Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 110 of 378
Found at i:30527040 original size:21 final size:20
Alignment explanation
Indices: 30527011--30527056 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
30527001 AAAAATGCAA
30527011 TCAACCTAACA-TGAATTAAAT
1 TCAACCTAA-ATTG-ATTAAAT
*
30527032 TCAAGCTAAATTGATTAAAT
1 TCAACCTAAATTGATTAAAT
30527052 T-AACC
1 TCAACC
30527057 ATTCCAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (20 bp):
TCAACCTAAATTGATTAAAT
Found at i:30533711 original size:36 final size:36
Alignment explanation
Indices: 30533664--30533737 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
30533654 GTCCCAAAAC
30533664 TACTATTCCGATTCCATTGAAAACGACCCGTTATAA
1 TACTATTCCGATTCCATTGAAAACGACCCGTTATAA
30533700 TACTATTCCGATTCCATTGAAAACGACCCGTTATAA
1 TACTATTCCGATTCCATTGAAAACGACCCGTTATAA
30533736 TA
1 TA
30533738 TTAACTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (36 bp):
TACTATTCCGATTCCATTGAAAACGACCCGTTATAA
Found at i:30536340 original size:46 final size:46
Alignment explanation
Indices: 30536273--30536553 Score: 314
Period size: 46 Copynumber: 6.1 Consensus size: 46
30536263 ATGTGATGAA
* *
30536273 AACATGATATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGC
1 AACATGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGC
*
30536319 AACATGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGC
1 AACATGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGC
* *
30536365 AACA-GAATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGC
1 AACATG-ATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGC
** * **
30536411 AACATGA-CGGGAATGAAAAAGACCATGGTTGAAAGATACCATGGC
1 AACATGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGC
** * * **
30536456 AATGTAACATGAAATGAACAAGACCATGGTTGAAAGATACCATGGC
1 AACATGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGC
* * * ** * * *
30536502 AACCTAACAAAAAATGAGTAAGACCATAGTTGAAAGACACTATGGC
1 AACATGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGC
*
30536548 ATCATG
1 AACATG
30536554 CCAAAGATAA
Statistics
Matches: 204, Mismatches: 28, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
45 36 0.18
46 167 0.82
47 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.20
Consensus pattern (46 bp):
AACATGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGC
Found at i:30536481 original size:91 final size:92
Alignment explanation
Indices: 30536292--30536504 Score: 286
Period size: 91 Copynumber: 2.3 Consensus size: 92
30536282 TGAAATGTGT
* * ***
30536292 AAGACCATGGTTGAAAGACACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGAT
1 AAGACCATGGTTGAAAGATACCATGGCAACATGATAGGAAATGAAAAAGACCATGGTTGAAAGAT
* ***
30536357 ACCATGGCAACAGAATATAAAATGTGT
66 ACCATGGCAACAGAACATAAAATGAAC
* *
30536384 AAGACCATGGTTGAAAGATACCATGGCAACATGA-CGGGAATGAAAAAGACCATGGTTGAAAGAT
1 AAGACCATGGTTGAAAGATACCATGGCAACATGATAGGAAATGAAAAAGACCATGGTTGAAAGAT
* *
30536448 ACCATGGCAA-TGTAACATGAAATGAAC
66 ACCATGGCAACAG-AACATAAAATGAAC
30536475 AAGACCATGGTTGAAAGATACCATGGCAAC
1 AAGACCATGGTTGAAAGATACCATGGCAAC
30536505 CTAACAAAAA
Statistics
Matches: 107, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
90 1 0.01
91 73 0.68
92 33 0.31
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.19
Consensus pattern (92 bp):
AAGACCATGGTTGAAAGATACCATGGCAACATGATAGGAAATGAAAAAGACCATGGTTGAAAGAT
ACCATGGCAACAGAACATAAAATGAAC
Found at i:30536538 original size:137 final size:137
Alignment explanation
Indices: 30536292--30536553 Score: 371
Period size: 137 Copynumber: 1.9 Consensus size: 137
30536282 TGAAATGTGT
* * ***
30536292 AAGACCATGGTTGAAAGACACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGAT
1 AAGACCATGGTTGAAAGACACCATGGCAACATAACATGAAATGAACAAGACCATGGTTGAAAGAT
* * * * *
30536357 ACCATGGCAACAGAATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACGGG
66 ACCATGGCAACAGAACAAAAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAACATGACGGG
30536422 AATGAAA
131 AATGAAA
* **
30536429 AAGACCATGGTTGAAAGATACCATGGCAATGTAACATGAAATGAACAAGACCATGGTTGAAAGAT
1 AAGACCATGGTTGAAAGACACCATGGCAACATAACATGAAATGAACAAGACCATGGTTGAAAGAT
** * *
30536494 ACCATGGCAACCTAACAAAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
66 ACCATGGCAACAGAACAAAAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAACATG
30536554 CCAAAGATAA
Statistics
Matches: 108, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
137 108 1.00
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (137 bp):
AAGACCATGGTTGAAAGACACCATGGCAACATAACATGAAATGAACAAGACCATGGTTGAAAGAT
ACCATGGCAACAGAACAAAAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAACATGACGGG
AATGAAA
Found at i:30536570 original size:91 final size:89
Alignment explanation
Indices: 30536291--30536571 Score: 271
Period size: 91 Copynumber: 3.1 Consensus size: 89
30536281 ATGAAATGTG
* * * *
30536291 TAAGACCATGGTTGAAAGACACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAAGAAATGAGTAAGACCATGGTTGAAAGA
* **
30536356 TACCATGGCAACA-GAATATAAAATGTG
66 TACCATGGC-ACATG--TA-AAGATGAA
* * **
30536383 TAAGACCATGGTTGAAAGATACCATGGCAACATGAC-GGGAATGAAAAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAAGAAATGAGTAAGACCATGGTTGAAAGA
30536447 TACCATGGCA-ATGTAACATGAAATGAA
66 TACCATGGCACATGTAA-A-G--ATGAA
* * * * *
30536474 CAAGACCATGGTTGAAAGATACCATGGCAACCTAACAAAAAATGAGTAAGACCATAGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAAGAAATGAGTAAGACCATGGTTGAAAGA
* * * *
30536539 CACTATGGCATCATGCCAAAGATAAA
66 TACCATGGCA-CATG-TAAAGATGAA
30536565 TAAGACC
1 TAAGACC
30536572 GTGGATGGGA
Statistics
Matches: 156, Mismatches: 24, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
87 1 0.01
88 3 0.02
89 1 0.01
90 2 0.01
91 78 0.50
92 64 0.41
93 1 0.01
94 4 0.03
95 2 0.01
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (89 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACAAGAAATGAGTAAGACCATGGTTGAAAGA
TACCATGGCACATGTAAAGATGAA
Found at i:30539814 original size:25 final size:25
Alignment explanation
Indices: 30539786--30539833 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
30539776 ACCTCACACG
30539786 CAAATTAAGAGTCATATCTATCTTA
1 CAAATTAAGAGTCATATCTATCTTA
*
30539811 CAAATTAAGAGTGATATCTATCT
1 CAAATTAAGAGTCATATCTATCT
30539834 AACTTGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (25 bp):
CAAATTAAGAGTCATATCTATCTTA
Found at i:30540365 original size:3 final size:3
Alignment explanation
Indices: 30540357--30540419 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
30540347 TTCATTCACC
30540357 TTA TTA TTA 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
30540405 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
30540420 AGTACTAGCT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:30542910 original size:15 final size:13
Alignment explanation
Indices: 30542872--30542916 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 13
30542862 TTTAAATGAC
30542872 AATAAAAATGCTAAA
1 AATAAAAA-G-TAAA
30542887 AATAAAAAGTAAA
1 AATAAAAAGTAAA
30542900 AATAAAGAAAGTAAA
1 AAT-AA-AAAGTAAA
30542915 AA
1 AA
30542917 CAACAAGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.25
14 3 0.11
15 18 0.64
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (13 bp):
AATAAAAAGTAAA
Found at i:30549241 original size:19 final size:19
Alignment explanation
Indices: 30549214--30549255 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
30549204 ACAAATTAAG
*
30549214 TTTAATTCCATTT-AAAATA
1 TTTAATTCC-TTTGAAAACA
*
30549233 TTTATTTCCTTTGAAAACA
1 TTTAATTCCTTTGAAAACA
30549252 TTTA
1 TTTA
30549256 CGTTGCGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTAATTCCTTTGAAAACA
Found at i:30550421 original size:8 final size:8
Alignment explanation
Indices: 30550404--30550444 Score: 73
Period size: 8 Copynumber: 5.1 Consensus size: 8
30550394 TTCACAAATG
30550404 TCGGCTTT
1 TCGGCTTT
*
30550412 TCGACTTT
1 TCGGCTTT
30550420 TCGGCTTT
1 TCGGCTTT
30550428 TCGGCTTT
1 TCGGCTTT
30550436 TCGGCTTT
1 TCGGCTTT
30550444 T
1 T
30550445 GCCGATCTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.02, C:0.24, G:0.22, T:0.51
Consensus pattern (8 bp):
TCGGCTTT
Found at i:30551905 original size:2 final size:2
Alignment explanation
Indices: 30551898--30551930 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
30551888 ACAATACTTT
30551898 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30551931 TTTCCCTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30551975 original size:15 final size:15
Alignment explanation
Indices: 30551941--30551972 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
30551931 TTTCCCTATC
30551941 TAATAATAATTATTA
1 TAATAATAATTATTA
30551956 TAATAATAATT-TTA
1 TAATAATAATTATTA
30551970 TAA
1 TAA
30551973 ATATATCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATAATAATTATTA
Found at i:30552095 original size:19 final size:18
Alignment explanation
Indices: 30552058--30552101 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
30552048 ATACATGCAG
30552058 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
30552075 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
30552094 TACTAATT
1 TAATAATT
30552102 AAAATTTCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:30554350 original size:34 final size:34
Alignment explanation
Indices: 30554312--30554379 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
30554302 TAAAAAATTT
30554312 AAAAGTAAAACATAAATTACCAAATCATAAAAAA
1 AAAAGTAAAACATAAATTACCAAATCATAAAAAA
* * *
30554346 AAAAGTAAAACCTACATTCCCAAATCATAAAAAA
1 AAAAGTAAAACATAAATTACCAAATCATAAAAAA
30554380 GAGAGAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.63, C:0.16, G:0.03, T:0.18
Consensus pattern (34 bp):
AAAAGTAAAACATAAATTACCAAATCATAAAAAA
Found at i:30555643 original size:53 final size:53
Alignment explanation
Indices: 30555523--30555730 Score: 267
Period size: 53 Copynumber: 3.9 Consensus size: 53
30555513 AACATTAAAG
* * * * * *
30555523 GACCATATCGTGTAAGATCGTAACTGGTGGGTTGTGG-ATAATATGGAAAAAA
1 GACCATATCGTGTAAGACCGTAATTGGTGGGTTATGGCATCATATGGGAAGAA
* * *
30555575 GACCATATTGTGTAAGACCGTAATTGGTGGGTTATGACATTATATGGGAAGAA
1 GACCATATCGTGTAAGACCGTAATTGGTGGGTTATGGCATCATATGGGAAGAA
* * *
30555628 GACCATAACGTGTAAGACCGTAACTT-GTGGATTATGGCATCATATAGGAAGAA
1 GACCATATCGTGTAAGACCGTAA-TTGGTGGGTTATGGCATCATATGGGAAGAA
* *
30555681 GACCATATCGTGTAAGATCATAATTGGTGGGTTATGGCATCATATGGGAA
1 GACCATATCGTGTAAGACCGTAATTGGTGGGTTATGGCATCATATGGGAA
30555731 AATCTAAGGA
Statistics
Matches: 134, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
52 34 0.25
53 98 0.73
54 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (53 bp):
GACCATATCGTGTAAGACCGTAATTGGTGGGTTATGGCATCATATGGGAAGAA
Found at i:30557457 original size:21 final size:21
Alignment explanation
Indices: 30557430--30557478 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
30557420 AGCTTTTTCA
30557430 AGCTTCTGTTCAAATCTTATG
1 AGCTTCTGTTCAAATCTTATG
* **
30557451 AGTTTCTGTTCAGCTCTTATG
1 AGCTTCTGTTCAAATCTTATG
30557472 AGCTTCT
1 AGCTTCT
30557479 ATTTAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (21 bp):
AGCTTCTGTTCAAATCTTATG
Found at i:30557476 original size:42 final size:42
Alignment explanation
Indices: 30557370--30557567 Score: 181
Period size: 42 Copynumber: 4.8 Consensus size: 42
30557360 GTGTTTTACT
* *
30557370 TTTC-GTTTAGCTCTTACGAGCTTTTGTTTAACTCATATGAG
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACTCATATGAG
* * * * * * *
30557411 TTTCCGTTCAGCTTTTTCAAGCTTCTGTTCAAATCTTATGAG
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACTCATATGAG
* * * *
30557453 TTTCTGTTCAGCTCTTATGAGCTTCTATTTAACTCATATGA-
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACTCATATGAG
* * *
30557494 TTT-T-TTTAGCTCTTACAAGCTTCTGTTCAACCCTTAT-AGG
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACTCATATGA-G
* * *
30557534 TTTCTATTTAGCTCTCACGAGATTCTGTTCAACT
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACT
30557568 TTCAAGCTTC
Statistics
Matches: 124, Mismatches: 28, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
38 1 0.01
39 26 0.21
40 4 0.03
41 8 0.06
42 85 0.69
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (42 bp):
TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACTCATATGAG
Found at i:30557547 original size:81 final size:83
Alignment explanation
Indices: 30557375--30557559 Score: 214
Period size: 81 Copynumber: 2.2 Consensus size: 83
30557365 TTACTTTTCG
* * * *
30557375 TTTAGCTCTTACGAGCTTTTGTTTAACTCATATGAGTTTCCGTTCAGCTTTTTCAAGCTTCTGTT
1 TTTAGCTCTTACGAGCTTCTATTTAACTCATATGAGTTT-CGTTCAGCTCTTACAAGCTTCTGTT
* *
30557440 CAAATCTTATGAGTTTCTG
65 CAAACCTTATGAGTTTCTA
* * * *
30557459 TTCAGCTCTTATGAGCTTCTATTTAACTCATATGA-TTT-TTTTAGCTCTTACAAGCTTCTGTTC
1 TTTAGCTCTTACGAGCTTCTATTTAACTCATATGAGTTTCGTTCAGCTCTTACAAGCTTCTGTTC
*
30557522 AACCCTTAT-AGGTTTCTA
66 AAACCTTATGA-GTTTCTA
* *
30557540 TTTAGCTCTCACGAGATTCT
1 TTTAGCTCTTACGAGCTTCT
30557560 GTTCAACTTT
Statistics
Matches: 85, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
80 1 0.01
81 50 0.59
83 3 0.04
84 31 0.36
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.45
Consensus pattern (83 bp):
TTTAGCTCTTACGAGCTTCTATTTAACTCATATGAGTTTCGTTCAGCTCTTACAAGCTTCTGTTC
AAACCTTATGAGTTTCTA
Found at i:30564727 original size:27 final size:27
Alignment explanation
Indices: 30564267--30564717 Score: 552
Period size: 27 Copynumber: 16.6 Consensus size: 27
30564257 AAAGTACTCC
*
30564267 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
*
30564294 C-AGTTTATAGAATTACTGTTTTACCCT
1 CGA-TTTACAGAATTACTGTTTTACCCT
** *
30564321 CGATTTGTAAAATTACTGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
* *
30564348 TGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
*
30564375 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACTGTTTTACCCT
* *
30564402 CGATTTATAGAATTACTATTTTTTACCCT
1 CGATTTACAGAATTAC--TGTTTTACCCT
30564431 CGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
* *
30564458 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
** * *
30564485 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
*
30564512 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
*
30564539 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACTGTTTTACCCT
* *
30564566 CGATTTATAGAATTACCGTTTTACCC-
1 CGATTTACAGAATTACTGTTTTACCCT
* * ** *
30564592 CTAATTTACATAATTACCATTTTACCCC
1 C-GATTTACAGAATTACTGTTTTACCCT
*
30564620 CGATTTACATAATTA-TCGTTTTACCCT
1 CGATTTACAGAATTACT-GTTTTACCCT
30564647 CGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
*
30564674 TGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACTGTTTTACCCT
*
30564701 CGATTTACAAAATTACT
1 CGATTTACAGAATTACT
30564718 AAAATACCCT
Statistics
Matches: 372, Mismatches: 40, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
26 4 0.01
27 338 0.91
28 5 0.01
29 25 0.07
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.41
Consensus pattern (27 bp):
CGATTTACAGAATTACTGTTTTACCCT
Found at i:30564740 original size:27 final size:27
Alignment explanation
Indices: 30564709--30564780 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
30564699 CTCGATTTAC
* **
30564709 AAAATTACTAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCTTAATTTGT
* **
30564736 GAAATTACCGCAATACCCTTAATTTGT
1 AAAATTACCAAAATACCCTTAATTTGT
*
30564763 AAAACTACCAAAATACCC
1 AAAATTACCAAAATACCC
30564781 CTGTATGGTA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.29
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTTAATTTGT
Found at i:30565988 original size:25 final size:25
Alignment explanation
Indices: 30565958--30566005 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
30565948 TTATAATATT
* *
30565958 AAAATGACCATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
30565983 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
30566006 GTTTATACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:30566072 original size:20 final size:20
Alignment explanation
Indices: 30566049--30566132 Score: 150
Period size: 20 Copynumber: 4.2 Consensus size: 20
30566039 TAAACATGGT
30566049 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
30566069 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
30566089 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
30566109 ATGTATGATATGCACATGAG
1 ATGTATGATATGCACATGAC
30566129 ATGT
1 ATGT
30566133 TCATAAATGC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:30566089 original size:11 final size:11
Alignment explanation
Indices: 30566053--30566127 Score: 63
Period size: 11 Copynumber: 7.4 Consensus size: 11
30566043 CATGGTATGT
30566053 ATGATATGCAC
1 ATGATATGCAC
* *
30566064 ATGACATG--T
1 ATGATATGCAC
30566073 ATGATATGCAC
1 ATGATATGCAC
*
30566084 ATGATATG--T
1 ATGATATGCAC
30566093 ATGATATGCAC
1 ATGATATGCAC
* *
30566104 ATGACATG--T
1 ATGATATGCAC
30566113 ATGATATGCAC
1 ATGATATGCAC
30566124 ATGA
1 ATGA
30566128 GATGTTCATA
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
9 22 0.46
11 26 0.54
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:30566235 original size:24 final size:24
Alignment explanation
Indices: 30566179--30566320 Score: 200
Period size: 24 Copynumber: 6.0 Consensus size: 24
30566169 GAGGAAGTGA
30566179 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
30566202 TAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
30566226 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
*
30566250 -AAAGGGCTTATGCCCCAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATC
* *
30566273 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
30566297 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
30566321 ATGATAAAGC
Statistics
Matches: 108, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
23 44 0.41
24 53 0.49
25 11 0.10
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:30566248 original size:47 final size:47
Alignment explanation
Indices: 30566178--30566321 Score: 218
Period size: 47 Copynumber: 3.0 Consensus size: 47
30566168 GGAGGAAGTG
30566178 AAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
* *
30566225 CAAAAGGGCTTATGCCCCAGTTATCAAAGGGCTTATGCCCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
* *
30566272 AAAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTATT-AAAG-GGCTTATGCC-CCAGTTAT
30566321 A
1 A
30566322 TGATAAAGCA
Statistics
Matches: 88, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
47 67 0.76
48 9 0.10
49 12 0.14
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (47 bp):
AAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
Found at i:30567715 original size:21 final size:21
Alignment explanation
Indices: 30567691--30567866 Score: 154
Period size: 21 Copynumber: 8.3 Consensus size: 21
30567681 TCTTACAAAC
* **
30567691 TTCTGTTTAACTGATATGAGT
1 TTCTGTTCAACTCTTATGAGT
* *
30567712 TTCTGTTCAGCTCTTATGAGC
1 TTCTGTTCAACTCTTATGAGT
30567733 TTCTGTTCAACTCTTATGAGT
1 TTCTGTTCAACTCTTATGAGT
*
30567754 TTCTGTTCAGCTCTTATGAGCT
1 TTCTGTTCAACTCTTATGAG-T
* * * *
30567776 TTTTGTTTAACTCATACGAGT
1 TTCTGTTCAACTCTTATGAGT
* * *
30567797 TTTTGTTCAGCTCTTATGAGC
1 TTCTGTTCAACTCTTATGAGT
* * *
30567818 TTCTATTCAACCCTTATGGGT
1 TTCTGTTCAACTCTTATGAGT
* * * * *
30567839 TTCTATTTAGCTCTTATAAGC
1 TTCTGTTCAACTCTTATGAGT
30567860 TTCTGTT
1 TTCTGTT
30567867 AAGATTTCGA
Statistics
Matches: 123, Mismatches: 31, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
21 107 0.87
22 16 0.13
ACGTcount: A:0.18, C:0.19, G:0.16, T:0.47
Consensus pattern (21 bp):
TTCTGTTCAACTCTTATGAGT
Found at i:30567736 original size:42 final size:42
Alignment explanation
Indices: 30567690--30567866 Score: 219
Period size: 42 Copynumber: 4.2 Consensus size: 42
30567680 CTCTTACAAA
* *
30567690 CTTCTGTTTAACTGATATGAGTTTCTGTTCAGCTCTTATGAG
1 CTTCTGTTCAACTCATATGAGTTTCTGTTCAGCTCTTATGAG
*
30567732 CTTCTGTTCAACTCTTATGAGTTTCTGTTCAGCTCTTATGAG
1 CTTCTGTTCAACTCATATGAGTTTCTGTTCAGCTCTTATGAG
* * * *
30567774 CTTTTTGTTTAACTCATACGAGTTTTTGTTCAGCTCTTATGAG
1 C-TTCTGTTCAACTCATATGAGTTTCTGTTCAGCTCTTATGAG
* * * * * * *
30567817 CTTCTATTCAACCCTTATGGGTTTCTATTTAGCTCTTATAAG
1 CTTCTGTTCAACTCATATGAGTTTCTGTTCAGCTCTTATGAG
30567859 CTTCTGTT
1 CTTCTGTT
30567867 AAGATTTCGA
Statistics
Matches: 114, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
42 77 0.68
43 37 0.32
ACGTcount: A:0.18, C:0.19, G:0.16, T:0.47
Consensus pattern (42 bp):
CTTCTGTTCAACTCATATGAGTTTCTGTTCAGCTCTTATGAG
Found at i:30567797 original size:85 final size:85
Alignment explanation
Indices: 30567694--30567861 Score: 255
Period size: 85 Copynumber: 2.0 Consensus size: 85
30567684 TACAAACTTC
* * * * *
30567694 TGTTTAACTGATATGAGTTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACTCTTATGAGTTTCTG
1 TGTTTAACTCATACGAGTTTCTGTTCAGCTCTTATGAGCTTCTATTCAACCCTTATGAGTTTCTA
*
30567759 TTCAGCTCTTATGAGCTTTT
66 TTCAGCTCTTATAAGCTTTT
* *
30567779 TGTTTAACTCATACGAGTTTTTGTTCAGCTCTTATGAGCTTCTATTCAACCCTTATGGGTTTCTA
1 TGTTTAACTCATACGAGTTTCTGTTCAGCTCTTATGAGCTTCTATTCAACCCTTATGAGTTTCTA
*
30567844 TTTAGCTCTTATAAGCTT
66 TTCAGCTCTTATAAGCTT
30567862 CTGTTAAGAT
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 74 1.00
ACGTcount: A:0.19, C:0.18, G:0.16, T:0.46
Consensus pattern (85 bp):
TGTTTAACTCATACGAGTTTCTGTTCAGCTCTTATGAGCTTCTATTCAACCCTTATGAGTTTCTA
TTCAGCTCTTATAAGCTTTT
Found at i:30574496 original size:20 final size:22
Alignment explanation
Indices: 30574460--30574507 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
30574450 TTTGGGGATA
30574460 AAGGGTGAAAAGT-AAAAGTTT
1 AAGGGTGAAAAGTAAAAAGTTT
30574481 AAGGG-GAAAA-TAAAAAAGTTT
1 AAGGGTGAAAAGT-AAAAAGTTT
*
30574502 GAGGGT
1 AAGGGT
30574508 TAAGGGAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 5 0.22
21 17 0.74
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (22 bp):
AAGGGTGAAAAGTAAAAAGTTT
Found at i:30576025 original size:13 final size:13
Alignment explanation
Indices: 30576008--30576037 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
30575998 TCTCCTTTTT
30576008 TTTTTCTTTCTTTC
1 TTTTTC-TTCTTTC
30576022 TTTTTCTTCTTTC
1 TTTTTCTTCTTTC
30576035 TTT
1 TTT
30576038 CCCCTTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCTTCTTTC
Found at i:30576031 original size:17 final size:16
Alignment explanation
Indices: 30576002--30576038 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
30575992 AAATTTTCTC
30576002 CTTT-TTTTTTTCTTT
1 CTTTCTTTTTTTCTTT
30576017 CTTTCTTTTTCTTCTTT
1 CTTTCTTTTT-TTCTTT
30576034 CTTTC
1 CTTTC
30576039 CCCTTGTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
16 5 0.25
17 11 0.55
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
CTTTCTTTTTTTCTTT
Found at i:30576266 original size:5 final size:5
Alignment explanation
Indices: 30576258--30576284 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
30576248 ATACTTTAAT
30576258 TATAA TATAA TATAA TATAA TATAA TA
1 TATAA TATAA TATAA TATAA TATAA TA
30576285 ATATTTTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:30583646 original size:16 final size:16
Alignment explanation
Indices: 30583612--30583664 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
30583602 AAGGCCTGAG
30583612 TCATGCAATACTCAAT
1 TCATGCAATACTCAAT
*
30583628 TCATG-AATACATCATT
1 TCATGCAATAC-TCAAT
* *
30583644 TCATACCATACTCAAT
1 TCATGCAATACTCAAT
30583660 TCATG
1 TCATG
30583665 AGTATATAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 5 0.17
16 21 0.70
17 4 0.13
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
TCATGCAATACTCAAT
Found at i:30588556 original size:293 final size:293
Alignment explanation
Indices: 30588029--30588611 Score: 1121
Period size: 293 Copynumber: 2.0 Consensus size: 293
30588019 CTGCAAATAT
*
30588029 AAGATAAGTAATTGTTAGAAAAGATCTACCTTTCCTAATTTGCCAATCTCATAAGTGCTGACAAA
1 AAGATAAGTAATTGTTAGAAAAGATCTACCCTTCCTAATTTGCCAATCTCATAAGTGCTGACAAA
* *
30588094 CCTTCTCCACTGAATAGAAACAAATAAGGGCTTAACGGGTCACCTTGGCGGAATCCCCTTGTTGC
66 CCTTCTCCACTGAATAGAAACAAATAAGGGCTTAACAGGTCACCTTGGCGCAATCCCCTTGTTGC
*
30588159 CCTGAAAATTGAGCCCTCTTCCCCATTAATTAAAATAGAGTATTTAACAGAATTAATACAACGGA
131 CCTAAAAATTGAGCCCTCTTCCCCATTAATTAAAATAGAGTATTTAACAGAATTAATACAACGGA
30588224 AAATAACATCCATAAATACTTCTGTACAACTCATTTTTGTCATTACCCCTTTGATAAAAGACCAT
196 AAATAACATCCATAAATACTTCTGTACAACTCATTTTTGTCATTACCCCTTTGATAAAAGACCAT
30588289 TTCACTCTATCATAAGCCTTACTCTTGTCAGAA
261 TTCACTCTATCATAAGCCTTACTCTTGTCAGAA
30588322 AAGATAAGTAATTGTTAGAAAAGATCTACCCTTCCTAATTTGCCAATCTCATAAGTGCTGACAAA
1 AAGATAAGTAATTGTTAGAAAAGATCTACCCTTCCTAATTTGCCAATCTCATAAGTGCTGACAAA
30588387 CCTTCTCCACTGAATAGAAACAAATAAGGGCTTAACAGGTCACCTTGGCGCAATCCCCTTGTTGC
66 CCTTCTCCACTGAATAGAAACAAATAAGGGCTTAACAGGTCACCTTGGCGCAATCCCCTTGTTGC
*
30588452 CTTAAAAATTGAGCCCTCTTCCCCATTAATTAAAATAGAGTATTTAACAGAATTAATACAACGGA
131 CCTAAAAATTGAGCCCTCTTCCCCATTAATTAAAATAGAGTATTTAACAGAATTAATACAACGGA
30588517 AAATAACATCCATAAATACTTCTGTACAACTCATTTTTGTCATTACCCCTTTGATAAAAGACCAT
196 AAATAACATCCATAAATACTTCTGTACAACTCATTTTTGTCATTACCCCTTTGATAAAAGACCAT
30588582 TTCACTCTATCATAAGCCTTACTCTTGTCA
261 TTCACTCTATCATAAGCCTTACTCTTGTCA
30588612 AGTTTCAAAG
Statistics
Matches: 285, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
293 285 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (293 bp):
AAGATAAGTAATTGTTAGAAAAGATCTACCCTTCCTAATTTGCCAATCTCATAAGTGCTGACAAA
CCTTCTCCACTGAATAGAAACAAATAAGGGCTTAACAGGTCACCTTGGCGCAATCCCCTTGTTGC
CCTAAAAATTGAGCCCTCTTCCCCATTAATTAAAATAGAGTATTTAACAGAATTAATACAACGGA
AAATAACATCCATAAATACTTCTGTACAACTCATTTTTGTCATTACCCCTTTGATAAAAGACCAT
TTCACTCTATCATAAGCCTTACTCTTGTCAGAA
Found at i:30592557 original size:17 final size:17
Alignment explanation
Indices: 30592535--30592582 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 17
30592525 ATTTTTTTAT
30592535 ATATTTTAATTATAAAA
1 ATATTTTAATTATAAAA
30592552 ATA-TTT-A-TATAAAA
1 ATATTTTAATTATAAAA
30592566 ATAATATTTAATT-TAAA
1 AT-AT-TTTAATTATAAA
30592583 TAAAAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
14 9 0.35
15 2 0.08
16 3 0.12
17 6 0.23
18 5 0.19
19 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATTTTAATTATAAAA
Found at i:30592585 original size:16 final size:16
Alignment explanation
Indices: 30592539--30592585 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
30592529 TTTTATATAT
30592539 TTTAATTATAAA-AATA
1 TTTAATT-TAAATAATA
**
30592555 TTTATATAAAAATAATA
1 TTTA-ATTTAAATAATA
30592572 TTTAATTTAAATAA
1 TTTAATTTAAATAA
30592586 AAAAATTAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTAATTTAAATAATA
Found at i:30598292 original size:40 final size:39
Alignment explanation
Indices: 30598127--30598310 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
30598117 AAATTGAATG
* * *
30598127 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
30598167 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
30598207 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
30598247 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
30598286 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
30598311 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:30598335 original size:80 final size:81
Alignment explanation
Indices: 30598167--30598355 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
30598157 GCTGGAAATT
* * * *
30598167 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
30598232 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
30598248 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
30598311 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
30598327 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
30598356 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:30606338 original size:39 final size:39
Alignment explanation
Indices: 30606288--30606387 Score: 125
Period size: 39 Copynumber: 2.6 Consensus size: 39
30606278 ATAACCGGGT
*
30606288 TAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC-ATCCGGC
1 TAAGACCCGAAGGCAATTGTGCGAGT--CATACTATCCGGC
*
30606327 TAAGACCCGAAGGC-ATTCGTGCGAGTCATTCTATCCGGC
1 TAAGACCCGAAGGCAATT-GTGCGAGTCATACTATCCGGC
*
30606366 TAAGACCCGAAGGCATTTGTGC
1 TAAGACCCGAAGGCAATTGTGC
30606388 AAATCGTGAT
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
37 1 0.02
38 5 0.09
39 46 0.85
40 2 0.04
ACGTcount: A:0.25, C:0.26, G:0.27, T:0.22
Consensus pattern (39 bp):
TAAGACCCGAAGGCAATTGTGCGAGTCATACTATCCGGC
Found at i:30606401 original size:39 final size:38
Alignment explanation
Indices: 30606288--30606403 Score: 124
Period size: 39 Copynumber: 3.0 Consensus size: 38
30606278 ATAACCGGGT
* * * *
30606288 TAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGC
1 TAAGACCCGAAGGCATTTGTGCAAGTCG-TATATCCGGC
* * * *
30606327 TAAGACCCGAAGGCATTCGTGCGAGTCATTCTATCCGGC
1 TAAGACCCGAAGGCATTTGTGCAAGTC-GTATATCCGGC
*
30606366 TAAGACCCGAAGGCATTTGTGCAAATCGTGATATCCGG
1 TAAGACCCGAAGGCATTTGTGCAAGTCGT-ATATCCGG
30606404 GTTAAGTCCC
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
38 1 0.02
39 62 0.98
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (38 bp):
TAAGACCCGAAGGCATTTGTGCAAGTCGTATATCCGGC
Found at i:30609154 original size:40 final size:37
Alignment explanation
Indices: 30609068--30609214 Score: 125
Period size: 40 Copynumber: 3.8 Consensus size: 37
30609058 ATTGAATGAT
* * * * *
30609068 ATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATTAT
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGC--G-AGTTAC
* * *
30609108 AACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTAC
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGT---TAC
**
30609148 ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTTT
1 ATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTTAC
*
30609185 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATCCGGGCTAAGACCCGAAGGCAATTGTGC
30609215 AAATCGTGAT
Statistics
Matches: 88, Mismatches: 14, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
37 29 0.33
38 2 0.02
39 3 0.03
40 54 0.61
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.22
Consensus pattern (37 bp):
ATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTAC
Found at i:30609229 original size:77 final size:77
Alignment explanation
Indices: 30609110--30609255 Score: 177
Period size: 77 Copynumber: 1.9 Consensus size: 77
30609100 GAAATTATAA
* * * *
30609110 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCATTCG
30609175 TGCGAGTTTTAT
66 TGCGAGTTTTAT
* * * * * * *
30609187 CCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGCCTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGCATTC
30609251 GTGCG
65 GTGCG
30609256 GGTTACCATA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
76 1 0.02
77 56 0.98
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.23
Consensus pattern (77 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCATTCG
TGCGAGTTTTAT
Found at i:30617244 original size:40 final size:40
Alignment explanation
Indices: 30617142--30617325 Score: 174
Period size: 40 Copynumber: 4.6 Consensus size: 40
30617132 AAATTGAATG
* * * * *
30617142 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TAGTT
* *
30617182 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
30617222 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
30617262 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
30617302 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
30617326 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 3 0.02
40 115 0.95
41 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:30620708 original size:16 final size:16
Alignment explanation
Indices: 30620687--30620731 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
30620677 TGTGGAATGC
*
30620687 TTTACTTTCTTTATAT
1 TTTACTTTCATTATAT
30620703 TTTACTTTCATTATAT
1 TTTACTTTCATTATAT
*
30620719 TTTACTTTAATTA
1 TTTACTTTCATTA
30620732 ACATTATGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTACTTTCATTATAT
Found at i:30627564 original size:17 final size:17
Alignment explanation
Indices: 30627523--30627570 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
30627513 AAAATATATA
*
30627523 ATTAATTTTAATAATTT
1 ATTAATTATAATAATTT
*
30627540 -TAATATTATAATAATTT
1 ATTA-ATTATAATAATTT
30627557 ATTAATTAATAATA
1 ATTAATT-ATAATA
30627571 TATATGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 2 0.08
17 15 0.60
18 8 0.32
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTAATTATAATAATTT
Found at i:30627569 original size:26 final size:27
Alignment explanation
Indices: 30627515--30627571 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
30627505 AAACAAATAA
*
30627515 AATA-TATAATTAATTTTAATAATTTT
1 AATATTATAATTAATTTTAATAATTAT
*
30627541 AATATTATAA-TAA-TTTATTAATTAAT
1 AATATTATAATTAATTTTAATAATT-AT
30627567 AATAT
1 AATAT
30627572 ATATGAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 9 0.33
26 13 0.48
27 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AATATTATAATTAATTTTAATAATTAT
Found at i:30627794 original size:2 final size:2
Alignment explanation
Indices: 30627787--30627829 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
30627777 CATATACTTT
30627787 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30627828 TA
1 TA
30627830 GTTTTCTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30628488 original size:41 final size:41
Alignment explanation
Indices: 30628438--30628537 Score: 173
Period size: 41 Copynumber: 2.4 Consensus size: 41
30628428 GGAATGTAGA
*
30628438 AAAACGCTTCCAGCTGGAAGCGCTTTCCGCGTGTTACCAGT
1 AAAATGCTTCCAGCTGGAAGCGCTTTCCGCGTGTTACCAGT
30628479 AAAATGCTTCCAGCTGGAAGCGCTTTCCGCGTGTTACCAGT
1 AAAATGCTTCCAGCTGGAAGCGCTTTCCGCGTGTTACCAGT
* *
30628520 AAAATGCTTTCAGTTGGA
1 AAAATGCTTCCAGCTGGA
30628538 CACGTTCCCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (41 bp):
AAAATGCTTCCAGCTGGAAGCGCTTTCCGCGTGTTACCAGT
Found at i:30628655 original size:22 final size:22
Alignment explanation
Indices: 30628621--30628683 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
30628611 CTTACTCATT
* * *
30628621 TCTCACAATATTCTCTAAAAGA
1 TCTCTCAAAATTCTCTAAAACA
*
30628643 TCTCTCAAAATTCTC-AAACCA
1 TCTCTCAAAATTCTCTAAAACA
*
30628664 -CTCTCGAAATTCTCTCAAAA
1 TCTCTCAAAATTCTCT-AAAA
30628684 TTCTTTCTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 13 0.39
21 4 0.12
22 16 0.48
ACGTcount: A:0.38, C:0.29, G:0.03, T:0.30
Consensus pattern (22 bp):
TCTCTCAAAATTCTCTAAAACA
Found at i:30631107 original size:32 final size:30
Alignment explanation
Indices: 30631034--30631114 Score: 99
Period size: 32 Copynumber: 2.6 Consensus size: 30
30631024 ACCAAGTTAG
* * **
30631034 TATTTGTTATCATTTAACAAATTAAAGTTG
1 TATTTGTTATCATTTCACAAATGAAAGTCA
30631064 TAATTTGTTATCATTTCACAAAATGAAAGCTCA
1 T-ATTTGTTATCATTTCAC-AAATGAAAG-TCA
30631097 TATTTGTTATCATTTCAC
1 TATTTGTTATCATTTCAC
30631115 GGAACTGCGT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
30 1 0.02
31 16 0.36
32 25 0.57
33 2 0.05
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (30 bp):
TATTTGTTATCATTTCACAAATGAAAGTCA
Found at i:30635010 original size:11 final size:11
Alignment explanation
Indices: 30634989--30635023 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
30634979 CCTTAATACC
30634989 AAAACCACTAAA
1 AAAACC-CTAAA
30635001 AAAACCCTAAA
1 AAAACCCTAAA
*
30635012 CAAACCCTAAA
1 AAAACCCTAAA
30635023 A
1 A
30635024 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.63, C:0.29, G:0.00, T:0.09
Consensus pattern (11 bp):
AAAACCCTAAA
Found at i:30637947 original size:20 final size:20
Alignment explanation
Indices: 30637922--30637985 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
30637912 TTAGATTCTT
30637922 TATTTATATGATATGGTTAC
1 TATTTATATGATATGGTTAC
* * **
30637942 TATTTAT-GGAGATTCTT--
1 TATTTATATGATATGGTTAC
30637959 TATTTATATGATATGGTTAC
1 TATTTATATGATATGGTTAC
30637979 TATTTAT
1 TATTTAT
30637986 GGATGAGACG
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 7 0.21
18 6 0.18
19 6 0.18
20 14 0.42
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (20 bp):
TATTTATATGATATGGTTAC
Found at i:30637964 original size:37 final size:37
Alignment explanation
Indices: 30637914--30637988 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
30637904 TAAAAGGGTT
30637914 AGATTCTTTATTTATATGATATGGTTACTATTTATGG
1 AGATTCTTTATTTATATGATATGGTTACTATTTATGG
30637951 AGATTCTTTATTTATATGATATGGTTACTATTTATGG
1 AGATTCTTTATTTATATGATATGGTTACTATTTATGG
30637988 A
1 A
30637989 TGAGACGTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.28, C:0.05, G:0.16, T:0.51
Consensus pattern (37 bp):
AGATTCTTTATTTATATGATATGGTTACTATTTATGG
Found at i:30645145 original size:40 final size:40
Alignment explanation
Indices: 30645101--30645229 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
30645091 TGCTGGAAAT
* *
30645101 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCGAGTGAC
* *
30645141 TATATCCGGGCTT-AGACCCGAAGGC-ATTCGTGCGAGTTAT
1 TATATCCGGG-TTAAGACCCGAAGGCAATT-GTGCGAGTGAC
* * * *
30645181 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCGA-GTGAC
30645221 TATATCCGG
1 TATATCCGG
30645230 TTATGTTCCG
Statistics
Matches: 75, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
39 5 0.07
40 66 0.88
41 4 0.05
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TATATCCGGGTTAAGACCCGAAGGCAATTGTGCGAGTGAC
Found at i:30647448 original size:95 final size:95
Alignment explanation
Indices: 30647261--30648052 Score: 917
Period size: 95 Copynumber: 8.4 Consensus size: 95
30647251 GGTGGTTTGG
* * * * *
30647261 AAATCAACTAA-TTAGATAAGATTGTTCATGATAATAAATCAAATGAACTTA-GTTGCAATCTTA
1 AAATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAAATGAACTTAGGCTGCAATCTTA
* ** *
30647324 AATCAGTGAGTTGTTTGAAGCAGCGATATT
66 AATCAGCGAGCCGTTTGGAGCAGCGATATT
* * * * *
30647354 AATTCAAG-TAACTCAGAGAAGACTGTTCATGATAGTAAATCAAATGAACTTAGGTTACGATCTT
1 AAATC-AGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAAATGAACTTAGGCTGCAATCTT
*
30647418 AAATCAGCGAGTCGTTTGGAGCAGCGATATT
65 AAATCAGCGAGCCGTTTGGAGCAGCGATATT
* * ***
30647449 AAATCAGCTAACTCAGAGAAGATTGTTCATGATAATAAATCAAATGAACTTAGACTATGATCTTA
1 AAATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAAATGAACTTAGGCTGCAATCTTA
* * * *
30647514 AATTACCGAGCCGTTTGGAGCAACAATATT
66 AATCAGCGAGCCGTTTGGAGCAGCGATATT
* * *
30647544 AAATAAACTAACTCAGATAAGATTGTTCATGATAGTAAATCAAATGAACTTAGGCTGCAATCTTA
1 AAATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAAATGAACTTAGGCTGCAATCTTA
* * * * *
30647609 AATGAGTGAGCCGTTGGGAGTAGCAATATT
66 AATCAGCGAGCCGTTTGGAGCAGCGATATT
** * * * * *
30647639 AAATCAATTAACTCAAAGAAGACTGTTCATGATAGTAAATCAAATGAACTCAAGCTGCAATATTA
1 AAATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAAATGAACTTAGGCTGCAATCTTA
* *
30647704 AATCAGTGAGCCGTTTGGAGTAGCGATATT
66 AATCAGCGAGCCGTTTGGAGCAGCGATATT
* * * * *
30647734 AAATCAGTTAACTCGGAGAAGATTGTTCATGATAGTAAATTAAACGAACTTAGGTTGCAATCTTA
1 AAATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAAATGAACTTAGGCTGCAATCTTA
* * * * *
30647799 AATCAGTGAACCGTTCGGAGCAACAATATT
66 AATCAGCGAGCCGTTTGGAGCAGCGATATT
* * * * * **
30647829 AAATCAGCTAACTTAGAGATGATTGTTCATAATAGTAAATCAAATAAACTTAAGCTGTGATCTTA
1 AAATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAAATGAACTTAGGCTGCAATCTTA
* * * **
30647894 AATTAGCGAGCTGCTTGGAGCAGTTATATT
66 AATCAGCGAGCCGTTTGGAGCAGCGATATT
*
30647924 AAATAAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAAATGAACTTA-GCTTGCAATCTT
1 AAATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAAATGAACTTAGGC-TGCAATCTT
* * *
30647988 AAATTAGCGAGCTGTTTGGAGCAACGATATT
65 AAATCAGCGAGCCGTTTGGAGCAGCGATATT
* *
30648019 AAATCAGCTAACTCAGATAAGATTGTTCACGATA
1 AAATCAGCTAACTCAGAGAAGATTGTTCATGATA
30648053 AATAAACTAA
Statistics
Matches: 597, Mismatches: 97, Indels: 8
0.85 0.14 0.01
Matches are distributed among these distances:
93 7 0.01
94 41 0.07
95 549 0.92
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (95 bp):
AAATCAGCTAACTCAGAGAAGATTGTTCATGATAGTAAATCAAATGAACTTAGGCTGCAATCTTA
AATCAGCGAGCCGTTTGGAGCAGCGATATT
Found at i:30651969 original size:47 final size:47
Alignment explanation
Indices: 30651915--30652044 Score: 179
Period size: 47 Copynumber: 2.8 Consensus size: 47
30651905 TCAATTAATA
* *
30651915 AGTACCTATACCATGACCCGTAGCCAAATCAAGGTAACTTATCCCGG
1 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCGG
* * * *
30651962 AGTACCTATATCATGGCCCGTAGCCAAATCAAGGTAACTCCTCTCTG
1 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCGG
* **
30652009 AATACCTATACCATGGCTTGTAGCCAAATCAAGGTA
1 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
30652045 TTATTCACAC
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 73 1.00
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.24
Consensus pattern (47 bp):
AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCGG
Found at i:30653615 original size:21 final size:21
Alignment explanation
Indices: 30653589--30653636 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
30653579 ATATCTAGAA
30653589 TGACCTGAATCTTCTCAGGGT
1 TGACCTGAATCTTCTCAGGGT
30653610 TGACCTGAATCTTCTCAGGGT
1 TGACCTGAATCTTCTCAGGGT
30653631 TGACCT
1 TGACCT
30653637 TTATGCCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (21 bp):
TGACCTGAATCTTCTCAGGGT
Found at i:30657112 original size:32 final size:32
Alignment explanation
Indices: 30657050--30657113 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 32
30657040 GTATACATTC
* *
30657050 AAATATCATATACATCTTTATTTTCATTCCAT
1 AAATATCATATACATCCTTATTCTCATTCCAT
* *
30657082 AAATAT-ATATATATCCTTATTCTGATTTCCAT
1 AAATATCATATACATCCTTATTCTCA-TTCCAT
30657114 CTTTATTTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.34, C:0.17, G:0.02, T:0.47
Consensus pattern (32 bp):
AAATATCATATACATCCTTATTCTCATTCCAT
Found at i:30661220 original size:28 final size:28
Alignment explanation
Indices: 30661180--30661234 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
30661170 TGCTAAATAT
*
30661180 AACACCGGCACAAAGTGCCTGCTACTAC
1 AACACCGGCACAAAGTACCTGCTACTAC
* *
30661208 AACACTGGTACAAAGTACCTGCTACTA
1 AACACCGGCACAAAGTACCTGCTACTA
30661235 AAATCACCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.35, C:0.31, G:0.16, T:0.18
Consensus pattern (28 bp):
AACACCGGCACAAAGTACCTGCTACTAC
Found at i:30670711 original size:45 final size:45
Alignment explanation
Indices: 30670647--30670771 Score: 169
Period size: 45 Copynumber: 2.8 Consensus size: 45
30670637 ACGCCTAAAT
*
30670647 TGAGTAAGACCATAGCTGAAAGATGTTATGGCATCAAGATAAAGA
1 TGAGTAAGACCATAGCTGAAAGATGTTATGACATCAAGATAAAGA
* * * * *
30670692 TGAGTAAGACCATGGCTGAAAGATGCTATGACATCATGGTAAATA
1 TGAGTAAGACCATAGCTGAAAGATGTTATGACATCAAGATAAAGA
* * *
30670737 GGACTAAGACCATAGCTGAAAGATGTTATGCCATC
1 TGAGTAAGACCATAGCTGAAAGATGTTATGACATC
30670772 CTTTGATAGT
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.23
Consensus pattern (45 bp):
TGAGTAAGACCATAGCTGAAAGATGTTATGACATCAAGATAAAGA
Found at i:30679024 original size:75 final size:75
Alignment explanation
Indices: 30678934--30679101 Score: 230
Period size: 75 Copynumber: 2.2 Consensus size: 75
30678924 TGAATAGGAG
*
30678934 TGTTTGGCTGTAGGTTTTGGATAGTCTAGGGTAAGAACACGCTATTCCTGGCTGGAAT-AGGAAT
1 TGTTTGGCTGCAGGTTTTGGATAGTCTAGGGTAAGAACACGCTATTCCTGGCTGGAATAAGG-AT
30678998 GGAATAAAGGT
65 GGAATAAAGGT
* * * ** *
30679009 TGTTTGGCTGCAGGTTTTGGATAGTTTATGGTAGGAACGTGCTATTCTTGGCTGGAATAAGGATG
1 TGTTTGGCTGCAGGTTTTGGATAGTCTAGGGTAAGAACACGCTATTCCTGGCTGGAATAAGGATG
* *
30679074 GAATGAGGGT
66 GAATAAAGGT
*
30679084 TGTTTGGCTGCAAGTTTT
1 TGTTTGGCTGCAGGTTTT
30679102 TTGTTTCCCT
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
75 79 0.96
76 3 0.04
ACGTcount: A:0.23, C:0.10, G:0.33, T:0.35
Consensus pattern (75 bp):
TGTTTGGCTGCAGGTTTTGGATAGTCTAGGGTAAGAACACGCTATTCCTGGCTGGAATAAGGATG
GAATAAAGGT
Found at i:30685612 original size:10 final size:10
Alignment explanation
Indices: 30685586--30685644 Score: 68
Period size: 10 Copynumber: 5.9 Consensus size: 10
30685576 TAAATTCTAT
30685586 AAGATAAATA
1 AAGATAAATA
30685596 CAA-ATAAATA
1 -AAGATAAATA
*
30685606 AAGATAATTA
1 AAGATAAATA
*
30685616 AAGATAATTA
1 AAGATAAATA
30685626 AAGATAAATGA
1 AAGATAAAT-A
30685637 AA-ATAAAT
1 AAGATAAAT
30685645 CCTAAAATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
9 2 0.05
10 37 0.84
11 5 0.11
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.24
Consensus pattern (10 bp):
AAGATAAATA
Found at i:30692049 original size:124 final size:122
Alignment explanation
Indices: 30691829--30692050 Score: 284
Period size: 124 Copynumber: 1.8 Consensus size: 122
30691819 GAATTATGTG
* * * * *
30691829 GAATGAAATATGGATGTATTGATTATTGATTTATGTGTGTATGAGTATTCGAATAATACCCGGGC
1 GAATGAAATATGGATGTAATGATCATTGATGTATGTGTGCATGAGAATTCGAATAATACCCGGGC
* * * **
30691894 TAAGTCCCGAAGGCGATTATGCTAGTGATTATAATTGTGTTTGAGCCTTAGTAACGA
66 TAAGCCCCGAAGACAATTATGCTAGAAATTATAATTGTGTTTGAGCCTTAGTAACGA
* * *
30691951 GAATGAAATATGTATGTCCAATGATCATTGATGTATGTGTGCATGAGAAATT-GAATGATATCCG
1 GAATGAAATATGGATGT--AATGATCATTGATGTATGTGTGCATGAG-AATTCGAATAATACCCG
*
30692015 GGCTAAGCCCCGAAGACAATTATGCTGGAAATTATA
63 GGCTAAGCCCCGAAGACAATTATGCTAGAAATTATA
30692051 TCCGGGTTAA
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
122 16 0.19
124 64 0.77
125 3 0.04
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (122 bp):
GAATGAAATATGGATGTAATGATCATTGATGTATGTGTGCATGAGAATTCGAATAATACCCGGGC
TAAGCCCCGAAGACAATTATGCTAGAAATTATAATTGTGTTTGAGCCTTAGTAACGA
Found at i:30692067 original size:40 final size:40
Alignment explanation
Indices: 30692008--30692149 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
30691998 AAATTGAATG
* * *
30692008 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
30692048 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGCGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
30692088 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
30692128 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
30692150 GCATTTGTGC
Statistics
Matches: 85, Mismatches: 16, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 3 0.04
40 82 0.96
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.21
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:30692173 original size:40 final size:39
Alignment explanation
Indices: 30692046--30692175 Score: 147
Period size: 40 Copynumber: 3.3 Consensus size: 39
30692036 ATGCTGGAAA
* * *
30692046 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGCGGC
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGC-A-CAGC
* *
30692087 -TATATCCGGGCTAAGACCCGAAGGCATTCGTGC-GAGTC
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCACAG-C
*
30692125 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGCACATGC
1 -TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCACA-GC
30692166 TTATATCCGG
1 TTATATCCGG
30692176 TTATATTCCG
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
40 70 0.93
41 2 0.03
42 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.25
Consensus pattern (39 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCACAGC
Found at i:30696993 original size:28 final size:28
Alignment explanation
Indices: 30696957--30697035 Score: 113
Period size: 28 Copynumber: 2.8 Consensus size: 28
30696947 GAATCATTCG
**
30696957 ATATTTCGCACACTAAGTTTCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
*
30696985 ATATCTCGCACACTAAGTGCCATTCTCA
1 ATATTTCGCACACTAAGTGCCATTCTCA
**
30697013 ATATTTCATACACTAAGTGCCAT
1 ATATTTCGCACACTAAGTGCCAT
30697036 ATTTGATTGC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.34
Consensus pattern (28 bp):
ATATTTCGCACACTAAGTGCCATTCTCA
Found at i:30708908 original size:21 final size:22
Alignment explanation
Indices: 30708875--30708915 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
30708865 TTCATTTATG
*
30708875 TTTCATTGGCACATA-ATCATA
1 TTTCATTGCCACATACATCATA
*
30708896 TTTCATTTCCACATACATCA
1 TTTCATTGCCACATACATCA
30708916 CAATACATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (22 bp):
TTTCATTGCCACATACATCATA
Found at i:30709346 original size:26 final size:26
Alignment explanation
Indices: 30709317--30709376 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 26
30709307 GCCCTGTGAA
* *
30709317 TCATTCGATATTTCGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
30709343 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
30709371 TCATTC
1 TCATTC
30709377 TCAATATTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 5 0.17
27 2 0.07
28 23 0.77
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:30709360 original size:28 final size:28
Alignment explanation
Indices: 30709324--30709398 Score: 123
Period size: 28 Copynumber: 2.7 Consensus size: 28
30709314 GAATCATTCG
30709324 ATATTTCGCACACTAAGTGTCATTCTCA
1 ATATTTCGCACACTAAGTGTCATTCTCA
*
30709352 ATATCTCGCACACTAAGTGTCATTCTCA
1 ATATTTCGCACACTAAGTGTCATTCTCA
* *
30709380 ATATTTCGTACACTGAGTG
1 ATATTTCGCACACTAAGTG
30709399 CCATATTTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (28 bp):
ATATTTCGCACACTAAGTGTCATTCTCA
Found at i:30723962 original size:2 final size:2
Alignment explanation
Indices: 30723955--30723988 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
30723945 AAAGGAAGTG
30723955 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30723989 GATTTTAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30724055 original size:16 final size:17
Alignment explanation
Indices: 30724022--30724060 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
30724012 AAGTTTTACA
*
30724022 AAAAAAAATTATAATTTT
1 AAAATAAATTAT-ATTTT
30724040 AAAATAAATTAT-TTTT
1 AAAATAAATTATATTTT
30724056 AAAAT
1 AAAAT
30724061 CTTATTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
18 11 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATAAATTATATTTT
Found at i:30734511 original size:14 final size:14
Alignment explanation
Indices: 30734492--30734518 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30734482 TTAGAATTTG
30734492 TTTTATTTTTAATT
1 TTTTATTTTTAATT
30734506 TTTTATTTTTAAT
1 TTTTATTTTTAAT
30734519 AATTTTATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTATTTTTAATT
Found at i:30734523 original size:17 final size:19
Alignment explanation
Indices: 30734501--30734545 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
30734491 GTTTTATTTT
30734501 TAATTTTTTA-TTTTT-AA
1 TAATTTTTTACTTTTTAAA
*
30734518 TAATTTTATACTTTTTAAA
1 TAATTTTTTACTTTTTAAA
*
30734537 TGATTTTTT
1 TAATTTTTT
30734546 CAGATTAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 5 0.22
19 9 0.39
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TAATTTTTTACTTTTTAAA
Found at i:30736743 original size:116 final size:116
Alignment explanation
Indices: 30736539--30736770 Score: 446
Period size: 116 Copynumber: 2.0 Consensus size: 116
30736529 ATGATAATGT
*
30736539 TTATATGTAAGACCATAGCTGGGCTATGGAATGAATGTAAAGGATGAATTAACGGATAAGACCAT
1 TTATATGTAAGACCATAGCTGGGCTATGGAATGAATGTAAAGGATGAATTAACAGATAAGACCAT
30736604 AACTGGGTTATGGCACTATGAATATAAGACCATGGCAGTGTTTATATGTAA
66 AACTGGGTTATGGCACTATGAATATAAGACCATGGCAGTGTTTATATGTAA
*
30736655 TTATATGTAAGACCATAGCTGGGCTATGGAATTAATGTAAAGGATGAATTAACAGATAAGACCAT
1 TTATATGTAAGACCATAGCTGGGCTATGGAATGAATGTAAAGGATGAATTAACAGATAAGACCAT
30736720 AACTGGGTTATGGCACTATGAATATAAGACCATGGCAGTGTTTATATGTAA
66 AACTGGGTTATGGCACTATGAATATAAGACCATGGCAGTGTTTATATGTAA
30736771 GATCATAGCT
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 114 1.00
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (116 bp):
TTATATGTAAGACCATAGCTGGGCTATGGAATGAATGTAAAGGATGAATTAACAGATAAGACCAT
AACTGGGTTATGGCACTATGAATATAAGACCATGGCAGTGTTTATATGTAA
Found at i:30736752 original size:33 final size:32
Alignment explanation
Indices: 30736710--30736842 Score: 93
Period size: 33 Copynumber: 4.3 Consensus size: 32
30736700 GAATTAACAG
30736710 ATAAGACCATAACTGGGTTATGGCACTATGAAT
1 ATAAGACCATAACTGGGTTATGGCACTATG-AT
** * *
30736743 ATAAGACCATGGCAGTGTT-T---A-TATG--
1 ATAAGACCATAACTGGGTTATGGCACTATGAT
* * * *
30736768 -TAAGATCATAGCTGGGCTATGGCACTCTGAT
1 ATAAGACCATAACTGGGTTATGGCACTATGAT
*
30736799 GATAAGACCATAACTGGGTTATGGCACTACGAAT
1 -ATAAGACCATAACTGGGTTATGGCACTATG-AT
*
30736833 GTAAGACCAT
1 ATAAGACCAT
30736843 GGCTAGGTCA
Statistics
Matches: 74, Mismatches: 16, Indels: 20
0.67 0.15 0.18
Matches are distributed among these distances:
24 13 0.18
25 1 0.01
28 5 0.07
29 4 0.05
32 1 0.01
33 48 0.65
34 2 0.03
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (32 bp):
ATAAGACCATAACTGGGTTATGGCACTATGAT
Found at i:30737770 original size:7 final size:8
Alignment explanation
Indices: 30737745--30737770 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
30737735 TTCTAATTTA
30737745 TTTCAATT
1 TTTCAATT
30737753 TTTCAATT
1 TTTCAATT
30737761 TTTCAATT
1 TTTCAATT
30737769 TT
1 TT
30737771 AATATAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTCAATT
Found at i:30738459 original size:12 final size:12
Alignment explanation
Indices: 30738442--30738475 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
30738432 CTGGTTGTGT
30738442 AAGCCACACGGC
1 AAGCCACACGGC
30738454 AAGCCACACGGC
1 AAGCCACACGGC
*
30738466 CAGCCACACG
1 AAGCCACACG
30738476 AGCGTGTGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.32, C:0.44, G:0.24, T:0.00
Consensus pattern (12 bp):
AAGCCACACGGC
Found at i:30740386 original size:31 final size:31
Alignment explanation
Indices: 30740351--30740412 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
30740341 TATAAGAAGA
30740351 GCATGAAACTCAACGCCAAGGCCATGCACAT
1 GCATGAAACTCAACGCCAAGGCCATGCACAT
* *
30740382 GCATGCAACTCAACGCCAAGGCTATGCACAT
1 GCATGAAACTCAACGCCAAGGCCATGCACAT
30740413 TCTCTTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.32, G:0.19, T:0.15
Consensus pattern (31 bp):
GCATGAAACTCAACGCCAAGGCCATGCACAT
Found at i:30743585 original size:33 final size:33
Alignment explanation
Indices: 30743543--30743609 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
30743533 GAAATTAGAC
30743543 ATCATTTCATTAGAGATCATGTCCAAAAAGGTA
1 ATCATTTCATTAGAGATCATGTCCAAAAAGGTA
30743576 ATCATTTCATTAGAGATCATGTCCAAAAAGGTA
1 ATCATTTCATTAGAGATCATGTCCAAAAAGGTA
30743609 A
1 A
30743610 AATAGTTCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (33 bp):
ATCATTTCATTAGAGATCATGTCCAAAAAGGTA
Found at i:30745123 original size:8 final size:8
Alignment explanation
Indices: 30745110--30745140 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
30745100 CTCATAAGAT
*
30745110 TATGTGTC
1 TATGTGAC
30745118 TATGTGAC
1 TATGTGAC
30745126 TATGTGAC
1 TATGTGAC
30745134 TATGTGA
1 TATGTGA
30745141 ATCCGGGTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.42
Consensus pattern (8 bp):
TATGTGAC
Found at i:30749643 original size:71 final size:71
Alignment explanation
Indices: 30749559--30749722 Score: 310
Period size: 71 Copynumber: 2.3 Consensus size: 71
30749549 CGATTTGTCT
30749559 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
30749624 CTTTCA
66 CTTTCA
*
30749630 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
30749695 CTTTCA
66 CTTTCA
*
30749701 CGTAGCTCTCTTGCCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
30749723 GATACATCTC
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 91 1.00
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
CTTTCA
Found at i:30749760 original size:71 final size:70
Alignment explanation
Indices: 30749559--30749756 Score: 231
Period size: 71 Copynumber: 2.8 Consensus size: 70
30749549 CGATTTGTCT
* * * * * *
30749559 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGCCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
30749624 CTTTCA
65 CTTTCA
* * * * *
30749630 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGCCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
30749695 CTTTCA
65 CTTTCA
* *
30749701 CGTAGCTCTCTTGCCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGCCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
30749757 TACAGGGTGT
Statistics
Matches: 118, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
68 22 0.19
69 1 0.01
70 1 0.01
71 94 0.80
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (70 bp):
CGTAGCTCTCTTGCCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:30758184 original size:40 final size:40
Alignment explanation
Indices: 30758140--30758325 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
30758130 GCTACTCGTT
* * *
30758140 CAAATACCTTCGGGACATAGCCCGG-TTATAGTAGCTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCACA
* *
30758180 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACA
*
30758220 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCACA
* * * * *
30758260 CAAATGCCTTC-GGATCTCAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCA-CA
30758301 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
30758326 CATCATTCGA
Statistics
Matches: 128, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
39 3 0.02
40 114 0.89
41 11 0.09
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACA
Found at i:30763527 original size:46 final size:46
Alignment explanation
Indices: 30763475--30763785 Score: 444
Period size: 46 Copynumber: 6.7 Consensus size: 46
30763465 GTGCTCCCTA
*
30763475 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 ATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
* *
30763521 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCGTGGCAACCTG
1 ATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
* *
30763567 ATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTG
1 ATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
*
30763613 ATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 ATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
* *
30763659 ACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
1 ATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
*** * *
30763705 ACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
1 ATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
* * * *
30763752 ACA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 ATATG-AAATGAGTAAGACCATGGTTGAAAGATAC
30763786 TATGACATCA
Statistics
Matches: 247, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
46 205 0.83
47 42 0.17
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
ATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
Found at i:30765551 original size:25 final size:25
Alignment explanation
Indices: 30765517--30765575 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
30765507 TTGTGACCAC
30765517 ACCCTCTAACCAAAGCCACGTTACA
1 ACCCTCTAACCAAAGCCACGTTACA
30765542 ACCCTCTAACCAAAGCCACGTTACA
1 ACCCTCTAACCAAAGCCACGTTACA
30765567 ACCCTCTAA
1 ACCCTCTAA
30765576 AAGACCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.36, C:0.41, G:0.07, T:0.17
Consensus pattern (25 bp):
ACCCTCTAACCAAAGCCACGTTACA
Found at i:30766717 original size:12 final size:13
Alignment explanation
Indices: 30766681--30766718 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
30766671 AAATATTTGA
30766681 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
30766694 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
30766708 CTTG-TCTTAAT
1 CTTGTTCTTAAT
30766719 ATTCTAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:30768111 original size:20 final size:20
Alignment explanation
Indices: 30768086--30768139 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
30768076 AAATCAATTT
30768086 AAAATGATTTTAACCAAGCC
1 AAAATGATTTTAACCAAGCC
* **
30768106 AAAATGATTTCAACCAAGTT
1 AAAATGATTTTAACCAAGCC
*
30768126 AAAATCATTTTAAC
1 AAAATGATTTTAAC
30768140 ACATCAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (20 bp):
AAAATGATTTTAACCAAGCC
Found at i:30773053 original size:25 final size:25
Alignment explanation
Indices: 30773025--30773073 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
30773015 ATATATATCA
30773025 TAAA-ATAGCACATAAAAGAAATAAT
1 TAAACATAGCACATAAAA-AAATAAT
*
30773050 TAAACATAGCATATAAAAAAATAA
1 TAAACATAGCACATAAAAAAATAA
30773074 AACTATGCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.65, C:0.08, G:0.06, T:0.20
Consensus pattern (25 bp):
TAAACATAGCACATAAAAAAATAAT
Found at i:30773586 original size:22 final size:21
Alignment explanation
Indices: 30773556--30773602 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
30773546 TACAAATTAA
30773556 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
30773578 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
30773599 ATCT
1 ATCT
30773603 AAGATTGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:30773608 original size:19 final size:19
Alignment explanation
Indices: 30773573--30773632 Score: 79
Period size: 17 Copynumber: 3.2 Consensus size: 19
30773563 AGATTACAAG
30773573 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
30773594 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
*
30773611 ATCATATCAAAGATTGCAT
1 ATCATATCTAAGATTGCAT
30773630 ATC
1 ATC
30773633 CTTAAAGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
17 16 0.44
19 11 0.31
20 1 0.03
21 8 0.22
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:30773856 original size:29 final size:29
Alignment explanation
Indices: 30773814--30773946 Score: 162
Period size: 29 Copynumber: 4.6 Consensus size: 29
30773804 AATCTCAGGA
*
30773814 TATTTTTTTAGAACCCATCTAGTCAAAAT
1 TATTTTTTCAGAACCCATCTAGTCAAAAT
* *
30773843 TATTTTTTTAGAACCCATCTCGTCAAAAT
1 TATTTTTTCAGAACCCATCTAGTCAAAAT
* *
30773872 TATTTTTTCAGAACTCATCTCGTCAAAAT
1 TATTTTTTCAGAACCCATCTAGTCAAAAT
* * *
30773901 TATGTTTCCAGAACCTATCTCA-TCAAAA-
1 TATTTTTTCAGAACCCATCT-AGTCAAAAT
*
30773929 TAATTTTTCAGAACCCAT
1 TATTTTTTCAGAACCCAT
30773947 TTCGATTTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
28 14 0.15
29 77 0.85
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (29 bp):
TATTTTTTCAGAACCCATCTAGTCAAAAT
Found at i:30774094 original size:23 final size:24
Alignment explanation
Indices: 30774047--30774095 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
30774037 TTAATCAATT
**
30774047 AAAACCATAAAACCCTAACCCTAA
1 AAAACCATAAAACCCTAACAATAA
*
30774071 AAAACC-TAAAACCCTAATAATAA
1 AAAACCATAAAACCCTAACAATAA
30774094 AA
1 AA
30774096 CCTTAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (24 bp):
AAAACCATAAAACCCTAACAATAA
Found at i:30774096 original size:14 final size:15
Alignment explanation
Indices: 30774077--30774109 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
30774067 CTAAAAAACC
30774077 TAAAACCCTAA-TAA
1 TAAAACCCTAATTAA
*
30774091 TAAAACCTTAATTAA
1 TAAAACCCTAATTAA
30774106 TAAA
1 TAAA
30774110 CTCTAAAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAAACCCTAATTAA
Found at i:30778950 original size:40 final size:40
Alignment explanation
Indices: 30778895--30778974 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
30778885 ATAAAATCAA
*
30778895 ACTCATCAATGATAGAATTTATTAAAAATTCTTAAACTAT
1 ACTCATCAATGATAGAATTTATTAAAAAATCTTAAACTAT
30778935 ACTCATCAATGATAGAATTTATTAAAAAATCTTAAACTAT
1 ACTCATCAATGATAGAATTTATTAAAAAATCTTAAACTAT
30778975 TTTTTTTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.36
Consensus pattern (40 bp):
ACTCATCAATGATAGAATTTATTAAAAAATCTTAAACTAT
Found at i:30781022 original size:20 final size:20
Alignment explanation
Indices: 30780970--30781025 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
30780960 TGAATATTAG
*
30780970 ATTAAATTAGATTAAATTTAAT
1 ATTAAATTA-A-TAAATTTAAC
*
30780992 ATTAAGA-TAATAACTTTAAC
1 ATTAA-ATTAATAAATTTAAC
30781012 ATTAAATTAATAAA
1 ATTAAATTAATAAA
30781026 ATATTATCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 1 0.03
20 19 0.66
21 1 0.03
22 7 0.24
23 1 0.03
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (20 bp):
ATTAAATTAATAAATTTAAC
Found at i:30782565 original size:55 final size:55
Alignment explanation
Indices: 30782490--30782601 Score: 188
Period size: 55 Copynumber: 2.0 Consensus size: 55
30782480 TATTTGAATC
* *
30782490 AAATGCTCATTTTGATTTTTTTACGAGATTACAAACTCGTTTAAATTATTTATTG
1 AAATACTCATTTTGATTTTTTTACGAGATTACAAACTCGTTTAAATTATCTATTG
* *
30782545 AAATACTCATTTTGATTTTTTTATGAGATTACGAACTCGTTTAAATTATCTATTG
1 AAATACTCATTTTGATTTTTTTACGAGATTACAAACTCGTTTAAATTATCTATTG
30782600 AA
1 AA
30782602 GTAAGTTGTC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (55 bp):
AAATACTCATTTTGATTTTTTTACGAGATTACAAACTCGTTTAAATTATCTATTG
Found at i:30784326 original size:30 final size:30
Alignment explanation
Indices: 30784287--30784343 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
30784277 TTTTATAAAT
30784287 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
30784317 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
30784344 AACAACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:30784534 original size:13 final size:13
Alignment explanation
Indices: 30784518--30784568 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
30784508 TTTAAAGCAA
30784518 ACTTTTTAAAAAC
1 ACTTTTTAAAAAC
* *
30784531 ACTTCTTAAAAGC
1 ACTTTTTAAAAAC
* *
30784544 ACTTTTTCACAAC
1 ACTTTTTAAAAAC
*
30784557 ATTTTTTAAAAA
1 ACTTTTTAAAAA
30784569 TACATTTCAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.41, C:0.18, G:0.02, T:0.39
Consensus pattern (13 bp):
ACTTTTTAAAAAC
Found at i:30784775 original size:18 final size:18
Alignment explanation
Indices: 30784768--30784827 Score: 120
Period size: 18 Copynumber: 3.3 Consensus size: 18
30784758 TTGATTAAAA
30784768 ATAAATTATATATTATAT
1 ATAAATTATATATTATAT
30784786 ATAAATTATATATTATAT
1 ATAAATTATATATTATAT
30784804 ATAAATTATATATTATAT
1 ATAAATTATATATTATAT
30784822 ATAAAT
1 ATAAAT
30784828 GTAAATATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATAAATTATATATTATAT
Found at i:30784782 original size:7 final size:7
Alignment explanation
Indices: 30784772--30784823 Score: 62
Period size: 7 Copynumber: 8.3 Consensus size: 7
30784762 TTAAAAATAA
30784772 ATTATAT
1 ATTATAT
30784779 ATTATAT
1 ATTATAT
30784786 A-TA-A-
1 ATTATAT
30784790 ATTATAT
1 ATTATAT
30784797 ATTATAT
1 ATTATAT
30784804 A-TA-A-
1 ATTATAT
30784808 ATTATAT
1 ATTATAT
30784815 ATTATAT
1 ATTATAT
30784822 AT
1 AT
30784824 AAATGTAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
4 2 0.05
5 6 0.15
6 6 0.15
7 25 0.64
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
ATTATAT
Found at i:30784788 original size:11 final size:11
Alignment explanation
Indices: 30784774--30784824 Score: 57
Period size: 11 Copynumber: 4.4 Consensus size: 11
30784764 AAAAATAAAT
30784774 TATATATTATA
1 TATATATTATA
*
30784785 TATAAATTATA
1 TATATATTATA
*
30784796 TATTATATATAAA
1 TA-TATAT-TATA
30784809 TTATATATTATA
1 -TATATATTATA
30784821 TATA
1 TATA
30784825 AATGTAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 16 0.48
12 7 0.21
13 8 0.24
14 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TATATATTATA
Found at i:30806676 original size:15 final size:15
Alignment explanation
Indices: 30806656--30806685 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30806646 CAAACTATGT
*
30806656 CTCTAATTTAGGAAA
1 CTCTAAGTTAGGAAA
30806671 CTCTAAGTTAGGAAA
1 CTCTAAGTTAGGAAA
30806686 GATACTAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (15 bp):
CTCTAAGTTAGGAAA
Found at i:30807382 original size:6 final size:6
Alignment explanation
Indices: 30807371--30807432 Score: 124
Period size: 6 Copynumber: 10.3 Consensus size: 6
30807361 TCTTCCTTTT
30807371 TGAAAA TGAAAA TGAAAA TGAAAA TGAAAA TGAAAA TGAAAA TGAAAA
1 TGAAAA TGAAAA TGAAAA TGAAAA TGAAAA TGAAAA TGAAAA TGAAAA
30807419 TGAAAA TGAAAA TG
1 TGAAAA TGAAAA TG
30807433 GCCTCTGTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.18
Consensus pattern (6 bp):
TGAAAA
Found at i:30820320 original size:31 final size:30
Alignment explanation
Indices: 30820251--30820307 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
30820241 TCAGAACTCG
* *
30820251 AGATATTTTTTAAACACCTTGAGAATCCCA
1 AGATAATTTTTAAACACCTCGAGAATCCCA
*
30820281 AGATAATTTTTAAACACCTCGGGAATC
1 AGATAATTTTTAAACACCTCGAGAATC
30820308 TCGGGATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (30 bp):
AGATAATTTTTAAACACCTCGAGAATCCCA
Found at i:30822036 original size:21 final size:21
Alignment explanation
Indices: 30822012--30822053 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
30822002 GTTTACCTAT
30822012 ATGGTTGCAACTTGAGGTATA
1 ATGGTTGCAACTTGAGGTATA
30822033 ATGGTTGCAACTTGAGGTATA
1 ATGGTTGCAACTTGAGGTATA
30822054 CTTAATCTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.33
Consensus pattern (21 bp):
ATGGTTGCAACTTGAGGTATA
Found at i:30824556 original size:40 final size:40
Alignment explanation
Indices: 30824486--30824783 Score: 431
Period size: 40 Copynumber: 7.5 Consensus size: 40
30824476 AAGCCAGGTA
* * * *
30824486 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
30824525 CCTTCGGGACATAGCCCGGATGTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
30824565 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
30824605 CCTTCGGGACTTAACCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
30824645 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
30824685 CCTTCGGGACTTAACCCGAATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
30824725 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
30824765 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
30824784 TTATCATCCG
Statistics
Matches: 237, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
39 13 0.05
40 224 0.95
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:30832671 original size:40 final size:40
Alignment explanation
Indices: 30832601--30832895 Score: 440
Period size: 40 Copynumber: 7.5 Consensus size: 40
30832591 CAAGCCAGTA
* * * *
30832601 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
30832640 CCTTCGGGACATAGCCCGGATGTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
30832680 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
30832720 CCTTCGGGACTTA-CCCGGATATAGTAACTCG-ACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
30832758 CCTTCGGGACTTAGCCC-GATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
30832797 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
30832837 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
30832877 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
30832896 TTATCATCCG
Statistics
Matches: 237, Mismatches: 13, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
38 34 0.14
39 57 0.24
40 146 0.62
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:30832809 original size:117 final size:115
Alignment explanation
Indices: 30832601--30832894 Score: 428
Period size: 117 Copynumber: 2.5 Consensus size: 115
30832591 CAAGCCAGTA
* * * * *
30832601 CCTTCGGGATTTAACCGGATATAGCTACTCGCTCGAATGCCTTCGGGACATAGCCCGGATGTAGT
1 CCTTCGGGACTTACCCGGATATAG-TACTCG--CAAATGCCTTCGGGACTTAGCCC-GATATAGT
*
30832666 AACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
62 AACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
30832720 CCTTCGGGACTTACCCGGATATAGTAACTCGACAAATGCCTTCGGGACTTAGCCCGATATAGTAA
1 CCTTCGGGACTTACCCGGATATAGT-ACTCG-CAAATGCCTTCGGGACTTAGCCCGATATAGTAA
30832785 CTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
64 CTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
30832837 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATGCCTTCGGGACTTAGCCCG
1 CCTTCGGGACTTA-CCCGGATA-TAGT-ACT--CGCAAATGCCTTCGGGACTTAGCCCG
30832895 GTTATCATCC
Statistics
Matches: 162, Mismatches: 8, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
117 74 0.46
118 35 0.22
119 51 0.31
120 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (115 bp):
CCTTCGGGACTTACCCGGATATAGTACTCGCAAATGCCTTCGGGACTTAGCCCGATATAGTAACT
CGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
Found at i:30832887 original size:157 final size:158
Alignment explanation
Indices: 30832601--30832895 Score: 452
Period size: 157 Copynumber: 1.9 Consensus size: 158
30832591 CAAGCCAGTA
* * * * * *
30832601 CCTTCGGGATTTAACCGGATATAGCTACTCGCTCGAATGCCTTCGGGACATAGCCCGGATGTAGT
1 CCTTCGGGACTTAACCCGATATAGCTACTCGCACAAATGCCTTCGGGACATAACCCGGATATAGT
*
30832666 AACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACT
66 AACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACT
30832731 TA-CCCGGATATAGTAACTCGACAAATG
131 TAGCCCGGATATAGTAACTCGACAAATG
* *
30832758 CCTTCGGGACTTAGCCCGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAG
1 CCTTCGGGACTTAACCCGATATAGCT-ACTCGCACAAATGCCTTCGGGACATAACCCGGATATAG
* *
30832822 TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATGCCTTCGGGA
65 TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTAGCACAAATGCCTTCGGGA
30832886 CTTAGCCCGG
129 CTTAGCCCGG
30832896 TTATCATCCG
Statistics
Matches: 124, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
156 2 0.02
157 117 0.94
158 5 0.04
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (158 bp):
CCTTCGGGACTTAACCCGATATAGCTACTCGCACAAATGCCTTCGGGACATAACCCGGATATAGT
AACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACT
TAGCCCGGATATAGTAACTCGACAAATG
Found at i:30835939 original size:22 final size:21
Alignment explanation
Indices: 30835884--30835941 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
30835874 TCTTTTAACA
30835884 CATAAACATTCAATTATATTGG
1 CATAAACA-TCAATTATATTGG
* *
30835906 CACAACCAATCAATTATATTGG
1 CATAAAC-ATCAATTATATTGG
30835928 CATAATACATCAAT
1 CATAA-ACATCAAT
30835942 AGAAATAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 28 0.93
23 2 0.07
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.31
Consensus pattern (21 bp):
CATAAACATCAATTATATTGG
Found at i:30839925 original size:21 final size:21
Alignment explanation
Indices: 30839888--30839927 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
30839878 GGGATTAAAT
*
30839888 CAAAATATAAAATAAATAACA
1 CAAAATATAAAAAAAATAACA
30839909 CAAAAT-TAAATAAAAATAA
1 CAAAATATAAA-AAAAATAA
30839928 AGACAAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (21 bp):
CAAAATATAAAAAAAATAACA
Found at i:30842920 original size:39 final size:39
Alignment explanation
Indices: 30842861--30843001 Score: 228
Period size: 39 Copynumber: 3.6 Consensus size: 39
30842851 AACATGTTTT
*
30842861 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
*
30842900 TGAGTATTGTGATATTTGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
*
30842939 TGAGTATTATGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * *
30842978 TGTGTAATGTGATACATGCTTAAA
1 TGAGTATTGTGATATATGCTTAAA
30843002 AGTGAATATG
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 94 1.00
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.45
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:30846435 original size:12 final size:12
Alignment explanation
Indices: 30846418--30846443 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
30846408 CTTCATATGA
30846418 TACCAAAATAAG
1 TACCAAAATAAG
30846430 TACCAAAATAAG
1 TACCAAAATAAG
30846442 TA
1 TA
30846444 AAGTTTTCAT
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:0.58, C:0.15, G:0.08, T:0.19
Consensus pattern (12 bp):
TACCAAAATAAG
Found at i:30846671 original size:27 final size:27
Alignment explanation
Indices: 30846633--30846687 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
30846623 TAAAAACAAC
30846633 TTAGTAAGTACTTCAAGAATTTAATGA
1 TTAGTAAGTACTTCAAGAATTTAATGA
*
30846660 TTAGTAAGTACTTTAAGAATTTAATGA
1 TTAGTAAGTACTTCAAGAATTTAATGA
30846687 T
1 T
30846688 AAGCCTACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (27 bp):
TTAGTAAGTACTTCAAGAATTTAATGA
Found at i:30848600 original size:170 final size:170
Alignment explanation
Indices: 30848299--30848620 Score: 452
Period size: 170 Copynumber: 1.9 Consensus size: 170
30848289 CTTTTTTAGT
* * * *
30848299 TTTTACGATTTAGTCCTTGTATTTTAATTACTAACCGTCTAATAAAATTACCTAACCAAATCTCG
1 TTTTACGATTTAGTCCTTGTACTTTAAGTACTAACCGTCTAATAAAATTACCTAACCAAAACTCA
* * * *
30848364 ATATAAATCTCAAGTAAGCTCATAAATATTAATAATTAATATTTACTGAATCGATTATTGGTATA
66 ATATAAATCTAAAGTAAGCTCATAAATATTAATAATTAATATTTACAGAATCAATGATTGGTATA
*
30848429 CGGTGTTCTGAAACAATCATTTTTGGTACACTTTTACAAA
131 CGGAGTTCTGAAACAATCATTTTTGGTACACTTTTACAAA
* *** *
30848469 TTTTATGATTTAGTCCTTGTACTTTAAGTACTAGTTGTCTACTAAAATTA-CTAGACCAAAACTC
1 TTTTACGATTTAGTCCTTGTACTTTAAGTACTAACCGTCTAATAAAATTACCTA-ACCAAAACTC
30848533 AATATAAATCTAAAGTTAA-CTCATAAATATTAATAATTAATATTTACAGAATCAATGATCT-GT
65 AATATAAATCTAAAG-TAAGCTCATAAATATTAATAATTAATATTTACAGAATCAATGAT-TGGT
* *
30848596 ATACGGAGTTCTGGAACCATCATTT
128 ATACGGAGTTCTGAAACAATCATTT
30848621 CTAGTGCCAG
Statistics
Matches: 133, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
169 3 0.02
170 126 0.95
171 4 0.03
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (170 bp):
TTTTACGATTTAGTCCTTGTACTTTAAGTACTAACCGTCTAATAAAATTACCTAACCAAAACTCA
ATATAAATCTAAAGTAAGCTCATAAATATTAATAATTAATATTTACAGAATCAATGATTGGTATA
CGGAGTTCTGAAACAATCATTTTTGGTACACTTTTACAAA
Found at i:30849468 original size:49 final size:49
Alignment explanation
Indices: 30849411--30849516 Score: 167
Period size: 49 Copynumber: 2.2 Consensus size: 49
30849401 GGAAGACAAG
* * *
30849411 TGTCGCGACACCCAACTTCGAGCTGTCAGAAGTTCCATTTGATGTTCAA
1 TGTCGCGACACCCAACTTCGAGCTATCAGAAATCCCATTTGATGTTCAA
*
30849460 TGTCGCGACACCCAACTTTGAGCTATCAGAAATCCCATTTGATGTTCAA
1 TGTCGCGACACCCAACTTCGAGCTATCAGAAATCCCATTTGATGTTCAA
*
30849509 TGACGCGA
1 TGTCGCGA
30849517 GACCTATATC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.27
Consensus pattern (49 bp):
TGTCGCGACACCCAACTTCGAGCTATCAGAAATCCCATTTGATGTTCAA
Found at i:30853833 original size:2 final size:2
Alignment explanation
Indices: 30853826--30853850 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30853816 GTATCTGCAT
30853826 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
30853851 GCTGAATTAA
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:30853898 original size:31 final size:29
Alignment explanation
Indices: 30853843--30853900 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 29
30853833 ATATATATAT
*
30853843 ATATATATGCTGAATTAAGTTGTAAAAGA
1 ATATAAATGCTGAATTAAGTTGTAAAAGA
30853872 ATATAAATG-TGAAGTTGAAGTATGTAAAA
1 ATATAAATGCTGAA-TT-AAGT-TGTAAAA
30853901 TATGAACTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 4 0.16
29 10 0.40
30 4 0.16
31 7 0.28
ACGTcount: A:0.47, C:0.02, G:0.19, T:0.33
Consensus pattern (29 bp):
ATATAAATGCTGAATTAAGTTGTAAAAGA
Found at i:30857666 original size:32 final size:31
Alignment explanation
Indices: 30857622--30857716 Score: 84
Period size: 32 Copynumber: 2.9 Consensus size: 31
30857612 TCAAGCCCAT
*
30857622 TGGGCCTAAGCCC-ATTCAGATAACAGTGATAC
1 TGGGCC-AAGCCCTATTCAGATAACAGT-AAAC
* * *
30857654 TGGGCCAGAGCCCTTTTCAGATTACAATAAAC
1 TGGGCCA-AGCCCTATTCAGATAACAGTAAAC
*
30857686 TGGGCCTTAGCCCCTTATTCAGATAACAGTA
1 TGGGCC-AAG-CCC-TATTCAGATAACAGTA
30857717 TGGCTCATAG
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
31 1 0.02
32 22 0.44
33 14 0.28
34 13 0.26
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (31 bp):
TGGGCCAAGCCCTATTCAGATAACAGTAAAC
Done.