Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007594.1 Corchorus capsularis cultivar CVL-1 contig07615, 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: 46896
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:4575 original size:22 final size:23
Alignment explanation
Indices: 4550--4595 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
4540 GTGTATAATC
*
4550 GGGACTCCT-TGTGAGAGCATTT
1 GGGACTCCTGTATGAGAGCATTT
*
4572 GGGACTCCTGTATGAGAGCGTTT
1 GGGACTCCTGTATGAGAGCATTT
4595 G
1 G
4596 TCTTGCTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.17, C:0.17, G:0.35, T:0.30
Consensus pattern (23 bp):
GGGACTCCTGTATGAGAGCATTT
Found at i:5248 original size:32 final size:31
Alignment explanation
Indices: 5186--5248 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
5176 AATTGATGCC
* * *
5186 AAAAAAAAAAGGTTCTAGTCCAGATTTCTTG
1 AAAAAAAAAAAGTTCTAGTCAAGATATCTTG
* *
5217 AAAAAAAAAAAGTTCCTAGTGAATATATCTTG
1 AAAAAAAAAAAGTT-CTAGTCAAGATATCTTG
5249 GTAGTCTCTG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (31 bp):
AAAAAAAAAAAGTTCTAGTCAAGATATCTTG
Found at i:8678 original size:1 final size:1
Alignment explanation
Indices: 8672--8710 Score: 78
Period size: 1 Copynumber: 39.0 Consensus size: 1
8662 CAGCAACAGG
8672 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8711 CCTCACTTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:10415 original size:37 final size:36
Alignment explanation
Indices: 10361--10490 Score: 117
Period size: 37 Copynumber: 3.6 Consensus size: 36
10351 AAAAAGATTG
10361 ATCAGTAAATT-GATAATTAAGAGTCAAGATAATGGTA
1 ATCAGTAAATTAG-TAATTAAGAGTCAAGATAAT-GTA
*
10398 ATCAGTAAATTAGTAATT-A-AGT-AAGAGGAGAT-TA
1 ATCAGTAAATTAGTAATTAAGAGTCAAGA-TA-ATGTA
* * * *
10432 ATCAGTAAATTGATTAATTCAGAGTCAAGGTAATAGCA
1 ATCAGTAAATT-AGTAATTAAGAGTCAAGATAAT-GTA
*
10470 ATCAGTAAATCAGTAATTAAG
1 ATCAGTAAATTAGTAATTAAG
10491 TGAAAAGAGA
Statistics
Matches: 76, Mismatches: 8, Indels: 18
0.75 0.08 0.18
Matches are distributed among these distances:
34 17 0.22
35 10 0.13
36 6 0.08
37 28 0.37
38 15 0.20
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.29
Consensus pattern (36 bp):
ATCAGTAAATTAGTAATTAAGAGTCAAGATAATGTA
Found at i:10439 original size:34 final size:35
Alignment explanation
Indices: 10396--10508 Score: 99
Period size: 34 Copynumber: 3.2 Consensus size: 35
10386 AAGATAATGG
10396 TAATCAGTAAATTAGTAATTAAGT-AAGAGGAGAT
1 TAATCAGTAAATTAGTAATTAAGTCAAGAGGAGAT
* *
10430 TAATCAGTAAATTGATTAATTCAGAGTCAAG-GTA-AT
1 TAATCAGTAAATT-AGTAATT-A-AGTCAAGAGGAGAT
* * * *
10466 AGCAATCAGTAAATCAGTAATTAAGTGAA-AAGAGAT
1 --TAATCAGTAAATTAGTAATTAAGTCAAGAGGAGAT
10502 TAATCAG
1 TAATCAG
10509 AGTCAAGGTA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
34 19 0.31
35 12 0.19
36 6 0.10
37 11 0.18
38 14 0.23
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (35 bp):
TAATCAGTAAATTAGTAATTAAGTCAAGAGGAGAT
Found at i:10473 original size:72 final size:71
Alignment explanation
Indices: 10347--10508 Score: 222
Period size: 72 Copynumber: 2.3 Consensus size: 71
10337 GCAAAAAGTA
* * * *
10347 AAGT-AAAA-AGATTGATCAGTAAATTGATAATTAAGAGTCAAGATAATGGTAATCAGTAAATTA
1 AAGTGAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGATAATAGCAATCAGTAAATCA
10410 GTAATT
66 GTAATT
* * *
10416 AAGT-AAGAGGAGATTAATCAGTAAATTGATTAATTCAGAGTCAAGGTAATAGCAATCAGTAAAT
1 AAGTGAA-AAGAGATTAATCAGTAAATTGA-TAATTAAGAGTCAAGATAATAGCAATCAGTAAAT
10480 CAGTAATT
64 CAGTAATT
10488 AAGTGAAAAGAGATTAATCAG
1 AAGTGAAAAGAGATTAATCAG
10509 AGTCAAGGTA
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
69 6 0.07
70 1 0.01
71 18 0.22
72 54 0.67
73 2 0.02
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (71 bp):
AAGTGAAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGATAATAGCAATCAGTAAATCA
GTAATT
Found at i:10646 original size:55 final size:55
Alignment explanation
Indices: 10443--10635 Score: 368
Period size: 55 Copynumber: 3.5 Consensus size: 55
10433 TCAGTAAATT
*
10443 GATTAATTCAGAGTCAAGGTAATAGCAATCAGTAAATCAGTAATTAAGTGAAAAGA
1 GATTAA-TCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTGAAAAGA
10499 GATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTGAAAAGA
1 GATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTGAAAAGA
10554 GATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTGAAAAGA
1 GATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTGAAAAGA
10609 GATTAATCAGAGTCAAGGTAATAGTAA
1 GATTAATCAGAGTCAAGGTAATAGTAA
10636 ATCAATAATC
Statistics
Matches: 136, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
55 130 0.96
56 6 0.04
ACGTcount: A:0.47, C:0.08, G:0.20, T:0.25
Consensus pattern (55 bp):
GATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTGAAAAGA
Found at i:10655 original size:48 final size:51
Alignment explanation
Indices: 10469--10666 Score: 258
Period size: 55 Copynumber: 3.8 Consensus size: 51
10459 AGGTAATAGC
10469 AATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAGGTAATAGT
1 AATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAGG----AGT
10524 AATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAGGTAATAGT
1 AATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAGG----AGT
10579 AATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAA-G-GT
1 AATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAGGAGT
* * * * *
10628 AAT-AGTAAATCAATAATCAAGTAAAAAGATAGTAATCAG
1 AATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAG
10667 TAAATTGATA
Statistics
Matches: 138, Mismatches: 5, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
48 31 0.22
49 5 0.04
54 1 0.01
55 101 0.73
ACGTcount: A:0.49, C:0.08, G:0.19, T:0.25
Consensus pattern (51 bp):
AATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAGGAGT
Found at i:11387 original size:16 final size:17
Alignment explanation
Indices: 11366--11399 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11356 GTAAGAAGGT
11366 CAAG-AATGGTATTAAG
1 CAAGAAATGGTATTAAG
11382 CAAGAAAATGGTATTAAG
1 CAAG-AAATGGTATTAAG
11400 TAAAAGATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
18 12 0.75
ACGTcount: A:0.47, C:0.06, G:0.24, T:0.24
Consensus pattern (17 bp):
CAAGAAATGGTATTAAG
Found at i:11422 original size:43 final size:42
Alignment explanation
Indices: 11257--11436 Score: 184
Period size: 43 Copynumber: 4.3 Consensus size: 42
11247 CAAGAGTGAA
**
11257 AAAAAATGGTATTAAACAAAAGAGT-AAAAATGGTATTAAGT
1 AAAAAATGGTATTAAGTAAAAGAGTCAAAAATGGTATTAAGT
*** * * *
11298 AAGGTATGGTATTAAGTAAAAAAGGTCAGAAATGGTATCAAGT
1 AAAAAATGGTATTAAGTAAAAGA-GTCAAAAATGGTATTAAGT
* * *
11341 AAAATATGGTATTAAGTAAGAAG-GTCAAGAATGGTATTAAGC
1 AAAAAATGGTATTAAGTAA-AAGAGTCAAAAATGGTATTAAGT
* * * *
11383 AAGAAAATGGTATTAAGTAAAAGATTAAAAAATGATATTAGGT
1 AA-AAAATGGTATTAAGTAAAAGAGTCAAAAATGGTATTAAGT
11426 AAAAAATGGTA
1 AAAAAATGGTA
11437 AAAGAAGTGA
Statistics
Matches: 112, Mismatches: 22, Indels: 9
0.78 0.15 0.06
Matches are distributed among these distances:
41 17 0.15
42 31 0.28
43 62 0.55
44 2 0.02
ACGTcount: A:0.51, C:0.03, G:0.21, T:0.26
Consensus pattern (42 bp):
AAAAAATGGTATTAAGTAAAAGAGTCAAAAATGGTATTAAGT
Found at i:13345 original size:86 final size:86
Alignment explanation
Indices: 13225--13384 Score: 293
Period size: 86 Copynumber: 1.9 Consensus size: 86
13215 CAAACAATCT
* * *
13225 TGAGCACTCTCGCTCGGTTTCTACAAACCAATCATCATATCAACAAAACCAAACATCAAACCAAA
1 TGAGCACTCTCGCTCAGTCTCTACAAACCAATCATCACATCAACAAAACCAAACATCAAACCAAA
13290 TAATCTCACGCTCGGTCTCTA
66 TAATCTCACGCTCGGTCTCTA
13311 TGAGCACTCTCGCTCAGTCTCTACAAACCAATCATCACATCAACAAAACCAAACATCAAACCAAA
1 TGAGCACTCTCGCTCAGTCTCTACAAACCAATCATCACATCAACAAAACCAAACATCAAACCAAA
13376 TAATCTCAC
66 TAATCTCAC
13385 ACACAACCGT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 71 1.00
ACGTcount: A:0.39, C:0.33, G:0.07, T:0.21
Consensus pattern (86 bp):
TGAGCACTCTCGCTCAGTCTCTACAAACCAATCATCACATCAACAAAACCAAACATCAAACCAAA
TAATCTCACGCTCGGTCTCTA
Found at i:26152 original size:10 final size:10
Alignment explanation
Indices: 26137--26165 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
26127 TTCAAAAAAA
26137 ATAATAATAT
1 ATAATAATAT
26147 ATAATAATAT
1 ATAATAATAT
26157 ATAATAATA
1 ATAATAATA
26166 ATGAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATAATAATAT
Found at i:26673 original size:78 final size:78
Alignment explanation
Indices: 26591--26828 Score: 325
Period size: 78 Copynumber: 3.2 Consensus size: 78
26581 TTGTTTAGGT
* *
26591 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTTTTTAATTAAATATAATATCTTTAT-A--
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCTTTATAACT
26652 A-T-TATTTT---A
65 ATTATATTTTACCA
* *
26661 TTTTACTATTTTACTTAACTAAAAACTCT-TTTTTATATAATTAAATCTAATATCTTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCTTTATAACTA
26725 TTATATTTTACCA
66 TTATATTTTACCA
** * *
26738 TTTTACTATTAAACTCAACTAAAAACTCAATTTTTATATAATTAAATATAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCTTTATAACTA
26803 TTATATTTTACCA
66 TTATATTTTACCA
26816 TTTTACTATTTTA
1 TTTTACTATTTTA
26829 ATTAAAAAAT
Statistics
Matches: 146, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
69 27 0.18
70 26 0.18
71 2 0.01
72 1 0.01
73 1 0.01
74 6 0.04
77 26 0.18
78 57 0.39
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.50
Consensus pattern (78 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCTTTATAACTA
TTATATTTTACCA
Found at i:26718 original size:69 final size:69
Alignment explanation
Indices: 26591--26822 Score: 259
Period size: 70 Copynumber: 3.2 Consensus size: 69
26581 TTGTTTAGGT
* *
26591 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTTTTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCT-TTTTTATATAATTAAATATAATATCTTTATAATT
26655 ATTTTA
64 ATTTTA
* *
26661 TTTTACTATTTTACTTAACTAAAAACTCTTTTTTATATAATTAAATCTAATATCTTTATAACTAT
1 TTTTACTATTTTACTCAACTAAAAACTCTTTTTTATATAATTAAATATAATATCTTTAT-A--A-
26726 TATATTTTACCA
62 T-TATTTT---A
** * * *
26738 TTTTACTATTAAACTCAACTAAAAACTCAATTTTTATATAATTAAATATAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTC-TTTTTTATATAATTAAATATAATATCTTTATAATTA
*
26803 TTATA
65 TTTTA
*
26808 TTTTACCATTTTACT
1 TTTTACTATTTTACT
26823 ATTTTAATTA
Statistics
Matches: 137, Mismatches: 15, Indels: 20
0.80 0.09 0.12
Matches are distributed among these distances:
69 27 0.20
70 39 0.28
71 2 0.01
72 1 0.01
73 6 0.04
74 6 0.04
75 1 0.01
77 27 0.20
78 28 0.20
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (69 bp):
TTTTACTATTTTACTCAACTAAAAACTCTTTTTTATATAATTAAATATAATATCTTTATAATTAT
TTTA
Found at i:26847 original size:70 final size:73
Alignment explanation
Indices: 26695--26847 Score: 186
Period size: 78 Copynumber: 2.1 Consensus size: 73
26685 ACTCTTTTTT
* *
26695 ATATAATTAAATCTAATATCTTTATAACTATTATATTTTACCATTTTACTATTAAACTCAACTAA
1 ATATAATTAAATATAATATCCTTATAACTATTATATTTTACCATTTTACTATT--A-TCAACTAA
* *
26760 AAACTCAATTTTT
63 AAA--CAATCTTG
* *
26773 ATATAATTAAATATAATATCCTTATAACTATTATATTTTACCATTTTACTATT-TTAA-TTAAAA
1 ATATAATTAAATATAATATCCTTATAACTATTATATTTTACCATTTTACTATTATCAACTAAAAA
26836 -AATCTTG
66 CAATCTTG
26843 ATATA
1 ATATA
26848 TTAGTTTTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
70 10 0.14
73 5 0.07
74 3 0.04
78 51 0.74
ACGTcount: A:0.42, C:0.12, G:0.01, T:0.46
Consensus pattern (73 bp):
ATATAATTAAATATAATATCCTTATAACTATTATATTTTACCATTTTACTATTATCAACTAAAAA
CAATCTTG
Found at i:28104 original size:32 final size:32
Alignment explanation
Indices: 28051--28124 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
28041 AAAAAATAGC
* * *
28051 CGAA-CCGACCCACCGGAGCGGCCTATCGTGG
1 CGAAGCCGCCCCACCGGAGCGGCCTACCCTGG
* *
28082 CGAAGCCGCCCCACCGGGGCGGCCTGCCCTGG
1 CGAAGCCGCCCCACCGGAGCGGCCTACCCTGG
*
28114 CTAAGCCGCCC
1 CGAAGCCGCCC
28125 TCTTGGGACG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 4 0.11
32 32 0.89
ACGTcount: A:0.15, C:0.45, G:0.32, T:0.08
Consensus pattern (32 bp):
CGAAGCCGCCCCACCGGAGCGGCCTACCCTGG
Found at i:28871 original size:2 final size:2
Alignment explanation
Indices: 28864--28901 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
28854 ATACTATCAC
28864 TA TA TA TA 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 TA TA TA TA
28902 CACACACACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29103 original size:24 final size:25
Alignment explanation
Indices: 29047--29101 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
29037 AACCCTAAAC
*
29047 TTCATTTCTAACAACTTCTTCAAAT
1 TTCATTTCTAACAACATCTTCAAAT
29072 TTCATTTCTAACAA-ATCTTCAAAT
1 TTCATTTCTAACAACATCTTCAAAT
29096 TT-ATTT
1 TTCATTT
29102 TCCTTCATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 4 0.14
24 11 0.38
25 14 0.48
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (25 bp):
TTCATTTCTAACAACATCTTCAAAT
Found at i:29129 original size:15 final size:14
Alignment explanation
Indices: 29111--29178 Score: 58
Period size: 15 Copynumber: 5.1 Consensus size: 14
29101 TTCCTTCATT
29111 TTAATCATAAACTAA
1 TTAA-CATAAACTAA
29126 TTAA-AT--ACTAA
1 TTAACATAAACTAA
29137 TTAATCATAAACTAA
1 TTAA-CATAAACTAA
*
29152 TT-AGAT--ACTAA
1 TTAACATAAACTAA
29163 TTAAACATAAACTAA
1 TT-AACATAAACTAA
29178 T
1 T
29179 AAACTAAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
11 16 0.37
13 9 0.21
14 1 0.02
15 17 0.40
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (14 bp):
TTAACATAAACTAA
Found at i:29140 original size:26 final size:26
Alignment explanation
Indices: 29111--29178 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
29101 TTCCTTCATT
29111 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
29137 TTAATCATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
29163 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
29179 AAACTAAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:29431 original size:21 final size:20
Alignment explanation
Indices: 29395--29438 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
29385 AAAATTGTAA
*
29395 AAAAGGGGACATTGTTTAGC
1 AAAAGGGGACATTGTTCAGC
29415 AAAAGGGAGACGA-TGTTCAGC
1 AAAAGGG-GAC-ATTGTTCAGC
29436 AAA
1 AAA
29439 CCCCATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 13 0.62
22 1 0.05
ACGTcount: A:0.41, C:0.11, G:0.30, T:0.18
Consensus pattern (20 bp):
AAAAGGGGACATTGTTCAGC
Found at i:29750 original size:15 final size:15
Alignment explanation
Indices: 29730--29767 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
29720 TTCATTTATC
*
29730 TATCTATATTATATA
1 TATCTATACTATATA
29745 TATCTATACTATATA
1 TATCTATACTATATA
*
29760 TATATATA
1 TATCTATA
29768 AAAGTACGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (15 bp):
TATCTATACTATATA
Found at i:30082 original size:108 final size:111
Alignment explanation
Indices: 29859--30082 Score: 314
Period size: 108 Copynumber: 2.0 Consensus size: 111
29849 ACTATTATAG
* *
29859 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTATTT
1 TTTTATTCTACTAAAAACTCTA--TTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
* * *
29924 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTCTAATATACAA
64 TATTTTTACCAAAAAATTTGGATATACTAAAATTATTATAATATAAAA
*
29972 TTTTATTCTACTAAAAACTCTA-TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTTTA
1 TTTTATTCTACTAAAAACTCTATTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTTTA
*
30034 TTTTTACCAAAAAATTTGGATATA-TAATAATGTATTATGAT-TAAAA
66 TTTTTACCAAAAAATTTGGATATACTAA-AAT-TATTATAATATAAAA
30080 TTT
1 TTT
30083 ATTATTTCCC
Statistics
Matches: 102, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
107 3 0.03
108 67 0.66
109 9 0.09
110 2 0.02
113 21 0.21
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.48
Consensus pattern (111 bp):
TTTTATTCTACTAAAAACTCTATTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTTTA
TTTTTACCAAAAAATTTGGATATACTAAAATTATTATAATATAAAA
Found at i:30326 original size:24 final size:26
Alignment explanation
Indices: 30275--30326 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
30265 TTACTCAACT
**
30275 AAAAACTCTATTTTTATTTTTCTATA
1 AAAAACTCTATTTTTATTTTAATATA
30301 AAAAACTCTATTTTTA-TTTAAT-TA
1 AAAAACTCTATTTTTATTTTAATATA
30325 AA
1 AA
30327 TCTAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 4 0.17
26 16 0.67
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (26 bp):
AAAAACTCTATTTTTATTTTAATATA
Found at i:30461 original size:158 final size:157
Alignment explanation
Indices: 30196--30524 Score: 357
Period size: 158 Copynumber: 2.1 Consensus size: 157
30186 TATATCATTT
** *
30196 TTACCATTTTACTATTTTAATTAAAAAAACTTAGATGTATTAGAAAATTTTAAATATACTTTTAT
1 TTACCATTTTACTATTTTAATTAAAAAAACTTAGACATATTAGAAAATTTTAAATATACTTTTAC
* *** * *
30261 AGTTTTACTCAACTAAAAACTCTATTTTTATTTTTCTATAAAAAACTCTATTTTTATTTAATTAA
66 AATTTTACTCAAC-AAAAACTCTATTACAATTATTCTAT-AAAAACTCTATTTTTATTCAATTAA
* *
30326 ATCT-AATATCCTT-ATAACTATTTTGTTG
129 AT-TGAATATCCTTAATAAATATTTTATTG
* *
30354 TTATCATTTTACTATTTTAATTAAAAAAACTTAGACATATTAG-AATTTTTAAAATATATTCTTT
1 TTACCATTTTACTATTTTAATTAAAAAAACTTAGACATATTAGAAAATTTT-AAATATA--CTTT
* * *
30418 TACAATTTT-TTTAGA-AATAAACT-T-TTACAATTATTCTACTAAAAACTCTATTTTTATTCGA
63 TACAATTTTACTCA-ACAA-AAACTCTATTACAATTATTCTA-TAAAAACTCTATTTTTATTCAA
** *
30479 TTAAATTGAATATTTTTAATAAATATTTTATTT
125 TTAAATTGAATATCCTTAATAAATATTTTATTG
30512 TTACCATTTTACT
1 TTACCATTTTACT
30525 TTTAAAATAT
Statistics
Matches: 143, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
156 1 0.01
157 48 0.34
158 75 0.52
159 7 0.05
160 12 0.08
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (157 bp):
TTACCATTTTACTATTTTAATTAAAAAAACTTAGACATATTAGAAAATTTTAAATATACTTTTAC
AATTTTACTCAACAAAAACTCTATTACAATTATTCTATAAAAACTCTATTTTTATTCAATTAAAT
TGAATATCCTTAATAAATATTTTATTG
Found at i:31339 original size:31 final size:31
Alignment explanation
Indices: 31283--31341 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
31273 TTTGTAAAAT
*
31283 TTTTGAAACGTCTATTGTACCCTTATTTAAC
1 TTTTGAAACGTCTATTATACCCTTATTTAAC
**
31314 TTTTGAAACGTCTATTATATTCTTATTT
1 TTTTGAAACGTCTATTATACCCTTATTT
31342 GTCTAACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.25, C:0.15, G:0.08, T:0.51
Consensus pattern (31 bp):
TTTTGAAACGTCTATTATACCCTTATTTAAC
Found at i:32045 original size:16 final size:17
Alignment explanation
Indices: 32026--32066 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
32016 TAGGTCTGGG
32026 TCATTTCAGG-TTCGGA
1 TCATTTCAGGATTCGGA
* *
32042 TCA-TTGAGGATTCGGG
1 TCATTTCAGGATTCGGA
32058 TCATTTCAG
1 TCATTTCAG
32067 TTCCGGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 5 0.25
16 11 0.55
17 4 0.20
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.37
Consensus pattern (17 bp):
TCATTTCAGGATTCGGA
Found at i:32986 original size:238 final size:229
Alignment explanation
Indices: 32577--33043 Score: 686
Period size: 238 Copynumber: 2.0 Consensus size: 229
32567 AAAATTGAGG
32577 GATGTTGACCGGTCACCTAATAACATTCAATATTCATTCTAAAACTGAAAACTCAGAAATTGCAA
1 GATGTTGACCGGTCACCTAATAACATTCAATATTCATTCTAAAACTGAAAACTCAGAAATTGCAA
* * *
32642 AAATAACTTTAACACCAGTATTTCGGTTTTGGATTAAGTGGATTTTTTTGGTCGAATCGGGTTGG
66 AAATAACTTTAACACCAGTATTTCGATTTTGGATTAAGCGGATTTTTTTGGTCGAATCGGGTTAG
*
32707 ATAGGGTTTGGCTTCAAGCAGTCGAGTTAGTAGCATACTTAAGATTTTAATTTTCATTTAATTTA
131 ATAAGGTTTGGCTTCAAGCAGTCGAGTTAGTAGCATACTTAAGATTTTAATTTTCATTTAATTTA
*
32772 AACATATTAGGTCACGTGCAAGGCACGTGAAAGT
196 AACATATTAGATCACGTGCAAGGCACGTGAAAGT
* * * *
32806 GATGTTGACCGGTCCCCTAATGACATTCAATGTTCATTCTCAAACTGAAAAC-CAGAAATTGCAA
1 GATGTTGACCGGTCACCTAATAACATTCAATATTCATTCTAAAACTGAAAACTCAGAAATTGCAA
*
32870 AAATAACTTTAACACCAGTGATTATAGGTCATTTCGATTTTGGATTGAGCGGA-TTTTTTGGTCG
66 AAATAACTTTAACACC---------A-GT-ATTTCGATTTTGGATTAAGCGGATTTTTTTGGTCG
* * * *
32934 AATCGGGTTAGATAAGGTTTGGTTTTAAGCGGTCGAGTTAGTAGTATACTTAAGATTTTAATTTT
120 AATCGGGTTAGATAAGGTTTGGCTTCAAGCAGTCGAGTTAGTAGCATACTTAAGATTTTAATTTT
*
32999 CATTTATTTTAAACATATTAGATCACGTGCAAGGCACGTGAAAGT
185 CATTTAATTTAAACATATTAGATCACGTGCAAGGCACGTGAAAGT
33044 AAACAATTAA
Statistics
Matches: 212, Mismatches: 15, Indels: 13
0.88 0.06 0.05
Matches are distributed among these distances:
228 28 0.13
229 48 0.23
237 1 0.00
238 115 0.54
239 20 0.09
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (229 bp):
GATGTTGACCGGTCACCTAATAACATTCAATATTCATTCTAAAACTGAAAACTCAGAAATTGCAA
AAATAACTTTAACACCAGTATTTCGATTTTGGATTAAGCGGATTTTTTTGGTCGAATCGGGTTAG
ATAAGGTTTGGCTTCAAGCAGTCGAGTTAGTAGCATACTTAAGATTTTAATTTTCATTTAATTTA
AACATATTAGATCACGTGCAAGGCACGTGAAAGT
Found at i:33398 original size:158 final size:162
Alignment explanation
Indices: 33206--33521 Score: 435
Period size: 166 Copynumber: 1.9 Consensus size: 162
33196 AGTTTTTTTA
* *
33206 TTTTAATGTATTTATTTTTTTAGAGAAATTCTACTCTACTAA-TC-TTTTTTTTTTGGCC-AGAG
1 TTTTAATGTATTTATATTTTTAGAGAAATTCTACTCTACTAATTCTTTTTTTTTTTGACCAAGAG
* *
33268 TACTCTACTAATCCGCCAACTATTTTTCACTTCTATTTTTTTTTCCTTTTTTCCAATTTTTCG-T
66 TACTCTACTAATCCACCAACTATTTTTCACTACTATTTTTTTTT-CTTTTTTCCAATTTTTCGTT
33332 TTATTTAAAAAATTATAAACTCTACTATCAATT
130 TTATTTAAAAAATTATAAACTCTACTATCAATT
33365 TTTTAATGTATTTA-ATTTTTAGAGAAATTCTACTCTACTAATCTTTCTTGTTTTTTTTTTGACC
1 TTTTAATGTATTTATATTTTTAGAGAAATTCTACTCTACTAA---TTC-T-TTTTTTTTTTGACC
*** * *
33429 AAGAGTACTCTACTAATCCATTGACTATTTTTCTCTACTATTTTTTTTTCTTTTTTTCAATTTTT
61 AAGAGTACTCTACTAATCCACCAACTATTTTTCACTACTATTTTTTTTTCTTTTTTCCAATTTTT
* *
33494 TGTTTTTTTTTAAAAAATTATAAACTCT
126 CG-TTTTATTTAAAAAATTATAAACTCT
33522 TTATAATTGC
Statistics
Matches: 136, Mismatches: 11, Indels: 12
0.86 0.07 0.08
Matches are distributed among these distances:
158 26 0.19
159 14 0.10
162 2 0.01
165 29 0.21
166 42 0.31
167 23 0.17
ACGTcount: A:0.25, C:0.15, G:0.06, T:0.54
Consensus pattern (162 bp):
TTTTAATGTATTTATATTTTTAGAGAAATTCTACTCTACTAATTCTTTTTTTTTTTGACCAAGAG
TACTCTACTAATCCACCAACTATTTTTCACTACTATTTTTTTTTCTTTTTTCCAATTTTTCGTTT
TATTTAAAAAATTATAAACTCTACTATCAATT
Found at i:35977 original size:21 final size:21
Alignment explanation
Indices: 35951--35994 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
35941 TAACAAACAA
** *
35951 TTCTTTCTGAATACATTTAAC
1 TTCTTTCCAAATAAATTTAAC
35972 TTCTTTCCAAATAAATTTAAC
1 TTCTTTCCAAATAAATTTAAC
35993 TT
1 TT
35995 TAGCTATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.18, G:0.02, T:0.48
Consensus pattern (21 bp):
TTCTTTCCAAATAAATTTAAC
Found at i:40948 original size:31 final size:31
Alignment explanation
Indices: 40912--41070 Score: 156
Period size: 31 Copynumber: 5.4 Consensus size: 31
40902 TTTTGTGCAC
* **
40912 GTGGCATGCCACGTGCCACTTTTTGAAACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
*
40943 GTGGCATGCCACGTGTCACTTTTTGGTACAC
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
* * *
40974 GTGGCGTGACATGTGTCACTTTTTGGTACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
41005 GT-G---G-CAC--G--ACTTTTTGGTACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
* * *
41027 GTGGCGTGCCACATGTCACTTTTTGGTACAC
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
*
41058 GTGGCGTGCCACG
1 GTGGCATGCCACG
41071 ACGGGCACCG
Statistics
Matches: 108, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
22 16 0.15
23 1 0.01
24 1 0.01
26 3 0.03
27 4 0.04
29 1 0.01
30 1 0.01
31 81 0.75
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.32
Consensus pattern (31 bp):
GTGGCATGCCACGTGTCACTTTTTGGTACAT
Found at i:41022 original size:53 final size:53
Alignment explanation
Indices: 40960--41062 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
40950 GCCACGTGTC
** *
40960 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
* *
41013 ACTTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGC
41063 GTGCCACGAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.36
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
Found at i:45818 original size:117 final size:116
Alignment explanation
Indices: 45692--45923 Score: 446
Period size: 117 Copynumber: 2.0 Consensus size: 116
45682 TCTACTTTTT
45692 TTTTTTGGATTTTCTCATGTGTTTATTTTGGAAAGAAATCAATTATCACTCCTTCAATAGGGAGC
1 TTTTTTGGATTTTCTCATGTGTTTATTTTGGAAAGAAATCAATTATCACTCCTTCAATAGGGAGC
45757 TTAGGTGTCTTCAATGGAGTTTAGTTATATCAACCCTCGGAAAACTGGTGCC
66 TTAGGTGTCTTCAATGGAGTTTAGTTATATCAACCCTCGG-AAACTGGTGCC
*
45809 TTTTTTGGATTTTCTCATGTGTTTATTTTGGAAAGAAATCAATTATCACTCCTTCAATGGGGAGC
1 TTTTTTGGATTTTCTCATGTGTTTATTTTGGAAAGAAATCAATTATCACTCCTTCAATAGGGAGC
45874 TTAGGTGTCTTCAATGGAGTTTAGTTATATCAACCCTCGGAAACTGGTGC
66 TTAGGTGTCTTCAATGGAGTTTAGTTATATCAACCCTCGGAAACTGGTGC
45924 TTTGCATTTG
Statistics
Matches: 114, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
116 10 0.09
117 104 0.91
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (116 bp):
TTTTTTGGATTTTCTCATGTGTTTATTTTGGAAAGAAATCAATTATCACTCCTTCAATAGGGAGC
TTAGGTGTCTTCAATGGAGTTTAGTTATATCAACCCTCGGAAACTGGTGCC
Found at i:46745 original size:43 final size:43
Alignment explanation
Indices: 46686--46795 Score: 102
Period size: 43 Copynumber: 2.6 Consensus size: 43
46676 AAGGGCATTT
*
46686 CTCTCTCCCCAAAGTCCCCAAACACAATT-ATAACACAG-GGACAA
1 CTCTCT-CTCAAAGTCCCCAAACACAATTCATAACACAGAGG-C-A
* * *
46730 CTCTCTCTCAAAGTCCTCAATCAC-ATTCTTAACACAGAGGCA
1 CTCTCTCTCAAAGTCCCCAAACACAATTCATAACACAGAGGCA
* * *
46772 -TCTATATCAAAGTCCCTAAACACA
1 CTCTCTCTCAAAGTCCCCAAACACA
46796 TGTAACACAA
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
41 18 0.33
42 4 0.07
43 24 0.44
44 8 0.15
ACGTcount: A:0.36, C:0.34, G:0.08, T:0.22
Consensus pattern (43 bp):
CTCTCTCTCAAAGTCCCCAAACACAATTCATAACACAGAGGCA
Done.