Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, whole genome shotgun sequence
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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 12 of 130
Found at i:3376912 original size:29 final size:30
Alignment explanation
Indices: 3376880--3376949 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 30
3376870 TTATTTTTAT
* *
3376880 TTTATTATTTTTTTGGTT-TTTTATCTATC
1 TTTATTATTTTTTTAGTTGATTTATCTATC
* * *
3376909 TTTA-AATTTTTTTAGTTGATTTATCTTTT
1 TTTATTATTTTTTTAGTTGATTTATCTATC
*
3376938 TTTATTAGTTTT
1 TTTATTATTTTT
3376950 ATCATTAGTT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
28 11 0.34
29 16 0.50
30 5 0.16
ACGTcount: A:0.17, C:0.04, G:0.07, T:0.71
Consensus pattern (30 bp):
TTTATTATTTTTTTAGTTGATTTATCTATC
Found at i:3377695 original size:3 final size:3
Alignment explanation
Indices: 3377684--3377729 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
3377674 GTTTTTTTAA
* *
3377684 TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3377730 TCTAAATTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:3377869 original size:62 final size:67
Alignment explanation
Indices: 3377803--3377944 Score: 161
Period size: 71 Copynumber: 2.1 Consensus size: 67
3377793 TGATTTTTCT
3377803 AAAATAAAA-TT-AAAAAAAAAAATTTTT-T-TTTTAGGA-AAAGTTGAAAGTATCAATTT-TCT
1 AAAATAAAATTTCAAAAAAAAAAATTTTTATATTTTAGGAGAAAGTTGAAAGTATCAATTTCTC-
3377862 TTA
65 TTA
* * *
3377865 AAAATAAAATTTCTAAAATAAAAATTTTTAAAAGTATTTTAGGAGAAAGTTGAAAGTATTAATTT
1 AAAATAAAATTTCAAAAAAAAAAATTTTT---A-TATTTTAGGAGAAAGTTGAAAGTATCAATTT
*
3377930 CTCTTG
62 CTCTTA
3377936 AAAATAAAA
1 AAAATAAAA
3377945 AGGTTTTAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
62 9 0.14
63 2 0.03
64 14 0.21
69 1 0.02
70 8 0.12
71 30 0.45
72 2 0.03
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.37
Consensus pattern (67 bp):
AAAATAAAATTTCAAAAAAAAAAATTTTTATATTTTAGGAGAAAGTTGAAAGTATCAATTTCTCT
TA
Found at i:3377884 original size:14 final size:15
Alignment explanation
Indices: 3377865--3377897 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3377855 ATTTTCTTTA
3377865 AAAAT-AAAATTTCT
1 AAAATAAAAATTTCT
*
3377879 AAAATAAAAATTTTT
1 AAAATAAAAATTTCT
3377894 AAAA
1 AAAA
3377898 GTATTTTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATAAAAATTTCT
Found at i:3378044 original size:57 final size:57
Alignment explanation
Indices: 3377894--3378159 Score: 199
Period size: 57 Copynumber: 4.7 Consensus size: 57
3377884 AAAAATTTTT
* * * * * * *
3377894 AAAAGTATTTTAGGAGAAAGTTGAAAGTATTAATTTCTCTTGAAAATAAAAAGGTTT-TAA
1 AAAAATATTTTAAGAAAAAGTTGAAAGTATCAATTT-T-TTTAAAATTAAAA--TTTCAAA
* * * * *
3377954 AAAAATATTTTTAGGAAAAAATTGAAAGCATCAATTTTTCTT-GAATTGAAATTTCAAA
1 AAAAATA-TTTTAAGAAAAAGTTGAAAGTATCAATTTTT-TTAAAATTAAAATTTCAAA
*
3378012 AAAAATATTTTAAGAAAAAGTTGATAGTATCAATTTTTTTCAAAATTAAAATTTCAAA
1 AAAAATATTTTAAGAAAAAGTTGAAAGTATCAATTTTTTT-AAAATTAAAATTTCAAA
* * * * *
3378070 AAAAA-AATTAAAG-AAAAGTTGAAAGTATCAATTTTGCTTAAAATAAAAACTTC---
1 AAAAATATTTTAAGAAAAAGTTGAAAGTATCAATTTT-TTTAAAATTAAAATTTCAAA
* * *
3378123 -CAAATGTTTTAAAGAAAAA-TTAAAAGTATCAATTTTT
1 AAAAATATTTT-AAGAAAAAGTTGAAAGTATCAATTTTT
3378160 CTTTTACAAA
Statistics
Matches: 169, Mismatches: 28, Indels: 25
0.76 0.13 0.11
Matches are distributed among these distances:
52 3 0.02
53 2 0.01
54 19 0.11
55 4 0.02
56 35 0.21
57 38 0.22
58 28 0.17
59 7 0.04
60 8 0.05
61 25 0.15
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.35
Consensus pattern (57 bp):
AAAAATATTTTAAGAAAAAGTTGAAAGTATCAATTTTTTTAAAATTAAAATTTCAAA
Found at i:3378248 original size:15 final size:16
Alignment explanation
Indices: 3378228--3378260 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3378218 AGTTAAATCA
3378228 TTATTT-TTTTTTATT
1 TTATTTCTTTTTTATT
*
3378243 TTATTTCTTTTTTCTT
1 TTATTTCTTTTTTATT
3378259 TT
1 TT
3378261 CTTAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (16 bp):
TTATTTCTTTTTTATT
Found at i:3378729 original size:24 final size:21
Alignment explanation
Indices: 3378702--3378744 Score: 59
Period size: 24 Copynumber: 1.9 Consensus size: 21
3378692 ACAAGTAAGA
3378702 TGATATATATAAACATATTTTATG
1 TGATATAT-TAAA-A-ATTTTATG
3378726 TGATATATTAAAAATTTTA
1 TGATATATTAAAAATTTTA
3378745 AAATATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 1 0.05
23 4 0.21
24 8 0.42
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (21 bp):
TGATATATTAAAAATTTTATG
Found at i:3379278 original size:24 final size:24
Alignment explanation
Indices: 3379251--3379301 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
3379241 TATTTTTAAT
*
3379251 AAATTTA-TTAAATTTAATGCAAAA
1 AAATTTATTTAAA-TCAATGCAAAA
*
3379275 AAATTTATTTAAATCAATTCAAAA
1 AAATTTATTTAAATCAATGCAAAA
3379299 AAA
1 AAA
3379302 AATATTACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATTTATTTAAATCAATGCAAAA
Found at i:3389209 original size:16 final size:16
Alignment explanation
Indices: 3389188--3389222 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3389178 AACATAATAT
3389188 AATTATAT-AATATAAA
1 AATTATATGAATA-AAA
3389204 AATTATATGAATAAAA
1 AATTATATGAATAAAA
3389220 AAT
1 AAT
3389223 ATGAATATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
AATTATATGAATAAAA
Found at i:3390712 original size:21 final size:22
Alignment explanation
Indices: 3390670--3390722 Score: 90
Period size: 22 Copynumber: 2.4 Consensus size: 22
3390660 CTTGAAATTA
3390670 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
3390692 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
3390713 ATAAATATAT
1 ATAAA-ATAT
3390723 ATAAATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 9 0.30
22 21 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:3392344 original size:21 final size:21
Alignment explanation
Indices: 3392314--3392368 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
3392304 TGATTTATAC
3392314 TTTT-TCTCTAAAAATTCATT
1 TTTTCTCTCTAAAAATTCATT
*
3392334 TTTTCTCTCTAAAAATTTATT
1 TTTTCTCTCTAAAAATTCATT
*
3392355 TTCTCTCTCTAAAA
1 TTTTCTCTCTAAAA
3392369 CCAAATCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 4 0.12
21 28 0.88
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTTCTCTCTAAAAATTCATT
Found at i:3392626 original size:21 final size:22
Alignment explanation
Indices: 3392583--3392634 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
3392573 AGAAAAATCC
3392583 ACAATAAAAAATTTAGTCACAA
1 ACAATAAAAAATTTAGTCACAA
3392605 A-AATAAAAAA-TTA-TCACCCAA
1 ACAATAAAAAATTTAGTCA--CAA
3392626 ACAATAAAA
1 ACAATAAAA
3392635 TACATAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 3 0.11
20 3 0.11
21 13 0.48
22 8 0.30
ACGTcount: A:0.63, C:0.15, G:0.02, T:0.19
Consensus pattern (22 bp):
ACAATAAAAAATTTAGTCACAA
Found at i:3393171 original size:21 final size:21
Alignment explanation
Indices: 3393145--3393217 Score: 87
Period size: 20 Copynumber: 3.5 Consensus size: 21
3393135 TTGATCTGAA
*
3393145 TTTAAAGAGAGAAAATGAATT
1 TTTAAAGAGAGAAAATGAAAT
* **
3393166 TTTAAA-AAAGAGTATGAAAT
1 TTTAAAGAGAGAAAATGAAAT
3393186 TTTAAAGAGAGAAAAT-AAAT
1 TTTAAAGAGAGAAAATGAAAT
3393206 TTTAAGAGAGAG
1 TTTAA-AGAGAG
3393218 TATGAATATA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 25 0.58
21 18 0.42
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.27
Consensus pattern (21 bp):
TTTAAAGAGAGAAAATGAAAT
Found at i:3393190 original size:41 final size:40
Alignment explanation
Indices: 3393145--3393223 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 40
3393135 TTGATCTGAA
*
3393145 TTTAAAGAGAGAAAATGAATTTTTAAAAAAGAGTATGAAAT
1 TTTAAAGAGAGAAAAT-AAATTTTAAAAAAGAGTATGAAAT
* *
3393186 TTTAAAGAGAGAAAATAAATTTTAAGAGAGAGTATGAA
1 TTTAAAGAGAGAAAATAAATTTTAAAAAAGAGTATGAA
3393224 TATAGATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 19 0.54
41 16 0.46
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (40 bp):
TTTAAAGAGAGAAAATAAATTTTAAAAAAGAGTATGAAAT
Found at i:3394053 original size:27 final size:27
Alignment explanation
Indices: 3394002--3394053 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
3393992 TAAATATAAA
*
3394002 ATAATATTATTTAATTTAATTTTATTT
1 ATAATATTATTTAATTTAATCTTATTT
* *
3394029 ATAATATTATTTTATTTTATCTTAT
1 ATAATATTATTTAATTTAATCTTAT
3394054 CATAACTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (27 bp):
ATAATATTATTTAATTTAATCTTATTT
Found at i:3406700 original size:19 final size:20
Alignment explanation
Indices: 3406655--3406711 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
3406645 AATTTTAAAA
**
3406655 TTTTAATAATAATTATATATG
1 TTTTAATAA-AAAAATATATG
3406676 TGTTTAATAAAAAAATATAT-
1 T-TTTAATAAAAAAATATATG
*
3406696 TTTTAAAAAATAAAAT
1 TTTTAATAAA-AAAAT
3406712 CATAATACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 8 0.26
20 6 0.19
21 9 0.29
22 8 0.26
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (20 bp):
TTTTAATAAAAAAATATATG
Found at i:3409990 original size:17 final size:16
Alignment explanation
Indices: 3409950--3409990 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3409940 TAAAATTAAA
3409950 ATTAAT-AAA-AAATT
1 ATTAATAAAATAAATT
3409964 ATTAATAAAATAAATT
1 ATTAATAAAATAAATT
*
3409980 TTTAGATAAAA
1 ATTA-ATAAAA
3409991 CTTGAACATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 6 0.26
15 3 0.13
16 8 0.35
17 6 0.26
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
ATTAATAAAATAAATT
Found at i:3410446 original size:14 final size:14
Alignment explanation
Indices: 3410420--3410465 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
3410410 TTTGTATTCG
3410420 TTTAAATTTTATTTA
1 TTTAAA-TTTATTTA
3410435 TTTAAATTTATTTA
1 TTTAAATTTATTTA
* *
3410449 ATTATGATTTATTTA
1 TTTA-AATTTATTTA
3410464 TT
1 TT
3410466 ATTTATGAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (14 bp):
TTTAAATTTATTTA
Found at i:3417379 original size:56 final size:56
Alignment explanation
Indices: 3417301--3417409 Score: 155
Period size: 56 Copynumber: 1.9 Consensus size: 56
3417291 CGAAATTATG
* * * *
3417301 AGTTTGTGGTTGTTAGTAATTACTGAGTAAACAACAAAAGCTGAGTCAATTATTTA
1 AGTTTGTGGTTCTTAGTAATTACTGAGTAAAAAACAAAAACTGAATCAATTATTTA
* * *
3417357 AGTTTGTGGTTCTTGGTTATTACTGATTAAAAAACAAAAACTGAATCAATTAT
1 AGTTTGTGGTTCTTAGTAATTACTGAGTAAAAAACAAAAACTGAATCAATTAT
3417410 CCAAAAGCAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 46 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (56 bp):
AGTTTGTGGTTCTTAGTAATTACTGAGTAAAAAACAAAAACTGAATCAATTATTTA
Found at i:3418310 original size:18 final size:18
Alignment explanation
Indices: 3418260--3418311 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
3418250 TAAAAAATTT
3418260 ATATAATATTTAAATTAAGA
1 ATATAATATTTAAATT-A-A
* *
3418280 ATATGATAATTAACATT-A
1 ATATAATATTTAA-ATTAA
3418298 ATATAATATTTAAA
1 ATATAATATTTAAA
3418312 ATTTATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 1 0.04
18 12 0.44
20 11 0.41
21 3 0.11
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (18 bp):
ATATAATATTTAAATTAA
Found at i:3418371 original size:18 final size:19
Alignment explanation
Indices: 3418348--3418389 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
3418338 TTTAAATTTA
3418348 ATTATATTAA-AAATAAAT
1 ATTATATTAATAAATAAAT
*
3418366 ATTATATTAATTAATAAAT
1 ATTATATTAATAAATAAAT
3418385 -TTATA
1 ATTATA
3418390 ATTTAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTATATTAATAAATAAAT
Found at i:3418415 original size:28 final size:28
Alignment explanation
Indices: 3418369--3418459 Score: 89
Period size: 28 Copynumber: 3.2 Consensus size: 28
3418359 AATAAATATT
3418369 ATATTA-ATTAATAAA-TTTATAATTTAA
1 ATATTATATTAA-AAATTTTATAATTTAA
* *
3418396 ATATTATATTAAAAATTTTAAAATTTAC
1 ATATTATATTAAAAATTTTATAATTTAA
* *
3418424 GTATTATATTAAATATTTAATTATAATTTAA
1 ATATTATATTAAA-AATT--TTATAATTTAA
3418455 A-ATTA
1 ATATTA
3418460 GAGCAATCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
27 9 0.17
28 27 0.52
29 3 0.06
30 4 0.08
31 9 0.17
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
ATATTATATTAAAAATTTTATAATTTAA
Found at i:3418879 original size:22 final size:21
Alignment explanation
Indices: 3418837--3418888 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3418827 TTCGAAATTA
**
3418837 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTAAAAAT
3418858 ATAAAATATTACTTTTAAAAAT
1 ATAAAATATTA-TTTTAAAAAT
3418880 AT-AAATATT
1 ATAAAATATT
3418889 TAAATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
ATAAAATATTATTTTAAAAAT
Found at i:3418892 original size:8 final size:8
Alignment explanation
Indices: 3418873--3418914 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
3418863 ATATTACTTT
*
3418873 TAAAAATA
1 TAAATATA
*
3418881 TAAATATT
1 TAAATATA
3418889 TAAATATA
1 TAAATATA
*
3418897 TAATTATA
1 TAAATATA
3418905 TAAATATA
1 TAAATATA
3418913 TA
1 TA
3418915 TAAATAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TAAATATA
Found at i:3418892 original size:16 final size:16
Alignment explanation
Indices: 3418871--3418920 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
3418861 AAATATTACT
3418871 TTTAAAAATATAAATA
1 TTTAAAAATATAAATA
* *
3418887 TTTAAATATATAATTA
1 TTTAAAAATATAAATA
*
3418903 TATAAATATATATAAATA
1 TTTAAA-A-ATATAAATA
3418921 AAAAATTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 19 0.70
18 8 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAAAAATATAAATA
Found at i:3418920 original size:26 final size:24
Alignment explanation
Indices: 3418878--3418929 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
3418868 ACTTTTAAAA
* *
3418878 ATATAAATATTTAAATATATAATT
1 ATATAAATATTTAAATAAAAAATT
3418902 ATATAAATATATATAAATAAAAAATT
1 ATATAAATAT-T-TAAATAAAAAATT
3418928 AT
1 AT
3418930 TTTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.42
25 1 0.04
26 13 0.54
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATATAAATATTTAAATAAAAAATT
Found at i:3419051 original size:21 final size:22
Alignment explanation
Indices: 3419025--3419072 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
3419015 TTCGAAATTA
**
3419025 ATAAAATATTA-TTTTTTAAAT
1 ATAAAATATTACTTTTAAAAAT
3419046 ATAAAATATTACTTTTAAAAAT
1 ATAAAATATTACTTTTAAAAAT
3419068 ATAAA
1 ATAAA
3419073 TATGTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAAAATATTACTTTTAAAAAT
Found at i:3419073 original size:21 final size:20
Alignment explanation
Indices: 3419024--3419075 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
3419014 ATTCGAAATT
**
3419024 AATA-AAATATTATTTTTTA
1 AATATAAATATTATTTTAAA
3419043 AATATAAAATATTACTTTTAAA
1 AATAT-AAATATTA-TTTTAAA
3419065 AATATAAATAT
1 AATATAAATAT
3419076 GTAAATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 4 0.14
21 14 0.50
22 10 0.36
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATAAATATTATTTTAAA
Found at i:3419073 original size:188 final size:188
Alignment explanation
Indices: 3418756--3419125 Score: 695
Period size: 188 Copynumber: 2.0 Consensus size: 188
3418746 GGATCGGATT
* *
3418756 ATGATGAATTTTTATTCGTTTTGAATTCGATTCGATTTGATAATGTATAAATCATATCTGATTCA
1 ATGATGAATTTTTATTCGTTTTGAACTCGATCCGATTTGATAATGTATAAATCATATCTGATTCA
3418821 ATTAAATTCGAAATTAATAAAATATTATTTTTTAAATATAAAATATTACTTTTAAAAATATAAAT
66 ATTAAATTCGAAATTAATAAAATATTATTTTTTAAATATAAAATATTACTTTTAAAAATATAAAT
*
3418886 ATTTAAATATATAATTATATAAATATATATAAATAAAAAATTATTTTTATATCGAATC
131 ATGTAAATATATAATTATATAAATATATATAAATAAAAAATTATTTTTATATCGAATC
*
3418944 ATGATGAATTTTTATTCGTTTTGAACTCGATCCGATTTGATAATGTATAAATCATATCTGATTTA
1 ATGATGAATTTTTATTCGTTTTGAACTCGATCCGATTTGATAATGTATAAATCATATCTGATTCA
*
3419009 ATTAGATTCGAAATTAATAAAATATTATTTTTTAAATATAAAATATTACTTTTAAAAATATAAAT
66 ATTAAATTCGAAATTAATAAAATATTATTTTTTAAATATAAAATATTACTTTTAAAAATATAAAT
3419074 ATGTAAATATATAATTATATAAATATATATAAATAAAAAATTATTTTTATAT
131 ATGTAAATATATAATTATATAAATATATATAAATAAAAAATTATTTTTATAT
3419126 AATATCAAAT
Statistics
Matches: 177, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
188 177 1.00
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (188 bp):
ATGATGAATTTTTATTCGTTTTGAACTCGATCCGATTTGATAATGTATAAATCATATCTGATTCA
ATTAAATTCGAAATTAATAAAATATTATTTTTTAAATATAAAATATTACTTTTAAAAATATAAAT
ATGTAAATATATAATTATATAAATATATATAAATAAAAAATTATTTTTATATCGAATC
Found at i:3419080 original size:8 final size:8
Alignment explanation
Indices: 3419061--3419102 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
3419051 ATATTACTTT
*
3419061 TAAAAATA
1 TAAATATA
*
3419069 TAAATATG
1 TAAATATA
3419077 TAAATATA
1 TAAATATA
*
3419085 TAATTATA
1 TAAATATA
3419093 TAAATATA
1 TAAATATA
3419101 TA
1 TA
3419103 TAAATAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (8 bp):
TAAATATA
Found at i:3419881 original size:45 final size:45
Alignment explanation
Indices: 3419815--3419907 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
3419805 GAAAAGAAAA
*
3419815 TATTCATCTAAGCAATCATTTGCCTTTAAGAGCAAAAATTAAACT
1 TATTCATCTAAGCAATCATTTGCCTTTAAGAACAAAAATTAAACT
*
3419860 TATTCATCTAAGCAATTATTTGCCTTTAAGAACAAAAATTAAACT
1 TATTCATCTAAGCAATCATTTGCCTTTAAGAACAAAAATTAAACT
3419905 TAT
1 TAT
3419908 CTAATGAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (45 bp):
TATTCATCTAAGCAATCATTTGCCTTTAAGAACAAAAATTAAACT
Found at i:3420476 original size:17 final size:17
Alignment explanation
Indices: 3420441--3420478 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3420431 TCAAAAAAGA
*
3420441 AAAATATAAAAATATTT
1 AAAATATAAAAATAATT
3420458 AAAATA-AAAAATAAATT
1 AAAATATAAAAAT-AATT
3420475 AAAA
1 AAAA
3420479 CGAAGGAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATATAAAAATAATT
Found at i:3422547 original size:14 final size:14
Alignment explanation
Indices: 3422528--3422577 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
3422518 AAAATTTTTA
*
3422528 ATTTTTATTATATT
1 ATTTTTATAATATT
* *
3422542 ATTTTTAAAATTTT
1 ATTTTTATAATATT
*
3422556 AATTCTTATAATATT
1 -ATTTTTATAATATT
3422571 ATTTTTA
1 ATTTTTA
3422578 AAAAATTTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTTTTATAATATT
Found at i:3422600 original size:29 final size:28
Alignment explanation
Indices: 3422504--3422602 Score: 101
Period size: 29 Copynumber: 3.3 Consensus size: 28
3422494 ATTTGACCCT
*
3422504 TATAGTATTATTTAAAAATTTTTAATTTTTA
1 TATATTATT-TTTAAAAA-TTTTAA-TTTTA
3422535 TTATATTATTTTT-AAAATTTTAATTCTTA
1 -TATATTATTTTTAAAAATTTTAATT-TTA
*
3422564 TAATATTATTTTTAAAAAATTTAATATTTA
1 T-ATATTATTTTTAAAAATTTTAAT-TTTA
*
3422594 TACATTATT
1 TATATTATT
3422603 ATCTGTCGAA
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
28 3 0.05
29 27 0.45
30 18 0.30
31 4 0.07
32 8 0.13
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (28 bp):
TATATTATTTTTAAAAATTTTAATTTTA
Found at i:3422601 original size:58 final size:57
Alignment explanation
Indices: 3422484--3422602 Score: 134
Period size: 58 Copynumber: 2.1 Consensus size: 57
3422474 AGTACTCTTC
* * * * *
3422484 TATTTTTAAAATTTGACCCTTATAGTATTATTTAAAAATTTTTAATTTTTATTATAT
1 TATTTTTAAAATTTAACCCTTATAATATTATTTAAAAATATTTAATATTTATTACAT
**
3422541 TATTTTTAAAATTTTAATTCTTATAATATTATTTTTAAAAA-ATTTAATATTTA-TACAT
1 TATTTTTAAAA-TTTAACCCTTATAATATTA--TTTAAAAATATTTAATATTTATTACAT
3422599 TATT
1 TATT
3422603 ATCTGTCGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
57 11 0.21
58 23 0.44
59 10 0.19
60 8 0.15
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (57 bp):
TATTTTTAAAATTTAACCCTTATAATATTATTTAAAAATATTTAATATTTATTACAT
Found at i:3425254 original size:105 final size:106
Alignment explanation
Indices: 3425071--3425282 Score: 399
Period size: 105 Copynumber: 2.0 Consensus size: 106
3425061 TAGGATTTCA
3425071 ATATAAAAGAGTTGGCACATAGCATAAAACTTGTGCATGATATTAGGAATTTATGACAGAGAAGG
1 ATATAAAAGAGTTGGCACATAGCATAAAACTTGTGCATGATATTAGGAATTTATGACAGAGAAGG
*
3425136 TAATTCAACATCACCAAAACCAAGTACTATGCCACAAACAG
66 TAATTCAACATCACCAAAACCAAGGACTATGCCACAAACAG
3425177 ATATAAAAGAGTTGGCACATAGCAT-AAACTTGTGCATGATATTAGGAATTTATGACAGAGAAGG
1 ATATAAAAGAGTTGGCACATAGCATAAAACTTGTGCATGATATTAGGAATTTATGACAGAGAAGG
*
3425241 TAATTTAACATCACCAAAACCAAGGACTATGCCACAAACAG
66 TAATTCAACATCACCAAAACCAAGGACTATGCCACAAACAG
3425282 A
1 A
3425283 GCGGGGAAAC
Statistics
Matches: 104, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
105 79 0.76
106 25 0.24
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (106 bp):
ATATAAAAGAGTTGGCACATAGCATAAAACTTGTGCATGATATTAGGAATTTATGACAGAGAAGG
TAATTCAACATCACCAAAACCAAGGACTATGCCACAAACAG
Found at i:3444516 original size:21 final size:21
Alignment explanation
Indices: 3444487--3444527 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3444477 CATAAAATGT
* *
3444487 TAAAATATAATGAATTATTTC
1 TAAAATATAATAAAGTATTTC
*
3444508 TAAATTATAATAAAGTATTT
1 TAAAATATAATAAAGTATTT
3444528 GTGATGTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (21 bp):
TAAAATATAATAAAGTATTTC
Found at i:3444608 original size:18 final size:18
Alignment explanation
Indices: 3444570--3444611 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
3444560 ATATTTAAAT
3444570 TATAA-ATTTATTAATTTA
1 TATAATATTTATT-ATTTA
3444588 TATAATATTTATT-TTTAA
1 TATAATATTTATTATTT-A
3444606 TATAAT
1 TATAAT
3444612 TAATTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.14
18 12 0.55
19 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATAATATTTATTATTTA
Found at i:3456061 original size:17 final size:17
Alignment explanation
Indices: 3456039--3456088 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
3456029 GAATAATAAA
3456039 ATATATTAAATTAAATT
1 ATATATTAAATTAAATT
**
3456056 ATATATTAAATT-TTTT
1 ATATATTAAATTAAATT
*
3456072 ATAT-TTAAAATAAATT
1 ATATATTAAATTAAATT
3456088 A
1 A
3456089 AATAAAATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 6 0.22
16 9 0.33
17 12 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATTAAATTAAATT
Found at i:3457114 original size:13 final size:13
Alignment explanation
Indices: 3457098--3457140 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
3457088 ATTCATCAAT
*
3457098 TTTTTTAATTTAA
1 TTTTTTAATATAA
3457111 TTTTTTAATAT-A
1 TTTTTTAATATAA
3457123 TTATTTTAATATAA
1 TT-TTTTAATATAA
3457137 TTTT
1 TTTT
3457141 AAATATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 3 0.11
13 21 0.78
14 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTTTAATATAA
Found at i:3457137 original size:26 final size:25
Alignment explanation
Indices: 3457100--3457149 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3457090 TCATCAATTT
* *
3457100 TTTTAATTTAATTTTTTAATATATTA
1 TTTTAATATAA-TTTTAAATATATTA
3457126 TTTTAATATAATTTTAAATATATT
1 TTTTAATATAATTTTAAATATATT
3457150 TAAAATTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTTAATATAATTTTAAATATATTA
Found at i:3457139 original size:11 final size:12
Alignment explanation
Indices: 3457113--3457150 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
3457103 TAATTTAATT
3457113 TTTTAATATATTA
1 TTTTAATATA-TA
3457126 TTTTAATATA-A
1 TTTTAATATATA
3457137 TTTTAA-ATATA
1 TTTTAATATATA
3457148 TTT
1 TTT
3457151 AAAATTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.12
11 11 0.46
13 10 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTTAATATATA
Found at i:3458847 original size:29 final size:30
Alignment explanation
Indices: 3458785--3458871 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 30
3458775 AATTCTAATG
* * *
3458785 AAAATAAATATTTTAAGATTTAATTAAATA
1 AAAATAAATATTTAAAAATTTAATTAATTA
* *
3458815 AAAA-AAATATTTAAAAATTAAATTAATTC
1 AAAATAAATATTTAAAAATTTAATTAATTA
* *
3458844 AAAATAAAAAATT-AAAATTTAATTAATT
1 AAAATAAATATTTAAAAATTTAATTAATT
3458872 GTAATAAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 38 0.79
30 10 0.21
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (30 bp):
AAAATAAATATTTAAAAATTTAATTAATTA
Found at i:3459536 original size:13 final size:13
Alignment explanation
Indices: 3459518--3459543 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3459508 TAAAAGTTCC
3459518 AAAAAAAGAAAGT
1 AAAAAAAGAAAGT
3459531 AAAAAAAGAAAGT
1 AAAAAAAGAAAGT
3459544 GTACTATTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (13 bp):
AAAAAAAGAAAGT
Found at i:3459981 original size:17 final size:19
Alignment explanation
Indices: 3459956--3460004 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 19
3459946 AATATTTAAT
3459956 TTAATTTAATAAAAAAT-A
1 TTAATTTAATAAAAAATAA
* *
3459974 TTAA-TTAAGATAAAATAA
1 TTAATTTAATAAAAAATAA
3459992 TTAATTTAATAAA
1 TTAATTTAATAAA
3460005 TTATAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 10 0.40
18 9 0.36
19 6 0.24
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TTAATTTAATAAAAAATAA
Found at i:3463256 original size:15 final size:16
Alignment explanation
Indices: 3463232--3463261 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3463222 TAATATGATA
3463232 ATATGAAATAAAAATT
1 ATATGAAATAAAAATT
3463248 ATATG-AATAAAAAT
1 ATATGAAATAAAAAT
3463262 ATTAAAATAA
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:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (16 bp):
ATATGAAATAAAAATT
Found at i:3467341 original size:3 final size:3
Alignment explanation
Indices: 3467335--3467360 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3467325 ATTATTATTA
3467335 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
3467361 CTATTTTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:3469326 original size:15 final size:16
Alignment explanation
Indices: 3469293--3469331 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
3469283 GTTACCAGCC
*
3469293 TTTTATTTTTTTACCTT
1 TTTTATTTTTGTA-CTT
3469310 TTTTATTTTTGTA-TT
1 TTTTATTTTTGTACTT
3469325 TTTTATT
1 TTTTATT
3469332 AATGTTTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
17 12 0.57
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTATTTTTGTACTT
Found at i:3469889 original size:53 final size:51
Alignment explanation
Indices: 3469679--3469901 Score: 159
Period size: 53 Copynumber: 4.3 Consensus size: 51
3469669 GTATAAGCTT
* * * *
3469679 AACAACTTT-AAAATTCTC-TTATGAAAAAAAACTTCTCTAGGTAGATG-TTC
1 AACAACTTTAAAAATTTTCATTTTG-AAAAAAGCTTCTCAAGGTAGA-GATTC
* ** *
3469729 AACAACTTTAAAAAATTTTCATTCTTGGAAAAAAGC-TCTTCTAGGTATTGACTC
1 AACAACTTT-AAAAATTTTCATT-TT-GAAAAAAGCTTC-TCAAGGTAGAGATTC
* * * * * * *
3469783 AAAAACTTTTAAAAAATTTCATATTGAAAAAGGCTTAT-ATAGGCAGAGGTTC
1 AACAAC-TTTAAAAATTTTCATTTTGAAAAAAGCTTCTCA-AGGTAGAGATTC
* *
3469835 AATAACTTTAAAATTTTCTTCATTTTGAAAAAAGCTTCTCAAGGTAGAGATTC
1 AACAACTTTAAAA-ATT-TTCATTTTGAAAAAAGCTTCTCAAGGTAGAGATTC
*
3469888 AACAACTTAAAAAA
1 AACAACTTTAAAAA
3469902 AAAATTTTCA
Statistics
Matches: 132, Mismatches: 28, Indels: 24
0.72 0.15 0.13
Matches are distributed among these distances:
50 9 0.07
51 7 0.05
52 30 0.23
53 47 0.36
54 35 0.27
55 4 0.03
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (51 bp):
AACAACTTTAAAAATTTTCATTTTGAAAAAAGCTTCTCAAGGTAGAGATTC
Found at i:3479172 original size:90 final size:90
Alignment explanation
Indices: 3479058--3479237 Score: 324
Period size: 90 Copynumber: 2.0 Consensus size: 90
3479048 CTTTATCGAT
3479058 GAAAGACCCTAATCTCATCTTTCACATTTTTTTTCATGATTGGATTAACTGCTCTAAGGTTTTTA
1 GAAAGACCCTAATCTCATCTTTCACATTTTTTTTCATGATTGGATTAACTGCTCTAAGGTTTTTA
*
3479123 GTGGATTGGACTCGTCATAAGTAAA
66 GTGGATCGGACTCGTCATAAGTAAA
* *
3479148 GAAAGACCCTAATCTCATCTTTCACATTTTTTTTCATGATTGGATTAATTGCTCTAAGGTTTTTG
1 GAAAGACCCTAATCTCATCTTTCACATTTTTTTTCATGATTGGATTAACTGCTCTAAGGTTTTTA
*
3479213 GTGGATCGGACTTGTCATAAGTAAA
66 GTGGATCGGACTCGTCATAAGTAAA
3479238 TTCTATTTAA
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.39
Consensus pattern (90 bp):
GAAAGACCCTAATCTCATCTTTCACATTTTTTTTCATGATTGGATTAACTGCTCTAAGGTTTTTA
GTGGATCGGACTCGTCATAAGTAAA
Found at i:3483544 original size:20 final size:20
Alignment explanation
Indices: 3483521--3483559 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3483511 CAAATCAAAT
3483521 TTAA-ATAAATATATAAATTA
1 TTAATATAAA-ATATAAATTA
*
3483541 TTAATATTAAATATAAATT
1 TTAATATAAAATATAAATT
3483560 TGATCCAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATATAAAATATAAATTA
Found at i:3484577 original size:2 final size:2
Alignment explanation
Indices: 3484570--3484609 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3484560 AGAGAAAAGA
3484570 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3484610 CTTAGGGACA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3493299 original size:82 final size:81
Alignment explanation
Indices: 3493143--3493302 Score: 232
Period size: 82 Copynumber: 2.0 Consensus size: 81
3493133 ACTTAAGGAG
* * * *
3493143 GAGTTCTGAATCTCACATCAGACATAAAAGGAAGGTCATGAGATATAAAAAGGTTTAGACCATCT
1 GAGTTCTGAATCTCACATCAGACATAAAAGAAAGGTCATGAAATATAAAAAAGTTTACACCATCT
3493208 CTTCCTTATAAGATGC
66 CTTCCTTATAAGATGC
* *
3493224 GAGTTCTGAATCTCACATC-GAACATAAAAGAAATGTCACTGAAATATAAAAAAGTTTACATCAT
1 GAGTTCTGAATCTCACATCAG-ACATAAAAGAAAGGTCA-TGAAATATAAAAAAGTTTACACCAT
*
3493288 CTTTTCCTTATAAGA
64 CTCTTCCTTATAAGA
3493303 CATCTTTGTA
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
80 1 0.01
81 34 0.49
82 35 0.50
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (81 bp):
GAGTTCTGAATCTCACATCAGACATAAAAGAAAGGTCATGAAATATAAAAAAGTTTACACCATCT
CTTCCTTATAAGATGC
Found at i:3503921 original size:16 final size:16
Alignment explanation
Indices: 3503887--3503923 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3503877 AAGCTGTTAG
3503887 CTCAA-TAATATTGAA
1 CTCAATTAATATTGAA
3503902 CTCAATTAAT-TTGAA
1 CTCAATTAATATTGAA
3503917 TCTCAAT
1 -CTCAAT
3503924 CACAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (16 bp):
CTCAATTAATATTGAA
Found at i:3504785 original size:79 final size:79
Alignment explanation
Indices: 3504652--3504798 Score: 215
Period size: 79 Copynumber: 1.9 Consensus size: 79
3504642 TTTTGAAGAT
* * * * * **
3504652 AGAGTCGTTCTTTACCATTATCCGAACACGATAGAAGTATAGGAGTAGATTCCTTTCGTATATAT
1 AGAGTCGTTCTTTACCATTATCCAAAAAAGACAGAAGTATAGGAGTAGACTCCTTTCACATATAT
3504717 ATAGAGAGAGAGAG
66 ATAGAGAGAGAGAG
3504731 AGAGTCGTTCTTTACCATTATCCAAAAAA-AGCAGAAGTATAGGAGTAGACTCCTTTCACATATA
1 AGAGTCGTTCTTTACCATTATCCAAAAAAGA-CAGAAGTATAGGAGTAGACTCCTTTCACATATA
3504795 TATA
65 TATA
3504799 TATATATATA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
78 1 0.02
79 59 0.98
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (79 bp):
AGAGTCGTTCTTTACCATTATCCAAAAAAGACAGAAGTATAGGAGTAGACTCCTTTCACATATAT
ATAGAGAGAGAGAG
Found at i:3504797 original size:2 final size:2
Alignment explanation
Indices: 3504790--3504830 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3504780 CTCCTTTCAC
3504790 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3504831 GAAGCTGCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3509126 original size:29 final size:29
Alignment explanation
Indices: 3509054--3509127 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 29
3509044 TTTATTCAAC
* *
3509054 ATAAAAATTTATCTAATTACAAATAAAAA
1 ATAAAAATTTATTTAAATACAAATAAAAA
* *
3509083 AT-TAAGTTTATTTAAATAC-AATAAAAA
1 ATAAAAATTTATTTAAATACAAATAAAAA
3509110 TATAAAAATTTATTTAAA
1 -ATAAAAATTTATTTAAA
3509128 AAAGTAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
27 8 0.22
28 15 0.41
29 14 0.38
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (29 bp):
ATAAAAATTTATTTAAATACAAATAAAAA
Found at i:3511292 original size:11 final size:12
Alignment explanation
Indices: 3511276--3511330 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 12
3511266 TTATTGTAGC
3511276 AAAAATTTAA-A
1 AAAAATTTAATA
3511287 AAAAATTTCAATA
1 AAAAATTT-AATA
3511300 AAAAATTTATACTA
1 AAAAATTTA-A-TA
*
3511314 AATCAATTTAATA
1 AA-AAATTTAATA
3511327 AAAA
1 AAAA
3511331 TTAATATTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
11 8 0.22
12 4 0.11
13 14 0.38
14 5 0.14
15 6 0.16
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAAATTTAATA
Found at i:3515945 original size:5 final size:5
Alignment explanation
Indices: 3515928--3515961 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
3515918 TTAAAAAAAG
*
3515928 AAATA ATAATA AAATA AAATA AAATA AAACA AAA
1 AAATA A-AATA AAATA AAATA AAATA AAATA AAA
3515962 AACATCATGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:3516026 original size:27 final size:28
Alignment explanation
Indices: 3515995--3516049 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
3515985 CTATAAACAC
* *
3515995 AAGTTATCATGCAA-TAATATAATATAT
1 AAGTTATCATACAATTAATATAAAATAT
*
3516022 AAGTTATCATATAATTAATATAAAATAT
1 AAGTTATCATACAATTAATATAAAATAT
3516050 CATACAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (28 bp):
AAGTTATCATACAATTAATATAAAATAT
Found at i:3516044 original size:21 final size:19
Alignment explanation
Indices: 3516011--3516067 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 19
3516001 TCATGCAATA
**
3516011 ATATAATATATAAGTTATC
1 ATATAATATATAAAATATC
3516030 ATATAATTAATATAAAATATC
1 ATATAA-T-ATATAAAATATC
* *
3516051 ATACAAATATATTAAAT
1 ATA-TAATATATAAAAT
3516068 TATGCCAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 6 0.19
20 9 0.29
21 14 0.45
22 2 0.06
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (19 bp):
ATATAATATATAAAATATC
Found at i:3516204 original size:17 final size:19
Alignment explanation
Indices: 3516174--3516210 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
3516164 AAACATTAAA
*
3516174 ATATAAATATAAATATAAT
1 ATATAAATATAAATAAAAT
3516193 ATATAAA-A-AAATAAAAT
1 ATATAAATATAAATAAAAT
3516210 A
1 A
3516211 AAAAAAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 1 0.06
19 7 0.41
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
ATATAAATATAAATAAAAT
Found at i:3517512 original size:42 final size:42
Alignment explanation
Indices: 3517420--3517528 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 42
3517410 TAGGCTTTTC
* * *
3517420 TAAACAGAGGCTAAACAACTTTAAATAAAAAATTGGCTCTTT
1 TAAACAAAGGCTAAATAACTTTAAATAAAAAATTGGCTCCTT
** * * *
3517462 TATTCAAAGGCTAAATAACTTTAAGTAAGAAA-TGAGTTCCTT
1 TAAACAAAGGCTAAATAACTTTAAATAAAAAATTG-GCTCCTT
* *
3517504 TAAACAAAGGTTAAGTAACTTTAAA
1 TAAACAAAGGCTAAATAACTTTAAA
3517529 ATAGGTGATT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
41 2 0.04
42 51 0.96
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (42 bp):
TAAACAAAGGCTAAATAACTTTAAATAAAAAATTGGCTCCTT
Found at i:3517971 original size:65 final size:65
Alignment explanation
Indices: 3517675--3518047 Score: 215
Period size: 65 Copynumber: 5.7 Consensus size: 65
3517665 CAAGGCCAAA
* * * *
3517675 ATGAGTGATCGAAATTAAACCAT-AAGTCAAAAAATATGAATGATATGGATTAAACCAAGGTTA-
1 ATGAGTGATCGAAATTAAACC-TCAAGTCAAAAAA-ATAAATGATTTGGATTGAACCAA-GATAG
3517738 AAG
63 AAG
* * * * * * * ** * *
3517741 ATGAGTGA-CCATTATTGAACCGCATGTTAGAAAAATAAATGATTTAAATTGAACCAATATTGAA
1 ATGAGTGATCGA-AATTAAACCTCAAGTCAAAAAAATAAATGATTTGGATTGAACCAAGATAGAA
3517805 G
65 G
** * * * * ** *
3517806 ATGAGTGATCGGGATCAAACCGT-AGGTTAAAAAAATAAATGA-CTAAATTGAACCAAGATCGAA
1 ATGAGTGATCGAAATTAAACC-TCAAGTCAAAAAAATAAATGATTTGGATTGAACCAAGATAGAA
3517869 G
65 G
* ** * * * *
3517870 ATGAGTGATTGGGATTGAA-TTGTAAGTTAAAAAAAATAAATGATTTGGATTGAACCAAGATAGA
1 ATGAGTGATCGAAATTAAACCT-CAAG-TCAAAAAAATAAATGATTTGGATTGAACCAAGATAGA
3517934 AG
64 AG
* * * * * *
3517936 ATAAGTGACCGAAATTGAACCTCAAGTCAAAAAAATAAATGATCTT-GATTGAGCCAAAATCGAA
1 ATGAGTGATCGAAATTAAACCTCAAGTCAAAAAAATAAATGAT-TTGGATTGAACCAAGATAGAA
*
3518000 A
65 G
* * * * *
3518001 ATAAGTGA-CTAGAACTAAACCACAAGT-AAAAAAATAAATGATCTGGA
1 ATGAGTGATCGA-AATTAAACCTCAAGTCAAAAAAATAAATGATTTGGA
3518048 CTAAGCCAAG
Statistics
Matches: 241, Mismatches: 53, Indels: 28
0.75 0.16 0.09
Matches are distributed among these distances:
62 1 0.00
63 1 0.00
64 57 0.24
65 120 0.50
66 61 0.25
67 1 0.00
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.24
Consensus pattern (65 bp):
ATGAGTGATCGAAATTAAACCTCAAGTCAAAAAAATAAATGATTTGGATTGAACCAAGATAGAAG
Found at i:3518066 original size:64 final size:65
Alignment explanation
Indices: 3517899--3518068 Score: 184
Period size: 65 Copynumber: 2.6 Consensus size: 65
3517889 TTGTAAGTTA
* * * * * *
3517899 AAAAAAATAAATGATTTGGATTGAA-CCAAGATAGAAGATAAGTGACCGAAATTGAACCTCAAGT
1 AAAAAAATAAATGATCTGGATT-AAGCCAAGATAGAAAATAAGTGACAGAAACTAAACCACAAGT
3517963 C
65 C
* * * *
3517964 AAAAAAATAAATGATCTTGATTGAGCCAAAATCGAAAATAAGTGACTAG-AACTAAACCACAAGT
1 AAAAAAATAAATGATCTGGATTAAGCCAAGATAGAAAATAAGTGAC-AGAAACTAAACCACAAGT
3518028 -
65 C
* * *
3518028 AAAAAAATAAATGATCTGGACTAAGCCAAGGTAAAAAATAA
1 AAAAAAATAAATGATCTGGATTAAGCCAAGATAGAAAATAA
3518069 TTAAGTCTGA
Statistics
Matches: 86, Mismatches: 17, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
64 35 0.41
65 50 0.58
66 1 0.01
ACGTcount: A:0.52, C:0.12, G:0.16, T:0.20
Consensus pattern (65 bp):
AAAAAAATAAATGATCTGGATTAAGCCAAGATAGAAAATAAGTGACAGAAACTAAACCACAAGTC
Found at i:3518354 original size:31 final size:30
Alignment explanation
Indices: 3518294--3518361 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
3518284 CAATTTAGAA
* *
3518294 ATTCA-AAGGTTCATCACAAAACTTCAAAG
1 ATTCATAAGGTTCATAACAAAACTGCAAAG
* *
3518323 ATTCATAAGGTTCCATAACAAAAGTGGAAAG
1 ATTCATAAGGTT-CATAACAAAACTGCAAAG
3518354 ATTC-TAAG
1 ATTCATAAG
3518362 ACTCCAAGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 5 0.15
30 10 0.30
31 18 0.55
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.25
Consensus pattern (30 bp):
ATTCATAAGGTTCATAACAAAACTGCAAAG
Found at i:3518438 original size:18 final size:18
Alignment explanation
Indices: 3518415--3518450 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3518405 CATAAATTCA
*
3518415 AGATTCGCAAAAGTTTTT
1 AGATTCGCAAAAATTTTT
*
3518433 AGATTCGTAAAAATTTTT
1 AGATTCGCAAAAATTTTT
3518451 TATTAGCAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (18 bp):
AGATTCGCAAAAATTTTT
Found at i:3519651 original size:19 final size:18
Alignment explanation
Indices: 3519629--3519664 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3519619 TTTTTCCTCC
3519629 TTTTACTTTTTTCTTTTCT
1 TTTTACTTTTTT-TTTTCT
*
3519648 TTTTGCTTTTTTTTTTC
1 TTTTACTTTTTTTTTTC
3519665 ACATCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.81
Consensus pattern (18 bp):
TTTTACTTTTTTTTTTCT
Found at i:3522913 original size:4 final size:4
Alignment explanation
Indices: 3522899--3522937 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
3522889 AGATATATGA
* * *
3522899 AAAT GAAT AAAT AAAT AAAT AAAC AAAC AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
3522938 ATACAAACAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:3523947 original size:23 final size:23
Alignment explanation
Indices: 3523912--3523965 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
3523902 ATATCATGCA
3523912 AATATTATCATGCAATAATAATAT
1 AATA-TATCATGCAATAATAATAT
3523936 AATATATCATGCAATAATAATAT
1 AATATATCATGCAATAATAATAT
*
3523959 ACTATAT
1 AATATAT
3523966 ATATATATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 25 0.86
24 4 0.14
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (23 bp):
AATATATCATGCAATAATAATAT
Found at i:3524059 original size:21 final size:21
Alignment explanation
Indices: 3524019--3524060 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3524009 ATATATAAGT
*
3524019 TATCATACAATTAATATAAAA
1 TATCATACAAATAATATAAAA
*
3524040 TATCATACAAAT-ATATTAAA
1 TATCATACAAATAATATAAAA
3524060 T
1 T
3524061 TTATGCCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.36
Consensus pattern (21 bp):
TATCATACAAATAATATAAAA
Found at i:3532249 original size:111 final size:111
Alignment explanation
Indices: 3532055--3532277 Score: 401
Period size: 111 Copynumber: 2.0 Consensus size: 111
3532045 CTATCTCATC
* * *
3532055 TCATCTGAGCCCATACATTATCTTCAAACTTCAATAAGTAAGGGGTGTGCATGTTTTTTCTCATA
1 TCATCTGAGCCCATACATTATCTTCAAACTTCAATAAGTAAAGGGTCTGCATGTTATTTCTCATA
*
3532120 TTCTTGATTGAGATAGCATTCCATTGTTACTCTTTGGAATGTCTGT
66 CTCTTGATTGAGATAGCATTCCATTGTTACTCTTTGGAATGTCTGT
3532166 TCATCTGAGCCCATACATTATCTTCAAACTTCAATAAGTAAAGGGTCTGCATGTTATTTCTCATA
1 TCATCTGAGCCCATACATTATCTTCAAACTTCAATAAGTAAAGGGTCTGCATGTTATTTCTCATA
*
3532231 CTCTTGATTGAGATAGCATTCCATTGTTACTTTTTGGAATGTCTGT
66 CTCTTGATTGAGATAGCATTCCATTGTTACTCTTTGGAATGTCTGT
3532277 T
1 T
3532278 TTAGTCTTGG
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.40
Consensus pattern (111 bp):
TCATCTGAGCCCATACATTATCTTCAAACTTCAATAAGTAAAGGGTCTGCATGTTATTTCTCATA
CTCTTGATTGAGATAGCATTCCATTGTTACTCTTTGGAATGTCTGT
Found at i:3533801 original size:19 final size:19
Alignment explanation
Indices: 3533777--3533814 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3533767 TCTACCCTGC
3533777 AATCACAACACTAGTACGT
1 AATCACAACACTAGTACGT
3533796 AATCACAACACTAGTACGT
1 AATCACAACACTAGTACGT
3533815 GGCCTTTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (19 bp):
AATCACAACACTAGTACGT
Found at i:3538090 original size:31 final size:31
Alignment explanation
Indices: 3538055--3538116 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
3538045 ACACTTATGG
*
3538055 GTGTTTTGAACTTCCTGCATGTGTCCAAATT
1 GTGTTTTGAACTTCCTACATGTGTCCAAATT
3538086 GTGTTTTGAACTTCCTACATGTGTCCAAATT
1 GTGTTTTGAACTTCCTACATGTGTCCAAATT
3538117 AGTTTTAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (31 bp):
GTGTTTTGAACTTCCTACATGTGTCCAAATT
Found at i:3544072 original size:68 final size:68
Alignment explanation
Indices: 3543949--3544082 Score: 171
Period size: 68 Copynumber: 2.0 Consensus size: 68
3543939 TTGCTGGGGA
* * * * *
3543949 AGATTGTTGGCAGATCGAAGGTTGATCGCATTCATCAATTTCATATACTCGAACACTGGTATTAA
1 AGATTGTTGACAGATCGAAGGTTGATCGCATTCATCAACTCCATATACTCAAACACTGGCATTAA
3544014 AGG
66 AGG
* * * *
3544017 AGATTGTTGACAGATCGAAGGTTG-GCTGCGTTCATCAACTCCATGTATTCAAACACTGGCATTA
1 AGATTGTTGACAGATCGAAGGTTGATC-GCATTCATCAACTCCATATACTCAAACACTGGCATTA
3544081 AA
65 AA
3544083 AGTTCGATTT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
67 1 0.02
68 55 0.98
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.30
Consensus pattern (68 bp):
AGATTGTTGACAGATCGAAGGTTGATCGCATTCATCAACTCCATATACTCAAACACTGGCATTAA
AGG
Found at i:3550748 original size:3 final size:3
Alignment explanation
Indices: 3550740--3550786 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
3550730 CATTTCAATT
**
3550740 TAA TAA TAA TAA TAA TAA TAA TAA TTT TAA -AA -AA TTAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
3550784 TAA
1 TAA
3550787 AAAAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 32 0.84
4 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3551702 original size:328 final size:324
Alignment explanation
Indices: 3551106--3551756 Score: 966
Period size: 328 Copynumber: 2.0 Consensus size: 324
3551096 TCAAACAACC
* * * *
3551106 CCCCAAATACCGAAACAGAAAAACGAAATAGATCTACAAAAAAGGAACCTTAGCGCCACAGCCGT
1 CCCCAAATACCGAAACAAAAAAACGAAACAGATCTACAAAAAAGGAACCTTAGCACCACAGCCGC
** *
3551171 CCTGAAACCAGAAAGAAAAATCATCAATTTAAGCCTGTCCCAAAAAAAAAAAATGAAGATCAGAA
66 CCTGAAACCAGAAAGAAAAATCATCAATTTAAGCCCATCCAAAAAAAAAAAAATGAAGATCAGAA
*
3551236 ACTTCAAAGACTAATTTGCAACTATTAAGGCTCTTTTAAGCAAAACGAAGGTCGAATTCAGAAAG
131 ACTTCAAAGACTAATTTGCAACTATTAAAGCTCTTTTAAGCAAAACGAAGGTCGAATTCAGAAAG
* * * *
3551301 AGGGCATCGAGAGGAATTTTTGGTGACTTTTTGACCCTTTTTTTATCACCAGTGACCACTACTGA
196 AGGGCATCGAGAGGAATTTTTGGTGACTTTTTGACCCTTTTTTGATCACCACTAACCACCACTGA
* *
3551366 CGGTAACCCACACGGCGGTAGGTGCAACGCAC-GACACCCGATTTCGATGAAACCAGAGAAAACT
261 CAGTAACCCACACGACGGTAGGTGCAACGCACAG-CACCCGATTTCGATGAAACCAGAGAAAACT
* * *
3551430 CCCCAAATATCGAAACAAAAAAATGAAACAGATCTACATAAAAGGAACCTTAGCACCACAGCCGC
1 CCCCAAATACCGAAACAAAAAAACGAAACAGATCTACAAAAAAGGAACCTTAGCACCACAGCCGC
* * *
3551495 CCTGAAACCA-AAAGAGAAATCATCAGTTTAAGCCCATCCAAAAAAAAAAAAAAAGATGAGCGAT
66 CCTGAAACCAGAAAGAAAAATCATCAATTTAAGCCCATCC---AAAAAAAAAAAA-ATGA-AGAT
* * *
3551559 CAGAAACTTCGAAGACTAATTTGCAACTATTAAAGCTCTTTTAGGCAAAACGAAGGTCGGATTCA
126 CAGAAACTTCAAAGACTAATTTGCAACTATTAAAGCTCTTTTAAGCAAAACGAAGGTCGAATTCA
*
3551624 GAAAGAGGGCGTCGAGAGGAATTTTTGGTGACTTTTTGA-CCTTTTTTCGATCACCACTAACCAC
191 GAAAGAGGGCATCGAGAGGAATTTTTGGTGACTTTTTGACCCTTTTTT-GATCACCACTAACCAC
* * * *
3551688 CATTGATAGTAACCCACACGACGGTCGGTGCAACGCACAGCACCCTATTTCGATGAAACCAGAGA
255 CACTGACAGTAACCCACACGACGGTAGGTGCAACGCACAGCACCCGATTTCGATGAAACCAGAGA
3551753 AAAC
320 AAAC
3551757 CCTAACTCTC
Statistics
Matches: 292, Mismatches: 28, Indels: 10
0.88 0.08 0.03
Matches are distributed among these distances:
323 25 0.09
324 68 0.23
326 11 0.04
327 12 0.04
328 175 0.60
329 1 0.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (324 bp):
CCCCAAATACCGAAACAAAAAAACGAAACAGATCTACAAAAAAGGAACCTTAGCACCACAGCCGC
CCTGAAACCAGAAAGAAAAATCATCAATTTAAGCCCATCCAAAAAAAAAAAAATGAAGATCAGAA
ACTTCAAAGACTAATTTGCAACTATTAAAGCTCTTTTAAGCAAAACGAAGGTCGAATTCAGAAAG
AGGGCATCGAGAGGAATTTTTGGTGACTTTTTGACCCTTTTTTGATCACCACTAACCACCACTGA
CAGTAACCCACACGACGGTAGGTGCAACGCACAGCACCCGATTTCGATGAAACCAGAGAAAACT
Found at i:3552506 original size:12 final size:11
Alignment explanation
Indices: 3552484--3552516 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3552474 TCGGTTCAAG
3552484 TAAAATTTTTT
1 TAAAATTTTTT
3552495 TAAAATTTTTT
1 TAAAATTTTTT
3552506 T--AATTTTTT
1 TAAAATTTTTT
3552515 TA
1 TA
3552517 TATATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.43
11 12 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TAAAATTTTTT
Found at i:3552972 original size:37 final size:39
Alignment explanation
Indices: 3552920--3552994 Score: 109
Period size: 37 Copynumber: 2.0 Consensus size: 39
3552910 CGCGTTTTCT
* *
3552920 AAAACCCCTAAAATCCGAAATCCTTTAAATCCAAACCCC
1 AAAACCCCTAAAATCCAAAATCCTTAAAATCCAAACCCC
*
3552959 AAAA-CCC-AAAATCCAAAATCCTTAAAATTCAAACCC
1 AAAACCCCTAAAATCCAAAATCCTTAAAATCCAAACCC
3552995 TTAAATCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 26 0.79
38 3 0.09
39 4 0.12
ACGTcount: A:0.48, C:0.33, G:0.01, T:0.17
Consensus pattern (39 bp):
AAAACCCCTAAAATCCAAAATCCTTAAAATCCAAACCCC
Found at i:3553028 original size:35 final size:36
Alignment explanation
Indices: 3552929--3553035 Score: 94
Period size: 37 Copynumber: 3.0 Consensus size: 36
3552919 TAAAACCCCT
* ** * *
3552929 AAAATCCGAAATCCTTTAAA-TCCAAACCCCAAAACCC
1 AAAATCCAAAATCCTCAAAACT-CAAACCCTAAAA-TC
* * *
3552966 AAAATCCAAAATCCTTAAAATTCAAACCCTTAAATC
1 AAAATCCAAAATCCTCAAAACTCAAACCCTAAAATC
3553002 AAAATCTC-AAA-CCTCAAAACTCAAACCCTAAAAT
1 AAAATC-CAAAATCCTCAAAACTCAAACCCTAAAAT
3553036 TTTCAAACTC
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
35 20 0.33
36 10 0.17
37 29 0.48
38 1 0.02
ACGTcount: A:0.50, C:0.30, G:0.01, T:0.20
Consensus pattern (36 bp):
AAAATCCAAAATCCTCAAAACTCAAACCCTAAAATC
Found at i:3553034 original size:14 final size:15
Alignment explanation
Indices: 3553002--3553056 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 15
3552992 CCCTTAAATC
3553002 AAAATCTCAAA-CCT
1 AAAATCTCAAACCCT
3553016 CAAAA-CTCAAACCCT
1 -AAAATCTCAAACCCT
* *
3553031 AAAATTTTCAAACTCT
1 AAAA-TCTCAAACCCT
3553047 AAAA-CTCAAA
1 AAAATCTCAAA
3553057 ACCTTAAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 15 0.44
15 7 0.21
16 12 0.35
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (15 bp):
AAAATCTCAAACCCT
Found at i:3553080 original size:31 final size:29
Alignment explanation
Indices: 3553008--3553086 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 29
3552998 AATCAAAATC
* **
3553008 TCAAACCTCAAAACTCAAACCCTAAAATTT
1 TCAAACCT-AAAACTCAAAACCTAAAACCT
*
3553038 TCAAACTCTAAAACTCAAAACCTTAAACCT
1 TCAAAC-CTAAAACTCAAAACCTAAAACCT
*
3553068 TCTATAACCTAAAATTCAA
1 TC-A-AACCTAAAACTCAA
3553087 GTCTTAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 25 0.61
31 13 0.32
32 3 0.07
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (29 bp):
TCAAACCTAAAACTCAAAACCTAAAACCT
Found at i:3569040 original size:17 final size:18
Alignment explanation
Indices: 3569018--3569051 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3569008 TCTAATCGAG
3569018 TTTTTA-TATTTAAATTT
1 TTTTTATTATTTAAATTT
*
3569035 TTTTTATTATTTTAATT
1 TTTTTATTATTTAAATT
3569052 AATAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTATTATTTAAATTT
Found at i:3577200 original size:3 final size:3
Alignment explanation
Indices: 3577192--3577235 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
3577182 CATGATGCAG
3577192 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3577236 CAGTGTCCCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3578138 original size:2 final size:2
Alignment explanation
Indices: 3578034--3578120 Score: 62
Period size: 2 Copynumber: 46.0 Consensus size: 2
3578024 ATATAACTAT
3578034 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA GT- TCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA T-A
* * * * *
3578075 TA TT TA TA T- TA TA TA AA AA TA AA TA -A T- TA AA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3578113 TA TA TA TA
1 TA TA TA TA
3578121 CATTAATATC
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
1 7 0.10
2 59 0.87
3 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3578514 original size:4 final size:4
Alignment explanation
Indices: 3578505--3578586 Score: 85
Period size: 4 Copynumber: 20.5 Consensus size: 4
3578495 ATTAAGTTTC
* * *
3578505 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATT TATT TATT
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
3578553 TATT TATA CT-TA TATT TATA TTTA TATT TATA TA
1 TATA TATA -TATA TATA TATA TATA TATA TATA TA
3578587 AATGTGTGTG
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
3 1 0.01
4 66 0.97
5 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (4 bp):
TATA
Found at i:3578516 original size:6 final size:6
Alignment explanation
Indices: 3578505--3578586 Score: 85
Period size: 6 Copynumber: 13.7 Consensus size: 6
3578495 ATTAAGTTTC
* * *
3578505 TATATA TATATA TATATA TATATA TATATA TATATA TATTTA TTTATT
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
3578553 TATTTA TACT-TA TATTTA TATTTA TATTTA TATA
1 TATATA TA-TATA TATATA TATATA TATATA TATA
3578587 AATGTGTGTG
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
5 1 0.02
6 64 0.97
7 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (6 bp):
TATATA
Found at i:3578522 original size:12 final size:12
Alignment explanation
Indices: 3578509--3578586 Score: 95
Period size: 12 Copynumber: 6.5 Consensus size: 12
3578499 AGTTTCTATA
*
3578509 TATATATATATA
1 TATATATATATT
*
3578521 TATATATATATA
1 TATATATATATT
3578533 TATATATATATT
1 TATATATATATT
* *
3578545 TATTTATTTATT
1 TATATATATATT
3578557 TATACT-TATATT
1 TATA-TATATATT
*
3578569 TATATTTATATT
1 TATATATATATT
3578581 TATATA
1 TATATA
3578587 AATGTGTGTG
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
11 1 0.02
12 56 0.97
13 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (12 bp):
TATATATATATT
Found at i:3579416 original size:30 final size:30
Alignment explanation
Indices: 3579377--3579454 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
3579367 AAATAAGTTT
* * *
3579377 TTAATTTTTAATTTATATCTAACTAAGCCC
1 TTAATTTTTAATTTATATCCAAATAAACCC
* * *
3579407 TTAACTTTTAACTTGTATCCAAATAAACCC
1 TTAATTTTTAATTTATATCCAAATAAACCC
3579437 TTAAATTTTTAATTTATA
1 TT-AATTTTTAATTTATA
3579455 CTTAAATAAG
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
30 26 0.68
31 12 0.32
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.46
Consensus pattern (30 bp):
TTAATTTTTAATTTATATCCAAATAAACCC
Found at i:3579462 original size:31 final size:30
Alignment explanation
Indices: 3579377--3579463 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 30
3579367 AAATAAGTTT
* *
3579377 TTAATTTTTAATTTATA-TCTAACTAAGCCC
1 TTAATTTTTAATTTATACT-TAAATAAACCC
* *
3579407 TTAACTTTTAACTTGTAT-C-CAAATAAACCC
1 TTAATTTTTAA-TT-TATACTTAAATAAACCC
3579437 TTAAATTTTTAATTTATACTTAAATAA
1 TT-AATTTTTAATTTATACTTAAATAA
3579464 GTTTTTAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
29 3 0.07
30 23 0.51
31 16 0.36
32 3 0.07
ACGTcount: A:0.38, C:0.15, G:0.02, T:0.45
Consensus pattern (30 bp):
TTAATTTTTAATTTATACTTAAATAAACCC
Found at i:3580701 original size:301 final size:301
Alignment explanation
Indices: 3580159--3580763 Score: 1165
Period size: 301 Copynumber: 2.0 Consensus size: 301
3580149 TTCTGACTGT
3580159 CGGATTCTCATTAATTGTCAAACGCGTTCCAAACATCAAAAGCTCAAAACTGATTGATCAGGACA
1 CGGATTCTCATTAATTGTCAAACGCGTTCCAAACATCAAAAGCTCAAAACTGATTGATCAGGACA
* *
3580224 CGTAATTTAGTGCCGAACACAGGTGAATGTTTCTCTACAATATGACCAATTCCACATCTGCAAGT
66 CGTAATTTAGTGCCGAACACAGGTGAATGTTTCTCTACAATATGACCAATTCCACAGCAGCAAGT
3580289 TGTAAAAGAACCGGAGAAGGGGTTTTAGACTTTGAGCACAAGCAACCAAACCACACTCCCACTTG
131 TGTAAAAGAACCGGAGAAGGGGTTTTAGACTTTGAGCACAAGCAACCAAACCACACTCCCACTTG
3580354 CTTCGTTTCAATTTTCAAAGCAATGGCGGCAGGGGTAAGACATGTAATTTAAAGCTCAAATTCTA
196 CTTCGTTTCAATTTTCAAAGCAATGGCGGCAGGGGTAAGACATGTAATTTAAAGCTCAAATTCTA
3580419 TACATTTTCGTCAATGGCTGCCAGTTTCCTTAACCATCCAA
261 TACATTTTCGTCAATGGCTGCCAGTTTCCTTAACCATCCAA
*
3580460 CGGATTCTCATTAGTTGTCAAACGCGTTCCAAACATCAAAAGCTCAAAACTGATTGATCAGGACA
1 CGGATTCTCATTAATTGTCAAACGCGTTCCAAACATCAAAAGCTCAAAACTGATTGATCAGGACA
* *
3580525 CGTAATTTAGTGCCGATCGCAGGTGAATGTTTCTCTACAATATGACCAATTCCACAGCAGCAAGT
66 CGTAATTTAGTGCCGAACACAGGTGAATGTTTCTCTACAATATGACCAATTCCACAGCAGCAAGT
3580590 TGTAAAAGAACCGGAGAAGGGGTTTTAGACTTTGAGCACAAGCAACCAAACCACACTCCCACTTG
131 TGTAAAAGAACCGGAGAAGGGGTTTTAGACTTTGAGCACAAGCAACCAAACCACACTCCCACTTG
3580655 CTTCGTTTCAATTTTCAAAGCAATGGCGGCAGGGGTAAGACATGTAATTTAAAGCTCAAATTCTA
196 CTTCGTTTCAATTTTCAAAGCAATGGCGGCAGGGGTAAGACATGTAATTTAAAGCTCAAATTCTA
3580720 TACATTTTCGTCAATGGCTGCCAGTTTCCTTAACCATCCAA
261 TACATTTTCGTCAATGGCTGCCAGTTTCCTTAACCATCCAA
3580761 CGG
1 CGG
3580764 CAAACTGACT
Statistics
Matches: 299, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
301 299 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (301 bp):
CGGATTCTCATTAATTGTCAAACGCGTTCCAAACATCAAAAGCTCAAAACTGATTGATCAGGACA
CGTAATTTAGTGCCGAACACAGGTGAATGTTTCTCTACAATATGACCAATTCCACAGCAGCAAGT
TGTAAAAGAACCGGAGAAGGGGTTTTAGACTTTGAGCACAAGCAACCAAACCACACTCCCACTTG
CTTCGTTTCAATTTTCAAAGCAATGGCGGCAGGGGTAAGACATGTAATTTAAAGCTCAAATTCTA
TACATTTTCGTCAATGGCTGCCAGTTTCCTTAACCATCCAA
Found at i:3582829 original size:132 final size:133
Alignment explanation
Indices: 3582666--3582932 Score: 353
Period size: 132 Copynumber: 2.0 Consensus size: 133
3582656 TAATCTCATA
* *
3582666 GAGACTTTATCTATTTATAAGCATACAAACTTGCCTATAAAAAATCTC-TTT-CTTCTTAAAATT
1 GAGACTTTATCTATTTATAAACATACAAACTTACCTATAAAAAATC-CATTTGCTT-TTAAAATT
* * * *
3582729 TTTCTTTTACAAGTTTCTTATCTATAAATTAATAATTAACCAATTCCAAACAAA-TCTTTTATAG
64 CTTATTTTACAAGTTTCTTATCAATAAATTAATAATTAACCAATCCCAAACAAATTCTTTTATAG
*
3582793 GATTT
129 AATTT
* * *
3582798 GAGACTTTAT-TAATTTATAAACATATAAACTTACCTATCAAGAATCCATTTGCTTTTAAAATTC
1 GAGACTTTATCT-ATTTATAAACATACAAACTTACCTATAAAAAATCCATTTGCTTTTAAAATTC
* * * *
3582862 TTATTTTGCAAGTTTCTTATCAATAAATTAATATTTAACCAATCCCCAACAAATTTTTTTATAGA
65 TTATTTTACAAGTTTCTTATCAATAAATTAATAATTAACCAATCCCAAACAAATTCTTTTATAGA
3582927 ATTT
130 ATTT
3582931 GA
1 GA
3582933 ATCGTTATTT
Statistics
Matches: 117, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
131 2 0.02
132 97 0.83
133 18 0.15
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (133 bp):
GAGACTTTATCTATTTATAAACATACAAACTTACCTATAAAAAATCCATTTGCTTTTAAAATTCT
TATTTTACAAGTTTCTTATCAATAAATTAATAATTAACCAATCCCAAACAAATTCTTTTATAGAA
TTT
Found at i:3591008 original size:19 final size:19
Alignment explanation
Indices: 3590980--3591024 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3590970 AATCACTTAA
*
3590980 TAAT-TAATT-AATAAATT
1 TAATATAATTAAATAAATC
3590997 TAAATATAATTAAATAAATC
1 T-AATATAATTAAATAAATC
3591017 TAATATAA
1 TAATATAA
3591025 AATTAGAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 1 0.04
18 3 0.12
19 12 0.50
20 8 0.33
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAATATAATTAAATAAATC
Found at i:3597334 original size:83 final size:83
Alignment explanation
Indices: 3597195--3597358 Score: 292
Period size: 83 Copynumber: 2.0 Consensus size: 83
3597185 CCCGCACTCA
* *
3597195 ACTTTGTGACACCCTCGTCACGGAGGTTGATCATCCTGCCTGCCTCCCTTGAGGTGTTTGACGTG
1 ACTTTGTGACACCCTCATCACGGAGGCTGATCATCCTGCCTGCCTCCCTTGAGGTGTTTGACGTG
3597260 GATCGAACGGTTTAGGAC
66 GATCGAACGGTTTAGGAC
*
3597278 ACTTTGTGACACTCTCATCACGGAGGCTGATCATCCTGCCTGCCTCCCTTGAGGTGTTTGACGTG
1 ACTTTGTGACACCCTCATCACGGAGGCTGATCATCCTGCCTGCCTCCCTTGAGGTGTTTGACGTG
*
3597343 GATTGAACGGTTTAGG
66 GATCGAACGGTTTAGG
3597359 GCTGATTTTG
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 77 1.00
ACGTcount: A:0.17, C:0.26, G:0.27, T:0.30
Consensus pattern (83 bp):
ACTTTGTGACACCCTCATCACGGAGGCTGATCATCCTGCCTGCCTCCCTTGAGGTGTTTGACGTG
GATCGAACGGTTTAGGAC
Found at i:3603556 original size:3 final size:3
Alignment explanation
Indices: 3603541--3603573 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
3603531 GAGATTACGC
*
3603541 GGA GGA GGC GGA GGA GGA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
3603574 AGAGTTGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.03, G:0.67, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:3606839 original size:2 final size:2
Alignment explanation
Indices: 3606828--3606857 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3606818 TGCTAACTGT
3606828 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3606858 GCATTAGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3617596 original size:2 final size:2
Alignment explanation
Indices: 3617589--3617617 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3617579 AGATGAGGAA
3617589 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3617618 TTTTAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3623476 original size:2 final size:2
Alignment explanation
Indices: 3623469--3623494 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3623459 GAGCCCTTCG
3623469 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
3623495 GAATAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3625474 original size:2 final size:2
Alignment explanation
Indices: 3625467--3625491 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3625457 AGAAAAAGTG
3625467 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3625492 TACACCGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3625938 original size:20 final size:20
Alignment explanation
Indices: 3625913--3625957 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
3625903 TTTGAAATTA
3625913 ATAAAATATTATTTTTAAAT
1 ATAAAATATTATTTTTAAAT
*
3625933 ATAAAATATTATTTTTTAAT
1 ATAAAATATTATTTTTAAAT
3625953 ATAAA
1 ATAAA
3625958 TATAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATAAAATATTATTTTTAAAT
Found at i:3625982 original size:8 final size:8
Alignment explanation
Indices: 3625951--3625989 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
3625941 TTATTTTTTA
3625951 ATATAAAT
1 ATATAAAT
3625959 ATA-AAATT
1 ATATAAA-T
*
3625967 AAATAAAT
1 ATATAAAT
3625975 ATATAAAT
1 ATATAAAT
3625983 ATATAAA
1 ATATAAA
3625990 ATTAATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 3 0.11
8 21 0.78
9 3 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
ATATAAAT
Found at i:3626008 original size:26 final size:26
Alignment explanation
Indices: 3625948--3626022 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 26
3625938 ATATTATTTT
* *
3625948 TTAATATAA-ATATAAAATTAAATAA
1 TTAATAAAATATATAAAATTAATTAA
*
3625973 AT-ATATAAATATATAAAATTAATTAA
1 TTAATA-AAATATATAAAATTAATTAA
*
3625999 TTAATAAAATA-ATTAAAAATAATT
1 TTAATAAAATATA-TAAAATTAATT
3626023 TTTTATATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
24 3 0.07
25 4 0.10
26 31 0.76
27 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
TTAATAAAATATATAAAATTAATTAA
Found at i:3627323 original size:24 final size:24
Alignment explanation
Indices: 3627283--3627331 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
3627273 TAAAATTTTT
* *
3627283 TTAATTATATTTTTAATTATTAATA
1 TTAATTATATTTATAATCA-TAATA
3627308 TTAATT-TATTTATAATCATAATA
1 TTAATTATATTTATAATCATAATA
3627331 T
1 T
3627332 GATATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.27
24 10 0.45
25 6 0.27
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TTAATTATATTTATAATCATAATA
Found at i:3628546 original size:108 final size:106
Alignment explanation
Indices: 3628424--3628630 Score: 299
Period size: 108 Copynumber: 1.9 Consensus size: 106
3628414 ACAATCTTCA
* * *
3628424 TCAATAAATTTTTATAAAGGATTATTGAAGGTATTTTTGGTCAAAAA-ATTCTTCAATAATCCAT
1 TCAATAAATTTTTATAAAGGATTATTAAAAGTATTTTTGATCAAAAATA-TCTTCAATAATCCAT
* *
3628488 TTCAAATTTTGTTGAGAGGATTATTGAAGGCACTTTTGGCCATC
65 TTCAAATTTT-TTAAG-GGATTATTGAAAGCACTTTTGGCCATC
* * *
3628532 TCAATAAATTTTTATGATGGATTATTAAAAGTATTTTTGATCAAAAATATCTTCAATAATCCTTT
1 TCAATAAATTTTTATAAAGGATTATTAAAAGTATTTTTGATCAAAAATATCTTCAATAATCCATT
*
3628597 TCAAATTTTTTAAGGGATTATTGAAAGCATTTTT
66 TCAAATTTTTTAAGGGATTATTGAAAGCACTTTT
3628631 TGGTCAAAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
106 18 0.20
107 4 0.04
108 66 0.74
109 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.43
Consensus pattern (106 bp):
TCAATAAATTTTTATAAAGGATTATTAAAAGTATTTTTGATCAAAAATATCTTCAATAATCCATT
TCAAATTTTTTAAGGGATTATTGAAAGCACTTTTGGCCATC
Found at i:3628695 original size:126 final size:124
Alignment explanation
Indices: 3628532--3628989 Score: 419
Period size: 126 Copynumber: 3.6 Consensus size: 124
3628522 TTTGGCCATC
* * *
3628532 TCAATAAATTTTTATGATGGATTATTAAAAGTATTTTTGATCAAAAATATC-TTCAATAATCCTT
1 TCAATAAATTTTTATGAGGGATTATTAAAGGTATTTTTGATCAAAAATA-CATTTAATAAT-CTT
* *
3628596 TTCAAATTTTTTAAGGGATTATTGAAAGCATTTTTTGGTCAAAAATACCTTCAATAATCCTCT
64 TTCAAATTTTTTAAGGGATTATTGAAAG-ATTTTTTGGCCAAAAATACCTTTAATAATCC-CT
* * * * * *
3628659 T-AATAAATTTTTATGAGGGATTATTGAAGGTGTTTTTGGTAAAAAATGCTTTTAATAATCTCTT
1 TCAATAAATTTTTATGAGGGATTATTAAAGGTATTTTTGATCAAAAATACATTTAATAATCT-TT
* * * * *
3628723 CCAAATATTTTCAAGAGATTATT-TAAGGTATTTTTGGCCAAAAATACCTTTAATAATCCCT
65 TCAAAT-TTTTTAAGGGATTATTGAAAGAT-TTTTTGGCCAAAAATACCTTTAATAATCCCT
* * ** * * * * *
3628784 TCCAA-AAA-TTTTAAGA-CGATTATTAAAGGCGTTTTTTATAAAAAATACATTGAATAATCCTA
1 T-CAATAAATTTTTATGAGGGATTATTAAAGGTATTTTTGATCAAAAATACATTTAATAATCTTT
* *** *
3628846 TCAATAAATTTTTATGAGGGATTATTGAAA-ATATTTTAAACCAAAAATACATTTAATAATCCCT
65 TC---AAATTTTT-TAAGGGATTATTGAAAGAT-TTTTTGGCCAAAAATACCTTTAATAATCCCT
* * *
3628910 TCCATAAATTTTTATGAGAGATTATTGAAGGTATTTTT-AGTCAAAAATACATTTAATAATCTTT
1 TCAATAAATTTTTATGAGGGATTATTAAAGGTATTTTTGA-TCAAAAATACATTTAATAATCTTT
*
3628974 TCAATTTTTTTCAAGG
65 TCAAATTTTTT-AAGG
3628990 TAAAAAACAC
Statistics
Matches: 267, Mismatches: 48, Indels: 34
0.77 0.14 0.10
Matches are distributed among these distances:
123 2 0.01
124 36 0.13
125 30 0.11
126 134 0.50
127 27 0.10
128 38 0.14
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (124 bp):
TCAATAAATTTTTATGAGGGATTATTAAAGGTATTTTTGATCAAAAATACATTTAATAATCTTTT
CAAATTTTTTAAGGGATTATTGAAAGATTTTTTGGCCAAAAATACCTTTAATAATCCCT
Found at i:3628704 original size:64 final size:65
Alignment explanation
Indices: 3628532--3628978 Score: 370
Period size: 64 Copynumber: 7.1 Consensus size: 65
3628522 TTTGGCCATC
* * * * * *
3628532 TCAATAAATTTTTATGATGGATTATTAAAAGTATTTTTGATCAAAAATATC-TTCAATAATCCTT
1 TCAATAAATTTTTATGAGGGATTATTGAAGGTATTTTTGGTCAAAAATA-CATTTAATAATCCTC
3628596 T
65 T
* * * * *
3628597 TC---AAATTTTT-TAAGGGATTATTGAAAGCATTTTTTGGTCAAAAATACCTTCAATAATCCTC
1 TCAATAAATTTTTATGAGGGATTATTGAAGGTA-TTTTTGGTCAAAAATACATTTAATAATCCTC
3628658 T
65 T
* * * *
3628659 T-AATAAATTTTTATGAGGGATTATTGAAGGTGTTTTTGGTAAAAAATGCTTTTAATAAT-CTCT
1 TCAATAAATTTTTATGAGGGATTATTGAAGGTATTTTTGGTCAAAAATACATTTAATAATCCTCT
* * * * * *
3628722 TCCAA-ATATTTTCA--AGAGATTATTTAAGGTATTTTTGGCCAAAAATACCTTTAATAATCC-C
1 T-CAATAAATTTTTATGAGGGATTATTGAAGGTATTTTTGGTCAAAAATACATTTAATAATCCTC
3628783 T
65 T
* * * ** ** * *
3628784 TCCAA-AAA-TTTTAAGA-CGATTATTAAAGGCGTTTTTTATAAAAAATACATTGAATAATCCT-
1 T-CAATAAATTTTTATGAGGGATTATTGAAGGTATTTTTGGTCAAAAATACATTTAATAATCCTC
*
3628845 A
65 T
** ****
3628846 TCAATAAATTTTTATGAGGGATTATTGAAAATATTTTAAACCAAAAATACATTTAATAATCC-CT
1 TCAATAAATTTTTATGAGGGATTATTGAAGGTATTTTTGGTCAAAAATACATTTAATAATCCTCT
* * * *
3628910 TCCATAAATTTTTATGAGAGATTATTGAAGGTATTTTTAGTCAAAAATACATTTAATAAT-CTTT
1 TCAATAAATTTTTATGAGGGATTATTGAAGGTATTTTTGGTCAAAAATACATTTAATAATCCTCT
3628974 TCAAT
1 TCAAT
3628979 TTTTTTCAAG
Statistics
Matches: 307, Mismatches: 58, Indels: 35
0.77 0.14 0.09
Matches are distributed among these distances:
61 23 0.07
62 121 0.39
63 15 0.05
64 129 0.42
65 19 0.06
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (65 bp):
TCAATAAATTTTTATGAGGGATTATTGAAGGTATTTTTGGTCAAAAATACATTTAATAATCCTCT
Found at i:3628868 original size:188 final size:189
Alignment explanation
Indices: 3628551--3628970 Score: 479
Period size: 188 Copynumber: 2.2 Consensus size: 189
3628541 TTTTATGATG
* * * * * * ** *
3628551 GATTATTAAAAGTATTTTTGATCAAAAATATCTTCAATAATCCTTTTCAAATTTTTTAAGGGATT
1 GATTATTAAAGGTATTTTTGGTCAAAAATACCTTTAATAATCCCTTCCAAAAATTTTAAGCGATT
* * * * *
3628616 ATTGAAAGCATTTTTTGGTCAAAAATACCTTCAATAATCCTCTTAATAAATTTTTATGAGGGATT
66 ATTGAAAGCATTTTTTGATAAAAAATACATTCAATAATCCTATCAATAAATTTTTATGAGGGATT
** * **** * * *
3628681 ATTGAAGGTGTTTTTGGTAAAAAATGCTTTTAATAATCTCTTCCA-AATATTTTCA-AGA
131 ATTGAAAATATTTTAAACAAAAAATACATTTAATAATCCCTTCCATAA-ATTTTCAGAGA
* *
3628739 GATTATTTAAGGTATTTTTGGCCAAAAATACCTTTAATAATCCCTTCCAAAAATTTTAAGACGAT
1 GATTATTAAAGGTATTTTTGGTCAAAAATACCTTTAATAATCCCTTCCAAAAATTTTAAG-CGAT
* *
3628804 TATT-AAAGGCGTTTTTT-ATAAAAAATACATTGAATAATCCTATCAATAAATTTTTATGAGGGA
65 TATTGAAA-GCATTTTTTGATAAAAAATACATTCAATAATCCTATCAATAAATTTTTATGAGGGA
* *
3628867 TTATTGAAAATATTTTAAACCAAAAATACATTTAATAATCCCTTCCATAAATTTTTATGAGA
129 TTATTGAAAATATTTTAAACAAAAAATACATTTAATAATCCCTTCCATAAATTTTCA-GAGA
* * *
3628929 GATTATTGAAGGTATTTTTAGTCAAAAATACATTTAATAATC
1 GATTATTAAAGGTATTTTTGGTCAAAAATACCTTTAATAATC
3628971 TTTTCAATTT
Statistics
Matches: 193, Mismatches: 34, Indels: 8
0.82 0.14 0.03
Matches are distributed among these distances:
188 135 0.70
189 17 0.09
190 41 0.21
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (189 bp):
GATTATTAAAGGTATTTTTGGTCAAAAATACCTTTAATAATCCCTTCCAAAAATTTTAAGCGATT
ATTGAAAGCATTTTTTGATAAAAAATACATTCAATAATCCTATCAATAAATTTTTATGAGGGATT
ATTGAAAATATTTTAAACAAAAAATACATTTAATAATCCCTTCCATAAATTTTCAGAGA
Found at i:3629307 original size:55 final size:56
Alignment explanation
Indices: 3629218--3629323 Score: 128
Period size: 55 Copynumber: 1.9 Consensus size: 56
3629208 CGTTTTTTAT
* ** *
3629218 CAAAAACACTTCAATAATCCTTTTCAAATTTTTTTA-GAG-GATTATTGAATGTGC
1 CAAAAACACTTCAATAATCCTCTTCAAAAATTTTTATGAGAAATTATTGAATGTGC
*
3629272 CAAAAATATCTTCAATAATCC-CTTCAATAAATTTTTATGAGAAATTATTGAA
1 CAAAAACA-CTTCAATAATCCTCTTCAA-AAATTTTTATGAGAAATTATTGAA
3629324 GGCGTTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
54 12 0.28
55 19 0.44
56 3 0.07
57 9 0.21
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (56 bp):
CAAAAACACTTCAATAATCCTCTTCAAAAATTTTTATGAGAAATTATTGAATGTGC
Found at i:3629526 original size:58 final size:58
Alignment explanation
Indices: 3629426--3629538 Score: 151
Period size: 58 Copynumber: 1.9 Consensus size: 58
3629416 AATCCATTCC
*
3629426 AAATTTTGTTGAAGGGATTATTGAAGGTGATTTTGATAAAAAAATACCTTCAATATCCT
1 AAATTTTGTTGAAGGGATTATTGAAGGTGATTTTAAT-AAAAAATACCTTCAATATCCT
* *
3629485 AAATTTT-TATGAA-GGATTATTGAATGT-ATTTTTAATCAAAAATACCTTCAATAT
1 AAATTTTGT-TGAAGGGATTATTGAAGGTGA-TTTTAATAAAAAATACCTTCAATAT
3629539 TCTCTCTCCA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
57 18 0.37
58 20 0.41
59 11 0.22
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (58 bp):
AAATTTTGTTGAAGGGATTATTGAAGGTGATTTTAATAAAAAATACCTTCAATATCCT
Found at i:3629534 original size:57 final size:58
Alignment explanation
Indices: 3629426--3629538 Score: 153
Period size: 57 Copynumber: 1.9 Consensus size: 58
3629416 AATCCATTCC
3629426 AAATTTTGTTGAAGGGATTATTGAAGGTGATTTTGATAAAAAAATACCTTCAATATCCT
1 AAATTTTGTTGAAGGGATTATTGAAGGTGATTTT-ATAAAAAAATACCTTCAATATCCT
*
3629485 AAATTTT-TATGAA-GGATTATTGAATGT-ATTTT-TAATCAAAAATACCTTCAATAT
1 AAATTTTGT-TGAAGGGATTATTGAAGGTGATTTTATAA--AAAAATACCTTCAATAT
3629539 TCTCTCTCCA
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
55 3 0.06
57 22 0.44
58 14 0.28
59 11 0.22
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (58 bp):
AAATTTTGTTGAAGGGATTATTGAAGGTGATTTTATAAAAAAATACCTTCAATATCCT
Found at i:3631612 original size:17 final size:16
Alignment explanation
Indices: 3631590--3631628 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3631580 TGGCCATAGC
3631590 TAATGATGAACTAATGA
1 TAATGATG-ACTAATGA
* *
3631607 TAATGATGATTTATGA
1 TAATGATGACTAATGA
3631623 TAATGA
1 TAATGA
3631629 ATTTACGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.36
Consensus pattern (16 bp):
TAATGATGACTAATGA
Found at i:3631796 original size:2 final size:2
Alignment explanation
Indices: 3631789--3631823 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3631779 TTAAATGAGC
3631789 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 T
3631824 GAAAACGATA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3638513 original size:30 final size:30
Alignment explanation
Indices: 3638479--3638548 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
3638469 TATATTTTAT
*
3638479 TTTATTTTTATCTTCATA-TTTTTAAATATA
1 TTTATTTTTAT-TTCATAGTTTATAAATATA
* **
3638509 TTTATTATTATTTCATAGTTTATATTTATA
1 TTTATTTTTATTTCATAGTTTATAAATATA
3638539 TTTATATTTT
1 TTTAT-TTTT
3638549 TTATGTCTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 6 0.18
30 24 0.73
31 3 0.09
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (30 bp):
TTTATTTTTATTTCATAGTTTATAAATATA
Found at i:3638536 original size:6 final size:6
Alignment explanation
Indices: 3638468--3638547 Score: 51
Period size: 6 Copynumber: 13.3 Consensus size: 6
3638458 GGTTCAATTG
* * * *
3638468 TTATAT TT-TAT TT-TAT TTTTAT CTTCATAT TTTTAA ATATAT TTAT-T
1 TTATAT TTATAT TTATAT TTATAT -TT-ATAT TTATAT TTATAT TTATAT
*
3638515 ATTAT-T TCATAGT TTATAT TTATAT TTATAT TT
1 -TTATAT TTATA-T TTATAT TTATAT TTATAT TT
3638548 TTTATGTCTT
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
5 14 0.24
6 33 0.56
7 9 0.15
8 3 0.05
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (6 bp):
TTATAT
Found at i:3638576 original size:14 final size:15
Alignment explanation
Indices: 3638557--3638613 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 15
3638547 TTTTATGTCT
3638557 TTTA-TTCATTTATC
1 TTTATTTCATTTATC
3638571 TTTATTTCACCTTTATC
1 TTTATTTCA--TTTATC
3638588 -TTATTTTC-TTTATC
1 TTTA-TTTCATTTATC
*
3638602 TTAATTTCATTT
1 TTTATTTCATTT
3638614 TTAATTTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
14 14 0.39
15 9 0.25
16 3 0.08
17 10 0.28
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTATTTCATTTATC
Found at i:3640771 original size:25 final size:26
Alignment explanation
Indices: 3640736--3640786 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
3640726 ATCAATAGTA
3640736 AAAAATATAATAACAACTT-TTAAAAT
1 AAAAATATAATAACAA-TTCTTAAAAT
*
3640762 AAAAA-ATAATAATAATTCTTAAAAT
1 AAAAATATAATAACAATTCTTAAAAT
3640787 TATATCTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 2 0.09
25 16 0.70
26 5 0.22
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (26 bp):
AAAAATATAATAACAATTCTTAAAAT
Found at i:3643076 original size:23 final size:23
Alignment explanation
Indices: 3643006--3643077 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 23
3642996 TTAATCTCTT
* *
3643006 AATTATGA-TTTTTTATTAAAAA
1 AATTACGATTTTTTTAATAAAAA
* ** ****
3643028 AGTTACTTTTTTTTTAATCTCTA
1 AATTACGATTTTTTTAATAAAAA
3643051 AATTACGATTTTTTTAATAAAAA
1 AATTACGATTTTTTTAATAAAAA
3643074 AATT
1 AATT
3643078 TCTAATGGCA
Statistics
Matches: 33, Mismatches: 16, Indels: 1
0.66 0.32 0.02
Matches are distributed among these distances:
22 4 0.12
23 29 0.88
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (23 bp):
AATTACGATTTTTTTAATAAAAA
Found at i:3647448 original size:2 final size:2
Alignment explanation
Indices: 3647443--3647468 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3647433 TATGTGTGTG
3647443 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3647469 AATGAAACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3651636 original size:2 final size:2
Alignment explanation
Indices: 3651629--3651655 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3651619 TGTTTAAAAC
3651629 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
3651656 CGTGTTATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3656634 original size:20 final size:22
Alignment explanation
Indices: 3656601--3656641 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3656591 GGCACAATTT
3656601 AAAATATTAAC-AAAAACTATA
1 AAAATATTAACAAAAAACTATA
*
3656622 AAAATA-TACCAAAAAACTAT
1 AAAATATTAACAAAAAACTAT
3656642 TTATATATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.66, C:0.12, G:0.00, T:0.22
Consensus pattern (22 bp):
AAAATATTAACAAAAAACTATA
Done.