Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007880.1 Hibiscus syriacus cultivar Beakdansim tig00110258_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: 1382630
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 5 of 5
Found at i:1128265 original size:23 final size:23
Alignment explanation
Indices: 1128209--1128266 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
1128199 TAAGCTACCA
1128209 AAAGGCAGAGAAAAACGTATCAC
1 AAAGGCAGAGAAAAACGTATCAC
* ** * * *
1128232 AAATGTGGAGATAAACGTGTCAT
1 AAAGGCAGAGAAAAACGTATCAC
1128255 AAAGGCAGAGAA
1 AAAGGCAGAGAA
1128267 TATATCACAA
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.48, C:0.12, G:0.26, T:0.14
Consensus pattern (23 bp):
AAAGGCAGAGAAAAACGTATCAC
Found at i:1132661 original size:141 final size:141
Alignment explanation
Indices: 1132415--1132797 Score: 450
Period size: 141 Copynumber: 2.7 Consensus size: 141
1132405 AGTCCACCTT
* * * * * * *
1132415 CGAGGTCAAAAACTGAGATTG-TGTAGGTTTGGATCTAAGCCTACGCCTT-ATGTCAAACAATTT
1 CGAGATCAAAAACAGAGA-TGCTGCAGGTTTGGATCTAAGCCTACG-CTTGAAGCCATACGATTT
* * * * * * *
1132478 GGAGATTCCAAATCCGAGTCACAACGAATCTAACGATGACATTGGCGATATGCAAAACAAAGACG
64 AGAGATTCCAAATCCGAGTCGCAACGATTCGAACGATGACATTGGCAAAATACAAAACAAAGACG
* *
1132543 A-TGACTCCACCTG
129 ACAG-CTCCACCCG
* * * * *
1132556 TGAGATCAATAACAGAGATGCTGCAGGTTTGGATCTAAGTCTACGCTTGAAGCCGTACGGTTTAG
1 CGAGATCAAAAACAGAGATGCTGCAGGTTTGGATCTAAGCCTACGCTTGAAGCCATACGATTTAG
* *
1132621 AGATTCCAAATCCGAGTCGCAACGATTCGAATGATGACATTTGCAAAATACAAAACAAAGACGAC
66 AGATTCCAAATCCGAGTCGCAACGATTCGAACGATGACATTGGCAAAATACAAAACAAAGACGAC
*
1132686 AGCTCCTCCCG
131 AGCTCCACCCG
* * *
1132697 CGAGGTCAAAAACAGAGATGCTGCAGGTTTGGATTTAAGCCTACGGTTGAAGCCATACGATTTAG
1 CGAGATCAAAAACAGAGATGCTGCAGGTTTGGATCTAAGCCTACGCTTGAAGCCATACGATTTAG
* *
1132762 -GATTCCAAATCCGAGTAGCAACGATTCGAACAATGA
66 AGATTCCAAATCCGAGTCGCAACGATTCGAACGATGA
1132798 AATTTGCGAT
Statistics
Matches: 204, Mismatches: 35, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
140 38 0.19
141 165 0.81
142 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (141 bp):
CGAGATCAAAAACAGAGATGCTGCAGGTTTGGATCTAAGCCTACGCTTGAAGCCATACGATTTAG
AGATTCCAAATCCGAGTCGCAACGATTCGAACGATGACATTGGCAAAATACAAAACAAAGACGAC
AGCTCCACCCG
Found at i:1132889 original size:18 final size:18
Alignment explanation
Indices: 1132866--1132903 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1132856 ATAACGACAA
1132866 TTCCGGCTG-CGAAGAATG
1 TTCCGG-TGACGAAGAATG
*
1132884 TTCCGGTGACGGAGAATG
1 TTCCGGTGACGAAGAATG
1132902 TT
1 TT
1132904 TGTGCCGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.26
Consensus pattern (18 bp):
TTCCGGTGACGAAGAATG
Found at i:1135137 original size:53 final size:53
Alignment explanation
Indices: 1135048--1135213 Score: 233
Period size: 53 Copynumber: 3.1 Consensus size: 53
1135038 CTAAGAAACA
* * * * * * *
1135048 ATTAGCAACATCACCAGGAGAACATTGCATAAGTTTAACGCCAGGATTCAAGC
1 ATTAACAACATCACGAGGAGAACGTTGCGTAGGTTTAACGCTAGGATTTAAGC
*
1135101 ATTAACAACATCACGAGGAGAACGTAGCGTAGGTTTAACGCTAGGATTTAAGC
1 ATTAACAACATCACGAGGAGAACGTTGCGTAGGTTTAACGCTAGGATTTAAGC
* * *
1135154 ATTAGCAACATCACGACGAGAACGTTGCGTAGGTTTAACGCTGGGATTTAAGC
1 ATTAACAACATCACGAGGAGAACGTTGCGTAGGTTTAACGCTAGGATTTAAGC
1135207 ATTAACA
1 ATTAACA
1135214 CCCAGCCACG
Statistics
Matches: 100, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 100 1.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (53 bp):
ATTAACAACATCACGAGGAGAACGTTGCGTAGGTTTAACGCTAGGATTTAAGC
Found at i:1137246 original size:20 final size:20
Alignment explanation
Indices: 1137223--1137263 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1137213 AAAGGTATGT
* *
1137223 AGTATGCGGATCAGGTCTGC
1 AGTATGCGGACCAAGTCTGC
1137243 AGTATGCGGACCAAGTCTGC
1 AGTATGCGGACCAAGTCTGC
1137263 A
1 A
1137264 AACATCTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.22
Consensus pattern (20 bp):
AGTATGCGGACCAAGTCTGC
Found at i:1137601 original size:12 final size:12
Alignment explanation
Indices: 1137586--1137627 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1137576 TTATTTAAAT
1137586 GGGTATTGGGCC
1 GGGTATTGGGCC
1137598 GGGTATTGGGCC
1 GGGTATTGGGCC
* * *
1137610 GAGAATCGGGCC
1 GGGTATTGGGCC
1137622 GGGTAT
1 GGGTAT
1137628 ATATATATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.14, C:0.17, G:0.48, T:0.21
Consensus pattern (12 bp):
GGGTATTGGGCC
Found at i:1137664 original size:31 final size:31
Alignment explanation
Indices: 1137626--1137708 Score: 112
Period size: 31 Copynumber: 2.6 Consensus size: 31
1137616 CGGGCCGGGT
1137626 ATATATATATATATTTAAATTAAATATATAA
1 ATATATATATATATTTAAATTAAATATATAA
* * * *
1137657 ATATATATTTTTATTTAAATTAAATTTATTA
1 ATATATATATATATTTAAATTAAATATATAA
*
1137688 ATATTATATATATATATAAAT
1 ATA-TATATATATATTTAAAT
1137709 AATTATTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 30 0.68
32 14 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
ATATATATATATATTTAAATTAAATATATAA
Found at i:1137782 original size:13 final size:13
Alignment explanation
Indices: 1137726--1137769 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
1137716 TTTAATATTT
*
1137726 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
*
1137738 ATCGGGGCAGGTA
1 ATCGGGGCGGGTA
*
1137751 ATCGGGGCGGATA
1 ATCGGGGCGGGTA
1137764 ATCGGG
1 ATCGGG
1137770 TAATCGGGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.18, C:0.16, G:0.48, T:0.18
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:1138488 original size:20 final size:20
Alignment explanation
Indices: 1138440--1138501 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
1138430 AATTTAAATC
*
1138440 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
1138460 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
1138478 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
1138497 AAAAT
1 AAAAT
1138502 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:1138551 original size:23 final size:23
Alignment explanation
Indices: 1138520--1138596 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
1138510 TATATTATAA
*
1138520 TATTAAAAAAATAATATTTAATT
1 TATTTAAAAAATAATATTTAATT
*
1138543 TATTTAAAAAATAATATTAAAATT
1 TATTTAAAAAATAATATT-TAATT
* * *
1138567 AATATCTATAATATAATA-TTAATT
1 --TATTTAAAAAATAATATTTAATT
1138591 TATTTA
1 TATTTA
1138597 TTTAAAAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
22 5 0.11
23 17 0.39
24 8 0.18
25 1 0.02
26 13 0.30
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTTAAAAAATAATATTTAATT
Found at i:1138641 original size:56 final size:53
Alignment explanation
Indices: 1138535--1138636 Score: 165
Period size: 53 Copynumber: 2.0 Consensus size: 53
1138525 AAAAAATAAT
*
1138535 ATTTAATTTATTTAAAAAATAATATTAAAATTAATATCTATAATATAATATTA
1 ATTTAATTTATTTAAAAAATAATATTAAAATTAAAATCTATAATATAATATTA
1138588 ATTT-ATTTATTTAAAAAATTAATATTAAAATTAAAATC-A-AATATAATAT
1 ATTTAATTTATTTAAAAAA-TAATATTAAAATTAAAATCTATAATATAATAT
1138637 AATATAAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
51 10 0.21
52 15 0.32
53 22 0.47
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (53 bp):
ATTTAATTTATTTAAAAAATAATATTAAAATTAAAATCTATAATATAATATTA
Found at i:1142728 original size:48 final size:48
Alignment explanation
Indices: 1142657--1142750 Score: 170
Period size: 48 Copynumber: 2.0 Consensus size: 48
1142647 TGGAAAACAC
* *
1142657 CCCATTTCCTCAATTAGCTACAACAAGATTGTTTTCATTTTCCCCAAG
1 CCCATTTCCTCAATCAGCTACAACAAGACTGTTTTCATTTTCCCCAAG
1142705 CCCATTTCCTCAATCAGCTACAACAAGACTGTTTTCATTTTCCCCA
1 CCCATTTCCTCAATCAGCTACAACAAGACTGTTTTCATTTTCCCCA
1142751 GATAAGGTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.27, C:0.32, G:0.07, T:0.34
Consensus pattern (48 bp):
CCCATTTCCTCAATCAGCTACAACAAGACTGTTTTCATTTTCCCCAAG
Found at i:1143768 original size:23 final size:23
Alignment explanation
Indices: 1143739--1143804 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
1143729 TTAACGAACG
*
1143739 TAAATGAACATAAACGAACATAA
1 TAAATGAACATAAACGAACACAA
1143762 TAAATGAACATAAACGAACACAA
1 TAAATGAACATAAACGAACACAA
* * *
1143785 TAAACGAATATAAACAAACA
1 TAAATGAACATAAACGAACA
1143805 ACACAAACAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (23 bp):
TAAATGAACATAAACGAACACAA
Found at i:1143770 original size:13 final size:13
Alignment explanation
Indices: 1143748--1143797 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
1143738 GTAAATGAAC
1143748 ATAAACGAACATA
1 ATAAACGAACATA
*
1143761 ATAAATGAAC---
1 ATAAACGAACATA
*
1143771 ATAAACGAACACA
1 ATAAACGAACATA
*
1143784 ATAAACGAATATA
1 ATAAACGAACATA
1143797 A
1 A
1143798 ACAAACAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
10 9 0.30
13 21 0.70
ACGTcount: A:0.62, C:0.14, G:0.08, T:0.16
Consensus pattern (13 bp):
ATAAACGAACATA
Found at i:1144088 original size:14 final size:14
Alignment explanation
Indices: 1144069--1144115 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
1144059 CCATCTGTTT
1144069 GAACATAAATGAAC
1 GAACATAAATGAAC
1144083 GAACATAAAT----
1 GAACATAAATGAAC
*
1144093 GAACATAAACGAAC
1 GAACATAAATGAAC
1144107 GAACATAAA
1 GAACATAAA
1144116 CGAGCATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
10 9 0.32
14 19 0.68
ACGTcount: A:0.60, C:0.15, G:0.13, T:0.13
Consensus pattern (14 bp):
GAACATAAATGAAC
Found at i:1144097 original size:24 final size:24
Alignment explanation
Indices: 1144068--1144115 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1144058 GCCATCTGTT
*
1144068 TGAACATAAATGAACGAACATAAA
1 TGAACATAAACGAACGAACATAAA
1144092 TGAACATAAACGAACGAACATAAA
1 TGAACATAAACGAACGAACATAAA
1144116 CGAGCATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (24 bp):
TGAACATAAACGAACGAACATAAA
Found at i:1144123 original size:24 final size:24
Alignment explanation
Indices: 1144069--1144123 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
1144059 CCATCTGTTT
* *
1144069 GAACATAAATGAACGAACATAAAT
1 GAACATAAACGAACGAACATAAAC
1144093 GAACATAAACGAACGAACATAAAC
1 GAACATAAACGAACGAACATAAAC
*
1144117 GAGCATA
1 GAACATA
1144124 TAATCGATCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.56, C:0.16, G:0.15, T:0.13
Consensus pattern (24 bp):
GAACATAAACGAACGAACATAAAC
Found at i:1151069 original size:301 final size:296
Alignment explanation
Indices: 1150596--1151315 Score: 984
Period size: 301 Copynumber: 2.4 Consensus size: 296
1150586 AAAGATACTA
* * * **
1150596 TCAAACTGTTTGACGAAAACTTCCAGAAT-TATC-TTTTCCTATCACTAACC-TATAAATTATCT
1 TCAAACTGTTTGACCAAAACTTCCAGAATCT-TCTTTTTCTTATCACT-ACCATATGAATCCTCT
* * * *
1150658 ATGTTTA-TTTATCTACACAATTTCTGTTACTAAATCCTAAAGAAGAAAACAGAAACTTCTCGGC
64 AT-ATTACTTTAGCTACAGAATTTCCGTTACTAAATCCTAAAGAAGAAAACAGAAACTTCTCGGC
* * **
1150722 TACTTTGCAAAGAACAAATTGATCCAAAAGCATTATAGAAACCAAAATAA-AAACAATCGAAAAT
128 TACTTTGCAAAGAAAAAATTGATCCAAAAGAATTATAGAAACCAAAATAAGAAA-AATAAAAAAT
*
1150786 CATTTTCATAATAAACACACTTCACTCAAAATAAAGTCACTGCAAATCATTGAAACACA-CAGCA
192 CATTTTCATAATAAACACACTTCAATCAAAATAAAGTCACTGCAAATCATTGAAACACACCAGCA
* **
1150850 TCCATCATCAAAATGATAAAATACAAGTATAGTAATGAAG
257 TCCATCATCAAAATGATAAAATACAAGTACAGTAACAAAG
*
1150890 TCAAACTGTTTGACCAAAACTTCCAGAATCTTCTTTTTCTTATCACTACCATATGAATCCTCAAT
1 TCAAACTGTTTGACCAAAACTTCCAGAATCTTCTTTTTCTTATCACTACCATATGAATCCTCTAT
* *
1150955 AATTACTTTAAGCTACAGACTTTCCGTTGCTAAATCCTAAAGAAGAAAACAGAAACTTCTCGGTC
66 -ATTACTTT-AGCTACAGAATTTCCGTTACTAAATCCTAAAGAAGAAAACAGAAAC-T-TC--TC
*
1151020 GGCTACTTTGCAAATAAAAAATTGATCCAAAAGAATTATAGAAACCAAAATAAGAAAAATAAAAA
125 GGCTACTTTGCAAAGAAAAAATTGATCCAAAAGAATTATAGAAACCAAAATAAGAAAAATAAAAA
* * *
1151085 ATCATTTTCATGATAAACACACTTCAATCAATATAAAGTCACTTCAAATCATTGAAACACACCAG
190 ATCATTTTCATAATAAACACACTTCAATCAAAATAAAGTCACTGCAAATCATTGAAACACACCAG
*
1151150 CATCCATCATCAAAATGATAAACTACAAGTACAGTAACAAAG
255 CATCCATCATCAAAATGATAAAATACAAGTACAGTAACAAAG
*
1151192 TCAAACTGTTTGACCAAAACTTCCAGAATCTTCTTTTTTTCTTATCACTACCATACGAATCCTCT
1 TCAAACTGTTTGACCAAAACTTCCAGAATCTTC--TTTTTCTTATCACTACCATATGAATCCTCT
* * * *
1151257 ATGTTCACTTTTAGCTACAGATTTTGCGTTACTAAATCCTAAAAAGAAGAAAACGGAAA
64 ATATT-AC-TTTAGCTACAGAATTTCCGTTACTAAATCCT--AAAGAAGAAAACAGAAA
1151316 TTTCATCACT
Statistics
Matches: 376, Mismatches: 33, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
294 33 0.09
295 26 0.07
296 3 0.01
297 41 0.11
298 1 0.00
299 2 0.01
301 115 0.31
302 77 0.20
303 2 0.01
304 57 0.15
305 3 0.01
306 16 0.04
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.28
Consensus pattern (296 bp):
TCAAACTGTTTGACCAAAACTTCCAGAATCTTCTTTTTCTTATCACTACCATATGAATCCTCTAT
ATTACTTTAGCTACAGAATTTCCGTTACTAAATCCTAAAGAAGAAAACAGAAACTTCTCGGCTAC
TTTGCAAAGAAAAAATTGATCCAAAAGAATTATAGAAACCAAAATAAGAAAAATAAAAAATCATT
TTCATAATAAACACACTTCAATCAAAATAAAGTCACTGCAAATCATTGAAACACACCAGCATCCA
TCATCAAAATGATAAAATACAAGTACAGTAACAAAG
Found at i:1153561 original size:32 final size:32
Alignment explanation
Indices: 1153525--1153590 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
1153515 TTCACTTAAG
*
1153525 TTTTTGGT-AAGTAAGTACCTAAAGTTATTTTT
1 TTTTTGGTAAAATAAGTACCTAAAG-TATTTTT
*
1153557 TTTTTGGTAAAATAGGTACCTAAAGTATTTTT
1 TTTTTGGTAAAATAAGTACCTAAAGTATTTTT
1153589 TT
1 TT
1153591 GTCAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 17 0.55
33 14 0.45
ACGTcount: A:0.29, C:0.06, G:0.15, T:0.50
Consensus pattern (32 bp):
TTTTTGGTAAAATAAGTACCTAAAGTATTTTT
Found at i:1153597 original size:29 final size:30
Alignment explanation
Indices: 1153555--1153613 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1153545 AAAGTTATTT
*
1153555 TTTTTTTGGT-AAAATAGGTACCTAAAGTA
1 TTTTTTTGGTAAAAATAGGTAACTAAAGTA
*
1153584 TTTTTTT-GTCAAAAATATGTAACTAAAGTA
1 TTTTTTTGGT-AAAAATAGGTAACTAAAGTA
1153614 CTTAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 2 0.08
29 7 0.27
30 17 0.65
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (30 bp):
TTTTTTTGGTAAAAATAGGTAACTAAAGTA
Found at i:1153760 original size:28 final size:28
Alignment explanation
Indices: 1153699--1153789 Score: 101
Period size: 28 Copynumber: 3.1 Consensus size: 28
1153689 GAGAATATTT
* * *
1153699 AAATAGTTTAGGTATCTATTTTGACATA
1 AAATATTTTAGGTACCTATTTTGACCTA
1153727 AAATATTTTAGGTACCTATTTTGACCTAA
1 AAATATTTTAGGTACCTATTTTGACCT-A
* * *
1153756 AATATAATTTTAGGTACTTGTTTTGACCAA
1 AA-AT-ATTTTAGGTACCTATTTTGACCTA
1153786 AAAT
1 AAAT
1153790 GTCAAAATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
28 24 0.44
29 5 0.09
30 5 0.09
31 20 0.37
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (28 bp):
AAATATTTTAGGTACCTATTTTGACCTA
Found at i:1153769 original size:31 final size:30
Alignment explanation
Indices: 1153705--1153789 Score: 102
Period size: 31 Copynumber: 2.9 Consensus size: 30
1153695 ATTTAAATAG
* *
1153705 TTTAGGTATCTATTTTGACAT-AAA-ATAT
1 TTTAGGTACCTATTTTGACCTAAAATATAT
1153733 TTTAGGTACCTATTTTGACCTAAAATATAAT
1 TTTAGGTACCTATTTTGACCTAAAATAT-AT
* * *
1153764 TTTAGGTACTTGTTTTGACCAAAAAT
1 TTTAGGTACCTATTTTGACCTAAAAT
1153790 GTCAAAATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
28 19 0.39
29 3 0.06
30 2 0.04
31 25 0.51
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.44
Consensus pattern (30 bp):
TTTAGGTACCTATTTTGACCTAAAATATAT
Found at i:1153931 original size:195 final size:195
Alignment explanation
Indices: 1153590--1153980 Score: 716
Period size: 195 Copynumber: 2.0 Consensus size: 195
1153580 AGTATTTTTT
1153590 TGTCAAAAATATGTAACTAAAGTACTTAATTTTTTTTTATCTAAGTACCTAAAATATTCTTTTAT
1 TGTCAAAAATATGTAACTAAAGTACTTAATTTTTTTTTATCTAAGTACCTAAAATATTCTTTTAT
1153655 TAATGTCAAATGTTAACTTTTTTAGAACTTAGATGAGAATATTTAAATAGTTTAGGTATCTATTT
66 TAATGTCAAATGTTAAC-TTTTTAGAACTTAGATGAGAATATTTAAATAGTTTAGGTATCTATTT
1153720 TGACATAAAATATTTTAGGTACCTATTTTGACCTAAAATATAATTTTAGGTACTTGTTTTGACCA
130 TGACATAAAATATTTTAGGTACCTATTTTGACCT-AAA-AT-ATTTTAGGTACTTGTTTTGACCA
1153785 AAAA
192 AAAA
1153789 TGTC-AAAATATGTAACTAAAGTACTTAA-TTTTTTTTATCTAAGTACCTAAAATATTCTTTTAT
1 TGTCAAAAATATGTAACTAAAGTACTTAATTTTTTTTTATCTAAGTACCTAAAATATTCTTTTAT
1153852 TAATGTCAAATGTTAAC-TTTTAGAACTTAGATGAGAATATTTAAATAGTTTAGGTATCTATTTT
66 TAATGTCAAATGTTAACTTTTTAGAACTTAGATGAGAATATTTAAATAGTTTAGGTATCTATTTT
*
1153916 GACATAAAATATTTTAGGTGCCTATTTTGACCTAAAATATTTTAGGTACTTGTTTTGACCAAAAA
131 GACATAAAATATTTTAGGTACCTATTTTGACCTAAAATATTTTAGGTACTTGTTTTGACCAAAAA
1153981 ATACTTTAGG
Statistics
Matches: 191, Mismatches: 1, Indels: 7
0.96 0.01 0.04
Matches are distributed among these distances:
192 27 0.14
193 2 0.01
194 3 0.02
195 79 0.41
197 52 0.27
198 24 0.13
199 4 0.02
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (195 bp):
TGTCAAAAATATGTAACTAAAGTACTTAATTTTTTTTTATCTAAGTACCTAAAATATTCTTTTAT
TAATGTCAAATGTTAACTTTTTAGAACTTAGATGAGAATATTTAAATAGTTTAGGTATCTATTTT
GACATAAAATATTTTAGGTACCTATTTTGACCTAAAATATTTTAGGTACTTGTTTTGACCAAAAA
Found at i:1153990 original size:29 final size:29
Alignment explanation
Indices: 1153894--1153996 Score: 122
Period size: 28 Copynumber: 3.6 Consensus size: 29
1153884 GAGAATATTT
*
1153894 AAATAGTTTAGGTA-TCTATTTTGA-CATA
1 AAATATTTTAGGTACT-TATTTTGACCATA
* *
1153922 AAATATTTTAGGTGCCTATTTTGACC-TA
1 AAATATTTTAGGTACTTATTTTGACCATA
* *
1153950 AAATATTTTAGGTACTTGTTTTGACCAAA
1 AAATATTTTAGGTACTTATTTTGACCATA
*
1153979 AAATACTTTAGGTACTTA
1 AAATATTTTAGGTACTTA
1153997 ATGAAAAGGA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
28 45 0.71
29 18 0.29
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.42
Consensus pattern (29 bp):
AAATATTTTAGGTACTTATTTTGACCATA
Found at i:1154451 original size:12 final size:12
Alignment explanation
Indices: 1154434--1154458 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1154424 ATGGGCCTGG
1154434 TCACTTGAGTTA
1 TCACTTGAGTTA
1154446 TCACTTGAGTTA
1 TCACTTGAGTTA
1154458 T
1 T
1154459 TTTCAAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (12 bp):
TCACTTGAGTTA
Found at i:1159770 original size:19 final size:19
Alignment explanation
Indices: 1159746--1159789 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
1159736 ACCAACTAAA
*
1159746 TCGCAATGCGATCGATAAT
1 TCGCAATACGATCGATAAT
1159765 TCGCAATACGATCGATAAT
1 TCGCAATACGATCGATAAT
1159784 TCGCAA
1 TCGCAA
1159790 CGTGATCTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (19 bp):
TCGCAATACGATCGATAAT
Found at i:1159840 original size:19 final size:21
Alignment explanation
Indices: 1159816--1159861 Score: 69
Period size: 19 Copynumber: 2.3 Consensus size: 21
1159806 GCAAATCGCA
1159816 TTGCGATAGTCCAAG-TT-CG
1 TTGCGATAGTCCAAGTTTACG
*
1159835 TTGCGATAGTCGAAGTTTACG
1 TTGCGATAGTCCAAGTTTACG
1159856 TTGCGA
1 TTGCGA
1159862 ATCTGGAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 14 0.58
20 2 0.08
21 8 0.33
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTTACG
Found at i:1160770 original size:4 final size:4
Alignment explanation
Indices: 1160763--1160801 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
1160753 TAACCTCTCT
* * *
1160763 CTCC CTCC CTCC CTCC TTTC CTCC CTCC TTCC CTCC CTC
1 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTC
1160802 TCTCTCTCTC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (4 bp):
CTCC
Found at i:1160785 original size:12 final size:12
Alignment explanation
Indices: 1160763--1160801 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1160753 TAACCTCTCT
*
1160763 CTCCCTCCCTCC
1 CTCCTTCCCTCC
*
1160775 CTCCTTTCCTCC
1 CTCCTTCCCTCC
1160787 CTCCTTCCCTCC
1 CTCCTTCCCTCC
1160799 CTC
1 CTC
1160802 TCTCTCTCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (12 bp):
CTCCTTCCCTCC
Found at i:1162048 original size:23 final size:23
Alignment explanation
Indices: 1162000--1162048 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1161990 GATCATTTTG
* * * *
1162000 TAACTTTTAATAGTCGAGGGAGT
1 TAACTTTCAATAATCGAGAGACT
1162023 TAACTTTCAATAATCGAGAGACT
1 TAACTTTCAATAATCGAGAGACT
1162046 TAA
1 TAA
1162049 TAAAATAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (23 bp):
TAACTTTCAATAATCGAGAGACT
Found at i:1162352 original size:2 final size:2
Alignment explanation
Indices: 1162345--1162373 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1162335 TCTCAACTCA
1162345 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1162374 CTCTTTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1162601 original size:31 final size:34
Alignment explanation
Indices: 1162566--1162648 Score: 118
Period size: 36 Copynumber: 2.5 Consensus size: 34
1162556 TAACGATGTT
1162566 AAAACGACGCCGTTTT-AAAA-AAAA-TTTAACC
1 AAAACGACGCCGTTTTAAAAATAAAATTTTAACC
*
1162597 AAAACGACGCCGTTTTAAAAAAATAAAATTTTCACC
1 AAAACGACGCCGTTTT--AAAAATAAAATTTTAACC
1162633 AAAACGACGCCGTTTT
1 AAAACGACGCCGTTTT
1162649 GAATCTATAT
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
31 16 0.35
34 4 0.09
35 4 0.09
36 22 0.48
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.24
Consensus pattern (34 bp):
AAAACGACGCCGTTTTAAAAATAAAATTTTAACC
Found at i:1168318 original size:80 final size:79
Alignment explanation
Indices: 1168221--1168379 Score: 257
Period size: 79 Copynumber: 2.0 Consensus size: 79
1168211 TGTTAATTTT
* *
1168221 TTTAACATTTCCGGTAAAGCGCTACTTAAAACATTATTTTTTTCTACC-AGAAATGTTAATATTG
1 TTTAACATTTCCGGTAAAACGCTACCTAAAACATTA-TTTTTTCTACCGA-AAATGTTAATATTG
*
1168285 GGCGCTACCTAAAATG
64 GACGCTACCTAAAATG
*
1168301 TTTAACATTTCCGGTAAAACGCTACCTAAAACATTATTTTTTCTATCGAAAATGTTAATATTGGA
1 TTTAACATTTCCGGTAAAACGCTACCTAAAACATTATTTTTTCTACCGAAAATGTTAATATTGGA
1168366 CGCTACCTAAAATG
66 CGCTACCTAAAATG
1168380 ATATTTTTTT
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
79 39 0.53
80 35 0.47
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.36
Consensus pattern (79 bp):
TTTAACATTTCCGGTAAAACGCTACCTAAAACATTATTTTTTCTACCGAAAATGTTAATATTGGA
CGCTACCTAAAATG
Found at i:1171861 original size:46 final size:46
Alignment explanation
Indices: 1171794--1171885 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
1171784 TTGCCTTTGG
1171794 CTCTAACATGGATTCCTTGTAATTACACCGGGGAAGCTGAGGATGA
1 CTCTAACATGGATTCCTTGTAATTACACCGGGGAAGCTGAGGATGA
1171840 CTCTAACATGGATTCCTTGTAATTACACCGGGGAAGCTGAGGATGA
1 CTCTAACATGGATTCCTTGTAATTACACCGGGGAAGCTGAGGATGA
1171886 ATTCATAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (46 bp):
CTCTAACATGGATTCCTTGTAATTACACCGGGGAAGCTGAGGATGA
Found at i:1180023 original size:73 final size:73
Alignment explanation
Indices: 1179904--1180071 Score: 336
Period size: 73 Copynumber: 2.3 Consensus size: 73
1179894 GTCAATGCTG
1179904 TAATGCAAGCATATACTTTCTCAAGGGTGTTCATTGAGCTACCATGTTGTGTTTGCTGAGTCTTT
1 TAATGCAAGCATATACTTTCTCAAGGGTGTTCATTGAGCTACCATGTTGTGTTTGCTGAGTCTTT
1179969 TTAGGTTA
66 TTAGGTTA
1179977 TAATGCAAGCATATACTTTCTCAAGGGTGTTCATTGAGCTACCATGTTGTGTTTGCTGAGTCTTT
1 TAATGCAAGCATATACTTTCTCAAGGGTGTTCATTGAGCTACCATGTTGTGTTTGCTGAGTCTTT
1180042 TTAGGTTA
66 TTAGGTTA
1180050 TAATGCAAGCATATACTTTCTC
1 TAATGCAAGCATATACTTTCTC
1180072 GAGCTTGACA
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 95 1.00
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.40
Consensus pattern (73 bp):
TAATGCAAGCATATACTTTCTCAAGGGTGTTCATTGAGCTACCATGTTGTGTTTGCTGAGTCTTT
TTAGGTTA
Found at i:1185591 original size:44 final size:47
Alignment explanation
Indices: 1185526--1185623 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 47
1185516 TTATTTTCGT
*
1185526 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTG
1 TTTTT-GAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTC
*
1185573 TTTTTGAAT-AA-GCATGCGAATTAGATATCATGCGGTTAGGATTTC
1 TTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTC
1185618 TTTTTG
1 TTTTTG
1185624 TGGATAACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
44 28 0.58
45 11 0.23
46 4 0.08
47 5 0.10
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (47 bp):
TTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTC
Found at i:1195211 original size:10 final size:10
Alignment explanation
Indices: 1195180--1195324 Score: 56
Period size: 9 Copynumber: 14.4 Consensus size: 10
1195170 TATTTTGCTT
1195180 AAAGAAGAAA
1 AAAGAAGAAA
* *
1195190 TAA-AAGAGA
1 AAAGAAGAAA
1195199 AAAGAAGAAA
1 AAAGAAGAAA
1195209 AAAGAA-AAA
1 AAAGAAGAAA
* * *
1195218 TGATGATGGAAA
1 -AAAGA-AGAAA
*
1195230 AAACGAAAAAA
1 AAA-GAAGAAA
1195241 AAACGAA-AAA
1 AAA-GAAGAAA
1195251 AAAGAA-AAA
1 AAAGAAGAAA
*
1195260 AAA-AA-TAA
1 AAAGAAGAAA
1195268 AAAGAAGAGAA
1 AAAGAAGA-AA
*
1195279 AAATGGAAAAAA
1 AAA--GAAGAAA
*
1195291 ATAAAAAGAGAA
1 A-AAGAAGA-AA
1195303 AAATG-A-AAA
1 AAA-GAAGAAA
1195312 AAAG-AGAAA
1 AAAGAAGAAA
1195321 AAAG
1 AAAG
1195325 GAGGGTTCAA
Statistics
Matches: 104, Mismatches: 17, Indels: 29
0.69 0.11 0.19
Matches are distributed among these distances:
8 9 0.09
9 33 0.32
10 23 0.22
11 22 0.21
12 11 0.11
13 6 0.06
ACGTcount: A:0.76, C:0.01, G:0.17, T:0.06
Consensus pattern (10 bp):
AAAGAAGAAA
Found at i:1195213 original size:17 final size:17
Alignment explanation
Indices: 1195180--1195321 Score: 52
Period size: 17 Copynumber: 8.2 Consensus size: 17
1195170 TATTTTGCTT
1195180 AAAGAAGAAATAAAAGAGA
1 AAAGAAG-AA-AAAAGAGA
1195199 AAAGAAGAAAAAAGA-A
1 AAAGAAGAAAAAAGAGA
*
1195215 AAATGATGATGGAAAAAACGAAA
1 AAA-GA--A--GAAAAAA-GAGA
* *
1195238 AAAAAACGAAAAAAAAGA
1 AAAGAA-GAAAAAAGAGA
1195256 AAA-AA-AAAATAA-A-A
1 AAAGAAGAAAA-AAGAGA
*
1195270 AGAAG-AGAAAAATG-GA
1 A-AAGAAGAAAAAAGAGA
1195286 AAA-AA-ATAAAAAGAGA
1 AAAGAAGA-AAAAAGAGA
*
1195302 AAA-ATGAAAAAAAGAGA
1 AAAGAAG-AAAAAAGAGA
1195319 AAA
1 AAA
1195322 AAGGAGGGTT
Statistics
Matches: 98, Mismatches: 7, Indels: 38
0.69 0.05 0.27
Matches are distributed among these distances:
14 3 0.03
15 17 0.17
16 18 0.18
17 22 0.22
18 8 0.08
19 15 0.15
20 1 0.01
21 7 0.07
22 3 0.03
23 4 0.04
ACGTcount: A:0.76, C:0.01, G:0.17, T:0.06
Consensus pattern (17 bp):
AAAGAAGAAAAAAGAGA
Found at i:1195243 original size:11 final size:11
Alignment explanation
Indices: 1195227--1195263 Score: 60
Period size: 10 Copynumber: 3.5 Consensus size: 11
1195217 ATGATGATGG
1195227 AAAAAACGAAA
1 AAAAAACGAAA
1195238 AAAAAACG-AA
1 AAAAAACGAAA
1195248 AAAAAA-GAAA
1 AAAAAACGAAA
1195258 AAAAAA
1 AAAAAA
1195264 ATAAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 1 0.04
10 16 0.64
11 8 0.32
ACGTcount: A:0.86, C:0.05, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAACGAAA
Found at i:1195264 original size:11 final size:11
Alignment explanation
Indices: 1195227--1195281 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
1195217 ATGATGATGG
*
1195227 AAAAAACGAAA
1 AAAAAAAGAAA
*
1195238 AAAAAACG--A
1 AAAAAAAGAAA
1195247 AAAAAAAGAAA
1 AAAAAAAGAAA
*
1195258 AAAAAAATAAA
1 AAAAAAAGAAA
* *
1195269 AAGAAGAGAAA
1 AAAAAAAGAAA
1195280 AA
1 AA
1195282 TGGAAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 8 0.22
11 29 0.78
ACGTcount: A:0.84, C:0.04, G:0.11, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:1195269 original size:20 final size:20
Alignment explanation
Indices: 1195227--1195323 Score: 72
Period size: 20 Copynumber: 4.7 Consensus size: 20
1195217 ATGATGATGG
* *
1195227 AAAAAACGAAAAAAAAACGA
1 AAAAAAAGAAAAAAAAAAGA
*
1195247 AAAAAAAGAAAAAAAAAATA
1 AAAAAAAGAAAAAAAAAAGA
* * **
1195267 AAAAGAAG-AGAAAAATGGA
1 AAAAAAAGAAAAAAAAAAGA
1195286 AAAAAATA-AAAAGAGAAAAATGA
1 AAAAAA-AGAAAA-A-AAAAA-GA
1195309 AAAAAAGAGAAAAAA
1 AAAAAA-AGAAAAAA
1195324 GGAGGGTTCA
Statistics
Matches: 58, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
19 12 0.21
20 27 0.47
21 1 0.02
22 4 0.07
23 10 0.17
24 4 0.07
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.04
Consensus pattern (20 bp):
AAAAAAAGAAAAAAAAAAGA
Found at i:1195321 original size:24 final size:24
Alignment explanation
Indices: 1195272--1195322 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1195262 AAATAAAAAG
*
1195272 AAGAGAAAAATGGAAAAAAATAAA
1 AAGAGAAAAATGGAAAAAAAGAAA
*
1195296 AAGAGAAAAATGAAAAAAAGAGAAA
1 AAGAGAAAAATGGAAAAAA-AGAAA
1195321 AA
1 AA
1195323 AGGAGGGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (24 bp):
AAGAGAAAAATGGAAAAAAAGAAA
Found at i:1196670 original size:51 final size:51
Alignment explanation
Indices: 1196613--1197165 Score: 866
Period size: 51 Copynumber: 10.9 Consensus size: 51
1196603 AAATTCGTTT
* *
1196613 GTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1196664 GTTGAAGA-TGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1196714 GTTGAAGATTGAGTCCTATACTCT-TGAAGGAATAGGGA-CGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1196763 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1196814 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* *
1196865 GTTGAAAATTGAGTCCTATA--CTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * *
1196914 GTTGAAG-TTGAGTCTTATACTCTCTGAATGAATAGGGAGCGGACAAATTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
1196964 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* *
1197015 GTTGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACTAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * ** *
1197066 GTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * *
1197117 ATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGAC
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
1197166 CCGTTTTATT
Statistics
Matches: 469, Mismatches: 23, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
48 11 0.02
49 69 0.15
50 111 0.24
51 245 0.52
54 2 0.00
55 31 0.07
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:1196898 original size:150 final size:151
Alignment explanation
Indices: 1196613--1197165 Score: 869
Period size: 150 Copynumber: 3.6 Consensus size: 151
1196603 AAATTCGTTT
*
1196613 GTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTTGTTGAAGA-TGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
1196677 CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTTGAA
66 CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTC-TGAA
1196742 GGAATAGGGA-CGGACAAGTTC
130 GGAATAGGGAGCGGACAAGTTC
*
1196763 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
* *
1196828 CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAAATTGAGTCCTATACTCTGAAT
66 CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTGAAG
1196893 GAATAGGGAGCGGACAAGTTC
131 GAATAGGGAGCGGACAAGTTC
* * *
1196914 GTTGAAG-TTGAGTCTTATACTCTCTGAATGAATAGGGAGCGGACAAATTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
* *
1196978 CCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATCGAGTCCTATACTCTCTGA
66 CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATA--CTCTGA
*
1197043 AGGAATAGGGAGCGGACTAGTTC
129 AGGAATAGGGAGCGGACAAGTTC
* ** **
1197066 GTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTTTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
* *
1197131 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGAC
62 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
1197166 CCGTTTTATT
Statistics
Matches: 371, Mismatches: 23, Indels: 11
0.92 0.06 0.03
Matches are distributed among these distances:
150 178 0.48
151 82 0.22
152 34 0.09
153 43 0.12
156 2 0.01
157 32 0.09
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (151 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTGAAG
GAATAGGGAGCGGACAAGTTC
Found at i:1196959 original size:201 final size:200
Alignment explanation
Indices: 1196613--1197165 Score: 831
Period size: 201 Copynumber: 2.7 Consensus size: 200
1196603 AAATTCGTTT
* *
1196613 GTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTTGTTGAAGA-TGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
*
1196677 CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTTGAA
66 CCTATA--CTCTGAAAGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTTGAA
*
1196742 GGAATAGGGACGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGA
129 GGAATAGGGACGGACAAATTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGA
1196807 CAAGTTC
194 CAAGTTC
*
1196814 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAAATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
* * *
1196879 CCTATACTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAG-TTGAGTCTTATACTCTCTGAAT
66 CCTATACTCTGAAAGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCT-TGAAG
*
1196943 GAATAGGGAGCGGACAAATTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGA
130 GAATAGGGA-CGGACAAATTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGA
1197008 CAAGTTC
194 CAAGTTC
* *
1197015 GTTGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACTAGTTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
** ** *
1197080 CCTATACTCCCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTTTTCGAGTTCTATACTCT
66 CCTATACT--CTGAAAGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-GAGTCCTATACTCT
*
1197145 CTGAAGGAATAGAGAGCGGAC
125 -TGAAGGAATAGGGA-CGGAC
1197166 CCGTTTTATT
Statistics
Matches: 322, Mismatches: 20, Indels: 13
0.91 0.06 0.04
Matches are distributed among these distances:
199 15 0.05
200 48 0.15
201 186 0.58
202 11 0.03
203 29 0.09
207 2 0.01
208 31 0.10
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (200 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
CCTATACTCTGAAAGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTTGAAGG
AATAGGGACGGACAAATTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
AGTTC
Found at i:1197200 original size:56 final size:54
Alignment explanation
Indices: 1196609--1197265 Score: 466
Period size: 51 Copynumber: 12.9 Consensus size: 54
1196599 AAGCAAATTC
* * * *
1196609 GTTTGTTGAAGATTG---AGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAA
1 GTTTATTGAAGATTGTTCAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCA
* * *
1196660 GTTTGTTGAAGA-TG---AGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTTATTGAAGATTGTTCAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCA
** * *
1196710 GTTCGTTGAAGATTG---AGTCCTATACTCT-TGAAGGAATAGGGA-CGGACAA
1 GTTTATTGAAGATTGTTCAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCA
** * *
1196759 GTTCGTTGAAGATTG---AGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTTATTGAAGATTGTTCAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCA
** * *
1196810 GTTCGTTGAAGATTG---AGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTTATTGAAGATTGTTCAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCA
** * * * *
1196861 GTTCGTTGAAAATTG---AGTCCTATA--CTCTGAATGAATAGGGAGCGGACAA
1 GTTTATTGAAGATTGTTCAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCA
** * * * *
1196910 GTTCGTTGAAG-TTG---AGTCTTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTTATTGAAGATTGTTCAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCA
* ** * * *
1196960 ATTCGTTGAAGATTG---AGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTTATTGAAGATTGTTCAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCA
** * * *
1197011 GTTCGTTGAAGATCG---AGTCCTATACTCTCTGAAGGAATAGGGAGCGGACTA
1 GTTTATTGAAGATTGTTCAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCA
** * * * *
1197062 GTTCGTTGAAGATTG---AGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCT
1 GTTTATTGAAGATTGTTCAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCA
* * *
1197113 GTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCC
1 GTTTATTGAAGATTGTTC-AGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCA
* * *
1197168 GTTTTATTAAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGC--A-C-
1 G-TTTATTGAAGATTGTTC-AGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCA
*
1197220 GTTTA-TGAAGATTGTTCGAGT-CT-TACT-TCCTGAAGGAATAGGGAGC
1 GTTTATTGAAGATTGTTC-AGTCCTATACTCT-CTGAAGGAATAGAGAGC
1197266 AGGCTCGTCA
Statistics
Matches: 558, Mismatches: 36, Indels: 27
0.90 0.06 0.04
Matches are distributed among these distances:
47 1 0.00
48 30 0.05
49 70 0.13
50 125 0.22
51 255 0.46
52 1 0.00
53 1 0.00
54 1 0.00
55 32 0.06
56 42 0.08
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (54 bp):
GTTTATTGAAGATTGTTCAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCA
Found at i:1206373 original size:108 final size:108
Alignment explanation
Indices: 1206184--1206403 Score: 440
Period size: 108 Copynumber: 2.0 Consensus size: 108
1206174 AGGTCAAATT
1206184 TCTAAAGAATGCATCCTCATCAACTCCTGCGTCTCCAGGCTCTCCATGCTTAAAGTCTGGAACAA
1 TCTAAAGAATGCATCCTCATCAACTCCTGCGTCTCCAGGCTCTCCATGCTTAAAGTCTGGAACAA
1206249 ACTTATCTCCTGAATCCCCGGCTAGGGAAGCTCTATTCTCATC
66 ACTTATCTCCTGAATCCCCGGCTAGGGAAGCTCTATTCTCATC
1206292 TCTAAAGAATGCATCCTCATCAACTCCTGCGTCTCCAGGCTCTCCATGCTTAAAGTCTGGAACAA
1 TCTAAAGAATGCATCCTCATCAACTCCTGCGTCTCCAGGCTCTCCATGCTTAAAGTCTGGAACAA
1206357 ACTTATCTCCTGAATCCCCGGCTAGGGAAGCTCTATTCTCATC
66 ACTTATCTCCTGAATCCCCGGCTAGGGAAGCTCTATTCTCATC
1206400 TCTA
1 TCTA
1206404 CCTTCTCTAC
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 112 1.00
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.28
Consensus pattern (108 bp):
TCTAAAGAATGCATCCTCATCAACTCCTGCGTCTCCAGGCTCTCCATGCTTAAAGTCTGGAACAA
ACTTATCTCCTGAATCCCCGGCTAGGGAAGCTCTATTCTCATC
Found at i:1210591 original size:31 final size:31
Alignment explanation
Indices: 1210549--1210612 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
1210539 ATTGAGTGCC
* * *
1210549 CATTTTGTTACAAATCAATAACGTTAGTGAT
1 CATTTTATTACAAACCAATAACGTTAATGAT
* *
1210580 CATTTTATTACAAACCGATAATGTTAATGAT
1 CATTTTATTACAAACCAATAACGTTAATGAT
1210611 CA
1 CA
1210613 ATATGTTTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (31 bp):
CATTTTATTACAAACCAATAACGTTAATGAT
Found at i:1213992 original size:43 final size:43
Alignment explanation
Indices: 1213700--1213993 Score: 252
Period size: 43 Copynumber: 6.9 Consensus size: 43
1213690 TTTAAACAAA
* * * * * *
1213700 AAACGCCACAATAGGTATTGATATTTAGCGGTGTTTGTGTGAC
1 AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTTTTCTCAC
* * * * *
1213743 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTGTGAC
1 AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTTTTCTCAC
* * * * *
1213786 AAACGCCGCAATAGGTAATGATATTTAGCAGCG-TTTTCCCAT
1 AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTTTTCTCAC
* * * * *
1213828 AAACGCCGCACTAGGTGTTGATGTTTTGCGGC-ATTTTCCCAC
1 AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTTTTCTCAC
* ** * * * * *
1213870 AAACGCCACCGTAGATTTTGATGTTTTGCGGTGTTTATTC-CAT
1 AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTT-TTCTCAC
* * *
1213913 AAACGCCGCAGTAGGTTTTGATGTTTTGCGGCGTTTTTCTCAC
1 AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTTTTCTCAC
* *
1213956 AAACGCCGCAATATGTATTGATTTTTTGCGGCGTTTTT
1 AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTTTT
1213994 GCTAAAAACA
Statistics
Matches: 212, Mismatches: 35, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
42 67 0.32
43 142 0.67
44 3 0.01
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (43 bp):
AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTTTTCTCAC
Found at i:1214096 original size:43 final size:42
Alignment explanation
Indices: 1213938--1214098 Score: 130
Period size: 43 Copynumber: 3.8 Consensus size: 42
1213928 TTTTGATGTT
* * * * *
1213938 TTGCGGCGTTTTTCTCACAAACGCCGC-AATATGTATTGATTTT
1 TTGCGGCGTTTTTGTTACAAACGCCGCTAA-ATGTA-TGGTATA
* * * * *
1213981 TTGCGGCGTTTTTGCTAAAAACACCAG-TAAA-GTTTTGTATA
1 TTGCGGCGTTTTTGTTACAAACGCC-GCTAAATGTATGGTATA
* * *
1214022 TAGCGGCGTTTCTAGGATACAAACGCCGCTAAATGTATGGTATA
1 TTGCGGCGTTT-T-TGTTACAAACGCCGCTAAATGTATGGTATA
1214066 TTGCGGCGTTTTTTGTTACAAACGCCGCTAAAT
1 TTGCGGCG-TTTTTGTTACAAACGCCGCTAAAT
1214099 AACACAGAAT
Statistics
Matches: 91, Mismatches: 20, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
41 13 0.14
42 4 0.04
43 52 0.57
44 19 0.21
45 3 0.03
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (42 bp):
TTGCGGCGTTTTTGTTACAAACGCCGCTAAATGTATGGTATA
Found at i:1214429 original size:21 final size:21
Alignment explanation
Indices: 1214404--1214498 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
1214394 CTGCTGATAT
1214404 GTTGCTTCTCTTTGTGCTGCC
1 GTTGCTTCTCTTTGTGCTGCC
*
1214425 GTTGCTTCTCTCTGTGCTGCC
1 GTTGCTTCTCTTTGTGCTGCC
*
1214446 GCTGCTTCTCTTTGTGCTGCC
1 GTTGCTTCTCTTTGTGCTGCC
* * *
1214467 GCTGCTTCT-TTCTCTGCTTCC
1 GTTGCTTCTCTT-TGTGCTGCC
*
1214488 GTTGCTGCTCT
1 GTTGCTTCTCT
1214499 GGTTGCTTCT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
20 2 0.03
21 62 0.95
22 1 0.02
ACGTcount: A:0.00, C:0.33, G:0.22, T:0.45
Consensus pattern (21 bp):
GTTGCTTCTCTTTGTGCTGCC
Found at i:1217958 original size:42 final size:42
Alignment explanation
Indices: 1217872--1218075 Score: 168
Period size: 41 Copynumber: 5.0 Consensus size: 42
1217862 GGCGTTGATA
* * * * *
1217872 AAAAAACGTCACTATTGATT-ACACTATTGTGGCATTTGT-T
1 AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTTTCT
* *
1217912 AAAAAATGCCACTATTGATTAAAACTATTGCAGCGTTTTTCT
1 AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTTTCT
* * * * *
1217954 -AAAAACGCCACTAGTGATTAACACTATTACGACGTTTGTCT
1 AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTTTCT
* * * ***
1217995 -AAAAATGCCACTATTTATTATCACTATTACGGCGTTTTAAG
1 AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTTTCT
* *
1218036 AATAAATGCCACTATATG-TGTAA-TCTATTGCGGCGTTTTT
1 AAAAAATGCCACTAT-TGAT-TAACACTATTGCGGCGTTTTT
1218076 GGTATAAACG
Statistics
Matches: 130, Mismatches: 29, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
40 18 0.14
41 80 0.62
42 29 0.22
43 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (42 bp):
AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTTTCT
Found at i:1217999 original size:82 final size:81
Alignment explanation
Indices: 1217873--1218032 Score: 196
Period size: 82 Copynumber: 2.0 Consensus size: 81
1217863 GCGTTGATAA
* * ** *
1217873 AAAAACGTCACTATTGATTACACTATTGTGGCATTTGTTAAAAAATGCCACTATTGATTAAAACT
1 AAAAACGCCACTAGTGATTACACTATTACGACATTTGTTAAAAAATGCCACTATTGATTAAAACT
*
1217938 ATTGCAGCGTTTTTCT
66 ATTACAGCGTTTTTCT
* * **
1217954 AAAAACGCCACTAGTGATTAACACTATTACGACGTTTGTCT-AAAAATGCCACTATTTATTATCA
1 AAAAACGCCACTAGTGATT-ACACTATTACGACATTTGT-TAAAAAATGCCACTATTGATTAAAA
*
1218018 CTATTACGGCGTTTT
64 CTATTACAGCGTTTT
1218033 AAGAATAAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
81 17 0.26
82 48 0.73
83 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (81 bp):
AAAAACGCCACTAGTGATTACACTATTACGACATTTGTTAAAAAATGCCACTATTGATTAAAACT
ATTACAGCGTTTTTCT
Found at i:1218105 original size:42 final size:41
Alignment explanation
Indices: 1218059--1218170 Score: 129
Period size: 39 Copynumber: 2.8 Consensus size: 41
1218049 ATATGTGTAA
* * * **
1218059 TCTATTGCGGCGTTTTTGGTATAAACGCTGCTAATTTACCAC
1 TCTATTACGGCGTTTTTGGTAAAAACGCCG-TAATAAACCAC
*
1218101 TCTATTACGGCG--TTTGGTAAAAAAGCCGTAATAAACCAC
1 TCTATTACGGCGTTTTTGGTAAAAACGCCGTAATAAACCAC
* *
1218140 CCTATTACGGCGTTTTTTGTAAAAACGCCGT
1 TCTATTACGGCGTTTTTGGTAAAAACGCCGT
1218171 TATATGTCAA
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
39 20 0.34
40 13 0.22
41 15 0.25
42 11 0.19
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (41 bp):
TCTATTACGGCGTTTTTGGTAAAAACGCCGTAATAAACCAC
Found at i:1230340 original size:16 final size:17
Alignment explanation
Indices: 1230319--1230352 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1230309 ACTATACACA
*
1230319 TGAATAGT-GAATTTTG
1 TGAATAGTAAAATTTTG
1230335 TGAATAGTAAAATTTTG
1 TGAATAGTAAAATTTTG
1230352 T
1 T
1230353 CGGCGATACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (17 bp):
TGAATAGTAAAATTTTG
Found at i:1234587 original size:11 final size:11
Alignment explanation
Indices: 1234571--1234595 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1234561 TGCTCATAGA
1234571 TATTATCAATT
1 TATTATCAATT
1234582 TATTATCAATT
1 TATTATCAATT
1234593 TAT
1 TAT
1234596 AATAAATCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTATCAATT
Found at i:1236666 original size:15 final size:15
Alignment explanation
Indices: 1236620--1236666 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1236610 TCGTGGAGGG
1236620 GATGCAATCCTCTGA
1 GATGCAATCCTCTGA
* **
1236635 GAAGCAGCCCT-TGGA
1 GATGCAATCCTCT-GA
1236650 GATGCAATCCTCTGA
1 GATGCAATCCTCTGA
1236665 GA
1 GA
1236667 AAGAACCCGA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 1 0.04
15 22 0.92
16 1 0.04
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.21
Consensus pattern (15 bp):
GATGCAATCCTCTGA
Found at i:1236681 original size:30 final size:30
Alignment explanation
Indices: 1236615--1236686 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
1236605 TAGGCTCGTG
* *
1236615 GAGGGGATGCAATCCTCTGAGAAGCAGCCC
1 GAGGAGATGCAATCCTCTGAGAAGCAACCC
**
1236645 TTGGAGATGCAATCCTCTGAGAAAG-AACCC
1 GAGGAGATGCAATCCTCTGAG-AAGCAACCC
*
1236675 GAGGAGAAGCAA
1 GAGGAGATGCAA
1236687 CCCTAGGAGG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 31 0.91
31 3 0.09
ACGTcount: A:0.33, C:0.22, G:0.31, T:0.14
Consensus pattern (30 bp):
GAGGAGATGCAATCCTCTGAGAAGCAACCC
Found at i:1238884 original size:2 final size:2
Alignment explanation
Indices: 1238879--1238914 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1238869 ATAATTTGTA
1238879 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
1238915 GATAAAAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1240977 original size:12 final size:12
Alignment explanation
Indices: 1240960--1240984 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1240950 ACAAAGTACC
1240960 ATTTGGTGCCTA
1 ATTTGGTGCCTA
1240972 ATTTGGTGCCTA
1 ATTTGGTGCCTA
1240984 A
1 A
1240985 ATTATTTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:1246596 original size:16 final size:16
Alignment explanation
Indices: 1246565--1246598 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1246555 ATAAACATCG
**
1246565 AGCTTAACGAGTAACA
1 AGCTTAACGAACAACA
1246581 AGCTTAACGAACAACA
1 AGCTTAACGAACAACA
1246597 AG
1 AG
1246599 TTTTTTTAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.15
Consensus pattern (16 bp):
AGCTTAACGAACAACA
Found at i:1258459 original size:49 final size:49
Alignment explanation
Indices: 1258399--1258522 Score: 185
Period size: 49 Copynumber: 2.5 Consensus size: 49
1258389 AAAACTGAAT
*
1258399 ACAAAAATCAAAATGAGGATTTAGCCTTTCATAGAGGATTCCAGCAGAA
1 ACAAAAATCAAAATGAGGATTTAGCCATTCATAGAGGATTCCAGCAGAA
* * * *
1258448 ACAGAAATCAAAATGAGGATTTAGCCATTCGTAGAGGTTTCCAGCCGAA
1 ACAAAAATCAAAATGAGGATTTAGCCATTCATAGAGGATTCCAGCAGAA
* *
1258497 ATAAAAATCAGAATGAGGATTTAGCC
1 ACAAAAATCAAAATGAGGATTTAGCC
1258523 CTCTGTAGAG
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 67 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (49 bp):
ACAAAAATCAAAATGAGGATTTAGCCATTCATAGAGGATTCCAGCAGAA
Found at i:1258667 original size:28 final size:28
Alignment explanation
Indices: 1258629--1258747 Score: 150
Period size: 28 Copynumber: 4.2 Consensus size: 28
1258619 ACGAGGTTCT
*
1258629 ATGCAGAATCAGGACGAGGACTAAGCCT
1 ATGCAGAATCAGGACGAGGACTAAGCCC
* *
1258657 ATGCAGAATCAGGATGGGGACTAAGCCC
1 ATGCAGAATCAGGACGAGGACTAAGCCC
* *
1258685 ATGCAGAATCAGAACGAGGAAC-GAGCTCCC
1 ATGCAGAATCAGGACGAGG-ACTAAG--CCC
*
1258715 ATGCAGAATCAGGACGGGGACTAAGCCC
1 ATGCAGAATCAGGACGAGGACTAAGCCC
1258743 ATGCA
1 ATGCA
1258748 AAATTAGTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
28 51 0.66
29 4 0.05
30 22 0.29
ACGTcount: A:0.34, C:0.24, G:0.29, T:0.13
Consensus pattern (28 bp):
ATGCAGAATCAGGACGAGGACTAAGCCC
Found at i:1261574 original size:19 final size:20
Alignment explanation
Indices: 1261550--1261626 Score: 63
Period size: 19 Copynumber: 4.0 Consensus size: 20
1261540 TTCGGTTTGC
1261550 AAAAAAACCGG-TTTTTTTT
1 AAAAAAACCGGATTTTTTTT
* **
1261569 AAAAAAACTGGATTTTTTCGG
1 AAAAAAACCGGATTTTTT-TT
* *
1261590 ATAAAAATCC--AGTTTTTTT
1 A-AAAAAACCGGATTTTTTTT
1261609 -AAAAAACCGGATTTTTTT
1 AAAAAAACCGGATTTTTTT
1261627 CCGGATAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
17 7 0.16
19 17 0.40
20 12 0.28
21 1 0.02
22 6 0.14
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (20 bp):
AAAAAAACCGGATTTTTTTT
Found at i:1261605 original size:41 final size:41
Alignment explanation
Indices: 1261551--1261647 Score: 117
Period size: 41 Copynumber: 2.4 Consensus size: 41
1261541 TCGGTTTGCA
* *
1261551 AAAAAACCGGTTTTTTTTAAAAAAACTGGA-TTTTTT-CGGAT
1 AAAAAACCAG-TTTTTTT-AAAAAACCGGATTTTTTTCCGGAT
*
1261592 AAAAATCCAGTTTTTTTAAAAAACCGGATTTTTTTCCGGAT
1 AAAAAACCAGTTTTTTTAAAAAACCGGATTTTTTTCCGGAT
* *
1261633 AAAAAATCGGTTTTT
1 AAAAAACCAGTTTTT
1261648 AATCTGATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
39 10 0.21
40 13 0.27
41 25 0.52
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.39
Consensus pattern (41 bp):
AAAAAACCAGTTTTTTTAAAAAACCGGATTTTTTTCCGGAT
Found at i:1262586 original size:18 final size:18
Alignment explanation
Indices: 1262563--1262630 Score: 127
Period size: 18 Copynumber: 3.8 Consensus size: 18
1262553 ATATAAATAG
1262563 AAAAATCTTATTTTTCAT
1 AAAAATCTTATTTTTCAT
1262581 AAAAATCTTATTTTTCAT
1 AAAAATCTTATTTTTCAT
1262599 AAAAATCTTATTTTTCAT
1 AAAAATCTTATTTTTCAT
*
1262617 AAAAATCTAATTTT
1 AAAAATCTTATTTT
1262631 CTTTTTATTG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (18 bp):
AAAAATCTTATTTTTCAT
Found at i:1262862 original size:23 final size:23
Alignment explanation
Indices: 1262791--1262871 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 23
1262781 TCAATAAGTA
*
1262791 TGTCTTTATGACACATTTTCATC
1 TGTCTTTATGACACATTTTCATT
** * *
1262814 TACCTTTATGACACGTTTTCAAT
1 TGTCTTTATGACACATTTTCATT
* *
1262837 TGTCTTTATGACACATTATCTTT
1 TGTCTTTATGACACATTTTCATT
1262860 TGTCTTT-TGACA
1 TGTCTTTATGACA
1262872 TGTTTTTCCG
Statistics
Matches: 47, Mismatches: 11, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
22 5 0.11
23 42 0.89
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.48
Consensus pattern (23 bp):
TGTCTTTATGACACATTTTCATT
Found at i:1266152 original size:14 final size:13
Alignment explanation
Indices: 1266135--1266176 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1266125 AAAAAACAAA
1266135 AATTATAAAAATAT
1 AATTATAAAAAT-T
1266149 AATT-TAAAAATT
1 AATTATAAAAATT
*
1266161 ATTTATAAAATATT
1 AATTATAAAA-ATT
1266175 AA
1 AA
1266177 AAATCTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 4 0.17
13 12 0.50
14 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTATAAAAATT
Found at i:1268508 original size:2 final size:2
Alignment explanation
Indices: 1268503--1268529 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1268493 AAAATATAAA
1268503 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1268530 ATCGGGGCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1272091 original size:58 final size:60
Alignment explanation
Indices: 1271956--1272112 Score: 196
Period size: 58 Copynumber: 2.6 Consensus size: 60
1271946 TATTTACACA
* *
1271956 TTTATTTTTTTGTTATTTACATTTCAGTACTTTATTTTTCCTGTTATTTACATTTATGCCT
1 TTTATTTTTCTGTTATTTACATTTCAGTCCTTTA-TTTTCCTGTTATTTACATTTATGCCT
** * *
1272017 TTTA-TTTTCTCATATTTATATTTCAGTCCTTTCATTTT-CTGTT-TTTACATTTTTG-CT
1 TTTATTTTTCTGTTATTTACATTTCAGTCCTTT-ATTTTCCTGTTATTTACATTTATGCCT
*
1272074 TTTATTTTTCTGTTATTTACATTTCTGTCCTTTAATTTT
1 TTTATTTTTCTGTTATTTACATTTCAGTCCTTT-ATTTT
1272113 ATGTACTTTA
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
57 6 0.07
58 40 0.48
59 5 0.06
60 27 0.33
61 5 0.06
ACGTcount: A:0.17, C:0.14, G:0.06, T:0.64
Consensus pattern (60 bp):
TTTATTTTTCTGTTATTTACATTTCAGTCCTTTATTTTCCTGTTATTTACATTTATGCCT
Found at i:1272107 original size:15 final size:15
Alignment explanation
Indices: 1272031--1272157 Score: 59
Period size: 15 Copynumber: 8.7 Consensus size: 15
1272021 TTTTCTCATA
* *
1272031 TTTATATTTCAGTCC
1 TTTACATTTCTGTCC
*
1272046 TTT-CATTTTCTGT-T
1 TTTACA-TTTCTGTCC
* *
1272060 TTTACATTTTTG-CT
1 TTTACATTTCTGTCC
** **
1272074 TTTATTTTTCTGTTA
1 TTTACATTTCTGTCC
1272089 TTTACATTTCTGTCC
1 TTTACATTTCTGTCC
* *
1272104 TTTA-ATTTTATGTAC
1 TTTACA-TTTCTGTCC
1272119 TTTA-A-TTCATGTCC
1 TTTACATTTC-TGTCC
* * *
1272133 TTTAAATTTCTGGCA
1 TTTACATTTCTGTCC
1272148 TTTACATTTC
1 TTTACATTTC
1272158 AGCCATTTAC
Statistics
Matches: 84, Mismatches: 20, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
13 2 0.02
14 28 0.33
15 51 0.61
16 3 0.04
ACGTcount: A:0.18, C:0.16, G:0.07, T:0.59
Consensus pattern (15 bp):
TTTACATTTCTGTCC
Found at i:1273927 original size:93 final size:93
Alignment explanation
Indices: 1273763--1273991 Score: 334
Period size: 93 Copynumber: 2.5 Consensus size: 93
1273753 CTCGTGTTTG
** * *
1273763 CTTGCGTACTCGTTAAATTAAACTAAATAAATTCATGTTTCCTCAGTGGAAGCATTGTGTGCTAA
1 CTTGCGTACTTATTAAATTAAACTAAATAAATTCATGTTTCCTCAGTGGAAACATTGAGTGCTAA
1273828 TAAGCTTGTA-GGTCTGTCATTTGTGTGT
66 TAAGCTTGTAGGGTC-GTCATTTGTGTGT
* * *
1273856 CTTGCGTACTTATTAAACTAAACTAAATAAATTAATGTTTCCTCAGTGGAAACATTGAGTGGTAA
1 CTTGCGTACTTATTAAATTAAACTAAATAAATTCATGTTTCCTCAGTGGAAACATTGAGTGCTAA
*
1273921 TGAGCTTGTAGGGTCGTCATTTGTGTGT
66 TAAGCTTGTAGGGTCGTCATTTGTGTGT
* * * *
1273949 GTTGCGTACTTATTCAATTATACTAAATAAATTCGTGTTTCCT
1 CTTGCGTACTTATTAAATTAAACTAAATAAATTCATGTTTCCT
1273992 TCATATGGAA
Statistics
Matches: 121, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
93 117 0.97
94 4 0.03
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (93 bp):
CTTGCGTACTTATTAAATTAAACTAAATAAATTCATGTTTCCTCAGTGGAAACATTGAGTGCTAA
TAAGCTTGTAGGGTCGTCATTTGTGTGT
Found at i:1277549 original size:2 final size:2
Alignment explanation
Indices: 1277542--1277567 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1277532 GTGTAGGACC
1277542 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
1277568 CCAGCGGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1281898 original size:14 final size:16
Alignment explanation
Indices: 1281879--1281916 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 16
1281869 TAAAATAAAT
1281879 TAATAATATA-ATA-A
1 TAATAATATATATATA
1281893 TAATAATATATTATATA
1 TAATAATATA-TATATA
1281910 TAATAAT
1 TAATAAT
1281917 TAAATATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.48
16 3 0.14
17 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATAATATATATATA
Found at i:1290261 original size:64 final size:63
Alignment explanation
Indices: 1290110--1290266 Score: 228
Period size: 62 Copynumber: 2.5 Consensus size: 63
1290100 TGTACTAAGT
* ** *
1290110 GTGCATCGATGCATAAAATGCATTCGATATTTTAAACACGCCTGAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTAAACAAACCTGAGTGCATCGATGCATGGCA
*
1290173 -TGTATCGATGCATAAAATGCATTCGATGTTTTCATAA-AAACCTGAGTGCATCGATGCATGGCA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTT-A-AACAAACCTGAGTGCATCGATGCATGGCA
*
1290236 GTGCATCGATGCATAATATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
1290267 CAATTTATTC
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
62 30 0.36
63 24 0.29
64 30 0.36
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTAAACAAACCTGAGTGCATCGATGCATGGCA
Found at i:1294777 original size:76 final size:76
Alignment explanation
Indices: 1294665--1294818 Score: 308
Period size: 76 Copynumber: 2.0 Consensus size: 76
1294655 AATTGATGTT
1294665 ATTAAAAATATTTATACTAAATTAATTTAATTATTTGTATACAAATATCAAAATGGTTGGAAAAT
1 ATTAAAAATATTTATACTAAATTAATTTAATTATTTGTATACAAATATCAAAATGGTTGGAAAAT
1294730 AAGTAGTTCAA
66 AAGTAGTTCAA
1294741 ATTAAAAATATTTATACTAAATTAATTTAATTATTTGTATACAAATATCAAAATGGTTGGAAAAT
1 ATTAAAAATATTTATACTAAATTAATTTAATTATTTGTATACAAATATCAAAATGGTTGGAAAAT
1294806 AAGTAGTTCAA
66 AAGTAGTTCAA
1294817 AT
1 AT
1294819 CAACGAGAAT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.38
Consensus pattern (76 bp):
ATTAAAAATATTTATACTAAATTAATTTAATTATTTGTATACAAATATCAAAATGGTTGGAAAAT
AAGTAGTTCAA
Found at i:1295072 original size:14 final size:15
Alignment explanation
Indices: 1295043--1295077 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1295033 TATATATATA
*
1295043 TAAAAGAAATATTAT
1 TAAAACAAATATTAT
1295058 TAAAACAAA-ATTAT
1 TAAAACAAATATTAT
1295072 TAAAAC
1 TAAAAC
1295078 TTACATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.29
Consensus pattern (15 bp):
TAAAACAAATATTAT
Found at i:1299148 original size:43 final size:44
Alignment explanation
Indices: 1299045--1299156 Score: 106
Period size: 43 Copynumber: 2.6 Consensus size: 44
1299035 GCGTTTGTAG
* *
1299045 ATAGGTTAGGTCAATTAGCAGCGTTTTTAAAACAAACGCCGCTA
1 ATAGGTTAGGTTATTTAGCAGCGTTTTTAAAACAAACGCCGCTA
* * * **
1299089 A-AAGTTATGCTT-TTTAGCAGTGTTTATT-TTACAAACGCCGC-A
1 ATAGGTTA-GGTTATTTAGCAGCGTTT-TTAAAACAAACGCCGCTA
*
1299131 ATAGGTTAGGTTATTTAGCGGCGTTT
1 ATAGGTTAGGTTATTTAGCAGCGTTT
1299157 GTAATAGTAA
Statistics
Matches: 53, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
42 5 0.09
43 43 0.81
44 5 0.09
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (44 bp):
ATAGGTTAGGTTATTTAGCAGCGTTTTTAAAACAAACGCCGCTA
Found at i:1301347 original size:14 final size:14
Alignment explanation
Indices: 1301325--1301363 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1301315 TTGCGGTTGT
1301325 GGTGATGGCTGCAC
1 GGTGATGGCTGCAC
* *
1301339 GGTGGTGGCTTCAC
1 GGTGATGGCTGCAC
*
1301353 TGTGATGGCTG
1 GGTGATGGCTG
1301364 GGCGTTAGAG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.10, C:0.18, G:0.44, T:0.28
Consensus pattern (14 bp):
GGTGATGGCTGCAC
Found at i:1301622 original size:42 final size:42
Alignment explanation
Indices: 1301454--1301775 Score: 417
Period size: 42 Copynumber: 7.9 Consensus size: 42
1301444 ATGGCGTTAG
* * * * * *
1301454 GTGCATGACTATAGCAGCGTTTATTACCAAAATGCCGCTAAA
1 GTGCATGATTATTGCGGCGTTTATTACAAAAACGCCACTAAA
* * *
1301496 GTGTATGATTATTGCGGCGTTTATTAGAAACACG-CACTAAA
1 GTGCATGATTATTGCGGCGTTTATTACAAAAACGCCACTAAA
* *
1301537 GTGCATGATTATTGCGGCGTTTA-T--AAAAACGCCGCTAAG
1 GTGCATGATTATTGCGGCGTTTATTACAAAAACGCCACTAAA
* *
1301576 GTGCATGATTATTACGGCGTTTATTACAAAAACGCCATTAAA
1 GTGCATGATTATTGCGGCGTTTATTACAAAAACGCCACTAAA
* *
1301618 GTGCATGACTATTGCGGCGTTTA-TA-AAAAACGCCATTAAA
1 GTGCATGATTATTGCGGCGTTTATTACAAAAACGCCACTAAA
* *
1301658 TTGCATGATTATTGCGGCGTTTATTTCAAAAACGCCACTAAA
1 GTGCATGATTATTGCGGCGTTTATTACAAAAACGCCACTAAA
*
1301700 GTGCATGATTATTGCGGCGTTTA-T-CTAAAACGCCACTAAA
1 GTGCATGATTATTGCGGCGTTTATTACAAAAACGCCACTAAA
*
1301740 GTGCATGACTATTGCGGCGTTTATTACAAAAACGCC
1 GTGCATGATTATTGCGGCGTTTATTACAAAAACGCC
1301776 GCCTTTTGAG
Statistics
Matches: 245, Mismatches: 27, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
38 6 0.02
39 27 0.11
40 75 0.31
41 33 0.13
42 104 0.42
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (42 bp):
GTGCATGATTATTGCGGCGTTTATTACAAAAACGCCACTAAA
Found at i:1301682 original size:82 final size:82
Alignment explanation
Indices: 1301454--1301775 Score: 432
Period size: 82 Copynumber: 3.9 Consensus size: 82
1301444 ATGGCGTTAG
* * * * * *
1301454 GTGCATGACTATAGCAGCGTTTATTACCAAAATGCCGCTAAAGTGTATGATTATTGCGGCGTTTA
1 GTGCATGACTATTGCGGCGTTTA-TA-AAAAACGCCACTAAAGTGCATGATTATTGCGGCGTTTA
* *
1301519 TTAGAAACACG-CACTAAA
64 TTACAAAAACGCCACTAAA
* * * *
1301537 GTGCATGATTATTGCGGCGTTTAT-AAAAACGCCGCTAAGGTGCATGATTATTACGGCGTTTATT
1 GTGCATGACTATTGCGGCGTTTATAAAAAACGCCACTAAAGTGCATGATTATTGCGGCGTTTATT
*
1301601 ACAAAAACGCCATTAAA
66 ACAAAAACGCCACTAAA
* *
1301618 GTGCATGACTATTGCGGCGTTTATAAAAAACGCCATTAAATTGCATGATTATTGCGGCGTTTATT
1 GTGCATGACTATTGCGGCGTTTATAAAAAACGCCACTAAAGTGCATGATTATTGCGGCGTTTATT
*
1301683 TCAAAAACGCCACTAAA
66 ACAAAAACGCCACTAAA
* ** *
1301700 GTGCATGATTATTGCGGCGTTTATCTAAAACGCCACTAAAGTGCATGACTATTGCGGCGTTTATT
1 GTGCATGACTATTGCGGCGTTTATAAAAAACGCCACTAAAGTGCATGATTATTGCGGCGTTTATT
1301765 ACAAAAACGCC
66 ACAAAAACGCC
1301776 GCCTTTTGAG
Statistics
Matches: 211, Mismatches: 26, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
80 42 0.20
81 29 0.14
82 120 0.57
83 20 0.09
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (82 bp):
GTGCATGACTATTGCGGCGTTTATAAAAAACGCCACTAAAGTGCATGATTATTGCGGCGTTTATT
ACAAAAACGCCACTAAA
Found at i:1301740 original size:122 final size:123
Alignment explanation
Indices: 1301454--1301775 Score: 429
Period size: 122 Copynumber: 2.6 Consensus size: 123
1301444 ATGGCGTTAG
* * * * * * * *
1301454 GTGCATGACTATAGCAGCGTTTATTACCAAAATGCCGCTAAAGTGTATGATTATTGCGGCGTTTA
1 GTGCATGATTATTGCGGCGTTTATTACAAAAACGCCACTAAAGTGCATGACTATTGCGGCGTTTA
* * * *
1301519 TTAGAAACACG-CACTAAAGTGCATGATTATTGCGGCGTTTATAAAAACGCCGCTAAG
66 TTACAAAAACGCCACTAAAGTGCATGATTATTGCGGCGTTTATAAAAACGCCACTAAA
* *
1301576 GTGCATGATTATTACGGCGTTTATTACAAAAACGCCATTAAAGTGCATGACTATTGCGGCGTTTA
1 GTGCATGATTATTGCGGCGTTTATTACAAAAACGCCACTAAAGTGCATGACTATTGCGGCGTTTA
* *
1301641 -TA-AAAAACGCCATTAAATTGCATGATTATTGCGGCGTTTATTTCAAAAACGCCACTAAA
66 TTACAAAAACGCCACTAAAGTGCATGATTATTGCGGCGTTTA--T-AAAAACGCCACTAAA
*
1301700 GTGCATGATTATTGCGGCGTTTA-T-CTAAAACGCCACTAAAGTGCATGACTATTGCGGCGTTTA
1 GTGCATGATTATTGCGGCGTTTATTACAAAAACGCCACTAAAGTGCATGACTATTGCGGCGTTTA
1301763 TTACAAAAACGCC
66 TTACAAAAACGCC
1301776 GCCTTTTGAG
Statistics
Matches: 176, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
120 6 0.03
121 30 0.17
122 92 0.52
123 4 0.02
124 44 0.25
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (123 bp):
GTGCATGATTATTGCGGCGTTTATTACAAAAACGCCACTAAAGTGCATGACTATTGCGGCGTTTA
TTACAAAAACGCCACTAAAGTGCATGATTATTGCGGCGTTTATAAAAACGCCACTAAA
Found at i:1309462 original size:2 final size:2
Alignment explanation
Indices: 1309455--1309480 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1309445 GTGTAGGACC
1309455 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
1309481 CCAGCGGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1313814 original size:14 final size:16
Alignment explanation
Indices: 1313795--1313832 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 16
1313785 TAAAATAAAT
1313795 TAATAATATA-ATA-A
1 TAATAATATATATATA
1313809 TAATAATATATTATATA
1 TAATAATATA-TATATA
1313826 TAATAAT
1 TAATAAT
1313833 TAAATATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.48
16 3 0.14
17 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATAATATATATATA
Found at i:1313938 original size:45 final size:46
Alignment explanation
Indices: 1313864--1313950 Score: 108
Period size: 45 Copynumber: 1.9 Consensus size: 46
1313854 ATATTTTTAA
* *
1313864 AAAACTATATTTTTTTCAAAAATGATATATACTATA-TATATGTTC
1 AAAACTATATTATTTTCAAAAAAGATATATACTATATTATATGTTC
*
1313909 AAAACTATA-TATTTT-AAAAAAGAACTATATATTATATTATAT
1 AAAACTATATTATTTTCAAAAAAG-A-TATATACTATATTATAT
1313951 ATATATATCA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
43 6 0.17
44 6 0.17
45 19 0.53
46 5 0.14
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (46 bp):
AAAACTATATTATTTTCAAAAAAGATATATACTATATTATATGTTC
Found at i:1337126 original size:49 final size:49
Alignment explanation
Indices: 1337066--1337189 Score: 185
Period size: 49 Copynumber: 2.5 Consensus size: 49
1337056 AAAACTGAAT
*
1337066 ACAAAAATCAAAATGAGGATTTAGCCTTTCATAGAGGATTCCAGCAGAA
1 ACAAAAATCAAAATGAGGATTTAGCCATTCATAGAGGATTCCAGCAGAA
* * * *
1337115 ACAGAAATCAAAATGAGGATTTAGCCATTCGTAGAGGTTTCCAGCCGAA
1 ACAAAAATCAAAATGAGGATTTAGCCATTCATAGAGGATTCCAGCAGAA
* *
1337164 ATAAAAATCAGAATGAGGATTTAGCC
1 ACAAAAATCAAAATGAGGATTTAGCC
1337190 CTCTGTAGAG
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 67 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (49 bp):
ACAAAAATCAAAATGAGGATTTAGCCATTCATAGAGGATTCCAGCAGAA
Found at i:1337334 original size:28 final size:28
Alignment explanation
Indices: 1337296--1337414 Score: 150
Period size: 28 Copynumber: 4.2 Consensus size: 28
1337286 ACGAGGTTCT
*
1337296 ATGCAGAATCAGGACGAGGACTAAGCCT
1 ATGCAGAATCAGGACGAGGACTAAGCCC
* *
1337324 ATGCAGAATCAGGATGGGGACTAAGCCC
1 ATGCAGAATCAGGACGAGGACTAAGCCC
* *
1337352 ATGCAGAATCAGAACGAGGAAC-GAGCTCCC
1 ATGCAGAATCAGGACGAGG-ACTAAG--CCC
*
1337382 ATGCAGAATCAGGACGGGGACTAAGCCC
1 ATGCAGAATCAGGACGAGGACTAAGCCC
1337410 ATGCA
1 ATGCA
1337415 AAATTAGTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
28 51 0.66
29 4 0.05
30 22 0.29
ACGTcount: A:0.34, C:0.24, G:0.29, T:0.13
Consensus pattern (28 bp):
ATGCAGAATCAGGACGAGGACTAAGCCC
Found at i:1340269 original size:25 final size:25
Alignment explanation
Indices: 1340238--1340321 Score: 75
Period size: 27 Copynumber: 3.3 Consensus size: 25
1340228 CCAGTTTTTT
1340238 TAAAAAACCTGGATTTTTTT-TCCGGA
1 TAAAAAACC-GG-TTTTTTTATCCGGA
*
1340264 TAAAAAACCGGTTTTTTTATCCGGTT
1 TAAAAAACCGGTTTTTTTATCCGG-A
* *
1340290 TGAAAAAAACCAG-TTTTTAATCCGG-
1 T--AAAAAACCGGTTTTTTTATCCGGA
1340315 TAAAAAA
1 TAAAAAA
1340322 ACCGATCGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
23 6 0.12
24 7 0.14
25 8 0.16
26 10 0.20
27 11 0.22
28 9 0.18
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (25 bp):
TAAAAAACCGGTTTTTTTATCCGGA
Found at i:1340295 original size:27 final size:27
Alignment explanation
Indices: 1340239--1340322 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 27
1340229 CAGTTTTTTT
1340239 AAAAAACCTGGATTTTTTT-TCCGG-AT-
1 AAAAAACC-GG-TTTTTTTATCCGGTATA
*
1340265 AAAAAACCGGTTTTTTTATCCGGTTTGA
1 AAAAAACCGGTTTTTTTATCCGGTAT-A
* *
1340293 AAAAAACCAG-TTTTTAATCCGGTA-A
1 AAAAAACCGGTTTTTTTATCCGGTATA
1340318 AAAAA
1 AAAAA
1340323 CCGATCGTTC
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
24 7 0.14
25 13 0.26
26 9 0.18
27 12 0.24
28 9 0.18
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (27 bp):
AAAAAACCGGTTTTTTTATCCGGTATA
Found at i:1341039 original size:119 final size:119
Alignment explanation
Indices: 1340808--1341024 Score: 296
Period size: 119 Copynumber: 1.8 Consensus size: 119
1340798 CTTTATTATT
* *
1340808 TTTTCTTTTCTTATATCACATCTCTATTTTCTTTTGTTTTTTAATCTTCAATAAACATGTCTTTA
1 TTTTCTTTTCTTATATCACATCTCTATTTTCTTTTATTTTTTAATCTTCAATAAACATATCTTTA
* * * * *
1340873 TGACACATTTTCATCTACCTTTATAATACGATTTCATCTACCTTTATGGCATCC
66 TAACACATTTTCATCCACCTTTATAACACAATTTAATCTACCTTTATGGCATCC
* *
1340927 TTTTCTTTTCTTATATCACATCTCTATTTTCTTTTATTTTTTAATGTTCAATAAGTC-TATCTTT
1 TTTTCTTTTCTTATATCACATCTCTATTTTCTTTTATTTTTTAATCTTCAATAA-ACATATCTTT
* *
1340991 ATAACACGTTTTTATCCA-CTATTATAACA-AATTT
65 ATAACACATTTTCATCCACCT-TTATAACACAATTT
1341025 TTAATTATCT
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
118 6 0.07
119 79 0.92
120 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.52
Consensus pattern (119 bp):
TTTTCTTTTCTTATATCACATCTCTATTTTCTTTTATTTTTTAATCTTCAATAAACATATCTTTA
TAACACATTTTCATCCACCTTTATAACACAATTTAATCTACCTTTATGGCATCC
Found at i:1341256 original size:19 final size:18
Alignment explanation
Indices: 1341224--1341292 Score: 120
Period size: 18 Copynumber: 3.8 Consensus size: 18
1341214 ATATAAACAG
1341224 AAAAATCTTATTTTTCAT
1 AAAAATCTTATTTTTCAT
1341242 AAAAATCTTATTTTTCATT
1 AAAAATCTTATTTTTCA-T
1341261 AAAAATCTTATTTTTCAT
1 AAAAATCTTATTTTTCAT
*
1341279 AAAAATCTAATTTT
1 AAAAATCTTATTTT
1341293 CTTTTTATTG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
18 31 0.63
19 18 0.37
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (18 bp):
AAAAATCTTATTTTTCAT
Found at i:1341524 original size:23 final size:22
Alignment explanation
Indices: 1341453--1341533 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 22
1341443 TCAATAAGTA
*
1341453 TGTCTTTATGACACATTTTCATC
1 TGTCTTTATGACACA-TTTCATT
** *
1341476 TACCTTTATGACACGATTTCAAT
1 TGTCTTTATGACAC-ATTTCATT
*
1341499 TGTCTTTATGACACATTATCTTT
1 TGTCTTTATGACACATT-TCATT
1341522 TGTCTTT-TGACA
1 TGTCTTTATGACA
1341534 TGTTTTTCCG
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
22 8 0.17
23 39 0.81
24 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.47
Consensus pattern (22 bp):
TGTCTTTATGACACATTTCATT
Found at i:1345155 original size:38 final size:39
Alignment explanation
Indices: 1345071--1345180 Score: 138
Period size: 38 Copynumber: 2.8 Consensus size: 39
1345061 TTATTTATAA
* *
1345071 TTCTCAAATTATTTCAC-TCTAACATTCTAGATTCCTAAT
1 TTCTTAAATTATTTCACAT-TAACATTCTAAATTCCTAAT
*
1345110 TTCTTAAATT-TTTCCACCA-TAACATT-TAAATTCTTAAT
1 TTCTTAAATTATTT-CA-CATTAACATTCTAAATTCCTAAT
1345148 TTCTTAAATTATTTCACATTAACATTCTAAATT
1 TTCTTAAATTATTTCACATTAACATTCTAAATT
1345181 ATTTTTTTAA
Statistics
Matches: 62, Mismatches: 3, Indels: 12
0.81 0.04 0.16
Matches are distributed among these distances:
37 2 0.03
38 32 0.52
39 27 0.44
40 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.01, T:0.46
Consensus pattern (39 bp):
TTCTTAAATTATTTCACATTAACATTCTAAATTCCTAAT
Found at i:1345243 original size:18 final size:18
Alignment explanation
Indices: 1345222--1345267 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
1345212 ACATTTGAAA
1345222 TTTAATTATAAT-TTTTGT
1 TTTAATTATAATATTTT-T
*
1345240 TTTAATTTTAATATTTTT
1 TTTAATTATAATATTTTT
1345258 TTTCAATTAT
1 TTT-AATTAT
1345268 GTAATTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTAATTATAATATTTTT
Found at i:1346024 original size:22 final size:20
Alignment explanation
Indices: 1345990--1346034 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
1345980 TAGTATATAT
1345990 TATATTTTAATTAATGATAA
1 TATATTTTAATTAATGATAA
* *
1346010 TATATATTTATATTATTGTTAA
1 TATAT-TTTA-ATTAATGATAA
1346032 TAT
1 TAT
1346035 TCAAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 4 0.19
22 12 0.57
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
TATATTTTAATTAATGATAA
Found at i:1351465 original size:13 final size:12
Alignment explanation
Indices: 1351447--1351479 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1351437 GTTAAAAAAA
1351447 TAAAAATATAATT
1 TAAAAATAT-ATT
1351460 TAAAAAT-TATT
1 TAAAAATATATT
1351471 TAAAAATAT
1 TAAAAATAT
1351480 TAAAAATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.53
12 2 0.11
13 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TAAAAATATATT
Found at i:1352713 original size:17 final size:17
Alignment explanation
Indices: 1352687--1352719 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
1352677 TTTTGTTTTT
1352687 AATTTATTTAAGTATTTA
1 AATTTATTTAA-TATTTA
1352705 AATTT-TTTAATATTT
1 AATTTATTTAATATTT
1352720 TATTTAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AATTTATTTAATATTTA
Found at i:1352721 original size:17 final size:19
Alignment explanation
Indices: 1352682--1352721 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
1352672 TAATATTTTG
*
1352682 TTTTTAATTTATTTAAGTA
1 TTTTAAATTTATTTAAGTA
1352701 -TTTAAATTT-TTTAA-TA
1 TTTTAAATTTATTTAAGTA
1352717 TTTTA
1 TTTTA
1352722 TTTAATCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 2 0.11
17 9 0.47
18 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTAAATTTATTTAAGTA
Found at i:1353859 original size:24 final size:24
Alignment explanation
Indices: 1353828--1353873 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1353818 AGATTATAGT
1353828 TATATAATTAGAATATAATTTTGA
1 TATATAATTAGAATATAATTTTGA
* *
1353852 TATATAATTAGATTATTATTTT
1 TATATAATTAGAATATAATTTT
1353874 AATAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (24 bp):
TATATAATTAGAATATAATTTTGA
Found at i:1354490 original size:27 final size:27
Alignment explanation
Indices: 1354460--1354517 Score: 86
Period size: 24 Copynumber: 2.3 Consensus size: 27
1354450 CAACCATATG
1354460 TGATGCCGCCACCGTCATTCCCTTACC
1 TGATGCCGCCACCGTCATTCCCTTACC
*
1354487 TGAT---GCCACCGTCGTTCCCTTACC
1 TGATGCCGCCACCGTCATTCCCTTACC
1354511 TGATGCC
1 TGATGCC
1354518 ACCGCCGCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 23 0.85
27 4 0.15
ACGTcount: A:0.14, C:0.41, G:0.17, T:0.28
Consensus pattern (27 bp):
TGATGCCGCCACCGTCATTCCCTTACC
Found at i:1354494 original size:24 final size:24
Alignment explanation
Indices: 1354467--1354521 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
1354457 ATGTGATGCC
1354467 GCCACCGTCATTCCCTTACCTGAT
1 GCCACCGTCATTCCCTTACCTGAT
*
1354491 GCCACCGTCGTTCCCTTACCTGAT
1 GCCACCGTCATTCCCTTACCTGAT
1354515 GCCACCG
1 GCCACCG
1354522 CCGCCACCGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.15, C:0.44, G:0.16, T:0.25
Consensus pattern (24 bp):
GCCACCGTCATTCCCTTACCTGAT
Found at i:1355139 original size:35 final size:34
Alignment explanation
Indices: 1355054--1355139 Score: 111
Period size: 34 Copynumber: 2.5 Consensus size: 34
1355044 TACTTACTTA
* * *
1355054 ATTTTGTTAATTTGGTTGGATTTATTTTTAATTT
1 ATTTTGTTAATTTTGTTGGATTTATTATTAATGT
*
1355088 ATTTTGTTAAATTTGTTGGACTTT-TTATTAATGT
1 ATTTTGTTAATTTTGTTGGA-TTTATTATTAATGT
1355122 ATTTTGGTTAATTTTGTT
1 ATTTT-GTTAATTTTGTT
1355140 TATTACCATT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
34 31 0.69
35 14 0.31
ACGTcount: A:0.21, C:0.01, G:0.15, T:0.63
Consensus pattern (34 bp):
ATTTTGTTAATTTTGTTGGATTTATTATTAATGT
Found at i:1355169 original size:35 final size:32
Alignment explanation
Indices: 1355134--1355214 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 32
1355124 TTTGGTTAAT
1355134 TTTGTT-TATTACCATTTAATATCAGTTATTGTAA
1 TTTGTTATATTACCATTTAATA-C--TTATTGTAA
1355168 TTTGTTTATCATTTACCATTTAATACTTATTGTAA
1 TTTG-TTAT-A-TTACCATTTAATACTTATTGTAA
*
1355203 GTTTGTTGTATT
1 -TTTGTTATATT
1355215 TAAAATTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
33 2 0.05
34 5 0.12
35 14 0.34
36 5 0.12
37 2 0.05
38 13 0.32
ACGTcount: A:0.26, C:0.09, G:0.10, T:0.56
Consensus pattern (32 bp):
TTTGTTATATTACCATTTAATACTTATTGTAA
Found at i:1360359 original size:5 final size:5
Alignment explanation
Indices: 1360317--1360375 Score: 59
Period size: 5 Copynumber: 12.0 Consensus size: 5
1360307 GCCGTTCGTT
* * * *
1360317 TTTTA TGTTA -TTTA TTTTGA GTTTA -TTTG TTGTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1360366 TTTTA TTTTA
1 TTTTA TTTTA
1360376 ATCACTAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
4 6 0.14
5 34 0.77
6 4 0.09
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:1360626 original size:15 final size:15
Alignment explanation
Indices: 1360606--1360751 Score: 58
Period size: 15 Copynumber: 9.9 Consensus size: 15
1360596 CTTTTATTCG
1360606 ATTTACATTTCTGTT
1 ATTTACATTTCTGTT
1360621 ATTTACATTT-TCG-T
1 ATTTACATTTCT-GTT
**
1360635 ACTTTATTTTTCCTGTT
1 A-TTTACATTT-CTGTT
* *
1360652 ATTTACATTTATGCCT
1 ATTTACATTTCTG-TT
* **
1360668 -TTTA-TTTTCTCAT
1 ATTTACATTTCTGTT
* * *
1360681 ATTTATATTTCAGTC
1 ATTTACATTTCTGTT
*
1360696 CTTT-CATTTTCTGTT
1 ATTTACA-TTTCTGTT
*
1360711 -TTTACATTAT-TGCT
1 ATTTACATT-TCTGTT
*
1360725 -TTTA-TTTTCTGTT
1 ATTTACATTTCTGTT
1360738 ATTTACATTTCTGT
1 ATTTACATTTCTGT
1360752 CCTTTAATTT
Statistics
Matches: 94, Mismatches: 23, Indels: 28
0.65 0.16 0.19
Matches are distributed among these distances:
12 1 0.01
13 6 0.06
14 28 0.30
15 47 0.50
16 9 0.10
17 3 0.03
ACGTcount: A:0.18, C:0.15, G:0.06, T:0.61
Consensus pattern (15 bp):
ATTTACATTTCTGTT
Found at i:1360741 original size:57 final size:58
Alignment explanation
Indices: 1360613--1360762 Score: 173
Period size: 57 Copynumber: 2.5 Consensus size: 58
1360603 TCGATTTACA
*
1360613 TTTCTGTTATTTACATTTTCGTACTTTATTTTTCCTGTTATTTACATTTATGCCTTTTAT
1 TTTCTGTTATTTACA-TTTCGTCCTTTA-TTTTCCTGTTATTTACATTTATGCCTTTTAT
** *
1360673 TTTCTCATATTTATATTTCAGTCCTTTCATTTT-CTGTT-TTTACA-TTATTG-CTTTTAT
1 TTTCTGTTATTTACATTTC-GTCCTTT-ATTTTCCTGTTATTTACATTTA-TGCCTTTTAT
1360730 TTTCTGTTATTTACATTTCTGTCCTTTAATTTT
1 TTTCTGTTATTTACATTTC-GTCCTTT-ATTTT
1360763 ATGTACTTTA
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
57 38 0.49
58 8 0.10
59 9 0.12
60 22 0.28
61 1 0.01
ACGTcount: A:0.17, C:0.15, G:0.06, T:0.62
Consensus pattern (58 bp):
TTTCTGTTATTTACATTTCGTCCTTTATTTTCCTGTTATTTACATTTATGCCTTTTAT
Found at i:1360761 original size:14 final size:14
Alignment explanation
Indices: 1360725--1360792 Score: 55
Period size: 15 Copynumber: 4.6 Consensus size: 14
1360715 CATTATTGCT
* **
1360725 TTTATTTTCTGTTA
1 TTTAATTTCTGTCC
1360739 TTTACATTTCTGTCC
1 TTTA-ATTTCTGTCC
* *
1360754 TTTAATTTTATGTAC
1 TTTAA-TTTCTGTCC
*
1360769 TTTAATTTATGTCC
1 TTTAATTTCTGTCC
1360783 TTTAAATTTC
1 TTT-AATTTC
1360793 AGGCATTTAC
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
14 16 0.36
15 28 0.64
ACGTcount: A:0.21, C:0.13, G:0.06, T:0.60
Consensus pattern (14 bp):
TTTAATTTCTGTCC
Found at i:1360801 original size:29 final size:29
Alignment explanation
Indices: 1360738--1360806 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
1360728 ATTTTCTGTT
* * * *
1360738 ATTTACATTTCTGTCCTTTAATTTTATGT
1 ATTTACATTTATGTCCTTTAATTTCAGGC
1360767 ACTTTA-ATTTATGTCCTTTAAATTTCAGGC
1 A-TTTACATTTATGTCCTTT-AATTTCAGGC
1360797 ATTTACATTT
1 ATTTACATTT
1360807 CAGCCATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
29 17 0.52
30 16 0.48
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (29 bp):
ATTTACATTTATGTCCTTTAATTTCAGGC
Found at i:1360817 original size:15 final size:15
Alignment explanation
Indices: 1360783--1360818 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1360773 ATTTATGTCC
* *
1360783 TTTAAATTTCAGGCA
1 TTTACATTTCAGCCA
1360798 TTTACATTTCAGCCA
1 TTTACATTTCAGCCA
1360813 TTTACA
1 TTTACA
1360819 CTTGGTGTGT
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:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (15 bp):
TTTACATTTCAGCCA
Found at i:1362577 original size:93 final size:93
Alignment explanation
Indices: 1362410--1362628 Score: 312
Period size: 93 Copynumber: 2.4 Consensus size: 93
1362400 CTCGTGTTTG
** * * *
1362410 CTTGCGTACTCGTTAAATTAAACTAAATAAATTTATGTTTCCTCAGTGGAAGCATTGTGTGCTAA
1 CTTGCGTACTTATTAAATTAAACTAAATAAATTAATGTTTCCTCAGTGGAAACATTGAGTGCTAA
* *
1362475 TAAGATTGTAGGTTTGTCATTTGTGTGT
66 TAAGATTGTAGGGTCGTCATTTGTGTGT
* *
1362503 CTTGCGTACTTATTAAACTAAACTAAATAAATTAATGTTTCCTCAGTGGAAACATTGAGTGGTAA
1 CTTGCGTACTTATTAAATTAAACTAAATAAATTAATGTTTCCTCAGTGGAAACATTGAGTGCTAA
* *
1362568 TGAGCTTGTAGGGTCGTCATTTGTGTGT
66 TAAGATTGTAGGGTCGTCATTTGTGTGT
* * *
1362596 GTTGCGTACTTATTCAATTATACTAAATAAATT
1 CTTGCGTACTTATTAAATTAAACTAAATAAATT
1362629 CGTGTAAACA
Statistics
Matches: 111, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 111 1.00
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.39
Consensus pattern (93 bp):
CTTGCGTACTTATTAAATTAAACTAAATAAATTAATGTTTCCTCAGTGGAAACATTGAGTGCTAA
TAAGATTGTAGGGTCGTCATTTGTGTGT
Found at i:1365790 original size:3 final size:3
Alignment explanation
Indices: 1365782--1365831 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
1365772 CACACATAAT
1365782 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1365830 TT
1 TT
1365832 CTCATGATTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1375301 original size:26 final size:26
Alignment explanation
Indices: 1375249--1375301 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1375239 CAACTCGACC
****
1375249 CTTGAGTAAATTTCATAAACCGTATG
1 CTTGAGTAAATTTCATAAAAAAAATG
1375275 CTTGAGTAAATTTCATAAAAAAAATG
1 CTTGAGTAAATTTCATAAAAAAAATG
1375301 C
1 C
1375302 CTCTTACACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (26 bp):
CTTGAGTAAATTTCATAAAAAAAATG
Found at i:1381659 original size:21 final size:21
Alignment explanation
Indices: 1381612--1381661 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1381602 AAACCCTATG
* *
1381612 GCGGAGGCATCTGAACTGACT
1 GCGGTGGCATCTGAAATGACT
*
1381633 GTGGTGGCATCTGAAATGGA-T
1 GCGGTGGCATCTGAAAT-GACT
1381654 GCGGTGGC
1 GCGGTGGC
1381662 GTTTGACCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.20, C:0.18, G:0.40, T:0.22
Consensus pattern (21 bp):
GCGGTGGCATCTGAAATGACT
Done.