Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold88
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: 1260485
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
File 3 of 8
Found at i:258530 original size:22 final size:22
Alignment explanation
Indices: 258502--258548 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 22
258492 CGTGTACATT
258502 ATTATTATTTATAACATATTTTATA
1 ATTA-TATTTA-AA-ATATTTTATA
258527 ATTATATTTAAAATATTTTATA
1 ATTATATTTAAAATATTTTATA
258549 TTAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.45
23 2 0.09
24 6 0.27
25 4 0.18
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTATATTTAAAATATTTTATA
Found at i:258549 original size:16 final size:16
Alignment explanation
Indices: 258524--258561 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
258514 AACATATTTT
*
258524 ATAATTATAT-TTAAA
1 ATAATTTTATATTAAA
258539 AT-ATTTTATATTAAA
1 ATAATTTTATATTAAA
258554 ATAATTTT
1 ATAATTTT
258562 TAAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 6 0.30
15 9 0.45
16 5 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATAATTTTATATTAAA
Found at i:258554 original size:15 final size:17
Alignment explanation
Indices: 258528--258561 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
258518 TATTTTATAA
258528 TTATATTTAAAAT-ATT
1 TTATATTTAAAATAATT
258544 TTATA-TTAAAATAATT
1 TTATATTTAAAATAATT
258560 TT
1 TT
258562 TAAATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATTTAAAATAATT
Found at i:258644 original size:18 final size:20
Alignment explanation
Indices: 258609--258648 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
258599 ATTAATTAAT
258609 TTATTTAATATTTATATTTTA
1 TTATTTAATA-TTATATTTTA
258630 TTATTTAATATTAT-TTTTA
1 TTATTTAATATTATATTTTA
258649 ATATAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 4 0.21
21 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTAATATTATATTTTA
Found at i:258760 original size:17 final size:16
Alignment explanation
Indices: 258738--258769 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
258728 TAAAATTTAT
258738 TTATTTAATGTTTTAAA
1 TTATTTAAT-TTTTAAA
258755 TTATTTAATTTTTAA
1 TTATTTAATTTTTAA
258770 TTTAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TTATTTAATTTTTAAA
Found at i:258831 original size:16 final size:15
Alignment explanation
Indices: 258804--258840 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
258794 ATTTTTTATA
258804 AATA-TTATTTAATT
1 AATATTTATTTAATT
258818 AATATTTATATTAATT
1 AATATTTAT-TTAATT
258834 AATATTT
1 AATATTT
258841 TCATATTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 4 0.19
15 4 0.19
16 13 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATATTTATTTAATT
Found at i:258834 original size:24 final size:23
Alignment explanation
Indices: 258778--258834 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
258768 AATTTAAAAA
* * *
258778 ATATAATTATTTATTTATTTTTT
1 ATATAATTATTTAATTAATATTT
*
258801 ATAAATATTATTTAATTAATATTT
1 ATATA-ATTATTTAATTAATATTT
258825 ATATTAATTA
1 ATA-TAATTA
258835 ATATTTTCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 4 0.15
24 22 0.81
25 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATATAATTATTTAATTAATATTT
Found at i:258921 original size:12 final size:12
Alignment explanation
Indices: 258906--258932 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
258896 ATTTTAAAAT
258906 AAAATTTAATTA
1 AAAATTTAATTA
258918 AAAATTTAATTA
1 AAAATTTAATTA
258930 AAA
1 AAA
258933 CATCGAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AAAATTTAATTA
Found at i:259191 original size:25 final size:25
Alignment explanation
Indices: 259163--259210 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
259153 TTTAATTTTT
*
259163 AAATTAAATTATTTTAGGTTTAATA
1 AAATTAAATTAATTTAGGTTTAATA
* *
259188 AAATTTAATTAATTTATGTTTAA
1 AAATTAAATTAATTTAGGTTTAA
259211 ATTATTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (25 bp):
AAATTAAATTAATTTAGGTTTAATA
Found at i:259603 original size:19 final size:19
Alignment explanation
Indices: 259575--259611 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
259565 AGTATTAAAT
* *
259575 ATAATTATTAATAAATTTA
1 ATAATCATTAAAAAATTTA
259594 ATAATCATTAAAAAATTT
1 ATAATCATTAAAAAATTT
259612 CGATTTTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAATCATTAAAAAATTTA
Found at i:260847 original size:21 final size:21
Alignment explanation
Indices: 260821--260863 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
260811 ATGATACTTT
*
260821 AAATATAAT-TATATTATATAA
1 AAATATAATATA-ATTACATAA
260842 AAATATAATATAATTACATAA
1 AAATATAATATAATTACATAA
260863 A
1 A
260864 TTGTTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AAATATAATATAATTACATAA
Found at i:273437 original size:17 final size:17
Alignment explanation
Indices: 273415--273450 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
273405 GTTGGATATC
273415 GCTTTTTAAGGATGGTT
1 GCTTTTTAAGGATGGTT
273432 GCTTTTTAAGGATGGTT
1 GCTTTTTAAGGATGGTT
273449 GC
1 GC
273451 ATAAATCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.08, G:0.31, T:0.44
Consensus pattern (17 bp):
GCTTTTTAAGGATGGTT
Found at i:279102 original size:2 final size:2
Alignment explanation
Indices: 279097--279128 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
279087 TGTGTGTGTG
279097 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
279129 CACACACATA
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:281362 original size:7 final size:7
Alignment explanation
Indices: 281326--281385 Score: 61
Period size: 7 Copynumber: 8.6 Consensus size: 7
281316 TTAAATTCTT
281326 AAATTTA
1 AAATTTA
*
281333 AAAGTTAA
1 AAA-TTTA
*
281341 AAATTAA
1 AAATTTA
281348 AAATTTTA
1 AAA-TTTA
281356 AAATTT-
1 AAATTTA
281362 AAATTT-
1 AAATTTA
281368 AAATTTA
1 AAATTTA
*
281375 AAATTTC
1 AAATTTA
281382 AAAT
1 AAAT
281386 GGAACCTAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
6 12 0.26
7 23 0.49
8 12 0.26
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (7 bp):
AAATTTA
Found at i:281385 original size:14 final size:15
Alignment explanation
Indices: 281326--281377 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
281316 TTAAATTCTT
*
281326 AAATTTAAAAGTTAA
1 AAATTTAAAAGTTTA
* *
281341 AAATTAAAAATTTTA
1 AAATTTAAAAGTTTA
281356 AAATTT-AAA-TTT-
1 AAATTTAAAAGTTTA
281368 AAATTTAAAA
1 AAATTTAAAA
281378 TTTCAAATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 6 0.19
13 6 0.19
14 3 0.09
15 17 0.53
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
AAATTTAAAAGTTTA
Found at i:284339 original size:20 final size:22
Alignment explanation
Indices: 284281--284341 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
284271 AAAAATAAAA
284281 AATTATAAA--TATTAATATTTT
1 AATTATAAATTTATTAA-ATTTT
*
284302 AATTTTAAATTTATTAAATTTT
1 AATTATAAATTTATTAAATTTT
*
284324 -ATTATAATTTTA-TAAATT
1 AATTATAAATTTATTAAATT
284342 AATTAGATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 6 0.17
21 18 0.51
22 5 0.14
23 6 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATTATAAATTTATTAAATTTT
Found at i:284512 original size:32 final size:32
Alignment explanation
Indices: 284450--284523 Score: 114
Period size: 31 Copynumber: 2.3 Consensus size: 32
284440 AAAAATGTTT
*
284450 TTATTTTAAATTTAATAATATTAAAATAAATA
1 TTATTTTTAATTTAATAATATTAAAATAAATA
*
284482 TT-TTTTTAATTTAATAATATTAAAGGTAAATA
1 TTATTTTTAATTTAATAATATTAAA-ATAAATA
284514 TTATTTTTAA
1 TTATTTTTAA
284524 ATTTTTTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
31 21 0.55
32 10 0.26
33 7 0.18
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (32 bp):
TTATTTTTAATTTAATAATATTAAAATAAATA
Found at i:285070 original size:24 final size:24
Alignment explanation
Indices: 285043--285089 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
285033 AATTAATTTT
*
285043 AAAAAATAGTGATTA-TTTTAAATA
1 AAAAAATA-TAATTATTTTTAAATA
*
285067 AAAATATATAATTATTTTTAAAT
1 AAAAAATATAATTATTTTTAAAT
285090 TTATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
AAAAAATATAATTATTTTTAAATA
Found at i:285122 original size:10 final size:11
Alignment explanation
Indices: 285104--285136 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
285094 ATTATTATTG
285104 ATATTTTTTAA
1 ATATTTTTTAA
285115 AT-TTTTTTAA
1 ATATTTTTTAA
285125 ATAATTTTTTAA
1 AT-ATTTTTTAA
285137 TTAAATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 2 0.10
12 8 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATATTTTTTAA
Found at i:285428 original size:2 final size:2
Alignment explanation
Indices: 285421--285470 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
285411 AAAGAAAATG
*
285421 AT AT AT AT AT AT AT GT AT AT AT -T AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
285461 AT AT -T AT AT A
1 AT AT AT AT AT A
285471 CCCACACACC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 3 0.07
2 40 0.93
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:285448 original size:19 final size:19
Alignment explanation
Indices: 285423--285470 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
285413 AGAAAATGAT
*
285423 ATATATATATATGTATATA
1 ATATATATATATATATATA
*
285442 TTATATATATATATATATA
1 ATATATATATATATATATA
285461 ATAT-TATATA
1 ATATATATATA
285471 CCCACACACC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 6 0.23
19 20 0.77
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
ATATATATATATATATATA
Found at i:288360 original size:21 final size:20
Alignment explanation
Indices: 288334--288373 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
288324 AAAAAATTAT
288334 TTTTAT-ATTAATATTTATATA
1 TTTTATAATTAA-A-TTATATA
288355 TTTTATAATTAAATTATAT
1 TTTTATAATTAAATTATAT
288374 TAATCAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTATAATTAAATTATATA
Found at i:292942 original size:36 final size:36
Alignment explanation
Indices: 292895--292966 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
292885 ATATCTGTAG
*
292895 CTTTCTTTCTTATATATTTTACCCTTTCATGGGCCA
1 CTTTCTTTCTTATATATTTTACCCTTTAATGGGCCA
* *
292931 CTTTCTTTCTTATATTTTTTACCTTTTAATGGGCCA
1 CTTTCTTTCTTATATATTTTACCCTTTAATGGGCCA
292967 TTGGAGATGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.17, C:0.22, G:0.08, T:0.53
Consensus pattern (36 bp):
CTTTCTTTCTTATATATTTTACCCTTTAATGGGCCA
Found at i:293045 original size:14 final size:13
Alignment explanation
Indices: 293025--293065 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
293015 TAAAAAAATT
293025 TAATTTTAAAAAA
1 TAATTTTAAAAAA
293038 TAAGTTTTATAAAAA
1 TAA-TTTTA-AAAAA
293053 -AA-TTTAAAAAA
1 TAATTTTAAAAAA
293064 TA
1 TA
293066 GATCAGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
11 5 0.20
12 5 0.20
13 3 0.12
14 7 0.28
15 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (13 bp):
TAATTTTAAAAAA
Found at i:293258 original size:13 final size:13
Alignment explanation
Indices: 293226--293272 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
293216 TTATTACGGA
*
293226 TATAATAAATATT
1 TATAATAAATAAT
*
293239 TAT-ATAATTAAT
1 TATAATAAATAAT
293251 TATAATAAAT-AT
1 TATAATAAATAAT
293263 TAATAATAAA
1 T-ATAATAAA
293273 AAAAATTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 13 0.45
13 16 0.55
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TATAATAAATAAT
Found at i:297165 original size:17 final size:18
Alignment explanation
Indices: 297143--297177 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
297133 TTAGATATAG
297143 TATTTTT-TTTTTATTTT
1 TATTTTTCTTTTTATTTT
*
297160 TATTTTTCTTTTTCTTTT
1 TATTTTTCTTTTTATTTT
297178 AAAAAAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.86
Consensus pattern (18 bp):
TATTTTTCTTTTTATTTT
Found at i:297719 original size:2 final size:2
Alignment explanation
Indices: 297714--297738 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
297704 AAAAAATAGT
297714 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
297739 GAGAGTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:301187 original size:34 final size:34
Alignment explanation
Indices: 301141--301325 Score: 248
Period size: 34 Copynumber: 5.5 Consensus size: 34
301131 GTAAAAACCA
*
301141 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
301175 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
301209 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
301243 CTATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
301277 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
301310 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
301326 TCTCCCACTT
Statistics
Matches: 133, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
33 18 0.14
34 111 0.83
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:305473 original size:19 final size:19
Alignment explanation
Indices: 305399--305473 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
305389 ACAGTAACCG
* **
305399 TATACTTGAATAGTACCCG
1 TATACGTGAATAGTACCTA
305418 TATACGTGAATAGTACCTA
1 TATACGTGAATAGTACCTA
305437 TATACGTGAATAGTACCTA
1 TATACGTGAATAGTACCTA
305456 TATACGTGAATAGTACCT
1 TATACGTGAATAGTACCT
305474 CGACAACCAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 53 1.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (19 bp):
TATACGTGAATAGTACCTA
Found at i:305823 original size:34 final size:34
Alignment explanation
Indices: 305777--305959 Score: 237
Period size: 34 Copynumber: 5.4 Consensus size: 34
305767 GTAAAAACCA
*
305777 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
305811 CCATTTAGTCAACAATGGTAAACC-ACCAAAT-TAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCT-C
* *
305845 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
305879 CTATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
305913 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
305946 CCATTTAATCAACA
1 CCATTTAATCAACA
305960 GTTAGGTGGA
Statistics
Matches: 131, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
33 17 0.13
34 109 0.83
35 5 0.04
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.27
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:306246 original size:7 final size:7
Alignment explanation
Indices: 306236--306269 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
306226 AATATTTAAT
306236 AAATTTA
1 AAATTTA
306243 AAATTTA
1 AAATTTA
306250 AAATTTA
1 AAATTTA
*
306257 ATATTTA
1 AAATTTA
*
306264 TAATTT
1 AAATTT
306270 TTTTATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (7 bp):
AAATTTA
Found at i:306246 original size:23 final size:23
Alignment explanation
Indices: 306215--306259 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
306205 ATTTATTTAT
* *
306215 ATTTGAAATATAATATTTAATAA
1 ATTTAAAATATAAAATTTAATAA
*
306238 ATTTAAAATTTAAAATTTAATA
1 ATTTAAAATATAAAATTTAATA
306260 TTTATAATTT
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:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
ATTTAAAATATAAAATTTAATAA
Found at i:308566 original size:27 final size:28
Alignment explanation
Indices: 308506--308588 Score: 84
Period size: 27 Copynumber: 3.0 Consensus size: 28
308496 TCTAATTCAA
* *
308506 ATTA-TTATTTGATAATAAAAATATTTT
1 ATTATTTATTTAATTATAAAAATATTTT
308533 -TTATTTAATTTAATTA-AAAAATATTTT
1 ATTATTT-ATTTAATTATAAAAATATTTT
* *
308560 ATT-TTTATTTATTTATAAATAATAATTT
1 ATTATTTATTTAATTATAAA-AATATTTT
308588 A
1 A
308589 AACTTTCGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
26 11 0.23
27 19 0.40
28 17 0.36
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (28 bp):
ATTATTTATTTAATTATAAAAATATTTT
Found at i:308951 original size:33 final size:32
Alignment explanation
Indices: 308914--308983 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
308904 AATAATATAA
308914 ATATAATATAAATTTACGAAGATATTAAAATTT
1 ATATAATATAAA-TTACGAAGATATTAAAATTT
** *
308947 ATATAATATAAATTATTAATATATTAAAATTT
1 ATATAATATAAATTACGAAGATATTAAAATTT
*
308979 TTATA
1 ATATA
308984 TAAATATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 21 0.64
33 12 0.36
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (32 bp):
ATATAATATAAATTACGAAGATATTAAAATTT
Found at i:308955 original size:17 final size:17
Alignment explanation
Indices: 308935--308983 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 17
308925 ATTTACGAAG
308935 ATATTAAAATTTATATA
1 ATATTAAAATTTATATA
*
308952 ATA-TAAATTATTA-AT-
1 ATATTAAAAT-TTATATA
*
308967 ATATTAAAATTTTTATA
1 ATATTAAAATTTATATA
308984 TAAATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
15 5 0.20
16 14 0.56
17 6 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATTAAAATTTATATA
Found at i:311828 original size:25 final size:25
Alignment explanation
Indices: 311789--311838 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
311779 AAAGAATTTT
*
311789 AATTTGAGTTCAAATACAATAATCA
1 AATTTGAGTTCAAATACAAAAATCA
*
311814 AATTTGAAGTT-AAATATAAAAATCA
1 AATTTG-AGTTCAAATACAAAAATCA
311839 GACCTAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (25 bp):
AATTTGAGTTCAAATACAAAAATCA
Found at i:320606 original size:2 final size:2
Alignment explanation
Indices: 320599--320636 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
320589 TATTAAATTT
320599 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
320637 CATTGTGGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:321095 original size:2 final size:2
Alignment explanation
Indices: 321088--321121 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
321078 TGCTTCTTCT
321088 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
321122 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:322363 original size:22 final size:23
Alignment explanation
Indices: 322330--322379 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
322320 CACTTCTCAT
*
322330 GCTTTTTCTTTT-TTGCTTTTTAA
1 GCTTTTTCTTTTCTT-CTTCTTAA
322353 GCTTTTT-TTTTCTTCTTCTTAA
1 GCTTTTTCTTTTCTTCTTCTTAA
322375 G-TTTT
1 GCTTTT
322380 ATTATTTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 4 0.16
22 12 0.48
23 9 0.36
ACGTcount: A:0.08, C:0.14, G:0.08, T:0.70
Consensus pattern (23 bp):
GCTTTTTCTTTTCTTCTTCTTAA
Found at i:323078 original size:16 final size:16
Alignment explanation
Indices: 323059--323125 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 16
323049 TTTTAAGTCT
*
323059 TTTTTGGTTCAAGTTA
1 TTTTCGGTTCAAGTTA
* * * *
323075 TTTTTGTTTCAAATCA
1 TTTTCGGTTCAAGTTA
*
323091 --TTCGGATTCAAGCTA
1 TTTTCGG-TTCAAGTTA
323106 TTTTCGGTTCAAGTTA
1 TTTTCGGTTCAAGTTA
323122 TTTT
1 TTTT
323126 AGTTTTGATT
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
14 3 0.08
15 6 0.15
16 25 0.64
17 5 0.13
ACGTcount: A:0.21, C:0.12, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTTCGGTTCAAGTTA
Found at i:323366 original size:16 final size:16
Alignment explanation
Indices: 323328--323366 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
323318 TTATTATCTC
*
323328 AGTCAATTCAGGTTAA
1 AGTCATTTCAGGTTAA
* *
323344 AGCCATTTCAGGTTTA
1 AGTCATTTCAGGTTAA
323360 AGTCATT
1 AGTCATT
323367 CTAGATTTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (16 bp):
AGTCATTTCAGGTTAA
Found at i:323768 original size:17 final size:17
Alignment explanation
Indices: 323746--323810 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 17
323736 ACCCATATAT
323746 TATTAAAATATTAATTA
1 TATTAAAATATTAATTA
* *
323763 TATTAATAT-TTAA-AA
1 TATTAAAATATTAATTA
323778 TATTATCATAATA-TAATTA
1 TATTA--A-AATATTAATTA
323797 TTATTAAAATATTA
1 -TATTAAAATATTA
323811 TTTTATATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
15 6 0.16
16 4 0.11
17 13 0.35
18 8 0.22
19 1 0.03
20 5 0.14
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTAAAATATTAATTA
Found at i:323908 original size:28 final size:29
Alignment explanation
Indices: 323877--323932 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
323867 TATGAAAAAC
*
323877 TATTTATAGTT-AAACTAATAAT-TTTTAA
1 TATTAATAGTTCAAA-TAATAATATTTTAA
*
323905 TATTAATATTTCAAATAATAATATTTTA
1 TATTAATAGTTCAAATAATAATATTTTA
323933 GTGATAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (29 bp):
TATTAATAGTTCAAATAATAATATTTTAA
Found at i:323915 original size:15 final size:15
Alignment explanation
Indices: 323886--323932 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
323876 CTATTTATAG
323886 TTAAACTAATAAT-TT
1 TTAAA-TAATAATATT
*
323901 TT-AATATTAATATT
1 TTAAATAATAATATT
*
323915 TCAAATAATAATATT
1 TTAAATAATAATATT
323930 TTA
1 TTA
323933 GTGATAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 6 0.23
14 5 0.19
15 15 0.58
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (15 bp):
TTAAATAATAATATT
Found at i:324943 original size:18 final size:18
Alignment explanation
Indices: 324920--324980 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
324910 GTTATTATTT
324920 AAAATTTTTATTTAGTTA
1 AAAATTTTTATTTAGTTA
*
324938 AAAATTATTA-TT--TT-
1 AAAATTTTTATTTAGTTA
324952 -AAATTTTTATTTAGTTA
1 AAAATTTTTATTTAGTTA
*
324969 CAAATTATTTAT
1 AAAATT-TTTAT
324981 AATTTATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
13 8 0.23
14 2 0.06
15 2 0.06
16 2 0.06
17 2 0.06
18 14 0.40
19 5 0.14
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (18 bp):
AAAATTTTTATTTAGTTA
Found at i:324948 original size:31 final size:31
Alignment explanation
Indices: 324911--324977 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
324901 TCAGCTTATG
324911 TTATTATTTAAAATTTTTATTTAGTTAAAAA
1 TTATTATTTAAAATTTTTATTTAGTTAAAAA
* *
324942 TTATTATTTTAAATTTTTATTTAGTTACAAA
1 TTATTATTTAAAATTTTTATTTAGTTAAAAA
324973 TTATT
1 TTATT
324978 TATAATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58
Consensus pattern (31 bp):
TTATTATTTAAAATTTTTATTTAGTTAAAAA
Found at i:324984 original size:28 final size:28
Alignment explanation
Indices: 324913--324985 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 28
324903 AGCTTATGTT
*
324913 ATTATTTAAAATTTTTATTTAGTTAAAA
1 ATTATTTATAATTTTTATTTAGTTAAAA
* *
324941 ATTATTATTTTAAATTTTTATTTAGTTACAA
1 ATTA-T-TTAT-AATTTTTATTTAGTTAAAA
324972 ATTATTTATAATTT
1 ATTATTTATAATTT
324986 ATAAAGCAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
28 9 0.24
29 4 0.11
30 3 0.08
31 22 0.58
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (28 bp):
ATTATTTATAATTTTTATTTAGTTAAAA
Found at i:328841 original size:60 final size:60
Alignment explanation
Indices: 328767--328885 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 60
328757 TAATGAAAAA
*
328767 TTTTACTGTAAATTTTATCAGATGTGACTTTTCGAAGGTTCTTTCTAATCATATTGAGAC
1 TTTTACTGTAAATTTTATCAGATATGACTTTTCGAAGGTTCTTTCTAATCATATTGAGAC
* *
328827 TTTTATTGTAAATTTTATTAGATATGACTTTTCGAAGGTTCTTTCTAATCATATTGAGA
1 TTTTACTGTAAATTTTATCAGATATGACTTTTCGAAGGTTCTTTCTAATCATATTGAGA
328886 TTAGATTCAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (60 bp):
TTTTACTGTAAATTTTATCAGATATGACTTTTCGAAGGTTCTTTCTAATCATATTGAGAC
Found at i:331586 original size:2 final size:2
Alignment explanation
Indices: 331579--331614 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
331569 CACTTGGTAC
331579 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
331615 GTATGAAGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:331878 original size:21 final size:23
Alignment explanation
Indices: 331831--331894 Score: 71
Period size: 26 Copynumber: 2.7 Consensus size: 23
331821 TTGAATTATT
331831 ATTTAATTATAAAATATTTGATTTAA
1 ATTTAATTATAAAATA--TGA-TTAA
331857 ATTTAATTATAAAATAT-A-TAA
1 ATTTAATTATAAAATATGATTAA
331878 ATATTAA-TATAAAATAT
1 AT-TTAATTATAAAATAT
331895 TTTTTAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
21 15 0.41
22 4 0.11
23 1 0.03
24 1 0.03
26 16 0.43
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTTAATTATAAAATATGATTAA
Found at i:333238 original size:20 final size:20
Alignment explanation
Indices: 333205--333339 Score: 85
Period size: 19 Copynumber: 6.8 Consensus size: 20
333195 CGTAAAATGC
333205 TTAAATATTAATATAATAATT
1 TTAAATA-TAATATAATAATT
333226 TTAAATAT-A-AT-ATAATT
1 TTAAATATAATATAATAATT
*
333243 TTAAATATAATATAATTTTATT
1 TTAAATATAATATAA--TAATT
*
333265 ATATAAAAATAATAT-A-AATAT
1 -T-TAAATATAATATAATAAT-T
*
333286 ATAAATAT-AT-TAA-AATT
1 TTAAATATAATATAATAATT
333303 TATATAAT-T-ATATAAT-ATT
1 T-TA-AATATAATATAATAATT
333322 TTAAATATAATTATAATA
1 TTAAATATAA-TATAATA
333340 TAAATATATA
Statistics
Matches: 91, Mismatches: 6, Indels: 34
0.69 0.05 0.26
Matches are distributed among these distances:
17 19 0.21
18 17 0.19
19 20 0.22
20 10 0.11
21 8 0.09
22 4 0.04
23 2 0.02
24 11 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAAATATAATATAATAATT
Found at i:333340 original size:20 final size:19
Alignment explanation
Indices: 333205--333340 Score: 97
Period size: 17 Copynumber: 6.9 Consensus size: 19
333195 CGTAAAATGC
333205 TTAAATATTAATATAATAATT
1 TTAAATA-TAATATAAT-ATT
333226 TTAAATATAATAT-A-ATT
1 TTAAATATAATATAATATT
333243 TTAAATATAATATAATTTTATT
1 TTAAATATAATATAA---TATT
*
333265 ATATAAAAATAATATAA-ATAT
1 -T-TAAATATAATATAATAT-T
* *
333286 ATAAATAT-AT-TAAAATT
1 TTAAATATAATATAATATT
333303 TATATAAT-T-ATATAATATT
1 T-TA-AATATAATATAATATT
333322 TTAAATATAATTATAATAT
1 TTAAATATAA-TATAATAT
333341 AAATATATAT
Statistics
Matches: 95, Mismatches: 5, Indels: 31
0.73 0.04 0.24
Matches are distributed among these distances:
17 23 0.24
18 13 0.14
19 18 0.19
20 16 0.17
21 8 0.08
22 3 0.03
23 1 0.01
24 13 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAAATATAATATAATATT
Found at i:333862 original size:15 final size:15
Alignment explanation
Indices: 333844--333874 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
333834 TAATATTTAA
*
333844 AAATAATTTTAAATT
1 AAATAATATTAAATT
333859 AAATAATATTAAATT
1 AAATAATATTAAATT
333874 A
1 A
333875 TAATTACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATAATATTAAATT
Found at i:333994 original size:19 final size:19
Alignment explanation
Indices: 333967--334010 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
333957 AATTTACGAT
333967 AATTATTAAGATTAA-ATATA
1 AATT-TTAA-ATTAATATATA
*
333987 AATTTTAAATTAATTTATA
1 AATTTTAAATTAATATATA
334006 AATTT
1 AATTT
334011 ACATATGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 5 0.23
19 13 0.59
20 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
AATTTTAAATTAATATATA
Found at i:334055 original size:15 final size:16
Alignment explanation
Indices: 334030--334059 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
334020 CCAATTATTT
334030 TAAAAATTTAAAAAGA
1 TAAAAATTTAAAAAGA
334046 TAAAAA-TTAAAAAG
1 TAAAAATTTAAAAAG
334060 TTTCAAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (16 bp):
TAAAAATTTAAAAAGA
Found at i:334673 original size:27 final size:25
Alignment explanation
Indices: 334639--334690 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
334629 AATAGATTAT
334639 TAAAATAAAAATTTTAT-ATAAATTTA
1 TAAAAT-AAAATTTTATAAT-AATTTA
*
334665 TAAAGATAAATTTTTATAATAATTTA
1 TAAA-ATAAAATTTTATAATAATTTA
334691 AATATACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
TAAAATAAAATTTTATAATAATTTA
Found at i:335340 original size:11 final size:11
Alignment explanation
Indices: 335304--335342 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
335294 TTTAAAAATA
335304 AAATTTA-ATT
1 AAATTTATATT
335314 AAAATTTATATT
1 -AAATTTATATT
335326 AAATTTATATT
1 AAATTTATATT
335337 AAATTT
1 AAATTT
335343 TGAGAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 24 0.89
12 3 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
AAATTTATATT
Found at i:340870 original size:356 final size:357
Alignment explanation
Indices: 340215--340926 Score: 1408
Period size: 356 Copynumber: 2.0 Consensus size: 357
340205 TGAGCTACTG
340215 GTTTATTTGGGTCATTTGCTAAATGTTTCTTGAAGCTGTAAAGATTAGTTAAGTGGCGAGTCAAA
1 GTTTATTTGGGTCATTTGCTAAATGTTTCTTGAAGCTGTAAAGATTAGTTAAGTGGCGAGTCAAA
340280 TGTGTTCGTAAAGATATGAAATTATTAGAGCATAAATGGTTTTGTGGATAACAGTATTTGTATGA
66 TGTGTTCGTAAAGATATGAAATTATTAGAGCATAAATGGTTTTGTGGATAACAGTATTTGTATGA
340345 TTTACATGTCAAAAAAAAAAAAAAAAAGTTAAACCACTTCTATAATATAAAAGAATTTTGTTGAA
131 TTTACATGTC-AAAAAAAAAAAAAAAAGTTAAACCACTTCTATAATATAAAAGAATTTTGTTGAA
340410 TTGGTTCAATTCTCCTGTTTCTAGTAAGGTGCTTTTTTTGGTAATGAAATTTTGAATTGCCTGTC
195 TTGGTTCAATTCTCCTGTTTCTAGTAAGGTGCTTTTTTTGGTAATGAAATTTTGAATTGCCTGTC
340475 ATGCGAGCCACCATCTTTTCAACCAATGTTCTTCCTTCCACATTTCTGTTGTTTGACTATTTTAT
260 ATGCGAGCCACCATCTTTTCAACCAATGTTCTTCCTTCCACATTTCTGTTGTTTGACTATTTTAT
340540 TTGCATTCTAGCTGATGATTAGGGGGTAATAAA
325 TTGCATTCTAGCTGATGATTAGGGGGTAATAAA
340573 GTTTATTTGGGTCATTTGCTAAATGTTTCTTGAAGCTGTAAAGATTAGTTAAGTGGCGAGTCAAA
1 GTTTATTTGGGTCATTTGCTAAATGTTTCTTGAAGCTGTAAAGATTAGTTAAGTGGCGAGTCAAA
340638 TGTGTTCGTAAAGATATGAAATTATTAGAGCATAAATGGTTTTGTGGATAACAGTATTTGTATGA
66 TGTGTTCGTAAAGATATGAAATTATTAGAGCATAAATGGTTTTGTGGATAACAGTATTTGTATGA
340703 TTTACATGTC-AAAAAAAAAAAAAAAGTTAAACCACTTCTATAATATAAAAGAATTTTGTTGAAT
131 TTTACATGTCAAAAAAAAAAAAAAAAGTTAAACCACTTCTATAATATAAAAGAATTTTGTTGAAT
340767 TGGTTCAATTCTCCTGTTTCTAGTAAGGTGCTTTTTTTGGTAATGAAATTTTGAATTGCCTGTCA
196 TGGTTCAATTCTCCTGTTTCTAGTAAGGTGCTTTTTTTGGTAATGAAATTTTGAATTGCCTGTCA
340832 TGCGAGCCACCATCTTTTCAACCAATGTTCTTCCTTCCACATTTCTGTTGTTTGACTATTTTATT
261 TGCGAGCCACCATCTTTTCAACCAATGTTCTTCCTTCCACATTTCTGTTGTTTGACTATTTTATT
340897 TGCATTCTAGCTGATGATTAGGGGGTAATA
326 TGCATTCTAGCTGATGATTAGGGGGTAATA
340927 TGAAAGACTG
Statistics
Matches: 354, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
356 214 0.60
358 140 0.40
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (357 bp):
GTTTATTTGGGTCATTTGCTAAATGTTTCTTGAAGCTGTAAAGATTAGTTAAGTGGCGAGTCAAA
TGTGTTCGTAAAGATATGAAATTATTAGAGCATAAATGGTTTTGTGGATAACAGTATTTGTATGA
TTTACATGTCAAAAAAAAAAAAAAAAGTTAAACCACTTCTATAATATAAAAGAATTTTGTTGAAT
TGGTTCAATTCTCCTGTTTCTAGTAAGGTGCTTTTTTTGGTAATGAAATTTTGAATTGCCTGTCA
TGCGAGCCACCATCTTTTCAACCAATGTTCTTCCTTCCACATTTCTGTTGTTTGACTATTTTATT
TGCATTCTAGCTGATGATTAGGGGGTAATAAA
Found at i:344090 original size:2 final size:2
Alignment explanation
Indices: 344083--344113 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
344073 ATGGTGCTGT
*
344083 TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
344114 CTAAAATCAT
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):
TA
Found at i:346202 original size:14 final size:14
Alignment explanation
Indices: 346183--346215 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
346173 TTCGAAAAAA
346183 AAAATATAAATATT
1 AAAATATAAATATT
*
346197 AAAATATAAATTTT
1 AAAATATAAATATT
346211 AAAAT
1 AAAAT
346216 TTATTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAATATAAATATT
Found at i:347182 original size:2 final size:2
Alignment explanation
Indices: 347175--347208 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
347165 ACCACCTTTC
347175 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
347209 AGATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:349010 original size:21 final size:23
Alignment explanation
Indices: 348970--349011 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
348960 TTACTCATTT
348970 TTATTACTTTTAATAATTTATCA
1 TTATTACTTTTAATAATTTATCA
348993 TTATTA-TTTTAA-AATTTAT
1 TTATTACTTTTAATAATTTAT
349012 ATTTGATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 6 0.32
23 6 0.32
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (23 bp):
TTATTACTTTTAATAATTTATCA
Found at i:349528 original size:2 final size:2
Alignment explanation
Indices: 349516--349549 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
349506 TCATATAATT
* *
349516 TA TA CA TA TA TA TA TA TA CA 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
349550 ATTAAAAGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:349535 original size:14 final size:14
Alignment explanation
Indices: 349507--349547 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
349497 GTAACCTTTT
*
349507 CATATA-ATTTATA
1 CATATATATATATA
349520 CATATATATATATA
1 CATATATATATATA
349534 CATATATATATATA
1 CATATATATATATA
349548 TAATTAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 6 0.23
14 20 0.77
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (14 bp):
CATATATATATATA
Found at i:350999 original size:18 final size:18
Alignment explanation
Indices: 350976--351012 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
350966 TCAAATTTAA
*
350976 TAAATTCAATGTTATTCG
1 TAAATTCAAAGTTATTCG
*
350994 TAAATTTAAAGTTATTCG
1 TAAATTCAAAGTTATTCG
351012 T
1 T
351013 GTGTTGGATT
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:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (18 bp):
TAAATTCAAAGTTATTCG
Found at i:353719 original size:2 final size:2
Alignment explanation
Indices: 353712--353741 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
353702 ACATATTACC
353712 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
353742 TAGGAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:355074 original size:2 final size:2
Alignment explanation
Indices: 355067--355099 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
355057 AAAGAATGAA
*
355067 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
355100 CGATGTAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:355271 original size:20 final size:20
Alignment explanation
Indices: 355246--355284 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
355236 GGCTCCATTT
355246 TCCCTCTCAAGTATCCCTCA
1 TCCCTCTCAAGTATCCCTCA
**
355266 TCCCTCTCTTGTATCCCTC
1 TCCCTCTCAAGTATCCCTC
355285 TTCAATTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.46, G:0.05, T:0.36
Consensus pattern (20 bp):
TCCCTCTCAAGTATCCCTCA
Found at i:359697 original size:27 final size:27
Alignment explanation
Indices: 359663--359733 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
359653 GCCACCCATT
359663 TGTTTGTCAAAAATGGTGGTTAT-TTTG
1 TGTTTGTCAAAAATGGTGGTT-TCTTTG
*
359690 TGTTTGTCAAAAATAGTGGTTTCCTTTG
1 TGTTTGTCAAAAATGGTGGTTT-CTTTG
* *
359718 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
359734 AGGCTTGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTTCTTTG
Found at i:361713 original size:5 final size:5
Alignment explanation
Indices: 361679--361724 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
361669 TTTTAAAATT
*
361679 TATAA TAT-A T-TGA TATATA TATATA TATAA TATAA TATAA TATAA T
1 TATAA TATAA TATAA TATA-A TATA-A TATAA TATAA TATAA TATAA T
361725 TAAAAATATC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
3 1 0.03
4 4 0.11
5 21 0.57
6 11 0.30
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (5 bp):
TATAA
Found at i:365262 original size:2 final size:2
Alignment explanation
Indices: 365255--365280 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
365245 TATGTCTGCA
365255 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
365281 GTTGAAACAA
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:375464 original size:19 final size:19
Alignment explanation
Indices: 375440--375485 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
375430 ACAAAAAAGT
*
375440 AACAAACGTCAAATAGACC
1 AACAAACATCAAATAGACC
375459 AACAAACATCAAATAGACC
1 AACAAACATCAAATAGACC
*
375478 AAAAAACA
1 AACAAACA
375486 ACCTATTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.61, C:0.24, G:0.07, T:0.09
Consensus pattern (19 bp):
AACAAACATCAAATAGACC
Found at i:377296 original size:2 final size:2
Alignment explanation
Indices: 377289--377353 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
377279 AGTAAACAAA
377289 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
377331 TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
377354 GCATTTATTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:380027 original size:20 final size:20
Alignment explanation
Indices: 380004--380043 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
379994 GAATTACATT
380004 TCCGACCATAGTTTGTCATA
1 TCCGACCATAGTTTGTCATA
380024 TCCGACCATAGTTTGTCATA
1 TCCGACCATAGTTTGTCATA
380044 GTTGAGCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (20 bp):
TCCGACCATAGTTTGTCATA
Found at i:383720 original size:20 final size:20
Alignment explanation
Indices: 383695--383736 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
383685 TGAACACATA
383695 ATCAGAAGATTAGACCAGAG
1 ATCAGAAGATTAGACCAGAG
383715 ATCAGAAGATTAGACCAGAG
1 ATCAGAAGATTAGACCAGAG
383735 AT
1 AT
383737 AGACAACAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.24, T:0.17
Consensus pattern (20 bp):
ATCAGAAGATTAGACCAGAG
Found at i:387354 original size:19 final size:20
Alignment explanation
Indices: 387330--387377 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
387320 AGTTTATAAA
387330 TTTAATTGA-ATTTTT-TATT
1 TTTAATT-ATATTTTTATATT
*
387349 TTTAATATATATTTTTATTTT
1 TTTAAT-TATATTTTTATATT
387370 TTTAATTA
1 TTTAATTA
387378 ATAATGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 7 0.28
20 9 0.36
21 9 0.36
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTAATTATATTTTTATATT
Found at i:387548 original size:42 final size:41
Alignment explanation
Indices: 387467--387550 Score: 98
Period size: 43 Copynumber: 2.0 Consensus size: 41
387457 TTTATTAAGT
* * **
387467 AAATAAATTTAATTAATTTAACTTTTATTTCAAATTTATAA
1 AAATAAATTTAATAAATTTAAATTAAATTTCAAATTTATAA
*
387508 AAATAAATTTTAATCAAATTTAAATTAAATTTTAAA-TTATAA
1 AAATAAA-TTTAAT-AAATTTAAATTAAATTTCAAATTTATAA
387550 A
1 A
387551 TTTCTATTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
41 7 0.19
42 13 0.36
43 16 0.44
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (41 bp):
AAATAAATTTAATAAATTTAAATTAAATTTCAAATTTATAA
Found at i:392008 original size:20 final size:21
Alignment explanation
Indices: 391983--392022 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
391973 TAGGATTATA
391983 AAAATATAACATAAA-ATATT
1 AAAATATAACATAAATATATT
392003 AAAATATAACATAAATATAT
1 AAAATATAACATAAATATAT
392023 AAATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAATATAACATAAATATATT
Found at i:392025 original size:20 final size:20
Alignment explanation
Indices: 391979--392025 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
391969 TAAATAGGAT
391979 TATA-AAAATATAACATAAA
1 TATATAAAATATAACATAAA
391998 -ATATTAAAATATAACATAAA
1 TATA-TAAAATATAACATAAA
392018 TATATAAA
1 TATATAAA
392026 TATTTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.12
20 19 0.76
21 3 0.12
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (20 bp):
TATATAAAATATAACATAAA
Found at i:392138 original size:8 final size:8
Alignment explanation
Indices: 392127--392249 Score: 55
Period size: 8 Copynumber: 15.1 Consensus size: 8
392117 CATAAATATA
392127 ATATAAAT
1 ATATAAAT
392135 ATATAAAT
1 ATATAAAT
*
392143 -TATTAGAT
1 ATA-TAAAT
392151 ATATCAAAATTT
1 ATAT--AAA--T
392163 ATATAAAT
1 ATATAAAT
392171 ATA-AATAT
1 ATATAA-AT
*
392179 ATATTACAT
1 ATA-TAAAT
392188 A-ATAAAAT
1 ATAT-AAAT
392196 ATATAAAT
1 ATATAAAT
*
392204 ATA-ATAT
1 ATATAAAT
*
392211 AAATAAAT
1 ATATAAAT
*
392219 A-AT-TAT
1 ATATAAAT
392225 ATAATAAAAT
1 AT-AT-AAAT
392235 ATATAAA-
1 ATATAAAT
392242 A-ATAAAT
1 ATATAAAT
392249 A
1 A
392250 ATTATAATAT
Statistics
Matches: 89, Mismatches: 9, Indels: 35
0.67 0.07 0.26
Matches are distributed among these distances:
6 8 0.09
7 14 0.16
8 43 0.48
9 9 0.10
10 10 0.11
12 5 0.06
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.37
Consensus pattern (8 bp):
ATATAAAT
Found at i:392204 original size:33 final size:33
Alignment explanation
Indices: 392162--392267 Score: 115
Period size: 33 Copynumber: 3.0 Consensus size: 33
392152 TATCAAAATT
*
392162 TATATAAATATAAATATATATTACATAATAAAA
1 TATATAAATATAAATATATATTATATAATAAAA
392195 TATATAAATATAATATAAATAAATAATTATATAATAAAA
1 TATATAAATATAA-AT--AT--AT-ATTATATAATAAAA
* *
392234 TATATAAAAATAAATA-ATTATAATATAATAAAA
1 TATATAAATATAAATATA-TATTATATAATAAAA
392267 T
1 T
392268 GTATGCATAG
Statistics
Matches: 63, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
33 28 0.44
34 3 0.05
36 3 0.05
38 4 0.06
39 25 0.40
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (33 bp):
TATATAAATATAAATATATATTATATAATAAAA
Found at i:392207 original size:18 final size:18
Alignment explanation
Indices: 392109--392267 Score: 101
Period size: 19 Copynumber: 8.4 Consensus size: 18
392099 TTATGATTCG
*
392109 ATAAAATACATAAATATA
1 ATAAAATATATAAATATA
392127 ATATAAATATATAAAT-TA
1 ATA-AAATATATAAATATA
* * *
392145 TTAGATATATCAAAATTTATATAA
1 ATA-AAATAT-ATAA---ATAT-A
* *
392169 ATATAAATATATATTACATA
1 ATA-AAATATATA-AATATA
392189 ATAAAATATATAAATATA
1 ATAAAATATATAAATATA
*
392207 ATATAAATAAATAATTATATA
1 ATA-AAATATATAA--ATATA
*
392228 ATAAAATATATAAAAATA
1 ATAAAATATATAAATATA
*
392246 A-ATAAT-TAT-AATATA
1 ATAAAATATATAAATATA
392261 ATAAAAT
1 ATAAAAT
392268 GTATGCATAG
Statistics
Matches: 110, Mismatches: 19, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
15 6 0.05
16 7 0.06
17 4 0.04
18 24 0.22
19 32 0.29
20 13 0.12
21 11 0.10
22 2 0.02
23 3 0.03
24 8 0.07
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.36
Consensus pattern (18 bp):
ATAAAATATATAAATATA
Found at i:392261 original size:15 final size:15
Alignment explanation
Indices: 392196--392261 Score: 50
Period size: 15 Copynumber: 4.4 Consensus size: 15
392186 ATAATAAAAT
*
392196 ATATAAATATAATATA
1 ATATAAATA-ATTATA
392212 A-ATAAATAATTAT-
1 ATATAAATAATTATA
392225 ATA-ATAA-AATATATAA
1 ATATA-AATAAT-TAT-A
*
392241 AAATAAATAATTATA
1 ATATAAATAATTATA
392256 ATATAA
1 ATATAA
392262 TAAAATGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 15
0.69 0.05 0.26
Matches are distributed among these distances:
13 5 0.12
14 10 0.25
15 13 0.32
16 8 0.20
17 4 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATAAATAATTATA
Found at i:400001 original size:1 final size:1
Alignment explanation
Indices: 399957--399987 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
399947 GTAGCATTGT
*
399957 GGGGGGGGGGGGGGGGGGGGGGGGGGTGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
399988 TTTGAGGGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.97, T:0.03
Consensus pattern (1 bp):
G
Found at i:400760 original size:25 final size:28
Alignment explanation
Indices: 400717--400768 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
400707 TTAATATATA
*
400717 TTTAAATATAAGTATAAAAT-ATAATTT
1 TTTAAATATAAGTAAAAAATAATAATTT
400744 TTTAAATAT-A-TAAAAAATAATAATT
1 TTTAAATATAAGTAAAAAATAATAATT
400769 ATATTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.30
26 7 0.30
27 9 0.39
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (28 bp):
TTTAAATATAAGTAAAAAATAATAATTT
Found at i:402714 original size:22 final size:22
Alignment explanation
Indices: 402684--402734 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
402674 TAAAAATATT
402684 TTAAAATATTTT-TATATTAATA
1 TTAAAATATTTTATA-ATTAATA
*
402706 TTAATATATTTTATAATTAA-A
1 TTAAAATATTTTATAATTAATA
*
402727 TTTAAATA
1 TTAAAATA
402735 AAAATATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 7 0.28
22 16 0.64
23 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAAAATATTTTATAATTAATA
Found at i:404151 original size:59 final size:59
Alignment explanation
Indices: 404059--404178 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
404049 TCAGTCATTG
404059 TTCATAATCCGTAAAAGGCCTGAGACTACTTAAGATTACCTAACATTACAAGTTTTGCC
1 TTCATAATCCGTAAAAGGCCTGAGACTACTTAAGATTACCTAACATTACAAGTTTTGCC
404118 TTCATAATCCGTAAAAGGCCTGAGACTACTTAAGATTACCTAACATTACAAGTTTTGCC
1 TTCATAATCCGTAAAAGGCCTGAGACTACTTAAGATTACCTAACATTACAAGTTTTGCC
404177 TT
1 TT
404179 AATATCTTTG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (59 bp):
TTCATAATCCGTAAAAGGCCTGAGACTACTTAAGATTACCTAACATTACAAGTTTTGCC
Found at i:404571 original size:55 final size:56
Alignment explanation
Indices: 404503--404616 Score: 167
Period size: 55 Copynumber: 2.0 Consensus size: 56
404493 TATTGCAACA
* * *
404503 ATCTTCATATTTGTAACTTGTACAGTGT-AACAAATTAGCATAATGGCAATATACT
1 ATCTTCATATTTGTAACTTGTACAGTGTAAAAAAATTAGAATAATGGCAATAAACT
* *
404558 ATCTTCATGTTTGTAACTTGTACAGTGTAAAAAAAATTAGAATAATGGTAATAAACT
1 ATCTTCATATTTGTAACTTGTACAGTGT-AAAAAAATTAGAATAATGGCAATAAACT
404615 AT
1 AT
404617 GTGCTCCTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
55 27 0.52
57 25 0.48
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (56 bp):
ATCTTCATATTTGTAACTTGTACAGTGTAAAAAAATTAGAATAATGGCAATAAACT
Found at i:409834 original size:13 final size:13
Alignment explanation
Indices: 409816--409840 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
409806 AAATTTAATA
409816 TAAATTGATTTTG
1 TAAATTGATTTTG
409829 TAAATTGATTTT
1 TAAATTGATTTT
409841 ATTATTTTAA
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:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TAAATTGATTTTG
Found at i:409958 original size:21 final size:22
Alignment explanation
Indices: 409934--409976 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
409924 ATTTGAATTG
409934 ATTTAAA-TTGAAAAAATTTTT
1 ATTTAAACTTGAAAAAATTTTT
*
409955 ATTTAAACTTGAACAAATTTTT
1 ATTTAAACTTGAAAAAATTTTT
409977 GCAAGTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (22 bp):
ATTTAAACTTGAAAAAATTTTT
Found at i:411425 original size:20 final size:20
Alignment explanation
Indices: 411402--411511 Score: 54
Period size: 20 Copynumber: 5.5 Consensus size: 20
411392 TAAAATATTT
411402 TATATTTATATAAATTTTAA
1 TATATTTATATAAATTTTAA
*
411422 TATA-TTA-AT-AATTTATAT
1 TATATTTATATAAATTT-TAA
* * *
411440 TATATATATTTATATCTTTATA
1 TATATTTATATAAAT-TTTA-A
*
411462 TCATATTTATACT--ATTTTTA
1 T-ATATTTATA-TAAATTTTAA
*
411482 TAT-TTTATATTATATTTTAA
1 TATATTTATA-TAAATTTTAA
*
411502 T-TTTTTATAT
1 TATATTTATAT
411512 CATATTTATA
Statistics
Matches: 69, Mismatches: 10, Indels: 23
0.68 0.10 0.23
Matches are distributed among these distances:
17 5 0.07
18 15 0.22
19 9 0.13
20 20 0.29
21 7 0.10
22 5 0.07
23 7 0.10
24 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (20 bp):
TATATTTATATAAATTTTAA
Found at i:411432 original size:18 final size:17
Alignment explanation
Indices: 411398--411496 Score: 59
Period size: 17 Copynumber: 5.9 Consensus size: 17
411388 TATTTAAAAT
411398 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
411415 ATTTTAATATATTA-AT-A
1 ATTTT-ATAT-TTATATAA
*
411432 A-TTTATA-TTATATAT
1 ATTTTATATTTATATAA
* *
411447 ATTTATATCTTTATATCAT
1 ATTT-TATATTTATAT-AA
*
411466 ATTTATACTATTT-T-TAT
1 ATTT-TA-TATTTATATAA
411483 ATTTTATA-TTATAT
1 ATTTTATATTTATAT
411497 TTTAATTTTT
Statistics
Matches: 68, Mismatches: 3, Indels: 23
0.72 0.03 0.24
Matches are distributed among these distances:
13 3 0.04
14 4 0.06
15 7 0.10
16 8 0.12
17 16 0.24
18 13 0.19
19 13 0.19
20 4 0.06
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:411439 original size:72 final size:80
Alignment explanation
Indices: 411384--411535 Score: 179
Period size: 80 Copynumber: 1.9 Consensus size: 80
411374 TCATATCATA
411384 ATCATATTTAAAATA-TTTTATA-TTTATA-TAAATTTTAATATATTAATAATTTATATTATATA
1 ATCATATTTAAAATATTTTTATATTTTATATTAAATTTTAATATATTAATAATTTATATTATATA
* *
411446 TATTTATATCTTTAT
66 TATTCATATCTATAT
* * * * *
411461 ATCATATTTATACTATTTTTATATTTTATATTATATTTTAATTTTTTATATCATATTTATATTAT
1 ATCATATTTAAAATATTTTTATATTTTATATTAAATTTTAATATATTA-AT-A-ATTTATATTAT
411526 ATA-ATT-ATAT
63 ATATATTCATAT
411536 TATGCATAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
77 13 0.20
78 7 0.11
79 6 0.09
80 14 0.22
81 6 0.09
82 4 0.06
83 14 0.22
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (80 bp):
ATCATATTTAAAATATTTTTATATTTTATATTAAATTTTAATATATTAATAATTTATATTATATA
TATTCATATCTATAT
Found at i:411488 original size:29 final size:29
Alignment explanation
Indices: 411439--411512 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
411429 ATAATTTATA
*
411439 TTATATATATTTATATCTTTATATCATAT
1 TTATATATTTTTATATCTTTATATCATAT
*
411468 TTATACTATTTTTATAT-TTTATATTATAT
1 TTATA-TATTTTTATATCTTTATATCATAT
411497 TT-TA-ATTTTTTATATC
1 TTATATA-TTTTTATATC
411513 ATATTTATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 1 0.03
27 9 0.22
28 2 0.05
29 18 0.45
30 10 0.25
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (29 bp):
TTATATATTTTTATATCTTTATATCATAT
Found at i:411504 original size:18 final size:19
Alignment explanation
Indices: 411396--411536 Score: 85
Period size: 18 Copynumber: 7.3 Consensus size: 19
411386 CATATTTAAA
411396 ATATTTTATA-TTTATA-T
1 ATATTTTATATTTTATATT
* *
411413 AAATTTTAATATATTAATAATTT
1 ATATTTT-ATAT-TTTAT-A-TT
*
411436 ATATTATATATATTTATATCT
1 ATATTTTATAT-TTTATAT-T
* * * *
411457 TTATATCATA-TTTATACT
1 ATATTTTATATTTTATATT
411475 AT-TTTTATATTTTATATT
1 ATATTTTATATTTTATATT
* *
411493 ATATTTTAATTTTTTATATC
1 ATATTTT-ATATTTTATATT
*
411513 ATA-TTTATATTATATAATT
1 ATATTTTATATTTTAT-ATT
411532 ATATT
1 ATATT
411537 ATGCATAATA
Statistics
Matches: 93, Mismatches: 19, Indels: 21
0.70 0.14 0.16
Matches are distributed among these distances:
17 11 0.12
18 21 0.23
19 18 0.19
20 19 0.20
21 9 0.10
22 9 0.10
23 6 0.06
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (19 bp):
ATATTTTATATTTTATATT
Found at i:411516 original size:20 final size:20
Alignment explanation
Indices: 411474--411518 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
411464 ATATTTATAC
* *
411474 TATTTTTATATTTTATATTA
1 TATTTTAATATTTTATATCA
*
411494 TATTTTAATTTTTTATATCA
1 TATTTTAATATTTTATATCA
411514 TATTT
1 TATTT
411519 ATATTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTTTAATATTTTATATCA
Found at i:411535 original size:13 final size:12
Alignment explanation
Indices: 411421--411538 Score: 67
Period size: 11 Copynumber: 10.2 Consensus size: 12
411411 ATAAATTTTA
411421 ATATATTAATAATT
1 ATATATT-AT-ATT
411435 -TATATTATA-T
1 ATATATTATATT
411445 ATAT-TTATATCT
1 ATATATTATAT-T
* *
411457 TTATATCATATTT
1 ATATATTATA-TT
411470 ATACTATT-T-TT
1 ATA-TATTATATT
*
411481 ATATTTTATATT
1 ATATATTATATT
*
411493 ATATTTTA-ATT
1 ATATATTATATT
*
411504 -T-T-TTATATC
1 ATATATTATATT
411513 ATAT-TTATATT
1 ATATATTATATT
411524 ATATAATTATATT
1 ATAT-ATTATATT
411537 AT
1 AT
411539 GCATAATATT
Statistics
Matches: 84, Mismatches: 7, Indels: 27
0.71 0.06 0.23
Matches are distributed among these distances:
8 3 0.04
9 3 0.04
10 11 0.13
11 24 0.29
12 16 0.19
13 23 0.27
14 4 0.05
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (12 bp):
ATATATTATATT
Found at i:411676 original size:2 final size:2
Alignment explanation
Indices: 411669--411693 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
411659 TTCTCAATTC
411669 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
411694 GTATGTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:411698 original size:4 final size:4
Alignment explanation
Indices: 411691--411727 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
411681 TATATATATA
411691 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
411728 TGATTACAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:412290 original size:3 final size:3
Alignment explanation
Indices: 412278--412315 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
412268 TGCCATAAAA
412278 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
412316 ATAGTTGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:412576 original size:16 final size:15
Alignment explanation
Indices: 412555--412585 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
412545 AAATATAATT
412555 TTTATA-AATTTAAA
1 TTTATATAATTTAAA
412569 TTTATATAATTTAAA
1 TTTATATAATTTAAA
412584 TT
1 TT
412586 GAATTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATATAATTTAAA
Found at i:413212 original size:2 final size:2
Alignment explanation
Indices: 413205--413233 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
413195 TCTTTAACAA
413205 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
413234 AAGACAGAAG
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:420977 original size:20 final size:20
Alignment explanation
Indices: 420954--421019 Score: 58
Period size: 20 Copynumber: 3.7 Consensus size: 20
420944 ACGTATTTAA
420954 AATATATTTATATAAATTTT
1 AATATATTTATATAAATTTT
*
420974 AATAT-GTT-TAT-AA--TT
1 AATATATTTATATAAATTTT
420989 --TATA-TTATATAAATTTT
1 AATATATTTATATAAATTTT
*
421006 AAAATATTTATATA
1 AATATATTTATATA
421020 TTTTGTATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 16
0.67 0.04 0.30
Matches are distributed among these distances:
13 5 0.14
14 3 0.08
15 4 0.11
17 4 0.11
18 3 0.08
19 5 0.14
20 12 0.33
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
AATATATTTATATAAATTTT
Found at i:420998 original size:32 final size:34
Alignment explanation
Indices: 420956--421032 Score: 104
Period size: 32 Copynumber: 2.3 Consensus size: 34
420946 GTATTTAAAA
* *
420956 TATATTTATATAAATTTTAATATGTTTATA-A-TT
1 TATA-TTATATAAATTTTAAAATATTTATATATTT
420989 TATATTATATAAATTTTAAAATATTTATATATTT
1 TATATTATATAAATTTTAAAATATTTATATATTT
*
421023 TGTATTATAT
1 TATATTATAT
421033 TTAATATTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
32 23 0.59
33 5 0.13
34 11 0.28
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (34 bp):
TATATTATATAAATTTTAAAATATTTATATATTT
Found at i:421029 original size:34 final size:32
Alignment explanation
Indices: 420947--421032 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 32
420937 ATTATAGACG
* * *
420947 TATTTAAAATATAT-TTATATAAATTTTAATA
1 TATTTATAATTTATATTATATAAATTTTAAAA
*
420978 TGTTTATAATTTATATTATATAAATTTTAAAA
1 TATTTATAATTTATATTATATAAATTTTAAAA
*
421010 TATTTATATATTTTGTATTATAT
1 TATTTATA-A-TTTATATTATAT
421033 TTAATATTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 11 0.24
32 23 0.50
33 1 0.02
34 11 0.24
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (32 bp):
TATTTATAATTTATATTATATAAATTTTAAAA
Found at i:421789 original size:19 final size:19
Alignment explanation
Indices: 421765--421814 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 19
421755 TTTTGAAGTT
421765 TTTTGTTTTAGAAATTAAA
1 TTTTGTTTTAGAAATTAAA
*
421784 TTTTG---T--AATTTAAA
1 TTTTGTTTTAGAAATTAAA
421798 TTTTGTTTTAGAAATTA
1 TTTTGTTTTAGAAATTA
421815 TTGAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 10
0.67 0.06 0.28
Matches are distributed among these distances:
14 12 0.50
16 1 0.04
17 1 0.04
19 10 0.42
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (19 bp):
TTTTGTTTTAGAAATTAAA
Found at i:421839 original size:2 final size:2
Alignment explanation
Indices: 421834--421869 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
421824 TTTTTAAAGC
* *
421834 AT AT AT AC AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
421870 TCTCTTATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:423956 original size:5 final size:5
Alignment explanation
Indices: 423930--423985 Score: 64
Period size: 5 Copynumber: 11.4 Consensus size: 5
423920 GTTTAATAAT
*
423930 TTATA -TAT- TTATA TTATAA TTATA TTATA TTTTAA TTAT- TTATA TTATA
1 TTATA TTATA TTATA TTAT-A TTATA TTATA TTAT-A TTATA TTATA TTATA
423979 TTATA TT
1 TTATA TT
423986 TAAAATTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 10 0.23
5 25 0.57
6 9 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:423976 original size:25 final size:27
Alignment explanation
Indices: 423938--423995 Score: 84
Period size: 25 Copynumber: 2.2 Consensus size: 27
423928 ATTTATATAT
*
423938 TTATATTATAATTATATTATATTT-TAA
1 TTAT-TTATAATTATATTATATTTAAAA
423965 TTATTTAT-ATTATATTATATTTAAAA
1 TTATTTATAATTATATTATATTTAAAA
423991 TTATT
1 TTATT
423996 AAATTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 14 0.48
26 11 0.38
27 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
TTATTTATAATTATATTATATTTAAAA
Found at i:424002 original size:31 final size:30
Alignment explanation
Indices: 423929--424008 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 30
423919 GGTTTAATAA
*
423929 TTTATATATTTATATTATAATTATATTATAT
1 TTTA-ATATTTATATTATAATTATATTAAAT
423960 TTTAATTATTTATATTAT-ATTATATTTAAAAT
1 TTTAA-TATTTATATTATAATTATA-TT-AAAT
*
423992 TATTAA-ATTTAAATTAT
1 T-TTAATATTTATATTAT
424009 TTAATCATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
30 7 0.16
31 28 0.65
32 4 0.09
33 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTAATATTTATATTATAATTATATTAAAT
Found at i:424968 original size:15 final size:15
Alignment explanation
Indices: 424948--424980 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
424938 TTATTTTAAA
*
424948 TAAATATAATTATTT
1 TAAATATAATTATAT
424963 TAAATATAATTATAT
1 TAAATATAATTATAT
424978 TAA
1 TAA
424981 TATGATATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAATATAATTATAT
Found at i:425197 original size:7 final size:7
Alignment explanation
Indices: 425187--425243 Score: 50
Period size: 7 Copynumber: 8.7 Consensus size: 7
425177 ATTATTACAT
425187 AAATATA
1 AAATATA
425194 AAATAT-
1 AAATATA
425200 AAATATA
1 AAATATA
* *
425207 ACACA-A
1 AAATATA
*
425213 AAAAATA
1 AAATATA
*
425220 AAATGT-
1 AAATATA
425226 -AATATA
1 AAATATA
425232 AAATATA
1 AAATATA
425239 AAATA
1 AAATA
425244 ATATAAATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
5 4 0.10
6 10 0.26
7 25 0.64
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (7 bp):
AAATATA
Found at i:425236 original size:17 final size:17
Alignment explanation
Indices: 425188--425250 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 17
425178 TTATTACATA
425188 AATATAAAATATAAATAT
1 AATATAAAATATAAA-AT
* * *
425206 AACACAAAAAAATAAAATGT
1 AATA-TAAAATATAAAA--T
425226 AATATAAAATATAAAAT
1 AATATAAAATATAAAAT
425243 AATATAAA
1 AATATAAA
425251 TAATATATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
17 9 0.25
18 4 0.11
19 19 0.53
20 4 0.11
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (17 bp):
AATATAAAATATAAAAT
Found at i:425300 original size:18 final size:17
Alignment explanation
Indices: 425275--425308 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
425265 TTATATAAAA
*
425275 TAAATTATTTAAATATT
1 TAAATTATATAAATATT
425292 TAAATTTATATAAATAT
1 TAAA-TTATATAAATAT
425309 AAAATATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATTATATAAATATT
Found at i:425300 original size:32 final size:36
Alignment explanation
Indices: 425252--425325 Score: 111
Period size: 34 Copynumber: 2.2 Consensus size: 36
425242 TAATATAAAT
*
425252 AATATATTAAATTTTATATAAA-ATAAATTA-TTTA
1 AATATATTAAATTTTATATAAATATAAAATATTTTA
425286 AATAT-TTAAA-TTTATATAAATATAAAATATTTTA
1 AATATATTAAATTTTATATAAATATAAAATATTTTA
425320 AATATA
1 AATATA
425326 ATTATAACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
32 10 0.28
33 12 0.33
34 14 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (36 bp):
AATATATTAAATTTTATATAAATATAAAATATTTTA
Found at i:425320 original size:34 final size:34
Alignment explanation
Indices: 425234--425325 Score: 109
Period size: 33 Copynumber: 2.7 Consensus size: 34
425224 GTAATATAAA
* **
425234 ATATAAAATAATATAAAT-AATATATTAAATTTT
1 ATATAAAATAAAATATTTAAATATATTAAATTTT
*
425267 ATATAAAATAAATTATTTAAATAT-TTAAA-TTT
1 ATATAAAATAAAATATTTAAATATATTAAATTTT
425299 ATATAAATATAAAATATTTTAAATATA
1 ATATAAA-ATAAAATA-TTTAAATATA
425326 ATTATAACAT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
32 10 0.20
33 26 0.52
34 14 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (34 bp):
ATATAAAATAAAATATTTAAATATATTAAATTTT
Found at i:425900 original size:17 final size:16
Alignment explanation
Indices: 425857--425903 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
425847 AATTTTAAAA
425857 AATATAAATAATAATTT
1 AATAT-AATAATAATTT
*
425874 AATATTATAATACATTTT
1 AATATAATAATA-A-TTT
425892 AA-ATAATAATAA
1 AATATAATAATAA
425904 AAATTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 7 0.27
17 14 0.54
18 5 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATAATAATAATTT
Found at i:425998 original size:21 final size:21
Alignment explanation
Indices: 425972--426018 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
425962 TATTTGATAA
425972 AAATAAAATATAAAAATAAT-T
1 AAATAAAATA-AAAAATAATAT
*
425993 AAATAAAATAAAAATTAATAT
1 AAATAAAATAAAAAATAATAT
426014 AAATA
1 AAATA
426019 TTTAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATAAAATAAAAAATAATAT
Found at i:426008 original size:16 final size:16
Alignment explanation
Indices: 425968--426016 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
425958 TAATTATTTG
*
425968 ATAAAAATAAAATATAA
1 ATAAAAATTAAATA-AA
*
425985 A-AATAATTAAATAAA
1 ATAAAAATTAAATAAA
426000 ATAAAAATTAATATAAA
1 ATAAAAATTAA-ATAAA
426017 TATTTAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 3 0.11
16 18 0.67
17 6 0.22
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAAATTAAATAAA
Found at i:426025 original size:29 final size:28
Alignment explanation
Indices: 425952--426027 Score: 77
Period size: 26 Copynumber: 2.8 Consensus size: 28
425942 AATTTTATAT
* *
425952 ATAATATAATTATTT-GATAAAAATAAA
1 ATAATATAAATATTTAAATAAAAATAAA
* *
425979 AT-ATAAAAATAATTAAAT-AAAATAAAA
1 ATAATATAAATATTTAAATAAAAAT-AAA
426006 ATTAATATAAATATTTAAATAA
1 A-TAATATAAATATTTAAATAA
426028 TTTAAAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
26 14 0.37
27 8 0.21
28 1 0.03
29 14 0.37
30 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (28 bp):
ATAATATAAATATTTAAATAAAAATAAA
Done.