Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 59 of 182
Found at i:18105128 original size:27 final size:27
Alignment explanation
Indices: 18105085--18105177 Score: 94
Period size: 27 Copynumber: 3.7 Consensus size: 27
18105075 TACTATTATA
* *
18105085 AATATACT-TTTTTAATATATTGTTTT
1 AATATACTGTTATAAATATATTGTTTT
18105111 AATATACTGTTATAAATATATTGTTTT
1 AATATACTGTTATAAATATATTGTTTT
* *
18105138 AATATAATGTT-T---TA-A--CTTTT
1 AATATACTGTTATAAATATATTGTTTT
18105158 AATATACTGTTATAAATATA
1 AATATACTGTTATAAATATA
18105178 CATCTAATTT
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
20 14 0.25
21 1 0.02
22 1 0.02
23 2 0.04
24 2 0.04
25 1 0.02
26 9 0.16
27 26 0.46
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (27 bp):
AATATACTGTTATAAATATATTGTTTT
Found at i:18105148 original size:13 final size:13
Alignment explanation
Indices: 18105061--18105152 Score: 103
Period size: 13 Copynumber: 6.9 Consensus size: 13
18105051 GGTTTCAACA
18105061 ATACTGTTTTAAT
1 ATACTGTTTTAAT
* *
18105074 ATACTATTATAAAT
1 ATACTGTT-TTAAT
*
18105088 ATACTTTTTTAAT
1 ATACTGTTTTAAT
*
18105101 ATATTGTTTTAAT
1 ATACTGTTTTAAT
*
18105114 ATACTGTTATAAAT
1 ATACTGTT-TTAAT
*
18105128 ATATTGTTTTAAT
1 ATACTGTTTTAAT
*
18105141 ATAATGTTTTAA
1 ATACTGTTTTAA
18105153 CTTTTAATAT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
13 44 0.67
14 22 0.33
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.53
Consensus pattern (13 bp):
ATACTGTTTTAAT
Found at i:18105703 original size:44 final size:44
Alignment explanation
Indices: 18105640--18105729 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
18105630 ATTATTTCTC
18105640 ATAAGTGCTTTTGAGTTAAAAAACACTTTTGAGCAAAAGTTAAA
1 ATAAGTGCTTTTGAGTTAAAAAACACTTTTGAGCAAAAGTTAAA
* *
18105684 ATAAGTGCTTTTGAGTTAAAAAATACTTTTGAGTAAAAGTTAAA
1 ATAAGTGCTTTTGAGTTAAAAAACACTTTTGAGCAAAAGTTAAA
18105728 AT
1 AT
18105730 TTATTATTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (44 bp):
ATAAGTGCTTTTGAGTTAAAAAACACTTTTGAGCAAAAGTTAAA
Found at i:18105714 original size:18 final size:20
Alignment explanation
Indices: 18105677--18105721 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
18105667 TTTGAGCAAA
*
18105677 AGTTAAAATAAGTGCTTTTG
1 AGTTAAAATAAGTACTTTTG
18105697 AGTTAAAA-AA-TACTTTTG
1 AGTTAAAATAAGTACTTTTG
18105715 AG-TAAAA
1 AGTTAAAA
18105722 GTTAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 5 0.21
18 9 0.38
19 2 0.08
20 8 0.33
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (20 bp):
AGTTAAAATAAGTACTTTTG
Found at i:18105726 original size:24 final size:23
Alignment explanation
Indices: 18105653--18105728 Score: 63
Period size: 24 Copynumber: 3.3 Consensus size: 23
18105643 AGTGCTTTTG
*
18105653 AGTTAAAAAACACTTTTGAGCAAA
1 AGTTAAAAAATACTTTTGAG-AAA
*
18105677 AGTTAAAATAAGTGCTTTT--G---
1 AGTTAAAA-AA-TACTTTTGAGAAA
18105697 AGTTAAAAAATACTTTTGAGTAAA
1 AGTTAAAAAATACTTTTGAG-AAA
18105721 AGTTAAAA
1 AGTTAAAA
18105729 TTTATTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 16
0.68 0.05 0.27
Matches are distributed among these distances:
18 6 0.15
19 2 0.05
20 9 0.22
24 17 0.41
25 2 0.05
26 5 0.12
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.32
Consensus pattern (23 bp):
AGTTAAAAAATACTTTTGAGAAA
Found at i:18106667 original size:19 final size:18
Alignment explanation
Indices: 18106627--18106710 Score: 64
Period size: 18 Copynumber: 4.6 Consensus size: 18
18106617 TTTTAGATTT
* *
18106627 TTTTTAACTTCTATTAGA
1 TTTTTAAGTTTTATTAGA
18106645 -TTTTAAGTTTTAGTTAGA
1 TTTTTAAGTTTTA-TTAGA
* **
18106663 TTTTTTAAATTCAATTAGA
1 -TTTTTAAGTTTTATTAGA
* *
18106682 TTTTTTAGATTTACTTAGA
1 TTTTTAAGTTTTA-TTAGA
18106701 -TTTTAAGTTT
1 TTTTTAAGTTT
18106711 AAACTTTAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
17 10 0.20
18 21 0.42
19 10 0.20
20 9 0.18
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.57
Consensus pattern (18 bp):
TTTTTAAGTTTTATTAGA
Found at i:18106680 original size:37 final size:38
Alignment explanation
Indices: 18106626--18106704 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
18106616 ATTTTAGATT
* * * *
18106626 TTTTTTAACTTCTATTAGA-TTTTAAGTTTTAGTTAGA
1 TTTTTTAAATTCAATTAGATTTTTAAGATTTACTTAGA
*
18106663 TTTTTTAAATTCAATTAGATTTTTTAGATTTACTTAGA
1 TTTTTTAAATTCAATTAGATTTTTAAGATTTACTTAGA
18106701 TTTT
1 TTTT
18106705 AAGTTTAAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 17 0.47
38 19 0.53
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.58
Consensus pattern (38 bp):
TTTTTTAAATTCAATTAGATTTTTAAGATTTACTTAGA
Found at i:18106704 original size:18 final size:19
Alignment explanation
Indices: 18106639--18106704 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
18106629 TTTAACTTCT
* *
18106639 ATTAGA-TTTTAAGTTTTA
1 ATTAGATTTTTTAGATTTA
* * *
18106657 GTTAGATTTTTTAAATTCA
1 ATTAGATTTTTTAGATTTA
18106676 ATTAGATTTTTTAGATTTA
1 ATTAGATTTTTTAGATTTA
*
18106695 CTTAGATTTT
1 ATTAGATTTT
18106705 AAGTTTAAAC
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
18 5 0.13
19 33 0.87
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.56
Consensus pattern (19 bp):
ATTAGATTTTTTAGATTTA
Found at i:18111447 original size:35 final size:35
Alignment explanation
Indices: 18111408--18111474 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
18111398 ATAAATGGTT
* * *
18111408 TACTGGCTCTACGGAGCGACATCATGGAAATGATC
1 TACTGGCTCTACAGAGCGACACCATGAAAATGATC
*
18111443 TACTGGTTCTACAGAGCGACACCATGAAAATG
1 TACTGGCTCTACAGAGCGACACCATGAAAATG
18111475 GTTTATTGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22
Consensus pattern (35 bp):
TACTGGCTCTACAGAGCGACACCATGAAAATGATC
Found at i:18113134 original size:25 final size:25
Alignment explanation
Indices: 18113072--18113125 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
18113062 TTAGTGTTAA
*
18113072 CGATTTATAGCTCGTGAGAGCATAC
1 CGATTCATAGCTCGTGAGAGCATAC
18113097 CGATTCATAGCTCGTGAGAGCATAC
1 CGATTCATAGCTCGTGAGAGCATAC
18113122 CGAT
1 CGAT
18113126 CTTCAGCTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (25 bp):
CGATTCATAGCTCGTGAGAGCATAC
Found at i:18113165 original size:25 final size:25
Alignment explanation
Indices: 18113080--18113171 Score: 91
Period size: 25 Copynumber: 3.7 Consensus size: 25
18113070 AACGATTTAT
*
18113080 AGCTCGTGA-GAGCATACCGATTCAT
1 AGCTCGT-ATGAGCATACCGATTCAC
*
18113105 AGCTCGTGA-GAGCATACCGA-TCTTC
1 AGCTCGT-ATGAGCATACCGATTC-AC
**
18113130 AGCTCAAATGAGCATACCGATTCAC
1 AGCTCGTATGAGCATACCGATTCAC
*
18113155 AGGTCGTATGAGCATAC
1 AGCTCGTATGAGCATAC
18113172 ATGTACATGA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
24 3 0.05
25 51 0.91
26 2 0.04
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (25 bp):
AGCTCGTATGAGCATACCGATTCAC
Found at i:18120766 original size:19 final size:18
Alignment explanation
Indices: 18120709--18120766 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 18
18120699 CACTCGCATA
18120709 AAAAAATTTATACTTATTTT
1 AAAAAATTT-TAC-TATTTT
* *
18120729 AAAGAAATTTTATTTTTTT
1 AAA-AAATTTTACTATTTT
*
18120748 ATCAAAATTTTACTATTTT
1 A-AAAAATTTTACTATTTT
18120767 TTTAATTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 19 0.61
20 6 0.19
21 6 0.19
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (18 bp):
AAAAAATTTTACTATTTT
Found at i:18122260 original size:18 final size:19
Alignment explanation
Indices: 18122224--18122260 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
18122214 GTTTAGTACT
18122224 GCTTAAAAAGTGCACTTTTA
1 GCTTAAAAAGT-CACTTTTA
18122244 GCTTAAAAAGT-ACTTTT
1 GCTTAAAAAGTCACTTTT
18122261 GAAATAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (19 bp):
GCTTAAAAAGTCACTTTTA
Found at i:18123765 original size:27 final size:27
Alignment explanation
Indices: 18123733--18123787 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
18123723 ACAGTCATAC
*
18123733 ATAACATAGAGAGCAT-ATAGTCATTTT
1 ATAACATAGAGA-AATAATAGTCATTTT
*
18123760 ATAACATAGGGAAATAATAGTCATTTT
1 ATAACATAGAGAAATAATAGTCATTTT
18123787 A
1 A
18123788 CCATGTAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.33
Consensus pattern (27 bp):
ATAACATAGAGAAATAATAGTCATTTT
Found at i:18130593 original size:37 final size:37
Alignment explanation
Indices: 18130523--18130614 Score: 123
Period size: 37 Copynumber: 2.5 Consensus size: 37
18130513 ACTTACAGAT
18130523 ATCCAACCGA-AACACGCCAAACGCTCATAAGAGCTA
1 ATCCAACCGATAACACGCCAAACGCTCATAAGAGCTA
* * * * *
18130559 ATCCAACCAATAACATGCTAAATGCTCATGAGAGCTA
1 ATCCAACCGATAACACGCCAAACGCTCATAAGAGCTA
*
18130596 ATACAACCGATAACACGCC
1 ATCCAACCGATAACACGCC
18130615 TCGGCACTAA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
36 9 0.20
37 37 0.80
ACGTcount: A:0.41, C:0.30, G:0.13, T:0.15
Consensus pattern (37 bp):
ATCCAACCGATAACACGCCAAACGCTCATAAGAGCTA
Found at i:18134115 original size:73 final size:74
Alignment explanation
Indices: 18134035--18134220 Score: 268
Period size: 73 Copynumber: 2.5 Consensus size: 74
18134025 GGGCAGATGT
* * *
18134035 ATAGCTCTTATGAGCATTTGGCATGTTATTGGTTGGATTATCTCTT-TGAGCATTTGGTGTGTTA
1 ATAGCTCTTATGAGCATTTGGCGTGTTATTGGTTGGATTAGCTCTTATGAGCATTTGGCGTGTTA
* *
18134099 TTGGTTGGA
66 TCGGATGGA
* * * *
18134108 ATAGCTCTTATGATCACTTAGCGTGTTATCGGTTGGATTAGCTCTTATGAGCATTTGGCGTGTTA
1 ATAGCTCTTATGAGCATTTGGCGTGTTATTGGTTGGATTAGCTCTTATGAGCATTTGGCGTGTTA
18134173 TCGGATGGA
66 TCGGATGGA
*
18134182 TTAGCTCTTATGAGCATTTGGCGTGTT-TTGGTTGGATTA
1 ATAGCTCTTATGAGCATTTGGCGTGTTATTGGTTGGATTA
18134221 CTTGTGTATT
Statistics
Matches: 98, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
73 51 0.52
74 47 0.48
ACGTcount: A:0.18, C:0.12, G:0.27, T:0.42
Consensus pattern (74 bp):
ATAGCTCTTATGAGCATTTGGCGTGTTATTGGTTGGATTAGCTCTTATGAGCATTTGGCGTGTTA
TCGGATGGA
Found at i:18134143 original size:37 final size:37
Alignment explanation
Indices: 18134036--18134220 Score: 266
Period size: 37 Copynumber: 5.1 Consensus size: 37
18134026 GGCAGATGTA
*
18134036 TAGCTCTTATGAGCATTTGGCATGTTATTGGTTGGAT
1 TAGCTCTTATGAGCATTTGGCGTGTTATTGGTTGGAT
* * *
18134073 TATCTCTT-TGAGCATTTGGTGTGTTATTGGTTGGAA
1 TAGCTCTTATGAGCATTTGGCGTGTTATTGGTTGGAT
* * * *
18134109 TAGCTCTTATGATCACTTAGCGTGTTATCGGTTGGAT
1 TAGCTCTTATGAGCATTTGGCGTGTTATTGGTTGGAT
* *
18134146 TAGCTCTTATGAGCATTTGGCGTGTTATCGGATGGAT
1 TAGCTCTTATGAGCATTTGGCGTGTTATTGGTTGGAT
18134183 TAGCTCTTATGAGCATTTGGCGTGTT-TTGGTTGGAT
1 TAGCTCTTATGAGCATTTGGCGTGTTATTGGTTGGAT
18134219 TA
1 TA
18134221 CTTGTGTATT
Statistics
Matches: 130, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
36 42 0.32
37 88 0.68
ACGTcount: A:0.18, C:0.12, G:0.28, T:0.43
Consensus pattern (37 bp):
TAGCTCTTATGAGCATTTGGCGTGTTATTGGTTGGAT
Found at i:18138819 original size:25 final size:25
Alignment explanation
Indices: 18138758--18138819 Score: 58
Period size: 25 Copynumber: 2.5 Consensus size: 25
18138748 GAATCAGTAT
* *
18138758 GCTCTCATGAGCTGTAAATTGGTAA
1 GCTCTCATGAGCTGTAAATCGATAA
18138783 GCT-T-ATACGAGCTG-AGAATCGATAA
1 GCTCTCAT--GAGCTGTA-AATCGATAA
18138808 GCTCTCATGAGC
1 GCTCTCATGAGC
18138820 CACAAATCGG
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
23 2 0.07
24 2 0.07
25 23 0.77
26 1 0.03
27 2 0.07
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.27
Consensus pattern (25 bp):
GCTCTCATGAGCTGTAAATCGATAA
Found at i:18138844 original size:25 final size:25
Alignment explanation
Indices: 18138773--18138845 Score: 60
Period size: 25 Copynumber: 2.9 Consensus size: 25
18138763 CATGAGCTGT
* * *
18138773 AAATTGGTAAGCTTATACGAGCTGA
1 AAATCGGTAAGCTCATACGAGCTCA
* * *
18138798 GAATCGATAAGCTC-TCATGAGC-CA
1 AAATCGGTAAGCTCAT-ACGAGCTCA
18138822 CAAATCGGTAAGCTCATACGAGCT
1 -AAATCGGTAAGCTCATACGAGCT
18138846 GTGGTGTGCC
Statistics
Matches: 35, Mismatches: 9, Indels: 7
0.69 0.18 0.14
Matches are distributed among these distances:
24 2 0.06
25 32 0.91
26 1 0.03
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (25 bp):
AAATCGGTAAGCTCATACGAGCTCA
Found at i:18145365 original size:12 final size:12
Alignment explanation
Indices: 18145348--18145373 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18145338 TTCTTGGAGG
18145348 GTATATTTGGTT
1 GTATATTTGGTT
18145360 GTATATTTGGTT
1 GTATATTTGGTT
18145372 GT
1 GT
18145374 GTTGGAGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (12 bp):
GTATATTTGGTT
Found at i:18145384 original size:34 final size:35
Alignment explanation
Indices: 18145326--18145395 Score: 115
Period size: 34 Copynumber: 2.0 Consensus size: 35
18145316 GTTGGGAGGC
*
18145326 TATATTTGGTTTTTCTTGGAGGGTATATTTGGTTG
1 TATATTTGGTTTGTCTTGGAGGGTATATTTGGTTG
*
18145361 TATATTTGG-TTGTGTTGGAGGGTATATTTGGTTG
1 TATATTTGGTTTGTCTTGGAGGGTATATTTGGTTG
18145395 T
1 T
18145396 GTTTGGAGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
34 24 0.73
35 9 0.27
ACGTcount: A:0.14, C:0.01, G:0.31, T:0.53
Consensus pattern (35 bp):
TATATTTGGTTTGTCTTGGAGGGTATATTTGGTTG
Found at i:18145389 original size:57 final size:58
Alignment explanation
Indices: 18145302--18145418 Score: 166
Period size: 57 Copynumber: 2.0 Consensus size: 58
18145292 TGTTTGAAGG
*
18145302 GTATATTTCATTGTGTTGGGAGGCTATATTTGGTT-TTTCTTGGAGGGTATATTTGGTT
1 GTATATTTCATTGTGTTGGGAGGCTATATTTGGTTGTGT-TTGGAGGGTATATTTGGTT
** * *
18145360 GTATATTTGGTTGTGTT-GGAGGGTATATTTGGTTGTGTTTGGAGGGTATGTTTGGTT
1 GTATATTTCATTGTGTTGGGAGGCTATATTTGGTTGTGTTTGGAGGGTATATTTGGTT
18145417 GT
1 GT
18145419 GCCTGGAGGC
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
57 36 0.68
58 17 0.32
ACGTcount: A:0.14, C:0.03, G:0.34, T:0.50
Consensus pattern (58 bp):
GTATATTTCATTGTGTTGGGAGGCTATATTTGGTTGTGTTTGGAGGGTATATTTGGTT
Found at i:18145405 original size:23 final size:23
Alignment explanation
Indices: 18145360--18145452 Score: 118
Period size: 23 Copynumber: 4.1 Consensus size: 23
18145350 ATATTTGGTT
18145360 GTATATTTGGTTGTG-TTGGAGG
1 GTATATTTGGTTGTGTTTGGAGG
18145382 GTATATTTGGTTGTGTTTGGAGG
1 GTATATTTGGTTGTGTTTGGAGG
* **
18145405 GTATGTTTGGTTGTGCCTGGAGG
1 GTATATTTGGTTGTGTTTGGAGG
* *
18145428 CTATGA-TTGGTTGTGTTTGGTGG
1 GTAT-ATTTGGTTGTGTTTGGAGG
18145451 GT
1 GT
18145453 GATAGTTTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
22 15 0.25
23 45 0.75
ACGTcount: A:0.11, C:0.03, G:0.41, T:0.45
Consensus pattern (23 bp):
GTATATTTGGTTGTGTTTGGAGG
Found at i:18145438 original size:80 final size:81
Alignment explanation
Indices: 18145290--18145441 Score: 191
Period size: 80 Copynumber: 1.9 Consensus size: 81
18145280 TTTAAGTGTA
* * * *
18145290 TGTGTTTGAAGGGTATATTTCATTGTGTTGGGAGGCTATATTTGGTTTTTCTTGGAGGGTATATT
1 TGTGTTTGAAGGGTATATTTCATTGTGTTGGGAGGCTATATTTGGTTGTGCCTGGAGGCTATATT
18145355 TGGTTGTATATTTGGT
66 TGGTTGTATATTTGGT
* ** * * *
18145371 TGTG-TTGGAGGGTATATTTGGTTGTGTTTGGAGGGTATGTTTGGTTGTGCCTGGAGGCTATGA-
1 TGTGTTTGAAGGGTATATTTCATTGTGTTGGGAGGCTATATTTGGTTGTGCCTGGAGGCTAT-AT
18145434 TTGGTTGT
65 TTGGTTGT
18145442 GTTTGGTGGG
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
80 55 0.92
81 5 0.08
ACGTcount: A:0.14, C:0.04, G:0.36, T:0.47
Consensus pattern (81 bp):
TGTGTTTGAAGGGTATATTTCATTGTGTTGGGAGGCTATATTTGGTTGTGCCTGGAGGCTATATT
TGGTTGTATATTTGGT
Found at i:18154571 original size:16 final size:17
Alignment explanation
Indices: 18154532--18154571 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
18154522 TTAAATTCAC
18154532 TCATTTAAGATTAATTT
1 TCATTTAAGATTAATTT
*
18154549 T-AATTAAGA-TAATTT
1 TCATTTAAGATTAATTT
18154564 TCATTTAA
1 TCATTTAA
18154572 TAAATGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 7 0.35
16 12 0.60
17 1 0.05
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (17 bp):
TCATTTAAGATTAATTT
Found at i:18158056 original size:21 final size:22
Alignment explanation
Indices: 18158027--18158073 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
18158017 CAGAAGGAGT
* *
18158027 GAGTAGTACTTCGCAGCAGATG
1 GAGTAGTACTCCGCAACAGATG
*
18158049 GAGT-GTACTCCGCAACAGGTG
1 GAGTAGTACTCCGCAACAGATG
18158070 GAGT
1 GAGT
18158074 TTGAGCAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAACAGATG
Found at i:18163704 original size:28 final size:28
Alignment explanation
Indices: 18163664--18163724 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
18163654 ATTATTTTCT
*
18163664 TTTGACAAAGAACTT-GAGGTTGAACTGA
1 TTTGACAAAGAACTTGGA-GTTGAACTAA
*
18163692 TTTGACTAAGAACTTGGAGTTGAACTAA
1 TTTGACAAAGAACTTGGAGTTGAACTAA
18163720 TTTGA
1 TTTGA
18163725 TTCTTGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 28 0.93
29 2 0.07
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (28 bp):
TTTGACAAAGAACTTGGAGTTGAACTAA
Found at i:18166285 original size:5 final size:5
Alignment explanation
Indices: 18166275--18166301 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
18166265 ACACTTTTTG
18166275 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
18166302 AGTTTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:18171033 original size:13 final size:13
Alignment explanation
Indices: 18171015--18171042 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
18171005 ATAAAATTGG
18171015 AAAGATGATAAAT
1 AAAGATGATAAAT
18171028 AAAGATGATAAAT
1 AAAGATGATAAAT
18171041 AA
1 AA
18171043 TAAAATAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (13 bp):
AAAGATGATAAAT
Found at i:18171576 original size:21 final size:20
Alignment explanation
Indices: 18171551--18171595 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
18171541 CCTAGAATTG
* *
18171551 AATTGAATTGAATTGATTATA
1 AATTGAATTAAATTGAGT-TA
*
18171572 AATTGTATTAAATTGAGTTA
1 AATTGAATTAAATTGAGTTA
18171592 AATT
1 AATT
18171596 TAGTCGTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.44
Consensus pattern (20 bp):
AATTGAATTAAATTGAGTTA
Found at i:18172055 original size:25 final size:25
Alignment explanation
Indices: 18172025--18172092 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 25
18172015 TCCGATATAT
*
18172025 GGCTCTTCGAAGCTTCCCGATTAAA
1 GGCTCTTCGGAGCTTCCCGATTAAA
* * * *
18172050 GTCTCTTTGTGAGCTTCCTGATTAAT
1 GGCTCTTCG-GAGCTTCCCGATTAAA
*
18172076 GGCTCTCCGGAGCTTCC
1 GGCTCTTCGGAGCTTCC
18172093 TAATATAGCT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
25 15 0.44
26 19 0.56
ACGTcount: A:0.16, C:0.28, G:0.22, T:0.34
Consensus pattern (25 bp):
GGCTCTTCGGAGCTTCCCGATTAAA
Found at i:18172244 original size:25 final size:25
Alignment explanation
Indices: 18172174--18172253 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
18172164 CCCATTATTG
*
18172174 GCTCGCATGAGCTTCCCGTTATATA
1 GCTCGCATGAGCTTCCCGTTACATA
* * **
18172199 G-TCTGGATAAGCTTCTTGTTACATA
1 GCTC-GCATGAGCTTCCCGTTACATA
* * *
18172224 GCTCACATGAGCTTCCCGTTATATG
1 GCTCGCATGAGCTTCCCGTTACATA
18172249 GCTCG
1 GCTCG
18172254 AAAGAAGACT
Statistics
Matches: 40, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
24 2 0.05
25 36 0.90
26 2 0.05
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (25 bp):
GCTCGCATGAGCTTCCCGTTACATA
Found at i:18179235 original size:21 final size:21
Alignment explanation
Indices: 18179211--18179251 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
18179201 GTCTAGGATG
*
18179211 TGAATTGAATTGAATTGATTA
1 TGAATTGAATTAAATTGATTA
*
18179232 TGAATTGTATTAAATTGATT
1 TGAATTGAATTAAATTGATT
18179252 TAAATTTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (21 bp):
TGAATTGAATTAAATTGATTA
Found at i:18179873 original size:25 final size:25
Alignment explanation
Indices: 18179820--18179906 Score: 70
Period size: 25 Copynumber: 3.5 Consensus size: 25
18179810 CTTACATGAA
* * *
18179820 CTTCCTAAT-TATGGCTCTTATAAG
1 CTTCCTATTATATAGCTCATATAAG
* *
18179844 TTTCCTATTATATAGCCTGA-ATAAG
1 CTTCCTATTATATAG-CTCATATAAG
* * *
18179869 CTTCCTGTTACATAGCTCATATGAG
1 CTTCCTATTATATAGCTCATATAAG
*
18179894 CTTCCCATTATAT
1 CTTCCTATTATAT
18179907 GACTCGAGAG
Statistics
Matches: 47, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
24 10 0.21
25 35 0.74
26 2 0.04
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.40
Consensus pattern (25 bp):
CTTCCTATTATATAGCTCATATAAG
Found at i:18184220 original size:31 final size:29
Alignment explanation
Indices: 18184157--18184225 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
18184147 CAAATTATTA
*
18184157 TTTTAGAAAGTTTTTAAATTTTTAACTTTC
1 TTTTAGAAAGTTTTTAAATTTTTAAC-ATC
18184187 TTTTAGAAAGTTTTTAGAATTTGTTATA-ATC
1 TTTTAGAAAGTTTTTA-AATTT-TTA-ACATC
18184218 TTTT-GAAA
1 TTTTAGAAA
18184226 AATATAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
30 20 0.57
31 11 0.31
32 3 0.09
33 1 0.03
ACGTcount: A:0.32, C:0.04, G:0.10, T:0.54
Consensus pattern (29 bp):
TTTTAGAAAGTTTTTAAATTTTTAACATC
Found at i:18185242 original size:30 final size:29
Alignment explanation
Indices: 18185177--18185242 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
18185167 TGAGTAGGTT
* *
18185177 AAAATTTAAGTCCCTCTACTTTTATTTTA
1 AAAATTTAAGCCCCTCTACTTTTAATTTA
*
18185206 AGAAATTT-AGCCCCTTTACTTTTTAGATTTA
1 A-AAATTTAAGCCCCTCTAC-TTTTA-ATTTA
18185237 AAAATT
1 AAAATT
18185243 CAATTGTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 10 0.32
30 16 0.52
31 5 0.16
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.45
Consensus pattern (29 bp):
AAAATTTAAGCCCCTCTACTTTTAATTTA
Found at i:18191184 original size:19 final size:19
Alignment explanation
Indices: 18191160--18191202 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
18191150 GACAGAAAGC
*
18191160 AAAAACAAGATAAAAACCT
1 AAAAACAAGAGAAAAACCT
*
18191179 AAAAACAAGAGAAAACCCT
1 AAAAACAAGAGAAAAACCT
18191198 AAAAA
1 AAAAA
18191203 GTGCAAGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.70, C:0.16, G:0.07, T:0.07
Consensus pattern (19 bp):
AAAAACAAGAGAAAAACCT
Found at i:18191958 original size:12 final size:12
Alignment explanation
Indices: 18191941--18191967 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
18191931 AATAAATCAT
18191941 ATATGTATATTA
1 ATATGTATATTA
18191953 ATATGTATATTA
1 ATATGTATATTA
18191965 ATA
1 ATA
18191968 GAAAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (12 bp):
ATATGTATATTA
Found at i:18192919 original size:24 final size:24
Alignment explanation
Indices: 18192864--18192938 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
18192854 AAAATATATA
*
18192864 AATAAAATAAT-AAATTTATTTAT
1 AATAAAATAATAAAATTAATTTAT
*
18192887 AATATAAATCATAAAATTAAATTTAT
1 AATA-AAATAATAAAATT-AATTTAT
*
18192913 -ATAAAATTATAAAA-TAATTTA-
1 AATAAAATAATAAAATTAATTTAT
18192934 AATAA
1 AATAA
18192939 TTTATTTGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
22 10 0.22
23 5 0.11
24 16 0.36
25 8 0.18
26 6 0.13
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (24 bp):
AATAAAATAATAAAATTAATTTAT
Found at i:18201750 original size:53 final size:53
Alignment explanation
Indices: 18201670--18201776 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
18201660 AACTAGTTTC
18201670 AGAACATGCTGAGTACAGTTGGCGACAAGAATTAATCATAGCTCACAAATTAT
1 AGAACATGCTGAGTACAGTTGGCGACAAGAATTAATCATAGCTCACAAATTAT
18201723 AGAACATGCTGAGTACAGTTGGCGACAAGAATTAATCATAGCTCACAAATTAT
1 AGAACATGCTGAGTACAGTTGGCGACAAGAATTAATCATAGCTCACAAATTAT
18201776 A
1 A
18201777 AATCCTTGCC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (53 bp):
AGAACATGCTGAGTACAGTTGGCGACAAGAATTAATCATAGCTCACAAATTAT
Found at i:18203412 original size:18 final size:18
Alignment explanation
Indices: 18203386--18203433 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
18203376 GAAATGTGAG
* *
18203386 AAATTATGTTCACATTTT
1 AAATGATGTTCACATTTC
18203404 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
*
18203422 AAATGGTGTTCA
1 AAATGATGTTCA
18203434 AATTGATGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:18203941 original size:72 final size:72
Alignment explanation
Indices: 18203862--18204171 Score: 455
Period size: 72 Copynumber: 4.3 Consensus size: 72
18203852 CAATGCTAAA
* * * * * *
18203862 CTAGTTTTATCGATAGTTATTTATGTGTGTTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTTATTTAT
18203927 GTGTAAT
66 GTGTAAT
18203934 CTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTTATTTAT
18203999 GTGTAAT
66 GTGTAAT
* * * * *
18204006 CTAGTTTTATCAATGGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATTTTCTACTTATGTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTTATTTAT
18204071 GTGTAAT
66 GTGTAAT
*
18204078 CTAGTTTTATTAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTTATTTAT
* *
18204143 ACT-AAAT
66 -GTGTAAT
*
18204150 -TAG-TTTATGAATAGTTGTTTAT
1 CTAGTTTTATCAATAGTTGTTTAT
18204172 ATATGATTTT
Statistics
Matches: 217, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
70 18 0.08
71 3 0.01
72 195 0.90
73 1 0.00
ACGTcount: A:0.24, C:0.06, G:0.16, T:0.55
Consensus pattern (72 bp):
CTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTTATTTAT
GTGTAAT
Found at i:18207152 original size:91 final size:91
Alignment explanation
Indices: 18206997--18207179 Score: 357
Period size: 91 Copynumber: 2.0 Consensus size: 91
18206987 AGGCGGGTAG
*
18206997 CCCAACCCATGAACAAATCTAGTCAGTACCATATCGGTGGATGTATTATTTTTGTTGGTACGTAC
1 CCCAACCCATGAACAAAACTAGTCAGTACCATATCGGTGGATGTATTATTTTTGTTGGTACGTAC
18207062 AACTATTAGCATGTTTCAGGGCATCA
66 AACTATTAGCATGTTTCAGGGCATCA
18207088 CCCAACCCATGAACAAAACTAGTCAGTACCATATCGGTGGATGTATTATTTTTGTTGGTACGTAC
1 CCCAACCCATGAACAAAACTAGTCAGTACCATATCGGTGGATGTATTATTTTTGTTGGTACGTAC
18207153 AACTATTAGCATGTTTCAGGGCATCA
66 AACTATTAGCATGTTTCAGGGCATCA
18207179 C
1 C
18207180 TTTAGGTTTA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (91 bp):
CCCAACCCATGAACAAAACTAGTCAGTACCATATCGGTGGATGTATTATTTTTGTTGGTACGTAC
AACTATTAGCATGTTTCAGGGCATCA
Found at i:18220481 original size:51 final size:52
Alignment explanation
Indices: 18220384--18220491 Score: 173
Period size: 51 Copynumber: 2.1 Consensus size: 52
18220374 ATAGAAATGG
* *
18220384 TGAAAATAGAGAAATGGGAAACATTTGGAAATGATTATGTTTTTCTCCAAAA
1 TGAAAATAGAGAAATGGGAAACATTTGGAAATGAATATGGTTTTCTCCAAAA
* *
18220436 TGAAAATAGAGAAAT-GGAATCATTTGGAAATGAATATGGTTTTCTCTAAAA
1 TGAAAATAGAGAAATGGGAAACATTTGGAAATGAATATGGTTTTCTCCAAAA
18220487 TGAAA
1 TGAAA
18220492 TTTAAAAATG
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
51 37 0.71
52 15 0.29
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (52 bp):
TGAAAATAGAGAAATGGGAAACATTTGGAAATGAATATGGTTTTCTCCAAAA
Found at i:18239154 original size:15 final size:15
Alignment explanation
Indices: 18239134--18239198 Score: 58
Period size: 15 Copynumber: 4.2 Consensus size: 15
18239124 TTGATAATTC
*
18239134 GAAAAATTAAGTGTT
1 GAAAAATTAAATGTT
*
18239149 GAAAAATTAAATGTGG
1 GAAAAATTAAATGT-T
* *
18239165 GAAAAAATTAAGTATT
1 G-AAAAATTAAATGTT
* *
18239181 GAAGATTTAAATGTT
1 GAAAAATTAAATGTT
18239196 GAA
1 GAA
18239199 TTTAAGTTAT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
15 26 0.67
16 2 0.05
17 11 0.28
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (15 bp):
GAAAAATTAAATGTT
Found at i:18242047 original size:5 final size:5
Alignment explanation
Indices: 18242037--18242065 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
18242027 TATCTGGAAA
18242037 GATTT GATTT GATTT GATTT GATTT GATT
1 GATTT GATTT GATTT GATTT GATTT GATT
18242066 GTGTAAATCT
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:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (5 bp):
GATTT
Found at i:18257306 original size:16 final size:17
Alignment explanation
Indices: 18257287--18257322 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
18257277 CTTTTTTTTT
18257287 TTTGAAT-TTTTATAAA
1 TTTGAATATTTTATAAA
18257303 TTTGAATATTTTATAAA
1 TTTGAATATTTTATAAA
18257320 TTT
1 TTT
18257323 TAAATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (17 bp):
TTTGAATATTTTATAAA
Found at i:18257333 original size:18 final size:18
Alignment explanation
Indices: 18257286--18257334 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
18257276 TCTTTTTTTT
18257286 TTTTGAATT-TTTATAAA
1 TTTTGAATTATTTATAAA
18257303 -TTTGAA-TATTTTATAAA
1 TTTTGAATTA-TTTATAAA
*
18257320 TTTTAAATTATTTAT
1 TTTTGAATTATTTAT
18257335 TAACATGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 1 0.04
16 6 0.22
17 8 0.30
18 10 0.37
19 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (18 bp):
TTTTGAATTATTTATAAA
Found at i:18273674 original size:31 final size:31
Alignment explanation
Indices: 18273637--18273703 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
18273627 CTAATAGCCC
* * *
18273637 TTTTTTTCTTTCCCAGT-TTGTTAAACCAATT
1 TTTTTTTCTCTCCC-GTATTGCTAAACAAATT
18273668 TTTTTTTCTCTCCCGTATTGCTAAACAAATT
1 TTTTTTTCTCTCCCGTATTGCTAAACAAATT
18273699 TTTTT
1 TTTTT
18273704 AGACTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.55
Consensus pattern (31 bp):
TTTTTTTCTCTCCCGTATTGCTAAACAAATT
Found at i:18278375 original size:13 final size:13
Alignment explanation
Indices: 18278357--18278381 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18278347 GAATTTATAT
18278357 GTGTGAAAATTTC
1 GTGTGAAAATTTC
18278370 GTGTGAAAATTT
1 GTGTGAAAATTT
18278382 TACCGTTTAA
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:18283032 original size:27 final size:27
Alignment explanation
Indices: 18282995--18283047 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
18282985 TTTTTTTTTA
*
18282995 TTTCTATTAAAAACGTCCGTTATAATTC
1 TTTCTATTAAAAACGTCCCTT-TAATTC
*
18283023 TTTCT-TTAAAAATGTCCCTTTAATT
1 TTTCTATTAAAAACGTCCCTTTAATT
18283048 TTTTGATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 13 0.57
28 5 0.22
ACGTcount: A:0.30, C:0.17, G:0.06, T:0.47
Consensus pattern (27 bp):
TTTCTATTAAAAACGTCCCTTTAATTC
Found at i:18283078 original size:13 final size:13
Alignment explanation
Indices: 18283060--18283085 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18283050 TTGATTTCAC
18283060 ATTACATAAATTA
1 ATTACATAAATTA
18283073 ATTACATAAATTA
1 ATTACATAAATTA
18283086 TTAAATTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTACATAAATTA
Found at i:18285751 original size:50 final size:50
Alignment explanation
Indices: 18285691--18286182 Score: 425
Period size: 50 Copynumber: 9.7 Consensus size: 50
18285681 TAAGGTTCGT
* *
18285691 CAGGGAAGTAAGATTCGCTGTTGTAACTTCAATCTGTTCCACTGCAACGC
1 CAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGC
* * * * * *
18285741 CAGGGCAGTAAGATTCGCCGTTGTAGCTTCAATCTGTGCCA-TGGAAGTAAGGTTCGT
1 CAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACT----GCAA----CGC
* * * * *
18285798 CAAGGAAGTAAGATTCACTATTGTAGCTTCAATCTGTTCCACTGCAACAC
1 CAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGC
* * * ** * *
18285848 CAAGGAAGTAAGATCCACTGTTGTAGCTTCAATCTTTTTAACTGCAATGT
1 CAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGC
* * * *
18285898 CGGGGAAGCAAAATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCACCGC
1 CAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGC
* ** * *
18285948 C-GGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCAATGT
1 CAGGG-AAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGC
* * * *
18285998 C-GAGAAAGCAAGATCCGCTGTTGTAGCTTTAATCTGTTCCACTGCACCGC
1 CAG-GGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGC
* * * * ** * *
18286048 TAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCAATGT
1 CAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGC
* * * *
18286098 C-GAGAAAGCAAGATCCGCTGTTGTAGCTTTAATCTGTTCCACTGCACCGC
1 CAG-GGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGC
* * *
18286148 TAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCT
1 CAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCT
18286183 TTTTAACTTG
Statistics
Matches: 353, Mismatches: 75, Indels: 28
0.77 0.16 0.06
Matches are distributed among these distances:
49 4 0.01
50 304 0.86
51 1 0.00
53 3 0.01
54 3 0.01
57 37 0.10
58 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (50 bp):
CAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGC
Found at i:18285805 original size:107 final size:107
Alignment explanation
Indices: 18285665--18285882 Score: 321
Period size: 107 Copynumber: 2.0 Consensus size: 107
18285655 AGTCTGTTCT
* * *
18285665 ATCTGTGCCAGGCAAATAAGGTTCGTCAGGGAAGTAAGATTCGCTGTTGTAACTTCAATCTGTTC
1 ATCTGTGCCAGGCAAATAAGGTTCGTCAAGGAAGTAAGATTCACTATTGTAACTTCAATCTGTTC
* * * * *
18285730 CACTGCAACGCCAGGGCAGTAAGATTCGCCGTTGTAGCTTCA
66 CACTGCAACACCAAGGAAGTAAGATCCACCGTTGTAGCTTCA
* *
18285772 ATCTGTGCCATGG-AAGTAAGGTTCGTCAAGGAAGTAAGATTCACTATTGTAGCTTCAATCTGTT
1 ATCTGTGCCA-GGCAAATAAGGTTCGTCAAGGAAGTAAGATTCACTATTGTAACTTCAATCTGTT
*
18285836 CCACTGCAACACCAAGGAAGTAAGATCCACTGTTGTAGCTTCA
65 CCACTGCAACACCAAGGAAGTAAGATCCACCGTTGTAGCTTCA
18285879 ATCT
1 ATCT
18285883 TTTTAACTGC
Statistics
Matches: 99, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
107 97 0.98
108 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (107 bp):
ATCTGTGCCAGGCAAATAAGGTTCGTCAAGGAAGTAAGATTCACTATTGTAACTTCAATCTGTTC
CACTGCAACACCAAGGAAGTAAGATCCACCGTTGTAGCTTCA
Found at i:18285957 original size:100 final size:100
Alignment explanation
Indices: 18285818--18286195 Score: 630
Period size: 100 Copynumber: 3.8 Consensus size: 100
18285808 AGATTCACTA
* * * *
18285818 TTGTAGCTTCAATCTGTTCCACTGCAACACCAAGGAAGTAAGATCCACTGTTGTAGCTTCAATCT
1 TTGTAGCTTCAATCTGTTCCACTGCACCGCCAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCT
* * *
18285883 TTTTAACTGCAATGTCGGGGAAGCAAAATCCGCTG
66 TTTTAACTGCAATGTCGAGAAAGCAAGATCCGCTG
**
18285918 TTGTAGCTTCAATCTGTTCCACTGCACCGCCGGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCT
1 TTGTAGCTTCAATCTGTTCCACTGCACCGCCAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCT
18285983 TTTTAACTGCAATGTCGAGAAAGCAAGATCCGCTG
66 TTTTAACTGCAATGTCGAGAAAGCAAGATCCGCTG
* *
18286018 TTGTAGCTTTAATCTGTTCCACTGCACCGCTAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCT
1 TTGTAGCTTCAATCTGTTCCACTGCACCGCCAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCT
18286083 TTTTAACTGCAATGTCGAGAAAGCAAGATCCGCTG
66 TTTTAACTGCAATGTCGAGAAAGCAAGATCCGCTG
* *
18286118 TTGTAGCTTTAATCTGTTCCACTGCACCGCTAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCT
1 TTGTAGCTTCAATCTGTTCCACTGCACCGCCAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCT
18286183 TTTTAACTTGCAA
66 TTTTAAC-TGCAA
18286196 CCTCAGGGGT
Statistics
Matches: 264, Mismatches: 13, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
100 259 0.98
101 5 0.02
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (100 bp):
TTGTAGCTTCAATCTGTTCCACTGCACCGCCAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCT
TTTTAACTGCAATGTCGAGAAAGCAAGATCCGCTG
Found at i:18298993 original size:14 final size:14
Alignment explanation
Indices: 18298957--18298990 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
18298947 TCATCATTTG
18298957 CCTATAACCAAAAC
1 CCTATAACCAAAAC
18298971 CCTATAACCAAAAC
1 CCTATAACCAAAAC
18298985 CC-ATAA
1 CCTATAA
18298991 ACCCATGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:18299556 original size:25 final size:26
Alignment explanation
Indices: 18299528--18299581 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
18299518 ATATAGATTT
* *
18299528 TAAAATATATGTAT-ATATATGTATA
1 TAAAAAATATGTATGATATACGTATA
18299553 TAAAAAATATGTATGGATATACGTATA
1 TAAAAAATATGTAT-GATATACGTATA
18299580 TA
1 TA
18299582 TATTTTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 13 0.52
27 12 0.48
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (26 bp):
TAAAAAATATGTATGATATACGTATA
Found at i:18301891 original size:12 final size:12
Alignment explanation
Indices: 18301874--18301902 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
18301864 TGGACGAAAA
18301874 AAGGCCAATTCC
1 AAGGCCAATTCC
18301886 AAGGCCAATTCC
1 AAGGCCAATTCC
18301898 AAGGC
1 AAGGC
18301903 TACTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.31, G:0.21, T:0.14
Consensus pattern (12 bp):
AAGGCCAATTCC
Found at i:18302371 original size:25 final size:25
Alignment explanation
Indices: 18302343--18302406 Score: 101
Period size: 25 Copynumber: 2.6 Consensus size: 25
18302333 CTCATACGAG
*
18302343 CCAATATTGGGAAGGTTCAAGCGAA
1 CCAATATCGGGAAGGTTCAAGCGAA
* *
18302368 CCAATATCGAGAAGGTTCAAGCGAG
1 CCAATATCGGGAAGGTTCAAGCGAA
18302393 CCAATATCGGGAAG
1 CCAATATCGGGAAG
18302407 CTCCGGAGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.17
Consensus pattern (25 bp):
CCAATATCGGGAAGGTTCAAGCGAA
Found at i:18302431 original size:26 final size:26
Alignment explanation
Indices: 18302390--18302472 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 26
18302380 AGGTTCAAGC
*
18302390 GAGCCAA-T-ATCGGGAAGCTCCGGA
1 GAGCCAATTAATCGGGAAGCTCCGAA
*
18302414 GAGCCAATTAATCGGGAAGCTCATGAAA
1 GAGCCAATTAATCGGGAAGCTC-CG-AA
**
18302442 GAGCC-ATTAATTAGGAAGCTCCGAA
1 GAGCCAATTAATCGGGAAGCTCCGAA
18302467 GAGCCA
1 GAGCCA
18302473 TATATCGGGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
24 7 0.14
25 8 0.16
26 13 0.27
27 15 0.31
28 6 0.12
ACGTcount: A:0.35, C:0.22, G:0.28, T:0.16
Consensus pattern (26 bp):
GAGCCAATTAATCGGGAAGCTCCGAA
Found at i:18302641 original size:24 final size:25
Alignment explanation
Indices: 18302579--18302641 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 25
18302569 CAAGATCCAT
*
18302579 ATAATGGGAAGCTCATGAGAGCCAA
1 ATAACGGGAAGCTCATGAGAGCCAA
* * * *
18302604 ATATCAGGATGCTCATGAGAG-CTA
1 ATAACGGGAAGCTCATGAGAGCCAA
*
18302628 ATAACGGGACGCTC
1 ATAACGGGAAGCTC
18302642 TTTCGAGCTG
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
24 13 0.43
25 17 0.57
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (25 bp):
ATAACGGGAAGCTCATGAGAGCCAA
Found at i:18322950 original size:22 final size:23
Alignment explanation
Indices: 18322901--18322951 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
18322891 TTTATCGATG
* * *
18322901 ATAAATTTGAGACAAATATATTA
1 ATAAATTTAAAACAAATACATTA
18322924 A-AAATTTAAAACAAAT-CATTA
1 ATAAATTTAAAACAAATACATTA
18322945 ATAAATT
1 ATAAATT
18322952 AATGAATAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 5 0.21
22 18 0.75
23 1 0.04
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (23 bp):
ATAAATTTAAAACAAATACATTA
Found at i:18323597 original size:53 final size:51
Alignment explanation
Indices: 18323515--18323614 Score: 137
Period size: 53 Copynumber: 1.9 Consensus size: 51
18323505 TATGAAACTT
*
18323515 CCCCATTTCCTCAAAATCCAATCCATTTTCGCACTTTGTTCCAATCTTTATAA
1 CCCCATTTCCTCAAAATCCAATCCATTTTC-CACTATGTT-CAATCTTTATAA
* ** *
18323568 CCCCATTTCCTCAAAATCCCATCTTTTTTCCCCTATGTTCAATCTTT
1 CCCCATTTCCTCAAAATCCAATCCATTTTCCACTATGTTCAATCTTT
18323615 GAAATCTCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 8 0.19
52 7 0.17
53 27 0.64
ACGTcount: A:0.23, C:0.34, G:0.03, T:0.40
Consensus pattern (51 bp):
CCCCATTTCCTCAAAATCCAATCCATTTTCCACTATGTTCAATCTTTATAA
Found at i:18345346 original size:10 final size:10
Alignment explanation
Indices: 18345333--18345358 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
18345323 TATTTTTTTT
18345333 TATTTTAAAC
1 TATTTTAAAC
18345343 TATTTTAAAC
1 TATTTTAAAC
18345353 TATTTT
1 TATTTT
18345359 TTTATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (10 bp):
TATTTTAAAC
Found at i:18351000 original size:26 final size:26
Alignment explanation
Indices: 18350970--18351046 Score: 81
Period size: 26 Copynumber: 3.1 Consensus size: 26
18350960 CATAAATACT
18350970 GATGAACGGTCACATAGCACATTGTG
1 GATGAACGGTCACATAGCACATTGTG
** * *
18350996 GATGAACCATCACATAG---A-TATC
1 GATGAACGGTCACATAGCACATTGTG
*
18351018 GATGAACGGTCACATAGCACATCGTG
1 GATGAACGGTCACATAGCACATTGTG
18351044 GAT
1 GAT
18351047 AAACCACCAC
Statistics
Matches: 38, Mismatches: 9, Indels: 8
0.69 0.16 0.15
Matches are distributed among these distances:
22 17 0.45
23 1 0.03
25 1 0.03
26 19 0.50
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (26 bp):
GATGAACGGTCACATAGCACATTGTG
Found at i:18352860 original size:45 final size:45
Alignment explanation
Indices: 18352810--18352897 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
18352800 AAATATTGTT
* *
18352810 TAATCAACTGCTCAGAAAGTCACTACTATAACCTGCCTCTTCCTC
1 TAATCAACTGCTCAGAAAGTCAATACTATAACCTACCTCTTCCTC
*
18352855 TAATCAACTGCTCAGAGAGTCAATACTATAACCTACCTCTTCC
1 TAATCAACTGCTCAGAAAGTCAATACTATAACCTACCTCTTCC
18352898 GATAGTTAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.31, C:0.32, G:0.09, T:0.28
Consensus pattern (45 bp):
TAATCAACTGCTCAGAAAGTCAATACTATAACCTACCTCTTCCTC
Found at i:18355157 original size:68 final size:67
Alignment explanation
Indices: 18354919--18355236 Score: 205
Period size: 68 Copynumber: 4.7 Consensus size: 67
18354909 GGTTTAATGT
* * * * ** * *
18354919 GTAAGATCATAGCTGGGTTATGGTAGCATATGAAGTCTG-TCAAAACAATAAACAT-GATATTAC
1 GTAAGA-CATAGTTGGGCTATGGCAACATATGAAGTCTGCT-AGGACAGTAAACATGGA-ATTAT
18354982 ATTGC
63 ATTGC
* * * ** * ** * * *
18354987 GTAAGACCGTAGCTAGATTATGGCAGCATATGAAGTCCACCAAGACAGT-AATAT-GAGATTATA
1 GTAAGA-CATAGTTGGGCTATGGCAACATATGAAGTCTGCTAGGACAGTAAACATGGA-ATTATA
18355050 TTGC
64 TTGC
* * * * *
18355054 ATAAGACTATATTTGGGATATGGCATCATAAGAAGTCTGCTAGGACAGTAAACATGGAATTATAT
1 GTAAGAC-ATAGTTGGGCTATGGCAACATATGAAGTCTGCTAGGACAGTAAACATGGAATTATAT
18355119 TGC
65 TGC
* * * * *
18355122 GTAAGATCATGGTTGGGCTATAGCAACATATGAAGTCTG-TCATGATAGTAAACATGGGATTATA
1 GTAAGA-CATAGTTGGGCTATGGCAACATATGAAGTCTGCT-AGGACAGTAAACATGGAATTATA
*
18355186 TTGT
64 TTGC
* * ** *
18355190 GTAAGACCATAGCTGGGCTATGGTAGTATATGAAGTCCGCTAGGACA
1 GTAAGA-CATAGTTGGGCTATGGCAACATATGAAGTCTGCTAGGACA
18355237 AAGAACCAGG
Statistics
Matches: 195, Mismatches: 48, Indels: 14
0.76 0.19 0.05
Matches are distributed among these distances:
66 1 0.01
67 50 0.26
68 140 0.72
69 4 0.02
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.28
Consensus pattern (67 bp):
GTAAGACATAGTTGGGCTATGGCAACATATGAAGTCTGCTAGGACAGTAAACATGGAATTATATT
GC
Found at i:18358137 original size:9 final size:9
Alignment explanation
Indices: 18358122--18358223 Score: 134
Period size: 9 Copynumber: 11.4 Consensus size: 9
18358112 TTTGGTTAAA
18358122 AATTAACCG
1 AATTAACCG
*
18358131 GATTAACCG
1 AATTAACCG
18358140 AATTAACC-
1 AATTAACCG
*
18358148 AATTACCCG
1 AATTAACCG
18358157 AATTAACCG
1 AATTAACCG
*
18358166 AATTACCCG
1 AATTAACCG
*
18358175 AATTACCCG
1 AATTAACCG
18358184 AATTAACCG
1 AATTAACCG
*
18358193 AATTACCCG
1 AATTAACCG
*
18358202 AATTAACCA
1 AATTAACCG
*
18358211 AATTAACCA
1 AATTAACCG
18358220 AATT
1 AATT
18358224 GAATCACTAC
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
8 7 0.08
9 76 0.92
ACGTcount: A:0.42, C:0.25, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:18364228 original size:3 final size:3
Alignment explanation
Indices: 18364215--18364245 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
18364205 TTTAGTCCCG
18364215 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
18364246 GCTATGTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:18369506 original size:42 final size:42
Alignment explanation
Indices: 18369447--18369530 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
18369437 GTTGAACCTA
*
18369447 GGAAAAAGGTTAAAAGCTATTCTTCAGGGTCGGATGTACCGG
1 GGAAAAAGGTTAAAAGCTATTCTTCAGGGGCGGATGTACCGG
18369489 GGAAAAAGGTTAAAAGCTATTCTTCAGGGGCGGATGTACCGG
1 GGAAAAAGGTTAAAAGCTATTCTTCAGGGGCGGATGTACCGG
18369531 AAACAAATGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.31, C:0.14, G:0.32, T:0.23
Consensus pattern (42 bp):
GGAAAAAGGTTAAAAGCTATTCTTCAGGGGCGGATGTACCGG
Found at i:18371259 original size:46 final size:44
Alignment explanation
Indices: 18371188--18371488 Score: 197
Period size: 46 Copynumber: 6.8 Consensus size: 44
18371178 AGTAGATCGC
* *
18371188 ATCAGGTCTTATCTCCCTAAGGTTACAGTGGAGTAGACCGAAGA
1 ATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGA
* **
18371232 ATTTCAGGTCTTATCTCCCTGATGTTACAGTGGAGCAGATTGAAGCA
1 A--TCAGGTCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAG-A
* * * * *
18371279 A-GAGATCTTATCTCCTTGAGATTACAATGGAGCAGATCC-AAGA
1 ATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGCAGA-CCGAAGA
* * * **
18371322 CA-CA-ATCCTATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-A
1 -ATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGA
* * * * ** * * *
18371363 ATAAAGGATCTTATCTCTCTAAAGTTACAGCAGAGTAGATC---GC
1 AT-CAGG-TCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGA
* * *
18371406 ATCAGGTCTTATCTCCCTGAGGTTAAATTGGAGTAGACCGAAGA
1 ATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGA
* *
18371450 ATTTCAGATTTTATCTCCCTGAGGTTACAGTGGAGCAGA
1 A--TCAGGTCTTATCTCCCTGAGGTTACAGTGGAGCAGA
18371489 TTGAAGCTAG
Statistics
Matches: 195, Mismatches: 45, Indels: 32
0.72 0.17 0.12
Matches are distributed among these distances:
40 1 0.01
41 26 0.13
42 6 0.03
43 32 0.16
44 60 0.31
46 68 0.35
47 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
ATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGA
Found at i:18371304 original size:44 final size:44
Alignment explanation
Indices: 18371062--18371520 Score: 221
Period size: 44 Copynumber: 10.5 Consensus size: 44
18371052 GAAAAATTTC
* * * **
18371062 AGATCTTATCTCTCTGAGATTACAGCGGAGCAGATTGAAGCTGG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGCAAG
* ** ** **
18371106 TAG-TCTTATCTCCCTGAGATTACAGTGGGGTGGATTAAAATAA-
1 -AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGCAAG
* ** * * *
18371149 AGGATCTTATCTCTCTGA-AGTTACAGCAGAGTAGATCGCATC-AG
1 A-GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGCAAG
* * * * *
18371193 -G-TCTTATCTCCCTAAGGTTACAGTGGAGTAGACCGAAG-AATTTC
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGCAA---G
* *
18371237 AGGTCTTATCTCCCTGATG-TTACAGTGGAGCAGATTGAAGCAAG
1 AGATCTTATCTCCCTGA-GATTACAGTGGAGCAGATCGAAGCAAG
* * * *
18371281 AGATCTTATCTCCTTGAGATTACAATGGAGCAGATCCAAG-ACAC
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGCA-AG
* ** **
18371325 A-ATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAA-
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGCAAG
* * ** * * *
18371367 AGGATCTTATCTCTCT-AAAGTTACAGCAGAGTAGATCGCATC-AG
1 A-GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGCAAG
* * * * * *
18371411 -G-TCTTATCTCCCTGAGGTTAAATTGGAGTAGACCGAAG-AATTTC
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGCAA---G
* * * *
18371455 AGATTTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCTAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGCAAG
*
18371499 AGATCTTATTTCCCTGAGATTA
1 AGATCTTATCTCCCTGAGATTA
18371521 TAACGGAATA
Statistics
Matches: 307, Mismatches: 79, Indels: 57
0.69 0.18 0.13
Matches are distributed among these distances:
41 55 0.18
42 5 0.02
43 41 0.13
44 136 0.44
45 4 0.01
46 62 0.20
47 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (44 bp):
AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGCAAG
Found at i:18371345 original size:43 final size:44
Alignment explanation
Indices: 18371243--18371358 Score: 139
Period size: 43 Copynumber: 2.7 Consensus size: 44
18371233 TTTCAGGTCT
** * *
18371243 TATCTCCCTGATG-TTACAGTGGAGCAGATTGAAGCAAGAGATCT
1 TATCTCCCTGA-GATTACAGTGGAGCAGATCCAAGCAACAGATCC
* *
18371287 TATCTCCTTGAGATTACAATGGAGCAGATCCAAG-ACACA-ATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGATCCAAGCA-ACAGATCC
18371330 TATCTCCCTGAGATTACAGTGGAGCAGAT
1 TATCTCCCTGAGATTACAGTGGAGCAGAT
18371359 TAAAATAAAG
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
43 32 0.52
44 30 0.48
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (44 bp):
TATCTCCCTGAGATTACAGTGGAGCAGATCCAAGCAACAGATCC
Found at i:18371403 original size:87 final size:87
Alignment explanation
Indices: 18371243--18371403 Score: 193
Period size: 87 Copynumber: 1.9 Consensus size: 87
18371233 TTTCAGGTCT
* * ** **
18371243 TATCTCCCTGATGTTACAGTGGAGCAGATTGAAGCAAGAGATCTTATCTCCTTGAGATTACAATG
1 TATCTCCCTGATGTTACAGTGGAGCAGATTAAAGAAAGAGATCTTATCTCCTAAAGATTACAACA
18371308 GAGCAGATCCAAGACACAATCC
66 GAGCAGATCCAAGACACAATCC
*
18371330 TATCTCCCTGA-GATTACAGTGGAGCAGATTAAAATAAAG-GATCTTATCTCTCTAAAG-TTACA
1 TATCTCCCTGATG-TTACAGTGGAGCAGATT-AAAGAAAGAGATCTTATCTC-CTAAAGATTACA
* *
18371392 GCAGAGTAGATC
63 ACAGAGCAGATC
18371404 GCATCAGGTC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
86 1 0.02
87 52 0.84
88 9 0.15
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (87 bp):
TATCTCCCTGATGTTACAGTGGAGCAGATTAAAGAAAGAGATCTTATCTCCTAAAGATTACAACA
GAGCAGATCCAAGACACAATCC
Found at i:18371441 original size:218 final size:219
Alignment explanation
Indices: 18371062--18371622 Score: 777
Period size: 218 Copynumber: 2.6 Consensus size: 219
18371052 GAAAAATTTC
* * * ** * * * *
18371062 AGATCTTATCTCTCTGAGATTACAGCGGAGCAGATTGAAGCTGGTAGTCTTATCTCCCTGAGATT
1 AGATCTTATCTCCCTGAGATTACAACGGAACAGATCCAAGCTAGCAATCCTATCTCCCTGAGATT
*
18371127 ACAGTGGGGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCA
66 ACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCA
* * *
18371192 GGTCTTATCTCCCTAAGGTTACAGTGGAGTAGACCGAAGAATTTCAGGTCTTATCTCCCTGATGT
131 GGTCTTATCTCCCTAAGGTTAAAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGT
18371257 TACAGTGGAGCAGATTGAAGCAAG
196 TACAGTGGAGCAGATTGAAGCAAG
* * *
18371281 AGATCTTATCTCCTTGAGATTACAATGGAGCAGATCCAAGAC-A-CAATCCTATCTCCCTGAGAT
1 AGATCTTATCTCCCTGAGATTACAACGGAACAGATCCAAG-CTAGCAATCCTATCTCCCTGAGAT
** *
18371344 TACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGCAGAGTAGATCGCATC
65 TACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATC
* * *
18371409 AGGTCTTATCTCCCTGAGGTTAAATTGGAGTAGACCGAAGAATTTCAGATTTTATCTCCCTGAGG
130 AGGTCTTATCTCCCTAAGGTTAAAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGG
*
18371474 TTACAGTGGAGCAGATTGAAGCTAG
195 TTACAGTGGAGCAGATTGAAGCAAG
* * * ** * * *
18371499 AGATCTTATTTCCCTGAGATTATAACGGAATAGATTGAAGCTAGTAATCCTAACTCTCTGA-AGT
1 AGATCTTATCTCCCTGAGATTACAACGGAACAGATCCAAGCTAGCAATCCTATCTCCCTGAGA-T
* * *
18371563 TACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTTTGAAGTTACAGTAGAATAGATC
65 TACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATC
18371623 ACATTAGATT
Statistics
Matches: 300, Mismatches: 38, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
217 1 0.00
218 195 0.65
219 103 0.34
220 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (219 bp):
AGATCTTATCTCCCTGAGATTACAACGGAACAGATCCAAGCTAGCAATCCTATCTCCCTGAGATT
ACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCATCA
GGTCTTATCTCCCTAAGGTTAAAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGGT
TACAGTGGAGCAGATTGAAGCAAG
Found at i:18371882 original size:129 final size:129
Alignment explanation
Indices: 18371642--18371960 Score: 460
Period size: 129 Copynumber: 2.5 Consensus size: 129
18371632 TGAAGCCGAT
* ** * *
18371642 AATCCTGTCTCCCTAAAGTTACATGTGGAGTGGATTAAAACCACAAATCTTATCTCTCTGAAGTT
1 AATCCTATCTCCCTAAAGTTACA-GTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTT
* * * *
18371707 GCAGTAGAGCAGATTACATCCAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACGAAAGAAATC
65 ACAGTAGAGCAGATCACATCCAGTCTTATCTCTCTGAAGTTACAGTGGAGCAGACGAAAGAAATA
* *
18371772 AATCCTATCTCCCTAAAGTTACAGTGAAGCAGATTAAAATCACAGATCTTATCTCTCTAAAGTTA
1 AATCCTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTA
* * * *
18371837 CAGTAGAGTAGATCGCAT-CAGGTCTTATCTCTTTGAGGTTACAGTGGAGCAGACGAAAGAAATA
66 CAGTAGAGCAGATCACATCCA-GTCTTATCTCTCTGAAGTTACAGTGGAGCAGACGAAAGAAATA
* *
18371901 AATCCTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAACCATAGATCTTATCTCCCTAA
1 AATCCTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAA
18371961 GCAGTAGTGG
Statistics
Matches: 169, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
128 2 0.01
129 145 0.86
130 22 0.13
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (129 bp):
AATCCTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTAAAGTTA
CAGTAGAGCAGATCACATCCAGTCTTATCTCTCTGAAGTTACAGTGGAGCAGACGAAAGAAATA
Found at i:18371954 original size:44 final size:44
Alignment explanation
Indices: 18371649--18371960 Score: 196
Period size: 44 Copynumber: 7.2 Consensus size: 44
18371639 GATAATCCTG
** * *
18371649 TCTCCCTAAAGTTACATGTGGAGTGGATTAAAACCACAAATCTTA
1 TCTCCCTAAAGTTACA-GTGGAGCAGATTAAAACCATAGATCTTA
* * * * * *
18371694 TCTCTCTGAAGTTGCAGTAGAGCAGATTACATCC--AG-TCTTA
1 TCTCCCTAAAGTTACAGTGGAGCAGATTAAAACCATAGATCTTA
* * * ** * *
18371735 TCTCTCTGAAGTTGCAGTGGAGCAGACGAAAGA-AATCA-ATCCTA
1 TCTCCCTAAAGTTACAGTGGAGCAGATTAAA-ACCAT-AGATCTTA
* * *
18371779 TCTCCCTAAAGTTACAGTGAAGCAGATTAAAATCACAGATCTTA
1 TCTCCCTAAAGTTACAGTGGAGCAGATTAAAACCATAGATCTTA
* * * *
18371823 TCTCTCTAAAGTTACAGT--AG-AG--TAGATCGCATCAGGTCTTA
1 TCTCCCTAAAGTTACAGTGGAGCAGATTAAAAC-CAT-AGATCTTA
** * * ** * * *
18371864 TCTCTTTGAGGTTACAGTGGAGCAGACGAAAGA-AATAAATCCTA
1 TCTCCCTAAAGTTACAGTGGAGCAGATTAAA-ACCATAGATCTTA
18371908 TCTCCCTAAAGTTACAGTGGAGCAGATTAAAACCATAGATCTTA
1 TCTCCCTAAAGTTACAGTGGAGCAGATTAAAACCATAGATCTTA
18371952 TCTCCCTAA
1 TCTCCCTAA
18371961 GCAGTAGTGG
Statistics
Matches: 201, Mismatches: 50, Indels: 33
0.71 0.18 0.12
Matches are distributed among these distances:
39 3 0.01
40 2 0.01
41 56 0.28
42 3 0.01
43 5 0.02
44 115 0.57
45 15 0.07
46 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (44 bp):
TCTCCCTAAAGTTACAGTGGAGCAGATTAAAACCATAGATCTTA
Found at i:18372828 original size:5 final size:6
Alignment explanation
Indices: 18372800--18372826 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
18372790 GTTTGTTTCA
18372800 TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT
18372827 ATCTTCTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:18373508 original size:24 final size:24
Alignment explanation
Indices: 18373456--18373509 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
18373446 CATTTTTATA
*
18373456 ATATATATATATGTCTATAAATTT
1 ATATATATATATGTCTATAAATTC
*
18373480 TTATATATATATGTAC-AT-AATTAC
1 ATATATATATATGT-CTATAAATT-C
18373504 ATATAT
1 ATATAT
18373510 TATTTATACT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 4 0.16
24 20 0.80
25 1 0.04
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.48
Consensus pattern (24 bp):
ATATATATATATGTCTATAAATTC
Found at i:18373746 original size:28 final size:27
Alignment explanation
Indices: 18373691--18373752 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 27
18373681 CATGTATCTC
18373691 TTTTATAAATATACATACACGTACATAT
1 TTTTATAAATATACATACAC-TACATAT
*
18373719 TTTTATAAATATATATACA-TACTTATAT
1 TTTTATAAATATACATACACTAC--ATAT
18373747 TTTTAT
1 TTTTAT
18373753 TTTATAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 3 0.10
28 28 0.90
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (27 bp):
TTTTATAAATATACATACACTACATAT
Found at i:18380510 original size:16 final size:17
Alignment explanation
Indices: 18380489--18380525 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
18380479 GAAATAGCAG
*
18380489 AAATAAAAATTTAAA-T
1 AAATAAAAAATTAAATT
18380505 AAATAAAAAATTAAATT
1 AAATAAAAAATTAAATT
18380522 AAAT
1 AAAT
18380526 TGGAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATAAAAAATTAAATT
Found at i:18382151 original size:7 final size:7
Alignment explanation
Indices: 18382141--18382176 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
18382131 TTTTAAAATG
18382141 CATTTCC
1 CATTTCC
18382148 CATTTCC
1 CATTTCC
18382155 CATTTCC
1 CATTTCC
18382162 CATTTCC
1 CATTTCC
18382169 CATTTCC
1 CATTTCC
18382176 C
1 C
18382177 TAAGCCCGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.14, C:0.44, G:0.00, T:0.42
Consensus pattern (7 bp):
CATTTCC
Found at i:18383074 original size:54 final size:54
Alignment explanation
Indices: 18383012--18383119 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
18383002 TTTCATTGGG
18383012 TTGTTTTTAGTTTCAAGGAAGAAAATGACAAACTTGGTAAGAGAGAGATCGGAA
1 TTGTTTTTAGTTTCAAGGAAGAAAATGACAAACTTGGTAAGAGAGAGATCGGAA
*
18383066 TTGTTTTTAGTTTCAAGGAAGAAAATGACAAACTTGGTAAGAGAGAGATTGGAA
1 TTGTTTTTAGTTTCAAGGAAGAAAATGACAAACTTGGTAAGAGAGAGATCGGAA
18383120 GAGTAGATTG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (54 bp):
TTGTTTTTAGTTTCAAGGAAGAAAATGACAAACTTGGTAAGAGAGAGATCGGAA
Found at i:18392686 original size:65 final size:65
Alignment explanation
Indices: 18392582--18392711 Score: 251
Period size: 65 Copynumber: 2.0 Consensus size: 65
18392572 ATAGAAAATA
*
18392582 GGAAAATGGTATTCATCAGCTATTGCCTATTGTATCCTGGTTATTTCTATATTATCCTTTCTTTC
1 GGAAAATGGTATTCATCAGCTATTGCCTATTGTATCCTGGTTATTTCTATATTATCCTTACTTTC
18392647 GGAAAATGGTATTCATCAGCTATTGCCTATTGTATCCTGGTTATTTCTATATTATCCTTACTTTC
1 GGAAAATGGTATTCATCAGCTATTGCCTATTGTATCCTGGTTATTTCTATATTATCCTTACTTTC
18392712 CCTATTTGGG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.45
Consensus pattern (65 bp):
GGAAAATGGTATTCATCAGCTATTGCCTATTGTATCCTGGTTATTTCTATATTATCCTTACTTTC
Found at i:18396656 original size:20 final size:21
Alignment explanation
Indices: 18396621--18396659 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
18396611 TGAAGTAAGT
18396621 TTGAAATGGAAAAGTATTGGA
1 TTGAAATGGAAAAGTATTGGA
*
18396642 TTGAAAT-GTAAAGTATTG
1 TTGAAATGGAAAAGTATTG
18396660 CATGGTATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.26, T:0.33
Consensus pattern (21 bp):
TTGAAATGGAAAAGTATTGGA
Found at i:18415025 original size:17 final size:17
Alignment explanation
Indices: 18414991--18415032 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
18414981 ACAAACTAAT
* **
18414991 TATTTTATCATTTTATA
1 TATTTTATAATTCAATA
18415008 TATTTTATAATTCAATA
1 TATTTTATAATTCAATA
18415025 T-TTTTATA
1 TATTTTATA
18415033 TGATTTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTTTATAATTCAATA
Found at i:18418689 original size:23 final size:23
Alignment explanation
Indices: 18418634--18418691 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
18418624 TCGAATACGT
*
18418634 CACAAAGGCCAATCAAAATACAC
1 CACAAAGGCTAATCAAAATACAC
*
18418657 CACAAAGGCTAATCATAATACAC
1 CACAAAGGCTAATCAAAATACAC
*
18418680 TACAAAGGCTAA
1 CACAAAGGCTAA
18418692 CACAAAGGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.50, C:0.26, G:0.10, T:0.14
Consensus pattern (23 bp):
CACAAAGGCTAATCAAAATACAC
Found at i:18418703 original size:35 final size:35
Alignment explanation
Indices: 18418657--18418726 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
18418647 CAAAATACAC
* *
18418657 CACAAAGGCTAATCATAATACACTACAAAGGCTAA
1 CACAAAGGCTAATCAGAATACACCACAAAGGCTAA
*
18418692 CACAAAGGCTAATCAGAATACGCCACAAAGGCTAA
1 CACAAAGGCTAATCAGAATACACCACAAAGGCTAA
18418727 TCAGAATACG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.47, C:0.24, G:0.14, T:0.14
Consensus pattern (35 bp):
CACAAAGGCTAATCAGAATACACCACAAAGGCTAA
Found at i:18418722 original size:23 final size:23
Alignment explanation
Indices: 18418692--18418770 Score: 131
Period size: 23 Copynumber: 3.4 Consensus size: 23
18418682 CAAAGGCTAA
18418692 CACAAAGGCTAATCAGAATACGC
1 CACAAAGGCTAATCAGAATACGC
18418715 CACAAAGGCTAATCAGAATACGC
1 CACAAAGGCTAATCAGAATACGC
* * *
18418738 CACAAAGACTAATCATAATACAC
1 CACAAAGGCTAATCAGAATACGC
18418761 CACAAAGGCT
1 CACAAAGGCT
18418771 CTATTTGGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.46, C:0.27, G:0.14, T:0.14
Consensus pattern (23 bp):
CACAAAGGCTAATCAGAATACGC
Found at i:18418724 original size:58 final size:58
Alignment explanation
Indices: 18418634--18418749 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 58
18418624 TCGAATACGT
* * *
18418634 CACAAAGGCCAATCAAAATACACCACAAAGGCTAATCATAATACACTACAAAGGCTAA
1 CACAAAGGCCAATCAAAATACACCACAAAGGCTAATCAGAATACACCACAAAGACTAA
* * * *
18418692 CACAAAGGCTAATCAGAATACGCCACAAAGGCTAATCAGAATACGCCACAAAGACTAA
1 CACAAAGGCCAATCAAAATACACCACAAAGGCTAATCAGAATACACCACAAAGACTAA
18418750 TCATAATACA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.48, C:0.26, G:0.13, T:0.13
Consensus pattern (58 bp):
CACAAAGGCCAATCAAAATACACCACAAAGGCTAATCAGAATACACCACAAAGACTAA
Found at i:18419569 original size:28 final size:28
Alignment explanation
Indices: 18419472--18419569 Score: 90
Period size: 28 Copynumber: 3.5 Consensus size: 28
18419462 AAATTAACGC
** *
18419472 GCTTATCG-TATTATTCCGCACTTCAAT
1 GCTTATCGTTATTATTTTGCACTTCGAT
** * *
18419499 GCTTATCGTTGTAAAAATTTGCAGTTCGAT
1 GCTTATCG-T-TATTATTTTGCACTTCGAT
* *
18419529 GCTTATCGATATTATTTTGCACTTCGGT
1 GCTTATCGTTATTATTTTGCACTTCGAT
18419557 GCTTATCGTTATT
1 GCTTATCGTTATT
18419570 TACACTTTGT
Statistics
Matches: 54, Mismatches: 14, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
27 8 0.15
28 26 0.48
30 20 0.37
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.44
Consensus pattern (28 bp):
GCTTATCGTTATTATTTTGCACTTCGAT
Found at i:18429564 original size:43 final size:42
Alignment explanation
Indices: 18429512--18429792 Score: 285
Period size: 43 Copynumber: 6.6 Consensus size: 42
18429502 GGCAAATCAA
*
18429512 ATGCACAACATATTTGCAAATAAAAATTTCCATTAGGTTGTGG
1 ATGCACAACATATTTGCAAATAAAAATTT-CACTAGGTTGTGG
* * * * * *
18429555 ATGTACAACATATTTGTAGATAAAAACTGTAACTGGGTTGTGG
1 ATGCACAACATATTTGCAAATAAAAA-TTTCACTAGGTTGTGG
* * * **
18429598 ATGCACAACATATTTACAGAT-AAACTGCCACTAGGTTGTGG
1 ATGCACAACATATTTGCAAATAAAAATTTCACTAGGTTGTGG
* * *
18429639 ATGCACAACATATTTTCAAAAAAAAAATTGTCATTAGGTTGTGG
1 ATGCACAACATATTTGC-AAATAAAAATT-TCACTAGGTTGTGG
*
18429683 TTGCACAACATATTTGCAAATAAAAATTTTCACTAGGTTGTGG
1 ATGCACAACATATTTGCAAATAAAAA-TTTCACTAGGTTGTGG
* ** * * *
18429726 TTGCACAACATATTTGCAGCTAAAAATTGTCACTGGGCTATGG
1 ATGCACAACATATTTGCAAATAAAAATT-TCACTAGGTTGTGG
* *
18429769 ATGCACAGCATATTTGCAGATAAA
1 ATGCACAACATATTTGCAAATAAA
18429793 CTGTCACTCT
Statistics
Matches: 199, Mismatches: 33, Indels: 12
0.82 0.14 0.05
Matches are distributed among these distances:
41 29 0.15
42 7 0.04
43 132 0.66
44 31 0.16
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (42 bp):
ATGCACAACATATTTGCAAATAAAAATTTCACTAGGTTGTGG
Found at i:18429691 original size:128 final size:127
Alignment explanation
Indices: 18429512--18429786 Score: 336
Period size: 128 Copynumber: 2.1 Consensus size: 127
18429502 GGCAAATCAA
* * * *
18429512 ATGCACAACATATTTGCAAATAAAAATTTCCATTAGGTTGTGGATGTACAACATATTTGTAGATA
1 ATGCACAACATATTTGCAAAAAAAAATTTCCATTAGGTTGTGGATGCACAACATATTTGCAAATA
*
18429577 AAAACTGTAACTGGGTTGTGGATGCACAACATATTTACAGATAAACTGCCACTAGGTTGTGG
66 AAAACTGTAACTAGGTTGTGGATGCACAACATATTTACAGATAAACTGCCACTAGGTTGTGG
* *
18429639 ATGCACAACATATTTTCAAAAAAAAAATTGT-CATTAGGTTGTGGTTGCACAACATATTTGCAAA
1 ATGCACAACATATTTGC-AAAAAAAAATT-TCCATTAGGTTGTGGATGCACAACATATTTGCAAA
* * * * * * * * * * *
18429703 TAAAAATTTTCACTAGGTTGTGGTTGCACAACATATTTGCAGCTAAAAATTGTCACTGGGCTATG
64 TAAAAACTGTAACTAGGTTGTGGATGCACAACATATTTACAG--ATAAACTGCCACTAGGTTGTG
18429768 G
127 G
*
18429769 ATGCACAGCATATTTGCA
1 ATGCACAACATATTTGCA
18429787 GATAAACTGT
Statistics
Matches: 124, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
127 16 0.13
128 75 0.60
129 2 0.02
130 31 0.25
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (127 bp):
ATGCACAACATATTTGCAAAAAAAAATTTCCATTAGGTTGTGGATGCACAACATATTTGCAAATA
AAAACTGTAACTAGGTTGTGGATGCACAACATATTTACAGATAAACTGCCACTAGGTTGTGG
Found at i:18433471 original size:18 final size:19
Alignment explanation
Indices: 18433428--18433471 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
18433418 TTGTTGAGTT
* *
18433428 TATTAATGAGTATTTTATA
1 TATTGATGACTATTTTATA
18433447 TAATTGATGACTATTTTATA
1 T-ATTGATGACTATTTTATA
18433467 T-TTGA
1 TATTGA
18433472 ATTATTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 1 0.05
20 17 0.77
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.52
Consensus pattern (19 bp):
TATTGATGACTATTTTATA
Found at i:18442429 original size:19 final size:19
Alignment explanation
Indices: 18442405--18442448 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
18442395 AAATTTCAGA
18442405 ATTTTTAAAGTTTTTTT-AT
1 ATTTTTAAA-TTTTTTTAAT
18442424 ATTTTTAAATTTTTTTAAT
1 ATTTTTAAATTTTTTTAAT
18442443 ATTTTT
1 ATTTTT
18442449 TTTCAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
ATTTTTAAATTTTTTTAAT
Found at i:18443081 original size:17 final size:17
Alignment explanation
Indices: 18443055--18443088 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18443045 AAACTTTTAA
*
18443055 TTTTTGCTCAAAAATAT
1 TTTTTACTCAAAAATAT
18443072 TTTTTACTCAAAAATAT
1 TTTTTACTCAAAAATAT
18443089 ATTTGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTTTACTCAAAAATAT
Found at i:18445629 original size:14 final size:15
Alignment explanation
Indices: 18445607--18445644 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
18445597 CAATCAAACA
18445607 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
18445621 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
18445636 ACAGAAAAT
1 CCAGAAAAT
18445645 TAAAACATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:18445678 original size:34 final size:35
Alignment explanation
Indices: 18445611--18445676 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
18445601 CAAACACCAG
*
18445611 AAAATATTTTCCAGTAAATCATTTTACAGAAAATT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAATT
*
18445646 AAAACATTTTCCCG-AAATCATTTTAC-GAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
18445677 ATATTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.41
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAATT
Found at i:18458368 original size:39 final size:40
Alignment explanation
Indices: 18458325--18458492 Score: 148
Period size: 40 Copynumber: 4.2 Consensus size: 40
18458315 CTCGTTCAAG
* * * *
18458325 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGGATTATA-AAACTCACACGAA
* *
18458364 TGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
* * *
18458404 TGCCTTCGGGACTTAACCCGGAATTAGT--ATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTA-TAAAACTCACACGAA
* * * *
18458444 GGCCTTCGGGACTTAACCCGGAATTA-ATAACTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTATAAAACTCACACGAA
18458484 TGCCTTCGG
1 TGCCTTCGG
18458493 ATCTTAGTCC
Statistics
Matches: 111, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
39 26 0.23
40 81 0.73
41 3 0.03
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
Found at i:18458476 original size:80 final size:80
Alignment explanation
Indices: 18458360--18458545 Score: 229
Period size: 80 Copynumber: 2.3 Consensus size: 80
18458350 AGTAACTCAT
* * *
18458360 ACAATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTC-GGATCTTAACCCG
*
18458424 GA-ATTAGT-A-TCTCGC
65 GATA-TAGTCACT-TAGC
**
18458439 ACAAAGGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATGCCTTCGGATCTTAGTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATGCCTTCGGATCTTAACCC
18458503 GGATATAGTCACTTAGC
64 GGATATAGTCACTTAGC
*
18458520 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
18458546 CAGCATTCAA
Statistics
Matches: 94, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
79 11 0.12
80 72 0.77
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTCACTTAGC
Found at i:18458505 original size:40 final size:40
Alignment explanation
Indices: 18458362--18458545 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
18458352 TAACTCATAC
* *
18458362 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
18458402 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
18458442 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
18458482 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
18458523 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
18458546 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
39 8 0.06
40 105 0.85
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:18463551 original size:29 final size:29
Alignment explanation
Indices: 18463508--18463563 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
18463498 ATAGGGACCT
18463508 GATCAAATTAATCATTCTACTATTAAATG
1 GATCAAATTAATCATTCTACTATTAAATG
* * * *
18463537 GATCAATTTAGTCATTTTACTTTTAAA
1 GATCAAATTAATCATTCTACTATTAAA
18463564 AAGAATCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (29 bp):
GATCAAATTAATCATTCTACTATTAAATG
Found at i:18467568 original size:26 final size:26
Alignment explanation
Indices: 18467539--18467591 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
18467529 CATCCATGAC
18467539 TTAGTGAATAATTTAACCTTAATTTA
1 TTAGTGAATAATTTAACCTTAATTTA
*
18467565 TTAGTGAATAATTTAAGCTTAATTTA
1 TTAGTGAATAATTTAACCTTAATTTA
18467591 T
1 T
18467592 GTAAGTTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (26 bp):
TTAGTGAATAATTTAACCTTAATTTA
Found at i:18471110 original size:20 final size:20
Alignment explanation
Indices: 18471085--18471131 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
18471075 TTAGATTAGA
* *
18471085 TTAAAAGGGTATTTTTATGT
1 TTAAAAGAGTATTTTTAGGT
*
18471105 TTAAAAATAGTATTTTTAGGT
1 TT-AAAAGAGTATTTTTAGGT
18471126 TTAAAA
1 TTAAAA
18471132 ATTGGGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (20 bp):
TTAAAAGAGTATTTTTAGGT
Found at i:18471117 original size:21 final size:21
Alignment explanation
Indices: 18471093--18471133 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
18471083 GATTAAAAGG
*
18471093 GTATTTTTATGTTTAAAAATA
1 GTATTTTTAGGTTTAAAAATA
18471114 GTATTTTTAGGTTTAAAAAT
1 GTATTTTTAGGTTTAAAAAT
18471134 TGGGTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (21 bp):
GTATTTTTAGGTTTAAAAATA
Found at i:18481329 original size:18 final size:18
Alignment explanation
Indices: 18481306--18481343 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
18481296 CAAAAGTGTT
18481306 AATTAACAAGAAATATTG
1 AATTAACAAGAAATATTG
18481324 AATTAACAAGAAATATTG
1 AATTAACAAGAAATATTG
18481342 AA
1 AA
18481344 AGTTGTAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.58, C:0.05, G:0.11, T:0.26
Consensus pattern (18 bp):
AATTAACAAGAAATATTG
Found at i:18482700 original size:33 final size:33
Alignment explanation
Indices: 18482663--18482728 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
18482653 CAGATGATAC
18482663 TCGATAATAACATAATAGTTCAGATAAGATGCA
1 TCGATAATAACATAATAGTTCAGATAAGATGCA
18482696 TCGATAATAACATAATAGTTCAGATAAGATGCA
1 TCGATAATAACATAATAGTTCAGATAAGATGCA
18482729 AAACAGGTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.27
Consensus pattern (33 bp):
TCGATAATAACATAATAGTTCAGATAAGATGCA
Found at i:18483044 original size:7 final size:7
Alignment explanation
Indices: 18483034--18483063 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
18483024 ATGCAGATTA
18483034 CAGATAT
1 CAGATAT
18483041 CAGATAT
1 CAGATAT
18483048 CAGATAT
1 CAGATAT
18483055 CAGATAT
1 CAGATAT
18483062 CA
1 CA
18483064 ATTATGTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (7 bp):
CAGATAT
Found at i:18484804 original size:70 final size:69
Alignment explanation
Indices: 18484683--18484820 Score: 231
Period size: 70 Copynumber: 2.0 Consensus size: 69
18484673 ATCTTGAGAT
* *
18484683 AATATGAACATGTTTTAAAATAATACATTTTGTCTAATTATCCAAACTCTCCTTTTAAAGCTAAA
1 AATATGAACATATCTTAAAATAATACATTTTGTCTAATTATCCAAACTCTCCTTTTAAAGCTAAA
18484748 AGAC
66 AGAC
* *
18484752 AATATGAACATATCTTAAAATAATACTTTTTTGTCTAATTATCCAAAGTCTCCTTTTAAAGCTAA
1 AATATGAACATATCTTAAAATAATAC-ATTTTGTCTAATTATCCAAACTCTCCTTTTAAAGCTAA
18484817 AAGA
65 AAGA
18484821 ATAGAAAGAT
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
69 24 0.38
70 40 0.62
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (69 bp):
AATATGAACATATCTTAAAATAATACATTTTGTCTAATTATCCAAACTCTCCTTTTAAAGCTAAA
AGAC
Found at i:18487494 original size:27 final size:27
Alignment explanation
Indices: 18487456--18487515 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
18487446 ATAGGTGGTG
18487456 CCTATCTAGTAGGCACCACTGGCGACT
1 CCTATCTAGTAGGCACCACTGGCGACT
* * *
18487483 CCTATCTGGTAGGCGCCACTGGTGACT
1 CCTATCTAGTAGGCACCACTGGCGACT
18487510 CCTATC
1 CCTATC
18487516 AATAAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.18, C:0.33, G:0.23, T:0.25
Consensus pattern (27 bp):
CCTATCTAGTAGGCACCACTGGCGACT
Found at i:18487563 original size:15 final size:15
Alignment explanation
Indices: 18487539--18487572 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
18487529 AAATAAAAAT
18487539 AAAATTACATT-ATA
1 AAAATTACATTAATA
18487553 AAAATTTACATTAATA
1 AAAA-TTACATTAATA
18487569 AAAA
1 AAAA
18487573 ATCACAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 7 0.39
16 7 0.39
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAATTACATTAATA
Found at i:18487698 original size:105 final size:102
Alignment explanation
Indices: 18487548--18487840 Score: 407
Period size: 105 Copynumber: 2.9 Consensus size: 102
18487538 TAAAATTACA
*
18487548 TTATAAAAATTTACATTAATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAAC
1 TTATAAAAATTTACATTACTAAAAAATCACAAAAC-CTAAACTAAACACTAACAATTTATA-AA-
*
18487613 CTAATCATAAATTACTAACAAAATAACTATAAAATCTTTTT
63 CTAATCATAAATTACTAACAAAATAACTATAAAAT-TTTTC
*
18487654 TTTTAAAAA-TTACATTACTAAAAAATCACAAAATCCTAAACTAAACACTAACAATTTATAAACT
1 TTATAAAAATTTACATTACTAAAAAATCACAAAA-CCTAAACTAAACACTAACAATTTATAAACT
* * *
18487718 AATAATAAATTACTAACAAAATGACTATAACATTTTTC
65 AATCATAAATTACTAACAAAATAACTATAAAATTTTTC
* * * *
18487756 TTAAAAATAATTTACATTACTAATAAATCACAAAA-C-ATA--AAACTCTAACAATTTATAAACT
1 TTATAAA-AATTTACATTACTAAAAAATCACAAAACCTAAACTAAACACTAACAATTTATAAACT
18487817 AATCATAAATTACTAACAAAATAA
65 AATCATAAATTACTAACAAAATAA
18487841 TATTACATTA
Statistics
Matches: 171, Mismatches: 13, Indels: 13
0.87 0.07 0.07
Matches are distributed among these distances:
99 43 0.25
101 2 0.01
102 10 0.06
103 34 0.20
104 25 0.15
105 48 0.28
106 9 0.05
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (102 bp):
TTATAAAAATTTACATTACTAAAAAATCACAAAACCTAAACTAAACACTAACAATTTATAAACTA
ATCATAAATTACTAACAAAATAACTATAAAATTTTTC
Found at i:18500525 original size:18 final size:17
Alignment explanation
Indices: 18500504--18500542 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
18500494 ATTTTTGAAG
18500504 TTTAGAGAATTTTAATTT
1 TTTA-AGAATTTTAATTT
* *
18500522 TTTAATAATTTTACTTT
1 TTTAAGAATTTTAATTT
18500539 TTTA
1 TTTA
18500543 TTAAAATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (17 bp):
TTTAAGAATTTTAATTT
Found at i:18504809 original size:45 final size:45
Alignment explanation
Indices: 18504684--18504810 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 45
18504674 TACTAGAAAC
* * * *
18504684 GAGTAAAACCATAGCTAAAAAGACATTATGGCATCACGATTTTAAT
1 GAGTAAGACCATAGCT-AAAAGACGTTATGGCATCATGATTCTAAT
* * *
18504730 GAATAAGACC--AGCTGAAAGATGTTATGGCATCATGATTCTAAT
1 GAGTAAGACCATAGCTAAAAGACGTTATGGCATCATGATTCTAAT
* *
18504773 GAGTAAGACCATAGCTAAAAGACGCTATGACATCATGA
1 GAGTAAGACCATAGCTAAAAGACGTTATGGCATCATGA
18504811 ATCAGACGAA
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
43 33 0.49
44 4 0.06
45 22 0.33
46 8 0.12
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (45 bp):
GAGTAAGACCATAGCTAAAAGACGTTATGGCATCATGATTCTAAT
Found at i:18504874 original size:45 final size:45
Alignment explanation
Indices: 18504825--18504941 Score: 171
Period size: 45 Copynumber: 2.6 Consensus size: 45
18504815 GACGAACAAA
* * * *
18504825 ACCATTGTTAAAAGACACTATGGCATCAAATCGGGAATGAATAAG
1 ACCATGGTTGAAAGACACCATGGCATCAAATCAGGAATGAATAAG
* * *
18504870 ACCATGGTTGAAATACACCATGACATCAAGTCAGGAATGAATAAG
1 ACCATGGTTGAAAGACACCATGGCATCAAATCAGGAATGAATAAG
18504915 ACCATGGTTGAAAGACACCATGGCATC
1 ACCATGGTTGAAAGACACCATGGCATC
18504942 CTTCAACCAT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (45 bp):
ACCATGGTTGAAAGACACCATGGCATCAAATCAGGAATGAATAAG
Found at i:18506464 original size:20 final size:20
Alignment explanation
Indices: 18506425--18506466 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
18506415 GCATAATTGT
*
18506425 TTCTATTTTGATGTTGAATG
1 TTCTATTTTGATGGTGAATG
18506445 TTCTATTTTGTATGGT-AATG
1 TTCTATTTTG-ATGGTGAATG
18506465 TT
1 TT
18506467 TTGTAACCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.57
Consensus pattern (20 bp):
TTCTATTTTGATGGTGAATG
Found at i:18506998 original size:29 final size:29
Alignment explanation
Indices: 18506929--18507163 Score: 219
Period size: 29 Copynumber: 8.0 Consensus size: 29
18506919 ATTTTTGAAG
* *
18506929 AATAGTGCCAAAATTGTAAAATCT-GAAA
1 AATAGTGGCAAAACTGTAAAATCTAGAAA
*
18506957 AA-ACCTGTGGCAAAACTGTAAAGTCTAGAAA
1 AATA---GTGGCAAAACTGTAAAATCTAGAAA
18506988 AATAGTGGCAAAACTGTAAAATCTAGAAA
1 AATAGTGGCAAAACTGTAAAATCTAGAAA
* *
18507017 AATAGTGGCATAATTGTAAAATCTA-AAA
1 AATAGTGGCAAAACTGTAAAATCTAGAAA
* * * * * * *
18507045 AACCATTGTCACAATTATAAAATCTAAAAA
1 AA-TAGTGGCAAAACTGTAAAATCTAGAAA
* *
18507075 ATATAGTGTCAAAACTATAAAATCTA-AAA
1 A-ATAGTGGCAAAACTGTAAAATCTAGAAA
*
18507104 AACTAGTGGCACAACTGTAAAATCTAGAAA
1 AA-TAGTGGCAAAACTGTAAAATCTAGAAA
* *
18507134 ACACAGTGGCAAAATTGTAAAATCTA-AAA
1 A-ATAGTGGCAAAACTGTAAAATCTAGAAA
18507163 A
1 A
18507164 GTGACTGTGT
Statistics
Matches: 175, Mismatches: 21, Indels: 21
0.81 0.10 0.10
Matches are distributed among these distances:
27 1 0.01
28 8 0.05
29 93 0.53
30 64 0.37
31 8 0.05
32 1 0.01
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23
Consensus pattern (29 bp):
AATAGTGGCAAAACTGTAAAATCTAGAAA
Found at i:18507000 original size:59 final size:59
Alignment explanation
Indices: 18506931--18507163 Score: 233
Period size: 59 Copynumber: 4.0 Consensus size: 59
18506921 TTTTGAAGAA
* * *
18506931 TAGTGCCAAAATTGTAAAATCTGAAAAAACCT-GTGGCAAAACTGTAAAGTCTAGAAAAA-
1 TAGTGGCAAAACTGTAAAATCT-AAAAAACCTAGTGGCAAAACTGTAAAATCTA-AAAAAC
* *
18506990 TAGTGGCAAAACTGTAAAATCTAGAAAAA--TAGTGGCATAATTGTAAAATCTAAAAAAC
1 TAGTGGCAAAACTGTAAAATCTA-AAAAACCTAGTGGCAAAACTGTAAAATCTAAAAAAC
* * * * * * ** * *
18507048 CATTGTCACAATTATAAAATCTAAAAAATATAGTGTCAAAACTATAAAATCTAAAAAAC
1 TAGTGGCAAAACTGTAAAATCTAAAAAACCTAGTGGCAAAACTGTAAAATCTAAAAAAC
* * *
18507107 TAGTGGCACAACTGTAAAATCTAGAAAACAC-AGTGGCAAAATTGTAAAATCTAAAAA
1 TAGTGGCAAAACTGTAAAATCTAAAAAAC-CTAGTGGCAAAACTGTAAAATCTAAAAA
18507164 GTGACTGTGT
Statistics
Matches: 142, Mismatches: 26, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
57 11 0.08
58 36 0.25
59 95 0.67
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (59 bp):
TAGTGGCAAAACTGTAAAATCTAAAAAACCTAGTGGCAAAACTGTAAAATCTAAAAAAC
Found at i:18507033 original size:88 final size:86
Alignment explanation
Indices: 18506929--18507163 Score: 276
Period size: 88 Copynumber: 2.7 Consensus size: 86
18506919 ATTTTTGAAG
* * *
18506929 AATAGTGCCAAAATTGTAAAATCTGAAAAAACCTGTGGCAAAACTGTAAAGTCTAGAAAA-ATAG
1 AATAGTGGCAAAATTGTAAAATCT-AAAAAACCTGTGGCAAAATTGTAAAATCTA-AAAATATAG
*
18506993 TGGCAAAACTGTAAAATCTAGAAA
64 TGGCAAAACTATAAAATCTA-AAA
* * * *
18507017 AATAGTGGCATAATTGTAAAATCTAAAAAACCAT-TGTCACAATTATAAAATCTAAAAAATATAG
1 AATAGTGGCAAAATTGTAAAATCTAAAAAACC-TGTGGCAAAATTGTAAAATCT-AAAAATATAG
*
18507081 TGTCAAAACTATAAAATCTAAAA
64 TGGCAAAACTATAAAATCTAAAA
* * * *
18507104 AACTAGTGGCACAACTGTAAAATCTAGAAAACACAGTGGCAAAATTGTAAAATCTAAAAA
1 AA-TAGTGGCAAAATTGTAAAATCTAAAAAAC-CTGTGGCAAAATTGTAAAATCTAAAAA
18507164 GTGACTGTGT
Statistics
Matches: 125, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
87 31 0.25
88 77 0.62
89 17 0.14
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23
Consensus pattern (86 bp):
AATAGTGGCAAAATTGTAAAATCTAAAAAACCTGTGGCAAAATTGTAAAATCTAAAAATATAGTG
GCAAAACTATAAAATCTAAAA
Found at i:18516633 original size:138 final size:137
Alignment explanation
Indices: 18516386--18516639 Score: 366
Period size: 138 Copynumber: 1.8 Consensus size: 137
18516376 AGCCATAAAA
* * *
18516386 GGGTCTATTCACAAAAGCTGACAGTTGGAATATAGCTACACGATGTCGCTCACACAAGCTGACGA
1 GGGTCTACTCACAAAAGCTGACAGTCGGAATATAGCTACACAATGTCGCTCACACAAGCTGACGA
* *
18516451 GTATCCACAACAAATGACAGAACTCAACCATCGGTAGGACATTTAGGACCAGCACCCGAAACATG
66 GTATCCACAACAAATGACAGAACTCAACCATCGATAGAACATTTAGGACCAGCACCCGAAACATG
18516516 GTAACCT
131 GTAACCT
* * * *
18516523 GGGTCTACTCACACAAGCTGACGGTCGGAATATAAGCTACACAATG-CTGCTTACACAAGCTGAT
1 GGGTCTACTCACAAAAGCTGACAGTCGGAATAT-AGCTACACAATGTC-GCTCACACAAGCTGAC
* * * *
18516587 GAGTATCCATAACAAATGCCAGACCTCAGCCATCGATAGAACATTTAGGACCA
64 GAGTATCCACAACAAATGACAGAACTCAACCATCGATAGAACATTTAGGACCA
18516640 ACATTTGAAA
Statistics
Matches: 102, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
137 30 0.29
138 72 0.71
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (137 bp):
GGGTCTACTCACAAAAGCTGACAGTCGGAATATAGCTACACAATGTCGCTCACACAAGCTGACGA
GTATCCACAACAAATGACAGAACTCAACCATCGATAGAACATTTAGGACCAGCACCCGAAACATG
GTAACCT
Done.