Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold206
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: 2736418
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 22040 characters in sequence are not A, C, G, or T
File 18 of 20
Found at i:2394789 original size:14 final size:14
Alignment explanation
Indices: 2394749--2394794 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
2394739 CGATGAAAAC
2394749 TATA-ACATATATGA
1 TATACACATATAT-A
*
2394763 TA-ACAATATATATA
1 TATAC-ACATATATA
2394777 TATACACATATATA
1 TATACACATATATA
2394791 TATA
1 TATA
2394795 TGTTAACGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 1 0.04
14 17 0.63
15 9 0.33
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.37
Consensus pattern (14 bp):
TATACACATATATA
Found at i:2394789 original size:16 final size:15
Alignment explanation
Indices: 2394755--2394795 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
2394745 AAACTATAAC
2394755 ATATATGATA-ACAAT
1 ATATAT-ATATACAAT
2394770 ATATATATATACACAT
1 ATATATATATACA-AT
2394786 ATATATATAT
1 ATATATATAT
2394796 GTTAACGGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.12
15 9 0.38
16 12 0.50
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.39
Consensus pattern (15 bp):
ATATATATATACAAT
Found at i:2395144 original size:4 final size:4
Alignment explanation
Indices: 2395135--2395164 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
2395125 CACTAATCAA
*
2395135 CTCC CTCC CTCC CTCC CTCC CTCC TTCC CT
1 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CT
2395165 TTTAAGCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.70, G:0.00, T:0.30
Consensus pattern (4 bp):
CTCC
Found at i:2395506 original size:16 final size:17
Alignment explanation
Indices: 2395471--2395516 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
2395461 TTATTTTTAT
*
2395471 ATAATATAAATTACATA
1 ATAATATAAATTACAAA
2395488 AT-ATATAAATATA-AAA
1 ATAATATAAAT-TACAAA
*
2395504 ATAATATACATTA
1 ATAATATAAATTA
2395517 TATAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAATATAAATTACAAA
Found at i:2395593 original size:16 final size:17
Alignment explanation
Indices: 2395571--2395613 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
2395561 AAAGCTCTAT
2395571 TTTATTTTTTA-C-AAA
1 TTTATTTTTTATCTAAA
2395586 TATTATTTTTTATCTAAA
1 T-TTATTTTTTATCTAAA
2395604 TTTATTTTTT
1 TTTATTTTTT
2395614 GAATTTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 1 0.04
16 10 0.40
17 10 0.40
18 4 0.16
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATTTTTTATCTAAA
Found at i:2395798 original size:16 final size:17
Alignment explanation
Indices: 2395767--2395799 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2395757 AGAATCCATC
2395767 TTTTTTTTTGTTATTGAA
1 TTTTTTTTTG-TATTGAA
2395785 TTTTTTTTTG-ATTGA
1 TTTTTTTTTGTATTGA
2395800 TCAATATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
18 10 0.67
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (17 bp):
TTTTTTTTTGTATTGAA
Found at i:2396508 original size:21 final size:20
Alignment explanation
Indices: 2396476--2396517 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
2396466 AATTTTTATT
*
2396476 TAAATTTAAATATAAAATATA
1 TAAATTTAAATA-AAAAAATA
2396497 TAAATATT-AATAAAAAAATA
1 TAAAT-TTAAATAAAAAAATA
2396517 T
1 T
2396518 TTTTAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.42
21 9 0.47
22 2 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAATTTAAATAAAAAAATA
Found at i:2398719 original size:2 final size:2
Alignment explanation
Indices: 2398714--2398740 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2398704 TAACTCTAAA
2398714 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
2398741 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2399282 original size:2 final size:2
Alignment explanation
Indices: 2399275--2399314 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2399265 CACTTCCTTG
*
2399275 AT AT AT AT AT AT AT AT AT AT AC 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
2399315 TCATAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2401309 original size:23 final size:24
Alignment explanation
Indices: 2401257--2401311 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
2401247 GGTGACTTGT
2401257 TACATGAACCCTATTAAATATCTA
1 TACATGAACCCTATTAAATATCTA
* *
2401281 TACATGTACCCTAATT-AAT-TTTA
1 TACATGAACCCT-ATTAAATATCTA
2401304 TACATGAA
1 TACATGAA
2401312 TTACATGGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.37
24 14 0.52
25 3 0.11
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.36
Consensus pattern (24 bp):
TACATGAACCCTATTAAATATCTA
Found at i:2407273 original size:8 final size:10
Alignment explanation
Indices: 2407241--2407274 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
2407231 AATTTGAATA
2407241 ATATTTAATAT
1 ATATTTAA-AT
2407252 ATATTTAAAT
1 ATATTTAAAT
2407262 ATATTTAAAT
1 ATATTTAAAT
2407272 ATA
1 ATA
2407275 AATATAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 15 0.65
11 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
ATATTTAAAT
Found at i:2408087 original size:21 final size:21
Alignment explanation
Indices: 2408061--2408115 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
2408051 AAAGTTTGCG
* *
2408061 TTTTATTATGTTATTTTTATA
1 TTTTATTATATTATTTTTACA
2408082 TTTTATTATATTATTTTTACA
1 TTTTATTATATTATTTTTACA
*
2408103 TGTTATTTATATT
1 TTTTA-TTATATT
2408116 TATTACTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 23 0.77
22 7 0.23
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (21 bp):
TTTTATTATATTATTTTTACA
Found at i:2408778 original size:17 final size:18
Alignment explanation
Indices: 2408756--2408803 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
2408746 ATTAAATTTT
* *
2408756 TTAAATTTTTTTAA-ATA
1 TTAAATTATTTTAATAGA
2408773 TTAAATTATTTTAATAGA
1 TTAAATTATTTTAATAGA
2408791 TTAAATTATTTTA
1 TTAAATTATTTTA
2408804 TGTAACTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTAAATTATTTTAATAGA
Found at i:2409441 original size:18 final size:18
Alignment explanation
Indices: 2409416--2409450 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2409406 ATTATTAAAT
2409416 TAAAATTT-TTAAAAAAA
1 TAAAATTTATTAAAAAAA
2409433 TAAATATTTATTAAAAAA
1 TAAA-ATTTATTAAAAAA
2409451 TATTATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATTTATTAAAAAAA
Found at i:2409460 original size:32 final size:31
Alignment explanation
Indices: 2409397--2409460 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 31
2409387 TTTAGTTTTC
* *
2409397 AAAATTAATATTATTAAATTAAAATTTTTAAA
1 AAAATAAATATTATTAAA-TAAAATTATTAAA
2409429 AAAATAAATATTTATTAAA-AAATATTATTAAA
1 AAAATAAATA-TTATTAAATAAA-ATTATTAAA
2409461 TTAAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 3 0.11
32 17 0.61
33 8 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
AAAATAAATATTATTAAATAAAATTATTAAA
Found at i:2409466 original size:16 final size:16
Alignment explanation
Indices: 2409403--2409467 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
2409393 TTTCAAAATT
2409403 AATATTATTAAATTAA
1 AATATTATTAAATTAA
2409419 AAT-TT-TTAAA--AA
1 AATATTATTAAATTAA
* *
2409431 AATAAATATT-TATTAAAA
1 AAT-ATTATTAAATT--AA
2409449 AATATTATTAAATTAA
1 AATATTATTAAATTAA
2409465 AAT
1 AAT
2409468 TTAAATAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 16
0.65 0.07 0.28
Matches are distributed among these distances:
12 5 0.14
14 7 0.19
15 4 0.11
16 8 0.22
17 5 0.14
18 8 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATATTATTAAATTAA
Found at i:2409508 original size:19 final size:21
Alignment explanation
Indices: 2409469--2409510 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2409459 AATTAAAATT
2409469 TAAATAATAATATATAAATTTA
1 TAAATAATAATATAT-AATTTA
*
2409491 TAAATAATAA-ATATATTTTA
1 TAAATAATAATATATAATTTA
2409511 GTTTTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 4 0.21
22 10 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATAATAATATATAATTTA
Found at i:2409874 original size:15 final size:13
Alignment explanation
Indices: 2409844--2409870 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2409834 TTTAATAATT
2409844 TTATTTTTATAAA
1 TTATTTTTATAAA
2409857 TTATTTTTATAAA
1 TTATTTTTATAAA
2409870 T
1 T
2409871 ATTAAATTAT
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATTTTTATAAA
Found at i:2409878 original size:20 final size:20
Alignment explanation
Indices: 2409852--2409908 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
2409842 TTTTATTTTT
2409852 ATAAATTATTTTTATAAATA
1 ATAAATTATTTTTATAAATA
*
2409872 TTAAATTATATTTTAATAAATA
1 ATAAATTAT-TTTT-ATAAATA
2409894 AT-AA-TATTTTTATAA
1 ATAAATTATTTTTATAA
2409909 TAAAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 4 0.12
19 4 0.12
20 11 0.33
21 6 0.18
22 8 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAAATTATTTTTATAAATA
Found at i:2409916 original size:17 final size:18
Alignment explanation
Indices: 2409879--2409916 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2409869 ATATTAAATT
*
2409879 ATATTTTAATAAATAATA
1 ATATTTTAATAAATAAAA
*
2409897 ATATTTTTAT-AATAAAA
1 ATATTTTAATAAATAAAA
2409914 ATA
1 ATA
2409917 AAAATTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATTTTAATAAATAAAA
Found at i:2409927 original size:20 final size:21
Alignment explanation
Indices: 2409885--2409932 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
2409875 AATTATATTT
* * *
2409885 TAATAAATAATAATATTTTTA
1 TAATAAATAATAAAAATTATA
2409906 TAATAAA-AATAAAAATTATA
1 TAATAAATAATAAAAATTATA
2409926 TAA-AAAT
1 TAATAAAT
2409933 TTTTTAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 3 0.13
20 13 0.57
21 7 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATAAATAATAAAAATTATA
Found at i:2411064 original size:3 final size:3
Alignment explanation
Indices: 2411056--2411089 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2411046 CTACAATATC
2411056 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2411090 CTTACTACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2411175 original size:2 final size:2
Alignment explanation
Indices: 2411168--2411206 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2411158 TTGTTTTAAG
2411168 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2411207 TAATATAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2411389 original size:15 final size:15
Alignment explanation
Indices: 2411328--2411406 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
2411318 AATTATAATT
* *
2411328 ATAAATATATTTTTA
1 ATAAATATAATTATA
* *
2411343 ATAATATTATATTTATT
1 ATAA-A-TATAATTATA
* *
2411360 ATAAATTTAAATATA
1 ATAAATATAATTATA
*
2411375 ATAAATATTATTATA
1 ATAAATATAATTATA
* *
2411390 ATTATTATAATTATA
1 ATAAATATAATTATA
2411405 AT
1 AT
2411407 TTTTTATTTT
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
15 36 0.72
16 2 0.04
17 12 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATAAATATAATTATA
Found at i:2411393 original size:9 final size:9
Alignment explanation
Indices: 2411319--2411403 Score: 50
Period size: 9 Copynumber: 9.2 Consensus size: 9
2411309 ACAGAGTTAA
2411319 ATTATAATT
1 ATTATAATT
*
2411328 ATAAATATATT
1 AT-TATA-ATT
*
2411339 TTTAATAA-T
1 ATT-ATAATT
*
2411348 ATTATATTT
1 ATTATAATT
*
2411357 ATTATAAAT
1 ATTATAATT
2411366 -TTA-AATAT
1 ATTATAAT-T
* *
2411374 AATAAATATT
1 ATTATA-ATT
2411384 ATTATAATT
1 ATTATAATT
2411393 ATTATAATT
1 ATTATAATT
2411402 AT
1 AT
2411404 AATTTTTTAT
Statistics
Matches: 57, Mismatches: 11, Indels: 16
0.68 0.13 0.19
Matches are distributed among these distances:
7 2 0.04
8 7 0.12
9 29 0.51
10 10 0.18
11 9 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
ATTATAATT
Found at i:2411787 original size:22 final size:23
Alignment explanation
Indices: 2411734--2411790 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
2411724 ATTAATATAT
2411734 AATTTTAATTT-TATATTAAATTA
1 AATTTT-ATTTATATATTAAATTA
**
2411757 AATAATATTTATA-ATTAAATTA
1 AATTTTATTTATATATTAAATTA
2411779 AATTTTATTTAT
1 AATTTTATTTAT
2411791 TTGAATTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 23 0.79
23 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATTTTATTTATATATTAAATTA
Found at i:2411929 original size:14 final size:15
Alignment explanation
Indices: 2411905--2411941 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
2411895 TAATTAAAAG
2411905 TATAA-TTTATTAAT
1 TATAATTTTATTAAT
2411919 T-TAATTTTATTAAT
1 TATAATTTTATTAAT
2411933 TATAATTTT
1 TATAATTTT
2411942 TAACTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 11 0.52
15 7 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATAATTTTATTAAT
Found at i:2411949 original size:14 final size:14
Alignment explanation
Indices: 2411905--2411949 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
2411895 TAATTAAAAG
2411905 TATAATTTATTAAT
1 TATAATTTATTAAT
2411919 T-TAATTTTATTAAT
1 TATAA-TTTATTAAT
2411933 TATAATTT-TTAACT
1 TATAATTTATTAA-T
2411947 TAT
1 TAT
2411950 TAATAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 7 0.25
14 18 0.64
15 3 0.11
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (14 bp):
TATAATTTATTAAT
Found at i:2414786 original size:32 final size:33
Alignment explanation
Indices: 2414725--2414786 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
2414715 TTGATTTAAT
**
2414725 TAAAAATTAAAAATTATTTAATCTATTATTATA
1 TAAAAATTAAAAATTATTTAAAATATTATTATA
* *
2414758 TAAAAATTTAAATTTATTTAAAAT-TTATT
1 TAAAAATTAAAAATTATTTAAAATATTATT
2414787 TAATAATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 5 0.20
33 20 0.80
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (33 bp):
TAAAAATTAAAAATTATTTAAAATATTATTATA
Found at i:2415001 original size:20 final size:19
Alignment explanation
Indices: 2414950--2415002 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
2414940 TTTATCATAT
2414950 AATATTTATTT-AATATTAA
1 AATA-TTATTTAAATATTAA
* *
2414969 ATTATT-TTAAAATATTTAA
1 AATATTATTTAAATA-TTAA
2414988 AATATTATTTAAATA
1 AATATTATTTAAATA
2415003 AATTAATCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 2 0.07
18 6 0.22
19 12 0.44
20 7 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AATATTATTTAAATATTAA
Found at i:2416566 original size:20 final size:22
Alignment explanation
Indices: 2416531--2416576 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
2416521 TTTTTTGTAA
*
2416531 TTTTTAAAATTATTAT-TTTAT
1 TTTTTAAAATTATTATATATAT
*
2416552 TTTTTAAAA-TGTTATATATAT
1 TTTTTAAAATTATTATATATAT
2416573 TTTT
1 TTTT
2416577 ATATTTTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTTAAAATTATTATATATAT
Found at i:2416577 original size:20 final size:20
Alignment explanation
Indices: 2416530--2416577 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
2416520 TTTTTTTGTA
*
2416530 ATTTTTAAAATTATTATTTT
1 ATTTTTAAAATTATTATTAT
*
2416550 ATTTTTTAAAA-TGTTATATAT
1 A-TTTTTAAAATTATTAT-TAT
2416571 ATTTTTA
1 ATTTTTA
2416578 TATTTTTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTTTAAAATTATTATTAT
Found at i:2419050 original size:16 final size:15
Alignment explanation
Indices: 2419024--2419057 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2419014 AAATATATTT
2419024 TTATTATTTAAATAA
1 TTATTATTTAAATAA
*
2419039 TTATTAATTTAAATTA
1 TTATT-ATTTAAATAA
2419055 TTA
1 TTA
2419058 AAAAATACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATTATTTAAATAA
Found at i:2420150 original size:23 final size:22
Alignment explanation
Indices: 2420099--2420153 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
2420089 ATATTAAATT
*
2420099 TAATAAATTATTTTTATAATATA
1 TAATAAATT-TTTTTAAAATATA
*
2420122 T-A-AAATTTTTTTAAAAATTTA
1 TAATAAATTTTTTT-AAAATATA
2420143 TAATAAATTTT
1 TAATAAATTTT
2420154 AATAATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 5 0.19
21 12 0.44
22 2 0.07
23 8 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAATAAATTTTTTTAAAATATA
Found at i:2420452 original size:17 final size:17
Alignment explanation
Indices: 2420430--2420467 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
2420420 AATATTAATT
2420430 TATTAT-ATTTTATTTTA
1 TATTATAATTTT-TTTTA
2420447 TATTATAATTTTTTTTA
1 TATTATAATTTTTTTTA
2420464 TATT
1 TATT
2420468 TGTTTTATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTATAATTTTTTTTA
Found at i:2420708 original size:10 final size:10
Alignment explanation
Indices: 2420695--2420743 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
2420685 TATAATATAA
2420695 TAAATAAATT
1 TAAATAAATT
2420705 TAAAT-AATT
1 TAAATAAATT
2420714 ATAAATAATAATT
1 -TAAAT-A-AATT
2420727 TAAAT--ATT
1 TAAATAAATT
2420735 TAAATAAAT
1 TAAATAAAT
2420744 ATATAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
8 8 0.24
9 4 0.12
10 12 0.36
12 5 0.15
13 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TAAATAAATT
Found at i:2420719 original size:20 final size:19
Alignment explanation
Indices: 2420688--2420743 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
2420678 ATTAAAATAT
*
2420688 AATATAATAAATAAATTTA
1 AATATTATAAATAAATTTA
2420707 AATAATTATAAATAATAATTTA
1 AAT-ATTATAAAT-A-AATTTA
2420729 AATATT-TAAATAAAT
1 AATATTATAAATAAAT
2420744 ATATAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
18 3 0.09
19 4 0.12
20 13 0.39
21 4 0.12
22 9 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATATTATAAATAAATTTA
Found at i:2420736 original size:30 final size:34
Alignment explanation
Indices: 2420700--2420769 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 34
2420690 TATAATAAAT
2420700 AAATTTAAAT-AAT-TAT-AAATAATA-AT-TTA
1 AAATTTAAATAAATATATAAAATAATATATATTA
2420729 AATATTTAAATAAATATATAAAATAATATATATTA
1 AA-ATTTAAATAAATATATAAAATAATATATATTA
2420764 AAATTT
1 AAATTT
2420770 TATATTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
29 2 0.06
30 8 0.23
31 3 0.09
32 3 0.09
33 8 0.23
34 6 0.17
35 5 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
AAATTTAAATAAATATATAAAATAATATATATTA
Found at i:2420742 original size:12 final size:13
Alignment explanation
Indices: 2420727--2420765 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
2420717 AATAATAATT
2420727 TAAATAT-TTAAA
1 TAAATATATTAAA
*
2420739 TAAATATATAAAA
1 TAAATATATTAAA
2420752 TAATATATATTAAA
1 TAA-ATATATTAAA
2420766 ATTTTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 7 0.30
13 7 0.30
14 9 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAATATATTAAA
Found at i:2420750 original size:20 final size:21
Alignment explanation
Indices: 2420694--2420760 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 21
2420684 ATATAATATA
2420694 ATAAATAAAT-TTAAATAATT
1 ATAAATAAATATTAAATAATT
2420714 ATAAAT-AATAATTTAAAT-ATT
1 ATAAATAAAT-A-TTAAATAATT
2420735 -TAAATAAATATATAAAATAATAT
1 ATAAATAAATAT-T-AAATAAT-T
2420758 ATA
1 ATA
2420761 TTAAAATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
19 4 0.11
20 13 0.34
21 10 0.26
22 8 0.21
23 1 0.03
24 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAAATAAATATTAAATAATT
Found at i:2420825 original size:14 final size:14
Alignment explanation
Indices: 2420742--2420825 Score: 56
Period size: 13 Copynumber: 6.4 Consensus size: 14
2420732 ATTTAAATAA
*
2420742 ATATATAAAATAATAT
1 ATAT-TAAAATTAT-T
2420758 ATATTAAAATT-TT
1 ATATTAAAATTATT
2420771 ATATTAAAATT-TT
1 ATATTAAAATTATT
*
2420784 -TA--ATAATTATT
1 ATATTAAAATTATT
**
2420795 -T-TTAATTTTATT
1 ATATTAAAATTATT
*
2420807 TTATTAAAATTATT
1 ATATTAAAATTATT
2420821 ATATT
1 ATATT
2420826 TATATTTAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
10 5 0.09
11 3 0.05
12 8 0.15
13 15 0.27
14 14 0.25
15 6 0.11
16 4 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATTAAAATTATT
Found at i:2420831 original size:20 final size:19
Alignment explanation
Indices: 2420803--2420854 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
2420793 TTTTTAATTT
*
2420803 TATTT-TATTAAAATTATTA
1 TATTTATATTAAAA-TAATA
*
2420822 TATTTATATTTAAATAATA
1 TATTTATATTAAAATAATA
2420841 TATCTTATCATTAA
1 TAT-TTAT-ATTAA
2420855 TTATTTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 12 0.44
20 11 0.41
21 4 0.15
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTATATTAAAATAATA
Found at i:2422494 original size:2 final size:2
Alignment explanation
Indices: 2422489--2422515 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2422479 TTTTGGCTGT
2422489 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 T
2422516 TATGAACTTA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2431199 original size:16 final size:16
Alignment explanation
Indices: 2431180--2431212 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2431170 ATATAATATT
2431180 ATTTATATTT-ATTTAA
1 ATTTAT-TTTAATTTAA
2431196 ATTTATTTTAATTTAA
1 ATTTATTTTAATTTAA
2431212 A
1 A
2431213 ATGTGAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTATTTTAATTTAA
Found at i:2431416 original size:30 final size:30
Alignment explanation
Indices: 2431380--2431451 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
2431370 CTTTAAAATT
*
2431380 TATTAATCAAGTTTATAATTTTATGTTTTA
1 TATTAATCAAGTTTATAATTTTATATTTTA
* * *
2431410 TATTAATTAAGTTTTTAATTTTATATTTTG
1 TATTAATCAAGTTTATAATTTTATATTTTA
*
2431440 TATCAATCAAGT
1 TATTAATCAAGT
2431452 ACTTTCTGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (30 bp):
TATTAATCAAGTTTATAATTTTATATTTTA
Found at i:2432116 original size:15 final size:17
Alignment explanation
Indices: 2432082--2432116 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2432072 TTTGGACGAG
2432082 TATCAAATACAGATATA
1 TATCAAATACAGATATA
* *
2432099 TATCTAATACAAATATA
1 TATCAAATACAGATATA
2432116 T
1 T
2432117 TTAACTCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.34
Consensus pattern (17 bp):
TATCAAATACAGATATA
Found at i:2437344 original size:14 final size:15
Alignment explanation
Indices: 2437310--2437344 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
2437300 TTTCACATAT
2437310 TTTTCATTTCATGCA
1 TTTTCATTTCATGCA
2437325 TTTTCATTTCATGC-
1 TTTTCATTTCATGCA
2437339 TTTTCA
1 TTTTCA
2437345 CGTAACATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.17, C:0.20, G:0.06, T:0.57
Consensus pattern (15 bp):
TTTTCATTTCATGCA
Found at i:2437385 original size:5 final size:5
Alignment explanation
Indices: 2437369--2437545 Score: 183
Period size: 5 Copynumber: 35.4 Consensus size: 5
2437359 CATGCATAAT
* * * *
2437369 TTTCA TTGCA TTTCA TTTCA TTTCA TTTCA TTGCA TTGCA TTTCA TTGCA
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA
* * * * * *
2437419 TTGCA TTTCA TTACA TTGCA TTGCA TTTCA TTACA TTGCA TTTCA TTTCA
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA
* * * * * *
2437469 TTGCA TTGCA TTTCA TTGCA TTGCA TTTCA TTACA TTGCA TTTCA TTTCA
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA
* * *
2437519 TTACA TTGCA TTTCA TTTCA TTGCA TT
1 TTTCA TTTCA TTTCA TTTCA TTTCA TT
2437546 GGTTTCATGC
Statistics
Matches: 149, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 149 1.00
ACGTcount: A:0.22, C:0.20, G:0.08, T:0.50
Consensus pattern (5 bp):
TTTCA
Found at i:2437394 original size:20 final size:20
Alignment explanation
Indices: 2437369--2437546 Score: 221
Period size: 20 Copynumber: 8.7 Consensus size: 20
2437359 CATGCATAAT
*
2437369 TTTCATTGCATTTCATTTCA
1 TTTCATTGCATTGCATTTCA
* *
2437389 TTTCATTTCATTGCATTGCA
1 TTTCATTGCATTGCATTTCA
2437409 TTTCATTGCATTGCATTTCA
1 TTTCATTGCATTGCATTTCA
*
2437429 TTACATTGCATTGCATTTCA
1 TTTCATTGCATTGCATTTCA
* *
2437449 TTACATTGCATTTCATTTCA
1 TTTCATTGCATTGCATTTCA
* *
2437469 TTGCATTGCATTTCATTGCATTGCA
1 -T---TT-CATTGCATTGCATTTCA
*
2437494 TTTCATTACATTGCATTTCA
1 TTTCATTGCATTGCATTTCA
*
2437514 TTTCATTACATTGCATTTCA
1 TTTCATTGCATTGCATTTCA
2437534 TTTCATTGCATTG
1 TTTCATTGCATTG
2437547 GTTTCATGCA
Statistics
Matches: 139, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
20 120 0.86
21 3 0.02
24 2 0.01
25 14 0.10
ACGTcount: A:0.22, C:0.20, G:0.09, T:0.49
Consensus pattern (20 bp):
TTTCATTGCATTGCATTTCA
Found at i:2438457 original size:16 final size:15
Alignment explanation
Indices: 2438436--2438466 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2438426 GATTTCCATA
2438436 AAAATAATAACAAAAT
1 AAAATAATAA-AAAAT
2438452 AAAATAATAAAAAAT
1 AAAATAATAAAAAAT
2438467 TCTTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAATAATAAAAAAT
Found at i:2442591 original size:28 final size:27
Alignment explanation
Indices: 2442551--2442619 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 27
2442541 TAAAACCGGA
2442551 GTTGGAGTATCCCCTCA-GAAATAACGGG
1 GTTGGAGTATCCCC-CATG-AATAACGGG
* *
2442579 GTTGGAGTATCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCCATGAATAACGGG
2442606 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
2442620 GATTGTGAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (27 bp):
GTTGGAGTATCCCCCATGAATAACGGG
Found at i:2442701 original size:51 final size:53
Alignment explanation
Indices: 2442610--2442727 Score: 152
Period size: 51 Copynumber: 2.3 Consensus size: 53
2442600 AACGGGGTTG
* * *
2442610 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
*
2442663 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
* *
2442714 GAATATCCTCGATT
1 GAGTATCCCCGATT
2442728 GTGGAGAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
51 35 0.60
52 8 0.14
53 15 0.26
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:2445101 original size:13 final size:13
Alignment explanation
Indices: 2445083--2445108 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2445073 ACAAAGATCC
2445083 ATGTATCGATACA
1 ATGTATCGATACA
2445096 ATGTATCGATACA
1 ATGTATCGATACA
2445109 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2445104 original size:33 final size:33
Alignment explanation
Indices: 2445062--2445128 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2445052 AAAATTTCCA
***
2445062 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2445095 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2445128 A
1 A
2445129 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2445172 original size:19 final size:18
Alignment explanation
Indices: 2445148--2445215 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
2445138 CAGTAGCTAA
2445148 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2445167 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2445182 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2445199 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2445216 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:2445188 original size:13 final size:13
Alignment explanation
Indices: 2445170--2445194 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2445160 ACAATACTTA
2445170 TGTATCGATACAT
1 TGTATCGATACAT
2445183 TGTATCGATACA
1 TGTATCGATACA
2445195 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2445192 original size:32 final size:32
Alignment explanation
Indices: 2445151--2445213 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2445141 TAGCTAATTA
*
2445151 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2445183 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2445214 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2445295 original size:21 final size:21
Alignment explanation
Indices: 2445271--2445327 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2445261 CATTTGTAGG
2445271 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
2445292 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
2445313 ATGTATCGATACATT
1 ATGTATCGATACATT
2445328 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:2445358 original size:19 final size:19
Alignment explanation
Indices: 2445334--2445371 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2445324 CATTTAAATT
2445334 TTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTCAA
2445353 TTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTCAA
2445372 ACACTTTATC
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:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTTTTTTTTTTTTCAA
Found at i:2446048 original size:55 final size:55
Alignment explanation
Indices: 2445964--2446531 Score: 846
Period size: 55 Copynumber: 10.3 Consensus size: 55
2445954 ATAAATTGTA
* * * * * *
2445964 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
2446019 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
2446074 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
2446129 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
2446184 TCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
2446239 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
2446294 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
2446349 TCCTGCTCGTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
2446404 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
2446459 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
2446514 TCCTGCTCTTTGGGGACT
1 TCCTGCTCTTTGAGGACT
2446532 AAAAAGCGGA
Statistics
Matches: 479, Mismatches: 25, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
54 14 0.03
55 453 0.95
56 12 0.03
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:2446259 original size:26 final size:26
Alignment explanation
Indices: 2446230--2446319 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
2446220 GTGTGGGCTT
2446230 TGAAAGGTGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGAGGAC
** * * *
2446256 TGAAAGGTG-CCACCAACTTGTGTGGGC
1 TGAAAGGTGTCCTGC-TCTT-TGAGGAC
* *
2446283 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGAGGAC
2446311 TGAAAGGTG
1 TGAAAGGTG
2446320 CCACCAACTT
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
25 3 0.06
26 17 0.36
27 8 0.17
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGAGGAC
Found at i:2446348 original size:29 final size:29
Alignment explanation
Indices: 2446260--2446348 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
2446250 GAGGACTGAA
2446260 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
** * *
2446289 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA-
1 AGGTG-CCACCAACTTGTGTGGG-CTTTAAG
2446315 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
2446344 AGGTG
1 AGGTG
2446349 TCCTGCTCGT
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 8 0.18
27 9 0.20
28 9 0.20
29 13 0.29
30 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (29 bp):
AGGTGCCACCAACTTGTGTGGGCTTTAAG
Found at i:2447543 original size:25 final size:25
Alignment explanation
Indices: 2447515--2447563 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2447505 CTTTTCTCTC
2447515 TTTTTCTTTG-TTTTGTTTTTTTTGT
1 TTTTTCTTTGCTTTT-TTTTTTTTGT
*
2447540 TTTTTTTTTGCTTTTTTTTTTTTG
1 TTTTTCTTTGCTTTTTTTTTTTTG
2447564 CTCCTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.86
Consensus pattern (25 bp):
TTTTTCTTTGCTTTTTTTTTTTTGT
Found at i:2447546 original size:11 final size:12
Alignment explanation
Indices: 2447530--2447560 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2447520 CTTTGTTTTG
2447530 TTTTTTTTG-TT
1 TTTTTTTTGCTT
2447541 TTTTTTTTGCTT
1 TTTTTTTTGCTT
2447553 TTTTTTTT
1 TTTTTTTT
2447561 TTGCTCCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.00, C:0.03, G:0.06, T:0.90
Consensus pattern (12 bp):
TTTTTTTTGCTT
Found at i:2447554 original size:20 final size:19
Alignment explanation
Indices: 2447515--2447562 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
2447505 CTTTTCTCTC
* * *
2447515 TTTTTCTTTGTTTTGTTTT
1 TTTTTTTTTTTTTTGCTTT
2447534 TTTTGTTTTTTTTTTGCTTT
1 TTTT-TTTTTTTTTTGCTTT
2447554 TTTTTTTTT
1 TTTTTTTTT
2447563 GCTCCTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.88
Consensus pattern (19 bp):
TTTTTTTTTTTTTTGCTTT
Found at i:2447571 original size:15 final size:14
Alignment explanation
Indices: 2447498--2447577 Score: 62
Period size: 14 Copynumber: 5.9 Consensus size: 14
2447488 TTAAGCAGGT
*
2447498 TCTTTTTCTTTT-C
1 TCTTTTTTTTTTGC
*
2447511 TCTCTTTTTCTTTG-
1 TCT-TTTTTTTTTGC
2447525 T-TTTGTTTTTTT--
1 TCTTT-TTTTTTTGC
*
2447537 TGTTTTTTTTTTGC
1 TCTTTTTTTTTTGC
*
2447551 TTTTTTTTTTTTGC
1 TCTTTTTTTTTTGC
2447565 TCCTTTTTTTTTT
1 T-CTTTTTTTTTT
2447578 TGAAGAGAAG
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
12 10 0.18
13 13 0.24
14 22 0.40
15 10 0.18
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.81
Consensus pattern (14 bp):
TCTTTTTTTTTTGC
Found at i:2447571 original size:16 final size:14
Alignment explanation
Indices: 2447515--2447579 Score: 66
Period size: 14 Copynumber: 4.7 Consensus size: 14
2447505 CTTTTCTCTC
*
2447515 TTTTTCTTTG-TTT
1 TTTTTTTTTGCTTT
2447528 TGTTTTTTTTG---T
1 T-TTTTTTTTGCTTT
2447540 TTTTTTTTTGCTTT
1 TTTTTTTTTGCTTT
2447554 TTTTTTTTTGCTCCTT
1 TTTTTTTTTGCT--TT
2447570 TTTTTTTTTG
1 TTTTTTTTTG
2447580 AAGAGAAGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
11 9 0.20
12 2 0.04
13 1 0.02
14 21 0.47
16 12 0.27
ACGTcount: A:0.00, C:0.08, G:0.09, T:0.83
Consensus pattern (14 bp):
TTTTTTTTTGCTTT
Found at i:2447571 original size:25 final size:25
Alignment explanation
Indices: 2447521--2447579 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
2447511 TCTCTTTTTC
* **
2447521 TTTGTTTTGTTTTTTTTGTTTTTTT
1 TTTGTTTTGTTTTTTTTGCTCCTTT
2447546 TTTGCTTTT-TTTTTTTTGCTCCTTT
1 TTTG-TTTTGTTTTTTTTGCTCCTTT
*
2447571 TTTTTTTTG
1 TTTGTTTTG
2447580 AAGAGAAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 4 0.14
25 20 0.71
26 4 0.14
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (25 bp):
TTTGTTTTGTTTTTTTTGCTCCTTT
Found at i:2447867 original size:49 final size:49
Alignment explanation
Indices: 2447810--2448353 Score: 665
Period size: 49 Copynumber: 11.4 Consensus size: 49
2447800 GAGTACCAAA
*
2447810 TAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* * * * * *
2447859 TAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGCCCAATA
1 TAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* *
2447908 TAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* * *
2447957 TAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATA
1 TAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* *
2448006 TCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* * *
2448055 TAGCTGGCCTTGACTCAGCACATTGGCA----C--CTTTAAGTCCAATA
1 TAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* * *
2448098 TCGTTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* * *
2448147 TAGCTGGCCTTGACTCAGCACATTGGCA----C--CTTTAAGTCCAATA
1 TAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* * *
2448190 TCGTTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* *
2448239 TAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATA
1 TAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* *
2448282 TAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTCAATG
1 TAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAATG
2448334 TAGCTGGCCTTGAATCAGCA
1 TAGCTGGCCTTGAATCAGCA
2448354 CGTTGACATC
Statistics
Matches: 422, Mismatches: 52, Indels: 39
0.82 0.10 0.08
Matches are distributed among these distances:
43 113 0.27
45 3 0.01
47 2 0.00
49 271 0.64
50 1 0.00
52 32 0.08
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.32
Consensus pattern (49 bp):
TAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
Found at i:2447978 original size:98 final size:92
Alignment explanation
Indices: 2447891--2448354 Score: 714
Period size: 92 Copynumber: 4.9 Consensus size: 92
2447881 TTGGCACCTT
* * *
2447891 CACCATTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CTTTTATCTTTAAGTCCAA
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATC-TTCATCTTTAAGTCCAA
2447955 TGTAGCTGGCCTTGACTCAGCACATTGG
65 TGTAGCTGGCCTTGACTCAGCACATTGG
*
2447983 CACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAG
1 CA----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAG
2448048 TCCAATGTAGCTGGCCTTGACTCAGCACATTGG
60 TCCAATGTAGCTGGCCTTGACTCAGCACATTGG
* *
2448081 CACCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAAT
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAAT
2448146 GTAGCTGGCCTTGACTCAGCACATTGG
66 GTAGCTGGCCTTGACTCAGCACATTGG
* *
2448173 CACCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAAT
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAAT
*
2448238 GTAGCTGGCCTTGAATCAGCACATTGG
66 GTAGCTGGCCTTGACTCAGCACATTGG
* * *
2448265 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTC
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA--TCTT-CATCTTTAAGTCC
*
2448330 AATGTAGCTGGCCTTGAATCAGCAC
63 AATGTAGCTGGCCTTGACTCAGCAC
2448355 GTTGACATCC
Statistics
Matches: 351, Mismatches: 11, Indels: 17
0.93 0.03 0.04
Matches are distributed among these distances:
92 223 0.64
94 4 0.01
95 37 0.11
96 1 0.00
98 85 0.24
99 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (92 bp):
CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAAT
GTAGCTGGCCTTGACTCAGCACATTGG
Found at i:2448106 original size:43 final size:43
Alignment explanation
Indices: 2448041--2448314 Score: 323
Period size: 43 Copynumber: 6.1 Consensus size: 43
2448031 GCATCTTCAT
* * *
2448041 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
* *
2448084 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA----C
* * *
2448131 ATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
* *
2448176 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA----C
* *
2448223 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
*
2448268 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
2448311 CTTT
1 CTTT
2448315 TCCATCTTTA
Statistics
Matches: 197, Mismatches: 22, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
43 118 0.60
45 2 0.01
47 2 0.01
49 75 0.38
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
Found at i:2448555 original size:174 final size:174
Alignment explanation
Indices: 2448265--2448835 Score: 1088
Period size: 174 Copynumber: 3.3 Consensus size: 174
2448255 AGCACATTGG
2448265 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTC
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTC
2448330 AATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTG
66 AATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTG
2448395 GCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTT
131 GCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTT
2448439 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTC
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTC
2448504 AATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTG
66 AATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTG
2448569 GCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTT
131 GCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTT
* *
2448613 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTTC
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTC
*
2448678 AATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTG
66 AATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTG
2448743 GCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTT
131 GCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTT
* * *
2448787 CATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTT
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTT
2448836 CATCATCTCT
Statistics
Matches: 391, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 391 1.00
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.36
Consensus pattern (174 bp):
CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTC
AATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTG
GCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTT
Found at i:2449666 original size:13 final size:13
Alignment explanation
Indices: 2449648--2449672 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2449638 CATAAAATGT
2449648 TGTATCGATACAA
1 TGTATCGATACAA
2449661 TGTATCGATACA
1 TGTATCGATACA
2449673 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2449670 original size:33 final size:33
Alignment explanation
Indices: 2449628--2449694 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2449618 TTCAACGATT
2449628 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
2449661 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
2449694 T
1 T
2449695 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:2449753 original size:13 final size:13
Alignment explanation
Indices: 2449735--2449759 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2449725 ATTACTCAAA
2449735 TGTATCGATACAT
1 TGTATCGATACAT
2449748 TGTATCGATACA
1 TGTATCGATACA
2449760 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2449862 original size:52 final size:52
Alignment explanation
Indices: 2449768--2449895 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
2449758 CACTGATCTT
* *
2449768 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATT-AAA
2449819 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATTAAA
2449871 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2449896 TCATATTTCG
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
51 19 0.26
52 51 0.70
53 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCAATACACTATTAAA
Found at i:2453613 original size:16 final size:15
Alignment explanation
Indices: 2453592--2453622 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2453582 GATTTCCATA
2453592 AAAATAATAACAAAAT
1 AAAATAATAA-AAAAT
2453608 AAAATAATAAAAAAT
1 AAAATAATAAAAAAT
2453623 TCTTTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAATAATAAAAAAT
Found at i:2455150 original size:2 final size:2
Alignment explanation
Indices: 2455143--2455173 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2455133 TTTATCTTCA
*
2455143 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2455174 CACGTCAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2455284 original size:20 final size:20
Alignment explanation
Indices: 2455261--2455304 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2455251 TAATTAACAA
2455261 TCAA-AGTCAATCGATCAAAG
1 TCAATAGTCAAT-GATCAAAG
*
2455281 TCAATAGTTAATGATCAAAG
1 TCAATAGTCAATGATCAAAG
2455301 TCAA
1 TCAA
2455305 CCAAACCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (20 bp):
TCAATAGTCAATGATCAAAG
Found at i:2457637 original size:45 final size:45
Alignment explanation
Indices: 2457529--2457630 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 45
2457519 TTCGCTCACA
* *
2457529 TTTTAAACATATTTTTTAATAAAAATATTATCATATACCTACATT
1 TTTTAAACACATTTTTTAATAAAAATATTATCATATACCCACATT
* *
2457574 TTTTAAACACATTTTTTAATAAAAATATT-TC-TTTGCCCAC-TT
1 TTTTAAACACATTTTTTAATAAAAATATTATCATATACCCACATT
2457616 CTTTTAAACACATTT
1 -TTTTAAACACATTT
2457631 CTTTTAACAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
42 2 0.04
43 20 0.38
44 2 0.04
45 28 0.54
ACGTcount: A:0.37, C:0.15, G:0.01, T:0.47
Consensus pattern (45 bp):
TTTTAAACACATTTTTTAATAAAAATATTATCATATACCCACATT
Found at i:2457900 original size:23 final size:23
Alignment explanation
Indices: 2457869--2457913 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2457859 TTTTAATTAA
* *
2457869 TAATTTATTTAATCGTATTATAT
1 TAATATATTTAATCATATTATAT
*
2457892 TAATATATTTTATCATATTATA
1 TAATATATTTAATCATATTATA
2457914 ATTATTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (23 bp):
TAATATATTTAATCATATTATAT
Found at i:2457955 original size:32 final size:32
Alignment explanation
Indices: 2457884--2457983 Score: 91
Period size: 30 Copynumber: 3.2 Consensus size: 32
2457874 TATTTAATCG
* * * *
2457884 TATTATATTAATATATTTTATCATAT-TATAAT
1 TATTATTTTAAAATATTTTAT-ATTTATATAAA
2457916 TA-T-TTTTAAAATATTTTATATTTATATAAA
1 TATTATTTTAAAATATTTTATATTTATATAAA
* *
2457946 TATTATTTTATTAATAATTTATA-TTATATAAA
1 TATTATTTTA-AAATATTTTATATTTATATAAA
*
2457978 TTTTAT
1 TATTAT
2457984 ATTATGTATT
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
29 3 0.05
30 21 0.37
31 2 0.04
32 21 0.37
33 10 0.18
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (32 bp):
TATTATTTTAAAATATTTTATATTTATATAAA
Found at i:2457987 original size:16 final size:16
Alignment explanation
Indices: 2457928--2457988 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
2457918 TTTTTAAAAT
2457928 ATTTTATATTTATATAA
1 ATTTTATA-TTATATAA
* *
2457945 ATATTATTTTAT-TAA
1 ATTTTATATTATATAA
*
2457960 TAATTTATATTATATAA
1 -ATTTTATATTATATAA
2457977 ATTTTATATTAT
1 ATTTTATATTAT
2457989 GTATTAACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
15 3 0.08
16 24 0.67
17 9 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTATATTATATAA
Found at i:2458003 original size:18 final size:18
Alignment explanation
Indices: 2457980--2458032 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
2457970 TATATAAATT
*
2457980 TTATATTATGTATTAACA
1 TTATATTATATATTAACA
* *
2457998 TTATATCATATATTAAATA
1 TTATATTATATATT-AACA
2458017 TTATATATATATATTA
1 TTATAT-TATATATTA
2458033 TATTTTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 12 0.41
19 10 0.34
20 7 0.24
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (18 bp):
TTATATTATATATTAACA
Found at i:2458009 original size:7 final size:7
Alignment explanation
Indices: 2457884--2458035 Score: 63
Period size: 7 Copynumber: 22.1 Consensus size: 7
2457874 TATTTAATCG
2457884 TATTATA
1 TATTATA
*
2457891 TTAATATA
1 -TATTATA
*
2457899 TTTTATCA
1 TATTAT-A
2457907 TATTATA
1 TATTATA
2457914 -ATTAT-
1 TATTATA
* *
2457919 TTTTAAAA
1 TATT-ATA
*
2457927 TATTTTA
1 TATTATA
2457934 TATT-TA
1 TATTATA
*
2457940 TA-TAAA
1 TATTATA
*
2457946 TATTATTT
1 TATTA-TA
2457954 TATTA-A
1 TATTATA
2457960 TAATT-TA
1 T-ATTATA
2457967 TATTATA
1 TATTATA
*
2457974 TAAATTTTA
1 T--ATTATA
*
2457983 TATTATG
1 TATTATA
2457990 TATTA-A
1 TATTATA
*
2457996 CA-T-TA
1 TATTATA
*
2458001 TATCATA
1 TATTATA
*
2458008 TATTAAA
1 TATTATA
2458015 TATTATA
1 TATTATA
2458022 TA-TATA
1 TATTATA
2458028 TATTATA
1 TATTATA
2458035 T
1 T
2458036 TTTTATAATT
Statistics
Matches: 105, Mismatches: 23, Indels: 33
0.65 0.14 0.20
Matches are distributed among these distances:
5 4 0.04
6 25 0.24
7 50 0.48
8 20 0.19
9 6 0.06
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (7 bp):
TATTATA
Found at i:2458035 original size:18 final size:18
Alignment explanation
Indices: 2457884--2458036 Score: 68
Period size: 16 Copynumber: 9.2 Consensus size: 18
2457874 TATTTAATCG
*
2457884 TATTATAT-TAATATATTT
1 TATTATATAT-ATATATTA
*
2457902 TATCATAT-TATA-ATTA
1 TATTATATATATATATTA
* * *
2457918 T-TTTTA-AAATATTTTA
1 TATTATATATATATATTA
*
2457934 TATT-TATATAAATATTA
1 TATTATATATATATATTA
*
2457951 TTTTAT-TA-ATA-ATTTA
1 TATTATATATATATA-TTA
*
2457967 TATTATATA-A-ATTTTA
1 TATTATATATATATATTA
* *
2457983 TATTATGTAT-TAACATTA
1 TATTATATATAT-ATATTA
*
2458001 TATCATATAT-TA-A--A
1 TATTATATATATATATTA
2458015 TATTATATATATATATTA
1 TATTATATATATATATTA
2458033 TATT
1 TATT
2458037 TTTATAATTG
Statistics
Matches: 101, Mismatches: 19, Indels: 30
0.67 0.13 0.20
Matches are distributed among these distances:
14 10 0.10
15 9 0.09
16 34 0.34
17 21 0.21
18 27 0.27
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.56
Consensus pattern (18 bp):
TATTATATATATATATTA
Found at i:2458042 original size:13 final size:13
Alignment explanation
Indices: 2457965--2458035 Score: 53
Period size: 11 Copynumber: 5.8 Consensus size: 13
2457955 ATTAATAATT
2457965 TATATTATATA-A
1 TATATTATATATA
*
2457977 -ATTTTATAT-TA
1 TATATTATATATA
* *
2457988 TGTATTA-ACAT-
1 TATATTATATATA
*
2457999 TATATCATATATTA
1 TATATTATATA-TA
*
2458013 AATATTATATATA
1 TATATTATATATA
2458026 TATATTATAT
1 TATATTATAT
2458036 TTTTATAATT
Statistics
Matches: 43, Mismatches: 10, Indels: 11
0.67 0.16 0.17
Matches are distributed among these distances:
11 15 0.35
12 7 0.16
13 12 0.28
14 9 0.21
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (13 bp):
TATATTATATATA
Found at i:2458214 original size:33 final size:31
Alignment explanation
Indices: 2458177--2458241 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
2458167 CAATTTTATG
**
2458177 ATTGAAAAAATATGTCTTATATTTTTAAAATAC
1 ATTGAAAAAATA-GTCTT-TAGATTTAAAATAC
* *
2458210 ATTGAATATATAGTCTTTAGATTTAAAATAC
1 ATTGAAAAAATAGTCTTTAGATTTAAAATAC
2458241 A
1 A
2458242 CACAATTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 13 0.46
32 5 0.18
33 10 0.36
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.42
Consensus pattern (31 bp):
ATTGAAAAAATAGTCTTTAGATTTAAAATAC
Found at i:2459052 original size:15 final size:16
Alignment explanation
Indices: 2459032--2459064 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2459022 AATCTTTATG
*
2459032 TAATTATGA-AAAAAA
1 TAATTAAGAGAAAAAA
2459047 TAATTAAGAGAAAAAA
1 TAATTAAGAGAAAAAA
2459063 TA
1 TA
2459065 TTAGAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (16 bp):
TAATTAAGAGAAAAAA
Found at i:2459316 original size:20 final size:20
Alignment explanation
Indices: 2459291--2459341 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
2459281 GAATAATTTT
2459291 TAATTTTAAATTTTTAAAAA
1 TAATTTTAAATTTTTAAAAA
* *
2459311 TAATTTTTTATTTTTTAAAAA
1 TAA-TTTTAAATTTTTAAAAA
2459332 TAATTATTAA
1 TAATT-TTAA
2459342 TCATTCTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAATTTTAAATTTTTAAAAA
Found at i:2464172 original size:52 final size:52
Alignment explanation
Indices: 2464024--2464152 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
2464014 CGAAATATGA
*
2464024 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
* *
2464076 AAATTTGCCTGCATGTATTGATACATTTTATAGTGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
2464128 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
2464153 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:2464179 original size:13 final size:13
Alignment explanation
Indices: 2464161--2464185 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2464151 CAAAGATCAG
2464161 TGTATCGATACAA
1 TGTATCGATACAA
2464174 TGTATCGATACA
1 TGTATCGATACA
2464186 TTTTTTGGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2464627 original size:13 final size:14
Alignment explanation
Indices: 2464609--2464639 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2464599 TTTTATCTTT
2464609 TTTTAATA-TTTTA
1 TTTTAATATTTTTA
2464622 TTTTAATATTTTTA
1 TTTTAATATTTTTA
2464636 TTTT
1 TTTT
2464640 TTAGCATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTAATATTTTTA
Found at i:2465004 original size:19 final size:19
Alignment explanation
Indices: 2464982--2465019 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2464972 CATATAATTT
2464982 TTATAAAT-TTTGAATTTAA
1 TTATAAATATTT-AATTTAA
*
2465001 TTATTAATATTTAATTTAA
1 TTATAAATATTTAATTTAA
2465020 ATATTATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
TTATAAATATTTAATTTAA
Found at i:2466913 original size:30 final size:30
Alignment explanation
Indices: 2466879--2466938 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
2466869 GAAAAGAATT
*
2466879 AACA-TGT-TTTTAATTATTTTATCTTTTTTA
1 AACATTGTATTTTAA-TATTTT-TATTTTTTA
*
2466909 AACATTTTATTTTAATATTTTTATTTTTTA
1 AACATTGTATTTTAATATTTTTATTTTTTA
2466939 GCATTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 12 0.46
31 8 0.31
32 6 0.23
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (30 bp):
AACATTGTATTTTAATATTTTTATTTTTTA
Found at i:2466962 original size:16 final size:15
Alignment explanation
Indices: 2466941--2466997 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
2466931 ATTTTTTAGC
2466941 ATTAAAATTATGAAAT
1 ATTAAAATTAT-AAAT
*
2466957 ATTAAATTTATAAAT
1 ATTAAAATTATAAAT
* *
2466972 AAATTTAATATTATAGAT
1 --A-TTAAAATTATAAAT
2466990 ATTAAAAT
1 ATTAAAAT
2466998 ATTTTTGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
15 10 0.30
16 11 0.33
17 1 0.03
18 11 0.33
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (15 bp):
ATTAAAATTATAAAT
Found at i:2468398 original size:13 final size:12
Alignment explanation
Indices: 2468373--2468406 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
2468363 GGAATTATTA
2468373 AAAAAATTAAAAT
1 AAAAAA-TAAAAT
2468386 AATAAAATAAAAT
1 AA-AAAATAAAAT
2468399 AAAAAATA
1 AAAAAATA
2468407 TTTTGATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 10 0.50
14 4 0.20
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:2471589 original size:33 final size:33
Alignment explanation
Indices: 2471552--2471614 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
2471542 TTTACATAAC
* *
2471552 TAGTTTGCATTGTGGTTTTCTTTTTGAAGTCCT
1 TAGTTTGCATTCTGGTTATCTTTTTGAAGTCCT
*
2471585 TAGTTTGCATTCTGGTTATCTTTTTTAAGT
1 TAGTTTGCATTCTGGTTATCTTTTTGAAGT
2471615 ACTGTATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.14, C:0.11, G:0.19, T:0.56
Consensus pattern (33 bp):
TAGTTTGCATTCTGGTTATCTTTTTGAAGTCCT
Found at i:2471788 original size:57 final size:57
Alignment explanation
Indices: 2471719--2471890 Score: 263
Period size: 57 Copynumber: 3.0 Consensus size: 57
2471709 CTGTGCCTTA
* * * * *
2471719 TAACTTCGAGTCAACCATAATAGTAGAGAGCTATGTTGCTTCGATTTTTTATTTTTC
1 TAACTTCGAGTCAGCCATAATAGTGGAGAGCTATGTTGCTCCGATTCTTCATTTTTC
* * *
2471776 TAACTTCGAGTCAGTCATAATAGTGGAAAGCTATGTTGCTCCGATTCTTCATTTTTT
1 TAACTTCGAGTCAGCCATAATAGTGGAGAGCTATGTTGCTCCGATTCTTCATTTTTC
*
2471833 TAACTTCGAGTCAGCCATAATAGTGGAGAGCTATGTTGCTCCAATTCTTCATTTTTC
1 TAACTTCGAGTCAGCCATAATAGTGGAGAGCTATGTTGCTCCGATTCTTCATTTTTC
2471890 T
1 T
2471891 TGATGTACTG
Statistics
Matches: 103, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 103 1.00
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (57 bp):
TAACTTCGAGTCAGCCATAATAGTGGAGAGCTATGTTGCTCCGATTCTTCATTTTTC
Found at i:2474191 original size:43 final size:45
Alignment explanation
Indices: 2474114--2474205 Score: 107
Period size: 43 Copynumber: 2.1 Consensus size: 45
2474104 GTCCAAAAAC
* * * *
2474114 TTATTTTACTATTTAAAATTATATTAAAAATT-AA-AAATTATTT
1 TTATATTAATATTTAAAATTAAATTAAAAATTAAATAAAATATTT
* * *
2474157 TTATATTAATATTTATAATTAAATTTAAATTTAAATAAAATATTT
1 TTATATTAATATTTAAAATTAAATTAAAAATTAAATAAAATATTT
2474202 TTAT
1 TTAT
2474206 TATTTAAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 26 0.65
44 2 0.05
45 12 0.30
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (45 bp):
TTATATTAATATTTAAAATTAAATTAAAAATTAAATAAAATATTT
Found at i:2474627 original size:17 final size:17
Alignment explanation
Indices: 2474601--2474639 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
2474591 CATGATAAAA
* *
2474601 ATAATTAAAATATAA-T
1 ATAATAAAAAAATAATT
2474617 ATAATAAAAAAATAATT
1 ATAATAAAAAAATAATT
2474634 ATAATA
1 ATAATA
2474640 TATTAAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAATAAAAAAATAATT
Found at i:2474667 original size:7 final size:7
Alignment explanation
Indices: 2474651--2474692 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
2474641 ATTAAGTTTT
*
2474651 ATATAAA
1 ATATATA
2474658 ATATATA
1 ATATATA
2474665 ATATATTA
1 ATATA-TA
2474673 A-ATATA
1 ATATATA
2474679 AT-TATA
1 ATATATA
2474685 ATATATA
1 ATATATA
2474692 A
1 A
2474693 AAATATATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
6 9 0.29
7 19 0.61
8 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATATATA
Found at i:2474925 original size:2 final size:2
Alignment explanation
Indices: 2474862--2474912 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
2474852 TTACCCAAAC
*
2474862 AT AT AT AT AC 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
2474904 AT AT AT AT A
1 AT AT AT AT A
2474913 CACACACATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2485160 original size:21 final size:21
Alignment explanation
Indices: 2485136--2485178 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2485126 ACAGTAATTT
2485136 TTTAAATT-TGAATTTATTTAA
1 TTTAAATTAT-AATTTATTTAA
*
2485157 TTTAAATTATTATTTATTTAA
1 TTTAAATTATAATTTATTTAA
2485178 T
1 T
2485179 ATTTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTAAATTATAATTTATTTAA
Found at i:2487289 original size:13 final size:13
Alignment explanation
Indices: 2487273--2487302 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2487263 TAAACGTACC
2487273 ATTTTTATATCAT
1 ATTTTTATATCAT
2487286 ATTTTTATATCAT
1 ATTTTTATATCAT
2487299 ATTT
1 ATTT
2487303 AAGATAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTTTTATATCAT
Found at i:2488083 original size:16 final size:17
Alignment explanation
Indices: 2488047--2488084 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2488037 CTCTCTCTCC
*
2488047 TTTTTTTTCTTTTC-TT
1 TTTTTTTTCTTTTCATA
*
2488063 TTTTTTTTTTTTTCATA
1 TTTTTTTTCTTTTCATA
2488080 TTTTT
1 TTTTT
2488085 CCCCTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.05, C:0.08, G:0.00, T:0.87
Consensus pattern (17 bp):
TTTTTTTTCTTTTCATA
Found at i:2492425 original size:19 final size:19
Alignment explanation
Indices: 2492403--2492441 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2492393 AAAAACAAGA
2492403 AATAAATAAATCAACAAAT
1 AATAAATAAATCAACAAAT
2492422 AATAAATAAATCAACAAAT
1 AATAAATAAATCAACAAAT
2492441 A
1 A
2492442 CACCCAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (19 bp):
AATAAATAAATCAACAAAT
Found at i:2492740 original size:15 final size:15
Alignment explanation
Indices: 2492716--2492751 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2492706 GCGATGAACA
*
2492716 AAAAACCCAAAAACC
1 AAAAATCCAAAAACC
*
2492731 AAAAATCCAAAATCC
1 AAAAATCCAAAAACC
2492746 AAAAAT
1 AAAAAT
2492752 AATCTCTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.67, C:0.25, G:0.00, T:0.08
Consensus pattern (15 bp):
AAAAATCCAAAAACC
Found at i:2493204 original size:5 final size:5
Alignment explanation
Indices: 2493194--2493263 Score: 67
Period size: 5 Copynumber: 14.0 Consensus size: 5
2493184 GATTTACATT
*
2493194 ATATA ATATA ATATAA ATATA ATATA AAAT- ATAATA A-ATA ATATAA
1 ATATA ATATA ATAT-A ATATA ATATA ATATA AT-ATA ATATA ATAT-A
2493240 ATATA ATATA A-AT- ATATAA ATATA
1 ATATA ATATA ATATA ATAT-A ATATA
2493264 TTAAAATTTA
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
3 1 0.02
4 9 0.16
5 30 0.55
6 15 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
ATATA
Found at i:2493214 original size:11 final size:11
Alignment explanation
Indices: 2493193--2493255 Score: 80
Period size: 11 Copynumber: 5.9 Consensus size: 11
2493183 AGATTTACAT
2493193 TATATAATATAA
1 TATA-AATATAA
2493205 TATAAATATAA
1 TATAAATATAA
2493216 TATAAA-AT-A
1 TATAAATATAA
2493225 TA-ATAA-ATAA
1 TATA-AATATAA
2493235 TATAAATATAA
1 TATAAATATAA
2493246 TATAAATATA
1 TATAAATATA
2493256 TAAATATATT
Statistics
Matches: 47, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
8 1 0.02
9 7 0.15
10 7 0.15
11 28 0.60
12 4 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TATAAATATAA
Found at i:2493236 original size:19 final size:19
Alignment explanation
Indices: 2493203--2493268 Score: 75
Period size: 18 Copynumber: 3.6 Consensus size: 19
2493193 TATATAATAT
*
2493203 AATATAA-ATATAATATAA
1 AATATAATAAATAATATAA
2493221 AATATAATAAATAATAT-A
1 AATATAATAAATAATATAA
*
2493239 AATATAATATA-AATATATA
1 AATATAATAAATAATATA-A
*
2493258 AATATATTAAA
1 AATATAATAAA
2493269 ATTTATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
17 5 0.12
18 18 0.44
19 18 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AATATAATAAATAATATAA
Found at i:2493237 original size:30 final size:28
Alignment explanation
Indices: 2493193--2493286 Score: 111
Period size: 28 Copynumber: 3.2 Consensus size: 28
2493183 AGATTTACAT
2493193 TATATAATATAATATAAATATAATATAAAA
1 TATATAA-ATAATATAAATATAATAT-AAA
2493223 TATAATAAATAATATAAATATAATATAAA
1 TAT-ATAAATAATATAAATATAATATAAA
* *
2493252 TATATAAAT-ATATTAAA-ATTTATATAAG
1 TATATAAATAATA-TAAATA-TAATATAAA
2493280 TATATAA
1 TATATAA
2493287 TATTTTAATT
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
27 4 0.07
28 24 0.41
29 6 0.10
30 21 0.36
31 4 0.07
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (28 bp):
TATATAAATAATATAAATATAATATAAA
Found at i:2493285 original size:41 final size:36
Alignment explanation
Indices: 2493196--2493289 Score: 111
Period size: 35 Copynumber: 2.5 Consensus size: 36
2493186 TTTACATTAT
2493196 ATAATATAATATA-AATATAATATAAAATATAATAA
1 ATAATATAATATATAATATAATATAAAATATAATAA
*
2493231 ATAATATAA-ATATAATATAAATATATAAATATATTAAA
1 ATAATATAATATATAATAT-AATATA-AAATATAAT-AA
*
2493269 ATTTATATAAGTATATAATAT
1 A-TAATATAA-TATATAATAT
2493290 TTTAATTATA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
34 3 0.06
35 14 0.28
36 6 0.12
37 8 0.16
38 3 0.06
39 7 0.14
41 9 0.18
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (36 bp):
ATAATATAATATATAATATAATATAAAATATAATAA
Found at i:2493293 original size:20 final size:20
Alignment explanation
Indices: 2493234--2493284 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
2493224 ATAATAAATA
*
2493234 ATATAAATATAATATAAA--T
1 ATATAAATATATTA-AAATTT
2493253 ATATAAATATATTAAAATTT
1 ATATAAATATATTAAAATTT
*
2493273 ATATAAGTATAT
1 ATATAAATATAT
2493285 AATATTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 3 0.11
19 13 0.46
20 12 0.43
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
ATATAAATATATTAAAATTT
Found at i:2493926 original size:19 final size:19
Alignment explanation
Indices: 2493894--2493936 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
2493884 TAGTTTTCTA
* *
2493894 AAAAATTATTAATTTTTAAT
1 AAAAATTATAAATTATT-AT
2493914 AAAAATTA-AAATTATTAT
1 AAAAATTATAAATTATTAT
2493932 AAAAA
1 AAAAA
2493937 AATAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 6 0.29
20 8 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATTATAAATTATTAT
Found at i:2493937 original size:19 final size:20
Alignment explanation
Indices: 2493892--2493937 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
2493882 GGTAGTTTTC
* *
2493892 TAAAAAATTATTAATTTTTA
1 TAAAAAATTATAAATTATTA
2493912 -ATAAAAATTA-AAATTATTA
1 TA-AAAAATTATAAATTATTA
2493931 TAAAAAA
1 TAAAAAA
2493938 ATAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAAAAATTATAAATTATTA
Found at i:2494098 original size:2 final size:2
Alignment explanation
Indices: 2494091--2494136 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2494081 CATTAACAAT
2494091 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
2494133 TA TA
1 TA TA
2494137 ATGTGAACGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2495034 original size:16 final size:16
Alignment explanation
Indices: 2494991--2495063 Score: 76
Period size: 16 Copynumber: 4.4 Consensus size: 16
2494981 CGATTATTAT
*
2494991 AATATAAATATAATAAAA
1 AATAT-AATATGAT-AAA
*
2495009 AATTAAAATATGATAAA
1 AA-TATAATATGATAAA
2495026 AATATAATATGATATAA
1 AATATAATATGATA-AA
*
2495043 AA-ATAATATGATATA
1 AATATAATATGATAAA
2495058 AATATA
1 AATATA
2495064 TAATTATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
15 3 0.06
16 25 0.52
17 9 0.19
18 9 0.19
19 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (16 bp):
AATATAATATGATAAA
Found at i:2495059 original size:34 final size:34
Alignment explanation
Indices: 2494991--2495063 Score: 89
Period size: 32 Copynumber: 2.2 Consensus size: 34
2494981 CGATTATTAT
2494991 AATATAAATATAATAAAAAATTAAAATATGATAAA
1 AATAT-AATATAATAAAAAATTAAAATATGATAAA
* *
2495026 AATATAATATGATATAAAAA-T--AATATGATATA
1 AATATAATATAATA-AAAAATTAAAATATGATAAA
2495058 AATATA
1 AATATA
2495064 TAATTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 16 0.46
34 9 0.26
35 10 0.29
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (34 bp):
AATATAATATAATAAAAAATTAAAATATGATAAA
Found at i:2495098 original size:32 final size:33
Alignment explanation
Indices: 2495016--2495117 Score: 84
Period size: 32 Copynumber: 3.2 Consensus size: 33
2495006 AAAAATTAAA
* * * *
2495016 ATATGATAAAAATATA-ATATGATAT-AAAAATA
1 ATATAATAAAAATATATAAAT-ATATCAAAATTT
* * * * *
2495048 ATATGATATAAATATATAATTATTTTAAAATTT
1 ATATAATAAAAATATATAAATATATCAAAATTT
2495081 ATATAATAAAAAT-TATAAATATATCAAAATTT
1 ATATAATAAAAATATATAAATATATCAAAATTT
*
2495113 TTATA
1 ATATA
2495118 TATATTTTTT
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
32 38 0.68
33 18 0.32
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (33 bp):
ATATAATAAAAATATATAAATATATCAAAATTT
Done.