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: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 66 of 109
Found at i:21322534 original size:39 final size:39
Alignment explanation
Indices: 21322480--21322557 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
21322470 CTAGTGGAAG
21322480 GACCAATTGTACAAATATAATTAAGGCTAAAATAATTTT
1 GACCAATTGTACAAATATAATTAAGGCTAAAATAATTTT
21322519 GACCAATTGTACAAATATAATTAAGGCTAAAATAATTTT
1 GACCAATTGTACAAATATAATTAAGGCTAAAATAATTTT
21322558 TAATTAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (39 bp):
GACCAATTGTACAAATATAATTAAGGCTAAAATAATTTT
Found at i:21335067 original size:30 final size:30
Alignment explanation
Indices: 21335011--21335135 Score: 110
Period size: 30 Copynumber: 4.1 Consensus size: 30
21335001 CTCCCTAAGA
* * *
21335011 GAACCCCC-TGTATATGCGAACACCTATAGGT
1 GAACCCCCTTGCATATG-AAAC-CCTATAGGC
* *
21335042 GAATCCTCTTGCATATGAAACCCTATAGGC
1 GAACCCCCTTGCATATGAAACCCTATAGGC
* *
21335072 GAACCCCCTTGCATGTGAAACCCTATAGAC
1 GAACCCCCTTGCATATGAAACCCTATAGGC
* * * *
21335102 GAACCCCATTGTATGTG-AACCCTTATAGGT
1 GAACCCCCTTGCATATGAAACCC-TATAGGC
21335132 GAAC
1 GAAC
21335136 TCATATGTAA
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
29 5 0.06
30 58 0.73
31 9 0.11
32 7 0.09
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (30 bp):
GAACCCCCTTGCATATGAAACCCTATAGGC
Found at i:21335272 original size:28 final size:28
Alignment explanation
Indices: 21335220--21335318 Score: 99
Period size: 28 Copynumber: 3.5 Consensus size: 28
21335210 TGAACCATGT
*
21335220 TATGTGTGAACCCTAATGCATGCAAACCCA
1 TATGTGCGAACCC--ATGCATGCAAACCCA
* * * *
21335250 TATGTGTGAACCCCTGCAAGCAAACCCC
1 TATGTGCGAACCCATGCATGCAAACCCA
* * **
21335278 TATATGCGAGCCCATGCATGTGAACCCA
1 TATGTGCGAACCCATGCATGCAAACCCA
21335306 TATGTGCGAACCC
1 TATGTGCGAACCC
21335319 TTATATAAAT
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
28 43 0.77
30 13 0.23
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.21
Consensus pattern (28 bp):
TATGTGCGAACCCATGCATGCAAACCCA
Found at i:21335443 original size:23 final size:23
Alignment explanation
Indices: 21335413--21335489 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
21335403 TTATATTTCT
21335413 TGTGAACCCTAAATGTTGTTACA
1 TGTGAACCCTAAATGTTGTTACA
* **
21335436 TGTGAACCCTAAATATTACTACA
1 TGTGAACCCTAAATGTTGTTACA
* * *
21335459 TGCGAACGCTACATGTTGTTACA
1 TGTGAACCCTAAATGTTGTTACA
21335482 TGTGAACC
1 TGTGAACC
21335490 TATGTGTTTA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (23 bp):
TGTGAACCCTAAATGTTGTTACA
Found at i:21346376 original size:90 final size:91
Alignment explanation
Indices: 21346181--21346396 Score: 283
Period size: 90 Copynumber: 2.4 Consensus size: 91
21346171 TATCTATAAA
* * * * *
21346181 ATTCACAACTATCTGACAGCGCATTAACCTGCAACACTTGTGGTACACCTACCCATTTTTTTGGC
1 ATTCACAACTATCTGACAACGTATTAACCTGCAACACTGGTGGTACACCTACACATTATTTTGGC
*
21346246 AGCTCTTATATGCAAATATGTTGTGC
66 AGCTCTTATATACAAATATGTTGTGC
*
21346272 ATTCACAACTATCTGACAACGTATTAACCTGCAACACTGGTGGTTCATCC-ACACA-TATTTTGG
1 ATTCACAACTATCTGACAACGTATTAACCTGCAACACTGGTGGTACA-CCTACACATTATTTTGG
* * *
21346335 TAGCTCTTATCTACAAATGTGTTGTGC
65 CAGCTCTTATATACAAATATGTTGTGC
* * * *
21346362 ATTCACAACCATCTGGCAACATATTAACCTACAAC
1 ATTCACAACTATCTGACAACGTATTAACCTGCAAC
21346397 TTTGTGATTT
Statistics
Matches: 110, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
90 61 0.55
91 47 0.43
92 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.31
Consensus pattern (91 bp):
ATTCACAACTATCTGACAACGTATTAACCTGCAACACTGGTGGTACACCTACACATTATTTTGGC
AGCTCTTATATACAAATATGTTGTGC
Found at i:21347470 original size:280 final size:281
Alignment explanation
Indices: 21346952--21347511 Score: 883
Period size: 280 Copynumber: 2.0 Consensus size: 281
21346942 AATTATGCAT
21346952 AAAATCTTATTTTTATTAAATTAAAACCAAGTTGAATGTCACTTTTCCGCTACTAGTTTTTAGTT
1 AAAATCTTATTTTTATTAAATTAAAACCAAGTTGAATGTCACTTTTCCGCTACTAGTTTTTAGTT
* * *
21347017 AAATTTAAGGGTAATAAATAAATGGAAAGTTAACTAAGTTTTTCTTAAAAACGATCACCGTTACA
66 AAAATTAAGGGTAATAAATAAATAGAAAGTTAACTAAGTTTTTCTTAAAAACGATCACCATTACA
* * *
21347082 TATGAAGGTTAATTTAAAACAGTTTTTGACAACTTGTTGTCTTTTCTGAAAATTGTCTAAGTTTT
131 TATGAAGGTTAATCTAAAACAGTTTTTGACAACTTGTTATCTTTTCTGAAAATTGACTAAGTTTT
* * ** *
21347147 CTACTATAATAAACAAATATTTAATATGACTGTCTCGAAAACTCCGATAATTCTGGTAGGCCATT
196 CTACTATAATAAACAAATATTTAATATGACTATCTCAAAAACTCCGATAATTCTAATAGACCATT
*
21347212 TCGAAAACCTCCCTATTTTCG
261 TCGAAAACCTCCCCATTTTCG
* * *
21347233 AAAATTTTATTTTT-TTAAATTAAAACGAAGTTGAATGTCACTTTTCCGCTGCTAGTTTTTAGTT
1 AAAATCTTATTTTTATTAAATTAAAACCAAGTTGAATGTCACTTTTCCGCTACTAGTTTTTAGTT
*
21347297 AAAATTGAGGGTAATAAATAAATAGAAAGTTAACTAAGTTTTTCTTAAAAACGGA-CACCATTAC
66 AAAATTAAGGGTAATAAATAAATAGAAAGTTAACTAAGTTTTTCTTAAAAAC-GATCACCATTAC
* * *
21347361 ATATGAAGGTTAATCTAAAA-TGATTTTTTATAACTTGTTATCTTTTCTGAAAATTGACTAAGTT
130 ATATGAAGGTTAATCTAAAACAG-TTTTTGACAACTTGTTATCTTTTCTGAAAATTGACTAAGTT
* * *
21347425 TTCTACTATAATAAACAAATATTTAATATGACTATTTCAAAAACTCTGATAATTCTAATAGACTA
194 TTCTACTATAATAAACAAATATTTAATATGACTATCTCAAAAACTCCGATAATTCTAATAGACCA
21347490 TTTCGAAAACCTCCCCATTTTC
259 TTTCGAAAACCTCCCCATTTTC
21347512 TAATTTTTTA
Statistics
Matches: 255, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
279 1 0.00
280 239 0.94
281 15 0.06
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (281 bp):
AAAATCTTATTTTTATTAAATTAAAACCAAGTTGAATGTCACTTTTCCGCTACTAGTTTTTAGTT
AAAATTAAGGGTAATAAATAAATAGAAAGTTAACTAAGTTTTTCTTAAAAACGATCACCATTACA
TATGAAGGTTAATCTAAAACAGTTTTTGACAACTTGTTATCTTTTCTGAAAATTGACTAAGTTTT
CTACTATAATAAACAAATATTTAATATGACTATCTCAAAAACTCCGATAATTCTAATAGACCATT
TCGAAAACCTCCCCATTTTCG
Found at i:21348096 original size:2 final size:2
Alignment explanation
Indices: 21348089--21348113 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21348079 ATTTTCTCTT
21348089 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 T
21348114 TTACTTTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21348341 original size:27 final size:27
Alignment explanation
Indices: 21348290--21348342 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
21348280 AAACTTTAAA
* **
21348290 ATAATTTGTTATATGAAATTTTTTTTG
1 ATAATTTGTTATATAAAATAATTTTTG
*
21348317 ATAATTTTTTATATAAAATAATTTTT
1 ATAATTTGTTATATAAAATAATTTTT
21348343 CTTATATGAT
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:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (27 bp):
ATAATTTGTTATATAAAATAATTTTTG
Found at i:21349261 original size:45 final size:44
Alignment explanation
Indices: 21349169--21349261 Score: 105
Period size: 45 Copynumber: 2.1 Consensus size: 44
21349159 ATTTTATATT
* * * * *
21349169 ATTTTATAATTTTTTTATTAATATCTTAATAACCTAACAGTTGA
1 ATTTCATAATTTTTTTATCAATATATTAACAACCTAACAGTTAA
** *
21349213 ATTTCATAATTTTTTCTATCAATATATTAACAATTTAACCGTTAA
1 ATTTCATAATTTTTT-TATCAATATATTAACAACCTAACAGTTAA
21349258 ATTT
1 ATTT
21349262 ATCAATATAA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.49
Consensus pattern (44 bp):
ATTTCATAATTTTTTTATCAATATATTAACAACCTAACAGTTAA
Found at i:21362479 original size:22 final size:24
Alignment explanation
Indices: 21362454--21362497 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
21362444 TTCTATGTAT
21362454 TATTAA-T-TTTAAAAATATTTTA
1 TATTAATTATTTAAAAATATTTTA
*
21362476 TATTAATTATTTAAAAGTATTT
1 TATTAATTATTTAAAAATATTT
21362498 AAAATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 1 0.05
24 12 0.63
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
TATTAATTATTTAAAAATATTTTA
Found at i:21374303 original size:33 final size:33
Alignment explanation
Indices: 21374266--21374394 Score: 114
Period size: 33 Copynumber: 3.9 Consensus size: 33
21374256 AATCCAGACT
* * *
21374266 AGTAGCAGGGATGATGCCCCTATATGCAGCCCA
1 AGTAGCAGGGATGATGCCCCAATAAGCAGGCCA
* * ** *
21374299 AGTAGTAGGAATGATGTTCAAATAAGCAGGCCA
1 AGTAGCAGGGATGATGCCCCAATAAGCAGGCCA
* * * **
21374332 AGTAGCAGTGATGGTGCCCCCATAAGCAGGTTA
1 AGTAGCAGGGATGATGCCCCAATAAGCAGGCCA
* * *
21374365 AGTAGCAGCGATGATGCCTCAATAATCAGG
1 AGTAGCAGGGATGATGCCCCAATAAGCAGG
21374395 TTAAGTATTG
Statistics
Matches: 73, Mismatches: 23, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
33 73 1.00
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.20
Consensus pattern (33 bp):
AGTAGCAGGGATGATGCCCCAATAAGCAGGCCA
Found at i:21384790 original size:3 final size:3
Alignment explanation
Indices: 21384782--21384817 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
21384772 AAGGCAATAA
21384782 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
21384818 AATGTTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:21387508 original size:13 final size:13
Alignment explanation
Indices: 21387473--21387510 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
21387463 GAGATATTTG
*
21387473 TAATTTGAAAAGT
1 TAATTTGAAAACT
21387486 TAAGTTTGAAAACT
1 TAA-TTTGAAAACT
21387500 TAATTTGAAAA
1 TAATTTGAAAA
21387511 TTTGGAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (13 bp):
TAATTTGAAAACT
Found at i:21387824 original size:34 final size:34
Alignment explanation
Indices: 21387747--21387957 Score: 206
Period size: 34 Copynumber: 6.1 Consensus size: 34
21387737 TCACTTGTCT
* * * * * *
21387747 TTTCTTGCAAGGAATATTTCTTGTTCACGCATTA
1 TTTCTTGCAGGGAATCTCTCATGTTCACACATCA
* * *
21387781 TTTTGTTGCAGAGAATCTCTCATGTTTACACATCA
1 -TTTCTTGCAGGGAATCTCTCATGTTCACACATCA
* * * *
21387816 TTTCTTGCAGGGAATCTTTCCTCTTCACATATCA
1 TTTCTTGCAGGGAATCTCTCATGTTCACACATCA
* * * *
21387850 TTTCTTGCAGGGAATATTTCATGTTCACGCATTA
1 TTTCTTGCAGGGAATCTCTCATGTTCACACATCA
* *
21387884 TTTTGTTACAGGGAATCTCTCATGTTCACACATCA
1 -TTTCTTGCAGGGAATCTCTCATGTTCACACATCA
* *
21387919 TTTCTTGCAGGGAATCTCTCATATTCATACATCA
1 TTTCTTGCAGGGAATCTCTCATGTTCACACATCA
*
21387953 ATTCT
1 TTTCT
21387958 GGTATTATTT
Statistics
Matches: 142, Mismatches: 33, Indels: 3
0.80 0.19 0.02
Matches are distributed among these distances:
34 89 0.63
35 53 0.37
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (34 bp):
TTTCTTGCAGGGAATCTCTCATGTTCACACATCA
Found at i:21387915 original size:103 final size:103
Alignment explanation
Indices: 21387747--21387935 Score: 333
Period size: 103 Copynumber: 1.8 Consensus size: 103
21387737 TCACTTGTCT
* * *
21387747 TTTCTTGCAAGGAATATTTCTTGTTCACGCATTATTTTGTTGCAGAGAATCTCTCATGTTTACAC
1 TTTCTTGCAAGGAATATTTCATGTTCACGCATTATTTTGTTACAGAGAATCTCTCATGTTCACAC
21387812 ATCATTTCTTGCAGGGAATCTTTCCTCTTCACATATCA
66 ATCATTTCTTGCAGGGAATCTTTCCTCTTCACATATCA
* *
21387850 TTTCTTGCAGGGAATATTTCATGTTCACGCATTATTTTGTTACAGGGAATCTCTCATGTTCACAC
1 TTTCTTGCAAGGAATATTTCATGTTCACGCATTATTTTGTTACAGAGAATCTCTCATGTTCACAC
21387915 ATCATTTCTTGCAGGGAATCT
66 ATCATTTCTTGCAGGGAATCT
21387936 CTCATATTCA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 81 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (103 bp):
TTTCTTGCAAGGAATATTTCATGTTCACGCATTATTTTGTTACAGAGAATCTCTCATGTTCACAC
ATCATTTCTTGCAGGGAATCTTTCCTCTTCACATATCA
Found at i:21391016 original size:41 final size:39
Alignment explanation
Indices: 21390957--21391056 Score: 103
Period size: 39 Copynumber: 2.5 Consensus size: 39
21390947 CTTACTTTAT
* *
21390957 ATATTTTTTAGAATTTTTTTTTAAAT-TTTATAAATTTTTAAA
1 ATATATTTT-GAA-TTTTTTATAAATATTT-TAAA-TTTTAAA
* *
21390999 TATATATTTTGGATTTTTTATAAATATTTTGAATTTTAAA
1 -ATATATTTTGAATTTTTTATAAATATTTTAAATTTTAAA
*
21391039 ATTTATTTTGAATTTTTT
1 ATATATTTTGAATTTTTT
21391057 GTAATCTTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
39 16 0.32
40 7 0.14
41 14 0.28
42 5 0.10
43 8 0.16
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (39 bp):
ATATATTTTGAATTTTTTATAAATATTTTAAATTTTAAA
Found at i:21391749 original size:21 final size:21
Alignment explanation
Indices: 21391723--21391765 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
21391713 ATAAACAACA
**
21391723 TAATGGTTTTGCCTTTTAACT
1 TAATGGTTTTAACTTTTAACT
21391744 TAATGGTTTTAACTTTTAACT
1 TAATGGTTTTAACTTTTAACT
21391765 T
1 T
21391766 TAGAAAAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (21 bp):
TAATGGTTTTAACTTTTAACT
Found at i:21392930 original size:23 final size:23
Alignment explanation
Indices: 21392900--21392956 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
21392890 AGGTAAGATA
*
21392900 AGGAACCCCCTGACATCATGACG
1 AGGAACCCCCTGACATCACGACG
* *
21392923 AGGAACCCCCTGACATCGCGACT
1 AGGAACCCCCTGACATCACGACG
21392946 AGGAACCCCCT
1 AGGAACCCCCT
21392957 ATCGTCACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.28, C:0.39, G:0.21, T:0.12
Consensus pattern (23 bp):
AGGAACCCCCTGACATCACGACG
Found at i:21394602 original size:31 final size:29
Alignment explanation
Indices: 21394532--21394603 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
21394522 TATCTCAGTT
*
21394532 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTGAAATGTA
* * *
21394561 ACGTTTTAGTCACTTATGTTATCGTATTGTA
1 ACATTTTAGTCACTTATGTT-T-GAAATGTA
21394592 ACATTTTAGTCA
1 ACATTTTAGTCA
21394604 TTGAGCCGTC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 19 0.53
30 1 0.03
31 16 0.44
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.47
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTGAAATGTA
Found at i:21396272 original size:3 final size:3
Alignment explanation
Indices: 21396257--21396343 Score: 156
Period size: 3 Copynumber: 29.0 Consensus size: 3
21396247 TACTATGACT
*
21396257 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
21396305 TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21396344 NNNNNNNNNN
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:21398964 original size:22 final size:22
Alignment explanation
Indices: 21398894--21398964 Score: 108
Period size: 22 Copynumber: 3.2 Consensus size: 22
21398884 AAATTCAATA
*
21398894 TCAATTTCCTTCAAAAATTCTC
1 TCAAATTCCTTCAAAAATTCTC
21398916 TC-AATTCCGTTCAAAAATTCTC
1 TCAAATTCC-TTCAAAAATTCTC
*
21398938 TCAAATTCCTTCCAAAATTCTC
1 TCAAATTCCTTCAAAAATTCTC
21398960 TCAAA
1 TCAAA
21398965 CTCTCAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.11
22 34 0.76
23 6 0.13
ACGTcount: A:0.34, C:0.28, G:0.01, T:0.37
Consensus pattern (22 bp):
TCAAATTCCTTCAAAAATTCTC
Found at i:21398970 original size:30 final size:30
Alignment explanation
Indices: 21398935--21398993 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
21398925 TTCAAAAATT
*
21398935 CTCTCAAATTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
21398965 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
21398994 TTTCCTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:21398985 original size:52 final size:51
Alignment explanation
Indices: 21398913--21399015 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 51
21398903 TTCAAAAATT
* * *
21398913 CTCTCAATTCCGTTCAAAAATTCTCTCAAATTCCTTCCAAAATTCTCTCAAA
1 CTCTCAATTCCGTTCAAAAATCCTCTCAAATTCCTTCAAAAAATCTC-CAAA
* *
21398965 CTCTCAAATTCC-TTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCGTTCAAAAATCCTCTCAAATTCCTTCAAAAAATCTCCAAA
21399016 TCCATATTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
51 4 0.09
52 35 0.78
53 6 0.13
ACGTcount: A:0.34, C:0.32, G:0.01, T:0.33
Consensus pattern (51 bp):
CTCTCAATTCCGTTCAAAAATCCTCTCAAATTCCTTCAAAAAATCTCCAAA
Found at i:21399004 original size:21 final size:22
Alignment explanation
Indices: 21398965--21399006 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
21398955 TTCTCTCAAA
21398965 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
21398987 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
21399007 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:21399112 original size:29 final size:30
Alignment explanation
Indices: 21399052--21399112 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
21399042 AATTTCATTA
* *
21399052 TTTTAAGAAAATTTTAAAATTTTTTATTTT
1 TTTTAAGAAAATTTTAAAATTTTTAATATT
*
21399082 TTTTAA-ATAATTTTAAAATTTTTAATATT
1 TTTTAAGAAAATTTTAAAATTTTTAATATT
21399111 TT
1 TT
21399113 CAACAATGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 22 0.79
30 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTTAAGAAAATTTTAAAATTTTTAATATT
Found at i:21399232 original size:14 final size:15
Alignment explanation
Indices: 21399203--21399236 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
21399193 AAATTTTAAA
21399203 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
21399218 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
21399232 TTTTA
1 TTTTA
21399237 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:21414910 original size:30 final size:30
Alignment explanation
Indices: 21414874--21414943 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
21414864 AAAGATTGTA
21414874 AATAATTTTAAGTATTCAATCAAAAATTAT
1 AATAATTTTAAGTATTCAATCAAAAATTAT
**
21414904 AATAATTTTAAGTATTGTATCAAAAATTAT
1 AATAATTTTAAGTATTCAATCAAAAATTAT
21414934 AATAATTTTA
1 AATAATTTTA
21414944 TCAATATTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (30 bp):
AATAATTTTAAGTATTCAATCAAAAATTAT
Found at i:21416750 original size:6 final size:6
Alignment explanation
Indices: 21416735--21416794 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
21416725 ATTGAGCTTA
* * * * * *
21416735 TCATCG TCATTT TCATCT TCATCT CCATCT CCA-CA TCAATTT TCATCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC-ATCT TCATCT
21416783 TCATCT TCATCT
1 TCATCT TCATCT
21416795 CTAACATTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
5 2 0.05
6 39 0.91
7 2 0.05
ACGTcount: A:0.20, C:0.33, G:0.02, T:0.45
Consensus pattern (6 bp):
TCATCT
Found at i:21416810 original size:30 final size:30
Alignment explanation
Indices: 21416746--21416810 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
21416736 CATCGTCATT
* *
21416746 TTCATCTTCATCTCCATCTCCACATCAATT
1 TTCATCTTCATCTCCATCTCAACATCAATC
* *
21416776 TTCATCTTCATCTTCATCTCTAACAT-TATC
1 TTCATCTTCATCTCCATCTC-AACATCAATC
21416806 TTCAT
1 TTCAT
21416811 ATTGTTATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 26 0.87
31 4 0.13
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (30 bp):
TTCATCTTCATCTCCATCTCAACATCAATC
Found at i:21419775 original size:22 final size:22
Alignment explanation
Indices: 21419750--21419801 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
21419740 TTATCCATTC
*
21419750 AAATATTATAATAGAA-AATTTT
1 AAATATTA-AATAAAACAATTTT
*
21419772 AAATAATAAATAAAACAATTTT
1 AAATATTAAATAAAACAATTTT
21419794 AACATATT
1 AA-ATATT
21419802 CAACAAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 6 0.24
22 15 0.60
23 4 0.16
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (22 bp):
AAATATTAAATAAAACAATTTT
Found at i:21419913 original size:24 final size:23
Alignment explanation
Indices: 21419861--21419914 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
21419851 TTTTTTAAAT
*
21419861 TAATAATTTTAAATTAAATATTA
1 TAATATTTTTAAATTAAATATTA
21419884 TAAATATTTTTAAATATAAAT-TTAA
1 T-AATATTTTTAAAT-TAAATATT-A
21419909 TAATAT
1 TAATAT
21419915 AATGAAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 1 0.04
24 19 0.70
25 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATATTTTTAAATTAAATATTA
Found at i:21428484 original size:52 final size:52
Alignment explanation
Indices: 21428422--21428530 Score: 209
Period size: 52 Copynumber: 2.1 Consensus size: 52
21428412 ATACTTGACG
21428422 AGTTTATTCTCTAGCAATTTACGAGCCTTTTTAATACTTCTTATTGATTTTT
1 AGTTTATTCTCTAGCAATTTACGAGCCTTTTTAATACTTCTTATTGATTTTT
*
21428474 AGTTTATTCTCTAGCAATTTATGAGCCTTTTTAATACTTCTTATTGATTTTT
1 AGTTTATTCTCTAGCAATTTACGAGCCTTTTTAATACTTCTTATTGATTTTT
21428526 AGTTT
1 AGTTT
21428531 TTAATGTTAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.23, C:0.14, G:0.10, T:0.53
Consensus pattern (52 bp):
AGTTTATTCTCTAGCAATTTACGAGCCTTTTTAATACTTCTTATTGATTTTT
Found at i:21432433 original size:10 final size:11
Alignment explanation
Indices: 21432411--21432436 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21432401 AAATGACAAC
21432411 AAAATAGTAAA
1 AAAATAGTAAA
21432422 AAAATAGTAAA
1 AAAATAGTAAA
21432433 AAAA
1 AAAA
21432437 CAACAGCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (11 bp):
AAAATAGTAAA
Found at i:21437573 original size:60 final size:60
Alignment explanation
Indices: 21437493--21437613 Score: 188
Period size: 60 Copynumber: 2.0 Consensus size: 60
21437483 TAGAAGGAGA
* * * *
21437493 TTGTATTGTAGACTGAGCAGGTAAAGGATTAGTTGACATAGGGGAAGGTGTGAGAGTAGG
1 TTGTATTGTAGAATGAGCAGGTAAAGAAGTAGTTGACATAGGAGAAGGTGTGAGAGTAGG
* *
21437553 TTGTATTGTGGAATGGGCAGGTAAAGAAGTAGTTGACATAGGAGAAGGTGTGAGAGTAGG
1 TTGTATTGTAGAATGAGCAGGTAAAGAAGTAGTTGACATAGGAGAAGGTGTGAGAGTAGG
21437613 T
1 T
21437614 AATGTGGACC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.31, C:0.04, G:0.39, T:0.26
Consensus pattern (60 bp):
TTGTATTGTAGAATGAGCAGGTAAAGAAGTAGTTGACATAGGAGAAGGTGTGAGAGTAGG
Found at i:21440330 original size:13 final size:13
Alignment explanation
Indices: 21440312--21440337 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21440302 CTGTTAGCTT
21440312 CTTTAACAGAATA
1 CTTTAACAGAATA
21440325 CTTTAACAGAATA
1 CTTTAACAGAATA
21440338 ACTACTAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
CTTTAACAGAATA
Found at i:21441721 original size:32 final size:29
Alignment explanation
Indices: 21441679--21441774 Score: 101
Period size: 28 Copynumber: 3.2 Consensus size: 29
21441669 ATGATACATA
21441679 AAAT-ATTTTAGAATTTTAAATATAATAAT
1 AAATGATTTTAGAATTTTAAATATAAT-AT
*
21441708 AAATGATACTTTAGAATTTT-AATGATACAT-G
1 AAATGAT--TTTAGAATTTTAAAT-ATA-ATAT
21441739 AAAT-ATTTTAGAATTTTAAATATAATTAT
1 AAATGATTTTAGAATTTTAAATATAA-TAT
21441768 AAATGAT
1 AAATGAT
21441775 GTTTTTGAGT
Statistics
Matches: 56, Mismatches: 2, Indels: 17
0.75 0.03 0.23
Matches are distributed among these distances:
27 1 0.02
28 15 0.27
29 11 0.20
30 6 0.11
31 7 0.12
32 14 0.25
33 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (29 bp):
AAATGATTTTAGAATTTTAAATATAATAT
Found at i:21441743 original size:60 final size:60
Alignment explanation
Indices: 21441667--21441799 Score: 212
Period size: 60 Copynumber: 2.2 Consensus size: 60
21441657 GCTATAAATC
21441667 TAATGATACATAAAATATTTTAGAATTTTAAATATAATAATAAATGATACTTTAGAATTT
1 TAATGATACATAAAATATTTTAGAATTTTAAATATAATAATAAATGATACTTTAGAATTT
* * ** * *
21441727 TAATGATACATGAAATATTTTAGAATTTTAAATATAATTATAAATGATGTTTTTGAGTTT
1 TAATGATACATAAAATATTTTAGAATTTTAAATATAATAATAAATGATACTTTAGAATTT
21441787 TAATGATACATAA
1 TAATGATACATAA
21441800 TGTTGGCATC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (60 bp):
TAATGATACATAAAATATTTTAGAATTTTAAATATAATAATAAATGATACTTTAGAATTT
Found at i:21449223 original size:126 final size:126
Alignment explanation
Indices: 21448998--21449247 Score: 446
Period size: 126 Copynumber: 2.0 Consensus size: 126
21448988 ATCTTTACCT
*
21448998 ACTACTAATAGTAATAATTTCTGTGTTATTACCATATCAGTTTCTAACATATCTACTCTCGATTT
1 ACTACTAATAGTAATAATTTCTATGTTATTACCATATCAGTTTCTAACATATCTACTCTCGATTT
21449063 ATCATTGTTCTCGACTCAGTGGGTATTAAGGATGTTACAGTTAGGACTTGAATCCAAACCC
66 ATCATTGTTCTCGACTCAGTGGGTATTAAGGATGTTACAGTTAGGACTTGAATCCAAACCC
* *
21449124 ACTACTAATAGTAATAATTTTTATGTTATTACCATCTCAGTTTCTAACATATCTACTCTCGATTT
1 ACTACTAATAGTAATAATTTCTATGTTATTACCATATCAGTTTCTAACATATCTACTCTCGATTT
* **
21449189 ATCATTGTTCTCGACTTAGTGGGTATTTGGGATGTTACAGTTAGGACTTGAATCCAAAC
66 ATCATTGTTCTCGACTCAGTGGGTATTAAGGATGTTACAGTTAGGACTTGAATCCAAAC
21449248 TCGTTTGTCA
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
126 118 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (126 bp):
ACTACTAATAGTAATAATTTCTATGTTATTACCATATCAGTTTCTAACATATCTACTCTCGATTT
ATCATTGTTCTCGACTCAGTGGGTATTAAGGATGTTACAGTTAGGACTTGAATCCAAACCC
Found at i:21452866 original size:16 final size:16
Alignment explanation
Indices: 21452827--21452877 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 16
21452817 ATGACATATC
*
21452827 AATAAATAAT-TTAAAA
1 AATAAA-AATATTCAAA
21452843 ATATAAAAATATTCAAA
1 A-ATAAAAATATTCAAA
21452860 AATAAAAATATTCAAA
1 AATAAAAATATTCAAA
21452876 AA
1 AA
21452878 AATTATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 21 0.66
17 11 0.34
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (16 bp):
AATAAAAATATTCAAA
Found at i:21466932 original size:180 final size:181
Alignment explanation
Indices: 21466626--21466991 Score: 718
Period size: 180 Copynumber: 2.0 Consensus size: 181
21466616 TGTTTTCTGT
21466626 TAAA-AAAATTATCCTATACAATCAAACATTGTCATGTGTAAAAAGAAAAAAAACACAATTTTTT
1 TAAATAAAATTATCCTATACAATCAAACATTGTCATGTGTAAAAAGAAAAAAAACACAATTTTTT
21466690 AAATGTGAATTGGGGTAACAGGTATATAAAATGATAACACAAGTGTGAATATGATAAAAAAAAAT
66 AAATGTGAATTGGGGTAACAGGTATATAAAATGATAACACAAGTGTGAATATGATAAAAAAAAAT
21466755 CAAAATTTTTTTTTGAATTCAGGAGTTCTTTTTAAATTTTAAT-AAATTAA
131 CAAAATTTTTTTTTGAATTCAGGAGTTCTTTTTAAATTTTAATAAAATTAA
21466805 TAAATAAAATTATCCTATACAATCAAACATTGTCATGTGTAAAAAGAAAAAAAACACAATTTTTT
1 TAAATAAAATTATCCTATACAATCAAACATTGTCATGTGTAAAAAGAAAAAAAACACAATTTTTT
21466870 AAATGTGAATTGGGGTAACAGGTATATAAAATGATAACACAAGTGTGAATATGATAAAAAAAAAT
66 AAATGTGAATTGGGGTAACAGGTATATAAAATGATAACACAAGTGTGAATATGATAAAAAAAAAT
21466935 CAAAATTTTTTTTTGAATTCAGGAGTTCTTTTTAAATTTTAATAAAATTAA
131 CAAAATTTTTTTTTGAATTCAGGAGTTCTTTTTAAATTTTAATAAAATTAA
21466986 TAAATA
1 TAAATA
21466992 TATTTAATTA
Statistics
Matches: 185, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
179 4 0.02
180 168 0.91
181 13 0.07
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (181 bp):
TAAATAAAATTATCCTATACAATCAAACATTGTCATGTGTAAAAAGAAAAAAAACACAATTTTTT
AAATGTGAATTGGGGTAACAGGTATATAAAATGATAACACAAGTGTGAATATGATAAAAAAAAAT
CAAAATTTTTTTTTGAATTCAGGAGTTCTTTTTAAATTTTAATAAAATTAA
Found at i:21484868 original size:119 final size:120
Alignment explanation
Indices: 21484657--21484895 Score: 453
Period size: 119 Copynumber: 2.0 Consensus size: 120
21484647 ATAGTTTATT
* *
21484657 TGACTTACTAATTTAGCCTATAAATGGGTTCTTTTACAATCTAAAAATACACCCATTAGATTAGA
1 TGACTTACTAATTTAGCCTATAAATAGGCTCTTTTACAATCTAAAAATACACCCATTAGATTAGA
21484722 ACTCATAACACATTCAAAGAATTTTGTGTTTACGTTTTGAGGG-TCTTTGTTTTC
66 ACTCATAACACATTCAAAGAATTTTGTGTTTACGTTTTGAGGGTTCTTTGTTTTC
21484776 TGACTTACTAATTTAGCCTATAAATAGGCTCTTTTACAATCTAAAAATACACCCATTAGATTAGA
1 TGACTTACTAATTTAGCCTATAAATAGGCTCTTTTACAATCTAAAAATACACCCATTAGATTAGA
21484841 ACTCATAACACATTCAAAGAATTTTGTGTTTACGTTTTGAGGGTTCTTTGTTTTC
66 ACTCATAACACATTCAAAGAATTTTGTGTTTACGTTTTGAGGGTTCTTTGTTTTC
21484896 GGGTTTTCGG
Statistics
Matches: 117, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
119 106 0.91
120 11 0.09
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.39
Consensus pattern (120 bp):
TGACTTACTAATTTAGCCTATAAATAGGCTCTTTTACAATCTAAAAATACACCCATTAGATTAGA
ACTCATAACACATTCAAAGAATTTTGTGTTTACGTTTTGAGGGTTCTTTGTTTTC
Found at i:21487220 original size:14 final size:15
Alignment explanation
Indices: 21487203--21487231 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
21487193 AATTTTATAT
21487203 ATGAAATAT-TTTTA
1 ATGAAATATATTTTA
21487217 ATGAAATATATTTTA
1 ATGAAATATATTTTA
21487232 TTATTTAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
ATGAAATATATTTTA
Found at i:21487739 original size:6 final size:6
Alignment explanation
Indices: 21487715--21487749 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
21487705 TTTCTTATTA
21487715 ATAGATT ATAGATT ATAGAT ATAGAT ATAGAT ATA
1 ATAGA-T ATAGA-T ATAGAT ATAGAT ATAGAT ATA
21487750 TAAATATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 16 0.57
7 12 0.43
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (6 bp):
ATAGAT
Found at i:21487740 original size:20 final size:20
Alignment explanation
Indices: 21487715--21487763 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
21487705 TTTCTTATTA
*
21487715 ATAGATTATAGAT-TATAGAT
1 ATAGA-TATAGATATATAAAT
21487735 ATAGATATAGATATATAAAT
1 ATAGATATAGATATATAAAT
*
21487755 ATAAATATA
1 ATAGATATA
21487764 AATTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (20 bp):
ATAGATATAGATATATAAAT
Found at i:21487750 original size:14 final size:14
Alignment explanation
Indices: 21487715--21487763 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
21487705 TTTCTTATTA
21487715 ATAGAT-TATAGATT
1 ATAGATATATAGA-T
21487729 ATAG--ATATAGAT
1 ATAGATATATAGAT
*
21487741 ATAGATATATAAAT
1 ATAGATATATAGAT
*
21487755 ATAAATATA
1 ATAGATATA
21487764 AATTTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 5 0.17
13 6 0.20
14 19 0.63
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (14 bp):
ATAGATATATAGAT
Found at i:21488842 original size:37 final size:37
Alignment explanation
Indices: 21488795--21488865 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
21488785 AGTATTACTT
*
21488795 AATATTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
21488832 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
21488866 AAAAAAGTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:21488870 original size:19 final size:19
Alignment explanation
Indices: 21488801--21488869 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
21488791 ACTTAATATT
21488801 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
21488820 TTATTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAG
21488838 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
21488857 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
21488870 AAGTGAGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 20 0.47
19 23 0.53
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:21491228 original size:19 final size:18
Alignment explanation
Indices: 21491201--21491262 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
21491191 GTAAGGGTTA
* *
21491201 ATTTCATTTTTCTAATATT
1 ATTTAATTTTTATAAT-TT
21491220 ATTTAATTTTTATAATTT
1 ATTTAATTTTTATAATTT
*
21491238 AATTAATATTTTTTATAATTT
1 -ATT--TAATTTTTATAATTT
21491259 -TTTA
1 ATTTA
21491263 TAATAGCCGG
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 2 0.05
18 2 0.05
19 19 0.51
21 14 0.38
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTAATTTTTATAATTT
Found at i:21493279 original size:59 final size:59
Alignment explanation
Indices: 21493179--21493382 Score: 327
Period size: 59 Copynumber: 3.4 Consensus size: 59
21493169 ATTGATTTAT
* * *
21493179 TTTTGAATTTTTTTATACAAATTGTTTTTATATTGTTTTATTTAATAAAATAGAAGTTC
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTTATTTAATAAAATAGAAGTTC
* * *
21493238 TTTTCAATATTTTTGTAAAAATTATTTTAATATTGTTTTATTTAATAAAATAGAAGTTC
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTTATTTAATAAAATAGAAGTTC
* *
21493297 TTTTGAATAATTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTTATTTAATAAAATAGAAGTTC
21493356 TTTTGAATATTTTTGTACAAATATATT
1 TTTTGAATATTTTTGTACAAAT-TATT
21493383 ACTGGCTGTG
Statistics
Matches: 132, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
59 128 0.97
60 4 0.03
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (59 bp):
TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTTATTTAATAAAATAGAAGTTC
Found at i:21493466 original size:29 final size:29
Alignment explanation
Indices: 21493434--21493505 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
21493424 ATCCATCTCA
* *
21493434 TCAAAATAATTTTTTCAAAATACATCATG
1 TCAAAATTATTTTTTCAAAACACATCATG
* * * *
21493463 TCAAATTTATTTTTTCAGAACCCATCTTG
1 TCAAAATTATTTTTTCAAAACACATCATG
21493492 TCAAAATTATTTTT
1 TCAAAATTATTTTT
21493506 CCCAGAACAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.36, C:0.15, G:0.04, T:0.44
Consensus pattern (29 bp):
TCAAAATTATTTTTTCAAAACACATCATG
Found at i:21493512 original size:30 final size:29
Alignment explanation
Indices: 21493456--21493513 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
21493446 TTTCAAAATA
* *
21493456 CATCATGTCAAATTTATTTTTTCAGAACC
1 CATCATGTCAAAATTATTTTTCCAGAACC
*
21493485 CATCTTGTCAAAATTATTTTTCCCAGAAC
1 CATCATGTCAAAATTATTTTT-CCAGAAC
21493514 AATACTTAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (29 bp):
CATCATGTCAAAATTATTTTTCCAGAACC
Found at i:21504130 original size:44 final size:43
Alignment explanation
Indices: 21504037--21504242 Score: 288
Period size: 44 Copynumber: 4.6 Consensus size: 43
21504027 TTTGAGTACT
*
21504037 TCTGATCAAGGACAAGTGATAAGTGGTAGCTTAGCTACACTTA
1 TCTGATCAGGGACAAGTGATAAGTGGTAGCTTAGCTACACTTA
21504080 TCTGATCAGGGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGGGACAAGTGATAAGTGGTAGC-TTAGCTACACTTA
21504124 TCTGATCAGCGG-CAAGTGATAAGTGGTAGCATTAGCTACACTTA
1 TCTGATCAG-GGACAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
21504168 TCTGATCAGTGACAAGCGGCAAGTGATAAGTGGTAGCTTAGCTACACTTA
1 TCTGATCA--G----G-GACAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
21504218 TCTGATCAAGGACAAGTGATAAGTG
1 TCTGATCAGGGACAAGTGATAAGTG
21504243 ATCATACGTA
Statistics
Matches: 149, Mismatches: 5, Indels: 18
0.87 0.03 0.10
Matches are distributed among these distances:
43 43 0.29
44 62 0.42
45 2 0.01
46 1 0.01
49 1 0.01
50 22 0.15
51 18 0.12
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (43 bp):
TCTGATCAGGGACAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:21504243 original size:50 final size:51
Alignment explanation
Indices: 21504131--21504244 Score: 169
Period size: 50 Copynumber: 2.3 Consensus size: 51
21504121 TTATCTGATC
*
21504131 AGCGGCAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAGTGACA
1 AGCGACAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAGTGACA
*
21504182 AGCGGCAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAG-GACA
1 AGCGACAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATC-AGTGACA
* *
21504232 AGTGATAAGTGAT
1 AGCGACAAGTGAT
21504245 CATACGTAAG
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
50 34 0.58
51 25 0.42
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.25
Consensus pattern (51 bp):
AGCGACAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAGTGACA
Found at i:21506074 original size:23 final size:23
Alignment explanation
Indices: 21506047--21506092 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
21506037 GATACAAATG
21506047 TTAAGAGTGAAAATTGGGGTTGT
1 TTAAGAGTGAAAATTGGGGTTGT
21506070 TTAAGAGTGAAAATTGGGGTTGT
1 TTAAGAGTGAAAATTGGGGTTGT
21506093 ACACCAGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.35, T:0.35
Consensus pattern (23 bp):
TTAAGAGTGAAAATTGGGGTTGT
Found at i:21515493 original size:22 final size:22
Alignment explanation
Indices: 21515430--21515501 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
21515420 AAATTTAATA
*
21515430 ATTTTAAAAAATTA-AAGCACAT
1 ATTTTAAAAAATTATAA-CATAT
*
21515452 ATTTTAAAAAA-TAT-ATATAT
1 ATTTTAAAAAATTATAACATAT
21515472 -TTTTAAAAAAATTATAACATAT
1 ATTTT-AAAAAATTATAACATAT
21515494 ATTTTAAA
1 ATTTTAAA
21515502 TTTTAAAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
19 4 0.10
20 9 0.21
21 6 0.14
22 19 0.45
23 4 0.10
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (22 bp):
ATTTTAAAAAATTATAACATAT
Found at i:21516091 original size:22 final size:22
Alignment explanation
Indices: 21516028--21516099 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
21516018 AAATTTAATA
*
21516028 ATTTTAAAAAATTA-AAGCACAT
1 ATTTTAAAAAATTATAA-CATAT
*
21516050 ATTTTAAAAAA-TAT-ATATAT
1 ATTTTAAAAAATTATAACATAT
21516070 -TTTTAAAAAAATTATAACATAT
1 ATTTT-AAAAAATTATAACATAT
21516092 ATTTTAAA
1 ATTTTAAA
21516100 TTTTAAAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
19 4 0.10
20 9 0.21
21 6 0.14
22 19 0.45
23 4 0.10
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (22 bp):
ATTTTAAAAAATTATAACATAT
Found at i:21517071 original size:3 final size:3
Alignment explanation
Indices: 21517063--21517092 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
21517053 ATTAACCCAA
21517063 AAG AAG AAG AAG AAG AAG AAG AAG AGAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG A-AG AA
21517093 ATGGTGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:21519019 original size:22 final size:22
Alignment explanation
Indices: 21518977--21519020 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
21518967 GCATATACAT
*
21518977 ATAATAAGCTTTAAATTTTTTA
1 ATAATAAGCTTTAAATGTTTTA
*
21518999 ATAATAATGCTTTATA-GTTTTA
1 ATAATAA-GCTTTAAATGTTTTA
21519021 TATATAGGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.50
Consensus pattern (22 bp):
ATAATAAGCTTTAAATGTTTTA
Found at i:21519019 original size:23 final size:22
Alignment explanation
Indices: 21518977--21519019 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
21518967 GCATATACAT
*
21518977 ATAATAAGCTTTAAATTTTTTA
1 ATAATAAGCTTTAAAGTTTTTA
*
21518999 ATAATAATGCTTTATAGTTTT
1 ATAATAA-GCTTTAAAGTTTT
21519020 ATATATAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (22 bp):
ATAATAAGCTTTAAAGTTTTTA
Found at i:21525432 original size:41 final size:41
Alignment explanation
Indices: 21525371--21525512 Score: 223
Period size: 41 Copynumber: 3.5 Consensus size: 41
21525361 AATGAGATAA
*
21525371 TTCA-ACTTTACGTCTAGCAGGCTTGATGCTGGTGAAATGT
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGT
*
21525411 TTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAAATGT
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGT
* * *
21525452 TTCAGACTTTACGTCTAGTAGGCTTGATGCCGATGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGT
*
21525493 TTCACACTTTACGTCTAGCA
1 TTCAGACTTTACGTCTAGCA
21525513 AGCTAATTGC
Statistics
Matches: 93, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 4 0.04
41 89 0.96
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGT
Found at i:21525557 original size:82 final size:82
Alignment explanation
Indices: 21525375--21525557 Score: 188
Period size: 82 Copynumber: 2.2 Consensus size: 82
21525365 AGATAATTCA
* * * * * * * * *
21525375 ACTTTACGTCTAGCAGGCTTGATGCTGGTGAAATGTTTCAGACTTTATGTCTAGCAGGCTTGATG
1 ACTTTAAGCCTAGCAGGCTTGATGCCGATGAAATATTTCACACTTTACGTCTAGCAAGCTTAATG
**
21525440 CCGGTGAAATGTTTCAG
66 CCGGTGAAATGAATCAG
* * *
21525457 ACTTTACGTCTAGTAGGCTTGATGCCGATGAAATATTTCACACTTTACGTCTAGCAAGC-TAATT
1 ACTTTAAGCCTAGCAGGCTTGATGCCGATGAAATATTTCACACTTTACGTCTAGCAAGCTTAA-T
* *
21525521 GCCGGTGTATTGAATCAG
65 GCCGGTGAAATGAATCAG
**
21525539 GTTTTAAGCCTAGCAGGCT
1 ACTTTAAGCCTAGCAGGCT
21525558 AAGTGCCGGT
Statistics
Matches: 83, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
81 2 0.02
82 81 0.98
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (82 bp):
ACTTTAAGCCTAGCAGGCTTGATGCCGATGAAATATTTCACACTTTACGTCTAGCAAGCTTAATG
CCGGTGAAATGAATCAG
Found at i:21525938 original size:45 final size:46
Alignment explanation
Indices: 21525874--21525966 Score: 179
Period size: 45 Copynumber: 2.0 Consensus size: 46
21525864 TATATATTCG
21525874 ATTGTATGTGCATGATAAGTACATATATGACTTTGG-TAAATGTAT
1 ATTGTATGTGCATGATAAGTACATATATGACTTTGGATAAATGTAT
21525919 ATTGTATGTGCATGATAAGTACATATATGACTTTGGATAAATGTAT
1 ATTGTATGTGCATGATAAGTACATATATGACTTTGGATAAATGTAT
21525965 AT
1 AT
21525967 GGTAAATACA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 36 0.77
46 11 0.23
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.40
Consensus pattern (46 bp):
ATTGTATGTGCATGATAAGTACATATATGACTTTGGATAAATGTAT
Found at i:21536744 original size:25 final size:25
Alignment explanation
Indices: 21536685--21536737 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
21536675 AAAAAATGTC
* *
21536685 AAATTCAAGTATCAAATTAGACTAAAA
1 AAATT-AAATATCAAATTAGA-GAAAA
21536712 AAATTAAATATCAAATTAG-GAAAA
1 AAATTAAATATCAAATTAGAGAAAA
21536736 AA
1 AA
21536738 TTGTAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.25
26 13 0.54
27 5 0.21
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.25
Consensus pattern (25 bp):
AAATTAAATATCAAATTAGAGAAAA
Found at i:21561152 original size:31 final size:31
Alignment explanation
Indices: 21561117--21561185 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
21561107 TTTGATCCTC
*
21561117 TGCTGGTGCTGGTTCTTTGTTCTTCTGCTAG
1 TGCTGGTGCTGGTTCTTTGTTCCTCTGCTAG
*
21561148 TGCTGGTGCTGGTTCTTTGTTCCTCTGCTGG
1 TGCTGGTGCTGGTTCTTTGTTCCTCTGCTAG
21561179 TGCTGGT
1 TGCTGGT
21561186 TTTTTGTTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.01, C:0.20, G:0.32, T:0.46
Consensus pattern (31 bp):
TGCTGGTGCTGGTTCTTTGTTCCTCTGCTAG
Found at i:21561178 original size:19 final size:19
Alignment explanation
Indices: 21561179--21561236 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 19
21561169 CCTCTGCTGG
*
21561179 TGCTGGTTTTTTGTTCCTC
1 TGCTGGTTATTTGTTCCTC
21561198 TGCTGGTTATTTGTTCCTC
1 TGCTGGTTATTTGTTCCTC
**
21561217 TGCTGGTGCTTTGTTCCTC
1 TGCTGGTTATTTGTTCCTC
21561236 T
1 T
21561237 TCTCCACCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.02, C:0.22, G:0.22, T:0.53
Consensus pattern (19 bp):
TGCTGGTTATTTGTTCCTC
Found at i:21561226 original size:25 final size:25
Alignment explanation
Indices: 21561098--21561204 Score: 133
Period size: 25 Copynumber: 4.0 Consensus size: 25
21561088 TTTTGTTCTC
* *
21561098 TGCTGCTTCTTTGATCCTCTGCTGG
1 TGCTGGTTCTTTGTTCCTCTGCTGG
21561123 TGCTGGTTCTTTGTTCTTCTGCTAGTGCTGG
1 TGCTGGTTCTTTGTTC--CT-C---TGCTGG
21561154 TGCTGGTTCTTTGTTCCTCTGCTGG
1 TGCTGGTTCTTTGTTCCTCTGCTGG
*
21561179 TGCTGGTTTTTTGTTCCTCTGCTGG
1 TGCTGGTTCTTTGTTCCTCTGCTGG
21561204 T
1 T
21561205 TATTTGTTCC
Statistics
Matches: 73, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
25 45 0.62
27 2 0.03
28 2 0.03
29 2 0.03
31 22 0.30
ACGTcount: A:0.02, C:0.22, G:0.27, T:0.49
Consensus pattern (25 bp):
TGCTGGTTCTTTGTTCCTCTGCTGG
Found at i:21563982 original size:27 final size:27
Alignment explanation
Indices: 21563952--21564005 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
21563942 CGAAGGTAAG
21563952 ACCACCGTTTGGGGAAAGTGATGACGC
1 ACCACCGTTTGGGGAAAGTGATGACGC
21563979 ACCACCGTTTGGGGAAAGTGATGACGC
1 ACCACCGTTTGGGGAAAGTGATGACGC
21564006 GGACGATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.22, G:0.33, T:0.19
Consensus pattern (27 bp):
ACCACCGTTTGGGGAAAGTGATGACGC
Found at i:21569588 original size:3 final size:3
Alignment explanation
Indices: 21569580--21569610 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
21569570 AGTAATTGAC
21569580 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
21569611 TCGAAGATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:21570083 original size:7 final size:7
Alignment explanation
Indices: 21570073--21570109 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
21570063 TTAATTAATT
21570073 TTTTAAA
1 TTTTAAA
21570080 TTTTAAA
1 TTTTAAA
21570087 TTTTAAA
1 TTTTAAA
21570094 TTTTAAA
1 TTTTAAA
21570101 TTTTAAA
1 TTTTAAA
21570108 TT
1 TT
21570110 ATAGTAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTTAAA
Found at i:21576037 original size:9 final size:9
Alignment explanation
Indices: 21576023--21576097 Score: 91
Period size: 9 Copynumber: 8.4 Consensus size: 9
21576013 TTTGGTTAAA
21576023 AATTAACCG
1 AATTAACCG
21576032 AATTAACC-
1 AATTAACCG
21576040 AATT-ACCAG
1 AATTAACC-G
21576049 AATTAACCG
1 AATTAACCG
* *
21576058 GATTACCCG
1 AATTAACCG
21576067 AATTAACCG
1 AATTAACCG
*
21576076 AATTACCCG
1 AATTAACCG
*
21576085 AATTAACCA
1 AATTAACCG
21576094 AATT
1 AATT
21576098 GAATCACTAC
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
7 3 0.05
8 4 0.07
9 46 0.82
10 3 0.05
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:21576064 original size:18 final size:18
Alignment explanation
Indices: 21576023--21576097 Score: 107
Period size: 18 Copynumber: 4.2 Consensus size: 18
21576013 TTTGGTTAAA
*
21576023 AATTAACCGAATTAACC-
1 AATTACCCGAATTAACCG
*
21576040 AATTACCAGAATTAACCG
1 AATTACCCGAATTAACCG
*
21576058 GATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
*
21576076 AATTACCCGAATTAACCA
1 AATTACCCGAATTAACCG
21576094 AATT
1 AATT
21576098 GAATCACTAC
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
17 15 0.29
18 36 0.71
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.24
Consensus pattern (18 bp):
AATTACCCGAATTAACCG
Found at i:21579151 original size:43 final size:43
Alignment explanation
Indices: 21579032--21579192 Score: 182
Period size: 43 Copynumber: 3.7 Consensus size: 43
21579022 AGCAAGTCGC
* * * * *
21579032 AGCAATTGTATTGGCACACGAGGTGCATCATCGAATGAACCAA
1 AGCAATTATACTGGCACACGAAGTGCATCATTGGATGAACCAA
*
21579075 AGCAATTATATTGGCACACGAAGTGCATCATTGGATGAACCAA
1 AGCAATTATACTGGCACACGAAGTGCATCATTGGATGAACCAA
* * * **
21579118 AGCAATTATACTGGCACACGTAA-TTCATTATTGGATAAACTGA
1 AGCAATTATACTGGCACACG-AAGTGCATCATTGGATGAACCAA
*
21579161 AGTAATTATACTGGCACAC-ATAGTGCATCATT
1 AGCAATTATACTGGCACACGA-AGTGCATCATT
21579193 AGATAAACTG
Statistics
Matches: 102, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 98 0.96
44 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (43 bp):
AGCAATTATACTGGCACACGAAGTGCATCATTGGATGAACCAA
Found at i:21579198 original size:43 final size:43
Alignment explanation
Indices: 21579078--21579220 Score: 146
Period size: 43 Copynumber: 3.3 Consensus size: 43
21579068 GAACCAAAGC
* * ** *
21579078 AATTATATTGGCACACGA-AGTGCATCATTGGATGAACCAAAGC
1 AATTATACTGGCACAC-ATAGTGCATCATTGGATAAACTGAAGT
* * * *
21579121 AATTATACTGGCACACGTAATTCATTATTGGATAAACTGAAGT
1 AATTATACTGGCACACATAGTGCATCATTGGATAAACTGAAGT
*
21579164 AATTATACTGGCACACATAGTGCATCATTAGATAAACTGGAA-T
1 AATTATACTGGCACACATAGTGCATCATTGGATAAACT-GAAGT
* *
21579207 AATCATACTAGCAC
1 AATTATACTGGCAC
21579221 GTAATAGCAT
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
43 79 0.96
44 3 0.04
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (43 bp):
AATTATACTGGCACACATAGTGCATCATTGGATAAACTGAAGT
Found at i:21582202 original size:16 final size:19
Alignment explanation
Indices: 21582183--21582219 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
21582173 TGAATAGTTT
21582183 TTTATT-TG-AATG-ATAA
1 TTTATTATGAAATGTATAA
21582199 TTTATTATGAAATGTATAA
1 TTTATTATGAAATGTATAA
21582218 TT
1 TT
21582220 GTTTAAGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.33
17 2 0.11
18 4 0.22
19 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (19 bp):
TTTATTATGAAATGTATAA
Found at i:21589712 original size:12 final size:12
Alignment explanation
Indices: 21589695--21589720 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21589685 TTATGTAATT
21589695 AAATTTTAAATA
1 AAATTTTAAATA
21589707 AAATTTTAAATA
1 AAATTTTAAATA
21589719 AA
1 AA
21589721 TAGAACATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATTTTAAATA
Found at i:21590585 original size:19 final size:19
Alignment explanation
Indices: 21590561--21590602 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
21590551 TTTCACCTTG
21590561 ATGATAAAAAGATTTCCAC
1 ATGATAAAAAGATTTCCAC
21590580 ATGATAAAAAGATTTCCAC
1 ATGATAAAAAGATTTCCAC
21590599 ATGA
1 ATGA
21590603 AATTTCCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (19 bp):
ATGATAAAAAGATTTCCAC
Found at i:21595171 original size:20 final size:22
Alignment explanation
Indices: 21595133--21595174 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
21595123 TACATTTCAA
21595133 AACACAACTTTTGACTTTTTTT
1 AACACAACTTTTGACTTTTTTT
*
21595155 AACA-AACTTTTG-GTTTTTTT
1 AACACAACTTTTGACTTTTTTT
21595175 GAAAACAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 8 0.42
22 4 0.21
ACGTcount: A:0.26, C:0.14, G:0.07, T:0.52
Consensus pattern (22 bp):
AACACAACTTTTGACTTTTTTT
Found at i:21598261 original size:35 final size:34
Alignment explanation
Indices: 21598201--21598268 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 34
21598191 AAAAAATAAT
21598201 ATATGATTAAATTGAAAATAAAATTTAAATATTTC
1 ATATGATTAAATTGAAAATAAAATTTAAA-ATTTC
* *
21598236 ATATGCATTAAATT-AGAATATAATTTAAAATTT
1 ATATG-ATTAAATTGAAAATAAAATTTAAAATTT
21598269 AATTCAATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 4 0.13
35 18 0.60
36 8 0.27
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (34 bp):
ATATGATTAAATTGAAAATAAAATTTAAAATTTC
Found at i:21606352 original size:153 final size:154
Alignment explanation
Indices: 21606183--21606491 Score: 575
Period size: 153 Copynumber: 2.0 Consensus size: 154
21606173 AGAATTCTAG
*
21606183 AAGGTAATGATGATGTTTTTGATATTTTTAATTAATTAATTAGATAAATGTTATTTAATTAATAT
1 AAGGTAATGATGATGTTTGTGATATTTTTAATTAATTAATTAGATAAATGTTATTTAATTAATAT
21606248 TTTATTAAGATTTTTAGTATTATTTTATTATTAAATGATTAATATAAAAGGGAGGAAAGATGATG
66 TTTATTAAGATTTTTAGTATTATTTTATTATTAAATGATTAATATAAAAGGGAGGAAAGATGATG
21606313 -AAAAAATCATCACCTTTCCATGC
131 AAAAAAATCATCACCTTTCCATGC
21606336 AAGGTAATGATGATGTTTGTGATATTTTTAATTAATTAATTAGATAAATGTTATTTAATTAATAT
1 AAGGTAATGATGATGTTTGTGATATTTTTAATTAATTAATTAGATAAATGTTATTTAATTAATAT
*
21606401 TTTATTAAGATTTTTAGTATTATTTTATTATTAAATGATTAATATAAAAGGGTGGAAAGATGATG
66 TTTATTAAGATTTTTAGTATTATTTTATTATTAAATGATTAATATAAAAGGGAGGAAAGATGATG
* *
21606466 AAAAAAATTATCATCTTTCCATGC
131 AAAAAAATCATCACCTTTCCATGC
21606490 AA
1 AA
21606492 CCAACGCTAG
Statistics
Matches: 151, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
153 128 0.85
154 23 0.15
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.43
Consensus pattern (154 bp):
AAGGTAATGATGATGTTTGTGATATTTTTAATTAATTAATTAGATAAATGTTATTTAATTAATAT
TTTATTAAGATTTTTAGTATTATTTTATTATTAAATGATTAATATAAAAGGGAGGAAAGATGATG
AAAAAAATCATCACCTTTCCATGC
Found at i:21612673 original size:20 final size:18
Alignment explanation
Indices: 21612619--21612674 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 18
21612609 TCGAAACAGA
21612619 TTAATAAAAATTAAAC-TT
1 TTAA-AAAAATTAAACATT
21612637 TTAAAAAAACTTAAAACAGTT
1 TTAAAAAAA-TT-AAACA-TT
21612658 TCTAAAAAAATTAAACA
1 T-TAAAAAAATTAAACA
21612675 AATTTTATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 5 0.15
18 6 0.18
19 4 0.12
20 5 0.15
21 5 0.15
22 8 0.24
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (18 bp):
TTAAAAAAATTAAACATT
Found at i:21612685 original size:22 final size:21
Alignment explanation
Indices: 21612624--21612685 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
21612614 ACAGATTAAT
21612624 AAAAATTAAAC--TTTTA-AA
1 AAAAATTAAACAATTTTATAA
* * *
21612642 AAAACTTAAA-ACAGTTTCTAA
1 AAAAATTAAACA-ATTTTATAA
21612663 AAAAATTAAACAAATTTTATAA
1 AAAAATTAAAC-AATTTTATAA
21612685 A
1 A
21612686 GACTTTTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
18 9 0.28
20 3 0.09
21 11 0.34
22 8 0.25
23 1 0.03
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.31
Consensus pattern (21 bp):
AAAAATTAAACAATTTTATAA
Found at i:21618874 original size:30 final size:30
Alignment explanation
Indices: 21618838--21618901 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
21618828 AAAAAGACAA
* **
21618838 CTTATATTGGTAGATGAACCTAAACATGTC
1 CTTATATTAGTAGAAAAACCTAAACATGTC
* *
21618868 CTTATATTAGTAGAAAAACCTACACATTTC
1 CTTATATTAGTAGAAAAACCTAAACATGTC
21618898 CTTA
1 CTTA
21618902 GTCTAATTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (30 bp):
CTTATATTAGTAGAAAAACCTAAACATGTC
Found at i:21620410 original size:43 final size:43
Alignment explanation
Indices: 21620362--21620499 Score: 156
Period size: 43 Copynumber: 3.3 Consensus size: 43
21620352 TGTGGTTTCA
21620362 TGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTACG
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTACG
* * *
21620405 TGTAAGACCATGTCTAGGACATTGGCACCG-TAT-ATGATT-TG
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATGA-GATTACG
* * ** * * *
21620446 TGTAAGACCCTGTCTGGGATAGAGGCATCGATATGTGATAACA
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTACG
21620489 TGTAAGACCAT
1 TGTAAGACCAT
21620500 ATTTGGGATA
Statistics
Matches: 77, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
41 26 0.34
42 13 0.17
43 38 0.49
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTACG
Found at i:21620507 original size:43 final size:41
Alignment explanation
Indices: 21620360--21620526 Score: 102
Period size: 43 Copynumber: 4.0 Consensus size: 41
21620350 GGTGTGGTTT
* * * * *
21620360 CATGTAAGACCATGTCTGGGACATTGGCATCGATATGAGATTA
1 CATGTAAGACCATATCTGGGATA-AGGCATCG-TATGTGATAA
* * * * * * * *
21620403 CGTGTAAGACCATGTCTAGGACATTGGCACCGTATATGAT-T
1 CATGTAAGACCATATCTGGGATA-AGGCATCGTATGTGATAA
** * *
21620444 TGTGTAAGACCCTGTCTGGGATAGAGGCATCGATATGTGATAA
1 CATGTAAGACCATATCTGGGATA-AGGCATCG-TATGTGATAA
* * *
21620487 CATGTAAGACCATATTTGGGATATGGCATTGTATGTGATA
1 CATGTAAGACCATATCTGGGATAAGGCATCGTATGTGATA
21620527 TATGTGTTTC
Statistics
Matches: 100, Mismatches: 22, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
41 34 0.34
42 19 0.19
43 47 0.47
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (41 bp):
CATGTAAGACCATATCTGGGATAAGGCATCGTATGTGATAA
Found at i:21624457 original size:13 final size:13
Alignment explanation
Indices: 21624439--21624470 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
21624429 GACCTTGTCT
21624439 TAAGCAAGCTTCA
1 TAAGCAAGCTTCA
21624452 TAAGCAAGCTTCA
1 TAAGCAAGCTTCA
21624465 TCAAGC
1 T-AAGC
21624471 TAATTGAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.22
Consensus pattern (13 bp):
TAAGCAAGCTTCA
Found at i:21627478 original size:198 final size:198
Alignment explanation
Indices: 21627140--21627539 Score: 764
Period size: 198 Copynumber: 2.0 Consensus size: 198
21627130 CAAATAAGGG
21627140 ACATTATGCTTGATTACAACTGGTTTATTATATAAGTGCTAAATGATATGAAAAGTCTGTTATTG
1 ACATTATGCTTGATTACAACTGGTTTATTATATAAGTGCTAAATGATATGAAAAGTCTGTTATTG
21627205 GTTCTGTAAATTTTGGTAATGCTTCGTAACACTATTCTGGCGACATATATAGGTTAAGGGTGTTA
66 GTTCTGTAAATTTTGGTAATGCTTCGTAACACTATTCTGGCGACATATATAGGTTAAGGGTGTTA
*
21627270 CATTTATTGGTATCAGAGATACGGTTTAGTCGATTCTCAGAATAACGTAGCATGTACAGTCTAGT
131 CATTTATTGGTATCAGAGATACGGTTTAGTCGATTCTCAGAATAACGTAGAATGTACAGTCTAGT
21627335 TAT
196 TAT
21627338 ACATTATGCTTGATTACAACTGGTTTATTATATAAGTGCTAAATGATATGAAAAGTCTGTTATTG
1 ACATTATGCTTGATTACAACTGGTTTATTATATAAGTGCTAAATGATATGAAAAGTCTGTTATTG
* * *
21627403 GTTCTGTAAATTTTGGTAATGTTTCGTAACACTATTCTGGCGGCATATATAGGTTAGGGGTGTTA
66 GTTCTGTAAATTTTGGTAATGCTTCGTAACACTATTCTGGCGACATATATAGGTTAAGGGTGTTA
21627468 CATTTATTGGTATCAGAGATACGGTTTAGTCGATTCTCAGAATAACGTAGAATGTACAGTCTAGT
131 CATTTATTGGTATCAGAGATACGGTTTAGTCGATTCTCAGAATAACGTAGAATGTACAGTCTAGT
21627533 TAT
196 TAT
21627536 ACAT
1 ACAT
21627540 GCCATTATAT
Statistics
Matches: 198, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
198 198 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (198 bp):
ACATTATGCTTGATTACAACTGGTTTATTATATAAGTGCTAAATGATATGAAAAGTCTGTTATTG
GTTCTGTAAATTTTGGTAATGCTTCGTAACACTATTCTGGCGACATATATAGGTTAAGGGTGTTA
CATTTATTGGTATCAGAGATACGGTTTAGTCGATTCTCAGAATAACGTAGAATGTACAGTCTAGT
TAT
Found at i:21632993 original size:24 final size:24
Alignment explanation
Indices: 21632916--21632999 Score: 66
Period size: 24 Copynumber: 3.5 Consensus size: 24
21632906 ACAGCTTGAA
*
21632916 AGAGCGTCCCGTTATTAGCTC-TC
1 AGAGCGTCCCGTTAATAGCTCTTC
* * *
21632939 ATGAGC-TCCCCATTATATGGTTCTTGC
1 A-GAGCGT-CCCGTTA-ATAGCTCTT-C
21632966 -GAGCGTCCCGTTAATAGCTCTTC
1 AGAGCGTCCCGTTAATAGCTCTTC
*
21632989 AGAGCATCCCG
1 AGAGCGTCCCG
21633000 ATCGGTTGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 13
0.69 0.12 0.19
Matches are distributed among these distances:
23 3 0.07
24 26 0.57
25 14 0.30
26 2 0.04
27 1 0.02
ACGTcount: A:0.19, C:0.30, G:0.21, T:0.30
Consensus pattern (24 bp):
AGAGCGTCCCGTTAATAGCTCTTC
Found at i:21633132 original size:25 final size:26
Alignment explanation
Indices: 21633070--21633141 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
21633060 ATAGCTCTTC
* *
21633070 GTGAGCTTCTCT-ATTAAAGACTCTCT
1 GTGAGCTTC-CTGATTAATGGCTCTCT
21633096 GTGAGCTTCCTGATTAATGGCTCTCT
1 GTGAGCTTCCTGATTAATGGCTCTCT
21633122 G-GAGCTTCCTGA-T-ATGGCTC
1 GTGAGCTTCCTGATTAATGGCTC
21633142 GCTTGAACTT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
23 7 0.16
24 1 0.02
25 13 0.30
26 22 0.51
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (26 bp):
GTGAGCTTCCTGATTAATGGCTCTCT
Found at i:21633152 original size:23 final size:25
Alignment explanation
Indices: 21633101--21633152 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 25
21633091 TCTCTGTGAG
* *
21633101 CTTCCTGATTAATGGCTCTCTGGAG
1 CTTCCTGATTAATGGCTCGCTGGAA
*
21633126 CTTCCTGA-T-ATGGCTCGCTTGAA
1 CTTCCTGATTAATGGCTCGCTGGAA
21633149 CTTC
1 CTTC
21633153 TCGATATATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 15 0.62
24 1 0.04
25 8 0.33
ACGTcount: A:0.15, C:0.27, G:0.21, T:0.37
Consensus pattern (25 bp):
CTTCCTGATTAATGGCTCGCTGGAA
Found at i:21635761 original size:21 final size:21
Alignment explanation
Indices: 21635731--21635772 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
21635721 TTTTCCAAAG
*
21635731 ATGTGTATTGGATTAAATTGA
1 ATGTGAATTGGATTAAATTGA
* *
21635752 ATGTGAATTGTATTAAGTTGA
1 ATGTGAATTGGATTAAATTGA
21635773 GATAAATTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (21 bp):
ATGTGAATTGGATTAAATTGA
Found at i:21636264 original size:74 final size:74
Alignment explanation
Indices: 21636138--21636304 Score: 185
Period size: 74 Copynumber: 2.2 Consensus size: 74
21636128 TCCTAATAAT
* * * * * * * *
21636138 TGGCTCAAATGAGCTTCCTGATAAATGGCTCTCCGTAGTTTCCCGATTAATGGCTCTCTTGAGTT
1 TGGCTCGAATGAGCTTCCTGATAAATGGCTCGCAGTAGCTTCCCGATAAATGGCTCACATGAGCT
21636203 TCTCGATT-A
66 TCTCG-TTAA
* * *
21636212 TGGCTCGTATGAGCTTCCTGATAATTGGCTCGCAAG-AGCTTCTCGATAAATGGCTCACATGAGC
1 TGGCTCGAATGAGCTTCCTGATAAATGGCTCGC-AGTAGCTTCCCGATAAATGGCTCACATGAGC
21636276 TTCTCGTTACA
65 TTCTCGTTA-A
*
21636287 TGGCTCGAAAGAGCTTCC
1 TGGCTCGAATGAGCTTCC
21636305 CGATTACATG
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
73 2 0.03
74 57 0.74
75 18 0.23
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (74 bp):
TGGCTCGAATGAGCTTCCTGATAAATGGCTCGCAGTAGCTTCCCGATAAATGGCTCACATGAGCT
TCTCGTTAA
Found at i:21636279 original size:25 final size:25
Alignment explanation
Indices: 21636133--21636292 Score: 103
Period size: 25 Copynumber: 6.4 Consensus size: 25
21636123 GAGCTTCCTA
* *
21636133 ATAATTGGCTCAAATGAGCTTC-CTG
1 ATAAATGGCTCACATGAGCTTCTC-G
* * * *
21636158 ATAAATGGCTCTC-CGTAGTTTCCCG
1 ATAAATGGCTCACATG-AGCTTCTCG
* * * *
21636183 ATTAATGGCTCTCTTGAGTTTCTCG
1 ATAAATGGCTCACATGAGCTTCTCG
* **
21636208 AT-TATGGCTCGTATGAGCTTC-CTG
1 ATAAATGGCTCACATGAGCTTCTC-G
* * *
21636232 ATAATTGGCTCGCAAGAGCTTCTCG
1 ATAAATGGCTCACATGAGCTTCTCG
21636257 ATAAATGGCTCACATGAGCTTCTCG
1 ATAAATGGCTCACATGAGCTTCTCG
* *
21636282 TTACATGGCTC
1 ATAAATGGCTC
21636293 GAAAGAGCTT
Statistics
Matches: 107, Mismatches: 22, Indels: 12
0.76 0.16 0.09
Matches are distributed among these distances:
23 1 0.01
24 18 0.17
25 85 0.79
26 3 0.03
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (25 bp):
ATAAATGGCTCACATGAGCTTCTCG
Found at i:21636300 original size:25 final size:25
Alignment explanation
Indices: 21636237--21636318 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
21636227 TCCTGATAAT
* * *
21636237 TGGCTCGCAAGAGCTTCTCGATAAA
1 TGGCTCGAAAGAGCTTCTCGTTACA
*
21636262 TGGCTC-ACATGAGCTTCTCGTTACA
1 TGGCTCGA-AAGAGCTTCTCGTTACA
*
21636287 TGGCTCGAAAGAGCTTCCCGATTACA
1 TGGCTCGAAAGAGCTTCTCG-TTACA
21636313 T-GCTCG
1 TGGCTCG
21636319 TATGAGTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
25 41 0.85
26 7 0.15
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (25 bp):
TGGCTCGAAAGAGCTTCTCGTTACA
Found at i:21636324 original size:50 final size:50
Alignment explanation
Indices: 21636123--21636324 Score: 130
Period size: 50 Copynumber: 4.1 Consensus size: 50
21636113 TAGCTCTTCG
* * **
21636123 GAGCTTCCTAATAATTGGCTC-AAATGAGCTTCCTGATAAATGGCTC-TCC
1 GAGCTTCCTGATAATTGGCTCGAAA-GAGCTTCCCGATAAATGGCTCGTAT
* * **** * * *
21636172 GTAGTTTCCCGATTAA-TGGCTCTCTTGAGTTTCTCGAT-TATGGCTCGTAT
1 G-AGCTTCCTGA-TAATTGGCTCGAAAGAGCTTCCCGATAAATGGCTCGTAT
* * **
21636222 GAGCTTCCTGATAATTGGCTCGCAAGAGCTTCTCGATAAATGGCTCACAT
1 GAGCTTCCTGATAATTGGCTCGAAAGAGCTTCCCGATAAATGGCTCGTAT
* *
21636272 GAGCTT-CTCGTTACA-TGGCTCGAAAGAGCTTCCCGATTACAT-GCTCGTAT
1 GAGCTTCCT-GATA-ATTGGCTCGAAAGAGCTTCCCGA-TAAATGGCTCGTAT
21636322 GAG
1 GAG
21636325 TATTCTTGAA
Statistics
Matches: 117, Mismatches: 27, Indels: 17
0.73 0.17 0.11
Matches are distributed among these distances:
48 3 0.03
49 36 0.31
50 70 0.60
51 8 0.07
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (50 bp):
GAGCTTCCTGATAATTGGCTCGAAAGAGCTTCCCGATAAATGGCTCGTAT
Found at i:21638221 original size:5 final size:6
Alignment explanation
Indices: 21638207--21638231 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
21638197 AAATACACCA
21638207 TTTTCT TTTTCT TTTTCT TTTTCT T
1 TTTTCT TTTTCT TTTTCT TTTTCT T
21638232 CCCTATATTT
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:21643591 original size:3 final size:3
Alignment explanation
Indices: 21643585--21643615 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
21643575 CAGACGTAGT
21643585 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
21643616 TTCTCAGCGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:21643747 original size:3 final size:3
Alignment explanation
Indices: 21643741--21643771 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
21643731 CAGACGTAGT
21643741 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
21643772 TTCTCAGCGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:21643753 original size:156 final size:156
Alignment explanation
Indices: 21643501--21643813 Score: 617
Period size: 156 Copynumber: 2.0 Consensus size: 156
21643491 CAAAGCCATC
21643501 CCCATTACCATTTGCAAAGCTTAAGGATGTCTAGGGTGCACAGGATAACGCACCTTCATCATCAT
1 CCCATTACCATTTGCAAAGCTTAAGGATGTCTAGGGTGCACAGGATAACGCACCTTCATCATCAT
21643566 CATCATCGTCAGACGTAGTAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAATTCTCAGCGCTTGGA
66 CATCATCGTCAGACGTAGTAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAATTCTCAGCGCTTGGA
21643631 GGTGAAGAGAAATGAAGGACCTCCGT
131 GGTGAAGAGAAATGAAGGACCTCCGT
21643657 CCCATTACCATTTGCAAAGCTTAAGGATGTCTAGGGTGCACAGGATAACGCACCTTCATCATCAT
1 CCCATTACCATTTGCAAAGCTTAAGGATGTCTAGGGTGCACAGGATAACGCACCTTCATCATCAT
21643722 CATCATCGTCAGACGTAGTAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAATTCTCAGCGCTTGGA
66 CATCATCGTCAGACGTAGTAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAATTCTCAGCGCTTGGA
*
21643787 GGTGAAGAGAAATGAAGGCCCTCCGT
131 GGTGAAGAGAAATGAAGGACCTCCGT
21643813 C
1 C
21643814 ATGGCTGCCA
Statistics
Matches: 156, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 156 1.00
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (156 bp):
CCCATTACCATTTGCAAAGCTTAAGGATGTCTAGGGTGCACAGGATAACGCACCTTCATCATCAT
CATCATCGTCAGACGTAGTAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAATTCTCAGCGCTTGGA
GGTGAAGAGAAATGAAGGACCTCCGT
Found at i:21648057 original size:3 final size:3
Alignment explanation
Indices: 21648044--21648077 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
21648034 TGTAATCATG
21648044 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
21648078 GTTTTTAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:21656812 original size:17 final size:17
Alignment explanation
Indices: 21656792--21656826 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21656782 CAAAATTAAA
* *
21656792 TTTTTATAAATGTTTAT
1 TTTTTAAAAATGCTTAT
21656809 TTTTTAAAAATGCTTAT
1 TTTTTAAAAATGCTTAT
21656826 T
1 T
21656827 ATAATATGCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (17 bp):
TTTTTAAAAATGCTTAT
Found at i:21658010 original size:22 final size:21
Alignment explanation
Indices: 21657985--21658027 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
21657975 ATTGTAAGAA
21657985 GAAATAGAGCTGTAATTGAAAT
1 GAAATAGAGCTGTAA-TGAAAT
21658007 GAAATAGAGCTGTAATGAAAT
1 GAAATAGAGCTGTAATGAAAT
21658028 AGAGCTGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.47, C:0.05, G:0.23, T:0.26
Consensus pattern (21 bp):
GAAATAGAGCTGTAATGAAAT
Found at i:21658025 original size:16 final size:16
Alignment explanation
Indices: 21658004--21658042 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
21657994 CTGTAATTGA
21658004 AATGAAATAGAGCTGT
1 AATGAAATAGAGCTGT
21658020 AATGAAATAGAGCTGT
1 AATGAAATAGAGCTGT
21658036 AATGAAA
1 AATGAAA
21658043 CTTAGGGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.49, C:0.05, G:0.23, T:0.23
Consensus pattern (16 bp):
AATGAAATAGAGCTGT
Found at i:21658373 original size:57 final size:57
Alignment explanation
Indices: 21658268--21658401 Score: 153
Period size: 57 Copynumber: 2.3 Consensus size: 57
21658258 TTGTTATCAA
* * * * * *
21658268 ATTTTAATAAAATTATTGTTAAATATATTTTATTTAAAAAATAAATAATTTAACCAT
1 ATTTTAATATAATTATTATTAAATATAATTTATATAAAAAATAAATAATTTAACAAC
* ** *
21658325 ATTTTAACATAATTATTATTAAATATAATTTA-ATAAAATAATTTATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATATAATTTATATAAAA-AATAAATAATTTAACAAC
21658382 ATTCTTAATATAATTATTAT
1 ATT-TTAATATAATTATTAT
21658402 ATGAATTAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
56 5 0.08
57 44 0.69
58 15 0.23
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.47
Consensus pattern (57 bp):
ATTTTAATATAATTATTATTAAATATAATTTATATAAAAAATAAATAATTTAACAAC
Found at i:21662249 original size:26 final size:26
Alignment explanation
Indices: 21662220--21662269 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
21662210 TATAATAAAA
21662220 TAATATATATAAAA-ATATACATATTT
1 TAATATATA-AAAATATATACATATTT
* *
21662246 TAATATGTAAAAATATATATATAT
1 TAATATATAAAAATATATACATAT
21662270 ATATAAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (26 bp):
TAATATATAAAAATATATACATATTT
Found at i:21664869 original size:126 final size:126
Alignment explanation
Indices: 21664726--21664977 Score: 441
Period size: 126 Copynumber: 2.0 Consensus size: 126
21664716 TTATTGAATT
*
21664726 TTTATCAAATTATTGGTTTAAAATTATGGTTTTAGGTTTATTTGGAACCTATATATTGTATTTTC
1 TTTATCAAATTATTGGTTGAAAATTATGGTTTTAGGTTTATTTGGAACCTATATATTGTATTTTC
* * *
21664791 TTGTAGGAGGTTGCCTAAACTTAGTTAAAATTTTGAAAATTTTCTTTAAACCCTTTGCCTA
66 TTGTAGGAGGTTACCTAAACTTAGTCAAAATTTTGAAAATTTTCTTTAAAACCTTTGCCTA
*
21664852 TTTATCAAATTATTGGTTGAAAATTATGTTTTTAGGTTTATTTGGAACCTATATATTGTATTTTC
1 TTTATCAAATTATTGGTTGAAAATTATGGTTTTAGGTTTATTTGGAACCTATATATTGTATTTTC
* *
21664917 TTGTAGGAGGTTACCTAAACTTAGTCAAAATTTTGAAATTTTTTTTTAAAACCTTTGCCTA
66 TTGTAGGAGGTTACCTAAACTTAGTCAAAATTTTGAAAATTTTCTTTAAAACCTTTGCCTA
21664978 CACGTTGTTT
Statistics
Matches: 119, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 119 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (126 bp):
TTTATCAAATTATTGGTTGAAAATTATGGTTTTAGGTTTATTTGGAACCTATATATTGTATTTTC
TTGTAGGAGGTTACCTAAACTTAGTCAAAATTTTGAAAATTTTCTTTAAAACCTTTGCCTA
Found at i:21666522 original size:65 final size:65
Alignment explanation
Indices: 21666431--21666573 Score: 198
Period size: 65 Copynumber: 2.2 Consensus size: 65
21666421 GTATAATATA
* * * *
21666431 TATATATATACATGTGGTTCGAATGTATGTTTC-AATTTCCTTGAGCTGAATTTAATGTTATGAA
1 TATATATATATATGAGGTTCGAATGTATGTTACAAATTT-CTTGAGCTGAACTTAATGTTATGAA
21666495 T
65 T
* * *
21666496 TATATATATATATGAGGTTGGAATGTATGTTACAAATTTTTTTAGCTGAACTTAATGTTATGAAT
1 TATATATATATATGAGGTTCGAATGTATGTTACAAATTTCTTGAGCTGAACTTAATGTTATGAAT
*
21666561 TATATATACATAT
1 TATATATATATAT
21666574 ATATATATGT
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 64 0.93
66 5 0.07
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (65 bp):
TATATATATATATGAGGTTCGAATGTATGTTACAAATTTCTTGAGCTGAACTTAATGTTATGAAT
Found at i:21666809 original size:41 final size:40
Alignment explanation
Indices: 21666706--21666814 Score: 119
Period size: 41 Copynumber: 2.7 Consensus size: 40
21666696 CGTATCTGAG
* *
21666706 ATAATCAGGCTTTATGCCTAGCAGGCTTAATGCTGGTGAA
1 ATAATCAGGCTTTAAGCCTAGCAGGCTTAATGCCGGTGAA
* * * * *
21666746 ATATTTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGTA
1 ATA-ATCAGGCTTTAAGCCTAGCAGGCTTAATGCCGGTGAA
* *
21666787 CTGAATCAGGCTTCAAGCCTAGCAGGCT
1 AT-AATCAGGCTTTAAGCCTAGCAGGCT
21666815 ACGTGCCGGT
Statistics
Matches: 55, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
40 3 0.05
41 51 0.93
42 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (40 bp):
ATAATCAGGCTTTAAGCCTAGCAGGCTTAATGCCGGTGAA
Found at i:21670323 original size:19 final size:18
Alignment explanation
Indices: 21670299--21670334 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
21670289 ATTGTATTTT
21670299 TATCGATACCATCTTTTGA
1 TATCGATACCAT-TTTTGA
21670318 TATCGATACCATTTTTG
1 TATCGATACCATTTTTG
21670335 CATTTTGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.44
Consensus pattern (18 bp):
TATCGATACCATTTTTGA
Found at i:21671763 original size:6 final size:6
Alignment explanation
Indices: 21671752--21671783 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
21671742 TTTTGGGTTT
21671752 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TT
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TT
21671784 TAAGGTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.47, T:0.38
Consensus pattern (6 bp):
TTAGGG
Found at i:21672183 original size:125 final size:125
Alignment explanation
Indices: 21671961--21672373 Score: 682
Period size: 125 Copynumber: 3.3 Consensus size: 125
21671951 ATTTATTAAG
* * * * * * *
21671961 GAAATCGCTCCTACGTTGACGCGTTTTTGATACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAT
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGATTCTGAAAAAATAATTTCGAGTTGAC
* * * * *
21672026 GTTTCTGAGCAAATAGTATAAAAAAAGTTTCAAGCAAGATGTTTTATCAGAAGAATTTCT
66 GTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTTT
*
21672086 GAAATCACTCCCACGTGGACGCGCTTTTGCTACAGTAGATTCTGAAAAAATAATTTCGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGATTCTGAAAAAATAATTTCGAGTTGAC
21672151 GTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTTT
66 GTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTTT
* *
21672211 GAAATCGCTCCCATGTGGACGCACTTTTGCTACAGTAGATTCTGAAAAAATAATTTCGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGATTCTGAAAAAATAATTTCGAGTTGAC
*
21672276 GTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAAAATTTTT
66 GTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTTT
21672336 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAG
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAG
21672374 CATGTTTGGG
Statistics
Matches: 269, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
125 269 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (125 bp):
GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGATTCTGAAAAAATAATTTCGAGTTGAC
GTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTTT
Found at i:21675618 original size:28 final size:29
Alignment explanation
Indices: 21675559--21675624 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 29
21675549 CAAAATATTC
* * *
21675559 AAAATAAACTATTTTGTACTTTATTACATT
1 AAAATAAACTATTTTGTAC-TAAATAAATT
*
21675589 AATATAAACTATTTTGTAC-AAATAAATT
1 AAAATAAACTATTTTGTACTAAATAAATT
21675617 AAAATAAA
1 AAAATAAA
21675625 AATCAATCTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 13 0.42
30 18 0.58
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAATAAACTATTTTGTACTAAATAAATT
Found at i:21675995 original size:18 final size:18
Alignment explanation
Indices: 21675969--21676011 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
21675959 GACTAGGAAA
* * *
21675969 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
21675987 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
21676005 AGGATAC
1 AGGATAC
21676012 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:21676129 original size:30 final size:30
Alignment explanation
Indices: 21676095--21676162 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
21676085 GTGCTATTGC
21676095 TGGGCCTGATGAAGTTATGGGCACT-GATGA
1 TGGGCCTGATGAAGTTATGGGC-CTCGATGA
* * * * *
21676125 TGGGCCGGGTGAATTTCTGGGCCTCGTTGA
1 TGGGCCTGATGAAGTTATGGGCCTCGATGA
21676155 TGGGCCTG
1 TGGGCCTG
21676163 CGTCGTCGTC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.15, C:0.18, G:0.40, T:0.28
Consensus pattern (30 bp):
TGGGCCTGATGAAGTTATGGGCCTCGATGA
Found at i:21678632 original size:33 final size:32
Alignment explanation
Indices: 21678590--21678656 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
21678580 GGTAAGACAT
21678590 TTTCCACAGCTCATCTCTT-CACTCTCTTCACCC
1 TTTCCACAGC-C-TCTCTTACACTCTCTTCACCC
*
21678623 TTTCCACAGCCTCTTTTCACACTCTCTTCACCC
1 TTTCCACAGCCTCTCTT-ACACTCTCTTCACCC
21678656 T
1 T
21678657 AACGATTGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 5 0.16
32 1 0.03
33 25 0.81
ACGTcount: A:0.15, C:0.45, G:0.03, T:0.37
Consensus pattern (32 bp):
TTTCCACAGCCTCTCTTACACTCTCTTCACCC
Found at i:21678686 original size:14 final size:14
Alignment explanation
Indices: 21678667--21678696 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21678657 AACGATTGCA
21678667 GCCTCATCATCTCT
1 GCCTCATCATCTCT
*
21678681 GCCTCATCTTCTCT
1 GCCTCATCATCTCT
21678695 GC
1 GC
21678697 TAGTTCACCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.43, G:0.10, T:0.37
Consensus pattern (14 bp):
GCCTCATCATCTCT
Found at i:21679782 original size:33 final size:33
Alignment explanation
Indices: 21679740--21679804 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
21679730 GGTAAGACAT
21679740 TTTCCACAGC-TCATCTCTTCACTCTCTTCACCC
1 TTTCCACAGCTTC-TCTCTTCACTCTCTTCACCC
*
21679773 TTTCCACAGCTTCTCTTTTCACTCTCTTCACC
1 TTTCCACAGCTTCTCTCTTCACTCTCTTCACC
21679805 TAAAGATTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.14, C:0.43, G:0.03, T:0.40
Consensus pattern (33 bp):
TTTCCACAGCTTCTCTCTTCACTCTCTTCACCC
Found at i:21679835 original size:14 final size:14
Alignment explanation
Indices: 21679816--21679845 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21679806 AAAGATTGCA
21679816 GCCTCATCATCTCT
1 GCCTCATCATCTCT
*
21679830 GCCTCATCTTCTCT
1 GCCTCATCATCTCT
21679844 GC
1 GC
21679846 TAGTTCACCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.43, G:0.10, T:0.37
Consensus pattern (14 bp):
GCCTCATCATCTCT
Found at i:21681312 original size:20 final size:20
Alignment explanation
Indices: 21681287--21681326 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
21681277 AATATTTTTC
*
21681287 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
21681307 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
21681327 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:21681328 original size:34 final size:35
Alignment explanation
Indices: 21681275--21681341 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
21681265 CAAACACCAG
* *
21681275 AAAATATTTTTCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
21681310 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
21681342 TATTTTATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:21683523 original size:17 final size:17
Alignment explanation
Indices: 21683501--21683568 Score: 64
Period size: 17 Copynumber: 3.8 Consensus size: 17
21683491 ACAAACAGTA
*
21683501 GATGTATAATTTCGTTT
1 GATGTATAATTTCATTT
*
21683518 GATGTATAATTTCTTTT
1 GATGTATAATTTCATTT
* * *
21683535 GGTTGGATTATTTTTCATTT
1 -GATGTA-TA-ATTTCATTT
21683555 GATGTATAATTTCA
1 GATGTATAATTTCA
21683569 GATATTTGTT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
17 21 0.52
18 6 0.15
19 6 0.15
20 7 0.17
ACGTcount: A:0.24, C:0.06, G:0.16, T:0.54
Consensus pattern (17 bp):
GATGTATAATTTCATTT
Done.