Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005606.1 Hibiscus syriacus cultivar Beakdansim tig00013040_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: 3509357
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:3259556 original size:23 final size:21
Alignment explanation
Indices: 3259530--3259584 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 21
3259520 TTTTTTCTTT
3259530 TTTTTCTTTTATTCTTTTCTGAA
1 TTTTTCTTTT-TTCTTTT-TGAA
**
3259553 TTTTTCACTTTTTTCTTTTTGTC
1 TTTTT--CTTTTTTCTTTTTGAA
3259576 TTTTTCTTT
1 TTTTTCTTT
3259585 CTTTTTGCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 4 0.14
23 12 0.43
24 7 0.25
25 5 0.18
ACGTcount: A:0.07, C:0.15, G:0.04, T:0.75
Consensus pattern (21 bp):
TTTTTCTTTTTTCTTTTTGAA
Found at i:3263245 original size:15 final size:16
Alignment explanation
Indices: 3263227--3263257 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3263217 ATTTCTTGCC
3263227 ATTTCC-TTTCTTATT
1 ATTTCCATTTCTTATT
3263242 ATTTCCATTTCTTATT
1 ATTTCCATTTCTTATT
3263258 TCATATTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTCCATTTCTTATT
Found at i:3263481 original size:15 final size:15
Alignment explanation
Indices: 3263459--3263497 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
3263449 AAGCAACAAG
3263459 AAGAAAAAGAAAGA-A
1 AAGAAAAA-AAAGAGA
3263474 TAAGAAAAAAAAGAGA
1 -AAGAAAAAAAAGAGA
3263490 AAGAAAAA
1 AAGAAAAA
3263498 GACTCCTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (15 bp):
AAGAAAAAAAAGAGA
Found at i:3263733 original size:15 final size:16
Alignment explanation
Indices: 3263694--3263735 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
3263684 TGAGTTGTAA
*
3263694 TTTATCTTCATTTTCTC
1 TTTAT-TTCATTTCCTC
3263711 TTTATTTCATTTCCT-
1 TTTATTTCATTTCCTC
*
3263726 TTTCTTTCAT
1 TTTATTTCAT
3263736 CTATTCTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 9 0.39
16 9 0.39
17 5 0.22
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATTTCATTTCCTC
Found at i:3264984 original size:13 final size:13
Alignment explanation
Indices: 3264966--3264990 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3264956 TTTAAGTCCA
3264966 TGTGATGTTCCTG
1 TGTGATGTTCCTG
3264979 TGTGATGTTCCT
1 TGTGATGTTCCT
3264991 ATTTTACTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.16, G:0.28, T:0.48
Consensus pattern (13 bp):
TGTGATGTTCCTG
Found at i:3267114 original size:2 final size:2
Alignment explanation
Indices: 3267107--3267150 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3267097 TATGAACCAC
3267107 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
3267149 AT
1 AT
3267151 CTTATTTTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3268268 original size:14 final size:14
Alignment explanation
Indices: 3268249--3268276 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3268239 TAAGATATTA
3268249 TTTCCATCACCATC
1 TTTCCATCACCATC
3268263 TTTCCATCACCATC
1 TTTCCATCACCATC
3268277 CTCAATCACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:3269154 original size:18 final size:18
Alignment explanation
Indices: 3269128--3269163 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3269118 ACCAGTCACA
3269128 ACCCAACCCGTTGACCCG
1 ACCCAACCCGTTGACCCG
*
3269146 ACCCGACCCGTTGACCCG
1 ACCCAACCCGTTGACCCG
3269164 TTAACCGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.50, G:0.19, T:0.11
Consensus pattern (18 bp):
ACCCAACCCGTTGACCCG
Found at i:3271704 original size:12 final size:12
Alignment explanation
Indices: 3271689--3271758 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
3271679 GATACATTAC
3271689 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
3271701 CTGATTTCTGAT
1 CTGAATTCTGTT
*
3271713 CTGGATTCTGTT
1 CTGAATTCTGTT
*
3271725 CTG-ATATCTGAT
1 CTGAAT-TCTGTT
3271737 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
3271749 TTGATTTCTG
1 CTGAATTCTG
3271759 ATATCTCTAT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:3271757 original size:48 final size:48
Alignment explanation
Indices: 3271652--3271760 Score: 141
Period size: 48 Copynumber: 2.3 Consensus size: 48
3271642 AAATATTTTA
* * *
3271652 TCTGATTTCCGA-CTTGAATTCTGTTCTGATACATTACCTGAATTCTGT
1 TCTGATTTCTGATC-TGGATTCTGTTCTGATACATGACCTGAATTCTGT
*
3271700 TCTGATTTCTGATCTGGATTCTGTTCTGATATC-TGATCTGAATTCTGT
1 TCTGATTTCTGATCTGGATTCTGTTCTGATA-CATGACCTGAATTCTGT
*
3271748 TTTGATTTCTGAT
1 TCTGATTTCTGAT
3271761 ATCTCTATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
48 52 0.96
49 2 0.04
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (48 bp):
TCTGATTTCTGATCTGGATTCTGTTCTGATACATGACCTGAATTCTGT
Found at i:3271758 original size:24 final size:24
Alignment explanation
Indices: 3271652--3271760 Score: 123
Period size: 24 Copynumber: 4.5 Consensus size: 24
3271642 AAATATTTTA
*
3271652 TCTGATTTCCGA-CTTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
* * *
3271676 TCTGA-TACATTACCTGAATTCTGT
1 TCTGATTTC-TGATCTGAATTCTGT
*
3271700 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
3271724 TCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
3271748 TTTGATTTCTGAT
1 TCTGATTTCTGAT
3271761 ATCTCTATTT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
23 2 0.03
24 66 0.93
25 3 0.04
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:3273842 original size:8 final size:8
Alignment explanation
Indices: 3273829--3273888 Score: 56
Period size: 8 Copynumber: 7.5 Consensus size: 8
3273819 AACCCGACCC
3273829 GACCCGTT
1 GACCCGTT
3273837 GACCC---
1 GACCCGTT
3273842 GACCCGTT
1 GACCCGTT
3273850 GACCCGTT
1 GACCCGTT
3273858 GA-CCGTT
1 GACCCGTT
3273865 GACCGGCGTT
1 GACC--CGTT
3273875 GACCACTGTT
1 GACC-C-GTT
3273885 GACC
1 GACC
3273889 AAAACTTTGA
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
5 5 0.11
7 7 0.16
8 16 0.36
9 1 0.02
10 15 0.34
ACGTcount: A:0.15, C:0.37, G:0.27, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:3273842 original size:13 final size:13
Alignment explanation
Indices: 3273824--3273855 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
3273814 GTCACAACCC
3273824 GACCCGACCCGTT
1 GACCCGACCCGTT
3273837 GACCCGACCCGTT
1 GACCCGACCCGTT
3273850 GACCCG
1 GACCCG
3273856 TTGACCGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.47, G:0.25, T:0.12
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:3273865 original size:15 final size:16
Alignment explanation
Indices: 3273845--3273878 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
3273835 TTGACCCGAC
3273845 CCGTTGACC-CGTTGA
1 CCGTTGACCGCGTTGA
3273860 CCGTTGACCGGCGTTGA
1 CCGTTGACC-GCGTTGA
3273877 CC
1 CC
3273879 ACTGTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.12, C:0.35, G:0.29, T:0.24
Consensus pattern (16 bp):
CCGTTGACCGCGTTGA
Found at i:3276400 original size:24 final size:24
Alignment explanation
Indices: 3276366--3276433 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
3276356 ATACATTACC
* *
3276366 TGAATTATGTTCTGATTTCTGATA
1 TGAATTCTGTTATGATTTCTGATA
* * *
3276390 TGGATTCTGTTATGATATCTGATC
1 TGAATTCTGTTATGATTTCTGATA
*
3276414 TGAATTCTGTTTTGATTTCT
1 TGAATTCTGTTATGATTTCT
3276434 CACATCTCCG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.21, C:0.10, G:0.18, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTGATA
Found at i:3276406 original size:48 final size:48
Alignment explanation
Indices: 3276328--3276433 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 48
3276318 AAATATTTTA
* *
3276328 TCTGATTTCTGACTTGAATTCTATTCTGATA-CATTACCTGAATTATGT
1 TCTGATTTCTGACTTGAATTCTATTATGATATC-TGACCTGAATTATGT
* * * *
3276376 TCTGATTTCTGA-TATGGATTCTGTTATGATATCTGATCTGAATTCTGT
1 TCTGATTTCTGACT-TGAATTCTATTATGATATCTGACCTGAATTATGT
*
3276424 TTTGATTTCT
1 TCTGATTTCT
3276434 CACATCTCCG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
47 1 0.02
48 47 0.96
49 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (48 bp):
TCTGATTTCTGACTTGAATTCTATTATGATATCTGACCTGAATTATGT
Found at i:3282858 original size:23 final size:21
Alignment explanation
Indices: 3282828--3282870 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
3282818 TTTGGTGCTG
*
3282828 AAAACAAGTTAAGAAACAAGATT
1 AAAACAAGATAA-AAA-AAGATT
3282851 AAAACAAGATAAAAAAAGAT
1 AAAACAAGATAAAAAAAGAT
3282871 AAAGGAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.67, C:0.07, G:0.12, T:0.14
Consensus pattern (21 bp):
AAAACAAGATAAAAAAAGATT
Found at i:3291642 original size:24 final size:25
Alignment explanation
Indices: 3291615--3291666 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
3291605 AAGAAAAATC
* *
3291615 AGAAAAG-AAAGTGAAGCACTCAAA
1 AGAAAAGAAAAATCAAGCACTCAAA
*
3291639 AG-AAAGAAAAATCCAGCACTCAAA
1 AGAAAAGAAAAATCAAGCACTCAAA
3291663 AGAA
1 AGAA
3291667 GAAAAAGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
23 4 0.17
24 18 0.78
25 1 0.04
ACGTcount: A:0.60, C:0.15, G:0.17, T:0.08
Consensus pattern (25 bp):
AGAAAAGAAAAATCAAGCACTCAAA
Found at i:3294455 original size:11 final size:13
Alignment explanation
Indices: 3294423--3294452 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3294413 TGGCCAAAGA
3294423 TGAAAAGGTATGT
1 TGAAAAGGTATGT
3294436 TGAAAAGGTATG-
1 TGAAAAGGTATGT
3294448 TGAAA
1 TGAAA
3294453 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:3297703 original size:24 final size:24
Alignment explanation
Indices: 3297668--3297722 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
3297658 CTTTCTTTCT
**
3297668 TTTTCTTATTTTTTAGTGCTTAAC
1 TTTTCTTATTTTGGAGTGCTTAAC
* *
3297692 TTTTCTTCTTTTGGAGTGCTTGAC
1 TTTTCTTATTTTGGAGTGCTTAAC
3297716 TTTTCTT
1 TTTTCTT
3297723 GGCTGATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.11, C:0.15, G:0.13, T:0.62
Consensus pattern (24 bp):
TTTTCTTATTTTGGAGTGCTTAAC
Found at i:3304996 original size:23 final size:23
Alignment explanation
Indices: 3304969--3305013 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3304959 TAGTGAAAAG
3304969 ATGAAGATGACAATGGAATGGTA
1 ATGAAGATGACAATGGAATGGTA
* * *
3304992 ATGAATATGGCAATGGGATGGT
1 ATGAAGATGACAATGGAATGGT
3305014 GATAGAGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.04, G:0.33, T:0.24
Consensus pattern (23 bp):
ATGAAGATGACAATGGAATGGTA
Found at i:3305422 original size:19 final size:20
Alignment explanation
Indices: 3305384--3305426 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
3305374 GAACCCCCTT
*
3305384 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
3305404 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
3305423 TGAA
1 TGAA
3305427 GATAAATGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:3308473 original size:26 final size:26
Alignment explanation
Indices: 3308411--3308474 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
3308401 GGTTAGGGTC
* *
3308411 TAGAAATGGCTATGATAGGGGTATAA
1 TAGAAATGGTTATGATAGGGGTAGAA
*
3308437 TAGAAATGGTTATGATAGGGGTAGGA
1 TAGAAATGGTTATGATAGGGGTAGAA
*
3308463 TAGAAAAGGTTA
1 TAGAAATGGTTA
3308475 AGAAATGGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.39, C:0.02, G:0.33, T:0.27
Consensus pattern (26 bp):
TAGAAATGGTTATGATAGGGGTAGAA
Found at i:3308764 original size:17 final size:17
Alignment explanation
Indices: 3308742--3308776 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3308732 GTAGGGGTCA
3308742 TTTTCTT-TTCTTTTTGT
1 TTTTCTTCTT-TTTTTGT
3308759 TTTTCTTCTTTTTTTGT
1 TTTTCTTCTTTTTTTGT
3308776 T
1 T
3308777 GCTTTTGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (17 bp):
TTTTCTTCTTTTTTTGT
Found at i:3308782 original size:20 final size:20
Alignment explanation
Indices: 3308744--3308782 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3308734 AGGGGTCATT
*
3308744 TTCTTTTCTTTTTGTTTTTC
1 TTCTTTTCTTTTTGCTTTTC
3308764 TTCTTTT-TTTGTTGCTTTT
1 TTCTTTTCTTT-TTGCTTTT
3308783 GTTGTAGCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (20 bp):
TTCTTTTCTTTTTGCTTTTC
Found at i:3309606 original size:19 final size:20
Alignment explanation
Indices: 3309565--3309607 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3309555 GAAACCCCTT
*
3309565 TGAAAACACATGATTTCTAA
1 TGAAAACACATAATTTCTAA
*
3309585 TGAAAATACATAATTT-TAA
1 TGAAAACACATAATTTCTAA
3309604 TGAA
1 TGAA
3309608 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (20 bp):
TGAAAACACATAATTTCTAA
Found at i:3313003 original size:20 final size:22
Alignment explanation
Indices: 3312968--3313007 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
3312958 CATGCTTAAT
3312968 CATTCATTTGTTAGCTCATATG
1 CATTCATTTGTTAGCTCATATG
3312990 CATTCA-TT-TTAGCTCATA
1 CATTCATTTGTTAGCTCATA
3313008 GGTCTTACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (22 bp):
CATTCATTTGTTAGCTCATATG
Found at i:3314468 original size:23 final size:24
Alignment explanation
Indices: 3314422--3314479 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 24
3314412 AGTGCATTTC
* *
3314422 ATCAAGTGGCATCAGAAGCCTCAT
1 ATCAAGTGGTATAAGAAGCCTCAT
3314446 ATCAAGTGGTATAAG-AGCCTCAT
1 ATCAAGTGGTATAAGAAGCCTCAT
*
3314469 ATCAAGCGGTA
1 ATCAAGTGGTA
3314480 ATCAGAGCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 18 0.58
24 13 0.42
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.22
Consensus pattern (24 bp):
ATCAAGTGGTATAAGAAGCCTCAT
Found at i:3314612 original size:28 final size:28
Alignment explanation
Indices: 3314581--3314647 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
3314571 AAGAAAAATC
*
3314581 AGAAAAGAAAGTGAAGCACTC-AAAAGAA
1 AGAAAAGAAAGTCAAGCACTCAAAAAG-A
*
3314609 AGAAGAA-AAA-TCCAGCACTCAAAAAGA
1 AGAA-AAGAAAGTCAAGCACTCAAAAAGA
3314636 AGAAAAGCAAAG
1 AGAAAAG-AAAG
3314648 AAAAGGAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
26 2 0.06
27 13 0.41
28 15 0.47
29 2 0.06
ACGTcount: A:0.61, C:0.13, G:0.19, T:0.06
Consensus pattern (28 bp):
AGAAAAGAAAGTCAAGCACTCAAAAAGA
Found at i:3322822 original size:24 final size:21
Alignment explanation
Indices: 3322788--3322830 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
3322778 TCCACAAGAC
*
3322788 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
3322810 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
3322831 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:3327990 original size:23 final size:23
Alignment explanation
Indices: 3327963--3328016 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
3327953 AAAAATCAGA
*
3327963 AAAGAAAGTGAAGCACTCAAAAG
1 AAAGAAAATGAAGCACTCAAAAG
**
3327986 AAAGAAAAATTCAGCACTCAAAAG
1 AAAG-AAAATGAAGCACTCAAAAG
3328010 -AAGAAAA
1 AAAGAAAA
3328017 ACAAAGTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 7 0.26
24 16 0.59
ACGTcount: A:0.61, C:0.13, G:0.17, T:0.09
Consensus pattern (23 bp):
AAAGAAAATGAAGCACTCAAAAG
Found at i:3329178 original size:19 final size:20
Alignment explanation
Indices: 3329154--3329196 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3329144 AGCATTTATC
*
3329154 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
3329173 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
3329193 TTCA
1 TTCA
3329197 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:3333428 original size:15 final size:15
Alignment explanation
Indices: 3333393--3333421 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3333383 GTGCTTCAAC
3333393 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
3333407 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
3333422 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:3335128 original size:35 final size:36
Alignment explanation
Indices: 3335055--3335153 Score: 121
Period size: 35 Copynumber: 2.8 Consensus size: 36
3335045 GTGCTTGCAT
* *
3335055 CATCTTCCATCACCATTTTCAAGCCTATAACATCAC
1 CATCTTCCATTACCATTGTCAAGCCTATAACATCAC
* * *
3335091 CATCTTCCATTACCATTGT-ACGCCTATATCATTAC
1 CATCTTCCATTACCATTGTCAAGCCTATAACATCAC
* *
3335126 CATATTCCATTACCATT-TCATGCCTATA
1 CATCTTCCATTACCATTGTCAAGCCTATA
3335154 TGACCACCAA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
34 1 0.02
35 37 0.67
36 17 0.31
ACGTcount: A:0.28, C:0.32, G:0.04, T:0.35
Consensus pattern (36 bp):
CATCTTCCATTACCATTGTCAAGCCTATAACATCAC
Found at i:3338982 original size:18 final size:18
Alignment explanation
Indices: 3338947--3338995 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 18
3338937 ATAATTGGTT
3338947 TAAGAAATGAATAATAAT-A
1 TAAG-AATGAA-AATAATAA
3338966 TAAGTAATGAAAATAATAA
1 TAAG-AATGAAAATAATAA
3338985 TAAGAATGAAA
1 TAAGAATGAAA
3338996 TGAAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.24
Consensus pattern (18 bp):
TAAGAATGAAAATAATAA
Found at i:3340960 original size:15 final size:15
Alignment explanation
Indices: 3340931--3340973 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3340921 TGCTGCAACA
* *
3340931 AAAAGCAAAAGAAAG
1 AAAAGAAAAAAAAAG
3340946 AAAA-AAAACAAAAAG
1 AAAAGAAAA-AAAAAG
3340961 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
3340974 TACTCCTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 3 0.12
15 17 0.71
16 4 0.17
ACGTcount: A:0.84, C:0.05, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAAAAG
Found at i:3341295 original size:17 final size:17
Alignment explanation
Indices: 3341270--3341302 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3341260 ATTCTACCTC
3341270 TACCATAACCATTTCTA
1 TACCATAACCATTTCTA
*
3341287 TACCCTAACCATTTCT
1 TACCATAACCATTTCT
3341303 TTTTAAGCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.36
Consensus pattern (17 bp):
TACCATAACCATTTCTA
Found at i:3343895 original size:19 final size:20
Alignment explanation
Indices: 3343871--3343913 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3343861 AGCATTTATC
*
3343871 TTCATTA-AAATTATGTATT
1 TTCATTATAAATCATGTATT
*
3343890 TTCATTATAAATCATGTGTT
1 TTCATTATAAATCATGTATT
3343910 TTCA
1 TTCA
3343914 AAGGGGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (20 bp):
TTCATTATAAATCATGTATT
Found at i:3344304 original size:23 final size:23
Alignment explanation
Indices: 3344269--3344328 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
3344259 CACCATCTTC
3344269 CATCACCATTTTTCACGCCTATAA
1 CATCACCA-TTTTCACGCCTATAA
3344293 CATCACCATTTTCACGCCTATAA
1 CATCACCATTTTCACGCCTATAA
3344316 CATCACCATTTTC
1 CATCACCATTTTC
3344329 CATCACCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 28 0.78
24 8 0.22
ACGTcount: A:0.28, C:0.35, G:0.03, T:0.33
Consensus pattern (23 bp):
CATCACCATTTTCACGCCTATAA
Found at i:3344355 original size:35 final size:35
Alignment explanation
Indices: 3344293--3344383 Score: 128
Period size: 35 Copynumber: 2.6 Consensus size: 35
3344283 ACGCCTATAA
*
3344293 CATCACCATTTTCACGCCTATAACATCACCATTTTC
1 CATCACCA-TTTCACGCCTATAACATCACCATCTTC
* * *
3344329 CATCACCATTGCACACCTATATCATCACCATCTTC
1 CATCACCATTTCACGCCTATAACATCACCATCTTC
*
3344364 TATCACCATTTCACGCCTAT
1 CATCACCATTTCACGCCTAT
3344384 TTAACCACCA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 40 0.83
36 8 0.17
ACGTcount: A:0.27, C:0.37, G:0.03, T:0.32
Consensus pattern (35 bp):
CATCACCATTTCACGCCTATAACATCACCATCTTC
Found at i:3344393 original size:35 final size:34
Alignment explanation
Indices: 3344293--3344394 Score: 98
Period size: 35 Copynumber: 2.9 Consensus size: 34
3344283 ACGCCTATAA
*
3344293 CATCACCATTTTCACGCCTA-TAACATCACCATTTTC
1 CATCACCA-TTTCACGCCTATTAAC--CACCATCTTC
* * * *
3344329 CATCACCATTGCACACCTATATCATCACCATCTTC
1 CATCACCATTTCACGCCTAT-TAACCACCATCTTC
*
3344364 TATCACCATTTCACGCCTATTTAACCACCAT
1 CATCACCATTTCACGCCTA-TTAACCACCAT
3344395 TCCCTTACCA
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
35 42 0.79
36 9 0.17
37 2 0.04
ACGTcount: A:0.28, C:0.37, G:0.03, T:0.31
Consensus pattern (34 bp):
CATCACCATTTCACGCCTATTAACCACCATCTTC
Found at i:3344550 original size:16 final size:16
Alignment explanation
Indices: 3344529--3344564 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3344519 CTTTGATAAC
3344529 ATTTTTATCCATTTCA
1 ATTTTTATCCATTTCA
* *
3344545 ATTTTTTTCCATTTCC
1 ATTTTTATCCATTTCA
3344561 ATTT
1 ATTT
3344565 CCTTTTCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTTATCCATTTCA
Found at i:3353364 original size:33 final size:33
Alignment explanation
Indices: 3353322--3353390 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
3353312 GTTGATGAAT
*
3353322 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
3353355 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
3353388 GAA
1 GAA
3353391 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:3362331 original size:19 final size:19
Alignment explanation
Indices: 3362307--3362344 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3362297 ATAATAATAC
3362307 ATTTATTTACCGATTTTAT
1 ATTTATTTACCGATTTTAT
3362326 ATTTATTTACCGATTTTAT
1 ATTTATTTACCGATTTTAT
3362345 TGAATAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.58
Consensus pattern (19 bp):
ATTTATTTACCGATTTTAT
Found at i:3364945 original size:24 final size:24
Alignment explanation
Indices: 3364891--3364945 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
3364881 AAAAAATCAG
*
3364891 AAAAG-AAGCACTCAAAAAGAAGA
1 AAAAGAAAACACTCAAAAAGAAGA
**
3364914 AATTGAAAACACTC-AAAAGAAGAA
1 AAAAGAAAACACTCAAAAAGAAG-A
3364938 AAAAGAAA
1 AAAAGAAA
3364946 GAAAATTTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.67, C:0.11, G:0.15, T:0.07
Consensus pattern (24 bp):
AAAAGAAAACACTCAAAAAGAAGA
Found at i:3372654 original size:21 final size:21
Alignment explanation
Indices: 3372615--3372654 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3372605 ATGTATTCTT
* * *
3372615 ATTAGCTCATAGACTTTATAC
1 ATTAGCTCACACACATTATAC
3372636 ATTAGCTCACACACATTAT
1 ATTAGCTCACACACATTAT
3372655 GAGATGATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (21 bp):
ATTAGCTCACACACATTATAC
Found at i:3376142 original size:201 final size:201
Alignment explanation
Indices: 3375797--3376204 Score: 807
Period size: 201 Copynumber: 2.0 Consensus size: 201
3375787 GCCAGAATTC
3375797 TTATGGTTGAAAAACTTGGTTTAACAACATCAAAACATCCCACTCCATATAAACTCCAATGGTTC
1 TTATGGTTGAAAAACTTGGTTTAACAACATCAAAACATCCCACTCCATATAAACTCCAATGGTTC
3375862 AATGAAGGAGGTGAGTTGAACGTTACCAAACAGGTTCTAATTCCTTTTTCAGTTGGTAGGTATAA
66 AATGAAGGAGGTGAGTTGAACGTTACCAAACAGGTTCTAATTCCTTTTTCAGTTGGTAGGTATAA
3375927 GGATGAGGAGCTTTGTGACATTGTCTGATACGATCATGCCAAGGGCCAAACTTCTTCAACACATG
131 GGATGAGGAGCTTTGTGACATTGTCTGATACGATCATGCCAAGGGCCAAACTTCTTCAACACATG
3375992 ATCACT
196 ATCACT
3375998 TTATGGTTGAAAAACTTGGTTTAACAACATCAAAACATCCCACTCCATATAAACTCCAATGGTTC
1 TTATGGTTGAAAAACTTGGTTTAACAACATCAAAACATCCCACTCCATATAAACTCCAATGGTTC
3376063 AATGAAGGAGGTGAGTTGAACGTTACCAAACAGGTTCTAATTCCTTTTTCAGTTGGTAGGTATAA
66 AATGAAGGAGGTGAGTTGAACGTTACCAAACAGGTTCTAATTCCTTTTTCAGTTGGTAGGTATAA
3376128 GGATGAGGAGCTTTGTGACATTGTCTGATACGATCATGCCAAGGGCCAAACTTCTTCAACACATG
131 GGATGAGGAGCTTTGTGACATTGTCTGATACGATCATGCCAAGGGCCAAACTTCTTCAACACATG
3376193 ATCACT
196 ATCACT
*
3376199 TCATGG
1 TTATGG
3376205 AGGTTTTGCC
Statistics
Matches: 206, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 206 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (201 bp):
TTATGGTTGAAAAACTTGGTTTAACAACATCAAAACATCCCACTCCATATAAACTCCAATGGTTC
AATGAAGGAGGTGAGTTGAACGTTACCAAACAGGTTCTAATTCCTTTTTCAGTTGGTAGGTATAA
GGATGAGGAGCTTTGTGACATTGTCTGATACGATCATGCCAAGGGCCAAACTTCTTCAACACATG
ATCACT
Found at i:3378066 original size:31 final size:31
Alignment explanation
Indices: 3378031--3378132 Score: 82
Period size: 31 Copynumber: 3.2 Consensus size: 31
3378021 TTCCTTTTCT
3378031 TCCTTTTATAAGACCACCCTTCATTATTCAA
1 TCCTTTTATAAGACCACCCTTCATTATTCAA
* *** * *
3378062 TCCTTGCATAGTAAGTGAACCTTTCTTCCTT-TTC-T
1 TCCTT--TTA-TAA--G-ACCACCCTTCATTATTCAA
3378097 TCCTTTTATAAGACCACCCTTCATTATTCAA
1 TCCTTTTATAAGACCACCCTTCATTATTCAA
3378128 TCCTT
1 TCCTT
3378133 CTACCTTTCT
Statistics
Matches: 51, Mismatches: 12, Indels: 16
0.65 0.15 0.20
Matches are distributed among these distances:
29 9 0.18
30 4 0.08
31 10 0.20
32 3 0.06
33 4 0.08
34 3 0.06
35 5 0.10
36 4 0.08
37 9 0.18
ACGTcount: A:0.24, C:0.28, G:0.06, T:0.42
Consensus pattern (31 bp):
TCCTTTTATAAGACCACCCTTCATTATTCAA
Found at i:3378081 original size:66 final size:66
Alignment explanation
Indices: 3377999--3378132 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
3377989 GTGAGTATCT
3377999 TTGCATAGTAAGTGAACCTTTCTTCCTTTTCTTCCTTTTATAAGACCACCCTTCATTATTCAATC
1 TTGCATAGTAAGTGAACCTTTCTTCCTTTTCTTCCTTTTATAAGACCACCCTTCATTATTCAATC
3378064 C
66 C
3378065 TTGCATAGTAAGTGAACCTTTCTTCCTTTTCTTCCTTTTATAAGACCACCCTTCATTATTCAATC
1 TTGCATAGTAAGTGAACCTTTCTTCCTTTTCTTCCTTTTATAAGACCACCCTTCATTATTCAATC
3378130 C
66 C
3378131 TT
1 TT
3378133 CTACCTTTCT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.22, C:0.27, G:0.07, T:0.43
Consensus pattern (66 bp):
TTGCATAGTAAGTGAACCTTTCTTCCTTTTCTTCCTTTTATAAGACCACCCTTCATTATTCAATC
C
Found at i:3380411 original size:20 final size:17
Alignment explanation
Indices: 3380388--3380462 Score: 77
Period size: 15 Copynumber: 4.5 Consensus size: 17
3380378 AAATTTTGGC
*
3380388 TTTTTTGGCTCTTTTTTT
1 TTTTTTTGC-CTTTTTTT
3380406 ATTTTTTTGCC--TTTTT
1 -TTTTTTTGCCTTTTTTT
3380422 TTTTTTTGCCTTTTTTT
1 TTTTTTTGCCTTTTTTT
*
3380439 GTTTTTTG--TTTTTTT
1 TTTTTTTGCCTTTTTTT
3380454 GTTTTTTTG
1 -TTTTTTTG
3380463 AAAAAAAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
15 17 0.34
16 12 0.24
17 12 0.24
18 1 0.02
19 8 0.16
ACGTcount: A:0.01, C:0.08, G:0.11, T:0.80
Consensus pattern (17 bp):
TTTTTTTGCCTTTTTTT
Found at i:3380435 original size:33 final size:34
Alignment explanation
Indices: 3380388--3380462 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 34
3380378 AAATTTTGGC
* *
3380388 TTTTTTGGCTCTTTTTTTATTTTTTTGCCTTTTT-
1 TTTTTTTGCTCTTTTTTT-GTTTTTTGCCTTTTTG
**
3380422 TTTTTTTGC-CTTTTTTTGTTTTTTGTTTTTTTG
1 TTTTTTTGCTCTTTTTTTGTTTTTTGCCTTTTTG
3380455 TTTTTTTG
1 TTTTTTTG
3380463 AAAAAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 12 0.33
33 16 0.44
34 8 0.22
ACGTcount: A:0.01, C:0.08, G:0.11, T:0.80
Consensus pattern (34 bp):
TTTTTTTGCTCTTTTTTTGTTTTTTGCCTTTTTG
Found at i:3380443 original size:8 final size:8
Alignment explanation
Indices: 3380399--3380462 Score: 69
Period size: 8 Copynumber: 8.0 Consensus size: 8
3380389 TTTTTGGCTC
*
3380399 TTTTTTTA
1 TTTTTTTG
3380407 TTTTTTTG
1 TTTTTTTG
**
3380415 CCTTTTT-
1 TTTTTTTG
3380422 TTTTTTTG
1 TTTTTTTG
3380430 CCTTTTTTTG
1 --TTTTTTTG
3380440 -TTTTTTG
1 TTTTTTTG
3380447 TTTTTTTG
1 TTTTTTTG
3380455 TTTTTTTG
1 TTTTTTTG
3380463 AAAAAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
7 12 0.26
8 27 0.57
10 8 0.17
ACGTcount: A:0.02, C:0.06, G:0.09, T:0.83
Consensus pattern (8 bp):
TTTTTTTG
Found at i:3397283 original size:29 final size:29
Alignment explanation
Indices: 3397251--3397306 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
3397241 TCTCTTTTTC
3397251 TTTTCTTT-TCTACTTTTCT-TCTTTTCTGA
1 TTTT-TTTCTCTACTTTT-TGTCTTTTCTGA
*
3397280 TTTTTTTCTCTTCTTTTTGTCTTTTCT
1 TTTTTTTCTCTACTTTTTGTCTTTTCT
3397307 TTCTTTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.04, C:0.20, G:0.04, T:0.73
Consensus pattern (29 bp):
TTTTTTTCTCTACTTTTTGTCTTTTCTGA
Found at i:3397288 original size:16 final size:16
Alignment explanation
Indices: 3397251--3397293 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
3397241 TCTCTTTTTC
3397251 TTTTCTTTTCTACTTT
1 TTTTCTTTTCTACTTT
*
3397267 TCTTCTTTTCTGA-TTT
1 TTTTCTTTTCT-ACTTT
*
3397283 TTTTCTCTTCT
1 TTTTCTTTTCT
3397294 TTTTGTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 22 0.96
17 1 0.04
ACGTcount: A:0.05, C:0.21, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTTCTTTTCTACTTT
Found at i:3397304 original size:21 final size:22
Alignment explanation
Indices: 3397263--3397310 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
3397253 TTCTTTTCTA
3397263 CTTT-TCTTCTTTTCTGATTTT
1 CTTTCTCTTCTTTTCTGATTTT
*
3397284 -TTTCTCTTCTTTT-TGTCTTTT
1 CTTTCTCTTCTTTTCTG-ATTTT
3397305 CTTTCT
1 CTTTCT
3397311 TTTTGTACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 5 0.22
21 13 0.57
22 5 0.22
ACGTcount: A:0.02, C:0.21, G:0.04, T:0.73
Consensus pattern (22 bp):
CTTTCTCTTCTTTTCTGATTTT
Found at i:3397312 original size:17 final size:18
Alignment explanation
Indices: 3397283--3397316 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3397273 TTTCTGATTT
3397283 TTTTCTCTTCTTTTTGTC
1 TTTTCTCTTCTTTTTGTC
3397301 TTTTCT-TTCTTTTTGT
1 TTTTCTCTTCTTTTTGT
3397317 ACTCCAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.00, C:0.18, G:0.06, T:0.76
Consensus pattern (18 bp):
TTTTCTCTTCTTTTTGTC
Found at i:3397313 original size:29 final size:29
Alignment explanation
Indices: 3397239--3397314 Score: 68
Period size: 29 Copynumber: 2.6 Consensus size: 29
3397229 TCCTTTTGAA
* *
3397239 CTTCTCTT-TTTCTTTTCTTTTCTACTTTT
1 CTTCTTTTCTTTCTTTT-TTCTCTACTTTT
* *
3397268 CTTCTTTTCTGAT-TTTTTTCTCTTCTTTT
1 CTTCTTTTCT-TTCTTTTTTCTCTACTTTT
3397297 -TGTCTTTTCTTTCTTTTT
1 CT-TCTTTTCTTTCTTTTT
3397315 GTACTCCAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
28 2 0.05
29 30 0.79
30 5 0.13
31 1 0.03
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74
Consensus pattern (29 bp):
CTTCTTTTCTTTCTTTTTTCTCTACTTTT
Found at i:3398008 original size:20 final size:19
Alignment explanation
Indices: 3397983--3398032 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
3397973 GCTGAATGGT
*
3397983 TACATGATGTTTCGGATAGA
1 TACATGATGTTTAGGA-AGA
*
3398003 TACATGA-CTTTAGGAAGA
1 TACATGATGTTTAGGAAGA
*
3398021 TACATAATGTTT
1 TACATGATGTTT
3398033 TAAAATGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 9 0.36
19 9 0.36
20 7 0.28
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (19 bp):
TACATGATGTTTAGGAAGA
Found at i:3403389 original size:5 final size:5
Alignment explanation
Indices: 3403379--3403438 Score: 54
Period size: 5 Copynumber: 11.8 Consensus size: 5
3403369 GAACTTCTCT
*
3403379 TTTTC TTTTC TTTTC TTCTT- TTCTTC TTTTC TTCTC TTCTT- TTTGTC
1 TTTTC TTTTC TTTTC TT-TTC TT-TTC TTTTC TTTTC TT-TTC TTT-TC
3403426 TTTTC TTTT- TTTT
1 TTTTC TTTTC TTTT
3403439 GCACTCCAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
4 5 0.10
5 35 0.73
6 8 0.17
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:3403389 original size:13 final size:12
Alignment explanation
Indices: 3403373--3403436 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 12
3403363 CTTTTTGAAC
3403373 TTCTCTTTTTCTT
1 TTCT-TTTTTCTT
3403386 TTCTTTTCTTCTT
1 TTCTTTT-TTCTT
3403399 TTCTTCTTTTCTTCT
1 TTCTT-TTTTC-T-T
3403414 CTTCTTTTTGTCTT
1 -TTCTTTTT-TCTT
3403428 TTCTTTTTT
1 TTCTTTTTT
3403437 TTGCACTCCA
Statistics
Matches: 45, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
12 4 0.09
13 25 0.56
14 4 0.09
15 5 0.11
16 7 0.16
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.77
Consensus pattern (12 bp):
TTCTTTTTTCTT
Found at i:3403397 original size:8 final size:8
Alignment explanation
Indices: 3403386--3403419 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
3403376 TCTTTTTCTT
3403386 TTCTTTTC
1 TTCTTTTC
3403394 TTCTTTTC
1 TTCTTTTC
3403402 TTCTTTTC
1 TTCTTTTC
*
3403410 TTCTCTTC
1 TTCTTTTC
3403418 TT
1 TT
3403420 TTTGTCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (8 bp):
TTCTTTTC
Found at i:3403405 original size:16 final size:16
Alignment explanation
Indices: 3403382--3403432 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
3403372 CTTCTCTTTT
3403382 TCTT-TTCTTTTCTTC
1 TCTTCTTCTTTTCTTC
*
3403397 TTTTCTTCTTTTCTTC
1 TCTTCTTCTTTTCTTC
*
3403413 TCTTCTT-TTTGTCTTT
1 TCTTCTTCTTT-TCTTC
3403429 TCTT
1 TCTT
3403433 TTTTTTGCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 6 0.19
16 25 0.81
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTTCTTCTTTTCTTC
Found at i:3403405 original size:21 final size:20
Alignment explanation
Indices: 3403372--3403434 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 20
3403362 TCTTTTTGAA
3403372 CTTCTCTTTTTCTTTTCTTTT
1 CTTCT-TTTTTCTTTTCTTTT
*
3403393 CTTCTTTTCTTCTTTTCTTCT
1 CTTCTTTT-TTCTTTTCTTTT
3403414 CTTCTTTTTGTCTTTTCTTTT
1 CTTCTTTTT-TCTTTTCTTTT
3403435 TTTTGCACTC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.11
21 34 0.89
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.75
Consensus pattern (20 bp):
CTTCTTTTTTCTTTTCTTTT
Found at i:3405496 original size:24 final size:24
Alignment explanation
Indices: 3405444--3405501 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
3405434 CTTTTCTTTG
*
3405444 CTTTTC-TTCTTTTTGAGTGCTGGA
1 CTTTTCTTTC-TTTTGAGTGCTGCA
* *
3405468 TTTTTCTTTCTTTTGAGTGCTTCA
1 CTTTTCTTTCTTTTGAGTGCTGCA
3405492 CTTTT-TTTCT
1 CTTTTCTTTCT
3405502 GATTTTTCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 5 0.17
24 21 0.72
25 3 0.10
ACGTcount: A:0.07, C:0.17, G:0.14, T:0.62
Consensus pattern (24 bp):
CTTTTCTTTCTTTTGAGTGCTGCA
Found at i:3406347 original size:17 final size:17
Alignment explanation
Indices: 3406325--3406358 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3406315 TAAATGGCTC
3406325 TTCATCTTGGCGCCTAA
1 TTCATCTTGGCGCCTAA
3406342 TTCATCTTGGCGCCTAA
1 TTCATCTTGGCGCCTAA
3406359 ATGAACCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (17 bp):
TTCATCTTGGCGCCTAA
Found at i:3410703 original size:13 final size:13
Alignment explanation
Indices: 3410685--3410710 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3410675 AACACCTTTG
3410685 ACATACCTTTTCA
1 ACATACCTTTTCA
3410698 ACATACCTTTTCA
1 ACATACCTTTTCA
3410711 TCTTTAGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATACCTTTTCA
Found at i:3413528 original size:32 final size:31
Alignment explanation
Indices: 3413469--3413530 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 31
3413459 TTTCATTGCT
*
3413469 TTTCTTCCTTTTGAGTGCTGGATTTTCTTTC
1 TTTCTTCCTTTTGAGTGCTGGAATTTCTTTC
* **
3413500 TTTCTTTCTTTTTGAGTGCTTTAATTTCTTT
1 TTTC-TTCCTTTTGAGTGCTGGAATTTCTTT
3413531 TCCGATTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 4 0.15
32 22 0.85
ACGTcount: A:0.08, C:0.16, G:0.13, T:0.63
Consensus pattern (31 bp):
TTTCTTCCTTTTGAGTGCTGGAATTTCTTTC
Found at i:3416008 original size:21 final size:21
Alignment explanation
Indices: 3415969--3416008 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3415959 ATGCATTATT
* * *
3415969 ATTAGCTCATAGACTTTATAC
1 ATTAGCTCACACACATTATAC
3415990 ATTAGCTCACACACATTAT
1 ATTAGCTCACACACATTAT
3416009 GAGATAATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (21 bp):
ATTAGCTCACACACATTATAC
Found at i:3422742 original size:17 final size:17
Alignment explanation
Indices: 3422720--3422752 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3422710 ACAAAAAGCA
3422720 AAAAGA-AAGAAGAAAAC
1 AAAAGAGAA-AAGAAAAC
3422737 AAAAGAGAAAAGAAAA
1 AAAAGAGAAAAGAAAA
3422753 GACTCCTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAGAGAAAAGAAAAC
Found at i:3443530 original size:14 final size:14
Alignment explanation
Indices: 3443511--3443541 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3443501 TGATGAATTA
3443511 ATGAATAAATCTTC
1 ATGAATAAATCTTC
*
3443525 ATGAATATATCTTC
1 ATGAATAAATCTTC
3443539 ATG
1 ATG
3443542 GCTGAATCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (14 bp):
ATGAATAAATCTTC
Found at i:3449838 original size:10 final size:10
Alignment explanation
Indices: 3449825--3449849 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3449815 AAATTTTGGC
3449825 TTTTTTGTTT
1 TTTTTTGTTT
3449835 TTTTTTGTTT
1 TTTTTTGTTT
3449845 TTTTT
1 TTTTT
3449850 GTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:3455145 original size:34 final size:34
Alignment explanation
Indices: 3455101--3455169 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
3455091 TTTTCATTCA
3455101 TCAACACATGTCATGCATGTTAATTATCTCATAT
1 TCAACACATGTCATGCATGTTAATTATCTCATAT
* *
3455135 TCAACCCATGTCATGCATGTTAATTATTTCATAT
1 TCAACACATGTCATGCATGTTAATTATCTCATAT
3455169 T
1 T
3455170 AGTTTTGCAT
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:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (34 bp):
TCAACACATGTCATGCATGTTAATTATCTCATAT
Found at i:3473789 original size:19 final size:20
Alignment explanation
Indices: 3473748--3473798 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
3473738 GAAACCCCTT
*
3473748 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
3473768 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
3473787 TGAAGATACATG
1 TGAAAATACATG
3473799 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:3474748 original size:30 final size:31
Alignment explanation
Indices: 3474708--3474767 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
3474698 ACATGCTGCC
**
3474708 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
3474739 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
3474768 TAAAGCTATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:3477968 original size:19 final size:20
Alignment explanation
Indices: 3477927--3477977 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
3477917 GAAACCCCTT
*
3477927 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
3477947 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
3477966 TGAAGATACATG
1 TGAAAATACATG
3477978 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:3478927 original size:30 final size:31
Alignment explanation
Indices: 3478887--3478946 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
3478877 ACATGCTGCC
**
3478887 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
3478918 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
3478947 TAAAGCTATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:3479513 original size:34 final size:34
Alignment explanation
Indices: 3479474--3479542 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
3479464 TTTTCATTCA
3479474 TCAACACATGCCATGCATGTTAATTATCTCATAT
1 TCAACACATGCCATGCATGTTAATTATCTCATAT
* *
3479508 TCAACACATGTCATGCATGTTAATTATTTCATAT
1 TCAACACATGCCATGCATGTTAATTATCTCATAT
3479542 T
1 T
3479543 AGTTTTGCAT
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:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (34 bp):
TCAACACATGCCATGCATGTTAATTATCTCATAT
Found at i:3485864 original size:13 final size:11
Alignment explanation
Indices: 3485823--3485907 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
3485813 ACAATCTGTC
3485823 CATCACCATTAT
1 CATCACCA-TAT
*
3485835 CA-CGCCTATAT
1 CATCACC-ATAT
3485846 CATCACCATAGT
1 CATCACCATA-T
3485858 CCATCACCATTAT
1 -CATCACCA-TAT
*
3485871 CA-CGCCTATAT
1 CATCACC-ATAT
3485882 CATCACCATATT
1 CATCACCATA-T
3485894 CCATCACCATAT
1 -CATCACCATAT
3485906 CA
1 CA
3485908 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:3485867 original size:36 final size:36
Alignment explanation
Indices: 3485820--3485924 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
3485810 GATACAATCT
3485820 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
3485856 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
3485892 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
3485925 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:3486090 original size:15 final size:15
Alignment explanation
Indices: 3486066--3486101 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3486056 TTTGATAACT
*
3486066 ATTCTATCCATTTCA
1 ATTCTTTCCATTTCA
3486081 ATTCTTTCCATTTCA
1 ATTCTTTCCATTTCA
*
3486096 TTTCTT
1 ATTCTT
3486102 AATTATCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTCTTTCCATTTCA
Found at i:3486379 original size:11 final size:11
Alignment explanation
Indices: 3486363--3486403 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
3486353 TTTGGAGTGC
3486363 AAAAGAAAAGA
1 AAAAGAAAAGA
3486374 AAAAG--AAGA
1 AAAAGAAAAGA
**
3486383 AAATCAAAAGA
1 AAAAGAAAAGA
3486394 AAAAGAAAAG
1 AAAAGAAAAG
3486404 TGAAGCAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
9 7 0.29
11 17 0.71
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:3491049 original size:46 final size:49
Alignment explanation
Indices: 3490968--3491077 Score: 113
Period size: 46 Copynumber: 2.3 Consensus size: 49
3490958 ATAACTAATG
*
3490968 AATAAAATAATAATAATAAACTAAACATATATTAA-C-T-CTAATTCCT
1 AATAAAATAATAATAATAAAATAAACATATATTAACCATACTAATTCCT
* * *
3491014 AATAAAATAATAATAACTAAAGAT-AATAT-TTTTAACCCAATATTAATTCCT
1 AATAAAATAATAATAA-TAAA-ATAAACATATATTAA-CC-ATACTAATTCCT
3491065 AATAAAATAATAA
1 AATAAAATAATAA
3491078 ATCTAATCCT
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
46 21 0.40
47 8 0.15
48 2 0.04
50 1 0.02
51 21 0.40
ACGTcount: A:0.55, C:0.11, G:0.01, T:0.33
Consensus pattern (49 bp):
AATAAAATAATAATAATAAAATAAACATATATTAACCATACTAATTCCT
Found at i:3492147 original size:9 final size:9
Alignment explanation
Indices: 3492133--3492168 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
3492123 AAGTATGGGT
3492133 AGAAATATC
1 AGAAATATC
3492142 AGAAATATC
1 AGAAATATC
*
3492151 AAAAATATC
1 AGAAATATC
3492160 AGAAATATC
1 AGAAATATC
3492169 CTAGTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.58, C:0.11, G:0.08, T:0.22
Consensus pattern (9 bp):
AGAAATATC
Found at i:3494791 original size:11 final size:11
Alignment explanation
Indices: 3494777--3494836 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
3494767 AAATTTTGGC
3494777 TTTTTTGGCTTT
1 TTTTTTGGC-TT
**
3494789 TTTTTTACCTT
1 TTTTTTGGCTT
*
3494800 TTTTTTGCCTT
1 TTTTTTGGCTT
* *
3494811 TTTTTTTGTTT
1 TTTTTTGGCTT
*
3494822 TTTTTTTG-TT
1 TTTTTTGGCTT
3494832 TTTTT
1 TTTTT
3494837 GAAGAAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
10 7 0.17
11 28 0.67
12 7 0.17
ACGTcount: A:0.02, C:0.08, G:0.08, T:0.82
Consensus pattern (11 bp):
TTTTTTGGCTT
Found at i:3494794 original size:12 final size:12
Alignment explanation
Indices: 3494777--3494829 Score: 56
Period size: 11 Copynumber: 4.6 Consensus size: 12
3494767 AAATTTTGGC
3494777 TTTTTTGGCTTT
1 TTTTTTGGCTTT
* *
3494789 TTTTTT-ACCTT
1 TTTTTTGGCTTT
*
3494800 TTTTTTGCCTTT
1 TTTTTTGGCTTT
*
3494812 TTTTTT-GTTTT
1 TTTTTTGGCTTT
3494823 TTTTTTG
1 TTTTTTG
3494830 TTTTTTTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
11 18 0.55
12 15 0.45
ACGTcount: A:0.02, C:0.09, G:0.09, T:0.79
Consensus pattern (12 bp):
TTTTTTGGCTTT
Found at i:3494824 original size:23 final size:22
Alignment explanation
Indices: 3494777--3494836 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
3494767 AAATTTTGGC
*
3494777 TTTTTTGGCTTTTTTTTTACCT
1 TTTTTTTGCTTTTTTTTTACCT
***
3494799 TTTTTTTGCCTTTTTTTTTGTTT
1 TTTTTTTG-CTTTTTTTTTACCT
3494822 TTTTTTTG-TTTTTTT
1 TTTTTTTGCTTTTTTT
3494837 GAAGAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 7 0.21
22 7 0.21
23 19 0.58
ACGTcount: A:0.02, C:0.08, G:0.08, T:0.82
Consensus pattern (22 bp):
TTTTTTTGCTTTTTTTTTACCT
Found at i:3494834 original size:12 final size:11
Alignment explanation
Indices: 3494798--3494836 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
3494788 TTTTTTTACC
*
3494798 TTTTTTTTGCCT
1 TTTTTTTTG-TT
3494810 TTTTTTTTGTT
1 TTTTTTTTGTT
3494821 TTTTTTTTGTT
1 TTTTTTTTGTT
3494832 TTTTT
1 TTTTT
3494837 GAAGAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:3497011 original size:36 final size:35
Alignment explanation
Indices: 3496964--3497068 Score: 149
Period size: 36 Copynumber: 2.9 Consensus size: 35
3496954 AATACAATAT
3496964 GTCCATCACCATTATCACGTCTATATCATCACCATA
1 GTCCATCACCATTATCACG-CTATATCATCACCATA
3497000 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACG-CTATATCATCACCATA
* * *
3497036 TTCCATCACTA-TATCACGCATATATTATCACCA
1 GTCCATCACCATTATCACGC-TATATCATCACCA
3497069 ACTTATAAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
34 1 0.02
35 19 0.30
36 44 0.69
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.30
Consensus pattern (35 bp):
GTCCATCACCATTATCACGCTATATCATCACCATA
Found at i:3497036 original size:11 final size:11
Alignment explanation
Indices: 3496986--3497051 Score: 53
Period size: 13 Copynumber: 5.5 Consensus size: 11
3496976 TATCACGTCT
3496986 ATATCATCACC
1 ATATCATCACC
3496997 ATAGTCCATCACC
1 ATA-T-CATCACC
*
3497010 ATTATCA-CGCC
1 A-TATCATCACC
3497021 TATATCATCACC
1 -ATATCATCACC
*
3497033 ATATTCCATCACT
1 ATA-T-CATCACC
3497046 ATATCA
1 ATATCA
3497052 CGCATATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
11 16 0.36
12 9 0.20
13 18 0.40
14 2 0.04
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (11 bp):
ATATCATCACC
Found at i:3497234 original size:15 final size:15
Alignment explanation
Indices: 3497210--3497239 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3497200 TTAGATAACT
3497210 ATTCTATCCATTTCA
1 ATTCTATCCATTTCA
*
3497225 ATTCTTTCCATTTCA
1 ATTCTATCCATTTCA
3497240 TTTTTTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTCTATCCATTTCA
Found at i:3501727 original size:679 final size:679
Alignment explanation
Indices: 3500430--3501791 Score: 2625
Period size: 679 Copynumber: 2.0 Consensus size: 679
3500420 CCACCAAACT
3500430 AAGGCATAGTCCACGAATTCCATAGCAGCAAGCCTGACCTTCTTTTGCTCCATATAATTTTGGCA
1 AAGGCATAGTCCACGAATTCCATAGCAGCAAGCCTGACCTTCTTTTGCTCCATATAATTTTGGCA
*
3500495 TTCAAAAATGTGTTCAATCTTGATTACCCAATCAAGATAGGCTTCAGGATTAGTTCGTCCTTGAA
66 TTCAAAAATGTGTTCAATCTTGATTACCCAATCAAGATAGGCTTCAGGATCAGTTCGTCCTTGAA
3500560 ATAGAGGAATGGTCACTTTGATGTTGCTGAAGTTGTCATTCTGATTTCGATGACCATCTCTTCGT
131 ATAGAGGAATGGTCACTTTGATGTTGCTGAAGTTGTCATTCTGATTTCGATGACCATCTCTTCGT
3500625 GCTACTGATGTTACTTCAGCCTCCTCTTCTTCGAATTCTTCTTCCATTCTAGGGAGATTTACTCT
196 GCTACTGATGTTACTTCAGCCTCCTCTTCTTCGAATTCTTCTTCCATTCTAGGGAGATTTACTCT
3500690 TCGATTCCCTAAAGATGCTTCAAATTGGTCCATACGATCATGCAAAGGCTCCAATTCTAATTTTA
261 TCGATTCCCTAAAGATGCTTCAAATTGGTCCATACGATCATGCAAAGGCTCCAATTCTAATTTTA
3500755 GATATCTGGCCATTTCATGCATGATTGCTTGAGTTTGTAAATTAGGGGCATCACTTTCAGGGGTT
326 GATATCTGGCCATTTCATGCATGATTGCTTGAGTTTGTAAATTAGGGGCATCACTTTCAGGGGTT
3500820 CATCCTAGACTTCAAGACATGGTTAGTGAAATAAGAAAAGAATAAGATGTGTAAAAGACCTTACC
391 CATCCTAGACTTCAAGACATGGTTAGTGAAATAAGAAAAGAATAAGATGTGTAAAAGACCTTACC
3500885 AGAATGTACTCTCACAAAGCCTCACGAGTCACTCCAAGGAAACTTGAATGTCACTCAATCCGCTC
456 AGAATGTACTCTCACAAAGCCTCACGAGTCACTCCAAGGAAACTTGAATGTCACTCAATCCGCTC
3500950 GTGTTTGCACTCTAGGACTTAATAATGGCTTTTACTTGTCCTCTTCTGATCTCACACACGCTCCA
521 GTGTTTGCACTCTAGGACTTAATAATGGCTTTTACTTGTCCTCTTCTGATCTCACACACGCTCCA
* *
3501015 GCCTTTTTCCTCTCAATTCTCTTATCCCAAGTTCTAGAGAACTTTACTCAAGATCGTATTAAGTA
586 GCCTTTTTCCTCTCAATTCTCTTATCCCAAGTTCTAGAGAACTTTACTCAAGACCGTATCAAGTA
3501080 AATTTCTACTTGTTTGGCGTCGGCTGTAA
651 AATTTCTACTTGTTTGGCGTCGGCTGTAA
* *
3501109 AAGGCATATTCCATGAATTCCATAGCAGCAAGCCTGACCTTCTTTTGCTCCATATAATTTTGGCA
1 AAGGCATAGTCCACGAATTCCATAGCAGCAAGCCTGACCTTCTTTTGCTCCATATAATTTTGGCA
3501174 TTCAAAAATGTGTTCAATCTTGATTACCCAATCAAGATAGGCTTCAGGATCAGTTCGTCCTTGAA
66 TTCAAAAATGTGTTCAATCTTGATTACCCAATCAAGATAGGCTTCAGGATCAGTTCGTCCTTGAA
3501239 ATAGAGGAATGGTCACTTTGATGTTGCTGAAGTTGTCATTCTGATTTCGATGACCATCTCTTCGT
131 ATAGAGGAATGGTCACTTTGATGTTGCTGAAGTTGTCATTCTGATTTCGATGACCATCTCTTCGT
3501304 GCTACTGATGTTACTTCAGCCTCCTCTTCTTCGAATTCTTCTTCCATTCTAGGGAGATTTACTCT
196 GCTACTGATGTTACTTCAGCCTCCTCTTCTTCGAATTCTTCTTCCATTCTAGGGAGATTTACTCT
3501369 TCGATTCCCTAAAGATGCTTCAAATTGGTCCATACGATCATGCAAAGGCTCCAATTCTAATTTTA
261 TCGATTCCCTAAAGATGCTTCAAATTGGTCCATACGATCATGCAAAGGCTCCAATTCTAATTTTA
3501434 GATATCTGGCCATTTCATGCATGATTGCTTGAGTTTGTAAATTAGGGGCATCACTTTCAGGGGTT
326 GATATCTGGCCATTTCATGCATGATTGCTTGAGTTTGTAAATTAGGGGCATCACTTTCAGGGGTT
*
3501499 CATCCTAGACTTCGAGACATGGTTAGTGAAATAAGAAAAGAATAAGATGTGTAAAAGACCTTACC
391 CATCCTAGACTTCAAGACATGGTTAGTGAAATAAGAAAAGAATAAGATGTGTAAAAGACCTTACC
* *
3501564 AGAATGTACTCTCACAAATCCTCACGAGTCACTCCAAGGAAACTTGAATGTCACTCAATCCTCTC
456 AGAATGTACTCTCACAAAGCCTCACGAGTCACTCCAAGGAAACTTGAATGTCACTCAATCCGCTC
* *
3501629 GTGTTTGCATTCTTGGACTTAATAATGGCTTTTACTTGTCCTCTTCTGATCTCACACACGCTCCA
521 GTGTTTGCACTCTAGGACTTAATAATGGCTTTTACTTGTCCTCTTCTGATCTCACACACGCTCCA
3501694 GCCTTTTTCCTCTCAATTCTCTTATCCCAAGTTCTAGAGAACTTTACTCAAGACCGTATCAAGTA
586 GCCTTTTTCCTCTCAATTCTCTTATCCCAAGTTCTAGAGAACTTTACTCAAGACCGTATCAAGTA
*
3501759 AATTTTTACTTGTTTGGCGTCGGCTGTAA
651 AATTTCTACTTGTTTGGCGTCGGCTGTAA
3501788 AAGG
1 AAGG
3501792 GTTAGTAGGA
Statistics
Matches: 672, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
679 672 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (679 bp):
AAGGCATAGTCCACGAATTCCATAGCAGCAAGCCTGACCTTCTTTTGCTCCATATAATTTTGGCA
TTCAAAAATGTGTTCAATCTTGATTACCCAATCAAGATAGGCTTCAGGATCAGTTCGTCCTTGAA
ATAGAGGAATGGTCACTTTGATGTTGCTGAAGTTGTCATTCTGATTTCGATGACCATCTCTTCGT
GCTACTGATGTTACTTCAGCCTCCTCTTCTTCGAATTCTTCTTCCATTCTAGGGAGATTTACTCT
TCGATTCCCTAAAGATGCTTCAAATTGGTCCATACGATCATGCAAAGGCTCCAATTCTAATTTTA
GATATCTGGCCATTTCATGCATGATTGCTTGAGTTTGTAAATTAGGGGCATCACTTTCAGGGGTT
CATCCTAGACTTCAAGACATGGTTAGTGAAATAAGAAAAGAATAAGATGTGTAAAAGACCTTACC
AGAATGTACTCTCACAAAGCCTCACGAGTCACTCCAAGGAAACTTGAATGTCACTCAATCCGCTC
GTGTTTGCACTCTAGGACTTAATAATGGCTTTTACTTGTCCTCTTCTGATCTCACACACGCTCCA
GCCTTTTTCCTCTCAATTCTCTTATCCCAAGTTCTAGAGAACTTTACTCAAGACCGTATCAAGTA
AATTTCTACTTGTTTGGCGTCGGCTGTAA
Found at i:3502026 original size:23 final size:24
Alignment explanation
Indices: 3501977--3502029 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
3501967 TTCTTTACTT
* *
3501977 TTTC-TTCTTTTGAGTGCTGGATT
1 TTTCTTTCTTTTGAGTGCTGCATC
*
3502000 TTTCTTTCTTTTGAGTGCTTCA-C
1 TTTCTTTCTTTTGAGTGCTGCATC
3502023 TTTCTTT
1 TTTCTTT
3502030 TTTGATTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.08, C:0.17, G:0.15, T:0.60
Consensus pattern (24 bp):
TTTCTTTCTTTTGAGTGCTGCATC
Found at i:3506708 original size:14 final size:14
Alignment explanation
Indices: 3506689--3506721 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3506679 AGTGCTTCAA
3506689 CTTTTCTTTCTT-TT
1 CTTTTCTTT-TTCTT
3506703 CTTTTCTTTTTCTT
1 CTTTTCTTTTTCTT
3506717 CTTTT
1 CTTTT
3506722 TGAGTGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTTCTTTTTCTT
Found at i:3506762 original size:22 final size:24
Alignment explanation
Indices: 3506711--3506762 Score: 81
Period size: 22 Copynumber: 2.2 Consensus size: 24
3506701 TTCTTTTCTT
3506711 TTTCTTCTTTTTGAGTGCTTTCAA
1 TTTCTTCTTTTTGAGTGCTTTCAA
*
3506735 TTTCTTC-TTTTGAGTGC-TTCGA
1 TTTCTTCTTTTTGAGTGCTTTCAA
3506757 TTTCTT
1 TTTCTT
3506763 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 10 0.37
23 10 0.37
24 7 0.26
ACGTcount: A:0.10, C:0.17, G:0.13, T:0.60
Consensus pattern (24 bp):
TTTCTTCTTTTTGAGTGCTTTCAA
Found at i:3508749 original size:28 final size:28
Alignment explanation
Indices: 3508717--3508770 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
3508707 TGAATTAACT
3508717 AAACAAATGATGAACATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
3508745 AAACAAATGATGAACATGCTGTTATG
1 AAACAAATGATGAACATGCTGTTATG
3508771 TGAATGTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.26
Consensus pattern (28 bp):
AAACAAATGATGAACATGCTGTTATGCA
Done.