Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006111.1 Corchorus capsularis cultivar CVL-1 contig06129, 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: 49391
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:7310 original size:165 final size:165
Alignment explanation
Indices: 7034--7479 Score: 515
Period size: 165 Copynumber: 2.7 Consensus size: 165
7024 TGAGTCATTT
* * *
7034 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTATGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAATTATTTAAT-CCCTCAAGAATCAAAAGTTAGGATAT
** * * * * ** **
7099 TTAAGTAATCTGCAAAGTAGGTAAAGACGAGAAAGATTAGTTCTCTAGCT-CATCATCAA-TCCT
64 TTAAGTAATCTGCAAAGTAGAAAAAGACGAAAAAAATAAGTTCTCTAACTCCAAAAGAAAGT-CT
* * *
7162 TGAT-GGGATCTTTTATTAATTCCACTACCCTATTCAA
128 TGATAGGGATATTTTAGTAATTCCACTACCCTATTAAA
* * *
7199 GTCCATTGAGAAATGACCAAAAAGATTACTTATTTAATCGCCTCCAGAATCAAAAGTTAGGATAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAATTATTTAATC-CCTCAAGAATCAAAAGTTAGGATAT
* *
7264 TTAAGTAATCTGCCAAGTAGAAAAATACGAAAAAAATAAGTTCTCTAACTCCAAAAGAAAGTCTT
64 TTAAGTAATCTGCAAAGTAGAAAAAGACGAAAAAAATAAGTTCTCTAACTCCAAAAGAAAGTCTT
* *
7329 GGTAGGGATATTTTAGTAATTCCACTACTCTATTAAA
129 GATAGGGATATTTTAGTAATTCCACTACCCTATTAAA
* * *
7366 GTCAATTGGGATATGACCAAAAAGTCTAATTATTTAATCCCTCAAGAATCAAAACTTAGGATATT
1 GTCAATTGAGAAATGACCAAAAAGT-TAATTATTTAATCCCTCAAGAATCAAAAGTTAGGATATT
* * * * *
7431 TAAGTAATCTGTTAAA-TGGGAAAAGAC-AAAAAAATTAGTTCTCTCACTC
65 TAAGTAATCTG-CAAAGTAGAAAAAGACGAAAAAAATAAGTTCTCTAACTC
7480 ATTAATACGG
Statistics
Matches: 239, Mismatches: 36, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
164 1 0.00
165 119 0.50
166 54 0.23
167 65 0.27
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.30
Consensus pattern (165 bp):
GTCAATTGAGAAATGACCAAAAAGTTAATTATTTAATCCCTCAAGAATCAAAAGTTAGGATATTT
AAGTAATCTGCAAAGTAGAAAAAGACGAAAAAAATAAGTTCTCTAACTCCAAAAGAAAGTCTTGA
TAGGGATATTTTAGTAATTCCACTACCCTATTAAA
Found at i:7546 original size:15 final size:15
Alignment explanation
Indices: 7526--7558 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
7516 TATTTATTCA
7526 AATCTATCTATCACT
1 AATCTATCTATCACT
7541 AATCTATCTATCACT
1 AATCTATCTATCACT
7556 AAT
1 AAT
7559 TGCAACAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.39
Consensus pattern (15 bp):
AATCTATCTATCACT
Found at i:13491 original size:39 final size:39
Alignment explanation
Indices: 13379--13491 Score: 92
Period size: 37 Copynumber: 2.9 Consensus size: 39
13369 TCAATCTATT
*
13379 TAACTACAAATCACATTGTAAATTGTATGATTTTTTTTT
1 TAACTACAAATCACATTGTAAATTGTATGATTTTTTTTC
* ** * * **
13418 TTAC--CTTATCAAGGATT-TCACATTCAATGA--TTTTTTC
1 TAACTACAAATC-A-CATTGT-AAATTGTATGATTTTTTTTC
13455 TAACTACAAATCACATTGTAAATTGTATGATTTTTTT
1 TAACTACAAATCACATTGTAAATTGTATGATTTTTTT
13492 CCTTATTAAA
Statistics
Matches: 51, Mismatches: 15, Indels: 16
0.62 0.18 0.20
Matches are distributed among these distances:
37 24 0.47
38 4 0.08
39 23 0.45
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (39 bp):
TAACTACAAATCACATTGTAAATTGTATGATTTTTTTTC
Found at i:16694 original size:3 final size:3
Alignment explanation
Indices: 16688--16719 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
16678 CTACTACTAC
16688 ATA ATA ATA ATA ATA ATA ATA ATA ATA TATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A
16720 GAGGCTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:17370 original size:15 final size:16
Alignment explanation
Indices: 17321--17377 Score: 64
Period size: 15 Copynumber: 3.6 Consensus size: 16
17311 TTGGAACCAT
17321 ATGACCCAAAACCGAAAA
1 ATGACCC-AAACC-AAAA
*
17339 A-CACCCAAACCAAAA
1 ATGACCCAAACCAAAA
*
17354 ATGACCCAAACC-CAA
1 ATGACCCAAACCAAAA
17369 ATGACCCAA
1 ATGACCCAA
17378 CATTTTAGCG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 16 0.46
16 14 0.40
17 4 0.11
18 1 0.03
ACGTcount: A:0.53, C:0.35, G:0.07, T:0.05
Consensus pattern (16 bp):
ATGACCCAAACCAAAA
Found at i:20589 original size:20 final size:21
Alignment explanation
Indices: 20552--20591 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
20542 TCATATTACA
*
20552 TATGTTACCTATTTTATGATT
1 TATGTTACCTAATTTATGATT
20573 TATGTTA-CTAATTTATGAT
1 TATGTTACCTAATTTATGAT
20592 AATTTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (21 bp):
TATGTTACCTAATTTATGATT
Found at i:24857 original size:7 final size:7
Alignment explanation
Indices: 24845--24875 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
24835 CAATGTCTTC
24845 TTTTTAA
1 TTTTTAA
24852 TTTTTAA
1 TTTTTAA
24859 TTTTTAA
1 TTTTTAA
24866 TTTTTAA
1 TTTTTAA
24873 TTT
1 TTT
24876 CCAGATTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTAA
Found at i:25245 original size:22 final size:22
Alignment explanation
Indices: 25220--25780 Score: 198
Period size: 22 Copynumber: 25.7 Consensus size: 22
25210 ATGATCCCAT
25220 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* ** *
25242 TATGAAATTTTAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
25264 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
25286 TAT-AAATTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* * * *
25307 TATGAAGTTTGGTTAACC-TCTT
1 TATGAAATTTTGATAACCTTC-C
* * *
25329 TAAGTAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
25351 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
25373 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
25396 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * **
25417 ATATGATATATTGATAACCATGT
1 -TATGAAATTTTGATAACCTTCC
* *
25440 TATGAAAATTT-A-AACACCTCC
1 TATGAAATTTTGATAAC-CTTCC
* *
25461 ATATG-AATTGTT-AGTAATC-ACAC
1 -TATGAAATT-TTGA-TAACCTTC-C
* * * *
25484 TCTAAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
* *
25506 TATGAAATTGTGATAACC-TCGT
1 TATGAAATTTTGATAACCTTC-C
*
25528 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
*
25551 TATAAAATTTTGATAAACC-TCGC
1 TATGAAATTTTGAT-AACCTTC-C
* * *
25574 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
25596 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
*
25613 TAT-AAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** *
25634 TATGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
25656 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* *
25678 TATGAAATTTTGATCTACATAT--
1 TATGAAATTTTGAT-AACCT-TCC
* *
25700 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* * **
25722 TGTGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
* ** *
25744 TATGAAATTTTAATAAGTTTCA
1 TATGAAATTTTGATAACCTTCC
25766 TATGAAATTTTGATA
1 TATGAAATTTTGATA
25781 TCCTCCCTGA
Statistics
Matches: 400, Mismatches: 103, Indels: 72
0.70 0.18 0.13
Matches are distributed among these distances:
16 11 0.03
17 3 0.01
20 4 0.01
21 36 0.09
22 272 0.68
23 70 0.17
24 4 0.01
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:25409 original size:45 final size:45
Alignment explanation
Indices: 25351--25436 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
25341 AAGACCTCAA
* * *
25351 TATGAAATTTTGATAACTTCCCA-ATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACCT-CCATATGAAATATTGATAACCAACAC
* *
25396 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCA
25437 TGTTATGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.09
45 32 0.91
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAACAC
Found at i:25536 original size:44 final size:43
Alignment explanation
Indices: 25334--25785 Score: 221
Period size: 44 Copynumber: 10.3 Consensus size: 43
25324 CTCTTTAAGT
* *
25334 AATTTTGA-AGACCTCAATATGAAATTTTGATAA-CTTCCCAATGA
1 AATTTTGATA-ACCTCATTATGAAATTTTGATAATC-T-CCTATGA
* * * * *
25378 AATTTTGATAACCAACACTATGAGATGTTGATAACCTCCATATGA
1 AATTTTGATAACC-TCATTATGAAATTTTGATAATCTCC-TATGA
* * * * * *
25423 TATATTGATAACCAT-GTTATGAAAATTT-AAACACCTCCATATG-
1 AATTTTGATAACC-TCATTATGAAATTTTGATA-ATCTCC-TATGA
* * * * * *
25466 AATTGTT-AGTAATCACACTCTAAAATTTTGATAATCACACTATGA
1 AATT-TTGA-TAACCTCATTATGAAATTTTGATAATCTC-CTATGA
* * *
25511 AATTGTGATAACCTCGTTATGAAATTTTGATAAATCTTCCTATAA
1 AATTTTGATAACCTCATTATGAAATTTTGAT-AATC-TCCTATGA
** * * *
25556 AATTTTGATAAACCTCGCTATAAAATTTTGATAACTTTCTTATGA
1 AATTTTGAT-AACCTCATTATGAAATTTTGATAA-TCTCCTATGA
* *
25601 AATCTTGATAA---C--TAT-AAATTTTGATAACCTCCCTATGA
1 AATTTTGATAACCTCATTATGAAATTTTGATAATCT-CCTATGA
** *
25639 TTTTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCTATGA
1 AATTTTGATAACCTCATTATGAAATTTTGATAATCT-CCTATGA
* * * * *
25683 AATTTTGATCTACAT-ATTATGAAATTTTGATAACCCTCTTGTGA
1 AATTTTGAT-AACCTCATTATGAAATTTTGATAA-TCTCCTATGA
* * * * * *
25727 AATTTTGA-AAACTAAACTATGAAATTTTAATAAGTTTCATATGA
1 AATTTTGATAACCT-CATTATGAAATTTTGATAA-TCTCCTATGA
*
25771 AATTTTGATATCCTC
1 AATTTTGATAACCTC
25786 CCTGAATTTT
Statistics
Matches: 309, Mismatches: 71, Indels: 56
0.71 0.16 0.13
Matches are distributed among these distances:
37 1 0.00
38 26 0.08
39 3 0.01
41 2 0.01
42 2 0.01
43 8 0.03
44 161 0.52
45 83 0.27
46 23 0.07
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39
Consensus pattern (43 bp):
AATTTTGATAACCTCATTATGAAATTTTGATAATCTCCTATGA
Found at i:25562 original size:23 final size:23
Alignment explanation
Indices: 25532--25611 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 23
25522 CCTCGTTATG
25532 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTTCCTATA
*
25555 AAATTTTGATAAA-CCTCGCTATA
1 AAATTTTGATAAATCTTC-CTATA
* * *
25578 AAATTTTGATAACT-TTCTTATG
1 AAATTTTGATAAATCTTCCTATA
*
25600 AAATCTTGATAA
1 AAATTTTGATAA
25612 CTATAAATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
22 17 0.35
23 32 0.65
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCCTATA
Found at i:25610 original size:45 final size:45
Alignment explanation
Indices: 25486--25611 Score: 134
Period size: 45 Copynumber: 2.8 Consensus size: 45
25476 AATCACACTC
* *
25486 TAAAATTTTGAT-AATC-ACACTATGAAATTGTGAT-AACCTCGTTA
1 TAAAATTTTGATAAATCTTC-CTATGAAATT-TGATAAACCTCGCTA
* *
25530 TGAAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCGCTA
1 TAAAATTTTGATAAATCTTCCTATGAAA-TTTGATAAACCTCGCTA
* *
25576 TAAAATTTTGATAACT-TTCTTATGAAATCTTGATAA
1 TAAAATTTTGATAAATCTTCCTATGAAAT-TTGATAA
25612 CTATAAATTT
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
44 12 0.17
45 31 0.45
46 26 0.38
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.40
Consensus pattern (45 bp):
TAAAATTTTGATAAATCTTCCTATGAAATTTGATAAACCTCGCTA
Found at i:25647 original size:38 final size:39
Alignment explanation
Indices: 25573--25691 Score: 105
Period size: 38 Copynumber: 2.9 Consensus size: 39
25563 ATAAACCTCG
* * *
25573 CTATAAAATTTTGATAACTTTCTTATGAAATCTTGATAA
1 CTATAAAATTTTGATAACCTCCCTATGAAATCTTGATAA
** *
25612 CTAT-AAATTTTGATAACCTCCCTATGATTTTTTGATAA
1 CTATAAAATTTTGATAACCTCCCTATGAAATCTTGATAA
* * *
25650 CCTCATTATGAAATTTTGTTAATCTCCCTATGAAATTTTGAT
1 -CT-A-TA--AAATTTTGATAACCTCCCTATGAAATCTTGAT
25692 CTACATATTA
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
38 28 0.44
39 6 0.09
40 1 0.02
41 1 0.02
44 28 0.44
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (39 bp):
CTATAAAATTTTGATAACCTCCCTATGAAATCTTGATAA
Found at i:25813 original size:20 final size:20
Alignment explanation
Indices: 25768--25814 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
25758 AAGTTTCATA
25768 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
* * *
25788 TG-AATTTTTATATCTTCCT
1 TGAAATTTTGATATCCTCCC
25807 TGAAATTT
1 TGAAATTT
25815 AAATTACTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.49
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:25996 original size:44 final size:44
Alignment explanation
Indices: 25928--26071 Score: 128
Period size: 44 Copynumber: 3.3 Consensus size: 44
25918 CACATTTTTG
* ** * *
25928 AAAA-TTTGATAACCTCTTTATGAAATTTTGATAACCTCTTTAT
1 AAAATTTTGATAACCCCGCTATGAAATTTTGATAACCACATTAT
* * * * *
25971 AAAATTTTGTTGACCCCTCTATGAAATTCTGATAATCACATTAT
1 AAAATTTTGATAACCCCGCTATGAAATTTTGATAACCACATTAT
** * * * *
26015 GTAATTTTGATAACCTCGCTTTGAAATTTTGATAACAACACTAT
1 AAAATTTTGATAACCCCGCTATGAAATTTTGATAACCACATTAT
*
26059 GAAATTTTGATAA
1 AAAATTTTGATAA
26072 TCTTTCTATA
Statistics
Matches: 80, Mismatches: 20, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
43 4 0.05
44 76 0.95
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (44 bp):
AAAATTTTGATAACCCCGCTATGAAATTTTGATAACCACATTAT
Found at i:26042 original size:66 final size:66
Alignment explanation
Indices: 25945--26073 Score: 161
Period size: 66 Copynumber: 2.0 Consensus size: 66
25935 GATAACCTCT
* * * ** *
25945 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCTCTATGAAATTCTGATAATCAC
1 TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATCAC
26010 A
66 A
* * *
26011 TTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAACACTATGAAATTTTGATAATC
1 TTATGAAATTTTGATAACCTC-CTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATC
26074 TTTCTATAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
66 51 0.96
67 2 0.04
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (66 bp):
TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATCAC
A
Found at i:26080 original size:22 final size:22
Alignment explanation
Indices: 25926--26112 Score: 107
Period size: 22 Copynumber: 8.5 Consensus size: 22
25916 ATCACATTTT
*
25926 TGAAAATTTGATAACCTCTT-TA
1 TGAAATTTTGATAACCT-TTCTA
25948 TGAAATTTTGATAACCTCTT-TA
1 TGAAATTTTGATAACCT-TTCTA
* * * **
25970 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTTTCTA
* *
25992 TGAAATTCTGATAATCAC-AT-TA
1 TGAAATTTTGATAA-C-CTTTCTA
* ** *
26014 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCTTTCTA
****
26036 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTTTCTA
*
26058 TGAAATTTTGATAATCTTTCTA
1 TGAAATTTTGATAACCTTTCTA
*
26080 T-AAA-TTTGATAATCTGATCTCTA
1 TGAAATTTTGATAACCT--T-TCTA
26103 TGAAATTTTG
1 TGAAATTTTG
26113 GTACTCCTTA
Statistics
Matches: 129, Mismatches: 26, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
20 12 0.09
21 5 0.04
22 97 0.75
23 7 0.05
24 4 0.03
25 4 0.03
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTTCTA
Found at i:26200 original size:22 final size:22
Alignment explanation
Indices: 26150--26200 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
26140 TAACATTCAT
*
26150 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCACACC
* * *
26172 ATAAAATTTTGATAACCTCCCC
1 ATGAAATTTTGATAACCACACC
26194 ATGAAAT
1 ATGAAAT
26201 ATTTAATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACC
Found at i:26364 original size:24 final size:22
Alignment explanation
Indices: 26300--26464 Score: 84
Period size: 22 Copynumber: 7.3 Consensus size: 22
26290 TTGTGATAAT
*
26300 TAACC-ACCTTATGAAATTTCAA
1 TAACCAACC-TATGAAATTTTAA
* *
26322 TAACCAACCTAAGAGATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
26344 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTTAA
**
26368 TAACC-ACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* *
26390 TAACCAGTACACTATGGAATTTTGA
1 TAACCA--AC-CTATGAAATTTTAA
** *
26415 TAACC-TTCTCATGAAATTGTAA
1 TAACCAACCT-ATGAAATTTTAA
*** *
26437 TAACCATTTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
26459 TAACCA
1 TAACCA
26465 TATAGAGACA
Statistics
Matches: 115, Mismatches: 19, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
21 3 0.03
22 69 0.60
23 6 0.05
24 17 0.15
25 20 0.17
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:26382 original size:22 final size:23
Alignment explanation
Indices: 26354--26419 Score: 89
Period size: 25 Copynumber: 2.8 Consensus size: 23
26344 TAACCTGATC
26354 CTATGAAATTTTGGTAACC-ACA
1 CTATGAAATTTTGGTAACCAACA
26376 CTATGAAATTTTGGTAACCAGTACA
1 CTATGAAATTTTGGTAACCA--ACA
* *
26401 CTATGGAATTTTGATAACC
1 CTATGAAATTTTGGTAACC
26420 TTCTCATGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
22 19 0.49
25 20 0.51
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (23 bp):
CTATGAAATTTTGGTAACCAACA
Found at i:26661 original size:19 final size:19
Alignment explanation
Indices: 26630--26666 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
26620 TATTGAAATT
26630 TAAAAATTGAAATTAAAAG
1 TAAAAATTGAAATTAAAAG
26649 TAAAATATT-AAATTAAAA
1 TAAAA-ATTGAAATTAAAA
26667 AAATAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
TAAAAATTGAAATTAAAAG
Found at i:27015 original size:31 final size:31
Alignment explanation
Indices: 26980--27039 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
26970 TGGCAATTTA
* *
26980 GAAATATGTTTTAAAGAA-AAGGGTACAATTG
1 GAAATATATTTTAAA-AATAAGAGTACAATTG
27011 GAAATATATTTTAAAAATAAGAGTACAAT
1 GAAATATATTTTAAAAATAAGAGTACAAT
27040 CGAAAAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.50, C:0.03, G:0.17, T:0.30
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGAGTACAATTG
Found at i:30680 original size:7 final size:7
Alignment explanation
Indices: 30643--30678 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
30633 TGTTGACCAG
30643 AATCCAA
1 AATCCAA
30650 AATCCAA
1 AATCCAA
30657 AATCCAA
1 AATCCAA
*
30664 AACCCAA
1 AATCCAA
*
30671 ATTCCAA
1 AATCCAA
30678 A
1 A
30679 TTTATTTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.56, C:0.31, G:0.00, T:0.14
Consensus pattern (7 bp):
AATCCAA
Found at i:30946 original size:22 final size:21
Alignment explanation
Indices: 30919--30975 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
30909 TGCTACAACT
30919 TTTTTTTTAATTAAAATGATTC
1 TTTTTTTTAA-TAAAATGATTC
30941 TTTTTTGGTTAA-AAAATGATTC
1 TTTTTT--TTAATAAAATGATTC
* *
30963 TCTATTTTAATAA
1 TTTTTTTTAATAA
30976 TGGAGGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
20 4 0.13
21 2 0.07
22 20 0.67
24 4 0.13
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.54
Consensus pattern (21 bp):
TTTTTTTTAATAAAATGATTC
Found at i:39730 original size:19 final size:18
Alignment explanation
Indices: 39706--39745 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
39696 TTGAAGATTT
*
39706 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
39725 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
39743 ATT
1 ATT
39746 ATTTCAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:40375 original size:12 final size:11
Alignment explanation
Indices: 40344--40382 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
40334 TCACAATTTC
40344 TTTTCTTCTAT
1 TTTTCTTCTAT
40355 TTTTC-TCTAGT
1 TTTTCTTCTA-T
40366 TTTTCTTCTAAT
1 TTTTCTTCT-AT
40378 TTTTC
1 TTTTC
40383 CTAAGGGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 4 0.16
11 11 0.44
12 9 0.36
13 1 0.04
ACGTcount: A:0.10, C:0.18, G:0.03, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAT
Found at i:42725 original size:87 final size:88
Alignment explanation
Indices: 42508--42730 Score: 229
Period size: 87 Copynumber: 2.6 Consensus size: 88
42498 AATTTTTAGG
* * ** * *
42508 TGCAAATTCTGTGGAAACTGATAAGGTGGAGAATAGTTTGAATTC-AA-TTGAATGTGATCTTCC
1 TGCAAAATCTTTGGAAACTGATTTGGTGGAGAATAGTTTGAATTCAAATTTCAA-GTGACCTTCC
* * * *
42571 TAATGGAGTTATGGGTGGTTATGG
65 TAATGGAGTTATGAGTAGTAATGA
* * * *
42595 TGCAAAATCTTTGGAAAAT-ATTATGGTAGAGAACAGTTGGAATTCAAATTTCAA-TGACCTTCC
1 TGCAAAATCTTTGGAAACTGATT-TGGTGGAGAATAGTTTGAATTCAAATTTCAAGTGACCTTCC
*
42658 TAATGGAGTTATGATTAGTAATGA
65 TAATGGAGTTATGAGTAGTAATGA
* * * *
42682 TGCAAAATCTTTGGAAACTGATTTGGTGGTGGATATTTTGAATTTAAAT
1 TGCAAAATCTTTGGAAACTGATTTGGTGGAGAATAGTTTGAATTCAAAT
42731 CGGAGTGGTC
Statistics
Matches: 109, Mismatches: 23, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
86 2 0.02
87 98 0.90
88 5 0.05
89 4 0.04
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (88 bp):
TGCAAAATCTTTGGAAACTGATTTGGTGGAGAATAGTTTGAATTCAAATTTCAAGTGACCTTCCT
AATGGAGTTATGAGTAGTAATGA
Found at i:43833 original size:31 final size:31
Alignment explanation
Indices: 43775--43834 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
43765 TCAATAATGG
* *
43775 AGGGTGCAATGTGGAACAAAAACAAAATATT
1 AGGGTGCAAAGTGGAACAAAAAAAAAATATT
*
43806 AGGGTGCAAAGT-GATCAAAATAAAAAATA
1 AGGGTGCAAAGTGGAACAAAA-AAAAAATA
43835 AGGGCGTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.52, C:0.08, G:0.22, T:0.18
Consensus pattern (31 bp):
AGGGTGCAAAGTGGAACAAAAAAAAAATATT
Found at i:43838 original size:29 final size:30
Alignment explanation
Indices: 43775--43847 Score: 69
Period size: 29 Copynumber: 2.4 Consensus size: 30
43765 TCAATAATGG
* *
43775 AGGGTGCAATGTGGAACAAAAACAAAATATT
1 AGGGTGCAAAGT-GAACAAAAACAAAATATA
*
43806 AGGGTGCAAAGTGATCAAAATA-AAAA-ATA
1 AGGGTGCAAAGTGAACAAAA-ACAAAATATA
* *
43835 AGGGCGTAAAGTG
1 AGGGTGCAAAGTG
43848 GATCTCCATA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 13 0.36
30 11 0.31
31 12 0.33
ACGTcount: A:0.48, C:0.08, G:0.26, T:0.18
Consensus pattern (30 bp):
AGGGTGCAAAGTGAACAAAAACAAAATATA
Done.