Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 106 of 356
Found at i:33387089 original size:24 final size:24
Alignment explanation
Indices: 33387060--33387121 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
33387050 CAACCATATT
* * *
33387060 TGCACACATAGTGCTA-ATTACAC
1 TGCACACATAGTGCCATAGTAAAC
33387083 TCGCACACATAGTGCCATAGTAAAC
1 T-GCACACATAGTGCCATAGTAAAC
33387108 TGCACACATAGTGC
1 TGCACACATAGTGC
33387122 ATTGGATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.03
24 27 0.79
25 6 0.18
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (24 bp):
TGCACACATAGTGCCATAGTAAAC
Found at i:33392071 original size:38 final size:38
Alignment explanation
Indices: 33391981--33392071 Score: 137
Period size: 38 Copynumber: 2.4 Consensus size: 38
33391971 GCAAGCTATA
* * * *
33391981 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
1 TGCTGGTATTATATTCGGGTTAAATCCCGCAGGCCTAG
*
33392019 TGCTGGTAATATATTCGGGTTAAATCCCGCAGGCCTAG
1 TGCTGGTATTATATTCGGGTTAAATCCCGCAGGCCTAG
33392057 TGCTGGTATTATATT
1 TGCTGGTATTATATT
33392072 AGGGCCTTCG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (38 bp):
TGCTGGTATTATATTCGGGTTAAATCCCGCAGGCCTAG
Found at i:33392134 original size:43 final size:43
Alignment explanation
Indices: 33392068--33392222 Score: 256
Period size: 43 Copynumber: 3.6 Consensus size: 43
33392058 GCTGGTATTA
* * *
33392068 TATTAGGGCCTTCGTGCCTAGCAGACTTCGTGCCAGTGATATG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
* * *
33392111 TATTCGGGCCTTCATGCCTAGCAGGCTTCGTACCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
33392154 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
33392197 TATTCGGGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
33392223 GTAATGCCGG
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 103 1.00
ACGTcount: A:0.14, C:0.26, G:0.30, T:0.30
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTG
Found at i:33394970 original size:41 final size:41
Alignment explanation
Indices: 33394925--33395142 Score: 305
Period size: 41 Copynumber: 5.3 Consensus size: 41
33394915 CGTTTTAACA
* * * * * *
33394925 AAAACGCCACTAAA-AACAGAGTAATAGCGGCGTTTTTTGTT
1 AAAACGCCGCTAAAGACCAGAGCATTAGCGGCG-CTTTTGGT
**
33394966 AAAACGCCGCTAAA-AATAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGT
*
33395006 AAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTCGGT
1 AAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGT
33395047 AAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGT
* * *
33395088 AAAATGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTTTGAT
1 AAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGT
33395129 AAAACGCCGCTAAA
1 AAAACGCCGCTAAA
33395143 AGTCATATAA
Statistics
Matches: 162, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 20 0.12
41 142 0.88
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (41 bp):
AAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGT
Found at i:33396393 original size:14 final size:14
Alignment explanation
Indices: 33396374--33396446 Score: 56
Period size: 14 Copynumber: 5.1 Consensus size: 14
33396364 AAATCTTCAA
33396374 AAAAATTAAAATTT
1 AAAAATTAAAATTT
* * *
33396388 AAAAATAAAAAATA
1 AAAAATTAAAATTT
* *
33396402 AAAAATAAAAACTT
1 AAAAATTAAAATTT
*
33396416 AAAAATTTAATATTT
1 AAAAA-TTAAAATTT
* * *
33396431 AATATTTAATATTT
1 AAAAATTAAAATTT
33396445 AA
1 AA
33396447 TAGTTTAGTC
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
14 39 0.81
15 9 0.19
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAAATTAAAATTT
Found at i:33396398 original size:6 final size:7
Alignment explanation
Indices: 33396373--33396412 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
33396363 AAAATCTTCA
33396373 AAAAAAT
1 AAAAAAT
* *
33396380 TAAAATT
1 AAAAAAT
*
33396387 TAAAAAT
1 AAAAAAT
33396394 AAAAAAT
1 AAAAAAT
33396401 AAAAAAT
1 AAAAAAT
33396408 AAAAA
1 AAAAA
33396413 CTTAAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (7 bp):
AAAAAAT
Found at i:33396447 original size:7 final size:7
Alignment explanation
Indices: 33396420--33396453 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
33396410 AAACTTAAAA
33396420 ATTTAAT
1 ATTTAAT
33396427 ATTTAAT
1 ATTTAAT
33396434 ATTTAAT
1 ATTTAAT
33396441 ATTTAAT
1 ATTTAAT
33396448 AGTTTA
1 A-TTTA
33396454 GTCCATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 22 0.85
8 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (7 bp):
ATTTAAT
Found at i:33399387 original size:15 final size:16
Alignment explanation
Indices: 33399367--33399397 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
33399357 GTTTTTATCT
33399367 TATATATGAT-TAAAA
1 TATATATGATCTAAAA
33399382 TATATATGATCTAAAA
1 TATATATGATCTAAAA
33399398 GCAAGAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (16 bp):
TATATATGATCTAAAA
Found at i:33403620 original size:23 final size:23
Alignment explanation
Indices: 33403594--33403639 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
33403584 AATCGAGTTG
*
33403594 GGTATGGGGTGTTACATGTTCAT
1 GGTATGGGGTGTTACAGGTTCAT
33403617 GGTATGGGGTGTTACAGGTTCAT
1 GGTATGGGGTGTTACAGGTTCAT
33403640 ACTTGGGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.17, C:0.09, G:0.37, T:0.37
Consensus pattern (23 bp):
GGTATGGGGTGTTACAGGTTCAT
Found at i:33404552 original size:17 final size:16
Alignment explanation
Indices: 33404502--33404543 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
33404492 TAATTTTGGT
33404502 TTTGTTCTTCTTA-TTC
1 TTTGTT-TTCTTATTTC
*
33404518 -TTCTTTTCTTATTTC
1 TTTGTTTTCTTATTTC
33404533 TTTGTTTTCTT
1 TTTGTTTTCTT
33404544 TTGTTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 6 0.27
15 7 0.32
16 9 0.41
ACGTcount: A:0.05, C:0.17, G:0.05, T:0.74
Consensus pattern (16 bp):
TTTGTTTTCTTATTTC
Found at i:33404558 original size:20 final size:21
Alignment explanation
Indices: 33404518--33404563 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
33404508 CTTCTTATTC
33404518 TTCTTTTCTTATTTCTTTGTT
1 TTCTTTTCTTATTTCTTTGTT
* *
33404539 TTCTTTTGTTCTTT-TTTGTT
1 TTCTTTTCTTATTTCTTTGTT
*
33404559 CTCTT
1 TTCTT
33404564 GAGATTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.02, C:0.15, G:0.07, T:0.76
Consensus pattern (21 bp):
TTCTTTTCTTATTTCTTTGTT
Found at i:33413217 original size:22 final size:23
Alignment explanation
Indices: 33413174--33413223 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
33413164 ATTGTCAATT
* **
33413174 AAATTATATTAATTGATTTTTTA
1 AAATAATATTAATTGAAATTTTA
33413197 AAATAATATTAATT-AAATTTTA
1 AAATAATATTAATTGAAATTTTA
*
33413219 GAATA
1 AAATA
33413224 TTATGTTTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (23 bp):
AAATAATATTAATTGAAATTTTA
Found at i:33413217 original size:23 final size:23
Alignment explanation
Indices: 33413174--33413217 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
33413164 ATTGTCAATT
* * *
33413174 AAATTATATTAATTGATTTTTTA
1 AAATAATATTAATTAAATTTTTA
33413197 AAATAATATTAATTAAATTTT
1 AAATAATATTAATTAAATTTT
33413218 AGAATATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
AAATAATATTAATTAAATTTTTA
Found at i:33413437 original size:39 final size:39
Alignment explanation
Indices: 33413364--33413438 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
33413354 TACTAATGGG
* * *
33413364 TGGTACAAAATTTAGACTAGTGATAAAATTGTTATTGGA
1 TGGTACAAAATTTAGACTAATAATAAAATAGTTATTGGA
*
33413403 TGGTACAAAATTTAGACTAATAATTAAATAGTTATT
1 TGGTACAAAATTTAGACTAATAATAAAATAGTTATT
33413439 TGAGTTTGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.37
Consensus pattern (39 bp):
TGGTACAAAATTTAGACTAATAATAAAATAGTTATTGGA
Found at i:33416696 original size:19 final size:19
Alignment explanation
Indices: 33416672--33416708 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
33416662 CATTGAATGT
33416672 TGGCCTATAATGGTTATGA
1 TGGCCTATAATGGTTATGA
*
33416691 TGGCCTATGATGGTTATG
1 TGGCCTATAATGGTTATG
33416709 TTAGTTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.11, G:0.30, T:0.38
Consensus pattern (19 bp):
TGGCCTATAATGGTTATGA
Found at i:33420893 original size:55 final size:56
Alignment explanation
Indices: 33420828--33420942 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
33420818 AGCATGGCTG
* * *
33420828 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAAACGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
* * *
33420884 CCAGA-ACAGATATACGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
33420939 CCAG
1 CCAG
33420943 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.57
56 21 0.41
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (56 bp):
CCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
Found at i:33420939 original size:28 final size:27
Alignment explanation
Indices: 33420853--33420942 Score: 101
Period size: 27 Copynumber: 3.2 Consensus size: 27
33420843 GTGACAGAGT
*
33420853 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
** *
33420882 CACCAGAACAGAT-ATACGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCA-TGC
33420909 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
33420937 CACCAG
1 CACCAG
33420943 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19
Consensus pattern (27 bp):
CACCAGAACAGATAATTTGTGGCATGC
Found at i:33421095 original size:28 final size:28
Alignment explanation
Indices: 33421048--33421112 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
33421038 AAATTAACCC
*
33421048 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
*
33421076 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
*
33421104 TGGGGGTAT
1 TAGGGGTAT
33421113 TCTAGTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Found at i:33421387 original size:8 final size:8
Alignment explanation
Indices: 33421360--33421390 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
33421350 CCAAAATACT
33421360 GGCTTTTC
1 GGCTTTTC
*
33421368 GGCATTTC
1 GGCTTTTC
33421376 GGCTTTTC
1 GGCTTTTC
33421384 GGCTTTT
1 GGCTTTT
33421391 ACCGATCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.03, C:0.23, G:0.26, T:0.48
Consensus pattern (8 bp):
GGCTTTTC
Found at i:33422901 original size:29 final size:28
Alignment explanation
Indices: 33422832--33422901 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
33422822 GTTACATGAC
* ** *
33422832 GGGCCATATGAATGTGATTGGGCTCGAT
1 GGGCCATATGAATGAGATTGGGCTAAAA
33422860 GGGCCATATGAATGAGATTGGGCCTAAAA
1 GGGCCATATGAATGAGATTGGG-CTAAAA
*
33422889 GGGCCAAATGAAT
1 GGGCCATATGAAT
33422902 AAGTATGGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 21 0.58
29 15 0.42
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.23
Consensus pattern (28 bp):
GGGCCATATGAATGAGATTGGGCTAAAA
Found at i:33424169 original size:17 final size:18
Alignment explanation
Indices: 33424136--33424169 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33424126 TTCAAAGAAG
33424136 GGTTTTCAATGAAAACAA
1 GGTTTTCAATGAAAACAA
*
33424154 GGTTTTCGAT-AAAACA
1 GGTTTTCAATGAAAACA
33424170 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAA
Found at i:33430690 original size:39 final size:39
Alignment explanation
Indices: 33430636--33430714 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
33430626 AGCGCTTGTT
* * **
33430636 TATAGTCTAAGCTCGACTTACCTTTCTGTTGAATGATCA
1 TATAGTCTAAGCTCGACCTACCTCTCCATTGAATGATCA
33430675 TATAGTCTAAGCTCGACCTACCTCTCCATTGAATGATCA
1 TATAGTCTAAGCTCGACCTACCTCTCCATTGAATGATCA
33430714 T
1 T
33430715 GGTGGTTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (39 bp):
TATAGTCTAAGCTCGACCTACCTCTCCATTGAATGATCA
Found at i:33436872 original size:21 final size:21
Alignment explanation
Indices: 33436814--33436873 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
33436804 AACACATAAA
* *
33436814 TGCCTGAA-ACGACAAATGAGG
1 TGCCT-AATACGACACACGAGG
33436835 TGCCTAATACGACACACGAGG
1 TGCCTAATACGACACACGAGG
33436856 TGCCTAATATACGACACA
1 TGCCT-A-ATACGACACA
33436874 TAAAGTGCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.06
21 21 0.62
22 1 0.03
23 10 0.29
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.17
Consensus pattern (21 bp):
TGCCTAATACGACACACGAGG
Found at i:33436881 original size:23 final size:21
Alignment explanation
Indices: 33436805--33436881 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 21
33436795 TCAGTATATA
33436805 ACACATAAA-TGCCTGAA-ACG
1 ACACATAAAGTGCCT-AATACG
* * *
33436825 ACAAATGAGGTGCCTAATACG
1 ACACATAAAGTGCCTAATACG
** *
33436846 ACACACGAGGTGCCTAATATACG
1 ACACATAAAGTGCCT-A-ATACG
33436869 ACACATAAAGTGC
1 ACACATAAAGTGC
33436882 TTGATTGGCA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
20 8 0.18
21 21 0.47
22 1 0.02
23 15 0.33
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.17
Consensus pattern (21 bp):
ACACATAAAGTGCCTAATACG
Found at i:33437763 original size:13 final size:13
Alignment explanation
Indices: 33437747--33437772 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33437737 CTATTTCTCC
33437747 TTTTTCTTTCTTT
1 TTTTTCTTTCTTT
33437760 TTTTTCTTTCTTT
1 TTTTTCTTTCTTT
33437773 CTCCTTACTT
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:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTCTTTCTTT
Found at i:33438067 original size:7 final size:7
Alignment explanation
Indices: 33438055--33438079 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
33438045 TTTTTAACTT
33438055 AATAATA
1 AATAATA
33438062 AATAATA
1 AATAATA
33438069 AATAATA
1 AATAATA
33438076 AATA
1 AATA
33438080 TCTTTTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAATA
Found at i:33438096 original size:37 final size:37
Alignment explanation
Indices: 33438034--33438104 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
33438024 ATTATTTAAT
33438034 TAATAAATATCTTTTTAACTTAATAATAAA-TAATAAA
1 TAATAAATATCTTTTTAACTTAATAA-AAAGTAATAAA
33438071 TAATAAATATCTTTTT-ACTTAAATAAAAAGTAAT
1 TAATAAATATCTTTTTAACTT-AATAAAAAGTAAT
33438105 TAAGTATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
36 7 0.22
37 25 0.78
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (37 bp):
TAATAAATATCTTTTTAACTTAATAAAAAGTAATAAA
Found at i:33449326 original size:41 final size:41
Alignment explanation
Indices: 33449243--33449352 Score: 107
Period size: 41 Copynumber: 2.7 Consensus size: 41
33449233 ATAGTGATAT
* *
33449243 TCGGGCTTTGAGCCTAGCAAGCCTTGTGCTGGTGAATTAAA
1 TCGGGCTTTGAGCCTAGCAAGCCTTGTGCCGGTGAATAAAA
* *
33449284 TCGGGCTTT-ATGCCTAGCAAG-CTTATTGCCGGTGTATAAAA
1 TCGGGCTTTGA-GCCTAGCAAGCCTT-GTGCCGGTGAATAAAA
*** * *
33449325 TCAAACTTTGAGTCTACCAAGCCTTGTG
1 TCGGGCTTTGAGCCTAGCAAGCCTTGTG
33449353 TCAGTGTGTG
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
40 4 0.07
41 47 0.85
42 4 0.07
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (41 bp):
TCGGGCTTTGAGCCTAGCAAGCCTTGTGCCGGTGAATAAAA
Found at i:33461750 original size:36 final size:36
Alignment explanation
Indices: 33461694--33461849 Score: 124
Period size: 36 Copynumber: 4.3 Consensus size: 36
33461684 AATCCCACCA
* * * *
33461694 AAACACACCAGATGCTCATAAGAGCTAGTCCATCCG
1 AAACATACCAAATGCCCATAAGAGCTAATCCATCCG
*
33461730 AAACATACCAAATGCCCATAAGAGCTAATCCATTCG
1 AAACATACCAAATGCCCATAAGAGCTAATCCATCCG
* * * *
33461766 ACACATACC-GATGGCTCC-GAAGAGCTAATCCAACCG
1 AAACATACCAAAT-GC-CCATAAGAGCTAATCCATCCG
* *
33461802 AAACACACC-AATGGCTCCGA-AA-AGCTAATCCAACCG
1 AAACATACCAAAT-GC-CC-ATAAGAGCTAATCCATCCG
*
33461838 AAACACACCAAA
1 AAACATACCAAA
33461850 CTAGAGAGTA
Statistics
Matches: 102, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
35 2 0.02
36 94 0.92
37 6 0.06
ACGTcount: A:0.40, C:0.31, G:0.14, T:0.14
Consensus pattern (36 bp):
AAACATACCAAATGCCCATAAGAGCTAATCCATCCG
Found at i:33475404 original size:49 final size:49
Alignment explanation
Indices: 33475332--33475432 Score: 184
Period size: 49 Copynumber: 2.1 Consensus size: 49
33475322 TGCATTTGTT
*
33475332 AATCCAAAGGGCAAAACCAGGAATTCATAGTGCCCATACCTTGTGTGAA
1 AATCCAAAAGGCAAAACCAGGAATTCATAGTGCCCATACCTTGTGTGAA
*
33475381 AATCCAAAAGGCAAAACCAGGAATTCGTAGTGCCCATACCTTGTGTGAA
1 AATCCAAAAGGCAAAACCAGGAATTCATAGTGCCCATACCTTGTGTGAA
33475430 AAT
1 AAT
33475433 TTATCTTCTA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (49 bp):
AATCCAAAAGGCAAAACCAGGAATTCATAGTGCCCATACCTTGTGTGAA
Found at i:33476850 original size:57 final size:58
Alignment explanation
Indices: 33476724--33476865 Score: 173
Period size: 57 Copynumber: 2.5 Consensus size: 58
33476714 CATTATAGAA
* * * *
33476724 AGGATTTAGCCTGGACGGGTAATCCTGATATAATCTCTCTCGAGCATATGTTACAACT
1 AGGATTTAGCCTGGACTGGTAATCCTGATATAAGCTCTCTCGAGCATACGTTACAAAT
* * * *
33476782 AGGGTTTAGCCTGGACTGGTAATCCT-AGT-TGAGCTCTTTTGAGCATACGTTACATAAT
1 AGGATTTAGCCTGGACTGGTAATCCTGA-TATAAGCTCTCTCGAGCATACGTTACA-AAT
33476840 -GGATTTAGCCTGGACTGGTAATCCTG
1 AGGATTTAGCCTGGACTGGTAATCCTG
33476866 TAATATGATA
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
57 45 0.62
58 27 0.38
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (58 bp):
AGGATTTAGCCTGGACTGGTAATCCTGATATAAGCTCTCTCGAGCATACGTTACAAAT
Found at i:33479663 original size:2 final size:2
Alignment explanation
Indices: 33479656--33479721 Score: 114
Period size: 2 Copynumber: 33.0 Consensus size: 2
33479646 ACCAGAACAA
*
33479656 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
33479698 CT CT CT CT CT CT CT CC CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT
33479722 TTTCAAAATC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:33481630 original size:6 final size:6
Alignment explanation
Indices: 33481612--33481668 Score: 55
Period size: 6 Copynumber: 9.3 Consensus size: 6
33481602 AAGAAACATT
* *
33481612 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATCAG- GTGACAGA ATCAAA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
33481661 ATCAGA AT
1 ATCAGA AT
33481669 GTGAATGCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
5 2 0.05
6 35 0.83
7 4 0.10
8 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.18
Consensus pattern (6 bp):
ATCAGA
Found at i:33481835 original size:27 final size:26
Alignment explanation
Indices: 33481787--33481846 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
33481777 GCGAGGCTGC
*
33481787 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
33481814 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
33481840 TAGATAT
1 CAGATAT
33481847 ATATATGTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:33481933 original size:27 final size:26
Alignment explanation
Indices: 33481885--33481936 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
33481875 GCGAGGCTGC
*
33481885 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
33481911 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
33481937 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:33482212 original size:27 final size:27
Alignment explanation
Indices: 33482182--33482672 Score: 558
Period size: 27 Copynumber: 18.2 Consensus size: 27
33482172 GGTAAAATGG
* * * *
33482182 TAATTTTACCCCACAAGGGTATCTCGA
1 TAATTCTACCCTACAGGGGTATTTCGA
33482209 TAATTCTACCCTACAGGGGTATTTC-A
1 TAATTCTACCCTACAGGGGTATTTCGA
* *
33482235 GTAATTATACCCTACAGGGGTATTTCGG
1 -TAATTCTACCCTACAGGGGTATTTCGA
* * * * *
33482263 TATTTCTACCTTATAAGGGTATTTCGG
1 TAATTCTACCCTACAGGGGTATTTCGA
*
33482290 TAATTCTACCCTACAGGGGTATTT-TA
1 TAATTCTACCCTACAGGGGTATTTCGA
* *
33482316 GTAATTCTACCCTATAGGGGTATTTCGG
1 -TAATTCTACCCTACAGGGGTATTTCGA
* *
33482344 TATTTTTACCCTACAGGGGTATTTCGA
1 TAATTCTACCCTACAGGGGTATTTCGA
* * * * *
33482371 TATTTTTATCCTACAGGTGTATTTCGG
1 TAATTCTACCCTACAGGGGTATTTCGA
* * *
33482398 TATTTCTACCCTACAAGGGTATTTCGG
1 TAATTCTACCCTACAGGGGTATTTCGA
*
33482425 TAATTCTACCCTATAGGGGTATTTC-A
1 TAATTCTACCCTACAGGGGTATTTCGA
*
33482451 GTAATTCTACCCTACAGGGGTATTTCGG
1 -TAATTCTACCCTACAGGGGTATTTCGA
*
33482479 TAATTCTACCCTACAGGGGTATTTCGG
1 TAATTCTACCCTACAGGGGTATTTCGA
*
33482506 TAATTCTACCCTACAGGGGTATTTCGG
1 TAATTCTACCCTACAGGGGTATTTCGA
* *
33482533 TAATTCTACCCTATAAGGGTATTTCGA
1 TAATTCTACCCTACAGGGGTATTTCGA
* * *
33482560 TATTTCTACCCTACAAGGGTATTTTGA
1 TAATTCTACCCTACAGGGGTATTTCGA
* *
33482587 TATTTCTACCCTACAAGGGTATTTC-A
1 TAATTCTACCCTACAGGGGTATTTCGA
* * * *
33482613 GTATTTCTACCCTACAAGGGTATTTTGG
1 -TAATTCTACCCTACAGGGGTATTTCGA
*
33482641 TAATTCTACCCTACAGGGGTATTTCAA
1 TAATTCTACCCTACAGGGGTATTTCGA
33482668 TAATT
1 TAATT
33482673 TTGTAAATCG
Statistics
Matches: 405, Mismatches: 51, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
26 2 0.00
27 403 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (27 bp):
TAATTCTACCCTACAGGGGTATTTCGA
Found at i:33482304 original size:81 final size:81
Alignment explanation
Indices: 33482184--33482665 Score: 633
Period size: 81 Copynumber: 6.0 Consensus size: 81
33482174 TAAAATGGTA
* * * * *
33482184 ATTT-TACCCCACAAGGGTATCTCGATAATTCTACCCTACAGGGGTATTTCAGTAATTATACCCT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCT
33482248 ACAGGGGTATTTCGGT
66 ACAGGGGTATTTCGGT
* * **
33482264 ATTTCTACCTTATAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCT
*
33482329 ATAGGGGTATTTCGGT
66 ACAGGGGTATTTCGGT
* * * * * * * *
33482345 ATTTTTACCCTACAGGGGTATTTCGATATTTTTATCCTACAGGTGTATTTCGGTATTTCTACCCT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCT
*
33482410 ACAAGGGTATTTCGGT
66 ACAGGGGTATTTCGGT
* * * *
33482426 AATTCTACCCTATAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCT
33482491 ACAGGGGTATTTCGGT
66 ACAGGGGTATTTCGGT
* * * * * *
33482507 AATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTATAAGGGTATTTCGATATTTCTACCCT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCT
* * *
33482572 ACAAGGGTATTTTGAT
66 ACAGGGGTATTTCGGT
* * * *
33482588 ATTTCTACCCTACAAGGGTATTTCAGTATTTCTACCCTACAAGGGTATTTTGGTAATTCTACCCT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCT
33482653 ACAGGGGTATTTC
66 ACAGGGGTATTTC
33482666 AATAATTTTG
Statistics
Matches: 349, Mismatches: 52, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
80 4 0.01
81 345 0.99
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (81 bp):
ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCT
ACAGGGGTATTTCGGT
Found at i:33482687 original size:27 final size:27
Alignment explanation
Indices: 33482657--33482972 Score: 103
Period size: 27 Copynumber: 11.7 Consensus size: 27
33482647 TACCCTACAG
* *
33482657 GGGTATTTCAATAATTTTGTAAATCGA
1 GGGTATTTCAGTAATTTTATAAATCGA
*** * * **
33482684 GGGTAAAACGGTAATTCTATAAATTAA
1 GGGTATTTCAGTAATTTTATAAATCGA
* * *
33482711 GGGTACTTT-GGTAATTTTACAAGTCGA
1 GGGTA-TTTCAGTAATTTTATAAATCGA
*
33482738 GGGTATTTCAATAATTTTA-AAAGTCGA
1 GGGTATTTCAGTAATTTTATAAA-TCGA
* * *
33482765 GGGTATTTCAGTAATTTCACAAAT-TA
1 GGGTATTTCAGTAATTTTATAAATCGA
** * * *
33482791 GGGGTATTTTGGTTATTTTACAAA-CTA
1 -GGGTATTTCAGTAATTTTATAAATCGA
* * *
33482818 GGGGTATTT-TGATAATTTTACAAA-CAA
1 -GGGTATTTCAG-TAATTTTATAAATCGA
** * *
33482845 GGGGTATTTTGGTAATTTTACAAA-CTAA
1 -GGGTATTTCAGTAATTTTATAAATC-GA
* * * *
33482873 GGGTATTT-TGATAATTTTACAAACCAA
1 GGGTATTTCAG-TAATTTTATAAATCGA
** * *
33482900 GGGTATTTTGGTAATTTTACAAA-CCA
1 GGGTATTTCAGTAATTTTATAAATCGA
** * * *
33482926 GGGGTATTTTGGTGATTTTATAAACCAA
1 -GGGTATTTCAGTAATTTTATAAATCGA
33482954 GGGTA-TTCTAGTAATTTTA
1 GGGTATTTC-AGTAATTTTA
33482973 CAAACCAGAG
Statistics
Matches: 234, Mismatches: 40, Indels: 30
0.77 0.13 0.10
Matches are distributed among these distances:
26 12 0.05
27 212 0.91
28 10 0.04
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.39
Consensus pattern (27 bp):
GGGTATTTCAGTAATTTTATAAATCGA
Found at i:33482779 original size:81 final size:79
Alignment explanation
Indices: 33482628--33483022 Score: 271
Period size: 81 Copynumber: 4.9 Consensus size: 79
33482618 TCTACCCTAC
* ** * ***
33482628 AAGGGTATTTTGGTAATTCTACCCTAC-AGGGGTATTTCAATAATTTTGTAAATCGAGGGTAAAA
1 AAGGGTATTTTGGTAATTTTA-CAAACGAGGGGTATTTCAATAATTTT-AAAATCGAGGGTATTT
*
33482692 CGGTAATTCTATAAATT
64 CGGTAATT-TACAAATT
* *
33482709 AAGGGTACTTTGGTAATTTTACAAGTCGA-GGGTATTTCAATAATTTTAAAAGTCGAGGGTATTT
1 AAGGGTATTTTGGTAATTTTACAA-ACGAGGGGTATTTCAATAATTTTAAAA-TCGAGGGTATTT
*
33482773 CAGTAATTTCACAAATT
64 CGGTAATTT-ACAAATT
* * * ** *
33482790 AGGGGTATTTTGGTTATTTTACAAACTAGGGGTATTTTGATAATTTTACAAA-CAAGGGGTATTT
1 AAGGGTATTTTGGTAATTTTACAAACGAGGGGTATTTCAATAATTTTA-AAATCGA-GGGTATTT
* *
33482854 TGGTAATTTTACAAACT
64 CGGTAA-TTTACAAATT
* * * *** *
33482871 AAGGGTATTTTGATAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAA-CCAGGGGTATTT
1 AAGGGTATTTTGGTAATTTTACAAACGAGGGGTATTTCAATAATTTTA-AAATCGA-GGGTATTT
* * * **
33482935 TGGTGATTTTATAAACC
64 CGGT-AATTTACAAATT
* * * * ** * * *
33482952 AAGGGTATTCTAGTAATTTTACAAACCAGAGGTATTT-TGTAATTTGT-AAACCAAGGGTATTTT
1 AAGGGTATTTTGGTAATTTTACAAACGAGGGGTATTTCAATAATTT-TAAAATCGAGGGTATTTC
33483015 GGTAATTT
65 GGTAATTT
33483023 CGTAAACTAA
Statistics
Matches: 263, Mismatches: 40, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
78 4 0.02
79 15 0.06
80 18 0.07
81 218 0.83
82 8 0.03
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.38
Consensus pattern (79 bp):
AAGGGTATTTTGGTAATTTTACAAACGAGGGGTATTTCAATAATTTTAAAATCGAGGGTATTTCG
GTAATTTACAAATT
Found at i:33482977 original size:27 final size:26
Alignment explanation
Indices: 33482709--33483022 Score: 251
Period size: 27 Copynumber: 11.7 Consensus size: 26
33482699 TCTATAAATT
**
33482709 AAGGGTACTTTGGTAATTTTACAAGTC
1 AAGGGTA-TTTGGTAATTTTACAAACC
* ** *
33482736 GAGGGTATTTCAATAATTTTA-AAAGTC
1 AAGGGTATTT-GGTAATTTTACAAA-CC
* * * **
33482763 GAGGGTATTTCAGTAATTTCACAAATT
1 AAGGGTATTT-GGTAATTTTACAAACC
* * *
33482790 AGGGGTATTTTGGTTATTTTACAAACT
1 AAGGGTA-TTTGGTAATTTTACAAACC
* *
33482817 AGGGGTATTTTGATAATTTTACAAA-C
1 AAGGGTA-TTTGGTAATTTTACAAACC
*
33482843 AAGGGGTATTTTGGTAATTTTACAAACT
1 AA-GGGTA-TTTGGTAATTTTACAAACC
*
33482871 AAGGGTATTTTGATAATTTTACAAACC
1 AAGGGTA-TTTGGTAATTTTACAAACC
33482898 AAGGGTATTTTGGTAATTTTACAAACC
1 AAGGGTA-TTTGGTAATTTTACAAACC
* * *
33482925 AGGGGTATTTTGGTGATTTTATAAACC
1 AAGGGTA-TTTGGTAATTTTACAAACC
*
33482952 AAGGGTATTCTAGTAATTTTACAAACC
1 AAGGGTATT-TGGTAATTTTACAAACC
*
33482979 -AGAGGTATTTTGTAATTTGT--AAACC
1 AAG-GGTATTTGGTAATTT-TACAAACC
33483004 AAGGGTATTTTGGTAATTT
1 AAGGGTA-TTTGGTAATTT
33483023 CGTAAACTAA
Statistics
Matches: 245, Mismatches: 31, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
25 9 0.04
26 30 0.12
27 198 0.81
28 8 0.03
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (26 bp):
AAGGGTATTTGGTAATTTTACAAACC
Found at i:33487184 original size:59 final size:59
Alignment explanation
Indices: 33487118--33487255 Score: 147
Period size: 60 Copynumber: 2.3 Consensus size: 59
33487108 CCAACTGTGT
* *
33487118 TGATATGGGCAAGGCCCAATAT-ATCTCG-ACTTGTATA-GGGCTACGGCCCAGATTGATAC
1 TGATATGGGCAAGGCCCAATATGCTCT-GTAC-TGTA-AGGGGCTACGGCCCAGATTAATAC
* * * * *
33487177 TGATATGGGCTAGGCCCAGTATGCTCTGTTACTGTAAGGGGCTATGGCCCATATTAATAT
1 TGATATGGGCAAGGCCCAATATGCTCTG-TACTGTAAGGGGCTACGGCCCAGATTAATAC
33487237 TGATATGGGCTAAGGCCCA
1 TGATATGGGC-AAGGCCCA
33487256 GTTAACACTA
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
59 22 0.33
60 35 0.53
61 9 0.14
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (59 bp):
TGATATGGGCAAGGCCCAATATGCTCTGTACTGTAAGGGGCTACGGCCCAGATTAATAC
Found at i:33489367 original size:29 final size:29
Alignment explanation
Indices: 33489331--33489400 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
33489321 TAGTTTTCGT
*
33489331 AAGAAAGCCTTTATGGCGATATCTGTTAA
1 AAGAAAGCCTTTATGACGATATCTGTTAA
* * * * *
33489360 AAGGAAGCTTTTGTGACGATATTTTTTAA
1 AAGAAAGCCTTTATGACGATATCTGTTAA
*
33489389 AAGAAATCCTTT
1 AAGAAAGCCTTT
33489401 TTGGTTGTTT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (29 bp):
AAGAAAGCCTTTATGACGATATCTGTTAA
Found at i:33491674 original size:16 final size:18
Alignment explanation
Indices: 33491653--33491685 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
33491643 CATACAAGCT
33491653 CCAAAAT-ATAG-TAGTA
1 CCAAAATGATAGATAGTA
33491669 CCAAAATGATAGATAGT
1 CCAAAATGATAGATAGT
33491686 GTGACGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.24
Consensus pattern (18 bp):
CCAAAATGATAGATAGTA
Found at i:33492291 original size:86 final size:89
Alignment explanation
Indices: 33492182--33492343 Score: 215
Period size: 86 Copynumber: 1.8 Consensus size: 89
33492172 ATCGGCAATC
* * * *
33492182 AGCCTGCTAGGTTTAAAAACCCGAAT-TCAT-TCACCGGCATT-TCGCCTGCTAGGCTC-GAGGC
1 AGCCTGCTAGGCTCAAAAACCCGAATAT-ATCTCACCGGCATTATAGCCTGCTAGGCTCAAAGGC
33492243 CCGAATAGTATCTCACCGGCATTAT
65 CCGAATAGTATCTCACCGGCATTAT
** *
33492268 AGCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACTGGCATTATAGCCTGCTAGGCTCAAAGGC
1 AGCCTGCTAGGCTCAAAAACCCGAATA-TATCTCACCGGCATTATAGCCTGCTAGGCTCAAAGGC
33492333 CCGAATAGTAT
65 CCGAATAGTAT
33492344 TGTGCGATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
86 22 0.34
87 2 0.03
88 11 0.17
89 14 0.22
90 15 0.23
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (89 bp):
AGCCTGCTAGGCTCAAAAACCCGAATATATCTCACCGGCATTATAGCCTGCTAGGCTCAAAGGCC
CGAATAGTATCTCACCGGCATTAT
Found at i:33492296 original size:45 final size:45
Alignment explanation
Indices: 33492212--33492343 Score: 223
Period size: 45 Copynumber: 3.0 Consensus size: 45
33492202 CCGAATTCAT
* *
33492212 TCACCGGCATT-TCGCCTGCTAGGCTC-GAGGCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
33492255 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
*
33492300 TCACTGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTAT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTAT
33492344 TGTGCGATAT
Statistics
Matches: 84, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
43 11 0.13
44 14 0.17
45 59 0.70
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.23
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
Found at i:33493236 original size:47 final size:47
Alignment explanation
Indices: 33493148--33493288 Score: 241
Period size: 47 Copynumber: 3.0 Consensus size: 47
33493138 AAAATTTTCT
* * *
33493148 TTAACTAAGAAACTTATCC-GAAATAATAAGGGCAAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATATTAAGAGCAAATTTAACAAGC
33493194 TTAACTAAGTAACTTATCCGGAAATATTAAGAGCAAATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATATTAAGAGCAAATTTAACAAGC
33493241 TTAACTAAGTAACTTATCCGGAAATATTAAGAGC-AATTTAACAAGC
1 TTAACTAAGTAACTTATCCGGAAATATTAAGAGCAAATTTAACAAGC
33493287 TT
1 TT
33493289 TAAATTCAAC
Statistics
Matches: 91, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
46 32 0.35
47 59 0.65
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.28
Consensus pattern (47 bp):
TTAACTAAGTAACTTATCCGGAAATATTAAGAGCAAATTTAACAAGC
Found at i:33503971 original size:29 final size:29
Alignment explanation
Indices: 33503938--33504032 Score: 97
Period size: 29 Copynumber: 3.3 Consensus size: 29
33503928 AGAAAAAAAT
*
33503938 CCTTTGTGGCAAAACTTTGGAAAGGCAAG
1 CCTTTGTGGCAAAACTCTGGAAAGGCAAG
** *
33503967 CCTTTGTGGC-GGAC-CTGCTAAAGGACAA-
1 CCTTTGTGGCAAAACTCTG-GAAAGG-CAAG
* *
33503995 CCTTTGTTGCAAAACTCTAGAAAGGCAAG
1 CCTTTGTGGCAAAACTCTGGAAAGGCAAG
33504024 CCTTTGTGG
1 CCTTTGTGG
33504033 TGAACCTATT
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
27 2 0.04
28 19 0.37
29 28 0.55
30 2 0.04
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.25
Consensus pattern (29 bp):
CCTTTGTGGCAAAACTCTGGAAAGGCAAG
Found at i:33504046 original size:57 final size:57
Alignment explanation
Indices: 33503938--33504102 Score: 186
Period size: 57 Copynumber: 2.9 Consensus size: 57
33503928 AGAAAAAAAT
* * * * * **
33503938 CCTTTGTGGCAAAACTTTGGAAAGGCAAGCCTTTGTGGCGGACCTGCTAAAGGACAA
1 CCTTTGTAGCAAAACTCTAGAAAGGCAAGCCTTTGTGGTGAACCTATTAAAGGACAA
* * *
33503995 CCTTTGTTGCAAAACTCTAGAAAGGCAAGCCTTTGTGGTGAACCTATTAAAGGATAG
1 CCTTTGTAGCAAAACTCTAGAAAGGCAAGCCTTTGTGGTGAACCTATTAAAGGACAA
* * * * * *
33504052 CTTTTGTAGAAAAAATCTAGAAAGGTAAGCCTTTGCGGTGAACCTCTTAAA
1 CCTTTGTAGCAAAACTCTAGAAAGGCAAGCCTTTGTGGTGAACCTATTAAA
33504103 TGATGCCTTT
Statistics
Matches: 92, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 92 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.27
Consensus pattern (57 bp):
CCTTTGTAGCAAAACTCTAGAAAGGCAAGCCTTTGTGGTGAACCTATTAAAGGACAA
Found at i:33504162 original size:27 final size:27
Alignment explanation
Indices: 33504110--33504162 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
33504100 AAATGATGCC
*
33504110 TTTGTGGCAAGACTCTGAATGGAAAGTA
1 TTTGTGGC-AGACTCTGAATGAAAAGTA
*
33504138 TTTGTGGC-GACTACTTAATGAAAAG
1 TTTGTGGCAGACT-CTGAATGAAAAG
33504163 GACGCCATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 4 0.18
27 10 0.45
28 8 0.36
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.30
Consensus pattern (27 bp):
TTTGTGGCAGACTCTGAATGAAAAGTA
Found at i:33504206 original size:28 final size:28
Alignment explanation
Indices: 33504173--33504257 Score: 98
Period size: 28 Copynumber: 3.0 Consensus size: 28
33504163 GACGCCATTA
*
33504173 TGGAAATCTCTAGATAAGGAAGCCTTTG
1 TGGAAATCTCTGGATAAGGAAGCCTTTG
* * * *
33504201 TTGAAATCTCTGGATAATGAAGCCATTA
1 TGGAAATCTCTGGATAAGGAAGCCTTTG
* * *
33504229 TGGCAATCTTTGGATAAGGAAACCTTTG
1 TGGAAATCTCTGGATAAGGAAGCCTTTG
33504257 T
1 T
33504258 AGCTATCGCT
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (28 bp):
TGGAAATCTCTGGATAAGGAAGCCTTTG
Found at i:33506788 original size:46 final size:46
Alignment explanation
Indices: 33506712--33506837 Score: 137
Period size: 46 Copynumber: 2.7 Consensus size: 46
33506702 GTTTAAGTAT
* * * * ***
33506712 TTAATATGCCTTGAGTCTATTTAATATGTTCTAATTAGATTC-GGTAA
1 TTAATATGTCTTAAGT-TATTTAATGTGTTCTAATTAG-TACAACCAA
* *
33506759 TTAATATGTCTTAAGTTAATTAATGTGTTCTAATTAGTACAACCAT
1 TTAATATGTCTTAAGTTATTTAATGTGTTCTAATTAGTACAACCAA
33506805 TTAATATGTCTTAAGTTTATTTAATGTGTTCTA
1 TTAATATGTCTTAAG-TTATTTAATGTGTTCTA
33506838 GTTAATATAG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
45 2 0.03
46 35 0.52
47 30 0.45
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.47
Consensus pattern (46 bp):
TTAATATGTCTTAAGTTATTTAATGTGTTCTAATTAGTACAACCAA
Found at i:33506856 original size:47 final size:47
Alignment explanation
Indices: 33506712--33506866 Score: 143
Period size: 47 Copynumber: 3.3 Consensus size: 47
33506702 GTTTAAGTAT
* * * * * *
33506712 TTAATATGCCTTGAGTCTATTTAATATGTTCTAATTAGAT-TCGGTAA
1 TTAATATGTCTTAAGTTTATTTAATGTGTTCTAATTA-ATATAGCTAA
* * * * * *
33506759 TTAATATGTCTTAAG-TTAATTAATGTGTTCTAATTAGTACAACCAT
1 TTAATATGTCTTAAGTTTATTTAATGTGTTCTAATTAATATAGCTAA
* *
33506805 TTAATATGTCTTAAGTTTATTTAATGTGTTCTAGTTAATATAGCTAC
1 TTAATATGTCTTAAGTTTATTTAATGTGTTCTAATTAATATAGCTAA
* *
33506852 TTAATGTGTCATAAG
1 TTAATATGTCTTAAG
33506867 CTTAGACAAT
Statistics
Matches: 85, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
45 1 0.01
46 34 0.40
47 50 0.59
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.45
Consensus pattern (47 bp):
TTAATATGTCTTAAGTTTATTTAATGTGTTCTAATTAATATAGCTAA
Found at i:33518237 original size:13 final size:14
Alignment explanation
Indices: 33518207--33518240 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
33518197 TCAACTGATT
33518207 AAAATTCAATAAATA
1 AAAATTCAAT-AATA
33518222 AAAATTCAAT-ATA
1 AAAATTCAATAATA
33518235 AAAATT
1 AAAATT
33518241 ATTATTGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.47
15 10 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATTCAATAATA
Found at i:33518902 original size:41 final size:41
Alignment explanation
Indices: 33518845--33518925 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
33518835 ATTCAATGCC
33518845 AAAATAGGGTTACGGAGCATTACCGGACATATCATACAATT
1 AAAATAGGGTTACGGAGCATTACCGGACATATCATACAATT
33518886 AAAATAGGGTTACGGAGCATTACCGGACATATCATACAAT
1 AAAATAGGGTTACGGAGCATTACCGGACATATCATACAAT
33518926 CACACATACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (41 bp):
AAAATAGGGTTACGGAGCATTACCGGACATATCATACAATT
Found at i:33529327 original size:14 final size:15
Alignment explanation
Indices: 33529308--33529337 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33529298 GTTTATTATA
33529308 TGTG-AAGTATCATG
1 TGTGAAAGTATCATG
33529322 TGTGAAAGTATCATG
1 TGTGAAAGTATCATG
33529337 T
1 T
33529338 CTAAATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.37
Consensus pattern (15 bp):
TGTGAAAGTATCATG
Found at i:33531266 original size:43 final size:43
Alignment explanation
Indices: 33531205--33531368 Score: 240
Period size: 43 Copynumber: 3.8 Consensus size: 43
33531195 AATGTGATAT
*
33531205 TCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAGATAATA
1 TCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGATAATA
* *
33531248 TCGGGCTTTGGGCCTAGCAGGCTATAATGCCGGTGAGATAATA
1 TCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGATAATA
* * *
33531291 TCGGGCTTCGAGCCTAGCAGGCTATAATGTCGGTGAAATGATA
1 TCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGATAATA
* * *
33531334 TCGGGCTTCAAGCCTAGCAGGCGA-AATGCTGGTGA
1 TCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGA
33531369 ATGAGTTCAG
Statistics
Matches: 111, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
42 9 0.08
43 102 0.92
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (43 bp):
TCGGGCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGATAATA
Found at i:33534466 original size:51 final size:48
Alignment explanation
Indices: 33534343--33534484 Score: 137
Period size: 51 Copynumber: 2.9 Consensus size: 48
33534333 CAAGATCTTG
*
33534343 TTTATTTAATTATTT-TTCAGATATGATGTTTTAAATAAATATAAATA
1 TTTATTTAATTATTTGTTCAGATCTGATGTTTTAAATAAATATAAATA
* * * * *
33534390 TTTATTTAATTTGTTTTGTTTAGATCTGGTGTTTTTACATGAATATAAATA
1 TTTATTTAA-TT-ATTTGTTCAGATCTGATG-TTTTAAATAAATATAAATA
*
33534441 TTTGTTTATATTATTTGTTCAAGATCT--TGTATTTAATATAAATA
1 TTTATTTA-ATTATTTGTTC-AGATCTGATGT-TTTAA-ATAAATA
33534485 GTTATATTTA
Statistics
Matches: 76, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
47 9 0.12
48 3 0.04
49 9 0.12
50 22 0.29
51 32 0.42
52 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.54
Consensus pattern (48 bp):
TTTATTTAATTATTTGTTCAGATCTGATGTTTTAAATAAATATAAATA
Found at i:33539018 original size:18 final size:20
Alignment explanation
Indices: 33538977--33539024 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
33538967 ATTGCTTCTC
33538977 AAAAATATTTTTTAAAGATA
1 AAAAATATTTTTTAAAGATA
*
33538997 AAAAATATTTTTTTAA-AT-
1 AAAAATATTTTTTAAAGATA
33539015 AAAAATATTT
1 AAAAATATTT
33539025 CTAAACAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 10 0.37
19 2 0.07
20 15 0.56
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
AAAAATATTTTTTAAAGATA
Found at i:33541965 original size:22 final size:23
Alignment explanation
Indices: 33541924--33541967 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
33541914 TAATAATGGT
33541924 TTAAAACATGTAAAACATTTTTC
1 TTAAAACATGTAAAACATTTTTC
* *
33541947 TTAAAAC-TTTAAAATATTTTT
1 TTAAAACATGTAAAACATTTTT
33541968 AAATTACATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (23 bp):
TTAAAACATGTAAAACATTTTTC
Found at i:33542034 original size:56 final size:56
Alignment explanation
Indices: 33541973--33542089 Score: 207
Period size: 56 Copynumber: 2.1 Consensus size: 56
33541963 TTTTTAAATT
*
33541973 ACATCAGCACTTCAAGTAAAATAATAAAAATATTAATAAAAAAACAGTTTATATAA
1 ACATCAACACTTCAAGTAAAATAATAAAAATATTAATAAAAAAACAGTTTATATAA
* *
33542029 ACATCAACACTTCAAGTAAAATAATAAAAATATTAATAAAAAAGCGGTTTATATAA
1 ACATCAACACTTCAAGTAAAATAATAAAAATATTAATAAAAAAACAGTTTATATAA
33542085 ACATC
1 ACATC
33542090 CAAATATATC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (56 bp):
ACATCAACACTTCAAGTAAAATAATAAAAATATTAATAAAAAAACAGTTTATATAA
Found at i:33542875 original size:8 final size:8
Alignment explanation
Indices: 33542862--33542890 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
33542852 TATTTATTTT
33542862 AAAAAATA
1 AAAAAATA
33542870 AAAAAAT-
1 AAAAAATA
33542877 AAAAAATA
1 AAAAAATA
33542885 AAAAAA
1 AAAAAA
33542891 GCATTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAATA
Found at i:33542879 original size:15 final size:15
Alignment explanation
Indices: 33542861--33542890 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
33542851 ATATTTATTT
33542861 TAAAAAATAAAAAAA
1 TAAAAAATAAAAAAA
33542876 TAAAAAATAAAAAAA
1 TAAAAAATAAAAAAA
33542891 GCATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (15 bp):
TAAAAAATAAAAAAA
Found at i:33543047 original size:32 final size:34
Alignment explanation
Indices: 33542993--33543063 Score: 101
Period size: 32 Copynumber: 2.1 Consensus size: 34
33542983 AATTTTAGAA
33542993 AAAAAACTATAAAAATAGAATTTAGAAAAATTAT
1 AAAAAACTATAAAAATAGAATTTAGAAAAATTAT
* **
33543027 AAAAAA-T-TAAAAATATAATTTTTAAAAATTAT
1 AAAAAACTATAAAAATAGAATTTAGAAAAATTAT
33543059 AAAAA
1 AAAAA
33543064 TGAAAATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 27 0.79
33 1 0.03
34 6 0.18
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (34 bp):
AAAAAACTATAAAAATAGAATTTAGAAAAATTAT
Found at i:33543052 original size:23 final size:22
Alignment explanation
Indices: 33543026--33543089 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 22
33543016 AGAAAAATTA
* *
33543026 TAAAAAATTAAAAATATAATTTT
1 TAAAAAATTAAAAATA-AAATAT
*
33543049 TAAAAATTATAAAAATGAAAATAT
1 TAAAAAAT-TAAAAAT-AAAATAT
*
33543073 TAAAATATTAAAAATAA
1 TAAAAAATTAAAAATAA
33543090 TAGAAATCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
22 2 0.06
23 14 0.41
24 17 0.50
25 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
TAAAAAATTAAAAATAAAATAT
Found at i:33543084 original size:32 final size:31
Alignment explanation
Indices: 33543018--33543096 Score: 79
Period size: 32 Copynumber: 2.5 Consensus size: 31
33543008 TAGAATTTAG
* * *
33543018 AAAAATTATAAAAAATTAAAAATATAATTTTT
1 AAAAATTAT-AAAAATGAAAAATATAAATATT
33543050 AAAAATTATAAAAATG-AAAATATTAAAATATT
1 AAAAATTATAAAAATGAAAAATA-T-AAATATT
* *
33543082 AAAAATAATAGAAAT
1 AAAAATTATAAAAAT
33543097 CATTTAGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 6 0.15
31 7 0.17
32 27 0.68
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (31 bp):
AAAAATTATAAAAATGAAAAATATAAATATT
Found at i:33543124 original size:23 final size:25
Alignment explanation
Indices: 33543083--33543130 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 25
33543073 TAAAATATTA
33543083 AAAATAATAGAAATCATTTAGAAAAT
1 AAAATAATAGAAATCATTTA-AAAAT
33543109 AAAAT-ATA-AAAT-ATTTAAAAAT
1 AAAATAATAGAAATCATTTAAAAAT
33543131 TATAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 5 0.23
24 4 0.18
25 3 0.14
26 5 0.23
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (25 bp):
AAAATAATAGAAATCATTTAAAAAT
Found at i:33553613 original size:12 final size:12
Alignment explanation
Indices: 33553596--33553621 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
33553586 TATCACGAAC
33553596 AAAATGATACCG
1 AAAATGATACCG
33553608 AAAATGATACCG
1 AAAATGATACCG
33553620 AA
1 AA
33553622 CATAATTTGT
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:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (12 bp):
AAAATGATACCG
Found at i:33555531 original size:28 final size:28
Alignment explanation
Indices: 33555468--33555590 Score: 185
Period size: 28 Copynumber: 4.4 Consensus size: 28
33555458 ATATTAAGTC
*
33555468 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
33555495 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
33555523 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
33555551 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
33555580 CGCACACTTAG
1 CGCACACTTAG
33555591 CGCCAATCTC
Statistics
Matches: 89, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
27 22 0.25
28 51 0.57
29 16 0.18
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:33570026 original size:41 final size:40
Alignment explanation
Indices: 33569868--33570043 Score: 170
Period size: 35 Copynumber: 4.5 Consensus size: 40
33569858 ACCCAAGTAT
* * ** * *
33569868 CTTCGGGATTTAG-CCGAATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAAGC
* * *
33569906 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCA-TAAA--
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAAGC
* *
33569943 --TCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAAGC
*
33569981 CTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCAC-TAGCACAAAAGC
33570022 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
33570044 CATTCGAATA
Statistics
Matches: 111, Mismatches: 17, Indels: 17
0.77 0.12 0.12
Matches are distributed among these distances:
35 28 0.25
36 2 0.02
38 11 0.10
39 19 0.17
40 20 0.18
41 28 0.25
42 3 0.03
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAAGC
Found at i:33579871 original size:79 final size:80
Alignment explanation
Indices: 33579736--33579915 Score: 231
Period size: 79 Copynumber: 2.3 Consensus size: 80
33579726 ACCCAAGTAT
* * * *
33579736 CTTCGGGATTTAG-CCGGATATAACCACTCGCACAAGGCCTTCGGGTCTTAGCCCGGATATGGTC
1 CTTCGGGACTTAGCCCGGATATAACCACTAGCACAAGGCCTTCGGATCTTAGCCCGGATATAGTC
* *
33579800 AC-TAGCATAAATG-
66 ACTTAGCACAAAAGC
** * * *
33579813 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGCCTTCGGATCTTAGTCCGGATATAGT
1 CTTCGGGACTTAGCCCGGATATAACCACTAGCAC-AAGGCCTTCGGATCTTAGCCCGGATATAGT
33579878 CACTTAGCACAAAAGC
65 CACTTAGCACAAAAGC
33579894 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
33579916 CATTCGAATA
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
77 12 0.14
78 16 0.18
79 29 0.33
80 9 0.10
81 22 0.25
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAACCACTAGCACAAGGCCTTCGGATCTTAGCCCGGATATAGTC
ACTTAGCACAAAAGC
Found at i:33579898 original size:41 final size:40
Alignment explanation
Indices: 33579736--33579915 Score: 215
Period size: 39 Copynumber: 4.5 Consensus size: 40
33579726 ACCCAAGTAT
* ** * *
33579736 CTTCGGGATTTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
33579774 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATG-
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
33579813 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
33579853 CTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCAC-TAGCACAAATGC
33579894 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
33579916 CATTCGAATA
Statistics
Matches: 120, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
38 11 0.09
39 53 0.44
40 25 0.21
41 28 0.23
42 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:33589650 original size:41 final size:40
Alignment explanation
Indices: 33589487--33589667 Score: 224
Period size: 40 Copynumber: 4.5 Consensus size: 40
33589477 ACCCAAGTAT
* ** * *
33589487 CTTCGGGATTTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
33589525 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
33589565 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
33589605 CTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCAC-TAGCACAAATGC
33589646 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
33589668 CATTCGAATA
Statistics
Matches: 122, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
38 11 0.09
39 18 0.15
40 62 0.51
41 28 0.23
42 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:33589666 original size:81 final size:79
Alignment explanation
Indices: 33589487--33589667 Score: 238
Period size: 81 Copynumber: 2.3 Consensus size: 79
33589477 ACCCAAGTAT
* * * *
33589487 CTTCGGGATTTAG-CCGGATATAACCACTCGCACAAGGCCTTCGGGTCTTAGCCCGGATATGGTC
1 CTTCGGGACTTAGCCCGGATATAACCACTAGCACAAGGCCTTCGGATCTTAGCCCGGATATAGTC
* *
33589551 ACTAGCATAAATGC
66 ACTAGCACAAAAGC
** * * *
33589565 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGCCTTCGGATCTTAGTCCGGATATAGT
1 CTTCGGGACTTAGCCCGGATATAACCACTAGCAC-AAGGCCTTCGGATCTTAGCCCGGATATAGT
33589630 CACTTAGCACAAAAGC
65 CAC-TAGCACAAAAGC
33589646 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
33589668 CATTCGAATA
Statistics
Matches: 89, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
78 12 0.13
79 16 0.18
80 29 0.33
81 32 0.36
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.25
Consensus pattern (79 bp):
CTTCGGGACTTAGCCCGGATATAACCACTAGCACAAGGCCTTCGGATCTTAGCCCGGATATAGTC
ACTAGCACAAAAGC
Found at i:33593909 original size:40 final size:40
Alignment explanation
Indices: 33593854--33594035 Score: 278
Period size: 40 Copynumber: 4.6 Consensus size: 40
33593844 ATTCGGATTG
*
33593854 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
*
33593894 ATAACCGGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
33593934 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
* *
33593974 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA-CT
* **
33594014 ATATCC-GGCTAAACCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
33594036 TACTTGGTTT
Statistics
Matches: 133, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 16 0.12
40 117 0.88
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.21
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
Found at i:33595929 original size:19 final size:20
Alignment explanation
Indices: 33595892--33595929 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
33595882 GATCTCATGG
*
33595892 ATCTGGGCCGTACATAGGCC
1 ATCTGGGCCGGACATAGGCC
33595912 ATCTGGGCCGGA-ATAGGC
1 ATCTGGGCCGGACATAGGC
33595930 TAAATGGGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.21, C:0.26, G:0.34, T:0.18
Consensus pattern (20 bp):
ATCTGGGCCGGACATAGGCC
Found at i:33596070 original size:29 final size:28
Alignment explanation
Indices: 33596038--33596111 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 28
33596028 TTCGGGTCAG
33596038 ATGGGCCATATGAATGTGATTTGGGCCTA
1 ATGGGCCATATGAATGTGA-TTGGGCCTA
*
33596067 ATGGGCCATATGAATGAGATTGGGCCTA
1 ATGGGCCATATGAATGTGATTGGGCCTA
* *
33596095 ATGGGCCAGATGCATGT
1 ATGGGCCATATGAATGT
33596112 ATGTAGACTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 23 0.56
29 18 0.44
ACGTcount: A:0.26, C:0.15, G:0.32, T:0.27
Consensus pattern (28 bp):
ATGGGCCATATGAATGTGATTGGGCCTA
Found at i:33596098 original size:28 final size:29
Alignment explanation
Indices: 33596038--33596102 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
33596028 TTCGGGTCAG
*
33596038 ATGGGCCATATGAATGTGATTTGGGCCTA
1 ATGGGCCATATGAATGAGATTTGGGCCTA
33596067 ATGGGCCATATGAATGAGA-TTGGGCCTA
1 ATGGGCCATATGAATGAGATTTGGGCCTA
33596095 ATGGGCCA
1 ATGGGCCA
33596103 GATGCATGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
28 17 0.49
29 18 0.51
ACGTcount: A:0.26, C:0.15, G:0.32, T:0.26
Consensus pattern (29 bp):
ATGGGCCATATGAATGAGATTTGGGCCTA
Found at i:33596426 original size:26 final size:27
Alignment explanation
Indices: 33596388--33596448 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
33596378 CAAGGTAAGT
*
33596388 AAAA-ACCCGTAATAAG-AAAATTACC
1 AAAATACCCCTAATAAGTAAAATTACC
** *
33596413 AAAATACCCCTAATTTGTGAAATTACC
1 AAAATACCCCTAATAAGTAAAATTACC
33596440 AAAATACCC
1 AAAATACCC
33596449 TCAACTTGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 4 0.13
26 9 0.30
27 17 0.57
ACGTcount: A:0.49, C:0.23, G:0.07, T:0.21
Consensus pattern (27 bp):
AAAATACCCCTAATAAGTAAAATTACC
Found at i:33596439 original size:27 final size:27
Alignment explanation
Indices: 33596405--33596533 Score: 104
Period size: 27 Copynumber: 4.8 Consensus size: 27
33596395 CGTAATAAGA
*
33596405 AAATTACCAAAATACCCCTAATTTGTG
1 AAATTACCAAAATACCCCTAACTTGTG
33596432 AAATTACCAAAATA-CCCTCAACTTGT-
1 AAATTACCAAAATACCCCT-AACTTGTG
* * * *
33596458 ACAATTATCGAAATA-CCCTCGACTTGTA
1 A-AATTACCAAAATACCCCT-AACTTGTG
* **
33596486 AAATTACCAAAATGCCCCTAA-GGGTG
1 AAATTACCAAAATACCCCTAACTTGTG
* *
33596512 AGAATGACTAAAATACCCCTAA
1 A-AATTACCAAAATACCCCTAA
33596534 GTGTTGAATG
Statistics
Matches: 83, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
26 8 0.10
27 70 0.84
28 5 0.06
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.25
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTAACTTGTG
Found at i:33603348 original size:55 final size:55
Alignment explanation
Indices: 33603215--33603357 Score: 164
Period size: 55 Copynumber: 2.6 Consensus size: 55
33603205 ATAAAGGTCT
* ** * *
33603215 ACGCCCGTGTTATTTTGGCAA-GTTCGGCCACGGTTGCTTGGCACGGGCGTGTTGC
1 ACGCCCATGTTATTTTGG-AAGGTTCGGCCACGGTTGCCAGGCACGGGCATGTCGC
* *
33603270 ACGCCCATGTTAATTT-GACAGGTTCGGCCACGGTTTCCAGGCACGGGCATGTCGC
1 ACGCCCATGTTATTTTGGA-AGGTTCGGCCACGGTTGCCAGGCACGGGCATGTCGC
* * *
33603325 ACGCCCATTTTGTTTTGGAAGGTTCGCCCACGG
1 ACGCCCATGTTATTTTGGAAGGTTCGGCCACGG
33603358 CCATGTCACA
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
53 1 0.01
54 2 0.03
55 69 0.93
56 2 0.03
ACGTcount: A:0.15, C:0.27, G:0.31, T:0.27
Consensus pattern (55 bp):
ACGCCCATGTTATTTTGGAAGGTTCGGCCACGGTTGCCAGGCACGGGCATGTCGC
Found at i:33611185 original size:31 final size:31
Alignment explanation
Indices: 33611150--33611210 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
33611140 TGGCCCCATT
33611150 CTTTCTAATCTTATCTACCAGAGGCTTAATA
1 CTTTCTAATCTTATCTACCAGAGGCTTAATA
33611181 CTTTCTAATCTTATCTACCAGAGGCTTAAT
1 CTTTCTAATCTTATCTACCAGAGGCTTAAT
33611211 TAACTGAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.39
Consensus pattern (31 bp):
CTTTCTAATCTTATCTACCAGAGGCTTAATA
Found at i:33613107 original size:42 final size:42
Alignment explanation
Indices: 33612995--33613111 Score: 112
Period size: 42 Copynumber: 2.8 Consensus size: 42
33612985 TAGAAAACAT
* * * *
33612995 ATACAATGCCAATAT-CCAGACATGGTCTTACATGTAATCAA
1 ATACGATGCCAATATCCCAAACATGGTCTTACACGAAATCAA
* * * * *
33613036 ATATCGATGCCACTGTCTCAAACAGGGTCTTACACGAAA-CTAG
1 ATA-CGATGCCAATATCCCAAACATGGTCTTACACGAAATC-AA
*
33613079 ATACGATGCCAATATCCCAAATATGGTCTTACA
1 ATACGATGCCAATATCCCAAACATGGTCTTACA
33613112 TGTAAAACAG
Statistics
Matches: 59, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
41 3 0.05
42 35 0.59
43 21 0.36
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.26
Consensus pattern (42 bp):
ATACGATGCCAATATCCCAAACATGGTCTTACACGAAATCAA
Found at i:33615035 original size:24 final size:24
Alignment explanation
Indices: 33615007--33615055 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
33614997 TAGTTCAATT
* *
33615007 TTCATAGATCAGCCCGTTCAGAGA
1 TTCATAGATCAACCCATTCAGAGA
*
33615031 TTCATAGATCAACCTATTCAGAGA
1 TTCATAGATCAACCCATTCAGAGA
33615055 T
1 T
33615056 GACAGTAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (24 bp):
TTCATAGATCAACCCATTCAGAGA
Found at i:33617741 original size:43 final size:43
Alignment explanation
Indices: 33617680--33617765 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
33617670 TGTATTAAGC
* *
33617680 ATTGTAATTATTATGCTTTTAGTTCTTTGATATTGCATAAATT
1 ATTGTAATAATTATGCTTTTAGTGCTTTGATATTGCATAAATT
33617723 ATTGTAATAATTATGCTTTTAGTGCTTTGATATTGCATAAATT
1 ATTGTAATAATTATGCTTTTAGTGCTTTGATATTGCATAAATT
33617766 GTATATACGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.29, C:0.07, G:0.13, T:0.51
Consensus pattern (43 bp):
ATTGTAATAATTATGCTTTTAGTGCTTTGATATTGCATAAATT
Found at i:33617896 original size:40 final size:40
Alignment explanation
Indices: 33617801--33617900 Score: 128
Period size: 40 Copynumber: 2.5 Consensus size: 40
33617791 CGATGACAAA
33617801 TCGGCTATTTGTGGCACTTAGTGTGCGATTCGACAAAGCT
1 TCGGCTATTTGTGGCACTTAGTGTGCGATTCGACAAAGCT
* * * ** *
33617841 TCAGATATTTGTGGCACTTAGTGTGCGATTTGTGATAGCT
1 TCGGCTATTTGTGGCACTTAGTGTGCGATTCGACAAAGCT
* *
33617881 TCGGCTATGTATGGCACTTA
1 TCGGCTATTTGTGGCACTTA
33617901 ACATGCGAGA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (40 bp):
TCGGCTATTTGTGGCACTTAGTGTGCGATTCGACAAAGCT
Found at i:33619861 original size:14 final size:14
Alignment explanation
Indices: 33619828--33619862 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
33619818 ATATGGTTCA
*
33619828 ACAAAATAACAAAC
1 ACAAAACAACAAAC
33619842 -CAAAACAACAAAC
1 ACAAAACAACAAAC
33619855 ACAAAACA
1 ACAAAACA
33619863 CTTGAGGACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.71, C:0.26, G:0.00, T:0.03
Consensus pattern (14 bp):
ACAAAACAACAAAC
Found at i:33624072 original size:26 final size:26
Alignment explanation
Indices: 33624037--33624101 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
33624027 TCAATCACAA
33624037 TTCTT-TTATTTCTA-TTCTGTACTTT
1 TTCTTATTATTTCTACTTCTG-ACTTT
* *
33624062 TTCTTATTATTTTTACTTTTGACTTT
1 TTCTTATTATTTCTACTTCTGACTTT
33624088 TTCTTAATT-TTTCT
1 TTCTT-ATTATTTCT
33624102 TTGTCGCACA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 5 0.15
26 22 0.65
27 7 0.21
ACGTcount: A:0.14, C:0.14, G:0.03, T:0.69
Consensus pattern (26 bp):
TTCTTATTATTTCTACTTCTGACTTT
Found at i:33643849 original size:29 final size:28
Alignment explanation
Indices: 33643807--33643861 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
33643797 CAGTTATGCC
33643807 GATTTGGCCTTGGGCCATGCATATCAGCT
1 GATTTGGCCTTGGGCCATG-ATATCAGCT
*
33643836 GATTTGGCTTTGGGCCATGATATCAG
1 GATTTGGCCTTGGGCCATGATATCAG
33643862 TACTTTGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (28 bp):
GATTTGGCCTTGGGCCATGATATCAGCT
Found at i:33651147 original size:49 final size:48
Alignment explanation
Indices: 33651070--33651249 Score: 201
Period size: 49 Copynumber: 3.8 Consensus size: 48
33651060 GGGGTAAGGT
* *
33651070 GCTGTTGCCATGTCCCAGACATGGTCTTACATTGGCTATCATCTTCGA
1 GCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTTCGA
* * * *
33651118 GGCTGATGCCATGTCCCAGACATAGTCTTACACTAGCTCTCA-CATGTCTA
1 -GCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATC-T-TCGA
*
33651168 TGCTGATGCCATGTCCCAGACATGGTCTTACACTGAC-A-CATC-TCGTA
1 -GCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTTCG-A
*
33651215 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCT
1 GCTGATGCCATGTCCCAGACATGGTCTTACACTGGCT
33651250 TACGTCCCGA
Statistics
Matches: 112, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
44 12 0.11
45 14 0.12
46 8 0.07
47 1 0.01
48 3 0.03
49 38 0.34
50 36 0.32
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (48 bp):
GCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCTTCGA
Found at i:33655903 original size:42 final size:42
Alignment explanation
Indices: 33655826--33655905 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
33655816 TGCAGAGGAC
* *
33655826 ACACGGCCAGAACACATGCCCATGTGGCAAGCCGTGTGTCAT
1 ACACGGCCAGAACACACGCCCATGTGGCAACCCGTGTGTCAT
* * *
33655868 ACACGGCCTAG-ACACACGCCCGTGTGTCTACCCGTGTG
1 ACACGGCC-AGAACACACGCCCATGTGGCAACCCGTGTG
33655906 GACAAAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
42 30 0.94
43 2 0.06
ACGTcount: A:0.23, C:0.34, G:0.26, T:0.17
Consensus pattern (42 bp):
ACACGGCCAGAACACACGCCCATGTGGCAACCCGTGTGTCAT
Found at i:33662786 original size:17 final size:17
Alignment explanation
Indices: 33662744--33662789 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
33662734 TATCATTTAC
33662744 CATTTATCGGGCATTAT
1 CATTTATCGGGCATTAT
* *
33662761 TATTAATCGGGCACTT-T
1 CATTTATCGGGCA-TTAT
33662778 CATTTATCGGGC
1 CATTTATCGGGC
33662790 TATAACGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 22 0.92
18 2 0.08
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.39
Consensus pattern (17 bp):
CATTTATCGGGCATTAT
Found at i:33667567 original size:21 final size:21
Alignment explanation
Indices: 33667516--33667569 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
33667506 TTACAGGCTC
* *
33667516 GCACGCCCATGTGATCCGAGG
1 GCACGCCCGTGTGACCCGAGG
*
33667537 GACATGCCCGTGTGACCCTG-GG
1 G-CACGCCCGTGTGACCC-GAGG
33667559 GCACGCCCGTG
1 GCACGCCCGTG
33667570 CTGCAGGCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 10 0.37
22 16 0.59
23 1 0.04
ACGTcount: A:0.15, C:0.35, G:0.35, T:0.15
Consensus pattern (21 bp):
GCACGCCCGTGTGACCCGAGG
Found at i:33672333 original size:17 final size:17
Alignment explanation
Indices: 33672291--33672336 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
33672281 TATCATTTAC
33672291 CATTTATCGGGCATTAT
1 CATTTATCGGGCATTAT
* *
33672308 TATTGATCGGGCACTT-T
1 CATTTATCGGGCA-TTAT
33672325 CATTTATCGGGC
1 CATTTATCGGGC
33672337 TATAATGAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 22 0.92
18 2 0.08
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (17 bp):
CATTTATCGGGCATTAT
Found at i:33698735 original size:20 final size:20
Alignment explanation
Indices: 33698703--33698775 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
33698693 TTGTACGGGA
*
33698703 TTGCACTTTGGTGCCTCTGT
1 TTGCACTTCGGTGCCTCTGT
*
33698723 TTGCATTTCGGTGCCTCTAG-
1 TTGCACTTCGGTGCCTCT-GT
* *
33698743 TTGCACTTCAGTGCCTCTAT
1 TTGCACTTCGGTGCCTCTGT
*
33698763 TTACACTTCGGTG
1 TTGCACTTCGGTG
33698776 TCTAATGCGT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 43 0.98
21 1 0.02
ACGTcount: A:0.11, C:0.26, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGCACTTCGGTGCCTCTGT
Found at i:33699766 original size:20 final size:20
Alignment explanation
Indices: 33699728--33699775 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
33699718 TAAATTCTAA
* **
33699728 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGATAATT
33699748 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
33699768 AAA-ATAAA
1 AAAGATAAA
33699776 ATCCTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:33704811 original size:27 final size:26
Alignment explanation
Indices: 33704785--33705189 Score: 515
Period size: 27 Copynumber: 15.0 Consensus size: 26
33704775 GGAAAGTTAT
*
33704785 CGAAATACCCCTGTAGGTTAGAATTA
1 CGAAATACCCCTGTAGGGTAGAATTA
*
33704811 TCGAAATACCCTTGTAGGGTAGAATTA
1 -CGAAATACCCCTGTAGGGTAGAATTA
*
33704838 CCGAAATACCCTTGTAGGGTAGAATTA
1 -CGAAATACCCCTGTAGGGTAGAATTA
*
33704865 CCGAAATACCCTTGTAGGGTAGAATTA
1 -CGAAATACCCCTGTAGGGTAGAATTA
* *
33704892 CTGAAATACCCTTATAGGGTAGAATTA
1 C-GAAATACCCCTGTAGGGTAGAATTA
*
33704919 TCGAAATACCCTTGTAGGGTAGAATTA
1 -CGAAATACCCCTGTAGGGTAGAATTA
33704946 CCGAAATACCCCTGTAGGGTAGAATTA
1 -CGAAATACCCCTGTAGGGTAGAATTA
33704973 TCGAAATACCCCTGTAGGGTAGAATTA
1 -CGAAATACCCCTGTAGGGTAGAATTA
*
33705000 CTGAAATACTCCTGTAGGGTAGAATTA
1 C-GAAATACCCCTGTAGGGTAGAATTA
* * *
33705027 CTAAAATACCCTTGTATGGTAGAATTA
1 C-GAAATACCCCTGTAGGGTAGAATTA
*
33705054 CCGAAATACCCTTGTAGGGTAGAATTA
1 -CGAAATACCCCTGTAGGGTAGAATTA
33705081 CCGAAATACCCCTGTAGGGTAGAATTA
1 -CGAAATACCCCTGTAGGGTAGAATTA
*
33705108 CTGAAATACCCCTGTAGGATAGAATTA
1 C-GAAATACCCCTGTAGGGTAGAATTA
*
33705135 CTAAAATACCCCTGTAGGGTAGAATTA
1 C-GAAATACCCCTGTAGGGTAGAATTA
* * *
33705162 CCAAGATACCCTTGT-GGTGTAAAATTA
1 CGAA-ATACCCCTGTAGG-GTAGAATTA
33705189 C
1 C
33705190 CATTTTGCCC
Statistics
Matches: 349, Mismatches: 22, Indels: 14
0.91 0.06 0.04
Matches are distributed among these distances:
26 7 0.02
27 340 0.97
28 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (26 bp):
CGAAATACCCCTGTAGGGTAGAATTA
Found at i:33704870 original size:81 final size:80
Alignment explanation
Indices: 33704785--33705190 Score: 575
Period size: 81 Copynumber: 5.0 Consensus size: 80
33704775 GGAAAGTTAT
*
33704785 CGAAATACCCCTGTAGGTTAGAATTATCGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCT
1 CGAAATACCCCTGTAGGGTAGAATTA-CGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCT
33704850 TGTAGGGTAGAATTAC
65 TGTAGGGTAGAATTAC
* * *
33704866 CGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCTTATAGGGTAGAATTATCGAAATACCCT
1 CGAAATACCCCTGTAGGGTAGAATTAC-GAAATACCCTTGTAGGGTAGAATTACCGAAATACCCT
33704931 TGTAGGGTAGAATTAC
65 TGTAGGGTAGAATTAC
* *
33704947 CGAAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACTGAAATACTCC
1 CGAAATACCCCTGTAGGGTAGAATTA-CGAAATACCCTTGTAGGGTAGAATTACCGAAATAC-CC
33705012 -TGTAGGGTAGAATTAC
64 TTGTAGGGTAGAATTAC
** * * *
33705028 TAAAATACCCTTGTATGGTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCC
1 CGAAATACCCCTGTAGGGTAGAATTA-CGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCT
33705093 TGTAGGGTAGAATTAC
65 TGTAGGGTAGAATTAC
* * * *
33705109 TGAAATACCCCTGTAGGATAGAATTACTAAAATACCCCTGTAGGGTAGAATTACC-AAGATACCC
1 CGAAATACCCCTGTAGGGTAGAATTAC-GAAATACCCTTGTAGGGTAGAATTACCGAA-ATACCC
*
33705173 TTGT-GGTGTAAAATTAC
64 TTGTAGG-GTAGAATTAC
33705190 C
1 C
33705191 ATTTTGCCCC
Statistics
Matches: 293, Mismatches: 25, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
80 8 0.03
81 282 0.96
82 3 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (80 bp):
CGAAATACCCCTGTAGGGTAGAATTACGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCTT
GTAGGGTAGAATTAC
Found at i:33705447 original size:28 final size:28
Alignment explanation
Indices: 33705415--33705504 Score: 123
Period size: 28 Copynumber: 3.3 Consensus size: 28
33705405 GGAGGAAGCG
33705415 TTCTGGTGGCTATTCCACAAATATCTGT
1 TTCTGGTGGCTATTCCACAAATATCTGT
* *
33705443 TTCTGGTGGTTATGCCACAAATATCTG-
1 TTCTGGTGGCTATTCCACAAATATCTGT
33705470 TTCTGGTGGCT-TTGCCAC-AATATCTGT
1 TTCTGGTGGCTATT-CCACAAATATCTGT
*
33705497 ATCTGGTG
1 TTCTGGTG
33705505 ACTCTGTCAC
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.16
27 21 0.38
28 25 0.45
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (28 bp):
TTCTGGTGGCTATTCCACAAATATCTGT
Found at i:33705485 original size:27 final size:26
Alignment explanation
Indices: 33705414--33705524 Score: 127
Period size: 27 Copynumber: 4.1 Consensus size: 26
33705404 TGGAGGAAGC
33705414 GTTCTGGTGGCTATT-CCACAAATATCT
1 GTTCTGGTGGCT-TTGCCAC-AATATCT
33705441 GTTTCTGGTGG-TTATGCCACAAATATCT
1 G-TTCTGGTGGCTT-TGCCAC-AATATCT
33705469 GTTCTGGTGGCTTTGCCACAATATCT
1 GTTCTGGTGGCTTTGCCACAATATCT
* * *
33705495 GTATCTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTTTGCCACAATATCT
33705522 GTT
1 GTT
33705525 GGCTGATCGA
Statistics
Matches: 76, Mismatches: 3, Indels: 11
0.84 0.03 0.12
Matches are distributed among these distances:
26 11 0.14
27 41 0.54
28 24 0.32
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (26 bp):
GTTCTGGTGGCTTTGCCACAATATCT
Found at i:33705516 original size:54 final size:54
Alignment explanation
Indices: 33705414--33705524 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
33705404 TGGAGGAAGC
* **
33705414 GTTCTGGTGGCTATTCCACAAATATCTGTTTCTGGTGGTTATGCCACAAATATCT
1 GTTCTGGTGGCTATTCCACAAATATCTGTATCTGGTGACTATGCCAC-AATATCT
* *
33705469 GTTCTGGTGGCT-TTGCCAC-AATATCTGTATCTGGTGACTCTGTCACAATATCT
1 GTTCTGGTGGCTATT-CCACAAATATCTGTATCTGGTGACTATGCCACAATATCT
33705522 GTT
1 GTT
33705525 GGCTGATCGA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
53 10 0.20
54 24 0.48
55 16 0.32
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (54 bp):
GTTCTGGTGGCTATTCCACAAATATCTGTATCTGGTGACTATGCCACAATATCT
Found at i:33705857 original size:27 final size:27
Alignment explanation
Indices: 33705827--33705883 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
33705817 ATTCTGTTAA
* *
33705827 GTGGCTTTGCCACATTATCTG-ATTCTG
1 GTGGCTCTGCCACAATATCTGTA-TCTG
33705854 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTCTGCCACAATATCTGTATCTG
33705881 GTG
1 GTG
33705884 ACTTCGTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.37
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTATCTG
Found at i:33706073 original size:31 final size:31
Alignment explanation
Indices: 33706028--33706090 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
33706018 ATTTTGATTT
*
33706028 TAATTCTATTACCTGACACTGATTCTAATTC
1 TAATTCTATCACCTGACACTGATTCTAATTC
* ** *
33706059 TAATTCTGTCACCTGATTCTGATTCTGATTC
1 TAATTCTATCACCTGACACTGATTCTAATTC
33706090 T
1 T
33706091 CATTTTGATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (31 bp):
TAATTCTATCACCTGACACTGATTCTAATTC
Found at i:33706080 original size:6 final size:6
Alignment explanation
Indices: 33706071--33706111 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
33706061 ATTCTGTCAC
* * *
33706071 CTGATT CTGATT CTGATT CTCATT TTGATT CTAATT CTGAT
1 CTGATT CTGATT CTGATT CTGATT CTGATT CTGATT CTGAT
33706112 AATGTTTCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.12, T:0.51
Consensus pattern (6 bp):
CTGATT
Found at i:33706120 original size:18 final size:17
Alignment explanation
Indices: 33706099--33706132 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
33706089 CTCATTTTGA
33706099 TTCTAATTCTGATAATGT
1 TTCTAATTCTG-TAATGT
*
33706117 TTCTTATTCTGTAATG
1 TTCTAATTCTGTAATG
33706133 GGCTAAGGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (17 bp):
TTCTAATTCTGTAATGT
Found at i:33711671 original size:10 final size:11
Alignment explanation
Indices: 33711638--33711671 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
33711628 TGCTATTTCC
33711638 TTAAAGTTTGT
1 TTAAAGTTTGT
33711649 TTAAAGTTTGT
1 TTAAAGTTTGT
33711660 TTAAAG-TTGT
1 TTAAAGTTTGT
33711670 TT
1 TT
33711672 TTTCTTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.26
11 17 0.74
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (11 bp):
TTAAAGTTTGT
Found at i:33713515 original size:48 final size:48
Alignment explanation
Indices: 33713410--33713541 Score: 192
Period size: 48 Copynumber: 2.7 Consensus size: 48
33713400 CGAATTATAA
* *
33713410 CTTGATTTGGCTTCGGGCCATGGTATAGGTGTATTTCGGAGATGAGTTAC
1 CTTGATTTGGCTTCGGGCCATGGTATA-G-GTACTTCGGAGATAAGTTAC
* *
33713460 CTTGATTTGGCTACGGGCCATGGTATAGGTACTTCGGGGATAAGTTAC
1 CTTGATTTGGCTTCGGGCCATGGTATAGGTACTTCGGAGATAAGTTAC
* *
33713508 CTTGATTTGGCTTCAGGCCATGGTCTAGGTACTT
1 CTTGATTTGGCTTCGGGCCATGGTATAGGTACTT
33713542 ATCGATTGTG
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
48 48 0.64
49 1 0.01
50 26 0.35
ACGTcount: A:0.18, C:0.17, G:0.30, T:0.35
Consensus pattern (48 bp):
CTTGATTTGGCTTCGGGCCATGGTATAGGTACTTCGGAGATAAGTTAC
Found at i:33715355 original size:40 final size:40
Alignment explanation
Indices: 33715285--33715380 Score: 106
Period size: 40 Copynumber: 2.4 Consensus size: 40
33715275 CTATCGGTCT
* **
33715285 CGCACACTAAGTGCCATATATAATCGAAGTTATTTC-AATA
1 CGCACACTAAGTGCCATATATAATCAAAGTTATCCCGAA-A
* * *
33715325 CGCACACTAAGTGCTATTTAT-AGCTAAAGTTATCCCGAAA
1 CGCACACTAAGTGCCATATATAATC-AAAGTTATCCCGAAA
33715365 CGCACACTAAGTGCCA
1 CGCACACTAAGTGCCA
33715381 AACATAGTCG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
39 2 0.04
40 43 0.91
41 2 0.04
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (40 bp):
CGCACACTAAGTGCCATATATAATCAAAGTTATCCCGAAA
Found at i:33719607 original size:30 final size:30
Alignment explanation
Indices: 33719573--33719638 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
33719563 TTCGGAGTAT
* **
33719573 TTTACTAAAAAAGGCCCATTTTTAATTTTA
1 TTTACTAAAAAAGGCCCACTTAAAATTTTA
* * *
33719603 TTTAC-GAAAATGGGCCACTTAAAATTTTA
1 TTTACTAAAAAAGGCCCACTTAAAATTTTA
33719632 TTTACTA
1 TTTACTA
33719639 GAATGGGCCA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (30 bp):
TTTACTAAAAAAGGCCCACTTAAAATTTTA
Found at i:33719855 original size:24 final size:24
Alignment explanation
Indices: 33719827--33719883 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
33719817 TTTATAAGTG
*
33719827 TTAGGGTTTTATTTGTTTTAGGGT
1 TTAGGGTTTTATTTATTTTAGGGT
33719851 TTAGGGTTTTATTTATTTTAGGGT
1 TTAGGGTTTTATTTATTTTAGGGT
33719875 TTAGGGTTT
1 TTAGGGTTT
33719884 AAGAGAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.14, C:0.00, G:0.28, T:0.58
Consensus pattern (24 bp):
TTAGGGTTTTATTTATTTTAGGGT
Found at i:33719923 original size:28 final size:28
Alignment explanation
Indices: 33719889--33719987 Score: 141
Period size: 28 Copynumber: 3.6 Consensus size: 28
33719879 GGTTTAAGAG
* * * *
33719889 AAAATAAATCAAGATTTAGGGATTTTAA
1 AAAATAAATTAGGGTTTAGGAATTTTAA
33719917 AAAATAAATTAGGGTTTAGGAATTTTAA
1 AAAATAAATTAGGGTTTAGGAATTTTAA
33719945 AAAATAAATTAGGGTTTAGGAATTTT-A
1 AAAATAAATTAGGGTTTAGGAATTTTAA
33719972 AAAA-AAATTA-GGTTTA
1 AAAATAAATTAGGGTTTA
33719988 AGGTTTTAGG
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
25 6 0.09
26 6 0.09
27 5 0.07
28 50 0.75
ACGTcount: A:0.48, C:0.01, G:0.16, T:0.34
Consensus pattern (28 bp):
AAAATAAATTAGGGTTTAGGAATTTTAA
Found at i:33720307 original size:128 final size:126
Alignment explanation
Indices: 33720066--33720871 Score: 827
Period size: 126 Copynumber: 6.4 Consensus size: 126
33720056 TTTGTACAAA
* * * * * * * * * *
33720066 CAGCAAAAGTATTGGAAAAAAGCTCCCAACTGGACTCTATTTTTGTCCA-AAGTTTGTGAAAAAA
1 CAGCAAAAGTACT-GAAAAAAGCTCCCAGCTAGACGCTCTTTTTCTACAGTAGTTTCTAAAAAAA
* ** * * * * * *
33720130 TAATTTTGAGAAGACGGTTATGAAAAAATAGGTTCAAAAGCGGTTCAAGCAAGATGTACTGT
65 TAATTTTGAAAAGATAGTTATGAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGT
* * ** *
33720192 CAGCAAAAGTACTGAAAAAAGTTCCCAGCTGGATACTCTTTTTCTACAGTAGTTTTTTAAAAAAA
1 CAGCAAAAGTACTGAAAAAAGCTCCCAGCTAGACGCTCTTTTTCTACAGTAG-TTTCT-AAAAAA
* * * * * *
33720257 ATAATTTTGAGAAGATGGTTCTAAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCATTAT
64 ATAATTTTGAAAAGATAGTTATGAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGT
* * * * * *
33720320 TAGCAAAAGTATTGAAGAAAGCTCCTAGCTAGACGCTCTTTTTCTATAGTAGTTTCTAGAAAAAT
1 CAGCAAAAGTACTGAAAAAAGCTCCCAGCTAGACGCTCTTTTTCTACAGTAGTTTCTAAAAAAAT
* * * * * *
33720385 AATTTTGAAAATACAGTTTTGAAAAAATAAGGTAAAAAATGCTT-AGAGCAGGATGCACTAT
66 AATTTTGAAAAGATAGTTATGAAAAAATAGGGTAAAAAACGCTTCA-AGCAGGATGCACTGT
* * * * * * *
33720446 CAACAAAAGTATTGAAGAAAGCTCCTAGCTAGATGCTCTTTTTCTATAGTAGTTTCTAGAAAAAT
1 CAGCAAAAGTACTGAAAAAAGCTCCCAGCTAGACGCTCTTTTTCTACAGTAGTTTCTAAAAAAAT
* * * *
33720511 AATATTGAAAATATAGTTTTGAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGTACTGT
66 AATTTTGAAAAGATAGTTATGAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGT
* * *
33720572 CAGCAAAAGTACTAAAAAAAGCTCCCAGCTAGACGCTCTTTTTCTACAATAGTTTCT-GAAAAA-
1 CAGCAAAAGTACTGAAAAAAGCTCCCAGCTAGACGCTCTTTTTCTACAGTAGTTTCTAAAAAAAT
* * * *
33720635 AA-TTTAAAAAGATAGTTATGAAATAAT---GTAAAAAACGCTTCAAGCAAGATGCATTGT
66 AATTTTGAAAAGATAGTTATGAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGT
** * * * * *
33720692 CAGCAAAAGTGTTGAAAAAAGCTTCTAGCTAGACACTCTTTTTCGACAATAGTTTCTAAAAAAAA
1 CAGCAAAAGTACTGAAAAAAGCTCCCAGCTAGACGCTCTTTTTCTACAGTAGTTTCT-AAAAAAA
* * * * *
33720757 TAATTTTGAGGAAGATGGTTCTAAAAAAATAGAGTAAAAAAACGCTTCAAGCAGGATGCACTGT
65 TAATTTTGA-AAAGATAGTTATGAAAAAATAGGGT-AAAAAACGCTTCAAGCAGGATGCACTGT
* *
33720821 CAACAAAAGTACTGAAAAAAGCTCCCAGCTAGACTCTCTTTTTCTACAGTA
1 CAGCAAAAGTACTGAAAAAAGCTCCCAGCTAGACGCTCTTTTTCTACAGTA
33720872 CATCCTGCTT
Statistics
Matches: 575, Mismatches: 91, Indels: 25
0.83 0.13 0.04
Matches are distributed among these distances:
120 77 0.13
122 5 0.01
123 22 0.04
124 6 0.01
125 50 0.09
126 235 0.41
127 9 0.02
128 102 0.18
129 69 0.12
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (126 bp):
CAGCAAAAGTACTGAAAAAAGCTCCCAGCTAGACGCTCTTTTTCTACAGTAGTTTCTAAAAAAAT
AATTTTGAAAAGATAGTTATGAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGT
Found at i:33727010 original size:20 final size:20
Alignment explanation
Indices: 33726966--33727004 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
33726956 AGGGACTAAA
* *
33726966 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
33726986 ATGAAAAATTCTAAAATTT
1 ATGAAAAATTCTAAAATTT
33727005 TTTGAATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:33736574 original size:16 final size:16
Alignment explanation
Indices: 33736553--33736583 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33736543 CTACAATGGT
*
33736553 TGAAATGCCGAAAAGC
1 TGAAATGCCAAAAAGC
33736569 TGAAATGCCAAAAAG
1 TGAAATGCCAAAAAG
33736584 TAGGTTGTCG
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (16 bp):
TGAAATGCCAAAAAGC
Found at i:33737328 original size:33 final size:32
Alignment explanation
Indices: 33737281--33737344 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
33737271 CTGATTGTAT
*
33737281 ACTGTACTGATACTGTA-TTGGGCTCAGGCCCC
1 ACTGTACTGATACTG-AGATGGGCTCAGGCCCC
*
33737313 ACTGATACTGTTACTGAGATGGGCTCAGGCCC
1 ACTG-TACTGATACTGAGATGGGCTCAGGCCC
33737345 AGACTGCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 5 0.18
33 23 0.82
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (32 bp):
ACTGTACTGATACTGAGATGGGCTCAGGCCCC
Found at i:33738275 original size:42 final size:42
Alignment explanation
Indices: 33738133--33738275 Score: 97
Period size: 42 Copynumber: 3.4 Consensus size: 42
33738123 AATAAGATGC
* * * * ** *
33738133 CAACGCCATGTCCTATACGTGGTCTTACATGGGATCTCACAT
1 CAACGCCATATCCCAGACGTGGTCTTACACGAAATCTCATAT
*** * ** * *
33738175 CGTTGCCATATCCCAAATATGGTCTTATACGAAATCTCATTT
1 CAACGCCATATCCCAGACGTGGTCTTACACGAAATCTCATAT
** * * * *
33738217 TGATGTCATGTTCCAGACGTGGTCTTACACGAAATCTCATAT
1 CAACGCCATATCCCAGACGTGGTCTTACACGAAATCTCATAT
33738259 CAACGCCATATCCCAGA
1 CAACGCCATATCCCAGA
33738276 TATAGTCTTA
Statistics
Matches: 71, Mismatches: 30, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (42 bp):
CAACGCCATATCCCAGACGTGGTCTTACACGAAATCTCATAT
Found at i:33738284 original size:42 final size:42
Alignment explanation
Indices: 33738179--33738287 Score: 110
Period size: 42 Copynumber: 2.6 Consensus size: 42
33738169 TCACATCGTT
* * * ** *
33738179 GCCATATCCCAAATATGGTCTTATACGAAATCTCATTTTGAT
1 GCCATATCCCAGATATGGTCTTACACGAAATCTCATATCAAC
* * * **
33738221 GTCATGTTCCAGACGTGGTCTTACACGAAATCTCATATCAAC
1 GCCATATCCCAGATATGGTCTTACACGAAATCTCATATCAAC
*
33738263 GCCATATCCCAGATATAGTCTTACA
1 GCCATATCCCAGATATGGTCTTACA
33738288 TGATAACAAA
Statistics
Matches: 50, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (42 bp):
GCCATATCCCAGATATGGTCTTACACGAAATCTCATATCAAC
Found at i:33750954 original size:16 final size:16
Alignment explanation
Indices: 33750933--33750964 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
33750923 CTGCAAAAAG
33750933 AAAACTAGTTAATTAT
1 AAAACTAGTTAATTAT
*
33750949 AAAACTAGTTAGTTAT
1 AAAACTAGTTAATTAT
33750965 TATATGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (16 bp):
AAAACTAGTTAATTAT
Found at i:33752778 original size:16 final size:16
Alignment explanation
Indices: 33752757--33752788 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
33752747 GATGTAACGC
*
33752757 CCCAAAAATCTCGAAA
1 CCCAAAAATCCCGAAA
33752773 CCCAAAAATCCCGAAA
1 CCCAAAAATCCCGAAA
33752789 TCCTGAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.34, G:0.06, T:0.09
Consensus pattern (16 bp):
CCCAAAAATCCCGAAA
Found at i:33754273 original size:29 final size:29
Alignment explanation
Indices: 33754235--33754334 Score: 130
Period size: 29 Copynumber: 3.5 Consensus size: 29
33754225 AATGTGGCTA
33754235 GGCCTAATGGGCCATATAAATGTGATTTG
1 GGCCTAATGGGCCATATAAATGTGATTTG
* *
33754264 GGCCTAATGGGCCATATACAGGTGATTTG
1 GGCCTAATGGGCCATATAAATGTGATTTG
* ** *
33754293 GGCCTAATGGGTCATAGGAATATGA-TTG
1 GGCCTAATGGGCCATATAAATGTGATTTG
*
33754321 GGCTTAATGGGCCA
1 GGCCTAATGGGCCA
33754335 AATACAGGTA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
28 15 0.25
29 46 0.75
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (29 bp):
GGCCTAATGGGCCATATAAATGTGATTTG
Found at i:33754334 original size:57 final size:58
Alignment explanation
Indices: 33754235--33754343 Score: 157
Period size: 57 Copynumber: 1.9 Consensus size: 58
33754225 AATGTGGCTA
* * *
33754235 GGCCTAATGGGCCATATAAATGTGATTTGGGCCTAATGGGCCATATACAGGTGATTTG
1 GGCCTAATGGGCCATAGAAATATGATTTGGGCCTAATGGGCCAAATACAGGTGATTTG
* * *
33754293 GGCCTAATGGGTCATAGGAATATGA-TTGGGCTTAATGGGCCAAATACAGGT
1 GGCCTAATGGGCCATAGAAATATGATTTGGGCCTAATGGGCCAAATACAGGT
33754344 ATGTGAAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
57 24 0.53
58 21 0.47
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (58 bp):
GGCCTAATGGGCCATAGAAATATGATTTGGGCCTAATGGGCCAAATACAGGTGATTTG
Done.