Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015981.1 Corchorus capsularis cultivar CVL-1 contig16002, 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: 25341
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:122 original size:37 final size:38
Alignment explanation
Indices: 44--122 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
34 ATAATTACCC
* *
44 ATTTAATTTTGCCTTTTGTCTTAGTTTCCAATCGTTGT
1 ATTTAATTTTGCCTTTTGTCTTAGTCTCCAATCGTTCT
* *
82 ATTTAATTTTGCTTTTTGTCTTTGTCTCCAA-CGTTCT
1 ATTTAATTTTGCCTTTTGTCTTAGTCTCCAATCGTTCT
119 ATTT
1 ATTT
123 GGGCTTAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 9 0.24
38 28 0.76
ACGTcount: A:0.15, C:0.16, G:0.11, T:0.57
Consensus pattern (38 bp):
ATTTAATTTTGCCTTTTGTCTTAGTCTCCAATCGTTCT
Found at i:1547 original size:22 final size:22
Alignment explanation
Indices: 1494--1547 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1484 TCTATGTGGC
*
1494 TATCAAAATTTCATAAGATGGT
1 TATCAAAATTTCAGAAGATGGT
* * *
1516 TATTATAATTTCACGAGGA-GGT
1 TATCAAAATTTCA-GAAGATGGT
1538 TATCAAAATT
1 TATCAAAATT
1548 CCATAGTGTG
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCAGAAGATGGT
Found at i:1560 original size:22 final size:22
Alignment explanation
Indices: 1535--1597 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
1525 TTCACGAGGA
* *
1535 GGTTATCAAAATTCCATAGTGT
1 GGTTACCAAAATTTCATAGTGT
*
1557 GGTTACCATAATTTCATAGTGT
1 GGTTACCAAAATTTCATAGTGT
*
1579 GGTTACCAAATTTTCATAG
1 GGTTACCAAAATTTCATAG
1598 GATGAGGTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (22 bp):
GGTTACCAAAATTTCATAGTGT
Found at i:1712 original size:22 final size:22
Alignment explanation
Indices: 1687--2078 Score: 132
Period size: 22 Copynumber: 17.6 Consensus size: 22
1677 ATCAAAGAGA
* *
1687 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
1709 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
*
1731 TTAACAAAATTTCATTAG-GAGG
1 TTATCAAAATTTCA-TAGTGAGG
* * *
1753 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
* *
1775 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
*
1797 TTATCAAAATTTCATA-TGAAGA
1 TTATCAAAATTTCATAGTG-AGG
* *
1819 TTAT-AAAAGTCTCAATTTCA-TAAGG
1 TTATCAAAA-TTTC-A--T-AGTGAGG
* * * *
1844 AGTACCAAAATTTGATAG-AAGG
1 -TTATCAAAATTTCATAGTGAGG
* * *
1866 CTATC-AAATCTCATAAAGT-A-A
1 TTATCAAAATTTCAT--AGTGAGG
* * **
1887 TTATCGAAATTTCATAGAGATAAAA
1 TTATCAAAATTTCAT--AG-TGAGG
*
1912 TTATCAAAATTT-ATA-TGAAGA
1 TTATCAAAATTTCATAGTG-AGG
* **
1933 TTATCAAAATTTCATACTGTTG
1 TTATCAAAATTTCATAGTGAGG
*
1955 TTATCAAAATTTCA-AATCGAGG
1 TTATCAAAATTTCATAGT-GAGG
* * * *
1977 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGAGG
*
1999 TTATCAGAATTTCATA--GAGG
1 TTATCAAAATTTCATAGTGAGG
* ** *
2019 TGTCAACAAAATTTTGTTA-AGAGG
1 T-T-ATCAAAA-TTTCATAGTGAGG
**
2043 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
*
2065 TTATCAAATTTTCA
1 TTATCAAAATTTCA
2079 AAATGTGATT
Statistics
Matches: 284, Mismatches: 54, Indels: 64
0.71 0.13 0.16
Matches are distributed among these distances:
20 11 0.04
21 40 0.14
22 179 0.63
23 20 0.07
24 8 0.03
25 16 0.06
26 6 0.02
27 4 0.01
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:1921 original size:25 final size:22
Alignment explanation
Indices: 1885--1948 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 22
1875 CTCATAAAGT
*
1885 AATTATCGAAATTTCATAGAGATAA
1 AATTATCAAAATTTCATA-AG--AA
*
1910 AATTATCAAAATTT-ATATGAA
1 AATTATCAAAATTTCATAAGAA
*
1931 GATTATCAAAATTTCATA
1 AATTATCAAAATTTCATA
1949 CTGTTGTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 15 0.43
22 3 0.09
23 1 0.03
24 3 0.09
25 13 0.37
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (22 bp):
AATTATCAAAATTTCATAAGAA
Found at i:2003 original size:44 final size:44
Alignment explanation
Indices: 1911--2097 Score: 147
Period size: 44 Copynumber: 4.3 Consensus size: 44
1901 TAGAGATAAA
* * *
1911 ATTATCAAAATTT-ATAT-GAAGATTATCAAAATTTCATACTGTTG
1 ATTATCAAAATTTCAAATAG-AGGTTATCAAAATTTCATAATG-TG
* *
1955 -TTATCAAAATTTCAAATCGAGGTTATCAAAATTACATAATGTG
1 ATTATCAAAATTTCAAATAGAGGTTATCAAAATTTCATAATGTG
* * ** *
1998 ATTATCAGAATTTC--ATAGAGGTGTCAACAAAATTTTGTTAA-GAG
1 ATTATCAAAATTTCAAATAGAGGT-T-ATCAAAA-TTTCATAATGTG
* * *
2042 GTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGTG
1 ATTATCAAAATTTCA-AATAGAGGTTATCAAAATTTCATAATGTG
2086 ATTA-CAAAATTT
1 ATTATCAAAATTT
2098 TCATATTGGT
Statistics
Matches: 113, Mismatches: 20, Indels: 21
0.73 0.13 0.14
Matches are distributed among these distances:
42 7 0.06
43 28 0.25
44 64 0.57
45 7 0.06
46 6 0.05
47 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (44 bp):
ATTATCAAAATTTCAAATAGAGGTTATCAAAATTTCATAATGTG
Found at i:2219 original size:19 final size:20
Alignment explanation
Indices: 2184--2231 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 20
2174 TTATGGAGTA
2184 ATCAAAATTACAGGGAGGAT
1 ATCAAAATTACAGGGAGGAT
*
2204 ATCAAAATT-CATGGAGGAT
1 ATCAAAATTACAGGGAGGAT
2223 ATCAAAATT
1 ATCAAAATT
2232 TCATATGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCAAAATTACAGGGAGGAT
Found at i:2296 original size:22 final size:22
Alignment explanation
Indices: 2271--2324 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2261 AAGATTCTCG
* *
2271 AAATTTCATAGTATA-GTTATTA
1 AAATTTCATAGGA-AGGTTATCA
2293 AAATTTCATAGGAAGGTTATCA
1 AAATTTCATAGGAAGGTTATCA
2315 AAATTTCATA
1 AAATTTCATA
2325 ATGGGATCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (22 bp):
AAATTTCATAGGAAGGTTATCA
Found at i:3014 original size:55 final size:55
Alignment explanation
Indices: 2948--3110 Score: 220
Period size: 55 Copynumber: 3.0 Consensus size: 55
2938 TAGAACTTTC
* * *
2948 TTCAAGGAACACTGGGAGATTAC-GAAGATTTCAAGCGAGTGTCAGCGTTGAAGCT
1 TTCAAGGAACACTGGGAGATCACTG-AGATCTCAAGCGAGTGTCAGCATTGAAGCT
*
3003 TTCAAGGAACACTGGGAGATCACTGAGATCTCAAGCGAGTGTCGGCATTGAAGCT
1 TTCAAGGAACACTGGGAGATCACTGAGATCTCAAGCGAGTGTCAGCATTGAAGCT
* * ** * *
3058 TTCAAGGAACACTAGGAAATCAAGGAGATCTCAGGCGAGCGTCAGCATTGAAG
1 TTCAAGGAACACTGGGAGATCACTGAGATCTCAAGCGAGTGTCAGCATTGAAG
3111 GTTGATAGGA
Statistics
Matches: 96, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
55 95 0.99
56 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (55 bp):
TTCAAGGAACACTGGGAGATCACTGAGATCTCAAGCGAGTGTCAGCATTGAAGCT
Found at i:3326 original size:21 final size:21
Alignment explanation
Indices: 3302--3341 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3292 ACTGGCGGGC
3302 TTTACTTGCTAAGGAAGGCAT
1 TTTACTTGCTAAGGAAGGCAT
*
3323 TTTACTTGCTGAGGAAGGC
1 TTTACTTGCTAAGGAAGGC
3342 GAACTCTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (21 bp):
TTTACTTGCTAAGGAAGGCAT
Found at i:4182 original size:156 final size:155
Alignment explanation
Indices: 3883--4174 Score: 328
Period size: 156 Copynumber: 1.9 Consensus size: 155
3873 CACCCCAAAC
* *
3883 TGTCCTTAAATGAAAAACTAACATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAACTTTGCCA
1 TGTCATTAAATGAAAAACTAACATAAGTTTTTCATTCTAAGTCTCAATGAGCTG-AACTTTGCCA
** * *
3948 AGGTACTTAGAATATTTCCATAAGACTATGGAAAAAATTATAAGTAAAACCGAACTCCCCTTGAT
65 AGGTACTTAGAATATCACCATAAGACTATGGAAAAAATTATAAGAAAAACCGAACTCCCCTAGAT
* *
4013 GGTGAACTAGGTTTCTTTTCCTGAGT
130 AGAGAACTAGGTTTCTTTTCCTGAGT
* *
4039 TGTCATTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAATGAAGCTG-A-TTTTCCA
1 TGTCATTAAATGAAAAACTAACATAAGTTTTTCATTCTAAGTCTCAATG-AGCTGAACTTTGCCA
* * * *
4101 CCA-GTAGACTTAGATTATCACCGTAA-AGCTAT-GAGAAAAATTCTAAGAAAAACCGAACT-CT
65 --AGGT--ACTTAGAATATCACCATAAGA-CTATGGA-AAAAATTATAAGAAAAACCGAACTCCC
4162 CTAGCATAGAGAA
124 CTAG-ATAGAGAA
4175 GTTGGTTTGA
Statistics
Matches: 114, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
153 6 0.05
154 3 0.03
155 12 0.11
156 93 0.82
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.30
Consensus pattern (155 bp):
TGTCATTAAATGAAAAACTAACATAAGTTTTTCATTCTAAGTCTCAATGAGCTGAACTTTGCCAA
GGTACTTAGAATATCACCATAAGACTATGGAAAAAATTATAAGAAAAACCGAACTCCCCTAGATA
GAGAACTAGGTTTCTTTTCCTGAGT
Found at i:9510 original size:2 final size:2
Alignment explanation
Indices: 9469--9496 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9459 CATTATATGC
9469 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
9497 GAATATGAAT
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:12097 original size:2 final size:2
Alignment explanation
Indices: 12090--12128 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
12080 AGCTTCATGC
*
12090 TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12129 ACAATATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14802 original size:2 final size:2
Alignment explanation
Indices: 14795--14824 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
14785 ATTTATAGCT
14795 TA 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 TA
14825 ACCTTCATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16957 original size:30 final size:30
Alignment explanation
Indices: 16922--16984 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
16912 TATATTAAAT
16922 ACACAAACAAATAAATTACAAAGAAAACTC
1 ACACAAACAAATAAATTACAAAGAAAACTC
16952 ACACAAACAAATAAATTACAAAGAAAACTC
1 ACACAAACAAATAAATTACAAAGAAAACTC
16982 ACA
1 ACA
16985 TTCCGTAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.63, C:0.21, G:0.03, T:0.13
Consensus pattern (30 bp):
ACACAAACAAATAAATTACAAAGAAAACTC
Found at i:21505 original size:12 final size:11
Alignment explanation
Indices: 21488--21522 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 11
21478 AACATTCTTC
21488 ATATATATA-T
1 ATATATATATT
21498 ATATATATATT
1 ATATATATATT
21509 ATACTATATATT
1 ATA-TATATATT
21521 AT
1 AT
21523 TTTTAACTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.39
11 4 0.17
12 10 0.43
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
ATATATATATT
Found at i:22046 original size:3 final size:3
Alignment explanation
Indices: 22040--22076 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
22030 TGTGTTTTGG
*
22040 GAA GAA GAA GAA TAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
22077 GAGGAGGAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:22625 original size:79 final size:79
Alignment explanation
Indices: 22487--22646 Score: 257
Period size: 79 Copynumber: 2.0 Consensus size: 79
22477 TCACTATTGA
* ** * *
22487 CTGATTTCATCACTCCCTCCTCAAGTTGGCTCGTGAAGACTCGCAACACCCAACTTGAACATTAA
1 CTGATTTCATCACTCCCTCCTCAAGTTGGCACGTGAAGACTCAAAACACCCAACATGAACACTAA
22552 TGATTCAAACCGAT
66 TGATTCAAACCGAT
* *
22566 CTGATTTCATCACTCCCTCCTCAAGTTGGCACGTGAAGACTCAAAACGCCTAACATGAACACTAA
1 CTGATTTCATCACTCCCTCCTCAAGTTGGCACGTGAAGACTCAAAACACCCAACATGAACACTAA
22631 TGATTCAAACCGAT
66 TGATTCAAACCGAT
22645 CT
1 CT
22647 TTTTCCAAGG
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 74 1.00
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.26
Consensus pattern (79 bp):
CTGATTTCATCACTCCCTCCTCAAGTTGGCACGTGAAGACTCAAAACACCCAACATGAACACTAA
TGATTCAAACCGAT
Found at i:23479 original size:85 final size:84
Alignment explanation
Indices: 23330--23700 Score: 480
Period size: 85 Copynumber: 4.4 Consensus size: 84
23320 GGCAGCTTTT
* * * * *
23330 AACTAGCCTCCCCTTTTTGAAGGTTCTACGCCA-CCCTACAGGAACTAACCTCCCCTTTTCGAAG
1 AACTAACCTCCCCTTTTCGAAGGTTTTACGACACCCCGA-AGGAACTAACCTCCCCTTTTCGAAG
23394 GTTTTACGCCAACCCCGCAGG
65 GTTTTACGCC-ACCCCGCAGG
* * * *
23415 AATTGACCTCCCCTTTTCGAAGGTTTAACGACACCCCGAAGGAACTAACCTCCCTTTTTCGAAGG
1 AACTAACCTCCCCTTTTCGAAGGTTTTACGACACCCCGAAGGAACTAACCTCCCCTTTTCGAAGG
23480 TTTTACGCCACCCCGCAGG
66 TTTTACGCCACCCCGCAGG
* *
23499 AACTAACCTCCCCTTTTCGAAGGTTTTTAC-ACCACCCCGCAGGAATTAACCTCCCCTTTTCGAA
1 AACTAACCTCCCCTTTTCGAAGG-TTTTACGA-CACCCCGAAGGAACTAACCTCCCCTTTTCGAA
* *
23563 GG-TTTACGCCA-CCGGTAGG
64 GGTTTTACGCCACCCCGCAGG
* *
23582 AACTAACCTCCCCCTTTTCGAAGGTTTTACGCCATCCCCGCAGGAACTAACCTCCCCTTTTCGAA
1 AACTAACCT-CCCCTTTTCGAAGGTTTTACGACA-CCCCGAAGGAACTAACCTCCCCTTTTCGAA
* **
23647 GATTTTACGCCACCTTGCAGG
64 GGTTTTACGCCACCCCGCAGG
* *
23668 GACTAACCTCCCTTTTTCGAAGGTTTTACGACA
1 AACTAACCTCCCCTTTTCGAAGGTTTTACGACA
23701 ACCTGCAGGA
Statistics
Matches: 252, Mismatches: 26, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
83 23 0.09
84 85 0.34
85 127 0.50
86 17 0.07
ACGTcount: A:0.23, C:0.34, G:0.16, T:0.26
Consensus pattern (84 bp):
AACTAACCTCCCCTTTTCGAAGGTTTTACGACACCCCGAAGGAACTAACCTCCCCTTTTCGAAGG
TTTTACGCCACCCCGCAGG
Found at i:23556 original size:127 final size:125
Alignment explanation
Indices: 23330--23700 Score: 530
Period size: 127 Copynumber: 2.9 Consensus size: 125
23320 GGCAGCTTTT
* * **
23330 AACTAGCCTCCCCTTTTT-GAAGGTTCTACGCCACCCTACAGGAACTAACCTCCCCTTTTCGAAG
1 AACTAACCTCCCCTTTTTCGAAGGTTTTACGCCACCCCGCAGGAACTAACCTCCCCTTTTCGAAG
*
23394 GTTTTACGCCAACCCCGCAGGAATTGACCTCCCCTTTTCGAAGGTTTAACGACACCCCGAAGG
66 GTTTTACGCC-ACCCCGCAGGAATTAACCTCCCCTTTTCGAAGGTTT-ACGACA-CCCGAAGG
23457 AACTAACCT-CCCTTTTTCGAAGGTTTTACGCCACCCCGCAGGAACTAACCTCCCCTTTTCGAAG
1 AACTAACCTCCCCTTTTTCGAAGGTTTTACGCCACCCCGCAGGAACTAACCTCCCCTTTTCGAAG
* * * *
23521 GTTTTTACACCACCCCGCAGGAATTAACCTCCCCTTTTCGAAGGTTTACGCCACCGGTAGG
66 G-TTTTACGCCACCCCGCAGGAATTAACCTCCCCTTTTCGAAGGTTTACGACACCCGAAGG
*
23582 AACTAACCTCCCCCTTTTCGAAGGTTTTACGCCATCCCCGCAGGAACTAACCTCCCCTTTTCGAA
1 AACTAACCTCCCCTTTTTCGAAGGTTTTACGCCA-CCCCGCAGGAACTAACCTCCCCTTTTCGAA
* ** * * *
23647 GATTTTACGCCACCTTGCAGGGACTAACCTCCCTTTTTCGAAGGTTTTACGACA
65 GGTTTTACGCCACCCCGCAGGAATTAACCTCCCCTTTTCGAAGG-TTTACGACA
23701 ACCTGCAGGA
Statistics
Matches: 221, Mismatches: 18, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
125 15 0.07
126 72 0.33
127 126 0.57
128 8 0.04
ACGTcount: A:0.23, C:0.34, G:0.16, T:0.26
Consensus pattern (125 bp):
AACTAACCTCCCCTTTTTCGAAGGTTTTACGCCACCCCGCAGGAACTAACCTCCCCTTTTCGAAG
GTTTTACGCCACCCCGCAGGAATTAACCTCCCCTTTTCGAAGGTTTACGACACCCGAAGG
Found at i:23709 original size:42 final size:42
Alignment explanation
Indices: 23330--23697 Score: 506
Period size: 42 Copynumber: 8.7 Consensus size: 42
23320 GGCAGCTTTT
* * * **
23330 AACTAGCCTCCCCTTTTTGAAGGTTCTACGCCACCCTACAGG
1 AACTAACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGG
23372 AACTAACCTCCCCTTTTCGAAGGTTTTACGCCAACCCCGCAGG
1 AACTAACCTCCCCTTTTCGAAGGTTTTACGCC-ACCCCGCAGG
* * * * *
23415 AATTGACCTCCCCTTTTCGAAGGTTTAACGACACCCCGAAGG
1 AACTAACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGG
*
23457 AACTAACCTCCCTTTTTCGAAGGTTTTACGCCACCCCGCAGG
1 AACTAACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGG
*
23499 AACTAACCTCCCCTTTTCGAAGGTTTTTACACCACCCCGCAGG
1 AACTAACCTCCCCTTTTCGAAGG-TTTTACGCCACCCCGCAGG
* * *
23542 AATTAACCTCCCCTTTTCGAAGG-TTTACGCCA-CCGGTAGG
1 AACTAACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGG
23582 AACTAACCTCCCCCTTTTCGAAGGTTTTACGCCATCCCCGCAGG
1 AACTAACCT-CCCCTTTTCGAAGGTTTTACGCCA-CCCCGCAGG
* **
23626 AACTAACCTCCCCTTTTCGAAGATTTTACGCCACCTTGCAGG
1 AACTAACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGG
* *
23668 GACTAACCTCCCTTTTTCGAAGGTTTTACG
1 AACTAACCTCCCCTTTTCGAAGGTTTTACG
23698 ACAACCTGCA
Statistics
Matches: 289, Mismatches: 31, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
40 14 0.05
41 22 0.08
42 139 0.48
43 99 0.34
44 15 0.05
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.27
Consensus pattern (42 bp):
AACTAACCTCCCCTTTTCGAAGGTTTTACGCCACCCCGCAGG
Done.