Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008943.1 Hibiscus syriacus cultivar Beakdansim tig00112264_pilon, 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: 1742779
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 5 of 5
Found at i:1479061 original size:19 final size:20
Alignment explanation
Indices: 1479037--1479091 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
1479027 TATCCTTTAT
1479037 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
1479056 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
*
1479076 -TATTATTATTCCATTA
1 TTATT-TTATTTCATTA
1479092 TTAGTCCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 4 0.13
19 12 0.39
20 12 0.39
21 3 0.10
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:1484515 original size:19 final size:20
Alignment explanation
Indices: 1484491--1484539 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
1484481 TATCCTTTAT
1484491 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
1484510 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
1484530 -TATTATTATT
1 TTATT-TTATT
1484540 CCCTTATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:1490199 original size:15 final size:17
Alignment explanation
Indices: 1490176--1490209 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1490166 TTTAGATAGG
1490176 TTTAGTTTATTA-TTAT
1 TTTAGTTTATTAGTTAT
1490192 TTTA-TTTATTAGTTAT
1 TTTAGTTTATTAGTTAT
1490208 TT
1 TT
1490210 AGGACATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTAGTTTATTAGTTAT
Found at i:1492054 original size:19 final size:19
Alignment explanation
Indices: 1492030--1492066 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1492020 TGGCCAAGAG
1492030 CATGTATCTTCATTAAAAT
1 CATGTATCTTCATTAAAAT
* *
1492049 CATGTATTTTTATTAAAA
1 CATGTATCTTCATTAAAA
1492067 AAAATCATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (19 bp):
CATGTATCTTCATTAAAAT
Found at i:1505908 original size:18 final size:17
Alignment explanation
Indices: 1505875--1505924 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 17
1505865 GCTATTTTTT
*
1505875 CAAAAAAAAA-ATCAAA
1 CAAAAAAAAAGAGCAAA
1505891 CAAAAAAAAAGAGGCAAA
1 CAAAAAAAAAGA-GCAAA
1505909 -AAACAAAAAAGA-CAAA
1 CAAA-AAAAAAGAGCAAA
1505925 ATTTCAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 14 0.47
17 4 0.13
18 12 0.40
ACGTcount: A:0.78, C:0.12, G:0.08, T:0.02
Consensus pattern (17 bp):
CAAAAAAAAAGAGCAAA
Found at i:1510970 original size:20 final size:21
Alignment explanation
Indices: 1510945--1510983 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1510935 ATGAATCTTC
1510945 ATTAAA-ATCATGTATTTTTT
1 ATTAAACATCATGTATTTTTT
1510965 ATTAAACATCATGTATTTT
1 ATTAAACATCATGTATTTT
1510984 CAAAGGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTAAACATCATGTATTTTTT
Found at i:1512793 original size:35 final size:37
Alignment explanation
Indices: 1512747--1512826 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
1512737 TTTGAGAATT
* *
1512747 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCATGATAATGGAAGATGGACTA
* *
1512782 TGGTGATGATATAGGTATGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCATGATAATGGAAGATGGACTA
1512819 TGGTGATG
1 TGGTGATG
1512827 GAAATAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 19 0.49
36 4 0.10
37 16 0.41
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCATGATAATGGAAGATGGACTA
Found at i:1512803 original size:11 final size:11
Alignment explanation
Indices: 1512747--1512826 Score: 56
Period size: 11 Copynumber: 6.7 Consensus size: 11
1512737 TTTGAGAATT
1512747 TGGTGATGATA
1 TGGTGATGATA
*
1512758 TAGGCG-TGATA
1 T-GGTGATGATA
1512769 TGGTGATGGACTA
1 TGGTGAT-GA-TA
1512782 TGGTGATGATA
1 TGGTGATGATA
1512793 TAGGT-ATGATAA
1 T-GGTGATGAT-A
*
1512805 TGGAAGATGGATTA
1 TGG-TGAT-GA-TA
1512819 TGGTGATG
1 TGGTGATG
1512827 GAAATAGTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
10 3 0.05
11 18 0.33
12 13 0.24
13 14 0.25
14 6 0.11
15 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.33
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:1512828 original size:13 final size:13
Alignment explanation
Indices: 1512767--1512828 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
1512757 ATAGGCGTGA
*
1512767 TATGGTGATGGAC
1 TATGGTGATGGAT
1512780 TATGGTGAT-GA-
1 TATGGTGATGGAT
1512791 TATAGGT-AT-GAT
1 TAT-GGTGATGGAT
* *
1512803 AATGGAAGATGGAT
1 TATGG-TGATGGAT
1512817 TATGGTGATGGA
1 TATGGTGATGGA
1512829 AATAGTATCT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
11 9 0.22
12 7 0.17
13 17 0.43
14 7 0.17
ACGTcount: A:0.31, C:0.02, G:0.35, T:0.32
Consensus pattern (13 bp):
TATGGTGATGGAT
Found at i:1518475 original size:35 final size:37
Alignment explanation
Indices: 1518424--1518508 Score: 111
Period size: 35 Copynumber: 2.4 Consensus size: 37
1518414 GGAAATTTGA
* * *
1518424 GAATTTGGTGATGATATAGGCGTGAT-ATGG-TGATG
1 GAATATGGTGATGATATAGGCATGATAATGGAAGATG
*
1518459 GAATATGGTGATGATATAGGTATGATAATGGAAGATG
1 GAATATGGTGATGATATAGGCATGATAATGGAAGATG
*
1518496 GATTATGGTGATG
1 GAATATGGTGATG
1518509 GAAATAGTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
35 23 0.53
36 4 0.09
37 16 0.37
ACGTcount: A:0.31, C:0.01, G:0.35, T:0.33
Consensus pattern (37 bp):
GAATATGGTGATGATATAGGCATGATAATGGAAGATG
Found at i:1518483 original size:11 final size:12
Alignment explanation
Indices: 1518430--1518485 Score: 57
Period size: 11 Copynumber: 4.8 Consensus size: 12
1518420 TTGAGAATTT
1518430 GGTGATGATATA
1 GGTGATGATATA
*
1518442 GGCG-TGATAT-
1 GGTGATGATATA
1518452 GGTGATGGA-ATA
1 GGTGAT-GATATA
1518464 TGGTGATGATATA
1 -GGTGATGATATA
1518477 GGT-ATGATA
1 GGTGATGATA
1518486 ATGGAAGATG
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
10 3 0.08
11 15 0.41
12 10 0.27
13 9 0.24
ACGTcount: A:0.30, C:0.02, G:0.36, T:0.32
Consensus pattern (12 bp):
GGTGATGATATA
Found at i:1518510 original size:13 final size:13
Alignment explanation
Indices: 1518449--1518510 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
1518439 ATAGGCGTGA
*
1518449 TATGGTGATGGAA
1 TATGGTGATGGAT
1518462 TATGGTGAT-GA-
1 TATGGTGATGGAT
1518473 TATAGGT-AT-GAT
1 TAT-GGTGATGGAT
* *
1518485 AATGGAAGATGGAT
1 TATGG-TGATGGAT
1518499 TATGGTGATGGA
1 TATGGTGATGGA
1518511 AATAGTATCT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
11 9 0.22
12 7 0.17
13 17 0.43
14 7 0.17
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (13 bp):
TATGGTGATGGAT
Found at i:1530666 original size:13 final size:13
Alignment explanation
Indices: 1530648--1530681 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
1530638 ACTATCTATT
1530648 CATCACCACCTTC
1 CATCACCACCTTC
1530661 CATCACCACCTTC
1 CATCACCACCTTC
1530674 CATCACCA
1 CATCACCA
1530682 TTTTCACACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.26, C:0.53, G:0.00, T:0.21
Consensus pattern (13 bp):
CATCACCACCTTC
Found at i:1535823 original size:35 final size:37
Alignment explanation
Indices: 1535777--1535856 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
1535767 TTTGAGAATT
*
1535777 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
1535812 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
1535849 TGGTGATG
1 TGGTGATG
1535857 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:1539893 original size:35 final size:37
Alignment explanation
Indices: 1539847--1539922 Score: 111
Period size: 35 Copynumber: 2.1 Consensus size: 37
1539837 TTTGAGAATT
*
1539847 TGGTGATGATATAGGCGTAAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTAATAATGGAAGATGGACTA
* *
1539882 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTAATAATGGAAGATGGACTA
1539919 TGGT
1 TGGT
1539923 TATGGAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 20 0.56
36 4 0.11
37 12 0.33
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.32
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTAATAATGGAAGATGGACTA
Found at i:1543912 original size:35 final size:37
Alignment explanation
Indices: 1543866--1543945 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
1543856 TTTGAGAATT
*
1543866 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
1543901 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
1543938 TGGTGATG
1 TGGTGATG
1543946 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:1551675 original size:21 final size:22
Alignment explanation
Indices: 1551651--1551693 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
1551641 AAGCTCATGT
1551651 CCTT-TTATTGAAGAGTCACAG
1 CCTTATTATTGAAGAGTCACAG
*
1551672 CCTTAGATTCTTGAAGAGTCAC
1 CCTT--ATTATTGAAGAGTCAC
1551694 GTCCTTTGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 4 0.22
24 14 0.78
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (22 bp):
CCTTATTATTGAAGAGTCACAG
Found at i:1553354 original size:17 final size:17
Alignment explanation
Indices: 1553332--1553374 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
1553322 GTAGGAGTCT
1553332 TTTTCTTTTCTCTT-TTG
1 TTTTCTTTT-TCTTGTTG
1553349 TTTTCTTCTTTCTTGTTG
1 TTTTCTT-TTTCTTGTTG
1553367 TTTT-TTTT
1 TTTTCTTTT
1553375 GTTGTAGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 13 0.54
18 9 0.38
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (17 bp):
TTTTCTTTTTCTTGTTG
Found at i:1557870 original size:35 final size:37
Alignment explanation
Indices: 1557824--1557903 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
1557814 TTTGAGAATT
*
1557824 TGGTGATGATATAGGCGTGAT-ATGG-TGACGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGACGGACTA
* *
1557859 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGACGGACTA
1557896 TGGTGATG
1 TGGTGATG
1557904 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.05, G:0.38, T:0.30
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGACGGACTA
Found at i:1568620 original size:22 final size:22
Alignment explanation
Indices: 1568559--1568613 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
1568549 ACATTTTGGA
*
1568559 TTTGTTTTGGCTTTTTTTGTTT
1 TTTGTTTTTGCTTTTTTTGTTT
1568581 TTT-TTTTTGCCTTTTTTTTGTTT
1 TTTGTTTTTG-C-TTTTTTTGTTT
1568604 TTTGTTTTTG
1 TTTGTTTTTG
1568614 TTATTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.17
22 4 0.14
23 14 0.48
24 6 0.21
ACGTcount: A:0.00, C:0.05, G:0.15, T:0.80
Consensus pattern (22 bp):
TTTGTTTTTGCTTTTTTTGTTT
Found at i:1572530 original size:23 final size:23
Alignment explanation
Indices: 1572504--1572555 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
1572494 TTTCTTTTTT
1572504 TTTCTTCTTTTGAGTGCTTTTAA
1 TTTCTTCTTTTGAGTGCTTTTAA
*
1572527 TTTCTTCTTTTGAGTGCTTTTAT
1 TTTCTTCTTTTGAGTGCTTTTAA
1572550 TTTCTT
1 TTTCTT
1572556 TGCTGATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.10, C:0.13, G:0.12, T:0.65
Consensus pattern (23 bp):
TTTCTTCTTTTGAGTGCTTTTAA
Found at i:1590712 original size:25 final size:25
Alignment explanation
Indices: 1590660--1590712 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
1590650 TTTTCTTTGC
* *
1590660 TTTTCTTCTTTTTGAGTGCTGTATT
1 TTTTCTTCTTTTGGAGTGCTGTACT
1590685 TTTTCTTCTTTTGGAGTGCT-TGACT
1 TTTTCTTCTTTTGGAGTGCTGT-ACT
1590710 TTT
1 TTT
1590713 ATTTGTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.08, C:0.13, G:0.17, T:0.62
Consensus pattern (25 bp):
TTTTCTTCTTTTGGAGTGCTGTACT
Found at i:1602636 original size:18 final size:19
Alignment explanation
Indices: 1602595--1602633 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1602585 CTATCTTTAT
1602595 TTATTTCATTTCATTCTTA
1 TTATTTCATTTCATTCTTA
1602614 TTATTT-ATTTCATTACTTA
1 TTATTTCATTTCATT-CTTA
1602633 T
1 T
1602634 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTTCATTTCATTCTTA
Found at i:1604088 original size:18 final size:18
Alignment explanation
Indices: 1604067--1604105 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1604057 CTTTAACCTT
1604067 ACAACACTTACCACGACA
1 ACAACACTTACCACGACA
* *
1604085 ACAACATTTGCCACGACA
1 ACAACACTTACCACGACA
1604103 ACA
1 ACA
1604106 CCATTCATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.36, G:0.08, T:0.13
Consensus pattern (18 bp):
ACAACACTTACCACGACA
Found at i:1611851 original size:18 final size:18
Alignment explanation
Indices: 1611825--1611868 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1611815 GTGAAGTATG
*
1611825 AATGGTGTTGTCGTGGCA
1 AATGTTGTTGTCGTGGCA
*
1611843 AATGTTGTTGTCGTGGTA
1 AATGTTGTTGTCGTGGCA
*
1611861 AGTGTTGT
1 AATGTTGT
1611869 AAGGTTAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.07, G:0.36, T:0.41
Consensus pattern (18 bp):
AATGTTGTTGTCGTGGCA
Found at i:1617594 original size:8 final size:8
Alignment explanation
Indices: 1617574--1617607 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
1617564 TCTTTTTGAA
1617574 CTTCTCTTT
1 CTTCT-TTT
1617583 -TTCTTTT
1 CTTCTTTT
1617590 CTTCTTTT
1 CTTCTTTT
1617598 CTTCTTTT
1 CTTCTTTT
1617606 CT
1 CT
1617608 GATTTTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 3 0.12
8 21 0.88
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (8 bp):
CTTCTTTT
Found at i:1624158 original size:8 final size:8
Alignment explanation
Indices: 1624137--1624196 Score: 63
Period size: 8 Copynumber: 7.8 Consensus size: 8
1624127 GCTATTTTTT
1624137 AAAAAAA-
1 AAAAAAAC
1624144 AATAAAAAC
1 AA-AAAAAC
1624153 AAAAAAA-
1 AAAAAAAC
***
1624160 GGCAAAAC
1 AAAAAAAC
1624168 AAAAAAAC
1 AAAAAAAC
1624176 AAAAAAAC
1 AAAAAAAC
1624184 -AAAAAAC
1 AAAAAAAC
1624191 AAAAAA
1 AAAAAA
1624197 GCCAAAATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
7 13 0.30
8 28 0.65
9 2 0.05
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.02
Consensus pattern (8 bp):
AAAAAAAC
Found at i:1624173 original size:23 final size:23
Alignment explanation
Indices: 1624137--1624196 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1624127 GCTATTTTTT
* *
1624137 AAAAAAAAATAAAAACAAAAAAAG
1 AAAAAACAA-AAAAACAAAAAAAC
**
1624161 GCAAAACAAAAAAACAAAAAAAC
1 AAAAAACAAAAAAACAAAAAAAC
1624184 AAAAAACAAAAAA
1 AAAAAACAAAAAA
1624197 GCCAAAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 24 0.80
24 6 0.20
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.02
Consensus pattern (23 bp):
AAAAAACAAAAAAACAAAAAAAC
Found at i:1624203 original size:15 final size:15
Alignment explanation
Indices: 1624137--1624196 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
1624127 GCTATTTTTT
*
1624137 AAAAAAAAATAAAAAC
1 AAAAAAACA-AAAAAC
***
1624153 AAAAAAAGGCAAAAC
1 AAAAAAACAAAAAAC
1624168 AAAAAAACAAAAAA-
1 AAAAAAACAAAAAAC
1624182 ACAAAAAACAAAAAA
1 A-AAAAAACAAAAAA
1624197 GCCAAAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
14 1 0.03
15 29 0.78
16 7 0.19
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.02
Consensus pattern (15 bp):
AAAAAAACAAAAAAC
Found at i:1628785 original size:19 final size:21
Alignment explanation
Indices: 1628736--1628788 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1628726 TGAAACCCCT
1628736 TTGAAAATACATGATTTTTAA
1 TTGAAAATACATGATTTTTAA
*
1628757 ATGAAAATACATGA-TTTT-A
1 TTGAAAATACATGATTTTTAA
*
1628776 TTGAAGATACATG
1 TTGAAAATACATG
1628789 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.41
20 4 0.14
21 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (21 bp):
TTGAAAATACATGATTTTTAA
Found at i:1629972 original size:19 final size:20
Alignment explanation
Indices: 1629948--1629990 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1629938 AGCATTTATC
*
1629948 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
1629967 TTCATTAAAAATCATGTATT
1 TTCATTAAAAATCATGTATT
1629987 TTCA
1 TTCA
1629991 AAGGGGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:1631227 original size:14 final size:14
Alignment explanation
Indices: 1631208--1631242 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1631198 CAAATAGTCC
1631208 AACTAGCTGAGTTT
1 AACTAGCTGAGTTT
1631222 AACTAGCTGAGTTT
1 AACTAGCTGAGTTT
*
1631236 AGCTAGC
1 AACTAGC
1631243 CTTAAGCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (14 bp):
AACTAGCTGAGTTT
Found at i:1633098 original size:35 final size:37
Alignment explanation
Indices: 1633049--1633126 Score: 115
Period size: 35 Copynumber: 2.2 Consensus size: 37
1633039 TTGAGAATTC
* *
1633049 GTGATGATATAGGCGTGAT-ATGG-TGATGGACTATG
1 GTGATGATACAGGCGTGATAATGGAAGATGGACTATG
*
1633084 GTGATGATACAGGCGTGATAATGGAAGATGGATTATG
1 GTGATGATACAGGCGTGATAATGGAAGATGGACTATG
1633121 GTGATG
1 GTGATG
1633127 GAAATAGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 18 0.47
36 4 0.11
37 16 0.42
ACGTcount: A:0.28, C:0.05, G:0.37, T:0.29
Consensus pattern (37 bp):
GTGATGATACAGGCGTGATAATGGAAGATGGACTATG
Found at i:1638694 original size:35 final size:37
Alignment explanation
Indices: 1638648--1638727 Score: 101
Period size: 35 Copynumber: 2.2 Consensus size: 37
1638638 TTTGAGAATT
** * *
1638648 TGGTGATGATATAGGCGTGCTA-TGG-TGATGGACTA
1 TGGTGATGATATACACGTGATAGTGGAAGATGGACTA
*
1638683 TGGTGATGATATACACGTGATAGTGGAAGATGGATTA
1 TGGTGATGATATACACGTGATAGTGGAAGATGGACTA
1638720 TGGTGATG
1 TGGTGATG
1638728 GAAATAGTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
35 19 0.50
36 3 0.08
37 16 0.42
ACGTcount: A:0.26, C:0.06, G:0.36, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATACACGTGATAGTGGAAGATGGACTA
Found at i:1642284 original size:13 final size:13
Alignment explanation
Indices: 1642261--1642324 Score: 55
Period size: 13 Copynumber: 5.2 Consensus size: 13
1642251 ATAAGATACT
1642261 ATCTGTCCATCACC
1 ATCT-TCCATCACC
1642275 ATCTTCCATCACC
1 ATCTTCCATCACC
** *
1642288 AT-TT-CATGTCT
1 ATCTTCCATCACC
*
1642299 AT-AT-CATCACC
1 ATCTTCCATCACC
1642310 ATCTTCCATCACC
1 ATCTTCCATCACC
1642323 AT
1 AT
1642325 TCACGTTTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
11 13 0.32
12 3 0.08
13 20 0.50
14 4 0.10
ACGTcount: A:0.25, C:0.38, G:0.03, T:0.34
Consensus pattern (13 bp):
ATCTTCCATCACC
Found at i:1642314 original size:35 final size:34
Alignment explanation
Indices: 1642268--1642346 Score: 122
Period size: 35 Copynumber: 2.3 Consensus size: 34
1642258 ACTATCTGTC
*
1642268 CATCACCATCTTCCATCACCATTTCATGTCTATAT
1 CATCACCATCTTCCATCACCA-TTCACGTCTATAT
*
1642303 CATCACCATCTTCCATCACCATTCACGTTTATAT
1 CATCACCATCTTCCATCACCATTCACGTCTATAT
*
1642337 CATCATCATC
1 CATCACCATC
1642347 CCTTAACCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 20 0.49
35 21 0.51
ACGTcount: A:0.27, C:0.35, G:0.03, T:0.35
Consensus pattern (34 bp):
CATCACCATCTTCCATCACCATTCACGTCTATAT
Found at i:1642752 original size:17 final size:16
Alignment explanation
Indices: 1642722--1642760 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
1642712 GTGCTACAAC
* *
1642722 AAAAAGCAACAAGAAA
1 AAAAAACAAAAAGAAA
1642738 GAAAAAACAAAAAGAAA
1 -AAAAAACAAAAAGAAA
1642755 AAAAAA
1 AAAAAA
1642761 GACTCCTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAACAAAAAGAAA
Found at i:1642756 original size:14 final size:14
Alignment explanation
Indices: 1642729--1642762 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1642719 AACAAAAAGC
1642729 AACAAGAAAGAAAA
1 AACAAGAAAGAAAA
1642743 AACAA-AAAGAAAA
1 AACAAGAAAGAAAA
*
1642756 AAAAAGA
1 AACAAGA
1642763 CTCCTACAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (14 bp):
AACAAGAAAGAAAA
Found at i:1645722 original size:22 final size:22
Alignment explanation
Indices: 1645697--1645738 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1645687 CAATTCATTT
1645697 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
1645719 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
1645739 CCAACACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:1646062 original size:9 final size:9
Alignment explanation
Indices: 1646060--1646099 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
1646050 AAAAACCAAA
1646060 AAAAAAACC
1 AAAAAAACC
1646069 AAAAAAACC
1 AAAAAAACC
*
1646078 AAAAAAA-A
1 AAAAAAACC
1646086 AAAAAAAGCC
1 AAAAAAA-CC
1646096 AAAA
1 AAAA
1646100 TTTCAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 7 0.26
9 16 0.59
10 4 0.15
ACGTcount: A:0.82, C:0.15, G:0.03, T:0.00
Consensus pattern (9 bp):
AAAAAAACC
Found at i:1646064 original size:12 final size:12
Alignment explanation
Indices: 1646047--1646087 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
1646037 TTTGCTATTT
1646047 AAAAAAAACCAA
1 AAAAAAAACCAA
1646059 AAAAAAAACC--
1 AAAAAAAACCAA
1646069 -AAAAAAACCAA
1 AAAAAAAACCAA
1646080 AAAAAAAA
1 AAAAAAAA
1646088 AAAAAGCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 9 0.35
12 17 0.65
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAACCAA
Found at i:1646074 original size:21 final size:21
Alignment explanation
Indices: 1646048--1646087 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1646038 TTGCTATTTA
1646048 AAAAAAACCAAAAAAAAAACC
1 AAAAAAACCAAAAAAAAAACC
1646069 AAAAAAACCAAAAAAAAAA
1 AAAAAAACCAAAAAAAAAA
1646088 AAAAAGCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (21 bp):
AAAAAAACCAAAAAAAAAACC
Found at i:1646081 original size:18 final size:18
Alignment explanation
Indices: 1646047--1646099 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
1646037 TTTGCTATTT
1646047 AAAAAAAA-CCAAAAAAAA
1 AAAAAAAAGCC-AAAAAAA
*
1646065 AACCAAAAAAACCAAAAAAA
1 AA--AAAAAAGCCAAAAAAA
1646085 AAAAAAAAGCCAAAA
1 AAAAAAAAGCCAAAA
1646100 TTTCAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 14 0.45
20 15 0.48
21 2 0.06
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGCCAAAAAAA
Found at i:1656871 original size:8 final size:8
Alignment explanation
Indices: 1656834--1656877 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
1656824 AAATTTTGGC
1656834 TTTTTTT-
1 TTTTTTTG
1656841 TTTTTTGTG
1 TTTTTT-TG
1656850 TTTTTTTG
1 TTTTTTTG
**
1656858 CCTTTTTG
1 TTTTTTTG
1656866 TTTTTTTG
1 TTTTTTTG
1656874 TTTT
1 TTTT
1656878 GTAAAACAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
7 6 0.19
8 19 0.61
9 6 0.19
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.84
Consensus pattern (8 bp):
TTTTTTTG
Found at i:1657251 original size:15 final size:16
Alignment explanation
Indices: 1657231--1657272 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
1657221 AATTAGAATA
1657231 AAATAAATAAAAGAT-
1 AAATAAATAAAAGATG
*
1657246 AAATAAATGAAAGATG
1 AAATAAATAAAAGATG
1657262 AAATAAGATAA
1 AAATAA-ATAA
1657273 TAAAGAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 14 0.61
16 6 0.26
17 3 0.13
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (16 bp):
AAATAAATAAAAGATG
Found at i:1661380 original size:8 final size:8
Alignment explanation
Indices: 1661369--1661418 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
1661359 AAATTTTGGC
1661369 TTTTTTG-
1 TTTTTTGT
1661376 TTTTTT-T
1 TTTTTTGT
1661383 TTTTTTGT
1 TTTTTTGT
*
1661391 GTTTTTTGC
1 -TTTTTTGT
*
1661400 CTTTTTGT
1 TTTTTTGT
1661408 TTTTTTGT
1 TTTTTTGT
1661416 TTT
1 TTT
1661419 GTAAAACAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
7 12 0.33
8 17 0.47
9 7 0.19
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.84
Consensus pattern (8 bp):
TTTTTTGT
Found at i:1661389 original size:31 final size:31
Alignment explanation
Indices: 1661354--1661418 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
1661344 TTTTTTGAAA
* *
1661354 TTTTGAAATTTTGGCTTTTTTGTTTTTTTTT
1 TTTTGAAATTTTGGCCTTTTTGTTTTTTTGT
*** *
1661385 TTTTGTGTTTTTTGCCTTTTTGTTTTTTTGT
1 TTTTGAAATTTTGGCCTTTTTGTTTTTTTGT
1661416 TTT
1 TTT
1661419 GTAAAACAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.05, C:0.05, G:0.14, T:0.77
Consensus pattern (31 bp):
TTTTGAAATTTTGGCCTTTTTGTTTTTTTGT
Found at i:1661412 original size:15 final size:15
Alignment explanation
Indices: 1661370--1661412 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1661360 AATTTTGGCT
***
1661370 TTTTTGTTTTTTTTT
1 TTTTTGTTTTTTGCC
1661385 TTTTGTGTTTTTTGCC
1 TTTT-TGTTTTTTGCC
1661401 TTTTTGTTTTTT
1 TTTTTGTTTTTT
1661413 TGTTTTGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.84
Consensus pattern (15 bp):
TTTTTGTTTTTTGCC
Found at i:1661416 original size:23 final size:23
Alignment explanation
Indices: 1661369--1661418 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1661359 AAATTTTGGC
** *
1661369 TTTTTTGTTTTTTTTTTTTTGTG
1 TTTTTTGCCTTTTTGTTTTTGTG
*
1661392 TTTTTTGCCTTTTTGTTTTTTTG
1 TTTTTTGCCTTTTTGTTTTTGTG
1661415 TTTT
1 TTTT
1661419 GTAAAACAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.84
Consensus pattern (23 bp):
TTTTTTGCCTTTTTGTTTTTGTG
Found at i:1665976 original size:15 final size:16
Alignment explanation
Indices: 1665953--1665982 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1665943 AAATTTTGGC
1665953 TTTTGTTTTTTTTGTG
1 TTTTGTTTTTTTTGTG
1665969 TTTT-TTTTTTTTGT
1 TTTTGTTTTTTTTGT
1665983 TTTGTAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (16 bp):
TTTTGTTTTTTTTGTG
Found at i:1670479 original size:13 final size:13
Alignment explanation
Indices: 1670461--1670492 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1670451 AAATTTTGGC
1670461 TTTTGTGTTTTTT
1 TTTTGTGTTTTTT
1670474 TTTTGTGTTTTTT
1 TTTTGTGTTTTTT
1670487 TTTTGT
1 TTTTGT
1670493 TTTGTAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (13 bp):
TTTTGTGTTTTTT
Found at i:1680232 original size:22 final size:22
Alignment explanation
Indices: 1680200--1680241 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1680190 TTGGTGCTGG
*
1680200 AAACAATATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
1680222 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
1680242 AAATGAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.17
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:1684596 original size:11 final size:11
Alignment explanation
Indices: 1684572--1684616 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
1684562 TTGGTGCTGG
1684572 AAACAAGATAA
1 AAACAAGATAA
* *
1684583 AAATAAGATTA
1 AAACAAGATAA
1684594 AAACAAGATAA
1 AAACAAGATAA
1684605 AGAA-AAGATAA
1 A-AACAAGATAA
1684616 A
1 A
1684617 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:1684600 original size:22 final size:22
Alignment explanation
Indices: 1684572--1684613 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1684562 TTGGTGCTGG
1684572 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
1684594 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
1684614 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:1687277 original size:31 final size:31
Alignment explanation
Indices: 1687242--1687303 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1687232 GCTTCTATGT
1687242 AAGAATTAGGTAATGTGAGCTATGATTGAAG
1 AAGAATTAGGTAATGTGAGCTATGATTGAAG
1687273 AAGAATTAGGTAATGTGAGCTATGATTGAAG
1 AAGAATTAGGTAATGTGAGCTATGATTGAAG
1687304 GTCATGAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.03, G:0.29, T:0.29
Consensus pattern (31 bp):
AAGAATTAGGTAATGTGAGCTATGATTGAAG
Found at i:1691327 original size:35 final size:35
Alignment explanation
Indices: 1691281--1691349 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
1691271 ATACTATTTG
* *
1691281 TCCATCACCATTTCATGCCTATATCATCACCATCT
1 TCCATCACCATTTCACGCCTATATCATCAACATCT
1691316 TCCATCACCATTTCACGCCTATATCATCAACATC
1 TCCATCACCATTTCACGCCTATATCATCAACATC
1691350 CCTTAACCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.28, C:0.38, G:0.03, T:0.32
Consensus pattern (35 bp):
TCCATCACCATTTCACGCCTATATCATCAACATCT
Found at i:1692177 original size:6 final size:6
Alignment explanation
Indices: 1692166--1692199 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
1692156 GTGTTGCAAC
*
1692166 AAAAGA AAAAGA AAGAAGA AAAACA AAAAGA AAA
1 AAAAGA AAAAGA AA-AAGA AAAAGA AAAAGA AAA
1692200 TAAAAAGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:1692186 original size:13 final size:12
Alignment explanation
Indices: 1692166--1692199 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1692156 GTGTTGCAAC
*
1692166 AAAAGAAAAAGA
1 AAAAGAAAAACA
1692178 AAGAAGAAAAACA
1 AA-AAGAAAAACA
1692191 AAAAGAAAA
1 AAAAGAAAA
1692200 TAAAAAGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAACA
Found at i:1698121 original size:15 final size:17
Alignment explanation
Indices: 1698089--1698121 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1698079 TCAATGTTTT
1698089 TCTTCAAAGCATCTTGA
1 TCTTCAAAGCATCTTGA
1698106 TCTTCAAA-CA-CTTGA
1 TCTTCAAAGCATCTTGA
1698121 T
1 T
1698122 TTGGTAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.36
Consensus pattern (17 bp):
TCTTCAAAGCATCTTGA
Found at i:1699109 original size:26 final size:26
Alignment explanation
Indices: 1699079--1699137 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
1699069 CTTGCTTTTC
*
1699079 TCTTTT-TGAGATTTTTTTCTTTTTAT
1 TCTTTTCTGA-ATTTTCTTCTTTTTAT
*
1699105 TCTTTTCTGAATTTTCTTCTTTTT-G
1 TCTTTTCTGAATTTTCTTCTTTTTAT
1699130 TCTTTTCT
1 TCTTTTCT
1699138 TTTTGCACTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 8 0.27
26 19 0.63
27 3 0.10
ACGTcount: A:0.08, C:0.14, G:0.07, T:0.71
Consensus pattern (26 bp):
TCTTTTCTGAATTTTCTTCTTTTTAT
Found at i:1706466 original size:11 final size:11
Alignment explanation
Indices: 1706460--1706487 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1706450 TATTTTTTTG
1706460 TTTTTTTGCCT
1 TTTTTTTGCCT
1706471 TTTTTTTGCCT
1 TTTTTTTGCCT
1706482 TTTTTT
1 TTTTTT
1706488 GTTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTTGCCT
Found at i:1708586 original size:90 final size:89
Alignment explanation
Indices: 1708442--1708606 Score: 285
Period size: 90 Copynumber: 1.8 Consensus size: 89
1708432 TTTTATAGCT
*
1708442 AAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATTG
1 AAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAAGCTATATTTAATTAATTG
* *
1708507 GAATTTAATAATCCTCTTATATCC
66 AAATTAAATAATCCTCTTATATCC
*
1708531 AAGTTACCCTAATCATATTAGGGATTTTATTATTTTAAATTAATTAAAGCTATATTTAATTAATT
1 AAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAAGCTATATTTAATTAATT
1708596 GAAATTAAATA
65 GAAATTAAATA
1708607 TTCAGGATTA
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
89 23 0.32
90 48 0.68
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (89 bp):
AAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAAGCTATATTTAATTAATTG
AAATTAAATAATCCTCTTATATCC
Found at i:1708636 original size:20 final size:21
Alignment explanation
Indices: 1708568--1708637 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
1708558 TATTATTTTA
1708568 AATTAATTAAAGC-TATATTT
1 AATTAATTAAAGCATATATTT
** * *
1708588 AATTAATTGAAATTAAATATTC
1 AATTAATT-AAAGCATATATTT
1708610 AGGATT-ATTAAAGCATATATTT
1 A--ATTAATTAAAGCATATATTT
1708632 AATTAA
1 AATTAA
1708638 CTCTAGATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 9
0.69 0.15 0.17
Matches are distributed among these distances:
20 11 0.30
21 4 0.11
22 16 0.43
23 3 0.08
24 3 0.08
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.41
Consensus pattern (21 bp):
AATTAATTAAAGCATATATTT
Found at i:1710204 original size:19 final size:20
Alignment explanation
Indices: 1710180--1710222 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1710170 AGCATTTATC
*
1710180 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
1710199 TTCATTAAAAATCATGTATT
1 TTCATTAAAAATCATGTATT
1710219 TTCA
1 TTCA
1710223 AAGGGGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:1710581 original size:13 final size:13
Alignment explanation
Indices: 1710563--1710587 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1710553 GATACTATCT
1710563 TTCCATCACCATA
1 TTCCATCACCATA
1710576 TTCCATCACCAT
1 TTCCATCACCAT
1710588 TCACGCATAT
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:0.28, C:0.40, G:0.00, T:0.32
Consensus pattern (13 bp):
TTCCATCACCATA
Found at i:1713269 original size:35 final size:37
Alignment explanation
Indices: 1713223--1713299 Score: 122
Period size: 35 Copynumber: 2.1 Consensus size: 37
1713213 TGAGAATTTA
*
1713223 GTGATGATATAGGCGTGAT-ATGG-TGATGGACTATG
1 GTGATGATATAGGCGTGATAATGGAAGATGGACTATG
*
1713258 GTGATGATATAGGCGTGATAATGGAAGATGGATTATG
1 GTGATGATATAGGCGTGATAATGGAAGATGGACTATG
1713295 GTGAT
1 GTGAT
1713300 AGAAATAGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 19 0.50
36 4 0.11
37 15 0.39
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (37 bp):
GTGATGATATAGGCGTGATAATGGAAGATGGACTATG
Found at i:1718946 original size:35 final size:37
Alignment explanation
Indices: 1718900--1718979 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
1718890 TTTGATAATT
*
1718900 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
1718935 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
1718972 TGGTGATG
1 TGGTGATG
1718980 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:1721964 original size:15 final size:15
Alignment explanation
Indices: 1721944--1721980 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
1721934 AGAAGTATCA
1721944 GGGTGACATAGATAG
1 GGGTGACATAGATAG
1721959 GGGTGACATAGATAG
1 GGGTGACATAGATAG
1721974 GGGTGAC
1 GGGTGAC
1721981 GCCACAAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.30, C:0.08, G:0.43, T:0.19
Consensus pattern (15 bp):
GGGTGACATAGATAG
Found at i:1723625 original size:11 final size:11
Alignment explanation
Indices: 1723611--1723635 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1723601 CAAAAAAAAA
1723611 GAAGTGCAAGT
1 GAAGTGCAAGT
1723622 GAAGTGCAAGT
1 GAAGTGCAAGT
1723633 GAA
1 GAA
1723636 AAAAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (11 bp):
GAAGTGCAAGT
Found at i:1723682 original size:22 final size:26
Alignment explanation
Indices: 1723655--1723708 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
1723645 AAAATCAGCA
*
1723655 AAGAAA-TTG-AAGCACT-CAAAA-G
1 AAGAAATTTGTAAGCACTAAAAAATG
1723677 AAGAAATTTGTAAGCACTAAAAAATG
1 AAGAAATTTGTAAGCACTAAAAAATG
1723703 AAGAAA
1 AAGAAA
1723709 AAGAAAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 6 0.22
23 3 0.11
24 7 0.26
25 4 0.15
26 7 0.26
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (26 bp):
AAGAAATTTGTAAGCACTAAAAAATG
Found at i:1730798 original size:10 final size:10
Alignment explanation
Indices: 1730785--1730810 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1730775 AAAGAAAAAG
1730785 GAAATGGATA
1 GAAATGGATA
1730795 GAAATGGATA
1 GAAATGGATA
1730805 GAAATG
1 GAAATG
1730811 TTATCAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (10 bp):
GAAATGGATA
Found at i:1734652 original size:49 final size:49
Alignment explanation
Indices: 1734558--1734652 Score: 109
Period size: 49 Copynumber: 1.9 Consensus size: 49
1734548 CACACTCCAA
* * * * *
1734558 TTTGCCTTTTCATCACGACTAGGAGGGTTGGTTAGAGCCATTTATCGTG
1 TTTGCCTTTTCATCACGACTAGGAGGGCTCGATAGAGACACTTATCGTG
* ** *
1734607 TTTGTCTTTTCATTGCGACTAGGAGGGCTCGATAGGGACACTTATC
1 TTTGCCTTTTCATCACGACTAGGAGGGCTCGATAGAGACACTTATC
1734653 CATCTATTAT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
49 37 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (49 bp):
TTTGCCTTTTCATCACGACTAGGAGGGCTCGATAGAGACACTTATCGTG
Found at i:1735148 original size:21 final size:20
Alignment explanation
Indices: 1735133--1735176 Score: 65
Period size: 18 Copynumber: 2.2 Consensus size: 20
1735123 TAAAACAATC
1735133 AAAAAAACAAAAAAAAGGCAA
1 AAAAAAACAAAAAAAA-GCAA
1735154 AAAAAAAC-AAAAAAA-CAA
1 AAAAAAACAAAAAAAAGCAA
1735172 AAAAA
1 AAAAA
1735177 GCCAAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.35
20 7 0.30
21 8 0.35
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (20 bp):
AAAAAAACAAAAAAAAGCAA
Done.