Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008019.1 Corchorus capsularis cultivar CVL-1 contig08040, 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: 28128
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:691 original size:6 final size:6
Alignment explanation
Indices: 680--721 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
670 GTTTTTCTGT
* *
680 TTTTTG TTTTTG TTTTTG -TTTTG TTTTCG -TCTTG TTTTTG TT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TT
722 ACGCTGTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
5 8 0.27
6 22 0.73
ACGTcount: A:0.00, C:0.05, G:0.17, T:0.79
Consensus pattern (6 bp):
TTTTTG
Found at i:701 original size:11 final size:11
Alignment explanation
Indices: 680--721 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
670 GTTTTTCTGT
680 TTTTTGTTTTTG
1 TTTTTG-TTTTG
692 TTTTTGTTTTG
1 TTTTTGTTTTG
* *
703 TTTTCGTCTTG
1 TTTTTGTTTTG
714 TTTTTGTT
1 TTTTTGTT
722 ACGCTGTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 20 0.77
12 6 0.23
ACGTcount: A:0.00, C:0.05, G:0.17, T:0.79
Consensus pattern (11 bp):
TTTTTGTTTTG
Found at i:1370 original size:44 final size:44
Alignment explanation
Indices: 1287--1370 Score: 98
Period size: 44 Copynumber: 1.9 Consensus size: 44
1277 ATAGAAAGTA
* **
1287 TGGTAAGCAAAATTTCATTAGAAGGTTATCAAATTTTCATTGTG
1 TGGTAAGCAAAATTTCATAAGAAGGTTATCAAAGATTCATTGTG
* * *
1331 TGGTAAGTAAAATTTCATAATAA-GTTGATCAGAGATTCAT
1 TGGTAAGCAAAATTTCATAAGAAGGTT-ATCAAAGATTCAT
1371 AGTGAGATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
43 3 0.09
44 30 0.91
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (44 bp):
TGGTAAGCAAAATTTCATAAGAAGGTTATCAAAGATTCATTGTG
Found at i:1553 original size:22 final size:22
Alignment explanation
Indices: 1527--1613 Score: 104
Period size: 22 Copynumber: 4.0 Consensus size: 22
1517 AACATTTCGT
1527 AGGAGGTTAACAAAATTTCATA
1 AGGAGGTTAACAAAATTTCATA
** *
1549 AGGAGGTTGTCAAAAATTCATA
1 AGGAGGTTAACAAAATTTCATA
* *
1571 GGGAGGTTATCAAAATTTCATA
1 AGGAGGTTAACAAAATTTCATA
*
1593 AGGTGGTT-ACTAAAATTTCAT
1 AGGAGGTTAAC-AAAATTTCAT
1614 GAGGTGCTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
21 1 0.02
22 54 0.98
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (22 bp):
AGGAGGTTAACAAAATTTCATA
Found at i:1613 original size:44 final size:43
Alignment explanation
Indices: 1515--1613 Score: 119
Period size: 44 Copynumber: 2.3 Consensus size: 43
1505 AGTGTTCTTA
* * *
1515 TCAACATTTCGTAGGAGGTTAACAAAATTTCATAAGGAGGTTG
1 TCAAAATTTCATAGGAGGTTAACAAAATTTCATAAGGAGGTTC
* * *
1558 TCAAAAATTCATAGGGAGGTTATCAAAATTTCATAAGGTGGTTAC
1 TCAAAATTTCATA-GGAGGTTAACAAAATTTCATAAGGAGGTT-C
1603 T-AAAATTTCAT
1 TCAAAATTTCAT
1614 GAGGTGCTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
43 10 0.21
44 36 0.77
45 1 0.02
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.32
Consensus pattern (43 bp):
TCAAAATTTCATAGGAGGTTAACAAAATTTCATAAGGAGGTTC
Found at i:1786 original size:21 final size:22
Alignment explanation
Indices: 1672--1904 Score: 104
Period size: 22 Copynumber: 10.6 Consensus size: 22
1662 TAGGTGCTTT
*
1672 TCAAAATTTC--A-TGAGATTA
1 TCAAAATTTCATAGTGAGGTTA
* *
1691 TCAAAATTTCA-AATGAATGTTA
1 TCAAAATTTCATAGTG-AGGTTA
* *
1713 TCAAAATTTTATAGGGAGGTT-
1 TCAAAATTTCATAGTGAGGTTA
1734 TACAAAAATTTCATAGTGAGGTTA
1 T-C-AAAATTTCATAGTGAGGTTA
* * *
1758 TCAGAATTTCATGGT-AGGTTG
1 TCAAAATTTCATAGTGAGGTTA
* * *
1779 TCAAAATTTCATAATGTGATTA
1 TCAAAATTTCATAGTGAGGTTA
* * * *
1801 CCAATATTTTATCAG-AAGGTTA
1 TCAAAATTTCAT-AGTGAGGTTA
* * *
1823 TCAAAATTCCATAATGTGCGCTTA
1 TCAAAATTTCAT-A-GTGAGGTTA
* * * *
1847 CCAATATTTCATTA-AGCGGTTA
1 TCAAAATTTCA-TAGTGAGGTTA
* * * *
1869 TTAAAATTTTATATTGAGGTTT
1 TCAAAATTTCATAGTGAGGTTA
*
1891 TCAAAATTTTATAG
1 TCAAAATTTCATAG
1905 GAAAATTTAC
Statistics
Matches: 155, Mismatches: 46, Indels: 23
0.69 0.21 0.10
Matches are distributed among these distances:
19 10 0.06
20 1 0.01
21 22 0.14
22 85 0.55
23 22 0.14
24 14 0.09
25 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (22 bp):
TCAAAATTTCATAGTGAGGTTA
Found at i:1868 original size:46 final size:44
Alignment explanation
Indices: 1773--1876 Score: 111
Period size: 46 Copynumber: 2.3 Consensus size: 44
1763 ATTTCATGGT
* * * *
1773 AGGTTGTCAAAATTTCATAATGTGATTACCAATATTTTATCAGA
1 AGGTTATCAAAATTCCATAATGTGATTACCAATATTTCATAAGA
*
1817 AGGTTATCAAAATTCCATAATGTGCGCTTACCAATATTTCATTAAG-
1 AGGTTATCAAAATTCCATAATGT--GATTACCAATATTTCA-TAAGA
* *
1863 CGGTTATTAAAATT
1 AGGTTATCAAAATT
1877 TTATATTGAG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 21 0.42
46 26 0.52
47 3 0.06
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (44 bp):
AGGTTATCAAAATTCCATAATGTGATTACCAATATTTCATAAGA
Found at i:1941 original size:22 final size:21
Alignment explanation
Indices: 1871--1947 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 21
1861 AGCGGTTATT
*
1871 AAAATTTTATATTGAGGTTTTC
1 AAAATTTTATATGGAGG-TTTC
**
1893 AAAATTTTATA-GGAAAATTTAC
1 AAAATTTTATATGG-AGGTTT-C
1915 AAAATTTTATATGGAGGTTCTC
1 AAAATTTTATATGGAGGTT-TC
*
1937 GAAATTTTATA
1 AAAATTTTATA
1948 GTACCGTCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
21 4 0.09
22 38 0.84
23 3 0.07
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.43
Consensus pattern (21 bp):
AAAATTTTATATGGAGGTTTC
Found at i:2023 original size:20 final size:20
Alignment explanation
Indices: 1972--2026 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
1962 ACTTAGTGTA
1972 ATTATCAAAATTTTATACGG
1 ATTATCAAAATTTTATACGG
**
1992 ATGTTATCAAAATTTTATATTG
1 A--TTATCAAAATTTTATACGG
*
2014 ATTATTAAAATTT
1 ATTATCAAAATTT
2027 CATAACGGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.40
22 18 0.60
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (20 bp):
ATTATCAAAATTTTATACGG
Found at i:2246 original size:6 final size:6
Alignment explanation
Indices: 2230--2260 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2220 GTACTTTTAT
2230 ATATA- ATATAG ATATAG ATATAG ATATAG AT
1 ATATAG ATATAG ATATAG ATATAG ATATAG AT
2261 TAGGCCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (6 bp):
ATATAG
Found at i:4058 original size:2 final size:2
Alignment explanation
Indices: 4051--4078 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4041 TTCATGCATG
4051 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4079 GTAGTAAAAA
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):
TA
Found at i:10164 original size:2 final size:2
Alignment explanation
Indices: 10157--10197 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
10147 AAATGGAAAA
*
10157 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AT AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
10198 TAAAAAATCG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.02
Consensus pattern (2 bp):
AG
Found at i:10655 original size:21 final size:21
Alignment explanation
Indices: 10630--10673 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
10620 TACTTTGGGG
**
10630 TTTGCTATTTACCGCCCCCCT
1 TTTGCTAAATACCGCCCCCCT
10651 TTTGCTAAATACCGCCCCCCT
1 TTTGCTAAATACCGCCCCCCT
10672 TT
1 TT
10674 CTATAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.41, G:0.09, T:0.36
Consensus pattern (21 bp):
TTTGCTAAATACCGCCCCCCT
Found at i:10915 original size:22 final size:23
Alignment explanation
Indices: 10880--10926 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
10870 GTAGTTAATC
*
10880 ATAAATTAACTAATTAAA-ACTA
1 ATAAACTAACTAATTAAATACTA
*
10902 ATAAACTAAGTAATTAAATACTA
1 ATAAACTAACTAATTAAATACTA
10925 AT
1 AT
10927 TAATTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (23 bp):
ATAAACTAACTAATTAAATACTA
Found at i:10938 original size:22 final size:22
Alignment explanation
Indices: 10891--10940 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
10881 TAAATTAACT
*
10891 AATTAAAACTAATAAACTAAGT
1 AATTAAAACTAATAAACTAAGA
* *
10913 AATTAAATACTAATTAATTAA-A
1 AATTAAA-ACTAATAAACTAAGA
10935 AATTAA
1 AATTAA
10941 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (22 bp):
AATTAAAACTAATAAACTAAGA
Found at i:10941 original size:15 final size:15
Alignment explanation
Indices: 10904--10942 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
10894 TAAAACTAAT
*
10904 AAACTAAGTAATTAA
1 AAACTAATTAATTAA
*
10919 ATACTAATTAATTAA
1 AAACTAATTAATTAA
*
10934 AAATTAATT
1 AAACTAATT
10943 TTAAAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (15 bp):
AAACTAATTAATTAA
Found at i:13425 original size:75 final size:75
Alignment explanation
Indices: 13302--13452 Score: 293
Period size: 75 Copynumber: 2.0 Consensus size: 75
13292 GACTAAAGCT
13302 AATGAAAGGGATTTAATTTTCAAAGTCTTCCAACCATTCTGATTTGTTAAATCCCTTTCTGATTT
1 AATGAAAGGGATTTAATTTTCAAAGTCTTCCAACCATTCTGATTTGTTAAATCCCTTTCTGATTT
13367 TCAACTTGGG
66 TCAACTTGGG
*
13377 AATGAAAGGGATTTAATTTTCAAAGTCTTCCAACCATTCTGATTTGTTAAATCCGTTTCTGATTT
1 AATGAAAGGGATTTAATTTTCAAAGTCTTCCAACCATTCTGATTTGTTAAATCCCTTTCTGATTT
13442 TCAACTTGGG
66 TCAACTTGGG
13452 A
1 A
13453 GGTCCCTATA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (75 bp):
AATGAAAGGGATTTAATTTTCAAAGTCTTCCAACCATTCTGATTTGTTAAATCCCTTTCTGATTT
TCAACTTGGG
Found at i:13541 original size:31 final size:31
Alignment explanation
Indices: 13506--13573 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
13496 AAAAAATCGA
13506 TCAATTTAGCCCCTCTACTCACAAGATTGGG
1 TCAATTTAGCCCCTCTACTCACAAGATTGGG
* *
13537 TCAATTTAGTCTCTCTACTCACAAGATTGGG
1 TCAATTTAGCCCCTCTACTCACAAGATTGGG
13568 TCAATT
1 TCAATT
13574 GAGTTTTAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (31 bp):
TCAATTTAGCCCCTCTACTCACAAGATTGGG
Found at i:15625 original size:22 final size:22
Alignment explanation
Indices: 15590--15631 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
15580 GCGTCAAAAT
*
15590 TAAAGCTTGACCGCTCGCGGTC
1 TAAAGCTTGACCGCGCGCGGTC
* *
15612 TAAAGTTTGCCCGCGCGCGG
1 TAAAGCTTGACCGCGCGCGG
15632 CTTGGACCAA
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:0.17, C:0.31, G:0.31, T:0.21
Consensus pattern (22 bp):
TAAAGCTTGACCGCGCGCGGTC
Found at i:16745 original size:17 final size:17
Alignment explanation
Indices: 16723--16760 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
16713 TTCCATCCAT
16723 CCAGCACTGACCACTTG
1 CCAGCACTGACCACTTG
16740 CCAGCACTGACCACTTG
1 CCAGCACTGACCACTTG
16757 CCAG
1 CCAG
16761 TTTCAATCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.24, C:0.42, G:0.18, T:0.16
Consensus pattern (17 bp):
CCAGCACTGACCACTTG
Found at i:24439 original size:31 final size:31
Alignment explanation
Indices: 24404--24463 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
24394 TTTTCCGATC
*
24404 GTACCCTTATTTTTAAAATATATTTCTAATT
1 GTACCCTTATTTTTAAAACATATTTCTAATT
*
24435 GTACCCTTTTTTTTAAAACATATTTCTAA
1 GTACCCTTATTTTTAAAACATATTTCTAA
24464 ATTACCATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.50
Consensus pattern (31 bp):
GTACCCTTATTTTTAAAACATATTTCTAATT
Found at i:25983 original size:151 final size:149
Alignment explanation
Indices: 25709--25998 Score: 408
Period size: 151 Copynumber: 1.9 Consensus size: 149
25699 TACAAGTACA
*
25709 AATAATGGAAAACTTTATGTTTTCCGATTGTACCTTTTTTCCAAATATATTTCTAAATTGACATT
1 AATAATGGAAAACTTTATGTTTTCCGATTGCACCTTTTTTCCAAATATATTTCTAAATTGACATT
* *
25774 ATTAAAATTTATTATTTAAAAATTAATTATAAAATTTCAATTTAGACCGAATTATAAGTTTGTAA
66 ATTAAAATTTATTATTT--AAATTAATTATAAAATTTCAATTTAAAACGAATTATAAGTTTGTAA
25839 AATTGATTTTCATTAATGAAC
129 AATTGATTTTCATTAATGAAC
* **
25860 AATAATAGG-AAACTTTATGTTTTCCGGTTGCACCCTTTTTTCCAAATATATTTCTAAATTTCCA
1 AATAAT-GGAAAACTTTATGTTTTCCGATTGCA-CCTTTTTTCCAAATATATTTCTAAATTGACA
*
25924 TTATTAAAATTTAGTATAATTT-TATT-ATT-TAAAATTTTCAATTTAAAACGAATTATAAGTTT
64 TTATTAAAATTTA-T-T-ATTTAAATTAATTATAAAA-TTTCAATTTAAAACGAATTATAAGTTT
*
25986 GTCAAATTGATTT
125 GTAAAATTGATTT
25999 CAGTCAGTGT
Statistics
Matches: 125, Mismatches: 8, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
150 5 0.04
151 67 0.54
152 47 0.38
153 1 0.01
154 1 0.01
155 4 0.03
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (149 bp):
AATAATGGAAAACTTTATGTTTTCCGATTGCACCTTTTTTCCAAATATATTTCTAAATTGACATT
ATTAAAATTTATTATTTAAATTAATTATAAAATTTCAATTTAAAACGAATTATAAGTTTGTAAAA
TTGATTTTCATTAATGAAC
Found at i:26693 original size:22 final size:22
Alignment explanation
Indices: 26567--26708 Score: 88
Period size: 22 Copynumber: 6.3 Consensus size: 22
26557 TTGTCTCTAT
* **
26567 GTGGTTATCAAAATTTCATAAA
1 GTGGTTATTAAAATTTCATAGG
* * *
26589 ATGATTATTATAATTTCAT-GAG
1 GTGGTTATTAAAATTTCATAG-G
* * * * *
26611 GAGATTATCAAAATTGCATAGT
1 GTGGTTATTAAAATTTCATAGG
*
26633 GTGGTTATCAAAAATTTCATAGG
1 GTGGTTAT-TAAAATTTCATAGG
* * *
26656 ATCAAGTTATTAAAATTTCTTAGG
1 GT--GGTTATTAAAATTTCATAGG
* *
26680 TTGGTTATTGAAATTTCATAGG
1 GTGGTTATTAAAATTTCATAGG
26702 GTGGTTA
1 GTGGTTA
26709 ATTATCACAA
Statistics
Matches: 89, Mismatches: 26, Indels: 10
0.71 0.21 0.08
Matches are distributed among these distances:
22 58 0.65
23 13 0.15
24 13 0.15
25 5 0.06
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.39
Consensus pattern (22 bp):
GTGGTTATTAAAATTTCATAGG
Found at i:26789 original size:22 final size:21
Alignment explanation
Indices: 26744--26889 Score: 98
Period size: 22 Copynumber: 6.6 Consensus size: 21
26734 ATCAAAGAGA
* **
26744 TTATCAAAATGTCATAGCAAGG
1 TTAT-AAAATTTCATAGTGAGG
*
26766 TTATAAGAATTTCATAGTGTGG
1 TTATAA-AATTTCATAGTGAGG
* *
26788 TTAACAAAATTTTATTAG-GAGG
1 TT-ATAAAATTTCA-TAGTGAGG
* * *
26810 TTACTAATATTTCATGGGGAGG
1 TTA-TAAAATTTCATAGTGAGG
* *
26832 TTATCAAAATTTTATAGTGTGG
1 TTAT-AAAATTTCATAGTGAGG
26854 TTATCAAAATTTCATA-TGAAGG
1 TTAT-AAAATTTCATAGTG-AGG
26876 TTATAAAAGTTTCA
1 TTATAAAA-TTTCA
26890 ATTTCATAAG
Statistics
Matches: 98, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
21 12 0.12
22 80 0.82
23 6 0.06
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (21 bp):
TTATAAAATTTCATAGTGAGG
Found at i:26879 original size:44 final size:44
Alignment explanation
Indices: 26744--27723 Score: 250
Period size: 44 Copynumber: 22.5 Consensus size: 44
26734 ATCAAAGAGA
* ** *
26744 TTATCAAAATGTCATAGCAAGGTTAT-AAGAATTTCATAGTG-TGG
1 TTATCAAAATTTCATAGTGAGGTTATCAA-AATTTCATA-TGAAGG
* * * ** *
26788 TTAACAAAATTTTATTAG-GAGGTTA-CTAATATTTCATGGGGAGG
1 TTATCAAAATTTCA-TAGTGAGGTTATC-AAAATTTCATATGAAGG
* *
26832 TTATCAAAATTTTATAGTGTGGTTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATATGAAGG
* * * *
26876 TTAT-AAAAGTTTCAATTTCA-TAAGGAGTACCAAAATTTGATA-GAAGG
1 TTATCAAAA-TTTC-A--T-AGTGAGG-TTATCAAAATTTCATATGAAGG
* * * * *
26923 TTATC-AAATCTCATAGAGTGATTATCAAAATTTCATA-GAGATCGAA
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATATGA-A--G-G
* * *
26969 TTATCAAAATTT-ATA-TAAAGATTATCAAAATTTCATAGTG-ATG
1 TTATCAAAATTTCATAGT-GAGGTTATCAAAATTTCATA-TGAAGG
* * * *
27012 TTATCAAAATTTCA-ATGCGAGGTTATCAAAATTGCATAATG-TGA
1 TTATCAAAATTTCATA-GTGAGGTTATCAAAATTTCAT-ATGAAGG
* * * * * *
27056 TTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATA-AAGAGG
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATATGA-AGG
* * * * * *
27100 TTATCAAATTTTCAAAATGTGATTA-CAAAAATTTCATA-G-TGG
1 TTATCAAAATTTCATAGTGAGGTTATC-AAAATTTCATATGAAGG
* * *
27142 ---T----ATTTC-TGGGGAGGTTATCAAAATTTCATAGTG-TGG
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATA-TGAAGG
* * * * *
27178 TTA-CCAAA--T--TAG-GAAGGTTATTAAACTTTTATTATGGA-G
1 TTATCAAAATTTCATAGTG-AGGTTATCAAAATTTCA-TATGAAGG
* * *
27217 TAATCAAAATTTC--AGGGAGGATATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATATGAAGG
* * * *
27259 TTATCAAAATTTCATAGTTTA-GTTTTCAAAATTTCATAAGATGG
1 TTATCAAAATTTCATAG-TGAGGTTATCAAAATTTCATATGAAGG
* *
27303 TTATCAAAATTTCATAGT-ATGTAGATCAAAATTTCATAATG-AGG
1 TTATCAAAATTTCATAGTGAGGT-TATCAAAATTTCAT-ATGAAGG
** * *
27347 TTATCAAAAAATCATAG-GCAGCTTATCAAAA--T--T-TGTA-G
1 TTATCAAAATTTCATAGTG-AGGTTATCAAAATTTCATATGAAGG
* * * * **
27385 TTATCAAGATTTCATAAG-AAAGTTATCAAAATTTTATA-GGGGG
1 TTATCAAAATTTCAT-AGTGAGGTTATCAAAATTTCATATGAAGG
* *
27428 TTTATCAAAATTTTATAG-GAAGATTTATCAAAATTTCATAGTG-AGG
1 -TTATCAAAATTTCATAGTG-AG-GTTATCAAAATTTCATA-TGAAGG
* * * *
27474 TTATCACAATTTCATAGTGTGATTATCAAAATTTCCTAACAATTCATATGGAGG
1 TTATCAAAATTTCATAGTGAGGTTATCAAAA-----T-----TTCATATGAAGG
* * * * * * * *
27528 TTTTTAAATTTTCATAATGTGGTTATCAATATATCATATGGAGG
1 TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATATGAAGG
* * * * * * *
27572 TTATCAACATCTCATATTGAGGTCT-TCAAAATTCCTTAGGGAGG
1 TTATCAAAATTTCATAGTGAGGT-TATCAAAATTTCATATGAAGG
* * ** * ** *
27616 TTAACAAAATTTCATAAG-AAGGTTAAAAAAAATT-ATAAAAAGA
1 TTATCAAAATTTCAT-AGTGAGGTTATCAAAATTTCATATGAAGG
* ** * * *
27659 TTCTTGAAATTTCATAGT-ATCGTTATTAAAATTTCATAGGAAGG
1 TTATCAAAATTTCATAGTGA-GGTTATCAAAATTTCATATGAAGG
*
27703 TTATCAAAATTTCATAATGAG
1 TTATCAAAATTTCATAGTGAG
27724 ATCATAAAAA
Statistics
Matches: 682, Mismatches: 165, Indels: 178
0.67 0.16 0.17
Matches are distributed among these distances:
34 16 0.02
35 5 0.01
36 4 0.01
38 26 0.04
39 25 0.04
40 9 0.01
41 5 0.01
42 55 0.08
43 59 0.09
44 321 0.47
45 50 0.07
46 33 0.05
47 22 0.03
48 15 0.02
49 2 0.00
53 2 0.00
54 33 0.05
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (44 bp):
TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATATGAAGG
Found at i:26889 original size:66 final size:66
Alignment explanation
Indices: 26763--26889 Score: 161
Period size: 66 Copynumber: 1.9 Consensus size: 66
26753 TGTCATAGCA
* * *
26763 AGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTTATTAGGAGGTTACTAATATTTCATGGG
1 AGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTCATTAGAAGGTTACTAAAATTTCATGGG
26828 G
66 G
* *
26829 AGGTTATCAA-AATTTTATAGTGTGGTTATCAAAATTTCA-TATGAAGGTTA-TAAAAGTTTCA
1 AGGTTAT-AAGAATTTCATAGTGTGGTTAACAAAATTTCATTA-GAAGGTTACTAAAA-TTTCA
26890 ATTTCATAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
65 6 0.11
66 45 0.85
67 2 0.04
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.39
Consensus pattern (66 bp):
AGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTCATTAGAAGGTTACTAAAATTTCATGGG
G
Found at i:26958 original size:22 final size:22
Alignment explanation
Indices: 26889--27138 Score: 146
Period size: 22 Copynumber: 11.5 Consensus size: 22
26879 TAAAAGTTTC
* *
26889 AATTTCATA-AG-GAGTACCAA
1 AATTTCATAGAGTGATTATCAA
*
26909 AATTTGATAGAAG-G-TTATC-A
1 AATTTCATAG-AGTGATTATCAA
*
26929 AATCTCATAGAGTGATTATCAA
1 AATTTCATAGAGTGATTATCAA
26951 AATTTCATAGAGATCGAATTATCAA
1 AATTTCATAGAG-T-G-ATTATCAA
* **
26976 AATTT-ATATAAAGATTATCAA
1 AATTTCATAGAGTGATTATCAA
*
26997 AATTTCATAGTGATG-TTATCAA
1 AATTTCATAGAG-TGATTATCAA
*
27019 AATTTCAATGCGAG-G-TTATCAA
1 AATTTC-AT-AGAGTGATTATCAA
*
27041 AATTGCATA-ATGTGATTATCAA
1 AATTTCATAGA-GTGATTATCAA
* * * *
27063 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAGAGTGATTATCAA
* * * *
27085 AATTTTATAAAGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* *
27107 ATTTTCA-AAATGTGATTA-CAAA
1 AATTTCATAGA-GTGATTATC-AA
27129 AATTTCATAG
1 AATTTCATAG
27139 TGGTATTTCT
Statistics
Matches: 178, Mismatches: 33, Indels: 35
0.72 0.13 0.14
Matches are distributed among these distances:
19 3 0.02
20 19 0.11
21 28 0.16
22 102 0.57
23 6 0.03
24 7 0.04
25 13 0.07
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
AATTTCATAGAGTGATTATCAA
Found at i:27067 original size:66 final size:66
Alignment explanation
Indices: 26988--27140 Score: 175
Period size: 66 Copynumber: 2.3 Consensus size: 66
26978 TTTATATAAA
* * * ** *
26988 GATTATCAAAATTTCATAGTGATGTTATCAAAATTTCAAT-GCGAGGTTATCAAAATTGCATAAT
1 GATTATCAAAATTTCATAGTGAGGTCAACAAAATTT-AATAAAGAGGTTATCAAAATTGCAAAAT
27052 GT
65 GT
* * * * *
27054 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGGTTATCAAATTTTCAAAATG
1 GATTATCAAAATTTCATAGTGAGGTCAACAAAATTTAATAAAGAGGTTATCAAAATTGCAAAATG
27119 T
66 T
27120 GATTA-CAAAAATTTCATAGTG
1 GATTATC-AAAATTTCATAGTG
27141 GTATTTCTGG
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
65 3 0.04
66 70 0.96
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.35
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGTGAGGTCAACAAAATTTAATAAAGAGGTTATCAAAATTGCAAAATG
T
Found at i:27266 original size:22 final size:22
Alignment explanation
Indices: 27238--27508 Score: 161
Period size: 22 Copynumber: 12.5 Consensus size: 22
27228 TCAGGGAGGA
27238 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
27260 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
27282 TTTCAAAATTTCATAAGATGGT
1 TATCAAAATTTCATATGAAGGT
* *
27304 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
*
27325 AGATCAAAATTTCATAATG-AGGT
1 -TATCAAAATTTCAT-ATGAAGGT
** * * *
27348 TATCAAAAAATCATAGGCAGCT
1 TATCAAAATTTCATATGAAGGT
*
27370 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
27386 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* **
27408 TATCAAAATTTTATA-GGGGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
27430 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
27453 TATCAAAATTTCATAGTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * *
27475 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
27497 TATCAAAATTTC
1 TATCAAAATTTC
27509 CTAACAATTC
Statistics
Matches: 194, Mismatches: 39, Indels: 32
0.73 0.15 0.12
Matches are distributed among these distances:
16 8 0.04
17 2 0.01
18 2 0.01
20 2 0.01
21 9 0.05
22 144 0.74
23 25 0.13
24 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:27354 original size:66 final size:64
Alignment explanation
Indices: 27219--27508 Score: 204
Period size: 66 Copynumber: 4.5 Consensus size: 64
27209 TTATGGAGTA
** * * *
27219 ATCAAAATTTCAGGGA-GGA-TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTA-G
1 ATCAAAATTTCATAGATGGATTATCAAAATTTCATA-GTA-GTTATCAAAATTTCATA-ATGAGG
27281 TT
63 TT
* *
27283 TTCAAAATTTCATAAGATGG-TTATCAAAATTTCATAGTATGTAGATCAAAATTTCATAATGAGG
1 ATCAAAATTTCAT-AGATGGATTATCAAAATTTCATAGTA-GT-TATCAAAATTTCATAATGAGG
27347 TT
63 TT
** *** * * *
27349 ATCAAAAAATCATAGGCAGCTTATCAAAA-TT--T-GTAGTTATCAAGATTTCATAA-GAAAGTT
1 ATCAAAATTTCATAGATGGATTATCAAAATTTCATAGTAGTTATCAAAATTTCATAATG-AGGTT
* ** * * * *
27409 ATCAAAATTTTATAGGGGGTTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGTGAGG
1 ATCAAAATTTCATAGATGGATTATCAAAATTTCATA-GTAG--TTATCAAAATTTCATAATGAGG
27474 TT
63 TT
*
27476 ATCACAATTTCATAG-TGTGATTATCAAAATTTC
1 ATCAAAATTTCATAGATG-GATTATCAAAATTTC
27509 CTAACAATTC
Statistics
Matches: 178, Mismatches: 32, Indels: 29
0.74 0.13 0.12
Matches are distributed among these distances:
59 1 0.01
60 41 0.23
61 4 0.02
62 3 0.02
63 2 0.01
64 11 0.06
65 16 0.09
66 54 0.30
67 45 0.25
68 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (64 bp):
ATCAAAATTTCATAGATGGATTATCAAAATTTCATAGTAGTTATCAAAATTTCATAATGAGGTT
Found at i:27564 original size:22 final size:23
Alignment explanation
Indices: 27539--27587 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
27529 TTTTAAATTT
* *
27539 TCATAAT-GTGGTTATCAATATA
1 TCATAATGGAGGTTATCAACATA
*
27561 TCAT-ATGGAGGTTATCAACATC
1 TCATAATGGAGGTTATCAACATA
27583 TCATA
1 TCATA
27588 TTGAGGTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (23 bp):
TCATAATGGAGGTTATCAACATA
Found at i:27588 original size:22 final size:22
Alignment explanation
Indices: 27548--27594 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
27538 TTCATAATGT
*
27548 GGTTATCAATATATCATATGGA
1 GGTTATCAACATATCATATGGA
* *
27570 GGTTATCAACATCTCATATTGA
1 GGTTATCAACATATCATATGGA
27592 GGT
1 GGT
27595 CTTCAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (22 bp):
GGTTATCAACATATCATATGGA
Found at i:27638 original size:22 final size:22
Alignment explanation
Indices: 27613--27719 Score: 74
Period size: 22 Copynumber: 4.9 Consensus size: 22
27603 TTCCTTAGGG
*
27613 AGGTTAACAAAATTTCATAAGA
1 AGGTTATCAAAATTTCATAAGA
** * *
27635 AGGTTAAAAAAAATT-ATAAAA
1 AGGTTATCAAAATTTCATAAGA
* * **
27656 AGATTCTTGAAATTTCAT-AGTA
1 AGGTTATCAAAATTTCATAAG-A
** * *
27678 TCGTTATTAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAAGA
27700 AGGTTATCAAAATTTCATAA
1 AGGTTATCAAAATTTCATAA
27720 TGAGATCATA
Statistics
Matches: 62, Mismatches: 20, Indels: 6
0.70 0.23 0.07
Matches are distributed among these distances:
21 15 0.24
22 46 0.74
23 1 0.02
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAAGA
Done.