Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 26 of 120
Found at i:6768654 original size:16 final size:17
Alignment explanation
Indices: 6768622--6768654 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6768612 AATCTAAATC
6768622 AAATAAAAATGATACAAT
1 AAATAAAAA-GATACAAT
6768640 AAATAAAAA-ATACAA
1 AAATAAAAAGATACAA
6768655 AAACTTAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (17 bp):
AAATAAAAAGATACAAT
Found at i:6772605 original size:6 final size:6
Alignment explanation
Indices: 6772594--6772621 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
6772584 TCGACTCTCT
6772594 CACCGC CACCGC CACCGC CACCGC CACC
1 CACCGC CACCGC CACCGC CACCGC CACC
6772622 ATCACTCGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.68, G:0.14, T:0.00
Consensus pattern (6 bp):
CACCGC
Found at i:6775435 original size:29 final size:29
Alignment explanation
Indices: 6775402--6775467 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
6775392 AATAGTTCAT
*
6775402 AATTTTATAATTTTAAAAAATTAAATTAA
1 AATTTTATAATTTTAAAAAATTAAAGTAA
* * * *
6775431 AATTTTATGATTTTAAGAGATTAAAGTAT
1 AATTTTATAATTTTAAAAAATTAAAGTAA
6775460 AATTTTAT
1 AATTTTAT
6775468 TTTTATTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (29 bp):
AATTTTATAATTTTAAAAAATTAAAGTAA
Found at i:6776460 original size:18 final size:18
Alignment explanation
Indices: 6776437--6776471 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6776427 AACAATTTTA
*
6776437 TTTCTTCTCTTTCTCATT
1 TTTCTTATCTTTCTCATT
6776455 TTTCTTATCTTTCTCAT
1 TTTCTTATCTTTCTCAT
6776472 CATAATATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTCTTATCTTTCTCATT
Found at i:6776539 original size:15 final size:15
Alignment explanation
Indices: 6776519--6776549 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6776509 GTCGTCATCT
6776519 TCATCATCATAATAA
1 TCATCATCATAATAA
*
6776534 TCATCATCGTAATAA
1 TCATCATCATAATAA
6776549 T
1 T
6776550 ATTCTTCATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.35
Consensus pattern (15 bp):
TCATCATCATAATAA
Found at i:6776540 original size:18 final size:18
Alignment explanation
Indices: 6776519--6776564 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
6776509 GTCGTCATCT
6776519 TCATCATCATAATAATCA
1 TCATCATCATAATAATCA
* * * *
6776537 TCATCGTAATAATATTCT
1 TCATCATCATAATAATCA
6776555 TCATCATCAT
1 TCATCATCAT
6776565 CGTCATCACC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.39
Consensus pattern (18 bp):
TCATCATCATAATAATCA
Found at i:6780621 original size:13 final size:13
Alignment explanation
Indices: 6780588--6780614 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6780578 TTACACACTT
6780588 TAGTCTTATATCA
1 TAGTCTTATATCA
6780601 TAGTCTTATATCA
1 TAGTCTTATATCA
6780614 T
1 T
6780615 TTTCTTACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (13 bp):
TAGTCTTATATCA
Found at i:6781453 original size:28 final size:31
Alignment explanation
Indices: 6781415--6781489 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 31
6781405 AAAAAAAGAA
*
6781415 TTATCAATTTTTAAGGGT-TCCAATTT-TTAT
1 TTAT-AATTTTTAAGGGTCTCAAATTTATTAT
*
6781445 TT-TAATTTTTAAGGGTCTCAAATTTATTTT
1 TTATAATTTTTAAGGGTCTCAAATTTATTAT
6781475 TTACTAATTTTTAAG
1 TTA-TAATTTTTAAG
6781490 AGACCAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 13 0.33
29 8 0.21
30 7 0.18
32 11 0.28
ACGTcount: A:0.28, C:0.08, G:0.09, T:0.55
Consensus pattern (31 bp):
TTATAATTTTTAAGGGTCTCAAATTTATTAT
Found at i:6781506 original size:31 final size:32
Alignment explanation
Indices: 6781447--6781507 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
6781437 ATTTTTATTT
* *
6781447 TAATTTTTAAGGGTCTCAAATTTATTTTTTAC
1 TAATTTTTAAGAGACTCAAATTTATTTTTTAC
*
6781479 TAATTTTTAAGAGAC-CAAATTTTTTTTTT
1 TAATTTTTAAGAGACTCAAATTTATTTTTT
6781508 CAACTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.54
Consensus pattern (32 bp):
TAATTTTTAAGAGACTCAAATTTATTTTTTAC
Found at i:6781997 original size:15 final size:15
Alignment explanation
Indices: 6781932--6781999 Score: 50
Period size: 15 Copynumber: 4.4 Consensus size: 15
6781922 ATATTATTGA
6781932 AAATAT-TTAAT-AT
1 AAATATATTAATAAT
* * *
6781945 TAATATTTTATTAAT
1 AAATATATTAATAAT
*
6781960 AAATATTTATTACAATTAT
1 AAATA--TATT--AATAAT
6781979 AAATATATTAATAAT
1 AAATATATTAATAAT
6781994 AAATAT
1 AAATAT
6782000 TTTGTAATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
13 5 0.12
14 4 0.10
15 17 0.40
17 7 0.17
19 9 0.21
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATATATTAATAAT
Found at i:6782431 original size:27 final size:27
Alignment explanation
Indices: 6782401--6782467 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
6782391 GGTGCCCATT
6782401 TGACAGGCGGCACTAGAGGTGCCTACC
1 TGACAGGCGGCACTAGAGGTGCCTACC
* *
6782428 TGACAGGCGGCATTAGAGGTGCCTATC
1 TGACAGGCGGCACTAGAGGTGCCTACC
*
6782455 TGACAGGCAGCAC
1 TGACAGGCGGCAC
6782468 CAAAGGCAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.24, C:0.27, G:0.33, T:0.16
Consensus pattern (27 bp):
TGACAGGCGGCACTAGAGGTGCCTACC
Found at i:6784898 original size:15 final size:15
Alignment explanation
Indices: 6784858--6784898 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
6784848 AACCCGTATC
6784858 AATA-TTTTT-TTTA
1 AATATTTTTTATTTA
*
6784871 AAT-TTTATTATTTA
1 AATATTTTTTATTTA
6784885 AATATTTTTTATTT
1 AATATTTTTTATTT
6784899 GTTTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 7 0.30
14 7 0.30
15 9 0.39
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
AATATTTTTTATTTA
Found at i:6786200 original size:14 final size:14
Alignment explanation
Indices: 6786181--6786207 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6786171 GTGTGATATT
6786181 AAATTTTGTTTATG
1 AAATTTTGTTTATG
6786195 AAATTTTGTTTAT
1 AAATTTTGTTTAT
6786208 TAGACAATCA
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:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (14 bp):
AAATTTTGTTTATG
Found at i:6798175 original size:15 final size:14
Alignment explanation
Indices: 6798156--6798243 Score: 54
Period size: 15 Copynumber: 6.0 Consensus size: 14
6798146 TAATTCATAT
6798156 TTTAATAATAATTA
1 TTTAATAATAATTA
*
6798170 TATTAAAAAT-ATTA
1 T-TTAATAATAATTA
* *
6798184 TTAAATTATATATTA
1 TTTAATAATA-ATTA
* *
6798199 TTTTATTAA-ATTGTA
1 -TTTAATAATAAT-TA
6798214 TTTAATAATAATTA
1 TTTAATAATAATTA
*
6798228 TGTTAAAATATAATTA
1 T-TTAATA-ATAATTA
6798244 AATAAATTAA
Statistics
Matches: 55, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
13 5 0.09
14 17 0.31
15 21 0.38
16 12 0.22
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TTTAATAATAATTA
Found at i:6798273 original size:57 final size:58
Alignment explanation
Indices: 6798147--6798282 Score: 163
Period size: 58 Copynumber: 2.3 Consensus size: 58
6798137 CATTTTTACT
*
6798147 AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAATTATATATTATTTTATTA
1 AATT-ATA-TTTAATAATAATTATATTAAAAATATTAATAAATTATATATTATTTTATTA
* *
6798207 AATTGTATTTAATAATAATTATGTTAAAATATAATTAAATAAATTA-A-ATT-TTTT-TTA
1 AATTATATTTAATAATAATTATATTAAAA-AT-ATT-AATAAATTATATATTATTTTATTA
*
6798264 CATTATATTTAATAATAAT
1 AATTATATTTAATAATAAT
6798283 CATTAAAATA
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
57 20 0.29
58 25 0.37
59 7 0.10
60 8 0.12
61 8 0.12
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (58 bp):
AATTATATTTAATAATAATTATATTAAAAATATTAATAAATTATATATTATTTTATTA
Found at i:6801930 original size:58 final size:58
Alignment explanation
Indices: 6801842--6801987 Score: 174
Period size: 58 Copynumber: 2.5 Consensus size: 58
6801832 ATATATTATA
* *
6801842 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAA-AT-ATT-ATTAAATTACAT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAATATAATTAAATAAATTA-AT
* *
6801899 ATTATTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATAAATTAAT
1 A-T-TTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
*
6801959 ATTTTTATTCAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
6801988 CATTAAAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
57 1 0.01
58 47 0.61
59 11 0.14
60 10 0.13
61 8 0.10
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
Found at i:6802126 original size:39 final size:44
Alignment explanation
Indices: 6802071--6802175 Score: 114
Period size: 46 Copynumber: 2.5 Consensus size: 44
6802061 TTTCTTATGC
*
6802071 TATTACAGCATC-ATTCCATT-CAACCAA-ACACAA-GAA-TA-T
1 TATTACAGC-TCTATTCCATTCCAACCAACAAACAATGAATTACT
*
6802110 TATTACAGCTCTATTCCATTCCAATCAACCAAACAATTGAATTACT
1 TATTACAGCTCTATTCCATTCCAACCAA-CAAACAA-TGAATTACT
*
6802156 GATTACAGCTCTATTCCATT
1 TATTACAGCTCTATTCCATT
6802176 ACAGCTATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
38 2 0.04
39 17 0.31
40 6 0.11
42 5 0.09
44 3 0.05
45 2 0.04
46 20 0.36
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (44 bp):
TATTACAGCTCTATTCCATTCCAACCAACAAACAATGAATTACT
Found at i:6802174 original size:46 final size:44
Alignment explanation
Indices: 6802082--6802175 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
6802072 ATTACAGCAT
* *
6802082 CATTCCATTCAACCAAACACAAGAATATTATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
*
6802126 CATTCCAATCAACCAAACA-ATTGAATTACTGATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACA-AGAA-TA-TGATTACAGCTCTATTC
6802172 CATT
1 CATT
6802176 ACAGCTATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 21 0.48
45 2 0.05
46 20 0.45
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
Found at i:6802178 original size:16 final size:16
Alignment explanation
Indices: 6802157--6802212 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
6802147 TGAATTACTG
6802157 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
6802173 ATTACAGCTATATTCC
1 ATTACAGCTCTATTCC
*
6802189 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
6802205 ATTACAGC
1 ATTACAGC
6802213 GAACCAAACG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.29, C:0.30, G:0.05, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:6806428 original size:25 final size:25
Alignment explanation
Indices: 6806399--6806448 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
6806389 TTCTAAGAGA
6806399 ATACTTTTGAATATGTAAACTAAAT
1 ATACTTTTGAATATGTAAACTAAAT
6806424 ATACTTTTGAATATGTAAACTAAAT
1 ATACTTTTGAATATGTAAACTAAAT
6806449 TTATTTTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (25 bp):
ATACTTTTGAATATGTAAACTAAAT
Found at i:6808381 original size:17 final size:16
Alignment explanation
Indices: 6808361--6808403 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
6808351 TTTTGGGACA
6808361 AAAAATATTTATAAAAT
1 AAAAATATTT-TAAAAT
6808378 AAAAATATTGTT-AAAT
1 AAAAATATT-TTAAAAT
6808394 -AAAATATTTT
1 AAAAATATTTT
6808404 TAAACTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.08
15 8 0.32
16 4 0.16
17 10 0.40
18 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AAAAATATTTTAAAAT
Found at i:6808399 original size:15 final size:16
Alignment explanation
Indices: 6808361--6808407 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
6808351 TTTTGGGACA
6808361 AAAAATATT-TATAAAAT
1 AAAAATATTGT-T-AAAT
6808378 AAAAATATTGTTAAAT
1 AAAAATATTGTTAAAT
*
6808394 -AAAATATTTTTAAA
1 AAAAATATTGTTAAA
6808408 CTTTTCAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 13 0.46
16 4 0.14
17 10 0.36
18 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
AAAAATATTGTTAAAT
Found at i:6808511 original size:17 final size:16
Alignment explanation
Indices: 6808485--6808524 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
6808475 AAAAATTTTA
*
6808485 ATTTTTACTCAGAAAT
1 ATTTTTACTCAAAAAT
6808501 ATTTTTGACTCAAAAAT
1 ATTTTT-ACTCAAAAAT
*
6808518 ACTTTTA
1 ATTTTTA
6808525 AAATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (16 bp):
ATTTTTACTCAAAAAT
Found at i:6810257 original size:36 final size:36
Alignment explanation
Indices: 6810216--6810307 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 36
6810206 CTTTTGAACG
* *
6810216 AGATATCATGTCTTCTCAATCCCAAGCTCCTGAGC-
1 AGATATCATGTCTTCTCAATCCCAAGCTCCTAAACT
*
6810251 ATGATATCAAGTCTTC-C--T---AAGCTCCTAAACT
1 A-GATATCATGTCTTCTCAATCCCAAGCTCCTAAACT
6810282 AGATATCATGTCTTCTCAATCCCAAG
1 AGATATCATGTCTTCTCAATCCCAAG
6810308 ATCTTGAACG
Statistics
Matches: 45, Mismatches: 4, Indels: 15
0.70 0.06 0.23
Matches are distributed among these distances:
30 23 0.51
31 2 0.04
33 2 0.04
35 2 0.04
36 16 0.36
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.30
Consensus pattern (36 bp):
AGATATCATGTCTTCTCAATCCCAAGCTCCTAAACT
Found at i:6810337 original size:30 final size:30
Alignment explanation
Indices: 6810301--6810367 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
6810291 GTCTTCTCAA
*
6810301 TCCCAAGATCTTGAACGAGATATCGAGTCT
1 TCCCAAGATCTTGAACAAGATATCGAGTCT
* * *
6810331 TCCCAAGCTCTTGAACAAGATATTGGGTCT
1 TCCCAAGATCTTGAACAAGATATCGAGTCT
*
6810361 TCTCAAG
1 TCCCAAG
6810368 TTCCTAAACG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (30 bp):
TCCCAAGATCTTGAACAAGATATCGAGTCT
Found at i:6810366 original size:66 final size:66
Alignment explanation
Indices: 6810196--6810353 Score: 210
Period size: 66 Copynumber: 2.4 Consensus size: 66
6810186 AAATATTGGA
* * * *
6810196 TCTTCCCAAGCTTTTGAACGAGATATCATGTCTTCTCAATCCCAAGCTCCTGAGCATGATATCAA
1 TCTTCCCAAGCTCTTGAACAAGATATCATGTCTTCTCAATCCCAAGATCCTGAACATGATATCAA
6810261 G
66 G
* * * * * *
6810262 TCTTCCTAAGCTCCTAAACTAGATATCATGTCTTCTCAATCCCAAGATCTTGAACGA-GATATCG
1 TCTTCCCAAGCTCTTGAACAAGATATCATGTCTTCTCAATCCCAAGATCCTGAAC-ATGATATCA
6810326 AG
65 AG
6810328 TCTTCCCAAGCTCTTGAACAAGATAT
1 TCTTCCCAAGCTCTTGAACAAGATAT
6810354 TGGGTCTTCT
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
66 77 0.99
67 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (66 bp):
TCTTCCCAAGCTCTTGAACAAGATATCATGTCTTCTCAATCCCAAGATCCTGAACATGATATCAA
G
Found at i:6811516 original size:35 final size:35
Alignment explanation
Indices: 6811470--6811542 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
6811460 GGAATTCTAC
6811470 CAATACCATATTTCACCATTAGAGTTCTACCGGTA
1 CAATACCATATTTCACCATTAGAGTTCTACCGGTA
6811505 CAATACCATATTTCACCATTAGAGTTCTACCGGTA
1 CAATACCATATTTCACCATTAGAGTTCTACCGGTA
6811540 CAA
1 CAA
6811543 ATGGAGAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.30
Consensus pattern (35 bp):
CAATACCATATTTCACCATTAGAGTTCTACCGGTA
Found at i:6819152 original size:6 final size:6
Alignment explanation
Indices: 6819150--6819183 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
6819140 TGCTCACGCT
6819150 CACTCA CACTCA CACTCA CACTCA CACTCA CACT
1 CACTCA CACTCA CACTCA CACTCA CACTCA CACT
6819184 TATTTGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (6 bp):
CACTCA
Found at i:6823612 original size:32 final size:32
Alignment explanation
Indices: 6823549--6823614 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
6823539 TATCACAGTA
* * *
6823549 TTTTTATAATTTTTTAAATGATTAAATAAATT
1 TTTTTATAATTTTTGAAAAGATAAAATAAATT
*
6823581 TTTTTATCA-TTTTGAAAAGATAAAATGAAATT
1 TTTTTATAATTTTTGAAAAGATAAAAT-AAATT
6823613 TT
1 TT
6823615 ATCATATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 14 0.48
32 15 0.52
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (32 bp):
TTTTTATAATTTTTGAAAAGATAAAATAAATT
Found at i:6833841 original size:2 final size:2
Alignment explanation
Indices: 6833836--6833875 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
6833826 AAAAAAAAAA
6833836 AT 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 AT
6833876 GCCTTTGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6834551 original size:14 final size:14
Alignment explanation
Indices: 6834532--6834558 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6834522 TCAGATTCTG
6834532 AAAACTAGAAATGT
1 AAAACTAGAAATGT
6834546 AAAACTAGAAATG
1 AAAACTAGAAATG
6834559 AACTTTCCTC
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:0.59, C:0.07, G:0.15, T:0.19
Consensus pattern (14 bp):
AAAACTAGAAATGT
Found at i:6834954 original size:230 final size:225
Alignment explanation
Indices: 6834556--6834984 Score: 639
Period size: 230 Copynumber: 1.9 Consensus size: 225
6834546 AAAACTAGAA
*
6834556 ATGAACTTTCCTCTAAGTGGTGGTTGTGTACCAAGTGCATAATGTCACTGCAGAGCTCATTATAC
1 ATGAACTTTCCTCTAAGTGGTGGTTGTGTACCAAGTGCATAATGTCACTGCAGAGATCATTATAC
* * * *
6834621 CGTAAACTACAGGTAACAACCTCTGTGCACTGGAATTGCACAGTAAGGCCTCACAATCTATTGGT
66 CGAAAACTACAGGTAACAACCCCTGTGCACTGGAATTGCACAGCAAGGCATCACAATCTATTGGT
** * *
6834686 TGCTGTTTCTATGTGCAACAATATAGGACGAAAGCAACTAATAGTTACACTACCCCACCCTCCCA
131 TGCTGTTTCTATGCCCAACAATATAGGACGAAAGCAACTAAAAGTTACACTACCCCACCATCCCA
6834751 TAAGTTTTGCCTACTATTTGCTTGACTTGC
196 TAAGTTTTGCCTACTATTTGCTTGACTTGC
* **
6834781 ATGAACTTTCCTTTAAGTGGTGGTTGTGTAATGAA-TGCATAATGTTCACTGCAGCA-ATCATTA
1 ATGAACTTTCCTCTAAGTGGTGGTTGTGT-ACCAAGTGCATAATG-TCACTGCAG-AGATCATTA
*
6834844 TACCGAAAACTACAGGTAACAAACAACCCCTGTGCACTGGAATTGCACAGCAAGTCATCACAATC
63 TACCGAAAACTACAGGT----AACAACCCCTGTGCACTGGAATTGCACAGCAAGGCATCACAATC
6834909 TATTGGTTGCTG-TTCTTATGCCCAACAATATAGGACGAAAGCAACTAAAAGTTACACTACCCCA
124 TATTGGTTGCTGTTTC-TATGCCCAACAATATAGGACGAAAGCAACTAAAAGTTACACTACCCCA
*
6834973 TCATCCCATAAG
188 CCATCCCATAAG
6834985 GATTATGATT
Statistics
Matches: 182, Mismatches: 14, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
225 37 0.20
226 34 0.19
227 1 0.01
229 3 0.02
230 107 0.59
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (225 bp):
ATGAACTTTCCTCTAAGTGGTGGTTGTGTACCAAGTGCATAATGTCACTGCAGAGATCATTATAC
CGAAAACTACAGGTAACAACCCCTGTGCACTGGAATTGCACAGCAAGGCATCACAATCTATTGGT
TGCTGTTTCTATGCCCAACAATATAGGACGAAAGCAACTAAAAGTTACACTACCCCACCATCCCA
TAAGTTTTGCCTACTATTTGCTTGACTTGC
Found at i:6837631 original size:29 final size:29
Alignment explanation
Indices: 6837598--6837662 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
6837588 ACAACATATT
6837598 AACATAAGTGAATAAAACGTAACATTTCA
1 AACATAAGTGAATAAAACGTAACATTTCA
* *
6837627 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGAATAAAACGTAACATTTCA
6837656 AACATAA
1 AACATAA
6837663 ATAACTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.52, C:0.14, G:0.09, T:0.25
Consensus pattern (29 bp):
AACATAAGTGAATAAAACGTAACATTTCA
Found at i:6837669 original size:29 final size:29
Alignment explanation
Indices: 6837610--6837678 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
6837600 CATAAGTGAA
* * *
6837610 TAAAACGTAACATTTCAAACATAAGTGAC
1 TAAAATGTAACATTTCAAACATAAATAAC
6837639 TAAAATGTAACATTTCAAACATAAATAAC
1 TAAAATGTAACATTTCAAACATAAATAAC
*
6837668 TAAAATATAAC
1 TAAAATGTAAC
6837679 TTGAGGTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.54, C:0.14, G:0.06, T:0.26
Consensus pattern (29 bp):
TAAAATGTAACATTTCAAACATAAATAAC
Found at i:6838652 original size:20 final size:21
Alignment explanation
Indices: 6838614--6838654 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
6838604 AAAAAAAAAA
*
6838614 TCATGTTTTTGTTGCTGTTTT
1 TCATGTTTTTGTTACTGTTTT
*
6838635 TCATG-TTTTGTTATTGTTTT
1 TCATGTTTTTGTTACTGTTTT
6838655 CTTACTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.07, C:0.07, G:0.17, T:0.68
Consensus pattern (21 bp):
TCATGTTTTTGTTACTGTTTT
Found at i:6840726 original size:17 final size:17
Alignment explanation
Indices: 6840704--6840738 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
6840694 ATTAAGAATC
6840704 GGATTGAATTTATTTAA
1 GGATTGAATTTATTTAA
6840721 GGATTGAATTTATTTAA
1 GGATTGAATTTATTTAA
6840738 G
1 G
6840739 TATGAAGGGA
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:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (17 bp):
GGATTGAATTTATTTAA
Found at i:6841195 original size:2 final size:2
Alignment explanation
Indices: 6841188--6841221 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6841178 TTATTGAAAA
6841188 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
6841222 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:6841226 original size:2 final size:2
Alignment explanation
Indices: 6841221--6841257 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
6841211 TCTCTCTCTC
*
6841221 TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
6841258 GCATGTGAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6850013 original size:9 final size:9
Alignment explanation
Indices: 6849999--6850032 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
6849989 TTAATTTTAT
6849999 AATACATTA
1 AATACATTA
6850008 AATACATTA
1 AATACATTA
6850017 AATACATTA
1 AATACATTA
6850026 AAT-CATT
1 AATACATT
6850033 TTTACATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.16
9 21 0.84
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (9 bp):
AATACATTA
Found at i:6850079 original size:18 final size:19
Alignment explanation
Indices: 6850049--6850084 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
6850039 TATTAAATCA
6850049 TATTTTCATGTATTTAATG
1 TATTTTCATGTATTTAATG
6850068 TATTTT-ATGTATTTAAT
1 TATTTTCATGTATTTAAT
6850085 AGTTGAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.61
Consensus pattern (19 bp):
TATTTTCATGTATTTAATG
Found at i:6855162 original size:6 final size:6
Alignment explanation
Indices: 6855153--6855187 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
6855143 CCAAAATTAA
6855153 AAATGG AAATGG AAATGG AAATGG AAATGG AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATG
6855188 ATTCATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:6855374 original size:25 final size:25
Alignment explanation
Indices: 6855334--6855405 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 25
6855324 ATATTTTCTC
*
6855334 AAAATTTTATCGGGGGTTAAATCGA-A
1 AAAATTTTATC-GGGGTAAAATC-ATA
*
6855360 AAAATTTTATCGGGGTAAAATCATC
1 AAAATTTTATCGGGGTAAAATCATA
*
6855385 AAAATTTTATTGGGGTAAAAT
1 AAAATTTTATCGGGGTAAAAT
6855406 AAGGATGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
24 1 0.02
25 30 0.71
26 11 0.26
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.33
Consensus pattern (25 bp):
AAAATTTTATCGGGGTAAAATCATA
Found at i:6855969 original size:37 final size:37
Alignment explanation
Indices: 6855928--6856008 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 37
6855918 TGCCACTAAA
6855928 ATTGTTAAACTAAAAGCATGTTAAACAGGTCACTGAG
1 ATTGTTAAACTAAAAGCATGTTAAACAGGTCACTGAG
* * * * *
6855965 ATTGTTAAACTGAAAGCATGTTAAGCATGTCATTGAT
1 ATTGTTAAACTAAAAGCATGTTAAACAGGTCACTGAG
6856002 ATTGTTA
1 ATTGTTA
6856009 TCGTTACCGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (37 bp):
ATTGTTAAACTAAAAGCATGTTAAACAGGTCACTGAG
Found at i:6857160 original size:49 final size:49
Alignment explanation
Indices: 6857057--6857166 Score: 123
Period size: 49 Copynumber: 2.2 Consensus size: 49
6857047 TAATGTAGAT
** * *
6857057 AAGCCACCAGGTAACGCAGACAAGCTTCTAGAAACAGAATATTGTGGTT
1 AAGCCACCAAATAATGCAGACAAGCTTCTAGAAACAGAATATTGTGGTC
* * * * *
6857106 GAGCCATCAAATAATGCAGTCAAGCTAT-TAGATACAGAATATTTTGGTC
1 AAGCCACCAAATAATGCAGACAAGCT-TCTAGAAACAGAATATTGTGGTC
6857155 AAGCCACCAAAT
1 AAGCCACCAAAT
6857167 TTGTTGATAT
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
49 48 0.98
50 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (49 bp):
AAGCCACCAAATAATGCAGACAAGCTTCTAGAAACAGAATATTGTGGTC
Found at i:6865627 original size:15 final size:16
Alignment explanation
Indices: 6865559--6865637 Score: 83
Period size: 15 Copynumber: 5.1 Consensus size: 16
6865549 TTCACTATAG
* *
6865559 TTTCAAAATCTATAGT
1 TTTCACAATCTAAAGT
*
6865575 TTTCAAAATCTAAA-T
1 TTTCACAATCTAAAGT
* *
6865590 TTTCACAGTCTATAG-
1 TTTCACAATCTAAAGT
6865605 TTTCACAATCTAAAGT
1 TTTCACAATCTAAAGT
*
6865621 TTT-ACAATTTAAAGT
1 TTTCACAATCTAAAGT
6865636 TT
1 TT
6865638 CAATATATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
15 38 0.70
16 16 0.30
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (16 bp):
TTTCACAATCTAAAGT
Found at i:6866379 original size:20 final size:19
Alignment explanation
Indices: 6866351--6866388 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
6866341 ATCTCAAACC
6866351 ACAATCCAAAATAATAATA
1 ACAATCCAAAATAATAATA
*
6866370 ACAATACCAAAATACTAAT
1 ACAAT-CCAAAATAATAAT
6866389 TATTTAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.21
Consensus pattern (19 bp):
ACAATCCAAAATAATAATA
Found at i:6866817 original size:48 final size:49
Alignment explanation
Indices: 6866743--6866860 Score: 132
Period size: 48 Copynumber: 2.4 Consensus size: 49
6866733 ATATGACACT
* * * * *
6866743 AATAATGTGGACAAGCCACCATATAATGC-ATCCAAGTTGCTAGAAATAA
1 AATATTGTGGACAAGCCACCAGATAATACAAT-CAAGCTGCCAGAAATAA
* *
6866792 AATATTGTGG-CAAGCCACTAGATAATACAATCAAGCTGCCAGATATAA
1 AATATTGTGGACAAGCCACCAGATAATACAATCAAGCTGCCAGAAATAA
* *
6866840 AATATTATGGTCAAGCCACCA
1 AATATTGTGGACAAGCCACCA
6866861 CTTTTGCAGG
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
48 38 0.66
49 20 0.34
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (49 bp):
AATATTGTGGACAAGCCACCAGATAATACAATCAAGCTGCCAGAAATAA
Found at i:6867086 original size:35 final size:35
Alignment explanation
Indices: 6867041--6867135 Score: 127
Period size: 35 Copynumber: 2.7 Consensus size: 35
6867031 AATTTATCAC
* *
6867041 AGTGACATGCTTTACATGCGAATCAGAATCAATAT
1 AGTGGCATGCTTAACATGCGAATCAGAATCAATAT
**
6867076 AGTGGCATGCTTAACATGCGAATCAGAATCGGTAT
1 AGTGGCATGCTTAACATGCGAATCAGAATCAATAT
* * *
6867111 AATGGCATGCTTAATATGCAAATCA
1 AGTGGCATGCTTAACATGCGAATCA
6867136 AAATATCAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (35 bp):
AGTGGCATGCTTAACATGCGAATCAGAATCAATAT
Found at i:6875440 original size:51 final size:51
Alignment explanation
Indices: 6875363--6875492 Score: 206
Period size: 51 Copynumber: 2.5 Consensus size: 51
6875353 TAGACGAAAG
* * *
6875363 GGTCCGATGACTAAGTGTCATCGTGAGTGAATGAATCCTTTATGGATTAAT
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTGTATGGATTAAA
* *
6875414 GGTCCAATGACTAAGTGTCATTGTGAGTAAATGAATCCTGTATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTGTATGGATTAAA
*
6875465 GCTCCGATGACTAAGTGTCATCGTGAGT
1 GGTCCGATGACTAAGTGTCATCGTGAGT
6875493 TTATAGATTC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 71 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTGTATGGATTAAA
Found at i:6877022 original size:26 final size:26
Alignment explanation
Indices: 6876982--6877136 Score: 88
Period size: 25 Copynumber: 6.1 Consensus size: 26
6876972 GTCTTCCAAA
* * *
6876982 AATTTAGCTCATACGAGCCTAGATAG
1 AATTTAGCTCTTACGAGCCCAGACAG
*
6877008 AGTTTAGCTCTTACGAGCCCAGACAG
1 AATTTAGCTCTTACGAGCCCAGACAG
* * * *
6877034 AATATCGCTCTTACGAG-CCAGTCAA
1 AATTTAGCTCTTACGAGCCCAGACAG
* * ** * *
6877059 AATATCGCTCTTATAAG-TCAAACAG
1 AATTTAGCTCTTACGAGCCCAGACAG
* *
6877084 AATATCA-CTCTTACGAG-CCAAACAG
1 AAT-TTAGCTCTTACGAGCCCAGACAG
* *
6877109 AATATCA-CTCTTACGAG-CCAAACAG
1 AAT-TTAGCTCTTACGAGCCCAGACAG
6877134 AAT
1 AAT
6877137 AACGCTCCTT
Statistics
Matches: 107, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
25 71 0.66
26 36 0.34
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (26 bp):
AATTTAGCTCTTACGAGCCCAGACAG
Found at i:6877062 original size:25 final size:25
Alignment explanation
Indices: 6877014--6877151 Score: 161
Period size: 25 Copynumber: 5.5 Consensus size: 25
6877004 ATAGAGTTTA
*
6877014 GCTCTTACGAGCCCAGACAGAATATC
1 GCTCTTACGAG-CCAAACAGAATATC
** *
6877040 GCTCTTACGAGCCAGTCAAAATATC
1 GCTCTTACGAGCCAAACAGAATATC
** *
6877065 GCTCTTATAAGTCAAACAGAATATC
1 GCTCTTACGAGCCAAACAGAATATC
*
6877090 ACTCTTACGAGCCAAACAGAATATC
1 GCTCTTACGAGCCAAACAGAATATC
* *
6877115 ACTCTTACGAGCCAAACAGAATAAC
1 GCTCTTACGAGCCAAACAGAATATC
6877140 GCTCCTT-CGAGC
1 GCT-CTTACGAGC
6877152 TAGAATCAGA
Statistics
Matches: 97, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
25 83 0.86
26 14 0.14
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (25 bp):
GCTCTTACGAGCCAAACAGAATATC
Found at i:6882232 original size:16 final size:15
Alignment explanation
Indices: 6882211--6882240 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
6882201 CAAATAAATA
6882211 AAAAATAAAAATAAAC
1 AAAAAT-AAAATAAAC
6882227 AAAAATAAAATAAA
1 AAAAATAAAATAAA
6882241 AATAAAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAAATAAAATAAAC
Found at i:6882236 original size:21 final size:21
Alignment explanation
Indices: 6882212--6882251 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6882202 AAATAAATAA
6882212 AAAATAAAAATAAACAAAAAT
1 AAAATAAAAATAAACAAAAAT
*
6882233 AAAATAAAAATAAAGAAAA
1 AAAATAAAAATAAACAAAA
6882252 TTGTATCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (21 bp):
AAAATAAAAATAAACAAAAAT
Found at i:6882243 original size:11 final size:11
Alignment explanation
Indices: 6882202--6882246 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
6882192 AAATTTAAAC
6882202 AAATAAATAA-A
1 AAATAAA-AATA
6882213 AAATAAAAAT-
1 AAATAAAAATA
*
6882223 AAACAAAAATA
1 AAATAAAAATA
6882234 AAATAAAAATA
1 AAATAAAAATA
6882245 AA
1 AA
6882247 GAAAATTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 11 0.37
11 19 0.63
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:6885337 original size:3 final size:3
Alignment explanation
Indices: 6885329--6885353 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6885319 TTTCTAAAAT
6885329 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
6885354 AATTATTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:6885606 original size:9 final size:9
Alignment explanation
Indices: 6885589--6885792 Score: 65
Period size: 9 Copynumber: 21.0 Consensus size: 9
6885579 TGATGTAAAC
*
6885589 TTATCAAAA
1 TTATAAAAA
6885598 TTATAAAAA
1 TTATAAAAA
**
6885607 CTTATAAGTA
1 -TTATAAAAA
6885617 TTATAAAAA
1 TTATAAAAA
6885626 -TATAATAAA
1 TTATAA-AAA
6885635 TCTCAT--AAA
1 T-T-ATAAAAA
6885644 TTATAAAAA
1 TTATAAAAA
**
6885653 AAATATAAAA
1 TTATA-AAAA
*
6885663 TTAATAAAAC
1 TT-ATAAAAA
*
6885673 TTATTTAAAA
1 TTA-TAAAAA
*
6885683 -TATTCAAAA
1 TTA-TAAAAA
*
6885692 TTAAAAAAA
1 TTATAAAAA
6885701 TGTATCAGAAAAAA
1 T-TAT----AAAAA
*
6885715 TTGTAAAAAA
1 TTAT-AAAAA
6885725 TTATAAAAAA
1 TTAT-AAAAA
* *
6885735 ATATTAAAA
1 TTATAAAAA
**
6885744 TTATTGAAA
1 TTATAAAAA
*
6885753 TTGATATAAAC
1 TT-ATA-AAAA
6885764 TTATAAAAA
1 TTATAAAAA
6885773 TTATATAAAAA
1 -T-TATAAAAA
*
6885784 TCATAAAAA
1 TTATAAAAA
6885793 CTTGAGTTAC
Statistics
Matches: 148, Mismatches: 27, Indels: 40
0.69 0.13 0.19
Matches are distributed among these distances:
7 2 0.01
8 6 0.04
9 65 0.44
10 49 0.33
11 16 0.11
12 2 0.01
13 2 0.01
14 6 0.04
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.32
Consensus pattern (9 bp):
TTATAAAAA
Found at i:6885715 original size:23 final size:21
Alignment explanation
Indices: 6885688--6885743 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 21
6885678 TAAAATATTC
*
6885688 AAAATTAAAAAAATGTATCAGAA
1 AAAATTAAAAAAAT-TAT-AAAA
*
6885711 AAAATTGTAAAAAATTATAAAA
1 AAAATT-AAAAAAATTATAAAA
6885733 AAATATTAAAA
1 AAA-ATTAAAA
6885744 TTATTGAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 9 0.32
23 12 0.43
24 7 0.25
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (21 bp):
AAAATTAAAAAAATTATAAAA
Found at i:6885724 original size:10 final size:10
Alignment explanation
Indices: 6885709--6885792 Score: 57
Period size: 10 Copynumber: 8.5 Consensus size: 10
6885699 AATGTATCAG
*
6885709 AAAAAATTGT
1 AAAAAATTAT
6885719 AAAAAATTAT
1 AAAAAATTAT
*
6885729 AAAAAAATAT
1 AAAAAATTAT
*
6885739 -TAAAATTAT
1 AAAAAATTAT
**
6885748 -TGAAATTGAT
1 AAAAAATT-AT
* *
6885758 ATAAACTTAT
1 AAAAAATTAT
6885768 -AAAAATTAT
1 AAAAAATTAT
*
6885777 ATAAAAATCAT
1 A-AAAAATTAT
6885788 AAAAA
1 AAAAA
6885793 CTTGAGTTAC
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
9 20 0.33
10 26 0.43
11 14 0.23
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:6885762 original size:20 final size:19
Alignment explanation
Indices: 6885550--6885792 Score: 87
Period size: 19 Copynumber: 12.7 Consensus size: 19
6885540 AAGATAAGAA
*
6885550 AAAAATATAAAAA-TAT-T
1 AAAATTATAAAAATTATAT
* *
6885567 -AAA-TATTAAAATTGATGT
1 AAAATTATAAAAATT-ATAT
* *
6885585 AAACTTATCAAAATTATA-
1 AAAATTATAAAAATTATAT
**
6885603 AAAACTTATAAGTATTATA-
1 AAAA-TTATAAAAATTATAT
*
6885622 AAAA-TATAATAAATCT-CAT
1 AAAATTATAA-AAAT-TATAT
**
6885641 -AAATTATAAAAAAAATAT
1 AAAATTATAAAAATTATAT
* *
6885659 AAAATTAATAAAACTTATTT
1 AAAATT-ATAAAAATTATAT
* *
6885679 AAAA-TATTCAAAATTA-AA
1 AAAATTA-TAAAAATTATAT
* *
6885697 AAAATGTATCAGAAAAAATTGTAA
1 AAAAT-TAT----AAAAATTATAT
*
6885721 AAAATTATAAAAA-AATATT
1 AAAATTATAAAAATTATA-T
**
6885740 AAAATTATTGAAATTGATAT
1 AAAATTATAAAAATT-ATAT
*
6885760 AAACTTATAAAAATTATAT
1 AAAATTATAAAAATTATAT
*
6885779 AAAAATCATAAAAA
1 -AAAATTATAAAAA
6885793 CTTGAGTTAC
Statistics
Matches: 166, Mismatches: 35, Indels: 47
0.67 0.14 0.19
Matches are distributed among these distances:
15 7 0.04
16 4 0.02
17 7 0.04
18 22 0.13
19 59 0.36
20 48 0.29
21 3 0.02
23 9 0.05
24 7 0.04
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.32
Consensus pattern (19 bp):
AAAATTATAAAAATTATAT
Found at i:6894338 original size:20 final size:21
Alignment explanation
Indices: 6894291--6894338 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
6894281 CCCCTTTTGA
*
6894291 TGGGTTTTCTTTATGAGAGTT
1 TGGGTTTTATTTATGAGAGTT
*
6894312 AGGGTTTTATTT-TCGAGA-TT
1 TGGGTTTTATTTAT-GAGAGTT
6894332 TGGGTTT
1 TGGGTTT
6894339 GTACATTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.15, C:0.04, G:0.29, T:0.52
Consensus pattern (21 bp):
TGGGTTTTATTTATGAGAGTT
Found at i:6895524 original size:3 final size:3
Alignment explanation
Indices: 6895516--6895549 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
6895506 AAGGATATTG
6895516 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
6895550 TCCACTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6896035 original size:21 final size:21
Alignment explanation
Indices: 6896009--6896056 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
6895999 TCTTTTTAAA
* *
6896009 AAAATATTTAAATTTAATTAT-
1 AAAATATATAAATATAA-TATC
6896030 AAAATATATAAATATAATATC
1 AAAATATATAAATATAATATC
6896051 AAAATA
1 AAAATA
6896057 AATTTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATATATAAATATAATATC
Found at i:6898559 original size:21 final size:20
Alignment explanation
Indices: 6898529--6898573 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
6898519 AATTCATTCC
**
6898529 TTTATTTTTATTTTTTAAAA
1 TTTATTTTTAAATTTTAAAA
6898549 TTTAGTTTTTAAATTTTAAAA
1 TTTA-TTTTTAAATTTTAAAA
6898570 TTTA
1 TTTA
6898574 AGTTAAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTATTTTTAAATTTTAAAA
Found at i:6902236 original size:59 final size:58
Alignment explanation
Indices: 6902066--6902255 Score: 202
Period size: 60 Copynumber: 3.2 Consensus size: 58
6902056 TTAATATGAT
* * *
6902066 ATTTGGTACTTGAATTTGATACTTTTTTTTAATTTGGTATCTAAATTTTTTTTTGACCCA
1 ATTTGGTACTTGAACTTGATATTTTTTTTTAATTTGGTATCTAAA--CTTTTTTGACCCA
* ** * *
6902126 ATTTGGTA-TCTGAACTTGATATTTTTTCTTAATTCAGTGTCGAAACTTTTTTTGACCCA
1 ATTTGGTACT-TGAACTTGATATTTTTTTTTAATTTGGTATCTAAAC-TTTTTTGACCCA
* * * **
6902185 ATTTGATACTTGAACTTGACATTTTTTTTCTAATTTGGTACCTAAACTTTTTTAGATTCA
1 ATTTGGTACTTGAACTTGATATTTTTTTT-TAATTTGGTATCTAAACTTTTTT-GACCCA
6902245 ATTTGGTACTT
1 ATTTGGTACTT
6902256 AAATTTATTA
Statistics
Matches: 106, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
59 43 0.41
60 63 0.59
ACGTcount: A:0.24, C:0.13, G:0.12, T:0.51
Consensus pattern (58 bp):
ATTTGGTACTTGAACTTGATATTTTTTTTTAATTTGGTATCTAAACTTTTTTGACCCA
Found at i:6902505 original size:58 final size:57
Alignment explanation
Indices: 6902395--6902542 Score: 165
Period size: 58 Copynumber: 2.6 Consensus size: 57
6902385 AATTAATATT
* * * * *
6902395 AAAAAAGATTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCATATACCAAATTGGACTC
1 AAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTT-ATATACAAAATTGAAC-A
* *
6902454 TAAAAAGTTTAAGTA-CAAATTAGGAAAAAGTGTCAAGTT-TGAGTACAAAATTGAACA
1 AAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTAT-A-TACAAAATTGAACA
* *
6902511 AAAAAACTTTAGGTACCAAATTAGAAAAAAGT
1 AAAAAAGTTTAGGTACCAAATTAGGAAAAAGT
6902543 AACAAGCTCA
Statistics
Matches: 75, Mismatches: 11, Indels: 7
0.81 0.12 0.08
Matches are distributed among these distances:
56 1 0.01
57 13 0.17
58 49 0.65
59 12 0.16
ACGTcount: A:0.50, C:0.10, G:0.16, T:0.24
Consensus pattern (57 bp):
AAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTATATACAAAATTGAACA
Found at i:6902557 original size:58 final size:57
Alignment explanation
Indices: 6902403--6902562 Score: 146
Period size: 58 Copynumber: 2.7 Consensus size: 57
6902393 TTAAAAAAGA
* ** *
6902403 TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCATA-TACCAAATTGGACTCTAAAAAGT
1 TTAGGTACCAAATTA-GAAAAA-AGTCAAGTTCA-AGTACCAAATTGAACTAAAAAAACT
* * ** *
6902462 TTAAGTA-CAAATTAGGAAAAAGTGTCAAGTTTGAGTACAAAATTGAAC-AAAAAAACT
1 TTAGGTACCAAATTA-GAAAAA-AGTCAAGTTCAAGTACCAAATTGAACTAAAAAAACT
*
6902519 TTAGGTACCAAATTAGAAAAAAGTAACAAGCTCAAGTACCAAAT
1 TTAGGTACCAAATTAGAAAAAAGT--CAAGTTCAAGTACCAAAT
6902563 GCTATATTAA
Statistics
Matches: 82, Mismatches: 15, Indels: 9
0.77 0.14 0.08
Matches are distributed among these distances:
56 2 0.02
57 19 0.23
58 55 0.67
59 6 0.07
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (57 bp):
TTAGGTACCAAATTAGAAAAAAGTCAAGTTCAAGTACCAAATTGAACTAAAAAAACT
Found at i:6905230 original size:15 final size:16
Alignment explanation
Indices: 6905210--6905239 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6905200 TTTAATCTTT
6905210 TAAAAATTA-TAAAAA
1 TAAAAATTATTAAAAA
6905225 TAAAAATTATTAAAA
1 TAAAAATTATTAAAA
6905240 CAATAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAAAATTATTAAAAA
Found at i:6905606 original size:29 final size:30
Alignment explanation
Indices: 6905555--6905624 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 30
6905545 AATGCATACG
* *
6905555 ATTAAA-TAAAAAAAAATTCATA-TGTATA
1 ATTAAATTAAAAAAAAAATCATATTGTAAA
6905583 ATTAAATTAAAATAAAAAAT-ATATTTGTAAA
1 ATTAAATTAAAA-AAAAAATCATA-TTGTAAA
*
6905614 ATTACATTAAA
1 ATTAAATTAAA
6905625 GCATAATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 6 0.17
29 8 0.23
30 6 0.17
31 15 0.43
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (30 bp):
ATTAAATTAAAAAAAAAATCATATTGTAAA
Found at i:6906276 original size:12 final size:12
Alignment explanation
Indices: 6906259--6906284 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6906249 GTAGTCTCCC
6906259 TTCTTTTCTTCT
1 TTCTTTTCTTCT
6906271 TTCTTTTCTTCT
1 TTCTTTTCTTCT
6906283 TT
1 TT
6906285 GTCTTGTTAT
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:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
TTCTTTTCTTCT
Found at i:6930249 original size:25 final size:25
Alignment explanation
Indices: 6930221--6930275 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
6930211 CGTAAGAGTA
* *
6930221 ATATTTTATTTGTCTCGTAAAAACG
1 ATATTTTATCTGGCTCGTAAAAACG
* * *
6930246 ATATTTTGTCTGGCTCGTAAGAGCG
1 ATATTTTATCTGGCTCGTAAAAACG
6930271 ATATT
1 ATATT
6930276 CTTTTTTGCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (25 bp):
ATATTTTATCTGGCTCGTAAAAACG
Found at i:6930275 original size:50 final size:50
Alignment explanation
Indices: 6930195--6930319 Score: 137
Period size: 50 Copynumber: 2.5 Consensus size: 50
6930185 AGACGATGAA
* *
6930195 GATATTTTGTCTTGCTCGTAAGAGTAATATT-TTATTTGTCTCGTAAA-AAC
1 GATATTTTGTCTGGCTCGTAAGAGCAATATTCTTATTTG-CTCG-AAAGAAC
* * * *
6930245 GATATTTTGTCTGGCTCGTAAGAGCGATATTCTTTTTTGCTTGAAAGAGC
1 GATATTTTGTCTGGCTCGTAAGAGCAATATTCTTATTTGCTCGAAAGAAC
* *
6930295 GATACTCTGTCTGGGCTCGTAAGAG
1 GATATTTTGTCT-GGCTCGTAAGAG
6930320 ATAAACTCTG
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
49 3 0.05
50 43 0.67
51 18 0.28
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.39
Consensus pattern (50 bp):
GATATTTTGTCTGGCTCGTAAGAGCAATATTCTTATTTGCTCGAAAGAAC
Found at i:6938540 original size:25 final size:25
Alignment explanation
Indices: 6938505--6938628 Score: 140
Period size: 25 Copynumber: 4.9 Consensus size: 25
6938495 AGACTATGAA
6938505 GATATTCTGTTTGGCTCGTAAGAGC
1 GATATTCTGTTTGGCTCGTAAGAGC
* *
6938530 GATATTTTGTTTGGCTCGTAAGAGT
1 GATATTCTGTTTGGCTCGTAAGAGC
* * * *
6938555 GACATTCTATCTAGCTCGTAAGAGC
1 GATATTCTGTTTGGCTCGTAAGAGC
* * *
6938580 GATATTCTGTCTGGTTCGAAAGAGC
1 GATATTCTGTTTGGCTCGTAAGAGC
* *
6938605 GATACTCTGTCTGGGCTCGTAAGA
1 GATATTCTGT-TTGGCTCGTAAGA
6938629 ACTAAACTCT
Statistics
Matches: 80, Mismatches: 18, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
25 71 0.89
26 9 0.11
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.34
Consensus pattern (25 bp):
GATATTCTGTTTGGCTCGTAAGAGC
Found at i:6942156 original size:22 final size:22
Alignment explanation
Indices: 6942128--6942205 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 22
6942118 TCTTTATACC
6942128 TTCTTTTCTTTTTATTTTCTTT
1 TTCTTTTCTTTTTATTTTCTTT
** *
6942150 TTCTTTTCCCTTCATTTTC-TT
1 TTCTTTTCTTTTTATTTTCTTT
** *
6942171 CCCTTTT-TTTCT-TTTTCTTT
1 TTCTTTTCTTTTTATTTTCTTT
6942191 TTCTTCTTCTCTTTT
1 TTCTT-TTCT-TTTT
6942206 CCTACCCTGA
Statistics
Matches: 40, Mismatches: 12, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
19 5 0.12
20 6 0.15
21 9 0.22
22 17 0.43
23 3 0.08
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (22 bp):
TTCTTTTCTTTTTATTTTCTTT
Found at i:6943203 original size:8 final size:7
Alignment explanation
Indices: 6943180--6943209 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
6943170 AGAGATGAAG
6943180 AAGAAAA
1 AAGAAAA
6943187 AAGAAAA
1 AAGAAAA
6943194 AAGAAGAA
1 AAGAA-AA
6943202 AAGAAAA
1 AAGAAAA
6943209 A
1 A
6943210 GGGAAGAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:6943217 original size:16 final size:15
Alignment explanation
Indices: 6943180--6943209 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6943170 AGAGATGAAG
6943180 AAGAA-AAAAGAAAA
1 AAGAAGAAAAGAAAA
6943194 AAGAAGAAAAGAAAA
1 AAGAAGAAAAGAAAA
6943209 A
1 A
6943210 GGGAAGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAGAAGAAAAGAAAA
Found at i:6945805 original size:47 final size:47
Alignment explanation
Indices: 6945746--6945890 Score: 254
Period size: 47 Copynumber: 3.1 Consensus size: 47
6945736 TTTTATTTTA
*
6945746 AACCGTAAACCCAATAAATAATAAACTTGTATCAAAATACCATAACT
1 AACCTTAAACCCAATAAATAATAAACTTGTATCAAAATACCATAACT
*
6945793 AACCTTAAACCCAATAAATAGTAAACTTGTATCAAAATACCATAACT
1 AACCTTAAACCCAATAAATAATAAACTTGTATCAAAATACCATAACT
* *
6945840 AACCTTAAACCCAATAAATAATAAACTTGCATGAAAATACCATAACT
1 AACCTTAAACCCAATAAATAATAAACTTGTATCAAAATACCATAACT
6945887 AACC
1 AACC
6945891 CTTTACAAAA
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 93 1.00
ACGTcount: A:0.50, C:0.22, G:0.04, T:0.23
Consensus pattern (47 bp):
AACCTTAAACCCAATAAATAATAAACTTGTATCAAAATACCATAACT
Found at i:6945808 original size:24 final size:24
Alignment explanation
Indices: 6945781--6945855 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
6945771 CTTGTATCAA
6945781 AATACCATAACTAACCTTAAACCC
1 AATACCATAACTAACCTTAAACCC
* * * * * **
6945805 AATA-AAT-AGTAAACTTGTATCAA
1 AATACCATAACTAACCTT-AAACCC
6945828 AATACCATAACTAACCTTAAACCC
1 AATACCATAACTAACCTTAAACCC
6945852 AATA
1 AATA
6945856 AATAATAAAC
Statistics
Matches: 34, Mismatches: 14, Indels: 6
0.63 0.26 0.11
Matches are distributed among these distances:
22 7 0.21
23 8 0.24
24 12 0.35
25 7 0.21
ACGTcount: A:0.49, C:0.24, G:0.03, T:0.24
Consensus pattern (24 bp):
AATACCATAACTAACCTTAAACCC
Found at i:6945860 original size:23 final size:23
Alignment explanation
Indices: 6945787--6945860 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
6945777 TCAAAATACC
6945787 ATAACTAACCTTAAACCCAATAA
1 ATAACTAACCTTAAACCCAATAA
* * * * ** *
6945810 AT-AGTAAACTTGTATCAAAATACC
1 ATAACTAACCTT-AAACCCAATA-A
6945834 ATAACTAACCTTAAACCCAATAA
1 ATAACTAACCTTAAACCCAATAA
6945857 ATAA
1 ATAA
6945861 TAAACTTGCA
Statistics
Matches: 34, Mismatches: 14, Indels: 6
0.63 0.26 0.11
Matches are distributed among these distances:
22 7 0.21
23 12 0.35
24 8 0.24
25 7 0.21
ACGTcount: A:0.51, C:0.22, G:0.03, T:0.24
Consensus pattern (23 bp):
ATAACTAACCTTAAACCCAATAA
Found at i:6947689 original size:145 final size:145
Alignment explanation
Indices: 6947426--6947692 Score: 507
Period size: 145 Copynumber: 1.8 Consensus size: 145
6947416 TTGTTCATTC
6947426 ATGATTATATATTTTATAGACAAATAAATTCAAAAGGATAGAGGCTAATTTTGTCATGTTTGAAT
1 ATGATTATATATTTTATAGACAAATAAATTCAAAAGGATAGAGGCTAATTTTGTCATGTTTGAAT
6947491 GTGCATCTGTATTGTCATTGCTTTTTGTTAGTCTAAGTCCTCAGTCAGGTAGCATCCTAAGGTGC
66 GTGCATCTGTATTGTCATTGCTTTTTGTTAGTCTAAGTCCTCAGTCAGGTAGCATCCTAAGGTGC
6947556 CCAAGAATTCTGCAA
131 CCAAGAATTCTGCAA
* *
6947571 ATGATTATATATTTTATAGACAAATAAATTCAGAAGGATAGAGGCTATTTTTGTCATGTTTGAAT
1 ATGATTATATATTTTATAGACAAATAAATTCAAAAGGATAGAGGCTAATTTTGTCATGTTTGAAT
*
6947636 GTGCATCTGTCTTGTCATTGCTTTTTGTTAGTCTAAGTCCTCAGTCAGGTAGCATCC
66 GTGCATCTGTATTGTCATTGCTTTTTGTTAGTCTAAGTCCTCAGTCAGGTAGCATCC
6947693 CCAAGAATTC
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
145 119 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (145 bp):
ATGATTATATATTTTATAGACAAATAAATTCAAAAGGATAGAGGCTAATTTTGTCATGTTTGAAT
GTGCATCTGTATTGTCATTGCTTTTTGTTAGTCTAAGTCCTCAGTCAGGTAGCATCCTAAGGTGC
CCAAGAATTCTGCAA
Found at i:6950572 original size:30 final size:30
Alignment explanation
Indices: 6950538--6950600 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
6950528 GTCTTTAGAC
* * *
6950538 TTAGATTAGCATTGTTTTTGAGAGGTTTTT
1 TTAGATTAGCATTATTTTTGAGAGATGTTT
**
6950568 TTAGATTTTCATTATTTTTGAGAGATGTTT
1 TTAGATTAGCATTATTTTTGAGAGATGTTT
6950598 TTA
1 TTA
6950601 AAAAATGTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.22, C:0.03, G:0.19, T:0.56
Consensus pattern (30 bp):
TTAGATTAGCATTATTTTTGAGAGATGTTT
Found at i:6950676 original size:16 final size:17
Alignment explanation
Indices: 6950657--6950692 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
6950647 AAATATTTAG
*
6950657 TATTTTAA-ATATGAAA
1 TATTTTAACATATAAAA
6950673 TATTTTAACATATAAAA
1 TATTTTAACATATAAAA
6950690 TAT
1 TAT
6950693 AAATTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
TATTTTAACATATAAAA
Found at i:6951375 original size:24 final size:23
Alignment explanation
Indices: 6951301--6951381 Score: 117
Period size: 23 Copynumber: 3.5 Consensus size: 23
6951291 CGTTTGTTTA
6951301 ATGTTCACGAACATTAATCGAAC
1 ATGTTCACGAACATTAATCGAAC
* *
6951324 ATGTTCACGAATATTAAACGAAC
1 ATGTTCACGAACATTAATCGAAC
* *
6951347 ATGTTCACTAACATATAATTGAAC
1 ATGTTCACGAACAT-TAATCGAAC
6951371 ATGTTCACGAA
1 ATGTTCACGAA
6951382 TAATAATGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 33 0.66
24 17 0.34
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (23 bp):
ATGTTCACGAACATTAATCGAAC
Found at i:6951501 original size:12 final size:12
Alignment explanation
Indices: 6951474--6951520 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
6951464 TCATTAATAA
6951474 ATAAACGAGC-T
1 ATAAACGAGCTT
6951485 ATAAACGAGCTT
1 ATAAACGAGCTT
**
6951497 ATAAACGAGCCA
1 ATAAACGAGCTT
*
6951509 ATAAATGAGCTT
1 ATAAACGAGCTT
6951521 GTTCGTGTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 10 0.33
12 20 0.67
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.21
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:6951518 original size:24 final size:23
Alignment explanation
Indices: 6951474--6951520 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
6951464 TCATTAATAA
*
6951474 ATAAACGAGCTATAAACGAGCTT
1 ATAAACGAGCAATAAACGAGCTT
*
6951497 ATAAACGAGCCAATAAATGAGCTT
1 ATAAACGAG-CAATAAACGAGCTT
6951521 GTTCGTGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.21
Consensus pattern (23 bp):
ATAAACGAGCAATAAACGAGCTT
Found at i:6954450 original size:22 final size:24
Alignment explanation
Indices: 6954425--6954469 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
6954415 TATTCTATCC
6954425 ATATTT-TTTTAATTT-TTTTAAA
1 ATATTTATTTTAATTTATTTTAAA
*
6954447 ATATTTATTTTATTTTATTTTAA
1 ATATTTATTTTAATTTATTTTAA
6954470 TATTTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 8 0.40
24 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
ATATTTATTTTAATTTATTTTAAA
Found at i:6961152 original size:312 final size:315
Alignment explanation
Indices: 6960528--6961361 Score: 1381
Period size: 312 Copynumber: 2.6 Consensus size: 315
6960518 TTCTAGTAGA
* *
6960528 TAATCTCTTTTAAATGTTGATGAATTCTATTGACTATTAATTGTATACGGAAGTATCTATTAATG
1 TAATCTCTTTTAAATGTTGATGAATTCTATAGACTATTAATTGTATAAGGAAGTATCTATTAATG
* * *
6960593 TTAGATTCACATTGATTTTTATTCAATTCTTCTCATCTATTTATATTTGGATTTAACTGTTTTGA
66 TTAGATTCACATTGAGTTTTATTCAATTCTTCTCATCTGTTTATATTTGGATTTAACTATTTTGA
* * *
6960658 CCACAAAAGTGGGATTGCAGTCACAGTCACAATCACTGAAAGGTGCGGTGACAAGTTAGATTAAC
131 CCACAGAAGTGCGATTGCAATCACAGTCAC-ATCAC--AAAGGTGCGGTGACAAGTTAGATTAAC
*
6960723 AAGAAAGACCTGATGCAACAAGGAAGCAACTACTTCTGACGAGAAGTGCCTAGGTGCGATGTAAG
193 AAGCAAGACCTGATGCAACAAGGAAGCAACTACTTCTGACGAGAAGTGCCTAGGTGCGATGTAAG
6960788 AGGAGCAATTAAGGGAAGATTCTAGTAGACTAGGAATAACATGCTTCAATTTATCTTT
258 AGGAGCAATTAAGGGAAGATTCTAGTAGACTAGGAATAACATGCTTCAATTTATCTTT
* * *
6960846 TAATCTCTTTTAAGTGTTGATGAGTTCTATAGATTATTAATTGTATAAGGAAGTATCTATTAATG
1 TAATCTCTTTTAAATGTTGATGAATTCTATAGACTATTAATTGTATAAGGAAGTATCTATTAATG
*
6960911 TTAGATTCACATTGAGTTTTATTCAATTCTTCTCATCTGTTTATATTTGGATTTAATTATTTTGA
66 TTAGATTCACATTGAGTTTTATTCAATTCTTCTCATCTGTTTATATTTGGATTTAACTATTTTGA
*
6960976 CCATAGAAGTGCGATTGCAATCACAGTCAC-T-A-AAAGGTGCGGTGACAAGTTAGATTAACAAG
131 CCACAGAAGTGCGATTGCAATCACAGTCACATCACAAAGGTGCGGTGACAAGTTAGATTAACAAG
* * * *
6961038 CAAGACCTGATGTAACAAGGAAGCGACTGCTTCTGACGAGAAGTGCCTAGGTGCTAT-TGAAGAG
196 CAAGACCTGATGCAACAAGGAAGCAACTACTTCTGACGAGAAGTGCCTAGGTGCGATGT-AAGAG
*
6961102 GAGCAATTAAGGGAAGATTCTGGTAGACTAGGAATAACATGCTTCAATTTATCTTT
260 GAGCAATTAAGGGAAGATTCTAGTAGACTAGGAATAACATGCTTCAATTTATCTTT
*
6961158 TAATCTCTTTTAAATGTTGATGAATTCTATTA-ACTATTAATTGTATATGGAAGTATCTATTAAT
1 TAATCTCTTTTAAATGTTGATGAATTCTA-TAGACTATTAATTGTATAAGGAAGTATCTATTAAT
6961222 GTTAGATTCACATTGAGTTTTATTCAATTCTTCTCATCTGTTTATATTTGGATTTAACTATTTTG
65 GTTAGATTCACATTGAGTTTTATTCAATTCTTCTCATCTGTTTATATTTGGATTTAACTATTTTG
6961287 ACCACAGAAGTGCGATTGCAATCACAGTCACAATCACTGAAAGGTGCGGTGACAAGTTAGATTAA
130 ACCACAGAAGTGCGATTGCAATCACAGTCAC-ATCAC--AAAGGTGCGGTGACAAGTTAGATTAA
6961352 CAAGCAAGAC
192 CAAGCAAGAC
6961362 AATGGAAGTT
Statistics
Matches: 483, Mismatches: 25, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
311 1 0.00
312 293 0.61
313 2 0.00
314 1 0.00
315 2 0.00
316 1 0.00
318 183 0.38
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (315 bp):
TAATCTCTTTTAAATGTTGATGAATTCTATAGACTATTAATTGTATAAGGAAGTATCTATTAATG
TTAGATTCACATTGAGTTTTATTCAATTCTTCTCATCTGTTTATATTTGGATTTAACTATTTTGA
CCACAGAAGTGCGATTGCAATCACAGTCACATCACAAAGGTGCGGTGACAAGTTAGATTAACAAG
CAAGACCTGATGCAACAAGGAAGCAACTACTTCTGACGAGAAGTGCCTAGGTGCGATGTAAGAGG
AGCAATTAAGGGAAGATTCTAGTAGACTAGGAATAACATGCTTCAATTTATCTTT
Found at i:6967521 original size:18 final size:18
Alignment explanation
Indices: 6967493--6967545 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
6967483 TGTGAGTATT
6967493 GAGACAGAAGAAGAAAAGA
1 GAGA-AGAAGAAGAAAAGA
6967512 GAGAAGAAGAAGGAAAAGA
1 GAGAAGAAGAA-GAAAAGA
* *
6967531 -AGAGGAGGAAGAAAA
1 GAGAAGAAGAAGAAAA
6967546 AGAATAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 5 0.16
18 15 0.48
19 11 0.35
ACGTcount: A:0.62, C:0.02, G:0.36, T:0.00
Consensus pattern (18 bp):
GAGAAGAAGAAGAAAAGA
Found at i:6968009 original size:17 final size:17
Alignment explanation
Indices: 6967950--6968009 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
6967940 ATGCATTTCA
*
6967950 TTTAATTGTTATTACAT
1 TTTAATTGTTCTTACAT
*
6967967 TTTTATTG-TCTCTACAT
1 TTTAATTGTTCT-TACAT
*
6967984 TTTATTTGTTCTTACAT
1 TTTAATTGTTCTTACAT
*
6968001 TTGAATTGT
1 TTTAATTGT
6968010 AGTTGCATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
16 2 0.06
17 30 0.86
18 3 0.09
ACGTcount: A:0.22, C:0.10, G:0.08, T:0.60
Consensus pattern (17 bp):
TTTAATTGTTCTTACAT
Found at i:6978348 original size:25 final size:26
Alignment explanation
Indices: 6978262--6978331 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 26
6978252 CAAATATACT
* *
6978262 AAAAATAAAAAGATAAAAGAGTAAATAAGC
1 AAAAAT-AAAA-AT-AAATAGTAAAT-AGA
6978292 AAAAATAAAAATAAATAGTAAATAGA
1 AAAAATAAAAATAAATAGTAAATAGA
6978318 AAAAAT-AAAATAAA
1 AAAAATAAAAATAAA
6978332 GTGATATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
25 8 0.21
26 8 0.21
27 10 0.26
28 2 0.05
29 4 0.11
30 6 0.16
ACGTcount: A:0.74, C:0.01, G:0.09, T:0.16
Consensus pattern (26 bp):
AAAAATAAAAATAAATAGTAAATAGA
Found at i:6979825 original size:23 final size:23
Alignment explanation
Indices: 6979777--6979825 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
6979767 TTAGGGTTTG
*
6979777 TTTGTAAATGGGATTTGGGTTAT
1 TTTGTAAATGGGATTTGGCTTAT
*
6979800 TTTGTAAAT-GGATCTTGGCTTTT
1 TTTGTAAATGGGAT-TTGGCTTAT
6979823 TTT
1 TTT
6979826 AATTAAAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.18, C:0.04, G:0.24, T:0.53
Consensus pattern (23 bp):
TTTGTAAATGGGATTTGGCTTAT
Found at i:6982612 original size:26 final size:27
Alignment explanation
Indices: 6982541--6982615 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 27
6982531 TCTTGATAAA
6982541 TATTAAATTAAATTTAATAG-TAAATCT
1 TATTAAATTAAATTTAAT-GTTAAATCT
* ** *
6982568 TATTAAAAT-AATAGAATGTTTAA-CT
1 TATTAAATTAAATTTAATGTTAAATCT
*
6982593 TGTTAAATTAAATTTAATGTTAA
1 TATTAAATTAAATTTAATGTTAA
6982616 GATAATAACT
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
25 10 0.27
26 19 0.51
27 8 0.22
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.44
Consensus pattern (27 bp):
TATTAAATTAAATTTAATGTTAAATCT
Found at i:6982695 original size:37 final size:37
Alignment explanation
Indices: 6982626--6982696 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
6982616 GATAATAACT
6982626 TTAATATTAAATTAATAAAATACTATTAAAATAAGAA
1 TTAATATTAAATTAATAAAATACTATTAAAATAAGAA
*
6982663 TTAA-ATTAAATTAAATATTAA-ACTATTAAAATAA
1 TTAATATTAAATT-AATA-AAATACTATTAAAATAA
6982697 TATTATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 8 0.26
37 21 0.68
38 2 0.06
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (37 bp):
TTAATATTAAATTAATAAAATACTATTAAAATAAGAA
Found at i:6986141 original size:34 final size:34
Alignment explanation
Indices: 6986103--6986180 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 34
6986093 CCAATATCAG
* *
6986103 ATCAGAATGTCACATTACCAGAAATATATAGCAA
1 ATCAGAATGTCACATTACCAAAAACATATAGCAA
* * * * * *
6986137 ATCAGAATTTCATATTTCTAAAAACATATATCAT
1 ATCAGAATGTCACATTACCAAAAACATATAGCAA
6986171 ATCAGAATGT
1 ATCAGAATGT
6986181 TATATCAGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (34 bp):
ATCAGAATGTCACATTACCAAAAACATATAGCAA
Found at i:6991478 original size:22 final size:22
Alignment explanation
Indices: 6991435--6991478 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
6991425 ATGTGAACAT
*
6991435 TAAAATAATATTAAGATGACTA
1 TAAAATAATATTAAAATGACTA
*
6991457 TAAAA-AATATATAAAATTACTA
1 TAAAATAATAT-TAAAATGACTA
6991479 AATATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (22 bp):
TAAAATAATATTAAAATGACTA
Found at i:6992474 original size:17 final size:17
Alignment explanation
Indices: 6992433--6992474 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
6992423 AGAAAATTAA
6992433 AAAATATATAAATTCATT
1 AAAAT-TATAAATTCATT
*
6992451 AACATTATAAATT-ATT
1 AAAATTATAAATTCATT
6992467 AATAATTA
1 AA-AATTA
6992475 AATCTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 5 0.24
17 12 0.57
18 4 0.19
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATTATAAATTCATT
Found at i:7000015 original size:16 final size:17
Alignment explanation
Indices: 6999994--7000036 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
6999984 TTAACATTAT
*
6999994 AAAATAATTTTTAAA-A
1 AAAATAATTTATAAATA
7000010 AAAATATATTTATAAATA
1 AAAATA-ATTTATAAATA
*
7000028 AAGATAATT
1 AAAATAATT
7000037 AGAATGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 6 0.26
17 11 0.48
18 6 0.26
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
AAAATAATTTATAAATA
Found at i:7006475 original size:6 final size:6
Alignment explanation
Indices: 7006466--7006494 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
7006456 ACAAAAAAAC
7006466 AGCCAT AGCCAT AGCCAT AGCCAT AGCCA
1 AGCCAT AGCCAT AGCCAT AGCCAT AGCCA
7006495 AATAAAATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.34, G:0.17, T:0.14
Consensus pattern (6 bp):
AGCCAT
Found at i:7011592 original size:23 final size:23
Alignment explanation
Indices: 7011566--7011615 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
7011556 ATATGACAAA
*
7011566 TTGTACAGCAAAAATACAATGAG
1 TTGTACAACAAAAATACAATGAG
* * *
7011589 TTGTACAACGAAAATTCAGTGAG
1 TTGTACAACAAAAATACAATGAG
7011612 TTGT
1 TTGT
7011616 GGTTTAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (23 bp):
TTGTACAACAAAAATACAATGAG
Found at i:7011980 original size:53 final size:54
Alignment explanation
Indices: 7011812--7011986 Score: 187
Period size: 54 Copynumber: 3.3 Consensus size: 54
7011802 ACATGAGAAA
* ** * *
7011812 GTTGCGATCTTAAATC-AGC-AACTACAAGATT-ATGGAAATTTTGTAAGTATAAG
1 GTTGCGATCTTAAATCGA-CAAACCACAAGATTCA-AAAAATCTTGTAAGTGTAAG
* * * *
7011865 GTTGCGATCTTAAATCGACGAGCCACAAGATTCAAAAAATCTTATAAATGTAAG
1 GTTGCGATCTTAAATCGACAAACCACAAGATTCAAAAAATCTTGTAAGTGTAAG
* *
7011919 GTTGCGATCTTAAATCGGCAAACCGCAAGATTC-AAAAATCTTGTAAGTGTAAG
1 GTTGCGATCTTAAATCGACAAACCACAAGATTCAAAAAATCTTGTAAGTGTAAG
* *
7011972 GCTACGATCTTAAAT
1 GTTGCGATCTTAAAT
7011987 TGGTGAGCCG
Statistics
Matches: 103, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
53 48 0.47
54 54 0.52
55 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (54 bp):
GTTGCGATCTTAAATCGACAAACCACAAGATTCAAAAAATCTTGTAAGTGTAAG
Found at i:7012002 original size:53 final size:54
Alignment explanation
Indices: 7011847--7012003 Score: 190
Period size: 53 Copynumber: 2.9 Consensus size: 54
7011837 AAGATTATGG
* * * *
7011847 AAATTTTGTAAGTATAAGGTTGCGATCTTAAATCGACGAGCCACAAGATTCAAA
1 AAATCTTGTAAGTGTAAGGTTGCGATCTTAAATCGGCGAGCCGCAAGATTCAAA
* * * *
7011901 AAATCTTATAAATGTAAGGTTGCGATCTTAAATCGGCAAACCGCAAGATTC-AA
1 AAATCTTGTAAGTGTAAGGTTGCGATCTTAAATCGGCGAGCCGCAAGATTCAAA
* * * * *
7011954 AAATCTTGTAAGTGTAAGGCTACGATCTTAAATTGGTGAGCCGTAAGATT
1 AAATCTTGTAAGTGTAAGGTTGCGATCTTAAATCGGCGAGCCGCAAGATT
7012004 TGAAAAAAAA
Statistics
Matches: 86, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
53 43 0.50
54 43 0.50
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (54 bp):
AAATCTTGTAAGTGTAAGGTTGCGATCTTAAATCGGCGAGCCGCAAGATTCAAA
Found at i:7012083 original size:81 final size:82
Alignment explanation
Indices: 7011930--7012091 Score: 193
Period size: 81 Copynumber: 2.0 Consensus size: 82
7011920 TTGCGATCTT
* * * * **
7011930 AAATCGGCAAACCGCAAGATTCAAAAATCTTGTAAGTGTAAGGCTACGATCTTAAATTGGTGAGC
1 AAATCGGCAAACCACAAGATTCAAAAATCTTGTAAGTATAAGGCTACGATATTAAATCGGCAAGC
**
7011995 CGTAAGATTT-GAAAAA
66 CACAAGATTTAGAAAAA
* * * *
7012011 AAATCGGCAAACTACAAGATTTC-CAAATCTTTTAAGTATAAGGCTGCGATATTAAATCGGCAAG
1 AAATCGGCAAACCACAAGA-TTCAAAAATCTTGTAAGTATAAGGCTACGATATTAAATCGGCAAG
7012075 CCACAAGATTTAGAAAA
65 CCACAAGATTTAGAAAA
7012092 TCTGGTAAGT
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
81 59 0.88
82 8 0.12
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (82 bp):
AAATCGGCAAACCACAAGATTCAAAAATCTTGTAAGTATAAGGCTACGATATTAAATCGGCAAGC
CACAAGATTTAGAAAAA
Found at i:7012120 original size:54 final size:54
Alignment explanation
Indices: 7012011--7012230 Score: 246
Period size: 54 Copynumber: 4.1 Consensus size: 54
7012001 ATTTGAAAAA
* ** * ** *
7012011 AAATCGGCAAACTACAAGATTT-CCAAATCTTTTAAGTATAAGGCTGCGATATT
1 AAATCGGCAAACCACAAGATTTAGAAAATCTTGTAAGTATAAGGCTATGATCTT
* * *
7012064 AAATCGGCAAGCCACAAGATTTAGAAAATCTGGTAAGTATAAGGTTATGATCTT
1 AAATCGGCAAACCACAAGATTTAGAAAATCTTGTAAGTATAAGGCTATGATCTT
* * * * *
7012118 AAATCAGCAAACCGCAAGATTCAAAAAATCTTGTAAGTATAAGGCTATTATCTT
1 AAATCGGCAAACCACAAGATTTAGAAAATCTTGTAAGTATAAGGCTATGATCTT
** * * *
7012172 AAATCAACAAGCCACAAGA-TTCGAAAATCTTGTAAGTATAAGGCTGTGATCTT
1 AAATCGGCAAACCACAAGATTTAGAAAATCTTGTAAGTATAAGGCTATGATCTT
7012225 AAATCG
1 AAATCG
7012231 ATGAGCCGTA
Statistics
Matches: 139, Mismatches: 27, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
53 54 0.39
54 85 0.61
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (54 bp):
AAATCGGCAAACCACAAGATTTAGAAAATCTTGTAAGTATAAGGCTATGATCTT
Found at i:7012222 original size:107 final size:107
Alignment explanation
Indices: 7012035--7012260 Score: 294
Period size: 107 Copynumber: 2.1 Consensus size: 107
7012025 CAAGATTTCC
* * **
7012035 AAATCTTTTAAGTATAAGGCTGCGATATTAAATCGGCAAGCCACAAGATTTAGAAAATCTGGTAA
1 AAATCTTGTAAGTATAAGGCTACGATATTAAATCAACAAGCCACAAGATTTAGAAAATCTGGTAA
*
7012100 GTATAAGGTTATGATCTTAAATC-AGCAAACCGCAAGATTCAAA
66 GTATAAGGCTATGATCTTAAATCGAG--AACCGCAAGATTCAAA
** * * *
7012143 AAATCTTGTAAGTATAAGGCTATTATCTTAAATCAACAAGCCACAAGA-TTCGAAAATCTTGTAA
1 AAATCTTGTAAGTATAAGGCTACGATATTAAATCAACAAGCCACAAGATTTAGAAAATCTGGTAA
* * *
7012207 GTATAAGGCTGTGATCTTAAATCGATGAGCCGTAAGATTCAAA
66 GTATAAGGCTATGATCTTAAATCGA-GAACCGCAAGATTCAAA
7012250 AAATCTTGTAA
1 AAATCTTGTAA
7012261 TTAGTAAATT
Statistics
Matches: 103, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
107 60 0.58
108 42 0.41
109 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (107 bp):
AAATCTTGTAAGTATAAGGCTACGATATTAAATCAACAAGCCACAAGATTTAGAAAATCTGGTAA
GTATAAGGCTATGATCTTAAATCGAGAACCGCAAGATTCAAA
Found at i:7013630 original size:36 final size:37
Alignment explanation
Indices: 7013560--7013661 Score: 118
Period size: 36 Copynumber: 2.8 Consensus size: 37
7013550 TCGTTATTCG
* *
7013560 TTTTACTCCCTATTGACCCCAAGGGTCATGATGCTCA-
1 TTTTACTCCCTGTTGA-CCCAAAGGTCATGATGCTCAT
* * *
7013597 TTTTACTCCTTGTTGACCTAAAGGTCATTATGCTCAT
1 TTTTACTCCCTGTTGACCCAAAGGTCATGATGCTCAT
* *
7013634 TTTTA-TCCGTGTTGATCCAAAGGTCATG
1 TTTTACTCCCTGTTGACCCAAAGGTCATG
7013662 CTTGTTACCA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
36 36 0.65
37 19 0.35
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.38
Consensus pattern (37 bp):
TTTTACTCCCTGTTGACCCAAAGGTCATGATGCTCAT
Found at i:7021311 original size:12 final size:12
Alignment explanation
Indices: 7021296--7021329 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
7021286 AAGAACGTTT
7021296 TAATATTAATAA
1 TAATATTAATAA
*
7021308 TAATATTATTAA
1 TAATATTAATAA
*
7021320 TAACATTAAT
1 TAATATTAAT
7021330 GACATTAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATATTAATAA
Found at i:7021387 original size:18 final size:17
Alignment explanation
Indices: 7021298--7021392 Score: 56
Period size: 18 Copynumber: 5.6 Consensus size: 17
7021288 GAACGTTTTA
7021298 ATATTAATAATAA-TAT
1 ATATTAATAATAATTAT
*
7021314 -TATTAATAA-CATTAAT
1 ATATTAATAATAATT-AT
* * *
7021330 GACATTAATGATAGTTAT
1 -ATATTAATAATAATTAT
* *
7021348 GGTAATAATAATAA--AT
1 -ATATTAATAATAATTAT
*
7021364 ACATTAATAATAATTAT
1 ATATTAATAATAATTAT
7021381 AATATTAATAAT
1 -ATATTAATAAT
7021393 GATGAAAAAT
Statistics
Matches: 57, Mismatches: 14, Indels: 14
0.67 0.16 0.16
Matches are distributed among these distances:
14 1 0.02
15 20 0.35
16 4 0.07
17 2 0.04
18 28 0.49
19 2 0.04
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (17 bp):
ATATTAATAATAATTAT
Found at i:7021390 original size:33 final size:32
Alignment explanation
Indices: 7021300--7021392 Score: 82
Period size: 33 Copynumber: 2.8 Consensus size: 32
7021290 ACGTTTTAAT
*
7021300 ATTAATAATAA-TATTATTAATAACATTAATGAC
1 ATTAATAATAATTATTATTAAT-A-ATAAATGAC
* * *
7021333 ATTAATGATAGTTATGGTAATAATAATAAAT-AC
1 ATTAATAATAATTAT--TATTAATAATAAATGAC
7021366 ATTAATAATAATTATAATATTAATAAT
1 ATTAATAATAATTAT--TATTAATAAT
7021393 GATGAAAAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
33 33 0.69
34 8 0.17
35 1 0.02
36 6 0.12
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (32 bp):
ATTAATAATAATTATTATTAATAATAAATGAC
Found at i:7022530 original size:30 final size:31
Alignment explanation
Indices: 7022484--7022573 Score: 82
Period size: 29 Copynumber: 3.0 Consensus size: 31
7022474 CCTTAAACTA
* * *
7022484 TCCAGAAATTATATTTTGACCCTTGAACTTCT
1 TCCAAAAATTACATTTTAACCC-TGAACTTCT
7022516 T-C-AAAATTACATTTTTAACCC-GAAC--CT
1 TCCAAAAATTACA-TTTTAACCCTGAACTTCT
*
7022543 TCCAAAAATTACATTTTTACCCTCGAACTTC
1 TCCAAAAATTACATTTTAACCCT-GAACTTC
7022574 CAAAAATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
27 3 0.06
28 9 0.19
29 13 0.28
30 11 0.23
31 9 0.19
32 2 0.04
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.37
Consensus pattern (31 bp):
TCCAAAAATTACATTTTAACCCTGAACTTCT
Found at i:7022597 original size:59 final size:59
Alignment explanation
Indices: 7022484--7022655 Score: 149
Period size: 58 Copynumber: 2.9 Consensus size: 59
7022474 CCTTAAACTA
* * * * *
7022484 TCCAGAAATTATATTTTGACCCTTGAACTTCTTC-AAAATTACATTTTT-AACCCGAACCT
1 TCCAAAAATTACATTTTTACCCTCGAACTTC--CAAAAATTATATTTTTGAACCCGAACCT
* * **
7022543 TCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTTTATTTTTGACCCCG-ATTT
1 TCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTATATTTTTGAACCCGAACCT
* * *
7022601 TCTAAAAATTACCA-TTTTA-CCTCCGAA-TATCCAAAAATTCTATTTTTGATCCCGA
1 TCCAAAAATTA-CATTTTTACCCT-CGAACT-TCCAAAAATTATATTTTTGAACCCGA
7022656 TTTTTCTAAA
Statistics
Matches: 95, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
57 5 0.05
58 56 0.59
59 34 0.36
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.38
Consensus pattern (59 bp):
TCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTATATTTTTGAACCCGAACCT
Found at i:7022655 original size:29 final size:28
Alignment explanation
Indices: 7022518--7022647 Score: 108
Period size: 29 Copynumber: 4.5 Consensus size: 28
7022508 GAACTTCTTC
*
7022518 AAAATTAC-ATTTTTAACCCGAACCTTCCA
1 AAAATTACTATTTTTACCCCGAA--TTCCA
7022547 AAAATTAC-ATTTTTACCCTCGAACTTCCA
1 AAAATTACTATTTTTACCC-CGAA-TTCCA
* * *
7022576 AAAATT-TTATTTTTGACCCCGATTTTCTA
1 AAAATTACTATTTTT-ACCCCGA-ATTCCA
*
7022605 AAAATTACCA-TTTTACCTCCGAATATCCA
1 AAAATTACTATTTTTACC-CCGAAT-TCCA
7022634 AAAATT-CTATTTTT
1 AAAATTACTATTTTT
7022648 GATCCCGATT
Statistics
Matches: 84, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
28 6 0.07
29 69 0.82
30 9 0.11
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (28 bp):
AAAATTACTATTTTTACCCCGAATTCCA
Found at i:7022669 original size:59 final size:57
Alignment explanation
Indices: 7022546--7022976 Score: 397
Period size: 59 Copynumber: 7.4 Consensus size: 57
7022536 CGAACCTTCC
*
7022546 AAAAATTA-CATTTTTACCCTCGAACT-TCCAAAAATTTTATTTTTGACCCCGA-TTTTCT
1 AAAAATTACCA-TTTTACCC-CGAA-TATCCAAAAA-TTTATTTTTGATCCCGATTTTTCT
7022604 AAAAATTACCATTTTACCTCCGAATATCCAAAAATTCTATTTTTGATCCCGATTTTTCT
1 AAAAATTACCATTTTACC-CCGAATATCCAAAAATT-TATTTTTGATCCCGATTTTTCT
* * * * * *
7022663 AAAAATTATCATTTTATCCCCAAATGTCCAAAAATTTCGTTTTTGATCTCGATTCTTCT
1 AAAAATTACCATTTTA-CCCCGAATATCCAAAAATTT-ATTTTTGATCCCGATTTTTCT
* * * ** *
7022722 AAAAATTATCGTTTTACCCCCAAATATCCAAAAATTCCGTTTATGATCCCGATTTTTCT
1 AAAAATTACCATTTTA-CCCCGAATATCCAAAAATT-TATTTTTGATCCCGATTTTTCT
*
7022781 AAAAATTACCATTTTACGCCCGAATATCCAAAAATTTCATTTTTGATCTCGATTTTTCT
1 AAAAATTACCATTTTAC-CCCGAATATCCAAAAATTT-ATTTTTGATCCCGATTTTTCT
** * * * *
7022840 AAAAATTATAATTTTACCCTCGGATGTCCAAAAATTTCGTTTTTGAAT-CTGATTTTTCT
1 AAAAATTACCATTTTACCC-CGAATATCCAAAAATTT-ATTTTTG-ATCCCGATTTTTCT
* ** * * * * * *
7022899 AAAAATTACCGTTTTACACTTGGAT-TTCTAAAATTTCATTTTTAACCCCAAATTTTTCT
1 AAAAATTACCATTTTAC-CCCGAATATCCAAAAATTT-ATTTTTGATCCC-GATTTTTCT
7022958 -AAAATTACCATTTTACCCC
1 AAAAATTACCATTTTACCCC
7022977 TCGAGAGTCC
Statistics
Matches: 315, Mismatches: 43, Indels: 31
0.81 0.11 0.08
Matches are distributed among these distances:
57 5 0.02
58 76 0.24
59 229 0.73
60 5 0.02
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (57 bp):
AAAAATTACCATTTTACCCCGAATATCCAAAAATTTATTTTTGATCCCGATTTTTCT
Found at i:7022769 original size:118 final size:117
Alignment explanation
Indices: 7022572--7022915 Score: 449
Period size: 118 Copynumber: 2.9 Consensus size: 117
7022562 CCCTCGAACT
* * * * *
7022572 TCCAAAAATTTTATTTTTGACCCCGATTTTCTAAAAATTACCATTTTACCTCCGAATATCCAAAA
1 TCCAAAAATTTCATTTTTGATCTCGATTTTCTAAAAATTATCATTTTACCCCCGAATATCCAAAA
** * *
7022637 ATTCTATTTTTGATCCCGATTTTTCTAAAAATTATCATTTTATC-CCCAAATG
66 ATTCCGTTTTTGATCCCGATTTTTCTAAAAATTACCATTTTA-CGCCCAAATA
* * *
7022689 TCCAAAAATTTCGTTTTTGATCTCGATTCTTCTAAAAATTATCGTTTTACCCCCAAATATCCAAA
1 TCCAAAAATTTCATTTTTGATCTCGATT-TTCTAAAAATTATCATTTTACCCCCGAATATCCAAA
* *
7022754 AATTCCGTTTATGATCCCGATTTTTCTAAAAATTACCATTTTACGCCCGAATA
65 AATTCCGTTTTTGATCCCGATTTTTCTAAAAATTACCATTTTACGCCCAAATA
* * * *
7022807 TCCAAAAATTTCATTTTTGATCTCGATTTTTCTAAAAATTATAATTTTACCCTCGGATGTCCAAA
1 TCCAAAAATTTCATTTTTGATCTCGA-TTTTCTAAAAATTATCATTTTACCCCCGAATATCCAAA
* * *
7022872 AATTTCGTTTTTGAAT-CTGATTTTTCTAAAAATTACCGTTTTAC
65 AATTCCGTTTTTG-ATCCCGATTTTTCTAAAAATTACCATTTTAC
7022916 ACTTGGATTT
Statistics
Matches: 198, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
117 25 0.13
118 169 0.85
119 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.41
Consensus pattern (117 bp):
TCCAAAAATTTCATTTTTGATCTCGATTTTCTAAAAATTATCATTTTACCCCCGAATATCCAAAA
ATTCCGTTTTTGATCCCGATTTTTCTAAAAATTACCATTTTACGCCCAAATA
Found at i:7022990 original size:177 final size:177
Alignment explanation
Indices: 7022572--7022976 Score: 534
Period size: 177 Copynumber: 2.3 Consensus size: 177
7022562 CCCTCGAACT
* *
7022572 TCCAAAAATTTTATTTTTGACCCCGA-TTTTCTAAAAATTACCATTTTACCTCCGAATATCCAAA
1 TCCAAAAATTTCATTTTTGACCCCGATTTTTCTAAAAATTACCATTTTACCCCCGAATATCCAAA
*
7022636 AATTCTATTTTTGATCCCGATTTTTCTAAAAATTATCATTTTATCCCCAAATGTCCAAAAATTTC
66 AATTCTATTTTTGATCCCGATTTTTCTAAAAATTATAATTTTATCCCCAAATGTCCAAAAATTTC
* *
7022701 GTTTTTGATCTCGATTCTTCTAAAAATTATCGTTTTACCCCCAAATA
131 GTTTTTGATCTCGATTCTTCTAAAAATTACCGTTTTACACCCAAATA
* * * * *
7022748 TCCAAAAATTCCGTTTATGATCCCGATTTTTCTAAAAATTACCATTTTACGCCCGAATATCCAAA
1 TCCAAAAATTTCATTTTTGACCCCGATTTTTCTAAAAATTACCATTTTACCCCCGAATATCCAAA
* **
7022813 AATT-TCATTTTTGATCTCGATTTTTCTAAAAATTATAATTTTA-CCCTCGGATGTCCAAAAATT
66 AATTCT-ATTTTTGATCCCGATTTTTCTAAAAATTATAATTTTATCCC-CAAATGTCCAAAAATT
* ****
7022876 TCGTTTTTGAATCT-GATTTTTCTAAAAATTACCGTTTTACACTTGGAT-
129 TCGTTTTTG-ATCTCGATTCTTCTAAAAATTACCGTTTTACACCCAAATA
* * * *
7022924 TTCTAAAATTTCATTTTTAACCCCAAATTTTTCT-AAAATTACCATTTTACCCC
1 TCCAAAAATTTCATTTTTGACCCC-GATTTTTCTAAAAATTACCATTTTACCCC
7022977 TCGAGAGTCC
Statistics
Matches: 197, Mismatches: 27, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
176 60 0.30
177 133 0.68
178 4 0.02
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.41
Consensus pattern (177 bp):
TCCAAAAATTTCATTTTTGACCCCGATTTTTCTAAAAATTACCATTTTACCCCCGAATATCCAAA
AATTCTATTTTTGATCCCGATTTTTCTAAAAATTATAATTTTATCCCCAAATGTCCAAAAATTTC
GTTTTTGATCTCGATTCTTCTAAAAATTACCGTTTTACACCCAAATA
Found at i:7033328 original size:94 final size:93
Alignment explanation
Indices: 7033171--7033357 Score: 320
Period size: 94 Copynumber: 2.0 Consensus size: 93
7033161 AAATAGATAA
7033171 ATATATATATAAAATAATAAATGCTATATTGGTCAAGAGGATTTAAGATTTAAAGCATGATGCTA
1 ATATATATATAAAATAATAAATGCTATATTGGTCAAGAGGATTTAAGATTTAAAGCATGATGCTA
*
7033236 GCATTAATAGAGTTGCAGTTTTGATTAT
66 GCATTAATAAAGTTGCAGTTTTGATTAT
* * *
7033264 ATATATATATAGAATAATAAATGTTGTATTGGGTCAAGAGGATTTAAGATTTAAAGCATGATGCT
1 ATATATATATAAAATAATAAATGCTATATT-GGTCAAGAGGATTTAAGATTTAAAGCATGATGCT
*
7033329 AGCATTAGTAAAGTTGCAGTTTTGATTAT
65 AGCATTAATAAAGTTGCAGTTTTGATTAT
7033358 TCATACCTTT
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
93 27 0.31
94 61 0.69
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.37
Consensus pattern (93 bp):
ATATATATATAAAATAATAAATGCTATATTGGTCAAGAGGATTTAAGATTTAAAGCATGATGCTA
GCATTAATAAAGTTGCAGTTTTGATTAT
Found at i:7035952 original size:25 final size:23
Alignment explanation
Indices: 7035911--7035957 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
7035901 CAAATTAGGG
7035911 AATTATTGTTTAGATTTAATTTT
1 AATTATTGTTTAGATTTAATTTT
*
7035934 AATTATCTTTTTAGAATTTAATTT
1 AATTAT-TGTTTAG-ATTTAATTT
7035958 GGATCCAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 6 0.29
25 9 0.43
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTTT
Found at i:7043419 original size:92 final size:88
Alignment explanation
Indices: 7043311--7043485 Score: 242
Period size: 92 Copynumber: 1.9 Consensus size: 88
7043301 TAATTAAGCT
*
7043311 TTTTTTTTACACTCAATTGAGCACTTGAACTTTCAAAATACATAAAAAAAAAACTCTCAAACTTC
1 TTTTTTTTACACTCAATTGAGCACTTGAACTTTCAAAATACAT--AAAAAAAACTCTCAAAATTC
7043376 TTCAAAGAAAAGCAATTAAGCCCCTAC
64 TTC-AA-AAAAGCAATTAAGCCCCTAC
* * * * * * *
7043403 TTTTTTTTCCACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAATACTCTCAAAATTTTT
1 TTTTTTTTACACTCAATTGAGCACTTGAACTTTCAAAATACATAAAAAAAACTCTCAAAATTCTT
7043468 CAAAAAAGCAATTAAGCC
66 CAAAAAAGCAATTAAGCC
7043486 TTTGCTCTTA
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
88 15 0.20
89 2 0.03
90 19 0.25
92 39 0.52
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.32
Consensus pattern (88 bp):
TTTTTTTTACACTCAATTGAGCACTTGAACTTTCAAAATACATAAAAAAAACTCTCAAAATTCTT
CAAAAAAGCAATTAAGCCCCTAC
Found at i:7043617 original size:21 final size:22
Alignment explanation
Indices: 7043578--7043621 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
7043568 AACTTTAGAA
*
7043578 TTTATAAAAAAATTCAAAATTT
1 TTTATAAAAAAAGTCAAAATTT
*
7043600 TTTATAAAAATAGT-AAAATTT
1 TTTATAAAAAAAGTCAAAATTT
7043621 T
1 T
7043622 ATAGAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TTTATAAAAAAAGTCAAAATTT
Found at i:7043833 original size:9 final size:9
Alignment explanation
Indices: 7043819--7044005 Score: 84
Period size: 9 Copynumber: 20.2 Consensus size: 9
7043809 TTTTGGTAAG
7043819 ATAATTTTT
1 ATAATTTTT
7043828 ATAATTTTT
1 ATAATTTTT
*
7043837 -TACGAATTTT
1 ATA--ATTTTT
*
7043847 ATATTTCTTT
1 ATAATT-TTT
*
7043857 AT-ATTCTGT
1 ATAATT-TTT
7043866 ATAATGTTCTT
1 ATAAT-TT-TT
* *
7043877 ATGA-CTTT
1 ATAATTTTT
*
7043885 ATAAAATTTT
1 AT-AATTTTT
7043895 ATAATTTTT
1 ATAATTTTT
*
7043904 -TATATTTCT
1 ATA-ATTTTT
7043913 AT-ATATTTT
1 ATAAT-TTTT
7043922 ATAATTTTT
1 ATAATTTTT
7043931 -TACGATTTTT
1 ATA--ATTTTT
*
7043941 ATAAAATTTT
1 AT-AATTTTT
7043951 AT-ATTTTT
1 ATAATTTTT
*
7043959 ATATTTTTT
1 ATAATTTTT
**
7043968 ACGATTTTT
1 ATAATTTTT
*
7043977 ATATTTTTT
1 ATAATTTTT
*
7043986 CTAATTTTT
1 ATAATTTTT
7043995 A-ATATTTTT
1 ATA-ATTTTT
7044004 AT
1 AT
7044006 TAAAATTTAA
Statistics
Matches: 133, Mismatches: 25, Indels: 39
0.68 0.13 0.20
Matches are distributed among these distances:
8 20 0.15
9 70 0.53
10 34 0.26
11 8 0.06
12 1 0.01
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (9 bp):
ATAATTTTT
Found at i:7043942 original size:56 final size:56
Alignment explanation
Indices: 7043843--7043964 Score: 160
Period size: 56 Copynumber: 2.2 Consensus size: 56
7043833 TTTTTACGAA
* *
7043843 TTTTATATTTCTTTATATTCTGTATAATGTTCTTATGACTTTATAAAATTTTATAATT
1 TTTTATATTTCTATATATTCTGTATAATGTTCTTACGACTTTATAAAATTTTAT-A-T
* *
7043901 TTTTATATTTCTATATATT-T-TATAAT-TTTTTACGATTTTTATAAAATTTTATAT
1 TTTTATATTTCTATATATTCTGTATAATGTTCTTACGA-CTTTATAAAATTTTATAT
7043955 TTTTATATTT
1 TTTTATATTT
7043965 TTTACGATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
54 11 0.19
55 8 0.14
56 21 0.36
57 1 0.02
58 18 0.31
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (56 bp):
TTTTATATTTCTATATATTCTGTATAATGTTCTTACGACTTTATAAAATTTTATAT
Found at i:7043993 original size:36 final size:37
Alignment explanation
Indices: 7043907--7044003 Score: 126
Period size: 36 Copynumber: 2.6 Consensus size: 37
7043897 AATTTTTTAT
7043907 ATTTCTATATATTTTATAATTTTTTACGATTTTTATAAA
1 ATTTCTATAT-TTTTAT-ATTTTTTACGATTTTTATAAA
**
7043946 ATTT-TATATTTTTATATTTTTTACGATTTTTATATT
1 ATTTCTATATTTTTATATTTTTTACGATTTTTATAAA
*
7043982 TTTTCTA-ATTTTTAATATTTTT
1 ATTTCTATATTTTT-ATATTTTT
7044004 ATTAAAATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
36 28 0.53
37 16 0.30
38 5 0.09
39 4 0.08
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (37 bp):
ATTTCTATATTTTTATATTTTTTACGATTTTTATAAA
Done.