Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008007.1 Hibiscus syriacus cultivar Beakdansim tig00110469_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: 1953294
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 11
Found at i:585969 original size:45 final size:45
Alignment explanation
Indices: 585885--586038 Score: 211
Period size: 45 Copynumber: 3.4 Consensus size: 45
585875 GGTATATGGT
* * *
585885 TTATGGAAT-AATGACAAGTGTATTGGTAAAATAAACTTACGAGC
1 TTATGGAATAAATGATAAGTATATTGGTAAAATAAGCTTACGAGC
* *
585929 TTATGGAATAAATGGTAAGTATATGGGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGATAAGTATATTGGTAAAATAAGCTTACGAGC
* *
585974 TTATGTGATTAAATGATAAGTATTTTGGTAAAATAAGCTTACGAGC
1 TTATG-GAATAAATGATAAGTATATTGGTAAAATAAGCTTACGAGC
* *
586020 TTATGGGATAAATGGTAAG
1 TTATGGAATAAATGATAAG
586039 AAATTTTATA
Statistics
Matches: 96, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
44 9 0.09
45 46 0.48
46 41 0.43
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (45 bp):
TTATGGAATAAATGATAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:586045 original size:46 final size:45
Alignment explanation
Indices: 585907--586038 Score: 201
Period size: 46 Copynumber: 2.9 Consensus size: 45
585897 GACAAGTGTA
* * *
585907 TTGGTAAAATAAACTTACGAGCTTATGGAATAAATGGTAAGTATA
1 TTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATT
* * *
585952 TGGGTAAAATAAGCTTACGAGCTTATGTGATTAAATGATAAGTATT
1 TTGGTAAAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAGTATT
585998 TTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 TTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
586039 AAATTTTATA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 36 0.47
46 41 0.53
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.32
Consensus pattern (45 bp):
TTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATT
Found at i:588332 original size:29 final size:29
Alignment explanation
Indices: 588283--588361 Score: 131
Period size: 29 Copynumber: 2.7 Consensus size: 29
588273 TTGGCCATAG
*
588283 GTCGCCATGCCTTCCCGGCGACCTACTAC
1 GTCGCCATGGCTTCCCGGCGACCTACTAC
* *
588312 GTTGCCATGGCTTCCCAGCGACCTACTAC
1 GTCGCCATGGCTTCCCGGCGACCTACTAC
588341 GTCGCCATGGCTTCCCGGCGA
1 GTCGCCATGGCTTCCCGGCGA
588362 GCTGCATAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.14, C:0.41, G:0.24, T:0.22
Consensus pattern (29 bp):
GTCGCCATGGCTTCCCGGCGACCTACTAC
Found at i:588637 original size:23 final size:23
Alignment explanation
Indices: 588611--588671 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
588601 TGTGAATTCA
588611 GCTGCATTATTGCAGCACTTATT
1 GCTGCATTATTGCAGCACTTATT
*
588634 GCTGCATTATTGCAGCCCTTATT
1 GCTGCATTATTGCAGCACTTATT
588657 GCTGCATTATTGCAG
1 GCTGCATTATTGCAG
588672 TCCTTCAGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38
Consensus pattern (23 bp):
GCTGCATTATTGCAGCACTTATT
Found at i:588645 original size:11 final size:11
Alignment explanation
Indices: 588611--588669 Score: 73
Period size: 11 Copynumber: 5.2 Consensus size: 11
588601 TGTGAATTCA
588611 GCTGCATTATT
1 GCTGCATTATT
*
588622 GCAGCACTTATT
1 GCTGCA-TTATT
588634 GCTGCATTATT
1 GCTGCATTATT
* *
588645 GCAGCCCTTATT
1 GCTG-CATTATT
588657 GCTGCATTATT
1 GCTGCATTATT
588668 GC
1 GC
588670 AGTCCTTCAG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 21 0.52
12 19 0.47
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.39
Consensus pattern (11 bp):
GCTGCATTATT
Found at i:588826 original size:23 final size:23
Alignment explanation
Indices: 588788--588849 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
588778 AAAGAAAGTG
*
588788 AGAAGAGAGCAAGGGAAAAGAGGA
1 AGAAGA-AGAAAGGGAAAAGAGGA
*
588812 AGAAGAATAAAGGGAAAAGAGGA
1 AGAAGAAGAAAGGGAAAAGAGGA
*
588835 ATAAGAAGAAAGGGA
1 AGAAGAAGAAAGGGA
588850 TAGCACAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 28 0.82
24 6 0.18
ACGTcount: A:0.58, C:0.02, G:0.37, T:0.03
Consensus pattern (23 bp):
AGAAGAAGAAAGGGAAAAGAGGA
Found at i:588945 original size:39 final size:36
Alignment explanation
Indices: 588902--588999 Score: 124
Period size: 39 Copynumber: 2.6 Consensus size: 36
588892 TTATTATTTT
**
588902 AAATTATTAGTTTGTTAGTTTATGGTTTAAGGTAAAACA
1 AAATT-TTAGTTAATTAGTTTA--GTTTAAGGTAAAACA
588941 AAATTTTAGTTAATTAGCTAGTTAGTTTAAGGTAAAACA
1 AAATTTTAGTTAATTAG-T--TTAGTTTAAGGTAAAACA
588980 AAATTTTAGTTAATTAGTTT
1 AAATTTTAGTTAATTAGTTT
589000 GTCAGTTTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
36 2 0.04
38 11 0.20
39 38 0.70
41 3 0.06
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (36 bp):
AAATTTTAGTTAATTAGTTTAGTTTAAGGTAAAACA
Found at i:589007 original size:39 final size:39
Alignment explanation
Indices: 588926--589010 Score: 143
Period size: 39 Copynumber: 2.2 Consensus size: 39
588916 TTAGTTTATG
*
588926 GTTTAAGGTAAAACAAAATTTTAGTTAATTAGCTAGTTA
1 GTTTAAGGTAAAACAAAATTTTAGTTAATTAGCTAGTCA
* *
588965 GTTTAAGGTAAAACAAAATTTTAGTTAATTAGTTTGTCA
1 GTTTAAGGTAAAACAAAATTTTAGTTAATTAGCTAGTCA
589004 GTTTAAG
1 GTTTAAG
589011 TTTTATTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.40
Consensus pattern (39 bp):
GTTTAAGGTAAAACAAAATTTTAGTTAATTAGCTAGTCA
Found at i:589127 original size:28 final size:27
Alignment explanation
Indices: 589088--589140 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
589078 TATATTAAAA
589088 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
589116 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
589141 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:589146 original size:27 final size:29
Alignment explanation
Indices: 589087--589151 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
589077 ATATATTAAA
589087 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
589116 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
589142 AAATAGTTAA
1 AAATAATTAA
589152 GTTATATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:589387 original size:21 final size:21
Alignment explanation
Indices: 589361--589400 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
589351 GATAATGAGT
589361 TTGTTAGTTTAAATTATATTA
1 TTGTTAGTTTAAATTATATTA
*
589382 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAATTATAT
589401 CATATAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAATTATATTA
Found at i:589625 original size:30 final size:30
Alignment explanation
Indices: 589579--589698 Score: 127
Period size: 30 Copynumber: 4.3 Consensus size: 30
589569 AGTTAATTTT
* *
589579 TTTAGTAG-TAAA-TTATAATTAAA-AATCG
1 TTTATTAGTTAAAGTTAT-ATTAAAGAATAG
*
589607 TTTATTAGTTTAAGTTATATTAAAGAATAG
1 TTTATTAGTTAAAGTTATATTAAAGAATAG
589637 TTTATTAGTTAAAGTTATATTAAAG---A-
1 TTTATTAGTTAAAGTTATATTAAAGAATAG
589663 ---A-TAGTTAAAGTTATATTAAAGAATAG
1 TTTATTAGTTAAAGTTATATTAAAGAATAG
589689 TTTATTAGTT
1 TTTATTAGTT
589699 GTTTAAGGGA
Statistics
Matches: 77, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
22 20 0.26
23 1 0.01
25 1 0.01
27 1 0.01
28 7 0.09
29 10 0.13
30 37 0.48
ACGTcount: A:0.42, C:0.01, G:0.12, T:0.44
Consensus pattern (30 bp):
TTTATTAGTTAAAGTTATATTAAAGAATAG
Found at i:589637 original size:22 final size:22
Alignment explanation
Indices: 589612--589692 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 22
589602 AATCGTTTAT
589612 TAGTTTAAGTTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
589634 TAGTTTATTAGTTAAAGTTATATTAAAGAA
1 TAG-----T--TTA-AGTTATATTAAAGAA
*
589664 TAGTTAAAGTTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
589686 TAGTTTA
1 TAGTTTA
589693 TTAGTTGTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
22 24 0.49
23 2 0.04
25 1 0.02
27 1 0.02
29 3 0.06
30 18 0.37
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (22 bp):
TAGTTTAAGTTATATTAAAGAA
Found at i:589642 original size:15 final size:16
Alignment explanation
Indices: 589619--589669 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
589609 TATTAGTTTA
589619 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
***
589635 AGTT-TATTAGTTAA-
1 AGTTATATTAAAGAAT
589649 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
589665 AGTTA
1 AGTTA
589670 AAGTTATATT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 4 0.15
15 14 0.52
16 9 0.33
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (16 bp):
AGTTATATTAAAGAAT
Found at i:589661 original size:11 final size:11
Alignment explanation
Indices: 589645--589683 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
589635 AGTTTATTAG
589645 TTAAAGTTATA
1 TTAAAGTTATA
*
589656 TTAAAG-AATA
1 TTAAAGTTATA
589666 GTTAAAGTTATA
1 -TTAAAGTTATA
589678 TTAAAG
1 TTAAAG
589684 AATAGTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (11 bp):
TTAAAGTTATA
Found at i:593134 original size:17 final size:17
Alignment explanation
Indices: 593114--593151 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
593104 TTTTTTTTAA
593114 AAACACTAA-ATATTTTT
1 AAACAC-AATATATTTTT
*
593131 AAACACAATATTTTTTT
1 AAACACAATATATTTTT
593148 AAAC
1 AAAC
593152 GGAATTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.39
Consensus pattern (17 bp):
AAACACAATATATTTTT
Found at i:593616 original size:45 final size:50
Alignment explanation
Indices: 593567--593669 Score: 135
Period size: 50 Copynumber: 2.1 Consensus size: 50
593557 GATAATAACA
* *
593567 AATTAATTAATTTTTT-T-T-ATAT-TTA-ATAACTTAAACTAAGAAACT
1 AATTAATTAATTTTTTATATAATATAATATATAACTTAAACTAACAAACT
*
593612 AATTAACTAATTTTTTATATAATATAATATATAACTTAAACTAACAAACT
1 AATTAATTAATTTTTTATATAATATAATATATAACTTAAACTAACAAACT
593662 AATATAAT
1 AAT-TAAT
593670 ATAACTTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
45 15 0.31
46 1 0.02
47 1 0.02
48 4 0.08
49 2 0.04
50 22 0.46
51 3 0.06
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.43
Consensus pattern (50 bp):
AATTAATTAATTTTTTATATAATATAATATATAACTTAAACTAACAAACT
Found at i:593671 original size:28 final size:30
Alignment explanation
Indices: 593631--593693 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
593621 ATTTTTTATA
593631 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
593661 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
593689 TAATA
1 TAATA
593694 ATTTATACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 26 0.79
29 1 0.03
30 6 0.18
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:593700 original size:28 final size:28
Alignment explanation
Indices: 593635--593700 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
593625 TTTATATAAT
593635 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
593663 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
593691 ATAATTTATA
1 ATAATATATA
593701 CTAACAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 2 0.06
28 31 0.89
29 2 0.06
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:593703 original size:21 final size:21
Alignment explanation
Indices: 593670--593718 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
593660 CTAATATAAT
593670 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
593691 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
593712 ATTAACT
1 A-TAACT
593719 AAATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:594231 original size:29 final size:29
Alignment explanation
Indices: 594183--594265 Score: 103
Period size: 29 Copynumber: 2.9 Consensus size: 29
594173 GGTTAAGTTT
* * * *
594183 GGTCGCCGGGACTGCTTGGCAACCTACAA
1 GGTCGCTGGGAGTGCATGGCGACCTACAA
***
594212 GGTCGCTGGGAGTGCATGGCGACCTTGTA
1 GGTCGCTGGGAGTGCATGGCGACCTACAA
594241 GGTCGCTGGGAGTGCATGGCGACCT
1 GGTCGCTGGGAGTGCATGGCGACCT
594266 GTGTTGGGGG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.16, C:0.25, G:0.39, T:0.20
Consensus pattern (29 bp):
GGTCGCTGGGAGTGCATGGCGACCTACAA
Found at i:597706 original size:24 final size:25
Alignment explanation
Indices: 597679--597725 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
597669 ATTCAAATAA
*
597679 TAATTTT-CAAACAAAATCAATCAT
1 TAATTTTGCAAAAAAAATCAATCAT
*
597703 TAATTTTGTAAAAAAAATCAATC
1 TAATTTTGCAAAAAAAATCAATC
597726 TAAAATCTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.34
Consensus pattern (25 bp):
TAATTTTGCAAAAAAAATCAATCAT
Found at i:598228 original size:18 final size:19
Alignment explanation
Indices: 598205--598240 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
598195 AAGATTTGTA
598205 ATTATT-TATTTTAATAGT
1 ATTATTATATTTTAATAGT
*
598223 ATTATTATTTTTTAATAG
1 ATTATTATATTTTAATAG
598241 AAACCGCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (19 bp):
ATTATTATATTTTAATAGT
Found at i:598779 original size:23 final size:23
Alignment explanation
Indices: 598693--598779 Score: 113
Period size: 23 Copynumber: 3.8 Consensus size: 23
598683 TCACAAAGGT
* *
598693 AGAGATAAACGTG-ACACAAAGGT
1 AGAGATAAACGTGCA-ACATAGGC
* *
598716 ATAGATAAGCGTGCAACATAGGC
1 AGAGATAAACGTGCAACATAGGC
598739 AGAGATAAACGTGCAACATAGGC
1 AGAGATAAACGTGCAACATAGGC
*
598762 AGAGATAAACGTGTAACA
1 AGAGATAAACGTGCAACA
598780 CAAACAAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
23 55 0.98
24 1 0.02
ACGTcount: A:0.45, C:0.15, G:0.25, T:0.15
Consensus pattern (23 bp):
AGAGATAAACGTGCAACATAGGC
Found at i:598817 original size:12 final size:13
Alignment explanation
Indices: 598800--598828 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
598790 TATTCTTATT
598800 AAAAAATAAA-AG
1 AAAAAATAAAGAG
598812 AAAAAATAAAGAG
1 AAAAAATAAAGAG
598825 AAAA
1 AAAA
598829 GAGAACCGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (13 bp):
AAAAAATAAAGAG
Found at i:606532 original size:2 final size:2
Alignment explanation
Indices: 606525--606611 Score: 174
Period size: 2 Copynumber: 43.5 Consensus size: 2
606515 ATTTCTCCTC
606525 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
606567 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
606609 CT C
1 CT C
606612 GTTTGTCTGT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:609063 original size:18 final size:19
Alignment explanation
Indices: 609028--609064 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
609018 CACGGAATGT
609028 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
609048 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
609065 TTATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:609248 original size:638 final size:643
Alignment explanation
Indices: 608435--609593 Score: 2008
Period size: 638 Copynumber: 1.8 Consensus size: 643
608425 AAGATTATCA
*
608435 GGGAATGTTGTATTTTGTGTTTGGTTGGTTTAGCAGGAATGTAAGATTACCGTGTTTGGTTAAAG
1 GGGAATGTTGTATTTTGTGTTTGGTTGGTTTAACAGGAATGTAAGATTACCGTGTTTGGTTAAAG
*
608500 GAATAAAAGATTATTGGAATATATATTTGACCAAATTGTCCTTATTATATATTTGTATAATATTA
66 GAATAAAAGATTATTGGAATATATATTTGACCAAATTATCCTTATTATATATTTGTATAATATTA
608565 CAAATTGTAAAATATTTATATATTTTCTTTAAAAAATTAAATTCATAATATTTATATAA-TTTTT
131 CAAATTGTAAAATATTTATATATTTTCTTTAAAAAATTAAATTCATAATATTTATATAATTTTTT
* *
608629 TTACAAAATTAAAAATATAAAAAAGGTTTAATGAAAGGGT-AAAAAAAATTTTAACCCCTGAACT
196 TTACAAAATTAAAAATATAAAAAAAGTTTAATGAAAGGGTAAAAAAAAATTTTAACCCCTGAACC
*
608693 TCATATAAAATTTTAATTATAGA-TTTTTTTATAAATCTAAAATAATTTAAAGATAAATTT-TAA
261 TCATATAAAATTTTAATTATAGATTTTTTTTATAAATCTAAAATAATTTAAAGAAAAATTTGT-A
* * *
608756 ATTTAACTTTCGTAGAATTTTTATTATCCAATGACAGAAGAATGATA-TTTT-AAAAAAATAAAA
325 ATTTAACCTTCGTAGAATTTTTATTATCCAATAACAGAAGAATGATACTTTTGAAAAAAACAAAA
* * * *
608819 ATTTAAGGGCATTTTAGTCCAAAACGCCGGTAATGTTACAATACCTAATGGAATGG-AGGTAATG
390 ATTTAAAGGCATTTTAGTCCAAAACGCCGGTAATGTTACAATACATAAGGGAA-GGAAAGTAATG
* * *
608883 ACATTTCCAATAATATACCCAAAAAAATCTACTATCGGTAATAAAACATTATCGGGAGTGAGATT
454 ACATTCCCAATAATATACCCAAAAAAATCTACTATCGGTAATAAAACATTACCGGGAATGAGATT
608948 TTCGACCAACCAAACATGGGAATGTGGGATTACAATCCTTGAACCAAACACCCTTAGGGTGCGTT
519 TTCGACCAACCAAACATGGGAATGTGGGATTACAATCCTTGAACCAAACACCCTTAGGGTGCGTT
609013 TGGTTCACGGAATGTAAGATTACCAGTGGGAATAAAAGATTACCAGGGAATATTATTACT
584 TGGTTCACGGAATGTAAGATTACCAGTGGGAATAAAAGATTACCAGGGAATATTATTACT
*
609073 GGGAATGTTGTATTTTGTGTTTGGTTGGTTTAACAGGAATGTAAGATTATCGTGTTTGGTTAAAG
1 GGGAATGTTGTATTTTGTGTTTGGTTGGTTTAACAGGAATGTAAGATTACCGTGTTTGGTTAAAG
* *
609138 GAATAAAAGATTATTGGAATGTATATTTGACCAAATTATCTTTATTATATATTTGTATAATATTA
66 GAATAAAAGATTATTGGAATATATATTTGACCAAATTATCCTTATTATATATTTGTATAATATTA
609203 CAAATTGTAAAATATTTATATATTTTCTTTAAAAAATTAAATTCATAATATTTATATAATTTTTT
131 CAAATTGTAAAATATTTATATATTTTCTTTAAAAAATTAAATTCATAATATTTATATAATTTTTT
609268 TTACAAAATTAAAAATATAAAAAAAGTTTAATGAAAGGGTAAAAAAAAATTTTAACCCCTGAACC
196 TTACAAAATTAAAAATATAAAAAAAGTTTAATGAAAGGGTAAAAAAAAATTTTAACCCCTGAACC
*
609333 TCATATAAAATTTTAATTATAGATTTTTTTTGTAAATCTAAAATAATTTAAAGAAAAATTTGTAA
261 TCATATAAAATTTTAATTATAGATTTTTTTTATAAATCTAAAATAATTTAAAGAAAAATTTGTAA
*
609398 TTTAACCTTCGTAGAATTTTTATTATTCAATAACAGAAGAATGATACTTTTGGAAAAAAAACAAA
326 TTTAACCTTCGTAGAATTTTTATTATCCAATAACAGAAGAATGATACTTTT-G-AAAAAAACAAA
609463 AATTTAAAGGCATTTTAGTCCAAAACGCCGGTAATGTTACAATACATAAGGGAAGGAAAGTAATG
389 AATTTAAAGGCATTTTAGTCCAAAACGCCGGTAATGTTACAATACATAAGGGAAGGAAAGTAATG
** * **
609528 ACATTCCCGGTAATATACCCCAAAAAATCTACTATTTGTAATAAAACATTACCGGGAATGAGATT
454 ACATTCCCAATAATATACCCAAAAAAATCTACTATCGGTAATAAAACATTACCGGGAATGAGATT
609593 T
519 T
609594 CCAGTTAACC
Statistics
Matches: 487, Mismatches: 25, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
638 184 0.38
639 44 0.09
640 46 0.09
641 80 0.16
642 5 0.01
644 2 0.00
645 126 0.26
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.36
Consensus pattern (643 bp):
GGGAATGTTGTATTTTGTGTTTGGTTGGTTTAACAGGAATGTAAGATTACCGTGTTTGGTTAAAG
GAATAAAAGATTATTGGAATATATATTTGACCAAATTATCCTTATTATATATTTGTATAATATTA
CAAATTGTAAAATATTTATATATTTTCTTTAAAAAATTAAATTCATAATATTTATATAATTTTTT
TTACAAAATTAAAAATATAAAAAAAGTTTAATGAAAGGGTAAAAAAAAATTTTAACCCCTGAACC
TCATATAAAATTTTAATTATAGATTTTTTTTATAAATCTAAAATAATTTAAAGAAAAATTTGTAA
TTTAACCTTCGTAGAATTTTTATTATCCAATAACAGAAGAATGATACTTTTGAAAAAAACAAAAA
TTTAAAGGCATTTTAGTCCAAAACGCCGGTAATGTTACAATACATAAGGGAAGGAAAGTAATGAC
ATTCCCAATAATATACCCAAAAAAATCTACTATCGGTAATAAAACATTACCGGGAATGAGATTTT
CGACCAACCAAACATGGGAATGTGGGATTACAATCCTTGAACCAAACACCCTTAGGGTGCGTTTG
GTTCACGGAATGTAAGATTACCAGTGGGAATAAAAGATTACCAGGGAATATTATTACT
Found at i:609952 original size:20 final size:24
Alignment explanation
Indices: 609910--609958 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 24
609900 TTTAGATATC
609910 ATTTTATATTTTTATCAATAATTT
1 ATTTTATATTTTTATCAATAATTT
609934 ATTTTA-ATTTTT-T-AA-AATTT
1 ATTTTATATTTTTATCAATAATTT
609954 ATTTT
1 ATTTT
609959 TAATAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.40
21 2 0.08
22 1 0.04
23 6 0.24
24 6 0.24
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
ATTTTATATTTTTATCAATAATTT
Found at i:616077 original size:21 final size:22
Alignment explanation
Indices: 616037--616077 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
616027 AATCCTTATC
*
616037 TATTGTAAATGTTCTCATTTAA
1 TATTGTAAATATTCTCATTTAA
616059 TATTGTAAATATT-TCATTT
1 TATTGTAAATATTCTCATTT
616078 GTCATTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (22 bp):
TATTGTAAATATTCTCATTTAA
Found at i:618598 original size:23 final size:25
Alignment explanation
Indices: 618566--618618 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
618556 ATAATTAAGT
*
618566 AGAAACATTAAATACT-AAACATTA
1 AGAAACATTAAATAATAAAACATTA
618590 AGAAA-ATTAAATAATAAAAACATTA
1 AGAAACATTAAATAAT-AAAACATTA
618615 AGAA
1 AGAA
618619 TCAAAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 9 0.35
24 5 0.19
25 12 0.46
ACGTcount: A:0.64, C:0.08, G:0.06, T:0.23
Consensus pattern (25 bp):
AGAAACATTAAATAATAAAACATTA
Found at i:623354 original size:13 final size:11
Alignment explanation
Indices: 623318--623372 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 11
623308 CATTTGTTCA
*
623318 ATTTTTATTTT
1 ATTTTTCTTTT
623329 A-TTTTCAATTTT
1 ATTTTTC--TTTT
623341 ATTTTTCTGATTT
1 ATTTTTCT--TTT
623354 ATTTTT-TTTT
1 ATTTTTCTTTT
623364 ATTTTTCTT
1 ATTTTTCTT
623373 AGAATTTTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
10 13 0.35
11 4 0.11
12 6 0.16
13 14 0.38
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.76
Consensus pattern (11 bp):
ATTTTTCTTTT
Found at i:627407 original size:20 final size:19
Alignment explanation
Indices: 627384--627436 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
627374 TATGTTATTT
**
627384 TATTAAATATTATTTTCAAA
1 TATTAAATATTAAATT-AAA
627404 TATTAAATATTAAAATTAAA
1 TATTAAATATT-AAATTAAA
627424 TATTAAATATTAA
1 TATTAAATATTAA
627437 TATAGGTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 25 0.83
21 3 0.10
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
TATTAAATATTAAATTAAA
Found at i:627411 original size:7 final size:7
Alignment explanation
Indices: 627384--627436 Score: 67
Period size: 7 Copynumber: 7.9 Consensus size: 7
627374 TATGTTATTT
627384 TATTAAA
1 TATTAAA
627391 TATT--A
1 TATTAAA
*
627396 TTTTCAAA
1 TATT-AAA
627404 TATTAAA
1 TATTAAA
627411 TATTAAA
1 TATTAAA
627418 -ATTAAA
1 TATTAAA
627424 TATTAAA
1 TATTAAA
627431 TATTAA
1 TATTAA
627437 TATAGGTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 4 0.10
6 6 0.15
7 26 0.65
8 4 0.10
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (7 bp):
TATTAAA
Found at i:627439 original size:13 final size:14
Alignment explanation
Indices: 627384--627436 Score: 67
Period size: 13 Copynumber: 3.9 Consensus size: 14
627374 TATGTTATTT
627384 TATTAAATATT--A
1 TATTAAATATTAAA
*
627396 TTTTCAAATATTAAA
1 TATT-AAATATTAAA
627411 TATTAAA-ATTAAA
1 TATTAAATATTAAA
627424 TATTAAATATTAA
1 TATTAAATATTAA
627437 TATAGGTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 3 0.09
13 20 0.57
14 8 0.23
15 4 0.11
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
TATTAAATATTAAA
Found at i:627503 original size:13 final size:13
Alignment explanation
Indices: 627487--627519 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
627477 TAAAATGACT
627487 AAATTAAA-TAATA
1 AAATTAAAGTAA-A
627500 AAATTAAAGTAAA
1 AAATTAAAGTAAA
627513 AAATTAA
1 AAATTAA
627520 TACCTCACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 16 0.84
14 3 0.16
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (13 bp):
AAATTAAAGTAAA
Found at i:627506 original size:70 final size:70
Alignment explanation
Indices: 627373--627506 Score: 175
Period size: 70 Copynumber: 1.9 Consensus size: 70
627363 AATCTAATTT
* * * * *
627373 TTATGTTATTTTATTAAATATTATTTTCAAATATTAAATATTAAAATTAAATATTAAATATTAAT
1 TTATGTTATTTTATTAAATATTATTATCAAAAATAAAATACTAAAATTAAATAATAAATATTAAT
627438 ATAGG
66 ATAGG
627443 TTATGTTATTTTATTAAATATTATGTAAT-AAAAATAAAATGACT-AAATTAAATAATAAA-ATT
1 TTATGTTATTTTATTAAATATTAT-T-ATCAAAAATAAAAT-ACTAAAATTAAATAATAAATATT
627505 AA
63 AA
627507 AGTAAAAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
70 29 0.52
71 24 0.43
72 3 0.05
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (70 bp):
TTATGTTATTTTATTAAATATTATTATCAAAAATAAAATACTAAAATTAAATAATAAATATTAAT
ATAGG
Found at i:638725 original size:43 final size:43
Alignment explanation
Indices: 638669--638942 Score: 203
Period size: 43 Copynumber: 6.4 Consensus size: 43
638659 GGTAACAAAA
**
638669 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTGTT-GGAC
1 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTT-TTCCAAC
* *** *
638712 AAACGCCGTAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
1 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTTTCCAAC
*** * * *
638755 AAACGCCGCAATAGGTGTTGAGATATAGCGGAGTTTTTCCCAC
1 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTTTCCAAC
*** * * * *
638798 AAACGCCGCAATAGGTGTTGAGATTTAACGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTTTCCAAC
*** * * *
638841 AAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTTTCCAAC
* * * * **
638884 AAACACCGCAA-AAG-ATCTGGTATATAGCGGCGTTTTTTAGAAC
1 AAACGCCGCAATAGGTAAC-GATATATAGCGGCG-TTTTTCCAAC
*
638927 AAACGCCGCAAAAGGT
1 AAACGCCGCAATAGGT
638943 CATATCTATA
Statistics
Matches: 197, Mismatches: 29, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
41 1 0.01
42 15 0.08
43 179 0.91
44 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (43 bp):
AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTTTCCAAC
Found at i:638781 original size:86 final size:86
Alignment explanation
Indices: 638669--638894 Score: 310
Period size: 86 Copynumber: 2.6 Consensus size: 86
638659 GGTAACAAAA
** * ** *
638669 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTGTT-GGACAAACGCCGTAATAGGTGTTGA
1 AAACGCCGCAATAGGTATTGAGATATAGCGGCGTTT-TTCCCACAAACGCCGCAATAGGTGTTGA
* *
638733 TATTTAGCGGCGTTTTTCCAAC
65 GATTTAACGGCGTTTTTCCAAC
* *
638755 AAACGCCGCAATAGGTGTTGAGATATAGCGGAGTTTTTCCCACAAACGCCGCAATAGGTGTTGAG
1 AAACGCCGCAATAGGTATTGAGATATAGCGGCGTTTTTCCCACAAACGCCGCAATAGGTGTTGAG
*
638820 ATTTAACGGCGTTTTTCCCAC
66 ATTTAACGGCGTTTTTCCAAC
* * *
638841 AAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACCGCAA
1 AAACGCCGCAATAGGTATTGAGATATAGCGGCGTTTTTCCCACAAACGCCGCAA
638895 AAGATCTGGT
Statistics
Matches: 124, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
85 2 0.02
86 122 0.98
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (86 bp):
AAACGCCGCAATAGGTATTGAGATATAGCGGCGTTTTTCCCACAAACGCCGCAATAGGTGTTGAG
ATTTAACGGCGTTTTTCCAAC
Found at i:638921 original size:86 final size:86
Alignment explanation
Indices: 638737--638943 Score: 265
Period size: 86 Copynumber: 2.4 Consensus size: 86
638727 TGTTGATATT
*
638737 TAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTGTTGAGATATAGCGGAGTTTTTCCCACAAAC
1 TAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTCTTGAGATATAGCGGAGTTTTTCCCACAAAC
* * * * *
638802 GCCGCAATAGGTGTTGAGATT
66 ACCGCAAAAGATGCTGAGATA
* * * *
638823 TAACGGCGTTTTTCCCACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAAC
1 TAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTCTTGAGATATAGCGGAGTTTTTCCCACAAAC
638888 ACCGCAAAAGAT-CTG-GTATA
66 ACCGCAAAAGATGCTGAG-ATA
** *
638908 TAGCGGCGTTTTTTAGAACAAACGCCGCAAAAGGTC
1 TAGCGGCG-TTTTTCCAACAAACGCCGCAATAGGTC
638944 ATATCTATAG
Statistics
Matches: 104, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
84 1 0.01
85 11 0.11
86 92 0.88
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (86 bp):
TAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTCTTGAGATATAGCGGAGTTTTTCCCACAAAC
ACCGCAAAAGATGCTGAGATA
Found at i:638921 original size:129 final size:129
Alignment explanation
Indices: 638710--638942 Score: 317
Period size: 129 Copynumber: 1.8 Consensus size: 129
638700 CGTTTGTTGG
* * * * * * *
638710 ACAAACGCCGTAATAGGTGTTGATATTTAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTGTTG
1 ACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCAACAAACACCGCAAAAGATGCTG
* * *
638775 AGATATAGCGGAGTTTTTCCCACAAACGCCGCAATAGGTGTTGAGATTTAACGGCGTTTTTCCC
66 AGATATAGCGGAGTTTTTACAACAAACGCCGCAAAAGGTGTTGAGATTTAACGGCGTTTTTCCC
*
638839 ACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACCGCAAAAGAT-CTG
1 ACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCAACAAACACCGCAAAAGATGCTG
* *
638903 -GTATATAGCGGCGTTTTTTAGAACAAACGCCGCAAAAGGT
66 AG-ATATAGCGGAG-TTTTTACAACAAACGCCGCAAAAGGT
638943 CATATCTATA
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
127 1 0.01
128 12 0.13
129 76 0.85
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (129 bp):
ACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCAACAAACACCGCAAAAGATGCTG
AGATATAGCGGAGTTTTTACAACAAACGCCGCAAAAGGTGTTGAGATTTAACGGCGTTTTTCCC
Found at i:639116 original size:21 final size:21
Alignment explanation
Indices: 639090--639148 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
639080 ATTTTCCAAT
*
639090 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
639111 AAACTTAAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
**
639132 AAAAATGAAATCCATAA
1 AAACTTGAAATCCATAA
639149 TAATAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:639230 original size:41 final size:41
Alignment explanation
Indices: 639175--639373 Score: 247
Period size: 42 Copynumber: 4.8 Consensus size: 41
639165 ACATTAACGT
639175 AAAACGCCACTAAAGTACGAGTCTATAGTGGCGTTTGTATA
1 AAAACGCCACTAAAGTACGAGTCTATAGTGGCGTTTGTATA
* * * *
639216 AAAACGCCACTAAAGTACTACTCTATCGTGACGTTTTGTATA
1 AAAACGCCACTAAAGTACGAGTCTATAGTGGCG-TTTGTATA
* * *
639258 AAAACACCGCTAAAGT-CGAGTCTATAGCGGCGTTTGTATA
1 AAAACGCCACTAAAGTACGAGTCTATAGTGGCGTTTGTATA
** * * * *
639298 AAAACGCTGCTAAAGTACTACTCTATCGTGGCGTTTTATATA
1 AAAACGCCACTAAAGTACGAGTCTATAGTGGCG-TTTGTATA
*
639340 AAAACGCCACTAAAGTACGAGTCTATAGCGGCGT
1 AAAACGCCACTAAAGTACGAGTCTATAGTGGCGT
639374 CCGCTAAAGT
Statistics
Matches: 131, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
40 22 0.17
41 53 0.40
42 56 0.43
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (41 bp):
AAAACGCCACTAAAGTACGAGTCTATAGTGGCGTTTGTATA
Found at i:639290 original size:82 final size:83
Alignment explanation
Indices: 639175--639373 Score: 328
Period size: 82 Copynumber: 2.4 Consensus size: 83
639165 ACATTAACGT
*
639175 AAAACGCCACTAAAGTACGAGTCTATAGTGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCT
1 AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCT
*
639240 ATCGTGACGTTTTGTATA
66 ATCGTGACGTTTTATATA
* * **
639258 AAAACACCGCTAAAGT-CGAGTCTATAGCGGCGTTTGTATAAAAACGCTGCTAAAGTACTACTCT
1 AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCT
*
639322 ATCGTGGCGTTTTATATA
66 ATCGTGACGTTTTATATA
639340 AAAACGCCACTAAAGTACGAGTCTATAGCGGCGT
1 AAAACGCCACTAAAGTACGAGTCTATAGCGGCGT
639374 CCGCTAAAGT
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
82 75 0.71
83 31 0.29
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (83 bp):
AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCT
ATCGTGACGTTTTATATA
Found at i:643059 original size:27 final size:29
Alignment explanation
Indices: 643029--643094 Score: 93
Period size: 27 Copynumber: 2.3 Consensus size: 29
643019 AAATATTAAG
643029 ATTATTATATAT-TATTAAAATAA-AAT-T
1 ATTATTAT-TATCTATTAAAATAATAATAT
*
643056 ATTATAATTATCTATTAAAATAATAATAT
1 ATTATTATTATCTATTAAAATAATAATAT
643085 ATTATTATTA
1 ATTATTATTA
643095 ATTATATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 3 0.09
27 18 0.53
28 3 0.09
29 10 0.29
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
ATTATTATTATCTATTAAAATAATAATAT
Found at i:643072 original size:30 final size:33
Alignment explanation
Indices: 643032--643101 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 33
643022 TATTAAGATT
*
643032 ATTATATATTATTAA-AATAA-A-ATTATTA-TA
1 ATTATATATTA-AAATAATAATATATTATTATTA
*
643062 ATTATCTATTAAAATAATAATATATTATTATTA
1 ATTATATATTAAAATAATAATATATTATTATTA
643095 ATTATAT
1 ATTATAT
643102 TAATTACTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 2 0.06
30 15 0.45
31 1 0.03
32 7 0.21
33 8 0.24
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (33 bp):
ATTATATATTAAAATAATAATATATTATTATTA
Found at i:643104 original size:9 final size:10
Alignment explanation
Indices: 643052--643115 Score: 51
Period size: 11 Copynumber: 6.2 Consensus size: 10
643042 ATTAAAATAA
643052 AATTATTA-T
1 AATTATTATT
643061 AATTATCTATT
1 AATTAT-TATT
* * *
643072 AAAATAATAAT
1 -AATTATTATT
643083 ATATTATTATT
1 A-ATTATTATT
643094 AATTA-TATT
1 AATTATTATT
643103 AATTACTTATT
1 AATTA-TTATT
643114 AA
1 AA
643116 AACAATAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
9 15 0.35
10 7 0.16
11 17 0.40
12 4 0.09
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (10 bp):
AATTATTATT
Found at i:643114 original size:42 final size:45
Alignment explanation
Indices: 643037--643150 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 45
643027 AGATTATTAT
* * *
643037 ATATTATTAAAATA-AAATTATTATAATTATCTATTAAAATAATA
1 ATATTATTAATATATTAATTATTATAATTATCTATTAAAACAATA
643081 ATA-TATT-AT-TATTAATTA-TATTAATTA-CTTATTAAAACAATA
1 ATATTATTAATATATTAATTATTA-TAATTATC-TATTAAAACAATA
**
643123 ATATTATTAATATATTAAAAATTATAAT
1 ATATTATTAATATATTAATTATTATAAT
643151 ATTAAAATAG
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
41 5 0.09
42 27 0.47
43 8 0.14
44 5 0.09
45 11 0.19
46 2 0.03
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.46
Consensus pattern (45 bp):
ATATTATTAATATATTAATTATTATAATTATCTATTAAAACAATA
Found at i:645286 original size:29 final size:29
Alignment explanation
Indices: 645252--645309 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
645242 AAAATAGGCA
645252 CCCTAAAACAAAACAGAATTAAAATATCC
1 CCCTAAAACAAAACAGAATTAAAATATCC
*
645281 CCCTAAAACAAAACAGAATTGAAATATCC
1 CCCTAAAACAAAACAGAATTAAAATATCC
645310 GTCCCGGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.53, C:0.24, G:0.05, T:0.17
Consensus pattern (29 bp):
CCCTAAAACAAAACAGAATTAAAATATCC
Found at i:647853 original size:2 final size:2
Alignment explanation
Indices: 647846--647885 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
647836 ATCGATTCTA
647846 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
647886 TCTTATCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:649466 original size:12 final size:11
Alignment explanation
Indices: 649439--649469 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
649429 CAATCATCGA
649439 ATTTTTAGTTC
1 ATTTTTAGTTC
649450 ATTTTTAGTTC
1 ATTTTTAGTTC
649461 ATTTTTAGT
1 ATTTTTAGT
649470 AAATTCTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.06, G:0.10, T:0.65
Consensus pattern (11 bp):
ATTTTTAGTTC
Found at i:650353 original size:29 final size:29
Alignment explanation
Indices: 650311--650389 Score: 149
Period size: 29 Copynumber: 2.7 Consensus size: 29
650301 ATGGCCATAA
650311 GACGCCATGCAATCCAGGCGATCTTGTAG
1 GACGCCATGCAATCCAGGCGATCTTGTAG
650340 GACGCCATGCAATCCAGGCGATCTTGTAG
1 GACGCCATGCAATCCAGGCGATCTTGTAG
*
650369 GACGCCATGTAATCCAGGCGA
1 GACGCCATGCAATCCAGGCGA
650390 CATACGGGGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (29 bp):
GACGCCATGCAATCCAGGCGATCTTGTAG
Found at i:650416 original size:21 final size:21
Alignment explanation
Indices: 650390--650436 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
650380 ATCCAGGCGA
650390 CATACGGGGTGACATACGAGC
1 CATACGGGGTGACATACGAGC
650411 CATACGGGGTGACATACGAGC
1 CATACGGGGTGACATACGAGC
650432 CATAC
1 CATAC
650437 AAGCCATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.26, G:0.30, T:0.15
Consensus pattern (21 bp):
CATACGGGGTGACATACGAGC
Found at i:650435 original size:9 final size:9
Alignment explanation
Indices: 650423--650462 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
650413 TACGGGGTGA
650423 CATACGAGC
1 CATACGAGC
*
650432 CATACAAGC
1 CATACGAGC
650441 CATATACGAGC
1 C--ATACGAGC
650452 CATACGAGC
1 CATACGAGC
650461 CA
1 CA
650463 ATGGAGAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 19 0.70
11 8 0.30
ACGTcount: A:0.38, C:0.33, G:0.17, T:0.12
Consensus pattern (9 bp):
CATACGAGC
Found at i:650449 original size:20 final size:20
Alignment explanation
Indices: 650424--650462 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
650414 ACGGGGTGAC
650424 ATACGAGCCATACAAGCCAT
1 ATACGAGCCATACAAGCCAT
*
650444 ATACGAGCCATACGAGCCA
1 ATACGAGCCATACAAGCCA
650463 ATGGAGAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (20 bp):
ATACGAGCCATACAAGCCAT
Found at i:650505 original size:28 final size:28
Alignment explanation
Indices: 650465--650521 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
650455 ACGAGCCAAT
* *
650465 GGAGAGGTCGCCATGCAGTCTTATACGA
1 GGAGAGGTCGCCATGCAGGCTTAGACGA
650493 GGAGAGGTCGCCATGCAGGCTTAGACGA
1 GGAGAGGTCGCCATGCAGGCTTAGACGA
650521 G
1 G
650522 TCATACGAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.21, G:0.37, T:0.18
Consensus pattern (28 bp):
GGAGAGGTCGCCATGCAGGCTTAGACGA
Found at i:650590 original size:29 final size:29
Alignment explanation
Indices: 650558--650615 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
650548 ATGCAGCCTA
650558 GGCGACCTTGTAGGTCGCCATGTAGTCCC
1 GGCGACCTTGTAGGTCGCCATGTAGTCCC
650587 GGCGACCTTGTAGGTCGCCATGTAGTCCC
1 GGCGACCTTGTAGGTCGCCATGTAGTCCC
650616 ATGTAGTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.14, C:0.31, G:0.31, T:0.24
Consensus pattern (29 bp):
GGCGACCTTGTAGGTCGCCATGTAGTCCC
Found at i:650976 original size:25 final size:26
Alignment explanation
Indices: 650926--650976 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
650916 CTTGGTCGCC
**
650926 GAGATTGCAGCCGAAGAAAGGGAGAA
1 GAGATTGCAGCCGAAGAAAGAAAGAA
650952 GAGATTGCAGCCG-AGAAAGAAAGAA
1 GAGATTGCAGCCGAAGAAAGAAAGAA
650977 AGGGAGAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.45, C:0.12, G:0.35, T:0.08
Consensus pattern (26 bp):
GAGATTGCAGCCGAAGAAAGAAAGAA
Found at i:651178 original size:41 final size:41
Alignment explanation
Indices: 651133--651221 Score: 92
Period size: 41 Copynumber: 2.2 Consensus size: 41
651123 TATATGATTG
* *
651133 TTAGTTTAAG-TT-ATAGTATACATAAATTAAAAATTATTTAA
1 TTAGTTTAAGTTTGATAGT-TACAT-AATTAAAAAATAATTAA
* * * *
651174 TTAGTATATGTTTGATAGTTATATAGTTAAAAAATAATTAA
1 TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
651215 TTAGTTT
1 TTAGTTT
651222 GTTTTATTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 28 0.72
42 6 0.15
43 5 0.13
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (41 bp):
TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
Found at i:651245 original size:47 final size:47
Alignment explanation
Indices: 651202--651292 Score: 134
Period size: 45 Copynumber: 2.0 Consensus size: 47
651192 TTATATAGTT
*
651202 AAAAAA-TAATTAATTAGTTTGTTTTA-TT-AATAGTTAGTTATATA
1 AAAAAATTAATTAATTAGTTTGTGTTAGTTAAATAGTTAGTTATATA
*
651246 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAATTAATTAATTAGTTTGTGTTAGTTAAATAGTT-AGTTATAT
651293 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 6 0.15
45 18 0.44
46 2 0.05
47 7 0.17
48 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (47 bp):
AAAAAATTAATTAATTAGTTTGTGTTAGTTAAATAGTTAGTTATATA
Found at i:651264 original size:45 final size:45
Alignment explanation
Indices: 651161--651292 Score: 130
Period size: 45 Copynumber: 3.0 Consensus size: 45
651151 TACATAAATT
* * * * *
651161 AAAAATTATTTAATTAGTAT-ATGT-TTGATAGTTA--TATAGTTA
1 AAAAATTATTTAATTAGTTTGTTTTATTAATAGTTAGTTATA-TAA
*
651203 AAAAA-TAATTAATTAGTTTGTTTTATTAATAGTTAGTTATATAA
1 AAAAATTATTTAATTAGTTTGTTTTATTAATAGTTAGTTATATAA
*
651247 AAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAATTATTTAATTAGTTTGTTTTA-TT-AATAGTT-AGTTATAT
651293 TTGTTTGTTG
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
41 12 0.16
42 7 0.09
43 9 0.12
44 7 0.09
45 22 0.30
46 2 0.03
47 7 0.09
48 8 0.11
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (45 bp):
AAAAATTATTTAATTAGTTTGTTTTATTAATAGTTAGTTATATAA
Found at i:651370 original size:32 final size:33
Alignment explanation
Indices: 651334--651410 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 33
651324 TTAGTTAGTA
651334 AGTTTATTAGTAG-TATA-TTATAATGAAAA-AAT
1 AGTTTATTAGTAGTTATAGTTAT-AT-AAAAGAAT
*
651366 AGTTTATTAGTTAGTTTTAGTTATATAAAAGAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAGAAT
*
651400 ATTTTATTAGT
1 AGTTTATTAGT
651411 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
32 10 0.26
33 8 0.21
34 17 0.44
35 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (33 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAGAAT
Found at i:653669 original size:17 final size:17
Alignment explanation
Indices: 653647--653679 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
653637 CAATGATTTT
*
653647 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
653664 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
653680 AATATTTAGT
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:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:653696 original size:24 final size:22
Alignment explanation
Indices: 653664--653732 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
653654 AAATCATTAC
653664 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
* *
653686 TAGTAAATCAACTATTTTAAATCA-T
1 TAGT--ATCAAATA-ATTAAAT-ATT
653711 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
653733 AACAATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.03
22 11 0.29
23 7 0.18
24 7 0.18
25 11 0.29
26 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (22 bp):
TAGTATCAAATAATTAAATATT
Found at i:653900 original size:20 final size:20
Alignment explanation
Indices: 653872--653913 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
653862 TAGTATTCTA
* *
653872 TAATTATTAGTAATAATTAT
1 TAATCATTAGTAATAATCAT
*
653892 TAATCATTAGTATTAATCAT
1 TAATCATTAGTAATAATCAT
653912 TA
1 TA
653914 TTATAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (20 bp):
TAATCATTAGTAATAATCAT
Found at i:653905 original size:13 final size:13
Alignment explanation
Indices: 653889--653913 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
653879 TAGTAATAAT
653889 TATTAATCATTAG
1 TATTAATCATTAG
653902 TATTAATCATTA
1 TATTAATCATTA
653914 TTATAAATAA
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:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
TATTAATCATTAG
Found at i:653933 original size:11 final size:11
Alignment explanation
Indices: 653913--653948 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
653903 ATTAATCATT
653913 ATTA-TAAATA
1 ATTACTAAATA
653923 ATTACTAAATA
1 ATTACTAAATA
*
653934 ATAACTAAATA
1 ATTACTAAATA
653945 ATTA
1 ATTA
653949 TTATAAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 4 0.17
11 19 0.83
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (11 bp):
ATTACTAAATA
Found at i:653976 original size:12 final size:13
Alignment explanation
Indices: 653887--654484 Score: 252
Period size: 12 Copynumber: 45.1 Consensus size: 13
653877 ATTAGTAATA
*
653887 ATTATTAATCATT
1 ATTATAAATCATT
* *
653900 AGTATTAATCATT
1 ATTATAAATCATT
653913 ATTATAAAT-A--
1 ATTATAAATCATT
653923 ATTACTAAAT-A--
1 ATTA-TAAATCATT
* *
653934 ATAACTAAATAATT
1 ATTA-TAAATCATT
653948 ATTATAAAATCATT
1 ATTAT-AAATCATT
*
653962 ATTAT-AATGATT
1 ATTATAAATCATT
653974 ATTATCAAATCATT
1 ATTAT-AAATCATT
653988 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
654007 AAATATTTAAATCATT
1 --AT-TATAAATCATT
654023 A-T-TAAATCATT
1 ATTATAAATCATT
* *
654034 TTTAT-AATGATT
1 ATTATAAATCATT
*
654046 ATTACTAAATTATT
1 ATTA-TAAATCATT
*
654060 ATTAT-AATGATT
1 ATTATAAATCATT
654072 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
654086 ACTAT-AATGATT
1 ATTATAAATCATT
654098 ATTATCAAATCATT
1 ATTAT-AAATCATT
*
654112 A--CTAAATC-TT
1 ATTATAAATCATT
* * * * *
654122 CA-AATCATTAAAT
1 -ATTATAAATCATT
654135 ATT-TAAATCATT
1 ATTATAAATCATT
654147 A-T-TAAATCATT
1 ATTATAAATCATT
* *
654158 TTTAT-AATGATT
1 ATTATAAATCATT
654170 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
654184 ATTAT-AATGATT
1 ATTATAAATCATT
654196 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
654210 ACTAT-AATGATT
1 ATTATAAATCATT
654222 ATTATCAAATCATT
1 ATTAT-AAATCATT
654236 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
654255 AAATATTTAAATCATT
1 --AT-TATAAATCATT
654271 A-T-TAAATCATT
1 ATTATAAATCATT
* *
654282 TTTAT-AATGATT
1 ATTATAAATCATT
654294 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
654308 ATTAT-AATGATT
1 ATTATAAATCATT
654320 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
654334 ACTAT-AATGATT
1 ATTATAAATCATT
654346 ATTATCAAATCATT
1 ATTAT-AAATCATT
654360 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
654379 AAATATTTAAATCATT
1 --AT-TATAAATCATT
654395 A-T-TAAATCATT
1 ATTATAAATCATT
* *
654406 TTTAT-AATGATT
1 ATTATAAATCATT
654418 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
654432 ATTAT-AATGATT
1 ATTATAAATCATT
654444 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
654458 ACTAT-AATGATT
1 ATTATAAATCATT
654470 ATTATCAAATCATT
1 ATTAT-AAATCATT
654484 A
1 A
654485 CTAAATCATC
Statistics
Matches: 459, Mismatches: 62, Indels: 127
0.71 0.10 0.20
Matches are distributed among these distances:
10 6 0.01
11 58 0.13
12 151 0.33
13 33 0.07
14 133 0.29
15 3 0.01
16 24 0.05
17 3 0.01
18 9 0.02
19 33 0.07
20 3 0.01
21 3 0.01
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (13 bp):
ATTATAAATCATT
Found at i:653983 original size:26 final size:26
Alignment explanation
Indices: 653945--654484 Score: 427
Period size: 26 Copynumber: 21.7 Consensus size: 26
653935 TAACTAAATA
*
653945 ATTATTATAAAATCATTATTATAATG
1 ATTATTATCAAATCATTATTATAATG
* *
653971 ATTATTATCAAATCATTACTA-AATC
1 ATTATTATCAAATCATTATTATAATG
* * * * *
653996 ATCA-AATC-ATTAAATATT-TAA--
1 ATTATTATCAAATCATTATTATAATG
* * *
654017 ATCATTATTAAATCATTTTTATAATG
1 ATTATTATCAAATCATTATTATAATG
*
654043 ATTATTA-CTAAATTATTATTATAATG
1 ATTATTATC-AAATCATTATTATAATG
*
654069 ATTATTATCAAATCATTACTATAATG
1 ATTATTATCAAATCATTATTATAATG
*
654095 ATTATTATCAAATCATTACTA-AAT-
1 ATTATTATCAAATCATTATTATAATG
* * * * *
654119 CTTCA-AATC-ATTAAATATT-TAA--
1 ATT-ATTATCAAATCATTATTATAATG
* * *
654141 ATCATTATTAAATCATTTTTATAATG
1 ATTATTATCAAATCATTATTATAATG
654167 ATTATTA-CTAAATCATTATTATAATG
1 ATTATTATC-AAATCATTATTATAATG
*
654193 ATTATTATCAAATCATTACTATAATG
1 ATTATTATCAAATCATTATTATAATG
* *
654219 ATTATTATCAAATCATTACTA-AATC
1 ATTATTATCAAATCATTATTATAATG
* * * * *
654244 ATCA-AATC-ATTAAATATT-TAA--
1 ATTATTATCAAATCATTATTATAATG
* * *
654265 ATCATTATTAAATCATTTTTATAATG
1 ATTATTATCAAATCATTATTATAATG
654291 ATTATTA-CTAAATCATTATTATAATG
1 ATTATTATC-AAATCATTATTATAATG
*
654317 ATTATTATCAAATCATTACTATAATG
1 ATTATTATCAAATCATTATTATAATG
* *
654343 ATTATTATCAAATCATTACTA-AATC
1 ATTATTATCAAATCATTATTATAATG
* * * * *
654368 ATCA-AATC-ATTAAATATT-TAA--
1 ATTATTATCAAATCATTATTATAATG
* * *
654389 ATCATTATTAAATCATTTTTATAATG
1 ATTATTATCAAATCATTATTATAATG
654415 ATTATTA-CTAAATCATTATTATAATG
1 ATTATTATC-AAATCATTATTATAATG
*
654441 ATTATTATCAAATCATTACTATAATG
1 ATTATTATCAAATCATTATTATAATG
654467 ATTATTATCAAATCATTA
1 ATTATTATCAAATCATTA
654485 CTAAATCATC
Statistics
Matches: 408, Mismatches: 73, Indels: 66
0.75 0.13 0.12
Matches are distributed among these distances:
21 13 0.03
22 9 0.02
23 56 0.14
24 26 0.06
25 22 0.05
26 278 0.68
27 4 0.01
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (26 bp):
ATTATTATCAAATCATTATTATAATG
Found at i:654112 original size:124 final size:124
Alignment explanation
Indices: 653902--654542 Score: 1155
Period size: 124 Copynumber: 5.2 Consensus size: 124
653892 TAATCATTAG
* * * * * * *
653902 TATT-AATCATTATTATAA--ATAATTACTAAATAATAACTA-AATAATTATTATAAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
*
653963 TTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
*
654022 TATTAAATCATTTTTATAATGATTATTACTAAATTATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
*
654087 CTATAATGATTATTATCAAATCATTACTAAATCTTCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
654146 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
654211 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
654270 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
654335 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
654394 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
654459 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
*
654518 TATTAAATCATTATTATAATGATTA
1 TATTAAATCATTTTTATAATGATTA
654543 ATAAATACAT
Statistics
Matches: 505, Mismatches: 12, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
120 4 0.01
121 13 0.03
123 17 0.03
124 471 0.93
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (124 bp):
TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
Found at i:654427 original size:150 final size:145
Alignment explanation
Indices: 654144--654487 Score: 412
Period size: 150 Copynumber: 2.3 Consensus size: 145
654134 TATTTAAATC
* *
654144 ATTATTAAATCATTTTTATAATGATTATTA-CTAAATCATTATTATAATGATTATTATCAAATCA
1 ATTA-TAAATCATTATTATAATGATTATTATC-AAATCATTACTATAATGATTATTATCAAATCA
* * *
654208 TTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTAT
64 TTACTATAATCATAATCATCAAATCATTA-TAAATCAT---ATCATTAAATATTTAAATCATTAT
*
654273 TAAATCATTTTTATAATGATT
125 TAAATCATTATTATAATGATT
654294 ATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
1 ATTA-TAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
* *
654359 TACTA-AATCATCAAATCATTAAAT-ATT-TAAATCAT-T-ATTAAATCATTTTTATAATGATTA
65 TACTATAATCAT--AATCATCAAATCATTATAAATCATATCATTAAAT-A--TTTA-AATCATTA
654419 TTACTAAATCATTATTATAATGATT
124 -T--TAAATCATTATTATAATGATT
*
654444 ATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTA
1 ATTAT-AAATCATTATTATAATGATTATTATCAAATCATTACTA
654488 AATCATCAAA
Statistics
Matches: 173, Mismatches: 10, Indels: 22
0.84 0.05 0.11
Matches are distributed among these distances:
143 7 0.04
144 2 0.01
146 4 0.02
147 7 0.04
148 9 0.05
149 6 0.03
150 129 0.75
151 9 0.05
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (145 bp):
ATTATAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATT
ACTATAATCATAATCATCAAATCATTATAAATCATATCATTAAATATTTAAATCATTATTAAATC
ATTATTATAATGATT
Found at i:657427 original size:26 final size:24
Alignment explanation
Indices: 657369--657427 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
657359 CTAATAAACC
*
657369 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
657393 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
657421 TAATAAT
1 TAATAAT
657428 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:658274 original size:28 final size:30
Alignment explanation
Indices: 658234--658296 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
658224 ATTTTTTATA
*
658234 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
658264 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
658292 TAATA
1 TAATA
658297 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:658303 original size:28 final size:28
Alignment explanation
Indices: 658238--658303 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
658228 TTTATATAAT
*
658238 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
658266 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
658294 ATAATTTATA
1 ATAATATATA
658304 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:658306 original size:21 final size:21
Alignment explanation
Indices: 658273--658321 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
658263 CTAATATAAT
658273 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
658294 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
658315 ATTAACT
1 A-TAACT
658322 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:658870 original size:20 final size:20
Alignment explanation
Indices: 658845--658917 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 20
658835 CCATGCACAG
658845 CATGCATCCCACAACTCCCC
1 CATGCATCCCACAACTCCCC
**
658865 CATGCATTCCCACGTC-CCATGCAC
1 CATGCA-TCCCACAACTCC---C-C
658889 ATCATGCATCCCACAACTCCCC
1 --CATGCATCCCACAACTCCCC
658911 CATGCAT
1 CATGCAT
658918 GCTCCAATAC
Statistics
Matches: 41, Mismatches: 4, Indels: 16
0.67 0.07 0.26
Matches are distributed among these distances:
20 15 0.37
21 7 0.17
22 1 0.02
23 2 0.05
24 1 0.02
25 7 0.17
26 8 0.20
ACGTcount: A:0.25, C:0.48, G:0.08, T:0.19
Consensus pattern (20 bp):
CATGCATCCCACAACTCCCC
Found at i:658884 original size:46 final size:46
Alignment explanation
Indices: 658825--658917 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
658815 CCATGCACAG
658825 TTCCCACGTCCCATGCACAGCATGCATCCCACAACTCCCCCATGCA
1 TTCCCACGTCCCATGCACAGCATGCATCCCACAACTCCCCCATGCA
*
658871 TTCCCACGTCCCATGCACATCATGCATCCCACAACTCCCCCATGCA
1 TTCCCACGTCCCATGCACAGCATGCATCCCACAACTCCCCCATGCA
658917 T
1 T
658918 GCTCCAATAC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.24, C:0.47, G:0.10, T:0.19
Consensus pattern (46 bp):
TTCCCACGTCCCATGCACAGCATGCATCCCACAACTCCCCCATGCA
Found at i:659019 original size:29 final size:29
Alignment explanation
Indices: 658977--659038 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
658967 AATACCACAC
*
658977 AGGTCGCTCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
659006 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
659035 AGGT
1 AGGT
659039 TACTGTAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.18, C:0.34, G:0.32, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCCA
Found at i:659473 original size:3 final size:3
Alignment explanation
Indices: 659465--659528 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
659455 GGGACTAACT
* * * *
659465 AAG AAG AAG AAG AAA AAG AA- AAG AA- ATG AAGG AGG AGG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG AAG
659509 AAG AAG AAGG AAG AAAG AAG
1 AAG AAG AA-G AAG -AAG AAG
659529 GGAGGAAGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
2 3 0.06
3 39 0.78
4 8 0.16
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:659536 original size:19 final size:18
Alignment explanation
Indices: 659485--659536 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 18
659475 AGAAAAAGAA
659485 AAGAAATGAAGGAGG-AGG
1 AAGAAA-GAAGGAGGAAGG
*
659503 AAG-AAGAA-GAAGAAGG
1 AAGAAAGAAGGAGGAAGG
659519 AAGAAAGAAGGGAGGAAG
1 AAGAAAGAA-GGAGGAAG
659537 AAGTTGTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 3 0.11
16 9 0.32
17 7 0.25
18 3 0.11
19 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.42, T:0.02
Consensus pattern (18 bp):
AAGAAAGAAGGAGGAAGG
Found at i:665565 original size:3 final size:3
Alignment explanation
Indices: 665509--665554 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
665499 GTAAATTGTA
665509 AAT AA- AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
665555 TTAAATAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:667087 original size:12 final size:12
Alignment explanation
Indices: 667070--667111 Score: 84
Period size: 12 Copynumber: 3.5 Consensus size: 12
667060 ATGAACTGAA
667070 CGTTCAGCGAAC
1 CGTTCAGCGAAC
667082 CGTTCAGCGAAC
1 CGTTCAGCGAAC
667094 CGTTCAGCGAAC
1 CGTTCAGCGAAC
667106 CGTTCA
1 CGTTCA
667112 TGAACCGTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.19
Consensus pattern (12 bp):
CGTTCAGCGAAC
Found at i:667098 original size:24 final size:23
Alignment explanation
Indices: 667070--667119 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 23
667060 ATGAACTGAA
667070 CGTTCAGCGAACCGTTCAGCGAAC
1 CGTTCAGCGAACCGTTCA-CGAAC
*
667094 CGTTCAGCGAACCGTTCATGAAC
1 CGTTCAGCGAACCGTTCACGAAC
667117 CGT
1 CGT
667120 ACGGCGGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTTCAGCGAACCGTTCACGAAC
Found at i:667262 original size:24 final size:24
Alignment explanation
Indices: 667235--667307 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
667225 CGTTCATTTA
667235 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
667259 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * *
667283 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
667307 C
1 C
667308 ATTCATTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
24 43 0.96
25 2 0.04
ACGTcount: A:0.10, C:0.15, G:0.26, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:667264 original size:14 final size:14
Alignment explanation
Indices: 667245--667300 Score: 84
Period size: 14 Copynumber: 4.3 Consensus size: 14
667235 CGTTCGTGAA
667245 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
667259 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
667273 CG-T---TTATGTT
1 CGTTCGGTTATGTT
667283 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
667297 CGTT
1 CGTT
667301 TATGTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.07, C:0.14, G:0.27, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:667320 original size:24 final size:24
Alignment explanation
Indices: 667246--667307 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
667236 GTTCGTGAAC
*
667246 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
667270 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
667294 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
667308 ATTCATTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.08, C:0.13, G:0.26, T:0.53
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGGTTAT
Found at i:668411 original size:16 final size:16
Alignment explanation
Indices: 668390--668456 Score: 84
Period size: 16 Copynumber: 4.3 Consensus size: 16
668380 GTCTCCAACG
668390 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
668406 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
** *
668422 TTTATGTTCGTGCGCG
1 TTTATGTTCGTGTTCA
668438 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
668452 TTTAT
1 TTTAT
668457 TAAATGAACG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 5 0.11
16 40 0.89
ACGTcount: A:0.10, C:0.12, G:0.21, T:0.57
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:668429 original size:32 final size:32
Alignment explanation
Indices: 668388--668448 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
668378 GGGTCTCCAA
**
668388 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGCGCATTTATGTTCGTGTT
*
668420 CGTTTATGTTCGTGCGCGTTTATGTTCGT
1 CGTTTATGTTCGTGCGCATTTATGTTCGT
668449 TTATTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.08, C:0.15, G:0.25, T:0.52
Consensus pattern (32 bp):
CGTTTATGTTCGTGCGCATTTATGTTCGTGTT
Found at i:668538 original size:16 final size:16
Alignment explanation
Indices: 668517--668547 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
668507 AAAAAAAAAT
668517 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
668533 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
668548 ATTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:673658 original size:43 final size:43
Alignment explanation
Indices: 673590--673675 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
673580 ACTTTGGTTC
* *
673590 GGTTGTAATATGTTAGTTTGATATATTTGTAGATTGTTACTTT
1 GGTTGTAATATATTAATTTGATATATTTGTAGATTGTTACTTT
*
673633 GGTTGTAATATATTAATTT-AGTATATTTGTGGATTGTTACTTT
1 GGTTGTAATATATTAATTTGA-TATATTTGTAGATTGTTACTTT
673676 AGAGTTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
42 1 0.03
43 38 0.97
ACGTcount: A:0.24, C:0.02, G:0.20, T:0.53
Consensus pattern (43 bp):
GGTTGTAATATATTAATTTGATATATTTGTAGATTGTTACTTT
Found at i:673992 original size:2 final size:2
Alignment explanation
Indices: 673974--674007 Score: 50
Period size: 2 Copynumber: 16.0 Consensus size: 2
673964 ACCCCTACAC
673974 AT AT GAT AT ACT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
674008 TTCCACTCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 26 0.87
3 4 0.13
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:678061 original size:2 final size:2
Alignment explanation
Indices: 678056--678080 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
678046 ATATGCATAC
678056 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 A
678081 AGCACTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:678635 original size:23 final size:23
Alignment explanation
Indices: 678588--678636 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
678578 AATAACATAT
**
678588 TAGGTAACGCTTATATAATGTAA
1 TAGGTAACGCTTATATAATAAAA
*
678611 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAACGCTTATATAATAAAA
678634 TAG
1 TAG
678637 ACATTTAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (23 bp):
TAGGTAACGCTTATATAATAAAA
Found at i:682418 original size:20 final size:20
Alignment explanation
Indices: 682375--682433 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
682365 TTTAATGTTG
**
682375 AAGTGG-TTTAGGGGTTTT-
1 AAGTGGTTTTAGGTTTTTTA
682393 AAGTGGTTTTAGGTTTTTTA
1 AAGTGGTTTTAGGTTTTTTA
*
682413 AAGTGGTTTAAGGTTTTTTA
1 AAGTGGTTTTAGGTTTTTTA
682433 A
1 A
682434 GTTGTTTAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
18 6 0.17
19 10 0.28
20 20 0.56
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (20 bp):
AAGTGGTTTTAGGTTTTTTA
Found at i:682442 original size:38 final size:39
Alignment explanation
Indices: 682375--682452 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
682365 TTTAATGTTG
*
682375 AAGTGGTTTAGGGGTTTTAAGTGGTTTTA-GGTTTTTTA
1 AAGTGGTTTAGGGGTTTTAAGTGGTTTTAGGGGTTTTTA
** *
682413 AAGTGGTTTAAGGTTTTTTAAGTTG-TTTAGGGGTTTTTA
1 AAGTGGTTT-AGGGGTTTTAAGTGGTTTTAGGGGTTTTTA
682452 A
1 A
682453 TATTTATAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
38 13 0.38
39 21 0.62
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (39 bp):
AAGTGGTTTAGGGGTTTTAAGTGGTTTTAGGGGTTTTTA
Found at i:682450 original size:19 final size:19
Alignment explanation
Indices: 682375--682452 Score: 88
Period size: 19 Copynumber: 4.1 Consensus size: 19
682365 TTTAATGTTG
682375 AAGTGGTTTAGGGG-TTTT
1 AAGTGGTTTAGGGGTTTTT
*
682393 AAGTGGTTTTA-GGTTTTTT
1 AAGTGG-TTTAGGGGTTTTT
* *
682412 AAAGTGGTTTAAGGTTTTTT
1 -AAGTGGTTTAGGGGTTTTT
*
682432 AAGTTGTTTAGGGGTTTTT
1 AAGTGGTTTAGGGGTTTTT
682451 AA
1 AA
682453 TATTTATAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
18 8 0.15
19 30 0.58
20 14 0.27
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (19 bp):
AAGTGGTTTAGGGGTTTTT
Found at i:685648 original size:24 final size:24
Alignment explanation
Indices: 685604--685650 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
685594 CCTTATTTTG
**
685604 AGATTGAGAGTTTGAGAGTTTTAA
1 AGATTGAGAGTTAAAGAGTTTTAA
685628 AGATTGAGAGTTAAA-AGGTTTTA
1 AGATTGAGAGTTAAAGA-GTTTTA
685651 GAAGTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.36, C:0.00, G:0.28, T:0.36
Consensus pattern (24 bp):
AGATTGAGAGTTAAAGAGTTTTAA
Found at i:686048 original size:170 final size:169
Alignment explanation
Indices: 685755--686294 Score: 642
Period size: 170 Copynumber: 3.2 Consensus size: 169
685745 TTTTTTTGTT
* * *
685755 AGAGATTCTCTGAGAAAAGGAAAAACACTTCCCCTGGAA--TACTCTTTTCCTCTTTGTCGGATT
1 AGAGATTCTCTGAGAAAAGGAAAAACGCTTCCCCTGGAACGT-CTCTTTT-CTTTTTGTCAGATT
* * * * * * * *
685818 TTATATGGAAGTCTCAATCTATTATATTAAGATATCTTTAGATAGTATGGGAAATATTCCCGTCA
64 TTATACGGAAGTCTTAATCTATTATGTTGAGATTTCTGTAGATAGTA-GGGAACTATTCCCATCA
* *
685883 GACCAATATAATGTTTGATGGGATGAGACACTTTAACATGGC
128 GACCAATATAATGTTTGATGGGATGAGACACTATGACATGGC
* * * *
685925 AGAGATTCTCTGACAAAAGGAAAAACGCTTCCCCTGGAACGTGTCTTTTCTTTTTTTCTGATTTT
1 AGAGATTCTCTGAGAAAAGGAAAAACGCTTCCCCTGGAACGTCTCTTTTCTTTTTGTCAGATTTT
* *
685990 ATACGGAAGTCTTAATCTATTATGTTGGGATTTCTGTAGGTAGTAGGGGAACTATTCCCATCAGA
66 ATACGGAAGTCTTAATCTATTATGTTGAGATTTCTGTAGATAGTA-GGGAACTATTCCCATCAGA
** * * *
686055 ATAATAAAATGTTTGATGGGATGAGACACTATGATATGGT
130 CCAATATAATGTTTGATGGGATGAGACACTATGACATGGC
* * * * *
686095 AGAGATTCTCTGAGAAAAGAAAAAACGCTTGCCCTGGAACG-CACATTT-TTTTCGTCAGATTTT
1 AGAGATTCTCTGAGAAAAGGAAAAACGCTTCCCCTGGAACGTCTCTTTTCTTTTTGTCAGATTTT
* * * *
686158 AT-CAGGAAGTCTTAGTCCATTATGCTGAGATTTC-GATAGATAGTATGGAACTATTCCCATCAG
66 ATAC-GGAAGTCTTAATCTATTATGTTGAGATTTCTG-TAGATAGTAGGGAACTATTCCCATCAG
* *
686221 ACCGATATAATGTTTGATGGGATGAGACACTATGACATGAC
129 ACCAATATAATGTTTGATGGGATGAGACACTATGACATGGC
* * *
686262 AAAGATTCTTTGAGAAAAGGAAAGACGCTTCCC
1 AGAGATTCTCTGAGAAAAGGAAAAACGCTTCCC
686295 GTAGAACGCG
Statistics
Matches: 315, Mismatches: 51, Indels: 11
0.84 0.14 0.03
Matches are distributed among these distances:
167 81 0.26
168 48 0.15
169 4 0.01
170 175 0.56
171 6 0.02
172 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (169 bp):
AGAGATTCTCTGAGAAAAGGAAAAACGCTTCCCCTGGAACGTCTCTTTTCTTTTTGTCAGATTTT
ATACGGAAGTCTTAATCTATTATGTTGAGATTTCTGTAGATAGTAGGGAACTATTCCCATCAGAC
CAATATAATGTTTGATGGGATGAGACACTATGACATGGC
Found at i:688308 original size:21 final size:21
Alignment explanation
Indices: 688282--688335 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
688272 CCGTGTAGTA
*
688282 GTGGCATCTGAATCGGTTGGG
1 GTGGCATCTGAATCGATTGGG
* *
688303 GTGGCATCTAAATCGATTGTG
1 GTGGCATCTGAATCGATTGGG
688324 GTGGCATCTGAA
1 GTGGCATCTGAA
688336 CCGGAAGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.15, G:0.35, T:0.30
Consensus pattern (21 bp):
GTGGCATCTGAATCGATTGGG
Found at i:688670 original size:2 final size:2
Alignment explanation
Indices: 688663--688694 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
688653 TTGGAACTAA
688663 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
688695 TCTTATCAAA
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:689852 original size:16 final size:17
Alignment explanation
Indices: 689812--689857 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
689802 TGCAAAAAAT
*
689812 AATAAAAATAATTAGTAC
1 AATAAAAAT-ATTAGTAA
689830 AAT-AAAATATTA-TAA
1 AATAAAAATATTAGTAA
689845 AATAAAAATATTA
1 AATAAAAATATTA
689858 AATAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 5 0.19
16 13 0.50
17 5 0.19
18 3 0.12
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
AATAAAAATATTAGTAA
Found at i:690294 original size:29 final size:29
Alignment explanation
Indices: 690245--690300 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
690235 TCACATTGTC
*
690245 AGAAATGGTGCTAGATTGGTAAAATTTAG
1 AGAAATGGTGCTAGATCGGTAAAATTTAG
* * *
690274 AGAATTGGTGCTTGATCGGTAATATTT
1 AGAAATGGTGCTAGATCGGTAAAATTT
690301 TAATATTAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.36
Consensus pattern (29 bp):
AGAAATGGTGCTAGATCGGTAAAATTTAG
Found at i:696965 original size:17 final size:19
Alignment explanation
Indices: 696943--696985 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
696933 TGCTGGTCGG
696943 ATATCG-AC-TCATCGCTT
1 ATATCGCACTTCATCGCTT
*
696960 ATATCGCTCTTCATCGCTT
1 ATATCGCACTTCATCGCTT
696979 ATATCGC
1 ATATCGC
696986 TTATATCGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 1 0.04
19 16 0.70
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.37
Consensus pattern (19 bp):
ATATCGCACTTCATCGCTT
Found at i:696967 original size:9 final size:9
Alignment explanation
Indices: 696953--696995 Score: 61
Period size: 9 Copynumber: 4.7 Consensus size: 9
696943 ATATCGACTC
696953 ATCGCTTAT
1 ATCGCTTAT
696962 ATCGCTCT-T
1 ATCGCT-TAT
696971 CATCGCTTAT
1 -ATCGCTTAT
696981 ATCGCTTAT
1 ATCGCTTAT
696990 ATCGCT
1 ATCGCT
696996 CTTCATCGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 23 0.74
10 8 0.26
ACGTcount: A:0.19, C:0.28, G:0.12, T:0.42
Consensus pattern (9 bp):
ATCGCTTAT
Found at i:700125 original size:36 final size:36
Alignment explanation
Indices: 700084--700182 Score: 180
Period size: 36 Copynumber: 2.8 Consensus size: 36
700074 ATTTATCCAT
*
700084 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
700120 TATCAGCTTTGGTACATTCGTCTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
700156 TATCAGCTTTGGTACATTCGTGTATCA
1 TATCAGCTTTGGTACATTCGTGTATCA
700183 TTGTCCAGCA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:702398 original size:21 final size:21
Alignment explanation
Indices: 702372--702416 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
702362 GATTTCTGGG
* *
702372 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
702393 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
702414 CAA
1 CAA
702417 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:703250 original size:31 final size:31
Alignment explanation
Indices: 703212--703336 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
703202 AGGGTCGAGG
703212 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
703243 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
703274 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
703305 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
703336 G
1 G
703337 GTCCTTCGGG
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:706514 original size:21 final size:21
Alignment explanation
Indices: 706488--706532 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
706478 GATTTCTGGG
* *
706488 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
706509 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
706530 CAA
1 CAA
706533 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:707372 original size:31 final size:31
Alignment explanation
Indices: 707334--707458 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
707324 AGGGTCGAGG
707334 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
707365 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
707396 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
707427 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
707458 G
1 G
707459 GTCCTTCGGG
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:709870 original size:25 final size:25
Alignment explanation
Indices: 709833--709890 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
709823 TGGGCCATGT
**
709833 GATTTCAGCAGAAGGAATTGTAGTA
1 GATTTCAAAAGAAGGAATTGTAGTA
709858 GATTTCAAAAGAAGGAATTGTAGTA
1 GATTTCAAAAGAAGGAATTGTAGTA
709883 GATTTCAA
1 GATTTCAA
709891 GAAATTGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (25 bp):
GATTTCAAAAGAAGGAATTGTAGTA
Found at i:714276 original size:36 final size:36
Alignment explanation
Indices: 714230--714400 Score: 270
Period size: 36 Copynumber: 4.8 Consensus size: 36
714220 ATTTATCCAT
*
714230 TATCAACTTTGATACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
* *
714266 TATCAGCTTTGCTATATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
*
714302 GATCAGCTTTGATACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
* *
714338 TATCATCTTTGATACATTCATGTATCAATGTTATCA
1 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
* *
714374 TATCAGCTTTGGTACATTCATGTATCA
1 TATCAGCTTTGATACATTCGTGTATCA
714401 TTGTCCAGCA
Statistics
Matches: 124, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 124 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
Found at i:715735 original size:2 final size:2
Alignment explanation
Indices: 715728--715759 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
715718 AAACATTTTA
715728 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
715760 GTTTTGACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:715869 original size:38 final size:38
Alignment explanation
Indices: 715746--716179 Score: 403
Period size: 36 Copynumber: 11.3 Consensus size: 38
715736 ATATATATAT
* * * * *
715746 ATATATATAATATAGTTTTGACAAGCATGTTTTAAAAACA
1 ATATATATTATATAGTTTTTA-AAACAT-TTTTGAAAATA
* *
715786 TTTATATATTATATAGTTTTTAAAACATTTTTTGAATATA
1 -ATATATATTATATAGTTTTTAAAACA-TTTTTGAAAATA
*
715826 TATATATATTATATAGTTTTTAAAACA-TTGTGAAAACTA
1 -ATATATATTATATAGTTTTTAAAACATTTTTGAAAA-TA
715865 ATATA-A-TATATAGTTTTTAAAACATTTTTTGAAAAT-
1 ATATATATTATATAGTTTTTAAAACA-TTTTTGAAAATA
715901 ATATATATTATATAGTTTTTAAAACA-TTTTGAAAACTA
1 ATATATATTATATAGTTTTTAAAACATTTTTGAAAA-TA
* *
715939 ATGTA-A-TATATAGGTTTTAAAACATTTTTTGAAAAT-
1 ATATATATTATATAGTTTTTAAAACA-TTTTTGAAAATA
* *
715975 ATATATGTTATATACTTTTTAAAACA-TTTTGAAAATA
1 ATATATATTATATAGTTTTTAAAACATTTTTGAAAATA
* * *
716012 A-ATATAATATATAATTTTTAAAAATATTTTTG--AA-A
1 ATATATATTATATAGTTTTT-AAAACATTTTTGAAAATA
*
716047 ATATATATTATATAGTTTTTAAAACA-TTTTGGAAATA
1 ATATATATTATATAGTTTTTAAAACATTTTTGAAAATA
*
716084 TATATAATATTATATAGTTTTTGAAAAATCATTTTTGAAAATG
1 -ATAT-ATATTATATAGTTTTT--AAAA-CATTTTTGAAAATA
* * * *
716127 CT-TATAATATATAGTTTTTAAAATAACATTTTAGAAATTA
1 ATATATATTATATAGTTTTT--AA-AACATTTTTGAAAATA
*
716167 ATATATTTTATAT
1 ATATATATTATAT
716180 TTTTGAAATT
Statistics
Matches: 331, Mismatches: 35, Indels: 54
0.79 0.08 0.13
Matches are distributed among these distances:
34 5 0.02
35 7 0.02
36 98 0.30
37 13 0.04
38 76 0.23
39 18 0.05
40 68 0.21
41 34 0.10
42 3 0.01
43 9 0.03
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (38 bp):
ATATATATTATATAGTTTTTAAAACATTTTTGAAAATA
Found at i:715919 original size:74 final size:73
Alignment explanation
Indices: 715789--716149 Score: 471
Period size: 74 Copynumber: 4.8 Consensus size: 73
715779 AAAAACATTT
*
715789 ATATATTATATAGTTTTTAAAACATTTTTTGAATATATATATATATTATATAGTTTTTAAAACAT
1 ATATAATATATAGTTTTTAAAACATTTTTTGAA-A-ATATATATATTATATAGTTTTTAAAACAT
*
715854 TGTGAAAACTA
64 TTTGAAAA-TA
715865 ATATAATATATAGTTTTTAAAACATTTTTTGAAAATATATATATTATATAGTTTTTAAAACATTT
1 ATATAATATATAGTTTTTAAAACATTTTTTGAAAATATATATATTATATAGTTTTTAAAACATTT
715930 TGAAAACTA
66 TGAAAA-TA
* * * *
715939 ATGTAATATATAGGTTTTAAAACATTTTTTGAAAATATATATGTTATATACTTTTTAAAACATTT
1 ATATAATATATAGTTTTTAAAACATTTTTTGAAAATATATATATTATATAGTTTTTAAAACATTT
716004 TGAAAATAA
66 TGAAAAT-A
*
716013 ATATAATATATAATTTTTAAAA-ATATTTTTG-AAA-ATATATATTATATAGTTTTTAAAACATT
1 ATATAATATATAGTTTTTAAAACAT-TTTTTGAAAATATATATATTATATAGTTTTTAAAACATT
716075 TTGGAAATATA
65 TT-GAAA-ATA
* * *
716086 TATAATATTATATAGTTTTTGAAAA-ATCATTTTTGAAAATGCT-TATAATATATAGTTTTTAAA
1 -AT-ATAATATATAGTTTTT-AAAACAT--TTTTTGAAAAT-ATATATATTATATAGTTTTTAAA
716149 A
60 A
716150 TAACATTTTA
Statistics
Matches: 259, Mismatches: 15, Indels: 19
0.88 0.05 0.06
Matches are distributed among these distances:
72 28 0.11
73 11 0.04
74 136 0.53
75 15 0.06
76 38 0.15
77 7 0.03
78 3 0.01
79 20 0.08
80 1 0.00
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (73 bp):
ATATAATATATAGTTTTTAAAACATTTTTTGAAAATATATATATTATATAGTTTTTAAAACATTT
TGAAAATA
Found at i:716201 original size:4 final size:4
Alignment explanation
Indices: 716192--716247 Score: 75
Period size: 4 Copynumber: 14.8 Consensus size: 4
716182 TTGAAATTGT
716192 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTA -TTA TTTA -TTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
716237 -TTA TTTTA TTT
1 TTTA -TTTA TTT
716248 TTTTGTTCAG
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
3 12 0.24
4 34 0.69
5 3 0.06
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:721823 original size:64 final size:66
Alignment explanation
Indices: 721699--721844 Score: 190
Period size: 64 Copynumber: 2.2 Consensus size: 66
721689 TTTTTCAGAG
* * * * *
721699 TGATGCACCGATGCACCAATCCATGCATCGATGCACCATGAATTATTTTGAAACATCGAATGCAT
1 TGATGCATCGATGCACCAAGCCATGCATCGATGCACCATGAACTATTTTAAAACATCGAATGCAC
721764 T
66 T
* *
721765 TGATGCATCGATGCACC-AGCCATGCATCGATGCACTC-TG-GCTATTTTAAAACATCGAATGTA
1 TGATGCATCGATGCACCAAGCCATGCATCGATGCAC-CATGAACTATTTTAAAACATCGAATGCA
721827 CT
65 CT
*
721829 TGATGCATCAATGCAC
1 TGATGCATCGATGCAC
721845 TCTTAGTGCA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
64 35 0.49
65 19 0.27
66 17 0.24
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (66 bp):
TGATGCATCGATGCACCAAGCCATGCATCGATGCACCATGAACTATTTTAAAACATCGAATGCAC
T
Found at i:721860 original size:64 final size:62
Alignment explanation
Indices: 721742--721864 Score: 149
Period size: 64 Copynumber: 1.9 Consensus size: 62
721732 CACCATGAAT
* * * *
721742 TATTTTGAAACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGC
1 TATTTTAAAACATCGAATGCACTTGATGCATCAATGCACCAG-C-TGCACCGATGCACTCTGGC
*
721806 TATTTTAAAACATCGAATGTACTTGATGCATCAATGCACTCTTAG-TGCACCGATGCACT
1 TATTTTAAAACATCGAATGCACTTGATGCATCAATGCAC-C--AGCTGCACCGATGCACT
721865 AAGGGTCCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
64 48 0.94
65 1 0.02
67 2 0.04
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (62 bp):
TATTTTAAAACATCGAATGCACTTGATGCATCAATGCACCAGCTGCACCGATGCACTCTGGC
Found at i:729307 original size:21 final size:21
Alignment explanation
Indices: 729265--729308 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
729255 ACTCTGGGAG
* *
729265 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
729286 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
729307 CT
1 CT
729309 CCTCCGGCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:730049 original size:12 final size:12
Alignment explanation
Indices: 730032--730059 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
730022 AAGGGGAGTA
730032 ATTTCAAAATTG
1 ATTTCAAAATTG
730044 ATTTCAAAATTG
1 ATTTCAAAATTG
730056 ATTT
1 ATTT
730060 TTCAAAGAAA
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:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (12 bp):
ATTTCAAAATTG
Found at i:732879 original size:85 final size:84
Alignment explanation
Indices: 732736--733047 Score: 398
Period size: 85 Copynumber: 3.7 Consensus size: 84
732726 TTTTTAAGAC
* * * * * *
732736 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCCCCGAGTTCGATT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACC-AAAGACCCTCGAGTTCGATT
732801 ACACTCAGCTTCGAGGGCAA
65 ACACTCAGCTTCGAGGGCAA
* * *
732821 ATCATTTGCAGCATAACTTAAGTCGAGAATGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCCTCGAGTTCGATT
* * * *
732886 ACGCTCAGC-TCCAAGGCAC
65 ACACTCAGCTTCGAGGGCAA
* * *
732905 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTG---CCAAAGACCCTCAAGTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCCTCGAGTTCGATTA
*
732967 CACTCAACTTCGAGGGCAA
66 CACTCAGCTTCGAGGGCAA
* *
732986 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAATACCTTCGAGTTCG
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCCTCGAGTTCG
733048 TGATACATGC
Statistics
Matches: 192, Mismatches: 29, Indels: 12
0.82 0.12 0.05
Matches are distributed among these distances:
80 26 0.14
81 44 0.23
84 43 0.22
85 76 0.40
86 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (84 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCCTCGAGTTCGATTA
CACTCAGCTTCGAGGGCAA
Done.