Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012390.1 Corchorus olitorius cultivar O-4 contig12423, 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: 57601
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:11138 original size:23 final size:25
Alignment explanation
Indices: 11112--11158 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
11102 ATTCCCATCA
*
11112 GAAAAG-AAT-AAAAAGAAGAAAGT
1 GAAAAGAAATGAAAAAGAAAAAAGT
11135 GAAAAGAAATGAAAAAGAAAAAAG
1 GAAAAGAAATGAAAAAGAAAAAAG
11159 ATAAATTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 3 0.14
25 12 0.57
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.06
Consensus pattern (25 bp):
GAAAAGAAATGAAAAAGAAAAAAGT
Found at i:12978 original size:9 final size:9
Alignment explanation
Indices: 12964--12997 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
12954 GCAACCAGTT
12964 AAAAAAATG
1 AAAAAAATG
12973 -AAAAAATG
1 AAAAAAATG
12981 AAAAAAATG
1 AAAAAAATG
12990 AAGAAAAA
1 AA-AAAAA
12998 ACAAAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.35
9 10 0.43
10 5 0.22
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (9 bp):
AAAAAAATG
Found at i:15165 original size:48 final size:47
Alignment explanation
Indices: 15097--15235 Score: 149
Period size: 45 Copynumber: 3.0 Consensus size: 47
15087 AGTCAACCGA
* *
15097 CTTTTTCCATTTTCAGCAGTTATGAAAGTTGGCCTCATAACAAGTCAT
1 CTTTTT-CATTTTCAGCAGTTATCAAAGTTGGCCTCAGAACAAGTCAT
* * *
15145 CTTTTTCAGTTTTCAACAGTTATCAAAGTCGACCTCAGAAC-AG--AT
1 CTTTTTCA-TTTTCAGCAGTTATCAAAGTTGGCCTCAGAACAAGTCAT
* * * *
15190 CTTTCTCAATTTTTAGTAGTCATCAAAGTTGGCCTCAGAACAAGTC
1 CTTTTTC-ATTTTCAGCAGTTATCAAAGTTGGCCTCAGAACAAGTC
15236 TTTTCTCAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
45 34 0.46
46 3 0.04
47 4 0.05
48 33 0.45
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (47 bp):
CTTTTTCATTTTCAGCAGTTATCAAAGTTGGCCTCAGAACAAGTCAT
Found at i:15266 original size:46 final size:45
Alignment explanation
Indices: 15166--15274 Score: 132
Period size: 45 Copynumber: 2.4 Consensus size: 45
15156 TTCAACAGTT
*
15166 ATCAAAGTCGACCTCAGAACAGATCTTTCTCAATTTTTAGTAGTC
1 ATCAAAGTTGACCTCAGAACAGATCTTTCTCAATTTTTAGTAGTC
* *
15211 ATCAAAGTTGGCCTCAGAACA-AGTCTTTTCTCAA-TTTTAGTAGTT
1 ATCAAAGTTGACCTCAGAACAGA-TC-TTTCTCAATTTTTAGTAGTC
* *
15256 TTTAACAGTTGACCTCAGA
1 ATCAA-AGTTGACCTCAGA
15275 GCAGGTTTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
44 1 0.02
45 34 0.62
46 20 0.36
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (45 bp):
ATCAAAGTTGACCTCAGAACAGATCTTTCTCAATTTTTAGTAGTC
Found at i:17553 original size:79 final size:78
Alignment explanation
Indices: 17372--17609 Score: 314
Period size: 79 Copynumber: 3.0 Consensus size: 78
17362 AGGGAATAGG
* ** * * * * *
17372 AACAACACCTCCCGACGAGGAAGGGCAAACTAAGAATTTAGACAACACTTTCCGATAGGGAAAGG
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGAGTATTTAGACAACACCTTCCGGT-GGGAAAGG
17437 CAAACTGGTTATTTA
65 CAAACTGG-TATTTA
*
17452 AACAACACCTTCCGGTGGGGAAGGGCAAACTGAGTATTTAGACTACACCTTCCGGTGGGAAAGCG
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGAGTATTTAGACAACACCTTCCGGTGGGAAAG-G
17517 CAAACTGGTATTTA
65 CAAACTGGTATTTA
* * * *
17531 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATCTAAACAACACCTTCCGGTGGGGAAGGG
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGAGTATTTAGACAACACCTTCCGGT-GGGAAAGG
17596 CAAACTGGGTATTT
65 CAAACT-GGTATTT
17610 GGACTAGACA
Statistics
Matches: 141, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
79 72 0.51
80 69 0.49
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20
Consensus pattern (78 bp):
AACAACACCTTCCGGTGGGGAAGGGCAAACTGAGTATTTAGACAACACCTTCCGGTGGGAAAGGC
AAACTGGTATTTA
Found at i:17602 original size:40 final size:40
Alignment explanation
Indices: 17372--17609 Score: 298
Period size: 40 Copynumber: 6.0 Consensus size: 40
17362 AGGGAATAGG
* ** * ** *
17372 AACAACACCTCCCGACGAGGAAGGGCAAACTAAGAATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
* * * * * *
17412 GACAACACTTTCCGATAGGGAAAGGCAAACTGGTTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
*
17452 AACAACACCTTCCGGTGGGGAAGGGCAAACTGAGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
* * * *
17492 GACTACACCTTCCGGTGGGAAAGCGCAAACT-GGTATTTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
*
17531 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATCTA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
17571 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTT
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTT
17610 GGACTAGACA
Statistics
Matches: 168, Mismatches: 29, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 34 0.20
40 134 0.80
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20
Consensus pattern (40 bp):
AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA
Found at i:24852 original size:13 final size:13
Alignment explanation
Indices: 24829--24862 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
24819 TTCTTTAAAA
24829 AAAACAAAAAAAGC
1 AAAA-AAAAAAAGC
24843 AAAAAAAAAAAGC
1 AAAAAAAAAAAGC
24856 AAAAAAA
1 AAAAAAA
24863 TAGATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGC
Found at i:26177 original size:11 final size:11
Alignment explanation
Indices: 26161--26187 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
26151 GTTAACCAAT
26161 ATAATAATTTG
1 ATAATAATTTG
26172 ATAATAATTTG
1 ATAATAATTTG
26183 ATAAT
1 ATAAT
26188 TTCTTATTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (11 bp):
ATAATAATTTG
Found at i:27125 original size:21 final size:21
Alignment explanation
Indices: 27087--27128 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
27077 GTGATTTAAT
** *
27087 TATCAAAATTTGTGGTTTGAC
1 TATCAAAAAGTGTCGTTTGAC
27108 TATCAAAAAGTGTCGTTTGAC
1 TATCAAAAAGTGTCGTTTGAC
27129 CATGCATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (21 bp):
TATCAAAAAGTGTCGTTTGAC
Found at i:27280 original size:54 final size:54
Alignment explanation
Indices: 27144--27363 Score: 327
Period size: 54 Copynumber: 4.1 Consensus size: 54
27134 ATATATAATG
* * * * * * *
27144 AATGGTTTTTTTGTGGTTTGACTATCAGACTTT--GGTTTAACTATACATGTAC
1 AATGATTTTTTTGTGGCTTAACTATCAAACTTTGGGGTTTGACCATGCATGTAC
*
27196 AATGATGTTTTTTGTGGTTTAACTATCAAACTTTGGGGTTTGACCATGCATGTAC
1 AATGAT-TTTTTTGTGGCTTAACTATCAAACTTTGGGGTTTGACCATGCATGTAC
27251 AATGATTTTTTTGTGGCTTAACTATCAAACTTTGGGGTTTGACCATGCATGTAC
1 AATGATTTTTTTGTGGCTTAACTATCAAACTTTGGGGTTTGACCATGCATGTAC
* *
27305 AATGATTTTTTTGTGGCTTGACTATCAAACTTTGGGGTTTGACCATGCATCTAC
1 AATGATTTTTTTGTGGCTTAACTATCAAACTTTGGGGTTTGACCATGCATGTAC
27359 AATGA
1 AATGA
27364 AATGCTATTA
Statistics
Matches: 156, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
52 5 0.03
53 25 0.16
54 104 0.67
55 22 0.14
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (54 bp):
AATGATTTTTTTGTGGCTTAACTATCAAACTTTGGGGTTTGACCATGCATGTAC
Found at i:27452 original size:21 final size:21
Alignment explanation
Indices: 27426--27467 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
27416 GTGATTTAAA
**
27426 TATCAAACTTTGGGGTTTGCT
1 TATCAAACTCCGGGGTTTGCT
*
27447 TATCAAAGTCCGGGGTTTGCT
1 TATCAAACTCCGGGGTTTGCT
27468 CATGTATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (21 bp):
TATCAAACTCCGGGGTTTGCT
Found at i:27584 original size:21 final size:21
Alignment explanation
Indices: 27560--27599 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
27550 TGGTTTAGCT
27560 ACCAAACTTCGGGGTTTGATC
1 ACCAAACTTCGGGGTTTGATC
*
27581 ACCAAACTTTGGGGTTTGA
1 ACCAAACTTCGGGGTTTGA
27600 CCATCATCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (21 bp):
ACCAAACTTCGGGGTTTGATC
Found at i:27673 original size:54 final size:54
Alignment explanation
Indices: 27609--27876 Score: 286
Period size: 54 Copynumber: 4.9 Consensus size: 54
27599 ACCATCATCC
* *
27609 TTTGGAGTTTGACCATGCATGTACAATGATGTTTTTGGGGTTTGACTATTAAAA
1 TTTGGGGTTTGACCATGCATGTACAATGATGTTTTTGTGGTTTGACTATTAAAA
* * * ** *
27663 TTTGGGGTTTGACCATGCATATACTATGAAATGTTTTTTTGTGATTTGACTATCGAAC
1 TTTGGGGTTTGACCATGCATGTACAATG--ATG--TTTTTGTGGTTTGACTATTAAAA
* * *
27721 TTTGGGGTTTGACCATGCATGCATAATGATGTTTTTTGTGGTTTAACTATTAAAA
1 TTTGGGGTTTGACCATGCATGTACAATGATG-TTTTTGTGGTTTGACTATTAAAA
** * * * *
27776 -TTGGGGTTTGACTGTGCATATACAATGAAATTTTTTTGTGGTTTGACTATTGAAT
1 TTTGGGGTTTGACCATGCATGTACAATG--ATGTTTTTGTGGTTTGACTATTAAAA
* * *
27831 TTTGGGGTTTGATCATGCATGTGCAATGATGTTTTTGGGGTTTGAC
1 TTTGGGGTTTGACCATGCATGTACAATGATGTTTTTGTGGTTTGAC
27877 CATGCATATA
Statistics
Matches: 174, Mismatches: 33, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
54 63 0.36
55 39 0.22
56 30 0.17
58 42 0.24
ACGTcount: A:0.23, C:0.09, G:0.24, T:0.43
Consensus pattern (54 bp):
TTTGGGGTTTGACCATGCATGTACAATGATGTTTTTGTGGTTTGACTATTAAAA
Found at i:27860 original size:110 final size:112
Alignment explanation
Indices: 27608--27873 Score: 378
Period size: 112 Copynumber: 2.4 Consensus size: 112
27598 GACCATCATC
* *
27608 CTTTGGAGTTTGACCATGCATGTACAATGATG-TTTTTGGGGTTTGACTATTAAAATTTGGGGTT
1 CTTTGGGGTTTGACCATGCATGTACAATGATGTTTTTTGGGGTTTAACTATTAAAATTTGGGGTT
*
27672 TGACCATGCATATACTATGAAATGTTTTTTTGTGATTTGACTATCGAA
66 TGACCATGCATATACAATGAAA-GTTTTTTTGTGATTTGACTATCGAA
* * *
27720 CTTTGGGGTTTGACCATGCATGCATAATGATGTTTTTTGTGGTTTAACTATTAAAA-TTGGGGTT
1 CTTTGGGGTTTGACCATGCATGTACAATGATGTTTTTTGGGGTTTAACTATTAAAATTTGGGGTT
** * *
27784 TGACTGTGCATATACAATGAAA-TTTTTTTGTGGTTTGACTATTGAA
66 TGACCATGCATATACAATGAAAGTTTTTTTGTGATTTGACTATCGAA
* * *
27830 TTTTGGGGTTTGATCATGCATGTGCAATGATG-TTTTTGGGGTTT
1 CTTTGGGGTTTGACCATGCATGTACAATGATGTTTTTTGGGGTTT
27874 GACCATGCAT
Statistics
Matches: 137, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
109 11 0.08
110 49 0.36
112 56 0.41
113 21 0.15
ACGTcount: A:0.23, C:0.09, G:0.24, T:0.44
Consensus pattern (112 bp):
CTTTGGGGTTTGACCATGCATGTACAATGATGTTTTTTGGGGTTTAACTATTAAAATTTGGGGTT
TGACCATGCATATACAATGAAAGTTTTTTTGTGATTTGACTATCGAA
Found at i:27872 original size:33 final size:35
Alignment explanation
Indices: 27830--27911 Score: 105
Period size: 33 Copynumber: 2.4 Consensus size: 35
27820 GACTATTGAA
* * *
27830 TTTTGGGGTTTGATCATGCATGTGCAATG-A-TGT
1 TTTTGGGGTTTGACCATGCATATACAATGAATTGT
*
27863 TTTTGGGGTTTGACCATGCATATACAATGAATTTT
1 TTTTGGGGTTTGACCATGCATATACAATGAATTGT
*
27898 TTTTGTGGTTTGAC
1 TTTTGGGGTTTGAC
27912 TATTGAACTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
33 26 0.62
34 1 0.02
35 15 0.36
ACGTcount: A:0.20, C:0.10, G:0.26, T:0.45
Consensus pattern (35 bp):
TTTTGGGGTTTGACCATGCATATACAATGAATTGT
Found at i:31068 original size:16 final size:15
Alignment explanation
Indices: 31047--31151 Score: 84
Period size: 16 Copynumber: 6.4 Consensus size: 15
31037 AGTGACTGGC
31047 GGTGGTAGCCGGCGGT
1 GGTGGT-GCCGGCGGT
31063 GGTGGTTGCCGGCGGT
1 GGTGG-TGCCGGCGGT
*
31079 GCTGGTGACCGGCGGTGGT
1 GGTGGTG-CCGGC---GGT
31098 GGTGGTTGCCGGCGGT
1 GGTGG-TGCCGGCGGT
*
31114 GCTGGTGACCGGCGGT
1 GGTGGTG-CCGGCGGT
* **
31130 GGTAGTGGTGGCCGGT
1 GGTGGTGCCGG-CGGT
31146 GGTGGT
1 GGTGGT
31152 TGGTTTCCGG
Statistics
Matches: 73, Mismatches: 8, Indels: 16
0.75 0.08 0.16
Matches are distributed among these distances:
15 6 0.08
16 52 0.71
17 1 0.01
19 12 0.16
20 2 0.03
ACGTcount: A:0.04, C:0.18, G:0.55, T:0.23
Consensus pattern (15 bp):
GGTGGTGCCGGCGGT
Found at i:31098 original size:19 final size:19
Alignment explanation
Indices: 31076--31151 Score: 72
Period size: 19 Copynumber: 4.2 Consensus size: 19
31066 GGTTGCCGGC
31076 GGTGCTGGTGACCGGCGGT
1 GGTGCTGGTGACCGGCGGT
*
31095 GGTGGTGGTTG-CCGGC---
1 GGTGCTGG-TGACCGGCGGT
31111 GGTGCTGGTGACCGGCGGT
1 GGTGCTGGTGACCGGCGGT
* *
31130 GGTAG-TGGTGGCCGGTGGT
1 GGT-GCTGGTGACCGGCGGT
31149 GGT
1 GGT
31152 TGGTTTCCGG
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
15 2 0.04
16 12 0.26
19 30 0.64
20 3 0.06
ACGTcount: A:0.04, C:0.17, G:0.55, T:0.24
Consensus pattern (19 bp):
GGTGCTGGTGACCGGCGGT
Found at i:31106 original size:35 final size:35
Alignment explanation
Indices: 31060--31149 Score: 153
Period size: 35 Copynumber: 2.6 Consensus size: 35
31050 GGTAGCCGGC
31060 GGTGGTGGTTGCCGGCGGTGCTGGTGACCGGCGGT
1 GGTGGTGGTTGCCGGCGGTGCTGGTGACCGGCGGT
31095 GGTGGTGGTTGCCGGCGGTGCTGGTGACCGGCGGT
1 GGTGGTGGTTGCCGGCGGTGCTGGTGACCGGCGGT
* * *
31130 GGTAGTGGTGGCCGGTGGTG
1 GGTGGTGGTTGCCGGCGGTG
31150 GTTGGTTTCC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.03, C:0.18, G:0.56, T:0.23
Consensus pattern (35 bp):
GGTGGTGGTTGCCGGCGGTGCTGGTGACCGGCGGT
Found at i:31714 original size:9 final size:9
Alignment explanation
Indices: 31702--31760 Score: 61
Period size: 8 Copynumber: 6.7 Consensus size: 9
31692 ATAAAAATAA
31702 AAAAAAGAG
1 AAAAAAGAG
*
31711 -AAAAGGAG
1 AAAAAAGAG
*
31719 AAAAAAGAAA
1 AAAAAAG-AG
31729 AAAAAAGGAG
1 AAAAAA-GAG
31739 AAAAAAGA-
1 AAAAAAGAG
31747 AAAAAA-AG
1 AAAAAAGAG
31755 AAAAAA
1 AAAAAA
31761 ATAAATTAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
7 1 0.02
8 19 0.45
9 7 0.17
10 14 0.33
11 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:31732 original size:27 final size:29
Alignment explanation
Indices: 31700--31761 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
31690 TTATAAAAAT
* *
31700 AAAAAAAA-GAG-AAAAGGAGAAAAAAGA
1 AAAAAAAAGGAGAAAAAAGAAAAAAAAGA
31727 AAAAAAAAGGAGAAAAAAGAAAAAAAAGA
1 AAAAAAAAGGAGAAAAAAGAAAAAAAAGA
31756 AAAAAA
1 AAAAAA
31762 TAAATTAAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 8 0.26
28 3 0.10
29 20 0.65
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (29 bp):
AAAAAAAAGGAGAAAAAAGAAAAAAAAGA
Found at i:31734 original size:20 final size:20
Alignment explanation
Indices: 31711--31753 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
31701 AAAAAAAGAG
31711 AAAAGGAGAAAAAAGAAAAA
1 AAAAGGAGAAAAAAGAAAAA
31731 AAAAGGAGAAAAAAGAAAAA
1 AAAAGGAGAAAAAAGAAAAA
31751 AAA
1 AAA
31754 GAAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (20 bp):
AAAAGGAGAAAAAAGAAAAA
Found at i:31761 original size:9 final size:9
Alignment explanation
Indices: 31694--31761 Score: 66
Period size: 9 Copynumber: 7.4 Consensus size: 9
31684 CGTCATTTAT
*
31694 AAAAATAAA
1 AAAAAGAAA
31703 AAAAAGAGAA
1 AAAAAGA-AA
**
31713 AAGGAGAAA
1 AAAAAGAAA
31722 AAAGAA-AAA
1 AAA-AAGAAA
* *
31731 AAAAGGAGA
1 AAAAAGAAA
31740 AAAAAGAAA
1 AAAAAGAAA
31749 AAAAAGAAA
1 AAAAAGAAA
31758 AAAA
1 AAAA
31762 TAAATTAAGC
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
8 1 0.02
9 38 0.81
10 8 0.17
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:44470 original size:77 final size:77
Alignment explanation
Indices: 44336--44907 Score: 451
Period size: 77 Copynumber: 7.4 Consensus size: 77
44326 ACGAATTCTC
* * * * *
44336 AAGTTGACATCGGTTGGCCTTCTAAAAAAGTTTT-GAAAGTTAGTATCAGTTGACCTTCTTTAAA
1 AAGTTGGCATCGGTTGGCCTTCTAAAAAAGTTTTCAAAAGTTGGTATCGGTTGGCCTTCTTTAAA
*
44400 ATTAAGCTTTCAA
66 ATCAAGCTTTC-A
* * *
44413 AAGTTGGCATCTGTTGGCCTTCT-AAAAAGTTCTCAAAAGTTGGCATCGGTTGGCCTTCTTTAAA
1 AAGTTGGCATCGGTTGGCCTTCTAAAAAAGTTTTCAAAAGTTGGTATCGGTTGGCCTTCTTTAAA
* *
44477 GTCAAGTTTTCA
66 ATCAAGCTTTCA
* * * * *
44489 AGAGTTGGTATCGGTTGACCTTCTCTAAAAATCGAGTTTTTAAAAGATGGTATCTGTTGGCCTTC
1 A-AGTTGGCATCGGTTGGCC-T-TCTAAAAA---AGTTTTCAAAAGTTGGTATCGGTTGGCCTTC
*
44554 --T-AAA--AAGTTTTCA
60 TTTAAAATCAAGCTTTCA
** *
44567 AAGTTGGCATCGGTTGGCCTTCTAAAAAATGTTTTC-GGAGTTGGTATCGGTTGGCCTTCTCTAA
1 AAGTTGGCATCGGTTGGCCTTCTAAAAAA-GTTTTCAAAAGTTGGTATCGGTTGGCCTTCT-TTA
*
44631 AAATCGAGCTTTTC-
64 AAATCAAGC-TTTCA
44645 AAGTTGGCATCGGTTGGCCTTCT-AAAAAGTTTTC-AAAGTTGGTATCGGTTGGCCTTCTTTAAA
1 AAGTTGGCATCGGTTGGCCTTCTAAAAAAGTTTTCAAAAGTTGGTATCGGTTGGCCTTCTTTAAA
*
44708 ATCAA-ATTTCCA
66 ATCAAGCTTT-CA
* * * *
44720 AAGTTGGCATCGGGTGGCTTTCTTTAAAATCGAGTTTTTTCAAAAGTTGGCATCGGTTGGCCTTC
1 AAGTTGGCATCGGTTGGCCTTC--TAAAA--AAG--TTTTCAAAAGTTGGTATCGGTTGGCCTTC
* * *
44785 --T-AGA--GAGTTTTCA
60 TTTAAAATCAAGCTTTCA
* ** * *
44798 AAGTTGGTATCGGTTGGCCTTCTTAAAGTTTTGAGTCTTC-AAAGTCGGTATCGGTTGGCCTTCT
1 AAGTTGGCATCGGTTGGCCTTC-TAAA----AAAGTTTTCAAAAGTTGGTATCGGTTGGCCTTCT
* * * ** *
44862 TGAGGATTTGAGTTTTCA
61 TTA-AAATCAAGCTTTCA
44880 AAGTTGGCATCGGTTGGCCTTCTAAAAA
1 AAGTTGGCATCGGTTGGCCTTCTAAAAA
44908 GTTAGTATCA
Statistics
Matches: 402, Mismatches: 56, Indels: 74
0.76 0.11 0.14
Matches are distributed among these distances:
72 20 0.05
73 8 0.02
74 1 0.00
75 36 0.09
76 64 0.16
77 100 0.25
78 61 0.15
79 13 0.03
80 10 0.02
81 6 0.01
82 35 0.09
83 48 0.12
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (77 bp):
AAGTTGGCATCGGTTGGCCTTCTAAAAAAGTTTTCAAAAGTTGGTATCGGTTGGCCTTCTTTAAA
ATCAAGCTTTCA
Found at i:44582 original size:118 final size:114
Alignment explanation
Indices: 44336--44910 Score: 606
Period size: 118 Copynumber: 5.0 Consensus size: 114
44326 ACGAATTCTC
* * * * * *
44336 AAGTTGACATCGGTTGGCCTTC-TAAA-AAAGTTTTGAAAGTTAGTATCAGTTGACCTTCTTTAA
1 AAGTTGGCATCGGTTGGCCTTCTTAAATAAAGTTTTCAAAGTTGGTATCGGTTGGCCTTCTTAAA
** * * *
44399 AATTAAGCTTTCAAAAGTTGGCATCTGTTGGCCTTCTAAAAAGTTCTCAA
66 AATCGAGCTTTTAAAAGTTGGCATCGGTTGGCCTTCTAAAAAGTTTTC-A
* *
44449 AAGTTGGCATCGGTTGGCCTTCTTTAAAGTCAAGTTTTCAAGAGTTGGTATCGGTTGACCTTCTC
1 AAGTTGGCATCGGTTGGCCTTC-TTAAA-TAAAGTTTTCAA-AGTTGGTATCGGTTGGCCTTCT-
* * * *
44514 TAAAAATCGAGTTTTTAAAAGATGGTATCTGTTGGCCTTCTAAAAAGTTTTCA
62 TAAAAATCGAGCTTTTAAAAGTTGGCATCGGTTGGCCTTCTAAAAAGTTTTCA
**
44567 AAGTTGGCATCGGTTGGCCTTC-TAAA-AAATGTTTTCGGAGTTGGTATCGGTTGGCCTTCTCTA
1 AAGTTGGCATCGGTTGGCCTTCTTAAATAAA-GTTTTCAAAGTTGGTATCGGTTGGCCTTCT-TA
*
44630 AAAATCGAGCTTTT-CAAGTTGGCATCGGTTGGCCTTCTAAAAAGTTTTCA
64 AAAATCGAGCTTTTAAAAGTTGGCATCGGTTGGCCTTCTAAAAAGTTTTCA
* * * * *
44680 AAGTTGGTATCGGTTGGCCTTCTTTAAAATCAAA-TTTCCAAAGTTGGCATCGGGTGGCTTTCTT
1 AAGTTGGCATCGGTTGGCCTTC-TT-AAAT-AAAGTTTTCAAAGTTGGTATCGGTTGGCCTTCTT
* * * *
44744 TAAAATCGAGTTTTTTCAAAAGTTGGCATCGGTTGGCCTTCTAGAGAGTTTTCA
63 AAAAATCGAG-CTTTT-AAAAGTTGGCATCGGTTGGCCTTCTAAAAAGTTTTCA
* ** * *
44798 AAGTTGGTATCGGTTGGCCTTCTTAAAGTTTTGAGTCTTCAAAGTCGGTATCGGTTGGCCTTCTT
1 AAGTTGGCATCGGTTGGCCTTCTTAAA---TAAAGTTTTCAAAGTTGGTATCGGTTGGCCTTCTT
** * * *
44863 GAGGATTTGAG-TTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAAGTT
63 -AAAAATCGAGCTTTTAAAAGTTGGCATCGGTTGGCCTTCTAAAAAGTT
44911 AGTATCAGTT
Statistics
Matches: 392, Mismatches: 50, Indels: 36
0.82 0.10 0.08
Matches are distributed among these distances:
113 74 0.19
114 39 0.10
115 21 0.05
116 37 0.09
117 41 0.10
118 106 0.27
119 69 0.18
120 5 0.01
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (114 bp):
AAGTTGGCATCGGTTGGCCTTCTTAAATAAAGTTTTCAAAGTTGGTATCGGTTGGCCTTCTTAAA
AATCGAGCTTTTAAAAGTTGGCATCGGTTGGCCTTCTAAAAAGTTTTCA
Found at i:44773 original size:43 final size:39
Alignment explanation
Indices: 44336--44902 Score: 318
Period size: 41 Copynumber: 14.6 Consensus size: 39
44326 ACGAATTCTC
* *
44336 AAGTTGACATCGGTTGGCCTTC--TAAAA--AAGTTTTGA
1 AAGTTGGCATCGGTTGGCCTTCTTTAAAATCAA-TTTTCA
* * * * * *
44372 AAGTTAGTATCAGTTGACCTTCTTTAAAATTAAGCTTTCAA
1 AAGTTGGCATCGGTTGGCCTTCTTTAAAATCAA-TTTTC-A
* * *
44413 AAGTTGGCATCTGTTGGCCTTC--TAAAA--AGTTCTCAA
1 AAGTTGGCATCGGTTGGCCTTCTTTAAAATCAATTTTC-A
*
44449 AAGTTGGCATCGGTTGGCCTTCTTTAAAGTCAAGTTTTCA
1 AAGTTGGCATCGGTTGGCCTTCTTTAAAATCAA-TTTTCA
* * * * *
44489 AGAGTTGGTATCGGTTGACCTTCTCTAAAAATCGAGTTTTTAA
1 A-AGTTGGCATCGGTTGGCCTTCT-TTAAAATC-A-ATTTTCA
* * * *
44532 AAGATGGTATCTGTTGGCCTTC--TAAAA--AGTTTTCA
1 AAGTTGGCATCGGTTGGCCTTCTTTAAAATCAATTTTCA
** * *
44567 AAGTTGGCATCGGTTGGCCTTCTAAAAAAT--GTTTTCG
1 AAGTTGGCATCGGTTGGCCTTCTTTAAAATCAATTTTCA
* * * *
44604 GAGTTGGTATCGGTTGGCCTTCTCTAAAAATCGAGCTTTTC-
1 AAGTTGGCATCGGTTGGCCTTCT-TTAAAATC-A-ATTTTCA
*
44645 AAGTTGGCATCGGTTGGCCTTC--TAAAA--AGTTTTCA
1 AAGTTGGCATCGGTTGGCCTTCTTTAAAATCAATTTTCA
* *
44680 AAGTTGGTATCGGTTGGCCTTCTTTAAAATCAAATTTCCA
1 AAGTTGGCATCGGTTGGCCTTCTTTAAAATC-AATTTTCA
* * *
44720 AAGTTGGCATCGGGTGGCTTTCTTTAAAATCGAGTTTTTTCAA
1 AAGTTGGCATCGGTTGGCCTTCTTTAAAATC-A--ATTTTC-A
* * *
44763 AAGTTGGCATCGGTTGGCCTTC--T-AGA-GAGTTTTCA
1 AAGTTGGCATCGGTTGGCCTTCTTTAAAATCAATTTTCA
* * * * *
44798 AAGTTGGTATCGGTTGGCCTTC-TTAAAGTTTTGAGTCTTCA
1 AAGTTGGCATCGGTTGGCCTTCTTTAAA---ATCAATTTTCA
* * * ** * *
44839 AAGTCGGTATCGGTTGGCCTTCTTGAGGATTTGAGTTTTCA
1 AAGTTGGCATCGGTTGGCCTTCTTTA--AAATCAATTTTCA
44880 AAGTTGGCATCGGTTGGCCTTCT
1 AAGTTGGCATCGGTTGGCCTTCT
44903 AAAAAGTTAG
Statistics
Matches: 424, Mismatches: 67, Indels: 75
0.75 0.12 0.13
Matches are distributed among these distances:
34 5 0.01
35 68 0.16
36 50 0.12
37 38 0.09
38 20 0.05
39 9 0.02
40 46 0.11
41 124 0.29
42 35 0.08
43 28 0.07
44 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (39 bp):
AAGTTGGCATCGGTTGGCCTTCTTTAAAATCAATTTTCA
Found at i:44781 original size:231 final size:232
Alignment explanation
Indices: 44336--44910 Score: 698
Period size: 231 Copynumber: 2.5 Consensus size: 232
44326 ACGAATTCTC
* * * * *
44336 AAGTTGACATCGGTTGGCCTTCTAAAAAA-GTTTT-GAAAGTTAGTATCAGTTGACCTTCTTTAA
1 AAGTTGGCATCGGTTGGCCTTCTAAAAAATGTTTTCG-AAGTTGGTATCGGTTGGCCTTCTTAAA
* *
44399 AATTAAGC-TTTCAAAAGTTGGCATCTGTTGGCCTTCTAAAAAGTTCTCAAAAGTTGGCATCGGT
65 AATTGAGCTTTTC-AAAGTTGGCATCGGTTGGCCTTCTAAAAAGTTCTCAAAAGTTGGCATCGGT
* * * * *
44463 TGGCCTTCTTTAAAGTCAAGTTTTCAAGAGTTGGTATCGGTTGACCTTCTCTAAAAATCGAGTTT
129 TGGCCTTCTTTAAAATCAAATTTCCAAGAGTTGGCATCGGGTGACCTTCTCTAAAAATCGAGTTT
* *
44528 TTAAAAGATGGTATCTGTTGGCCTTCTAAAAAGTTTTCA
194 TTAAAAGATGGCATCGGTTGGCCTTCTAAAAAGTTTTCA
*
44567 AAGTTGGCATCGGTTGGCCTTCTAAAAAATGTTTTCGGAGTTGGTATCGGTTGGCCTTCTCTAAA
1 AAGTTGGCATCGGTTGGCCTTCTAAAAAATGTTTTCGAAGTTGGTATCGGTTGGCCTTCT-TAAA
* * *
44632 AATCGAGCTTTTC-AAGTTGGCATCGGTTGGCCTTCTAAAAAGTTTTC-AAAGTTGGTATCGGTT
65 AATTGAGCTTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAAGTTCTCAAAAGTTGGCATCGGTT
* * *
44695 GGCCTTCTTTAAAATCAAATTTCCAA-AGTTGGCATCGGGTGGCTTTCT-TTAAAATCGAGTTTT
130 GGCCTTCTTTAAAATCAAATTTCCAAGAGTTGGCATCGGGTGACCTTCTCTAAAAATCGAG-TTT
* * *
44758 TTCAAAAGTTGGCATCGGTTGGCCTTCTAGAGAGTTTTCA
194 TT-AAAAGATGGCATCGGTTGGCCTTCTAAAAAGTTTTCA
* *** * * *
44798 AAGTTGGTATCGGTTGGCCTTCTTAAAGTTTTGAGTCTTCAAAGTCGGTATCGGTTGGCCTTCTT
1 AAGTTGGCATCGGTTGGCCTTC-TAAA-AAAT--GTTTTCGAAGTTGGTATCGGTTGGCCTTCTT
** *
44863 GAGGATTTGAG-TTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAAGTT
62 -AAAAATTGAGCTTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAAGTT
44911 AGTATCAGTT
Statistics
Matches: 296, Mismatches: 36, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
229 10 0.03
230 23 0.08
231 119 0.40
232 60 0.20
233 11 0.04
234 10 0.03
235 63 0.21
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (232 bp):
AAGTTGGCATCGGTTGGCCTTCTAAAAAATGTTTTCGAAGTTGGTATCGGTTGGCCTTCTTAAAA
ATTGAGCTTTTCAAAGTTGGCATCGGTTGGCCTTCTAAAAAGTTCTCAAAAGTTGGCATCGGTTG
GCCTTCTTTAAAATCAAATTTCCAAGAGTTGGCATCGGGTGACCTTCTCTAAAAATCGAGTTTTT
AAAAGATGGCATCGGTTGGCCTTCTAAAAAGTTTTCA
Found at i:46235 original size:16 final size:16
Alignment explanation
Indices: 46214--46264 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
46204 AGTGACCGGC
46214 GGTGGTAGCCGGCGGT
1 GGTGGTAGCCGGCGGT
* * *
46230 GGTGGTTGCCGACAGT
1 GGTGGTAGCCGGCGGT
* *
46246 GTTGGTGGCCGGCGGT
1 GGTGGTAGCCGGCGGT
46262 GGT
1 GGT
46265 TGGTTTCCGG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.06, C:0.18, G:0.53, T:0.24
Consensus pattern (16 bp):
GGTGGTAGCCGGCGGT
Done.