Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016422.1 Corchorus olitorius cultivar O-4 contig16455, 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: 110126
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2342 original size:71 final size:71
Alignment explanation
Indices: 2190--2388 Score: 240
Period size: 71 Copynumber: 2.8 Consensus size: 71
2180 ATTTCTGTTA
* * * * *
2190 GTAGATTCATCCACCATATCCAAATTCGTGAAATCAGAG-CAAAAT-TGAGCAAAACTCTAGACA
1 GTAGATTCATCCACCATATCCAGATTCGTG--ACCCGAGTC-GAATCAGAGCAAAACTCTAGACA
*
2253 TCTATGTTG
63 TCTACGTTG
*
2262 GTAGATTCATCCACCATATCCAGATTCGTGACCCGAGTCGAATCAGAGCAAAACTCTAGACGTCT
1 GTAGATTCATCCACCATATCCAGATTCGTGACCCGAGTCGAATCAGAGCAAAACTCTAGACATCT
*
2327 CCGTTG
66 ACGTTG
* * * * *
2333 GTAGATTCATCCATCATATCCAGATTCGTGACCCAAGTTGAATCAAAACAAAACTC
1 GTAGATTCATCCACCATATCCAGATTCGTGACCCGAGTCGAATCAGAGCAAAACTC
2389 CGGATACCAG
Statistics
Matches: 112, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
70 8 0.07
71 75 0.67
72 29 0.26
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (71 bp):
GTAGATTCATCCACCATATCCAGATTCGTGACCCGAGTCGAATCAGAGCAAAACTCTAGACATCT
ACGTTG
Found at i:2578 original size:29 final size:29
Alignment explanation
Indices: 2545--2616 Score: 144
Period size: 29 Copynumber: 2.5 Consensus size: 29
2535 TTGCAATACC
2545 TTCAAGTTTCTATTTAAAGGAGTTTTTTA
1 TTCAAGTTTCTATTTAAAGGAGTTTTTTA
2574 TTCAAGTTTCTATTTAAAGGAGTTTTTTA
1 TTCAAGTTTCTATTTAAAGGAGTTTTTTA
2603 TTCAAGTTTCTATT
1 TTCAAGTTTCTATT
2617 AATATAAATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.26, C:0.08, G:0.12, T:0.53
Consensus pattern (29 bp):
TTCAAGTTTCTATTTAAAGGAGTTTTTTA
Found at i:20614 original size:20 final size:21
Alignment explanation
Indices: 20591--20630 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20581 CCACGAAACC
*
20591 GCCTCCGT-TCACTACAAGCG
1 GCCTCCGTCTCACCACAAGCG
*
20611 GCCTCCTTCTCACCACAAGC
1 GCCTCCGTCTCACCACAAGC
20631 ACTACCTGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.20, C:0.45, G:0.15, T:0.20
Consensus pattern (21 bp):
GCCTCCGTCTCACCACAAGCG
Found at i:28979 original size:15 final size:15
Alignment explanation
Indices: 28954--29109 Score: 101
Period size: 15 Copynumber: 10.8 Consensus size: 15
28944 CCCATCTGAC
*
28954 TGCAGTTCATGTAAA
1 TGCACTTCATGTAAA
* *
28969 TGCCCTTCATGTAAT
1 TGCACTTCATGTAAA
*
28984 TGCAGTTCATGTAAA
1 TGCACTTCATGTAAA
* * *
28999 TGCCCTTCATGTGAT
1 TGCACTTCATGTAAA
**
29014 TGCGGTTC------A
1 TGCACTTCATGTAAA
*
29023 TGCAGTTCATGTAAA
1 TGCACTTCATGTAAA
* *
29038 TGTC-CTTCATGCAAC
1 TG-CACTTCATGTAAA
*
29053 TGCAGTTCATGTAAA
1 TGCACTTCATGTAAA
* * *
29068 TGCCCTTCATGCAAC
1 TGCACTTCATGTAAA
*
29083 TGCACTTCATGTAAC
1 TGCACTTCATGTAAA
29098 TGCACTTCATGT
1 TGCACTTCATGT
29110 TTTAGCTGCT
Statistics
Matches: 107, Mismatches: 26, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
9 7 0.07
14 1 0.01
15 98 0.92
16 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (15 bp):
TGCACTTCATGTAAA
Found at i:28988 original size:30 final size:30
Alignment explanation
Indices: 28952--29109 Score: 163
Period size: 30 Copynumber: 5.0 Consensus size: 30
28942 TGCCCATCTG
28952 ACTGCAGTTCATGTAAATGCCCTTCATGTA
1 ACTGCAGTTCATGTAAATGCCCTTCATGTA
*
28982 ATTGCAGTTCATGTAAATGCCCTTCATGTGA
1 ACTGCAGTTCATGTAAATGCCCTTCATGT-A
* * *
29013 TTGCGGTTCATGCAGTTCATGTAAATGTCCTTCATGCA
1 -------AC-TGCAGTTCATGTAAATGCCCTTCATGTA
*
29051 ACTGCAGTTCATGTAAATGCCCTTCATGCA
1 ACTGCAGTTCATGTAAATGCCCTTCATGTA
* * *
29081 ACTGCACTTCATGTAACTGCACTTCATGT
1 ACTGCAGTTCATGTAAATGCCCTTCATGT
29110 TTTAGCTGCT
Statistics
Matches: 108, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
30 80 0.74
31 2 0.02
38 1 0.01
39 25 0.23
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (30 bp):
ACTGCAGTTCATGTAAATGCCCTTCATGTA
Found at i:29061 original size:39 final size:39
Alignment explanation
Indices: 28984--29063 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 39
28974 TTCATGTAAT
** * *
28984 TGCAGTTCATGTAAATGCCCTTCATGTGATTGCGGTTCA
1 TGCAGTTCATGTAAATGCCCTTCATGCAACTGCAGTTCA
*
29023 TGCAGTTCATGTAAATGTCCTTCATGCAACTGCAGTTCA
1 TGCAGTTCATGTAAATGCCCTTCATGCAACTGCAGTTCA
29062 TG
1 TG
29064 TAAATGCCCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (39 bp):
TGCAGTTCATGTAAATGCCCTTCATGCAACTGCAGTTCA
Found at i:29092 original size:69 final size:69
Alignment explanation
Indices: 28954--29093 Score: 208
Period size: 69 Copynumber: 2.0 Consensus size: 69
28944 CCCATCTGAC
* * ** * **
28954 TGCAGTTCATGTAAATGCCCTTCATGTAATTGCAGTTCATGTAAATGCCCTTCATGTGATTGCGG
1 TGCAGTTCATGTAAATGCCCTTCATGCAACTGCAGTTCATGTAAATGCCCTTCATGCAACTGCAC
29019 TTCA
66 TTCA
*
29023 TGCAGTTCATGTAAATGTCCTTCATGCAACTGCAGTTCATGTAAATGCCCTTCATGCAACTGCAC
1 TGCAGTTCATGTAAATGCCCTTCATGCAACTGCAGTTCATGTAAATGCCCTTCATGCAACTGCAC
29088 TTCA
66 TTCA
29092 TG
1 TG
29094 TAACTGCACT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (69 bp):
TGCAGTTCATGTAAATGCCCTTCATGCAACTGCAGTTCATGTAAATGCCCTTCATGCAACTGCAC
TTCA
Found at i:34079 original size:21 final size:21
Alignment explanation
Indices: 34034--34092 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
34024 CTGTTTGACA
* *
34034 ACTGTACAGATGAGATTA--C
1 ACTGTACATATGAGATTATGT
*
34053 ACTGTACATATTAGATTATGT
1 ACTGTACATATGAGATTATGT
34074 ACTGTACATATGAGATTAT
1 ACTGTACATATGAGATTAT
34093 TAGAACAGCG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.47
21 18 0.53
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (21 bp):
ACTGTACATATGAGATTATGT
Found at i:45163 original size:30 final size:30
Alignment explanation
Indices: 45089--45164 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 30
45079 TACCGTGCAA
* *
45089 GTCCCTCTACTTATAAAAAAGGATCAATTTG
1 GTCCCTCTACTTA-CAAAAACGATCAATTTG
*
45120 GT-CCTCTTA-TTACAAAAACTATCAATTTG
1 GTCCCTC-TACTTACAAAAACGATCAATTTG
45149 GTCCCTCTACTTACAA
1 GTCCCTCTACTTACAA
45165 TTTGATGTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 18 0.46
30 17 0.44
31 4 0.10
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (30 bp):
GTCCCTCTACTTACAAAAACGATCAATTTG
Found at i:53685 original size:3 final size:3
Alignment explanation
Indices: 53677--53702 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
53667 GATTGTAGAC
53677 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
53703 AATGGGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:55977 original size:40 final size:40
Alignment explanation
Indices: 55915--55995 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
55905 ACTTGACCCT
* *
55915 CCTAATAATTAAGGAAATAAATTAAATTCAGGTTTAGCCC
1 CCTAATAATCAAGGAAATAAATTAAATCCAGGTTTAGCCC
55955 CCTAATAATCAAGGTAAA-AAATTAAATCCAGGTTTAGCCC
1 CCTAATAATCAAGG-AAATAAATTAAATCCAGGTTTAGCCC
55995 C
1 C
55996 TAGTTATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 35 0.92
41 3 0.08
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (40 bp):
CCTAATAATCAAGGAAATAAATTAAATCCAGGTTTAGCCC
Found at i:60613 original size:19 final size:19
Alignment explanation
Indices: 60589--60626 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
60579 CTGTTTAGCA
60589 ACTGTACAAATAAGATTAT
1 ACTGTACAAATAAGATTAT
* *
60608 ACTGTACAGATCAGATTAT
1 ACTGTACAAATAAGATTAT
60627 TAGAGCAGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (19 bp):
ACTGTACAAATAAGATTAT
Found at i:69460 original size:7 final size:7
Alignment explanation
Indices: 69444--69480 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
69434 GTAGTTCCAA
69444 CCCCCAC
1 CCCCCAC
69451 CCCCC-C
1 CCCCCAC
69457 CCCCCAC
1 CCCCCAC
*
69464 CCCCCTC
1 CCCCCAC
69471 CCCCCAC
1 CCCCCAC
69478 CCC
1 CCC
69481 AACTTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.08, C:0.89, G:0.00, T:0.03
Consensus pattern (7 bp):
CCCCCAC
Found at i:69462 original size:13 final size:14
Alignment explanation
Indices: 69444--69480 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
69434 GTAGTTCCAA
69444 CCCCCACCCCCC-C
1 CCCCCACCCCCCTC
69457 CCCCCACCCCCCTC
1 CCCCCACCCCCCTC
69471 CCCCCACCCC
1 CCCCCACCCC
69481 AACTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.08, C:0.89, G:0.00, T:0.03
Consensus pattern (14 bp):
CCCCCACCCCCCTC
Found at i:85015 original size:13 final size:16
Alignment explanation
Indices: 84979--85012 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
84969 AAAAACATTA
84979 ATTATAATACGACAAT
1 ATTATAATACGACAAT
84995 ATTATAATACGACAAT
1 ATTATAATACGACAAT
85011 AT
1 AT
85013 AATGTACGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.32
Consensus pattern (16 bp):
ATTATAATACGACAAT
Found at i:87617 original size:42 final size:42
Alignment explanation
Indices: 87569--87648 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
87559 GAGGTATGCC
*
87569 TATCTCATGGCCTTTCAAGCAGCATTTTAGGTGAGGTATTTT
1 TATCTCATGGCCTTTCAAGCAGCATTTTAGGTCAGGTATTTT
* *
87611 TATCTCATGGCCTTTCTAGGAGCATTTTAGGTCAGGTA
1 TATCTCATGGCCTTTCAAGCAGCATTTTAGGTCAGGTA
87649 CTAACATACT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (42 bp):
TATCTCATGGCCTTTCAAGCAGCATTTTAGGTCAGGTATTTT
Found at i:89117 original size:14 final size:15
Alignment explanation
Indices: 89093--89121 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
89083 TCCCAAGACC
89093 AAAACTCCAGAGCAA
1 AAAACTCCAGAGCAA
89108 AAAACT-CAGAGCAA
1 AAAACTCCAGAGCAA
89122 TCCAAAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.24, G:0.14, T:0.07
Consensus pattern (15 bp):
AAAACTCCAGAGCAA
Found at i:102529 original size:21 final size:21
Alignment explanation
Indices: 102505--102545 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
102495 TGGCTGCGTT
102505 TAGTAGAGTGGTGCGGTAGCG
1 TAGTAGAGTGGTGCGGTAGCG
102526 TAGTAGAGTGGTGCGGTAGC
1 TAGTAGAGTGGTGCGGTAGC
102546 CGTGCGATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.46, T:0.24
Consensus pattern (21 bp):
TAGTAGAGTGGTGCGGTAGCG
Found at i:102690 original size:49 final size:49
Alignment explanation
Indices: 102613--102708 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 49
102603 TTAGGTACCC
*
102613 TACAGATGAGATTATTAGAGCAGTGATTGAAACAGAGTTTACACTTATG
1 TACAGATGAGATTATTAGAGCAGCGATTGAAACAGAGTTTACACTTATG
*
102662 TACATATGAGATTATTAGAGCAGCGATTGAAACAGAGTTTACACTTA
1 TACAGATGAGATTATTAGAGCAGCGATTGAAACAGAGTTTACACTTA
102709 AATTCCGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (49 bp):
TACAGATGAGATTATTAGAGCAGCGATTGAAACAGAGTTTACACTTATG
Found at i:103729 original size:14 final size:14
Alignment explanation
Indices: 103710--103740 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
103700 ATAATTAGTA
103710 TTACAGATCATTCT
1 TTACAGATCATTCT
*
103724 TTACAGATCATTTT
1 TTACAGATCATTCT
103738 TTA
1 TTA
103741 ATAAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.48
Consensus pattern (14 bp):
TTACAGATCATTCT
Found at i:107103 original size:21 final size:21
Alignment explanation
Indices: 107077--107119 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
107067 AATGATTGTC
107077 TTGATTGTTTCTTGTGAATTG
1 TTGATTGTTTCTTGTGAATTG
107098 TTGATTGTTTCTTGTGAATTG
1 TTGATTGTTTCTTGTGAATTG
107119 T
1 T
107120 GTTGCCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.05, G:0.23, T:0.58
Consensus pattern (21 bp):
TTGATTGTTTCTTGTGAATTG
Found at i:107686 original size:50 final size:51
Alignment explanation
Indices: 107546--107696 Score: 198
Period size: 51 Copynumber: 3.0 Consensus size: 51
107536 CTCAAATGTT
* * * *
107546 TAAAAGAGTTTAGTAATTAGGAGACCGATGAGAGCTGTCTCTCTAAACATC
1 TAAAAGAGTTTAGTAATTAGGAGACCGATGGGAGATGTCTCCCCAAACATC
* *
107597 TAAACA-ATTTTAGTAATTAGGAGACCGATAGGAGATGTCTCCCCAAACATC
1 TAAA-AGAGTTTAGTAATTAGGAGACCGATGGGAGATGTCTCCCCAAACATC
** *
107648 TAAAAGA-TTTAGTAATTAGGAGATTGATGGGAGTTGTCTCCCCAAACAT
1 TAAAAGAGTTTAGTAATTAGGAGACCGATGGGAGATGTCTCCCCAAACAT
107697 TTAATTAAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
50 39 0.44
51 48 0.55
52 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.28
Consensus pattern (51 bp):
TAAAAGAGTTTAGTAATTAGGAGACCGATGGGAGATGTCTCCCCAAACATC
Found at i:107730 original size:43 final size:43
Alignment explanation
Indices: 107684--107826 Score: 211
Period size: 43 Copynumber: 3.4 Consensus size: 43
107674 ATGGGAGTTG
* *
107684 TCTCCCCAAACATTTAATTAAAAAAAGTGACCGATGAGAGCTG
1 TCTCTCCAAACATTTAATTAAAAAAAGTGACCGATGAGAGCTA
* *
107727 TCTCTCCAAACATTTAGTT---AAAAGTGATCGATGAGAGCTA
1 TCTCTCCAAACATTTAATTAAAAAAAGTGACCGATGAGAGCTA
*
107767 TCTCTCCAAACATTTAATTAAAAAAAGTGACCTATGAGAGCTA
1 TCTCTCCAAACATTTAATTAAAAAAAGTGACCGATGAGAGCTA
*
107810 TCTCTCCAAACAATTAA
1 TCTCTCCAAACATTTAA
107827 AAAAGTGACC
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
40 37 0.42
43 52 0.58
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.27
Consensus pattern (43 bp):
TCTCTCCAAACATTTAATTAAAAAAAGTGACCGATGAGAGCTA
Found at i:107853 original size:144 final size:142
Alignment explanation
Indices: 107705--107969 Score: 397
Period size: 144 Copynumber: 1.9 Consensus size: 142
107695 ATTTAATTAA
* *
107705 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAGTT-AAAAGTGATCGATGAGAGCTATC
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAGTGATCGATAAGAGCTATC
* *
107769 TCTCCAAACATTTAATTAAAAAAAGTGACCTATGAGAGCTATCTCTCCAAACAATTAAAAAAGTG
66 TCTCCAAA-ATTTAA--AAAAAAAGTGACCGATGAGAGCCATCTCTCCAAACAATTAAAAAAGTG
107834 ACCAACACTAAAAAT
128 ACCAACACTAAAAAT
* * *
107849 AAAAAGTGACTGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAGTGATTGATAAGAGCTGTC
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAGTGATCGATAAGAGCTATC
* * * *
107914 TCTCCAAAATTTAAATAAAAAGTGACCGATGTGAGCCGTCTCTCCAAACATTTAAA
66 TCTCCAAAATTTAAAAAAAAAGTGACCGATGAGAGCCATCTCTCCAAACAATTAAA
107970 GAAAAAGTGA
Statistics
Matches: 109, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
142 36 0.33
144 45 0.41
145 28 0.26
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (142 bp):
AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAGTGATCGATAAGAGCTATC
TCTCCAAAATTTAAAAAAAAAGTGACCGATGAGAGCCATCTCTCCAAACAATTAAAAAAGTGACC
AACACTAAAAAT
Found at i:108086 original size:42 final size:42
Alignment explanation
Indices: 107849--110126 Score: 2122
Period size: 42 Copynumber: 55.4 Consensus size: 42
107839 CACTAAAAAT
*
107849 AAAAAGTGACTGATGAGAGCTGTCTCTCCAAACATTTAATT-
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
** * *
107890 AAAAAGTGATTGATAAGAGCTGTCTCTCCAAA-ATTTAAAT-
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* *
107930 AAAAAGTGACCGATGTGAGCCGTCTCTCCAAACATTTAA--A
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * *
107970 GAAAAAGTGACCGATGAGAACTCTCTCTCCAAATATTTAATT-
1 -AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * * **
108012 -AAAAGTGACTGATGTGAGCTATCTCTTTAAACATTTAATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * *
108053 AAAAATTGATCGATGAGAGCTGTCTCTCCAAACATTTAAAT-
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* *
108094 AAAAAGTGACCGATGAGAGCTATTTCTCCAAACATTTAATT-
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* *
108135 -AAAAGTGATCGATGAGAGCTATCTCTCCAAACATTTAATTAA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT-A
* *
108177 AAAAAGTGACCGATGAGAGCTTTCTCT-CAAA-A--CAATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * * *
108215 AAAAA-TAGACCGATGATAGGTATCTCTACAAAC----AATTA
1 AAAAAGT-GACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* *
108253 AAAAAGTGACCGATGAGAGCTATCTCTCCAAACATTCCAAACATTTAA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATT---TA-A-TT-A
* * *
108301 CTAAAAAGTGACAGATGAGAGCTATCTCTTCAAACATTT-A-TA
1 --AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
*
108343 TAAAAAGTGACCGATGAGAGCTGACTCTCCAAACATTTAATT-
1 -AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * *
108385 AAAAAGTGACCGATGAGAGTTATCTCTCCAAACATTTAAAT-
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* *
108426 AAAAAGTGACCGATGAGAGCTGTTTCTCTAAACATTTAATT-
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
*
108467 -AAAAGTGACCGATGAGAGCTGTCTCTCTAAACATTTAATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
*
108508 AAAAAATGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* *
108550 AAAAAGTGACTGATGAGAGCCGTCTCTCCAAACATTTAATT-
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
108591 -AAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT-A
*
108633 AAAAAGTGACTGATGAGAGCTGTCTCTCCAAACATTTAATT-
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
*
108674 -AAAAGTGACCGATGAGAGCTATCTCTCCAAACATTTAATTAA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT-A
* *
108716 AAAAAGTGATCGATGAGAGC--TCTCT-CAAA-A--CAATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * * * *
108752 AAAAAGTGACCGATGAGAGCTATCTAT-CAAAAAATAAATT-
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
** *
108792 AAAAAGTGATTGATGAGAGCTGTCTCT-CAAA-A--CAATT-
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * * * *
108829 AAAAAGTGATCGATGAGAGCTATCTCTCAAAACAATAAATT-
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
*
108870 AAAAAGTGACCGATGAGAGCTGTCTCT-CAAA-A--CAATT-
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * * * *
108907 AAAAAGGGACCGATGAGAGGTATCTCTCCAAACAATAAATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * * *
108949 AAAAAGTGACTGATGAGTGCTGCCTCT-CAAA-A--CAATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * * * *
108987 AAAAAGTGATCGATGAGAGCTATCTCTCAAAACAATAAATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * * *
109029 AAAAAGCGACCGATGAGAGCTGTCTCTCAAAACAATAAATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
*
109071 AAAAAGTGACCGATGAGAGCTGTCTCT-CAAA-A--CAATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * * *
109109 AAAAAG-GAACCGATGAGAGGTATCTCTCCAAACAATAAATTA
1 AAAAAGTG-ACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * * *
109151 AAAAAGTGACTGATGAGTGCTGCCTCT-CAAA-A--CAATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * * * *
109189 AAAAAGTGATCGATGAGAGCTATCTCTCAAAACAATAAATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
** *
109231 AAAAAGTGACCGATGAGAGCCATCTCTCTAAACATTTAATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* *
109273 AAAAAGTGAACGATGAGAGTTGTCTCTCCAAACATTTAATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* *
109315 AAAAGGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTG
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
109357 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
*
109399 AAAAAGTGATCGATGAGAGCTGTCTCTCCAAACATTTAATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * *
109441 AAAAAGTAACCGATGAGAGCTGTCTCTCCAAGCATTTAAATA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* ** *
109483 AAAAAGTGACCGATGAGAGCTATCTCTTTAAACATTCAATT-
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
*
109524 -AAAAGTGACCGATGAGAGCTATCTCTCCAAACATTTAATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * * * *
109565 AAAAATTTACCAATGAGAGCTGTCTCTCAAAACAATT-A--A
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * * * *
109604 AAAAAGTGACCTATGAGAGCTATCTCTGCAAACAATAAATT-
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * *
109645 AAAAACTGACCGATGAGAACTGTCTCT-CAAA-A--CAATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * * *
109683 AAAAAGTGACCGATAAGAGCTATCCCTTCAAAC----AATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * * * *** ** * * *
109721 AAAAAGTGGCCAACATTAAAAAAAAAGTGAC-CGATGAGAGC-TGTCT-CTCCA
1 AAAAAGTGACC--GA-T--GAGAGCTGTCTCTCCA--A-A-CAT-T-TAAT-TA
* *** * * * *** *
109772 AACATTTAA-TTAAAAAGTGACTGATG-AGAGCTAT-CTCGC-TTAACATTTA
1 AA-A---AAGTGACCGA-TGA--GA-GCTG-TCTCTCCAAACATTTA-A-TTA
* *
109821 AATAAAAAGTGATCGATGAGAGCTATCTCTCCAAACATTT-ATT-
1 AA---AAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* *
109864 GAAAAGTGACCGATTAGAGCTGTCTCTCCAAACATTTAATT-
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
*
109905 AATAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* * *
109947 AAAAGGTGACCGATGAGAGTTGTCTCTCCAAACATTTAAAT-
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
*
109988 AAAAAGTGACTGATGAGAGCTGTCTCTCCAAACATTTAATT-
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
*
110029 AAAAA-TGATCGATGAGAGCTGTCTCTCCAAACATTTAATTA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
* *
110070 AAAAAGTGACCGATGAGAGCTATCTCTCCAAACATTTAATAA
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
110112 AAAAAGTGACCGATG
1 AAAAAGTGACCGATG
Statistics
Matches: 1879, Mismatches: 249, Indels: 217
0.80 0.11 0.09
Matches are distributed among these distances:
36 20 0.01
37 67 0.04
38 190 0.10
39 61 0.03
40 368 0.20
41 380 0.20
42 617 0.33
43 90 0.05
44 3 0.00
45 8 0.00
46 6 0.00
47 4 0.00
48 7 0.00
49 8 0.00
50 37 0.02
51 4 0.00
52 6 0.00
54 1 0.00
55 2 0.00
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (42 bp):
AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTA
Found at i:109790 original size:41 final size:41
Alignment explanation
Indices: 109742--110126 Score: 576
Period size: 41 Copynumber: 9.4 Consensus size: 41
109732 AACATTAAAA
109742 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* * * ** *
109783 AAAAAGTGACTGATGAGAGCTATCTCGCTTAACATTTAAAT
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* *
109824 AAAAAGTGATCGATGAGAGCTATCTCTCCAAACATTT-ATT
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* *
109864 GAAAAGTGACCGATTAGAGCTGTCTCTCCAAACATTTAATT
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
*
109905 AATAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* *
109946 AAAAAGGTGACCGATGAGAGTTGTCTCTCCAAACATTTAAAT
1 AAAAA-GTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
*
109988 AAAAAGTGACTGATGAGAGCTGTCTCTCCAAACATTTAATT
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
*
110029 AAAAA-TGATCGATGAGAGCTGTCTCTCCAAACATTTAATT
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* *
110069 AAAAAAGTGACCGATGAGAGCTATCTCTCCAAACATTTAATAA
1 -AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAAT-T
110112 AAAAAGTGACCGATG
1 AAAAAGTGACCGATG
Statistics
Matches: 309, Mismatches: 30, Indels: 9
0.89 0.09 0.03
Matches are distributed among these distances:
40 68 0.22
41 155 0.50
42 86 0.28
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (41 bp):
AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
Found at i:109919 original size:81 final size:82
Alignment explanation
Indices: 109732--110126 Score: 580
Period size: 81 Copynumber: 4.8 Consensus size: 82
109722 AAAAGTGGCC
* *
109732 AACA-TTAAAAAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAGTGACTGA
1 AACATTTAAATAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAGTGACCGA
* * **
109796 TGAGAGCTATCTCGCTT
66 TGAGAGCTGTCTCTCCA
* * *
109813 AACATTTAAATAAAAAGTGATCGATGAGAGCTATCTCTCCAAACATTT-ATTGAAAAGTGACCGA
1 AACATTTAAATAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAGTGACCGA
*
109877 TTAGAGCTGTCTCTCCA
66 TGAGAGCTGTCTCTCCA
* *
109894 AACATTTAATTAATAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAGGTGACCG
1 AACATTTAAATAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAA-GTGACCG
*
109959 ATGAGAGTTGTCTCTCCA
65 ATGAGAGCTGTCTCTCCA
* *
109977 AACATTTAAATAAAAAGTGACTGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAA-TGATCGA
1 AACATTTAAATAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAGTGACCGA
110041 TGAGAGCTGTCTCTCCA
66 TGAGAGCTGTCTCTCCA
* * *
110058 AACATTTAATTAAAAAAGTGACCGATGAGAGCTATCTCTCCAAACATTTAATAAAAAAAGTGACC
1 AACATTTAAAT-AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAAT-TAAAAAGTGACC
110123 GATG
64 GATG
Statistics
Matches: 281, Mismatches: 27, Indels: 9
0.89 0.09 0.03
Matches are distributed among these distances:
81 106 0.38
82 85 0.30
83 82 0.29
84 8 0.03
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.27
Consensus pattern (82 bp):
AACATTTAAATAAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATTAAAAAGTGACCGA
TGAGAGCTGTCTCTCCA
Done.