Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012361.1 Corchorus olitorius cultivar O-4 contig12394, 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: 44754
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:16115 original size:32 final size:32
Alignment explanation
Indices: 16074--16139 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
16064 TCTTTTAGTT
16074 AGCTGCATTGCATAGCAAATTCTATATATGCC
1 AGCTGCATTGCATAGCAAATTCTATATATGCC
*
16106 AGCTGCATTGCATAGCAGATTCTATATATGCC
1 AGCTGCATTGCATAGCAAATTCTATATATGCC
16138 AG
1 AG
16140 GAGTTCCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (32 bp):
AGCTGCATTGCATAGCAAATTCTATATATGCC
Found at i:29643 original size:329 final size:327
Alignment explanation
Indices: 28547--29674 Score: 1288
Period size: 331 Copynumber: 3.4 Consensus size: 327
28537 AACGCCTTCA
* *
28547 AAACAA-ATTTCAGATGCTCGTAAAAA-CAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGA
1 AAACAAGA-TTCAGATGCTCGTAAAAATAAATCCTTAAATCCAATGTAGCTGAGATTTGGTTCGA
* * * * *
28610 TGAATATAAATATTTCAAGGAGTCTTTACGCCAAAAATTATGCAAAACTAAGCCGGGGCCCCGTA
65 TGAATATAGATAATTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTAAGCCGGGGCTCCGGA
* *
28675 AAGCGTTTTTAGCCAAAAACCGTGATGGTAGTACACGATTTTGGCTAAAATTTTGTAAAAACTGA
130 ACGCGTTTTTAGCCAAAAACCGTGAT-G-AGTACACGATTTTGGCTAAAATTTTGCAAAAACTGA
* * * * * * *
28740 CCCAAAAAATTTTTTCTCAATTTTTTGCCACAATAATGAGAAAAATTATATAAATAAATGCC-AA
193 -CCAAAAAATTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAATTATATAATTCAACGCCAAA
** * * * *
28804 AAGTTAGAAGGATTTTTT-ACGCTTTTAATATCGTTTCTCCAATTTTTTTCCGAATTTATTTCTT
257 AAAATAGAAGGGTTTTTTCACACTTCTAATATCGTTT-TCCAA--TTTTTCCGAATTTATTTCTA
28868 ATTAAATCG
319 ATTAAATCG
* * * *
28877 ACACAAGATTCAGATGCTCGTAAAAATAAATCCTTGAATCCAATGTTGCTGAGATTTGATTCGAT
1 AAACAAGATTCAGATGCTCGTAAAAATAAATCCTTAAATCCAATGTAGCTGAGATTTGGTTCGAT
* * * * * ***
28942 GAATATAGATAATTTAAGGAGTCTTTATGTCAAAAATCATACAAAACTGAA-CCAGGGCTTTAGA
66 GAATATAGATAATTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACT-AAGCCGGGGCTCCGGA
** * * *
29006 ACGCGTTTTTAGGAAAAAAACCGTGATG-GTATATGATTTCGGCTAAAATTTTGCAAAAACTGAC
130 ACGCGTTTTTA-GCCAAAAACCGTGATGAGTACACGATTTTGGCTAAAATTTTGCAAAAACTGA-
* * ** *
29070 CCGAAAATTTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAAACATATAATTCAACCCCAAAA
193 CCAAAAAATTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAATTATATAATTCAACGCCAAAA
* * * ** *
29135 ATATTGAA-GGATTTTTCACACTTCTAATATCGTTTTTCCTTTTTTTTTCCCGAATTTATTTTTA
258 AAATAGAAGGGTTTTTTCACACTTCTAATATCG-TTTTCC--AATTTTT-CCGAATTTATTTCTA
29199 ATTAAATCG
319 ATTAAATCG
* * * *
29208 AAACAAAATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTAACTGAGATTTGGTTCGAT
1 AAACAAGATTCAGATGCTCGTAAAAATAAATCCTTAAATCCAATGTAGCTGAGATTTGGTTCGAT
* * * * *
29273 GAATATAGATATTTGAA-GATGTCTTTACGCCATAAATCATGCCAAACTAAGTCGGGGCTCCGGA
66 GAATATAGATAATTCAAGGA-GTCTTTACGCCAAAAATCATGCAAAACTAAGCCGGGGCTCCGGA
* * * **
29337 ACGGGTTTTTAGCCAAAAACCTTGATGACTACACGATTTTGGCTTCAATTTTGCAAAAACTGACC
130 ACGCGTTTTTAGCCAAAAACCGTGATGAGTACACGATTTTGGCTAAAATTTTGCAAAAACTGACC
* *
29402 AAAAAATTTTTCCCTCAATTCATTGCCACAATACTTAGAAAAATTATATAATTCAACGCCAAAAA
195 AAAAAATTTTT-CCTCAATTCTTTGCCACAATACTCAGAAAAATTATATAATTCAACGCCAAAAA
* * * *
29467 AATGGAAGGGTTTTTTCACACTTCTAATATCGATTTTCCGATTTTTCTGATTTTATTTCTAATTA
259 AATAGAAGGGTTTTTTCACACTTCTAATATCG-TTTTCCAATTTTTCCGAATTTATTTCTAATTA
29532 AATCG
323 AATCG
* * * *
29537 AAACGAGATTCAGATGCTCGTAAAAATAAATCCTTCAATCCATTGTAGCTGAGATTTGGTTTGAT
1 AAACAAGATTCAGATGCTCGTAAAAATAAATCCTTAAATCCAATGTAGCTGAGATTTGGTTCGAT
* * * * * *
29602 GAATTTAGGTAATTCAAGGTGCCTTTACGCAAAAAATCATGCAAAACTGTA-CCGGGGC-CC-GA
66 GAATATAGATAATTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACT-AAGCCGGGGCTCCGGA
*
29664 ACGCGGTTTTA
130 ACGCGTTTTTA
29675 CCCTCGTTTA
Statistics
Matches: 666, Mismatches: 115, Indels: 37
0.81 0.14 0.05
Matches are distributed among these distances:
327 11 0.02
328 2 0.00
329 208 0.31
330 87 0.13
331 314 0.47
332 44 0.07
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (327 bp):
AAACAAGATTCAGATGCTCGTAAAAATAAATCCTTAAATCCAATGTAGCTGAGATTTGGTTCGAT
GAATATAGATAATTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTAAGCCGGGGCTCCGGAA
CGCGTTTTTAGCCAAAAACCGTGATGAGTACACGATTTTGGCTAAAATTTTGCAAAAACTGACCA
AAAAATTTTTCCTCAATTCTTTGCCACAATACTCAGAAAAATTATATAATTCAACGCCAAAAAAA
TAGAAGGGTTTTTTCACACTTCTAATATCGTTTTCCAATTTTTCCGAATTTATTTCTAATTAAAT
CG
Found at i:32115 original size:331 final size:333
Alignment explanation
Indices: 30882--33451 Score: 3150
Period size: 331 Copynumber: 7.8 Consensus size: 333
30872 TTCCTGGGAA
* * *
30882 AGTACACGATTTTGGCTAAAATTTTGCAAAATCTGACCCG-AAATTTTTTTTCTTCAACTCCTTG
1 AGTACACGATTTTGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTTTC-TCAATTCTTTG
* * *
30946 CCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGGTTTTCACGCTTCAA
65 CCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGTTTTTCACGCTTCTA
* *
31011 ATATCGTTTTTCTATTTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
130 ATATCGTTTTTCCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * * * *
31076 GTAAAAATAAATCCTTAAATCCAATGTGGCTGAGACTTGGTTTGATGAATTTAGATAATTGAAGG
195 GTAAAAATAAATCCTTAAATCCAATGTAGCTGAGATTTGGTTCGATGAATATAGATAATTCAAGG
* * ** *
31141 ATTATTTACGCCAAAAATCATGCAAAACTGAGCC-GGGCCCTGGAACGATTTTTTAGCCAAAAAT
260 AGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGGCCC-GGAACGCGTTTTTAGCCAAAAAC
31205 CGTGATGGTT
324 CGTGATGGTT
* * *
31215 AGTAAACGATTTTCGCTAAAATTTTGCAAAAACTGACCAG-AAATTTTTTTT-TCAATTCTTTGC
1 AGTACACGATTTTGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTTTCTCAATTCTTTGC
* * * * *
31278 CATAATACTCATAAAAAATATATAATTCAATGCCAAAAACATTGAAGGGTTTTTCACACTTCTAA
66 CACAATACTCAGAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGTTTTTCACGCTTCTAA
* * * * * *
31343 TATTGTTTTT-CATTTTTTTTCCGAATTAATTTCTGATTAAATCGAAGCAAGATTTAGATACT-G
131 TATCGTTTTTCCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
* ** * * * *
31406 TAAAAA-CAATCCTTAAATATAATGTAGCTGATATTTGGTTCGATCAATATAGATATTTCAAGAA
196 TAAAAATAAATCCTTAAATCCAATGTAGCTGAGATTTGGTTCGATGAATATAGATAATTCAAGGA
* *
31470 GTCTTTACGCCAAAAATCATGCAAAACTAAGCCGGGGCCCGGAATGCGTTTTTAGCCAAAAACCG
261 GTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGGCCCGGAACGCGTTTTTAGCCAAAAACCG
31535 TGATGG--
326 TGATGGTT
* * **
31541 -GTACACGATTTTTGCTAAAATTTTGCAAAAAATGACCCGAAAA-TTTTTTTCTCAATTCTAAGG
1 AGTACACGATTTTGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTTTCTCAATTCT-TTG
* * * * * *
31604 CCACAATACTCAGAAAAATTATATAAATCAACACCAAAAAAATTGAAGGATTTTTTACGCTTCTA
65 CCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGTTTTTCACGCTTCTA
* * *
31669 ATATCGTTTTCCCA-TTTTTTTCCGAATTTATTTCTTATTAAATCGACACAAGATTCAGATGCTC
130 ATATCGTTTTTCCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * * * *
31733 ATAAAAATAAATCCTTAAATCCAATGTTGTTGAGATTTGATTCGATGAATATAGATAATTTAAGG
195 GTAAAAATAAATCCTTAAATCCAATGTAGCTGAGATTTGGTTCGATGAATATAGATAATTCAAGG
* ** * *
31798 AGTCTTTACGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCATAACACGTTTTTAG-GAAATAA
260 AGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGG-CCCGGAACGCGTTTTTAGCCAAA-AA
31862 CCGTGATGGTT
323 CCGTGATGGTT
*
31873 AGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTTTCTCAATTCTTTGC
1 AGTACACGATTTTGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTTTCTCAATTCTTTGC
* ** * * *
31938 CACAATACTCTGAAAAAGCATATAATTCAACCCCATAAATATTGAAGGGTTTTTCACTCTTCTAA
66 CACAATACTCAGAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGTTTTTCACGCTTCTAA
* * *
32003 TATCG-TTTT-C-TTTTTTTTCCGATTTTATTTCTAATTAAATCGAAACAAGATTCAGATGCCCA
131 TATCGTTTTTCCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
* * * * *
32065 TAAAAACAAATCCTTAAATCCAATGTAACTGAAATTTGGTTCGATGAATATAGATATTTGAAGGA
196 TAAAAATAAATCCTTAAATCCAATGTAGCTGAGATTTGGTTCGATGAATATAGATAATTCAAGGA
* * * * * *
32130 ATCTTGACGCCATAAATCATGCCAAACTGAGTCGGGGCCTTGGAACGCGTTTTTAGCCAAAAACC
261 GTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGGCC-CGGAACGCGTTTTTAGCCAAAAACC
*
32195 TTGAT-G--
325 GTGATGGTT
* * * * * *
32201 ACTACACGATTTTGGTTTAAATTTTGCAAAAACTGACCCGAAAA-ATTTTTCCTCAATTCATTGC
1 AGTACACGATTTTGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTTTCTCAATTCTTTGC
* * * * * *
32265 CACAATACTTAGAAAAATTATTTAATTCAACGCTAAAAAAATTGAAGGGTTTTTCACACTTCTAA
66 CACAATACTCAGAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGTTTTTCACGCTTCTAA
* * * *
32330 TATCATTTTTCCGA--TTTTTTCTGATTTTATTTCTAATTAAATCGAAACAAGATTTAGATGCTC
131 TATCGTTTTTCC-ATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * * *
32393 GTAAAAATAAATCCTTAAATCCAATGTATCTGAGATTTGATTCGATGAATTTAGGTAATTCAAGG
195 GTAAAAATAAATCCTTAAATCCAATGTAGCTGAGATTTGGTTCGATGAATATAGATAATTCAAGG
* * * * *
32458 AGTCTTTACG-CACAAAATCATACAAAACTGTGCCGGAGTCCAGAACGCGTTTTTAGCCAAAAAC
260 AGTCTTTACGCCA-AAAATCATGCAAAACTGAGCCGGGGCCCGGAACGCGTTTTTAGCCAAAAAC
*
32522 TGTGATGGTT
324 CGTGATGGTT
* * *
32532 AGTACACGATTTTGGCTAAAAATTTGCAAAAATCTAACCCGAAAATTTTTTCT-TCAATTCTTTG
1 AGTACACGATTTTGGCTAAAATTTTGCAAAAA-CTGACCCGAAAATTTTTTTTCTCAATTCTTTG
* *
32596 CCATAATACTCAGAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGTCTTTCACGCTTCTA
65 CCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGTTTTTCACGCTTCTA
*
32661 ATATCGTTTTTCCAATTTTTTTT---AATTTATTTTTAATTAAATCGAAACAAGATTCAGATGCT
130 ATATCGTTTTTCC-ATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCT
* * * * * * *
32723 CGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGACTTGGTTTGATTAATTTTGATAATTGAAG
194 CGTAAAAATAAATCCTTAAATCCAATGTAGCTGAGATTTGGTTCGATGAATATAGATAATTCAAG
* * * * * * *
32788 GAGTCTTTATGTCAAAAATCATACAGAACTGAGGCGAGGACCCAGAACGCGTTTTTAGCCAAAAA
259 GAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCG-GGGCCCGGAACGCGTTTTTAGCCAAAAA
32853 CC------G-T
323 CCGTGATGGTT
* **
32857 -G-ACACTATTTTGAATAAAATTTTGCAAAAACTGATCCC-AAAATTTTTTTTCTCAATTCTTTG
1 AGTACACGATTTTGGCTAAAATTTTGCAAAAACTGA-CCCGAAAATTTTTTTTCTCAATTCTTTG
* * * *
32919 CCACATTACTCAGAAAAAATATATAATTTAACGCCAAAAAGATTGAAGGGTTATTCACGCTTCTA
65 CCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGTTTTTCACGCTTCTA
* ** * * * *
32984 ATATCATTTTTTAATTTTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGGTCCA
130 ATATCGTTTTTCCATTTTTTTT-CCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCT
* * * * *
33049 CGTAAAAATAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTTGATGAATTTAGATAATTCAAG
194 CGTAAAAATAAATCCTTAAATCCAATGTAGCTGAGATTTGGTTCGATGAATATAGATAATTCAAG
* * *
33114 GAGTCTTTACACCAAAAATCATGCAAAACTGAGACGGGGCCCGGAACGCGTTTTTAGCAAAAAAC
259 GAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGGCCCGGAACGCGTTTTTAGCCAAAAAC
33179 CGTGATGGTT
324 CGTGATGGTT
* * * ** * * *
33189 AGTAAACGATTTTCGCTAAAATTTTGCAAAAACTTACTAGAAAAATTTTTCT-TCAATTTTTTGC
1 AGTACACGATTTTGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTTTCTCAATTCTTTGC
** * *
33253 CACAATACTCAGAAAAAATATATAATTCAACGTTAAAAATATTAAAGGGTTTTTCACACTTCTAA
66 CACAATACTCAGAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGTTTTTCACGCTTCTAA
* * * * *
33318 TATCGTTTTTCAATTTTTTTCCCGAATTAATTTCTGATTAAATCGAAACAAGATTCAAATGCTCG
131 TATCGTTTTTCCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
* * * * *
33383 TAAAAA-CAATCCTTAAACCCAATTTAACTGAGATTCGGTTCGATGAATATAGAT-ATGTCAAGG
196 TAAAAATAAATCCTTAAATCCAATGTAGCTGAGATTTGGTTCGATGAATATAGATAAT-TCAAGG
33446 AGTCTT
260 AGTCTT
33452 ATTTTGTTTC
Statistics
Matches: 1915, Mismatches: 275, Indels: 96
0.84 0.12 0.04
Matches are distributed among these distances:
322 23 0.01
323 108 0.06
324 1 0.00
325 70 0.04
326 135 0.07
327 184 0.10
328 183 0.10
329 230 0.12
330 75 0.04
331 435 0.23
332 171 0.09
333 241 0.13
334 59 0.03
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (333 bp):
AGTACACGATTTTGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTTTCTCAATTCTTTGC
CACAATACTCAGAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGTTTTTCACGCTTCTAA
TATCGTTTTTCCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
TAAAAATAAATCCTTAAATCCAATGTAGCTGAGATTTGGTTCGATGAATATAGATAATTCAAGGA
GTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGGCCCGGAACGCGTTTTTAGCCAAAAACCG
TGATGGTT
Found at i:32284 original size:660 final size:655
Alignment explanation
Indices: 30883--33438 Score: 3199
Period size: 660 Copynumber: 3.9 Consensus size: 655
30873 TCCTGGGAAA
* * * * *
30883 GTACACGATTTTGGCTAAAATTTTGCAAAATCTGACCCGAAATTTTTTTTCTTCAACTCCTTGCC
1 GTACACGATTTTGGCTAAAATTTTGCAAAAACTGACCCGAAA-ATTTTTTCCTCAATTCATTGCC
* * *
30948 ACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGGTTTTCACGCTTCAAAT
65 ACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAAT
* * *
31013 ATCGTTTTTCTATTTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
130 ATCGTTTTCCAATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * * * *
31078 AAAAATAAATCCTTAAATCCAATGTGGCTGAGACTTGGTTTGATGAATTTAGATAATTGAAGGAT
195 AAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGATTCGATGAATTTAGATAATTCAAGGAG
* * * * *
31143 TATTTACGCCAAAAATCATGCAAAACTGAGCCGGGCCCTGGAACGA-TTTTTTAGCCAAAAATCG
260 TCTTTACGCCAAAAATCATGCAAAACTGAGCGGGGCCC-AGAAC-ACGTTTTTAGCCAAAAACCG
*
31207 TGATGGTTAGTAAACGATTTTCGCTAAAATTTTGCAAAAACTGACCAG-AAATTTTTTTTTCAAT
323 TGATGGTTAGTAAACGATTTTCGCTAAAATTTTGCAAAAACTGACCAGAAAATTTTTTCTTCAAT
* * * *
31271 TCTTTGCCATAATACTCATAAAAAATATATAATTCAATGCCAAAAACATTGAAGGGTTTTTCACA
388 TCTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGTTTTTCACA
* * * *
31336 CTTCTAATATTGTTTTTCATTTTTTTTCCGAATTAATTTCTGATTAAATCGAAGCAAGATTTAGA
453 CTTCTAATATCGTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGA
* * ** * * * *
31401 T-ACTGTAAAAACAATCCTTAAATATAATGTAGCTGATATTTGGTTCGATCAATATAGATATTTC
518 TGCCCGTAAAAACAATCCTTAAATCCAATGTAACTGAGATTTGGTTCGATGAATATAGATATTTG
* * *
31465 AA-GAAGTCTTTACGCCAAAAATCATGCAAAACTAAGCCGGGGCCCGGAATGCGTTTTTAGCCAA
583 AAGGAA-TCTTTACGCCAAAAATCATGCCAAACTGAGCCGGGGCCCGGAACGCGTTTTTAGCCAA
31529 AAACCGTGAT
647 AAACC-TGAT
* * * **
31539 GGGTACACGATTTTTGCTAAAATTTTGCAAAAAATGACCCGAAAATTTTTTTCTCAATTCTAAGG
1 --GTACACGATTTTGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTCCTCAATTC-ATTG
* * * * *
31604 CCACAATACTCAGAAAAATTATATAAATCAACACCAAAAAAATTGAAGGATTTTTTACGCTTCTA
63 CCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTA
* * *
31669 ATATCGTTTTCCCA-TTTTTTTCCGAATTTATTTCTTATTAAATCGACACAAGATTCAGATGCTC
128 ATATCGTTTTCCAATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * * * *
31733 ATAAAAATAAATCCTTAAATCCAATGTTGTTGAGATTTGATTCGATGAATATAGATAATTTAAGG
193 GTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGATTCGATGAATTTAGATAATTCAAGG
* *
31798 AGTCTTTACGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCATAACACGTTTTTAG-GAAATAA
258 AGTCTTTACGCCAAAAATCATGCAAAACTGAG-CGGGG-CCCAGAACACGTTTTTAGCCAAA-AA
* * *
31862 CCGTGATGGTTAGTACACGA-TTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTTTC
320 CCGTGATGGTTAGTAAACGATTTTC-GCTAAAATTTTGCAAAAACTGACCAGAAAATTTTTTCT-
* ** * *
31926 TCAATTCTTTGCCACAATACTCTGAAAAAGCATATAATTCAACCCCATAAATATTGAAGGGTTTT
383 TCAATTCTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGTTTT
* * *
31991 TCACTCTTCTAATATCG-TTTTC-TTTTTTTTCCGATTTTATTTCTAATTAAATCGAAACAAGAT
448 TCACACTTCTAATATCGTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
* *
32054 TCAGATGCCCATAAAAACAAATCCTTAAATCCAATGTAACTGAAATTTGGTTCGATGAATATAGA
513 TCAGATGCCCGTAAAAAC-AATCCTTAAATCCAATGTAACTGAGATTTGGTTCGATGAATATAGA
* * * *
32119 TATTTGAAGGAATCTTGACGCCATAAATCATGCCAAACTGAGTCGGGGCCTTGGAACGCGTTTTT
577 TATTTGAAGGAATCTTTACGCCAAAAATCATGCCAAACTGAGCCGGGGCC-CGGAACGCGTTTTT
32184 AGCCAAAAACCTTGAT
641 AGCCAAAAACC-TGAT
* * *
32200 GACTACACGATTTTGGTTTAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCAATTCATTGC
1 G--TACACGATTTTGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTCCTCAATTCATTGC
* * * * *
32265 CACAATACTTAGAAAAATTATTTAATTCAACGCTAAAAAAATTGAAGGGTTTTTCACACTTCTAA
64 CACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAA
* * * * *
32330 TATCATTTTTCCGA--TTTTTTCTGATTTTATTTCTAATTAAATCGAAACAAGATTTAGATGCTC
129 TATC-GTTTTCCAATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
** *
32393 GTAAAAATAAATCCTTAAATCCAATGTATCTGAGATTTGATTCGATGAATTTAGGTAATTCAAGG
193 GTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGATTCGATGAATTTAGATAATTCAAGG
* * * * *
32458 AGTCTTTACG-CACAAAATCATACAAAACTGTGCCGGAGTCCAGAACGCGTTTTTAGCCAAAAAC
258 AGTCTTTACGCCA-AAAATCATGCAAAACTGAG-CGGGGCCCAGAACACGTTTTTAGCCAAAAAC
* * * * * *
32522 TGTGATGGTTAGTACACGATTTTGGCTAAAAATTTGCAAAAATCTAACCCGAAAATTTTTTCTTC
321 CGTGATGGTTAGTAAACGATTTTCGCTAAAATTTTGCAAAAA-CTGACCAGAAAATTTTTTCTTC
* *
32587 AATTCTTTGCCATAATACTCAGAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGTCTTTC
385 AATTCTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGTTTTTC
* * *
32652 ACGCTTCTAATATCGTTTTTCCAATTTTTTTT---AATTTATTTTTAATTAAATCGAAACAAGAT
450 ACACTTCTAATATCGTTTTT-C-ATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
* * ** * * * * *
32714 TCAGATGCTCGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGACTTGGTTTGATTAATTTTGA
513 TCAGATGCCCGTAAAAA-CAATCCTTAAATCCAATGTAACTGAGATTTGGTTCGATGAATATAGA
* * * * * * * *
32779 TAATTGAAGGAGTCTTTATGTCAAAAATCAT-ACAGAACTGAGGCGAGGACCCAGAACGCGTTTT
577 TATTTGAAGGAATCTTTACGCCAAAAATCATGCCA-AACTGAGCCG-GGGCCCGGAACGCGTTTT
32843 TAGCCAAAAACC-G-T
640 TAGCCAAAAACCTGAT
* ** * *
32857 G-ACACTATTTTGAATAAAATTTTGCAAAAACTGATCCC-AAAATTTTTTTTCTCAATTCTTTGC
1 GTACACGATTTTGGCTAAAATTTTGCAAAAACTGA-CCCGAAAA-TTTTTTCCTCAATTCATTGC
* * * *
32920 CACATTACTCAGAAAAAATATATAATTTAACGCCAAAAAGATTGAAGGGTTATTCACGCTTCTAA
64 CACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAA
* ** * * * *
32985 TATCATTTTTTAATTTTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGGTCCAC
129 TATCGTTTTCCAATTTTTTTT-CCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * * *
33050 GTAAAAATAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTTGATGAATTTAGATAATTCAAGG
193 GTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGATTCGATGAATTTAGATAATTCAAGG
* * * *
33115 AGTCTTTACACCAAAAATCATGCAAAACTGAGACGGGGCCCGGAACGCGTTTTTAGCAAAAAACC
258 AGTCTTTACGCCAAAAATCATGCAAAACTGAG-CGGGGCCCAGAACACGTTTTTAGCCAAAAACC
* * *
33180 GTGATGGTTAGTAAACGATTTTCGCTAAAATTTTGCAAAAACTTACTAGAAAAATTTTTCTTCAA
322 GTGATGGTTAGTAAACGATTTTCGCTAAAATTTTGCAAAAACTGACCAGAAAATTTTTTCTTCAA
* ** *
33245 TTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGTTAAAAATATTAAAGGGTTTTTCAC
387 TTCTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGTTTTTCAC
* *
33310 ACTTCTAATATCGTTTTTCAATTTTTTTCCCGAATTAATTTCTGATTAAATCGAAACAAGATTCA
452 ACTTCTAATATCGTTTTTC-ATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCA
* * * * *
33375 AATGCTCGTAAAAACAATCCTTAAACCCAATTTAACTGAGATTCGGTTCGATGAATATAGATAT
516 GATGCCCGTAAAAACAATCCTTAAATCCAATGTAACTGAGATTTGGTTCGATGAATATAGATAT
33439 GTCAAGGAGT
Statistics
Matches: 1640, Mismatches: 223, Indels: 71
0.85 0.12 0.04
Matches are distributed among these distances:
654 38 0.02
655 90 0.05
656 102 0.06
657 379 0.23
658 256 0.16
659 159 0.10
660 515 0.31
661 93 0.06
663 8 0.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (655 bp):
GTACACGATTTTGGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTCCTCAATTCATTGCCA
CAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATA
TCGTTTTCCAATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
AAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGATTCGATGAATTTAGATAATTCAAGGAGT
CTTTACGCCAAAAATCATGCAAAACTGAGCGGGGCCCAGAACACGTTTTTAGCCAAAAACCGTGA
TGGTTAGTAAACGATTTTCGCTAAAATTTTGCAAAAACTGACCAGAAAATTTTTTCTTCAATTCT
TTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGTTTTTCACACTT
CTAATATCGTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGC
CCGTAAAAACAATCCTTAAATCCAATGTAACTGAGATTTGGTTCGATGAATATAGATATTTGAAG
GAATCTTTACGCCAAAAATCATGCCAAACTGAGCCGGGGCCCGGAACGCGTTTTTAGCCAAAAAC
CTGAT
Found at i:37922 original size:49 final size:49
Alignment explanation
Indices: 37850--37980 Score: 253
Period size: 49 Copynumber: 2.7 Consensus size: 49
37840 AAAAAGATAC
*
37850 TGTACACTACTACATGATCTAATCAAATATGATCTAATCAACTTTTCTT
1 TGTACACTACTACATGATCTAATCACATATGATCTAATCAACTTTTCTT
37899 TGTACACTACTACATGATCTAATCACATATGATCTAATCAACTTTTCTT
1 TGTACACTACTACATGATCTAATCACATATGATCTAATCAACTTTTCTT
37948 TGTACACTACTACATGATCTAATCACATATGAT
1 TGTACACTACTACATGATCTAATCACATATGAT
37981 ATGTAAATAT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
49 81 1.00
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.37
Consensus pattern (49 bp):
TGTACACTACTACATGATCTAATCACATATGATCTAATCAACTTTTCTT
Found at i:44154 original size:15 final size:15
Alignment explanation
Indices: 44136--44165 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44126 TTCTCCCCGT
*
44136 CCTCCTCCTCCTCTG
1 CCTCCCCCTCCTCTG
44151 CCTCCCCCTCCTCTG
1 CCTCCCCCTCCTCTG
44166 ATGAACCCCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.63, G:0.07, T:0.30
Consensus pattern (15 bp):
CCTCCCCCTCCTCTG
Found at i:44235 original size:27 final size:26
Alignment explanation
Indices: 44208--44361 Score: 218
Period size: 27 Copynumber: 5.7 Consensus size: 26
44198 CACGTCCCCC
* *
44208 CTTCCTCCGCCTCTGCCTCTCCCGCCC
1 CTTCCTCCGCCTCCGCCTC-CCCGCCT
* * *
44235 CCTGCTCCGCCTCTGCCTCTCCCGCCT
1 CTTCCTCCGCCTCCGCCTC-CCCGCCT
44262 CTTCCTCCGCCTCCGCCTCCCCTGCCT
1 CTTCCTCCGCCTCCGCCTCCCC-GCCT
44289 CTTCCTCCGCCTCCGCCTCCCCTGCCT
1 CTTCCTCCGCCTCCGCCTCCCC-GCCT
44316 CTTCCTCCGCCTCCGCCTCCTCCGCCT
1 CTTCCTCCGCCTCCGCCTCC-CCGCCT
44343 CTTCCTCCGCCTCCGCCTC
1 CTTCCTCCGCCTCCGCCTC
44362 GTCCGCCGCC
Statistics
Matches: 119, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
26 3 0.03
27 114 0.96
28 2 0.02
ACGTcount: A:0.00, C:0.62, G:0.12, T:0.26
Consensus pattern (26 bp):
CTTCCTCCGCCTCCGCCTCCCCGCCT
Found at i:44261 original size:15 final size:15
Alignment explanation
Indices: 44214--44268 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
44204 CCCCCTTCCT
44214 CCGCCTCTGCCTCTC
1 CCGCCTCTGCCTCTC
44229 CCGCC-C--CCTGCT-
1 CCGCCTCTGCCT-CTC
44241 CCGCCTCTGCCTCTC
1 CCGCCTCTGCCTCTC
*
44256 CCGCCTCTTCCTC
1 CCGCCTCTGCCTC
44269 CGCCTCCGCC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 8 0.24
13 3 0.09
14 3 0.09
15 20 0.59
ACGTcount: A:0.00, C:0.62, G:0.13, T:0.25
Consensus pattern (15 bp):
CCGCCTCTGCCTCTC
Found at i:44289 original size:21 final size:21
Alignment explanation
Indices: 44270--44343 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 21
44260 CTCTTCCTCC
*
44270 GCCTCCGCCTCC-CCTGCCTCT
1 GCCTCCGCCTCCGCCT-CCCCT
*
44291 TCCTCCGCCTCCGCCTCCCCT
1 GCCTCCGCCTCCGCCTCCCCT
**
44312 GCCTCTTCCTCCGCCTCCGCCT
1 GCCTCCGCCTCCGCCTCC-CCT
44334 -CCTCCGCCTC
1 GCCTCCGCCTC
44344 TTCCTCCGCC
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 38 0.86
22 6 0.14
ACGTcount: A:0.00, C:0.64, G:0.12, T:0.24
Consensus pattern (21 bp):
GCCTCCGCCTCCGCCTCCCCT
Found at i:44335 original size:6 final size:6
Alignment explanation
Indices: 44265--44361 Score: 77
Period size: 6 Copynumber: 17.7 Consensus size: 6
44255 CCCGCCTCTT
**
44265 CCTCCG CCTCCG CCTCC- CCT--G CCTCTT CCTCCG CCTCCG CCTCC-
1 CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG
** **
44309 CCT--G CCTCTT CCTCCG CCTCCG CCT--- CCTCCG CCTCTT CCTCCG
1 CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG
44352 CCTCCG CCTC
1 CCTCCG CCTC
44362 GTCCGCCGCC
Statistics
Matches: 72, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
3 3 0.04
4 6 0.08
5 6 0.08
6 57 0.79
ACGTcount: A:0.00, C:0.64, G:0.11, T:0.25
Consensus pattern (6 bp):
CCTCCG
Done.