Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold71
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: 5741892
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 121862 characters in sequence are not A, C, G, or T
File 17 of 33
Found at i:2662254 original size:15 final size:15
Alignment explanation
Indices: 2662198--2662242 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 15
2662188 TTAAAAAAAT
2662198 AAAATAAATTAATTAAA
1 AAAATAAA--AATTAAA
2662215 AAAATGTAAAAATTAAA
1 AAAA--TAAAAATTAAA
2662232 AAAATAAAAAT
1 AAAATAAAAAT
2662243 AAATAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 7 0.27
17 15 0.58
19 4 0.15
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (15 bp):
AAAATAAAAATTAAA
Found at i:2662264 original size:39 final size:38
Alignment explanation
Indices: 2662187--2662267 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 38
2662177 ATATTTAATG
2662187 ATTAAAAAAATAAAATAAATTAATTAAAAAAATGTAAAA
1 ATTAAAAAAATAAAATAAATTAATTAAAAAAA-GTAAAA
*
2662226 ATTAAAAAAATAAAAATAAA-TAATATAAACAACA-TAAAA
1 ATTAAAAAAAT-AAAATAAATTAAT-TAAA-AAAAGTAAAA
2662265 ATT
1 ATT
2662268 CATTATAAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
39 23 0.61
40 12 0.32
41 3 0.08
ACGTcount: A:0.72, C:0.02, G:0.01, T:0.25
Consensus pattern (38 bp):
ATTAAAAAAATAAAATAAATTAATTAAAAAAAGTAAAA
Found at i:2662573 original size:11 final size:13
Alignment explanation
Indices: 2662547--2662578 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
2662537 TATTATATAT
2662547 TTTGAGTTTAAAA
1 TTTGAGTTTAAAA
2662560 TTTGA-TTT-AAA
1 TTTGAGTTTAAAA
2662571 TTTGAGTT
1 TTTGAGTT
2662579 GAATTTAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.44
12 5 0.28
13 5 0.28
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (13 bp):
TTTGAGTTTAAAA
Found at i:2662990 original size:17 final size:18
Alignment explanation
Indices: 2662943--2662991 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
2662933 TAACAGTTTA
2662943 ATTTT-TTATTTAAATTTG
1 ATTTTATTA-TTAAATTTG
* *
2662961 ATTTCATTCTTAAATTT-
1 ATTTTATTATTAAATTTG
2662978 ATTTTATTATTAAA
1 ATTTTATTATTAAA
2662992 AAAATTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 12 0.46
18 12 0.46
19 2 0.08
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (18 bp):
ATTTTATTATTAAATTTG
Found at i:2663019 original size:16 final size:16
Alignment explanation
Indices: 2662980--2663023 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
2662970 TTAAATTTAT
*
2662980 TTTATTATTAAAAAAA
1 TTTAATATTAAAAAAA
*
2662996 TTAAAATATTAAAAAAA
1 TT-TAATATTAAAAAAA
2663013 TTTAATATTAA
1 TTTAATATTAA
2663024 TATTTATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTAATATTAAAAAAA
Found at i:2665080 original size:14 final size:13
Alignment explanation
Indices: 2665049--2665090 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
2665039 AATCAAATAC
2665049 ATATTT-TTATTA
1 ATATTTATTATTA
2665061 ATTATTTATTATATA
1 A-TATTTATTAT-TA
2665076 ATATTTATTTATTA
1 ATATTTA-TTATTA
2665090 A
1 A
2665091 AATTGTTTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.04
13 5 0.19
14 13 0.50
15 7 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATATTTATTATTA
Found at i:2667177 original size:2 final size:2
Alignment explanation
Indices: 2667170--2667211 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2667160 TTTAATAGCC
2667170 AT 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 AT
2667212 CAAACTCTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2667467 original size:13 final size:13
Alignment explanation
Indices: 2667449--2667475 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2667439 AACGAAAATT
2667449 CAAACAAACAAAC
1 CAAACAAACAAAC
2667462 CAAACAAACAAAC
1 CAAACAAACAAAC
2667475 C
1 C
2667476 TTTTGGCTAG
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:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAACAAACAAAC
Found at i:2667536 original size:3 final size:3
Alignment explanation
Indices: 2667528--2667556 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2667518 GAATCATGAT
2667528 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2667557 GCAGGAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2669956 original size:15 final size:15
Alignment explanation
Indices: 2669945--2669984 Score: 66
Period size: 14 Copynumber: 2.8 Consensus size: 15
2669935 CATTAAATAT
2669945 TTAAA-AAATAAAAA
1 TTAAATAAATAAAAA
2669959 TTAAATAAATAAAAA
1 TTAAATAAATAAAAA
2669974 -TAAATAAATAA
1 TTAAATAAATAA
2669985 TGTAAATAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
TTAAATAAATAAAAA
Found at i:2672815 original size:16 final size:15
Alignment explanation
Indices: 2672791--2672847 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 15
2672781 CATATTTTAT
2672791 TAATAATTTACTTTAAA
1 TAAT-ATTTA-TTTAAA
*
2672808 TAATATTTATTTAATG
1 TAATATTTATTTAA-A
*
2672824 TAAAATTTATTTTAAA
1 TAATATTTA-TTTAAA
2672840 -AATATTTA
1 TAATATTTA
2672848 AAATCTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 12 0.35
16 13 0.38
17 9 0.26
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
TAATATTTATTTAAA
Found at i:2683925 original size:1 final size:1
Alignment explanation
Indices: 2683921--2683953 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
2683911 TCGTCTCCCG
*
2683921 CCCCCCCCTCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2683954 GGCCCAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:2683937 original size:13 final size:13
Alignment explanation
Indices: 2683915--2683953 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
2683905 AAAGCCTCGT
*
2683915 CTCCCGCCCCCCC
1 CTCCCCCCCCCCC
2683928 CTCCCCCCCCCCC
1 CTCCCCCCCCCCC
2683941 C-CCCCCCCCCCC
1 CTCCCCCCCCCCC
2683953 C
1 C
2683954 GGCCCAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 12 0.48
13 13 0.52
ACGTcount: A:0.00, C:0.92, G:0.03, T:0.05
Consensus pattern (13 bp):
CTCCCCCCCCCCC
Found at i:2684031 original size:16 final size:17
Alignment explanation
Indices: 2684010--2684044 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2684000 ACAAATCACT
2684010 TTTCCTTTT-TCTTTAA
1 TTTCCTTTTCTCTTTAA
*
2684026 TTTCCTTTTCTTTTTAA
1 TTTCCTTTTCTCTTTAA
2684043 TT
1 TT
2684045 AATTTATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTCCTTTTCTCTTTAA
Found at i:2684040 original size:21 final size:22
Alignment explanation
Indices: 2684008--2684049 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2683998 AGACAAATCA
**
2684008 CTTTTCCTTTTTCTTTAATTTC
1 CTTTTCCTTTTTAATTAATTTC
2684030 CTTTT-CTTTTTAATTAATTT
1 CTTTTCCTTTTTAATTAATTT
2684050 ATTCTTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (22 bp):
CTTTTCCTTTTTAATTAATTTC
Found at i:2686492 original size:19 final size:21
Alignment explanation
Indices: 2686442--2686495 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
2686432 ATTGAATTAT
*
2686442 TATAATAAATTATATAAAAAA
1 TATAAAAAATTATATAAAAAA
*
2686463 TAAAAATAAATT-TATAAAAAA
1 TATAAA-AAATTATATAAAAAA
2686484 -ATAAAAAATTAT
1 TATAAAAAATTAT
2686496 TTGACGAGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 5 0.18
20 5 0.18
21 13 0.46
22 5 0.18
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TATAAAAAATTATATAAAAAA
Found at i:2686497 original size:22 final size:23
Alignment explanation
Indices: 2686445--2686490 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
2686435 GAATTATTAT
2686445 AATAAA-TTATATAAAAAATAAA
1 AATAAATTTATATAAAAAATAAA
2686467 AATAAATTTATA-AAAAAATAAA
1 AATAAATTTATATAAAAAATAAA
2686489 AA
1 AA
2686491 ATTATTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (23 bp):
AATAAATTTATATAAAAAATAAA
Found at i:2686781 original size:19 final size:19
Alignment explanation
Indices: 2686741--2686783 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2686731 AAAATGATGC
*
2686741 ATAAATTTCTTTAAAATAT
1 ATAAATTTCTGTAAAATAT
*
2686760 ATAAATTT-TGTAACAATTT
1 ATAAATTTCTGTAA-AATAT
2686779 ATAAA
1 ATAAA
2686784 ACCGATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (19 bp):
ATAAATTTCTGTAAAATAT
Found at i:2686910 original size:2 final size:2
Alignment explanation
Indices: 2686903--2686951 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2686893 ATTTTTAAGG
2686903 AT 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 AT
2686945 AT AT AT A
1 AT AT AT A
2686952 AAGAACAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2690212 original size:18 final size:18
Alignment explanation
Indices: 2690185--2690227 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2690175 AAAAAGCCCG
*
2690185 TATTTAATGAGGAACCAA
1 TATTTGATGAGGAACCAA
* *
2690203 TATTTGATGAGGAGCCAG
1 TATTTGATGAGGAACCAA
2690221 TATTTGA
1 TATTTGA
2690228 CGAAGAAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (18 bp):
TATTTGATGAGGAACCAA
Found at i:2691034 original size:16 final size:16
Alignment explanation
Indices: 2690984--2691050 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 16
2690974 AACCACAAAT
2690984 TTTCTAAGAATCATAGA
1 TTTCT-AGAATCATAGA
** * *
2691001 AAT-TAGAATCGTATA
1 TTTCTAGAATCATAGA
2691016 TTTCT-GTAATCATAGA
1 TTTCTAG-AATCATAGA
*
2691032 TTTCTAGAATTATAGA
1 TTTCTAGAATCATAGA
2691048 TTT
1 TTT
2691051 TCAACTATAA
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
15 11 0.29
16 25 0.66
17 2 0.05
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (16 bp):
TTTCTAGAATCATAGA
Found at i:2691770 original size:12 final size:12
Alignment explanation
Indices: 2691753--2691777 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2691743 AATTTAACCC
2691753 ATTTCATTATTT
1 ATTTCATTATTT
2691765 ATTTCATTATTT
1 ATTTCATTATTT
2691777 A
1 A
2691778 CTACATGACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTCATTATTT
Found at i:2695268 original size:20 final size:20
Alignment explanation
Indices: 2695231--2695269 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2695221 ACTAATTAAA
*
2695231 TATTATCTTTTATATATAAG
1 TATTATCTTGTATATATAAG
2695251 TATTGATCTTGTAT-TATAA
1 TATT-ATCTTGTATATATAA
2695270 TACATTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.54
Consensus pattern (20 bp):
TATTATCTTGTATATATAAG
Found at i:2698011 original size:2 final size:2
Alignment explanation
Indices: 2698004--2698040 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2697994 AATTATTAGG
*
2698004 TA TA TA TA TA TA TA TA CA 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 T
2698041 TATCTGGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2698182 original size:22 final size:22
Alignment explanation
Indices: 2698154--2698196 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2698144 TCACATTGCT
2698154 TTATAAAAAATCACATCAAAAG
1 TTATAAAAAATCACATCAAAAG
* *
2698176 TTATAAAAAATTATATCAAAA
1 TTATAAAAAATCACATCAAAA
2698197 CTTAGCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.28
Consensus pattern (22 bp):
TTATAAAAAATCACATCAAAAG
Found at i:2698233 original size:21 final size:21
Alignment explanation
Indices: 2698182--2698299 Score: 82
Period size: 21 Copynumber: 5.7 Consensus size: 21
2698172 AAAGTTATAA
*
2698182 AAAATTATATCAAAACTTAGC
1 AAAATTATATCAAAACTTACC
*
2698203 AAAATAATATCAAAGA-TTACC
1 AAAATTATATCAAA-ACTTACC
* * **
2698224 ATAATTATATTTAAAA-TTATT
1 AAAATTATA-TCAAAACTTACC
* *
2698245 AAAATTATATAAAAAC-TATC
1 AAAATTATATCAAAACTTACC
**
2698265 AAAATTATATTCAAAAC-TATT
1 AAAATTATA-TCAAAACTTACC
*
2698286 AAAATCATATCAAA
1 AAAATTATATCAAA
2698300 GATTAATAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
20 22 0.28
21 53 0.66
22 5 0.06
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAATTATATCAAAACTTACC
Found at i:2698249 original size:42 final size:41
Alignment explanation
Indices: 2698203--2698342 Score: 140
Period size: 42 Copynumber: 3.4 Consensus size: 41
2698193 AAAACTTAGC
*
2698203 AAAATAATATCAAAGATTACCATAATTATATTTAAAATTATT
1 AAAATTATATCAAAGATTA-CATAATTATATTTAAAATTATT
* * * * *
2698245 AAAATTATAT-AAAAACTATCAAAATTATATTCAAAACTATT
1 AAAATTATATCAAAGATTA-CATAATTATATTTAAAATTATT
* * *
2698286 AAAATCATATCAAAGATTA-ATAAATTTATATTTAAAGTTACT
1 AAAATTATATCAAAGATTACAT-AA-TTATATTTAAAATTATT
*
2698328 CAAATTATATCAAAG
1 AAAATTATATCAAAG
2698343 GTTGTTTATT
Statistics
Matches: 78, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
40 1 0.01
41 36 0.46
42 41 0.53
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.36
Consensus pattern (41 bp):
AAAATTATATCAAAGATTACATAATTATATTTAAAATTATT
Found at i:2698272 original size:83 final size:83
Alignment explanation
Indices: 2698182--2698337 Score: 210
Period size: 83 Copynumber: 1.9 Consensus size: 83
2698172 AAAGTTATAA
*
2698182 AAAATTATA-TCAAAACTTAGCAAAATAATATCAAAGATTACCAT-AA-TTATATTTAAAATTAT
1 AAAATTATATTCAAAAC-TAGCAAAATAATATCAAAGATTA--ATAAATTTATATTTAAAATTAC
2698244 TAAAATTATATAAAAACTATC
63 TAAAATTATATAAAAACTATC
** * * *
2698265 AAAATTATATTCAAAACTATTAAAATCATATCAAAGATTAATAAATTTATATTTAAAGTTACTCA
1 AAAATTATATTCAAAACTAGCAAAATAATATCAAAGATTAATAAATTTATATTTAAAATTACTAA
2698330 AATTATAT
66 AATTATAT
2698338 CAAAGGTTGT
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
81 2 0.03
82 2 0.03
83 53 0.83
84 7 0.11
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.36
Consensus pattern (83 bp):
AAAATTATATTCAAAACTAGCAAAATAATATCAAAGATTAATAAATTTATATTTAAAATTACTAA
AATTATATAAAAACTATC
Found at i:2698316 original size:21 final size:20
Alignment explanation
Indices: 2698287--2698342 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
2698277 AAAACTATTA
*
2698287 AAATCATATCAAAGATTAAT-
1 AAATTATATCAAAG-TTAATC
* *
2698307 AAATTTATATTTAAAGTTACTC
1 AAA-TTATA-TCAAAGTTAATC
2698329 AAATTATATCAAAG
1 AAATTATATCAAAG
2698343 GTTGTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
20 8 0.28
21 13 0.45
22 8 0.28
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (20 bp):
AAATTATATCAAAGTTAATC
Found at i:2699958 original size:19 final size:19
Alignment explanation
Indices: 2699922--2699959 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2699912 TAAACACATT
*
2699922 AATATTTTTTATTTTTTAA
1 AATATTTTTTATTATTTAA
2699941 AATATTTTTT-TATATTTAA
1 AATATTTTTTAT-TATTTAA
2699960 TTAATTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
AATATTTTTTATTATTTAA
Found at i:2700738 original size:17 final size:15
Alignment explanation
Indices: 2700718--2700758 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
2700708 TAATATTCGG
2700718 TTAAATTTAATGTTTT
1 TTAAATTTAAT-TTTT
2700734 ATTAAATTTAATTTTT
1 -TTAAATTTAATTTTT
2700750 TT-AATTTAA
1 TTAAATTTAA
2700759 ATATTAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.29
15 2 0.08
16 4 0.17
17 11 0.46
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (15 bp):
TTAAATTTAATTTTT
Found at i:2700914 original size:16 final size:17
Alignment explanation
Indices: 2700882--2700919 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
2700872 TATAAATTTA
*
2700882 TAAAAGAATTAAAATAT
1 TAAAAAAATTAAAATAT
2700899 TAAAAAAATT-AAATAT
1 TAAAAAAATTAAAATAT
2700915 TAAAA
1 TAAAA
2700920 TATTAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
TAAAAAAATTAAAATAT
Found at i:2700916 original size:24 final size:23
Alignment explanation
Indices: 2700889--2700936 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 23
2700879 TTATAAAAGA
2700889 ATTAAAATATTAAAAAAATTAAAT
1 ATTAAAATATTAAAAAAA-TAAAT
*
2700913 ATTAAAATATTAATAAAATAAAT
1 ATTAAAATATTAAAAAAATAAAT
2700936 A
1 A
2700937 AATTTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATTAAAATATTAAAAAAATAAAT
Found at i:2701440 original size:3 final size:3
Alignment explanation
Indices: 2701432--2701484 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
2701422 ACTCATAATA
* * * *
2701432 TAT TAT TAT AAT TAT TAT TTT TAT TAT TAA TAT TAT TA- TAA TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2701478 TAT TAT T
1 TAT TAT T
2701485 TAATTTATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2703741 original size:22 final size:23
Alignment explanation
Indices: 2703704--2703746 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
2703694 TTATATAATA
2703704 ATATTTTTATCATT-AATTATTT
1 ATATTTTTATCATTAAATTATTT
2703726 ATATTTTTAT-ATTTAAATTAT
1 ATATTTTTATCA-TTAAATTAT
2703747 AAAAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 1 0.05
22 12 0.63
23 6 0.32
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
ATATTTTTATCATTAAATTATTT
Found at i:2703767 original size:49 final size:49
Alignment explanation
Indices: 2703714--2703836 Score: 130
Period size: 49 Copynumber: 2.5 Consensus size: 49
2703704 ATATTTTTAT
*
2703714 CATTAATTATTTATATTTTTAT-ATTTAAATTATAAAAAATTATTAAATA
1 CATTAATTATTTATATTTTTATAAATTAAATTA-AAAAAATTATTAAATA
* *
2703763 CATTAAAATT-TTTA-AATTTTATAAATTAAATTAAAAAAATTATTATATA
1 CATT--AATTATTTATATTTTTATAAATTAAATTAAAAAAATTATTAAATA
* *
2703812 -TTTTATTATTTATTATTTTT-TAAAT
1 CATTAATTATTTA-TATTTTTATAAAT
2703837 ATATAATAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
46 3 0.05
47 4 0.06
48 7 0.11
49 31 0.50
50 13 0.21
51 4 0.06
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (49 bp):
CATTAATTATTTATATTTTTATAAATTAAATTAAAAAAATTATTAAATA
Found at i:2706056 original size:30 final size:32
Alignment explanation
Indices: 2706020--2706078 Score: 104
Period size: 30 Copynumber: 1.9 Consensus size: 32
2706010 AATGTGGTTT
2706020 CGTGTTAGATTCCAT-GG-GATTACTTACATC
1 CGTGTTAGATTCCATGGGTGATTACTTACATC
2706050 CGTGTTAGATTCCATGGGTGATTACTTAC
1 CGTGTTAGATTCCATGGGTGATTACTTAC
2706079 GGTTACAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 15 0.56
31 2 0.07
32 10 0.37
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (32 bp):
CGTGTTAGATTCCATGGGTGATTACTTACATC
Found at i:2708427 original size:2 final size:2
Alignment explanation
Indices: 2708415--2708455 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2708405 GACTTCCACC
*
2708415 TA TA AA 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
2708456 GGTTCTTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2716057 original size:18 final size:17
Alignment explanation
Indices: 2716034--2716067 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2716024 ACCTTATATA
*
2716034 TATATATATATTAAAATT
1 TATATAAAT-TTAAAATT
2716052 TATATAAATTTAAAAT
1 TATATAAATTTAAAAT
2716068 ATTTTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATATAAATTTAAAATT
Found at i:2716057 original size:26 final size:26
Alignment explanation
Indices: 2715987--2716057 Score: 63
Period size: 30 Copynumber: 2.6 Consensus size: 26
2715977 TAATAAAATA
2715987 ATTAAAATATTATAT-TAAATATATAT
1 ATTAAAAT-TTATATATAAATATATAT
* * *
2716013 TTTCAAATTTTACCTTATATATATATATAT
1 ATT-AAAATTTA---TATATAAATATATAT
2716043 ATTAAAATTTATATA
1 ATTAAAATTTATATA
2716058 AATTTAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
26 9 0.26
27 4 0.11
29 10 0.29
30 12 0.34
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTAAAATTTATATATAAATATATAT
Found at i:2717015 original size:38 final size:39
Alignment explanation
Indices: 2716973--2717061 Score: 103
Period size: 38 Copynumber: 2.4 Consensus size: 39
2716963 ATTCACGTTA
*
2716973 GAATTCCT-TAGTCACCAGCCATCAGCCAATTCCAAATT
1 GAATTCCTCTAGTCACCAGCCACCAGCCAATTCCAAATT
* * * * *
2717011 GAATT-TTCTAGTCGCTAGCCACCGGCCAATTTCAAATT
1 GAATTCCTCTAGTCACCAGCCACCAGCCAATTCCAAATT
2717049 GAATT-CTCTAGTC
1 GAATTCCTCTAGTC
2717062 GTCAGCCGCC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 1 0.02
38 42 0.98
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (39 bp):
GAATTCCTCTAGTCACCAGCCACCAGCCAATTCCAAATT
Found at i:2717086 original size:35 final size:36
Alignment explanation
Indices: 2717039--2717141 Score: 127
Period size: 35 Copynumber: 2.8 Consensus size: 36
2717029 CCACCGGCCA
*
2717039 ATTTCAAATTGAATTCTCTAGTCGTCAGCCGCCAG-
1 ATTTCAAATTGAATTCTCTAATCGTCAGCCGCCAGC
* * * *
2717074 TTTTCAAATTGAATTCTCTAACCGTTAGTCGCCAGCC
1 ATTTCAAATTGAATTCTCTAATCGTCAGCCGCCAG-C
*
2717111 AATTTCAAATTGAATTCTCTAATTGTCAGCC
1 -ATTTCAAATTGAATTCTCTAATCGTCAGCC
2717142 AATCCAATTT
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
35 30 0.55
38 25 0.45
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (36 bp):
ATTTCAAATTGAATTCTCTAATCGTCAGCCGCCAGC
Found at i:2717132 original size:38 final size:38
Alignment explanation
Indices: 2716995--2717133 Score: 158
Period size: 38 Copynumber: 3.7 Consensus size: 38
2716985 CACCAGCCAT
* * * * *
2716995 CAGCCAATTCCAAATTGAATTTTCTAGTCGCTAGCCAC
1 CAGCCAATTTCAAATTGAATTCTCTAATCGTTAGCCGC
* * *
2717033 CGGCCAATTTCAAATTGAATTCTCTAGTCGTCAGCCGC
1 CAGCCAATTTCAAATTGAATTCTCTAATCGTTAGCCGC
* * *
2717071 CAG---TTTTCAAATTGAATTCTCTAACCGTTAGTCGC
1 CAGCCAATTTCAAATTGAATTCTCTAATCGTTAGCCGC
2717106 CAGCCAATTTCAAATTGAATTCTCTAAT
1 CAGCCAATTTCAAATTGAATTCTCTAAT
2717134 TGTCAGCCAA
Statistics
Matches: 84, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
35 30 0.36
38 54 0.64
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (38 bp):
CAGCCAATTTCAAATTGAATTCTCTAATCGTTAGCCGC
Found at i:2721794 original size:21 final size:20
Alignment explanation
Indices: 2721751--2721815 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
2721741 CAATCGTTAA
*
2721751 TTAATTTTAAATTAAATTC-T
1 TTAATTTTTAATT-AATTCAT
2721771 TTAATTTTTAATTAATTCAAT
1 TTAATTTTTAATTAATTC-AT
*
2721792 TTAA-ATTTAATTTAATTCAT
1 TTAATTTTTAA-TTAATTCAT
2721812 TTAA
1 TTAA
2721816 AAGGATACGC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.12
20 23 0.57
21 12 0.30
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAATTTTTAATTAATTCAT
Found at i:2722228 original size:13 final size:14
Alignment explanation
Indices: 2722199--2722229 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2722189 CAGCTAAAAC
2722199 AAAAACAAAAGGAA
1 AAAAACAAAAGGAA
*
2722213 AAAAACAGAAGGAA
1 AAAAACAAAAGGAA
2722227 AAA
1 AAA
2722230 TGGCAGAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.06, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAACAAAAGGAA
Found at i:2724514 original size:26 final size:25
Alignment explanation
Indices: 2724456--2724521 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
2724446 ATAGCTGTCT
*
2724456 TTTTTTAATAGTTTTATCAATTTCAA
1 TTTTTTAATAATTTTATCAATTT-AA
*
2724482 TTTTTTAATAATTTTAATTAATTT-A
1 TTTTTTAATAATTTT-ATCAATTTAA
*
2724507 TTTATTTAAAAATTT
1 TTT-TTTAATAATTT
2724522 AATACTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.11
26 24 0.69
27 7 0.20
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.61
Consensus pattern (25 bp):
TTTTTTAATAATTTTATCAATTTAA
Found at i:2725701 original size:50 final size:50
Alignment explanation
Indices: 2725647--2725951 Score: 461
Period size: 50 Copynumber: 6.1 Consensus size: 50
2725637 AGGTGTTGTC
* *
2725647 ATTGTTAACTATTCTTCACCAATCTTTGACAATAGAAAGAGGTGACCGTA
1 ATTGTTAACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGTA
* *
2725697 ATTGTTAACTATT-TTCACCAACCTTTAACAATAGAGAGAGGT-AGTCGTA
1 ATTGTTAACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGA-CCGTA
* * *
2725746 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCATA
1 ATTGTTAACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGTA
*
2725796 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGTA
1 ATTGTTAACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGTA
* * *
2725846 ATTGTTAACTATTTTTCACCAACCTTTGACAATAGAGAGAGGTGGCTGTA
1 ATTGTTAACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGTA
* * *
2725896 ATTGTTAACTATTTTTCACCAACTTTTGATAATAGAGAGAGGTGACCGTA
1 ATTGTTAACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGTA
2725946 ATTGTT
1 ATTGTT
2725952 GACTCTAAGC
Statistics
Matches: 233, Mismatches: 19, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
48 1 0.00
49 42 0.18
50 189 0.81
51 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (50 bp):
ATTGTTAACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGTA
Found at i:2729184 original size:50 final size:50
Alignment explanation
Indices: 2729120--2729479 Score: 343
Period size: 50 Copynumber: 7.2 Consensus size: 50
2729110 AAGTGTTGCC
* * **
2729120 ATTGTTGATTATTCTTCACCAACCTTTGATAATAGAAAGAAGTGGTCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAAAGAAGTGACCGTA
* *
2729170 ATTGTTGATTATTCTTCACCAACTTTTGACAATA-AAGAGAAGTGACCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAA-AGAAGTGACCGTA
* * * * *
2729220 ATTGTTGAGTATTCTTTACCAACCTTTGACAATCGAGAGAGGTGACCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAAAGAAGTGACCGTA
* * * * *
2729270 ATTGTTGACTATTCTTCACCAACCTTTAACAGTAGAGAG-AGATGATCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAAAGAAG-TGACCGTA
* * * **
2729320 ATTGTTAACTATTTTTCATCAATTTTTGACAATAGAAAG-AGATGACCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAAAGAAG-TGACCGTA
* * * * * **
2729370 ATTGTTGACTATTCTTTATCAACCTTTAACAATAGAGAG-AGATAACTATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAAAGAAG-TGACCGTA
* * * * *
2729420 ATTGTTAACTATTTTTCATCAACTTTTGACAATAGAAAG-AGTTGATCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAAAGAAG-TGACCGTA
2729470 ATTGTTGACT
1 ATTGTTGACT
2729480 TTAAACAACT
Statistics
Matches: 257, Mismatches: 50, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
49 3 0.01
50 253 0.98
51 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAAAGAAGTGACCGTA
Found at i:2729245 original size:100 final size:100
Alignment explanation
Indices: 2729120--2729479 Score: 411
Period size: 100 Copynumber: 3.6 Consensus size: 100
2729110 AAGTGTTGCC
* * * * ** *
2729120 ATTGTTGATTATTCTTCACCAACCTTTGATAATAGAAAGA-AGTGGTCGTAATTGTTGATTATTC
1 ATTGTTAACTATTTTTCACCAACCTTTGACAATAGAAAGAGA-TGACCGTAATTGTTGACTATTC
* * * *
2729184 TTCACCAACTTTTGACAATAAAGAGA-AGTGACCGTA
65 TTCACCAACCTTTAACAATAGAGAGAGA-TGACCATA
* * * * *
2729220 ATTGTTGAGTATTCTTT-ACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATTC
1 ATTGTTAACTATT-TTTCACCAACCTTTGACAATAGAAAGAGATGACCGTAATTGTTGACTATTC
* *
2729284 TTCACCAACCTTTAACAGTAGAGAGAGATGATCATA
65 TTCACCAACCTTTAACAATAGAGAGAGATGACCATA
* **
2729320 ATTGTTAACTATTTTTCATCAATTTTTGACAATAGAAAGAGATGACCGTAATTGTTGACTATTCT
1 ATTGTTAACTATTTTTCACCAACCTTTGACAATAGAAAGAGATGACCGTAATTGTTGACTATTCT
* * * *
2729385 TTATCAACCTTTAACAATAGAGAGAGATAACTATA
66 TCACCAACCTTTAACAATAGAGAGAGATGACCATA
* * * *
2729420 ATTGTTAACTATTTTTCATCAACTTTTGACAATAGAAAGAGTTGATCGTAATTGTTGACT
1 ATTGTTAACTATTTTTCACCAACCTTTGACAATAGAAAGAGATGACCGTAATTGTTGACT
2729480 TTAAACAACT
Statistics
Matches: 224, Mismatches: 32, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
99 3 0.01
100 218 0.97
101 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (100 bp):
ATTGTTAACTATTTTTCACCAACCTTTGACAATAGAAAGAGATGACCGTAATTGTTGACTATTCT
TCACCAACCTTTAACAATAGAGAGAGATGACCATA
Found at i:2729393 original size:150 final size:150
Alignment explanation
Indices: 2729120--2729475 Score: 439
Period size: 150 Copynumber: 2.4 Consensus size: 150
2729110 AAGTGTTGCC
* * * * *
2729120 ATTGTTGATTATTCTTCACCAACCTTTGATAATAGAAAGA-AGTGGTCGTAATTGTTGATTATTC
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAAAGAGA-TGATCGTAATTGTTAACTATTC
* *
2729184 TTCACCAACTTTTGACAATAAAGAGAAGTGACCGTAATTGTTGAGTATTCTTTACCAACCTTTGA
65 TTCACCAACTTTTGACAATAAAGAGAAGTGACCGTAATTGTTGACTATTCTTTACCAACCTTTAA
* * * *
2729249 CAATCGAGAGAGGTGACCGTA
130 CAATAGAGAGAGATAACCATA
* * * * *
2729270 ATTGTTGACTATTCTTCACCAACCTTTAACAGTAGAGAGAGATGATCATAATTGTTAACTATTTT
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAAAGAGATGATCGTAATTGTTAACTATTCT
* * *
2729335 TCATCAATTTTTGACAATAGAA-AG-AGATGACCGTAATTGTTGACTATTCTTTATCAACCTTTA
66 TCACCAACTTTTGACAATA-AAGAGAAG-TGACCGTAATTGTTGACTATTCTTTACCAACCTTTA
*
2729398 ACAATAGAGAGAGATAACTATA
129 ACAATAGAGAGAGATAACCATA
* * * * *
2729420 ATTGTTAACTATTTTTCATCAACTTTTGACAATAGAAAGAGTTGATCGTAATTGTT
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAAAGAGATGATCGTAATTGTT
2729476 GACTTTAAAC
Statistics
Matches: 174, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
149 2 0.01
150 169 0.97
151 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (150 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAAAGAGATGATCGTAATTGTTAACTATTCT
TCACCAACTTTTGACAATAAAGAGAAGTGACCGTAATTGTTGACTATTCTTTACCAACCTTTAAC
AATAGAGAGAGATAACCATA
Found at i:2731572 original size:2 final size:2
Alignment explanation
Indices: 2731565--2731604 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2731555 AAGTAATTAA
2731565 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
2731605 GTCTATAGAA
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:2732669 original size:60 final size:60
Alignment explanation
Indices: 2732598--2732718 Score: 174
Period size: 60 Copynumber: 2.0 Consensus size: 60
2732588 ATTATTTATT
* * *
2732598 ATAAATTGTAAATATTTTTAATTC-CGTAACACA-TTTTGTATTTCCCTTAAAATATTGAAA
1 ATAAATTGTAAATATTTTTAATTCTC-CAACACATTTTTGTAATT-CCTTAAAATATTAAAA
*
2732658 ATAAATTGTAAATATTTTTAATTCTCCAACACATTTTTTTAATTCCTTAAAATATTAAAA
1 ATAAATTGTAAATATTTTTAATTCTCCAACACATTTTTGTAATTCCTTAAAATATTAAAA
2732718 A
1 A
2732719 ATAATAAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
60 46 0.84
61 9 0.16
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (60 bp):
ATAAATTGTAAATATTTTTAATTCTCCAACACATTTTTGTAATTCCTTAAAATATTAAAA
Found at i:2733272 original size:18 final size:19
Alignment explanation
Indices: 2733241--2733288 Score: 64
Period size: 17 Copynumber: 2.6 Consensus size: 19
2733231 TCAAATTAAA
*
2733241 ATTTAATTTA-TTATTATT
1 ATTTAATATATTTATTATT
2733259 -TTTAATATATTTATTATT
1 ATTTAATATATTTATTATT
2733277 ATTTACATATAT
1 ATTTA-ATATAT
2733289 ATATATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 8 0.31
18 8 0.31
19 4 0.15
20 6 0.23
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTAATATATTTATTATT
Found at i:2735684 original size:36 final size:41
Alignment explanation
Indices: 2735600--2735690 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
2735590 TTAAGGAATG
* *
2735600 AAAGAAAAGAAAAGAGAGGGAAGTAAATGAAAAGGAAAGGA
1 AAAGAAAAGAAAAGAGAGGCAAGTAAATGAAAAGGAAAGCA
*
2735641 AAAGAAAAGAAAAGA-A-GCAAG-AAA-G-AAAGGAAATCA
1 AAAGAAAAGAAAAGAGAGGCAAGTAAATGAAAAGGAAAGCA
*
2735677 AAGGAAAAAGAAAA
1 AAAG-AAAAGAAAA
2735691 ATTATAGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
36 12 0.27
37 10 0.22
38 3 0.07
39 4 0.09
40 1 0.02
41 15 0.33
ACGTcount: A:0.68, C:0.02, G:0.26, T:0.03
Consensus pattern (41 bp):
AAAGAAAAGAAAAGAGAGGCAAGTAAATGAAAAGGAAAGCA
Found at i:2737629 original size:78 final size:75
Alignment explanation
Indices: 2737534--2737846 Score: 387
Period size: 75 Copynumber: 4.1 Consensus size: 75
2737524 GGTGGGGGAG
*
2737534 ACTTGTATGCCTCCTTAGGAGGAGGAGGAGGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGA
1 ACTTGTATGGCTCCTTAGGA-G-GG-GGAGGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGA
2737599 GGGGGAGACTTGT
63 GGGGGAGACTTGT
* ** * * *
2737612 ACTTGTATGGTTCCTTAGGAGGGGGAGG-GGGAGACTTGTACTTGTATGTTTCCT-TACGAGGGG
1 ACTTGTATGGCTCCTTAGGAGGGGGAGGAGGG-GACTTGTACTTGTA----AACTGGAGGAGGTG
2737675 GAGGGGGAGACTTGT
61 GAGGGGGAGACTTGT
* * * *
2737690 ACTTGTATGGTTCCTTAGGAGGGGGTGGAGGGGACTTGTACTTGTAAACCGGAGGAGGTGGTGGG
1 ACTTGTATGGCTCCTTAGGAGGGGGAGGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGAGGG
2737755 GGAGACTTGT
66 GGAGACTTGT
* * * * *
2737765 ATTTGTATGGCTCCTTAGGTGGAGGAGGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGTGGA
1 ACTTGTATGGCTCCTTAGGAGGGGGAGGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGAGGG
2737830 GGAGACTTGT
66 GGAGACTTGT
*
2737840 ATTTGTA
1 ACTTGTA
2737847 GGGGTGTGGC
Statistics
Matches: 206, Mismatches: 22, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
74 4 0.02
75 114 0.55
76 2 0.01
77 1 0.00
78 80 0.39
79 5 0.02
ACGTcount: A:0.20, C:0.11, G:0.42, T:0.27
Consensus pattern (75 bp):
ACTTGTATGGCTCCTTAGGAGGGGGAGGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGAGGG
GGAGACTTGT
Found at i:2737632 original size:39 final size:39
Alignment explanation
Indices: 2737589--2737810 Score: 265
Period size: 39 Copynumber: 5.8 Consensus size: 39
2737579 TGTAAACTGG
*
2737589 AGGAGGTGGAGGGGGAGACTTGTACTTGTATGGTTCCTT
1 AGGAGGGGGAGGGGGAGACTTGTACTTGTATGGTTCCTT
*
2737628 AGGAGGGGGAGGGGGAGACTTGTACTTGTATGTTTCCTT
1 AGGAGGGGGAGGGGGAGACTTGTACTTGTATGGTTCCTT
*
2737667 ACGAGGGGGAGGGGGAGACTTGTACTTGTATGGTTCCTT
1 AGGAGGGGGAGGGGGAGACTTGTACTTGTATGGTTCCTT
* ** **
2737706 AGGAGGGGGTGGAGGG-GACTTGTACTTGTA---AACCGG
1 AGGAGGGGGAGG-GGGAGACTTGTACTTGTATGGTTCCTT
* * * *
2737742 AGGAGGTGGTGGGGGAGACTTGTATTTGTATGGCTCCTT
1 AGGAGGGGGAGGGGGAGACTTGTACTTGTATGGTTCCTT
* *
2737781 AGGTGGAGGAGGAGGG-GACTTGTACTTGTA
1 AGGAGGGGGAGG-GGGAGACTTGTACTTGTA
2737811 AACTGGAGGA
Statistics
Matches: 157, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
35 3 0.02
36 26 0.17
39 122 0.78
40 6 0.04
ACGTcount: A:0.19, C:0.10, G:0.43, T:0.28
Consensus pattern (39 bp):
AGGAGGGGGAGGGGGAGACTTGTACTTGTATGGTTCCTT
Found at i:2737795 original size:75 final size:75
Alignment explanation
Indices: 2737491--2737846 Score: 386
Period size: 75 Copynumber: 4.7 Consensus size: 75
2737481 TGGCGGTGGT
* * * * *
2737491 GGAGGAGACTTGTATTTGTAAACTGGTGGGGGTGGT-GGGG-GA---G-ACTTGTATGCCTCCTT
1 GGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGTGGGGGAGACTTGTACTTGTATGGCTCCTT
2737550 AGGAGGAGGAGGA
66 ---AGGAGGAGGA
* *
2737563 GGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGAGGGGGAGACTTGTACTTGTATGGTTCCTT
1 GGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGTGGGGGAGACTTGTACTTGTATGGCTCCTT
*
2737628 AGGAGGGGGA
66 AGGAGGAGGA
** * * * * *
2737638 GG-GGGAGACTTGTACTTGTATGTTTCCT-TACGAGGGGGAGGGGGAGACTTGTACTTGTATGGT
1 GGAGGG-GACTTGTACTTGTA----AACTGGAGGAGGTGGTGGGGGAGACTTGTACTTGTATGGC
* *
2737701 TCCTTAGGAGGGGGT
61 TCCTTAGGAGGAGGA
* *
2737716 GGAGGGGACTTGTACTTGTAAACCGGAGGAGGTGGTGGGGGAGACTTGTATTTGTATGGCTCCTT
1 GGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGTGGGGGAGACTTGTACTTGTATGGCTCCTT
*
2737781 AGGTGGAGGA
66 AGGAGGAGGA
* *
2737791 GGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGTGGAGGAGACTTGTATTTGTA
1 GGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGTGGGGGAGACTTGTACTTGTA
2737847 GGGGTGTGGC
Statistics
Matches: 243, Mismatches: 28, Indels: 23
0.83 0.10 0.08
Matches are distributed among these distances:
72 31 0.13
73 4 0.02
74 6 0.02
75 120 0.49
77 1 0.00
78 76 0.31
79 5 0.02
ACGTcount: A:0.20, C:0.10, G:0.43, T:0.27
Consensus pattern (75 bp):
GGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGTGGGGGAGACTTGTACTTGTATGGCTCCTT
AGGAGGAGGA
Found at i:2737824 original size:39 final size:38
Alignment explanation
Indices: 2737711--2737833 Score: 99
Period size: 39 Copynumber: 3.2 Consensus size: 38
2737701 TCCTTAGGAG
* *
2737711 GGGGTGGAGGGGACTTGTACTTGTAAACCGGAGGAGGT
1 GGGGAGGAGGGGACTTGTACTTGTAAACTGGAGGAGGT
* * * ** ****
2737749 GGTG-GG-GGAGACTTGTATTTGTATGGCT-CCTTAGGT
1 GGGGAGGAGGGGACTTGTACTTGTA-AACTGGAGGAGGT
2737785 GGAGGAGGAGGGGACTTGTACTTGTAAACTGGAGGAGGT
1 GG-GGAGGAGGGGACTTGTACTTGTAAACTGGAGGAGGT
2737824 GGTGGAGGAG
1 GG-GGAGGAG
2737834 ACTTGTATTT
Statistics
Matches: 60, Mismatches: 20, Indels: 9
0.67 0.22 0.10
Matches are distributed among these distances:
36 21 0.35
37 4 0.07
38 7 0.12
39 28 0.47
ACGTcount: A:0.20, C:0.09, G:0.46, T:0.24
Consensus pattern (38 bp):
GGGGAGGAGGGGACTTGTACTTGTAAACTGGAGGAGGT
Found at i:2738091 original size:87 final size:87
Alignment explanation
Indices: 2737926--2738092 Score: 226
Period size: 87 Copynumber: 1.9 Consensus size: 87
2737916 CACTGGAGGT
* * * *
2737926 GGTGGAGACTTATACTTGTAAACAGGTGATGGTGGGGGTGGAGACTTGTACTTGTAGGGGTGCTT
1 GGTGGAGACTTATACTTGTAAACAGGAGATGGTGGGGGAGGAGACTTGTACTTGTAAGGCTGCTT
*
2737991 GGGTGGTGATGGTGGTGGTGGC
66 GGGCGGTGATGGTGGTGGTGGC
* * * * *
2738013 GGTGGTGACTTGTACTTGTAAACTGGAGTTGGTGGGGGAGGAGACTTGTACTTGTAAGGCTTCTT
1 GGTGGAGACTTATACTTGTAAACAGGAGATGGTGGGGGAGGAGACTTGTACTTGTAAGGCTGCTT
* *
2738078 TGGCGGTGGTGGTGG
66 GGGCGGTGATGGTGG
2738093 AGTATACACC
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
87 68 1.00
ACGTcount: A:0.16, C:0.09, G:0.44, T:0.31
Consensus pattern (87 bp):
GGTGGAGACTTATACTTGTAAACAGGAGATGGTGGGGGAGGAGACTTGTACTTGTAAGGCTGCTT
GGGCGGTGATGGTGGTGGTGGC
Found at i:2738839 original size:23 final size:23
Alignment explanation
Indices: 2738791--2738840 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2738781 CTCCTTTTGG
* *
2738791 TTTTTAAAATTATTTTTATTTAA
1 TTTTTAAAATTATTTATACTTAA
*
2738814 TTTTTTAAATTATTTAATACTT-A
1 TTTTTAAAATTATTT-ATACTTAA
2738837 TTTT
1 TTTT
2738841 CTTTTATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTTTAAAATTATTTATACTTAA
Found at i:2742839 original size:13 final size:14
Alignment explanation
Indices: 2742813--2742847 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
2742803 TCTTAAAACT
2742813 TTTTAAAAACATAA
1 TTTTAAAAACATAA
2742827 TTTTAAAAA-ATAA
1 TTTTAAAAACATAA
2742840 TTATTAAA
1 TT-TTAAA
2742848 GATGATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (14 bp):
TTTTAAAAACATAA
Found at i:2742986 original size:23 final size:23
Alignment explanation
Indices: 2742955--2742999 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2742945 TAATTTTATT
*
2742955 TTTAATTAAGTGATAT-AATTTAA
1 TTTAATTAAAT-ATATAAATTTAA
*
2742978 TTTACTTAAATATATAAATTTA
1 TTTAATTAAATATATAAATTTA
2743000 TATACTGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (23 bp):
TTTAATTAAATATATAAATTTAA
Found at i:2744559 original size:3 final size:3
Alignment explanation
Indices: 2744551--2744585 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
2744541 AGTAAATTTA
*
2744551 AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2744586 GAAACCTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2745791 original size:8 final size:8
Alignment explanation
Indices: 2745778--2745802 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2745768 CTTTTAAAAG
2745778 TAAAATAA
1 TAAAATAA
2745786 TAAAATAA
1 TAAAATAA
2745794 TAAAATAA
1 TAAAATAA
2745802 T
1 T
2745803 TTTTTTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
TAAAATAA
Found at i:2749038 original size:34 final size:34
Alignment explanation
Indices: 2748987--2749171 Score: 223
Period size: 34 Copynumber: 5.5 Consensus size: 34
2748977 GTAAAAACCA
*
2748987 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGAAACCTACCAAATCTC
* * *
2749021 CCATTTAGTCAATAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-AAACCTACCAAATCTC
* *
2749055 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGAAACCTACCAAATCTC
* * * *
2749089 CCATTTAATCAACAATGGTAAGCTACCAAATTTT
1 CCATTTAATCAACAATGGAAACCTACCAAATCTC
* *
2749123 CCATTTAGTCAACAATGGTAAACC-ACCAAATC-A
1 CCATTTAATCAACAATGG-AAACCTACCAAATCTC
2749156 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
2749172 TCTCCCACTT
Statistics
Matches: 131, Mismatches: 17, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
33 18 0.14
34 106 0.81
35 7 0.05
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGAAACCTACCAAATCTC
Found at i:2749106 original size:68 final size:68
Alignment explanation
Indices: 2748987--2749171 Score: 246
Period size: 68 Copynumber: 2.7 Consensus size: 68
2748977 GTAAAAACCA
* * * *
2748987 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAATAATGGTAAACCACCAAAT
1 CCATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAAAT
2749052 CAC
66 CAC
* * *
2749055 CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAAAT
***
2749120 TTT
66 CAC
* * *
2749123 CCATTTAGTCAACAATGGTAAACCACCAAATC-ACCATTTAATCAACAAT
1 CCATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAATCAACAAT
2749172 TCTCCCACTT
Statistics
Matches: 104, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 16 0.15
68 88 0.85
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (68 bp):
CCATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAAAT
CAC
Found at i:2753264 original size:19 final size:19
Alignment explanation
Indices: 2753237--2753299 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
2753227 TCACGTGTAC
* *
2753237 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
2753256 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
2753275 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
2753294 AGTACC
1 AGTACC
2753300 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:2753657 original size:34 final size:34
Alignment explanation
Indices: 2753606--2753786 Score: 215
Period size: 34 Copynumber: 5.4 Consensus size: 34
2753596 GTAAAAACCA
*
2753606 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGAAACCTACCAAATCTC
* * *
2753640 CCATTTAGTCAATAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-AAACCTACCAAATCTC
* *
2753674 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGAAACCTACCAAATCTC
* * * *
2753708 CCATTTAATCAACAATGGTAAGCTACCAAATTTT
1 CCATTTAATCAACAATGGAAACCTACCAAATCTC
* *
2753742 CCATTTAGTCAACAATGGTAAACC-ACCAAATC-A
1 CCATTTAATCAACAATGG-AAACCTACCAAATCTC
2753775 CCATTTAATCAA
1 CCATTTAATCAA
2753787 GAGAGAGAAA
Statistics
Matches: 127, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
33 14 0.11
34 106 0.83
35 7 0.06
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGAAACCTACCAAATCTC
Found at i:2753725 original size:68 final size:68
Alignment explanation
Indices: 2753606--2753786 Score: 238
Period size: 68 Copynumber: 2.7 Consensus size: 68
2753596 GTAAAAACCA
* * * *
2753606 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAATAATGGTAAACCACCAAAT
1 CCATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAAAT
2753671 CAC
66 CAC
* * *
2753674 CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAAAT
***
2753739 TTT
66 CAC
* * *
2753742 CCATTTAGTCAACAATGGTAAACCACCAAATC-ACCATTTAATCAA
1 CCATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAATCAA
2753787 GAGAGAGAAA
Statistics
Matches: 100, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 12 0.12
68 88 0.88
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.26
Consensus pattern (68 bp):
CCATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAAAT
CAC
Found at i:2754665 original size:36 final size:36
Alignment explanation
Indices: 2754625--2754908 Score: 217
Period size: 36 Copynumber: 7.7 Consensus size: 36
2754615 GTGAGGTGGT
* * *
2754625 GGTGGTGGAGGAGACTTGTATTTGTAAACGGGAGGG
1 GGTGGTGGAGGAGACTTGTACTTGTAAACCGGAGGA
* ** **
2754661 GGTGGTGGGGGAGACTTGTACTTGTATGGCTCCTTAGGA
1 GGTGGTGGAGGAGACTTGTACTTGTA---AACCGGAGGA
* * * *
2754700 GGAGGAGGAGGGGACTTGTACTTGTAAACTGGAGGA
1 GGTGGTGGAGGAGACTTGTACTTGTAAACCGGAGGA
* * ** **
2754736 GGTGGAGGGGGAGACTTGTACTTGTATGGTTCCTTAGGA
1 GGTGGTGGAGGAGACTTGTACTTGTA---AACCGGAGGA
* *
2754775 GGGGGTGGAGGGGACTTGTACTTGTAAACCGGAGGA
1 GGTGGTGGAGGAGACTTGTACTTGTAAACCGGAGGA
* *** *****
2754811 GGTGGTGGGGGAGACTTGTACTTGTATGGCTCCTTA
1 GGTGGTGGAGGAGACTTGTACTTGTAAACCGGAGGA
* * *
2754847 GGTGGAGGAGGGGACTTGTACTTGTAAACTGGAGGA
1 GGTGGTGGAGGAGACTTGTACTTGTAAACCGGAGGA
*
2754883 GGTGGTGGAGGAGACTTGTATTTGTA
1 GGTGGTGGAGGAGACTTGTACTTGTA
2754909 GGGGTGTGGC
Statistics
Matches: 183, Mismatches: 59, Indels: 12
0.72 0.23 0.05
Matches are distributed among these distances:
36 130 0.71
39 53 0.29
ACGTcount: A:0.20, C:0.10, G:0.43, T:0.27
Consensus pattern (36 bp):
GGTGGTGGAGGAGACTTGTACTTGTAAACCGGAGGA
Found at i:2754718 original size:75 final size:75
Alignment explanation
Indices: 2754631--2754908 Score: 427
Period size: 75 Copynumber: 3.7 Consensus size: 75
2754621 TGGTGGTGGT
* * * *
2754631 GGAGGAGACTTGTATTTGTAAACGGGAGGGGGTGGTGGGGGAGACTTGTACTTGTATGGCTCCTT
1 GGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGTGGGGGAGACTTGTACTTGTATGGCTCCTT
2754696 AGGAGGAGGA
66 AGGAGGAGGA
* *
2754706 GGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGAGGGGGAGACTTGTACTTGTATGGTTCCTT
1 GGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGTGGGGGAGACTTGTACTTGTATGGCTCCTT
* *
2754771 AGGAGGGGGT
66 AGGAGGAGGA
*
2754781 GGAGGGGACTTGTACTTGTAAACCGGAGGAGGTGGTGGGGGAGACTTGTACTTGTATGGCTCCTT
1 GGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGTGGGGGAGACTTGTACTTGTATGGCTCCTT
*
2754846 ---AGGTGGA
66 AGGAGGAGGA
* *
2754853 GGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGTGGAGGAGACTTGTATTTGTA
1 GGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGTGGGGGAGACTTGTACTTGTA
2754909 GGGGTGTGGC
Statistics
Matches: 187, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
72 58 0.31
75 129 0.69
ACGTcount: A:0.21, C:0.10, G:0.43, T:0.27
Consensus pattern (75 bp):
GGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGTGGGGGAGACTTGTACTTGTATGGCTCCTT
AGGAGGAGGA
Found at i:2754992 original size:54 final size:55
Alignment explanation
Indices: 2754874--2754997 Score: 130
Period size: 54 Copynumber: 2.3 Consensus size: 55
2754864 GTACTTGTAA
* * * * *
2754874 ACTGGAGGAGGTGGTGGAGGAGACTTGTATTTGTAGGGGTGTGGCTTAGGTGGTG
1 ACTGGAGGTGGTGGAGGAGGAGACTTGTACTTGTAGGGGTGGGGCGTAGGTGGTG
* * *
2754929 A-TGGTGGTGGTGGAGGAGGAGATTTGTACTTGTAAGGTGGTGGGGGGTA-GT-GT-
1 ACTGGAGGTGGTGGAGGAGGAGACTTGTACTTGT-AGG-GGTGGGGCGTAGGTGGTG
2754982 ACTGGAGGTGGTGGAG
1 ACTGGAGGTGGTGGAG
2754998 ACTTATACTT
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
53 1 0.02
54 42 0.74
55 6 0.11
56 8 0.14
ACGTcount: A:0.17, C:0.04, G:0.51, T:0.28
Consensus pattern (55 bp):
ACTGGAGGTGGTGGAGGAGGAGACTTGTACTTGTAGGGGTGGGGCGTAGGTGGTG
Found at i:2755109 original size:138 final size:139
Alignment explanation
Indices: 2754859--2755114 Score: 322
Period size: 138 Copynumber: 1.8 Consensus size: 139
2754849 TGGAGGAGGG
* * * *
2754859 GACTTGTACTTGTAAACTGGAGGAGGTGGTGGAGGAGACTTGTATTTGTAGGGGTGTGGCTTAGG
1 GACTTATACTTGTAAACGGGAGGAGGTGGGGGAGGAGACTTGTACTTGTAGGGGTGTGGCTTAGG
* * *
2754924 TGGTGATGGTGGTGGTGGAGGAGGAGATTTGTACTTGTAAGGTGGTGG-GGGGTAGTGTACTGGA
66 TGGTGATGGTGGTGGTGGAGGAGGAGACTTGTACTTATAAGGAGGTGGAGGGGTAGTGTACTGGA
2754988 GGTGGTGGA
131 GGTGGTGGA
* * * *
2754997 GACTTATACTTGTAAACGGGCGGTGGTGGGGGTGGAGACTTGTACTTGTA-GGG-GT-GCTTGGG
1 GACTTATACTTGTAAACGGGAGGAGGTGGGGGAGGAGACTTGTACTTGTAGGGGTGTGGCTTAGG
* * * *
2755059 TGGTGATGGTGGTGGTGGCGGTGGGGACTTGTATTTATAAACTGGAGGTGGAGGGG
66 TGGTGATGGTGGTGGTGGAGGAGGAGACTTGTACTTAT-AA--GGAGGTGGAGGGG
2755115 GAGGAGACTT
Statistics
Matches: 99, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
135 38 0.38
136 4 0.04
137 3 0.03
138 50 0.51
139 4 0.04
ACGTcount: A:0.17, C:0.07, G:0.47, T:0.29
Consensus pattern (139 bp):
GACTTATACTTGTAAACGGGAGGAGGTGGGGGAGGAGACTTGTACTTGTAGGGGTGTGGCTTAGG
TGGTGATGGTGGTGGTGGAGGAGGAGACTTGTACTTATAAGGAGGTGGAGGGGTAGTGTACTGGA
GGTGGTGGA
Found at i:2755220 original size:36 final size:34
Alignment explanation
Indices: 2755144--2755220 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 34
2755134 TGGGTGCTTT
*
2755144 GGTGGAGGTGGGGGAGACTTATACTTGTAAACTG
1 GGTGGAGGTGGGGGAGACTTATACTTGTAAACGG
* *
2755178 GG-GGAGGTGGAGGAGGAGACTTGTACTTGT-AAGGG
1 GGTGGAGGT-G-GG-GGAGACTTATACTTGTAAACGG
2755213 GGTGGAGG
1 GGTGGAGG
2755221 GTAATGCACT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
33 6 0.17
34 3 0.08
35 7 0.19
36 20 0.56
ACGTcount: A:0.22, C:0.06, G:0.49, T:0.22
Consensus pattern (34 bp):
GGTGGAGGTGGGGGAGACTTATACTTGTAAACGG
Found at i:2755264 original size:162 final size:161
Alignment explanation
Indices: 2754984--2755316 Score: 395
Period size: 162 Copynumber: 2.1 Consensus size: 161
2754974 GGTAGTGTAC
* * * *
2754984 TGGAGGTGGTGGAGACTTATACTTGTAAACGGGCGGTGGTGGGGGTGGAGACTTGTACTTGTAGG
1 TGGAGGTGGGGGAGACTTATACTTGTAAACGGGCGGAGGTGGAGGAGGAGACTTGTACTTGTAGG
* * * * * * *
2755049 GGTGCTTGGGTGGTGATGGTGGTGGTGGCGGTGGGGACTTGTATTTATAAACTGGAGGTGGAGGG
66 GGTGC-TGGGTGGTAATGCTGGAGGAGGCGGTGGAGACTTATACTTATAAACTGGAGGTGGAGGG
* *
2755114 GGAGGAGACTTGTACTTATATGGGTGCTTTGG
130 GGAGGAGACTTGTACTTATAAGGCTGCTTTGG
2755146 TGGAGGTGGGGGAGACTTATACTTGTAAACTGGG-GGAGGTGGAGGAGGAGACTTGTACTTGTAA
1 TGGAGGTGGGGGAGACTTATACTTGTAAAC-GGGCGGAGGTGGAGGAGGAGACTTGTACTTGT-A
* * * *
2755210 GGGG-G-TGGAG-GGTAATGCACTGGAGGAGGTGGTGGAGATTTATACTTGTAAACTGGAGTTGG
64 GGGGTGCTGG-GTGGTAATG--CTGGAGGAGGCGGTGGAGACTTATACTTATAAACTGGAGGTGG
* * *
2755272 TGGGGGAGGAGACTTGTACTTGTAAGGCTTCTTTGG
126 AGGGGGAGGAGACTTGTACTTATAAGGCTGCTTTGG
*
2755308 TGGTGGTGG
1 TGGAGGTGG
2755317 TGGTGGAGAA
Statistics
Matches: 145, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
160 9 0.06
161 1 0.01
162 127 0.88
163 8 0.06
ACGTcount: A:0.19, C:0.08, G:0.45, T:0.29
Consensus pattern (161 bp):
TGGAGGTGGGGGAGACTTATACTTGTAAACGGGCGGAGGTGGAGGAGGAGACTTGTACTTGTAGG
GGTGCTGGGTGGTAATGCTGGAGGAGGCGGTGGAGACTTATACTTATAAACTGGAGGTGGAGGGG
GAGGAGACTTGTACTTATAAGGCTGCTTTGG
Found at i:2755657 original size:2 final size:2
Alignment explanation
Indices: 2755650--2755684 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2755640 GCCATGATAA
2755650 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 A
2755685 AAATGTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2757396 original size:34 final size:34
Alignment explanation
Indices: 2757358--2757466 Score: 114
Period size: 34 Copynumber: 3.2 Consensus size: 34
2757348 TTATGTTGGC
* * *
2757358 TAAATGGATGGTTTGCTAGTTTGTTATTGTTGAT
1 TAAATGGATGATTTGATAGTTTGTCATTGTTGAT
* * *
2757392 TAAATAGG-CGATTTGGT-GATTTATCATTGTTGAT
1 TAAAT-GGATGATTTGATAG-TTTGTCATTGTTGAT
* *
2757426 TAAATTGATGATTTGATAGTTTGTCATTGTTGAC
1 TAAATGGATGATTTGATAGTTTGTCATTGTTGAT
2757460 TAAATGG
1 TAAATGG
2757467 CTAAAAGATA
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
33 2 0.03
34 55 0.92
35 3 0.05
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.46
Consensus pattern (34 bp):
TAAATGGATGATTTGATAGTTTGTCATTGTTGAT
Found at i:2761964 original size:34 final size:34
Alignment explanation
Indices: 2761922--2762071 Score: 216
Period size: 34 Copynumber: 4.4 Consensus size: 34
2761912 AAGTGGGAGA
2761922 ATTGTTGACTAAATGAGTGATTTGGTGGTTTG-C
1 ATTGTTGACTAAATGAGTGATTTGGTGGTTTGTC
* *
2761955 AATTGTTGACTAAATGGGTGATTTGGTAGTTTG-C
1 -ATTGTTGACTAAATGAGTGATTTGGTGGTTTGTC
* * *
2761989 TATTGTTGATTAGATGAGTGATTTGATGGTTTGTC
1 -ATTGTTGACTAAATGAGTGATTTGGTGGTTTGTC
2762024 ATTGTTGACTAAATG-GTGATTTGGTGGTTTGTC
1 ATTGTTGACTAAATGAGTGATTTGGTGGTTTGTC
2762057 ATTGTTGACTAAATG
1 ATTGTTGACTAAATG
2762072 GCTAAAAGAT
Statistics
Matches: 104, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
33 32 0.31
34 71 0.68
35 1 0.01
ACGTcount: A:0.22, C:0.05, G:0.29, T:0.44
Consensus pattern (34 bp):
ATTGTTGACTAAATGAGTGATTTGGTGGTTTGTC
Found at i:2765114 original size:23 final size:24
Alignment explanation
Indices: 2765088--2765133 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2765078 GCCACTCCAT
*
2765088 TTCATATT-TTTTTTTCTTTTTTC
1 TTCATATTCTTTCTTTCTTTTTTC
*
2765111 TTCATCTTCTTTCTTTCTTTTTT
1 TTCATATTCTTTCTTTCTTTTTT
2765134 ACCTAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (24 bp):
TTCATATTCTTTCTTTCTTTTTTC
Found at i:2766160 original size:32 final size:32
Alignment explanation
Indices: 2766105--2766962 Score: 1504
Period size: 32 Copynumber: 26.8 Consensus size: 32
2766095 AAAATGGTGA
* * * *
2766105 TTTGAAAAGCGTTGCCACTGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
2766137 TTTTAAATGGGTTGCCACCGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2766169 TTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2766201 TTTGAAATGGGTTGCCACCTACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2766233 TTT-AGAATGGGTTGCCACCGACCTGTGTGGGC
1 TTTGA-AATGGGTTGCCACCGACTTGTGTGGGC
*
2766265 TTTGAAATGGGTTGCCACCGACCTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2766297 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2766329 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2766361 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2766393 TTTGAAATGGGTTGCCACCGACCTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2766425 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2766457 TTTGAAATGGGTTGCCACCGACCTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2766489 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2766521 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2766553 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2766585 TTTGAAATGGGTTGCCACCGACCTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2766617 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2766649 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2766681 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2766713 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
2766745 TTTGGAATGGGTTGCCACCGACCTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2766777 TTTGAAATGGGTTGCCACCGACCTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2766809 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2766841 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2766873 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2766905 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
2766937 TTTGGAATGGG-TGCCACAGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
2766963 GATTTAAAAG
Statistics
Matches: 797, Mismatches: 27, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
31 14 0.02
32 782 0.98
33 1 0.00
ACGTcount: A:0.16, C:0.20, G:0.34, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:2766980 original size:27 final size:27
Alignment explanation
Indices: 2766945--2767518 Score: 882
Period size: 27 Copynumber: 21.0 Consensus size: 27
2766935 GCTTTGGAAT
* *
2766945 GGGTGCCACAGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
** *
2766972 GGACGCCACGAAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2766999 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
2767026 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2767053 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
2767081 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
2767108 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
2767136 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2767163 GGGTGCCACGGAGTTGT-GATCTTAAAA
1 GGGTGCCACGGAGTTGTGGA-CTTAAAA
*
2767190 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
2767217 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
*
2767245 GGGTGCCACGGAGTTGTGGTCTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
2767273 GGGTGTCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2767300 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
2767327 GGGTGCCACGGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2767354 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
2767382 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
2767409 GGGTGCCACGGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2767436 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
2767464 GGGT-CCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
2767490 GGATGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
2767518 G
1 G
2767519 AAAATACCAC
Statistics
Matches: 500, Mismatches: 37, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
26 11 0.02
27 348 0.70
28 141 0.28
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:2767209 original size:109 final size:108
Alignment explanation
Indices: 2766945--2767518 Score: 875
Period size: 109 Copynumber: 5.3 Consensus size: 108
2766935 GCTTTGGAAT
* * **
2766945 GGGTGCCACAGAGTTGTGGATTTAAAAGGACGCCAC-GAAGTTGTGGACTTAAAAGGGTGCCACG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAG-AGTTGTGGACTTAAAAGGGTGCCACG
* *
2767009 GAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAA
65 GAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
*
2767053 GGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCAC
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAG-GGTGCCAC
*
2767118 GGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
64 GGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
*
2767163 GGGTGCCACGGAGTTGT-GATCTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCAC
1 GGGTGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAG-GGTGCCAC
* *
2767227 GGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGTCTTTAAAA
64 GGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAA
* *
2767273 GGGTGTCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGG
*
2767338 AGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAA
66 AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAA
* * *
2767382 GGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTAAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGG
*
2767447 AGTTGTGGACTTTAAAAGGGT-CCACAGAGTTGTGGACTTAAAA
66 AGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
*
2767490 GGATGCCACGGAGTTGTGGACTTTAAAAG
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAG
2767519 AAAATACCAC
Statistics
Matches: 436, Mismatches: 22, Indels: 15
0.92 0.05 0.03
Matches are distributed among these distances:
108 44 0.10
109 257 0.59
110 133 0.31
111 2 0.00
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (108 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGG
AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:2767245 original size:164 final size:162
Alignment explanation
Indices: 2766945--2767518 Score: 891
Period size: 164 Copynumber: 3.5 Consensus size: 162
2766935 GCTTTGGAAT
* * ** *
2766945 GGGTGCCACAGAGTTGTGGATTTAAAAGGACGCCACGAAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
*
2767010 AGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACT
66 AGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-
*
2767075 TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
130 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
* *
2767108 GAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1 G-GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
* *
2767173 GAGTTGT-GATCTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCACGGAGTTATGG
65 GAGTTGTGGA-CTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAG-GGTGCCACGGAGTTGTGG
*
2767237 ACTTAAAAGGGTGCCACGGAGTTGTGGTCTTTAAAA
128 ACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAA
*
2767273 GGGTGTCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
* * *
2767338 AGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGAC
66 AGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC
*
2767403 TTAAAAGGGTGCCACGGAGTTGTGGACTAAAAA
130 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
* *
2767436 GGGTGCCACGGAGTTGTGGACTTTAAAAGGGT-CCACAGAGTTGTGGACTTAAAAGGATGCCACG
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
2767500 GAGTTGTGGACTTTAAAAG
65 GAGTTGTGGAC-TTAAAAG
2767519 AAAATACCAC
Statistics
Matches: 377, Mismatches: 26, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
163 69 0.18
164 274 0.73
165 34 0.09
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (162 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
AGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACT
TAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:2768577 original size:1 final size:1
Alignment explanation
Indices: 2768571--2768605 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
2768561 GGTGAAAAGG
**
2768571 TTTTTTTTTTTTTTTTTGGTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2768606 AGGATTAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (1 bp):
T
Found at i:2768593 original size:19 final size:19
Alignment explanation
Indices: 2768569--2768605 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2768559 AGGGTGAAAA
2768569 GGTTTTTTTTTTTTTTTTT
1 GGTTTTTTTTTTTTTTTTT
2768588 GGTTTTTTTTTTTTTTTT
1 GGTTTTTTTTTTTTTTTT
2768606 AGGATTAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (19 bp):
GGTTTTTTTTTTTTTTTTT
Found at i:2775396 original size:23 final size:24
Alignment explanation
Indices: 2775370--2775415 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2775360 GCCACTCCAT
*
2775370 TTCATATT-TTTTTTTCTTTTTTC
1 TTCATATTCTTTCTTTCTTTTTTC
*
2775393 TTCATCTTCTTTCTTTCTTTTTT
1 TTCATATTCTTTCTTTCTTTTTT
2775416 ACCTAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (24 bp):
TTCATATTCTTTCTTTCTTTTTTC
Found at i:2777179 original size:6 final size:6
Alignment explanation
Indices: 2777168--2777232 Score: 55
Period size: 6 Copynumber: 10.7 Consensus size: 6
2777158 TTTATCGATT
* *
2777168 TATAAA TATAAA TAT-AA TATAAA TTATTAAA -A-ATA TTTAAA TTATAAA
1 TATAAA TATAAA TATAAA TATAAA -TA-TAAA TATAAA TATAAA -TATAAA
2777216 TATAAA TATAATA TATA
1 TATAAA TATAA-A TATA
2777233 TTTAATAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
4 2 0.04
5 5 0.10
6 25 0.52
7 12 0.25
8 4 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (6 bp):
TATAAA
Found at i:2777188 original size:11 final size:11
Alignment explanation
Indices: 2777172--2777230 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
2777162 TCGATTTATA
2777172 AATATAAATAT
1 AATATAAATAT
2777183 AATATAAAT-T
1 AATATAAATAT
*
2777193 -AT-TAAAAAT
1 AATATAAATAT
*
2777202 -ATTTAAATTAT
1 AATATAAA-TAT
2777213 AAATATAAATAT
1 -AATATAAATAT
2777225 AATATA
1 AATATA
2777231 TATTTAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
8 4 0.10
9 5 0.12
10 5 0.12
11 17 0.43
12 3 0.08
13 6 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AATATAAATAT
Found at i:2777975 original size:25 final size:27
Alignment explanation
Indices: 2777947--2778005 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
2777937 TTACTAATAA
* *
2777947 AAAATTTTAA-TTAA-TATTATATATT
1 AAAATTTTAACTTAATTAGTACATATT
* *
2777972 AAAATTATAACTTAATTAGTACATTTT
1 AAAATTTTAACTTAATTAGTACATATT
2777999 AAAATTT
1 AAAATTT
2778006 ATAAACTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 9 0.33
26 4 0.15
27 14 0.52
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (27 bp):
AAAATTTTAACTTAATTAGTACATATT
Found at i:2784770 original size:26 final size:25
Alignment explanation
Indices: 2784722--2784770 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
2784712 TTTATGTTCA
*
2784722 TATATATATATTTCTTGAAAAAATT
1 TATATATATATTTCTTCAAAAAATT
2784747 TATATAGTAT-TTATCTTCAAAAAA
1 TATATA-TATATT-TCTTCAAAAAA
2784771 CAAAAGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (25 bp):
TATATATATATTTCTTCAAAAAATT
Found at i:2788934 original size:32 final size:33
Alignment explanation
Indices: 2788896--2788957 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
2788886 TACAATTATA
*
2788896 TAAATTTTTATATGTTAATA-ATTCATTTTAAG
1 TAAATTTTGATATGTTAATATATTCATTTTAAG
* *
2788928 TAAATTTTGATATGTTCATATATTCGTTTT
1 TAAATTTTGATATGTTAATATATTCATTTT
2788958 GCATTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 18 0.69
33 8 0.31
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (33 bp):
TAAATTTTGATATGTTAATATATTCATTTTAAG
Found at i:2789547 original size:34 final size:34
Alignment explanation
Indices: 2789499--2789578 Score: 142
Period size: 34 Copynumber: 2.4 Consensus size: 34
2789489 TATCTTTTAG
*
2789499 CCATTTAGTTAATAATGGCAAACCACCAAATCAC
1 CCATTTAGTCAATAATGGCAAACCACCAAATCAC
*
2789533 TCATTTAGTCAATAATGGCAAACCACCAAATCAC
1 CCATTTAGTCAATAATGGCAAACCACCAAATCAC
2789567 CCATTTAGTCAA
1 CCATTTAGTCAA
2789579 CAATTCTCCC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.25
Consensus pattern (34 bp):
CCATTTAGTCAATAATGGCAAACCACCAAATCAC
Found at i:2794056 original size:34 final size:34
Alignment explanation
Indices: 2794018--2794126 Score: 146
Period size: 34 Copynumber: 3.2 Consensus size: 34
2794008 TCTTTTAGCC
* *
2794018 ATTTAGTCAATAATGGCAAACCACTAAATCACCT
1 ATTTAGTCAATAATGACAAACCACAAAATCACCT
* * **
2794052 ATTTAATCAACAATGACAAACCACAAAATTGCCT
1 ATTTAGTCAATAATGACAAACCACAAAATCACCT
**
2794086 ATTTAGTCAATAATGACAAACCACCGAATCACCT
1 ATTTAGTCAATAATGACAAACCACAAAATCACCT
2794120 ATTTAGT
1 ATTTAGT
2794127 TAACACTTAT
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (34 bp):
ATTTAGTCAATAATGACAAACCACAAAATCACCT
Found at i:2800489 original size:36 final size:36
Alignment explanation
Indices: 2800449--2800732 Score: 172
Period size: 36 Copynumber: 7.6 Consensus size: 36
2800439 GTGGGGTGGT
* *
2800449 GGTGGAGGAGGAGACTTGTATTTGTAAACGGGAGGG
1 GGTGGAGGAGGAGACTTGTACTTGTAAACGGGAGGA
* * ** *
2800485 GGTGGTGGGGGAGACTTGTACTTGTATGGCTCCTTAGGAGGA
1 GGTGGAGGAGGAGACTTGTACTTGTA----AAC--GGGAGGA
* *
2800527 GGAGGAGGAGGGGACTTGTACTTGTAAACGGGAGGA
1 GGTGGAGGAGGAGACTTGTACTTGTAAACGGGAGGA
* ** ***
2800563 GGTGGAGGGGGAGACTTGTACTTGTATGGTTCCTTAGGA
1 GGTGGAGGAGGAGACTTGTACTTGTA---AACGGGAGGA
* * * *
2800602 GGGGGAGGAGGGGACTTATACTTGTAAACTGGAGGA
1 GGTGGAGGAGGAGACTTGTACTTGTAAACGGGAGGA
* * * ** *** *
2800638 GGTGGTGGGGGGGACTTGTACTTGTATGGCTCCTTAGGT
1 GGTGGAGGAGGAGACTTGTACTTGTA---AACGGGAGGA
* * *
2800677 GGAGGAGGAGGGGACTTGTACTTGTAAACTGGAGGA
1 GGTGGAGGAGGAGACTTGTACTTGTAAACGGGAGGA
*
2800713 GGTGGTGGAGGAGACTTGTA
1 GGTGGAGGAGGAGACTTGTA
2800733 TTGGTAGGGG
Statistics
Matches: 183, Mismatches: 53, Indels: 24
0.70 0.20 0.09
Matches are distributed among these distances:
36 100 0.55
38 1 0.01
39 54 0.30
40 1 0.01
42 27 0.15
ACGTcount: A:0.21, C:0.09, G:0.45, T:0.25
Consensus pattern (36 bp):
GGTGGAGGAGGAGACTTGTACTTGTAAACGGGAGGA
Found at i:2800609 original size:75 final size:75
Alignment explanation
Indices: 2800452--2800732 Score: 427
Period size: 75 Copynumber: 3.7 Consensus size: 75
2800442 GGGTGGTGGT
* * *
2800452 GGAGGAGGAGACTTGTATTTGTAAACGGGAGGGGGTGGTGGGGGAGACTTGTACTTGTATGGCTC
1 GGAGGAGGGGACTTGTACTTGTAAACGGGAGGAGGTGGTGGGGGAGACTTGTACTTGTATGGCTC
2800517 CTTAGGAGGAGG
66 CTTAGGA-G-GG
* *
2800529 AGGAGGAGGGGACTTGTACTTGTAAACGGGAGGAGGTGGAGGGGGAGACTTGTACTTGTATGGTT
1 -GGAGGAGGGGACTTGTACTTGTAAACGGGAGGAGGTGGTGGGGGAGACTTGTACTTGTATGGCT
2800594 CCTTAGGAGGG
65 CCTTAGGAGGG
* * *
2800605 GGAGGAGGGGACTTATACTTGTAAACTGGAGGAGGTGGTGGGGGGGACTTGTACTTGTATGGCTC
1 GGAGGAGGGGACTTGTACTTGTAAACGGGAGGAGGTGGTGGGGGAGACTTGTACTTGTATGGCTC
* *
2800670 CTTAGGTGGA
66 CTTAGGAGGG
* *
2800680 GGAGGAGGGGACTTGTACTTGTAAACTGGAGGAGGTGGTGGAGGAGACTTGTA
1 GGAGGAGGGGACTTGTACTTGTAAACGGGAGGAGGTGGTGGGGGAGACTTGTA
2800733 TTGGTAGGGG
Statistics
Matches: 188, Mismatches: 15, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
75 118 0.63
76 2 0.01
77 1 0.01
78 67 0.36
ACGTcount: A:0.22, C:0.09, G:0.44, T:0.25
Consensus pattern (75 bp):
GGAGGAGGGGACTTGTACTTGTAAACGGGAGGAGGTGGTGGGGGAGACTTGTACTTGTATGGCTC
CTTAGGAGGG
Found at i:2800848 original size:90 final size:86
Alignment explanation
Indices: 2800761--2801131 Score: 260
Period size: 90 Copynumber: 4.4 Consensus size: 86
2800751 AGGTGGTGAG
2800761 GGTGGTGGTGGAGGAGGAGACTTGTACTTGTAAGGTGGTGGGGGGTAGTGCACTGGAGGTGGTGG
1 GGTGGTGGTGGAGGAGGAGACTTGTACTTGTAAGGTGGTGGGGGGT-GTGCACTGGAGGTGGTGG
*
2800826 AGACTTGTACTTGTAAACT---
65 AGACTTATACTTGTAAACTGGA
* * * * * * * * *
2800845 GGTGTTGGTGGGGGTGGAGACTTGTACTTGTACGGGTGCTTGGGTGGTGATGGAGGTGGTGGTGG
1 GGTGGTGGTGGAGGAGGAGACTTGTACTTGTA-AGGTG-GTGGGGGGTG-TGCA-CTGGAGGTGG
*
2800910 TGGGGACTTATACTTGTAAACTGGA
62 TGGAGACTTATACTTGTAAACTGGA
* * * * * * *
2800935 GGTGG-AG-GG-GGAGGAGACTTGTACTTGT-A-----TGGGTGCTTTG--GTGGTGGTGGGGGA
1 GGTGGTGGTGGAGGAGGAGACTTGTACTTGTAAGGTGGTGGGGGGTGTGCACTGGAGGTGGTGGA
2800989 GACTTATACTTGTAAAC---A
66 GACTTATACTTGTAAACTGGA
* * * * * *
2801007 GGGGGAGGAGGAGGAGGAGACTTGTACTTGTAAGGGGGTGGAGGGTAATGCACTGGTGGAGGAGG
1 GGTGGTGGTGGAGGAGGAGACTTGTACTTGTAAGGTGGTGGGGGGT-GTGCAC---T---GGAGG
*
2801072 TGGTGGAGATTTATACTTGTAAACTGGA
59 TGGTGGAGACTTATACTTGTAAACTGGA
*
2801100 -GT--TGGTGGGGGAGGAGACTTGTACTTGTAAGG
1 GGTGGTGGTGGAGGAGGAGACTTGTACTTGTAAGG
2801132 CTTCTTTGGT
Statistics
Matches: 226, Mismatches: 33, Indels: 50
0.73 0.11 0.16
Matches are distributed among these distances:
72 5 0.02
73 1 0.00
74 2 0.01
75 48 0.21
76 1 0.00
78 2 0.01
79 7 0.03
81 5 0.02
82 2 0.01
84 29 0.13
85 5 0.02
86 10 0.04
87 47 0.21
88 2 0.01
89 1 0.00
90 57 0.25
92 1 0.00
93 1 0.00
ACGTcount: A:0.19, C:0.08, G:0.46, T:0.27
Consensus pattern (86 bp):
GGTGGTGGTGGAGGAGGAGACTTGTACTTGTAAGGTGGTGGGGGGTGTGCACTGGAGGTGGTGGA
GACTTATACTTGTAAACTGGA
Found at i:2800899 original size:36 final size:35
Alignment explanation
Indices: 2800818--2800899 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 35
2800808 GTGCACTGGA
*
2800818 GGTGGTGGAGACTTGTACTTGTAAACTGGTGTTGGT
1 GGTGGTGGAGACTTGTACTTGT-AACGGGTGTTGGT
*
2800854 GGGGGTGGAGACTTGTACTTGT-ACGGGTGCTTGGGT
1 GGTGGTGGAGACTTGTACTTGTAACGGGTG-TT-GGT
*
2800890 GGTGATGGAG
1 GGTGGTGGAG
2800900 GTGGTGGTGG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
34 6 0.15
35 2 0.05
36 32 0.80
ACGTcount: A:0.15, C:0.09, G:0.45, T:0.32
Consensus pattern (35 bp):
GGTGGTGGAGACTTGTACTTGTAACGGGTGTTGGT
Found at i:2800932 original size:87 final size:87
Alignment explanation
Indices: 2800818--2801128 Score: 297
Period size: 87 Copynumber: 3.7 Consensus size: 87
2800808 GTGCACTGGA
* * * * *
2800818 GGTGGTGGAGACTTGTACTTGTAAACTGGTGTTGGTGGGGGTGGAGACTTGTACTTGTACGGGTG
1 GGTGGTGGAGACTTATACTTGTAAACTGGAGGTGGAGGGGGAGGAGACTTGTACTTGTACGGGTG
2800883 CTTGGGTGGTGATGGAGGTGGT
66 CTTGGGTGGTGATGGAGGTGGT
* *
2800905 GGTGGTGGGGACTTATACTTGTAAACTGGAGGTGGAGGGGGAGGAGACTTGTACTTGTATGGGTG
1 GGTGGTGGAGACTTATACTTGTAAACTGGAGGTGGAGGGGGAGGAGACTTGTACTTGTACGGGTG
2800970 CTT---T-G-G-T---GGTGGT
66 CTTGGGTGGTGATGGAGGTGGT
* * * * *
2800983 -G-GG-GGAGACTTATACTTGTAAACAGGGGGAGGAGGAGGAGGAGACTTGTACTTGTAAGGGGG
1 GGTGGTGGAGACTTATACTTGTAAACTGGAGGTGGAGGGGGAGGAGACTTGTACTTGT-A-CGGG
** ** * * *
2801045 TG-GAGGGTAATGCACTGGTGGAGGA
64 TGCTTGGGTGGTG-A-TGGAGGTGGT
* * *
2801070 GGTGGTGGAGATTTATACTTGTAAACTGGAGTTGGTGGGGGAGGAGACTTGTACTTGTA
1 GGTGGTGGAGACTTATACTTGTAAACTGGAGGTGGAGGGGGAGGAGACTTGTACTTGTA
2801129 AGGCTTCTTT
Statistics
Matches: 183, Mismatches: 25, Indels: 30
0.77 0.11 0.13
Matches are distributed among these distances:
75 47 0.26
76 3 0.02
77 6 0.03
78 6 0.03
79 1 0.01
81 2 0.01
82 1 0.01
83 1 0.01
84 2 0.01
87 65 0.36
88 1 0.01
89 3 0.02
90 45 0.25
ACGTcount: A:0.20, C:0.08, G:0.44, T:0.28
Consensus pattern (87 bp):
GGTGGTGGAGACTTATACTTGTAAACTGGAGGTGGAGGGGGAGGAGACTTGTACTTGTACGGGTG
CTTGGGTGGTGATGGAGGTGGT
Found at i:2800939 original size:138 final size:139
Alignment explanation
Indices: 2800689--2800944 Score: 315
Period size: 138 Copynumber: 1.8 Consensus size: 139
2800679 AGGAGGAGGG
* *
2800689 GACTTGTACTTGTAAACTGGAGGAGGTGGTGGAGGAGACTTGTATTGGTAGGGGTGTGGCTTAGG
1 GACTTGTACTTGTAAACTGGAGGAGGTGGGGGAGGAGACTTGTATTGGTAGCGGTGTGGCTTAGG
* * *
2800754 TGGTGAGGGTGGTGGTGGAGGAGGAGACTTGTACTTGTAAGGTGGTGG-GGGGTAGTGCACTGGA
66 TGGTGAGGGAGGTGGTGGAGGAGGAGACTTATACTTGTAAGGAGGTGGAGGGGTAGTGCACTGGA
2800818 GGTGGTGGA
131 GGTGGTGGA
* ** * *
2800827 GACTTGTACTTGTAAACTGGTGTTGGTGGGGGTGGAGACTTGTACTT-GTA-CGG-GT-GCTTGG
1 GACTTGTACTTGTAAACTGGAGGAGGTGGGGGAGGAGACTTGTA-TTGGTAGCGGTGTGGCTTAG
* * * *
2800888 GTGGTGATGGAGGTGGTGGTGGTGGGGACTTATACTTGTAAACTGGAGGTGGAGGGG
65 GTGGTGAGGGAGGTGGTGGAGGAGGAGACTTATACTTGT-AA--GGAGGTGGAGGGG
2800945 GAGGAGACTT
Statistics
Matches: 99, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
135 38 0.38
136 4 0.04
137 2 0.02
138 49 0.49
139 6 0.06
ACGTcount: A:0.17, C:0.07, G:0.47, T:0.29
Consensus pattern (139 bp):
GACTTGTACTTGTAAACTGGAGGAGGTGGGGGAGGAGACTTGTATTGGTAGCGGTGTGGCTTAGG
TGGTGAGGGAGGTGGTGGAGGAGGAGACTTATACTTGTAAGGAGGTGGAGGGGTAGTGCACTGGA
GGTGGTGGA
Found at i:2800954 original size:36 final size:36
Alignment explanation
Indices: 2800895--2801039 Score: 103
Period size: 36 Copynumber: 3.9 Consensus size: 36
2800885 TGGGTGGTGA
* * * *
2800895 TGGAGGTGGTGGTGGTGGGGACTTATACTTGTAAAC
1 TGGAGGTGGAGGGGGAGGAGACTTATACTTGTAAAC
* ***
2800931 TGGAGGTGGAGGGGGAGGAGACTTGTACTTGTATGGG
1 TGGAGGTGGAGGGGGAGGAGACTTATACTTGTA-AAC
** *
2800968 TGCTTTGGTGGTGGTGGG-GGAGACTTATACTTGTAAAC
1 TG--GAGGTGGAGG-GGGAGGAGACTTATACTTGTAAAC
* * * * *
2801006 AGGGGGAGGAGGAGGAGGAGACTTGTACTTGTAA
1 TGGAGGTGGAGGGGGAGGAGACTTATACTTGTAA
2801040 GGGGGTGGAG
Statistics
Matches: 82, Mismatches: 22, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
35 2 0.02
36 51 0.62
37 2 0.02
38 1 0.01
39 23 0.28
40 3 0.04
ACGTcount: A:0.21, C:0.08, G:0.44, T:0.27
Consensus pattern (36 bp):
TGGAGGTGGAGGGGGAGGAGACTTATACTTGTAAAC
Found at i:2800996 original size:75 final size:75
Alignment explanation
Indices: 2800899--2801038 Score: 228
Period size: 75 Copynumber: 1.9 Consensus size: 75
2800889 TGGTGATGGA
* * *
2800899 GGTGGTGGTGGTGGGGACTTATACTTGTAAACTGGAGGTGGAGGGGGAGGAGACTTGTACTTGTA
1 GGTGGTGGTGGTGGGGACTTATACTTGTAAACAGGAGGAGGAGGAGGAGGAGACTTGTACTTGTA
2800964 TGGGTGCTTT
66 TGGGTGCTTT
*
2800974 GGTGGTGGTGG-GGGAGACTTATACTTGTAAACAGGGGGAGGAGGAGGAGGAGACTTGTACTTGT
1 GGTGGTGGTGGTGGG-GACTTATACTTGTAAACAGGAGGAGGAGGAGGAGGAGACTTGTACTTGT
2801038 A
65 A
2801039 AGGGGGTGGA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
74 3 0.05
75 57 0.95
ACGTcount: A:0.21, C:0.08, G:0.44, T:0.27
Consensus pattern (75 bp):
GGTGGTGGTGGTGGGGACTTATACTTGTAAACAGGAGGAGGAGGAGGAGGAGACTTGTACTTGTA
TGGGTGCTTT
Found at i:2803244 original size:2 final size:2
Alignment explanation
Indices: 2803237--2803266 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2803227 TATTATAGAC
2803237 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
2803267 TCTACAATAA
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:2803556 original size:3 final size:3
Alignment explanation
Indices: 2803548--2803579 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2803538 TTTCTCTAGT
*
2803548 TTA TTA TTA TTA ATA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2803580 TCTAGAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2805193 original size:14 final size:14
Alignment explanation
Indices: 2805174--2805204 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2805164 TTCGTATCAA
*
2805174 TTAAATCTTTTTTG
1 TTAAATCCTTTTTG
2805188 TTAAATCCTTTTTG
1 TTAAATCCTTTTTG
2805202 TTA
1 TTA
2805205 CTAAAACCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.06, T:0.61
Consensus pattern (14 bp):
TTAAATCCTTTTTG
Found at i:2808263 original size:13 final size:13
Alignment explanation
Indices: 2808245--2808283 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
2808235 TGGGTCAGTC
2808245 TGGGTATGTTATT
1 TGGGTATGTTATT
*
2808258 TGGGTATATTATT
1 TGGGTATGTTATT
2808271 TGGGCTATGTTAT
1 TGGG-TATGTTAT
2808284 GAGTCTTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.18, C:0.03, G:0.28, T:0.51
Consensus pattern (13 bp):
TGGGTATGTTATT
Found at i:2808464 original size:3 final size:3
Alignment explanation
Indices: 2808456--2808491 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2808446 CCATTTCATA
2808456 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
2808492 ATTTTTCTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:2815311 original size:2 final size:2
Alignment explanation
Indices: 2815301--2815344 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
2815291 AATATATCAT
* *
2815301 TC TC CC TC TC TC AC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2815343 TC
1 TC
2815345 AATAACATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.02, C:0.52, G:0.00, T:0.45
Consensus pattern (2 bp):
TC
Found at i:2816601 original size:3 final size:3
Alignment explanation
Indices: 2816593--2816625 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2816583 TCAACTTTGC
2816593 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2816626 TAAAACTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2828526 original size:2 final size:2
Alignment explanation
Indices: 2828513--2828565 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
2828503 TGTCCTTTGA
* * * *
2828513 AT AT AC AT AT AT AT AT AT GT AT AT AT GT CT 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 AT
2828555 AT AT AT AT AT A
1 AT AT AT AT AT A
2828566 AGGAGCATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2830849 original size:11 final size:11
Alignment explanation
Indices: 2830816--2830856 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
2830806 TAAAAAGGAA
2830816 ATAAATTATAAT
1 ATAAATT-TAAT
*
2830828 ATTAAAATTAAT
1 A-TAAATTTAAT
2830840 ATAAATTTAAT
1 ATAAATTTAAT
2830851 ATAAAT
1 ATAAAT
2830857 ATATAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 15 0.58
12 6 0.23
13 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATAAATTTAAT
Found at i:2830853 original size:28 final size:27
Alignment explanation
Indices: 2830822--2830886 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
2830812 GGAAATAAAT
2830822 TATAATAT-TAAA-ATTAATATAAATTTAA
1 TATAATATATAAATATT-ATA-AAATTT-A
*
2830850 TATAAATATATAAATATTTTAAAATTTA
1 TAT-AATATATAAATATTATAAAATTTA
2830878 TATAATATA
1 TATAATATA
2830887 AATTATTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
27 6 0.18
28 7 0.21
29 11 0.33
30 6 0.18
31 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TATAATATATAAATATTATAAAATTTA
Found at i:2830896 original size:25 final size:29
Alignment explanation
Indices: 2830842--2830894 Score: 76
Period size: 26 Copynumber: 1.9 Consensus size: 29
2830832 AAATTAATAT
2830842 AAATTTAATATAAATATATAAATATTTTA
1 AAATTTAATATAAATATATAAATATTTTA
*
2830871 AAATTT-ATAT-AATATA-AATTATTT
1 AAATTTAATATAAATATATAAATATTT
2830895 AATTAACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
27 6 0.26
28 4 0.17
29 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
AAATTTAATATAAATATATAAATATTTTA
Found at i:2831649 original size:32 final size:33
Alignment explanation
Indices: 2831613--2831688 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 33
2831603 TTTAATACAT
*
2831613 TTATATATTTACGTAATTTTAATTTTA-TTATA
1 TTATATATTTAAGTAATTTTAATTTTATTTATA
* * *
2831645 TTATAT-TTTAATTATTTTTTATTTTATTTATA
1 TTATATATTTAAGTAATTTTAATTTTATTTATA
2831677 TTATATATTTAA
1 TTATATATTTAA
2831689 ATTTATCTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 16 0.42
32 17 0.45
33 5 0.13
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (33 bp):
TTATATATTTAAGTAATTTTAATTTTATTTATA
Found at i:2831658 original size:16 final size:16
Alignment explanation
Indices: 2831634--2831688 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
2831624 CGTAATTTTA
2831634 ATTTT-ATTATATTAT
1 ATTTTAATTATATTAT
* *
2831649 ATTTTAATTATTTTTT
1 ATTTTAATTATATTAT
*
2831665 ATTTTATTTATATTAT
1 ATTTTAATTATATTAT
2831681 ATATTTAA
1 AT-TTTAA
2831689 ATTTATCTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
15 5 0.16
16 23 0.72
17 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTTAATTATATTAT
Found at i:2833848 original size:26 final size:26
Alignment explanation
Indices: 2833817--2833870 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
2833807 TATGTATATG
2833817 TATTATA-A-TTAATTATCATTTTATTA
1 TATTATATACTTAATT-TCATTTT-TTA
*
2833843 TATTATATACTTAATTTTATTTTTTA
1 TATTATATACTTAATTTCATTTTTTA
2833869 TA
1 TA
2833871 ATTTATTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 12 0.48
27 7 0.28
28 6 0.24
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (26 bp):
TATTATATACTTAATTTCATTTTTTA
Found at i:2833856 original size:28 final size:29
Alignment explanation
Indices: 2833806--2833870 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
2833796 TTTTAAAAAA
2833806 TTATGTATATGTATTATAATTAATTATCATT
1 TTAT-TATATGTATTATAATTAATT-TCATT
* *
2833837 TTATTATAT-TA-TATACTTAATTTTATT
1 TTATTATATGTATTATAATTAATTTCATT
2833864 TT-TTATA
1 TTATTATA
2833871 ATTTATTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 5 0.16
27 6 0.19
28 10 0.31
29 2 0.06
30 5 0.16
31 4 0.12
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (29 bp):
TTATTATATGTATTATAATTAATTTCATT
Found at i:2834154 original size:22 final size:22
Alignment explanation
Indices: 2834111--2834154 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2834101 ATTGTAATTT
*
2834111 TTTATGATTATTTTGTACTATA
1 TTTATGATTATTTTATACTATA
*
2834133 TTTAT-ATTATGTTTATATTATA
1 TTTATGATTAT-TTTATACTATA
2834155 ATCGTAATTA
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:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTATGATTATTTTATACTATA
Found at i:2834508 original size:32 final size:33
Alignment explanation
Indices: 2834449--2834516 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
2834439 CAACACAATA
*
2834449 AAAATGAATATATGAATATATTCAAATTTATAT
1 AAAATGAATATATGAATATATTAAAATTTATAT
* * *
2834482 AAAAT-AATTTATTAATATTTTAAAATTTATAT
1 AAAATGAATATATGAATATATTAAAATTTATAT
2834514 AAA
1 AAA
2834517 CATATAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 26 0.84
33 5 0.16
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (33 bp):
AAAATGAATATATGAATATATTAAAATTTATAT
Found at i:2835336 original size:16 final size:15
Alignment explanation
Indices: 2835299--2835339 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
2835289 AATAAAAAAT
2835299 AAAATAATT-AT-TA
1 AAAATAATTAATATA
2835312 AAAA-AATTAATATA
1 AAAATAATTAATATA
2835326 AAAATATATTAATA
1 AAAATA-ATTAATA
2835340 AATTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.17
13 6 0.25
14 6 0.25
15 1 0.04
16 7 0.29
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAATAATTAATATA
Found at i:2836338 original size:9 final size:9
Alignment explanation
Indices: 2836324--2836433 Score: 54
Period size: 9 Copynumber: 12.3 Consensus size: 9
2836314 GTAATATAAT
2836324 TATATTTTA
1 TATATTTTA
2836333 TATATTTTA
1 TATATTTTA
2836342 TAT-TTATT-
1 TATATT-TTA
2836350 TA-ATTTT-
1 TATATTTTA
*
2836357 T-TATATT-
1 TATATTTTA
*
2836364 TATATTATA
1 TATATTTTA
*
2836373 TAAATTTTTAA
1 TATA-TTTT-A
2836384 TATATTTATA
1 TATATTT-TA
* *
2836394 TAATTTTTTT
1 T-ATATTTTA
*
2836404 TATATTTTT
1 TATATTTTA
*
2836413 TACA-TTTA
1 TATATTTTA
2836421 TCATATTTTA
1 T-ATATTTTA
2836431 TAT
1 TAT
2836434 TACATTTATA
Statistics
Matches: 78, Mismatches: 12, Indels: 22
0.70 0.11 0.20
Matches are distributed among these distances:
7 8 0.10
8 14 0.18
9 31 0.40
10 15 0.19
11 10 0.13
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (9 bp):
TATATTTTA
Done.