Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, 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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 20 of 147
Found at i:4288111 original size:15 final size:15
Alignment explanation
Indices: 4288037--4288105 Score: 84
Period size: 15 Copynumber: 4.3 Consensus size: 15
4288027 AAAAATCTAA
4288037 TATATATATATATATAT
1 TATAT-TATAT-TATAT
*
4288054 ATATATATATCTATATAT
1 -TATAT-TATAT-TATAT
4288072 TATATTATATTATAT
1 TATATTATATTATAT
4288087 TATATTATATTATAT
1 TATATTATATTATAT
4288102 TATA
1 TATA
4288106 ACATATAAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
15 24 0.49
16 4 0.08
17 5 0.10
18 16 0.33
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATTATATTATAT
Found at i:4291614 original size:10 final size:11
Alignment explanation
Indices: 4291599--4291623 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4291589 GTTTTTTTGT
4291599 ATTTTTTGGAA
1 ATTTTTTGGAA
4291610 ATTTTTTGGAA
1 ATTTTTTGGAA
4291621 ATT
1 ATT
4291624 CCAAAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (11 bp):
ATTTTTTGGAA
Found at i:4291697 original size:30 final size:30
Alignment explanation
Indices: 4291642--4291700 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
4291632 ATGTTGAATT
*
4291642 TTTCGATGAAAATTCAAGTTTTTTGGTGAC
1 TTTCGATGAAAAATCAAGTTTTTTGGTGAC
*
4291672 TTTCTGATGAAAAATCCAG-TTTTTGGTGA
1 TTTC-GATGAAAAATCAAGTTTTTTGGTGA
4291701 TAAAATCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.42
Consensus pattern (30 bp):
TTTCGATGAAAAATCAAGTTTTTTGGTGAC
Found at i:4292092 original size:15 final size:15
Alignment explanation
Indices: 4292067--4292104 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
4292057 AAGGTTTTTT
4292067 TATTT-TTATTTATC
1 TATTTATTATTTATC
*
4292081 TATTTATTATTTATT
1 TATTTATTATTTATC
*
4292096 TGTTTATTA
1 TATTTATTA
4292105 ATTTTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (15 bp):
TATTTATTATTTATC
Found at i:4292158 original size:4 final size:4
Alignment explanation
Indices: 4292071--4292139 Score: 50
Period size: 4 Copynumber: 16.5 Consensus size: 4
4292061 TTTTTTTATT
* * * * *
4292071 TTTA TTTA TCTA TTTA -TTA TTTA TTTG TTTA TTAA TTTT TTTAA TTTTG
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A -TTTA
4292120 TTCTCA TTTA TTTA TTTA TT
1 TT-T-A TTTA TTTA TTTA TT
4292140 AAATTGAAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
3 3 0.06
4 40 0.80
5 2 0.04
6 5 0.10
ACGTcount: A:0.22, C:0.04, G:0.03, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:4292529 original size:60 final size:59
Alignment explanation
Indices: 4292201--4292732 Score: 527
Period size: 60 Copynumber: 9.1 Consensus size: 59
4292191 TAAAAATGAA
* * * * **
4292201 AAAAAAATGTTTTTG-GAAAAATTTGAAAGTATCAATTTTCCTTGAAAACGAAAATTT-
1 AAAAAAGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAAAATTTC
* * * * * * *
4292258 -TAAAA-TGTTTCT-AGGAAAAGTTGAAAATATCAATTTT-TCTTAAAAATAAAAATTTG
1 AAAAAAGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCT-TTGAAAATAAAAATTTC
* * * *
4292314 AAAAATGTATTTTTGAG-GAAAGTTGAAAGTGTCAATTTT-TATTGACAAA-AAGAATTTC
1 AAAAAAGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCT-TTGA-AAATAAAAATTTC
*
4292372 AAAAAAGATATTTTTGAG-AAAA-TTGAAAGTATCAATTTTCCTT-AGAAATAAAAATTTC
1 AAAAAAG-TATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTGA-AAATAAAAATTTC
* * *
4292430 AAAAAATTATTTTTGA-AGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGAATTTT
1 AAAAAAGTATTTTTGAGA-AAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAAAATTTC
* * *
4292489 AAACAAGGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGAATTTC
1 AAA-AAAGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAAAATTTC
* * * * *
4292549 AAAAAAAGTATTTTTTAGGAAAAGTTGAAAGTATCAATTTTCTTTAAAAAAAAAAAATTC
1 -AAAAAAGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAAAATTTC
* *
4292609 AAAAAAAGCATTTTTGAGAAAAAGTTGAAAGTATCAATTTT-TCTTGAAAATAACAATTTC
1 -AAAAAAGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCT-TTGAAAATAAAAATTTC
** * * *
4292669 AAAAAGAACATTTTTGAGGAAAAGTTGAAACTATCAATTTT-TCTTGAAAATAAAAATTTT
1 AAAAA-AGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCT-TTGAAAATAAAAATTTC
4292729 AAAA
1 AAAA
4292733 TGCTTAAAGG
Statistics
Matches: 402, Mismatches: 54, Indels: 35
0.82 0.11 0.07
Matches are distributed among these distances:
55 40 0.10
56 4 0.01
57 16 0.04
58 77 0.19
59 58 0.14
60 203 0.50
61 4 0.01
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (59 bp):
AAAAAAGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAAAATTTC
Found at i:4292592 original size:120 final size:120
Alignment explanation
Indices: 4292200--4292732 Score: 594
Period size: 120 Copynumber: 4.5 Consensus size: 120
4292190 CTAAAAATGA
* * * * * **
4292200 AAAAAAAATGTTTTTG-GAAAAATTTGAAAGTATCAATTTTCCTTGAAAACGAAAATTTT--AAA
1 AAAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAAAATTTTAAAAA
* * * * * *
4292262 A--TGTTTCT-AGGAAAAGTTGAAAATATCAATTTTTCTTAAAAATAAAAATTT-
66 AGGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAATTTC
* * * * *
4292313 GAAAAATGTATTTTTGAGG-AAAGTTGAAAGTGTCAATTTT-TATTGACAAA-AAGAATTTCAAA
1 AAAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCT-TTGA-AAATAAAAATTTTAAA
*
4292375 AAAGATATTTTTGAG-AAAA-TTGAAAGTATCAATTTTCCTT-AGAAATAAAAATTTC
64 AAAGGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGA-AAATAAAAATTTC
* * * *
4292430 -AAAAAATTATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGAATTTTAAACA
1 AAAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAAAATTTTAAAAA
*
4292494 AGGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGAATTTC
66 AGGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAATTTC
* * * * *
4292549 AAAAAAAGTATTTTTTAGGAAAAGTTGAAAGTATCAATTTTCTTTAAAAAAAAAAAATTCAAAAA
1 AAAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAAAATTTTAAAAA
* * * *
4292614 AAGCATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAACAATTTC
66 AGGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAATTTC
* *
4292669 AAAAAGAA-CATTTTTGAGGAAAAGTTGAAACTATCAATTTT-TCTTGAAAATAAAAATTTTAAA
1 AAAAA-AAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCT-TTGAAAATAAAAATTTTAAA
4292732 A
64 A
4292733 TGCTTAAAGG
Statistics
Matches: 358, Mismatches: 43, Indels: 31
0.83 0.10 0.07
Matches are distributed among these distances:
113 41 0.11
114 4 0.01
115 5 0.01
116 49 0.14
117 57 0.16
118 7 0.02
119 34 0.09
120 159 0.44
121 2 0.01
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (120 bp):
AAAAAAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAAAATTTTAAAAA
AGGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAATTTC
Found at i:4303456 original size:57 final size:54
Alignment explanation
Indices: 4303328--4303531 Score: 182
Period size: 57 Copynumber: 3.7 Consensus size: 54
4303318 TATTTCTCTT
* * * * * *
4303328 AAAAACAAAAAGA--TCAAATTGATAACCCGTAAAAGGCAG-TTGATTTCAAAA
1 AAAAAAAAAAAGAGCTCAAATTGAAAACCCATAAAGGGCGGTTTGATTTAAAAA
* *
4303379 AAAAAAAAAAAGAACTCAAATTGAAAACCCATAAAGGGCGGTTTGAATTAAAAA
1 AAAAAAAAAAAGAGCTCAAATTGAAAACCCATAAAGGGCGGTTTGATTTAAAAA
* * * * *
4303433 AAAAAAGGCAAAAAGAGCACAAATTGAAAAACGATAAA-GGTGGTTTTAGTTTAAAAAA
1 AAAAAA---AAAAAGAGCTCAAATTGAAAACCCATAAAGGGCGGTTTGA-TTT-AAAAA
* *
4303491 AAAAAATAAAAAGGAGCTTAAATTGAAAACCCACAAAGGGC
1 AAAAAA-AAAAA-GAGCTCAAATTGAAAACCCATAAAGGGC
4303532 AATTTGAGTC
Statistics
Matches: 122, Mismatches: 21, Indels: 13
0.78 0.13 0.08
Matches are distributed among these distances:
51 12 0.10
53 22 0.18
54 16 0.13
56 13 0.11
57 46 0.38
58 13 0.11
ACGTcount: A:0.55, C:0.11, G:0.16, T:0.17
Consensus pattern (54 bp):
AAAAAAAAAAAGAGCTCAAATTGAAAACCCATAAAGGGCGGTTTGATTTAAAAA
Found at i:4303563 original size:45 final size:45
Alignment explanation
Indices: 4303505--4303671 Score: 124
Period size: 45 Copynumber: 3.5 Consensus size: 45
4303495 AATAAAAAGG
4303505 AGCTTAAATTGAAAACCCACAAAGGGCAATTTGAGTCAGAAAAAA
1 AGCTTAAATTGAAAACCCACAAAGGGCAATTTGAGTCAGAAAAAA
* * *
4303550 AGCTTAAATTGAAAA-CCAGTAAAGGGTAGTTTGAGTTCA-AAAAAA
1 AGCTTAAATTGAAAACCCA-CAAAGGGCAATTTGAG-TCAGAAAAAA
* * * * *
4303595 CTTGGGGGGCTCAAATTGAAAACCCACAAAAGGCAATTTGAGTTAGAAAATGA
1 -------AGCTTAAATTGAAAACCCACAAAGGGCAATTTGAGTCAGAAAA-AA
* *
4303648 TG-TCTAAATTGAAAACCCAAAAAG
1 AGCT-TAAATTGAAAACCCACAAAG
4303672 ACAGCATAGA
Statistics
Matches: 94, Mismatches: 15, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
44 3 0.03
45 35 0.37
46 21 0.22
51 2 0.02
52 29 0.31
53 4 0.04
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.21
Consensus pattern (45 bp):
AGCTTAAATTGAAAACCCACAAAGGGCAATTTGAGTCAGAAAAAA
Found at i:4304696 original size:85 final size:85
Alignment explanation
Indices: 4304562--4304827 Score: 383
Period size: 85 Copynumber: 3.1 Consensus size: 85
4304552 TTTCGACTTT
* * * *
4304562 GTCCAAGTTATT-ATTTCAGACTTCGATTCAGTCCAAGTTATTTTGTTTTGGATTTTGACTTTTG
1 GTCCAAGTTATTCATTTCAGACTTCGGTTCAGTCCAGGTAATTTTGTTTTGGATTTTGACTTATG
4304626 TCAAATCCTTT-TTTGGCTTA
66 TCAAAT-CTTTATTTGGCTTA
* * * * * *
4304646 ATCCAAGTTATTCATTTTAGACTTTGGTTCAGTCCAGGTCATTTTATTTTGGATGTTGACTTATG
1 GTCCAAGTTATTCATTTCAGACTTCGGTTCAGTCCAGGTAATTTTGTTTTGGATTTTGACTTATG
* *
4304711 TTAGATCTTTATTTGGCTTA
66 TCAAATCTTTATTTGGCTTA
*
4304731 GTCTAAGTTATTCATTTCAGACTTCGGTTCAGTCCAGGTAATTTTGTTTTGGATTTTGACTTATG
1 GTCCAAGTTATTCATTTCAGACTTCGGTTCAGTCCAGGTAATTTTGTTTTGGATTTTGACTTATG
*
4304796 TCAAATCTTTATTTGGTTTA
66 TCAAATCTTTATTTGGCTTA
4304816 GTCCAAGTTATT
1 GTCCAAGTTATT
4304828 TCAAACTTCG
Statistics
Matches: 158, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
84 15 0.09
85 143 0.91
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (85 bp):
GTCCAAGTTATTCATTTCAGACTTCGGTTCAGTCCAGGTAATTTTGTTTTGGATTTTGACTTATG
TCAAATCTTTATTTGGCTTA
Found at i:4306004 original size:23 final size:23
Alignment explanation
Indices: 4305972--4306031 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
4305962 TTTATTTCTA
*
4305972 TTTATCTATTTATTATTTATTTG
1 TTTATTTATTTATTATTTATTTG
* *
4305995 TTTATTTATTT-TAAATTTTTTTG
1 TTTATTTATTTAT-TATTTATTTG
*
4306018 CTTATTTATTTATT
1 TTTATTTATTTATT
4306032 TATTAAATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 1 0.03
23 28 0.93
24 1 0.03
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (23 bp):
TTTATTTATTTATTATTTATTTG
Found at i:4306054 original size:4 final size:4
Alignment explanation
Indices: 4305970--4306035 Score: 55
Period size: 4 Copynumber: 17.0 Consensus size: 4
4305960 TTTTTATTTC
* * * * *
4305970 TATT TATC TATT TA-T TATT TATT TGTT TATT TATT T-TA AATT TTTT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
**
4306016 TGCT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT
4306036 AAATTGAAAT
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
3 4 0.09
4 43 0.91
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:4306339 original size:120 final size:119
Alignment explanation
Indices: 4306123--4306802 Score: 606
Period size: 120 Copynumber: 5.7 Consensus size: 119
4306113 CTAGGAAATT
* **
4306123 TTGAATGTATCAATTTTCCTTGAAAACGAAAATTTT--AAAA-T-GTTTCT-AGGAAAAGTTGAA
1 TTGAAAGTATCAATTTTCCTTGAAAATAAAAATTTTGAAAAAGTAGTTT-TAAGGAAAAGTTGAA
* * *
4306183 AGCATCAATTTTTCTTGAAAATAAAAATTTCAAAAAAAGGTAGTTTTGAGGAAAAG
65 AGTATCAATTTTTCTTGAAAATAAAAATTTC-AAAAAAGGTATTTTTGAAGAAAAG
* *
4306239 TTGAAAATATCAATTTTCCTTGAAAATAAAAATTTTGAAAAAGTAGTTTTAAGTAAAAGTTGAAA
1 TTGAAAGTATCAATTTTCCTTGAAAATAAAAATTTTGAAAAAGTAGTTTTAAGGAAAAGTTGAAA
* * *
4306304 GTATTAATTTTTCTTGAAAATAAAAAATTTCAAAAAAGATATTTTTGAAAAAAAG
66 GTATCAATTTTTCTTGAAAAT-AAAAATTTCAAAAAAGGTATTTTTGAAGAAAAG
* ** *
4306359 TTGAAAGTATCAATTTTCTTTCCAAATAAAAATTTTGAAAAAGTATTTTTGAA-G-AAAGTTGAA
1 TTGAAAGTATCAATTTTCCTTGAAAATAAAAATTTTGAAAAAGTAGTTTT-AAGGAAAAGTTGAA
* * * * *
4306422 AGTATCAATTTTCCTT-AGAAAT-AAAATATCAAAATA-GAATTTTTGAAGAAAAA
65 AGTATCAATTTTTCTTGA-AAATAAAAATTTCAAAAAAGGTATTTTTGAAGAAAAG
* ** * *
4306475 TTGAAAGTATCAATTTTTCTTGAAAATAAAAATTTCAAAAAAGGTATTTTTGAGGAAAAGTTGAA
1 TTGAAAGTATCAATTTTCCTTGAAAATAAAAATTTTGAAAAA-GTAGTTTTAAGGAAAAGTTGAA
* * *
4306540 A-TATCAATTTTTGTTGAAAATAAAAACTTCAAAAAATGG-ATTTTTGAGGAAAAG
65 AGTATCAATTTTTCTTGAAAATAAAAATTTCAAAAAA-GGTATTTTTGAAGAAAAG
* *
4306594 TTGAAAGTATCAATTTTGTATCAATTTTCCTTG-AAA-AAAAA-TTTGAAAAAAAGGTATTTTTG
1 TT----G-A--AA----GTATCAATTTTCCTTGAAAATAAAAATTTTG--AAAAA-GTAGTTTTA
* * * * *
4306656 AGG-AAAGTTAAAAGTATCGA-TTTTCTTTGAAAATGAAAATTTTGAAAAAA--TATTTTTGAGG
52 AGGAAAAGTTGAAAGTATCAATTTTTC-TTGAAAAT-AAAAATTTCAAAAAAGGTATTTTTGAAG
*
4306717 AAAAA
115 AAAAG
* * * ** ** * *
4306722 TTGAAAGTATCAATTTTCTTTAAAAATAACAATTTCAAAAAAACATTTTTGAGGAAAAGTTGAAA
1 TTGAAAGTATCAATTTTCCTTGAAAATAAAAATTTTGAAAAAGTAGTTTTAAGGAAAAGTTGAAA
*
4306787 GTATCAAATTTTCTTG
66 GTATCAATTTTTCTTG
4306803 TATAAAAGCA
Statistics
Matches: 469, Mismatches: 58, Indels: 72
0.78 0.10 0.12
Matches are distributed among these distances:
116 82 0.17
117 61 0.13
118 53 0.11
119 53 0.11
120 104 0.22
121 13 0.03
123 2 0.00
124 2 0.00
126 2 0.00
127 2 0.00
128 34 0.07
129 34 0.07
130 27 0.06
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (119 bp):
TTGAAAGTATCAATTTTCCTTGAAAATAAAAATTTTGAAAAAGTAGTTTTAAGGAAAAGTTGAAA
GTATCAATTTTTCTTGAAAATAAAAATTTCAAAAAAGGTATTTTTGAAGAAAAG
Found at i:4306433 original size:58 final size:59
Alignment explanation
Indices: 4306123--4306801 Score: 616
Period size: 59 Copynumber: 11.3 Consensus size: 59
4306113 CTAGGAAATT
* * ** * *
4306123 TTGAATGTATCAATTTTCCTTGAAAACGAAAATTTT--AAAA-TGTTTCT-AGGAAAAG
1 TTGAAAGTATCAATTTTCTTTGAAAATAAAAATTTTAAAAAAGTATTTTTGAGGAAAAG
* * *
4306178 TTGAAAGCATCAATTTT-TCTTGAAAATAAAAATTTCAAAAAAAGGTAGTTTTGAGGAAAAG
1 TTGAAAGTATCAATTTTCT-TTGAAAATAAAAATTT-TAAAAAA-GTATTTTTGAGGAAAAG
* * * * * *
4306239 TTGAAAATATCAATTTTCCTTGAAAATAAAAATTTTGAAAAAGTAGTTTTAAGTAAAAG
1 TTGAAAGTATCAATTTTCTTTGAAAATAAAAATTTTAAAAAAGTATTTTTGAGGAAAAG
* * **
4306298 TTGAAAGTATTAATTTT-TCTTGAAAATAAAAAATTTCAAAAAAGATATTTTTGAAAAAAAG
1 TTGAAAGTATCAATTTTCT-TTGAAAAT-AAAAATTTTAAAAAAG-TATTTTTGAGGAAAAG
** * *
4306359 TTGAAAGTATCAATTTTCTTTCCAAATAAAAATTTTGAAAAAGTATTTTTGAAG-AAAG
1 TTGAAAGTATCAATTTTCTTTGAAAATAAAAATTTTAAAAAAGTATTTTTGAGGAAAAG
* * * * * * *
4306417 TTGAAAGTATCAATTTTCCTT-AGAAAT-AAAATATCAAAATAGAATTTTTGAAGAAAAA
1 TTGAAAGTATCAATTTTCTTTGA-AAATAAAAATTTTAAAAAAGTATTTTTGAGGAAAAG
*
4306475 TTGAAAGTATCAATTTT-TCTTGAAAATAAAAATTTCAAAAAAGGTATTTTTGAGGAAAAG
1 TTGAAAGTATCAATTTTCT-TTGAAAATAAAAATTTTAAAAAA-GTATTTTTGAGGAAAAG
* * *
4306535 TTGAAA-TATCAATTTT-TGTTGAAAATAAAAACTTCAAAAAATGGATTTTTGAGGAAAAG
1 TTGAAAGTATCAATTTTCT-TTGAAAATAAAAATTTTAAAAAA-GTATTTTTGAGGAAAAG
*
4306594 TTGAAAGTATCAATTTTGTATCAATTTTCCTTG-AAA-AAAAATTTGAAAAAAAGGTATTTTTGA
1 TTGAAAGTATCAA--TT-T-TC-----T--TTGAAAATAAAAATTT-TAAAAAA-GTATTTTTGA
4306657 GG-AAAG
53 GGAAAAG
* * * *
4306663 TTAAAAGTATCGATTTTCTTTGAAAATGAAAATTTTGAAAAAA-TATTTTTGAGGAAAAA
1 TTGAAAGTATCAATTTTCTTTGAAAATAAAAATTTT-AAAAAAGTATTTTTGAGGAAAAG
* * * **
4306722 TTGAAAGTATCAATTTTCTTTAAAAATAACAATTTCAAAAAAACATTTTTGAGGAAAAG
1 TTGAAAGTATCAATTTTCTTTGAAAATAAAAATTTTAAAAAAGTATTTTTGAGGAAAAG
4306781 TTGAAAGTATCAAATTTTCTT
1 TTGAAAGTATC-AATTTTCTT
4306802 GTATAAAAGC
Statistics
Matches: 520, Mismatches: 67, Indels: 69
0.79 0.10 0.11
Matches are distributed among these distances:
55 29 0.06
57 21 0.04
58 78 0.15
59 177 0.34
60 86 0.17
61 73 0.14
62 3 0.01
63 1 0.00
64 1 0.00
65 2 0.00
66 1 0.00
67 2 0.00
69 22 0.04
70 21 0.04
71 3 0.01
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (59 bp):
TTGAAAGTATCAATTTTCTTTGAAAATAAAAATTTTAAAAAAGTATTTTTGAGGAAAAG
Found at i:4306489 original size:27 final size:27
Alignment explanation
Indices: 4306403--4306492 Score: 69
Period size: 27 Copynumber: 3.2 Consensus size: 27
4306393 TTGAAAAAGT
*
4306403 ATTTTTGAAG-AAAGTTGAAAGTATCA
1 ATTTTTGAAGAAAAATTGAAAGTATCA
* * *
4306429 ATTTTCCTTAGAA-ATAAAATATCAAAATA-GA
1 A-TTT--TT-GAAGA-AAAAT-TGAAAGTATCA
4306460 ATTTTTGAAGAAAAATTGAAAGTATCA
1 ATTTTTGAAGAAAAATTGAAAGTATCA
4306487 ATTTTT
1 ATTTTT
4306493 CTTGAAAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 17
0.67 0.10 0.24
Matches are distributed among these distances:
26 7 0.15
27 18 0.38
28 3 0.06
29 2 0.04
30 6 0.12
31 6 0.12
32 6 0.12
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.37
Consensus pattern (27 bp):
ATTTTTGAAGAAAAATTGAAAGTATCA
Found at i:4306644 original size:69 final size:71
Alignment explanation
Indices: 4306541--4306679 Score: 185
Period size: 69 Copynumber: 2.0 Consensus size: 71
4306531 AAAGTTGAAA
** * *
4306541 TATCAATTTTTGTTGAAAATAAAAACTTCAAAAAATGG-ATTTTTGAGGAAAAGTTGAAAGTATC
1 TATCAATTTTCCTTGAAAATAAAAACTTCAAAAAAAGGTATTTTTGAGG-AAAGTTAAAAGTATC
4306605 AATTTTG
65 AATTTTG
* * *
4306612 TATCAATTTTCCTTG-AAA-AAAAATTTGAAAAAAAGGTATTTTTGAGGAAAGTTAAAAGTATCG
1 TATCAATTTTCCTTGAAAATAAAAACTTCAAAAAAAGGTATTTTTGAGGAAAGTTAAAAGTATCA
4306675 ATTTT
66 ATTTT
4306680 CTTTGAAAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
69 34 0.57
70 13 0.22
71 13 0.22
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (71 bp):
TATCAATTTTCCTTGAAAATAAAAACTTCAAAAAAAGGTATTTTTGAGGAAAGTTAAAAGTATCA
ATTTTG
Found at i:4306663 original size:128 final size:130
Alignment explanation
Indices: 4306481--4306738 Score: 366
Period size: 128 Copynumber: 2.0 Consensus size: 130
4306471 AAAATTGAAA
* * *
4306481 GTATCAATTTTTCTTGAAAATAAAAATTTCAAAAAAGGTATTTTTGAGGAAAAGTTGAAA-TATC
1 GTATCAATTTTCCTTGAAAATAAAAATTTAAAAAAAGGTATTTTTGAGGAAAAGTTAAAAGTATC
*
4306545 AATTTT-TGTTGAAAAT-AAAAACTTCAAAAAATGGATTTTTGAGGAAAAGTTGAAAGTATCAAT
66 AATTTTCT-TTGAAAATGAAAAACTTCAAAAAAT--ATTTTTGAGGAAAAATTGAAAGTATCAAT
4306608 TTT
128 TTT
4306611 GTATCAATTTTCCTTG-AAA-AAAAATTTGAAAAAAAGGTATTTTTGAGG-AAAGTTAAAAGTAT
1 GTATCAATTTTCCTTGAAAATAAAAATTT-AAAAAAAGGTATTTTTGAGGAAAAGTTAAAAGTAT
* ** *
4306673 CGATTTTCTTTGAAAATGAAAATTTTGAAAAAATATTTTTGAGGAAAAATTGAAAGTATCAATTT
65 CAATTTTCTTTGAAAATGAAAAACTTCAAAAAATATTTTTGAGGAAAAATTGAAAGTATCAATTT
4306738 T
130 T
4306739 CTTTAAAAAT
Statistics
Matches: 116, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
128 48 0.41
129 39 0.34
130 29 0.25
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (130 bp):
GTATCAATTTTCCTTGAAAATAAAAATTTAAAAAAAGGTATTTTTGAGGAAAAGTTAAAAGTATC
AATTTTCTTTGAAAATGAAAAACTTCAAAAAATATTTTTGAGGAAAAATTGAAAGTATCAATTTT
Found at i:4306697 original size:188 final size:188
Alignment explanation
Indices: 4306423--4306798 Score: 487
Period size: 188 Copynumber: 2.0 Consensus size: 188
4306413 AAAGTTGAAA
* * * *
4306423 GTATCAATTTTCCTTAGAAATAAAATATCAAAATAGAATTTTTGAAGAAAAATTGAAAGTATCAA
1 GTATCAATTTTCCTTAGAAAAAAAATATAAAAAAAGAATTTTTGAAGAAAAATTAAAAGTATCAA
*
4306488 TTTTTCTTGAAAATAAAAA-TTTCAAAAAAGGTATTTTTGAGGAAAAGTTGAAA-TATCAATTTT
66 TTTTTCTTGAAAATAAAAATTTTCAAAAAA--TATTTTTGAGGAAAAATTGAAAGTATCAATTTT
* **
4306551 -TGTTGAAAATAAAAACTTCAAAAAATGGATTTTTGAGGAAAAGTTGAAAGTATC-AATTTT
129 CT-TTAAAAATAAAAACTTCAAAAAA-ACATTTTTGAGGAAAAGTTGAAAGTATCAAATTTT
* * * *
4306611 GTATCAATTTTCCTT-GAAAAAAAATTTGAAAAAAAGGTATTTTTG-AGGAAAGTTAAAAGTATC
1 GTATCAATTTTCCTTAGAAAAAAAATAT-AAAAAAA-GAATTTTTGAAGAAAAATTAAAAGTATC
* * *
4306674 GA-TTTTCTTTGAAAATGAAAATTTTGAAAAAATATTTTTGAGGAAAAATTGAAAGTATCAATTT
64 AATTTTTC-TTGAAAATAAAAATTTTCAAAAAATATTTTTGAGGAAAAATTGAAAGTATCAATTT
* *
4306738 TCTTTAAAAATAACAATTTCAAAAAAACATTTTTGAGGAAAAGTTGAAAGTATCAAATTTT
128 TCTTTAAAAATAAAAACTTCAAAAAAACATTTTTGAGGAAAAGTTGAAAGTATCAAATTTT
4306799 CTTGTATAAA
Statistics
Matches: 164, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
187 62 0.38
188 84 0.51
189 18 0.11
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (188 bp):
GTATCAATTTTCCTTAGAAAAAAAATATAAAAAAAGAATTTTTGAAGAAAAATTAAAAGTATCAA
TTTTTCTTGAAAATAAAAATTTTCAAAAAATATTTTTGAGGAAAAATTGAAAGTATCAATTTTCT
TTAAAAATAAAAACTTCAAAAAAACATTTTTGAGGAAAAGTTGAAAGTATCAAATTTT
Found at i:4307401 original size:26 final size:25
Alignment explanation
Indices: 4307366--4307414 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
4307356 TTTTTAGGAG
*
4307366 AATTCATGAATGCTCTTGATATTGA
1 AATTCATGAATGATCTTGATATTGA
4307391 AATTGCATGAATGATCTTGATATT
1 AATT-CATGAATGATCTTGATATT
4307415 TTGATGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (25 bp):
AATTCATGAATGATCTTGATATTGA
Found at i:4313358 original size:2 final size:2
Alignment explanation
Indices: 4313351--4313377 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4313341 ACTCAATCAA
4313351 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
4313378 AATCAAACAA
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:4314929 original size:21 final size:23
Alignment explanation
Indices: 4314873--4314929 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 23
4314863 TAAAATTTAT
*
4314873 TATTA-TATTA-AGAATTAAAAA
1 TATTATTATTATATAATTAAAAA
* *
4314894 TATTATTATTTTATAATTTAAAA
1 TATTATTATTATATAATTAAAAA
4314917 T-TT-TTATTATATA
1 TATTATTATTATATA
4314930 TAAATTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 14 0.47
22 6 0.20
23 10 0.33
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATTATTATTATATAATTAAAAA
Found at i:4314936 original size:24 final size:23
Alignment explanation
Indices: 4314863--4314936 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 23
4314853 AGTAAAATAA
*
4314863 TAAAATTTATTATTATATTAAGAAT
1 TAAAATTT-TTATTATATTAA-ATT
* * *
4314888 TAAAAATATTATTATTTTATAATT
1 TAAAATTTTTATTATATTA-AATT
4314912 TAAAATTTTTATTATATATAAATT
1 TAAAATTTTTATTATAT-TAAATT
4314936 T
1 T
4314937 TAATATAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
24 31 0.77
25 9 0.22
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (23 bp):
TAAAATTTTTATTATATTAAATT
Found at i:4319200 original size:2 final size:2
Alignment explanation
Indices: 4319193--4319224 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
4319183 TCACATTGAA
4319193 AT AT AT AT AT -T AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4319225 TCCTCTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:4319983 original size:6 final size:6
Alignment explanation
Indices: 4319972--4319999 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
4319962 TTGTGAGTCA
4319972 AGCTCG AGCTCG AGCTCG AGCTCG AGCT
1 AGCTCG AGCTCG AGCTCG AGCTCG AGCT
4320000 GTGTCGGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.32, T:0.18
Consensus pattern (6 bp):
AGCTCG
Found at i:4320677 original size:16 final size:16
Alignment explanation
Indices: 4320656--4320687 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4320646 GAGACTTATG
*
4320656 ATAAATTTAAATCCCT
1 ATAAATCTAAATCCCT
4320672 ATAAATCTAAATCCCT
1 ATAAATCTAAATCCCT
4320688 TACAAAATAT
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:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAAATCTAAATCCCT
Found at i:4322705 original size:108 final size:108
Alignment explanation
Indices: 4322515--4322721 Score: 333
Period size: 108 Copynumber: 1.9 Consensus size: 108
4322505 TACTTATTTC
* * **
4322515 CAACTTGTCATCTCACTCTTTTATGCACGATAGCTTTTACCTCCCAAATGCTCTTTAGCTTTTAC
1 CAACTTGTCATCTCACTCTTTTATGCACGATAACTTTTACATCCCAAATGCTCTCAAGCTTTTAC
* *
4322580 CTTTCAAATGCTTTCCATGTGAATGATGGATGCTACCTTAAAT
66 CTTCCAAATGCTCTCCATGTGAATGATGGATGCTACCTTAAAT
* *
4322623 CAACTTGTCATCTCACTCTTTTATGCACTATAACTTTTACATCCTAAATGCTCTCAAGCTTTTAC
1 CAACTTGTCATCTCACTCTTTTATGCACGATAACTTTTACATCCCAAATGCTCTCAAGCTTTTAC
*
4322688 CTTCCAAATGCTCTCCATGTGAGTGATGGATGCT
66 CTTCCAAATGCTCTCCATGTGAATGATGGATGCT
4322722 GCCTAACTCA
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
108 90 1.00
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (108 bp):
CAACTTGTCATCTCACTCTTTTATGCACGATAACTTTTACATCCCAAATGCTCTCAAGCTTTTAC
CTTCCAAATGCTCTCCATGTGAATGATGGATGCTACCTTAAAT
Found at i:4328170 original size:156 final size:161
Alignment explanation
Indices: 4327962--4328277 Score: 376
Period size: 164 Copynumber: 2.0 Consensus size: 161
4327952 TCTATCATTC
* *
4327962 AACATTCTAATTGAACATTTAATCAACCAATGTATACGATTAGATCTAATGTAATTATACTGATA
1 AACATTCTAATTGAACATTTAATCAACCAATGTATACAATTAAATCTAATGTAATTATACTGATA
** * * *
4328027 -TCAATTTACGT-CTAA-ACCAAAAACT-AAAATAAAATAGATGTAAGGAAAATTTTTT-AAAAT
66 TTCAATTTACGTCCTAACAAAAAAAAATAAAAACAAAATAAATGTAA-GAAAATTTTTTAAAAAT
*
4328087 TCAAAATACTTGTTAAAAAATTATAATATAAT
130 TCAAAATACTTGCTAAAAAATTATAATATAAT
** * **
4328119 AACATTCTAATTGAACA-TTAATCATTTC-ATGTGTACAATTAAATCTAATGTAATTATGTTGAT
1 AACATTCTAATTGAACATTTAATCA-ACCAATGTATACAATTAAATCTAATGTAATTATACTGAT
* *
4328182 ATTTAATTTATGTCCTAACAAAAAAAAATAAAACAAAACAAAATAAATGTAAGAAAATTTTTTAA
65 ATTCAATTTACGTCCTAACAAAAAAAAAT---A-AAAACAAAATAAATGTAAGAAAATTTTTTAA
* *
4328247 AAATTTAAAATACTTGCTAAAAAATTCTAAT
126 AAATTCAAAATACTTGCTAAAAAATTATAAT
4328278 TTTCTCTAGA
Statistics
Matches: 132, Mismatches: 17, Indels: 13
0.81 0.10 0.08
Matches are distributed among these distances:
156 38 0.29
157 27 0.20
158 4 0.03
159 7 0.05
163 11 0.08
164 45 0.34
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.34
Consensus pattern (161 bp):
AACATTCTAATTGAACATTTAATCAACCAATGTATACAATTAAATCTAATGTAATTATACTGATA
TTCAATTTACGTCCTAACAAAAAAAAATAAAAACAAAATAAATGTAAGAAAATTTTTTAAAAATT
CAAAATACTTGCTAAAAAATTATAATATAAT
Found at i:4328218 original size:15 final size:15
Alignment explanation
Indices: 4328198--4328228 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4328188 TTTATGTCCT
4328198 AACAAAAAAAAATAA
1 AACAAAAAAAAATAA
*
4328213 AACAAAACAAAATAA
1 AACAAAAAAAAATAA
4328228 A
1 A
4328229 TGTAAGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.10, G:0.00, T:0.06
Consensus pattern (15 bp):
AACAAAAAAAAATAA
Found at i:4328551 original size:2 final size:2
Alignment explanation
Indices: 4328544--4328584 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
4328534 AGTTTTATTT
* *
4328544 TA TA TA TA TA TA TA TA TA TA TA TA CA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4328585 GGAAGAAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4329113 original size:28 final size:30
Alignment explanation
Indices: 4329063--4329127 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
4329053 TTAAAATTTT
*
4329063 ATAAAAAATTATATATGAATTTAAT-AAAA
1 ATAAAAAATTATATATAAATTTAATGAAAA
*
4329092 ATAAAAAA-TATAT-TAAAGTTTACTGAAAA
1 ATAAAAAATTATATATAAA-TTTAATGAAAA
*
4329121 AGAAAAA
1 ATAAAAA
4329128 TAATCATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 3 0.10
28 10 0.32
29 18 0.58
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (30 bp):
ATAAAAAATTATATATAAATTTAATGAAAA
Found at i:4329227 original size:9 final size:9
Alignment explanation
Indices: 4329201--4329234 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
4329191 ATGAAATTAA
4329201 TAAATATTT
1 TAAATATTT
4329210 TAAATTATTT
1 TAAA-TATTT
*
4329220 TTAATATTT
1 TAAATATTT
4329229 TAAATA
1 TAAATA
4329235 ATAATTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TAAATATTT
Found at i:4329667 original size:29 final size:27
Alignment explanation
Indices: 4329611--4329687 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 27
4329601 TAAATATTAA
4329611 TTTTAATG-AAA-TTTTTTCAGTATAAAT
1 TTTTAATGAAAATTTTTTTCA--ATAAAT
4329638 TTTTAATGAAAATTTTTTTCAATCACAAT
1 TTTTAATGAAAATTTTTTTCAAT-A-AAT
* *
4329667 TATT-AT-AATATTTTTTTCAAT
1 TTTTAATGAAAATTTTTTTCAAT
4329688 TGTAATTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
27 24 0.55
28 6 0.14
29 14 0.32
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.53
Consensus pattern (27 bp):
TTTTAATGAAAATTTTTTTCAATAAAT
Found at i:4331030 original size:25 final size:25
Alignment explanation
Indices: 4330994--4331074 Score: 105
Period size: 25 Copynumber: 3.3 Consensus size: 25
4330984 TAACCTTTGT
4330994 TTTTATTAGTTTAATATTATAATTA
1 TTTTATTAGTTTAATATTATAATTA
*
4331019 TTTTATTTGTTTAATA-TA-AA-TA
1 TTTTATTAGTTTAATATTATAATTA
* *
4331041 TTTTTATTAGTTTAAAATAATAATTA
1 -TTTTATTAGTTTAATATTATAATTA
4331067 TTTTATTA
1 TTTTATTA
4331075 ATTTTTAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
22 2 0.04
23 16 0.33
24 3 0.06
25 25 0.52
26 2 0.04
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (25 bp):
TTTTATTAGTTTAATATTATAATTA
Found at i:4331084 original size:25 final size:24
Alignment explanation
Indices: 4330994--4331084 Score: 71
Period size: 25 Copynumber: 3.7 Consensus size: 24
4330984 TAACCTTTGT
*
4330994 TTTTATTA-GTTTAATATTATAATTA
1 TTTTATTATTTTTAATA--ATAATTA
* *
4331019 TTTTATT-TGTTTAAT-ATAAATA
1 TTTTATTATTTTTAATAATAATTA
**
4331041 TTTTTATTAGTTTAAAATAATAATTA
1 -TTTTATTA-TTTTTAATAATAATTA
4331067 TTTTATTAATTTTTAATA
1 TTTTATT-ATTTTTAATA
4331085 CTATTTTTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
22 6 0.11
23 7 0.13
25 33 0.62
26 7 0.13
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.59
Consensus pattern (24 bp):
TTTTATTATTTTTAATAATAATTA
Found at i:4331151 original size:9 final size:8
Alignment explanation
Indices: 4331134--4331188 Score: 56
Period size: 8 Copynumber: 6.4 Consensus size: 8
4331124 TTTATTTAAA
4331134 AATAATTT
1 AATAATTT
4331142 AATAATTTT
1 AATAA-TTT
4331151 AATAATTT
1 AATAATTT
*
4331159 ATTAATTT
1 AATAATTT
*
4331167 TATAAATATT
1 AAT-AAT-TT
4331177 AAATAATTT
1 -AATAATTT
4331186 AAT
1 AAT
4331189 TTTTTTGTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 19 0.49
9 13 0.33
10 5 0.13
11 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
AATAATTT
Found at i:4331156 original size:17 final size:17
Alignment explanation
Indices: 4331134--4331168 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
4331124 TTTATTTAAA
4331134 AATAATTTAATAATTTT
1 AATAATTTAATAATTTT
*
4331151 AATAATTTATTAATTTT
1 AATAATTTAATAATTTT
4331168 A
1 A
4331169 TAAATATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATAATTTAATAATTTT
Found at i:4332162 original size:12 final size:11
Alignment explanation
Indices: 4332138--4332177 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
4332128 TTTGAGATTT
4332138 TTTTG-TTTG-
1 TTTTGTTTTGA
4332147 TTTTGTTTTGTA
1 TTTTGTTTTG-A
4332159 TTTTGTTTTGA
1 TTTTGTTTTGA
4332170 TTTT-TTTT
1 TTTTGTTTT
4332178 AAAATTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 5 0.18
10 8 0.29
11 5 0.18
12 10 0.36
ACGTcount: A:0.05, C:0.00, G:0.15, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTGA
Found at i:4332568 original size:107 final size:105
Alignment explanation
Indices: 4332352--4332729 Score: 413
Period size: 107 Copynumber: 3.6 Consensus size: 105
4332342 AAAAATCTCA
* * * * * *
4332352 AAAATCTTTGAATGCTCCTCTCAATCAGAGGCATTAAAACTTTGAAAATTATAATCTTTTGCCCA
1 AAAATCTTTGAATGCTCATCCCAATCAGAGGCATTGAAACTTTGAAAATTAAAATGTTTTGCCGA
* * *
4332417 ATGGTCTTAGAGATTATGCCCAAAAGTCTTTGAAATCTTTG
66 A-GGTCTTGGAGATCATGCCCAAAGGTCTTTGAAATCTTTG
* * * ** *
4332458 AAAATATTTGAATGCTCTTCCTAATCAGAGGCATTGGGACTTTGAAAATTTAAAATGATTTGCCT
1 AAAATCTTTGAATGCTCATCCCAATCAGAGGCATTGAAACTTTGAAAA-TTAAAATGTTTTGCC-
* * *
4332523 GGAGGTCTTGGAGATCATGCTCAGAGGTCTTTGAAATCTTTG
64 GAAGGTCTTGGAGATCATGCCCAAAGGTCTTTGAAATCTTTG
* *
4332565 AAAATCTTTGAATGCTCATCCCAATCAAAGGCATTGAAAC-TTCAAAATT-AAATGTTTTTGCCC
1 AAAATCTTTGAATGCTCATCCCAATCAGAGGCATTGAAACTTTGAAAATTAAAATG-TTTTG-CC
* * * * **
4332628 GAAGGTCTTGAAAATCACGCCCAAAGGTCTTAT-AGATC-TAA
64 GAAGGTCTTGGAGATCATGCCCAAAGGTCTT-TGAAATCTTTG
* *
4332669 AAAATCTTTGAACGTTCATCCCAATCAGAGGCATTGAAACTTTGAAAATTTAAAATGTTTT
1 AAAATCTTTGAATGCTCATCCCAATCAGAGGCATTGAAACTTTGAAAA-TTAAAATGTTTT
4332730 ACTGAGTGAT
Statistics
Matches: 226, Mismatches: 38, Indels: 16
0.81 0.14 0.06
Matches are distributed among these distances:
104 43 0.19
105 41 0.18
106 56 0.25
107 85 0.38
108 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (105 bp):
AAAATCTTTGAATGCTCATCCCAATCAGAGGCATTGAAACTTTGAAAATTAAAATGTTTTGCCGA
AGGTCTTGGAGATCATGCCCAAAGGTCTTTGAAATCTTTG
Found at i:4333514 original size:14 final size:15
Alignment explanation
Indices: 4333495--4333523 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4333485 TTTTTTTTTT
4333495 GTGATGC-AATGCAA
1 GTGATGCAAATGCAA
4333509 GTGATGCAAATGCAA
1 GTGATGCAAATGCAA
4333524 ATGTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.21
Consensus pattern (15 bp):
GTGATGCAAATGCAA
Found at i:4335032 original size:20 final size:20
Alignment explanation
Indices: 4334982--4335040 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
4334972 CTTTTCACCC
4334982 ATTCATTTTTTTTCCTTATTTT
1 ATTCA-TTTTTTTCCTT-TTTT
*
4335004 ATTC-CTTTTTTCC-TTTTT
1 ATTCATTTTTTTCCTTTTTT
4335022 ATTTCATTTTTTT-CTTTTT
1 A-TTCATTTTTTTCCTTTTT
4335041 CTTTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 5 0.16
19 5 0.16
20 18 0.56
22 4 0.12
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (20 bp):
ATTCATTTTTTTCCTTTTTT
Found at i:4335050 original size:19 final size:19
Alignment explanation
Indices: 4335000--4335056 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
4334990 TTTTTCCTTA
* *
4335000 TTTTA-TTCCTTTTTTCCT
1 TTTTATTTCATTTTTTTCT
4335018 TTTTATTTCATTTTTTTCT
1 TTTTATTTCATTTTTTTCT
*
4335037 TTTTCTTT--TTTTTTT-T
1 TTTTATTTCATTTTTTTCT
4335053 TTTT
1 TTTT
4335057 TCATTGAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 5 0.14
17 7 0.20
18 5 0.14
19 18 0.51
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTATTTCATTTTTTTCT
Found at i:4335055 original size:15 final size:15
Alignment explanation
Indices: 4335017--4335054 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
4335007 CCTTTTTTCC
*
4335017 TTTTTATTTCATTTT
1 TTTTTTTTTCATTTT
*
4335032 TTTCTTTTTC-TTTT
1 TTTTTTTTTCATTTT
4335046 TTTTTTTTT
1 TTTTTTTTT
4335055 TTTCATTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.05, C:0.08, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTTTTTCATTTT
Found at i:4343241 original size:8 final size:8
Alignment explanation
Indices: 4343208--4343238 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
4343198 ACTTTGAAGA
4343208 CTTTTTTT
1 CTTTTTTT
4343216 CTTTTTTT
1 CTTTTTTT
4343224 CTTTTTTT
1 CTTTTTTT
4343232 -TTTTTTT
1 CTTTTTTT
4343239 TTTGGTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
CTTTTTTT
Found at i:4343350 original size:20 final size:16
Alignment explanation
Indices: 4343308--4343345 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
4343298 TTCTTCTAAG
4343308 AAACCATTCAAAACAC
1 AAACCATTCAAAACAC
4343324 AAACCATTCAAAACAC
1 AAACCATTCAAAACAC
4343340 AAACCA
1 AAACCA
4343346 ACCATAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.58, C:0.32, G:0.00, T:0.11
Consensus pattern (16 bp):
AAACCATTCAAAACAC
Found at i:4343722 original size:5 final size:6
Alignment explanation
Indices: 4343708--4343732 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4343698 ACCCATCTCC
4343708 TTTTCT TTTTCT TTTTCT TTTTCT T
1 TTTTCT TTTTCT TTTTCT TTTTCT T
4343733 CTCCTTCCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:4344433 original size:144 final size:145
Alignment explanation
Indices: 4344165--4344508 Score: 370
Period size: 144 Copynumber: 2.4 Consensus size: 145
4344155 GGATTATAAA
* * * * * * *
4344165 ACACAAAAAATAATGAAAAATTATAAAATTGAGATATAAAAAGTTTCATAAAAATTTGAGCTTCG
1 ACACCAAAAATAATGAAATATTATGAAATTAAGATATAAAAAGTTTCATAAAAATCTGAACTTCA
* * * * *
4344230 AAAGATCAAATTACAAAAATACCCTTATATGGGTATTTTAGTATTTTTACATTTTTTGGGATAC-
66 AAAGATCAAATTACAAAAATACCCTTATAAGGGTATTTTAGTAATTTCACACTTCTTGGGATACA
*
4344294 TCTGTGATTTCAAAT
131 GCTGTGATTTCAAAT
* * * * * * *
4344309 GCATCAAAAATTATGAAATATTATGAAATTAAGATTTGAAAGGTTTCATAGAAATCTGAAC-TCA
1 ACACCAAAAATAATGAAATATTATGAAATTAAGATATAAAAAGTTTCATAAAAATCTGAACTTCA
* * * *
4344373 AGAAGATTAAATTACGAAAATACCTTTATAAGGGTATTTT-GATAATTTCACACTTCTTGGGGTA
66 A-AAGATCAAATTACAAAAATACCCTTATAAGGGTATTTTAG-TAATTTCACACTTCTTGGGATA
4344437 CAGCTGTGATTTCAAAT
129 CAGCTGTGATTTCAAAT
* * * * * * *
4344454 ACACCAAAAATCATAAAATATTATGAAATCAATATCTAAAAAATTTCATGAAAAT
1 ACACCAAAAATAATGAAATATTATGAAATTAAGATATAAAAAGTTTCATAAAAAT
4344509 ATCCCTTATA
Statistics
Matches: 161, Mismatches: 36, Indels: 5
0.80 0.18 0.02
Matches are distributed among these distances:
143 4 0.02
144 100 0.62
145 57 0.35
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (145 bp):
ACACCAAAAATAATGAAATATTATGAAATTAAGATATAAAAAGTTTCATAAAAATCTGAACTTCA
AAAGATCAAATTACAAAAATACCCTTATAAGGGTATTTTAGTAATTTCACACTTCTTGGGATACA
GCTGTGATTTCAAAT
Found at i:4359431 original size:22 final size:22
Alignment explanation
Indices: 4359328--4359555 Score: 78
Period size: 22 Copynumber: 10.4 Consensus size: 22
4359318 ATAAGAAATG
* **
4359328 ATTTGTAAGACTTTTGGGCATA
1 ATTTGTAAGACTTCTAAGCATA
* * *
4359350 ATTTGTAAAACCTC-CAGACATA
1 ATTTGTAAGACTTCTAAG-CATA
* * *
4359372 ATTTATAAGGCTTCCAAGCATA
1 ATTTGTAAGACTTCTAAGCATA
*
4359394 ATTT-TCAAGACTTCTAAGCATG
1 ATTTGT-AAGACTTCTAAGCATA
* *
4359416 ATTTGTAAGACCTCT-AGTTATA
1 ATTTGTAAGACTTCTAAG-CATA
* * * **
4359438 GTTTGAAAGGCATTC-GGGCATA
1 ATTTGTAAGAC-TTCTAAGCATA
*
4359460 ATTT-TCAAAACCTTC-AAGCATA
1 ATTTGT-AAGA-CTTCTAAGCATA
* **
4359482 ATTTGTAAAGCCTT-TGGGCATA
1 ATTTGT-AAGACTTCTAAGCATA
* * * *
4359504 ATTCT-CAAGACCTCTAAACATG
1 ATT-TGTAAGACTTCTAAGCATA
* *
4359526 ATTTGTAAGACCTCT-GGCATA
1 ATTTGTAAGACTTCTAAGCATA
4359547 ATTTGTAAG
1 ATTTGTAAG
4359556 CCTATCAGAC
Statistics
Matches: 148, Mismatches: 44, Indels: 29
0.67 0.20 0.13
Matches are distributed among these distances:
21 22 0.15
22 115 0.78
23 11 0.07
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (22 bp):
ATTTGTAAGACTTCTAAGCATA
Found at i:4359530 original size:44 final size:44
Alignment explanation
Indices: 4359453--4359549 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 44
4359443 AAAGGCATTC
* * *
4359453 GGGCATAATTTTCAAAACCTTCAAGCATAATTTGTAA-AGCCTTT
1 GGGCATAATTCTCAAAACCTTCAAACATAATTTGTAAGA-CCTCT
* *
4359497 GGGCATAATTCTCAAGACC-TCTAAACATGATTTGTAAGACCTCT
1 GGGCATAATTCTCAAAACCTTC-AAACATAATTTGTAAGACCTCT
4359541 -GGCATAATT
1 GGGCATAATT
4359550 TGTAAGCCTA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
43 11 0.24
44 34 0.74
45 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (44 bp):
GGGCATAATTCTCAAAACCTTCAAACATAATTTGTAAGACCTCT
Found at i:4359581 original size:65 final size:65
Alignment explanation
Indices: 4359477--4359686 Score: 183
Period size: 65 Copynumber: 3.2 Consensus size: 65
4359467 AAACCTTCAA
** * *
4359477 GCATAATTTGTAAAGCCTTTGGGCATAATTCTCAAGACCTCTAAACATGATTTGTAAGACCTCTG
1 GCATAATTTGTAAAGCCTTCAGACATAATTCTCAAGACCTCCAAACATGATTTGTAAGACCTCTG
* * **
4359542 GCATAATTTGT-AAGCCTATCAGACATAATTTTCAAGACCTCCAAACATGATTTGTAAAATTTTC
1 GCATAATTTGTAAAGCCT-TCAGACATAATTCTCAAGACCTCCAAACATGATTTGTAAGA-CCTC
**
4359606 AA
64 TG
* ** * * * * *
4359608 GCATAATTT-TGAAGGCCTTTGGTCATAATTCTCAAGACCT-CTAGCATGATTTATAAGACTTTC
1 GCATAATTTGT-AAAGCCTTCAGACATAATTCTCAAGACCTCCAAACATGATTTGTAAGAC-CTC
*
4359671 GG
64 TG
*
4359673 GCATAATTTTTAAA
1 GCATAATTTGTAAA
4359687 ACTTCCAAGC
Statistics
Matches: 116, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
64 6 0.05
65 75 0.65
66 30 0.26
67 5 0.04
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (65 bp):
GCATAATTTGTAAAGCCTTCAGACATAATTCTCAAGACCTCCAAACATGATTTGTAAGACCTCTG
Found at i:4359589 original size:22 final size:22
Alignment explanation
Indices: 4359510--4359598 Score: 67
Period size: 22 Copynumber: 4.1 Consensus size: 22
4359500 CATAATTCTC
* *
4359510 AAGACCTCTAAACATGATTTGT
1 AAGACCTCCAAACATAATTTGT
***
4359532 AAGACCT-CTGGCATAATTTGT
1 AAGACCTCCAAACATAATTTGT
* *
4359553 AAG-CCTATCAGACATAATTT-T
1 AAGACCT-CCAAACATAATTTGT
*
4359574 CAAGACCTCCAAACATGATTTGT
1 -AAGACCTCCAAACATAATTTGT
4359597 AA
1 AA
4359599 AATTTTCAAG
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
20 3 0.06
21 13 0.25
22 32 0.62
23 4 0.08
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.30
Consensus pattern (22 bp):
AAGACCTCCAAACATAATTTGT
Found at i:4363310 original size:24 final size:24
Alignment explanation
Indices: 4363273--4363336 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
4363263 AATTTTATAT
*
4363273 ATAATAAAAATTTTAAATTATAAA
1 ATAATAATAATTTTAAATTATAAA
* * * *
4363297 ATAATAATATTTTTAATTTTTAAT
1 ATAATAATAATTTTAAATTATAAA
4363321 ATAATAATAAATTTTA
1 ATAATAAT-AATTTTA
4363337 TTATTTTACT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 27 0.82
25 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATAATAATAATTTTAAATTATAAA
Found at i:4366077 original size:13 final size:13
Alignment explanation
Indices: 4366061--4366087 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4366051 ATTAAAAATA
4366061 AAAAAAATTTTTT
1 AAAAAAATTTTTT
4366074 AAAAAAATTTTTT
1 AAAAAAATTTTTT
4366087 A
1 A
4366088 TCGATAAAAT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAAAAATTTTTT
Found at i:4366996 original size:21 final size:21
Alignment explanation
Indices: 4366940--4366997 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 21
4366930 TTGACATAAC
* *
4366940 TATTAAAATAGTAAAATTATT
1 TATTACAATATTAAAATTATT
4366961 TATTACTAAATATATTAAAATTATT
1 TATTAC---A-ATATTAAAATTATT
4366986 TATTACAATATT
1 TATTACAATATT
4366998 TATTAATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
21 10 0.32
22 1 0.03
24 1 0.03
25 19 0.61
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (21 bp):
TATTACAATATTAAAATTATT
Found at i:4367003 original size:25 final size:25
Alignment explanation
Indices: 4366943--4366991 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
4366933 ACATAACTAT
*
4366943 TAAA-ATAGTAAAATTATTTATTAC
1 TAAATATATTAAAATTATTTATTAC
4366967 TAAATATATTAAAATTATTTATTAC
1 TAAATATATTAAAATTATTTATTAC
4366992 AATATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (25 bp):
TAAATATATTAAAATTATTTATTAC
Found at i:4367091 original size:21 final size:22
Alignment explanation
Indices: 4367065--4367113 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
4367055 TATTATATCA
4367065 TAATATTAAAATAGTAATAT-T
1 TAATATTAAAATAGTAATATAT
*
4367086 TAATATTAAAATAGTTATATAT
1 TAATATTAAAATAGTAATATAT
4367108 T-ATATT
1 TAATATT
4367114 GATAGTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TAATATTAAAATAGTAATATAT
Found at i:4367239 original size:10 final size:10
Alignment explanation
Indices: 4367224--4367281 Score: 63
Period size: 10 Copynumber: 6.2 Consensus size: 10
4367214 CATATAATTA
4367224 AAATAATATT
1 AAATAATATT
4367234 AAATAATATT
1 AAATAATATT
4367244 -AAT--TATT
1 AAATAATATT
4367251 AAATAATA--
1 AAATAATATT
*
4367259 AAATATTATTT
1 AAATAATA-TT
4367270 AAATAATATT
1 AAATAATATT
4367280 AA
1 AA
4367282 TATTTATTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 4 0.10
8 10 0.25
9 3 0.08
10 16 0.40
11 7 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AAATAATATT
Found at i:4367266 original size:22 final size:21
Alignment explanation
Indices: 4367238--4367302 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 21
4367228 AATATTAAAT
4367238 AATATTAATTATTAAATAATAA
1 AATATT-ATTATTAAATAATAA
*
4367260 AATATTA-T-TTAAATAATATT
1 AATATTATTATTAAATAATA-A
*
4367280 AATATTTATTACTAATATAATAA
1 AATA-TTATTATTAA-ATAATAA
4367303 TATAAATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
19 10 0.29
20 5 0.14
21 4 0.11
22 7 0.20
23 3 0.09
24 6 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
AATATTATTATTAAATAATAA
Found at i:4367272 original size:36 final size:36
Alignment explanation
Indices: 4367217--4367351 Score: 107
Period size: 36 Copynumber: 3.7 Consensus size: 36
4367207 AAATATTCAT
*
4367217 ATAATTAAAATAATA-TTAAATAATATTAATTATTAA
1 ATAA-TAAAATATTATTTAAATAATATTAATTATTAA
*
4367253 ATAATAAAATATTATTTAAATAATATTAA-TATTTA
1 ATAATAAAATATTATTTAAATAATATTAATTATTAA
* * * * * *
4367288 TTACTAATATAATAATATAAAT--TATTTATTATTGAA
1 ATAATAAAAT-ATTATTTAAATAATATTAATTATT-AA
* *
4367324 ATATTAAAATATTTATGTTTAATAATAT
1 ATAATAAAATA-TTAT-TTAAATAATAT
4367352 ACAAAATTAA
Statistics
Matches: 76, Mismatches: 15, Indels: 13
0.73 0.14 0.12
Matches are distributed among these distances:
34 5 0.07
35 26 0.34
36 38 0.50
37 4 0.05
39 3 0.04
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (36 bp):
ATAATAAAATATTATTTAAATAATATTAATTATTAA
Found at i:4367273 original size:19 final size:18
Alignment explanation
Indices: 4367217--4367277 Score: 70
Period size: 17 Copynumber: 3.3 Consensus size: 18
4367207 AAATATTCAT
*
4367217 ATAATTAAAATAATATTAA
1 ATAA-TAAAATATTATTAA
**
4367236 ATAATATTA-ATTATTAA
1 ATAATAAAATATTATTAA
4367253 ATAATAAAATATTATTTAA
1 ATAATAAAATATTA-TTAA
4367272 ATAATA
1 ATAATA
4367278 TTAATATTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 14 0.40
18 7 0.20
19 14 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAATAAAATATTATTAA
Found at i:4367287 original size:17 final size:17
Alignment explanation
Indices: 4367227--4367287 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
4367217 ATAATTAAAA
4367227 TAATA-TTAAATAATAT
1 TAATATTTAAATAATAT
*
4367243 TAAT-TATTAAATAATAAAA
1 TAATAT-TTAAATAAT--AT
*
4367262 TATTATTTAAATAATAT
1 TAATATTTAAATAATAT
4367279 TAATATTTA
1 TAATATTTA
4367288 TTACTAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
16 4 0.11
17 18 0.50
19 13 0.36
20 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAATATTTAAATAATAT
Found at i:4367290 original size:46 final size:46
Alignment explanation
Indices: 4367215--4367315 Score: 109
Period size: 46 Copynumber: 2.2 Consensus size: 46
4367205 TAAAATATTC
* * * *
4367215 ATATAATTAAAATAATATTAAATAATATTAATTAT-TAAATAATAAA
1 ATATTATTTAAATAATATTAAATAATATTACTAATAT-AATAATAAA
* *
4367261 ATATTATTTAAATAATATT-AATATTTATTACTAATATAATAATATA
1 ATATTATTTAAATAATATTAAATA-ATATTACTAATATAATAATAAA
4367307 A-ATTATTTA
1 ATATTATTTA
4367316 TTATTGAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
45 12 0.26
46 34 0.72
47 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (46 bp):
ATATTATTTAAATAATATTAAATAATATTACTAATATAATAATAAA
Found at i:4372995 original size:19 final size:20
Alignment explanation
Indices: 4372959--4372998 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
4372949 AAAAAAAAAA
4372959 TTATATATTTTATTAATTTTT
1 TTATATATTTTA-TAATTTTT
4372980 TTATATATTTTA-AATTTTT
1 TTATATATTTTATAATTTTT
4372999 ATAAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATATATTTTATAATTTTT
Found at i:4382144 original size:16 final size:18
Alignment explanation
Indices: 4382110--4382300 Score: 84
Period size: 18 Copynumber: 10.8 Consensus size: 18
4382100 ATGCTACAAT
4382110 TATTATATTAATAAAATAA
1 TATTATATTAAT-AAATAA
*
4382129 TATT-T-TTATTAAATAA
1 TATTATATTAATAAATAA
4382145 CTATTATATTAATAAATAA
1 -TATTATATTAATAAATAA
* *
4382164 TA--CTATTAATATATTAA
1 TATTATATTAATA-AATAA
*
4382181 -A--AAATT-AT-AAT-A
1 TATTATATTAATAAATAA
* *
4382193 TATTACATTAATTATATAA
1 TATTATATTAA-TAAATAA
* *
4382212 TA-TATCAATTATATTAATTA
1 TATTAT--ATTA-ATAAATAA
*
4382232 TAATATATTAATAAATAA
1 TATTATATTAATAAATAA
* *
4382250 TATAATATTAACAAATAA
1 TATTATATTAATAAATAA
* *
4382268 TACATT-TTTTATTAAAATAA
1 T--ATTATATTAAT-AAATAA
4382288 TATT-TATTAATAA
1 TATTATATTAATAA
4382301 TATATTAATA
Statistics
Matches: 130, Mismatches: 24, Indels: 38
0.68 0.12 0.20
Matches are distributed among these distances:
12 1 0.01
13 3 0.02
15 6 0.05
16 19 0.15
17 15 0.12
18 38 0.29
19 25 0.19
20 19 0.15
21 4 0.03
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
TATTATATTAATAAATAA
Found at i:4382251 original size:15 final size:15
Alignment explanation
Indices: 4382135--4382329 Score: 70
Period size: 15 Copynumber: 12.8 Consensus size: 15
4382125 ATAATATTTT
* *
4382135 TATTAAATAACTATTA
1 TATT-AATAAATAATA
4382151 TATTAATAAATAATA
1 TATTAATAAATAATA
*
4382166 CTATTAATATATTAA-A
1 -TATTAATA-AATAATA
*
4382182 -A--AAT-TATAATA
1 TATTAATAAATAATA
*
4382193 TATTACATTAAT--TA
1 TATTA-ATAAATAATA
*
4382207 TA-TAATATATCAATTA
1 TATTAATAAAT-AA-TA
*
4382223 TATTAAT-TATAATA
1 TATTAATAAATAATA
4382237 TATTAATAAATAATATAA
1 TATTAATAAAT-A-AT-A
*
4382255 TATTAACAAATAATACA
1 TATTAATAAATAAT--A
* *
4382272 TTTTTTATTAAAATAATA
1 --TATTAAT-AAATAATA
*
4382290 T-TT-ATTAATAATA
1 TATTAATAAATAATA
*
4382303 TATTAATAAATAACA
1 TATTAATAAATAATA
*
4382318 TAGTAATAAATA
1 TATTAATAAATA
4382330 TTATTATATT
Statistics
Matches: 137, Mismatches: 19, Indels: 47
0.67 0.09 0.23
Matches are distributed among these distances:
10 3 0.02
11 1 0.01
12 8 0.06
13 10 0.07
14 18 0.13
15 36 0.26
16 26 0.19
17 12 0.09
18 12 0.09
19 4 0.03
20 7 0.05
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.43
Consensus pattern (15 bp):
TATTAATAAATAATA
Found at i:4383027 original size:22 final size:22
Alignment explanation
Indices: 4383002--4383043 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4382992 TGTATATTTA
* *
4383002 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
4383024 TATTTGTATCCCTAAAATTA
1 TATTTGTATCCCTAAAATTA
4383044 GGATAGACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:4383307 original size:25 final size:24
Alignment explanation
Indices: 4383255--4383318 Score: 94
Period size: 25 Copynumber: 2.7 Consensus size: 24
4383245 AAAATTTTCA
* *
4383255 GCCTTCATTGCTG-ACTTTTTTAG
1 GCCTTCATTGCCGAACTTGTTTAG
4383278 GCCTTCATTGCCGAATCTTGTTTAG
1 GCCTTCATTGCCGAA-CTTGTTTAG
4383303 GCCTTCATTGCCGAAC
1 GCCTTCATTGCCGAAC
4383319 CCTTTCAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
23 12 0.32
24 2 0.05
25 23 0.62
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.39
Consensus pattern (24 bp):
GCCTTCATTGCCGAACTTGTTTAG
Found at i:4396617 original size:130 final size:130
Alignment explanation
Indices: 4396393--4396704 Score: 376
Period size: 130 Copynumber: 2.4 Consensus size: 130
4396383 TTTGTGTAAT
* **** ** * *
4396393 ATAAATGCCTTAATTGAGTGAATATAAGACATG-AGGTTATTATCAATTACGGCGTGGGTTTAAT
1 ATAAATGCCTTAATTGAGTGAATATAAGAAATGAAAAAAATTATCAATTACAACGTAGGTTAAAT
** *
4396457 ATAAACGCCTTAATTGAGTGAATATAAGAATTGATAAA-AGCTTTCAATTTTGGCCTTTTGAAAA
66 ATAAACGCCTTAATTGAGTGAATATAAGAATTGATAAATA-CTTTCAATTAAGGACTTTTGAAAA
4396521 A
130 A
* * *
4396522 ATAAAGGCCTTAAATGAGTGAATATAAGAAATGAAAAAAATTGTCAATTACAACGTAGGTTAAAT
1 ATAAATGCCTTAATTGAGTGAATATAAGAAATGAAAAAAATTATCAATTACAACGTAGGTTAAAT
* * *** *
4396587 ATAAACGCCTTAATTGAGTGTATATAAGAATTGATAAATACTTTCAATTAAGGAGTTTTTTTAAT
66 ATAAACGCCTTAATTGAGTGAATATAAGAATTGATAAATACTTTCAATTAAGGACTTTTGAAAAA
* *
4396652 ATAAATGCCTTAATTGAGTGAATATAAGAATCAGGAAAAAAACTATCAATTAC
1 ATAAATGCCTTAATTGAGTGAATATAAGAA--ATGAAAAAAATTATCAATTAC
4396705 GGCGTCCTTC
Statistics
Matches: 153, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
129 30 0.20
130 104 0.68
131 1 0.01
132 18 0.12
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.32
Consensus pattern (130 bp):
ATAAATGCCTTAATTGAGTGAATATAAGAAATGAAAAAAATTATCAATTACAACGTAGGTTAAAT
ATAAACGCCTTAATTGAGTGAATATAAGAATTGATAAATACTTTCAATTAAGGACTTTTGAAAAA
Found at i:4396736 original size:67 final size:65
Alignment explanation
Indices: 4396390--4396737 Score: 240
Period size: 65 Copynumber: 5.3 Consensus size: 65
4396380 ACATTTGTGT
* * **** * **
4396390 AATATAAATGCCTTAATTGAGTGAATATAAG-ACATG-AGGTTATTATCAATTACGGCGTGGGTT
1 AATATAAACGCCTTAATTGAGTGAATATAAGAATATGAAAAAAACTATCAATTACGGCGT-CCTT
*
4396453 T
65 A
* * * ** * *
4396454 AATATAAACGCCTTAATTGAGTGAATATAAGAAT-TGATAAAAGCTTTCAATTTTGGCCT-TTTG
1 AATATAAACGCCTTAATTGAGTGAATATAAGAATATGAAAAAAACTATCAATTACGGCGTCCTT-
4396517 AA
65 -A
* * * * * ** **
4396519 AAAATAAAGGCCTTAAATGAGTGAATATAAGAA-ATGAAAAAAATTGTCAATTACAACGTAGGTT
1 AATATAAACGCCTTAATTGAGTGAATATAAGAATATGAAAAAAACTATCAATTACGGCGT-CCTT
4396583 A
65 A
* * * * * * **
4396584 AATATAAACGCCTTAATTGAGTGTATATAAGAAT-TGATAAATACTTTCAATTAAGGAGTTTTTT
1 AATATAAACGCCTTAATTGAGTGAATATAAGAATATGAAAAAAACTATCAATTACGGCG-TCCTT
*
4396648 T
65 A
* *
4396649 AATATAAATGCCTTAATTGAGTGAATATAAGAATCAGGAAAAAAACTATCAATTACGGCGTCCTT
1 AATATAAACGCCTTAATTGAGTGAATATAAGAAT-ATGAAAAAAACTATCAATTACGGCGTCCTT
4396714 CA
65 -A
* *
4396716 AACATATACGCCTTAATTGAGT
1 AATATAAACGCCTTAATTGAGT
4396738 CAAAACAAAA
Statistics
Matches: 215, Mismatches: 57, Indels: 21
0.73 0.19 0.07
Matches are distributed among these distances:
63 2 0.01
64 32 0.15
65 138 0.64
66 4 0.02
67 39 0.18
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (65 bp):
AATATAAACGCCTTAATTGAGTGAATATAAGAATATGAAAAAAACTATCAATTACGGCGTCCTTA
Found at i:4398011 original size:15 final size:15
Alignment explanation
Indices: 4397991--4398029 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
4397981 TTACCGTTGC
*
4397991 TGGAGCCTCCTCTGA
1 TGGAGCATCCTCTGA
4398006 TGGAGCATCCTCTGA
1 TGGAGCATCCTCTGA
4398021 TGGAGCATC
1 TGGAGCATC
4398030 ACCATCATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (15 bp):
TGGAGCATCCTCTGA
Found at i:4402044 original size:53 final size:53
Alignment explanation
Indices: 4401964--4402071 Score: 189
Period size: 53 Copynumber: 2.0 Consensus size: 53
4401954 TTTCAGTGTT
*
4401964 CACTCTATTAGTGTAATTCGATCTTTCCACCATATATCCTAAAAAGCTATGTG
1 CACTCTATTAGTGTAATTCGATCTTTCCACCATATATCCCAAAAAGCTATGTG
* *
4402017 CACTCTATTAGTGTAATTTGATCTTTCCACCATATATCCCAAAAGGCTATGTG
1 CACTCTATTAGTGTAATTCGATCTTTCCACCATATATCCCAAAAAGCTATGTG
4402070 CA
1 CA
4402072 GGCTATGTGT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (53 bp):
CACTCTATTAGTGTAATTCGATCTTTCCACCATATATCCCAAAAAGCTATGTG
Found at i:4409530 original size:14 final size:16
Alignment explanation
Indices: 4409499--4409530 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
4409489 ATTTATTATA
4409499 AAAATTATTAATTAAT
1 AAAATTATTAATTAAT
4409515 AAAATT-TTAA-TAAT
1 AAAATTATTAATTAAT
4409529 AA
1 AA
4409531 CTTTATATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 4 0.25
16 6 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATTATTAATTAAT
Found at i:4409618 original size:11 final size:11
Alignment explanation
Indices: 4409597--4410494 Score: 82
Period size: 11 Copynumber: 85.0 Consensus size: 11
4409587 TAACACTTTA
4409597 ATTAA-TTAAT
1 ATTAATTTAAT
4409607 ATTAATTTAAT
1 ATTAATTTAAT
* **
4409618 AAT-ATGAAAT
1 ATTAATTTAAT
*
4409628 ATTAATTTATT
1 ATTAATTTAAT
* * *
4409639 AAT-ACTGAAT
1 ATTAATTTAAT
*
4409649 TTTAATTTAAT
1 ATTAATTTAAT
4409660 AATT--TTGTAAT
1 -ATTAATT-TAAT
*
4409671 A-TCATTT-A-
1 ATTAATTTAAT
4409679 ATTAATTTAAT
1 ATTAATTTAAT
* *
4409690 AATATTTTAAT
1 ATTAATTTAAT
*
4409701 AAT-ATTT-AT
1 ATTAATTTAAT
4409710 -TTAATTCTAAT
1 ATTAATT-TAAT
*
4409721 ATTATTTTAAT
1 ATTAATTTAAT
*
4409732 AATAGATAATTAAT
1 ATTA-AT--TTAAT
*
4409746 -TTATTATTAAT
1 ATTAAT-TTAAT
* *
4409757 TTTCTATTT--T
1 ATT-AATTTAAT
4409767 ATTAATTTTAAT
1 ATTAA-TTTAAT
4409779 ATT-ATGTTAAT
1 ATTAAT-TTAAT
*
4409790 ATT-ATTTGAT
1 ATTAATTTAAT
*
4409800 ATTAA-ATAAT
1 ATTAATTTAAT
4409810 ATT-A--T-AT
1 ATTAATTTAAT
4409817 ATTAA-TTAAT
1 ATTAATTTAAT
* *
4409827 ATT-ACTAAAT
1 ATTAATTTAAT
*
4409837 ATTCATTT--T
1 ATTAATTTAAT
* * *
4409846 ACT-CTTAAAT
1 ATTAATTTAAT
4409856 ATTAATTTAAT
1 ATTAATTTAAT
* **
4409867 A-TGATGAAAT
1 ATTAATTTAAT
4409877 ATTAATTTAAT
1 ATTAATTTAAT
* * *
4409888 AAT-ATTGATT
1 ATTAATTTAAT
*
4409898 ATTAAATTAAT
1 ATTAATTTAAT
* *
4409909 AAT-ATTAAAT
1 ATTAATTTAAT
*
4409919 ATCAATTTAAT
1 ATTAATTTAAT
* * *
4409930 AAT-AGTGAAT
1 ATTAATTTAAT
4409940 ATTAATTTAAT
1 ATTAATTTAAT
** *
4409951 AACATTTTAAT
1 ATTAATTTAAT
*
4409962 AGT-ATTT-A-
1 ATTAATTTAAT
*
4409970 ATTAATTTCAT
1 ATTAATTTAAT
*
4409981 AAT-ATGTTAAT
1 ATTAAT-TTAAT
* *
4409992 GTTATTTTCAA-
1 ATTAATTT-AAT
4410003 ATT-ATTT-A-
1 ATTAATTTAAT
*
4410011 ATTAATTTTCAT
1 ATTAA-TTTAAT
*
4410023 ATAAATTATAAT
1 ATTAATT-TAAT
4410035 ATT-ATTTAATT
1 ATTAATTTAA-T
*
4410046 AATCTAATATGAAT
1 -AT-TAAT-TTAAT
**
4410060 ATTCTTTTAAT
1 ATTAATTTAAT
4410071 ATT-ATTTAAT
1 ATTAATTTAAT
*
4410081 A--ACATTAAAT
1 ATTA-ATTTAAT
*
4410091 ATGAATTTAAT
1 ATTAATTTAAT
* *
4410102 ATT-GTTAAAT
1 ATTAATTTAAT
* **
4410112 ATTAACTTAGG
1 ATTAATTTAAT
* *
4410123 ATT-ATTAAAC
1 ATTAATTTAAT
** *
4410133 GCTAATTAAAT
1 ATTAATTTAAT
* *
4410144 AAT-ATTAAAT
1 ATTAATTTAAT
**
4410154 ATTGTTTTAAT
1 ATTAATTTAAT
4410165 ATT-ATTTAGAAT
1 ATTAATTT--AAT
* *
4410177 AATAGTATTACAT
1 ATTAAT-TTA-AT
*
4410190 ATTTATTT-A-
1 ATTAATTTAAT
4410199 A-TAATTTGAAT
1 ATTAATTT-AAT
* *
4410210 ATTAGTATAAT
1 ATTAATTTAAT
*
4410221 ATT-ATTGAAT
1 ATTAATTTAAT
*
4410231 ATTAATTTAAC
1 ATTAATTTAAT
*
4410242 AAT-A-TTAACT
1 ATTAATTTAA-T
*
4410252 ATTAATTTAAG
1 ATTAATTTAAT
* *
4410263 AAT-ATTAAAT
1 ATTAATTTAAT
*
4410273 AATAATTTAAT
1 ATTAATTTAAT
4410284 ATT-ATTT-A-
1 ATTAATTTAAT
* *
4410292 ATTAATGTAAC
1 ATTAATTTAAT
** *
4410303 AACATTTTAAT
1 ATTAATTTAAT
*
4410314 GTT-ATTTAAT
1 ATTAATTTAAT
** * **
4410324 -GGATTTTACG
1 ATTAATTTAAT
*
4410334 ATT-ATGTTAAG
1 ATTAAT-TTAAT
4410345 ATT-ATTTAAT
1 ATTAATTTAAT
*
4410355 ATT-ACTT-A-
1 ATTAATTTAAT
* **
4410363 GTTAATTTCCT
1 ATTAATTTAAT
4410374 ATTAATTTAAT
1 ATTAATTTAAT
*
4410385 ATAAATTTAATACT
1 ATTAATTT-A-A-T
4410399 AAATTAATTGTAAT
1 --ATTAATT-TAAT
* *
4410413 ATTATTTTACT
1 ATTAATTTAAT
*
4410424 -TTTATTT--T
1 ATTAATTTAAT
*
4410432 ATTAATTTTAT
1 ATTAATTTAAT
4410443 ATT-ATTTAATT
1 ATTAATTTAA-T
4410454 ATT--TTTAAT
1 ATTAATTTAAT
* *
4410463 ATGAATTTATT
1 ATTAATTTAAT
*
4410474 ATTATTTTAAT
1 ATTAATTTAAT
4410485 A-TAATTTAAT
1 ATTAATTTAAT
4410495 TAATTTTAAC
Statistics
Matches: 618, Mismatches: 176, Indels: 188
0.63 0.18 0.19
Matches are distributed among these distances:
7 5 0.01
8 23 0.04
9 47 0.08
10 210 0.34
11 239 0.39
12 57 0.09
13 13 0.02
14 12 0.02
15 4 0.01
16 7 0.01
17 1 0.00
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (11 bp):
ATTAATTTAAT
Found at i:4409630 original size:21 final size:21
Alignment explanation
Indices: 4409604--4409662 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
4409594 TTAATTAATT
4409604 AATATTAATTTAATAATA-TG
1 AATATTAATTTAATAATACTG
*
4409624 AAATATTAATTTATTAATACTG
1 -AATATTAATTTAATAATACTG
*
4409646 AATTTTAATTTAATAAT
1 AATATTAATTTAATAAT
4409663 TTTGTAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 32 0.94
22 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (21 bp):
AATATTAATTTAATAATACTG
Found at i:4409727 original size:31 final size:30
Alignment explanation
Indices: 4409650--4409829 Score: 131
Period size: 31 Copynumber: 5.9 Consensus size: 30
4409640 ATACTGAATT
*
4409650 TTAATTTAATAATT-TTGTAAT-ATCATTTAA
1 TTAATTTAAT-ATTATTTTAATAAT-ATTTAA
* *
4409680 TTAATTTAATAATATTTTAATAATATTTAT
1 TTAATTTAATATTATTTTAATAATATTTAA
**
4409710 TTAATTCTAATATTATTTTAATAATAGATAA
1 TTAATT-TAATATTATTTTAATAATATTTAA
* *
4409741 TTAATTTATTATTAATTTT-CT-AT-TTT-A
1 TTAATTTAATATT-ATTTTAATAATATTTAA
* *
4409768 TTAATTTTAATATTATGTTAATATTATTTGATA
1 TTAA-TTTAATATTATTTTAATAATATTT-A-A
*
4409801 TTAA-ATAATATTATATATTAATTAATATT
1 TTAATTTAATATTAT-T-TTAA-TAATATT
4409830 ACTAAATATT
Statistics
Matches: 118, Mismatches: 18, Indels: 24
0.74 0.11 0.15
Matches are distributed among these distances:
27 9 0.08
28 10 0.08
29 5 0.04
30 37 0.31
31 42 0.36
33 9 0.08
34 6 0.05
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (30 bp):
TTAATTTAATATTATTTTAATAATATTTAA
Found at i:4409729 original size:17 final size:16
Alignment explanation
Indices: 4409680--4409731 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
4409670 TATCATTTAA
*
4409680 TTAATTTAATAATATT
1 TTAATTTAATATTATT
4409696 TTAA--TAATATT-TAT
1 TTAATTTAATATTAT-T
4409710 TTAATTCTAATATTATT
1 TTAATT-TAATATTATT
4409727 TTAAT
1 TTAAT
4409732 AATAGATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
13 1 0.03
14 11 0.37
16 4 0.13
17 13 0.43
18 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TTAATTTAATATTATT
Found at i:4409755 original size:72 final size:71
Alignment explanation
Indices: 4409595--4409758 Score: 165
Period size: 72 Copynumber: 2.3 Consensus size: 71
4409585 TATAACACTT
* * *
4409595 TAATTAATTAATATTAATTTAATAATATGAAATATTAATTTATTAATACTGAATTTTAATTTAAT
1 TAATTAATTTATATTAATTTAATAATATGAAATAATAATTTATTAATACTGAATATTAATTTAAT
*
4409660 AATTTTG
66 AA-TTAG
* ** * *
4409667 TAATATCATTTA-ATTAATTTAATAATATTTTAATAAT-ATTTATTTAATTCT-AATATTATTTT
1 TAAT-TAATTTATATTAATTTAATAATA-TGAAATAATAATTTA-TTAATACTGAATATTAATTT
4409729 AATAA-TAG
63 AATAATTAG
4409737 ATAATTAATTTATTATTAATTT
1 -TAATTAATTTA-TATTAATTT
4409759 TCTATTTTAT
Statistics
Matches: 76, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
70 8 0.11
71 4 0.05
72 46 0.61
73 18 0.24
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (71 bp):
TAATTAATTTATATTAATTTAATAATATGAAATAATAATTTATTAATACTGAATATTAATTTAAT
AATTAG
Found at i:4409811 original size:20 final size:17
Alignment explanation
Indices: 4409798--4409830 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4409788 ATATTATTTG
4409798 ATATTAAATAATATTAT
1 ATATTAAATAATATTAT
*
4409815 ATATTAATTAATATTA
1 ATATTAAATAATATTA
4409831 CTAAATATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATTAAATAATATTAT
Found at i:4409878 original size:21 final size:22
Alignment explanation
Indices: 4409852--4409952 Score: 113
Period size: 21 Copynumber: 4.8 Consensus size: 22
4409842 TTTTACTCTT
4409852 AAATATTAATTTAAT-AT-GATG
1 AAATATTAATTTAATAATAG-TG
*
4409873 AAATATTAATTTAATAATATTG
1 AAATATTAATTTAATAATAGTG
* * *
4409895 -ATTATTAAATTAATAATA-TT
1 AAATATTAATTTAATAATAGTG
*
4409915 AAATATCAATTTAATAATAGTG
1 AAATATTAATTTAATAATAGTG
4409937 -AATATTAATTTAATAA
1 AAATATTAATTTAATAA
4409953 CATTTTAATA
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
20 1 0.01
21 61 0.91
22 5 0.07
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.44
Consensus pattern (22 bp):
AAATATTAATTTAATAATAGTG
Found at i:4409952 original size:42 final size:43
Alignment explanation
Indices: 4409853--4409952 Score: 141
Period size: 42 Copynumber: 2.4 Consensus size: 43
4409843 TTTACTCTTA
* *
4409853 AATATTAATTTAAT-ATGATGAAATATTAATTTAATAATATTG
1 AATATTAATTTAATAATGATGAAATATCAATTTAATAATAGTG
* * *
4409895 ATTATTAAATTAATAAT-ATTAAATATCAATTTAATAATAGTG
1 AATATTAATTTAATAATGATGAAATATCAATTTAATAATAGTG
4409937 AATATTAATTTAATAA
1 AATATTAATTTAATAA
4409953 CATTTTAATA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 48 0.96
43 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.44
Consensus pattern (43 bp):
AATATTAATTTAATAATGATGAAATATCAATTTAATAATAGTG
Found at i:4410210 original size:33 final size:35
Alignment explanation
Indices: 4410141--4410217 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 35
4410131 ACGCTAATTA
*
4410141 AATAATATTAAATATTGTTTTAATATTATTTAGAAT
1 AATAGTATTAAATATTGTTTTAATA-TATTTAGAAT
*
4410177 AATAGTATTACATATT-TATTTAATA-ATTT-GAAT
1 AATAGTATTAAATATTGT-TTTAATATATTTAGAAT
*
4410210 ATTAGTAT
1 AATAGTAT
4410218 AATATTATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 11 0.30
34 4 0.11
35 1 0.03
36 21 0.57
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.49
Consensus pattern (35 bp):
AATAGTATTAAATATTGTTTTAATATATTTAGAAT
Found at i:4410247 original size:21 final size:21
Alignment explanation
Indices: 4410188--4410289 Score: 100
Period size: 21 Copynumber: 4.9 Consensus size: 21
4410178 ATAGTATTAC
*
4410188 ATATTTATTTAATAAT-TTGA
1 ATATTAATTTAATAATATTGA
* * *
4410208 ATATTAGTATAATATTATTGA
1 ATATTAATTTAATAATATTGA
*
4410229 ATATTAATTTAACAATATT-A
1 ATATTAATTTAATAATATTGA
* *
4410249 ACTATTAATTTAAGAATATTAA
1 A-TATTAATTTAATAATATTGA
* *
4410271 ATAATAATTTAATATTATT
1 ATATTAATTTAATAATATT
4410290 TAATTAATGT
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
20 14 0.21
21 51 0.76
22 2 0.03
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (21 bp):
ATATTAATTTAATAATATTGA
Found at i:4410440 original size:14 final size:15
Alignment explanation
Indices: 4410411--4410453 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
4410401 ATTAATTGTA
*
4410411 ATATTATTTTACTTTT
1 ATATTA-TTTAATTTT
*
4410427 ATTTTA-TTAATTTT
1 ATATTATTTAATTTT
4410441 ATATTATTTAATT
1 ATATTATTTAATT
4410454 ATTTTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 12 0.52
15 6 0.26
16 5 0.22
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
ATATTATTTAATTTT
Found at i:4410484 original size:22 final size:22
Alignment explanation
Indices: 4410430--4410492 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
4410420 TACTTTTATT
* *
4410430 TTATTAATTTT-ATATTATTTA
1 TTATTATTTTTAATATAATTTA
4410451 --ATTATTTTTAATATGAATTTA
1 TTATTATTTTTAATAT-AATTTA
4410472 TTATTA-TTTTAATATAATTTA
1 TTATTATTTTTAATATAATTTA
4410493 ATTAATTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
19 8 0.22
20 4 0.11
21 11 0.31
22 9 0.25
23 4 0.11
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTATTATTTTTAATATAATTTA
Found at i:4410502 original size:10 final size:10
Alignment explanation
Indices: 4410427--4410503 Score: 56
Period size: 10 Copynumber: 7.7 Consensus size: 10
4410417 TTTTACTTTT
4410427 ATTTT-ATTA
1 ATTTTAATTA
4410436 ATTTTATATT-
1 ATTTTA-ATTA
4410446 A-TTTAATTA
1 ATTTTAATTA
*
4410455 TTTTTAATATGA
1 ATTTTAAT-T-A
*
4410467 ATTTATTATT-
1 ATTT-TAATTA
4410477 ATTTTAATATA
1 ATTTTAAT-TA
4410488 A-TTTAATTA
1 ATTTTAATTA
4410497 ATTTTAA
1 ATTTTAA
4410504 CAAAAAATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 19
0.70 0.05 0.25
Matches are distributed among these distances:
8 3 0.06
9 15 0.28
10 23 0.43
11 5 0.09
12 5 0.09
13 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (10 bp):
ATTTTAATTA
Found at i:4410611 original size:12 final size:10
Alignment explanation
Indices: 4410585--4410685 Score: 57
Period size: 10 Copynumber: 9.6 Consensus size: 10
4410575 TATATAATTA
4410585 AATTAATATT
1 AATTAATATT
4410595 AATTAATTATCT
1 AATTAA-TAT-T
4410607 AATTAAATATTAT
1 AATT-AATA-T-T
4410620 AATTAATATT
1 AATTAATATT
*
4410630 -ATTTA-ATT
1 AATTAATATT
* *
4410638 AATGAA-ATA
1 AATTAATATT
*
4410647 AAATAATATT
1 AATTAATATT
4410657 AATTAATCATAAT
1 AATTAAT-AT--T
4410670 AATTAGA-ATT
1 AATTA-ATATT
4410680 AATTAA
1 AATTAA
4410686 ACATATAAAG
Statistics
Matches: 72, Mismatches: 9, Indels: 21
0.71 0.09 0.21
Matches are distributed among these distances:
8 3 0.04
9 14 0.19
10 21 0.29
11 6 0.08
12 13 0.18
13 14 0.19
14 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (10 bp):
AATTAATATT
Found at i:4410630 original size:27 final size:25
Alignment explanation
Indices: 4410568--4410639 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 25
4410558 GGTGAATTAT
*
4410568 TTAATAATATATAATTAAATTAATA
1 TTAATATTATATAATTAAATTAATA
* *
4410593 TTAATTAATTATCTAATTAAATATTATAA
1 TTAA-T-ATTATATAATTAAAT-TAAT-A
*
4410622 TTAATATTATTTAATTAA
1 TTAATATTATATAATTAA
4410640 TGAAATAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 4 0.10
26 1 0.03
27 25 0.64
28 4 0.10
29 5 0.13
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (25 bp):
TTAATATTATATAATTAAATTAATA
Found at i:4410704 original size:30 final size:30
Alignment explanation
Indices: 4410670--4410735 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
4410660 TAATCATAAT
*
4410670 AATTAGAATTAATTAAACATATAA-AGACAA
1 AATTAAAATTAATTAAACATATAAGA-ACAA
**
4410700 AATTAAAATTAATTAAATGTATAAGAACAA
1 AATTAAAATTAATTAAACATATAAGAACAA
4410730 AATTAA
1 AATTAA
4410736 TCGATAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.61, C:0.05, G:0.06, T:0.29
Consensus pattern (30 bp):
AATTAAAATTAATTAAACATATAAGAACAA
Found at i:4415116 original size:30 final size:33
Alignment explanation
Indices: 4415053--4415120 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 33
4415043 GACCTCAAAG
*
4415053 TTAAAAATGATATATTATTTAAAATTTTATAAAAA
1 TTAAAAATGATATAATATTTAAAA--TTATAAAAA
4415088 TTAAAAAT-ATATAAT-TTTAAAA-TATAAAAA
1 TTAAAAATGATATAATATTTAAAATTATAAAAA
4415118 TTA
1 TTA
4415121 TATTTTATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
30 11 0.34
33 7 0.22
34 6 0.19
35 8 0.25
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (33 bp):
TTAAAAATGATATAATATTTAAAATTATAAAAA
Found at i:4415134 original size:22 final size:23
Alignment explanation
Indices: 4415084--4415127 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
4415074 AAATTTTATA
4415084 AAAAT-TAAAAATATATAATTTT
1 AAAATATAAAAATATATAATTTT
4415106 AAAATATAAAAAT-TAT-ATTTT
1 AAAATATAAAAATATATAATTTT
4415127 A
1 A
4415128 TATATATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.29
22 8 0.38
23 7 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAATATAAAAATATATAATTTT
Found at i:4416933 original size:13 final size:13
Alignment explanation
Indices: 4416917--4416941 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4416907 AAGAGAAGAA
4416917 AGAGAGAGAGAGT
1 AGAGAGAGAGAGT
4416930 AGAGAGAGAGAG
1 AGAGAGAGAGAG
4416942 AGAAATAACA
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:0.48, T:0.04
Consensus pattern (13 bp):
AGAGAGAGAGAGT
Found at i:4417837 original size:2 final size:2
Alignment explanation
Indices: 4417832--4417878 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
4417822 GAGAGATCTT
* *
4417832 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GT GA TA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4417874 GA GA G
1 GA GA G
4417879 TATAAAATTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.49, T:0.04
Consensus pattern (2 bp):
GA
Found at i:4421012 original size:14 final size:13
Alignment explanation
Indices: 4420982--4421022 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
4420972 TGAATTATTA
*
4420982 TATAATTTTTTAT
1 TATAATTTTTAAT
4420995 TATAATTTATTAAT
1 TATAATTT-TTAAT
4421009 TATAATATTTTAAT
1 TATAAT-TTTTAAT
4421023 AAAATAATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 8 0.32
14 15 0.60
15 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATAATTTTTAAT
Found at i:4421890 original size:28 final size:28
Alignment explanation
Indices: 4421852--4421936 Score: 93
Period size: 29 Copynumber: 3.0 Consensus size: 28
4421842 AATTTAATAA
* *
4421852 ATTAAAA-AAATATATTTTATAATTTTT
1 ATTAAAATAAATATAATATATAATTTTT
*
4421879 ATTAAAATAAATTATAATATATATTTTTT
1 ATTAAAATAAA-TATAATATATAATTTTT
4421908 A-TAAAATAAAATATAAATATATGAATTTT
1 ATTAAAAT-AAATAT-AATATAT-AATTTT
4421937 AATATTTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
27 7 0.14
28 12 0.24
29 25 0.51
30 5 0.10
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (28 bp):
ATTAAAATAAATATAATATATAATTTTT
Found at i:4430985 original size:22 final size:21
Alignment explanation
Indices: 4430959--4431027 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 21
4430949 AGACCAAAAT
*
4430959 ATAAATAAGAAAATAATAATAA
1 ATAAAAAAGAAAATAA-AATAA
* *
4430981 ATAAAAAATAGAATAAAATAAA
1 ATAAAAAAGAAAATAAAAT-AA
*
4431003 ATTAAAAAATAAAATTAAAACTAA
1 A-TAAAAAAGAAAA-TAAAA-TAA
4431027 A
1 A
4431028 ATTGGGCCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 3 0.08
22 16 0.41
23 11 0.28
24 8 0.21
25 1 0.03
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (21 bp):
ATAAAAAAGAAAATAAAATAA
Found at i:4430988 original size:17 final size:16
Alignment explanation
Indices: 4430959--4431003 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
4430949 AGACCAAAAT
*
4430959 ATAAATAAGAAAATAATA
1 ATAAATAA-AAAAT-AGA
4430977 ATAAATAAAAAATAGA
1 ATAAATAAAAAATAGA
4430993 ATAAAATAAAA
1 AT-AAATAAAA
4431004 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 4 0.16
17 13 0.52
18 8 0.32
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (16 bp):
ATAAATAAAAAATAGA
Found at i:4430993 original size:24 final size:23
Alignment explanation
Indices: 4430973--4431028 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
4430963 ATAAGAAAAT
4430973 AATAATAAATAAAAAATAGAATAA
1 AATAA-AAATAAAAAATAGAATAA
* *
4430997 AATAAAATTAAAAAATAAAATTAA
1 AATAAAAATAAAAAATAGAA-TAA
4431021 AACTAAAA
1 AA-TAAAA
4431029 TTGGGCCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 13 0.46
24 10 0.36
25 5 0.18
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (23 bp):
AATAAAAATAAAAAATAGAATAA
Found at i:4431022 original size:12 final size:13
Alignment explanation
Indices: 4430995--4431022 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4430985 AAAATAGAAT
4430995 AAAATAAAATTAA
1 AAAATAAAATTAA
4431008 AAAATAAAATTAA
1 AAAATAAAATTAA
4431021 AA
1 AA
4431023 CTAAAATTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAATAAAATTAA
Found at i:4432177 original size:18 final size:18
Alignment explanation
Indices: 4432154--4432195 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
4432144 CAAAGAATTT
4432154 CATGGCATTAAAATTTAA
1 CATGGCATTAAAATTTAA
4432172 CATGGCATTAAAATTTAA
1 CATGGCATTAAAATTTAA
4432190 CATGGC
1 CATGGC
4432196 CTTATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (18 bp):
CATGGCATTAAAATTTAA
Found at i:4432578 original size:24 final size:24
Alignment explanation
Indices: 4432524--4432572 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
4432514 ATTACAAAAA
* *
4432524 TGCA-TTTGAAAAATTATTTTATT
1 TGCATTTTTAAAAAATATTTTATT
4432547 TGCATTTTTAAAAAATATTTCTATT
1 TGCATTTTTAAAAAATATTT-TATT
4432572 T
1 T
4432573 TATTTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 4 0.18
24 13 0.59
25 5 0.23
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (24 bp):
TGCATTTTTAAAAAATATTTTATT
Found at i:4434219 original size:16 final size:16
Alignment explanation
Indices: 4434175--4434220 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 16
4434165 AATAAAATGA
* *
4434175 TTTATTATATATATAT
1 TTTATTATATTTAGAT
4434191 TTTATTTCATATTTAGAT
1 TTTA-TT-ATATTTAGAT
4434209 TTTATTATATTT
1 TTTATTATATTT
4434221 TAATTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 10 0.38
17 4 0.15
18 12 0.46
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTATTATATTTAGAT
Found at i:4434773 original size:22 final size:21
Alignment explanation
Indices: 4434742--4434782 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4434732 TTCTTGGTAT
*
4434742 ATATAAAAAAATTTAAATATAA
1 ATAT-AAAAAACTTAAATATAA
*
4434764 ATATAGAAAACTTAAATAT
1 ATATAAAAAACTTAAATAT
4434783 TTAAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (21 bp):
ATATAAAAAACTTAAATATAA
Found at i:4438295 original size:22 final size:22
Alignment explanation
Indices: 4438268--4438319 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
4438258 ATATGATTAT
*
4438268 TATTAT-TAGTATTATCATATCA
1 TATTATATAGTATAAT-ATATCA
4438290 TATTATATAGTATAATATATCA
1 TATTATATAGTATAATATATCA
*
4438312 TATCATAT
1 TATTATAT
4438320 TAATACTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (22 bp):
TATTATATAGTATAATATATCA
Found at i:4438367 original size:10 final size:9
Alignment explanation
Indices: 4438234--4438388 Score: 56
Period size: 10 Copynumber: 16.3 Consensus size: 9
4438224 GTCTCTTTTG
4438234 TATATATTAT
1 TATATA-TAT
* *
4438244 TGTAGTATAA
1 TATA-TATAT
4438254 TAGTATATGAT
1 TA-TATAT-AT
4438265 TAT-TATTAT
1 TATATA-TAT
4438274 TAGTAT-TAT
1 TA-TATATAT
*
4438283 CATATCATAT
1 TATAT-ATAT
4438293 TATATAGTA-
1 TATATA-TAT
4438302 TA-ATATAT
1 TATATATAT
*
4438310 CATATCATAT
1 TATAT-ATAT
4438320 TA-ATACTAT
1 TATATA-TAT
*
4438329 TATAT-TTT
1 TATATATAT
*
4438337 TATTTATCAT
1 TATATAT-AT
4438347 TATTAGTATAT
1 TA-TA-TATAT
4438358 TATATCATAT
1 TATAT-ATAT
4438368 TACTAT-TAT
1 TA-TATATAT
4438377 TAT-TATTAT
1 TATATA-TAT
4438386 TAT
1 TAT
4438389 TATTATTTAC
Statistics
Matches: 111, Mismatches: 12, Indels: 45
0.66 0.07 0.27
Matches are distributed among these distances:
7 3 0.03
8 15 0.14
9 35 0.32
10 39 0.35
11 16 0.14
12 3 0.03
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (9 bp):
TATATATAT
Found at i:4438379 original size:3 final size:3
Alignment explanation
Indices: 4438326--4438395 Score: 58
Period size: 3 Copynumber: 24.3 Consensus size: 3
4438316 ATATTAATAC
* * * *
4438326 TAT TA- TAT TTT TATT TAT CAT TAT TAG TA- TAT TA- TAT CA- TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
4438368 TAC TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4438396 TACATTTTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
2 7 0.13
3 43 0.81
4 3 0.06
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:4439229 original size:24 final size:24
Alignment explanation
Indices: 4439202--4439274 Score: 83
Period size: 24 Copynumber: 2.9 Consensus size: 24
4439192 AGTTTCATTT
4439202 TTTCATTTTATTTTTATTTTTTGA
1 TTTCATTTTATTTTTATTTTTTGA
* *
4439226 TTTCATTTGATTTTATTTATTTTTTTA
1 TTTCATTT--TATT-TTTATTTTTTGA
**
4439253 GCTCATTTTATTTTTATTTTTT
1 TTTCATTTTATTTTTATTTTTT
4439275 ATGGTTTTAG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
24 18 0.44
25 3 0.07
26 3 0.07
27 17 0.41
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.74
Consensus pattern (24 bp):
TTTCATTTTATTTTTATTTTTTGA
Found at i:4439258 original size:27 final size:28
Alignment explanation
Indices: 4439214--4439271 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
4439204 TCATTTTATT
**
4439214 TTTATTTTTTGATTTCATTTGA-TTTTA
1 TTTATTTTTTGAGCTCATTTGATTTTTA
* *
4439241 TTTATTTTTTTAGCTCATTTTATTTTTA
1 TTTATTTTTTGAGCTCATTTGATTTTTA
4439269 TTT
1 TTT
4439272 TTTATGGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 18 0.69
28 8 0.31
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.72
Consensus pattern (28 bp):
TTTATTTTTTGAGCTCATTTGATTTTTA
Found at i:4439381 original size:17 final size:17
Alignment explanation
Indices: 4439356--4439394 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
4439346 AAAAAAATAT
*
4439356 ATAAAAAAACATTTTCAA
1 ATAAAAAATC-TTTTCAA
4439374 ATAAAAAATCTTTTCAA
1 ATAAAAAATCTTTTCAA
4439391 ATAA
1 ATAA
4439395 GTTTTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (17 bp):
ATAAAAAATCTTTTCAA
Found at i:4448488 original size:117 final size:120
Alignment explanation
Indices: 4448281--4448716 Score: 479
Period size: 126 Copynumber: 3.6 Consensus size: 120
4448271 AGAGAGAGTA
* * *
4448281 ATTTCTGATTTAGGACAGG-TTGGGGAAAGTCTACCAGTTTAGAGATATAAGTTTTAAGGTTTAT
1 ATTTCTGATTTAGGACAGGTTTGGAG-AAGTCTACCTGCTTAGAGATATAAGTTTTAAGGTTTAT
*
4448345 GGTTTACCGTTTA-TGATAGGAATTTAGGGAATGGGGTTTGGGAGTCAAAGA-GG-G
65 GGTTTACCGTTTATTG-TAGGAATTTAGGGAATAGGGTTTGGGAGTCAAAGAGGGTG
* * * * *
4448399 -TTTCTGATTTAGGACAGGTTTGGAGAAGCCTACCTGCTTACAGATGTGAGTTTTAAAGTTTATG
1 ATTTCTGATTTAGGACAGGTTTGGAGAAGTCTACCTGCTTAGAGATATAAGTTTTAAGGTTTATG
* *
4448463 GTTTACCGTTTATTGTAGGAATTTAGGGAATAGGGTTGGGGAGTGAAAGAGGTCGGATG
66 GTTTACCGTTTATTGTAGGAATTTAGGGAATAGGGTTTGGGAGTCAAAGA-G--GG-TG
* * * * *
4448522 TAATTTCTGATTTAGGATAGGTTTGGAGAAGTGTACCTGCTTGGAGGTATAAGTTTTAATGTTTA
1 --ATTTCTGATTTAGGACAGGTTTGGAGAAGTCTACCTGCTTAGAGATATAAGTTTTAAGGTTTA
* * * * *
4448587 TGATTTACTGTTTATGGTAGGAATTTA-GGAATAGGGTTTGGAAGTTAAAGAGGGTCAGTTG
64 TGGTTTACCGTTTATTGTAGGAATTTAGGGAATAGGGTTTGGGAGTCAAAGA-GG---G-TG
* * *
4448648 TCATTTCTGATTTTGTACAGGTTTGGAGAAGTCTACCTGCTTAGAGATATGAGTTTTAAGGTTTA
1 --ATTTCTGATTTAGGACAGGTTTGGAGAAGTCTACCTGCTTAGAGATATAAGTTTTAAGGTTTA
4448713 TGGT
64 TGGT
4448717 AGGAATTTAG
Statistics
Matches: 267, Mismatches: 37, Indels: 20
0.82 0.11 0.06
Matches are distributed among these distances:
117 94 0.35
118 7 0.03
121 2 0.01
123 2 0.01
125 23 0.09
126 139 0.52
ACGTcount: A:0.26, C:0.07, G:0.30, T:0.37
Consensus pattern (120 bp):
ATTTCTGATTTAGGACAGGTTTGGAGAAGTCTACCTGCTTAGAGATATAAGTTTTAAGGTTTATG
GTTTACCGTTTATTGTAGGAATTTAGGGAATAGGGTTTGGGAGTCAAAGAGGGTG
Found at i:4449861 original size:16 final size:16
Alignment explanation
Indices: 4449840--4449871 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4449830 TATAAAGGAG
4449840 GAATCACTTTCATGAT
1 GAATCACTTTCATGAT
*
4449856 GAATCACTTTGATGAT
1 GAATCACTTTCATGAT
4449872 AAGCCATGAT
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:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (16 bp):
GAATCACTTTCATGAT
Found at i:4451582 original size:47 final size:47
Alignment explanation
Indices: 4451511--4451603 Score: 125
Period size: 47 Copynumber: 2.0 Consensus size: 47
4451501 TCAGGATATT
*
4451511 TTGCATATGGTTACATTTAATTGAAAAAAT-TAGTCAGTGTTAAAGAG
1 TTGCATATGGTTACAGTTAATTGAAAAAATATAGTCA-TGTTAAAGAG
* * **
4451558 TTGCATATGGTTATAGTTAGTTGAAAAGTTATAGTCATGTTAAAGA
1 TTGCATATGGTTACAGTTAATTGAAAAAATATAGTCATGTTAAAGA
4451604 TACTATGCAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 34 0.85
48 6 0.15
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.38
Consensus pattern (47 bp):
TTGCATATGGTTACAGTTAATTGAAAAAATATAGTCATGTTAAAGAG
Found at i:4453966 original size:19 final size:19
Alignment explanation
Indices: 4453944--4453983 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
4453934 CCTAAAAGTA
4453944 ATTTTAATTT-ATTTATATT
1 ATTTTAATTTAATTTAT-TT
*
4453963 ATTTTTATTTAATTTATTT
1 ATTTTAATTTAATTTATTT
4453982 AT
1 AT
4453984 GTTTTGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTTTAATTTAATTTATTT
Found at i:4454033 original size:17 final size:17
Alignment explanation
Indices: 4454011--4454051 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
4454001 AAAAATAATA
*
4454011 TAAATTTTGATTTTTTT
1 TAAATTTTGATTTTATT
*
4454028 TAAATTATGATTTTATT
1 TAAATTTTGATTTTATT
*
4454045 TAGATTT
1 TAAATTT
4454052 AAAATTTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (17 bp):
TAAATTTTGATTTTATT
Found at i:4454535 original size:20 final size:21
Alignment explanation
Indices: 4454507--4454555 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
4454497 TTGTTATTTT
*
4454507 TTTACTTATTTATT-TCTATA
1 TTTATTTATTTATTCTCTATA
* *
4454527 TTTATTTATTTATTCTTTATT
1 TTTATTTATTTATTCTCTATA
4454548 TTTATTTA
1 TTTATTTA
4454556 GGTTTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTATTTATTTATTCTCTATA
Found at i:4454553 original size:17 final size:18
Alignment explanation
Indices: 4454512--4454568 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
4454502 ATTTTTTTAC
* *
4454512 TTATTTATTTCTATATTTAT
1 TTATTTAGTTCTTTA-TT-T
4454532 TTATTTA-TTCTTTATTT
1 TTATTTAGTTCTTTATTT
*
4454549 TTATTTAGGT-TTTATTT
1 TTATTTAGTTCTTTATTT
4454566 TTA
1 TTA
4454569 CCTATTGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 18 0.53
18 3 0.09
19 6 0.18
20 7 0.21
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.72
Consensus pattern (18 bp):
TTATTTAGTTCTTTATTT
Found at i:4465636 original size:2 final size:2
Alignment explanation
Indices: 4465631--4465664 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
4465621 TTGACGTGTG
* *
4465631 TA TA TA TA TA TA TA TA TG TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4465665 GACACATACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4468604 original size:2 final size:2
Alignment explanation
Indices: 4468597--4468629 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4468587 CATCTCTTTC
4468597 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4468630 AGAGTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4470186 original size:2 final size:2
Alignment explanation
Indices: 4470179--4470210 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4470169 ACATTGTTAC
4470179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4470211 TCCAATTCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4472904 original size:14 final size:15
Alignment explanation
Indices: 4472874--4472904 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4472864 AAAATTTATG
4472874 AATTTATTTTTTAAA
1 AATTTATTTTTTAAA
4472889 AATTTATTTTTTAAA
1 AATTTATTTTTTAAA
4472904 A
1 A
4472905 CCCTTGAAAT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
AATTTATTTTTTAAA
Found at i:4473037 original size:13 final size:14
Alignment explanation
Indices: 4473012--4473041 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4473002 GATTTATCTC
4473012 AAAATTAATTTTTA
1 AAAATTAATTTTTA
4473026 AAAATTAATTTTTA
1 AAAATTAATTTTTA
4473040 AA
1 AA
4473042 TTTATAAAAT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAAATTAATTTTTA
Found at i:4474875 original size:8 final size:8
Alignment explanation
Indices: 4474860--4474895 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
4474850 TTTTTTAAAC
4474860 TATAAATA
1 TATAAATA
*
4474868 TTTAAATA
1 TATAAATA
*
4474876 TATAATTA
1 TATAAATA
4474884 TATAAATA
1 TATAAATA
4474892 TATA
1 TATA
4474896 TAAATAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
TATAAATA
Done.