Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold151
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: 367700
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
File 3 of 4
Found at i:219846 original size:77 final size:74
Alignment explanation
Indices: 219713--219863 Score: 189
Period size: 77 Copynumber: 2.0 Consensus size: 74
219703 ATTATTTGTA
*
219713 CACTTTTATCTTTATATATGTATTTATATATATAGTGAATATAATTTTATATTAATTTTGAAAAA
1 CACTTTTATCTTTATATATGTATTTATATATATAGTGAATATAATTTTAGATTAATTTTGAAAAA
*
219778 GTTATCTTT
66 ATTATCTTT
* * *
219787 CACTTTTATTTTTATATATGTATTTTTTATATATATTA-TTAAT-TAAATTTTGGATTAATTTTG
1 CACTTTTATCTTTATATATGTA---TTTATATATA-TAGTGAATAT-AATTTTAGATTAATTTTG
*
219850 AAAAAATTTTCTTT
61 AAAAAATTATCTTT
219864 TTTTCTTAAG
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
74 21 0.32
76 1 0.02
77 42 0.64
78 2 0.03
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.56
Consensus pattern (74 bp):
CACTTTTATCTTTATATATGTATTTATATATATAGTGAATATAATTTTAGATTAATTTTGAAAAA
ATTATCTTT
Found at i:221836 original size:6 final size:6
Alignment explanation
Indices: 221801--221832 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
221791 GTGGAGGCTA
*
221801 TGACAG TGACAG TGACAG TGACAG TGTCAG TG
1 TGACAG TGACAG TGACAG TGACAG TGACAG TG
221833 TCAGAACAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.34, T:0.22
Consensus pattern (6 bp):
TGACAG
Found at i:224046 original size:16 final size:16
Alignment explanation
Indices: 224016--224081 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 16
224006 ATTATAATAT
* *
224016 TATAATATATCATAAA
1 TATAAAATATAATAAA
*
224032 TTTAAAATATAATAAA
1 TATAAAATATAATAAA
*
224048 TATATAATA-AATAAA
1 TATAAAATATAATAAA
224063 -ATAATATATATAA-AAA
1 TATAA-A-ATATAATAAA
224079 TAT
1 TAT
224082 TTTAATATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
14 3 0.08
15 7 0.17
16 26 0.65
17 4 0.10
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
TATAAAATATAATAAA
Found at i:224066 original size:23 final size:20
Alignment explanation
Indices: 224035--224080 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
224025 TCATAAATTT
*
224035 AAAATATAATAA-ATATATA
1 AAAATAAAATAATATATATA
224054 ATAAATAAAATAATATATATA
1 A-AAATAAAATAATATATATA
224075 AAAATA
1 AAAATA
224081 TTTTAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 15 0.62
21 8 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAATAAAATAATATATATA
Found at i:224128 original size:29 final size:28
Alignment explanation
Indices: 224073--224128 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
224063 ATAATATATA
*
224073 TAAAAATATTTTAATATATTTATAAATT
1 TAAAAATATTTTAATATATATATAAATT
*
224101 TAAAAATTTTATTAATA-ATATATCAAAT
1 TAAAAATATT-TTAATATATATAT-AAAT
224129 AATAGTTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
TAAAAATATTTTAATATATATATAAATT
Found at i:224398 original size:18 final size:18
Alignment explanation
Indices: 224339--224405 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
224329 ATAATTTAAT
224339 TATT-TTAAAATATTCAA
1 TATTATTAAAATATTCAA
* * * *
224356 TGTCATTATAAT-TTTAA
1 TATTATTAAAATATTCAA
* *
224373 TATAATTAAAATATTGAA
1 TATTATTAAAATATTCAA
224391 TATTATTAAAATATT
1 TATTATTAAAATATT
224406 ATTATTTACA
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
17 15 0.38
18 24 0.62
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (18 bp):
TATTATTAAAATATTCAA
Found at i:224442 original size:18 final size:17
Alignment explanation
Indices: 224369--224442 Score: 58
Period size: 18 Copynumber: 4.0 Consensus size: 17
224359 CATTATAATT
* *
224369 TTAATATAATTAAAATA
1 TTAATATTACTAAAATA
*
224386 TTGAATATTATTAAAATA
1 TT-AATATTACTAAAATA
*
224404 TTATTATTTACATACATAATA
1 TTAATA-TTAC-TA-A-AATA
224425 TTAAGTATTACTAAAATA
1 TTAA-TATTACTAAAATA
224443 ATATTAAATG
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
17 5 0.11
18 23 0.49
19 3 0.06
20 3 0.06
21 11 0.23
22 2 0.04
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (17 bp):
TTAATATTACTAAAATA
Found at i:224481 original size:39 final size:39
Alignment explanation
Indices: 224438--224535 Score: 101
Period size: 39 Copynumber: 2.5 Consensus size: 39
224428 AGTATTACTA
* * *
224438 AAATAATATT-AAATGATTTGTAATCTAAAGTATATTATT
1 AAATAATATTAAAAT-AATTATAATCTAAAATATATTATT
* * *
224477 AAATATTATTAAAATAATTATATTTTAAAATATATTATT
1 AAATAATATTAAAATAATTATAATCTAAAATATATTATT
* *
224516 AAATATTTTTAAAAT-ATTAT
1 AAATAATATTAAAATAATTAT
224536 TCAATATTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
38 5 0.10
39 42 0.82
40 4 0.08
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (39 bp):
AAATAATATTAAAATAATTATAATCTAAAATATATTATT
Found at i:224513 original size:17 final size:17
Alignment explanation
Indices: 224479--224514 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
224469 ATATTATTAA
224479 ATATTATTAAAATAATT
1 ATATTATTAAAATAATT
224496 ATATT-TTAAAATATATT
1 ATATTATTAAAATA-ATT
224513 AT
1 AT
224515 TAAATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTATTAAAATAATT
Found at i:224546 original size:24 final size:23
Alignment explanation
Indices: 224469--224653 Score: 105
Period size: 21 Copynumber: 8.4 Consensus size: 23
224459 AATCTAAAGT
224469 ATATTATTAA-A-TATTATTAAA
1 ATATTATTAATATTATTATTAAA
224490 ATA--ATT-ATATT-TTA--AAA
1 ATATTATTAATATTATTATTAAA
*
224507 TATATTATTAA-A-TATTTTTAAA
1 -ATATTATTAATATTATTATTAAA
*
224529 ATATTATTCAATATTATTATAAAA
1 ATATTATT-AATATTATTATTAAA
*
224553 ATATT-TTAAT-GTATTATTAAA
1 ATATTATTAATATTATTATTAAA
*
224574 ATATTTTTCATATTATATAATTATTAAA
1 ATATTATT-A-A-TAT-T-ATTATTAAA
*
224602 ATATT-TCAATA-TATTATT-AA
1 ATATTATTAATATTATTATTAAA
* * **
224622 ATATT-GTATACATTATTAAAAAA
1 ATATTATTA-ATATTATTATTAAA
224645 ATATTATTA
1 ATATTATTA
224654 TAATAAATAA
Statistics
Matches: 128, Mismatches: 13, Indels: 43
0.70 0.07 0.23
Matches are distributed among these distances:
17 3 0.02
18 4 0.03
19 8 0.06
20 15 0.12
21 34 0.27
22 16 0.12
23 11 0.09
24 18 0.14
25 2 0.02
26 1 0.01
27 2 0.02
28 14 0.11
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (23 bp):
ATATTATTAATATTATTATTAAA
Found at i:224605 original size:49 final size:45
Alignment explanation
Indices: 224468--224626 Score: 135
Period size: 49 Copynumber: 3.4 Consensus size: 45
224458 TAATCTAAAG
* * *
224468 TATATTATT-AAATATTATTAAAATAATTATATTTTAAAATATATTATTAA
1 TATATTATTAAAATATTATT-CAAT-A-T-TATTATAAAA-ATATT-TCAA
* *
224518 -ATATTTTTAAAATATTATTCAATATTATTATAAAAATATTTTAA
1 TATATTATTAAAATATTATTCAATATTATTATAAAAATATTTCAA
* * *
224562 TGTATTATTAAAATATTTTTCATATTATATAATTATTAAAATATTTCAA
1 TATATTATTAAAATATTATTCA-A-TAT-T-ATTATAAAAATATTTCAA
224611 TATATTATT-AAATATT
1 TATATTATTAAAATATT
224627 GTATACATTA
Statistics
Matches: 94, Mismatches: 9, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
44 4 0.04
45 23 0.24
46 10 0.11
47 4 0.04
48 9 0.10
49 34 0.36
50 10 0.11
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.51
Consensus pattern (45 bp):
TATATTATTAAAATATTATTCAATATTATTATAAAAATATTTCAA
Found at i:224626 original size:28 final size:28
Alignment explanation
Indices: 224567--224626 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
224557 TTTAATGTAT
* *
224567 TATTAAAATATTTTTCATATTATATAAT
1 TATTAAAATATTTATCATATTATATAAA
224595 TATTAAAATATTTCAAT-ATATTAT-TAAA
1 TATTAAAATATTT--ATCATATTATATAAA
224623 TATT
1 TATT
224627 GTATACATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 20 0.71
29 7 0.25
30 1 0.04
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (28 bp):
TATTAAAATATTTATCATATTATATAAA
Found at i:224638 original size:19 final size:17
Alignment explanation
Indices: 224583--224641 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 17
224573 AATATTTTTC
224583 ATATTATATAATTATTAAA
1 ATATT-TATAATTATT-AA
224602 ATATTTCAATATATTATTAA
1 ATATTT--ATA-ATTATTAA
224622 ATATTGTATACATTATTAA
1 ATATT-TATA-ATTATTAA
224641 A
1 A
224642 AAAATATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 1 0.03
19 17 0.49
20 10 0.29
21 7 0.20
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (17 bp):
ATATTTATAATTATTAA
Found at i:225271 original size:68 final size:68
Alignment explanation
Indices: 225196--225324 Score: 231
Period size: 68 Copynumber: 1.9 Consensus size: 68
225186 GTTTTGAATA
*
225196 TTTTATATTTATTTATTCATAATAAATTTATTTATAAATTAAATTATTTGTTATATTTGATTGGA
1 TTTTATATTTATTTATTCATAATAAATTTATTTACAAATTAAATTATTTGTTATATTTGATTGGA
225261 TAT
66 TAT
* *
225264 TTTTATATTTATTTATTTATAATAAATTTATTTACAAATTAAATTATTTGTTATGTTTGAT
1 TTTTATATTTATTTATTCATAATAAATTTATTTACAAATTAAATTATTTGTTATATTTGAT
225325 GAGTTTGATT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 58 1.00
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (68 bp):
TTTTATATTTATTTATTCATAATAAATTTATTTACAAATTAAATTATTTGTTATATTTGATTGGA
TAT
Found at i:225463 original size:20 final size:19
Alignment explanation
Indices: 225427--225466 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
225417 TATTTTTATT
225427 TAAATTTAATTATAAAATA
1 TAAATTTAATTATAAAATA
225446 TAAATATTAA-TATAAAA-A
1 TAAAT-TTAATTATAAAATA
225464 TAA
1 TAA
225467 TTTTTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 12 0.60
20 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATTTAATTATAAAATA
Found at i:225522 original size:13 final size:13
Alignment explanation
Indices: 225504--225528 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
225494 AGTATAACCT
225504 TAAAAAATTTAAG
1 TAAAAAATTTAAG
225517 TAAAAAATTTAA
1 TAAAAAATTTAA
225529 AATTTTTTAA
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:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
TAAAAAATTTAAG
Found at i:226422 original size:17 final size:18
Alignment explanation
Indices: 226387--226424 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
226377 ATACGCAAAT
* *
226387 AAATTTTTATTTTTATTA
1 AAATTTTAATTATTATTA
226405 AAATTTTAATTATT-TTA
1 AAATTTTAATTATTATTA
226422 AAA
1 AAA
226425 CTTATTTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
AAATTTTAATTATTATTA
Found at i:226468 original size:24 final size:23
Alignment explanation
Indices: 226421--226464 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
226411 TAATTATTTT
* *
226421 AAAACTTATTTTGATAAAAATAA
1 AAAAATTATTTTAATAAAAATAA
*
226444 AAAAATTATTTTAATATAAAT
1 AAAAATTATTTTAATAAAAAT
226465 TAAATATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
AAAAATTATTTTAATAAAAATAA
Found at i:226508 original size:30 final size:29
Alignment explanation
Indices: 226434--226539 Score: 85
Period size: 30 Copynumber: 3.6 Consensus size: 29
226424 ACTTATTTTG
**
226434 ATAAAAATAA-AAAAATTATTTTAATATA
1 ATAAAAATAATAAATTTTATTTTAATATA
* *
226462 A-ATTAAATATTAAAATTTTATTTTAATATA
1 ATA-AAAATAAT-AAATTTTATTTTAATATA
*
226492 ATAAAAATACATAAA-TTTA-TTTAGATAAA
1 ATAAAAATA-ATAAATTTTATTTTA-ATATA
*
226521 ATAATAAAAAATAAATTTT
1 ATAA-AAATAATAAATTTT
226540 TTATTATTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
27 1 0.02
28 10 0.16
29 17 0.27
30 32 0.52
31 2 0.03
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (29 bp):
ATAAAAATAATAAATTTTATTTTAATATA
Found at i:226523 original size:29 final size:28
Alignment explanation
Indices: 226478--226542 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
226468 ATATTAAAAT
* *
226478 TTTATTTTAATATAATAA-AAATACATAAA
1 TTTA-TTTAATAAAATAATAAA-AAATAAA
226507 TTTATTTAGATAAAATAATAAAAAATAAA
1 TTTATTTA-ATAAAATAATAAAAAATAAA
226536 TTT-TTTA
1 TTTATTTA
226543 TTATTTTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 8 0.25
29 21 0.66
30 3 0.09
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
TTTATTTAATAAAATAATAAAAAATAAA
Found at i:226652 original size:21 final size:21
Alignment explanation
Indices: 226628--226673 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
226618 CCAATATTTC
226628 AATTATCATAATTTTTTATTA
1 AATTATCATAATTTTTTATTA
226649 AATTATCATAATTTTTTATTA
1 AATTATCATAATTTTTTATTA
226670 AATT
1 AATT
226674 GATTATACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTATCATAATTTTTTATTA
Found at i:226775 original size:15 final size:16
Alignment explanation
Indices: 226748--226789 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
226738 AATAATAAGA
*
226748 AAAAAATTATATTTTT
1 AAAAAATTATATTATT
*
226764 TAAAAATT-TATTATT
1 AAAAAATTATATTATT
226779 AAAAAATTATA
1 AAAAAATTATA
226790 AAAACTACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAAAAATTATATTATT
Found at i:227024 original size:2 final size:2
Alignment explanation
Indices: 227017--227058 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
227007 TAAATAGATA
227017 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
227059 GAAGTGAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:228296 original size:11 final size:11
Alignment explanation
Indices: 228280--228318 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
228270 CTAAATTTAT
228280 ATATATATTTG
1 ATATATATTTG
228291 ATATATATTTG
1 ATATATATTTG
228302 --A-ATATTTG
1 ATATATATTTG
228310 ATAT-TATTT
1 ATATATATTT
228319 TCTAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
8 7 0.28
9 1 0.04
10 6 0.24
11 11 0.44
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (11 bp):
ATATATATTTG
Found at i:229404 original size:52 final size:52
Alignment explanation
Indices: 229316--229425 Score: 166
Period size: 52 Copynumber: 2.1 Consensus size: 52
229306 TCGCTTGTTA
* * * * *
229316 CTAATTACTAGCGATTTTTAAAACTAATTTTGTTTTACTTTCATCTACGTTC
1 CTAACTACTAACGATTTTTAAAACTAATTTTATTTTAATTTCATCCACGTTC
*
229368 CTAACTACTAACGATTTTTAAAATTAATTTTATTTTAATTTCATCCACGTTC
1 CTAACTACTAACGATTTTTAAAACTAATTTTATTTTAATTTCATCCACGTTC
229420 CTAACT
1 CTAACT
229426 TAATCTGGTG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.46
Consensus pattern (52 bp):
CTAACTACTAACGATTTTTAAAACTAATTTTATTTTAATTTCATCCACGTTC
Found at i:230343 original size:68 final size:68
Alignment explanation
Indices: 230212--230347 Score: 200
Period size: 68 Copynumber: 2.0 Consensus size: 68
230202 ACACTCTTAC
* * * * * **
230212 AATATGTGGTTGTGATTGCACCAAGTGTATTGCTGAGACTGTACCAAGTGTATGGCGGTTATAAT
1 AATATGTGGGTGAGATGGCACCAAGTGTATGGCTGAGACTGTACCAAGTGCATGGCGAATATAAT
230277 ACT
66 ACT
*
230280 AATATGTGGGTGAGATGGCACCAAGTGTATGGCTGAGACTGTACCAAGTGCATGGTGAATATAAT
1 AATATGTGGGTGAGATGGCACCAAGTGTATGGCTGAGACTGTACCAAGTGCATGGCGAATATAAT
230345 ACT
66 ACT
230348 TTTAGAGACT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 60 1.00
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (68 bp):
AATATGTGGGTGAGATGGCACCAAGTGTATGGCTGAGACTGTACCAAGTGCATGGCGAATATAAT
ACT
Found at i:231385 original size:7 final size:6
Alignment explanation
Indices: 231369--231401 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
231359 ATGGGATAAA
231369 AAAAAG AAAAAG AAAAAG AAAAAG AAAACAG AA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA-AG AA
231402 TTTCTAGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 22 0.85
7 4 0.15
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:231741 original size:24 final size:21
Alignment explanation
Indices: 231709--231756 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 21
231699 TTATATTAAT
231709 ATATATTTTAATTAAATTTAAATA
1 ATATATTTT-ATT--ATTTAAATA
*
231733 ATATTTTTTATTATTTAAATA
1 ATATATTTTATTATTTAAATA
231754 ATA
1 ATA
231757 ATCAAAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 12 0.52
23 3 0.13
24 8 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATATTTTATTATTTAAATA
Found at i:232952 original size:20 final size:20
Alignment explanation
Indices: 232916--232979 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
232906 AAATTTAAAT
232916 AATGTTGATAA-AAATATTAA
1 AATGTT-ATAATAAATATTAA
* *
232936 AATGTTATAATATATATAAAA
1 AATGTTATAATAAATAT-TAA
*
232957 AATATTA-ACATAAATATTAA
1 AATGTTATA-ATAAATATTAA
232977 AAT
1 AAT
232980 ATTTATTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
19 4 0.11
20 17 0.47
21 15 0.42
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.36
Consensus pattern (20 bp):
AATGTTATAATAAATATTAA
Found at i:235491 original size:13 final size:13
Alignment explanation
Indices: 235473--235498 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
235463 TTTATCTTAA
235473 GATACTTAACACT
1 GATACTTAACACT
235486 GATACTTAACACT
1 GATACTTAACACT
235499 ACACTGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
GATACTTAACACT
Found at i:236765 original size:19 final size:19
Alignment explanation
Indices: 236728--236767 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
236718 ATTTATTCTT
*
236728 ATTATTTAAAAAATTTATA
1 ATTATTTAAAAAATATATA
236747 ATTATTTAAAATAAATATATA
1 ATTATTT-AAA-AAATATATA
236768 TAATAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 3 0.17
21 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTATTTAAAAAATATATA
Found at i:236927 original size:31 final size:28
Alignment explanation
Indices: 236892--236953 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 28
236882 ATATGGTAAG
236892 TATATTATTATTTAAAAAAACTATTTTTGTA
1 TATATTATTATTT-AAAAAA-TATTTTT-TA
* *
236923 TATATTTTTATTTTAAAAATATTTTTTA
1 TATATTATTATTTAAAAAATATTTTTTA
236951 TAT
1 TAT
236954 TTTTAGAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 5 0.17
29 7 0.24
30 5 0.17
31 12 0.41
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (28 bp):
TATATTATTATTTAAAAAATATTTTTTA
Found at i:237751 original size:31 final size:31
Alignment explanation
Indices: 237667--237752 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 31
237657 CAGTTTTATT
* *
237667 TATTTAAATTAAAAATTAATTTAATTAATTTTAA
1 TATTAAAATTAAAAA--AA-TTAATTAATATTAA
* ***
237701 TATTAAAATTGATCGAATTAATTAATATTAA
1 TATTAAAATTAAAAAAATTAATTAATATTAA
*
237732 TTTTAAAATTAAAAAAATTAA
1 TATTAAAATTAAAAAAATTAA
237753 ATCGATATTA
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
31 29 0.71
32 2 0.05
34 10 0.24
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (31 bp):
TATTAAAATTAAAAAAATTAATTAATATTAA
Found at i:237803 original size:9 final size:9
Alignment explanation
Indices: 237791--237820 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
237781 GATTTTTTTA
237791 ATTTTAAAT
1 ATTTTAAAT
237800 ATTTTAAAT
1 ATTTTAAAT
237809 ATTTTAAAT
1 ATTTTAAAT
237818 ATT
1 ATT
237821 AATTTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTTTAAAT
Found at i:237908 original size:5 final size:5
Alignment explanation
Indices: 237898--237957 Score: 81
Period size: 5 Copynumber: 12.6 Consensus size: 5
237888 CTTTAAACTG
* *
237898 ATTAA ATTAA ATTGA ATT-- ATTAA ACT-A ATTAA ATTAA ATTAA ATTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA
237945 ATTAA ATTAA ATT
1 ATTAA ATTAA ATT
237958 TTTTAATTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
3 3 0.06
4 3 0.06
5 43 0.88
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (5 bp):
ATTAA
Found at i:237908 original size:27 final size:26
Alignment explanation
Indices: 237870--237936 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
237860 TTAATCGAAT
237870 TGATT-AATTAAATCAA-TACTTTAAAC
1 TGATTAAATTAAATCAATTA--TTAAAC
*
237896 TGATTAAATTAAATTGAATTATTAAAC
1 TGATTAAATTAAA-TCAATTATTAAAC
*
237923 TAATTAAATTAAAT
1 TGATTAAATTAAAT
237937 TAAATTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
26 6 0.17
27 25 0.69
28 3 0.08
29 2 0.06
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (26 bp):
TGATTAAATTAAATCAATTATTAAAC
Found at i:237937 original size:27 final size:27
Alignment explanation
Indices: 237890--237943 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
237880 AATCAATACT
* *
237890 TTAAACTGATTAAATTAAATTGAATTA
1 TTAAACTAATTAAATTAAATTAAATTA
237917 TTAAACTAATTAAATTAAATTAAATTA
1 TTAAACTAATTAAATTAAATTAAATTA
237944 AATTAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (27 bp):
TTAAACTAATTAAATTAAATTAAATTA
Found at i:238257 original size:17 final size:18
Alignment explanation
Indices: 238227--238260 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
238217 TTATTTAAAA
238227 TAAAGAGATATTTTATTT
1 TAAAGAGATATTTTATTT
*
238245 TAAAGA-ATTTTTTATT
1 TAAAGAGATATTTTATT
238261 AAAATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAAGAGATATTTTATTT
Found at i:242152 original size:24 final size:26
Alignment explanation
Indices: 242099--242154 Score: 80
Period size: 24 Copynumber: 2.2 Consensus size: 26
242089 GGTGGCTAGT
* *
242099 CAACAAAAGCCACCCTTTGTGTTTGT
1 CAACAAAAGCCACCCTATGTGTTTGC
242125 CAACAAAAGCCA-CC-ATGTGTTTGC
1 CAACAAAAGCCACCCTATGTGTTTGC
242149 CAACAA
1 CAACAA
242155 TGGTGGTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 14 0.50
25 2 0.07
26 12 0.43
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (26 bp):
CAACAAAAGCCACCCTATGTGTTTGC
Found at i:244787 original size:21 final size:22
Alignment explanation
Indices: 244758--244803 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
244748 TGTTCAGACA
** *
244758 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
244780 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
244801 AGT
1 AGT
244804 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:246718 original size:24 final size:26
Alignment explanation
Indices: 246667--246724 Score: 93
Period size: 24 Copynumber: 2.3 Consensus size: 26
246657 TGGGTGGCTA
*
246667 GTCAACAAAAGCCACCCTTTGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
246693 GTCAACAAAAGCCA-CC-ATGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
246717 GTCAACAA
1 GTCAACAA
246725 TGGTGGTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 15 0.48
25 2 0.06
26 14 0.45
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (26 bp):
GTCAACAAAAGCCACCCTATGTGTTT
Found at i:252255 original size:31 final size:30
Alignment explanation
Indices: 252195--252259 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
252185 ATACAGGCTA
*
252195 ATTGTACAAGGATGGTTTTGGTAGGAAATT
1 ATTGTACAAGGATGGTTTTGGTAGCAAATT
* * * *
252225 CATTGTACGAGGGTGGTTTTGTTTGCAAATT
1 -ATTGTACAAGGATGGTTTTGGTAGCAAATT
252256 ATTG
1 ATTG
252260 GGCGGTGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.25, C:0.06, G:0.29, T:0.40
Consensus pattern (30 bp):
ATTGTACAAGGATGGTTTTGGTAGCAAATT
Found at i:253603 original size:23 final size:22
Alignment explanation
Indices: 253548--253609 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
253538 ATCTATATAC
253548 AAATATAAA-ATATAAAATTAT
1 AAATATAAATATATAAAATTAT
* * *
253569 AAATATTTAATATCTAAAATTTT
1 AAATA-TAAATATATAAAATTAT
*
253592 AAATATCAAATAAATAAA
1 AAATAT-AAATATATAAA
253610 GTACAAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 5 0.16
22 4 0.12
23 23 0.72
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATATAAATATATAAAATTAT
Found at i:254211 original size:22 final size:22
Alignment explanation
Indices: 254139--254211 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
254129 AAAGAATTTC
* * *
254139 ACTTATTTGATTATCTTAAAATT
1 ACTT-TTTGATTTTTTTATAATT
* * *
254162 AATTTTTAATTTTTTTAT-TTT
1 ACTTTTTGATTTTTTTATAATT
*
254183 GATTTTTTGATTTTTTTATAATT
1 -ACTTTTTGATTTTTTTATAATT
254206 ACTTTT
1 ACTTTT
254212 AAAAACAATT
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
21 2 0.05
22 31 0.82
23 5 0.13
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (22 bp):
ACTTTTTGATTTTTTTATAATT
Found at i:255974 original size:2 final size:2
Alignment explanation
Indices: 255967--255998 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
255957 TTTAGATACA
255967 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
255999 TAATGTAATT
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):
AT
Found at i:256277 original size:4 final size:4
Alignment explanation
Indices: 256268--256294 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
256258 TTGTAAGCAA
256268 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
256295 AACTCTGCAA
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:256779 original size:2 final size:2
Alignment explanation
Indices: 256713--256765 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
256703 AAGTTTGCTT
256713 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
256755 TA TA TA TA TA T
1 TA TA TA TA TA T
256766 TTCTAATTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:259748 original size:24 final size:24
Alignment explanation
Indices: 259700--259749 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
259690 TAAAATAATA
*
259700 TAAAATTTAAAATTACTTTTATAT
1 TAAAATTTAAAATTAATTTTATAT
*
259724 TAAAATTTATAATTAAATTTT-TAT
1 TAAAATTTAAAATT-AATTTTATAT
259748 TA
1 TA
259750 TTTAGACAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TAAAATTTAAAATTAATTTTATAT
Found at i:261631 original size:77 final size:77
Alignment explanation
Indices: 261532--261696 Score: 280
Period size: 77 Copynumber: 2.2 Consensus size: 77
261522 GATATTATGA
*
261532 ATATATTAAAT-ATTTTAAAATTTTTTATATATTT-AAAGGATTATATTTTGGACTCATATTCAA
1 ATATATTAAATAATTTTAAAATTTTTTATATATTTGAAA-GATTATATTTTAGACTCATATTCAA
*
261595 ATGTATTAGACAT
65 ATATATTAGACAT
*
261608 ATATTTTAAATAATTTTAAAATTTTTTATATATTTGAAAGATTATATTTTAGACTCATATTCAAA
1 ATATATTAAATAATTTTAAAATTTTTTATATATTTGAAAGATTATATTTTAGACTCATATTCAAA
261673 TATATTAGACAT
66 TATATTAGACAT
261685 ATATATTAAATA
1 ATATATTAAATA
261697 TAAATATAAA
Statistics
Matches: 83, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
76 10 0.12
77 70 0.84
78 3 0.04
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (77 bp):
ATATATTAAATAATTTTAAAATTTTTTATATATTTGAAAGATTATATTTTAGACTCATATTCAAA
TATATTAGACAT
Found at i:261688 original size:21 final size:22
Alignment explanation
Indices: 261651--261698 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
261641 TTGAAAGATT
*
261651 ATATTTTAGACTCATAT-TCAA
1 ATATATTAGACTCATATATCAA
*
261672 ATATATTAGACAT-ATATATTAA
1 ATATATTAGAC-TCATATATCAA
261694 ATATA
1 ATATA
261699 AATATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (22 bp):
ATATATTAGACTCATATATCAA
Found at i:264115 original size:27 final size:29
Alignment explanation
Indices: 264061--264133 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 29
264051 CTCTATTACA
264061 ATAATATTATAAAATTTATAATATAAAT-T
1 ATAATATT-TAAAATTTATAATATAAATAT
264090 ATTAATATATTAAAATTTAT-A-A-AAATAT
1 A-TAATAT-TTAAAATTTATAATATAAATAT
*
264118 AAAATATTTTAAAATT
1 ATAATA-TTTAAAATT
264134 ATCATAACAC
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
27 16 0.41
28 4 0.10
29 2 0.05
30 16 0.41
31 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
ATAATATTTAAAATTTATAATATAAATAT
Found at i:266609 original size:17 final size:17
Alignment explanation
Indices: 266587--266626 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
266577 TTCTGATTCT
**
266587 TTATATTTTTTAAATAA
1 TTATATTTGATAAATAA
*
266604 TTATATTTGATAAATAT
1 TTATATTTGATAAATAA
266621 TTATAT
1 TTATAT
266627 ATAAAAATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TTATATTTGATAAATAA
Found at i:269106 original size:20 final size:20
Alignment explanation
Indices: 269076--269122 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
269066 TACGCATGAC
269076 AAATA-TAATT-ATATTATTA
1 AAATATTAATTAAT-TTATTA
*
269095 AATTATTAATTAATTTATTA
1 AAATATTAATTAATTTATTA
269115 AAATATTA
1 AAATATTA
269123 TCATACCTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.17
20 18 0.75
21 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATATTAATTAATTTATTA
Found at i:270802 original size:31 final size:31
Alignment explanation
Indices: 270764--270824 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
270754 GGATTCAGTT
270764 AAATACAAAAAACTTTTATAAAATAATAATA
1 AAATACAAAAAACTTTTATAAAATAATAATA
* *
270795 AAATACAAAAGACTTTTTTAAAATAATAAT
1 AAATACAAAAAACTTTTATAAAATAATAAT
270825 TCACTATGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.31
Consensus pattern (31 bp):
AAATACAAAAAACTTTTATAAAATAATAATA
Found at i:271832 original size:72 final size:72
Alignment explanation
Indices: 271745--271962 Score: 339
Period size: 72 Copynumber: 3.0 Consensus size: 72
271735 TCCTGAAAGC
* * *
271745 TTATTATCACACAAATATAACATTTTCAAACTAGAAAGATTTCCAATTGC-TTCAGGAATTTGAC
1 TTATTATCACTCAAATATAACATTCTCAAGCTAGAAAGATTTCCAATTGCATT-AGGAATTTGAC
*
271809 CTTCCAGG
65 CTTCCAGA
* *
271817 TTATTATCATTCAAATATAACATTCCCAAGCTAGAAAGATTTCCAATTGCATTAGGAATTTGACC
1 TTATTATCACTCAAATATAACATTCTCAAGCTAGAAAGATTTCCAATTGCATTAGGAATTTGACC
271882 TTCCAGA
66 TTCCAGA
* * *
271889 TAATTATTACTCAAATATAGCATTCTCAAGCTAGAAAGATTTCCAATTGCATTAGGAATTTGACC
1 TTATTATCACTCAAATATAACATTCTCAAGCTAGAAAGATTTCCAATTGCATTAGGAATTTGACC
271954 TTCCAGA
66 TTCCAGA
271961 TT
1 TT
271963 GCTTTCAGTT
Statistics
Matches: 133, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
72 131 0.98
73 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (72 bp):
TTATTATCACTCAAATATAACATTCTCAAGCTAGAAAGATTTCCAATTGCATTAGGAATTTGACC
TTCCAGA
Found at i:272786 original size:13 final size:13
Alignment explanation
Indices: 272754--272779 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
272744 ATTTTATTAA
272754 ATATTAATTAATT
1 ATATTAATTAATT
272767 ATATTAATTAATT
1 ATATTAATTAATT
272780 GAGTTAAACT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATTAATTAATT
Found at i:273363 original size:14 final size:15
Alignment explanation
Indices: 273328--273356 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
273318 TGTTATATTA
273328 AAATTTTATAGTTTT
1 AAATTTTATAGTTTT
273343 AAATTTTAT-GTTTT
1 AAATTTTATAGTTTT
273357 TTATTTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (15 bp):
AAATTTTATAGTTTT
Found at i:273755 original size:32 final size:32
Alignment explanation
Indices: 273712--273780 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
273702 TTTATTATAT
273712 TATTAAATATATTAAAATT-TCAAATATAAATA
1 TATTAAATATATTAAAATTATCAAAT-TAAATA
* * *
273744 TATTAAGTATATTAAATTTATCATATTAAATA
1 TATTAAATATATTAAAATTATCAAATTAAATA
273776 TATTA
1 TATTA
273781 TGTTACTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 28 0.85
33 5 0.15
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (32 bp):
TATTAAATATATTAAAATTATCAAATTAAATA
Found at i:273780 original size:9 final size:9
Alignment explanation
Indices: 273712--273760 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
273702 TTTATTATAT
273712 TATTAAATA
1 TATTAAATA
273721 TATTAAA-A
1 TATTAAATA
*
273729 T-TTCAA-A
1 TATTAAATA
273736 TA-TAAATA
1 TATTAAATA
*
273744 TATTAAGTA
1 TATTAAATA
273753 TATTAAAT
1 TATTAAAT
273761 TTATCATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
7 9 0.27
8 5 0.15
9 19 0.58
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (9 bp):
TATTAAATA
Found at i:274311 original size:40 final size:43
Alignment explanation
Indices: 274244--274354 Score: 119
Period size: 44 Copynumber: 2.7 Consensus size: 43
274234 TAAGTTATTA
*
274244 TTATATT-TA-AAATATTATATATTTATATA-TTA-AT-A-AT
1 TTATATTATATAAATATTATAAATTTATATATTTATATCATAT
*
274281 TTATATTATATAAATTTTAATAAATTTATATATTTATATCATAT
1 TTATATTATATAAATATT-ATAAATTTATATATTTATATCATAT
274325 TTATATTATATTTAAA-ATTATTAAATTTAT
1 TTATATTATA--TAAATATTA-TAAATTTAT
274355 TAATATATAT
Statistics
Matches: 61, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
37 7 0.11
38 2 0.03
39 6 0.10
40 12 0.20
41 3 0.05
42 2 0.03
43 1 0.02
44 13 0.21
45 11 0.18
46 4 0.07
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (43 bp):
TTATATTATATAAATATTATAAATTTATATATTTATATCATAT
Found at i:279404 original size:15 final size:16
Alignment explanation
Indices: 279384--279424 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
279374 CCCAAATAAA
279384 AAATTTTAAAT-TCAT
1 AAATTTTAAATATCAT
279399 AAA-TTTAAATATCAT
1 AAATTTTAAATATCAT
*
279414 AAATTTCAAAT
1 AAATTTTAAAT
279425 CTAAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 7 0.30
15 10 0.43
16 6 0.26
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATTTTAAATATCAT
Found at i:280027 original size:26 final size:27
Alignment explanation
Indices: 279965--280039 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
279955 AATATTTATT
*
279965 ATATATTTATATTATTTTTTAATATATC
1 ATATA-TTATATTATTTTTTAAAATATC
* *
279993 ATATTTTATATTATTTTTTAAAAT-TT
1 ATATATTATATTATTTTTTAAAATATC
* *
280019 TTATATTATATTCATATTTTA
1 ATATATTATATT-ATTTTTTA
280040 TATTATATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 11 0.28
27 25 0.62
28 4 0.10
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.63
Consensus pattern (27 bp):
ATATATTATATTATTTTTTAAAATATC
Found at i:280571 original size:31 final size:30
Alignment explanation
Indices: 280535--280626 Score: 105
Period size: 31 Copynumber: 2.9 Consensus size: 30
280525 AATTCAATGA
280535 ATTAAATATAGA-TACTTGTAAATTTGATAAT
1 ATTAAATATA-ATTA-TTGTAAATTTGATAAT
* * *
280566 ATTAAACAAAATTATTTATAAATTTGATGAAT
1 ATTAAATATAATTA-TTGTAAATTTGAT-AAT
280598 ATTAAATATAATTATTCGTAAATTTGATA
1 ATTAAATATAATTATT-GTAAATTTGATA
280627 GTTCATAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
30 1 0.02
31 25 0.49
32 25 0.49
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (30 bp):
ATTAAATATAATTATTGTAAATTTGATAAT
Found at i:280611 original size:32 final size:31
Alignment explanation
Indices: 280535--280626 Score: 114
Period size: 32 Copynumber: 2.9 Consensus size: 31
280525 AATTCAATGA
*
280535 ATTAAATATAGA-TACTTGTAAATTTGATAAT
1 ATTAAATATA-ATTATTTGTAAATTTGATAAT
* * *
280566 ATTAAACAAAATTATTTATAAATTTGATGAAT
1 ATTAAATATAATTATTTGTAAATTTGAT-AAT
*
280598 ATTAAATATAATTATTCGTAAATTTGATA
1 ATTAAATATAATTATTTGTAAATTTGATA
280627 GTTCATAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
30 1 0.02
31 23 0.45
32 27 0.53
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (31 bp):
ATTAAATATAATTATTTGTAAATTTGATAAT
Found at i:281010 original size:5 final size:5
Alignment explanation
Indices: 281000--281038 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
280990 TATTAATAAT
*
281000 TTATA TTATA -TATA TTATT TTATA TTATA TTTATA TTAT
1 TTATA TTATA TTATA TTATA TTATA TTATA -TTATA TTAT
281039 TTTTTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 4 0.13
5 21 0.70
6 5 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTATA
Found at i:281023 original size:19 final size:20
Alignment explanation
Indices: 280999--281041 Score: 70
Period size: 19 Copynumber: 2.1 Consensus size: 20
280989 ATATTAATAA
280999 TTTATATTATA-TATATTAT
1 TTTATATTATATTATATTAT
281018 TTTATATTATATTTATATTAT
1 TTTATATTATA-TTATATTAT
281039 TTT
1 TTT
281042 TTTAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 11 0.50
21 11 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATATTATATTATATTAT
Found at i:282619 original size:19 final size:19
Alignment explanation
Indices: 282591--282627 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
282581 GGTTGTCGAG
* *
282591 GCACTGTTTACGTATACAA
1 GCACTATTTACATATACAA
282610 GCACTATTTACATATACA
1 GCACTATTTACATATACA
282628 GTTATTGTGC
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:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (19 bp):
GCACTATTTACATATACAA
Found at i:286726 original size:34 final size:35
Alignment explanation
Indices: 286688--286771 Score: 145
Period size: 34 Copynumber: 2.5 Consensus size: 35
286678 AGGTGGGAGA
*
286688 ATTGTTGACTAAATAGG-TGATTTGGTGGTTTGCC
1 ATTGTTGACTAAATAGGATGATTTGGTAGTTTGCC
286722 ATTGTTGACTAAAT-GGATGATTTGGTAGTTTGCC
1 ATTGTTGACTAAATAGGATGATTTGGTAGTTTGCC
286756 ATTGTTGACTAAATAG
1 ATTGTTGACTAAATAG
286772 CTAAAAGATA
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
33 2 0.04
34 44 0.94
35 1 0.02
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.40
Consensus pattern (35 bp):
ATTGTTGACTAAATAGGATGATTTGGTAGTTTGCC
Found at i:287703 original size:16 final size:16
Alignment explanation
Indices: 287682--287736 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
287672 TAGGAAGGAA
287682 GGAAAATTAAAAAGAT
1 GGAAAATTAAAAAGAT
*
287698 GGAAAATTGAAAGAGA-
1 GGAAAATT-AAAAAGAT
*
287714 GGAAAATTTGAAAA-AT
1 GGAAAA-TTAAAAAGAT
287730 GGAAAAT
1 GGAAAAT
287737 ATTTTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 2 0.06
16 23 0.70
17 8 0.24
ACGTcount: A:0.58, C:0.00, G:0.24, T:0.18
Consensus pattern (16 bp):
GGAAAATTAAAAAGAT
Found at i:287726 original size:17 final size:16
Alignment explanation
Indices: 287681--287728 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
287671 ATAGGAAGGA
287681 AGGAAAATT-AAAAAG
1 AGGAAAATTGAAAAAG
*
287696 ATGGAAAATTGAAAGAG
1 A-GGAAAATTGAAAAAG
287713 AGGAAAATTTGAAAAA
1 AGGAAAA-TTGAAAAA
287729 TGGAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 14 0.50
17 13 0.46
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (16 bp):
AGGAAAATTGAAAAAG
Found at i:288819 original size:25 final size:24
Alignment explanation
Indices: 288756--288822 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 24
288746 ATCAATTCTG
*
288756 ATTTGAATTTAAAAAAATTCAATCA
1 ATTTG-ATTTAATAAAATTCAATCA
* *
288781 A-TTCATTCTAAATAAAATTTAATCTA
1 ATTTGATT-T-AATAAAATTCAATC-A
288807 ATTTGATTTAATAAAA
1 ATTTGATTTAATAAAA
288823 AAATAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
23 3 0.09
24 3 0.09
25 20 0.59
26 3 0.09
27 5 0.15
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.40
Consensus pattern (24 bp):
ATTTGATTTAATAAAATTCAATCA
Found at i:289099 original size:16 final size:16
Alignment explanation
Indices: 289078--289144 Score: 73
Period size: 16 Copynumber: 4.2 Consensus size: 16
289068 TAAACCCGAT
**
289078 TAACTTAAATTTAAAA
1 TAACTTAAACCTAAAA
289094 TAACTTAAACCTAAAA
1 TAACTTAAACCTAAAA
*
289110 T-AGTATAAACCTAAAA
1 TAACT-TAAACCTAAAA
* *
289126 TAACTTAAAACTACAA
1 TAACTTAAACCTAAAA
289142 TAA
1 TAA
289145 TTCAAACTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
15 2 0.05
16 39 0.91
17 2 0.05
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.28
Consensus pattern (16 bp):
TAACTTAAACCTAAAA
Found at i:289159 original size:32 final size:32
Alignment explanation
Indices: 289089--289178 Score: 94
Period size: 32 Copynumber: 2.8 Consensus size: 32
289079 AACTTAAATT
* *
289089 TAAAATAACTTAAACCTAAAATAGTATAAACC
1 TAAAATAACTTAAAACTAAAATAATATAAACC
* *
289121 TAAAATAACTTAAAACTACAATAAT-TCAAACT
1 TAAAATAACTTAAAACTAAAATAATAT-AAACC
* *
289153 TGAAATAA-TTCGAAACTAAAATAATA
1 TAAAATAACTT-AAAACTAAAATAATA
289179 CGAATAAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
31 3 0.06
32 45 0.94
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (32 bp):
TAAAATAACTTAAAACTAAAATAATATAAACC
Found at i:289174 original size:16 final size:16
Alignment explanation
Indices: 289120--289182 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
289110 TAGTATAAAC
*
289120 CTAAAATAACTT-AAAA
1 CTAAAATAA-TTCGAAA
*
289136 CTACAATAATTC-AAA
1 CTAAAATAATTCGAAA
*
289151 CTTGAAATAATTCGAAA
1 C-TAAAATAATTCGAAA
*
289168 CTAAAATAATACGAA
1 CTAAAATAATTCGAA
289183 TAAAAAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 6 0.15
16 29 0.74
17 4 0.10
ACGTcount: A:0.56, C:0.14, G:0.05, T:0.25
Consensus pattern (16 bp):
CTAAAATAATTCGAAA
Found at i:290055 original size:21 final size:22
Alignment explanation
Indices: 290031--290074 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
290021 TACTTTTATT
290031 TAAAT-TTAATTATAAAAA-ATA
1 TAAATATTAA-TATAAAAATATA
*
290052 TAAATATTTATATAAAAATATA
1 TAAATATTAATATAAAAATATA
290074 T
1 T
290075 TTTAATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:293666 original size:16 final size:17
Alignment explanation
Indices: 293645--293678 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
293635 ATAATATGAA
293645 AAAAATAATAT-AATAT
1 AAAAATAATATAAATAT
293661 AAAAATAATATAAATAT
1 AAAAATAATATAAATAT
293678 A
1 A
293679 TGAATGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAATAATATAAATAT
Found at i:293712 original size:22 final size:26
Alignment explanation
Indices: 293662--293712 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
293652 ATATAATATA
293662 AAAATAATATAAATATATGAATGTATT
1 AAAATAATATAAATATA-GAATGTATT
293689 AAAAT-ATATAAA-ATA-AAT-TATT
1 AAAATAATATAAATATAGAATGTATT
293711 AA
1 AA
293713 TATTTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.25
23 3 0.12
25 3 0.12
26 7 0.29
27 5 0.21
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (26 bp):
AAAATAATATAAATATAGAATGTATT
Found at i:293758 original size:20 final size:20
Alignment explanation
Indices: 293719--293772 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
293709 TTAATATTTT
*
293719 ATAATTTAATTAATAATATA
1 ATAATTTAAATAATAATATA
293739 ATAATTTAAAT-ATAATTATA
1 ATAATTTAAATAATAA-TATA
**
293759 A-AATAAAAATAATA
1 ATAATTTAAATAATA
293773 TGAATATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAATTTAAATAATAATATA
Found at i:293787 original size:15 final size:15
Alignment explanation
Indices: 293769--293802 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
293759 AAATAAAAAT
*
293769 AATATGAATATGTTC
1 AATATAAATATGTTC
*
293784 AATATAAATATGTTT
1 AATATAAATATGTTC
293799 AATA
1 AATA
293803 ATCTCATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (15 bp):
AATATAAATATGTTC
Found at i:294354 original size:15 final size:15
Alignment explanation
Indices: 294320--294371 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
294310 TATTATATAT
294320 TTATATAAATTTTAATA
1 TTATATAAA-TTTAA-A
294337 TTATA-ATAATTTAAA
1 TTATATA-AATTTAAA
294352 TTATATAAATTTAAA
1 TTATATAAATTTAAA
294367 -TATAT
1 TTATAT
294372 TTATATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
14 5 0.15
15 14 0.42
16 7 0.21
17 7 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATATAAATTTAAA
Found at i:294392 original size:19 final size:18
Alignment explanation
Indices: 294314--294401 Score: 60
Period size: 18 Copynumber: 4.9 Consensus size: 18
294304 TTAAGGTATT
*
294314 ATATATTTATATAAATTTTA
1 ATATATTTATAT--ATTTAA
*
294334 ATAT-TATA-ATAATTTAA
1 ATATATTTATAT-ATTTAA
*
294351 AT-TA--TATAAATTTAA
1 ATATATTTATATATTTAA
*
294366 ATATATTTATATATTTAT
1 ATATATTTATATATTTAA
294384 ATGATATTTATATTATTT
1 AT-ATATTTATA-TATTT
294402 TTTATGTAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
15 10 0.18
16 4 0.07
17 8 0.14
18 13 0.23
19 12 0.21
20 9 0.16
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (18 bp):
ATATATTTATATATTTAA
Found at i:295568 original size:2 final size:2
Alignment explanation
Indices: 295561--295599 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
295551 TTGCATTGTA
295561 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
295600 GGGTTTTAAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:296211 original size:22 final size:22
Alignment explanation
Indices: 296167--296211 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
296157 TATTATCATG
296167 TTAAAATATATATAACATGATTA
1 TTAAAATATATATAACA-GATTA
*
296190 TTAACAATATATATCACA-ATTA
1 TTAA-AATATATATAACAGATTA
296212 ATTATGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 4 0.20
24 12 0.60
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (22 bp):
TTAAAATATATATAACAGATTA
Found at i:297105 original size:16 final size:16
Alignment explanation
Indices: 297084--297114 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
297074 ATTTACTGAA
*
297084 ATGTACTGATATCAAG
1 ATGTACTAATATCAAG
297100 ATGTACTAATATCAA
1 ATGTACTAATATCAA
297115 AACAAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (16 bp):
ATGTACTAATATCAAG
Found at i:297782 original size:32 final size:34
Alignment explanation
Indices: 297727--297825 Score: 118
Period size: 32 Copynumber: 3.0 Consensus size: 34
297717 ATAATTTAAA
297727 ATAATAATATAAATATATAAATATATTAAAATTT
1 ATAATAATATAAATATATAAATATATTAAAATTT
*
297761 ATAA-AATATAAAT-TATTAATATATTAAAATTT
1 ATAATAATATAAATATATAAATATATTAAAATTT
* *
297793 AT-AT-ATA-AAATATTTTAAATATAATTATAATTT
1 ATAATAATATAAATA-TATAAATAT-ATTAAAATTT
297826 TTAAAAAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
30 4 0.07
31 4 0.07
32 27 0.47
33 18 0.32
34 4 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (34 bp):
ATAATAATATAAATATATAAATATATTAAAATTT
Found at i:297798 original size:14 final size:14
Alignment explanation
Indices: 297747--297803 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
297737 AAATATATAA
297747 ATATATTAAAATTT
1 ATATATTAAAATTT
* *
297761 ATAAAATATAAATTATTA
1 AT-ATAT-TAAA--ATTT
297779 ATATATTAAAATTT
1 ATATATTAAAATTT
297793 ATATA-TAAAAT
1 ATATATTAAAAT
297804 ATTTTAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
13 6 0.17
14 10 0.29
15 3 0.09
16 8 0.23
17 3 0.09
18 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATATTAAAATTT
Found at i:297825 original size:18 final size:17
Alignment explanation
Indices: 297710--297826 Score: 66
Period size: 16 Copynumber: 6.9 Consensus size: 17
297700 TGATATGATT
*
297710 ATATAATATAATTTAAA
1 ATATAATATAATTTTAA
*
297727 ATAATAATATAAATATATAA
1 AT-ATAATAT-AAT-TTTAA
* *
297747 ATATATTAAAATTTATAA
1 ATATAATATAATTT-TAA
297765 A-AT-ATA-AATTATT-A
1 ATATAATATAATT-TTAA
* * *
297779 ATATATTA-AAATTTAT
1 ATATAATATAATTTTAA
*
297795 ATATAAAAT-ATTTTAA
1 ATATAATATAATTTTAA
297811 ATATAATTATAATTTT
1 ATATAA-TATAATTTT
297827 TAAAAAATAT
Statistics
Matches: 75, Mismatches: 14, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
14 2 0.03
15 9 0.12
16 25 0.33
17 7 0.09
18 19 0.25
19 8 0.11
20 5 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATATAATTTTAA
Found at i:298109 original size:17 final size:15
Alignment explanation
Indices: 298075--298130 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 15
298065 ATATTATATG
298075 AATATAAAAAATTAA
1 AATATAAAAAATTAA
298090 AATATAAAAAATTTATA
1 AATATAAAAAA-TTA-A
*
298107 AATAAATAAATATATTAA
1 AAT--ATAAA-AAATTAA
298125 AATATA
1 AATATA
298131 TACCTAACGT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
15 11 0.31
16 6 0.17
17 4 0.11
18 4 0.11
19 8 0.23
20 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AATATAAAAAATTAA
Found at i:298568 original size:13 final size:13
Alignment explanation
Indices: 298550--298574 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
298540 GAGATCGAGT
298550 TATTTATATATTG
1 TATTTATATATTG
298563 TATTTATATATT
1 TATTTATATATT
298575 TTTATATTTT
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:0.04, T:0.64
Consensus pattern (13 bp):
TATTTATATATTG
Found at i:298701 original size:27 final size:27
Alignment explanation
Indices: 298631--298705 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
298621 AAAGTCATCA
* *
298631 TTTATTTGTCAAAAATAGTAATTATTT
1 TTTATTTGTCAAAAATGGTGATTATTT
* * *
298658 TGTATTTGTTAAAAATGGTGGTT-TCTT
1 TTTATTTGTCAAAAATGGTGATTAT-TT
298685 TTTATTTGTCAAAAATGGTGA
1 TTTATTTGTCAAAAATGGTGA
298706 CATGTTATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 1 0.03
27 38 0.97
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (27 bp):
TTTATTTGTCAAAAATGGTGATTATTT
Found at i:301684 original size:21 final size:21
Alignment explanation
Indices: 301658--301709 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
301648 GGTATTTACA
*
301658 AAGAAATATGGATCTTCTAGC
1 AAGAAAGATGGATCTTCTAGC
301679 AAGAAAGATGGATCTTCTAGC
1 AAGAAAGATGGATCTTCTAGC
301700 AAGAAAGATG
1 AAGAAAGATG
301710 TTCGCTACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (21 bp):
AAGAAAGATGGATCTTCTAGC
Found at i:303672 original size:13 final size:13
Alignment explanation
Indices: 303650--303683 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
303640 AGACTCCCTC
303650 ATCCCTCTCTTGT
1 ATCCCTCTCTTGT
*
303663 ATCTCTCTCTTGT
1 ATCCCTCTCTTGT
303676 ATCCCTCT
1 ATCCCTCT
303684 TCAATTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.09, C:0.38, G:0.06, T:0.47
Consensus pattern (13 bp):
ATCCCTCTCTTGT
Found at i:304613 original size:6 final size:6
Alignment explanation
Indices: 304602--304632 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
304592 TTTATGATTG
304602 TAATTA TAATTA TAATTA TAATTA TAATTA T
1 TAATTA TAATTA TAATTA TAATTA TAATTA T
304633 TGTGTTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATTA
Found at i:305946 original size:20 final size:20
Alignment explanation
Indices: 305921--305966 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
305911 AAATAGAGGC
*
305921 TCCCTCCTCCATCTCAGGTA
1 TCCCTCATCCATCTCAGGTA
* **
305941 TCCCTCATCCTTCTCTTGTA
1 TCCCTCATCCATCTCAGGTA
305961 TCCCTC
1 TCCCTC
305967 TTCAATTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.46, G:0.07, T:0.37
Consensus pattern (20 bp):
TCCCTCATCCATCTCAGGTA
Found at i:310488 original size:20 final size:20
Alignment explanation
Indices: 310463--310508 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
310453 AAATAGAGGC
*
310463 TCCCTCCTCCATCTCAGGTA
1 TCCCTCATCCATCTCAGGTA
* **
310483 TCCCTCATCCTTCTCTTGTA
1 TCCCTCATCCATCTCAGGTA
310503 TCCCTC
1 TCCCTC
310509 TTCAATTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.46, G:0.07, T:0.37
Consensus pattern (20 bp):
TCCCTCATCCATCTCAGGTA
Found at i:310879 original size:20 final size:20
Alignment explanation
Indices: 310856--310905 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
310846 TTAATTCGAT
310856 TTAAATTATTATTTATTT-AA
1 TTAAATTATT-TTTATTTAAA
*
310876 TTAAAAATATTTTTATTTAAA
1 TT-AAATTATTTTTATTTAAA
*
310897 TTTAATTAT
1 TTAAATTAT
310906 AAAAATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTAAATTATTTTTATTTAAA
Found at i:310935 original size:18 final size:19
Alignment explanation
Indices: 310907--310944 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
310897 TTTAATTATA
310907 AAAATATATAAATATTAAT
1 AAAATATATAAATATTAAT
*
310926 AAAA-ATATAAATTTTAAT
1 AAAATATATAAATATTAAT
310944 A
1 A
310945 TTTTTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATATATAAATATTAAT
Found at i:310972 original size:20 final size:18
Alignment explanation
Indices: 310947--311000 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
310937 TTTTAATATT
310947 TTTTAAATAATAATAAAAAA
1 TTTTAAATAA-AAT-AAAAA
* *
310967 TTTTAAATTAAATCAAAA
1 TTTTAAATAAAATAAAAA
*
310985 TTTTAAA-AAATTAAAA
1 TTTTAAATAAAATAAAA
311001 TAAAAATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 6 0.21
18 11 0.38
19 3 0.10
20 9 0.31
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
TTTTAAATAAAATAAAAA
Found at i:314261 original size:24 final size:24
Alignment explanation
Indices: 314233--314278 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
314223 AATAAAAATT
314233 AGCTACCAATTTTGACAAACAACA
1 AGCTACCAATTTTGACAAACAACA
* *
314257 AGCTACCATTTTTTACAAACAA
1 AGCTACCAATTTTGACAAACAA
314279 AAAATAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (24 bp):
AGCTACCAATTTTGACAAACAACA
Found at i:314301 original size:27 final size:26
Alignment explanation
Indices: 314261--314330 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 26
314251 ACAACAAGCT
*
314261 ACCATTTTTTACAAACAAAAAATAACC
1 ACCATATTTTACAAACAAAAAA-AACC
* **
314288 ACCATATTTGACAAATACAAAGGAAACC
1 ACCATATTTTAC-AA-ACAAAAAAAACC
314316 ACCATATTTTACAAA
1 ACCATATTTTACAAA
314331 TACAAAGGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
26 1 0.03
27 12 0.33
28 17 0.47
29 6 0.17
ACGTcount: A:0.50, C:0.21, G:0.04, T:0.24
Consensus pattern (26 bp):
ACCATATTTTACAAACAAAAAAAACC
Found at i:314320 original size:28 final size:28
Alignment explanation
Indices: 314284--314338 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
314274 AACAAAAAAT
314284 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
*
314312 AACCACCATATTTTACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
314339 GTGGCATTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.49, C:0.22, G:0.09, T:0.20
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:318709 original size:27 final size:28
Alignment explanation
Indices: 318669--318738 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
318659 ACAACAAGCT
* *
318669 ACCATTTTTTACAAACA-AAAA-ATAACC
1 ACCATATTTGACAAACATAAAAGA-AACC
* *
318696 ACCATATTTGACAAATATAAAAGAAATC
1 ACCATATTTGACAAACATAAAAGAAACC
318724 ACCATATTTGACAAA
1 ACCATATTTGACAAA
318739 TACAAAAGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 14 0.38
28 22 0.59
29 1 0.03
ACGTcount: A:0.51, C:0.19, G:0.04, T:0.26
Consensus pattern (28 bp):
ACCATATTTGACAAACATAAAAGAAACC
Found at i:319206 original size:16 final size:17
Alignment explanation
Indices: 319182--319222 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
319172 TTAATAATTT
*
319182 TAAATATAATAT-AATA
1 TAAAAATAATATAAATA
319198 TAAAAATAATATAAATA
1 TAAAAATAATATAAATA
*
319215 TATAAATA
1 TAAAAATA
319223 TATTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAAATAATATAAATA
Found at i:319217 original size:8 final size:8
Alignment explanation
Indices: 319182--319230 Score: 53
Period size: 9 Copynumber: 5.6 Consensus size: 8
319172 TTAATAATTT
319182 TAAATATAA
1 TAAATAT-A
319191 TATAATATA
1 TA-AATATA
*
319200 AAAATAATA
1 TAAAT-ATA
319209 TAAATATA
1 TAAATATA
319217 TAAATATA
1 TAAATATA
319225 TTAAAT
1 -TAAAT
319231 TTTATATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 14 0.40
9 16 0.46
10 5 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
TAAATATA
Found at i:319229 original size:17 final size:17
Alignment explanation
Indices: 319182--319230 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
319172 TTAATAATTT
*
319182 TAAATATAATATAATATA
1 TAAATATATTA-AATATA
*
319200 AAAATA-ATATAAATATA
1 TAAATATAT-TAAATATA
319217 TAAATATATTAAAT
1 TAAATATATTAAAT
319231 TTTATATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAATATATTAAATATA
Found at i:319267 original size:32 final size:33
Alignment explanation
Indices: 319203--319281 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 33
319193 TAATATAAAA
*
319203 ATAATATAAATATATAAATATATTAAATTTTAT
1 ATAAAATAAATATATAAATATATTAAATTTTAT
* *
319236 ATAAAATAAAT-TATTAATATTTTATAA-TTTAT
1 ATAAAATAAATATATAAATATATTA-AATTTTAT
319268 ATAAATATATAATA
1 ATAAA-ATA-AATA
319282 ATTTAAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
32 21 0.54
33 15 0.38
34 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
ATAAAATAAATATATAAATATATTAAATTTTAT
Found at i:319688 original size:26 final size:25
Alignment explanation
Indices: 319653--319702 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
319643 TTTTAATAAA
*
319653 AATATATTAATTATTAAATTAAATT
1 AATATATTAATAATTAAATTAAATT
*
319678 AATATATTTAATAATTATATTAAAT
1 AATATA-TTAATAATTAAATTAAAT
319703 ACATTGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AATATATTAATAATTAAATTAAATT
Found at i:320002 original size:5 final size:5
Alignment explanation
Indices: 319984--320143 Score: 78
Period size: 5 Copynumber: 33.8 Consensus size: 5
319974 ATTTAATATT
* *
319984 TTATA -TAT- TTATA TTATA TT-TA TT-TA TT-TAA TTATA TTAAA TTATT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTAT-A TTATA TTATA TTATA
* * * *
320030 TTAAA ATATTA TGTAT- TTAT- TTAAA TT-TA -TATA TTA-A TAATA -TATA
1 TTATA TTA-TA T-TATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * * *
320076 TTATA TAAAA TT-TA ATATA TTA-A -TATA TTTATA TTATA TTTATA TTATT
1 TTATA TTATA TTATA TTATA TTATA TTATA -TTATA TTATA -TTATA TTATA
*
320125 TTTTA TTATA TTATA TTAT
1 TTATA TTATA TTATA TTAT
320144 TTTTCAAAAA
Statistics
Matches: 117, Mismatches: 22, Indels: 32
0.68 0.13 0.19
Matches are distributed among these distances:
3 3 0.03
4 34 0.29
5 66 0.56
6 12 0.10
7 2 0.02
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:320032 original size:23 final size:23
Alignment explanation
Indices: 319980--320032 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
319970 ATAAATTTAA
* *
319980 TATTTTATATATTTATATTATAT
1 TATTTTATATAATTATATTAAAT
*
320003 T-TATTTATTTAATTATATTAAAT
1 TAT-TTTATATAATTATATTAAAT
320026 TATTTTA
1 TATTTTA
320033 AAATATTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 1 0.04
23 23 0.92
24 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTTTATATAATTATATTAAAT
Found at i:320083 original size:14 final size:14
Alignment explanation
Indices: 320057--320114 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
320047 TATTTAAATT
320057 TATATATTA-ATAA
1 TATATATTATATAA
320070 TATATATTATATAA
1 TATATATTATATAA
* * *
320084 AATTTAATATATTAA
1 TATATATTATA-TAA
*
320099 TATAT-TTATATTA
1 TATATATTATATAA
320112 TAT
1 TAT
320115 TTATATTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
13 14 0.39
14 16 0.44
15 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATATATTATATAA
Found at i:320087 original size:31 final size:33
Alignment explanation
Indices: 320052--320114 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
320042 GTATTTATTT
320052 AAATTT-ATATATTAATA-ATATATATTATATA
1 AAATTTAATATATTAATATATATATATTATATA
*
320083 AAATTTAATATATTAATATATTTATATTATAT
1 AAATTTAATATATTAATATATATATATTATAT
320115 TTATATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 6 0.21
32 11 0.38
33 12 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
AAATTTAATATATTAATATATATATATTATATA
Found at i:320114 original size:21 final size:21
Alignment explanation
Indices: 319986--320192 Score: 64
Period size: 21 Copynumber: 10.0 Consensus size: 21
319976 TTAATATTTT
319986 ATATATTTATATTATAT-TT-
1 ATATATTTATATTATATATTA
* *
320005 ATTTATTTA-ATTATAT-TAA
1 ATATATTTATATTATATATTA
**
320024 AT-TATTT-TAAAATATTATGT-
1 ATATATTTATATTATA-TAT-TA
* *
320044 ATTTATTTAAATTTATATATTA
1 ATATATTTATA-TTATATATTA
*
320066 ATA-ATATATATTATATAAAATTTA
1 ATATATTTATATTATAT---A-TTA
* *
320090 ATATATTAATA-TATTTA-TA
1 ATATATTTATATTATATATTA
* * *
320109 TTATATTTATATTATTTTTTA
1 ATATATTTATATTATATATTA
* *
320130 TTATA-TTATATTAT-TTTTCA
1 ATATATTTATATTATATATT-A
*
320150 A-AAATTTTATATTATAT-TTA
1 ATATA-TTTATATTATATATTA
* * *
320170 CTTTATATATAATTATATATTA
1 ATATATTTAT-ATTATATATTA
320192 A
1 A
320193 ATTTCGCTTT
Statistics
Matches: 141, Mismatches: 24, Indels: 43
0.68 0.12 0.21
Matches are distributed among these distances:
18 17 0.12
19 28 0.20
20 29 0.21
21 38 0.27
22 10 0.07
23 4 0.03
24 10 0.07
25 5 0.04
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATATTTATATTATATATTA
Found at i:320463 original size:27 final size:27
Alignment explanation
Indices: 320433--320501 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
320423 ATGCTTTATA
320433 ATTAAAAATTT-TATAATTATTTTAA-AT
1 ATTAAAAATTTATATAA--ATTTTAATAT
* * *
320460 ATTATATATTTATTTAAATTTTAATAT
1 ATTAAAAATTTATATAAATTTTAATAT
*
320487 ATTAATAATTTATAT
1 ATTAAAAATTTATAT
320502 TTTTATATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
26 7 0.21
27 22 0.67
28 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
ATTAAAAATTTATATAAATTTTAATAT
Found at i:320477 original size:19 final size:20
Alignment explanation
Indices: 320434--320489 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
320424 TGCTTTATAA
* * *
320434 TTAAAAATTTTATAATTATT
1 TTAAATATTATATATTTATT
320454 TTAAATATTATATATTTA-T
1 TTAAATATTATATATTTATT
*
320473 TTAAATTTTAATATATT
1 TTAAATATT-ATATATT
320490 AATAATTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.29
20 22 0.71
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTAAATATTATATATTTATT
Found at i:320501 original size:15 final size:16
Alignment explanation
Indices: 320479--320520 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
320469 TTATTTAAAT
320479 TTTAATATATTAATAA
1 TTTAATATATTAATAA
* * *
320495 TTT-ATATTTTTATAT
1 TTTAATATATTAATAA
320510 TTTAATATATT
1 TTTAATATATT
320521 TATATGATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTAATATATTAATAA
Found at i:320503 original size:23 final size:24
Alignment explanation
Indices: 320450--320525 Score: 84
Period size: 23 Copynumber: 3.1 Consensus size: 24
320440 ATTTTATAAT
320450 TATTTTAA-ATATTATATATTTATTTA
1 TATTTTAATATATTA-ATA--TATTTA
*
320476 AATTTTAATATATTAATA-ATTTA
1 TATTTTAATATATTAATATATTTA
* *
320499 TATTTTTATATTTTAATATATTTA
1 TATTTTAATATATTAATATATTTA
320523 TAT
1 TAT
320526 GATATTTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
23 20 0.45
24 8 0.18
26 10 0.23
27 6 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TATTTTAATATATTAATATATTTA
Found at i:323017 original size:27 final size:29
Alignment explanation
Indices: 322983--323044 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
322973 CAAATACAAT
* *
322983 ATATATAAAATAAT-TAAATATAAAATAA
1 ATATATAAAACAATATAAACATAAAATAA
* *
323011 A-ATATAATACAATATGAACATAAAATAA
1 ATATATAAAACAATATAAACATAAAATAA
323039 ATATAT
1 ATATAT
323045 TAACGTATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 10 0.36
28 14 0.50
29 4 0.14
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.31
Consensus pattern (29 bp):
ATATATAAAACAATATAAACATAAAATAA
Found at i:323024 original size:22 final size:21
Alignment explanation
Indices: 322974--323041 Score: 77
Period size: 20 Copynumber: 3.2 Consensus size: 21
322964 TACACGATAC
*
322974 AAATACAATAT-ATATAAAAT
1 AAATACAATATAAAATAAAAT
*
322994 AATTA-AATATAAAATAAAAT
1 AAATACAATATAAAATAAAAT
*
323014 ATAATACAATATGAACATAAAAT
1 A-AATACAATAT-AAAATAAAAT
323037 AAATA
1 AAATA
323042 TATTAACGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 5 0.12
20 13 0.32
21 3 0.08
22 9 0.22
23 10 0.25
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.28
Consensus pattern (21 bp):
AAATACAATATAAAATAAAAT
Found at i:323455 original size:2 final size:2
Alignment explanation
Indices: 323448--323475 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
323438 GTAAAGAACA
323448 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
323476 TAAGTCTACA
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:325706 original size:33 final size:35
Alignment explanation
Indices: 325664--325728 Score: 107
Period size: 33 Copynumber: 1.9 Consensus size: 35
325654 AAAAAATATT
*
325664 TTATTAAATAATATTTT-TAAT-ATTACTTTTGAA
1 TTATTAAATAATATTTTATAATAAATACTTTTGAA
325697 TTATTAAATAATATTTTATAATAAATACTTTT
1 TTATTAAATAATATTTTATAATAAATACTTTT
325729 TAAATTTAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 17 0.59
34 4 0.14
35 8 0.28
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.54
Consensus pattern (35 bp):
TTATTAAATAATATTTTATAATAAATACTTTTGAA
Done.