Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014933.1 Corchorus olitorius cultivar O-4 contig14966, 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: 96029
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3096 original size:3 final size:3
Alignment explanation
Indices: 3088--3117 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3078 ATTCAGTCTC
3088 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
3118 GTTTGTTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:22997 original size:2 final size:2
Alignment explanation
Indices: 22990--23017 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22980 CAGAATGGAA
22990 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23018 GGTAATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23222 original size:2 final size:2
Alignment explanation
Indices: 23209--23238 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
23199 ATAATTTGCC
*
23209 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23239 GTTGTCTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:27055 original size:82 final size:82
Alignment explanation
Indices: 26918--27080 Score: 281
Period size: 82 Copynumber: 2.0 Consensus size: 82
26908 TGATAATCAC
* *
26918 ACTCAAACAAGTGGACACCAAATGGATCATGGCAGCAGAAACAATCAATGGAAGCATAAGCGTTA
1 ACTCAAACAAGAGGACACCAAATGGATCATGCCAGCAGAAACAATCAATGGAAGCATAAGCGTTA
26983 AGTCGAAATAGACTTCT
66 AGTCGAAATAGACTTCT
* *
27000 ACTCAAACAAGAGGACACCAAATGGATCATGCCAGCAGAAACAATCAATGGAAGCATATGCTTTA
1 ACTCAAACAAGAGGACACCAAATGGATCATGCCAGCAGAAACAATCAATGGAAGCATAAGCGTTA
*
27065 AGTCGAATTAGACTTC
66 AGTCGAAATAGACTTC
27081 ATGAAAATCA
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 76 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (82 bp):
ACTCAAACAAGAGGACACCAAATGGATCATGCCAGCAGAAACAATCAATGGAAGCATAAGCGTTA
AGTCGAAATAGACTTCT
Found at i:28469 original size:9 final size:9
Alignment explanation
Indices: 28455--28480 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
28445 AAAAACCCCA
28455 AACAGCCCT
1 AACAGCCCT
28464 AACAGCCCT
1 AACAGCCCT
28473 AACAGCCC
1 AACAGCCC
28481 AAACCCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.46, G:0.12, T:0.08
Consensus pattern (9 bp):
AACAGCCCT
Found at i:32339 original size:44 final size:44
Alignment explanation
Indices: 32276--32360 Score: 170
Period size: 44 Copynumber: 1.9 Consensus size: 44
32266 TTCCATAAAC
32276 AAGAATCTCGATGAGCAACTATTATTAGAGAGAATATCATATTG
1 AAGAATCTCGATGAGCAACTATTATTAGAGAGAATATCATATTG
32320 AAGAATCTCGATGAGCAACTATTATTAGAGAGAATATCATA
1 AAGAATCTCGATGAGCAACTATTATTAGAGAGAATATCATA
32361 GGAAGAGAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (44 bp):
AAGAATCTCGATGAGCAACTATTATTAGAGAGAATATCATATTG
Found at i:32715 original size:18 final size:18
Alignment explanation
Indices: 32684--32718 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
32674 TGGTTAACAT
**
32684 CTCAGGGAGGTAAAATAG
1 CTCAGGGACCTAAAATAG
32702 CTCAGGGACCTAAAATA
1 CTCAGGGACCTAAAATA
32719 AAAATAAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (18 bp):
CTCAGGGACCTAAAATAG
Found at i:41185 original size:20 final size:19
Alignment explanation
Indices: 41155--41204 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
41145 TCCTGAAATC
*
41155 ATATAA-AAAAAGCTCAGAA
1 ATATAATAAAAA-ATCAGAA
41174 AGTATAATAAAAAATCAGAA
1 A-TATAATAAAAAATCAGAA
41194 ATCATAATAAA
1 AT-ATAATAAA
41205 GAATATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 20 0.74
21 5 0.19
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.20
Consensus pattern (19 bp):
ATATAATAAAAAATCAGAA
Found at i:62295 original size:15 final size:15
Alignment explanation
Indices: 62245--62295 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
62235 TTCATCCTAA
62245 TTAAGCAAGGGTTTT
1 TTAAGCAAGGGTTTT
* *
62260 TTAA-CAGAGACAGTTTA
1 TTAAGCA-AG--GGTTTT
62277 TTAAGCAAGGGTTTT
1 TTAAGCAAGGGTTTT
62292 TTAA
1 TTAA
62296 CAGAGACAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
14 2 0.07
15 14 0.50
17 10 0.36
18 2 0.07
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (15 bp):
TTAAGCAAGGGTTTT
Found at i:63917 original size:16 final size:16
Alignment explanation
Indices: 63896--63927 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
63886 TTTTGAGGAC
63896 ATGAATCAAGTTTTAT
1 ATGAATCAAGTTTTAT
63912 ATGAATCAAGTTTTAT
1 ATGAATCAAGTTTTAT
63928 CTGATTCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (16 bp):
ATGAATCAAGTTTTAT
Found at i:64937 original size:17 final size:16
Alignment explanation
Indices: 64890--64940 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
64880 CATGTAATCT
*
64890 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
*
64906 TTGCATTACTGGTGATC
1 TTG-ATCACTGGTGATC
*
64923 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
64940 T
1 T
64941 GGGGGGTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:67028 original size:53 final size:53
Alignment explanation
Indices: 66948--67051 Score: 208
Period size: 53 Copynumber: 2.0 Consensus size: 53
66938 TTAGAGAATA
66948 TATTTGAATATTAAAAATTTAATTAATTATGAAATGGGTACTTGTCAACATTT
1 TATTTGAATATTAAAAATTTAATTAATTATGAAATGGGTACTTGTCAACATTT
67001 TATTTGAATATTAAAAATTTAATTAATTATGAAATGGGTACTTGTCAACAT
1 TATTTGAATATTAAAAATTTAATTAATTATGAAATGGGTACTTGTCAACAT
67052 CTTAAGTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (53 bp):
TATTTGAATATTAAAAATTTAATTAATTATGAAATGGGTACTTGTCAACATTT
Found at i:72677 original size:16 final size:16
Alignment explanation
Indices: 72656--72687 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
72646 CAAAACTATT
*
72656 CCCTAAATGACACATG
1 CCCTAAAGGACACATG
72672 CCCTAAAGGACACATG
1 CCCTAAAGGACACATG
72688 TCAACCCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.31, G:0.16, T:0.16
Consensus pattern (16 bp):
CCCTAAAGGACACATG
Found at i:74471 original size:31 final size:31
Alignment explanation
Indices: 74433--74513 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
74423 TAGATCCAGT
*
74433 TAAGTAGAGGGACTC-AATTGACACCAAATTG
1 TAAGTAGAGGGAC-CAAATTAACACCAAATTG
* * *
74464 TAAGTAGATGAACCAAATTAAGACCAAATTG
1 TAAGTAGAGGGACCAAATTAACACCAAATTG
74495 TAAGT-GAGGGAACCAAATT
1 TAAGTAGAGGG-ACCAAATT
74514 GACAATTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
30 4 0.10
31 38 0.90
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.22
Consensus pattern (31 bp):
TAAGTAGAGGGACCAAATTAACACCAAATTG
Found at i:74536 original size:31 final size:34
Alignment explanation
Indices: 74492--74555 Score: 98
Period size: 31 Copynumber: 2.0 Consensus size: 34
74482 TAAGACCAAA
74492 TTGTAAGTGAGGGAACCAAATTGA-CAATTTTTT
1 TTGTAAGTGAGGGAACCAAATTGATCAATTTTTT
*
74525 TTGT-AGT-AGGGAACCAAATTGATCCATTTTT
1 TTGTAAGTGAGGGAACCAAATTGATCAATTTTT
74556 GTTAGTAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 15 0.52
32 10 0.34
33 4 0.14
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (34 bp):
TTGTAAGTGAGGGAACCAAATTGATCAATTTTTT
Found at i:74568 original size:32 final size:31
Alignment explanation
Indices: 74501--74568 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
74491 ATTGTAAGTG
* *
74501 AGGGAACCAAATTGACAATTTTTTTTGTAGT
1 AGGGAACCAAATTGACAATTTTTTTAGTAGA
*
74532 AGGGAACCAAATTGATCCATTTTTGTTAGTA-A
1 AGGGAACCAAATTGA-CAATTTTT-TTAGTAGA
74564 AGGGA
1 AGGGA
74569 CATGTACGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 15 0.47
32 12 0.38
33 5 0.16
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (31 bp):
AGGGAACCAAATTGACAATTTTTTTAGTAGA
Found at i:76380 original size:19 final size:20
Alignment explanation
Indices: 76342--76392 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
76332 TAATAATCCC
76342 ATATGTACAGTACCTAATCTA
1 ATATGTACAGTA-CTAATCTA
* *
76363 ATATGTACAGT-GTAATCTC
1 ATATGTACAGTACTAATCTA
*
76382 ATCTGTACAGT
1 ATATGTACAGT
76393 TGTTAAATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 16 0.59
21 11 0.41
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (20 bp):
ATATGTACAGTACTAATCTA
Found at i:89772 original size:19 final size:20
Alignment explanation
Indices: 89748--89805 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
89738 CTGTTTGGCA
89748 ACTGTACAGATGAGATTA-C
1 ACTGTACAGATGAGATTAGC
* *
89767 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA-GC
*
89788 ACGGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
89806 TAAGAGCAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (20 bp):
ACTGTACAGATGAGATTAGC
Found at i:90453 original size:26 final size:28
Alignment explanation
Indices: 90400--90453 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
90390 TTTTGACATT
90400 AACAAAACACACAACCAGATGTACCAAAAA
1 AACAAAACACACAACCAGA--TACCAAAAA
90430 AACAAAACACAC-ACCAGA-ACCAAA
1 AACAAAACACACAACCAGATACCAAA
90454 TTTCTATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 6 0.25
29 6 0.25
30 12 0.50
ACGTcount: A:0.61, C:0.30, G:0.06, T:0.04
Consensus pattern (28 bp):
AACAAAACACACAACCAGATACCAAAAA
Found at i:92894 original size:45 final size:45
Alignment explanation
Indices: 92822--92908 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
92812 GGATAGTTTG
* * *
92822 AGCACTCGGCAATCATGGAGCCAAAGCTCTCTTTGATTTCCTTAA
1 AGCACTCGGCAATCATGAAGCCAAAGCTCTCCTTGATCTCCTTAA
* * * *
92867 AGCATTCGGCAATCATGAATCCTAAGCTTTCCTTGATCTCCT
1 AGCACTCGGCAATCATGAAGCCAAAGCTCTCCTTGATCTCCT
92909 GCACGTTCTC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (45 bp):
AGCACTCGGCAATCATGAAGCCAAAGCTCTCCTTGATCTCCTTAA
Found at i:93558 original size:71 final size:72
Alignment explanation
Indices: 93442--93588 Score: 242
Period size: 71 Copynumber: 2.0 Consensus size: 72
93432 GGAGCACCAC
*
93442 TGTGTCTTCTCGTGTACCTTCGTGTCTGGCCTCGCCTCACTGCGGAGAGCCTCTGTCTTCTCCTG
1 TGTGTCTTCTCGCGTACCTTCGTGTCTGGCCTCGCCTCACTGCGGAGAGCCTCTGTCTTCTCCTG
93507 T-CTTCA
66 TACTTCA
* * *
93513 TGTGTCTTCTCGCGTACCTTCGTGTCTGGCCTTGCCTCACTGCGGAGAGCCTGTGTCTTCTCGTG
1 TGTGTCTTCTCGCGTACCTTCGTGTCTGGCCTCGCCTCACTGCGGAGAGCCTCTGTCTTCTCCTG
93578 TACCTTCA
66 TA-CTTCA
93586 TGT
1 TGT
93589 CTGGCCTCGC
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 62 0.89
73 8 0.11
ACGTcount: A:0.07, C:0.32, G:0.24, T:0.37
Consensus pattern (72 bp):
TGTGTCTTCTCGCGTACCTTCGTGTCTGGCCTCGCCTCACTGCGGAGAGCCTCTGTCTTCTCCTG
TACTTCA
Found at i:93568 original size:51 final size:51
Alignment explanation
Indices: 93513--93622 Score: 184
Period size: 51 Copynumber: 2.2 Consensus size: 51
93503 CCTGTCTTCA
* *
93513 TGTGTCTTCTCGCGTACCTTCGTGTCTGGCCTTGCCTCACTGCGGAGAGCC
1 TGTGTCTTCTCGCGTACCTTCATGTCTGGCCTCGCCTCACTGCGGAGAGCC
*
93564 TGTGTCTTCTCGTGTACCTTCATGTCTGGCCTCGCCTCACTGCGGAGAGCC
1 TGTGTCTTCTCGCGTACCTTCATGTCTGGCCTCGCCTCACTGCGGAGAGCC
*
93615 TCTGTCTT
1 TGTGTCTT
93623 GTGTCTTCGC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.08, C:0.33, G:0.25, T:0.34
Consensus pattern (51 bp):
TGTGTCTTCTCGCGTACCTTCATGTCTGGCCTCGCCTCACTGCGGAGAGCC
Found at i:95162 original size:333 final size:325
Alignment explanation
Indices: 94379--96028 Score: 1548
Period size: 333 Copynumber: 5.0 Consensus size: 325
94369 CATAGTAGAA
* *
94379 TAATTCGGAAAAAAATTGAAAAACGATAGTAGAATAGTTAAAAGCCCGTCAATCTTTTTGGCGTT
1 TAATTCGGAAAAAAATTGAAAAACGATATTAGAATAGTGAAAAGCCCGTCAATCTTTTTGGCGTT
* *
94444 GAATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTCAGGAAAAACTTCTCAAGTCA----GT
66 GAATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTCAGGAAAAACTTCTCAGGTCATTTTTT
** * *
94505 TTTTAGCCGAAATCGTGTACT----ATCACGATTTTTGGGCTAAAAACGCGTTTTGGGGCCCCGG
131 TTTTAGCCGAAATCGTGTACTAAGCATCACGATTTTTGGGCTAAAAACGCGTTCCGGAGCCCCGA
* * * * * * *
94566 CTCAGTTATACATGATTTTAGGCAGAAAGACTTCTTGAAATATCTACATATATCTAGCCAAATCT
196 CTCAATTATACATGATTTTAGGCACAAAGACTCCCTGAAATATCTATATATATCGAACCAAATCT
* * * ** * *
94631 GAGCCACAGTGGATTTAAAGATTTGTTTTTATGAGCATCTTAATCTTGTTTCGATTTAAATAAAT
261 CAACCACAGTGGATTTAAGGATTTGTTTTTACAAGCATCTAAATCTTGTTTCGATTTAAAGAAAT
* * * * * * ** * *
94696 AAATTCGAAAAAGAAAATGGAAAATCGGTTTTAGAAGCGTGAATAA-CCC-TTAATTTTTTTTGG
1 TAATTCG-GAAA-AAAATTGAAAAACGATATTAGAATAGTGAA-AAGCCCGTCAA-TCTTTTTGG
* ** * * * * *
94759 CGTTGAAATATATATTTTTTCCAAGTATTGTGGTAAAAAAATTGAGGAAAAACTTTTCGGGTCAT
62 CGTTGAATTATATATTTTTTCTGAGTATTTTGG-CAAAAAATTCAGGAAAAACTTCTCAGGTCAT
*
94824 TTTTTGGAAAATTTTAGCCGAAATCGTGTACTAACCATCACTG-TTTTT-GGCTAAAAAACGCGT
126 TTTTT------TTTTAGCCGAAATCGTGTACTAAGCATCAC-GATTTTTGGGCT-AAAAACGCGT
* * * *
94887 TCCGGAG-CCCGACTCAATTTTGCATGATTTTTGGCACAAAGAGTCCCTGAAATATCTATAT-TC
183 TCCGGAGCCCCGACTCAATTATACATGATTTTAGGCACAAAGACTCCCTGAAATATCTATATAT-
* * * *
94950 ATCGAACTAAATCTCAACCACATTGGATATAAGGATTTGTTTTTACAAGCATCTAAATCTTTTTT
247 ATCGAACCAAATCTCAACCACAGTGGATTTAAGGATTTGTTTTTACAAGCATCTAAATCTTGTTT
95015 CGATTTAATTAGAAAT
312 CGATTTAA--AGAAAT
* *
95031 TAATTCGGAAAAAAATTGAAAAACGATAGTAGAATAGTTAAAAGCCCGTCAATCTTTTTGGCGTT
1 TAATTCGGAAAAAAATTGAAAAACGATATTAGAATAGTGAAAAGCCCGTCAATCTTTTTGGCGTT
* *
95096 GAATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTCAGGAAAAACTTCTCAAGTCA---GTT
66 GAATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTCAGGAAAAACTTCTCAGGTCATTTTTT
* * ** *
95158 TTTT-GCCGAAATCATGTACTAAGTATCACGATTTTTGGGCTAAAAACGCGTTTTGGAGCCCCGG
131 TTTTAGCCGAAATCGTGTACTAAGCATCACGATTTTTGGGCTAAAAACGCGTTCCGGAGCCCCGA
* * * * * * * *
95222 CTCAGTTATACATGATTTTAGGAAGAAAGACTTCTTGAAAGATCTATATATATCTAGCCAAATCT
196 CTCAATTATACATGATTTTAGGCACAAAGACTCCCTGAAATATCTATATATATCGAACCAAATCT
* * * *
95287 GC-GCCACAGTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAAATAAA
261 -CAACCACAGTGGATTTAAGGATTTGTTTTTACAAGCATCTAAATCTTGTTTCGATTTAAAGAAA
95351 T
325 T
* * * * * * ** * * *
95352 AAATTCGAAAAAAAAATGGAAAATCGGTTTTAGAAGCGTGAATAA-CCCTTAATATTTTTTTGGC
1 TAATTCG-GAAAAAAATTGAAAAACGATATTAGAATAGTGAA-AAGCCCGTCA-ATCTTTTTGGC
* ** * * *
95416 GTTGAATTATATATTTTTTCCGAGTATTGTTGTAAAAAAATTGAGGAAAAACTTTTCGGGTCATT
63 GTTGAATTATATATTTTTTCTGAGTATT-TTGGCAAAAAATTCAGGAAAAACTTCTCAGGTCATT
* * * * *
95481 TTTTGGAAAATTTTATCCGAAATCGCGTACAAAGCATCACTATTTTT-GGCTAAAAATGCGTTCC
127 TTTT------TTTTAGCCGAAATCGTGTACTAAGCATCACGATTTTTGGGCTAAAAACGCGTTCC
* * * *
95545 GGAG-CCCGACTCAATTTTGCATGATTTTTGGCACAAAGAGTCCCTGAAATATCTATAT-TCATC
186 GGAGCCCCGACTCAATTATACATGATTTTAGGCACAAAGACTCCCTGAAATATCTATATAT-ATC
* *
95608 GAACTAAATCTCAACCACATTGGATTTAAGGA-TT-TTTTTACAAGCATCTAAATCTT-TTTCCG
250 GAACCAAATCTCAACCACAGTGGATTTAAGGATTTGTTTTTACAAGCATCTAAATCTTGTTT-CG
*
95670 TATTAATAAGAAAT
314 -ATTTA-AAGAAAT
*
95684 TAATTCGGAAAAAAAATTGAAAAACGATATTAGAATAGTGAAAAGCCCATCAATCTTTTTGGCGT
1 TAATTCGG-AAAAAAATTGAAAAACGATATTAGAATAGTGAAAAGCCCGTCAATCTTTTTGGCGT
* *
95749 TAAATTATATATTTTTTGCTGAATATTTTGGCAAAAAAGTTCAGGAAAAATCTTCTCAGGTCA--
65 TGAATTATATATTTTTT-CTGAGTATTTTGGCAAAAAA-TTCAGGAAAAA-CTTCTCAGGTCATT
* * * * **
95812 -ATTTTTTAGCAGAAATCGTGTACTAACTAACCATCACGATTTTT-GGTTAAAAACGCGTTTTTG
127 TTTTTTTTAGCCGAAATCGTG---T-ACTAAGCATCACGATTTTTGGGCTAAAAACGCG--TTCC
* * * * * * * *
95875 GGGGCCTCGGCTCAGTTATACACGATTTTAGGCAGAAAGACTTCTTGAAATATCTATAT-TCATC
186 GGAGCCCCGACTCAATTATACATGATTTTAGGCACAAAGACTCCCTGAAATATCTATATAT-ATC
* * ** * * * * *
95939 TAGCTGAATTTGAGCCACAGTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGA
250 GAACCAAATCTCAACCACAGTGGATTTAAGGATTTGTTTTTACAAGCATCTAAATCTTGTTTCGA
*
96004 TTTAAA-TAAT
315 TTTAAAGAAAT
96014 TAAATTC-GAAAAAAA
1 T-AATTCGGAAAAAAA
96029 G
Statistics
Matches: 1068, Mismatches: 199, Indels: 120
0.77 0.14 0.09
Matches are distributed among these distances:
317 6 0.01
318 6 0.01
319 62 0.06
320 27 0.03
321 12 0.01
322 72 0.07
323 152 0.14
324 45 0.04
327 3 0.00
328 27 0.03
329 12 0.01
330 55 0.05
331 127 0.12
332 166 0.16
333 225 0.21
334 59 0.06
335 12 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (325 bp):
TAATTCGGAAAAAAATTGAAAAACGATATTAGAATAGTGAAAAGCCCGTCAATCTTTTTGGCGTT
GAATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTCAGGAAAAACTTCTCAGGTCATTTTTT
TTTTAGCCGAAATCGTGTACTAAGCATCACGATTTTTGGGCTAAAAACGCGTTCCGGAGCCCCGA
CTCAATTATACATGATTTTAGGCACAAAGACTCCCTGAAATATCTATATATATCGAACCAAATCT
CAACCACAGTGGATTTAAGGATTTGTTTTTACAAGCATCTAAATCTTGTTTCGATTTAAAGAAAT
Found at i:95794 original size:656 final size:654
Alignment explanation
Indices: 94379--96028 Score: 2760
Period size: 656 Copynumber: 2.5 Consensus size: 654
94369 CATAGTAGAA
94379 TAATTCGGAAAAAAATTGAAAAACGATAGTAGAATAGTTAAAAGCCCGTCAATCTTTTTGGCGTT
1 TAATTCGGAAAAAAATTGAAAAACGATAGTAGAATAGTTAAAAGCCCGTCAATCTTTTTGGCGTT
94444 GAATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTCAGGAAAAACTTCTCAAGTCAGTTTTT
66 GAATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTCAGGAAAAACTTCTCAAGTCAGTTTTT
*
94509 AGCCGAAATCGTGTAC---TATCACGATTTTTGGGCTAAAAACGCGTTTTGGGGCCCCGGCTCAG
131 TGCCGAAATCGTGTACTAATATCACGATTTTTGGGCTAAAAACGCGTTTTGGGGCCCCGGCTCAG
*
94571 TTATACATGATTTTAGGCAGAAAGACTTCTTGAAATATCTACATATATCTAGCCAAATCTGAGCC
196 TTATACATGATTTTAGGCAGAAAGACTTCTTGAAATATCTATATATATCTAGCCAAATCTGAGCC
* *
94636 ACAGTGGATTTAAAGATTTGTTTTTATGAGCATCTTAATCTTGTTTCGATTTAAATAAATAAATT
261 ACAGTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAAATAAATAAATT
94701 CGAAAAAGAAAATGGAAAATCGGTTTTAGAAGCGTGAATAACCCTTAATTTTTTTTGGCGTTGAA
326 CGAAAAA-AAAATGGAAAATCGGTTTTAGAAGCGTGAATAACCCTTAATTTTTTTTGGCGTTGAA
94766 ATATATATTTTTTCCAAGTATTGTGGTAAAAAAATTGAGGAAAAACTTTTCGGGTCATTTTTTGG
390 ATATATATTTTTTCCAAGTATTGTGGTAAAAAAATTGAGGAAAAACTTTTCGGGTCATTTTTTGG
* * *
94831 AAAATTTTAGCCGAAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAAACGCGTTCCGGAGCC
455 AAAATTTTAGCCGAAATCGCGTACAAACCATCACTATTTTTGGCTAAAAAACGCGTTCCGGAGCC
94896 CGACTCAATTTTGCATGATTTTTGGCACAAAGAGTCCCTGAAATATCTATATTCATCGAACTAAA
520 CGACTCAATTTTGCATGATTTTTGGCACAAAGAGTCCCTGAAATATCTATATTCATCGAACTAAA
* *
94961 TCTCAACCACATTGGATATAAGGATTTGTTTTTACAAGCATCTAAATCTTTTTTCGATTTAATTA
585 TCTCAACCACATTGGATATAAGGATTTGTTTTTACAAGCATCTAAATCTTTTTCCGATTTAATAA
95026 GAAAT
650 GAAAT
95031 TAATTCGGAAAAAAATTGAAAAACGATAGTAGAATAGTTAAAAGCCCGTCAATCTTTTTGGCGTT
1 TAATTCGGAAAAAAATTGAAAAACGATAGTAGAATAGTTAAAAGCCCGTCAATCTTTTTGGCGTT
95096 GAATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTCAGGAAAAACTTCTCAAGTCAGTTTTT
66 GAATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTCAGGAAAAACTTCTCAAGTCAGTTTTT
* *
95161 TGCCGAAATCATGTACTAAGTATCACGATTTTTGGGCTAAAAACGCGTTTTGGAGCCCCGGCTCA
131 TGCCGAAATCGTGTACTAA-TATCACGATTTTTGGGCTAAAAACGCGTTTTGGGGCCCCGGCTCA
* * *
95226 GTTATACATGATTTTAGGAAGAAAGACTTCTTGAAAGATCTATATATATCTAGCCAAATCTGCGC
195 GTTATACATGATTTTAGGCAGAAAGACTTCTTGAAATATCTATATATATCTAGCCAAATCTGAGC
95291 CACAGTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAAATAAATAAAT
260 CACAGTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAAATAAATAAAT
95356 TCGAAAAAAAAATGGAAAATCGGTTTTAGAAGCGTGAATAACCCTTAATATTTTTTTGGCGTTGA
325 TCGAAAAAAAAATGGAAAATCGGTTTTAGAAGCGTGAATAACCCTTAAT-TTTTTTTGGCGTTGA
* * *
95421 ATTATATATTTTTTCCGAGTATTGTTGTAAAAAAATTGAGGAAAAACTTTTCGGGTCATTTTTTG
389 AATATATATTTTTTCCAAGTATTGTGGTAAAAAAATTGAGGAAAAACTTTTCGGGTCATTTTTTG
* * *
95486 GAAAATTTTATCCGAAATCGCGTACAAAGCATCACTATTTTTGGCT-AAAAATGCGTTCCGGAGC
454 GAAAATTTTAGCCGAAATCGCGTACAAACCATCACTATTTTTGGCTAAAAAACGCGTTCCGGAGC
95550 CCGACTCAATTTTGCATGATTTTTGGCACAAAGAGTCCCTGAAATATCTATATTCATCGAACTAA
519 CCGACTCAATTTTGCATGATTTTTGGCACAAAGAGTCCCTGAAATATCTATATTCATCGAACTAA
*
95615 ATCTCAACCACATTGGATTTAAGGA-TT-TTTTTACAAGCATCTAAATCTTTTTCCG-TATTAAT
584 ATCTCAACCACATTGGATATAAGGATTTGTTTTTACAAGCATCTAAATCTTTTTCCGAT-TTAAT
95677 AAGAAAT
648 AAGAAAT
* * *
95684 TAATTCGGAAAAAAAATTGAAAAACGATATTAGAATAGTGAAAAGCCCATCAATCTTTTTGGCGT
1 TAATTCGG-AAAAAAATTGAAAAACGATAGTAGAATAGTTAAAAGCCCGTCAATCTTTTTGGCGT
* * * *
95749 TAAATTATATATTTTTTGCTGAATATTTTGGCAAAAAAGTTCAGGAAAAATCTTCTCAGGTCAAT
65 TGAATTATATATTTTTT-CTGAGTATTTTGGCAAAAAA-TTCAGGAAAAA-CTTCTCAAGTCAGT
* *
95814 TTTTTAGCAGAAATCGTGTACTAACTAACCATCACGATTTTT-GGTTAAAAACGCGTTTTTGGGG
127 TTTTT-GCCGAAATCGTGTACTAA-T----ATCACGATTTTTGGGCTAAAAACGCG-TTTT-GGG
* *
95878 GCCTCGGCTCAGTTATACACGATTTTAGGCAGAAAGACTTCTTGAAATATCTATAT-TCATCTAG
184 GCCCCGGCTCAGTTATACATGATTTTAGGCAGAAAGACTTCTTGAAATATCTATATAT-ATCTAG
** *
95942 CTGAATTTGAGCCACAGTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTT
248 CCAAATCTGAGCCACAGTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTT
*
96007 AAATAATTAAATTCGAAAAAAA
313 AAATAAATAAATTCGAAAAAAA
96029 G
Statistics
Matches: 938, Mismatches: 42, Indels: 25
0.93 0.04 0.02
Matches are distributed among these distances:
652 145 0.15
653 46 0.05
654 71 0.08
655 166 0.18
656 305 0.33
657 17 0.02
658 17 0.02
661 12 0.01
662 17 0.02
663 142 0.15
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (654 bp):
TAATTCGGAAAAAAATTGAAAAACGATAGTAGAATAGTTAAAAGCCCGTCAATCTTTTTGGCGTT
GAATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTCAGGAAAAACTTCTCAAGTCAGTTTTT
TGCCGAAATCGTGTACTAATATCACGATTTTTGGGCTAAAAACGCGTTTTGGGGCCCCGGCTCAG
TTATACATGATTTTAGGCAGAAAGACTTCTTGAAATATCTATATATATCTAGCCAAATCTGAGCC
ACAGTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCTTGTTTCGATTTAAATAAATAAATT
CGAAAAAAAAATGGAAAATCGGTTTTAGAAGCGTGAATAACCCTTAATTTTTTTTGGCGTTGAAA
TATATATTTTTTCCAAGTATTGTGGTAAAAAAATTGAGGAAAAACTTTTCGGGTCATTTTTTGGA
AAATTTTAGCCGAAATCGCGTACAAACCATCACTATTTTTGGCTAAAAAACGCGTTCCGGAGCCC
GACTCAATTTTGCATGATTTTTGGCACAAAGAGTCCCTGAAATATCTATATTCATCGAACTAAAT
CTCAACCACATTGGATATAAGGATTTGTTTTTACAAGCATCTAAATCTTTTTCCGATTTAATAAG
AAAT
Done.