Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022461.1 Corchorus olitorius cultivar O-4 contig22494, 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: 23048
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4067 original size:43 final size:43
Alignment explanation
Indices: 3998--4105 Score: 180
Period size: 43 Copynumber: 2.5 Consensus size: 43
3988 TGGCTTTAAG
* *
3998 ATATCGCGTCTCTTCTCACTCCCGCATCAAGACTGTTTTGGTT
1 ATATCGCATCTCTTCTCACTCACGCATCAAGACTGTTTTGGTT
*
4041 ATATTGCATCTCTTCTCACTCACGCATCAAGACTGTTTTGGTT
1 ATATCGCATCTCTTCTCACTCACGCATCAAGACTGTTTTGGTT
*
4084 ATATCGCATCTCTTTTCACTCA
1 ATATCGCATCTCTTCTCACTCA
4106 TGCAGCTGTG
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.19, C:0.29, G:0.13, T:0.39
Consensus pattern (43 bp):
ATATCGCATCTCTTCTCACTCACGCATCAAGACTGTTTTGGTT
Found at i:4756 original size:120 final size:122
Alignment explanation
Indices: 4552--4791 Score: 333
Period size: 120 Copynumber: 2.0 Consensus size: 122
4542 CATTGCATTG
* * * * *
4552 ATTTGCTTGCTGTGATTTTCCTTTTTCTGCTACGATGGTTTCTTGATAGTGTTTCTTCTCGTCTG
1 ATTTGCTTGCTGTGAGTATCCTTTTTCTGCTACGATGGTTTCTAGATAATGTTTCTTCTCCTCTG
** *
4617 CAGTTGTCTTCCCATTGGAGCTGAGTTTATCCATGTGGCAGCTAGGATTGCCTTCAA
66 CAGTTGTCTTCCCATTGGAGCTGAGCATATCCATGTGGCAGCAAGGATTGCCTTCAA
* * **
4674 ATTTGC-TGTTGTGAGTATCCTTTTTCTGTTTTGATGGTTTCTAGATAATG-TTCTTCTCCTCTG
1 ATTTGCTTGCTGTGAGTATCCTTTTTCTGCTACGATGGTTTCTAGATAATGTTTCTTCTCCTCTG
*
4737 CAGTTGTC-TCTCCATTGGAGCTGAGCATATCCTTGTGGCAGCAAGGATTGCCTTC
66 CAGTTGTCTTC-CCATTGGAGCTGAGCATATCCATGTGGCAGCAAGGATTGCCTTC
4792 CTGTCTCGAG
Statistics
Matches: 104, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
119 2 0.02
120 60 0.58
121 36 0.35
122 6 0.06
ACGTcount: A:0.15, C:0.20, G:0.22, T:0.43
Consensus pattern (122 bp):
ATTTGCTTGCTGTGAGTATCCTTTTTCTGCTACGATGGTTTCTAGATAATGTTTCTTCTCCTCTG
CAGTTGTCTTCCCATTGGAGCTGAGCATATCCATGTGGCAGCAAGGATTGCCTTCAA
Found at i:4919 original size:40 final size:40
Alignment explanation
Indices: 4862--5234 Score: 593
Period size: 40 Copynumber: 9.2 Consensus size: 40
4852 ATTGAGGGCC
*
4862 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
1 AATGTGAA-TAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
4903 AATGTGAATAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
4943 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
1 AATGTGAA-TAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
4984 AATGTGAATAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
* *
5024 AATGTGAATAAGGCAAGTTCAATGTCATTTGGGAAATTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
5064 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAATGTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
5104 AATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAATGTTG
1 AATGTGAA-TAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
* * *
5145 AATGTGATTAAGGCAAGTTCAATGTCAATTGGAAAATTTG
1 AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
5185 AATGTGAATCAAGGCAAGTTCAATGTCAATTGGGAAAGTTT
1 AATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
5226 TATGTGAAT
1 AATGTGAAT
5235 GCGCTGCGTA
Statistics
Matches: 314, Mismatches: 15, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
40 191 0.61
41 123 0.39
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.30
Consensus pattern (40 bp):
AATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
Found at i:4960 original size:81 final size:81
Alignment explanation
Indices: 4862--5234 Score: 613
Period size: 81 Copynumber: 4.6 Consensus size: 81
4852 ATTGAGGGCC
*
4862 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATG
1 AATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATG
*
4927 TGAATTGGGAAAGTTG
66 TCAATTGGGAAAGTTG
*
4943 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATG
1 AATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATG
*
5008 TGAATTGGGAAAGTTG
66 TCAATTGGGAAAGTTG
* *
5024 AATGTGAA-TAAGGCAAGTTCAATGTCATTTGGGAAATTTGAATGTGAATAAGGCAAGTTCAATG
1 AATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATG
*
5088 TCAATTGGGAATGTTG
66 TCAATTGGGAAAGTTG
* *
5104 AATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAATGTTGAATGTGATTAAGGCAAGTTCAATG
1 AATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATG
* *
5169 TCAATTGGAAAATTTG
66 TCAATTGGGAAAGTTG
* **
5185 AATGTGAATCAAGGCAAGTTCAATGTCAATTGGGAAAGTTTTATGTGAAT
1 AATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAAAGTTGAATGTGAAT
5235 GCGCTGCGTA
Statistics
Matches: 274, Mismatches: 17, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
80 75 0.27
81 199 0.73
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.30
Consensus pattern (81 bp):
AATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATG
TCAATTGGGAAAGTTG
Found at i:5023 original size:121 final size:122
Alignment explanation
Indices: 4862--5234 Score: 624
Period size: 121 Copynumber: 3.1 Consensus size: 122
4852 ATTGAGGGCC
4862 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATG
1 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATG
* * *
4927 TGAATTGGGAAAGTTGAATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
66 TCAATTGGGAAATTTGAATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
4984 AATGTGAA-TAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATG
1 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATG
* *
5048 TCATTTGGGAAATTTGAATGTGAA-TAAGGCAAGTTCAATGTCAATTGGGAATGTTG
66 TCAATTGGGAAATTTGAATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
* * *
5104 AATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAATGTTGAATGTGATTAAGGCAAGTTCAATG
1 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATG
* * *
5169 TCAATTGGAAAATTTGAATGTGAATCAAGGCAAGTTCAATGTCAATTGGGAAAGTTT
66 TCAATTGGGAAATTTGAATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
*
5226 TATGTGAAT
1 AATGTGAAT
5235 GCGCTGCGTA
Statistics
Matches: 235, Mismatches: 14, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
120 38 0.16
121 152 0.65
122 45 0.19
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.30
Consensus pattern (122 bp):
AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTGAATGTGAATAAGGCAAGTTCAATG
TCAATTGGGAAATTTGAATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAAAGTTG
Found at i:8444 original size:333 final size:332
Alignment explanation
Indices: 7601--8447 Score: 903
Period size: 333 Copynumber: 2.5 Consensus size: 332
7591 TTTAATAAAT
* * *
7601 TTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATACTCGTAAAAG
1 TTTTTCATATTTTTTC-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAC
* * *
7665 AACTCCTTAAATTCAATGTGGCTAAGATTTGATTAAATGAATATAGATATTTCATTCAAGGAGTC
65 AAATCCTTAAATCCAATGTGGCTGAGATTTGATTAAATGAAT-TAGATA--T--TTCAAGGAGTC
* * * ** * *
7730 TCGGCACCAAAAATCATGCAAAATTG-AGTC-GGGCCATGAAATGCGTTTTTA-ACCGAAAACCG
125 TCGGCGCCAAAAATCATGCAAAACTGTAGCCGGGGCCCCGAAATGCGTTTTTAGCCCAAAAACCG
* * * *
7792 TGATCGTGAATACACGATTTTGGTTAAAATTTTGCAAAAACTGACCCGAAAGATTTTTCCATCAA
190 TAATCATGAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAGATTTTTCCATCAA
* * * * *
7857 TTTTTGACTAAAATACTCATAAAAAATATATAATTTAACGTCAAAAAGATTGGAGGACTTTTCAT
255 TTTTTGACCAAAATACTCATAAAAAATACATAATTCAACGCCAAAAAGATTGAAGGACTTTTCAT
*
7922 GCTTTTAATATCG
320 GCTTCTAATATCG
* * *
7935 TTTTTCATATTTTTAT-GAATTAATTTCTACTTAAATCGAAACAAGA-TCTGGATGCTCATAAGA
1 TTTTTCATATTTTT-TCGAATTAATTTCTAATTAAATCGAAACAAGATTC-AGATGCTCGTAA-A
* * * * * * *
7998 GCAAATTCTTCAATCCAATGTAGCTGAGATTAGATTAAATG-ATTACTGATATCTCAAAGAGTCT
63 ACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAAATGAATTA--GATATTTCAAGGAGTCT
* ** * *
8062 TGGCGCCAAAAATCATGCAAAACT-TAGCCGGGATCCCGGAACGCGTTTTTAGCCCAAAAACCGT
126 CGGCGCCAAAAATCATGCAAAACTGTAGCCGGGGCCCCGAAATGCGTTTTTAGCCCAAAAACCGT
* * * * *
8126 AATTAT-AATTACACGATTTCGGCTAGAATTTTGTAAAAATTGACTCGAAAG-TTATTTCC-TCA
191 AATCATGAA-TACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAGATT-TTTCCATCA
* **
8188 ATTTTT-ATCCACAATACTCAT-AAAAATCACATAATTCAACGCCAAAAAGATTGAAGGGTTTTT
254 ATTTTTGA-CCAAAATACTCATAAAAAAT-ACATAATTCAACGCCAAAAAGATTGAAGGACTTTT
8251 CATGCTTCTAATATCG
317 CATGCTTCTAATATCG
* * * ***
8267 TTTTTCCTATTATTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGTTTTA
1 TTTTTCATATT-TTTT-CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* *
8332 CAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATGTAGATATTTCAAGGAGTCTCG
64 CAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAAATGAAT-TAGATATTTCAAGGAGTCTCG
* ** **
8397 GTGTAAAAAATCATGCAACGCTGTA-CCGGGGCCCCGAAATGCGTTTTTAGC
128 GCGCCAAAAATCATGCAAAACTGTAGCCGGGGCCCCGAAATGCGTTTTTAGC
8448 AAAAAAAACC
Statistics
Matches: 419, Mismatches: 74, Indels: 41
0.78 0.14 0.08
Matches are distributed among these distances:
331 41 0.10
332 94 0.22
333 150 0.36
334 88 0.21
335 45 0.11
336 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (332 bp):
TTTTTCATATTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAACA
AATCCTTAAATCCAATGTGGCTGAGATTTGATTAAATGAATTAGATATTTCAAGGAGTCTCGGCG
CCAAAAATCATGCAAAACTGTAGCCGGGGCCCCGAAATGCGTTTTTAGCCCAAAAACCGTAATCA
TGAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAGATTTTTCCATCAATTTTTG
ACCAAAATACTCATAAAAAATACATAATTCAACGCCAAAAAGATTGAAGGACTTTTCATGCTTCT
AATATCG
Found at i:11346 original size:655 final size:644
Alignment explanation
Indices: 10137--11837 Score: 2110
Period size: 655 Copynumber: 2.6 Consensus size: 644
10127 AAATATAATG
* * * * * *
10137 TGGTTGAGATTTTGTTAGATGAATATAGATATTTCAATGAGTCTCGGTGCAAAAAATCATGCAAC
1 TGGTTGGGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATTCAAA
** * * * *
10202 GCTGTACCGGGGCCCCGAAACACGTTTTTAGCCAAAAACCGTGAT--TTCGATTAACGTACGATT
66 ATTGAACC-GGGCCCTGGAACACGTTTTTAGCCAAAAATCGTGATGATT--ATT-AC--ACGATT
* * * * * * ** *
10265 TCGGCT-AATATTTTGCAAAAATTA-ACCAGAAATATTTTTCCTAAATTTTTTTCTAAAATACTC
125 TCGGCTAAAT-TTTTGCAAAAAATAGACCCGAAAGATATCTCCTCAATTTTAGT-TATAATACTC
* * * * * * *
10328 ATAAAATATTTATAATTCAACTCCAAAAAGATTGGA-GGAGTTTTCTTACTTTTAATAT-AGTTT
188 ATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGAATTTAC--GCTTTTAATATCA-TTT
* * *
10391 TTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAA
250 TTCATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAA
* * * *
10456 TTCTTAAATGCAATGAGGCTGAGA---T-TTA-AT--ATAGATATTTCAGGGAGTTTCGACGCCA
315 TTCTTAAATGCAATGAGGCTGAGATTTTATTAGATGAATAGATATTTCAAGGAGTGTCGGCACCA
* * * * * *
10514 AAAATCATGCAAAACTGAGTCAGGACCTCGAAATGCATTTTTATCAAAAAAATAGTGATGGTTAG
380 AAAACCATGCAAAACTGAGTCAGGACCCCGAAACGCATTTTTAGCAAAAAAACAGTGATGATTAG
* *
10579 TACACGATTTCGGCTAAAATTTTGCAAAAAATGACCAGAAAAATATTCTCTCAATTTTTAGCGAC
445 TACACGATTTCGGCTAAAATTTTGCAAAAAATGACCAGAAAAATA-TCTCTCAATTTTTAACCAC
* * * * *
10644 AATACTTATGAAAAACATATAATTCAATGCCAAAAAAATTGAAGGGCTTTACACGCTTTTAATAT
509 AATACTCATAAAAAACATATAATTCAATGACAAAAAAATTGAAGGGCTTTACACACTTCTAATAT
* * * *
10709 TGTTTTTCCTA-TTTTTTCTGAATTAATTTCTAATTAAAACGAAACGTGATTCAAATGTTTGTAA
574 CGTTTTTCCTATTTTTTTCCGAATTAATTTCTAATTAAAACAAAACATGATTCAAATGTTTGTAA
10773 AAACAA
639 AAACAA
* *
10779 TGGTTGGGATTTGGGTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAGAAATCATTCAAA
1 TGGTTGGGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATTCAAA
10844 ATTGAACCGGGCCCTGGAACACGTTTTTAGCCAAAAATCGTGATGATTATTACACGATTTCGGCT
66 ATTGAACCGGGCCCTGGAACACGTTTTTAGCCAAAAATCGTGATGATTATTACACGATTTCGGCT
*
10909 AAATTTTTGCAAAAAAAAAAAAAAGACCCGAAAGATATCTCCTCAATTTTAAGTTATAATACTCA
131 AAATTTTTGC------AAAAAATAGACCCGAAAGATATCTCCTCAATTTT-AGTTATAATACTCA
* *
10974 TAAAAAACTATATAATTCAACGCCAATAAGATTGAAGGGAATTTAACGCTTTCAATATCATTTTT
189 TAAAAAA-TATATAATTCAACGCCAAAAAGATTGAAGGGAATTT-ACGCTTTTAATATCATTTTT
* *
11039 CATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATTCTCGTAAAAACAAATC
252 CATATTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATT
* * * *
11104 CTTAAATGTAACGTGGCTAAGATTTTATTAGATGAACGTAGATATTTCAAGGAGTGTCGGC-CTC
317 CTTAAATGCAATGAGGCTGAGATTTTATTAGATGAA--TAGATATTTCAAGGAGTGTCGGCAC-C
* * ** * *
11168 AAAAACCATTCAAAACTGTGTTGGGGCCCCGAAACGCGTTTTTAGCAAAAAAAAACAGTGATGAT
379 AAAAACCATGCAAAACTGAGTCAGGACCCCGAAACGCATTTTTAGC--AAAAAAACAGTGATGAT
* *
11233 TAGTACACGATTTCGGCTAAAATTTTGCAAAAGATGACCAGATAAATA-CTCTCAATTTTTAACC
442 TAGTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCAGAAAAATATCTCTCAATTTTTAACC
* * *
11297 ACAATACTCATAAAAAATATATAATTCATTGACAAAAAAATTGAAGGGCTTTTCACACTTCTAAT
507 ACAATACTCATAAAAAACATATAATTCAATGACAAAAAAATTGAAGGGCTTTACACACTTCTAAT
11362 ATCGTTTTTCCTATTTTTTTCCGAATTAATTTCTAATTAAAACAAAACATGATTCAAATGTTTGT
572 ATCGTTTTTCCTATTTTTTTCCGAATTAATTTCTAATTAAAACAAAACATGATTCAAATGTTTGT
11427 AAAAACAA
637 AAAAACAA
* * * *
11435 TGGTTGGGATTTGGTTAGATGTATATAGATATTTGAAGG-GATCTCAGTGCCAAAAATCAATCAA
1 TGGTTGGGATTTGGTTAGATGAATATAGATATTTCAAGGAG-TCTCGGTGCCAAAAATCATTCAA
* * ** * *
11499 AATTGAACCAGGCCCTGGAACGCG-TTTTAGCTTAAAATTGTGATGATTATTACACGATTTCGTC
65 AATTGAACCGGGCCCTGGAACACGTTTTTAGCCAAAAATCGTGATGATTATTACACGATTTCGGC
* * *
11563 TAAAATTTTGC-AAAAATTGACCCGAAAGATATCTCCTCAATTTTTAGTCATAATACTCAT-AAA
130 TAAATTTTTGCAAAAAATAGACCCGAAAGATATCTCCTCAA-TTTTAGTTATAATACTCATAAAA
** * * *
11626 AATATATAATTCAACGCCCAAAAAGATTGAAGGGCTTTTCATGATTTTAATATCGTTTTTCATAT
194 AATATATAATTCAACG-CCAAAAAGATTGAAGGGAATTT-ACGCTTTTAATATCATTTTTCATAT
*
11691 TTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATTCTTA
257 TTTTT-TGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATTCTTA
* *
11756 AATGCAATGAGGCTGGGATTTTATTAGATGAGTATAGATATTTCAAAGAGTGTCGGCACCAAAAA
321 AATGCAATGAGGCTGAGATTTTATTAGATGA--ATAGATATTTCAAGGAGTGTCGGCACCAAAAA
11821 CCATGCAAAACTGAGTC
384 CCATGCAAAACTGAGTC
11838 GGGCCTCGAA
Statistics
Matches: 915, Mismatches: 109, Indels: 64
0.84 0.10 0.06
Matches are distributed among these distances:
638 18 0.02
639 3 0.00
640 2 0.00
641 36 0.04
642 62 0.07
643 2 0.00
644 6 0.01
645 36 0.04
646 131 0.14
647 57 0.06
648 166 0.18
649 6 0.01
650 4 0.00
651 2 0.00
653 1 0.00
654 1 0.00
655 187 0.20
656 134 0.15
657 61 0.07
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (644 bp):
TGGTTGGGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATTCAAA
ATTGAACCGGGCCCTGGAACACGTTTTTAGCCAAAAATCGTGATGATTATTACACGATTTCGGCT
AAATTTTTGCAAAAAATAGACCCGAAAGATATCTCCTCAATTTTAGTTATAATACTCATAAAAAA
TATATAATTCAACGCCAAAAAGATTGAAGGGAATTTACGCTTTTAATATCATTTTTCATATTTTT
TTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATTCTTAAATGC
AATGAGGCTGAGATTTTATTAGATGAATAGATATTTCAAGGAGTGTCGGCACCAAAAACCATGCA
AAACTGAGTCAGGACCCCGAAACGCATTTTTAGCAAAAAAACAGTGATGATTAGTACACGATTTC
GGCTAAAATTTTGCAAAAAATGACCAGAAAAATATCTCTCAATTTTTAACCACAATACTCATAAA
AAACATATAATTCAATGACAAAAAAATTGAAGGGCTTTACACACTTCTAATATCGTTTTTCCTAT
TTTTTTCCGAATTAATTTCTAATTAAAACAAAACATGATTCAAATGTTTGTAAAAACAA
Found at i:13895 original size:50 final size:50
Alignment explanation
Indices: 13825--14145 Score: 543
Period size: 50 Copynumber: 6.4 Consensus size: 50
13815 AGACAACACG
*
13825 CGAAGGTACACGAGAAGACAGAGGCCTCCACAGTGAGGCGAGGCCAGACA
1 CGAAGGTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCCAGACA
* * *
13875 CGAAGCTACACGAGAAGACAGAAGCCTCTGCAGTGAGGCGAGGCCAGACA
1 CGAAGGTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCCAGACA
*
13925 CGAAGGTACACGAGAAGACAGAGGCCTCCGTAGTGAGGCGAGGCCAAGACA
1 CGAAGGTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCC-AGACA
*
13976 CGAAGGTACACGAGAAGACAGAAGCCTCCGCAGTGAGGCGAGGCCAGACA
1 CGAAGGTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCCAGACA
* * *
14026 CGAAGATACACGAGAGGACAGAGGCCTCCGCAGTGAGGCGAGCCCAGACA
1 CGAAGGTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCCAGACA
14076 CGAAGGTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCCAGACA
1 CGAAGGTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCCAGACA
*
14126 CGAAGCTACACGAGAAGACA
1 CGAAGGTACACGAGAAGACA
14146 CAACACACAC
Statistics
Matches: 252, Mismatches: 18, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
50 204 0.81
51 48 0.19
ACGTcount: A:0.34, C:0.26, G:0.34, T:0.07
Consensus pattern (50 bp):
CGAAGGTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCCAGACA
Found at i:14099 original size:151 final size:150
Alignment explanation
Indices: 13825--14145 Score: 552
Period size: 151 Copynumber: 2.1 Consensus size: 150
13815 AGACAACACG
* *
13825 CGAAGGTACACGAGAAGACAGAGGCCTCCACAGTGAGGCGAGGCCAGACACGAAGCTACACGAGA
1 CGAAGGTACACGAGAAGACAGAAGCCTCCACAGTGAGGCGAGGCCAGACACGAAGATACACGAGA
* *
13890 AGACAGAAGCCTCTGCAGTGAGGCGAGGCCAGACACGAAGGTACACGAGAAGACAGAGGCCTCCG
66 AGACAGAAGCCTCCGCAGTGAGGCGAGCCCAGACACGAAGGTACACGAGAAGACAGAGGCCTCCG
*
13955 TAGTGAGGCGAGGCCAAGACA
131 CAGTGAGGCGAGGCC-AGACA
*
13976 CGAAGGTACACGAGAAGACAGAAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGATACACGAGA
1 CGAAGGTACACGAGAAGACAGAAGCCTCCACAGTGAGGCGAGGCCAGACACGAAGATACACGAGA
* *
14041 GGACAGAGGCCTCCGCAGTGAGGCGAGCCCAGACACGAAGGTACACGAGAAGACAGAGGCCTCCG
66 AGACAGAAGCCTCCGCAGTGAGGCGAGCCCAGACACGAAGGTACACGAGAAGACAGAGGCCTCCG
14106 CAGTGAGGCGAGGCCAGACA
131 CAGTGAGGCGAGGCCAGACA
*
14126 CGAAGCTACACGAGAAGACA
1 CGAAGGTACACGAGAAGACA
14146 CAACACACAC
Statistics
Matches: 161, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
150 24 0.15
151 137 0.85
ACGTcount: A:0.34, C:0.26, G:0.34, T:0.07
Consensus pattern (150 bp):
CGAAGGTACACGAGAAGACAGAAGCCTCCACAGTGAGGCGAGGCCAGACACGAAGATACACGAGA
AGACAGAAGCCTCCGCAGTGAGGCGAGCCCAGACACGAAGGTACACGAGAAGACAGAGGCCTCCG
CAGTGAGGCGAGGCCAGACA
Done.