Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011191.1 Corchorus capsularis cultivar CVL-1 contig11212, 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: 70029
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:559 original size:18 final size:17
Alignment explanation
Indices: 523--588 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 17
513 TGTATACATG
*
523 ATATATATATAGTACTATA
1 ATATAT-TATACTA-TATA
*
542 TTATATTATACATATATA
1 ATATATTATAC-TATATA
*
560 ATATATTATACTATAATGC
1 ATATATTATACTAT-AT-A
579 ATATATTATA
1 ATATATTATA
589 GGGCATATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 3 0.08
18 20 0.50
19 17 0.43
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (17 bp):
ATATATTATACTATATA
Found at i:699 original size:35 final size:35
Alignment explanation
Indices: 657--724 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
647 TATATTACCA
657 GATCAATCATAATTAATTTTCTTCAAAAAAAAAAT
1 GATCAATCATAATTAATTTTCTTCAAAAAAAAAAT
692 GATCAATCATAATTAATTTTCTTCAAAAAAAAA
1 GATCAATCATAATTAATTTTCTTCAAAAAAAAA
725 TTTATGATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.34
Consensus pattern (35 bp):
GATCAATCATAATTAATTTTCTTCAAAAAAAAAAT
Found at i:1032 original size:2 final size:2
Alignment explanation
Indices: 1025--1051 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1015 TTCTGGCCAA
1025 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
1052 GTTTGCAGCT
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:10663 original size:21 final size:20
Alignment explanation
Indices: 10637--10675 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
10627 TCATGAACAG
10637 CCACCGGCCTTTGTTGTTACT
1 CCACCGGCCTTTG-TGTTACT
10658 CCACCGGCCTTTGTGTTA
1 CCACCGGCCTTTGTGTTA
10676 AAAGTAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.10, C:0.33, G:0.21, T:0.36
Consensus pattern (20 bp):
CCACCGGCCTTTGTGTTACT
Found at i:12317 original size:73 final size:73
Alignment explanation
Indices: 12194--12340 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 73
12184 GTGTTTATGA
*
12194 ATGGAAAATACCATTGTAGGATTAGGCATAGGCCATTAAACCATTGAATAGATATGAATACTTAA
1 ATGGAAAATACCATTGTAGGATTAGGCATAGGCCATTAAACCATTAAATAGATATGAATACTTAA
12259 TGATGTGG
66 TGATGTGG
12267 ATGGAAAATACCATTGTAGGATTAGGCATAGGCCATTAAACCATTAAATAGATATGAATACTTAA
1 ATGGAAAATACCATTGTAGGATTAGGCATAGGCCATTAAACCATTAAATAGATATGAATACTTAA
12332 TGATGTGG
66 TGATGTGG
12340 A
1 A
12341 AAGTATCCGT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (73 bp):
ATGGAAAATACCATTGTAGGATTAGGCATAGGCCATTAAACCATTAAATAGATATGAATACTTAA
TGATGTGG
Found at i:16931 original size:50 final size:50
Alignment explanation
Indices: 16877--16975 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
16867 CGTGTCTATC
16877 TGTTTCATAAGAGTTAGCATAGAAGAATGTCTGCAGTTTATGTGCTCCCA
1 TGTTTCATAAGAGTTAGCATAGAAGAATGTCTGCAGTTTATGTGCTCCCA
*
16927 TGTTTCATAAGAGTTAGCATAGAAGAATGTCTGCGGTTTATGTGCTCCC
1 TGTTTCATAAGAGTTAGCATAGAAGAATGTCTGCAGTTTATGTGCTCCC
16976 CTTGTATAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.34
Consensus pattern (50 bp):
TGTTTCATAAGAGTTAGCATAGAAGAATGTCTGCAGTTTATGTGCTCCCA
Found at i:18481 original size:26 final size:27
Alignment explanation
Indices: 18452--18505 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
18442 GAATTATATC
18452 TTTT-GAGCAAAATTCTTTCAGTTGAT
1 TTTTAGAGCAAAATTCTTTCAGTTGAT
18478 TTTTAGAGCAAAATTCTTTCAGTTGAT
1 TTTTAGAGCAAAATTCTTTCAGTTGAT
18505 T
1 T
18506 AAAAGAGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (27 bp):
TTTTAGAGCAAAATTCTTTCAGTTGAT
Found at i:18512 original size:27 final size:27
Alignment explanation
Indices: 18456--18512 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
18446 TATATCTTTT
***
18456 GAGCAAAATTCTTTCAGTTGATTTTTA
1 GAGCAAAATTCTTTCAGTTGATTAAAA
18483 GAGCAAAATTCTTTCAGTTGATTAAAA
1 GAGCAAAATTCTTTCAGTTGATTAAAA
18510 GAG
1 GAG
18513 AACTGAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.37
Consensus pattern (27 bp):
GAGCAAAATTCTTTCAGTTGATTAAAA
Found at i:18947 original size:29 final size:31
Alignment explanation
Indices: 18894--18951 Score: 102
Period size: 29 Copynumber: 1.9 Consensus size: 31
18884 ATTTTGTCCC
18894 CTGAACTTGTACATTTTGGACGTTTTGCCTA
1 CTGAACTTGTACATTTTGGACGTTTTGCCTA
18925 CTGAACTT-TA-ATTTTGGACGTTTTGCC
1 CTGAACTTGTACATTTTGGACGTTTTGCC
18952 CCCTAAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 17 0.63
30 2 0.07
31 8 0.30
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (31 bp):
CTGAACTTGTACATTTTGGACGTTTTGCCTA
Found at i:21934 original size:14 final size:14
Alignment explanation
Indices: 21915--21945 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
21905 AAAAATAACA
21915 ATAATCATTTTCTT
1 ATAATCATTTTCTT
21929 ATAATCATTTTCTT
1 ATAATCATTTTCTT
21943 ATA
1 ATA
21946 TATTTCTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (14 bp):
ATAATCATTTTCTT
Found at i:29394 original size:57 final size:57
Alignment explanation
Indices: 29313--29438 Score: 164
Period size: 57 Copynumber: 2.2 Consensus size: 57
29303 CAAGAAATTG
* * *
29313 AAAAAAAAAAACCAAGCAACTACCAACCCGTTTGGCCCCATCTCTCTCTA-TTCAAA
1 AAAAAAAAAAACCAAGCAACTACCAACCCATTCGGCCCCACCTCTCTCTATTTCAAA
* * * *
29369 AAAAAAAAAAAGCAAGCAAACTACCAATCCATTCGGCCCCACCTTTTTCTATTTCAAA
1 AAAAAAAAAAACCAAGC-AACTACCAACCCATTCGGCCCCACCTCTCTCTATTTCAAA
29427 AAAAAAAGAAAA
1 AAAAAAA-AAAA
29439 AAAAGTAAGG
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
56 16 0.27
57 27 0.45
58 13 0.22
59 4 0.07
ACGTcount: A:0.47, C:0.27, G:0.07, T:0.19
Consensus pattern (57 bp):
AAAAAAAAAAACCAAGCAACTACCAACCCATTCGGCCCCACCTCTCTCTATTTCAAA
Found at i:29945 original size:58 final size:59
Alignment explanation
Indices: 29857--30247 Score: 546
Period size: 58 Copynumber: 6.7 Consensus size: 59
29847 AGCAATATCG
* * **
29857 ATCGAGCATCCCTCGGTCGCACGACCAAGTGGGCATCCCCCACTCATGTAATAAGA-CG
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGATAA
* *
29915 ATCGAGCATCCCTCGGTCGCACGGCCAAGTGGGCATCCCCCACTCATGGAATAA-ATAA
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGATAA
* *
29973 ATCGAGCATCCCTCGGTCACACGGCCCAGTGGGCATCCCCCACTCATGCAATAAGA-AA
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGATAA
* *
30031 ACCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCACACTCATGTAAT-AGATAA
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGATAA
* * *
30089 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCTACTCACGCAATAAGA-AA
1 ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGATAA
* *
30147 A-CGGAGCATCTCTCGGTCACACGGCCAAGTGGGCATCCCCCACCCATGTAATAA-ATAA
1 ATC-GAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGATAA
* * *
30205 ATCAAGCATCCCTCGGTCGCATGGCCCAA-TGGGCATCCCCCAC
1 ATCGAGCATCCCTCGGTCACACGG-CCAAGTGGGCATCCCCCAC
30248 ACGTGCAAGA
Statistics
Matches: 300, Mismatches: 25, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
57 6 0.02
58 285 0.95
59 9 0.03
ACGTcount: A:0.27, C:0.35, G:0.21, T:0.17
Consensus pattern (59 bp):
ATCGAGCATCCCTCGGTCACACGGCCAAGTGGGCATCCCCCACTCATGTAATAAGATAA
Found at i:30857 original size:29 final size:29
Alignment explanation
Indices: 30771--30890 Score: 136
Period size: 29 Copynumber: 4.2 Consensus size: 29
30761 GAAAGAAAAG
* *
30771 GTGGTAGTACGCCC-CCAAGGCTCACGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
* * * *
30799 GTGATAGCACTCCCTCCAAAGTTCTCGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
*
30828 GTGGTAGTACTCCCTCCAAAGCTCAAGAA
1 GTGGTAGTACTCCCTCCAAAGCTCACGAA
*
30857 GTGGTAGTACGT-CCTCCAAACCTCACGAA
1 GTGGTAGTAC-TCCCTCCAAAGCTCACGAA
*
30886 ATGGT
1 GTGGT
30891 TGTATTTGGA
Statistics
Matches: 76, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
28 11 0.14
29 64 0.84
30 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.21
Consensus pattern (29 bp):
GTGGTAGTACTCCCTCCAAAGCTCACGAA
Found at i:31002 original size:53 final size:54
Alignment explanation
Indices: 30943--31161 Score: 257
Period size: 53 Copynumber: 4.0 Consensus size: 54
30933 GCACCGTACA
*
30943 ACCATTTTGGTCGAGCGCCGTACA-ACCATCTTGGAAGAGAGCGCCGTACATCC
1 ACCATTTTGGACGAGCGCCGTACACACCATCTTGGAAGAGAGCGCCGTACATCC
*
30996 ACCATTTCGGACGAGCGCCGTACA-ACCATCTTGGAAGAGAGCGCCGTACATCC
1 ACCATTTTGGACGAGCGCCGTACACACCATCTTGGAAGAGAGCGCCGTACATCC
** * * *
31049 ACCATTTTGGACGAGCGTTGTACATCCACCATTTTGG-A-CGAGCGTCGTACATCC
1 ACCATTTTGGACGAGCGCCGTACA--CACCATCTTGGAAGAGAGCGCCGTACATCC
* * * *
31103 ACCATATTGGAAGAGAGCGCCGTACATCCACCATCTTGGATGAGAGCACCGTACATCC
1 ACCATTTTGG-A-CGAGCGCCGTACA--CACCATCTTGGAAGAGAGCGCCGTACATCC
31161 A
1 A
31162 TATTGGAAAA
Statistics
Matches: 142, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
53 72 0.51
54 23 0.16
55 2 0.01
56 31 0.22
58 14 0.10
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (54 bp):
ACCATTTTGGACGAGCGCCGTACACACCATCTTGGAAGAGAGCGCCGTACATCC
Found at i:31130 original size:29 final size:28
Alignment explanation
Indices: 30895--31161 Score: 247
Period size: 27 Copynumber: 9.9 Consensus size: 28
30885 AATGGTTGTA
30895 TTTGGACGAGAGCGCCGTACATCCACCAT
1 TTTGGA-GAGAGCGCCGTACATCCACCAT
* *
30924 TTTGGA-CGAGCACCGTACA---ACCAT
1 TTTGGAGAGAGCGCCGTACATCCACCAT
**
30948 TTTGG-TCGAGCGCCGTACA---ACCAT
1 TTTGGAGAGAGCGCCGTACATCCACCAT
*
30972 CTTGGAAGAGAGCGCCGTACATCCACCAT
1 TTTGG-AGAGAGCGCCGTACATCCACCAT
* *
31001 TTCGGA-CGAGCGCCGTACA---ACCAT
1 TTTGGAGAGAGCGCCGTACATCCACCAT
*
31025 CTTGGAAGAGAGCGCCGTACATCCACCAT
1 TTTGG-AGAGAGCGCCGTACATCCACCAT
* **
31054 TTTGGA-CGAGCGTTGTACATCCACCAT
1 TTTGGAGAGAGCGCCGTACATCCACCAT
* *
31081 TTTGGA-CGAGCGTCGTACATCCACCAT
1 TTTGGAGAGAGCGCCGTACATCCACCAT
*
31108 ATTGGAAGAGAGCGCCGTACATCCACCAT
1 TTTGG-AGAGAGCGCCGTACATCCACCAT
* *
31137 CTTGGATGAGAGCACCGTACATCCA
1 TTTGGA-GAGAGCGCCGTACATCCA
31162 TATTGGAAAA
Statistics
Matches: 202, Mismatches: 22, Indels: 28
0.80 0.09 0.11
Matches are distributed among these distances:
24 39 0.19
25 1 0.00
26 24 0.12
27 71 0.35
28 4 0.02
29 63 0.31
ACGTcount: A:0.26, C:0.30, G:0.24, T:0.21
Consensus pattern (28 bp):
TTTGGAGAGAGCGCCGTACATCCACCAT
Found at i:31315 original size:28 final size:28
Alignment explanation
Indices: 31284--31391 Score: 117
Period size: 28 Copynumber: 4.2 Consensus size: 28
31274 AAGATGGAGT
31284 GCTCCCAATGACCACGAAGCGGTAGTAC
1 GCTCCCAATGACCACGAAGCGGTAGTAC
31312 GCT-CCAAT--------AGCGGTAGTAC
1 GCTCCCAATGACCACGAAGCGGTAGTAC
*
31331 GCTCCCAACGACCACGAAGCGGTAGTAC
1 GCTCCCAATGACCACGAAGCGGTAGTAC
* * *
31359 GCTCCCAATGACCGCAAAGCGATAGTAC
1 GCTCCCAATGACCACGAAGCGGTAGTAC
31387 GCTCC
1 GCTCC
31392 AAAAGCGGTA
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
19 14 0.21
20 4 0.06
27 5 0.08
28 43 0.65
ACGTcount: A:0.28, C:0.33, G:0.24, T:0.15
Consensus pattern (28 bp):
GCTCCCAATGACCACGAAGCGGTAGTAC
Found at i:31398 original size:19 final size:19
Alignment explanation
Indices: 31374--31414 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
31364 CAATGACCGC
*
31374 AAAGCGATAGTACGCTCCA
1 AAAGCGATAGAACGCTCCA
*
31393 AAAGCGGTAGAACGCTCCA
1 AAAGCGATAGAACGCTCCA
31412 AAA
1 AAA
31415 AAAAAATCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.12
Consensus pattern (19 bp):
AAAGCGATAGAACGCTCCA
Found at i:32553 original size:25 final size:24
Alignment explanation
Indices: 32514--32560 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
32504 TCTGAACTTC
32514 AATTTTGGACATTTTGCCCCCTGA
1 AATTTTGGACATTTTGCCCCCTGA
*
32538 AATTTTGGGACGTTTTGCCCCCT
1 AATTTT-GGACATTTTGCCCCCT
32561 CAGCCTAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (24 bp):
AATTTTGGACATTTTGCCCCCTGA
Found at i:41285 original size:3 final size:3
Alignment explanation
Indices: 41277--41305 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
41267 GTAAGGCAAA
41277 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41306 ATAAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:45729 original size:19 final size:18
Alignment explanation
Indices: 45696--45731 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
45686 TTGAAATAAT
45696 TCTTCAATAATCTTCAAA
1 TCTTCAATAATCTTCAAA
*
45714 TCTTCAAATTATCTTCAA
1 TCTTC-AATAATCTTCAA
45732 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAA
Found at i:52872 original size:14 final size:14
Alignment explanation
Indices: 52853--52880 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52843 CTTTGATATT
52853 TTTGGAGATGGAAA
1 TTTGGAGATGGAAA
52867 TTTGGAGATGGAAA
1 TTTGGAGATGGAAA
52881 ATGGAGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (14 bp):
TTTGGAGATGGAAA
Found at i:61571 original size:22 final size:20
Alignment explanation
Indices: 61546--61595 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
61536 AACATTTGAG
61546 TTATATAAATATTAAAATAAAA
1 TTATA-AAATATTAAAA-AAAA
*
61568 TTATGAAAATA-TATAAAAAA
1 TTAT-AAAATATTAAAAAAAA
61588 TTATAAAA
1 TTATAAAA
61596 AAATTATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.15
20 8 0.31
21 4 0.15
22 9 0.35
23 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
TTATAAAATATTAAAAAAAA
Found at i:63662 original size:58 final size:58
Alignment explanation
Indices: 63593--63702 Score: 211
Period size: 58 Copynumber: 1.9 Consensus size: 58
63583 TTACAAAATT
*
63593 TGTTTCTGAGTTCTATTATGAGAGAGAGTTTAAGTCAATGTTTATAGGGTTATCCAAG
1 TGTTTCTGAGTTCTATTATGAGAGAGAGTTTAAGTCAATATTTATAGGGTTATCCAAG
63651 TGTTTCTGAGTTCTATTATGAGAGAGAGTTTAAGTCAATATTTATAGGGTTA
1 TGTTTCTGAGTTCTATTATGAGAGAGAGTTTAAGTCAATATTTATAGGGTTA
63703 CACAGACAGG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (58 bp):
TGTTTCTGAGTTCTATTATGAGAGAGAGTTTAAGTCAATATTTATAGGGTTATCCAAG
Found at i:69411 original size:139 final size:139
Alignment explanation
Indices: 69161--69485 Score: 508
Period size: 139 Copynumber: 2.3 Consensus size: 139
69151 CTTTGATTAC
69161 ATAATCATCAATCAATTACAACTTTGATTGGCAAAATTAACTAACGACATATTCAATAATTTATT
1 ATAATCATCAATCAATTACAACTTTGATTGGCAAAATTAACTAACGACATATTCAATAATTTATT
* * *
69226 TTTTTGTAACATAATTACTAATTGATTTATTTATTTATGGTAA-TTTTTTCGTGGCGATTTTATG
66 TTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATTTTTTTCGTAGCGA-TTAATG
*
69290 GTAAAATCAT
130 GTAAAATCAA
* * *
69300 ATAATCATCAATCAATTACAACTTTGATTGACAAAATTAACTAACGACATGTTGAATAATTTATT
1 ATAATCATCAATCAATTACAACTTTGATTGGCAAAATTAACTAACGACATATTCAATAATTTATT
* * * *
69365 TTTTGGTAACATAATTATTAATTGATTTATTTCTTTATGTTAATTTTTTTGGTAGCGATTAATGG
66 TTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATTTTTTTCGTAGCGATTAATGG
*
69430 TAAAATTAA
131 TAAAATCAA
* *
69439 ATAATTATCAATCAATTACGACTTTGATTGGCAAAATTAACTAACGA
1 ATAATCATCAATCAATTACAACTTTGATTGGCAAAATTAACTAACGA
69486 TCACTAACTT
Statistics
Matches: 170, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
139 158 0.93
140 12 0.07
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.42
Consensus pattern (139 bp):
ATAATCATCAATCAATTACAACTTTGATTGGCAAAATTAACTAACGACATATTCAATAATTTATT
TTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATTTTTTTCGTAGCGATTAATGG
TAAAATCAA
Found at i:69669 original size:20 final size:20
Alignment explanation
Indices: 69644--69681 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
69634 ATTTAGTGAA
69644 TTACTAAATACCGCCCCCTT
1 TTACTAAATACCGCCCCCTT
**
69664 TTACTAGCTACCGCCCCC
1 TTACTAAATACCGCCCCC
69682 CTTTGGACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.45, G:0.08, T:0.26
Consensus pattern (20 bp):
TTACTAAATACCGCCCCCTT
Found at i:69691 original size:22 final size:20
Alignment explanation
Indices: 69652--69691 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
69642 AATTACTAAA
*
69652 TACCGCCCCCTTTTACTAGC
1 TACCGCCCCCTTTGACTAGC
69672 TACCGCCCCCCTTTGGACTA
1 TACCG-CCCCCTTT-GACTA
69692 TTTTGCCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.45, G:0.12, T:0.28
Consensus pattern (20 bp):
TACCGCCCCCTTTGACTAGC
Found at i:69882 original size:29 final size:29
Alignment explanation
Indices: 69827--69884 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
69817 TTTTTGGATT
* *
69827 GAAAGTATGTTTTTTTTAACAAAAAAAAA
1 GAAAGTATGTTTTTTTAAAAAAAAAAAAA
69856 GAAAGTATG-TTTTTTAAAAAAATAAAAAA
1 GAAAGTATGTTTTTTTAAAAAAA-AAAAAA
69885 TAAATATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (29 bp):
GAAAGTATGTTTTTTTAAAAAAAAAAAAA
Done.