Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016461.1 Corchorus olitorius cultivar O-4 contig16494, 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: 51273
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:776 original size:316 final size:316
Alignment explanation
Indices: 1--1107 Score: 1438
Period size: 316 Copynumber: 3.4 Consensus size: 316
* ** ** *
1 GTACTAACCATCACAGTTTTTTTGCTAAAATCGCGTTTCGGAACCCCGGTTCAGTTTTTTATGA-
1 GTACTAACCATCAC-G-GTTTTTGCTAAAATCGCGTTTCGGGGCCCCGGTTCAGTTTTGCAAGAT
* * * *
65 TTTTAGAGCCAAGACTAATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATAAGATTT
64 TTTTGGTGCCAAGACTCATTCAAATATCTATATTCATCTAACCAAATCTCAGCCACA-AAGATTT
* *
130 AAAGATATATTTTTATGAGTATCTGAATTTTGTTTCGATTTAATTTGAAAGAATTCGAAAAAATT
128 AAAGATATA-TTTTACGAGTATCT-AATTTTGTTTCGATTTAA-TT------A---GAAATAATT
* *
195 TGAAAAATAATAATAGAAGCGTGAAAAGCCCTTGAATCCATTTGGCGTTGAATTATATATTTTTT
181 CGAAAAATAATAATAGAAGCGTGAAAAGCCCTTGAATCCTTTTGGCGTTGAATTATATATTTTTT
* * *** *
260 ATGAGTGTTGTGGCCAAAAATCATGAAAAACATTTTCGGGTCAATTTTTGCAAAATTTTAG-TCG
246 ATGAGTATTATGGCCAAAAATTGCGAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTTAGCT-G
324 AAACCGT
310 AAACCGT
* * *
331 GTACTAACCATCACAGTTTTTTCTAAAATCTCGTTTCGGGGCCCCGGTTCAGTGTTT-CAAGATT
1 GTACTAACCATCACGGTTTTTGCTAAAATCGCGTTTCGGGGCCCCGGTTCAGT-TTTGCAAGATT
* * * *
395 TTTGGTGCCAATACTCATGCTAATATCTATATTCCTCTAACCAAATCAT-AGCCACAAAAGATTT
65 TTTGGTGCCAAGACTCATTCAAATATCTATATTCATCTAACCAAATC-TCAGCCAC-AAAGATTT
*
459 AAAGATATATCTTTACGAGTATCATATTTTTGTTTCGATTTAATTAGAAATAATTCGAAAAATAA
128 AAAGATATAT-TTTACGAGTATC-TAATTTTGTTTCGATTTAATTAGAAATAATTCGAAAAATAA
*
524 TAATAGAAGCGTGAAAAGCCCTTGAATCCTTTTGGCGTTGAATTATATA-TTTTTATAAGTATTA
191 TAATAGAAGCGTGAAAAGCCCTTGAATCCTTTTGGCGTTGAATTATATATTTTTTATGAGTATTA
* * * *
588 TGGCCAAAAATTGCGAAAAATATTTTCGGATCAGTTTTTGCAAACTTTTTGCTGAAACCGT
256 TGGCCAAAAATTGCGAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTTAGCTGAAACCGT
** * *
649 GTACTAA-TGT-ACGGTTGTTGCTAAAATCGCGTTTCAGGGCCCCGGTTCAGTTTTGCAAGATTT
1 GTACTAACCATCACGGTTTTTGCTAAAATCGCGTTTCGGGGCCCCGGTTCAGTTTTGCAAGATTT
* *
712 TTGGTGCCAAGACTCATTCAAATATCTATATTCATCTAACCAAATCTCAGCCTCGAATGATTTAA
66 TTGGTGCCAAGACTCATTCAAATATCTATATTCATCTAACCAAATCTCAGCCAC-AAAGATTTAA
777 AGATATATTCTTACGAGTATCTTAATTTTGTTTCGATTTAATTAGAAATAATTCGAAAAAATTTG
130 AGATATATT-TTACGAGTATC-TAATTTTGTTTCGATTTAATTAGAAATAATTC----------G
842 AAAAATAATAATAGAAGCGTGAAAAGCCCTTGAATCCTTTTGGCGTTGAATTATATATTTTTTAT
183 AAAAATAATAATAGAAGCGTGAAAAGCCCTTGAATCCTTTTGGCGTTGAATTATATATTTTTTAT
*
907 GAGTATTATGGCCGAAAATTGCGAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTTAGCTGAAA
248 GAGTATTATGGCCAAAAATTGCGAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTTAGCTGAAA
972 CCGT
313 CCGT
* *
976 GTACTAAAACCATCACGGTTTTTGCTAAAATCACGTTTCGGGGCCCAGGTTCAGTTTTGCAAGAT
1 GTACT--AACCATCACGGTTTTTGCTAAAATCGCGTTTCGGGGCCCCGGTTCAGTTTTGCAAGAT
* *
1041 TTTTTGTGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCAC-AAGATTTA
64 TTTTGGTGCCAAGACTCATTCAAATATCTATATTCATCTAACCAAATCTCAGCCACAAAGATTTA
1105 AAG
129 AAG
1108 GAAAATTTTT
Statistics
Matches: 688, Mismatches: 64, Indels: 51
0.86 0.08 0.06
Matches are distributed among these distances:
315 5 0.01
316 150 0.22
317 1 0.00
318 70 0.10
319 66 0.10
322 1 0.00
326 58 0.08
327 75 0.11
328 39 0.06
329 105 0.15
330 18 0.03
331 100 0.15
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (316 bp):
GTACTAACCATCACGGTTTTTGCTAAAATCGCGTTTCGGGGCCCCGGTTCAGTTTTGCAAGATTT
TTGGTGCCAAGACTCATTCAAATATCTATATTCATCTAACCAAATCTCAGCCACAAAGATTTAAA
GATATATTTTACGAGTATCTAATTTTGTTTCGATTTAATTAGAAATAATTCGAAAAATAATAATA
GAAGCGTGAAAAGCCCTTGAATCCTTTTGGCGTTGAATTATATATTTTTTATGAGTATTATGGCC
AAAAATTGCGAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTTAGCTGAAACCGT
Found at i:1293 original size:226 final size:227
Alignment explanation
Indices: 899--1335 Score: 682
Period size: 226 Copynumber: 1.9 Consensus size: 227
889 GAATTATATA
* *
899 TTTTTTATGAGTATTATGGCCGAAAATTGCGAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTT
1 TTTTTTATGAGTATTATGCCCAAAAATTGCGAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTT
* *
964 AGCTGAAACCGTGTACTAAAACCATCACGGTTTTTGCTAAAATCACGTTTCGGGGCCCAGGTTCA
66 AGCCGAAACCGTGTACTAAAACCATCACGGTTTTTGCTAAAATCACGTTTCGGGGCCCAGATTCA
* *
1029 GTTTTGCAAGATTTTTTGTGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGC
131 GTTTTGCAAGATTTTTGGAGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGC
1094 CAC-AAGATTTAAAGGAAAATTTTTAGGTGAG
196 CACAAAGATTTAAAGGAAAATTTTTAGGTGAG
* *
1125 TTTTTTATGAGTATTGTGCCCAAAAATTGTGAAAAACATTCTT-GGGTCAGTTTTTGCAAAATTT
1 TTTTTTATGAGTATTATGCCCAAAAATTGCGAAAAACATT-TTCGGGTCAGTTTTTGCAAAATTT
* * * * * * *
1189 TAGCCGAAATCGTGTACTAACACCATCATGGTTTTTTGGTAAATTCGCGTTTCGGGGCCCCGATT
65 TAGCCGAAACCGTGTACTAAAACCATCACGG-TTTTTGCTAAAATCACGTTTCGGGGCCCAGATT
*
1254 CAGTTTTGCATGA-TTTTGGAGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCA
129 CAGTTTTGCAAGATTTTTGGAGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCA
1318 GCCACATAAGATTTAAAG
194 GCCACA-AAGATTTAAAG
1336 ATATATTTTT
Statistics
Matches: 191, Mismatches: 16, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
226 138 0.72
227 42 0.22
228 11 0.06
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (227 bp):
TTTTTTATGAGTATTATGCCCAAAAATTGCGAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTT
AGCCGAAACCGTGTACTAAAACCATCACGGTTTTTGCTAAAATCACGTTTCGGGGCCCAGATTCA
GTTTTGCAAGATTTTTGGAGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGC
CACAAAGATTTAAAGGAAAATTTTTAGGTGAG
Found at i:1799 original size:330 final size:330
Alignment explanation
Indices: 1126--2983 Score: 2865
Period size: 330 Copynumber: 5.6 Consensus size: 330
1116 TTAGGTGAGT
* * *
1126 TTTTTATGAGTATTGTGCCCAAAAATTGTGAAAAACATTCTT-GGGTCAGTTTTTGCAAAATTTT
1 TTTTTATGAGTATTGTGGCCAGAAATTGCGAAAAACATT-TTCGGGTCAGTTTTTGCAAAATTTT
* * * * *
1190 AGCCGAAATCGTGTACTAACACCATCATGGTTTTTTGGTAAATTCGCGTTTCGGGGCCCCGATTC
65 AGCCGAAACCGTGTACT-A-ACCATCACGG-TTTTTGCTAAAATCGCGTTTCGGGGCCCCGGTTC
* * *
1255 AGTTTTGCATGA-TTTTGGAGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAG
127 AGTTTTGCAAGATTTTTGGTGCCAAGACTCATTCAAATATCTATATTCATCTAACCAAATCTCAG
* *
1319 CCACATAAGATTTAAAGATATATTTTTACGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATA
192 CCACAAAAGATTTAAAGATATATCTTTACGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATA
*
1384 ATTCCAAAAAAAATTGAAAAATAATAATAGAAGCGTGAAAAGCCCTTGAATCCTTTTGGCGTTGA
257 ATT-CGAAAAAAATTGAAAAATAATAATAGAAGCGTGAAAAGCCCTTGAATCCTTTTGGCGTTGA
1449 ATTATATAT-
321 ATTATATATG
*
1458 TTTTTATGAGTATTATGGCC-GAAAATTGCGAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTT
1 TTTTTATGAGTATTGTGGCCAG-AAATTGCGAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTT
*
1522 AGCCGAAACCGTGTACTAACCATCACGGTTTTTGCTAAAATCGCGTTTCGGGACCCCGGTTCAGT
65 AGCCGAAACCGTGTACTAACCATCACGGTTTTTGCTAAAATCGCGTTTCGGGGCCCCGGTTCAGT
* * *
1587 TTTTCAAGATTTTTGGTGCCAATACTCATTCAAATATCTATATTCCTCTAACCAAATCTCAGCCA
130 TTTGCAAGATTTTTGGTGCCAAGACTCATTCAAATATCTATATTCATCTAACCAAATCTCAGCCA
* * *
1652 CAAAAAATTTAAAAATATATCTTTACGAGTATCTGAATTTAGTTTCGATTTAATTAGAAATAATT
195 CAAAAGATTTAAAGATATATCTTTACGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATAATT
1717 CGAAAAAAATTGAAAAATAATAATAGAAGCGTGAAAAGCCCTTGAATCCTTTTGGCGTTGAATTA
260 CGAAAAAAATTGAAAAATAATAATAGAAGCGTGAAAAGCCCTTGAATCCTTTTGGCGTTGAATTA
1782 TATATG
325 TATATG
* * * * *
1788 TTTTGATGAGTATTGTGGCCAGAAATTGCGAAATACATTTTGGGGTCAGTTTTCGTAAAATTTTA
1 TTTTTATGAGTATTGTGGCCAGAAATTGCGAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTTA
* * * *
1853 ACCGAAACTGTGTACTAACCATCACGGTTTTTGCTAAAATCCCGTTTCGGGGCCCCGTTTCAGTT
66 GCCGAAACCGTGTACTAACCATCACGGTTTTTGCTAAAATCGCGTTTCGGGGCCCCGGTTCAGTT
* * *
1918 TTGCAAGATTTTTGGTGCCGAGACTCATTCAAATCTCTATATTCATCTAACCAAATCTCAGCCAT
131 TTGCAAGATTTTTGGTGCCAAGACTCATTCAAATATCTATATTCATCTAACCAAATCTCAGCCAC
1983 AAAAGATTTAAAGATATATCTTTACGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATAATTC
196 AAAAGATTTAAAGATATATCTTTACGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATAATTC
*
2048 GAAAAAATTTGAAAAATAATAATAGAAGCGAT-AAAAGCCCTTGAATCCTTTTGGCGTTGAATTA
261 GAAAAAAATTGAAAAATAATAATAGAAGCG-TGAAAAGCCCTTGAATCCTTTTGGCGTTGAATTA
2112 TATATG
325 TATATG
* *
2118 -TTTTATGAGTATTGTGGCCAGAAATAGCAAAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTT
1 TTTTTATGAGTATTGTGGCCAGAAATTGC-GAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTT
* * * *
2182 AGCCTAAACCGTGTACTAACCATCACGATTTTTGCTAAAATTGCGTTTCGGGGCCCCGGTTCTGT
65 AGCCGAAACCGTGTACTAACCATCACGGTTTTTGCTAAAATCGCGTTTCGGGGCCCCGGTTCAGT
* *
2247 TTTGCAAGATTTTTGGTGCCAAGACTCATTCAAATATCTATATTGATCTAACCAAATCTCAGCGA
130 TTTGCAAGATTTTTGGTGCCAAGACTCATTCAAATATCTATATTCATCTAACCAAATCTCAGCCA
*
2312 CAAAAGATTTAAAGATATATCTTTACGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATTATT
195 CAAAAGATTTAAAGATATATCTTTACGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATAATT
* * *
2377 CGAAAAAAATTGAAAAATAGTAATAGAAGCGTGAAAAGCCCTTGAATCCTTTTGACGTTTAATTA
260 CGAAAAAAATTGAAAAATAATAATAGAAGCGTGAAAAGCCCTTGAATCCTTTTGGCGTTGAATTA
2442 TATATG
325 TATATG
* * * *
2448 -TTTTATGAGTATTTTGGCCAGAAATTGCAAAAAACATTTTCGGGTCAGTTTTCGTAAAATTTTA
1 TTTTTATGAGTATTGTGGCCAGAAATTGCGAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTTA
* * *
2512 ACCGAAACTGTGTACTAACCATCACGGTTTTTTGGTAAAATCGCGTTTCGGGGCCCCGGTTCAGT
66 GCCGAAACCGTGTACTAACCATCACGG-TTTTTGCTAAAATCGCGTTTCGGGGCCCCGGTTCAGT
** * *
2577 TTTGCATTATTTTTGGAGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCA
130 TTTGCAAGATTTTTGGTGCCAAGACTCATTCAAATATCTATATTCATCTAACCAAATCTCAGCCA
* * *
2642 CATAGGATTTAAAGATATAT-TTTTCGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATAATT
195 CAAAAGATTTAAAGATATATCTTTACGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATAATT
*
2706 CGAAAAAATTTGAAAAATAATAATAGAAGCGAT-AAAAGCCCTTGAATCCTTTTGGCGTTGAATT
260 CGAAAAAAATTGAAAAATAATAATAGAAGCG-TGAAAAGCCCTTGAATCCTTTTGGCGTTGAATT
2770 ATATAT-
324 ATATATG
* * * *
2776 TTTTTATGAGTATTGTGGCCAAAAATTGCGAAAAAATATTTTTGGGTCAGTTTTTGTAAAATTTT
1 TTTTTATGAGTATTGTGGCCAGAAATTGCG-AAAAACATTTTCGGGTCAGTTTTTGCAAAATTTT
* * * *
2841 AGCCGAAACCGTGTACTAACCATCACTGTTTTTGCTAAAATCGCGTTTCTGGGCCCCGGTGCAAT
65 AGCCGAAACCGTGTACTAACCATCACGGTTTTTGCTAAAATCGCGTTTCGGGGCCCCGGTTCAGT
* * *
2906 TTTGCAAGATTTTTGGTGCCAAGACTCATT-ATAATATCTATATTCATCTAACTAAATTTCAGAC
130 TTTGCAAGATTTTTGGTGCCAAGACTCATTCA-AATATCTATATTCATCTAACCAAATCTCAGCC
*
2970 ACATAAGATTTAAA
194 ACAAAAGATTTAAA
2984 AATAAATTTT
Statistics
Matches: 1400, Mismatches: 113, Indels: 29
0.91 0.07 0.02
Matches are distributed among these distances:
328 1 0.00
329 427 0.31
330 895 0.64
331 5 0.00
332 72 0.05
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (330 bp):
TTTTTATGAGTATTGTGGCCAGAAATTGCGAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTTA
GCCGAAACCGTGTACTAACCATCACGGTTTTTGCTAAAATCGCGTTTCGGGGCCCCGGTTCAGTT
TTGCAAGATTTTTGGTGCCAAGACTCATTCAAATATCTATATTCATCTAACCAAATCTCAGCCAC
AAAAGATTTAAAGATATATCTTTACGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATAATTC
GAAAAAAATTGAAAAATAATAATAGAAGCGTGAAAAGCCCTTGAATCCTTTTGGCGTTGAATTAT
ATATG
Found at i:2773 original size:659 final size:655
Alignment explanation
Indices: 1127--2987 Score: 2987
Period size: 659 Copynumber: 2.8 Consensus size: 655
1117 TAGGTGAGTT
* * * * * *
1127 TTTTATGAGTATTGTGCCCAAAAATTGTGAAAAACATTCTTGGGTCAGTTTTTGCAAAATTTTAG
1 TTTTATGAGTATTGTGGCCAGAAATTGCGAAAAACATT-TTGGGTCAGTTTTCGTAAAATTTTAA
* *
1192 CCGAAA-TCGTGTACTAACACCATCATGGTTTTTTGGTAAATTCGCGTTTCGGGGCCCCGATTCA
65 CCGAAACT-GTGTACT-A-ACCATCACGGTTTTTTGGTAAAATCGCGTTTCGGGGCCCCGATTCA
1256 GTTTTGCATGA-TTTTGGAGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGC
127 GTTTTGCATGATTTTTGGAGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGC
1320 CACATAAGATTTAAAGATATATTTTTACGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATAA
192 CACATAAGATTTAAAGATATATTTTT-CGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATAA
* *
1385 TTCCAAAAAAAATTGAAAAATAATAATAGAAGCG-TGAAAAGCCCTTGAATCCTTTTGGCGTTGA
256 TT-CGAAAAAATTTGAAAAATAATAATAGAAGCGAT-AAAAGCCCTTGAATCCTTTTGGCGTTGA
* *
1449 ATTATATATTTTTTATGAGTATTATGGCC-GAAAATTGCGAAAAACATTTTCGGGTCAGTTTTTG
319 ATTATATATTTTTTATGAGTATTGTGGCCAG-AAATTGCAAAAAACATTTTCGGGTCAGTTTTTG
*
1513 CAAAATTTTAGCCGAAACCGTGTACTAACCATCACGGTTTTTGCTAAAATCGCGTTTCGGGACCC
383 CAAAATTTTAGCCGAAACCGTGTACTAACCATCAC-GTTTTTGCTAAAATCGCGTTTCGGGGCCC
* * *
1578 CGGTTCAGTTTTTCAAGATTTTTGGTGCCAATACTCATTCAAATATCTATATTCCTCTAACCAAA
447 CGGTTCAGTTTTGCAAGATTTTTGGTGCCAAGACTCATTCAAATATCTATATTCATCTAACCAAA
*
1643 TCTCAGCCACAAAAAATTTAAAAATATATCTTTACGAGTATCTGAATTTAGTTTCGATTTAATTA
512 TCTCAG-CACAAAAGATTTAAAAATATATCTTTACGAGTATCTGAATTTAGTTTCGATTTAATTA
*
1708 GAAATAATTCGAAAAAAATTGAAAAATAATAATAGAAGCGTGAAAAGCCCTTGAATCCTTTTGGC
576 GAAATAATTCGAAAAAAATTGAAAAATAATAATAGAAGCGTGAAAAGCCCTTGAATCCTTTTGAC
1773 GTTGAATTATATATG
641 GTTGAATTATATATG
*
1788 TTTTGATGAGTATTGTGGCCAGAAATTGCGAAATACATTTTGGGGTCAGTTTTCGTAAAATTTTA
1 TTTT-ATGAGTATTGTGGCCAGAAATTGCGAAAAACATTTT-GGGTCAGTTTTCGTAAAATTTTA
* * *
1853 ACCGAAACTGTGTACTAACCATCACGG-TTTTTGCTAAAATCCCGTTTCGGGGCCCCGTTTCAGT
64 ACCGAAACTGTGTACTAACCATCACGGTTTTTTGGTAAAATCGCGTTTCGGGGCCCCGATTCAGT
* * * * *
1917 TTTGCAAGATTTTTGGTGCCGAGACTCATTCAAATCTCTATATTCATCTAACCAAATCTCAGCCA
129 TTTGCATGATTTTTGGAGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCA
* * *
1982 TAAAAGATTTAAAGATATATCTTTACGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATAATT
194 CATAAGATTTAAAGATATAT-TTTTCGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATAATT
2047 CGAAAAAATTTGAAAAATAATAATAGAAGCGATAAAAGCCCTTGAATCCTTTTGGCGTTGAATTA
258 CGAAAAAATTTGAAAAATAATAATAGAAGCGATAAAAGCCCTTGAATCCTTTTGGCGTTGAATTA
* *
2112 TATATGTTTTATGAGTATTGTGGCCAGAAATAGCAAAAAAACATTTTCGGGTCAGTTTTTGCAAA
323 TATATTTTTTATGAGTATTGTGGCCAGAAATTGC-AAAAAACATTTTCGGGTCAGTTTTTGCAAA
* *
2177 ATTTTAGCCTAAACCGTGTACTAACCATCACGATTTTTGCTAAAATTGCGTTTCGGGGCCCCGGT
387 ATTTTAGCCGAAACCGTGTACTAACCATCACG-TTTTTGCTAAAATCGCGTTTCGGGGCCCCGGT
* *
2242 TCTGTTTTGCAAGATTTTTGGTGCCAAGACTCATTCAAATATCTATATTGATCTAACCAAATCTC
451 TCAGTTTTGCAAGATTTTTGGTGCCAAGACTCATTCAAATATCTATATTCATCTAACCAAATCTC
* *
2307 AGCGACAAAAGATTTAAAGATATATCTTTACGAGTATCTGAATTTTGTTTCGATTTAATTAGAAA
516 AGC-ACAAAAGATTTAAAAATATATCTTTACGAGTATCTGAATTTAGTTTCGATTTAATTAGAAA
* * *
2372 TTATTCGAAAAAAATTGAAAAATAGTAATAGAAGCGTGAAAAGCCCTTGAATCCTTTTGACGTTT
580 TAATTCGAAAAAAATTGAAAAATAATAATAGAAGCGTGAAAAGCCCTTGAATCCTTTTGACGTTG
2437 AATTATATATG
645 AATTATATATG
* *
2448 TTTTATGAGTATTTTGGCCAGAAATTGCAAAAAACATTTTCGGGTCAGTTTTCGTAAAATTTTAA
1 TTTTATGAGTATTGTGGCCAGAAATTGCGAAAAACATTTT-GGGTCAGTTTTCGTAAAATTTTAA
*
2513 CCGAAACTGTGTACTAACCATCACGGTTTTTTGGTAAAATCGCGTTTCGGGGCCCCGGTTCAGTT
65 CCGAAACTGTGTACTAACCATCACGGTTTTTTGGTAAAATCGCGTTTCGGGGCCCCGATTCAGTT
*
2578 TTGCATTATTTTTGGAGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCAC
130 TTGCATGATTTTTGGAGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCAC
*
2643 ATAGGATTTAAAGATATATTTTTCGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATAATTCG
195 ATAAGATTTAAAGATATATTTTTCGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATAATTCG
2708 AAAAAATTTGAAAAATAATAATAGAAGCGATAAAAGCCCTTGAATCCTTTTGGCGTTGAATTATA
260 AAAAAATTTGAAAAATAATAATAGAAGCGATAAAAGCCCTTGAATCCTTTTGGCGTTGAATTATA
* * * *
2773 TATTTTTTATGAGTATTGTGGCCAAAAATTGCGAAAAAATATTTTTGGGTCAGTTTTTGTAAAAT
325 TATTTTTTATGAGTATTGTGGCCAGAAATTGC-AAAAAACATTTTCGGGTCAGTTTTTGCAAAAT
* *
2838 TTTAGCCGAAACCGTGTACTAACCATCACTGTTTTTGCTAAAATCGCGTTTCTGGGCCCCGGTGC
389 TTTAGCCGAAACCGTGTACTAACCATCAC-GTTTTTGCTAAAATCGCGTTTCGGGGCCCCGGTTC
* * *
2903 AATTTTGCAAGATTTTTGGTGCCAAGACTCATT-ATAATATCTATATTCATCTAACTAAATTTCA
453 AGTTTTGCAAGATTTTTGGTGCCAAGACTCATTCA-AATATCTATATTCATCTAACCAAATCTCA
*
2967 GACACATAAGATTTAAAAATA
517 G-CACAAAAGATTTAAAAATA
2988 AATTTTTAGG
Statistics
Matches: 1110, Mismatches: 76, Indels: 30
0.91 0.06 0.02
Matches are distributed among these distances:
658 1 0.00
659 517 0.47
660 517 0.47
661 10 0.01
662 64 0.06
663 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (655 bp):
TTTTATGAGTATTGTGGCCAGAAATTGCGAAAAACATTTTGGGTCAGTTTTCGTAAAATTTTAAC
CGAAACTGTGTACTAACCATCACGGTTTTTTGGTAAAATCGCGTTTCGGGGCCCCGATTCAGTTT
TGCATGATTTTTGGAGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACA
TAAGATTTAAAGATATATTTTTCGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATAATTCGA
AAAAATTTGAAAAATAATAATAGAAGCGATAAAAGCCCTTGAATCCTTTTGGCGTTGAATTATAT
ATTTTTTATGAGTATTGTGGCCAGAAATTGCAAAAAACATTTTCGGGTCAGTTTTTGCAAAATTT
TAGCCGAAACCGTGTACTAACCATCACGTTTTTGCTAAAATCGCGTTTCGGGGCCCCGGTTCAGT
TTTGCAAGATTTTTGGTGCCAAGACTCATTCAAATATCTATATTCATCTAACCAAATCTCAGCAC
AAAAGATTTAAAAATATATCTTTACGAGTATCTGAATTTAGTTTCGATTTAATTAGAAATAATTC
GAAAAAAATTGAAAAATAATAATAGAAGCGTGAAAAGCCCTTGAATCCTTTTGACGTTGAATTAT
ATATG
Found at i:3171 original size:227 final size:227
Alignment explanation
Indices: 2776--3210 Score: 615
Period size: 227 Copynumber: 1.9 Consensus size: 227
2766 AATTATATAT
* * * * *
2776 TTTTTATGAGTATTGTGGCCAAAAATTGCGAAAAAATATTTTTGGGTCAGTTTTTGTAAAATTTT
1 TTTTTATCAGTATTGTGCCCAAAAATTGCGAAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTT
* * *
2841 AGCCGAAACCGTGTACTAACCATCACTGTTTTTGCTAAAATCGCGTTTCTGGGCCCCGGTGCAAT
66 AGCCGAAACCATGTACTAACCATCACGGTTTTTGCTAAAATCGCGTTTCGGGGCCCCGGTGCAAT
* *
2906 TTTGCAAGATTTTTGGTGCCAAGACTCATTATAATATCTATATTCATCTAA-CTAAATTTCAGAC
131 TTTGCAAGATTTTTGGAGCCAAGACTCATTATAATATCTATATTCATCTAATC-AAATCTCAGAC
2970 ACATAAGATTTAAAAATAAATTTTTAGGTGAGA
195 ACATAAGATTTAAAAATAAATTTTTAGGTGAGA
* * *
3003 TTTTTATCAGTATTGTGCCCAAAATTTGTG-AAAAACATTTTCGGGTCATTTTTTGCAAAATTTT
1 TTTTTATCAGTATTGTGCCCAAAAATTGCGAAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTT
* * * * * * *
3067 AGCTGAAATCATGTATTAACCATCACGGTTTTTTGGTAAAATCGCGTTTCGGGGCCCCTGTTCAG
66 AGCCGAAACCATGTACTAACCATCACGG-TTTTTGCTAAAATCGCGTTTCGGGGCCCCGGTGCAA
** *
3132 TTTTGCATTATTTTTGGAGCCAAGACTCATTGA-AATATCTATATTCATCTAATCAAATCTCAGC
130 TTTTGCAAGATTTTTGGAGCCAAGACTCATT-ATAATATCTATATTCATCTAATCAAATCTCAGA
3196 CACATAAGATTTAAA
194 CACATAAGATTTAAA
3211 GATATATTCT
Statistics
Matches: 182, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
226 53 0.29
227 127 0.70
228 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (227 bp):
TTTTTATCAGTATTGTGCCCAAAAATTGCGAAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTT
AGCCGAAACCATGTACTAACCATCACGGTTTTTGCTAAAATCGCGTTTCGGGGCCCCGGTGCAAT
TTTGCAAGATTTTTGGAGCCAAGACTCATTATAATATCTATATTCATCTAATCAAATCTCAGACA
CATAAGATTTAAAAATAAATTTTTAGGTGAGA
Found at i:3602 original size:542 final size:547
Alignment explanation
Indices: 2448--3846 Score: 2095
Period size: 542 Copynumber: 2.5 Consensus size: 547
2438 ATTATATATG
* * ** * *
2448 TTTTATGAGTATTTTGGCCAGAAA-TTGCAAAAAACATTTTCGGGTCAGTTTTCGTAAAATTTTA
1 TTTTATGAGTATTGTGCCCA-AAATTTGTGAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTTA
*
2512 ACCGAAA-CTGTGTACTAACCATCACGGTTTTTTGGTAAAATCGCGTTTCGGGGCCCCGGTTCAG
65 GCCGAAATC-GTGTACTAACCATCACGGTTTTTTGGTAAAATCGCGTTTCGGGGCCCCGGTTCAG
2576 TTTTGCATTATTTTTGGAGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCC
129 TTTTGCATTATTTTTGGAGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCC
*
2641 ACATAGGATTTAAAGATATATTTT-TCGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATAAT
194 ACATAAGATTTAAAGATATATTTTAT-GAGTATCTGAATTTTGTTTCGATTTAATTAGAAATAAT
*
2705 TCGAAAAAATTTGAAAAATAATAATAGAAGCGAT-AAAAGCCCTTGAATCCTTTTGGCGTTGAAT
258 TCGAAAAAATTTGAAAAATAATAATAGAAGCG-TGAAAAGCCCATGAATCCTTTTGGCGTTGAAT
* * *
2769 TATATATTTTTTATGAGTATTGTGGCCAAAAATTGCGAAAAAATATTTTTGGGTCAGTTTTTGTA
322 TATATATTTTTTATGAGTATTGTGGCC----A---CGAAAAAATATTTTCGAGTCAGTTTTTGCA
* *
2834 AAATTTTAGCCGAAACCGTGTACTAACCATCACTGTTTTTGCTAAAATCGCGTTTCTGGGCCCCG
380 AAATTTTAACCGAAACCGTG-A-TAACCATCACGGTTTTTGCTAAAATCGCGTTTCTGGGCCCCG
*
2899 GTGCAATTTTGCAAGATTTTTGGTGCCAAGACTCATTATAATATCTATATTCATCTAACTAAATT
443 GTGCAATTTTGCAAGATTTTTGGTGCCAAGACTCATTATAATATCTATATTCATCTAACAAAATT
2964 TCAGACACATAAGATTTAAAAATAAATTTTTAGGTGAGAT
508 TCAGACACATAAGATTTAAAAATAAATTTTTAGGTGAGAT
* *
3004 TTTTATCAGTATTGTGCCCAAAATTTGTGAAAAACATTTTCGGGTCATTTTTTGCAAAATTTTAG
1 TTTTATGAGTATTGTGCCCAAAATTTGTGAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTTAG
* * * *
3069 CTGAAATCATGTATTAACCATCACGGTTTTTTGGTAAAATCGCGTTTCGGGGCCCCTGTTCAGTT
66 CCGAAATCGTGTACTAACCATCACGGTTTTTTGGTAAAATCGCGTTTCGGGGCCCCGGTTCAGTT
*
3134 TTGCATTATTTTTGGAGCCAAGACTCATTGAAATATCTATATTCATCTAATCAAATCTCAGCCAC
131 TTGCATTATTTTTGGAGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCAC
*
3199 ATAAGATTTAAAGATATATTCTTATGAGTATATGAATTTTGTTTCGATTTAATTAGAAATAATTC
196 ATAAGATTTAAAGATATATT-TTATGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATAATTC
* *
3264 GAACAAATTTGAAAAATAATAATAGAAGCGTGAAAAGGCCATGAATCCTTTTGGCGTTGAATTAT
260 GAAAAAATTTGAAAAATAATAATAGAAGCGTGAAAAGCCCATGAATCCTTTTGGCGTTGAATTAT
3329 ATATTTTTTATGAGTATTGTGG-C-CG-AAAAA-ATTTTCGAGTCAGTTTTTGCAAAATTTTAAC
325 ATATTTTTTATGAGTATTGTGGCCACGAAAAAATATTTTCGAGTCAGTTTTTGCAAAATTTTAAC
* * * *
3390 CGAAACCGTG-T-ACCATTACGGTTTTTGCTAAAATCGCGTTT-TGGGGTCCCGGTTCAGTTTTG
390 CGAAACCGTGATAACCATCACGGTTTTTGCTAAAATCGCGTTTCT-GGGCCCCGGTGCAATTTTG
* *
3452 CAAGATTTTTTGTGCCAAGACTCATTGA-AATATCTATATTCATCTAACAAAATTTCAGCCACAT
454 CAAGATTTTTGGTGCCAAGACTCATT-ATAATATCTATATTCATCTAACAAAATTTCAGACACAT
* *
3516 AAGATTTAAAGAA-AAATTTTTAGTTGAGTT
518 AAGATTTAAA-AATAAATTTTTAGGTGAGAT
* *
3546 TTTTATGAGTATTGTGCCCAAAATTTGTGAAAAGCATTTTCGGGTCAGTTTTTGCAATATTTTAG
1 TTTTATGAGTATTGTGCCCAAAATTTGTGAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTTAG
* *
3611 CCGAAATCGTGTACTAACCATCATGGTTTTTTGGTAAAATCGCGTTTCGGTGCCCCGGTTCAGTT
66 CCGAAATCGTGTACTAACCATCACGGTTTTTTGGTAAAATCGCGTTTCGGGGCCCCGGTTCAGTT
* * *
3676 TTGCATGATTTTTGGAGCCAAGACTCATTGAAATATCTATAGTCATCTAACCAAATCTCAGCAAC
131 TTGCATTATTTTTGGAGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCAC
* * * * *
3741 ATAATATTTAAAGATATGTTTTCACGAGTATCTAAATTTTGTTTCGATTTATTTAGAAAGTAATT
196 ATAAGATTTAAAGATATATTTT-ATGAGTATCTGAATTTTGTTTCGATTTAATTAGAAA-TAATT
* * **
3806 AGAAAAAACTTGAAAAATAATAATAGAAAAGTGAAAAGCCC
259 CGAAAAAATTTGAAAAATAATAATAGAAGCGTGAAAAGCCC
3847 TTCGATTCAT
Statistics
Matches: 774, Mismatches: 59, Indels: 33
0.89 0.07 0.04
Matches are distributed among these distances:
541 3 0.00
542 359 0.46
543 44 0.06
546 37 0.05
547 5 0.01
548 2 0.00
555 3 0.00
556 196 0.25
557 124 0.16
558 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (547 bp):
TTTTATGAGTATTGTGCCCAAAATTTGTGAAAAACATTTTCGGGTCAGTTTTTGCAAAATTTTAG
CCGAAATCGTGTACTAACCATCACGGTTTTTTGGTAAAATCGCGTTTCGGGGCCCCGGTTCAGTT
TTGCATTATTTTTGGAGCCAAGACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCAC
ATAAGATTTAAAGATATATTTTATGAGTATCTGAATTTTGTTTCGATTTAATTAGAAATAATTCG
AAAAAATTTGAAAAATAATAATAGAAGCGTGAAAAGCCCATGAATCCTTTTGGCGTTGAATTATA
TATTTTTTATGAGTATTGTGGCCACGAAAAAATATTTTCGAGTCAGTTTTTGCAAAATTTTAACC
GAAACCGTGATAACCATCACGGTTTTTGCTAAAATCGCGTTTCTGGGCCCCGGTGCAATTTTGCA
AGATTTTTGGTGCCAAGACTCATTATAATATCTATATTCATCTAACAAAATTTCAGACACATAAG
ATTTAAAAATAAATTTTTAGGTGAGAT
Found at i:4586 original size:332 final size:332
Alignment explanation
Indices: 3976--4918 Score: 1292
Period size: 334 Copynumber: 2.8 Consensus size: 332
3966 GCTCAGTTTT
* * *
3976 GATTTTTGATG-CAAAAAATCACT-AACATATC-ATTATTCATCTAACCAAATCTTAGCCACATA
1 GATTTTTGATGAC-AAAACTCATTGAA-ATATCTA-TATTCATCTAACCAAATCTCAGCCACATA
*
4038 AGATTTAAAGATATGTTTTTACGAATATCTGAATTTTGTTTCGATTTAATTACAAAGTAATT---
63 AGATTTAAAGATATGTTTTTACGAGTATCTGAATTTTGTTTCGATTTAATTAC-AAGTAATTAAA
*
4100 AAAAAATTGAAAAATATTAATAGAAGAGTGAAAAGCCCTTCAATCCTTTTGGCATTGAATTATAT
127 AAAAAATTGAAAAATAATAATAGAAGAGTGAAAAGCCCTTCAATCCTTTTGGCATTGAATTATAT
*
4165 ATTTTTTATGAGTATTGTGGCCAAAATTTGCGAAAAACATTTTCTCGTCAGTTTTTGCAAAATTT
192 ATTTTTTATGAGTATTGTGGCCAAAAATTGCGAAAAACATTTTCTCGTCAGTTTTTGCAAAATTT
* * * *
4230 TAGCCGAAACTGTGTACTAACCATCACGG-TTCTTGGCTAAAATCGCGTTTCGGGGCCCCGGTTT
257 TAGCCGAAACCGTGTACCAACCATCACGGTTTCTTGGCTAAAATCGCGTTTCCGGGCCCCGATTT
4294 -AGTTTTGCAA
322 AAGTTTTGCAA
* *
4304 GATTTTTGATGCCACGAA-TCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATAAG
1 GATTTTTGATGACA-AAACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATAAG
* * *
4368 ATTTAAAGATATGTTTTTACGAGTATCTGATTTTTGTTTTGATTTAATTAGAATGTAATTACAAA
65 ATTTAAAGATATGTTTTTACGAGTATCTGAATTTTGTTTCGATTTAATTACAA-GTAATTA-AAA
* * * *
4433 AAAAATTGAAAAATAATAAAAGAAGAGTGAAAAGCCCTTCAATCCTTTTGGCGTTAAATTCTATA
128 AAAAATTGAAAAATAATAATAGAAGAGTGAAAAGCCCTTCAATCCTTTTGGCATTGAATTATATA
* * *
4498 TTTTTCATGAGTATTGTGGCCAAAAATAGCGAAAAACATTTTCTCGTTAGTTTTTGCAAAATTTT
193 TTTTTTATGAGTATTGTGGCCAAAAATTGCGAAAAACATTTTCTCGTCAGTTTTTGCAAAATTTT
** * * * * *
4563 AGCAAAAACCGTTTACCAACCATCACGGTTTTTTTGCTAAAATCGTGTTTCCGGGTCCCGATTTA
258 AGCCGAAACCGTGTACCAACCATCACGGTTTCTTGGCTAAAATCGCGTTTCCGGGCCCCGATTTA
4628 AGTTTTGCAA
323 AGTTTTGCAA
* * * *
4638 GATTTTTGGTGACAAAACTCATTGAAATATCTATATTTATCTAATCAAATCTCAGCCACATAATA
1 GATTTTTGATGACAAAACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATAAGA
* * * * *
4703 TTTAAAAAAATGTTTTTACGAGTATCTGAATTTTGTTTCAATTTAATTATAAATAATTAGAAAAA
66 TTTAAAGATATGTTTTTACGAGTATCTGAATTTTGTTTCGATTTAATTACAAGTAATT--AAAAA
* * * *
4768 AAAATTGAAAAATAATAATAGAAGCGTTATAAGCCCTTCAATCATTTTGGCATTGAATTATATAT
129 AAAATTGAAAAATAATAATAGAAGAGTGAAAAGCCCTTCAATCCTTTTGGCATTGAATTATATAT
* * * **
4833 TTTTTATGAGTAATGTGGTCAAAAATTGCAAAAAAAAACATTTTCGGGTCAGTTTTTGCAAAATT
194 TTTTTATGAGTATTGTGGCCAAAAATTGC---GAAAAACATTTTCTCGTCAGTTTTTGCAAAATT
4898 TTAGCCGAAACCGTGTACCAA
256 TTAGCCGAAACCGTGTACCAA
4919 ATCTCAGCCA
Statistics
Matches: 539, Mismatches: 59, Indels: 25
0.87 0.09 0.04
Matches are distributed among these distances:
327 2 0.00
328 104 0.19
329 6 0.01
332 145 0.27
333 36 0.07
334 198 0.37
335 1 0.00
337 47 0.09
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (332 bp):
GATTTTTGATGACAAAACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATAAGA
TTTAAAGATATGTTTTTACGAGTATCTGAATTTTGTTTCGATTTAATTACAAGTAATTAAAAAAA
AATTGAAAAATAATAATAGAAGAGTGAAAAGCCCTTCAATCCTTTTGGCATTGAATTATATATTT
TTTATGAGTATTGTGGCCAAAAATTGCGAAAAACATTTTCTCGTCAGTTTTTGCAAAATTTTAGC
CGAAACCGTGTACCAACCATCACGGTTTCTTGGCTAAAATCGCGTTTCCGGGCCCCGATTTAAGT
TTTGCAA
Found at i:6248 original size:336 final size:328
Alignment explanation
Indices: 4914--6675 Score: 2196
Period size: 327 Copynumber: 5.3 Consensus size: 328
4904 GAAACCGTGT
* * *
4914 ACCAAATCTCAGCCACAAAAGATTTAAAGATATATCTTTACAAGTATCTGAATTTTGTTTCGATT
1 ACCAAATCTCAGCCACATAAGATTTAAAGATATATTTTTACGAGTATCTGAATTTTGTTTCGATT
* *
4979 TAATTAGAAA-TAATTCGAAAAAAATTGAAAAATAATAATAGAAGCGTGAAAA-CCCTTAAATCC
66 TAATTAGAAAGTAATTAG-AAAAAATTGAAAAATAATAATAGAAGCGTGAAAAGCCCTTCAATCC
*
5042 TTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGACCAAAAATTGCGAAAAATAAATTCTC
130 TTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGCG-AAAA-AAATT-TC
* * * *
5107 GTGTCAGTTTTTGCAAAATTTTAGCTGAAGTCGTGTACTAACCATCGCGGTTTTTGCTAAAATCG
192 GGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGCTAAAATCG
* * *
5172 TGTTTCAGGGCCCCGGTTCAGTTTTGCAAAATTTTTGGTGCCAAGACTCATTCAAATATCTATAT
257 CGTTTCAGGGCCCCGGTTCAGTTTTGCAAGATTTTTGGTGCCAAGACTCATTGAAATATCTATAT
5237 TCATCTA
322 TCATCTA
* *
5244 ACCAAATCTCAGCCACATAAGATTTAAAGATATATTTTTACGAGTATCTTAATTTGGTTTCGATT
1 ACCAAATCTCAGCCACATAAGATTTAAAGATATATTTTTACGAGTATCTGAATTTTGTTTCGATT
* * *
5309 TAATTAG-AAGTAATTAGAAAAATTTG-AAAATAATAATAGAAGCGTGAAATGCCCTTGAATCCT
66 TAATTAGAAAGTAATTAGAAAAAATTGAAAAATAATAATAGAAGCGTGAAAAGCCCTTCAATCCT
* * * *
5372 TTTGGCGTTGAATTATATATTTTTTATGAGTATTATTGTCAAAAATTGCGAAAAACATTTTCGGG
131 TTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGCGAAAAA-AATTTCGGG
* * *
5437 TCAGTTTTTGCAAAATTTTAGCCGAAACCGTTTACTAACTATCACGGTTTTTGCTAAAATCGCGT
195 TCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGCTAAAATCGCGT
*
5502 TTCAGGGCCCCGGTTCAGTTTTGCAAGATTTTTGGTGCCAAGACTCATTCAAATATCTATATTCA
260 TTCAGGGCCCCGGTTCAGTTTTGCAAGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCA
5567 TCTA
325 TCTA
*
5571 ACCAAATCTCAGCCACGA-AAGATTTAAAGATAT-TATCTTACGAGTATCTGAATTTTGTTTCGA
1 ACCAAATCTCAGCCAC-ATAAGATTTAAAGATATAT-TTTTACGAGTATCTGAATTTTGTTTCGA
* * * *
5634 TTTAATTAGAAA-TAATTCGAAAATATTTGAAAAACAATAATAGAAGCGTGAAAAGCCCTTGAAT
64 TTTAATTAGAAAGTAATTAGAAAA-AATTGAAAAATAATAATAGAAGCGTGAAAAGCCCTTCAAT
* * * * *
5698 ACTTTTGTCGTTGAATTATATACTTTTTTATGAGTGTTGTGACCAAAAATTGCGAAAAATATTTT
128 CCTTTTGGCGTTGAATTATATA-TTTTTTATGAGTATTGTGGCCAAAAATTGCGAAAAA-AATTT
* * * * *
5763 CGGATCAGTTTTTGCAAAATTTTAGCTGAGACCGTGTACTAACCATCACGATTTTTTGCTAAAAT
191 CGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACG-GTTTTTGCTAAAAT
* *
5828 CGCGTTTCGGGGCCCCGGTTCAGTTTTGCAAGATTTATGGTGCCAAGACTCATTGAAATATCTAT
255 CGCGTTTCAGGGCCCCGGTTCAGTTTTGCAAGATTTTTGGTGCCAAGACTCATTGAAATATCTAT
5893 ATTCATCTA
320 ATTCATCTA
* *
5902 ACCAAATCTCAGCCACATAAGATTTGAAGATATGTTTTTACGAGTATCTGAATTTTGTTTCGATT
1 ACCAAATCTCAGCCACATAAGATTTAAAGATATATTTTTACGAGTATCTGAATTTTGTTTCGATT
* *
5967 TAATTAGAAAGTAATTAGAATAAAATTGAAAAAAAATAATAATAGAAGCGTGAAAAACCCTTCTA
66 TAATTAGAAAGTAATTAGAA-AAAATTG---AAAAATAATAATAGAAGCGTGAAAAGCCCTTCAA
** * * * * *
6032 TAATTTTGACATTAAATTCTATATTTTTTTATGAGTATTGTGGCCAAAAATAGCGAAAAAAATTT
127 TCCTTTTGGCGTTGAATTATATA-TTTTTTATGAGTATTGTGGCCAAAAATTGCGAAAAAAATTT
** * * * *
6097 CGGGTCTA-TTTTTGCAAAAAAAATTAGCCGAAATCGGGTACTAACCAACACAGTTTTTGGTTAA
191 CGGGTC-AGTTTTTGC--AAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTT-GCTAA
* * * ** * * ** *
6161 AATGGCGTTCCGGGGCCCCGACTCAGTTTTGGATGATTTTTTATGCCAAGAATCATTGAAATATC
252 AATCGCGTTTCAGGGCCCCGGTTCAGTTTTGCAAGATTTTTGGTGCCAAGACTCATTGAAATATC
*
6226 TTTATTCATCTA
317 TATATTCATCTA
* * *
6238 ACCAAATCTCAGCCACATAAGATTTAAAGATATGTTTTTACGAGCATCTGAATTTTTTTTCGATT
1 ACCAAATCTCAGCCACATAAGATTTAAAGATATATTTTTACGAGTATCTGAATTTTGTTTCGATT
* *
6303 TAATTAGAAAGTAATTAGAAAAAAATTAAAAAATAATAATAGAAGCGTGAAAAGCCCATCAATCC
66 TAATTAGAAAGTAATTAG-AAAAAATTGAAAAATAATAATAGAAGCGTGAAAAGCCCTTCAATCC
* *
6368 TTTTGGCGTTGGATTATATATTTTTTATGAGTATTATGGCCAAAAATTATG-GAAATAAAATTTC
130 TTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAA-T-TGCGAAA-AAAATTTC
* * * * *
6432 GGGTCAGTTTTTGCAAAATTTT-GACCAAAATTGTGTACTTAACTATAACGGTTTTTTTGTTAAA
192 GGGTCAGTTTTTGCAAAATTTTAG-CCGAAATCGTGTAC-TAACCATCACGG--TTTTTGCTAAA
* * * * * ** * * *
6496 ATCGTG-TTCCGGGCCCCTGGCTCAGTTTTGCATGATATTTGACGTCAAGGCTCATTGAACTATC
253 ATCGCGTTTCAGGGCCCC-GGTTCAGTTTTGCAAGATTTTTGGTGCCAAGACTCATTGAAATATC
*
6560 TATATTCATCTT
317 TATATTCATCTA
* ** ** * * * *
6572 ACCAAATCTCAGCTACATTGGATCCAAGGATTTATTTTTACGATTATCTGAATTTTGTTTCTATT
1 ACCAAATCTCAGCCACATAAGATTTAAAGATATATTTTTACGAGTATCTGAATTTTGTTTCGATT
** * * *
6637 TAATTTTAAATTAATTCGAAAAAATATGGAAAAACAATA
66 TAATTAGAAAGTAATTAGAAAAAAT-T-GAAAAATAATA
6676 TATTAAAGCT
Statistics
Matches: 1255, Mismatches: 144, Indels: 61
0.86 0.10 0.04
Matches are distributed among these distances:
326 1 0.00
327 206 0.16
328 38 0.03
329 119 0.09
330 155 0.12
331 154 0.12
332 55 0.04
333 79 0.06
334 162 0.13
335 101 0.08
336 183 0.15
337 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (328 bp):
ACCAAATCTCAGCCACATAAGATTTAAAGATATATTTTTACGAGTATCTGAATTTTGTTTCGATT
TAATTAGAAAGTAATTAGAAAAAATTGAAAAATAATAATAGAAGCGTGAAAAGCCCTTCAATCCT
TTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGCGAAAAAAATTTCGGGT
CAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGCTAAAATCGCGTT
TCAGGGCCCCGGTTCAGTTTTGCAAGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCAT
CTA
Found at i:6787 original size:35 final size:36
Alignment explanation
Indices: 6727--6794 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
6717 GCTCTATATA
* *
6727 TTTTTAGTTTTTATTAAAAACTGGATTTATTTTATT
1 TTTTTAATTGTTATTAAAAACTGGATTTATTTTATT
* *
6763 TTTTTAATTGTTATTACAAA-TGGATTTTTTTT
1 TTTTTAATTGTTATTAAAAACTGGATTTATTTT
6795 TCTCTCTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 11 0.39
36 17 0.61
ACGTcount: A:0.26, C:0.03, G:0.09, T:0.62
Consensus pattern (36 bp):
TTTTTAATTGTTATTAAAAACTGGATTTATTTTATT
Found at i:26435 original size:13 final size:13
Alignment explanation
Indices: 26419--26448 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
26409 AATCTATACT
*
26419 AATTATCTATGTG
1 AATTATCCATGTG
26432 AATTATCCATGTG
1 AATTATCCATGTG
26445 AATT
1 AATT
26449 GTAAAGTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (13 bp):
AATTATCCATGTG
Found at i:26598 original size:19 final size:18
Alignment explanation
Indices: 26569--26616 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
26559 TTATTTATAT
26569 CATTTAAAAAAAACTACC
1 CATTTAAAAAAAACTACC
*
26587 TATTTAAAAAAAACTACC
1 CATTTAAAAAAAACTACC
26605 CATTTAAAAAAA
1 CATTTAAAAAAA
26617 TACCACAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.17, G:0.00, T:0.25
Consensus pattern (18 bp):
CATTTAAAAAAAACTACC
Found at i:27065 original size:17 final size:17
Alignment explanation
Indices: 27043--27090 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
27033 GTAATATTTG
*
27043 ATCACTAGTGATCTCGC
1 ATCACTAGTGATCTCAC
* *
27060 ATCACTGGTGATCTTAC
1 ATCACTAGTGATCTCAC
*
27077 ATTACTAGTGATCT
1 ATCACTAGTGATCT
27091 GGGGGTGATC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (17 bp):
ATCACTAGTGATCTCAC
Found at i:35374 original size:172 final size:172
Alignment explanation
Indices: 35084--35433 Score: 693
Period size: 172 Copynumber: 2.0 Consensus size: 172
35074 AGAAAAAAGG
35084 GAAA-TAATTCAATACAGAAGCTGAAATGAAAGCTACATTAGAACAACAATATCTTTTGAAGAAG
1 GAAATTAATTCAATACAGAAGCTGAAATGAAAGCTACATTAGAACAACAATATCTTTTGAAGAAG
35148 GTTCTCATGTCAATGACTACATATTTAATCTCCCCTATCTCAATTTCAGACCTAAACGGTTGTAA
66 GTTCTCATGTCAATGACTACATATTTAATCTCCCCTATCTCAATTTCAGACCTAAACGGTTGTAA
35213 AGTTCAAATATTTCTTTTCTTCAAATTGTATCCTTGATCAAA
131 AGTTCAAATATTTCTTTTCTTCAAATTGTATCCTTGATCAAA
35255 GAAATTAATTCAATACAGAAGCTGAAATGAAAGCTACATTAGAACAACAATATCTTTTGAAGAAG
1 GAAATTAATTCAATACAGAAGCTGAAATGAAAGCTACATTAGAACAACAATATCTTTTGAAGAAG
35320 GTTCTCATGTCAATGACTACATATTTAATCTCCCCTATCTCAATTTCAGACCTAAACGGTTGTAA
66 GTTCTCATGTCAATGACTACATATTTAATCTCCCCTATCTCAATTTCAGACCTAAACGGTTGTAA
35385 AGTTCAAATATTTCTTTTCTTCAAATTGTATCCTTGATCAAA
131 AGTTCAAATATTTCTTTTCTTCAAATTGTATCCTTGATCAAA
35427 GAAATTA
1 GAAATTA
35434 GAAATGACTA
Statistics
Matches: 178, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
171 4 0.02
172 174 0.98
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (172 bp):
GAAATTAATTCAATACAGAAGCTGAAATGAAAGCTACATTAGAACAACAATATCTTTTGAAGAAG
GTTCTCATGTCAATGACTACATATTTAATCTCCCCTATCTCAATTTCAGACCTAAACGGTTGTAA
AGTTCAAATATTTCTTTTCTTCAAATTGTATCCTTGATCAAA
Found at i:39473 original size:21 final size:21
Alignment explanation
Indices: 39448--39503 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
39438 CGCGAGCTAC
39448 TCGAGCTCGACTCGAAAAAAT
1 TCGAGCTCGACTCGAAAAAAT
* * *
39469 TCGAGTTCGGCTCG-GAAAAT
1 TCGAGCTCGACTCGAAAAAAT
39489 TCGAGC-CGAGCTCGA
1 TCGAGCTCGA-CTCGA
39504 GCTCGAGCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 2 0.07
20 14 0.50
21 12 0.43
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.20
Consensus pattern (21 bp):
TCGAGCTCGACTCGAAAAAAT
Found at i:43091 original size:2 final size:2
Alignment explanation
Indices: 43084--43119 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
43074 CATTGCATGT
*
43084 GA GA GA GA GA GA GA GG GA GA GA GA GA GA GA GA -A GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
43120 CAAAGGGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Done.