Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold57
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: 4071704
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82236 characters in sequence are not A, C, G, or T
File 25 of 27
Found at i:3522929 original size:2 final size:2
Alignment explanation
Indices: 3522917--3523022 Score: 53
Period size: 2 Copynumber: 55.0 Consensus size: 2
3522907 AATAAATTAA
* * * *
3522917 AT AT AT TT AT AT AT -T AT TT TT AT AT AT CAT AA AT -T 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
* * * * * *
3522958 A- AT AT AT -T AT TT AT AA AT -T TT A- AT AT AT TT AT TT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3522996 AT TT AT AT CAT AT AT AT AT AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT
3523023 TTAATTTTTT
Statistics
Matches: 77, Mismatches: 19, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
1 6 0.08
2 67 0.87
3 4 0.05
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (2 bp):
AT
Found at i:3522940 original size:11 final size:11
Alignment explanation
Indices: 3522920--3523050 Score: 55
Period size: 11 Copynumber: 11.9 Consensus size: 11
3522910 AAATTAAATA
3522920 TATTTATATAT
1 TATTTATATAT
*
3522931 TATTTTTATA-
1 TATTTATATAT
* *
3522941 TA-TCATAAAT
1 TATTTATATAT
3522951 TATATATAATATAT
1 TAT-T-T-ATATAT
*
3522965 TATTTATA-AA
1 TATTTATATAT
3522975 T-TTTA-ATA-
1 TATTTATATAT
*
3522983 TATTTATTTATT
1 TATTTATATA-T
3522995 TATTTATATCAT
1 TATTTATAT-AT
*
3523007 ATATATATATAT
1 -TATTTATATAT
3523019 ATATTTA-AT-T
1 -TATTTATATAT
*
3523029 TTTTTATTATATT
1 TATTTA-TATA-T
3523042 TATTT-TATA
1 TATTTATATA
3523051 AGATATGTCA
Statistics
Matches: 91, Mismatches: 13, Indels: 32
0.67 0.10 0.24
Matches are distributed among these distances:
8 2 0.02
9 18 0.20
10 9 0.10
11 20 0.22
12 19 0.21
13 15 0.16
14 8 0.09
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTATATAT
Found at i:3522973 original size:25 final size:23
Alignment explanation
Indices: 3522945--3523025 Score: 67
Period size: 25 Copynumber: 3.4 Consensus size: 23
3522935 TTTATATATC
3522945 ATAAATTATATATAATATATTATTT
1 ATAAATT-TATAT-ATATATTATTT
3522970 ATAAATTT-TA-ATATATTTATTT
1 ATAAATTTATATATATA-TTATTT
** *
3522992 ATTTATTTATATCATATATATATAT
1 ATAAATTTATAT-ATATAT-TATTT
*
3523017 ATATATTTA
1 ATAAATTTA
3523026 ATTTTTTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
21 5 0.11
22 12 0.26
23 4 0.09
24 2 0.04
25 24 0.51
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (23 bp):
ATAAATTTATATATATATTATTT
Found at i:3526984 original size:2 final size:2
Alignment explanation
Indices: 3526923--3526969 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3526913 TTAAAAAGGA
3526923 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3526965 AT AT A
1 AT AT A
3526970 CACTTATACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3530576 original size:2 final size:2
Alignment explanation
Indices: 3530569--3530597 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3530559 AAACAGGAAA
3530569 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 A
3530598 CACCTGAACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3532200 original size:35 final size:36
Alignment explanation
Indices: 3532146--3532213 Score: 88
Period size: 35 Copynumber: 1.9 Consensus size: 36
3532136 TATATATAAA
*
3532146 ATAAATTTAAGTTTATATTTGA-TTT-ATTTTAATTC
1 ATAAATTTAAATTTATATTT-ATTTTAATTTTAATTC
3532181 ATAAATTTAAA-TTATTATTTATTTTAATTTTAA
1 ATAAATTTAAATTTA-TATTTATTTTAATTTTAA
3532214 AAAATACAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 4 0.14
35 18 0.62
36 7 0.24
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.57
Consensus pattern (36 bp):
ATAAATTTAAATTTATATTTATTTTAATTTTAATTC
Found at i:3532246 original size:17 final size:18
Alignment explanation
Indices: 3532221--3532255 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3532211 TAAAAAATAC
3532221 AAATGATTT-TTATATAA
1 AAATGATTTATTATATAA
*
3532238 AAATTATTTATTATATAA
1 AAATGATTTATTATATAA
3532256 TTAAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
AAATGATTTATTATATAA
Found at i:3532263 original size:53 final size:52
Alignment explanation
Indices: 3532189--3532297 Score: 118
Period size: 52 Copynumber: 2.2 Consensus size: 52
3532179 TCATAAATTT
* * * *
3532189 AAATTA-TTATT-TAT-TTTAATTTTAAA-AAATACAAATGATTTTTATATAA
1 AAATTATTTATTATATAATTAAATTTAAATAAAAACAAATGATTTTAAT-TAA
* * *
3532238 AAATTATTTATTATATAATTAAATTTAAATAAAAATATATTATTTTAATTAA
1 AAATTATTTATTATATAATTAAATTTAAATAAAAACAAATGATTTTAATTAA
3532290 AAATTATT
1 AAATTATT
3532298 ATTTTGGACT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
49 6 0.12
50 5 0.10
51 3 0.06
52 21 0.43
53 14 0.29
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (52 bp):
AAATTATTTATTATATAATTAAATTTAAATAAAAACAAATGATTTTAATTAA
Found at i:3532290 original size:20 final size:19
Alignment explanation
Indices: 3532261--3532302 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
3532251 TATAATTAAA
3532261 TTTAAATAAAAATATATTAT
1 TTTAAATAAAAAT-TATTAT
*
3532281 TTTAATTAAAAATTATTAT
1 TTTAAATAAAAATTATTAT
3532300 TTT
1 TTT
3532303 GGACTGAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTAAATAAAAATTATTAT
Found at i:3532294 original size:32 final size:32
Alignment explanation
Indices: 3532229--3532290 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
3532219 ACAAATGATT
*
3532229 TTTATATAAAAATTATTTATTATATAATTAAA
1 TTTAAATAAAAATTATTTATTATATAATTAAA
3532261 TTTAAATAAAAA-TATATTATT-T-TAATTAAA
1 TTTAAATAAAAATTAT-TTATTATATAATTAAA
3532291 AATTATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 8 0.29
31 4 0.14
32 16 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
TTTAAATAAAAATTATTTATTATATAATTAAA
Found at i:3532338 original size:6 final size:6
Alignment explanation
Indices: 3532327--3532352 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3532317 TAAAATAATA
3532327 AAATTT AAATTT AAATTT AAATTT AA
1 AAATTT AAATTT AAATTT AAATTT AA
3532353 TCGAATCGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AAATTT
Found at i:3533826 original size:14 final size:14
Alignment explanation
Indices: 3533807--3533833 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3533797 CCACCATTGT
3533807 TCGTAAATTGTAAA
1 TCGTAAATTGTAAA
3533821 TCGTAAATTGTAA
1 TCGTAAATTGTAA
3533834 TTTGAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (14 bp):
TCGTAAATTGTAAA
Found at i:3534323 original size:22 final size:20
Alignment explanation
Indices: 3534298--3534353 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 20
3534288 TATTAAAAAT
3534298 TATTTTTATATTAATATTTATA
1 TATTTTTATATTAA-ATTTA-A
3534320 TATTTTTATAATTAAATTTAA
1 TATTTTTAT-ATTAAATTTAA
3534341 TAATTTTT-TATTA
1 T-ATTTTTATATTA
3534354 TAAATTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.12
21 3 0.09
22 20 0.62
23 5 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTATATTAAATTTAA
Found at i:3534349 original size:23 final size:22
Alignment explanation
Indices: 3534300--3534369 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 22
3534290 TTAAAAATTA
3534300 TTTTTATATTAATATTT-AT-AT
1 TTTTTATATTAA-ATTTAATAAT
3534321 ATTTTTATAATTAAATTTAATAAT
1 -TTTTTAT-ATTAAATTTAATAAT
*
3534345 TTTTTAT-TATAAATTAAATTAAT
1 TTTTTATAT-TAAATTTAA-TAAT
3534368 TT
1 TT
3534370 AACTTAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
21 1 0.02
22 19 0.45
23 20 0.48
24 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTTATATTAAATTTAATAAT
Found at i:3544278 original size:2 final size:2
Alignment explanation
Indices: 3544271--3544304 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3544261 CTGACTCTAA
*
3544271 AT AT AT AT AT AT AT AA 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
3544305 GAAAGTTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3549574 original size:7 final size:7
Alignment explanation
Indices: 3549548--3549596 Score: 53
Period size: 7 Copynumber: 6.6 Consensus size: 7
3549538 AATAATAACG
3549548 TATTTTT
1 TATTTTT
3549555 ATATTTATTT
1 -TA-TT-TTT
3549565 TATTTTT
1 TATTTTT
3549572 TATTTTT
1 TATTTTT
*
3549579 TATATTT
1 TATTTTT
*
3549586 TATATTT
1 TATTTTT
3549593 TATT
1 TATT
3549597 ATATTATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
7 26 0.70
8 4 0.11
9 4 0.11
10 3 0.08
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (7 bp):
TATTTTT
Found at i:3549586 original size:21 final size:22
Alignment explanation
Indices: 3549553--3549613 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
3549543 TAACGTATTT
3549553 TTATATT-TATTTTATTTTTTA
1 TTATATTATATTTTATTTTTTA
* *
3549574 TT-TTTTATATTTTATATTTTA
1 TTATATTATATTTTATTTTTTA
3549595 TTATATTATATTTATATTT
1 TTATATTATATTT-TATTT
3549614 AAAATATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.09
21 17 0.52
22 9 0.27
23 4 0.12
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (22 bp):
TTATATTATATTTTATTTTTTA
Found at i:3549600 original size:10 final size:11
Alignment explanation
Indices: 3549552--3549613 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
3549542 ATAACGTATT
3549552 TTTATA-TTTA
1 TTTATATTTTA
*
3549562 TTTTATTTTTTA
1 -TTTATATTTTA
*
3549574 TTT-T-TTATA
1 TTTATATTTTA
3549583 TTTTATATTTTA
1 -TTTATATTTTA
*
3549595 -TTATATTATA
1 TTTATATTTTA
3549605 TTTATATTT
1 TTTATATTT
3549614 AAAATATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
9 4 0.10
10 13 0.32
11 16 0.39
12 8 0.20
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATATTTTA
Found at i:3549608 original size:28 final size:28
Alignment explanation
Indices: 3549560--3549613 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
3549550 TTTTTATATT
* *
3549560 TATTTTATTTTTTATTTTTTATATTTTA
1 TATTTTATTTATTATTATTTATATTTTA
3549588 TATTTTATTATATTA-TATTTATATTT
1 TATTTTATT-TATTATTATTTATATTT
3549614 AAAATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (28 bp):
TATTTTATTTATTATTATTTATATTTTA
Found at i:3549640 original size:15 final size:14
Alignment explanation
Indices: 3549622--3549671 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
3549612 TTAAAATATT
3549622 TTTTATTAATATAAA
1 TTTTATT-ATATAAA
3549637 TTTTA-TATATTAATA
1 TTTTATTATA-TAA-A
3549652 TTTTAATTATATAAA
1 TTTT-ATTATATAAA
3549667 TTTTA
1 TTTTA
3549672 AAATATTTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
13 3 0.10
14 5 0.16
15 15 0.48
16 4 0.13
17 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTATTATATAAA
Found at i:3549664 original size:30 final size:28
Alignment explanation
Indices: 3549576--3549671 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 28
3549566 ATTTTTTATT
* *
3549576 TTTTATATTTTATATTTTATTATAT-TA
1 TTTTATATTTAATATTTTATTATATAAA
3549603 TATTTATATTTAAAATATTTTTTATTAATATAAA
1 T-TTTATATTT--AATA--TTTTATT-ATATAAA
3549637 TTTTATATATTAATATTTTAATTATATAAA
1 TTTTATAT-TTAATATTTT-ATTATATAAA
3549667 TTTTA
1 TTTTA
3549672 AAATATTTAC
Statistics
Matches: 58, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
27 1 0.02
28 9 0.16
30 19 0.33
31 3 0.05
32 11 0.19
33 11 0.19
34 4 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTATATTTAATATTTTATTATATAAA
Found at i:3549672 original size:15 final size:14
Alignment explanation
Indices: 3549630--3549677 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
3549620 TTTTTTATTA
3549630 ATATAAATTTT-AT
1 ATATAAATTTTAAT
3549643 ATATTAATATTTTAATT
1 ATA-TAA-ATTTTAA-T
*
3549660 ATATAAATTTTAAA
1 ATATAAATTTTAAT
3549674 ATAT
1 ATAT
3549678 TTACGTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 3 0.10
14 7 0.23
15 12 0.40
16 4 0.13
17 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATAAATTTTAAT
Found at i:3550195 original size:18 final size:16
Alignment explanation
Indices: 3550161--3550217 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 16
3550151 TAATTTCACA
*
3550161 AATAAAATTAATAAAAT
1 AATAAAATT-TTAAAAT
3550178 AATAAATATTTTTAAAAT
1 AATAAA-A-TTTTAAAAT
3550196 ATATTAAAATTTTAAAA-
1 A-A-TAAAATTTTAAAAT
3550213 AATAA
1 AATAA
3550218 TTAAAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
15 3 0.09
16 1 0.03
17 7 0.20
18 16 0.46
19 4 0.11
20 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AATAAAATTTTAAAAT
Found at i:3550213 original size:19 final size:19
Alignment explanation
Indices: 3550168--3550223 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
3550158 ACAAATAAAA
3550168 TTAATAAAATAA-TAAATATT
1 TTAA-AAAATAATTAAA-ATT
*
3550188 TT-TAAAATATATTAAAATT
1 TTAAAAAATA-ATTAAAATT
3550207 TTAAAAAATAATTAAAA
1 TTAAAAAATAATTAAAA
3550224 ATAAAACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
18 6 0.19
19 13 0.42
20 12 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAAAAATAATTAAAATT
Found at i:3550224 original size:20 final size:20
Alignment explanation
Indices: 3550168--3550225 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
3550158 ACAAATAAAA
*
3550168 TTAATAAAATAA-TAAATATT
1 TTAA-AAAATAATTAAAAATT
*
3550188 TT-TAAAATATATT-AAAATT
1 TTAAAAAATA-ATTAAAAATT
3550207 TTAAAAAATAATTAAAAAT
1 TTAAAAAATAATTAAAAAT
3550226 AAAACATGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 6 0.19
19 11 0.35
20 14 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAAAAAATAATTAAAAATT
Found at i:3558659 original size:16 final size:17
Alignment explanation
Indices: 3558622--3558659 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3558612 GAAAAGAATC
*
3558622 ATTAAATTTTAATTTAT
1 ATTAAATTTTAATATAT
*
3558639 TTTAAA-TTTAATATAT
1 ATTAAATTTTAATATAT
3558655 ATTAA
1 ATTAA
3558660 CTATAAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTAAATTTTAATATAT
Found at i:3562426 original size:2 final size:2
Alignment explanation
Indices: 3562419--3562447 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3562409 TAATATTATG
3562419 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 T
3562448 GATTATCTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3564479 original size:26 final size:26
Alignment explanation
Indices: 3564435--3564485 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
3564425 TATATATGAT
** *
3564435 AAAAAATATTATCTCTTTAAATATAA
1 AAAAAATATTAAATATTTAAATATAA
*
3564461 AAAAAATATTAAATATTTACATATA
1 AAAAAATATTAAATATTTAAATATA
3564486 TTTAATACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (26 bp):
AAAAAATATTAAATATTTAAATATAA
Found at i:3565147 original size:22 final size:21
Alignment explanation
Indices: 3565119--3565184 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
3565109 GATTCTGTCT
3565119 AAATTATTAATTAATAATAAAA
1 AAATTATT-ATTAATAATAAAA
* *
3565141 AAATTATTTTTAATTATAAAA
1 AAATTATTATTAATAATAAAA
* *
3565162 ATATATAAATATTAAT-ATAAAA
1 A-A-ATTATTATTAATAATAAAA
3565184 A
1 A
3565185 TTTATTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 12 0.32
22 16 0.43
23 9 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATTATTATTAATAATAAAA
Found at i:3565159 original size:21 final size:22
Alignment explanation
Indices: 3565119--3565162 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3565109 GATTCTGTCT
3565119 AAATTATTAATTAATAATAAAA
1 AAATTATTAATTAATAATAAAA
* *
3565141 AAATTATT-TTTAATTATAAAA
1 AAATTATTAATTAATAATAAAA
3565162 A
1 A
3565163 TATATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AAATTATTAATTAATAATAAAA
Found at i:3565443 original size:5 final size:5
Alignment explanation
Indices: 3565428--3565456 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3565418 TGCCCATATC
3565428 TTTTA -TTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
3565457 AATCTACCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:3574522 original size:26 final size:25
Alignment explanation
Indices: 3574453--3574560 Score: 135
Period size: 25 Copynumber: 4.3 Consensus size: 25
3574443 TTAAAAAGTG
* * * *
3574453 TTAAAAATTATTTATTGTTAAATTA
1 TTAAAAAATAATTATTATTAAAATA
* *
3574478 TTAAAAAATAATTACTATTAAAACA
1 TTAAAAAATAATTATTATTAAAATA
3574503 TTAAAATAATAATTATTATTAAAATA
1 TTAAAA-AATAATTATTATTAAAATA
* *
3574529 TTAAAAAATATTTATTATGAAAATA
1 TTAAAAAATAATTATTATTAAAATA
3574554 TTAAAAA
1 TTAAAAA
3574561 TACATTACTA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
25 49 0.68
26 23 0.32
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (25 bp):
TTAAAAAATAATTATTATTAAAATA
Found at i:3575956 original size:28 final size:28
Alignment explanation
Indices: 3575914--3575970 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
3575904 AGAGGAACAC
*
3575914 ATTGTTACTTCTTTGATTTGATACTGTT
1 ATTGTTACTTCTTTGATTTGAGACTGTT
*
3575942 ATTGTTACTTTTTTGATTTGAGACTGTT
1 ATTGTTACTTCTTTGATTTGAGACTGTT
3575970 A
1 A
3575971 GATTTTGACC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.19, C:0.09, G:0.16, T:0.56
Consensus pattern (28 bp):
ATTGTTACTTCTTTGATTTGAGACTGTT
Found at i:3577951 original size:19 final size:18
Alignment explanation
Indices: 3577911--3577956 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
3577901 TTAAATTTAT
3577911 TTAATTATATTTTGATTGA
1 TTAATT-TATTTTGATTGA
3577930 TTAATTTA-TTTGATTGTTA
1 TTAATTTATTTTGATTG--A
3577949 TTAATTTA
1 TTAATTTA
3577957 GTAATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.32
18 2 0.08
19 15 0.60
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (18 bp):
TTAATTTATTTTGATTGA
Found at i:3578281 original size:2 final size:2
Alignment explanation
Indices: 3578276--3578304 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3578266 ATTTAAAATA
3578276 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 A
3578305 AAAGAAATGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3581407 original size:2 final size:2
Alignment explanation
Indices: 3581400--3581427 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3581390 CAGCCCATGA
3581400 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
3581428 TTATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3581984 original size:2 final size:2
Alignment explanation
Indices: 3581974--3582002 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3581964 TTTTTGGTTC
3581974 AT AT A- 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
3582003 TGAATTGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3582292 original size:2 final size:2
Alignment explanation
Indices: 3582287--3582316 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3582277 TTTCCTATCT
*
3582287 TA TA TA TA CA 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
3582317 AATTTATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3582824 original size:17 final size:18
Alignment explanation
Indices: 3582802--3582840 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3582792 TTTTGATTAG
3582802 ATTTA-TTAATTTTTTAA
1 ATTTATTTAATTTTTTAA
* *
3582819 ATTTATTTGATTTTTTAG
1 ATTTATTTAATTTTTTAA
3582837 ATTT
1 ATTT
3582841 TATAATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
ATTTATTTAATTTTTTAA
Found at i:3583151 original size:6 final size:7
Alignment explanation
Indices: 3583126--3583161 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
3583116 ACTAAACGTA
3583126 GGAAAAG
1 GGAAAAG
3583133 GGAAAAG
1 GGAAAAG
*
3583140 GGGAAAG
1 GGAAAAG
3583147 GGAAAAG
1 GGAAAAG
3583154 GGAAAAG
1 GGAAAAG
3583161 G
1 G
3583162 ATAAAAGCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (7 bp):
GGAAAAG
Found at i:3585234 original size:17 final size:17
Alignment explanation
Indices: 3585214--3585247 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3585204 AAATAGTAGA
3585214 TAAATAATAAATAAATT
1 TAAATAATAAATAAATT
**
3585231 TAAATTTTAAATAAATT
1 TAAATAATAAATAAATT
3585248 AAAAAAATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATAATAAATAAATT
Found at i:3586190 original size:18 final size:18
Alignment explanation
Indices: 3586132--3586193 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
3586122 TTTTAAAATT
* *
3586132 ATATTAAATA-ATTTTAA
1 ATATAAAATATATTATAA
*
3586149 ATATAAAAATATATTATAC
1 ATAT-AAAATATATTATAA
* * *
3586168 CTATAACATATTTTATAA
1 ATATAAAATATATTATAA
3586186 ATATAAAA
1 ATATAAAA
3586194 ATAAAATAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
17 4 0.12
18 22 0.65
19 8 0.24
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATAAAATATATTATAA
Found at i:3587005 original size:22 final size:23
Alignment explanation
Indices: 3586980--3587025 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
3586970 AAAGACCATG
* *
3586980 ATGACAAAAGTAAAAA-GTTAAA
1 ATGAAAAAAATAAAAAGGTTAAA
3587002 ATGAAAAAAATAAAAAGGTTAAA
1 ATGAAAAAAATAAAAAGGTTAAA
3587025 A
1 A
3587026 CATCTATGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.67, C:0.02, G:0.13, T:0.17
Consensus pattern (23 bp):
ATGAAAAAAATAAAAAGGTTAAA
Found at i:3597394 original size:7 final size:7
Alignment explanation
Indices: 3597382--3597446 Score: 64
Period size: 7 Copynumber: 9.4 Consensus size: 7
3597372 ATTCAATGTA
3597382 TTTAAAT
1 TTTAAAT
3597389 TTTAAAT
1 TTTAAAT
3597396 TTTAAAT
1 TTTAAAT
3597403 TTTAACA-
1 TTTAA-AT
3597410 TTTATAA-
1 TTTA-AAT
*
3597417 TTT-ATT
1 TTTAAAT
*
3597423 TTTTAAT
1 TTTAAAT
*
3597430 TTTAAGT
1 TTTAAAT
3597437 TTTAAAT
1 TTTAAAT
3597444 TTT
1 TTT
3597447 TTTATTAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
5 1 0.02
6 3 0.06
7 43 0.88
8 2 0.04
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (7 bp):
TTTAAAT
Found at i:3598609 original size:6 final size:6
Alignment explanation
Indices: 3598600--3598661 Score: 70
Period size: 6 Copynumber: 10.3 Consensus size: 6
3598590 AGAGCTACTC
* * * *
3598600 CCACCA CCACCT CCACCT CCACCT CCACCT CCTCCA CCGCCT CCACCT
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT
* *
3598648 CCGCCA CCACCT CC
1 CCACCT CCACCT CC
3598662 GCCAGAAGGG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.16, C:0.68, G:0.03, T:0.13
Consensus pattern (6 bp):
CCACCT
Found at i:3598627 original size:18 final size:18
Alignment explanation
Indices: 3598600--3598661 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
3598590 AGAGCTACTC
* *
3598600 CCACCACCACCTCCACCT
1 CCACCTCCACCTCCACCA
*
3598618 CCACCTCCACCTCCTCCA
1 CCACCTCCACCTCCACCA
* *
3598636 CCGCCTCCACCTCCGCCA
1 CCACCTCCACCTCCACCA
3598654 CCACCTCC
1 CCACCTCC
3598662 GCCAGAAGGG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.16, C:0.68, G:0.03, T:0.13
Consensus pattern (18 bp):
CCACCTCCACCTCCACCA
Found at i:3602110 original size:3 final size:3
Alignment explanation
Indices: 3602102--3602134 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
3602092 TAAACTCCAT
3602102 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3602135 AAAAACGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:3603229 original size:2 final size:2
Alignment explanation
Indices: 3603224--3603250 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3603214 ACACACACAC
3603224 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3603251 GTAATTGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3605419 original size:17 final size:17
Alignment explanation
Indices: 3605391--3605436 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
3605381 CATAAGAAGA
*
3605391 TTAAAATAAAAATTTTAT
1 TTAAATTAAAAA-TTTAT
3605409 TTAAATTAAAAATTTAT
1 TTAAATTAAAAATTTAT
3605426 TTAAATATAAA
1 TTAAAT-TAAA
3605437 TTATAAGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAATTAAAAATTTAT
Found at i:3606027 original size:12 final size:14
Alignment explanation
Indices: 3606007--3606039 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3605997 TAAATTAAAA
3606007 AATATATAAA-TTTT
1 AATATA-AAATTTTT
3606021 AATATAAAATTTTT
1 AATATAAAATTTTT
3606035 AATAT
1 AATAT
3606040 TTTAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATAAAATTTTT
Found at i:3607541 original size:15 final size:15
Alignment explanation
Indices: 3607521--3607569 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
3607511 GATGGCTTAA
3607521 TATATTTATAATATT
1 TATATTTATAATATT
*
3607536 TATATTAATAATATT
1 TATATTTATAATATT
*
3607551 ATTTATTTAT--TATT
1 -TATATTTATAATATT
3607565 TATAT
1 TATAT
3607570 AAAATAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 4 0.14
14 4 0.14
15 14 0.48
16 7 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATATTTATAATATT
Found at i:3607596 original size:15 final size:15
Alignment explanation
Indices: 3607576--3607619 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
3607566 ATATAAAATA
3607576 ATATAAATTTATAAT
1 ATATAAATTTATAAT
* *
3607591 ATATAAATATAAAAT
1 ATATAAATTTATAAT
*
3607606 A-ATATATTTATAAT
1 ATATAAATTTATAAT
3607620 TAAAAATAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATAAATTTATAAT
Found at i:3607634 original size:29 final size:30
Alignment explanation
Indices: 3607566--3607627 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
3607556 TTTATTATTT
*
3607566 ATATAAAATAATATAAATTTATAATATATAA
1 ATATAAAATAATAT-AATTTATAATATAAAA
3607597 ATATAAAATAATAT-ATTTATAAT-TAAAA
1 ATATAAAATAATATAATTTATAATATAAAA
3607625 ATA
1 ATA
3607628 ATTAAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 7 0.23
29 9 0.30
31 14 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (30 bp):
ATATAAAATAATATAATTTATAATATAAAA
Found at i:3619660 original size:2 final size:2
Alignment explanation
Indices: 3619653--3619698 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3619643 TCAAGTGTCC
3619653 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3619695 CT CT
1 CT CT
3619699 TGTTATTGGC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3620126 original size:2 final size:2
Alignment explanation
Indices: 3620119--3620144 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3620109 ATGTAAAAGA
3620119 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
3620145 TACATTGGAA
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):
AT
Found at i:3627116 original size:3 final size:3
Alignment explanation
Indices: 3627108--3627148 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
3627098 TAACTCTGTC
*
3627108 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG ATG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
3627149 CACCTCGATC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.02, C:0.00, G:0.32, T:0.66
Consensus pattern (3 bp):
TTG
Found at i:3630765 original size:2 final size:2
Alignment explanation
Indices: 3630746--3630783 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
3630736 TATTTTATCT
*
3630746 TA TA TT TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA T
3630784 TAATCCATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3632141 original size:6 final size:6
Alignment explanation
Indices: 3632130--3632167 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
3632120 TTAATTAACT
3632130 AATTTA AATTTA AATTTA AATTT- AATTT- AATTTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATT
3632168 AATAAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
AATTTA
Found at i:3632158 original size:5 final size:5
Alignment explanation
Indices: 3632113--3632170 Score: 50
Period size: 5 Copynumber: 11.6 Consensus size: 5
3632103 AAATTTTAAA
*
3632113 AATTT AA-TT AA-TT AA-CT AATTT AAATTT AAATTT AAATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT -AATTT -AATTT -AATTT AATTT
*
3632158 AATTT AAATT AAT
1 AATTT AATTT AAT
3632171 AAAAATATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
4 11 0.23
5 19 0.40
6 17 0.36
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (5 bp):
AATTT
Found at i:3632219 original size:17 final size:17
Alignment explanation
Indices: 3632197--3632231 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3632187 TAAAACCAAT
*
3632197 TAATTCGAATTTAAAAA
1 TAATTCGAATCTAAAAA
3632214 TAATTCGAATCTAAAAA
1 TAATTCGAATCTAAAAA
3632231 T
1 T
3632232 TAATAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (17 bp):
TAATTCGAATCTAAAAA
Found at i:3632234 original size:53 final size:54
Alignment explanation
Indices: 3632172--3632277 Score: 160
Period size: 53 Copynumber: 2.0 Consensus size: 54
3632162 TAAATTAATA
* *
3632172 AAAATATTAATAATTTAAAACCAATTAATTCGAATTTAAAAATAATTCGAATCT
1 AAAATATTAATAATTTAAAACCAATTAATTCAAATTTAAAAATAACTCGAATCT
** *
3632226 AAAA-ATTAATAATTTAAAATTAATTGATTCAAATTTAAAAATAACTCGAATC
1 AAAATATTAATAATTTAAAACCAATTAATTCAAATTTAAAAATAACTCGAATC
3632278 CGAAATGATT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
53 43 0.91
54 4 0.09
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (54 bp):
AAAATATTAATAATTTAAAACCAATTAATTCAAATTTAAAAATAACTCGAATCT
Found at i:3632299 original size:16 final size:16
Alignment explanation
Indices: 3632280--3632331 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
3632270 CTCGAATCCG
*
3632280 AAATGATTTAAACTTA
1 AAATGATTTAAACTCA
* ** *
3632296 AAATGACTCGAACTCG
1 AAATGATTTAAACTCA
*
3632312 AAATGATTTAAACTCG
1 AAATGATTTAAACTCA
3632328 AAAT
1 AAAT
3632332 AATCCGAACC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (16 bp):
AAATGATTTAAACTCA
Found at i:3632299 original size:32 final size:31
Alignment explanation
Indices: 3632263--3632350 Score: 106
Period size: 32 Copynumber: 2.7 Consensus size: 31
3632253 TTCAAATTTA
*
3632263 AAAATAACTCGAATCCGAAATGATTTAAACTT
1 AAAATAACTCGAA-CCGAAATGATTTAAACTC
*
3632295 AAAATGACTCGAACTCGAAATGATTTAAACTC
1 AAAATAACTCGAAC-CGAAATGATTTAAACTC
*
3632327 GAAATAA-TCCGAACCCGAAATGAT
1 AAAATAACT-CGAA-CCGAAATGAT
3632351 CCTAACAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
31 2 0.04
32 46 0.94
33 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.24
Consensus pattern (31 bp):
AAAATAACTCGAACCGAAATGATTTAAACTC
Found at i:3633139 original size:60 final size:59
Alignment explanation
Indices: 3633033--3633145 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 59
3633023 GTAAAAAATC
****
3633033 TAAAATAACTTAAACTCGATAAATCCAATTGTTAAATTTGATTGACTCAAATCTAAACT
1 TAAAATAACTTAAACTCGATAAATCCAATTGTTAAACCCAATTGACTCAAATCTAAACT
* * *
3633092 TAAAATGACTTAAACTCGATTTAATCCTAA-TGTTAAACCCAATTGACTCGAATC
1 TAAAATAACTTAAACTCGA-TAAATCC-AATTGTTAAACCCAATTGACTCAAATC
3633146 CAGAATGACT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
59 18 0.40
60 25 0.56
61 2 0.04
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.33
Consensus pattern (59 bp):
TAAAATAACTTAAACTCGATAAATCCAATTGTTAAACCCAATTGACTCAAATCTAAACT
Found at i:3633745 original size:2 final size:2
Alignment explanation
Indices: 3633732--3633765 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3633722 TACGTAATTA
*
3633732 AT AT AC 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
3633766 TGGAGGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3640766 original size:98 final size:100
Alignment explanation
Indices: 3640589--3640782 Score: 266
Period size: 98 Copynumber: 1.9 Consensus size: 100
3640579 AAATGCCACG
* *
3640589 CACACACTCAAGCAACACAAACATGACTGATATTAACATGGTATAGGCTATCTAACAAAAGTTGC
1 CACACACTCAAGCAACACAAACA-GA--GATATTAACATGGTATAGCCTATCTAACAAAAGTTAC
** *
3640654 ACATACCTTGGAGGTGGGATAGGAGGAAACAAGTCACT
63 ACATACCTCAGAGGTGGGACAGGAGGAAACAAGTCACT
* * *
3640692 CACACACTCAAGCAACACAAAC-G-GATATTAGCATGGTATAGCCTATTTAACAAATGTTACACA
1 CACACACTCAAGCAACACAAACAGAGATATTAACATGGTATAGCCTATCTAACAAAAGTTACACA
*
3640755 TACCTCAGAGGTTGGACAGGAGGAAACA
66 TACCTCAGAGGTGGGACAGGAGGAAACA
3640783 TGTAACTTTG
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
98 59 0.72
101 1 0.01
103 22 0.27
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (100 bp):
CACACACTCAAGCAACACAAACAGAGATATTAACATGGTATAGCCTATCTAACAAAAGTTACACA
TACCTCAGAGGTGGGACAGGAGGAAACAAGTCACT
Found at i:3645586 original size:27 final size:28
Alignment explanation
Indices: 3645551--3645617 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
3645541 GATTTAAAAT
*
3645551 AAATTTTTAATAA-TTTAATTAACATAA
1 AAATTTTTAATAATTTTAATAAACATAA
* * *
3645578 AAATTTTTAACAAATTTTAATAAATATCA
1 AAATTTTTAA-TAATTTTAATAAACATAA
3645607 AAATTTTTAAT
1 AAATTTTTAAT
3645618 TATAATTACA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
27 10 0.30
28 2 0.06
29 21 0.64
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (28 bp):
AAATTTTTAATAATTTTAATAAACATAA
Found at i:3648681 original size:2 final size:2
Alignment explanation
Indices: 3648668--3648704 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3648658 ATGAGATTAT
*
3648668 TA TA TG 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 T
3648705 TCATGCTGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3650084 original size:13 final size:14
Alignment explanation
Indices: 3650066--3650094 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3650056 ATATATTTAT
3650066 AATAAAAAT-ATAA
1 AATAAAAATAATAA
3650079 AATAAAAATAATAA
1 AATAAAAATAATAA
3650093 AA
1 AA
3650095 ATTATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AATAAAAATAATAA
Found at i:3650583 original size:30 final size:30
Alignment explanation
Indices: 3650549--3650612 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
3650539 TTTTTTATTT
* * *
3650549 TTTAAAT-TATTTTTAAATAATATATATATA
1 TTTAAATATAATTATAAATAATA-AGATATA
*
3650579 TTTAAATATAATTATAAATAGTAAGATATA
1 TTTAAATATAATTATAAATAATAAGATATA
3650609 TTTA
1 TTTA
3650613 TATCGAATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 17 0.59
31 12 0.41
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
TTTAAATATAATTATAAATAATAAGATATA
Found at i:3663413 original size:29 final size:28
Alignment explanation
Indices: 3663381--3663446 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
3663371 TTAAATTTAA
*
3663381 ATTATTATTTATATAATAAAAAATATTTT
1 ATTATTATTTAAATAAT-AAAAATATTTT
* * *
3663410 ATTA-AAATTAAATTATAAAAATATTTT
1 ATTATTATTTAAATAATAAAAATATTTT
3663437 -TTATT-TTTAA
1 ATTATTATTTAA
3663447 TATCATTTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
26 7 0.23
27 11 0.37
28 8 0.27
29 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
ATTATTATTTAAATAATAAAAATATTTT
Found at i:3668967 original size:13 final size:13
Alignment explanation
Indices: 3668949--3668974 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3668939 TTATTATTTT
3668949 AAATATATAATAA
1 AAATATATAATAA
3668962 AAATATATAATAA
1 AAATATATAATAA
3668975 TTTTTTAATT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATATATAATAA
Found at i:3669454 original size:21 final size:22
Alignment explanation
Indices: 3669408--3669454 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
3669398 ATTATTAAAT
* *
3669408 TAATAAAAATATTATTTATTAA
1 TAATAAAAATATTATATAATAA
3669430 -AATAAAAATATTA-ATAATAA
1 TAATAAAAATATTATATAATAA
3669450 TAATA
1 TAATA
3669455 TTTTAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAATAAAAATATTATATAATAA
Found at i:3677224 original size:3 final size:3
Alignment explanation
Indices: 3677216--3677252 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3677206 TCTACGCTAT
3677216 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3677253 AGTTTCTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3677280 original size:18 final size:18
Alignment explanation
Indices: 3677248--3677284 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3677238 TAATAATAAT
*
3677248 AATAAAGTTTCTAATTAA
1 AATAAAATTTCTAATTAA
*
3677266 AATAAAATTTTTAATTAA
1 AATAAAATTTCTAATTAA
3677284 A
1 A
3677285 TTTTACATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (18 bp):
AATAAAATTTCTAATTAA
Found at i:3677342 original size:18 final size:19
Alignment explanation
Indices: 3677315--3677354 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
3677305 TGATATTAAT
*
3677315 TTAATTAAAAATTAA-AAA
1 TTAATCAAAAATTAATAAA
3677333 TTAATCAAAAATTAATAAA
1 TTAATCAAAAATTAATAAA
3677352 TTA
1 TTA
3677355 TATATGTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
TTAATCAAAAATTAATAAA
Found at i:3678555 original size:13 final size:13
Alignment explanation
Indices: 3678539--3678564 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3678529 AATTATTATT
3678539 TTAAATTAAAAAA
1 TTAAATTAAAAAA
3678552 TTAAATTAAAAAA
1 TTAAATTAAAAAA
3678565 GATTTATTAT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAAATTAAAAAA
Found at i:3678762 original size:23 final size:23
Alignment explanation
Indices: 3678700--3678775 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
3678690 TTAAGAAAAT
* *
3678700 AAAAAATAATATTTAATTAAATTTA
1 AAAAAATAACATTTAA-CAAA-TTA
* *
3678725 AAAAATTTACA-TTAACAAATTA
1 AAAAAATAACATTTAACAAATTA
**
3678747 AAAAAATAACATTTAAGGAATTA
1 AAAAAATAACATTTAACAAATTA
3678770 AAAAAA
1 AAAAAA
3678776 ATTTATCATT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
22 12 0.29
23 18 0.43
24 4 0.10
25 8 0.19
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.30
Consensus pattern (23 bp):
AAAAAATAACATTTAACAAATTA
Found at i:3678772 original size:108 final size:109
Alignment explanation
Indices: 3678571--3678773 Score: 252
Period size: 108 Copynumber: 1.9 Consensus size: 109
3678561 AAAAGATTTA
* *
3678571 TTATTATTTTTTTAATAAAATTAAAAATAATATTTAATTAAATTAAAAAAATTACACTAAAAAAT
1 TTATTATTTTTTTAAGAAAATAAAAAATAATATTTAATTAAATTAAAAAAATTACACTAAAAAAT
* * * ***
3678636 TAAAATATTAATTATATGTTTTTATAAAAATAAAAAGTATTTTT
66 TAAAAAATAAATTATAAGTGAATATAAAAATAAAAAGTATTTTT
* * *
3678680 TTATTA-TTTTTTAAGAAAATAAAAAATAATATTTAATTAAATTTAAAAAATTTACATTAACAAA
1 TTATTATTTTTTTAAGAAAATAAAAAATAATATTTAATTAAA-TTAAAAAAATTACACTAAAAAA
3678744 TTAAAAAAATAACATT-TAAG-GAAT-TAAAAA
65 TT-AAAAAATAA-ATTATAAGTGAATATAAAAA
3678774 AAATTTATCA
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
108 39 0.49
109 28 0.35
110 10 0.12
111 3 0.04
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (109 bp):
TTATTATTTTTTTAAGAAAATAAAAAATAATATTTAATTAAATTAAAAAAATTACACTAAAAAAT
TAAAAAATAAATTATAAGTGAATATAAAAATAAAAAGTATTTTT
Found at i:3679211 original size:121 final size:121
Alignment explanation
Indices: 3679073--3679439 Score: 440
Period size: 120 Copynumber: 3.1 Consensus size: 121
3679063 AAAAAATATT
3679073 ATTATAAT-AAAAA-CTTTTTTAATTTAAAATTTTTTATTTTTAAAAACATAATAATTAATATTT
1 ATTATAATAAAAAACCTTTTTTAATTTAAAATTTTTTATTTTTAAAAACATAATAATTAATATTT
*
3679136 TAATTTGTTAATGTAAATTTTTAAA-TTGAATTAAATATTTTTTTATTTTATTAAAA
66 TAATTTGTTAATGTAATTTTTTAAACTT-AATTAAATATTTTTTTATTTTATTAAAA
*
3679192 ATTATAATAAAAAACC--TTTTATTTTAAAATTTTTTATTTTTATAAAAACATAATAATTAA-AT
1 ATTATAATAAAAAACCTTTTTTAATTTAAAATTTTTTA-TTTT-TAAAAACATAATAATTAATAT
3679254 TTTAATTTGTTAATGTAATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAA
64 TTTAATTTGTTAATGTAATTTTTTAAACTTAATTAAATATT-TTTTT-ATTTTATTAAAA
* * * *
3679314 A--ATAATAATAAACCCTTTTATTTTTATTTAAAATTTTTTA-TTAT-GAAA-A-AATAATTAAT
1 ATTATAATAA-AAAACC--TT-TTTTAATTTAAAATTTTTTATTTTTAAAAACATAATAATTAAT
* * *
3679373 ATTTTAATTTGTTAATATAATTTTCTTTAAAGTTAATTAAATA--TTATT-TTTTATTAAAA
62 ATTTTAATTTGTTAATGTAA-TTT-TTTAAACTTAATTAAATATTTTTTTATTTTATTAAAA
*
3679432 ATAATAAT
1 ATTATAAT
3679440 TAATATAAAT
Statistics
Matches: 220, Mismatches: 10, Indels: 35
0.83 0.04 0.13
Matches are distributed among these distances:
118 12 0.05
119 27 0.12
120 73 0.33
121 51 0.23
122 19 0.09
123 18 0.08
124 2 0.01
126 18 0.08
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (121 bp):
ATTATAATAAAAAACCTTTTTTAATTTAAAATTTTTTATTTTTAAAAACATAATAATTAATATTT
TAATTTGTTAATGTAATTTTTTAAACTTAATTAAATATTTTTTTATTTTATTAAAA
Found at i:3679444 original size:121 final size:121
Alignment explanation
Indices: 3679088--3679444 Score: 414
Period size: 121 Copynumber: 2.9 Consensus size: 121
3679078 AATAAAAACT
* *
3679088 TTTTTAATTTAAAATTTTTTATTTTTAAAAACATAATAATTAATATTTTAATTTGTTAATGTAAA
1 TTTTT-ATTTAAAATTTTTTATTTATAAAAACATAATAATTAATATTTTAATTTGTTAATGTAAT
* *
3679153 TTTTTAAATTGAATTAAATATTTTTTTATTTTATTAAAAATTATAATAA-AAAACCTTTTA
65 TTTTTAAATT-AATTAAATA--TTATT-TTTTATTAAAAATAATAATAATAAAACCTTTTA
3679213 ----T-TTTAAAATTTTTTATTTTTATAAAAACATAATAATTAA-ATTTTAATTTGTTAATGTAA
1 TTTTTATTTAAAATTTTTTA--TTTATAAAAACATAATAATTAATATTTTAATTTGTTAATGTAA
* *
3679272 TTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAA-AATAATAATAAACCCTTTTA
64 TTTTTTAAA-TTAATTAAATATTATTTTT--TATTA--AAAATAATAATAATAAAACCTTTTA
* *
3679334 TTTTTATTTAAAATTTTTTA-TTAT-GAAA-A-AATAATTAATATTTTAATTTGTTAATATAATT
1 TTTTTATTTAAAATTTTTTATTTATAAAAACATAATAATTAATATTTTAATTTGTTAATGTAA-T
3679395 TTCTTTAAAGTTAATTAAATATTATTTTTTATTAAAAATAATAATTAATA
65 TT-TTTAAA-TTAATTAAATATTATTTTTTATTAAAAATAATAA-TAATA
3679445 TAAATTTCTC
Statistics
Matches: 204, Mismatches: 10, Indels: 40
0.80 0.04 0.16
Matches are distributed among these distances:
117 3 0.01
118 4 0.02
119 22 0.11
120 58 0.28
121 67 0.33
122 6 0.03
123 29 0.14
125 1 0.00
126 14 0.07
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (121 bp):
TTTTTATTTAAAATTTTTTATTTATAAAAACATAATAATTAATATTTTAATTTGTTAATGTAATT
TTTTAAATTAATTAAATATTATTTTTTATTAAAAATAATAATAATAAAACCTTTTA
Found at i:3680241 original size:19 final size:18
Alignment explanation
Indices: 3680208--3680249 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
3680198 TACATGTATT
*
3680208 ATTACTTTTTATTTAAAA
1 ATTATTTTTTATTTAAAA
*
3680226 ATTATTTTTATATTTATAA
1 ATTATTTTT-TATTTAAAA
3680245 ATTAT
1 ATTAT
3680250 AAAAAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTATTTTTTATTTAAAA
Found at i:3680275 original size:28 final size:29
Alignment explanation
Indices: 3680222--3680276 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
3680212 CTTTTTATTT
**
3680222 AAAAATTATTTTTATATTTATAAATTATA
1 AAAAATTATTTTTATATCAATAAATTATA
*
3680251 AAAAATTATTTTTAT-TCAATTAATTA
1 AAAAATTATTTTTATATCAATAAATTA
3680277 ATATAGTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
AAAAATTATTTTTATATCAATAAATTATA
Found at i:3680526 original size:11 final size:11
Alignment explanation
Indices: 3680510--3680558 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
3680500 TTATTACTTG
3680510 TTATTTATAAA
1 TTATTTATAAA
* *
3680521 TTATTTTTAAT
1 TTATTTATAAA
3680532 TTATTTATAAA
1 TTATTTATAAA
* *
3680543 TTAATTA-AAT
1 TTATTTATAAA
3680553 TTATTT
1 TTATTT
3680559 TTTAAAAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 7 0.23
11 24 0.77
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:3680538 original size:22 final size:21
Alignment explanation
Indices: 3680510--3680558 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
3680500 TTATTACTTG
* *
3680510 TTATTTATAAATTATTTTTAAT
1 TTATTTATAAATTA-ATTAAAT
3680532 TTATTTATAAATTAATTAAAT
1 TTATTTATAAATTAATTAAAT
3680553 TTATTT
1 TTATTT
3680559 TTTAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATTTATAAATTAATTAAAT
Found at i:3680698 original size:289 final size:294
Alignment explanation
Indices: 3680094--3680737 Score: 831
Period size: 289 Copynumber: 2.2 Consensus size: 294
3680084 TTTACATGTA
* * * *
3680094 TTATTTTTCGATAACGACTTACATACGAGTTTTCTTTTATCTGTAAAATAACCAAG-AAAAATTT
1 TTATTTTTCGATAACGACTTAAATACGAGCTTTCCTTTATCTGTAAAATGACCAAGAAAAAATTT
* * *
3680158 ATTGTACATGAATTATTTTTATTAAAATTAATTAATATTGTACATGTATTATTACTTTTTATTTA
66 ATTATACATGAATTATTTTTATTAAAATTAATTAATATTGTACATGAATTATTACTTGTTATTTA
* *
3680223 AAAATTATTTTTATATTTATAAATTATAAAAAATTATTTTTATTCAATTAATTAATATAGTACAT
131 AAAATTATTTTTATATTTATAAATTATAAAAAATTATTTTTATTCAATAAATTAATATAATACAT
* * ** * ** * **
3680288 GTATTATTTTTATAATTGATAGATTTTAAATTTATGTTAGCCAACAATATTTTACTTTTTTTTAT
196 GTATCATTTTTATAATTGATAAAAATTAAATTTACGTTAGCCAACAATAAATTAATTTTTTCGAT
** *
3680353 AATGACTTATTTTAGATTTACAGAAGCACACATT
261 AACAACTTATTTCAGATTTACAGAAGCACACATT
* * *
3680387 TTATTTTTTGGTAACGACTTAAATACGAGCTTTCCTTTATCTGTAAAATGACTAAGAAAAAATTT
1 TTATTTTTCGATAACGACTTAAATACGAGCTTTCCTTTATCTGTAAAATGACCAAGAAAAAATTT
* * * *
3680452 ATTATCCATGTATTATTTTTATTAAAATTAATTAATATTGTGCGTGAATTATTACTTGTTATTTA
66 ATTATACATGAATTATTTTTATTAAAATTAATTAATATTGTACATGAATTATTACTTGTTATTTA
* **
3680517 TAAATTATTTTTAATTTATTTATAAATTA-ATTAAATT-TATTTT-TT-AA-AAATTAAT-TAAT
131 AAAATTATTTTT-A--TATTTATAAATTATAAAAAATTAT-TTTTATTCAATAAATTAATATAAT
* *
3680576 A-TTGTA-CA-TTTTATAATTGTTAAAAATTAAATTTACGTTAGCCAACAATAAATTAATTTTTT
192 ACATGTATCATTTTTATAATTGATAAAAATTAAATTTACGTTAGCCAACAATAAATTAATTTTTT
* * *
3680638 CGATAACAACTTATTTCGGATTTACATATGCACACATT
257 CGATAACAACTTATTTCAGATTTACAGAAGCACACATT
* *
3680676 TTATTTTTCGATAACAACTTAAATACGAACTTTCCTTTATCTGTAAAATGACCAAGAAAAAA
1 TTATTTTTCGATAACGACTTAAATACGAGCTTTCCTTTATCTGTAAAATGACCAAGAAAAAA
3680738 GTTTCCTCAA
Statistics
Matches: 304, Mismatches: 42, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
289 133 0.44
290 1 0.00
291 4 0.01
292 4 0.01
293 56 0.18
294 79 0.26
295 4 0.01
296 10 0.03
297 13 0.04
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (294 bp):
TTATTTTTCGATAACGACTTAAATACGAGCTTTCCTTTATCTGTAAAATGACCAAGAAAAAATTT
ATTATACATGAATTATTTTTATTAAAATTAATTAATATTGTACATGAATTATTACTTGTTATTTA
AAAATTATTTTTATATTTATAAATTATAAAAAATTATTTTTATTCAATAAATTAATATAATACAT
GTATCATTTTTATAATTGATAAAAATTAAATTTACGTTAGCCAACAATAAATTAATTTTTTCGAT
AACAACTTATTTCAGATTTACAGAAGCACACATT
Found at i:3684369 original size:85 final size:89
Alignment explanation
Indices: 3684156--3684399 Score: 302
Period size: 85 Copynumber: 2.8 Consensus size: 89
3684146 GCAGTCTTTC
* *
3684156 CTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATAATT-AATGCATTAGTCTAATCCTTATA
1 CTTTTTTTCTATAAAAAA-AATCTGATTCTCAGATATAATTCAA-GCATTAGTCTAATCCTTACA
* **
3684220 GTATGACATTTACAATCAATTAATCTTT
64 GTCTGACATTT--AATCAATTAATCTAA
* * *
3684248 CTTTTTTTTCTAT-AAAAAAATGTGATTCTCAAATATAATTCAAGCATTAGTCTAAT-TTTACAG
1 C-TTTTTTTCTATAAAAAAAATCTGATTCTCAGATATAATTCAAGCATTAGTCTAATCCTTACAG
*
3684311 TCTGACATTT-A-CAATTAGTC-AA
65 TCTGACATTTAATCAATTAATCTAA
* *
3684333 CTTTTTTTCTATAAAAAAAATCTGATTCTCAGATATAATTCATGTATTAGTCTAATCCTTACAGT
1 CTTTTTTTCTATAAAAAAAATCTGATTCTCAGATATAATTCAAGCATTAGTCTAATCCTTACAGT
3684398 CT
66 CT
3684400 TTCTTTTTTC
Statistics
Matches: 134, Mismatches: 14, Indels: 14
0.83 0.09 0.09
Matches are distributed among these distances:
84 11 0.08
85 40 0.30
86 17 0.13
87 1 0.01
90 14 0.10
91 32 0.24
92 8 0.06
93 11 0.08
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (89 bp):
CTTTTTTTCTATAAAAAAAATCTGATTCTCAGATATAATTCAAGCATTAGTCTAATCCTTACAGT
CTGACATTTAATCAATTAATCTAA
Found at i:3684537 original size:68 final size:69
Alignment explanation
Indices: 3684333--3684537 Score: 313
Period size: 70 Copynumber: 3.0 Consensus size: 69
3684323 AATTAGTCAA
* *
3684333 CTTTTTTTCTATAAAAAAAATCTGATTCTCAGATATAATTCATGTATTAGTCTAATCCTTACAGT
1 CTTTTTTTCTATAAAAAAAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAGT
3684398 CTTT
66 CTTT
* * * *
3684402 CTTTTTTCCTATAAAAAAGAATATGATTCTCAGATACAATTCATGCATTAGTCTAATCCTTGGAG
1 CTTTTTTTCTATAAAAAA-AATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAG
3684467 TCTTT
65 TCTTT
* **
3684472 CTTTTTTTCTAT-AAAAAAATCTGATTCTCAGATATAATTTATGCATTAGTCTAATATTTGCAGT
1 CTTTTTTTCTATAAAAAAAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAGT
3684536 CT
66 CT
3684538 GACATTTATA
Statistics
Matches: 122, Mismatches: 13, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
68 43 0.35
69 22 0.18
70 57 0.47
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (69 bp):
CTTTTTTTCTATAAAAAAAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAGT
CTTT
Found at i:3684635 original size:92 final size:92
Alignment explanation
Indices: 3684465--3684730 Score: 377
Period size: 88 Copynumber: 3.0 Consensus size: 92
3684455 TAATCCTTGG
* *
3684465 AGTCTTTC-TTTTTTTCTAT-AAAAAAATCTGATTCTCAGATATAATTTATGCATTAGTCTAAT-
1 AGTCTTTCTTTTTTTTCTATAAAAAAAATCTGATTCTCAGATATAATTCATACATTAGTCTAATC
*
3684527 ATTTGCAGTCTGACATTTATAATCAATC
66 A-TTGCAGTCTGACATTTACAATCAATC
*
3684555 AGTCTTTCTTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCAT-CATTAGTTTAAT
1 AGTCTTTCTTTTTTTTCTATAAAAAA-AATCTGATTCTCAGATATAATTCATACATTAGTCTAAT
* * *
3684619 CCTTGCAGTATAACATTTACAATCAATC
65 CATTGCAGTCTGACATTTACAATCAATC
* *
3684647 A-AC--T-TTTTTTTTCTATAAAAAAAATTTGATTCTCAGATATAATTCATACATTAGTCTAATC
1 AGTCTTTCTTTTTTTTCTATAAAAAAAATCTGATTCTCAGATATAATTCATACATTAGTCTAATC
3684708 ATTGCAGTCTGACATTTACAATC
66 ATTGCAGTCTGACATTTACAATC
3684731 GATTCTCAAA
Statistics
Matches: 159, Mismatches: 12, Indels: 12
0.87 0.07 0.07
Matches are distributed among these distances:
87 24 0.15
88 50 0.31
89 1 0.01
90 8 0.05
91 12 0.08
92 40 0.25
93 24 0.15
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (92 bp):
AGTCTTTCTTTTTTTTCTATAAAAAAAATCTGATTCTCAGATATAATTCATACATTAGTCTAATC
ATTGCAGTCTGACATTTACAATCAATC
Found at i:3684738 original size:57 final size:57
Alignment explanation
Indices: 3684674--3684787 Score: 174
Period size: 57 Copynumber: 2.0 Consensus size: 57
3684664 AAAAAAATTT
* * *
3684674 GATTCTCAGATATAATTCATACATTAGTCTAATCATTGCAGTCTGACATTTACAATC
1 GATTCTCAAATATAATTCATACATTAGTCTAATCATTACAATCTGACATTTACAATC
* * *
3684731 GATTCTCAAATATAATTCATGCATTAGTCTAATCTTTACAATCTGACATTTATAATC
1 GATTCTCAAATATAATTCATACATTAGTCTAATCATTACAATCTGACATTTACAATC
3684788 AATCAACTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (57 bp):
GATTCTCAAATATAATTCATACATTAGTCTAATCATTACAATCTGACATTTACAATC
Found at i:3684778 original size:237 final size:238
Alignment explanation
Indices: 3684489--3684926 Score: 679
Period size: 236 Copynumber: 1.8 Consensus size: 238
3684479 TCTATAAAAA
* * * *
3684489 AATCTGATTCTCAGATATAATTTATGCATTAGTCTAATATTTGCAGTCTGACATTTATAATCAAT
1 AATCTGATTCTCAAATATAATTCATGCATTAGTCTAATATTTACAATCTGACATTTATAATCAAT
* *
3684554 C-AGTCTTTCTTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCAT-CATTAGTTTA
66 CAACT-TTTC-TTTTTTTCTATAAAAAAGAAT-TGATTCTCAGATATAATTCATACATTAGTCTA
* *
3684617 ATCCTTGCAGTATAACATTTACAATCAATCAACTTTTTTTTTCTATAAAAAA-AATTTGAT-TCT
128 ATCCTTGCAGTATAACATTTACAATCAATCAACTTTTTTTTTCCATAAAAAAGAATTCGATGT-T
*
3684680 CAGATATAATTCATACATTAGTCTAATCATTGCAGTCTGACATTTAC
192 AAGATATAATTCATACATTAGTCTAATCATTGCAGTCTGACATTTAC
*
3684727 AATC-GATTCTCAAATATAATTCATGCATTAGTCTAATCTTTACAATCTGACATTTATAATCAAT
1 AATCTGATTCTCAAATATAATTCATGCATTAGTCTAATATTTACAATCTGACATTTATAATCAAT
3684791 CAACTTTTCTTTTTTTCTATAAAAAAGAATTGATTCTCAGATATAATTCATACATTAGTCTAATC
66 CAACTTTTCTTTTTTTCTATAAAAAAGAATTGATTCTCAGATATAATTCATACATTAGTCTAATC
* * * *
3684856 TTTGCAGTCTGATATTTACAATCAATCAACTTTTTTTTTCCATAAAAAAGAATTCGATGTTAAGA
131 CTTGCAGTATAACATTTACAATCAATCAACTTTTTTTTTCCATAAAAAAGAATTCGATGTTAAGA
3684921 TATAAT
196 TATAAT
3684927 CACATTTATT
Statistics
Matches: 182, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
235 21 0.12
236 77 0.42
237 77 0.42
238 7 0.04
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (238 bp):
AATCTGATTCTCAAATATAATTCATGCATTAGTCTAATATTTACAATCTGACATTTATAATCAAT
CAACTTTTCTTTTTTTCTATAAAAAAGAATTGATTCTCAGATATAATTCATACATTAGTCTAATC
CTTGCAGTATAACATTTACAATCAATCAACTTTTTTTTTCCATAAAAAAGAATTCGATGTTAAGA
TATAATTCATACATTAGTCTAATCATTGCAGTCTGACATTTAC
Found at i:3684841 original size:148 final size:145
Alignment explanation
Indices: 3684582--3684878 Score: 445
Period size: 148 Copynumber: 2.0 Consensus size: 145
3684572 TATAAAAAAG
* * * *
3684582 AATCTGATTCTCAGATATAATTCATCATTAGTTTAATCCTTGCAGTATAACATTTACAATCAATC
1 AATCTGATTCTCAAATATAATTCATCATTAGTCTAATCCTTACAATATAACATTTACAATCAATC
3684647 AACTTTTTTTTTCTATAAAAAAAATTTGATTCTCAGATATAATTCATACATTAGTCTAATCATTG
66 AACTTTTTTTTTCTATAAAAAAAATTTGATTCTCAGATATAATTCATACATTAGTCTAATCATTG
3684712 CAGTCTGACATTTAC
131 CAGTCTGACATTTAC
* * * *
3684727 AATC-GATTCTCAAATATAATTCATGCATTAGTCTAATCTTTACAATCTGACATTTATAATCAAT
1 AATCTGATTCTCAAATATAATTCAT-CATTAGTCTAATCCTTACAATATAACATTTACAATCAAT
3684791 CAACTTTTCTTTTTTTCTATAAAAAAGAA-TTGATTCTCAGATATAATTCATACATTAGTCTAAT
65 CAAC--TT-TTTTTTTCTATAAAAAA-AATTTGATTCTCAGATATAATTCATACATTAGTCTAAT
* *
3684855 CTTTGCAGTCTGATATTTAC
126 CATTGCAGTCTGACATTTAC
3684875 AATC
1 AATC
3684879 AATCAACTTT
Statistics
Matches: 137, Mismatches: 10, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
144 19 0.14
145 40 0.29
147 2 0.01
148 74 0.54
149 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.41
Consensus pattern (145 bp):
AATCTGATTCTCAAATATAATTCATCATTAGTCTAATCCTTACAATATAACATTTACAATCAATC
AACTTTTTTTTTCTATAAAAAAAATTTGATTCTCAGATATAATTCATACATTAGTCTAATCATTG
CAGTCTGACATTTAC
Found at i:3684886 original size:91 final size:89
Alignment explanation
Indices: 3684729--3684926 Score: 274
Period size: 91 Copynumber: 2.2 Consensus size: 89
3684719 ACATTTACAA
* * *
3684729 TCGATTCTCAAATATAATTCATGCATTAGTCTAATCTTTACAATCTGACATTTATAATCAATCAA
1 TCGATTCTCAGATATAATTCATACATTAGTCTAATCTTTACAATCTGACATTTACAATCAATCAA
*
3684794 CTTTTCTTTTTTTCTATAAAAAAGAAT
66 C--TT-TTTTTTTCCATAAAAAAGAAT
* * *
3684821 T-GATTCTCAGATATAATTCATACATTAGTCTAATCTTTGCAGTCTGATATTTACAATCAATCAA
1 TCGATTCTCAGATATAATTCATACATTAGTCTAATCTTTACAATCTGACATTTACAATCAATCAA
3684885 CTTTTTTTTTCCATAAAAAAGAAT
66 CTTTTTTTTTCCATAAAAAAGAAT
*
3684909 TCGATGT-TAAGATATAAT
1 TCGAT-TCTCAGATATAAT
3684927 CACATTTATT
Statistics
Matches: 96, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
88 21 0.22
89 15 0.16
90 1 0.01
91 58 0.60
92 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (89 bp):
TCGATTCTCAGATATAATTCATACATTAGTCTAATCTTTACAATCTGACATTTACAATCAATCAA
CTTTTTTTTTCCATAAAAAAGAAT
Found at i:3685917 original size:123 final size:123
Alignment explanation
Indices: 3685556--3685922 Score: 421
Period size: 123 Copynumber: 3.0 Consensus size: 123
3685546 TATTATTTTT
* * * * *
3685556 AATAAATAATAATATGTAATTAATTTTAAAAAATTTTATATTAATAAATTAAAATATT-A--ATT
1 AATAAAAAATAATATTTAATTAAGTTT-AAAAA-TTTACATTAACAAATTAAAATATTAATTATT
* * *
3685618 -T-TTTTAACAATAAAAAAATTTAAATAAAAATAAAAAA-TGTTTATTTATTATTATTTTTAATA
64 ATGTTTTAAAAAT-AAAAAATTT---T-AAAATAAAAAAGTTTTTA-TTATTATAATTTTTAATA
3685680 A
123 A
* * *
3685681 AATTAAAAATAATATTTAATAAAGTTTAAAAAATTACATTAACAAATTAAAA-ATTAATTATTAT
1 AATAAAAAATAATATTTAATTAAGTTTAAAAATTTACATTAACAAATTAAAATATTAATTATTAT
*
3685745 GTTTTTATAAAAATAAAAAATTTTAAAAT-AAAAAGCTTTT-TTATTATAATTTTTAATAA
66 G--TTT-TAAAAATAAAAAATTTTAAAATAAAAAAGTTTTTATTATTATAATTTTTAATAA
3685804 AATAAAAAATAATATTTAATTCAA-TTTAAAAATTTACATTAACAAATTAAAATATTAATTATTA
1 AATAAAAAATAATATTTAATT-AAGTTTAAAAATTTACATTAACAAATTAAAATATTAATTATTA
* *
3685868 TGTTTTAAAAATAAAAAATTTTAAATTAAAAAAGTTTTTATTATAATAATATTTT
65 TGTTTTAAAAATAAAAAATTTTAAAATAAAAAAGTTTTTATTATTATAAT-TTTT
3685923 TTATTTTTTA
Statistics
Matches: 210, Mismatches: 18, Indels: 29
0.82 0.07 0.11
Matches are distributed among these distances:
121 21 0.10
122 16 0.08
123 91 0.43
124 29 0.14
125 33 0.16
126 2 0.01
129 12 0.06
130 6 0.03
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (123 bp):
AATAAAAAATAATATTTAATTAAGTTTAAAAATTTACATTAACAAATTAAAATATTAATTATTAT
GTTTTAAAAATAAAAAATTTTAAAATAAAAAAGTTTTTATTATTATAATTTTTAATAA
Found at i:3686249 original size:22 final size:23
Alignment explanation
Indices: 3686206--3686295 Score: 85
Period size: 23 Copynumber: 3.9 Consensus size: 23
3686196 AATAATGATA
**
3686206 AATTTTTTTAATTCCTTAAATGT
1 AATTTTTTTAATTTATTAAATGT
*
3686229 TATTTTTTTAATTTATT-AATGT
1 AATTTTTTTAATTTATTAAATGT
*
3686251 AAATTTTTTTAAATTTAATTAAATAT
1 -AATTTTTTT-AATTT-ATTAAATGT
* *
3686277 CA-TTTTTTATTTTATTAAA
1 AATTTTTTTAATTTATTAAA
3686296 AAATAATAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
22 11 0.20
23 26 0.46
24 11 0.20
25 4 0.07
26 4 0.07
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (23 bp):
AATTTTTTTAATTTATTAAATGT
Found at i:3686258 original size:24 final size:24
Alignment explanation
Indices: 3686185--3686272 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 24
3686175 GAATAGAGAG
3686185 TTTTTT-ATTTGAA-TAATGATAAAT
1 TTTTTTAATTT-AATTAATG-TAAAT
** *
3686209 TTTTTTAA-TTCCTTAAATGT-TAT
1 TTTTTTAATTTAATT-AATGTAAAT
3686232 TTTTTTAATTT-ATTAATGTAAAT
1 TTTTTTAATTTAATTAATGTAAAT
3686255 TTTTTTAAATTTAATTAA
1 TTTTTT-AATTTAATTAA
3686273 ATATCATTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
22 5 0.10
23 20 0.38
24 17 0.33
25 10 0.19
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (24 bp):
TTTTTTAATTTAATTAATGTAAAT
Found at i:3686283 original size:47 final size:47
Alignment explanation
Indices: 3686185--3686294 Score: 118
Period size: 47 Copynumber: 2.3 Consensus size: 47
3686175 GAATAGAGAG
* ** * *
3686185 TTTTTT-ATTTGAATAATGATAAATTTTTTTAATTCCTTAAATGTTAT
1 TTTTTTAATTT-ATTAATGATAAATTTTTTTAATTAATTAAATATCAT
3686232 TTTTTTAATTTATTAATG-TAAATTTTTTTAAATTTAATTAAATATCA-
1 TTTTTTAATTTATTAATGATAAATTTTTTT-AA-TTAATTAAATATCAT
*
3686279 TTTTTTATTTTATTAA
1 TTTTTTAATTTATTAA
3686295 AAAATAATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
46 11 0.20
47 29 0.54
48 14 0.26
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.60
Consensus pattern (47 bp):
TTTTTTAATTTATTAATGATAAATTTTTTTAATTAATTAAATATCAT
Found at i:3686427 original size:36 final size:35
Alignment explanation
Indices: 3686278--3686433 Score: 104
Period size: 36 Copynumber: 4.3 Consensus size: 35
3686268 ATTAAATATC
*
3686278 ATTTTTTATTTTATTAAAAAATAATAATAATAAAT
1 ATTTTTAATTTTATTAAAAAATAATAATAATAAAT
* * *
3686313 ACTTTTTATTTTTA-TAAAAACATATCATTAATATTTAAT
1 A-TTTTTAATTTTATTAAAAA-ATA--A-TAATAATAAAT
* ** ** * *
3686352 -TTTTTAATGTAATTTTTTTAATTTAATTA-AAT-ATT
1 ATTTTTAAT-T--TTATTAAAAAATAATAATAATAAAT
3686387 ATTTTTAATTTTATTAAAAAATAATAATAATAAAT
1 ATTTTTAATTTTATTAAAAAATAATAATAATAAAT
3686422 CATTTTTAATTT
1 -ATTTTTAATTT
3686434 AATTTTTTAA
Statistics
Matches: 88, Mismatches: 20, Indels: 25
0.66 0.15 0.19
Matches are distributed among these distances:
33 11 0.12
34 3 0.03
35 12 0.14
36 34 0.39
37 9 0.10
38 3 0.03
39 9 0.10
40 4 0.05
41 3 0.03
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.53
Consensus pattern (35 bp):
ATTTTTAATTTTATTAAAAAATAATAATAATAAAT
Found at i:3686460 original size:109 final size:111
Alignment explanation
Indices: 3686236--3686436 Score: 300
Period size: 109 Copynumber: 1.8 Consensus size: 111
3686226 TGTTATTTTT
* *
3686236 TTAATTTATTAATGTAAATTTTTTTAAATTTAATTAAATATCATTTTTTATTTTATTAAAAAATA
1 TTAATTTTTTAATGTAAATTTTTTTAAATTTAATTAAATATCATTTTTAATTTTATTAAAAAATA
* * ** *
3686301 ATAATAATAAATACTTTTTATTTTTATAAAAACATATCATTAATAT
66 ATAATAATAAATACTTTTTAATTTAATAAAAACATATCAAAAATAA
*
3686347 TTAATTTTTTAATGT-AATTTTTTT-AATTTAATTAAATATTATTTTTAATTTTATTAAAAAATA
1 TTAATTTTTTAATGTAAATTTTTTTAAATTTAATTAAATATCATTTTTAATTTTATTAAAAAATA
3686410 ATAATAATAAAT-CATTTTTAATTTAAT
66 ATAATAATAAATAC-TTTTTAATTTAAT
3686437 TTTTTAATTT
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
108 1 0.01
109 60 0.71
110 9 0.11
111 14 0.17
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (111 bp):
TTAATTTTTTAATGTAAATTTTTTTAAATTTAATTAAATATCATTTTTAATTTTATTAAAAAATA
ATAATAATAAATACTTTTTAATTTAATAAAAACATATCAAAAATAA
Found at i:3686980 original size:4 final size:4
Alignment explanation
Indices: 3686971--3686997 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3686961 AACATCCGTT
3686971 CTTC CTTC CTTC CTTC CTTC CTTC CTT
1 CTTC CTTC CTTC CTTC CTTC CTTC CTT
3686998 TCCCTCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (4 bp):
CTTC
Found at i:3692246 original size:2 final size:2
Alignment explanation
Indices: 3692239--3692270 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3692229 TTGGAATTAT
3692239 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
3692271 ATGTTGGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3692721 original size:14 final size:14
Alignment explanation
Indices: 3692684--3692714 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3692674 GTAATATTAT
*
3692684 ATATAATTATATGA
1 ATATAATAATATGA
3692698 ATATAATAATATGA
1 ATATAATAATATGA
3692712 ATA
1 ATA
3692715 AAGTAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (14 bp):
ATATAATAATATGA
Found at i:3692776 original size:15 final size:16
Alignment explanation
Indices: 3692758--3692808 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 16
3692748 ATATATTTTA
3692758 AAATTTATAT-AATAT
1 AAATTTATATAAATAT
3692773 AAA-TTAT-TAACATATT
1 AAATTTATATAA-ATA-T
3692789 AATATTTATATAAATAT
1 AA-ATTTATATAAATAT
3692806 AAA
1 AAA
3692809 ATATTTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
13 1 0.03
14 5 0.17
15 6 0.20
16 4 0.13
17 4 0.13
18 7 0.23
19 3 0.10
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTTATATAAATAT
Found at i:3692813 original size:19 final size:19
Alignment explanation
Indices: 3692784--3692866 Score: 75
Period size: 19 Copynumber: 4.4 Consensus size: 19
3692774 AATTATTAAC
*
3692784 ATATTAATATTTATATAAAT
1 ATATAAATA-TTATATAAAT
3692804 ATA-AAATATT-T-TAAAT
1 ATATAAATATTATATAAAT
**
3692820 ATAATATAATAAAATA-AAAT
1 AT-ATA-AATATTATATAAAT
*
3692840 ACATAAATATTATATAAAT
1 ATATAAATATTATATAAAT
3692859 ATATAAAT
1 ATATAAAT
3692867 TTTTAGATCT
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
16 7 0.14
17 2 0.04
18 10 0.20
19 22 0.44
20 9 0.18
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATAAATATTATATAAAT
Found at i:3692815 original size:59 final size:57
Alignment explanation
Indices: 3692750--3692871 Score: 137
Period size: 59 Copynumber: 2.1 Consensus size: 57
3692740 AATAAATTAT
* * *
3692750 ATATTTTAAAAT-TTATATAATATAAAT-TATTAACATATTAATATTTATATAAATATA-AA
1 ATATTTTAAAATATAATATAATA-AAATAAAAT-ACATA--AATA-TTATATAAATATATAA
3692809 ATATTTT-AAATATAATATAATAAAATAAAATACATAAATATTATATAAATATATAA
1 ATATTTTAAAATATAATATAATAAAATAAAATACATAAATATTATATAAATATATAA
3692865 AT-TTTTA
1 ATATTTTA
3692872 GATCTAATGA
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
55 17 0.30
56 8 0.14
58 13 0.23
59 18 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (57 bp):
ATATTTTAAAATATAATATAATAAAATAAAATACATAAATATTATATAAATATATAA
Found at i:3692864 original size:28 final size:29
Alignment explanation
Indices: 3692789--3692865 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 29
3692779 TTAACATATT
**
3692789 AATATT-TATATAA-ATATAAAATATTTTA
1 AATATTATATA-AATATATAAAATATCATA
* *
3692817 AATATAATAT-AATAAAATAAAATA-CATA
1 AATATTATATAAAT-ATATAAAATATCATA
3692845 AATATTATATAAATATATAAA
1 AATATTATATAAATATATAAA
3692866 TTTTTAGATC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
27 2 0.05
28 22 0.56
29 15 0.38
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (29 bp):
AATATTATATAAATATATAAAATATCATA
Found at i:3700311 original size:21 final size:21
Alignment explanation
Indices: 3700287--3700328 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3700277 TATTTTTAAT
*
3700287 ATTTTAAATT-AATGTTAAAAA
1 ATTTCAAATTAAAT-TTAAAAA
*
3700308 ATTTCAATTTAAATTTAAAAA
1 ATTTCAAATTAAATTTAAAAA
3700329 CATAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
ATTTCAAATTAAATTTAAAAA
Found at i:3705008 original size:19 final size:20
Alignment explanation
Indices: 3704980--3705026 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
3704970 TATTATATAT
*
3704980 ATATATAAATTAAT-TAAAA
1 ATATAAAAATTAATATAAAA
* *
3704999 ATATAAAAATTTATATAAAT
1 ATATAAAAATTAATATAAAA
3705019 ATATAAAA
1 ATATAAAA
3705027 TTTTAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATATAAAAATTAATATAAAA
Found at i:3705026 original size:20 final size:20
Alignment explanation
Indices: 3704973--3705044 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
3704963 TATGAATTAT
* * *
3704973 TATATATATATATAAATTAA
1 TATAAATATATAAAAATTTA
*
3704993 T-TAAAAATATAAAAATTTA
1 TATAAATATATAAAAATTTA
*
3705012 TATAAATATATAAAATTTTA
1 TATAAATATATAAAAATTTA
*
3705032 AATATAAT-TATAA
1 TATA-AATATATAA
3705045 TATATGATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 15 0.35
20 25 0.58
21 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TATAAATATATAAAAATTTA
Found at i:3709798 original size:2 final size:2
Alignment explanation
Indices: 3709791--3709827 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3709781 ACCGTCAAAT
3709791 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 T
3709828 CCTTTCGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3711397 original size:3 final size:3
Alignment explanation
Indices: 3711389--3711430 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
3711379 TACATTCATT
*
3711389 TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3711431 CGAGTTAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3712442 original size:8 final size:8
Alignment explanation
Indices: 3712429--3712516 Score: 62
Period size: 8 Copynumber: 11.4 Consensus size: 8
3712419 TAATATAAAA
3712429 ATTAATAT
1 ATTAATAT
3712437 ATTAATAT
1 ATTAATAT
*
3712445 ATTAAAAT
1 ATTAATAT
*
3712453 TTTATATAAT
1 ATTA-AT-AT
*
3712463 ATAAATA-
1 ATTAATAT
*
3712470 ATTAATTT
1 ATTAATAT
3712478 ATTAA-A-
1 ATTAATAT
3712484 ATT--TAT
1 ATTAATAT
3712490 ATTAATAT
1 ATTAATAT
3712498 A-TAATAT
1 ATTAATAT
*
3712505 TTTAAATAT
1 ATT-AATAT
3712514 ATT
1 ATT
3712517 TATTATATAA
Statistics
Matches: 61, Mismatches: 10, Indels: 17
0.69 0.11 0.19
Matches are distributed among these distances:
5 1 0.02
6 6 0.10
7 11 0.18
8 29 0.48
9 10 0.16
10 4 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATTAATAT
Found at i:3712475 original size:33 final size:35
Alignment explanation
Indices: 3712431--3712516 Score: 115
Period size: 33 Copynumber: 2.5 Consensus size: 35
3712421 ATATAAAAAT
3712431 TAATATATTAATATATTAAAATTT-TATATAATATA
1 TAATATATTAATATATTAAAATTTATAT-TAATATA
*
3712466 -AATA-ATTAATTTATTAAAATTTATATTAATATA
1 TAATATATTAATATATTAAAATTTATATTAATATA
*
3712499 TAATATTTTAAATATATT
1 TAATATATT-AATATATT
3712517 TATTATATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 24 0.55
34 11 0.25
35 2 0.05
36 7 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (35 bp):
TAATATATTAATATATTAAAATTTATATTAATATA
Found at i:3712499 original size:40 final size:40
Alignment explanation
Indices: 3712404--3712504 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 40
3712394 TTATATAAAA
*
3712404 ATTAAAAATATAATATAATATAAAAATTAATATATTAATAT
1 ATTAAAATTAT-ATATAATATAAAAATTAATATATTAATAT
* *
3712445 ATTAAAATTTTATATAATATAAATAATTAATTTATTAA-A-
1 ATTAAAATTATATATAATATAAA-AATTAATATATTAATAT
* *
3712484 ATTTATATTAATATATAATAT
1 ATTAAAATT-ATATATAATAT
3712505 TTTAAATATA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
39 7 0.13
40 23 0.44
41 22 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (40 bp):
ATTAAAATTATATATAATATAAAAATTAATATATTAATAT
Found at i:3712508 original size:20 final size:20
Alignment explanation
Indices: 3712434--3712508 Score: 58
Period size: 20 Copynumber: 4.1 Consensus size: 20
3712424 TAAAAATTAA
*
3712434 TATATTAATATATTAAAATTT
1 TATATTAATATA-TAATATTT
*
3712455 TATA-TAATATA-AATA-AT
1 TATATTAATATATAATATTT
*
3712472 TA-ATT--TAT-TAA-AATT
1 TATATTAATATATAATATTT
3712487 TATATTAATATATAATATTT
1 TATATTAATATATAATATTT
3712507 TA
1 TA
3712509 AATATATTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 17
0.67 0.06 0.27
Matches are distributed among these distances:
14 1 0.02
15 8 0.19
16 4 0.10
17 4 0.10
18 6 0.14
19 3 0.07
20 12 0.29
21 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATATTAATATATAATATTT
Found at i:3715920 original size:63 final size:66
Alignment explanation
Indices: 3715842--3715964 Score: 225
Period size: 63 Copynumber: 1.9 Consensus size: 66
3715832 AAACTTACCG
3715842 TGCCAAAGATGACTCTTACAAAAGAACTACTATGAA-TTAGCTTAT-A-TTGCTGTCCTACGTAC
1 TGCCAAAGATGACTCTTACAAAAGAACTACTATGAATTTAGCTTATAATTTGCTGTCCTACGTAC
3715904 A
66 A
3715905 TGCCAAAGATGACTCTTACAAAAGAACTACTATGAATTTAGCTTATAATTTGCTGTCCTA
1 TGCCAAAGATGACTCTTACAAAAGAACTACTATGAATTTAGCTTATAATTTGCTGTCCTA
3715965 TACGTACAGG
Statistics
Matches: 57, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
63 36 0.63
64 9 0.16
65 1 0.02
66 11 0.19
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.32
Consensus pattern (66 bp):
TGCCAAAGATGACTCTTACAAAAGAACTACTATGAATTTAGCTTATAATTTGCTGTCCTACGTAC
A
Found at i:3716551 original size:6 final size:6
Alignment explanation
Indices: 3716540--3716564 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3716530 CCAGTACGGC
3716540 CAGCCT CAGCCT CAGCCT CAGCCT C
1 CAGCCT CAGCCT CAGCCT CAGCCT C
3716565 GTATGTACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.52, G:0.16, T:0.16
Consensus pattern (6 bp):
CAGCCT
Found at i:3719433 original size:3 final size:3
Alignment explanation
Indices: 3719425--3719470 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
3719415 ATCTTGAATG
*
3719425 TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3719471 AATGCGGCGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3722732 original size:2 final size:2
Alignment explanation
Indices: 3722725--3722763 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3722715 TATACTTCGT
3722725 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
3722764 TTTAAACCCA
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:3723226 original size:10 final size:10
Alignment explanation
Indices: 3723211--3723243 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3723201 CTCAAATTTG
3723211 AAAAAAAA-A
1 AAAAAAAATA
3723220 AAAAAAAATA
1 AAAAAAAATA
*
3723230 AAAGAAAATA
1 AAAAAAAATA
3723240 AAAA
1 AAAA
3723244 TTAGTTGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.91, C:0.00, G:0.03, T:0.06
Consensus pattern (10 bp):
AAAAAAAATA
Done.