Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004123.1 Hibiscus syriacus cultivar Beakdansim tig00009023_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: 1596068
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1478566 original size:19 final size:19
Alignment explanation
Indices: 1478544--1478674 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
1478534 CGAAATTAAA
*
1478544 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1478563 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
1478579 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1478596 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
1478610 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1478629 TTCGCATTGTGA--TTC--
1 TTCGCATTGCGATTTTCAT
*
1478644 -TCTCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1478662 TTCGCATTGCGAT
1 TTCGCATTGCGAT
1478675 AGTAATTTCC
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 26 0.32
16 9 0.11
17 9 0.11
19 38 0.46
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:1478590 original size:33 final size:32
Alignment explanation
Indices: 1478548--1478674 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
1478538 ATTAAATTCG
1478548 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
1478581 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
1478614 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
1478647 CATTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1478675 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1478637 original size:66 final size:66
Alignment explanation
Indices: 1478541--1478673 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
1478531 ACGCGAAATT
* *
1478541 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATTTTCATTTCGCATTGC
1478606 G
66 G
* *
1478607 AAATTAGCGTTGCGATTTTCATTTCGCATTGTGATTCTCTCATTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATTTTCATTTCGCATTGC
1478672 G
66 G
1478673 A
1 A
1478674 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATTTTCATTTCGCATTGC
G
Found at i:1480979 original size:12 final size:12
Alignment explanation
Indices: 1480962--1480986 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1480952 TCTTCGGGGA
1480962 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1480974 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1480986 C
1 C
1480987 AGTATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1481195 original size:24 final size:24
Alignment explanation
Indices: 1481161--1481214 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1481151 CTGAAACATC
* *
1481161 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
1481185 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
1481209 ATCAAA
1 ATCAAA
1481215 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:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:1482299 original size:20 final size:20
Alignment explanation
Indices: 1482274--1482331 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
1482264 ATTCATTTGA
1482274 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1482294 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
1482314 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1482332 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1482391 original size:19 final size:19
Alignment explanation
Indices: 1482350--1482413 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
1482340 GAAATGAAAA
1482350 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1482366 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1482383 TCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
*
1482402 GCGCATTGCGAT
1 TCGCATTGCGAT
1482414 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
14 11 0.27
16 3 0.07
17 3 0.07
19 24 0.59
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1482520 original size:14 final size:14
Alignment explanation
Indices: 1482501--1482537 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1482491 CATCAATTAA
1482501 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1482515 ACAAATCATCTTTT
1 ACAAATCAACATTT
1482529 ACAAATCAA
1 ACAAATCAA
1482538 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1484466 original size:19 final size:19
Alignment explanation
Indices: 1484386--1484503 Score: 86
Period size: 20 Copynumber: 6.4 Consensus size: 19
1484376 TAGTTTACTT
* *
1484386 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1484406 TCGCAACGCGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
1484425 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
1484445 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* *
1484464 TCGTAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
1484478 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
1484496 TCGCAACG
1 TCGCAACG
1484504 ACAAAATCGC
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
14 9 0.11
15 1 0.01
16 2 0.03
17 2 0.03
18 12 0.15
19 24 0.30
20 29 0.37
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1484479 original size:14 final size:14
Alignment explanation
Indices: 1484460--1484517 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1484450 ATGCGAAATG
*
1484460 AAAATCGTAACGAC
1 AAAATCGCAACGAC
*
1484474 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1484490 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1484506 AAAATCGCAACG
1 AAAATCGCAACG
1484518 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1484504 original size:32 final size:33
Alignment explanation
Indices: 1484444--1484522 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
1484434 GGAAATGGCT
* *
1484444 ATCGCAATGCGAAATGAAAATCGTAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1484477 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1484509 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1484523 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1484570 original size:14 final size:14
Alignment explanation
Indices: 1484551--1484640 Score: 72
Period size: 14 Copynumber: 5.9 Consensus size: 14
1484541 TTTCATTTCG
1484551 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1484565 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
1484581 CGCATTGCAATTTTGT
1 CG--TTGCGATTTTGT
*
1484597 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1484613 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
1484629 CATTGCGATTTT
1 CGTTGCGATTTT
1484641 CATTTCGCAT
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 29 0.48
16 15 0.25
18 17 0.28
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1484581 original size:32 final size:33
Alignment explanation
Indices: 1484534--1484654 Score: 201
Period size: 32 Copynumber: 3.7 Consensus size: 33
1484524 ACAAATCGCA
*
1484534 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
1484567 TTGCGA-TTTCATTTCGCATTGCAATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
1484599 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1484631 TTGCGATTTTCATTTCGCATTGCG
1 TTGCGATTTTCATTTCGCATTGCG
1484655 TTAGCCATTT
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
32 60 0.72
33 23 0.28
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1484683 original size:20 final size:19
Alignment explanation
Indices: 1484640--1484695 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
1484630 ATTGCGATTT
* *
1484640 TCATTTCGCATTGCGTTAG
1 TCATTTCGCGTTGCGATAG
*
1484659 CCATTTCCGCGTTGCGATAG
1 TCATTT-CGCGTTGCGATAG
*
1484679 TCATTTTCGTGTTGCGA
1 TCA-TTTCGCGTTGCGA
1484696 AAGTAAACTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 5 0.17
20 22 0.73
21 3 0.10
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.39
Consensus pattern (19 bp):
TCATTTCGCGTTGCGATAG
Found at i:1485203 original size:18 final size:18
Alignment explanation
Indices: 1485177--1485221 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1485167 GTCGATCAGA
*
1485177 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1485195 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1485213 TGATGGCTC
1 TGATGGCTC
1485222 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1486565 original size:20 final size:20
Alignment explanation
Indices: 1486540--1486577 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1486530 AATAGTTTCT
1486540 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1486560 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1486578 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1486868 original size:22 final size:22
Alignment explanation
Indices: 1486841--1486884 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1486831 GATGGAGATA
1486841 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1486863 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1486885 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:1487097 original size:20 final size:20
Alignment explanation
Indices: 1487072--1487124 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1487062 GATTATGTAT
1487072 TATCGCGTTGCGAAAGTCAA-
1 TATCGCGTTGCGAAAGT-AAG
1487092 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
1487112 TATCTCGTTGCGA
1 TATCGCGTTGCGA
1487125 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:1487158 original size:20 final size:19
Alignment explanation
Indices: 1487052--1487166 Score: 77
Period size: 20 Copynumber: 5.7 Consensus size: 19
1487042 CGCTTTGAAA
*
1487052 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGA-TA-GTAGT
* * *
1487073 ATCGCGTTGCGAAAGTCAAT
1 ATCGCATTGCGATAGT-AGT
* *
1487093 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGT-AGT
* * * *
1487113 ATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGA--TAGTAGT
1487134 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGT-AGT
1487154 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1487167 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
19 5 0.06
20 47 0.61
21 23 0.30
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.35
Consensus pattern (19 bp):
ATCGCATTGCGATAGTAGT
Found at i:1487184 original size:21 final size:21
Alignment explanation
Indices: 1487155--1487247 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
1487145 ATAGTCAGTA
1487155 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1487176 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1487196 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * * **
1487217 CCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1487237 TCGCATTGCGA
1 TCGCATTGCGA
1487248 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.17, C:0.26, G:0.18, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:1487185 original size:41 final size:42
Alignment explanation
Indices: 1487089--1487228 Score: 135
Period size: 41 Copynumber: 3.4 Consensus size: 42
1487079 TTGCGAAAGT
* * * *
1487089 CAATATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-G
1 CAATATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCC
* * * *
1487130 TATTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCC
1 CAATATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCC
* **
1487172 CAAT-TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCC
1 CAATATCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCC
*
1487213 CAAT-CCGCGTTGCGAT
1 CAATATCGCGTTGCGAT
1487229 TTACTTATTC
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 3 0.04
41 76 0.94
42 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (42 bp):
CAATATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCC
Found at i:1487229 original size:41 final size:41
Alignment explanation
Indices: 1487155--1487247 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
1487145 ATAGTCAGTA
*
1487155 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATCCGCGTTGCGATTTACTTAT
1487196 TCGCATTGCGATTTTCCCAATCCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATCCGCGTTGCGATTTACTTAT
1487237 TCGCATTGCGA
1 TCGCATTGCGA
1487248 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.26, G:0.18, T:0.39
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATCCGCGTTGCGATTTACTTAT
Found at i:1493930 original size:21 final size:22
Alignment explanation
Indices: 1493882--1493934 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 22
1493872 CCCTCGAGGG
1493882 GTATCGATACACATTCAAGGAAT
1 GTATCGATACACATTCAAGG-AT
*
1493905 GTATCGGTACACATTCAAGG-T
1 GTATCGATACACATTCAAGGAT
1493926 GTATCGATA
1 GTATCGATA
1493935 TATAGCAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 9 0.32
23 19 0.68
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (22 bp):
GTATCGATACACATTCAAGGAT
Found at i:1495502 original size:19 final size:19
Alignment explanation
Indices: 1495478--1495538 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
1495468 AAACCGAAAC
1495478 CGGTTTTTTCGGTTCGGTT
1 CGGTTTTTTCGGTTCGGTT
*
1495497 CGGTTTTTT---TAACGGTT
1 CGGTTTTTTCGGT-TCGGTT
*
1495514 CGGGTTTTTCGGTTCGGTT
1 CGGTTTTTTCGGTTCGGTT
1495533 CGGTTT
1 CGGTTT
1495539 ATCGGTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 1 0.03
17 13 0.38
19 19 0.56
20 1 0.03
ACGTcount: A:0.03, C:0.15, G:0.31, T:0.51
Consensus pattern (19 bp):
CGGTTTTTTCGGTTCGGTT
Found at i:1495537 original size:18 final size:18
Alignment explanation
Indices: 1495482--1495545 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
1495472 CGAAACCGGT
1495482 TTTTTCGGTTCGGTTCGG
1 TTTTTCGGTTCGGTTCGG
1495500 TTTTT---TTAACGGTTCGGG
1 TTTTTCGGTT--CGGTTC-GG
1495518 TTTTTCGGTTCGGTTCGG
1 TTTTTCGGTTCGGTTCGG
*
1495536 TTTATCGGTT
1 TTTTTCGGTT
1495546 TTTCAATAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
15 2 0.05
17 6 0.15
18 23 0.59
19 6 0.15
21 2 0.05
ACGTcount: A:0.05, C:0.14, G:0.30, T:0.52
Consensus pattern (18 bp):
TTTTTCGGTTCGGTTCGG
Found at i:1499990 original size:19 final size:19
Alignment explanation
Indices: 1499963--1500010 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
1499953 TTGACCAAGT
*
1499963 GTATTGGTACCTCCCAGTG
1 GTATCGGTACCTCCCAGTG
1499982 GTATCGGTACCTCCCAGTG
1 GTATCGGTACCTCCCAGTG
1500001 GTATCGGTAC
1 GTATCGGTAC
1500011 ACTAATTGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (19 bp):
GTATCGGTACCTCCCAGTG
Found at i:1502128 original size:34 final size:34
Alignment explanation
Indices: 1502080--1502148 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
1502070 TAAAAAATAA
1502080 AAAAAACCAAACCAACCTGGCCAAGCAGAAGGAG
1 AAAAAACCAAACCAACCTGGCCAAGCAGAAGGAG
* *
1502114 AAAAAACCATACCAACCTGGCCGAGCAGAAGGAG
1 AAAAAACCAAACCAACCTGGCCAAGCAGAAGGAG
1502148 A
1 A
1502149 CAACATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.48, C:0.26, G:0.22, T:0.04
Consensus pattern (34 bp):
AAAAAACCAAACCAACCTGGCCAAGCAGAAGGAG
Found at i:1503262 original size:20 final size:20
Alignment explanation
Indices: 1503230--1503268 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1503220 CTATTTTTGG
*
1503230 ATTTTTTGTTTAATGTAATC
1 ATTTTTTGTTTAACGTAATC
1503250 ATTTTTT-TCTTAACGTAAT
1 ATTTTTTGT-TTAACGTAAT
1503269 AAATAAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.59
Consensus pattern (20 bp):
ATTTTTTGTTTAACGTAATC
Found at i:1505171 original size:38 final size:37
Alignment explanation
Indices: 1505120--1505222 Score: 163
Period size: 38 Copynumber: 2.7 Consensus size: 37
1505110 CGCAACTTAC
1505120 AATGTTACATTTTT-ACTAATATTTTCGGTTGAACAAAA
1 AATGTTACATTTTTCA-TAATATTTTCGGTTGAA-AAAA
1505158 AATGTTACATTTTTCATAATATTTTCGGTTGAAAAAA
1 AATGTTACATTTTTCATAATATTTTCGGTTGAAAAAA
*
1505195 AGATGTTACATTTTTCATAACATTTTCG
1 A-ATGTTACATTTTTCATAATATTTTCG
1505223 ATTGTCAACC
Statistics
Matches: 62, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
37 5 0.08
38 56 0.90
39 1 0.02
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.44
Consensus pattern (37 bp):
AATGTTACATTTTTCATAATATTTTCGGTTGAAAAAA
Found at i:1506696 original size:25 final size:24
Alignment explanation
Indices: 1506651--1506703 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 24
1506641 TAACGTTTGT
*
1506651 AAAATTAGACATCTAGATTGATCGAA
1 AAAATTAGACATCTACATTGA--GAA
*
1506677 AAAATTAGACA-CTACTTTGAGAA
1 AAAATTAGACATCTACATTGAGAA
1506700 AAAA
1 AAAA
1506704 AATATAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.28
25 7 0.28
26 11 0.44
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.25
Consensus pattern (24 bp):
AAAATTAGACATCTACATTGAGAA
Found at i:1510306 original size:30 final size:30
Alignment explanation
Indices: 1510272--1510331 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1510262 ATCAAGAGCC
1510272 TTTAGGCTGGCCTTTGCTTGGGCGCCGAAA
1 TTTAGGCTGGCCTTTGCTTGGGCGCCGAAA
*
1510302 TTTAGGTTGGCCTTTGCTTGGGCGCCGAAA
1 TTTAGGCTGGCCTTTGCTTGGGCGCCGAAA
1510332 CAATTTACTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.13, C:0.22, G:0.33, T:0.32
Consensus pattern (30 bp):
TTTAGGCTGGCCTTTGCTTGGGCGCCGAAA
Found at i:1514011 original size:15 final size:15
Alignment explanation
Indices: 1513926--1514011 Score: 72
Period size: 15 Copynumber: 6.0 Consensus size: 15
1513916 GAAAATATTA
*
1513926 ATATTTTAAAATAAT
1 ATATTTTATAATAAT
*
1513941 ATATTTTATAACAAT
1 ATATTTTATAATAAT
*
1513956 ATA-TTTATAATCA-
1 ATATTTTATAATAAT
**
1513969 AT-TTTTAT-ATTTT
1 ATATTTTATAATAAT
* * *
1513982 AAATGTTAAAATAAT
1 ATATTTTATAATAAT
1513997 ATATTTTATAATAAT
1 ATATTTTATAATAAT
1514012 TTATACATTC
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
12 2 0.04
13 8 0.15
14 12 0.23
15 31 0.58
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (15 bp):
ATATTTTATAATAAT
Found at i:1514092 original size:19 final size:19
Alignment explanation
Indices: 1514068--1514107 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1514058 CGCTCCTAAC
1514068 TTATATATTTTATAATGAT
1 TTATATATTTTATAATGAT
1514087 TTATATATTTTATAATGAT
1 TTATATATTTTATAATGAT
1514106 TT
1 TT
1514108 TCTGACGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
TTATATATTTTATAATGAT
Found at i:1521236 original size:24 final size:20
Alignment explanation
Indices: 1521204--1521261 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
1521194 ATGCATGTGT
1521204 AGTGCATCGATGCACCCGTTAAGG
1 AGTGCATCGATGCA-CCG-T-A-G
* *
1521228 AGTGCATCGATACACTGTAG
1 AGTGCATCGATGCACCGTAG
1521248 AGTGCATCGATGCA
1 AGTGCATCGATGCA
1521262 TACCTTCATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
21 1 0.03
22 1 0.03
23 2 0.06
24 13 0.42
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (20 bp):
AGTGCATCGATGCACCGTAG
Found at i:1522948 original size:9 final size:9
Alignment explanation
Indices: 1522934--1523014 Score: 108
Period size: 9 Copynumber: 8.7 Consensus size: 9
1522924 AGGGTTGGAA
1522934 ACCGGTTTG
1 ACCGGTTTG
1522943 ACCGGTTCTG
1 ACCGGTT-TG
*
1522953 ATCGGTTTG
1 ACCGGTTTG
1522962 ACCGGTTTG
1 ACCGGTTTG
1522971 ACCGGTTTG
1 ACCGGTTTG
1522980 AACCGGTTTG
1 -ACCGGTTTG
* *
1522990 ACCGATCTG
1 ACCGGTTTG
1522999 ACCCGGTTTG
1 A-CCGGTTTG
1523009 ACCGGT
1 ACCGGT
1523015 CTACCCGACC
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
9 39 0.62
10 24 0.38
ACGTcount: A:0.14, C:0.25, G:0.31, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1522960 original size:19 final size:18
Alignment explanation
Indices: 1522934--1523014 Score: 108
Period size: 19 Copynumber: 4.3 Consensus size: 18
1522924 AGGGTTGGAA
1522934 ACCGGTTTGACCGGTTCTG
1 ACCGGTTTGACCGGTT-TG
*
1522953 ATCGGTTTGACCGGTTTG
1 ACCGGTTTGACCGGTTTG
1522971 ACCGGTTTGAACCGGTTTG
1 ACCGGTTTG-ACCGGTTTG
* *
1522990 ACCGATCTGACCCGGTTTG
1 ACCGGTTTGA-CCGGTTTG
1523009 ACCGGT
1 ACCGGT
1523015 CTACCCGACC
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
18 11 0.20
19 44 0.80
ACGTcount: A:0.14, C:0.25, G:0.31, T:0.31
Consensus pattern (18 bp):
ACCGGTTTGACCGGTTTG
Found at i:1522974 original size:28 final size:28
Alignment explanation
Indices: 1522934--1523014 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 28
1522924 AGGGTTGGAA
*
1522934 ACCGGTTTGACCGGTTCTG-ATCGGTTTG
1 ACCGGTTTGACCGGTT-TGAACCGGTTTG
1522962 ACCGGTTTGACCGGTTTGAACCGGTTTG
1 ACCGGTTTGACCGGTTTGAACCGGTTTG
* *
1522990 ACCGATCTGACCCGGTTTG-ACCGGT
1 ACCGGTTTGA-CCGGTTTGAACCGGT
1523015 CTACCCGACC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
27 2 0.04
28 38 0.79
29 8 0.17
ACGTcount: A:0.14, C:0.25, G:0.31, T:0.31
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTGAACCGGTTTG
Found at i:1530188 original size:9 final size:9
Alignment explanation
Indices: 1530174--1530281 Score: 117
Period size: 9 Copynumber: 11.3 Consensus size: 9
1530164 AGGGCTGGAA
1530174 ACCGGTTTG
1 ACCGGTTTG
*
1530183 ACCGGTTTTCA
1 ACCGG-TTT-G
*
1530194 ACCGATTCTG
1 ACCGGTT-TG
*
1530204 ACCAGTTTG
1 ACCGGTTTG
*
1530213 ATCGGTTTCG
1 ACCGGTTT-G
1530223 ACCGGTTTG
1 ACCGGTTTG
1530232 ACCGGTTTCG
1 ACCGGTTT-G
1530242 ACCGGTTTG
1 ACCGGTTTG
1530251 ACCGGTTTCG
1 ACCGGTTT-G
1530261 ACCGGTTTG
1 ACCGGTTTG
*
1530270 ACCGGTCTG
1 ACCGGTTTG
1530279 ACC
1 ACC
1530282 CGACTGACCC
Statistics
Matches: 84, Mismatches: 9, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
9 43 0.51
10 36 0.43
11 5 0.06
ACGTcount: A:0.14, C:0.27, G:0.28, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1530206 original size:21 final size:20
Alignment explanation
Indices: 1530173--1530211 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1530163 GAGGGCTGGA
* *
1530173 AACCGGTTTGACCGGTTTTC
1 AACCGATTTGACCAGTTTTC
1530193 AACCGATTCTGACCAGTTT
1 AACCGATT-TGACCAGTTT
1530212 GATCGGTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.33
Consensus pattern (20 bp):
AACCGATTTGACCAGTTTTC
Found at i:1530230 original size:19 final size:19
Alignment explanation
Indices: 1530203--1530275 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
1530193 AACCGATTCT
* *
1530203 GACCAGTTTGATCGGTTTC
1 GACCGGTTTGACCGGTTTC
1530222 GACCGGTTTGACCGGTTTC
1 GACCGGTTTGACCGGTTTC
1530241 GACCGGTTTGACCGGTTTC
1 GACCGGTTTGACCGGTTTC
1530260 GACCGGTTTGACCGGT
1 GACCGGTTTGACCGGT
1530276 CTGACCCGAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.12, C:0.25, G:0.32, T:0.32
Consensus pattern (19 bp):
GACCGGTTTGACCGGTTTC
Found at i:1547155 original size:2 final size:2
Alignment explanation
Indices: 1547150--1547214 Score: 103
Period size: 2 Copynumber: 32.5 Consensus size: 2
1547140 AGGAACCAAA
* *
1547150 AC AC AC AC AC AC AC AC AC AC AC AT AC AC AC AC AC AT AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
1547192 AC AC AT AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC A
1547215 TACATACATA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.45, G:0.00, T:0.05
Consensus pattern (2 bp):
AC
Found at i:1547228 original size:12 final size:12
Alignment explanation
Indices: 1547150--1547222 Score: 114
Period size: 12 Copynumber: 6.2 Consensus size: 12
1547140 AGGAACCAAA
*
1547150 ACACACACACAC
1 ACACACACACAT
1547162 ACACACACACAT
1 ACACACACACAT
1547174 ACACACACACAT
1 ACACACACACAT
1547186 ACACACACACAT
1 ACACACACACAT
1547198 ACACACACAC--
1 ACACACACACAT
*
1547208 ACACACATACAT
1 ACACACACACAT
1547220 ACA
1 ACA
1547223 TACATATTCC
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
10 9 0.16
12 48 0.84
ACGTcount: A:0.51, C:0.42, G:0.00, T:0.07
Consensus pattern (12 bp):
ACACACACACAT
Found at i:1547924 original size:15 final size:15
Alignment explanation
Indices: 1547890--1547932 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
1547880 CTCTAACACA
1547890 CAAAGAAC-AAAAAC
1 CAAAGAACAAAAAAC
*
1547904 C-CAGAACAAAAAAC
1 CAAAGAACAAAAAAC
1547918 CAAAGAACAACAAAA
1 CAAAGAACAA-AAAA
1547933 AAAAAACCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 5 0.21
14 8 0.33
15 7 0.29
16 4 0.17
ACGTcount: A:0.70, C:0.23, G:0.07, T:0.00
Consensus pattern (15 bp):
CAAAGAACAAAAAAC
Found at i:1548471 original size:21 final size:21
Alignment explanation
Indices: 1548442--1548488 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1548432 AATATGTAAA
*
1548442 TCGCATTGCGATTTTTCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
1548463 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
1548484 TCGCA
1 TCGCA
1548489 ACGCGAAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1548494 original size:21 final size:21
Alignment explanation
Indices: 1548449--1548494 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1548439 AAATCGCATT
* ***
1548449 GCGATTTTTCAAATTCGCGTT
1 GCGATTTTCCAAATTCGCAAC
1548470 GCGATTTTCCAAATTCGCAAC
1 GCGATTTTCCAAATTCGCAAC
1548491 GCGA
1 GCGA
1548495 AAGTCAAATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (21 bp):
GCGATTTTCCAAATTCGCAAC
Found at i:1548659 original size:22 final size:22
Alignment explanation
Indices: 1548634--1548675 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1548624 GGCGACATCC
*
1548634 GTCCCCATCTCCGACGAAATTT
1 GTCCCCATCTCCGACAAAATTT
*
1548656 GTCCCCATTTCCGACAAAAT
1 GTCCCCATCTCCGACAAAAT
1548676 CCGTCTATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.36, G:0.12, T:0.26
Consensus pattern (22 bp):
GTCCCCATCTCCGACAAAATTT
Found at i:1550951 original size:4 final size:4
Alignment explanation
Indices: 1550942--1550983 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
1550932 TTTTTCGGCA
* * *
1550942 TTAT TTAT TTAT TTAT TTAC TTAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1550984 TTAGCGGCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:1551170 original size:42 final size:42
Alignment explanation
Indices: 1551123--1551245 Score: 117
Period size: 42 Copynumber: 2.9 Consensus size: 42
1551113 GCCCGATGCA
* * *
1551123 CCTATCATCATTCAAGATGCGCC-TCCTATCGTTCAAGAGGCC
1 CCTATCATCATTCAAGAAGC-CCATCCCACCGTTCAAGAGGCC
1551165 CCTATCATCA-TCGAAGAAGCCCATCCCACCGTTCAAGAGGCC
1 CCTATCATCATTC-AAGAAGCCCATCCCACCGTTCAAGAGGCC
** * * * *
1551207 CCTGCCATCGTTCAAGAGGTCC-TGCCCGCCGTTCAAGAG
1 CCTATCATCATTCAAGAAGCCCAT-CCCACCGTTCAAGAG
1551246 CCCGATTCAC
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
41 5 0.07
42 61 0.90
43 2 0.03
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.21
Consensus pattern (42 bp):
CCTATCATCATTCAAGAAGCCCATCCCACCGTTCAAGAGGCC
Found at i:1551202 original size:21 final size:20
Alignment explanation
Indices: 1551178--1551248 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
1551168 ATCATCATCG
1551178 AAGAAGCCCATCCCACCGTTC
1 AAGAAGCCC-TCCCACCGTTC
* * *
1551199 AAGAGGCCCCTGCCATCGTTC
1 AAGAAG-CCCTCCCACCGTTC
* * *
1551220 AAGAGGTCCTGCCCGCCGTTC
1 AAGAAGCCCT-CCCACCGTTC
1551241 AAG-AGCCC
1 AAGAAGCCC
1551249 GATTCACATG
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
20 6 0.15
21 30 0.77
22 3 0.08
ACGTcount: A:0.23, C:0.39, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGAAGCCCTCCCACCGTTC
Found at i:1551232 original size:20 final size:21
Alignment explanation
Indices: 1551128--1551225 Score: 74
Period size: 21 Copynumber: 4.7 Consensus size: 21
1551118 ATGCACCTAT
* * *
1551128 CATCATTCAAGATGCGCCT-C
1 CATCGTTCAAGAGGCCCCTGC
**
1551148 CTATCGTTCAAGAGGCCCCTAT
1 C-ATCGTTCAAGAGGCCCCTGC
* * * *
1551170 CATC-ATCGAAGAAGCCCATCC
1 CATCGTTC-AAGAGGCCCCTGC
*
1551191 CACCGTTCAAGAGGCCCCTGC
1 CATCGTTCAAGAGGCCCCTGC
1551212 CATCGTTCAAGAGG
1 CATCGTTCAAGAGG
1551226 TCCTGCCCGC
Statistics
Matches: 59, Mismatches: 15, Indels: 7
0.73 0.19 0.09
Matches are distributed among these distances:
20 3 0.05
21 53 0.90
22 3 0.05
ACGTcount: A:0.26, C:0.35, G:0.19, T:0.20
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTGC
Found at i:1552696 original size:61 final size:62
Alignment explanation
Indices: 1552596--1552735 Score: 176
Period size: 66 Copynumber: 2.2 Consensus size: 62
1552586 TTTTACATTG
*
1552596 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTA-TTTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
* ** * *
1552656 AAAGTTTATTTGTTTAATTTGATTTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA--TTTTT-CTTGATTAATTGATTTGT
1552721 A
62 A
1552722 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
1552736 GTTTCTAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
60 16 0.24
61 17 0.25
64 4 0.06
66 30 0.45
ACGTcount: A:0.31, C:0.01, G:0.16, T:0.52
Consensus pattern (62 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
Found at i:1553089 original size:39 final size:39
Alignment explanation
Indices: 1553033--1553121 Score: 142
Period size: 39 Copynumber: 2.3 Consensus size: 39
1553023 ACTCAAGTTG
1553033 TAGATTTTGATTTCCTTTTGCTTGGCACCATATCAGATT
1 TAGATTTTGATTTCCTTTTGCTTGGCACCATATCAGATT
* * * *
1553072 TTGATTTTGATTTCCTTTTGTTTGGCACCATATGAGCTT
1 TAGATTTTGATTTCCTTTTGCTTGGCACCATATCAGATT
1553111 TAGATTTTGAT
1 TAGATTTTGAT
1553122 GAGCATCGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.49
Consensus pattern (39 bp):
TAGATTTTGATTTCCTTTTGCTTGGCACCATATCAGATT
Found at i:1553870 original size:25 final size:25
Alignment explanation
Indices: 1553836--1553910 Score: 141
Period size: 25 Copynumber: 3.0 Consensus size: 25
1553826 ATTATTTTTC
*
1553836 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
1553861 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
1553886 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
1553911 TAATTGATTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.25
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:1553883 original size:14 final size:13
Alignment explanation
Indices: 1553835--1553909 Score: 50
Period size: 14 Copynumber: 5.8 Consensus size: 13
1553825 CATTATTTTT
*
1553835 CCAAATAATGTAC
1 CCAAACAATGTAC
1553848 CCATAACAATGT--
1 CCA-AACAATGTAC
* *
1553860 TCAAATAATGTAC
1 CCAAACAATGTAC
1553873 CCACAACAATGT--
1 CCA-AACAATGTAC
* *
1553885 TCAAATAATGTAC
1 CCAAACAATGTAC
1553898 CCACAACAATGT
1 CCA-AACAATGT
1553910 TTAATTGATT
Statistics
Matches: 46, Mismatches: 9, Indels: 13
0.68 0.13 0.19
Matches are distributed among these distances:
11 14 0.30
12 4 0.09
13 7 0.15
14 21 0.46
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (13 bp):
CCAAACAATGTAC
Found at i:1554415 original size:18 final size:18
Alignment explanation
Indices: 1554389--1554429 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1554379 AGGTGAAGCC
* *
1554389 GATTGTGATTGGGATTTT
1 GATTTTGATTGCGATTTT
1554407 GATTTTGATTGCGATTTT
1 GATTTTGATTGCGATTTT
1554425 GATTT
1 GATTT
1554430 CCTTTTGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.02, G:0.27, T:0.54
Consensus pattern (18 bp):
GATTTTGATTGCGATTTT
Found at i:1556714 original size:24 final size:24
Alignment explanation
Indices: 1556680--1556733 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1556670 CCATCACATC
1556680 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1556704 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1556728 ATCAAA
1 ATCAAA
1556734 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1557661 original size:19 final size:19
Alignment explanation
Indices: 1557637--1557687 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
1557627 ACTAAAACCT
1557637 GTTGCGAAATT-AAATTCGA
1 GTTGCGAAATTGAAATTC-A
*
1557656 GTTGCGAATTTGAAATTCA
1 GTTGCGAAATTGAAATTCA
*
1557675 GTTGCGAATTTGA
1 GTTGCGAAATTGA
1557688 CTTTCGCGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 24 0.80
20 6 0.20
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (19 bp):
GTTGCGAAATTGAAATTCA
Found at i:1557673 original size:20 final size:20
Alignment explanation
Indices: 1557637--1557766 Score: 90
Period size: 20 Copynumber: 6.6 Consensus size: 20
1557627 ACTAAAACCT
*
1557637 GTTGCGAAATT-AAATTCGA
1 GTTGCGAATTTGAAATTCGA
1557656 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
** *
1557675 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGAAATTCGA
**
1557695 GTTGCG-ATTT-ACATATTCTT
1 GTTGCGAATTTGA-A-ATTCGA
* * *
1557715 GTTGCGAAATTGGAAACT-GG
1 GTTGCG-AATTTGAAATTCGA
* * *
1557735 GTTGCGAAATTGGAATTCGC
1 GTTGCGAATTTGAAATTCGA
1557755 GTTGCGAATTTG
1 GTTGCGAATTTG
1557767 TTGGTCATTT
Statistics
Matches: 85, Mismatches: 18, Indels: 15
0.72 0.15 0.13
Matches are distributed among these distances:
18 1 0.01
19 38 0.45
20 39 0.46
21 2 0.02
22 4 0.05
23 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGA
Found at i:1561228 original size:2 final size:2
Alignment explanation
Indices: 1561221--1561252 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1561211 ATAAACTTTA
1561221 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
1561253 TCAAATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1569901 original size:13 final size:13
Alignment explanation
Indices: 1569885--1569961 Score: 79
Period size: 13 Copynumber: 5.9 Consensus size: 13
1569875 TAAATAGACC
1569885 TATTAAATAAAAT
1 TATTAAATAAAAT
*
1569898 TATTTAATAAAAT
1 TATTAAATAAAAT
*
1569911 TATTTAATAAAAT
1 TATTAAATAAAAT
1569924 TATTTAAATATAAAT
1 TA-TTAAATA-AAAT
1569939 TA-TAAA-AAACAT
1 TATTAAATAAA-AT
*
1569951 GATT-AATAAAA
1 TATTAAATAAAA
1569962 AATATTGACA
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
11 2 0.04
12 7 0.12
13 35 0.62
14 6 0.11
15 6 0.11
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (13 bp):
TATTAAATAAAAT
Found at i:1570040 original size:23 final size:24
Alignment explanation
Indices: 1569987--1570040 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
1569977 CAATGATTAA
*
1569987 ATGTAAATTAATATAGTTTAATTT
1 ATGTAAATTAATACAGTTTAATTT
**
1570011 ACATAAATT-ATACAGTTTAATTT
1 ATGTAAATTAATACAGTTTAATTT
1570034 ATGTAAA
1 ATGTAAA
1570041 GAAAAAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (24 bp):
ATGTAAATTAATACAGTTTAATTT
Found at i:1570317 original size:12 final size:11
Alignment explanation
Indices: 1570291--1570330 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1570281 GATAATGATA
*
1570291 ATTTAAATAAC
1 ATTTGAATAAC
*
1570302 ATTTGATATAAA
1 ATTTGA-ATAAC
1570314 ATTTGAATAAC
1 ATTTGAATAAC
1570325 ATTTGA
1 ATTTGA
1570331 GTTAATTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (11 bp):
ATTTGAATAAC
Found at i:1570611 original size:20 final size:20
Alignment explanation
Indices: 1570588--1570640 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1570578 AATTACAAGA
1570588 CAACAACAGACATTAGGCAG
1 CAACAACAGACATTAGGCAG
*
1570608 CAACAACAGGCATTAGGCAG
1 CAACAACAGACATTAGGCAG
*
1570628 CAACAGCAGACAT
1 CAACAACAGACAT
1570641 CATTTATGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.26, G:0.21, T:0.09
Consensus pattern (20 bp):
CAACAACAGACATTAGGCAG
Found at i:1579185 original size:12 final size:12
Alignment explanation
Indices: 1579168--1579195 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1579158 CAGACATACC
1579168 AAAAAAGAAAGA
1 AAAAAAGAAAGA
1579180 AAAAAAGAAAGA
1 AAAAAAGAAAGA
1579192 AAAA
1 AAAA
1579196 CACATAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAGA
Found at i:1581113 original size:2 final size:2
Alignment explanation
Indices: 1581106--1581136 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1581096 AATAAAATTA
1581106 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1581137 TATTTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1581323 original size:2 final size:2
Alignment explanation
Indices: 1581318--1581352 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1581308 ACACACACAC
1581318 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1581353 AATGAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1581980 original size:23 final size:22
Alignment explanation
Indices: 1581936--1581977 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1581926 ACTCAACCCC
1581936 CTCATATTCTCTTTTCATTTCT
1 CTCATATTCTCTTTTCATTTCT
* * *
1581958 CTCATTTTTTCTTTTTATTT
1 CTCATATTCTCTTTTCATTT
1581978 TCTTTACAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (22 bp):
CTCATATTCTCTTTTCATTTCT
Found at i:1582787 original size:18 final size:18
Alignment explanation
Indices: 1582766--1582811 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1582756 TAAGAAAAGA
1582766 AATAAATAAAATAAAAAC
1 AATAAATAAAATAAAAAC
* *
1582784 AAT-AATATAGATAAAAAT
1 AATAAATA-AAATAAAAAC
1582802 AA-AAATAAAA
1 AATAAATAAAA
1582812 ATAGTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (18 bp):
AATAAATAAAATAAAAAC
Found at i:1584659 original size:7 final size:7
Alignment explanation
Indices: 1584644--1584713 Score: 54
Period size: 7 Copynumber: 9.7 Consensus size: 7
1584634 TATTTATTTA
*
1584644 TTTTATT
1 TTTTCTT
1584651 TTTTC-T
1 TTTTCTT
1584657 TTTTCTCT
1 TTTTCT-T
*
1584665 TTTTCTC
1 TTTTCTT
1584672 TTTT-TT
1 TTTTCTT
1584678 TTTTCATTT
1 TTTTC--TT
1584687 TTTTCTT
1 TTTTCTT
*
1584694 TTTGTCAT
1 TTT-TCTT
*
1584702 TTTTCAT
1 TTTTCTT
1584709 TTTTC
1 TTTTC
1584714 CTTCTTCGGG
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
6 11 0.21
7 22 0.42
8 13 0.25
9 7 0.13
ACGTcount: A:0.06, C:0.14, G:0.01, T:0.79
Consensus pattern (7 bp):
TTTTCTT
Found at i:1584679 original size:20 final size:20
Alignment explanation
Indices: 1584650--1584696 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
1584640 TTTATTTTAT
*
1584650 TTTTTCTTTTTCTCTTTTTCTC
1 TTTTT-TTTTTC-ATTTTTCTC
*
1584672 TTTTTTTTTTCATTTTTTTC
1 TTTTTTTTTTCATTTTTCTC
1584692 TTTTT
1 TTTTT
1584697 GTCATTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 12 0.52
21 6 0.26
22 5 0.22
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTTTTTTTCATTTTTCTC
Found at i:1584687 original size:28 final size:27
Alignment explanation
Indices: 1584644--1584705 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
1584634 TATTTATTTA
1584644 TTTTATTTTTTCTTTTTCTCTTTTTCTC
1 TTTT-TTTTTTCTTTTTCTCTTTTTCTC
* *
1584672 TTTTTTTTTTCATTTTTTTCTTTTTGTC
1 TTTTTTTTTTC-TTTTTCTCTTTTTCTC
*
1584700 ATTTTT
1 TTTTTT
1584706 CATTTTTCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 7 0.23
28 23 0.77
ACGTcount: A:0.05, C:0.13, G:0.02, T:0.81
Consensus pattern (27 bp):
TTTTTTTTTTCTTTTTCTCTTTTTCTC
Found at i:1584713 original size:44 final size:43
Alignment explanation
Indices: 1584631--1584713 Score: 98
Period size: 43 Copynumber: 1.9 Consensus size: 43
1584621 TTGAACCACC
*
1584631 TTTTATTTATTTATTTTATTTTTTCTTTTTCTCTTTTTCTCTT
1 TTTTATTTATTTATTTTATTTTTTCTTTTTCTATTTTTCTCTT
* *
1584674 TTTTTTTTCATTT-TTTTCTTTTTGTCATTTTTC-ATTTTTC
1 TTTTATTT-ATTTATTTTATTTTT-TC-TTTTTCTATTTTTC
1584714 CTTCTTCGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
43 16 0.47
44 12 0.35
45 6 0.18
ACGTcount: A:0.08, C:0.12, G:0.01, T:0.78
Consensus pattern (43 bp):
TTTTATTTATTTATTTTATTTTTTCTTTTTCTATTTTTCTCTT
Found at i:1590619 original size:23 final size:23
Alignment explanation
Indices: 1590553--1590628 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
1590543 TCTCAAAGGA
*
1590553 CCACATAGGTTTGCACCGAAATG
1 CCACATAGGTTTGCACCGAAGTG
* *
1590576 CCAAATAGGTTTGCACCGAAGTT
1 CCACATAGGTTTGCACCGAAGTG
*
1590599 TCACATAGGTTTGCACCGAAGTG
1 CCACATAGGTTTGCACCGAAGTG
*
1590622 ACACATA
1 CCACATA
1590629 TTTGTCCCAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (23 bp):
CCACATAGGTTTGCACCGAAGTG
Found at i:1590650 original size:21 final size:21
Alignment explanation
Indices: 1590626--1590666 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1590616 GAAGTGACAC
1590626 ATATTTGTCCCAAAAGACCAT
1 ATATTTGTCCCAAAAGACCAT
* * *
1590647 ATATTTTTCCCGAAGGACCA
1 ATATTTGTCCCAAAAGACCA
1590667 CATAAGACCC
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:0.24, G:0.12, T:0.29
Consensus pattern (21 bp):
ATATTTGTCCCAAAAGACCAT
Found at i:1590830 original size:21 final size:21
Alignment explanation
Indices: 1590804--1590854 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1590794 CATAGAGTTT
*
1590804 GTTCACATTCACTGGTTCAAA
1 GTTCACATTCACTGATTCAAA
* *
1590825 GTTCACATTCACTTATTTAAA
1 GTTCACATTCACTGATTCAAA
1590846 GTTCACATT
1 GTTCACATT
1590855 TCCATAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (21 bp):
GTTCACATTCACTGATTCAAA
Found at i:1591330 original size:53 final size:54
Alignment explanation
Indices: 1591242--1591363 Score: 149
Period size: 53 Copynumber: 2.3 Consensus size: 54
1591232 AATATTTCCC
* *
1591242 TTCAAGGATATCGATACCTCCTCATGGTACCGATACCAAAATAGCATTCGAT-A
1 TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAAAATAGCATTCGATGA
* * * ** * *
1591295 TTCAAGGGTATCGATACCTCCTTAAGGTTCTGATACCAATCTGGCATTCGATGT
1 TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAAAATAGCATTCGATGA
1591349 TTCAA-GGTATCGATA
1 TTCAAGGGTATCGATA
1591364 TCATCTTTCA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 54 0.92
54 5 0.08
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (54 bp):
TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAAAATAGCATTCGATGA
Done.