Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013034.1 Corchorus capsularis cultivar CVL-1 contig13055, 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: 79891
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:11544 original size:29 final size:29
Alignment explanation
Indices: 11476--11537 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 29
11466 TTAAAATTTT
*
11476 AAGCATATTACTAATTTTTTACCCAAAAAA
1 AAGCATATTACTAATTTTGTA-CCAAAAAA
*
11506 AAGCATATTACTAATTTTGT-CCTAAAAA
1 AAGCATATTACTAATTTTGTACCAAAAAA
11534 AAGC
1 AAGC
11538 CCTATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 11 0.37
30 19 0.63
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.32
Consensus pattern (29 bp):
AAGCATATTACTAATTTTGTACCAAAAAA
Found at i:12635 original size:337 final size:340
Alignment explanation
Indices: 12021--12693 Score: 1054
Period size: 337 Copynumber: 2.0 Consensus size: 340
12011 CCACAGTAGA
12021 AGTTACATTTATCAAGCAAAAAATTAATTATAAGTCAAATAAAATAATCGCACGTTAGGGAAATA
1 AGTTACATTTATCAAGCAAAAAATTAATTATAAGTCAAATAAAATAATCGCACGTTAGGGAAATA
**** * *
12086 ATAAATTTTAATCATAATACATTAAACTATCAAATATTTCTGTCAATCACAGTAACATTTTAAAT
66 ATAAATTTTAATCATAATACATTAAACTATCAAATAAAGATATCAATCACAATAACATTTTAAAT
*
12151 TAAAATGGTAAAAATAAAATATTATAAAATATTCAATTTAATTAAATGAAAATAGATTTTTTAAT
131 TAAAATGGTAAAAATAAAATATTATAAAATATTCAATTTAATTAAATGAAAATAGAGTTTTTAAT
*
12216 AGAATAAAACTATGTATTAAAAAATTTTAATATATCCAAATTCTTATTGAAAAATAGTAAAATGG
196 AGAATAAAACTATATATTAAAAAATTTTAATATATCCAAATTCTTATTGAAAAATAGTAAAATGG
*
12281 TAAAAATAAAGTAATTATAAAGATATT-A-TA-TT-TAATTGAATAAAAATAGAATTTTTAGTGG
261 TAAAAATAAAGTAATTATAAAGATATTAATTATTTATAATTGAATAAAAATAGAATTTTTAGTAG
12342 AATAAAACCAATAAG
326 AATAAAACCAATAAG
* * *
12357 AGTTACA-TTATCAAGCAAAACATTAATTATAAGTCAAATAAAATATTTC-TACGTTAGGGAAAT
1 AGTTACATTTATCAAGCAAAAAATTAATTATAAGTCAAATAAAATA-ATCGCACGTTAGGGAAAT
*
12420 AATAAATTTTAATCATAATACATTAAA-TATCAAATGGAAAGATATCAATCACAATAACTTTTTA
65 AATAAATTTTAATCATAATACATTAAACTATCAAAT--AAAGATATCAATCACAATAACATTTTA
* * *
12484 AATTAAAATGGTAAAAATAAAATAATTATAAACTATTGAATTTAATTAAATGAAAATATAGTTTT
128 AATTAAAATGGTAAAAATAAAAT-ATTATAAAATATTCAATTTAATTAAATGAAAATAGAGTTTT
* *
12549 TAATAGAATAAAACTGTATATTAAAAAATTTTAATATATCCAAATTTTTATTGAAAAATAGTAAA
192 TAATAGAATAAAACTATATATTAAAAAATTTTAATATATCCAAATTCTTATTGAAAAATAGTAAA
*
12614 ATGGTAAAAATAAAGTAATTATAAAGATATTAAATTTATTTAATAATTGAATAAAATTAGAATTT
257 ATGGTAAAAATAAAGTAATTATAAAGATATT-AA-TTATTT-ATAATTGAATAAAAATAGAATTT
*
12679 TTAGTAGACTAAAAC
319 TTAGTAGAATAAAAC
12694 TACAATAGTT
Statistics
Matches: 306, Mismatches: 20, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
334 8 0.03
335 77 0.25
336 52 0.17
337 130 0.42
339 1 0.00
341 2 0.01
342 2 0.01
344 34 0.11
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (340 bp):
AGTTACATTTATCAAGCAAAAAATTAATTATAAGTCAAATAAAATAATCGCACGTTAGGGAAATA
ATAAATTTTAATCATAATACATTAAACTATCAAATAAAGATATCAATCACAATAACATTTTAAAT
TAAAATGGTAAAAATAAAATATTATAAAATATTCAATTTAATTAAATGAAAATAGAGTTTTTAAT
AGAATAAAACTATATATTAAAAAATTTTAATATATCCAAATTCTTATTGAAAAATAGTAAAATGG
TAAAAATAAAGTAATTATAAAGATATTAATTATTTATAATTGAATAAAAATAGAATTTTTAGTAG
AATAAAACCAATAAG
Found at i:17546 original size:21 final size:21
Alignment explanation
Indices: 17491--17546 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
17481 AGAGACAAAA
* *
17491 GAAAGAAATCAATGAGATAACC
1 GAAAGAAATC-ATGAAAGAACC
**
17513 -AAA-AAATTGTGAAAGAACC
1 GAAAGAAATCATGAAAGAACC
17532 GAAAGAAATCATGAA
1 GAAAGAAATCATGAA
17547 GAAATCAAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
19 8 0.31
20 7 0.27
21 11 0.42
ACGTcount: A:0.57, C:0.11, G:0.18, T:0.14
Consensus pattern (21 bp):
GAAAGAAATCATGAAAGAACC
Found at i:18496 original size:22 final size:21
Alignment explanation
Indices: 18444--19009 Score: 127
Period size: 22 Copynumber: 26.0 Consensus size: 21
18434 TATGATCCCA
18444 TTATGAAATTTTGATAACCTC
1 TTATGAAATTTTGATAACCTC
*
18465 TTATGAAATTTTGATAACGGTAC
1 TTATGAAATTTTGATAAC-CT-C
* ** * * *
18488 -TATGGAATTTCAAGAATCTTT
1 TTATGAAATTTTGATAA-CCTC
* ** *
18509 TTAT-AATTTTTTTTAACTTTC
1 TTATGAAATTTTGATAAC-CTC
*
18530 TTATGAAATTTTGTTAACCTCC
1 TTATGAAATTTTGATAACCT-C
* * *
18552 CTAAGGAATTTTGA-ATACCTC
1 TTATGAAATTTTGATA-ACCTC
* *
18573 AATATGAAATTTTGATAACTTCC
1 -TTATGAAATTTTGATAACCT-C
** *
18596 CAATGAAATTTTGATAACCAAC
1 TTATGAAATTTTGATAACC-TC
* * * *
18618 ACTATGAGATGTTGATAACTTCC
1 -TTATGAAATTTTGATAACCT-C
* * * *
18641 ATATGATATATTGATAACCAC
1 TTATGAAATTTTGATAACCTC
* * * *
18662 TTTATAAAAATTTAAAAACCTCC
1 -TTATGAAATTTTGATAACCT-C
* *
18685 ATATG-AATTGTT-AGTAATCACAC
1 TTATGAAATT-TTGA-TAA-C-CTC
* *
18708 TT-TAAAATTTTGATAATCACAC
1 TTATGAAATTTTGATAA-C-CTC
* *
18730 -CATGAAATTGTGATAACCTC
1 TTATGAAATTTTGATAACCTC
* * *
18750 GCTATGAAATTTTGATAAATCTT
1 -TTATGAAATTTTGAT-AACCTC
* *
18773 TCTATAAAATTTTAATAAACCTCC
1 T-TATGAAATTTTGAT-AACCT-C
* * *
18797 CTATAAAATTTTGATAACTTTC
1 TTATGAAATTTTGATAAC-CTC
* *
18819 TTATGAAATCTTGATGA---C
1 TTATGAAATTTTGATAACCTC
* *
18837 -TA-CAAATTTTGATAAGCTCC
1 TTATGAAATTTTGATAACCT-C
* **
18857 CTATGATTTTTTGATAACCTC
1 TTATGAAATTTTGATAACCTC
* *
18878 ATTATGAAATTTTGTTAATCTCC
1 -TTATGAAATTTTGATAACCT-C
** * *
18901 CCATGAAATTTTGATCTACATAC
1 TTATGAAATTTTGAT-AACCT-C
18924 -TATGAAATTTTGATAACCCTC
1 TTATGAAATTTTGATAA-CCTC
* *
18945 TTATGAAATTCTGA-AAACTAAAC
1 TTATGAAATTTTGATAACCT---C
**
18968 -TATGAAAAATTGATAACCTTC
1 TTATGAAATTTTGATAACC-TC
* *
18989 ATATGAAATTTTGATATCCTC
1 TTATGAAATTTTGATAACCTC
19010 ACTGAATTTT
Statistics
Matches: 394, Mismatches: 105, Indels: 92
0.67 0.18 0.16
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
18 1 0.00
20 6 0.02
21 49 0.12
22 252 0.64
23 72 0.18
24 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (21 bp):
TTATGAAATTTTGATAACCTC
Found at i:18633 original size:45 final size:45
Alignment explanation
Indices: 18575--18660 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
18565 AATACCTCAA
* *
18575 TATGAAATTTTGATAACTTCCCA-ATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACTT-CCATATGAAATATTGATAACCAACAC
* *
18620 TATGAGATGTTGATAACTTCCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACTTCCATATGAAATATTGATAACCA
18661 CTTTATAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 3 0.08
45 33 0.92
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (45 bp):
TATGAAATGTTGATAACTTCCATATGAAATATTGATAACCAACAC
Found at i:18782 original size:23 final size:23
Alignment explanation
Indices: 18734--18813 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
18724 TCACACCATG
* * *
18734 AAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAACCTCCCTATA
* **
18756 AAATTTTGATAAATCTTTCTATA
1 AAATTTTGATAAACCTCCCTATA
*
18779 AAATTTTAATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
18802 AAATTTTGATAA
1 AAATTTTGATAA
18814 CTTTCTTATG
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 9 0.19
23 38 0.81
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:19067 original size:19 final size:19
Alignment explanation
Indices: 18995--19061 Score: 107
Period size: 19 Copynumber: 3.5 Consensus size: 19
18985 CTTCATATGA
*
18995 AATTTTGATATCCTCACTG
1 AATTTTGATATCCTCCCTG
19014 AATTTTGATATCCTCCCTG
1 AATTTTGATATCCTCCCTG
*
19033 AATTTTGGTATCCTCCCTG
1 AATTTTGATATCCTCCCTG
19052 AAATTTTGAT
1 -AATTTTGAT
19062 TACTCCATCA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 36 0.82
20 8 0.18
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (19 bp):
AATTTTGATATCCTCCCTG
Found at i:19192 original size:22 final size:22
Alignment explanation
Indices: 19167--19411 Score: 134
Period size: 22 Copynumber: 11.3 Consensus size: 22
19157 AATCAGATTT
*
19167 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
*
19189 TGAAATTTTGATAACATCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
19211 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
19233 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
19255 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
**
19277 TGAAATTTTGATAACAAC---A
1 TGAAATTTTGATAACCTCTTTA
19296 CTGAAATTTTGATAA--TCTTCATA
1 -TGAAATTTTGATAACCTCTT--TA
*
19319 T-AAATTTTGATAATCATATCTTTA
1 TGAAATTTTGATAA-C--CTCTTTA
* * * *
19343 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTTTA
* *
19365 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
19385 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCTTTA
19405 TGAAATT
1 TGAAATT
19412 GAGACTTTTA
Statistics
Matches: 169, Mismatches: 38, Indels: 34
0.70 0.16 0.14
Matches are distributed among these distances:
18 1 0.01
19 2 0.01
20 30 0.18
21 25 0.15
22 90 0.53
23 3 0.02
24 3 0.02
25 11 0.07
26 4 0.02
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:19235 original size:44 final size:43
Alignment explanation
Indices: 19142--19292 Score: 126
Period size: 44 Copynumber: 3.4 Consensus size: 43
19132 AAAAATACCA
* * * *
19142 CTATGAAATTTTTG-TAATCAGATTTTGAAAA-TTTGATAACCTCT
1 CTATGAAA-TTTTGATAA-CACATTAT-AAAATTTTGATAACCCCG
* * * * *
19186 TTATGAAATTTTGATAACATCTTTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAACA-CATTATAAAATTTTGATAACCCCG
** *
19230 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAA-CACATTATAAAATTTTGATAACCCCG
*
19274 CTTTGAAATTTTGATAACA
1 CTATGAAATTTTGATAACA
19293 ACACTGAAAT
Statistics
Matches: 87, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
43 13 0.15
44 72 0.83
45 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.43
Consensus pattern (43 bp):
CTATGAAATTTTGATAACACATTATAAAATTTTGATAACCCCG
Found at i:19337 original size:18 final size:19
Alignment explanation
Indices: 19299--19337 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
19289 AACAACACTG
19299 AAATTTTGATAATCTTCATAT
1 AAATTTTGATAA--TTCATAT
19320 AAATTTTGATAA-TCATAT
1 AAATTTTGATAATTCATAT
19338 CTTTATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
21 12 0.67
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (19 bp):
AAATTTTGATAATTCATAT
Found at i:19446 original size:22 final size:22
Alignment explanation
Indices: 19167--19527 Score: 112
Period size: 22 Copynumber: 16.3 Consensus size: 22
19157 AATCAGATTT
* *
19167 TGAAAATTTGATAACC-TCTTTA
1 TGAAATTTTGATAACCTTC-ATA
19189 TGAAATTTTGATAACATCTT--TA
1 TGAAATTTTGATAAC--CTTCATA
* * * *
19211 TAAAATTTTGTTGACCCCTC-TA
1 TGAAATTTTGAT-AACCTTCATA
* *
19233 TGAAATTTTGATAATC-ACATTA
1 TGAAATTTTGATAACCTTCA-TA
* * *
19255 TGTAATTTTGATAACC-TCGCTT
1 TGAAATTTTGATAACCTTC-ATA
** *
19277 TGAAATTTTGATAA-CAACA-C
1 TGAAATTTTGATAACCTTCATA
*
19297 TGAAATTTTGATAATCTTCATA
1 TGAAATTTTGATAACCTTCATA
* *
19319 T-AAATTTTGATAATCATATCTTTA
1 TGAAATTTTGATAA-CCT-TC-ATA
*
19343 TGAAATTTCGATAATCAC-TC-TA
1 TGAAATTTTGATAA-C-CTTCATA
*
19365 TGAGA-TTTGATAACCTTC-TA
1 TGAAATTTTGATAACCTTCATA
* * *
19385 TCAAATTTTGGTACTCCTT-ATGAAA
1 TGAAATTTTGATA-ACCTTCAT---A
*
19410 TTGAGACTTTT-ATAACCTTCATA
1 -TGA-AATTTTGATAACCTTCATA
*
19433 TGAAATTTTGATAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
* * **
19455 TAAAATTTTGATAACCTCCCGA
1 TGAAATTTTGATAACCTTCATA
* *
19477 TGAAGTATT-AGTAACCTTC-TAA
1 TGAAATTTTGA-TAACCTTCAT-A
* *
19499 TGAAATTTTGTTAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
19521 TGAAATT
1 TGAAATT
19528 CGTATAACCT
Statistics
Matches: 253, Mismatches: 52, Indels: 68
0.68 0.14 0.18
Matches are distributed among these distances:
19 1 0.00
20 23 0.09
21 42 0.17
22 144 0.57
23 7 0.03
24 6 0.02
25 19 0.08
26 6 0.02
27 5 0.02
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCATA
Found at i:19652 original size:24 final size:22
Alignment explanation
Indices: 19591--19753 Score: 84
Period size: 22 Copynumber: 7.3 Consensus size: 22
19581 TTGTGATAAT
* *
19591 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
19613 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
**
19635 TAA-CATGATCCTATGAAATTTTGG
1 TAACCA--A-CCTATGAAATTTTAA
* **
19659 TAA-CTACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* **
19681 TAATC-ACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* *
19703 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* * *
19725 TAACC-TCCTCATGGAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
19747 TAACCAA
1 TAACCAA
19754 AGTAAAATAT
Statistics
Matches: 120, Mismatches: 14, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
21 5 0.04
22 97 0.81
23 2 0.02
24 16 0.13
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.32
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:19729 original size:22 final size:22
Alignment explanation
Indices: 19645--19729 Score: 134
Period size: 22 Copynumber: 3.9 Consensus size: 22
19635 TAACATGATC
*
19645 CTATGAAATTTTGGTAACTACA
1 CTATGAAATTTTGGTAACCACA
*
19667 CTATGAAATTTTGGTAATCACA
1 CTATGAAATTTTGGTAACCACA
19689 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* *
19711 CTATGGAATTTTGATAACC
1 CTATGAAATTTTGGTAACC
19730 TCCTCATGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:19738 original size:22 final size:22
Alignment explanation
Indices: 19645--19752 Score: 101
Period size: 22 Copynumber: 4.9 Consensus size: 22
19635 TAACATGATC
* * *
19645 CTATGAAATTTTGGTAACTACA
1 CTATGGAATTTTGATAACCACA
* * *
19667 CTATGAAATTTTGGTAATCACA
1 CTATGGAATTTTGATAACCACA
* *
19689 CTATGAAATTTTGGTAACCACA
1 CTATGGAATTTTGATAACCACA
*
19711 CTATGGAATTTTGATAACCTC-
1 CTATGGAATTTTGATAACCACA
* *
19732 CTCATGGAATTATAATAACCA
1 CT-ATGGAATTTTGATAACCA
19753 AAGTAAAATA
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
21 2 0.03
22 74 0.97
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (22 bp):
CTATGGAATTTTGATAACCACA
Found at i:22458 original size:20 final size:20
Alignment explanation
Indices: 22433--22491 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
22423 ATTATAAAAT
22433 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTTTTAAA
*
22453 AATAATAACTAACTTTTAAA
1 AATAATAACTAATTTTTAAA
*
22473 AATAATAACTAATTATTAA
1 AATAATAACTAATTTTTAA
22492 CTTTAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (20 bp):
AATAATAACTAATTTTTAAA
Found at i:22458 original size:23 final size:22
Alignment explanation
Indices: 22427--22484 Score: 79
Period size: 20 Copynumber: 2.8 Consensus size: 22
22417 AATCATATTA
22427 TAAAATAATAATAACTAA-TTT
1 TAAAATAATAATAACTAACTTT
*
22448 TTAAA-AATAATAACTAACTTT
1 TAAAATAATAATAACTAACTTT
22469 T-AAA-AATAATAACTAA
1 TAAAATAATAATAACTAA
22485 TTATTAACTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 27 0.77
21 8 0.23
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAAATAATAATAACTAACTTT
Found at i:23224 original size:18 final size:18
Alignment explanation
Indices: 23177--23224 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
23167 TATCTTTCTA
23177 TAATTAATAAAAAAAGTT
1 TAATTAATAAAAAAAGTT
*
23195 TAATGAATAAAAATAA-TAT
1 TAATTAATAAAAA-AAGT-T
23214 TAATTAA-AAAA
1 TAATTAATAAAA
23225 TATTATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (18 bp):
TAATTAATAAAAAAAGTT
Found at i:23910 original size:22 final size:21
Alignment explanation
Indices: 23885--24047 Score: 100
Period size: 22 Copynumber: 7.5 Consensus size: 21
23875 GAGGTTATTG
23885 AAATTTCATGATGTAGTTATCA
1 AAATTTCAT-ATGTAGTTATCA
* **
23907 AAATTTTCATAGAGCGGTTA-C-
1 AAA-TTTCATA-TGTAGTTATCA
* *
23928 CAATTTTATAGTGT-GATTATCA
1 AAATTTCATA-TGTAG-TTATCA
* * *
23950 AAATTTTATAGGAAGATTATCA
1 AAATTTCATATGTAG-TTATCA
*
23972 AAATTTCACAT-TGAGGTTATCA
1 AAATTTCATATGT-A-GTTATCA
*
23994 AAATTTCATAGTGTGGTTATCA
1 AAATTTCATA-TGTAGTTATCA
*
24016 AAATTTCACAGTGTAGTTATCA
1 AAATTTCATA-TGTAGTTATCA
*
24038 AATTTTCATA
1 AAATTTCATA
24048 GGAGGTTATT
Statistics
Matches: 111, Mismatches: 20, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
19 1 0.01
20 11 0.10
21 4 0.04
22 81 0.73
23 13 0.12
24 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.39
Consensus pattern (21 bp):
AAATTTCATATGTAGTTATCA
Found at i:23994 original size:44 final size:43
Alignment explanation
Indices: 23944--24082 Score: 147
Period size: 44 Copynumber: 3.2 Consensus size: 43
23934 TATAGTGTGA
* *
23944 TTATCAAAATTTTATAGGAAGATTATCAAAATTTCACATTGAGG
1 TTATCAAAATTTTATAGG-AGGTTATCAAAATTTCACAATGAGG
* * *
23988 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAGTGTA-G
1 TTATCAAAATTTTATAG-GAGGTTATCAAAATTTCACAATG-AGG
** * *
24032 TTATC-AAATTTTCATAGGAGGTTATTGAAATTTCATAACGAGG
1 TTATCAAAATTTT-ATAGGAGGTTATCAAAATTTCACAATGAGG
24075 TTATCAAA
1 TTATCAAA
24083 TTAATTTCAC
Statistics
Matches: 79, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
42 1 0.01
43 29 0.37
44 47 0.59
45 2 0.03
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.37
Consensus pattern (43 bp):
TTATCAAAATTTTATAGGAGGTTATCAAAATTTCACAATGAGG
Found at i:24014 original size:66 final size:65
Alignment explanation
Indices: 23899--24112 Score: 173
Period size: 66 Copynumber: 3.2 Consensus size: 65
23889 TTCATGATGT
* * * * * * *
23899 AGTTATCAAAATTTTCATAGAGCGGTTA-C-CAATTTTATAGTGTGATTATCAAAATTTTATAG-
1 AGTTATCAAAA-TTTCACAG-GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAGT
23961 GA
64 GA
*
23963 AGATTATCAAAATTTCACATTGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAGT
1 AG-TTATCAAAATTTCACA-GGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAGT
*
24028 GT
64 GA
* * ** ** *
24030 AGTTATCAAATTTTCATAGGAGGTTATTGAAATTTCATAACGAGGTTATCAAATTAATTTCACAG
1 AGTTATCAAAATTTCACAGGAGGTTATCAAAATTTCATAGTGTGGTTATC-AA--AATTTCACAG
*
24095 TGT
63 TGA
* *
24098 GGTTATCAATATTTC
1 AGTTATCAAAATTTC
24113 TACGCTAGCA
Statistics
Matches: 122, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
64 14 0.11
65 36 0.30
66 44 0.36
67 3 0.02
68 25 0.20
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (65 bp):
AGTTATCAAAATTTCACAGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAGTGA
Found at i:27786 original size:11 final size:11
Alignment explanation
Indices: 27770--27794 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
27760 ATATATACAA
27770 AAATAAGAAAT
1 AAATAAGAAAT
27781 AAATAAGAAAT
1 AAATAAGAAAT
27792 AAA
1 AAA
27795 ATTATTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (11 bp):
AAATAAGAAAT
Found at i:36550 original size:35 final size:35
Alignment explanation
Indices: 36504--36574 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
36494 AGGCACAAAC
*
36504 GCCGTTAATGCTTAACTCTTAACAGTGTCAAGATA
1 GCCGTTAATGCTTAACACTTAACAGTGTCAAGATA
*
36539 GCCGTTAATGCTTAGCACTTAACAGTGTCAAGATA
1 GCCGTTAATGCTTAACACTTAACAGTGTCAAGATA
36574 G
1 G
36575 ATCTCGTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (35 bp):
GCCGTTAATGCTTAACACTTAACAGTGTCAAGATA
Found at i:47260 original size:12 final size:13
Alignment explanation
Indices: 47231--47261 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
47221 TTGAATATGT
47231 TTTTTCATAATTA
1 TTTTTCATAATTA
47244 TTTTTCATAATTA
1 TTTTTCATAATTA
47257 TTTTT
1 TTTTT
47262 AAGACTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTCATAATTA
Found at i:47362 original size:21 final size:21
Alignment explanation
Indices: 47336--47411 Score: 116
Period size: 21 Copynumber: 3.5 Consensus size: 21
47326 ACTTAAAATT
47336 ACAACTTAAATAAAGTTAAAA
1 ACAACTTAAATAAAGTTAAAA
47357 ACAACTTAAATAAAGTTAAAA
1 ACAACTTAAATAAAGTTAAAA
*
47378 TTACAACTTAAATAAATTTAAAA
1 --ACAACTTAAATAAAGTTAAAA
*
47401 ACAACATAAAT
1 ACAACTTAAAT
47412 TACACCATAG
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
21 31 0.61
23 20 0.39
ACGTcount: A:0.61, C:0.11, G:0.03, T:0.26
Consensus pattern (21 bp):
ACAACTTAAATAAAGTTAAAA
Found at i:47376 original size:27 final size:23
Alignment explanation
Indices: 47328--47400 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
47318 TATGTTTAAC
47328 TTAAAATTACAACTTAAATAAAG
1 TTAAAATTACAACTTAAATAAAG
47351 TTAAAA--ACAACTTAAATAAAG
1 TTAAAATTACAACTTAAATAAAG
*
47372 TTAAAATTACAACTTAAATAAAT
1 TTAAAATTACAACTTAAATAAAG
47395 TTAAAA
1 TTAAAA
47401 ACAACATAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
21 21 0.45
23 26 0.55
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.30
Consensus pattern (23 bp):
TTAAAATTACAACTTAAATAAAG
Found at i:47378 original size:44 final size:44
Alignment explanation
Indices: 47328--47411 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
47318 TATGTTTAAC
*
47328 TTAAAATTACAACTTAAATAAAGTTAAAAACAACTTAAATAAAG
1 TTAAAATTACAACTTAAATAAAGTTAAAAACAACATAAATAAAG
*
47372 TTAAAATTACAACTTAAATAAATTTAAAAACAACATAAAT
1 TTAAAATTACAACTTAAATAAAGTTAAAAACAACATAAAT
47412 TACACCATAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.29
Consensus pattern (44 bp):
TTAAAATTACAACTTAAATAAAGTTAAAAACAACATAAATAAAG
Found at i:47910 original size:15 final size:16
Alignment explanation
Indices: 47882--47911 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
47872 GTTCATTTCG
47882 TCATTTTCTTTCTTTT
1 TCATTTTCTTTCTTTT
47898 TCATTTT-TTTCTTT
1 TCATTTTCTTTCTTT
47912 CTTCCTCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (16 bp):
TCATTTTCTTTCTTTT
Found at i:52685 original size:12 final size:12
Alignment explanation
Indices: 52670--52703 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
52660 ATTTCATCTT
*
52670 CATCTTCATCCC
1 CATCCTCATCCC
*
52682 CATCCCCATCCC
1 CATCCTCATCCC
52694 CATCCTCATC
1 CATCCTCATC
52704 TTTAGAGGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.18, C:0.56, G:0.00, T:0.26
Consensus pattern (12 bp):
CATCCTCATCCC
Found at i:58675 original size:26 final size:26
Alignment explanation
Indices: 58641--58695 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
58631 TGGATCTTCT
*
58641 TTCAATAATTTCCCAATAACTGGATC
1 TTCAATAATTTCCCAATAACTGAATC
* *
58667 TTCAATAATTTTCCAATAATTGAATC
1 TTCAATAATTTCCCAATAACTGAATC
58693 TTC
1 TTC
58696 TTTGAAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (26 bp):
TTCAATAATTTCCCAATAACTGAATC
Found at i:58802 original size:16 final size:16
Alignment explanation
Indices: 58781--58815 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
58771 ATCTAAAATA
*
58781 CTTCAGAGTTTTTCTG
1 CTTCAGAGCTTTTCTG
58797 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
58813 CTT
1 CTT
58816 TCTGAATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.49
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:59640 original size:63 final size:64
Alignment explanation
Indices: 59564--59684 Score: 217
Period size: 63 Copynumber: 1.9 Consensus size: 64
59554 TAGTTCATTT
*
59564 TTTTTTGTGCTCTAAGTTTTGCGTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGTCTTTC
1 TTTTTTGTGCTCTAAGTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGTCTTTC
*
59628 TTTTTT-TGCTCTAATTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAG
1 TTTTTTGTGCTCTAAGTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAG
59685 CCTGCTATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
63 49 0.89
64 6 0.11
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.44
Consensus pattern (64 bp):
TTTTTTGTGCTCTAAGTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGTCTTTC
Found at i:68480 original size:2 final size:2
Alignment explanation
Indices: 68473--68511 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
68463 AGAAAATTAT
*
68473 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
68512 ATATATGCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:68880 original size:18 final size:18
Alignment explanation
Indices: 68835--68899 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 18
68825 ATAAGGAATC
*
68835 TGATTTTGATGATGCTCT
1 TGATTTTGATGATGCTGT
*
68853 TG-TATT--TGATGCTGT
1 TGATTTTGATGATGCTGT
* *
68868 TGATTTTGATGATGTTGA
1 TGATTTTGATGATGCTGT
*
68886 TGATTCTGATGATG
1 TGATTTTGATGATG
68900 ATGATTATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 10 0.26
16 3 0.08
17 3 0.08
18 22 0.58
ACGTcount: A:0.18, C:0.06, G:0.26, T:0.49
Consensus pattern (18 bp):
TGATTTTGATGATGCTGT
Found at i:70245 original size:2 final size:2
Alignment explanation
Indices: 70238--70265 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
70228 AATTAATGAA
70238 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
70266 CATGAGGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72193 original size:25 final size:26
Alignment explanation
Indices: 72165--72216 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
72155 TTAGTAGAAT
*
72165 AATTGT-AAA-AATTTATTTCTAAAAA
1 AATTGTAAAAGAATATATTT-TAAAAA
72190 AATTGTAAAAGAATATATTTTAAAAA
1 AATTGTAAAAGAATATATTTTAAAAA
72216 A
1 A
72217 TTTCTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 6 0.25
26 10 0.42
27 8 0.33
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (26 bp):
AATTGTAAAAGAATATATTTTAAAAA
Found at i:73400 original size:2 final size:2
Alignment explanation
Indices: 73393--73443 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
73383 TCTCAAAACT
* * * *
73393 TA TA TA TA AA TA TA CA TA CA TA TG T- TA 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 TA TA TA TA
73434 TA TA TA TA TA
1 TA TA TA TA TA
73444 AATTAGCACC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:74257 original size:21 final size:22
Alignment explanation
Indices: 74231--74271 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
74221 TTGTAGGTGA
*
74231 TGATGTGATT-ACTATGGTACT
1 TGATGTGATTAACAATGGTACT
*
74252 TGATGTTATTAACAATGGTA
1 TGATGTGATTAACAATGGTA
74272 ACCTTTTGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.41
Consensus pattern (22 bp):
TGATGTGATTAACAATGGTACT
Found at i:77550 original size:10 final size:11
Alignment explanation
Indices: 77530--77555 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
77520 GGGGAATAAG
77530 AAAGAAAAAAA
1 AAAGAAAAAAA
77541 AAAGAAAAAAA
1 AAAGAAAAAAA
77552 AAAG
1 AAAG
77556 CCAAATAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Done.