Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015372.1 Corchorus olitorius cultivar O-4 contig15405, 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: 85753
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3020 original size:20 final size:20
Alignment explanation
Indices: 2995--3034 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2985 GTCCCCTCGA
*
2995 TAACTAAGTGCTATTGCAAT
1 TAACTAAGAGCTATTGCAAT
3015 TAACTAAGAGCTATTGCAAT
1 TAACTAAGAGCTATTGCAAT
3035 GAGATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
TAACTAAGAGCTATTGCAAT
Found at i:6966 original size:11 final size:11
Alignment explanation
Indices: 6946--6975 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
6936 GACTTTATTC
*
6946 TAAAAGAAAAG
1 TAAAAAAAAAG
6957 TAAAAAAAAAG
1 TAAAAAAAAAG
6968 TAAAAAAA
1 TAAAAAAA
6976 TCAGGCTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (11 bp):
TAAAAAAAAAG
Found at i:14274 original size:31 final size:29
Alignment explanation
Indices: 14232--14296 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 29
14222 GCTTAATACC
14232 CAAATTAGCTCCTTAACTATCCATTTTGGGA
1 CAAATTAGCTCCTTAACT-T-CATTTTGGGA
* **
14263 CAAATTGGCTCCTTAACTTTTTTTTGGGA
1 CAAATTAGCTCCTTAACTTCATTTTGGGA
14292 CAAAT
1 CAAAT
14297 AAATCCCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 13 0.42
30 1 0.03
31 17 0.55
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (29 bp):
CAAATTAGCTCCTTAACTTCATTTTGGGA
Found at i:19006 original size:51 final size:52
Alignment explanation
Indices: 18946--19051 Score: 169
Period size: 52 Copynumber: 2.1 Consensus size: 52
18936 CATGTTTATC
* *
18946 AAAATGAAATAAAGCTATCA-GTTTATCACAAAACGGAAAAGTCGCAACAAG
1 AAAATGAAATAAAGCTAGCAGGTTTATCACAAAACAGAAAAGTCGCAACAAG
* *
18997 AAAATGAAATAAAGCTAGCAGGTTTATCATAAACCAGAAAAGTCGCAACAAG
1 AAAATGAAATAAAGCTAGCAGGTTTATCACAAAACAGAAAAGTCGCAACAAG
19049 AAA
1 AAA
19052 GTTAAAATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
51 19 0.38
52 31 0.62
ACGTcount: A:0.52, C:0.15, G:0.16, T:0.17
Consensus pattern (52 bp):
AAAATGAAATAAAGCTAGCAGGTTTATCACAAAACAGAAAAGTCGCAACAAG
Found at i:19450 original size:160 final size:160
Alignment explanation
Indices: 19182--19826 Score: 1139
Period size: 160 Copynumber: 4.0 Consensus size: 160
19172 TACGGATTTG
19182 AAAG-ACCAAACCCGCAGCACTGGTTCCAGCTTCCATGGGATTGCCTGGCACCAAACCCCAATGA
1 AAAGTACCAAACCCGCAGCACTGGTTCCAGCTTCCATGGGATTGCCTGGCACCAAACCCCAATGA
* *
19246 TAAAAAACGCACGAACGGAGGTAAGCCTAGCCCGATGTGGCATCCCGCAGAACTCGAGAGATGGC
66 TAAAAAACGCACGAACGGAGGTAAGCCTGGCCTGATGTGGCATCCCGCAGAACTCGAGAGATGGC
19311 AAAAGACTCAACAACAGGAATGTGGCCCTT
131 AAAAGACTCAACAACAGGAATGTGGCCCTT
19341 AAAGTACCAAACCCGCAGCACTGGTTCCAGCTTCCATGGGATTGCCTGGCACCAAACCCCAATGA
1 AAAGTACCAAACCCGCAGCACTGGTTCCAGCTTCCATGGGATTGCCTGGCACCAAACCCCAATGA
*
19406 TAAAAAACGCACGAACGGAGGTAAGCCTGGCCTGATGTGGCATCCCGCAGAACTCGAGAGATGGA
66 TAAAAAACGCACGAACGGAGGTAAGCCTGGCCTGATGTGGCATCCCGCAGAACTCGAGAGATGGC
19471 AAAAGACTCAACAACAGGAATGTGGCCCTT
131 AAAAGACTCAACAACAGGAATGTGGCCCTT
* *
19501 AAAGTATCAAACCCGCAGCACTGGTTCCAACTTCCATGGGATTGCCTGGCACCAAACCCCAATGA
1 AAAGTACCAAACCCGCAGCACTGGTTCCAGCTTCCATGGGATTGCCTGGCACCAAACCCCAATGA
* * *
19566 TCAAAAACGCACGAACGGAGGTAAGCCTGACCTGATGTGGCATCCCGCAGAACTCGAGAAATGGC
66 TAAAAAACGCACGAACGGAGGTAAGCCTGGCCTGATGTGGCATCCCGCAGAACTCGAGAGATGGC
*
19631 AAAAGACTCAATAACAGGAATGTGGCCCTT
131 AAAAGACTCAACAACAGGAATGTGGCCCTT
* *
19661 AAAGTACCAAACCCGCAACACTGGTTCCAGTTTCCATGGGATTGCCTGGCACCAAACCCCAATGA
1 AAAGTACCAAACCCGCAGCACTGGTTCCAGCTTCCATGGGATTGCCTGGCACCAAACCCCAATGA
* *
19726 TCAAAAACGCACGAACGGAGGTAAGCCTGGCCTGATGTGGCATCCCGCAGAACTCGAGATATGGC
66 TAAAAAACGCACGAACGGAGGTAAGCCTGGCCTGATGTGGCATCCCGCAGAACTCGAGAGATGGC
* * *
19791 AAAAGACTCAATAACAAGAAGGTGGCCCTT
131 AAAAGACTCAACAACAGGAATGTGGCCCTT
19821 AAAGTA
1 AAAGTA
19827 TCGAACATAA
Statistics
Matches: 467, Mismatches: 18, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
159 4 0.01
160 463 0.99
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (160 bp):
AAAGTACCAAACCCGCAGCACTGGTTCCAGCTTCCATGGGATTGCCTGGCACCAAACCCCAATGA
TAAAAAACGCACGAACGGAGGTAAGCCTGGCCTGATGTGGCATCCCGCAGAACTCGAGAGATGGC
AAAAGACTCAACAACAGGAATGTGGCCCTT
Found at i:20171 original size:13 final size:13
Alignment explanation
Indices: 20153--20180 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
20143 AAAGATTGAG
20153 ATCTAAAACACAT
1 ATCTAAAACACAT
20166 ATCTAAAACACAT
1 ATCTAAAACACAT
20179 AT
1 AT
20181 AATGATAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.25
Consensus pattern (13 bp):
ATCTAAAACACAT
Found at i:21539 original size:21 final size:21
Alignment explanation
Indices: 21513--21591 Score: 65
Period size: 21 Copynumber: 3.6 Consensus size: 21
21503 CCGTTTAGTA
21513 ATATATATAATTAAATATATT
1 ATATATATAATTAAATATATT
21534 ATATATAT-A-T-AATAATATT
1 ATATATATAATTAAAT-ATATT
* *
21553 AGATATATGTAATTACATATATAATA
1 --ATATATATAATTA-A-ATAT-ATT
21579 ATATATATAATTA
1 ATATATATAATTA
21592 TTAAACGGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
18 3 0.07
19 6 0.13
20 1 0.02
21 15 0.33
22 1 0.02
23 1 0.02
24 12 0.26
25 3 0.07
26 4 0.09
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (21 bp):
ATATATATAATTAAATATATT
Found at i:21551 original size:19 final size:20
Alignment explanation
Indices: 21529--21589 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 20
21519 ATAATTAAAT
21529 ATATTATATATATATAATA-
1 ATATTATATATATATAATAC
* *
21548 ATATTAGATATATGTAATTAC
1 ATATTATATATATATAA-TAC
21569 ATATATAATAATATATATAAT
1 ATAT-T-AT-ATATATATAAT
21590 TATTAAACGG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 15 0.45
20 2 0.06
21 4 0.12
22 1 0.03
23 2 0.06
24 9 0.27
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (20 bp):
ATATTATATATATATAATAC
Found at i:21559 original size:28 final size:31
Alignment explanation
Indices: 21522--21582 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
21512 AATATATATA
*
21522 ATTAAATATAT-T-A-TATATATATAATAAT
1 ATTAAATATATGTAATTACATATATAATAAT
*
21550 ATTAGATATATGTAATTACATATATAATAAT
1 ATTAAATATATGTAATTACATATATAATAAT
21581 AT
1 AT
21583 ATATAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 10 0.36
29 1 0.04
30 1 0.04
31 16 0.57
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (31 bp):
ATTAAATATATGTAATTACATATATAATAAT
Found at i:25288 original size:15 final size:15
Alignment explanation
Indices: 25268--25302 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
25258 GGACTATTAT
25268 GAATGG-CCAAAATTC
1 GAATGGTCC-AAATTC
25283 GAATGGTCCAAATTC
1 GAATGGTCCAAATTC
25298 GAATG
1 GAATG
25303 TTTGGAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.89
16 2 0.11
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (15 bp):
GAATGGTCCAAATTC
Found at i:33801 original size:123 final size:123
Alignment explanation
Indices: 33593--33821 Score: 377
Period size: 123 Copynumber: 1.9 Consensus size: 123
33583 TGCTCTTCCA
* ** *
33593 TGATATTAACAATATCTCTTTTTACCAAATCCAAATTGAATTGAAATAAATGGTTATGGTTTGGA
1 TGATATTAACAATATCTCTTTTTACCAAATCCAAATTGAATTGAAACAAATAATTATGGTTTGCA
* *
33658 CTCTTCGTGTACCCATCTAAGTTGGATTCTCATTAACCACAACAATGTTGCTCTCTCG
66 CTCTTCGTGCACCCATCTAAGTTGGATTCTCATTAAACACAACAATGTTGCTCTCTCG
* * *
33716 TGATATTAACAATATTTCTTTTTGCCAAATCCAAATTGAATTGACACAAATAATTATGGTTTGCA
1 TGATATTAACAATATCTCTTTTTACCAAATCCAAATTGAATTGAAACAAATAATTATGGTTTGCA
33781 CTCTTCGTGCACCCATCTAAGTTGGATTCTCATTAAACACA
66 CTCTTCGTGCACCCATCTAAGTTGGATTCTCATTAAACACA
33822 GTCTTTTATT
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
123 97 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (123 bp):
TGATATTAACAATATCTCTTTTTACCAAATCCAAATTGAATTGAAACAAATAATTATGGTTTGCA
CTCTTCGTGCACCCATCTAAGTTGGATTCTCATTAAACACAACAATGTTGCTCTCTCG
Found at i:55387 original size:18 final size:18
Alignment explanation
Indices: 55364--55402 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
55354 TAAGTAATAT
*
55364 ATACTATATCTTATTTTA
1 ATACTATATCTTATTTGA
55382 ATACTATATCTTATTTGA
1 ATACTATATCTTATTTGA
55400 ATA
1 ATA
55403 TTTTTGTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (18 bp):
ATACTATATCTTATTTGA
Found at i:55886 original size:32 final size:31
Alignment explanation
Indices: 55850--55919 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 31
55840 TTTTTTCAAA
55850 TAAAAA-AGCCACGTTCATACAATTTCAGAAAT
1 TAAAAATA-CCACGTTCATACAATTT-AGAAAT
* * *
55882 TAAAAATATCATGTTCATACAATTTTGAAAT
1 TAAAAATACCACGTTCATACAATTTAGAAAT
55913 TAAAAAT
1 TAAAAAT
55920 GGCCATAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 12 0.35
32 21 0.62
33 1 0.03
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.31
Consensus pattern (31 bp):
TAAAAATACCACGTTCATACAATTTAGAAAT
Found at i:60093 original size:18 final size:18
Alignment explanation
Indices: 60072--60136 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
60062 TGAAGACGAT
60072 GAAGAAGAAGAAGAGGAG
1 GAAGAAGAAGAAGAGGAG
* *
60090 GAAGAAGATGATGAGGAG
1 GAAGAAGAAGAAGAGGAG
* * * *
60108 GATGACGAGGACGAGGAG
1 GAAGAAGAAGAAGAGGAG
60126 GAAGAAGAAGA
1 GAAGAAGAAGA
60137 GAAAGTAATA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.48, C:0.03, G:0.45, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAGAAGAGGAG
Found at i:60105 original size:15 final size:15
Alignment explanation
Indices: 60063--60106 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
60053 GAAGGAAAAT
* *
60063 GAAGACGATGAAGAA
1 GAAGAAGATGAGGAA
*
60078 GAAGAAGAGGAGGAA
1 GAAGAAGATGAGGAA
*
60093 GAAGATGATGAGGA
1 GAAGAAGATGAGGA
60107 GGATGACGAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.50, C:0.02, G:0.41, T:0.07
Consensus pattern (15 bp):
GAAGAAGATGAGGAA
Found at i:79103 original size:30 final size:30
Alignment explanation
Indices: 79063--79130 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
79053 ATCCTAAATT
*
79063 TAGGAACTTATAAATATCATTTGGTTAAAC
1 TAGGAGCTTATAAATATCATTTGGTTAAAC
79093 TAGGAGCTTATAAATATCATTTGGTTAAAC
1 TAGGAGCTTATAAATATCATTTGGTTAAAC
79123 TAGGAGCT
1 TAGGAGCT
79131 AAACTTGGTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (30 bp):
TAGGAGCTTATAAATATCATTTGGTTAAAC
Found at i:81881 original size:334 final size:332
Alignment explanation
Indices: 81253--82058 Score: 868
Period size: 334 Copynumber: 2.4 Consensus size: 332
81243 AAAAAGCTAG
* * * *
81253 ATCTAACCAAATCTCAGCAACATTTGATTTAAGAATTTGTTTTTACGAGCATCGGAATCTTGTTT
1 ATCTAATCAAATCTCAGCAACATTGGATTTAAGAATTTGATTTTACGAGCATCTGAATCTTGTTT
* ** * * *
81318 CCATTTAATTAGAAATTAATAAAG-AAACAATAAGAAATACGATATTAAAAGCGTAAAAAGCCCC
66 CGATTTAATTAGAAATTAATTCAGAAAAAAATAGGAAAAACGATATTAAAAGCGTAAAAAGCCCC
* * * ** *
81382 CATCTTTTTGGCGTTGAATTATATATTCTTATGAGTTTTTAGCCAAAAGTTGAGGAGAAATCTTT
131 AATCTTTTTAGCATTGAAAAATATATTCTTAAGAGTTTTTAGCCAAAAGTTGAGGAGAAATCTTT
* * * *
81447 CGTGTCAATTTTTGCAAAAATTTAGCCGAAATCGTGTACTAACTAACAATTATAGTTTTTGGCTA
196 CGGGTCAATTTTTACAAAAATTTAGCCGAAATCGTG-A-TAACTAACAATCACAGTTTTTGGCTA
* * *
81512 AAAATGCGTTTCCGGCGACCCGCCTCAATTTTGCATGATTTTTTGACTCCGAGACTACTTGAA-A
259 AAAAAGCGTTTCCGGCGACCCGCCTCAATTTTGCATGA-TTTTTGACGCCAAGACTACTT-AAGA
*
81576 TATCTATATTC
322 TATCCATATTC
* * * * *
81587 ATCTAATCAAATCTCAACCACATGGGATTTAAGGATTTGATTTTACGAGCATCTTAATCTTGTTT
1 ATCTAATCAAATCTCAGCAACATTGGATTTAAGAATTTGATTTTACGAGCATCTGAATCTTGTTT
* * *
81652 CGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATTAGAAA-CGTCAAAATCCC
66 CGATTTAATTAGAAATTAATTCAGAAAAAAATAGGAAAAACGATATTA-AAAGCGTAAAAAGCCC
* *
81716 TTCAATCTTTTTAGCATTTAAAAATATAATT-TTAAGAGTATTTTAGCTGAAAA-TTGAGGA-AA
130 --CAATCTTTTTAGCATTGAAAAATAT-ATTCTTAAGAGT-TTTTAGC-CAAAAGTTGAGGAGAA
* * * * *
81778 TATCTTTTGGGTCCATTTTTTACAAAATTTTAGGCGAAATCGTG-TAA-TAACCATCACCA-TTT
190 -ATCTTTCGGGT-CAATTTTTACAAAAATTTAGCCGAAATCGTGATAACTAACAATCA-CAGTTT
* * * * *
81840 TTGGCTAAAAAAGCG-TTCTGG-GGCACCGGCTCAGA-TTTGCATGATTTTTGGCGCCAAGACTC
252 TTGGCTAAAAAAGCGTTTCCGGCGAC-CCGCCTCA-ATTTTGCATGATTTTTGACGCCAAGACTA
81902 CTTAAGATATCCATATTC
315 CTTAAGATATCCATATTC
* * *
81920 ATCTAATCAAATCTCAGCTACGTTGGATTTAAGAATTT-CTTTTACGAGCAT-TAGAATCTTGTT
1 ATCTAATCAAATCTCAGCAACATTGGATTTAAGAATTTGATTTTACGAGCATCT-GAATCTTGTT
* * * * * *
81983 TCGATTTAATTAAAAATTAATTCTGAAAAATAT-GAAAAAACGATATTAAAAGTGTGAAAAGTCC
65 TCGATTTAATTAGAAATTAATTCAGAAAAAAATAGGAAAAACGATATTAAAAGCGTAAAAAG-CC
82047 TCCAATCTTTTT
129 -CCAATCTTTTT
82059 GGTGTTAATT
Statistics
Matches: 397, Mismatches: 58, Indels: 37
0.81 0.12 0.08
Matches are distributed among these distances:
330 3 0.01
331 31 0.08
332 55 0.14
333 64 0.16
334 97 0.24
335 55 0.14
336 7 0.02
337 28 0.07
338 26 0.07
339 31 0.08
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (332 bp):
ATCTAATCAAATCTCAGCAACATTGGATTTAAGAATTTGATTTTACGAGCATCTGAATCTTGTTT
CGATTTAATTAGAAATTAATTCAGAAAAAAATAGGAAAAACGATATTAAAAGCGTAAAAAGCCCC
AATCTTTTTAGCATTGAAAAATATATTCTTAAGAGTTTTTAGCCAAAAGTTGAGGAGAAATCTTT
CGGGTCAATTTTTACAAAAATTTAGCCGAAATCGTGATAACTAACAATCACAGTTTTTGGCTAAA
AAAGCGTTTCCGGCGACCCGCCTCAATTTTGCATGATTTTTGACGCCAAGACTACTTAAGATATC
CATATTC
Found at i:83470 original size:330 final size:331
Alignment explanation
Indices: 82184--84146 Score: 1941
Period size: 330 Copynumber: 5.9 Consensus size: 331
82174 AACTGACCCG
* ** * * * *
82184 AAAATTTTTCCTCAATACTTTGCCACAATACTTTGAAAAAATATATGATTGAACCCCATAAATTT
1 AAAATTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATTGAACGCCAAAAAATT
* * * * *
82249 GAAGGGTTTTTCACACTTCAAATATCATTTTTCAAATTTTTT-TGGATCAATTTCTAATTAAATC
66 GAAGGGTTTTTCACGCTTCAAATATCGTTTTTCTAATTTTTTCTGAATCAATTTATAATTAAATC
* * * ** * *
82313 GAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTAA-ATCCAATGTGATTGGGATTTCGTTCG
131 GAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAATA-ACAATGTGGCTGAGATTTGGTTCG
* * * * * *
82377 ATGAATAT-GTATATATTTGAAGGAGTCTTTACGCCAAAAATTATTCAAAACTAAGC-CAAGTAC
195 ATGAATATAG-ATA-A-TTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCGGAA-TTC
* *
82440 CCGGAACACGTTTTTCGCAAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAACTTTGCAAA
256 CCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAACTTTGCAAA
* * *
82505 AATTGACTCAA
321 ACTTGAATCGA
* * * * *
82516 AAAATTTATCCTCAATTCTTTGCCACAAAACTAAGAAAAAATATATAATTTAATGCCCAAAAAAT
1 AAAATTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATTGAACG-CCAAAAAAT
* * * ** *
82581 TGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCTAATTTTTTTTCCGTATTTATTTCA-AACTA
65 TGAAGGGTTTTTCACGCTTCAAATATCGTTTTTCTAA--TTTTTTCTGAATCAATTT-ATAATTA
* * * * * **
82645 AATCGAAACAAGATTC-GGTAGCTTGTACAAATAAATCCTTAATAACAATGTGGCTGAAATTTTT
127 AATCGAAACAAGATTCAGAT-GCTCGTAAAAAGAAATCCTTAATAACAATGTGGCTGAGATTTGG
* * *
82709 TTCGATGAATATAGATAATTCAAGGAGTCTTTACGCCAAAAATCATTCAAAACTGAGTCGGGA-C
191 TTCGATGAATATAGATAATTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAG-CGGAATT
** * * * * * * * *
82773 CCCGGAACATGTTTTTAGCCAAGAACCGTGATGATTAATACACGATTTTGGCAAAAATTTTGCAA
255 CCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAACTTTGC-A
82838 AAAC-TG-ATCCGA
319 AAACTTGAAT-CGA
** * * * * *
82850 AATTTTTTTCCTAAATTCTTTTCCACAACACTCAG-AAAAATATATGATTGAACTCCAAAAAATT
1 AAAATTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATTGAACGCCAAAAAA-T
* * *
82914 TGAAGGGCTTTTCACGCTTCAAATATCGTTTTTCAAATTTTTTTTTCTGAATCAATTTCTAATTA
65 TGAAGGGTTTTTCACGCTTCAAATATCGTTTTTCTAA---TTTTTTCTGAATCAATTTATAATTA
* * ** *
82979 AATTGAAACAAGATTCAGATGCTTGTAAAAAGAAATCCTTAATCTCAATGTGGCTGGGATTTGGT
127 AATCGAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAATAACAATGTGGCTGAGATTTGGT
* * * * * ***
83044 TTGATG-A-AT--AT-A-TCAAGGAGTCTTTATGGCAAAAATCATGCAAAACTAAGCCGAGGCCC
192 TCGATGAATATAGATAATTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCGGAATTCC
83103 CGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAACTTTGCAAAA
257 CGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAACTTTGCAAAA
83168 CTTGAATCGA
322 CTTGAATCGA
* * * *
83178 AAAATTTTTCCTCAATTTTTTGCCACAATACTAAGAAAAAATATAAAATTCAACGCCAAAAAATT
1 AAAATTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATTGAACGCCAAAAAATT
* * * * ** *
83243 GAAGGGTTTTTCACGTTTCTAATATCATTTTTCCAA-TTTTTCTGAATTTATTTATAATTGAATC
66 GAAGGGTTTTTCACGCTTCAAATATCGTTTTTCTAATTTTTTCTGAATCAATTTATAATTAAATC
* * * * *
83307 GAAACAAGATTCAGATGCTCGTAAAAGGAGATCCTTAA-ATGCAATGTTGCTGAGATTTGGCTCG
131 GAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAATA-ACAATGTGGCTGAGATTTGGTTCG
* * * * * * *
83371 ATAAATATAGATATTTCAAGGAGTCTTTACTCCCAAAATCAGGCAAAATTGAGTCGGAATTCCAG
195 ATGAATATAGATAATTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAG-CGGAATTCCCG
*
83436 GAACGCG-TTTTAGCAAAAAACCGTGATGGTTAGTAAACGATTTCGACTAAAACTTTGCAAAA-T
259 GAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAACTTTGCAAAACT
**
83499 TGACCCGA
324 TGAATCGA
* * *
83507 AAAGTTTTTCCTCAATTCTTTGCCACAATACTCAGAAGAAATATATAATTCAACGCCAAAAAAAT
1 AAAATTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATTGAACGCC-AAAAAAT
* * *
83572 TGAAGGG-TTTTCACGCTTCAAATATCGTTTTTCTAATTTTTTCCGTAT--TTTTATCAAATTAA
65 TGAAGGGTTTTTCACGCTTCAAATATCGTTTTTCTAATTTTTTCTGAATCAATTTAT--AATTAA
* * * * * * * *
83634 ATTGAAACAAGATTCGGTTGCTTGTACAAACATATCCTTAATAACAATGTGGCTGAGATTTTGTT
128 ATCGAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAATAACAATGTGGCTGAGATTTGGTT
* * *
83699 CGATGAATATAGATAATTCAAGGAGTCTTTACGGCAAAAATCATTCAAAACTGAGCCGG-GTTCC
193 CGATGAATATAGATAATTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAG-CGGAATTCC
* * * *
83763 CGGAACGTGTTTTTAGCAAAAAACCGTGATGGTTATTACACGATTT-TAGCTAAAATTTTGCAAA
257 CGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGA-CTAAAACTTTGC-AA
*
83827 AAC-TG-ACCTG-
320 AACTTGAATC-GA
* * *
83837 -AAA---TTCCTCAATTCTTTGCCACAACACTCTG-AAAAATATATAATTGAACACCAAAAAATT
1 AAAATTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATTGAACGCCAAAAAA-T
* * * * ** *
83897 TAAAGGGCTTTTC-CGTCTTCAAATATCGTCTTTATAATTTTTTTTTCCAAAATCAATTTCTAAT
65 TGAAGGGTTTTTCACG-CTTCAAATATCGTTTTTCTAA---TTTTTT-CTGAATCAATTTATAAT
* * * * *
83961 TAAATCGAAATAAGATTCAGATGGTCGTAAAAAGAGA-CTCTTAA-ATGCAATGTTGCTGAGATT
125 TAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAAATC-CTTAATA-ACAATGTGGCTGAGATT
* * * *
84024 T-GTCTCGATGAATATAGATAATTCAAGGAGTCTTTACACCAATAATCAGGCAAAATTGAGCCGG
188 TGGT-TCGATGAATATAGATAATTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAG-CGG
* * * *
84088 AA-TCCCGGGACGAGTTTTTGGCAAAAAACCGTGATGGTTAGTACACGATTTCGATTAAA
251 AATTCCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGACTAAA
84147 TATCGAAATA
Statistics
Matches: 1352, Mismatches: 227, Indels: 106
0.80 0.13 0.06
Matches are distributed among these distances:
324 85 0.06
325 28 0.02
326 52 0.04
327 7 0.01
328 161 0.12
329 134 0.10
330 421 0.31
331 22 0.02
332 60 0.04
333 92 0.07
334 198 0.15
335 16 0.01
336 74 0.05
337 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (331 bp):
AAAATTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATAATTGAACGCCAAAAAATT
GAAGGGTTTTTCACGCTTCAAATATCGTTTTTCTAATTTTTTCTGAATCAATTTATAATTAAATC
GAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAATAACAATGTGGCTGAGATTTGGTTCGA
TGAATATAGATAATTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCGGAATTCCCGGA
ACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAACTTTGCAAAACTTG
AATCGA
Found at i:83981 original size:660 final size:654
Alignment explanation
Indices: 82150--84146 Score: 2275
Period size: 660 Copynumber: 3.0 Consensus size: 654
82140 TGCCAAAATC
* * *
82150 CGATTTTGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTTCCTCAATACTTTGCCACAATAC
1 CGATTTCGACTAAAAT-TTGCAAAAACTGACCCGAAAATTTTTCCTCAATTCTTTGCCACAATAC
** * * * * *
82215 TTTGAAAAAATATATGATTGAACCCCATAAATTTGAAGGGTTTTTCACACTTCAAATATCATTTT
65 TCAG-AAAAATATATGATTGAACCCAAAAAATTTGAAGGGCTTTTCACGCTTCAAATATCGTTTT
* * * *
82280 TCAAATTTTTT-TGGATCAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAA
129 TCAAATTTTTTCTGAATCAATTTCTAATTAAATTGAAACAAGATTCAGATGCTTGTAAAAACAAA
* ** *
82344 TCCTTAA-ATCCAATGTGATTGGGATTTCGTTCGATGAATATGTATATATTTGAAGGAGTCTTTA
194 TCCTTAATA-ACAATGTGGCTGGGATTTCGTTCGATGAATATG-ATA-A-TTCAAGGAGTCTTTA
* * ** * *
82408 CGCCAAAAATTATTCAAAACTAAGCCAAGTACCCGGAACACGTTTTTCGCAAAAAACCGTGATGG
255 CGGCAAAAATCATTCAAAACTAAGCCGGGTACCCGGAACGCGTTTTTAGCAAAAAACCGTGATGG
* **
82473 TTAGTACACGATTTCGACTAAAACTTTGCAAAAATTGACTCAAAAAATTTATCCTCAATTCTTTG
320 TTAGTACACGATTTCGACTAAAACTTTGCAAAAACTGAC-C-TGAAA-TT-TCCTCAATTCTTTG
*
82538 CCACAAAACTAAGAAAAAATATATAATTTAATGCCCAAAAAATTGAAGGGTTTTTCACG-CTTCT
381 CCACAAAACTAAGAAAAAATATATAATTCAA--CCCAAAAAATTGAAGGGTTTTTCACGTCTTCT
* * * *
82602 AATATCGTTTTTCTAATTTTTTTTCCGTATTTATTTCAAACTAAATCGAAACAAGATTC-GGTAG
444 AATATCGTTTTTCTAATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAT-G
* * * * * * * *
82666 CTTGTACAAATAAATCCTT-AATAACAATGTGGCTGAAATTTTTTTCGATGAATATAGATAATTC
508 CTCGTA-AAAGAGATCCTTAAAT-GCAATGTTGCTGAGATTTGTCTCGATGAATATAGATAATTC
* ** * * * *
82730 AAGGAGTCTTTACGCCAAAAATCATTCAAAACTGAGTCGGGACCCCGGAAC-ATGTTTTTAGCCA
571 AAGGAGTCTTTAC-CCCAAAATCAGGCAAAATTGAGTCGGAATCCCGGAACGA-GTTTTTAGCAA
* * *
82794 AGAACCGTGATGATTAATACA
634 AAAACCGTGATGGTTAGTACA
* * * * * * * *
82815 CGATTTTGGCAAAAATTTTGCAAAAACTGATCCGAAATTTTTTTCCTAAATTCTTTTCCACAACA
1 CGATTTCGACTAAAA-TTTGCAAAAACTGACCCGAAA-ATTTTTCCTCAATTCTTTGCCACAATA
82880 CTCAGAAAAATATATGATTGAACTCCAAAAAATTTGAAGGGCTTTTCACGCTTCAAATATCGTTT
64 CTCAGAAAAATATATGATTGAAC-CCAAAAAATTTGAAGGGCTTTTCACGCTTCAAATATCGTTT
82945 TTCAAATTTTTTTTTCTGAATCAATTTCTAATTAAATTGAAACAAGATTCAGATGCTTGTAAAAA
128 TTCAAA---TTTTTTCTGAATCAATTTCTAATTAAATTGAAACAAGATTCAGATGCTTGTAAAAA
* ** * *
83010 GAAATCCTTAATCTCAATGTGGCTGGGATTTGGTTTGATG-A-AT-AT-A-TCAAGGAGTCTTTA
190 CAAATCCTTAATAACAATGTGGCTGGGATTTCGTTCGATGAATATGATAATTCAAGGAGTCTTTA
* * *
83070 TGGCAAAAATCATGCAAAACTAAGCCGAGG-CCCCGGAACGCGTTTTTAGCAAAAAACCGTGATG
255 CGGCAAAAATCATTCAAAACTAAGCCG-GGTACCCGGAACGCGTTTTTAGCAAAAAACCGTGATG
* *
83134 GTTAGTACACGATTTCGACTAAAACTTTGC-AAAACTTGA-ATCGAAAAATTTTTCCTCAATTTT
319 GTTAGTACACGATTTCGACTAAAACTTTGCAAAAAC-TGACCT-G--AAA--TTTCCTCAATTCT
* *
83197 TTGCCACAATACTAAGAAAAAATATAAAATTCAACGCCAAAAAATTGAAGGGTTTTTCACGT-TT
378 TTGCCACAAAACTAAGAAAAAATATATAATTCAAC-CCAAAAAATTGAAGGGTTTTTCACGTCTT
* * * * *
83261 CTAATATCATTTTTCCAA---TTTTTCTGAATTTATTTATAATTGAATCGAAACAAGATTCAGAT
442 CTAATATCGTTTTTCTAATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAT
* * *
83323 GCTCGTAAAAGGAGATCCTTAAATGCAATGTTGCTGAGATTTGGCTCGATAAATATAGATATTTC
507 GCTCGTAAAA-GAGATCCTTAAATGCAATGTTGCTGAGATTTGTCTCGATGAATATAGATAATTC
* *
83388 AAGGAGTCTTTACTCCCAAAATCAGGCAAAATTGAGTCGGAATTCCAGGAACGCG-TTTTAGCAA
571 AAGGAGTCTTTAC-CCCAAAATCAGGCAAAATTGAGTCGGAA-TCCCGGAACGAGTTTTTAGCAA
*
83452 AAAACCGTGATGGTTAGTAAA
634 AAAACCGTGATGGTTAGTACA
*
83473 CGATTTCGACTAAAACTTTGC-AAAATTGACCCGAAAAGTTTTTCCTCAATTCTTTGCCACAATA
1 CGATTTCGACTAAAA-TTTGCAAAAACTGACCCGAAAA-TTTTTCCTCAATTCTTTGCCACAATA
* * *
83537 CTCAGAAGAAATATATAATTCAACGCCAAAAAAATTGAAGGG-TTTTCACGCTTCAAATATCGTT
64 CTCAGAA-AAATATATGATTGAAC-CCAAAAAATTTGAAGGGCTTTTCACGCTTCAAATATCGTT
* * * ** * * * *
83601 TTTCTAATTTTTTCCGTAT-TTTTATCAAATTAAATTGAAACAAGATTCGGTTGCTTGTACAAAC
127 TTTCAAATTTTTTCTGAATCAATT-TCTAATTAAATTGAAACAAGATTCAGATGCTTGTAAAAAC
* * *
83665 ATATCCTTAATAACAATGTGGCTGAGATTTTGTTCGATGAATATAGATAATTCAAGGAGTCTTTA
191 AAATCCTTAATAACAATGTGGCTGGGATTTCGTTCGATGAATAT-GATAATTCAAGGAGTCTTTA
* * *
83730 CGGCAAAAATCATTCAAAACTGAGCCGGGTTCCCGGAACGTGTTTTTAGCAAAAAACCGTGATGG
255 CGGCAAAAATCATTCAAAACTAAGCCGGGTACCCGGAACGCGTTTTTAGCAAAAAACCGTGATGG
* * *
83795 TTATTACACGATTT-TAGCTAAAATTTTGCAAAAACTGACCTGAAA-TTCCTCAATTCTTTGCCA
320 TTAGTACACGATTTCGA-CTAAAACTTTGCAAAAACTGACCTGAAATTTCCTCAATTCTTTGCCA
* ** * * * *
83858 CAACACTCTG-AAAAATATATAATTGAACACCAAAAAATTTAAAGGGCTTTTC-CGTCTTCAAAT
384 CAAAACTAAGAAAAAATATATAATTCAAC-CCAAAAAA-TTGAAGGGTTTTTCACGTCTTCTAAT
* * * ** * *
83921 ATCGTCTTTATAATTTTTTTTTCCAAAATCAATTTCTAATTAAATCGAAATAAGATTCAGATGGT
447 ATCGTTTTTCTAA-TTTTTTTTCC-GAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCT
83986 CGTAAAAAGAGA-CTCTTAAATGCAATGTTGCTGAGATTTGTCTCGATGAATATAGATAATTCAA
510 CGT-AAAAGAGATC-CTTAAATGCAATGTTGCTGAGATTTGTCTCGATGAATATAGATAATTCAA
* * * *
84050 GGAGTCTTTACACCAATAATCAGGCAAAATTGAGCCGGAATCCCGGGACGAGTTTTTGGCAAAAA
573 GGAGTCTTTACCCCAA-AATCAGGCAAAATTGAGTCGGAATCCCGGAACGAGTTTTTAGCAAAAA
84115 ACCGTGATGGTTAGTACA
637 ACCGTGATGGTTAGTACA
*
84133 CGATTTCGATTAAA
1 CGATTTCGACTAAA
84147 TATCGAAATA
Statistics
Matches: 1138, Mismatches: 149, Indels: 95
0.82 0.11 0.07
Matches are distributed among these distances:
653 2 0.00
654 105 0.09
655 52 0.05
656 2 0.00
657 74 0.07
658 193 0.17
659 37 0.03
660 261 0.23
661 57 0.05
662 143 0.13
663 4 0.00
664 1 0.00
665 51 0.04
666 70 0.06
668 2 0.00
669 7 0.01
670 77 0.07
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (654 bp):
CGATTTCGACTAAAATTTGCAAAAACTGACCCGAAAATTTTTCCTCAATTCTTTGCCACAATACT
CAGAAAAATATATGATTGAACCCAAAAAATTTGAAGGGCTTTTCACGCTTCAAATATCGTTTTTC
AAATTTTTTCTGAATCAATTTCTAATTAAATTGAAACAAGATTCAGATGCTTGTAAAAACAAATC
CTTAATAACAATGTGGCTGGGATTTCGTTCGATGAATATGATAATTCAAGGAGTCTTTACGGCAA
AAATCATTCAAAACTAAGCCGGGTACCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTA
CACGATTTCGACTAAAACTTTGCAAAAACTGACCTGAAATTTCCTCAATTCTTTGCCACAAAACT
AAGAAAAAATATATAATTCAACCCAAAAAATTGAAGGGTTTTTCACGTCTTCTAATATCGTTTTT
CTAATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAGAGA
TCCTTAAATGCAATGTTGCTGAGATTTGTCTCGATGAATATAGATAATTCAAGGAGTCTTTACCC
CAAAATCAGGCAAAATTGAGTCGGAATCCCGGAACGAGTTTTTAGCAAAAAACCGTGATGGTTAG
TACA
Found at i:84679 original size:563 final size:559
Alignment explanation
Indices: 83628--84709 Score: 1360
Period size: 563 Copynumber: 1.9 Consensus size: 559
83618 ATTTTTATCA
* * * ** * * *
83628 AATTAAATTGAAACAAGATTCGGTTGCTTGTACAAACATATCCTTAATAACAATGTGGCTGAGAT
1 AATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAATAACAAAGTGGCTGAGAT
* * * * *
83693 TTTGTTCGATGAATATAGATAATTCAAGGAGTCTTTACGGCAAAAATCATTCAAAACTGAGCCGG
66 TTGGTTCGATGAATATAGACAATTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTAAGCCGG
* * * *
83758 GTTCCCGGAACGTGTTTTTAGCAAAAAACCGTGATGGTTATTACACGATTTTAGCTAAAATTTTG
131 GTCCCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTTAGCTAAAACTTTG
* ** * *
83823 CAAAAACTGACCTGAAATTCCTCAATTCTTTGCCACAACACTCTGAAAAATATATAATTGAACAC
196 CAAAAACTAACCTGAAATTCCTCAATTCTTTGCCACAACACTAGGAAAAATATAAAATTCAACAC
*
83888 CAAAAAATTTAAAGGGCTTTTCCGTCTTCAAATATCGTCTTTATAATTTTTTTTTCCAAAATCAA
261 CAAAAAATTTAAAGGGCTTTTCCGTCTTCAAATATCGTCTTTACAA---TTTTTTCCAAAATCAA
* * *
83953 TTTCTAATTAAATCGAAATAAGATTCAGATGGTCGTAAAAAGAGACTCTTAAATGCAATGTTGCT
323 TTTATAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAGACTCTTAAATGCAATGTTGCT
* *
84018 GAGATTTGTCTCGATGAATATAGATAATTCAAGGAGTCTTTACACCAATAATCAGGCAAAATTGA
388 GAGATTTGGCTCGATAAATATAGATAATTCAAGGAGTCTTTACACCAATAATCAGGCAAAATTGA
* ** * *
84083 GCCGGAATCCCGGGACGAGTTTTTGGCAAAAAACCGTGATGGTTAGTACACGATTTCGATTAAAT
453 GCCGGAATCCCGGAACGAGTTTTTAACAAAAAACCGTGATGGTTAGTAAACGATTTCGACTAAAT
84148 ATCGAAATATCATTTTTAAATGTTTTTTCAGAATCAATTTCT
518 ATCGAAATATCATTTTTAAATGTTTTTTCAGAATCAATTTCT
* * *
84190 AATTAAATCGAAACAAGATTCAGATGCTCATAAAAATAAATCCTTAA-ATCCAAAGTGGCTGGGA
1 AATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAATA-ACAAAGTGGCTGAGA
* ** * *
84254 TTTGGTTCGATGAGTATTTACATTTCAAGGAGTCTTTACTCCAAAAATCATGCAAAACTAAGCCG
65 TTTGGTTCGATGAATATAGACAATTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTAAGCCG
*
84319 AGG-CCCCGGAACGCGTTTTTAGCAAAAAAACCGTGATGGTTAGTACACGATTTT-GATTAAAAC
130 -GGTCCCCGGAACGCGTTTTTAGC-AAAAAACCGTGATGGTTAGTACACGATTTTAG-CTAAAAC
* *
84382 TTTGCAAAAATTAA-CTCGAAATTTTTTTCCTCAATTCTTTGCCACAATACTAAGGAAAAATATA
192 TTTGCAAAAACTAACCT-GAAA-----TTCCTCAATTCTTTGCCACAACACT-AGGAAAAATATA
* * * * *
84446 AAATTCAACGA-CAAAAAA-TTGAAGGGTTTTTCACG-CTTCTAATATCGTTTTTCCAA-TTTTT
250 AAATTCAAC-ACCAAAAAATTTAAAGGGCTTTTC-CGTCTTCAAATATCGTCTTTACAATTTTTT
* ** * *
84507 CC-GAATTTATTTATAATTGAATCGAAACAAGATTCAGATGCTCGTAAAAGGAGA-TCCTTAAAT
313 CCAAAATCAATTTATAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAGACT-CTTAAAT
* * *
84570 GCAATGTTGCTGAGATTTGGCTTGATAAATATAGATATTTCAAGGAGTCTTTACTCCCAA-AATC
377 GCAATGTTGCTGAGATTTGGCTCGATAAATATAGATAATTCAAGGAGTCTTTAC-ACCAATAATC
* * * *
84634 AGGCAAAATTGAGTCGGAATTCTGGAACGCG-TTTTAACAAAAAAACCGTGATGGTTAGTAAACG
441 AGGCAAAATTGAGCCGGAATCCCGGAACGAGTTTTTAAC-AAAAAACCGTGATGGTTAGTAAACG
84698 ATTTCGACTAAA
505 ATTTCGACTAAA
84710 ACTTTGCCAA
Statistics
Matches: 443, Mismatches: 61, Indels: 31
0.83 0.11 0.06
Matches are distributed among these distances:
561 1 0.00
562 133 0.30
563 218 0.49
564 11 0.02
568 53 0.12
569 26 0.06
570 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (559 bp):
AATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAATAACAAAGTGGCTGAGAT
TTGGTTCGATGAATATAGACAATTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTAAGCCGG
GTCCCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTTAGCTAAAACTTTG
CAAAAACTAACCTGAAATTCCTCAATTCTTTGCCACAACACTAGGAAAAATATAAAATTCAACAC
CAAAAAATTTAAAGGGCTTTTCCGTCTTCAAATATCGTCTTTACAATTTTTTCCAAAATCAATTT
ATAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAGACTCTTAAATGCAATGTTGCTGAG
ATTTGGCTCGATAAATATAGATAATTCAAGGAGTCTTTACACCAATAATCAGGCAAAATTGAGCC
GGAATCCCGGAACGAGTTTTTAACAAAAAACCGTGATGGTTAGTAAACGATTTCGACTAAATATC
GAAATATCATTTTTAAATGTTTTTTCAGAATCAATTTCT
Found at i:84809 original size:330 final size:330
Alignment explanation
Indices: 84170--85368 Score: 1290
Period size: 331 Copynumber: 3.6 Consensus size: 330
84160 TTTTTAAATG
* ** * * * *
84170 TTTTTTCAGAATCAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAATAAATCCTT
1 TTTTTTCCGAATTTATTTATAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAGATCCTT
* * * ** * *
84235 AAATCCAAAGTGGCTGGGATTTGGTTCGATGAGTATTTACATTTCAAGGAGTCTTTACTCCAAAA
66 AAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATAATTCAAGGAGTCTTTACTCCAAAA
* * * *
84300 ATCATGCAAAACTAAGCC-GAGGCCCCGGAACGCGTTTTTAGCAAAAAAACCGTGATGGTTAGTA
131 ATCAGGCAAAACTGAGCCGGA-ACCCCGGAACGCGTTTTTAAC-AAAAAACCGTGATGGTTAGTA
* * * * *
84364 CACGATTTTGATTAAAACTTTGCAAAAATTAACTCGAAATTTTTTTCCTCAATTCTTTGCCACAA
194 AACGA-TTTGACTAAAACTTTGCCAAAATTGACCCGAAATTTTTTTCCTCAATTCTTTGCCACAA
* * **
84429 TACTAAGGAAAAATATAAAATTCAACGAC-AAAAAATTGAAGGGTTTTTCACGCTTCTAATATCG
258 TACTCA-GAAAAATATATAATTCAACCCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCG
*
84493 TTTTTCCAA
322 TTTTTCTAA
* *
84502 -TTTTTCCGAATTTATTTATAATTGAATCGAAACAAGATTCAGATGCTCGTAAAAGGAGATCCTT
1 TTTTTTCCGAATTTATTTATAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAGATCCTT
* * * * *
84566 AAATGCAATGTTGCTGAGATTTGGCTT-GATAAATATAGATATTTCAAGGAGTCTTTACTCCCAA
66 AAATCCAATGTGGCTGAGATTTGG-TTCGATGAATATAGATAATTCAAGGAGTCTTTACTCCAAA
* * ** *
84630 AATCAGGCAAAATTGAGTCGGAATTCTGGAACGCG-TTTTAACAAAAAAACCGTGATGGTTAGTA
130 AATCAGGCAAAACTGAGCCGGAACCCCGGAACGCGTTTTTAAC-AAAAAACCGTGATGGTTAGTA
** *
84694 AACGATTTCGACTAAAACTTTGCCAAAATTGACCCGAAAAGTTTTTCCTCAATTCCTTGCCACAA
194 AACGATTT-GACTAAAACTTTGCCAAAATTGACCCGAAATTTTTTTCCTCAATTCTTTGCCACAA
*
84759 TACTCAGAAAAAATATATAATTCAACTCCAAAAAAATTGAAGGG-TTTTCACGCTTCTAATATCG
258 TACTCAG-AAAAATATATAATTCAACCCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCG
84823 TTTTTCTAA
322 TTTTTCTAA
* * * * * * * *
84832 TTTTTTCCGTATTTTTTTCA-AATTAAATCGAAACAAGATTCGGTTGCTTGTAGAAACATATCCT
1 TTTTTTCCGAATTTATTT-ATAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAGATCCT
* * * **
84896 T-AATAACAATGTGGCTGAGATTTTGTTCGAGGAATATAGATAATTCAAGGAGTCTTTACGGCAA
65 TAAAT-CCAATGTGGCTGAGATTTGGTTCGATGAATATAGATAATTCAAGGAGTCTTTACTCCAA
** * * * * *
84960 AAATCATTCAAAACTGAGCCGGGACCCCAGAACGTG-TTTTAAGCAAAAAATCGTGATGGTTATT
129 AAATCAGGCAAAACTGAGCCGGAACCCCGGAACGCGTTTTTAA-CAAAAAACCGTGATGGTTAGT
* * * *
85024 ACACGATTTTAGCTAAAATTTTG-CAAAATCTGACCTGAAATTTTTTTCCTCAATTCTTTGCCAC
193 AAACGATTTGA-CTAAAACTTTGCCAAAAT-TGACCCGAAATTTTTTTCCTCAATTCTTTGCCAC
* * * * * *
85088 AACACTCTGAAAAATATATAATTGAACCCCAAAAAATTTAAAGGGTCTTTTCACGCTTCAAATAT
256 AATACTCAGAAAAATATATAATTCAACCCCAAAAAAATTGAAGGGT-TTTTCACGCTTCTAATAT
*
85153 CATTTTTCTAA
320 CGTTTTTCTAA
* ** * * *
85164 TTTTTTTTTCCAAAATCAATTTCTAATTAAATCGAAATAAGATTCAGATGGTCGTAAAAAGAGA-
1 ---TTTTTTCC-GAATTTATTTATAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAGAT
* * *
85228 CTCTTAAATCCAATGTTGCTGAGATTT-GTCTCGATGAATATAGATAATTCAAGGAGTATTTACA
62 C-CTTAAATCCAATGTGGCTGAGATTTGGT-TCGATGAATATAGATAATTCAAGGAGTCTTTACT
* * * * * * **
85292 CCAATAATCAGGAAAAATTGAGCCGGAATCCCGGGACGAGTTTTTGGCAAAAAACCGTGATGGTT
125 CCAAAAATCAGGCAAAACTGAGCCGGAACCCCGGAACGCGTTTTTAACAAAAAACCGTGATGGTT
85357 AGTACAA-GATTT
190 AGTA-AACGATTT
85369 TGATTAAATA
Statistics
Matches: 721, Mismatches: 122, Indels: 44
0.81 0.14 0.05
Matches are distributed among these distances:
329 4 0.01
330 176 0.24
331 348 0.48
332 33 0.05
335 11 0.02
336 141 0.20
337 8 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (330 bp):
TTTTTTCCGAATTTATTTATAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAGATCCTT
AAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATAATTCAAGGAGTCTTTACTCCAAAA
ATCAGGCAAAACTGAGCCGGAACCCCGGAACGCGTTTTTAACAAAAAACCGTGATGGTTAGTAAA
CGATTTGACTAAAACTTTGCCAAAATTGACCCGAAATTTTTTTCCTCAATTCTTTGCCACAATAC
TCAGAAAAATATATAATTCAACCCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTT
TCTAA
Found at i:85029 original size:894 final size:889
Alignment explanation
Indices: 83292--85032 Score: 2132
Period size: 894 Copynumber: 1.9 Consensus size: 889
83282 TTCTGAATTT
* * * * * * *
83292 ATTTATAATTGAATCGAAACAAGATTCAGATGCTCGTAAAAGGAGATCCTTAAATGCAATGTTGC
1 ATTTATAATTAAATCGAAACAAGATTCAGATGCTCATAAAAAGAAATCCTTAAATCCAAAGTGGC
* * * *
83357 TGAGATTTGGCTCGATAAATATAGATATTTCAAGGAGTCTTTACTCCCAAAATCAGGCAAAATTG
66 TGAGATTTGGCTCGATAAATATAGACATTTCAAGGAGTCTTTACTCCAAAAATCAGGCAAAACTA
* **
83422 AGTCGGAATTCCAGGAACGCGTTTTAGCAAAAAACCGTGATGGTTAGTAAACGATTTCGACTAAA
131 AGTCCGAAGCCCAGGAACGCGTTTTAGCAAAAAACCGTGATGGTTAGTAAACGATTTCGACTAAA
* *
83487 ACTTTGCAAAATTGACCCGAAAAGTTTTTCCTCAATTCTTTGCCACAATACTCAGAAGAAATATA
196 ACTTTGCAAAATTAACCCGAAAAGTTTTTCCTCAATTCTTTGCCACAATACTAAGAAGAAATATA
* * *
83552 TAATTCAACGCCAAAAAAATTGAAGGGTTTTCACGCTTCAAATATCGTTTTTCTAATTTTTTCCG
261 AAATTCAACGACAAAAAAATTGAAGGGTTTTCACGCTTCAAATATCGTTTTTCCAATTTTTTCCG
* * * * * *
83617 TATTTTTATCAAATTAAATTGAAACAAGATTCGGTTGCTTGTACAAACATATCCTTAATAACAAT
326 AATTTTTAT-AAATTAAATCGAAACAAGATTCAGATGCTCGTACAAACAGATCCTTAATAACAAT
* * * **
83682 GTGGCTGAGATTTTGTTCGATGAATATAGATAATTCAAGGAGTCTTTACGGCAAAAATCATTCAA
390 GTGGCTGAGATTTGGTTCGATAAATATAGATAATTCAAGGAGTCTTTACGCCAAAAATCAGGCAA
* * * * * *
83747 AACTGAGCCGGGTTCCCGGAACGTGTTTTTAGCAAAAAACCGTGATGGTTATTACACGATTTTAG
455 AACTGAGCCGGATTCCCGGAACGCGTTTTTAACAAAAAACCGTGATGGTTAGTAAACGATTTGAG
* * * *
83812 CTAAAATTTTGCAAAAACTGACCTGAAATTCCTCAATTCTTTGCCACAACACTCTGAAAAATATA
520 CTAAAACTTTGCAAAAACTGACCCGAAATTCCTCAATTCCTTGCCACAACACTCAGAAAAATATA
* *
83877 TAATTGAACACCAAAAAATTTAAAGGGCTTTTCCGTCTTCAAATATCGTCTTTATAATTTTTTTT
585 TAATTCAACACCAAAAAAATTAAAGGGCTTTTCCGTCTTCAAATATCGTCTTTATAA--TTTTTT
* * * *
83942 TCCAAAATCAATTTCTAATTAAATCGAAATAAGATTCAGATGGTCGTAAAAAGAGACTCTTAAAT
648 TCCAAAATCAATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAGACTCTTAAAT
* * * *
84007 GCAATGTTGCTGAGATTTGTCTCGATGAATATAGATAATTCAAGGAGTCTTTACACCAATAATCA
713 ACAATGTGGCTGAGATTTGTCTCGAGGAATATAGATAATTCAAGGAGTCTTTACACCAAAAATCA
* * * * **
84072 GGCAAAATTGAGCCGGAATCCCGGGACGAGTTTTTGGCAAAAAACCGTGATGGTTAGTACACGAT
778 GGCAAAACTGAGCCGGAACCCCAGAACGAGTTTTAAGCAAAAAACCGTGATGGTTAGTACACGAT
84137 TTCGATTAAATATCGAAATATCATTTTTAAATGTTTTTTCAGAATCA
843 TTCGATTAAATATCGAAATATCATTTTTAAATGTTTTTTCAGAATCA
* *
84184 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAATAAATCCTTAAATCCAAAGTGGC
1 ATTTATAATTAAATCGAAACAAGATTCAGATGCTCATAAAAAGAAATCCTTAAATCCAAAGTGGC
* * * * ** *
84249 TGGGATTTGGTTCGATGAGTATTTACATTTCAAGGAGTCTTTACTCCAAAAATCATGCAAAACTA
66 TGAGATTTGGCTCGATAAATATAGACATTTCAAGGAGTCTTTACTCCAAAAATCAGGCAAAACTA
* * * * *
84314 AG-CCGAGGCCCCGGAACGCGTTTTTAGCAAAAAAACCGTGATGGTTAGTACACGATTTTGATTA
131 AGTCCGAAGCCCAGGAACGCG-TTTTAGC-AAAAAACCGTGATGGTTAGTAAACGATTTCGACTA
* **
84378 AAACTTTGCAAAAATTAACTCGAAATTTTTTTCCTCAATTCTTTGCCACAATACTAAGGAA-AAA
194 AAACTTTGC-AAAATTAACCCGAAAAGTTTTTCCTCAATTCTTTGCCACAATACTAA-GAAGAAA
*
84442 TATAAAATTCAACGAC-AAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCAA-TTT
257 TATAAAATTCAACGACAAAAAAATTGAAGGG-TTTTCACGCTTCAAATATCGTTTTTCCAATTTT
* *
84505 TTCCGAATTTATT-TATAATTGAATCGAAACAAGATTCAGATGCTCGTA-AAAGGAGATCCTTAA
321 TTCCGAATTT-TTATA-AATTAAATCGAAACAAGATTCAGATGCTCGTACAAA-CAGATCCTTAA
* * * * *
84568 -ATGCAATGTTGCTGAGATTTGGCTT-GATAAATATAGATATTTCAAGGAGTCTTTACTCCCAAA
383 TA-ACAATGTGGCTGAGATTTGG-TTCGATAAATATAGATAATTCAAGGAGTCTTTACGCCAAAA
* * *
84631 ATCAGGCAAAATTGAGTCGGAATT-CTGGAACGCG-TTTTAACAAAAAAACCGTGATGGTTAGTA
446 ATCAGGCAAAACTGAGCCGG-ATTCCCGGAACGCGTTTTTAAC-AAAAAACCGTGATGGTTAGTA
* *
84694 AACGATTTCGA-CTAAAACTTTGCCAAAATTGACCCGAAAAGTTTTTCCTCAATTCCTTGCCACA
509 AACGATTT-GAGCTAAAACTTTGCAAAAACTGACCCG-AAA----TTCCTCAATTCCTTGCCACA
* * * *
84758 ATACTCAGAAAAAATATATAATTCAACTCCAAAAAAATTGAAGGG-TTTTCACG-CTTCTAATAT
568 ACACTCAG-AAAAATATATAATTCAACACCAAAAAAATTAAAGGGCTTTTC-CGTCTTCAAATAT
* * ** *** * * *
84821 CGTTTTTCTAA-TTTTTTCC-GTATTTTTTTCAAATTAAATCGAAACAAGATTCGGTTGCTTGTA
631 CGTCTTTATAATTTTTTTCCAAAATCAATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTA
* *
84884 GAAACATA-TCCTT-AATAACAATGTGGCTGAGATTTTGT-TCGAGGAATATAGATAATTCAAGG
696 AAAACAGACT-CTTAAAT-ACAATGTGGCTGAGA-TTTGTCTCGAGGAATATAGATAATTCAAGG
** ** * * *
84946 AGTCTTTACGGCAAAAATCATTCAAAACTGAGCCGGGACCCCAGAACGTGTTTTAAGCAAAAAAT
758 AGTCTTTACACCAAAAATCAGGCAAAACTGAGCCGGAACCCCAGAACGAGTTTTAAGCAAAAAAC
*
85011 CGTGATGGTTATTACACGATTT
823 CGTGATGGTTAGTACACGATTT
85033 TAGCTAAAAT
Statistics
Matches: 716, Mismatches: 110, Indels: 44
0.82 0.13 0.05
Matches are distributed among these distances:
891 13 0.02
892 130 0.18
893 230 0.32
894 245 0.34
895 16 0.02
898 48 0.07
899 34 0.05
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (889 bp):
ATTTATAATTAAATCGAAACAAGATTCAGATGCTCATAAAAAGAAATCCTTAAATCCAAAGTGGC
TGAGATTTGGCTCGATAAATATAGACATTTCAAGGAGTCTTTACTCCAAAAATCAGGCAAAACTA
AGTCCGAAGCCCAGGAACGCGTTTTAGCAAAAAACCGTGATGGTTAGTAAACGATTTCGACTAAA
ACTTTGCAAAATTAACCCGAAAAGTTTTTCCTCAATTCTTTGCCACAATACTAAGAAGAAATATA
AAATTCAACGACAAAAAAATTGAAGGGTTTTCACGCTTCAAATATCGTTTTTCCAATTTTTTCCG
AATTTTTATAAATTAAATCGAAACAAGATTCAGATGCTCGTACAAACAGATCCTTAATAACAATG
TGGCTGAGATTTGGTTCGATAAATATAGATAATTCAAGGAGTCTTTACGCCAAAAATCAGGCAAA
ACTGAGCCGGATTCCCGGAACGCGTTTTTAACAAAAAACCGTGATGGTTAGTAAACGATTTGAGC
TAAAACTTTGCAAAAACTGACCCGAAATTCCTCAATTCCTTGCCACAACACTCAGAAAAATATAT
AATTCAACACCAAAAAAATTAAAGGGCTTTTCCGTCTTCAAATATCGTCTTTATAATTTTTTTCC
AAAATCAATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAGACTCTTAAATACA
ATGTGGCTGAGATTTGTCTCGAGGAATATAGATAATTCAAGGAGTCTTTACACCAAAAATCAGGC
AAAACTGAGCCGGAACCCCAGAACGAGTTTTAAGCAAAAAACCGTGATGGTTAGTACACGATTTC
GATTAAATATCGAAATATCATTTTTAAATGTTTTTTCAGAATCA
Done.