Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014470.1 Corchorus capsularis cultivar CVL-1 contig14491, 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: 116929
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:652 original size:19 final size:19
Alignment explanation
Indices: 614--652 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
604 TTCTTATATG
* **
614 TAACCGTTTCACCATTGTT
1 TAACCGTTTCACAACCGTT
633 TAACCGTTTCACAACCGTT
1 TAACCGTTTCACAACCGTT
652 T
1 T
653 TGGGTCTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.28, G:0.10, T:0.38
Consensus pattern (19 bp):
TAACCGTTTCACAACCGTT
Found at i:1320 original size:201 final size:201
Alignment explanation
Indices: 974--1974 Score: 1237
Period size: 201 Copynumber: 5.0 Consensus size: 201
964 TTGGTTTAAA
* ** * *
974 ATAAGAAAATTTACACAATACACCGTCAGTGGAGTTTAGCAGACTACATGTGCGGGGTTTAACTT
1 ATAAGAAAAATTATGCAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTT
* **
1039 TAAGGGTTGACATGTGTACCCTTAGGGAATATATATTAATATTAAATATTTAATTATGAAATATG
66 TAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGG
* * *
1104 GTATATGTCAACTTTTTAACCCACTTATGGAGTTCAAAATTTATACTGATAGTGTATTGTATAAT
131 GTATGTGTCAACTTTTTAACCCGCTTATGGAGTTCAAAATTTATACTGACAGTGTATTGTATAAT
1169 AATCCT
196 AATCCT
* * *
1175 TTAAGAAAAATTATGCAATACGCCGTCCGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTT
1 ATAAGAAAAATTATGCAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTT
* * * *
1240 TAAGGGTTGAGATGTGTACCTTTAGGGAATATATATTAATGTTAAATATTTAATTATGAAATGGG
66 TAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGG
*
1305 GTATGTGTCAACTTTTTAACCCGCTTATGGAGTTCGAAATTTATACTGACAGTGTATTGTATAAT
131 GTATGTGTCAACTTTTTAACCCGCTTATGGAGTTCAAAATTTATACTGACAGTGTATTGTATAAT
1370 AATCCT
196 AATCCT
* * *
1376 ATAAGAAAAATTATGCAATACACCATTAGTGGAGTTTAGCAAACTGCACGTGCGGGGTTTAACTT
1 ATAAGAAAAATTATGCAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTT
* *
1441 TAAGGGTTGACATGTGTACCCTTAGGAAATATGTATTAATATTAAATATTTGATTATGAAATGGG
66 TAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGG
* * * *
1506 ATATGTGTCAAC-TTTTAACCCGCTTATAGAATCCAAAATTTATACTGACAGTGTATTGTATAAT
131 GTATGTGTCAACTTTTTAACCCGCTTATGGAGTTCAAAATTTATACTGACAGTGTATTGTATAAT
*
1570 AATCGT
196 AATCCT
* * * * ** *
1576 ATAAGAAAATTTATGCAATAAACTGTCAGTGTAGTTTAGCAGACTGCACGCACGAGG------TT
1 ATAAGAAAAATTATGCAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTT
* *
1635 TAAGGGTTGACATGTGT-CCTCTTAGGGAATATGTATTAATATTTTATATTAATTAATTATGAAA
66 TAAGGGTTGACATGTGTACC-CTTAGGGAATATGTATTAATA--TTA-AATATTTAATTATGAAA
* * * * * *
1699 T-GGGTATGCGTCAACTTCTTAACCCGCTCATGAAGTTCAAAA-TT-TACAGACAATGTATTGTA
127 TGGGGTATGTGTCAACTTTTTAACCCGCTTATGGAGTTCAAAATTTATACTGACAGTGTATTGTA
*
1761 TAACAATCCT
192 TAATAATCCT
* * * **
1771 ATAA-AAAAATTATACAATACACCGTTAGTAGAGTTTAGCAGACTGCACGTGCATGG-----C-T
1 ATAAGAAAAATTATGCAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTT
* * *
1829 TAAGGGTTGACATGTGTCCCCTTAAGGAAAATGTATTAATATTAAATATTTAATTAATTATGAAA
66 TAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATA--T--TTAATTATGAAA
* * ** * * *
1894 TTGAGGTATGTGTCAACTTCTTAACTAGCTTATGGAGTCCAAAATTTACATTGACAGTGTATTGT
127 -TGGGGTATGTGTCAACTTTTTAACCCGCTTATGGAGTTCAAAATTTATACTGACAGTGTATTGT
*
1959 ACAATAATCCTT
191 ATAATAATCC-T
1971 ATAA
1 ATAA
1975 TAAAGCTTAC
Statistics
Matches: 695, Mismatches: 89, Indels: 33
0.85 0.11 0.04
Matches are distributed among these distances:
191 3 0.00
192 3 0.00
193 2 0.00
194 117 0.17
195 42 0.06
196 18 0.03
197 69 0.10
198 2 0.00
199 21 0.03
200 105 0.15
201 313 0.45
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (201 bp):
ATAAGAAAAATTATGCAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTT
TAAGGGTTGACATGTGTACCCTTAGGGAATATGTATTAATATTAAATATTTAATTATGAAATGGG
GTATGTGTCAACTTTTTAACCCGCTTATGGAGTTCAAAATTTATACTGACAGTGTATTGTATAAT
AATCCT
Found at i:20276 original size:21 final size:20
Alignment explanation
Indices: 20234--20276 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
20224 TGGGTTCCTG
* *
20234 TGAAAAAAGTTGAAGGCTTT
1 TGAAAAAAGTTGAAGCCATT
*
20254 TGAAACAAAGTTGTAGCCATT
1 TGAAA-AAAGTTGAAGCCATT
20275 TG
1 TG
20277 TTCTGCAGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.30
Consensus pattern (20 bp):
TGAAAAAAGTTGAAGCCATT
Found at i:23908 original size:27 final size:27
Alignment explanation
Indices: 23872--23935 Score: 119
Period size: 27 Copynumber: 2.3 Consensus size: 27
23862 ATTTCTGGAA
23872 AACAAGGGAAATGGACAATTAAAAAGG
1 AACAAGGGAAATGGACAATTAAAAAGG
23899 AACAAGGGAAATGGACAATTAAAAAGG
1 AACAAGGGAAATGGACAATTAAAAAGG
23926 AACAGAGGGA
1 AACA-AGGGA
23936 GTAATTACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 31 0.86
28 5 0.14
ACGTcount: A:0.55, C:0.08, G:0.28, T:0.09
Consensus pattern (27 bp):
AACAAGGGAAATGGACAATTAAAAAGG
Found at i:29097 original size:22 final size:22
Alignment explanation
Indices: 29071--29135 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 22
29061 GGGTTAGTAT
*
29071 GTGGCCGTGAGATTCGGTCATA
1 GTGGCCGTGAGATTCGGCCATA
* *
29093 GTGGCCGTGGGATTCGGCCATG
1 GTGGCCGTGAGATTCGGCCATA
*
29115 GTGGTCGTGAGATTCGGCCAT
1 GTGGCCGTGAGATTCGGCCAT
29136 CCTTCAAAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.14, C:0.20, G:0.40, T:0.26
Consensus pattern (22 bp):
GTGGCCGTGAGATTCGGCCATA
Found at i:33054 original size:22 final size:22
Alignment explanation
Indices: 33028--33069 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
33018 ACTAAAGACT
33028 GTGGCCGTGAGATTCGGCCATA
1 GTGGCCGTGAGATTCGGCCATA
33050 GTGGCCGTGAGATTCGGCCA
1 GTGGCCGTGAGATTCGGCCA
33070 CATGATGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.17, C:0.24, G:0.38, T:0.21
Consensus pattern (22 bp):
GTGGCCGTGAGATTCGGCCATA
Found at i:33246 original size:22 final size:22
Alignment explanation
Indices: 33220--33284 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 22
33210 GGGTTAGTAT
33220 GTGGCCGTGAGATTCGGCCATA
1 GTGGCCGTGAGATTCGGCCATA
* * *
33242 GTGGCCGTGGGATTCGACCATG
1 GTGGCCGTGAGATTCGGCCATA
*
33264 GTGGTCGTGAGATTCGGCCAT
1 GTGGCCGTGAGATTCGGCCAT
33285 CCTTCAAAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.15, C:0.22, G:0.38, T:0.25
Consensus pattern (22 bp):
GTGGCCGTGAGATTCGGCCATA
Found at i:37153 original size:2 final size:2
Alignment explanation
Indices: 37146--37177 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
37136 CTTTATAGTC
37146 AT AT 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 AT AT
37178 CAAATGAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55974 original size:2 final size:2
Alignment explanation
Indices: 55967--56000 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55957 AGTGGGTAGA
55967 AT AT AT 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 AT AT AT
56001 TGTTGATAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59861 original size:53 final size:53
Alignment explanation
Indices: 59781--59883 Score: 197
Period size: 53 Copynumber: 1.9 Consensus size: 53
59771 TATCATTTCA
*
59781 CAACAAAATTTGATTTCTTAACTGAATTTTCTTAAGAGAATTTATAAAATTCG
1 CAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATTCG
59834 CAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAAT
1 CAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAAT
59884 AAAAAAGCCG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.40
Consensus pattern (53 bp):
CAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAATTCG
Found at i:63331 original size:26 final size:26
Alignment explanation
Indices: 63299--63364 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
63289 CACGTGCGAT
* * *
63299 GTCACGTGTTGAGGT-GTCCGTTGGAG
1 GTCACGTGTGGA-GTCGTACGTTGGAA
*
63325 GTTACGTGTGGAGTCGTACGTTGGAA
1 GTCACGTGTGGAGTCGTACGTTGGAA
63351 GTCACGTGTGGAGT
1 GTCACGTGTGGAGT
63365 GCCAACTGGC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 2 0.06
26 32 0.94
ACGTcount: A:0.15, C:0.14, G:0.41, T:0.30
Consensus pattern (26 bp):
GTCACGTGTGGAGTCGTACGTTGGAA
Found at i:63454 original size:23 final size:23
Alignment explanation
Indices: 63428--63552 Score: 144
Period size: 23 Copynumber: 5.4 Consensus size: 23
63418 CCAGGTTTGT
* *
63428 AAGTGGTCGGTCGCTAGACTTAG
1 AAGTGGTCGGTCGCTAGGCTTGG
* * *
63451 AAGTGGTTGGACACTAGGCTTAGG
1 AAGTGGTCGGTCGCTAGGCTT-GG
*
63475 -AGTGGTCGGTCGCTAGACTTGG
1 AAGTGGTCGGTCGCTAGGCTTGG
* *
63497 AGGTGGTCGGGCGCTAGGCTTGG
1 AAGTGGTCGGTCGCTAGGCTTGG
*
63520 GAGTGGTCGGTCGCTAGGCTTGG
1 AAGTGGTCGGTCGCTAGGCTTGG
*
63543 AAGTTGTCGG
1 AAGTGGTCGG
63553 GCGCCAAGCA
Statistics
Matches: 83, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
22 2 0.02
23 80 0.96
24 1 0.01
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.26
Consensus pattern (23 bp):
AAGTGGTCGGTCGCTAGGCTTGG
Found at i:63553 original size:46 final size:46
Alignment explanation
Indices: 63429--63556 Score: 184
Period size: 46 Copynumber: 2.8 Consensus size: 46
63419 CAGGTTTGTA
* * * *
63429 AGTGGTCGGTCGCTAGACTTAGAAGTGGTTGGACACTAGGCTTAGG
1 AGTGGTCGGTCGCTAGACTTGGAAGTGGTCGGGCGCTAGGCTTAGG
* *
63475 AGTGGTCGGTCGCTAGACTTGGAGGTGGTCGGGCGCTAGGCTTGGG
1 AGTGGTCGGTCGCTAGACTTGGAAGTGGTCGGGCGCTAGGCTTAGG
* *
63521 AGTGGTCGGTCGCTAGGCTTGGAAGTTGTCGGGCGC
1 AGTGGTCGGTCGCTAGACTTGGAAGTGGTCGGGCGC
63557 CAAGCAATTG
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.15, C:0.17, G:0.43, T:0.25
Consensus pattern (46 bp):
AGTGGTCGGTCGCTAGACTTGGAAGTGGTCGGGCGCTAGGCTTAGG
Found at i:68456 original size:39 final size:38
Alignment explanation
Indices: 68401--68476 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
68391 CTCATGAGTC
68401 ATGATTTCCTTCTTTCTTTAATTCCTTTTTTT-TTGAAGT
1 ATGATTTCCTTCTTTCTTT--TTCCTTTTTTTGTTGAAGT
*
68440 ATGATTTCCCTT-TTTCTTTTTCTTTTTTTTGTTGAAG
1 ATGATTT-CCTTCTTTCTTTTTCCTTTTTTTGTTGAAG
68477 GAGATTTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
37 10 0.29
38 6 0.18
39 14 0.41
40 4 0.12
ACGTcount: A:0.13, C:0.14, G:0.09, T:0.63
Consensus pattern (38 bp):
ATGATTTCCTTCTTTCTTTTTCCTTTTTTTGTTGAAGT
Found at i:69227 original size:22 final size:22
Alignment explanation
Indices: 69202--69278 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
69192 CTCTCTATGC
69202 AATTTTGATAATCTCTCC-ATAA
1 AATTTTGATAATCTC-CCTATAA
* * *
69224 AATTTTCATAACCTCCCTATGA
1 AATTTTGATAATCTCCCTATAA
* * *
69246 AATTTTGTTAATATCCCTAGAA
1 AATTTTGATAATCTCCCTATAA
*
69268 AATTTGGATAA
1 AATTTTGATAA
69279 GCACAAATTT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
21 2 0.05
22 41 0.95
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (22 bp):
AATTTTGATAATCTCCCTATAA
Found at i:69333 original size:22 final size:21
Alignment explanation
Indices: 69304--69447 Score: 81
Period size: 22 Copynumber: 6.6 Consensus size: 21
69294 AATTCAGTCC
*
69304 CTATGAAATTTTGTTAACCTT
1 CTATGAAATTTTGATAACCTT
* *
69325 CTTATGAAATTTTGATAATCATA
1 C-TATGAAATTTTGATAA-CCTT
* * *
69348 CTATAAAATTTCGATAACTTT
1 CTATGAAATTTTGATAACCTT
* * *
69369 CGTATGAAATTTTGTTGACCTCC
1 C-TATGAAATTTTGATAACCT-T
* * * *
69392 CTAAGAAATTCTAATGAACTTT
1 CTATGAAATTTTGAT-AACCTT
* * *
69414 TTATAAAATTTTGATAACATTT
1 CTATGAAATTTTGATAAC-CTT
*
69436 GTATGAAATTTT
1 CTATGAAATTTT
69448 AGATCATGTG
Statistics
Matches: 90, Mismatches: 27, Indels: 11
0.70 0.21 0.09
Matches are distributed among these distances:
21 7 0.08
22 76 0.84
23 7 0.08
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.44
Consensus pattern (21 bp):
CTATGAAATTTTGATAACCTT
Found at i:69384 original size:66 final size:66
Alignment explanation
Indices: 69305--69447 Score: 164
Period size: 66 Copynumber: 2.2 Consensus size: 66
69295 ATTCAGTCCC
* * * * *
69305 TATGAAATTTTGTTAACCTTCTTATGAAATTTTGAT-AATCATACTATAAAATTTCGATAAC-TT
1 TATGAAATTTTGTTAACCTCCCTAAGAAATTCTAATGAA-CATACTATAAAATTTCGATAACATT
69368 TCG
65 T-G
* * ** *
69371 TATGAAATTTTGTTGACCTCCCTAAGAAATTCTAATGAACTTTTTATAAAATTTTGATAACATTT
1 TATGAAATTTTGTTAACCTCCCTAAGAAATTCTAATGAACATACTATAAAATTTCGATAACATTT
69436 G
66 G
69437 TATGAAATTTT
1 TATGAAATTTT
69448 AGATCATGTG
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
66 60 0.92
67 5 0.08
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (66 bp):
TATGAAATTTTGTTAACCTCCCTAAGAAATTCTAATGAACATACTATAAAATTTCGATAACATTT
G
Found at i:71533 original size:2 final size:2
Alignment explanation
Indices: 71528--71553 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
71518 TTATATAGTG
71528 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
71554 GTAAGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:72580 original size:2 final size:2
Alignment explanation
Indices: 72573--72598 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
72563 AATTGAGGCC
72573 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
72599 AAATTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:84881 original size:16 final size:16
Alignment explanation
Indices: 84860--84890 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
84850 AATTTTAAGT
84860 TGATGTTTCGTTGATA
1 TGATGTTTCGTTGATA
*
84876 TGATGTTTTGTTGAT
1 TGATGTTTCGTTGAT
84891 TCTGAAAATT
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:0.16, C:0.03, G:0.26, T:0.55
Consensus pattern (16 bp):
TGATGTTTCGTTGATA
Found at i:86889 original size:11 final size:11
Alignment explanation
Indices: 86861--86890 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
86851 TTGACATTTA
*
86861 GCTACGAACTT
1 GCTACGGACTT
86872 GCTACGGACTT
1 GCTACGGACTT
86883 GCTACGGA
1 GCTACGGA
86891 TAAGTAGACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.23
Consensus pattern (11 bp):
GCTACGGACTT
Found at i:87226 original size:26 final size:25
Alignment explanation
Indices: 87197--87249 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
87187 ATTATTAACA
87197 AAAG-TAATTATTATATATACTTTATC
1 AAAGATAATTATT-TATATA-TTTATC
*
87223 AAAGTATAATTATTTTTATATTTATC
1 AAAG-ATAATTATTTATATATTTATC
87249 A
1 A
87250 TTAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 11 0.46
27 5 0.21
28 8 0.33
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.49
Consensus pattern (25 bp):
AAAGATAATTATTTATATATTTATC
Found at i:96677 original size:21 final size:21
Alignment explanation
Indices: 96651--96693 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
96641 AGAGATGTGT
96651 TCTATTGGAGAAATTATTAGG
1 TCTATTGGAGAAATTATTAGG
96672 TCTATTGGAGAAATTATTAGG
1 TCTATTGGAGAAATTATTAGG
96693 T
1 T
96694 GGAACCAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.40
Consensus pattern (21 bp):
TCTATTGGAGAAATTATTAGG
Found at i:100022 original size:14 final size:14
Alignment explanation
Indices: 100003--100031 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
99993 AAAAGCTTTG
100003 GTCTGAAATTTGGA
1 GTCTGAAATTTGGA
100017 GTCTGAAATTTGGA
1 GTCTGAAATTTGGA
100031 G
1 G
100032 CAATTTCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.31, T:0.34
Consensus pattern (14 bp):
GTCTGAAATTTGGA
Found at i:102873 original size:109 final size:110
Alignment explanation
Indices: 102682--102978 Score: 431
Period size: 109 Copynumber: 2.7 Consensus size: 110
102672 TAAATTAAAA
*
102682 TGGTAAAAATAAA--AATATATATAAAATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGT
1 TGGTAAAAATAAAGTAAT-TATA-AAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGT
*
102744 AGAATAAAATTGTATATTAG-AAAAAATTTTAATATATCCAAATTCTT
63 AGAATAAAATTGTATATTAGAAAAAAATTTGAATATATCCAAATTCTT
*
102791 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAATTTTTAGTAGA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
* *
102856 ATAAAATTGTATATTAGAAAAAAATTTGAGTATATCCAAATTTTT
66 ATAAAATTGTATATTAGAAAAAAATTTGAATATATCCAAATTCTT
* *
102901 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTA
102966 GTAGAATAAAATT
61 GTAGAATAAAATT
102979 ATAATAGTTA
Statistics
Matches: 171, Mismatches: 8, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
109 69 0.40
110 67 0.39
111 5 0.03
112 1 0.01
115 29 0.17
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (110 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAAATTTGAATATATCCAAATTCTT
Found at i:106613 original size:2 final size:2
Alignment explanation
Indices: 106606--106633 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
106596 ATTTTATAGA
106606 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
106634 GGAAGTTTTC
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
Done.