Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009074.1 Hibiscus syriacus cultivar Beakdansim tig00112507_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2143704
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1153362 original size:18 final size:19
Alignment explanation
Indices: 1153339--1153384 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
1153329 TAAAAATATT
1153339 TTTAATGTTAATATGT-AA
1 TTTAATGTTAATATGTGAA
1153357 TTTAAT-TTAATATGTGAA
1 TTTAATGTTAATATGTGAA
1153375 TTTAA-GTTAA
1 TTTAATGTTAA
1153385 CATATATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (19 bp):
TTTAATGTTAATATGTGAA
Found at i:1155968 original size:2 final size:2
Alignment explanation
Indices: 1155961--1156003 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1155951 CATCACTAAC
1155961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1156003 A
1 A
1156004 ATCACACCGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1156674 original size:24 final size:25
Alignment explanation
Indices: 1156618--1156681 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 25
1156608 TATTATACAT
*
1156618 TATATATATATTA-CACTATTCACAA
1 TATATATATATTATTACTA-TCACAA
*
1156643 TATATATATATTATTACTA-CACTA
1 TATATATATATTATTACTATCACAA
1156667 TATATATATATTATT
1 TATATATATATTATT
1156682 TTACAACATC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 19 0.53
25 13 0.36
26 4 0.11
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (25 bp):
TATATATATATTATTACTATCACAA
Found at i:1158016 original size:17 final size:16
Alignment explanation
Indices: 1157985--1158018 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1157975 TTCGTTTTCA
1157985 TTTTTTTATTCATTTT
1 TTTTTTTATTCATTTT
*
1158001 TTTTTTTACTTTATTTT
1 TTTTTTTA-TTCATTTT
1158018 T
1 T
1158019 ATAACCATTT
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:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTTATTCATTTT
Found at i:1158042 original size:6 final size:6
Alignment explanation
Indices: 1158026--1158056 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1158016 TTTATAACCA
1158026 TTTTA- TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
1158057 ATTTTATTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:1158045 original size:57 final size:57
Alignment explanation
Indices: 1157979--1158111 Score: 135
Period size: 57 Copynumber: 2.3 Consensus size: 57
1157969 TTTTTCTTCG
* * *
1157979 TTTTCATTTTTTTATTCATTTTTTTTTTTACTTTATTT-TTATAACCATTTTATTTTA
1 TTTTTATTTTTTTATTCATTTATTTTATTACTTTATTTCTT-TAACCATTTTATTTTA
* * * * *
1158036 TTTTTATTTTTATT-TTTATTTATTTTATTACTTTCTTTCTTTTATCGTTTTATTTTA
1 TTTTTATTTTT-TTATTCATTTATTTTATTACTTTATTTCTTTAACCATTTTATTTTA
1158093 TTTCATTATTTTATTTATT
1 TTT--TTATTTT-TTTATT
1158112 TAACCACTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
57 46 0.74
58 4 0.06
59 9 0.15
60 3 0.05
ACGTcount: A:0.18, C:0.08, G:0.01, T:0.74
Consensus pattern (57 bp):
TTTTTATTTTTTTATTCATTTATTTTATTACTTTATTTCTTTAACCATTTTATTTTA
Found at i:1158111 original size:17 final size:17
Alignment explanation
Indices: 1158028--1158112 Score: 73
Period size: 18 Copynumber: 4.9 Consensus size: 17
1158018 TATAACCATT
*
1158028 TTATTTTATTT-TTATTT
1 TTATTTTATTTATT-TTA
1158045 TTATTTTTATTTATTTTA
1 TTA-TTTTATTTATTTTA
* * *
1158063 TTACTTTCTTTCTTTTA
1 TTATTTTATTTATTTTA
** *
1158080 TCGTTTTATTTTATTTCA
1 TTATTTTA-TTTATTTTA
1158098 TTATTTTATTTATTT
1 TTATTTTATTTATTT
1158113 AACCACTTTC
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
17 25 0.47
18 26 0.49
19 2 0.04
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.75
Consensus pattern (17 bp):
TTATTTTATTTATTTTA
Found at i:1160592 original size:46 final size:45
Alignment explanation
Indices: 1160471--1160614 Score: 261
Period size: 45 Copynumber: 3.2 Consensus size: 45
1160461 ATCAATAAAT
* *
1160471 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAACATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1160516 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1160561 TTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTT-ATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1160607 TTACCATT
1 TTACCATT
1160615 AGTATGATTT
Statistics
Matches: 96, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
45 52 0.54
46 44 0.46
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
Found at i:1160775 original size:59 final size:58
Alignment explanation
Indices: 1160615--1160919 Score: 204
Period size: 59 Copynumber: 5.2 Consensus size: 58
1160605 ACTTACCATT
* * * * *
1160615 AGTATGATTTTGTTACCATTTTAGCACATGAAATACCCTATGTGAAAATCCATAC-CATT
1 AGTATGATTTTCTTACCTTTTTAGCACAT-AAATGCCCTATCTGAAAATCCATACAC-TC
* * * * * * **
1160674 AGTATGATTTCCTTATCTTTGTAGCACCCTTAGTGCTTTATCTGAAAATCCATACACTC
1 AGTATGATTTTCTTACCTTTTTAGCA-CATAAATGCCCTATCTGAAAATCCATACACTC
* * ***
1160733 AGTATGATTCTCTTACCTTTTTAGCACATAAAATGCCCTATCTGGAAATCCATATTTTC
1 AGTATGATTTTCTTACCTTTTTAGCACAT-AAATGCCCTATCTGAAAATCCATACACTC
* * * * * * * * *
1160792 AATATGATTTTCTTATC-ATTTAGCACACTCAGTGCCCCATATGGAAATCTATACACTC
1 AGTATGATTTTCTTACCTTTTTAGCACA-TAAATGCCCTATCTGAAAATCCATACACTC
* * * * * * * *
1160850 AGTATGATTTCCTTATC-ATTTAGCACACTCAGTGCTCC-ATATGGAAATCTATACACTC
1 AGTATGATTTTCTTACCTTTTTAGCACA-TAAATGC-CCTATCTGAAAATCCATACACTC
1160908 AGTATGATTTTC
1 AGTATGATTTTC
1160920 CTTATCATTT
Statistics
Matches: 200, Mismatches: 41, Indels: 11
0.79 0.16 0.04
Matches are distributed among these distances:
58 96 0.48
59 101 0.50
60 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (58 bp):
AGTATGATTTTCTTACCTTTTTAGCACATAAATGCCCTATCTGAAAATCCATACACTC
Found at i:1160880 original size:30 final size:30
Alignment explanation
Indices: 1160844--1160941 Score: 80
Period size: 30 Copynumber: 3.3 Consensus size: 30
1160834 GGAAATCTAT
1160844 ACACTCAGTATGATTTCCTTATCATTTAGC
1 ACACTCAGTATGATTTCCTTATCATTTAGC
* * * * *
1160874 ACACTCAG--TG--CTCCATATGGAAATCTA-T
1 ACACTCAGTATGATTTCCTTAT---CATTTAGC
1160902 ACACTCAGTATGATTTTCCTTATCATTTAGC
1 ACACTCAGTATGA-TTTCCTTATCATTTAGC
1160933 ACACTCAGT
1 ACACTCAGT
1160942 GTTTCATATG
Statistics
Matches: 49, Mismatches: 10, Indels: 17
0.64 0.13 0.22
Matches are distributed among these distances:
26 6 0.12
28 10 0.20
29 4 0.08
30 14 0.29
31 9 0.18
33 6 0.12
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (30 bp):
ACACTCAGTATGATTTCCTTATCATTTAGC
Found at i:1160950 original size:59 final size:58
Alignment explanation
Indices: 1160674--1160995 Score: 353
Period size: 59 Copynumber: 5.5 Consensus size: 58
1160664 CCATACCATT
* * * ** * * *
1160674 AGTATGATTTCCTTATCTTTGTAGCACCCTTAGTGCTTTATCTGAAAATCCATACACTC
1 AGTATGATTTCCTTATCATT-TAGCACACTCAGTGCTCCATATGGAAATCTATACACTC
* * * * * * ***
1160733 AGTATGA-TTCTCTTACCTTTTTAGCACA-TAAAATGC-CCTATCTGGAAATCCATATTTTC
1 AGTATGATTTC-CTTATC-ATTTAGCACACT-CAGTGCTCC-ATATGGAAATCTATACACTC
* * *
1160792 AATATGATTTTCTTATCATTTAGCACACTCAGTGCCCCATATGGAAATCTATACACTC
1 AGTATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTC
1160850 AGTATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTC
1 AGTATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTC
* *
1160908 AGTATGATTTTCCTTATCATTTAGCACACTCAGTGTTTCATATGGAAATCTATACACTC
1 AGTATGA-TTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTC
*
1160967 AGTATGATTTCCTTATTATTTTAGCACAC
1 AGTATGATTTCCTTATCA-TTTAGCACAC
1160996 AAAGTGCCAT
Statistics
Matches: 227, Mismatches: 27, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
58 104 0.46
59 118 0.52
60 5 0.02
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (58 bp):
AGTATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTC
Found at i:1169259 original size:27 final size:28
Alignment explanation
Indices: 1169188--1169266 Score: 74
Period size: 27 Copynumber: 2.9 Consensus size: 28
1169178 CTAAAAATAT
*
1169188 TAATAATTACAAAAATT-AATT-TATAAAC
1 TAATAA-TA-AAAAATTAAATTAAATAAAC
1169216 TAATAATAAAAAATTAAA-TAAATAAAC
1 TAATAATAAAAAATTAAATTAAATAAAC
* * * *
1169243 TATTACTAATAATTTAAATTAAAT
1 TAATAATAAAAAATTAAATTAAAT
1169267 TAAAATTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 8 0.19
27 24 0.56
28 11 0.26
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (28 bp):
TAATAATAAAAAATTAAATTAAATAAAC
Found at i:1169395 original size:21 final size:21
Alignment explanation
Indices: 1169363--1169426 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
1169353 CTGCAAAAAA
1169363 TAAAATAA-TTAAATAAAATAC
1 TAAAA-AATTTAAATAAAATAC
1169384 TAAAAAATTTAAATAAAATAC
1 TAAAAAATTTAAATAAAATAC
*
1169405 TAATAAAATATTAAATAGAATA
1 TAA-AAAAT-TTAAATAAAATA
1169427 AAATATACAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
20 2 0.05
21 21 0.54
22 5 0.13
23 11 0.28
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (21 bp):
TAAAAAATTTAAATAAAATAC
Found at i:1169426 original size:12 final size:12
Alignment explanation
Indices: 1169360--1169426 Score: 70
Period size: 11 Copynumber: 5.8 Consensus size: 12
1169350 TAACTGCAAA
1169360 AAATAAAATAATT
1 AAATAAAAT-ATT
*
1169373 AAATAAAATACT
1 AAATAAAATATT
1169385 -AA-AAAAT-TT
1 AAATAAAATATT
*
1169394 AAATAAAATACT
1 AAATAAAATATT
1169406 -AATAAAATATT
1 AAATAAAATATT
*
1169417 AAATAGAATA
1 AAATAAAATA
1169427 AAATATACAT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
9 1 0.02
10 7 0.16
11 17 0.38
12 11 0.24
13 9 0.20
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.28
Consensus pattern (12 bp):
AAATAAAATATT
Found at i:1172948 original size:27 final size:27
Alignment explanation
Indices: 1172916--1172977 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
1172906 TGATTGCATG
*
1172916 AGGTGACTCAAAATGCATAATATGACT
1 AGGTGACTCAAAATGCACAATATGACT
1172943 AGGTGACTCAAAATGCACAATATGACT
1 AGGTGACTCAAAATGCACAATATGACT
1172970 AGGTGACT
1 AGGTGACT
1172978 TATGCAAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (27 bp):
AGGTGACTCAAAATGCACAATATGACT
Found at i:1175054 original size:21 final size:20
Alignment explanation
Indices: 1175029--1175068 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1175019 ATTGATACCC
1175029 CAATACTAGAGTATCGATACT
1 CAATAC-AGAGTATCGATACT
*
1175050 CAATACATAGTATCGATAC
1 CAATACAGAGTATCGATAC
1175069 CACTGCACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (20 bp):
CAATACAGAGTATCGATACT
Found at i:1179754 original size:26 final size:22
Alignment explanation
Indices: 1179703--1179757 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 22
1179693 TATATTAGGG
*
1179703 TATAATGTATATTTTTTTATTA
1 TATAGTGTATATTTTTTTATTA
1179725 -ATAGTGTATAGTTATTTTTAATATA
1 TATAGTGTATA-TT-TTTTT-AT-TA
1179750 TATAGTGT
1 TATAGTGT
1179758 GTGGTCATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 9 0.33
22 2 0.07
23 5 0.19
24 2 0.07
25 2 0.07
26 7 0.26
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (22 bp):
TATAGTGTATATTTTTTTATTA
Found at i:1179829 original size:20 final size:20
Alignment explanation
Indices: 1179747--1179830 Score: 57
Period size: 20 Copynumber: 4.3 Consensus size: 20
1179737 TATTTTTAAT
1179747 ATATATAGTGTGTGGTCATA
1 ATATATAGTGTGTGGTCATA
* * * * **
1179767 TTATATAGTATATAGTTTTA
1 ATATATAGTGTGTGGTCATA
** * *
1179787 ATATAT--TGT-TTATGATC
1 ATATATAGTGTGTGGTCATA
1179804 ATATATAGTGTGTGGTCATA
1 ATATATAGTGTGTGGTCATA
1179824 ATATATA
1 ATATATA
1179831 ATATATAGTT
Statistics
Matches: 44, Mismatches: 17, Indels: 6
0.66 0.25 0.09
Matches are distributed among these distances:
17 9 0.20
18 2 0.05
19 3 0.07
20 30 0.68
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATATATAGTGTGTGGTCATA
Found at i:1180116 original size:20 final size:21
Alignment explanation
Indices: 1180075--1180119 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
1180065 ATATTATATT
*
1180075 AATATAAGTCCAATAAAAATA
1 AATACAAGTCCAATAAAAATA
*
1180096 AATACAAGTCC-ATAGAAATA
1 AATACAAGTCCAATAAAAATA
1180116 AATA
1 AATA
1180120 AGATTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.60, C:0.11, G:0.07, T:0.22
Consensus pattern (21 bp):
AATACAAGTCCAATAAAAATA
Found at i:1183270 original size:12 final size:12
Alignment explanation
Indices: 1183244--1183291 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
1183234 TATTAACATA
*
1183244 TTTAA-AATATA
1 TTTAATAATATT
*
1183255 TTTATTAATATT
1 TTTAATAATATT
1183267 TTTAATAATATAT
1 TTTAATAATAT-T
*
1183280 TATAATAATATT
1 TTTAATAATATT
1183292 ATTACAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
11 4 0.13
12 16 0.52
13 11 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTAATAATATT
Found at i:1183285 original size:22 final size:23
Alignment explanation
Indices: 1183223--1183300 Score: 75
Period size: 24 Copynumber: 3.3 Consensus size: 23
1183213 CATTTTAATA
* * *
1183223 AAAATATTAATTATTAACATATTT
1 AAAATA-TATTTATTAATATTTTT
1183247 AAAATATATTTATTAATATTTTT
1 AAAATATATTTATTAATATTTTT
* *
1183270 AATAATATATTATAATAATATTATT
1 AA-AATATATT-TATTAATATTTTT
*
1183295 ACAATA
1 AAAATA
1183301 ATATACTCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
23 16 0.35
24 18 0.39
25 12 0.26
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (23 bp):
AAAATATATTTATTAATATTTTT
Found at i:1183292 original size:11 final size:11
Alignment explanation
Indices: 1183271--1183377 Score: 53
Period size: 11 Copynumber: 9.6 Consensus size: 11
1183261 AATATTTTTA
1183271 ATAAT-ATATT
1 ATAATAATATT
1183281 ATAATAATATT
1 ATAATAATATT
1183292 ATTACAATAATA-T
1 A-T--AATAATATT
*
1183305 ACTCAATTATATT
1 A-T-AATAATATT
1183318 ATAATAATA-T
1 ATAATAATATT
* * *
1183328 ATGACACTATT
1 ATAATAATATT
* **
1183339 ATATTCTTATT
1 ATAATAATATT
*
1183350 TTAATAATA-T
1 ATAATAATATT
1183360 ATAATAA-ATT
1 ATAATAATATT
1183370 ATTAATAA
1 A-TAATAA
1183378 AAGTTATACT
Statistics
Matches: 73, Mismatches: 16, Indels: 15
0.70 0.15 0.14
Matches are distributed among these distances:
9 1 0.01
10 21 0.29
11 30 0.41
12 9 0.12
13 5 0.07
14 7 0.10
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.45
Consensus pattern (11 bp):
ATAATAATATT
Found at i:1183294 original size:14 final size:14
Alignment explanation
Indices: 1183260--1183304 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1183250 ATATATTTAT
1183260 TAATATT-TT-TAA
1 TAATATTATTATAA
1183272 TAATA-TATTATAA
1 TAATATTATTATAA
*
1183285 TAATATTATTACAA
1 TAATATTATTATAA
1183299 TAATAT
1 TAATAT
1183305 ACTCAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 1 0.03
12 7 0.24
13 8 0.28
14 13 0.45
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
TAATATTATTATAA
Found at i:1183326 original size:26 final size:26
Alignment explanation
Indices: 1183269--1183343 Score: 62
Period size: 26 Copynumber: 2.8 Consensus size: 26
1183259 TTAATATTTT
* * * *
1183269 TAATAATATATTATAATAATATTATTA
1 TAATAATATACT-CAATTATATTATAA
*
1183296 CAATAATATACTCAATTATATTATAA
1 TAATAATATACTCAATTATATTATAA
* *
1183322 TAAT-ATATGACACTATTATATT
1 TAATAATAT-ACTCAATTATATT
1183344 CTTATTTTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
25 4 0.10
26 25 0.64
27 10 0.26
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.44
Consensus pattern (26 bp):
TAATAATATACTCAATTATATTATAA
Found at i:1183732 original size:22 final size:20
Alignment explanation
Indices: 1183680--1183733 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
1183670 ATTACTCTAA
*
1183680 TATTTTTAAAATAATAATAT
1 TATTTTTATAATAATAATAT
1183700 TAAGTTTTTATAATAAATAATAT
1 T-A-TTTTTATAAT-AATAATAT
1183723 TATTTATTATA
1 TATTT-TTATA
1183734 TTTTATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 1 0.03
21 4 0.14
22 15 0.52
23 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TATTTTTATAATAATAATAT
Found at i:1184827 original size:13 final size:13
Alignment explanation
Indices: 1184809--1184851 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
1184799 AAAATGAATT
*
1184809 AAAAATATATTTA
1 AAAAATATAGTTA
1184822 AAAAAT-TAGTT-
1 AAAAATATAGTTA
*
1184833 AAAAATAAAGTTA
1 AAAAATATAGTTA
1184846 AAAAAT
1 AAAAAT
1184852 TACTTTGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 6 0.23
12 8 0.31
13 12 0.46
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (13 bp):
AAAAATATAGTTA
Found at i:1184834 original size:24 final size:24
Alignment explanation
Indices: 1184798--1184853 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
1184788 AAAAACATAT
* * *
1184798 AAAAATGAATTAAAAATATATTTA
1 AAAAATTAATTAAAAATAAAGTTA
*
1184822 AAAAATTAGTTAAAAATAAAGTTA
1 AAAAATTAATTAAAAATAAAGTTA
1184846 AAAAATTA
1 AAAAATTA
1184854 CTTTGCAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.30
Consensus pattern (24 bp):
AAAAATTAATTAAAAATAAAGTTA
Found at i:1184836 original size:11 final size:12
Alignment explanation
Indices: 1184807--1184849 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
1184797 TAAAAATGAA
*
1184807 TTAAAAATATAT
1 TTAAAAATATAG
1184819 TTAAAAA-ATTAG
1 TTAAAAATA-TAG
*
1184831 TTAAAAATAAAG
1 TTAAAAATATAG
1184843 TTAAAAA
1 TTAAAAA
1184850 ATTACTTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 1 0.04
12 25 0.93
13 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (12 bp):
TTAAAAATATAG
Found at i:1185696 original size:31 final size:31
Alignment explanation
Indices: 1185629--1185688 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1185619 CAATTTAAGG
*
1185629 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
1185660 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
1185689 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:1185780 original size:19 final size:19
Alignment explanation
Indices: 1185753--1185818 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 19
1185743 AATGTTTTTA
* *
1185753 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
*
1185772 TGAACAGTAAATTACTCTT
1 TGAACAGTAAATTACTATT
* * *
1185791 TGAATAGTAAATCACTGTT
1 TGAACAGTAAATTACTATT
1185810 TGAACAGTA
1 TGAACAGTA
1185819 CCCGAGGCTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:1185950 original size:21 final size:21
Alignment explanation
Indices: 1185924--1185965 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1185914 ATTTGAATAT
*
1185924 TATGAAGAGGTATCGATTCCC
1 TATGAAGAGGTACCGATTCCC
*
1185945 TATGAAGGGGTACCGATTCCC
1 TATGAAGAGGTACCGATTCCC
1185966 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
TATGAAGAGGTACCGATTCCC
Found at i:1186027 original size:21 final size:21
Alignment explanation
Indices: 1185994--1186033 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1185984 TTTTTACAGA
*
1185994 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
1186016 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
1186034 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1187194 original size:19 final size:20
Alignment explanation
Indices: 1187170--1187217 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1187160 AACGATTTTC
*
1187170 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
1187189 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1187209 TTTTGAAAA
1 TTTTGAAAA
1187218 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1188546 original size:31 final size:31
Alignment explanation
Indices: 1188479--1188538 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1188469 CAATTTAAGG
*
1188479 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
1188510 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
1188539 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:1188635 original size:19 final size:19
Alignment explanation
Indices: 1188613--1188667 Score: 83
Period size: 19 Copynumber: 2.9 Consensus size: 19
1188603 GAAAATTAAT
1188613 TTACTATTTGAACAGTAAA
1 TTACTATTTGAACAGTAAA
*
1188632 TTACTATTTGAATAGTAAA
1 TTACTATTTGAACAGTAAA
* *
1188651 TCACTGTTTGAACAGTA
1 TTACTATTTGAACAGTA
1188668 TCCGAGGCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (19 bp):
TTACTATTTGAACAGTAAA
Found at i:1188798 original size:21 final size:21
Alignment explanation
Indices: 1188772--1188813 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1188762 ATTTGAATAT
*
1188772 TATGAAGAGGTATCGATTCCC
1 TATGAAGAGGTACCGATTCCC
*
1188793 TATGAAGGGGTACCGATTCCC
1 TATGAAGAGGTACCGATTCCC
1188814 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
TATGAAGAGGTACCGATTCCC
Found at i:1191217 original size:60 final size:60
Alignment explanation
Indices: 1191124--1191240 Score: 216
Period size: 60 Copynumber: 1.9 Consensus size: 60
1191114 ATGAAAAATG
*
1191124 AAATTAGGGTTTTTAATGTTAGATAGGAACTTTCGGTTAATTGGAGTATGGGTCCTTAAA
1 AAATTAGGGTTTTTAATGTTAGATAGGAACTTTCGGTTAACTGGAGTATGGGTCCTTAAA
*
1191184 AAATTAGGGTTTTTAATGTTAGATAGGAGCTTTCGGTTAACTGGAGTATGGGTCCTT
1 AAATTAGGGTTTTTAATGTTAGATAGGAACTTTCGGTTAACTGGAGTATGGGTCCTT
1191241 GAAGTTTTGG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.27, C:0.08, G:0.26, T:0.38
Consensus pattern (60 bp):
AAATTAGGGTTTTTAATGTTAGATAGGAACTTTCGGTTAACTGGAGTATGGGTCCTTAAA
Found at i:1193039 original size:24 final size:24
Alignment explanation
Indices: 1192996--1193044 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
1192986 TATATATATA
1192996 TATTTATTTTTTAATAATTTAATT
1 TATTTATTTTTTAATAATTTAATT
1193020 TATTTAGTATTTTT-AT-ATTTAATT
1 TATTTA-T-TTTTTAATAATTTAATT
1193044 T
1 T
1193045 TTAAACATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 15 0.65
25 3 0.13
26 5 0.22
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TATTTATTTTTTAATAATTTAATT
Found at i:1193046 original size:39 final size:38
Alignment explanation
Indices: 1192994--1193079 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 38
1192984 TATATATATA
* * *
1192994 TATATTTATTTTTTAATA-ATTTAATTTATTTAGTATTTT
1 TATATTTAATTTTTAA-ACATTTAAATAATTTAGTA-TTT
*
1193033 TATATTTAATTTTTAAACATTTAAATAATTTTGTATTT
1 TATATTTAATTTTTAAACATTTAAATAATTTAGTATTT
*
1193071 TAAATTTAA
1 TATATTTAA
1193080 ATTTCAGAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
38 12 0.29
39 29 0.71
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.60
Consensus pattern (38 bp):
TATATTTAATTTTTAAACATTTAAATAATTTAGTATTT
Found at i:1196134 original size:165 final size:164
Alignment explanation
Indices: 1195863--1196194 Score: 607
Period size: 165 Copynumber: 2.0 Consensus size: 164
1195853 TGTAATGATG
1195863 CCTGCTATGCTTCTACCAAACTATGCTGCAATTGCATTGATTCAAAGTTGCAACATTGTTTGCTT
1 CCTGCTATGCTTCTACCAAACTATGCTGCAATTGCATTGATTCAAAGTTGCAACATTGTTTGCTT
1195928 TAAAGTTTAAACTGAATTTGATAAATGAAAGTTTATGTTCCTGGAAACTGG-GCATCGGTCAATG
66 TAAAGTTTAAACTGAATTTGATAAATGAAAGTTTATGTTCCTGGAAACTGGTGCATCGGT--ATG
1195992 -TTCAAATAGTACAATGCGTTCTTCATGTTTCATGC
129 CTTCAAATAGTACAATGCGTTCTTCATGTTTCATGC
1196027 CCTGCTATAGCTTCTACC-AACTATGCTGCAATTGCATTGAGTTCAAAGTTGCAACATTGTTTGC
1 CCTGCTAT-GCTTCTACCAAACTATGCTGCAATTGCATTGA-TTCAAAGTTGCAACATTGTTTGC
1196091 TTTAAAGTTTAAACTGAATTTGATAAATGAAAGTTTATGTTCCTGGAAACTGGTGCATCGGTATG
64 TTTAAAGTTTAAACTGAATTTGATAAATGAAAGTTTATGTTCCTGGAAACTGGTGCATCGGTATG
1196156 CTTCAAATAGTACAATGCGTTCTTCATGTTTCATGC
129 CTTCAAATAGTACAATGCGTTCTTCATGTTTCATGC
1196192 CCT
1 CCT
1196195 AAAGTTGGTT
Statistics
Matches: 164, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
164 33 0.20
165 123 0.75
166 8 0.05
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (164 bp):
CCTGCTATGCTTCTACCAAACTATGCTGCAATTGCATTGATTCAAAGTTGCAACATTGTTTGCTT
TAAAGTTTAAACTGAATTTGATAAATGAAAGTTTATGTTCCTGGAAACTGGTGCATCGGTATGCT
TCAAATAGTACAATGCGTTCTTCATGTTTCATGC
Found at i:1199538 original size:21 final size:20
Alignment explanation
Indices: 1199514--1199552 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1199504 CATGTCACCC
1199514 CTTCCCCCTCTCCCTCCCCGT
1 CTTCCCCCT-TCCCTCCCCGT
* *
1199535 CTTCTCCCTTCTCTCCCC
1 CTTCCCCCTTCCCTCCCC
1199553 CTGCCATGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.00, C:0.64, G:0.03, T:0.33
Consensus pattern (20 bp):
CTTCCCCCTTCCCTCCCCGT
Found at i:1199943 original size:15 final size:16
Alignment explanation
Indices: 1199923--1199956 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1199913 AAATTTTAAA
1199923 AAATTAGAT-ATTTTT
1 AAATTAGATGATTTTT
*
1199938 AAATTATATGATTTTT
1 AAATTAGATGATTTTT
1199954 AAA
1 AAA
1199957 AAAAAGTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
AAATTAGATGATTTTT
Found at i:1204206 original size:21 final size:21
Alignment explanation
Indices: 1204181--1204220 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1204171 TTTTATTCTG
1204181 AGCAATGATTATGATTCTTCA
1 AGCAATGATTATGATTCTTCA
1204202 AGCAATGATTATGATTCTT
1 AGCAATGATTATGATTCTT
1204221 ACTGATTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (21 bp):
AGCAATGATTATGATTCTTCA
Found at i:1204327 original size:16 final size:16
Alignment explanation
Indices: 1204302--1204334 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1204292 TCTAAAGTGC
1204302 AACAAAACAAAT-CAA
1 AACAAAACAAATACAA
1204317 AACACAAACAAATACAA
1 AACA-AAACAAATACAA
1204334 A
1 A
1204335 GTTCGATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.73, C:0.21, G:0.00, T:0.06
Consensus pattern (16 bp):
AACAAAACAAATACAA
Found at i:1207952 original size:131 final size:131
Alignment explanation
Indices: 1207712--1207955 Score: 314
Period size: 131 Copynumber: 1.9 Consensus size: 131
1207702 TAATTAAAAT
** *
1207712 AAATTAATATATAATTTATAAAAATATGATATTTATTTATTTAAGAATATCAGAAAAGAACTTTT
1 AAATTAATATATAATTTATAAAAATAAAATATTTATTTATTTAAGAATATCAGAAAAGAACTTCT
* * * *
1207777 AGGTGCTTTAAGGCAACCCATTTCTTAATATTAATAAATGAATAAATAAAAAACATTTTCCTAAT
66 AGGTGCTTTAAGACAACCAATTTCTTAATATGAATAAATAAATAAATAAAAAACATTTTCCTAAT
1207842 A
131 A
* * *
1207843 AAATTAATATATAATTTATAAAAGA-AAAATATTTATTTATTTAA-AATTATCATAATAGGACTT
1 AAATTAATATATAATTTATAAAA-ATAAAATATTTATTTATTTAAGAA-TATCAGAAAAGAACTT
* * **
1207906 CTAGTTGCTTTAAGATAGTCAATTTCTTAATATCGAA-AAATAAATAAATA
64 CTAGGTGCTTTAAGACAACCAATTTCTTAATAT-GAATAAATAAATAAATA
1207956 TTTTTATTTA
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
130 2 0.02
131 91 0.95
132 3 0.03
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (131 bp):
AAATTAATATATAATTTATAAAAATAAAATATTTATTTATTTAAGAATATCAGAAAAGAACTTCT
AGGTGCTTTAAGACAACCAATTTCTTAATATGAATAAATAAATAAATAAAAAACATTTTCCTAAT
A
Found at i:1209442 original size:14 final size:12
Alignment explanation
Indices: 1209429--1209491 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
1209419 TATTTGTAAT
1209429 TATTTATTAATAA
1 TATTTA-TAATAA
*
1209442 TA-ATATAATAA
1 TATTTATAATAA
1209453 TATTTATAATAA
1 TATTTATAATAA
* *
1209465 TAAATAATAATAA
1 T-ATTTATAATAA
* *
1209478 TAATAATAATAA
1 TATTTATAATAA
1209490 TA
1 TA
1209492 ATAATGTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
11 8 0.18
12 24 0.55
13 12 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TATTTATAATAA
Found at i:1209444 original size:3 final size:3
Alignment explanation
Indices: 1209436--1209541 Score: 121
Period size: 3 Copynumber: 36.0 Consensus size: 3
1209426 AATTATTTAT
* *
1209436 TAA TAA TAA T-A TAA TAA TAT TTA TAA TAA TAAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
*
1209481 TAA TAA TAA TAA TAA TGTA TAA TAA TAA TAA TAA -AA -AA TAA -AA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1209524 AAA TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
1209542 AAGCAAACTG
Statistics
Matches: 89, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
2 8 0.09
3 76 0.85
4 5 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1209478 original size:28 final size:28
Alignment explanation
Indices: 1209429--1209513 Score: 97
Period size: 28 Copynumber: 3.1 Consensus size: 28
1209419 TATTTGTAAT
1209429 TATTTAT--TAAT-AATAAT-ATAATAA
1 TATTTATAATAATAAATAATAATAATAA
1209453 TATTTATAATAATAAATAATAATAATAA
1 TATTTATAATAATAAATAATAATAATAA
* *
1209481 TAATAATAATAATAATGTATAATAATAATAA
1 TATTTATAATAATAA---ATAATAATAATAA
1209512 TA
1 TA
1209514 AAAAATAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
24 7 0.13
26 4 0.08
27 6 0.12
28 20 0.38
31 15 0.29
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (28 bp):
TATTTATAATAATAAATAATAATAATAA
Found at i:1209824 original size:45 final size:45
Alignment explanation
Indices: 1209667--1210014 Score: 588
Period size: 45 Copynumber: 7.7 Consensus size: 45
1209657 GATGGAAATG
* *
1209667 TTGAAAACATCATGCAGTGAAGGACTTACAGATGACCCGAAGGTTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
*
1209713 TTAAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
* * *
1209759 TTGAAAATATCATGCTCTGAAGGGCTTACAGATGACCTGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1209804 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
1209849 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1209894 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
**
1209939 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACTTGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
1209984 TTGAAAACATCATGCATTGAAGGGCTTACAG
1 TTGAAAACATCATGCACTGAAGGGCTTACAG
1210015 TGTGGGAAAT
Statistics
Matches: 287, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
45 205 0.71
46 82 0.29
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.25
Consensus pattern (45 bp):
TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
Found at i:1210699 original size:22 final size:22
Alignment explanation
Indices: 1210672--1210723 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
1210662 AATAAAGCTT
1210672 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
1210694 TTATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1210716 TCATCTTT
1 TCATCTTT
1210724 AAAGAATGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1211293 original size:23 final size:23
Alignment explanation
Indices: 1211263--1211318 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
1211253 TTAGCATCTT
*
1211263 CTCCGCCGTCTCTGCTCCAACTG
1 CTCCGCCGTCTCTACTCCAACTG
*
1211286 CTCCGCCGCCTCTACTCCAACTG
1 CTCCGCCGTCTCTACTCCAACTG
1211309 CTCCGCCGTC
1 CTCCGCCGTC
1211319 ATGTTCCCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.09, C:0.52, G:0.16, T:0.23
Consensus pattern (23 bp):
CTCCGCCGTCTCTACTCCAACTG
Found at i:1213569 original size:53 final size:53
Alignment explanation
Indices: 1213500--1213609 Score: 177
Period size: 53 Copynumber: 2.1 Consensus size: 53
1213490 TGGCACGCCT
*
1213500 AGATGTTCGTAAAGCTTTTGAAAAGA-ATTCATAATTTCCTCTGTTTTCTGCAC
1 AGATGTTCATAAAGCTTTTGAAAA-ACATTCATAATTTCCTCTGTTTTCTGCAC
* *
1213553 AGATGTTCATAAAGCTTTTGAAAAACATTCATCATTTCCTGTGTTTTCTGCAC
1 AGATGTTCATAAAGCTTTTGAAAAACATTCATAATTTCCTCTGTTTTCTGCAC
1213606 AGAT
1 AGAT
1213610 TTCTGGTCAG
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
52 1 0.02
53 52 0.98
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (53 bp):
AGATGTTCATAAAGCTTTTGAAAAACATTCATAATTTCCTCTGTTTTCTGCAC
Found at i:1214598 original size:70 final size:72
Alignment explanation
Indices: 1214485--1214730 Score: 230
Period size: 75 Copynumber: 3.4 Consensus size: 72
1214475 CATAATGATG
* * * * * *
1214485 TGGGCCTTCAGTATGCCCCAACATTTACTGATATGAACGTTCAAAAT-G-TTATTCCAATTTCTG
1 TGGGCTTTCAGCATGCCCCAACATTTGCTAATAAGAACGTTCAAAATCGCATATTCCAATTTCTG
1214548 ATTAAAA
66 ATTAAAA
*
1214555 TGGGCTTTCAGCATGCCCCATCATTTGCTAATACAG-ACGTTCAAAATGCGCCAATATTCCAATT
1 TGGGCTTTCAGCATGCCCCAACATTTGCTAATA-AGAACGTTCAAAAT-CG-C-ATATTCCAATT
*
1214619 TCTGATTGAAA
62 TCTGATTAAAA
* * *** * * *
1214630 TGGGCTTTCAGCATGCCCCAACATTTGTTGACGTGAACATTCAAAATGCATCAATATTCCTGA-T
1 TGGGCTTTCAGCATGCCCCAACATTTGCTAATAAGAACGTTCAAAAT-C-GC-ATATTCC-AATT
* *
1214694 TATGATTGAAA
62 TCTGATTAAAA
1214705 TGGGCTTTCAGCATGCCCCAACATTT
1 TGGGCTTTCAGCATGCCCCAACATTT
1214731 ACTTCTTGTT
Statistics
Matches: 149, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
70 39 0.26
71 1 0.01
72 1 0.01
74 1 0.01
75 106 0.71
76 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.32
Consensus pattern (72 bp):
TGGGCTTTCAGCATGCCCCAACATTTGCTAATAAGAACGTTCAAAATCGCATATTCCAATTTCTG
ATTAAAA
Found at i:1214635 original size:75 final size:75
Alignment explanation
Indices: 1214534--1214730 Score: 258
Period size: 75 Copynumber: 2.6 Consensus size: 75
1214524 TTCAAAATGT
* * *
1214534 TATTCCAATTTCTGATTAAAATGGGCTTTCAGCATGCCCCATCATTTGCTAAT-AC-AG-ACGTT
1 TATTCCAATTTCTGATTGAAATGGGCTTTCAGCATGCCCCAACATTTG-T--TGACGAGAACATT
*
1214596 CAAAATGCGCCAA
63 CAAAATGCACCAA
*
1214609 TATTCCAATTTCTGATTGAAATGGGCTTTCAGCATGCCCCAACATTTGTTGACGTGAACATTCAA
1 TATTCCAATTTCTGATTGAAATGGGCTTTCAGCATGCCCCAACATTTGTTGACGAGAACATTCAA
*
1214674 AATGCATCAA
66 AATGCACCAA
* *
1214684 TATTCCTGA-TTATGATTGAAATGGGCTTTCAGCATGCCCCAACATTT
1 TATTCC-AATTTCTGATTGAAATGGGCTTTCAGCATGCCCCAACATTT
1214731 ACTTCTTGTT
Statistics
Matches: 110, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
72 1 0.01
73 2 0.02
74 2 0.02
75 104 0.95
76 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.32
Consensus pattern (75 bp):
TATTCCAATTTCTGATTGAAATGGGCTTTCAGCATGCCCCAACATTTGTTGACGAGAACATTCAA
AATGCACCAA
Found at i:1214885 original size:17 final size:17
Alignment explanation
Indices: 1214863--1214896 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1214853 TTGGTTCACT
1214863 CTCAACGTCTGTTTAAC
1 CTCAACGTCTGTTTAAC
1214880 CTCAACGTCTGTTTAAC
1 CTCAACGTCTGTTTAAC
1214897 TTGAATATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (17 bp):
CTCAACGTCTGTTTAAC
Found at i:1221943 original size:2 final size:2
Alignment explanation
Indices: 1221936--1221972 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1221926 ATAAAGAAGA
1221936 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1221973 ATAGTATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1222813 original size:131 final size:131
Alignment explanation
Indices: 1222670--1222913 Score: 355
Period size: 131 Copynumber: 1.9 Consensus size: 131
1222660 TAATTAAAAT
** * *
1222670 AAATTAATATATAATTTATAAAAATAGGATATTTATTTATTTAAGAATATCAGAAAAAAACTTCT
1 AAATTAATATATAATTTATAAAAATAAAATATTTATTTATATAAAAATATCAGAAAAAAACTTCT
* * *
1222735 AGATGCTTTAAGACAACCCATTTCTTAATAT-TAATAAATGAATAAATAAAAAACATTTTCCTAA
66 AGATGCTTTAAGACAACCAATTTCTTAATATCGAA-AAATAAATAAATAAAAAACATTTTCCTAA
1222799 TA
130 TA
* * **
1222801 AAATTAATATATATTTTATAAAAGTAAAATATTTATTTATATAAAAATATCAGAAAAGGACTTCT
1 AAATTAATATATAATTTATAAAAATAAAATATTTATTTATATAAAAATATCAGAAAAAAACTTCT
* *
1222866 AGTTGCTTTAAGACAATCAATTTCTTAATATCGAAAAATAAATAAATA
66 AGATGCTTTAAGACAACCAATTTCTTAATATCGAAAAATAAATAAATA
1222914 TTTTTATTTA
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
131 97 0.98
132 2 0.02
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (131 bp):
AAATTAATATATAATTTATAAAAATAAAATATTTATTTATATAAAAATATCAGAAAAAAACTTCT
AGATGCTTTAAGACAACCAATTTCTTAATATCGAAAAATAAATAAATAAAAAACATTTTCCTAAT
A
Found at i:1224143 original size:22 final size:22
Alignment explanation
Indices: 1224118--1224174 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
1224108 ATATACAAGC
1224118 TACAAAGTGAACCTACAGATGA
1 TACAAAGTGAACCTACAGATGA
*
1224140 TACAAAGTGAACCTACAGATGG
1 TACAAAGTGAACCTACAGATGA
*
1224162 GACAAAGTGAACC
1 TACAAAGTGAACC
1224175 CACAAAGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (22 bp):
TACAAAGTGAACCTACAGATGA
Found at i:1226040 original size:106 final size:106
Alignment explanation
Indices: 1225767--1226461 Score: 1219
Period size: 106 Copynumber: 6.5 Consensus size: 106
1225757 TGAATGAAAT
*
1225767 TTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
1 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
* * *
1225832 TTCGCTGTGAAGTTGAAATTGACTCTGGAATTGGGAAGTTG
66 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
* *
1225873 TTTTTTTTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATA
1 ---TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1225938 TCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
63 TCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
1225982 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
1 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
1226047 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
66 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
* *
1226088 TTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCC
1 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
*
1226153 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTG
66 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
*
1226194 TTTGTTGACAACCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
1 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
1226259 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
66 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
* *
1226300 TTTGTTGACAACCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCC
1 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
* *
1226365 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTG
66 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
* *
1226406 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCGAGT
1 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1226462 GGCACGATAT
Statistics
Matches: 563, Mismatches: 23, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
106 463 0.82
109 100 0.18
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
Found at i:1227006 original size:17 final size:19
Alignment explanation
Indices: 1226973--1227008 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
1226963 TGTTGAATCC
1226973 CCAAATAATGCCCCAATAT
1 CCAAATAATGCCCCAATAT
1226992 CCAAA-AATG-CCCAATAT
1 CCAAATAATGCCCCAATAT
1227009 TTGATATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 4 0.24
19 5 0.29
ACGTcount: A:0.44, C:0.31, G:0.06, T:0.19
Consensus pattern (19 bp):
CCAAATAATGCCCCAATAT
Found at i:1228130 original size:8 final size:7
Alignment explanation
Indices: 1228118--1228186 Score: 59
Period size: 8 Copynumber: 9.1 Consensus size: 7
1228108 TGATTTTTGC
1228118 TCTTTTT
1 TCTTTTT
1228125 TCCTTTTGT
1 T-CTTTT-T
*
1228134 TCTTGTT
1 TCTTTTT
1228141 TCTCTTTT
1 TCT-TTTT
1228149 TCTTTGTT
1 TCTTT-TT
1228157 T-TTTTT
1 TCTTTTT
*
1228163 GCTTTTT
1 TCTTTTT
1228170 TGCTTCTTT
1 T-CTT-TTT
1228179 TCTTTTT
1 TCTTTTT
1228186 T
1 T
1228187 GTTCTTGATT
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
6 2 0.04
7 19 0.37
8 24 0.47
9 6 0.12
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (7 bp):
TCTTTTT
Found at i:1228131 original size:16 final size:17
Alignment explanation
Indices: 1228112--1228165 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
1228102 ACTTTTTGAT
*
1228112 TTTTGCTCTTTTTTC-C
1 TTTTGCTCTTGTTTCTC
*
1228128 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
*
1228145 TTTTTCT-TTGTTT-T-
1 TTTTGCTCTTGTTTCTC
1228159 TTTTGCT
1 TTTTGCT
1228166 TTTTTGCTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 6 0.19
15 1 0.03
16 19 0.59
17 6 0.19
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:1228185 original size:16 final size:16
Alignment explanation
Indices: 1228159--1228192 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1228149 TCTTTGTTTT
1228159 TTTTGCTTTTTTGCTTC
1 TTTTGCTTTTTTG-TTC
1228176 TTTT-CTTTTTTGTTC
1 TTTTGCTTTTTTGTTC
1228191 TT
1 TT
1228193 GATTGGATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.76
Consensus pattern (16 bp):
TTTTGCTTTTTTGTTC
Found at i:1230081 original size:5 final size:5
Alignment explanation
Indices: 1230071--1230099 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1230061 GCAAGTGATG
1230071 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1230100 GAAAGATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:1231380 original size:22 final size:22
Alignment explanation
Indices: 1231355--1231411 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
1231345 ATATACAAGC
1231355 TACAAAGTGAACCTACAGATGA
1 TACAAAGTGAACCTACAGATGA
*
1231377 TACAAAGTGAACCTACAGATGG
1 TACAAAGTGAACCTACAGATGA
*
1231399 GACAAAGTGAACC
1 TACAAAGTGAACC
1231412 CACAAAGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (22 bp):
TACAAAGTGAACCTACAGATGA
Found at i:1233514 original size:3 final size:3
Alignment explanation
Indices: 1233506--1233584 Score: 90
Period size: 3 Copynumber: 26.0 Consensus size: 3
1233496 AATTATTTAT
** *
1233506 TAA TAA TAA T-A TAA TAA TTT TTA TAA TAA TAA TAA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
1233551 TAA TAA TAA TAAA TAA TAA TAA -ATA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TA-A TAA TAA TAA
1233585 AAGCAAACTG
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
2 3 0.04
3 57 0.85
4 7 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1233547 original size:32 final size:28
Alignment explanation
Indices: 1233506--1233582 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 28
1233496 AATTATTTAT
*
1233506 TAATAATAATATAATAATTTTTATAAT-AA
1 TAATAATAATATAATAA--TTAATAATAAA
1233535 TAATAATAATAATAAATAA-TAATAATAAA
1 TAATAATAAT-AT-AATAATTAATAATAAA
1233564 TAATAATAAATATAATAAT
1 TAATAAT-AATATAATAAT
1233583 AAAAGCAAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
28 11 0.26
29 21 0.50
30 5 0.12
31 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
TAATAATAATATAATAATTAATAATAAA
Found at i:1233567 original size:35 final size:34
Alignment explanation
Indices: 1233506--1233585 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 34
1233496 AATTATTTAT
* **
1233506 TAATAATAATATAATAATTTTTATAATAAT-AATAA
1 TAATAATAA-ATAATAATATAAATAATAATAAAT-A
1233541 TAATAATAAATAATAATAATAAATAATAATAAATA
1 TAATAATAAATAATAAT-ATAAATAATAATAAATA
1233576 TAATAATAAA
1 TAATAATAAA
1233586 AGCAAACTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
34 8 0.20
35 29 0.73
36 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (34 bp):
TAATAATAAATAATAATATAAATAATAATAAATA
Found at i:1236650 original size:39 final size:40
Alignment explanation
Indices: 1236601--1236694 Score: 113
Period size: 39 Copynumber: 2.4 Consensus size: 40
1236591 ATAGTAATGA
1236601 AAATAA-ATAAGATAAAAAAAATTAAAAA-CAAATGAA-AT
1 AAATAAGATAAGATAAAAAAAA-TAAAAATCAAATGAAGAT
** *
1236639 AAATAAGATAAGATAAAGGAAATAAAAATTAAATGAAGAT
1 AAATAAGATAAGATAAAAAAAATAAAAATCAAATGAAGAT
* *
1236679 AAATAGGATAATATAA
1 AAATAAGATAAGATAA
1236695 TAAAGGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 12 0.25
39 20 0.42
40 16 0.33
ACGTcount: A:0.68, C:0.01, G:0.11, T:0.20
Consensus pattern (40 bp):
AAATAAGATAAGATAAAAAAAATAAAAATCAAATGAAGAT
Found at i:1236781 original size:41 final size:38
Alignment explanation
Indices: 1236696--1236809 Score: 99
Period size: 41 Copynumber: 2.9 Consensus size: 38
1236686 ATAATATAAT
* *
1236696 AAAGGAAAAAATAATAAAAAAT-ATAAAGAAA-AAGAAA
1 AAAGGAAAAAATAA-AAAATATAATAAAGAAATAAAAAA
* *
1236733 AAGGGAAAAAATAAAAAATATAATAAATAAATAAAAACTA
1 AAAGGAAAAAATAAAAAATATAATAAAGAAATAAAAA--A
* *
1236773 GAAAGGAAAAACA-AATAAATACAATAAAGATAATAAA
1 -AAAGGAAAAA-ATAAAAAATATAATAAAGA-AATAAA
1236810 TAAATAAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
36 6 0.10
37 21 0.34
38 4 0.06
40 1 0.02
41 23 0.37
42 7 0.11
ACGTcount: A:0.74, C:0.03, G:0.10, T:0.14
Consensus pattern (38 bp):
AAAGGAAAAAATAAAAAATATAATAAAGAAATAAAAAA
Found at i:1236862 original size:3 final size:3
Alignment explanation
Indices: 1236856--1236909 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
1236846 ATATATACGT
* * * * *
1236856 TAA TAA TAA TAA TAA AAA CAA TGA TAA TAA TAA TAA TAG TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1236904 AAA TAA
1 TAA TAA
1236910 AAAATATATA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:1236869 original size:21 final size:20
Alignment explanation
Indices: 1236835--1236909 Score: 55
Period size: 21 Copynumber: 3.8 Consensus size: 20
1236825 TATATAATGA
*
1236835 TAATAAAAAAAATATATACGT
1 TAATAATAAAAATA-ATACGT
* * **
1236856 TAATAATAATAATAAAAACAA
1 TAATAATAAAAAT-AATACGT
* *
1236877 TGATAATAATAATAATA-GT
1 TAATAATAAAAATAATACGT
1236896 T-ATAATAAAAATAA
1 TAATAATAAAAATAA
1236910 AAAATATATA
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
18 12 0.28
19 1 0.02
20 3 0.07
21 26 0.60
22 1 0.02
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (20 bp):
TAATAATAAAAATAATACGT
Found at i:1236917 original size:18 final size:18
Alignment explanation
Indices: 1236858--1236923 Score: 51
Period size: 18 Copynumber: 3.4 Consensus size: 18
1236848 ATATACGTTA
*
1236858 ATAATAATAATAAAAACAAT
1 ATAATAAAAAT-AAAA-AAT
* * **
1236878 GATAATAATAATAATAGTT
1 -ATAATAAAAATAAAAAAT
1236897 ATAATAAAAATAAAAAAT
1 ATAATAAAAATAAAAAAT
1236915 ATATATAAA
1 ATA-ATAAA
1236924 TACGTATAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 17 0.46
19 6 0.16
20 3 0.08
21 11 0.30
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.29
Consensus pattern (18 bp):
ATAATAAAAATAAAAAAT
Found at i:1236961 original size:5 final size:5
Alignment explanation
Indices: 1236951--1237084 Score: 68
Period size: 5 Copynumber: 27.2 Consensus size: 5
1236941 GTAAAAAAAG
* * * * *
1236951 AAATA AAATA ATAATA AAAT- AAA-C AAATA AAA-A TAATA AAA-G GATTA
1 AAATA AAATA A-AATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
* * * **
1236998 AAATA AAATA AAAT- AAATA AATATA TATATA ATATT GTATA AAAT- AAA-A
1 AAATA AAATA AAATA AAATA AA-ATA -AAATA AAATA AAATA AAATA AAATA
1237047 AAATAA GAAATA AAATAA AAATA AAATA AAA-A AAATA A
1 AAAT-A -AAATA AAAT-A AAATA AAATA AAATA AAATA A
1237085 GAAAGATAAA
Statistics
Matches: 100, Mismatches: 15, Indels: 28
0.70 0.10 0.20
Matches are distributed among these distances:
4 24 0.24
5 53 0.53
6 18 0.18
7 5 0.05
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (5 bp):
AAATA
Found at i:1237041 original size:41 final size:40
Alignment explanation
Indices: 1236953--1237070 Score: 112
Period size: 41 Copynumber: 2.8 Consensus size: 40
1236943 AAAAAAAGAA
*
1236953 ATAAAATAATAATAAAATAAACAAATAAAAATAATAAAAGG
1 ATAAAATAA-AATAAAATAAATAAATAAAAATAATAAAAGG
* ** *
1236994 ATTAAAATAAAATAAAATAAATAAATATATATATAAT-ATTGT
1 A-TAAAATAAAATAAAATAAATAAATA-A-AAATAATAAAAGG
* *
1237036 ATAAAATAAAAAAATAAGAAATAAAATAAAAATAA
1 ATAAAATAAAATAA-AATAAAT-AAATAAAAATAA
1237071 AATAAAAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
41 34 0.53
42 19 0.30
43 11 0.17
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (40 bp):
ATAAAATAAAATAAAATAAATAAATAAAAATAATAAAAGG
Found at i:1237998 original size:17 final size:16
Alignment explanation
Indices: 1237976--1238015 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
1237966 ATTTATAATG
*
1237976 TAAATATATAATATATA
1 TAAATATAGAAT-TATA
1237993 TAAATATAGAATTATA
1 TAAATATAGAATTATA
1238009 -AAATATA
1 TAAATATA
1238016 ATTTGTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.32
16 4 0.18
17 11 0.50
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
TAAATATAGAATTATA
Found at i:1238740 original size:84 final size:84
Alignment explanation
Indices: 1238602--1239537 Score: 1223
Period size: 84 Copynumber: 11.2 Consensus size: 84
1238592 TGACAGATAG
* * *
1238602 CCCTTCTTGCTTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAG
1 CCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
*
1238667 GTCTTTGGTTGGCAGATAA
66 GTCTTTGGTTGGCAAATAA
* * * *
1238686 CCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCATTGGAGCTGAGCGTAGTCGAACTCAAAG
1 CCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
*
1238751 GTCTTTTGG-TGGAAAATAA
66 GTC-TTTGGTTGGCAAATAA
* * *
1238770 CCCTTCTATCCTTGAGCTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
*
1238835 GTCTTTGGTTGGCATATAA
66 GTCTTTGGTTGGCAAATAA
* *
1238854 CCTTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
*
1238919 GTCTTTTGG-TGGCAGATAA
66 GTC-TTTGGTTGGCAAATAA
* * * ** *
1238938 CCCTTCTAGCCTTAAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTTAAACTCAAAG
1 CCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
*
1239003 GTCTTCGGTTGGCAAATAA
66 GTCTTTGGTTGGCAAATAA
* *
1239022 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
** *
1239087 GTCTTTTATTGGAAAATAA
66 GTCTTTGGTTGGCAAATAA
* * * * *
1239106 CCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCAAAG
1 CCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
*
1239171 GTCTTTTGTTGG-AAGATAA
66 GTCTTTGGTTGGCAA-ATAA
* * * * * ***
1239190 CCCTTCTAACCTTGAGTTATGCTGCAAATGATATGCCTTTGAGCTGATCGTAGTCAAACGAAAAG
1 CCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
**
1239255 GTCTTTTATTGGCAAATAA
66 GTCTTTGGTTGGCAAATAA
* * * * * * * *
1239274 CCCTTCTTGCCTTTAGCTATGTTGGAAATGATGTGCCTTGGAGTTGAGCATAGTCGAACTCAAAG
1 CCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* *
1239339 GTCTTTGGTTAGCAGATAA
66 GTCTTTGGTTGGCAAATAA
* * * *
1239358 CCTTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGAACTTGAAG
1 CCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
**
1239423 GTCTTTTATTGGCAAATAA
66 GTCTTTGGTTGGCAAATAA
* * *
1239442 CCCTTCTTGCCTTGAGCTATGTTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAG
1 CCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* *
1239507 GTCTTT-GCTGACAAATAA
66 GTCTTTGGTTGGCAAATAA
*
1239525 CCCTTCTCGCCTT
1 CCCTTCTAGCCTT
1239538 AAGTTAAGCT
Statistics
Matches: 741, Mismatches: 105, Indels: 13
0.86 0.12 0.02
Matches are distributed among these distances:
83 32 0.04
84 697 0.94
85 12 0.02
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (84 bp):
CCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
GTCTTTGGTTGGCAAATAA
Found at i:1238881 original size:168 final size:168
Alignment explanation
Indices: 1238586--1239549 Score: 1392
Period size: 168 Copynumber: 5.7 Consensus size: 168
1238576 AACTCGACAA
* * * * * *
1238586 TTTTATTGACAGATAGCCCTTCTTGCTTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGC
1 TTTTATTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
* *
1238651 ATAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATG
66 ATAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
* *
1238716 ATATGCATTGGAGCTGAGCGTAGTCGAACTCAAAGGTC
131 ATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
** * * *
1238754 TTTTGGTGGAAAATAACCCTTCTAT-CCTTGAGCTATGCTGCAAATGATGTGCCTTGAAGCTGAG
1 TTTTATTGGCAAATAACCCTTCT-TGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAG
* * * *
1238818 CGTAGTCGAACTCGAAGGTCTTTGGTTGGCATATAACCTTTCTAGCCTTGAGTTATGCTGCAAAT
65 CATAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
1238883 GATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
130 GATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
** * * *
1238922 TTTTGGTGGCAGATAACCCTTCTAGCCTTAAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTATTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
* ** * *
1238987 GTAGTTAAACTCAAAGGTCTTCGGTTGGCAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
66 ATAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
*
1239052 ATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
131 ATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
*
1239090 TTTTATTGGAAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTATTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
* * * * *
1239155 GTAGTCAAACTCAAAGGTCTTTTGTTGGAAGATAACCCTTCTAACCTTGAGTTATGCTGCAAATG
66 ATAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
* * * ***
1239220 ATATGCCTTTGAGCTGATCGTAGTCAAACGAAAAGGTC
131 ATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
* * *
1239258 TTTTATTGGCAAATAACCCTTCTTGCCTTTAGCTATGTTGGAAATGATGTGCCTTGGAGTTGAGC
1 TTTTATTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
* *
1239323 ATAGTCGAACTCAAAGGTCTTTGGTTAGCAGATAACCTTTCTAGCCTTGAGTTATGCTGCAAATG
66 ATAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
* *
1239388 ATATGCCTTTGAGCTGAGCGTAGTCGAACTTGAAGGTC
131 ATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
*
1239426 TTTTATTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATATGCCTTGGAGCTGAGC
1 TTTTATTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
* * * * * * *
1239491 ATAGTCGAACTCGAAGGTCTTT-GCTGACAAATAACCCTTCTCGCCTTAAGTTAAGCTGC
66 ATAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGC
1239550 CGATAGTTTC
Statistics
Matches: 718, Mismatches: 76, Indels: 5
0.90 0.10 0.01
Matches are distributed among these distances:
167 29 0.04
168 688 0.96
169 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (168 bp):
TTTTATTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
ATAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
ATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
Found at i:1240879 original size:95 final size:96
Alignment explanation
Indices: 1240676--1240879 Score: 252
Period size: 98 Copynumber: 2.1 Consensus size: 96
1240666 GGCTTGCTGA
** * * * * *
1240676 ATCCATAAAGTTGGGGCGTTTAACCAATTGCTTTAGAGGGACAGCTCAATATCATTGTATAGATA
1 ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGCACAACTCAAGATCATTG-ATA-ATA
* *
1240741 TTATAATCACCTCTATCAGGCTAGCTTAATATT
64 TTATAATCACCTCTATCAGACTAGCTGAATATT
*
1240774 ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGCACAACTCAAGCTCCATTG-T-ATAT
1 ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGCACAACTCAAGAT-CATTGATAATAT
*
1240837 TATAATCACCT-TGATCAGACTAGCTGAATCTT
65 TATAATCACCTCT-ATCAGACTAGCTGAATATT
1240869 ATCCATAAAGC
1 ATCCATAAAGC
1240880 TGGGGTGATG
Statistics
Matches: 93, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
94 1 0.01
95 42 0.45
97 1 0.01
98 44 0.47
99 5 0.05
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (96 bp):
ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGCACAACTCAAGATCATTGATAATATT
ATAATCACCTCTATCAGACTAGCTGAATATT
Found at i:1245080 original size:11 final size:11
Alignment explanation
Indices: 1245064--1245088 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1245054 TTTATTTCAA
1245064 TTCACTTGCAC
1 TTCACTTGCAC
1245075 TTCACTTGCAC
1 TTCACTTGCAC
1245086 TTC
1 TTC
1245089 TTTTTGGTAT
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:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:1249816 original size:63 final size:63
Alignment explanation
Indices: 1249696--1249840 Score: 159
Period size: 63 Copynumber: 2.3 Consensus size: 63
1249686 CGATGCACAG
* * ** * *
1249696 GGAGTGCTTCGATGCACCCATTAAAATGGAAACATCGAATGCGATTGGTGCATCGATGTATAA
1 GGAGTGCATCGATGCACCCACTAAAATACAAACATCGAATGCGATTGATGCACCGATGTATAA
* * *
1249759 GGAGTGCATCGATGCATCCC-CTAAAATACAAACATCGAATGGGATTTATGCACCGATGCAT-A
1 GGAGTGCATCGATGCA-CCCACTAAAATACAAACATCGAATGCGATTGATGCACCGATGTATAA
* *
1249821 GATAGTTCATCGATGCACCC
1 G-GAGTGCATCGATGCACCC
1249841 GTCTAGGGAT
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
62 5 0.07
63 61 0.88
64 3 0.04
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (63 bp):
GGAGTGCATCGATGCACCCACTAAAATACAAACATCGAATGCGATTGATGCACCGATGTATAA
Found at i:1250618 original size:32 final size:31
Alignment explanation
Indices: 1250577--1250684 Score: 121
Period size: 31 Copynumber: 3.5 Consensus size: 31
1250567 GAGTCGAGGG
*
1250577 TTTACCTATGTTCTACGGAACATATAGACAA
1 TTTACCTATGTTCTACGGAACATATGGACAA
*
1250608 TTTTACCTATG-TCTTTC-GAGACATATGGACAA
1 -TTTACCTATGTTC-TACGGA-ACATATGGACAA
* * *
1250640 TATACCTATGTTCTAAGGAACATATGGATAA
1 TTTACCTATGTTCTACGGAACATATGGACAA
*
1250671 TTTACCTAGGTTCT
1 TTTACCTATGTTCT
1250685 TTGGGACCTA
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
31 37 0.58
32 27 0.42
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (31 bp):
TTTACCTATGTTCTACGGAACATATGGACAA
Found at i:1250686 original size:63 final size:62
Alignment explanation
Indices: 1250579--1250700 Score: 165
Period size: 63 Copynumber: 2.0 Consensus size: 62
1250569 GTCGAGGGTT
* *
1250579 TACCTATGTTCTACGGAACATATAGACAATTTTACCTATGTCTTTCGAGACATATGGACAATA
1 TACCTATGTTCTAAGGAACATATAGACAATTTTACCTAGGTCTTT-GAGACATATGGACAATA
* * * *
1250642 TACCTATGTTCTAAGGAACATATGGATAA-TTTACCTAGGTTCTTTGGGACCTATGGACA
1 TACCTATGTTCTAAGGAACATATAGACAATTTTACCTAGG-TCTTTGAGACATATGGACA
1250701 GTTGCCGAGG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
62 21 0.40
63 31 0.60
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (62 bp):
TACCTATGTTCTAAGGAACATATAGACAATTTTACCTAGGTCTTTGAGACATATGGACAATA
Found at i:1250697 original size:31 final size:31
Alignment explanation
Indices: 1250577--1250700 Score: 115
Period size: 31 Copynumber: 4.0 Consensus size: 31
1250567 GAGTCGAGGG
** * *
1250577 TTTACCTATGTTCTACGGAACATATAGACAA
1 TTTACCTATGTTCTTTGGGACATATGGACAA
*
1250608 TTTTACCTATG-TCTTTCGAGACATATGGACAA
1 -TTTACCTATGTTCTTT-GGGACATATGGACAA
* ** * *
1250640 TATACCTATGTTCTAAGGAACATATGGATAA
1 TTTACCTATGTTCTTTGGGACATATGGACAA
* *
1250671 TTTACCTAGGTTCTTTGGGACCTATGGACA
1 TTTACCTATGTTCTTTGGGACATATGGACA
1250701 GTTGCCGAGG
Statistics
Matches: 72, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
31 47 0.65
32 25 0.35
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (31 bp):
TTTACCTATGTTCTTTGGGACATATGGACAA
Found at i:1250714 original size:30 final size:30
Alignment explanation
Indices: 1250672--1250752 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
1250662 TATGGATAAT
* *
1250672 TTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTACCGAGGTTCTTTGTGACCTATGGACAG
* * * *
1250702 TTGCCGAGGTTCTTTATGACCTCTGGATAG
1 TTACCGAGGTTCTTTGTGACCTATGGACAG
*
1250732 TTACCG-GGGTCTTTGTGACCT
1 TTACCGAGGTTCTTTGTGACCT
1250753 CTGAATAGGT
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 13 0.31
30 29 0.69
ACGTcount: A:0.16, C:0.21, G:0.27, T:0.36
Consensus pattern (30 bp):
TTACCGAGGTTCTTTGTGACCTATGGACAG
Found at i:1253511 original size:63 final size:62
Alignment explanation
Indices: 1253430--1253586 Score: 183
Period size: 63 Copynumber: 2.5 Consensus size: 62
1253420 TTCAGTGTGT
* * * ** *
1253430 ATCGATGCATAGGGAGTGCATCGATGCACCCATTAAAATGGAAACATCAAATGGG-TTTGGTGC
1 ATCGATGCATAAGAAGTGCATCGATGCACCC-CTAAAATACAAACATCAAATGGGATTT-ATGC
*
1253493 ATCGATGCATAAGAAGTGCATCGATGCATCCCCTAAAATACAAACATCGAATGGGATTTATGC
1 ATCGATGCATAAGAAGTGCATCGATGCA-CCCCTAAAATACAAACATCAAATGGGATTTATGC
* *
1253556 ACCGATGTAT-AGATAGTGCATCGATGCACCC
1 ATCGATGCATAAGA-AGTGCATCGATGCACCC
1253587 GTCTAGGGAT
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
62 6 0.07
63 70 0.85
64 6 0.07
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (62 bp):
ATCGATGCATAAGAAGTGCATCGATGCACCCCTAAAATACAAACATCAAATGGGATTTATGC
Found at i:1254358 original size:31 final size:31
Alignment explanation
Indices: 1254320--1254446 Score: 132
Period size: 31 Copynumber: 4.1 Consensus size: 31
1254310 AGAGTCGAGG
*
1254320 GTTTACCTATGTTCTACGGAACATATTGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* *
1254351 GTTTACCTATGTGT-TTC-AAGACATATGGACA
1 GTTTACCTATGT-TCTACGGA-ACATATGGACA
* *
1254382 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* ** * *
1254413 GTTTACCTAGGTTCTTTGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
1254444 GTT
1 GTT
1254447 GACGAGGTTC
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
30 2 0.03
31 75 0.95
32 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:1254466 original size:30 final size:31
Alignment explanation
Indices: 1254405--1254488 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 31
1254395 CTAAGGAACA
* * *
1254405 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAGTTGACCGAGGTTCTTTAGGACC
*
1254436 TATGGACAGTTGA-CGAGGTTCTTTATGACC
1 TATGGACAGTTGACCGAGGTTCTTTAGGACC
* * *
1254466 TCTGGATAGTT-ACCG-GGGTCTTT
1 TATGGACAGTTGACCGAGGTTCTTT
1254489 GTGACCTCTG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
29 8 0.18
30 25 0.56
31 12 0.27
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (31 bp):
TATGGACAGTTGACCGAGGTTCTTTAGGACC
Found at i:1256527 original size:40 final size:41
Alignment explanation
Indices: 1256462--1256553 Score: 118
Period size: 40 Copynumber: 2.3 Consensus size: 41
1256452 AATAGTAATG
1256462 AAAATAA-ATAAGATAAAAAACAATAAAAAAACAAATGAA-A
1 AAAATAAGATAAGATAAAAAACAATAAAAAAA-AAATGAAGA
* *
1256502 AAAATAAGATAAGATAAAGAA-AATAAAAATAAAATGAAGA
1 AAAATAAGATAAGATAAAAAACAATAAAAAAAAAATGAAGA
* *
1256542 TAAATAGGATAA
1 AAAATAAGATAA
1256554 ATATAATAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
39 7 0.15
40 27 0.59
41 12 0.26
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (41 bp):
AAAATAAGATAAGATAAAAAACAATAAAAAAAAAATGAAGA
Found at i:1256553 original size:26 final size:25
Alignment explanation
Indices: 1256501--1256635 Score: 74
Period size: 25 Copynumber: 5.5 Consensus size: 25
1256491 AACAAATGAA
*
1256501 AAAAATAAGATAAGATAAAGAAAAT
1 AAAAATAAAATAAGATAAAGAAAAT
* **
1256526 AAAAATAAAATGAAGATAAATAGGAT
1 AAAAATAAAAT-AAGATAAAGAAAAT
* *
1256552 AAATATAATA-AAGA-AAA-AATAAT
1 AAAAATAAAATAAGATAAAGAA-AAT
1256575 AAAAA-AAATATAAAGA-AAA-AATAAT
1 AAAAATAAA-AT-AAGATAAAGAA-AAT
1256600 AAAAA-AAATATAAAGA-AAA-AATAAT
1 AAAAATAAA-AT-AAGATAAAGAA-AAT
1256625 AAAAA-AAAATA
1 AAAAATAAAATA
1256636 TAAAGAAAAA
Statistics
Matches: 95, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
22 3 0.03
23 11 0.12
24 6 0.06
25 56 0.59
26 19 0.20
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (25 bp):
AAAAATAAAATAAGATAAAGAAAAT
Found at i:1256573 original size:14 final size:14
Alignment explanation
Indices: 1256556--1256645 Score: 124
Period size: 13 Copynumber: 7.0 Consensus size: 14
1256546 TAGGATAAAT
1256556 ATAATAAAGAAAAA
1 ATAATAAAGAAAAA
1256570 ATAAT-AA-AAAAA
1 ATAATAAAGAAAAA
1256582 AT-ATAAAGAAAAA
1 ATAATAAAGAAAAA
1256595 ATAAT-AA-AAAAA
1 ATAATAAAGAAAAA
1256607 AT-ATAAAGAAAAA
1 ATAATAAAGAAAAA
1256620 ATAATAAA-AAAAA
1 ATAATAAAGAAAAA
1256633 AT-ATAAAGAAAAA
1 ATAATAAAGAAAAA
1256646 GAAACAAGGG
Statistics
Matches: 69, Mismatches: 0, Indels: 15
0.82 0.00 0.18
Matches are distributed among these distances:
11 4 0.06
12 23 0.33
13 30 0.43
14 12 0.17
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (14 bp):
ATAATAAAGAAAAA
Found at i:1256644 original size:11 final size:12
Alignment explanation
Indices: 1256565--1256645 Score: 87
Period size: 12 Copynumber: 6.5 Consensus size: 12
1256555 TATAATAAAG
1256565 AAAAAATAATAA
1 AAAAAATAATAA
1256577 AAAAAAT-ATAAA
1 AAAAAATAAT-AA
1256589 GAAAAAATAATAA
1 -AAAAAATAATAA
1256602 AAAAAAT-ATAAA
1 AAAAAATAAT-AA
1256614 GAAAAAATAATAA
1 -AAAAAATAATAA
1256627 AAAAAA-ATATAA
1 AAAAAATA-ATAA
1256639 AGAAAAA
1 A-AAAAA
1256646 GAAACAAGGG
Statistics
Matches: 61, Mismatches: 0, Indels: 15
0.80 0.00 0.20
Matches are distributed among these distances:
11 5 0.08
12 29 0.48
13 23 0.38
14 4 0.07
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (12 bp):
AAAAAATAATAA
Found at i:1256659 original size:26 final size:25
Alignment explanation
Indices: 1256559--1256645 Score: 165
Period size: 25 Copynumber: 3.4 Consensus size: 25
1256549 GATAAATATA
1256559 ATAAAGAAAAAATAATAAAAAAAAT
1 ATAAAGAAAAAATAATAAAAAAAAT
1256584 ATAAAGAAAAAATAATAAAAAAAAT
1 ATAAAGAAAAAATAATAAAAAAAAT
1256609 ATAAAGAAAAAATAATAAAAAAAAAT
1 ATAAAGAAAAAATAAT-AAAAAAAAT
1256635 ATAAAGAAAAA
1 ATAAAGAAAAA
1256646 GAAACAAGGG
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 41 0.67
26 20 0.33
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (25 bp):
ATAAAGAAAAAATAATAAAAAAAAT
Found at i:1256686 original size:26 final size:26
Alignment explanation
Indices: 1256657--1256821 Score: 66
Period size: 26 Copynumber: 6.4 Consensus size: 26
1256647 AAACAAGGGA
1256657 AAAATTAAAATATATAATAAATAAAT
1 AAAATTAAAATATATAATAAATAAAT
* * * *
1256683 AAAAACTAGAAAGGAAAAAAATAAATACAAT
1 -AAAATTA-AAA--TATATAATAAATA-AAT
1256714 AAAGATTAAAA-ATA-AATTAAATAAAT
1 AAA-ATTAAAATATATAA-TAAATAAAT
*
1256740 TAAA-T-AAAT-TA-AATAAA-AAA-
1 AAAATTAAAATATATAATAAATAAAT
*
1256760 AAGAATATATAAAT-GATAAT-AA-AAAT
1 AA-AAT-TA-AAATATATAATAAATAAAT
* *
1256786 AAAAATAAAATATATACATTAAT-AAT
1 AAAATTAAAATATATA-ATAAATAAAT
*
1256812 AAAAATAAAA
1 AAAATTAAAA
1256822 ATAATGATAA
Statistics
Matches: 109, Mismatches: 11, Indels: 37
0.69 0.07 0.24
Matches are distributed among these distances:
20 1 0.01
21 5 0.05
22 4 0.04
23 12 0.11
24 6 0.06
25 15 0.14
26 27 0.25
27 14 0.13
28 3 0.03
30 16 0.15
31 6 0.06
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (26 bp):
AAAATTAAAATATATAATAAATAAAT
Found at i:1256735 original size:9 final size:9
Alignment explanation
Indices: 1256723--1256756 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
1256713 TAAAGATTAA
1256723 AAATAAATT
1 AAATAAATT
1256732 AAATAAATT
1 AAATAAATT
1256741 AAATAAATT
1 AAATAAATT
1256750 AAATAAA
1 AAATAAA
1256757 AAAAAGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AAATAAATT
Found at i:1256785 original size:12 final size:12
Alignment explanation
Indices: 1256750--1256825 Score: 55
Period size: 12 Copynumber: 6.0 Consensus size: 12
1256740 TAAATAAATT
1256750 AAATAAAAA-AA
1 AAATAAAAATAA
*
1256761 AGAATATATAAATGA
1 A-AATA-A-AAATAA
*
1256776 TAATAAAAATAA
1 AAATAAAAATAA
1256788 AAATAAAATATATA
1 AAATAAAA-ATA-A
* * *
1256802 CATTAATAATAA
1 AAATAAAAATAA
1256814 AAATAAAAATAA
1 AAATAAAAATAA
1256826 TGATAATAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
11 1 0.02
12 26 0.53
13 8 0.16
14 13 0.27
15 1 0.02
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (12 bp):
AAATAAAAATAA
Found at i:1256811 original size:32 final size:32
Alignment explanation
Indices: 1256750--1256825 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
1256740 TAAATAAATT
* *
1256750 AAATAAAAAAAAGAATATATAAATGATAATAA
1 AAATAAAAATAAGAATATATAAATAATAATAA
*
1256782 AAATAAAAATAA-AATATATACATTAATAATAA
1 AAATAAAAATAAGAATATATA-AATAATAATAA
1256814 AAATAAAAATAA
1 AAATAAAAATAA
1256826 TGATAATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 8 0.20
32 32 0.80
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (32 bp):
AAATAAAAATAAGAATATATAAATAATAATAA
Found at i:1257037 original size:22 final size:21
Alignment explanation
Indices: 1256999--1257042 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
1256989 TAAATAAAAA
1256999 AAATTAAAAAGATAAAAGAATT
1 AAATTAAAAAGATAAAA-AATT
*
1257021 AAATTAAAAGGGA-AAAAAATT
1 AAATTAAAA-AGATAAAAAATT
1257042 A
1 A
1257043 GGGGATGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 13 0.65
23 2 0.10
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.20
Consensus pattern (21 bp):
AAATTAAAAAGATAAAAAATT
Found at i:1257423 original size:65 final size:63
Alignment explanation
Indices: 1257343--1257522 Score: 213
Period size: 65 Copynumber: 2.8 Consensus size: 63
1257333 GAATAAATTG
* * *
1257343 AACATTGAATACATTTCATGCATCAATGCACATACTATGCATCGATGCACTCAGAG-T-TTTATG
1 AACATCGAATGCATTTCATGCATCGATGCACAT-CTATGCATCGATGCACTCAG-GCTATTT-TG
1257406 AA
63 -A
* *
1257408 AACATCGAATGCATTTGATGCATCGATGCACCATCCATGCATCGATGCACTCAGGCTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCA-CATCTATGCATCGATGCACTCAGGCTATTTTGA
* *
1257472 AACATCGAATGCATTTTATGTATCGATGCA-ATCTTAGTGCATCGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCACATC-TA-TGCATCGATGCACT
1257523 AAGGGTCCAA
Statistics
Matches: 102, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
62 3 0.03
63 1 0.01
64 44 0.43
65 48 0.47
66 6 0.06
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACATCTATGCATCGATGCACTCAGGCTATTTTGA
Found at i:1263338 original size:21 final size:22
Alignment explanation
Indices: 1263309--1263367 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
1263299 TGCATCCCTT
1263309 TGAATGTGCATCGATACA-CCA
1 TGAATGTGCATCGATACAGCCA
* * * *
1263330 TGAAGGTGCACCGATGCATGCCT
1 TGAATGTGCATCGATACA-GCCA
1263353 TGAATGTGCATCGAT
1 TGAATGTGCATCGAT
1263368 GCACACTGCC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 15 0.50
23 15 0.50
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (22 bp):
TGAATGTGCATCGATACAGCCA
Found at i:1263361 original size:23 final size:22
Alignment explanation
Indices: 1263290--1263370 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 22
1263280 ACACTTAACA
1263290 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCAT-CC-TTGAAT
* * *
1263314 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATGCATCCTTGAAT
*
1263335 GTGCACCGATGCATGCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
1263358 GTGCATCGATGCA
1 GTGCATCGATGCA
1263371 CACTGCCCTG
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
21 15 0.32
22 2 0.04
23 18 0.38
24 12 0.26
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:1265649 original size:12 final size:12
Alignment explanation
Indices: 1265632--1265696 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
1265622 TAAAGGGGAG
1265632 AAGTGTTAGAGT
1 AAGTGTTAGAGT
1265644 AAGTGTTAGAGT
1 AAGTGTTAGAGT
** *
1265656 AAG-GGGAGTAAT
1 AAGTGTTAG-AGT
1265668 AGAAGTGTTAGAGT
1 --AAGTGTTAGAGT
*
1265682 AAGTATTAGAGT
1 AAGTGTTAGAGT
1265694 AAG
1 AAG
1265697 AGGGAGTAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 3 0.07
12 31 0.74
14 5 0.12
15 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (12 bp):
AAGTGTTAGAGT
Found at i:1265673 original size:38 final size:39
Alignment explanation
Indices: 1265630--1265705 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 39
1265620 GTTAAAGGGG
*
1265630 AGAAGTGTTAGAGTAAGTGTTAGAGTAAG-GGGAGTAAT
1 AGAAGTGTTAGAGTAAGTATTAGAGTAAGAGGGAGTAAT
1265668 AGAAGTGTTAGAGTAAGTATTAGAGTAAGAGGGAGTAA
1 AGAAGTGTTAGAGTAAGTATTAGAGTAAGAGGGAGTAA
1265706 GTTTTCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 28 0.78
39 8 0.22
ACGTcount: A:0.39, C:0.00, G:0.36, T:0.25
Consensus pattern (39 bp):
AGAAGTGTTAGAGTAAGTATTAGAGTAAGAGGGAGTAAT
Found at i:1266187 original size:64 final size:65
Alignment explanation
Indices: 1266079--1266203 Score: 193
Period size: 64 Copynumber: 1.9 Consensus size: 65
1266069 GAATGTATTT
1266079 CATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCAGC
1 CATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCAGC
* *
1266144 CATGCATCGATGCACTCAG-GCTATTT-TG-AAACATTGAATGCATTTTATGCATCGATGCAC
1 CATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCGAATGCATTTGATGCATCGATGCAC
1266204 TCTTAGTGCA
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
64 31 0.55
65 22 0.39
66 3 0.05
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (65 bp):
CATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCAGC
Found at i:1267776 original size:25 final size:26
Alignment explanation
Indices: 1267743--1267811 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 26
1267733 ACCATAATAA
*
1267743 ATATAATATGATTTATAATGTA-AA-T
1 ATATAATAT-ATTTATAATGCAGAATT
*
1267768 ATATAATATATATA-AATGCAGAATT
1 ATATAATATATTTATAATGCAGAATT
*
1267793 ATATAATATAATTTGTAAT
1 ATATAATAT-ATTTATAAT
1267812 ATTAGATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 5 0.14
24 6 0.17
25 19 0.53
26 3 0.08
27 3 0.08
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.42
Consensus pattern (26 bp):
ATATAATATATTTATAATGCAGAATT
Found at i:1270072 original size:27 final size:27
Alignment explanation
Indices: 1270034--1270095 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
1270024 GTTAAGAAAT
1270034 CGAGTCGAATATTTATCGAGTTTTGAC
1 CGAGTCGAATATTTATCGAGTTTTGAC
1270061 CGAGTCGAATATTTATCGAGTTTTGAC
1 CGAGTCGAATATTTATCGAGTTTTGAC
1270088 CGAGTCGA
1 CGAGTCGA
1270096 TCTCGAGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (27 bp):
CGAGTCGAATATTTATCGAGTTTTGAC
Found at i:1270706 original size:34 final size:34
Alignment explanation
Indices: 1270666--1270744 Score: 149
Period size: 34 Copynumber: 2.3 Consensus size: 34
1270656 CGGAAATATT
*
1270666 TTATATATATAATTAATATAAAATATATAAAATA
1 TTATATATATAATTAATATAAAAAATATAAAATA
1270700 TTATATATATAATTAATATAAAAAATATAAAATA
1 TTATATATATAATTAATATAAAAAATATAAAATA
1270734 TTATATATATA
1 TTATATATATA
1270745 TATATATATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (34 bp):
TTATATATATAATTAATATAAAAAATATAAAATA
Found at i:1270707 original size:36 final size:35
Alignment explanation
Indices: 1270659--1270746 Score: 142
Period size: 34 Copynumber: 2.5 Consensus size: 35
1270649 CCGAACCCGG
*
1270659 AAATATTTTATATATATAATTAATATAAAATATATA
1 AAATA-TTTATATATATAATTAATATAAAAAATATA
1270695 AAATA-TTATATATATAATTAATATAAAAAATATA
1 AAATATTTATATATATAATTAATATAAAAAATATA
1270729 AAATATTATATATATATA
1 AAATATT-TATATATATA
1270747 TATATATAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
34 33 0.67
35 1 0.02
36 15 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (35 bp):
AAATATTTATATATATAATTAATATAAAAAATATA
Found at i:1270818 original size:13 final size:13
Alignment explanation
Indices: 1270800--1270824 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1270790 AACCTGGCCC
1270800 GAAAAAAATCCCT
1 GAAAAAAATCCCT
1270813 GAAAAAAATCCC
1 GAAAAAAATCCC
1270825 GGATACTCGA
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:0.56, C:0.24, G:0.08, T:0.12
Consensus pattern (13 bp):
GAAAAAAATCCCT
Found at i:1271395 original size:19 final size:19
Alignment explanation
Indices: 1271363--1271401 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1271353 CTTTATTTTT
1271363 TTAATAAAAATAAAAATTA
1 TTAATAAAAATAAAAATTA
* *
1271382 TTAATTAAATTAAAAATTA
1 TTAATAAAAATAAAAATTA
1271401 T
1 T
1271402 CGAATTTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TTAATAAAAATAAAAATTA
Found at i:1271878 original size:24 final size:25
Alignment explanation
Indices: 1271841--1271891 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
1271831 CAATTGTTAA
* *
1271841 AATGATAAACGAACACAAATGAACG
1 AATGATAAAAGAACACAAACGAACG
*
1271866 AATG-TAAAAGAACATAAACGAACG
1 AATGATAAAAGAACACAAACGAACG
1271890 AA
1 AA
1271892 CATAAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.59, C:0.14, G:0.16, T:0.12
Consensus pattern (25 bp):
AATGATAAAAGAACACAAACGAACG
Found at i:1271897 original size:24 final size:24
Alignment explanation
Indices: 1271845--1271898 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1271835 TGTTAAAATG
* * *
1271845 ATAAACGAACACAAATGAACGAAT
1 ATAAAAGAACACAAACGAACGAAC
* *
1271869 GTAAAAGAACATAAACGAACGAAC
1 ATAAAAGAACACAAACGAACGAAC
1271893 ATAAAA
1 ATAAAA
1271899 TTAATTGAGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.61, C:0.15, G:0.13, T:0.11
Consensus pattern (24 bp):
ATAAAAGAACACAAACGAACGAAC
Found at i:1273256 original size:26 final size:27
Alignment explanation
Indices: 1273227--1273281 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
1273217 AGACATGAAA
1273227 TTAAACTACAAGAATGATCGAAT-GAG
1 TTAAACTACAAGAATGATCGAATGGAG
* ** *
1273253 TTAAAGTATGAGAGTGATCGAATGGAG
1 TTAAACTACAAGAATGATCGAATGGAG
1273280 TT
1 TT
1273282 GATTACTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.40, C:0.07, G:0.25, T:0.27
Consensus pattern (27 bp):
TTAAACTACAAGAATGATCGAATGGAG
Found at i:1277919 original size:14 final size:14
Alignment explanation
Indices: 1277902--1277960 Score: 77
Period size: 13 Copynumber: 4.4 Consensus size: 14
1277892 GTTTGATTCA
1277902 ACCCATTGACTTTG
1 ACCCATTGACTTTG
*
1277916 ACCCAGTGACTTTG
1 ACCCATTGACTTTG
*
1277930 A-CCGTTGACTTTG
1 ACCCATTGACTTTG
*
1277943 A-CCATTGACTTTA
1 ACCCATTGACTTTG
1277956 ACCCA
1 ACCCA
1277961 AAAAGTCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
13 22 0.56
14 17 0.44
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (14 bp):
ACCCATTGACTTTG
Found at i:1282599 original size:20 final size:22
Alignment explanation
Indices: 1282570--1282609 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
1282560 TACAATGATT
1282570 TAAAAAAAA-T-CTATTTTTAC
1 TAAAAAAAATTACTATTTTTAC
*
1282590 TAAAATAAATTACTATTTTT
1 TAAAAAAAATTACTATTTTT
1282610 TATACTATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 1 0.06
22 8 0.47
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAAAAAAATTACTATTTTTAC
Found at i:1283354 original size:24 final size:24
Alignment explanation
Indices: 1283321--1283403 Score: 78
Period size: 24 Copynumber: 3.3 Consensus size: 24
1283311 TAGACTGAAT
*
1283321 ATAAACGAATGAACATAAACAAAC
1 ATAAATGAATGAACATAAACAAAC
* *
1283345 ATAAATGAATGAATGA-AAATAATGTAC
1 ATAAATGAATGAA-CATAAACAA---AC
* *
1283372 ATAAATGAACGAACATAAACTAAC
1 ATAAATGAATGAACATAAACAAAC
1283396 ATAAATGA
1 ATAAATGA
1283404 GCAAATTATC
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
24 27 0.57
25 1 0.02
26 1 0.02
27 18 0.38
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.19
Consensus pattern (24 bp):
ATAAATGAATGAACATAAACAAAC
Found at i:1283389 original size:23 final size:24
Alignment explanation
Indices: 1283352--1283403 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
1283342 AACATAAATG
* **
1283352 AATGAATGAAAATAATGT-ACATA
1 AATGAACGAAAATAAACTAACATA
*
1283375 AATGAACGAACATAAACTAACATA
1 AATGAACGAAAATAAACTAACATA
1283399 AATGA
1 AATGA
1283404 GCAAATTATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.58, C:0.10, G:0.12, T:0.21
Consensus pattern (24 bp):
AATGAACGAAAATAAACTAACATA
Found at i:1286736 original size:13 final size:13
Alignment explanation
Indices: 1286692--1286738 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1286682 CTGTTCTTTG
*
1286692 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
1286706 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
1286718 TTTATTTAAAATAA
1 -ATATTTAAAATAA
1286732 ATATTTA
1 ATATTTA
1286739 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:1288165 original size:12 final size:12
Alignment explanation
Indices: 1288139--1288244 Score: 66
Period size: 12 Copynumber: 8.8 Consensus size: 12
1288129 AATAATATTT
*
1288139 ATATATATATTTA
1 ATATATATA-ATA
*
1288152 ATATATTTAAT-
1 ATATATATAATA
1288163 A-ATA-ATAATA
1 ATATATATAATA
1288173 ATGATA-ATAATA
1 AT-ATATATAATA
1288185 ATA-ATAATAATA
1 ATATAT-ATAATA
1288197 ATGATA-ATAATA
1 AT-ATATATAATA
1288209 ATAATAATATTAATA
1 AT-AT-ATA-TAATA
1288224 ATA-ATTATAATA
1 ATATA-TATAATA
1288236 ATA-ATATAA
1 ATATATATAA
1288245 ATTAATTAAT
Statistics
Matches: 78, Mismatches: 4, Indels: 24
0.74 0.04 0.23
Matches are distributed among these distances:
9 4 0.05
10 5 0.06
11 7 0.09
12 40 0.51
13 12 0.15
14 3 0.04
15 7 0.09
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (12 bp):
ATATATATAATA
Found at i:1288167 original size:3 final size:3
Alignment explanation
Indices: 1288159--1288241 Score: 130
Period size: 3 Copynumber: 27.7 Consensus size: 3
1288149 TTAATATATT
* *
1288159 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1288207 TAA TAA TAA TAT TAA TAA TAA TTA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1288242 TAAATTAATT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Done.