Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016103.1 Corchorus capsularis cultivar CVL-1 contig16124, 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: 45143
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7397 original size:2 final size:2
Alignment explanation
Indices: 7390--7425 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
7380 TTGTATGTGT
*
7390 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7426 AAAGTACTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:7963 original size:32 final size:32
Alignment explanation
Indices: 7910--7989 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
7900 TTTTTCTTTG
* * * *
7910 AAACACCACAATTTAGTGGCGTTTCTTTAACA
1 AAACGCCACTATTTAGCGGCGTTTCTTAAACA
7942 AAACGCCACTATTTAGCGGCGTTTCTTAAACA
1 AAACGCCACTATTTAGCGGCGTTTCTTAAACA
*
7974 AAATGTCC-CTATTTAG
1 AAACG-CCACTATTTAG
7990 TGGCATTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 40 0.95
33 2 0.05
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.31
Consensus pattern (32 bp):
AAACGCCACTATTTAGCGGCGTTTCTTAAACA
Found at i:8535 original size:21 final size:21
Alignment explanation
Indices: 8511--8561 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
8501 ATGTTGGAGG
8511 TTTATTTTACATTGTTAGTT-A
1 TTTATTTTACATTGTT-GTTAA
* * * *
8532 TTTAATTTGCTTTGTTTTTAA
1 TTTATTTTACATTGTTGTTAA
8553 TTTATTTTA
1 TTTATTTTA
8562 ATTTAGAATT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.22, C:0.04, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTATTTTACATTGTTGTTAA
Found at i:10109 original size:27 final size:27
Alignment explanation
Indices: 10066--10199 Score: 162
Period size: 27 Copynumber: 5.0 Consensus size: 27
10056 AATCCTCGGC
*
10066 CCCCATCATAATAACCCGGCTGAGCAG
1 CCCCATCATAGTAACCCGGCTGAGCAG
*
10093 CCCCATCATAGTGACCCGGCTGAGCAG
1 CCCCATCATAGTAACCCGGCTGAGCAG
** * * *
10120 CCATATCATTGTAACCTGGCTGAGCTG
1 CCCCATCATAGTAACCCGGCTGAGCAG
* *
10147 TCCCATCATAGTAACCGGGCTGAGCA-
1 CCCCATCATAGTAACCCGGCTGAGCAG
*
10173 CCCTCATCATAGTAACCCGGCTAAGCA
1 CCC-CATCATAGTAACCCGGCTGAGCA
10200 CACTCAAACT
Statistics
Matches: 89, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
26 2 0.02
27 87 0.98
ACGTcount: A:0.26, C:0.34, G:0.21, T:0.19
Consensus pattern (27 bp):
CCCCATCATAGTAACCCGGCTGAGCAG
Found at i:23141 original size:33 final size:33
Alignment explanation
Indices: 23095--23160 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
23085 CCTCATCAAA
* *
23095 TTCAATATGAATTTTAATCTTGGCCATTTATTT
1 TTCAATATGAATTTCAATCTTGGCCATTGATTT
* *
23128 TTCAATGTTAATTTCAATCTTGGCCATTGATTT
1 TTCAATATGAATTTCAATCTTGGCCATTGATTT
23161 ATGTTTTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.50
Consensus pattern (33 bp):
TTCAATATGAATTTCAATCTTGGCCATTGATTT
Found at i:23348 original size:31 final size:29
Alignment explanation
Indices: 23289--23349 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 29
23279 TTAATTAATC
**
23289 ATTAATTATTTGTAATAGTATATTAAACT
1 ATTAATTATTTGTAATAGTATACAAAACT
23318 ATTAATTATTAATGTAACTA-TATACAAAACT
1 ATTAATTATT--TGTAA-TAGTATACAAAACT
23349 A
1 A
23350 GAAATATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 10 0.37
31 15 0.56
32 2 0.07
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.43
Consensus pattern (29 bp):
ATTAATTATTTGTAATAGTATACAAAACT
Found at i:23880 original size:31 final size:33
Alignment explanation
Indices: 23844--23912 Score: 115
Period size: 31 Copynumber: 2.2 Consensus size: 33
23834 AACTCTATTT
23844 TAAACATGCGCAAAAGAATCCTG-ATAAAAAAA
1 TAAACATGCGCAAAAGAATCCTGCATAAAAAAA
*
23876 -AAACATGCGCAAAAGAATCCTGCTTAAAAAAA
1 TAAACATGCGCAAAAGAATCCTGCATAAAAAAA
23908 TAAAC
1 TAAAC
23913 TTCTATATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 22 0.65
32 8 0.24
33 4 0.12
ACGTcount: A:0.55, C:0.17, G:0.12, T:0.16
Consensus pattern (33 bp):
TAAACATGCGCAAAAGAATCCTGCATAAAAAAA
Found at i:24347 original size:16 final size:16
Alignment explanation
Indices: 24326--24356 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24316 TGCACGGAAA
*
24326 ATAAATGGTACATATC
1 ATAAATGGTAAATATC
24342 ATAAATGGTAAATAT
1 ATAAATGGTAAATAT
24357 GAGATAGCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.32
Consensus pattern (16 bp):
ATAAATGGTAAATATC
Found at i:25403 original size:65 final size:63
Alignment explanation
Indices: 25303--25435 Score: 185
Period size: 64 Copynumber: 2.1 Consensus size: 63
25293 ATCTGCGGCG
* * *
25303 TTTTTGCATAAAACGCCATTGAATGGTGGCATTTGTGTAAAAAACGCCACTGGTCAGTGGCGTT
1 TTTTTGCATAAAACGCCACTGAATGGTGGCATTTGTGT-AAAAACGCCACTGATCACTGGCGTT
* * * *
25367 TTTTCTGCATAAAGCGCCACTGATTGGTGGCTTTTGTGTAAAAACGCCACTGATCACTGGCTTT
1 TTTT-TGCATAAAACGCCACTGAATGGTGGCATTTGTGTAAAAACGCCACTGATCACTGGCGTT
25431 TTTTT
1 TTTTT
25436 TTTTACAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
63 1 0.02
64 30 0.49
65 30 0.49
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (63 bp):
TTTTTGCATAAAACGCCACTGAATGGTGGCATTTGTGTAAAAACGCCACTGATCACTGGCGTT
Found at i:25428 original size:30 final size:30
Alignment explanation
Indices: 25328--25431 Score: 91
Period size: 34 Copynumber: 3.3 Consensus size: 30
25318 CCATTGAATG
* *
25328 GTGGCATTTGTGTAAAAAACGCCACTGGTCA
1 GTGGCTTTTGTGT-AAAAACGCCACTGATCA
* * * **
25359 GTGGCGTTTTTTCTGCATAAAGCGCCACTGATTG
1 GTGGC---TTTTGTGTA-AAAACGCCACTGATCA
25393 GTGGCTTTTGTGTAAAAACGCCACTGATCA
1 GTGGCTTTTGTGTAAAAACGCCACTGATCA
*
25423 CTGGCTTTT
1 GTGGCTTTT
25432 TTTTTTTTAC
Statistics
Matches: 56, Mismatches: 13, Indels: 9
0.72 0.17 0.12
Matches are distributed among these distances:
30 21 0.38
31 12 0.21
33 1 0.02
34 22 0.39
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (30 bp):
GTGGCTTTTGTGTAAAAACGCCACTGATCA
Found at i:25570 original size:32 final size:32
Alignment explanation
Indices: 25532--25677 Score: 163
Period size: 32 Copynumber: 4.6 Consensus size: 32
25522 ACAGATTACA
25532 TTAGTGGCGTTTTCTTCAATATGTGCCACAAT
1 TTAGTGGCGTTTTCTTCAATATGTGCCACAAT
*
25564 TTAGTGGCGTTTTCTTCGATATGTGCCACAAT
1 TTAGTGGCGTTTTCTTCAATATGTGCCACAAT
* *
25596 TTAGTGGCCTTTTCTTCAGA-ATTTGCCACTAA-
1 TTAGTGGCGTTTTCTTCA-ATATGTGCCAC-AAT
** * * * *
25628 GCAGTGGCGTTTTGTTCTATA-GCAGCCACTAT
1 TTAGTGGCGTTTTCTTCAATATG-TGCCACAAT
25660 TTAGTGGCGTTTTCTTCA
1 TTAGTGGCGTTTTCTTCA
25678 GTAAACGCCA
Statistics
Matches: 93, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
31 2 0.02
32 88 0.95
33 3 0.03
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (32 bp):
TTAGTGGCGTTTTCTTCAATATGTGCCACAAT
Found at i:25688 original size:64 final size:64
Alignment explanation
Indices: 25566--25691 Score: 157
Period size: 64 Copynumber: 2.0 Consensus size: 64
25556 GCCACAATTT
* **
25566 AGTGGCGTTTTCTTCGATATGTGCCACAATTTAGTGGCCTTTTCTTCAGAATTTGCCACTAAGC
1 AGTGGCGTTTTCTTCGATATGAGCCACAATTTAGTGGCCTTTTCTTCAGAATACGCCACTAAGC
* * * *
25630 AGTGGCGTTTTGTTCTATA-GCAGCCACTATTTAGTGGCGTTTTCTTCAGTAA-ACGCCACTAA
1 AGTGGCGTTTTCTTCGATATG-AGCCACAATTTAGTGGCCTTTTCTTCAG-AATACGCCACTAA
25692 AATGGAGTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
63 1 0.02
64 50 0.94
65 2 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (64 bp):
AGTGGCGTTTTCTTCGATATGAGCCACAATTTAGTGGCCTTTTCTTCAGAATACGCCACTAAGC
Found at i:27411 original size:43 final size:43
Alignment explanation
Indices: 27350--27453 Score: 167
Period size: 43 Copynumber: 2.4 Consensus size: 43
27340 AAAAATAGTA
27350 TACTGCC-AA-AGTATACTTCATAATTTCAGAACTTCATAATT
1 TACTGCCAAACAGTATACTTCATAATTTCAGAACTTCATAATT
*
27391 TACTGCCAAACAGTATACTTCATATTTTCAGAACTTCATAATT
1 TACTGCCAAACAGTATACTTCATAATTTCAGAACTTCATAATT
27434 TACTGCCAAAAACAGTATAC
1 TACTGCC--AAACAGTATAC
27454 AGGATTTAGC
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
41 7 0.12
42 2 0.03
43 38 0.66
45 11 0.19
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.34
Consensus pattern (43 bp):
TACTGCCAAACAGTATACTTCATAATTTCAGAACTTCATAATT
Found at i:31826 original size:40 final size:40
Alignment explanation
Indices: 31771--31872 Score: 143
Period size: 40 Copynumber: 2.5 Consensus size: 40
31761 TTAAAACCTT
**
31771 AATTCAGTGTAATTAAGAAAAGTTAAGAAAAGTAGGTCTC
1 AATTCAGTGTAATTAAGAAAAGTTAAGAAAAGTAAATCTC
*
31811 AATTCAGTGTAATTAAGAGAAA-TTAAGAAAAGTAAATCTT
1 AATTCAGTGTAATTAAGA-AAAGTTAAGAAAAGTAAATCTC
* *
31851 AATTCAGGGTAATTAACAAAAG
1 AATTCAGTGTAATTAAGAAAAG
31873 CAAAGTCTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
39 3 0.05
40 49 0.89
41 3 0.05
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (40 bp):
AATTCAGTGTAATTAAGAAAAGTTAAGAAAAGTAAATCTC
Found at i:31854 original size:30 final size:31
Alignment explanation
Indices: 31831--31977 Score: 129
Period size: 31 Copynumber: 4.5 Consensus size: 31
31821 AATTAAGAGA
31831 AATTAAGAAAAGTAAA-TCTTAATTCAGGGT
1 AATTAAGAAAAGTAAAGTCTTAATTCAGGGT
* *
31861 AATTAACAAAAGCAAAGTCTTAATTCAGGGT
1 AATTAAGAAAAGTAAAGTCTTAATTCAGGGT
*
31892 AATTAAGAAAAGTAAACACAGTCAAAGTCTTAATT--TGGT
1 AATT-----AAG--AA-A-AGT-AAAGTCTTAATTCAGGGT
* * *
31931 AATTAAGAAAAGCAAAGTCTGAATTCAAGGT
1 AATTAAGAAAAGTAAAGTCTTAATTCAGGGT
31962 AATTAAGAAAAGTAAA
1 AATTAAGAAAAGTAAA
31978 CACAGTTAAA
Statistics
Matches: 95, Mismatches: 9, Indels: 25
0.74 0.07 0.19
Matches are distributed among these distances:
29 11 0.12
30 16 0.17
31 37 0.39
32 2 0.02
34 3 0.03
36 2 0.02
38 2 0.02
39 8 0.08
40 2 0.02
41 12 0.13
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.26
Consensus pattern (31 bp):
AATTAAGAAAAGTAAAGTCTTAATTCAGGGT
Found at i:31945 original size:70 final size:70
Alignment explanation
Indices: 31793--32014 Score: 245
Period size: 70 Copynumber: 3.1 Consensus size: 70
31783 TTAAGAAAAG
* * * * *
31793 TTAAGAAAAG-TAGGTCTCAATTCAGTGTAATTAAGAGAAATTAAGA-AAAGTAAA-TCTTAATT
1 TTAAGAAAAGCAAAGTCTCAATTCAGGGTAATTAAGA-AAAGTAA-ACACAGTAAAGTCTTAATT
31855 CAGGGTAA
64 -AGGGTAA
* *
31863 TTAACAAAAGCAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAAAGTCTTAATT-
1 TTAAGAAAAGCAAAGTCTCAATTCAGGGTAATTAAGAAAAGTAAACACAGT-AAAGTCTTAATTA
*
31927 TGGTAA
65 GGGTAA
* * * * *
31933 TTAAGAAAAGCAAAGTCTGAATTCAAGGTAATTAAGAAAAGTAAACACAGTTAAAGTTTTAGCTC
1 TTAAGAAAAGCAAAGTCTCAATTCAGGGTAATTAAGAAAAGTAAACACAG-TAAAGTCTTA-ATT
31998 AGGGTAA
64 AGGGTAA
32005 TTAAGAAAAG
1 TTAAGAAAAG
32015 TAAGCACAGT
Statistics
Matches: 130, Mismatches: 15, Indels: 12
0.83 0.10 0.08
Matches are distributed among these distances:
69 1 0.01
70 79 0.61
71 27 0.21
72 23 0.18
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.27
Consensus pattern (70 bp):
TTAAGAAAAGCAAAGTCTCAATTCAGGGTAATTAAGAAAAGTAAACACAGTAAAGTCTTAATTAG
GGTAA
Found at i:31965 original size:111 final size:111
Alignment explanation
Indices: 31869--32084 Score: 319
Period size: 111 Copynumber: 1.9 Consensus size: 111
31859 GTAATTAACA
*
31869 AAAG-CAAAGTCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAAAGTCTTAATTTGGTAA
1 AAAGTCAAAGTCTTAACTCAGGGTAATTAAGAAAAGTAAACACAGTCAAAGTCTTAATTTGGTAA
31933 TTAAGAAAAGCAAAGTCTGAATTCAAGGTAATTAAGAAAAGTAAAC
66 TTAAGAAAAGCAAAGTCTGAATTCAAGGTAATTAAGAAAAGTAAAC
* * * * * *
31979 ACAGTTAAAGTTTTAGCTCAGGGTAATTAAGAAAAGTAAGCACAGTCGAAGTCTTAATTTGGTAA
1 AAAGTCAAAGTCTTAACTCAGGGTAATTAAGAAAAGTAAACACAGTCAAAGTCTTAATTTGGTAA
* *
32044 TTAAGAAAAGCAAAGTCTTG-ATTCATGGAAATTAAGTAAAA
66 TTAAGAAAAGCAAAGTC-TGAATTCAAGGTAATTAAG-AAAA
32085 ACAGTAAAAG
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
110 3 0.03
111 85 0.90
112 6 0.06
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.26
Consensus pattern (111 bp):
AAAGTCAAAGTCTTAACTCAGGGTAATTAAGAAAAGTAAACACAGTCAAAGTCTTAATTTGGTAA
TTAAGAAAAGCAAAGTCTGAATTCAAGGTAATTAAGAAAAGTAAAC
Found at i:31989 original size:41 final size:41
Alignment explanation
Indices: 31943--32053 Score: 127
Period size: 41 Copynumber: 2.8 Consensus size: 41
31933 TTAAGAAAAG
*
31943 CAAAGTCTGAATTCAAGGTAATTAAGAAAAGTAAACACAGT
1 CAAAGTCTTAATTCAAGGTAATTAAGAAAAGTAAACACAGT
* * ** * *
31984 TAAAGTTTTAGCTCAGGGTAATTAAGAAAAGTAAGCACAGT
1 CAAAGTCTTAATTCAAGGTAATTAAGAAAAGTAAACACAGT
* *
32025 CGAAGTCTTAATT--TGGTAATTAAGAAAAG
1 CAAAGTCTTAATTCAAGGTAATTAAGAAAAG
32054 CAAAGTCTTG
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
39 15 0.26
41 42 0.74
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (41 bp):
CAAAGTCTTAATTCAAGGTAATTAAGAAAAGTAAACACAGT
Found at i:32103 original size:37 final size:37
Alignment explanation
Indices: 32064--32336 Score: 287
Period size: 37 Copynumber: 7.2 Consensus size: 37
32054 CAAAGTCTTG
* *
32064 ATTCATGGAAATTAAGTAAAAACAGTAAAAGGACTTG
1 ATTCATGGAAATTAAGTAAAAACAGTCAAAGGACTTA
* *
32101 ATTCA-GGTTAATCAAGTAAACACAACAGTCAAAGGACTTA
1 ATTCATGG-AAATTAAGT-AA-A-AACAGTCAAAGGACTTA
* **
32141 ATTCAAGGAAATTAAGTAAAAGTAGTCAAAGGACTTA
1 ATTCATGGAAATTAAGTAAAAACAGTCAAAGGACTTA
* ** * *
32178 ATTCAGGGAAATTAAGTAAAAGTAGTAAAATGACTTA
1 ATTCATGGAAATTAAGTAAAAACAGTCAAAGGACTTA
* **
32215 ATTCATGGTAATTAAGTAAAAGTAGTCAAAGGACTTA
1 ATTCATGGAAATTAAGTAAAAACAGTCAAAGGACTTA
* * *
32252 ATTCATGGTAATTAAGTAAACACAGTAGTCAAAGTACTTA
1 ATTCATGGAAATTAAGTAAA-A-A-CAGTCAAAGGACTTA
* * *
32292 ATTCAGGGAAATTAAGTAAAATCAGTCAAAGGACATA
1 ATTCATGGAAATTAAGTAAAAACAGTCAAAGGACTTA
32329 ATTCATGG
1 ATTCATGG
32337 TAATCAGGTA
Statistics
Matches: 204, Mismatches: 24, Indels: 16
0.84 0.10 0.07
Matches are distributed among these distances:
36 2 0.01
37 133 0.65
38 4 0.02
39 4 0.02
40 59 0.29
41 2 0.01
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (37 bp):
ATTCATGGAAATTAAGTAAAAACAGTCAAAGGACTTA
Found at i:32279 original size:114 final size:113
Alignment explanation
Indices: 32064--32348 Score: 362
Period size: 114 Copynumber: 2.5 Consensus size: 113
32054 CAAAGTCTTG
* * *
32064 ATTCATGGAAATTAAGTAAAAACAGTAAAAGGACTTGATTCA-GGTTAATCAAGTAAACACAACA
1 ATTCAGGGAAATTAAGT-AAAATAGTAAAAGGACTTAATTCATGG-TAATCAAGTAAACACAACA
32128 GTCAAAGGACTTAATTCAAGGAAATTAAGTAAAAGTAGTCAAAGGACTTA
64 GTCAAAGGACTTAATTCAAGGAAATTAAGTAAAAGTAGTCAAAGGACTTA
* * **
32178 ATTCAGGGAAATTAAGTAAAAGTAGTAAAATGACTTAATTCATGGTAATTAAGT-AA-A-AGTAG
1 ATTCAGGGAAATTAAGTAAAA-TAGTAAAAGGACTTAATTCATGGTAATCAAGTAAACACAACAG
* * *
32240 TCAAAGGACTTAATTCATGGTAATTAAGTAAACACAGTAGTCAAAGTACTTA
65 TCAAAGGACTTAATTCAAGGAAATTAAGT-AA-A-AGTAGTCAAAGGACTTA
* * *
32292 ATTCAGGGAAATTAAGTAAAATCAGTCAAAGGACATAATTCATGGTAATCAGGTAAA
1 ATTCAGGGAAATTAAGTAAAAT-AGTAAAAGGACTTAATTCATGGTAATCAAGTAAA
32349 GTAAAGCACA
Statistics
Matches: 149, Mismatches: 15, Indels: 13
0.84 0.08 0.07
Matches are distributed among these distances:
111 30 0.20
112 3 0.02
113 8 0.05
114 104 0.70
115 4 0.03
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (113 bp):
ATTCAGGGAAATTAAGTAAAATAGTAAAAGGACTTAATTCATGGTAATCAAGTAAACACAACAGT
CAAAGGACTTAATTCAAGGAAATTAAGTAAAAGTAGTCAAAGGACTTA
Found at i:32348 original size:151 final size:151
Alignment explanation
Indices: 32064--32348 Score: 403
Period size: 151 Copynumber: 1.9 Consensus size: 151
32054 CAAAGTCTTG
*
32064 ATTCATGGAAATTAAGTAAAAACAGTAAAAGGACTTGATTCAGGTTAATCAAGTAAACACAACAG
1 ATTCATGGAAATTAAGTAAAAACAGTAAAAGGACTTAATTCAGGTTAATCAAGTAAACACAACAG
* *
32129 TCAAAGGACTTAATTCAAGGAAATTAAGTAAAAGTAGTCAAAGGACTTAATTCAGGGAAATTAAG
66 TCAAAGGACTTAATTCAAGGAAATTAAGTAAAAGTAGTCAAAGGACATAATTCAGGGAAATCAAG
32194 TAAAAGTAGTAAAATGACTTA
131 TAAAAGTAGTAAAATGACTTA
* ** * * **
32215 ATTCATGGTAATTAAGTAAAAGTAGTCAAAGGACTTAATTCATGG-TAATTAAGTAAACACAGTA
1 ATTCATGGAAATTAAGTAAAAACAGTAAAAGGACTTAATTCA-GGTTAATCAAGTAAACACAACA
* * * *
32279 GTCAAAGTACTTAATTCAGGGAAATTAAGTAAAA-TCAGTCAAAGGACATAATTCATGGTAATCA
65 GTCAAAGGACTTAATTCAAGGAAATTAAGTAAAAGT-AGTCAAAGGACATAATTCAGGGAAATCA
*
32343 GGTAAA
129 AGTAAA
32349 GTAAAGCACA
Statistics
Matches: 117, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
150 1 0.01
151 114 0.97
152 2 0.02
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (151 bp):
ATTCATGGAAATTAAGTAAAAACAGTAAAAGGACTTAATTCAGGTTAATCAAGTAAACACAACAG
TCAAAGGACTTAATTCAAGGAAATTAAGTAAAAGTAGTCAAAGGACATAATTCAGGGAAATCAAG
TAAAAGTAGTAAAATGACTTA
Found at i:32391 original size:41 final size:41
Alignment explanation
Indices: 32344--32675 Score: 372
Period size: 41 Copynumber: 8.1 Consensus size: 41
32334 TGGTAATCAG
*
32344 GTAAAGTAAAGCACATACTTAATTTCAAGGAAAGAAATTAA
1 GTAAAGTAAAGCACAGACTTAATTTCAAGGAAAGAAATTAA
* * * *
32385 GTAAAGTATAGCACATACTTAATTTCAAGGAAGGAAATTAG
1 GTAAAGTAAAGCACAGACTTAATTTCAAGGAAAGAAATTAA
** * *
32426 GTAAAGTTTAGCACGGACTTAATTTCAAGGAAGGAAATTAA
1 GTAAAGTAAAGCACAGACTTAATTTCAAGGAAAGAAATTAA
** * *
32467 GTAAAGTATGGCACAGACTTAATTTCAATGAAAGAAATTAG
1 GTAAAGTAAAGCACAGACTTAATTTCAAGGAAAGAAATTAA
*
32508 GTAAA-TAGTAAGCACAGACTTAATTTCAA-GAAAGGAAATTAG
1 GTAAAGTA--AAGCACAGACTTAATTTCAAGGAAA-GAAATTAA
*
32550 GTAAAG-AATAGCACAGACTTAATTTCAA-GAAATGAAATTAG
1 GTAAAGTAA-AGCACAGACTTAATTTCAAGGAAA-GAAATTAA
* *
32591 GTAAAG-ACAAGCACAAACTTAATTTCAAGGAAGGAAATT-A
1 GTAAAGTA-AAGCACAGACTTAATTTCAAGGAAAGAAATTAA
* *
32631 GCTAAAG-ACAAGCACAGACTTAATTTCAGGGAAGGAAATTAA
1 G-TAAAGTA-AAGCACAGACTTAATTTCAAGGAAAGAAATTAA
32673 GTA
1 GTA
32676 GAGTTAATAA
Statistics
Matches: 261, Mismatches: 21, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
40 4 0.02
41 219 0.84
42 38 0.15
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.24
Consensus pattern (41 bp):
GTAAAGTAAAGCACAGACTTAATTTCAAGGAAAGAAATTAA
Found at i:32429 original size:82 final size:83
Alignment explanation
Indices: 32342--32671 Score: 413
Period size: 82 Copynumber: 4.0 Consensus size: 83
32332 CATGGTAATC
* *
32342 AGGTAAAGTA-AAGCACATACTTAATTTCAAGGAAAGAAATTAAGTAAAGTATAGCACATACTTA
1 AGGTAAAGTACAAGCACAGACTTAATTTCAAGGAAAGAAATTAAGTAAAGTATAGCACAGACTTA
32406 ATTTCAAGGAAGGAAATT
66 ATTTCAAGGAAGGAAATT
** * * *
32424 AGGTAAAGT-TTAGCACGGACTTAATTTCAAGGAAGGAAATTAAGTAAAGTATGGCACAGACTTA
1 AGGTAAAGTACAAGCACAGACTTAATTTCAAGGAAAGAAATTAAGTAAAGTATAGCACAGACTTA
* *
32488 ATTTCAATGAAAGAAATT
66 ATTTCAAGGAAGGAAATT
* * *
32506 AGGTAAA-TAGTAAGCACAGACTTAATTTCAA-GAAAGGAAATTAGGTAAAGAATAGCACAGACT
1 AGGTAAAGTA-CAAGCACAGACTTAATTTCAAGGAAA-GAAATTAAGTAAAGTATAGCACAGACT
* *
32569 TAATTTCAAGAAATGAAATT
64 TAATTTCAAGGAAGGAAATT
* * *
32589 AGGTAAAG-ACAAGCACAAACTTAATTTCAAGGAAGGAAATT-AGCTAAAG-ACAAGCACAGACT
1 AGGTAAAGTACAAGCACAGACTTAATTTCAAGGAAAGAAATTAAG-TAAAGTA-TAGCACAGACT
*
32651 TAATTTCAGGGAAGGAAATT
64 TAATTTCAAGGAAGGAAATT
32671 A
1 A
32672 AGTAGAGTTA
Statistics
Matches: 215, Mismatches: 25, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
81 3 0.01
82 141 0.66
83 71 0.33
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.24
Consensus pattern (83 bp):
AGGTAAAGTACAAGCACAGACTTAATTTCAAGGAAAGAAATTAAGTAAAGTATAGCACAGACTTA
ATTTCAAGGAAGGAAATT
Found at i:32537 original size:165 final size:165
Alignment explanation
Indices: 32352--32658 Score: 449
Period size: 165 Copynumber: 1.9 Consensus size: 165
32342 AGGTAAAGTA
* * * *
32352 AAGCACATACTTAATTTCAAGGAAA-GAAATTAAGTAAAGTATAGCACATACTTAATTTCAAGGA
1 AAGCACAGACTTAATTTCAA-GAAAGGAAATTAAGTAAAGAATAGCACAGACTTAATTTCAAGAA
*** ** **
32416 AGGAAATTAGGTAAAGTTTAGCACGGACTTAATTTCAAGGAAGGAAATTAAG-TAAAGTA-TGGC
65 AGGAAATTAGGTAAAGACAAGCACAAACTTAATTTCAAGGAAGGAAATT-AGCTAAAG-ACAAGC
32479 ACAGACTTAATTTCAATGAAAGAAATTAGGTAAATAGT
128 ACAGACTTAATTTCAATGAAAGAAATTAGGTAAATAGT
*
32517 AAGCACAGACTTAATTTCAAGAAAGGAAATTAGGTAAAGAATAGCACAGACTTAATTTCAAGAAA
1 AAGCACAGACTTAATTTCAAGAAAGGAAATTAAGTAAAGAATAGCACAGACTTAATTTCAAGAAA
*
32582 TGAAATTAGGTAAAGACAAGCACAAACTTAATTTCAAGGAAGGAAATTAGCTAAAGACAAGCACA
66 GGAAATTAGGTAAAGACAAGCACAAACTTAATTTCAAGGAAGGAAATTAGCTAAAGACAAGCACA
32647 GACTTAATTTCA
131 GACTTAATTTCA
32659 GGGAAGGAAA
Statistics
Matches: 126, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
164 7 0.06
165 119 0.94
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.24
Consensus pattern (165 bp):
AAGCACAGACTTAATTTCAAGAAAGGAAATTAAGTAAAGAATAGCACAGACTTAATTTCAAGAAA
GGAAATTAGGTAAAGACAAGCACAAACTTAATTTCAAGGAAGGAAATTAGCTAAAGACAAGCACA
GACTTAATTTCAATGAAAGAAATTAGGTAAATAGT
Found at i:32735 original size:32 final size:32
Alignment explanation
Indices: 32681--32864 Score: 172
Period size: 32 Copynumber: 5.5 Consensus size: 32
32671 AAGTAGAGTT
** *
32681 AATAAAGGGCTTATTTCAGGGTAATTAAGTAG
1 AATAAAGAACTTAATTCAGGGTAATTAAGTAG
* * *
32713 AATAAAGAACTTAATTCTGGGTACTTAAGTAA
1 AATAAAGAACTTAATTCAGGGTAATTAAGTAG
*
32745 AATAAAGAACATAATTCAGGGTAATTAAGTAG
1 AATAAAGAACTTAATTCAGGGTAATTAAGTAG
* * *
32777 AATAAAGAACTTAATCCAAGGTAATTAAGTGGATTC
1 AATAAAGAACTTAATTCAGGGTAATTAAGT--A--G
*
32813 AATAAA-ATAGCTTAATTCAAGGTAATTAAGTGGAG
1 AATAAAGA-A-CTTAATTCAGGGTAATTAAGT--AG
32848 TCAATAAAGAACTTAAT
1 --AATAAAGAACTTAAT
32865 CTAAAAAGAG
Statistics
Matches: 127, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
32 81 0.64
34 1 0.01
35 1 0.01
36 13 0.10
37 30 0.24
38 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (32 bp):
AATAAAGAACTTAATTCAGGGTAATTAAGTAG
Found at i:43930 original size:21 final size:22
Alignment explanation
Indices: 43885--43933 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
43875 TAAAATGGGT
*
43885 AATCA-AGAGTTTTCAAGATTT
1 AATCAGAGAGTTTTCAAGATTA
43906 AATCAGAGA-TTTTCAA-ATTCA
1 AATCAGAGAGTTTTCAAGATT-A
43927 AATCAGA
1 AATCAGA
43934 TTTAGTGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 3 0.12
21 19 0.76
22 3 0.12
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (22 bp):
AATCAGAGAGTTTTCAAGATTA
Done.