Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 89 of 93
Found at i:35170776 original size:23 final size:22
Alignment explanation
Indices: 35170733--35170776 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
35170723 TTTATTATAT
* * *
35170733 TTAATTAATTTTTTATCTTAAA
1 TTAAATAAATTTTTATATTAAA
35170755 TTAAATAAATTTTTATGATTAA
1 TTAAATAAATTTTTAT-ATTAA
35170777 CAATTTAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TTAAATAAATTTTTATATTAAA
Found at i:35171080 original size:24 final size:25
Alignment explanation
Indices: 35171019--35171082 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 25
35171009 ATGATATAAA
35171019 AATAATAATTAA-T-ATT-TTAATT
1 AATAATAATTAATTAATTATTAATT
35171041 AATAATAATTAATTAATTATTAATT
1 AATAATAATTAATTAATTATTAATT
*
35171066 -ATAA-AATTTATTTAATT
1 AATAATAA-TTAATTAATT
35171083 TAAAATAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
22 12 0.32
23 3 0.08
24 16 0.43
25 6 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AATAATAATTAATTAATTATTAATT
Found at i:35171099 original size:28 final size:28
Alignment explanation
Indices: 35171068--35171138 Score: 83
Period size: 27 Copynumber: 2.5 Consensus size: 28
35171058 TATTAATTAT
*
35171068 AAAATTTATTTAATTTAAAATAAAAATAA
1 AAAATTTATTTAA-ATAAAATAAAAATAA
*
35171097 AAAATTT-TATTAAATATAATAAAAAT-A
1 AAAATTTAT-TTAAATAAAATAAAAATAA
*
35171124 AATATTTATTTAAAT
1 AAAATTTATTTAAAT
35171139 TTTTAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 13 0.35
28 13 0.35
29 11 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
AAAATTTATTTAAATAAAATAAAAATAA
Found at i:35171137 original size:27 final size:26
Alignment explanation
Indices: 35171066--35171138 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 26
35171056 ATTATTAATT
*
35171066 ATAAAATTTATTTAATTTAAAATAAAA
1 ATAAAATTTATTTAA-ATAAAATAAAA
*
35171093 ATAAAAAATTT-TATTAAATATAATAAAA
1 AT--AAAATTTAT-TTAAATAAAATAAAA
35171121 ATAAATATTTATTTAAAT
1 ATAAA-ATTTATTTAAAT
35171139 TTTTAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
26 3 0.08
27 12 0.31
28 13 0.33
29 11 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
ATAAAATTTATTTAAATAAAATAAAA
Found at i:35176116 original size:17 final size:17
Alignment explanation
Indices: 35176096--35176141 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
35176086 AATACGAGTT
35176096 TTATATATTTTATTAAA
1 TTATATATTTTATTAAA
*
35176113 TTATAT-TTTTAATAAA
1 TTATATATTTTATTAAA
*
35176129 ATA-ATTATTTTAT
1 TTATA-TATTTTAT
35176142 AATAAAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 1 0.04
16 12 0.50
17 11 0.46
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATATATTTTATTAAA
Found at i:35176128 original size:16 final size:16
Alignment explanation
Indices: 35176096--35176147 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
35176086 AATACGAGTT
*
35176096 TTATATATTTTATTAAA
1 TTATAT-TTTTAATAAA
35176113 TTATATTTTTAATAAAA
1 TTATATTTTTAAT-AAA
*
35176130 TAATTATTTTATAATAAA
1 TTA-TATTTT-TAATAAA
35176148 ATGACATCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 6 0.20
17 11 0.37
18 9 0.30
19 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATATTTTTAATAAA
Found at i:35181847 original size:33 final size:33
Alignment explanation
Indices: 35181810--35181874 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
35181800 ATTGGTGGGT
* *
35181810 ACTGGAATTGGTGCTGGAGTTGGGCTTGTCGGA
1 ACTGGAATAGGTGCTGGAGTTGGGATTGTCGGA
**
35181843 ACTGGTGTAGGTGCTGGAGTTGGGATTGTCGG
1 ACTGGAATAGGTGCTGGAGTTGGGATTGTCGG
35181875 GAGTGGCCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.14, C:0.11, G:0.45, T:0.31
Consensus pattern (33 bp):
ACTGGAATAGGTGCTGGAGTTGGGATTGTCGGA
Found at i:35197754 original size:25 final size:25
Alignment explanation
Indices: 35197720--35197771 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
35197710 AAGTATGGCC
35197720 ATTGAGAATACTAGCATGCATCCTT
1 ATTGAGAATACTAGCATGCATCCTT
35197745 ATTGAGAATACTAGCATGCATCCTT
1 ATTGAGAATACTAGCATGCATCCTT
35197770 AT
1 AT
35197772 ATTATCCTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (25 bp):
ATTGAGAATACTAGCATGCATCCTT
Found at i:35199510 original size:2 final size:2
Alignment explanation
Indices: 35199503--35199554 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
35199493 CAGTTATGTA
** *
35199503 AT AT AT AT AT GC AT AT AT AT AT AT AT AT AT AT AT GT 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
35199545 AT AT AT AT AT
1 AT AT AT AT AT
35199555 TCACATGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35199520 original size:12 final size:12
Alignment explanation
Indices: 35199497--35199554 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
35199487 GAGTTACAGT
35199497 TATGTAATATATA
1 TATGT-ATATATA
*
35199510 TATGCATATATA
1 TATGTATATATA
*
35199522 TATATATATATA
1 TATGTATATATA
35199534 TATGTATATATA
1 TATGTATATATA
*
35199546 TATATATAT
1 TATGTATAT
35199555 TCACATGTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
12 36 0.90
13 4 0.10
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (12 bp):
TATGTATATATA
Found at i:35217207 original size:30 final size:30
Alignment explanation
Indices: 35217160--35217232 Score: 112
Period size: 30 Copynumber: 2.4 Consensus size: 30
35217150 ATGAGAACTT
*
35217160 TTTGACTTGGA-TTTTTTTTAATAAAAGTTC
1 TTTG-CTTGGATTTTTTTTTAATAAAAATTC
*
35217190 TTTGCTTGGATTTTTTTTTAGTAAAAATTC
1 TTTGCTTGGATTTTTTTTTAATAAAAATTC
35217220 TTTGCTTGGATTT
1 TTTGCTTGGATTT
35217233 AAGAGATGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 6 0.15
30 34 0.85
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.56
Consensus pattern (30 bp):
TTTGCTTGGATTTTTTTTTAATAAAAATTC
Found at i:35220186 original size:18 final size:19
Alignment explanation
Indices: 35220149--35220186 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
35220139 AAAGTCATAA
35220149 TATTCAAAAAAGCTTTTAAAT
1 TATTCAAAAAA-C-TTTAAAT
35220170 TATTCAAAAAA-TTTAAA
1 TATTCAAAAAACTTTAAA
35220187 ATAAATCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
21 11 0.65
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.37
Consensus pattern (19 bp):
TATTCAAAAAACTTTAAAT
Found at i:35220283 original size:28 final size:29
Alignment explanation
Indices: 35220224--35220281 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
35220214 TATATTTTTA
35220224 TATTTTTATTTTAGATCAAATAAATCTTT
1 TATTTTTATTTTAGATCAAATAAATCTTT
35220253 TATTTTTATTTT-GAATCAAATAAATCTTT
1 TATTTTTATTTTAG-ATCAAATAAATCTTT
35220282 ATAAATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.55
Consensus pattern (29 bp):
TATTTTTATTTTAGATCAAATAAATCTTT
Found at i:35227867 original size:13 final size:14
Alignment explanation
Indices: 35227849--35227877 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
35227839 ATATGTATTT
35227849 ATTAAAG-ATATAA
1 ATTAAAGAATATAA
35227862 ATTAAAGAATATAA
1 ATTAAAGAATATAA
35227876 AT
1 AT
35227878 GAAAACAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (14 bp):
ATTAAAGAATATAA
Found at i:35229012 original size:24 final size:24
Alignment explanation
Indices: 35228985--35229185 Score: 121
Period size: 24 Copynumber: 8.6 Consensus size: 24
35228975 ACACGCTATG
* *
35228985 ATGTTACACGTTATGTACAAAAAT
1 ATGTTACACGTCATGTACAAAAAC
*
35229009 ATGTTACACGTCATGTGCAAAAAC
1 ATGTTACACGTCATGTACAAAAAC
* * *
35229033 ATGTGACACGTCATGGT----TAAG
1 ATGTTACACGTCAT-GTACAAAAAC
* ** *
35229054 TTGTTACACACCATGTACAGAAAC
1 ATGTTACACGTCATGTACAAAAAC
*
35229078 ATGTGACACG-CTATGTACAAAAAC
1 ATGTTACACGTC-ATGTACAAAAAC
* ** **
35229102 ATGTAACACGTCATG---ATTAGG
1 ATGTTACACGTCATGTACAAAAAC
* ** *
35229123 TTGTTACACACCATGTACAGAAAC
1 ATGTTACACGTCATGTACAAAAAC
*
35229147 ATGTGACACGTCATGTACAAAAAC
1 ATGTTACACGTCATGTACAAAAAC
* *
35229171 ATGTGACACGCCATG
1 ATGTTACACGTCATG
35229186 GTTAGGTTGT
Statistics
Matches: 132, Mismatches: 35, Indels: 20
0.71 0.19 0.11
Matches are distributed among these distances:
20 2 0.02
21 25 0.19
23 1 0.01
24 101 0.77
25 3 0.02
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (24 bp):
ATGTTACACGTCATGTACAAAAAC
Found at i:35229207 original size:69 final size:69
Alignment explanation
Indices: 35228997--35229200 Score: 320
Period size: 69 Copynumber: 3.0 Consensus size: 69
35228987 GTTACACGTT
* * * * *
35228997 ATGTACAAAAATATGTTACACGTCATGTGCAAAAACATGTGACACGTCATGGTTAAGTTGTTACA
1 ATGTACAGAAACATGTGACACGTCATGTACAAAAACATGTGACACGTCATGGTTAGGTTGTTACA
35229062 CACC
66 CACC
* *
35229066 ATGTACAGAAACATGTGACACG-CTATGTACAAAAACATGTAACACGTCATGATTAGGTTGTTAC
1 ATGTACAGAAACATGTGACACGTC-ATGTACAAAAACATGTGACACGTCATGGTTAGGTTGTTAC
35229130 ACACC
65 ACACC
*
35229135 ATGTACAGAAACATGTGACACGTCATGTACAAAAACATGTGACACGCCATGGTTAGGTTGTTACA
1 ATGTACAGAAACATGTGACACGTCATGTACAAAAACATGTGACACGTCATGGTTAGGTTGTTACA
35229200 C
66 C
35229201 GTCATGTTGA
Statistics
Matches: 123, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
68 1 0.01
69 121 0.98
70 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (69 bp):
ATGTACAGAAACATGTGACACGTCATGTACAAAAACATGTGACACGTCATGGTTAGGTTGTTACA
CACC
Found at i:35229485 original size:158 final size:157
Alignment explanation
Indices: 35229152--35229470 Score: 475
Period size: 158 Copynumber: 2.0 Consensus size: 157
35229142 GAAACATGTG
* **
35229152 ACACGTCATGTACAAAAA-CATGTGACACGCCATGGTTAGGTTGTTACACGTCATGTTGAAAAAA
1 ACACGTCATGTACAAAAATC-TGTGACAAGCCATAATTAGGTTGTTACACGTCATGTTGAAAAAA
* * *
35229216 ATACTATTGTTACACGCCATGTATAAAAACATATTACACGTCATGGTTAAAAAAAGTTGTTACAT
65 ATACTATTGTTACACGCCATCTACAAAAACATATTACACGTCATGGTTAAAAAAAGTCGTTACAT
* *
35229281 GCCATGTTGAAAAACAAATATTGTTGTT
130 GCCATGTTGAAAAACAAAAATTATTGTT
35229309 ACACGTCATGTACAAAAATCTGTGACAAGCCATAATTAGGTTGTTACACGTCATGTTGAAAAAAA
1 ACACGTCATGTACAAAAATCTGTGACAAGCCATAATTAGGTTGTTACACGTCATGTTG-AAAAAA
* * *
35229374 ATACTATTGTTACACGTCATCTACAAAAATATGTTACACG-CTATGGTTAAAAAAAGTCGTTACA
65 ATACTATTGTTACACGCCATCTACAAAAACATATTACACGTC-ATGGTTAAAAAAAGTCGTTACA
35229438 CT-CCATGTTGAAAAA-AAAAATTATTGTT
129 -TGCCATGTTGAAAAACAAAAATTATTGTT
35229466 ACACG
1 ACACG
35229471 CTATGTTGAA
Statistics
Matches: 147, Mismatches: 11, Indels: 8
0.89 0.07 0.05
Matches are distributed among these distances:
157 70 0.48
158 76 0.52
159 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.29
Consensus pattern (157 bp):
ACACGTCATGTACAAAAATCTGTGACAAGCCATAATTAGGTTGTTACACGTCATGTTGAAAAAAA
TACTATTGTTACACGCCATCTACAAAAACATATTACACGTCATGGTTAAAAAAAGTCGTTACATG
CCATGTTGAAAAACAAAAATTATTGTT
Found at i:35229489 original size:26 final size:26
Alignment explanation
Indices: 35229398--35229491 Score: 77
Period size: 26 Copynumber: 3.5 Consensus size: 26
35229388 CGTCATCTAC
35229398 AAAAATA-TGTTACACGCTATGGTT-A
1 AAAAATATTGTTACACGCTAT-GTTGA
* * *
35229423 AAAAA-AGTCGTTACACTCCATGTTGAAAAA
1 AAAAATA-TTGTTACACGCTATGTTG----A
35229453 AAAAATTATTGTTACACGCTATGTTGA
1 AAAAA-TATTGTTACACGCTATGTTGA
35229480 AAAAATATTGTT
1 AAAAATATTGTT
35229492 GTTACACGAC
Statistics
Matches: 54, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
24 1 0.02
25 8 0.15
26 17 0.31
27 6 0.11
30 6 0.11
31 15 0.28
32 1 0.02
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.32
Consensus pattern (26 bp):
AAAAATATTGTTACACGCTATGTTGA
Found at i:35229511 original size:27 final size:28
Alignment explanation
Indices: 35229480--35229551 Score: 85
Period size: 27 Copynumber: 2.6 Consensus size: 28
35229470 GCTATGTTGA
35229480 AAAAATATTGTTGTTACACGACATAT-TC
1 AAAAATATTGTTGTTACACGACA-ATGTC
***
35229508 AAAAATATT-TTGTTACACTTTAATGTC
1 AAAAATATTGTTGTTACACGACAATGTC
*
35229535 TAAAATATTGTTGTTAC
1 AAAAATATTGTTGTTAC
35229552 TTACGAACCA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 2 0.05
27 20 0.53
28 16 0.42
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.42
Consensus pattern (28 bp):
AAAAATATTGTTGTTACACGACAATGTC
Found at i:35229511 original size:29 final size:28
Alignment explanation
Indices: 35229450--35229525 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 28
35229440 CCATGTTGAA
* * *
35229450 AAAAAAAATTATTGTTACACGCTATGTTG
1 AAAAAATATT-TTGTTACACGCTATATTC
35229479 AAAAAATATTGTTGTTACACGAC-ATATTC
1 AAAAAATATT-TTGTTACACG-CTATATTC
35229508 -AAAAATATTTTGTTACAC
1 AAAAAATATTTTGTTACAC
35229526 TTTAATGTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 9 0.21
28 9 0.21
29 23 0.55
30 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.36
Consensus pattern (28 bp):
AAAAAATATTTTGTTACACGCTATATTC
Found at i:35229824 original size:159 final size:155
Alignment explanation
Indices: 35229535--35229837 Score: 473
Period size: 159 Copynumber: 1.9 Consensus size: 155
35229525 CTTTAATGTC
*
35229535 TAAAATATTGTTGTTACTTACGAACCAAAACTTCAAATCTTCTCAACTTTTTTCTTTTTTTGTTG
1 TAAAATATTGTTGTTACTTACGAACCAAAACTTCAAATCTTCTCAACTCTTTTCTTTTTTTGTTG
*
35229600 TTTTTTTTGACAATTTGGCACAGATTAAATTGTTTCTAACATCTTTTCATAAATCAAAATACAAA
66 TTTTTTTTGACAATTTGGCACAGATTAAAGTGTTTCTAACATCTTTTCATAAATCAAAATAC-AA
35229665 TATTTTTTTTATCTAAACCACCTACNGCT
130 -A-TTTTTTTATCTAAACCACCTAC-GCT
* * *
35229694 TAAAATTTTGTTGTTACTTATGAACCAAAACTTCAAATCTTTTCAACTCTTTTCATTTTTTT-TT
1 TAAAATATTGTTGTTACTTACGAACCAAAACTTCAAATCTTCTCAACTCTTTTC-TTTTTTTGTT
* * * *
35229758 GTTTTTTTTGACAATTTGGCACTGATTATAGTGTTTCTAACATGTTTTCATTAATCAAAATACAA
65 GTTTTTTTTGACAATTTGGCACAGATTAAAGTGTTTCTAACATCTTTTCATAAATCAAAATACAA
35229823 ATTTTTTTATCTAAA
130 ATTTTTTTATCTAAA
35229838 ATACTTATTT
Statistics
Matches: 134, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
156 14 0.10
157 1 0.01
158 2 0.01
159 110 0.82
160 7 0.05
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (155 bp):
TAAAATATTGTTGTTACTTACGAACCAAAACTTCAAATCTTCTCAACTCTTTTCTTTTTTTGTTG
TTTTTTTTGACAATTTGGCACAGATTAAAGTGTTTCTAACATCTTTTCATAAATCAAAATACAAA
TTTTTTTATCTAAACCACCTACGCT
Found at i:35231546 original size:31 final size:31
Alignment explanation
Indices: 35231487--35231570 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
35231477 GTATTAAAAG
* *
35231487 ATAAGAATTTTTTGACTTGGA--TTTTTTTTA
1 ATAAAAATTCTTTG-CTTGGATTTTTTTTTTA
*
35231517 ATAAAAGTTCTTTGCTTGGATTTTTTTTTTA
1 ATAAAAATTCTTTGCTTGGATTTTTTTTTTA
*
35231548 GTAAAAATTCTTTGCTTGGATTT
1 ATAAAAATTCTTTGCTTGGATTT
35231571 AAGAGATGAG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
29 6 0.13
30 11 0.23
31 30 0.64
ACGTcount: A:0.25, C:0.06, G:0.14, T:0.55
Consensus pattern (31 bp):
ATAAAAATTCTTTGCTTGGATTTTTTTTTTA
Found at i:35234442 original size:18 final size:18
Alignment explanation
Indices: 35234419--35234481 Score: 69
Period size: 18 Copynumber: 3.7 Consensus size: 18
35234409 TTGATAATGT
35234419 TGCTGCCACTGTTCCTAA
1 TGCTGCCACTGTTCCTAA
* *
35234437 TGCTGCCTCTGTCCCT-A
1 TGCTGCCACTGTTCCTAA
*
35234454 --CTGCCACTATTCCTAA
1 TGCTGCCACTGTTCCTAA
*
35234470 TGCTGCCTCTGT
1 TGCTGCCACTGT
35234482 CCCTGTTGCC
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
15 11 0.31
16 1 0.03
17 1 0.03
18 22 0.63
ACGTcount: A:0.13, C:0.37, G:0.16, T:0.35
Consensus pattern (18 bp):
TGCTGCCACTGTTCCTAA
Found at i:35234493 original size:33 final size:33
Alignment explanation
Indices: 35234421--35234485 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
35234411 GATAATGTTG
*
35234421 CTGCCACTGTTCCTAATGCTGCCTCTGTCCCTA
1 CTGCCACTATTCCTAATGCTGCCTCTGTCCCTA
35234454 CTGCCACTATTCCTAATGCTGCCTCTGTCCCT
1 CTGCCACTATTCCTAATGCTGCCTCTGTCCCT
35234486 GTTGCCACCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.12, C:0.40, G:0.14, T:0.34
Consensus pattern (33 bp):
CTGCCACTATTCCTAATGCTGCCTCTGTCCCTA
Found at i:35239266 original size:22 final size:23
Alignment explanation
Indices: 35239238--35239284 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
35239228 TACCTGATTC
*
35239238 TCCTGGTTTTCCTC-AACGTTTA
1 TCCTGGTTTTCCTCTAACGTCTA
*
35239260 TCCTGGTTTTGCTCTAACGTCTA
1 TCCTGGTTTTCCTCTAACGTCTA
35239283 TC
1 TC
35239285 TGACTTGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.13, C:0.28, G:0.15, T:0.45
Consensus pattern (23 bp):
TCCTGGTTTTCCTCTAACGTCTA
Found at i:35262798 original size:30 final size:30
Alignment explanation
Indices: 35262742--35262798 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
35262732 TATGTAAAGA
*
35262742 TAAAATTTTAAATTTATGAATATATTTGTT
1 TAAAATTTTAAATTTATAAATATATTTGTT
* *
35262772 TAAAA-TTTATAATTTTTAAATTTATTT
1 TAAAATTTTA-AATTTATAAATATATTT
35262799 ATTAATAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 4 0.17
30 19 0.83
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (30 bp):
TAAAATTTTAAATTTATAAATATATTTGTT
Found at i:35266555 original size:29 final size:29
Alignment explanation
Indices: 35266522--35266652 Score: 131
Period size: 30 Copynumber: 4.4 Consensus size: 29
35266512 TACTTTTAAA
*
35266522 TTTTTATATTTTTATTACATTTAATCAAG
1 TTTTTATATTTTTATTAAATTTAATCAAG
** *
35266551 TTTTTATATTTTTATTTTAAATCAAAT-AAT
1 TTTTTATATTTTTA--TTAAATTTAATCAAG
**
35266581 TTTTTATATTTTTATTATGTTTAATCAAG
1 TTTTTATATTTTTATTAAATTTAATCAAG
** *
35266610 TTTTTATATTTTTATTTTAAATCAAAT-AAA
1 TTTTTATATTTTTA--TTAAATTTAATCAAG
35266640 TTTTTATATTTTT
1 TTTTTATATTTTT
35266653 TATTTTAAAT
Statistics
Matches: 83, Mismatches: 14, Indels: 9
0.78 0.13 0.08
Matches are distributed among these distances:
28 7 0.08
29 30 0.36
30 31 0.37
31 15 0.18
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (29 bp):
TTTTTATATTTTTATTAAATTTAATCAAG
Found at i:35266592 original size:59 final size:59
Alignment explanation
Indices: 35266518--35266652 Score: 243
Period size: 59 Copynumber: 2.3 Consensus size: 59
35266508 TTAATACTTT
35266518 TAAATTTTTATATTTTTATTACATTTAATCAAGTTTTTATATTTTTATTTTAAATCAAA
1 TAAATTTTTATATTTTTATTACATTTAATCAAGTTTTTATATTTTTATTTTAAATCAAA
* **
35266577 TAATTTTTTATATTTTTATTATGTTTAATCAAGTTTTTATATTTTTATTTTAAATCAAA
1 TAAATTTTTATATTTTTATTACATTTAATCAAGTTTTTATATTTTTATTTTAAATCAAA
35266636 TAAATTTTTATATTTTT
1 TAAATTTTTATATTTTT
35266653 TATTTTAAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 72 1.00
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (59 bp):
TAAATTTTTATATTTTTATTACATTTAATCAAGTTTTTATATTTTTATTTTAAATCAAA
Found at i:35266656 original size:31 final size:30
Alignment explanation
Indices: 35266518--35266671 Score: 163
Period size: 31 Copynumber: 5.2 Consensus size: 30
35266508 TTAATACTTT
* **
35266518 TAAATTTTTATATTTTTA--TTACATTTAA
1 TAAATTTTTATATTTTTATTTTAAATCAAA
*
35266546 TCAAGTTTTTATATTTTTATTTTAAATCAAA
1 T-AAATTTTTATATTTTTATTTTAAATCAAA
* ** **
35266577 TAATTTTTTATATTTTTA--TTATGTTTAA
1 TAAATTTTTATATTTTTATTTTAAATCAAA
*
35266605 TCAAGTTTTTATATTTTTATTTTAAATCAAA
1 T-AAATTTTTATATTTTTATTTTAAATCAAA
35266636 TAAATTTTTATATTTTTTATTTTAAATCAAA
1 TAAATTTTTATA-TTTTTATTTTAAATCAAA
35266667 TAAAT
1 TAAAT
35266672 ACTTTTAATT
Statistics
Matches: 104, Mismatches: 15, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
28 8 0.08
29 32 0.31
30 26 0.25
31 38 0.37
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (30 bp):
TAAATTTTTATATTTTTATTTTAAATCAAA
Found at i:35283597 original size:3 final size:3
Alignment explanation
Indices: 35283589--35283620 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
35283579 GCAAATCCTT
35283589 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
35283621 TGTAGAAGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:35293318 original size:2 final size:2
Alignment explanation
Indices: 35293311--35293342 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35293301 TGACTATTAG
35293311 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35293343 AAATCAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35303645 original size:6 final size:6
Alignment explanation
Indices: 35303637--35303721 Score: 76
Period size: 6 Copynumber: 15.2 Consensus size: 6
35303627 GTTTTTTTCA
* * *
35303637 AGAGAA AGAGAG AGAGAG AGAGAG AGAGAG -GAG-G AGA-AG -GAAATN
1 AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGA-G
*
35303682 A-AGA- AGA-AG AGAGAG AGAGAG AGAGAG AGAGAG GGAGAG A
1 AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG A
35303722 AGGGAAAACT
Statistics
Matches: 66, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
4 5 0.08
5 11 0.17
6 50 0.76
ACGTcount: A:0.52, C:0.00, G:0.46, T:0.01
Consensus pattern (6 bp):
AGAGAG
Found at i:35303652 original size:4 final size:4
Alignment explanation
Indices: 35303637--35303721 Score: 76
Period size: 4 Copynumber: 22.8 Consensus size: 4
35303627 GTTTTTTTCA
* * *
35303637 AGAG AAAG AGAG AGAG AGAG AGAG AGAG AG-G AG-G AGA- AG-G AAATN
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGA-G
*
35303682 A-AG A-AG A-AG AGAG AGAG AGAG AGAG AGAG AGAG GGAG AGA
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGA
35303722 AGGGAAAACT
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
3 16 0.23
4 52 0.75
5 1 0.01
ACGTcount: A:0.52, C:0.00, G:0.46, T:0.01
Consensus pattern (4 bp):
AGAG
Found at i:35306324 original size:2 final size:2
Alignment explanation
Indices: 35306277--35306306 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
35306267 CACCCCACGT
35306277 TC TC TC TC TC TC TC TC TC T- TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
35306307 GTCAGCGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:35325912 original size:20 final size:20
Alignment explanation
Indices: 35325872--35325912 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
35325862 TATGTTTGTT
35325872 TTTTTAGTATCATTTTAATTA
1 TTTTTAGTAT-ATTTTAATTA
35325893 TTTTTAGTAT-TTTTACATTA
1 TTTTTAGTATATTTTA-ATTA
35325913 ATATATATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 4 0.21
21 10 0.53
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTTAGTATATTTTAATTA
Found at i:35332232 original size:2 final size:2
Alignment explanation
Indices: 35332225--35332254 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
35332215 CTATTGTGTC
35332225 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35332255 AAACTATTAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35336488 original size:12 final size:12
Alignment explanation
Indices: 35336471--35336495 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35336461 ATAACATGTA
35336471 AATAAAAAAATT
1 AATAAAAAAATT
35336483 AATAAAAAAATT
1 AATAAAAAAATT
35336495 A
1 A
35336496 TACTCGATAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAAAAAAATT
Found at i:35336539 original size:14 final size:13
Alignment explanation
Indices: 35336520--35336549 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
35336510 TTTTAGACTC
35336520 ATAAAATATAACAT
1 ATAAAATATAA-AT
35336534 ATAAAATATAAAT
1 ATAAAATATAAAT
35336547 ATA
1 ATA
35336550 CTCGAACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAAAATATAAAT
Found at i:35336665 original size:16 final size:18
Alignment explanation
Indices: 35336631--35336668 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
35336621 ATTTCAATAA
35336631 AAAAAAAGAGAAAGAGAG
1 AAAAAAAGAGAAAGAGAG
*
35336649 AAAAAAATA-AAAGGAGAG
1 AAAAAAAGAGAAA-GAGAG
35336667 AA
1 AA
35336669 GCATGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (18 bp):
AAAAAAAGAGAAAGAGAG
Found at i:35339509 original size:6 final size:6
Alignment explanation
Indices: 35339498--35339522 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
35339488 TTTATTTATA
35339498 TAATAT TAATAT TAATAT TAATAT T
1 TAATAT TAATAT TAATAT TAATAT T
35339523 TTATCTAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATAT
Found at i:35342223 original size:2 final size:2
Alignment explanation
Indices: 35342216--35342244 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35342206 TAATCTCTGT
35342216 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
35342245 TCATAGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35349646 original size:76 final size:75
Alignment explanation
Indices: 35349520--35349670 Score: 293
Period size: 76 Copynumber: 2.0 Consensus size: 75
35349510 CAAAATCTGA
35349520 TTTGGAGAAGCCAACCACATTACGACTAATGTTTTCACCTTCTTCACACACTAAGCCAACTTCAA
1 TTTGGAGAAGCCAACCACATTACGACTAATGTTTTCACCTTCTTCACACACTAAGCCAACTTCAA
35349585 TAGTACCTTT
66 TAGTACCTTT
35349595 NTTTGGAGAAGCCAACCACATTACGACTAATGTTTTCACCTTCTTCACACACTAAGCCAACTTCA
1 -TTTGGAGAAGCCAACCACATTACGACTAATGTTTTCACCTTCTTCACACACTAAGCCAACTTCA
35349660 ATAGTACCTTT
65 ATAGTACCTTT
35349671 AGGTGTTTTC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.30
Consensus pattern (75 bp):
TTTGGAGAAGCCAACCACATTACGACTAATGTTTTCACCTTCTTCACACACTAAGCCAACTTCAA
TAGTACCTTT
Found at i:35354715 original size:160 final size:164
Alignment explanation
Indices: 35354410--35354737 Score: 459
Period size: 160 Copynumber: 2.0 Consensus size: 164
35354400 AACCAACTTA
* * * ** *
35354410 CCAAACAGTTTTAAGTTAATTTTAAAAATTATTATTTTTTACAAAAGTTTCGTAATAATTTTTAA
1 CCAAACAGTTTTAACTTAATTTTAAAAATTAATATTTTTCACAAAAACTCCGTAATAATTTTTAA
* * * * *
35354475 GCTAAAAAATTTAAACTAACCAAATTTTTACTTTTTTTTTCTTTCCTCTTTTTTCTTCATTTTTC
66 GCTAAAAAATTTAAACTAACCAAATCTTTA-TTTTTTCTCCTCTCCTCTTTTTTCTTCACTTTTC
*
35354540 TTTTCTTCTTAATTCAAGTTGATTACTCTCTTCAC
130 TTTTCTTCCTAATTCAAGTTGATTACTCTCTTCAC
* * *
35354575 CCAAACAGTTTTAACTTAA-TTTAAAATTTAATATTTTTCGCAAAAACTCCGTAATAATTTTTAC
1 CCAAACAGTTTTAACTTAATTTTAAAAATTAATATTTTTCACAAAAACTCCGTAATAATTTTTAA
*
35354639 G-TATAAAAA-TTAAACTAACCAAA-CTTT-TTTTTTCTCCTCTCCTCTTTTTTCTTCGCTTTTC
66 GCTA-AAAAATTTAAACTAACCAAATCTTTATTTTTTCTCCTCTCCTCTTTTTTCTTCACTTTTC
35354700 TTTTCTTCCTAATTCAAGTTGATTACTCTCTTCAC
130 TTTTCTTCCTAATTCAAGTTGATTACTCTCTTCAC
35354735 CCA
1 CCA
35354738 TCAACCAGGT
Statistics
Matches: 146, Mismatches: 16, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
160 66 0.45
162 3 0.02
163 16 0.11
164 43 0.29
165 18 0.12
ACGTcount: A:0.29, C:0.19, G:0.04, T:0.48
Consensus pattern (164 bp):
CCAAACAGTTTTAACTTAATTTTAAAAATTAATATTTTTCACAAAAACTCCGTAATAATTTTTAA
GCTAAAAAATTTAAACTAACCAAATCTTTATTTTTTCTCCTCTCCTCTTTTTTCTTCACTTTTCT
TTTCTTCCTAATTCAAGTTGATTACTCTCTTCAC
Found at i:35355206 original size:29 final size:28
Alignment explanation
Indices: 35355152--35355206 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
35355142 ATCGTCAAAT
35355152 CATTCTTTTATTTTTCCTTTTGTTTTAC
1 CATTCTTTTATTTTTCCTTTTGTTTTAC
*
35355180 CATTTTTTTCATTTTTCTCTTTT-TTTT
1 CATTCTTTT-ATTTTTC-CTTTTGTTTT
35355207 CTCTCACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 8 0.33
29 11 0.46
30 5 0.21
ACGTcount: A:0.09, C:0.16, G:0.02, T:0.73
Consensus pattern (28 bp):
CATTCTTTTATTTTTCCTTTTGTTTTAC
Found at i:35363498 original size:9 final size:9
Alignment explanation
Indices: 35363484--35363511 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
35363474 TTTAAAAAGG
35363484 AGTTCGGTT
1 AGTTCGGTT
35363493 AGTTCGGTT
1 AGTTCGGTT
35363502 AGTTCGGTT
1 AGTTCGGTT
35363511 A
1 A
35363512 TTTGATATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.14, C:0.11, G:0.32, T:0.43
Consensus pattern (9 bp):
AGTTCGGTT
Found at i:35371690 original size:14 final size:15
Alignment explanation
Indices: 35371651--35371692 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
35371641 TATTATAATA
35371651 TTTTATTTATTCATAT
1 TTTTATTT-TTCATAT
*
35371667 TTTGTATTTTTCA-CT
1 TTT-TATTTTTCATAT
35371682 TTTTATTTTTC
1 TTTTATTTTTC
35371693 CCTGTGTTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 8 0.33
15 4 0.17
16 7 0.29
17 5 0.21
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTTATTTTTCATAT
Found at i:35399989 original size:17 final size:18
Alignment explanation
Indices: 35399957--35399990 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35399947 ATTGAAATTG
35399957 AAAAAAAGAAAGAAATGA
1 AAAAAAAGAAAGAAATGA
*
35399975 AAAAAAATAAA-AAATG
1 AAAAAAAGAAAGAAATG
35399991 CATGATACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (18 bp):
AAAAAAAGAAAGAAATGA
Found at i:35401883 original size:3 final size:3
Alignment explanation
Indices: 35401869--35401898 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
35401859 GTAAATATTT
*
35401869 ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
35401899 TATACGAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:35438530 original size:2 final size:2
Alignment explanation
Indices: 35438525--35438559 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
35438515 CTTTTTTCTA
35438525 AT AT AT AT AT AT AT AT AT AT AT -T 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
35438560 CACTATTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:35438846 original size:160 final size:161
Alignment explanation
Indices: 35438531--35438849 Score: 448
Period size: 159 Copynumber: 2.0 Consensus size: 161
35438521 TCTAATATAT
*
35438531 ATATATATATATATATTATATATATATATCACTATTTTCTTTTGCAAAGCATAATGAACTTTAAT
1 ATATATATATATATATTATATATATATATCACTATTTTCTTTTGAAAAGCATAATGAACTTTAAT
* *
35438596 TAATTAAAATATAATGATCGTGTAATTAGAATATACTAAAAATTGCAAATATGATTATTAAAACT
66 TAATTAAAATATAATGATCGTATAATTAAAATATACTAAAAATTGCAAATATGATTATTAAAACT
*
35438661 ATCATATATGTACTATGACAGTTACGTGTAA
131 ATCATATATGTACCATGACAGTTACGTGTAA
* * *** *
35438692 ATATGTATATATATA-TATATAT-TATTTTTTTATTTT-TATTTGAAAAGCATCATGGAA-TTTA
1 ATATATATATATATATTATATATATATATCACTATTTTCT-TTTGAAAAGCATAAT-GAACTTTA
* * *
35438753 ATTAATTAAAATTTAATGATCGTATAATTAAAATATACTAAAAAATTGCAAATATGATTGTTACA
64 ATTAATTAAAATATAATGATCGTATAATTAAAATATACT-AAAAATTGCAAATATGATTATTAAA
* *
35438818 GCTATCATATATGTACCATGATAGTTACGTGT
128 ACTATCATATATGTACCATGACAGTTACGTGT
35438850 TAATTATTTA
Statistics
Matches: 140, Mismatches: 15, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
158 1 0.01
159 63 0.45
160 62 0.44
161 14 0.10
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.41
Consensus pattern (161 bp):
ATATATATATATATATTATATATATATATCACTATTTTCTTTTGAAAAGCATAATGAACTTTAAT
TAATTAAAATATAATGATCGTATAATTAAAATATACTAAAAATTGCAAATATGATTATTAAAACT
ATCATATATGTACCATGACAGTTACGTGTAA
Found at i:35439487 original size:17 final size:17
Alignment explanation
Indices: 35439465--35439497 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35439455 GAATTGCCTT
35439465 AAAAAAAGATTTATTTG
1 AAAAAAAGATTTATTTG
*
35439482 AAAAAAATATTTATTT
1 AAAAAAAGATTTATTT
35439498 AAATTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (17 bp):
AAAAAAAGATTTATTTG
Found at i:35443998 original size:2 final size:2
Alignment explanation
Indices: 35443991--35444021 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35443981 AATAACAGTG
35443991 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
35444022 TATCAAGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35452148 original size:17 final size:17
Alignment explanation
Indices: 35452123--35452160 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
35452113 AAAAACAACC
35452123 TTTTTTCTC-CTTTTTT
1 TTTTTTCTCACTTTTTT
35452139 TTTTTCTCTCACTTTTTT
1 TTTTT-TCTCACTTTTTT
35452157 TTTT
1 TTTT
35452161 CCTTTCCACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.25
17 4 0.20
18 11 0.55
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTCTCACTTTTTT
Found at i:35472444 original size:30 final size:30
Alignment explanation
Indices: 35472403--35472469 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
35472393 TTTCTCACTC
35472403 TTCTTTCAAGTCATAGCTGAACATTTACCA
1 TTCTTTCAAGTCATAGCTGAACATTTACCA
*
35472433 TTCTTTGAAGTCATAGCTGAACATTTACCA
1 TTCTTTCAAGTCATAGCTGAACATTTACCA
35472463 TTCTTTC
1 TTCTTTC
35472470 TCGCTTAGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.40
Consensus pattern (30 bp):
TTCTTTCAAGTCATAGCTGAACATTTACCA
Found at i:35473101 original size:66 final size:66
Alignment explanation
Indices: 35472995--35473118 Score: 187
Period size: 66 Copynumber: 1.9 Consensus size: 66
35472985 ACTTTTAGTA
* *
35472995 AATTTTCTATTCAAATTTCTCTCAAATTTAAAAATAAGATATTTTTATTTTATGTAATCGAGCAT
1 AATTTTCTATTCAAATTTATCTCAAATTTAAAAATAAGATATTTTTACTTTATGTAATCGAGCAT
35473060 G
66 G
* * *
35473061 AATTTT-TAATTCGAATTTATCTCAAATTTAAATATAAGATATTTTTACTTTCTGTAAT
1 AATTTTCT-ATTCAAATTTATCTCAAATTTAAAAATAAGATATTTTTACTTTATGTAAT
35473119 TTTCAAGTCG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
65 1 0.02
66 51 0.98
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (66 bp):
AATTTTCTATTCAAATTTATCTCAAATTTAAAAATAAGATATTTTTACTTTATGTAATCGAGCAT
G
Found at i:35481604 original size:32 final size:31
Alignment explanation
Indices: 35481557--35481616 Score: 102
Period size: 32 Copynumber: 1.9 Consensus size: 31
35481547 AAATACAAAC
*
35481557 TTTTTTTTAATGTTAATCCTGGTCTGAGGTT
1 TTTTTTTTAAAGTTAATCCTGGTCTGAGGTT
35481588 TTTTTTTTGAAAGTTAATCCTGGTCTGAG
1 TTTTTTTT-AAAGTTAATCCTGGTCTGAG
35481617 TCATGCCCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 8 0.30
32 19 0.70
ACGTcount: A:0.18, C:0.10, G:0.20, T:0.52
Consensus pattern (31 bp):
TTTTTTTTAAAGTTAATCCTGGTCTGAGGTT
Found at i:35492944 original size:29 final size:29
Alignment explanation
Indices: 35492911--35493016 Score: 158
Period size: 29 Copynumber: 3.7 Consensus size: 29
35492901 GAAGGGAGAC
35492911 ACAAGATTTTTCAATTTTCTTTATTTGGT
1 ACAAGATTTTTCAATTTTCTTTATTTGGT
* * *
35492940 ACAAGATTTTTCAATTTTCTTCATTCGGG
1 ACAAGATTTTTCAATTTTCTTTATTTGGT
*
35492969 ACAAGATATTTCAATTTTCTTTATTTGGT
1 ACAAGATTTTTCAATTTTCTTTATTTGGT
* *
35492998 AAAAGATTTTTCCATTTTC
1 ACAAGATTTTTCAATTTTC
35493017 AATTAAGGCA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.50
Consensus pattern (29 bp):
ACAAGATTTTTCAATTTTCTTTATTTGGT
Found at i:35494398 original size:17 final size:15
Alignment explanation
Indices: 35494356--35494390 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
35494346 ATTTGAGGCC
* *
35494356 AGAGAAGGTGGGGAG
1 AGAGAGGGTGGAGAG
35494371 AGAGAGGGTGGAGAG
1 AGAGAGGGTGGAGAG
35494386 AGAGA
1 AGAGA
35494391 CGCGGTGGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.57, T:0.06
Consensus pattern (15 bp):
AGAGAGGGTGGAGAG
Found at i:35523581 original size:14 final size:13
Alignment explanation
Indices: 35523559--35523601 Score: 61
Period size: 14 Copynumber: 3.3 Consensus size: 13
35523549 TTAAAATATT
35523559 TTTTATTTTTTTA
1 TTTTATTTTTTTA
35523572 TTTGTATTTTTTTA
1 TTT-TATTTTTTTA
*
35523586 TTTTA-ATTTTTA
1 TTTTATTTTTTTA
35523598 TTTT
1 TTTT
35523602 CATTAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 10 0.36
13 5 0.18
14 13 0.46
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.81
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:35523651 original size:24 final size:23
Alignment explanation
Indices: 35523609--35523667 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
35523599 TTTCATTAAT
35523609 TTTAAATATTAATGATTTTATAA-
1 TTTAAATATTAATGATTTTA-AAC
35523632 TTTAAATATTAAT-ATCTTTTAAAC
1 TTTAAATATTAATGA--TTTTAAAC
*
35523656 TTTAAATTTTAA
1 TTTAAATATTAA
35523668 ATATTGATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
22 1 0.03
23 15 0.47
24 16 0.50
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (23 bp):
TTTAAATATTAATGATTTTAAAC
Found at i:35523895 original size:27 final size:27
Alignment explanation
Indices: 35523864--35523915 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
35523854 GGTAGTAACT
* *
35523864 TAACATATTATAATAGATATAAATATG
1 TAACATATCATAATAAATATAAATATG
*
35523891 TAACATATCATAATAAATATGAATA
1 TAACATATCATAATAAATATAAATA
35523916 GATATTACGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.35
Consensus pattern (27 bp):
TAACATATCATAATAAATATAAATATG
Found at i:35527951 original size:19 final size:19
Alignment explanation
Indices: 35527922--35527970 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
35527912 ATATATATAT
35527922 ATAAA-ATTCAATATGCAA
1 ATAAATATTCAATATGCAA
35527940 ATAAATATTCAATATGCAA
1 ATAAATATTCAATATGCAA
*
35527959 ACAAATAATTCA
1 ATAAAT-ATTCA
35527971 GAAAGACTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 5 0.18
19 18 0.64
20 5 0.18
ACGTcount: A:0.55, C:0.12, G:0.04, T:0.29
Consensus pattern (19 bp):
ATAAATATTCAATATGCAA
Found at i:35534744 original size:27 final size:27
Alignment explanation
Indices: 35534713--35534767 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
35534703 TTGGGAGAAA
35534713 CCTCATCAGTGTTTGTGGGAAAGAACT
1 CCTCATCAGTGTTTGTGGGAAAGAACT
* *
35534740 CCTCATCCGTGTTTGTGGGAAATAACT
1 CCTCATCAGTGTTTGTGGGAAAGAACT
35534767 C
1 C
35534768 ATCAGAGGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (27 bp):
CCTCATCAGTGTTTGTGGGAAAGAACT
Found at i:35540395 original size:56 final size:56
Alignment explanation
Indices: 35540309--35540421 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
35540299 TCAGCTACTG
*
35540309 TTGGTGAGTAAGAAATTTGGTTTTGCATAATTTTGCTTTAGATTAGAGAGATCATT
1 TTGGTGAGTAAGAAATTTGGTTTTGCATAATTTTGCTTGAGATTAGAGAGATCATT
* *
35540365 TTGGTGGGTAAGAAATTTGGTTTTGCATAATTTTGCTTGAGGTTAGAGAGATCATT
1 TTGGTGAGTAAGAAATTTGGTTTTGCATAATTTTGCTTGAGATTAGAGAGATCATT
35540421 T
1 T
35540422 CTTACAGGTG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.27, C:0.05, G:0.26, T:0.42
Consensus pattern (56 bp):
TTGGTGAGTAAGAAATTTGGTTTTGCATAATTTTGCTTGAGATTAGAGAGATCATT
Found at i:35549832 original size:26 final size:26
Alignment explanation
Indices: 35549774--35549832 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
35549764 GTTCCATAAG
35549774 TTTTTTAAATTAATATAAATATAACT
1 TTTTTTAAATTAATATAAATATAACT
** * *
35549800 TCCTTTAAATT-ATATACATATTATCT
1 TTTTTTAAATTAATATAAATA-TAACT
35549826 TTTTTTA
1 TTTTTTA
35549833 CTCATTTGAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTTTTAAATTAATATAAATATAACT
Found at i:35550208 original size:54 final size:54
Alignment explanation
Indices: 35550144--35550248 Score: 192
Period size: 54 Copynumber: 1.9 Consensus size: 54
35550134 TCAATCAAGA
35550144 ATCAACGTTTTTAAATTCTAATTCTATCACATAATCACATCACTAAACTACATT
1 ATCAACGTTTTTAAATTCTAATTCTATCACATAATCACATCACTAAACTACATT
* *
35550198 ATCAACGTTTTTAAATTCTGATTCTATCACATAATCACATCATTAAACTAC
1 ATCAACGTTTTTAAATTCTAATTCTATCACATAATCACATCACTAAACTAC
35550249 GTCATATATC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.37
Consensus pattern (54 bp):
ATCAACGTTTTTAAATTCTAATTCTATCACATAATCACATCACTAAACTACATT
Found at i:35556717 original size:27 final size:28
Alignment explanation
Indices: 35556661--35556720 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
35556651 TAATCGTGTT
*
35556661 ATCGTGTTCAAACGTATAAACGTGTTTA
1 ATCGTGTTCAAACATATAAACGTGTTTA
35556689 ATCGTGTTCAAACATAT-AACGTGTTTA
1 ATCGTGTTCAAACATATAAACGTGTTTA
35556716 ATCGT
1 ATCGT
35556721 ATTATAGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 15 0.48
28 16 0.52
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (28 bp):
ATCGTGTTCAAACATATAAACGTGTTTA
Found at i:35558672 original size:31 final size:33
Alignment explanation
Indices: 35558608--35558672 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
35558598 CTTTAAGATA
* *
35558608 TTTATAAATGTTTCAATGCCCTCCTTACAATATT
1 TTTACAAATGTTTCAATCCCCTCC-TACAATATT
35558642 TTTACAAAT-TTTCAATCCCCTCC-ACAATATT
1 TTTACAAATGTTTCAATCCCCTCCTACAATATT
35558673 AAAGTGCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 8 0.28
33 13 0.45
34 8 0.28
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.42
Consensus pattern (33 bp):
TTTACAAATGTTTCAATCCCCTCCTACAATATT
Found at i:35571723 original size:2 final size:2
Alignment explanation
Indices: 35571716--35571769 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
35571706 GATGATGATG
35571716 GA GA GA GA GA 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 GA GA GA GA GA
35571758 GA GA GA GA GA GA
1 GA GA GA GA GA GA
35571770 CGAACGAACG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35571842 original size:2 final size:2
Alignment explanation
Indices: 35571835--35571867 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35571825 NNNNNNNNNN
35571835 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
35571868 ATGAGAGCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35575552 original size:104 final size:104
Alignment explanation
Indices: 35575383--35575572 Score: 269
Period size: 104 Copynumber: 1.8 Consensus size: 104
35575373 AATTTAATAA
* * * *
35575383 TATTATTCCTTTTTTAATCTTTTAATTTTATTTTCATTAAAATTTTAAAATATTAATAATTTATT
1 TATTATTCATTTTTTAATCTTTTAATTTAATTTTCATTAAAAATTTAAAACATTAATAATTTATT
*
35575448 ATTAACTTACTAATATAATTTTTATTATTTCTCTATTTG
66 ATTAAATTACTAATATAATTTTTATTATTTCTCTATTTG
35575487 TATT-TTCATTTTTTAATCTTTTAATTTAAATTTTCATTAAAAATTT-AAACATTAA-AATTTTT
1 TATTATTCATTTTTTAATCTTTTAATTT-AATTTTCATTAAAAATTTAAAACATTAATAA--TTT
* *
35575549 ATTATTAAATTATTAATTTAATTT
63 ATTATTAAATTACTAATATAATTT
35575573 CTTTCTACTT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
102 2 0.03
103 30 0.39
104 44 0.58
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.58
Consensus pattern (104 bp):
TATTATTCATTTTTTAATCTTTTAATTTAATTTTCATTAAAAATTTAAAACATTAATAATTTATT
ATTAAATTACTAATATAATTTTTATTATTTCTCTATTTG
Found at i:35582544 original size:62 final size:62
Alignment explanation
Indices: 35582447--35582571 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
35582437 GCTTACACTT
35582447 TACACAATGTGAGAAAAGGAAAAACAATGAAGTTTGAACAACTCTTTCTATTAGTGCAGACA
1 TACACAATGTGAGAAAAGGAAAAACAATGAAGTTTGAACAACTCTTTCTATTAGTGCAGACA
*
35582509 TACACAATGTGAGAAAAGGAAAACCAATGAAGTTTGAACAACTCTTTCTATTAGTGCAGACA
1 TACACAATGTGAGAAAAGGAAAAACAATGAAGTTTGAACAACTCTTTCTATTAGTGCAGACA
35582571 T
1 T
35582572 GGTGCAAGAG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (62 bp):
TACACAATGTGAGAAAAGGAAAAACAATGAAGTTTGAACAACTCTTTCTATTAGTGCAGACA
Found at i:35584756 original size:123 final size:123
Alignment explanation
Indices: 35584537--35584784 Score: 424
Period size: 123 Copynumber: 2.0 Consensus size: 123
35584527 ACCACACCGT
* ** *
35584537 GAAAGAGGTAATTATGGAAGCAGAATCCCATCCCGTTATTGTTCCGCCAGGCGAGAACAAGGCTC
1 GAAAGAGGTAATCATGGAAGCAGAATCCCATCCCGTTATCCTCCCGCCAGGCGAGAACAAGGCTC
*
35584602 TTTACGACTTCGCGGAGATGTCACGGACACTGTACCATGCAGAAAAGAAAGTCGTTGC
66 TTTACAACTTCGCGGAGATGTCACGGACACTGTACCATGCAGAAAAGAAAGTCGTTGC
* *
35584660 GAAAGAGGTAATCATGGAAGCAGAATCCCATCCCGTTATCCTCCCGCCTGGTGAGAACAAGGCTC
1 GAAAGAGGTAATCATGGAAGCAGAATCCCATCCCGTTATCCTCCCGCCAGGCGAGAACAAGGCTC
*
35584725 TTTACAACTTCGCGGAGATGTCACGGGCACTGTACCATGCAGAAAAGAAAGTCGTTGC
66 TTTACAACTTCGCGGAGATGTCACGGACACTGTACCATGCAGAAAAGAAAGTCGTTGC
35584783 GA
1 GA
35584785 GGAGATTGAA
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
123 117 1.00
ACGTcount: A:0.30, C:0.24, G:0.26, T:0.21
Consensus pattern (123 bp):
GAAAGAGGTAATCATGGAAGCAGAATCCCATCCCGTTATCCTCCCGCCAGGCGAGAACAAGGCTC
TTTACAACTTCGCGGAGATGTCACGGACACTGTACCATGCAGAAAAGAAAGTCGTTGC
Found at i:35586770 original size:3 final size:3
Alignment explanation
Indices: 35586762--35586790 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
35586752 CTTTGCTCAG
35586762 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
35586791 TTGGCAATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.34, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:35596181 original size:18 final size:19
Alignment explanation
Indices: 35596144--35596187 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
35596134 AATAAATAAT
*
35596144 TATTAATAATATCCTTAGA
1 TATTAATAATATCATTAGA
*
35596163 TATTCATAATAT-ATTAGA
1 TATTAATAATATCATTAGA
35596181 TATTAAT
1 TATTAAT
35596188 GTATAATACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (19 bp):
TATTAATAATATCATTAGA
Found at i:35596777 original size:17 final size:17
Alignment explanation
Indices: 35596755--35596800 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
35596745 TAACAATATT
35596755 TATGTATAAATTAAATA
1 TATGTATAAATTAAATA
*
35596772 TATGTATATA-T-AATA
1 TATGTATAAATTAAATA
*
35596787 TATTTATACAATTA
1 TATGTATA-AATTA
35596801 TATAGATTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
15 11 0.48
16 2 0.09
17 10 0.43
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (17 bp):
TATGTATAAATTAAATA
Found at i:35606947 original size:21 final size:21
Alignment explanation
Indices: 35606913--35606961 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
35606903 ATAAGTTATA
35606913 GAAAAATCTAAATT-ATATATT
1 GAAAAATCTAAATTGA-ATATT
* *
35606934 GAAAAGTCTGAATTGAATATT
1 GAAAAATCTAAATTGAATATT
*
35606955 GAGAAAT
1 GAAAAAT
35606962 TTATATTATG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.49, C:0.04, G:0.14, T:0.33
Consensus pattern (21 bp):
GAAAAATCTAAATTGAATATT
Found at i:35623672 original size:13 final size:12
Alignment explanation
Indices: 35623642--35623684 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
35623632 ATTATTAATA
*
35623642 AAAATTAAATTA
1 AAAATTAAATTT
35623654 ATAAATTAAAATTT
1 A-AAATT-AAATTT
*
35623668 AAAATTATATTT
1 AAAATTAAATTT
35623680 AAAAT
1 AAAAT
35623685 ACTTAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 11 0.41
13 10 0.37
14 6 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATTAAATTT
Found at i:35625883 original size:21 final size:22
Alignment explanation
Indices: 35625850--35625898 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
35625840 AAACGATATT
35625850 ATAAAATTTTTAAAA-AATAAA
1 ATAAAATTTTTAAAATAATAAA
*
35625871 AGTAAAA-TTTTAAAATATTAAA
1 A-TAAAATTTTTAAAATAATAAA
35625893 ATAAAA
1 ATAAAA
35625899 CAAAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
ATAAAATTTTTAAAATAATAAA
Found at i:35627062 original size:84 final size:85
Alignment explanation
Indices: 35626937--35627104 Score: 240
Period size: 81 Copynumber: 2.0 Consensus size: 85
35626927 ATTAGAAAAG
35626937 ATAGAGAGAGAGAGGAGGGATGAATTAAAATTTTTAGAAATGTATTAGAAATAAGAAAATAGGGA
1 ATAGAGAGAGAGAGGAGGGATGAATTAAAATTTTTAGAAATGTATT-GAAAT-AGAAAA-A-GGA
35627002 A-GGGGGAGAGAGAAG-AAGAGGA
62 AGGGGGGAGAGAGAAGAAAGAGGA
*
35627024 NATAGAGAGAGAGA-GAGGGATG-A-TAAAATTTTT-GAAATGTATTGAAATAGAAAAATGAAGG
1 -ATAGAGAGAGAGAGGAGGGATGAATTAAAATTTTTAGAAATGTATTGAAATAGAAAAAGGAAGG
35627085 GGGGAGAGAGAAGAAAGAGG
65 GGGGAGAGAGAAGAAAGAGG
35627105 GAAGCAAAGG
Statistics
Matches: 77, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
80 3 0.04
81 15 0.19
82 12 0.16
83 5 0.06
84 10 0.13
85 10 0.13
86 1 0.01
87 8 0.10
88 13 0.17
ACGTcount: A:0.48, C:0.00, G:0.35, T:0.17
Consensus pattern (85 bp):
ATAGAGAGAGAGAGGAGGGATGAATTAAAATTTTTAGAAATGTATTGAAATAGAAAAAGGAAGGG
GGGAGAGAGAAGAAAGAGGA
Found at i:35627908 original size:15 final size:15
Alignment explanation
Indices: 35627888--35627922 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
35627878 CATGGTAGTT
35627888 GAAAAAAGATAAAAA-
1 GAAAAAAGA-AAAAAG
35627903 GAAAAAAGAAAAAAG
1 GAAAAAAGAAAAAAG
35627918 GAAAA
1 GAAAA
35627923 CAATCAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (15 bp):
GAAAAAAGAAAAAAG
Found at i:35627914 original size:6 final size:7
Alignment explanation
Indices: 35627888--35627922 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
35627878 CATGGTAGTT
35627888 GAAAAAA
1 GAAAAAA
35627895 GATAAAAA
1 GA-AAAAA
35627903 GAAAAAA
1 GAAAAAA
35627910 GAAAAAA
1 GAAAAAA
35627917 GGAAAA
1 -GAAAA
35627923 CAATCAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 14 0.54
8 12 0.46
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (7 bp):
GAAAAAA
Found at i:35629971 original size:16 final size:16
Alignment explanation
Indices: 35629946--35629990 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
35629936 AAGGCTCAAG
35629946 AAGAAGAGAGAAAAGAAA
1 AAGAAGAGA-AAAA-AAA
*
35629964 GAGAAGAGAAAAAAAA
1 AAGAAGAGAAAAAAAA
35629980 AAGAAGA-AAAA
1 AAGAAGAGAAAA
35629991 CCCAACCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.16
16 9 0.36
17 4 0.16
18 8 0.32
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AAGAAGAGAAAAAAAA
Found at i:35645416 original size:3 final size:3
Alignment explanation
Indices: 35645408--35645435 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
35645398 GAAGCTAAGC
35645408 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
35645436 TAAAGCCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:35651031 original size:14 final size:15
Alignment explanation
Indices: 35651014--35651042 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
35651004 GTAAAAGAAA
35651014 TCCCAGAA-AAACTT
1 TCCCAGAAGAAACTT
35651028 TCCCAGAAGAAACTT
1 TCCCAGAAGAAACTT
35651043 GAGAAATCCT
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:0.41, C:0.28, G:0.10, T:0.21
Consensus pattern (15 bp):
TCCCAGAAGAAACTT
Found at i:35655673 original size:34 final size:34
Alignment explanation
Indices: 35655630--35655695 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
35655620 TTTTATTAGG
*
35655630 GAGTAAAAGATTTTGAATGAACCCCGACGCCTGT
1 GAGTAAAAGATTTTGAATGAACCCCAACGCCTGT
*
35655664 GAGTAAAAGATTTTGAATGAACCGCAACGCCT
1 GAGTAAAAGATTTTGAATGAACCCCAACGCCT
35655696 CTAACTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (34 bp):
GAGTAAAAGATTTTGAATGAACCCCAACGCCTGT
Found at i:35665999 original size:3 final size:3
Alignment explanation
Indices: 35665991--35666015 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35665981 TTCCTCATGT
35665991 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
35666016 TATTGCAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:35670417 original size:5 final size:5
Alignment explanation
Indices: 35670395--35670507 Score: 54
Period size: 5 Copynumber: 21.8 Consensus size: 5
35670385 TATGCAAACA
* * *
35670395 CTTTT C-TTT GTTTC CTTTT CTTTT CTTTAT TTTTT CTCTTT -TTTT C-TTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTT-T CTTTT CT-TTT CTTTT CTTTT
* * * *
35670444 CTTTT TTTTGT CTCTT CTCATT CATTTT -TTTCT CTGTTT CTTTT GTTTT
1 CTTTT CTTT-T CTTTT CT-TTT C-TTTT CTTT-T CT-TTT CTTTT CTTTT
*
35670493 TTATTT CTTTT CTTT
1 CT-TTT CTTTT CTTT
35670508 AATATATATA
Statistics
Matches: 82, Mismatches: 14, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
4 13 0.16
5 43 0.52
6 23 0.28
7 3 0.04
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.75
Consensus pattern (5 bp):
CTTTT
Found at i:35670444 original size:25 final size:26
Alignment explanation
Indices: 35670410--35670459 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
35670400 CTTTGTTTCC
35670410 TTTTCTTTTCTTTATTTTT-TCTCTTT
1 TTTTCTTTTCTTT-TTTTTGTCTCTTT
35670436 TTTTC-TTTCTTTTTTTTGTCTCTT
1 TTTTCTTTTCTTTTTTTTGTCTCTT
35670460 CTCATTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.22
25 13 0.57
26 5 0.22
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (26 bp):
TTTTCTTTTCTTTTTTTTGTCTCTTT
Found at i:35670459 original size:13 final size:12
Alignment explanation
Indices: 35670405--35670459 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
35670395 CTTTTCTTTG
*
35670405 TTTC-CTTTTCT
1 TTTCTCTTTTTT
*
35670416 TTTCT-TTATTT
1 TTTCTCTTTTTT
35670427 TTTCTCTTTTTT
1 TTTCTCTTTTTT
35670439 TCTT-TCTTTTTT
1 T-TTCTCTTTTTT
35670451 TTGTCTCTT
1 TT-TCTCTT
35670460 CTCATTCATT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
11 14 0.39
12 16 0.44
13 6 0.17
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTCTCTTTTTT
Found at i:35670492 original size:21 final size:21
Alignment explanation
Indices: 35670413--35670507 Score: 59
Period size: 21 Copynumber: 4.5 Consensus size: 21
35670403 TGTTTCCTTT
* *
35670413 TCTTTTC-TTTATTTTTTCTC
1 TCTTTTCTTTTGTTTTTTATC
* * *
35670433 TTTTTTTCTTTCTTTTTTTTGTC
1 -TCTTTTCTTT-TGTTTTTTATC
* * **
35670456 TCTTCTCATTCATTTTTT-TC
1 TCTTTTCTTTTGTTTTTTATC
*
35670476 TCTGTTTCTTTTGTTTTTTATT
1 TCT-TTTCTTTTGTTTTTTATC
35670498 TCTTTTCTTT
1 TCTTTTCTTT
35670508 AATATATATA
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
20 5 0.09
21 30 0.53
22 13 0.23
23 9 0.16
ACGTcount: A:0.04, C:0.17, G:0.03, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTGTTTTTTATC
Found at i:35670535 original size:127 final size:131
Alignment explanation
Indices: 35670396--35670650 Score: 457
Period size: 127 Copynumber: 2.0 Consensus size: 131
35670386 ATGCAAACAC
*
35670396 TTTTCTTTGTTTCCTTTTCTTTTCTTTATTTTTTCTCTTTTTTTCTTTCTTT-TTTTT-GTCTCT
1 TTTTCTTTGTTTCCTTTTCTTTTCTTTATTTTTTCTCTTTTTTTCTTTCTTTCTTTTTAATCTCT
35670459 TCTCATTCATTTTTTTCTCT-GTTTCTTTTGTTTTTTATTTCTTTTCTT-TA-ATATATATATAC
66 TCTCATTCATTTTTTTCT-TAGTTTCTTTTGTTTTTTATTTCTTTTCTTATATATATATATATAC
35670521 AA
130 AA
35670523 TTTTCTTTGTTTCCTTTTCTTTTCTTTATTTTTTCTCTTTTTTTCTTTCTTTCTTTTTAATCTCT
1 TTTTCTTTGTTTCCTTTTCTTTTCTTTATTTTTTCTCTTTTTTTCTTTCTTTCTTTTTAATCTCT
35670588 TCTCATTCATTTTTTTCTTAGTTTCTTTTGTTTTTTATTTCTTTTCTTATATATATATATATA
66 TCTCATTCATTTTTTTCTTAGTTTCTTTTGTTTTTTATTTCTTTTCTTATATATATATATATA
35670651 TTCCTACCCT
Statistics
Matches: 122, Mismatches: 1, Indels: 6
0.95 0.01 0.05
Matches are distributed among these distances:
127 52 0.43
128 6 0.05
129 51 0.42
130 2 0.02
131 11 0.09
ACGTcount: A:0.11, C:0.15, G:0.03, T:0.71
Consensus pattern (131 bp):
TTTTCTTTGTTTCCTTTTCTTTTCTTTATTTTTTCTCTTTTTTTCTTTCTTTCTTTTTAATCTCT
TCTCATTCATTTTTTTCTTAGTTTCTTTTGTTTTTTATTTCTTTTCTTATATATATATATATACA
A
Found at i:35670563 original size:18 final size:18
Alignment explanation
Indices: 35670536--35670580 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
35670526 TCTTTGTTTC
35670536 CTTT-TCTTTTCTTTATTT
1 CTTTCTCTTTT-TTTATTT
*
35670554 -TTTCTCTTTTTTTCTTT
1 CTTTCTCTTTTTTTATTT
35670571 CTTTCT-TTTT
1 CTTTCTCTTTT
35670581 AATCTCTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (18 bp):
CTTTCTCTTTTTTTATTT
Found at i:35670569 original size:8 final size:8
Alignment explanation
Indices: 35670537--35670580 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
35670527 CTTTGTTTCC
35670537 TTTTCTTT
1 TTTTCTTT
*
35670545 TCTTTATTT
1 T-TTTCTTT
35670554 TTTCTCTTT
1 TTT-TCTTT
35670563 TTTTCTTT
1 TTTTCTTT
*
35670571 CTTTCTTT
1 TTTTCTTT
35670579 TT
1 TT
35670581 AATCTCTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
8 16 0.53
9 14 0.47
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTCTTT
Found at i:35670580 original size:14 final size:14
Alignment explanation
Indices: 35670523--35670580 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
35670513 ATATATACAA
* *
35670523 TTTTCTTTGTTTCC
1 TTTTCTTTCTTTCT
*
35670537 TTTTCTTTTCTTTAT
1 TTTTC-TTTCTTTCT
*
35670552 TTTT-TCTC-TT-T
1 TTTTCTTTCTTTCT
35670563 TTTTCTTTCTTTCT
1 TTTTCTTTCTTTCT
35670577 TTTT
1 TTTT
35670581 AATCTCTTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
11 5 0.14
12 5 0.14
13 5 0.14
14 10 0.29
15 10 0.29
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTCTTTCTTTCT
Found at i:35670580 original size:16 final size:16
Alignment explanation
Indices: 35670538--35670632 Score: 57
Period size: 16 Copynumber: 5.5 Consensus size: 16
35670528 TTTGTTTCCT
* *
35670538 TTTCTTTTCTTTATTTT
1 TTTCTTTT-TTTCTTTC
35670555 TTCTCTTTTTTTCTTTC
1 TT-TCTTTTTTTCTTTC
35670572 TTTCTTTTTAATCTCTTCTC
1 TTTCTTTTT--T-TCTT-TC
* **
35670592 ATTCATTTTTTTCTTAG
1 TTTC-TTTTTTTCTTTC
*
35670609 TTTCTTTTGTTT-TTTA
1 TTTCTTTT-TTTCTTTC
35670625 TTTCTTTT
1 TTTCTTTT
35670633 CTTATATATA
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
16 21 0.33
17 16 0.25
18 11 0.17
19 5 0.08
20 5 0.08
21 5 0.08
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.75
Consensus pattern (16 bp):
TTTCTTTTTTTCTTTC
Found at i:35671079 original size:40 final size:40
Alignment explanation
Indices: 35671035--35671111 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
35671025 GTTGAAAATG
* *
35671035 TGATGCATTAGGATTTTATTTTTTTTAGGTTTTAAACTCT
1 TGATGCATTAGGATTTTATTTTCTTGAGGTTTTAAACTCT
* * *
35671075 TGATGCCTTGGGATTTTGTTTTCTTGAGGTTTTAAAC
1 TGATGCATTAGGATTTTATTTTCTTGAGGTTTTAAAC
35671112 CCTCAACCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.19, C:0.09, G:0.19, T:0.52
Consensus pattern (40 bp):
TGATGCATTAGGATTTTATTTTCTTGAGGTTTTAAACTCT
Found at i:35675088 original size:51 final size:51
Alignment explanation
Indices: 35675012--35675127 Score: 169
Period size: 51 Copynumber: 2.3 Consensus size: 51
35675002 GTTAACATTC
* * *
35675012 CTAATCCTTGTACAATACGATATCTAAACTATTAAGACTTGGAATAAATTA
1 CTAATCCTTGTATAACACAATATCTAAACTATTAAGACTTGGAATAAATTA
**
35675063 CTAATCCTTGTATAACACAATATCTAAACTATTAAGACTTTTAATAAATTA
1 CTAATCCTTGTATAACACAATATCTAAACTATTAAGACTTGGAATAAATTA
* *
35675114 CTAATGCTTCTATA
1 CTAATCCTTGTATA
35675128 GGACATGTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (51 bp):
CTAATCCTTGTATAACACAATATCTAAACTATTAAGACTTGGAATAAATTA
Found at i:35682236 original size:21 final size:24
Alignment explanation
Indices: 35682210--35682253 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 24
35682200 TACTGAGTAT
35682210 CCTCAATTA-A-A-AAAAAAAAAC
1 CCTCAATTATATATAAAAAAAAAC
35682231 CCTCAATTATATATAAAAAAAAA
1 CCTCAATTATATATAAAAAAAAA
35682254 TTAATACTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 1 0.05
23 1 0.05
24 9 0.45
ACGTcount: A:0.64, C:0.16, G:0.00, T:0.20
Consensus pattern (24 bp):
CCTCAATTATATATAAAAAAAAAC
Found at i:35690601 original size:2 final size:2
Alignment explanation
Indices: 35690594--35690628 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
35690584 AAGTTAGTAG
35690594 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35690629 GCTATTTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35690792 original size:28 final size:28
Alignment explanation
Indices: 35690760--35690813 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
35690750 GACGACCACC
*
35690760 AATTGAAAAAGAAGACCACCCATTGACA
1 AATTGAAAAAGAAGACCACCAATTGACA
* *
35690788 AATTGAAAGAGATGACCACCAATTGA
1 AATTGAAAAAGAAGACCACCAATTGA
35690814 TATATGGGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.48, C:0.19, G:0.17, T:0.17
Consensus pattern (28 bp):
AATTGAAAAAGAAGACCACCAATTGACA
Found at i:35695052 original size:25 final size:25
Alignment explanation
Indices: 35695024--35695073 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
35695014 CCTTCACTAA
35695024 TTCTCCCCAAACTTATCCTTATATG
1 TTCTCCCCAAACTTATCCTTATATG
* ** *
35695049 TTCTCCGCTCACTTATCCTTGTATG
1 TTCTCCCCAAACTTATCCTTATATG
35695074 GTTATTTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.18, C:0.32, G:0.08, T:0.42
Consensus pattern (25 bp):
TTCTCCCCAAACTTATCCTTATATG
Found at i:35695673 original size:2 final size:2
Alignment explanation
Indices: 35695666--35695693 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35695656 GATAGTCATA
35695666 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
35695694 CAAGTTTTAT
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):
AT
Found at i:35699079 original size:25 final size:25
Alignment explanation
Indices: 35699043--35699091 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
35699033 TTGGGTCACT
35699043 AAGTCTACAAATTGGGATAGAAGCG
1 AAGTCTACAAATTGGGATAGAAGCG
* *
35699068 AAGTCTATAAATTGGGGTAGAAGC
1 AAGTCTACAAATTGGGATAGAAGC
35699092 AGAGTGACAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.39, C:0.10, G:0.29, T:0.22
Consensus pattern (25 bp):
AAGTCTACAAATTGGGATAGAAGCG
Found at i:35703766 original size:27 final size:27
Alignment explanation
Indices: 35703725--35703777 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
35703715 AAAACCCAAA
* * *
35703725 TCCATTGTTCTAACCGAATCAAGCAAT
1 TCCATGGTTCCAACCGAACCAAGCAAT
*
35703752 TCCATGGTTCCAACCGTACCAAGCAA
1 TCCATGGTTCCAACCGAACCAAGCAA
35703778 CCCAGCACCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.32, C:0.30, G:0.13, T:0.25
Consensus pattern (27 bp):
TCCATGGTTCCAACCGAACCAAGCAAT
Found at i:35708875 original size:2 final size:2
Alignment explanation
Indices: 35708868--35708901 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
35708858 TGCAAAAATA
35708868 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
35708902 GTATGTATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35711017 original size:17 final size:16
Alignment explanation
Indices: 35710977--35711017 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
35710967 ATATTAATAT
*
35710977 ATAAA-TTATTTTTTG
1 ATAAATTTACTTTTTG
35710992 ATAAATTTACTTTTTG
1 ATAAATTTACTTTTTG
35711008 ATAAACTTTA
1 ATAAA-TTTA
35711018 AATTTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.22
16 14 0.61
17 4 0.17
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (16 bp):
ATAAATTTACTTTTTG
Found at i:35712637 original size:16 final size:16
Alignment explanation
Indices: 35712600--35712644 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
35712590 AATTGAAATT
* *
35712600 AAAAAAGAAAAAGGAA
1 AAAAAAGTAAAAGAAA
*
35712616 AAAAAAGTAAATGAAA
1 AAAAAAGTAAAAGAAA
*
35712632 AAAAAATTAAAAG
1 AAAAAAGTAAAAG
35712645 TAAATATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (16 bp):
AAAAAAGTAAAAGAAA
Found at i:35712927 original size:10 final size:10
Alignment explanation
Indices: 35712912--35712950 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
35712902 AATTATTAAT
35712912 TATTTTTATA
1 TATTTTTATA
35712922 TA-TTTT-TA
1 TATTTTTATA
35712930 -ATTTTTATA
1 TATTTTTATA
35712939 TATTTTTA-A
1 TATTTTTATA
35712948 TAT
1 TAT
35712951 AATTAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
7 1 0.04
8 6 0.23
9 10 0.38
10 9 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TATTTTTATA
Found at i:35712933 original size:17 final size:17
Alignment explanation
Indices: 35712913--35712948 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
35712903 ATTATTAATT
35712913 ATTTTTATATATTTTTA
1 ATTTTTATATATTTTTA
35712930 ATTTTTATATATTTTTA
1 ATTTTTATATATTTTTA
35712947 AT
1 AT
35712949 ATAATTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTATATATTTTTA
Found at i:35717736 original size:35 final size:35
Alignment explanation
Indices: 35717692--35717789 Score: 133
Period size: 35 Copynumber: 2.8 Consensus size: 35
35717682 TTGTACAGAA
* *
35717692 AACAACTAGAACAAGTGTAGTGCTACTTCATACAG
1 AACAACTAGAACAAGTGAAGTGCTACTTCACACAG
* * * *
35717727 AATAACTAGAACAAGTAAAGCGCTACTTCACGCAG
1 AACAACTAGAACAAGTGAAGTGCTACTTCACACAG
*
35717762 AACAACTAGAACAAGTGAAGTACTACTT
1 AACAACTAGAACAAGTGAAGTGCTACTT
35717790 AAAGCAGAAG
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.20
Consensus pattern (35 bp):
AACAACTAGAACAAGTGAAGTGCTACTTCACACAG
Found at i:35718086 original size:29 final size:29
Alignment explanation
Indices: 35718047--35718108 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
35718037 TTCTACCTTA
*
35718047 TTCTCGTATACCTATT-TATGTACAGCTTC
1 TTCTCGTATACCTATTCT-CGTACAGCTTC
* *
35718076 TTCTCTTATACCTGTTCTCGTACAGCTTC
1 TTCTCGTATACCTATTCTCGTACAGCTTC
35718105 TTCT
1 TTCT
35718109 TTTGTAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.16, C:0.27, G:0.10, T:0.47
Consensus pattern (29 bp):
TTCTCGTATACCTATTCTCGTACAGCTTC
Found at i:35718126 original size:29 final size:29
Alignment explanation
Indices: 35718066--35718126 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
35718056 ACCTATTTAT
* *
35718066 GTACAGCTTCTTCTCTTATACCTGTTCTC
1 GTACAGCTTCTTCTCTTATAACTGTTCAC
* * *
35718095 GTACAGCTTCTTCTTTTGTAACTTTTCAC
1 GTACAGCTTCTTCTCTTATAACTGTTCAC
35718124 GTA
1 GTA
35718127 TATCTCTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.16, C:0.26, G:0.11, T:0.46
Consensus pattern (29 bp):
GTACAGCTTCTTCTCTTATAACTGTTCAC
Found at i:35720751 original size:18 final size:18
Alignment explanation
Indices: 35720728--35720771 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
35720718 GATAAAGGCC
* *
35720728 CATGAAACAAGGGTTTCT
1 CATGAAAAAAGAGTTTCT
35720746 CATGAAAAAAGAGTTTCT
1 CATGAAAAAAGAGTTTCT
35720764 CATGAAAA
1 CATGAAAA
35720772 GGGCATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (18 bp):
CATGAAAAAAGAGTTTCT
Found at i:35721018 original size:93 final size:95
Alignment explanation
Indices: 35720859--35721046 Score: 344
Period size: 93 Copynumber: 2.0 Consensus size: 95
35720849 TATGTTTCTG
35720859 GACTCGCATCCAGTGACGTCAAAGCAGAACGAGGGTGTAAGAACAAGTTAGAAGAACGTCAAACA
1 GACTCGCATCCAGTGACGTCAAAGCAGAACGAGGGTGTAAGAACAAGTTAGAAGAACGTCAAACA
*
35720924 AGTTGCCTGCGAC-T-TGGGCAACACCATT
66 AGTTGCCTACGACTTGTGGGCAACACCATT
*
35720952 GACTCGCATCCAGTGACGTCAAAGCAGAACGAGGGTGTGAGAACAAGTTAGAAGAACGTCAAACA
1 GACTCGCATCCAGTGACGTCAAAGCAGAACGAGGGTGTAAGAACAAGTTAGAAGAACGTCAAACA
35721017 AGTTGCCTACGACTTGTGGGCAACACCATT
66 AGTTGCCTACGACTTGTGGGCAACACCATT
35721047 TTCTCGGAAT
Statistics
Matches: 91, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
93 76 0.84
94 1 0.01
95 14 0.15
ACGTcount: A:0.34, C:0.22, G:0.26, T:0.18
Consensus pattern (95 bp):
GACTCGCATCCAGTGACGTCAAAGCAGAACGAGGGTGTAAGAACAAGTTAGAAGAACGTCAAACA
AGTTGCCTACGACTTGTGGGCAACACCATT
Found at i:35724126 original size:9 final size:9
Alignment explanation
Indices: 35724114--35724143 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
35724104 ATTAAAAAAA
35724114 TTAATAATT
1 TTAATAATT
*
35724123 TTAATAAAT
1 TTAATAATT
35724132 TTAATAATT
1 TTAATAATT
35724141 TTA
1 TTA
35724144 TATATTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TTAATAATT
Found at i:35724150 original size:17 final size:18
Alignment explanation
Indices: 35724114--35724153 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
35724104 ATTAAAAAAA
35724114 TTAATAATTTTAATAAAT
1 TTAATAATTTTAATAAAT
*
35724132 TTAATAATTTT-ATATAT
1 TTAATAATTTTAATAAAT
35724149 TTAAT
1 TTAAT
35724154 TATATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATAATTTTAATAAAT
Found at i:35724160 original size:22 final size:22
Alignment explanation
Indices: 35724147--35724189 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
35724137 AATTTTATAT
*
35724147 ATTTAATTATATAAAATTATTA
1 ATTTAATTATATAATATTATTA
*
35724169 ATTTAATTAT-TAATAATATTA
1 ATTTAATTATATAATATTATTA
35724190 CTTATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTAATTATATAATATTATTA
Found at i:35724827 original size:2 final size:2
Alignment explanation
Indices: 35724820--35724850 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35724810 ATGATAAATG
35724820 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35724851 TGCTAGTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35744625 original size:16 final size:16
Alignment explanation
Indices: 35744604--35744634 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35744594 TAAAAAAATT
35744604 AAATAATTACTTTATG
1 AAATAATTACTTTATG
*
35744620 AAATAATTATTTTAT
1 AAATAATTACTTTAT
35744635 TCCGTTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (16 bp):
AAATAATTACTTTATG
Done.