Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018500.1 Corchorus olitorius cultivar O-4 contig18533, 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: 27000
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:935 original size:118 final size:118
Alignment explanation
Indices: 720--951 Score: 437
Period size: 118 Copynumber: 2.0 Consensus size: 118
710 TGATTGGCAC
*
720 CATGTGGCGCCACAGGTGGAGGGAGAAGTGCAGGCAGGTTGACTTGTCTCTGATCTTGGGCTACT
1 CATGTGGCGCCACAGGTGGAGGGAGAAGTGCAGGCAGGTTGACTTGTCTCGGATCTTGGGCTACT
785 TGTTGGATCTGCCCCCGAGTCTATCTTACACTTGACCAATCTGAGCCAGAAAT
66 TGTTGGATCTGCCCCCGAGTCTATCTTACACTTGACCAATCTGAGCCAGAAAT
838 CATGTGGCGCCACAGGTGGAGGGAGAAGTGCAGGCAGGTTGACTTGTCTCGGATCTTGGGCTACT
1 CATGTGGCGCCACAGGTGGAGGGAGAAGTGCAGGCAGGTTGACTTGTCTCGGATCTTGGGCTACT
* *
903 TGTTGGATCTGCCCCCGAGTCTATTTTCCACTTGACCAATCTGAGCCAG
66 TGTTGGATCTGCCCCCGAGTCTATCTTACACTTGACCAATCTGAGCCAG
952 GATGTTCTCA
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 111 1.00
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (118 bp):
CATGTGGCGCCACAGGTGGAGGGAGAAGTGCAGGCAGGTTGACTTGTCTCGGATCTTGGGCTACT
TGTTGGATCTGCCCCCGAGTCTATCTTACACTTGACCAATCTGAGCCAGAAAT
Found at i:4243 original size:1 final size:1
Alignment explanation
Indices: 4237--4269 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
4227 GGCTATCTAT
4237 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4270 GAACAAAGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6798 original size:39 final size:39
Alignment explanation
Indices: 6744--6822 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
6734 CATGTTTGCA
6744 TTGTCTCGGAATATATAGTTAACATATTTGAAGACAACT
1 TTGTCTCGGAATATATAGTTAACATATTTGAAGACAACT
**
6783 TTGTCTCGGAATATATAGTTCGCATATTTGAAGACAACT
1 TTGTCTCGGAATATATAGTTAACATATTTGAAGACAACT
6822 T
1 T
6823 AAATTATTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (39 bp):
TTGTCTCGGAATATATAGTTAACATATTTGAAGACAACT
Found at i:12741 original size:29 final size:29
Alignment explanation
Indices: 12695--12751 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
12685 TAGGTCACTC
12695 TATGTGATGAGTTCAAGTACAATTGGGTG
1 TATGTGATGAGTTCAAGTACAATTGGGTG
* * *
12724 TATGTGGTGAGTTTAAGTTCAATTGGGT
1 TATGTGATGAGTTCAAGTACAATTGGGT
12752 CTAAGAGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.25, C:0.05, G:0.32, T:0.39
Consensus pattern (29 bp):
TATGTGATGAGTTCAAGTACAATTGGGTG
Found at i:12765 original size:206 final size:208
Alignment explanation
Indices: 12407--12807 Score: 707
Period size: 206 Copynumber: 1.9 Consensus size: 208
12397 TCTTTCACAC
* *
12407 TTTTGACTCGAAGGTAATTACTAATTAGTCTCAAGTGTGGGATACTCTTGGTAAAACCAAAAAAA
1 TTTTGACTCGAAAGTAATTACTAATTAGTCTCAAGTCTGGGATACTCTTGGTAAAACC--AAAAA
*
12472 AAAAAATTAGGTCACTCTATGTGATGAGTTCAAGTTCAATTGGGTGTATGTAGTGAGTTTAAGTT
64 AAAAAATTAGGTCACTCTATGTGATGAGTTCAAGTACAATTGGGTGTATGTAGTGAGTTTAAGTT
* *
12537 CAGTTGGGTGTAAGAGACTCTCTGTGGTGAGTTTAAACTCAATTGGGTGTATTTGGTGAGTTTAA
129 CAATTGGGTCTAAGAGACTCTCTGTGGTGAGTTTAAACTCAATTGGGTGTATTTGGTGAGTTTAA
12602 TATGTGATGCAGTGT
194 TATGTGATGCAGTGT
12617 TTTTGACTCGAAAGTAATTACTAATTAGTCTCAAGTCTGGGATACTCTTGGTAAAA-C-AAAAAA
1 TTTTGACTCGAAAGTAATTACTAATTAGTCTCAAGTCTGGGATACTCTTGGTAAAACCAAAAAAA
*
12680 AAAATTAGGTCACTCTATGTGATGAGTTCAAGTACAATTGGGTGTATGTGGTGAGTTTAAGTTCA
66 AAAATTAGGTCACTCTATGTGATGAGTTCAAGTACAATTGGGTGTATGTAGTGAGTTTAAGTTCA
*
12745 ATTGGGTCTAAGAGACTCTCTGTGGTGAGTTTAAATTCAATTGGGTGTATTTGGTGAGTTTAA
131 ATTGGGTCTAAGAGACTCTCTGTGGTGAGTTTAAACTCAATTGGGTGTATTTGGTGAGTTTAA
12808 GTTTAATTAG
Statistics
Matches: 184, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
206 129 0.70
209 1 0.01
210 54 0.29
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.35
Consensus pattern (208 bp):
TTTTGACTCGAAAGTAATTACTAATTAGTCTCAAGTCTGGGATACTCTTGGTAAAACCAAAAAAA
AAAATTAGGTCACTCTATGTGATGAGTTCAAGTACAATTGGGTGTATGTAGTGAGTTTAAGTTCA
ATTGGGTCTAAGAGACTCTCTGTGGTGAGTTTAAACTCAATTGGGTGTATTTGGTGAGTTTAATA
TGTGATGCAGTGT
Found at i:22127 original size:20 final size:22
Alignment explanation
Indices: 22099--22153 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
22089 TTTTATGAAA
*
22099 TTTGTTAATC-AC-TATAAAAT
1 TTTGATAATCTACATATAAAAT
*
22119 TTTGATAATCTCCATATAAAAT
1 TTTGATAATCTACATATAAAAT
22141 TTTGATAAT-TACA
1 TTTGATAATCTACA
22154 CTCTAAAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.30
21 4 0.13
22 17 0.57
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (22 bp):
TTTGATAATCTACATATAAAAT
Found at i:22160 original size:22 final size:23
Alignment explanation
Indices: 22108--22166 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 23
22098 ATTTGTTAAT
*
22108 CACTATAAAATTTTGATAATCTC
1 CACTATAAAATTTTGATAATCTA
22131 CA-TATAAAATTTTGATAAT-TA
1 CACTATAAAATTTTGATAATCTA
*
22152 CACTCTAAAGATTTT
1 CACTATAAA-ATTTT
22167 ATGATGATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 3 0.09
22 22 0.69
23 7 0.22
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (23 bp):
CACTATAAAATTTTGATAATCTA
Found at i:22282 original size:22 final size:22
Alignment explanation
Indices: 22255--22305 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
22245 TTCCTAATAA
22255 AAATTTTAACAACCA-CCTAATG
1 AAATTTTAACAACCACCCT-ATG
* * *
22277 AAATTTTGATAACTACCCTATG
1 AAATTTTAACAACCACCCTATG
22299 AAATTTT
1 AAATTTT
22306 GATAAACTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (22 bp):
AAATTTTAACAACCACCCTATG
Found at i:22306 original size:22 final size:22
Alignment explanation
Indices: 22274--22640 Score: 75
Period size: 22 Copynumber: 16.7 Consensus size: 22
22264 CAACCACCTA
22274 ATGAAATTTTGATAACTACCCT
1 ATGAAATTTTGATAACTACCCT
* *
22296 ATGAAATTTTGATAAACT-TCCA
1 ATGAAATTTTGAT-AACTACCCT
* * * **
22318 ATGAAATGTTGGTAAGCGCACATT
1 ATGAAATTTTGATAA-C-TACCCT
* * * * *
22342 ATGATATCTTGGTAACCT-TCCG
1 ATGAAATTTTGATAA-CTACCCT
* * * **
22364 ATAAAATATTGGTAA-TCACATT
1 ATGAAATTTTGATAACT-ACCCT
*
22386 ATAAAATTTTGATAAACATA-CC-
1 ATGAAATTTTGAT-AAC-TACCCT
* * *
22408 ATGAAATTGTGATACCT-CACT
1 ATGAAATTTTGATAACTACCCT
*
22429 ATGAAATTTTTATAAATCT-CCCT
1 ATGAAATTTTGAT-AA-CTACCCT
* *
22452 AT-AACATTTTGATGACCT-CCAT
1 ATGAA-ATTTTGAT-AACTACCCT
* * * *
22474 TTCAAATTTTGAAAACCA-CCT
1 ATGAAATTTTGATAACTACCCT
* * * *
22495 CATGAAATCTTGATAACCATCTT
1 -ATGAAATTTTGATAACTACCCT
22518 ATGAAATTTTGATAAC-ATCCCT
1 ATGAAATTTTGATAACTA-CCCT
* * *
22540 AT-AAATTTTTTATAGCCT-CCTT
1 ATGAAA-TTTTGATA-ACTACCCT
*
22562 AT-AAACTTTTGTTAAC--CTCCT
1 ATGAAA-TTTTGATAACTAC-CCT
* ** *
22583 ACGAAATTTTGATAAGAACACT
1 ATGAAATTTTGATAACTACCCT
* * *
22605 ATTAAATTTTGATAAC-CCCCA
1 ATGAAATTTTGATAACTACCCT
22626 ATGAAATTTTGATAA
1 ATGAAATTTTGATAA
22641 TTAATTACAC
Statistics
Matches: 247, Mismatches: 72, Indels: 53
0.66 0.19 0.14
Matches are distributed among these distances:
20 4 0.02
21 51 0.21
22 149 0.60
23 27 0.11
24 15 0.06
25 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (22 bp):
ATGAAATTTTGATAACTACCCT
Found at i:22747 original size:21 final size:22
Alignment explanation
Indices: 22677--22749 Score: 85
Period size: 22 Copynumber: 3.4 Consensus size: 22
22667 CTTACCTTTG
* *
22677 AAATTTTGTTAATCTCCCAATA
1 AAATTTTGTTAATCTCACTATA
** * *
22699 AAATTTTGAGAACCACACTATA
1 AAATTTTGTTAATCTCACTATA
22721 AAATTTTGTTAATCTCACTAT-
1 AAATTTTGTTAATCTCACTATA
22742 AAATTTTG
1 AAATTTTG
22750 ATAAATTCAT
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 8 0.20
22 33 0.80
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (22 bp):
AAATTTTGTTAATCTCACTATA
Found at i:22768 original size:43 final size:44
Alignment explanation
Indices: 22675--22770 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 44
22665 GACTTACCTT
* *
22675 TGAAATTTTGTTAATCTCCCAATAAAATTTTGAGAACCACACTA
1 TGAAATTTTGTTAATCTCACAATAAAATTTTGAGAAACACACTA
* * * ** *
22719 TAAAATTTTGTTAATCTCACTAT-AAATTTTGATAAATTCATTA
1 TGAAATTTTGTTAATCTCACAATAAAATTTTGAGAAACACACTA
22762 TGAAATTTT
1 TGAAATTTT
22771 AGCTACCACA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
43 23 0.53
44 20 0.47
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (44 bp):
TGAAATTTTGTTAATCTCACAATAAAATTTTGAGAAACACACTA
Found at i:22770 original size:22 final size:21
Alignment explanation
Indices: 22677--22770 Score: 66
Period size: 22 Copynumber: 4.3 Consensus size: 21
22667 CTTACCTTTG
* * *
22677 AAATTTTGTTAATCTCCCAAT
1 AAATTTTGTAAATCTCACTAT
* *
22698 AAAATTTTG-AGAACCACACTAT
1 -AAATTTTGTA-AATCTCACTAT
*
22720 AAAATTTTGTTAATCTCACTAT
1 -AAATTTTGTAAATCTCACTAT
*
22742 AAATTTTGATAAAT-TCATTAT
1 AAATTTTG-TAAATCTCACTAT
22763 GAAATTTT
1 -AAATTTT
22771 AGCTACCACA
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
21 14 0.24
22 44 0.76
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.41
Consensus pattern (21 bp):
AAATTTTGTAAATCTCACTAT
Found at i:22852 original size:22 final size:22
Alignment explanation
Indices: 22814--22965 Score: 91
Period size: 22 Copynumber: 7.0 Consensus size: 22
22804 CCTCTGAAAT
*
22814 ACCACATTAT-AATATTTTGATA
1 ACCACACTATGAA-ATTTTGATA
22836 ACCACACTATGAAATTTTGATA
1 ACCACACTATGAAATTTTGATA
* * * *
22858 ATCTC-CCCTCTAAAATTTCGATA
1 A-C-CACACTATGAAATTTTGATA
* * * *
22881 ACCTCCCCATGAAATTTTG-TT
1 ACCACACTATGAAATTTTGATA
* * *
22902 A-C-CTCTATGAAATTGTGATT
1 ACCACACTATGAAATTTTGATA
** *
22922 ATTACACTATGAAATTTTGGTA
1 ACCACACTATGAAATTTTGATA
*
22944 ACAACACT-TGAAATTTTGATA
1 ACCACACTATGAAATTTTGATA
22965 A
1 A
22966 GCTCACTCTA
Statistics
Matches: 102, Mismatches: 21, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
19 12 0.12
20 4 0.04
21 16 0.16
22 51 0.50
23 18 0.18
24 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (22 bp):
ACCACACTATGAAATTTTGATA
Found at i:23028 original size:22 final size:21
Alignment explanation
Indices: 23003--23256 Score: 125
Period size: 22 Copynumber: 11.7 Consensus size: 21
22993 TATAAGCACA
23003 CTATGAAATTTTGATAATCTTC
1 CTATGAAATTTTGATAA-CTTC
* *
23025 CTATGAAATTTTAATAACCTC
1 CTATGAAATTTTGATAACTTC
* **
23046 CATAT-AAGATTTCGATAATCGCC
1 C-TATGAA-ATTTTGATAA-CTTC
***
23069 CTATGAAATTTTGATAACCAGA
1 CTATGAAATTTTGATAA-CTTC
* * *
23091 ATATGAAATTTTGGTAACCTCC
1 CTATGAAATTTTGATAA-CTTC
* *
23113 CTATGAAATTTTAACAACCTTC
1 CTATGAAATTTTGATAA-CTTC
* * *
23135 CCATG-AATTTCGATAACCTC
1 CTATGAAATTTTGATAACTTC
*
23155 CTTATGAAATTTTGATAACATC
1 C-TATGAAATTTTGATAACTTC
* * * *
23177 CCATGAAATTGTAATAACTAC
1 CTATGAAATTTTGATAACTTC
* * * * *
23198 ACTATAAAATTTTAACATCCTAC
1 -CTATGAAATTTTGATA-ACTTC
* **
23221 CTATGAAATTTTGGTAACCAC
1 CTATGAAATTTTGATAACTTC
*
23242 ACTATAAAATTTTGA
1 -CTATGAAATTTTGA
23257 GAACCGAACT
Statistics
Matches: 176, Mismatches: 47, Indels: 18
0.73 0.20 0.07
Matches are distributed among these distances:
20 4 0.02
21 35 0.20
22 128 0.73
23 9 0.05
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (21 bp):
CTATGAAATTTTGATAACTTC
Found at i:23063 original size:44 final size:43
Alignment explanation
Indices: 23008--23173 Score: 154
Period size: 44 Copynumber: 3.8 Consensus size: 43
22998 GCACACTATG
* *
23008 AAATTTTGATAATCTTCCTATGAAATTTTAATAACCTCCATAT
1 AAATTTCGATAATCTCCCTATGAAATTTTAATAACCTCCATAT
* * ***
23051 AAGATTTCGATAATCGCCCTATGAAATTTTGATAACCAGAATAT
1 AA-ATTTCGATAATCTCCCTATGAAATTTTAATAACCTCCATAT
* * * * *
23095 GAAATTTTGGTAACCTCCCTATGAAATTTTAACAACCTTCC-CAT
1 -AAATTTCGATAATCTCCCTATGAAATTTTAATAACC-TCCATAT
* * * *
23139 GAATTTCGATAACCTCCTTATGAAATTTTGATAAC
1 AAATTTCGATAATCTCCCTATGAAATTTTAATAAC
23174 ATCCCATGAA
Statistics
Matches: 97, Mismatches: 23, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
43 31 0.32
44 64 0.66
45 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (43 bp):
AAATTTCGATAATCTCCCTATGAAATTTTAATAACCTCCATAT
Found at i:23194 original size:43 final size:43
Alignment explanation
Indices: 23105--23214 Score: 109
Period size: 43 Copynumber: 2.6 Consensus size: 43
23095 GAAATTTTGG
* *
23105 TAACCTCCCTATGAAATTTTAACAACCTTCCCATGAATTTCGA
1 TAACCTCCCTATGAAATTTTAACAACCATCCCATGAATTTCAA
* * *
23148 TAACCTCCTTATGAAATTTTGATAA-CATCCCATGAAATTGT-AA
1 TAACCTCCCTATGAAATTTTAACAACCATCCCATG-AATT-TCAA
* *
23191 TAA-CTACACTATAAAATTTTAACA
1 TAACCT-CCCTATGAAATTTTAACA
23215 TCCTACCTAT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
42 10 0.19
43 43 0.80
44 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (43 bp):
TAACCTCCCTATGAAATTTTAACAACCATCCCATGAATTTCAA
Found at i:23244 original size:44 final size:44
Alignment explanation
Indices: 23092--23287 Score: 146
Period size: 44 Copynumber: 4.5 Consensus size: 44
23082 ATAACCAGAA
* * * *
23092 TATGAAATTTTGGTAACCTCCCTATGAAATTTTAACAACCTTCC
1 TATGAAATTTTGGTAACCACACTATAAAATTTTAACAACCTACC
* * * * * * * *
23136 CATG-AATTTCGATAACCTC-CTTATGAAATTTTGATAACAT-CC
1 TATGAAATTTTGGTAACCACAC-TATAAAATTTTAACAACCTACC
* * ** * *
23178 CATGAAATTGTAATAACTACACTATAAAATTTTAACATCCTACC
1 TATGAAATTTTGGTAACCACACTATAAAATTTTAACAACCTACC
* * * *
23222 TATGAAATTTTGGTAACCACACTATAAAATTTTGAGAACCGAAC
1 TATGAAATTTTGGTAACCACACTATAAAATTTTAACAACCTACC
* *
23266 TATAAAATTTTAGTAACCACAC
1 TATGAAATTTTGGTAACCACAC
23288 AATGAATTTT
Statistics
Matches: 120, Mismatches: 28, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
42 7 0.06
43 53 0.44
44 60 0.50
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (44 bp):
TATGAAATTTTGGTAACCACACTATAAAATTTTAACAACCTACC
Found at i:23303 original size:21 final size:22
Alignment explanation
Indices: 22987--23303 Score: 107
Period size: 22 Copynumber: 14.5 Consensus size: 22
22977 CTCACTATGT
* * *
22987 AATTTTTATAAGCACACTATGA
1 AATTTTGATAACCACACTATAA
** *
23009 AATTTTGATAATCTTC-CTATGA
1 AATTTTGATAA-CCACACTATAA
* *
23031 AATTTTAATAACCTC-CATATAA
1 AATTTTGATAACCACAC-TATAA
* * * * * *
23053 GATTTCGATAATCGCCCTATGA
1 AATTTTGATAACCACACTATAA
* * *
23075 AATTTTGATAACCAGAATATGA
1 AATTTTGATAACCACACTATAA
* * * *
23097 AATTTTGGTAACCTCCCTATGA
1 AATTTTGATAACCACACTATAA
* * * * *
23119 AATTTTAACAACCTTC-CCAT-G
1 AATTTTGATAACC-ACACTATAA
* * *
23140 AATTTCGATAACCTC-CTTATGA
1 AATTTTGATAACCACAC-TATAA
* *
23162 AATTTTGATAA-CATC-CCATGA
1 AATTTTGATAACCA-CACTATAA
* * *
23183 AATTGTAATAACTACACTATAA
1 AATTTTGATAACCACACTATAA
* * * *
23205 AATTTTAACATCCTAC-CTATGA
1 AATTTTGATAACC-ACACTATAA
*
23227 AATTTTGGTAACCACACTATAA
1 AATTTTGATAACCACACTATAA
*
23249 AATTTTGAGAACCGA-ACTATAA
1 AATTTTGATAACC-ACACTATAA
* *
23271 AATTTT-AGTAACCACACAAT-G
1 AATTTTGA-TAACCACACTATAA
23292 AATTTTGATAAC
1 AATTTTGATAAC
23304 TTCCAAAATT
Statistics
Matches: 222, Mismatches: 58, Indels: 31
0.71 0.19 0.10
Matches are distributed among these distances:
20 3 0.01
21 45 0.20
22 167 0.75
23 7 0.03
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.34
Consensus pattern (22 bp):
AATTTTGATAACCACACTATAA
Found at i:23632 original size:10 final size:10
Alignment explanation
Indices: 23602--23639 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
23592 GTACTTTTAT
23602 ATATAGTATAG
1 ATATAG-ATAG
23613 ATA-A-ATAG
1 ATATAGATAG
23621 ATATAGATAG
1 ATATAGATAG
23631 ATATAGATA
1 ATATAGATA
23640 TATTTCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.28
9 1 0.04
10 14 0.56
11 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.32
Consensus pattern (10 bp):
ATATAGATAG
Found at i:24470 original size:65 final size:65
Alignment explanation
Indices: 24400--24531 Score: 264
Period size: 65 Copynumber: 2.0 Consensus size: 65
24390 AATATATTTA
24400 ATAAAAAAGGGTACAATAGGAAAACATAAAATTTCCCTTTATTCGTACTTTTATATATAGTATAG
1 ATAAAAAAGGGTACAATAGGAAAACATAAAATTTCCCTTTATTCGTACTTTTATATATAGTATAG
24465 ATAAAAAAGGGTACAATAGGAAAACATAAAATTTCCCTTTATTCGTACTTTTATATATAGTATAG
1 ATAAAAAAGGGTACAATAGGAAAACATAAAATTTCCCTTTATTCGTACTTTTATATATAGTATAG
24530 AT
1 AT
24532 TAGTAAAATG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (65 bp):
ATAAAAAAGGGTACAATAGGAAAACATAAAATTTCCCTTTATTCGTACTTTTATATATAGTATAG
Done.