Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 10 of 345
Found at i:3276235 original size:38 final size:38
Alignment explanation
Indices: 3276111--3276227 Score: 102
Period size: 37 Copynumber: 3.1 Consensus size: 38
3276101 ATAATTAATA
*
3276111 AATATATAATACAAGTAAAATATAATAATA-AT-ATAAAAAT
1 AATATATAATA-AA-TAATA-ATAATAATATATGA-AAAAAT
* * *
3276151 AATGATGT-A-AAATAATAATAATAATTTGTGAAAAAAT
1 AAT-ATATAATAAATAATAATAATAATATATGAAAAAAT
3276188 AATATATAATAAATAATAATAAT-ATATAT-AATAAAAT
1 AATATATAATAAATAATAATAATAATATATGAA-AAAAT
3276225 AAT
1 AAT
3276228 CTTATAATGT
Statistics
Matches: 64, Mismatches: 7, Indels: 15
0.74 0.08 0.17
Matches are distributed among these distances:
36 13 0.20
37 27 0.42
38 16 0.25
39 1 0.02
40 4 0.06
41 3 0.05
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (38 bp):
AATATATAATAAATAATAATAATAATATATGAAAAAAT
Found at i:3278864 original size:30 final size:30
Alignment explanation
Indices: 3278830--3278905 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
3278820 AGTATATTTT
3278830 ATTTTTTTATTTAAAAAAATAAAAAAATT-A
1 ATTTTTTTATTTAAAAAAA-AAAAAAATTAA
* * * *
3278860 ATTTTTATATGTTAAATAAAAAATAATTTAA
1 ATTTTTTTAT-TTAAAAAAAAAAAAAATTAA
3278891 ATTTTTTTA-TTAAAA
1 ATTTTTTTATTTAAAA
3278906 TATTTATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 5 0.13
30 16 0.42
31 17 0.45
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (30 bp):
ATTTTTTTATTTAAAAAAAAAAAAAATTAA
Found at i:3284623 original size:21 final size:22
Alignment explanation
Indices: 3284594--3284640 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3284584 CAGAAGGAGT
*
3284594 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
3284616 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
3284637 GAGT
1 GAGT
3284641 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:3291325 original size:30 final size:29
Alignment explanation
Indices: 3291291--3291360 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
3291281 TTATTAAACC
* *
3291291 CTTCAAAATTTTTAAAATTCTCATTAGATT
1 CTTCAAAATTTTTAAAATT-TAATTAAATT
** *
3291321 CTTCAATTTTTTTTAAATTTAATTAAATT
1 CTTCAAAATTTTTAAAATTTAATTAAATT
*
3291350 ATTCAAAATTT
1 CTTCAAAATTT
3291361 AGTGTCAATA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.51
Consensus pattern (29 bp):
CTTCAAAATTTTTAAAATTTAATTAAATT
Found at i:3294790 original size:18 final size:19
Alignment explanation
Indices: 3294767--3294813 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
3294757 ATTTCGTTTG
3294767 ATATTAATTGAATA-TAAT
1 ATATTAATTGAATAGTAAT
**
3294785 ATATTAATTTTATAGTTAAT
1 ATATTAATTGAATAG-TAAT
3294805 ATATTAATT
1 ATATTAATT
3294814 TTCCTTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 12 0.48
20 13 0.52
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (19 bp):
ATATTAATTGAATAGTAAT
Found at i:3295622 original size:30 final size:31
Alignment explanation
Indices: 3295587--3295646 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
3295577 TTTTAGGGAT
3295587 AAATAT-CAAAATTATACATGAATTTTGATC
1 AAATATGCAAAATTATACATGAATTTTGATC
* * *
3295617 AAATATGTAATATTATACATTAATTTTGAT
1 AAATATGCAAAATTATACATGAATTTTGAT
3295647 TTTATACAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.42
Consensus pattern (31 bp):
AAATATGCAAAATTATACATGAATTTTGATC
Found at i:3298375 original size:23 final size:23
Alignment explanation
Indices: 3298349--3298393 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
3298339 TCTATTTATA
* *
3298349 GTAACAAATCTTAATTTTAATTT
1 GTAACAAACCTTAATATTAATTT
**
3298372 GTAAGTAACCTTAATATTAATT
1 GTAACAAACCTTAATATTAATT
3298394 AAATGATAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (23 bp):
GTAACAAACCTTAATATTAATTT
Found at i:3302078 original size:30 final size:30
Alignment explanation
Indices: 3302044--3302103 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
3302034 TATTTTATTA
3302044 TTAATTTTGTTATTATTTTAAAGGTATTTG
1 TTAATTTTGTTATTATTTTAAAGGTATTTG
3302074 TTAATTTTGTTATTATTTTAAAGGTATTTG
1 TTAATTTTGTTATTATTTTAAAGGTATTTG
3302104 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.00, G:0.13, T:0.60
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGTATTTG
Found at i:3303546 original size:12 final size:12
Alignment explanation
Indices: 3303529--3303553 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3303519 ATGAATTGGT
3303529 ACCTCAATATTG
1 ACCTCAATATTG
3303541 ACCTCAATATTG
1 ACCTCAATATTG
3303553 A
1 A
3303554 AAAAGAAAAC
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:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (12 bp):
ACCTCAATATTG
Found at i:3307285 original size:6 final size:6
Alignment explanation
Indices: 3307274--3307300 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3307264 TATATAATAA
3307274 ATATAG ATATAG ATATAG ATATAG ATA
1 ATATAG ATATAG ATATAG ATATAG ATA
3307301 GGCTACCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (6 bp):
ATATAG
Found at i:3307423 original size:6 final size:6
Alignment explanation
Indices: 3307414--3307441 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3307404 ATCTATATTT
3307414 ATATAC ATATAC ATATAC ATATAC ATAT
1 ATATAC ATATAC ATATAC ATATAC ATAT
3307442 TTTAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATAC
Found at i:3314606 original size:18 final size:18
Alignment explanation
Indices: 3314580--3314614 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3314570 TCGGATCACC
*
3314580 TTTGTTTTAATAAAACGT
1 TTTGGTTTAATAAAACGT
*
3314598 TTTGGTTTACTAAAACG
1 TTTGGTTTAATAAAACG
3314615 ACATTTTGGT
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:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (18 bp):
TTTGGTTTAATAAAACGT
Found at i:3316169 original size:31 final size:28
Alignment explanation
Indices: 3316100--3316162 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
3316090 ATATATATGC
*
3316100 ATATATATAGAA-GTTTTAAAATAAAAA
1 ATATATATAAAATGTTTTAAAATAAAAA
**
3316127 ATATATA-AAAATGTTTTAAAATAAGTA
1 ATATATATAAAATGTTTTAAAATAAAAA
3316154 ATATATATA
1 ATATATATA
3316163 GTAAAATCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 3 0.10
27 27 0.87
28 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (28 bp):
ATATATATAAAATGTTTTAAAATAAAAA
Found at i:3321157 original size:30 final size:30
Alignment explanation
Indices: 3321119--3321215 Score: 133
Period size: 30 Copynumber: 3.2 Consensus size: 30
3321109 ATAGTAATTG
* *
3321119 GCAGCCATCACATCCTGTCGCACACAATC-
1 GCAGCCATCGCATCCTGTCGCACGCAATCA
* *
3321148 GCTAGCCATCGTATCCTGTCACACGCAATCA
1 GC-AGCCATCGCATCCTGTCGCACGCAATCA
*
3321179 GCAACCATCGCATCCTGTCGCACGCAATCA
1 GCAGCCATCGCATCCTGTCGCACGCAATCA
3321209 GCAGCCA
1 GCAGCCA
3321216 CCATATCCAA
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
29 2 0.03
30 54 0.93
31 2 0.03
ACGTcount: A:0.27, C:0.39, G:0.16, T:0.18
Consensus pattern (30 bp):
GCAGCCATCGCATCCTGTCGCACGCAATCA
Found at i:3321230 original size:30 final size:30
Alignment explanation
Indices: 3321169--3321231 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
3321159 TATCCTGTCA
* * **
3321169 CACGCAATCAGCAACCATCGCATCCTGTCG
1 CACGCAATCAGCAACCACCACATCCAATCG
* *
3321199 CACGCAATCAGCAGCCACCATATCCAATCG
1 CACGCAATCAGCAACCACCACATCCAATCG
3321229 CAC
1 CAC
3321232 CCTGTGCGCC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.41, G:0.14, T:0.14
Consensus pattern (30 bp):
CACGCAATCAGCAACCACCACATCCAATCG
Found at i:3321750 original size:71 final size:72
Alignment explanation
Indices: 3321601--3321743 Score: 207
Period size: 71 Copynumber: 2.0 Consensus size: 72
3321591 TGTGATGGCG
* * * * * *
3321601 GAATATGCCAGTAGCATGTTTTTAATCTGTTAAAGTATATGTGCAATTAGCATGTTCTGATCTGT
1 GAATATGCCAATAGCATGTTTTTAACCTGTTAAACTATATGTGCAACTAGCATGTTCTAATCTAT
3321666 TTTATCT
66 TTTATCT
* *
3321673 GAATATGCCAATAGCAT-TTTTTTACCTGTTAAACTATATGTGCAACTAGTATGTTCTAATCTAT
1 GAATATGCCAATAGCATGTTTTTAACCTGTTAAACTATATGTGCAACTAGCATGTTCTAATCTAT
3321737 TTTATCT
66 TTTATCT
3321744 ATATATGGGC
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
71 47 0.75
72 16 0.25
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (72 bp):
GAATATGCCAATAGCATGTTTTTAACCTGTTAAACTATATGTGCAACTAGCATGTTCTAATCTAT
TTTATCT
Found at i:3326230 original size:18 final size:18
Alignment explanation
Indices: 3326204--3326238 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3326194 TCGGATTACC
*
3326204 TTTATTTTAATAAAACGT
1 TTTAGTTTAATAAAACGT
*
3326222 TTTAGTTTATTAAAACG
1 TTTAGTTTAATAAAACG
3326239 GTGTTTTTGG
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:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (18 bp):
TTTAGTTTAATAAAACGT
Found at i:3326950 original size:16 final size:16
Alignment explanation
Indices: 3326926--3326968 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
3326916 TTTGGGCTGG
*
3326926 TTTAGTTTGTATGGGT
1 TTTAATTTGTATGGGT
* *
3326942 TTTAATTTGTTTTGGT
1 TTTAATTTGTATGGGT
*
3326958 TTTAATCTGTA
1 TTTAATTTGTA
3326969 ATGGACTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.16, C:0.02, G:0.21, T:0.60
Consensus pattern (16 bp):
TTTAATTTGTATGGGT
Found at i:3332015 original size:44 final size:45
Alignment explanation
Indices: 3331929--3332015 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 45
3331919 TATCGCACAG
* * *
3331929 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCTGGTGAGA
1 TACTATTCGGGCCTTCGAGCCTAGCAGGCGATAATGCCGGTGAGA
3331974 TACTATTCGGG-CTTCGAGCCTAGCAGGCGA-AATGCCCGGTGA
1 TACTATTCGGGCCTTCGAGCCTAGCAGGCGATAATG-CCGGTGA
3332016 ATGAATTCAG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 4 0.11
44 23 0.61
45 11 0.29
ACGTcount: A:0.22, C:0.23, G:0.30, T:0.25
Consensus pattern (45 bp):
TACTATTCGGGCCTTCGAGCCTAGCAGGCGATAATGCCGGTGAGA
Found at i:3334076 original size:26 final size:23
Alignment explanation
Indices: 3333931--3334060 Score: 111
Period size: 23 Copynumber: 5.5 Consensus size: 23
3333921 ATCAGGTAGT
*
3333931 TCACAAAGAACCATATCGGGAAGC
1 TCACAAAGAGCC-TATCGGGAAGC
3333955 TCACAAAGAGCCTATCGGGAAGC
1 TCACAAAGAGCCTATCGGGAAGC
** * * *
3333978 TC-CGGATAGCCATATATCAGGAAGT
1 TCACAAAGAGCC---TATCGGGAAGC
**
3334003 TCA-AGCGAGCACTATCGGGAAGC
1 TCACAAAGAGC-CTATCGGGAAGC
*
3334026 TCACAAAGAGCCTATCGGAAAGC
1 TCACAAAGAGCCTATCGGGAAGC
*
3334049 TCACGAAGAGCC
1 TCACAAAGAGCC
3334061 ATATATCGGG
Statistics
Matches: 85, Mismatches: 15, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
22 6 0.07
23 47 0.55
24 16 0.19
25 15 0.18
26 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.15
Consensus pattern (23 bp):
TCACAAAGAGCCTATCGGGAAGC
Found at i:3336221 original size:20 final size:21
Alignment explanation
Indices: 3336168--3336243 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 21
3336158 CTAAATAATT
* *
3336168 AATAATTAAATA-ATAA-TAA
1 AATAATAAAATATCTAATTAA
*
3336187 AATAATAAAATATCTTATTAA
1 AATAATAAAATATCTAATTAA
*
3336208 AATAAT-ATATATCTAATTAAA
1 AATAATAAAATATCTAATT-AA
*
3336229 TAATCATAAAATATC
1 -AATAATAAAATATC
3336244 ATCAACATCA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 11 0.24
20 12 0.27
21 11 0.24
22 5 0.11
23 6 0.13
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (21 bp):
AATAATAAAATATCTAATTAA
Found at i:3338003 original size:21 final size:19
Alignment explanation
Indices: 3337966--3338029 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 19
3337956 TTTTCTTAAA
*
3337966 AATTAATTTTG-GAAAATCT
1 AATTATTTTTGAGAAAAT-T
3337985 CAATTATTTTTGAGAAAATT
1 -AATTATTTTTGAGAAAATT
*
3338005 AATTTTGATTTTGAGAAAATT
1 AATTAT--TTTTGAGAAAATT
3338026 AATT
1 AATT
3338030 TTGATCAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
19 5 0.13
20 11 0.28
21 23 0.59
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.45
Consensus pattern (19 bp):
AATTATTTTTGAGAAAATT
Found at i:3338030 original size:21 final size:21
Alignment explanation
Indices: 3337992--3338034 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3337982 TCTCAATTAT
3337992 TTTTGAGAAAATTAATTTTGA
1 TTTTGAGAAAATTAATTTTGA
3338013 TTTTGAGAAAATTAATTTTGA
1 TTTTGAGAAAATTAATTTTGA
3338034 T
1 T
3338035 CAAGTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (21 bp):
TTTTGAGAAAATTAATTTTGA
Found at i:3338679 original size:17 final size:17
Alignment explanation
Indices: 3338657--3338693 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3338647 ATCTAATACT
3338657 TATCAAGATAAGTATTA
1 TATCAAGATAAGTATTA
3338674 TATCAAGATAAGTATTA
1 TATCAAGATAAGTATTA
3338691 TAT
1 TAT
3338694 TAATTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (17 bp):
TATCAAGATAAGTATTA
Found at i:3339918 original size:18 final size:17
Alignment explanation
Indices: 3339883--3339915 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3339873 CTTTTTATTC
3339883 TTTTATTATTTCATTTA
1 TTTTATTATTTCATTTA
3339900 TTTTACTTATTT-ATTT
1 TTTTA-TTATTTCATTT
3339916 TATCATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTATTTCATTTA
Found at i:3342993 original size:13 final size:13
Alignment explanation
Indices: 3342947--3343005 Score: 63
Period size: 13 Copynumber: 4.6 Consensus size: 13
3342937 AATGTGTATG
3342947 TATTATATATAT-
1 TATTATATATATA
3342959 T-TT-TA-ATACTA
1 TATTATATATA-TA
3342970 TATTATGTATATATA
1 TATTA--TATATATA
3342985 TATTATATATATA
1 TATTATATATATA
3342998 TATTATAT
1 TATTATAT
3343006 TTTTATGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
9 3 0.08
10 3 0.08
11 3 0.08
12 3 0.08
13 16 0.40
15 9 0.22
16 3 0.08
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (13 bp):
TATTATATATATA
Found at i:3343022 original size:13 final size:12
Alignment explanation
Indices: 3342947--3343022 Score: 50
Period size: 13 Copynumber: 6.1 Consensus size: 12
3342937 AATGTGTATG
3342947 TATTATATATATT
1 TATTATATAT-TT
*
3342960 T-TTAATACTATAT
1 TATT-ATA-TATTT
*
3342973 TATGTATATA-TA
1 TAT-TATATATTT
*
3342985 TATTATATATATA
1 TATTATATAT-TT
3342998 TATTATAT-TTT
1 TATTATATATTT
3343009 TATGTATATATTT
1 TAT-TATATATTT
3343022 T
1 T
3343023 TAATATCACA
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
11 10 0.20
12 11 0.22
13 22 0.43
14 7 0.14
15 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (12 bp):
TATTATATATTT
Found at i:3343494 original size:21 final size:21
Alignment explanation
Indices: 3343470--3343513 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3343460 TATGTTTTAC
3343470 TATAAATCACGTTATTTTTCT
1 TATAAATCACGTTATTTTTCT
3343491 TATAAATCACGTTATTTTTCT
1 TATAAATCACGTTATTTTTCT
3343512 TA
1 TA
3343514 CTCAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.52
Consensus pattern (21 bp):
TATAAATCACGTTATTTTTCT
Found at i:3346540 original size:5 final size:5
Alignment explanation
Indices: 3346530--3346560 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
3346520 TTGTGTGTTC
3346530 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T
3346561 ACAAATTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:3350971 original size:5 final size:5
Alignment explanation
Indices: 3350961--3350988 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3350951 TTGTGTGTTC
3350961 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
3350989 TACAAATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:3356757 original size:15 final size:15
Alignment explanation
Indices: 3356737--3356765 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3356727 ATGTAATGTT
3356737 ATTATTATTATTACC
1 ATTATTATTATTACC
3356752 ATTATTATTATTAC
1 ATTATTATTATTAC
3356766 TAATATGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATTATTATTACC
Found at i:3361463 original size:21 final size:20
Alignment explanation
Indices: 3361437--3361483 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 20
3361427 ATTTATCAAA
3361437 GTCTTTTTCTCTGTCTTTTTT
1 GTCTTTTT-TCTGTCTTTTTT
3361458 GTC-TTTTTCTGTCTTTTTT
1 GTCTTTTTTCTGTCTTTTTT
3361477 GT-TTTTT
1 GTCTTTTT
3361484 ATTTTTCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 18 0.72
20 4 0.16
21 3 0.12
ACGTcount: A:0.00, C:0.15, G:0.11, T:0.74
Consensus pattern (20 bp):
GTCTTTTTTCTGTCTTTTTT
Found at i:3361470 original size:10 final size:9
Alignment explanation
Indices: 3361448--3361483 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
3361438 TCTTTTTCTC
3361448 TGTCTTTTT
1 TGTCTTTTT
3361457 TGTCTTTTT
1 TGTCTTTTT
3361466 CTGTCTTTTT
1 -TGTCTTTTT
3361476 TGT-TTTTT
1 TGTCTTTTT
3361484 ATTTTTCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 5 0.19
9 12 0.46
10 9 0.35
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (9 bp):
TGTCTTTTT
Found at i:3361848 original size:9 final size:8
Alignment explanation
Indices: 3361834--3361881 Score: 60
Period size: 8 Copynumber: 5.8 Consensus size: 8
3361824 TCTTATATTA
3361834 TTTTTTAC
1 TTTTTTAC
3361842 TTTTTTTAC
1 -TTTTTTAC
3361851 ATTTTTTAC
1 -TTTTTTAC
*
3361860 TTTTTAAC
1 TTTTTTAC
*
3361868 TTTTTAAC
1 TTTTTTAC
3361876 TTTTTT
1 TTTTTT
3361882 TCTTATATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
8 20 0.56
9 16 0.44
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTTTAC
Found at i:3361855 original size:10 final size:9
Alignment explanation
Indices: 3361834--3361882 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
3361824 TCTTATATTA
3361834 TTTTTTACT
1 TTTTTTACT
*
3361843 TTTTTTACA
1 TTTTTTACT
3361852 TTTTTTAC-
1 TTTTTTACT
*
3361860 TTTTTAAC-
1 TTTTTTACT
*
3361868 TTTTTAACT
1 TTTTTTACT
3361877 TTTTTT
1 TTTTTT
3361883 CTTATATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
8 15 0.42
9 21 0.58
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTTTACT
Found at i:3361856 original size:18 final size:18
Alignment explanation
Indices: 3361833--3361882 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 18
3361823 TTCTTATATT
3361833 ATTTTTTACTTTTTTTAC
1 ATTTTTTACTTTTTTTAC
*
3361851 ATTTTTTAC-TTTTTAAC
1 ATTTTTTACTTTTTTTAC
*
3361868 -TTTTTAACTTTTTTT
1 ATTTTTTACTTTTTTT
3361883 CTTATATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 7 0.25
17 12 0.43
18 9 0.32
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTTTTACTTTTTTTAC
Found at i:3361946 original size:18 final size:17
Alignment explanation
Indices: 3361925--3361996 Score: 90
Period size: 18 Copynumber: 4.0 Consensus size: 17
3361915 TTTTTTAAGT
*
3361925 TTTATATTATTTTCTTAA
1 TTTATATTATTAT-TTAA
*
3361943 TTTATTTTACTTATTTAA
1 TTTATATTA-TTATTTAA
3361961 TTTATATTATTAATTTAA
1 TTTATATTATT-ATTTAA
3361979 TTTATATTATTAATTTAA
1 TTTATATTATT-ATTTAA
3361997 AAAATTATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
17 2 0.04
18 44 0.90
19 3 0.06
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTATATTATTATTTAA
Found at i:3361965 original size:36 final size:37
Alignment explanation
Indices: 3361898--3361996 Score: 100
Period size: 36 Copynumber: 2.7 Consensus size: 37
3361888 ATTTTGTATC
*
3361898 TTTCTTAAATTT-TTTT-CTTTTTTAAGTTTTATATTAT
1 TTTCTT-AATTTATTTTACTTATTTAAG-TTTATATTAT
3361935 TTTCTTAATTTATTTTACTTATTTAA-TTTATATTAT
1 TTTCTTAATTTATTTTACTTATTTAAGTTTATATTAT
* *
3361971 TAAT-TTAATTTATATTA-TTAATTTAA
1 T-TTCTTAATTTATTTTACTT-ATTTAA
3361997 AAAATTATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
35 2 0.04
36 34 0.62
37 11 0.20
38 8 0.15
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (37 bp):
TTTCTTAATTTATTTTACTTATTTAAGTTTATATTAT
Found at i:3362004 original size:21 final size:21
Alignment explanation
Indices: 3361962--3362019 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
3361952 CTTATTTAAT
*
3361962 TTATATTATTAATTT---AAT
1 TTATATTATTAATTTAAAAAA
3361980 TTATATTATTAATTTAAAAAA
1 TTATATTATTAATTTAAAAAA
*
3362001 TTATAATA-TATATTTAAAA
1 TTATATTATTA-ATTTAAAA
3362020 TGTTTTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 15 0.44
20 2 0.06
21 17 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATATTATTAATTTAAAAAA
Found at i:3362032 original size:21 final size:20
Alignment explanation
Indices: 3362008--3362046 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3361998 AAATTATAAT
3362008 ATATATTTAAAATGTTTTATA
1 ATATATTTAAAAT-TTTTATA
* *
3362029 ATATTTTTTAAATTTTTA
1 ATATATTTAAAATTTTTA
3362047 ATTATCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
ATATATTTAAAATTTTTATA
Found at i:3362126 original size:37 final size:36
Alignment explanation
Indices: 3362085--3362155 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
3362075 TTTATATATA
* *
3362085 TATTTGTGAAATTAATTATTTATAAATTTTAAAAATG
1 TATTTGTCAAATTAATTATTTA-AAATTGTAAAAATG
* *
3362122 TATTTTTCAAATTAATTTTTTAAAATTGTAAAAA
1 TATTTGTCAAATTAATTATTTAAAATTGTAAAAA
3362156 AATAATTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 11 0.37
37 19 0.63
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (36 bp):
TATTTGTCAAATTAATTATTTAAAATTGTAAAAATG
Found at i:3362848 original size:10 final size:9
Alignment explanation
Indices: 3362830--3362932 Score: 66
Period size: 10 Copynumber: 10.8 Consensus size: 9
3362820 TAAAATTTAA
3362830 AAAATATTT
1 AAAATATTT
3362839 AAAATCATTT
1 AAAAT-ATTT
*
3362849 AAAATATTAA
1 AAAATATT-T
3362859 AAAATATTT
1 AAAATATTT
*
3362868 TAAATCATTT
1 AAAAT-ATTT
* *
3362878 TAAATGTTTT
1 AAAAT-ATTT
*
3362888 ATAATA-TT
1 AAAATATTT
3362896 AAAATATATT
1 AAAATAT-TT
*
3362906 -TAATATTT
1 AAAATATTT
3362914 AAAAATAATTT
1 -AAAAT-ATTT
3362925 GAAAATAT
1 -AAAATAT
3362933 ATTTTTAATA
Statistics
Matches: 74, Mismatches: 12, Indels: 15
0.73 0.12 0.15
Matches are distributed among these distances:
8 9 0.12
9 17 0.23
10 39 0.53
11 9 0.12
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (9 bp):
AAAATATTT
Found at i:3362854 original size:19 final size:18
Alignment explanation
Indices: 3362830--3362932 Score: 66
Period size: 19 Copynumber: 5.4 Consensus size: 18
3362820 TAAAATTTAA
3362830 AAAATATTTAAAATCATTT
1 AAAATATTTAAAAT-ATTT
*
3362849 AAAATATTAAAAAATATTT
1 AAAATATT-TAAAATATTT
* * *
3362868 TAAATCATTTTAAATGTTTT
1 AAAAT-ATTTAAAAT-ATTT
*
3362888 ATAATA-TTAAAATATATT
1 AAAATATTTAAAATAT-TT
*
3362906 -TAATATTTAAAAATAATTT
1 AAAATATTT-AAAAT-ATTT
3362925 GAAAATAT
1 -AAAATAT
3362933 ATTTTTAATA
Statistics
Matches: 65, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
17 6 0.09
18 10 0.15
19 28 0.43
20 16 0.25
21 5 0.08
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
AAAATATTTAAAATATTT
Found at i:3362858 original size:29 final size:28
Alignment explanation
Indices: 3362820--3362918 Score: 101
Period size: 29 Copynumber: 3.5 Consensus size: 28
3362810 AAATTCTATG
3362820 TAAAATTTAAAAAATATTTAAAATCATT
1 TAAAATTTAAAAAATATTTAAAATCATT
*
3362848 TAAAATATTAAAAAATATTTTAAATCATT
1 TAAAAT-TTAAAAAATATTTAAAATCATT
* ** * *
3362877 TTAAATGTTTTATAATA-TTAAAATATATT
1 TAAAAT-TTAAAAAATATTTAAAAT-CATT
*
3362906 TAATATTTAAAAA
1 TAAAATTTAAAAA
3362919 TAATTTGAAA
Statistics
Matches: 56, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
28 16 0.29
29 40 0.71
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (28 bp):
TAAAATTTAAAAAATATTTAAAATCATT
Found at i:3362930 original size:30 final size:32
Alignment explanation
Indices: 3362888--3362961 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 32
3362878 TAAATGTTTT
3362888 ATAATATTAAAATATA-TTTAATATTTA-AAA
1 ATAATATTAAAATATATTTTAATATTTATAAA
3362918 ATAAT-TTGAAAATATATTTTTAATATTTATAAAA
1 ATAATATT-AAAATATA-TTTTAATATTTAT-AAA
3362952 ATATATATTA
1 ATA-ATATTA
3362962 TAAAACATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
29 2 0.05
30 13 0.35
32 11 0.30
34 6 0.16
35 3 0.08
36 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (32 bp):
ATAATATTAAAATATATTTTAATATTTATAAA
Found at i:3366428 original size:30 final size:30
Alignment explanation
Indices: 3366392--3366514 Score: 147
Period size: 30 Copynumber: 4.1 Consensus size: 30
3366382 GGTCAAATGG
* * * *
3366392 ACTCGAACCGCCTATATCCAGGTGATATGA
1 ACTCGAACCACCCATGTCCGGGTGATATGA
3366422 ACTCGAACCACCCATGTCCGGGTGATATGA
1 ACTCGAACCACCCATGTCCGGGTGATATGA
* *
3366452 ACTCAAATCACCCATGTCCGGGTGATATGA
1 ACTCGAACCACCCATGTCCGGGTGATATGA
* * * * *
3366482 ACTTGAACCACCTATGTCTGGTTTATATGA
1 ACTCGAACCACCCATGTCCGGGTGATATGA
3366512 ACT
1 ACT
3366515 GCTCTGGGAC
Statistics
Matches: 80, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 80 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (30 bp):
ACTCGAACCACCCATGTCCGGGTGATATGA
Found at i:3369542 original size:28 final size:27
Alignment explanation
Indices: 3369491--3369547 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
3369481 CAAAATAATA
* * *
3369491 AAAATATATATTTAATATATATTTTTT
1 AAAATATATATTTAATAGAAATTTATT
*
3369518 AAAATTTATATTTATATAGAAATTTATT
1 AAAATATATATTTA-ATAGAAATTTATT
3369546 AA
1 AA
3369548 TAGTCACATC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (27 bp):
AAAATATATATTTAATAGAAATTTATT
Found at i:3369677 original size:21 final size:21
Alignment explanation
Indices: 3369649--3369692 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
3369639 TCAAAAAAAG
3369649 AATTT-AAAAATAATATT-TAA
1 AATTTAAAAAAT-ATATTATAA
3369669 AATTGTAAAAAATATATTATAA
1 AATT-TAAAAAATATATTATAA
3369691 AA
1 AA
3369693 CATTTTAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.19
21 6 0.29
22 11 0.52
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AATTTAAAAAATATATTATAA
Found at i:3369848 original size:27 final size:28
Alignment explanation
Indices: 3369818--3369877 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 28
3369808 TTTAAAAAAA
* * *
3369818 TATTTAAAATATTATGATTTCTTATAT-
1 TATTTAAAAAATTATAATTTCTTAAATG
*
3369845 TA-TTAAAAAATTATAATTTTTTAAATG
1 TATTTAAAAAATTATAATTTCTTAAATG
3369872 TATTTA
1 TATTTA
3369878 GTATTTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 20 0.74
27 4 0.15
28 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (28 bp):
TATTTAAAAAATTATAATTTCTTAAATG
Found at i:3370045 original size:21 final size:22
Alignment explanation
Indices: 3370021--3370063 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3370011 AAAAAAAGAA
*
3370021 AAAAAT-ATATTTAATATTTAT
1 AAAAATAATATTTAAAATTTAT
3370042 -AAAATAATATTTAAAATTTAT
1 AAAAATAATATTTAAAATTTAT
3370063 A
1 A
3370064 TTTATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAAATAATATTTAAAATTTAT
Found at i:3370051 original size:14 final size:14
Alignment explanation
Indices: 3370032--3370069 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3370022 AAAATATATT
3370032 TAATATTTATAAAA
1 TAATATTTATAAAA
*
3370046 TAATATTTA-AAAT
1 TAATATTTATAAAA
*
3370059 TTATATTTATA
1 TAATATTTATA
3370070 TTTAAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATATTTATAAAA
Found at i:3370244 original size:20 final size:24
Alignment explanation
Indices: 3370219--3370265 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 24
3370209 AAAATTAATA
3370219 AAATATTA-AAAA-T-AT-ATTTC
1 AAATATTATAAAACTAATAATTTC
3370239 AAATATTATAAAACTAATAATTTC
1 AAATATTATAAAACTAATAATTTC
3370263 AAA
1 AAA
3370266 ACTAATTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.35
21 4 0.17
22 1 0.04
23 2 0.09
24 8 0.35
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATATTATAAAACTAATAATTTC
Found at i:3370417 original size:23 final size:20
Alignment explanation
Indices: 3370371--3370417 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 20
3370361 AAATTTAAAA
3370371 AAAATATTATAAAACATTTT
1 AAAATATTATAAAACATTTT
*
3370391 -AAATATATATTACAAATATTTT
1 AAAATAT-TA-TA-AAACATTTT
3370413 AAAAT
1 AAAAT
3370418 TAATAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 6 0.27
20 2 0.09
21 2 0.09
22 8 0.36
23 4 0.18
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATATTATAAAACATTTT
Found at i:3370430 original size:23 final size:23
Alignment explanation
Indices: 3370337--3370430 Score: 79
Period size: 23 Copynumber: 4.2 Consensus size: 23
3370327 TAAAGTTAAA
3370337 AAATATTTTTAAAAATAATAAT-T
1 AAATA-TTTTAAAAATAATAATAT
* *
3370360 AAA-A-TTTAAAAAAAATATTAT
1 AAATATTTTAAAAATAATAATAT
* * * *
3370381 AAAACATTTTAAATAT-ATATTAC
1 -AAATATTTTAAAAATAATAATAT
*
3370404 AAATATTTTAAAATTAATAATAT
1 AAATATTTTAAAAATAATAATAT
3370427 AAAT
1 AAAT
3370431 TAAATAAGCA
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
20 13 0.23
21 1 0.02
22 16 0.29
23 19 0.34
24 7 0.12
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATATTTTAAAAATAATAATAT
Found at i:3370464 original size:18 final size:18
Alignment explanation
Indices: 3370414--3370465 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
3370404 AAATATTTTA
*
3370414 AAATTAATAATATAAATT
1 AAATAAATAATATAAATT
** *
3370432 AAATAAGCAAAATAAATT
1 AAATAAATAATATAAATT
3370450 AAGA-AAATAATATAAA
1 AA-ATAAATAATATAAA
3370466 ACTTAAAAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
18 25 0.96
19 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (18 bp):
AAATAAATAATATAAATT
Found at i:3371719 original size:18 final size:17
Alignment explanation
Indices: 3371679--3371717 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3371669 CCTAAATGTG
*
3371679 ATTTTATCTTCTTTATT
1 ATTTTATCTTATTTATT
3371696 ATTTTACTCTTATTT-TT
1 ATTTTA-TCTTATTTATT
3371713 ATTTT
1 ATTTT
3371718 TATTTTTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTATCTTATTTATT
Found at i:3371782 original size:13 final size:13
Alignment explanation
Indices: 3371764--3371817 Score: 63
Period size: 13 Copynumber: 3.9 Consensus size: 13
3371754 TATATACATC
3371764 ATAATAAAAAAAT
1 ATAATAAAAAAAT
*
3371777 ATAATAAAAATAT
1 ATAATAAAAAAAT
*
3371790 ATATACAAAACAAAT
1 ATA-ATAAAA-AAAT
3371805 ATAAATAAAAAAA
1 AT-AATAAAAAAA
3371818 ATTTACCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
13 15 0.44
14 8 0.24
15 10 0.29
16 1 0.03
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (13 bp):
ATAATAAAAAAAT
Found at i:3371819 original size:15 final size:15
Alignment explanation
Indices: 3371769--3371819 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
3371759 ACATCATAAT
3371769 AAAAAAATAT-AAT-
1 AAAAAAATATAAATA
* * *
3371782 AAAAATATATATACA
1 AAAAAAATATAAATA
*
3371797 AAACAAATATAAATA
1 AAAAAAATATAAATA
3371812 AAAAAAAT
1 AAAAAAAT
3371820 TTACCTTTTC
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 9 0.32
14 1 0.04
15 18 0.64
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.22
Consensus pattern (15 bp):
AAAAAAATATAAATA
Found at i:3371850 original size:11 final size:11
Alignment explanation
Indices: 3371834--3371868 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
3371824 CTTTTCCCCC
3371834 CTCCCTTCTCT
1 CTCCCTTCTCT
3371845 CTCCCTTCTCT
1 CTCCCTTCTCT
3371856 CTTCCC-TCTCT
1 C-TCCCTTCTCT
3371867 CT
1 CT
3371869 TCTTTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 18 0.78
12 4 0.17
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:3372379 original size:11 final size:11
Alignment explanation
Indices: 3372355--3372397 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
3372345 TTCTAATACG
*
3372355 TATATATATTA
1 TATATATTTTA
*
3372366 TATGTATTTTA
1 TATATATTTTA
* *
3372377 TATATATTATG
1 TATATATTTTA
3372388 TATATATTTT
1 TATATATTTT
3372398 TTAATGCCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TATATATTTTA
Found at i:3379748 original size:20 final size:21
Alignment explanation
Indices: 3379716--3379776 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
3379706 TTATTAATAT
3379716 TATAT-TTAGTTATATA-CCTA
1 TATATCTTAGTTATATATCC-A
*
3379736 TATATCTTATTATATATATCCA
1 TATATCTTAGT-TATATATCCA
*
3379758 TATATCTTAATATATATAT
1 TATATCTTAGT-TATATAT
3379777 GTGCATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.14
21 4 0.11
22 25 0.69
23 2 0.06
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.51
Consensus pattern (21 bp):
TATATCTTAGTTATATATCCA
Found at i:3379760 original size:22 final size:23
Alignment explanation
Indices: 3379726--3379776 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
3379716 TATATTTAGT
*
3379726 TATATA-CCTATATATCTTATTA
1 TATATATCCTATATATCTTAATA
3379748 TATATATCC-ATATATCTTAATA
1 TATATATCCTATATATCTTAATA
3379770 TATATAT
1 TATATAT
3379777 GTGCATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (23 bp):
TATATATCCTATATATCTTAATA
Found at i:3391735 original size:43 final size:43
Alignment explanation
Indices: 3391540--3391877 Score: 190
Period size: 43 Copynumber: 7.7 Consensus size: 43
3391530 CAAAATTTGA
* *
3391540 TCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATATAG
1 TCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATTTAG
* * * *
3391583 CCTGC-TCACTCCTGCTCAGTGAAGATAAG-GCTGGTGATTGGAA
1 TCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGT-ATT-TAG
* * * * *** * *
3391626 TCTGCTCCA-TCGCCGGT-ACGTGGAGATAAGATTCATCAAAATTCG
1 TCTGCTTCACTC-CTGCTCA-GTGAAGATAAGA-TC-TGGTATTTAG
* *
3391671 ATCTGTTTCACTTCTGCTCAGTGAAGATAAGATCTGGTATTTAG
1 -TCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATTTAG
* * * * * *
3391715 CCTGCTCCACTCCTGCTCAGTGAAGATAAG-GCTGATGATTGGAA
1 TCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGT-ATT-TAG
* * * * ***
3391759 TCTGCTCCA-TCGCCGGT-ACGTGGAGATAAGATTCATCAAAATTT-G
1 TCTGCTTCACTC-CTGCTCA-GTGAAGATAAGA-TC-T-GGTATTTAG
3391804 ATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGT-TTATAG
1 -TCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATT-TAG
*
3391848 CCTGCTTCACTCCTGCTCAGTGAAGATAAG
1 TCTGCTTCACTCCTGCTCAGTGAAGATAAG
3391878 GCTGATGATT
Statistics
Matches: 216, Mismatches: 55, Indels: 48
0.68 0.17 0.15
Matches are distributed among these distances:
41 4 0.02
42 32 0.15
43 74 0.34
44 44 0.20
45 4 0.02
46 47 0.22
47 10 0.05
48 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (43 bp):
TCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATTTAG
Found at i:3391782 original size:133 final size:133
Alignment explanation
Indices: 3391399--3392021 Score: 910
Period size: 133 Copynumber: 4.7 Consensus size: 133
3391389 GATCTGCTGT
* * *
3391399 AATTTGATCTGCTTTACTCCTGCTCAGTAAAGATAAGATCT-GTATGTTTAGCCTACTTCACTCC
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTA--TTTAGCCTGCTTCACTCC
* * ** * * * * ** * *
3391463 TGCTCAATGAAGATAAGGCTGGTGGCTGAAATCTACTCCATTGCCGATATATAGAGATAAGACTC
64 TGCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTC
*
3391528 GCCAA
129 ACCAA
* *
3391533 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTAGTATATAGCCTGC-TCACTCCTG
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATTTAGCCTGCTTCACTCCTG
* *
3391597 CTCAGTGAAGATAAGGCTGGTGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCAT
66 CTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCAC
3391662 CAA
131 CAA
* * * *
3391665 AATTCGATCTGTTTCACTTCTGCTCAGTGAAGATAAGATCTGGTATTTAGCCTGCTCCACTCCTG
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATTTAGCCTGCTTCACTCCTG
*
3391730 CTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCAT
66 CTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCAC
3391795 CAA
131 CAA
3391798 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGT-TTATAGCCTGCTTCACTCCT
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATT-TAGCCTGCTTCACTCCT
3391862 GCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCA
65 GCTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCA
3391927 CCAA
130 CCAA
* * * * *
3391931 AATTTGATCTGCTCCGCTCCTGCTCAGCGAAGATAAGATCTGCTATATTTAACCTGCTTCACTCC
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTG--GTATTTAGCCTGCTTCACTCC
3391996 TGCTCAGTGAAGATAAGGCTGATGAT
64 TGCTCAGTGAAGATAAGGCTGATGAT
3392022 ATCTGTAATC
Statistics
Matches: 449, Mismatches: 34, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
132 116 0.26
133 247 0.55
134 39 0.09
135 45 0.10
136 2 0.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (133 bp):
AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATTTAGCCTGCTTCACTCCTG
CTCAGTGAAGATAAGGCTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAGATAAGATTCAC
CAA
Found at i:3403951 original size:16 final size:16
Alignment explanation
Indices: 3403930--3403979 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 16
3403920 CGAAAATGAT
3403930 ATAATAAGTATAATAA
1 ATAATAAGTATAATAA
*
3403946 ATAAT-AGTGTAA-AA
1 ATAATAAGTATAATAA
*
3403960 A-AATAA-TACAATAA
1 ATAATAAGTATAATAA
3403974 ATAATA
1 ATAATA
3403980 GGAAAATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
13 6 0.21
14 7 0.25
15 10 0.36
16 5 0.18
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (16 bp):
ATAATAAGTATAATAA
Found at i:3406214 original size:31 final size:31
Alignment explanation
Indices: 3406176--3406244 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
3406166 GAAGAAAGGT
3406176 ACTAATATTAACATTATATTAAGCAAAGCAA
1 ACTAATATTAACATTATATTAAGCAAAGCAA
3406207 ACTAATATTAACATTATATTAAGCAAAGCAA
1 ACTAATATTAACATTATATTAAGCAAAGCAA
3406238 ACATAAT
1 AC-TAAT
3406245 TACCACATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 33 0.89
32 4 0.11
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (31 bp):
ACTAATATTAACATTATATTAAGCAAAGCAA
Found at i:3410951 original size:27 final size:30
Alignment explanation
Indices: 3410891--3410957 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 30
3410881 GTATTTTAGA
3410891 ATACATGAACTATAATTTAATGTGCAATTAT
1 ATACATGAACTATAATTT-ATGTGCAATTAT
* *
3410922 ATACATGAACT-T-ATTT-TGTGCACTTTT
1 ATACATGAACTATAATTTATGTGCAATTAT
3410949 ATACATGAA
1 ATACATGAA
3410958 ATCTTGATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 18 0.53
29 4 0.12
30 1 0.03
31 11 0.32
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.40
Consensus pattern (30 bp):
ATACATGAACTATAATTTATGTGCAATTAT
Found at i:3411411 original size:22 final size:21
Alignment explanation
Indices: 3411375--3411415 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
3411365 TAATTTTTTA
3411375 CCACTTAATTTTTTAATTTAAC
1 CCACTTAATTTTTT-ATTTAAC
3411397 CCACTGTAA-TTTTTATTTA
1 CCACT-TAATTTTTTATTTA
3411416 TTTTAGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 10 0.56
23 3 0.17
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.51
Consensus pattern (21 bp):
CCACTTAATTTTTTATTTAAC
Found at i:3412388 original size:14 final size:14
Alignment explanation
Indices: 3412365--3412418 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
3412355 AATATAAAAT
3412365 ATTT-TTTATTTAA
1 ATTTATTTATTTAA
*
3412378 ATTTATTTATTAAA
1 ATTTATTTATTTAA
* *
3412392 AATTATTAATTTAA
1 ATTTATTTATTTAA
*
3412406 TATTTATATATTT
1 -ATTTATTTATTT
3412419 GATTTAATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
13 4 0.12
14 19 0.59
15 9 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTTATTTATTTAA
Found at i:3412441 original size:16 final size:15
Alignment explanation
Indices: 3412400--3412441 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
3412390 AAAATTATTA
*
3412400 ATTTAATATTTATAT
1 ATTTAATATTAATAT
*
3412415 ATTTGAT-TTAATAT
1 ATTTAATATTAATAT
3412429 ATCTTAATATTAA
1 AT-TTAATATTAA
3412442 CAGAGTTACC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 8 0.36
15 10 0.45
16 4 0.18
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (15 bp):
ATTTAATATTAATAT
Found at i:3412948 original size:3 final size:3
Alignment explanation
Indices: 3412940--3412965 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3412930 TTTGTTCTAC
3412940 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
3412966 TTATTATCTT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:3415386 original size:14 final size:15
Alignment explanation
Indices: 3415367--3415395 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3415357 TTTTTACTTA
3415367 AAAAAATA-AAAAAT
1 AAAAAATATAAAAAT
3415381 AAAAAATATAAAAAT
1 AAAAAATATAAAAAT
3415396 GGTTAAGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAAATATAAAAAT
Found at i:3415391 original size:16 final size:15
Alignment explanation
Indices: 3415365--3415394 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
3415355 TTTTTTTACT
3415365 TAAAAAAATAAAAAA
1 TAAAAAAATAAAAAA
3415380 TAAAAAATATAAAAA
1 TAAAAAA-ATAAAAA
3415395 TGGTTAAGAA
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:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
TAAAAAAATAAAAAA
Found at i:3418191 original size:23 final size:19
Alignment explanation
Indices: 3418142--3418178 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3418132 CCCTGTTTTA
*
3418142 CCCTCTGCCTCTTCTGTTC
1 CCCTTTGCCTCTTCTGTTC
3418161 CCCTTTGCCTCTTCTGTT
1 CCCTTTGCCTCTTCTGTT
3418179 TCGCCCGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.43, G:0.11, T:0.46
Consensus pattern (19 bp):
CCCTTTGCCTCTTCTGTTC
Found at i:3418210 original size:5 final size:5
Alignment explanation
Indices: 3418203--3418261 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
3418193 CCCTCCGTTT
* * * *
3418203 CTTTT CTTTT CTTTG CTTTG CTTTG CTTTCTC CTTTG CTTT- C-TTC CTTTG
1 CTTTG CTTTG CTTTG CTTTG CTTTG C-TT-TG CTTTG CTTTG CTTTG CTTTG
3418253 CTTTG CTTT
1 CTTTG CTTT
3418262 CTCCAGTCGA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
3 2 0.04
4 2 0.04
5 36 0.78
6 4 0.09
7 2 0.04
ACGTcount: A:0.00, C:0.25, G:0.10, T:0.64
Consensus pattern (5 bp):
CTTTG
Found at i:3418215 original size:10 final size:10
Alignment explanation
Indices: 3418200--3418261 Score: 56
Period size: 10 Copynumber: 6.2 Consensus size: 10
3418190 GCTCCCTCCG
*
3418200 TTTCTTTTCT
1 TTTCTTTGCT
3418210 TTTCTTTGCT
1 TTTCTTTGCT
*
3418220 TTGCTTTGCT
1 TTTCTTTGCT
3418230 TTCTCCTTTGC-
1 TT-T-CTTTGCT
*
3418241 TTTC-TTCCT
1 TTTCTTTGCT
*
3418250 TTGCTTTGCT
1 TTTCTTTGCT
3418260 TT
1 TT
3418262 CTCCAGTCGA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
8 3 0.07
9 4 0.10
10 27 0.64
11 2 0.05
12 6 0.14
ACGTcount: A:0.00, C:0.24, G:0.10, T:0.66
Consensus pattern (10 bp):
TTTCTTTGCT
Found at i:3418240 original size:12 final size:13
Alignment explanation
Indices: 3418223--3418256 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
3418213 CTTTGCTTTG
3418223 CTTTGCTTTC-TC
1 CTTTGCTTTCTTC
3418235 CTTTGCTTTCTTC
1 CTTTGCTTTCTTC
3418248 CTTTGCTTT
1 CTTTGCTTT
3418257 GCTTTCTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.00, C:0.29, G:0.09, T:0.62
Consensus pattern (13 bp):
CTTTGCTTTCTTC
Found at i:3418281 original size:31 final size:30
Alignment explanation
Indices: 3418218--3418287 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
3418208 CTTTTCTTTG
* * *
3418218 CTTTGCTTTGCTTTCTCCTTTGCTTTCTTC
1 CTTTGCTTTGCTTTCTCCGTCGCTATCTTC
3418248 CTTTGCTTTGCTTTCTCCAGTCGAC-ATCTTC
1 CTTTGCTTTGCTTTCTCC-GTCG-CTATCTTC
3418279 CTTTGCTTT
1 CTTTGCTTT
3418288 CTCCAGTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 18 0.51
31 16 0.46
32 1 0.03
ACGTcount: A:0.04, C:0.30, G:0.11, T:0.54
Consensus pattern (30 bp):
CTTTGCTTTGCTTTCTCCGTCGCTATCTTC
Found at i:3420152 original size:19 final size:19
Alignment explanation
Indices: 3420128--3420165 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3420118 AAAGTGTGCA
3420128 TTTGTGCATTGGTATGTCG
1 TTTGTGCATTGGTATGTCG
3420147 TTTGTGCATTGGTATGTCG
1 TTTGTGCATTGGTATGTCG
3420166 GTGAGGGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.32, T:0.47
Consensus pattern (19 bp):
TTTGTGCATTGGTATGTCG
Found at i:3420615 original size:18 final size:18
Alignment explanation
Indices: 3420569--3420616 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
3420559 TATAAGAATA
*
3420569 TTAATTATTA-ATA-ATT
1 TTAATTATAATATATATT
3420585 TT-ATTA-AATTATATATT
1 TTAATTATAA-TATATATT
3420602 TTAATTATAATATAT
1 TTAATTATAATATAT
3420617 TTAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 4 0.15
16 5 0.19
17 5 0.19
18 9 0.35
19 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATTATAATATATATT
Found at i:3420621 original size:15 final size:15
Alignment explanation
Indices: 3420586--3420637 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
3420576 TTAATAATTT
*
3420586 TATTAAATTAT-ATA
1 TATTTAATTATAATA
3420600 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
3420614 TATTTAATAATAAT-
1 TATTTAATTATAATA
3420628 TATGTTAATT
1 TAT-TTAATT
3420638 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:3420704 original size:66 final size:65
Alignment explanation
Indices: 3420634--3420828 Score: 182
Period size: 56 Copynumber: 3.1 Consensus size: 65
3420624 TAATTATGTT
3420634 AATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTTTAA
1 AATTT-TATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTTTAA
3420699 G
65 G
* * * * * *
3420700 AATTTTA--TTA-A--ATTATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATT-ATGTTA
1 AATTTTATTTTATAGTATCATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTAATTTTA
*
3420754 AT
64 AG
* *
3420756 T--TATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAA
1 AATTTTATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATT-TTAA
3420819 G
65 G
3420820 AATTTTATT
1 AATTTTATT
3420829 AAATTATATA
Statistics
Matches: 95, Mismatches: 18, Indels: 32
0.66 0.12 0.22
Matches are distributed among these distances:
54 3 0.03
56 20 0.21
57 6 0.06
58 1 0.01
59 13 0.14
60 13 0.14
61 1 0.01
62 6 0.06
63 16 0.17
64 4 0.04
65 2 0.02
66 10 0.11
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.50
Consensus pattern (65 bp):
AATTTTATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTTTAAG
Found at i:3420734 original size:119 final size:120
Alignment explanation
Indices: 3420552--3420872 Score: 619
Period size: 119 Copynumber: 2.7 Consensus size: 120
3420542 ATTGTTTTAT
*
3420552 TAAATT-ATATAAGAATATTAATTATTAATAATTTTATTAAATTATATATTTTAATTATAATATA
1 TAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
3420616 TTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAG
66 TTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAG
3420671 TAAATTCATATAAGAATATTAATT-TTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
1 TAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
3420735 TTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAG
66 TTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAG
3420790 TAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
1 TAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
3420855 TTTAATAATAATTATGTT
66 TTTAATAATAATTATGTT
3420873 TAAATATGAT
Statistics
Matches: 199, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
119 124 0.62
120 75 0.38
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.50
Consensus pattern (120 bp):
TAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATA
TTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAG
Found at i:3420740 original size:15 final size:15
Alignment explanation
Indices: 3420705--3420756 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
3420695 TTAAGAATTT
*
3420705 TATTAAATTAT-ATA
1 TATTTAATTATAATA
3420719 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
3420733 TATTTAATAATAAT-
1 TATTTAATTATAATA
3420747 TATGTTAATT
1 TAT-TTAATT
3420757 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:3420855 original size:16 final size:16
Alignment explanation
Indices: 3420834--3420875 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
3420824 TTATTAAATT
*
3420834 ATATATTTTAATTATA
1 ATATATTTTAATAATA
3420850 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
3420865 AT-TATGTTTAA
1 ATATAT-TTTAA
3420876 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:3420860 original size:15 final size:15
Alignment explanation
Indices: 3420825--3420866 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3420815 TTAAGAATTT
*
3420825 TATTAAATTAT-ATA
1 TATTTAATTATAATA
3420839 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
3420853 TATTTAATAATAAT
1 TATTTAATTATAAT
3420867 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:3425752 original size:17 final size:18
Alignment explanation
Indices: 3425715--3425752 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
3425705 GATTGAGAGT
* *
3425715 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
3425733 GAAAAGAAAT-TGAAAAA
1 GAAAAGAAATGTGAAAAA
3425750 GAA
1 GAA
3425753 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.63, C:0.03, G:0.24, T:0.11
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:3425765 original size:13 final size:12
Alignment explanation
Indices: 3425734--3425788 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
3425724 TGTGAAACAG
*
3425734 AAAAGAAATTGA
1 AAAAGAAGTTGA
3425746 AAAAGAAGTTGA
1 AAAAGAAGTTGA
*
3425758 AGAAAGAAG-AGA
1 A-AAAGAAGTTGA
*
3425770 AAATG-AGTTAGA
1 AAAAGAAGTT-GA
3425782 AAAAGAA
1 AAAAGAA
3425789 ACAAAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 21 0.62
13 8 0.24
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.13
Consensus pattern (12 bp):
AAAAGAAGTTGA
Found at i:3431177 original size:17 final size:17
Alignment explanation
Indices: 3431155--3431197 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
3431145 TAACAATTAA
*
3431155 TATTAATTGCTTAAATG
1 TATTAATTACTTAAATG
3431172 TATTAATTACTTAAATG
1 TATTAATTACTTAAATG
3431189 TATTAATTA
1 TATTAATTA
3431198 TTGATATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.49
Consensus pattern (17 bp):
TATTAATTACTTAAATG
Found at i:3437700 original size:67 final size:66
Alignment explanation
Indices: 3437621--3437782 Score: 182
Period size: 67 Copynumber: 2.4 Consensus size: 66
3437611 CAAAATCTAG
* * * * *
3437621 ACCTGAAACTGATGCTTAACTATAAAATTTTACGAGCATTTTGT-CCTATTAACTTATGCCTGCT
1 ACCTG-AACTGATGCTTAGCTATAAAA-TTTACAAGCATTTTGTAAC-AGTAACCTATGCCTGCT
3437685 GCCA
63 GCCA
* * *
3437689 ATCTGAACTGATGCTCAGCTATATAAATTTACAAGCATTTTGTAACAGTAGCCTATGCCTGCTGC
1 ACCTGAACTGATGCTTAGCTATA-AAATTTACAAGCATTTTGTAACAGTAACCTATGCCTGCTGC
3437754 CA
65 CA
**
3437756 ACCTGAGACCCATGCTTAGCTATAAAA
1 ACCTGA-ACTGATGCTTAGCTATAAAA
3437783 AATTTTCATG
Statistics
Matches: 79, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
67 57 0.72
68 22 0.28
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (66 bp):
ACCTGAACTGATGCTTAGCTATAAAATTTACAAGCATTTTGTAACAGTAACCTATGCCTGCTGCC
A
Found at i:3443007 original size:216 final size:215
Alignment explanation
Indices: 3442388--3443066 Score: 952
Period size: 216 Copynumber: 3.1 Consensus size: 215
3442378 CTTTTAATGG
* * * *
3442388 CATTTTTTTTGTTAGCCATAATTCCTCACTTGTTAAGGAGTTTTAATGACTAAAGATATTAACAA
1 CATTTTTTTAGCTAGCCATAATTCCTCACTTGTAAAGGAGTTTTAATGGCTAAAGATATTAACAA
3442453 TGTCACGCTAGCTTGTAGAAAGATTATCGCCAACTTGAGAATTCAAGCTAGGATTATTCTCATTC
66 TGTCACGCTAGCTTGTAGAAAGATTATCGCCAACTTGAGAATTCAAGCTAGGATTATTCTCATTC
* * * * * *
3442518 GACAAACCC-TCTCTTGATGCACAAACAGGGATCAACTCATGAAAAAGGAAATCAACATTTAAGC
131 GACGAACCCTTCTTTTGATGCACAAACAGGGATCGACTCATGCAAAAGGAAGTCAACAATTAAGC
* *
3442582 AAACATCTGTTGCTCGGTAGGA
196 -AACATTTGTTGCTTGGTA-GA
3442604 C-TTTTTTTAGCTAGCCATAATTCCTCACTTGTAAAGGAAGTTTTAATGGCTAAAGATATTAACA
1 CATTTTTTTAGCTAGCCATAATTCCTCACTTGTAAAGG-AGTTTTAATGGCTAAAGATATTAACA
* * * * * *
3442668 ATGTCATGCTAGCTTATAGAAATATTATCGCCAAACTTAACAATGTCAAGCTAAGATTATTCTCA
65 ATGTCACGCTAGCTTGTAGAAAGATTATCGCC-AACTTGAGAAT-TCAAGCTAGGATTATTCTCA
* * * *
3442733 TTCAATGAACCCTTTTTTTGATGCACAAACAGGGATCGACTCATGCAAAAAGAAGTCAACAATTA
128 TTCGACGAACCCTTCTTTTGATGCACAAACAGGGATCGACTCATGCAAAAGGAAGTCAACAATTA
3442798 AGCAACATTTGTTGCTTGGTAGA
193 AGCAACATTTGTTGCTTGGTAGA
* * *
3442821 CATCTTTTTTAGCTAGCCATAAGTCCTCACTTGTCAAGGAGTTGTAATGGCTAAAGATATTAACA
1 CAT-TTTTTTAGCTAGCCATAATTCCTCACTTGTAAAGGAGTTTTAATGGCTAAAGATATTAACA
* * * * * * *
3442886 ATGTCACGTTAACTTGCAGAAAGATTATCGCCAATTTGAGAATTCAAGCTAGGATTTTTTTTATT
65 ATGTCACGCTAGCTTGTAGAAAGATTATCGCCAACTTGAGAATTCAAGCTAGGATTATTCTCATT
* * * *
3442951 CGACGAACCCTTCTTTTGATGCACAAATAGAGATTGACTCGTGCAAAAGGAAGTCAACAATTAAG
130 CGACGAACCCTTCTTTTGATGCACAAACAGGGATCGACTCATGCAAAAGGAAGTCAACAATTAAG
3443016 CAACATTTGTTGCTTGGTAGA
195 CAACATTTGTTGCTTGGTAGA
3443037 CA--TTTTTAGCTAGCCATAATTCCTCACTTG
1 CATTTTTTTAGCTAGCCATAATTCCTCACTTG
3443067 GTGTTTTTAT
Statistics
Matches: 410, Mismatches: 47, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
213 27 0.07
215 33 0.08
216 153 0.37
217 20 0.05
218 96 0.23
219 81 0.20
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Consensus pattern (215 bp):
CATTTTTTTAGCTAGCCATAATTCCTCACTTGTAAAGGAGTTTTAATGGCTAAAGATATTAACAA
TGTCACGCTAGCTTGTAGAAAGATTATCGCCAACTTGAGAATTCAAGCTAGGATTATTCTCATTC
GACGAACCCTTCTTTTGATGCACAAACAGGGATCGACTCATGCAAAAGGAAGTCAACAATTAAGC
AACATTTGTTGCTTGGTAGA
Found at i:3451031 original size:18 final size:17
Alignment explanation
Indices: 3451008--3451042 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3450998 AATAAAACAT
3451008 TTAATTATAAATTTTTTA
1 TTAATT-TAAATTTTTTA
*
3451026 TTAATTTTAATTTTTTA
1 TTAATTTAAATTTTTTA
3451043 AAAATAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTAATTTAAATTTTTTA
Found at i:3451058 original size:16 final size:16
Alignment explanation
Indices: 3451039--3451072 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3451029 ATTTTAATTT
3451039 TTTAAAAATAAA-TTAC
1 TTTAAAAA-AAATTTAC
3451055 TTTAAAAAAAATTTAC
1 TTTAAAAAAAATTTAC
3451071 TT
1 TT
3451073 AGCGGTCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.18
16 14 0.82
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTAAAAAAAATTTAC
Found at i:3455110 original size:18 final size:20
Alignment explanation
Indices: 3455070--3455111 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
3455060 ATTTTTTTAT
* *
3455070 TAATATAATAACTATAATTA
1 TAATATAATAAATATAATGA
3455090 TAATA-AATAAATAT-ATGA
1 TAATATAATAAATATAATGA
3455108 TAAT
1 TAAT
3455112 TAAAAACAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 8 0.40
20 5 0.25
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
TAATATAATAAATATAATGA
Found at i:3456439 original size:20 final size:20
Alignment explanation
Indices: 3456414--3456455 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
3456404 TATATACACA
3456414 TTTTTTGTCTTACCATAGAT
1 TTTTTTGTCTTACCATAGAT
*
3456434 TTTTTTGTCTTACGATAGAT
1 TTTTTTGTCTTACCATAGAT
3456454 TT
1 TT
3456456 GGTCATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.57
Consensus pattern (20 bp):
TTTTTTGTCTTACCATAGAT
Found at i:3457218 original size:27 final size:27
Alignment explanation
Indices: 3457181--3457234 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
3457171 AAGTTTTTCT
*
3457181 TTTTTATTGAAAAACTAAAATTAATTC
1 TTTTTACTGAAAAACTAAAATTAATTC
*
3457208 TTTTTACTGAAAAGCTAAAATTAATTC
1 TTTTTACTGAAAAACTAAAATTAATTC
3457235 AAAAAGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (27 bp):
TTTTTACTGAAAAACTAAAATTAATTC
Found at i:3459074 original size:11 final size:11
Alignment explanation
Indices: 3459058--3459083 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3459048 TTTATTTTAC
3459058 TATTTTGTTAT
1 TATTTTGTTAT
3459069 TATTTTGTTAT
1 TATTTTGTTAT
3459080 TATT
1 TATT
3459084 ATTTTTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (11 bp):
TATTTTGTTAT
Found at i:3459094 original size:36 final size:38
Alignment explanation
Indices: 3459039--3459118 Score: 103
Period size: 36 Copynumber: 2.2 Consensus size: 38
3459029 AATTGTTGTT
* * **
3459039 TTATT-TTATTTTATTTTACTATTTTGTTATTATTTTG
1 TTATTATTATTTTATTTTACTATTTTGCTATCATTTCA
3459076 TTATTATTA-TTT-TTTTACTATTTTGCTATCATTTCA
1 TTATTATTATTTTATTTTACTATTTTGCTATCATTTCA
3459112 TTATTAT
1 TTATTAT
3459119 GTGGCTATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 27 0.71
37 8 0.21
38 3 0.08
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.69
Consensus pattern (38 bp):
TTATTATTATTTTATTTTACTATTTTGCTATCATTTCA
Found at i:3459097 original size:25 final size:24
Alignment explanation
Indices: 3459045--3459100 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
3459035 TGTTTTATTT
* *
3459045 TATTTTATTTTACTATTTTGTTAT
1 TATTTTGTTTTACTATTTTGTTAC
* *
3459069 TATTTTGTTATTATTATTTTTTTAC
1 TATTTTGTT-TTACTATTTTGTTAC
3459094 TATTTTG
1 TATTTTG
3459101 CTATCATTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 8 0.30
25 19 0.70
ACGTcount: A:0.20, C:0.04, G:0.05, T:0.71
Consensus pattern (24 bp):
TATTTTGTTTTACTATTTTGTTAC
Found at i:3468755 original size:10 final size:9
Alignment explanation
Indices: 3468730--3468831 Score: 69
Period size: 10 Copynumber: 10.7 Consensus size: 9
3468720 AATACAAAAA
*
3468730 ATAAAAATCA
1 ATAAAAAT-T
*
3468740 ATAAAAGTT
1 ATAAAAATT
3468749 ATAAAAATT
1 ATAAAAATT
* *
3468758 ATTAAATTT
1 ATAAAAATT
*
3468767 ATTAAAAATA
1 A-TAAAAATT
3468777 ATATAAAATT
1 ATA-AAAATT
*
3468787 CTTAAAAATT
1 -ATAAAAATT
*
3468797 ATAAAATTTT
1 ATAAAA-ATT
* *
3468807 ATAAAAGTC
1 ATAAAAATT
3468816 ATAAAAAATT
1 AT-AAAAATT
3468826 ATAAAA
1 ATAAAA
3468832 TGCATCAAAA
Statistics
Matches: 71, Mismatches: 16, Indels: 11
0.72 0.16 0.11
Matches are distributed among these distances:
9 30 0.42
10 39 0.55
11 2 0.03
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:3468763 original size:19 final size:19
Alignment explanation
Indices: 3468730--3468831 Score: 75
Period size: 19 Copynumber: 5.3 Consensus size: 19
3468720 AATACAAAAA
* *
3468730 ATAAAAATCAATAAAAGTT
1 ATAAAAATCATTAAAATTT
*
3468749 ATAAAAATTATT-AAATTT
1 ATAAAAATCATTAAAATTT
*
3468767 ATTAAAAATAATATAAAATTCT
1 A-TAAAAATCAT-TAAAATT-T
*
3468789 -TAAAAATTA-TAAAATTTT
1 ATAAAAATCATTAAAA-TTT
* * *
3468807 ATAAAAGTCATAAAAAATT
1 ATAAAAATCATTAAAATTT
3468826 ATAAAA
1 ATAAAA
3468832 TGCATCAAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
18 12 0.18
19 36 0.54
20 13 0.19
21 5 0.07
22 1 0.01
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (19 bp):
ATAAAAATCATTAAAATTT
Found at i:3468783 original size:39 final size:38
Alignment explanation
Indices: 3468730--3468831 Score: 118
Period size: 39 Copynumber: 2.7 Consensus size: 38
3468720 AATACAAAAA
*
3468730 ATAAAAATCA-ATAAAAGTTATAAAAATTATTAAA-TTT
1 ATAAAAATCATATAAAA-TTATAAAAATTATAAAATTTT
* *
3468767 ATTAAAAATAATATAAAATTCTTAAAAATTATAAAATTTT
1 A-TAAAAATCATATAAAATT-ATAAAAATTATAAAATTTT
* *
3468807 ATAAAAGTCATAAAAAATTATAAAA
1 ATAAAAATCATATAAAATTATAAAA
3468832 TGCATCAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
37 1 0.02
38 15 0.28
39 34 0.63
40 4 0.07
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (38 bp):
ATAAAAATCATATAAAATTATAAAAATTATAAAATTTT
Found at i:3468801 original size:29 final size:29
Alignment explanation
Indices: 3468752--3468831 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 29
3468742 AAAAGTTATA
* *
3468752 AAAATTATT-AAATTTATTAAAAATAATAT
1 AAAATTCTTAAAAATTA-TAAAAATAATAT
**
3468781 AAAATTCTTAAAAATTAT-AAAATTTTAT
1 AAAATTCTTAAAAATTATAAAAATAATAT
* *
3468809 AAAAGTCATAAAAAATTATAAAA
1 AAAATTC-TTAAAAATTATAAAA
3468832 TGCATCAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
28 14 0.33
29 19 0.45
30 9 0.21
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (29 bp):
AAAATTCTTAAAAATTATAAAAATAATAT
Found at i:3469034 original size:9 final size:9
Alignment explanation
Indices: 3469022--3469199 Score: 53
Period size: 9 Copynumber: 19.0 Consensus size: 9
3469012 TTTTGATACG
3469022 ATAATTTTT
1 ATAATTTTT
3469031 ATAATTTTT
1 ATAATTTTT
* *
3469040 TTACTAGTTTT
1 ATA--ATTTTT
*
3469051 ATATTTCTTT
1 ATAATT-TTT
**
3469061 ATTTTTTTT
1 ATAATTTTT
3469070 ATAATTTTCTT
1 ATAA-TTT-TT
* *
3469081 ATGA-CTTT
1 ATAATTTTT
**
3469089 ATAAAAGTTT
1 AT-AATTTTT
3469099 ATAATTTTTTT
1 ATAA--TTTTT
3469110 GATAA-TTTT
1 -ATAATTTTT
3469119 AT-ATATTTT
1 ATAAT-TTTT
3469128 ATAATTTTT
1 ATAATTTTT
3469137 -TACGA-TTTT
1 ATA--ATTTTT
**
3469146 ATAAAAGTTT
1 AT-AATTTTT
*
3469156 ACAATTTTT
1 ATAATTTTT
*
3469165 ATATTTTTT
1 ATAATTTTT
*
3469174 ATGATTTTT
1 ATAATTTTT
**
3469183 AT-GGTTTT
1 ATAATTTTT
3469191 ATAATTTTT
1 ATAATTTTT
3469200 TTGCCACATG
Statistics
Matches: 124, Mismatches: 26, Indels: 38
0.66 0.14 0.20
Matches are distributed among these distances:
7 1 0.01
8 14 0.11
9 65 0.52
10 24 0.19
11 16 0.13
12 4 0.03
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (9 bp):
ATAATTTTT
Found at i:3469082 original size:20 final size:20
Alignment explanation
Indices: 3469025--3469082 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
3469015 TGATACGATA
* *
3469025 ATTTTTATAATTTTTTTACT
1 ATTTTTATAATTTTCTTATT
*
3469045 AGTTTTAT-A-TTTCTTTATT
1 ATTTTTATAATTTTC-TTATT
*
3469064 TTTTTTATAATTTTCTTAT
1 ATTTTTATAATTTTCTTAT
3469083 GACTTTATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 3 0.10
19 11 0.37
20 12 0.40
21 4 0.13
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (20 bp):
ATTTTTATAATTTTCTTATT
Found at i:3469101 original size:29 final size:28
Alignment explanation
Indices: 3469067--3469171 Score: 108
Period size: 29 Copynumber: 3.8 Consensus size: 28
3469057 CTTTATTTTT
*
3469067 TTTATAATTTTCTTATGACTTTATAAAAG
1 TTTATAATTTT-TTATGATTTTATAAAAG
* * *
3469096 TTTATAATTTTTTTGATAATTTTAT-ATAT
1 TTTATAA-TTTTTT-ATGATTTTATAAAAG
*
3469125 TTTATAATTTTTTACGATTTTATAAAAG
1 TTTATAATTTTTTATGATTTTATAAAAG
*
3469153 TTTACAA-TTTTTAT-ATTTT
1 TTTATAATTTTTTATGATTTT
3469172 TTATGATTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
26 5 0.08
27 14 0.22
28 14 0.22
29 18 0.29
30 12 0.19
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.59
Consensus pattern (28 bp):
TTTATAATTTTTTATGATTTTATAAAAG
Found at i:3472163 original size:68 final size:67
Alignment explanation
Indices: 3472055--3472191 Score: 265
Period size: 68 Copynumber: 2.0 Consensus size: 67
3472045 ACATACACTG
3472055 TTTACCTTTAGAGTGTTTTGTAGATGCACTAATTCAGTCATGACCTGACATAGTGCATAATTTAA
1 TTTACCTTTAGAGTGTTTTGTAGATGCACTAATTCAGTCATGACCTGACATAGTGCATAATTTAA
3472120 CT
66 CT
3472122 TTTACCTTTAAGAGTGTTTTGTAGATGCACTAATTCAGTCATGACCTGACATAGTGCATAATTTA
1 TTTACCTTT-AGAGTGTTTTGTAGATGCACTAATTCAGTCATGACCTGACATAGTGCATAATTTA
3472187 ACT
65 ACT
3472190 TT
1 TT
3472192 GTTCCCGTCA
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
67 9 0.13
68 60 0.87
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (67 bp):
TTTACCTTTAGAGTGTTTTGTAGATGCACTAATTCAGTCATGACCTGACATAGTGCATAATTTAA
CT
Found at i:3474627 original size:23 final size:21
Alignment explanation
Indices: 3474598--3474666 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 21
3474588 TTCTTTCATT
3474598 TTTTTTAATATATGTTGTAGG
1 TTTTTTAATATATGTTGTAGG
* *
3474619 TTGTGTTTATTGAT-TGTTGTAGAA
1 TT-T-TTTAAT-ATATGTTGTAG-G
*
3474643 TTTTTTAATTTATGTTGTAGG
1 TTTTTTAATATATGTTGTAGG
3474664 TTT
1 TTT
3474667 CATGTTTGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
21 6 0.16
22 14 0.37
23 14 0.37
24 4 0.11
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.59
Consensus pattern (21 bp):
TTTTTTAATATATGTTGTAGG
Found at i:3474658 original size:22 final size:21
Alignment explanation
Indices: 3474598--3474662 Score: 60
Period size: 23 Copynumber: 3.0 Consensus size: 21
3474588 TTCTTTCATT
* *
3474598 TTTTTTAATATATGTTGTAGG
1 TTTTTTAATTTATGTTGTAGA
*
3474619 TTGTGTTT-ATTGATTGTTGTAGAA
1 TT-T-TTTAATTTA-TGTTGTAG-A
3474643 TTTTTTAATTTATGTTGTAG
1 TTTTTTAATTTATGTTGTAG
3474663 GTTTCATGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
21 2 0.06
22 15 0.43
23 16 0.46
24 2 0.06
ACGTcount: A:0.22, C:0.00, G:0.20, T:0.58
Consensus pattern (21 bp):
TTTTTTAATTTATGTTGTAGA
Found at i:3478255 original size:15 final size:15
Alignment explanation
Indices: 3478235--3478264 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3478225 TTTAATCTTT
*
3478235 TATAAATTATAAAAA
1 TATAAACTATAAAAA
3478250 TATAAACTATAAAAA
1 TATAAACTATAAAAA
3478265 ATTAAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TATAAACTATAAAAA
Found at i:3484122 original size:21 final size:21
Alignment explanation
Indices: 3484079--3484140 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 21
3484069 GAGCAGAAAT
3484079 TAAAATATAAATTTT-TTGAATG
1 TAAAATAT-AATTTTATT-AATG
3484101 TCAAAATATAATTTTATT-ATG
1 T-AAAATATAATTTTATTAATG
3484122 TATAAATTTATAATTTTAT
1 TA-AAA--TATAATTTTAT
3484141 AAAATTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
20 1 0.03
21 7 0.20
22 7 0.20
23 20 0.57
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (21 bp):
TAAAATATAATTTTATTAATG
Found at i:3490216 original size:22 final size:21
Alignment explanation
Indices: 3490174--3490217 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
3490164 AAAGAGATGA
* *
3490174 AGAAGGAAGGAAAATAGAAGG
1 AGAAGGAAGGAAAAAAAAAGG
*
3490195 AGAAGAGAATGAAAAAAAAAGG
1 AGAAG-GAAGGAAAAAAAAAGG
3490217 A
1 A
3490218 AAAGTTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.05
Consensus pattern (21 bp):
AGAAGGAAGGAAAAAAAAAGG
Found at i:3494298 original size:31 final size:31
Alignment explanation
Indices: 3494263--3494321 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
3494253 GCCCAGTAAC
3494263 TTAAAT-AAACACTTTTGAATAGATCAGTGAT
1 TTAAATGAAA-ACTTTTGAATAGATCAGTGAT
*
3494294 TTAAATGAAAACTTTTGAATAGTTCAGT
1 TTAAATGAAAACTTTTGAATAGATCAGT
3494322 TATAATTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 23 0.88
32 3 0.12
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (31 bp):
TTAAATGAAAACTTTTGAATAGATCAGTGAT
Found at i:3499931 original size:15 final size:15
Alignment explanation
Indices: 3499905--3499942 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3499895 GGATTAATCG
3499905 TATATATTAATT-TAAT
1 TATAT-TTAATTAT-AT
3499921 TATATTTAATTATAT
1 TATATTTAATTATAT
3499936 TATATTT
1 TATATTT
3499943 TTTATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATATTTAATTATAT
Found at i:3500559 original size:26 final size:26
Alignment explanation
Indices: 3500529--3500583 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 26
3500519 TTAAAGAAAA
*
3500529 TATTAA-TAT-TATAAAACTA-A-AT
1 TATTAATTATATATAAAAATATATAT
3500551 TATTAATTATATATAAAAATATATAT
1 TATTAATTATATATAAAAATATATAT
3500577 TATTAAT
1 TATTAAT
3500584 GGTTTCTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 6 0.21
23 3 0.11
24 9 0.32
25 1 0.04
26 9 0.32
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
TATTAATTATATATAAAAATATATAT
Found at i:3509682 original size:9 final size:9
Alignment explanation
Indices: 3509616--3509690 Score: 55
Period size: 9 Copynumber: 8.3 Consensus size: 9
3509606 AAACCTTGAT
3509616 GATGACGAG
1 GATGACGAG
*
3509625 GATGAGGA-
1 GATGACGAG
*
3509633 GATGTCTG-G
1 GATGAC-GAG
*
3509642 AGATGACGGG
1 -GATGACGAG
* *
3509652 GATGAAGTG
1 GATGACGAG
* *
3509661 GATGAAGAT
1 GATGACGAG
3509670 GATGACGAG
1 GATGACGAG
3509679 GATGACGAG
1 GATGACGAG
3509688 GAT
1 GAT
3509691 CATAATGATT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
8 4 0.08
9 42 0.81
10 6 0.12
ACGTcount: A:0.32, C:0.07, G:0.44, T:0.17
Consensus pattern (9 bp):
GATGACGAG
Found at i:3509690 original size:27 final size:28
Alignment explanation
Indices: 3509613--3509690 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 28
3509603 AGAAAACCTT
* **
3509613 GATGATGACGAGGATGAGGA-GATGTCTG
1 GATGATGACGAGGATGAAGAGGATG-CAA
* *
3509641 GA-GATGACGGGGATGAAGTGGATG-AA
1 GATGATGACGAGGATGAAGAGGATGCAA
*
3509667 GATGATGACGAGGATGACGAGGAT
1 GATGATGACGAGGATGAAGAGGAT
3509691 CATAATGATT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
26 2 0.05
27 32 0.80
28 6 0.15
ACGTcount: A:0.32, C:0.06, G:0.44, T:0.18
Consensus pattern (28 bp):
GATGATGACGAGGATGAAGAGGATGCAA
Found at i:3521041 original size:20 final size:21
Alignment explanation
Indices: 3521018--3521061 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
3521008 TGACTTAGAC
*
3521018 AAAAAAATAAATTTAAT-TTA
1 AAAAAAATAAATCTAATATTA
* *
3521038 AAAAATATCAATCTAATATTA
1 AAAAAAATAAATCTAATATTA
3521059 AAA
1 AAA
3521062 CAATTTAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAAAAATAAATCTAATATTA
Found at i:3528355 original size:28 final size:29
Alignment explanation
Indices: 3528286--3528343 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
3528276 AACTATAATT
* *
3528286 GGTATTCAAATAAGCCCTTAATCTTTAAC
1 GGTATCCAAATAAGCCCTTAATCCTTAAC
3528315 TGGTATCCAAATAAG-CCTTAA-CCTTAAC
1 -GGTATCCAAATAAGCCCTTAATCCTTAAC
3528343 G
1 G
3528344 TATACCTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 1 0.04
28 6 0.23
29 6 0.23
30 13 0.50
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.31
Consensus pattern (29 bp):
GGTATCCAAATAAGCCCTTAATCCTTAAC
Found at i:3535756 original size:16 final size:17
Alignment explanation
Indices: 3535735--3535772 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3535725 GTAAATTACT
* *
3535735 AAAAAATACATAT-TAA
1 AAAAAAGACAAATGTAA
3535751 AAAAAAGACAAATGTAA
1 AAAAAAGACAAATGTAA
3535768 AAAAA
1 AAAAA
3535773 TTGAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (17 bp):
AAAAAAGACAAATGTAA
Done.