Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020826.1 Corchorus olitorius cultivar O-4 contig20859, 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: 84856
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:1140 original size:325 final size:323
Alignment explanation
Indices: 11--1959 Score: 2605
Period size: 323 Copynumber: 6.0 Consensus size: 323
1 CTTTAAATTT
* * ** * * * *
11 TTTTTCCAATTTTTTTACTAAATTTATTTTTATTTAACTGTAAACAAGATTTAGACGGTCGTAAA
1 TTTTTGCATTTTTTTTACCGAATTTATTTCTATTTAACTGTAAACAAGATTCAGATGCTCGTAAA
**
76 CACAAATTCTTAAATTTATTGTGGATGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCT
66 CACAAATTCTTAAATCCATTGTGGATGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCT
* * * * *
141 TTCTGCCAAAAATCATGCAAAAATGAGCTGGGGCACCGAAATGCGATTTTAGCCAAAATCCGTGA
131 TTCTGCCAAAAATCATGCAAAACTGAGC-CGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGA
*
206 TAGTTAGTACACGATTTCGGCTAAAATCTGACTCGTAAAATTTTTTTCACAAATTTTTTTTCCAT
195 TAGTTAGTACACGATTTCGGCTAAAATCTGAATCG-AAAATTTTTTTCAC-AA-TTTTTTTCCAT
* *
271 AATACTCAGAAAAAAATATATAATTCAACGCCATAAAAATTTAAGGGTTTTTCACGCTTC-AATA
257 AATACTCAG-AAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATA
335 TCG
321 TCG
* * * * * **
338 TTTTTTGCGCTTTTTTTTTGCCGAATTTATTTCTATTTAACTTTAAAAAACATTCAGATTATCGT
1 -TTTTT--GCATTTTTTTTACCGAATTTATTTCTATTTAACTGTAAACAAGATTCAGATGCTCGT
* * * * *
403 AAAAACAAATTCTTAAATCCATTGT-GACTGGGATTTGTTTAGATGAATGTAGATATTTCAAGGA
63 AAACACAAATTCTTAAATCCATTGTGGA-TGAGATTTGGTTCGATGAATATAGATATTTCAAGGA
* * *
467 GTTTTTCTGCCAAAAATCATGCAAAACTAAGCCGGGGCGCCGAAATGCATTTTTAGCCAAAAACC
127 GTCTTTCTGCCAAAAATCATGCAAAACTGAGCC-GGGCGCCGAAATGCGTTTTTAGCCAAAAACC
* * *
532 GTTATAGTTAGTACACGATTTCGGCGAAAATCTGAATCGAAAATTTTTTTCTCAATTTTTTTTCC
191 GTGATAGTTAGTACACGATTTCGGCTAAAATCTGAATCGAAAATTTTTTTCACAA-TTTTTTTCC
* * * * *
597 ATAATACTCAGAAAAAATATTTAATTCAAGGCCAAAATAATTGAAGGGTTTTTTACGCTT-TTAT
255 ATAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAAT
*
661 TTC-
320 ATCG
* * * * * * *
664 TTTTTCCAATTTTTTTACTGAATTTATTTTTATTTAACTGTAAACAAGATTTAGACGGTCGTAAA
1 TTTTTGCATTTTTTTTACCGAATTTATTTCTATTTAACTGTAAACAAGATTCAGATGCTCGTAAA
** *
729 CACAAATTCTTAAATTTATTGTGGATGATATTTGGTTCGATGAATATAGATATTTCAAGGAGTCT
66 CACAAATTCTTAAATCCATTGTGGATGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCT
* *
794 TTCTGCCAAAAATCATGCAAAACTGAGCCTGGGCGCCTAAATGCGTTTTTAGCCAAAAACCGTTA
131 TTCTGCCAAAAATCATGCAAAACTGAGCC-GGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGA
* *
859 TAGTTAGTACACGATTTCGGCTAAAATCTGACTCGGAAATTTTTTTCACAATTTTTTTCCATAAT
195 TAGTTAGTACACGATTTCGGCTAAAATCTGAATCGAAAATTTTTTTCACAATTTTTTTCCATAAT
* *
924 ACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGATTTTCACGCTTCTAGTATCG
260 ACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCG
* * * *
988 TTTTTGCATTTTTTTTTACCGAATTTATTTCCATTTAACTTTAAAAAAGATTCAGATTCTCGTAA
1 TTTTTGCA-TTTTTTTTACCGAATTTATTTCTATTTAACTGTAAACAAGATTCAGATGCTCGTAA
* * * * *
1053 AAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAGGAGTC
65 ACACAAATTCTTAAATCCATTGTGGATGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTC
* * * * *
1118 TTTCTGCCAAAAATCATGCAAAAATGAGCCGAGGCGCCAAAATGCGTTTTTACCCACAAATCGTG
130 TTTCTGCCAAAAATCATGCAAAACTGAGCCG-GGCGCCGAAATGCGTTTTTAGCCAAAAACCGTG
*
1183 ATAGTTAGTACACGATTTCGG-TCAAAATCTGAATCGAAACA-TTTTTTCTCAATTTTTTTCCAT
194 ATAGTTAGTACACGATTTCGGCT-AAAATCTGAATCGAAA-ATTTTTTTCACAATTTTTTTCCAT
* * *
1246 AATACTCAGAAAAAATATATAATTCAACACCATAAAAATTGAAGGGCTTTTCACGCTTCTAATAT
257 AATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATAT
1311 CG
322 CG
** * *
1313 TTTTCCCA-TTTTTTT-CCGGAATTTATTTCTATTTAACTCTAAACAAGATTTAGATGCTCGTAA
1 TTTTTGCATTTTTTTTACC-GAATTTATTTCTATTTAACTGTAAACAAGATTCAGATGCTCGTAA
*
1376 ACACAAATTCTTAAATCCATTGTGGATGAGATTTGTTTCGATGAATATAGATATTTCAAGGAGTC
65 ACACAAATTCTTAAATCCATTGTGGATGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTC
* ** * *
1441 TTTCTGTCAAAAATCATGCAAAACTGAGCC-GAAGCCAAAATGCGTTTTTAGCCAAAACCCGTGA
130 TTTCTGCCAAAAATCATGCAAAACTGAGCCGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGA
* *
1505 TAGTTAGTACACGATTTCGGCTAAAATCTGACTCGGAAAA--TTTTTCACAATTTTTTTCGATAA
195 TAGTTAGTACACGATTTCGGCTAAAATCTGAATC-GAAAATTTTTTTCACAATTTTTTTCCATAA
* *
1568 TACTCAGAAAAAATATATAATTCAACGCC-AAAAAATTGAA-GGTTTTTCACGCTTTTAGTATTC
259 TACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATA-TC
1631 G
323 G
* ** * *
1632 TTTTTGCATATTTTTCCCCGAATTTGTTTCTATTTAACTGTAAACAAGATTCAGATTCTCGTAAA
1 TTTTTGCATTTTTTTTACCGAATTTATTTCTATTTAACTGTAAACAAGATTCAGATGCTCGTAAA
* * **
1697 CACAAATTCTTAAATCCATTGTGGTTGAGATTTGGTTCGAGGAATATAGATATTTCAAGGAAACT
66 CACAAATTCTTAAATCCATTGTGGATGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCT
* *
1762 TTCTGCCGAAAATCATGCAAAACTGAAGCAGGGCG-CGAAATGCGTTTTTAGCCAAAAACCGTGA
131 TTCTGCCAAAAATCATGCAAAACTG-AGCCGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGA
* * *
1826 TAG-TAGTACACGATTTCGCCTAAAATCTGAATCGAAAAATTTTTTCTCAATTTCTTTTCCATAA
195 TAGTTAGTACACGATTTCGGCTAAAATCTGAATCGAAAATTTTTTTCACAATTT-TTTTCCATAA
* * ** * * *
1890 TATTCGGAAAAAATATATAATTCAACGTAAAAAAAAATGAAGGATTTTTCACACTTCTAATATCG
259 TACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCG
1955 TTTTT
1 TTTTT
1960 TATACATAAG
Statistics
Matches: 1423, Mismatches: 173, Indels: 55
0.86 0.10 0.03
Matches are distributed among these distances:
318 17 0.01
319 24 0.02
320 207 0.15
321 107 0.08
322 107 0.08
323 364 0.26
324 27 0.02
325 290 0.20
326 1 0.00
327 47 0.03
328 28 0.02
329 15 0.01
330 189 0.13
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (323 bp):
TTTTTGCATTTTTTTTACCGAATTTATTTCTATTTAACTGTAAACAAGATTCAGATGCTCGTAAA
CACAAATTCTTAAATCCATTGTGGATGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCT
TTCTGCCAAAAATCATGCAAAACTGAGCCGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGAT
AGTTAGTACACGATTTCGGCTAAAATCTGAATCGAAAATTTTTTTCACAATTTTTTTCCATAATA
CTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCG
Found at i:1337 original size:648 final size:645
Alignment explanation
Indices: 12--1958 Score: 2892
Period size: 648 Copynumber: 3.0 Consensus size: 645
2 TTTAAATTTT
*
12 TTTTCCAATTTTTTTACTAAATTTATTTTTATTTAACTGTAAACAAGATTTAGACGGTCGTAAAC
1 TTTTCCAATTTTTTTACTGAATTTATTTTTATTTAACTGTAAACAAGATTTAGACGGTCGTAAAC
77 ACAAATTCTTAAATTTATTGTGGATGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTT
66 ACAAATTCTTAAATTTATTGTGGATGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTT
* * * * *
142 TCTGCCAAAAATCATGCAAAAATGAG-CTGGGGCACCGAAATGCGATTTTAGCCAAAATCCGTGA
131 TCTGCCAAAAATCATGCAAAACTGAGCCT-GGGCGCCAAAATGCGTTTTTAGCCAAAAACCGTGA
*
206 TAGTTAGTACACGATTTCGGCTAAAATCTGACTCGTAAAATTTTTTTCACAAATTTTTTTTCCAT
195 TAGTTAGTACACGATTTCGGCTAAAATCTGACTCG-GAAATTTTTTTCAC-AA-TTTTTTTCCAT
* * *
271 AATACTCAGAAAAAAATATATAATTCAACGCCATAAAAATTTAAGGGTTTTTCACGCTTC-AATA
257 AATACTCAG-AAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAGTA
* * * *
335 TCGTTTTTTGCGCTTTTTTTTTGCCGAATTTATTTCTATTTAACTTTAAAAAACATTCAGATTAT
321 TCG-TTTTTGC-ATTTTTTTTTACCGAATTTATTTCTATTTAACTTTAAAAAAGATTCAGATTCT
* * * *
400 CGTAAAAACAAATTCTTAAATCCATTGTGACTGGGATTTGTTTAGATGAATGTAGATATTTCAAG
384 CGTAAAAACAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAG
* * *
465 GAGTTTTTCTGCCAAAAATCATGCAAAACTAAGCCGGGGCGCCGAAATGCATTTTTAGCCAAAAA
449 GAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCC-GGGCGCCGAAATGCGTTTTTAGCCAAAAA
*
530 CCGTTATAGTTAGTACACGATTTCGGCGAAAATCTGAATCGAAAATTTTTTTCTCAATTTTTTTT
513 CCGTGATAGTTAGTACACGATTTCGGCGAAAATCTGAATCGAAAA-TTTTTTCTCAA-TTTTTTT
* * * *
595 CCATAATACTCAGAAAAAATATTTAATTCAAGGCCAAAATAATTGAAGGGTTTTTTACGCTT-TT
576 CCATAATACTCAGAAAAAATATATAATTCAACGCCAAAA-AATTGAAGGGTTTTTCACGCTTCTA
* *
659 ATTTCT
640 ATATCG
665 TTTTCCAATTTTTTTACTGAATTTATTTTTATTTAACTGTAAACAAGATTTAGACGGTCGTAAAC
1 TTTTCCAATTTTTTTACTGAATTTATTTTTATTTAACTGTAAACAAGATTTAGACGGTCGTAAAC
*
730 ACAAATTCTTAAATTTATTGTGGATGATATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTT
66 ACAAATTCTTAAATTTATTGTGGATGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTT
* *
795 TCTGCCAAAAATCATGCAAAACTGAGCCTGGGCGCCTAAATGCGTTTTTAGCCAAAAACCGTTAT
131 TCTGCCAAAAATCATGCAAAACTGAGCCTGGGCGCCAAAATGCGTTTTTAGCCAAAAACCGTGAT
860 AGTTAGTACACGATTTCGGCTAAAATCTGACTCGGAAATTTTTTTCACAATTTTTTTCCATAATA
196 AGTTAGTACACGATTTCGGCTAAAATCTGACTCGGAAATTTTTTTCACAATTTTTTTCCATAATA
*
925 CTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGATTTTCACGCTTCTAGTATCGTT
261 CTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAGTATCGTT
*
990 TTTGCATTTTTTTTTACCGAATTTATTTCCATTTAACTTTAAAAAAGATTCAGATTCTCGTAAAA
326 TTTGCATTTTTTTTTACCGAATTTATTTCTATTTAACTTTAAAAAAGATTCAGATTCTCGTAAAA
* *
1055 ACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTT
391 ACAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTT
* * * * *
1120 TCTGCCAAAAATCATGCAAAAATGAGCCGAGGCGCCAAAATGCGTTTTTACCCACAAATCGTGAT
456 TCTGCCAAAAATCATGCAAAACTGAGCCG-GGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGAT
1185 AGTTAGTACACGATTTCGGTC-AAAATCTGAATCGAAACATTTTTTCTCAATTTTTTTCCATAAT
520 AGTTAGTACACGATTTCGG-CGAAAATCTGAATCGAAA-ATTTTTTCTCAATTTTTTTCCATAAT
* *
1249 ACTCAGAAAAAATATATAATTCAACACCATAAAAATTGAAGGGCTTTTCACGCTTCTAATATCG
583 ACTCAGAAAAAATATATAATTCAACGCCA-AAAAATTGAAGGGTTTTTCACGCTTCTAATATCG
* * * * * * *
1313 TTTTCCCATTTTTTTCCGGAATTTATTTCTATTTAACTCTAAACAAGATTTAGATGCTCGTAAAC
1 TTTTCCAATTTTTTTACTGAATTTATTTTTATTTAACTGTAAACAAGATTTAGACGGTCGTAAAC
** *
1378 ACAAATTCTTAAATCCATTGTGGATGAGATTTGTTTCGATGAATATAGATATTTCAAGGAGTCTT
66 ACAAATTCTTAAATTTATTGTGGATGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTT
* ** *
1443 TCTGTCAAAAATCATGCAAAACTGAGCC--GAAGCCAAAATGCGTTTTTAGCCAAAACCCGTGAT
131 TCTGCCAAAAATCATGCAAAACTGAGCCTGGGCGCCAAAATGCGTTTTTAGCCAAAAACCGTGAT
* *
1506 AGTTAGTACACGATTTCGGCTAAAATCTGACTCGGAAA-ATTTTTCACAATTTTTTTCGATAATA
196 AGTTAGTACACGATTTCGGCTAAAATCTGACTCGGAAATTTTTTTCACAATTTTTTTCCATAATA
*
1570 CTCAGAAAAAATATATAATTCAACGCC-AAAAAATTGAA-GGTTTTTCACGCTTTTAGTATTCGT
261 CTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAGTA-TCGT
* ** * * *
1633 TTTTGCA-TATTTTTCCCCGAATTTGTTTCTATTTAACTGTAAACAAGATTCAGATTCTCGTAAA
325 TTTTGCATTTTTTTTTACCGAATTTATTTCTATTTAACTTTAAAAAAGATTCAGATTCTCGTAAA
* * * * **
1697 CACAAATTCTTAAATCCATTGTGGTTGAGATTTGGTTCGAGGAATATAGATATTTCAAGGAAACT
390 AACAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCT
* *
1762 TTCTGCCGAAAATCATGCAAAACTGAAGCAGGGCG-CGAAATGCGTTTTTAGCCAAAAACCGTGA
455 TTCTGCCAAAAATCATGCAAAACTG-AGCCGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGA
* *
1826 TAG-TAGTACACGATTTCGCCTAAAATCTGAATCGAAAAATTTTTTCTCAATTTCTTTTCCATAA
519 TAGTTAGTACACGATTTCGGCGAAAATCTGAATCG-AAAATTTTTTCTCAATTT-TTTTCCATAA
* * ** * * *
1890 TATTCGGAAAAAATATATAATTCAACGTAAAAAAAAATGAAGGATTTTTCACACTTCTAATATCG
582 TACTCAGAAAAAATATATAATTCAACG-CCAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCG
1955 TTTT
1 TTTT
1959 TTATACATAA
Statistics
Matches: 1187, Mismatches: 94, Indels: 37
0.90 0.07 0.03
Matches are distributed among these distances:
640 1 0.00
641 43 0.04
642 99 0.08
643 153 0.13
644 26 0.02
645 51 0.04
646 68 0.06
647 61 0.05
648 368 0.31
649 56 0.05
650 26 0.02
651 2 0.00
652 13 0.01
653 218 0.18
654 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (645 bp):
TTTTCCAATTTTTTTACTGAATTTATTTTTATTTAACTGTAAACAAGATTTAGACGGTCGTAAAC
ACAAATTCTTAAATTTATTGTGGATGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTT
TCTGCCAAAAATCATGCAAAACTGAGCCTGGGCGCCAAAATGCGTTTTTAGCCAAAAACCGTGAT
AGTTAGTACACGATTTCGGCTAAAATCTGACTCGGAAATTTTTTTCACAATTTTTTTCCATAATA
CTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAGTATCGTT
TTTGCATTTTTTTTTACCGAATTTATTTCTATTTAACTTTAAAAAAGATTCAGATTCTCGTAAAA
ACAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTT
TCTGCCAAAAATCATGCAAAACTGAGCCGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
GTTAGTACACGATTTCGGCGAAAATCTGAATCGAAAATTTTTTCTCAATTTTTTTCCATAATACT
CAGAAAAAATATATAATTCAACGCCAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCG
Found at i:9661 original size:31 final size:31
Alignment explanation
Indices: 9623--9687 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
9613 TCTGGAATGT
*
9623 GATCACGTGTGGCCGTTATTACGGTAGATGA
1 GATCACGTGTGGCCGTGATTACGGTAGATGA
9654 GATCACGTGTGGCCGTGATTACGGTAGATGA
1 GATCACGTGTGGCCGTGATTACGGTAGATGA
9685 GAT
1 GAT
9688 TGTTATGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.23, C:0.15, G:0.34, T:0.28
Consensus pattern (31 bp):
GATCACGTGTGGCCGTGATTACGGTAGATGA
Found at i:19057 original size:27 final size:26
Alignment explanation
Indices: 19016--19069 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
19006 CATATACTTT
19016 TTTTTTGGCACAATAACTTCATATAC
1 TTTTTTGGCACAATAACTTCATATAC
* *
19042 TTTTTTGGCATTAATAATTTCATATAC
1 TTTTTTGGCA-CAATAACTTCATATAC
19069 T
1 T
19070 GTAGTATGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 10 0.40
27 15 0.60
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (26 bp):
TTTTTTGGCACAATAACTTCATATAC
Found at i:26716 original size:2 final size:2
Alignment explanation
Indices: 26709--26735 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
26699 CATATACCAC
26709 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
26736 GAACATGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28866 original size:30 final size:30
Alignment explanation
Indices: 28832--28894 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
28822 TCGAAAGACT
28832 GTAGTTTCTACTACGTATACTAATATACTA
1 GTAGTTTCTACTACGTATACTAATATACTA
* *
28862 GTAGTTTCTACTACGTATATTAGTATACTA
1 GTAGTTTCTACTACGTATACTAATATACTA
28892 GTA
1 GTA
28895 TCATTATTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (30 bp):
GTAGTTTCTACTACGTATACTAATATACTA
Found at i:30180 original size:21 final size:19
Alignment explanation
Indices: 30153--30209 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 19
30143 TTGAACCCAA
30153 ATAATCTCATCTGTACAAT
1 ATAATCTCATCTGTACAAT
* *
30172 ACCTAATCTAATCTGTACAGT
1 A--TAATCTCATCTGTACAAT
*
30193 ATAATTTCATCTGTACA
1 ATAATCTCATCTGTACA
30210 GTTACTAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 15 0.47
21 17 0.53
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (19 bp):
ATAATCTCATCTGTACAAT
Found at i:30204 original size:19 final size:19
Alignment explanation
Indices: 30153--30211 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
30143 TTGAACCCAA
*
30153 ATAATCTCATCTGTACAAT
1 ATAATCTCATCTGTACAGT
*
30172 ACCTAATCTAATCTGTACAGT
1 A--TAATCTCATCTGTACAGT
*
30193 ATAATTTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
30212 TACTAAACAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.37
Consensus pattern (19 bp):
ATAATCTCATCTGTACAGT
Found at i:48570 original size:8 final size:8
Alignment explanation
Indices: 48559--48599 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
48549 TGAAAAACAA
48559 AAAAAAAC
1 AAAAAAAC
48567 AAAAAAAC
1 AAAAAAAC
48575 AAAAAAAC
1 AAAAAAAC
*
48583 CAAAAAA-
1 AAAAAAAC
48590 AAAAAAAC
1 AAAAAAAC
48598 AA
1 AA
48600 CAAATGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:48574 original size:18 final size:18
Alignment explanation
Indices: 48551--48603 Score: 74
Period size: 17 Copynumber: 3.1 Consensus size: 18
48541 AATGAACATG
48551 AAAAACAAAAAAAAACAA
1 AAAAACAAAAAAAAACAA
*
48569 AAAAAC-AAAAAAACCAA
1 AAAAACAAAAAAAAACAA
*
48586 AAAAA-AAAAAACAACAA
1 AAAAACAAAAAAAAACAA
48603 A
1 A
48604 TGAAAATGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 25 0.81
18 6 0.19
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAACAAAAAAAAACAA
Found at i:48587 original size:26 final size:26
Alignment explanation
Indices: 48551--48603 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
48541 AATGAACATG
48551 AAAAACAAAAAAAAACAAAAA-AACAA
1 AAAAACAAAAAAAAA-AAAAACAACAA
*
48577 AAAAACCAAAAAAAAAAAAACAACAA
1 AAAAACAAAAAAAAAAAAAACAACAA
48603 A
1 A
48604 TGAAAATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (26 bp):
AAAAACAAAAAAAAAAAAAACAACAA
Found at i:48609 original size:17 final size:14
Alignment explanation
Indices: 48551--48599 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
48541 AATGAACATG
48551 AAAAACAAAAAAAA
1 AAAAACAAAAAAAA
* *
48565 ACAAA-AAAACAAA
1 AAAAACAAAAAAAA
*
48578 AAAACCAAAAAAAA
1 AAAAACAAAAAAAA
48592 AAAAACAA
1 AAAAACAA
48600 CAAATGAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAACAAAAAAAA
Found at i:56026 original size:25 final size:27
Alignment explanation
Indices: 55966--56029 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 27
55956 TAGCAGTGGA
*
55966 CGAACTATATTGTTCTTTGTTATTTTGG
1 CGAACTATATTGTTCTTTGTTAATTT-G
55994 ACGAACTATATTGTTCTTTGTTAATTT-
1 -CGAACTATATTGTTCTTTGTTAATTTG
56021 C-AACTATAT
1 CGAACTATAT
56030 AATTGCTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
25 8 0.24
26 1 0.03
29 25 0.74
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (27 bp):
CGAACTATATTGTTCTTTGTTAATTTG
Done.