Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006202.1 Corchorus capsularis cultivar CVL-1 contig06221, 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: 4226
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Found at i:67 original size:23 final size:23
Alignment explanation
Indices: 10--98 Score: 72
Period size: 25 Copynumber: 3.8 Consensus size: 23
1 TGATAATCA
* *
10 CACTATAAAATTGTGAT-AACCT
1 CACTATAAAATTTTAATAAACCT
* * * *
32 CGCTATGACATTTTAATAAATCT
1 CACTATAAAATTTTAATAAACCT
*
55 TACTATAAAATTTTGATATAAACCT
1 CACTATAAAATTTT-A-ATAAACCT
* *
80 CCCTATAAAATTTTGATAA
1 CACTATAAAATTTTAATAA
99 CTTTCTTACA
Statistics
Matches: 50, Mismatches: 14, Indels: 5
0.72 0.20 0.07
Matches are distributed among these distances:
22 12 0.24
23 18 0.36
24 1 0.02
25 19 0.38
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (23 bp):
CACTATAAAATTTTAATAAACCT
Found at i:157 original size:22 final size:22
Alignment explanation
Indices: 124--263 Score: 117
Period size: 22 Copynumber: 6.5 Consensus size: 22
114 TGATAACTAC
*
124 AAATTTTAATAACCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
** **
146 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCCCTATG
** *
168 AAATTTTCTTAATCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
*
190 AAATTTTGATAACC-CTCTTATG
1 AAATTTTGATAACCTC-CCTATG
* **
212 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCT-CCCTATG
*
234 AAATTTTGATATCCTCCC--TG
1 AAATTTTGATAACCTCCCTATG
254 AAATTTTGAT
1 AAATTTTGAT
264 TATTCCATAA
Statistics
Matches: 90, Mismatches: 24, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
20 12 0.13
21 4 0.04
22 71 0.79
23 3 0.03
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCTATG
Found at i:394 original size:22 final size:22
Alignment explanation
Indices: 369--474 Score: 81
Period size: 22 Copynumber: 4.8 Consensus size: 22
359 AATCACATTT
369 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* *
391 TGAAATTTTGATAACCTCGTTA
1 TGAAAATTTGATAACCTCTTTA
* * * *
413 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTTTA
* * *
435 TG-AAATTCTGATAATCACATTA
1 TGAAAATT-TGATAACCTCTTTA
* *
457 TGTAATTTTGATAACCTC
1 TGAAAATTTGATAACCTC
475 GCTTTAAAAT
Statistics
Matches: 63, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
21 5 0.08
22 54 0.86
23 4 0.06
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:464 original size:44 final size:44
Alignment explanation
Indices: 344--492 Score: 138
Period size: 44 Copynumber: 3.4 Consensus size: 44
334 AGAAATACCA
* * *
344 CTATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCT
1 CTATGAAA-TTTTGATAATCACATTATGAAATTTTGATAACCCCT
* * * * * * *
388 TTATGAAATTTTGATAACCTCGTTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
* * * *
432 CTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
* *
476 CTTTAAAATTTTGATAA
1 CTATGAAATTTTGATAA
493 CAAGTTAACA
Statistics
Matches: 80, Mismatches: 24, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
43 5 0.06
44 75 0.94
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
Found at i:485 original size:22 final size:22
Alignment explanation
Indices: 371--493 Score: 69
Period size: 22 Copynumber: 5.6 Consensus size: 22
361 TCACATTTTG
371 AAAA-TTTGATAACCT--CTTT
1 AAAATTTTGATAACCTCGCTTT
390 ATGAAATTTTGATAACCTCG-TTAT
1 A--AAATTTTGATAACCTCGCTT-T
* * * * *
414 AAAATTTTGTTGACCCCTCTAT
1 AAAATTTTGATAACCTCGCTTT
* * *
436 GAAATTCTGATAA--TCACATTAT
1 AAAATTTTGATAACCTCGC-TT-T
**
458 GTAATTTTGATAACCTCGCTTT
1 AAAATTTTGATAACCTCGCTTT
480 AAAATTTTGATAAC
1 AAAATTTTGATAAC
494 AAGTTAACAA
Statistics
Matches: 76, Mismatches: 17, Indels: 19
0.68 0.15 0.17
Matches are distributed among these distances:
19 1 0.01
20 2 0.03
21 4 0.05
22 59 0.78
23 5 0.07
24 5 0.07
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
AAAATTTTGATAACCTCGCTTT
Found at i:579 original size:22 final size:23
Alignment explanation
Indices: 506--605 Score: 86
Period size: 21 Copynumber: 4.5 Consensus size: 23
496 GTTAACAACA
*
506 CTATGAAATTTTGATAATCTTC-
1 CTATGAAATTTTGATAATCTACT
*
528 CTAT-AAATTTTGATAATCTGATAT
1 CTATGAAATTTTGATAATCT-A-CT
*
552 CTATGAAATTTCGATAAT-TACT
1 CTATGAAATTTTGATAATCTACT
* *
574 CTATGAGA-TTTGATAACCT--T
1 CTATGAAATTTTGATAATCTACT
*
594 CTATCAAATTTT
1 CTATGAAATTTT
606 TGTTCTCCTT
Statistics
Matches: 63, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
20 7 0.11
21 25 0.40
22 13 0.21
23 1 0.02
24 5 0.08
25 12 0.19
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (23 bp):
CTATGAAATTTTGATAATCTACT
Found at i:939 original size:23 final size:22
Alignment explanation
Indices: 909--963 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
899 CAATAAAATT
*
909 TTGATAACCAACACTATGAGATG
1 TTGATAACCAACA-TATGAGATA
* *
932 TTGATAACCTACATATGATATA
1 TTGATAACCAACATATGAGATA
*
954 TTAATAACCA
1 TTGATAACCA
964 CGTTATGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (22 bp):
TTGATAACCAACATATGAGATA
Found at i:1028 original size:22 final size:22
Alignment explanation
Indices: 994--1049 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
984 CCTCCATATG
* * *
994 AATTGTTAGTAATCACACTCTGA
1 AATTGTGA-TAATCACACTATAA
*
1017 AATTTTGATAATCACACTATAA
1 AATTGTGATAATCACACTATAA
1039 AATTGTGATAA
1 AATTGTGATAA
1050 CCTCGCTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (22 bp):
AATTGTGATAATCACACTATAA
Found at i:1088 original size:23 final size:23
Alignment explanation
Indices: 1031--1119 Score: 72
Period size: 25 Copynumber: 3.8 Consensus size: 23
1021 TTGATAATCA
* *
1031 CACTATAAAATTGTGAT-AACCT
1 CACTATAAAATTTTAATAAACCT
* * * *
1053 CGCTATGACATTTTAATAAATCT
1 CACTATAAAATTTTAATAAACCT
*
1076 TACTATAAAATTTTGATATAAACCT
1 CACTATAAAATTTT-A-ATAAACCT
* *
1101 CCCTATAAAATTTTGATAA
1 CACTATAAAATTTTAATAA
1120 CTTTCTTACA
Statistics
Matches: 50, Mismatches: 14, Indels: 5
0.72 0.20 0.07
Matches are distributed among these distances:
22 12 0.24
23 18 0.36
24 1 0.02
25 19 0.38
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (23 bp):
CACTATAAAATTTTAATAAACCT
Found at i:1195 original size:22 final size:22
Alignment explanation
Indices: 1145--1262 Score: 89
Period size: 22 Copynumber: 5.5 Consensus size: 22
1135 TGATAACTAC
*
1145 AAATTTTAATAACCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
** **
1167 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCCCTATG
** *
1189 AAATTTTCTTAATCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
* **
1211 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCT-CCCTATG
* *
1233 CAATTTTGATATCCTCCC-A-G
1 AAATTTTGATAACCTCCCTATG
1253 AAATTTTGAT
1 AAATTTTGAT
1263 TACTCCATAA
Statistics
Matches: 71, Mismatches: 23, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
20 10 0.14
21 5 0.07
22 53 0.75
23 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCTATG
Found at i:1393 original size:22 final size:22
Alignment explanation
Indices: 1368--1492 Score: 71
Period size: 22 Copynumber: 5.7 Consensus size: 22
1358 AATCACATTT
* *
1368 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCGCCTTA
*
1390 TGAAATTTTGATAACCGCCTTA
1 TGAAAATTTGATAACCGCCTTA
* *
1412 T-AAAATTTTGTTGACC-CCTCTA
1 TGAAAA-TTTGATAACCGCCT-TA
* * *
1434 TG-AAATTCTGATAATCACATTA
1 TGAAAATT-TGATAACCGCCTTA
* *
1456 TGTAATTTTGATAACATCG-CTT-
1 TGAAAATTTGATAAC--CGCCTTA
*
1478 TGAAATTTTGATAAC
1 TGAAAATTTGATAAC
1493 AAGTTAACAA
Statistics
Matches: 80, Mismatches: 15, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
21 8 0.10
22 63 0.79
23 8 0.10
24 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (22 bp):
TGAAAATTTGATAACCGCCTTA
Found at i:1463 original size:44 final size:44
Alignment explanation
Indices: 1343--1491 Score: 138
Period size: 44 Copynumber: 3.4 Consensus size: 44
1333 AGAAATACCA
* * *
1343 CTATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCT
1 CTATGAAA-TTTTGATAATCACATTATGAAATTTTGATAACCCCT
* * * * * * *
1387 TTATGAAATTTTGATAACCGCCTTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
* * ** *
1431 CTATGAAATTCTGATAATCACATTATGTAATTTTGATAACATCG
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
*
1475 CTTTGAAATTTTGATAA
1 CTATGAAATTTTGATAA
1492 CAAGTTAACA
Statistics
Matches: 80, Mismatches: 24, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
43 5 0.06
44 75 0.94
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
Found at i:1534 original size:21 final size:24
Alignment explanation
Indices: 1505--1583 Score: 96
Period size: 22 Copynumber: 3.5 Consensus size: 24
1495 GTTAACAACA
1505 CTATGAAATTTTGATAATCT-TC-
1 CTATGAAATTTTGATAATCTATCT
1527 CTAT-AAATTTTGATAATCTGATCT
1 CTATGAAATTTTGATAATCT-ATCT
*
1551 CTATGAAATTTCGATAAT-TA-CT
1 CTATGAAATTTTGATAATCTATCT
*
1573 CTATGAGATTT
1 CTATGAAATTT
1584 AATAACCTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
21 15 0.29
22 16 0.31
23 3 0.06
24 5 0.10
25 12 0.24
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (24 bp):
CTATGAAATTTTGATAATCTATCT
Found at i:1885 original size:31 final size:30
Alignment explanation
Indices: 1821--1885 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
1811 TGGCAATTTA
* * * *
1821 GAAATATGTTTTTAAAAAAGAGTACAGTTG
1 GAAATATATTTTAAAAAAAGAGTACAATCG
*
1851 GAAATATATTTTAAAAATAAGGGTACAATCG
1 GAAATATATTTTAAAAA-AAGAGTACAATCG
1882 GAAA
1 GAAA
1886 ACATAAAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 15 0.52
31 14 0.48
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (30 bp):
GAAATATATTTTAAAAAAAGAGTACAATCG
Found at i:1921 original size:2 final size:2
Alignment explanation
Indices: 1914--1957 Score: 63
Period size: 2 Copynumber: 22.0 Consensus size: 2
1904 TTCGTACTTT
*
1914 TA TA TA TA GTA TA GA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1956 TA
1 TA
1958 GAGTAATTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1955 original size:999 final size:1002
Alignment explanation
Indices: 1--1865 Score: 3199
Period size: 999 Copynumber: 1.9 Consensus size: 1002
1 TGATAATCACACTATAAAATTGTGATAACCTCGCTATGACATTTTAATAAATCTTACTATAAAAT
1 TGATAATCACACTATAAAATTGTGATAACCTCGCTATGACATTTTAATAAATCTTACTATAAAAT
66 TTTGATATAAACCTCCCTATAAAATTTTGATAACTTTCTTACAAATCTTGATAACTACAAATTTT
66 TTTGATATAAACCTCCCTATAAAATTTTGATAACTTTCTTACAAATCTTGATAACTACAAATTTT
131 AATAACCTCCCTATGATTTTTTGATAACCTCATTATGAAATTTTCTTAATCTCCCTATGAAATTT
131 AATAACCTCCCTATGATTTTTTGATAACCTCATTATGAAATTTTCTTAA-CT-CC----------
*
196 TGATAACCCTCTTATGAAATTTTGAAAACTAAACTATGAAATTTTGATATCCTCCCTGAAATTTT
184 T--T-A-CCTCTTATGAAATTTTGAAAACTAAACTATGAAATTTTGATATCCTCCCAGAAATTTT
*
261 GATTATTCCATAATAAAAGTTTAATAACCTTCCTAATTTGGTAACCATACTATGAAATTTTGATA
245 GATTACTCCATAATAAAAGTTTAATAACCTTCCTAATTTGGTAACCATACTATGAAATTTTGATA
326 ACCTCCCCAGAAATACCACTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTA
310 ACCTCCCCAGAAATACCACTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTA
* *
391 TGAAATTTTGATAACCTCGTTATAAAATTTTGTTGACCCCTCTATGAAATTCTGATAATCACATT
375 TGAAATTTTGATAACCGCCTTATAAAATTTTGTTGACCCCTCTATGAAATTCTGATAATCACATT
*
456 ATGTAATTTTGATAACCTCGCTTTAAAATTTTGATAACAAGTTAACAACACTATGAAATTTTGAT
440 ATGTAATTTTGATAACATCGCTTTAAAATTTTGATAACAAGTTAACAACACTATGAAATTTTGAT
*
521 AATCTTCCTATAAATTTTGATAATCTGATATCTATGAAATTTCGATAATTACTCTATGAGATTTG
505 AATCTTCCTATAAATTTTGATAATCTGATATCTATGAAATTTCGATAATTACTCTATGAGATTTA
*
586 ATAACCTTCTATCAAATTTTTGTTCTCCTTACGAAATTGAGACTTTTATAACCTTCATATGAAAT
570 ATAACCTTCTATCAAATTTTTG-TCTACTTACGAAATTGAGACTTTTATAACCTTCATATGAAAT
* * *
651 TGGAAACAAAGGCAAAAGGTAAAATTAAATAGGACATTGGAAACTCAAAGCCAAATTGACTTTCT
634 TGGAAACAAAGACAAAAGGCAAAATTAAATAGGACATTGGAAACTCAAAGCCAAATTGACTTTAT
* *
716 AATAATTAATAATATACATATTATATATAATCTAATAATTAATAATGGAATAATTTATGATTAAA
699 AATAATTAATAATAGACATATTATAAATAATCTAATAATTAATAATGGAATAATTTATGATTAAA
*
781 AAAATAATGAAATAATTAAAATATTATTTAGTAATGTCAATTTAGAAATATGTTTTAAAAAAAAG
764 AAAATAATGAAATAATTAAAATATTATTTAGTAATGGCAATTTAGAAATATGTTTTAAAAAAAAG
* * * ***
846 GGTACAATTGGAAATATATTTTCAATTGTACATATTTCCAATTGATAATTTCCCAATAAAATTTT
829 AGTACAATTGGAAATATATTTTAAATGGTACATA-TTCCAAAACATAATTTCCCAATAAAATTTT
* *
911 GATAACCAACACTATGAGATGTTGATAACCTACATATGATATATTAATAACCACGTTATGAAAAT
893 GATAA-CAACACTATGAGATATTGATAACATACATATGATATATTAATAACCACGTTATGAAAAT
976 TTAAAAAACCTCCATATGAATTGTTAGTAATCACACTCTGAAATTT
957 TTAAAAAACCTCCATATGAATTGTTAGTAATCACACTCTGAAATTT
1022 TGATAATCACACTATAAAATTGTGATAACCTCGCTATGACATTTTAATAAATCTTACTATAAAAT
1 TGATAATCACACTATAAAATTGTGATAACCTCGCTATGACATTTTAATAAATCTTACTATAAAAT
1087 TTTGATATAAACCTCCCTATAAAATTTTGATAACTTTCTTACAAATCTTGATAACTACAAATTTT
66 TTTGATATAAACCTCCCTATAAAATTTTGATAACTTTCTTACAAATCTTGATAACTACAAATTTT
1152 AATAACCTCCCTATGATTTTTTGATAACCTCATTATGAAATTTTCTTAA-T-C-T-CC-C-TATG
131 AATAACCTCCCTATGATTTTTTGATAACCTCATTATGAAATTTTCTTAACTCCTTACCTCTTATG
*
1211 AAATTTTGAAAACTAAACTATGCAATTTTGATATCCTCCCAGAAATTTTGATTACTCCATAATAA
196 AAATTTTGAAAACTAAACTATGAAATTTTGATATCCTCCCAGAAATTTTGATTACTCCATAATAA
1276 AAGTTTAATAACCTTCCTAATTTGGTAACCATACTATGAAATTTTGATAACCTCCCCAGAAATAC
261 AAGTTTAATAACCTTCCTAATTTGGTAACCATACTATGAAATTTTGATAACCTCCCCAGAAATAC
1341 CACTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACC
326 CACTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACC
1406 GCCTTATAAAATTTTGTTGACCCCTCTATGAAATTCTGATAATCACATTATGTAATTTTGATAAC
391 GCCTTATAAAATTTTGTTGACCCCTCTATGAAATTCTGATAATCACATTATGTAATTTTGATAAC
*
1471 ATCGCTTTGAAATTTTGATAACAAGTTAACAACACTATGAAATTTTGATAATCTTCCTATAAATT
456 ATCGCTTTAAAATTTTGATAACAAGTTAACAACACTATGAAATTTTGATAATCTTCCTATAAATT
*
1536 TTGATAATCTGATCTCTATGAAATTTCGATAATTACTCTATGAGATTTAATAACCTTCTATCAAA
521 TTGATAATCTGATATCTATGAAATTTCGATAATTACTCTATGAGATTTAATAACCTTCTATCAAA
* * *
1601 -TTTTG-GTACTTATGAAATTGAGACTTTTATAACCTTCATATGAAATTGGAAACAAAGATAAAA
586 TTTTTGTCTACTTACGAAATTGAGACTTTTATAACCTTCATATGAAATTGGAAACAAAGACAAAA
*
1664 GGCAAAATTAAATAGGACATTGGAAACTCAAAGCTAAATTGACTTTATAATAATTAATAATAGAC
651 GGCAAAATTAAATAGGACATTGGAAACTCAAAGCCAAATTGACTTTATAATAATTAATAATAGAC
* * *
1729 GTATTATAAATAATCTAATAATTAATAATGGAATAATTTATGATTAAAAAAATAATGGAATGATT
716 ATATTATAAATAATCTAATAATTAATAATGGAATAATTTATGATTAAAAAAATAATGAAATAATT
* *
1794 AAAATATTATTTAGTAATGGCAATTTAGAAATATGTTTT-TAAAAAAGAGTACAGTTGGAAATAT
781 AAAATATTATTTAGTAATGGCAATTTAGAAATATGTTTTAAAAAAAAGAGTACAATTGGAAATAT
1858 ATTTTAAA
846 ATTTTAAA
1866 AATAAGGGTA
Statistics
Matches: 817, Mismatches: 27, Indels: 26
0.94 0.03 0.03
Matches are distributed among these distances:
995 29 0.04
996 213 0.26
998 5 0.01
999 385 0.47
1000 1 0.00
1001 2 0.00
1004 1 0.00
1017 1 0.00
1019 1 0.00
1021 179 0.22
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.37
Consensus pattern (1002 bp):
TGATAATCACACTATAAAATTGTGATAACCTCGCTATGACATTTTAATAAATCTTACTATAAAAT
TTTGATATAAACCTCCCTATAAAATTTTGATAACTTTCTTACAAATCTTGATAACTACAAATTTT
AATAACCTCCCTATGATTTTTTGATAACCTCATTATGAAATTTTCTTAACTCCTTACCTCTTATG
AAATTTTGAAAACTAAACTATGAAATTTTGATATCCTCCCAGAAATTTTGATTACTCCATAATAA
AAGTTTAATAACCTTCCTAATTTGGTAACCATACTATGAAATTTTGATAACCTCCCCAGAAATAC
CACTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACC
GCCTTATAAAATTTTGTTGACCCCTCTATGAAATTCTGATAATCACATTATGTAATTTTGATAAC
ATCGCTTTAAAATTTTGATAACAAGTTAACAACACTATGAAATTTTGATAATCTTCCTATAAATT
TTGATAATCTGATATCTATGAAATTTCGATAATTACTCTATGAGATTTAATAACCTTCTATCAAA
TTTTTGTCTACTTACGAAATTGAGACTTTTATAACCTTCATATGAAATTGGAAACAAAGACAAAA
GGCAAAATTAAATAGGACATTGGAAACTCAAAGCCAAATTGACTTTATAATAATTAATAATAGAC
ATATTATAAATAATCTAATAATTAATAATGGAATAATTTATGATTAAAAAAATAATGAAATAATT
AAAATATTATTTAGTAATGGCAATTTAGAAATATGTTTTAAAAAAAAGAGTACAATTGGAAATAT
ATTTTAAATGGTACATATTCCAAAACATAATTTCCCAATAAAATTTTGATAACAACACTATGAGA
TATTGATAACATACATATGATATATTAATAACCACGTTATGAAAATTTAAAAAACCTCCATATGA
ATTGTTAGTAATCACACTCTGAAATTT
Found at i:3714 original size:18 final size:18
Alignment explanation
Indices: 3691--3727 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3681 TTTGAGAGTG
*
3691 GGCAAAAAATCCAAAATT
1 GGCAAAAAATCAAAAATT
*
3709 GGCAAAATATCAAAAATT
1 GGCAAAAAATCAAAAATT
3727 G
1 G
3728 AAGCTCATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.14, G:0.14, T:0.19
Consensus pattern (18 bp):
GGCAAAAAATCAAAAATT
Done.