Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023878.1 Corchorus olitorius cultivar O-4 contig23911, 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: 72037
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:14407 original size:13 final size:13
Alignment explanation
Indices: 14389--14413 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14379 TATTATTATT
14389 ATTTTTAATTTTA
1 ATTTTTAATTTTA
14402 ATTTTTAATTTT
1 ATTTTTAATTTT
14414 TTACATGATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTTAATTTTA
Found at i:34961 original size:31 final size:31
Alignment explanation
Indices: 34875--34961 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
34865 GGTATTGCTG
*
34875 ACATGGCAATGCCACGTCTGACAAAAACGCC
1 ACATGGCAATGCCACGTCTGACCAAAACGCC
* * * *
34906 ACGTGGCAATGACACAT-TGAACCAAAATGCC
1 ACATGGCAATGCCACGTCTG-ACCAAAACGCC
* *
34937 ACATGGCAATGCCGCGTCAGACCAA
1 ACATGGCAATGCCACGTCTGACCAA
34962 GACACCGATG
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
30 2 0.05
31 41 0.93
32 1 0.02
ACGTcount: A:0.36, C:0.30, G:0.21, T:0.14
Consensus pattern (31 bp):
ACATGGCAATGCCACGTCTGACCAAAACGCC
Found at i:35042 original size:15 final size:15
Alignment explanation
Indices: 35022--35055 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
35012 TAGGATTCCA
35022 CTAAGATGGTGCCAC
1 CTAAGATGGTGCCAC
*
35037 CTAAGATGGTGTCAC
1 CTAAGATGGTGCCAC
35052 CTAA
1 CTAA
35056 TCAAATCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (15 bp):
CTAAGATGGTGCCAC
Found at i:36004 original size:11 final size:11
Alignment explanation
Indices: 35980--36014 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
35970 TTGACAGCGC
35980 AACAAAAACAA
1 AACAAAAACAA
* *
35991 AACGAAAACGA
1 AACAAAAACAA
36002 AACAAAAACAA
1 AACAAAAACAA
36013 AA
1 AA
36015 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:53484 original size:37 final size:37
Alignment explanation
Indices: 53430--53513 Score: 150
Period size: 37 Copynumber: 2.3 Consensus size: 37
53420 GAAGTACGTA
53430 TTGATTTGTTTCTCTTTAGTCAGCATGTTAGTATGTC
1 TTGATTTGTTTCTCTTTAGTCAGCATGTTAGTATGTC
* *
53467 TTGGTTTGTTTCTCTTTAGTCAGCATGTTTGTATGTC
1 TTGATTTGTTTCTCTTTAGTCAGCATGTTAGTATGTC
53504 TTGATTTGTT
1 TTGATTTGTT
53514 GTCAGCATGT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.13, C:0.12, G:0.20, T:0.55
Consensus pattern (37 bp):
TTGATTTGTTTCTCTTTAGTCAGCATGTTAGTATGTC
Found at i:63815 original size:19 final size:19
Alignment explanation
Indices: 63791--63827 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
63781 TGCATCTGTA
*
63791 ACCGTTTTACCACCGTTTG
1 ACCGTTTCACCACCGTTTG
63810 ACCGTTTCACCACCGTTT
1 ACCGTTTCACCACCGTTT
63828 TGGGCCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.35, G:0.14, T:0.35
Consensus pattern (19 bp):
ACCGTTTCACCACCGTTTG
Found at i:63903 original size:21 final size:21
Alignment explanation
Indices: 63878--63935 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 21
63868 GCTGCTCTAA
63878 TAATCTCATATGTACAGTACC
1 TAATCTCATATGTACAGTACC
* * **
63899 TAATCTAATCTGTACA--ATG
1 TAATCTCATATGTACAGTACC
63918 TAATCTCATATGTACAGT
1 TAATCTCATATGTACAGT
63936 TGCTAAACAG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
19 15 0.52
21 14 0.48
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.36
Consensus pattern (21 bp):
TAATCTCATATGTACAGTACC
Found at i:65276 original size:334 final size:335
Alignment explanation
Indices: 64307--65865 Score: 1742
Period size: 333 Copynumber: 4.7 Consensus size: 335
64297 CACAATGTCG
* * *
64307 GCAAAAATTGACGC-GAAAGATTTTTTCCTCAATTCTTGGCGACAATACTCATAAAAAAAAGATA
1 GCAAAAATTGAC-CTGAAAGATTTTTTACTCAATTTTTGGCCACAATACTCAT--AAAAAAGATA
* * * * * * *
64371 CAATTTAACGCCAAAAAGATTGAAGGACTTTTC-CTACTTTTAATATCGATTTTCCTA-TTTCTT
63 TAATTCAACGCCAAAAATATTGAAGGGCTTTTCAC-GCTTCTAATATCGATTTTCCTATTTTTTT
* * * * ** *
64434 CT-GAATTAATTTCTAATTAAATC-AAA-AACGTTTTCTGATACTCGTAAAAACAAATCATTAAA
127 CTCAAATTAATATCTAATTAAATCGAAACAA-G-ATTCAGATGTTCGTAAAAACAAATCCTTAAA
** * * * * *
64496 TCCAATGTACCTGAAATTTGGTTAGATGAATGTAGATATTTTAAGGAGTCTTAGCGCCAAAAATC
190 TCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTGGCGCCAAAAATC
* * * * * *
64561 ATATAAAACTGAGTC-GGGGCCTGGAACGCGTTTTTAGCCAAAAATCGTGA-----CGT------
255 ATACAAAACAGAGACTGGGCCCTGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAA
64614 TTTCGACTAAAATTTT
320 TTTCGACTAAAATTTT
* * *
64630 GCAAAAATGGACCCGAAAGA-TTTTTACCTCAGTTTTTGGCCACAATACTCATAAAAAAAGATAT
1 GCAAAAATTGACCTGAAAGATTTTTTA-CTCAATTTTTGGCCACAATACTCAT-AAAAAAGATAT
* *
64694 AATTCAACGTCAAAAATATTGAAGGGCTTTTCGCGCTTCTAATATCG---TT--T-TTTTTTT-T
64 AATTCAACGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGATTTTCCTATTTTTTTCT
* * * *
64752 CAAATTAATATCTAATTAAATCGAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATTCA
129 CAAATTAATATCTAATTAAATCGAAACAAGATTCAGATGTTCGTAAAAACAAATCCTTAAATCCA
* * * * * * * *
64817 ATGTGGCAGAGATTTGGTTAGATAAATATAGATATTTCGAGGATTTTTTGCGCCAAAAATCATGC
194 ATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTGGCGCCAAAAATCATAC
* * * * * *
64882 AAACCTA-AGCCGGGGCCCTGGAACGCGTTTTTAGCTAAAAACCGTTATGGTT-GAACACAATTT
259 AAAAC-AGAGACTGGGCCCTGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTT
* *
64945 CGGCTAAAGTTTT
323 CGACTAAAATTTT
* * * *
64958 GCAAAAATTGACCTGAAAGATTATTTACTCAATTTTTGGCCAAAATAGTCATAAATAAGATATAA
1 GCAAAAATTGACCTGAAAGATTTTTTACTCAATTTTTGGCCACAATACTCATAAAAAAGATATAA
** * *
65023 TTCAATTCCAAAAATATTGAAGGGCTTTTCACGCTTCAAATATCGTTTTTCCTATTTTTTTCTCA
66 TTCAACGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGATTTTCCTATTTTTTTCTCA
65088 AATTAATATCTAATTAAATCGAAACAAGATTCAGATGTTCGTAAAAACAAATCCTTAAATCCAAT
131 AATTAATATCTAATTAAATCGAAACAAGATTCAGATGTTCGTAAAAACAAATCCTTAAATCCAAT
** * * *
65153 GTGGCTGAGATTTATTTATATGAATATACACATTTCAAGAAGTCTTGGCGCCAAAAATCATACAA
196 GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTGGCGCCAAAAATCATACAA
*
65218 AACAGAG-CTGGGCCCTGGAACGCGTTTTTAGACAAAAACCGTGATGGTTAGTACACAATTTTCG
261 AACAGAGACTGGGCCCTGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAA-TTTCG
65282 AC-AAAATTTT
325 ACTAAAATTTT
* *
65292 GCAAAAATTGACCTGAAAGATTTTTTTCTCAATTTTT-GCCAACAATACTCAGAAAAAAGATATA
1 GCAAAAATTGACCTGAAAGATTTTTTACTCAATTTTTGGCC-ACAATACTCATAAAAAAGATATA
* * * *
65356 ATTCAACGCCAAAAGTATTGAAGGGTTTTTCACGCTTCTGATATTGATTTTCCTA-TTTTTTC-C
65 ATTCAACGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGATTTTCCTATTTTTTTCTC
* * * * * *
65419 GAATTAATTTTTAATTAAATCGAAA-ACAGTTTCTGATGCTT-GTAAAAACAAATCCATAAATCC
130 AAATTAATATCTAATTAAATCGAAACA-AGATTCAGATG-TTCGTAAAAACAAATCCTTAAATCC
* * * * *
65482 AATGTGGCTGAGATTTGGTTAGATTAATATAGTTATTTCAATG-ATTCTTGCCTCCAAAAATCAT
193 AATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAA-GAAGTCTTGGCGCCAAAAATCAT
* * * * * *
65546 GCAAAACTGAGAC-GGAGCCCCGGAACGCGTTTTTAGCCAAAATCAGTGATTGGTTATTACACAA
257 ACAAAACAGAGACTGG-GCCCTGGAACGCGTTTTTAGCCAAAAACCGTGA-TGGTTAGTACACAA
*
65610 TTTCGGCTAAAA-TTT
320 TTTCGACTAAAATTTT
* * *
65625 -CAGAAAATTGACCTGAAAGATTTTTTCCTCTATTTTTGGCTACAATACTCATAAAAAAGATATA
1 GCA-AAAATTGACCTGAAAGATTTTTTACTCAATTTTTGGCCACAATACTCATAAAAAAGATATA
* * * *
65689 ATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCAAATATCGTTTTTCCT-TTTTTTT-TC
65 ATTCAACGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGATTTTCCTATTTTTTTCTC
* *
65752 AAATTAATATTTAATTAAATCGAAACAAGATTCAGATGTTCGTAAAAATAAATCCTTAAATCCAA
130 AAATTAATATCTAATTAAATCGAAACAAGATTCAGATGTTCGTAAAAACAAATCCTTAAATCCAA
* *
65817 TGTGGCTGAGATTTGGTTAGATGAATATAAACATTTCAAGAAGTCTTGG
195 TGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTGG
65866 TGTTAGGCAC
Statistics
Matches: 1046, Mismatches: 144, Indels: 82
0.82 0.11 0.06
Matches are distributed among these distances:
316 1 0.00
317 112 0.11
318 35 0.03
319 4 0.00
322 57 0.05
323 40 0.04
327 52 0.05
328 54 0.05
329 5 0.00
330 2 0.00
331 1 0.00
332 122 0.12
333 300 0.29
334 255 0.24
335 6 0.01
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (335 bp):
GCAAAAATTGACCTGAAAGATTTTTTACTCAATTTTTGGCCACAATACTCATAAAAAAGATATAA
TTCAACGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGATTTTCCTATTTTTTTCTCA
AATTAATATCTAATTAAATCGAAACAAGATTCAGATGTTCGTAAAAACAAATCCTTAAATCCAAT
GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTCTTGGCGCCAAAAATCATACAA
AACAGAGACTGGGCCCTGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGA
CTAAAATTTT
Found at i:67925 original size:332 final size:330
Alignment explanation
Indices: 67169--68222 Score: 1208
Period size: 332 Copynumber: 3.2 Consensus size: 330
67159 TCACTTGGCA
* * ** * * * * *
67169 CCAAAACTCATACAAAACAAAGTCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTT
1 CCAAAAATCATGCAAAACTGAGACGGAGCCCCGGAACGCGTTTTTAGCAAAAAACCGTGAT-G-A
*
67234 A-GTA-CACAATTTTCGGCTAAAATTTTGCAAAAAAATTGACCCGAAAGATTTTTTCCTCGAATT
64 ACGTATGACAATTTT-GGCTAAAATTTTG--AAAAAATTGACCCGAAAGA-TTTTTCCTC-AATT
* * * * * *
67297 TTGGCCACAATACTCATAAGAAAGATATAACTCAATGCCGAAAAGATTGTAGGGCTTTTCACGTT
124 TTGGCCACAATACTCATAAAAAAGATATAAATCAACGCCAAAAAGATTGAAGGGCTTTTCACGCT
* * *
67362 TCTAATATAGTTTTTCCTATTTTTTTTCAAATTAATATCTTATTAAATCGAAACAAGATTCAGAT
189 TCTAATATCGTTTTTCCTA-TTTTTTTCAAATTAATATCTAATTAAATCGAAA-AAGATTTAGAT
*
67427 ACTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATACATATTTC
252 ACTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTC
* ** *
67492 GAGGAGTTTTGGTG
317 AATAAGTCTTGGTG
* * * * * * **
67506 CC-ATAATCATACAAAACTGAGCCGGTGCCCCGGAACGCGTTTTTAGCCAAAAACCGTTATGGTT
1 CCAAAAATCATGCAAAACTGAGACGGAGCCCCGGAACGCGTTTTTAGCAAAAAACCGTGAT-GAA
* * * * *
67570 GGTTTGCCAA-TTTAGCT-AAATTTTGTAAAAATTGACCCGAAAGATATTTTCCTCAATTTTTGG
65 CGTATGACAATTTTGGCTAAAATTTTGAAAAAATTGACCCGAAAGAT-TTTTCCTCAA-TTTTGG
* * *
67633 CCACAATACTCATAAAAAAGATATAATTCAACGACAAAAAGATTGAAGGGATTTTCACGCTTCTA
128 CCACAATACTCATAAAAAAGATATAAATCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTA
*
67698 ATATCGTTTTTCCTACTTTTTTTCAAATTAATATCTAATTAAATCGAAATAAGATTTAGATGCTC
193 ATATCGTTTTTCCTA-TTTTTTTCAAATTAATATCTAATTAAATCGAAA-AAGATTTAGATACTC
* * *
67763 GTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTTGTTAAATGAATATAGATATTTCAATA
256 GTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAATA
67828 AGTCTTGGTG
321 AGTCTTGGTG
* * *
67838 CCAAAAATCATGCAAAACGGAGACGGAGCCCCGGAATGCGTTTTGAGCAAAAAACCGTGAT-AAC
1 CCAAAAATCATGCAAAACTGAGACGGAGCCCCGGAACGCGTTTTTAGCAAAAAACCGTGATGAAC
* * *
67902 GTAT-ACAATTTTGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTGTCTCCTCAACTTATGGC
66 GTATGACAATTTTGGCTAAAATTTTGAAAAAATTGACCCGAAAGATT-TTTCCTCAA-TTTTGGC
* * *
67966 CACAATACTCATAAAAAATATATAAATCAACGCCAAAAATATTGAAGGGCTTTTCA-GACTTTTA
129 CACAATACTCATAAAAAAGATATAAATCAACGCCAAAAAGATTGAAGGGCTTTTCACG-CTTCTA
* * * * * * * *
68030 ATATCGTTTTCCCTA-TTTTTTCTGAATTAATTTATAATTAAATCGAAAATGGTTTCCGATTCTC
193 ATATCGTTTTTCCTATTTTTTTC-AAATTAATATCTAATTAAATCGAAAAAGATTT-AGATACTC
** * * * * *
68094 GTAAAAGTAATTCCTTAAACCCAATGTGGCTGATATTTGGTTAGATGAATATTGATATTTCAATT
256 GTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAATA
* *
68159 GGTCTTGGCG
321 AGTCTTGGTG
** *
68169 CCAAAAATCATGCAAAACTGAGATAGAGCCCCGAAACGCGTTTTTAGTCAAAAA
1 CCAAAAATCATGCAAAACTGAGACGGAGCCCCGGAACGCGTTTTTAG-CAAAAA
68223 TAGTGATATT
Statistics
Matches: 618, Mismatches: 87, Indels: 29
0.84 0.12 0.04
Matches are distributed among these distances:
330 15 0.02
331 146 0.24
332 334 0.54
333 49 0.08
334 8 0.01
335 4 0.01
336 57 0.09
337 5 0.01
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (330 bp):
CCAAAAATCATGCAAAACTGAGACGGAGCCCCGGAACGCGTTTTTAGCAAAAAACCGTGATGAAC
GTATGACAATTTTGGCTAAAATTTTGAAAAAATTGACCCGAAAGATTTTTCCTCAATTTTGGCCA
CAATACTCATAAAAAAGATATAAATCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATA
TCGTTTTTCCTATTTTTTTCAAATTAATATCTAATTAAATCGAAAAAGATTTAGATACTCGTAAA
AACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAATAAGTCT
TGGTG
Found at i:69694 original size:331 final size:328
Alignment explanation
Indices: 69014--70027 Score: 1071
Period size: 331 Copynumber: 3.0 Consensus size: 328
69004 TAGTTATGGG
* * * * * **
69014 TAAAAACGCGTTCCGAGGCCCTGCCTCAATTTTGTATGATTT-TAGGCGCCAAGACTCATTGAAA
1 TAAAAACGCATTACGGGGCCCCGACTCAATTTTAAATGATTTCT-GGC-CCAAGACTCATTGAAA
* ** * *
69078 TATGTATATTCATCTAACCAAATCAAAG-CACATTAGATTTAAGGATTTATTTTTACGAGTATCT
64 TATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTATTTTTACGAGCATC-
* **
69142 GAAACCGATTTCGATTTAATTAGAAATTAATAAGGAAAAATATAGGAAAATCGATATTAGAAGCG
128 GAAACCGTTTTCGATTTAATTAGAAATTAATTCGGAAAAATATAGGAAAATCGATATTAGAAGCG
* * * *
69207 TGAGGAAGCCTTTCAATCTTTTCGGTGTTGAATTAAATATTTATTATGATTATTTTGGCCAACAA
193 TGA--AAGCCTTTCAATCTTTTTGGTGTTGAATTAAATATTTATTATGAGTA-TTTGGTCAAAAA
* ** * * *
69272 TT-AACGAAAAATCTTTCGGATCAATTTTTGCAATATTTTAGATGAAATTGTGTTCTAACCATCA
255 TTGAA-GAAAAATCTTTCGG-TCAATTTTTGCAAAATTTTACCTGAAATCGTGTACTAACAATCA
*
69336 TGGATTTTG-GC
318 CGG-TTTTGTGC
** * * * * *
69347 TAAAAACGTGTTACGGGGTCCCGGCTTAATTTTAAATGATTTTTGTCACCAAGACTCATTGAAAT
1 TAAAAACGCATTACGGGGCCCCGACTCAATTTTAAATGATTTCTGGC-CCAAGACTCATTGAAAT
* * * * *
69412 AACTATATTCATCTAACCAAATCTCAGCCACATCGGATTTAAGGATTTGTTTATACGAGCAGCAG
65 ATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTATTTTTACGAGCATC-G
* *
69477 AAACCGTTTTCGATTTAATTAAAAATTAATTCGG-AAAA-A-AGGAAAATCGATATTAGAAGCAT
129 AAACCGTTTTCGATTTAATTAGAAATTAATTCGGAAAAATATAGGAAAATCGATATTAGAAGCGT
* ** * *
69539 GAAAGGCCCTTT-AATCTTTTTTGTAATGAATTAAATAATTATTTTGAGTATTGTGGTCAAAAAT
194 GAAA-G-CCTTTCAATCTTTTTGGTGTTGAATTAAATATTTATTATGAGTATT-TGGTCAAAAAT
* * * *
69603 TGAGGAAAAAATCTTTCAGGTCAATTTTTGAAAAATTTTACCTGAAATCGTCTACTAACTATCAC
256 TGAAG-AAAAATCTTTC-GGTCAATTTTTGCAAAATTTTACCTGAAATCGTGTACTAACAATCAC
69668 GGTTTTGTGC
319 GGTTTTGTGC
* **
69678 TAAAAACGCATTACGGGGCCCCGACTCAGTTTTGCATGATTTCTGGCCCTAAGACTCATTGAAAT
1 TAAAAACGCATTACGGGGCCCCGACTCAATTTTAAATGATTTCTGGCCC-AAGACTCATTGAAAT
* * *
69743 ATCTATATTCATCTAAACAAATCTCAGCCACATTGGATTTAA-GATTTTTTCTTTTACCAGCATC
65 ATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGA-TTTAT-TTTTACGAGCATC
** *
69807 TCAACCTTGTTTT-GATTTAATTAGAAATTAATTCGGAAAAATATAGGAAATTCGATATTAGAAG
128 GAAACC--GTTTTCGATTTAATTAGAAATTAATTCGGAAAAATATAGGAAAATCGATATTAGAAG
* * * * * *
69871 GGTAAAAAGCCTTTCAATCTTTCTGGCGTTGAATTATATATTTATTATGAGTATTTTGTACAAAA
191 CGT-GAAAGCCTTTCAATCTTTTTGGTGTTGAATTAAATATTTATTATGAGTATTTGGT-CAAAA
* * * * * *
69936 ATTGAAGAAAAATCTCTCGGGTAAATTTTTTCTAAATTTTAGCC-GAAATCATGTACTACCAATC
254 ATTGAAGAAAAATCTTTC-GGTCAATTTTTGCAAAATTTTA-CCTGAAATCGTGTACTAACAATC
*
70000 ACGATTTT-TGTC
317 ACGGTTTTGTG-C
70012 TAAAAACGCATTACGG
1 TAAAAACGCATTACGG
70028 AACTCCGGCT
Statistics
Matches: 568, Mismatches: 91, Indels: 43
0.81 0.13 0.06
Matches are distributed among these distances:
329 4 0.01
330 52 0.09
331 180 0.32
332 35 0.06
333 90 0.16
334 138 0.24
335 66 0.12
336 3 0.01
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (328 bp):
TAAAAACGCATTACGGGGCCCCGACTCAATTTTAAATGATTTCTGGCCCAAGACTCATTGAAATA
TCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTATTTTTACGAGCATCGAA
ACCGTTTTCGATTTAATTAGAAATTAATTCGGAAAAATATAGGAAAATCGATATTAGAAGCGTGA
AAGCCTTTCAATCTTTTTGGTGTTGAATTAAATATTTATTATGAGTATTTGGTCAAAAATTGAAG
AAAAATCTTTCGGTCAATTTTTGCAAAATTTTACCTGAAATCGTGTACTAACAATCACGGTTTTG
TGC
Found at i:70839 original size:331 final size:332
Alignment explanation
Indices: 70208--71769 Score: 2142
Period size: 331 Copynumber: 4.7 Consensus size: 332
70198 TTATTATGAG
* * * * *
70208 TATCGTGTACTGAA-AATCACCGTTTTTTGGCTAAAAACTCTTTACGGGGTCCGAACTCAATTTT
1 TATCGTGTACT-AACCATCA-CGGTTTTTGGTTAAAAACTCTTTACGGGGTCCCAGCTCAATTTT
*
70272 AAATGATTTTTGGCGCCAAGCCTCATTAAAATATCTATATTTATCTAACAAAATCTCAATCACAT
64 ACATGATTTTTGGCGCCAAGCCTCATTAAAATATCTATATTTATCTAACAAAATCTCAATCACAT
* *
70337 TGGATTTTAG-ATTTTTTTTACCGGCATTAGAAATCTGTTTCGATTTAAGTAGAAATTAATTCGG
129 TGGATTTTAGAATTTTTTTTACCAGCATCAGAAATCTGTTTCGATTTAAGTAGAAATTAATTCGG
* * *
70401 AAAAATATAGGAAATTCGATATTAGAAGCGTAAAAAGCCTTTCAATCTTTTTGGCGTTAAATTAT
194 AAAAATATAGGAAATTCGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGGAGTTGAATTAT
* * *
70466 ATATTTATTATGAGCATTTTGTACAAAATTTGAAGAAAAATCTTTCAGGTCAATTTTTGGAATAT
259 ATATTTATTATGAGTATTTTGTACAAAAATTGAAGAAAAATCTTTCAGGTCAATTTTTGCAATAT
70531 TTTAGCTGA
324 TTTAGCTGA
*
70540 TATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACTCTTTACGGGGTCCCAGTTCAATTTTAC
1 TATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACTCTTTACGGGGTCCCAGCTCAATTTTAC
* * *
70605 ATGATTTTTGGCTCCAAGCCTCATTGAAATATCTATATTTATTTAACAAAATCTCAATCACATTG
66 ATGATTTTTGGCGCCAAGCCTCATTAAAATATCTATATTTATCTAACAAAATCTCAATCACATTG
70670 GATTTTAGAATTTTTTTTACCAGCATCAGAAATCTGTTTCGATTTAAGTAGAAATTAATTCGGAA
131 GATTTTAGAATTTTTTTTACCAGCATCAGAAATCTGTTTCGATTTAAGTAGAAATTAATTCGGAA
* * *
70735 AAATATAGGAAAATCGATATTAGAAGCTTGAAAAGCCTTTTAATCTTTTTGGAGTTGAATTATAT
196 AAATATAGGAAATTCGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGGAGTTGAATTATAT
*
70800 ATTTATTATGATTATTTTGTAC-AAAATTGAATG-AAAATCTTTCAGGTCAATTTTTGCAATATT
261 ATTTATTATGAGTATTTTGTACAAAAATTGAA-GAAAAATCTTTCAGGTCAATTTTTGCAATATT
70863 TTAGCTGA
325 TTAGCTGA
* * * * * *
70871 TATCGTGTATTAACCATCACGGTTTTTGGCTAAAAACGCGTTACGGCGTCCCAGCTCAGTTTTAC
1 TATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACTCTTTACGGGGTCCCAGCTCAATTTTAC
* * * ** * *
70936 ATGATTTTTGGCGCCAAGCCTCATTAAAATTTTTATCTTTATCTAATTAGATCTCAATCATATTG
66 ATGATTTTTGGCGCCAAGCCTCATTAAAATATCTATATTTATCTAACAAAATCTCAATCACATTG
* * * *
71001 GATTTAAGAATTTTTTTTACTAGCATCAGAAATCTGTTTCGATTTAATTAGAAATTAATTCCGAA
131 GATTTTAGAATTTTTTTTACCAGCATCAGAAATCTGTTTCGATTTAAGTAGAAATTAATTCGGAA
* * *
71066 AAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCTTTCAATC-TTTTGGACGTTGAGTCATA
196 AAATATAGGAAATTCGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGGA-GTTGAATTATA
* * *
71130 TACTTATTATGAGTATTTTGTACAAAAATTGAAGAAAAATCTTTCAGGTAAATTGTTT-CAAAAT
260 TATTTATTATGAGTATTTTGTACAAAAATTGAAGAAAAATCTTTCAGGTCAATT-TTTGCAATAT
*
71194 TTTAGCCGA
324 TTTAGCTGA
* * * * * * ** ** *
71203 AATCATGTACTAACCATCACGATTTTT-GTCTAAAAACGCATT-CCGGAACTCTGGCTCAGTTTT
1 TATCGTGTACTAACCATCACGGTTTTTGGT-TAAAAACTCTTTACGGGGTC-CCAGCTCAATTTT
* ** * * * * * **
71266 GCATGATTTTTGGAACCAAGACTCATT-GAATAATCCATATTCATCTAACCAAATCTCAGCCACA
64 ACATGATTTTTGGCGCCAAGCCTCATTAAAAT-ATCTATATTTATCTAACAAAATCTCAATCACA
** * * * * * *
71330 TTGGATTAAAG-ATTTTTTTTACGAGCTTCTG-AACCTTGTTTCAATTTAATTAGAAATTAATTC
128 TTGGATTTTAGAATTTTTTTTACCAGCATCAGAAATC-TGTTTCGATTTAAGTAGAAATTAATTC
* * * * * *
71393 AGAAAATTATAGGAAATTCCATATTAGAAGTGTGTAAAGCCTTTCAATCTTTTTGGCGTTGAATT
192 GGAAAAATATAGGAAATTCGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGGAGTTGAATT
* *
71458 ATAAATTTATTATGAGTATTTTGTACAAAAATTGAAGAAAAATATTTCAGGTCAATTTTTGCAAT
257 ATATATTTATTATGAGTATTTTGTACAAAAATTGAAGAAAAATCTTTCAGGTCAATTTTTGCAAT
*
71523 ATTTCAGCTGA
322 ATTTTAGCTGA
*
71534 TATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACTCTTTACGGGGTCCCAGTTCAATTTTAC
1 TATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACTCTTTACGGGGTCCCAGCTCAATTTTAC
71599 ATGATTTTTGGCGCCAAGCCTCATTAAAATATCTATATTTATCTAAGC-AAATCTCAATCACATT
66 ATGATTTTTGGCGCCAAGCCTCATTAAAATATCTATATTTATCTAA-CAAAATCTCAATCACATT
* * *
71663 GGATGTTAGAATTTTTTTTACCAGCATCAGAAATCTGTTTCGATTTAAATAGAAATTAA-TCGTA
130 GGATTTTAGAATTTTTTTTACCAGCATCAGAAATCTGTTTCGATTTAAGTAGAAATTAATTCGGA
*
71727 AAAATATAGGAAATTCGATATTAGAAGCGTAAAAAGCCTTTCA
195 AAAATATAGGAAATTCGATATTAGAAGCGTGAAAAGCCTTTCA
71770 GGTCAATTTT
Statistics
Matches: 1072, Mismatches: 139, Indels: 39
0.86 0.11 0.03
Matches are distributed among these distances:
330 13 0.01
331 710 0.66
332 343 0.32
333 6 0.01
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (332 bp):
TATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACTCTTTACGGGGTCCCAGCTCAATTTTAC
ATGATTTTTGGCGCCAAGCCTCATTAAAATATCTATATTTATCTAACAAAATCTCAATCACATTG
GATTTTAGAATTTTTTTTACCAGCATCAGAAATCTGTTTCGATTTAAGTAGAAATTAATTCGGAA
AAATATAGGAAATTCGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGGAGTTGAATTATAT
ATTTATTATGAGTATTTTGTACAAAAATTGAAGAAAAATCTTTCAGGTCAATTTTTGCAATATTT
TAGCTGA
Found at i:71491 original size:663 final size:662
Alignment explanation
Indices: 70208--71769 Score: 2180
Period size: 663 Copynumber: 2.4 Consensus size: 662
70198 TTATTATGAG
* * * *
70208 TATCGTGTACTGAA-AATCACCGTTTTTTGGCTAAAAACTCTTTACGGGGTCCGAACTCAATTTT
1 TATCGTGTACT-AACCATCA-CGGTTTTTGGCTAAAAACTCTTTACGGGGTCCCAGCTCAATTTT
*
70272 AAATGATTTTTGGCGCCAAGCCTCATTAAAATATCTATATTTATCTAACAAAATCTCAATCACAT
64 ACATGATTTTTGGCGCCAAGCCTCATTAAAATATCTATATTTATCTAACAAAATCTCAATCACAT
* * * *
70337 TGGATTTTAG-ATTTTTTTTACCGGCATTAGAAATCTGTTTCGATTTAAGTAGAAATTAATTCGG
129 TGGA-TTTAGAATTTTTTTTACCAGCATCAGAAATCTGTTTCGATTTAAATAGAAATTAATTCCG
*
70401 AAAAATATAGGAAATTCGATATTAGAAGCGTAAAAAGCCTTTCAATCTTTTTGGCGTTAAATTAT
193 AAAAATATAGGAAATTCGATATTAGAAGCGTAAAAAGCCTTTCAATCTTTTTGGCGTTAAATCAT
* * * * *
70466 ATATTTATTATGAGCATTTTGTACAAAATTTGAAGAAAAATCTTTCAGGTCAATTTTTGGAATAT
258 ATACTTATTATGAGCATTTTGTACAAAAATTGAAGAAAAATCTTTCAGGTAAATTTTTGCAAAAT
* * * * * * ** *
70531 TTTAGCTGATATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACTCTTTACGGGGTCCCAGTT
323 TTTAGCCGAAATCATGTACTAACCATCACGATTTTTGGTTAAAAACGCATTACGGACTCCCAGCT
** * * * *
70596 CAATTTTACATGATTTTTGGCTCCAAGCCTCATTGAAATATCTATATTTATTTAACAAAATCTCA
388 CAATTTTACATGATTTTTGGAACCAAGACTCATTGAAATATCCATATTCATCTAACAAAATCTCA
* ** *
70661 ATCACATTGGATTTTAGAATTTTTTTTACCAGCATCAGAAATCTGTTTCGATTTAAGTAGAAATT
453 ACCACATTGGATTAAAGAATTTTTTTTACCAGCATCAGAAATCTGTTTCAATTTAAGTAGAAATT
* * *
70726 AATTCGGAAAAATATAGGAAAATCGATATTAGAAGCTTGAAAAGCCTTTTAATCTTTTTGGAGTT
518 AATTCAGAAAAATATAGGAAAATCCATATTAGAAGCTTGAAAAGCCTTTCAATCTTTTTGGAGTT
* * *
70791 GAATTATATATTTATTATGATTATTTTGTACAAAATTGAATG-AAAATCTTTCAGGTCAATTTTT
583 GAATTATAAATTTATTATGAGTATTTTGTACAAAATTGAA-GAAAAATATTTCAGGTCAATTTTT
*
70855 GCAATATTTTAGCTGA
647 GCAATATTTCAGCTGA
* * * * *
70871 TATCGTGTATTAACCATCACGGTTTTTGGCTAAAAACGCGTTACGGCGTCCCAGCTCAGTTTTAC
1 TATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACTCTTTACGGGGTCCCAGCTCAATTTTAC
* * * ** * *
70936 ATGATTTTTGGCGCCAAGCCTCATTAAAATTTTTATCTTTATCTAATTAGATCTCAATCATATTG
66 ATGATTTTTGGCGCCAAGCCTCATTAAAATATCTATATTTATCTAACAAAATCTCAATCACATTG
* *
71001 GATTTAAGAATTTTTTTTACTAGCATCAGAAATCTGTTTCGATTTAATTAGAAATTAATTCCGAA
131 GATTT-AGAATTTTTTTTACCAGCATCAGAAATCTGTTTCGATTTAAATAGAAATTAATTCCGAA
* * * *
71066 AAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCTTTCAATC-TTTTGGACGTTGAGTCATA
195 AAATATAGGAAATTCGATATTAGAAGCGTAAAAAGCCTTTCAATCTTTTTGG-CGTTAAATCATA
*
71130 TACTTATTATGAGTATTTTGTACAAAAATTGAAGAAAAATCTTTCAGGTAAATTGTTT-CAAAAT
259 TACTTATTATGAGCATTTTGTACAAAAATTGAAGAAAAATCTTTCAGGTAAATT-TTTGCAAAAT
* **
71194 TTTAGCCGAAATCATGTACTAACCATCACGATTTTT-GTCTAAAAACGCATTCCGGAACT-CTGG
323 TTTAGCCGAAATCATGTACTAACCATCACGATTTTTGGT-TAAAAACGCATTACGG-ACTCCCAG
* * *
71257 CTCAGTTTTGCATGATTTTTGGAACCAAGACTCATTG-AATAATCCATATTCATCTAACCAAATC
386 CTCAATTTTACATGATTTTTGGAACCAAGACTCATTGAAAT-ATCCATATTCATCTAACAAAATC
* * * * * *
71321 TCAGCCACATTGGATTAAAG-ATTTTTTTTACGAGCTTCTG-AACCTTGTTTCAATTTAATTAGA
450 TCAACCACATTGGATTAAAGAATTTTTTTTACCAGCATCAGAAATC-TGTTTCAATTTAAGTAGA
* * *
71384 AATTAATTCAGAAAATTATAGGAAATTCCATATTAGAAG-TGTGTAAAGCCTTTCAATCTTTTTG
514 AATTAATTCAGAAAAATATAGGAAAATCCATATTAGAAGCT-TGAAAAGCCTTTCAATCTTTTTG
*
71448 GCGTTGAATTATAAATTTATTATGAGTATTTTGTACAAAAATTGAAGAAAAATATTTCAGGTCAA
578 GAGTTGAATTATAAATTTATTATGAGTATTTTGTAC-AAAATTGAAGAAAAATATTTCAGGTCAA
71513 TTTTTGCAATATTTCAGCTGA
642 TTTTTGCAATATTTCAGCTGA
* *
71534 TATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACTCTTTACGGGGTCCCAGTTCAATTTTAC
1 TATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACTCTTTACGGGGTCCCAGCTCAATTTTAC
71599 ATGATTTTTGGCGCCAAGCCTCATTAAAATATCTATATTTATCTAAGC-AAATCTCAATCACATT
66 ATGATTTTTGGCGCCAAGCCTCATTAAAATATCTATATTTATCTAA-CAAAATCTCAATCACATT
71663 GGATGTTAGAATTTTTTTTACCAGCATCAGAAATCTGTTTCGATTTAAATAGAAATTAA-T-CGT
130 GGAT-TTAGAATTTTTTTTACCAGCATCAGAAATCTGTTTCGATTTAAATAGAAATTAATTCCG-
71726 AAAAATATAGGAAATTCGATATTAGAAGCGTAAAAAGCCTTTCA
193 AAAAATATAGGAAATTCGATATTAGAAGCGTAAAAAGCCTTTCA
71770 GGTCAATTTT
Statistics
Matches: 792, Mismatches: 92, Indels: 31
0.87 0.10 0.03
Matches are distributed among these distances:
661 9 0.01
662 279 0.35
663 498 0.63
664 6 0.01
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (662 bp):
TATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACTCTTTACGGGGTCCCAGCTCAATTTTAC
ATGATTTTTGGCGCCAAGCCTCATTAAAATATCTATATTTATCTAACAAAATCTCAATCACATTG
GATTTAGAATTTTTTTTACCAGCATCAGAAATCTGTTTCGATTTAAATAGAAATTAATTCCGAAA
AATATAGGAAATTCGATATTAGAAGCGTAAAAAGCCTTTCAATCTTTTTGGCGTTAAATCATATA
CTTATTATGAGCATTTTGTACAAAAATTGAAGAAAAATCTTTCAGGTAAATTTTTGCAAAATTTT
AGCCGAAATCATGTACTAACCATCACGATTTTTGGTTAAAAACGCATTACGGACTCCCAGCTCAA
TTTTACATGATTTTTGGAACCAAGACTCATTGAAATATCCATATTCATCTAACAAAATCTCAACC
ACATTGGATTAAAGAATTTTTTTTACCAGCATCAGAAATCTGTTTCAATTTAAGTAGAAATTAAT
TCAGAAAAATATAGGAAAATCCATATTAGAAGCTTGAAAAGCCTTTCAATCTTTTTGGAGTTGAA
TTATAAATTTATTATGAGTATTTTGTACAAAATTGAAGAAAAATATTTCAGGTCAATTTTTGCAA
TATTTCAGCTGA
Done.