Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014711.1 Corchorus capsularis cultivar CVL-1 contig14732, 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: 3075
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Found at i:561 original size:112 final size:111
Alignment explanation
Indices: 342--554 Score: 257
Period size: 112 Copynumber: 1.9 Consensus size: 111
332 AAAAGTCGTG
* ** * **
342 TGTTGGAATGAGATGAGCTTGATAGACAGCGGTATGCACAAACAAAGCTCTCCTCGAAGTGCAAA
1 TGTTGGAATGAGATGAACTTGATAGACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAA
* * * *
407 GCATCAACTTTGCGGGTTTGTATGCAACACATCGTTCGTAGCGGTT
66 ACATCAACTTTGAGGGTTTGTATGCAAAACATCATTCGTAGCGGTT
* ** * *
453 TGTTGGAGTGAGATGAACTTTTTGGACAGCCCTATGCACAAACAAAAGCTTTCCTAGAAGCCCAA
1 TGTTGGAATGAGATGAACTTGATAGACAGCCCTATGCACAAAC-AAAGCTCTCCTAGAAGCCCAA
*
518 AACCTCAACTTTGAGCGG-TTGTATGCAAAACATCATT
65 AACATCAACTTTGAG-GGTTTGTATGCAAAACATCATT
555 TTTAGCGAAA
Statistics
Matches: 84, Mismatches: 16, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
111 36 0.43
112 46 0.55
113 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (111 bp):
TGTTGGAATGAGATGAACTTGATAGACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAA
ACATCAACTTTGAGGGTTTGTATGCAAAACATCATTCGTAGCGGTT
Found at i:873 original size:158 final size:157
Alignment explanation
Indices: 459--876 Score: 407
Period size: 158 Copynumber: 2.6 Consensus size: 157
449 GGTTTGTTGG
* * * * * *
459 AGTGAGATGAACTTTTTGGACAGCCCTATGCACAAACAAAAGCTTTCCTAGAAGCCCAAAACCTC
1 AGTGAGATGAGCTTGTTGGACAGCCCTATGCACAAAC-AAAGCTTTCCTCGAAGTCCAAAGCATC
* * * * * *
524 AACTTTGAGCGGTTGTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGATGAATTTTTTG
65 AACTTTGTGAGTTTGTATGC-AAACATCGTTCTTAGAGAAA-GCTCATTCCAGATGAATTTTTTG
* *
589 CGCTACGAGTGCTCAAATGTCGTGCGTCGA
128 CGCAACGAGTGCTCAAAGGTCGTGCGTCGA
* * *
619 AGTGCA-ATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCGTC
1 AGTG-AGATGAGCTTGTTGGACAGCCCTATGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCATC
* * * * * * **
683 AA-TTT-TGCACATTTTTGTGCTAAACATAGTTCTTAGTAG-AA-CTCTTTCTAGATGCGTTTTT
65 AACTTTGTG-A-GTTTGTATGC-AAACATCGTTCTTAG-AGAAAGCTCATTCCAGATGAATTTTT
* *
744 TCGCGCAACGAGT-CGTCAAAGGTCTTGTGTCGA
126 T-GCGCAACGAGTGC-TCAAAGGTCGTGCGTCGA
* * * * *
777 AGTGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTTCGAAGCATCA
1 AGTGAGATGAGCTTGTTGGACAGCCCTATGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCATCA
842 ACTTTGTGAGTTTGTATGCAACACATCGTTCTTAG
66 ACTTTGTGAGTTTGTATGCAA-ACATCGTTCTTAG
877 CGGTTTGCCG
Statistics
Matches: 209, Mismatches: 39, Indels: 22
0.77 0.14 0.08
Matches are distributed among these distances:
157 22 0.11
158 103 0.49
159 49 0.23
160 34 0.16
161 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (157 bp):
AGTGAGATGAGCTTGTTGGACAGCCCTATGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCATCA
ACTTTGTGAGTTTGTATGCAAACATCGTTCTTAGAGAAAGCTCATTCCAGATGAATTTTTTGCGC
AACGAGTGCTCAAAGGTCGTGCGTCGA
Found at i:1213 original size:157 final size:157
Alignment explanation
Indices: 885--1305 Score: 426
Period size: 158 Copynumber: 2.7 Consensus size: 157
875 AGCGGTTTGC
* * * *
885 CGGAATGAGATGA-ACTTTTTGGACAGCCCTGTGCATAAACAAAGCTTTCCTAGAAGCCTAAAAC
1 CGGAATGAGATGAGA-TTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCC-A-AATCC-AAAGC
* * *
949 CTCAACTTTG-AGCGTTTGTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGTTGCATTT
62 CTCAACTTTGCAGCGTTTGTATGCAAAACATCATTCTTAGCGAAAGACTCATTCCAGATGCATTT
*
1013 TTTGCGCAACGAGTGCTCAAATGTCGTGCGT
127 TTTGCGCAACGAGTGCTCAAAAGTCGTGCGT
* *
1044 C-GAATTGTGATGAGATTGTTGGACTGCCCTGTGCACAAACAAAGCTTTCACAAATTCCAAAGCC
1 CGGAA-TGAGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTC-CAAA-TCCAAAGCC
* * * * ** *
1108 TCAACTTTGCA-CGTTTTTGTGCTAAACAT-AGTTCTTAGC-AAA-ACTCTTTCTGGATGCGTTT
63 TCAACTTTGCAGCGTTTGTATGCAAAACATCA-TTCTTAGCGAAAGACTCATTCCAGATGCATTT
*
1169 TTTCGCGCAACGAGTGCTCAAAAGTCGTGTGT
127 TTT-GCGCAACGAGTGCTCAAAAGTCGTGCGT
* * * * * * *
1201 CGGAATGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCA
1 CGGAATGAGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCT-T--TCCAAATCCAAAGCC
* * *
1266 TCAACTTTGC-GAGTTTGTATGCAACACATCGTTCTTAGCG
63 TCAACTTTGCAGCGTTTGTATGCAAAACATCATTCTTAGCG
1306 GTTTGTCGGA
Statistics
Matches: 215, Mismatches: 33, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
156 16 0.07
157 66 0.31
158 84 0.39
159 45 0.21
160 4 0.02
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (157 bp):
CGGAATGAGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCAAATCCAAAGCCTCA
ACTTTGCAGCGTTTGTATGCAAAACATCATTCTTAGCGAAAGACTCATTCCAGATGCATTTTTTG
CGCAACGAGTGCTCAAAAGTCGTGCGT
Found at i:1283 original size:427 final size:428
Alignment explanation
Indices: 1--2164 Score: 3135
Period size: 428 Copynumber: 5.1 Consensus size: 428
* * *
1 ATGCAACACATCGTTCTTAGCGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTATGTAGA
1 ATGCAACACATCGTTCTTAGCGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCACA
* * * * * *
66 AACAAAACTTTACTCGAAGCCCAAAACCTCAACTCTGAGTGGTTGTATGCAAAACATCATTTTTT
66 AACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTTTA
*
131 GCGAAAGCCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGC
131 GCGAAAGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGC
* * * *
196 GCTGAGATTGTTGGACAGCCCTGTGCAGAAACAATGCTTT-CACGAATTCCAAAGCCTCAACTTT
196 GATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCACGAAGTCCAAAGCCTCAACTTT
* *
260 GCGCGTTTTTGTGCTAGAA-ATAGTTCTTAGCAAAACTCTTTCT-GAATGCGTTTTTTCGCGCAA
261 GCACATTTTTGTGCTA-AACATAGTTCTTAGCAAAACTCTTTCTAG-ATGCGTTTTTTCGCGCAA
* *
323 CGAGTGCTCAAAAGTCGTGTGTTGGAATGAGATGAGCTTGATAGACAGCGGTATGCACAAACAAA
324 CGAGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGATAGACAGCGCTATGCACAAACAAA
* *
388 GCTCTCCTCGAAGTGCAAAGCATCAACTTTGCGGGTTTGT
389 GCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGAGTTTGT
* * *
428 ATGCAACACATCGTTCGTAGCGGTTTGTTGGAGTGAGATGAACTTTTTGGACAGCCCTATGCACA
1 ATGCAACACATCGTTCTTAGCGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCACA
493 AACAAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTTT
66 AAC-AAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTTT
* * *
558 AGCGAAAGGCTCATTCCAGATGAATTTTTTGCGCTACGAGTGCTCAAATGTCGTGCGTCGAAGTG
130 AGCGAAAGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTG
* * * *
623 CAATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCGTCAATTT
195 CGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCACGAAGTCCAAAGCCTCAACTT
* *
688 TGCACATTTTTGTGCTAAACATAGTTCTTAGTAGAACTCTTTCTAGATGCGTTTTTTCGCGCAAC
260 TGCACATTTTTGTGCTAAACATAGTTCTTAGCAAAACTCTTTCTAGATGCGTTTTTTCGCGCAAC
* * *
753 GAGT-CGTCAAAGGTCTTGTGTC-GAAGTGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAA
325 GAGTGC-TCAAAAGTCGTGTGTCGGAA-TGAGATGAGCTTGATAGACAGCGCTATGCACAAACAA
* * *
816 AGCTCTCCTCGAAGTTCGAAGCATCAACTTTGTGAGTTTGT
388 AGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGAGTTTGT
* * *
857 ATGCAACACATCGTTCTTAGCGGTTTGCCGGAATGAGATGAACTTTTTGGACAGCCCTGTGCATA
1 ATGCAACACATCGTTCTTAGCGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCACA
* *
922 AACAAAGCTTTCCTAGAAGCCTAAAACCTCAACTTTGAGCGTTTGTATGCAAAACATCATTTTTA
66 AACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTTTA
* *
987 GCGAAAGGCTCATTCCAGTTGCATTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGT
131 GCGAAAGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGC
* * *
1052 GATGAGATTGTTGGACTGCCCTGTGCACAAACAAAGCTTT-CACAAATTCCAAAGCCTCAACTTT
196 GATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCACGAAGTCCAAAGCCTCAACTTT
* *
1116 GCACGTTTTTGTGCTAAACATAGTTCTTAGCAAAACTCTTTCTGGATGCGTTTTTTCGCGCAACG
261 GCACATTTTTGTGCTAAACATAGTTCTTAGCAAAACTCTTTCTAGATGCGTTTTTTCGCGCAACG
*
1181 AGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGC
326 AGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGATAGACAGCGCTATGCACAAACAAAGC
1246 TCTCCTCGAAGTCCAAAGCATCAACTTTGCGAGTTTGT
391 TCTCCTCGAAGTCCAAAGCATCAACTTTGCGAGTTTGT
*
1284 ATGCAACACATCGTTCTTAGCGGTTTGTCGGAATGAGATGAACTTTTTGGACAGCCCTGTGCACA
1 ATGCAACACATCGTTCTTAGCGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCACA
* * * * *
1349 AACAAAGCTTCCCTAGAAGCCCAAAACCTCAACTTTGAGCGTTTGTGTGCAAAACATCGTTTTGA
66 AACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTTTA
* ** * * * *
1414 G-GAACAGGCTCATTCCAGATGCGTTTTTTGCGCATTGAGTGCTTAAATGTCATGCGTCGGAGTG
131 GCGAA-AGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTG
* * * * * * *
1478 AGTTGAGCA-TGTTGGAAAGCCCTTTGCACAAACAAAGTTTTCCCCGAAGTCCAAAACCTCAACT
195 CGATGAG-ATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCACGAAGTCCAAAGCCTCAACT
* * * * *
1542 TAT-CATCA-TTTTGTGCAAAACATCGTTGTTAGCAAAACTCTTTTTCCAGATGCGATTTTTTTG
259 T-TGCA-CATTTTTGTGCTAAACATAGTTCTTAGCAAAACTC--TTTCTAGATGCG-TTTTTTCG
* * * ** * ** * *
1605 TGCAATGAGTGCTCAAAAGTCGTTTGTTAGAGTGAGATGAGCAAGATGGACAGCCCTATGCACAA
319 CGCAACGAGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGATAGACAGCGCTATGCACAA
* * **
1670 ACAAAGCTCTCCTCGAAGTCGAAAGCATCAACTTTGCGTGAATGT
384 ACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGAGTTTGT
* * ** *
1715 ATGCCAA-ACATCGTTCTTAGCGGTGTGTCGGAGTGAGATGAGCAATTTGGACAACCCTGTGCAC
1 ATG-CAACACATCGTTCTTAGCGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCAC
* *
1779 AAACAAAGCTTTCTTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGTAAAACATCATTTTT
65 AAACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTTT
* *
1844 AGCGAAAGGCTCATTCGAGATGCATTTTTTGCGCTACGAGTGCTCAAATGTCGTGCGTCGAATTG
130 AGCGAAAGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTG
* * *
1909 CGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCGTCAATTT
195 CGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCACGAAGTCCAAAGCCTCAACTT
* *
1974 TGCACATTTTTGTGCTAAACATAGTTCTTAGTAGAACTCTTTCTAGATGCGTTTTTTCGCGCAAC
260 TGCACATTTTTGTGCTAAACATAGTTCTTAGCAAAACTCTTTCTAGATGCGTTTTTTCGCGCAAC
* * *
2039 GAGTGCTCAAAGGTCGTGTGTCGGAGTGAGATGAGCTTGCTAGACAGCGCTATGCACAAACAAAG
325 GAGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGATAGACAGCGCTATGCACAAACAAAG
* * *
2104 CTCTCCTCGAAGTCGAAAGCATCAACATTGCGCGTTTGT
390 CTCTCCTCGAAGTCCAAAGCATCAACTTTGCGAGTTTGT
*
2143 TTGCAACACATCGTTCTTAGCG
1 ATGCAACACATCGTTCTTAGCG
2165 AAAGGCTCAT
Statistics
Matches: 1550, Mismatches: 165, Indels: 43
0.88 0.09 0.02
Matches are distributed among these distances:
426 3 0.00
427 447 0.29
428 491 0.32
429 239 0.15
430 15 0.01
431 349 0.23
432 6 0.00
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.29
Consensus pattern (428 bp):
ATGCAACACATCGTTCTTAGCGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCACA
AACAAAGCTTTCCTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTTTA
GCGAAAGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGC
GATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCACGAAGTCCAAAGCCTCAACTTT
GCACATTTTTGTGCTAAACATAGTTCTTAGCAAAACTCTTTCTAGATGCGTTTTTTCGCGCAACG
AGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGATAGACAGCGCTATGCACAAACAAAGC
TCTCCTCGAAGTCCAAAGCATCAACTTTGCGAGTTTGT
Found at i:1373 original size:111 final size:111
Alignment explanation
Indices: 1198--1409 Score: 291
Period size: 111 Copynumber: 1.9 Consensus size: 111
1188 AAAAGTCGTG
* * * *
1198 TGTCGGAATGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAA
1 TGTCGGAATGAGATGAACTTGTTAGACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAA
* * *
1263 GCATCAACTTTGCGAGTTTGTATGCAACACATCGTTCTTAGCGGTT
66 ACATCAACTTTGAGAGTTTGTATGCAAAACATCGTTCTTAGCGGTT
* * *
1309 TGTCGGAATGAGATGAACTTTTTGGACAGCCCTGTGCACAAACAAAGCT-TCCCTAGAAGCCCAA
1 TGTCGGAATGAGATGAACTTGTTAGACAGCCCTATGCACAAACAAAGCTCT-CCTAGAAGCCCAA
* * *
1373 AACCTCAACTTTGAGCGTTTGTGTGCAAAACATCGTT
65 AACATCAACTTTGAGAGTTTGTATGCAAAACATCGTT
1410 TTGAGGAACA
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
110 1 0.01
111 86 0.99
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (111 bp):
TGTCGGAATGAGATGAACTTGTTAGACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAA
ACATCAACTTTGAGAGTTTGTATGCAAAACATCGTTCTTAGCGGTT
Found at i:1703 original size:161 final size:158
Alignment explanation
Indices: 1331--1704 Score: 392
Period size: 161 Copynumber: 2.3 Consensus size: 158
1321 ATGAACTTTT
* * * * *
1331 TGGACAGCCCTGTGCACAAACAAAGCTTCCCTAGAAGCCCAAAACCTCAACTTTGAGCGTTTGTG
1 TGGACAGCCCTATGCACAAACAAAGCTT-CCTCGAAGTCCAAAACCTCAACTTTCAGCATTTGTG
* * * * *
1396 TGCAAAACATCGTTTTGAGGAACAGGCTCATTCCAGATGCGTTTTTTGCGCATTGAGTGCTTAAA
65 TGCAAAACATCGTTTTGAGCAAAACGCTCATTCCAGATGCGTTTTTTGCGCAATGAGTGCTCAAA
* * * * *
1461 TGTCATGCGTCGGAGTGAGTTGAGCATGT
130 AGTCATGCGTCAGAGTGAGATGAGCAAGA
* * * * *
1490 TGGAAAGCCCTTTGCACAAACAAAGTTTTCCCCGAAGTCCAAAACCTCAACTTATCATCATTT-T
1 TGGACAGCCCTATGCACAAACAAAG-CTTCCTCGAAGTCCAAAACCTCAACTT-TCAGCATTTGT
* ** *
1554 GTGCAAAACATCGTTGTT-AGCAAAACTCTTTTTCCAGATGCGATTTTTTTGTGCAATGAGTGCT
64 GTGCAAAACATCGTT-TTGAGCAAAACGCTCATTCCAGATGCG--TTTTTTGCGCAATGAGTGCT
* ** *
1618 CAAAAGTCGTTTGTTAGAGTGAGATGAGCAAGA
126 CAAAAGTCATGCGTCAGAGTGAGATGAGCAAGA
* * *
1651 TGGACAGCCCTATGCACAAACAAAGCTCTCCTCGAAGTCGAAAGCATCAACTTT
1 TGGACAGCCCTATGCACAAACAAAGCT-TCCTCGAAGTCCAAAACCTCAACTTT
1705 GCGTGAATGT
Statistics
Matches: 175, Mismatches: 34, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
159 78 0.45
160 12 0.07
161 85 0.49
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (158 bp):
TGGACAGCCCTATGCACAAACAAAGCTTCCTCGAAGTCCAAAACCTCAACTTTCAGCATTTGTGT
GCAAAACATCGTTTTGAGCAAAACGCTCATTCCAGATGCGTTTTTTGCGCAATGAGTGCTCAAAA
GTCATGCGTCAGAGTGAGATGAGCAAGA
Found at i:1828 original size:111 final size:111
Alignment explanation
Indices: 1634--1847 Score: 257
Period size: 111 Copynumber: 1.9 Consensus size: 111
1624 TCGTTTGTTA
* * * * *
1634 GAGTGAGATGAGCAAGATGGACAGCCCTATGCACAAACAAAGCTCTCCTCGAAGTCGAAAGCATC
1 GAGTGAGATGAGCAAGATGGACAACCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAAACATC
* * * *
1699 AACTTTGCGTGAATGTATGCCAAACATCGTTCTTAGCGGTGTGTCG
66 AACTTTGAGCGAATGTATGCAAAACATCATTCTTAGCGGTGTGTCG
** * * * *
1745 GAGTGAGATGAGCAATTTGGACAACCCTGTGCACAAACAAAGCTTTCTTAGAAGCCCAAAACCTC
1 GAGTGAGATGAGCAAGATGGACAACCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAAACATC
** * *
1810 AACTTTGAGCGGTTGTATGTAAAACATCATTTTTAGCG
66 AACTTTGAGCGAATGTATGCAAAACATCATTCTTAGCG
1848 AAAGGCTCAT
Statistics
Matches: 84, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
111 84 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24
Consensus pattern (111 bp):
GAGTGAGATGAGCAAGATGGACAACCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAAACATC
AACTTTGAGCGAATGTATGCAAAACATCATTCTTAGCGGTGTGTCG
Found at i:2085 original size:158 final size:156
Alignment explanation
Indices: 1861--2456 Score: 687
Period size: 158 Copynumber: 3.8 Consensus size: 156
1851 GGCTCATTCG
* * *
1861 AGATGCATTTTTTGCGCTACGAGTGCTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGAC
1 AGATGCATTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGAGATGAGATTGTTAGAC
* * * * * *
1926 AGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCGTCAATTTTGCACATTTTTGTGCTA
66 AGCCCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGCGTTTTTGTGCTA
1991 AACATAGTTCTTAGTAGAACTCTTTCT
131 AACATAGTTCTTAG-AGAACTCTTTCT
* * * * * * *
2018 AGATGCGTTTTTTCGCGCAACGAGTGCTCAAAGGTCGTGTGTCGGAGTGAGATGAGCTTGCTAGA
1 AGATGCATTTTTT-GCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGAGATGAGATTGTTAGA
* * *
2083 CAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCGAAAGCATCAACATTGCGCGTTTGTT-TGC
65 CAGCCCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGCGTTT-TTGTGC
* * * *
2147 -AACACATCGTTCTTAGCGAAAGGCTCATTCC
129 TAA-ACATAGTTCTTAGAG-AA--CTCTTTCT
* *
2178 AGATGCATTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGAC
1 AGATGCATTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGAGATGAGATTGTTAGAC
* * * * * * *
2243 AGCCCTGTGCAGAAACAAAGCT-TTCACGAATTCCAAAGCCTCAACTTTGCGCGTTTTTGTGTTA
66 AGCCCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGCGTTTTTGTGCTA
*
2307 AACATAGTTCTTAGCAAAACTCTTTCT
131 AACATAGTTCTTAG-AGAACTCTTTCT
* * * ** * *
2334 CGATGCGTTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGTATGGGAA-TGAGATGAGCTTGTTAG
1 AGATGCATTTTTT-GCGCAACGAGTGCTCAAATGTCGTGCGT-CGAATTGAGATGAGATTGTTAG
* * *
2398 CCAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGAGTTT
64 ACAGCCCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGCGTTT
2457 GTATGCAACA
Statistics
Matches: 362, Mismatches: 65, Indels: 23
0.80 0.14 0.05
Matches are distributed among these distances:
156 17 0.05
157 76 0.21
158 184 0.51
159 67 0.19
160 18 0.05
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (156 bp):
AGATGCATTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGAGATGAGATTGTTAGAC
AGCCCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGCGTTTTTGTGCTA
AACATAGTTCTTAGAGAACTCTTTCT
Found at i:2422 original size:316 final size:317
Alignment explanation
Indices: 1774--2480 Score: 1083
Period size: 316 Copynumber: 2.2 Consensus size: 317
1764 GACAACCCTG
* * * * * * * * * *
1774 TGCACAAACAAAGCTTTCTTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGTATGTAAAACATCA
1 TGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGCGTTTGTATGCAACACATCA
* * *
1839 TTTTTAGCGAAAGGCTCATTCGAGATGCATTTTTTGCGCTACGAGTGCTCAAATGTCGTGCGTCG
66 TTCTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCG
* *
1904 AATTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCTCGAAGTCCAAAGCGTC
131 AATTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCACGAAGTCCAAAGCCTC
* * *
1969 AATTTTGCACATTTTTGTGCTAAACATAGTTCTTAGTAGAACTCTTTCTAGATGCGTTTTTTCGC
196 AACTTTGCACATTTTTGTGCTAAACATAGTTCTTAGCAAAACTCTTTCTAGATGCGTTTTTTCGC
* * *
2034 GCAACGAGTGCTCAAAGGTCGTGTGTCGGAGTGAGATGAGCTTGCTAGACAGCGCTA
261 GCAACGAGTGCTCAAAAGTCGTGTATCGGAATGAGATGAGCTTGCTAGACAGCGCTA
* * * *
2091 TGCACAAACAAAGCTCTCCTCGAAGTCGAAAGCATCAACATTGCGCGTTTGTTTGCAACACATCG
1 TGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGCGTTTGTATGCAACACATCA
2156 TTCTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCG
66 TTCTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCG
* *
2221 AATTGCGATGAGATTGTTGGACAGCCCTGTGCAGAAACAAAGCTTT-CACGAATTCCAAAGCCTC
131 AATTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCACGAAGTCCAAAGCCTC
* * * *
2285 AACTTTGCGCGTTTTTGTGTTAAACATAGTTCTTAGCAAAACTCTTTCTCGATGCGTTTTTTCGC
196 AACTTTGCACATTTTTGTGCTAAACATAGTTCTTAGCAAAACTCTTTCTAGATGCGTTTTTTCGC
* * *
2350 GCAACGAGTGCTCAAAAGTCGTGTATGGGAATGAGATGAGCTTGTTAGCCAGCGCTA
261 GCAACGAGTGCTCAAAAGTCGTGTATCGGAATGAGATGAGCTTGCTAGACAGCGCTA
* *
2407 TGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGAGTTTGTATGCAACACTTCA
1 TGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGCGTTTGTATGCAACACATCA
2472 TTCTTAGCG
66 TTCTTAGCG
2481 GTTTGTCGGA
Statistics
Matches: 350, Mismatches: 40, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
316 192 0.55
317 158 0.45
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (317 bp):
TGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGCGTTTGTATGCAACACATCA
TTCTTAGCGAAAGGCTCATTCCAGATGCATTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCG
AATTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCACGAAGTCCAAAGCCTC
AACTTTGCACATTTTTGTGCTAAACATAGTTCTTAGCAAAACTCTTTCTAGATGCGTTTTTTCGC
GCAACGAGTGCTCAAAAGTCGTGTATCGGAATGAGATGAGCTTGCTAGACAGCGCTA
Found at i:2556 original size:111 final size:111
Alignment explanation
Indices: 2381--2591 Score: 246
Period size: 111 Copynumber: 1.9 Consensus size: 111
2371 TGTATGGGAA
* * * * * *
2381 TGAGATGAGCTTGTTAGCCAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAAC
1 TGAGATGAACTTGTTAGACAGCCCTATGCACAAACAAAGCTCTACTAGAAGGCCAAAGCATCAAC
* * * *
2446 TTTGCG-AGTTTGTATGCAACACTTCATTCTTAGCGGTTTGTCGGAG
66 TTTGAGCAG-TTCTATGCAAAACATCATTCTTAGCGGTTTGTCGGAG
* * * * *
2492 TGAGATGAACTTTTTGGACAGCCCTATGCAGAAACAAAGCTTTACTAGAAGGCCAAAATC-TCAA
1 TGAGATGAACTTGTTAGACAGCCCTATGCACAAACAAAGCTCTACTAGAAGGCC-AAAGCATCAA
*
2556 CTTTGAGCAGTTCTATGCAAAACATCATTTTTAGCG
65 CTTTGAGCAGTTCTATGCAAAACATCATTCTTAGCG
2592 AAAGGCTCAT
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
111 76 0.93
112 6 0.07
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (111 bp):
TGAGATGAACTTGTTAGACAGCCCTATGCACAAACAAAGCTCTACTAGAAGGCCAAAGCATCAAC
TTTGAGCAGTTCTATGCAAAACATCATTCTTAGCGGTTTGTCGGAG
Found at i:2739 original size:744 final size:749
Alignment explanation
Indices: 1309--2909 Score: 2215
Period size: 744 Copynumber: 2.1 Consensus size: 749
1299 CTTAGCGGTT
* * * * * * * *
1309 TGTCGGAATGAGATGAACTTTTTGGACAGCCCTGTGCACAAACAAAGCT-TCCCTAGAAGCCCAA
1 TGTCGGAGTGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCT-CCTCGAAGTCCAA
* * * * *
1373 AACCTCAACTTTGAGCGTTTGTGTGCAAAACATCGTT-TTGAG-GAACAGGCTCATTCCAGATGC
65 AGCATCAACTTTGCGCGTTTGTATGCAACACATCGTTCTT-AGCGAACAGGCTCATTCCAGATGC
* ** * * *
1436 GTTTTTTGCGCATTGAGTGCTTAAATGTCATGCGTCGGAGTGAGTTGAGCATGTTGGAAAGCCCT
129 ATTTTTTGCGCAACGAGTGCTCAAATGTCATGCGTCGAAGTGAGATGAGCATGTTGGAAAGCCCT
* * * * *
1501 TTGCACAAACAAAGTTTTCCCCGAAGTCCAAAACCTCAACTTATCATCATTTTGTGCAAAACATC
194 GTGCACAAACAAAGCTTTCCACGAAGTCCAAAACCTCAACTTATCAGCATTTTGTGCAAAACATA
* * * * * * *
1566 GTTGTTAGCAAAACTCTTTTTCCAGATGCGATTTTTTTGTGCAATGAGTGCTCAAAAGTCGTTTG
259 GTTCTTAGCAAAACTCTTTCTCCAGATGCGATTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGTA
* * * *
1631 TTAGAGTGAGATGAGCAAGATGGACAGCCCTATGCACAAACAAAGCTCTCCTCGAAGTCGAAAGC
324 TGAGAATGAGATGAGCAAGATAGACAGCCCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGC
* * *
1696 ATCAACTTTGCGTGAATGTATGCCAAACATCGTTCTTAGCGGTGTGTCGGAGTGAGATGAGCAAT
389 ATCAACTTTGCGAGAATGTATGCCAAACATCATTCTTAGCGGTGTGTCGGAGTGAGATGAACAAT
* * *
1761 TTGGACAACCCTGTGCACAAACAAAGCTTTCTTAGAAGCCCAAAACCTCAACTTTGAGCGGTTGT
454 TTGGACAACCCTATGCACAAACAAAGCTTTCTTAGAAGCCCAAAACCTCAACTTTGAGCAGTTCT
* * * *
1826 ATGTAAAACATCATTTTTAGCGAAAGGCTCATTCGAGATGCATTTTTTGCGCTACGAGTGCTCAA
519 ATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGAAGCATTTTTTGCGCAACGAGTGCTCAA
* *
1891 ATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCCTCGA
584 ATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAACCCTGTGCACAAACAAAGCTTTCCACGA
* * * *
1956 AGTCCAAAGCGTCAATTTTGCACATTTTTGTGCTAAACATAGTTCTTAGTAGAACTCTTTCTAGA
649 AGTCCAAAGCCTCAACTTTGCACATTTTTGTGCTAAACATAGTTCATAGCAGAACTCTTTCTAGA
* *
2021 TGCGTTTTTTCGCGCAACGAGTGCT-CAAAGGTCGTG
714 TGCGTTTTTTCGCACAACGAGTGCTAAAAAGG-CGTG
* *
2057 TGTCGGAGTGAGATGAGCTTGCTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCGAAA
1 TGTCGGAGTGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAA
* *
2122 GCATCAACATTGCGCGTTTGTTTGCAACACATCGTTCTTAGCGAA-AGGCTCATTCCAGATGCAT
66 GCATCAACTTTGCGCGTTTGTATGCAACACATCGTTCTTAGCGAACAGGCTCATTCCAGATGCAT
* * * *
2186 TTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGCGATGAG-ATTGTTGGACAGCCCTG
131 TTTTTGCGCAACGAGTGCTCAAATGTCATGCGTCGAAGTGAGATGAGCA-TGTTGGAAAGCCCTG
* * * * **
2250 TGCAGAAACAAAGCTTT-CACGAATTCCAAAGCCTCAACTT-TGC-GCGTTTTTGTGTTAAACAT
195 TGCACAAACAAAGCTTTCCACGAAGTCCAAAACCTCAACTTAT-CAGC-ATTTTGTGCAAAACAT
2312 AGTTCTTAGCAAAACTCTTTCT-C-GATGCG-TTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGT
258 AGTTCTTAGCAAAACTCTTTCTCCAGATGCGATTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGT
* ** * * *
2374 ATGGGAATGAGATGAGCTTGTTAGCCAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAG
323 ATGAGAATGAGATGAGCAAGATAGACAGCCCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAG
** * * *
2439 CATCAACTTTGCGAGTTTGTATG-CAACACTTCATTCTTAGCGGTTTGTCGGAGTGAGATGAACT
388 CATCAACTTTGCGAGAATGTATGCCAA-ACATCATTCTTAGCGGTGTGTCGGAGTGAGATGAACA
* * * * *
2503 TTTTGGACAGCCCTATGCAGAAACAAAGCTTTAC-TAGAAGGCCAAAATCTCAACTTTGAGCAGT
452 ATTTGGACAACCCTATGCACAAACAAAGCTTT-CTTAGAAGCCCAAAACCTCAACTTTGAGCAGT
2567 TCTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGAAAGCATTTTTTGCGCAACGAGTGC
516 TCTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAG-AAGCATTTTTTGCGCAACGAGTGC
2632 TCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAACCCTGTGCACAAACAAAGCTTT-C
580 TCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAACCCTGTGCACAAACAAAGCTTTCC
***
2696 ACGAAGTCCAAAGCCTCAACTTTGCGTGTTTTTGTGCTAAACATAGTTCATAGCAGAACTCTTTC
645 ACGAAGTCCAAAGCCTCAACTTTGCACATTTTTGTGCTAAACATAGTTCATAGCAGAACTCTTTC
*
2761 TGGATGCGTTTTTTCGCACAACGAGTGCTAAAAAAGGCGTG
710 TAGATGCGTTTTTTCGCACAACGAGTGCT-AAAAAGGCGTG
2802 TGTCGGAGTGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAA
1 TGTCGGAGTGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAA
*
2867 GCATCAACTTTGCGTGTTTGTATGCAACACATCGTTCTTAGCG
66 GCATCAACTTTGCGCGTTTGTATGCAACACATCGTTCTTAGCG
2910 GTTTGTCGGA
Statistics
Matches: 751, Mismatches: 91, Indels: 25
0.87 0.10 0.03
Matches are distributed among these distances:
743 3 0.00
744 312 0.42
745 198 0.26
746 8 0.01
747 54 0.07
748 170 0.23
749 6 0.01
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (749 bp):
TGTCGGAGTGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAA
GCATCAACTTTGCGCGTTTGTATGCAACACATCGTTCTTAGCGAACAGGCTCATTCCAGATGCAT
TTTTTGCGCAACGAGTGCTCAAATGTCATGCGTCGAAGTGAGATGAGCATGTTGGAAAGCCCTGT
GCACAAACAAAGCTTTCCACGAAGTCCAAAACCTCAACTTATCAGCATTTTGTGCAAAACATAGT
TCTTAGCAAAACTCTTTCTCCAGATGCGATTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGTATG
AGAATGAGATGAGCAAGATAGACAGCCCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCAT
CAACTTTGCGAGAATGTATGCCAAACATCATTCTTAGCGGTGTGTCGGAGTGAGATGAACAATTT
GGACAACCCTATGCACAAACAAAGCTTTCTTAGAAGCCCAAAACCTCAACTTTGAGCAGTTCTAT
GCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGAAGCATTTTTTGCGCAACGAGTGCTCAAAT
GTCGTGCGTCGAATTGCGATGAGATTGTTGGACAACCCTGTGCACAAACAAAGCTTTCCACGAAG
TCCAAAGCCTCAACTTTGCACATTTTTGTGCTAAACATAGTTCATAGCAGAACTCTTTCTAGATG
CGTTTTTTCGCACAACGAGTGCTAAAAAGGCGTG
Found at i:2997 original size:111 final size:111
Alignment explanation
Indices: 2802--3013 Score: 271
Period size: 111 Copynumber: 1.9 Consensus size: 111
2792 AAAAGGCGTG
* * * * *
2802 TGTCGGAGTGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAA
1 TGTCGGAATGAGATGAACTTGTTAGACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAA
* * *** *
2867 GCATCAACTTTGCGTGTTTGTATGCAACACATCGTTCTTAGCGGTT
66 ACATAAACTTTGAACGTTTGTATGCAAAACATCGTTCTTAGCGGTT
* * * *
2913 TGTCGGAATGAGATGAACTTTTTGGACAGCCCTTTGCACAAACAAAGCTTTCCTAGAAGCCCAAA
1 TGTCGGAATGAGATGAACTTGTTAGACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAA
* *
2978 ACCTAAACTTTGAACGTTTGTGTGCAAAACATCGTT
66 ACATAAACTTTGAACGTTTGTATGCAAAACATCGTT
3014 TTGAGGAACA
Statistics
Matches: 84, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
111 84 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (111 bp):
TGTCGGAATGAGATGAACTTGTTAGACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAA
ACATAAACTTTGAACGTTTGTATGCAAAACATCGTTCTTAGCGGTT
Found at i:3009 original size:429 final size:427
Alignment explanation
Indices: 2057--3068 Score: 1506
Period size: 429 Copynumber: 2.4 Consensus size: 427
2047 AAAGGTCGTG
* ** * * * * * *
2057 TGTCGGAGTGAGATGAGCTTGCTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCGAAA
1 TGTCGGAGTGAGATGAACTTTTTGGACAGCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAAA
* * * * * * *
2122 GCATCAACATTGCGCGTTTGTTTGCAACACATCGTTCTTAGCGAAAGGCTCATTCCAGATGCATT
66 ACCTCAACTTTGAGCGTTTGTATGCAAAACATCGTTTTTAGCGAAAGGCTCATTCCAGATGCATT
*
2187 TTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAGCCCTGTG
131 TTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAACCCTGTG
* * *
2252 CAGAAACAAAGCTTTCACGAATTCCAAAGCCTCAACTTTGCGCGTTTTTGTGTTAAACATAGTTC
196 CACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGCGCGTTTTTGTGCTAAACATAGTTC
* * * * *
2317 TTAGCAAAACTCTTTCTCGATGCGTTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGTATGGGAAT
261 ATAGCAAAACTCTTTCTCGATGCGTTTTTTCGCACAACGAGTGCTAAAAAGGCGTGTATCGGAAT
*
2382 GAGATGAGCTTGTTAGCCAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACT
326 GAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACT
*
2447 TTGCGAGTTTGTATGCAACACTTCATTCTTAGCGGTT
391 TTGCGAGTTTGTATGCAACACATCATTCTTAGCGGTT
* * *
2484 TGTCGGAGTGAGATGAACTTTTTGGACAGCCCTATGCAGAAACAAAGCTTTACTAGAAGGCCAAA
1 TGTCGGAGTGAGATGAACTTTTTGGACAGCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAAA
* * * *
2549 ATCTCAACTTTGAGCAG-TTCTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGAAAGCA
66 ACCTCAACTTTGAGC-GTTTGTATGCAAAACATCGTTTTTAGCGAAAGGCTCATTCCAG-ATGCA
2613 TTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAACCCTG
129 TTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAACCCTG
*
2678 TGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGCGTGTTTTTGTGCTAAACATAGT
194 TGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGCGCGTTTTTGTGCTAAACATAGT
* * *
2743 TCATAGCAGAACTCTTTCTGGATGCGTTTTTTCGCACAACGAGTGCTAAAAAAGGCGTGTGTCGG
259 TCATAGCAAAACTCTTTCTCGATGCGTTTTTTCGCACAACGAGTGCT-AAAAAGGCGTGTATCGG
*
2808 AGTGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCA
323 AATGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCA
* *
2873 ACTTTGCGTGTTTGTATGCAACACATCGTTCTTAGCGGTT
388 ACTTTGCGAGTTTGTATGCAACACATCATTCTTAGCGGTT
* *
2913 TGTCGGAATGAGATGAACTTTTTGGACAGCCCTTTGCACAAACAAAGCTTTCCTAGAAGCCCAAA
1 TGTCGGAGTGAGATGAACTTTTTGGACAGCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAAA
* * * * ** *
2978 ACCTAAACTTTGAACGTTTGTGTGCAAAACATCGTTTTGAG-GAACAACCTCATTCCAGATGCGT
66 ACCTCAACTTTGAGCGTTTGTATGCAAAACATCGTTTTTAGCGAA-AGGCTCATTCCAGATGCAT
* *
3042 TTTTTGCGCAATGAGTGCTTAAATGTC
130 TTTTTGCGCAACGAGTGCTCAAATGTC
3069 ATGTGTC
Statistics
Matches: 522, Mismatches: 58, Indels: 9
0.89 0.10 0.02
Matches are distributed among these distances:
427 100 0.19
428 206 0.39
429 216 0.41
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (427 bp):
TGTCGGAGTGAGATGAACTTTTTGGACAGCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAAA
ACCTCAACTTTGAGCGTTTGTATGCAAAACATCGTTTTTAGCGAAAGGCTCATTCCAGATGCATT
TTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAACCCTGTG
CACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGCGCGTTTTTGTGCTAAACATAGTTC
ATAGCAAAACTCTTTCTCGATGCGTTTTTTCGCACAACGAGTGCTAAAAAGGCGTGTATCGGAAT
GAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACT
TTGCGAGTTTGTATGCAACACATCATTCTTAGCGGTT
Found at i:3047 original size:428 final size:426
Alignment explanation
Indices: 2057--3068 Score: 1497
Period size: 428 Copynumber: 2.4 Consensus size: 426
2047 AAAGGTCGTG
* ** * * * * * *
2057 TGTCGGAGTGAGATGAGCTTGCTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCGAAA
1 TGTCGGAGTGAGATGAACTTTTTGGACAGCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAAA
* * * * * *
2122 GCATCAACATTGCGCGTTTGTTTGCAACACATCGTTCTTAGCGAAAGGCTCATTCCAGATGCATT
66 ACCTCAACTTTGAGCGTTTGTATGCAAAACATCGTT-TTAGCGAAAGGCTCATTCCAGATGCATT
*
2187 TTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAGCCCTGTG
130 TTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAACCCTGTG
* * *
2252 CAGAAACAAAGCTTTCACGAATTCCAAAGCCTCAACTTTGCGCGTTTTTGTGTTAAACATAGTTC
195 CACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGCGCGTTTTTGTGCTAAACATAGTTC
* * * * *
2317 TTAGCAAAACTCTTTCTCGATGCGTTTTTTCGCGCAACGAGTGCTCAAAAGTCGTGTATGGGAAT
260 ATAGCAAAACTCTTTCTCGATGCGTTTTTTCGCACAACGAGTGCTAAAAAGGCGTGTATCGGAAT
*
2382 GAGATGAGCTTGTTAGCCAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACT
325 GAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACT
*
2447 TTGCGAGTTTGTATGCAACACTTCATTCTTAGCGGTT
390 TTGCGAGTTTGTATGCAACACATCATTCTTAGCGGTT
* * *
2484 TGTCGGAGTGAGATGAACTTTTTGGACAGCCCTATGCAGAAACAAAGCTTTACTAGAAGGCCAAA
1 TGTCGGAGTGAGATGAACTTTTTGGACAGCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAAA
* * * *
2549 ATCTCAACTTTGAGCAG-TTCTATGCAAAACATCATTTTTAGCGAAAGGCTCATTCCAGAAAGCA
66 ACCTCAACTTTGAGC-GTTTGTATGCAAAACATC-GTTTTAGCGAAAGGCTCATTCCAG-ATGCA
2613 TTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAACCCTG
128 TTTTTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAACCCTG
*
2678 TGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGCGTGTTTTTGTGCTAAACATAGT
193 TGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGCGCGTTTTTGTGCTAAACATAGT
* * *
2743 TCATAGCAGAACTCTTTCTGGATGCGTTTTTTCGCACAACGAGTGCTAAAAAAGGCGTGTGTCGG
258 TCATAGCAAAACTCTTTCTCGATGCGTTTTTTCGCACAACGAGTGCT-AAAAAGGCGTGTATCGG
*
2808 AGTGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCA
322 AATGAGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCA
* *
2873 ACTTTGCGTGTTTGTATGCAACACATCGTTCTTAGCGGTT
387 ACTTTGCGAGTTTGTATGCAACACATCATTCTTAGCGGTT
* *
2913 TGTCGGAATGAGATGAACTTTTTGGACAGCCCTTTGCACAAACAAAGCTTTCCTAGAAGCCCAAA
1 TGTCGGAGTGAGATGAACTTTTTGGACAGCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAAA
* * * ** *
2978 ACCTAAACTTTGAACGTTTGTGTGCAAAACATCGTTTTGAG-GAACAACCTCATTCCAGATGCGT
66 ACCTCAACTTTGAGCGTTTGTATGCAAAACATCGTTTT-AGCGAA-AGGCTCATTCCAGATGCAT
* *
3042 TTTTTGCGCAATGAGTGCTTAAATGTC
129 TTTTTGCGCAACGAGTGCTCAAATGTC
3069 ATGTGTC
Statistics
Matches: 522, Mismatches: 56, Indels: 13
0.88 0.09 0.02
Matches are distributed among these distances:
427 98 0.19
428 212 0.41
429 212 0.41
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (426 bp):
TGTCGGAGTGAGATGAACTTTTTGGACAGCCCTATGCACAAACAAAGCTTTCCTAGAAGCCCAAA
ACCTCAACTTTGAGCGTTTGTATGCAAAACATCGTTTTAGCGAAAGGCTCATTCCAGATGCATTT
TTTGCGCAACGAGTGCTCAAATGTCGTGCGTCGAATTGCGATGAGATTGTTGGACAACCCTGTGC
ACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTTTGCGCGTTTTTGTGCTAAACATAGTTCA
TAGCAAAACTCTTTCTCGATGCGTTTTTTCGCACAACGAGTGCTAAAAAGGCGTGTATCGGAATG
AGATGAGCTTGTTAGACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGCATCAACTT
TGCGAGTTTGTATGCAACACATCATTCTTAGCGGTT
Done.