTGAATTATATACTTTTCCCG
196 AAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATTGAATTATATACTTTTCCCG
12973 ACTATTGTGTGAAAAAATTGAGGAAAAATTTTTCGGCTCAATTTTTGCAAAATTTTTGCCGAAAT
261 ACTATTGTGTGAAAAAATTGAGGAAAAATTTTTCGGCTCAATTTTTGCAAAATTTTTGCCGAAAT
13038 CGTGTAC
326 CGTGTAC
13045 TATCCATCACGGTTTTT
1 TATCCATCACGGTTTTT
Statistics
Matches: 333, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
330 293 0.88
331 3 0.01
332 37 0.11
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (332 bp):
TATCCATCACGGTTTTTGGCAAAAAAGGTGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTA
ACCCCAAGACTCTTTGAAATATCTATATTTATCAAACCAAATCTCAGCCACAATTGATTTAAAGA
CGTGTTTTTACGAGCATCGGAATCTTGTTTCGATTTCTACTAGAAATTAATTAAAAAAAATAGGA
AAAACGATATTAGAAGCGTGAAAAGCCTTTTAATCTTTTTGGCATTGAATTATATACTTTTCCCG
ACTATTGTGTGAAAAAATTGAGGAAAAATTTTTCGGCTCAATTTTTGCAAAATTTTTGCCGAAAT
CGTGTAC
Done.