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 5 of 378
Found at i:1402692 original size:19 final size:17
Alignment explanation
Indices: 1402670--1402712 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
1402660 CTGGGAAAAA
1402670 AATAATTTTGATAAATTAG
1 AATAATTTT-A-AAATTAG
1402689 AATAATATTTAAAATTAG
1 AATAAT-TTTAAAATTAG
1402707 AA-AATT
1 AATAATT
1402713 AAAACTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 3 0.13
18 9 0.39
19 7 0.30
20 3 0.13
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (17 bp):
AATAATTTTAAAATTAG
Found at i:1403229 original size:11 final size:11
Alignment explanation
Indices: 1403199--1403244 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
1403189 AACAAATTTA
*
1403199 TTCTTTTTACT
1 TTCTTTTTTCT
*
1403210 TTCTTTTTTTT
1 TTCTTTTTTCT
1403221 TTCTTTTTTCCT
1 TTCTTTTTT-CT
1403233 TCTCTTTTTTCT
1 T-TCTTTTTTCT
1403245 CCCCATTTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 18 0.60
12 4 0.13
13 8 0.27
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
TTCTTTTTTCT
Found at i:1409595 original size:17 final size:19
Alignment explanation
Indices: 1409573--1409608 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
1409563 ATTAATTCGA
1409573 AATTTAAT-ATT-TATTTT
1 AATTTAATCATTGTATTTT
1409590 AATTTAATCATTGTATTTT
1 AATTTAATCATTGTATTTT
1409609 TTTTTTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 3 0.18
19 6 0.35
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (19 bp):
AATTTAATCATTGTATTTT
Found at i:1413530 original size:2 final size:2
Alignment explanation
Indices: 1413523--1413559 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1413513 AAATAAATAA
1413523 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1413560 AAATATGGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1417861 original size:136 final size:137
Alignment explanation
Indices: 1417617--1418021 Score: 442
Period size: 149 Copynumber: 2.9 Consensus size: 137
1417607 AAACAATAAT
* * * * * *
1417617 CGAAGATTAGCAGAGAAGAGAGAACAACTTCGAAAGCTGGTAACCACTTCAAAGTTATCGAAATT
1 CGAAGATTAGCAGAGAAGAGAGAACAATTTCG-ACGCTCGTAATCACTACAAAGCTATCGAAATT
* *
1417682 CGATCAAACGAAC-TTCATAATTC-AGCTATAAAACAACCATCCATCACCCAAAAAAA-AAAAAA
65 CTATCAAACGAACTTTCATAATTCGA-CTATAAAACAACGATCCATCACCCAAAAAAAGAAAAAA
1417744 ATTCAAAAG
129 ATTCAAAAG
* * *
1417753 CGAAGGTTAGCAGAGAAGAGAGAACGATTTCGACGCTCGTAATCACTCCAAAGCTATCGAAATTC
1 CGAAGATTAGCAGAGAAGAGAGAACAATTTCGACGCTCGTAATCACTACAAAGCTATCGAAATTC
**
1417818 TATCAAACGAACTTTCATAATTCGACTATAAAACAACGATCCATCACAAAAAAAAAAAAAGAAAG
66 TATCAAACGAACTTTCATAATTCGACTATAAAACAACGATCCATCAC----------CCA-AAA-
1417883 AAAGAAAAAAATTCAAAAG
119 AAAGAAAAAAATTCAAAAG
* * * * *
1417902 CGAAGATTAGCAGAGCAGATAGAACAATTTCGACGCTCGTAATCACTACAAATCTTTCTAAATT-
1 CGAAGATTAGCAGAGAAGAGAGAACAATTTCGACGCTCGTAATCACTACAAAGCTATCGAAATTC
* ** *
1417966 TGATCAAACGAACTTGCATAACCCGACTATTAAACAACGATCCATCA-CCAAAAAAA
66 T-ATCAAACGAACTTTCATAATTCGACTATAAAACAACGATCCATCACCCAAAAAAA
1418022 TTCAAACAAC
Statistics
Matches: 227, Mismatches: 26, Indels: 32
0.80 0.09 0.11
Matches are distributed among these distances:
135 39 0.17
136 63 0.28
137 4 0.02
138 1 0.00
146 1 0.00
147 3 0.01
148 4 0.02
149 112 0.49
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.20
Consensus pattern (137 bp):
CGAAGATTAGCAGAGAAGAGAGAACAATTTCGACGCTCGTAATCACTACAAAGCTATCGAAATTC
TATCAAACGAACTTTCATAATTCGACTATAAAACAACGATCCATCACCCAAAAAAAGAAAAAAAT
TCAAAAG
Found at i:1424883 original size:2 final size:2
Alignment explanation
Indices: 1424876--1424913 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1424866 GGTCTTAGAC
1424876 AT AT 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 AT AT
1424914 TTCAATTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1433351 original size:16 final size:17
Alignment explanation
Indices: 1433308--1433356 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
1433298 TAGACATGAA
*
1433308 ATAAATTATTAATTAAT
1 ATAAATTATTAAATAAT
*
1433325 ATAAATT-TTAAATATT
1 ATAAATTATTAAATAAT
*
1433341 A-AAATTATTAATTAAT
1 ATAAATTATTAAATAAT
1433357 CCATTAACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 5 0.19
16 15 0.56
17 7 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAAATTATTAAATAAT
Found at i:1438212 original size:21 final size:22
Alignment explanation
Indices: 1438168--1438226 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 22
1438158 AATTCTTCTT
1438168 TTTTTTTTATATTGAAGTAAATAAGA
1 TTTTTTTTAT-TTG--G-AAATAAGA
1438194 -TTTTTTTATTTGGAAATAAGA
1 TTTTTTTTATTTGGAAATAAGA
1438215 TTTTTTTTATTT
1 TTTTTTTTATTT
1438227 AGACTTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 8 0.25
22 12 0.38
24 3 0.09
25 9 0.28
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (22 bp):
TTTTTTTTATTTGGAAATAAGA
Found at i:1438975 original size:43 final size:43
Alignment explanation
Indices: 1438910--1438998 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
1438900 TCAATCAATT
1438910 TAGTGAATTTCATTTTTGGCCTTTTTCTGTTATGGGTTGGGCC
1 TAGTGAATTTCATTTTTGGCCTTTTTCTGTTATGGGTTGGGCC
*
1438953 TAGTGAATTTCATTTTTTGCCTTTTTCTGTTATGGGTTGGGCC
1 TAGTGAATTTCATTTTTGGCCTTTTTCTGTTATGGGTTGGGCC
1438996 TAG
1 TAG
1438999 AGGGTTATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.12, C:0.13, G:0.25, T:0.49
Consensus pattern (43 bp):
TAGTGAATTTCATTTTTGGCCTTTTTCTGTTATGGGTTGGGCC
Found at i:1442921 original size:31 final size:31
Alignment explanation
Indices: 1442886--1442945 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
1442876 CTTTTAACCC
*
1442886 CTAAATCTGA-TAATTAGATTCATTTTGGTAT
1 CTAAAT-TGAGTAATTAGATTCAATTTGGTAT
*
1442917 CTAAATTTAGTAATTAGATTCAATTTGGT
1 CTAAATTGAGTAATTAGATTCAATTTGGT
1442946 CATTGATCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.45
Consensus pattern (31 bp):
CTAAATTGAGTAATTAGATTCAATTTGGTAT
Found at i:1455014 original size:23 final size:23
Alignment explanation
Indices: 1454984--1455029 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1454974 TCTCGCAAAT
1454984 TATATTTGAAATATATAATATTC
1 TATATTTGAAATATATAATATTC
1455007 TATATTTGAAATATATAATATTC
1 TATATTTGAAATATATAATATTC
1455030 AGTAACTTGT
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:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (23 bp):
TATATTTGAAATATATAATATTC
Found at i:1472639 original size:20 final size:20
Alignment explanation
Indices: 1472614--1472654 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1472604 TAATTCTTAA
1472614 TATTTTGCAGTTTTTATTTT
1 TATTTTGCAGTTTTTATTTT
** *
1472634 TATTTTTTATTTTTTATTTT
1 TATTTTGCAGTTTTTATTTT
1472654 T
1 T
1472655 GGATTTGGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.02, G:0.05, T:0.78
Consensus pattern (20 bp):
TATTTTGCAGTTTTTATTTT
Found at i:1472640 original size:7 final size:7
Alignment explanation
Indices: 1472624--1472654 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1472614 TATTTTGCAG
1472624 TTTTTA-
1 TTTTTAT
1472630 TTTTTAT
1 TTTTTAT
1472637 TTTTTAT
1 TTTTTAT
1472644 TTTTTAT
1 TTTTTAT
1472651 TTTT
1 TTTT
1472655 GGATTTGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTAT
Found at i:1476925 original size:15 final size:15
Alignment explanation
Indices: 1476905--1476934 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1476895 TTTAATCTTT
*
1476905 TATAAATTATAAAAA
1 TATAAACTATAAAAA
1476920 TATAAACTATAAAAA
1 TATAAACTATAAAAA
1476935 ATTAAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TATAAACTATAAAAA
Found at i:1483613 original size:21 final size:21
Alignment explanation
Indices: 1483575--1483615 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1483565 AATTTTCTAT
*
1483575 TTTAGTTGCAATGTAATTTAG
1 TTTAGTTGAAATGTAATTTAG
1483596 TTTAGTTGAAAATG-AATTTA
1 TTTAGTTG-AAATGTAATTTA
1483616 ATTGTTGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.46
Consensus pattern (21 bp):
TTTAGTTGAAATGTAATTTAG
Found at i:1484688 original size:18 final size:18
Alignment explanation
Indices: 1484665--1484708 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1484655 CTCCAACAGT
*
1484665 AAAAAAAATTGAAAAAGA
1 AAAAAAAACTGAAAAAGA
* *
1484683 AAAAAATACTGAAAACGA
1 AAAAAAAACTGAAAAAGA
1484701 AAAAAAAA
1 AAAAAAAA
1484709 AAAAATAGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.77, C:0.05, G:0.09, T:0.09
Consensus pattern (18 bp):
AAAAAAAACTGAAAAAGA
Found at i:1485052 original size:145 final size:149
Alignment explanation
Indices: 1484778--1485098 Score: 427
Period size: 145 Copynumber: 2.2 Consensus size: 149
1484768 CTAGTGTATA
* *
1484778 TTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTCTTCGTATTTTTTTATTTTCGT
1 TTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTATTCG-A-TTATTTATTTTCGT
* * * *
1484843 ATCTTATTTTTTAAAATATATTATATTCGTATTTTATTTCTTCATATTATTTTAGTACATAATGT
64 ATATTATTTTTTAAAATATATTATATTCGTATTTTATTTCTTCATATTATTTTAGCAAAAAATGT
*
1484908 TTCAAATGTATTATTTAAGTG
129 TTCAAATGTATTATGTAAGTG
** *
1484929 TTTTTTATATTTTTTTAATAAAT-ACCCTTATTTT-AGCACTTTATTC-A-TATTT-TTTTCGTA
1 TTTTTTATATTAATTTAATAAATAACCCTGATTTTGA-CACTTTATTCGATTATTTATTTTCGTA
* * * *
1484989 TATTATTTTTTAAAATATATTATTTTCGTATTTTATTTTTTTATATTGTTTTAGCAAAAAATGTT
65 TATTATTTTTTAAAATATATTATATTCGTATTTTATTTCTTCATATTATTTTAGCAAAAAATGTT
1485054 TCAAATGTATTATGTAAGTG
130 TCAAATGTATTATGTAAGTG
*
1485074 TTTCTTTTACATTAATTTAATAAAT
1 -TT-TTTTATATTAATTTAATAAAT
1485099 GTATTATTTT
Statistics
Matches: 150, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
145 84 0.56
146 6 0.04
147 18 0.12
148 1 0.01
149 1 0.01
150 19 0.13
151 21 0.14
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.56
Consensus pattern (149 bp):
TTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTATTCGATTATTTATTTTCGTAT
ATTATTTTTTAAAATATATTATATTCGTATTTTATTTCTTCATATTATTTTAGCAAAAAATGTTT
CAAATGTATTATGTAAGTG
Found at i:1485433 original size:145 final size:150
Alignment explanation
Indices: 1485165--1485491 Score: 425
Period size: 145 Copynumber: 2.2 Consensus size: 150
1485155 ATTTAAGAAG
** *
1485165 AAAGTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAGAAACACTTAAATAATACATTTGA
1 AAAGTGCCAAAATCAGGGTTATTTATTAAAAAAAAATAAAAGAAACACTTAAATAATACATTTGA
* * *
1485230 AACATTTTTCGCTAAAACAATATAAAAAATAAAATAAGAAAATAATATATTTTAAAAAATAATAT
66 AACATTTGTCACTAAAACAATATAAAAAATAAAATAAGAAAATAATATATTTTAAAAAATAAGAT
* *
1485295 ACG-A-AAAAAAATATGAAT
131 ACGAATAAAAAAATACGAAA
*
1485313 AAAGTGCTAAAATCAGGGTTATTTATTAAAAAAAAAT-AAA-AAA-ACTTAAATAATACATTTGA
1 AAAGTGCCAAAATCAGGGTTATTTATTAAAAAAAAATAAAAGAAACACTTAAATAATACATTTGA
* * ** *
1485375 AACATTATGT-ACTAAAATAATATGAAGAAATAAAATACTAATATAATATATTTT-AAAAATAAG
66 AACATT-TGTCACTAAAACAATAT-AAAAAATAAAATAAGAAAATAATATATTTTAAAAAATAAG
1485438 ATACGAAAATAAAAAAATACGAAA
129 ATACG--AATAAAAAAATACGAAA
* *
1485462 AAAGTGCCAAAATCAAGATTATTTATTAAA
1 AAAGTGCCAAAATCAGGGTTATTTATTAAA
1485492 TTAATATAAA
Statistics
Matches: 156, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
145 49 0.31
146 31 0.20
147 3 0.02
148 34 0.22
149 39 0.25
ACGTcount: A:0.57, C:0.07, G:0.08, T:0.28
Consensus pattern (150 bp):
AAAGTGCCAAAATCAGGGTTATTTATTAAAAAAAAATAAAAGAAACACTTAAATAATACATTTGA
AACATTTGTCACTAAAACAATATAAAAAATAAAATAAGAAAATAATATATTTTAAAAAATAAGAT
ACGAATAAAAAAATACGAAA
Found at i:1485561 original size:18 final size:18
Alignment explanation
Indices: 1485538--1485592 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
1485528 CAACATGACC
*
1485538 CATTTTTTATTTTTTTTT
1 CATTTTTAATTTTTTTTT
* *
1485556 CATTTTCAGTATTTTTTTT
1 CATTTTTAAT-TTTTTTTT
1485575 C-TTTTTCAATTTTTTTTT
1 CATTTTT-AATTTTTTTTT
1485593 ACTGTTGGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 19 0.63
19 11 0.37
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.76
Consensus pattern (18 bp):
CATTTTTAATTTTTTTTT
Found at i:1485592 original size:19 final size:19
Alignment explanation
Indices: 1485547--1485592 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1485537 CCATTTTTTA
*
1485547 TTTTTTTTTCATTTTCAGT
1 TTTTTTTTTCATTTTCAAT
* *
1485566 ATTTTTTTTCTTTTTCAAT
1 TTTTTTTTTCATTTTCAAT
1485585 TTTTTTTT
1 TTTTTTTT
1485593 ACTGTTGGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTTTTTTCATTTTCAAT
Found at i:1490549 original size:17 final size:17
Alignment explanation
Indices: 1490527--1490565 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1490517 CCTTTATTGG
1490527 ATCATTCTACTAA-AATA
1 ATCATTCTACTAATAA-A
*
1490544 ATCATTCTATTAATAAA
1 ATCATTCTACTAATAAA
1490561 ATCAT
1 ATCAT
1490566 AAAAACTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (17 bp):
ATCATTCTACTAATAAA
Found at i:1495921 original size:75 final size:75
Alignment explanation
Indices: 1495798--1495940 Score: 259
Period size: 75 Copynumber: 1.9 Consensus size: 75
1495788 GAGAGGAGGG
*
1495798 ATGGTGGAAAGATGTAGAATGGGAGGATGAATCCACTCGAGTTGCTTTTCTCCCTTCTTTCAAAC
1 ATGGTGGAAAGATGTAGAATGGGAGGATGAATCCACTCGAATTGCTTTTCTCCCTTCTTTCAAAC
1495863 CTGAGGTGGA
66 CTGAGGTGGA
* *
1495873 ATGGTGGAAAGATGTAGAATGGGAGGATGAATCCAGTCGAATTGCTTTTCTCTCTTCTTTCAAAC
1 ATGGTGGAAAGATGTAGAATGGGAGGATGAATCCACTCGAATTGCTTTTCTCCCTTCTTTCAAAC
1495938 CTG
66 CTG
1495941 GTCTATTCTA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (75 bp):
ATGGTGGAAAGATGTAGAATGGGAGGATGAATCCACTCGAATTGCTTTTCTCCCTTCTTTCAAAC
CTGAGGTGGA
Found at i:1496704 original size:15 final size:14
Alignment explanation
Indices: 1496680--1496721 Score: 66
Period size: 15 Copynumber: 2.9 Consensus size: 14
1496670 ATTTTAATAA
1496680 TAAAAAATTATTAT
1 TAAAAAATTATTAT
*
1496694 TATATAAATTATTAT
1 TA-AAAAATTATTAT
1496709 TAAAAAATTATTA
1 TAAAAAATTATTA
1496722 AAAACCAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAAAAATTATTAT
Found at i:1497327 original size:22 final size:22
Alignment explanation
Indices: 1497302--1497346 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1497292 GTATCAAAAA
1497302 TGTTATCACTATAATTTTTGGG
1 TGTTATCACTATAATTTTTGGG
1497324 TGTTATCACTATAATTTTTGGG
1 TGTTATCACTATAATTTTTGGG
1497346 T
1 T
1497347 ACTAAAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.09, G:0.18, T:0.51
Consensus pattern (22 bp):
TGTTATCACTATAATTTTTGGG
Found at i:1528457 original size:19 final size:17
Alignment explanation
Indices: 1528412--1528451 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1528402 TAAAATTTTA
* *
1528412 AAAAAATGAATTATATT
1 AAAAAATTAAATATATT
1528429 AAAAAATTAAATATATT
1 AAAAAATTAAATATATT
1528446 AAAAAA
1 AAAAAA
1528452 GGTTAAGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
AAAAAATTAAATATATT
Found at i:1528503 original size:62 final size:62
Alignment explanation
Indices: 1528427--1528545 Score: 220
Period size: 62 Copynumber: 1.9 Consensus size: 62
1528417 ATGAATTATA
1528427 TTAAAAAATTAAATATATTAAAAAAGGTTAAGCATAACCAATTTTAAAATTTTAATAAATTT
1 TTAAAAAATTAAATATATTAAAAAAGGTTAAGCATAACCAATTTTAAAATTTTAATAAATTT
* *
1528489 TTAAAAAATTAAATATATTAAAAAATGTTAAGTATAACCAATTTTAAAATTTTAATA
1 TTAAAAAATTAAATATATTAAAAAAGGTTAAGCATAACCAATTTTAAAATTTTAATA
1528546 TGTTCAATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (62 bp):
TTAAAAAATTAAATATATTAAAAAAGGTTAAGCATAACCAATTTTAAAATTTTAATAAATTT
Found at i:1528677 original size:16 final size:17
Alignment explanation
Indices: 1528623--1528691 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
1528613 GAGAAAATTT
* *
1528623 TTTTTAATATATTTAAAT
1 TTTTAAATATA-TTAAAA
*
1528641 TTTTAAA-AAACTTAAAAA
1 TTTTAAATATA-TT-AAAA
*
1528659 ATTTAAATATATTAAAA
1 TTTTAAATATATTAAAA
*
1528676 TTTTAAATATGTTAAA
1 TTTTAAATATATTAAA
1528692 GAAAATATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
17 22 0.54
18 17 0.41
19 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (17 bp):
TTTTAAATATATTAAAA
Found at i:1528725 original size:80 final size:78
Alignment explanation
Indices: 1528634--1528799 Score: 183
Period size: 80 Copynumber: 2.1 Consensus size: 78
1528624 TTTTAATATA
* * ** * *
1528634 TTTAAATTTTTAAAAAACTTAAAAAATTTAAATATATTAAAATTTTAAATATGTTAAAGAAAATA
1 TTTAAAATTTTAAAAAACTCAAAAAATCAAAATATATTAAAATTTTAAACATATTAAA-AAAAT-
1528699 TT-AAGTA-TAACCAAT
64 TTGAAGTATTAA--AAT
* * * * *
1528714 TTTAAAATTTTAATATACTCAATATATCAAAATATATTAAAATTTTGAACATATTAAAAAAATTT
1 TTTAAAATTTTAAAAAACTCAAAAAATCAAAATATATTAAAATTTTAAACATATTAAAAAAATTT
1528779 GAAGTATTAAAAT
66 GAAGTATTAAAAT
1528792 TTTAAAAT
1 TTTAAAAT
1528800 ATTTTTTAAT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
78 13 0.18
79 10 0.14
80 50 0.68
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (78 bp):
TTTAAAATTTTAAAAAACTCAAAAAATCAAAATATATTAAAATTTTAAACATATTAAAAAAATTT
GAAGTATTAAAAT
Found at i:1528769 original size:17 final size:16
Alignment explanation
Indices: 1528747--1528802 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
1528737 ATATCAAAAT
1528747 ATATTAAAATTTTGAA
1 ATATTAAAATTTTGAA
*
1528763 CATATTAAAAAAATTTGAA
1 -ATATT--AAAATTTTGAA
* *
1528782 GTATTAAAATTTTAAA
1 ATATTAAAATTTTGAA
1528798 ATATT
1 ATATT
1528803 TTTTAATAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 13 0.41
17 5 0.16
18 4 0.12
19 10 0.31
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (16 bp):
ATATTAAAATTTTGAA
Found at i:1528774 original size:19 final size:18
Alignment explanation
Indices: 1528752--1528790 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1528742 AAAATATATT
*
1528752 AAAATTTTGAACATATTAA
1 AAAAATTTGAA-ATATTAA
*
1528771 AAAAATTTGAAGTATTAA
1 AAAAATTTGAAATATTAA
1528789 AA
1 AA
1528791 TTTTAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (18 bp):
AAAAATTTGAAATATTAA
Found at i:1529246 original size:36 final size:37
Alignment explanation
Indices: 1529169--1529246 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 37
1529159 ATCTTCGTAC
* * * *
1529169 ATTTTTTAATCAACAAATTTTGATATATTTTTATCAT
1 ATTTTTTAATCAACAAATTATGACATATTATTATCAA
*
1529206 ATTTTTTAATCAACAAATTATGCCCAT-TTATT-TCAA
1 ATTTTTTAATCAACAAATTATG-ACATATTATTATCAA
1529242 ATTTT
1 ATTTT
1529247 AAATTAATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
36 8 0.23
37 25 0.71
38 2 0.06
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.51
Consensus pattern (37 bp):
ATTTTTTAATCAACAAATTATGACATATTATTATCAA
Found at i:1536404 original size:17 final size:17
Alignment explanation
Indices: 1536382--1536416 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1536372 GCCCAATTTA
1536382 ACTAATGTTTAATGAAT
1 ACTAATGTTTAATGAAT
1536399 ACTAATGTTTAATGAAT
1 ACTAATGTTTAATGAAT
1536416 A
1 A
1536417 AACAACACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (17 bp):
ACTAATGTTTAATGAAT
Found at i:1538687 original size:2 final size:2
Alignment explanation
Indices: 1538680--1538713 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1538670 AAACTAGATG
* *
1538680 TA TA TA TA TA TA TA TA TA TA TA GA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1538714 CAAATTAGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1541196 original size:25 final size:25
Alignment explanation
Indices: 1541168--1541218 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1541158 TCCTTCCATT
*
1541168 TTCTCT-TCTTCTTTTATTCTTCTTC
1 TTCTCTAT-TTCTTTTATTATTCTTC
*
1541193 TTCTCTATTTCTTTTCTTATTCTTC
1 TTCTCTATTTCTTTTATTATTCTTC
1541218 T
1 T
1541219 ACTGCCCAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (25 bp):
TTCTCTATTTCTTTTATTATTCTTC
Found at i:1541671 original size:2 final size:2
Alignment explanation
Indices: 1541664--1541693 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1541654 ACTCAAATCA
1541664 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
1541694 TTGTTTGCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1541942 original size:2 final size:2
Alignment explanation
Indices: 1541935--1541959 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1541925 TTCATATTTG
1541935 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1541960 CATTTTCAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1545383 original size:23 final size:23
Alignment explanation
Indices: 1545348--1545393 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1545338 TAGTTGATCC
1545348 TGTTAAAAATTATTA-ATTTAATT
1 TGTTAAAAATTATTATA-TTAATT
* *
1545371 TGTTGAAATTTATTATATTAATT
1 TGTTAAAAATTATTATATTAATT
1545394 CTTTTAACCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (23 bp):
TGTTAAAAATTATTATATTAATT
Found at i:1546149 original size:32 final size:32
Alignment explanation
Indices: 1546108--1546171 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1546098 GGATCATGAG
1546108 TTGATTTCACAAGGGGTTCAAAAGTTCTTGAA
1 TTGATTTCACAAGGGGTTCAAAAGTTCTTGAA
1546140 TTGATTTCACAAGGGGTTCAAAAGTTCTTGAA
1 TTGATTTCACAAGGGGTTCAAAAGTTCTTGAA
1546172 CAATCCCCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.34
Consensus pattern (32 bp):
TTGATTTCACAAGGGGTTCAAAAGTTCTTGAA
Found at i:1546810 original size:31 final size:31
Alignment explanation
Indices: 1546775--1546836 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1546765 AAATATGTAT
1546775 ACTTAACAAGGGATAAAGAAACTAGAATTTA
1 ACTTAACAAGGGATAAAGAAACTAGAATTTA
1546806 ACTTAACAAGGGATAAAGAAACTAGAATTTA
1 ACTTAACAAGGGATAAAGAAACTAGAATTTA
1546837 CTTTTTGATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.23
Consensus pattern (31 bp):
ACTTAACAAGGGATAAAGAAACTAGAATTTA
Found at i:1547016 original size:14 final size:14
Alignment explanation
Indices: 1546997--1547023 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1546987 TTATATGTCT
1546997 ATGTAAATGTATAA
1 ATGTAAATGTATAA
1547011 ATGTAAATGTATA
1 ATGTAAATGTATA
1547024 TGAATCTTAC
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:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (14 bp):
ATGTAAATGTATAA
Found at i:1551436 original size:20 final size:20
Alignment explanation
Indices: 1551399--1551436 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1551389 ATTTTCAATT
*
1551399 ATTAATATTTTTTATAGTCA
1 ATTAATATTTTGTATAGTCA
1551419 ATTAATATTATTGT-TAGT
1 ATTAATATT-TTGTATAGT
1551437 TAATGTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (20 bp):
ATTAATATTTTGTATAGTCA
Found at i:1561706 original size:36 final size:35
Alignment explanation
Indices: 1561666--1561778 Score: 85
Period size: 36 Copynumber: 3.2 Consensus size: 35
1561656 AGACTAATAT
1561666 TAATATATAGCTCAACTTTAAATTTAGTCAGAACCC
1 TAATATATA-CTCAACTTTAAATTTAGTCAGAACCC
* *
1561702 TAATATGATTA-TCAAATATTAAAAAATT--TCAGAA---
1 TAATAT-A-TACTCAACT-TT--AAATTTAGTCAGAACCC
* *
1561736 TAATATATAACTTAACTTTAAATTTAGTCAAAACCC
1 TAATATAT-ACTCAACTTTAAATTTAGTCAGAACCC
1561772 TAATATA
1 TAATATA
1561779 ATTACTAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 24
0.66 0.07 0.27
Matches are distributed among these distances:
31 5 0.08
32 1 0.02
33 9 0.15
34 10 0.17
36 18 0.31
37 9 0.15
38 2 0.03
39 5 0.08
ACGTcount: A:0.46, C:0.13, G:0.05, T:0.35
Consensus pattern (35 bp):
TAATATATACTCAACTTTAAATTTAGTCAGAACCC
Found at i:1567208 original size:14 final size:14
Alignment explanation
Indices: 1567189--1567255 Score: 62
Period size: 14 Copynumber: 4.7 Consensus size: 14
1567179 GTTTGCAGGT
*
1567189 AAAATGTTTTCCGG
1 AAAATGATTTCCGG
*
1567203 AAAATGATTTCTGG
1 AAAATGATTTCCGG
* * *
1567217 AAAATAATTTCTTGA
1 AAAATGATTTC-CGG
* *
1567232 AAAATAATTTCTGG
1 AAAATGATTTCCGG
1567246 AAAATGATTT
1 AAAATGATTT
1567256 ACTTTTCTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 33 0.72
15 13 0.28
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.37
Consensus pattern (14 bp):
AAAATGATTTCCGG
Found at i:1567237 original size:15 final size:15
Alignment explanation
Indices: 1567203--1567249 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
1567193 TGTTTTCCGG
* *
1567203 AAAATGATTTC-TGG
1 AAAATAATTTCTTGA
1567217 AAAATAATTTCTTGA
1 AAAATAATTTCTTGA
*
1567232 AAAATAATTTCTGGA
1 AAAATAATTTCTTGA
1567247 AAA
1 AAA
1567250 TGATTTACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 10 0.34
15 19 0.66
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (15 bp):
AAAATAATTTCTTGA
Found at i:1584579 original size:32 final size:32
Alignment explanation
Indices: 1584541--1584606 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
1584531 TTACTCACTC
1584541 TATTTTATATTGATTAGATTGTAATTGTAATT
1 TATTTTATATTGATTAGATTGTAATTGTAATT
1584573 TATTTTATATTGATTAGATTGTAATTGTAATT
1 TATTTTATATTGATTAGATTGTAATTGTAATT
1584605 TA
1 TA
1584607 GAGAATTTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (32 bp):
TATTTTATATTGATTAGATTGTAATTGTAATT
Found at i:1586659 original size:9 final size:10
Alignment explanation
Indices: 1586637--1586673 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
1586627 AATGACTCCT
*
1586637 AAAATTTTTG
1 AAAATTTTTA
1586647 AAAATTTTT-
1 AAAATTTTTA
1586656 AAAATTTTTA
1 AAAATTTTTA
1586666 AAAATTTT
1 AAAATTTT
1586674 CATTATACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.35
10 17 0.65
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (10 bp):
AAAATTTTTA
Found at i:1586660 original size:19 final size:19
Alignment explanation
Indices: 1586636--1586673 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1586626 TAATGACTCC
*
1586636 TAAAATTTTTGAAAATTTT
1 TAAAATTTTTAAAAATTTT
1586655 TAAAATTTTTAAAAATTTT
1 TAAAATTTTTAAAAATTTT
1586674 CATTATACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TAAAATTTTTAAAAATTTT
Found at i:1592715 original size:21 final size:22
Alignment explanation
Indices: 1592689--1592734 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1592679 CCACAACCTA
1592689 ATATTA-ATTTCTATATTTT-TT
1 ATATTACATTTCTAT-TTTTATT
*
1592710 ATATTACATTTTTATTTTTATT
1 ATATTACATTTCTATTTTTATT
1592732 ATA
1 ATA
1592735 ATTCACTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (22 bp):
ATATTACATTTCTATTTTTATT
Found at i:1601872 original size:31 final size:31
Alignment explanation
Indices: 1601837--1601904 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
1601827 TAAAAGCTAG
1601837 TGACTT-AATTGAAAACGTTT-GAATAATTCAA
1 TGACTTGAATT-AAAAC-TTTCGAATAATTCAA
* *
1601868 TGACTTGAATTAAAACTTTCGAATAATTTAG
1 TGACTTGAATTAAAACTTTCGAATAATTCAA
1601899 TGACTT
1 TGACTT
1601905 TTTGGTAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 3 0.09
31 26 0.79
32 4 0.12
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (31 bp):
TGACTTGAATTAAAACTTTCGAATAATTCAA
Found at i:1616094 original size:16 final size:16
Alignment explanation
Indices: 1616075--1616113 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
1616065 ATCAGAAAAA
1616075 AATCAAATTTTGAGTT
1 AATCAAATTTTGAGTT
1616091 AATCAAA--TTGAGTT
1 AATCAAATTTTGAGTT
*
1616105 ATTCAAATT
1 AATCAAATT
1616114 ATTCAAGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
14 13 0.65
16 7 0.35
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (16 bp):
AATCAAATTTTGAGTT
Found at i:1616304 original size:21 final size:19
Alignment explanation
Indices: 1616278--1616349 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 19
1616268 TCTCTCAACA
1616278 AAAATTACAAAATAATTTTC
1 AAAATT-CAAAATAATTTTC
* *
1616298 ACAAATTTTAAAATAATTTTT
1 A-AAA-TTCAAAATAATTTTC
*
1616319 AAAATTCAAAAT-ATTTATA
1 AAAATTCAAAATAATTT-TC
*
1616338 AAAATTCTAAAT
1 AAAATTCAAAAT
1616350 TTTAAATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
18 4 0.09
19 19 0.43
20 4 0.09
21 15 0.34
22 2 0.05
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTC
Found at i:1625728 original size:20 final size:20
Alignment explanation
Indices: 1625703--1625750 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1625693 TATTTCATAA
*
1625703 AAAAATTTAGATC-AAATTAT
1 AAAAATATAGA-CAAAATTAT
*
1625723 AAAAATATATACAAAATTAT
1 AAAAATATAGACAAAATTAT
1625743 AAAAATAT
1 AAAAATAT
1625751 TTATAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAAATATAGACAAAATTAT
Found at i:1625819 original size:20 final size:20
Alignment explanation
Indices: 1625794--1625837 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1625784 AAAATTATTT
*
1625794 AATAAAATAATAATTTTATA
1 AATAAAATAATAATCTTATA
1625814 AATAAAATAATAATCTTATA
1 AATAAAATAATAATCTTATA
1625834 AATA
1 AATA
1625838 TAACAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
AATAAAATAATAATCTTATA
Found at i:1628374 original size:17 final size:17
Alignment explanation
Indices: 1628354--1628442 Score: 55
Period size: 17 Copynumber: 5.3 Consensus size: 17
1628344 TTTGTTTTTG
1628354 TTTTTTTCTTTTAATTA
1 TTTTTTTCTTTTAATTA
*
1628371 TTTTCCTT-TTTTAATTA
1 TTTT-TTTCTTTTAATTA
*
1628388 TTTGTGTTTCCATTTTAATCA
1 TTT-T-TTT-C-TTTTAATTA
* *
1628409 -ATTTTT-TTTT--GT-
1 TTTTTTTCTTTTAATTA
1628421 TTTTTTTCTTTTAATTA
1 TTTTTTTCTTTTAATTA
1628438 TTTTT
1 TTTTT
1628443 GTTTCCATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 20
0.65 0.11 0.24
Matches are distributed among these distances:
13 5 0.09
14 4 0.08
15 4 0.08
16 1 0.02
17 21 0.40
18 8 0.15
19 1 0.02
20 1 0.02
21 8 0.15
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.73
Consensus pattern (17 bp):
TTTTTTTCTTTTAATTA
Found at i:1628440 original size:67 final size:70
Alignment explanation
Indices: 1628304--1628441 Score: 219
Period size: 73 Copynumber: 2.0 Consensus size: 70
1628294 TTTCCTTTTT
1628304 TTTTTTAATTATCTGTGTTTCCATTTTAATCAATTTTTTTTTTGTTTTTGTTTTTTTCTTTTAAT
1 TTTTTTAATTATCTGTGTTTCCATTTTAATCAATTTTTTTTTTG---TTGTTTTTTTCTTTTAAT
1628369 TATTTTCC
63 TATTTTCC
*
1628377 TTTTTTAATTATTTGTGTTTCCATTTTAATCAA-TTTTTTTTTG-T-TTTTTTTCTTTTAATTAT
1 TTTTTTAATTATCTGTGTTTCCATTTTAATCAATTTTTTTTTTGTTGTTTTTTTCTTTTAATTAT
1628439 TTT
66 TTT
1628442 TGTTTCCATT
Statistics
Matches: 64, Mismatches: 1, Indels: 6
0.90 0.01 0.08
Matches are distributed among these distances:
67 21 0.33
68 1 0.02
72 10 0.16
73 32 0.50
ACGTcount: A:0.16, C:0.08, G:0.05, T:0.71
Consensus pattern (70 bp):
TTTTTTAATTATCTGTGTTTCCATTTTAATCAATTTTTTTTTTGTTGTTTTTTTCTTTTAATTAT
TTTCC
Found at i:1628467 original size:50 final size:49
Alignment explanation
Indices: 1628379--1628473 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 49
1628369 TATTTTCCTT
* **
1628379 TTTTAATTATTTGTGTTTCCATTTTAATCAATTTTTTTTTGTTTTTTTTC
1 TTTTAATTATTTGTGTTTCCATTTTAACCAA-TCCTTTTTGTTTTTTTTC
*
1628429 TTTTAATTATTTTTGTTTCCATTTTGAACCAA-CCTTTTTGTTTTT
1 TTTTAATTATTTGTGTTTCCATTTT-AACCAATCCTTTTTGTTTTT
1628474 ATGCTTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
49 11 0.28
50 24 0.60
51 5 0.12
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.66
Consensus pattern (49 bp):
TTTTAATTATTTGTGTTTCCATTTTAACCAATCCTTTTTGTTTTTTTTC
Found at i:1630067 original size:64 final size:64
Alignment explanation
Indices: 1629944--1630061 Score: 147
Period size: 61 Copynumber: 1.9 Consensus size: 64
1629934 AAAAATACGC
* **
1629944 AAGTACTTAATTGGGACAAGAAAAAAAAAGCTCAAGTATCAAATTGAATATTAAAACTAAACTT
1 AAGTACTTAATTGGGACAAGAAAAAAAAAGCTCAAGTATCAAATTGAAAAAAAAAACTAAACTT
1630008 AAGTACTTAATTGCGG-C-A-AAAAAAAAA-CTCAAGTATC-AATTAGAAAAACAAAAA
1 AAGTACTTAATTG-GGACAAGAAAAAAAAAGCTCAAGTATCAAATT-GAAAAA-AAAAA
1630062 TACTAATTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
60 4 0.08
61 14 0.29
62 13 0.27
63 1 0.02
64 14 0.29
65 2 0.04
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.22
Consensus pattern (64 bp):
AAGTACTTAATTGGGACAAGAAAAAAAAAGCTCAAGTATCAAATTGAAAAAAAAAACTAAACTT
Found at i:1643574 original size:15 final size:15
Alignment explanation
Indices: 1643554--1643602 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
1643544 AGTTTTAAAT
1643554 ATTAAAAATAAAGAA
1 ATTAAAAATAAAGAA
* * *
1643569 ATTAAATATATA-AT
1 ATTAAAAATAAAGAA
*
1643583 TTTAAAAATAAAGAA
1 ATTAAAAATAAAGAA
1643598 ATTAA
1 ATTAA
1643603 TTAACCTGGC
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (15 bp):
ATTAAAAATAAAGAA
Found at i:1647758 original size:30 final size:31
Alignment explanation
Indices: 1647667--1647751 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 31
1647657 TTACAAAATG
* *
1647667 GTCATTAAACTATTCGAA-AGTTTTCATTTAA
1 GTCACTAAACTATTC-AAGAGTTTTTATTTAA
1647698 GTCACTAAACTATTCAAGAGTTTTTATTTAA
1 GTCACTAAACTATTCAAGAGTTTTTATTTAA
**
1647729 GTCACTAGGCTATT-AAG-GTTTTT
1 GTCACTAAACTATTCAAGAGTTTTT
1647752 TTTTTAAAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
29 6 0.12
30 5 0.10
31 38 0.78
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (31 bp):
GTCACTAAACTATTCAAGAGTTTTTATTTAA
Found at i:1650514 original size:24 final size:23
Alignment explanation
Indices: 1650481--1650525 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1650471 ATAGCTAGAG
* *
1650481 AAAAACTTATTGATAATATTTTTT
1 AAAAAATTATTAATAA-ATTTTTT
1650505 AAAAAATTATTAATAAATTTT
1 AAAAAATTATTAATAAATTTT
1650526 ATGCAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
AAAAAATTATTAATAAATTTTTT
Found at i:1651724 original size:23 final size:24
Alignment explanation
Indices: 1651690--1651738 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
1651680 CCAATTGGGA
* *
1651690 AAAAAAAGTTCAAGTATCAAATTG
1 AAAAAAAGTTCAAGTACCAAAGTG
*
1651714 AAAAAAA-TTCAGGTACCAAAGTG
1 AAAAAAAGTTCAAGTACCAAAGTG
1651737 AA
1 AA
1651739 TATTGAAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.55, C:0.10, G:0.14, T:0.20
Consensus pattern (24 bp):
AAAAAAAGTTCAAGTACCAAAGTG
Found at i:1666240 original size:13 final size:13
Alignment explanation
Indices: 1666208--1666246 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1666198 TGATTTGATC
1666208 TAATT-TTT-ATA
1 TAATTATTTAATA
1666219 -AATTA-TTAATA
1 TAATTATTTAATA
1666230 TAATTATTTAATA
1 TAATTATTTAATA
1666243 TAAT
1 TAAT
1666247 ATTATTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 6 0.25
11 3 0.12
12 5 0.21
13 10 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAATTATTTAATA
Found at i:1666252 original size:15 final size:14
Alignment explanation
Indices: 1666215--1666253 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
1666205 ATCTAATTTT
1666215 TATAAATTA-TTAA
1 TATAAATTATTTAA
1666228 TAT-AATTATTTAA
1 TATAAATTATTTAA
1666241 TATAATATTATTT
1 TATAA-ATTATTT
1666254 TATGTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.22
13 10 0.43
14 1 0.04
15 7 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATAAATTATTTAA
Found at i:1672378 original size:80 final size:80
Alignment explanation
Indices: 1672176--1672939 Score: 646
Period size: 80 Copynumber: 9.6 Consensus size: 80
1672166 AACATCATTG
* * * * * * * * *
1672176 GTTTTTCCTCTTGAAAATTCTCAGAAAATATTCACAGATTCACTCAAAAGGAAATATAGAAAGAG
1 GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATT-ACTC--AAGGAAATACAGCAAGAA
*
1672241 CAAAAGGGTATCAGAA-TT
63 CAAAAGGGCATCA-AACTT
* *
1672259 GGTTTCCCTTCATGCAAATTCCAAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAGAACA
1 GTTTTCCC-TCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAGAAC-
*
1672324 AAAAGGGCA-CAAACTC
64 AAAAGGGCATCAAACTT
* * * * *
1672340 GTTTTCCCTCAAGCGAATTCCCATAAAATTTTCACAAATTGCTCAAGCAAATACAGCAAGAACAA
1 GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAGAAC-A
*
1672405 AAAGGGCA-CAAACTA
65 AAAGGGCATCAAACTT
* * * * * *
1672420 GTTTTCCGTCAAGCGAATTCCCATAAAATTTTCACAAATTACTCAAGCAAATACAGCAAGAGCAA
1 GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAGAACAA
*
1672485 AAGGGAATC-AACATT
66 AAGGGCATCAAAC-TT
** * ** * *
1672500 GTTTTCCCTCATGCAAATTCCCAGAAAAAATTCACAGAGAACT-AAGGAAATACATCAA-AAGTA
1 GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAGAA-CA
* *
1672563 AAAGGACATCAAATTT
65 AAAGGGCATCAAACTT
* * * * *
1672579 GGTCT-CCTCTTGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGCAAATACAGCAAGAGCAA
1 GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAGAACAA
*
1672643 AAGGGAATC-AACATT
66 AAGGGCATCAAAC-TT
** * ** *
1672658 GTTTTCCCTCATGCAAATTCCCAGAAAAAATTCACAGAGAACT-AAGGAAATACATCAA-AAGCA
1 GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAGAA-CA
* *
1672721 AAAGGACATCAAATTT
65 AAAGGGCATCAAACTT
* * * *
1672737 GGTCT-CCTCTTGCAAATTCCCAGAAAATTTTCACAAATTACTGAAGGAAATACAGCAA-AAGCA
1 GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAGAA-CA
* *
1672800 AAAGGGTATCGAA-TT
65 AAAGGGCATCAAACTT
* * * *
1672815 GATTTCTCCCT--T-CAAATTCCCAGAAAAAATTTCACAAATTACTCAAGCAAATACAACAAGAG
1 G-TTT-TCCCTCATGCAAATTCCCAG-AAAATTTTCACAAATTACTCAAGGAAATACAGCAAGAA
* * **
1672877 CAAAATGGG-ACCTAACCA
63 CAAAA-GGGCATCAAACTT
* * *
1672895 GTGTTCCCTCACT-CAAATTCCCAGAAAAAATTTCACATATTACTC
1 GTTTTCCCTCA-TGCAAATTCCCAG-AAAATTTTCACAAATTACTC
1672940 CAGAAAAACT
Statistics
Matches: 561, Mismatches: 96, Indels: 50
0.79 0.14 0.07
Matches are distributed among these distances:
78 85 0.15
79 166 0.30
80 205 0.37
81 61 0.11
82 8 0.01
83 10 0.02
84 26 0.05
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.23
Consensus pattern (80 bp):
GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAGAACAA
AAGGGCATCAAACTT
Found at i:1672626 original size:158 final size:157
Alignment explanation
Indices: 1672271--1672850 Score: 738
Period size: 158 Copynumber: 3.7 Consensus size: 157
1672261 TTTCCCTTCA
* * * *
1672271 TGCAAATTCCAAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAGAACAAAAAGGGCA-CA
1 TGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGCAAATACAGCAAGAGC-AAAAGGGAATCA
* * * * ** * *** * *
1672335 AACTCGTTTTCCCTCAAGCGAATTCCCATAAAATTTTCACAAATTGCTCAAGCAAATACAGCAAG
65 AA-TTGTTTTCCCTCATGCAAATTCCCAGAAAAAATTCACAGAGAACT-AAGGAAATACATCAA-
* * * * * * *
1672400 AACAAAAAGGGCA-CAAACTAGTTTTCCGTCA
127 AAGAAAAAGGACATCAAATTTGGTCTCC-TCT
* * *
1672431 AGCGAATTCCCATAAAATTTTCACAAATTACTCAAGCAAATACAGCAAGAGCAAAAGGGAATCAA
1 TGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGCAAATACAGCAAGAGCAAAAGGGAATCAA
1672496 CATTGTTTTCCCTCATGCAAATTCCCAGAAAAAATTCACAGAGAACTAAGGAAATACATCAAAAG
66 -ATTGTTTTCCCTCATGCAAATTCCCAGAAAAAATTCACAGAGAACTAAGGAAATACATCAAAAG
*
1672561 TAAAAGGACATCAAATTTGGTCTCCTCT
130 AAAAAGGACATCAAATTTGGTCTCCTCT
1672589 TGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGCAAATACAGCAAGAGCAAAAGGGAATCAA
1 TGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGCAAATACAGCAAGAGCAAAAGGGAATCAA
1672654 CATTGTTTTCCCTCATGCAAATTCCCAGAAAAAATTCACAGAGAACTAAGGAAATACATCAAAAG
66 -ATTGTTTTCCCTCATGCAAATTCCCAGAAAAAATTCACAGAGAACTAAGGAAATACATCAAAAG
*
1672719 CAAAAGGACATCAAATTTGGTCTCCTCT
130 AAAAAGGACATCAAATTTGGTCTCCTCT
* * * * *
1672747 TGCAAATTCCCAGAAAATTTTCACAAATTACTGAAGGAAATACAGCAAAAGCAAAAGGGTATCGA
1 TGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGCAAATACAGCAAGAGCAAAAGGGAATCAA
1672812 ATTGATTTCTCCCT--T-CAAATTCCCAGAAAAAATTTCACA
66 ATTG-TTT-TCCCTCATGCAAATTCCCAGAAAAAA-TTCACA
1672851 AATTACTCAA
Statistics
Matches: 378, Mismatches: 36, Indels: 15
0.88 0.08 0.03
Matches are distributed among these distances:
156 17 0.04
157 11 0.03
158 229 0.61
159 36 0.10
160 84 0.22
161 1 0.00
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.23
Consensus pattern (157 bp):
TGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGCAAATACAGCAAGAGCAAAAGGGAATCAA
ATTGTTTTCCCTCATGCAAATTCCCAGAAAAAATTCACAGAGAACTAAGGAAATACATCAAAAGA
AAAAGGACATCAAATTTGGTCTCCTCT
Found at i:1677600 original size:75 final size:75
Alignment explanation
Indices: 1677473--1677625 Score: 261
Period size: 75 Copynumber: 2.0 Consensus size: 75
1677463 CTTCGTTCTC
* *
1677473 CAAAGGATTGTCCTAATATAACATAGCCAGCGACAAAAAGAATCAAATTACAGCATTTAAACTTC
1 CAAAGGATTGTCCTAATATAACATAGCCAGCAACAAAAAGAATCAAACTACAGCATTTAAACTTC
1677538 AATAATACAG
66 AATAATACAG
* *
1677548 CAAAGGATTGTCCTGATATAACATAGCCAGCAACAAAAAGAATCAGACTACAGCATTTAAACTTC
1 CAAAGGATTGTCCTAATATAACATAGCCAGCAACAAAAAGAATCAAACTACAGCATTTAAACTTC
*
1677613 AATAGTACAG
66 AATAATACAG
1677623 CAA
1 CAA
1677626 CATGAGGCTA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.22
Consensus pattern (75 bp):
CAAAGGATTGTCCTAATATAACATAGCCAGCAACAAAAAGAATCAAACTACAGCATTTAAACTTC
AATAATACAG
Found at i:1681341 original size:160 final size:156
Alignment explanation
Indices: 1680920--1681564 Score: 626
Period size: 150 Copynumber: 4.2 Consensus size: 156
1680910 AGGAAGTAAC
* * *
1680920 AAAAAACGAGGCAATTAGACTGAAA-GGTATCGAAATAAAATTGAAAAAAAAAACACAAA---AA
1 AAAAAACAAGGCAATTAGACT-AAAGGGTATTGAAATAAATTTGAAAAAAAAAA-A-AAACCTAA
* * * *
1680981 ACCAGAGTCAAGAACACCACGAAAGATCAAATGCTCAAGCGAATAACCAATAAAACGGA-GATTT
63 CCCAGAGCCAAGAACACCATGAAAGATCAAATGCTCAAGCGAATAACCAATAAAAC-AATGATTT
* * *
1681045 TCAGCAAAATTAGAGATATGAAGTT------
127 TCAGCAAAA-TCGAGCTAAGAAGTTAAAAAA
* *
1681070 AAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAATTTG-AAAAAAAAAAAAACCTAACTC
1 AAAAAACAAGGCAATTAGACTAAAGGGTATTGAAATAAATTTGAAAAAAAAAAAAAACCTAACCC
* * * *
1681134 AGAGCCAAGAACACCATGAAAGATCAAATGGTCAAACGAACAACCAATATAACAATGATTTTCAG
66 AGAGCCAAGAACACCATGAAAGATCAAATGCTCAAGCGAATAACCAATAAAACAATGATTTTCAG
*
1681199 CAAAATCGAGCTAGGAAGTTTAAAAAAA
131 CAAAATCGAGCTAAGAAG-TT-AAAAAA
* * *
1681227 AAAAAACCAAGGCACTTAGACTAAAGAGTATTGAGATAAATTTGAAAAGAAAAAAAAAACCTAAC
1 AAAAAA-CAAGGCAATTAGACTAAAGGGTATTGAAATAAATTTGAAAA-AAAAAAAAAACCTAAC
*
1681292 CCAGAGCCAAAAACACCATGAAAGATCAAATGCTCAAGCGAATAACCAATAAAACAATGATTTTC
64 CCAGAGCCAAGAACACCATGAAAGATCAAATGCTCAAGCGAATAACCAATAAAACAATGATTTTC
* * *
1681357 AACGAAATCGAACTAAGAAG-TAAAAAA
129 AGCAAAATCGAGCTAAGAAGTTAAAAAA
* * * *
1681384 AAAAAA-AGGGTAATTAGAGTAAAGGGTATTGGAATAAATTTG-----AAAAAAAAA---AACCC
1 AAAAAACAAGGCAATTAGACTAAAGGGTATTGAAATAAATTTGAAAAAAAAAAAAAACCTAACCC
* *** * * * * *
1681440 AGAGCCAAGAATC-TCACCCAAGCTCGAATGCTCAAACGAACAACCAATAAAGCAATGATTTTCA
66 AGAGCCAAGAA-CACCATGAAAGATCAAATGCTCAAGCGAATAACCAATAAAACAATGATTTTCA
* * *
1681504 GCAAATTCGAGCTATGAAG-T----CA
130 GCAAAATCGAGCTAAGAAGTTAAAAAA
* *
1681526 AAAAAACAAGGCAATTATACTAAAGGGAATTGAAATAAA
1 AAAAAACAAGGCAATTAGACTAAAGGGTATTGAAATAAA
1681565 ATCGAAAAGC
Statistics
Matches: 418, Mismatches: 59, Indels: 43
0.80 0.11 0.08
Matches are distributed among these distances:
142 7 0.02
143 26 0.06
146 72 0.17
147 4 0.01
148 1 0.00
149 32 0.08
150 101 0.24
155 29 0.07
157 18 0.04
158 34 0.08
159 3 0.01
160 91 0.22
ACGTcount: A:0.52, C:0.15, G:0.16, T:0.17
Consensus pattern (156 bp):
AAAAAACAAGGCAATTAGACTAAAGGGTATTGAAATAAATTTGAAAAAAAAAAAAAACCTAACCC
AGAGCCAAGAACACCATGAAAGATCAAATGCTCAAGCGAATAACCAATAAAACAATGATTTTCAG
CAAAATCGAGCTAAGAAGTTAAAAAA
Found at i:1681470 original size:146 final size:144
Alignment explanation
Indices: 1681002--1681657 Score: 415
Period size: 146 Copynumber: 4.4 Consensus size: 144
1680992 GAACACCACG
* * * * * * *
1681002 AAAGATCAAATGCTCAAGCGAATAACCAATAAAACGGA-GATTTTCAGCAAAATTAGAGA-TATG
1 AAAGCTCAAATGCTCAAACGAACAACCAATAAAAC-AATGATTTTCAAC-AAATTCGA-ACTAAG
* * * * * * *
1681065 AAGT-TAAAAAACAAGGCAATTAGAGTAAAGGGTATTGAAATAAATTTGAAAAAAAAAAAAACCT
63 AAGTAAAAAAAAAAAGGCAATTAGACTAAAGGGAATTGAAATAAAATCG-AAAACAAAAAAA-C-
* * **
1681129 AACTCAGAGCCAAGAA-CACCATG
125 --C-CAAAGCCAAGAATC-TCACC
* * * * * * *
1681152 AAAGATCAAATGGTCAAACGAACAACCAATATAACAATGATTTTCAGCAAAATCGAGCTAGGAAG
1 AAAGCTCAAATGCTCAAACGAACAACCAATAAAACAATGATTTTCAACAAATTCGAACTAAGAAG
* * * * * * *
1681217 TTTAAAAAAAAAAAAACCAAGGCACTTAGACTAAAGAGTATTGAGATAAATTTGAAAAGAAAAAA
66 --T----AAAAAAAAA--AAGGCAATTAGACTAAAGGGAATTGAAATAAAATCG-AAA-ACAAAA
* * * ***
1681282 AAAACCTAACCCAGAGCCAAAAACACC
121 AAACCCAAAGCCA-AG--AATCTCACC
* * *
1681309 ATGAAAGATCAAATGCTCAAGCGAATAACCAATAAAACAATGATTTTCAACGAAA-TCGAACTAA
1 ---AAAGCTCAAATGCTCAAACGAACAACCAATAAAACAATGATTTTCAAC-AAATTCGAACTAA
* * * * * *
1681373 GAAGTAAAAAAAAAAAAAGGGTAATTAGAGTAAAGGGTATTGGAATAAATTTGAAAA-AAAAAAA
62 GAAGT--AAAAAAAAAAA-GGCAATTAGACTAAAGGGAATTGAAATAAAATCGAAAACAAAAAAA
*
1681437 CCCAGAGCCAAGAATCTCACC
124 CCCAAAGCCAAGAATCTCACC
* * * * * *
1681458 CAAGCTCGAATGCTCAAACGAACAACCAATAAAGCAATGATTTTCAGCAAATTCGAGCTATGAAG
1 AAAGCTCAAATGCTCAAACGAACAACCAATAAAACAATGATTTTCAACAAATTCGAACTAAGAAG
* * * * **
1681523 TCAAAAAAACAAGGCAATTATACTAAAGGGAATTGAAATAAAATCGAAAAGCACACTAACCCAAA
66 TAAAAAAAAAAAGGCAATTAGACTAAAGGGAATTGAAATAAAATCGAAAA-CAAAAAAACCCAAA
1681588 GCCAAGAATCTCACC
130 GCCAAGAATCTCACC
* * *
1681603 AAAGCTCAAATGCTCAAACGAACAACCAAAAACAAAAATGATTTTCAGCAAATTC
1 AAAGCTCAAATGCTCAAACGAACAACCAATAA-AACAATGATTTTCAACAAATTC
1681658 TAGCTGGGAA
Statistics
Matches: 411, Mismatches: 70, Indels: 54
0.77 0.13 0.10
Matches are distributed among these distances:
143 31 0.08
144 9 0.02
145 56 0.14
146 73 0.18
149 19 0.05
150 41 0.10
151 3 0.01
152 13 0.03
153 1 0.00
154 10 0.02
155 31 0.08
156 17 0.04
157 4 0.01
158 37 0.09
159 9 0.02
160 54 0.13
161 3 0.01
ACGTcount: A:0.51, C:0.17, G:0.15, T:0.18
Consensus pattern (144 bp):
AAAGCTCAAATGCTCAAACGAACAACCAATAAAACAATGATTTTCAACAAATTCGAACTAAGAAG
TAAAAAAAAAAAGGCAATTAGACTAAAGGGAATTGAAATAAAATCGAAAACAAAAAAACCCAAAG
CCAAGAATCTCACC
Found at i:1682639 original size:30 final size:31
Alignment explanation
Indices: 1682580--1682640 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1682570 TAATTATACG
* *
1682580 CATGAAATTTTGATTGTGGTTCAAATGTATA
1 CATGAAACTTTGATTGTGATTCAAATGTATA
*
1682611 CATGAAACTTTGATT-TGATTCAATTGTATA
1 CATGAAACTTTGATTGTGATTCAAATGTATA
1682641 TATTTAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (31 bp):
CATGAAACTTTGATTGTGATTCAAATGTATA
Found at i:1685735 original size:2 final size:2
Alignment explanation
Indices: 1685728--1685768 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1685718 TAATTTTACT
1685728 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1685769 CCTCTTCCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1688699 original size:60 final size:60
Alignment explanation
Indices: 1688576--1688700 Score: 187
Period size: 60 Copynumber: 2.1 Consensus size: 60
1688566 TGAATAGTTA
* * * *
1688576 GGTGAGCAAAAAAGAAATGTACTAATAGTTGAGTGACCATTTTGTAACTTTTCATAGTTG
1 GGTGACCAAAAAAGAAATGTACTAATACTTGAGTGACCATTTTATAACTTTTCATAGTCG
* * *
1688636 GGTGACCAAAGAAGAAATTTACTAATACTTGAGTGACTATTTTATAACTTTTCATAGTCG
1 GGTGACCAAAAAAGAAATGTACTAATACTTGAGTGACCATTTTATAACTTTTCATAGTCG
1688696 GGTGA
1 GGTGA
1688701 AAAAATGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (60 bp):
GGTGACCAAAAAAGAAATGTACTAATACTTGAGTGACCATTTTATAACTTTTCATAGTCG
Found at i:1691121 original size:10 final size:10
Alignment explanation
Indices: 1691099--1691128 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1691089 TTTATTAGTA
1691099 AAAATAAAA-
1 AAAATAAAAG
1691108 AAAATAAAAG
1 AAAATAAAAG
1691118 AAAATAAAAG
1 AAAATAAAAG
1691128 A
1 A
1691129 GAGGATAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (10 bp):
AAAATAAAAG
Found at i:1692213 original size:30 final size:31
Alignment explanation
Indices: 1692177--1692240 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
1692167 ACTTATTTTA
1692177 TTGTTAA-TTTTCTTATTATTTTAAAGACAT
1 TTGTTAATTTTTCTTATTATTTTAAAGACAT
* * *
1692207 TTGTTAATTTTTTTTATTATTTTAGAGGCAT
1 TTGTTAATTTTTCTTATTATTTTAAAGACAT
1692238 TTG
1 TTG
1692241 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.59
Consensus pattern (31 bp):
TTGTTAATTTTTCTTATTATTTTAAAGACAT
Found at i:1693397 original size:29 final size:29
Alignment explanation
Indices: 1693355--1693413 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
1693345 AAAGTGATTT
*
1693355 AAATGAAATAATTA-GGGCTAAAATGATA
1 AAATGAAAAAATTAGGGGCTAAAATGATA
*
1693383 AAATGAAAAATATTAGGGGCTAAAATTATA
1 AAATGAAAAA-ATTAGGGGCTAAAATGATA
1693413 A
1 A
1693414 TTAAGCATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 9 0.33
29 4 0.15
30 14 0.52
ACGTcount: A:0.54, C:0.03, G:0.17, T:0.25
Consensus pattern (29 bp):
AAATGAAAAAATTAGGGGCTAAAATGATA
Found at i:1700475 original size:32 final size:29
Alignment explanation
Indices: 1700407--1700477 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
1700397 CATATCATTA
* *
1700407 TAAAATAAATATAATTCATGCAAAAAAAATT
1 TAAAA-AAATATAATTCAT-AAAAAAAAAAT
*
1700438 TAAAAATATATAATTCATAAAAAAATAAGAT
1 TAAAAAAATATAATTCATAAAAAAA-AA-AT
1700469 TAAAAAAAT
1 TAAAAAAAT
1700478 TTAAAATTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 6 0.18
30 14 0.41
31 14 0.41
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.28
Consensus pattern (29 bp):
TAAAAAAATATAATTCATAAAAAAAAAAT
Found at i:1702822 original size:240 final size:239
Alignment explanation
Indices: 1702376--1702922 Score: 783
Period size: 240 Copynumber: 2.3 Consensus size: 239
1702366 TTATCAAGAT
* * * * * *
1702376 ATTGAGACTACCCCTTCAAGATTTTGTTGTCCATAGATAACCATGTATTTAGCCTTTATTTATTC
1 ATTGAGAATGCCCTTTCAAGATTTTGTTGTCCAAATATAACCATGAATTTAGCCTTTATTTATTC
* * * * * *
1702441 CCCCCTATATAATAAAATTGGTCAAATTTCATTGAAAGTACCTCTATTATTTGTTTTTTTCACAA
66 CCCCATAAATAATAAAATCGGTCAAATTTCATAGAAACTACCTCTATTATTTGTTTTTTTCAAAA
* * *
1702506 ATTTAGCCTCTCTACTATAATTTAATAATTTCTTAGGTGATTGGAGGGTACCGAATCAAGTTACA
131 ATTTAACCTCTCTACTATAATTTAATAATTTCTTAGGTGAGTGGAGAGTACCGAATCAAGTTACA
*
1702571 GTTCAAGAGAGTGGGATTACATCAACAAAGTTTGAATAATGGTC
196 GTTCAAGAGAGTGGGATTACATCAACAAAGTTTGAATAATGATC
1702615 ATTGAGAATGCCCTTTCAAGATTTTGTTGTCCAAATATAACCATGAATTTAGCCTTTATTTA-T-
1 ATTGAGAATGCCCTTTCAAGATTTTGTTGTCCAAATATAACCATGAATTTAGCCTTTATTTATTC
* *
1702678 CCCCATAAATAATAAAATCGGTCAAATTTCATAGAAACTCCCTCTATTATTTATTTTTTTTTCCA
66 CCCCATAAATAATAAAATCGGTCAAATTTCATAGAAACTACCTCTATTA-TT-TGTTTTTTT-CA
* * * *
1702743 AAAATTTAATCTCTCTACTATAATTTGATCATTTCTTGGGTGAGTGGAGAGTACCGAATCAAGTT
128 AAAATTTAACCTCTCTACTATAATTTAATAATTTCTTAGGTGAGTGGAGAGTACCGAATCAAGTT
* *
1702808 ACAGTTCAAGAGAGTGGGATTATATCAACAAAGTTTGACTAATGATC
193 ACAGTTCAAGAGAGTGGGATTACATCAACAAAGTTTGAATAATGATC
* * * * *
1702855 ATTGAGAGTGTCCTTTTCAAGATTTTGCTGCCCAAATATAACCATGAATTTAGCCTTTATTTTTT
1 ATTGAGAATG-CCCTTTCAAGATTTTGTTGTCCAAATATAACCATGAATTTAGCCTTTATTTATT
1702920 CCC
65 CCC
1702923 TCTAAAATCA
Statistics
Matches: 273, Mismatches: 29, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
237 43 0.16
238 3 0.01
239 64 0.23
240 112 0.41
241 48 0.18
242 1 0.00
243 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (239 bp):
ATTGAGAATGCCCTTTCAAGATTTTGTTGTCCAAATATAACCATGAATTTAGCCTTTATTTATTC
CCCCATAAATAATAAAATCGGTCAAATTTCATAGAAACTACCTCTATTATTTGTTTTTTTCAAAA
ATTTAACCTCTCTACTATAATTTAATAATTTCTTAGGTGAGTGGAGAGTACCGAATCAAGTTACA
GTTCAAGAGAGTGGGATTACATCAACAAAGTTTGAATAATGATC
Found at i:1710333 original size:137 final size:137
Alignment explanation
Indices: 1710088--1710374 Score: 513
Period size: 137 Copynumber: 2.1 Consensus size: 137
1710078 CATTGGGCCT
** * *
1710088 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGATACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1710153 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
1710217 CATATGC
131 CATATGC
1710224 AAGCCCATTTGGGTAACAGTGATACTGGGCCAAAGCCCTTTTTCAGATTACAATAAACTGGGCCT
1 AAGCCCATTTGGGTAACAGTGATACTGGGCCAAAGCCC-TTTTCAGATTACAATAAACTGGGCCT
*
1710289 TAGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAA
65 TAGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAA
1710354 ACATATGC
130 ACATATGC
1710362 AAGCCCATTTGGG
1 AAGCCCATTTGGG
1710375 GAGACTACTC
Statistics
Matches: 144, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
136 34 0.24
137 88 0.61
138 22 0.15
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGATACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
CATATGC
Found at i:1712197 original size:26 final size:26
Alignment explanation
Indices: 1712161--1712270 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
1712151 CATGAATTTC
*
1712161 TTATCATGAAACATTTACCTAAACCA
1 TTATCATGAAACATTTACCTAACCCA
1712187 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
1712213 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
*
1712239 TTGTCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
1712265 TTATCA
1 TTATCA
1712271 ATTTGTATCA
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:1721651 original size:21 final size:21
Alignment explanation
Indices: 1721610--1721652 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1721600 AAAACAATCG
*
1721610 TTGAATTTTGAAACGTTTTAA
1 TTGAATTTTGAAACGTATTAA
*
1721631 TTGAATTTTTTAAA-GTATTAA
1 TTGAA-TTTTGAAACGTATTAA
1721652 T
1 T
1721653 ATCGTCTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (21 bp):
TTGAATTTTGAAACGTATTAA
Found at i:1730988 original size:23 final size:23
Alignment explanation
Indices: 1730962--1731010 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
1730952 TTTGAATCAG
1730962 TTTTCTTTAATTTTTAATAA-TTAT
1 TTTTCTTT-ATTTTT-ATAATTTAT
1730986 TTTTCTTTATTTTTATAATTTAT
1 TTTTCTTTATTTTTATAATTTAT
1731009 TT
1 TT
1731011 AATTAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 4 0.17
23 12 0.50
24 8 0.33
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTCTTTATTTTTATAATTTAT
Found at i:1734590 original size:30 final size:29
Alignment explanation
Indices: 1734541--1734608 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
1734531 TGTTTGGGTC
*
1734541 AGGACTAAAATTTTAAAATTAAAAAGTACA
1 AGGACTAAAATTATAAAATTAAAAA-TACA
*
1734571 AGGACTAAAATTGAT-AAATTTAAAATACA
1 AGGACTAAAATT-ATAAAATTAAAAATACA
* *
1734600 TGAACTAAA
1 AGGACTAAA
1734609 TCCACAACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 11 0.33
30 21 0.64
31 1 0.03
ACGTcount: A:0.56, C:0.07, G:0.10, T:0.26
Consensus pattern (29 bp):
AGGACTAAAATTATAAAATTAAAAATACA
Found at i:1735761 original size:2 final size:2
Alignment explanation
Indices: 1735756--1735782 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1735746 ACTCTCTTAC
1735756 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1735783 ATTTTGTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1737527 original size:13 final size:13
Alignment explanation
Indices: 1737505--1737535 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1737495 ACGATTTAAC
*
1737505 GATCAGTATGGTA
1 GATCAATATGGTA
1737518 GATCAATATGGTA
1 GATCAATATGGTA
1737531 GATCA
1 GATCA
1737536 GTACATGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (13 bp):
GATCAATATGGTA
Found at i:1738254 original size:21 final size:19
Alignment explanation
Indices: 1738222--1738266 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
1738212 TTTCGGTTAT
*
1738222 CTTTTTTTAATTTTTAGTG
1 CTTTTTTGAATTTTTAGTG
1738241 ACTTTTTCTGAATTTTTAGTG
1 -CTTTTT-TGAATTTTTAGTG
1738262 CTTTT
1 CTTTT
1738267 AAGTGATAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.16, C:0.09, G:0.11, T:0.64
Consensus pattern (19 bp):
CTTTTTTGAATTTTTAGTG
Found at i:1740551 original size:30 final size:29
Alignment explanation
Indices: 1740482--1740551 Score: 68
Period size: 30 Copynumber: 2.3 Consensus size: 29
1740472 GGGTTTGCTT
* * *
1740482 AAAATTTTCAAAAATTTTAGAGACTTAATT
1 AAAATTTT-AAAAATTATAGAGACATAATG
* *
1740512 AGAATTTTTAAAAATTATAGAAGGCATAATG
1 A-AAATTTTAAAAATTATAG-AGACATAATG
1740543 AAAATTTTA
1 AAAATTTTA
1740552 GAATCACATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
30 18 0.56
31 14 0.44
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (29 bp):
AAAATTTTAAAAATTATAGAGACATAATG
Found at i:1751033 original size:15 final size:16
Alignment explanation
Indices: 1751010--1751047 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1751000 TTAATAAAAA
1751010 AATAA-TTAAAAATTT
1 AATAATTTAAAAATTT
*
1751025 AA-AATTTAAAATTTT
1 AATAATTTAAAAATTT
1751040 AATAATTT
1 AATAATTT
1751048 GTAATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 13 0.65
16 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATAATTTAAAAATTT
Found at i:1751794 original size:62 final size:61
Alignment explanation
Indices: 1751672--1751795 Score: 144
Period size: 61 Copynumber: 2.0 Consensus size: 61
1751662 AAATTGATAA
* * *
1751672 AAAAATAAATAATGTAATCATATTTTAATATAATTATTATTTAATATAATTTAATAAAAAT
1 AAAAATAAATAATGTAATAATATTTTAATATAAATATTATTTAATATAAATTAATAAAAAT
* * * *
1751733 AAAAATATATAATTTAATAATGTTTTTAATATAAATATT-TTT-ATATTAAATTATATTAAAAT
1 AAAAATAAATAATGTAATAAT-ATTTTAATATAAATATTATTTAATA-TAAATTA-ATAAAAAT
1751795 A
1 A
1751796 TTTTTTAGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
60 3 0.06
61 27 0.51
62 23 0.43
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (61 bp):
AAAAATAAATAATGTAATAATATTTTAATATAAATATTATTTAATATAAATTAATAAAAAT
Found at i:1751796 original size:32 final size:31
Alignment explanation
Indices: 1751767--1751828 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
1751757 TTTAATATAA
*
1751767 ATATT-TTTATATTAAATTATATTAAAATAT
1 ATATTATTTATATTAAATTATAGTAAAATAT
* *
1751797 TTTTTAGTTTATATTAAATTATAGTAAAATAT
1 ATATTA-TTTATATTAAATTATAGTAAAATAT
1751829 TTAAAATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 3 0.11
32 24 0.89
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (31 bp):
ATATTATTTATATTAAATTATAGTAAAATAT
Found at i:1752284 original size:22 final size:22
Alignment explanation
Indices: 1752238--1752280 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1752228 ACAAAATTAT
*
1752238 TAAATATTTAAATAATATAATA
1 TAAATATTTAAATAATATAAAA
1752260 TAAATATTTTAAA-AAT-TAAAA
1 TAAATA-TTTAAATAATATAAAA
1752281 ATAATATGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATTTAAATAATATAAAA
Found at i:1755373 original size:25 final size:23
Alignment explanation
Indices: 1755339--1755401 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 23
1755329 TTAAAAAAAA
1755339 TAAAATATTTAA-AATATAATTTT
1 TAAAATATTTAATAAT-TAATTTT
1755362 ATATAAATATTTATATAATTAATTTT
1 -TA-AAATATTTA-ATAATTAATTTT
1755388 TAAAATTATTTAAT
1 TAAAA-TATTTAAT
1755402 TTAAATTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
24 7 0.20
25 17 0.49
26 8 0.23
27 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TAAAATATTTAATAATTAATTTT
Found at i:1757462 original size:20 final size:20
Alignment explanation
Indices: 1757438--1757484 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1757428 ATTTAATTTA
*
1757438 ATTGCATTGTGTG-TTGTTT
1 ATTGCATTGGGTGTTTGTTT
1757457 ACTTGC-TTGGGTGTTTGTTT
1 A-TTGCATTGGGTGTTTGTTT
1757477 -TTGCATTG
1 ATTGCATTG
1757485 CGTATGAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 4 0.17
19 10 0.42
20 10 0.42
ACGTcount: A:0.09, C:0.09, G:0.28, T:0.55
Consensus pattern (20 bp):
ATTGCATTGGGTGTTTGTTT
Found at i:1760173 original size:30 final size:30
Alignment explanation
Indices: 1760109--1760181 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
1760099 TTTTAAAATT
* **
1760109 TTTTAAAATTTTAATTATCTCCCTCAAAGT
1 TTTTAAAATTTTAATTATCTCCCTAAAAAC
1760139 TTTTAAAAGTTTTAATTATAC-CCC-AAAAAC
1 TTTTAAAA-TTTTAATTAT-CTCCCTAAAAAC
1760169 TTTTAAAAATTTT
1 TTTT-AAAATTTT
1760182 GATCAGAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
30 19 0.51
31 17 0.46
32 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.03, T:0.45
Consensus pattern (30 bp):
TTTTAAAATTTTAATTATCTCCCTAAAAAC
Found at i:1761775 original size:17 final size:20
Alignment explanation
Indices: 1761739--1761777 Score: 57
Period size: 17 Copynumber: 2.1 Consensus size: 20
1761729 CACGCCATTA
1761739 AATTTAATAGAAGAAATTTT
1 AATTTAATAGAAGAAATTTT
1761759 AATTTAA-A-AAG-AATTTT
1 AATTTAATAGAAGAAATTTT
1761776 AA
1 AA
1761778 AATCTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 3 0.16
19 1 0.05
20 7 0.37
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (20 bp):
AATTTAATAGAAGAAATTTT
Found at i:1763754 original size:24 final size:24
Alignment explanation
Indices: 1763722--1763769 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1763712 TAATACTTTT
*
1763722 AATGCATACAAACTTAAAAAAGAG
1 AATGCATACAAACGTAAAAAAGAG
1763746 AATGCATACAAACGTAAAAAAGAG
1 AATGCATACAAACGTAAAAAAGAG
1763770 CAATCTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.58, C:0.12, G:0.15, T:0.15
Consensus pattern (24 bp):
AATGCATACAAACGTAAAAAAGAG
Found at i:1764021 original size:23 final size:23
Alignment explanation
Indices: 1763993--1764050 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
1763983 ATTATTAAAT
*
1763993 TTATTATATTATATA-ATCTAATA
1 TTATTATATTATATACA-CTAACA
1764016 TTATTAGTA-TATATACACTAACA
1 TTATTA-TATTATATACACTAACA
1764039 TATATTATATTA
1 T-TATTATATTA
1764051 ACAAATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (23 bp):
TTATTATATTATATACACTAACA
Found at i:1766125 original size:24 final size:23
Alignment explanation
Indices: 1766093--1766160 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 23
1766083 TAATTTAACC
*
1766093 TTTTAAAAATTATAAAAATATAA
1 TTTTTAAAATTATAAAAATATAA
* *
1766116 TTTTTTAAAATAATAAAATTAT-A
1 -TTTTTAAAATTATAAAAATATAA
*
1766139 TTTTTACTAA-TATAAAAATATA
1 TTTTTA-AAATTATAAAAATATA
1766161 TAATTTAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
22 15 0.42
23 3 0.08
24 18 0.50
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (23 bp):
TTTTTAAAATTATAAAAATATAA
Found at i:1766162 original size:24 final size:22
Alignment explanation
Indices: 1766103--1766162 Score: 61
Period size: 25 Copynumber: 2.6 Consensus size: 22
1766093 TTTTAAAAAT
1766103 TATAAAAATATA-ATTTTTTAA
1 TATAAAAATATATATTTTTTAA
*
1766124 AATAATAAA-ATTATATTTTTACTAA
1 TATAA-AAATA-TATATTTTT--TAA
1766149 TATAAAAATATATA
1 TATAAAAATATATA
1766163 ATTTAATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
21 5 0.16
22 5 0.16
23 6 0.19
24 7 0.23
25 8 0.26
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TATAAAAATATATATTTTTTAA
Found at i:1768863 original size:4 final size:4
Alignment explanation
Indices: 1768854--1768882 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1768844 AGGTTCTTTG
1768854 ATAA ATAA ATAA ATAA ATAA ATAA A-AA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
1768883 CTCGAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:1777049 original size:25 final size:25
Alignment explanation
Indices: 1777022--1777070 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
1777012 AAAAAGTTAC
1777022 AAATTATAAAAAAATGA-AAAAAATCA
1 AAATT-TAAAAAAAT-ATAAAAAATCA
1777048 AAATTTAAAAAAATATAAAAAAT
1 AAATTTAAAAAAATATAAAAAAT
1777071 GTTCATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 1 0.05
25 16 0.73
26 5 0.23
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (25 bp):
AAATTTAAAAAAATATAAAAAATCA
Found at i:1780786 original size:31 final size:31
Alignment explanation
Indices: 1780751--1780821 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
1780741 TTAATATATT
*
1780751 ATTTGGTATTTGAATTTGGCTTAAACATTCA
1 ATTTGGTATTTGAATTTGACTTAAACATTCA
* * * *
1780782 ATTTGGTACTTGAGTTTGACTTTAATATTCA
1 ATTTGGTATTTGAATTTGACTTAAACATTCA
*
1780813 ATTTAGTAT
1 ATTTGGTAT
1780822 CTAAACCAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.28, C:0.08, G:0.15, T:0.48
Consensus pattern (31 bp):
ATTTGGTATTTGAATTTGACTTAAACATTCA
Found at i:1780972 original size:23 final size:23
Alignment explanation
Indices: 1780942--1780985 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1780932 CATTGAAGCT
1780942 AAATTCAAATACCAAATTGAAAA
1 AAATTCAAATACCAAATTGAAAA
*
1780965 AAATTCAAGTACCAAATTGAA
1 AAATTCAAATACCAAATTGAA
1780986 TATTAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.23
Consensus pattern (23 bp):
AAATTCAAATACCAAATTGAAAA
Found at i:1782006 original size:29 final size:30
Alignment explanation
Indices: 1781968--1782033 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
1781958 TCAGGATTGT
* *
1781968 ATCAAATTAGTCCCTCTATTATT-AAATGA
1 ATCAAATTAGTCCCTCTACTATTAAAAAGA
* *
1781997 ATCAATTTAGTCCCTGTACTATTAAAAAGA
1 ATCAAATTAGTCCCTCTACTATTAAAAAGA
1782027 ATCAAAT
1 ATCAAAT
1782034 AATGCCAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.35
Consensus pattern (30 bp):
ATCAAATTAGTCCCTCTACTATTAAAAAGA
Found at i:1784174 original size:5 final size:5
Alignment explanation
Indices: 1784164--1784189 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1784154 TGATGTTTTA
1784164 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
1784190 TTTAAAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:1792399 original size:31 final size:31
Alignment explanation
Indices: 1792361--1792441 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
1792351 ACCCTATAAA
1792361 TTTTTGAAACTTTTCATTATGCAT-TTTAATT
1 TTTTTGAAACTTTTCATTATGC-TCTTTAATT
*
1792392 TTTTTGAAAAC-TTTAATTATGCTCTTTAATT
1 TTTTTG-AAACTTTTCATTATGCTCTTTAATT
* * *
1792423 TTTTTCAAAATTCTCATTA
1 TTTTTGAAACTTTTCATTA
1792442 ATCTAAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
30 4 0.10
31 34 0.81
32 4 0.10
ACGTcount: A:0.28, C:0.11, G:0.05, T:0.56
Consensus pattern (31 bp):
TTTTTGAAACTTTTCATTATGCTCTTTAATT
Found at i:1793402 original size:2 final size:2
Alignment explanation
Indices: 1793395--1793428 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1793385 TTATACATAC
1793395 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
1793429 TATGGTGGTG
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:1793926 original size:2 final size:2
Alignment explanation
Indices: 1793921--1793961 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1793911 ATCTTTTATG
1793921 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1793962 GATGTTTTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1796302 original size:41 final size:41
Alignment explanation
Indices: 1796250--1796331 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
1796240 CTTTGAAAGC
1796250 TTTGAATTATTATTGGGTTAATGTAATCTTTAGTCCTTGAA
1 TTTGAATTATTATTGGGTTAATGTAATCTTTAGTCCTTGAA
1796291 TTTGAATTATTATTGGGTTAATGTAATCTTTAGTCCTTGAA
1 TTTGAATTATTATTGGGTTAATGTAATCTTTAGTCCTTGAA
1796332 CTTGTCAACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.49
Consensus pattern (41 bp):
TTTGAATTATTATTGGGTTAATGTAATCTTTAGTCCTTGAA
Found at i:1796759 original size:2 final size:2
Alignment explanation
Indices: 1796748--1796777 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1796738 CTTTTTGTTG
1796748 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1796778 CATAATGGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1801502 original size:20 final size:20
Alignment explanation
Indices: 1801465--1801503 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1801455 GAATCATATA
*
1801465 TTTATATAATATACAAAAAC
1 TTTATATAATATAAAAAAAC
1801485 TTTATATAAGT-TAAAAAAA
1 TTTATATAA-TATAAAAAAA
1801504 AAAATTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (20 bp):
TTTATATAATATAAAAAAAC
Found at i:1807899 original size:29 final size:30
Alignment explanation
Indices: 1807845--1807920 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
1807835 CCTTATACTA
* * *
1807845 TTAATAATATAGGGAGTAAATCGATCCA-T
1 TTAATAATAGAGGGATTAAATCGATCAAGT
* *
1807874 TTAATAATAGAGGGATTAATTTGATCAAGT
1 TTAATAATAGAGGGATTAAATCGATCAAGT
*
1807904 TCTTATAATAGAGGGAT
1 T-TAATAATAGAGGGAT
1807921 CTCACATGCA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 23 0.59
30 2 0.05
31 14 0.36
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (30 bp):
TTAATAATAGAGGGATTAAATCGATCAAGT
Found at i:1810198 original size:313 final size:317
Alignment explanation
Indices: 1809502--1810222 Score: 827
Period size: 318 Copynumber: 2.3 Consensus size: 317
1809492 CAAATTTCTT
* * * * *
1809502 AATTCATAAAATAAGAATCAAGATACATGAATCCATACAAGTATTAGTCATACCAATATCAATTA
1 AATTCATGAAACAAGAA-CAAGATACATGAATCCATACAAGTATTAATCACACCAATATCAATCA
* * * * * * * * * *
1809567 GGTTCAGTTATTAACACCATTAAAACGTACAAAGAGCACAGGGATTTGGGTATATTTTAATCTTT
65 AGTCCAATCATTAACACCATTAAAAAGTACAAAGAGCACAGCGACTTGCGAATATTTTAACCTTT
* *
1809632 AAACAGGTTTTGTTTTTCTTCCCCAACTTCATTTCTCAAACCTAATACTTTCATCCAAACCATTC
130 AAACAGGTATTGTTTTGCTTCCCCAACTTCATTTCTCAAACCTAATACTTTCATCCAAA-CATTC
** * *
1809697 ATTCCAAAAAACGAACAAAACTTCGAGCTTGAACAAGTGGGTTGACCCTCGGAAAAGCCTTAAAG
194 ACCCCAAAAAACGAACAAAACTTCGAGCTTGAACAAGTGCGTTGACCCTCGGAAAAGCCCTAAAG
* * *
1809762 GGGGCAACTTGGATCACCAAGATTGGGTGGTCTAAAAATCTGGTTAAACACTACCACAA
259 GGAGCAACTTGGATCACCAAGATTGAGTGGTCTAAAAATATGGTTAAACACTACCACAA
* * * *
1809821 ATTTTATGAAATAAGAACAAGATATATGAATCCATACAAGTATTAATCACACCAATATCAATCAA
1 AATTCATGAAACAAGAACAAGATACATGAATCCATACAAGTATTAATCACACCAATATCAATCAA
* * *
1809886 GTCCAATCGTTAACATCGTTAAAAAGTACAAAGAGCACAGCGACTT-CGAACTATTTTAACCTTT
66 GTCCAATCATTAACACCATTAAAAAGTACAAAGAGCACAGCGACTTGCGAA-TATTTTAACCTTT
* * * * *
1809950 AAA-TGG-ATTGTTGTTGCTTCCTCAACTTTATTTGTCAAATCTAATACTTTCATCC-AA-A-TC
130 AAACAGGTATTGTT-TTGCTTCCCCAACTTCATTTCTCAAACCTAATACTTTCATCCAAACATTC
* *
1810010 ACCCCAAAAGATC-AA-AATGAGTCTTCGAGCTTGAACAAGT-CGTTCGACCCTC-GAACAAGCC
194 ACCCCAAAA-AACGAACAA--A-ACTTCGAGCTTGAACAAGTGCGTT-GACCCTCGGAA-AAGCC
* * * * * *
1810071 CT-AAGGGAGCAGCTTGGATCACCATGATTGAGTTGTCTAAAAATATTGTTAAACCCTACCCCAA
253 CTAAAGGGAGCAACTTGGATCACCAAGATTGAGTGGTCTAAAAATATGGTTAAACACTACCACAA
* *
1810135 AATTCATG-AACAAGAACAAGATACATGAACCCATACAAGTATTAATCACACCAATAACAATCAA
1 AATTCATGAAACAAGAACAAGATACATGAATCCATACAAGTATTAATCACACCAATATCAATCAA
* * *
1810199 TTCTAATTATTAACACCATTAAAA
66 GTCCAATCATTAACACCATTAAAA
1810223 CATACACAAA
Statistics
Matches: 340, Mismatches: 54, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
312 2 0.01
313 81 0.24
314 69 0.20
315 31 0.09
316 7 0.02
317 41 0.12
318 95 0.28
319 14 0.04
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (317 bp):
AATTCATGAAACAAGAACAAGATACATGAATCCATACAAGTATTAATCACACCAATATCAATCAA
GTCCAATCATTAACACCATTAAAAAGTACAAAGAGCACAGCGACTTGCGAATATTTTAACCTTTA
AACAGGTATTGTTTTGCTTCCCCAACTTCATTTCTCAAACCTAATACTTTCATCCAAACATTCAC
CCCAAAAAACGAACAAAACTTCGAGCTTGAACAAGTGCGTTGACCCTCGGAAAAGCCCTAAAGGG
AGCAACTTGGATCACCAAGATTGAGTGGTCTAAAAATATGGTTAAACACTACCACAA
Found at i:1812632 original size:30 final size:30
Alignment explanation
Indices: 1812573--1812632 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1812563 GACTATATCA
* *
1812573 AAAAAAAAATTTAGGGTCGGAAATTTAATT
1 AAAAAAAAATTTAGGGTCGAAAATATAATT
*
1812603 AAAAAAAATTTTAGAGGTC-AAAATATAATT
1 AAAAAAAAATTTAG-GGTCGAAAATATAATT
1812633 TATCTTGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.30
Consensus pattern (30 bp):
AAAAAAAAATTTAGGGTCGAAAATATAATT
Found at i:1814321 original size:19 final size:20
Alignment explanation
Indices: 1814284--1814322 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1814274 AGAAGGATAA
*
1814284 CATCATCTTTATTTGTTTTT
1 CATCATCTTTATTTCTTTTT
*
1814304 CATC-TCTTTTTTTCTTTTT
1 CATCATCTTTATTTCTTTTT
1814323 TTTTTCCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.10, C:0.18, G:0.03, T:0.69
Consensus pattern (20 bp):
CATCATCTTTATTTCTTTTT
Found at i:1814334 original size:20 final size:20
Alignment explanation
Indices: 1814311--1814360 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1814301 TTTCATCTCT
* *
1814311 TTTTTTCTTTTTTTTTTCCC
1 TTTTTTCTTATTTTTATCCC
* *
1814331 TTTTTTGTAATTTTTATCCC
1 TTTTTTCTTATTTTTATCCC
1814351 TTTTTATCTT
1 TTTTT-TCTT
1814361 GTTTCATTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.08, C:0.16, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTTTCTTATTTTTATCCC
Found at i:1817925 original size:4 final size:4
Alignment explanation
Indices: 1817918--1817944 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1817908 ATATGTATAT
1817918 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1817945 TATATATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1820873 original size:3 final size:3
Alignment explanation
Indices: 1820859--1820899 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
1820849 ACCACACAAT
*
1820859 TGA TGT TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1820900 GTAGCAGCAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.29, C:0.00, G:0.34, T:0.37
Consensus pattern (3 bp):
TGA
Found at i:1832632 original size:15 final size:15
Alignment explanation
Indices: 1832612--1832642 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1832602 AGCAATAAAC
1832612 AATTACCTGACCAGT
1 AATTACCTGACCAGT
1832627 AATTACCTGACCAGT
1 AATTACCTGACCAGT
1832642 A
1 A
1832643 CTCTCGAGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (15 bp):
AATTACCTGACCAGT
Found at i:1834305 original size:16 final size:17
Alignment explanation
Indices: 1834284--1834320 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1834274 CTAGCTTGAA
*
1834284 TTTTAAAT-TTTTTATT
1 TTTTAAATATTTTAATT
1834300 TTTT-AATATTTTAATT
1 TTTTAAATATTTTAATT
1834316 TTTTA
1 TTTTA
1834321 GATACATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTAAATATTTTAATT
Found at i:1834785 original size:31 final size:31
Alignment explanation
Indices: 1834738--1834798 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1834728 AGAGAATGCC
*
1834738 CAAAATATAAACGATCTAAAACGTGAGTGAA
1 CAAAATAGAAACGATCTAAAACGTGAGTGAA
* *
1834769 CAAAATAGAAATGATCTAAAACGTTAGTGA
1 CAAAATAGAAACGATCTAAAACGTGAGTGA
1834799 CTAAATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.21
Consensus pattern (31 bp):
CAAAATAGAAACGATCTAAAACGTGAGTGAA
Found at i:1834959 original size:8 final size:8
Alignment explanation
Indices: 1834946--1834974 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1834936 CTGAATCTTA
1834946 TTTTTTCT
1 TTTTTTCT
1834954 TTTTTTCT
1 TTTTTTCT
1834962 TTTTTTCT
1 TTTTTTCT
1834970 TTTTT
1 TTTTT
1834975 GTGATGGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTCT
Done.