Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008478.1 Hibiscus syriacus cultivar Beakdansim tig00111309_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1476524
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1010144 original size:11 final size:11
Alignment explanation
Indices: 1010130--1010205 Score: 59
Period size: 11 Copynumber: 6.5 Consensus size: 11
1010120 ATAACTTAAT
1010130 AATAATAATAA
1 AATAATAATAA
*
1010141 AATAATCATAA
1 AATAATAATAA
1010152 AGATAATAATTTAA
1 A-ATAATAA--TAA
1010166 ACAT-AT-ATCAA
1 A-ATAATAAT-AA
1010177 AAGTAATAATAA
1 AA-TAATAATAA
1010189 AATAA-AATAA
1 AATAATAATAA
1010199 TAATAAT
1 -AATAAT
1010206 TAAAATGAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
10 7 0.13
11 23 0.43
12 13 0.25
13 4 0.08
14 6 0.11
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (11 bp):
AATAATAATAA
Found at i:1011618 original size:3 final size:3
Alignment explanation
Indices: 1011610--1011661 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
1011600 ATATATATAT
* * *
1011610 TAA TAA TAA TAA TAA TAA TATT TAG TAA TAA TAA -ATT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA TAA TAA
1011656 TAA TAA
1 TAA TAA
1011662 AATTTAAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
2 1 0.02
3 37 0.90
4 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1011623 original size:31 final size:36
Alignment explanation
Indices: 1011588--1011660 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
1011578 TTTGGGCTTG
*
1011588 TAATATATA-T-ATATATATATATTAATAATAATAATAA
1 TAATATATAGTAATA-ATAAAT-TTAATAATAATAAT-A
*
1011625 TAATATTTAGTAATAATAAATTTAATAATAATAATA
1 TAATATATAGTAATAATAAATTTAATAATAATAATA
1011661 AAATTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 1 0.03
37 22 0.69
38 6 0.19
39 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (36 bp):
TAATATATAGTAATAATAAATTTAATAATAATAATA
Found at i:1011630 original size:25 final size:25
Alignment explanation
Indices: 1011588--1011657 Score: 68
Period size: 28 Copynumber: 2.6 Consensus size: 25
1011578 TTTGGGCTTG
*
1011588 TAATATATATATATATATATATTAATAA
1 TAATA-ATA-ATA-ATATATAGTAATAA
*
1011616 TAATAATAATAATATTTAGTAATAA
1 TAATAATAATAATATATAGTAATAA
1011641 TAAATTTAATAATAATA
1 T-AA--TAATAATAATA
1011658 ATAAAATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
25 13 0.35
26 5 0.14
27 3 0.08
28 16 0.43
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (25 bp):
TAATAATAATAATATATAGTAATAA
Found at i:1015595 original size:2 final size:2
Alignment explanation
Indices: 1015555--1015581 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1015545 TATGATTGAC
1015555 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1015582 GGTTAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1019696 original size:13 final size:13
Alignment explanation
Indices: 1019678--1019704 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1019668 AGGTACCTGA
1019678 TTTTTTTTTGTTT
1 TTTTTTTTTGTTT
1019691 TTTTTTTTTGTTT
1 TTTTTTTTTGTTT
1019704 T
1 T
1019705 CTTGGATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (13 bp):
TTTTTTTTTGTTT
Found at i:1021100 original size:39 final size:39
Alignment explanation
Indices: 1021052--1021185 Score: 119
Period size: 39 Copynumber: 3.4 Consensus size: 39
1021042 CTACTTAGAA
* * *
1021052 GTATGGGTACCAGAATATCAATATGAGAACTGTTTCAGC
1 GTATAGGTACCAAAATATCAATATGAGAACCGTTTCAGC
* * * * *
1021091 GTATAGGTACCAAAATATTAGTAAGGGAACCGTTTCAGA
1 GTATAGGTACCAAAATATCAATATGAGAACCGTTTCAGC
* * * *
1021130 GTATAGGCACCATAATTTCATTAT-AGGAACCGTGTT-AGC
1 GTATAGGTACCAAAATATCAATATGA-GAACCGT-TTCAGC
*
1021169 GTATAAGTACCAAAATA
1 GTATAGGTACCAAAATA
1021186 GTTGTATAAG
Statistics
Matches: 73, Mismatches: 20, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
39 71 0.97
40 2 0.03
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.28
Consensus pattern (39 bp):
GTATAGGTACCAAAATATCAATATGAGAACCGTTTCAGC
Found at i:1021353 original size:40 final size:40
Alignment explanation
Indices: 1021249--1021478 Score: 234
Period size: 40 Copynumber: 5.8 Consensus size: 40
1021239 TTACAATAAA
* * **
1021249 GGTGATGTATTG-A-ATGAGATCACACCGAAATAGGAGAGT
1 GGTGATGTATTGTACATGATA-CACACCTAAATACAAGAGT
** *
1021288 GGTGATGTATTTGTACGGGATACACACCTAAACACAAGAGT
1 GGTGATGTA-TTGTACATGATACACACCTAAATACAAGAGT
* * * **
1021329 GGTGATGTATTGTACATAATACACA-CTCAATTACAATAAA
1 GGTGATGTATTGTACATGATACACACCT-AAATACAAGAGT
* *
1021369 GGTGATGTATTATACGTGATACACACCTAAATACAAGAGT
1 GGTGATGTATTGTACATGATACACACCTAAATACAAGAGT
* * **
1021409 GGTGATGTATTGTACGA-AATGCACACCTAAATACGGGAGT
1 GGTGATGTATTGTAC-ATGATACACACCTAAATACAAGAGT
1021449 GGTGATGTATTGTACATGATACACACCTAA
1 GGTGATGTATTGTACATGATACACACCTAA
1021479 TTAATAGAAT
Statistics
Matches: 154, Mismatches: 30, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
39 12 0.08
40 112 0.73
41 27 0.18
42 3 0.02
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.27
Consensus pattern (40 bp):
GGTGATGTATTGTACATGATACACACCTAAATACAAGAGT
Found at i:1021481 original size:120 final size:120
Alignment explanation
Indices: 1021236--1021474 Score: 338
Period size: 120 Copynumber: 2.0 Consensus size: 120
1021226 GTATTAGTAC
* **
1021236 CAATTACAATAAAGGTGATGTATTGAATGAGATCACACCGAAATAGGAGAGTGGTGATGTATTTG
1 CAATTACAATAAAGGTGATGTATTGAACGAGATCACACCGAAATACAAGAGTGGTGATGTATTTG
**
1021301 TACGGGATACACACCTAAACACAAGAGTGGTGATGTATTGTACATAATACACACT
66 TACGAAATACACACCTAAACACAAGAGTGGTGATGTATTGTACATAATACACACT
* *
1021356 CAATTACAATAAAGGTGATGTATT-ATACGTGATACACACCTAAATACAAGAGTGGTGATGTA-T
1 CAATTACAATAAAGGTGATGTATTGA-ACGAGAT-CACACCGAAATACAAGAGTGGTGATGTATT
* * ** *
1021419 TGTACGAAATGCACACCTAAATACGGGAGTGGTGATGTATTGTACATGATACACAC
64 TGTACGAAATACACACCTAAACACAAGAGTGGTGATGTATTGTACATAATACACAC
1021475 CTAATTAATA
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
119 1 0.01
120 79 0.75
121 25 0.24
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (120 bp):
CAATTACAATAAAGGTGATGTATTGAACGAGATCACACCGAAATACAAGAGTGGTGATGTATTTG
TACGAAATACACACCTAAACACAAGAGTGGTGATGTATTGTACATAATACACACT
Found at i:1023811 original size:17 final size:16
Alignment explanation
Indices: 1023789--1023822 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1023779 AACCACATGG
1023789 ACGAGAAACAAGAAAAA
1 ACGAGAAA-AAGAAAAA
*
1023806 ACGAGAAAAATAAAAA
1 ACGAGAAAAAGAAAAA
1023822 A
1 A
1023823 TCAAGTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.74, C:0.09, G:0.15, T:0.03
Consensus pattern (16 bp):
ACGAGAAAAAGAAAAA
Found at i:1026666 original size:14 final size:14
Alignment explanation
Indices: 1026647--1026676 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1026637 GAGCGATACC
1026647 TCGTAATAATGATA
1 TCGTAATAATGATA
1026661 TCGTAATAATGATA
1 TCGTAATAATGATA
1026675 TC
1 TC
1026677 AACGGAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (14 bp):
TCGTAATAATGATA
Found at i:1033963 original size:65 final size:65
Alignment explanation
Indices: 1033859--1033989 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
1033849 CATTTTCATT
* *
1033859 TCCATTTAAAACATACGATATGGTATCAAAATAGACATACATGATATAAGAATACTTTTATGAAC
1 TCCATTTAAAACATACGATATGGTACCAAAATAGACATACATGATATAAGAATACTTTTATAAAC
*
1033924 TCCATTTAAAACATACGATATGGTACCAAAATAGACATACATGATATCAGAATACTTTTATAAAC
1 TCCATTTAAAACATACGATATGGTACCAAAATAGACATACATGATATAAGAATACTTTTATAAAC
1033989 T
1 T
1033990 GGAGCTCTGT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (65 bp):
TCCATTTAAAACATACGATATGGTACCAAAATAGACATACATGATATAAGAATACTTTTATAAAC
Found at i:1034463 original size:17 final size:19
Alignment explanation
Indices: 1034428--1034466 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
1034418 AGTATAATGC
1034428 ATCATCATATGCAACACACA
1 ATCATCATA-GCAACACACA
1034448 ATCATCATA-CAA-ACACA
1 ATCATCATAGCAACACACA
1034465 AT
1 AT
1034467 GATAACACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 3 0.16
20 9 0.47
ACGTcount: A:0.49, C:0.28, G:0.03, T:0.21
Consensus pattern (19 bp):
ATCATCATAGCAACACACA
Found at i:1035412 original size:20 final size:20
Alignment explanation
Indices: 1035387--1035491 Score: 77
Period size: 20 Copynumber: 5.2 Consensus size: 20
1035377 ATTGATACTT
* *
1035387 TAATTCCAGTACTGGTATTG
1 TAATTCCAATACTAGTATTG
*
1035407 TAATTCCAATA-TTGATATTG
1 TAATTCCAATACTAG-TATTG
** * * *
1035427 TAATTATAGTACCAATATTG
1 TAATTCCAATACTAGTATTG
* * * *
1035447 TAATTCCAATATTTGTACTA
1 TAATTCCAATACTAGTATTG
*
1035467 TAATTCTAATACTAGTATTG
1 TAATTCCAATACTAGTATTG
1035487 TAATT
1 TAATT
1035492 ATAGTATCAA
Statistics
Matches: 61, Mismatches: 22, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
19 2 0.03
20 59 0.97
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.44
Consensus pattern (20 bp):
TAATTCCAATACTAGTATTG
Found at i:1035423 original size:40 final size:40
Alignment explanation
Indices: 1035372--1035491 Score: 145
Period size: 40 Copynumber: 3.0 Consensus size: 40
1035362 CAAAAATTCC
* *
1035372 CCAATATTGATACTTTAATTCCAGTACTGGTATTGTAATT
1 CCAATATTGATACTTTAATTCTAGTACTAGTATTGTAATT
* * *
1035412 CCAATATTGATA-TTGTAATTATAGTACCAATATTGTAATT
1 CCAATATTGATACTT-TAATTCTAGTACTAGTATTGTAATT
* *
1035452 CCAATATTTG-TACTATAATTCTAATACTAGTATTGTAATT
1 CCAATA-TTGATACTTTAATTCTAGTACTAGTATTGTAATT
1035492 ATAGTATCAA
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
39 2 0.03
40 61 0.91
41 4 0.06
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.43
Consensus pattern (40 bp):
CCAATATTGATACTTTAATTCTAGTACTAGTATTGTAATT
Found at i:1038548 original size:44 final size:44
Alignment explanation
Indices: 1038500--1038683 Score: 133
Period size: 44 Copynumber: 4.2 Consensus size: 44
1038490 AATAGGTGTG
* * * * *
1038500 GTATATAGCGATGTTTTTTGGATACAAATACCGTAAAAGGTCTT
1 GTATATAGCGACGTTTGTCGGATACAAACACCGTAAAAGGACTT
* * * *
1038544 GTATATAGCGGCGTTTGTCGGATATAAACGCCGTTAAAGGACTT
1 GTATATAGCGACGTTTGTCGGATACAAACACCGTAAAAGGACTT
* * * * * *
1038588 GTATATATC-ATCATTTGTCGTATATAAACGCC-TCTAAAGGACTT
1 GTATATAGCGA-CGTTTGTCGGATACAAACACCGT-AAAAGGACTT
* * **
1038632 GTATATAGCTG-CGTTTGTCAGATATAAACGTCGCT-AAAGGACTT
1 GTATATAGC-GACGTTTGTCGGATACAAACACCG-TAAAAGGACTT
1038676 GTATATAG
1 GTATATAG
1038684 TGGCATTTTT
Statistics
Matches: 116, Mismatches: 18, Indels: 12
0.79 0.12 0.08
Matches are distributed among these distances:
43 1 0.01
44 114 0.98
46 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (44 bp):
GTATATAGCGACGTTTGTCGGATACAAACACCGTAAAAGGACTT
Found at i:1039052 original size:21 final size:21
Alignment explanation
Indices: 1039028--1039080 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1039018 GCTGATATGT
*
1039028 TGCTTCTCTCTGTGCTTCCGA
1 TGCTGCTCTCTGTGCTTCCGA
*
1039049 TGCTGCTCTCTGTGCTTCCGC
1 TGCTGCTCTCTGTGCTTCCGA
1039070 TGCTGCTCTCT
1 TGCTGCTCTCT
1039081 CTGTTTACCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.02, C:0.36, G:0.21, T:0.42
Consensus pattern (21 bp):
TGCTGCTCTCTGTGCTTCCGA
Found at i:1045480 original size:45 final size:45
Alignment explanation
Indices: 1045389--1045648 Score: 425
Period size: 45 Copynumber: 5.8 Consensus size: 45
1045379 GTTAAACATG
* * *
1045389 AAAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTAGT
1 AAAATAAGCTTACGAGCTTATGGAGTAAATGGTAAGTATATTGGT
*
1045433 AAAATAAGTTTACGAGCTTATGGAGTAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAGTAAATGGTAAGTATATTGGT
* *
1045478 AAAATAAGCTTACGAGCTTATGGAGTAAATGATAAGTATATTAGT
1 AAAATAAGCTTACGAGCTTATGGAGTAAATGGTAAGTATATTGGT
1045523 AAAATAAGCTTACGAGCTTATGGAGTAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAGTAAATGGTAAGTATATTGGT
*
1045568 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAGTAAATGGTAAGTATATTGGT
*
1045613 AAAATAAGCTTACGAGCTTATAGGA-TAAATGATAAG
1 AAAATAAGCTTACGAGCTTAT-GGAGTAAATGGTAAG
1045649 AAATTTTATA
Statistics
Matches: 203, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
44 24 0.12
45 176 0.87
46 3 0.01
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAGTAAATGGTAAGTATATTGGT
Found at i:1047078 original size:21 final size:21
Alignment explanation
Indices: 1047042--1047083 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
1047032 ACAAATGATA
1047042 ATGTTGTGGCAAAATGAGATGG
1 ATGTTGTGGCAAAATGA-ATGG
1047064 ATGTTGTGG-AAAATGAATGG
1 ATGTTGTGGCAAAATGAATGG
1047084 TTGTGGTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 7 0.35
22 9 0.45
ACGTcount: A:0.33, C:0.02, G:0.36, T:0.29
Consensus pattern (21 bp):
ATGTTGTGGCAAAATGAATGG
Found at i:1048654 original size:20 final size:20
Alignment explanation
Indices: 1048617--1048659 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1048607 ATTCTACCAC
*
1048617 ATGCAACTATATGCTCCTAA
1 ATGCAACTACATGCTCCTAA
* *
1048637 ATGCACCTACATGGTCCTAA
1 ATGCAACTACATGCTCCTAA
1048657 ATG
1 ATG
1048660 AGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.28
Consensus pattern (20 bp):
ATGCAACTACATGCTCCTAA
Found at i:1058998 original size:2 final size:2
Alignment explanation
Indices: 1058991--1059021 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1058981 GAAAGAAAAG
1058991 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 T
1059022 TTCCTGATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1061467 original size:13 final size:13
Alignment explanation
Indices: 1061449--1061473 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1061439 GCGATAATGA
1061449 GGTTAATGAAAAG
1 GGTTAATGAAAAG
1061462 GGTTAATGAAAA
1 GGTTAATGAAAA
1061474 ACGTATTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (13 bp):
GGTTAATGAAAAG
Found at i:1064282 original size:42 final size:42
Alignment explanation
Indices: 1064235--1064325 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
1064225 TATAAAAACC
* ** * *
1064235 CTATTGTGGCATTTTTGCTACAGACGCCGC-TAAATTACTACT
1 CTATTGTAGCATTTGGGCTAAAAACGCCGCAT-AATTACTACT
*
1064277 CTATTGCAGCATTTGGGCTAAAAACGCCGCATAATTACTACT
1 CTATTGTAGCATTTGGGCTAAAAACGCCGCATAATTACTACT
1064319 CTATTGT
1 CTATTGT
1064326 TGCGTTTGTA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 40 0.98
43 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.34
Consensus pattern (42 bp):
CTATTGTAGCATTTGGGCTAAAAACGCCGCATAATTACTACT
Found at i:1075966 original size:3 final size:3
Alignment explanation
Indices: 1075958--1076050 Score: 152
Period size: 3 Copynumber: 31.0 Consensus size: 3
1075948 ATTTATTTAT
*
1075958 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1076006 TTA TCA TTA -TA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1076051 AAAATAATAA
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.02
3 79 0.94
4 3 0.04
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1077520 original size:17 final size:17
Alignment explanation
Indices: 1077451--1077520 Score: 50
Period size: 17 Copynumber: 3.9 Consensus size: 17
1077441 TATTTTTATT
1077451 ATTATTATAGTCATATAA
1 ATTATTATA-TCATATAA
*
1077469 ATATATATATATAATAATAA
1 AT-TAT-TATATCAT-ATAA
* * * *
1077489 TTTATTTTTTTATATAA
1 ATTATTATATCATATAA
*
1077506 ATTATTTTATCATAT
1 ATTATTATATCATAT
1077521 TTTAATATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
17 16 0.39
18 7 0.17
19 9 0.22
20 9 0.22
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (17 bp):
ATTATTATATCATATAA
Found at i:1078260 original size:17 final size:18
Alignment explanation
Indices: 1078238--1078273 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1078228 TTTCTTTTCA
1078238 ATTTTTAT-ATACTTATT
1 ATTTTTATAATACTTATT
*
1078255 ATTTTTATAATATTTATT
1 ATTTTTATAATACTTATT
1078273 A
1 A
1078274 ATATTTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTTATAATACTTATT
Found at i:1079924 original size:20 final size:20
Alignment explanation
Indices: 1079895--1079935 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1079885 CCTTCATATA
*
1079895 TTTACATTTGCATTTGCATT
1 TTTACATTTGCATTTACATT
* *
1079915 TTTACGTTTGTATTTACATT
1 TTTACATTTGCATTTACATT
1079935 T
1 T
1079936 GCATATTTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.59
Consensus pattern (20 bp):
TTTACATTTGCATTTACATT
Found at i:1082760 original size:26 final size:25
Alignment explanation
Indices: 1082724--1082775 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
1082714 TCTTATACTC
1082724 ATCCAGCAAAGAAAGAAAAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAA-AAAA
*
1082750 ATCCAGCAAAGAAAGAAGAAAAAAA
1 ATCCAGCAAAGAAAGAAAAAAAAAA
1082775 A
1 A
1082776 GAAAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.69, C:0.12, G:0.15, T:0.04
Consensus pattern (25 bp):
ATCCAGCAAAGAAAGAAAAAAAAAA
Found at i:1082778 original size:12 final size:11
Alignment explanation
Indices: 1082761--1082825 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
1082751 TCCAGCAAAG
1082761 AAAGAAGAAAAA
1 AAAGAA-AAAAA
1082773 AAAG-AAAAAA
1 AAAGAAAAAAA
* **
1082783 AATGAATGAAA
1 AAAGAAAAAAA
**
1082794 ACGGAAAAAAA
1 AAAGAAAAAAA
*
1082805 AAGGAAAAAGAA
1 AAAGAAAAA-AA
1082817 AAAGAAAAA
1 AAAGAAAAA
1082826 GGGGAGAATT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
10 8 0.19
11 20 0.48
12 14 0.33
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:1082813 original size:19 final size:19
Alignment explanation
Indices: 1082771--1082827 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 19
1082761 AAAGAAGAAA
*
1082771 AAAAAGAAAAA-AAATGAATG
1 AAAAAGAAAAAGAAA--AAGG
* *
1082791 AAAACGGAAAA-AAAAAGG
1 AAAAAGAAAAAGAAAAAGG
1082809 AAAAAGAAAAAGAAAAAGG
1 AAAAAGAAAAAGAAAAAGG
1082828 GGAGAATTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 12 0.39
19 7 0.23
20 12 0.39
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (19 bp):
AAAAAGAAAAAGAAAAAGG
Found at i:1085129 original size:110 final size:108
Alignment explanation
Indices: 1084928--1085142 Score: 276
Period size: 110 Copynumber: 2.0 Consensus size: 108
1084918 CAATGCCATG
1084928 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTGGAAGTGTTCTTTGAGTTATCTGATATG
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTGGAAGTGTTCTTTGAGTTATCTGATATG
* *
1084993 GTTTGGTATGAACCCAAAAACCATCATTGGATTTA-AAAGATAATT
66 GTTCGGTAAGAACCC-AAAACCATCA-TGGA-TTAGAAAGATAATT
* * * *
1085038 TGCTCATGGTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAG-T-TCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATC-T-TGGAAGTGTTCTTTGAGTTATCTGATA
*
1085101 TGGTTCGGTAAGAATTCC-AAACCAATCATGGATTAGAAAGAT
64 TGGTTCGGTAAGAA-CCCAAAACC-ATCATGGATTAGAAAGAT
1085143 GAACATGATC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
108 3 0.03
109 15 0.16
110 54 0.58
111 4 0.04
112 17 0.18
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (108 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTGGAAGTGTTCTTTGAGTTATCTGATATG
GTTCGGTAAGAACCCAAAACCATCATGGATTAGAAAGATAATT
Found at i:1087693 original size:22 final size:22
Alignment explanation
Indices: 1087662--1087716 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
1087652 ATCTACACTC
1087662 TTCAAAGATG-CTAGATTCCCTT
1 TTCAAAGATGAC-AGATTCCCTT
* *
1087684 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
1087706 TTCAAAGATGA
1 TTCAAAGATGA
1087717 AAGCTTTATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:1088296 original size:113 final size:114
Alignment explanation
Indices: 1088104--1088540 Score: 772
Period size: 113 Copynumber: 3.9 Consensus size: 114
1088094 TTTCAAAGAT
*
1088104 TCAAATCCATCATTTGATGGATCAGCTTTTTCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
* *
1088169 AAGAAGAAAAAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
1088218 TCAAATCCATCATTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
* *
1088282 AAGAAGGAAGAAGAAATACATAATGAGAAGAATTTGTTCAACCTTTTTC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
1088331 TCAAATCAATCATTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAAAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1088395 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
1088444 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
*
1088509 AAGAAAGAAGAA-AAAGTTCATAATGAGAAGAA
66 AAGAAGGAAGAAGAAA-TTCATAATGAGAAGAA
1088541 CTCATCTGAA
Statistics
Matches: 309, Mismatches: 12, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
113 220 0.71
114 89 0.29
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (114 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:1088532 original size:40 final size:40
Alignment explanation
Indices: 1088479--1088580 Score: 170
Period size: 40 Copynumber: 2.5 Consensus size: 40
1088469 CTTTTCCAGA
1088479 AAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAG
1 AAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAG
*
1088519 AAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
1 AAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAG
*
1088559 AGGAAA-TTCATAATGAGAAGAA
1 A-AAAAGTTCATAATGAGAAGAA
1088581 ATTGATCAAC
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
40 56 0.95
41 3 0.05
ACGTcount: A:0.52, C:0.09, G:0.22, T:0.18
Consensus pattern (40 bp):
AAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAG
Found at i:1088552 original size:154 final size:153
Alignment explanation
Indices: 1088363--1088693 Score: 536
Period size: 154 Copynumber: 2.2 Consensus size: 153
1088353 CAGCTTTTCC
* *
1088363 AGAAAAAGTTCATAATGAAAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAA
* * *
1088428 TTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAAT
66 TTGATCAACCTTTTGCTCAAATCCATCACTTGATAGATCAGCTTTTCCAG-AAAAAGTTCATAAT
1088493 GAGAAGAACTCATCTGAAGAAAGA
130 GAGAAGAACTCATCTGAAGAAAGA
*
1088517 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAATTCATAATGAGAAGAAA
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAA
* ** *
1088582 TTGATCAACCTTTTGTTTGAATTCATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATG
66 TTGATCAACCTTTTGCTCAAATCCATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATG
* *
1088647 AGAAGGACTCATCTGAAGAAGGA
131 AGAAGAACTCATCTGAAGAAAGA
*
1088670 AGAAGAAGTTCATAATGAGAAGAA
1 AGAAAAAGTTCATAATGAGAAGAA
1088694 TTTGTTCGAC
Statistics
Matches: 164, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
153 59 0.36
154 105 0.64
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (153 bp):
AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAA
TTGATCAACCTTTTGCTCAAATCCATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATG
AGAAGAACTCATCTGAAGAAAGA
Found at i:1088648 original size:113 final size:113
Alignment explanation
Indices: 1088517--1088936 Score: 583
Period size: 113 Copynumber: 3.7 Consensus size: 113
1088507 TGAAGAAAGA
* *
1088517 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAATTCATAATGAGAAGAAA
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAA
* * *
1088582 TTGATCAACCTTTTGTTTGAATTCATCACTTGATAGATCAGCTTTTCC
66 TTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGATCAACTTTTCC
* *
1088630 AGAAAAAGTTCATAATGAGAAGGACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAA
* * * **
1088695 TTGTTCGACCTTTTGTTTGAATTCATCATTTGATGGATCAACATCCCC
66 TTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGATCAACTTTTCC
* *
1088743 AGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAATAAGAAGTTCATAATGAGAAGA
1 A--GAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
* * * *
1088807 ACTTGTTCAA-CTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCC
64 AATTGTTCAACCTTTT-GTTTGAATTCATCACTTGATGGATCAACTTTTCC
* * * **
1088857 AGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGC
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAA
*
1088922 TTGTTCGACCTTTTG
66 TTGTTCAACCTTTTG
1088937 CATGACTCTA
Statistics
Matches: 274, Mismatches: 28, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
112 35 0.13
113 140 0.51
114 65 0.24
115 34 0.12
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (113 bp):
AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAA
TTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGATCAACTTTTCC
Found at i:1088725 original size:267 final size:267
Alignment explanation
Indices: 1088250--1088809 Score: 863
Period size: 267 Copynumber: 2.1 Consensus size: 267
1088240 CAGCTTTTCC
*
1088250 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATACATAATGAGAAGAAT
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATACATAATGAGAAGAAA
* * *
1088315 TTGTTCAACCTTTTTCTCAAATCAATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATG
66 TTGATCAACCTTTTTCTCAAATCAATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATG
1088380 AAAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
131 AAAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
* * **
1088445 CAAATCCATCATTTGATGGATCAGCTTTTCCAG-AAAAAAGTTCATAATGAGAAGAACTCATCTG
196 CAAATCCATCATTTGATGGATCAACATCCCCAGTAAAAAAGTTCATAATGAGAAGAACTCATCTG
1088509 AAGAAAGA
261 AAG-AAGA
* *
1088517 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAATTCATAATGAGAAGAAA
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATACATAATGAGAAGAAA
* * *
1088582 TTGATCAACCTTTTGTTTGAATTC-ATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAAT
66 TTGATCAACCTTTT-TCTCAAATCAATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAAT
* * * * *
1088646 GAGAAGGACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCGACCTTTTGT
130 GAAAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * *
1088711 TTGAATTCATCATTTGATGGATCAACATCCCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCT
195 TCAAATCCATCATTTGATGGATCAACATCCCCAGTAAAAAAGTTCATAATGAGAAGAACTCATCT
1088776 GAAGAAGA
260 GAAGAAGA
* *
1088784 ATAAGAAGTTCATAATGAGAAGAACT
1 AGAAAAAGTTCATAATGAGAAGAACT
1088810 TGTTCAACTT
Statistics
Matches: 266, Mismatches: 25, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
267 228 0.86
268 38 0.14
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (267 bp):
AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATACATAATGAGAAGAAA
TTGATCAACCTTTTTCTCAAATCAATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATG
AAAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
CAAATCCATCATTTGATGGATCAACATCCCCAGTAAAAAAGTTCATAATGAGAAGAACTCATCTG
AAGAAGA
Found at i:1088833 original size:227 final size:228
Alignment explanation
Indices: 1088518--1088936 Score: 662
Period size: 227 Copynumber: 1.8 Consensus size: 228
1088508 GAAGAAAGAA
*
1088518 GAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAATTCATAATGAGAAGAAAT
1 GAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAAT
* * * *
1088583 TGATCAACCTTTTGTTTGAATTCATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATGA
66 TGATCAACCTTTTGCTCGAATTCATCACTCGATAGATCAACTTTTCCAGAAAAAGTTCATAATGA
* * *
1088648 GAAGGACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCGACCTTTTGTTT
131 GAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTGTTT
1088713 GAATTCATCATTTGATGGATCAACATCCCCAGT
196 GAATTCATCATTTGATGGATCAACATCCCCAGT
* * * *
1088746 GAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAATAAGAAGTTCATAATGAGAAGAACT
1 GAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAAT
* * * *
1088810 TGTTCAA-CTTTTCGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATG
66 TGATCAACCTTTT-GCTCGAATTCATCACTCGATAGATCAACTTTTCCAGAAAAAGTTCATAATG
*
1088874 AGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTG
130 AGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTG
1088937 CATGACTCTA
Statistics
Matches: 173, Mismatches: 17, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
226 5 0.03
227 133 0.77
228 35 0.20
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (228 bp):
GAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAAT
TGATCAACCTTTTGCTCGAATTCATCACTCGATAGATCAACTTTTCCAGAAAAAGTTCATAATGA
GAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTGTTT
GAATTCATCATTTGATGGATCAACATCCCCAGT
Found at i:1088869 original size:380 final size:380
Alignment explanation
Indices: 1088139--1088919 Score: 1183
Period size: 380 Copynumber: 2.1 Consensus size: 380
1088129 CTTTTTCAGA
*
1088139 AAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAAGAAATTCATAATGAGAAGAATTT
1 AAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAAGAAATTCATAATGAGAAGAAATT
* * *
1088204 GTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAG
66 GATCAACCTTTTGCTCAAATCCATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATGAG
1088269 AAGAACTCATCTGAAGAAGGAAGAAGAAATACATAATGAGAAGAATTTGTTCAACCTTTTTCTCA
131 AAGAACTCATCTGAAGAAGGAAGAAGAAATACATAATGAGAAGAATTTGTTCAACCTTTTTCTCA
* * **
1088334 AATCAATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAAAAGAACTCATCTGAAGA
196 AATCAATCATTTGATGGATCAACATCCCCAGAAAAAGTTCATAATGAAAAGAACTCATCTGAAGA
* * *
1088399 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGG
261 AGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGG
*
1088464 ATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAG
326 ATCAACTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAG
* * *
1088519 AAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAATTCATAATGAGAAGAAATT
1 AAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAAGAAATTCATAATGAGAAGAAATT
* ** *
1088584 GATCAACCTTTTGTTTGAATTCATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATGAG
66 GATCAACCTTTTGCTCAAATCCATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATGAG
* * * * * *
1088649 AAGGACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCGACCTTTTGTTTG
131 AAGAACTCATCTGAAGAAGGAAGAAGAAATACATAATGAGAAGAATTTGTTCAACCTTTT-TCTC
* * *
1088714 AATTC-ATCATTTGATGGATCAACATCCCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGA
195 AAATCAATCATTTGATGGATCAACATCCCCA--GAAAAAGTTCATAATGAAAAGAACTCATCTGA
* * * *
1088778 AGAA-GAATAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTCGAATTCATCACTCG
258 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTT-GCTCAAATCCATCACTCG
* *
1088841 ATGGATCAACTTTTCCAG-AGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAG
322 ATGGATCAACTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAG
*
1088899 AAGAAGTTCATAATGAGAAGA
1 AAAAAGTTCATAATGAGAAGA
1088920 GCTTGTTCGA
Statistics
Matches: 362, Mismatches: 35, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
380 259 0.72
381 69 0.19
382 34 0.09
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (380 bp):
AAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAAGAAATTCATAATGAGAAGAAATT
GATCAACCTTTTGCTCAAATCCATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATGAG
AAGAACTCATCTGAAGAAGGAAGAAGAAATACATAATGAGAAGAATTTGTTCAACCTTTTTCTCA
AATCAATCATTTGATGGATCAACATCCCCAGAAAAAGTTCATAATGAAAAGAACTCATCTGAAGA
AGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGG
ATCAACTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAG
Found at i:1089003 original size:17 final size:17
Alignment explanation
Indices: 1088981--1089039 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
1088971 CAGCATTTCC
1088981 AGAAGAAGTTCACAATG
1 AGAAGAAGTTCACAATG
*
1088998 AGAAGAA-CTCATCTGAA-G
1 AGAAGAAGTTCA-C--AATG
1089016 AAGAAGAAGTTCACAATG
1 -AGAAGAAGTTCACAATG
1089034 AGAAGA
1 AGAAGA
1089040 GCTTGTTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
16 3 0.09
17 16 0.47
18 2 0.06
19 10 0.29
20 3 0.09
ACGTcount: A:0.49, C:0.12, G:0.24, T:0.15
Consensus pattern (17 bp):
AGAAGAAGTTCACAATG
Found at i:1095536 original size:36 final size:36
Alignment explanation
Indices: 1095496--1095598 Score: 179
Period size: 36 Copynumber: 2.9 Consensus size: 36
1095486 ACGGTGATGG
*
1095496 ACATTGATACACGAATGTACCAAAGATGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
1095532 ACATTGATACACGAATATACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
1095568 ACATTGATACACGAATGTATCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
1095599 ATGGAGAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.25
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:1099802 original size:20 final size:22
Alignment explanation
Indices: 1099745--1099802 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 22
1099735 GTATAAGGAG
*
1099745 TGCATCGATGCACATGTTAAAGGA
1 TGCATCGATGCAC-TGTT-AAGAA
* *
1099769 TGCATCGGTACACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
1099789 TGCATCGATGCACT
1 TGCATCGATGCACT
1099803 TCAAGGGGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 15 0.52
22 1 0.03
23 2 0.07
24 11 0.38
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:1100788 original size:27 final size:23
Alignment explanation
Indices: 1100730--1100777 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1100720 GATTAATTAA
1100730 GTAAATGATGAGTGTATGTCTCT
1 GTAAATGATGAGTGTATGTCTCT
1100753 GTAAATGATGAGTGTATGTCTCT
1 GTAAATGATGAGTGTATGTCTCT
1100776 GT
1 GT
1100778 GTATATTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (23 bp):
GTAAATGATGAGTGTATGTCTCT
Found at i:1105168 original size:15 final size:15
Alignment explanation
Indices: 1105148--1105178 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1105138 TGTCACTTCT
1105148 TCATCTCTATTTTAA
1 TCATCTCTATTTTAA
1105163 TCATCTCTATTTTAA
1 TCATCTCTATTTTAA
1105178 T
1 T
1105179 ATTATTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.55
Consensus pattern (15 bp):
TCATCTCTATTTTAA
Found at i:1105265 original size:29 final size:29
Alignment explanation
Indices: 1105233--1105292 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
1105223 TTGACCCTTC
* *
1105233 AATTTTCTAAAA-TTTCAATTTAGTTACTA
1 AATTTTC-AAAACTTACAATTTAGTCACTA
*
1105262 AATTTTCAAAACTTACATTTTAGTCACTA
1 AATTTTCAAAACTTACAATTTAGTCACTA
1105291 AA
1 AA
1105293 CAAAATTTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.43
Consensus pattern (29 bp):
AATTTTCAAAACTTACAATTTAGTCACTA
Found at i:1106378 original size:21 final size:20
Alignment explanation
Indices: 1106354--1106403 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
1106344 GTTTTATACT
1106354 AAATATAATCTAATAGTAATA
1 AAATATAAT-TAATAGTAATA
* **
1106375 AAATTATTATTAATTTTAATA
1 AAA-TATAATTAATAGTAATA
1106396 AAATATAA
1 AAATATAA
1106404 AATTCTCCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
AAATATAATTAATAGTAATA
Found at i:1126621 original size:14 final size:14
Alignment explanation
Indices: 1126604--1126637 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1126594 TTAGAGAAAG
1126604 AGTCAACAGGTCAA-
1 AGTCAAC-GGTCAAC
1126618 AGTCAACGGTCAAC
1 AGTCAACGGTCAAC
1126632 AGTCAA
1 AGTCAA
1126638 TGATCAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.41, C:0.24, G:0.21, T:0.15
Consensus pattern (14 bp):
AGTCAACGGTCAAC
Found at i:1141811 original size:41 final size:43
Alignment explanation
Indices: 1141706--1141897 Score: 126
Period size: 43 Copynumber: 4.4 Consensus size: 43
1141696 ATAGGTCAAG
* * * *
1141706 ATCTATAGCAGC-GTTTTTGTAAC-AAGATCGTAAAATGTCAGATAT
1 ATCTATAGCAGCTTTTTTTGGAACAAACACCGTAAAATGTC----AT
* *
1141751 ATATATAGCGGCATTTTTTT-GAACAAACACCGTAAAATGTCAT
1 ATCTATAGCAGC-TTTTTTTGGAACAAACACCGTAAAATGTCAT
* ** **
1141794 ATCTATAGCAGCTTTTTTTTGGAAAAAACGTCACAAAATGTCA-
1 ATCTATAGCAGC-TTTTTTTGGAACAAACACCGTAAAATGTCAT
* * * * *
1141837 ATCTATATC-GGTGTTTTTGGAACAAACGCCGTAAAA-GTCAG
1 ATCTATAGCAGCTTTTTTTGGAACAAACACCGTAAAATGTCAT
*
1141878 ATCTATAGCGGCATTTTTTT
1 ATCTATAGCAGC-TTTTTTT
1141898 AAACAAATGC
Statistics
Matches: 116, Mismatches: 24, Indels: 16
0.74 0.15 0.10
Matches are distributed among these distances:
40 4 0.03
41 28 0.24
42 2 0.02
43 33 0.28
44 17 0.15
45 10 0.09
46 3 0.03
47 19 0.16
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (43 bp):
ATCTATAGCAGCTTTTTTTGGAACAAACACCGTAAAATGTCAT
Found at i:1145215 original size:17 final size:18
Alignment explanation
Indices: 1145176--1145217 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
1145166 AAGAGAATGA
*
1145176 AAAAATAGGTGAAGTGGG
1 AAAAATAGGTGAAGTGAG
1145194 AAAAATAGGTGAAGTGAG
1 AAAAATAGGTGAAGTGAG
1145212 AAAAAT
1 AAAAAT
1145218 GAAAAAGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (18 bp):
AAAAATAGGTGAAGTGAG
Found at i:1145330 original size:42 final size:42
Alignment explanation
Indices: 1145261--1145707 Score: 473
Period size: 42 Copynumber: 10.7 Consensus size: 42
1145251 TTATAAATTT
* * * * *
1145261 GCGGCGTTTGTAAACAAAAATGACACTAAAGTACGAGTCTATA
1 GCGGCGTTTGT-TATAAAAACGCCACTAAAGTACTAGTCTATA
* * * *
1145304 GCGGTGTTTGTTCTAAAAACGCCACTAACA-TAATACTCTATA
1 GCGGCGTTTGTTATAAAAACGCCACTAA-AGTACTAGTCTATA
* * *
1145346 GCGGCGTTT-TTACAATAACGCCACTAAAGTTA-TGAGTCTTTA
1 GCGGCGTTTGTTATAAAAACGCCACTAAAG-TACT-AGTCTATA
* * * *
1145388 ACGGCGTTTG-TAT-ACAACGCCACTAAAGTACGATTCTATA
1 GCGGCGTTTGTTATAAAAACGCCACTAAAGTACTAGTCTATA
* *
1145428 GCGGCATTTGTTCA-AAAAACACCACTAAAGTACTAGTCTATA
1 GCGGCGTTTGTT-ATAAAAACGCCACTAAAGTACTAGTCTATA
* *
1145470 GCGGCGTTTGTATAAAAAAACGCCATTAAAGTACTAGTCTATA
1 GCGGCGTTTGT-TATAAAAACGCCACTAAAGTACTAGTCTATA
* * * *
1145513 GTGGCGTTT-TTATAAATACGCCACTAAAGTAC-AGTCTTTG
1 GCGGCGTTTGTTATAAAAACGCCACTAAAGTACTAGTCTATA
*
1145553 GCGGCATTTG-TATAAAAACGCCACTAAAGTACTAGTCTATA
1 GCGGCGTTTGTTATAAAAACGCCACTAAAGTACTAGTCTATA
** * *
1145594 GCGGCGTTTAATATAAAAACGCCACTAAAGTACAAGTATATA
1 GCGGCGTTTGTTATAAAAACGCCACTAAAGTACTAGTCTATA
* *
1145636 GCGGCGTTTG-TATAAAAACACCACTAAAGTACTAGTCTTTA
1 GCGGCGTTTGTTATAAAAACGCCACTAAAGTACTAGTCTATA
* *
1145677 GCGGCGTTTGTTCTAAAAACACCACTAAAGT
1 GCGGCGTTTGTTATAAAAACGCCACTAAAGT
1145708 TCAAGTGTTT
Statistics
Matches: 338, Mismatches: 51, Indels: 31
0.80 0.12 0.07
Matches are distributed among these distances:
40 51 0.15
41 101 0.30
42 140 0.41
43 46 0.14
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (42 bp):
GCGGCGTTTGTTATAAAAACGCCACTAAAGTACTAGTCTATA
Found at i:1145570 original size:83 final size:83
Alignment explanation
Indices: 1145261--1145713 Score: 486
Period size: 83 Copynumber: 5.4 Consensus size: 83
1145251 TTATAAATTT
* * * * * * *
1145261 GCGGCGTTTGTAAACAAAAATGACACTAAAGTACGAGTCTATAGCGGTGTTTGTTCTAAAAACGC
1 GCGGCGTTTGT-TATAAAAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTG-TATAAAAACGC
* *
1145326 CACTAACA-TAATACTCTATA
64 CACTAA-AGTACTAGTCTATA
* * ** * * *
1145346 GCGGCGTTT-TTACAATAACGCCACTAAAGTTATGAGTCTTTAACGGCGTTTGTAT-ACAACGCC
1 GCGGCGTTTGTTATAAAAACGCCACTAAAG-TACAAGTCTATAGCGGCGTTTGTATAAAAACGCC
* *
1145409 ACTAAAGTACGATTCTATA
65 ACTAAAGTACTAGTCTATA
* * *
1145428 GCGGCATTTGTTCA-AAAAACACCACTAAAGTACTAGTCTATAGCGGCGTTTGTATAAAAAAACG
1 GCGGCGTTTGTT-ATAAAAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTAT--AAAAACG
*
1145492 CCATTAAAGTACTAGTCTATA
63 CCACTAAAGTACTAGTCTATA
* * * * *
1145513 GTGGCGTTT-TTATAAATACGCCACTAAAGTAC-AGTCTTTGGCGGCATTTGTATAAAAACGCCA
1 GCGGCGTTTGTTATAAAAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCA
1145576 CTAAAGTACTAGTCTATA
66 CTAAAGTACTAGTCTATA
** * *
1145594 GCGGCGTTTAATATAAAAACGCCACTAAAGTACAAGTATATAGCGGCGTTTGTATAAAAACACCA
1 GCGGCGTTTGTTATAAAAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCA
*
1145659 CTAAAGTACTAGTCTTTA
66 CTAAAGTACTAGTCTATA
* * *
1145677 GCGGCGTTTGTTCTAAAAACACCACTAAAGTTCAAGT
1 GCGGCGTTTGTTATAAAAACGCCACTAAAGTACAAGT
1145714 GTTTTATGGC
Statistics
Matches: 312, Mismatches: 46, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
81 36 0.12
82 71 0.23
83 127 0.41
84 39 0.12
85 39 0.12
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (83 bp):
GCGGCGTTTGTTATAAAAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCA
CTAAAGTACTAGTCTATA
Found at i:1145570 original size:124 final size:124
Alignment explanation
Indices: 1145284--1145707 Score: 516
Period size: 124 Copynumber: 3.4 Consensus size: 124
1145274 ACAAAAATGA
** * * *
1145284 CACTAAAGTACGAGTCTATAGCGGTGTTTGTTCTAAAAACGCCACTAACA-TAATACTCTATAGC
1 CACTAAAGTACGAGTCTATAGCGGCATTTGTTCTAAAAACACCACTAA-AGTACTAGTCTATAGC
* * * * *
1145348 GGCGTTTT-TACAATAACGCCACTAAAGTTA-TGAGTCTTTAACGGCGTTTGTATACAACGC
65 GGCGTTTTATAAAAAAACGCCACTAAAG-TACT-AGTCTATAGCGGCGTTTGTATAAAACGC
* *
1145408 CACTAAAGTACGATTCTATAGCGGCATTTGTTCAAAAAACACCACTAAAGTACTAGTCTATAGCG
1 CACTAAAGTACGAGTCTATAGCGGCATTTGTTCTAAAAACACCACTAAAGTACTAGTCTATAGCG
* * *
1145473 GCGTTTGTATAAAAAAACGCCATTAAAGTACTAGTCTATAGTGGCGTTTTTATAAATACGC
66 GCGTTT-TATAAAAAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTATAAA-ACGC
* * * *
1145534 CACTAAAGTAC-AGTCTTTGGCGGCATTTG-TATAAAAACGCCACTAAAGTACTAGTCTATAGCG
1 CACTAAAGTACGAGTCTATAGCGGCATTTGTTCTAAAAACACCACTAAAGTACTAGTCTATAGCG
* * * * *
1145597 GCGTTTAATATAAAAACGCCACTAAAGTACAAGTATATAGCGGCGTTTGTATAAAAACAC
66 GCGTTTTATAAAAAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTAT-AAAACGC
* * *
1145657 CACTAAAGTACTAGTCTTTAGCGGCGTTTGTTCTAAAAACACCACTAAAGT
1 CACTAAAGTACGAGTCTATAGCGGCATTTGTTCTAAAAACACCACTAAAGT
1145708 TCAAGTGTTT
Statistics
Matches: 259, Mismatches: 33, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
123 54 0.21
124 118 0.46
125 55 0.21
126 32 0.12
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29
Consensus pattern (124 bp):
CACTAAAGTACGAGTCTATAGCGGCATTTGTTCTAAAAACACCACTAAAGTACTAGTCTATAGCG
GCGTTTTATAAAAAAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTATAAAACGC
Found at i:1147161 original size:26 final size:24
Alignment explanation
Indices: 1147119--1147186 Score: 68
Period size: 26 Copynumber: 2.8 Consensus size: 24
1147109 TTATAAATTC
*
1147119 TATTAATTAT-TTATTAAAGTAATAG
1 TATTAATTATATT-TTAAA-AAATAG
*
1147144 TATTATATTATATTTTAAAAAATAT
1 TATTA-ATTATATTTTAAAAAATAG
1147169 TAATTAA-TATATTTTAAA
1 T-ATTAATTATATTTTAAA
1147187 TATATTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
24 11 0.29
25 11 0.29
26 14 0.37
27 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (24 bp):
TATTAATTATATTTTAAAAAATAG
Found at i:1147197 original size:23 final size:24
Alignment explanation
Indices: 1147152--1147204 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
1147142 AGTATTATAT
1147152 TATATTTTAAAAAATATTAATTAA
1 TATATTTTAAAAAATATTAATTAA
* *
1147176 TATATTTT-AAATATATTTATTAA
1 TATATTTTAAAAAATATTAATTAA
*
1147199 AATATT
1 TATATT
1147205 ATTAGATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TATATTTTAAAAAATATTAATTAA
Found at i:1147206 original size:11 final size:11
Alignment explanation
Indices: 1147162--1147208 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
1147152 TATATTTTAA
1147162 AAAATATTAATT
1 AAAATATT-ATT
*
1147174 AATATATT-TT
1 AAAATATTATT
1147184 AAATATATTTATT
1 AAA-ATA-TTATT
1147197 AAAATATTATT
1 AAAATATTATT
1147208 A
1 A
1147209 GATTATCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
10 4 0.13
11 9 0.30
12 12 0.40
13 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
AAAATATTATT
Found at i:1147272 original size:18 final size:18
Alignment explanation
Indices: 1147210--1147273 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
1147200 ATATTATTAG
*
1147210 ATTATCATATTAAT-ATTA
1 ATTA-CATATTAATAATTT
*
1147228 AATACATA--AATAATGTT
1 ATTACATATTAATAAT-TT
1147245 ATT-CATTATTAATAATTT
1 ATTACA-TATTAATAATTT
1147263 ATTACATATTA
1 ATTACATATTA
1147274 TTAAAATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
15 3 0.08
16 4 0.11
17 9 0.24
18 13 0.35
19 8 0.22
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTACATATTAATAATTT
Found at i:1147344 original size:33 final size:33
Alignment explanation
Indices: 1147301--1147363 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1147291 ATGTTATTAT
*
1147301 AATATAATTAAATATTTT-ATTATAATATTAAA
1 AATATAATTAAATATTTTAATAATAATATTAAA
1147333 AATATATATTAAATATTTTAATAATAATATT
1 AATATA-ATTAAATATTTTAATAATAATATT
1147364 TTGATTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 6 0.21
33 12 0.43
34 10 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
AATATAATTAAATATTTTAATAATAATATTAAA
Found at i:1147395 original size:13 final size:13
Alignment explanation
Indices: 1147310--1147395 Score: 55
Period size: 11 Copynumber: 7.1 Consensus size: 13
1147300 TAATATAATT
1147310 AAATATTTTATTA
1 AAATATTTTATTA
*
1147323 TAATA--TTA--A
1 AAATATTTTATTA
*
1147332 AAATA-TATATT-
1 AAATATTTTATTA
*
1147343 AAATATTTTAATA
1 AAATATTTTATTA
1147356 ATAATATTTTGATTA
1 A-AATATTTT-ATTA
1147371 AAATGA---TATTA
1 AAAT-ATTTTATTA
1147382 AAATATTTTATTA
1 AAATATTTTATTA
1147395 A
1 A
1147396 TTATAAATTC
Statistics
Matches: 56, Mismatches: 6, Indels: 22
0.67 0.07 0.26
Matches are distributed among these distances:
9 5 0.09
10 3 0.05
11 16 0.29
12 5 0.09
13 11 0.20
14 11 0.20
15 5 0.09
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (13 bp):
AAATATTTTATTA
Found at i:1163582 original size:20 final size:22
Alignment explanation
Indices: 1163557--1163596 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
1163547 ATATTATTGT
*
1163557 ACTATTTTA-TTTTA-ATTTAA
1 ACTATTATACTTTTATATTTAA
1163577 ACTATTATACTTTTATATTT
1 ACTATTATACTTTTATATTT
1163597 TTTTTATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 5 0.29
22 4 0.24
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (22 bp):
ACTATTATACTTTTATATTTAA
Found at i:1170280 original size:31 final size:31
Alignment explanation
Indices: 1170238--1170296 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1170228 GGTTAACGGA
*
1170238 ATGTAAAATTACCTGTGGGAATAAAAAAGGT
1 ATGTAAAATTACCAGTGGGAATAAAAAAGGT
*
1170269 ATGTAAGATTACCAGTGGGAATAAAAAA
1 ATGTAAAATTACCAGTGGGAATAAAAAA
1170297 ATATCGGGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.47, C:0.07, G:0.22, T:0.24
Consensus pattern (31 bp):
ATGTAAAATTACCAGTGGGAATAAAAAAGGT
Found at i:1171616 original size:2 final size:2
Alignment explanation
Indices: 1171609--1171633 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1171599 CTTTTTACTA
1171609 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1171634 ATACAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1186851 original size:34 final size:32
Alignment explanation
Indices: 1186798--1186867 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1186788 CCTTACAAAC
*
1186798 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
1186830 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
1186864 TCCC
1 TCCC
1186868 CTTTATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:1187175 original size:21 final size:21
Alignment explanation
Indices: 1187150--1187191 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1187140 CCAGAATGAG
*
1187150 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1187171 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1187192 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1187227 original size:19 final size:19
Alignment explanation
Indices: 1187203--1187269 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1187193 TATTCAAATA
*
1187203 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAT
*
1187222 TTACTGTTCAAATAGTAAT
1 TTACTGTTCAAACAGTAAT
* *
1187241 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAACAGTAAT
*
1187260 TTACTATTCA
1 TTACTGTTCA
1187270 TAAAAACATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.40
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAT
Found at i:1187382 original size:30 final size:31
Alignment explanation
Indices: 1187335--1187425 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
1187325 AAATTTTGAA
1187335 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1187364 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1187395 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1187426 CCTTAAATTG
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 11 0.18
31 38 0.63
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1187613 original size:24 final size:24
Alignment explanation
Indices: 1187584--1187633 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1187574 TAAGCTCCCC
1187584 TTTTTTCATTAAGAAATTGAATTT
1 TTTTTTCATTAAGAAATTGAATTT
*
1187608 TTTTTTTATTAAGAAATTGAATTT
1 TTTTTTCATTAAGAAATTGAATTT
1187632 TT
1 TT
1187634 CAAACTAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (24 bp):
TTTTTTCATTAAGAAATTGAATTT
Found at i:1190194 original size:34 final size:32
Alignment explanation
Indices: 1190141--1190210 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1190131 CCTTACAAAC
*
1190141 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
1190173 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
1190207 TCCC
1 TCCC
1190211 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:1190505 original size:30 final size:31
Alignment explanation
Indices: 1190458--1190548 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
1190448 AAATTTTGAA
1190458 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
*
1190487 TAAATTCAATTCAAGTCCAAAAATCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1190518 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1190549 CCTTAAATTG
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 11 0.19
30 11 0.19
31 37 0.63
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1190702 original size:32 final size:33
Alignment explanation
Indices: 1190664--1190735 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 33
1190654 AATATCACAC
*
1190664 TTAAAAAAT-TCCGATCCGAACCCG-AATTTATT
1 TTAAAAAATATCCGACCCGAACCCGAAATTT-TT
*
1190696 TT-AAAAATATCCGACCCGATCCCGAAATTTTT
1 TTAAAAAATATCCGACCCGAACCCGAAATTTTT
1190728 TTAAAAAA
1 TTAAAAAA
1190736 ATCTAACCCG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 6 0.17
32 19 0.54
33 10 0.29
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (33 bp):
TTAAAAAATATCCGACCCGAACCCGAAATTTTT
Found at i:1190745 original size:32 final size:32
Alignment explanation
Indices: 1190664--1190747 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 32
1190654 AATATCACAC
* * *
1190664 TTAAAAAATTCCGATCCGAACCCGAATTTATT
1 TTAAAAAAATCCAACCCGAACCCGAATTTATT
* * *
1190696 TTAAAAATATCCGACCCGATCCCGAAATTT-TT
1 TTAAAAAAATCCAACCCGAACCCG-AATTTATT
*
1190728 TTAAAAAAATCTAACCCGAA
1 TTAAAAAAATCCAACCCGAA
1190748 TACCAAAAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 38 0.88
33 5 0.12
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (32 bp):
TTAAAAAAATCCAACCCGAACCCGAATTTATT
Found at i:1194706 original size:18 final size:18
Alignment explanation
Indices: 1194680--1194715 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1194670 GGTGCTTGAA
*
1194680 TCCAGGGTTTCAAATAGC
1 TCCAAGGTTTCAAATAGC
1194698 TCCAAGGTTTCAAATAGC
1 TCCAAGGTTTCAAATAGC
1194716 AGCCGAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (18 bp):
TCCAAGGTTTCAAATAGC
Found at i:1201177 original size:29 final size:30
Alignment explanation
Indices: 1201146--1201216 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
1201136 GATTTTTCAG
*
1201146 AAAATAAATTA-TTAGAATTTGAATTATAGA
1 AAAATAAATTACTGA-AATTTGAATTATAGA
*
1201176 AAAATAAATTACTGAAATTTGAATTCT-GA
1 AAAATAAATTACTGAAATTTGAATTATAGA
*
1201205 AAAATGAATTAC
1 AAAATAAATTAC
1201217 ATTTCTGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 13 0.35
30 22 0.59
31 2 0.05
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.34
Consensus pattern (30 bp):
AAAATAAATTACTGAAATTTGAATTATAGA
Found at i:1201212 original size:14 final size:15
Alignment explanation
Indices: 1201165--1201216 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
1201155 TATTAGAATT
1201165 TGAATTA-TAGAAAAA
1 TGAATTACT-GAAAAA
* **
1201180 TAAATTACTGAAATT
1 TGAATTACTGAAAAA
1201195 TGAATT-CTGAAAAA
1 TGAATTACTGAAAAA
1201209 TGAATTAC
1 TGAATTAC
1201217 ATTTCTGAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 12 0.41
15 16 0.55
16 1 0.03
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.33
Consensus pattern (15 bp):
TGAATTACTGAAAAA
Found at i:1201589 original size:29 final size:26
Alignment explanation
Indices: 1201556--1201617 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 26
1201546 TTACTAAAAT
1201556 ATTATTTAAATATATAAATAAAATTATTC
1 ATTA-TTAAATATAT-AA-AAAATTATTC
1201585 ATTATTAAATATATAAAAAATTATT-
1 ATTATTAAATATATAAAAAATTATTC
1201610 ATATATTA
1 AT-TATTA
1201618 TTAAAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
25 2 0.06
26 14 0.44
27 2 0.06
28 10 0.31
29 4 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTATTAAATATATAAAAAATTATTC
Found at i:1201604 original size:26 final size:27
Alignment explanation
Indices: 1201555--1201630 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 27
1201545 TTTACTAAAA
1201555 TATTATTTAAATATATAAATAAAATTAT
1 TATTA-TTAAATATATAAATAAAATTAT
1201583 TCATTATTAAATATATAAA-AAATTATTAT
1 T-ATTATTAAATATATAAATAAA--ATTAT
1201612 ATATTATTAAA-ATA-AAATA
1 -TATTATTAAATATATAAATA
1201631 TAATATCTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
27 6 0.14
28 18 0.42
29 18 0.42
30 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (27 bp):
TATTATTAAATATATAAATAAAATTAT
Found at i:1201669 original size:28 final size:28
Alignment explanation
Indices: 1201585--1201696 Score: 84
Period size: 28 Copynumber: 3.8 Consensus size: 28
1201575 AAAATTATTC
* *
1201585 ATTATTAAATATATAAA-AAATTATTATAT
1 ATTATTAAA-ATA-AAATATATTATTTTAT
* *
1201614 ATTATTAAAATAAAATATAATATCTTAT
1 ATTATTAAAATAAAATATATTATTTTAT
* *
1201642 ATTATTATAATATAAT-TGATTATTTTAT
1 ATTATTAAAATAAAATAT-ATTATTTTAT
*
1201670 ATAATATTAAAAATAATATTATATTAT
1 AT--TATT-AAAATAA-AATATATTAT
1201697 AAATATTAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
27 4 0.06
28 35 0.54
29 9 0.14
30 4 0.06
31 5 0.08
32 7 0.11
33 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (28 bp):
ATTATTAAAATAAAATATATTATTTTAT
Found at i:1201688 original size:17 final size:17
Alignment explanation
Indices: 1201668--1201701 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1201658 TGATTATTTT
1201668 ATATAATATTAAAAATA
1 ATATAATATTAAAAATA
* *
1201685 ATATTATATTATAAATA
1 ATATAATATTAAAAATA
1201702 TTAATAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATATTAAAAATA
Found at i:1201716 original size:50 final size:49
Alignment explanation
Indices: 1201662--1201778 Score: 116
Period size: 50 Copynumber: 2.4 Consensus size: 49
1201652 TATAATTGAT
*
1201662 TATTTTATATAATATTAAAAATAATATTAT-ATTATAAAT-ATTAATAAATA
1 TATTTTATATAATATTAAAAATAATATTATGATGA-AAATGA-TAATAAA-A
* * * * *
1201712 TATTTTAAAT-ATTTTAATAATTAATATTTTGATGAAAATGATATTAAAA
1 TATTTTATATAATATTAA-AAATAATATTATGATGAAAATGATAATAAAA
1201761 TATTTTAT-TAATATTAAA
1 TATTTTATATAATATTAAA
1201779 TTCATAAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
48 2 0.04
49 20 0.36
50 29 0.53
51 4 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.48
Consensus pattern (49 bp):
TATTTTATATAATATTAAAAATAATATTATGATGAAAATGATAATAAAA
Found at i:1203452 original size:3 final size:3
Alignment explanation
Indices: 1203444--1203471 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1203434 TTAAATTTCG
1203444 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1203472 GTCCCTATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1204530 original size:5 final size:6
Alignment explanation
Indices: 1204495--1204527 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1204485 AGACACGTAT
*
1204495 GACCAA GACCAC GACCAC GACCAC GACC-C GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACC
1204528 CGAGACGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.33, C:0.48, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:1205038 original size:5 final size:5
Alignment explanation
Indices: 1205030--1205070 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
1205020 CCGTCTCGTC
1205030 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG TCG
1205071 TGGTAATACG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.27
Consensus pattern (5 bp):
TCGGG
Found at i:1205059 original size:6 final size:6
Alignment explanation
Indices: 1205033--1205074 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
1205023 TCTCGTCTCG
1205033 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1205075 AATACGTGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.00, C:0.17, G:0.55, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:1205233 original size:20 final size:20
Alignment explanation
Indices: 1205208--1205259 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1205198 ACTGTAGACT
1205208 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
*
1205228 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
1205248 ATCGCAACGCGA
1 ATCGCAACGCGA
1205260 TTTTCAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:1206527 original size:4 final size:4
Alignment explanation
Indices: 1206518--1206542 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1206508 AACAGTGGTT
1206518 ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA A
1206543 ATATTTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:1209399 original size:35 final size:35
Alignment explanation
Indices: 1209353--1209422 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
1209343 TTCGATAAAA
1209353 CATTATTAACCTTATATTTCTTATTTTAATTATCG
1 CATTATTAACCTTATATTTCTTATTTTAATTATCG
1209388 CATTATTAACCTTATATTTCTTATTTTAATTATCG
1 CATTATTAACCTTATATTTCTTATTTTAATTATCG
1209423 ATAGTTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.14, G:0.03, T:0.54
Consensus pattern (35 bp):
CATTATTAACCTTATATTTCTTATTTTAATTATCG
Found at i:1211397 original size:14 final size:14
Alignment explanation
Indices: 1211361--1211398 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1211351 AATAAATAAG
*
1211361 AATAAAAAAGGGATA
1 AATAAAAAA-GGAAA
1211376 AAT-AAAAAGGAAA
1 AATAAAAAAGGAAA
1211389 AATAAAAAAG
1 AATAAAAAAG
1211399 AGATAACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 7 0.33
14 11 0.52
15 3 0.14
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.11
Consensus pattern (14 bp):
AATAAAAAAGGAAA
Found at i:1211685 original size:18 final size:17
Alignment explanation
Indices: 1211648--1211683 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 17
1211638 ACATATAAAT
1211648 ATAAATATAAAAAATAA
1 ATAAATATAAAAAATAA
1211665 ATAAATGATAAAATAATAA
1 ATAAAT-ATAAAA-AATAA
1211684 TATTACTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 6 0.35
19 5 0.29
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
ATAAATATAAAAAATAA
Found at i:1211765 original size:2 final size:2
Alignment explanation
Indices: 1211758--1211804 Score: 71
Period size: 2 Copynumber: 24.0 Consensus size: 2
1211748 TAAAGGAATA
1211758 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1211798 AT GAT AT
1 AT -AT AT
1211805 CAAATAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.05
2 38 0.90
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1221786 original size:44 final size:43
Alignment explanation
Indices: 1221702--1221787 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 43
1221692 CTTCTTAAAT
* *
1221702 TTTTAACTTTTTCTTTTATCTTTCATTATTAATTTCTCTTTCA
1 TTTTAACTTTTCCTTTTATCTTTCATTATTAATCTCTCTTTCA
* * *
1221745 TTTTAACTTTTACCTTTTCTCTTTCTTTCATTCATCT-TCTTTC
1 TTTTAACTTTT-CCTTTTATCTTTCATT-ATTAATCTCTCTTTC
1221788 TTTGTTATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
43 11 0.31
44 19 0.53
45 6 0.17
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (43 bp):
TTTTAACTTTTCCTTTTATCTTTCATTATTAATCTCTCTTTCA
Found at i:1240312 original size:27 final size:28
Alignment explanation
Indices: 1240282--1240346 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
1240272 AAATAAAGAA
*
1240282 ATAAATAAACAAAATAG-ATAAAATGAG
1 ATAAATAAACAAAATAGAATAAAATAAG
1240309 ATAAATAAA-AAAATAGAATAAAATAAG
1 ATAAATAAACAAAATAGAATAAAATAAG
1240336 A-AATATAAACA
1 ATAA-ATAAACA
1240347 CCAAAAAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
26 9 0.26
27 24 0.71
28 1 0.03
ACGTcount: A:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (28 bp):
ATAAATAAACAAAATAGAATAAAATAAG
Found at i:1240517 original size:18 final size:17
Alignment explanation
Indices: 1240480--1240515 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 17
1240470 ACATATAAAT
1240480 ATAAATATAAAAAATAA
1 ATAAATATAAAAAATAA
1240497 ATAAATGATAAAATAATAA
1 ATAAAT-ATAAAA-AATAA
1240516 TATTACTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 6 0.35
19 5 0.29
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
ATAAATATAAAAAATAA
Found at i:1241557 original size:16 final size:16
Alignment explanation
Indices: 1241536--1241574 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
1241526 AAAGGGTGCA
1241536 ATTGGGCTGCCGATGT
1 ATTGGGCTGCCGATGT
*
1241552 ATTGGGTTGCCGATGT
1 ATTGGGCTGCCGATGT
1241568 ATTGGGC
1 ATTGGGC
1241575 CTGTACAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.13, C:0.15, G:0.38, T:0.33
Consensus pattern (16 bp):
ATTGGGCTGCCGATGT
Found at i:1241659 original size:16 final size:17
Alignment explanation
Indices: 1241625--1241673 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
1241615 ATAAATGAAC
*
1241625 ATATATATTTATTATATA
1 ATATATATTTA-TAAATA
1241643 ATATA-ATTTATAAATA
1 ATATATATTTATAAATA
*
1241659 AAATATATTATATAA
1 ATATATATT-TATAA
1241674 TATTAATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 9 0.33
17 8 0.30
18 10 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATTTATAAATA
Found at i:1241663 original size:18 final size:19
Alignment explanation
Indices: 1241615--1241666 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
1241605 AAATAAATAA
*
1241615 ATAAATGAACATATATATTT
1 ATAAAT-AAAATATATATTT
* *
1241635 AT-TATATAATATA-ATTT
1 ATAAATAAAATATATATTT
1241652 ATAAATAAAATATAT
1 ATAAATAAAATATAT
1241667 TATATAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 5
0.71 0.14 0.14
Matches are distributed among these distances:
17 6 0.24
18 15 0.60
19 2 0.08
20 2 0.08
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
ATAAATAAAATATATATTT
Found at i:1243321 original size:3 final size:3
Alignment explanation
Indices: 1243313--1243345 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1243303 CAAGTATATG
1243313 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1243346 CACATTGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1247735 original size:31 final size:31
Alignment explanation
Indices: 1247694--1247756 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
1247684 TTTCGTTGCG
* *
1247694 ATCGGGTCCGAGTTTGGTTGGAGAAGTATGA
1 ATCGGATCCGAGTTTGGTTGGACAAGTATGA
1247725 ATCGGATCCGAGTTTGGTTGGACAAGTATGA
1 ATCGGATCCGAGTTTGGTTGGACAAGTATGA
1247756 A
1 A
1247757 CGACGCCTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.11, G:0.35, T:0.29
Consensus pattern (31 bp):
ATCGGATCCGAGTTTGGTTGGACAAGTATGA
Found at i:1255058 original size:128 final size:128
Alignment explanation
Indices: 1254830--1255083 Score: 445
Period size: 128 Copynumber: 2.0 Consensus size: 128
1254820 GTACCACCTC
* * * *
1254830 CCATGGAACTAAATTGACACCGCCGATGTCCCACACATTTCCCCGTATGAATCGTCTGTTAAGAG
1 CCATGGAACAAAATTGACACCGCCGATGTCCCACACATTTCCCCATACGAATCGTCTGATAAGAG
1254895 CTTCTATCTTATTGCAAATCTTCCGGGGCAAAACCGTTGATTGCATCGTGTAAATAGGAAGCG
66 CTTCTATCTTATTGCAAATCTTCCGGGGCAAAACCGTTGATTGCATCGTGTAAATAGGAAGCG
1254958 CCATGGAACAAAATTGACACCGCCGATGTCCCACACATTTCCCCATACGAATCGTCTGATAAGAG
1 CCATGGAACAAAATTGACACCGCCGATGTCCCACACATTTCCCCATACGAATCGTCTGATAAGAG
* * *
1255023 CTTCTATTTTATTGTAAATCTTCCGGGGCAAAACCGTTGATTGCATTGTGTAAATAGGAAG
66 CTTCTATCTTATTGCAAATCTTCCGGGGCAAAACCGTTGATTGCATCGTGTAAATAGGAAG
1255084 TGCCGCTAAA
Statistics
Matches: 119, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
128 119 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (128 bp):
CCATGGAACAAAATTGACACCGCCGATGTCCCACACATTTCCCCATACGAATCGTCTGATAAGAG
CTTCTATCTTATTGCAAATCTTCCGGGGCAAAACCGTTGATTGCATCGTGTAAATAGGAAGCG
Found at i:1256798 original size:31 final size:32
Alignment explanation
Indices: 1256760--1256833 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 32
1256750 ACTACAGGTT
* *
1256760 GATTGAATTTGAGGTTATGATGATT-GAATTG
1 GATTGAATTTGAGGTTAGGATGATTAGAATAG
1256791 GATTGAATTTGAGGTTAGGATGATTAGAATAG
1 GATTGAATTTGAGGTTAGGATGATTAGAATAG
*
1256823 CA-TGAATTTGA
1 GATTGAATTTGA
1256834 TCATAGGAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
31 33 0.85
32 6 0.15
ACGTcount: A:0.32, C:0.01, G:0.28, T:0.38
Consensus pattern (32 bp):
GATTGAATTTGAGGTTAGGATGATTAGAATAG
Found at i:1257865 original size:4 final size:4
Alignment explanation
Indices: 1257856--1258130 Score: 550
Period size: 4 Copynumber: 68.8 Consensus size: 4
1257846 TTTTCCTTAA
1257856 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1257904 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1257952 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1258000 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1258048 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1258096 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1258131 TAGTTAGATT
Statistics
Matches: 271, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 271 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:1263889 original size:54 final size:55
Alignment explanation
Indices: 1263815--1263922 Score: 164
Period size: 54 Copynumber: 2.0 Consensus size: 55
1263805 CTTTTAAGGC
* *
1263815 TAACATATTTTTTTATGATAAGAGTATGTATATGTACAAGATTTTATATTAAAAGT
1 TAACATA-TTTTTTATGATAAGAGTACGGATATGTACAAGATTTTATATTAAAAGT
**
1263871 TAACATA-TTTTTATGATAAGAGTACGGATATGTTTAAGATTTTATATTAAAA
1 TAACATATTTTTTATGATAAGAGTACGGATATGTACAAGATTTTATATTAAAA
1263923 AGATAAATGT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 41 0.85
56 7 0.15
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.44
Consensus pattern (55 bp):
TAACATATTTTTTATGATAAGAGTACGGATATGTACAAGATTTTATATTAAAAGT
Found at i:1263934 original size:29 final size:29
Alignment explanation
Indices: 1263900--1263978 Score: 140
Period size: 29 Copynumber: 2.7 Consensus size: 29
1263890 GAGTACGGAT
1263900 ATGTTTAAGATTTTATATTAAAAAGATAA
1 ATGTTTAAGATTTTATATTAAAAAGATAA
1263929 ATGTTTAAGATTTTATATTAAAAAGATAA
1 ATGTTTAAGATTTTATATTAAAAAGATAA
**
1263958 ATGTTTAAGAAGTTATATTAA
1 ATGTTTAAGATTTTATATTAA
1263979 GATAAAAAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (29 bp):
ATGTTTAAGATTTTATATTAAAAAGATAA
Found at i:1266586 original size:42 final size:41
Alignment explanation
Indices: 1266535--1266690 Score: 138
Period size: 42 Copynumber: 3.7 Consensus size: 41
1266525 AGTTAATCAA
* *
1266535 TAGCCGCGTTTATAGTAAAAACGCCGCAATAGAGT-ATACATT
1 TAGCGGCGTTTATA-TAAAAATGCCGCAATAGAGTGATA-ATT
* * *
1266577 TAGCGGCGTTT-TAGCT-AAAATGCCGTAATAGAGTGTTAATG
1 TAGCGGCGTTTATA--TAAAAATGCCGCAATAGAGTGATAATT
** * * *
1266618 TAGCGATGTTTATATCATAAATGCCGCAATAGAGTGGTAAAT
1 TAGCGGCGTTTATAT-AAAAATGCCGCAATAGAGTGATAATT
*
1266660 TAGCGGCGTTTATATATAAAATGCCTCAATA
1 TAGCGGCGTTTATATA-AAAATGCCGCAATA
1266691 TGGTTGTTTA
Statistics
Matches: 91, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
40 1 0.01
41 30 0.33
42 60 0.66
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (41 bp):
TAGCGGCGTTTATATAAAAATGCCGCAATAGAGTGATAATT
Found at i:1268471 original size:22 final size:22
Alignment explanation
Indices: 1268391--1268475 Score: 89
Period size: 22 Copynumber: 3.9 Consensus size: 22
1268381 GAGGGTTTAT
** *
1268391 AGTGGTCCTTCAAGACATATCC
1 AGTGGTCCTTCGGGACGTATCC
* * * * *
1268413 AGTGGTCCTTTGGAATGCATTC
1 AGTGGTCCTTCGGGACGTATCC
*
1268435 AGTGGTCCTTTGGGACGTATCC
1 AGTGGTCCTTCGGGACGTATCC
1268457 AGTGGTCCTTCGGGACGTA
1 AGTGGTCCTTCGGGACGTA
1268476 GCGGTCCTTC
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACGTATCC
Found at i:1275368 original size:22 final size:22
Alignment explanation
Indices: 1275343--1275428 Score: 74
Period size: 22 Copynumber: 4.1 Consensus size: 22
1275333 ATTCGGGATA
* **
1275343 TATCCAGTTGTCCTTTGGGACG
1 TATCCAGTGGTCCTTCAGGACG
1275365 TATCCAGTGGTCCTTCAGGACG
1 TATCCAGTGGTCCTTCAGGACG
* *
1275387 --T--AGTGGTCCTTCGGGACA
1 TATCCAGTGGTCCTTCAGGACG
*
1275405 TATCAAGTGGTCCTT-AGGGACG
1 TATCCAGTGGTCCTTCA-GGACG
1275427 TA
1 TA
1275429 ATGGTCCTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
18 15 0.29
20 2 0.04
22 35 0.67
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (22 bp):
TATCCAGTGGTCCTTCAGGACG
Found at i:1275393 original size:18 final size:18
Alignment explanation
Indices: 1275370--1275443 Score: 60
Period size: 18 Copynumber: 3.9 Consensus size: 18
1275360 GGACGTATCC
1275370 AGTGGTCCTTCAGGACGT
1 AGTGGTCCTTCAGGACGT
* *
1275388 AGTGGTCCTTCGGGACATAT
1 AGTGGTCCTTCAGGAC--GT
1275408 CAAGTGGTCCTT-AGGGACGT
1 --AGTGGTCCTTCA-GGACGT
* *
1275428 AATGGTCCTTCGGGAC
1 AGTGGTCCTTCAGGAC
1275444 AAATATTCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
18 28 0.64
20 2 0.05
22 14 0.32
ACGTcount: A:0.19, C:0.22, G:0.32, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCAGGACGT
Found at i:1275403 original size:40 final size:40
Alignment explanation
Indices: 1275352--1275444 Score: 134
Period size: 40 Copynumber: 2.3 Consensus size: 40
1275342 ATATCCAGTT
* * * *
1275352 GTCCTTTGGGACGTATCCAGTGGTCCTTCA-GGACGTAGTG
1 GTCCTTCGGGACATATCAAGTGGTCCTT-AGGGACGTAATG
1275392 GTCCTTCGGGACATATCAAGTGGTCCTTAGGGACGTAATG
1 GTCCTTCGGGACATATCAAGTGGTCCTTAGGGACGTAATG
1275432 GTCCTTCGGGACA
1 GTCCTTCGGGACA
1275445 AATATTCACT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 1 0.02
40 47 0.98
ACGTcount: A:0.18, C:0.23, G:0.31, T:0.28
Consensus pattern (40 bp):
GTCCTTCGGGACATATCAAGTGGTCCTTAGGGACGTAATG
Found at i:1278729 original size:2 final size:2
Alignment explanation
Indices: 1278722--1278749 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1278712 TTTATAAGTT
1278722 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1278750 AGTTTATAAG
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):
TA
Found at i:1279419 original size:6 final size:6
Alignment explanation
Indices: 1279408--1279744 Score: 607
Period size: 6 Copynumber: 57.3 Consensus size: 6
1279398 GTGTGTATGT
1279408 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
* *
1279456 TGTGTA TGTGTA TGAGTA TGTGTA TATGTA TGTGTA TGTGTA TGTGTA
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
1279504 TGTGTA TGTGTA TGTGTA TGTGTA TGT-TA TGTGTA TGTGTA TGTGTA
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
1279551 --TGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA --TGTA TGTGTA
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
1279595 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
1279643 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
1279691 TGTGTA --TGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
1279737 TGTGTA TG
1 TGTGTA TG
1279745 CGTCTATATG
Statistics
Matches: 320, Mismatches: 4, Indels: 14
0.95 0.01 0.04
Matches are distributed among these distances:
4 12 0.04
5 5 0.02
6 303 0.95
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.50
Consensus pattern (6 bp):
TGTGTA
Found at i:1283075 original size:7 final size:7
Alignment explanation
Indices: 1283057--1283097 Score: 73
Period size: 7 Copynumber: 5.7 Consensus size: 7
1283047 TCCAGAGTTC
1283057 TCTTCTCT
1 TCTTC-CT
1283065 TCTTCCT
1 TCTTCCT
1283072 TCTTCCT
1 TCTTCCT
1283079 TCTTCCT
1 TCTTCCT
1283086 TCTTCCT
1 TCTTCCT
1283093 TCTTC
1 TCTTC
1283098 ATACGTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 28 0.85
8 5 0.15
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (7 bp):
TCTTCCT
Found at i:1284605 original size:31 final size:31
Alignment explanation
Indices: 1284567--1284631 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1284557 AGAGTCGAGG
* *
1284567 GTTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTTACCTAGGTTCTTCCG-GACATATGGACA
*
1284598 GTTTACCTAGGTTCTTCCGGACCTATGGACA
1 GTTTACCTAGGTTCTTCCGGACATATGGACA
1284629 GTT
1 GTT
1284632 GCTGAGGTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 24 0.80
32 6 0.20
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCCGGACATATGGACA
Found at i:1289655 original size:21 final size:21
Alignment explanation
Indices: 1289604--1289674 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
1289594 AAAAGAGAGA
* *
1289604 AGCAGCAGAAGCAGCCAAAGC
1 AGCAGCGGAAACAGCCAAAGC
* *
1289625 AGCAGTGGAAACAGCCAGAGC
1 AGCAGCGGAAACAGCCAAAGC
* * ** *
1289646 AGTAGCGGAATCAGAGAAAGA
1 AGCAGCGGAAACAGCCAAAGC
1289667 AGCAGCGG
1 AGCAGCGG
1289675 CAGCACAGAG
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.41, C:0.21, G:0.34, T:0.04
Consensus pattern (21 bp):
AGCAGCGGAAACAGCCAAAGC
Found at i:1289688 original size:21 final size:21
Alignment explanation
Indices: 1289664--1289733 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
1289654 AATCAGAGAA
*
1289664 AGAAGCAGCGGCAGCACAGAG
1 AGAAGCAGCGACAGCACAGAG
* **
1289685 AGAAGCAGTGACAATACAGAG
1 AGAAGCAGCGACAGCACAGAG
*
1289706 AGAAGTAGCGACAGCACAGAG
1 AGAAGCAGCGACAGCACAGAG
1289727 AGAAGCA
1 AGAAGCA
1289734 ACATATCAGC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.44, C:0.19, G:0.33, T:0.04
Consensus pattern (21 bp):
AGAAGCAGCGACAGCACAGAG
Found at i:1289747 original size:42 final size:42
Alignment explanation
Indices: 1289654--1289748 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
1289644 GCAGTAGCGG
* *
1289654 AATCAG-AGAAAGAAGCAGCGGCAGCACAGAGAGAAGCAGTGAC
1 AATCAGCAGAGAGAAGCAGCGACAGCACAGAGAGAAGCA--GAC
*
1289697 AAT-A-CAGAGAGAAGTAGCGACAGCACAGAGAGAAGCA-AC
1 AATCAGCAGAGAGAAGCAGCGACAGCACAGAGAGAAGCAGAC
1289736 ATATCAGCAGAGA
1 A-ATCAGCAGAGA
1289749 TGTGAAGAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
39 3 0.07
40 2 0.04
41 1 0.02
42 36 0.80
43 3 0.07
ACGTcount: A:0.46, C:0.18, G:0.29, T:0.06
Consensus pattern (42 bp):
AATCAGCAGAGAGAAGCAGCGACAGCACAGAGAGAAGCAGAC
Found at i:1290108 original size:41 final size:43
Alignment explanation
Indices: 1290051--1290167 Score: 130
Period size: 44 Copynumber: 2.7 Consensus size: 43
1290041 ATTCTGTGTT
* * *
1290051 ATTTAGTGGCGTTTGTA-A-AAAAACGCCGCAATATGCTGTAC
1 ATTTAGCGGCGTTTGTATACAAAAACGCCGCAATATACTATAC
* * *
1290092 ATTTAGCGGTGTTTGTATACTAGAAACGTCGCAATATACTATAC
1 ATTTAGCGGCGTTTGTATAC-AAAAACGCCGCAATATACTATAC
* *
1290136 ATTTAGCAGCGTTTGTATACTAGAAACGCCGC
1 ATTTAGCGGCGTTTGTATAC-AAAAACGCCGC
1290168 TAATGCTCAA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 15 0.23
42 1 0.02
44 48 0.75
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (43 bp):
ATTTAGCGGCGTTTGTATACAAAAACGCCGCAATATACTATAC
Found at i:1290128 original size:44 final size:44
Alignment explanation
Indices: 1290071--1290167 Score: 149
Period size: 44 Copynumber: 2.2 Consensus size: 44
1290061 GTTTGTAAAA
* * * *
1290071 AAACGCCGCAATATGCTGTACATTTAGCGGTGTTTGTATACTAG
1 AAACGCCGCAATATACTATACATTTAGCAGCGTTTGTATACTAG
*
1290115 AAACGTCGCAATATACTATACATTTAGCAGCGTTTGTATACTAG
1 AAACGCCGCAATATACTATACATTTAGCAGCGTTTGTATACTAG
1290159 AAACGCCGC
1 AAACGCCGC
1290168 TAATGCTCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (44 bp):
AAACGCCGCAATATACTATACATTTAGCAGCGTTTGTATACTAG
Found at i:1290237 original size:43 final size:42
Alignment explanation
Indices: 1290159--1290317 Score: 126
Period size: 43 Copynumber: 3.7 Consensus size: 42
1290149 TGTATACTAG
* * *
1290159 AAACGCCGCT-AATGCTC-AACCCTTATTGCGTCATTTTCGATA
1 AAACGCCGCTAAAT-CTCAAAACC-TACTGCGCCATTTTCGATA
* * *
1290201 CAAACGCCACTAAATCTAAAAACCTACTGCGCCATTTGTGGGA-A
1 -AAACGCCGCTAAATCTCAAAACCTACTGCGCCATTT-T-CGATA
* * * * **
1290245 AAACGCCGCAAAATATCAAAACCTACTGCGGCGTTTTTAAGTA
1 AAACGCCGCTAAATCTCAAAACCTACTGCGCCATTTTCGA-TA
*
1290288 AAACGCCGCTAAATCTCAATACCTACTGCG
1 AAACGCCGCTAAATCTCAAAACCTACTGCG
1290318 GTGTTTTTCC
Statistics
Matches: 93, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 80 0.86
44 9 0.10
45 2 0.02
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (42 bp):
AAACGCCGCTAAATCTCAAAACCTACTGCGCCATTTTCGATA
Found at i:1290318 original size:43 final size:43
Alignment explanation
Indices: 1290202--1290384 Score: 143
Period size: 43 Copynumber: 4.3 Consensus size: 43
1290192 TTTTCGATAC
* * * * * **
1290202 AAACGCCACTAAATCTAAAAACCTACTGCGCCATTTGTGGGAA
1 AAACGCCGCTAAATCTCAAAACCTACTGCGGCGTTTTTAAGAA
* * *
1290245 AAACGCCGCAAAATATCAAAACCTACTGCGGCGTTTTTAAGTA
1 AAACGCCGCTAAATCTCAAAACCTACTGCGGCGTTTTTAAGAA
* * ***
1290288 AAACGCCGCTAAATCTCAATACCTACTGCGGTGTTTTTCCTAA
1 AAACGCCGCTAAATCTCAAAACCTACTGCGGCGTTTTTAAGAA
* * * * * ** *
1290331 AAACACTGCTAAA-CATCAACACCTATTGCGGTGTTTTTCTGAC
1 AAACGCCGCTAAATC-TCAAAACCTACTGCGGCGTTTTTAAGAA
1290374 AAACGCCGCTA
1 AAACGCCGCTA
1290385 TATGTTGTCA
Statistics
Matches: 112, Mismatches: 27, Indels: 2
0.79 0.19 0.01
Matches are distributed among these distances:
42 1 0.01
43 111 0.99
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAATCTCAAAACCTACTGCGGCGTTTTTAAGAA
Found at i:1295961 original size:19 final size:19
Alignment explanation
Indices: 1295937--1295976 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1295927 CTTTCATGTG
1295937 TGTAGTTTGAGATTGAAAT
1 TGTAGTTTGAGATTGAAAT
1295956 TGTAGTTTGAGATTGAAAT
1 TGTAGTTTGAGATTGAAAT
1295975 TG
1 TG
1295977 AAAGGGGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (19 bp):
TGTAGTTTGAGATTGAAAT
Found at i:1301804 original size:565 final size:564
Alignment explanation
Indices: 1300736--1301864 Score: 1848
Period size: 565 Copynumber: 2.0 Consensus size: 564
1300726 CCAGCCTTAC
* ** *
1300736 AAATCTTTCTAAGGGGTGGTAACAAGGACTTTGACCCACTATCTATAGGGAGATAGGAACCATAA
1 AAATCTTTCTAAGGGGTGGTAACAAGGACTTGGACCCACTATCTATAGAAAGATAGGAACCACAA
*
1300801 GTATCAAGGGAAGAAGAGGTTGATGCCACAAGTAAATAAATTACTTGATAAGTCGATAAAAATCA
66 GTATCAAGGGAAGAAGAGGTTGATGCCACAAGTAAATAAATTACTTGATAAGTCAATAAAAATCA
*
1300866 CAAGGACTTAAGAAAAGAGAATAATATAACTTTAAATTATAAGAAAGTGTGCTTACAAATGAATA
131 CAAGGACTTAAGAAAAGAGAATAATATAACTTTAAATTATAAGAAAGTGTGCTTACAAAAGAATA
* * * *
1300931 GAACTATCCTATTTATAGTTTTTGAAGGGACTTAGCCGAATTGTTACATGGTGGTTCGGCCAGCC
196 GAACTAGCCCATTTATAGTTTTTGAAGGAACTTAGCCGAATGGTTACATGGTGGTTCGGCCAGCC
* * * *
1300996 CTTGTGTCCCTCTTTAATGACATAATTAATTAATTAATAACATGAAAAATATAGGTGTTGGTTCG
261 CTTGTATCCCTCTATAATGACATAATTAATTAATTAATAACATGAAAAATATAGGTGCTGGTTCA
* * *
1301061 GTTGGAATAGAGGAGCATGTCTCATGGCCGAATAGCACTTGAATCCCTTTAAGTTTGCGCCAATT
326 GTTGGAATAGAGGAGCATGTCTCATGGCCGAATAACACTTGAATCCCTTCAAGTTGGCGCCAATT
1301126 TGGATGAGAAATGATGCTTGGCCGAATGGTGAGGTTACCATTCATCATTGCGCCTAAATGGAGTC
391 TGGATGAGAAATGATGCTTGGCCGAATGGTGAGGTTACCATTCATCATTGCGCCTAAATGGAGTC
** * * * * * *
1301191 ACACGCATAGCACATGGCATGGCTTATCAGAAGGCGTGCACATGGCTTTCTAGGATGCTTGTGGT
456 ACACAAATAACACATGGCATGGATGATCACAAGACATGCACATGGCTTTCTAGGATGCTTGTGGT
*
1301256 AAGGTTGCAACCATAGGATGATGTCTTGAAGTCCTTGGGCAGCT
521 AAGGTTGCAACCATAGGATGATGTATTGAAGTCCTTGGGCAGCT
* *
1301300 AAATCTTTCTAAGGGGTGGTAACAAGGACTTGGACCCA-TAATTTATAGAAAGATATGAACCACA
1 AAATCTTTCTAAGGGGTGGTAACAAGGACTTGGACCCACT-ATCTATAGAAAGATAGGAACCACA
* * *
1301364 AGTATCAAGGGAATAAGGGGTTGATGCCACAAGTAAATAAATTACTTGATAAGTCAATAAAAGTC
65 AGTATCAAGGGAAGAAGAGGTTGATGCCACAAGTAAATAAATTACTTGATAAGTCAATAAAAATC
* *
1301429 ACAAGGACTTAAGAAAAGAGAATAATCTCACTTTAAATTATAAGAAAGGTGTGCTTACAAAAGAA
130 ACAAGGACTTAAGAAAAGAGAATAATATAACTTTAAATTATAAGAAA-GTGTGCTTACAAAAGAA
* * * *
1301494 TAGTACTAGCCCATTTATAGTTTTTGAAGGAACTTGGTCGAATGGTTATATGGTGGTTCGGCCAG
194 TAGAACTAGCCCATTTATAGTTTTTGAAGGAACTTAGCCGAATGGTTACATGGTGGTTCGGCCAG
*
1301559 CCCTTGTATCCCTCTATAATGACATAATTAATTAATTAATAACATGAAAAATATATGTGCTGGTT
259 CCCTTGTATCCCTCTATAATGACATAATTAATTAATTAATAACATGAAAAATATAGGTGCTGGTT
*
1301624 CAGTTGGAATAGAGGAGCATGTCTCATGGCCGAATAACACTTGAATCCCTTCAAGTTGGTGCCAA
324 CAGTTGGAATAGAGGAGCATGTCTCATGGCCGAATAACACTTGAATCCCTTCAAGTTGGCGCCAA
*
1301689 TTTGGATGAGAAATGATGCTTGGCCGAATGGTGAGGTTGCCATTCATC-TTGCCGCCTAAATGGA
389 TTTGGATGAGAAATGATGCTTGGCCGAATGGTGAGGTTACCATTCATCATTG-CGCCTAAATGGA
*
1301753 GTCACACAAATAACACATGGCTTGGATGATCACAAGACATGCACATGGCTTTCTAGGATGCTTGT
453 GTCACACAAATAACACATGGCATGGATGATCACAAGACATGCACATGGCTTTCTAGGATGCTTGT
1301818 GGTAAGGTTGCAACCATAGGATGATGTATTGAAGTCCTTGGGCAGCT
518 GGTAAGGTTGCAACCATAGGATGATGTATTGAAGTCCTTGGGCAGCT
1301865 TAGAGATGAA
Statistics
Matches: 521, Mismatches: 41, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
563 1 0.00
564 165 0.32
565 355 0.68
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (564 bp):
AAATCTTTCTAAGGGGTGGTAACAAGGACTTGGACCCACTATCTATAGAAAGATAGGAACCACAA
GTATCAAGGGAAGAAGAGGTTGATGCCACAAGTAAATAAATTACTTGATAAGTCAATAAAAATCA
CAAGGACTTAAGAAAAGAGAATAATATAACTTTAAATTATAAGAAAGTGTGCTTACAAAAGAATA
GAACTAGCCCATTTATAGTTTTTGAAGGAACTTAGCCGAATGGTTACATGGTGGTTCGGCCAGCC
CTTGTATCCCTCTATAATGACATAATTAATTAATTAATAACATGAAAAATATAGGTGCTGGTTCA
GTTGGAATAGAGGAGCATGTCTCATGGCCGAATAACACTTGAATCCCTTCAAGTTGGCGCCAATT
TGGATGAGAAATGATGCTTGGCCGAATGGTGAGGTTACCATTCATCATTGCGCCTAAATGGAGTC
ACACAAATAACACATGGCATGGATGATCACAAGACATGCACATGGCTTTCTAGGATGCTTGTGGT
AAGGTTGCAACCATAGGATGATGTATTGAAGTCCTTGGGCAGCT
Found at i:1302258 original size:22 final size:20
Alignment explanation
Indices: 1302212--1302267 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 20
1302202 AGAATGCTCG
*
1302212 AATGGTACCGATACCCCCAT
1 AATGGTATCGATACCCCCAT
1302232 -A-GGTATCGATACCCCCAT
1 AATGGTATCGATACCCCCAT
1302250 GCAATGGTATCGATACCC
1 --AATGGTATCGATACCC
1302268 TAAGGCATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 16 0.52
19 1 0.03
21 1 0.03
22 13 0.42
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (20 bp):
AATGGTATCGATACCCCCAT
Done.