Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 9 of 32
Found at i:1050816 original size:20 final size:20
Alignment explanation
Indices: 1050791--1050835 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1050781 TAAATTTAAA
1050791 TATTATAATTCA-TATATTTT
1 TATTAT-ATTCATTATATTTT
*
1050811 TATTATATTTATTATATTTT
1 TATTATATTCATTATATTTT
1050831 T-TTAT
1 TATTAT
1050836 GTTATAATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTATATTCATTATATTTT
Found at i:1050892 original size:19 final size:17
Alignment explanation
Indices: 1050864--1050913 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
1050854 ATATTATTTT
1050864 ATATAAATTTTAATATA
1 ATATAAATTTTAATATA
* *
1050881 ATATTAAAATTTAA-ATT
1 ATA-TAAATTTTAATATA
1050898 ATATAAATTTTAATAT
1 ATATAAATTTTAATAT
1050914 TTTTATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 9 0.32
17 10 0.36
18 9 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATAAATTTTAATATA
Found at i:1051552 original size:14 final size:13
Alignment explanation
Indices: 1051533--1051562 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
1051523 ATCATTTGAC
1051533 AAAAATAAATAACA
1 AAAAATAAATAA-A
1051547 AAAAATAAATAAA
1 AAAAATAAATAAA
1051560 AAA
1 AAA
1051563 TAAAAAACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAATAAATAAA
Found at i:1051558 original size:18 final size:18
Alignment explanation
Indices: 1051535--1051569 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1051525 CATTTGACAA
*
1051535 AAATAAATAACAAAAAAT
1 AAATAAAAAACAAAAAAT
*
1051553 AAATAAAAAATAAAAAA
1 AAATAAAAAACAAAAAA
1051570 CACCCCTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (18 bp):
AAATAAAAAACAAAAAAT
Found at i:1052513 original size:25 final size:26
Alignment explanation
Indices: 1052468--1052518 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
1052458 TATCTATTTT
*
1052468 TTTAAAATATCAAATTAAATTTTAAA
1 TTTAAAATATCAAATTAAATTGTAAA
*
1052494 TTTAAATATAT-AACTT-AATTGTAAA
1 TTTAAA-ATATCAAATTAAATTGTAAA
1052519 ATCAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 8 0.36
26 10 0.45
27 4 0.18
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (26 bp):
TTTAAAATATCAAATTAAATTGTAAA
Found at i:1053165 original size:10 final size:10
Alignment explanation
Indices: 1053135--1053205 Score: 53
Period size: 10 Copynumber: 7.6 Consensus size: 10
1053125 CTATTTATCG
*
1053135 TTAATAAAAT
1 TTAATAATAT
1053145 TTAA-AAT-T
1 TTAATAATAT
1053153 TTAATAATAT
1 TTAATAATAT
1053163 TT-ATAA-A-
1 TTAATAATAT
* *
1053170 ATAATAATTT
1 TTAATAATAT
1053180 TTAATAATAT
1 TTAATAATAT
* * *
1053190 ATATTAAAAT
1 TTAATAATAT
1053200 TTAATA
1 TTAATA
1053206 TGATCCAATA
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
7 1 0.02
8 10 0.22
9 9 0.20
10 26 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
TTAATAATAT
Found at i:1053169 original size:27 final size:29
Alignment explanation
Indices: 1053138--1053205 Score: 90
Period size: 27 Copynumber: 2.4 Consensus size: 29
1053128 TTTATCGTTA
*
1053138 ATAAAATTTAA-AA-TTTTAATAATATTT
1 ATAAAATTTAATAATTTTTAATAATATAT
1053165 ATAAAA--TAATAATTTTTAATAATATAT
1 ATAAAATTTAATAATTTTTAATAATATAT
1053192 ATTAAAATTTAATA
1 A-TAAAATTTAATA
1053206 TGATCCAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
25 3 0.09
26 2 0.06
27 20 0.57
28 5 0.14
30 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
ATAAAATTTAATAATTTTTAATAATATAT
Found at i:1054936 original size:22 final size:22
Alignment explanation
Indices: 1054906--1054957 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1054896 TTTAAATAAA
*
1054906 AATTATAAAAAATTT-TACTTT
1 AATTTTAAAAAATTTATACTTT
* *
1054927 AACTTTTAAAAATTTTATATTTT
1 AA-TTTTAAAAAATTTATACTTT
1054950 AATTTTAA
1 AATTTTAA
1054958 TATTTCAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 2 0.08
22 17 0.65
23 7 0.27
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (22 bp):
AATTTTAAAAAATTTATACTTT
Found at i:1055100 original size:17 final size:16
Alignment explanation
Indices: 1055074--1055115 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
1055064 TAATGAATAA
*
1055074 AATTATAAAATTTTAT
1 AATTATAAAATATTAT
1055090 AATTAATAAAATATTAT
1 AATT-ATAAAATATTAT
*
1055107 TATTATAAA
1 AATTATAAA
1055116 TAATATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTATAAAATATTAT
Found at i:1055545 original size:2 final size:2
Alignment explanation
Indices: 1055538--1055581 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1055528 GATCAGCCAA
1055538 AT AT AT AT AT 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 AT AT AT AT AT
1055580 AT
1 AT
1055582 TTGTTAGTGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1056316 original size:17 final size:18
Alignment explanation
Indices: 1056294--1056344 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 18
1056284 TTATATAATA
1056294 AAATATTATTTAAA-TTT
1 AAATATTATTTAAATTTT
*
1056311 AAATATTAATATAAATTTTT
1 AAATATT-ATTTAAA-TTTT
*
1056331 TAATATTATTTAAA
1 AAATATTATTTAAA
1056345 ATAATAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 7 0.25
18 6 0.21
19 6 0.21
20 9 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATATTATTTAAATTTT
Found at i:1056325 original size:18 final size:17
Alignment explanation
Indices: 1056294--1056328 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1056284 TTATATAATA
*
1056294 AAATATTATTTAAATTT
1 AAATATTATATAAATTT
1056311 AAATATTAATATAAATTT
1 AAATATT-ATATAAATTT
1056329 TTTAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATATTATATAAATTT
Found at i:1056346 original size:20 final size:19
Alignment explanation
Indices: 1056294--1056346 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
1056284 TTATATAATA
1056294 AAATATTATTT-AAA-TTT
1 AAATATTATTTAAAATTTT
* *
1056311 AAATATTAATATAAATTTTT
1 AAATATT-ATTTAAAATTTT
*
1056331 TAATATTATTTAAAAT
1 AAATATTATTTAAAAT
1056347 AATAAAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 7 0.25
18 3 0.11
19 9 0.32
20 9 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATATTATTTAAAATTTT
Found at i:1058318 original size:20 final size:20
Alignment explanation
Indices: 1058276--1058317 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1058266 GATACAAGGG
1058276 AAAGAAAGAAAGAAAGAAGA
1 AAAGAAAGAAAGAAAGAAGA
**
1058296 AAAGAAAGATGGAAA-AAGA
1 AAAGAAAGAAAGAAAGAAGA
1058315 AAA
1 AAA
1058318 ATTCATACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (20 bp):
AAAGAAAGAAAGAAAGAAGA
Found at i:1064347 original size:22 final size:20
Alignment explanation
Indices: 1064322--1064380 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 20
1064312 TTATATTTAT
1064322 TATATATATATAAATTACATAA
1 TATATATATATAAATTA-AT-A
*
1064344 TATATAAATATAAAATTAATA
1 TATATATATAT-AAATTAATA
1064365 TATAT-TATAT-AATTAA
1 TATATATATATAAATTAA
1064381 AAATTAACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 6 0.18
20 4 0.12
21 6 0.18
22 12 0.35
23 6 0.18
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
TATATATATATAAATTAATA
Found at i:1069794 original size:20 final size:20
Alignment explanation
Indices: 1069750--1069787 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1069740 ATTTAAATAT
1069750 TATTTTTATATAAAAAATTA
1 TATTTTTATATAAAAAATTA
*
1069770 TATTTTTAT-TAATAAATT
1 TATTTTTATATAAAAAATT
1069788 TTAATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTTTTATATAAAAAATTA
Found at i:1071947 original size:87 final size:87
Alignment explanation
Indices: 1071801--1071970 Score: 295
Period size: 87 Copynumber: 2.0 Consensus size: 87
1071791 CTCTGATGAT
* * *
1071801 TCAATCTCAACCCGCAATTCTCTCTGACACTCATCTCCCTTGCGCTTCGGAGTCGACTTTTCAGC
1 TCAATCTCAAACCGCAATTCTCTCTGACAATCATCTCCCTTGCGCTTCAGAGTCGACTTTTCAGC
*
1071866 TTTAAAATCAGTCTCTCCAGCA
66 TTTAAAATAAGTCTCTCCAGCA
*
1071888 TCAATTTCAAACCGCAATTCTCTCTGACAATCATCTCCCTTGCGCTTCAGAGTCGACTTTTCAGC
1 TCAATCTCAAACCGCAATTCTCTCTGACAATCATCTCCCTTGCGCTTCAGAGTCGACTTTTCAGC
1071953 TTTAAAATAAGTCTCTCC
66 TTTAAAATAAGTCTCTCC
1071971 CGCAGAACCA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 78 1.00
ACGTcount: A:0.24, C:0.32, G:0.12, T:0.32
Consensus pattern (87 bp):
TCAATCTCAAACCGCAATTCTCTCTGACAATCATCTCCCTTGCGCTTCAGAGTCGACTTTTCAGC
TTTAAAATAAGTCTCTCCAGCA
Found at i:1074543 original size:17 final size:17
Alignment explanation
Indices: 1074506--1074553 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
1074496 AATTTTATAT
*
1074506 TTTTATTTTCTTATAAAA
1 TTTTATTTT-TAATAAAA
*
1074524 TTTTATTTTTAATAAGA
1 TTTTATTTTTAATAAAA
*
1074541 TTTAAATTTTTAA
1 TTT-TATTTTTAA
1074554 CTTCTTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTTATTTTTAATAAAA
Found at i:1074663 original size:15 final size:17
Alignment explanation
Indices: 1074642--1074687 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
1074632 TAATTAGTGT
1074642 TTAAATATAAAAATC-A
1 TTAAATATAAAAATCAA
1074658 -TAAATATATAAAATCAA
1 TTAAATATA-AAAATCAA
1074675 TTAAAT-TAAAAAT
1 TTAAATATAAAAAT
1074688 TTTAATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 8 0.30
16 11 0.41
17 3 0.11
18 5 0.19
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAATATAAAAATCAA
Found at i:1074715 original size:22 final size:19
Alignment explanation
Indices: 1074687--1074733 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 19
1074677 AAATTAAAAA
1074687 TTTTAATATTAATTAATTTAAT
1 TTTTAATATTAA-TAA-TT-AT
1074709 TTTTAATATTAATAATTAT
1 TTTTAATATTAATAATTAT
1074728 TTTTAA
1 TTTTAA
1074734 AAATTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.32
20 2 0.08
21 3 0.12
22 12 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTAATATTAATAATTAT
Found at i:1074991 original size:17 final size:17
Alignment explanation
Indices: 1074969--1075005 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1074959 TGTTTATTTA
1074969 TATATTTTAAATATATT
1 TATATTTTAAATATATT
**
1074986 TATATTTTATTTATATT
1 TATATTTTAAATATATT
1075003 TAT
1 TAT
1075006 TAAAATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATATTTTAAATATATT
Found at i:1075203 original size:16 final size:16
Alignment explanation
Indices: 1075182--1075214 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1075172 TAAATAAAAA
1075182 AATAATAATATTAATT
1 AATAATAATATTAATT
1075198 AATAATAATATTAATT
1 AATAATAATATTAATT
1075214 A
1 A
1075215 TATTATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATAATATTAATT
Found at i:1075742 original size:19 final size:20
Alignment explanation
Indices: 1075677--1075742 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 20
1075667 CTAAACATTT
1075677 ATTTTTATTGTAATTAAA-AATA
1 ATTTTTATT-T-A-TAAATAATA
* *
1075699 TTTTTTATTTATAATTAATA
1 ATTTTTATTTATAAATAATA
1075719 A-TTTTA-TTATAAATAATA
1 ATTTTTATTTATAAATAATA
1075737 ATTTTT
1 ATTTTT
1075743 TAAAAAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 12 0.32
19 12 0.32
20 5 0.13
21 1 0.03
22 8 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
ATTTTTATTTATAAATAATA
Found at i:1075746 original size:15 final size:16
Alignment explanation
Indices: 1075706--1075754 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 16
1075696 ATATTTTTTA
*
1075706 TTTATAATTAATAATTT
1 TTTATAAATAATAA-TT
1075723 TATTATAAATAATAATT
1 T-TTATAAATAATAATT
1075740 TTT-TAAA-AA-AATT
1 TTTATAAATAATAATT
1075753 TT
1 TT
1075755 AATATTACTG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 6 0.20
14 2 0.07
15 4 0.13
16 2 0.07
17 4 0.13
18 12 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTATAAATAATAATT
Found at i:1076362 original size:20 final size:20
Alignment explanation
Indices: 1076334--1076385 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1076324 AAGTAAAAAA
1076334 ATTTATTAAAATTTTAATTT
1 ATTTATTAAAATTTTAATTT
* *
1076354 ATTTTTTAAAATTTTTA-TT
1 ATTTATTAAAATTTTAATTT
*
1076373 -TTTATAAAAATTT
1 ATTTATTAAAATTT
1076386 AATAAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 11 0.39
19 2 0.07
20 15 0.54
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTATTAAAATTTTAATTT
Found at i:1081006 original size:16 final size:15
Alignment explanation
Indices: 1080987--1081022 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1080977 ATTTAATTTA
1080987 TTTAATTTTTAATAAT
1 TTTAATTTTTAA-AAT
*
1081003 TTTATTTTTTAAAAT
1 TTTAATTTTTAAAAT
1081018 TTTAA
1 TTTAA
1081023 AATATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTAATTTTTAAAAT
Found at i:1081558 original size:19 final size:20
Alignment explanation
Indices: 1081534--1081611 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 20
1081524 AGGCACAAAT
1081534 ATAATAAAAATAT-TAAAAC
1 ATAATAAAAATATATAAAAC
*
1081553 ATAATAAAAATATATATAAC
1 ATAATAAAAATATATAAAAC
1081573 ATAACATCAAAAATA-ATAAAA-
1 AT-A-AT-AAAAATATATAAAAC
1081594 AT-ATAATATAATATATAA
1 ATAATAA-A-AATATATAA
1081612 TTATATTAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
17 2 0.04
18 3 0.06
19 17 0.34
20 11 0.22
21 3 0.06
22 7 0.14
23 7 0.14
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
ATAATAAAAATATATAAAAC
Found at i:1081599 original size:8 final size:9
Alignment explanation
Indices: 1081534--1081596 Score: 54
Period size: 9 Copynumber: 6.3 Consensus size: 9
1081524 AGGCACAAAT
1081534 ATAATAAAA
1 ATAATAAAA
*
1081543 ATATTAAAA
1 ATAATAAAA
1081552 CATAATAAAA
1 -ATAATAAAA
*
1081562 ATATATATAAC
1 ATA-ATA-AAA
1081573 ATAACATCAAAA
1 AT-A-AT-AAAA
1081585 ATAATAAAA
1 ATAATAAAA
1081594 ATA
1 ATA
1081597 TAATATAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
9 18 0.41
10 13 0.30
11 5 0.11
12 7 0.16
13 1 0.02
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.25
Consensus pattern (9 bp):
ATAATAAAA
Found at i:1081622 original size:28 final size:28
Alignment explanation
Indices: 1081591--1081693 Score: 70
Period size: 33 Copynumber: 3.5 Consensus size: 28
1081581 AAAAATAATA
1081591 AAAATATAATATAATATATAATTATATT
1 AAAATATAATATAATATATAATTATATT
*
1081619 AAAAATCTGTATAATATAAAATTATAAATT-TATT
1 -AAAA----TATAATATAATA-TAT-AATTATATT
*
1081653 AAAAT-TTATATAAATATATAA-TAT-TT
1 AAAATATAATAT-AATATATAATTATATT
*
1081679 TAAATATAATTATAA
1 AAAATATAA-TATAA
1081694 AAATATCTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 22
0.69 0.06 0.26
Matches are distributed among these distances:
26 7 0.12
27 7 0.12
28 11 0.19
29 8 0.14
33 15 0.25
34 7 0.12
35 4 0.07
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (28 bp):
AAAATATAATATAATATATAATTATATT
Found at i:1081632 original size:33 final size:31
Alignment explanation
Indices: 1081595--1081682 Score: 87
Period size: 33 Copynumber: 2.9 Consensus size: 31
1081585 ATAATAAAAA
1081595 TATAATATAATATATAATTATATTAAAAATCT
1 TATAATATAATATATAATTATATTAAAAAT-T
*
1081627 GTATAATATAAAATTATAAATT-TATT-AAAATT
1 -TATAATATAATA-TAT-AATTATATTAAAAATT
*
1081659 TAT-ATA-AATATATAA-TATTTTAAA
1 TATAATATAATATATAATTATATTAAA
1081683 TATAATTATA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
26 1 0.02
27 5 0.10
28 5 0.10
29 3 0.06
30 3 0.06
31 3 0.06
32 1 0.02
33 16 0.33
34 7 0.15
35 4 0.08
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (31 bp):
TATAATATAATATATAATTATATTAAAAATT
Found at i:1082297 original size:15 final size:15
Alignment explanation
Indices: 1082273--1082303 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1082263 TAATAGAATA
*
1082273 TTAAATTTTTAATTT
1 TTAAAATTTTAATTT
1082288 TTAAAATTTTAATTT
1 TTAAAATTTTAATTT
1082303 T
1 T
1082304 AATTTTTATA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTAAAATTTTAATTT
Found at i:1084287 original size:28 final size:32
Alignment explanation
Indices: 1084251--1084312 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1084241 ATGTATGATT
*
1084251 AAAATT-TATTTAAT-TATT-ATTTTTTTTAA
1 AAAATTATATTTAATATATTAATTTTTATTAA
1084280 AAAATTATATTTAATATATTAATTTTTATTAA
1 AAAATTATATTTAATATATTAATTTTTATTAA
1084312 A
1 A
1084313 TTTAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 6 0.21
30 8 0.28
31 4 0.14
32 11 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
AAAATTATATTTAATATATTAATTTTTATTAA
Found at i:1084313 original size:29 final size:27
Alignment explanation
Indices: 1084248--1084316 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 27
1084238 TACATGTATG
1084248 ATTAAAATTTATTTAATTATTATTTTT
1 ATTAAAATTTATTTAATTATTATTTTT
*
1084275 TTTAAAAAATTATATTTAATATATTAATTTTT
1 ATT--AAAATT-TATTTAAT-TATT-ATTTTT
1084307 ATT-AAATTTA
1 ATTAAAATTTA
1084317 AAAATAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
27 2 0.06
28 2 0.06
29 11 0.31
30 8 0.23
31 4 0.11
32 8 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
ATTAAAATTTATTTAATTATTATTTTT
Found at i:1085598 original size:17 final size:16
Alignment explanation
Indices: 1085576--1085620 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1085566 TTTTAAAAAT
1085576 AATTTATTAAATATTTA
1 AATTTA-TAAATATTTA
1085593 AATTTA-AAATAATTTA
1 AATTTATAAAT-ATTTA
*
1085609 AAATTATAAATA
1 AATTTATAAATA
1085621 ATATATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 4 0.16
16 11 0.44
17 10 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTTATAAATATTTA
Found at i:1085621 original size:17 final size:17
Alignment explanation
Indices: 1085583--1085622 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
1085573 AATAATTTAT
*
1085583 TAAAT-ATTTAAATTTA
1 TAAATAATTTAAAATTA
1085599 -AAATAATTTAAAATTA
1 TAAATAATTTAAAATTA
1085615 TAAATAAT
1 TAAATAAT
1085623 ATATTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 10 0.48
17 7 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATAATTTAAAATTA
Found at i:1087149 original size:13 final size:14
Alignment explanation
Indices: 1087086--1087158 Score: 62
Period size: 14 Copynumber: 5.2 Consensus size: 14
1087076 ATTTAATTTT
1087086 TAATATAATTTAAAA
1 TAATA-AATTTAAAA
* *
1087101 T-ATAAAAATAAAAA
1 TAAT-AAATTTAAAA
* *
1087115 TATTTATATTTAAAA
1 TA-ATAAATTTAAAA
1087130 TAATAAATTTAAAA
1 TAATAAATTTAAAA
1087144 -AATAAA-TTAAAA
1 TAATAAATTTAAAA
1087156 TAA
1 TAA
1087159 AATAAAATAA
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
12 6 0.13
13 8 0.17
14 20 0.43
15 11 0.24
16 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAATAAATTTAAAA
Found at i:1089405 original size:2 final size:2
Alignment explanation
Indices: 1089398--1089427 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1089388 CTAGGTACTA
1089398 CT CT 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 CT CT
1089428 TGCTTGATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1089794 original size:14 final size:14
Alignment explanation
Indices: 1089752--1089797 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1089742 AATTTTTTAT
*
1089752 TATATATTTTTAAA
1 TATATATATTTAAA
1089766 TATATATATTT--A
1 TATATATATTTAAA
*
1089778 TATTTATATTTAAA
1 TATATATATTTAAA
1089792 TATATA
1 TATATA
1089798 AAAATTATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 11 0.41
14 16 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATATATATTTAAA
Found at i:1094453 original size:7 final size:7
Alignment explanation
Indices: 1094431--1094460 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
1094421 AAGTATTATT
1094431 AAATATA
1 AAATATA
1094438 AAATAATA
1 AAAT-ATA
1094446 AAATATA
1 AAATATA
1094453 AAATATA
1 AAATATA
1094460 A
1 A
1094461 TTAATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAATATA
Found at i:1094473 original size:54 final size:55
Alignment explanation
Indices: 1094432--1094556 Score: 142
Period size: 47 Copynumber: 2.4 Consensus size: 55
1094422 AGTATTATTA
1094432 AATATAAAATAATAAAATATAAAATATAATT-AATT-TTAA--TT--TATTA-TA
1 AATATAAAATAATAAAATATAAAATATAATTAAATTATTAATTTTAATATTATTA
* * *
1094480 AACAT-AAATAATAAAATAT-AAATATTATTAAATTATTAAATTTAAATTATTATTA
1 AATATAAAATAATAAAATATAAAATATAATTAAATTATT-AATTTTAA-TATTATTA
1094535 AATATAAAATAATAAAATATAA
1 AATATAAAATAATAAAATATAA
1094557 CTATTAAAAG
Statistics
Matches: 62, Mismatches: 4, Indels: 13
0.78 0.05 0.16
Matches are distributed among these distances:
46 9 0.15
47 18 0.29
48 6 0.10
49 2 0.03
51 1 0.02
54 5 0.08
55 6 0.10
56 14 0.23
57 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (55 bp):
AATATAAAATAATAAAATATAAAATATAATTAAATTATTAATTTTAATATTATTA
Found at i:1094530 original size:25 final size:24
Alignment explanation
Indices: 1094484--1094550 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
1094474 ATTATAAACA
1094484 TAAATAATAAAATATAAATATTAT
1 TAAATAATAAAATATAAATATTAT
* * *
1094508 TAAATTATTAAATTTAAATTATTAT
1 TAAATAATAAAATATAAA-TATTAT
1094533 TAAAT-ATAAAATAATAAA
1 TAAATAATAAAAT-ATAAA
1094551 ATATAACTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 21 0.58
25 15 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TAAATAATAAAATATAAATATTAT
Found at i:1094585 original size:56 final size:54
Alignment explanation
Indices: 1094430--1094587 Score: 132
Period size: 54 Copynumber: 2.9 Consensus size: 54
1094420 TAAGTATTAT
* *
1094430 TAAAT-ATAAAATAATAAA-A-TATAAAATATAATTAATTTTAAT-TTATTATAAACA
1 TAAATAATAAAAT-ATAAATATTAT-AAA-AT-ATTAAATATAATATTATTATAAACA
* * *
1094484 TAAATAATAAAATATAAATATTATTAAATTATTAAATTTAA-ATTATTATTAAATA
1 TAAATAATAAAATATAAATATTA-TAAAATATTAAATATAATATTATTA-TAAACA
*
1094539 TAAAATAATAAAATATAACTATTA-AAAGATA-TAAATAATAATATTATTA
1 T-AAATAATAAAATATAAATATTATAAA-ATATTAAAT-ATAATATTATTA
1094588 ATTATATTAT
Statistics
Matches: 88, Mismatches: 6, Indels: 18
0.79 0.05 0.16
Matches are distributed among these distances:
54 34 0.39
55 20 0.23
56 33 0.38
57 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (54 bp):
TAAATAATAAAATATAAATATTATAAAATATTAAATATAATATTATTATAAACA
Found at i:1096968 original size:20 final size:20
Alignment explanation
Indices: 1096921--1096971 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1096911 TATTTATCGA
* * *
1096921 TATAAATATATTTAAATATT
1 TATATATATATTTAAAAAAT
* *
1096941 TTTTTATATATTTAAAAAAT
1 TATATATATATTTAAAAAAT
1096961 TATATATATAT
1 TATATATATAT
1096972 ATATATCAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATATATATATTTAAAAAAT
Found at i:1096999 original size:17 final size:18
Alignment explanation
Indices: 1096968--1097005 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1096958 AATTATATAT
*
1096968 ATATATATATCAAATAAA
1 ATATATATATAAAATAAA
1096986 ATATA-ATATAAAATAAA
1 ATATATATATAAAATAAA
1097003 ATA
1 ATA
1097006 AAAAATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
ATATATATATAAAATAAA
Found at i:1098593 original size:4 final size:4
Alignment explanation
Indices: 1098566--1098615 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
1098556 ATGTATGTAT
* * * *
1098566 AGAG AGAT AGAT AGAT AGAT AGAG AGAG AGAG AGAG AGAG AGAG AGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
1098614 AG
1 AG
1098616 TTTTAGCTGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.42, T:0.08
Consensus pattern (4 bp):
AGAG
Found at i:1104955 original size:16 final size:17
Alignment explanation
Indices: 1104934--1104983 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 17
1104924 TAAATATATT
1104934 TAAATTTTATATAA-AA
1 TAAATTTTATATAATAA
*
1104950 TAAATTATTA-ATAATGA
1 TAAATT-TTATATAATAA
1104967 TAAATTTTATATGAATA
1 TAAATTTTATAT-AATA
1104984 TGTAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 13 0.46
17 12 0.43
18 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (17 bp):
TAAATTTTATATAATAA
Found at i:1105012 original size:15 final size:15
Alignment explanation
Indices: 1104994--1105036 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1104984 TGTAAAATTT
1104994 TAAAAATAAAAAATA
1 TAAAAATAAAAAATA
* *
1105009 TAAAAATATAAATTA
1 TAAAAATAAAAAATA
* *
1105024 TTAAATTAAAAAA
1 TAAAAATAAAAAA
1105037 AAAAGTTACC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAAAATAAAAAATA
Found at i:1106227 original size:21 final size:20
Alignment explanation
Indices: 1106192--1106231 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
1106182 TTTATATTCG
1106192 ATTTTTTATATTTAAATTAAT
1 ATTTTTTATATTT-AATTAAT
1106213 ATTTTTTA-ATATTAATTAA
1 ATTTTTTATAT-TTAATTAA
1106232 AAATAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTTTATATTTAATTAAT
Found at i:1108065 original size:17 final size:18
Alignment explanation
Indices: 1108028--1108074 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 18
1108018 ATATTTAATT
1108028 TAAAATTAA-TTAACATA
1 TAAAATTAATTTAACATA
1108045 -AAAATTAATTTAA-ATA
1 TAAAATTAATTTAACATA
1108061 TAAAATTATATTTA
1 TAAAATTA-ATTTA
1108075 GCGTCGTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 11 0.41
17 11 0.41
18 5 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAATTAATTTAACATA
Found at i:1109961 original size:12 final size:13
Alignment explanation
Indices: 1109940--1109971 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1109930 TTCCCCCTGT
1109940 TTCT-TCTTCTTC
1 TTCTCTCTTCTTC
1109952 TTC-CTCTTCTTC
1 TTCTCTCTTCTTC
1109964 TTCTCTCT
1 TTCTCTCT
1109972 CCAAAGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (13 bp):
TTCTCTCTTCTTC
Found at i:1111101 original size:16 final size:18
Alignment explanation
Indices: 1111070--1111103 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1111060 TTAAAATTTG
1111070 TTATATTTATATTTTTTA
1 TTATATTTATATTTTTTA
1111088 TTATA-TTA-ATTTTTTA
1 TTATATTTATATTTTTTA
1111104 AAATATATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATATTTATATTTTTTA
Found at i:1111489 original size:19 final size:19
Alignment explanation
Indices: 1111441--1111489 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
1111431 AGTATAAAAT
1111441 TAATTTAATTTATATATTTA
1 TAATTT-ATTTATATATTTA
1111461 TAATTT-TTTATATGATTTA
1 TAATTTATTTATAT-ATTTA
1111480 T-ATTTATTTA
1 TAATTTATTTA
1111490 ATCTGATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 11 0.41
19 10 0.37
20 6 0.22
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TAATTTATTTATATATTTA
Found at i:1111680 original size:23 final size:23
Alignment explanation
Indices: 1111652--1111697 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1111642 TTTAAAAACT
1111652 CACAAACATAATAAATATAATTA
1 CACAAACATAATAAATATAATTA
*
1111675 CACAAATATAATAAATATAATTA
1 CACAAACATAATAAATATAATTA
1111698 TACTATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (23 bp):
CACAAACATAATAAATATAATTA
Found at i:1112028 original size:21 final size:24
Alignment explanation
Indices: 1111982--1112032 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 24
1111972 TTAAAATTTT
1111982 ATTTAATATTATTATTATATTAAA
1 ATTTAATATTATTATTATATTAAA
1112006 ATTT-ATA-TATT-TTATAATT-AA
1 ATTTAATATTATTATTAT-ATTAAA
1112027 ATTTAA
1 ATTTAA
1112033 ATAAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 10 0.40
22 8 0.32
23 3 0.12
24 4 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTAATATTATTATTATATTAAA
Found at i:1112907 original size:14 final size:14
Alignment explanation
Indices: 1112883--1112924 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
1112873 AATGATTTAG
*
1112883 GATGAAATGAAATA
1 GATGGAATGAAATA
*
1112897 GATTGAATGAAATA
1 GATGGAATGAAATA
*
1112911 GGTGGAATGAAATA
1 GATGGAATGAAATA
1112925 ATTATTTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (14 bp):
GATGGAATGAAATA
Found at i:1116324 original size:14 final size:14
Alignment explanation
Indices: 1116305--1116344 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1116295 TGATTTTGGA
*
1116305 TGGAATGGAATGGG
1 TGGAATGGAATAGG
1116319 TGGAATGGAATAGG
1 TGGAATGGAATAGG
* *
1116333 TGAAATAGAATA
1 TGGAATGGAATA
1116345 ATTATTTTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.23
Consensus pattern (14 bp):
TGGAATGGAATAGG
Found at i:1116560 original size:28 final size:28
Alignment explanation
Indices: 1116520--1116587 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
1116510 TCATCCAAAG
* *
1116520 ATACCTTTTCATAAAAGATGGTGTTTAT
1 ATACCTTTTCATAAAAGATGATGTCTAT
1116548 ATACCTTTTCATAAAAGATGATGTCTAT
1 ATACCTTTTCATAAAAGATGATGTCTAT
*
1116576 ATACTTTTTCAT
1 ATACCTTTTCAT
1116588 CCAATGTGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.44
Consensus pattern (28 bp):
ATACCTTTTCATAAAAGATGATGTCTAT
Found at i:1116930 original size:29 final size:27
Alignment explanation
Indices: 1116872--1116932 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
1116862 AAATTTAACT
*
1116872 TATAAACTAATTTTTTTACAATTGATG
1 TATAAACTAATTTTTTTACAATTGAAG
* **
1116899 TATAAAGTAATTATTTTTTGAATTGAAAG
1 TATAAACTAATT-TTTTTACAATTG-AAG
1116928 TATAA
1 TATAA
1116933 GAATTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 11 0.39
28 10 0.36
29 7 0.25
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (27 bp):
TATAAACTAATTTTTTTACAATTGAAG
Found at i:1117568 original size:18 final size:20
Alignment explanation
Indices: 1117537--1117578 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
1117527 TAATATATTT
*
1117537 TTAAATTAAGTAAT-TTT-A
1 TTAAATAAAGTAATATTTAA
*
1117555 TTAAATAAATTAATATTTAA
1 TTAAATAAAGTAATATTTAA
1117575 TTAA
1 TTAA
1117579 TTTATAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 12 0.60
19 3 0.15
20 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAAATAAAGTAATATTTAA
Found at i:1118334 original size:21 final size:20
Alignment explanation
Indices: 1118292--1118352 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
1118282 ATTATTATTT
* *
1118292 ATTTAATAAAAAATTATTTAA
1 ATTTAATATAAAA-TATATAA
1118313 ATTTAATTATAAAATATATAA
1 ATTTAA-TATAAAATATATAA
* *
1118334 ATAATAATCTAAAATATAT
1 AT-TTAATATAAAATATAT
1118353 TTTTAATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 25 0.74
22 9 0.26
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTTAATATAAAATATATAA
Found at i:1119487 original size:16 final size:17
Alignment explanation
Indices: 1119456--1119513 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
1119446 AATAATAAAT
*
1119456 TTTTTTAGTTTATTTAA
1 TTTTTTAGTTTTTTTAA
*
1119473 TTTTTTATTTTTTTATAA
1 TTTTTTAGTTTTTT-TAA
* *
1119491 TTTTATA-TTTTTTAAA
1 TTTTTTAGTTTTTTTAA
1119507 TTATTTT
1 TT-TTTT
1119514 TTATTAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
16 4 0.12
17 21 0.62
18 9 0.26
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (17 bp):
TTTTTTAGTTTTTTTAA
Found at i:1119491 original size:18 final size:18
Alignment explanation
Indices: 1119456--1119518 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
1119446 AATAATAAAT
* *
1119456 TTTTTTAGTTTATT-TAA
1 TTTTTTATTTTTTTATAA
1119473 TTTTTTATTTTTTTATAA
1 TTTTTTATTTTTTTATAA
* * *
1119491 TTTTATATTTTTTAAATTA
1 TTTTTTATTTTTT-TATAA
1119510 TTTTTTATT
1 TTTTTTATT
1119519 AATTTTATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 12 0.32
18 15 0.39
19 11 0.29
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTTTTATTTTTTTATAA
Found at i:1119526 original size:16 final size:15
Alignment explanation
Indices: 1119475--1119528 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
1119465 TTATTTAATT
1119475 TTTTATTTTTTTATAA
1 TTTTATTTTTTT-TAA
*
1119491 TTTTATATTTTTTAA
1 TTTTATTTTTTTTAA
*
1119506 -ATTATTTTTTATTAA
1 TTTTATTTTTT-TTAA
1119521 TTTTATTT
1 TTTTATTT
1119529 GAAAATTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.25
15 7 0.22
16 17 0.53
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTATTTTTTTTAA
Found at i:1119778 original size:4 final size:4
Alignment explanation
Indices: 1119769--1119794 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1119759 TTTTATTATC
1119769 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
1119795 CAATCAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:1125743 original size:22 final size:24
Alignment explanation
Indices: 1125716--1125760 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1125706 ATGAAAAATT
1125716 AAAATA-AAA-AA-ATTAATTTTAA
1 AAAATATAAATAATATT-ATTTTAA
1125738 AAAATATAAATAATATTATTTTA
1 AAAATATAAATAATATTATTTTA
1125761 TTCATCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 8 0.40
25 3 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAAATATAAATAATATTATTTTAA
Found at i:1126527 original size:23 final size:25
Alignment explanation
Indices: 1126479--1126529 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
1126469 AAGTCGATAA
*
1126479 AAAATTTTATATTTAATAAATTATT
1 AAAATTTTATATTTAATAAATGATT
*
1126504 AAAATTTTGTA-TTAA-AAATGATT
1 AAAATTTTATATTTAATAAATGATT
1126527 AAA
1 AAA
1126530 TAAAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.42
24 4 0.17
25 10 0.42
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (25 bp):
AAAATTTTATATTTAATAAATGATT
Found at i:1129574 original size:2 final size:2
Alignment explanation
Indices: 1129567--1129594 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1129557 ATTTTTAAGG
1129567 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
1129595 ACTTAGAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1133956 original size:7 final size:6
Alignment explanation
Indices: 1133925--1133955 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
1133915 TATAAATTAA
1133925 TTAAAT TTAAAT TTAAAT TTAAAT CTTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT -TTAAAT
1133956 CAATTTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (6 bp):
TTAAAT
Found at i:1133960 original size:17 final size:16
Alignment explanation
Indices: 1133939--1133979 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1133929 ATTTAAATTT
1133939 AAATTTAAATC-TTAA
1 AAATTTAAATCATTAA
1133954 ATCAATTT-AATCATTAA
1 A--AATTTAAATCATTAA
1133971 AAATTTAAA
1 AAATTTAAA
1133980 ACTCAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
15 6 0.27
16 6 0.27
17 10 0.45
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATTTAAATCATTAA
Found at i:1135322 original size:2 final size:2
Alignment explanation
Indices: 1135315--1135351 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1135305 AAAACCCTCA
1135315 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
1135352 AGATATGAAC
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:1136100 original size:16 final size:15
Alignment explanation
Indices: 1136055--1136098 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1136045 GGACTCCGTA
1136055 TTTATATAAATTTAT
1 TTTATATAAATTTAT
*
1136070 TATAT-TAATAATTTAT
1 TTTATAT-A-AATTTAT
1136086 TTTATATAAATTT
1 TTTATATAAATTT
1136099 TAAAATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 1 0.04
15 10 0.42
16 12 0.50
17 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTATATAAATTTAT
Found at i:1136134 original size:27 final size:27
Alignment explanation
Indices: 1136095--1136147 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1136085 TTTTATATAA
1136095 ATTTTAAAATATTTATTTAT-TTGTATC
1 ATTTTAAAATATTT-TTTATATTGTATC
* *
1136122 ATTTTATATTATTTTTTATATTGTAT
1 ATTTTAAAATATTTTTTATATTGTAT
1136148 TACATAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (27 bp):
ATTTTAAAATATTTTTTATATTGTATC
Found at i:1137446 original size:22 final size:22
Alignment explanation
Indices: 1137420--1137462 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1137410 TATTTTTATT
1137420 TAAAT-TTAATTATAAAAATATA
1 TAAATATT-ATTATAAAAATATA
1137442 TAAATATTATTATAAAAATAT
1 TAAATATTATTATAAAAATAT
1137463 TTTTTTACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATATTATTATAAAAATATA
Found at i:1138794 original size:26 final size:24
Alignment explanation
Indices: 1138764--1138826 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 24
1138754 TTTTTATTTT
*
1138764 ATTAAAATATTAATATTTAATAAATA
1 ATTAAAATATTAATATATAA-AAA-A
* *
1138790 TTTAAAATTTTAAATATATAAAAAA
1 ATTAAAATATT-AATATATAAAAAA
1138815 ATTAAAA-ATTAA
1 ATTAAAATATTAA
1138827 ATAAATTCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 2 0.06
24 2 0.06
25 7 0.23
26 12 0.39
27 8 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATTAAAATATTAATATATAAAAAA
Found at i:1141523 original size:2 final size:2
Alignment explanation
Indices: 1141516--1141542 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1141506 GTCTCACTAA
1141516 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
1141543 GAGAGAGAGA
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:1143203 original size:20 final size:19
Alignment explanation
Indices: 1143154--1143203 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1143144 GTTATCGTAA
1143154 ATTTATTTAAAAATTAAATT
1 ATTT-TTTAAAAATTAAATT
* * *
1143174 ATTATGTAAAAATTTTAATT
1 ATTTTTTAAAAA-TTAAATT
1143194 ATTTTTTAAA
1 ATTTTTTAAA
1143204 GTTTAAATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
ATTTTTTAAAAATTAAATT
Found at i:1144533 original size:40 final size:39
Alignment explanation
Indices: 1144452--1144533 Score: 94
Period size: 40 Copynumber: 2.1 Consensus size: 39
1144442 GATTAAGTAC
* * *
1144452 TATATAAAAATATAATACAAATATTATATATTTAATAAA
1 TATAAAAAAATATAATACAAATATTATAAATATAATAAA
* *
1144491 TATAAAAATAATATAATATAATATATT-TAAATATAATTAA
1 TATAAAAA-AATATAATACAA-ATATTATAAATATAATAAA
1144531 TAT
1 TAT
1144534 TTAATATTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 7 0.19
40 24 0.67
41 5 0.14
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (39 bp):
TATAAAAAAATATAATACAAATATTATAAATATAATAAA
Found at i:1144535 original size:17 final size:15
Alignment explanation
Indices: 1144505--1144585 Score: 56
Period size: 17 Copynumber: 5.1 Consensus size: 15
1144495 AAAATAATAT
1144505 AATATAATATATTTA
1 AATATAATATATTTA
1144520 AATATAATTAATATTTA
1 AATATAA-T-ATATTTA
* *
1144537 ATATTTAAATGTATTT-
1 A-ATAT-AATATATTTA
* *
1144553 ATTATATACATATTTA
1 AATATA-ATATATTTA
*
1144569 AGATATAACATATTTA
1 A-ATATAATATATTTA
1144585 A
1 A
1144586 TAATTTATAT
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
14 1 0.02
15 15 0.29
16 13 0.25
17 17 0.33
18 4 0.08
19 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATAATATATTTA
Found at i:1144540 original size:24 final size:24
Alignment explanation
Indices: 1144513--1144622 Score: 75
Period size: 24 Copynumber: 4.6 Consensus size: 24
1144503 ATAATATAAT
1144513 ATATTTAAATATAATTAATATTTA
1 ATATTTAAATATAATTAATATTTA
* * * *
1144537 ATATTTAAATGTATTTATTATATA
1 ATATTTAAATATAATTAATATTTA
*
1144561 CATATTTAAGATATAA--CATATTTA
1 -ATATTTAA-ATATAATTAATATTTA
* * *
1144585 ATAATTTATAT-TATTTTATATTT-
1 AT-ATTTAAATATAATTAATATTTA
*
1144608 ATATTATTAATATAA
1 ATATT-TAAATATAA
1144623 AAATATGAGA
Statistics
Matches: 64, Mismatches: 15, Indels: 14
0.69 0.16 0.15
Matches are distributed among these distances:
22 5 0.08
23 9 0.14
24 38 0.59
25 8 0.12
26 4 0.06
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
ATATTTAAATATAATTAATATTTA
Found at i:1144646 original size:2 final size:2
Alignment explanation
Indices: 1144639--1144677 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1144629 GAGATAACAC
1144639 AT 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 AT A
1144678 CACACACACG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1145573 original size:13 final size:13
Alignment explanation
Indices: 1145555--1145623 Score: 52
Period size: 13 Copynumber: 5.1 Consensus size: 13
1145545 TTAATCAAAT
1145555 ATATTTTTATTTA
1 ATATTTTTATTTA
*
1145568 ATATTTTTAAAATTTT
1 ATATTTTT---ATTTA
*
1145584 ATATTTCT-TTTA
1 ATATTTTTATTTA
1145596 TATATTTTATATTTA
1 -ATATTTT-TATTTA
*
1145611 AT-TTTTTAATTA
1 ATATTTTTATTTA
1145623 A
1 A
1145624 AAAATCGAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
12 9 0.20
13 18 0.40
14 3 0.07
15 4 0.09
16 11 0.24
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (13 bp):
ATATTTTTATTTA
Found at i:1148370 original size:2 final size:2
Alignment explanation
Indices: 1148363--1148387 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1148353 ATAGACATGC
1148363 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
1148388 GGAGAGAGAG
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:1148394 original size:2 final size:2
Alignment explanation
Indices: 1148389--1148420 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1148379 ATATATATAG
1148389 GA GA GA 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 GA GA GA
1148421 AGCCGCTTGA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1149671 original size:22 final size:22
Alignment explanation
Indices: 1149624--1149707 Score: 75
Period size: 21 Copynumber: 4.0 Consensus size: 22
1149614 TTATGATGGA
* *
1149624 ATTTGAATT-AATT-ATAAAAA
1 ATTTAAATTAAATTAATAAAAT
* *
1149644 AATTAAATTAAATTAATAAATT
1 ATTTAAATTAAATTAATAAAAT
* *
1149666 ATTTAATTTAAA-TATTAAAAT
1 ATTTAAATTAAATTAATAAAAT
* *
1149687 ATTTAAATTTAATTCATAAAA
1 ATTTAAATTAAATTAATAAAA
1149708 AAATTTTTTG
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
20 7 0.14
21 21 0.43
22 21 0.43
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (22 bp):
ATTTAAATTAAATTAATAAAAT
Found at i:1149920 original size:8 final size:8
Alignment explanation
Indices: 1149907--1149946 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
1149897 AAATTTATCA
1149907 TATTTTTT
1 TATTTTTT
1149915 TATTTTTAAT
1 TATTTTT--T
1149925 TATTTTTT
1 TATTTTTT
*
1149933 TATTTTTA
1 TATTTTTT
1149941 TATTTT
1 TATTTT
1149947 ACGAGATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 21 0.72
10 8 0.28
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (8 bp):
TATTTTTT
Found at i:1157487 original size:2 final size:2
Alignment explanation
Indices: 1157480--1157530 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1157470 ATTATCTCAC
1157480 CT CT CT CT CT CT CT CT 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 CT CT CT CT CT CT CT CT
1157522 CT CT CT CT C
1 CT CT CT CT C
1157531 GTTTATATCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1159333 original size:22 final size:23
Alignment explanation
Indices: 1159300--1159342 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1159290 AAATGATAAA
1159300 TATTAAAATATAAATTTTAAATT
1 TATTAAAATATAAATTTTAAATT
*
1159323 TATT-AAATATAATTTTTAAA
1 TATTAAAATATAAATTTTAAA
1159343 AATAATGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTAAAATATAAATTTTAAATT
Found at i:1161132 original size:2 final size:2
Alignment explanation
Indices: 1161125--1161171 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1161115 GTTGGTTTTG
1161125 AT AT AT AT AT 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 AT AT AT AT AT
1161167 AT AT A
1 AT AT A
1161172 ATAATAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1161396 original size:26 final size:28
Alignment explanation
Indices: 1161364--1161426 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 28
1161354 AAAAATTTTG
* *
1161364 TATATTTTTTTATTT-TTTA-TATAATT
1 TATATTTTTTAATTTAATTATTATAATT
*
1161390 TATATTTATTTAATTTAATTATTATATTT
1 TATATTT-TTTAATTTAATTATTATAATT
1161419 TATATTTT
1 TATATTTT
1161427 ATTTTAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 7 0.23
27 7 0.23
28 4 0.13
29 13 0.42
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (28 bp):
TATATTTTTTAATTTAATTATTATAATT
Found at i:1161522 original size:33 final size:33
Alignment explanation
Indices: 1161463--1161565 Score: 84
Period size: 33 Copynumber: 3.0 Consensus size: 33
1161453 AATTTTGAGT
* *
1161463 AAATTAAAATTTTTAATTACTT-TATTTATTAAAA
1 AAATT-AAATTATTAAATA-TTATATTTATTAAAA
***
1161497 AAATTAAATTATTAAATATTATATTTA-TACTTT
1 AAATTAAATTATTAAATATTATATTTATTA-AAA
* *
1161530 CAATTAATATAATATAAATATTATATTTATTAAAA
1 AAATTAA-ATTAT-TAAATATTATATTTATTAAAA
1161565 A
1 A
1161566 CTTTACATGC
Statistics
Matches: 53, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
32 4 0.08
33 23 0.43
34 9 0.17
35 15 0.28
36 2 0.04
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.48
Consensus pattern (33 bp):
AAATTAAATTATTAAATATTATATTTATTAAAA
Found at i:1166349 original size:19 final size:19
Alignment explanation
Indices: 1166327--1166380 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
1166317 TTATTAAAAG
1166327 ATATTGATATATAATATTT
1 ATATTGATATATAATATTT
* *
1166346 ATATTTAAATAT-ATATTT
1 ATATTGATATATAATATTT
*
1166364 AAATATGATATA-AATAT
1 ATAT-TGATATATAATAT
1166381 ATATTTTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (19 bp):
ATATTGATATATAATATTT
Found at i:1166362 original size:12 final size:12
Alignment explanation
Indices: 1166345--1166386 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
1166335 ATATAATATT
1166345 TATATTTAAATA
1 TATATTTAAATA
1166357 TATATTTAAATA
1 TATATTTAAATA
1166369 TGATA--TAAATA
1 T-ATATTTAAATA
1166380 TATATTT
1 TATATTT
1166387 TTAAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 3 0.11
11 7 0.26
12 14 0.52
13 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (12 bp):
TATATTTAAATA
Found at i:1168803 original size:3 final size:3
Alignment explanation
Indices: 1168797--1168822 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1168787 ATATTATTGC
1168797 TGT TGT TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TG
1168823 AATTCTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (3 bp):
TGT
Found at i:1169599 original size:4 final size:4
Alignment explanation
Indices: 1169585--1169615 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
1169575 AGCCAGCCAT
1169585 ATAA ATCAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA AT-AA ATAA ATAA ATAA ATAA ATAA AT
1169616 TGTGGATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:1169720 original size:2 final size:2
Alignment explanation
Indices: 1169713--1169756 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1169703 CTGCATGGAA
1169713 AT AT AT AT AT 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 AT AT AT AT AT
1169755 AT
1 AT
1169757 TTGCTCCTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1169967 original size:26 final size:28
Alignment explanation
Indices: 1169915--1169993 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
1169905 ATATTATTAT
1169915 TAATATTTTATAATTAATTTAAATAAAAA
1 TAATATTTTAT-ATTAATTTAAATAAAAA
* *
1169944 TAATATTTTAT-TT-A-TTAAATTAAAT
1 TAATATTTTATATTAATTTAAATAAAAA
* *
1169969 TAAATTATTTTATTTTATTTTAAAT
1 T-AA-TATTTTATATTAATTTAAAT
1169994 CTAATTTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
25 10 0.24
26 3 0.07
27 10 0.24
28 2 0.05
29 11 0.26
30 6 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TAATATTTTATATTAATTTAAATAAAAA
Found at i:1169973 original size:29 final size:30
Alignment explanation
Indices: 1169915--1169983 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
1169905 ATATTATTAT
* *
1169915 TAATATTTTA-TAATTAATTTAAATAAAAA
1 TAATATTTTATTTATTAAATTAAATAAAAA
*
1169944 TAATATTTTATTTATTAAATTAAAT-TAAA
1 TAATATTTTATTTATTAAATTAAATAAAAA
1169973 T--TATTTTATTT
1 TAATATTTTATTT
1169984 TATTTTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 10 0.28
29 14 0.39
30 12 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
TAATATTTTATTTATTAAATTAAATAAAAA
Found at i:1170006 original size:21 final size:20
Alignment explanation
Indices: 1169967--1170016 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
1169957 ATTAAATTAA
* *
1169967 ATTAAATTATTTTATTTTAT
1 ATTAAATTAATTTAATTTAT
*
1169987 TTTAAATCTAATTTAATTTAT
1 ATTAAAT-TAATTTAATTTAT
1170008 ATTAAATTA
1 ATTAAATTA
1170017 TCAAATCAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTAAATTAATTTAATTTAT
Found at i:1170992 original size:34 final size:35
Alignment explanation
Indices: 1170915--1170993 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 35
1170905 GTATTAAATA
*
1170915 AAATTTTTAAAAATAATAAATAAATAATTTTTATT
1 AAATTTTTATAAATAATAAATAAATAATTTTTATT
* * * * *
1170950 -GATGTTTATAAGTATTAATTAAATAATTTTT-TT
1 AAATTTTTATAAATAATAAATAAATAATTTTTATT
1170983 AAATTTTTATA
1 AAATTTTTATA
1170994 TATTTAAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
33 2 0.06
34 33 0.94
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (35 bp):
AAATTTTTATAAATAATAAATAAATAATTTTTATT
Found at i:1171035 original size:11 final size:11
Alignment explanation
Indices: 1171008--1171041 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1170998 TAAAAAATTA
*
1171008 TATATTTATATT
1 TATATTTA-AAT
1171020 TATATTTAAAT
1 TATATTTAAAT
1171031 TATATTTAAAT
1 TATATTTAAAT
1171042 ATAAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TATATTTAAAT
Found at i:1171046 original size:17 final size:17
Alignment explanation
Indices: 1171013--1171055 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1171003 AATTATATAT
* *
1171013 TTATATTTATATTTAAA
1 TTATATTTAAATATAAA
1171030 TTATATTTAAATATAAA
1 TTATATTTAAATATAAA
1171047 -TAT-TTTAAA
1 TTATATTTAAA
1171056 AAATAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 6 0.25
16 3 0.12
17 15 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATATTTAAATATAAA
Found at i:1175994 original size:22 final size:19
Alignment explanation
Indices: 1175966--1176007 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
1175956 ATCAATTGAT
1175966 TATTTAAATAATATTTTATATA
1 TATTTAAAT--TATTTTA-ATA
1175988 TATTTAAATTATTTTAATA
1 TATTTAAATTATTTTAATA
1176007 T
1 T
1176008 TAAATAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 7 0.35
22 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTAAATTATTTTAATA
Found at i:1179247 original size:30 final size:29
Alignment explanation
Indices: 1179213--1179307 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 29
1179203 ATTTGCATAT
1179213 AAATAAGATTTTAATTTTTAATTTATAAAC
1 AAATAA-ATTTTAATTTTTAATTTATAAAC
* * * * *
1179243 AAATAAACTCTTAATATTTATTTTATACAT
1 AAATAAA-TTTTAATTTTTAATTTATAAAC
* * *
1179273 AAATTAATTTTAATTTTTTATTT-TATAC
1 AAATAAATTTTAATTTTTAATTTATAAAC
1179301 AAATAAA
1 AAATAAA
1179308 AATATAAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
28 9 0.18
29 13 0.25
30 29 0.57
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.48
Consensus pattern (29 bp):
AAATAAATTTTAATTTTTAATTTATAAAC
Found at i:1179417 original size:15 final size:15
Alignment explanation
Indices: 1179397--1179434 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1179387 TTTATTCTCT
1179397 AATAATAATGT-ATAA
1 AATAATAAT-TCATAA
1179412 AATAATAATTCATAA
1 AATAATAATTCATAA
*
1179427 AAGAATAA
1 AATAATAA
1179435 AGGCTTCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (15 bp):
AATAATAATTCATAA
Found at i:1179754 original size:21 final size:24
Alignment explanation
Indices: 1179730--1179804 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 24
1179720 AATACGCCAC
1179730 TAATTATA-A-ATAA-AAATAAAA
1 TAATTATAGATATAATAAATAAAA
*
1179751 TAATTTTAGATATAATAAATAAAA
1 TAATTATAGATATAATAAATAAAA
* *
1179775 AAAGTAATAAGATATAATATAA-AAAA
1 TAA-TTAT-AGATATAATA-AATAAAA
1179801 TAAT
1 TAAT
1179805 ATAAAAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.16
22 1 0.02
23 4 0.09
24 10 0.23
25 3 0.07
26 16 0.37
27 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (24 bp):
TAATTATAGATATAATAAATAAAA
Found at i:1179796 original size:12 final size:12
Alignment explanation
Indices: 1179788--1179813 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1179778 GTAATAAGAT
1179788 ATAATATAAAAA
1 ATAATATAAAAA
1179800 ATAATATAAAAA
1 ATAATATAAAAA
1179812 AT
1 AT
1179814 TTAAAATTTA
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
ATAATATAAAAA
Found at i:1180333 original size:10 final size:10
Alignment explanation
Indices: 1180312--1180348 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1180302 TAGTGATTCG
1180312 TATTAA-TTA
1 TATTAATTTA
1180321 TATTAATTTA
1 TATTAATTTA
1180331 TA-TAATTTTA
1 TATTAA-TTTA
1180341 TATTAATT
1 TATTAATT
1180349 ATTATTGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.36
10 13 0.52
11 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TATTAATTTA
Found at i:1180553 original size:15 final size:15
Alignment explanation
Indices: 1180511--1180561 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 15
1180501 TTTTATATGG
1180511 TATTAAAAATTT-TAAA
1 TATT-AAAATTTAT-AA
1180527 TATTAAATATTTATAA
1 TATTAAA-ATTTATAA
*
1180543 TTTTAAAATTTATATA
1 TATTAAAATTTATA-A
1180559 TAT
1 TAT
1180562 GTATATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 10 0.33
16 19 0.63
17 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATTAAAATTTATAA
Found at i:1185969 original size:20 final size:20
Alignment explanation
Indices: 1185926--1185983 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
1185916 GATACATTGA
* * * *
1185926 AATGTATCCATACATGTATG
1 AATGTATCGATACATTTTTC
1185946 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* *
1185966 AATGGATCGATATATTTT
1 AATGTATCGATACATTTT
1185984 GACTTTTTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:1194907 original size:20 final size:19
Alignment explanation
Indices: 1194865--1194907 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
1194855 TAGAACCAAA
**
1194865 AAATTTTTTTGACTCTACT
1 AAATTTTTTTGACTCTAAG
*
1194884 AAATTATTTTTGACTTTAAG
1 AAATT-TTTTTGACTCTAAG
1194904 AAAT
1 AAAT
1194908 ATATAAATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (19 bp):
AAATTTTTTTGACTCTAAG
Found at i:1195322 original size:30 final size:28
Alignment explanation
Indices: 1195288--1195380 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 28
1195278 TATTACATCC
1195288 AATAAATTATTAACTTTTAATTTACACTTA
1 AATAAATTATTAA-TTTTAATTTACAC-TA
1195318 AATAAGATT-TTAATTTTTAAATTGTACAC-A
1 AATAA-ATTATTAA-TTTT-AATT-TACACTA
*
1195348 AATAAATTATTAATATTTAATTTATACATA
1 AATAAATTATTAAT-TTTAATTTACAC-TA
1195378 AAT
1 AAT
1195381 TAACTTTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
28 4 0.07
29 8 0.15
30 30 0.56
31 7 0.13
32 5 0.09
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.45
Consensus pattern (28 bp):
AATAAATTATTAATTTTAATTTACACTA
Found at i:1196520 original size:52 final size:51
Alignment explanation
Indices: 1196441--1196543 Score: 152
Period size: 52 Copynumber: 2.0 Consensus size: 51
1196431 GGTATATCAG
* *
1196441 CCTAACAATATTAATACGCCATCAATCATAAATAAAGATAAGGTAATTTTA
1 CCTAACAATATTAATACGCCACCAATCATAAATAAAGATAAGATAATTTTA
* * *
1196492 CCTAACAATATTTAATAGGCCACCAATCATAAATAAAGGTACGATAATTTTA
1 CCTAACAATA-TTAATACGCCACCAATCATAAATAAAGATAAGATAATTTTA
1196544 GTTATGGTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 10 0.22
52 36 0.78
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.29
Consensus pattern (51 bp):
CCTAACAATATTAATACGCCACCAATCATAAATAAAGATAAGATAATTTTA
Found at i:1196613 original size:24 final size:24
Alignment explanation
Indices: 1196584--1196680 Score: 85
Period size: 24 Copynumber: 4.1 Consensus size: 24
1196574 ATGATATTAA
*
1196584 AAATAATATGAATAAAATATATAT
1 AAATAATATGATTAAAATATATAT
* *
1196608 AAATAAATAT-ATTAAAATTTAAAT
1 AAAT-AATATGATTAAAATATATAT
* *
1196632 AATATAA-ATTATTAATATATATAT
1 AA-ATAATATGATTAAAATATATAT
*
1196656 ATATAATATG-TT-AAATATAATAT
1 AAATAATATGATTAAAATAT-ATAT
1196679 AA
1 AA
1196681 TTATGATATA
Statistics
Matches: 58, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
22 5 0.09
23 13 0.22
24 33 0.57
25 7 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (24 bp):
AAATAATATGATTAAAATATATAT
Found at i:1196649 original size:13 final size:15
Alignment explanation
Indices: 1196586--1196715 Score: 73
Period size: 14 Copynumber: 9.2 Consensus size: 15
1196576 GATATTAAAA
* *
1196586 ATAATATGAATA-AA
1 ATAATATAAATATAT
*
1196600 ATATATATAAATAAAT
1 ATA-ATATAAATATAT
* * *
1196616 ATATTA-AAATTTAA
1 ATAATATAAATATAT
1196630 ATAATATAAAT-TAT
1 ATAATATAAATATAT
*
1196644 -TAATATATATATAT
1 ATAATATAAATATAT
** *
1196658 ATAATAT-GTTAAAT
1 ATAATATAAATATAT
1196672 ATAATAT-AAT-TAT
1 ATAATATAAATATAT
1196685 GAT-ATATAAA-A-AT
1 -ATAATATAAATATAT
*
1196698 ATAATATATATATAT
1 ATAATATAAATATAT
1196713 ATA
1 ATA
1196716 CTTAATACTA
Statistics
Matches: 89, Mismatches: 16, Indels: 21
0.71 0.13 0.17
Matches are distributed among these distances:
12 2 0.02
13 23 0.26
14 35 0.39
15 25 0.28
16 4 0.04
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
ATAATATAAATATAT
Found at i:1196653 original size:2 final size:2
Alignment explanation
Indices: 1196646--1196715 Score: 53
Period size: 2 Copynumber: 37.5 Consensus size: 2
1196636 TAAATTATTA
* *
1196646 AT AT AT AT AT AT AT A- AT AT GT -T AA AT AT A- AT AT A- AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1196683 AT GAT AT AT AA AA AT AT A- 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
1196716 CTTAATACTA
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
1 6 0.11
2 48 0.86
3 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1197207 original size:10 final size:10
Alignment explanation
Indices: 1197175--1197237 Score: 55
Period size: 10 Copynumber: 6.7 Consensus size: 10
1197165 GTATTAATAG
1197175 TATATTATTT
1 TATATTATTT
1197185 TA-A-T-TTT
1 TATATTATTT
*
1197192 TGTATTATTT
1 TATATTATTT
*
1197202 TATATTA-AT
1 TATATTATTT
*
1197211 TATATTAATT
1 TATATTATTT
1197221 TATATCT-TTT
1 TATAT-TATTT
1197231 TATATTA
1 TATATTA
1197238 ATCATATTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
7 4 0.10
8 2 0.05
9 11 0.26
10 24 0.57
11 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (10 bp):
TATATTATTT
Found at i:1197215 original size:9 final size:9
Alignment explanation
Indices: 1197201--1197248 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
1197191 TTGTATTATT
1197201 TTATATTAA
1 TTATATTAA
1197210 TTATATTAA
1 TTATATTAA
**
1197219 TTTATATCTTT
1 -TTATAT-TAA
1197230 TTATATTAA
1 TTATATTAA
*
1197239 TCATATTAA
1 TTATATTAA
1197248 T
1 T
1197249 CGATATTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 19 0.59
10 12 0.38
11 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (9 bp):
TTATATTAA
Found at i:1197233 original size:20 final size:19
Alignment explanation
Indices: 1197175--1197239 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
1197165 GTATTAATAG
*
1197175 TATATT-ATTT-TAATTTT
1 TATATTAATTTATATTTTT
* * **
1197192 TGTATTATTTTATATTAAT
1 TATATTAATTTATATTTTT
1197211 TATATTAATTTATATCTTTT
1 TATATTAATTTATAT-TTTT
1197231 TATATTAAT
1 TATATTAAT
1197240 CATATTAATC
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
17 5 0.14
18 3 0.08
19 17 0.47
20 11 0.31
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
TATATTAATTTATATTTTT
Found at i:1197254 original size:29 final size:29
Alignment explanation
Indices: 1197199--1197254 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1197189 TTTTGTATTA
* **
1197199 TTTTATATTAATTATATTAATTTATATCT
1 TTTTATATTAATCATATTAATCGATATCT
1197228 TTTTATATTAATCATATTAATCGATAT
1 TTTTATATTAATCATATTAATCGATAT
1197255 TTTATATTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (29 bp):
TTTTATATTAATCATATTAATCGATATCT
Found at i:1197324 original size:22 final size:21
Alignment explanation
Indices: 1197282--1197325 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1197272 GAGATTTTAT
** *
1197282 TTTTTATTTTTTTCTTGATTA
1 TTTTTATTTTTTTAATAATTA
1197303 TTTTTACTTTTTTTAATAATTA
1 TTTTTA-TTTTTTTAATAATTA
1197325 T
1 T
1197326 ATTAAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTTATTTTTTTAATAATTA
Done.