Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011717.1 Corchorus capsularis cultivar CVL-1 contig11738, 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: 29864
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:368 original size:125 final size:125
Alignment explanation
Indices: 214--650 Score: 348
Period size: 125 Copynumber: 3.3 Consensus size: 125
204 ATATTGAATT
* * *
214 TAATTAAATGAAAATAGAGTCTTTCGTAGAATAAAACAGTATATTAAAAATTTTAATATATCCAA
1 TAATTAAATAAAAATAGAGTTTTTAGTAGAATAAAACAGTATATTAAAAATTTTAATATATCCAA
279 TTTTTATTGAAAAATAGTAAAATTGTCAAAATAAAGAAACTATAAAGAAATTAGATTTAA
66 TTTTTATTGAAAAATAGTAAAATTGTCAAAATAAAGAAACTATAAAGAAATTAGATTTAA
* ** * * *
339 TAATTGAATAAAAATAGAGTTTTTAGTAGAATAAAACTACAATCGTTTAAGCAAGGGTATTTAAG
1 TAATTAAATAAAAATAGAGTTTTTAGTAGAATAAAAC-AGTAT--ATTAA--AA--AT-TTTAAT
* * * * * *
404 AGAT---ATATTCA--AAAAAATAAGGATATAATGGTCGATTCAAAAGTTTTAAAATGGTAAA-A
58 ATATCCAATTTTTATTGAAAAAT-A-G-TAAAAT--T-G--TCAAAA----T-AAA--G-AAACT
*
463 ATAAA-ATAATTATAAAATATTGAA
107 ATAAAGA-AA-T-T-AGAT-TT-AA
* * *
487 TTTAATTAAATGAAAATAGAGTTTTTCGTAGAATAAAACTGTATATTAAAAATTTTAATATATCC
1 --TAATTAAATAAAAATAGAGTTTTTAGTAGAATAAAACAGTATATTAAAAATTTTAATATATCC
552 AATTTTTATTGAAAAATAGTAAAATTGTCAAAATAAAGAAACTATAAAGAAATTAGATTTAA
64 AATTTTTATTGAAAAATAGTAAAATTGTCAAAATAAAGAAACTATAAAGAAATTAGATTTAA
* *
614 TAATTGAATAAAAATAGAGTTTTTAGTAGAACAAAAC
1 TAATTAAATAAAAATAGAGTTTTTAGTAGAATAAAAC
651 TACAATCGTT
Statistics
Matches: 237, Mismatches: 36, Indels: 78
0.68 0.10 0.22
Matches are distributed among these distances:
125 66 0.28
126 3 0.01
127 2 0.01
128 12 0.05
129 4 0.02
130 9 0.04
131 9 0.04
132 9 0.04
133 10 0.04
134 4 0.02
135 1 0.00
136 6 0.03
139 6 0.03
140 1 0.00
141 4 0.02
142 10 0.04
143 9 0.04
144 9 0.04
145 9 0.04
146 4 0.02
147 12 0.05
148 2 0.01
149 2 0.01
150 34 0.14
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.33
Consensus pattern (125 bp):
TAATTAAATAAAAATAGAGTTTTTAGTAGAATAAAACAGTATATTAAAAATTTTAATATATCCAA
TTTTTATTGAAAAATAGTAAAATTGTCAAAATAAAGAAACTATAAAGAAATTAGATTTAA
Found at i:671 original size:275 final size:275
Alignment explanation
Indices: 174--724 Score: 1066
Period size: 275 Copynumber: 2.0 Consensus size: 275
164 ACCTTTTAAA
174 TTAAAATGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATGAAAATAGAGTCTTTC
1 TTAAAATGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATGAAAATAGAGTCTTTC
239 GTAGAATAAAACAGTATATTAAAAATTTTAATATATCCAATTTTTATTGAAAAATAGTAAAATTG
66 GTAGAATAAAACAGTATATTAAAAATTTTAATATATCCAATTTTTATTGAAAAATAGTAAAATTG
304 TCAAAATAAAGAAACTATAAAGAAATTAGATTTAATAATTGAATAAAAATAGAGTTTTTAGTAGA
131 TCAAAATAAAGAAACTATAAAGAAATTAGATTTAATAATTGAATAAAAATAGAGTTTTTAGTAGA
*
369 ATAAAACTACAATCGTTTAAGCAAGGGTATTTAAGAGATATATTCAAAAAAATAAGGATATAATG
196 ACAAAACTACAATCGTTTAAGCAAGGGTATTTAAGAGATATATTCAAAAAAATAAGGATATAATG
434 GTCGATTCAAAAGTT
261 GTCGATTCAAAAGTT
*
449 TTAAAATGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATGAAAATAGAGTTTTTC
1 TTAAAATGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATGAAAATAGAGTCTTTC
*
514 GTAGAATAAAACTGTATATTAAAAATTTTAATATATCCAATTTTTATTGAAAAATAGTAAAATTG
66 GTAGAATAAAACAGTATATTAAAAATTTTAATATATCCAATTTTTATTGAAAAATAGTAAAATTG
579 TCAAAATAAAGAAACTATAAAGAAATTAGATTTAATAATTGAATAAAAATAGAGTTTTTAGTAGA
131 TCAAAATAAAGAAACTATAAAGAAATTAGATTTAATAATTGAATAAAAATAGAGTTTTTAGTAGA
*
644 ACAAAACTACAATCGTTTAATCAAGGGTATTTAAGAGATATATTCAAAAAAATAAGGATATAATG
196 ACAAAACTACAATCGTTTAAGCAAGGGTATTTAAGAGATATATTCAAAAAAATAAGGATATAATG
709 GTCGATTCAAAAGTT
261 GTCGATTCAAAAGTT
724 T
1 T
725 CTCAAAACTC
Statistics
Matches: 272, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
275 272 1.00
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.33
Consensus pattern (275 bp):
TTAAAATGGTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATGAAAATAGAGTCTTTC
GTAGAATAAAACAGTATATTAAAAATTTTAATATATCCAATTTTTATTGAAAAATAGTAAAATTG
TCAAAATAAAGAAACTATAAAGAAATTAGATTTAATAATTGAATAAAAATAGAGTTTTTAGTAGA
ACAAAACTACAATCGTTTAAGCAAGGGTATTTAAGAGATATATTCAAAAAAATAAGGATATAATG
GTCGATTCAAAAGTT
Found at i:1571 original size:29 final size:30
Alignment explanation
Indices: 1527--1590 Score: 114
Period size: 29 Copynumber: 2.2 Consensus size: 30
1517 TTTAATCGAA
1527 TAAAA-ATAGAGTTTTTAGTAGAATAATTG
1 TAAAAGATAGAGTTTTTAGTAGAATAATTG
1556 TAAAAGATAGAG-TTTTAGTAGAATAATTG
1 TAAAAGATAGAGTTTTTAGTAGAATAATTG
1585 TAAAAG
1 TAAAAG
1591 TTTATTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 28 0.82
30 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (30 bp):
TAAAAGATAGAGTTTTTAGTAGAATAATTG
Found at i:1616 original size:26 final size:26
Alignment explanation
Indices: 1580--1630 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 26
1570 TTAGTAGAAT
1580 AATTGTAAAAG-TTTATTTTTAAAAAA
1 AATTGTAAAAGATTTA-TTTTAAAAAA
1606 AATTGTAAAAGAATTTATTTTAAAA
1 AATTGTAAAAG-ATTTATTTTAAAA
1631 GTTCTAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 11 0.48
27 8 0.35
28 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (26 bp):
AATTGTAAAAGATTTATTTTAAAAAA
Found at i:1782 original size:28 final size:26
Alignment explanation
Indices: 1710--1803 Score: 86
Period size: 27 Copynumber: 3.5 Consensus size: 26
1700 AGATTTAATT
* *
1710 AAATAAAA-ATAGAGTTTTTTTACAGAA
1 AAATAAAATATTGAGTTTTTTT-GAG-A
*
1737 AAATAAAA-ATAGAGTTTTTAGTTGAGTA
1 AAATAAAATATTGAGTTTTT--TTGAG-A
1765 AAATAAAATATTGA-TTTTTTTGAGA
1 AAATAAAATATTGAGTTTTTTTGAGA
*
1790 TAATAAAATATTGA
1 AAATAAAATATTGA
1804 ATTTATTTAA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
25 14 0.23
26 5 0.08
27 19 0.32
28 16 0.27
29 6 0.10
ACGTcount: A:0.49, C:0.01, G:0.13, T:0.37
Consensus pattern (26 bp):
AAATAAAATATTGAGTTTTTTTGAGA
Found at i:2077 original size:4 final size:4
Alignment explanation
Indices: 2065--2105 Score: 59
Period size: 4 Copynumber: 10.5 Consensus size: 4
2055 ACTTTTATAT
2065 ATAG TATAG ATAG AT-- ATAG ATAG ATAG ATAG ATAG ATAG AT
1 ATAG -ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
2106 GGATTAAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.06
4 28 0.82
5 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.29
Consensus pattern (4 bp):
ATAG
Found at i:2093 original size:18 final size:19
Alignment explanation
Indices: 2060--2098 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
2050 TTCGTACTTT
*
2060 TATATATAGTATAGATAGA
1 TATAGATAGTATAGATAGA
2079 TATAGATAG-ATAGATAGA
1 TATAGATAGTATAGATAGA
2097 TA
1 TA
2099 GATAGATGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (19 bp):
TATAGATAGTATAGATAGA
Found at i:4899 original size:19 final size:21
Alignment explanation
Indices: 4863--4904 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
4853 ATAATCCTCC
*
4863 TTAAAAAAACAATTTTTTCCT
1 TTAAAAAAACAATCTTTTCCT
4884 TTAAAAAAA-AA-CTTTTCCT
1 TTAAAAAAACAATCTTTTCCT
4903 TT
1 TT
4905 TCTACTTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 9 0.45
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAAAAAAACAATCTTTTCCT
Found at i:11825 original size:5 final size:5
Alignment explanation
Indices: 11815--11858 Score: 54
Period size: 5 Copynumber: 9.0 Consensus size: 5
11805 TAGTAAAAAG
* * *
11815 AGAAA AGAAA AG-CA GGAAA AGAAT AGAAA AGAAA AGAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
11859 GAGCTCTTCC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
4 2 0.06
5 30 0.94
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.02
Consensus pattern (5 bp):
AGAAA
Found at i:13245 original size:32 final size:32
Alignment explanation
Indices: 13197--13263 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
13187 AATGAAACTC
* *
13197 TGTAAGACCCATTTTTGG-AAGTAGGTGTTTAA
1 TGTAAGAACCAATTTTGGTAAGTAGG-GTTTAA
13229 TGTAAGAACCAATTTTGGTAAGTAGGGTTTAA
1 TGTAAGAACCAATTTTGGTAAGTAGGGTTTAA
13261 TGT
1 TGT
13264 GGTGGAGTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 25 0.78
33 7 0.22
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.37
Consensus pattern (32 bp):
TGTAAGAACCAATTTTGGTAAGTAGGGTTTAA
Found at i:17761 original size:58 final size:58
Alignment explanation
Indices: 17661--17785 Score: 232
Period size: 58 Copynumber: 2.2 Consensus size: 58
17651 AGTAAACATG
*
17661 AGTGGTAGAGAGAAAAATAACAGTGGTTATTGCTTACAAGGGGGGAAAAAGAAAACAA
1 AGTGTTAGAGAGAAAAATAACAGTGGTTATTGCTTACAAGGGGGGAAAAAGAAAACAA
*
17719 AGTGTTAGAGAGAAAAATAACAGTGGTTATTGCTTACGAGGGGGGAAAAAGAAAACAA
1 AGTGTTAGAGAGAAAAATAACAGTGGTTATTGCTTACAAGGGGGGAAAAAGAAAACAA
17777 AGTGTTAGA
1 AGTGTTAGA
17786 TGCACCCATA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 65 1.00
ACGTcount: A:0.45, C:0.06, G:0.30, T:0.19
Consensus pattern (58 bp):
AGTGTTAGAGAGAAAAATAACAGTGGTTATTGCTTACAAGGGGGGAAAAAGAAAACAA
Found at i:21953 original size:3 final size:3
Alignment explanation
Indices: 21945--21984 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
21935 TCTCTTAAAT
21945 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
21985 CTATACTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:22066 original size:31 final size:30
Alignment explanation
Indices: 22026--22100 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 30
22016 AAACTTTATG
22026 TTTTCCAATTGTACCCTTATTTTT-AAAACATA
1 TTTT-CAATTGTA-CCTT-TTTTTAAAAACATA
22058 TTTTCAATTGTACCTTTTTTTAAAAAACATA
1 TTTTCAATTGTACCTTTTTTT-AAAAACATA
*
22089 TTTCTAAATTGT
1 TTT-TCAATTGT
22101 CATTACGAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
29 5 0.13
30 4 0.10
31 19 0.49
32 11 0.28
ACGTcount: A:0.32, C:0.15, G:0.04, T:0.49
Consensus pattern (30 bp):
TTTTCAATTGTACCTTTTTTTAAAAACATA
Found at i:22184 original size:155 final size:156
Alignment explanation
Indices: 22013--22324 Score: 513
Period size: 155 Copynumber: 2.0 Consensus size: 156
22003 TACGAATAAG
* *
22013 GGGAAACTTTATGTTTTCCAATTGTACCCTTATTTTTAAAACATATTTTCAATTGTA-CCTTTTT
1 GGGAAACTTTACGTTTTCCAATTGTACCCATATTTTTAAAACATATTTTCAATTGTACCCTTTTT
* * * *
22077 TTAAAAAACATATTTCTAAATTGTCATTAC-GAGTAATATTTTAATTATTCAATTA-TTTTTTAA
66 TT--AAAACATATTTCTAAATTGCCACTACTAAATAATATTTTAATTATTCAATTATTTTTTTAA
22140 TCATAAATTATTCCATTATTAATTATTA
129 TCATAAATTATTCCATTATTAATTATTA
*
22168 GGGAAACTTTACGTTTTCCGATTGTACCCATATTTTTAAAACATATTTTCAATTGTACCCTTTTT
1 GGGAAACTTTACGTTTTCCAATTGTACCCATATTTTTAAAACATATTTTCAATTGTACCCTTTTT
*
22233 TTAAAACATATTTCTAAATTGCCACTACTAAATAATATTTTAATTATTCCATTATTTTTTTAATC
66 TTAAAACATATTTCTAAATTGCCACTACTAAATAATATTTTAATTATTCAATTATTTTTTTAATC
22298 ATAAATTATTCCATTATTAATTATTA
131 ATAAATTATTCCATTATTAATTATTA
22324 G
1 G
22325 ATTATATAAT
Statistics
Matches: 146, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
154 24 0.16
155 76 0.52
156 46 0.32
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.47
Consensus pattern (156 bp):
GGGAAACTTTACGTTTTCCAATTGTACCCATATTTTTAAAACATATTTTCAATTGTACCCTTTTT
TTAAAACATATTTCTAAATTGCCACTACTAAATAATATTTTAATTATTCAATTATTTTTTTAATC
ATAAATTATTCCATTATTAATTATTA
Found at i:22236 original size:30 final size:31
Alignment explanation
Indices: 22188--22245 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
22178 ACGTTTTCCG
22188 ATTGTACCCATATTTTTAAAACATATTTTCA
1 ATTGTACCCATATTTTTAAAACATATTTTCA
*
22219 ATTGTACCC-TTTTTTTAAAACATATTT
1 ATTGTACCCATATTTTTAAAACATATTT
22246 CTAAATTGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.33, C:0.16, G:0.03, T:0.48
Consensus pattern (31 bp):
ATTGTACCCATATTTTTAAAACATATTTTCA
Found at i:22253 original size:31 final size:31
Alignment explanation
Indices: 22188--22253 Score: 98
Period size: 30 Copynumber: 2.1 Consensus size: 31
22178 ACGTTTTCCG
*
22188 ATTGTACCCATATTTTTAAAACATATTTTCA
1 ATTGTACCCATATTTTTAAAACATATTTTAA
*
22219 ATTGTACCC-TTTTTTTAAAACATATTTCTAA
1 ATTGTACCCATATTTTTAAAACATATTT-TAA
22250 ATTG
1 ATTG
22254 CCACTACTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.47
Consensus pattern (31 bp):
ATTGTACCCATATTTTTAAAACATATTTTAA
Found at i:26605 original size:2 final size:2
Alignment explanation
Indices: 26600--26654 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
26590 CTTTTTTTAT
26600 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
26642 AC AC AC AC AC AC A
1 AC AC AC AC AC AC A
26655 TATATATATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:27035 original size:7 final size:7
Alignment explanation
Indices: 27016--27066 Score: 77
Period size: 7 Copynumber: 7.1 Consensus size: 7
27006 GGGATAAGTG
27016 GAAAAAA
1 GAAAAAA
27023 TG-AAAAA
1 -GAAAAAA
27030 GAAAAAA
1 GAAAAAA
27037 GAAAAAA
1 GAAAAAA
27044 GAAAAAA
1 GAAAAAA
27051 GAAAAAA
1 GAAAAAA
27058 GAAAGAAA
1 GAAA-AAA
27066 G
1 G
27067 GAAACGAGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 1 0.02
7 35 0.85
8 5 0.12
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (7 bp):
GAAAAAA
Found at i:27162 original size:44 final size:44
Alignment explanation
Indices: 27086--27231 Score: 175
Period size: 44 Copynumber: 3.2 Consensus size: 44
27076 AAGAGCAACG
* *
27086 ATGGTTTTCAAAAAATAGTCATGGTTTACAAAAGGTTTTGATAAA
1 ATGGTTTTC-AAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA
*
27131 ATGGTTTTCAAAAAGAGTCGTGGTTTTCAAAAGGTTTTGATAAA
1 ATGGTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA
* * * *
27175 ATGTTTTTTTTCAAGAAGAATCATGGTTTTCAAGAGGGTTTTGATAAA
1 ATG---GTTTTCAAAAAGAGTCATGGTTTTCAA-AAGGTTTTGATAAA
*
27223 AGGGTTTTC
1 ATGGTTTTC
27232 CAAAGTTGCA
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
44 35 0.40
45 14 0.16
47 23 0.26
48 15 0.17
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (44 bp):
ATGGTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA
Found at i:27581 original size:13 final size:12
Alignment explanation
Indices: 27563--27591 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
27553 TGACAAAGAT
27563 AAAAAAAAAATG
1 AAAAAAAAAATG
27575 AAAAAAAAAATG
1 AAAAAAAAAATG
27587 AAAAA
1 AAAAA
27592 TGAAAATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAAAAAAAATG
Found at i:27963 original size:20 final size:18
Alignment explanation
Indices: 27936--27995 Score: 70
Period size: 17 Copynumber: 3.3 Consensus size: 18
27926 AGTGCATTGA
27936 AAAAAAAAGAGAGAGAAAG
1 AAAAAAAAGAGA-AGAAAG
*
27955 AAAATAAAAGAAAAGAAA-
1 AAAA-AAAAGAGAAGAAAG
*
27973 AGAAAAAA-AGAAGAAAG
1 AAAAAAAAGAGAAGAAAG
27990 AAAAAA
1 AAAAAA
27996 GGAAAATGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 7 0.20
17 9 0.26
18 3 0.09
19 9 0.26
20 7 0.20
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (18 bp):
AAAAAAAAGAGAAGAAAG
Found at i:27968 original size:5 final size:5
Alignment explanation
Indices: 27951--27993 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
27941 AAAGAGAGAG
* *
27951 AAAGA AAATA AAAGA AAAGA AAAGA AAAAA AGAAG- AAAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA A-AAGA AAAGA AAA
27994 AAGGAAAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 3 0.09
5 27 0.84
6 2 0.06
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:29074 original size:29 final size:29
Alignment explanation
Indices: 29032--29088 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
29022 ATGTTTATTG
*
29032 ATCCAAGGCGATCTTTCTTGAGTTAATTA
1 ATCCAAGGCGATCTTTCTTCAGTTAATTA
*
29061 ATCCAGGGCGATCTTTCTTCAGTTAATT
1 ATCCAAGGCGATCTTTCTTCAGTTAATT
29089 TCAATTGGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.39
Consensus pattern (29 bp):
ATCCAAGGCGATCTTTCTTCAGTTAATTA
Found at i:29113 original size:35 final size:35
Alignment explanation
Indices: 29063--29197 Score: 164
Period size: 35 Copynumber: 3.9 Consensus size: 35
29053 GTTAATTAAT
* * * **
29063 CCAGGGCGATCTTTCTTCAGTTAATTTCAATTGGT
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAC
* *
29098 CCAGGGCGGTATTTCTTGAGTTTATTTCAGTTGAC
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAC
* *
29133 CCAGGGTGGTCTTTCTTCAGCTTATTTCAGTTGAC
1 CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAC
*
29168 CCAGGGTGGTCTTTC-TCTAGTTTATTTCAG
1 CCAGGGCGGTCTTTCTTC-AGTTTATTTCAG
29198 AATGATCGAT
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
34 2 0.02
35 85 0.98
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (35 bp):
CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGAC
Found at i:29309 original size:119 final size:119
Alignment explanation
Indices: 29158--29531 Score: 640
Period size: 119 Copynumber: 3.1 Consensus size: 119
29148 TTCAGCTTAT
*
29158 TTCAGTTGACCCAGGGTGGTCTTTCTCTAGTTTATTTCAGAATGATCGATTCAGTCGACCCAGGG
1 TTCAGTTGACCCAGGGTGGTCTTTCTCCAGTTTATTTCAGAATGATCGATTCAGTCGACCCAGGG
29223 CGGTCTTTCTTTAGTAGCTTCCAAGTTTATCCAAGTTTATGTTAGAATGATCGA
66 CGGTCTTTCTTTAGTAGCTTCCAAGTTTATCCAAGTTTATGTTAGAATGATCGA
29277 TTCAGTTGACCCAGGGTGGTCTTTCTCCAGTTTATTTCAGAATGATCGATTCAGTCGACCCAGGG
1 TTCAGTTGACCCAGGGTGGTCTTTCTCCAGTTTATTTCAGAATGATCGATTCAGTCGACCCAGGG
*
29342 CGGTCTTTCTTTAGTAGCTTCCAAGTTTATCCAAGTCTATGTTAGAATGATCGA
66 CGGTCTTTCTTTAGTAGCTTCCAAGTTTATCCAAGTTTATGTTAGAATGATCGA
* * * * *
29396 TTCAGTTGACCCAGGGTGGTTTTTCTTCAGTTCATGTCAGAATGATCGATTCGGTCGACCCAGGG
1 TTCAGTTGACCCAGGGTGGTCTTTCTCCAGTTTATTTCAGAATGATCGATTCAGTCGACCCAGGG
* * * * *
29461 TGGTCTTTCTTCAGTAGTTTCCACGTTTATCCAAGTTTATATTAGAATGATCGA
66 CGGTCTTTCTTTAGTAGCTTCCAAGTTTATCCAAGTTTATGTTAGAATGATCGA
29515 TTCAGTTGACCCAGGGT
1 TTCAGTTGACCCAGGGT
29532 AGTTTTTCAT
Statistics
Matches: 242, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
119 242 1.00
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.36
Consensus pattern (119 bp):
TTCAGTTGACCCAGGGTGGTCTTTCTCCAGTTTATTTCAGAATGATCGATTCAGTCGACCCAGGG
CGGTCTTTCTTTAGTAGCTTCCAAGTTTATCCAAGTTTATGTTAGAATGATCGA
Found at i:29328 original size:49 final size:49
Alignment explanation
Indices: 29256--29351 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 49
29246 AGTTTATCCA
* *
29256 AGTTTATGTTAGAATGATCGATTCAGTTGACCCAGGGTGGTCTTTCTCC
1 AGTTTATGTTAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTCC
29305 AGTTTAT-TTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCT
1 AGTTTATGTT-AGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCT
29352 TTAGTAGCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
48 2 0.05
49 42 0.95
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (49 bp):
AGTTTATGTTAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTCC
Found at i:29457 original size:49 final size:49
Alignment explanation
Indices: 29380--29475 Score: 156
Period size: 49 Copynumber: 2.0 Consensus size: 49
29370 ATCCAAGTCT
* * *
29380 ATGTTAGAATGATCGATTCAGTTGACCCAGGGTGGTTTTTCTTCAGTTC
1 ATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTC
*
29429 ATGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGT
1 ATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGT
29476 AGTTTCCACG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (49 bp):
ATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAGTTC
Found at i:29619 original size:33 final size:34
Alignment explanation
Indices: 29555--29624 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
29545 TGGTTTCCAG
* *
29555 TTGATCCAGGGTGGTCTTTATCAGGTTATTCA-GT
1 TTGATCCAGGGTGGTCTTCATCAAG-TATTCATGT
29589 TTGATCCAGGGTGGTCTTCATCAAAG-ATTCATGT
1 TTGATCCAGGGTGGTCTTCATC-AAGTATTCATGT
29623 TT
1 TT
29625 AAATTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 5 0.16
34 25 0.78
35 2 0.06
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (34 bp):
TTGATCCAGGGTGGTCTTCATCAAGTATTCATGT
Done.