Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 13 of 295
Found at i:4103633 original size:57 final size:58
Alignment explanation
Indices: 4103563--4103695 Score: 196
Period size: 57 Copynumber: 2.3 Consensus size: 58
4103553 GATAAAATTG
* * * *
4103563 AATAGTTGGGTGACTATTTTATAACTTTTTAGAGTTGGGTGACCAAAAAAAAT-TACT
1 AATAGTTGAGTGACTATTTTATAACTTTTCAGAGTTGGATGACAAAAAAAAATCTACT
* *
4103620 AATAGTTGAGTGACCATTTTATAACTTTTCATAGTTGGATGACAAAAAAAAATCTACT
1 AATAGTTGAGTGACTATTTTATAACTTTTCAGAGTTGGATGACAAAAAAAAATCTACT
*
4103678 AATAGTTGAGTGGCTATT
1 AATAGTTGAGTGACTATT
4103696 AATATAATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
57 47 0.70
58 20 0.30
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (58 bp):
AATAGTTGAGTGACTATTTTATAACTTTTCAGAGTTGGATGACAAAAAAAAATCTACT
Found at i:4106209 original size:12 final size:12
Alignment explanation
Indices: 4106192--4106224 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
4106182 CGGCCTGCCC
4106192 ATATTAATTTTT
1 ATATTAATTTTT
4106204 ATATT-ATTTTT
1 ATATTAATTTTT
4106215 ATA-TAATTTT
1 ATATTAATTTT
4106225 AAAATATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:4106382 original size:30 final size:30
Alignment explanation
Indices: 4106346--4106406 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
4106336 CAACTTAACA
*
4106346 AGCAAATGCCTCTAAAATAATAACAAAATT
1 AGCAAATGCCTCTAAAATAATAAAAAAATT
* *
4106376 AGCAAATGTCTTTAAAATAATAAAAAAATT
1 AGCAAATGCCTCTAAAATAATAAAAAAATT
4106406 A
1 A
4106407 ATAAAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.26
Consensus pattern (30 bp):
AGCAAATGCCTCTAAAATAATAAAAAAATT
Found at i:4106403 original size:11 final size:11
Alignment explanation
Indices: 4106389--4106418 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
4106379 AAATGTCTTT
4106389 AAAATAATAAA
1 AAAATAATAAA
4106400 AAAATTAATAAA
1 AAAA-TAATAAA
4106412 AAAATAA
1 AAAATAA
4106419 GTTTTATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAATAATAAA
Found at i:4106465 original size:22 final size:22
Alignment explanation
Indices: 4106440--4106482 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4106430 TATCCAAACA
4106440 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* *
4106462 ATAATAGCAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
4106483 AATAGAGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.14, G:0.12, T:0.16
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:4106469 original size:11 final size:11
Alignment explanation
Indices: 4106447--4106509 Score: 58
Period size: 11 Copynumber: 5.7 Consensus size: 11
4106437 ACAATAACAA
*
4106447 CAAAATAGTAG
1 CAAAATAATAG
*
4106458 CAACATAATAG
1 CAAAATAATAG
*
4106469 CAAAATAGTAG
1 CAAAATAATAG
*
4106480 CAAAATAGAGAG
1 CAAAATA-ATAG
4106492 -AAAATAATAAG
1 CAAAATAAT-AG
4106503 -AAAATAA
1 CAAAATAA
4106510 AATTTAAAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
10 1 0.02
11 40 0.93
12 2 0.05
ACGTcount: A:0.62, C:0.08, G:0.14, T:0.16
Consensus pattern (11 bp):
CAAAATAATAG
Found at i:4106495 original size:22 final size:22
Alignment explanation
Indices: 4106447--4106497 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
4106437 ACAATAACAA
* *
4106447 CAAAATAGTAGCAACATAATAG
1 CAAAATAGTAGCAAAATAAGAG
4106469 CAAAATAGTAGCAAAATAGAGAG
1 CAAAATAGTAGCAAAATA-AGAG
4106492 -AAAATA
1 CAAAATA
4106498 ATAAGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 23 0.88
23 3 0.12
ACGTcount: A:0.59, C:0.10, G:0.16, T:0.16
Consensus pattern (22 bp):
CAAAATAGTAGCAAAATAAGAG
Found at i:4110370 original size:4 final size:4
Alignment explanation
Indices: 4110361--4110389 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
4110351 CCCTTTTCTA
4110361 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
4110390 CACGTTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:4121584 original size:19 final size:19
Alignment explanation
Indices: 4121541--4121584 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4121531 TTAACCCTCT
*
4121541 TAATATATTATATGGTATA
1 TAATATATTATATAGTATA
*
4121560 TAATATATTA-ATAGTTTA
1 TAATATATTATATAGTATA
4121578 T-ATATAT
1 TAATATAT
4121585 GCATCAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 6 0.26
18 7 0.30
19 10 0.43
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (19 bp):
TAATATATTATATAGTATA
Found at i:4124463 original size:26 final size:27
Alignment explanation
Indices: 4124426--4124476 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
4124416 TTCTTTCTTT
*
4124426 TTTTTGTTTTATAGATTTTTGCGTAAA
1 TTTTTGTTTTATAAATTTTTGCGTAAA
4124453 TTTTT-TTTTATAAATTTTTGCGTA
1 TTTTTGTTTTATAAATTTTTGCGTA
4124477 CAGCAATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.22, C:0.04, G:0.12, T:0.63
Consensus pattern (27 bp):
TTTTTGTTTTATAAATTTTTGCGTAAA
Found at i:4133194 original size:18 final size:18
Alignment explanation
Indices: 4133171--4133206 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4133161 TCTAATTCAC
4133171 TTTAATTTACCCAATCAA
1 TTTAATTTACCCAATCAA
4133189 TTTAATTTACCCAATCAA
1 TTTAATTTACCCAATCAA
4133207 AGCTTACTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTAATTTACCCAATCAA
Found at i:4136017 original size:3 final size:3
Alignment explanation
Indices: 4136011--4136055 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
4136001 GCTGCCATGA
* *
4136011 AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG -AG AAA AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
4136056 GGGAGGCGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:4136776 original size:3 final size:3
Alignment explanation
Indices: 4136770--4136801 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
4136760 CCCGCCGCCC
4136770 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
4136802 CATGGCAGCA
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:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:4136844 original size:27 final size:27
Alignment explanation
Indices: 4136814--4136897 Score: 159
Period size: 27 Copynumber: 3.1 Consensus size: 27
4136804 TGGCAGCAGC
4136814 ACCGGTGCCGCCTATGGGGTACCCTCA
1 ACCGGTGCCGCCTATGGGGTACCCTCA
*
4136841 ACCGGTGCCGCCTATGGGGTACCCTCC
1 ACCGGTGCCGCCTATGGGGTACCCTCA
4136868 ACCGGTGCCGCCTATGGGGTACCCTCA
1 ACCGGTGCCGCCTATGGGGTACCCTCA
4136895 ACC
1 ACC
4136898 TATATTTTAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.14, C:0.39, G:0.29, T:0.18
Consensus pattern (27 bp):
ACCGGTGCCGCCTATGGGGTACCCTCA
Found at i:4142498 original size:80 final size:81
Alignment explanation
Indices: 4142363--4142524 Score: 272
Period size: 80 Copynumber: 2.0 Consensus size: 81
4142353 CCCTTACATG
* *
4142363 TTGAGAACGAAGAAAAATGGGTTACTGATATGACTCTTGAAATTGTTACCATAAAACACTTTGAT
1 TTGAGAACGAAGAAAAATAGGTTACTGA-ATGACTCTTGAAATTGTTACCATAAAACACTTTGAC
4142428 CTTAGAGATGAGAAAAT
65 CTTAGAGATGAGAAAAT
* *
4142445 TTGAGAACGGAGAAAAATATGTTACTG-ATGACTCTTGAAATTGTTACCATAAAACACTTTGACC
1 TTGAGAACGAAGAAAAATAGGTTACTGAATGACTCTTGAAATTGTTACCATAAAACACTTTGACC
4142509 TTAGAGATGAGAAAAT
66 TTAGAGATGAGAAAAT
4142525 GTATAGTATA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
80 52 0.68
82 24 0.32
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (81 bp):
TTGAGAACGAAGAAAAATAGGTTACTGAATGACTCTTGAAATTGTTACCATAAAACACTTTGACC
TTAGAGATGAGAAAAT
Found at i:4143548 original size:3 final size:3
Alignment explanation
Indices: 4143540--4143567 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4143530 ACCAAATATG
4143540 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4143568 GGTGGAATGC
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4146978 original size:21 final size:22
Alignment explanation
Indices: 4146949--4146995 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
4146939 CAGAAGGAGT
*
4146949 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
4146971 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
4146992 GAGT
1 GAGT
4146996 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:4154852 original size:19 final size:19
Alignment explanation
Indices: 4154809--4154854 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
4154799 TATGTGCTTA
4154809 AAATTTTATAAATTTATAT
1 AAATTTTATAAATTTATAT
*
4154828 ATAATTTTA-AAATTATATCT
1 A-AATTTTATAAATT-TATAT
4154848 AAATTTT
1 AAATTTT
4154855 TACGCGTGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
AAATTTTATAAATTTATAT
Found at i:4154855 original size:20 final size:20
Alignment explanation
Indices: 4154809--4154856 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
4154799 TATGTGCTTA
*
4154809 AAATTTTATAAATTTATATAT
1 AAATTTT-TAAAATTATATAT
*
4154830 -AA-TTTTAAAATTATATCT
1 AAATTTTTAAAATTATATAT
4154848 AAATTTTTA
1 AAATTTTTA
4154857 CGCGTGGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 11 0.48
19 5 0.22
20 7 0.30
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
AAATTTTTAAAATTATATAT
Found at i:4161316 original size:46 final size:48
Alignment explanation
Indices: 4161244--4161346 Score: 147
Period size: 46 Copynumber: 2.2 Consensus size: 48
4161234 GACAGGACAG
* * * *
4161244 GACAGAAATGAGCCATGTAAGTCCATATCA-GT-TATATGGCTTTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
*
4161290 GACAGGAATGAGCCATGTAAGCCCATATTATATATATATGGCATTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
4161338 GACAGGAAT
1 GACAGGAAT
4161347 AATTCATGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
46 27 0.54
47 1 0.02
48 22 0.44
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (48 bp):
GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
Found at i:4165189 original size:46 final size:48
Alignment explanation
Indices: 4165117--4165219 Score: 147
Period size: 46 Copynumber: 2.2 Consensus size: 48
4165107 GACAGGACAG
* * * *
4165117 GACAGAAATGAGCCATGTAAGTCCATATCA-GT-TATATGGCTTTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
*
4165163 GACAGGAATGAGCCATGTAAGCCCATATTATATATATATGGCATTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
4165211 GACAGGAAT
1 GACAGGAAT
4165220 AATTCATGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
46 27 0.54
47 1 0.02
48 22 0.44
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (48 bp):
GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
Found at i:4171028 original size:111 final size:111
Alignment explanation
Indices: 4170834--4171052 Score: 341
Period size: 111 Copynumber: 2.0 Consensus size: 111
4170824 ACATGTATAA
* * *
4170834 TTTTGGTTAAGAGTTTATTGTCATAAATATTATAAGGCTCGATTTTAAGAAACTTTTTAAACTTT
1 TTTTGGTTAAGAGTTTATTGTCATAAATATCACAAGGCTCAATTTTAAGAAACTTTTTAAACTTT
* * *
4170899 CACCGTGCTTAAAAACACTATTTTGTAAATCA-ATTTTTTCAACCGT
66 CACCATGCTTAAAAACACTATTTTATAAA-CAGATTTTTCCAACCGT
* *
4170945 TTTTGGTTAAGAGTTTATTGTTATAAATATCACAATGCTCAATTTTAAGAAACTTTTTAAACTTT
1 TTTTGGTTAAGAGTTTATTGTCATAAATATCACAAGGCTCAATTTTAAGAAACTTTTTAAACTTT
*
4171010 TACCATGCTTAAAAACACTATTTTATAAACAGATTTTTCCAAC
66 CACCATGCTTAAAAACACTATTTTATAAACAGATTTTTCCAAC
4171053 AGTTAGGTCT
Statistics
Matches: 98, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
110 2 0.02
111 96 0.98
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (111 bp):
TTTTGGTTAAGAGTTTATTGTCATAAATATCACAAGGCTCAATTTTAAGAAACTTTTTAAACTTT
CACCATGCTTAAAAACACTATTTTATAAACAGATTTTTCCAACCGT
Found at i:4175709 original size:14 final size:13
Alignment explanation
Indices: 4175682--4175708 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4175672 TCTTTAAATC
4175682 TAAATCATTTTTT
1 TAAATCATTTTTT
4175695 TAAATCATTTTTT
1 TAAATCATTTTTT
4175708 T
1 T
4175709 TTCTTTTCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (13 bp):
TAAATCATTTTTT
Found at i:4188077 original size:120 final size:120
Alignment explanation
Indices: 4187864--4188103 Score: 453
Period size: 120 Copynumber: 2.0 Consensus size: 120
4187854 GTTTTATGAG
*
4187864 TCAAAGTGGTGGTTCCTTTGCTTTTTTAATTATTAATTTTTGGCTGTATCAACAGTCACAAGAAA
1 TCAAAGTGGTGGTTCCTTTGCTTTTTTAATTATTAATTTTTGGCTGAATCAACAGTCACAAGAAA
*
4187929 CTTTGACAAGAATTTTGGGAACTTTTGAAAGTTCAGTCTATGTTTTATGCTTGTT
66 CTTTGACAAGAATTTTGGGAACCTTTGAAAGTTCAGTCTATGTTTTATGCTTGTT
*
4187984 TCAAAGTGGTGGTTCCTTTGCTTTTTTAATTATTAATTTTTGGCTGAATCAACAGTTACAAGAAA
1 TCAAAGTGGTGGTTCCTTTGCTTTTTTAATTATTAATTTTTGGCTGAATCAACAGTCACAAGAAA
4188049 CTTTGACAAGAATTTTGGGAACCTTTGAAAGTTCAGTCTATGTTTTATGCTTGTT
66 CTTTGACAAGAATTTTGGGAACCTTTGAAAGTTCAGTCTATGTTTTATGCTTGTT
4188104 GCATACATGC
Statistics
Matches: 117, Mismatches: 3, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
120 117 1.00
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.43
Consensus pattern (120 bp):
TCAAAGTGGTGGTTCCTTTGCTTTTTTAATTATTAATTTTTGGCTGAATCAACAGTCACAAGAAA
CTTTGACAAGAATTTTGGGAACCTTTGAAAGTTCAGTCTATGTTTTATGCTTGTT
Found at i:4201530 original size:11 final size:11
Alignment explanation
Indices: 4201516--4201565 Score: 68
Period size: 11 Copynumber: 4.7 Consensus size: 11
4201506 TTTCAATATT
4201516 CTCTCAAATTC
1 CTCTCAAATTC
4201527 CTCTCAAA-T-
1 CTCTCAAATTC
*
4201536 CTCTCAAATTT
1 CTCTCAAATTC
*
4201547 CTCTTAAATTC
1 CTCTCAAATTC
4201558 CTCTCAAA
1 CTCTCAAA
4201566 ACTCTCGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.24
10 2 0.06
11 24 0.71
ACGTcount: A:0.30, C:0.32, G:0.00, T:0.38
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:4201540 original size:20 final size:21
Alignment explanation
Indices: 4201508--4201565 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
4201498 ATTCAATCTT
4201508 TCAATATTCTCTCAAATTCCTC
1 TCAA-ATTCTCTCAAATTCCTC
*
4201530 TCAAA-TCTCTCAAATTTCTC
1 TCAAATTCTCTCAAATTCCTC
*
4201550 TTAAATTCCTCTCAAA
1 TCAAATT-CTCTCAAA
4201566 ACTCTCGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 18 0.56
21 2 0.06
22 12 0.38
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (21 bp):
TCAAATTCTCTCAAATTCCTC
Found at i:4202744 original size:23 final size:21
Alignment explanation
Indices: 4202713--4202779 Score: 89
Period size: 21 Copynumber: 3.1 Consensus size: 21
4202703 CCTGATCAGT
4202713 ATACGACACATAAAGTGCCTG
1 ATACGACACATAAAGTGCCTG
** *
4202734 ATACGACACACGAGGTGCCTG
1 ATACGACACATAAAGTGCCTG
4202755 AAATACGACACATAAAGTGCCTG
1 --ATACGACACATAAAGTGCCTG
4202778 AT
1 AT
4202780 CAGTAAAGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
21 20 0.53
23 18 0.47
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (21 bp):
ATACGACACATAAAGTGCCTG
Found at i:4203174 original size:15 final size:15
Alignment explanation
Indices: 4203149--4203221 Score: 101
Period size: 15 Copynumber: 4.8 Consensus size: 15
4203139 TCATATATAT
4203149 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
4203165 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
4203180 AATAATTTCAATCAA
1 TATAAATTCAATCAA
* *
4203195 AATAATTTCAATCAA
1 TATAAATTCAATCAA
4203210 TATAAATTCAAT
1 TATAAATTCAAT
4203222 AAATTCATCG
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
15 49 0.92
16 4 0.08
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:4203241 original size:45 final size:44
Alignment explanation
Indices: 4203152--4203242 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 44
4203142 TATATATTAT
** *
4203152 ATAATTCAATCAATATAAATTCAATCAAAATAATTTCAATCAAA
1 ATAATTCAATCAATATAAATTCAATCAAAATAATCGCAACCAAA
* *
4203196 ATAATTTCAATCAATATAAATTCAAT-AAATTCATCGCATACCAAA
1 ATAA-TTCAATCAATATAAATTCAATCAAAATAATCGCA-ACCAAA
4203241 AT
1 AT
4203243 CAATCCATTC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
44 12 0.30
45 28 0.70
ACGTcount: A:0.52, C:0.15, G:0.01, T:0.32
Consensus pattern (44 bp):
ATAATTCAATCAATATAAATTCAATCAAAATAATCGCAACCAAA
Found at i:4204466 original size:21 final size:20
Alignment explanation
Indices: 4204442--4204485 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
4204432 TCCCCTGCTC
*
4204442 TCTATTTCGTTTCATTCTGTT
1 TCTATTTCCTTTC-TTCTGTT
*
4204463 TCTATTTCCTTTCTTTTGTT
1 TCTATTTCCTTTCTTCTGTT
4204483 TCT
1 TCT
4204486 TTAGTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.07, C:0.20, G:0.07, T:0.66
Consensus pattern (20 bp):
TCTATTTCCTTTCTTCTGTT
Found at i:4204505 original size:5 final size:5
Alignment explanation
Indices: 4204492--4204523 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
4204482 TTCTTTAGTT
4204492 TATATA TATAA TATAA TATAA TATAA TATAA T
1 TATA-A TATAA TATAA TATAA TATAA TATAA T
4204524 TAAAACATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TATAA
Found at i:4206660 original size:116 final size:116
Alignment explanation
Indices: 4206456--4206865 Score: 739
Period size: 116 Copynumber: 3.5 Consensus size: 116
4206446 CGTGGCCCTT
*
4206456 TAAAATGGAAATTATTTTAAATAAGGCAACATTTTGAATATTTTTATATTATTTCATGTAATTAG
1 TAAAATGAAAATTATTTTAAATAAGGCAACATTTTGAATATTTTTATATTATTTCATGTAATTAG
*
4206521 ATAAAAGGTTGTTTTAAACAAAGTAATTGTAATTTACTTTTATATTTTTAA
66 ATAAAAGGTTGTTTTAAATAAAGTAATTGTAATTTACTTTTATATTTTTAA
*
4206572 TAAAATGGAAATTATTTTAAATAAGGCAACATTTTGAATATTTTTATATTATTTCATGTAATTAG
1 TAAAATGAAAATTATTTTAAATAAGGCAACATTTTGAATATTTTTATATTATTTCATGTAATTAG
4206637 ATAAAAGGTTGTTTTAAATAAAGTAATTGTAATTTACTTTTATATTTTTAA
66 ATAAAAGGTTGTTTTAAATAAAGTAATTGTAATTTACTTTTATATTTTTAA
* * *
4206688 TAAAATGAAAATTATTTTAAATAAGGCAACATTTTGAATATTTTTATATTATTTCATGTGATAAT
1 TAAAATGAAAATTATTTTAAATAAGGCAACATTTTGAATATTTTTATATTATTTCATGTAATTAG
*
4206753 ATAAAAGGTTGTTTTAAATAAAGTAATTATAATTTACTTTTATATTTTTAA
66 ATAAAAGGTTGTTTTAAATAAAGTAATTGTAATTTACTTTTATATTTTTAA
* *
4206804 TAAAATGAAAATTATTTTAAATAAAGCAATATTTTGAATATTTTTATATTATTTCATGTAAT
1 TAAAATGAAAATTATTTTAAATAAGGCAACATTTTGAATATTTTTATATTATTTCATGTAAT
4206866 AAAATATAAA
Statistics
Matches: 285, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 285 1.00
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (116 bp):
TAAAATGAAAATTATTTTAAATAAGGCAACATTTTGAATATTTTTATATTATTTCATGTAATTAG
ATAAAAGGTTGTTTTAAATAAAGTAATTGTAATTTACTTTTATATTTTTAA
Found at i:4208318 original size:49 final size:49
Alignment explanation
Indices: 4208198--4208387 Score: 211
Period size: 49 Copynumber: 3.7 Consensus size: 49
4208188 GATAATAACA
* ** *
4208198 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTC-GTGATGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCACT--TGG
* * *
4208249 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCACTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCACTTGG
*
4208298 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAGGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---A-CTT--GG
4208353 ATGCCAATGCCATGTCCCAGACATGGTCTTACATG
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATG
4208388 AGATCTCTTT
Statistics
Matches: 119, Mismatches: 12, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
49 42 0.35
50 4 0.03
51 34 0.29
52 1 0.01
53 3 0.03
55 2 0.02
56 33 0.28
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCACTTGG
Found at i:4208511 original size:13 final size:13
Alignment explanation
Indices: 4208490--4208521 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4208480 GCTTGGATCA
*
4208490 TCATCAAATAAAT
1 TCATAAAATAAAT
4208503 TCATAAAATAAAT
1 TCATAAAATAAAT
4208516 TCATAA
1 TCATAA
4208522 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:4208768 original size:30 final size:30
Alignment explanation
Indices: 4208733--4208790 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
4208723 CCTCGACTCT
*
4208733 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
4208763 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
4208791 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:4212836 original size:126 final size:126
Alignment explanation
Indices: 4212604--4213142 Score: 783
Period size: 126 Copynumber: 4.3 Consensus size: 126
4212594 GCCCAAGTTA
* * * * * * *
4212604 TTTCAGAAACCACTATAACAAAAGAGCATCCACGTGGGAACTTTTTTCAGTACTTTTGCTGAAAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
* * **
4212669 TGCATCCTGCTTGAAGCATTTTTGATACTATTTATGCAGACACGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* * * *
4212730 TTTCAGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
* *
4212795 TGCATCCTGTTTGAAGCGTTTTT-ACCACTATTTGCGTAGACACGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGA-CACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* * * * *
4212856 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCATGTGGAATCTTCTTTTAGTACTTTTGCTGACAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
* *
4212921 TGCATCCTGCTTGAAGCGTTTTTTACACTATTTGCACAGACACGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* * *
4212982 TTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTCCTTTCAGTACTTTTGCTGACAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
* *
4213047 TGCATCCTGCTTGAAGCGTTTTTGACACCATTTGCGCAGACACGTCTTCTCAAATTTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* *
4213108 TTTCAAAGACTACTGTAGTAAAAGAGCGTCCACGT
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGT
4213143 AGAAGCTTTT
Statistics
Matches: 373, Mismatches: 38, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
125 1 0.00
126 371 0.99
127 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.34
Consensus pattern (126 bp):
TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
Found at i:4213321 original size:98 final size:98
Alignment explanation
Indices: 4213186--4213429 Score: 275
Period size: 98 Copynumber: 2.5 Consensus size: 98
4213176 AAGTTATCCT
* *
4213186 AAACCCCAAACCCTAATTTATTTGATTTTTT-TCTTAAATACCCTAAAAC-CTAAAATCC-TAAT
1 AAACCCTAAACTCTAATTTATTTGATTTTTTCT-TTAAA-ACCCTAAAACAC-AAAA-CCATAAT
* * *
4213248 CTAATTTTTTTTAAATTTA-TAATTAATTTACTCAAG
62 CTAATTTTTTTTAAAATTAGTAATTAATTTAATCAAC
* * *
4213284 TAACCCTAAACTCTAATTTATTTGATTTTTTCTTTAAAAACC-ATAAACACGAAACCATAATCTA
1 AAACCCTAAACTCTAATTTATTTGATTTTTTCTTTAAAACCCTA-AAACACAAAACCATAATCTA
*
4213348 ATTTTTTTTAAAATTAGTAATTAATTTAATTAAC
65 ATTTTTTTTAAAATTAGTAATTAATTTAATCAAC
* * *
4213382 AAACACTAAA-TCTTAATTTATTTAATTTTTTTCCTTAAAACCCTAAAA
1 AAACCCTAAACTC-TAATTTATTTGA-TTTTTTCTTTAAAACCCTAAAA
4213430 TTTAAAAATT
Statistics
Matches: 124, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
96 3 0.02
97 34 0.27
98 67 0.54
99 19 0.15
100 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (98 bp):
AAACCCTAAACTCTAATTTATTTGATTTTTTCTTTAAAACCCTAAAACACAAAACCATAATCTAA
TTTTTTTTAAAATTAGTAATTAATTTAATCAAC
Found at i:4219863 original size:9 final size:9
Alignment explanation
Indices: 4219848--4219898 Score: 84
Period size: 9 Copynumber: 5.7 Consensus size: 9
4219838 GTATTTTTCT
4219848 GTAATTCGG
1 GTAATTCGG
*
4219857 TTAATTCGG
1 GTAATTCGG
*
4219866 TTAATTCGG
1 GTAATTCGG
4219875 GTAATTCGG
1 GTAATTCGG
4219884 GTAATTCGG
1 GTAATTCGG
4219893 GTAATT
1 GTAATT
4219899 TTTAACCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 40 1.00
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (9 bp):
GTAATTCGG
Found at i:4222384 original size:12 final size:13
Alignment explanation
Indices: 4222359--4222403 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
4222349 TTTTCTTAAC
*
4222359 AATAATTCTAAAA
1 AATAAATCTAAAA
4222372 AATAAAT-TAAAA
1 AATAAATCTAAAA
*
4222384 AATAAATCTTAAA
1 AATAAATCTAAAA
4222397 AATAAAT
1 AATAAAT
4222404 ACAAATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 12 0.41
13 17 0.59
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAAATCTAAAA
Found at i:4222716 original size:13 final size:14
Alignment explanation
Indices: 4222692--4222721 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4222682 ATTTTAAATT
4222692 TTTAGAAATTTTTA
1 TTTAGAAATTTTTA
4222706 TTTAG-AATTTTTA
1 TTTAGAAATTTTTA
4222719 TTT
1 TTT
4222722 TTAAAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTAGAAATTTTTA
Found at i:4225609 original size:20 final size:20
Alignment explanation
Indices: 4225584--4225626 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
4225574 ATCGGTATTC
4225584 TTATCCTGAATTTCAGGATT
1 TTATCCTGAATTTCAGGATT
* *
4225604 TTATCCTGAATTTTAGTATT
1 TTATCCTGAATTTCAGGATT
4225624 TTA
1 TTA
4225627 ATTTAGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.51
Consensus pattern (20 bp):
TTATCCTGAATTTCAGGATT
Found at i:4230056 original size:6 final size:6
Alignment explanation
Indices: 4230045--4230076 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
4230035 CTAAATTAAT
*
4230045 AAAATA AAAATA AAAATA AAAATA AAACTA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AA
4230077 TAAAACAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:4230662 original size:10 final size:10
Alignment explanation
Indices: 4230639--4230738 Score: 95
Period size: 9 Copynumber: 10.4 Consensus size: 10
4230629 ATTAAGATTA
*
4230639 AATTTTAAAT
1 AATTTTTAAT
*
4230649 -ATTTTTATT
1 AATTTTTAAT
4230658 AATTTTTAAT
1 AATTTTTAAT
*
4230668 AA-TTTTAGT
1 AATTTTTAAT
4230677 AATTTCTT-AT
1 AATTT-TTAAT
*
4230687 AATTCTTAAT
1 AATTTTTAAT
4230697 -ATTTTTAAAT
1 AATTTTT-AAT
*
4230707 AATTTTTTAT
1 AATTTTTAAT
4230717 -ATTTTTAAT
1 AATTTTTAAT
4230726 AATTTTT-AT
1 AATTTTTAAT
4230735 AATT
1 AATT
4230739 ATTTGAAAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 8 0.11
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:4230663 original size:19 final size:19
Alignment explanation
Indices: 4230639--4230738 Score: 62
Period size: 19 Copynumber: 5.2 Consensus size: 19
4230629 ATTAAGATTA
4230639 AATTTTAAATATTTTTATT
1 AATTTTAAATATTTTTATT
* * *
4230658 AATTTTTAATAATTTTAGT
1 AATTTTAAATATTTTTATT
* * *
4230677 AATTTCT-TATAATTCTTAAT
1 AATTT-TAAAT-ATTTTTATT
* *
4230697 ATTTTTAAATAATTTT-TT
1 AATTTTAAATATTTTTATT
*
4230715 ATATTTTTAATAATTTTTA-T
1 A-ATTTTAAAT-ATTTTTATT
4230735 AATT
1 AATT
4230739 ATTTGAAAAT
Statistics
Matches: 60, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
18 2 0.03
19 38 0.63
20 20 0.33
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (19 bp):
AATTTTAAATATTTTTATT
Found at i:4230664 original size:20 final size:20
Alignment explanation
Indices: 4230635--4230738 Score: 76
Period size: 20 Copynumber: 5.3 Consensus size: 20
4230625 TTGAATTAAG
*
4230635 ATTAAATTTTAAATATTTTT
1 ATTAATTTTTAAATATTTTT
*
4230655 ATTAATTTTT-AATAATTTT
1 ATTAATTTTTAAATATTTTT
* * *
4230674 AGTAATTTCTTATA-ATTCTT
1 ATTAATTT-TTAAATATTTTT
* *
4230694 AAT-ATTTTTAAATAATTTT
1 ATTAATTTTTAAATATTTTT
4230713 -TTATATTTTT-AATAATTTTT
1 ATTA-ATTTTTAAAT-ATTTTT
4230733 A-TAATT
1 ATTAATT
4230739 ATTTGAAAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
18 5 0.08
19 29 0.45
20 30 0.46
21 1 0.02
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.61
Consensus pattern (20 bp):
ATTAATTTTTAAATATTTTT
Found at i:4230681 original size:29 final size:30
Alignment explanation
Indices: 4230639--4230731 Score: 106
Period size: 29 Copynumber: 3.2 Consensus size: 30
4230629 ATTAAGATTA
4230639 AATTTTAAAT-ATTTTTATTAATTTTTAAT
1 AATTTTAAATAATTTTTATTAATTTTTAAT
* *
4230668 AATTTT-AGTAATTTCTTA-TAATTCTTAAT
1 AATTTTAAATAATTT-TTATTAATTTTTAAT
*
4230697 ATTTTTAAATAA-TTTT-TTATATTTTTAAT
1 AATTTTAAATAATTTTTATTA-ATTTTTAAT
4230726 AATTTT
1 AATTTT
4230732 TATAATTATT
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
28 6 0.11
29 40 0.75
30 7 0.13
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.61
Consensus pattern (30 bp):
AATTTTAAATAATTTTTATTAATTTTTAAT
Found at i:4231415 original size:19 final size:19
Alignment explanation
Indices: 4231393--4231458 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
4231383 GTTTTCGTCG
*
4231393 GAAATGGTAATTTTTGTGA
1 GAAATGGTAATTTTTGTCA
* *
4231412 GAAATGATTAGTTTTTGTCA
1 GAAATG-GTAATTTTTGTCA
* *
4231432 AAAATGGTAATTTGTGTCA
1 GAAATGGTAATTTTTGTCA
4231451 GAAATGGT
1 GAAATGGT
4231459 TGGAAACAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 23 0.61
20 15 0.39
ACGTcount: A:0.33, C:0.03, G:0.24, T:0.39
Consensus pattern (19 bp):
GAAATGGTAATTTTTGTCA
Found at i:4231424 original size:39 final size:39
Alignment explanation
Indices: 4231381--4231456 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
4231371 ATTCCCAAAC
** * *
4231381 TAGTTTTCGTCGGAAATGGTAATTTTTGTGAGAAATGAT
1 TAGTTTTCGTCAAAAATGGTAATTTGTGTCAGAAATGAT
*
4231420 TAGTTTTTGTCAAAAATGGTAATTTGTGTCAGAAATG
1 TAGTTTTCGTCAAAAATGGTAATTTGTGTCAGAAATG
4231457 GTTGGAAACA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.30, C:0.05, G:0.24, T:0.41
Consensus pattern (39 bp):
TAGTTTTCGTCAAAAATGGTAATTTGTGTCAGAAATGAT
Found at i:4242614 original size:112 final size:109
Alignment explanation
Indices: 4242465--4242675 Score: 300
Period size: 108 Copynumber: 1.9 Consensus size: 109
4242455 TTGTCAATAT
4242465 AATATAATAATAAAGAATAAAAGATATTTCCATCAATTCATATACATATCATATAATAATAAACT
1 AATATAATAATAAAGAATAAAAGATATTTCCATCAATTCATATACATAT--TAT-ATAATAAA-T
* *
4242530 TTACATCCAATAAGTACTTCAATTATTTTATATAAAAAAACTCTAATG
62 TTACATACAATAAGCACTTCAATTATTTTATATAAAAAAACTCTAATG
* * *
4242578 AATATAATAA-AAATAATAAAATATAATTT-CATCAATTCATATGCATATTATATAATAAATTTA
1 AATATAATAATAAAGAATAAAAGAT-ATTTCCATCAATTCATATACATATTATATAATAAATTTA
* *
4242641 CATACAATAAGCATTTTAATTATTTTATATAAAAA
65 CATACAATAAGCACTTCAATTATTTTATATAAAAA
4242676 GCCTTATTAA
Statistics
Matches: 90, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
108 35 0.39
109 8 0.09
110 3 0.03
112 30 0.33
113 14 0.16
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (109 bp):
AATATAATAATAAAGAATAAAAGATATTTCCATCAATTCATATACATATTATATAATAAATTTAC
ATACAATAAGCACTTCAATTATTTTATATAAAAAAACTCTAATG
Found at i:4255885 original size:20 final size:19
Alignment explanation
Indices: 4255845--4255898 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
4255835 ATTTTAAAAT
* *
4255845 AAATATTATAAAACATTTA
1 AAATATTATAAAAAATATA
4255864 AAATATTATAAAAAATAATA
1 AAATATTATAAAAAAT-ATA
*
4255884 AACA-ATTTTAAAAAA
1 AA-ATATTATAAAAAA
4255899 AAACCAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 15 0.50
20 14 0.47
21 1 0.03
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATATTATAAAAAATATA
Found at i:4268745 original size:22 final size:22
Alignment explanation
Indices: 4268715--4268757 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4268705 AGATATAAAC
*
4268715 TATTTTAAAT-TCTTTTATTATG
1 TATTGTAAATCTC-TTTATTATG
4268737 TATTGTAAATCTCTTTATTAT
1 TATTGTAAATCTCTTTATTAT
4268758 CATTTATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (22 bp):
TATTGTAAATCTCTTTATTATG
Found at i:4279646 original size:3 final size:3
Alignment explanation
Indices: 4279559--4279637 Score: 122
Period size: 3 Copynumber: 26.3 Consensus size: 3
4279549 GTACTTTTGC
4279559 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
4279607 TAT TAT TAT CAT TTT TAC TAT TAT TAG TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4279638 GGTATTATTG
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:4279847 original size:38 final size:37
Alignment explanation
Indices: 4279768--4279851 Score: 102
Period size: 36 Copynumber: 2.3 Consensus size: 37
4279758 AATTTGTTTA
*
4279768 ATATATATATACGTATACTCATATTTCTTTTTTTATAT
1 ATATATATATACATATAC-CATATTTCTTTTTTTATAT
*
4279806 ATATCTATATACATATA-CATATTT-TTATTTTTATA-
1 ATATATATATACATATACCATATTTCTT-TTTTTATAT
4279841 AGTATATATAT
1 A-TATATATAT
4279852 TTATATGTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
35 3 0.07
36 23 0.56
38 15 0.37
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (37 bp):
ATATATATATACATATACCATATTTCTTTTTTTATAT
Found at i:4282991 original size:27 final size:28
Alignment explanation
Indices: 4282942--4283009 Score: 99
Period size: 27 Copynumber: 2.5 Consensus size: 28
4282932 TTAAAGACAC
4282942 TATTATAAATATAATAAATATTTTATTA
1 TATTATAAATATAATAAATATTTTATTA
4282970 TATTATAAA-A-AAGTAAATATTTTATTA
1 TATTATAAATATAA-TAAATATTTTATTA
4282997 TA-T-TAAATATAAT
1 TATTATAAATATAAT
4283010 TTTTAAAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
25 4 0.11
26 5 0.14
27 19 0.51
28 9 0.24
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (28 bp):
TATTATAAATATAATAAATATTTTATTA
Found at i:4284593 original size:22 final size:23
Alignment explanation
Indices: 4284566--4284608 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
4284556 TTATAATCAA
4284566 ATATAAACACATAATT-TTATTT
1 ATATAAACACATAATTATTATTT
* *
4284588 ATATAAATATATAATTATTAT
1 ATATAAACACATAATTATTAT
4284609 ATTTTATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATAAACACATAATTATTATTT
Found at i:4285795 original size:24 final size:24
Alignment explanation
Indices: 4285768--4285819 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
4285758 TTAGTAAGTC
*
4285768 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
4285792 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
4285816 AAAT
1 AAAT
4285820 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:4291920 original size:36 final size:36
Alignment explanation
Indices: 4291870--4291941 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
4291860 CCGCATAATT
* *
4291870 GAGTTTTTGTCATTAATCAAAATAGAAAAGAGAAAA
1 GAGTTTTTGCCATTAATCAAAAGAGAAAAGAGAAAA
4291906 GAGTTTTTGCCATTAATCAAAAGAGAAAAGAGAAAA
1 GAGTTTTTGCCATTAATCAAAAGAGAAAAGAGAAAA
4291942 TATACTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (36 bp):
GAGTTTTTGCCATTAATCAAAAGAGAAAAGAGAAAA
Found at i:4292284 original size:39 final size:38
Alignment explanation
Indices: 4292241--4292404 Score: 109
Period size: 40 Copynumber: 4.2 Consensus size: 38
4292231 TAAAAAACAT
*
4292241 TAAAAAAATATAAAAATTTATAAATATCATAATAACTTA
1 TAAAAAAATATAAAAATTTATAAAAATCATAATAA-TTA
* * * * ** * * *
4292280 TAAAATAATTCTAAAAA-TCATAAAGATTTTTATATTTT
1 TAAAA-AAATATAAAAATTTATAAAAATCATAATAATTA
* * *
4292318 TAAAAAATTATAAAAACTTATAAAAAAC-TAATAAATTA
1 TAAAAAAATATAAAAATTTATAAAAATCATAAT-AATTA
* *
4292356 TAAACAAATGTATAAAAATGTATAAAAAT-ATATATGAATTA
1 TAAA-AAA-ATATAAAAATTTATAAAAATCATA-AT-AATTA
4292397 TAAAAAAA
1 TAAAAAAA
4292405 ATCATTTATC
Statistics
Matches: 95, Mismatches: 23, Indels: 14
0.72 0.17 0.11
Matches are distributed among these distances:
37 13 0.14
38 21 0.22
39 20 0.21
40 30 0.32
41 11 0.12
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (38 bp):
TAAAAAAATATAAAAATTTATAAAAATCATAATAATTA
Found at i:4292383 original size:11 final size:10
Alignment explanation
Indices: 4292318--4292383 Score: 57
Period size: 10 Copynumber: 6.6 Consensus size: 10
4292308 TTTATATTTT
4292318 TAAAAAATTA
1 TAAAAAATTA
*
4292328 TAAAAACTTA
1 TAAAAAATTA
*
4292338 TAAAAAA--C
1 TAAAAAATTA
*
4292346 TAATAAATTA
1 TAAAAAATTA
4292356 TAAACAAATGTA
1 TAAA-AAAT-TA
4292368 T-AAAAATGTA
1 TAAAAAAT-TA
4292378 TAAAAA
1 TAAAAA
4292384 TATATATGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
8 6 0.13
10 26 0.58
11 10 0.22
12 3 0.07
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:4292389 original size:20 final size:19
Alignment explanation
Indices: 4292320--4292402 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
4292310 TATATTTTTA
4292320 AAAAAT-TATAAAAACTTAT
1 AAAAATATATAAAAA-TTAT
*
4292339 AAAAA-ACTA-ATAAATTAT
1 AAAAATA-TATAAAAATTAT
*
4292357 AAACAAATGTATAAAAATGTAT
1 -AA-AAATATATAAAAAT-TAT
**
4292379 AAAAATATATATGAATTAT
1 AAAAATATATAAAAATTAT
4292398 AAAAA
1 AAAAA
4292403 AAATCATTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
18 4 0.08
19 19 0.37
20 18 0.35
21 7 0.14
22 3 0.06
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
AAAAATATATAAAAATTAT
Found at i:4292403 original size:20 final size:18
Alignment explanation
Indices: 4292318--4292403 Score: 66
Period size: 20 Copynumber: 4.4 Consensus size: 18
4292308 TTTATATTTT
*
4292318 TAAAAAATTATAAAAACTTA
1 TAAAAAA-TATATAAA-TTA
4292338 TAAAAAACTA-ATAAATTA
1 TAAAAAA-TATATAAATTA
*
4292356 TAAACAAATGTATAAAAATGTA
1 TAAA-AAA--TATATAAAT-TA
*
4292378 TAAAAATATATATGAATTA
1 TAAAAA-ATATATAAATTA
4292397 TAAAAAA
1 TAAAAAA
4292404 AATCATTTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
18 8 0.15
19 15 0.27
20 18 0.33
21 7 0.13
22 7 0.13
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
TAAAAAATATATAAATTA
Found at i:4307070 original size:24 final size:24
Alignment explanation
Indices: 4307038--4307087 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
4307028 TATGTATTTT
*
4307038 CATAATCAAATACAAATACAGATG
1 CATAATCAAATACAAATACAAATG
* * *
4307062 CATATTCAAATTCAGATACAAATG
1 CATAATCAAATACAAATACAAATG
4307086 CA
1 CA
4307088 GACACATATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.18, G:0.08, T:0.24
Consensus pattern (24 bp):
CATAATCAAATACAAATACAAATG
Found at i:4308652 original size:152 final size:153
Alignment explanation
Indices: 4308470--4308774 Score: 567
Period size: 152 Copynumber: 2.0 Consensus size: 153
4308460 TTACCACTAA
*
4308470 ACCAGCAGATACATTCTTATTAACAATTAAGCAAAAATATAATATAACCCTTACGAACCAAGTCA
1 ACCAGCAGACACATTCTTATTAACAATTAAGCAAAAATATAATATAACCCTTACGAACCAAGTCA
*
4308535 GATATAATTTCAAAATTAATAGAAATATTCCATATGC-AAAAAAAACGAACACAAGTCCTAAAAC
66 GATATAATTTCAAAATTAATAGAAATATTCCATATGCAAAAAAAAAAGAACACAAGTCCTAAAAC
4308599 ACACAACCAGAACACCTAACCAC
131 ACACAACCAGAACACCTAACCAC
4308622 ACCAGCAGACACATTCTTATTAACAATTAAGCAAAAATATAATATAACCCTTACGAACCAAGTCA
1 ACCAGCAGACACATTCTTATTAACAATTAAGCAAAAATATAATATAACCCTTACGAACCAAGTCA
* *
4308687 GATATAATTTCAAAATTAATGGAAATATTCCATATGCAAAAAAAAAAGAACACAAGTCCTCAAAC
66 GATATAATTTCAAAATTAATAGAAATATTCCATATGCAAAAAAAAAAGAACACAAGTCCTAAAAC
4308752 ACACAACCAGAACACCTAACCAC
131 ACACAACCAGAACACCTAACCAC
4308775 TGAACCAGAT
Statistics
Matches: 148, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
152 100 0.68
153 48 0.32
ACGTcount: A:0.49, C:0.23, G:0.08, T:0.21
Consensus pattern (153 bp):
ACCAGCAGACACATTCTTATTAACAATTAAGCAAAAATATAATATAACCCTTACGAACCAAGTCA
GATATAATTTCAAAATTAATAGAAATATTCCATATGCAAAAAAAAAAGAACACAAGTCCTAAAAC
ACACAACCAGAACACCTAACCAC
Found at i:4315832 original size:36 final size:35
Alignment explanation
Indices: 4315778--4315846 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 35
4315768 AAATAGTATT
* * *
4315778 ATTATTTTTATGTATTAAACCAATAATTTATATTTA
1 ATTATTATTATATATTAAA-CAATAATTCATATTTA
* *
4315814 ATTATTATTATATTTTAAACTATAATTCATATT
1 ATTATTATTATATATTAAACAATAATTCATATT
4315847 AAAAGTATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 12 0.43
36 16 0.57
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (35 bp):
ATTATTATTATATATTAAACAATAATTCATATTTA
Found at i:4321996 original size:39 final size:39
Alignment explanation
Indices: 4321927--4322020 Score: 104
Period size: 39 Copynumber: 2.4 Consensus size: 39
4321917 ACCAATATGG
* *
4321927 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTT-GT
1 CACCCAGTGCCTCATCGGATAGTCCAAAGTAA-AGTTGGT
* *
4321966 CACCCAGTGTCTCATCGGCCTAG-CCAAAGTAAAGTTGGT
1 CACCCAGTGCCTCATCGG-ATAGTCCAAAGTAAAGTTGGT
*
4322005 -ACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
4322021 AATCTATCCG
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
38 18 0.38
39 26 0.55
40 3 0.06
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCAAAGTAAAGTTGGT
Found at i:4323616 original size:5 final size:5
Alignment explanation
Indices: 4323598--4323628 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
4323588 TTTCTTTTAT
4323598 ATATA ATAATA ATATA ATATA ATATA ATATA
1 ATATA AT-ATA ATATA ATATA ATATA ATATA
4323629 CTTAATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:4324458 original size:24 final size:24
Alignment explanation
Indices: 4324422--4324473 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
4324412 GAGTTTAAGC
*
4324422 GAGCCATGTCAGGAAGCTCAT-AA
1 GAGCCATATCAGGAAGCTCATAAA
*
4324445 GAGCCTATATCAGGATGCTCATAAA
1 GAGCC-ATATCAGGAAGCTCATAAA
4324470 GAGC
1 GAGC
4324474 TGCGTTTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.20
24 14 0.56
25 6 0.24
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (24 bp):
GAGCCATATCAGGAAGCTCATAAA
Found at i:4327184 original size:18 final size:18
Alignment explanation
Indices: 4327163--4327201 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4327153 GATTGAGAGT
* *
4327163 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
4327181 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
4327199 GAA
1 GAA
4327202 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:4330944 original size:13 final size:13
Alignment explanation
Indices: 4330926--4330950 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4330916 AATAATAATC
4330926 TCATGTATCCATG
1 TCATGTATCCATG
4330939 TCATGTATCCAT
1 TCATGTATCCAT
4330951 TATCCAACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (13 bp):
TCATGTATCCATG
Found at i:4334208 original size:38 final size:39
Alignment explanation
Indices: 4334161--4334236 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
4334151 AAATCAAAAT
4334161 TTATTTTAATATAATA-TTATAGTATTATGCATACTTTA
1 TTATTTTAATATAATATTTATAGTATTATGCATACTTTA
*
4334199 TTATTTTAATATAATATTTATAGTATTATGCGTACTTT
1 TTATTTTAATATAATATTTATAGTATTATGCATACTTT
4334237 TATTTGGTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 16 0.44
39 20 0.56
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (39 bp):
TTATTTTAATATAATATTTATAGTATTATGCATACTTTA
Found at i:4336193 original size:28 final size:30
Alignment explanation
Indices: 4336147--4336233 Score: 99
Period size: 31 Copynumber: 2.9 Consensus size: 30
4336137 GTACCAACTT
*
4336147 GAGAAAAAAATATAATTTAAATATCT-AT-TGT
1 GAGAAAAAAA-A-AATTTAAATA-CTAATATGA
*
4336178 G-GCAAAAAAAAATTTAAATACTAATATGA
1 GAGAAAAAAAAAATTTAAATACTAATATGA
4336207 GAGAAAAAATAAAATTTAAATACTAAT
1 GAGAAAAAA-AAAATTTAAATACTAAT
4336234 TTGGGGGTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
27 2 0.04
28 12 0.24
29 4 0.08
30 13 0.27
31 18 0.37
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.29
Consensus pattern (30 bp):
GAGAAAAAAAAAATTTAAATACTAATATGA
Found at i:4336743 original size:3 final size:3
Alignment explanation
Indices: 4336735--4336796 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
4336725 TATGTATACG
4336735 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
4336783 TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TT
4336797 TTTTGTGCAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:4339721 original size:23 final size:23
Alignment explanation
Indices: 4339676--4339721 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4339666 ATATTTTTCA
* *
4339676 TTTAATAATTTTAAAATAGTTAT
1 TTTAATAATATTAAAATAATTAT
4339699 TTTAATAA-ATTAAATATAATTAT
1 TTTAATAATATTAAA-ATAATTAT
4339722 GAAAATGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTAATAATATTAAAATAATTAT
Found at i:4341376 original size:20 final size:20
Alignment explanation
Indices: 4341347--4341384 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4341337 TTGGGTCCAT
*
4341347 TTTTTTATGATTTTTTTAGA
1 TTTTTAATGATTTTTTTAGA
4341367 TTTTTAATGATTTTTTTA
1 TTTTTAATGATTTTTTTA
4341385 ATGTCCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (20 bp):
TTTTTAATGATTTTTTTAGA
Found at i:4341387 original size:12 final size:11
Alignment explanation
Indices: 4341345--4341384 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
4341335 TTTTGGGTCC
4341345 ATTTTTTTATG
1 ATTTTTTTATG
4341356 ATTTTTTTA-G
1 ATTTTTTTATG
*
4341366 A-TTTTTAATG
1 ATTTTTTTATG
4341376 ATTTTTTTA
1 ATTTTTTTA
4341385 ATGTCCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 6 0.24
10 4 0.16
11 15 0.60
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (11 bp):
ATTTTTTTATG
Found at i:4346544 original size:28 final size:27
Alignment explanation
Indices: 4346491--4346545 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
4346481 GGTTATATAT
*
4346491 ATAATATTTTAAAAGTAAATATAATAA
1 ATAATATTTAAAAAGTAAATATAATAA
* *
4346518 ATAATATTTAAATAATTTAATATAATAA
1 ATAATATTTAAA-AAGTAAATATAATAA
4346546 TTTTACTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
ATAATATTTAAAAAGTAAATATAATAA
Found at i:4346750 original size:23 final size:22
Alignment explanation
Indices: 4346703--4346753 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
4346693 ATCTAGTAAC
4346703 TATATAAATTTATTATCATTAA
1 TATATAAATTTATTATCATTAA
* *
4346725 TATATAAGTTTA--ATTATTATA
1 TATATAAATTTATTATCATTA-A
4346746 TATATAAA
1 TATATAAA
4346754 ATAATTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 6 0.24
21 8 0.32
22 11 0.44
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TATATAAATTTATTATCATTAA
Found at i:4346931 original size:6 final size:6
Alignment explanation
Indices: 4346883--4346912 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
4346873 TATATTATTT
4346883 AATATAA AATATA AATATA AATATA AATAT
1 AATAT-A AATATA AATATA AATATA AATAT
4346913 TTATTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AATATA
Found at i:4347057 original size:21 final size:21
Alignment explanation
Indices: 4347023--4347073 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
4347013 CGTTATTTTT
* * * *
4347023 AATCTAACCGCTACAGTATCC
1 AATCTCACCACTACAATAACC
*
4347044 AATCTCACCACTACAATAACT
1 AATCTCACCACTACAATAACC
4347065 AATCTCACC
1 AATCTCACC
4347074 GCCACCGCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.35, G:0.04, T:0.24
Consensus pattern (21 bp):
AATCTCACCACTACAATAACC
Found at i:4349520 original size:44 final size:44
Alignment explanation
Indices: 4349457--4349545 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
4349447 TTACACTATG
4349457 TTTTAACCCTTATTGAATTTGAATCATTATTTCTTTTTGTTATT
1 TTTTAACCCTTATTGAATTTGAATCATTATTTCTTTTTGTTATT
4349501 TTTTAACCCTTATTGAATTTGAATCATTATTTCTTTTTGTTATT
1 TTTTAACCCTTATTGAATTTGAATCATTATTTCTTTTTGTTATT
4349545 T
1 T
4349546 CTTCAAATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.22, C:0.11, G:0.07, T:0.60
Consensus pattern (44 bp):
TTTTAACCCTTATTGAATTTGAATCATTATTTCTTTTTGTTATT
Found at i:4352399 original size:16 final size:18
Alignment explanation
Indices: 4352378--4352415 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
4352368 ATTGTTACTA
4352378 TTTTAAAGT-TTA-ATAT
1 TTTTAAAGTATTATATAT
*
4352394 TTTTAATGTATTATATAT
1 TTTTAAAGTATTATATAT
4352412 TTTT
1 TTTT
4352416 TTAAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 3 0.16
18 8 0.42
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTTAAAGTATTATATAT
Found at i:4359824 original size:51 final size:51
Alignment explanation
Indices: 4359748--4359864 Score: 207
Period size: 51 Copynumber: 2.3 Consensus size: 51
4359738 TGGATCACAT
*
4359748 TTATCACTTGTCACTTGTCACTGATCAAATAAGTGTAGCTGAGGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAAATAAGTATAGCTGAGGCTACCAC
* *
4359799 TTATCACTTGTCACTTGTCACTGATCAGATAAGTATAGCTGAGGCTACGAC
1 TTATCACTTGTCACTTGTCACTGATCAAATAAGTATAGCTGAGGCTACCAC
4359850 TTATCACTTGTCACT
1 TTATCACTTGTCACT
4359865 GATCAGAAGT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAAATAAGTATAGCTGAGGCTACCAC
Found at i:4362638 original size:24 final size:24
Alignment explanation
Indices: 4362610--4362661 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
4362600 TTAGTAGGTC
*
4362610 AAATAAATTATGCTAATAAATACT
1 AAATAAATTATACTAATAAATACT
*
4362634 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
4362658 AAAT
1 AAAT
4362662 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:4363750 original size:4 final size:4
Alignment explanation
Indices: 4363741--4363806 Score: 132
Period size: 4 Copynumber: 16.5 Consensus size: 4
4363731 ATCTACTTCA
4363741 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4363789 TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TA
4363807 ATCTAGCTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 62 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:4376500 original size:20 final size:20
Alignment explanation
Indices: 4376475--4376521 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
4376465 AAGTGCAATA
4376475 AAATTAAGTGATCTTAACAT
1 AAATTAAGTGATCTTAACAT
4376495 AAATTAAGTGATCTTAACAT
1 AAATTAAGTGATCTTAACAT
4376515 AAATTAA
1 AAATTAA
4376522 TTGGCTGAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (20 bp):
AAATTAAGTGATCTTAACAT
Found at i:4388521 original size:20 final size:20
Alignment explanation
Indices: 4388496--4388542 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
4388486 AAGTGCAATA
4388496 AAATTAAGTGATCTTAACAT
1 AAATTAAGTGATCTTAACAT
4388516 AAATTAAGTGATCTTAACAT
1 AAATTAAGTGATCTTAACAT
4388536 AAATTAA
1 AAATTAA
4388543 TTGGCTGAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (20 bp):
AAATTAAGTGATCTTAACAT
Found at i:4403146 original size:26 final size:24
Alignment explanation
Indices: 4403085--4403148 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 24
4403075 TATAATTTAT
*
4403085 AAATTAATTTAATAATAATTAAAA
1 AAATTAATTTAATAATAATGAAAA
4403109 AAATTATTATTTAACTGAA-AATGATAAA
1 AAATTA--ATTTAA-T-AATAATGA-AAA
4403137 AAATTAATTTAA
1 AAATTAATTTAA
4403149 AAATGGTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
24 6 0.18
26 12 0.35
27 5 0.15
28 11 0.32
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (24 bp):
AAATTAATTTAATAATAATGAAAA
Found at i:4406214 original size:10 final size:10
Alignment explanation
Indices: 4406195--4406224 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
4406185 AAAATTTAAA
4406195 TAAAATTTTT
1 TAAAATTTTT
4406205 TAAAGATTTTT
1 TAAA-ATTTTT
4406216 TAAAATTTT
1 TAAAATTTT
4406225 ATATTCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (10 bp):
TAAAATTTTT
Found at i:4406360 original size:12 final size:12
Alignment explanation
Indices: 4406345--4406369 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4406335 TGATATATTC
4406345 TTTGAAATAATT
1 TTTGAAATAATT
4406357 TTTGAAATAATT
1 TTTGAAATAATT
4406369 T
1 T
4406370 AAGTGTTGTT
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TTTGAAATAATT
Found at i:4406711 original size:13 final size:14
Alignment explanation
Indices: 4406695--4406728 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
4406685 CGAAATTTTT
4406695 TAAATTAAAAAA-A
1 TAAATTAAAAAATA
*
4406708 TAAAATAAAAAATA
1 TAAATTAAAAAATA
4406722 TAAATTA
1 TAAATTA
4406729 TTTGAAAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAATTAAAAAATA
Found at i:4407627 original size:16 final size:16
Alignment explanation
Indices: 4407606--4407673 Score: 100
Period size: 16 Copynumber: 4.2 Consensus size: 16
4407596 TTTGGTTCGT
4407606 TGTATTAGATTAGAGG
1 TGTATTAGATTAGAGG
4407622 TGTATTAGATTAGAGG
1 TGTATTAGATTAGAGG
* * *
4407638 TGTATTGGATTAAAAG
1 TGTATTAGATTAGAGG
*
4407654 TGTATTGGATTAGAGG
1 TGTATTAGATTAGAGG
4407670 TGTA
1 TGTA
4407674 ATAGCAAATC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (16 bp):
TGTATTAGATTAGAGG
Found at i:4407933 original size:18 final size:17
Alignment explanation
Indices: 4407912--4407946 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
4407902 TTATTATTAA
*
4407912 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
4407930 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
4407947 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:4408710 original size:13 final size:13
Alignment explanation
Indices: 4408692--4408721 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4408682 TTAAAAGCTA
*
4408692 AATTCAGAAAAAC
1 AATTCAAAAAAAC
4408705 AATTCAAAAAAAC
1 AATTCAAAAAAAC
4408718 AATT
1 AATT
4408722 ACATGATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.13, G:0.03, T:0.20
Consensus pattern (13 bp):
AATTCAAAAAAAC
Found at i:4412367 original size:12 final size:12
Alignment explanation
Indices: 4412331--4412372 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
4412321 CTCATTCTCC
*
4412331 TTCTCCTTTTCT
1 TTCTCTTTTTCT
4412343 TTCTCTTTTTCT
1 TTCTCTTTTTCT
4412355 TTCT-TTTTCTCT
1 TTCTCTTTT-TCT
*
4412367 TCCTCT
1 TTCTCT
4412373 CCTTGCTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 4 0.15
12 21 0.81
13 1 0.04
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (12 bp):
TTCTCTTTTTCT
Found at i:4418020 original size:27 final size:27
Alignment explanation
Indices: 4417986--4418046 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
4417976 TCATAGAATT
4417986 TGCTTTCATTTTGTTTCAGTGCTTTGA
1 TGCTTTCATTTTGTTTCAGTGCTTTGA
4418013 TGCTTTCATTTTGTTTCAGTGCTTTGA
1 TGCTTTCATTTTGTTTCAGTGCTTTGA
4418040 TGCTTTC
1 TGCTTTC
4418047 TAGCGAGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.10, C:0.16, G:0.18, T:0.56
Consensus pattern (27 bp):
TGCTTTCATTTTGTTTCAGTGCTTTGA
Found at i:4421754 original size:22 final size:22
Alignment explanation
Indices: 4421719--4421761 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
4421709 ATTTTACTGC
4421719 TTTATGCTGCTGTTTTACTATT
1 TTTATGCTGCTGTTTTACTATT
* * *
4421741 TTTATGTTGTTGTTTTGCTAT
1 TTTATGCTGCTGTTTTACTAT
4421762 AATTTTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.09, G:0.16, T:0.63
Consensus pattern (22 bp):
TTTATGCTGCTGTTTTACTATT
Found at i:4422000 original size:14 final size:15
Alignment explanation
Indices: 4421976--4422005 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
4421966 GTATTATATT
4421976 TTTATAAAAAATTAA
1 TTTATAAAAAATTAA
4421991 TTTA-AAAAAATTAA
1 TTTATAAAAAATTAA
4422005 T
1 T
4422006 ACAGGCGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTATAAAAAATTAA
Found at i:4427663 original size:71 final size:71
Alignment explanation
Indices: 4427585--4427727 Score: 241
Period size: 71 Copynumber: 2.0 Consensus size: 71
4427575 GGGATTAGAA
* *
4427585 AGGTTTCTAGTTAAGCTTTTGTAAAGGCTAGATGGTTTTAGTTAAGCCATAAGAACTAGGAGGTA
1 AGGTTTCTAGTTAAGCCTTTGTAAAGGCTAGATGGTTTTAGTTAAGCCATAAAAACTAGGAGGTA
4427650 GGTTCT
66 GGTTCT
* * *
4427656 AGGTTTCTATTTAAGCCTTTGTAAAGGCTAGATGGTTTTAGTTAAGTCATAAAAACTAGGAGTTA
1 AGGTTTCTAGTTAAGCCTTTGTAAAGGCTAGATGGTTTTAGTTAAGCCATAAAAACTAGGAGGTA
4427721 GGTTCT
66 GGTTCT
4427727 A
1 A
4427728 TCTTAACCTT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.36
Consensus pattern (71 bp):
AGGTTTCTAGTTAAGCCTTTGTAAAGGCTAGATGGTTTTAGTTAAGCCATAAAAACTAGGAGGTA
GGTTCT
Found at i:4428564 original size:18 final size:17
Alignment explanation
Indices: 4428521--4428565 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
4428511 TAAATACATT
4428521 TAAAAACATAAAAACAAA
1 TAAAAA-ATAAAAACAAA
*
4428539 TATTAAAATAAGAAACAAA
1 TA-AAAAATAA-AAACAAA
4428558 TAAAAAAT
1 TAAAAAAT
4428566 GAGACTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.18
Consensus pattern (17 bp):
TAAAAAATAAAAACAAA
Found at i:4431103 original size:26 final size:28
Alignment explanation
Indices: 4431074--4431125 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
4431064 TATTGTCATC
*
4431074 TCATTTTATTTTAT-T-TTATTTTATTT
1 TCATTTCATTTTATGTGTTATTTTATTT
4431100 TCATTTCATTTTATGTGTTATTTTAT
1 TCATTTCATTTTATGTGTTATTTTAT
4431126 GGTTCCCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 13 0.57
27 1 0.04
28 9 0.39
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (28 bp):
TCATTTCATTTTATGTGTTATTTTATTT
Found at i:4431109 original size:31 final size:33
Alignment explanation
Indices: 4431058--4431125 Score: 95
Period size: 31 Copynumber: 2.1 Consensus size: 33
4431048 TTTGTACATA
4431058 TTATTATATTGTCATCTCATTTTAT-T-TTATT
1 TTATTATATTGTCATCTCATTTTATGTGTTATT
* * *
4431089 TTATTTTATTTTCATTTCATTTTATGTGTTATT
1 TTATTATATTGTCATCTCATTTTATGTGTTATT
4431122 TTAT
1 TTAT
4431126 GGTTCCCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 22 0.69
32 1 0.03
33 9 0.28
ACGTcount: A:0.21, C:0.07, G:0.04, T:0.68
Consensus pattern (33 bp):
TTATTATATTGTCATCTCATTTTATGTGTTATT
Found at i:4431141 original size:5 final size:5
Alignment explanation
Indices: 4431076--4431125 Score: 64
Period size: 5 Copynumber: 9.4 Consensus size: 5
4431066 TTGTCATCTC
*
4431076 ATTTT ATTTT ATTTT ATTTT ATTTT CATTTC ATTTT ATGTGTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT -ATTTT ATTTT AT-T-TT ATTTT
4431124 AT
1 AT
4431126 GGTTCCCTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
5 30 0.75
6 6 0.15
7 4 0.10
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (5 bp):
ATTTT
Found at i:4432494 original size:16 final size:15
Alignment explanation
Indices: 4432473--4432537 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 15
4432463 CCATGCTCTC
4432473 TTTTATTTTTTGAATT
1 TTTTATTTTTT-AATT
*
4432489 TTTTATTTTTTAAAAT
1 TTTTATTTTTT-AATT
*
4432505 TTTAATTTGCTTT-ATT
1 TTTTATTT--TTTAATT
4432521 TTTTATTTTTATAATT
1 TTTTATTTTT-TAATT
4432537 T
1 T
4432538 AAAAATTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
14 2 0.05
15 1 0.03
16 34 0.85
18 3 0.08
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.72
Consensus pattern (15 bp):
TTTTATTTTTTAATT
Found at i:4434893 original size:20 final size:21
Alignment explanation
Indices: 4434864--4434914 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
4434854 AATTTAGTCT
4434864 TTAACATTTA-TATTTATTTT-G
1 TTAA-ATTTATTA-TTATTTTAG
*
4434885 TTAATTTTATTATTATTTTAG
1 TTAAATTTATTATTATTTTAG
4434906 TTAAATTTA
1 TTAAATTTA
4434915 ACTAATAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (21 bp):
TTAAATTTATTATTATTTTAG
Found at i:4443299 original size:36 final size:36
Alignment explanation
Indices: 4443231--4443299 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
4443221 GTACTAAAAT
* * *
4443231 TAACAATAAAATAAGAGTTATAAAATATCAAAACAA
1 TAACAACAAAATAAGAGTAATAAAATAGCAAAACAA
*
4443267 TAACAACAAAAT-AGTAGTAATATAATAGCAAAA
1 TAACAACAAAATAAG-AGTAATAAAATAGCAAAA
4443300 TGTCATCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 2 0.07
36 26 0.93
ACGTcount: A:0.62, C:0.09, G:0.07, T:0.22
Consensus pattern (36 bp):
TAACAACAAAATAAGAGTAATAAAATAGCAAAACAA
Found at i:4455213 original size:15 final size:14
Alignment explanation
Indices: 4455188--4455222 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
4455178 TACTATTTAA
*
4455188 GGTTTATGGATTAT
1 GGTTTAGGGATTAT
4455202 GAGTTTAGGGATTAT
1 G-GTTTAGGGATTAT
4455217 GGTTTA
1 GGTTTA
4455223 TGATTTAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:4455216 original size:22 final size:21
Alignment explanation
Indices: 4455182--4455232 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
4455172 ATGAGTTACT
* *
4455182 ATTTAAGGTTTATGGATTATG
1 ATTTAGGGATTATGGATTATG
*
4455203 AGTTTAGGGATTATGGTTTATG
1 A-TTTAGGGATTATGGATTATG
4455225 ATTTAGGG
1 ATTTAGGG
4455233 GTTAGGGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.45
Consensus pattern (21 bp):
ATTTAGGGATTATGGATTATG
Found at i:4455242 original size:22 final size:22
Alignment explanation
Indices: 4455198--4455239 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
4455188 GGTTTATGGA
*
4455198 TTATGAGTTTAGGGATTATGGT
1 TTATGAGTTTAGGGATTAGGGT
*
4455220 TTATGA-TTTAGGGGTTAGGG
1 TTATGAGTTTAGGGATTAGGG
4455240 GTTCAAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (22 bp):
TTATGAGTTTAGGGATTAGGGT
Found at i:4456369 original size:81 final size:81
Alignment explanation
Indices: 4456228--4456387 Score: 194
Period size: 81 Copynumber: 2.0 Consensus size: 81
4456218 TGCCTTAATA
* *
4456228 CTTTTTCACAAAATCGGCTCCCCCCTCCCCCCCCAAAAAAATCCCAAAATTTGACATGAAATCTA
1 CTTTTTCACAAAATCAGCTCCCCCCTCCCCCCCCAAAAAAATCCCAAAATTTCACATGAAATCTA
*
4456293 TTCTTTTTTTTCCCTC
66 TTCTCTTTTTTCCCTC
* * ** * ** * * * *
4456309 CTTTTTCCCAAAATCAGTTCCCTTCTCCCTCCCCAATGAAATCCTAAAATTTCACCTGAAATTTC
1 CTTTTTCACAAAATCAGCTCCCCCCTCCCCCCCCAAAAAAATCCCAAAATTTCACATGAAATCTA
4456374 TTCTCTTTTTTCCC
66 TTCTCTTTTTTCCC
4456388 CCATTTTATT
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
81 65 1.00
ACGTcount: A:0.25, C:0.35, G:0.04, T:0.36
Consensus pattern (81 bp):
CTTTTTCACAAAATCAGCTCCCCCCTCCCCCCCCAAAAAAATCCCAAAATTTCACATGAAATCTA
TTCTCTTTTTTCCCTC
Found at i:4456701 original size:48 final size:48
Alignment explanation
Indices: 4456612--4456705 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
4456602 TTTCTTGGCT
* * *
4456612 TAAAAACGCCTAAGTCAGCCTAACTTCCACCGATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
4456660 TAAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
4456706 AGAATTCCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
47 4 0.10
48 37 0.90
ACGTcount: A:0.39, C:0.28, G:0.14, T:0.19
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:4459216 original size:48 final size:48
Alignment explanation
Indices: 4459127--4459220 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
4459117 TTTCTTGGCT
* * *
4459127 TAAAAACGCCTAAGTCAGCCTAACTTCCACCGATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
*
4459175 TAAAAACGCCTAAGTCAG-CTCAAC-TCGTAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
4459221 AGAATTCCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 4 0.10
48 36 0.90
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:4462933 original size:22 final size:23
Alignment explanation
Indices: 4462882--4462934 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
4462872 AGAAAACCAT
4462882 TTTAT-GTGTTAAATGCTGAAAA
1 TTTATGGTGTTAAATGCTGAAAA
* *
4462904 TTTA-GGTGTTAAATGTTG-CAA
1 TTTATGGTGTTAAATGCTGAAAA
4462925 TTTATGGTGT
1 TTTATGGTGT
4462935 CTGAAAGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.28, C:0.04, G:0.23, T:0.45
Consensus pattern (23 bp):
TTTATGGTGTTAAATGCTGAAAA
Found at i:4463974 original size:43 final size:43
Alignment explanation
Indices: 4463913--4464050 Score: 143
Period size: 43 Copynumber: 3.2 Consensus size: 43
4463903 CACGACTTGT
* * * * *
4463913 TTTAGCGACGTTTTTGGGAGAAGCGCCGTTAAAGGTCATGATC
1 TTTAGCGGCGTTTGTGGGAAAAGCGACGCTAAAGGTCATGATC
* * *
4463956 TTTAGCGGCGCTTGTGGGAAAAGCGACGCTAAAAGTCATGACTT
1 TTTAGCGGCGTTTGTGGGAAAAGCGACGCTAAAGGTCATGA-TC
* * * *
4464000 TTTA-CGGCGTTTGTGGAAAAAGTGTCGCTAAAGGTCATGACC
1 TTTAGCGGCGTTTGTGGGAAAAGCGACGCTAAAGGTCATGATC
*
4464042 TTTTGCGGC
1 TTTAGCGGC
4464051 ATTTTTTAGA
Statistics
Matches: 77, Mismatches: 16, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
42 3 0.04
43 69 0.90
44 5 0.06
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGACGCTAAAGGTCATGATC
Found at i:4465094 original size:21 final size:21
Alignment explanation
Indices: 4465069--4465152 Score: 64
Period size: 21 Copynumber: 4.0 Consensus size: 21
4465059 TTCTGCTCTG
4465069 CTCTG-CTACCATCGCTGCTGC
1 CTCTGCCT-CCATCGCTGCTGC
*
4465090 CTCTGCCTCCTTCGCTGCTGC
1 CTCTGCCTCCATCGCTGCTGC
** * * *
4465111 AGCTACCTCCCTCCCTGCTGC
1 CTCTGCCTCCATCGCTGCTGC
* *
4465132 CGCTGCCTTCC-TCGCTACTGC
1 CTCTGCC-TCCATCGCTGCTGC
4465153 ATCCGCTCTA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
21 46 0.90
22 5 0.10
ACGTcount: A:0.06, C:0.48, G:0.18, T:0.29
Consensus pattern (21 bp):
CTCTGCCTCCATCGCTGCTGC
Found at i:4465591 original size:13 final size:14
Alignment explanation
Indices: 4465565--4465593 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4465555 ACTAACGACG
4465565 AATTAAACCATTAT
1 AATTAAACCATTAT
4465579 AATTAAA-CATTAT
1 AATTAAACCATTAT
4465592 AA
1 AA
4465594 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:4470607 original size:9 final size:9
Alignment explanation
Indices: 4470593--4470736 Score: 91
Period size: 9 Copynumber: 16.0 Consensus size: 9
4470583 TAAGTATAAT
4470593 TAAGTTATG
1 TAAGTTATG
4470602 TAAGTTATG
1 TAAGTTATG
* * *
4470611 ATATGATATA
1 -TAAGTTATG
*
4470621 T-ATTTATG
1 TAAGTTATG
4470629 T-A-TTATG
1 TAAGTTATG
4470636 TAAGTTATG
1 TAAGTTATG
*
4470645 TAAATTATG
1 TAAGTTATG
*
4470654 TAAGTTATT
1 TAAGTTATG
**
4470663 TATCTTATG
1 TAAGTTATG
*
4470672 TAAATTATG
1 TAAGTTATG
*
4470681 TAAGATATGATA
1 TAAG-T-T-ATG
*
4470693 TATATTTATG
1 TA-AGTTATG
4470703 T-A-TTATG
1 TAAGTTATG
4470710 TAAGTTATG
1 TAAGTTATG
*
4470719 TAAATTATG
1 TAAGTTATG
*
4470728 TAAGATATG
1 TAAGTTATG
4470737 ATACATATTT
Statistics
Matches: 104, Mismatches: 22, Indels: 18
0.72 0.15 0.12
Matches are distributed among these distances:
7 12 0.12
8 8 0.08
9 66 0.63
10 10 0.10
11 2 0.02
12 5 0.05
13 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.15, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:4470653 original size:18 final size:18
Alignment explanation
Indices: 4470630--4470736 Score: 101
Period size: 18 Copynumber: 5.8 Consensus size: 18
4470620 ATATTTATGT
4470630 ATTATGTAAGTTATGTAA
1 ATTATGTAAGTTATGTAA
* *
4470648 ATTATGTAAGTTATTTAT
1 ATTATGTAAGTTATGTAA
* *
4470666 CTTATGTAAATTATGTAA
1 ATTATGTAAGTTATGTAA
* *
4470684 GATATGATATATATTTATGT--
1 -AT-T-ATGTA-AGTTATGTAA
4470704 ATTATGTAAGTTATGTAA
1 ATTATGTAAGTTATGTAA
*
4470722 ATTATGTAAGATATG
1 ATTATGTAAGTTATG
4470737 ATACATATTT
Statistics
Matches: 71, Mismatches: 12, Indels: 12
0.75 0.13 0.13
Matches are distributed among these distances:
16 7 0.10
17 4 0.06
18 45 0.63
19 3 0.04
20 1 0.01
21 4 0.06
22 7 0.10
ACGTcount: A:0.37, C:0.01, G:0.15, T:0.47
Consensus pattern (18 bp):
ATTATGTAAGTTATGTAA
Found at i:4473604 original size:38 final size:38
Alignment explanation
Indices: 4473553--4473652 Score: 182
Period size: 38 Copynumber: 2.6 Consensus size: 38
4473543 ATAAATAAAA
*
4473553 ACCTTGGCCACCTACTCCACCACCTTTGTTGGCCACCC
1 ACCTTAGCCACCTACTCCACCACCTTTGTTGGCCACCC
4473591 ACCTTAGCCACCTACTCCACCACCTTTGTTGGCCACCC
1 ACCTTAGCCACCTACTCCACCACCTTTGTTGGCCACCC
*
4473629 ACCTTAGCCACCAACTCCACCACC
1 ACCTTAGCCACCTACTCCACCACC
4473653 CTTGGCCACC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 60 1.00
ACGTcount: A:0.20, C:0.49, G:0.10, T:0.21
Consensus pattern (38 bp):
ACCTTAGCCACCTACTCCACCACCTTTGTTGGCCACCC
Found at i:4473775 original size:23 final size:22
Alignment explanation
Indices: 4473748--4473793 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
4473738 TTGGTTTTTA
4473748 TGGAGAAGGATTGTTCTTTGTTT
1 TGGAGAAGG-TTGTTCTTTGTTT
* * *
4473771 TGGAGGAGGTTTTTTTTTGTTT
1 TGGAGAAGGTTGTTCTTTGTTT
4473793 T
1 T
4473794 TTTGGAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.13, C:0.02, G:0.30, T:0.54
Consensus pattern (22 bp):
TGGAGAAGGTTGTTCTTTGTTT
Found at i:4474142 original size:3 final size:3
Alignment explanation
Indices: 4474128--4474212 Score: 63
Period size: 3 Copynumber: 28.3 Consensus size: 3
4474118 AAGCTTTGTT
* *
4474128 TTA TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
*
4474172 TT- TCTCA TGTA TATA TTA TTT TTA -TA TTA TTA TTA -TA TTA T
1 TTA T-T-A T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4474213 ATATGCCCTC
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
2 8 0.12
3 50 0.76
4 6 0.09
5 2 0.03
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Done.