Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016312.1 Corchorus capsularis cultivar CVL-1 contig16333, 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: 24932
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:724 original size:270 final size:268
Alignment explanation
Indices: 219--731 Score: 586
Period size: 270 Copynumber: 1.9 Consensus size: 268
209 AATGAGATTG
* * * *
219 TTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGCGCGTTTTTG
1 TTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGCCCAAAACCTCAACTTTGAGCGTTTGTG
* * * ** *
284 TGCTAAATATAGTTCTTAGCAAAACTCTTTCTGGATGTGTTTTTTCGCGCAACGAGTGCTCAAAA
66 TGCAAAACATAGTTCTTAGCAAAACTCATTCCAGATGCGTTTTTTCGCGCAACGAGTGCTCAAAA
* * * * ** * * *
349 GTCGTGTGTCGGAATGAGATGAGCTTGTTAGACAGGGCTATGCACAAACAGAGCTCTTCTCGATG
131 GTCATGAGTCGGAATAAGATGAGCATGTTAGACAGCCCTATGCACAAACAAAGCTCTTCCCGAAG
* * * *
414 TCCAAAGCATCAACTTTGCGCGTTTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAATGAGA
196 TCCAAAACATCAACTTTGCACCTTTGTATGCAAAACATCGTTCTTAGCGGTTTGTCGGAATGAGA
479 TGAACTTT
261 TGAACTTT
* *
487 TTGGAGAGCCGTGTGCACAAACAAAGCTTTC-CTAGAAGCCCAAAACCTCAACTTTGAGCGTTTG
1 TTGGACAGCCCTGTGCACAAACAAAGCTTTCAC--GAAGCCCAAAACCTCAACTTTGAGCGTTTG
* * * *
551 TGTGCAAAACATCGTT-TTGAGGAACAGGCTCATTCCAGATGCGTTTTTT-GCGCAATGAGTGCT
64 TGTGCAAAACATAGTTCTT-AGCAA-A-ACTCATTCCAGATGCGTTTTTTCGCGCAACGAGTGCT
* * * * * *
614 CAAATGTCATGAGTCGGAGTAAGTTGAGCATGTTAGACAGCCCTGTGCATAAACAAAG-TTTTCC
126 CAAAAGTCATGAGTCGGAATAAGATGAGCATGTTAGACAGCCCTATGCACAAACAAAGCTCTT-C
* * *
678 CCGAAGTCCAAAACCTCAACTTAT-CACCTTTTTGTGCAAAACATCGTTCTTAGC
190 CCGAAGTCCAAAACATCAACTT-TGCACCTTTGTATGCAAAACATCGTTCTTAGC
732 AAAACTCTTT
Statistics
Matches: 200, Mismatches: 38, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
267 1 0.00
268 31 0.16
269 46 0.23
270 104 0.52
271 18 0.09
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (268 bp):
TTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGCCCAAAACCTCAACTTTGAGCGTTTGTG
TGCAAAACATAGTTCTTAGCAAAACTCATTCCAGATGCGTTTTTTCGCGCAACGAGTGCTCAAAA
GTCATGAGTCGGAATAAGATGAGCATGTTAGACAGCCCTATGCACAAACAAAGCTCTTCCCGAAG
TCCAAAACATCAACTTTGCACCTTTGTATGCAAAACATCGTTCTTAGCGGTTTGTCGGAATGAGA
TGAACTTT
Found at i:949 original size:431 final size:426
Alignment explanation
Indices: 1--1105 Score: 1450
Period size: 431 Copynumber: 2.6 Consensus size: 426
* ** * *
1 TTTGCGCATTTGTATGCAACACATCGTTCTTAGAAGTTTGTCGGAGTAAGATGAACTTTTTGGAT
1 TTTGCGCGTTTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAGTGAGATGAACTTTTTGGAC
*
66 AGCCCTGTGCACAAATAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAA
66 AGCCCTGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAA
* * * *
131 AACATCATTTTTG-GCGATTA-GCTCATTCCAGATGCATTTTTTGCGCTACGAGTGCTCAAATAT
131 AACATC-CTTTTGAGCGA-AAGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCAAATGT
* * *
194 CTTGCCTCGAAATGCAA-TGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTC
194 CATGCGTCG-AA-GTAAGTGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTC
* * * * * * *
258 CAAAGCCTCAACTTTGCGCGTTTTTGTGCTAAATATAGTTCTTAGCAAAACTCTTTCTGGATGTG
257 CAAAACCTCAACTTTGCACCTTTTTGTGCAAAACATAGTTCTTAGCAAAACTCTTTCCGGATGCG
* * * ** * ***
323 TTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGTTAGACAGGGCT
322 TTTTTTCGAGCAACGACTGCTCAAAAGTCGTGTGTCAGAATGAGATGAGCAAGATAGACAACCCT
* * *
388 ATGCACAAACAGAGCTCTTCTCGATGTCCAAAGCATCAAC
387 ATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAAC
* *
428 TTTGCGCGTTTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAATGAGATGAACTTTTTGGAG
1 TTTGCGCGTTTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAGTGAGATGAACTTTTTGGAC
* * *
493 AGCCGTGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGTTTGTGTGCAA
66 AGCCCTGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAA
* * *
558 AACATCGTTTTGAG-GAACAGGCTCATTCCAGATGCGTTTTTTGCGCAATGAGTGCTCAAATGTC
131 AACATCCTTTTGAGCGAA-AGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCAAATGTC
* * * * * *
622 ATGAGTCGGAGTAAGTTGAGCA-TGTTAGACAGCCCTGTGCATAAACAAAGTTTTCCCCGAAGTC
195 ATGCGTCGAAGTAAG-TGAG-ATTGTTGGACAGCCCTGTGCACAAACAAAGCTTT-CACGAAGTC
*
686 CAAAACCTCAACTTAT-CACCTTTTTGTGCAAAACATCGTTCTTAGCAAAACTCTTTTTCCGGAT
257 CAAAACCTCAACTT-TGCACCTTTTTGTGCAAAACATAGTTCTTAGCAAAACTC--TTTCCGGAT
* * * * *
750 GCGATTTTTTTGAGCAATGACTGCTCAAAAGTCGTTTGTCAGAGTGAGATGAGCAAGATGGACAA
319 GCG-TTTTTTCGAGCAACGACTGCTCAAAAGTCGTGTGTCAGAATGAGATGAGCAAGATAGACAA
* *
815 CCCTATGCACAAAGAAAGCTCTCCTCGAAGTCTAAAGCATCAAC
383 CCCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAAC
* * * * *
859 TTTGCGCGTATGTATGCCAA-ACATCGTTCTTAGCGGTGTCTCGGAGTGAGATGAGCTATTTGGA
1 TTTGCGCGTTTGTATG-CAACACATCGTTCTTAGCGGTTTGTCGGAGTGAGATGAACTTTTTGGA
923 CAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCA
65 CAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCA
* *
988 AAACTTCCTTTTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCAAATGTC
130 AAACATCCTTTTGAGCGAAAGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCAAATGTC
* ** *
1053 GTGCGTCGAAGTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAATGCTT
195 ATGCGTCGAAGTAAG-TGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTT
1106 GTTAGGGAGC
Statistics
Matches: 587, Mismatches: 77, Indels: 24
0.85 0.11 0.03
Matches are distributed among these distances:
425 3 0.01
426 9 0.02
427 205 0.35
428 54 0.09
429 1 0.00
430 11 0.02
431 298 0.51
432 6 0.01
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (426 bp):
TTTGCGCGTTTGTATGCAACACATCGTTCTTAGCGGTTTGTCGGAGTGAGATGAACTTTTTGGAC
AGCCCTGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAA
AACATCCTTTTGAGCGAAAGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCAAATGTCA
TGCGTCGAAGTAAGTGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAA
ACCTCAACTTTGCACCTTTTTGTGCAAAACATAGTTCTTAGCAAAACTCTTTCCGGATGCGTTTT
TTCGAGCAACGACTGCTCAAAAGTCGTGTGTCAGAATGAGATGAGCAAGATAGACAACCCTATGC
ACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAAC
Found at i:985 original size:111 final size:111
Alignment explanation
Indices: 791--991 Score: 260
Period size: 111 Copynumber: 1.8 Consensus size: 111
781 TCGTTTGTCA
* * * * *
791 GAGTGAGATGAGCAAGATGGACAACCCTATGCACAAAGAAAGCTCTCCTCGAAGTCTAAAGCATC
1 GAGTGAGATGAGCAAGATGGACAACCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAAACATC
* *
856 AACTTTGCGCGTATGTATGCCAAACATCGTTCTTAGCGGTGTCTCG
66 AACTTTGAGCGTATGTATGCAAAACATCGTTCTTAGCGGTGTCTCG
* ** * * * *
902 GAGTGAGATGAGCTATTTGGACAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTC
1 GAGTGAGATGAGCAAGATGGACAACCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAAACATC
967 AACTTTGAGCGGT-TGTATGCAAAAC
66 AACTTTGAGC-GTATGTATGCAAAAC
992 TTCCTTTTTA
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
111 73 0.97
112 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (111 bp):
GAGTGAGATGAGCAAGATGGACAACCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAAACATC
AACTTTGAGCGTATGTATGCAAAACATCGTTCTTAGCGGTGTCTCG
Found at i:1984 original size:374 final size:375
Alignment explanation
Indices: 1294--2010 Score: 1103
Period size: 374 Copynumber: 1.9 Consensus size: 375
1284 TGCAAAACAT
* * *
1294 CATTTTTTGCGCTACGAGTGCTCAAATGTTGTGCGTCGAAGTGCAATGAGATTGTTGGACAGCCC
1 CATTTTTTGCGCAACGAGTGCTCAAATGTCGTGCATCGAAGTGCAATGAGATTGTTGGACAGCCC
* *
1359 TGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCATCAATTTTGCACATTTCTGTGCTAAACAT
66 TGTGCACAAACAAAGCTTTCCACGAAGTCCAAAGCATCAACTTTGCACATTTCTGTGCTAAACAT
* *
1424 AGTTCTTAGCAGAACTCTTTCTAGATGCATTTTTTCGTGCAACGAATGCTCAAAAGACGTGTGTC
131 AGTTCTTAGCAAAACTCTTTCTAGATGCATTTTTTCGCGCAACGAATGCTCAAAAGACGTGTGTC
* * *
1489 GGAGTGAGATGAGCTTGTTAGATAACACTATGCACAAACAAAGCTCTCCTCGAAGTCTAAAGCAT
196 GGAATGAGATGAGCTTGTTAGACAACACTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCAT
* * * * * *
1554 CACCTTTGGGCGTTTGTTTGCAACACATCGTTCTTAGCGGTGTGTTGGAGTGAGATGAGCTTTTT
261 CAACTTTGGGAGTTTGTATGCAACAAATCGTTCTTAGCGGTGTGTCGGAGTGAGATGAACTTTTT
*
1619 GAACAGTCCTATGCACAACATCATTTTTAGCGAAAGGCTCATTCAAGATG
326 GAACAGCCCTATGCACAACATCATTTTTAGCGAAAGGCTCATTCAAGATG
* * *
1669 CATTTTTTGCGCAACGAGTGGTCAAATGTCGTGCATCGAATTGCGATGAGATTGTTGGACAGCCC
1 CATTTTTTGCGCAACGAGTGCTCAAATGTCGTGCATCGAAGTGCAATGAGATTGTTGGACAGCCC
* * * *
1734 TGTGCACAAACAAAGCTTT-CACGAAGTCCAAAGCCTCAACTTTGCGCGTTTTTGTGCTAAACAT
66 TGTGCACAAACAAAGCTTTCCACGAAGTCCAAAGCATCAACTTTGCACATTTCTGTGCTAAACAT
* * * *
1798 AGTTCTTAGCAAAACTCTTTCTGGATGCGTTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGTGTC
131 AGTTCTTAGCAAAACTCTTTCTAGATGCATTTTTTCGCGCAACGAATGCTCAAAAGACGTGTGTC
* * *
1863 GGAATGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGATGTCCAAAGCAT
196 GGAATGAGATGAGCTTGTTAGACAACACTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCAT
* * *
1928 CAACTTTGTGAGTTTGTATGTAACAAATCGTTCTTAGCGGTTTGTCGGAGTGAGATGAACTTTTT
261 CAACTTTGGGAGTTTGTATGCAACAAATCGTTCTTAGCGGTGTGTCGGAGTGAGATGAACTTTTT
* *
1993 GGACAGCCCTGTGCACAA
326 GAACAGCCCTATGCACAA
2011 ACAAAGCTTT
Statistics
Matches: 306, Mismatches: 36, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
374 228 0.75
375 78 0.25
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (375 bp):
CATTTTTTGCGCAACGAGTGCTCAAATGTCGTGCATCGAAGTGCAATGAGATTGTTGGACAGCCC
TGTGCACAAACAAAGCTTTCCACGAAGTCCAAAGCATCAACTTTGCACATTTCTGTGCTAAACAT
AGTTCTTAGCAAAACTCTTTCTAGATGCATTTTTTCGCGCAACGAATGCTCAAAAGACGTGTGTC
GGAATGAGATGAGCTTGTTAGACAACACTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCAT
CAACTTTGGGAGTTTGTATGCAACAAATCGTTCTTAGCGGTGTGTCGGAGTGAGATGAACTTTTT
GAACAGCCCTATGCACAACATCATTTTTAGCGAAAGGCTCATTCAAGATG
Found at i:2262 original size:159 final size:160
Alignment explanation
Indices: 1971--2367 Score: 406
Period size: 159 Copynumber: 2.5 Consensus size: 160
1961 TTAGCGGTTT
* * * *
1971 GTCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGTCCAAAA
1 GTCGGAGTGAGATGAGCATGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAA
* * * ** * *
2036 CCTCAACTTTGAGCGTTTGTGTGCAAAACGTCGCTTTGAGGAAAAAGCTCATTCCAGATGC-TTT
66 CCTCAACTTTCAGCATTTGTGTGCAAAACATCGCTTTGAACAAAAACCTCATTCCAGATGCGATT
2100 TTTTGCCCAATGAGAGC-TAAAATGTCACGC
131 TTTTGCCCAATGAGAGCTTAAAA-GTCACGC
* * * *
2130 GTCGGAGTGAGTTGAGCATGTTGGACAGCCCTGTGCAAAAACAAAGTTTTCCCCGAAGTCCAAAA
1 GTCGGAGTGAGATGAGCATGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAA
* * * ** *
2195 CCTCAACTTATCATCATTT-TGTGCAAAACATCG-TTCTTAACAAAACCCTTTTTCCATATGCGA
66 CCTCAACTT-TCAGCATTTGTGTGCAAAACATCGCTT-TGAACAAAAACCTCATTCCAGATGCGA
** * * *
2258 TTTTTTTTTGTGCAATGAGTGCTTAAAAGTCATGT
129 ---TTTTTTGCCCAATGAGAGCTTAAAAGTCACGC
* * * * * * *
2293 GTCGGAGTGAGATGAGCAAGATGCACAGCCCTATGCACCAACAAAGCTCTCCTCGAAGTCCAAAG
1 GTCGGAGTGAGATGAGCATGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAA
*
2358 CATCAACTTT
66 CCTCAACTTT
2368 GCGCGTATGT
Statistics
Matches: 193, Mismatches: 38, Indels: 11
0.80 0.16 0.05
Matches are distributed among these distances:
158 2 0.01
159 96 0.50
160 6 0.03
162 1 0.01
163 83 0.43
164 5 0.03
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (160 bp):
GTCGGAGTGAGATGAGCATGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAA
CCTCAACTTTCAGCATTTGTGTGCAAAACATCGCTTTGAACAAAAACCTCATTCCAGATGCGATT
TTTTGCCCAATGAGAGCTTAAAAGTCACGC
Found at i:2352 original size:163 final size:159
Alignment explanation
Indices: 1995--2367 Score: 392
Period size: 163 Copynumber: 2.3 Consensus size: 159
1985 AACTTTTTGG
* * *
1995 ACAGCCCTGTGCACAAACAAAGCTTTCCTAGAAGTCCAAAACCTCAACTTTGAGCGTTTGTGTGC
1 ACAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAACCTCAACTTTCAGCATTTGTGTGC
* ** *
2060 AAAACGTCGCTTTGAGGAAAAAGCTCATTCCAGATGCTTTTTTTGCCCAATGAGAGCTAAAATGT
66 AAAACATCGCTTTGAACAAAAACCTCATTCCAGATGCTTTTTTTGCCCAATGAGAGCTAAAATGT
* * * *
2125 CACGCGTCGGAGTGAGTTGAGCATGTTGG
131 CACGCGTCGGAGTGAGATGAGCAAGATGC
* * * *
2154 ACAGCCCTGTGCAAAAACAAAGTTTTCCCCGAAGTCCAAAACCTCAACTTATCATCATTT-TGTG
1 ACAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAACCTCAACTT-TCAGCATTTGTGTG
* * ** * ** *
2218 CAAAACATCG-TTCTTAACAAAACCCTTTTTCCATATGCGATTTTTTTTTGTGCAATGAGTGCTT
65 CAAAACATCGCTT-TGAACAAAAACCTCATTCCAGATGC----TTTTTTTGCCCAATGAGAGC-T
* *
2282 AAAA-GTCATGTGTCGGAGTGAGATGAGCAAGATGC
124 AAAATGTCACGCGTCGGAGTGAGATGAGCAAGATGC
* * * * *
2317 ACAGCCCTATGCACCAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTT
1 ACAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAACCTCAACTTT
2368 GCGCGTATGT
Statistics
Matches: 174, Mismatches: 33, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
158 2 0.01
159 76 0.44
160 6 0.03
162 1 0.01
163 84 0.48
164 5 0.03
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (159 bp):
ACAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAACCTCAACTTTCAGCATTTGTGTGC
AAAACATCGCTTTGAACAAAAACCTCATTCCAGATGCTTTTTTTGCCCAATGAGAGCTAAAATGT
CACGCGTCGGAGTGAGATGAGCAAGATGC
Found at i:2455 original size:433 final size:427
Alignment explanation
Indices: 1628--2611 Score: 1190
Period size: 433 Copynumber: 2.3 Consensus size: 427
1618 TGAACAGTCC
* * * * * * * * * *
1628 TATGCACAACATCATTTTTAGCGAAAGGCTCATTCAAGATGCATTTTTTGCGCAACGAGTGGTCA
1 TATGCAAAACATCACTTTGAGCGAAAAGCTCATTCCAGATGCATTTTTTGCCCAATGAGAGCTAA
** * * * *
1693 AATGTCGTGCATCGAATTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACGA
66 AATGTCACGCGTGGAAGTGAGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACGA
* * * * **
1758 AGTCCAAAGCCTCAACTTTGCGCGTTTTTGTGCTAAACATAGTTCTTAGCAAAACTCTTTCTGGA
131 AGTCCAAAACCTCAACTTTGCGCGATTTTGTGCAAAACATAGTTCTTAACAAAACTCTTTCCAGA
* ** *
1823 TGCGTTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGTTAGACAG
196 TGCGTTTTTTCGCGCAACGAGTGCTCAAAAGTCATGTGTCGGAATGAGATGAGCAAGATAGACAG
* * * * *
1888 CGCTATGCACAAACAAAGCTCTCCTCGATGTCCAAAGCATCAACTTTGTGAGTTTGTATGTAACA
261 CCCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGAGTATGTATGCAACA
* *
1953 AATCGTTCTTAGCGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCACAAACAAAGC
326 AATCGTTCTTAGCGGTGTGTCGGAGTGAGATGAACTATTTGGACAGCCCTGTGCACAAACAAAGC
* *
2018 TTTCCTAGAAGTCCAAAACCTCAACTTTGAGCGTTTG
391 TTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTG
* * * *
2055 TGTGCAAAACGTCGCTTTGAG-GAAAAAGCTCATTCCAGATGCTTTTTTTGCCCAATGAGAGCTA
1 TATGCAAAACATCACTTTGAGCG-AAAAGCTCATTCCAGATGCATTTTTTGCCCAATGAGAGCTA
* * *
2119 AAATGTCACGCGTCGG-AGTGAGTTGAGCA-TGTTGGACAGCCCTGTGCAAAAACAAAGTTTTCC
65 AAATGTCACGCGT-GGAAGTGAGATGAG-ATTGTTGGACAGCCCTGTGCACAAACAAAGCTTT-C
* * * *
2182 CCGAAGTCCAAAACCTCAACTTAT-CATC-ATTTTGTGCAAAACATCGTTCTTAACAAAACCCTT
127 ACGAAGTCCAAAACCTCAACTT-TGC-GCGATTTTGTGCAAAACATAGTTCTTAACAAAA--CTC
* * * * * *
2245 TTTCCATATGCGATTTTTTTTTGTGCAATGAGTGCTTAAAAGTCATGTGTCGGAGTGAGATGAGC
188 TTTCCAGATGCG---TTTTTTCGCGCAACGAGTGCTCAAAAGTCATGTGTCGGAATGAGATGAGC
* *
2310 AAGAT-GCACAGCCCTATGCACCAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGCGT
250 AAGATAG-ACAGCCCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGAGT
* * * *
2374 ATGTATGCCAA-ACATCGTTCTTAGCGGTGTGTCGGAGTTAGATGAGCTATTTGGACAGCCTTGT
314 ATGTATG-CAACAAATCGTTCTTAGCGGTGTGTCGGAGTGAGATGAACTATTTGGACAGCCCTGT
2438 GCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTG
378 GCACAAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTG
* * * * * *
2488 TATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCGCAATGAGTGCTCA
1 TATGCAAAACATCACTTTGAGCGAAAAGCTCATTCCAGATGCATTTTTTGCCCAATGAGAGCTAA
** * *
2553 AATGTCGTGCGTGGAAGTGCGATGAGATTGTTGGACAGTCCTGTGCACAAACAAAGCTT
66 AATGTCACGCGTGGAAGTGAGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTT
2612 GTTAGGCAGT
Statistics
Matches: 466, Mismatches: 75, Indels: 26
0.82 0.13 0.05
Matches are distributed among these distances:
426 1 0.00
427 96 0.21
428 50 0.11
429 2 0.00
430 11 0.02
432 4 0.01
433 299 0.64
434 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (427 bp):
TATGCAAAACATCACTTTGAGCGAAAAGCTCATTCCAGATGCATTTTTTGCCCAATGAGAGCTAA
AATGTCACGCGTGGAAGTGAGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACGA
AGTCCAAAACCTCAACTTTGCGCGATTTTGTGCAAAACATAGTTCTTAACAAAACTCTTTCCAGA
TGCGTTTTTTCGCGCAACGAGTGCTCAAAAGTCATGTGTCGGAATGAGATGAGCAAGATAGACAG
CCCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGAGTATGTATGCAACA
AATCGTTCTTAGCGGTGTGTCGGAGTGAGATGAACTATTTGGACAGCCCTGTGCACAAACAAAGC
TTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTG
Found at i:2490 original size:111 final size:111
Alignment explanation
Indices: 2290--2510 Score: 273
Period size: 111 Copynumber: 2.0 Consensus size: 111
2280 TTAAAAGTCA
* * *
2290 TGTGTCGGAGTGAGATGAGCAAGATGCACAGCCCTATGCACCAACAAAGCTCTCCTCGAAGTCCA
1 TGTGTCGGAGTGAGATGAGCAAGATGCACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGCCCA
* * * *
2355 AAGCATCAACTTTGCGCGTATGTATGCCAAACATCGTTCTTAGCGG
66 AAACATCAACTTTGAGCGTATGTATGCAAAACATCATTCTTAGCGG
* * ** * * * *
2401 TGTGTCGGAGTTAGATGAGCTATTTGGACAGCCTTGTGCACAAACAAAGCTTTCCTAGAAGCCCA
1 TGTGTCGGAGTGAGATGAGCAAGATGCACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGCCCA
* *
2466 AAACCTCAACTTTGAGCGGT-TGTATGCAAAACATCATTTTTAGCG
66 AAACATCAACTTTGAGC-GTATGTATGCAAAACATCATTCTTAGCG
2511 AAAGGCTCAT
Statistics
Matches: 92, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
111 90 0.98
112 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.25
Consensus pattern (111 bp):
TGTGTCGGAGTGAGATGAGCAAGATGCACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGCCCA
AAACATCAACTTTGAGCGTATGTATGCAAAACATCATTCTTAGCGG
Found at i:6881 original size:26 final size:25
Alignment explanation
Indices: 6852--6920 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 25
6842 CTAAATGTGC
*
6852 AAATGATCAAAATGCCCTTAGTGCAG
1 AAATGA-CAAAATGCCCTTAGTGCAA
** *
6878 AAATGACCAAAATGCAATTGGTGCAA
1 AAATGA-CAAAATGCCCTTAGTGCAA
6904 AAATGACAAAAATGCCC
1 AAATGAC-AAAATGCCC
6921 CCTATGTGAC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
25 1 0.03
26 34 0.97
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (25 bp):
AAATGACAAAATGCCCTTAGTGCAA
Found at i:7192 original size:9 final size:9
Alignment explanation
Indices: 7178--7214 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
7168 CTTAAAGAGC
7178 ACAATGGAG
1 ACAATGGAG
7187 ACAATGGAG
1 ACAATGGAG
7196 ACAATGGAG
1 ACAATGGAG
7205 ATC-ATGGAG
1 A-CAATGGAG
7214 A
1 A
7215 GGATGAGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 26 0.96
10 1 0.04
ACGTcount: A:0.43, C:0.11, G:0.32, T:0.14
Consensus pattern (9 bp):
ACAATGGAG
Found at i:12872 original size:33 final size:32
Alignment explanation
Indices: 12835--12917 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 32
12825 TTGTTTTCAA
*
12835 CACAAACAACACCTAAATTAGATTTAGTGTCAT
1 CACAAACAACA-CTAAATTAGATTTAGTATCAT
*
12868 CACAAACAACACTCAAATTAGGTTTAGTATCAT
1 CACAAACAACACT-AAATTAGATTTAGTATCAT
*
12901 CGCAAACAACATCTAAA
1 CACAAACAACA-CTAAA
12918 ACACTCTTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
32 2 0.04
33 41 0.91
34 2 0.04
ACGTcount: A:0.45, C:0.23, G:0.08, T:0.24
Consensus pattern (32 bp):
CACAAACAACACTAAATTAGATTTAGTATCAT
Found at i:15967 original size:30 final size:30
Alignment explanation
Indices: 15927--15983 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
15917 TGTCTTCAAG
15927 TCCATAATAAGTCCTT-GGCGCATCATTCCT
1 TCCATAATAAG-CCTTGGGCGCATCATTCCT
*
15957 TCCATGATAAGCCTTGGGCGCATCATT
1 TCCATAATAAGCCTTGGGCGCATCATT
15984 TACTTTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.32
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCGCATCATTCCT
Found at i:20457 original size:19 final size:18
Alignment explanation
Indices: 20424--20459 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20414 TTGAAATAAT
20424 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
20442 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
20460 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:22489 original size:12 final size:12
Alignment explanation
Indices: 22474--22498 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22464 ATCAAATTAA
22474 ATGCAAAATGCC
1 ATGCAAAATGCC
22486 ATGCAAAATGCC
1 ATGCAAAATGCC
22498 A
1 A
22499 GTTTAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.24, G:0.16, T:0.16
Consensus pattern (12 bp):
ATGCAAAATGCC
Done.