Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012991.1 Corchorus capsularis cultivar CVL-1 contig13012, 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: 91946
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:1855 original size:125 final size:125
Alignment explanation
Indices: 1616--2094 Score: 608
Period size: 125 Copynumber: 3.8 Consensus size: 125
1606 TATTTTATTT
* * * * *
1616 GCATTTAGGTTCTAGTTTTCCCAAAATACCCTTTCGGACAAAGGGTCAGCTTCTTCACATTCTTG
1 GCATTTAGTTTC-AATTTTCCCAAAATACCCTTTCAGACAAAGGGT-TGTTTCTTCACATTCTTG
* * *
1681 CCCTTAGATTCAAGTTCCCAAAATACCCTTTTAGACAAAGGGTTTGTTTTGTCACATTTCTA
64 CTCTTAGATTCAAGTTCCCAAAATACCCTTTCAGACAAAGGGTTCGTTTTGTCACATTTCTA
1743 GCATTTAGTTTCAATTTTCCCAAAATACCCTTTCAGACAAAGGGTTGTTTCTTCACATTCTTGCT
1 GCATTTAGTTTCAATTTTCCCAAAATACCCTTTCAGACAAAGGGTTGTTTCTTCACATTCTTGCT
1808 CTTAGATTCAAGTTCCCAAAATACCCTTTCAGACAAAGGGTTCGTTTTGTCACATTTCTA
66 CTTAGATTCAAGTTCCCAAAATACCCTTTCAGACAAAGGGTTCGTTTTGTCACATTTCTA
* * * ** *
1868 GCATTCAGTTTCAATTTTCCC-AAATACTCTTTCGGACAAAGGGTTAATTCTGTCACACTCTTGC
1 GCATTTAGTTTCAATTTTCCCAAAATACCCTTTCAGACAAAGGGTTGTTTCT-TCACATTCTTGC
* * * * * *
1932 AT-TTAGTTTCAATTTCCCAGAATACCCTTTCCGACAAAGGG-TCAGTTTCGTCACATTCCTA
65 -TCTTAGATTCAAGTTCCCAAAATACCCTTTCAGACAAAGGGTTC-GTTTTGTCACATTTCTA
* * * *
1993 -CGTTTAAGTTT-AGTATTCCCAAAATACCCTTTCAGACAAAGGGTTAGTTTCTTCACATTCCTG
1 GCATTT-AGTTTCAATTTTCCCAAAATACCCTTTCAGACAAAGGGTT-GTTTCTTCACATTCTTG
* * * *
2056 CACTTAGATTCTATTTCCCAAAATACCCTTTCGGACAAA
64 CTCTTAGATTCAAGTTCCCAAAATACCCTTTCAGACAAA
2095 AGGTCAGTTT
Statistics
Matches: 310, Mismatches: 35, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
124 38 0.12
125 225 0.73
126 36 0.12
127 11 0.04
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (125 bp):
GCATTTAGTTTCAATTTTCCCAAAATACCCTTTCAGACAAAGGGTTGTTTCTTCACATTCTTGCT
CTTAGATTCAAGTTCCCAAAATACCCTTTCAGACAAAGGGTTCGTTTTGTCACATTTCTA
Found at i:2097 original size:63 final size:62
Alignment explanation
Indices: 1632--2104 Score: 474
Period size: 62 Copynumber: 7.6 Consensus size: 62
1622 AGGTTCTAGT
* * * * *
1632 TTTCCCAAAATACCCTTTCGGACAAAGGGTCAGCTTCTTCACATTCTTGCCCTTAGATTCAA
1 TTTCCCAAAATACCCTTTCAGACAAAGGGTTAGTTTCTTCACATTCCTGCACTTAGATTCAA
* * * * * *
1694 GTTCCCAAAATACCCTTTTAGACAAAGGGTTTGTTT-TGTCACATTTCTAGCATTTAGTTTCAA
1 TTTCCCAAAATACCCTTTCAGACAAAGGGTTAGTTTCT-TCACATTCCT-GCACTTAGATTCAA
* *
1757 TTTTCCCAAAATACCCTTTCAGACAAAGGGTT-GTTTCTTCACATTCTTGCTCTTAGATTCAA
1 -TTTCCCAAAATACCCTTTCAGACAAAGGGTTAGTTTCTTCACATTCCTGCACTTAGATTCAA
* * * *
1819 GTTCCCAAAATACCCTTTCAGACAAAGGGTTCGTTT-TGTCACATTTCTAGCA-TTCAGTTTCAA
1 TTTCCCAAAATACCCTTTCAGACAAAGGGTTAGTTTCT-TCACATTCCT-GCACTT-AGATTCAA
* * * * * * *
1882 TTTTCCC-AAATACTCTTTCGGACAAAGGGTTA-ATTCTGTCACACTCTTGCATTTAGTTTCAA
1 -TTTCCCAAAATACCCTTTCAGACAAAGGGTTAGTTTCT-TCACATTCCTGCACTTAGATTCAA
* * * * * ** * *
1944 TTTCCCAGAATACCCTTTCCGACAAAGGGTCAGTTTCGTCACATTCCTACGTTTA-AGTTTAG
1 TTTCCCAAAATACCCTTTCAGACAAAGGGTTAGTTTCTTCACATTCCTGCACTTAGA-TTCAA
*
2006 TATTCCCAAAATACCCTTTCAGACAAAGGGTTAGTTTCTTCACATTCCTGCACTTAGATTCTA
1 T-TTCCCAAAATACCCTTTCAGACAAAGGGTTAGTTTCTTCACATTCCTGCACTTAGATTCAA
* * *
2069 TTTCCCAAAATACCCTTTCGGACAAAAGGTCAGTTT
1 TTTCCCAAAATACCCTTTCAGACAAAGGGTTAGTTT
2105 AGCCATGTTT
Statistics
Matches: 338, Mismatches: 57, Indels: 32
0.79 0.13 0.07
Matches are distributed among these distances:
61 38 0.11
62 146 0.43
63 118 0.35
64 36 0.11
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (62 bp):
TTTCCCAAAATACCCTTTCAGACAAAGGGTTAGTTTCTTCACATTCCTGCACTTAGATTCAA
Found at i:14538 original size:21 final size:21
Alignment explanation
Indices: 14512--14564 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
14502 GCACTGGAGT
* *
14512 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAGGCAAACC
* *
14533 ACATGGGGCGCCATGCAAGCC
1 ACATGGGGCGCCAGGCAAACC
14554 ACAT-GGGCGCC
1 ACATGGGGCGCC
14565 CAACGCTAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.25, C:0.32, G:0.34, T:0.09
Consensus pattern (21 bp):
ACATGGGGCGCCAGGCAAACC
Found at i:19715 original size:50 final size:50
Alignment explanation
Indices: 19640--19781 Score: 239
Period size: 50 Copynumber: 2.8 Consensus size: 50
19630 GAAGACGATG
*
19640 GAATTGGAAGACAATTCGAAGGATAAGCGGAAGACGGTCCTTTTAAGATT
1 GAATTGGAAGACAATTCGAAGGATAAGCGGAAGACGATCCTTTTAAGATT
19690 GAATTGGAAGACAATTCGAAGGATAAGCGGAAGACGATCCTTTTAAGATT
1 GAATTGGAAGACAATTCGAAGGATAAGCGGAAGACGATCCTTTTAAGATT
* *
19740 GAATTGGAAGACAATTCGAAGGAGCTGATCGGAAGACGATCC
1 GAATTGGAAGACAATTCGAAGGA--TAAGCGGAAGACGATCC
19782 GTTCAAAAAT
Statistics
Matches: 87, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
50 72 0.83
52 15 0.17
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.22
Consensus pattern (50 bp):
GAATTGGAAGACAATTCGAAGGATAAGCGGAAGACGATCCTTTTAAGATT
Found at i:26399 original size:33 final size:34
Alignment explanation
Indices: 26327--26408 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 34
26317 CTATGATCAA
** *
26327 CCAAAACAGATTT-GTTTTCATCACAATTAGCAT
1 CCAAAACAGATTTAGTTTTCATCACAAACAACAT
26360 CCAAAACAGATTTAGTTTT-ATCACAAACAACA-
1 CCAAAACAGATTTAGTTTTCATCACAAACAACAT
*
26392 CCAAAAACAAATTTAGT
1 CC-AAAACAGATTTAGT
26409 GTCATTGCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
32 2 0.05
33 36 0.84
34 5 0.12
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.28
Consensus pattern (34 bp):
CCAAAACAGATTTAGTTTTCATCACAAACAACAT
Found at i:30034 original size:13 final size:14
Alignment explanation
Indices: 30016--30044 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
30006 ATAACCGGAC
30016 TTTGCATTCAT-CA
1 TTTGCATTCATGCA
30029 TTTGCATTCATGCA
1 TTTGCATTCATGCA
30043 TT
1 TT
30045 GAGTAGAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (14 bp):
TTTGCATTCATGCA
Found at i:34087 original size:18 final size:18
Alignment explanation
Indices: 34047--34093 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
34037 CAGGGTGGCT
34047 GAAGAAGA-AGAAGAGAG
1 GAAGAAGAGAGAAGAGAG
*
34064 GAAGAAGAGAGAAGCGCAG
1 GAAGAAGAGAGAAGAG-AG
34083 G-AGAAGAGAGA
1 GAAGAAGAGAGA
34094 GGGTCGAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 8 0.30
18 16 0.59
19 3 0.11
ACGTcount: A:0.53, C:0.04, G:0.43, T:0.00
Consensus pattern (18 bp):
GAAGAAGAGAGAAGAGAG
Found at i:34724 original size:37 final size:37
Alignment explanation
Indices: 34671--34746 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
34661 CTACCGTTTG
* *
34671 AGCCCAAAACGGTGGTGAACTGACCAACTGGTGGCTT
1 AGCCCAAAACGATGGTGAACTGACCAACTAGTGGCTT
* *
34708 AGCCCAAAACGATGGTGAACTGATCATCTAGTGGCTT
1 AGCCCAAAACGATGGTGAACTGACCAACTAGTGGCTT
34745 AG
1 AG
34747 GTGCAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (37 bp):
AGCCCAAAACGATGGTGAACTGACCAACTAGTGGCTT
Found at i:35377 original size:26 final size:26
Alignment explanation
Indices: 35324--35378 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
35314 TGGATCTTCT
**
35324 TTCAATAATTCCCCAATAACTGGGTC
1 TTCAATAATTCCCCAATAACTGAATC
* * *
35350 TTCAGTAATTCTCCAATAATTGAATC
1 TTCAATAATTCCCCAATAACTGAATC
35376 TTC
1 TTC
35379 TTTGAAAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (26 bp):
TTCAATAATTCCCCAATAACTGAATC
Found at i:39700 original size:16 final size:15
Alignment explanation
Indices: 39671--39718 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
39661 TATGACCCAA
*
39671 AACCGAAAAAGACCCG
1 AACC-AAAATGACCCG
*
39687 AACCAAAATTGACCCA
1 AACCAAAA-TGACCCG
*
39703 AACCCAAATGACCCG
1 AACCAAAATGACCCG
39718 A
1 A
39719 CATTTAAGCG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.48, C:0.33, G:0.12, T:0.06
Consensus pattern (15 bp):
AACCAAAATGACCCG
Found at i:42494 original size:39 final size:39
Alignment explanation
Indices: 42451--42567 Score: 146
Period size: 39 Copynumber: 3.0 Consensus size: 39
42441 TCTCTCTCCC
42451 CAAAGTCCCCAAACACATATAACACAGGGGCAACTTTCT
1 CAAAGTCCCCAAACACATATAACACAGGGGCAACTTTCT
* * * * *
42490 CAAAGTCCTCAAACACATATAACACAGAGTCATCTATACT
1 CAAAGTCCCCAAACACATATAACACAGGGGCAACT-TTCT
* * *
42530 -AAAGTCCCTAAACACATATAACACAAGGGCAATTTTCT
1 CAAAGTCCCCAAACACATATAACACAGGGGCAACTTTCT
42568 TCTCTATATG
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
38 3 0.05
39 58 0.91
40 3 0.05
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.21
Consensus pattern (39 bp):
CAAAGTCCCCAAACACATATAACACAGGGGCAACTTTCT
Found at i:44250 original size:27 final size:27
Alignment explanation
Indices: 44218--44273 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
44208 TTCCAGCAAT
44218 ACAACTCAGCTGCACCACAGCAACAAG
1 ACAACTCAGCTGCACCACAGCAACAAG
*
44245 ACAACTCAGCTGCACCACAGCAGCAAG
1 ACAACTCAGCTGCACCACAGCAACAAG
44272 AC
1 AC
44274 CAAACAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.39, C:0.38, G:0.16, T:0.07
Consensus pattern (27 bp):
ACAACTCAGCTGCACCACAGCAACAAG
Found at i:46561 original size:35 final size:35
Alignment explanation
Indices: 46516--46705 Score: 211
Period size: 35 Copynumber: 5.4 Consensus size: 35
46506 ATTTCATCAA
* * *
46516 ATTCAGCACTTGGGGGCTACAGCAACCCCTTCATC
1 ATTCAACACTTGGGGACTCCAGCAACCCCTTCATC
46551 ATTCAACACTTGGGGACTCCAGCAACCCCTTCATC
1 ATTCAACACTTGGGGACTCCAGCAACCCCTTCATC
* * *
46586 ATTCAACACTTGGGGACTCCAACAACTCCTTCCTC
1 ATTCAACACTTGGGGACTCCAGCAACCCCTTCATC
** *
46621 ATTCGCCACTTGGAGACTCCCA-CAACCCCTTCATC
1 ATTCAACACTTGGGGACT-CCAGCAACCCCTTCATC
* * * * * * *
46656 ATTCAACAATTGGGTACTTCAGCAGCTCATTCTTC
1 ATTCAACACTTGGGGACTCCAGCAACCCCTTCATC
*
46691 ATTCAATACTTGGGG
1 ATTCAACACTTGGGG
46706 GCTTCAACAA
Statistics
Matches: 129, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
34 2 0.02
35 124 0.96
36 3 0.02
ACGTcount: A:0.25, C:0.34, G:0.15, T:0.26
Consensus pattern (35 bp):
ATTCAACACTTGGGGACTCCAGCAACCCCTTCATC
Found at i:47355 original size:71 final size:72
Alignment explanation
Indices: 47063--47409 Score: 522
Period size: 72 Copynumber: 4.8 Consensus size: 72
47053 CCCATGGTCT
* * *
47063 TCTTCTTCATTGCGATTGTAGCCGAGGCAGTTCCCGCATTTGGCAGCCCTTCGCACAATCCTTAC
1 TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
*
47128 ATGATCA
66 ATGATTA
* * *
47135 TC-ACCTTCATTGTGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTC
1 TCTTCC-TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
*
47199 CATGATAA
65 CATGATTA
* *
47207 TCTTCCAT-ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCGGTCCTTCGCACAATCCTTA
1 TCTTCC-TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
**
47271 TGTGATTA
65 CATGATTA
*
47279 TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACA-TTGGCAGTCCTTCGCACAATCCTTAT
1 TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
*
47343 GTGATTA
66 ATGATTA
47350 TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACA-TTGGCAGTCCTTCGCACAATCC
1 TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCC
47410 ATGCTACTAC
Statistics
Matches: 254, Mismatches: 18, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
71 94 0.37
72 157 0.62
73 3 0.01
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (72 bp):
TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
ATGATTA
Found at i:48568 original size:20 final size:20
Alignment explanation
Indices: 48540--48577 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48530 TCGAAGTGTC
*
48540 ATAGCTGCGGCAGGGACAAT
1 ATAGCTGCGGCAGAGACAAT
*
48560 ATAGTTGCGGCAGAGACA
1 ATAGCTGCGGCAGAGACA
48578 GAAGCATGGC
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:0.32, C:0.18, G:0.34, T:0.16
Consensus pattern (20 bp):
ATAGCTGCGGCAGAGACAAT
Found at i:52824 original size:24 final size:24
Alignment explanation
Indices: 52797--52843 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
52787 AAACGGGAAG
52797 AAGAAGTAA-AAAGAGAAAAAAATA
1 AAGAAGTAAGAAA-AGAAAAAAATA
*
52821 AAGAGGTAAGTAAAAGAAAAAAA
1 AAGAAGTAAG-AAAAGAAAAAAA
52844 AGGGTAGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 8 0.40
25 9 0.45
26 3 0.15
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (24 bp):
AAGAAGTAAGAAAAGAAAAAAATA
Found at i:52824 original size:27 final size:26
Alignment explanation
Indices: 52794--52844 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
52784 AAGAAACGGG
52794 AAGAAG-AAGTAAAAAGAGAAAAAAATA
1 AAGAAGTAAGT-AAAAGA-AAAAAAATA
*
52821 AAGAGGTAAGTAAAAGAAAAAAAA
1 AAGAAGTAAGTAAAAGAAAAAAAA
52845 GGGTAGGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 7 0.32
27 11 0.50
28 4 0.18
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.08
Consensus pattern (26 bp):
AAGAAGTAAGTAAAAGAAAAAAAATA
Found at i:57555 original size:39 final size:39
Alignment explanation
Indices: 57510--57621 Score: 138
Period size: 39 Copynumber: 2.9 Consensus size: 39
57500 TTCTCTCTCC
*
57510 CTAAAGTCCCCAAACACATATAACACAGGGGCAACTCT-
1 CTAAAGTCCCCAAACACATATAACACAGGGGCAACTATA
* * *
57548 CTTAAAGTCCTCAAACACATATAACACAGAGTG-ATCTATA
1 C-TAAAGTCCCCAAACACATATAACACAG-GGGCAACTATA
* *
57588 CTAAAGTCCCTAAACACATATAACACAAGGGCAA
1 CTAAAGTCCCCAAACACATATAACACAGGGGCAA
57622 TTTTCTTCTC
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
38 3 0.05
39 55 0.90
40 3 0.05
ACGTcount: A:0.43, C:0.27, G:0.12, T:0.19
Consensus pattern (39 bp):
CTAAAGTCCCCAAACACATATAACACAGGGGCAACTATA
Found at i:59061 original size:23 final size:23
Alignment explanation
Indices: 59034--59077 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
59024 TAAGTCTCAT
*
59034 CTAATCTGAAACTTCTTTTGAAC
1 CTAATCCGAAACTTCTTTTGAAC
59057 CTAATCCGAAACTTCTTTTGA
1 CTAATCCGAAACTTCTTTTGA
59078 GTTTCACTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.39
Consensus pattern (23 bp):
CTAATCCGAAACTTCTTTTGAAC
Found at i:59758 original size:20 final size:21
Alignment explanation
Indices: 59735--59774 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
59725 TTATTAAAAA
59735 ATAA-TTTTTAAAAAAAATAT
1 ATAATTTTTTAAAAAAAATAT
59755 ATAATTTTTTTAAAAAAAAT
1 ATAA-TTTTTTAAAAAAAAT
59775 TTGGTGAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
22 14 0.78
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAATTTTTTAAAAAAAATAT
Found at i:75538 original size:56 final size:56
Alignment explanation
Indices: 75452--75563 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
75442 GACGCCTCCT
75452 CAAAGGTTCTCAAAATACTCACTATCTTTGAGCAATCACCCCAAACACGCTCGAAG
1 CAAAGGTTCTCAAAATACTCACTATCTTTGAGCAATCACCCCAAACACGCTCGAAG
75508 CAAAGGTTCTCAAAATACTCACTATCTTTGAGCAATCACCCCAAACACGCTCGAAG
1 CAAAGGTTCTCAAAATACTCACTATCTTTGAGCAATCACCCCAAACACGCTCGAAG
75564 AAAAAGGATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.21
Consensus pattern (56 bp):
CAAAGGTTCTCAAAATACTCACTATCTTTGAGCAATCACCCCAAACACGCTCGAAG
Found at i:89872 original size:19 final size:20
Alignment explanation
Indices: 89834--89874 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
89824 ACTATTCGAC
*
89834 TTTTAAACATTTAAAGAAGT
1 TTTTAAACATATAAAGAAGT
*
89854 TTTTAGACATATAAA-AAGT
1 TTTTAAACATATAAAGAAGT
89873 TT
1 TT
89875 GTAACCATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTAAACATATAAAGAAGT
Done.