Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014021.1 Corchorus capsularis cultivar CVL-1 contig14042, 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: 64511
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:112 original size:25 final size:23
Alignment explanation
Indices: 78--135 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 23
68 TCAAACCCTA
*
78 AACTTCATTTCTAACAACTTCTTC
1 AACTTCATTTCTAACAA-ATCTTC
102 GAACTTCATTTCTAACAAATCTTC
1 -AACTTCATTTCTAACAAATCTTC
*
126 AAATTCATTT
1 AACTTCATTT
136 TCCTTCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 9 0.29
24 5 0.16
25 17 0.55
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (23 bp):
AACTTCATTTCTAACAAATCTTC
Found at i:174 original size:26 final size:26
Alignment explanation
Indices: 145--212 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
135 TTCCTTCATT
145 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
171 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
197 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
213 AAACTAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:212 original size:15 final size:15
Alignment explanation
Indices: 145--225 Score: 51
Period size: 13 Copynumber: 6.1 Consensus size: 15
135 TTCCTTCATT
*
145 TTAATCATAAACTAA
1 TTAAACATAAACTAA
160 TT-AA-AT--ACTAA
1 TTAAACATAAACTAA
171 TTAATA-ATAAACTAA
1 TTAA-ACATAAACTAA
*
186 TT--AGAT--ACTAA
1 TTAAACATAAACTAA
197 TTAAACATAAACTAA
1 TTAAACATAAACTAA
212 -TAAAC-TAAA-TAA
1 TTAAACATAAACTAA
224 TT
1 TT
226 TTAATTAACT
Statistics
Matches: 54, Mismatches: 2, Indels: 22
0.69 0.03 0.28
Matches are distributed among these distances:
11 14 0.26
12 5 0.09
13 15 0.28
14 6 0.11
15 14 0.26
ACGTcount: A:0.56, C:0.10, G:0.01, T:0.33
Consensus pattern (15 bp):
TTAAACATAAACTAA
Found at i:236 original size:52 final size:51
Alignment explanation
Indices: 145--262 Score: 122
Period size: 52 Copynumber: 2.4 Consensus size: 51
135 TTCCTTCATT
* * *
145 TTAATCATAAACTAATTAAATACTAATTAATAATAAACTAATTAGATACTAA
1 TTAAACATAAACTAATTAAATAATAATTAATAATAAACTAATTA-AAACTAA
* *
197 TTAAACATAAACTAA-TAAACTAAATAATT-TTAATTAACTAATTAAAACTAA
1 TTAAACATAAACTAATTAAA-T-AATAATTAATAATAAACTAATTAAAACTAA
248 -T---CATAAACTAATTAA
1 TTAAACATAAACTAATTAA
263 TATTAAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
47 10 0.17
48 3 0.05
50 1 0.02
51 10 0.17
52 28 0.48
53 6 0.10
ACGTcount: A:0.55, C:0.10, G:0.01, T:0.34
Consensus pattern (51 bp):
TTAAACATAAACTAATTAAATAATAATTAATAATAAACTAATTAAAACTAA
Found at i:282 original size:10 final size:9
Alignment explanation
Indices: 264--298 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
254 ACTAATTAAT
264 ATTAAAAAA
1 ATTAAAAAA
*
273 TTTAAAAAA
1 ATTAAAAAA
282 ATTAAAAAA
1 ATTAAAAAA
291 ATTAAAAA
1 ATTAAAAA
299 GAAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
ATTAAAAAA
Found at i:796 original size:21 final size:21
Alignment explanation
Indices: 763--807 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
753 TAAAAAGGGG
** *
763 TTTGCTATTTACCGCCCCCCT
1 TTTGCTAAATACCACCCCCCT
*
784 TTTGCTAAATACCACCCCCTT
1 TTTGCTAAATACCACCCCCCT
805 TTT
1 TTT
808 TATAATTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.38, G:0.07, T:0.40
Consensus pattern (21 bp):
TTTGCTAAATACCACCCCCCT
Found at i:1117 original size:26 final size:26
Alignment explanation
Indices: 1088--1155 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
1078 TACTTAATTT
1088 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
1114 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
1140 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
1156 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:1155 original size:15 final size:13
Alignment explanation
Indices: 1058--1149 Score: 59
Period size: 11 Copynumber: 7.1 Consensus size: 13
1048 TATGATTAGT
*
1058 TTTAATTAGTTAA
1 TTTAATTAGTTTA
* * *
1071 TTAAAATTACTTAA
1 TT-TAATTAGTTTA
1085 TTT-ATTAGTTTA
1 TTTAATTAGTTTA
1097 TGTTTAATTAG--TA
1 --TTTAATTAGTTTA
*
1110 TCTAATTAGTTTA
1 TTTAATTAGTTTA
1123 TTATTAATTAG--TA
1 -T-TTAATTAGTTTA
1136 TTTAATTAGTTTA
1 TTTAATTAGTTTA
1149 T
1 T
1150 GATTAAAATG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
11 16 0.26
12 8 0.13
13 11 0.18
14 15 0.24
15 12 0.19
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (13 bp):
TTTAATTAGTTTA
Found at i:1199 original size:24 final size:25
Alignment explanation
Indices: 1165--1223 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
1155 AAATGAAGGA
*
1165 AAATGAA-TTTGAAG-ATTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
1188 AAATGAAGTTTGAAGAAGTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
1213 AAATGAAGTTT
1 AAATGAAGTTT
1224 AGGGTTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 7 0.21
25 19 0.58
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.36
Consensus pattern (25 bp):
AAATGAAGTTTGAAGAAGTTGTTAG
Found at i:10841 original size:8 final size:8
Alignment explanation
Indices: 10828--10854 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
10818 AACTGAGGTG
10828 TTTTTTCT
1 TTTTTTCT
10836 TTTTTTCT
1 TTTTTTCT
10844 TTTTTTCT
1 TTTTTTCT
10852 TTT
1 TTT
10855 CCATTCATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTCT
Found at i:14467 original size:5 final size:5
Alignment explanation
Indices: 14457--14484 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
14447 TTTTCAGTAT
14457 AAATG AAATG AAATG AAATG AAATG AAA
1 AAATG AAATG AAATG AAATG AAATG AAA
14485 ACATTCCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (5 bp):
AAATG
Found at i:16483 original size:30 final size:30
Alignment explanation
Indices: 16447--16531 Score: 161
Period size: 30 Copynumber: 2.8 Consensus size: 30
16437 ACTCGTTACC
16447 TCACCACAATGCCATACTTGTGTAGTTGCA
1 TCACCACAATGCCATACTTGTGTAGTTGCA
*
16477 TCACCACAAAGCCATACTTGTGTAGTTGCA
1 TCACCACAATGCCATACTTGTGTAGTTGCA
16507 TCACCACAATGCCATACTTGTGTAG
1 TCACCACAATGCCATACTTGTGTAG
16532 GAGGCCCTCA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.28
Consensus pattern (30 bp):
TCACCACAATGCCATACTTGTGTAGTTGCA
Found at i:23330 original size:69 final size:69
Alignment explanation
Indices: 23249--23390 Score: 284
Period size: 69 Copynumber: 2.1 Consensus size: 69
23239 GCTTCGAAGA
23249 CAAACCGCTTGTTGCGCAGGCTATCAAGATGCCATTTCTTGCAGTCTTCATTATTGAACTCAGTG
1 CAAACCGCTTGTTGCGCAGGCTATCAAGATGCCATTTCTTGCAGTCTTCATTATTGAACTCAGTG
23314 GAAT
66 GAAT
23318 CAAACCGCTTGTTGCGCAGGCTATCAAGATGCCATTTCTTGCAGTCTTCATTATTGAACTCAGTG
1 CAAACCGCTTGTTGCGCAGGCTATCAAGATGCCATTTCTTGCAGTCTTCATTATTGAACTCAGTG
23383 GAAT
66 GAAT
23387 CAAA
1 CAAA
23391 GTCACCAAAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (69 bp):
CAAACCGCTTGTTGCGCAGGCTATCAAGATGCCATTTCTTGCAGTCTTCATTATTGAACTCAGTG
GAAT
Found at i:24814 original size:5 final size:5
Alignment explanation
Indices: 24757--24798 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
24747 TTCAAAAAGT
*
24757 TTTTC TTTTC TTTTC TTTTC -CTTC TTTTTC TTTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC -TTTTC TTTTC T
24799 GCCCTAACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 3 0.09
5 21 0.64
6 9 0.27
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:39718 original size:12 final size:12
Alignment explanation
Indices: 39701--39735 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
39691 AGTTTTTTGG
39701 TGTGTGAGAGAT
1 TGTGTGAGAGAT
*
39713 TGTGTGTGAGAT
1 TGTGTGAGAGAT
*
39725 TGTGAGAGAGA
1 TGTGTGAGAGA
39736 AAAAGCTGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.43, T:0.31
Consensus pattern (12 bp):
TGTGTGAGAGAT
Found at i:40335 original size:22 final size:21
Alignment explanation
Indices: 40310--40881 Score: 231
Period size: 22 Copynumber: 26.5 Consensus size: 21
40300 TCCCATTAAA
40310 AAATTTTGATAACCTTCCTATG
1 AAATTTTGATAACC-TCCTATG
* * *
40332 AAATTTTAATAACGATACTATG
1 AAATTTTGATAAC-CTCCTATG
* * * * *
40354 GAATTTCGAGAACCT--TTTT
1 AAATTTTGATAACCTCCTATG
** *
40373 ATAATTTTTTTAACCTTCTTATG
1 A-AATTTTGATAACC-TCCTATG
* *
40396 AAATTTGGTTAACCTCCCT-TAG
1 AAATTTTGATAACCT-CCTAT-G
* *
40418 GAATTTTGA-AGACCTCAATATG
1 AAATTTTGATA-ACCTC-CTATG
* *
40440 AAATTTTGATAACTTCCCAATG
1 AAATTTTGATAACCT-CCTATG
*
40462 AAATTTTGATAACCAACACTATG
1 AAATTTTGATAACC-TC-CTATG
* **
40485 AGATGCTGATAACCTCCATATG
1 AAATTTTGATAACCTCC-TATG
* * * *
40507 ATATATTGATAACCACATTATG
1 AAATTTTGATAACCTC-CTATG
** * *
40529 AAAAATTAAAAACCTCCATATG
1 AAATTTTGATAACCTCC-TATG
* * *
40551 -AATTGTT-AGTAATCACACTCTG
1 AAATT-TTGA-TAACCTC-CTATG
* *
40573 AAATTTTGATAATCACACTATG
1 AAATTTTGATAACCTC-CTATG
*
40595 AAATTGTGATAACCTCGCTATG
1 AAATTTTGATAACCTC-CTATG
* *
40617 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGAT-AA-CCTCCTATG
*
40640 AAATTTCGATAAACCTCCCTAT-
1 AAATTTTGAT-AACCT-CCTATG
* *
40662 AATATTTTGATAACTTTCTTATG
1 AA-ATTTTGATAAC-CTCCTATG
* *
40685 AAATCTTGATAA----CTA-C
1 AAATTTTGATAACCTCCTATG
40701 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCT-CCTATG
** *
40723 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAACCTC-CTATG
* *
40745 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCT-CCTATG
* * *
40767 AAATTTTGATCTACATACTATG
1 AAATTTTGAT-AACCTCCTATG
* *
40789 AAATTTTGATAACCCTCTTGTG
1 AAATTTTGATAA-CCTCCTATG
* *
40811 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCT--CCTATG
* *
40833 AAATTTTGATATCCTCC-CTG
1 AAATTTTGATAACCTCCTATG
*
40853 -AATTTTGATATCCTCCT-TG
1 AAATTTTGATAACCTCCTATG
40872 AAATTTTGAT
1 AAATTTTGAT
40882 TACTCCATAA
Statistics
Matches: 411, Mismatches: 96, Indels: 88
0.69 0.16 0.15
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
19 20 0.05
20 22 0.05
21 18 0.04
22 269 0.65
23 66 0.16
24 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (21 bp):
AAATTTTGATAACCTCCTATG
Found at i:40425 original size:23 final size:22
Alignment explanation
Indices: 40382--40425 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
40372 TATAATTTTT
* *
40382 TTAACCTTCTTATGAAATTTGG
1 TTAACCTCCTTAGGAAATTTGG
*
40404 TTAACCTCCCTTAGGAATTTTG
1 TTAACCT-CCTTAGGAAATTTG
40426 AAGACCTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (22 bp):
TTAACCTCCTTAGGAAATTTGG
Found at i:40643 original size:23 final size:23
Alignment explanation
Indices: 40612--40696 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
40602 GATAACCTCG
*
40612 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* * *
40635 CTATAAAATTTCGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
* *
40658 CTATAATATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* * *
40680 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
40697 CTACAAATTT
Statistics
Matches: 49, Mismatches: 13, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
22 15 0.31
23 34 0.69
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.41
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:40789 original size:44 final size:44
Alignment explanation
Indices: 40310--41135 Score: 270
Period size: 44 Copynumber: 19.3 Consensus size: 44
40300 TCCCATTAAA
* *
40310 AAATTTTGATAACCTTCCTATGAAATTTTAATAACGAT-ACTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAAC-ATCACTATG
* * * *** ** * *
40354 GAATTTCGAGAACCTTTTTAT--AATTTTTTTAACCTTC-TTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAA-CATCACTATG
* * * * *
40396 AAATTTGGTTAACCTCCCT-TAGGAATTTTGA-AGACCTCAATATG
1 AAATTTTGATAACCTCCCTAT-GAAATTTTGATA-ACATCACTATG
* * *
40440 AAATTTTGATAACTTCCCAATGAAATTTTGATAACCAACACTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAA-CATCACTATG
* ** * * * *
40485 AGATGCTGATAACCTCCATATGATATATTGATAACCA-CATTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAA-CATCACTATG
** * * * *
40529 AAAAATTAAAAACCTCCATATG-AATTGTT-AGTAATCA-CACTCTG
1 AAATTTTGATAACCTCCCTATGAAATT-TTGA-TAA-CATCACTATG
* * * * * *
40573 AAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACATCACTATG
* * * * * *
40617 AAATTTTGATAAATCTTCCTATAAAATTTCGATAAACCTCCCTAT-
1 AAATTTTGAT-AACCTCCCTATGAAATTTTGAT-AACATCACTATG
* * * *
40662 AATATTTTGATAACTTTCTTATGAAATCTTGATAAC-T-AC----
1 AA-ATTTTGATAACCTCCCTATGAAATTTTGATAACATCACTATG
** * *
40701 AAATTTTGATAACCTCCCTATGATTTTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACATCACTATG
* * *
40745 AAATTTTGTTAATCTCCCTATGAAATTTTGATCTACAT-ACTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGAT-AACATCACTATG
* * * *
40789 AAATTTTGATAACC-CTCTTGTGAAATTTTGAAAAC-TAAACTATG
1 AAATTTTGATAACCTC-CCTATGAAATTTTGATAACAT-CACTATG
* * *
40833 AAATTTTGATATCCTCCC--TG-AATTTTGATATCCTC-CT-TG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACATCACTATG
* * * * * *
40872 AAATTTTGATTA-CTCCATAATAAAAGTTTAATAACCTTC-C--T-
1 AAATTTTGATAACCTCCCT-ATGAAATTTTGATAA-CATCACTATG
* * ** * *
40913 -AATTTAG-TAACCAT-ACTATGAAATTTTGATAATGTCCCCA-G
1 AAATTTTGATAACC-TCCCTATGAAATTTTGATAACATCACTATG
* * *
40954 -AA-----AT-A-C-CACTATGAAATTTTTG-TAATCA-CATTTTG
1 AAATTTTGATAACCTCCCTATGAAA-TTTTGATAA-CATCACTATG
* ** * ** *
40989 AAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTTTATA
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACATCACTATG
* * *
41033 AAATTTTGTTGACC-CCTCTATATGAAATTCTGATAA-ATCACATTATG
1 AAATTTTGATAACCTCC-C--TATGAAATTTTGATAACATCAC--TATG
* * * *
41080 TAATTTTGATAACCTCGCTTTGAAATTTTGATAACAACACTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACATCACTATG
41124 AAATTTTGATAA
1 AAATTTTGATAA
41136 TCTTTCTATA
Statistics
Matches: 572, Mismatches: 146, Indels: 128
0.68 0.17 0.15
Matches are distributed among these distances:
34 13 0.02
35 7 0.01
36 3 0.01
37 1 0.00
38 33 0.06
39 30 0.05
40 11 0.02
41 17 0.03
42 41 0.07
43 25 0.04
44 241 0.42
45 97 0.17
46 37 0.06
47 15 0.03
48 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (44 bp):
AAATTTTGATAACCTCCCTATGAAATTTTGATAACATCACTATG
Found at i:40887 original size:19 final size:20
Alignment explanation
Indices: 40831--40881 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
40821 AACTAAACTA
40831 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
40851 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
40870 TGAAATTTTGAT
1 TGAAATTTTGAT
40882 TACTCCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:41060 original size:24 final size:22
Alignment explanation
Indices: 40987--41236 Score: 127
Period size: 22 Copynumber: 11.3 Consensus size: 22
40977 AATCACATTT
*
40987 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
41009 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * *
41031 TAAAATTTTGTTGACCCCTCTATA
1 TGAAATTTTGAT-A-ACCTCTTTA
* * * *
41055 TGAAATTCTGATAAATCACATTA
1 TGAAATTTTGAT-AACCTCTTTA
* *
41078 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
41100 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
*
41122 TGAAATTTTGATAATCT-TTCTA
1 TGAAATTTTGATAACCTCTT-TA
* *
41144 T-AAATTTCGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTTTA
* * * * *
41168 TAAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTTTA
* *
41190 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
41210 TCAAATTTTGGT-ACTTC-TTA
1 TGAAATTTTGATAACCTCTTTA
41230 TGAAATT
1 TGAAATT
41237 GAGACTTTTA
Statistics
Matches: 171, Mismatches: 45, Indels: 26
0.71 0.19 0.11
Matches are distributed among these distances:
20 18 0.11
21 25 0.15
22 76 0.44
23 17 0.10
24 22 0.13
25 13 0.08
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:41271 original size:22 final size:22
Alignment explanation
Indices: 40987--41297 Score: 76
Period size: 22 Copynumber: 13.8 Consensus size: 22
40977 AATCACATTT
* *
40987 TGAAAATTTGATAACC-TCTTTA
1 TGAAATTTTGATAACCTTC-ATA
*
41009 TGAAATTTTGATAACC-TCTTTA
1 TGAAATTTTGATAACCTTC-ATA
* * * *
41031 TAAAATTTTGTTGACCCCTCTATA
1 TGAAATTTTGAT-AACCTTC-ATA
* * *
41055 TGAAATTCTGATAA-ATCACATTA
1 TGAAATTTTGATAACCT-TCA-TA
* * *
41078 TGTAATTTTGATAACC-TCGCTT
1 TGAAATTTTGATAACCTTC-ATA
**
41100 TGAAATTTTGATAA-CAACACTA
1 TGAAATTTTGATAACCTTCA-TA
*
41122 TGAAATTTTGATAATCTTTC-TA
1 TGAAATTTTGATAA-CCTTCATA
*
41144 T-AAATTTCGATAATCCGATCTC-TA
1 TGAAATTTTGATAA-CC--T-TCATA
* *
41168 TAAAATTTCGATAATCAC-TC-TA
1 TGAAATTTTGATAA-C-CTTCATA
*
41190 TGAGA-TTTGATAACCTTC-TA
1 TGAAATTTTGATAACCTTCATA
* * *
41210 TCAAATTTTGGT-A-CTTCTTA
1 TGAAATTTTGATAACCTTCATA
*
41230 TGAAATTGAGACTTTTATAACCTTCATA
1 TGAAA-T-----TTTGATAACCTTCATA
*
41258 TGAAATTTTGATAAACC-ACACTA
1 TGAAATTTTGAT-AACCTTCA-TA
*
41281 TAAAATTTTGATAACCT
1 TGAAATTTTGATAACCT
41298 CCCCATAAAA
Statistics
Matches: 220, Mismatches: 40, Indels: 57
0.69 0.13 0.18
Matches are distributed among these distances:
19 5 0.02
20 15 0.07
21 27 0.12
22 84 0.38
23 37 0.17
24 20 0.09
25 14 0.06
26 5 0.02
27 2 0.01
28 11 0.05
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCATA
Found at i:41305 original size:22 final size:23
Alignment explanation
Indices: 41260--41308 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
41250 CCTTCATATG
*
41260 AAATTTTGATAAACCACACTATA
1 AAATTTTGATAAACCACACCATA
* *
41283 AAATTTTGAT-AACCTCCCCATA
1 AAATTTTGATAAACCACACCATA
41305 AAAT
1 AAAT
41309 ATTTAATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.31
Consensus pattern (23 bp):
AAATTTTGATAAACCACACCATA
Found at i:41472 original size:24 final size:22
Alignment explanation
Indices: 41408--41547 Score: 72
Period size: 22 Copynumber: 6.3 Consensus size: 22
41398 TTGTGATAAT
41408 TAACC-ACCATATGAAATTTCAA
1 TAACCAACC-TATGAAATTTCAA
* *
41430 TAACCAACCTAAGAGATTTCAA
1 TAACCAACCTATGAAATTTCAA
* ***
41452 TAACCTGATCCTATGAAATTTTGG
1 TAACC--AACCTATGAAATTTCAA
* **
41476 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTCAA
*
41498 TAACC-TCCTCATGAAATTAT-AA
1 TAACCAACCT-ATGAAATT-TCAA
* * **
41520 TAACCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTCAA
41542 TAACCA
1 TAACCA
41548 CATAGAAACA
Statistics
Matches: 94, Mismatches: 16, Indels: 16
0.75 0.13 0.13
Matches are distributed among these distances:
21 4 0.04
22 67 0.71
23 7 0.07
24 16 0.17
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.31
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTCAA
Found at i:41515 original size:22 final size:21
Alignment explanation
Indices: 41460--41546 Score: 93
Period size: 22 Copynumber: 4.0 Consensus size: 21
41450 AATAACCTGA
*
41460 TCCTATGAAATTTTGGTAACC
1 TCCTATGAAATTTTGATAACC
* *
41481 ACACTATGGAATTTTGATAACC
1 TC-CTATGAAATTTTGATAACC
* *
41503 TCCTCATGAAATTATAATAACC
1 TCCT-ATGAAATTTTGATAACC
*
41525 ATCTTATGAAATTTTGATAACC
1 -TCCTATGAAATTTTGATAACC
41547 ACATAGAAAC
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
21 3 0.06
22 47 0.89
23 3 0.06
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (21 bp):
TCCTATGAAATTTTGATAACC
Found at i:41744 original size:19 final size:19
Alignment explanation
Indices: 41713--41749 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
41703 TATTGACATT
41713 TAAAAATTAAAATTAAAAC
1 TAAAAATTAAAATTAAAAC
41732 TAAAATATT-AAATTAAAA
1 TAAAA-ATTAAAATTAAAA
41750 AAATAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (19 bp):
TAAAAATTAAAATTAAAAC
Found at i:42174 original size:31 final size:31
Alignment explanation
Indices: 42127--42204 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 31
42117 TATTATTTAG
*
42127 TAATGGTA-ATTTAGAAATATGCTTTAAAGAA
1 TAATGGTACAATTAGAAATATGCTTTAAA-AA
*
42158 -AATGGTACAATTAGAAATATGTTTTAAAAA
1 TAATGGTACAATTAGAAATATGCTTTAAAAA
*
42188 TAA-GGTACAATCAGAAA
1 TAATGGTACAATTAGAAA
42205 ATATAAAGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 22 0.52
31 20 0.48
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31
Consensus pattern (31 bp):
TAATGGTACAATTAGAAATATGCTTTAAAAA
Found at i:42208 original size:31 final size:31
Alignment explanation
Indices: 42139--42204 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
42129 ATGGTAATTT
*
42139 AGAAATATGCTTTAAAGAAAATGGTACAATT
1 AGAAATATGCTTTAAAGAAAATGGTACAATC
*
42170 AGAAATATGTTTTAAA-AATAA-GGTACAATC
1 AGAAATATGCTTTAAAGAA-AATGGTACAATC
42200 AGAAA
1 AGAAA
42205 ATATAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 15 0.47
31 17 0.53
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (31 bp):
AGAAATATGCTTTAAAGAAAATGGTACAATC
Found at i:46792 original size:17 final size:17
Alignment explanation
Indices: 46746--46798 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
46736 AACACATGTA
* *
46746 ATCTTTGATCACCGGTG
1 ATCTTGGATCACTGGTG
*
46763 ATCTTGCATCACTGGTG
1 ATCTTGGATCACTGGTG
*
46780 ATCTTGGATCACTAGTG
1 ATCTTGGATCACTGGTG
46797 AT
1 AT
46799 ATGAGGGGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (17 bp):
ATCTTGGATCACTGGTG
Found at i:47285 original size:29 final size:28
Alignment explanation
Indices: 47230--47285 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
47220 GTTTAACATT
47230 AATTCTTGAGTCGTCACAAATTCAAAAAA
1 AATTCTTGAGTCGTCACAAA-TCAAAAAA
47259 AATTCTTGAGTCGTCACCAAA-CAAAAA
1 AATTCTTGAGTCGTCA-CAAATCAAAAA
47286 GGATCATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 6 0.23
29 16 0.62
30 4 0.15
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.25
Consensus pattern (28 bp):
AATTCTTGAGTCGTCACAAATCAAAAAA
Found at i:48069 original size:3 final size:3
Alignment explanation
Indices: 48063--48098 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
48053 TCATTTAACT
48063 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
48099 ATCAATATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:54848 original size:23 final size:23
Alignment explanation
Indices: 54819--54866 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
54809 TCATTAAAAG
54819 AAGATTAAAAAAATGCGGAGCCA
1 AAGATTAAAAAAATGCGGAGCCA
54842 AAGATTAAAAAAATGCGGAGCCA
1 AAGATTAAAAAAATGCGGAGCCA
54865 AA
1 AA
54867 ATTCCAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.54, C:0.12, G:0.21, T:0.12
Consensus pattern (23 bp):
AAGATTAAAAAAATGCGGAGCCA
Found at i:60505 original size:21 final size:23
Alignment explanation
Indices: 60467--60513 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
60457 TGGATTATTT
*
60467 AAAAATCTTATAAGAGTTATTAA
1 AAAAATCTTATAAGAGTTACTAA
60490 AAAAATCTTAT-A-AGTTACTAA
1 AAAAATCTTATAAGAGTTACTAA
60511 AAA
1 AAA
60514 TACACTAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.48
22 1 0.04
23 11 0.48
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (23 bp):
AAAAATCTTATAAGAGTTACTAA
Found at i:60550 original size:23 final size:23
Alignment explanation
Indices: 60474--60551 Score: 58
Period size: 23 Copynumber: 3.6 Consensus size: 23
60464 TTTAAAAATC
* *
60474 TTATAAGAGTTATTAAAAAA-ATC
1 TTATAAGA-TTAATAAAAAATATA
* *
60497 TTATAAG-TTACT-AAAAATACA
1 TTATAAGATTAATAAAAAATATA
* *
60518 --CTAAGCTTAATAAAAAATATA
1 TTATAAGATTAATAAAAAATATA
60539 TTATAAGATTAAT
1 TTATAAGATTAAT
60552 TAAGAAGTTC
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
19 4 0.10
20 9 0.21
21 13 0.31
23 16 0.38
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (23 bp):
TTATAAGATTAATAAAAAATATA
Found at i:62053 original size:3 final size:3
Alignment explanation
Indices: 62047--62071 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
62037 AAGAAGAAGA
62047 AGG AGG AGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG A
62072 CAAAAAGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
AGG
Done.