Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014019.1 Corchorus olitorius cultivar O-4 contig14052, 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: 91879
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:475 original size:22 final size:22
Alignment explanation
Indices: 450--494 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
440 TAAAATTTTG
* *
450 ATAACCTTTCTATGAAATTTCA
1 ATAACCATACTATGAAATTTCA
*
472 ATAACGATACTATGAAATTTCA
1 ATAACCATACTATGAAATTTCA
494 A
1 A
495 GAATATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.36
Consensus pattern (22 bp):
ATAACCATACTATGAAATTTCA
Found at i:536 original size:22 final size:22
Alignment explanation
Indices: 503--544 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
493 AAGAATATTT
*
503 TTATAAATTTTTTTTAACCTTC
1 TTATAAATTTTTGTTAACCTTC
525 TTATGAAA-TTTTGTTAACCT
1 TTAT-AAATTTTTGTTAACCT
545 CCCTAAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.55
Consensus pattern (22 bp):
TTATAAATTTTTGTTAACCTTC
Found at i:634 original size:22 final size:23
Alignment explanation
Indices: 586--640 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
576 CAATGAAATT
*
586 TTGATAACCAACACTATGAGATG
1 TTGATAACCAACACTATGAGATA
** *
609 TTGATAACCTCCA-TATGATATA
1 TTGATAACCAACACTATGAGATA
631 TTGATAACCA
1 TTGATAACCA
641 CGTTATGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (23 bp):
TTGATAACCAACACTATGAGATA
Found at i:704 original size:22 final size:22
Alignment explanation
Indices: 666--725 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
656 AAAACCTCCA
*
666 TATG-AATTGTTAGTAATCACAC
1 TATGAAATTGTGA-TAATCACAC
* * *
688 TCTGAAATTTTGATAATTACAC
1 TATGAAATTGTGATAATCACAC
710 TATGAAATTGTGATAA
1 TATGAAATTGTGATAA
726 CTTCGCTATG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
22 25 0.81
23 6 0.19
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (22 bp):
TATGAAATTGTGATAATCACAC
Found at i:734 original size:22 final size:22
Alignment explanation
Indices: 679--938 Score: 106
Period size: 22 Copynumber: 12.1 Consensus size: 22
669 GAATTGTTAG
* *
679 TAATCACACTCTGAAATTTTGA
1 TAATTACACTATGAAATTTTGA
*
701 TAATTACACTATGAAATTGTGA
1 TAATTACACTATGAAATTTTGA
*
723 TAACTT-CGCTATGAAATTTTGA
1 TAA-TTACACTATGAAATTTTGA
745 T-ATCCT-C-CTTATGAAATTTTGA
1 TAAT--TACAC-TATGAAATTTTGA
767 -AATT----TAT-AAATTTTGA
1 TAATTACACTATGAAATTTTGA
* * **
783 TAACCT-CCCTATGATTTTTTGA
1 TAA-TTACACTATGAAATTTTGA
* * *
805 TAACCT-CATTATGAAATTTTGT
1 TAA-TTACACTATGAAATTTTGA
*
827 TAATCT-CCCTATGAAATTTTGA
1 TAAT-TACACTATGAAATTTTGA
*
849 T--CTACAAACTATGAAATTTTGA
1 TAATTAC--ACTATGAAATTTTGA
** * *
871 TAA-CCCTCTTATGAAAATTTGA
1 TAATTACAC-TATGAAATTTTGA
* * *
893 AAACTAAACTATGAAATTTTGA
1 TAATTACACTATGAAATTTTGA
915 TAACCTT-CA-TATGAAATTTTGA
1 TAA--TTACACTATGAAATTTTGA
937 TA
1 TA
939 TCCTCCCTGA
Statistics
Matches: 185, Mismatches: 32, Indels: 42
0.71 0.12 0.16
Matches are distributed among these distances:
16 9 0.05
17 5 0.03
18 1 0.01
19 1 0.01
20 3 0.02
21 6 0.03
22 154 0.83
23 5 0.03
24 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (22 bp):
TAATTACACTATGAAATTTTGA
Found at i:758 original size:44 final size:44
Alignment explanation
Indices: 573--1725 Score: 321
Period size: 44 Copynumber: 27.0 Consensus size: 44
563 ACCTCAAACT
* ** * *
573 TCCCAATGAAATTTTGATAACCAACACTATGAGATGTTGATAACC
1 TCCCTATGAAATTTTGATAA-CTTCACTATGAAATTTTGATAACC
* * * * * *
618 TCCATATGATATATTGATAAC--CACGTTATGAAAATTTAAAAACC
1 TCCCTATGAAATTTTGATAACTTCAC--TATGAAATTTTGATAACC
* * * *
662 TCCATATG-AATTGTT-AGTAA-TCACACTCTGAAATTTTGATAA-T
1 TCCCTATGAAATT-TTGA-TAACT-TCACTATGAAATTTTGATAACC
* * * *
705 TACACTATGAAATTGTGATAACTTCGCTATGAAATTTTGATATCC
1 T-CCCTATGAAATTTTGATAACTTCACTATGAAATTTTGATAACC
*
750 TCCTTATGAAATTTTGA-AA-TT---TAT-AAATTTTGATAACC
1 TCCCTATGAAATTTTGATAACTTCACTATGAAATTTTGATAACC
** * * * *
788 TCCCTATGATTTTTTGATAACCTCATTATGAAATTTTGTTAATC
1 TCCCTATGAAATTTTGATAACTTCACTATGAAATTTTGATAACC
*
832 TCCCTATGAAATTTTGAT--CTACAAACTATGAAATTTTGATAACC
1 TCCCTATGAAATTTTGATAACTTC--ACTATGAAATTTTGATAACC
* * * **
876 -CTCTTATGAAAATTTGAAAACTAAACTATGAAATTTTGATAACC
1 TC-CCTATGAAATTTTGATAACTTCACTATGAAATTTTGATAACC
* * * * * *
920 TTCATATGAAATTTTGATATCCTC-C-CTGAAATTTTGATTA-C
1 TCCCTATGAAATTTTGATAACTTCACTATGAAATTTTGATAACC
* * ** *
961 TCCATAATAAAAGATTAATAACCTTC-C--T--AA-TTTGATAACC
1 TCCCT-ATGAAATTTTGATAA-CTTCACTATGAAATTTTGATAACC
* * * * *
1001 AT-ACTATGAAATCTTGATAACCTCCCCA--AAA-----AT-A-C
1 -TCCCTATGAAATTTTGATAACTTCACTATGAAATTTTGATAACC
* * * *
1036 -CACTATGAAATTTTGGTAA--TCACATTTTGAAAATTTGATAACC
1 TCCCTATGAAATTTTGATAACTTCAC--TATGAAATTTTGATAACC
** * * * * **
1079 TCTTTATGAAATTTTGATAACCTCTCTATAAAATTTTGGTGGCC
1 TCCCTATGAAATTTTGATAACTTCACTATGAAATTTTGATAACC
* * *
1123 -CCTCTATGAAATTTTGATAA-TAACATTATGTAATTTTGATAACC
1 TCC-CTATGAAATTTTGATAACT-TCACTATGAAATTTTGATAACC
* * * *
1167 TCGCTTTGAAATTTTGATAACAAT-ACTATGAAATTTTGATAATC
1 TCCCTATGAAATTTTGATAAC-TTCACTATGAAATTTTGATAACC
* * ** *
1211 TTCCTAT-AAATTTTGATAA-TTCGATCTCT---A-TGAGATAATC
1 TCCCTATGAAATTTTGATAACTTC-A-CTATGAAATTTTGATAACC
* ** * * *
1251 ACTTTATGAGATTTT-ATAACCTT--CTATCAAATTTTGGTAA--
1 TCCCTATGAAATTTTGATAA-CTTCACTATGAAATTTTGATAACC
* *
1291 TCCTTATGAAATTGAGACTTTTATAATCTTCA-TATGAAATTTTGATAACC
1 TCCCTATGAAA-T-----TTTGATAA-CTTCACTATGAAATTTTGATAACC
** * * * ** *
1341 TCCCCCTGAAATATTGATAACCTCCCCCTGAAATATT-AGTAACC
1 TCCCTATGAAATTTTGATAACTTCACTATGAAATTTTGA-TAACC
* * **
1385 TCCTTATGAAATTTTGTTAACCACACTATGAAATTCTT-ATAACC
1 TCCCTATGAAATTTTGATAACTTCACTATGAAATT-TTGATAACC
* * * *
1429 TCGCTATGACATTTTGATAA--T--C--T----CTTTAATAACC
1 TCCCTATGAAATTTTGATAACTTCACTATGAAATTTTGATAACC
** ** *
1463 TTTCTAT-AAATTTGTGATAA--T-ACTATGAAATTTCAATAATC
1 TCCCTATGAAATTT-TGATAACTTCACTATGAAATTTTGATAACC
* * * *
1504 TTCCTAAGAAATTTTAATAACCTGATC-CTATGAAATTTTGGTAACC
1 TCCCTATGAAATTTTGATAA-CT--TCACTATGAAATTTTGATAACC
* * * *
1550 ACACTATGAAATTTTGATAACCTTC-CCATGAAATTTTGATAACT
1 TCCCTATGAAATTTTGATAA-CTTCACTATGAAATTTTGATAACC
* * * ** * * *
1594 TTCATATGAAATTTTGGTAACCACACTATGGAATTTCGATAACT
1 TCCCTATGAAATTTTGATAACTTCACTATGAAATTTTGATAACC
** ** *
1638 TCTATATGAAATTTT-AGTAACCACACTATGGAATTTTGATAACC
1 TCCCTATGAAATTTTGA-TAACTTCACTATGAAATTTTGATAACC
* *
1682 T-CCTCATGAAATTATAATAAC--CATCTTATGAAATTTTGATAACC
1 TCCCT-ATGAAATTTTGATAACTTCA-C-TATGAAATTTTGATAACC
1726 ACACAGAGAC
Statistics
Matches: 819, Mismatches: 191, Indels: 197
0.68 0.16 0.16
Matches are distributed among these distances:
32 3 0.00
33 7 0.01
34 35 0.04
35 2 0.00
36 4 0.00
37 3 0.00
38 34 0.04
39 24 0.03
40 29 0.04
41 38 0.05
42 47 0.06
43 38 0.05
44 451 0.55
45 28 0.03
46 46 0.06
47 7 0.01
48 14 0.02
49 1 0.00
50 8 0.01
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (44 bp):
TCCCTATGAAATTTTGATAACTTCACTATGAAATTTTGATAACC
Found at i:760 original size:66 final size:64
Alignment explanation
Indices: 690--957 Score: 237
Period size: 66 Copynumber: 4.2 Consensus size: 64
680 AATCACACTC
* *
690 TGAAATTTTGATAATTACACTATGAAATTGTGATAACTTCGCTATGAAATTTTGATATCCTCCTT
1 TGAAATTTTGATAATT-CACTATGAAATTTTGATAACTTC-CTATGAAATTTTGATAACCTCCTT
755 A
64 A
* ** *
756 TGAAATTTTGA-AATT---TAT-AAATTTTGATAACCTCCCTATGATTTTTTGATAACCTCATTA
1 TGAAATTTTGATAATTCACTATGAAATTTTGATAA-CTTCCTATGAAATTTTGATAACCTCCTTA
* * * ***
816 TGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACAAACTATGAAATTTTGATAACC-CTCT
1 TGAAATTTTGATAAT-TCACTATGAAATTTTGAT-AACTTCCTATGAAATTTTGATAACCTC-CT
880 TA
63 TA
* * ** * *
882 TGAAAATTTGAAAACTAAACTATGAAATTTTGATAACCTTCATATGAAATTTTGATATCCTCC--
1 TGAAATTTTGATAA-TTCACTATGAAATTTTGATAA-CTTCCTATGAAATTTTGATAACCTCCTT
*
945 C
64 A
946 TGAAATTTTGAT
1 TGAAATTTTGAT
958 TACTCCATAA
Statistics
Matches: 161, Mismatches: 29, Indels: 26
0.75 0.13 0.12
Matches are distributed among these distances:
60 42 0.26
61 9 0.06
62 1 0.01
64 10 0.06
65 9 0.06
66 87 0.54
67 3 0.02
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (64 bp):
TGAAATTTTGATAATTCACTATGAAATTTTGATAACTTCCTATGAAATTTTGATAACCTCCTTA
Found at i:1088 original size:22 final size:22
Alignment explanation
Indices: 1063--1229 Score: 83
Period size: 22 Copynumber: 7.6 Consensus size: 22
1053 AATCACATTT
*
1063 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTCTA
*
1085 TGAAATTTTGATAACCTCTCTA
1 TGAAAATTTGATAACCTCTCTA
* ** *
1107 T-AAAATTTTGGTGGCCCCTCTA
1 TGAAAA-TTTGATAACCTCTCTA
* ***
1129 TGAAATTTTGATAATAACAT-TA
1 TGAAAATTTGATAACCTC-TCTA
* * * *
1151 TGTAATTTTGATAACCTCGCTT
1 TGAAAATTTGATAACCTCTCTA
* * *
1173 TGAAATTTTGATAACAAT-ACTA
1 TGAAAATTTGATAAC-CTCTCTA
* *
1195 TGAAATTTTGATAATCT-TCCTA
1 TGAAAATTTGATAACCTCT-CTA
*
1217 T-AAATTTTGATAA
1 TGAAAATTTGATAA
1230 TTCGATCTCT
Statistics
Matches: 112, Mismatches: 27, Indels: 13
0.74 0.18 0.09
Matches are distributed among these distances:
21 16 0.14
22 91 0.81
23 5 0.04
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTCTA
Found at i:1223 original size:21 final size:23
Alignment explanation
Indices: 1126--1230 Score: 87
Period size: 22 Copynumber: 4.8 Consensus size: 23
1116 GGTGGCCCCT
*
1126 CTATGAAATTTTGATAAT-AACA
1 CTATGAAATTTTGATAATCAATA
* * * *
1148 TTATGTAATTTTGATAA-C-CTCG
1 CTATGAAATTTTGATAATCAAT-A
*
1170 CTTTGAAATTTTGATAA-CAATA
1 CTATGAAATTTTGATAATCAATA
* *
1192 CTATGAAATTTTGATAATC-TTC
1 CTATGAAATTTTGATAATCAATA
1214 CTAT-AAATTTTGATAAT
1 CTATGAAATTTTGATAAT
1231 TCGATCTCTA
Statistics
Matches: 66, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
21 13 0.20
22 51 0.77
23 2 0.03
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (23 bp):
CTATGAAATTTTGATAATCAATA
Found at i:1350 original size:22 final size:22
Alignment explanation
Indices: 1325--1387 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
1315 AATCTTCATA
*
1325 TGAAATTTTGATAACCTCCCCC
1 TGAAATATTGATAACCTCCCCC
1347 TGAAATATTGATAACCTCCCCC
1 TGAAATATTGATAACCTCCCCC
1369 TGAAATATT-AGTAACCTCC
1 TGAAATATTGA-TAACCTCC
1388 TTATGAAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 1 0.03
22 38 0.97
ACGTcount: A:0.32, C:0.29, G:0.10, T:0.30
Consensus pattern (22 bp):
TGAAATATTGATAACCTCCCCC
Found at i:1394 original size:22 final size:22
Alignment explanation
Indices: 1324--1406 Score: 87
Period size: 22 Copynumber: 3.8 Consensus size: 22
1314 TAATCTTCAT
*
1324 ATGAAATTTTGATAACCTCCCC
1 ATGAAATATTGATAACCTCCCC
*
1346 CTGAAATATTGATAACCTCCCC
1 ATGAAATATTGATAACCTCCCC
* **
1368 CTGAAATATT-AGTAACCTCCTT
1 ATGAAATATTGA-TAACCTCCCC
* *
1390 ATGAAATTTTGTTAACC
1 ATGAAATATTGATAACC
1407 ACACTATGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
21 1 0.02
22 51 0.98
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.34
Consensus pattern (22 bp):
ATGAAATATTGATAACCTCCCC
Found at i:1427 original size:22 final size:22
Alignment explanation
Indices: 1323--1448 Score: 69
Period size: 22 Copynumber: 5.7 Consensus size: 22
1313 ATAATCTTCA
* *
1323 TATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCACAC
** * * *
1345 CCTGAAATATTGATAACCTCCC
1 TATGAAATTTTGATAACCACAC
** * *
1367 CCTGAAATATT-AGTAACCTC-C
1 TATGAAATTTTGA-TAACCACAC
*
1388 TTATGAAATTTTGTTAACCACAC
1 -TATGAAATTTTGATAACCACAC
* *
1411 TATGAAATTCTT-ATAACCTCGC
1 TATGAAATT-TTGATAACCACAC
*
1433 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
1449 TCTCTTTAAT
Statistics
Matches: 86, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
21 4 0.05
22 79 0.92
23 3 0.03
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:1515 original size:22 final size:23
Alignment explanation
Indices: 1489--1541 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
1479 ATAATACTAT
*
1489 GAAATTTCAATAATCT-TCCTAA
1 GAAATTTCAATAACCTATCCTAA
* *
1511 GAAATTTTAATAACCTGATCCTAT
1 GAAATTTCAATAACCT-ATCCTAA
1535 GAAATTT
1 GAAATTT
1542 TGGTAACCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 14 0.54
24 12 0.46
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (23 bp):
GAAATTTCAATAACCTATCCTAA
Found at i:1559 original size:22 final size:22
Alignment explanation
Indices: 1531--1729 Score: 167
Period size: 22 Copynumber: 9.0 Consensus size: 22
1521 TAACCTGATC
*
1531 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
*
1553 CTATGAAATTTTGATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
* **
1575 CCATGAAATTTTGATAACTTTCA
1 CTATGAAATTTTGATAAC-CACA
*
1598 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* * **
1619 CTATGGAATTTCGATAACTTCTA
1 CTATGAAATTTTGATAACCAC-A
1642 -TATGAAATTTT-AGTAACCACA
1 CTATGAAATTTTGA-TAACCACA
* *
1663 CTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* *
1684 CTCATGAAATTATAATAACCATC-
1 CT-ATGAAATTTTGATAACCA-CA
*
1707 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
1729 C
1 C
1730 AGAGACATGA
Statistics
Matches: 139, Mismatches: 27, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
21 7 0.05
22 127 0.91
23 5 0.04
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:1647 original size:66 final size:68
Alignment explanation
Indices: 1484--1725 Score: 223
Period size: 66 Copynumber: 3.6 Consensus size: 68
1474 TTGTGATAAT
* * *
1484 ACTATGAAATTTCAATAATCTTCCTAA-GAAATTTTAATAACCTGATCCTATGAAATTTTGGTAA
1 ACTATGAAATTTCGATAACCTT-CTAATGAAATTTTAATAACCTGATCATATGAAATTTTGGTAA
1548 CCAC
65 CCAC
* ** * *
1552 ACTATGAAATTTTGATAACCTTCCCATGAAATTTTGATAA-CT-TTCATATGAAATTTTGGTAAC
1 ACTATGAAATTTCGATAACCTTCTAATGAAATTTTAATAACCTGATCATATGAAATTTTGGTAAC
1615 CAC
66 CAC
* * * *
1618 ACTATGGAATTTCGATAA-CTTCTATATGAAATTTTAGTAACC--A-CACTATGGAATTTTGATA
1 ACTATGAAATTTCGATAACCTTCTA-ATGAAATTTTAATAACCTGATCA-TATGAAATTTTGGTA
*
1679 ACCTC
64 ACCAC
* * * *
1684 -CTCATGAAATTAT-AATAACCATCTTATGAAATTTTGATAACC
1 ACT-ATGAAATT-TCGATAACCTTCTAATGAAATTTTAATAACC
1726 ACACAGAGAC
Statistics
Matches: 143, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
65 8 0.06
66 94 0.66
67 10 0.07
68 31 0.22
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (68 bp):
ACTATGAAATTTCGATAACCTTCTAATGAAATTTTAATAACCTGATCATATGAAATTTTGGTAAC
CAC
Found at i:1930 original size:20 final size:20
Alignment explanation
Indices: 1892--1930 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1882 TATTGACATT
1892 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
1912 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
1931 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:6275 original size:15 final size:15
Alignment explanation
Indices: 6255--6284 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6245 CTCTATAACC
6255 TCATAAATCATATTT
1 TCATAAATCATATTT
6270 TCATAAATCATATTT
1 TCATAAATCATATTT
6285 ATTATATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (15 bp):
TCATAAATCATATTT
Found at i:6426 original size:19 final size:18
Alignment explanation
Indices: 6397--6438 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
6387 TGAGTAGTTT
* *
6397 TTAAGTAAAAATGTAATA
1 TTAAATAAAAATATAATA
6415 TATAAATAAAAATATAATA
1 T-TAAATAAAAATATAATA
6434 TTAAA
1 TTAAA
6439 ATAATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
TTAAATAAAAATATAATA
Found at i:6442 original size:19 final size:19
Alignment explanation
Indices: 6402--6438 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
6392 AGTTTTTAAG
*
6402 TAAAAATGTAATATATAAA
1 TAAAAATATAATATATAAA
6421 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
6439 ATAATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:6630 original size:15 final size:16
Alignment explanation
Indices: 6610--6646 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
6600 TTGAAGGATA
6610 TTTAAA-AATGTATTT
1 TTTAAAGAATGTATTT
*
6625 TTTAAAGAATTTA-TT
1 TTTAAAGAATGTATTT
6640 TTTAAAG
1 TTTAAAG
6647 GATATATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (16 bp):
TTTAAAGAATGTATTT
Found at i:8301 original size:42 final size:43
Alignment explanation
Indices: 8250--8343 Score: 147
Period size: 45 Copynumber: 2.2 Consensus size: 43
8240 AGTGCATTAT
*
8250 CTAA-ATTCTACTC-CATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCTCATCTCTAGATAATTCATCAAAATAAAG
8291 CTAATATTCTACTCATTCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACTC--TCATCTCTAGATAATTCATCAAAATAAAG
8336 CTAATATT
1 CTAATATT
8344 AGTTGTTGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 9 0.19
45 35 0.73
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACTCTCATCTCTAGATAATTCATCAAAATAAAG
Found at i:8470 original size:423 final size:414
Alignment explanation
Indices: 7694--8533 Score: 1448
Period size: 423 Copynumber: 2.0 Consensus size: 414
7684 ACTATATTTT
* *
7694 TTGTAGTTGTTTAAGTCGGTTAGTAAGAAGATATTGCATTGGCTATAAGTTAATCAGTTAGGAGA
1 TTGTAGTTGTTTAAGTCGGTTAGTAAGAAAATATTGCATTGGCTATAAGTTAATCAGTTAGAAGA
* *
7759 AACTCATACATCGAAACAAATAATTCGTATATATAAAGCAAAACACATGACCTCTATTTTATTCT
66 AACTCATACATCGAAACAAATAATTCGCATATATAAAGCAAAACACATGACCTCTATTTCATTCT
*
7824 AAAAGTGCATTATCTAAATTCTACTCCATCTCATCAAAATAAAGCTAATATTCTACTCCTCCATC
131 AAAAGTGCATTATCTAAATTCTACTCCATCTCATCAAAATAAAGCTAATATTCTACTCATCCATC
* *
7889 TCTAGATAATTCATCAAAATAAATCTAATATTAATTGTTGCTTGAAATGTATGTTGATTATCTAA
196 TCTAGATAATTCATCAAAATAAAGCTAATATTAATTGTTGCTTGAAATGTATGTTGATCATCTAA
*
7954 AAAAGCATACTACGCTGTGGTCATTTTTTAATCTTGATTGCACTTGTTGAATTAATGAACTCGGG
261 AAAAGCATACTACGCTGCGGTCATTTTTTAATCTTGATTGCACTTGTTGAATTAATGAACTCGGG
** *
8019 TAGGTGAAAGAATATGGCTTCTACATAA-GAATGCCTAATTTTTTGTAGTCAAGGAGCATGTATA
326 TAGGTGAAAGAATATGGCTTCTACATAAGGAATAACTAATTTTTTGTAGTCAAGGAGCATATATA
8083 GTTGTCGTAGGAAAATTGAATTAG
391 GTTGTCGTAGGAAAATTGAATTAG
8107 TTGTAGTTGTTTAAGTCGGTTAGTAAGAAAATATTGCATTGGCTATAAGTTAATCAGTTAGAAGA
1 TTGTAGTTGTTTAAGTCGGTTAGTAAGAAAATATTGCATTGGCTATAAGTTAATCAGTTAGAAGA
*
8172 AACTCATACATCGAAACAAATAATTCGCATATATAAAGCAAAACACATGACCTCTCTTTCATTCT
66 AACTCATACATCGAAACAAATAATTCGCATATATAAAGCAAAACACATGACCTCTATTTCATTCT
8237 AAAAGTGCATTATCTAAATTCTACTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCTA
131 AAAAGTGCATTATCTAAATTCTACTCCA--TC--------TCATCAAAATAAAGCTAATATTCTA
* *
8302 CTCATTCATCTCTAGATAATTCATCAAAATAAAGCTAATATTAGTTGTTGCTTGAAATGTATGTT
186 CTCATCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTAATTGTTGCTTGAAATGTATGTT
*
8367 GATCATCTAAAAAAGCATACTACGTTGCGGTCATTTTTTAATCTTGATTGCACTTGTTGAATTAA
251 GATCATCTAAAAAAGCATACTACGCTGCGGTCATTTTTTAATCTTGATTGCACTTGTTGAATTAA
8432 TGAACTCGGGTAGGTGAAAGAATATGGCTTCTACATAAGGAATAACTAATTTTTTGTAGTCAAGG
316 TGAACTCGGGTAGGTGAAAGAATATGGCTTCTACATAAGGAATAACTAATTTTTTGTAGTCAAGG
8497 AGCATATATAGTTGTCGTAGGAAAATTGAATTAG
381 AGCATATATAGTTGTCGTAGGAAAATTGAATTAG
8531 TTG
1 TTG
8534 AGAGTATTTG
Statistics
Matches: 401, Mismatches: 15, Indels: 11
0.94 0.04 0.03
Matches are distributed among these distances:
413 153 0.38
415 2 0.00
423 186 0.46
424 60 0.15
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (414 bp):
TTGTAGTTGTTTAAGTCGGTTAGTAAGAAAATATTGCATTGGCTATAAGTTAATCAGTTAGAAGA
AACTCATACATCGAAACAAATAATTCGCATATATAAAGCAAAACACATGACCTCTATTTCATTCT
AAAAGTGCATTATCTAAATTCTACTCCATCTCATCAAAATAAAGCTAATATTCTACTCATCCATC
TCTAGATAATTCATCAAAATAAAGCTAATATTAATTGTTGCTTGAAATGTATGTTGATCATCTAA
AAAAGCATACTACGCTGCGGTCATTTTTTAATCTTGATTGCACTTGTTGAATTAATGAACTCGGG
TAGGTGAAAGAATATGGCTTCTACATAAGGAATAACTAATTTTTTGTAGTCAAGGAGCATATATA
GTTGTCGTAGGAAAATTGAATTAG
Found at i:10506 original size:25 final size:25
Alignment explanation
Indices: 10456--10521 Score: 125
Period size: 24 Copynumber: 2.7 Consensus size: 25
10446 TTACTACATT
10456 AAAAATGAGTAGTTGCTTACTTAAA
1 AAAAATGAGTAGTTGCTTACTTAAA
10481 AAAAAT-AGTAGTTGCTTACTTAAA
1 AAAAATGAGTAGTTGCTTACTTAAA
10505 AAAAATGAGTAGTTGCT
1 AAAAATGAGTAGTTGCT
10522 AGTTTTCTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
24 24 0.60
25 16 0.40
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.32
Consensus pattern (25 bp):
AAAAATGAGTAGTTGCTTACTTAAA
Found at i:10930 original size:13 final size:13
Alignment explanation
Indices: 10909--10938 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
10899 ACTTCGCTTT
*
10909 ATAATTAGTATAG
1 ATAAGTAGTATAG
10922 ATAAGTAGTATAG
1 ATAAGTAGTATAG
10935 ATAA
1 ATAA
10939 TATAATAATA
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:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (13 bp):
ATAAGTAGTATAG
Found at i:11075 original size:22 final size:23
Alignment explanation
Indices: 11050--11104 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 23
11040 TATTTAAAAT
11050 TATGAATTC-AAGTCTCACGAGA
1 TATGAATTCAAAGTCTCACGAGA
*
11072 TATGAATTCAAAAAGTCTCACGAGG
1 TATGAATTC--AAAGTCTCACGAGA
11097 TATGAATT
1 TATGAATT
11105 TAGTTTTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 9 0.31
25 20 0.69
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (23 bp):
TATGAATTCAAAGTCTCACGAGA
Found at i:11126 original size:13 final size:13
Alignment explanation
Indices: 11108--11132 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11098 ATGAATTTAG
11108 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
11121 TTTTTTCTTTTT
1 TTTTTTCTTTTT
11133 TCGTGGTACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:11262 original size:15 final size:15
Alignment explanation
Indices: 11242--11272 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11232 ATATATAAAC
11242 AGTAACTTAAAATAT
1 AGTAACTTAAAATAT
*
11257 AGTAACTTCAAATAT
1 AGTAACTTAAAATAT
11272 A
1 A
11273 CATTCTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (15 bp):
AGTAACTTAAAATAT
Found at i:12803 original size:15 final size:16
Alignment explanation
Indices: 12785--12827 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
12775 ATGATAATAA
*
12785 AAACAAAAC-GAAAAC
1 AAACAAAACAAAAAAC
12800 AAACAAAACAAAAAAC
1 AAACAAAACAAAAAAC
12816 -AA-AAAACAAAAA
1 AAACAAAACAAAAA
12828 TAATATAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 10 0.38
15 11 0.42
16 5 0.19
ACGTcount: A:0.81, C:0.16, G:0.02, T:0.00
Consensus pattern (16 bp):
AAACAAAACAAAAAAC
Found at i:15820 original size:218 final size:218
Alignment explanation
Indices: 15441--15846 Score: 758
Period size: 218 Copynumber: 1.9 Consensus size: 218
15431 AATAAAATAT
* * *
15441 GGGTAATTATTTGATACATCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGACA
1 GGGTAATTATTTGATACACCGGCGATGTAAATTTTGGACTCCACAAGCGAGTTGTGGAGTTGACA
15506 CATGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACACATGTC
66 CATGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACACATGTC
*
15571 ACCCTTCAGGACCCGCTTGTGTAGTCTGCTAAACTCCACCGCCGGTGTATTGTATAATTTGCCAT
131 ACCCTTCAGGACCCGCTTGTGTAGCCTGCTAAACTCCACCGCCGGTGTATTGTATAATTTGCCAT
15636 AAAATATTTACATTTCTTTTTAA
196 AAAATATTTACATTTCTTTTTAA
15659 GGGTAATTATTTGATACACCGGCGATGTAAATTTTGGACTCCACAAGCGAGTTGTGGAGTTGACA
1 GGGTAATTATTTGATACACCGGCGATGTAAATTTTGGACTCCACAAGCGAGTTGTGGAGTTGACA
*
15724 CATGTCTATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACACATGTC
66 CATGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACACATGTC
*
15789 ACCCTTCAGGACCCGCTTGTGTAGCCTGCTAAACTCCACCGCCGTTGTATTGTATAAT
131 ACCCTTCAGGACCCGCTTGTGTAGCCTGCTAAACTCCACCGCCGGTGTATTGTATAAT
15847 CACAAAGTTG
Statistics
Matches: 182, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
218 182 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (218 bp):
GGGTAATTATTTGATACACCGGCGATGTAAATTTTGGACTCCACAAGCGAGTTGTGGAGTTGACA
CATGTCCATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACACATGTC
ACCCTTCAGGACCCGCTTGTGTAGCCTGCTAAACTCCACCGCCGGTGTATTGTATAATTTGCCAT
AAAATATTTACATTTCTTTTTAA
Found at i:31701 original size:14 final size:13
Alignment explanation
Indices: 31679--31712 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
31669 TTGACTTTAT
*
31679 TTATATATTATTA
1 TTATTTATTATTA
31692 TATATTTATTATTA
1 T-TATTTATTATTA
31706 TTATTTA
1 TTATTTA
31713 AAGAAAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:64590 original size:109 final size:108
Alignment explanation
Indices: 64394--64590 Score: 324
Period size: 109 Copynumber: 1.8 Consensus size: 108
64384 TGTTCACATT
* ** *
64394 CATTTCTTTATCTTTTCTTCCCAGTATTGTGGTTATTTCAGAGGCGAATGAAAATGGAAAAATAT
1 CATTACTTTATCTTTTCTTCCCAGTATTGTGGTTATTTCAGAGAAGAATGAAAAGGGAAAAATAT
64459 TAACATGACTATTAGGATAGTAAGGATATGAAATCCAAAACTAG
66 TAACA-GACTATTAGGATAGTAAGGATATGAAATCCAAAACTAG
64503 CATTACTTTATCTTTTCTTCCCAGTATTGTGGTTATTTCAGAGAAGAATGAAAAGGGAAAAATAT
1 CATTACTTTATCTTTTCTTCCCAGTATTGTGGTTATTTCAGAGAAGAATGAAAAGGGAAAAATAT
64568 TACGACA-ACTATTAGGATAGTAA
66 TA--ACAGACTATTAGGATAGTAA
64591 AAATACAAAA
Statistics
Matches: 82, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
109 79 0.96
111 3 0.04
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (108 bp):
CATTACTTTATCTTTTCTTCCCAGTATTGTGGTTATTTCAGAGAAGAATGAAAAGGGAAAAATAT
TAACAGACTATTAGGATAGTAAGGATATGAAATCCAAAACTAG
Found at i:64602 original size:109 final size:108
Alignment explanation
Indices: 64394--64613 Score: 316
Period size: 109 Copynumber: 2.0 Consensus size: 108
64384 TGTTCACATT
* ** *
64394 CATTTCTTTATCTTTTCTTCCCAGTATTGTGGTTATTTCAGAGGCGAATGAAAATGGAAAAATAT
1 CATTACTTTATCTTTTCTTCCCAGTATTGTGGTTATTTCAGAGAAGAATGAAAAGGGAAAAATAT
** ** *
64459 TAACATGACTATTAGGATAGTAAGGATATGAAATCCAAAACTAG
66 TAACA-GACTATTAGGATAGTAAAAATACAAAATCCAAAAATAG
64503 CATTACTTTATCTTTTCTTCCCAGTATTGTGGTTATTTCAGAGAAGAATGAAAAGGGAAAAATAT
1 CATTACTTTATCTTTTCTTCCCAGTATTGTGGTTATTTCAGAGAAGAATGAAAAGGGAAAAATAT
*
64568 TACGACA-ACTATTAGGATAGTAAAAATACAAAATCTAAAAATAG
66 TA--ACAGACTATTAGGATAGTAAAAATACAAAATCCAAAAATAG
64612 CA
1 CA
64614 CTCACATCAA
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
109 96 0.97
111 3 0.03
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (108 bp):
CATTACTTTATCTTTTCTTCCCAGTATTGTGGTTATTTCAGAGAAGAATGAAAAGGGAAAAATAT
TAACAGACTATTAGGATAGTAAAAATACAAAATCCAAAAATAG
Found at i:74652 original size:25 final size:24
Alignment explanation
Indices: 74624--74671 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
74614 CCGGATAATG
*
74624 TGATAACCTCATTGTCACTATATGA
1 TGATAACCT-ATTGCCACTATATGA
**
74649 TGATGCCCTATTGCCACTATATG
1 TGATAACCTATTGCCACTATATG
74672 GACAATAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (24 bp):
TGATAACCTATTGCCACTATATGA
Found at i:83007 original size:8 final size:8
Alignment explanation
Indices: 82994--83020 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
82984 TATTTTATCT
82994 TATCTTAC
1 TATCTTAC
83002 TATCTTAC
1 TATCTTAC
83010 TATCTTAC
1 TATCTTAC
83018 TAT
1 TAT
83021 TATATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (8 bp):
TATCTTAC
Found at i:83674 original size:118 final size:118
Alignment explanation
Indices: 83466--83695 Score: 406
Period size: 118 Copynumber: 1.9 Consensus size: 118
83456 GCAATCATCC
* **
83466 ACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTAAAATTTTCCACTTCAAATTAACTC
1 ACCACAACCATGAATATTGTTTTGAAGAATTTCAAGTCCTAAAATTTTCCACTTCAAACCAACTC
83531 ATCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAATGCTCT
66 ATCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAATGCTCT
**
83584 ACCACAACCATGAATATTGTTTTGAAGAATTTCAAGTCCTTGAATTTTCCACTTCAAACCAACTC
1 ACCACAACCATGAATATTGTTTTGAAGAATTTCAAGTCCTAAAATTTTCCACTTCAAACCAACTC
*
83649 TTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAA
66 ATCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAA
83696 CGCGTTAACA
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
118 106 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.33
Consensus pattern (118 bp):
ACCACAACCATGAATATTGTTTTGAAGAATTTCAAGTCCTAAAATTTTCCACTTCAAACCAACTC
ATCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAATGCTCT
Found at i:84605 original size:2 final size:2
Alignment explanation
Indices: 84592--84631 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
84582 GTTCACATGG
*
84592 TA TA TA TG TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
84632 GTGTGTGTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:85028 original size:22 final size:22
Alignment explanation
Indices: 84958--85255 Score: 107
Period size: 22 Copynumber: 13.3 Consensus size: 22
84948 TCAATCAAAC
*
84958 CAAAATTACATA-GGAAGGTTAT
1 CAAAATTTCATATGG-AGGTTAT
* * *
84980 CAAATTTTTATA-GTGTGGTTA-
1 CAAAATTTCATATG-GAGGTTAT
85001 CTAAAATTTCATATGGAGGTTAT
1 C-AAAATTTCATATGGAGGTTAT
** *
85024 CAAAACGTCATAGTGTA-GTTAT
1 CAAAATTTCATA-TGGAGGTTAT
* * * *
85046 CAAAATTCCATATAGACGTTAC
1 CAAAATTTCATATGGAGGTTAT
* ***
85068 CAAAATTTTATAAAAAGGTTAT
1 CAAAATTTCATATGGAGGTTAT
* *
85090 CAAAATTTC-T-TAGAGTGTCATT
1 CAAAATTTCATATGGAG-GTTA-T
* * *
85112 GACAAAATTTTATACGAAGGTTAT
1 --CAAAATTTCATATGGAGGTTAT
*
85136 CAAAATTT-ATA-GTGTGGTTAT
1 CAAAATTTCATATG-GAGGTTAT
*
85157 CAAAATTTCATAGGGAGGGAGGTTAT
1 CAAAATTTCAT----ATGGAGGTTAT
* * * * *
85183 CAAAGTATCCTAGGGAGGTTAA
1 CAAAATTTCATATGGAGGTTAT
*
85205 CAAAATTTCATA-GTAAGGTTA-
1 CAAAATTTCATATG-GAGGTTAT
85226 CAACAATTT--TATGGAGATGTTAT
1 CAA-AATTTCATATGGAG--GTTAT
85249 CAAAATT
1 CAAAATT
85256 AAATAAAGAG
Statistics
Matches: 208, Mismatches: 43, Indels: 50
0.69 0.14 0.17
Matches are distributed among these distances:
20 8 0.04
21 29 0.14
22 130 0.62
23 9 0.04
24 9 0.04
25 4 0.02
26 18 0.09
27 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATATGGAGGTTAT
Found at i:85146 original size:21 final size:21
Alignment explanation
Indices: 85114--85169 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
85104 GTGTCATTGA
85114 CAAAATTTTATACG-AAGGTTAT
1 CAAAA-TTTATA-GTAAGGTTAT
**
85136 CAAAATTTATAGTGTGGTTAT
1 CAAAATTTATAGTAAGGTTAT
85157 CAAAATTTCATAG
1 CAAAATTT-ATAG
85170 GGAGGGAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 1 0.03
21 20 0.67
22 9 0.30
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (21 bp):
CAAAATTTATAGTAAGGTTAT
Found at i:85196 original size:26 final size:26
Alignment explanation
Indices: 85151--85200 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
85141 TTTATAGTGT
*
85151 GGTTATCAAAATTTCATAGGGAGGGA
1 GGTTATCAAAATATCATAGGGAGGGA
* *
85177 GGTTATCAAAGTATCCTAGGGAGG
1 GGTTATCAAAATATCATAGGGAGG
85201 TTAACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.32, C:0.10, G:0.32, T:0.26
Consensus pattern (26 bp):
GGTTATCAAAATATCATAGGGAGGGA
Found at i:85392 original size:22 final size:22
Alignment explanation
Indices: 85315--85458 Score: 88
Period size: 22 Copynumber: 6.8 Consensus size: 22
85305 TTCATGGTGT
* *
85315 GGTTATCAAAATTTTATGAA-GA
1 GGTTATCAAAATTTCA-CAATGA
* *
85337 GGTTATCAAAATTTTCATAATGC
1 GGTTATCAAAA-TTTCACAATGA
*
85360 GGTTA-C--AATTTCACACTGA
1 GGTTATCAAAATTTCACAATGA
* * *
85379 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCACAATGA
* *
85401 GTTTATC-AAATTT-TC-AT-A
1 GGTTATCAAAATTTCACAATGA
* *
85419 GGTTATCGAAATTTCATAATGA
1 GGTTATCAAAATTTCACAATGA
* *
85441 TGTTATCAAATTTTCACA
1 GGTTATCAAAATTTCACA
85459 CCATTGTGAA
Statistics
Matches: 92, Mismatches: 21, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
18 6 0.07
19 20 0.22
20 3 0.03
21 8 0.09
22 45 0.49
23 10 0.11
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.40
Consensus pattern (22 bp):
GGTTATCAAAATTTCACAATGA
Found at i:85433 original size:18 final size:17
Alignment explanation
Indices: 85378--85436 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 17
85368 TTTCACACTG
85378 AGGTTATCAAAATTTCAT
1 AGGTTATC-AAATTTCAT
85396 AGTGTGTTTATCAAATTTTCAT
1 A--G-G-TTATCAAA-TTTCAT
85418 AGGTTATCGAAATTTCAT
1 AGGTTATC-AAATTTCAT
85436 A
1 A
85437 ATGATGTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
18 13 0.37
19 4 0.11
20 2 0.06
21 4 0.11
22 12 0.34
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (17 bp):
AGGTTATCAAATTTCAT
Found at i:85433 original size:40 final size:40
Alignment explanation
Indices: 85336--85456 Score: 131
Period size: 40 Copynumber: 3.0 Consensus size: 40
85326 TTTTATGAAG
** *
85336 AGGTTATCAAAATTTTCATAATGCGGTTA-C-AATTTCACACT
1 AGGTTATCAAAA-TTTCATAATGATGTTATCAAATTT-TCA-T
*
85377 GAGGTTATCAAAATTTCATAGTG-TGTTTATCAAATTTTCAT
1 -AGGTTATCAAAATTTCATAATGATG-TTATCAAATTTTCAT
*
85418 AGGTTATCGAAATTTCATAATGATGTTATCAAATTTTCA
1 AGGTTATCAAAATTTCATAATGATGTTATCAAATTTTCA
85457 CACCATTGTG
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
40 35 0.50
41 15 0.21
42 15 0.21
43 5 0.07
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (40 bp):
AGGTTATCAAAATTTCATAATGATGTTATCAAATTTTCAT
Found at i:85488 original size:39 final size:40
Alignment explanation
Indices: 85381--85493 Score: 106
Period size: 40 Copynumber: 2.8 Consensus size: 40
85371 CACACTGAGG
* * * **
85381 TTATCAAAATTTCATAGTGTGTTTATCAAATTTTCATAGG
1 TTATCGAAATTTCATAGTGTGGTTATCAAATTTTCACACA
*
85421 TTATCGAAATTTCATAATGAT-GTTATCAAATTTTCACACCA
1 TTATCGAAATTTCATAGTG-TGGTTATCAAATTTTCACA-CA
* *
85462 TTGT-G-AATTTCATAGTGTGGTGATCAATATTT
1 TTATCGAAATTTCATAGTGTGGTTATCAA-ATTT
85494 CTACGTTGGA
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
38 1 0.02
39 18 0.30
40 37 0.62
41 4 0.07
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (40 bp):
TTATCGAAATTTCATAGTGTGGTTATCAAATTTTCACACA
Found at i:85915 original size:70 final size:70
Alignment explanation
Indices: 85838--85982 Score: 272
Period size: 70 Copynumber: 2.1 Consensus size: 70
85828 TGCATGTTTG
* *
85838 TGTGTAGAACGTTGTTTTGGAGAAAATGTTTATTTCGAATGTGTTATTTGTGTAATCAATGCTCA
1 TGTGTAGAACATTGTTTTGGAGAAAATGTTTATTTCGAATGTGTTATTTGTGTAAGCAATGCTCA
85903 TATGT
66 TATGT
85908 TGTGTAGAACATTGTTTTGGAGAAAATGTTTATTTCGAATGTGTTATTTGTGTAAGCAATGCTCA
1 TGTGTAGAACATTGTTTTGGAGAAAATGTTTATTTCGAATGTGTTATTTGTGTAAGCAATGCTCA
85973 TATGT
66 TATGT
85978 TGTGT
1 TGTGT
85983 TTCAGAGTTA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.26, C:0.07, G:0.23, T:0.44
Consensus pattern (70 bp):
TGTGTAGAACATTGTTTTGGAGAAAATGTTTATTTCGAATGTGTTATTTGTGTAAGCAATGCTCA
TATGT
Found at i:86326 original size:223 final size:223
Alignment explanation
Indices: 85919--86366 Score: 835
Period size: 223 Copynumber: 2.0 Consensus size: 223
85909 GTGTAGAACA
*
85919 TTGTTTTGGAGAAAATGTTTATTTCGAATGTGTTATTTGTGTAAGCAATGCTCATATGTTGTGTT
1 TTGTTTTGGAGAAAATGTTTATTTCGAATGTATTATTTGTGTAAGCAATGCTCATATGTTGTGTT
*
85984 TCAGAGTTAGTAGAGCTTATTGGAAAATAGTTTGCCAAACAAAGTTTTCTTCAAAGACTAAAACC
66 TCAGAGTTAGTAGAACTTATTGGAAAATAGTTTGCCAAACAAAGTTTTCTTCAAAGACTAAAACC
*
86049 TCAATTGTGTGCAAAACATTTATTTATTTGAAAATGATCAAAACGATCTTTTTTTTAACCAACAC
131 TCAATTGTGTGCAAAACATTTATTTATTTGAAAATGATCAAAACGATCTTTTTTTAAACCAACAC
86114 TCTAATGTCATGTATTGAAATCAGTTAG
196 TCTAATGTCATGTATTGAAATCAGTTAG
86142 TTGTTTTGGAGAAAATGTTTATTTCGAATGTATTATTTGTGTAAGCAATGCTCATATGTTGTGTT
1 TTGTTTTGGAGAAAATGTTTATTTCGAATGTATTATTTGTGTAAGCAATGCTCATATGTTGTGTT
* *
86207 TCGGAGTTAGTAGAACTTATTGGAAAATAGTTTGCCAAACAAAGTTTTCTTCAAAGGCTAAAACC
66 TCAGAGTTAGTAGAACTTATTGGAAAATAGTTTGCCAAACAAAGTTTTCTTCAAAGACTAAAACC
86272 TCAA-TGTGTGCAAAACATTTATTTATTTGAAAATGATCAAAACGATCTTTTTTTTAAACCAACA
131 TCAATTGTGTGCAAAACATTTATTTATTTGAAAATGATCAAAACGATC-TTTTTTTAAACCAACA
86336 CTCTAATGTCATGTATTGAAATCAGTTAG
195 CTCTAATGTCATGTATTGAAATCAGTTAG
86365 TT
1 TT
86367 TATTGGAAAA
Statistics
Matches: 219, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
222 43 0.20
223 176 0.80
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.39
Consensus pattern (223 bp):
TTGTTTTGGAGAAAATGTTTATTTCGAATGTATTATTTGTGTAAGCAATGCTCATATGTTGTGTT
TCAGAGTTAGTAGAACTTATTGGAAAATAGTTTGCCAAACAAAGTTTTCTTCAAAGACTAAAACC
TCAATTGTGTGCAAAACATTTATTTATTTGAAAATGATCAAAACGATCTTTTTTTAAACCAACAC
TCTAATGTCATGTATTGAAATCAGTTAG
Found at i:86718 original size:21 final size:20
Alignment explanation
Indices: 86689--86757 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 20
86679 TTGATACATA
*
86689 TATAACTTTTTTCATAACCGT
1 TATAGCTTTTTTCATAA-CGT
*
86710 TATAGC-TTTTTGAGTAA--T
1 TATAGCTTTTTTCA-TAACGT
86728 TA-A-CTTTTTTCATAACTGT
1 TATAGCTTTTTTCATAAC-GT
86747 TATAGCTTTTT
1 TATAGCTTTTT
86758 GAGTAATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 14
0.69 0.05 0.25
Matches are distributed among these distances:
16 4 0.11
17 7 0.18
18 3 0.08
19 3 0.08
20 7 0.18
21 14 0.37
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (20 bp):
TATAGCTTTTTTCATAACGT
Found at i:86741 original size:37 final size:37
Alignment explanation
Indices: 86691--86767 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
86681 GATACATATA
86691 TAACTTTTTTCATAACCGTTATAGCTTTTTGAGTAAT
1 TAACTTTTTTCATAACCGTTATAGCTTTTTGAGTAAT
*
86728 TAACTTTTTTCATAACTGTTATAGCTTTTTGAGTAAT
1 TAACTTTTTTCATAACCGTTATAGCTTTTTGAGTAAT
86765 TAA
1 TAA
86768 GTATTGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (37 bp):
TAACTTTTTTCATAACCGTTATAGCTTTTTGAGTAAT
Found at i:87369 original size:42 final size:42
Alignment explanation
Indices: 87310--87392 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
87300 GTATTCCTCT
*
87310 GCTAGCATATTGATCCTCTCCTTCAGCTGCTCAGTCTCGAAC
1 GCTAGCATATTGATCCTCTCCTTCAACTGCTCAGTCTCGAAC
** *
87352 GCTAGCATATTGATCCTCTTTTTCAATTGCTCAGTCTCGAA
1 GCTAGCATATTGATCCTCTCCTTCAACTGCTCAGTCTCGAA
87393 TTTTATCTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (42 bp):
GCTAGCATATTGATCCTCTCCTTCAACTGCTCAGTCTCGAAC
Found at i:87752 original size:27 final size:27
Alignment explanation
Indices: 87722--87777 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
87712 CTTTTAGTAA
*
87722 ATTACCCCAATCAAAATCTCCAGTTTC
1 ATTACCCCAATCAAAATCTCCAATTTC
87749 ATTACCCCAATCAAAATCTCCAATTTC
1 ATTACCCCAATCAAAATCTCCAATTTC
87776 AT
1 AT
87778 CCCTAAGCGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.32, G:0.02, T:0.30
Consensus pattern (27 bp):
ATTACCCCAATCAAAATCTCCAATTTC
Found at i:88294 original size:98 final size:95
Alignment explanation
Indices: 88128--88324 Score: 313
Period size: 98 Copynumber: 2.0 Consensus size: 95
88118 AAGAAAATTC
* *
88128 TTGCTCAATTCAAATTGAAGGATTAAACATTGCTGAAGAAATTCAAGTAATTAAGATTCATTTAT
1 TTGCTCAATTCAAATTGAAGGATTAAACATTGCTCAAGAAATTCAAGGAATTAAGATTCATTTAT
88193 TCTGCAATTACATCTATTCGATTCTAACGA
66 TCTGCAATTACATCTATTCGATTCTAACGA
* *
88223 TTGCTCAATTCAAGAAATTTAAGGATTAAACATTGCTCAAGAAATTCAAGGAATTGAGATTCATT
1 TTGCTCAATTC---AAATTGAAGGATTAAACATTGCTCAAGAAATTCAAGGAATTAAGATTCATT
* *
88288 TATTCTGCAATTACATCTATTTGATTCTAATGA
63 TATTCTGCAATTACATCTATTCGATTCTAACGA
88321 TTGC
1 TTGC
88325 CTTTATTTAA
Statistics
Matches: 93, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
95 11 0.12
98 82 0.88
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (95 bp):
TTGCTCAATTCAAATTGAAGGATTAAACATTGCTCAAGAAATTCAAGGAATTAAGATTCATTTAT
TCTGCAATTACATCTATTCGATTCTAACGA
Found at i:88907 original size:31 final size:31
Alignment explanation
Indices: 88850--88908 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
88840 TTTGTAAAAC
*
88850 TTTTGAAACACCTATTGTACCGTTATTTAAT
1 TTTTGAAACACCTATTATACCGTTATTTAAT
**
88881 TTTTGAAACGTCTATTATATCC-TTATTT
1 TTTTGAAACACCTATTATA-CCGTTATTT
88909 GTCTGACATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 22 0.92
32 2 0.08
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.49
Consensus pattern (31 bp):
TTTTGAAACACCTATTATACCGTTATTTAAT
Found at i:90170 original size:23 final size:23
Alignment explanation
Indices: 90127--90170 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
90117 CTGAAAACTC
* *
90127 TATTTTTATTTAATTAAATTTAA
1 TATTTTTATTAAATAAAATTTAA
90150 TATTTTTA-TAAATAAATATTT
1 TATTTTTATTAAATAAA-ATTT
90171 TAATTTTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTTTTATTAAATAAAATTTAA
Found at i:91351 original size:31 final size:31
Alignment explanation
Indices: 91313--91373 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
91303 GAGTTTTGTA
91313 AAACTTTTGAA-CTGCCTATTATACCCTTATC
1 AAACTTTTGAATC-GCCTATTATACCCTTATC
* *
91344 AAACTTTTGAATCGTCTATTATATCCTTAT
1 AAACTTTTGAATCGCCTATTATACCCTTAT
91374 TTTTTTATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.43
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATTATACCCTTATC
Found at i:91520 original size:92 final size:93
Alignment explanation
Indices: 91410--91588 Score: 283
Period size: 92 Copynumber: 1.9 Consensus size: 93
91400 TTTTTTAAAT
* *
91410 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAA-TCAAATCTAATATCCTTATAA-C
1 TTTTATAGTTTTACTCAACTAAAAACTCTATGTTTATTTAAGT-AAATCTAATATCCTTA-AACC
*
91473 TATTTT-TTTTTACCATTTTACTATTCTAC
64 TATTTTATTTTTACCATATTACTATTCTAC
91502 TTTTATAGTTTTACTCAACTAAAAACTCTATGTTTATTTAAGTAAATCTAATATCCTTAAACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATGTTTATTTAAGTAAATCTAATATCCTTAAACCTA
*
91567 TTTTATTTTTACGATATTACTA
66 TTTTATTTTTACCATATTACTA
91589 ATTTAATTAA
Statistics
Matches: 80, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
91 2 0.03
92 62 0.77
93 16 0.20
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.49
Consensus pattern (93 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATGTTTATTTAAGTAAATCTAATATCCTTAAACCTA
TTTTATTTTTACCATATTACTATTCTAC
Done.