Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 10 of 93
Found at i:5158967 original size:21 final size:21
Alignment explanation
Indices: 5158942--5158994 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
5158932 ACTGGTCACT
5158942 ACGAACCCACACATTGTATCC
1 ACGAACCCACACATTGTATCC
5158963 ACGAACCCACACATTGTATCC
1 ACGAACCCACACATTGTATCC
5158984 ACGAACCCACA
1 ACGAACCCACA
5158995 GTCTGAGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.36, C:0.40, G:0.09, T:0.15
Consensus pattern (21 bp):
ACGAACCCACACATTGTATCC
Found at i:5171557 original size:18 final size:18
Alignment explanation
Indices: 5171531--5171638 Score: 110
Period size: 18 Copynumber: 6.0 Consensus size: 18
5171521 AGCCATTGAC
* *
5171531 CACGGAAAATGTCTTAAG
1 CACGAAAAATGTCTTACG
* *
5171549 CACGAAAAATATTTTACG
1 CACGAAAAATGTCTTACG
*
5171567 CAC-AGCAAATGTCTTACG
1 CACGA-AAAATGTCTTACG
* *
5171585 CACGACAAATGTCTTACA
1 CACGAAAAATGTCTTACG
* *
5171603 TATGAAAAATGTCTTACG
1 CACGAAAAATGTCTTACG
*
5171621 CAAGAAAAATGTCTTACG
1 CACGAAAAATGTCTTACG
5171639 TCTATGCCGA
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
17 1 0.01
18 72 0.97
19 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (18 bp):
CACGAAAAATGTCTTACG
Found at i:5173205 original size:30 final size:29
Alignment explanation
Indices: 5173134--5173206 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
5173124 TCAGAAAAAT
* * *
5173134 TCAAATAAACTCTTATACTTTTATTGTGT
1 TCAAATAAGCCCTTATACTTTTATTGTGG
* *
5173163 TC-AATCAAGCCCTTATACTTTTGTTTTGAG
1 TCAAAT-AAGCCCTTATACTTTTATTGTG-G
5173193 TCAAATAAGCCCTT
1 TCAAATAAGCCCTT
5173207 TTGACTAGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 3 0.08
29 20 0.56
30 10 0.28
31 3 0.08
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (29 bp):
TCAAATAAGCCCTTATACTTTTATTGTGG
Found at i:5173866 original size:25 final size:23
Alignment explanation
Indices: 5173827--5173882 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 23
5173817 GTTGATTATG
5173827 TGACATG-T-TGACATATTATAAT
1 TGACATGATATGACATATTA-AAT
*
5173849 TGACGATGATATGACATATTAATT
1 TGAC-ATGATATGACATATTAAAT
5173873 TGACATGATA
1 TGACATGATA
5173883 ACATGACAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 4 0.13
23 9 0.30
24 7 0.23
25 10 0.33
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (23 bp):
TGACATGATATGACATATTAAAT
Found at i:5174119 original size:6 final size:6
Alignment explanation
Indices: 5174108--5174171 Score: 51
Period size: 6 Copynumber: 10.5 Consensus size: 6
5174098 GCATTATGCT
* * *
5174108 AAAATA AAAATA AAAATTAA AAAATA ATAATAA AAAATA AGAA-A AAAACA
1 AAAATA AAAATA AAAA-T-A AAAATA AAAAT-A AAAATA AAAATA AAAATA
*
5174158 AATA-A AAAATA AAA
1 AAAATA AAAATA AAA
5174172 GCTGAAATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
5 8 0.17
6 27 0.57
7 7 0.15
8 5 0.11
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:5174146 original size:7 final size:7
Alignment explanation
Indices: 5174108--5174171 Score: 71
Period size: 7 Copynumber: 9.3 Consensus size: 7
5174098 GCATTATGCT
5174108 AAAAT-A
1 AAAATAA
5174114 AAAATAA
1 AAAATAA
*
5174121 AAATTAA
1 AAAATAA
5174128 AAAAT-A
1 AAAATAA
*
5174134 ATAATAA
1 AAAATAA
5174141 AAAATAA
1 AAAATAA
5174148 GAAAA-AA
1 -AAAATAA
5174155 ACAAATAA
1 A-AAATAA
5174163 AAAATAA
1 AAAATAA
5174170 AA
1 AA
5174172 GCTGAAATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
6 11 0.22
7 31 0.63
8 7 0.14
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.16
Consensus pattern (7 bp):
AAAATAA
Found at i:5175445 original size:24 final size:24
Alignment explanation
Indices: 5175389--5175451 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
5175379 TTTATCTAAC
5175389 AAATAAA-AAAATAAATTTGAAAT
1 AAATAAATAAAATAAATTTGAAAT
* * *
5175412 AAACATATAAAATAACTTT-AACAT
1 AAATAAATAAAATAAATTTGAA-AT
5175436 AAATAAAT-AAATAAAT
1 AAATAAATAAAATAAAT
5175452 GATTAAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
23 14 0.44
24 18 0.56
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.27
Consensus pattern (24 bp):
AAATAAATAAAATAAATTTGAAAT
Found at i:5176796 original size:50 final size:50
Alignment explanation
Indices: 5176738--5176837 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
5176728 GATCACCTTG
5176738 GTGATATTTAACACATAAAAATACAAAATAAATTATTATTTAGAAAGTTA
1 GTGATATTTAACACATAAAAATACAAAATAAATTATTATTTAGAAAGTTA
5176788 GTGATATTTAACACATAAAAATACAAAATAAATTATTATTTAGAAAGTTA
1 GTGATATTTAACACATAAAAATACAAAATAAATTATTATTTAGAAAGTTA
5176838 CCTTACCATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (50 bp):
GTGATATTTAACACATAAAAATACAAAATAAATTATTATTTAGAAAGTTA
Found at i:5179613 original size:111 final size:111
Alignment explanation
Indices: 5179394--5179697 Score: 412
Period size: 111 Copynumber: 2.7 Consensus size: 111
5179384 GTTTGCGCCG
* * * *
5179394 GCAGGAGAAAAGTTAGAGGGAGGAAGCTCGACCGTCGTTCCACCAGATCCGACGCAGGGAAGAGA
1 GCAGAAGAAAAGTGAGAGGGAGGAAGCTCGACCGTCGTGCCACCAGATCCGGCGCAGGGAAGAGA
* *
5179459 GGAGAGACACCCGATCGGCGCCAAAGGGGTTGGAAGCCGGCAAAGC
66 GGAGAGACACCCGATCGGCGCCAAAGGGGTTGAAAGCCAGCAAAGC
* * * *
5179505 GCAGAAGAATAGTGAGAGGGAGGAAGCTCGACTGTCGCGCCATCAGATCCGGCGCAGGGAAGAGA
1 GCAGAAGAAAAGTGAGAGGGAGGAAGCTCGACCGTCGTGCCACCAGATCCGGCGCAGGGAAGAGA
* * *
5179570 GGAGAGACACCCGATTGGCG-CTAAGGGGATTGAAAGTCAGCAAAGC
66 GGAGAGACACCCGATCGGCGCCAAAGGGG-TTGAAAGCCAGCAAAGC
* * * * * * *
5179616 ACAAAAGAAGAGTGAGAGGGAGGAAGCCCGACCATCGTGCCGCCAGATCCGGCACAGGGAAGAGA
1 GCAGAAGAAAAGTGAGAGGGAGGAAGCTCGACCGTCGTGCCACCAGATCCGGCGCAGGGAAGAGA
5179681 GGAGAGACACCCGATCG
66 GGAGAGACACCCGATCG
5179698 ACAGTAGAGA
Statistics
Matches: 168, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
110 7 0.04
111 161 0.96
ACGTcount: A:0.32, C:0.22, G:0.37, T:0.09
Consensus pattern (111 bp):
GCAGAAGAAAAGTGAGAGGGAGGAAGCTCGACCGTCGTGCCACCAGATCCGGCGCAGGGAAGAGA
GGAGAGACACCCGATCGGCGCCAAAGGGGTTGAAAGCCAGCAAAGC
Found at i:5180633 original size:19 final size:18
Alignment explanation
Indices: 5180597--5180648 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 18
5180587 AAAATTACTC
5180597 AATAAAAATAAT-AAATA
1 AATAAAAATAATAAAATA
*
5180614 AATAACAATAGATAAAATA
1 AATAAAAATA-ATAAAATA
* *
5180633 AATGATAATAATAAAA
1 AATAAAAATAATAAAA
5180649 ATTAAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 9 0.30
18 8 0.27
19 13 0.43
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (18 bp):
AATAAAAATAATAAAATA
Found at i:5180774 original size:22 final size:21
Alignment explanation
Indices: 5180737--5180782 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
5180727 TATATATAAC
* *
5180737 AAATAATAAAATAATAAAATA
1 AAATAAAAAAATAATAAAACA
5180758 AAATAAAAATAATAATAAAACA
1 AAATAAAAA-AATAATAAAACA
5180780 AAA
1 AAA
5180783 AATAGACAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (21 bp):
AAATAAAAAAATAATAAAACA
Found at i:5185366 original size:10 final size:10
Alignment explanation
Indices: 5185348--5185389 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
5185338 TATAATTAAT
5185348 TATATTAAAAA
1 TATA-TAAAAA
5185359 TATATAAAAA
1 TATATAAAAA
*
5185369 T-TAAAAAAA
1 TATATAAAAA
5185378 TATATAAAAA
1 TATATAAAAA
5185388 TA
1 TA
5185390 AAAATAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 8 0.29
10 16 0.57
11 4 0.14
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
TATATAAAAA
Found at i:5185368 original size:11 final size:11
Alignment explanation
Indices: 5185348--5185387 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
5185338 TATAATTAAT
*
5185348 TATATTAAAAA
1 TATATAAAAAA
5185359 TATAT-AAAAA
1 TATATAAAAAA
5185369 T-TA-AAAAAA
1 TATATAAAAAA
5185378 TATATAAAAA
1 TATATAAAAA
5185388 TAAAAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 8 0.31
10 8 0.31
11 10 0.38
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TATATAAAAAA
Found at i:5185380 original size:28 final size:28
Alignment explanation
Indices: 5185348--5185406 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 28
5185338 TATAATTAAT
5185348 TATATTAAAAATATATAAA-AATTAAAAAAA
1 TATA-TAAAAATA-A-AAATAATTAAAAAAA
*
5185378 TATATAAAAATAAAAATAATTAATAAAA
1 TATATAAAAATAAAAATAATTAAAAAAA
5185406 T
1 T
5185407 TATTTAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 3 0.11
28 12 0.44
29 8 0.30
30 4 0.15
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (28 bp):
TATATAAAAATAAAAATAATTAAAAAAA
Found at i:5185386 original size:18 final size:18
Alignment explanation
Indices: 5185354--5185408 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
5185344 TAATTATATT
5185354 AAAAATATATAAAAATTAA
1 AAAAATATAT-AAAATTAA
*
5185373 AAAAATATATAAAAATAA
1 AAAAATATATAAAATTAA
5185391 AAATAAT-TAATAAAATTA
1 AAA-AATAT-ATAAAATTA
5185409 TTTAATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 11 0.34
19 21 0.66
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAAATATATAAAATTAA
Found at i:5185405 original size:19 final size:19
Alignment explanation
Indices: 5185354--5185393 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
5185344 TAATTATATT
5185354 AAAAATATATAAAAATTAA
1 AAAAATATATAAAAATTAA
5185373 AAAAATATATAAAAA-TAA
1 AAAAATATATAAAAATTAA
5185391 AAA
1 AAA
5185394 TAATTAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAATATATAAAAATTAA
Found at i:5185567 original size:12 final size:12
Alignment explanation
Indices: 5185550--5185575 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5185540 TTTTCAACAG
5185550 TTATTTTTTTAT
1 TTATTTTTTTAT
5185562 TTATTTTTTTAT
1 TTATTTTTTTAT
5185574 TT
1 TT
5185576 TCAATCAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTATTTTTTTAT
Found at i:5185657 original size:21 final size:21
Alignment explanation
Indices: 5185618--5185657 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5185608 ATTTTTTCTT
*
5185618 ATATATAAAATTAATTTTTTA
1 ATATATAAAATTAACTTTTTA
* *
5185639 ATATATAATATTTACTTTT
1 ATATATAAAATTAACTTTT
5185658 GAATTTTNAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATATAAAATTAACTTTTTA
Found at i:5185683 original size:181 final size:183
Alignment explanation
Indices: 5185482--5185848 Score: 695
Period size: 181 Copynumber: 2.0 Consensus size: 183
5185472 TAAAAAGCTA
5185482 TTTATTTTCAACTATTTCTTTTATTTTCAATCAACTAATAGTCATATGTATTTAATTATTTTCAA
1 TTTATTTTCAACTATTTCTTTTATTTTCAATCAACTAATAGTCATATGTATTTAATTATTTTCAA
5185547 CAGTTA-TTTTTTTATTTATTTTTTTATTTTCAATCAATATATTTAATAATTTTTAACAGTTATT
66 CAGTTATTTTTTTTATTTATTTTTTTATTTTCAATCAATATATTTAATAATTTTTAACAGTTATT
5185611 TTTTCT-TATATATAAAATTAA-TTTTTTAATATATAATATTTACTTTTGAAT
131 TTTTCTATATATATAAAATTAATTTTTTTAATATATAATATTTACTTTTGAAT
5185662 TTTNATTTTCAACTATTTCTTTTATTTTCAATCAACTAATAGTCATATGTATTTAATTATTTTCA
1 TTT-ATTTTCAACTATTTCTTTTATTTTCAATCAACTAATAGTCATATGTATTTAATTATTTTCA
5185727 ACAGTTATTTTTTTTATTTATTTTTTTATTTTCAATCAATATATTTAATAATTTTTAACAGTTAT
65 ACAGTTATTTTTTTTATTTATTTTTTTATTTTCAATCAATATATTTAATAATTTTTAACAGTTAT
*
5185792 TTTTTTTATATATATAAAATTAATTTTTTTAATATATAATATTTACTTTTGAAT
130 TTTTTCTATATATATAAAATTAATTTTTTTAATATATAATATTTACTTTTGAAT
5185846 TTT
1 TTT
5185849 TCTTTTTCTT
Statistics
Matches: 182, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
180 3 0.02
181 68 0.37
182 63 0.35
183 15 0.08
184 33 0.18
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.58
Consensus pattern (183 bp):
TTTATTTTCAACTATTTCTTTTATTTTCAATCAACTAATAGTCATATGTATTTAATTATTTTCAA
CAGTTATTTTTTTTATTTATTTTTTTATTTTCAATCAATATATTTAATAATTTTTAACAGTTATT
TTTTCTATATATATAAAATTAATTTTTTTAATATATAATATTTACTTTTGAAT
Found at i:5185841 original size:22 final size:23
Alignment explanation
Indices: 5185793--5185841 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
5185783 AACAGTTATT
*
5185793 TTTTTTATATATATAAAATTAAT
1 TTTTTTATATATATAAAATTAAC
* *
5185816 TTTTTTA-ATATATAATATTTAC
1 TTTTTTATATATATAAAATTAAC
5185838 TTTT
1 TTTT
5185842 GAATTTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTTTATATATATAAAATTAAC
Found at i:5188933 original size:4 final size:4
Alignment explanation
Indices: 5188919--5188956 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
5188909 CTACCAAAAC
* *
5188919 TATA CATA TATA TATA TATA TATA TATA TATA TGTA TA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TA
5188957 GCATAGAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (4 bp):
TATA
Found at i:5188933 original size:6 final size:6
Alignment explanation
Indices: 5188919--5188956 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
5188909 CTACCAAAAC
* *
5188919 TATACA TATATA TATATA TATATA TATATA TATGTA TA
1 TATATA TATATA TATATA TATATA TATATA TATATA TA
5188957 GCATAGAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (6 bp):
TATATA
Found at i:5193447 original size:2 final size:2
Alignment explanation
Indices: 5193440--5193464 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5193430 ATGGCTCATC
5193440 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
5193465 CTTCTCATGA
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:5195683 original size:73 final size:74
Alignment explanation
Indices: 5195579--5195726 Score: 280
Period size: 73 Copynumber: 2.0 Consensus size: 74
5195569 TACTTATGGC
5195579 ACAAGAACCATTTGCCAGTATCCTTTCTTTCAACAAAAGAAAACATGGTTGTGGAC-TATCAATA
1 ACAAGAACCATTTGCCAGTATCCTTTCTTTCAACAAAAGAAAACATGGTTGTGGACTTATCAATA
5195643 TTTAAAATA
66 TTTAAAATA
5195652 ACAAGAACCATTTGCCAGTATCCTTTCTTTCAACAAAAGAAAACATGGTTGTGGACTTTATCAAT
1 ACAAGAACCATTTGCCAGTATCCTTTCTTTCAACAAAAGAAAACATGGTTGTGGAC-TTATCAAT
5195717 ATTTAAAATA
65 ATTTAAAATA
5195727 TATAACTAAA
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
73 56 0.77
75 17 0.23
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (74 bp):
ACAAGAACCATTTGCCAGTATCCTTTCTTTCAACAAAAGAAAACATGGTTGTGGACTTATCAATA
TTTAAAATA
Found at i:5201743 original size:17 final size:17
Alignment explanation
Indices: 5201723--5201757 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5201713 TTAAAAAAAA
*
5201723 ATATAAAAAATAATAAT
1 ATATAAAAAATAACAAT
*
5201740 ATATAAATAATAACAAT
1 ATATAAAAAATAACAAT
5201757 A
1 A
5201758 ACAATAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
ATATAAAAAATAACAAT
Found at i:5201827 original size:3 final size:3
Alignment explanation
Indices: 5201813--5201844 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
5201803 GAGGCTTGCA
5201813 AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5201845 TCATGATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5201894 original size:21 final size:21
Alignment explanation
Indices: 5201867--5201910 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5201857 TATATATATT
*
5201867 TAAAAAAA-AAGAAAAATAAA
1 TAAAAAAATAAAAAAAATAAA
*
5201887 TAAAAAAATATAAAAAATAAA
1 TAAAAAAATAAAAAAAATAAA
5201908 TAA
1 TAA
5201911 TATAATTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (21 bp):
TAAAAAAATAAAAAAAATAAA
Found at i:5201904 original size:17 final size:18
Alignment explanation
Indices: 5201870--5201907 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5201860 ATATATTTAA
5201870 AAAAAAAGAAAAATAAAT
1 AAAAAAAGAAAAATAAAT
* *
5201888 AAAAAAATATAAA-AAAT
1 AAAAAAAGAAAAATAAAT
5201905 AAA
1 AAA
5201908 TAATATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (18 bp):
AAAAAAAGAAAAATAAAT
Found at i:5203656 original size:15 final size:15
Alignment explanation
Indices: 5203636--5203677 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
5203626 ATAATTTTAT
*
5203636 TAATTATTTTTAATA
1 TAATTATTTATAATA
* *
5203651 TAATTAATTATATTA
1 TAATTATTTATAATA
5203666 TAATTA-TTATAA
1 TAATTATTTATAA
5203678 AATTATAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTATTTATAATA
Found at i:5204995 original size:19 final size:20
Alignment explanation
Indices: 5204962--5205001 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
5204952 ACATATGAGT
5204962 AAATAAAATAGAAATAAAAA
1 AAATAAAATAGAAATAAAAA
*
5204982 AAAT-AAATATAAATAAAAA
1 AAATAAAATAGAAATAAAAA
5205001 A
1 A
5205002 TATATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (20 bp):
AAATAAAATAGAAATAAAAA
Found at i:5205010 original size:15 final size:15
Alignment explanation
Indices: 5204961--5205010 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
5204951 AACATATGAG
5204961 TAAATAAAATAGAAATA
1 TAAATAAAA-A-AAATA
*
5204978 -AAA-AAAATAAATA
1 TAAATAAAAAAAATA
*
5204991 TAAATAAAAAATATA
1 TAAATAAAAAAAATA
5205006 TAAAT
1 TAAAT
5205011 TNATAATCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 5 0.18
14 3 0.11
15 17 0.61
16 3 0.11
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (15 bp):
TAAATAAAAAAAATA
Found at i:5205498 original size:514 final size:515
Alignment explanation
Indices: 5204494--5205527 Score: 1966
Period size: 514 Copynumber: 2.0 Consensus size: 515
5204484 TGTTAAATTT
5204494 AATTAATAATCAAAAGATTGATAATAGAAATATAAAACTATAATATGTAAAATACAAATAATTAA
1 AATTAATAATCAAAAGATTGATAATAGAAATATAAAACTATAATATGTAAAATACAAATAATTAA
5204559 AAATGATATATAAGATTAATAATTTTTTATATAATCAAAATTATTTAAAGACAATATGTTCAAGA
66 AAATGATATATAAGATTAATAATTTTTTATATAATCAAAATTATTTAAAGACAATATGTTCAAGA
5204624 TAATTTCATTTCAACTAAATATAAAACGTAAAAGATATAAAAAAATATACTCAAATTAATTTTCT
131 TAATTTCATTTCAACTAAATATAAAACGTAAAAGATATAAAAAAATATACTCAAATTAATTTTCT
5204689 CTTACATAATTAGAATTAATAAAAAAATGATACATTAATGAAAGTTTAAATAACAATATAACATT
196 CTTACATAATTAGAATTAATAAAAAAATGATACATTAATGAAAGTTTAAATAACAATATAACATT
5204754 ACAACTTAAATTTGAGAATTATATAATAATTTATTAATTTTTAAAAATTTAAAATGATTGAAAAT
261 ACAACTTAAATTTGAGAATTATATAATAATTTATTAATTTTTAAAAATTTAAAATGATTGAAAAT
5204819 AATCTACGTAACATAAAAAAGAAAAACATAGCAAATAAAATATAGAAACCACATAAGACATAACA
326 AATCTACGTAACATAAAAAAGAAAAACATAGCAAATAAAATATAGAAACCACATAAGACATAACA
* * *
5204884 AAAAAGAAAGAAAAAGGATATGATTAATGATTTGTAGAAATTTGAAAAAGAAATTATAAAAATTT
391 AAAAAGAAAGAAAAAGAATATGATTAATGATTTATAAAAATTTGAAAAAGAAATTATAAAAATTT
5204949 AGAACATATGAGTAAATAAAATAGAAATAAAAAAAATAAATATAAATAAAAAAT-ATATA
456 AGAACATATGAGTAAATAAAATAGAAATAAAAAAAATAAATATAAATAAAAAATAATATA
*
5205008 AATTNATAATCAAAAGATTGATAATAGAAATATAAAACTATAATATGTAAAATACAAATAATTAA
1 AATTAATAATCAAAAGATTGATAATAGAAATATAAAACTATAATATGTAAAATACAAATAATTAA
5205073 AAATGATATATAAGATTAATAATTTTTTATATAATCAAAATTATTTAAAGACAATATGTTCAAGA
66 AAATGATATATAAGATTAATAATTTTTTATATAATCAAAATTATTTAAAGACAATATGTTCAAGA
5205138 TAATTTCATTTCAACTAAATATAAAACGTAAAAGATATAAAAAAATATACTCAAATTAATTTTCT
131 TAATTTCATTTCAACTAAATATAAAACGTAAAAGATATAAAAAAATATACTCAAATTAATTTTCT
5205203 CTTACATAATTAGAATTAATAAAAAAATGATACATTAATGAAAGTTTAAATAACAATATAACATT
196 CTTACATAATTAGAATTAATAAAAAAATGATACATTAATGAAAGTTTAAATAACAATATAACATT
5205268 ACAACTTAAATTTGAGAATTATATAATAATTTATTAATTTTTAAAAATTTAAAATGATTGAAAAT
261 ACAACTTAAATTTGAGAATTATATAATAATTTATTAATTTTTAAAAATTTAAAATGATTGAAAAT
5205333 AATCTACGTAACATAAAAAAGAAAAACATAGCAAATAAAATATAGAAACCACATAAGACATAACA
326 AATCTACGTAACATAAAAAAGAAAAACATAGCAAATAAAATATAGAAACCACATAAGACATAACA
* *
5205398 AAAAAGAAAGAAGAAGAATAT-AGTTGATGATTTATAAAAATTTG-AAAAGAAAATTTATAAAAA
391 AAAAAGAAAGAAAAAGAATATGA-TTAATGATTTATAAAAATTTGAAAAAG-AAA-TTATAAAAA
5205461 TTTAGAACATATGAGTAAATAAAATAGAAATAAAAAAAATAAATATAAATAAAAAATAATATA
453 TTTAGAACATATGAGTAAATAAAATAGAAATAAAAAAAATAAATATAAATAAAAAATAATATA
5205524 AATT
1 AATT
5205528 GATAGAAAAA
Statistics
Matches: 510, Mismatches: 6, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
513 6 0.01
514 429 0.84
515 66 0.13
516 9 0.02
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.30
Consensus pattern (515 bp):
AATTAATAATCAAAAGATTGATAATAGAAATATAAAACTATAATATGTAAAATACAAATAATTAA
AAATGATATATAAGATTAATAATTTTTTATATAATCAAAATTATTTAAAGACAATATGTTCAAGA
TAATTTCATTTCAACTAAATATAAAACGTAAAAGATATAAAAAAATATACTCAAATTAATTTTCT
CTTACATAATTAGAATTAATAAAAAAATGATACATTAATGAAAGTTTAAATAACAATATAACATT
ACAACTTAAATTTGAGAATTATATAATAATTTATTAATTTTTAAAAATTTAAAATGATTGAAAAT
AATCTACGTAACATAAAAAAGAAAAACATAGCAAATAAAATATAGAAACCACATAAGACATAACA
AAAAAGAAAGAAAAAGAATATGATTAATGATTTATAAAAATTTGAAAAAGAAATTATAAAAATTT
AGAACATATGAGTAAATAAAATAGAAATAAAAAAAATAAATATAAATAAAAAATAATATA
Found at i:5205499 original size:15 final size:15
Alignment explanation
Indices: 5205476--5205525 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
5205466 AACATATGAG
*
5205476 TAAATAAAATAGAA-A
1 TAAAAAAAATA-AATA
5205491 TAAAAAAAATAAATA
1 TAAAAAAAATAAATA
5205506 TAAATAAAAA-ATAATA
1 TAAA-AAAAATA-AATA
5205522 TAAA
1 TAAA
5205526 TTGATAGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 2 0.06
15 16 0.52
16 13 0.42
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (15 bp):
TAAAAAAAATAAATA
Found at i:5205502 original size:20 final size:20
Alignment explanation
Indices: 5205477--5205526 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
5205467 ACATATGAGT
5205477 AAATAAAATAGAAATAAAAA
1 AAATAAAATAGAAATAAAAA
*
5205497 AAAT-AAATATAAATAAAAA
1 AAATAAAATAGAAATAAAAA
5205516 ATAATATAAAT
1 A-AATA-AAAT
5205527 TGATAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 15 0.58
20 7 0.27
22 4 0.15
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (20 bp):
AAATAAAATAGAAATAAAAA
Found at i:5205521 original size:16 final size:17
Alignment explanation
Indices: 5205494--5205526 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
5205484 ATAGAAATAA
5205494 AAAAAATAAATATAAAT
1 AAAAAATAAATATAAAT
5205511 AAAAAAT-AATATAAAT
1 AAAAAATAAATATAAAT
5205527 TGATAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAAATAAATATAAAT
Found at i:5208061 original size:103 final size:103
Alignment explanation
Indices: 5207882--5208088 Score: 405
Period size: 103 Copynumber: 2.0 Consensus size: 103
5207872 ACAGTCTTTC
5207882 TTCCCAAACCGGGTTGCAATGCCATCAGAGTCTCTCGCCAATTAGGCAAGAGACTTCACATGGTA
1 TTCCCAAACCGGGTTGCAATGCCATCAGAGTCTCTCGCCAATTAGGCAAGAGACTTCACATGGTA
5207947 TCCCCGTTATGGAAAATAAAGTTACTTTTCAATATATA
66 TCCCCGTTATGGAAAATAAAGTTACTTTTCAATATATA
5207985 TTCCCAAACCGGGTTGCAATGCCATCAGAGTCTCTCGCCAATTAGGCAAGAGACTTCACATGGTA
1 TTCCCAAACCGGGTTGCAATGCCATCAGAGTCTCTCGCCAATTAGGCAAGAGACTTCACATGGTA
*
5208050 TCCTCGTTATGGAAAATAAAGTTACTTTTCAATATATA
66 TCCCCGTTATGGAAAATAAAGTTACTTTTCAATATATA
5208088 T
1 T
5208089 ATATATATAT
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (103 bp):
TTCCCAAACCGGGTTGCAATGCCATCAGAGTCTCTCGCCAATTAGGCAAGAGACTTCACATGGTA
TCCCCGTTATGGAAAATAAAGTTACTTTTCAATATATA
Found at i:5208088 original size:2 final size:2
Alignment explanation
Indices: 5208081--5208117 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5208071 TTACTTTTCA
5208081 AT AT 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 AT AT A
5208118 ATAAATGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5208678 original size:56 final size:56
Alignment explanation
Indices: 5208612--5208770 Score: 169
Period size: 56 Copynumber: 2.9 Consensus size: 56
5208602 TCAGTTACTT
*
5208612 ACGGAA-TTTATTTGATAA-TTCCAATGAAAATCTACAACTAATGACTAAATCATCA
1 ACGGAATTTTA-TTGATAATTTCCAATGAAAATCTACAAGTAATGACTAAATCATCA
* * * * * * **
5208667 ATGGAATTTTATTAATAATTTCTAATGAAAATCTAGAGGTAATGAATAAATCATTG
1 ACGGAATTTTATTGATAATTTCCAATGAAAATCTACAAGTAATGACTAAATCATCA
* * * **
5208723 ACAGAATTTCATTGATAATTTTCAATGAAAATCTGTAAGTAATGACTA
1 ACGGAATTTTATTGATAATTTCCAATGAAAATCTACAAGTAATGACTA
5208771 CAGTATGTAC
Statistics
Matches: 83, Mismatches: 19, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
55 11 0.13
56 72 0.87
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.35
Consensus pattern (56 bp):
ACGGAATTTTATTGATAATTTCCAATGAAAATCTACAAGTAATGACTAAATCATCA
Found at i:5218188 original size:3 final size:3
Alignment explanation
Indices: 5218176--5218260 Score: 54
Period size: 3 Copynumber: 28.3 Consensus size: 3
5218166 GTTCAATTTA
* *
5218176 TAT TATT TAT TAT TAT TAT TAT T-T TATT TAT T-T TTT TAT TTT TA-
1 TAT TA-T TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
* *
5218220 TAT ATAT T-T GTAT CAT GAAT TAT TAT TAT TAT TAT T-T TAT T
1 TAT -TAT TAT -TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT T
5218261 GTTTGCAAGC
Statistics
Matches: 66, Mismatches: 6, Indels: 20
0.72 0.07 0.22
Matches are distributed among these distances:
2 9 0.14
3 45 0.68
4 12 0.18
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5218227 original size:20 final size:20
Alignment explanation
Indices: 5218191--5218228 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5218181 TTTATTATTA
*
5218191 TTATTATTTTATTTATTTTT
1 TTATTATTTTATATATTTTT
5218211 TTATT-TTTATATATATTT
1 TTATTATTT-TATATATTT
5218229 GTATCATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (20 bp):
TTATTATTTTATATATTTTT
Found at i:5218355 original size:5 final size:5
Alignment explanation
Indices: 5218345--5218377 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
5218335 GTATGTATTT
*
5218345 TTTTA TTTTA TTTTA TTTTA TTTT- TTTAA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
5218378 TTATTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:5218378 original size:9 final size:8
Alignment explanation
Indices: 5218340--5218382 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
5218330 TTTATGTATG
5218340 TATTTTTT
1 TATTTTTT
*
5218348 TATTTTAT
1 TATTTTTT
*
5218356 T-TTATTT
1 TATTTTTT
5218363 TATTTTTT
1 TATTTTTT
*
5218371 TAATTTTT
1 TATTTTTT
5218379 TATT
1 TATT
5218383 ATATATTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
7 5 0.18
8 23 0.82
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (8 bp):
TATTTTTT
Found at i:5219365 original size:29 final size:30
Alignment explanation
Indices: 5219319--5219375 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
5219309 ATACCTCTCT
*
5219319 TTTTTTTTTCATTATATTTT-TCTTTATTTA
1 TTTTTTTATCATTATATTTTAT-TTTATTTA
*
5219349 TTTTTTTAT-ATTTTATTTTATTTTATT
1 TTTTTTTATCATTATATTTTATTTTATT
5219376 ATAATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.79
Consensus pattern (30 bp):
TTTTTTTATCATTATATTTTATTTTATTTA
Found at i:5219370 original size:20 final size:19
Alignment explanation
Indices: 5219341--5219383 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
5219331 TATATTTTTC
* *
5219341 TTTATTTATTTTTTTATAT
1 TTTATTTATTTTATTATAA
5219360 TTTATTTTATTTTATTATAA
1 TTTA-TTTATTTTATTATAA
5219380 TTTA
1 TTTA
5219384 AATTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTATTTATTTTATTATAA
Found at i:5219383 original size:10 final size:10
Alignment explanation
Indices: 5219341--5219383 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
5219331 TATATTTTTC
5219341 TTTATT-TAT
1 TTTATTATAT
*
5219350 TTTTTTATAT
1 TTTATTATAT
*
5219360 TTTATTTTAT
1 TTTATTATAT
*
5219370 TTTATTATAA
1 TTTATTATAT
5219380 TTTA
1 TTTA
5219384 AATTTAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
9 5 0.18
10 23 0.82
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTATTATAT
Found at i:5222328 original size:19 final size:17
Alignment explanation
Indices: 5222290--5222338 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
5222280 TTCGTATCTA
* *
5222290 TTAAAATTTTAAAATTTT
1 TTAAAATTTT-TATTTTT
5222308 TTAATATATTTTTATTTTT
1 TTAA-A-ATTTTTATTTTT
5222327 TTAAAATTTTTA
1 TTAAAATTTTTA
5222339 AAATTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 7 0.26
18 5 0.19
19 10 0.37
20 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTAAAATTTTTATTTTT
Found at i:5222336 original size:9 final size:9
Alignment explanation
Indices: 5222290--5222344 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
5222280 TTCGTATCTA
5222290 TTAAAA-TT
1 TTAAAATTT
5222298 TTAAAATTTT
1 TTAAAA-TTT
5222308 TTAATATATTT
1 TTAA-A-ATTT
**
5222319 TT-ATTTTT
1 TTAAAATTT
5222327 TTAAAATTT
1 TTAAAATTT
5222336 TTAAAATTT
1 TTAAAATTT
5222345 ATTTGTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
8 11 0.29
9 13 0.34
10 7 0.18
11 6 0.16
12 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TTAAAATTT
Found at i:5233519 original size:14 final size:14
Alignment explanation
Indices: 5233497--5233536 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
5233487 TAAATTTTGT
5233497 CAGACAATTTTTTAA
1 CAGA-AATTTTTTAA
*
5233512 CAGAAATTTTTCAA
1 CAGAAATTTTTTAA
5233526 C-GAAATTTTTT
1 CAGAAATTTTTT
5233537 TGTTGAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 9 0.39
14 10 0.43
15 4 0.17
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (14 bp):
CAGAAATTTTTTAA
Found at i:5239163 original size:12 final size:13
Alignment explanation
Indices: 5239135--5239173 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
5239125 ACTGTTTAAT
5239135 ATTTTCAACGAAA
1 ATTTTCAACGAAA
5239148 ATTTTCAACGAAA
1 ATTTTCAACGAAA
* *
5239161 TTTTTCATCGAAA
1 ATTTTCAACGAAA
5239174 CCGTAAACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (13 bp):
ATTTTCAACGAAA
Found at i:5240693 original size:14 final size:14
Alignment explanation
Indices: 5240658--5240692 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
5240648 AAATCCCGTT
5240658 GAAAA-TTTCCAAC
1 GAAAATTTTCCAAC
5240671 GAAAATTTTCCAAC
1 GAAAATTTTCCAAC
5240685 G-AAATTTT
1 GAAAATTTT
5240693 TTCCGTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (14 bp):
GAAAATTTTCCAAC
Found at i:5241300 original size:2 final size:2
Alignment explanation
Indices: 5241288--5241320 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5241278 TTAATATGGA
*
5241288 AT AT GT 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
5241321 AAGAAAGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5258580 original size:23 final size:23
Alignment explanation
Indices: 5258554--5258599 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5258544 TCAATGTAAA
5258554 GCTTAAATACACAGAAAAACTAC
1 GCTTAAATACACAGAAAAACTAC
* *
5258577 GCTTAGATACACAGTAAAACTAC
1 GCTTAAATACACAGAAAAACTAC
5258600 CCTCAATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.22, G:0.11, T:0.20
Consensus pattern (23 bp):
GCTTAAATACACAGAAAAACTAC
Found at i:5265675 original size:15 final size:16
Alignment explanation
Indices: 5265647--5265676 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5265637 TTTCAAGAGA
5265647 TTCTTTTAGTTATTTT
1 TTCTTTTAGTTATTTT
5265663 TTCTTTT-GTTATTT
1 TTCTTTTAGTTATTT
5265677 GCATGCTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.10, C:0.07, G:0.07, T:0.77
Consensus pattern (16 bp):
TTCTTTTAGTTATTTT
Found at i:5282345 original size:16 final size:15
Alignment explanation
Indices: 5282324--5282371 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
5282314 TAATGTAGAG
5282324 AAATAAAATAAATAA
1 AAATAAAATAAATAA
* *
5282339 TAAATAAAATTAATTGA
1 -AAATAAAA-TAAATAA
*
5282356 AAAGAAAATAAATAA
1 AAATAAAATAAATAA
5282371 A
1 A
5282372 GAAAAAGTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 6 0.23
16 15 0.58
17 5 0.19
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (15 bp):
AAATAAAATAAATAA
Found at i:5282507 original size:15 final size:15
Alignment explanation
Indices: 5282487--5282517 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5282477 TGCCAATTCA
5282487 GAGGGGGGGGGGGGG
1 GAGGGGGGGGGGGGG
5282502 GAGGGGGGGGGGGGG
1 GAGGGGGGGGGGGGG
5282517 G
1 G
5282518 CGTACCCCAT
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:0.06, C:0.00, G:0.94, T:0.00
Consensus pattern (15 bp):
GAGGGGGGGGGGGGG
Found at i:5282509 original size:13 final size:13
Alignment explanation
Indices: 5282491--5282515 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5282481 AATTCAGAGG
5282491 GGGGGGGGGGGGA
1 GGGGGGGGGGGGA
5282504 GGGGGGGGGGGG
1 GGGGGGGGGGGG
5282516 GGCGTACCCC
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:0.04, C:0.00, G:0.96, T:0.00
Consensus pattern (13 bp):
GGGGGGGGGGGGA
Found at i:5282509 original size:14 final size:14
Alignment explanation
Indices: 5282490--5282516 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5282480 CAATTCAGAG
5282490 GGGGGGGGGGGGGA
1 GGGGGGGGGGGGGA
5282504 GGGGGGGGGGGGG
1 GGGGGGGGGGGGG
5282517 GCGTACCCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.04, C:0.00, G:0.96, T:0.00
Consensus pattern (14 bp):
GGGGGGGGGGGGGA
Found at i:5282673 original size:19 final size:18
Alignment explanation
Indices: 5282648--5282690 Score: 68
Period size: 20 Copynumber: 2.3 Consensus size: 18
5282638 TTTTTATAAA
5282648 TTTTTTTTTGAAAATTTTT
1 TTTTTTTTTG-AAATTTTT
5282667 CTTTTTTTTTGAAATTTTT
1 -TTTTTTTTTGAAATTTTT
5282686 TTTTT
1 TTTTT
5282691 GAAATATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 8 0.35
20 10 0.43
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (18 bp):
TTTTTTTTTGAAATTTTT
Found at i:5282675 original size:33 final size:34
Alignment explanation
Indices: 5282633--5282739 Score: 116
Period size: 34 Copynumber: 3.2 Consensus size: 34
5282623 TCTTTTTTAA
*
5282633 ATTTGTTTTTAT-AAATTTTTTTTTGAAA-ATTT
1 ATTTTTTTTTATGAAATTTTTTTTTGAAATATTT
*
5282665 -TTCTTTTTTTTTGAAATTTTTTTTTTGAAATATTT
1 ATT-TTTTTTTATGAAA-TTTTTTTTTGAAATATTT
** *
5282700 ATTTTTTTACATGTAATTTTTTTTTGAAATA--T
1 ATTTTTTTTTATGAAATTTTTTTTTGAAATATTT
5282732 ATTTTTTT
1 ATTTTTTT
5282740 GATATTTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
31 2 0.03
32 16 0.25
33 3 0.05
34 28 0.44
35 13 0.20
36 2 0.03
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.68
Consensus pattern (34 bp):
ATTTTTTTTTATGAAATTTTTTTTTGAAATATTT
Found at i:5282684 original size:13 final size:13
Alignment explanation
Indices: 5282668--5282759 Score: 60
Period size: 13 Copynumber: 6.3 Consensus size: 13
5282658 AAAATTTTTC
5282668 TTTTTTTTTGAAA
1 TTTTTTTTTGAAA
5282681 TTTTTTTTTTGAAATA
1 -TTTTTTTTTG-AA-A
*
5282697 TTTATTTTTTTACATGTAA
1 --T-TTTTTTT---TGAAA
5282716 TTTTTTTTTGAAA
1 TTTTTTTTTGAAA
*
5282729 TATATTTTTTTGATA
1 T-T-TTTTTTTGAAA
5282744 TTTTTTTTTG-AA
1 TTTTTTTTTGAAA
5282756 TTTT
1 TTTT
5282760 AAAAAAAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
12 5 0.08
13 13 0.20
14 12 0.18
15 13 0.20
16 8 0.12
17 3 0.05
18 7 0.11
19 1 0.02
20 1 0.02
21 2 0.03
ACGTcount: A:0.23, C:0.01, G:0.07, T:0.70
Consensus pattern (13 bp):
TTTTTTTTTGAAA
Found at i:5282736 original size:15 final size:15
Alignment explanation
Indices: 5282668--5282755 Score: 92
Period size: 14 Copynumber: 5.8 Consensus size: 15
5282658 AAAATTTTTC
5282668 TTTTTTTTTGAAAT-
1 TTTTTTTTTGAAATA
5282682 TTTTTTTTTGAAATA
1 TTTTTTTTTGAAATA
* *
5282697 TTTATTTTTTTACATGTAA
1 TTT-TTTTTTGA-A-AT-A
5282716 TTTTTTTTTGAAATA
1 TTTTTTTTTGAAATA
*
5282731 TATTTTTTTG--ATA
1 TTTTTTTTTGAAATA
5282744 TTTTTTTTTGAA
1 TTTTTTTTTGAA
5282756 TTTTAAAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
13 12 0.20
14 14 0.23
15 13 0.21
16 8 0.13
17 2 0.03
18 8 0.13
19 4 0.07
ACGTcount: A:0.24, C:0.01, G:0.07, T:0.68
Consensus pattern (15 bp):
TTTTTTTTTGAAATA
Found at i:5284246 original size:21 final size:21
Alignment explanation
Indices: 5284199--5284251 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
5284189 TTGATTTTGA
* *
5284199 ATGAAGGCATCAGTCTTTGTT
1 ATGAATGCATCAGTCTTTGTC
5284220 ATGAATGCATCAGTCTTTGTC
1 ATGAATGCATCAGTCTTTGTC
5284241 ATGAATTGCAT
1 ATGAA-TGCAT
5284252 GATCATATCC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 24 0.83
22 5 0.17
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (21 bp):
ATGAATGCATCAGTCTTTGTC
Found at i:5285029 original size:18 final size:19
Alignment explanation
Indices: 5284984--5285030 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
5284974 AGCTAAAGTA
*
5284984 AAAAAAAAAATGATATAGG
1 AAAAAATAAATGATATAGG
* *
5285003 AATAAATAAATGAT-TAGT
1 AAAAAATAAATGATATAGG
5285021 AAAAAATAAA
1 AAAAAATAAA
5285031 AAAAAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (19 bp):
AAAAAATAAATGATATAGG
Found at i:5285673 original size:25 final size:25
Alignment explanation
Indices: 5285626--5285673 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
5285616 TTATATAATC
*
5285626 ATAAAAAAATTATATACATAAATTT
1 ATAAAAAAATTATATACACAAATTT
*
5285651 ATAAAAAACA-TATATACGCAAAT
1 ATAAAAAA-ATTATATACACAAAT
5285674 AATAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 19 0.95
26 1 0.05
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.29
Consensus pattern (25 bp):
ATAAAAAAATTATATACACAAATTT
Found at i:5287731 original size:11 final size:11
Alignment explanation
Indices: 5287709--5287759 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
5287699 ACTTAGAGCC
*
5287709 TTTTTCTTCTT
1 TTTTTTTTCTT
*
5287720 TTTCTTTTCTT
1 TTTTTTTTCTT
5287731 TTTTTTTTCTCT
1 TTTTTTTTCT-T
5287743 TTTTTTTTCTT
1 TTTTTTTTCTT
5287754 TCTTTT
1 T-TTTT
5287760 GCTGCTCACC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
11 20 0.57
12 15 0.43
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:5287739 original size:16 final size:15
Alignment explanation
Indices: 5287708--5287759 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
5287698 AACTTAGAGC
* *
5287708 CTTTTTCTTCTTTTT
1 CTTTTTTTTTTTTTT
5287723 CTTTTCTTTTTTTTTT
1 CTTTT-TTTTTTTTTT
*
5287739 CTCTTTTTTTTTCTTT
1 CT-TTTTTTTTTTTTT
5287755 CTTTT
1 CTTTT
5287760 GCTGCTCACC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 8 0.25
16 21 0.66
17 3 0.09
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
CTTTTTTTTTTTTTT
Found at i:5287745 original size:12 final size:12
Alignment explanation
Indices: 5287709--5287752 Score: 63
Period size: 12 Copynumber: 3.6 Consensus size: 12
5287699 ACTTAGAGCC
5287709 TTTTTCTTCTTTT
1 TTTTTC-TCTTTT
5287722 TCTTTTCT-TTTT
1 T-TTTTCTCTTTT
5287734 TTTTTCTCTTTT
1 TTTTTCTCTTTT
5287746 TTTTTCT
1 TTTTTCT
5287753 TTCTTTTGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.21
12 16 0.55
13 2 0.07
14 5 0.17
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTCTCTTTT
Found at i:5287747 original size:9 final size:8
Alignment explanation
Indices: 5287709--5287759 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
5287699 ACTTAGAGCC
5287709 TTTTTCTT
1 TTTTTCTT
5287717 CTTTTTCTT
1 -TTTTTCTT
5287726 TTCTTT-TT
1 TT-TTTCTT
5287734 TTTTTCTCT
1 TTTTTCT-T
5287743 TTTTT-TT
1 TTTTTCTT
*
5287750 TCTTTCTT
1 TTTTTCTT
5287758 TT
1 TT
5287760 GCTGCTCACC
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 11 0.31
9 17 0.47
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTCTT
Found at i:5289592 original size:22 final size:22
Alignment explanation
Indices: 5289521--5289593 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
5289511 TAGAATTTTT
*
5289521 GTTAAAATTTTGTTGAAAATCC
1 GTTAAAATTTCGTTGAAAATCC
*** ** **
5289543 GTTAGAAATTTTCAACGAATTTTT
1 GTTA-AAA-TTTCGTTGAAAATCC
5289567 GTTAAAATTTCGTTGAAAATCC
1 GTTAAAATTTCGTTGAAAATCC
5289589 GTTAA
1 GTTAA
5289594 CGAAAATTTC
Statistics
Matches: 34, Mismatches: 15, Indels: 4
0.64 0.28 0.08
Matches are distributed among these distances:
22 17 0.50
23 6 0.18
24 11 0.32
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.41
Consensus pattern (22 bp):
GTTAAAATTTCGTTGAAAATCC
Found at i:5296108 original size:17 final size:18
Alignment explanation
Indices: 5296086--5296124 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
5296076 TTCTATTACC
5296086 TATATATGT-T-TATATTT
1 TATATATGTATGTAT-TTT
5296103 TATATATGTATGTATTTT
1 TATATATGTATGTATTTT
5296121 TATA
1 TATA
5296125 CTTGTTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 8 0.40
19 3 0.15
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (18 bp):
TATATATGTATGTATTTT
Found at i:5299247 original size:23 final size:22
Alignment explanation
Indices: 5299150--5299261 Score: 95
Period size: 22 Copynumber: 5.0 Consensus size: 22
5299140 TATTATTTAG
*
5299150 TATTATTTAAATT-TAATGAAGAA
1 TATTATTT-AATTATAAT-AAAAA
* *
5299173 TA-TATTTTATATTTTAATATTAAA
1 TATTA-TTTA-ATTATAATA-AAAA
5299197 TATTATTTAATTATAATAAAAA
1 TATTATTTAATTATAATAAAAA
* * *
5299219 TA-TATTTGTATTTTGATAAAAA
1 TATTATTT-AATTATAATAAAAA
5299241 TATTATTTAATTATAATAAAA
1 TATTATTTAATTATAATAAAA
5299262 GTTATTTTGA
Statistics
Matches: 72, Mismatches: 10, Indels: 15
0.74 0.10 0.15
Matches are distributed among these distances:
21 5 0.07
22 31 0.43
23 22 0.31
24 12 0.17
25 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (22 bp):
TATTATTTAATTATAATAAAAA
Found at i:5299247 original size:44 final size:46
Alignment explanation
Indices: 5299150--5299269 Score: 149
Period size: 44 Copynumber: 2.7 Consensus size: 46
5299140 TATTATTTAG
* *
5299150 TATTATTTAAATT-TAATGAAGAATATATTTTATATTTTAATATTAAA
1 TATTATTT-AATTATAAT-AAAAATATATTTTATATTTTAATATAAAA
* *
5299197 TATTATTTAATTATAATAAAAATATA-TTTGTATTTTGATA-AAAA
1 TATTATTTAATTATAATAAAAATATATTTTATATTTTAATATAAAA
*
5299241 TATTATTTAATTATAATAAAAGT-TATTTT
1 TATTATTTAATTATAATAAAAATATATTTT
5299270 GATTTTATTG
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
43 2 0.03
44 28 0.42
45 12 0.18
46 12 0.18
47 12 0.18
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (46 bp):
TATTATTTAATTATAATAAAAATATATTTTATATTTTAATATAAAA
Found at i:5299268 original size:20 final size:20
Alignment explanation
Indices: 5299193--5299268 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
5299183 ATTTTAATAT
*
5299193 TAAATATTATTTAATTATAA
1 TAAAAATTATTTAATTATAA
* * *
5299213 TAAAAATATATTTGTATTTTGA
1 TAAAAAT-TATTT-AATTATAA
5299235 TAAAAATATTATTTAATTATAA
1 T-AAAA-ATTATTTAATTATAA
*
5299257 TAAAAGTTATTT
1 TAAAAATTATTT
5299269 TGATTTTATT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
20 12 0.27
21 9 0.20
22 12 0.27
23 9 0.20
24 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
TAAAAATTATTTAATTATAA
Found at i:5299389 original size:62 final size:62
Alignment explanation
Indices: 5299309--5299541 Score: 175
Period size: 62 Copynumber: 3.5 Consensus size: 62
5299299 TAAAAAAAAT
* *
5299309 AAATTCTTTAATTTTAATAAAGAGTATTTTTTTTCATCATAGTTTTTTTTTTTTTAATTAAAC
1 AAATT-TTAAATTTTAATAAAAAGTATTTTTTTTCATCATAGTTTTTTTTTTTTTAATTAAAC
* * ** **
5299372 AAATTTTAAATTTTAATAAAAAGTATTTTTATCATTTACCCATTA-TTCCTTAACCATTTTTAAA
1 AAATTTTAAATTTTAATAAAAAGTATTTTT-T--TTCA-TCA-TAGTT--TT---TTTTTTTTTA
5299436 ATTANAAC
56 ATTA-AAC
* *
5299444 AAAAAAAAATTTTTAATTTTAATAAAGAGTA-TTTTTTTCATCATAGTTTTTTTGTTTTTTAATT
1 ------AAATTTTAAATTTTAATAAAAAGTATTTTTTTTCATCATAGTTTTTTT-TTTTTTAATT
5299508 -AAC
59 AAAC
5299511 AAATTTTTAAATTTTAATAAAAAGTATTTTT
1 AAA-TTTTAAATTTTAATAAAAAGTATTTTT
5299542 ATCATTTACC
Statistics
Matches: 131, Mismatches: 18, Indels: 42
0.69 0.09 0.22
Matches are distributed among these distances:
61 3 0.02
62 43 0.33
63 10 0.08
65 3 0.02
66 4 0.03
67 5 0.04
68 3 0.02
69 8 0.06
71 12 0.09
72 5 0.04
73 4 0.03
74 3 0.02
76 1 0.01
77 4 0.03
78 23 0.18
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (62 bp):
AAATTTTAAATTTTAATAAAAAGTATTTTTTTTCATCATAGTTTTTTTTTTTTTAATTAAAC
Found at i:5299467 original size:140 final size:141
Alignment explanation
Indices: 5299302--5299579 Score: 465
Period size: 140 Copynumber: 2.0 Consensus size: 141
5299292 TTATCTTTAA
5299302 AAAAAATAAATTCTTTAATTTTAATAAAGAGTATTTTTTTTCATCATAGTTTTTTT-TTTTTTAA
1 AAAAAATAAATTCTTTAATTTTAATAAAGAGTA-TTTTTTTCATCATAGTTTTTTTGTTTTTTAA
5299366 TTAAACAAA-TTTTAAATTTTAATAAAAAGTATTTTTATCATTTACCCATTATTCCTTAACCATT
65 TT-AACAAATTTTTAAATTTTAATAAAAAGTATTTTTATCATTTACCCATTATTCCTTAACCATT
5299430 TTTAAAATTANAAC
129 TTTAAAATTA-AAC
5299444 AAAAAA-AAATT-TTTAATTTTAATAAAGAGTATTTTTTTCATCATAGTTTTTTTGTTTTTTAAT
1 AAAAAATAAATTCTTTAATTTTAATAAAGAGTATTTTTTTCATCATAGTTTTTTTGTTTTTTAAT
* * * *
5299507 TAACAAATTTTTAAATTTTAATAAAAAGTATTTTTATCATTTACCCATTGTTCTTTGATCATTTT
66 TAACAAATTTTTAAATTTTAATAAAAAGTATTTTTATCATTTACCCATTATTCCTTAACCATTTT
5299572 TAAAATTA
131 TAAAATTA
5299580 TTCCTACCAA
Statistics
Matches: 130, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
139 28 0.22
140 91 0.70
141 5 0.04
142 6 0.05
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (141 bp):
AAAAAATAAATTCTTTAATTTTAATAAAGAGTATTTTTTTCATCATAGTTTTTTTGTTTTTTAAT
TAACAAATTTTTAAATTTTAATAAAAAGTATTTTTATCATTTACCCATTATTCCTTAACCATTTT
TAAAATTAAAC
Found at i:5299791 original size:37 final size:37
Alignment explanation
Indices: 5299743--5299818 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
5299733 AAGGAAACAA
*
5299743 TTTTAGTAAACTCTCGTCGTGTCTAACCAGTTGGTAT
1 TTTTAGTAAACTCTCATCGTGTCTAACCAGTTGGTAT
5299780 TTTTAGTAAACTCTCATCGTGTCTAACCAGTTGGTAT
1 TTTTAGTAAACTCTCATCGTGTCTAACCAGTTGGTAT
5299817 TT
1 TT
5299819 GAACCTTGGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.42
Consensus pattern (37 bp):
TTTTAGTAAACTCTCATCGTGTCTAACCAGTTGGTAT
Found at i:5320217 original size:23 final size:23
Alignment explanation
Indices: 5320187--5320241 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
5320177 TTGTTTGTTA
*
5320187 ATGTTGCATGCAGTTCCCTTGAT
1 ATGTTGCATGCAATTCCCTTGAT
5320210 ATGTTGCATGCAATTCCCTTGAT
1 ATGTTGCATGCAATTCCCTTGAT
5320233 ATGTTGCAT
1 ATGTTGCAT
5320242 TTGAAATGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (23 bp):
ATGTTGCATGCAATTCCCTTGAT
Found at i:5326312 original size:35 final size:35
Alignment explanation
Indices: 5326266--5326340 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
5326256 GATAGGGACA
5326266 GAGGGTACTAGATATTTTTACTTAAAAGAACCAGT
1 GAGGGTACTAGATATTTTTACTTAAAAGAACCAGT
*
5326301 GAGGGTACTAGATTTTTTTACTTAAAAGAACCAGT
1 GAGGGTACTAGATATTTTTACTTAAAAGAACCAGT
5326336 GAGGG
1 GAGGG
5326341 GCAGATATCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.31
Consensus pattern (35 bp):
GAGGGTACTAGATATTTTTACTTAAAAGAACCAGT
Found at i:5333191 original size:17 final size:17
Alignment explanation
Indices: 5333169--5333215 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
5333159 GATAAATAAT
5333169 TAAAAATTAATTAAAAA
1 TAAAAATTAATTAAAAA
* *
5333186 TAAAAAGTAA-AAAAAA
1 TAAAAATTAATTAAAAA
*
5333202 TAAATATTTAATTA
1 TAAA-AATTAATTA
5333216 GATACTTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
16 9 0.39
17 13 0.57
18 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
TAAAAATTAATTAAAAA
Found at i:5343462 original size:33 final size:33
Alignment explanation
Indices: 5343421--5343519 Score: 132
Period size: 33 Copynumber: 3.0 Consensus size: 33
5343411 TCTTAATATC
5343421 ATATATTTTATTTTTATTTTTTATTATAATTTT
1 ATATATTTTATTTTTATTTTTTATTATAATTTT
* *
5343454 ATATATTTTATTTTTATTTCTTAATATAATTTCT
1 ATATATTTTATTTTTATTTTTTATTATAATTT-T
5343488 -TATATTTTATATTTTATTTTATT-TTA-AATTTT
1 ATATATTTTAT-TTTTATTTT-TTATTATAATTTT
5343520 TTAAAAGACA
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
32 1 0.02
33 45 0.76
34 11 0.19
35 2 0.03
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTTTTATTATAATTTT
Found at i:5343609 original size:16 final size:18
Alignment explanation
Indices: 5343565--5343609 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
5343555 TATAACAATA
*
5343565 TAAATATATTTAATAAAG
1 TAAAAATATTTAATAAAG
5343583 TAACAAA-ATTT-A-AAAG
1 TAA-AAATATTTAATAAAG
5343599 TAAAAATATTT
1 TAAAAATATTT
5343610 TTAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 3 0.12
16 11 0.46
17 1 0.04
18 7 0.29
19 2 0.08
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (18 bp):
TAAAAATATTTAATAAAG
Found at i:5345942 original size:3 final size:3
Alignment explanation
Indices: 5345925--5345957 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
5345915 TTCTTCAACC
5345925 CTT CTT -TT C-T CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
5345958 CTGTTTCCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:5347567 original size:152 final size:152
Alignment explanation
Indices: 5347291--5347593 Score: 552
Period size: 152 Copynumber: 2.0 Consensus size: 152
5347281 AGGGTGCCAG
*
5347291 CTGTGTTTGTTTATCAAGAATCCATATTCAACCATTTGATAAGATTAAAACCCACATGTTGAGAA
1 CTGTGTTTGTTTATCAAGAATCCATATCCAACCATTTGATAAGATTAAAACCCACATGTTGAGAA
*
5347356 ACTTGATCGGTCAATCTAACATTGCTAAATGACAAGGTGCTGGCGGCCCTGATTAATCTTTGTTA
66 ACTTGATCGGTCAATCTAACATTGCTAAATGACAAGGTGCCGGCGGCCCTGATTAATCTTTGTTA
5347421 GATCTTCTTTACAATTAATTAA
131 GATCTTCTTTACAATTAATTAA
* *
5347443 CTGTGTTTGTTTATCAAGAATCCATATCCAACCATTTGATAAGATTATAACCCATATGTTGAGAA
1 CTGTGTTTGTTTATCAAGAATCCATATCCAACCATTTGATAAGATTAAAACCCACATGTTGAGAA
*
5347508 ACTTGATCGGTCAATCTAACATTGCTAAATGACAAGGTGCCGGCGGCCCTGATTAATCTTTGTTG
66 ACTTGATCGGTCAATCTAACATTGCTAAATGACAAGGTGCCGGCGGCCCTGATTAATCTTTGTTA
*
5347573 GATCTTCTTTATAATTAATTA
131 GATCTTCTTTACAATTAATTA
5347594 GTTATTGCAA
Statistics
Matches: 145, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
152 145 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (152 bp):
CTGTGTTTGTTTATCAAGAATCCATATCCAACCATTTGATAAGATTAAAACCCACATGTTGAGAA
ACTTGATCGGTCAATCTAACATTGCTAAATGACAAGGTGCCGGCGGCCCTGATTAATCTTTGTTA
GATCTTCTTTACAATTAATTAA
Found at i:5358801 original size:31 final size:29
Alignment explanation
Indices: 5358738--5358801 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
5358728 CTGAACCAGA
* **
5358738 AATATTAGCTGAATAAAAAAATATATCTG
1 AATATTAGCAGAATAAAAAAATATATAAG
*
5358767 AATATTAGCAGAGCTAAAAGAAATATATAAG
1 AATATTAGCAGA-ATAAAA-AAATATATAAG
5358798 AATA
1 AATA
5358802 AAACTTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 11 0.38
30 5 0.17
31 13 0.45
ACGTcount: A:0.55, C:0.06, G:0.12, T:0.27
Consensus pattern (29 bp):
AATATTAGCAGAATAAAAAAATATATAAG
Found at i:5365505 original size:2 final size:2
Alignment explanation
Indices: 5365498--5365523 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5365488 TTTGCAACAC
5365498 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
5365524 AAGTGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5367488 original size:9 final size:9
Alignment explanation
Indices: 5367474--5367503 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
5367464 ACACGATTAA
*
5367474 TAACACGTT
1 TAACACGAT
5367483 TAACACGAT
1 TAACACGAT
5367492 TAACACGAT
1 TAACACGAT
5367501 TAA
1 TAA
5367504 ATAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (9 bp):
TAACACGAT
Found at i:5367571 original size:12 final size:12
Alignment explanation
Indices: 5367554--5367578 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5367544 TTTAAAATCT
5367554 ATAATTATAAAA
1 ATAATTATAAAA
5367566 ATAATTATAAAA
1 ATAATTATAAAA
5367578 A
1 A
5367579 CAAAAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAATTATAAAA
Found at i:5368100 original size:2 final size:2
Alignment explanation
Indices: 5368095--5368128 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5368085 TATAAAAAAT
5368095 TA TA TA 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 TA TA TA
5368129 AATGCAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5370331 original size:19 final size:19
Alignment explanation
Indices: 5370304--5370366 Score: 53
Period size: 18 Copynumber: 3.5 Consensus size: 19
5370294 AATAGACTAG
*
5370304 AAATGAAAAAAATAAATAT
1 AAATAAAAAAAATAAATAT
* *
5370323 AAATAAAAATAAT-AATAC
1 AAATAAAAAAAATAAATAT
* *
5370341 AAATTAAAAGAA-AAA-AT
1 AAATAAAAAAAATAAATAT
5370358 AAA-AAAAAA
1 AAATAAAAAA
5370367 CTTTAAAGTT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
16 4 0.11
17 4 0.11
18 16 0.46
19 11 0.31
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (19 bp):
AAATAAAAAAAATAAATAT
Found at i:5370339 original size:18 final size:18
Alignment explanation
Indices: 5370304--5370366 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 18
5370294 AATAGACTAG
*
5370304 AAATGAAAAAAATAAATAT
1 AAAT-AAAAAAATAAATAC
5370323 AAATAAAAATAAT-AATAC
1 AAATAAAAA-AATAAATAC
5370341 AAATTAAAAGAAA-AAATA-
1 AAA-TAAAA-AAATAAATAC
5370359 AAA-AAAAA
1 AAATAAAAA
5370367 CTTTAAAGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
15 1 0.03
16 4 0.10
18 15 0.38
19 18 0.46
20 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATAAAAAAATAAATAC
Found at i:5379342 original size:2 final size:2
Alignment explanation
Indices: 5379335--5379360 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5379325 AACTAAGGCC
5379335 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
5379361 CTATGGTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5382676 original size:19 final size:19
Alignment explanation
Indices: 5382652--5382693 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
5382642 TTTAGTCAAA
5382652 ATTTAATATATTTTAATGC
1 ATTTAATATATTTTAATGC
5382671 ATTTAATATATTTTAATGC
1 ATTTAATATATTTTAATGC
5382690 ATTT
1 ATTT
5382694 TTTTCAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (19 bp):
ATTTAATATATTTTAATGC
Found at i:5385707 original size:14 final size:14
Alignment explanation
Indices: 5385688--5385720 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5385678 TAAACAACTT
5385688 ATTTATAAAA-TAGA
1 ATTTATAAAAGTA-A
5385702 ATTTATAAAAGTAA
1 ATTTATAAAAGTAA
5385716 ATTTA
1 ATTTA
5385721 CCAAACAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (14 bp):
ATTTATAAAAGTAA
Found at i:5387422 original size:7 final size:6
Alignment explanation
Indices: 5387396--5387420 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5387386 ATTTGATTAA
5387396 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
5387421 TACACATAAA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:5390295 original size:27 final size:27
Alignment explanation
Indices: 5390265--5390340 Score: 134
Period size: 27 Copynumber: 2.8 Consensus size: 27
5390255 TTCTTCAGGA
*
5390265 GGGAAGTGGCATTGAGTTTCTTCAATT
1 GGGAAGTGGAATTGAGTTTCTTCAATT
5390292 GGGAAGTGGAATTGAGTTTCTTCAATT
1 GGGAAGTGGAATTGAGTTTCTTCAATT
*
5390319 GGGAAGTGGAATTGAGCTTCTT
1 GGGAAGTGGAATTGAGTTTCTT
5390341 GAGTTCAGAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.24, C:0.09, G:0.32, T:0.36
Consensus pattern (27 bp):
GGGAAGTGGAATTGAGTTTCTTCAATT
Found at i:5414701 original size:27 final size:27
Alignment explanation
Indices: 5414670--5414721 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
5414660 ATCTATCAAA
5414670 GATTCAAGTGCATTTGCATTTTGCAAG
1 GATTCAAGTGCATTTGCATTTTGCAAG
*
5414697 GATTCAAGTGCGTTTGCATTTTGCA
1 GATTCAAGTGCATTTGCATTTTGCA
5414722 TGGAAGCAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
GATTCAAGTGCATTTGCATTTTGCAAG
Found at i:5419721 original size:14 final size:13
Alignment explanation
Indices: 5419701--5419735 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
5419691 TAAAAGAGGG
5419701 AGAAAAAAAGAAA
1 AGAAAAAAAGAAA
* *
5419714 AGACAAAAAGGAA
1 AGAAAAAAAGAAA
5419727 AGAAAAAAA
1 AGAAAAAAA
5419736 AAACAGTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAGAAA
Found at i:5425515 original size:2 final size:2
Alignment explanation
Indices: 5425508--5425538 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5425498 TATGCTAATA
5425508 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 A
5425539 AGGTATGTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5437596 original size:12 final size:12
Alignment explanation
Indices: 5437579--5437603 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5437569 TCATCATTGG
5437579 AGCTTTTTTTTA
1 AGCTTTTTTTTA
5437591 AGCTTTTTTTTA
1 AGCTTTTTTTTA
5437603 A
1 A
5437604 AAAAATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.64
Consensus pattern (12 bp):
AGCTTTTTTTTA
Found at i:5442736 original size:14 final size:13
Alignment explanation
Indices: 5442712--5442741 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
5442702 AGGGTGGTGG
5442712 TTTCTTCTCTCTC
1 TTTCTTCTCTCTC
5442725 TTTCTCTCTCTCTC
1 TTTCT-TCTCTCTC
5442739 TTT
1 TTT
5442742 TGTCAAGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTCTTCTCTCTC
Found at i:5450696 original size:21 final size:21
Alignment explanation
Indices: 5450670--5450715 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
5450660 TATGATAAGC
*
5450670 CATGGTTAGGTTGTTACACAT
1 CATGGTTAAGTTGTTACACAT
*
5450691 CATGGTTAAGTTGTTACACGT
1 CATGGTTAAGTTGTTACACAT
5450712 CATG
1 CATG
5450716 TACAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (21 bp):
CATGGTTAAGTTGTTACACAT
Found at i:5450745 original size:66 final size:66
Alignment explanation
Indices: 5450572--5450754 Score: 204
Period size: 66 Copynumber: 2.8 Consensus size: 66
5450562 GATTAGGTCA
* * * * **
5450572 TTACACACCATGTAAAAAAATATGTGACAACCCATGGTTAGGTTATTATATGTCATGGCTAAGTT
1 TTACACGCCATGTAAAAAAATATGTGACAAGCCATGGTTAGGTTGTTACACATCATGGCTAAGTT
5450637 G
66 G
* * * * * * *
5450638 TTATACGCCGTCTATAAAAATATATGATAAGCCATGGTTAGGTTGTTACACATCATGGTTAAGTT
1 TTACACGCCATGTAAAAAAATATGTGACAAGCCATGGTTAGGTTGTTACACATCATGGCTAAGTT
5450703 G
66 G
* * * **
5450704 TTACACGTCATGTACAAAAATATGTGACAAGTCATAATTAGGTTGTTACAC
1 TTACACGCCATGTAAAAAAATATGTGACAAGCCATGGTTAGGTTGTTACAC
5450755 GTTATGTACA
Statistics
Matches: 94, Mismatches: 23, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
66 94 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (66 bp):
TTACACGCCATGTAAAAAAATATGTGACAAGCCATGGTTAGGTTGTTACACATCATGGCTAAGTT
G
Found at i:5450764 original size:45 final size:45
Alignment explanation
Indices: 5450700--5450806 Score: 178
Period size: 45 Copynumber: 2.4 Consensus size: 45
5450690 TCATGGTTAA
5450700 GTTGTTACACGTCATGTACAAAAATATGTGACAAGTCATAATTAG
1 GTTGTTACACGTCATGTACAAAAATATGTGACAAGTCATAATTAG
* *
5450745 GTTGTTACACGTTATGTACAAAAATATGTGACAAGTCATGATTAG
1 GTTGTTACACGTCATGTACAAAAATATGTGACAAGTCATAATTAG
* *
5450790 ATTGTTACACATCATGT
1 GTTGTTACACGTCATGT
5450807 TGAAAAAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.34
Consensus pattern (45 bp):
GTTGTTACACGTCATGTACAAAAATATGTGACAAGTCATAATTAG
Found at i:5450840 original size:19 final size:20
Alignment explanation
Indices: 5450818--5450856 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
5450808 GAAAAAAAAT
5450818 ATTA-TTGTTACACGCCATA
1 ATTAGTTGTTACACGCCATA
5450837 ATTAGGTTGTTACACGCCAT
1 ATTA-GTTGTTACACGCCAT
5450857 GTTGAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
21 14 0.78
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (20 bp):
ATTAGTTGTTACACGCCATA
Found at i:5450886 original size:51 final size:52
Alignment explanation
Indices: 5450785--5450887 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 52
5450775 ACAAGTCATG
* *
5450785 ATTAGATTGTTACACATCATGTTGAAAAAAAATATTATTGTTACACGCCATA
1 ATTAGATTGTTACACACCATGTTGAAAAAAAATACTATTGTTACACGCCATA
* * *
5450837 ATTAGGTTGTTACACGCCATGTTG-AAAAAAATACTATTGTTACATGCCATA
1 ATTAGATTGTTACACACCATGTTGAAAAAAAATACTATTGTTACACGCCATA
5450888 TATAAAAACA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 25 0.54
52 21 0.46
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.34
Consensus pattern (52 bp):
ATTAGATTGTTACACACCATGTTGAAAAAAAATACTATTGTTACACGCCATA
Found at i:5450910 original size:24 final size:25
Alignment explanation
Indices: 5450890--5450947 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
5450880 ATGCCATATA
* *
5450890 TAAAAACA-TGTTACACACCATGGT
1 TAAAAAAAGTGTTACACACCATGAT
5450914 TAAAAAAAGTTGTTACACACCATG-T
1 TAAAAAAAG-TGTTACACACCATGAT
5450939 TGAAAAAAA
1 T-AAAAAAA
5450948 TATATTGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 7 0.23
25 2 0.07
26 21 0.70
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (25 bp):
TAAAAAAAGTGTTACACACCATGAT
Found at i:5450911 original size:54 final size:51
Alignment explanation
Indices: 5450792--5450921 Score: 136
Period size: 51 Copynumber: 2.5 Consensus size: 51
5450782 ATGATTAGAT
* * * ***
5450792 TGTTACACATCATGTTGAAAAAAAATATTATTGTTACACGCCATAATTAGGT
1 TGTTACACACCATGTTG-AAAAAAATACTATTGTTACACGCCATAATAAACA
* *
5450844 TGTTACACGCCATGTTGAAAAAAATACTATTGTTACATGCCATATATAAAAACA
1 TGTTACACACCATGTTGAAAAAAATACTATTGTTACACGCCATA-AT--AAACA
5450898 TGTTACACACCATGGTT-AAAAAAA
1 TGTTACACACCAT-GTTGAAAAAAA
5450922 GTTGTTACAC
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
51 25 0.38
52 17 0.26
54 20 0.31
55 3 0.05
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (51 bp):
TGTTACACACCATGTTGAAAAAAATACTATTGTTACACGCCATAATAAACA
Found at i:5450927 original size:26 final size:26
Alignment explanation
Indices: 5450898--5450947 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
5450888 TATAAAAACA
5450898 TGTTACACACCATGGTT-AAAAAAAGT
1 TGTTACACACCAT-GTTGAAAAAAAGT
5450924 TGTTACACACCATGTTGAAAAAAA
1 TGTTACACACCATGTTGAAAAAAA
5450948 TATATTGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (26 bp):
TGTTACACACCATGTTGAAAAAAAGT
Found at i:5451433 original size:23 final size:23
Alignment explanation
Indices: 5451407--5451472 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
5451397 TCTTGAAAGC
5451407 GCAAGAAAGAGAAATCTGAAAAT
1 GCAAGAAAGAGAAATCTGAAAAT
5451430 GCAAGAAAGAGAAATCTGAAAAT
1 GCAAGAAAGAGAAATCTGAAAAT
* * *
5451453 ACGAGAGAGAGAAATC-GAAA
1 GCAAGAAAGAGAAATCTGAAA
5451473 GGATAACAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 4 0.10
23 36 0.90
ACGTcount: A:0.56, C:0.09, G:0.24, T:0.11
Consensus pattern (23 bp):
GCAAGAAAGAGAAATCTGAAAAT
Found at i:5453128 original size:18 final size:17
Alignment explanation
Indices: 5453098--5453132 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5453088 AAGAGCGACA
*
5453098 GAGGAGAAGGAGAGGAG
1 GAGGAGAAAGAGAGGAG
5453115 GAGGAAGAAAGAGAGGAG
1 GAGG-AGAAAGAGAGGAG
5453133 CAGCTGTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (17 bp):
GAGGAGAAAGAGAGGAG
Found at i:5456388 original size:89 final size:89
Alignment explanation
Indices: 5456166--5456443 Score: 337
Period size: 89 Copynumber: 3.1 Consensus size: 89
5456156 CTCTCAACTC
* * * * * * * *
5456166 CTTCCTTTTCCAGTTGGCGACACAAGGCTGAAGCCCCAACTCTCTCTAAAACCGACGGCACAGGA
1 CTTCCTTTTTCAGTCGGCGACACAAGCCCGAAGGCCCAACTCTCTCTAGAACCGATGGCACAGCA
* * **
5456231 ACCCAGATCTGGTCAGCTCTCACTT
66 ACCCAGATCTTGTC-TCTCTTGCTT
* * *
5456256 CTTCCTTTTTCAGTCGGCGATAGAAGCCCGAA-GCCCTAGCTCTCTCTAGAACCGATGGCACAGC
1 CTTCCTTTTTCAGTCGGCGACACAAGCCCGAAGGCCC-AACTCTCTCTAGAACCGATGGCACAGC
5456320 AACCCAGATCTTGTCTCTCTTGCTT
65 AACCCAGATCTTGTCTCTCTTGCTT
* * * *
5456345 CTTCCTTTTTCAGTCGGTGACACAAGCCCGAAGGCCCAACTCTCTCTAGAATCGGTGGCACAACA
1 CTTCCTTTTTCAGTCGGCGACACAAGCCCGAAGGCCCAACTCTCTCTAGAACCGATGGCACAGCA
*
5456410 ACCCAGATCTTCTCTCTCTTGCTT
66 ACCCAGATCTTGTCTCTCTTGCTT
5456434 CTT--TTTTTCA
1 CTTCCTTTTTCA
5456444 CTGACGGCAA
Statistics
Matches: 163, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
87 7 0.04
89 89 0.55
90 67 0.41
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.28
Consensus pattern (89 bp):
CTTCCTTTTTCAGTCGGCGACACAAGCCCGAAGGCCCAACTCTCTCTAGAACCGATGGCACAGCA
ACCCAGATCTTGTCTCTCTTGCTT
Found at i:5460756 original size:2 final size:2
Alignment explanation
Indices: 5460708--5460745 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5460698 CTCTTTTAAT
5460708 TA TA TA TA TA 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 TA TA TA TA TA
5460746 AAATTATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5486409 original size:10 final size:10
Alignment explanation
Indices: 5486394--5486474 Score: 76
Period size: 10 Copynumber: 8.1 Consensus size: 10
5486384 GCCATCCCGA
5486394 TTTTTTT-TT
1 TTTTTTTATT
*
5486403 CTTTTTTATT
1 TTTTTTTATT
*
5486413 TATTTTTA-T
1 TTTTTTTATT
*
5486422 TTATTTTATT
1 TTTTTTTATT
*
5486432 TTATTTTATT
1 TTTTTTTATT
*
5486442 TATTTTTATT
1 TTTTTTTATT
5486452 TTTATTATTATT
1 TTT-TT-TTATT
*
5486464 TTTTTTAATT
1 TTTTTTTATT
5486474 T
1 T
5486475 ATGTGTCTAC
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
9 13 0.22
10 34 0.58
11 4 0.07
12 8 0.14
ACGTcount: A:0.17, C:0.01, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:5486428 original size:19 final size:19
Alignment explanation
Indices: 5486405--5486476 Score: 80
Period size: 19 Copynumber: 3.8 Consensus size: 19
5486395 TTTTTTTTCT
5486405 TTTTTATTTATTTTTATTTA
1 TTTTTATTTA-TTTTATTTA
5486425 -TTTTATTTTATTTTATTTA
1 TTTTTA-TTTATTTTATTTA
5486444 TTTTTATTT-TTATTA-TTA
1 TTTTTATTTATT-TTATTTA
*
5486462 TTTTT-TTTAATTTAT
1 TTTTTATTTATTTTAT
5486477 GTGTCTACAC
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
17 6 0.13
18 11 0.24
19 20 0.43
20 9 0.20
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTATTTATTTTATTTA
Found at i:5486431 original size:15 final size:14
Alignment explanation
Indices: 5486404--5486476 Score: 74
Period size: 15 Copynumber: 4.9 Consensus size: 14
5486394 TTTTTTTTTC
5486404 TTTTTTATTTATTT
1 TTTTTTATTTATTT
*
5486418 TTATTTATTTTATTT
1 TTTTTTA-TTTATTT
*
5486433 TATTTTATTTATTTT
1 TTTTTTATTTA-TTT
5486448 TATTTTTATTATTATTT
1 T-TTTTTA-T-TTATTT
*
5486465 TTTTTAATTTAT
1 TTTTTTATTTAT
5486477 GTGTCTACAC
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
14 14 0.29
15 17 0.35
16 10 0.20
17 5 0.10
18 3 0.06
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTATTTATTT
Found at i:5489310 original size:15 final size:15
Alignment explanation
Indices: 5489290--5489328 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
5489280 TTTATATTCT
*
5489290 TTTTTATTTTTTTCA
1 TTTTTATTCTTTTCA
5489305 TTTTTA-TCTTTTCA
1 TTTTTATTCTTTTCA
5489319 TTATTTATTC
1 TT-TTTATTC
5489329 ACTTCTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 9 0.43
15 10 0.48
16 2 0.10
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTATTCTTTTCA
Found at i:5489559 original size:26 final size:26
Alignment explanation
Indices: 5489529--5489601 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 26
5489519 GGCATCCATC
*
5489529 CACTTTTAATGATAAAATTATCTATT
1 CACTTCTAATGATAAAATTATCTATT
* *
5489555 CACTTCTAGTGATAAAATTAT-TCTT
1 CACTTCTAATGATAAAATTATCTATT
* * *
5489580 AAATTCTGATGATAAAATTATC
1 CACTTCTAATGATAAAATTATC
5489602 CTTAAATTCA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 20 0.51
26 19 0.49
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (26 bp):
CACTTCTAATGATAAAATTATCTATT
Found at i:5489592 original size:25 final size:24
Alignment explanation
Indices: 5489537--5489610 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 24
5489527 TCCACTTTTA
* * *
5489537 ATGATAAAATTATCTATTCACTTCT
1 ATGATAAAATTAT-TCTTAAATTCT
5489562 AGTGATAAAATTATTCTTAAATTCT
1 A-TGATAAAATTATTCTTAAATTCT
*
5489587 GATGATAAAATTATCCTTAAATTC
1 -ATGATAAAATTATTCTTAAATTC
5489611 ATAATTATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 30 0.70
26 13 0.30
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (24 bp):
ATGATAAAATTATTCTTAAATTCT
Found at i:5518111 original size:22 final size:22
Alignment explanation
Indices: 5518085--5518126 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5518075 TTTGAAATGC
5518085 GATTTGGCGTTTTATGTTTTAT
1 GATTTGGCGTTTTATGTTTTAT
*
5518107 GATTTGGGGTTTTATGTTTT
1 GATTTGGCGTTTTATGTTTT
5518127 TAAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.02, G:0.26, T:0.60
Consensus pattern (22 bp):
GATTTGGCGTTTTATGTTTTAT
Found at i:5518271 original size:45 final size:45
Alignment explanation
Indices: 5518206--5518340 Score: 162
Period size: 45 Copynumber: 3.0 Consensus size: 45
5518196 TCATGGTTAA
* * *
5518206 GTTGTCACACATCATATATAAAAATATGCGACATGTTATGATTAG
1 GTTGTCACACATCATGTATAAAAATATGCGACACGCTATGATTAG
*
5518251 GTTGTCACACATCATGTATAAAAATATACGACACGCTATGATTAG
1 GTTGTCACACATCATGTATAAAAATATGCGACACGCTATGATTAG
* * * * * * * *
5518296 ATTGTTACACGTTATGTATAAAAACATGTGACACGATATGGTTAG
1 GTTGTCACACATCATGTATAAAAATATGCGACACGCTATGATTAG
5518341 ATTATTATAC
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 77 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (45 bp):
GTTGTCACACATCATGTATAAAAATATGCGACACGCTATGATTAG
Done.