Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009074.1 Hibiscus syriacus cultivar Beakdansim tig00112507_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: 2143704
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:1949553 original size:19 final size:19
Alignment explanation
Indices: 1949493--1949559 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 19
1949483 AAAAAGTACT
*
1949493 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1949512 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
1949526 ATCGTAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1949545 ATCGCAACGCAAAAT
1 ATCGCAACGCGAAAT
1949560 TAAATTCGCG
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
14 9 0.24
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1949586 original size:19 final size:19
Alignment explanation
Indices: 1949564--1949714 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
1949554 CAAAATTAAA
1949564 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1949583 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1949598 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * *
1949616 TTTGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
1949630 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1949649 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1949664 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1949682 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1949701 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1949715 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1949610 original size:33 final size:32
Alignment explanation
Indices: 1949568--1949694 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
1949558 ATTAAATTCG
1949568 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* *
1949601 CGTTGCGATTTTCATTTTGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1949634 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1949667 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1949695 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1949641 original size:66 final size:66
Alignment explanation
Indices: 1949561--1949693 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
1949551 ACGCAAAATT
*
1949561 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTTGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1949626 G
66 G
*
1949627 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1949692 G
66 G
1949693 A
1 A
1949694 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1950826 original size:12 final size:12
Alignment explanation
Indices: 1950809--1950845 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
1950799 TCTTCGGGGA
1950809 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1950821 CTTTTTCTTCTT
1 CTTTTTCTTCTT
*
1950833 CTTTTACTTCTT
1 CTTTTTCTTCTT
1950845 C
1 C
1950846 AGGATTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1951054 original size:24 final size:24
Alignment explanation
Indices: 1951020--1951073 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1951010 CTGAAACATC
*
1951020 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
1951044 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1951068 ATCAAA
1 ATCAAA
1951074 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1951899 original size:21 final size:20
Alignment explanation
Indices: 1951856--1951905 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
1951846 TTTTCCTAAT
*
1951856 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
1951876 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
1951897 TCGCAATGC
1 TCGCAATGC
1951906 CATACTGACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:1951981 original size:20 final size:20
Alignment explanation
Indices: 1951934--1951983 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1951924 GAGATAATAC
1951934 AAAATCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
***
1951954 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
1951974 AAAATCGCAA
1 AAAATCGCAA
1951984 TCATCTTCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:1952247 original size:14 final size:16
Alignment explanation
Indices: 1952227--1952300 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
1952217 TGAAAATCGC
1952227 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
1952242 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
1952259 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
1952278 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
1952294 -TTGCGAT
1 ATTGCGAT
1952301 AGTCAGTTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:1952264 original size:19 final size:19
Alignment explanation
Indices: 1952223--1952290 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
1952213 GAAATGAAAA
1952223 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1952239 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1952256 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1952275 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1952291 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1952446 original size:14 final size:14
Alignment explanation
Indices: 1952427--1952479 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
1952417 CACCAATTAA
**
1952427 ACAAATCAACATTT
1 ACAAATCAATTTTT
*
1952441 ACAAATCATTTTTT
1 ACAAATCAATTTTT
*
1952455 ACAAATCATTTTTT
1 ACAAATCAATTTTT
1952469 ACAAATCAATT
1 ACAAATCAATT
1952480 AAACAATCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (14 bp):
ACAAATCAATTTTT
Found at i:1954371 original size:20 final size:20
Alignment explanation
Indices: 1954348--1954398 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1954338 ACTTAAAATC
1954348 GCAACGCGAAAATGACTATA
1 GCAACGCGAAAATGACTATA
* * *
1954368 GCAACGCGGAAATGGCTATC
1 GCAACGCGAAAATGACTATA
*
1954388 GCAATGCGAAA
1 GCAACGCGAAA
1954399 TGCAAATCGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.22, G:0.25, T:0.14
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATA
Found at i:1954407 original size:19 final size:17
Alignment explanation
Indices: 1954385--1954475 Score: 61
Period size: 14 Copynumber: 5.4 Consensus size: 17
1954375 GGAAATGGCT
1954385 ATCGCAATGCGAAATGCAA
1 ATCGCAAT-CGAAATG-AA
*
1954404 ATCGCAA-CGACA--AA
1 ATCGCAATCGAAATGAA
1954418 ATCGCAATACGAAATGAAA
1 ATCGCAAT-CGAAATG-AA
1954437 ATCGCAA-C-AACA--AA
1 ATCGCAATCGAA-ATGAA
*
1954451 ATCGCAATGCGAAATAAA
1 ATCGCAAT-CGAAATGAA
1954469 ATCGCAA
1 ATCGCAA
1954476 CGACAAAATC
Statistics
Matches: 59, Mismatches: 2, Indels: 23
0.70 0.02 0.27
Matches are distributed among these distances:
14 18 0.31
16 8 0.14
17 8 0.14
18 9 0.15
19 16 0.27
ACGTcount: A:0.49, C:0.22, G:0.15, T:0.13
Consensus pattern (17 bp):
ATCGCAATCGAAATGAA
Found at i:1954431 original size:33 final size:33
Alignment explanation
Indices: 1954385--1954489 Score: 176
Period size: 33 Copynumber: 3.2 Consensus size: 33
1954375 GGAAATGGCT
*
1954385 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
1954418 ATCGCAATACGAAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1954451 ATCGCAATGCGAAAT-AAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1954483 ATCGCAA
1 ATCGCAA
1954490 CGTGAAACAC
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
32 23 0.34
33 44 0.66
ACGTcount: A:0.50, C:0.23, G:0.15, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1954432 original size:13 final size:14
Alignment explanation
Indices: 1954402--1954491 Score: 72
Period size: 14 Copynumber: 5.8 Consensus size: 14
1954392 TGCGAAATGC
1954402 AAATCGCAACGACA
1 AAATCGCAACGACA
*
1954416 AAATCGCAATACGAAATGA
1 AAATCGC-A-ACG--A-CA
*
1954435 AAATCGCAACAACA
1 AAATCGCAACGACA
*
1954449 AAATCGCAATGCGAAATA
1 AAATCGCAA--CG--ACA
1954467 AAATCGCAACGACA
1 AAATCGCAACGACA
1954481 AAATCGCAACG
1 AAATCGCAACG
1954492 TGAAACACAA
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 30 0.49
15 2 0.03
16 6 0.10
17 2 0.03
18 13 0.21
19 8 0.13
ACGTcount: A:0.51, C:0.23, G:0.14, T:0.11
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:1954504 original size:65 final size:66
Alignment explanation
Indices: 1954385--1954507 Score: 178
Period size: 65 Copynumber: 1.9 Consensus size: 66
1954375 GGAAATGGCT
* * *
1954385 ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGCAATACGAAATGAAAATCGCAACAACAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACACGAAATCAAAATCGCAACAACAA
1954450 A
66 A
**
1954451 ATCGCAATGCGAAAT-AAAATCGCAACGACAAAATCGCAACGTGAAA-CACAAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACACGAAATCA-AAATCGCA
1954508 TTGCGACTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
64 1 0.02
65 35 0.69
66 15 0.29
ACGTcount: A:0.49, C:0.24, G:0.15, T:0.12
Consensus pattern (66 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACACGAAATCAAAATCGCAACAACAA
A
Found at i:1954557 original size:33 final size:33
Alignment explanation
Indices: 1954515--1954599 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 33
1954505 GCATTGCGAC
1954515 TTTCATTTCGCATTGCGATTTTGTCGTTGCAAT
1 TTTCATTTCGCATTGCGATTTTGTCGTTGCAAT
* **
1954548 TTTCATTTCGCATTGCAATTTTGTCGTTGGGAT
1 TTTCATTTCGCATTGCGATTTTGTCGTTGCAAT
1954581 TTTCATTTCGCATTGCGAT
1 TTTCATTTCGCATTGCGAT
1954600 AGCCATTTCC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.15, C:0.18, G:0.19, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCATTGCGATTTTGTCGTTGCAAT
Found at i:1954565 original size:19 final size:19
Alignment explanation
Indices: 1954503--1954569 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 19
1954493 GAAACACAAA
* *
1954503 TCGCATTGCGACTTTCATT
1 TCGCATTGCAATTTTCATT
* *
1954522 TCGCATTGCGA-TTT--TG
1 TCGCATTGCAATTTTCATT
1954538 TCG--TTGCAATTTTCATT
1 TCGCATTGCAATTTTCATT
1954555 TCGCATTGCAATTTT
1 TCGCATTGCAATTTT
1954570 GTCGTTGGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 5 0.12
15 3 0.08
16 4 0.10
17 4 0.10
18 3 0.08
19 21 0.52
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.46
Consensus pattern (19 bp):
TCGCATTGCAATTTTCATT
Found at i:1954608 original size:19 final size:20
Alignment explanation
Indices: 1954584--1954627 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1954574 TTGGGATTTT
1954584 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
1954603 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
1954623 CATTT
1 CATTT
1954628 TCATGTTGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:1954635 original size:20 final size:20
Alignment explanation
Indices: 1954593--1954638 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1954583 TCATTTCGCA
*
1954593 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCACG
* * *
1954613 TTGCGATAGTCATTTTCATG
1 TTGCGATAGCCATTTCCACG
1954633 TTGCGA
1 TTGCGA
1954639 AAGTAAACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCACG
Found at i:1955140 original size:18 final size:18
Alignment explanation
Indices: 1955114--1955158 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1955104 GTCGATCAGA
*
1955114 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
1955132 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
1955150 TGATGGCTC
1 TGATGGCTC
1955159 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:1956503 original size:20 final size:20
Alignment explanation
Indices: 1956478--1956520 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1956468 AATAGTTTCT
1956478 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
* *
1956498 GAAAATGACAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
1956518 GAA
1 GAA
1956521 TTTTGACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.21, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1956827 original size:22 final size:22
Alignment explanation
Indices: 1956800--1956843 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1956790 GATGGAGATA
1956800 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1956822 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1956844 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1957043 original size:21 final size:21
Alignment explanation
Indices: 1957017--1957085 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
1957007 GAAAATCACA
1957017 TTGCGATTATGTATTATCGCG
1 TTGCGATTATGTATTATCGCG
* * *
1957038 TTGCGA--AAGTCAGTATCTCG
1 TTGCGATTATGT-ATTATCGCG
* *
1957058 TTGCGATTTTGTATTATCGCA
1 TTGCGATTATGTATTATCGCG
1957079 TTGCGAT
1 TTGCGAT
1957086 AGTAAGTATC
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
19 3 0.08
20 13 0.35
21 19 0.51
22 2 0.05
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (21 bp):
TTGCGATTATGTATTATCGCG
Found at i:1957074 original size:41 final size:41
Alignment explanation
Indices: 1957015--1957124 Score: 143
Period size: 41 Copynumber: 2.7 Consensus size: 41
1957005 TTGAAAATCA
* *
1957015 CATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCT
1 CATTGCGATTATGTATTATCGCATTGCGAAAGTAAGTATCT
* * *
1957056 CGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCT
1 CATTGCGATTATGTATTATCGCATTGCGAAAGTAAGTATCT
*
1957097 CATTGCGA-TA-GTCAGTATCGCATTGCGA
1 CATTGCGATTATGT-ATTATCGCATTGCGA
1957125 TTTTTCCAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
39 2 0.03
40 15 0.25
41 43 0.72
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (41 bp):
CATTGCGATTATGTATTATCGCATTGCGAAAGTAAGTATCT
Found at i:1957100 original size:20 final size:20
Alignment explanation
Indices: 1957072--1957125 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1957062 GATTTTGTAT
1957072 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
1957092 TATCTCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1957112 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1957126 TTTTCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1957236 original size:21 final size:21
Alignment explanation
Indices: 1957196--1957236 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1957186 ACTGTAGACC
** *
1957196 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
1957217 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
1957237 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:1958566 original size:15 final size:15
Alignment explanation
Indices: 1958520--1958573 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
1958510 TCATATTGGA
* *
1958520 ATTCGAATATGTGGT
1 ATTCGGATATGTGTT
1958535 ATTC-GAGTATGTGTT
1 ATTCGGA-TATGTGTT
*
1958550 ATTCGGATATGTATT
1 ATTCGGATATGTGTT
1958565 ATTCGGATA
1 ATTCGGATA
1958574 GGATCGGATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.03
15 31 0.91
16 2 0.06
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (15 bp):
ATTCGGATATGTGTT
Found at i:1959914 original size:40 final size:40
Alignment explanation
Indices: 1959869--1959948 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
1959859 TGATGTATAA
*
1959869 GAGGATAATATTAAATATGTTCCGATGGTTCCACTTCCAT
1 GAGGATAATATTAAATATGTTCCAATGGTTCCACTTCCAT
1959909 GAGGATAATATTAAATATGTTCCAATGGTTCCACTTCCAT
1 GAGGATAATATTAAATATGTTCCAATGGTTCCACTTCCAT
1959949 CGATTGGAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (40 bp):
GAGGATAATATTAAATATGTTCCAATGGTTCCACTTCCAT
Found at i:1960080 original size:15 final size:15
Alignment explanation
Indices: 1960060--1960093 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1960050 TTGGATCGCT
1960060 TTTGTAATCCATATG
1 TTTGTAATCCATATG
*
1960075 TTTGTAATCTATATG
1 TTTGTAATCCATATG
1960090 TTTG
1 TTTG
1960094 AAAATGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.53
Consensus pattern (15 bp):
TTTGTAATCCATATG
Found at i:1962797 original size:21 final size:22
Alignment explanation
Indices: 1962772--1962822 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
1962762 AGTTGTGGGG
1962772 ATGTTTTTAGT-TTTTTATTAA
1 ATGTTTTTAGTATTTTTATTAA
* *
1962793 ATGTTTTTGGTATTTTTATTTA
1 ATGTTTTTAGTATTTTTATTAA
1962815 AT-TTTTTA
1 ATGTTTTTA
1962823 AATACTTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.22, C:0.00, G:0.10, T:0.69
Consensus pattern (22 bp):
ATGTTTTTAGTATTTTTATTAA
Found at i:1976187 original size:42 final size:43
Alignment explanation
Indices: 1976131--1976226 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 43
1976121 AAGATCATGT
* *
1976131 TATATAGTGCCATTT-TCACT-ACAAATGCC-ACAATTGATTACA
1 TATATAGTGGCATTTAT-ACTAACAAATGCCGAC-ATTGATCACA
*
1976173 TATATAGTGGCATTTATATTAACAAATGCCGACATTGATCACA
1 TATATAGTGGCATTTATACTAACAAATGCCGACATTGATCACA
*
1976216 TATATATTGGC
1 TATATAGTGGC
1976227 GCTTTTTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
42 16 0.34
43 29 0.62
44 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34
Consensus pattern (43 bp):
TATATAGTGGCATTTATACTAACAAATGCCGACATTGATCACA
Found at i:1976210 original size:43 final size:44
Alignment explanation
Indices: 1976151--1976248 Score: 128
Period size: 43 Copynumber: 2.2 Consensus size: 44
1976141 CATTTTCACT
*
1976151 ACAAATGCCACAATTGATTACATATATAGTGGC-ATTTATATTA
1 ACAAATGCCACAATTGATCACATATATAGTGGCGATTTATATTA
* * *
1976194 ACAAATGCCGAC-ATTGATCACATATATATTGGCGCTTTTTATTA
1 ACAAATGCC-ACAATTGATCACATATATAGTGGCGATTTATATTA
*
1976238 ACAAACGCCAC
1 ACAAATGCCAC
1976249 TATAGACAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 30 0.62
44 18 0.38
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (44 bp):
ACAAATGCCACAATTGATCACATATATAGTGGCGATTTATATTA
Found at i:1976305 original size:20 final size:20
Alignment explanation
Indices: 1976280--1976321 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1976270 ATATTCAAAA
*
1976280 TCATTTATTTTTCTTGATTT
1 TCATTTATTTTACTTGATTT
* *
1976300 TCATTTCTTTTACTTTATTT
1 TCATTTATTTTACTTGATTT
1976320 TC
1 TC
1976322 TTTTTCCTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.69
Consensus pattern (20 bp):
TCATTTATTTTACTTGATTT
Found at i:1978385 original size:175 final size:175
Alignment explanation
Indices: 1978085--1978405 Score: 561
Period size: 175 Copynumber: 1.8 Consensus size: 175
1978075 GCACAAAAAG
1978085 GGGGTGACCTAGCTTTACCCACAATAAATTGAACATGATTATGGAAATAAAAAAGTAAAAATTCC
1 GGGGTGACCTAGCTTTACCCACAATAAATTGAACATGATTATGGAAATAAAAAAGTAAAAATTCC
* * *
1978150 AACTATACCTGGCCTGAGAAAGAAACAGAGTTGAGAGAAGAAAAAAATGTGCTGGAAGAACGTTG
66 AACTATACCTGGCCTGAGAAAGAAACAGAGTTGAGAGAAGAAAAAAAGGAGCTAGAAGAACGTTG
1978215 AAGGAGAGCCCCCATTACCGTTCGCGAACGTCAAAACTAAGATTA
131 AAGGAGAGCCCCCATTACCGTTCGCGAACGTCAAAACTAAGATTA
* * *
1978260 GGGGTGGCCTAGCTTTACCCACAATGAATTGAACATGATTATGGAAATAAAAAAGTAAAAATTTC
1 GGGGTGACCTAGCTTTACCCACAATAAATTGAACATGATTATGGAAATAAAAAAGTAAAAATTCC
* * *
1978325 AACTATACCTGGCCTGAGAAAGAACCAGGGTTGATAGAAGAAAAAAAGGAGCTAGAAGAACGTTG
66 AACTATACCTGGCCTGAGAAAGAAACAGAGTTGAGAGAAGAAAAAAAGGAGCTAGAAGAACGTTG
1978390 AAGGAGAGCCCCCATT
131 AAGGAGAGCCCCCATT
1978406 GACATTTAGG
Statistics
Matches: 137, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
175 137 1.00
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.20
Consensus pattern (175 bp):
GGGGTGACCTAGCTTTACCCACAATAAATTGAACATGATTATGGAAATAAAAAAGTAAAAATTCC
AACTATACCTGGCCTGAGAAAGAAACAGAGTTGAGAGAAGAAAAAAAGGAGCTAGAAGAACGTTG
AAGGAGAGCCCCCATTACCGTTCGCGAACGTCAAAACTAAGATTA
Found at i:1980188 original size:81 final size:83
Alignment explanation
Indices: 1980077--1980267 Score: 221
Period size: 82 Copynumber: 2.3 Consensus size: 83
1980067 TATTGCCGCG
* * *
1980077 TTTGTA-AAAAACGCTGCTAAAATACTACTCTGTCATGACG-TTCTTGAAAAAC-GTCACTATGA
1 TTTGTATAAAAACGCTGTTAAAGTACTACTCTGTCATGACGTTTCTTGAAAAACACT-ACTATGA
*
1980139 ATGAATCC-TATTATGGCA-
65 ATGAA-CCATATTACGGCAT
* ** * * *
1980157 TTTGTATAAAAACGCCGTTAAAGTACTACTCTGTTGTGGCGTTTGTTGAAAAACACTACTATGTA
1 TTTGTATAAAAACGCTGTTAAAGTACTACTCTGTCATGACGTTTCTTGAAAAACACTACTATGAA
1980222 TGAACCATATTACGGCAT
66 TGAACCATATTACGGCAT
* *
1980240 TTTGTATAAAAACGTTGTTAACGTACTA
1 TTTGTATAAAAACGCTGTTAAAGTACTA
1980268 TTTTGCTATG
Statistics
Matches: 93, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
80 6 0.06
81 30 0.32
82 31 0.33
83 26 0.28
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (83 bp):
TTTGTATAAAAACGCTGTTAAAGTACTACTCTGTCATGACGTTTCTTGAAAAACACTACTATGAA
TGAACCATATTACGGCAT
Found at i:1982618 original size:2 final size:2
Alignment explanation
Indices: 1982611--1982649 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1982601 TTAAAAGTAG
1982611 TA TA TA TA TA TA TA TA TA TA TA 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 T
1982650 GAATTACGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1989610 original size:72 final size:72
Alignment explanation
Indices: 1989493--1989631 Score: 233
Period size: 72 Copynumber: 1.9 Consensus size: 72
1989483 TCTATTCACG
* *
1989493 ACCTCTTGAAATGAAGAGAGGTTAAGTGCTAATAACATCTTTTTCAGTCTAGGGCGTAAACTCTC
1 ACCTCTTGAAATGAAGAGAGGTTAAGTGCTAATAACAACTCTTTCAGTCTAGGGCGTAAACTCTC
1989558 CATAAAT
66 CATAAAT
* **
1989565 ACCTCTTGAAATGAAGAGAGGTTAAGTGTTAATAACAACTCTTTCAGTCTAGGGTTTAAACTCTC
1 ACCTCTTGAAATGAAGAGAGGTTAAGTGCTAATAACAACTCTTTCAGTCTAGGGCGTAAACTCTC
1989630 CA
66 CA
1989632 CAAACCATTC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (72 bp):
ACCTCTTGAAATGAAGAGAGGTTAAGTGCTAATAACAACTCTTTCAGTCTAGGGCGTAAACTCTC
CATAAAT
Found at i:1991093 original size:23 final size:23
Alignment explanation
Indices: 1991032--1991107 Score: 61
Period size: 23 Copynumber: 3.4 Consensus size: 23
1991022 AAATTGCACC
* *
1991032 GAAGTGCCACATAA--TTGTCCC
1 GAAGTGCCACATAAGTTTGTACT
* *
1991053 GAAG-GACCAAATAGGTTTGTACT
1 GAAGTG-CCACATAAGTTTGTACT
*
1991076 GAAGTGCCACATAAGTTTGCA-T
1 GAAGTGCCACATAAGTTTGTACT
1991098 GGAAGTGCCA
1 -GAAGTGCCA
1991108 TATATTTGTC
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
20 1 0.02
21 10 0.23
22 1 0.02
23 30 0.70
24 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.24
Consensus pattern (23 bp):
GAAGTGCCACATAAGTTTGTACT
Found at i:1991149 original size:21 final size:22
Alignment explanation
Indices: 1991106--1991154 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
1991096 ATGGAAGTGC
*
1991106 CATATATTTGTCCCGAATAACCA
1 CATA-ATTTGTCCCGAAGAACCA
*
1991129 CATAATTT-TCCCGAAGGACCA
1 CATAATTTGTCCCGAAGAACCA
*
1991150 AATAA
1 CATAA
1991155 AACCCTCGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 15 0.65
22 4 0.17
23 4 0.17
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (22 bp):
CATAATTTGTCCCGAAGAACCA
Found at i:1995669 original size:29 final size:29
Alignment explanation
Indices: 1995601--1995672 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 29
1995591 AAAGTTGTCA
* *
1995601 ATATCCCCATCCTGATTCTATATGGGATT
1 ATATCCCCATCTTGATTATATATGGGATT
* * * *
1995630 AAATACTCATCTTGATTATGTATGGGATT
1 ATATCCCCATCTTGATTATATATGGGATT
*
1995659 GTATCCCCATCTTG
1 ATATCCCCATCTTG
1995673 TTTCGATTTG
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (29 bp):
ATATCCCCATCTTGATTATATATGGGATT
Found at i:1999381 original size:2 final size:2
Alignment explanation
Indices: 1999374--1999453 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
1999364 ATTTCTTACC
1999374 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1999416 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1999454 TAATTTAAAG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1999998 original size:14 final size:14
Alignment explanation
Indices: 1999979--2000017 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1999969 GCTTTTTCTT
1999979 TATATATATATGTA
1 TATATATATATGTA
*
1999993 TATATATATATTTA
1 TATATATATATGTA
* *
2000007 TTTATTTATAT
1 TATATATATAT
2000018 CTTTGAACAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (14 bp):
TATATATATATGTA
Found at i:2005199 original size:22 final size:22
Alignment explanation
Indices: 2005171--2005221 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
2005161 CCATTTCGCG
*
2005171 TTGCGATAGTCTACAGTTGTTA
1 TTGCGATAGTCTACAGTTGTCA
*
2005193 TTGCGATAGTCTACAGTTGTCG
1 TTGCGATAGTCTACAGTTGTCA
2005215 TTGCGAT
1 TTGCGAT
2005222 TTTCCAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (22 bp):
TTGCGATAGTCTACAGTTGTCA
Found at i:2005328 original size:6 final size:6
Alignment explanation
Indices: 2005317--2005355 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
2005307 AAAGACACGT
2005317 ACGACC ACGACC ACGACC ACGACC -CGACC -CGACC -CGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
2005356 CGAGACGGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.45
6 18 0.55
ACGTcount: A:0.28, C:0.54, G:0.18, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:2005346 original size:5 final size:5
Alignment explanation
Indices: 2005318--2005358 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
2005308 AAGACACGTA
2005318 CGACC ACGACC ACGACC ACGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC -CGACC CGACC CGACC CGACC CGA
2005359 GACGGACGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.27, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:2007728 original size:36 final size:36
Alignment explanation
Indices: 2007687--2007762 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2007677 ATTTTCGGGA
*
2007687 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
2007723 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
2007759 TTTT
1 TTTT
2007763 TTTTGCTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:2009179 original size:18 final size:18
Alignment explanation
Indices: 2009152--2009189 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
2009142 TCTAAAATAT
2009152 AAAAGAT-AAAAATTTAA
1 AAAAGATAAAAAATTTAA
2009169 AAAAGGATAAAAAATTTAA
1 AAAA-GATAAAAAATTTAA
2009188 AA
1 AA
2009190 TTTTACTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 3 0.16
19 12 0.63
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (18 bp):
AAAAGATAAAAAATTTAA
Found at i:2022712 original size:2 final size:2
Alignment explanation
Indices: 2022705--2022732 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2022695 TGCATTGATG
2022705 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2022733 CATCATTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2023411 original size:78 final size:79
Alignment explanation
Indices: 2023280--2023479 Score: 269
Period size: 78 Copynumber: 2.5 Consensus size: 79
2023270 ACATTTTATT
* * * * *
2023280 TATGACATCATTTTATGCCAATAATGAACCCATATGCATTATTCTTTATTGCCGATAATGCACCC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCATTATTGCCGATAATGCACCC
*
2023345 ATATACATTTCAAC
66 ATATACAGTTCAAC
2023359 TATGGCATCCTTTCATGCCAATAATGCA-CCATATGCATTATTCAATTA-TGCCGATAATGCACC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTC-ATTATTGCCGATAATGCACC
* *
2023422 CATATGCAGTTCAGC
65 CATATACAGTTCAAC
* * * *
2023437 TGTGGCATCCTTTCATGCCACTAATGCATCCACATGCATTATT
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATT
2023480 ATTTTATGTT
Statistics
Matches: 108, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
78 68 0.63
79 40 0.37
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (79 bp):
TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCATTATTGCCGATAATGCACCC
ATATACAGTTCAAC
Found at i:2027555 original size:64 final size:64
Alignment explanation
Indices: 2027482--2027705 Score: 213
Period size: 64 Copynumber: 3.5 Consensus size: 64
2027472 TGTTTGAATG
* * **
2027482 TGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATTC
1 TGCATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTC
2027545 A
64 A
* * * **
2027546 TGCATCGATGTATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGG
1 TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
** *** * ** *
2027610 TGCATCGATGCATAAGG-AGTGCATCGATGCATCCCAGCAATAATGCTACATCGAATACCTTTTA
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
*
2027674 TGCACCGATGCATCA-GTAGTGCATCGATGCAT
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCAT
2027706 ACCTTCATTA
Statistics
Matches: 134, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
63 1 0.01
64 125 0.93
65 8 0.06
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
Found at i:2029390 original size:34 final size:34
Alignment explanation
Indices: 2029347--2029486 Score: 138
Period size: 34 Copynumber: 3.8 Consensus size: 34
2029337 TATGACATCA
*
2029347 TTTTATGCCAATAATGGACCCATATGCATTATTC
1 TTTTATGCCAATAATGCACCCATATGCATTATTC
2029381 TTTTATGCCAATAATGCACCCATATGCATTTCAACTATGGC
1 TTTTATGCCAATAATGCACCCATATGCA-TT--A-T-T--C
2029422 ATCCTTTCATGCCAATAATGCA-CCATATGCATTATTC
1 -T--TTT-ATGCCAATAATGCACCCATATGCATTATTC
** *
2029459 AATTATGCCGATAATGCACCCATATGCA
1 TTTTATGCCAATAATGCACCCATATGCA
2029487 GTTCAGCTGT
Statistics
Matches: 90, Mismatches: 4, Indels: 24
0.76 0.03 0.20
Matches are distributed among these distances:
33 13 0.14
34 38 0.42
35 2 0.02
37 2 0.02
38 1 0.01
39 2 0.02
40 1 0.01
41 2 0.02
42 1 0.01
43 2 0.02
44 12 0.13
45 14 0.16
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (34 bp):
TTTTATGCCAATAATGCACCCATATGCATTATTC
Found at i:2029465 original size:78 final size:79
Alignment explanation
Indices: 2029337--2029536 Score: 260
Period size: 78 Copynumber: 2.5 Consensus size: 79
2029327 ACATTTTATT
* * * * **
2029337 TATGACATCATTTTATGCCAATAATGGACCCATATGCATTATTCTTTTATGCCAATAATGCACCC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCAATTATGCCAATAATGCACCC
*
2029402 ATATGCATTTCAAC
66 ATATGCAGTTCAAC
*
2029416 TATGGCATCCTTTCATGCCAATAATGCA-CCATATGCATTATTCAATTATGCCGATAATGCACCC
1 TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCAATTATGCCAATAATGCACCC
*
2029480 ATATGCAGTTCAGC
66 ATATGCAGTTCAAC
* * * *
2029494 TGTGGCATCCTTTCATGCCACT-ATAGCATCCACATGCATTATT
1 TATGGCATCCTTTCATGCCAATAAT-GCACCCATATGCATTATT
2029537 ATTTTATGCT
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
77 2 0.02
78 68 0.64
79 37 0.35
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (79 bp):
TATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCAATTATGCCAATAATGCACCC
ATATGCAGTTCAAC
Found at i:2061874 original size:105 final size:105
Alignment explanation
Indices: 2061692--2061901 Score: 402
Period size: 105 Copynumber: 2.0 Consensus size: 105
2061682 ATTCGACCAG
*
2061692 TAGGTCTGTCTTGAAAATTTTAAATCAACCTAAGCTCTGATACCACTAAATGTAACCCCCTCAGA
1 TAGGTCTGTCATGAAAATTTTAAATCAACCTAAGCTCTGATACCACTAAATGTAACCCCCTCAGA
2061757 CCTATGCAGGTAACCTGATCTGATCTAGAGTGTCAGATTA
66 CCTATGCAGGTAACCTGATCTGATCTAGAGTGTCAGATTA
*
2061797 TAGGTGTGTCATGAAAATTTTAAATCAACCTAAGCTCTGATACCACTAAATGTAACCCCCTCAGA
1 TAGGTCTGTCATGAAAATTTTAAATCAACCTAAGCTCTGATACCACTAAATGTAACCCCCTCAGA
2061862 CCTATGCAGGTAACCTGATCTGATCTAGAGTGTCAGATTA
66 CCTATGCAGGTAACCTGATCTGATCTAGAGTGTCAGATTA
2061902 GGGCCATCGG
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 103 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (105 bp):
TAGGTCTGTCATGAAAATTTTAAATCAACCTAAGCTCTGATACCACTAAATGTAACCCCCTCAGA
CCTATGCAGGTAACCTGATCTGATCTAGAGTGTCAGATTA
Found at i:2067027 original size:33 final size:37
Alignment explanation
Indices: 2066990--2067064 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 37
2066980 TTATTATTCC
*
2066990 TTTACAATTTACTTTT-C-TTAATTTT-TCTTA-TTG
1 TTTACAACTTACTTTTACTTTAATTTTATCTTACTTG
* * *
2067023 TTTACACCTTAGTTTTACTTTAATTTTATTTTACTTG
1 TTTACAACTTACTTTTACTTTAATTTTATCTTACTTG
2067060 TTTAC
1 TTTAC
2067065 TTTAAAAGCC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
33 13 0.38
34 1 0.03
35 8 0.24
36 4 0.12
37 8 0.24
ACGTcount: A:0.21, C:0.13, G:0.04, T:0.61
Consensus pattern (37 bp):
TTTACAACTTACTTTTACTTTAATTTTATCTTACTTG
Found at i:2072883 original size:3 final size:3
Alignment explanation
Indices: 2072877--2072914 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2072867 TCTTTATCAT
2072877 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2072915 TTAAAACCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2072980 original size:3 final size:3
Alignment explanation
Indices: 2072972--2073018 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
2072962 TTCAAGCTCC
* *
2072972 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT A-T ATT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2073019 TTACTCATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:2073201 original size:24 final size:23
Alignment explanation
Indices: 2073174--2073218 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2073164 AAATCTAACG
2073174 AACCACTTCTCTTATTTTCTTTAA
1 AACC-CTTCTCTTATTTTCTTTAA
* *
2073198 AACCTTTTTCTTATTTTCTTT
1 AACCCTTCTCTTATTTTCTTT
2073219 TACCTCCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.20, C:0.22, G:0.00, T:0.58
Consensus pattern (23 bp):
AACCCTTCTCTTATTTTCTTTAA
Found at i:2075808 original size:13 final size:13
Alignment explanation
Indices: 2075790--2075817 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2075780 GGGTCTTATA
2075790 GACTATAACCAGC
1 GACTATAACCAGC
2075803 GACTATAACCAGC
1 GACTATAACCAGC
2075816 GA
1 GA
2075818 GTATCCGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.29, G:0.18, T:0.14
Consensus pattern (13 bp):
GACTATAACCAGC
Found at i:2077371 original size:23 final size:23
Alignment explanation
Indices: 2077328--2077371 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2077318 TAACTTTTAT
* *
2077328 TAATTTTTATTATATGTAATATA
1 TAATTTTTACTATATGCAATATA
2077351 TAATTTTATACTATAT-CAATA
1 TAATTTT-TACTATATGCAATA
2077372 AATTTTATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (23 bp):
TAATTTTTACTATATGCAATATA
Found at i:2078699 original size:22 final size:22
Alignment explanation
Indices: 2078682--2078741 Score: 113
Period size: 22 Copynumber: 2.8 Consensus size: 22
2078672 AGTACAAAAT
2078682 AAAA-AAGGTGGGTATACAACA
1 AAAAGAAGGTGGGTATACAACA
2078703 AAAAGAAGGTGGGTATACAACA
1 AAAAGAAGGTGGGTATACAACA
2078725 AAAAGAAGGTGGGTATA
1 AAAAGAAGGTGGGTATA
2078742 AAAATTTCGA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 4 0.11
22 34 0.89
ACGTcount: A:0.50, C:0.07, G:0.28, T:0.15
Consensus pattern (22 bp):
AAAAGAAGGTGGGTATACAACA
Found at i:2079284 original size:22 final size:23
Alignment explanation
Indices: 2079258--2079308 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
2079248 ATGACTTGAT
2079258 TATACAAAAT-AAGGTTTCAAAA
1 TATACAAAATAAAGGTTTCAAAA
*
2079280 TATACAAAATAAAGGTTTCAGAA
1 TATACAAAATAAAGGTTTCAAAA
2079303 TATACA
1 TATACA
2079309 TGTCCTCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (23 bp):
TATACAAAATAAAGGTTTCAAAA
Found at i:2079621 original size:16 final size:16
Alignment explanation
Indices: 2079600--2079631 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2079590 CTACATCTCC
2079600 GAGCTCATCCACCCCT
1 GAGCTCATCCACCCCT
2079616 GAGCTCATCCACCCCT
1 GAGCTCATCCACCCCT
2079632 CTAGTATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.50, G:0.12, T:0.19
Consensus pattern (16 bp):
GAGCTCATCCACCCCT
Found at i:2089787 original size:42 final size:42
Alignment explanation
Indices: 2089723--2089813 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 42
2089713 TGATTTATTT
* * *
2089723 GTGATACTAAATATCACCCTTATCATTGTTATCTGATGCTTA
1 GTGATACCAAATATCACCCTTATCATTCTTATCTGACGCTTA
* * * *
2089765 GTGATACCGAATATCACTCTTATCATTCTTGTCTGACGCTTG
1 GTGATACCAAATATCACCCTTATCATTCTTATCTGACGCTTA
2089807 GTGATAC
1 GTGATAC
2089814 TAAGGGACAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.38
Consensus pattern (42 bp):
GTGATACCAAATATCACCCTTATCATTCTTATCTGACGCTTA
Found at i:2092614 original size:11 final size:11
Alignment explanation
Indices: 2092598--2092630 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
2092588 ATAATTGATT
2092598 CTACTTTGTTG
1 CTACTTTGTTG
2092609 CTACTTTGTTG
1 CTACTTTGTTG
2092620 CTACTTTGTTG
1 CTACTTTGTTG
2092631 ACCATATAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.09, C:0.18, G:0.18, T:0.55
Consensus pattern (11 bp):
CTACTTTGTTG
Found at i:2095173 original size:2 final size:2
Alignment explanation
Indices: 2095162--2095223 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
2095152 TTGTAGTTTC
2095162 TA TA -A TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2095202 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
2095224 ATAGGGGAGT
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 56 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2098063 original size:3 final size:3
Alignment explanation
Indices: 2098057--2098098 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
2098047 TATTTTACGA
*
2098057 AAT AAT -AT AAT AAT AAT -AT AAT AAT AAT AAT AAA AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2098099 ATTTAGGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2098073 original size:11 final size:11
Alignment explanation
Indices: 2098057--2098097 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
2098047 TATTTTACGA
2098057 AATAATATAAT
1 AATAATATAAT
2098068 AATAATATAAT
1 AATAATATAAT
*
2098079 AATAATAATAAA
1 AATAAT-ATAAT
2098091 AATAATA
1 AATAATA
2098098 AATTTAGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AATAATATAAT
Found at i:2100972 original size:27 final size:26
Alignment explanation
Indices: 2100941--2101021 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 26
2100931 GTAATAAATC
2100941 ATGTGATAAGAATATGTGACATGAGTT
1 ATGTGATAAGAATATGTGA-ATGAGTT
*
2100968 ATGTGATAAGAATATGTG--TCA---
1 ATGTGATAAGAATATGTGAATGAGTT
*
2100989 ATGTGATAAGAATATGTGATAAGAGTT
1 ATGTGATAAGAATATGTGA-ATGAGTT
2101016 ATGTGA
1 ATGTGA
2101022 AAATAAGCTA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
21 18 0.40
24 3 0.07
27 24 0.53
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.33
Consensus pattern (26 bp):
ATGTGATAAGAATATGTGAATGAGTT
Found at i:2101021 original size:14 final size:13
Alignment explanation
Indices: 2100941--2101012 Score: 64
Period size: 13 Copynumber: 5.8 Consensus size: 13
2100931 GTAATAAATC
2100941 ATGTGATAAGAAT
1 ATGTGATAAGAAT
* * *
2100954 ATGTGACATGAGTT
1 ATGTGATAAGA-AT
2100968 ATGTGATAAGAAT
1 ATGTGATAAGAAT
*
2100981 ATGTG-T---CA-
1 ATGTGATAAGAAT
2100989 ATGTGATAAGAAT
1 ATGTGATAAGAAT
2101002 ATGTGATAAGA
1 ATGTGATAAGA
2101013 GTTATGTGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
8 5 0.11
9 2 0.04
12 2 0.04
13 26 0.58
14 10 0.22
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (13 bp):
ATGTGATAAGAAT
Found at i:2101476 original size:45 final size:46
Alignment explanation
Indices: 2101367--2101489 Score: 160
Period size: 46 Copynumber: 2.7 Consensus size: 46
2101357 AATTAAATTG
* * * *
2101367 AACATCGAATTCATTTCATGCACCGATGCACTGAGGATTTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCACTCAGGATTTTATGAA
* *
2101413 AACATCGAATGCATTTGATGCATCGATGCACTCTGGCTATTT-TG-A
1 AACATCGAATGCATTTGATGCATCGATGCACTCAGGAT-TTTATGAA
*
2101458 AACATCGAATGCACTTGATGCATCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCACT
2101490 GTTAGTGCAC
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
45 32 0.46
46 34 0.49
47 3 0.04
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (46 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCAGGATTTTATGAA
Found at i:2108746 original size:21 final size:21
Alignment explanation
Indices: 2108704--2108747 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2108694 ACTCCGGGAG
* * *
2108704 CTAGTTCCTCACGAGCTTCTC
1 CTAGCTCCTCAAGAGCTCCTC
*
2108725 CTAGCTCCTCAAGTGCTCCTC
1 CTAGCTCCTCAAGAGCTCCTC
2108746 CT
1 CT
2108748 CCTCCTCCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.41, G:0.14, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCAAGAGCTCCTC
Found at i:2109445 original size:25 final size:25
Alignment explanation
Indices: 2109417--2109491 Score: 150
Period size: 25 Copynumber: 3.0 Consensus size: 25
2109407 TTAAAGGGGC
2109417 GAAGTGTTATAGTAAGGGGGAGTAA
1 GAAGTGTTATAGTAAGGGGGAGTAA
2109442 GAAGTGTTATAGTAAGGGGGAGTAA
1 GAAGTGTTATAGTAAGGGGGAGTAA
2109467 GAAGTGTTATAGTAAGGGGGAGTAA
1 GAAGTGTTATAGTAAGGGGGAGTAA
2109492 TTTGCAATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.36, C:0.00, G:0.40, T:0.24
Consensus pattern (25 bp):
GAAGTGTTATAGTAAGGGGGAGTAA
Found at i:2109965 original size:65 final size:65
Alignment explanation
Indices: 2109860--2110019 Score: 173
Period size: 65 Copynumber: 2.5 Consensus size: 65
2109850 AATTAAATTG
* * * * *
2109860 AACATCGAATGCATTTCATGCACCGATGCA-CTGACTATGCACCGATGCACTGAGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACCAGACCATGCACCGATGCACTCAGGATATTT-TG
2109923 AA
65 -A
* * *
2109925 AACATCGAATGCATTTGATGCATCGATGCACCAG-CCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACCAGACCATGCACCGATGCACTCAGGATATTTTGA
* * * *
2109989 AATATCGAATGTACTTGATGTATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
2110020 TAAGGGTTCA
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 28 0.35
65 48 0.59
66 5 0.06
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACCAGACCATGCACCGATGCACTCAGGATATTTTGA
Found at i:2112327 original size:11 final size:11
Alignment explanation
Indices: 2112311--2112341 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2112301 CACCTCAGAC
*
2112311 TCGGATCCGTG
1 TCGGATACGTG
2112322 TCGGATACGTG
1 TCGGATACGTG
2112333 TCGGATACG
1 TCGGATACG
2112342 GGGGTGTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.16, C:0.23, G:0.35, T:0.26
Consensus pattern (11 bp):
TCGGATACGTG
Found at i:2114635 original size:42 final size:42
Alignment explanation
Indices: 2114558--2114713 Score: 260
Period size: 42 Copynumber: 3.7 Consensus size: 42
2114548 TGCAATATGG
2114558 GTATCGATACCTATGCAT-GTACCGATACCCTAGATAGGGAA
1 GTATCGATACCTATGCATGGTACCGATACCCTAGATAGGGAA
2114599 GTATCGATACCTATGCATGGTACCGATACCCTAGATAGGGAA
1 GTATCGATACCTATGCATGGTACCGATACCCTAGATAGGGAA
*
2114641 GTATCGATACTTATGCATGGTACCGATACCCTAGATAGGGAA
1 GTATCGATACCTATGCATGGTACCGATACCCTAGATAGGGAA
***
2114683 GTATCGATACCCTATGGGGGGTACCGATACC
1 GTATCGATA-CCTATGCATGGTACCGATACC
2114714 ACTACAAGAG
Statistics
Matches: 108, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
41 18 0.17
42 73 0.68
43 17 0.16
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (42 bp):
GTATCGATACCTATGCATGGTACCGATACCCTAGATAGGGAA
Found at i:2114648 original size:23 final size:23
Alignment explanation
Indices: 2114580--2114696 Score: 87
Period size: 23 Copynumber: 5.4 Consensus size: 23
2114570 ATGCATGTAC
2114580 CGATACCCTAGATAGGGAAGTAT
1 CGATACCCTAGATAGGGAAGTAT
*
2114603 CGATA-CCTATGCAT---G--GTAC
1 CGATACCCTA-G-ATAGGGAAGTAT
2114622 CGATACCCTAGATAGGGAAGTAT
1 CGATACCCTAGATAGGGAAGTAT
* *
2114645 CGATA-CTTATGCAT---G--GTAC
1 CGATACCCTA-G-ATAGGGAAGTAT
2114664 CGATACCCTAGATAGGGAAGTAT
1 CGATACCCTAGATAGGGAAGTAT
2114687 CGATACCCTA
1 CGATACCCTA
2114697 TGGGGGGTAC
Statistics
Matches: 72, Mismatches: 6, Indels: 32
0.65 0.05 0.29
Matches are distributed among these distances:
18 4 0.06
19 18 0.25
20 7 0.10
21 4 0.06
22 7 0.10
23 28 0.39
24 4 0.06
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (23 bp):
CGATACCCTAGATAGGGAAGTAT
Found at i:2114712 original size:20 final size:22
Alignment explanation
Indices: 2114576--2114713 Score: 71
Period size: 23 Copynumber: 6.5 Consensus size: 22
2114566 ACCTATGCAT
*
2114576 GTACCGATACCCTAGATAGGGAA
1 GTACCGATACCCTA-ATAGGGAG
* *
2114599 GTATCGATA-CCT-AT--GCATG
1 GTACCGATACCCTAATAGGGA-G
*
2114618 GTACCGATACCCTAGATAGGGAA
1 GTACCGATACCCTA-ATAGGGAG
* * *
2114641 GTATCGATA--CT--TATGCATG
1 GTACCGATACCCTAATAGGGA-G
*
2114660 GTACCGATACCCTAGATAGGGAA
1 GTACCGATACCCTA-ATAGGGAG
* *
2114683 GTATCGATACCCT-AT-GGGGG
1 GTACCGATACCCTAATAGGGAG
2114703 GTACCGATACC
1 GTACCGATACC
2114714 ACTACAAGAG
Statistics
Matches: 85, Mismatches: 18, Indels: 27
0.65 0.14 0.21
Matches are distributed among these distances:
18 6 0.07
19 16 0.19
20 18 0.21
21 6 0.07
22 5 0.06
23 28 0.33
24 6 0.07
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (22 bp):
GTACCGATACCCTAATAGGGAG
Found at i:2117189 original size:119 final size:119
Alignment explanation
Indices: 2117059--2117277 Score: 341
Period size: 119 Copynumber: 1.8 Consensus size: 119
2117049 TGAACATATT
** * * *
2117059 TTCATTTTTCTTTACTATAGTTTAGTATGATGATAATAATGAAAATGCATTAAAATTTTAATGAT
1 TTCATTTTTCTTTACTATAGTTTACCATGACGATAATAATAAAAATGAATT-AAATTTTAATGAT
*
2117124 CATATTT-AAATTTTAAAAGTACGAGGATTAAAATAAAACAAAAATAAACTTTAA
65 CATATTTCAAATTTTAAAAGTACGAAGATTAAAATAAAACAAAAATAAACTTTAA
* *
2117178 TTCATTTTTCTTTACTATGGTTTACCATGACGATAATAATAAAAATGAATTAAATTTTAATGGTC
1 TTCATTTTTCTTTACTATAGTTTACCATGACGATAATAATAAAAATGAATTAAATTTTAATGATC
*
2117243 ATATTTCAAATTTTAAAAGTATGAAGATTAAAATA
66 ATATTTCAAATTTTAAAAGTACGAAGATTAAAATA
2117278 TGAAGCTTAA
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
118 19 0.21
119 71 0.79
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (119 bp):
TTCATTTTTCTTTACTATAGTTTACCATGACGATAATAATAAAAATGAATTAAATTTTAATGATC
ATATTTCAAATTTTAAAAGTACGAAGATTAAAATAAAACAAAAATAAACTTTAA
Found at i:2117281 original size:14 final size:15
Alignment explanation
Indices: 2117255--2117287 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2117245 ATTTCAAATT
2117255 TTAAAAGTATGAAGA
1 TTAAAAGTATGAAGA
*
2117270 TTAAAA-TATGAAGC
1 TTAAAAGTATGAAGA
2117284 TTAA
1 TTAA
2117288 GTGAGTGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.52, C:0.03, G:0.15, T:0.30
Consensus pattern (15 bp):
TTAAAAGTATGAAGA
Found at i:2121875 original size:31 final size:31
Alignment explanation
Indices: 2121805--2121877 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
2121795 GCTTAATGCC
* *
2121805 CAAATAAGCGCTCAAACTATATCTTTTGTGT
1 CAAATAAGTGCTCAAACTATACCTTTTGTGT
2121836 CAAATAAGTGCTCAAACTATACCTTTTGTGT
1 CAAATAAGTGCTCAAACTATACCTTTTGTGT
2121867 CAAATAAGTGC
1 CAAATAAGTGC
2121878 ATACATTTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (31 bp):
CAAATAAGTGCTCAAACTATACCTTTTGTGT
Found at i:2127561 original size:25 final size:23
Alignment explanation
Indices: 2127506--2127562 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
2127496 AATCCGTATA
* * *
2127506 ATATATTATATATCTATATTTAT
1 ATATATTTTAAATCTATATTCAT
*
2127529 ATACATTTTAAATACTATATTACAT
1 ATATATTTTAAAT-CTATATT-CAT
2127554 ATATATTTT
1 ATATATTTT
2127563 CATAACTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 10 0.37
24 7 0.26
25 10 0.37
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATATTTTAAATCTATATTCAT
Found at i:2127624 original size:27 final size:28
Alignment explanation
Indices: 2127537--2127703 Score: 182
Period size: 30 Copynumber: 5.9 Consensus size: 28
2127527 ATATACATTT
*
2127537 TAAATACTATATTAC-ATATATA-TTTTC
1 TAAAAACTATATT-CTATATATATTTTTC
* * * *
2127564 --ATAACTATAATATATATTTATTTTTC
1 TAAAAACTATATTCTATATATATTTTTC
2127590 TAAAAAAACTATATTCTATATATATTTTTC
1 T--AAAAACTATATTCTATATATATTTTTC
*
2127620 TAAAAACTATATATATATATATATATATTTC
1 TAAAAACTATAT-TCTATATATAT-T-TTTC
*
2127651 TAAAAACTATATACTATATATA-TTTTC
1 TAAAAACTATATTCTATATATATTTTTC
2127678 TAAAAACTATATTCTATATATATTTT
1 TAAAAACTATATTCTATATATATTTT
2127704 ATTCAATATT
Statistics
Matches: 117, Mismatches: 13, Indels: 19
0.79 0.09 0.13
Matches are distributed among these distances:
25 14 0.12
26 5 0.04
27 25 0.21
28 15 0.13
29 10 0.09
30 32 0.27
31 16 0.14
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (28 bp):
TAAAAACTATATTCTATATATATTTTTC
Found at i:2127730 original size:59 final size:59
Alignment explanation
Indices: 2127514--2127700 Score: 205
Period size: 59 Copynumber: 3.3 Consensus size: 59
2127504 TAATATATTA
* * * * *
2127514 TATATCTATATTTATATACATTT-TAAATACTATATTAC-ATATATA-TTTTC--ATAAC
1 TATATATATATATATATATATTTCTAAAAACTATA-TACTATATATATTTTTCTAAAAAC
* *
2127569 TATA-ATATATAT-T-TATTTTTCTAAAAAAACTATATTCTATATATATTTTTCTAAAAAC
1 TATATATATATATATATATATTTCT--AAAAACTATATACTATATATATTTTTCTAAAAAC
2127627 TATATATATATATATATATATTTCTAAAAACTATATACTATATATA-TTTTCTAAAAAC
1 TATATATATATATATATATATTTCTAAAAACTATATACTATATATATTTTTCTAAAAAC
*
2127685 TATAT-TCTATATATAT
1 TATATATATATATATAT
2127701 TTTATTCAAT
Statistics
Matches: 112, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
52 5 0.04
53 2 0.02
54 8 0.07
55 20 0.18
56 5 0.04
57 10 0.09
58 25 0.22
59 28 0.25
60 1 0.01
61 8 0.07
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (59 bp):
TATATATATATATATATATATTTCTAAAAACTATATACTATATATATTTTTCTAAAAAC
Found at i:2128330 original size:81 final size:81
Alignment explanation
Indices: 2127933--2128375 Score: 510
Period size: 82 Copynumber: 5.4 Consensus size: 81
2127923 TAACACTTGA
* * * * * * * *
2127933 TCTGCTCCAATATGCTTTCAAGAGAGATCAGTCTTGATCTGTTCCTCTTTTTCGGGTAGTCAGAT
1 TCTGCTCCACTCTTCTTTC-AGGGAGATCAGACTTGATATGTTCCTCTTTTTTGGGTAGTCAAAT
2127998 CAATTTTGGAAGACGGG
65 CAATTTTGGAAGACGGG
* * * *
2128015 TCTCCTCCACTCTTGTTTCAAGGGAGATCAGACTTGATATGTTCCT-TTTTTTCGGGTAGACAAG
1 TCTGCTCCACTCTTCTTTC-AGGGAGATCAGACTTGATATGTTCCTCTTTTTT-GGGTAGTCAAA
*
2128079 TCAATTTTGGAAGACGAG
64 TCAATTTTGGAAGACGGG
* * * * *
2128097 TCTGCTCCGCTCTTCTTTCAGGGGAGATGATACTTGATATGTTCCTCTTTTTCGGGTAGTCAGAT
1 TCTGCTCCACTCTTCTTTCA-GGGAGATCAGACTTGATATGTTCCTCTTTTTTGGGTAGTCAAAT
**
2128162 CAATTTTGTTAGACGGG
65 CAATTTTGGAAGACGGG
** * * * *
2128179 TCTATTCCACTCTTCTTTTAGGGGAGATCAGACTTTATATGTTCCTCTTTTTTGGGTAGTTATAT
1 TCTGCTCCACTCTTCTTTCA-GGGAGATCAGACTTGATATGTTCCTCTTTTTTGGGTAGTCAAAT
* *
2128244 TAATTTTGGAAGATGGG
65 CAATTTTGGAAGACGGG
* * * *
2128261 TCTGCTCCACTCTTATTTCAGGGAGACCATACTTGATTTGTTCCTCTTTTTTGGGTAGTCAAATC
1 TCTGCTCCACTCTTCTTTCAGGGAGATCAGACTTGATATGTTCCTCTTTTTTGGGTAGTCAAATC
*
2128326 AATTTTAGAAGACGGG
66 AATTTTGGAAGACGGG
* *
2128342 TCTGCTCTACTCTTCTTTCAGGGGAGATAAGACT
1 TCTGCTCCACTCTTCTTTCA-GGGAGATCAGACT
2128376 CAAAATATCT
Statistics
Matches: 300, Mismatches: 57, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
81 76 0.25
82 219 0.73
83 5 0.02
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (81 bp):
TCTGCTCCACTCTTCTTTCAGGGAGATCAGACTTGATATGTTCCTCTTTTTTGGGTAGTCAAATC
AATTTTGGAAGACGGG
Found at i:2129362 original size:51 final size:51
Alignment explanation
Indices: 2129284--2129398 Score: 160
Period size: 51 Copynumber: 2.3 Consensus size: 51
2129274 TTACAGACAT
* * * * *
2129284 GTTGACTCCTTTACACT-AGAAAGTCAAGTTGACAAATGATACTACTGAAAA
1 GTTGACTCCTCT-CAGTGAGAAAATCAAGTTGAAAAATGATACTACTAAAAA
*
2129335 GTTGACTTCTCTCAGTGAGAAAATCAAGTTGAAAAATGATACTACTAAAAA
1 GTTGACTCCTCTCAGTGAGAAAATCAAGTTGAAAAATGATACTACTAAAAA
2129386 GTTGACTCCTCTC
1 GTTGACTCCTCTC
2129399 CACGACAAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 3 0.05
51 53 0.95
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (51 bp):
GTTGACTCCTCTCAGTGAGAAAATCAAGTTGAAAAATGATACTACTAAAAA
Found at i:2129630 original size:24 final size:24
Alignment explanation
Indices: 2129603--2129655 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
2129593 TCAATTGATA
2129603 TGCTTCTCTGTATCCGAGAATCTT
1 TGCTTCTCTGTATCCGAGAATCTT
* *
2129627 TGCTTTTTTGTATCCGAGAATCTT
1 TGCTTCTCTGTATCCGAGAATCTT
2129651 TGCTT
1 TGCTT
2129656 TTCTACTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (24 bp):
TGCTTCTCTGTATCCGAGAATCTT
Found at i:2129656 original size:24 final size:24
Alignment explanation
Indices: 2129611--2129657 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
2129601 TATGCTTCTC
2129611 TGTATCCGAGAATCTTTGCTTTTT
1 TGTATCCGAGAATCTTTGCTTTTT
2129635 TGTATCCGAGAATCTTTGCTTTT
1 TGTATCCGAGAATCTTTGCTTTT
2129658 CTACTACATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (24 bp):
TGTATCCGAGAATCTTTGCTTTTT
Found at i:2136246 original size:20 final size:20
Alignment explanation
Indices: 2136217--2136259 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2136207 ATTCCACCAC
2136217 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* * *
2136237 ATGCATCTATATGGTCTTAA
1 ATGCAACTATATGCTCCTAA
2136257 ATG
1 ATG
2136260 GGCTCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:2141868 original size:20 final size:20
Alignment explanation
Indices: 2141839--2141881 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2141829 ATTCCACCAC
2141839 ATGCAACTATATGCTCATAA
1 ATGCAACTATATGCTCATAA
* * *
2141859 ATGCATCTATATGGTCCTAA
1 ATGCAACTATATGCTCATAA
2141879 ATG
1 ATG
2141882 GGCTATTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCATAA
Done.