Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010991.1 Corchorus olitorius cultivar O-4 contig11023, 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: 1820
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Found at i:281 original size:154 final size:154
Alignment explanation
Indices: 1--340 Score: 538
Period size: 154 Copynumber: 2.2 Consensus size: 154
*
1 AACTATAATCGTTTTGGTGAGATTAGTTGACTGTGAAGATTTTAGCTCATTTGCAACACTTGTTA
1 AACTATAATCATTTTGGTGAGATTAGTTGACTGTGAAGATTTTAGCTCATTTGCAACACTTGTTA
* * *
66 TTTTGGGCCTATCGGGGCCCATTAGTTCAGATTTGAATCGTCTTCGATTTGGCAAACCTCAATTC
66 TTTTGGGCCTATCGGGGCCCATTAGTTCAGATTTGAATAGTCTTCCATTTGGCAAACCTCAATGC
*
131 TATTCTTTCCATTGTTTATGCCCT
131 TATTCTTTCCATTGTTTAAGCCCT
* * *
155 AACTATAATCATTTTGGTGAGATTAGTCGACT-TAGAAGGTTTTAGCTCATTTGGAACACTTGTT
1 AACTATAATCATTTTGGTGAGATTAGTTGACTGT-GAAGATTTTAGCTCATTTGCAACACTTGTT
* * *
219 ATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATATTCTTCCATTTGGCAAACCTCAATG
65 ATTTTGGGCCTATCGGGGCCCATTAGTTCAGATTTGAATAGTCTTCCATTTGGCAAACCTCAATG
* *
284 CTTTTCTTTCCATTGTTTAAGGCCT
130 CTATTCTTTCCATTGTTTAAGCCCT
*
309 AACTATAATCATTTTGGAGAGATTAGTTGACT
1 AACTATAATCATTTTGGTGAGATTAGTTGACT
341 ATGGCCTAAC
Statistics
Matches: 170, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
153 1 0.01
154 169 0.99
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (154 bp):
AACTATAATCATTTTGGTGAGATTAGTTGACTGTGAAGATTTTAGCTCATTTGCAACACTTGTTA
TTTTGGGCCTATCGGGGCCCATTAGTTCAGATTTGAATAGTCTTCCATTTGGCAAACCTCAATGC
TATTCTTTCCATTGTTTAAGCCCT
Found at i:481 original size:193 final size:193
Alignment explanation
Indices: 147--528 Score: 649
Period size: 193 Copynumber: 2.0 Consensus size: 193
137 TTCCATTGTT
147 TATGCCCTAACTATAATCATTTTGGTGAGATTAGTCGACTTAGAAGGTTTTAGCTCATTTGGAAC
1 TATGCCCTAACTATAATCATTTTGGTGAGATTAGTCGACTTAGAAGGTTTTAGCTCATTTGGAAC
* *
212 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATATTCTTCCATTTGGCAAAC
66 ACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGAATAGTCTTCCATTTGGCAAAC
277 CTCAATGCTTTTCTTTCCATTGTTTAAGGCCTAACTATAATCATTTTGGAGAGATTAGTTGAC
131 CTCAATGCTTTTCTTTCCATTGTTTAAGGCCTAACTATAATCATTTTGGAGAGATTAGTTGAC
* * * *
340 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTTGA-TTGTGAAGTTTTTAGCTCATTTGGAA
1 TATGCCCTAACTATAATCATTTTGGTGAGATTAGTCGACTT-AGAAGGTTTTAGCTCATTTGGAA
* * *
404 CACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGACTCGTCTTCGATTTGGCAAA
65 CACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGAATAGTCTTCCATTTGGCAAA
* *
469 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGT
130 CCTCAATGCTTTTCTTTCCATTGTTTAAGGCCTAACTATAATCATTTTGGAGAGATTAGT
529 CGATTGTGAA
Statistics
Matches: 177, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
192 2 0.01
193 175 0.99
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (193 bp):
TATGCCCTAACTATAATCATTTTGGTGAGATTAGTCGACTTAGAAGGTTTTAGCTCATTTGGAAC
ACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGAATAGTCTTCCATTTGGCAAAC
CTCAATGCTTTTCTTTCCATTGTTTAAGGCCTAACTATAATCATTTTGGAGAGATTAGTTGAC
Found at i:635 original size:153 final size:153
Alignment explanation
Indices: 340--682 Score: 580
Period size: 153 Copynumber: 2.2 Consensus size: 153
330 ATTAGTTGAC
* *
340 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTTGATTGTGAAGTTTTTAGCTCATTTGGAAC
1 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGATTGTGAAGTTTTTAGCTCATTTGGAAA
* * *
405 ACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGACTCGTCTTCGATTTGGCAAAC
66 ACTTGTTATTTTGGGCCTAAC-GGGCCCACTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAA
*
470 CTCAATGCTTTTCTTTCCATTGTT
130 CTCAATGATTTTCTTTCCATTGTT
*
494 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGATTGTGAAGTTTTTTAGCTCATTTGTAA
1 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGATTGTGAAG-TTTTTAGCTCATTTGGAA
*
559 AACTTGTTATTTTGGGCCTAAC-GGCCCAGTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAA
65 AACTTGTTATTTTGGGCCTAACGGGCCCACTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAA
623 CTCAATGATTTTCTTTCCATTGTT
130 CTCAATGATTTTCTTTCCATTGTT
*
647 TATGGCCTAACTATAATCATTTTTGTGAGATTAGTC
1 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
683 AACTATGGCC
Statistics
Matches: 179, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
153 97 0.54
154 45 0.25
155 37 0.21
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (153 bp):
TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGATTGTGAAGTTTTTAGCTCATTTGGAAA
ACTTGTTATTTTGGGCCTAACGGGCCCACTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAAC
TCAATGATTTTCTTTCCATTGTT
Found at i:739 original size:346 final size:346
Alignment explanation
Indices: 1--1029 Score: 1688
Period size: 346 Copynumber: 3.0 Consensus size: 346
*
1 AACTATAATCGTTTTGGTGAGATTAGTTGACTGTGAAGATTTTAGCTCATTTGCAACACTTGTTA
1 AACTATAATCATTTTGGTGAGATTAGTTGACTGTGAAGATTTTAGCTCATTTGCAACACTTGTTA
* *
66 TTTTGGGCCTATCGGGGCCCATTAGTTCAGATTTGAATCGTCTTCGATTTGGCAAACCTCAATTC
66 TTTTGGGCCTATCGGGGCCCATTAGTTCCGATTTGAATCGTCTTCGATTTGGCAAACCTCAATGC
* * * *
131 TATTCTTTCCATTGTTTATGCCCTAACTATAATCATTTTGGTGAGATTAGTCGACTTAGAAGGTT
131 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGACTTTGAAGTTT
* **
196 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATATT
196 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCACTAGTTCCGTTTTGAATCGT
* * *
261 CTTCCATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAAGGCCTAACTATAATCATTTTGG
260 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTTG
* **
326 AGAGATTAGTTGACTATGGCCT
325 TGAGATTAGTCAACTATGGCCT
* * *
348 AACTATAATCATTTTGGTGAGATTAGTTGATTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA
1 AACTATAATCATTTTGGTGAGATTAGTTGACTGTGAAGATTTTAGCTCATTTGCAACACTTGTTA
* * *
413 TTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGACTCGTCTTCGATTTGGCAAACCTCAATGC
66 TTTTGGGCCTATCGGGGCCCATTAGTTCCGATTTGAATCGTCTTCGATTTGGCAAACCTCAATGC
478 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGA-TTGTGAAGTT
131 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGACTT-TGAAG-T
* * * *
542 TTTTAGCTCATTTGTAAAACTTGTTATTTTGGGCCTAAC-GGCCCAGTAGTTCCGTTTTGAATCG
194 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCACTAGTTCCGTTTTGAATCG
* *
606 TCTTCGATTTGGCAAAACTCAATGATTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTT
259 TCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTT
671 GTGAGATTAGTCAACTATGGCCT
324 GTGAGATTAGTCAACTATGGCCT
*
694 AACTATAATCATGTTGGTGAGATTAGTTGACTGTGAAGATTTTAGCTCATTTGCAACACTTG-TA
1 AACTATAATCATTTTGGTGAGATTAGTTGACTGTGAAGATTTTAGCTCATTTGCAACACTTGTTA
758 -TTTGGGCCTATCGGGGCCCATTAGTTCCGATTTGAATCGTCTTCGATTTGGCAAACCTCAATGC
66 TTTTGGGCCTATCGGGGCCCATTAGTTCCGATTTGAATCGTCTTCGATTTGGCAAACCTCAATGC
* *
822 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTTGTTAGATTAGTCGACTTTGAAGTTT
131 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGACTTTGAAGTTT
*
887 TTAGTCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGACTCG
196 TTAG-CTCATTTGGAACACTTGTTATTTTGGGCCTATC-GGGCCCACTAGTTCCGTTTTGAATCG
952 TCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTT
259 TCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTT
1017 GGTGAGATTAGTC
324 -GTGAGATTAGTC
1030 GATTGTGAAG
Statistics
Matches: 632, Mismatches: 43, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
343 7 0.01
344 148 0.23
345 4 0.01
346 248 0.39
347 189 0.30
348 36 0.06
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (346 bp):
AACTATAATCATTTTGGTGAGATTAGTTGACTGTGAAGATTTTAGCTCATTTGCAACACTTGTTA
TTTTGGGCCTATCGGGGCCCATTAGTTCCGATTTGAATCGTCTTCGATTTGGCAAACCTCAATGC
TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGACTTTGAAGTTT
TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGCCCACTAGTTCCGTTTTGAATCGTC
TTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTTGT
GAGATTAGTCAACTATGGCCT
Found at i:820 original size:191 final size:192
Alignment explanation
Indices: 494--873 Score: 613
Period size: 191 Copynumber: 2.0 Consensus size: 192
484 TTCCATTGTT
* * * *
494 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGATTGTGAAGTTTTTTAGCTCATTTGTAA
1 TATGGCCTAACTATAATCATGTTGGTGAGATTAGTCGACTGTGAAGTATTTTAGCTCATTTGCAA
*
559 AACTTGTTATTTTGGGCCTAACGGCCCAGTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAAC
66 AACTTGTTATTTTGGGCCTAACGGCCCAGTAGTTCCGATTTGAATCGTCTTCGATTTGGCAAAAC
624 TCAATGATTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTTGTGAGATTAGTCAAC
131 TCAATGATTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTTGTGAGATTAGTCAAC
*
686 TATGGCCTAACTATAATCATGTTGGTGAGATTAGTTGACTGTGAAG-ATTTTAGCTCATTTGCAA
1 TATGGCCTAACTATAATCATGTTGGTGAGATTAGTCGACTGTGAAGTATTTTAGCTCATTTGCAA
* * *
750 CACTTG-TA-TTTGGGCCTATCGGGGCCCATTAGTTCCGATTTGAATCGTCTTCGATTTGGCAAA
66 AACTTGTTATTTTGGGCCTAAC--GGCCCAGTAGTTCCGATTTGAATCGTCTTCGATTTGGCAAA
* * *
813 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTTGTTAGATTAGTC
129 ACTCAATGATTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTTGTGAGATTAGTC
874 GACTTTGAAG
Statistics
Matches: 174, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
189 11 0.06
190 2 0.01
191 118 0.68
192 43 0.25
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (192 bp):
TATGGCCTAACTATAATCATGTTGGTGAGATTAGTCGACTGTGAAGTATTTTAGCTCATTTGCAA
AACTTGTTATTTTGGGCCTAACGGCCCAGTAGTTCCGATTTGAATCGTCTTCGATTTGGCAAAAC
TCAATGATTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTTGTGAGATTAGTCAAC
Found at i:965 original size:155 final size:154
Alignment explanation
Indices: 686--1182 Score: 788
Period size: 155 Copynumber: 3.2 Consensus size: 154
676 ATTAGTCAAC
* * * * *
686 TATGGCCTAACTATAATCATGTTGGTGAGATTAGTTGACTGTGAAGATTTTAGCTCATTTGCAAC
1 TATGGCCTAACTATAATCATTTTTGTGAGATTAGTCGACTTTGAAGTTTTTAGCTCATTTGCAAC
* *
751 ACTTG-TA-TTTGGGCCTATCGGGGCCCATTAGTTCCGATTTGAATCGTCTTCGATTTGGCAAAC
66 ACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAC
814 CTCAATGCTTTTCTTTCCATTGTT
131 CTCAATGCTTTTCTTTCCATTGTT
* *
838 TATGGCCTAACTATAATCATTTTTGTTAGATTAGTCGACTTTGAAGTTTTTAGTCTCATTTGGAA
1 TATGGCCTAACTATAATCATTTTTGTGAGATTAGTCGACTTTGAAGTTTTTAG-CTCATTTGCAA
*
903 CACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGACTCGTCTTCGATTTGGCAAA
65 CACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAA
968 CCTCAATGCTTTTCTTTCCATTGTT
130 CCTCAATGCTTTTCTTTCCATTGTT
*
993 TATGGCCTAACTATAATCATTTTTGGTGAGATTAGTCGA-TTGTGAAGTTTTTAGCTCTATTTGT
1 TATGGCCTAACTATAATCATTTTT-GTGAGATTAGTCGACTT-TGAAGTTTTTAGCTC-ATTTGC
* * * *
1057 AAAACTTGTTATCTTGGGCCTAAC--GGCCCAGTAGTTCCGTTTTGAATCGTCTTCGATTTGGCA
63 AACACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGAATCGTCTTCGATTTGGCA
1120 AACCTCAATGCTTTTCTTTCCATTGTT
128 AACCTCAATGCTTTTCTTTCCATTGTT
1147 TATGGCCTAACTATAATCATTTTTGTGAGATTAGTC
1 TATGGCCTAACTATAATCATTTTTGTGAGATTAGTC
1183 AACTATGGCC
Statistics
Matches: 322, Mismatches: 17, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
152 47 0.15
153 28 0.09
154 90 0.28
155 106 0.33
156 51 0.16
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (154 bp):
TATGGCCTAACTATAATCATTTTTGTGAGATTAGTCGACTTTGAAGTTTTTAGCTCATTTGCAAC
ACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAC
CTCAATGCTTTTCTTTCCATTGTT
Found at i:1080 original size:500 final size:499
Alignment explanation
Indices: 340--1682 Score: 2298
Period size: 500 Copynumber: 2.7 Consensus size: 499
330 ATTAGTTGAC
*
340 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTTGATTGTGAAGTTTTTAGCTCATTTGGAAC
1 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGATTGTGAAGTTTTTAGCTCATTTGGAAC
405 ACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGACTCGTCTTCGATTTGGCAAAC
66 ACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGACTCGTCTTCGATTTGGCAAAC
470 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGATTG
131 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGATTG
535 TGAAGTTTTTTAGCTCATTTGTAAAACTTGTTATTTTGGGCCTAACGGCCCAGTAGTTCCGTTTT
196 TGAAG-TTTTTAGCTCATTTGTAAAACTTGTTATTTTGGGCCTAACGGCCCAGTAGTTCCGTTTT
* *
600 GAATCGTCTTCGATTTGGCAAAACTCAATGATTTTCTTTCCATTGTTTATGGCCTAACTATAATC
260 GAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
665 ATTTTTGTGAGATTAGTCAACTATGGCCTAACTATAATCATGTTGGTGAGATTAGTTGACTGTGA
325 ATTTTTGTGAGATTAGTCAACTATGGCCTAACTATAATCATGTTGGTGAGATTAGTTGACTGTGA
*
730 AGATTTTAGCTCATTTGCAACACTTG-TA-TTTGGGCCTATCGGGGCCCATTAGTTCCGATTTGA
390 AGATTTTAGCTCATTTGCAACACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGATTTGA
*
793 ATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT
455 ATCGTCTTCGATTCGGCAAACCTCAATGCTTTTCTTTCCATTGTT
* *
838 TATGGCCTAACTATAATCATTTTTGTTAGATTAGTCGACTT-TGAAGTTTTTAGTCTCATTTGGA
1 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGA-TTGTGAAGTTTTTAG-CTCATTTGGA
902 ACACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGACTCGTCTTCGATTTGGCAA
64 ACACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGACTCGTCTTCGATTTGGCAA
967 ACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTTGGTGAGATTAGTCGA
129 ACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA-TTTTGGTGAGATTAGTCGA
*
1032 TTGTGAAGTTTTTAGCTCTATTTGTAAAACTTGTTATCTTGGGCCTAACGGCCCAGTAGTTCCGT
193 TTGTGAAGTTTTTAGCTC-ATTTGTAAAACTTGTTATTTTGGGCCTAACGGCCCAGTAGTTCCGT
1097 TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
257 TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
*
1162 ATCATTTTTGTGAGATTAGTCAACTATGGCCTAACTATAATCATTTTGGTGAGATTAGTTGACTG
322 ATCATTTTTGTGAGATTAGTCAACTATGGCCTAACTATAATCATGTTGGTGAGATTAGTTGACTG
* *
1227 TGAAGTTTTTAGCTCATTTGCAACACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTT
387 TGAAGATTTTAGCTCATTTGCAACACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGATT
*
1292 TGACTCGTCTTCGATTCGGCAAACCTCAATGCTTTTCTTTCCATTGTT
452 TGAATCGTCTTCGATTCGGCAAACCTCAATGCTTTTCTTTCCATTGTT
*
1340 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGATTGTGAAGTTTTTAGCTCATTCGGAAC
1 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGATTGTGAAGTTTTTAGCTCATTTGGAAC
* * * * *
1405 ACTTGTTATCTTGGGCCTAACGGGG-CCATTAGTTCCGTTTTGAATCTTCTTCGATTTGGCAAAC
66 ACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGACTCGTCTTCGATTTGGCAAAC
* * * * *
1469 CTCAAAGCTTTTCTTTCCATTGTTTATGGCATAACTATAATCATTTTAGTGAGATTAGTCCACTG
131 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGATTG
* * * * ** *
1534 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGACCCACTAAATACGTTT
196 TGAAGTTTTTAGCTCATTTGTAAAACTTGTTATTTTGGGCCTAACG-G-CCCAGTAGTTCCGTTT
* *
1599 TGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCATAACTATAAT
259 TGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
*
1664 CATTTTAGTGAGATTAGTC
324 CATTTTTGTGAGATTAGTC
1683 CACTGTGAAG
Statistics
Matches: 800, Mismatches: 36, Indels: 16
0.94 0.04 0.02
Matches are distributed among these distances:
498 74 0.09
499 167 0.21
500 397 0.50
501 38 0.05
502 124 0.16
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (499 bp):
TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGATTGTGAAGTTTTTAGCTCATTTGGAAC
ACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGACTCGTCTTCGATTTGGCAAAC
CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGATTG
TGAAGTTTTTAGCTCATTTGTAAAACTTGTTATTTTGGGCCTAACGGCCCAGTAGTTCCGTTTTG
AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
TTTTTGTGAGATTAGTCAACTATGGCCTAACTATAATCATGTTGGTGAGATTAGTTGACTGTGAA
GATTTTAGCTCATTTGCAACACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGATTTGAA
TCGTCTTCGATTCGGCAAACCTCAATGCTTTTCTTTCCATTGTT
Found at i:1322 original size:193 final size:193
Alignment explanation
Indices: 993--1375 Score: 644
Period size: 193 Copynumber: 2.0 Consensus size: 193
983 TTCCATTGTT
* *
993 TATGGCCTAACTATAATCATTTTTGGTGAGATTAGTCGATTGTGAAGTTTTTAGCTCTATTTGTA
1 TATGGCCTAACTATAATCATTTTTGGTGAGATTAGTCGACTGTGAAGTTTTTAGCTCTATTTGCA
* *
1058 AAACTTGTTATCTTGGGCCTAACGGCCCAGTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAC
66 AAACTTGTTATCTTGGGCCTAACGGCCCACTAGTTCCGTTTTGAATCGTCTTCGATTCGGCAAAC
*
1123 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTTGTGAGATTAGTCAAC
131 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCAAC
*
1186 TATGGCCTAACTATAATCA-TTTTGGTGAGATTAGTTGACTGTGAAGTTTTTAGCTC-ATTTGCA
1 TATGGCCTAACTATAATCATTTTTGGTGAGATTAGTCGACTGTGAAGTTTTTAGCTCTATTTGCA
* * * *
1249 ACACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGACTCGTCTTCGATTCGGCAA
66 AAACTTGTTATCTTGGGCCTAAC--GGCCCACTAGTTCCGTTTTGAATCGTCTTCGATTCGGCAA
1314 ACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
129 ACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTC
1376 GATTGTGAAG
Statistics
Matches: 178, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
191 26 0.15
192 35 0.20
193 117 0.66
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (193 bp):
TATGGCCTAACTATAATCATTTTTGGTGAGATTAGTCGACTGTGAAGTTTTTAGCTCTATTTGCA
AAACTTGTTATCTTGGGCCTAACGGCCCACTAGTTCCGTTTTGAATCGTCTTCGATTCGGCAAAC
CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCAAC
Found at i:1523 original size:346 final size:348
Alignment explanation
Indices: 838--1528 Score: 1217
Period size: 346 Copynumber: 2.0 Consensus size: 348
828 TTCCATTGTT
* * * *
838 TATGGCCTAACTATAATCATTTTTGTTAGATTAGTCGACTTTGAAGTTTTTAGTCTCATTTGGAA
1 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGACTGTGAAGTTTTTAGTCTCATTTGCAA
*
903 CACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGACTCGTCTTCGATTTGGCAAA
66 CACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGACTCGTCTTCGATTCGGCAAA
968 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTTGGTGAGATTAGTCGAT
131 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTTGGTGAGATTAGTCGAT
* *
1033 TGTGAAGTTTTTAGCTCTATTTGTAAAACTTGTTATCTTGGGCCTAACGGCCCAGTAGTTCCGTT
196 TGTGAAGTTTTTAGCTCTATTCGGAAAACTTGTTATCTTGGGCCTAACGGCCCAGTAGTTCCGTT
* *
1098 TTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAA
261 TTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCATAACTATAA
*
1163 TCATTTTTGTGAGATTAGTCAAC
326 TCATTTTAGTGAGATTAGTCAAC
*
1186 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTTGACTGTGAAGTTTTTAG-CTCATTTGCAA
1 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGACTGTGAAGTTTTTAGTCTCATTTGCAA
1250 CACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGACTCGTCTTCGATTCGGCAAA
66 CACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGACTCGTCTTCGATTCGGCAAA
1315 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA-TTTTGGTGAGATTAGTCGAT
131 CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTTGGTGAGATTAGTCGAT
* * *
1379 TGTGAAGTTTTTAGCTC-ATTCGGAACACTTGTTATCTTGGGCCTAACGGGGCCATTAGTTCCGT
196 TGTGAAGTTTTTAGCTCTATTCGGAAAACTTGTTATCTTGGGCCTAAC-GGCCCAGTAGTTCCGT
*
1443 TTTGAATCTTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCATAACTATA
260 TTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCATAACTATA
1508 ATCATTTTAGTGAGATTAGTC
325 ATCATTTTAGTGAGATTAGTC
1529 CACTGTGAAG
Statistics
Matches: 327, Mismatches: 15, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
345 27 0.08
346 133 0.41
347 118 0.36
348 49 0.15
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (348 bp):
TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGACTGTGAAGTTTTTAGTCTCATTTGCAA
CACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGACTCGTCTTCGATTCGGCAAA
CCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTTGGTGAGATTAGTCGAT
TGTGAAGTTTTTAGCTCTATTCGGAAAACTTGTTATCTTGGGCCTAACGGCCCAGTAGTTCCGTT
TTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTTTATGGCATAACTATAA
TCATTTTAGTGAGATTAGTCAAC
Found at i:1665 original size:154 final size:154
Alignment explanation
Indices: 1186--1818 Score: 1009
Period size: 154 Copynumber: 4.1 Consensus size: 154
1176 ATTAGTCAAC
* ** *
1186 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTTGACTGTGAAGTTTTTAGCTCATTTGCAAC
1 TATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
* *
1251 ACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGACTCGTCTTCGATTCGGCAAAC
66 ACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAC
*
1316 CTCAATGCTTTTCTTTCCATTGTT
131 CTCAAAGCTTTTCTTTCCATTGTT
* * * *
1340 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGATTGTGAAGTTTTTAGCTCATTCGGAAC
1 TATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
* * * *
1405 ACTTGTTATCTTGGGCCTAACGGGG-CCATTAGTTCCGTTTTGAATCTTCTTCGATTTGGCAAAC
66 ACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAC
1469 CTCAAAGCTTTTCTTTCCATTGTT
131 CTCAAAGCTTTTCTTTCCATTGTT
*
1493 TATGGCATAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
1 TATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
* * ** *
1558 ACTTGTTATTTTGGGCCTATCGAGACCCACTAAATACGTTTTGAATCGTCTTCGATTTGGCAAAC
66 ACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAC
1623 CTCAAAGCTTTTCTTTCCATTGTT
131 CTCAAAGCTTTTCTTTCCATTGTT
* *
1647 TATGGCATAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAA
1 TATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
* *
1712 ACATGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCG-TTTGAATCGTCTTCGATTTGGCAAAC
66 ACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAC
*
1776 CTCAATGCTTTTCTTTCCATTGTT
131 CTCAAAGCTTTTCTTTCCATTGTT
*
1800 TATGGCCTAACCATAATCA
1 TATGGCCTAACTATAATCA
1819 AT
Statistics
Matches: 442, Mismatches: 36, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
153 205 0.46
154 237 0.54
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.39
Consensus pattern (154 bp):
TATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
ACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAC
CTCAAAGCTTTTCTTTCCATTGTT
Found at i:1756 original size:307 final size:307
Alignment explanation
Indices: 1186--1818 Score: 1025
Period size: 307 Copynumber: 2.1 Consensus size: 307
1176 ATTAGTCAAC
* **
1186 TATGGCCTAACTATAATCATTTTGGTGAGATTAGTTGACTGTGAAGTTTTTAGCTCATTTGCAAC
1 TATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGCAAC
* * ** * *
1251 ACTTGTTATTTTGGGCCTATCGGGGCCCACTAGTTCCGTTTTGACTCGTCTTCGATTCGGCAAAC
66 ACTTGTTATTTTGGGCCTATCGAGACCCACTAAATACGTTTTGAATCGTCTTCGATTCGGCAAAC
* * * * *
1316 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCGATTG
131 CTCAAAGCTTTTCTTTCCATTGTTTATGGCATAACTATAATCATTTTAGTGAGATTAGTCCACTG
* *
1381 TGAAGTTTTTAGCTCATTCGGAACACTTGTTATCTTGGGCCTAACGGGGCCATTAGTTCCGTTTT
196 TGAAGTTTTTAGCTCATTCGGAAAACATGTTATCTTGGGCCTAACGGGGCCATTAGTTCCGTTTT
*
1446 GAATCTTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTT
261 GAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTT
* *
1493 TATGGCATAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
1 TATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGCAAC
*
1558 ACTTGTTATTTTGGGCCTATCGAGACCCACTAAATACGTTTTGAATCGTCTTCGATTTGGCAAAC
66 ACTTGTTATTTTGGGCCTATCGAGACCCACTAAATACGTTTTGAATCGTCTTCGATTCGGCAAAC
1623 CTCAAAGCTTTTCTTTCCATTGTTTATGGCATAACTATAATCATTTTAGTGAGATTAGTCCACTG
131 CTCAAAGCTTTTCTTTCCATTGTTTATGGCATAACTATAATCATTTTAGTGAGATTAGTCCACTG
* * *
1688 TGAAGTTTTTAGCTCATTTGGAAAACATGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCG-TT
196 TGAAGTTTTTAGCTCATTCGGAAAACATGTTATCTTGGGCCTAACGGGG-CCATTAGTTCCGTTT
*
1752 TGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT
260 TGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTT
*
1800 TATGGCCTAACCATAATCA
1 TATGGCCTAACTATAATCA
1819 AT
Statistics
Matches: 299, Mismatches: 26, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
307 287 0.96
308 12 0.04
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.39
Consensus pattern (307 bp):
TATGGCCTAACTATAATCATTTTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGCAAC
ACTTGTTATTTTGGGCCTATCGAGACCCACTAAATACGTTTTGAATCGTCTTCGATTCGGCAAAC
CTCAAAGCTTTTCTTTCCATTGTTTATGGCATAACTATAATCATTTTAGTGAGATTAGTCCACTG
TGAAGTTTTTAGCTCATTCGGAAAACATGTTATCTTGGGCCTAACGGGGCCATTAGTTCCGTTTT
GAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTTTCCATTGTT
Done.