Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006949.1 Corchorus capsularis cultivar CVL-1 contig06970, 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: 33499
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:55 original size:17 final size:17
Alignment explanation
Indices: 33--70 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
23 TTTTTTAATC
*
33 ATAAATTATTCCATTAT
1 ATAAATTATTACATTAT
*
50 ATAAATTATTAGATTAT
1 ATAAATTATTACATTAT
67 ATAA
1 ATAA
71 TACGTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (17 bp):
ATAAATTATTACATTAT
Found at i:1192 original size:22 final size:22
Alignment explanation
Indices: 1167--1292 Score: 114
Period size: 22 Copynumber: 5.7 Consensus size: 22
1157 ATCAAAGAGA
* *
1167 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
1189 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
*
1211 TTAACAAAATTTCATTAG-GAGG
1 TTATCAAAATTTCA-TAGTGAGG
* * *
1233 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
* * *
1255 TTATCAAAATTTTATAATGTGG
1 TTATCAAAATTTCATAGTGAGG
1277 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
1293 TAAATGTTAT
Statistics
Matches: 84, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
21 5 0.06
22 73 0.87
23 6 0.07
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:1547 original size:21 final size:22
Alignment explanation
Indices: 1471--1550 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
1461 CAAAATATGA
* *
1471 TTATCAGAATTTCATAGAG-GAG
1 TTATCAAAATTTCATAAAGAG-G
* * *
1493 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
*
1515 TTATCAAAATTTCATTAAGAGG
1 TTATCAAAATTTCATAAAGAGG
*
1537 TTATCAAATTTTCA
1 TTATCAAAATTTCA
1551 AAATGTGATT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
22 46 0.98
23 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGG
Found at i:1792 original size:22 final size:22
Alignment explanation
Indices: 1657--2125 Score: 222
Period size: 22 Copynumber: 21.6 Consensus size: 22
1647 TATGGAGTAC
* *
1657 TCAAAATTTC--AGGGAGGATA
1 TCAAAATTTCATAGTGAGGTTA
* *
1677 TCAAAATTTCATAGTTTA-GTTT
1 TCAAAATTTCATAG-TGAGGTTA
* *
1699 TCAAATTTTCATA-AGAGGGTTA
1 TCAAAATTTCATAGTGA-GGTTA
* * * *
1721 TCCAAATTTCATAG-CATGTAGA
1 TCAAAATTTCATAGTGAGGT-TA
* **
1743 TCAAAATTTCATAGGGAGAATA
1 TCAAAATTTCATAGTGAGGTTA
** *
1765 AAAAAATTTCATAATGAGGTTA
1 TCAAAATTTCATAGTGAGGTTA
**
1787 TCAAAAAATCATAGTGAGGTTA
1 TCAAAATTTCATAGTGAGGTTA
1809 TCAAAA-TT--T-GT-A-GTTA
1 TCAAAATTTCATAGTGAGGTTA
* * *
1825 TCAAGATTTCATAAG-AAAGTTA
1 TCAAAATTTCAT-AGTGAGGTTA
* *
1847 TCAAAATTTTATAGGGAGGTTTA
1 TCAAAATTTCATAGTGAGG-TTA
* *
1870 TCAAACTTT-ATAG-GAAGATTTA
1 TCAAAATTTCATAGTG-AG-GTTA
1892 TCAAAATTTCATAGTGAGGTTA
1 TCAAAATTTCATAGTGAGGTTA
* * *
1914 TCACAATTTCATAGTGTGATTA
1 TCAAAATTTCATAGTGAGGTTA
* * *
1936 TCAAAATTTCAGAGTGCGATTA
1 TCAAAATTTCATAGTGAGGTTA
* *
1958 -CTAACAA-TTCATA-TGGAGCTTT
1 TC-AA-AATTTCATAGT-GAGGTTA
* * ** *
1980 TTAAATTTTCATAACGTGGTTA
1 TCAAAATTTCATAGTGAGGTTA
*
2002 TCAATATATT-ATA-TGGAGGTTA
1 TCAAAAT-TTCATAGT-GAGGTTA
* * *
2024 TCAACATCTCATAGTGTTGGTTA
1 TCAAAATTTCATAGTG-AGGTTA
* * *
2047 TCAAAATTTCATTGGGAAGTTA
1 TCAAAATTTCATAGTGAGGTTA
*
2069 TCAAAATTTCATATTGAGGTCT-
1 TCAAAATTTCATAGTGAGGT-TA
* * *
2091 TCAAAATTCCTTAGGGAGGTTA
1 TCAAAATTTCATAGTGAGGTTA
*
2113 ACAAAATTTCATA
1 TCAAAATTTCATA
2126 AGAAGGTTAA
Statistics
Matches: 334, Mismatches: 81, Indels: 66
0.69 0.17 0.14
Matches are distributed among these distances:
16 9 0.03
17 3 0.01
18 2 0.01
19 2 0.01
20 11 0.03
21 13 0.04
22 251 0.75
23 42 0.13
24 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (22 bp):
TCAAAATTTCATAGTGAGGTTA
Found at i:1938 original size:44 final size:45
Alignment explanation
Indices: 1844--1951 Score: 125
Period size: 45 Copynumber: 2.4 Consensus size: 45
1834 CATAAGAAAG
* *
1844 TTATCAAAATTTTATAGGGAGGTTTATCAAACTTTATAGGAAGAT
1 TTATCAAAATTTCATAGTGAGGTTTATCAAACTTTATAGGAAGAT
*
1889 TTATCAAAATTTCATAGTGAGG-TTATCACAA-TTTCATAGTG-TGA-
1 TTATCAAAATTTCATAGTGAGGTTTATCA-AACTTT-ATAG-GAAGAT
*
1933 TTATCAAAATTTCAGAGTG
1 TTATCAAAATTTCATAGTG
1952 CGATTACTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
44 27 0.48
45 28 0.50
46 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (45 bp):
TTATCAAAATTTCATAGTGAGGTTTATCAAACTTTATAGGAAGAT
Found at i:2148 original size:22 final size:22
Alignment explanation
Indices: 2107--2148 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2097 TTCCTTAGGG
* * *
2107 AGGTTAACAAAATTTCATAAGA
1 AGGTTAAAAAAAATTAATAAGA
2129 AGGTTAAAAAAAATTAATAA
1 AGGTTAAAAAAAATTAATAA
2149 AAAGATTCTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.05, G:0.12, T:0.26
Consensus pattern (22 bp):
AGGTTAAAAAAAATTAATAAGA
Found at i:9651 original size:22 final size:22
Alignment explanation
Indices: 9626--9849 Score: 112
Period size: 22 Copynumber: 10.1 Consensus size: 22
9616 TTAATTGTTA
*
9626 ATAATCACACTCTGAAATTTTG
1 ATAATCACACTATGAAATTTTG
*
9648 ATAATCACACTATGAAATTGTG
1 ATAATCACACTATGAAATTTTG
* * *
9670 ATAACCACGCTATAAAATTTTG
1 ATAATCACACTATGAAATTTTG
* * * *
9692 ATAAACCTCCCTATAAAATTTTG
1 AT-AATCACACTATGAAATTTTG
** * *
9715 ATAACTTTC-TTATGAAATCTTG
1 ATAA-TCACACTATGAAATTTTG
* * * ***
9737 ATAACCTCCCTATGTTTTTTTG
1 ATAATCACACTATGAAATTTTG
* * * *
9759 ATAACCTCATTATGAAATGTTG
1 ATAATCACACTATGAAATTTTG
* * *
9781 TTAATCTCCCTATGAAATTTTG
1 ATAATCACACTATGAAATTTTG
* **
9803 ATAA-CCCTTTTATGAAATTTTG
1 ATAATCAC-ACTATGAAATTTTG
* *
9825 A-AAACTAAACTATGAAATTTTG
1 ATAATC-ACACTATGAAATTTTG
9847 ATA
1 ATA
9850 TCCTCCTTGA
Statistics
Matches: 156, Mismatches: 39, Indels: 13
0.75 0.19 0.06
Matches are distributed among these distances:
21 6 0.04
22 127 0.81
23 23 0.15
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
ATAATCACACTATGAAATTTTG
Found at i:9758 original size:44 final size:43
Alignment explanation
Indices: 9638--9849 Score: 149
Period size: 44 Copynumber: 4.8 Consensus size: 43
9628 AATCACACTC
* * * * * ** *
9638 TGAAATTTTGATAATCACACTATGAAATTGTGATAACCACGCTA
1 TGAAATCTTGATAACCTCCCTATGAAATTTTGATAACTTC-TTA
* * *
9682 TAAAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTCTTA
1 TGAAATCTTGAT-AACCTCCCTATGAAATTTTGATAAC-TTCTTA
*** *
9727 TGAAATCTTGATAACCTCCCTATGTTTTTTTGATAACCTCATTA
1 TGAAATCTTGATAACCTCCCTATGAAATTTTGATAACTTC-TTA
* * *
9771 TGAAATGTTGTTAATCTCCCTATGAAATTTTGATAACCCTT-TTA
1 TGAAATCTTGATAACCTCCCTATGAAATTTTGATAA--CTTCTTA
* * **
9815 TGAAATTTTGA-AAACTAAACTATGAAATTTTGATA
1 TGAAATCTTGATAACCT-CCCTATGAAATTTTGATA
9850 TCCTCCTTGA
Statistics
Matches: 134, Mismatches: 28, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
43 6 0.04
44 93 0.69
45 32 0.24
46 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (43 bp):
TGAAATCTTGATAACCTCCCTATGAAATTTTGATAACTTCTTA
Found at i:9999 original size:22 final size:22
Alignment explanation
Indices: 9974--10098 Score: 96
Period size: 22 Copynumber: 5.7 Consensus size: 22
9964 AATCACATTT
*
9974 TGAAAATTTGATAACCTTTTTA
1 TGAAAATTTGATAACCTCTTTA
*
9996 TGAAATTTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* *
10018 T-AAAATTTTGTTGACC-CTTCTA
1 TGAAAA-TTTGATAACCTCTT-TA
* * *
10040 TG-AAATTCTGATAATCACATTA
1 TGAAAATT-TGATAACCTCTTTA
* *
10062 TGTAATTTTGATAACCTCGTTT-
1 TGAAAATTTGATAACCTC-TTTA
*
10084 TGAAATTTTGATAAC
1 TGAAAATTTGATAAC
10099 AACACTATGA
Statistics
Matches: 82, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
21 8 0.10
22 66 0.80
23 8 0.10
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:10069 original size:44 final size:44
Alignment explanation
Indices: 9949--10119 Score: 161
Period size: 44 Copynumber: 3.9 Consensus size: 44
9939 AGAAATACCA
* * *
9949 CTATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTTT
1 CTATGAAA-TTTTGATAATCACATTATGAAATTTTGATAACCCTT
* * * * * * *
9993 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCTT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCTT
* *
10037 CTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCGTT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACC-C-TT
*
10083 -T-TGAAATTTTGATAA-CAACACTATGAAATTTTGATAA
1 CTATGAAATTTTGATAATC-ACATTATGAAATTTTGATAA
10120 TCTGATCTCT
Statistics
Matches: 101, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
43 6 0.06
44 91 0.90
45 2 0.02
46 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCTT
Found at i:10107 original size:66 final size:66
Alignment explanation
Indices: 9993--10121 Score: 163
Period size: 66 Copynumber: 2.0 Consensus size: 66
9983 GATAACCTTT
* * * *
9993 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCTTCTATGAAATTCTGATAATCAC
1 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGATAACACTACTATGAAATTCTGATAATCAC
10058 A
66 A
* * *
10059 TTATGTAATTTTGATAACCTCGTTT-TGAAATTTTGATAACAAC-ACTATGAAATTTTGATAATC
1 TTATGAAATTTTGATAACCTC-TTTATAAAATTTTGATAAC-ACTACTATGAAATTCTGATAATC
10122 TGATCTCTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
66 50 0.93
67 4 0.07
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (66 bp):
TTATGAAATTTTGATAACCTCTTTATAAAATTTTGATAACACTACTATGAAATTCTGATAATCAC
A
Found at i:10109 original size:22 final size:21
Alignment explanation
Indices: 10037--10119 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 21
10027 GTTGACCCTT
*
10037 CTATGAAATTCTGATAATCACA
1 CTATGAAATTTTGATAA-CACA
* * *
10059 TTATGTAATTTTGATAAC-CT
1 CTATGAAATTTTGATAACACA
*
10079 CGTTTTGAAATTTTGATAACAACA
1 C--TATGAAATTTTGATAAC-ACA
10103 CTATGAAATTTTGATAA
1 CTATGAAATTTTGATAA
10120 TCTGATCTCT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 44 0.92
24 2 0.04
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (21 bp):
CTATGAAATTTTGATAACACA
Found at i:10112 original size:88 final size:88
Alignment explanation
Indices: 9949--10115 Score: 212
Period size: 88 Copynumber: 1.9 Consensus size: 88
9939 AGAAATACCA
* * * **
9949 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTTTTTATGAAATTTTGATAACCTC
1 CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTGTTTATGAAATTTTGATAACAAC
**
10014 TTTATAAAATTTTGTTGACCCTT
66 ACTATAAAATTTTGTTGACCCTT
* *
10037 CTATGAAA-TTCTGATAATCACATTATGTAATTTTGATAACCTCGTTT-TGAAATTTTGATAACA
1 CTATGAAATTTCTG-TAATCACATTATGAAAATTTGATAACCT-GTTTATGAAATTTTGATAACA
*
10100 ACACTATGAAATTTTG
64 ACACTATAAAATTTTG
10116 ATAATCTGAT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 4 0.06
88 60 0.90
89 3 0.04
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.44
Consensus pattern (88 bp):
CTATGAAATTTCTGTAATCACATTATGAAAATTTGATAACCTGTTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTTGACCCTT
Found at i:10270 original size:22 final size:22
Alignment explanation
Indices: 10220--10340 Score: 74
Period size: 22 Copynumber: 5.5 Consensus size: 22
10210 TAACCTTCAT
* *
10220 ATGATATTTTGATAACCACACT-
1 ATGAAATTTTGATAACCTC-CTA
* *
10242 ATAAAATTTTGATAACCTCCTC
1 ATGAAATTTTGATAACCTCCTA
* *
10264 GTGAAATATT-AGTAACCTCCTA
1 ATGAAATTTTGA-TAACCTCCTA
*
10286 ATGAAATTTTGTTAA-CTACACT-
1 ATGAAATTTTGATAACCT-C-CTA
10308 ATGAAATTCTT-ATAACCTCTCT-
1 ATGAAATT-TTGATAACCTC-CTA
*
10330 ATGATATTTTG
1 ATGAAATTTTG
10341 TTAATCTCTT
Statistics
Matches: 78, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
21 7 0.09
22 65 0.83
23 6 0.08
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCCTA
Found at i:10427 original size:22 final size:22
Alignment explanation
Indices: 10378--10427 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
10368 AATCGTGATA
*
10378 ATTAACCACCCTAAGAAATTTC
1 ATTAACCAACCTAAGAAATTTC
* *
10400 AATAACCAACCTAAGAAATTTT
1 ATTAACCAACCTAAGAAATTTC
10422 ATTAAC
1 ATTAAC
10428 TTGATCCAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (22 bp):
ATTAACCAACCTAAGAAATTTC
Found at i:10452 original size:46 final size:45
Alignment explanation
Indices: 10402--10517 Score: 134
Period size: 44 Copynumber: 2.6 Consensus size: 45
10392 GAAATTTCAA
10402 TAACCAAC-CTAAGAAATTTT-ATTAACTTGATCCA-ATGAAATTTTGG
1 TAACCAACACTAAGAAATTTTGA-TAAC-T--TCCATATGAAATTTTGG
*
10448 TAACC-ACACTATGAAATTTTGATAACTTCCATATGAAATTTTGG
1 TAACCAACACTAAGAAATTTTGATAACTTCCATATGAAATTTTGG
* *
10492 TAACC-ACACTATGGAATTTTGATAAC
1 TAACCAACACTAAGAAATTTTGATAAC
10518 CTCCTCGTGA
Statistics
Matches: 65, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
43 4 0.06
44 37 0.57
45 3 0.05
46 20 0.31
47 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.34
Consensus pattern (45 bp):
TAACCAACACTAAGAAATTTTGATAACTTCCATATGAAATTTTGG
Found at i:10464 original size:22 final size:22
Alignment explanation
Indices: 10436--10561 Score: 109
Period size: 22 Copynumber: 5.7 Consensus size: 22
10426 ACTTGATCCA
*
10436 ATGAAATTTTGGTAACCACACT
1 ATGAAATTTTGATAACCACACT
10458 ATGAAATTTTGATAACTTC-CA-T
1 ATGAAATTTTGATAAC--CACACT
*
10480 ATGAAATTTTGGTAACCACACT
1 ATGAAATTTTGATAACCACACT
* *
10502 ATGGAATTTTGATAACCTC-CT
1 ATGAAATTTTGATAACCACACT
* * *
10523 CGTGAAATTATAATAA-CA-ATCTT
1 -ATGAAATTTTGATAACCACA-C-T
10546 ATGAAATTTTGATAAC
1 ATGAAATTTTGATAAC
10562 TACATAGAGA
Statistics
Matches: 82, Mismatches: 13, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
20 1 0.01
21 5 0.06
22 72 0.88
23 3 0.04
24 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACT
Found at i:10531 original size:44 final size:44
Alignment explanation
Indices: 10432--10521 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 44
10422 ATTAACTTGA
*
10432 TCCA-ATGAAATTTTGGTAACCACACTATGAAATTTTGATAACT
1 TCCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACC
*
10475 TCCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC
1 TCCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACC
10519 TCC
1 TCC
10522 TCGTGAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
43 4 0.09
44 40 0.91
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (44 bp):
TCCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACC
Found at i:11896 original size:30 final size:30
Alignment explanation
Indices: 11833--11898 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
11823 AGCAAGTTAA
* *
11833 AAATATGTTTTCAAAAAATGGTACAATTGG
1 AAATATGTTTTCAAAAAAAGGTACAATTCG
11863 AAATATG-TTTCAAAAATAAGGATACAA-TCG
1 AAATATGTTTTCAAAAA-AAGG-TACAATTCG
11893 AAATAT
1 AAATAT
11899 ATAAAGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 9 0.28
30 18 0.56
31 5 0.16
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.30
Consensus pattern (30 bp):
AAATATGTTTTCAAAAAAAGGTACAATTCG
Found at i:12933 original size:108 final size:108
Alignment explanation
Indices: 12739--12954 Score: 405
Period size: 108 Copynumber: 2.0 Consensus size: 108
12729 GTCAAATGTC
12739 CAAATTGGACCTAAACCTTTCGCGAGCTGCTCAATTTGAGTTTAAACCTTTAAGTTGAACCAAAT
1 CAAATTGGACCTAAACCTTTCGCGAGCTGCTCAATTTGAGTTTAAACCTTTAAGTTGAACCAAAT
*
12804 TGAGCCTAAACCTTTTCTAGATGCACCAAATTGGGCCTAAATT
66 TGAGCCTAAACCTTTTCTAGATGCACCAAATTGGACCTAAATT
12847 CAAATTGGACCTAAACCTTTCGCGAGCTGCTCAATTTGAGTTTAAACCTTTAAGTTGAACCAAAT
1 CAAATTGGACCTAAACCTTTCGCGAGCTGCTCAATTTGAGTTTAAACCTTTAAGTTGAACCAAAT
* *
12912 TGAGGCTAAACCTTTTTTAGATGCACCAAATTGGACCTAAATT
66 TGAGCCTAAACCTTTTCTAGATGCACCAAATTGGACCTAAATT
12955 TGATAGACGT
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 105 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (108 bp):
CAAATTGGACCTAAACCTTTCGCGAGCTGCTCAATTTGAGTTTAAACCTTTAAGTTGAACCAAAT
TGAGCCTAAACCTTTTCTAGATGCACCAAATTGGACCTAAATT
Found at i:13288 original size:21 final size:22
Alignment explanation
Indices: 13264--13309 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
13254 TTGAAAGAGC
13264 CCCAAATTTCTCAATT-AAAAA
1 CCCAAATTTCTCAATTAAAAAA
*
13285 CCC-ATTTTCTCAATTAAAAAA
1 CCCAAATTTCTCAATTAAAAAA
13306 CCCA
1 CCCA
13310 TGTTGAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.43, C:0.28, G:0.00, T:0.28
Consensus pattern (22 bp):
CCCAAATTTCTCAATTAAAAAA
Found at i:13295 original size:20 final size:21
Alignment explanation
Indices: 13270--13310 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
13260 GAGCCCCAAA
13270 TTTCTCAATT-AAAAACCCAT
1 TTTCTCAATTAAAAAACCCAT
13290 TTTCTCAATTAAAAAACCCAT
1 TTTCTCAATTAAAAAACCCAT
13311 GTTGAAAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.34
Consensus pattern (21 bp):
TTTCTCAATTAAAAAACCCAT
Found at i:16310 original size:19 final size:18
Alignment explanation
Indices: 16273--16312 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
16263 TTCTTGAAAT
*
16273 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
16291 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
16310 AAT
1 AAT
16313 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:17507 original size:53 final size:53
Alignment explanation
Indices: 17395--17495 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 53
17385 TATTTGAATG
* ** *
17395 TTTTGAAAAGACTTAAATTGAACACTTTGAAAACTTTGATGGGAACTTTCCCA
1 TTTTGAAAAGACCTAAATTGAACACTTTGAAAACTTTGATGAAAAATTTCCCA
* *
17448 ATTTGAAAAGACCTAAATTGAATACTTTGAAAAC-TTGATGAAAAATTT
1 TTTTGAAAAGACCTAAATTGAACACTTTGAAAACTTTGATGAAAAATTT
17496 TTGATTTTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
52 11 0.26
53 31 0.74
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.34
Consensus pattern (53 bp):
TTTTGAAAAGACCTAAATTGAACACTTTGAAAACTTTGATGAAAAATTTCCCA
Found at i:18587 original size:19 final size:19
Alignment explanation
Indices: 18563--18602 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
18553 AACTTAACTT
18563 ATCATAATATAATAGCAAA
1 ATCATAATATAATAGCAAA
18582 ATCATAATATAATAGCAAA
1 ATCATAATATAATAGCAAA
18601 AT
1 AT
18603 TAATTCGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (19 bp):
ATCATAATATAATAGCAAA
Found at i:23766 original size:24 final size:24
Alignment explanation
Indices: 23739--23787 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
23729 CTGGTTTTTG
*
23739 TTTCTGTTGTCATTTGTTTACCCC
1 TTTCTGCTGTCATTTGTTTACCCC
*
23763 TTTCTGCTGTCATTTGTTTTCCCC
1 TTTCTGCTGTCATTTGTTTACCCC
23787 T
1 T
23788 GCTTCAGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.06, C:0.27, G:0.12, T:0.55
Consensus pattern (24 bp):
TTTCTGCTGTCATTTGTTTACCCC
Found at i:25018 original size:14 final size:14
Alignment explanation
Indices: 24999--25041 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
24989 CATGGTATAA
24999 CTTATTTTCATATG
1 CTTATTTTCATATG
* *
25013 CTTATTTTTATATT
1 CTTATTTTCATATG
25027 CTT-TTTTCAT-TG
1 CTTATTTTCATATG
25039 CTT
1 CTT
25042 TGGACATTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 4 0.16
13 6 0.24
14 15 0.60
ACGTcount: A:0.16, C:0.14, G:0.05, T:0.65
Consensus pattern (14 bp):
CTTATTTTCATATG
Found at i:29444 original size:17 final size:17
Alignment explanation
Indices: 29394--29445 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
29384 ATCTTTCTCA
* *
29394 TTCTCCATATTCTCTTC
1 TTCTTCATATTCTCTTG
29411 TTCTTCATATTCTCTTG
1 TTCTTCATATTCTCTTG
29428 TTCTCTCA-ATTCTCTTG
1 TTCT-TCATATTCTCTTG
29445 T
1 T
29446 CTTTTTCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 29 0.91
18 3 0.09
ACGTcount: A:0.12, C:0.29, G:0.04, T:0.56
Consensus pattern (17 bp):
TTCTTCATATTCTCTTG
Found at i:29700 original size:30 final size:31
Alignment explanation
Indices: 29641--29710 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 31
29631 ACAAAGTTTA
* * *
29641 TTTAACATGCATAATCTCGTCTTCTACCTTTG
1 TTTATCATGCATAATCTCG-CTCCTACCTTTC
29673 TTTATCATGCATAATCTC-CTCCTACCTTTC
1 TTTATCATGCATAATCTCGCTCCTACCTTTC
29703 TTTATCAT
1 TTTATCAT
29711 TAAAAATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 18 0.51
32 17 0.49
ACGTcount: A:0.21, C:0.27, G:0.06, T:0.46
Consensus pattern (31 bp):
TTTATCATGCATAATCTCGCTCCTACCTTTC
Found at i:29790 original size:36 final size:35
Alignment explanation
Indices: 29743--29908 Score: 225
Period size: 33 Copynumber: 4.8 Consensus size: 35
29733 ACTACCTTAT
*
29743 ATATTAGTGGCATCTGAAGTTGTCACATGATCAAGA
1 ATATTAGTGGCACCTGAAGTTGTCACAT-ATCAAGA
*
29779 ATATTAGTGGCACCTGAAGTTGTCAC--ATCAAGC
1 ATATTAGTGGCACCTGAAGTTGTCACATATCAAGA
*
29812 ATAGTAGTGGCACCTGAAGTTGTCACATGATCAAGA
1 ATATTAGTGGCACCTGAAGTTGTCACAT-ATCAAGA
*
29848 ATATTAGTGGCACCTGAAATTGTCAC--ATCAA-A
1 ATATTAGTGGCACCTGAAGTTGTCACATATCAAGA
*
29880 CATATTAGTGACACCTGAAGTTGTCACAT
1 -ATATTAGTGGCACCTGAAGTTGTCACAT
29909 CAAAGAAATA
Statistics
Matches: 116, Mismatches: 8, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
32 1 0.01
33 60 0.52
36 55 0.47
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (35 bp):
ATATTAGTGGCACCTGAAGTTGTCACATATCAAGA
Found at i:29858 original size:69 final size:69
Alignment explanation
Indices: 29747--29908 Score: 279
Period size: 69 Copynumber: 2.3 Consensus size: 69
29737 CCTTATATAT
* * *
29747 TAGTGGCATCTGAAGTTGTCACATGATCAAGAATATTAGTGGCACCTGAAGTTGTCACATCAAGC
1 TAGTGGCACCTGAAGTTGTCACATGATCAAGAATATTAGTGGCACCTGAAATTGTCACATCAAAC
29812 ATAG
66 ATAG
29816 TAGTGGCACCTGAAGTTGTCACATGATCAAGAATATTAGTGGCACCTGAAATTGTCACATCAAAC
1 TAGTGGCACCTGAAGTTGTCACATGATCAAGAATATTAGTGGCACCTGAAATTGTCACATCAAAC
*
29881 ATAT
66 ATAG
*
29885 TAGTGACACCTGAAGTTGTCACAT
1 TAGTGGCACCTGAAGTTGTCACAT
29909 CAAAGAAATA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 88 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (69 bp):
TAGTGGCACCTGAAGTTGTCACATGATCAAGAATATTAGTGGCACCTGAAATTGTCACATCAAAC
ATAG
Found at i:31761 original size:16 final size:16
Alignment explanation
Indices: 31742--31777 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
31732 TGTTTTTTTT
31742 AATAAATATTTTATTC
1 AATAAATATTTTATTC
*
31758 AATAAATATTTTATTG
1 AATAAATATTTTATTC
31774 AATA
1 AATA
31778 TGTTTCTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
AATAAATATTTTATTC
Done.