Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 16 of 362
Found at i:5037221 original size:26 final size:26
Alignment explanation
Indices: 5037191--5037242 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
5037181 CACCAATGAA
*
5037191 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
5037217 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
5037243 CTTTCACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:5037253 original size:103 final size:103
Alignment explanation
Indices: 5037056--5037320 Score: 435
Period size: 103 Copynumber: 2.6 Consensus size: 103
5037046 TAACCGTTAT
* *
5037056 TGGTGGATCTCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
*
5037121 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTACATTTCAAAGATA
5037159 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTC-GGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
5037223 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTT-ACATTTCAAAGATA
* * **
5037262 TGGTGGATCA-CGCACATAGCACCACCAATGAACCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
5037321 TTTATATACA
Statistics
Matches: 153, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
102 28 0.18
103 124 0.81
104 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.19
Consensus pattern (103 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTACATTTCAAAGATA
Found at i:5042354 original size:24 final size:23
Alignment explanation
Indices: 5042302--5042354 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
5042292 ATCAAACATC
* *
5042302 ATAAAACACAAATATTCATCAAT
1 ATAAAACACAAACATTCATCAAA
* *
5042325 AGAAAACTCAAAACATTCATCAAA
1 ATAAAACAC-AAACATTCATCAAA
5042349 ATAAAA
1 ATAAAA
5042355 AATTCTGGCA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.60, C:0.17, G:0.02, T:0.21
Consensus pattern (23 bp):
ATAAAACACAAACATTCATCAAA
Found at i:5045600 original size:40 final size:38
Alignment explanation
Indices: 5045556--5045650 Score: 100
Period size: 40 Copynumber: 2.4 Consensus size: 38
5045546 ACCGTACCTT
**
5045556 TTGGTGTGTAGGGTTGGATGGGTTGATTATATCCCCATAC
1 TTGGTGTGTAGGGTTGGATGGGTCAATTATATCCCC--AC
* * * *
5045596 TTGGTGTGAAGGTTTGGGTGGGTCAATTCTATCCCCAC
1 TTGGTGTGTAGGGTTGGATGGGTCAATTATATCCCCAC
* *
5045634 ATGGTGTGTTGGGTTGG
1 TTGGTGTGTAGGGTTGG
5045651 TCGGAGATGG
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
38 15 0.33
40 30 0.67
ACGTcount: A:0.15, C:0.13, G:0.36, T:0.37
Consensus pattern (38 bp):
TTGGTGTGTAGGGTTGGATGGGTCAATTATATCCCCAC
Found at i:5049096 original size:45 final size:45
Alignment explanation
Indices: 5049047--5049265 Score: 330
Period size: 45 Copynumber: 4.9 Consensus size: 45
5049037 TCGGCCATGG
* * * *
5049047 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
* *
5049092 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
5049137 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
*
5049182 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
* * * **
5049227 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
5049266 TCCACCTCTT
Statistics
Matches: 160, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 160 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
Found at i:5049200 original size:90 final size:90
Alignment explanation
Indices: 5049047--5049265 Score: 375
Period size: 90 Copynumber: 2.4 Consensus size: 90
5049037 TCGGCCATGG
* *
5049047 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAATGCTTCCTTAAATTCTTCCA
1 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
5049112 TGAATTATGCATGATGTTGGTCAAA
66 TGAATTATGCATGATGTTGGTCAAA
* * *
5049137 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
1 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
5049202 TGAATTATGCATGATGTTGGTCAAA
66 TGAATTATGCATGATGTTGGTCAAA
* *
5049227 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTG
5049266 TCCACCTCTT
Statistics
Matches: 119, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 119 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (90 bp):
TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
TGAATTATGCATGATGTTGGTCAAA
Found at i:5052789 original size:45 final size:45
Alignment explanation
Indices: 5052740--5052958 Score: 330
Period size: 45 Copynumber: 4.9 Consensus size: 45
5052730 TCGGCCATGG
* * * *
5052740 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
*
5052785 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
*
5052830 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
*
5052875 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
* * * **
5052920 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
5052959 TCCACCTCTT
Statistics
Matches: 162, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 162 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
Found at i:5053093 original size:16 final size:16
Alignment explanation
Indices: 5053072--5053103 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5053062 CATTCTGCAT
5053072 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
5053088 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
5053104 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:5057917 original size:12 final size:12
Alignment explanation
Indices: 5057900--5057924 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5057890 TTTTAAAATT
5057900 ATGAATAATATA
1 ATGAATAATATA
5057912 ATGAATAATATA
1 ATGAATAATATA
5057924 A
1 A
5057925 AACATAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATGAATAATATA
Found at i:5057981 original size:11 final size:11
Alignment explanation
Indices: 5057965--5058006 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
5057955 TATACATAAC
5057965 ATATAATAAAA
1 ATATAATAAAA
* *
5057976 AAATAAT-AAT
1 ATATAATAAAA
5057986 ATATAATAAAA
1 ATATAATAAAA
5057997 ATATAATAAA
1 ATATAATAAA
5058007 TGTTATATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
ATATAATAAAA
Found at i:5057989 original size:21 final size:21
Alignment explanation
Indices: 5057960--5058005 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
5057950 TACGATATAC
5057960 ATAACATATAATAAAAAAATA
1 ATAACATATAATAAAAAAATA
* *
5057981 ATAATATATAATAAAAATATA
1 ATAACATATAATAAAAAAATA
5058002 ATAA
1 ATAA
5058006 ATGTTATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (21 bp):
ATAACATATAATAAAAAAATA
Found at i:5058004 original size:24 final size:24
Alignment explanation
Indices: 5057960--5058040 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 24
5057950 TACGATATAC
*
5057960 ATAACATATAATAAAA-A-AAT-A
1 ATAATATATAATAAAATATAATAA
5057981 ATAATATATAATAAAAATATAATAA
1 ATAATATATAAT-AAAATATAATAA
**
5058006 ATGTTATATAATAAAATATAATTTAA
1 ATAATATATAATAAAATATAA--TAA
5058032 AT-ATATATA
1 ATAATATATA
5058041 GGAAAATAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
21 11 0.22
22 4 0.08
23 1 0.02
24 12 0.24
25 17 0.34
26 5 0.10
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (24 bp):
ATAATATATAATAAAATATAATAA
Found at i:5060027 original size:205 final size:206
Alignment explanation
Indices: 5059671--5060252 Score: 1028
Period size: 205 Copynumber: 2.8 Consensus size: 206
5059661 AAATCTATTT
* *
5059671 CTTC-GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCA
1 CTTCTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAACA
* * *
5059735 CGCGAAAACCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
66 CGTGAAAGCCAAATCAGCTATGTCTTTGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
* *
5059800 TGGATCTTCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCATCGAAATG
131 TGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCATCAAAATG
5059865 GAGATGCCAGA
196 GAGATGCCAGA
*
5059876 CTT-TGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGTGTAAACA
1 CTTCTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAACA
*
5059940 CGTGAAAGCCAAATCAGCTATGTGTTTGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
66 CGTGAAAGCCAAATCAGCTATGTCTTTGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
5060005 TGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCATCAAAATG
131 TGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCATCAAAATG
5060070 GAGATGCCAGA
196 GAGATGCCAGA
*
5060081 CTTCT-ATTTGTTCTCTGACAATACAGATATGCCAAATCATCTTAGATTTGCTTCAGCGTAAAC-
1 CTTCTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAACA
5060144 CGTGAAAGCCAAATCAGCTATGTCTTTGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
66 CGTGAAAGCCAAATCAGCTATGTCTTTGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
* *
5060209 TGGATCTGCTTCAGTATAAACATCTGAATGTTAGATCTGTTATG
131 TGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATG
5060253 CTGCGGCCTA
Statistics
Matches: 361, Mismatches: 14, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
204 106 0.29
205 254 0.70
206 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (206 bp):
CTTCTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAACA
CGTGAAAGCCAAATCAGCTATGTCTTTGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
TGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCATCAAAATG
GAGATGCCAGA
Found at i:5072396 original size:12 final size:12
Alignment explanation
Indices: 5072379--5072403 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5072369 TTTTAAAATT
5072379 ATGAATAATATA
1 ATGAATAATATA
5072391 ATGAATAATATA
1 ATGAATAATATA
5072403 A
1 A
5072404 AACATAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATGAATAATATA
Found at i:5072514 original size:25 final size:24
Alignment explanation
Indices: 5072444--5072508 Score: 87
Period size: 25 Copynumber: 2.7 Consensus size: 24
5072434 TATACATAAC
* **
5072444 ATATAATAAAATATAATAAGTAAT
1 ATATAATAAAATATAATAAATGTT
5072468 ATATAATAAAAATATAATAAATGTT
1 ATATAAT-AAAATATAATAAATGTT
5072493 ATATAAT-AAATATAAT
1 ATATAATAAAATATAAT
5072509 TTAAATATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.24
24 7 0.19
25 21 0.57
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (24 bp):
ATATAATAAAATATAATAAATGTT
Found at i:5072542 original size:14 final size:14
Alignment explanation
Indices: 5072448--5072544 Score: 66
Period size: 14 Copynumber: 7.4 Consensus size: 14
5072438 CATAACATAT
*
5072448 AATAAAATATAATA
1 AATAATATATAATA
*
5072462 AGTAATATATAAT-
1 AATAATATATAATA
5072475 AA-AA-ATATAATA
1 AATAATATATAATA
**
5072487 AATGTTATATAATA
1 AATAATATATAATA
*
5072501 AAT-ATA-AT-TTA
1 AATAATATATAATA
5072512 AAT-ATATATAGGA-A
1 AATAATATATA--ATA
*
5072526 AATAATATATGATA
1 AATAATATATAATA
5072540 AATAA
1 AATAA
5072545 AAATTATATA
Statistics
Matches: 65, Mismatches: 9, Indels: 18
0.71 0.10 0.20
Matches are distributed among these distances:
11 15 0.23
12 8 0.12
13 4 0.06
14 32 0.49
15 6 0.09
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (14 bp):
AATAATATATAATA
Found at i:5072612 original size:26 final size:27
Alignment explanation
Indices: 5072548--5072612 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
5072538 TAAATAAAAA
5072548 TTATATATAAATATATAAATAGTACTTT
1 TTATA-ATAAATATATAAATAGTACTTT
* ** *
5072576 TAATAAT-AATATATGTATAGT-TTTT
1 TTATAATAAATATATAAATAGTACTTT
5072601 TTATAATAAATA
1 TTATAATAAATA
5072613 AATTATATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
25 9 0.29
26 16 0.52
27 2 0.06
28 4 0.13
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (27 bp):
TTATAATAAATATATAAATAGTACTTT
Found at i:5075724 original size:2 final size:2
Alignment explanation
Indices: 5075717--5075743 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5075707 TTAGAAAAAT
5075717 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5075744 TCAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5079983 original size:29 final size:30
Alignment explanation
Indices: 5079922--5079976 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
5079912 ACATAAGGTG
*
5079922 TAAAATTATTATTATATATTACTAATAAAT
1 TAAAATTAATATTATATATTACTAATAAAT
5079952 TAAAATTAATA-TATATATTA-TAATA
1 TAAAATTAATATTATATATTACTAATA
5079977 TGTTTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 5 0.21
29 9 0.38
30 10 0.42
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (30 bp):
TAAAATTAATATTATATATTACTAATAAAT
Found at i:5080054 original size:17 final size:19
Alignment explanation
Indices: 5080012--5080057 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
5080002 TATTATAGTA
*
5080012 ATAAAAGAAATAAAGAAAG
1 ATAAAAGAAATAAAGAAAC
*
5080031 ATAAAAGAAA-AAGGAAAC
1 ATAAAAGAAATAAAGAAAC
5080049 AT-AAAGAAA
1 ATAAAAGAAA
5080058 GAAAAAGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 7 0.28
18 8 0.32
19 10 0.40
ACGTcount: A:0.74, C:0.02, G:0.15, T:0.09
Consensus pattern (19 bp):
ATAAAAGAAATAAAGAAAC
Found at i:5089816 original size:23 final size:22
Alignment explanation
Indices: 5089790--5089843 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
5089780 TGTATACGCG
5089790 TACATAATAAAAATATATACTAA
1 TACATAATAAAAATA-ATACTAA
* *
5089813 TACATAATAATAATAATAGTAA
1 TACATAATAAAAATAATACTAA
5089835 TAC-TAATAA
1 TACATAATAA
5089844 TACTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 6 0.21
22 9 0.31
23 14 0.48
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.31
Consensus pattern (22 bp):
TACATAATAAAAATAATACTAA
Found at i:5089824 original size:3 final size:3
Alignment explanation
Indices: 5089793--5089862 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
5089783 ATACGCGTAC
* * * *
5089793 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATA GTA ATA CTA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
*
5089840 ATA ATA CTA ATA AT- ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
5089863 CAAGGATATT
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
2 4 0.08
3 43 0.81
4 6 0.11
ACGTcount: A:0.61, C:0.06, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:5090430 original size:8 final size:8
Alignment explanation
Indices: 5090417--5090441 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5090407 GGTGTTCGGC
5090417 GCAAGTGG
1 GCAAGTGG
5090425 GCAAGTGG
1 GCAAGTGG
5090433 GCAAGTGG
1 GCAAGTGG
5090441 G
1 G
5090442 GGGTAGATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.52, T:0.12
Consensus pattern (8 bp):
GCAAGTGG
Found at i:5091434 original size:17 final size:18
Alignment explanation
Indices: 5091402--5091439 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5091392 CTTGTTATTG
*
5091402 TATATAATTGATTTTTTT
1 TATATAATTGATTTTTGT
*
5091420 TATAT-ATTTATTTTTGT
1 TATATAATTGATTTTTGT
5091437 TAT
1 TAT
5091440 CTTCGCTCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
TATATAATTGATTTTTGT
Found at i:5092633 original size:23 final size:22
Alignment explanation
Indices: 5092592--5092636 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
5092582 TATTATTTCA
5092592 ATTATTATTTTATTAAAATAAT
1 ATTATTATTTTATTAAAATAAT
* *
5092614 ATTATTTTTATTATTTAAATAAT
1 ATTATTATT-TTATTAAAATAAT
5092637 TTGAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTATTATTTTATTAAAATAAT
Found at i:5096816 original size:20 final size:20
Alignment explanation
Indices: 5096775--5096818 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5096765 ATGAAATAAT
*
5096775 AAAAGAATAAAAAGAAAGAC
1 AAAAGAATAAAAAGAAAAAC
*
5096795 AAAAGAA-ACAAAGAAGAAAC
1 AAAAGAATAAAAAGAA-AAAC
5096815 AAAA
1 AAAA
5096819 CAGAAGCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.77, C:0.07, G:0.14, T:0.02
Consensus pattern (20 bp):
AAAAGAATAAAAAGAAAAAC
Found at i:5108835 original size:13 final size:13
Alignment explanation
Indices: 5108817--5108846 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5108807 ATTTTATTCT
*
5108817 TTTTTATTTCTTC
1 TTTTTATCTCTTC
5108830 TTTTTATCTCTTC
1 TTTTTATCTCTTC
5108843 TTTT
1 TTTT
5108847 CCTTTTCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTATCTCTTC
Found at i:5110940 original size:39 final size:39
Alignment explanation
Indices: 5110882--5110968 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
5110872 CTACTTTCAC
5110882 TTCTTCCTTTTTGGCTTCAACTTTTACAATCTCCTTCTT
1 TTCTTCCTTTTTGGCTTCAACTTTTACAATCTCCTTCTT
*
5110921 TTCTTCCTTTTTGGGTTCAACTTTTACAATCTCCTTCTT
1 TTCTTCCTTTTTGGCTTCAACTTTTACAATCTCCTTCTT
5110960 TTCTTCCTT
1 TTCTTCCTT
5110969 AGCCTCCATT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.11, C:0.28, G:0.06, T:0.55
Consensus pattern (39 bp):
TTCTTCCTTTTTGGCTTCAACTTTTACAATCTCCTTCTT
Found at i:5112194 original size:28 final size:29
Alignment explanation
Indices: 5112123--5112194 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 29
5112113 ATTTAAGTCG
* *
5112123 ATTTACCAAAATATGCTGATTTTTTTTTA
1 ATTTACCGAAATATGCTGATTTTTGTTTA
*
5112152 ATTTGA--GAATCTATGCTG-TTTTTGTTTA
1 ATTT-ACCGAA-ATATGCTGATTTTTGTTTA
5112180 ATTTACCGAAATATG
1 ATTTACCGAAATATG
5112195 TCAAATTTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
27 1 0.03
28 19 0.54
29 14 0.40
30 1 0.03
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (29 bp):
ATTTACCGAAATATGCTGATTTTTGTTTA
Found at i:5122165 original size:15 final size:14
Alignment explanation
Indices: 5122138--5122174 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
5122128 TGCGTCTTTC
5122138 TTTCTTTTTTCCTT
1 TTTCTTTTTTCCTT
5122152 TTTCTTTCTTTCCTT
1 TTTCTTT-TTTCCTT
*
5122167 TTTGTTTT
1 TTTCTTTT
5122175 CGTTTGGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (14 bp):
TTTCTTTTTTCCTT
Found at i:5122254 original size:21 final size:20
Alignment explanation
Indices: 5122206--5122256 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
5122196 TCTTCTTTTT
*
5122206 TTATTCATT-TACTTATTTTA
1 TTATT-ATTATACTTAGTTTA
5122226 TT-TTATTATACATTAGTTTA
1 TTATTATTATAC-TTAGTTTA
5122246 TTATTATTATA
1 TTATTATTATA
5122257 ATGTATATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 3 0.11
19 5 0.19
20 11 0.41
21 8 0.30
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (20 bp):
TTATTATTATACTTAGTTTA
Found at i:5123639 original size:51 final size:51
Alignment explanation
Indices: 5123526--5123629 Score: 172
Period size: 51 Copynumber: 2.0 Consensus size: 51
5123516 CTGATCACAT
*
5123526 TTATCACTTGTCACTAATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTAATCAGATAAGTGTAACTAAAACTACCACTTATCAC
* * *
5123577 TTATCACTTGTCACTGATCAGATATGTGTAACTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTAATCAGATAAGTGTAACTAAAACTACCACTTATCAC
5123628 TT
1 TT
5123630 GTTGCTTGTC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.34
Consensus pattern (51 bp):
TTATCACTTGTCACTAATCAGATAAGTGTAACTAAAACTACCACTTATCAC
Found at i:5132650 original size:34 final size:34
Alignment explanation
Indices: 5132600--5132667 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
5132590 AATTTTAATA
* *
5132600 AAAAGTATAAAAATATTTAAAATGTATTAAAAAT
1 AAAAGTATAAAAATATTTAAAAAGAATTAAAAAT
5132634 AAAA-TATAAAAAATATTTAAAAAGAATTAAAAAT
1 AAAAGTAT-AAAAATATTTAAAAAGAATTAAAAAT
5132668 TATAAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 3 0.10
34 28 0.90
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.29
Consensus pattern (34 bp):
AAAAGTATAAAAATATTTAAAAAGAATTAAAAAT
Found at i:5132954 original size:2 final size:2
Alignment explanation
Indices: 5132949--5132976 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5132939 AATGATTTAG
5132949 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
5132977 GAAACATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5133581 original size:19 final size:19
Alignment explanation
Indices: 5133545--5133583 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
5133535 AATAATATTA
* **
5133545 TTTTTATATATTTTAAAAT
1 TTTTTAAATATTAAAAAAT
5133564 TTTTTAAATATTAAAAAAT
1 TTTTTAAATATTAAAAAAT
5133583 T
1 T
5133584 AATTAAATGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTTAAATATTAAAAAAT
Found at i:5133991 original size:16 final size:16
Alignment explanation
Indices: 5133972--5134005 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5133962 TAAAAATATA
*
5133972 TAATTATTTTTTAATT
1 TAATTATCTTTTAATT
*
5133988 TAATTATCTTTTATTT
1 TAATTATCTTTTAATT
5134004 TA
1 TA
5134006 GTTAAAAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TAATTATCTTTTAATT
Found at i:5136607 original size:11 final size:11
Alignment explanation
Indices: 5136583--5136615 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5136573 TTTTTTTGTT
5136583 AAAATAAA-TA
1 AAAATAAATTA
*
5136593 AAAATATATTA
1 AAAATAAATTA
5136604 AAAATAAATTA
1 AAAATAAATTA
5136615 A
1 A
5136616 TAATGTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 7 0.35
11 13 0.65
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAATAAATTA
Found at i:5138076 original size:22 final size:22
Alignment explanation
Indices: 5138048--5138101 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
5138038 TTTTCGATTT
5138048 AATTATTTAATT-AATCAAAGTA
1 AATTATTTAATTCAATCAAA-TA
* *
5138070 ATTTATTTAATTCAATTAAATA
1 AATTATTTAATTCAATCAAATA
5138092 AATTATTTAA
1 AATTATTTAA
5138102 AAATATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (22 bp):
AATTATTTAATTCAATCAAATA
Found at i:5141276 original size:12 final size:12
Alignment explanation
Indices: 5141259--5141295 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
5141249 ATAAAAAATA
5141259 AAAAAATTCATT
1 AAAAAATTCATT
5141271 AAAAAATTCATT
1 AAAAAATTCATT
5141283 AAAAAATTCATT
1 AAAAAATTCATT
5141295 A
1 A
5141296 TTTTTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAAAATTCATT
Found at i:5141311 original size:18 final size:18
Alignment explanation
Indices: 5141284--5141340 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 18
5141274 AAATTCATTA
5141284 AAAAATTCATTATTTTTTT
1 AAAAA-TCATTATTTTTTT
***
5141303 AAAAATCATTA-TTTAAA
1 AAAAATCATTATTTTTTT
5141320 AAAAAT-ATTATTTTTTT
1 AAAAATCATTATTTTTTT
5141337 AAAA
1 AAAA
5141341 TAATCACGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
16 4 0.13
17 16 0.52
18 6 0.19
19 5 0.16
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAAATCATTATTTTTTT
Found at i:5142928 original size:20 final size:20
Alignment explanation
Indices: 5142903--5142942 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5142893 TGAAAAGTAG
5142903 GATTTAATTTCTGGTAATCT
1 GATTTAATTTCTGGTAATCT
5142923 GATTTAATTTCTGGTAATCT
1 GATTTAATTTCTGGTAATCT
5142943 TAGGACTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (20 bp):
GATTTAATTTCTGGTAATCT
Found at i:5157292 original size:41 final size:41
Alignment explanation
Indices: 5157085--5157281 Score: 308
Period size: 41 Copynumber: 4.8 Consensus size: 41
5157075 TTTATCGTTA
* * * * *
5157085 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAACGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
5157126 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
5157167 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
5157208 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
5157249 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
5157282 AAGAGCCGGT
Statistics
Matches: 147, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 142 0.97
42 2 0.01
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:5157550 original size:33 final size:33
Alignment explanation
Indices: 5157495--5157591 Score: 106
Period size: 33 Copynumber: 2.8 Consensus size: 33
5157485 GATAGATATG
*
5157495 TATATATATATGT-TGCATTCGGCATAGGTGAA
1 TATATATATGTGTATGCATTCGGCATAGGTGAA
*
5157527 TATATTTATGTGTATGCATTCGGCATAGGTGAA
1 TATATATATGTGTATGCATTCGGCATAGGTGAA
* * *
5157560 AATAAGTGTATGTATCTATGCATTCGGCATAG
1 TAT-A-TATATG--TGTATGCATTCGGCATAG
5157592 ATGGGTATAG
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 11 0.20
33 21 0.38
34 1 0.02
35 5 0.09
37 17 0.31
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (33 bp):
TATATATATGTGTATGCATTCGGCATAGGTGAA
Found at i:5164922 original size:41 final size:41
Alignment explanation
Indices: 5164756--5164911 Score: 226
Period size: 41 Copynumber: 3.8 Consensus size: 41
5164746 TTTATCGTTA
* * * * *
5164756 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAACGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
5164797 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
5164838 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
5164879 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
5164912 AAGAGCCGGT
Statistics
Matches: 106, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 101 0.95
42 2 0.02
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:5165216 original size:37 final size:32
Alignment explanation
Indices: 5165140--5165222 Score: 103
Period size: 32 Copynumber: 2.4 Consensus size: 32
5165130 ATATATATGT
* *
5165140 TGCATTCGGCATAGGTGAAATATTTATGTGTA
1 TGCATTCGGCATAGGTGAAATATGTATGTCTA
5165172 TGCATTCGGCATAGGTGAAAATAAGTGTATGTATCTA
1 TGCATTCGGCATAGGTG-AAAT-A-TGTATG--TCTA
5165209 TGCATTCGGCATAG
1 TGCATTCGGCATAG
5165223 ATGGGTATAG
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
32 17 0.39
33 4 0.09
34 1 0.02
35 5 0.11
37 17 0.39
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (32 bp):
TGCATTCGGCATAGGTGAAATATGTATGTCTA
Found at i:5166495 original size:9 final size:9
Alignment explanation
Indices: 5166450--5166497 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
5166440 CACTCAAATC
5166450 CAATTCTCTT
1 CAATTCTC-T
5166460 C-ATTCTCT
1 CAATTCTCT
**
5166468 TTATTCTCT
1 CAATTCTCT
*
5166477 CATTTCTCT
1 CAATTCTCT
5166486 CAATTCTCT
1 CAATTCTCT
5166495 CAA
1 CAA
5166498 GATTAGTTCC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
8 1 0.03
9 30 0.94
10 1 0.03
ACGTcount: A:0.19, C:0.31, G:0.00, T:0.50
Consensus pattern (9 bp):
CAATTCTCT
Found at i:5167473 original size:17 final size:19
Alignment explanation
Indices: 5167451--5167493 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
5167441 ATAAAAATAT
5167451 AATCTT-CA-ATGATATGC
1 AATCTTACATATGATATGC
*
5167468 AATCTTAGATATGATATGC
1 AATCTTACATATGATATGC
5167487 AATCTTA
1 AATCTTA
5167494 GAAGATATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 1 0.04
19 16 0.70
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (19 bp):
AATCTTACATATGATATGC
Found at i:5167483 original size:19 final size:19
Alignment explanation
Indices: 5167459--5167495 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
5167449 ATAATCTTCA
5167459 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5167478 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
5167496 AGATATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:5167521 original size:22 final size:22
Alignment explanation
Indices: 5167459--5167518 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 22
5167449 ATAATCTTCA
5167459 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
5167478 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
5167500 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
5167519 GATTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.43
22 8 0.23
23 12 0.34
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:5175399 original size:47 final size:47
Alignment explanation
Indices: 5175345--5175655 Score: 496
Period size: 47 Copynumber: 6.6 Consensus size: 47
5175335 TATTTGAATA
* *
5175345 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
5175392 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
5175439 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
5175488 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
5175535 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * * *
5175582 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTCATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
5175629 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
5175656 TCCCGAAGGG
Statistics
Matches: 249, Mismatches: 13, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
47 204 0.82
49 45 0.18
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:5175504 original size:143 final size:141
Alignment explanation
Indices: 5175345--5175655 Score: 532
Period size: 143 Copynumber: 2.2 Consensus size: 141
5175335 TATTTGAATA
5175345 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
5175410 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT
66 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCGAAT
* * *
5175475 GGCCGATGTGATG
129 GGCCAACGTCATG
5175488 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* *
5175553 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAGGGCCGAGTGG
66 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGG
5175618 CCAACGTCATG
131 CCAACGTCATG
* *
5175629 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
5175656 TCCCGAAGGG
Statistics
Matches: 160, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
141 54 0.34
143 106 0.66
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (141 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGG
CCAACGTCATG
Found at i:5176346 original size:37 final size:36
Alignment explanation
Indices: 5176305--5176388 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 36
5176295 TTTTGTTTTT
5176305 AAACACGAGAACTTTGAAACACAATAATAATTTTTGA
1 AAACACGAGAACTTTGAAACACAA-AATAATTTTTGA
** * **
5176342 AAACACGAAGATTTTTGAAACACGAAATTTTTTTTGA
1 AAACACG-AGAACTTTGAAACACAAAATAATTTTTGA
5176379 AAACAC-AGAA
1 AAACACGAGAA
5176389 TTTTTTTGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
35 3 0.08
37 23 0.57
38 14 0.35
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (36 bp):
AAACACGAGAACTTTGAAACACAAAATAATTTTTGA
Found at i:5176374 original size:17 final size:18
Alignment explanation
Indices: 5176334--5176373 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
5176324 CACAATAATA
5176334 ATTTTTGAAAACACGAAG
1 ATTTTTGAAAACACGAAG
5176352 ATTTTTG-AAACACGAA-
1 ATTTTTGAAAACACGAAG
5176368 ATTTTT
1 ATTTTT
5176374 TTTGAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 6 0.27
17 9 0.41
18 7 0.32
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (18 bp):
ATTTTTGAAAACACGAAG
Found at i:5176375 original size:19 final size:20
Alignment explanation
Indices: 5176335--5176395 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
5176325 ACAATAATAA
**
5176335 TTTTTGAAAACAC-GAA-GA
1 TTTTTGAAAACACAGAATTT
5176353 TTTTTG-AAACAC-GAAATTT
1 TTTTTGAAAACACAG-AATTT
5176372 TTTTTGAAAACACAGAATTT
1 TTTTTGAAAACACAGAATTT
5176392 TTTT
1 TTTT
5176396 GTTATTATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
17 7 0.19
18 8 0.22
19 6 0.16
20 15 0.41
21 1 0.03
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (20 bp):
TTTTTGAAAACACAGAATTT
Found at i:5176396 original size:19 final size:18
Alignment explanation
Indices: 5176335--5176396 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 18
5176325 ACAATAATAA
**
5176335 TTTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAATT
5176353 TTTTTG-AAACACGAAATTT
1 TTTTTGAAAACACG-AA-TT
5176372 TTTTTGAAAACACAGAATT
1 TTTTTGAAAACAC-GAATT
5176391 TTTTTG
1 TTTTTG
5176397 TTATTATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.18
18 8 0.21
19 14 0.37
20 8 0.21
21 1 0.03
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (18 bp):
TTTTTGAAAACACGAATT
Found at i:5176425 original size:17 final size:18
Alignment explanation
Indices: 5176405--5176452 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
5176395 TGTTATTATT
5176405 ATTTTGAAACACGTG-AA
1 ATTTTGAAACACGTGAAA
5176422 ATTTTGAAGACA--TGAAA
1 ATTTTGAA-ACACGTGAAA
5176439 ATTTTTGAAACACG
1 A-TTTTGAAACACG
5176453 ATTTTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.08
17 14 0.54
18 10 0.38
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (18 bp):
ATTTTGAAACACGTGAAA
Found at i:5177065 original size:23 final size:24
Alignment explanation
Indices: 5177034--5177099 Score: 93
Period size: 23 Copynumber: 2.9 Consensus size: 24
5177024 CACAAAGTGG
5177034 GCTGCTTCTTTCTTTTTCTTTTTT
1 GCTGCTTCTTTCTTTTTCTTTTTT
*
5177058 -CTGCTTCTTTCTTCTTCTTTTTT
1 GCTGCTTCTTTCTTTTTCTTTTTT
*
5177081 GCTGCTT-TTT-TTTTGCTTT
1 GCTGCTTCTTTCTTTTTCTTT
5177100 GTTTTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 7 0.18
23 25 0.66
24 6 0.16
ACGTcount: A:0.00, C:0.21, G:0.09, T:0.70
Consensus pattern (24 bp):
GCTGCTTCTTTCTTTTTCTTTTTT
Found at i:5177231 original size:20 final size:19
Alignment explanation
Indices: 5177208--5177272 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
5177198 ATCTTTTTTT
5177208 TTTTTATTTTATTTCTTTCC
1 TTTTTATTTT-TTTCTTTCC
*
5177228 TTTTCTATTTTTTTCTCTCC
1 TTTT-TATTTTTTTCTTTCC
*
5177248 TTTTTCTTTCTTTTTCTTT-C
1 TTTTT-ATT-TTTTTCTTTCC
5177268 TTTTT
1 TTTTT
5177273 CCTTTCTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
19 1 0.03
20 24 0.62
21 14 0.36
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTATTTTTTTCTTTCC
Found at i:5177236 original size:21 final size:20
Alignment explanation
Indices: 5177207--5177273 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 20
5177197 TATCTTTTTT
*
5177207 TTTTTTATTTTATTTCTTTCC
1 TTTTCTATTTT-TTTCTTTCC
*
5177228 TTTTCTATTTTTTTCTCTCC
1 TTTTCTATTTTTTTCTTTCC
*
5177248 TTTTTCT-TTCTTTTTCTTTCT
1 -TTTTCTATT-TTTTTCTTTCC
5177269 TTTTC
1 TTTTC
5177274 CTTTCTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 15 0.38
21 25 0.62
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTCTATTTTTTTCTTTCC
Found at i:5177253 original size:11 final size:10
Alignment explanation
Indices: 5177219--5177284 Score: 80
Period size: 10 Copynumber: 6.4 Consensus size: 10
5177209 TTTTATTTTA
*
5177219 TTTCTTTCCT
1 TTTCTTTCTT
5177229 TTTCTATT-TT
1 TTTCT-TTCTT
*
5177239 TTTCTCTCCTT
1 TTTCT-TTCTT
5177250 TTTCTTTCTT
1 TTTCTTTCTT
5177260 TTTCTTTCTT
1 TTTCTTTCTT
5177270 TTTCCTTTCTT
1 TTT-CTTTCTT
5177281 TTTC
1 TTTC
5177285 GGGTTAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
10 30 0.61
11 19 0.39
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:5177277 original size:21 final size:20
Alignment explanation
Indices: 5177219--5177284 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 20
5177209 TTTTATTTTA
*
5177219 TTTCTTTCCTTTTCTATT-TT
1 TTTCTTTCTTTTTCT-TTCTT
*
5177239 TTTCTCTCCTTTTTCTTTCTT
1 TTTCT-TTCTTTTTCTTTCTT
5177260 TTTCTTTCTTTTTCCTTTCTT
1 TTTCTTTCTTTTT-CTTTCTT
5177281 TTTC
1 TTTC
5177285 GGGTTAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTCTTTCTTTTTCTTTCTT
Found at i:5177838 original size:29 final size:30
Alignment explanation
Indices: 5177805--5177914 Score: 100
Period size: 30 Copynumber: 3.7 Consensus size: 30
5177795 TGTAATTTTT
*
5177805 AGAAAATTT-AGGATTAAAATGAAATTTAA
1 AGAAAATTTAAGGGTTAAAATGAAATTTAA
* * *
5177834 TGAAAGTTTAAGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTAAGGGT-TAAAATGAAATTTAA
* *
5177864 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTTAAGGGTTAAAATGAAATTTAA
* * *
5177893 GGAAAAGTTTAGGGGTCAAAAT
1 AGAAAA-TTTAAGGGTTAAAAT
5177915 ACAATTTTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
29 12 0.18
30 54 0.81
31 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.22, T:0.29
Consensus pattern (30 bp):
AGAAAATTTAAGGGTTAAAATGAAATTTAA
Found at i:5177860 original size:30 final size:30
Alignment explanation
Indices: 5177820--5177914 Score: 129
Period size: 30 Copynumber: 3.2 Consensus size: 30
5177810 ATTTAGGATT
*
5177820 AAAATGAAATTTAATGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
5177850 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
5177880 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAAGGGTC
5177910 AAAAT
1 AAAAT
5177915 ACAATTTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 2 0.04
30 55 0.96
ACGTcount: A:0.46, C:0.03, G:0.22, T:0.28
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAAGGGTC
Found at i:5177943 original size:13 final size:15
Alignment explanation
Indices: 5177917--5177951 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
5177907 GTCAAAATAC
5177917 AATTTTTATTTTTTA
1 AATTTTTATTTTTTA
5177932 AATTTTT-TTTTTTA
1 AATTTTTATTTTTTA
5177946 AATTTT
1 AATTTT
5177952 GAAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
AATTTTTATTTTTTA
Found at i:5178327 original size:54 final size:54
Alignment explanation
Indices: 5178193--5178574 Score: 640
Period size: 54 Copynumber: 7.0 Consensus size: 54
5178183 CACGTGAGCC
* *
5178193 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT--AA
*
5178248 AAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
* *
5178302 AAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTTGAAAATCAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
5178356 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
* *
5178410 AAGTCTCAACTCACCTCCCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
5178464 AAGGCTCAACTCACCTCTCGCAATATGAGTTGCTTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
5178518 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATCAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT-AA
5178573 AA
1 AA
5178575 TACCTCAATG
Statistics
Matches: 308, Mismatches: 17, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
54 256 0.83
55 41 0.13
56 11 0.04
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (54 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
Found at i:5178669 original size:72 final size:72
Alignment explanation
Indices: 5178519--5179586 Score: 1757
Period size: 72 Copynumber: 14.8 Consensus size: 72
5178509 AGAAATTAAA
** * * *
5178519 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATCAGAAATTGAAAATACCTCAAT
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAATTACCTCAAC
5178584 GTGTCTTG
65 GTGTCTTG
*
5178592 AGGCTCAACTCATTTCTCACAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
5178657 TGTCTTG
66 TGTCTTG
* *
5178664 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCA
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
*
5178729 TGTCCTG
66 TGTCTTG
*
5178736 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
5178801 TGTCTTG
66 TGTCTTG
* * *
5178808 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAAAAATTGAAAATACCTCAAT
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAATTACCTCAAC
5178873 GTGTCTTG
65 GTGTCTTG
5178881 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
5178946 TGTCTTG
66 TGTCTTG
*
5178953 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
5179018 TGTCTTG
66 TGTCTTG
* *
5179025 AGGCTCAACTCATTTCTCCCAATATGAGTTGAA-TTTGAAAACAAAAATTGAAATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
5179089 TGTCTTG
66 TGTCTTG
* *
5179096 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAAAAATTGAAAATACCTCAAC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAATTACCTCAAC
5179161 GTGTCTTG
65 GTGTCTTG
* *
5179169 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAAATACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
5179234 TGTCTTG
66 TGTCTTG
*
5179241 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTTTGAAAACAGAAATTGAAATTACCTCAG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAA--TTTTGAAAACAGAAATTGAAATTACCTCAA
*
5179306 CAATGTCCTTG
64 C-GTGT-CTTG
*
5179317 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAGCAGAAA-TGAAATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
5179381 TGTCTTG
66 TGTCTTG
*
5179388 AGGCTCAACTCATTTCTCGCAATATGAGTTG-ATTTTGAAAACAGAAATTGAAATTACCTCAACA
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
5179452 TGTCTTG
66 TGTCTTG
*
5179459 AGGCTCAACTCATTTCTCGCAATATGAGTTGATATTTTGAGAAGCAGAAATTGAAAATTACCTCA
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGA-AAACAGAAATTG-AAATTACCTCA
5179524 ACGTGTCTTG
63 ACGTGTCTTG
** * *
5179534 AGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTGAAAACATAGATTGAAA
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAA
5179587 AAAACATAAA
Statistics
Matches: 944, Mismatches: 39, Indels: 26
0.94 0.04 0.03
Matches are distributed among these distances:
70 15 0.02
71 161 0.17
72 419 0.44
73 207 0.22
74 53 0.06
75 52 0.06
76 37 0.04
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (72 bp):
AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
TGTCTTG
Found at i:5178776 original size:217 final size:216
Alignment explanation
Indices: 5178519--5179586 Score: 1766
Period size: 217 Copynumber: 4.9 Consensus size: 216
5178509 AGAAATTAAA
** * * * *
5178519 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATCAGAAATTGAAAATACCTCAAT
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAAAAATTGAAATTACCTCAAC
*
5178584 GTGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTA
65 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTA
5178649 CCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATT
130 CCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATT
* * *
5178714 GAAATTACCTCAGCATGTCCTG
195 GAAATTACCTCAACGTGTCTTG
5178736 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACG
* *
5178801 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAAAAATTGAAAATA
66 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAATTA
*
5178866 CCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATT
130 CCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATT
5178931 GAAATTACCTCAACGTGTCTTG
195 GAAATTACCTCAACGTGTCTTG
5178953 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACG
* *
5179018 TGTCTTGAGGCTCAACTCATTTCTCCCAATATGAGTTGAA-TTTGAAAACAAAAATTGAAATTAC
66 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTAC
*
5179082 CTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAAAAATT
131 CTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATT
*
5179147 GAAAATACCTCAACGTGTCTTG
195 GAAATTACCTCAACGTGTCTTG
*
5179169 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAAATACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACG
5179234 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTTTGAAAACAGAAATTGAAATT
66 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA--TTTTGAAAACAGAAATTGAAATT
* * *
5179299 ACCTCAGCAATGTCCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAGCAGAA
129 ACCTCAAC-GTGT-CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAA
5179364 A-TGAAATTACCTCAACGTGTCTTG
192 ATTGAAATTACCTCAACGTGTCTTG
* *
5179388 AGGCTCAACTCATTTCTCGCAATATGAGTTG-ATTTTGAAAACAGAAATTGAAATTACCTCAACA
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACG
*
5179452 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATATTTTGAGAAGCAGAAATTGAAAAT
66 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGA-AAACAGAAATTG-AAAT
** * *
5179517 TACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTGAAAACATAGA
128 TACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAA
5179581 TTGAAA
193 TTGAAA
5179587 AAAACATAAA
Statistics
Matches: 803, Mismatches: 37, Indels: 22
0.93 0.04 0.03
Matches are distributed among these distances:
215 70 0.09
216 220 0.27
217 283 0.35
218 83 0.10
219 94 0.12
220 8 0.01
221 45 0.06
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (216 bp):
AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACG
TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTAC
CTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTG
AAATTACCTCAACGTGTCTTG
Found at i:5179592 original size:16 final size:16
Alignment explanation
Indices: 5179571--5179603 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5179561 GTTGATTTTG
*
5179571 AAAACATAGATTGAAA
1 AAAACATAAATTGAAA
5179587 AAAACATAAATTGAAA
1 AAAACATAAATTGAAA
5179603 A
1 A
5179604 TACCTCAGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.06, G:0.09, T:0.18
Consensus pattern (16 bp):
AAAACATAAATTGAAA
Found at i:5179825 original size:122 final size:122
Alignment explanation
Indices: 5179587--5179903 Score: 503
Period size: 122 Copynumber: 2.6 Consensus size: 122
5179577 TAGATTGAAA
* * * *
5179587 AAAACATAAATTGAAAATACCTCAGGCTGTGAGCC-GAGGGCTCAACTCATCTCTCGCAATATGA
1 AAAACATAAACTAAAAATACCTC-GGC-GTG-CCCTGA-GGCTCAACTCATTTCTCGCAATATGA
* * *
5179651 GTTGATTTTGAAAAATAAGAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
62 GTTGATTTTAAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
5179712 AAAACATAAACTAAAAATA-CTCGGCGTGCCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 AAAACATAAACTAAAAATACCTCGGCGTGCCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
5179776 ATTTTCAAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
66 ATTTT-AAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
*
5179834 AAAACATAAACTAAAAATACCTCGGCGTGCCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTG
1 AAAACATAAACTAAAAATACCTCGGCGTGCCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
5179899 ATTTT
66 ATTTT
5179904 TTAAAAAAAT
Statistics
Matches: 181, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
121 36 0.20
122 73 0.40
123 52 0.29
124 3 0.02
125 17 0.09
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (122 bp):
AAAACATAAACTAAAAATACCTCGGCGTGCCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
ATTTTAAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
Found at i:5179918 original size:69 final size:71
Alignment explanation
Indices: 5179799--5179972 Score: 221
Period size: 69 Copynumber: 2.5 Consensus size: 71
5179789 AAAAATTAAA
* * * * **
5179799 AGGCTTAACTCACCTCTCGCAATATGAG-TCA-ATTTAAAACATAAACTAAAAATACCTCGGCGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACATAAACTAAAAATACCTCAACGT
5179862 GCCCTG
66 GCCCTG
* *
5179868 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTAAA-A-AAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACATAAACTAAAAATACCTCAACGT
* *
5179931 GTCTTG
66 GCCCTG
*
5179937 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
5179973 CTTGGAAAGC
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
69 83 0.90
70 3 0.03
71 6 0.07
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (71 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAACATAAACTAAAAATACCTCAACGT
GCCCTG
Found at i:5191727 original size:37 final size:36
Alignment explanation
Indices: 5191686--5191769 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 36
5191676 TTTTGTTTTT
5191686 AAACACGAGAACTTTGAAACACAATAATAATTTTTGA
1 AAACACGAGAACTTTGAAACACAA-AATAATTTTTGA
** * **
5191723 AAACACGAAGATTTTTGAAACACGAAATTTTTTTTGA
1 AAACACG-AGAACTTTGAAACACAAAATAATTTTTGA
5191760 AAACAC-AGAA
1 AAACACGAGAA
5191770 TTTTTTTGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
35 3 0.08
37 23 0.57
38 14 0.35
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (36 bp):
AAACACGAGAACTTTGAAACACAAAATAATTTTTGA
Found at i:5191755 original size:17 final size:18
Alignment explanation
Indices: 5191715--5191754 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
5191705 CACAATAATA
5191715 ATTTTTGAAAACACGAAG
1 ATTTTTGAAAACACGAAG
5191733 ATTTTTG-AAACACGAA-
1 ATTTTTGAAAACACGAAG
5191749 ATTTTT
1 ATTTTT
5191755 TTTGAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 6 0.27
17 9 0.41
18 7 0.32
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (18 bp):
ATTTTTGAAAACACGAAG
Found at i:5191756 original size:19 final size:20
Alignment explanation
Indices: 5191716--5191776 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
5191706 ACAATAATAA
**
5191716 TTTTTGAAAACAC-GAA-GA
1 TTTTTGAAAACACAGAATTT
5191734 TTTTTG-AAACAC-GAAATTT
1 TTTTTGAAAACACAG-AATTT
5191753 TTTTTGAAAACACAGAATTT
1 TTTTTGAAAACACAGAATTT
5191773 TTTT
1 TTTT
5191777 GTTATTATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
17 7 0.19
18 8 0.22
19 6 0.16
20 15 0.41
21 1 0.03
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (20 bp):
TTTTTGAAAACACAGAATTT
Found at i:5191777 original size:19 final size:18
Alignment explanation
Indices: 5191716--5191777 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 18
5191706 ACAATAATAA
**
5191716 TTTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAATT
5191734 TTTTTG-AAACACGAAATTT
1 TTTTTGAAAACACG-AA-TT
5191753 TTTTTGAAAACACAGAATT
1 TTTTTGAAAACAC-GAATT
5191772 TTTTTG
1 TTTTTG
5191778 TTATTATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.18
18 8 0.21
19 14 0.37
20 8 0.21
21 1 0.03
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (18 bp):
TTTTTGAAAACACGAATT
Found at i:5191806 original size:17 final size:18
Alignment explanation
Indices: 5191786--5191833 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
5191776 TGTTATTATT
5191786 ATTTTGAAACACGTG-AA
1 ATTTTGAAACACGTGAAA
5191803 ATTTTGAAGACA--TGAAA
1 ATTTTGAA-ACACGTGAAA
5191820 ATTTTTGAAACACG
1 A-TTTTGAAACACG
5191834 ATTTTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.08
17 14 0.54
18 10 0.38
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (18 bp):
ATTTTGAAACACGTGAAA
Found at i:5192448 original size:24 final size:24
Alignment explanation
Indices: 5192420--5192490 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
5192410 ACAAAGTGGG
5192420 CTGCTTCTTTCTTTTTCTTTTTTT
1 CTGCTTCTTTCTTTTTCTTTTTTT
* *
5192444 CTGCTTCTTTCTTCTTCTTTTTTG
1 CTGCTTCTTTCTTTTTCTTTTTTT
*
5192468 CTGCTT-TTT-TTTTGCTTTGTTTT
1 CTGCTTCTTTCTTTTTCTTT-TTTT
5192491 TTTTTTGGGC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
22 7 0.17
23 6 0.15
24 28 0.68
ACGTcount: A:0.00, C:0.20, G:0.08, T:0.72
Consensus pattern (24 bp):
CTGCTTCTTTCTTTTTCTTTTTTT
Found at i:5192464 original size:21 final size:20
Alignment explanation
Indices: 5192428--5192476 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
5192418 GGCTGCTTCT
*
5192428 TTCTTTTTCTTTTTTTCTGC
1 TTCTTTTTCTTCTTTTCTGC
*
5192448 TTCTTTCTTCTTCTTTTTTGC
1 TTCTTT-TTCTTCTTTTCTGC
*
5192469 TGCTTTTT
1 TTCTTTTT
5192477 TTTTGCTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.00, C:0.20, G:0.06, T:0.73
Consensus pattern (20 bp):
TTCTTTTTCTTCTTTTCTGC
Found at i:5192664 original size:10 final size:10
Alignment explanation
Indices: 5192608--5192664 Score: 60
Period size: 10 Copynumber: 5.4 Consensus size: 10
5192598 TTTTATTTTA
*
5192608 TTTTCTTTCC
1 TTTTCTTTCT
*
5192618 TTTTCTATTTT
1 TTTTCT-TTCT
*
5192629 TTTTCTCTCCTT
1 TTTTCT-TTC-T
5192641 TTTTCTTTCT
1 TTTTCTTTCT
5192651 TTTTCTTTCT
1 TTTTCTTTCT
5192661 TTTT
1 TTTT
5192665 TCCTTTCTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
10 21 0.54
11 11 0.28
12 7 0.18
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:5192665 original size:21 final size:21
Alignment explanation
Indices: 5192608--5192673 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
5192598 TTTTATTTTA
* *
5192608 TTTTCTTTC-CTTTTCTATTTT
1 TTTTCTTTCTTTTTTCT-TTCT
*
5192629 TTTTCTCTCCTTTTTTCTTTCT
1 TTTTCT-TTCTTTTTTCTTTCT
5192651 TTTTCTTTCTTTTTTCCTTTCT
1 TTTTCTTTCTTTTTT-CTTTCT
5192673 T
1 T
5192674 CTTCGGGTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
21 14 0.37
22 18 0.47
23 6 0.16
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTCTTTCTTTTTTCTTTCT
Found at i:5192665 original size:22 final size:21
Alignment explanation
Indices: 5192596--5192665 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
5192586 ATCTTTTTAT
5192596 TTTTTTATTTTATTTTCTTTCC
1 TTTTTTATTTT-TTTTCTTTCC
* *
5192618 TTTTCTATTTTTTTTCTCTCC
1 TTTTTTATTTTTTTTCTTTCC
*
5192639 TTTTTTCTTTCTTTTTCTTT-C
1 TTTTTTATTT-TTTTTCTTTCC
5192660 TTTTTT
1 TTTTTT
5192666 CCTTTCTTCT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 24 0.57
22 18 0.43
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTTTATTTTTTTTCTTTCC
Found at i:5193234 original size:29 final size:30
Alignment explanation
Indices: 5193201--5193317 Score: 105
Period size: 30 Copynumber: 3.9 Consensus size: 30
5193191 TGTAATTTTT
*
5193201 AGAAAATTT-AGGATTAAAATGAAATTTAA
1 AGAAAATTTAAGGGTTAAAATGAAATTTAA
* * *
5193230 TGAAAGTTTAAGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTAAGGGT-TAAAATGAAATTTAA
* *
5193260 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTTAAGGGTTAAAATGAAATTTAA
* * * *
5193289 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTAAGGGTTAAAATGAAATTT
5193318 TTATTTTTTA
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
29 12 0.16
30 60 0.82
31 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.30
Consensus pattern (30 bp):
AGAAAATTTAAGGGTTAAAATGAAATTTAA
Found at i:5193256 original size:30 final size:30
Alignment explanation
Indices: 5193216--5193317 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
5193206 ATTTAGGATT
*
5193216 AAAATGAAATTTAATGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
5193246 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
5193276 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAAGGGTC
*
5193306 AAAATGCAATTT
1 AAAATGAAATTT
5193318 TTATTTTTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 2 0.03
30 61 0.97
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAAGGGTC
Found at i:5193340 original size:14 final size:15
Alignment explanation
Indices: 5193316--5193348 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
5193306 AAAATGCAAT
5193316 TTTTATTTTTTAAAA
1 TTTTATTTTTTAAAA
5193331 TTTT-TTTTTTAAAA
1 TTTTATTTTTTAAAA
5193345 TTTT
1 TTTT
5193349 GAAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTATTTTTTAAAA
Found at i:5197131 original size:48 final size:49
Alignment explanation
Indices: 5197079--5197187 Score: 113
Period size: 50 Copynumber: 2.3 Consensus size: 49
5197069 ATAAAATAAT
* * *
5197079 TATAATATATAATATGAA-A-GT-ATATATGTAAAAATAATATTTAATATA
1 TATAATATATAATA-GAATACGTAATACAAGTAAAAAT-ATATATAATATA
5197127 TATAAATAATATAA-AGAATACGTAATACAAGTAAAAATATATATAATATA
1 TAT-AAT-ATATAATAGAATACGTAATACAAGTAAAAATATATATAATATA
5197177 TA-AATA-ATAAT
1 TATAATATATAAT
5197188 TTAAAATAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
46 4 0.08
47 1 0.02
48 9 0.17
49 5 0.10
50 21 0.40
51 12 0.23
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.35
Consensus pattern (49 bp):
TATAATATATAATAGAATACGTAATACAAGTAAAAATATATATAATATA
Found at i:5197177 original size:7 final size:7
Alignment explanation
Indices: 5197165--5197291 Score: 55
Period size: 7 Copynumber: 17.1 Consensus size: 7
5197155 AAGTAAAAAT
5197165 ATATATA
1 ATATATA
5197172 ATATATA
1 ATATATA
5197179 A-ATAATA
1 ATAT-ATA
* *
5197186 ATTTAAA
1 ATATATA
5197193 ATA-ATA
1 ATATATA
*
5197199 ATAGTTTGTA
1 ATA---TATA
* *
5197209 AAAAATA
1 ATATATA
5197216 ATATATA
1 ATATATA
5197223 ATAAATGATA
1 AT--AT-ATA
5197233 ATAATATA
1 AT-ATATA
5197241 A-A-ATA
1 ATATATA
*
5197246 ATGTATA
1 ATATATA
*
5197253 ATAAAATA
1 AT-ATATA
5197261 ATTATATA
1 A-TATATA
5197269 ATATATA
1 ATATATA
*
5197276 ATATAAA
1 ATATATA
5197283 GATATATA
1 -ATATATA
5197291 A
1 A
5197292 ACATTATGTG
Statistics
Matches: 90, Mismatches: 16, Indels: 28
0.67 0.12 0.21
Matches are distributed among these distances:
5 4 0.04
6 8 0.09
7 43 0.48
8 20 0.22
9 6 0.07
10 9 0.10
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (7 bp):
ATATATA
Found at i:5197194 original size:30 final size:31
Alignment explanation
Indices: 5197160--5197291 Score: 89
Period size: 30 Copynumber: 4.4 Consensus size: 31
5197150 AATACAAGTA
*
5197160 AAAATATAT-ATAATATATAAATAATAATTT
1 AAAATATATAATAATATATAAATAATAATAT
* * * *
5197190 AAAATA-ATAATAGTTTGTAAAAAATAATAT
1 AAAATATATAATAATATATAAATAATAATAT
* * * *
5197220 ATAATAAATGATAATA-ATATAA-AATAATGT
1 AAAATATATAATAATATATA-AATAATAATAT
*
5197250 ATAATA-A-AATAAT-TATATAATATATAATAT
1 AAAATATATAATAATATATA-AATA-ATAATAT
5197280 AAAGATATATAA
1 AAA-ATATATAA
5197292 ACATTATGTG
Statistics
Matches: 79, Mismatches: 14, Indels: 15
0.73 0.13 0.14
Matches are distributed among these distances:
28 11 0.14
29 4 0.05
30 50 0.63
31 11 0.14
32 1 0.01
33 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (31 bp):
AAAATATATAATAATATATAAATAATAATAT
Found at i:5197235 original size:20 final size:18
Alignment explanation
Indices: 5197213--5197278 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 18
5197203 TTTGTAAAAA
5197213 ATAATATATAATAAATGAT
1 ATAATATATAAT-AATGAT
*
5197232 AATAATATAAAATAATG-T
1 -ATAATATATAATAATGAT
*
5197250 ATAATA-A-AATAATTAT
1 ATAATATATAATAATGAT
5197266 ATAATATATAATA
1 ATAATATATAATA
5197279 TAAAGATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
15 6 0.15
16 8 0.20
17 7 0.17
18 5 0.12
19 4 0.10
20 11 0.27
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
ATAATATATAATAATGAT
Found at i:5197275 original size:23 final size:23
Alignment explanation
Indices: 5197210--5197278 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
5197200 TAGTTTGTAA
* *
5197210 AAAATAA-TATATAATAAATGAT
1 AAAATAATTATATAATATATAAT
* * *
5197232 AATAAT-ATAAAATAATGTATAAT
1 AA-AATAATTATATAATATATAAT
5197255 AAAATAATTATATAATATATAAT
1 AAAATAATTATATAATATATAAT
5197278 A
1 A
5197279 TAAAGATATA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
22 6 0.17
23 30 0.83
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (23 bp):
AAAATAATTATATAATATATAAT
Found at i:5197276 original size:15 final size:13
Alignment explanation
Indices: 5197210--5197282 Score: 58
Period size: 15 Copynumber: 5.2 Consensus size: 13
5197200 TAGTTTGTAA
5197210 AAAATAATATATAAT
1 AAAATAAT-TAT-AT
*
5197225 AAATGATAATAATAT
1 AAA--ATAATTATAT
5197240 AAAATAATGTATAAT
1 AAAATAAT-TAT-AT
5197255 AAAATAATTATAT
1 AAAATAATTATAT
* *
5197268 AATAT-ATAATAT
1 AAAATAATTATAT
5197280 AAA
1 AAA
5197283 GATATATAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
12 8 0.16
13 11 0.22
14 5 0.10
15 18 0.37
16 2 0.04
17 5 0.10
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (13 bp):
AAAATAATTATAT
Found at i:5197287 original size:20 final size:18
Alignment explanation
Indices: 5197213--5197288 Score: 68
Period size: 20 Copynumber: 4.2 Consensus size: 18
5197203 TTTGTAAAAA
*
5197213 ATAATATATAATAAATGAT
1 ATAATATAAAAT-AATGAT
5197232 AATAATATAAAATAATG-T
1 -ATAATATAAAATAATGAT
*
5197250 AT-A-ATAAAATAATTAT
1 ATAATATAAAATAATGAT
*
5197266 ATAATATATAATATAAAGAT
1 ATAATATA-AA-ATAATGAT
5197286 ATA
1 ATA
5197289 TAAACATTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
15 10 0.21
16 4 0.09
17 3 0.06
18 4 0.09
19 6 0.13
20 20 0.43
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (18 bp):
ATAATATAAAATAATGAT
Found at i:5200710 original size:220 final size:220
Alignment explanation
Indices: 5200343--5200911 Score: 976
Period size: 220 Copynumber: 2.6 Consensus size: 220
5200333 TGACCTGCAG
* * * *
5200343 GTGTTTACGCTGAAGCGGATCCAAGATGATTTAACATCCCTGTATTGTCAGAGAACAAATCGAAG
1 GTGTTTACGCTAAAGCAGATCTAAGATGATTTAACATCTCTGTATTGTCAGAGAACAAATCGAAG
* * * *
5200408 AAACAGATTTGACATCTCTATATTCGATGGAGAGAAGATCGAAGACATAGCAGATCTAACCTTCG
66 AAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTAACCTTCG
* *
5200473 GATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCTTGCGTTGACAAGGAGCAGATCG
131 GATGTCTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCTTACGTTGACAAGGAGCAGATCG
5200538 AAGACATAGCAGATTTGGCTTTCAC
196 AAGACATAGCAGATTTGGCTTTCAC
* *
5200563 GTGTTTACGCTAAAGCAGATCTAAGATGATTTAACATCTCTGTATTTTCAGAGAACAAATCAAAG
1 GTGTTTACGCTAAAGCAGATCTAAGATGATTTAACATCTCTGTATTGTCAGAGAACAAATCGAAG
*
5200628 AAACAGATTTGGCTTCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTAACCTTCG
66 AAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTAACCTTCG
5200693 GATGTCTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCTTACGTTGACAAGGAGCAGATCG
131 GATGTCTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCTTACGTTGACAAGGAGCAGATCG
5200758 AAGACATAGCAGATTTGGCTTTCAC
196 AAGACATAGCAGATTTGGCTTTCAC
* ** *
5200783 ATGTTTACGCTAAAGCAGATCTAAGATGATTTGGCATCTCTGTACTGTCAGAGAACAAATCGAAG
1 GTGTTTACGCTAAAGCAGATCTAAGATGATTTAACATCTCTGTATTGTCAGAGAACAAATCGAAG
*
5200848 AAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTGACCTTC
66 AAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTAACCTTC
5200912 ATTGAAGCAG
Statistics
Matches: 328, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
220 328 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (220 bp):
GTGTTTACGCTAAAGCAGATCTAAGATGATTTAACATCTCTGTATTGTCAGAGAACAAATCGAAG
AAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTAACCTTCG
GATGTCTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCTTACGTTGACAAGGAGCAGATCG
AAGACATAGCAGATTTGGCTTTCAC
Found at i:5200961 original size:78 final size:78
Alignment explanation
Indices: 5200853--5201208 Score: 525
Period size: 78 Copynumber: 4.4 Consensus size: 78
5200843 CGAAGAAACA
** * * * *
5200853 GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATCTGACCTTCATTGAA
5200918 GCAGATCCAAGAT
66 GCAGATCCAAGAT
*
5200931 GACTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATCTGACCTTCATTGAA
5200996 GCAGATCCAAGAT
66 GCAGATCCAAGAT
*
5201009 GATTTGGCATCTCTGTATTAGACGTATTAGACGGGGAGCAGATCGAAGACACAGCAGATCTGACC
1 GATTTGGCATCTC-----T----GTATTAGACGGGGAGCAGATCGAAGACACAACAGATCTGACC
5201074 TTCATTGAAGCAGATCCAAGAT
57 TTCATTGAAGCAGATCCAAGAT
* *
5201096 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAACATAT-TAGACCTTCATTGA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATCT-GACCTTCATTGA
5201160 AGCAGATCCAAGAT
65 AGCAGATCCAAGAT
5201174 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATC
5201209 TGACCTTCAT
Statistics
Matches: 256, Mismatches: 12, Indels: 20
0.89 0.04 0.07
Matches are distributed among these distances:
77 1 0.00
78 177 0.69
82 1 0.00
83 1 0.00
87 76 0.30
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (78 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATCTGACCTTCATTGAA
GCAGATCCAAGAT
Found at i:5201067 original size:165 final size:165
Alignment explanation
Indices: 5200868--5201197 Score: 590
Period size: 165 Copynumber: 2.0 Consensus size: 165
5200858 GGCATCTCCA
* *
5200868 TATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGA
1 TATTAGACGGAGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGA
5200933 CTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATCT-GACCTTCATTGAAG
66 CTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGAT-TAGACCTTCATTGAAG
5200997 CAGATCCAAGATGATTTGGCATCTCTGTATTAGACG
130 CAGATCCAAGATGATTTGGCATCTCTGTATTAGACG
*
5201033 TATTAGACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGA
1 TATTAGACGGAGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGA
* * *
5201098 TTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAACATATTAGACCTTCATTGAAGC
66 CTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATTAGACCTTCATTGAAGC
5201163 AGATCCAAGATGATTTGGCATCTCTGTATTAGACG
131 AGATCCAAGATGATTTGGCATCTCTGTATTAGACG
5201198 GGGAGCAGAT
Statistics
Matches: 158, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
164 1 0.01
165 157 0.99
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (165 bp):
TATTAGACGGAGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGA
CTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATTAGACCTTCATTGAAGC
AGATCCAAGATGATTTGGCATCTCTGTATTAGACG
Found at i:5201091 original size:87 final size:87
Alignment explanation
Indices: 5200945--5201197 Score: 400
Period size: 87 Copynumber: 3.0 Consensus size: 87
5200935 TGGCATCTCT
5200945 GTATTAGACGGGGAGCAGATCGAAGACACAACAGATCTGACCTTCATTGAAGCAGATCCAAGATG
1 GTATTAGACGGGGAGCAGATCGAAGACACAACAGATCTGACCTTCATTGAAGCAGATCCAAGATG
5201010 ATTTGGCATCTCTGTATTAGAC
66 ATTTGGCATCTCTGTATTAGAC
*
5201032 GTATTAGACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATG
1 GTATTAGACGGGGAGCAGATCGAAGACACAACAGATCTGACCTTCATTGAAGCAGATCCAAGATG
5201097 ATTTGGCATCTC-----T----
66 ATTTGGCATCTCTGTATTAGAC
* *
5201110 GTATTAGACGGGGAGCAGATCGAAGACATAACATAT-TAGACCTTCATTGAAGCAGATCCAAGAT
1 GTATTAGACGGGGAGCAGATCGAAGACACAACAGATCT-GACCTTCATTGAAGCAGATCCAAGAT
5201174 GATTTGGCATCTCTGTATTAGAC
65 GATTTGGCATCTCTGTATTAGAC
5201197 G
1 G
5201198 GGGAGCAGAT
Statistics
Matches: 152, Mismatches: 4, Indels: 20
0.86 0.02 0.11
Matches are distributed among these distances:
77 1 0.01
78 72 0.47
82 1 0.01
83 1 0.01
87 77 0.51
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (87 bp):
GTATTAGACGGGGAGCAGATCGAAGACACAACAGATCTGACCTTCATTGAAGCAGATCCAAGATG
ATTTGGCATCTCTGTATTAGAC
Found at i:5201283 original size:45 final size:44
Alignment explanation
Indices: 5201232--5201328 Score: 140
Period size: 44 Copynumber: 2.2 Consensus size: 44
5201222 TTTACATCGA
*
5201232 AGCAGATCCAAGATGACAGATTTGGCATCTCTGTATTAGACAGGG
1 AGCAGATCCAAGAAG-CAGATTTGGCATCTCTGTATTAGACAGGG
** * *
5201277 AGCAGATTGAAGAAGCAGATTTGGCGTCTCTGTATTAGACGGGG
1 AGCAGATCCAAGAAGCAGATTTGGCATCTCTGTATTAGACAGGG
5201321 AGCAGATC
1 AGCAGATC
5201329 AAATATAGCA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 34 0.74
45 12 0.26
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (44 bp):
AGCAGATCCAAGAAGCAGATTTGGCATCTCTGTATTAGACAGGG
Found at i:5205474 original size:88 final size:85
Alignment explanation
Indices: 5205139--5205481 Score: 280
Period size: 88 Copynumber: 3.9 Consensus size: 85
5205129 CTGAATAATT
* * * * *** * *
5205139 TTTTTTTTAATTTTTC-AGGATA-TATAATAATCACAATTTATTTTATTTTATTTTT-TTTATCA
1 TTTTTTTTAA-TTTTCGAGAAAATTATAATAATCACTATTTATTTTATTTCATTTTTGAGGAACT
* *
5205201 GGGCTTGAGTCTGGTACTGCA
65 TGGCTTGAGTCTGGTGCTGCA
* * * *
5205222 TTTTTTTTAATTTTTCGAGATAATTACAATAATCACTATTTATTTCATTTCATTTTTGAGGGACT
1 TTTTTTTTAA-TTTTCGAGAAAATTATAATAATCACTATTTATTTTATTTCATTTTTGAGGAACT
* * *
5205287 TCGGTTTGAGCCTGGCTGCTACAA
65 T-GGCTTGAGTCTGG-TGCTGC-A
* * * * *
5205311 TAATTCTTTTAATTTTCTA-ATATAAATATAATAATCACTATTTATTTTATTTTATTTTTGAGGT
1 T--TTTTTTTAATTTTCGAGA-A-AATTATAATAATCACTATTTATTTTATTTCATTTTTGAGGA
* *
5205375 ATTTGGTCTTGAGTCTGGTGTTGCA
62 ACTTGG-CTTGAGTCTGGTGCTGCA
* * *
5205400 GTTTTTTTTAGTTTTACGAGAAAATTATAATAATCACTAATTATTTTATTTCATTTTCGAGGAAC
1 -TTTTTTTTAATTTT-CGAGAAAATTATAATAATCACTATTTATTTTATTTCATTTTTGAGGAAC
*
5205465 TTGAGCTTGAGTATGGT
64 TTG-GCTTGAGTCTGGT
5205482 ACTGTAATAT
Statistics
Matches: 204, Mismatches: 41, Indels: 25
0.76 0.15 0.09
Matches are distributed among these distances:
83 16 0.08
84 3 0.01
85 29 0.14
86 1 0.00
87 11 0.05
88 66 0.32
89 8 0.04
90 14 0.07
91 56 0.27
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.50
Consensus pattern (85 bp):
TTTTTTTTAATTTTCGAGAAAATTATAATAATCACTATTTATTTTATTTCATTTTTGAGGAACTT
GGCTTGAGTCTGGTGCTGCA
Found at i:5205536 original size:96 final size:93
Alignment explanation
Indices: 5205424--5205595 Score: 238
Period size: 96 Copynumber: 1.8 Consensus size: 93
5205414 TACGAGAAAA
* * * *
5205424 TTATAATAATCACTAATTATTTTATTTCATTTTC-GAGGAACTTGAGCTTGAGTATGGTACTGTA
1 TTATAATAATAACTAATTATTTCATTTCATTTTCTG-GGAACTTGAACTTGAGTATGATACTGTA
5205488 ATATTTAGTTTTTTTTAATTTTTTTGAGATGG
65 A-ATTT--TTTTTTTTAATTTTTTTGAGATGG
* * *
5205520 TTATAATAATAACTAATTATTTCATTTCGTTTTCTGGGCACTTGAACTTGAGTATGATGCTGTAA
1 TTATAATAATAACTAATTATTTCATTTCATTTTCTGGGAACTTGAACTTGAGTATGATACTGTAA
5205585 ATTTTTTTTTT
66 ATTTTTTTTTT
5205596 AGAATAATTA
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
93 7 0.10
95 4 0.06
96 56 0.82
97 1 0.01
ACGTcount: A:0.27, C:0.09, G:0.15, T:0.50
Consensus pattern (93 bp):
TTATAATAATAACTAATTATTTCATTTCATTTTCTGGGAACTTGAACTTGAGTATGATACTGTAA
ATTTTTTTTTTTAATTTTTTTGAGATGG
Found at i:5205886 original size:86 final size:86
Alignment explanation
Indices: 5205693--5205903 Score: 223
Period size: 87 Copynumber: 2.4 Consensus size: 86
5205683 TAATTTTCTG
* * * *
5205693 GGATAATTATAATAATCACTTTTTATTTCATTTCATTTTTAGGGCACTTCGACTTGAGTCTATAC
1 GGATAATTATAATAATAACTATTTATTTCATTTCATTTTTAGGGCACTGCGACTTGAGTATATAC
5205758 TGCAATAATTTATTTTTAATCA
66 TGCAATAATTTATTTTT-ATCA
* * * ** * *
5205780 AGAAAATTATAATAATAACTATTTATTTCATTTCATTTTTAGGG-ACTGGGGTTTGAGTATGGTG
1 GGATAATTATAATAATAACTATTTATTTCATTTCATTTTTAGGGCACTGCGACTTGAGTAT-ATA
*
5205844 CTGTGAA-AAGTTTATTTGTT-T-A
65 CTG-CAATAA-TTTATTT-TTATCA
**
5205866 GGATAATTATAATAATAACTATTTATTTTGTTTCATTT
1 GGATAATTATAATAATAACTATTTATTTCATTTCATTT
5205904 CATTTTCAAT
Statistics
Matches: 104, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
86 46 0.44
87 47 0.45
88 9 0.09
89 2 0.02
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (86 bp):
GGATAATTATAATAATAACTATTTATTTCATTTCATTTTTAGGGCACTGCGACTTGAGTATATAC
TGCAATAATTTATTTTTATCA
Found at i:5206339 original size:85 final size:86
Alignment explanation
Indices: 5206223--5206431 Score: 214
Period size: 85 Copynumber: 2.4 Consensus size: 86
5206213 TTTCCAAGAA
* * * * *
5206223 AATTATAAAAATCATTATTTATTTC-TCTTCATGTT-TAGGACCCTTGGACTTGAGTC-TTATGC
1 AATTATAATAATCACTATTTATTTCAT-TTCAT-TTCGAGG-CACTTGGACTTG-GTCAAT-TGC
* *
5206285 TGCAACA-ATTT-TT-TTTTTGGGAT
61 TGCAACATATTTATTATTTCTGGAAT
5206308 AATTATAATAATCACTATTTATTTCATTTCATTTGCGAGGCACTTGGACTTGGTCAATTGCTGCA
1 AATTATAATAATCACTATTTATTTCATTTCATTT-CGAGGCACTTGGACTTGGTCAATTGCTGCA
*
5206373 ATATATTTATTAAAATTTCTGGAAT
65 ACATATTTATT---ATTTCTGGAAT
*
5206398 AATTATAATAATTACTATTTATTTCATTTCATTT
1 AATTATAATAATCACTATTTATTTCATTTCATTT
5206432 TCAAGGCATT
Statistics
Matches: 105, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
84 14 0.13
85 44 0.42
86 6 0.06
90 41 0.39
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (86 bp):
AATTATAATAATCACTATTTATTTCATTTCATTTCGAGGCACTTGGACTTGGTCAATTGCTGCAA
CATATTTATTATTTCTGGAAT
Found at i:5216014 original size:33 final size:33
Alignment explanation
Indices: 5215972--5216037 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
5215962 GAGGGAAATT
5215972 GGGTTTATATAATATATATCTCAAAGTATGGTC
1 GGGTTTATATAATATATATCTCAAAGTATGGTC
5216005 GGGTTTATATAATATATATCTCAAAGTATGGTC
1 GGGTTTATATAATATATATCTCAAAGTATGGTC
5216038 CATGTCCATT
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:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (33 bp):
GGGTTTATATAATATATATCTCAAAGTATGGTC
Found at i:5216330 original size:2 final size:2
Alignment explanation
Indices: 5216323--5216355 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5216313 CTTGAAAACT
5216323 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5216356 TTTTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5231328 original size:23 final size:22
Alignment explanation
Indices: 5231284--5231329 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
5231274 AAATTTTAGG
*
5231284 GTTTCTTTTTAAAGCTTAAAAT
1 GTTTCTTTTTAAAGATTAAAAT
* *
5231306 GTTTTTTTTTAAATGATTTAAAT
1 GTTTCTTTTTAAA-GATTAAAAT
5231329 G
1 G
5231330 GTGAAATTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.54
Consensus pattern (22 bp):
GTTTCTTTTTAAAGATTAAAAT
Found at i:5231838 original size:17 final size:17
Alignment explanation
Indices: 5231808--5231840 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5231798 TTCCAAACGC
5231808 TTTCATATACTATTATA
1 TTTCATATACTATTATA
5231825 TTTCTATATA-TATTAT
1 TTTC-ATATACTATTAT
5231841 CTATATTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTCATATACTATTATA
Found at i:5232047 original size:15 final size:16
Alignment explanation
Indices: 5232027--5232056 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5232017 AATTCATTTG
5232027 TATATTAC-TATTTAA
1 TATATTACTTATTTAA
5232042 TATATTACTTATTTA
1 TATATTACTTATTTA
5232057 TATTTTCCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATTACTTATTTAA
Found at i:5234172 original size:20 final size:20
Alignment explanation
Indices: 5234147--5234200 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
5234137 AGGGGCACAT
* *
5234147 GCCCGTATGGCCTGGGACAC
1 GCCCGTGTGGCCTGGAACAC
* *
5234167 GCCCGTGTGTCCTGGAACAT
1 GCCCGTGTGGCCTGGAACAC
5234187 GCCCGTGTGGCCTG
1 GCCCGTGTGGCCTG
5234201 CCCATGGGCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.11, C:0.33, G:0.35, T:0.20
Consensus pattern (20 bp):
GCCCGTGTGGCCTGGAACAC
Found at i:5235936 original size:21 final size:21
Alignment explanation
Indices: 5235877--5235928 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
5235867 GAAACAGAAA
* *
5235877 GTGCCTAAAACGACACACGAG
1 GTGCCTGAAACAACACACGAG
*
5235898 GTGCCTGATACAACACACGAG
1 GTGCCTGAAACAACACACGAG
5235919 GTGCCTGAAA
1 GTGCCTGAAA
5235929 TATGACACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.27, G:0.25, T:0.13
Consensus pattern (21 bp):
GTGCCTGAAACAACACACGAG
Found at i:5236347 original size:15 final size:14
Alignment explanation
Indices: 5236323--5236362 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
5236313 TATATATTAT
5236323 ATAATTCAATCAAA
1 ATAATTCAATCAAA
*
5236337 ATAATTTCAATCAAT
1 ATAA-TTCAATCAAA
5236352 ATAAATTCAAT
1 AT-AATTCAAT
5236363 AAATTCATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 17 0.74
16 2 0.09
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAATTCAATCAAA
Found at i:5237451 original size:13 final size:14
Alignment explanation
Indices: 5237433--5237461 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5237423 GATTAACTTC
5237433 ATAAATATTTT-TA
1 ATAAATATTTTCTA
5237446 ATAAATATTTTCTA
1 ATAAATATTTTCTA
5237460 AT
1 AT
5237462 CCATTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATATTTTCTA
Found at i:5237782 original size:13 final size:13
Alignment explanation
Indices: 5237764--5237794 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5237754 AGATAATTAG
5237764 CAAATCATACATA
1 CAAATCATACATA
5237777 CAAATCATACATA
1 CAAATCATACATA
*
5237790 TAAAT
1 CAAAT
5237795 TTATACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.26
Consensus pattern (13 bp):
CAAATCATACATA
Found at i:5238215 original size:37 final size:39
Alignment explanation
Indices: 5238119--5238217 Score: 114
Period size: 40 Copynumber: 2.6 Consensus size: 39
5238109 AACACACCAG
*
5238119 AATGGCGACCAACGCCTCATCGGATAGTTCAAAGCAAAT
1 AATGGCGACCAACGCCTCATCGGATAGTCCAAAGCAAAT
* * * *
5238158 AAGTGACGACCAACGTCTCATCGGCTAAG-CCGAAGC-AA-
1 AA-TGGCGACCAACGCCTCATCGGAT-AGTCCAAAGCAAAT
5238196 AATGGCGACCAACGCCTCATCG
1 AATGGCGACCAACGCCTCATCG
5238218 AATCTATCCG
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
37 18 0.35
38 2 0.04
39 4 0.08
40 25 0.49
41 2 0.04
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.15
Consensus pattern (39 bp):
AATGGCGACCAACGCCTCATCGGATAGTCCAAAGCAAAT
Found at i:5239215 original size:16 final size:16
Alignment explanation
Indices: 5239196--5239226 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5239186 TTTCTTTTGT
*
5239196 TTCTTTATTTTATTTA
1 TTCTTTATTTCATTTA
5239212 TTCTTTATTTCATTT
1 TTCTTTATTTCATTT
5239227 TATTTACTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (16 bp):
TTCTTTATTTCATTTA
Found at i:5239377 original size:3 final size:3
Alignment explanation
Indices: 5239350--5239432 Score: 55
Period size: 3 Copynumber: 27.0 Consensus size: 3
5239340 CTATCTCAAT
*
5239350 TAA TAGA TAA -AA T-A TAA TGA TAA TAA TAA TAA TAA TAA TAA GTAAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -T-AA
* ** *
5239396 TATC TTT TACT TAA TAA TAA TAA T-A TAA TAA TAA TAA
1 TA-A TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
5239433 GTAAATATCT
Statistics
Matches: 65, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
2 6 0.09
3 48 0.74
4 9 0.14
5 2 0.03
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:5239431 original size:42 final size:43
Alignment explanation
Indices: 5239364--5239454 Score: 166
Period size: 42 Copynumber: 2.1 Consensus size: 43
5239354 AGATAAAATA
*
5239364 TAATGATAATAATAATAATAATAATAAGTAAATATCTTTTACT
1 TAATAATAATAATAATAATAATAATAAGTAAATATCTTTTACT
5239407 TAATAATAATAAT-ATAATAATAATAAGTAAATATCTTTTACT
1 TAATAATAATAATAATAATAATAATAAGTAAATATCTTTTACT
5239449 TAATAA
1 TAATAA
5239455 ATAAGTAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 35 0.74
43 12 0.26
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (43 bp):
TAATAATAATAATAATAATAATAATAAGTAAATATCTTTTACT
Found at i:5245203 original size:3 final size:3
Alignment explanation
Indices: 5245182--5245231 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
5245172 GTAAGTATAA
* *
5245182 TAT TAG TAT TAA T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5245229 TAT
1 TAT
5245232 GAGTGGGAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 1 0.02
3 41 0.98
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:5246984 original size:72 final size:72
Alignment explanation
Indices: 5246908--5247045 Score: 188
Period size: 72 Copynumber: 1.9 Consensus size: 72
5246898 AATTTTATAA
* *
5246908 TGTAATTAGAAC-AGTTTGAAATTTGAAAACCAATTTAAAATTAAGATCATAATTTGGGATGCCT
1 TGTAATTAAAACGA-TTTGAAATTTGAAAACAAATTTAAAATTAAGATCATAATTTGGGATGCCT
5246972 GATGTAAT
65 GATGTAAT
* ** * * *
5246980 TGTAATTAAAACGATTTGAAATTTGAGAGTAAATTTAAAATTAAGATTATAGTTTGGGATGTCTG
1 TGTAATTAAAACGATTTGAAATTTGAAAACAAATTTAAAATTAAGATCATAATTTGGGATGCCTG
5247045 A
66 A
5247046 AGCAATTAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
72 56 0.98
73 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (72 bp):
TGTAATTAAAACGATTTGAAATTTGAAAACAAATTTAAAATTAAGATCATAATTTGGGATGCCTG
ATGTAAT
Found at i:5248630 original size:27 final size:28
Alignment explanation
Indices: 5248582--5248636 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
5248572 GAATAATGAG
** *
5248582 AATTAAAATGATCTTAGCCATTGGATTA
1 AATTAAAATGATCTTAAACATTAGATTA
*
5248610 AATT-AAATGATTTTAAACATTAGATTA
1 AATTAAAATGATCTTAAACATTAGATTA
5248637 TGTATTTATC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (28 bp):
AATTAAAATGATCTTAAACATTAGATTA
Found at i:5249290 original size:60 final size:60
Alignment explanation
Indices: 5249223--5249335 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
5249213 CACTTTTTCT
* * *
5249223 AATTTGGTACCTAAATTTGACACTTTTTCTTACGTTGGTA-CTAAATCTTTTTTGGGTTCC
1 AATTTGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCT-AATCTTTTTTGGGTTCC
* *
5249283 AATTTGGTACCTAAACTTGACTCTTTTTCCTAATTTGGTACCTAATCTTTTTT
1 AATTTGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTAATCTTTTTT
5249336 TGTTCGATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
60 45 0.96
61 2 0.04
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.48
Consensus pattern (60 bp):
AATTTGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTAATCTTTTTTGGGTTCC
Found at i:5249320 original size:31 final size:31
Alignment explanation
Indices: 5249195--5249327 Score: 109
Period size: 30 Copynumber: 4.4 Consensus size: 31
5249185 TTTTGTTCAG
* *
5249195 TTTGGTACTTAAACTTAACACTTTTT-CTAA
1 TTTGGTACCTAAACTTGACACTTTTTCCTAA
* * *
5249225 TTTGGTACCTAAATTTGACACTTTTTCTTAC
1 TTTGGTACCTAAACTTGACACTTTTTCCTAA
* *
5249256 GTTGGTA-CTAAATCTT----TTTTGGGTTCC-AA
1 TTTGGTACCTAAA-CTTGACACTTT---TTCCTAA
*
5249285 TTTGGTACCTAAACTTGACTCTTTTTCCTAA
1 TTTGGTACCTAAACTTGACACTTTTTCCTAA
5249316 TTTGGTACCTAA
1 TTTGGTACCTAA
5249328 TCTTTTTTTG
Statistics
Matches: 80, Mismatches: 12, Indels: 21
0.71 0.11 0.19
Matches are distributed among these distances:
27 3 0.04
29 10 0.12
30 40 0.50
31 24 0.30
33 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (31 bp):
TTTGGTACCTAAACTTGACACTTTTTCCTAA
Found at i:5249830 original size:59 final size:59
Alignment explanation
Indices: 5249731--5249867 Score: 168
Period size: 59 Copynumber: 2.3 Consensus size: 59
5249721 AACTCTTTGG
** * * * * *
5249731 TACCAAATTAGGAAAAAAATGTCAAGTTCAGGTACTAAATTGGGCCCAAAAAAGTTTA-A
1 TACCAAATTAGG-AAAAAATGTCAAGTTCAAATACCAAATTAGGACAAAAAAAATTTAGA
* *
5249790 GTATCAAATTAGGAAAAAGTGTCAAGTTCAAATACCAAATTAGGACAAAAAAAATTTAGA
1 -TACCAAATTAGGAAAAAATGTCAAGTTCAAATACCAAATTAGGACAAAAAAAATTTAGA
5249850 TACCAAATTAGGAAAAAA
1 TACCAAATTAGGAAAAAA
5249868 AAATGCCAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 53 0.82
60 12 0.18
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (59 bp):
TACCAAATTAGGAAAAAATGTCAAGTTCAAATACCAAATTAGGACAAAAAAAATTTAGA
Found at i:5252992 original size:31 final size:31
Alignment explanation
Indices: 5252921--5252994 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
5252911 AAATCTTAAC
*
5252921 AGTTCAGTGACTTAAATAAAAACTTTTGAATA
1 AGTT-AGTGACTTAAATAAAAACTTTTAAATA
* * *
5252953 ACTTAGTGACTTAAATGAAAATTTTTAAAT-
1 AGTTAGTGACTTAAATAAAAACTTTTAAATA
5252983 AGTTGAGTGACT
1 AGTT-AGTGACT
5252995 AACTTATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 3 0.08
31 30 0.83
32 3 0.08
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (31 bp):
AGTTAGTGACTTAAATAAAAACTTTTAAATA
Done.