Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold163
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: 1788591
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.32
Warning! 179834 characters in sequence are not A, C, G, or T
File 10 of 13
Found at i:1278240 original size:28 final size:27
Alignment explanation
Indices: 1278209--1278270 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
1278199 TGATATGATA
1278209 TAAATATTATAAAAATATATAA-ATTTAT
1 TAAATATTATAAAAATATATAATA-TT-T
*
1278237 TAAA-ATTTATATAAATATATAATATTT
1 TAAATA-TTATAAAAATATATAATATTT
1278264 TAAATAT
1 TAAATAT
1278271 AATTATTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
27 7 0.23
28 22 0.73
29 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TAAATATTATAAAAATATATAATATTT
Found at i:1278265 original size:20 final size:20
Alignment explanation
Indices: 1278206--1278256 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
1278196 ATATGATATG
*
1278206 ATATAAATAT-TATAAAA-AT
1 ATATAAATATAT-TAAAATTT
*
1278225 ATATAAATTTATTAAAATTT
1 ATATAAATATATTAAAATTT
1278245 ATATAAATATAT
1 ATATAAATATAT
1278257 AATATTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATAAATATATTAAAATTT
Found at i:1278722 original size:17 final size:17
Alignment explanation
Indices: 1278702--1278743 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1278692 TTTAAAAATT
1278702 ATATATATTTATATTAA
1 ATATATATTTATATTAA
* *
1278719 ATATATTTTTATATTTA
1 ATATATATTTATATTAA
1278736 ATGATATA
1 AT-ATATA
1278744 AAATTAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
ATATATATTTATATTAA
Found at i:1278796 original size:29 final size:29
Alignment explanation
Indices: 1278710--1278798 Score: 103
Period size: 29 Copynumber: 3.1 Consensus size: 29
1278700 TTATATATAT
*
1278710 TTATATTAAAT-ATATTTTTATATTTA-A
1 TTATATTAAATAATATTTTTATATTGATA
* *
1278737 TGATATAAAATTAATATTTTTATATTTGATA
1 TTATATTAAA-TAATATTTTTATA-TTGATA
1278768 TTAT-TTAAATAATATTTTTATATTCGATA
1 TTATATTAAATAATATTTTTATATT-GATA
1278797 TT
1 TT
1278799 TTTCGAATCC
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
27 8 0.15
28 3 0.06
29 30 0.58
30 7 0.13
31 4 0.08
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.56
Consensus pattern (29 bp):
TTATATTAAATAATATTTTTATATTGATA
Found at i:1278799 original size:15 final size:14
Alignment explanation
Indices: 1278750--1278801 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
1278740 TATAAAATTA
1278750 ATATTTTTATATTTG
1 ATATTTTTATA-TTG
* *
1278765 ATATTATTTA-AATA
1 ATATT-TTTATATTG
1278779 ATATTTTTATATTCG
1 ATATTTTTATATT-G
1278794 ATATTTTT
1 ATATTTTT
1278802 CGAATCCGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
13 4 0.13
14 8 0.27
15 14 0.47
16 4 0.13
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.62
Consensus pattern (14 bp):
ATATTTTTATATTG
Found at i:1280434 original size:18 final size:18
Alignment explanation
Indices: 1280411--1280467 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
1280401 AAAAATATAT
*
1280411 ATAAATATAATATATTTA
1 ATAAATAAAATATATTTA
* *
1280429 ATAAATAAAAT-TAATATG
1 ATAAATAAAATAT-ATTTA
* *
1280447 ATTAATACAATATATTTA
1 ATAAATAAAATATATTTA
1280465 ATA
1 ATA
1280468 TATTTGTTAT
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
17 1 0.03
18 27 0.93
19 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (18 bp):
ATAAATAAAATATATTTA
Found at i:1280436 original size:22 final size:23
Alignment explanation
Indices: 1280411--1280472 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 23
1280401 AAAAATATAT
1280411 ATAAATATAATATATTTAATA-A
1 ATAAATATAATATATTTAATACA
1280433 ATAAA-ATTAATATGA-TTAATACA
1 ATAAATA-TAATAT-ATTTAATACA
* *
1280456 ATATATTTAATATATTT
1 ATAAATATAATATATTT
1280473 GTTATATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
21 1 0.03
22 18 0.55
23 14 0.42
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
ATAAATATAATATATTTAATACA
Found at i:1280467 original size:9 final size:9
Alignment explanation
Indices: 1280455--1280513 Score: 63
Period size: 9 Copynumber: 7.0 Consensus size: 9
1280445 TGATTAATAC
1280455 AATATATTT
1 AATATATTT
1280464 AATATATTT
1 AATATATTT
**
1280473 GTTATA-TT
1 AATATATTT
1280481 --TATATTT
1 AATATATTT
*
1280488 AAAAT-TTT
1 AATATATTT
1280496 AATATATTT
1 AATATATTT
1280505 AATATATTT
1 AATATATTT
1280514 TATTTTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
6 4 0.10
7 2 0.05
8 9 0.21
9 27 0.64
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (9 bp):
AATATATTT
Found at i:1280500 original size:41 final size:42
Alignment explanation
Indices: 1280455--1280536 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 42
1280445 TGATTAATAC
*
1280455 AATATATTTAATATA-TTTGTTATATTTATATTTA-AAATTTT
1 AATATATTTAATATATTTTATTATATTT-TATTTATAAATTTT
*
1280496 AATATATTTAATATATTTTATTTTATTTTATTTATAAATTT
1 AATATATTTAATATATTTTATTATATTTTATTTATAAATTT
1280537 AACACCAAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 21 0.57
42 16 0.43
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (42 bp):
AATATATTTAATATATTTTATTATATTTTATTTATAAATTTT
Found at i:1281104 original size:3 final size:3
Alignment explanation
Indices: 1281096--1281141 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
1281086 AAATTTACAG
1281096 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1281142 AACCCCGCAG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1281241 original size:34 final size:32
Alignment explanation
Indices: 1281187--1281251 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1281177 CCAGTCTACA
*
1281187 TATATCTGCAGCTTGAAGAGAGACAAGTTTAT
1 TATATATGCAGCTTGAAGAGAGACAAGTTTAT
1281219 TATATATGCAGCTTGAAGAGAGACAAGTTTAT
1 TATATATGCAGCTTGAAGAGAGACAAGTTTAT
1281251 T
1 T
1281252 CGTTTCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (32 bp):
TATATATGCAGCTTGAAGAGAGACAAGTTTAT
Found at i:1281410 original size:2 final size:2
Alignment explanation
Indices: 1281403--1281432 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1281393 GAATTTCCCA
1281403 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
1281433 TTTATCAAAG
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:1282312 original size:17 final size:18
Alignment explanation
Indices: 1282290--1282323 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1282280 TCATTATATT
1282290 TAAATA-TATAAAAAATA
1 TAAATATTATAAAAAATA
*
1282307 TAAATATTTTAAAAAAT
1 TAAATATTATAAAAAAT
1282324 TATTATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAATATTATAAAAAATA
Found at i:1282563 original size:22 final size:22
Alignment explanation
Indices: 1282538--1282582 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1282528 AAAAAATATT
1282538 TTTTTATAA-ATATTTTATTTTA
1 TTTTTA-AATATATTTTATTTTA
* *
1282560 TTTTTAAATTTTTTTTATTTTA
1 TTTTTAAATATATTTTATTTTA
1282582 T
1 T
1282583 AATGAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTTAAATATATTTTATTTTA
Found at i:1282573 original size:20 final size:19
Alignment explanation
Indices: 1282534--1282584 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1282524 AAATAAAAAA
1282534 TATTTTTTTATAAATATTT
1 TATTTTTTTATAAATATTT
*
1282553 TATTTTATTTTTAAAT-TTT
1 TATTTT-TTTATAAATATTT
1282572 T-TTTATTTTATAA
1 TATTT-TTTTATAA
1282585 TGAATCAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 9 0.32
19 11 0.39
20 8 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTTTTTATAAATATTT
Found at i:1282760 original size:32 final size:32
Alignment explanation
Indices: 1282702--1282762 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
1282692 TATAATTATA
* * * *
1282702 ATTATTAAATTAAAAATAATATTATTTTTAAT
1 ATTAATAAAATAAAAATAAAAATATTTTTAAT
1282734 ATTAATAAAATAAAAATAAAAATATTTTT
1 ATTAATAAAATAAAAATAAAAATATTTTT
1282763 TATTATCTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
ATTAATAAAATAAAAATAAAAATATTTTTAAT
Found at i:1283235 original size:22 final size:23
Alignment explanation
Indices: 1283210--1283261 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
1283200 TTTATTTTAT
1283210 TATTTAAAAATATTTA-AATTAA
1 TATTTAAAAATATTTATAATTAA
* * *
1283232 TATTTATATATTTTTATAATTAA
1 TATTTAAAAATATTTATAATTAA
1283255 -ATTTAAA
1 TATTTAAA
1283262 TAAAAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTTAAAAATATTTATAATTAA
Found at i:1283970 original size:162 final size:162
Alignment explanation
Indices: 1283700--1284029 Score: 561
Period size: 162 Copynumber: 2.0 Consensus size: 162
1283690 TTGTGCCTCA
* *
1283700 CAATGACAGCAGAGTTAGGTAAGTTGTGGGAGAATCTAACGCTGACAGAGGAAGAAAAGGAATGC
1 CAATGACAGCAGAGTTAGGTAAGTTGTGGGACAATCTAACGCTAACAGAGGAAGAAAAGGAATGC
* **
1283765 GTAGACACAAAAGATATGGGAGACAGCAGCAATAGCGAGTGGTGCAACAAATGGTTGGGAGCAAA
66 GTAGACACAAAAGATATGGGAGACAGCAGCAATAGCAAGTGGTGCAACAAATGGCCGGGAGCAAA
*
1283830 ATTATTAACAAATCGTCCATGCAACAAAGAGG
131 ATTATTAACAAATCGTCCATACAACAAAGAGG
* * * *
1283862 CAATGACATCAGAGTTAGGTGAGTTTTGGGACAATCTAACGCTAACAGAGGGAGAAAAGGAATGC
1 CAATGACAGCAGAGTTAGGTAAGTTGTGGGACAATCTAACGCTAACAGAGGAAGAAAAGGAATGC
*
1283927 GTAGACACAAAAGATATGGGAGACAGCAGCAATAGCAAGTGGTGCAAGAAATGGCCGGGAGCAAA
66 GTAGACACAAAAGATATGGGAGACAGCAGCAATAGCAAGTGGTGCAACAAATGGCCGGGAGCAAA
1283992 ATTATTAACAAATCGTCCATACAACAAAGAGG
131 ATTATTAACAAATCGTCCATACAACAAAGAGG
1284024 CAATGA
1 CAATGA
1284030 TAAACACTCT
Statistics
Matches: 157, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
162 157 1.00
ACGTcount: A:0.41, C:0.15, G:0.28, T:0.17
Consensus pattern (162 bp):
CAATGACAGCAGAGTTAGGTAAGTTGTGGGACAATCTAACGCTAACAGAGGAAGAAAAGGAATGC
GTAGACACAAAAGATATGGGAGACAGCAGCAATAGCAAGTGGTGCAACAAATGGCCGGGAGCAAA
ATTATTAACAAATCGTCCATACAACAAAGAGG
Found at i:1287363 original size:5 final size:5
Alignment explanation
Indices: 1287350--1287423 Score: 66
Period size: 5 Copynumber: 15.4 Consensus size: 5
1287340 AATTTAATAT
* * *
1287350 TTATT TTATA TTATA TT-TA TTATT TTATA TTATA -T-TA TTATT TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* *
1287397 TTTTA TTATA -TATA TTAAA TTTATA TT
1 TTATA TTATA TTATA TTATA -TTATA TT
1287424 TTTATATAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
3 2 0.04
4 10 0.18
5 39 0.71
6 4 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (5 bp):
TTATA
Found at i:1287374 original size:19 final size:19
Alignment explanation
Indices: 1287350--1287403 Score: 92
Period size: 18 Copynumber: 2.9 Consensus size: 19
1287340 AATTTAATAT
1287350 TTATTTTATATTATATTTA
1 TTATTTTATATTATATTTA
1287369 TTATTTTATATTATA-TTA
1 TTATTTTATATTATATTTA
*
1287387 TTATTTTATATTTTATT
1 TTATTTTATATTATATT
1287404 ATATATATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
18 17 0.52
19 16 0.48
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATTTTATATTATATTTA
Found at i:1287398 original size:25 final size:25
Alignment explanation
Indices: 1287341--1287457 Score: 88
Period size: 24 Copynumber: 4.8 Consensus size: 25
1287331 TAATTATGAA
* *
1287341 ATTTAATA-TTTATTTTATATTA-T
1 ATTTTATATTTTATATTATATTATT
1287364 A-TTTATTATTTTATATTATATTATT
1 ATTTTA-TATTTTATATTATATTATT
1287389 ATTTTATA-TTT-TATTATATATATT
1 ATTTTATATTTTATATTATAT-TATT
* *
1287413 AAATTTATATTTT-TA-TATAATTTTT
1 -ATTTTATATTTTATATTAT-ATTATT
* *
1287438 ATATT-TATTTTACATTATAT
1 ATTTTATATTTTATATTATAT
1287458 ATCAATATTT
Statistics
Matches: 77, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
22 3 0.04
23 17 0.22
24 26 0.34
25 20 0.26
26 11 0.14
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (25 bp):
ATTTTATATTTTATATTATATTATT
Found at i:1287403 original size:30 final size:30
Alignment explanation
Indices: 1287341--1287457 Score: 105
Period size: 30 Copynumber: 3.8 Consensus size: 30
1287331 TAATTATGAA
*
1287341 ATTTAATATTTATTTTATATTATATTTATT
1 ATTTTATATTTATTTTATATTATATTTATT
*
1287371 ATTTTATATTATATTATTATTTTATATTTTATT
1 ATTTTATATT-TATT-TTATATTATA-TTTATT
* * * *
1287404 A-TATATATTAAATTTATATT-T-TTATATA
1 ATTTTATATTTATTTTATATTATATT-TATT
*
1287432 ATTTTTATATTTATTTTACATTATAT
1 A-TTTTATATTTATTTTATATTATAT
1287458 ATCAATATTT
Statistics
Matches: 68, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
27 2 0.03
28 4 0.06
29 1 0.01
30 30 0.44
31 7 0.10
32 17 0.25
33 7 0.10
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (30 bp):
ATTTTATATTTATTTTATATTATATTTATT
Found at i:1287429 original size:19 final size:19
Alignment explanation
Indices: 1287339--1287459 Score: 74
Period size: 19 Copynumber: 6.5 Consensus size: 19
1287329 TTTAATTATG
*
1287339 AAATTTA-ATATTTATTTT
1 AAATTTATATTTTTATTTT
*
1287357 ATA-TTATATTTATTATTTT
1 AAATTTATATTT-TTATTTT
* *
1287376 ATA-TTATATTATTATTTT
1 AAATTTATATTTTTATTTT
* * *
1287394 ATATTT-TATTATATATATT
1 AAATTTATATT-TTTATTTT
*
1287413 AAATTTATATTTTTA-TAT
1 AAATTTATATTTTTATTTT
* *
1287431 -AATTTTTATATTTATTTT
1 AAATTTATATTTTTATTTT
*
1287449 ACATTATATAT
1 AAATT-TATAT
1287460 CAATATTTTT
Statistics
Matches: 80, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
17 15 0.19
18 22 0.28
19 35 0.44
20 8 0.10
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.64
Consensus pattern (19 bp):
AAATTTATATTTTTATTTT
Found at i:1287600 original size:11 final size:11
Alignment explanation
Indices: 1287586--1287636 Score: 66
Period size: 12 Copynumber: 4.5 Consensus size: 11
1287576 TTAAATAAAT
1287586 ATTATATATTA
1 ATTATATATTA
*
1287597 ATTATATGATAA
1 ATTATAT-ATTA
*
1287609 AATATATATTAA
1 ATTATATATT-A
1287621 ATTATATATTA
1 ATTATATATTA
1287632 ATTAT
1 ATTAT
1287637 TAAAATAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
11 15 0.44
12 19 0.56
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (11 bp):
ATTATATATTA
Found at i:1288048 original size:16 final size:16
Alignment explanation
Indices: 1288024--1288069 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1288014 ACTTATATTA
1288024 AATTAAAATAAT-ATAGT
1 AATT-AAATAATAATA-T
*
1288041 AATTAAATATTAATAT
1 AATTAAATAATAATAT
1288057 AATTAAAT-ATAAT
1 AATTAAATAATAAT
1288070 TAACATGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 4 0.15
16 15 0.58
17 7 0.27
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
AATTAAATAATAATAT
Found at i:1289557 original size:20 final size:21
Alignment explanation
Indices: 1289512--1289573 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
1289502 AAATGAAAAG
**
1289512 ATAA-TTAAATATAATATTTTA
1 ATAATTTAAATATAATA-TAAA
*
1289533 A-AATTTATATA-AATATAAA
1 ATAATTTAAATATAATATAAA
1289552 ATAATTTAAATATAATATAAA
1 ATAATTTAAATATAATATAAA
1289573 A
1 A
1289574 AAATAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 3 0.09
20 15 0.44
21 16 0.47
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAATTTAAATATAATATAAA
Found at i:1289936 original size:5 final size:5
Alignment explanation
Indices: 1289928--1289999 Score: 56
Period size: 5 Copynumber: 13.4 Consensus size: 5
1289918 ATAATTTTAA
* * *
1289928 AATAT AATAT AAATAT TATAT AAAAAT AATTAA AATAT AATAT AATA-
1 AATAT AATAT -AATAT AATAT -AATAT AA-TAT AATAT AATAT AATAT
1289975 AATTAAT AATAT AAATAT AATAT AA
1 AA-T-AT AATAT -AATAT AATAT AA
1290000 ATTTATGAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
4 2 0.04
5 32 0.59
6 18 0.33
7 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:1289941 original size:11 final size:11
Alignment explanation
Indices: 1289927--1290001 Score: 74
Period size: 11 Copynumber: 7.4 Consensus size: 11
1289917 AATAATTTTA
1289927 AAATATAATAT
1 AAATATAATAT
*
1289938 AAATATTATAT
1 AAATATAATAT
*
1289949 AAAAATAAT-T
1 AAATATAATAT
1289959 AAAATATAATAT
1 -AAATATAATAT
1289971 -AATA-AAT-T
1 AAATATAATAT
1289979 --A-ATAATAT
1 AAATATAATAT
1289987 AAATATAATAT
1 AAATATAATAT
1289998 AAAT
1 AAAT
1290002 TTATGAATAT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
6 1 0.02
7 4 0.08
8 2 0.04
9 3 0.06
10 6 0.11
11 36 0.68
12 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AAATATAATAT
Found at i:1289982 original size:27 final size:28
Alignment explanation
Indices: 1289952--1290022 Score: 83
Period size: 27 Copynumber: 2.5 Consensus size: 28
1289942 ATTATATAAA
*
1289952 AATAATTAAAATATAATAT-AATAAATT
1 AATAATTAAAATATAATATAAATAAATG
**
1289979 AATAA-TATAAATATAATATAAATTTATG
1 AATAATTA-AAATATAATATAAATAAATG
1290007 AATATATTAAAATATA
1 AATA-ATTAAAATATA
1290023 TAGCATAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 2 0.05
27 16 0.43
28 9 0.24
29 8 0.22
30 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (28 bp):
AATAATTAAAATATAATATAAATAAATG
Found at i:1290222 original size:13 final size:14
Alignment explanation
Indices: 1290195--1290235 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1290185 TAAATGATAC
1290195 ATATTTAATAAAAT
1 ATATTTAATAAAAT
1290209 ATATTTAA-AAAAT
1 ATATTTAATAAAAT
*
1290222 A-A-TAAATAAAAT
1 ATATTTAATAAAAT
1290234 AT
1 AT
1290236 GAATTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
11 3 0.12
12 7 0.29
13 6 0.25
14 8 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATATTTAATAAAAT
Found at i:1290808 original size:19 final size:18
Alignment explanation
Indices: 1290771--1290810 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1290761 ACATAATTAT
*
1290771 AATATAATAAAATATATA
1 AATATAATAAAATACATA
*
1290789 AATATGATATAAATACATA
1 AATATAATA-AAATACATA
1290808 AAT
1 AAT
1290811 TATTAAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (18 bp):
AATATAATAAAATACATA
Found at i:1291522 original size:16 final size:17
Alignment explanation
Indices: 1291503--1291536 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1291493 TGACCATTTC
1291503 AAATAAAATAT-TTAAT
1 AAATAAAATATATTAAT
*
1291519 AAATCAAATATATTAAT
1 AAATAAAATATATTAAT
1291536 A
1 A
1291537 TAATTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATAAAATATATTAAT
Found at i:1292743 original size:48 final size:47
Alignment explanation
Indices: 1292671--1292763 Score: 134
Period size: 48 Copynumber: 2.0 Consensus size: 47
1292661 TTATTATAAA
*
1292671 AAATTTAAATTTTATATGTACATTAATTAAGTTGATTTCATTTGAAT
1 AAATTTAAATTTTATATGTACATTAACTAAGTTGATTTCATTTGAAT
* *
1292718 AAATTTATATCTTTATACT-TACATTAACTAAGTTGATTTCGTTTGA
1 AAATTTAAAT-TTTATA-TGTACATTAACTAAGTTGATTTCATTTGA
1292764 CTTTGGAGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
47 9 0.22
48 31 0.76
49 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.48
Consensus pattern (47 bp):
AAATTTAAATTTTATATGTACATTAACTAAGTTGATTTCATTTGAAT
Found at i:1293251 original size:16 final size:16
Alignment explanation
Indices: 1293212--1293252 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1293202 AATTTGATAT
1293212 TTATAT-TA-TATTAA
1 TTATATATATTATTAA
* *
1293226 TTAAAAATATTATTAA
1 TTATATATATTATTAA
1293242 TTATATATATT
1 TTATATATATT
1293253 TAATTGTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
14 4 0.19
15 2 0.10
16 15 0.71
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATATATATTATTAA
Found at i:1294397 original size:21 final size:22
Alignment explanation
Indices: 1294371--1294417 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1294361 TATATGAAAT
1294371 AAAATA-AAT-TATTAATATATA
1 AAAATATAATATATTAA-ATATA
*
1294392 AAAATATAATATTTTAAATATA
1 AAAATATAATATATTAAATATA
1294414 AAAA
1 AAAA
1294418 GTAACACGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 6 0.26
22 12 0.52
23 5 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAATATAATATATTAAATATA
Found at i:1294415 original size:22 final size:23
Alignment explanation
Indices: 1294359--1294417 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 23
1294349 CACATATAAA
*
1294359 AATATATGAAATAAAATAAATTATT
1 AATATAT-AAA-AATATAAATTATT
1294384 AATATATAAAAATATAATATT-TT
1 AATATATAAAAATATAA-ATTATT
1294407 AA-ATATAAAAA
1 AATATATAAAAA
1294418 GTAACACGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
22 9 0.28
23 10 0.31
24 6 0.19
25 7 0.22
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AATATATAAAAATATAAATTATT
Found at i:1294942 original size:14 final size:14
Alignment explanation
Indices: 1294902--1294944 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
1294892 TTTTTCTCCT
*
1294902 ATATATAAAATAAA
1 ATATATATAATAAA
*
1294916 ATATACAT-A-AAA
1 ATATATATAATAAA
1294928 ATATATATAATAAA
1 ATATATATAATAAA
1294942 ATA
1 ATA
1294945 AATTATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 10 0.42
13 2 0.08
14 12 0.50
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
ATATATATAATAAA
Found at i:1295043 original size:4 final size:4
Alignment explanation
Indices: 1295025--1295079 Score: 64
Period size: 4 Copynumber: 14.8 Consensus size: 4
1295015 TAAATTTTTT
*
1295025 TTTC TTT- TTTC -TTC TTTC TTTC CTTC TTTC TTT- TTT- TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
1295069 TTTC CTTC TTT
1 TTTC TTTC TTT
1295080 TTCACCTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
3 12 0.27
4 32 0.73
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:1295064 original size:22 final size:22
Alignment explanation
Indices: 1295026--1295082 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
1295016 AAATTTTTTT
1295026 TTCTTT-TTTCTTCTTTCTTTCC
1 TTCTTTCTTT-TTCTTTCTTTCC
* *
1295048 TTCTTTCTTTTTTTTTCTTTCT
1 TTCTTTCTTTTTCTTTCTTTCC
*
1295070 TTCCTTCTTTTTC
1 TTCTTTCTTTTTC
1295083 ACCTATTCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 27 0.90
23 3 0.10
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (22 bp):
TTCTTTCTTTTTCTTTCTTTCC
Found at i:1295065 original size:26 final size:26
Alignment explanation
Indices: 1295025--1295079 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
1295015 TAAATTTTTT
1295025 TTTCTTTTTTCTTCTTTCTTTCCTTC
1 TTTCTTTTTTCTTCTTTCTTTCCTTC
*
1295051 TTTCTTTTTTTTTCTTTCTTTCCTTC
1 TTTCTTTTTTCTTCTTTCTTTCCTTC
1295077 TTT
1 TTT
1295080 TTCACCTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTCTTTTTTCTTCTTTCTTTCCTTC
Found at i:1295091 original size:26 final size:26
Alignment explanation
Indices: 1295036--1295091 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
1295026 TTCTTTTTTC
*** *
1295036 TTCTTTCTTTCCTTCTTTCTTTTTTT
1 TTCTTTCTTTCCTTCTTTCTTACCTA
1295062 TTCTTTCTTTCCTTCTTT-TTCACCTA
1 TTCTTTCTTTCCTTCTTTCTT-ACCTA
1295088 TTCT
1 TTCT
1295092 AAAAAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.70
Consensus pattern (26 bp):
TTCTTTCTTTCCTTCTTTCTTACCTA
Found at i:1295759 original size:20 final size:21
Alignment explanation
Indices: 1295721--1295761 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1295711 GTAGTAAAAA
1295721 TTGTATGTATTTCTAATGTGT
1 TTGTATGTATTTCTAATGTGT
* *
1295742 TTGTAT-TATTTTTTATGTGT
1 TTGTATGTATTTCTAATGTGT
1295762 CAAAATTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.17, C:0.02, G:0.17, T:0.63
Consensus pattern (21 bp):
TTGTATGTATTTCTAATGTGT
Found at i:1295819 original size:36 final size:36
Alignment explanation
Indices: 1295751--1295819 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
1295741 TTTGTATTAT
* * *
1295751 TTTTTATGTGTCAAAATTACTATAAATTTATATAAA
1 TTTTTATATGTCAAAATTAATATAAATATATATAAA
*
1295787 TTTTTATATGTCAATAATTAATAT-TATATATAT
1 TTTTTATATGTCAA-AATTAATATAAATATATAT
1295820 TTTGGTACGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 20 0.71
37 8 0.29
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (36 bp):
TTTTTATATGTCAAAATTAATATAAATATATATAAA
Found at i:1296378 original size:15 final size:16
Alignment explanation
Indices: 1296357--1296394 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1296347 ATTTTTAAAT
1296357 AAATTTTA-TTAATTA
1 AAATTTTATTTAATTA
*
1296372 TAATTTTATTTAATTA
1 AAATTTTATTTAATTA
1296388 AAATTTT
1 AAATTTT
1296395 TATAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AAATTTTATTTAATTA
Found at i:1296673 original size:20 final size:21
Alignment explanation
Indices: 1296617--1296676 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
1296607 ATATTTATAA
1296617 AAAATATTTATA-ATATAACAT
1 AAAATA-TTATACATATAACAT
* * *
1296638 AAAAATAATATGCATATGACAT
1 -AAAATATTATACATATAACAT
1296660 -AAATATTATACATATAA
1 AAAATATTATACATATAA
1296677 AAATATATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
20 14 0.45
21 3 0.10
22 14 0.45
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (21 bp):
AAAATATTATACATATAACAT
Found at i:1296699 original size:37 final size:37
Alignment explanation
Indices: 1296636--1296715 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 37
1296626 ATAATATAAC
* * *
1296636 ATAAAAATAATATGCATATGACATAAA-TATTATACAT
1 ATAAAAATAATATGCAAATAAAATAAATTATTA-ACAT
*
1296673 ATAAAAATATATATG-AAATAAAATAAATTATTAATAT
1 ATAAAAATA-ATATGCAAATAAAATAAATTATTAACAT
1296710 ATAAAA
1 ATAAAA
1296716 TTTTTTATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 27 0.73
38 10 0.27
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (37 bp):
ATAAAAATAATATGCAAATAAAATAAATTATTAACAT
Found at i:1296723 original size:20 final size:20
Alignment explanation
Indices: 1296708--1296755 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
1296698 AATTATTAAT
1296708 ATATAAAATTTTTTATAAAA
1 ATATAAAATTTTTTATAAAA
* * *
1296728 ATATAATATTTATATAAAAAA
1 ATATAAAATTT-TTTATAAAA
1296749 ATATAAA
1 ATATAAA
1296756 TACAAATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATAAAATTTTTTATAAAA
Found at i:1296982 original size:13 final size:14
Alignment explanation
Indices: 1296909--1296997 Score: 51
Period size: 14 Copynumber: 6.3 Consensus size: 14
1296899 TTATAAAATT
*
1296909 TTTAATAAAAAAAAA
1 TTTAAT-AAATAAAA
*
1296924 TTATAATTAAT-AAA
1 TT-TAATAAATAAAA
* *
1296938 TTTATTTAAA-AATA
1 TTTA-ATAAATAAAA
1296952 TTTAATAAATAAAA
1 TTTAATAAATAAAA
*
1296966 -TTAA-AATTAAAA
1 TTTAATAAATAAAA
*
1296978 TTTAATTATATAAAAA
1 TTTAA-TAAAT-AAAA
1296994 TTTA
1 TTTA
1296998 TACAAATATA
Statistics
Matches: 56, Mismatches: 10, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
12 7 0.12
13 14 0.25
14 17 0.30
15 6 0.11
16 12 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TTTAATAAATAAAA
Found at i:1297049 original size:24 final size:23
Alignment explanation
Indices: 1297002--1297057 Score: 80
Period size: 24 Copynumber: 2.5 Consensus size: 23
1296992 AATTTATACA
*
1297002 AATATAAAATAA-ATTAAAATAT
1 AATATAAAATAATATTAAAAAAT
1297024 AATATAAACATAATATTAAAAAAT
1 AATATAAA-ATAATATTAAAAAAT
1297048 AAT-TAAAATA
1 AATATAAAATA
1297058 TAATATGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 11 0.35
23 8 0.26
24 12 0.39
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
AATATAAAATAATATTAAAAAAT
Found at i:1297060 original size:11 final size:11
Alignment explanation
Indices: 1297006--1297061 Score: 62
Period size: 11 Copynumber: 5.0 Consensus size: 11
1296996 TATACAAATA
1297006 TAAAATA-AAT
1 TAAAATATAAT
1297016 TAAAATATAAT
1 TAAAATATAAT
1297027 ATAAACATA-ATAT
1 -TAAA-ATATA-AT
*
1297040 TAAAAAATAAT
1 TAAAATATAAT
1297051 TAAAATATAAT
1 TAAAATATAAT
1297062 ATGATATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 7 0.18
11 17 0.44
12 10 0.26
13 5 0.13
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAATATAAT
Found at i:1297087 original size:22 final size:21
Alignment explanation
Indices: 1297054--1297095 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
1297044 AAATAATTAA
*
1297054 AATATAATATGATATAAATAT
1 AATATAATATGATAAAAATAT
1297075 AATATGAATATGATAAAAATA
1 AATAT-AATATGATAAAAATA
1297096 CATAAACATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (21 bp):
AATATAATATGATAAAAATAT
Found at i:1298086 original size:23 final size:25
Alignment explanation
Indices: 1298041--1298087 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1298031 AATACATAAA
*
1298041 TTTTTTCTCTTTTTCTTTCTTTCAT
1 TTTTTTCTCCTTTTCTTTCTTTCAT
1298066 TTTTTTCTCCTTTT-TTT-TTTCA
1 TTTTTTCTCCTTTTCTTTCTTTCA
1298088 ACTCTACCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 13 0.62
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTTTCTCCTTTTCTTTCTTTCAT
Found at i:1298479 original size:28 final size:29
Alignment explanation
Indices: 1298446--1298520 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
1298436 GTACATATAA
* *
1298446 AAATATATTAAAA-GAAA-ATAAAAATTAT
1 AAATATATAAAAATAAAAGATAAAAATT-T
*
1298474 AAATATATAAAAATAAAAGATAAATATTT
1 AAATATATAAAAATAAAAGATAAAAATTT
* *
1298503 AAATATAAAAAAAAAAAA
1 AAATATATAAAAATAAAA
1298521 CAAATCCTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
28 12 0.30
29 20 0.50
30 8 0.20
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (29 bp):
AAATATATAAAAATAAAAGATAAAAATTT
Found at i:1298498 original size:21 final size:21
Alignment explanation
Indices: 1298472--1298512 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1298462 AATAAAAATT
1298472 ATAAATATATAAAAATAAAAG
1 ATAAATATATAAAAATAAAAG
* *
1298493 ATAAATATTTAAATATAAAA
1 ATAAATATATAAAAATAAAA
1298513 AAAAAAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
ATAAATATATAAAAATAAAAG
Found at i:1299929 original size:20 final size:21
Alignment explanation
Indices: 1299904--1299959 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
1299894 AATACATAAA
1299904 ATAAAATA-AAT-TATTAATAT
1 ATAAAATATAATAT-TTAATAT
*
1299924 ATAAAAATATAATATTTTATAT
1 AT-AAAATATAATATTTAATAT
*
1299946 ATAAAAAATAATAT
1 ATAAAATATAATAT
1299960 AAATACAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 2 0.06
21 17 0.55
22 11 0.35
23 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAAAATATAATATTTAATAT
Found at i:1299932 original size:21 final size:22
Alignment explanation
Indices: 1299917--1299959 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1299907 AAATAAATTA
1299917 TTAATATATAAAAATATAATAT
1 TTAATATATAAAAATATAATAT
*
1299939 TTTATATATAAAAA-ATAATAT
1 TTAATATATAAAAATATAATAT
1299960 AAATACAAAT
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAATATATAAAAATATAATAT
Found at i:1299937 original size:26 final size:26
Alignment explanation
Indices: 1299901--1299976 Score: 72
Period size: 26 Copynumber: 3.1 Consensus size: 26
1299891 AAAAATACAT
*
1299901 AAAATAAAATAAATTATTAATATATA
1 AAAATATAATAAATTATTAATATATA
1299927 AAAATATAAT--ATT-TT-ATATATA
1 AAAATATAATAAATTATTAATATATA
* **
1299949 AAAA-ATAATATAAATACAAATATATA
1 AAAATATAATA-AATTATTAATATATA
1299975 AA
1 AA
1299977 TTTTTTTACT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
21 5 0.12
22 11 0.27
23 2 0.05
24 5 0.12
26 18 0.44
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (26 bp):
AAAATATAATAAATTATTAATATATA
Found at i:1299998 original size:15 final size:14
Alignment explanation
Indices: 1299977--1300010 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1299967 AATATATAAA
1299977 TTTTTTTACTTTTT
1 TTTTTTTACTTTTT
*
1299991 TCTTTTTTGCTTTTT
1 T-TTTTTTACTTTTT
1300006 TTTTT
1 TTTTT
1300011 CCCTCTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.03, C:0.09, G:0.03, T:0.85
Consensus pattern (14 bp):
TTTTTTTACTTTTT
Found at i:1300122 original size:12 final size:12
Alignment explanation
Indices: 1300105--1300140 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1300095 AGTATTATAA
1300105 ATAGATATAAAT
1 ATAGATATAAAT
*
1300117 ATAGATATAGAT
1 ATAGATATAAAT
1300129 ATAGATAGTAAA
1 ATAGATA-TAAA
1300141 GAAAACTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 18 0.86
13 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.31
Consensus pattern (12 bp):
ATAGATATAAAT
Found at i:1300124 original size:6 final size:6
Alignment explanation
Indices: 1300105--1300135 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1300095 AGTATTATAA
*
1300105 ATAGAT ATAAAT ATAGAT ATAGAT ATAGAT A
1 ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT A
1300136 GTAAAGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (6 bp):
ATAGAT
Found at i:1300316 original size:7 final size:7
Alignment explanation
Indices: 1300304--1300357 Score: 74
Period size: 7 Copynumber: 7.7 Consensus size: 7
1300294 TGTGATAAAT
1300304 TAAAAAA
1 TAAAAAA
1300311 TAAAAAA
1 TAAAAAA
1300318 TAAAAAA
1 TAAAAAA
1300325 TAAAAAA
1 TAAAAAA
* *
1300332 TAATATA
1 TAAAAAA
1300339 T-AAAAA
1 TAAAAAA
1300345 TAATAAAA
1 TAA-AAAA
1300353 TAAAA
1 TAAAA
1300358 TTTAAATTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 4 0.10
7 30 0.73
8 7 0.17
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAAAAA
Found at i:1300505 original size:43 final size:41
Alignment explanation
Indices: 1300458--1300540 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 41
1300448 AGTATCTAAT
* * *
1300458 AATATTGATTAAAATTTTTAAAAATATATATAATTAAATAAAA
1 AATATTAAATAAAATTTTT--AAATATAAATAATTAAATAAAA
* **
1300501 AATATTAAATATAATTTTTTTATATAAATAATTAAATAAA
1 AATATTAAATAAAATTTTTAAATATAAATAATTAAATAAA
1300541 TTTTAATCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 18 0.53
43 16 0.47
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (41 bp):
AATATTAAATAAAATTTTTAAATATAAATAATTAAATAAAA
Found at i:1301708 original size:20 final size:21
Alignment explanation
Indices: 1301685--1301751 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 21
1301675 TTTTTTATTA
* *
1301685 TTATTCAATATAAATTAT-AT
1 TTATTAAAAATAAATTATAAT
1301705 TTA-TAAAAATAAATTATAAT
1 TTATTAAAAATAAATTATAAT
*
1301725 TTA-TAATAAT-AA-T-TAAT
1 TTATTAAAAATAAATTATAAT
*
1301742 ATATTAAAAA
1 TTATTAAAAA
1301752 ATAATAATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 6 0.15
18 6 0.15
19 14 0.35
20 14 0.35
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (21 bp):
TTATTAAAAATAAATTATAAT
Found at i:1301716 original size:19 final size:19
Alignment explanation
Indices: 1301694--1301755 Score: 74
Period size: 19 Copynumber: 3.2 Consensus size: 19
1301684 ATTATTCAAT
1301694 ATAAATTATATTTATAAAA
1 ATAAATTATATTTATAAAA
*
1301713 ATAAATTATAATTTATAATA
1 ATAAATTAT-ATTTATAAAA
1301733 AT-AATTAATATATTA-AAAA
1 ATAAATT-ATAT-TTATAAAA
1301752 ATAA
1 ATAA
1301756 TAATTAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 20 0.54
20 17 0.46
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAATTATATTTATAAAA
Found at i:1301772 original size:15 final size:14
Alignment explanation
Indices: 1301727--1301769 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1301717 ATTATAATTT
*
1301727 ATAA-TAATAATTA
1 ATAATTAATAAATA
*
1301740 ATATATTAAAAAATA
1 ATA-ATTAATAAATA
1301755 ATAATTAATAAATA
1 ATAATTAATAAATA
1301769 A
1 A
1301770 ATACTAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 3 0.12
14 12 0.48
15 10 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAATTAATAAATA
Found at i:1301780 original size:22 final size:22
Alignment explanation
Indices: 1301729--1301770 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1301719 TATAATTTAT
*
1301729 AATAATAATTAATATATTAAAA
1 AATAATAATTAATATAATAAAA
1301751 AATAATAATTAATA-AATAAA
1 AATAATAATTAATATAATAAA
1301771 TACTAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAATAATTAATATAATAAAA
Found at i:1301954 original size:10 final size:11
Alignment explanation
Indices: 1301939--1301980 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
1301929 AATAACTTTT
1301939 TATAATTTAAA
1 TATAATTTAAA
1301950 T-TAATTT-AA
1 TATAATTTAAA
1301959 TATAATTTAAAA
1 TATAATTT-AAA
*
1301971 TATTATTTAA
1 TATAATTTAA
1301981 GATTAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 3 0.11
10 12 0.44
11 3 0.11
12 9 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TATAATTTAAA
Found at i:1306442 original size:13 final size:13
Alignment explanation
Indices: 1306426--1306452 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1306416 ATGAAAAAGA
1306426 GGGATTTTTTCTT
1 GGGATTTTTTCTT
1306439 GGGATTTTTTCTT
1 GGGATTTTTTCTT
1306452 G
1 G
1306453 TTTTGGTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.26, T:0.59
Consensus pattern (13 bp):
GGGATTTTTTCTT
Found at i:1308648 original size:14 final size:14
Alignment explanation
Indices: 1308631--1308752 Score: 62
Period size: 14 Copynumber: 8.7 Consensus size: 14
1308621 TAAATTATTA
1308631 ATATTTATATATAT
1 ATATTTATATATAT
1308645 ATATTT-TATATGATT
1 ATATTTATATAT-A-T
*
1308660 ATAATTTATGTTATAT
1 AT-ATTTAT-ATATAT
*
1308676 AAATTT-TAATATAT
1 ATATTTAT-ATATAT
* *
1308690 TTATTTTTATAT-T
1 ATATTTATATATAT
*
1308703 ATTTTTTATATAATATT
1 A-TATTTATAT-ATA-T
1308720 ATATTT-TA-AT-T
1 ATATTTATATATAT
1308731 AT-TTTATAT-TAT
1 ATATTTATATATAT
*
1308743 ATAATTATAT
1 ATATTTATAT
1308753 TAAATTTAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 29
0.67 0.09 0.24
Matches are distributed among these distances:
10 3 0.04
11 6 0.07
12 3 0.04
13 14 0.17
14 28 0.34
15 12 0.14
16 10 0.12
17 4 0.05
18 3 0.04
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (14 bp):
ATATTTATATATAT
Found at i:1308652 original size:15 final size:15
Alignment explanation
Indices: 1308634--1308727 Score: 79
Period size: 15 Copynumber: 6.3 Consensus size: 15
1308624 ATTATTAATA
1308634 TTTATATATATATAT
1 TTTATATATATATAT
*
1308649 TTTATATGAT-TATAA
1 TTTATAT-ATATATAT
* *
1308664 TTTATGTTATATAAAT
1 TTTAT-ATATATATAT
*
1308680 TTTA-ATATATTTAT
1 TTTATATATATATAT
*
1308694 TTT-TATAT-TATTT
1 TTTATATATATATAT
1308707 TTTATATAATATTATAT
1 TTTATAT-ATA-TATAT
1308724 TTTA
1 TTTA
1308728 ATTATTTTAT
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
13 6 0.10
14 17 0.28
15 20 0.33
16 10 0.16
17 8 0.13
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (15 bp):
TTTATATATATATAT
Found at i:1308693 original size:20 final size:21
Alignment explanation
Indices: 1308638--1308693 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
1308628 TTAATATTTA
*
1308638 TATATATATATTT-TATATGAT
1 TATA-ATATATTTATATATAAT
*
1308659 TATAATTTATGTTATATA-AAT
1 TATAATATAT-TTATATATAAT
*
1308680 TTTAATATATTTAT
1 TATAATATATTTAT
1308694 TTTTATATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
20 9 0.31
21 16 0.55
22 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
TATAATATATTTATATATAAT
Found at i:1308695 original size:29 final size:30
Alignment explanation
Indices: 1308602--1308725 Score: 91
Period size: 31 Copynumber: 4.1 Consensus size: 30
1308592 TGTATTATTT
*
1308602 TTTATGTTATAATTATATTTAAAT-TATTAATA
1 TTTATGTTAT-A-TATATTTTAATATATT-ATA
*
1308634 TTTAT-ATATATATATTTT-ATATGATTATAA
1 TTTATGTTATATATATTTTAATAT-ATTAT-A
*
1308664 TTTATGTTATATAAATTTTAATATATT-TA
1 TTTATGTTATATATATTTTAATATATTATA
*
1308693 -TT-T-TTATATTATTTTTTATATAATATTATA
1 TTTATGTTATA-TATATTTTA-AT-ATATTATA
1308723 TTT
1 TTT
1308726 TAATTATTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 21
0.74 0.06 0.20
Matches are distributed among these distances:
26 5 0.07
27 8 0.11
28 6 0.08
29 16 0.21
30 13 0.17
31 19 0.25
32 9 0.12
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (30 bp):
TTTATGTTATATATATTTTAATATATTATA
Found at i:1308708 original size:26 final size:28
Alignment explanation
Indices: 1308608--1308753 Score: 88
Period size: 29 Copynumber: 5.0 Consensus size: 28
1308598 ATTTTTTATG
*
1308608 TTATAATTATATTTAA-AT-TATTAATATT
1 TTAT-ATTATTTTTAATATATATT-ATATT
*
1308636 TATATATATATATTTTATATGATTATAATT-TATG
1 T-TATAT-TAT-TTTTA-AT-A-TAT-ATTATATT
* *
1308670 TTATATAAATTTTAATATAT-TTAT-TT
1 TTATATTATTTTTAATATATATTATATT
*
1308696 TTATATTATTTTTTATATAATATTATATT
1 TTATATTATTTTTAATAT-ATATTATATT
*
1308725 TTA-ATTATTTTATATTATATAATTATATT
1 TTATATTATTTT-TAATATAT-ATTATATT
1308754 AAATTTAAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 29
0.70 0.08 0.22
Matches are distributed among these distances:
26 18 0.19
27 3 0.03
28 20 0.22
29 24 0.26
30 6 0.06
31 6 0.06
32 1 0.01
33 6 0.06
34 5 0.05
35 1 0.01
36 3 0.03
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (28 bp):
TTATATTATTTTTAATATATATTATATT
Found at i:1308712 original size:38 final size:38
Alignment explanation
Indices: 1308670--1308742 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
1308660 ATAATTTATG
* *
1308670 TTATATAA-ATTTTAATATATTTATTTTTATATTATTTT
1 TTATATAATATTATAATATAATTA-TTTTATATTATTTT
* *
1308708 TTATATAATATTATATTTTAATTATTTTATATTAT
1 TTATATAATATTATAATATAATTATTTTATATTAT
1308743 ATAATTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
38 19 0.63
39 11 0.37
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (38 bp):
TTATATAATATTATAATATAATTATTTTATATTATTTT
Found at i:1308717 original size:31 final size:32
Alignment explanation
Indices: 1308682--1308753 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 32
1308672 ATATAAATTT
1308682 TAATATATTTATTTTTATATTA-TTT-T-TTATA
1 TAATATATTTA-TTTTA-ATTATTTTATATTATA
*
1308713 TAATAT-TATATTTTAATTATTTTATATTATA
1 TAATATATTTATTTTAATTATTTTATATTATA
1308744 TAATTATATT
1 TAA-TATATT
1308754 AAATTTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
28 4 0.12
29 8 0.24
30 4 0.12
31 14 0.41
32 3 0.09
33 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (32 bp):
TAATATATTTATTTTAATTATTTTATATTATA
Found at i:1308743 original size:29 final size:29
Alignment explanation
Indices: 1308640--1308753 Score: 98
Period size: 29 Copynumber: 4.0 Consensus size: 29
1308630 AATATTTATA
*
1308640 TATATATATTTTATATGATTATAATT-TATGT
1 TATAT-TATTTTATAT-A-TATAATTATATTT
*
1308671 TATATAAATTTTA-ATATAT--TTAT-TTT
1 TATAT-TATTTTATATATATAATTATATTT
*
1308697 TATATTATTTTTTATATA-ATATTATATTT
1 TATATTATTTTATATATATA-ATTATATTT
1308726 TA-ATTATTTTATATTATATAATTATATT
1 TATATTATTTTATA-TATATAATTATATT
1308754 AAATTTAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 18
0.75 0.05 0.19
Matches are distributed among these distances:
25 5 0.07
26 14 0.20
27 1 0.01
28 17 0.24
29 18 0.26
30 3 0.04
31 12 0.17
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
TATATTATTTTATATATATAATTATATTT
Found at i:1308758 original size:28 final size:28
Alignment explanation
Indices: 1308678--1308758 Score: 73
Period size: 28 Copynumber: 3.0 Consensus size: 28
1308668 TGTTATATAA
* *
1308678 ATTTTA-ATAT-AT-TTATTTTTATATT
1 ATTTTATATATAATATTATATTTAAATT
* *
1308703 ATTTTTTATATAATATTATATTTTAATT
1 ATTTTATATATAATATTATATTTAAATT
1308731 ATTTTATAT-TATATAATTATA-TTAAATT
1 ATTTTATATATA-AT-ATTATATTTAAATT
1308759 TAAAATTATC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
25 5 0.11
26 4 0.09
27 4 0.09
28 26 0.58
29 6 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
ATTTTATATATAATATTATATTTAAATT
Found at i:1309819 original size:11 final size:11
Alignment explanation
Indices: 1309791--1309834 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
1309781 AAATAAAAAA
* *
1309791 TAATTATAATA
1 TAATTAAAATT
1309802 TAA-TAAAATT
1 TAATTAAAATT
*
1309812 TAATTAAAAAT
1 TAATTAAAATT
1309823 TAATTAAAATT
1 TAATTAAAATT
1309834 T
1 T
1309835 TTAAATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 8 0.29
11 20 0.71
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TAATTAAAATT
Found at i:1309843 original size:24 final size:24
Alignment explanation
Indices: 1309809--1309885 Score: 75
Period size: 24 Copynumber: 3.0 Consensus size: 24
1309799 ATATAATAAA
*
1309809 ATTTAATTAAAAATTAATTAAAAT
1 ATTTAAATAAAAATTAATTAAAAT
*
1309833 TTTTAAATAAAAACTTATTATTTAAAA-
1 ATTTAAATAAAAA-TTA--A-TTAAAAT
*
1309860 ATTAAAATAAAAAATTAATTAAAAT
1 ATTTAAAT-AAAAATTAATTAAAAT
1309885 A
1 A
1309886 AAAAATTGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
24 17 0.40
25 5 0.12
27 10 0.23
28 11 0.26
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (24 bp):
ATTTAAATAAAAATTAATTAAAAT
Found at i:1309881 original size:17 final size:17
Alignment explanation
Indices: 1309859--1309892 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1309849 ATTATTTAAA
1309859 AATTAAAATAAAAAATT
1 AATTAAAATAAAAAATT
1309876 AATTAAAATAAAAAATT
1 AATTAAAATAAAAAATT
1309893 GATCAGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATTAAAATAAAAAATT
Found at i:1309964 original size:22 final size:22
Alignment explanation
Indices: 1309929--1309971 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1309919 AAATTTTATT
1309929 TAAATTTAATTATAAAAATAAA
1 TAAATTTAATTATAAAAATAAA
1309951 TAAATATTAA-TATAAAAATAA
1 TAAAT-TTAATTATAAAAATAA
1309972 TTTTTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATAAA
Found at i:1310105 original size:2 final size:2
Alignment explanation
Indices: 1310098--1310133 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1310088 AAAATATTTG
1310098 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
1310134 ACATTTAAGA
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):
TA
Found at i:1311473 original size:16 final size:16
Alignment explanation
Indices: 1311454--1311510 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 16
1311444 AATTTAAATT
1311454 AATTTTATTTTTTTAA
1 AATTTTATTTTTTTAA
*
1311470 AATTATTATTTATTTAA
1 AATT-TTATTTTTTTAA
* *
1311487 AA--ATATTTTTATTTA
1 AATTTTATTTTT-TTAA
1311502 AATTTTATT
1 AATTTTATT
1311511 ATAAAAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
14 6 0.19
15 5 0.16
16 4 0.12
17 17 0.53
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
AATTTTATTTTTTTAA
Found at i:1311480 original size:17 final size:17
Alignment explanation
Indices: 1311454--1311503 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
1311444 AATTTAAATT
*
1311454 AATT-TTATTTTTTTAA
1 AATTATTATTTATTTAA
1311470 AATTATTATTTATTTAA
1 AATTATTATTTATTTAA
*
1311487 AAATATT-TTTATTTAA
1 AATTATTATTTATTTAA
1311503 A
1 A
1311504 TTTTATTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AATTATTATTTATTTAA
Found at i:1311500 original size:20 final size:19
Alignment explanation
Indices: 1311438--1311501 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 19
1311428 TTTTAGATAA
* *
1311438 TTATTTAATTTAAATTAATT
1 TTATTT-ATTTAAAATATTT
* *
1311458 TTATTT-TTTTAAA-ATTA
1 TTATTTATTTAAAATATTT
1311475 TTATTTATTTAAAAATATTT
1 TTATTTATTT-AAAATATTT
1311495 TTATTTA
1 TTATTTA
1311502 AATTTTATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 8 0.23
18 8 0.23
19 3 0.09
20 16 0.46
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATTTATTTAAAATATTT
Found at i:1311510 original size:17 final size:16
Alignment explanation
Indices: 1311461--1311503 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
1311451 ATTAATTTTA
1311461 TTTT-TTTAAAATTAT
1 TTTTATTTAAAATTAT
*
1311476 TATTTATTTAAAAATAT
1 T-TTTATTTAAAATTAT
1311493 TTTTATTTAAA
1 TTTTATTTAAA
1311504 TTTTATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 1 0.04
16 13 0.52
17 11 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTATTTAAAATTAT
Found at i:1311518 original size:14 final size:15
Alignment explanation
Indices: 1311476--1311536 Score: 56
Period size: 14 Copynumber: 4.1 Consensus size: 15
1311466 TTAAAATTAT
1311476 TATTTATT-TAAAAA
1 TATTTATTATAAAAA
**
1311490 TATTT-TTATTTAAA
1 TATTTATTATAAAAA
1311504 T-TTTATTATAAAAA
1 TATTTATTATAAAAA
*
1311518 TATATATTAATATAAAA
1 TATTTATT-ATA-AAAA
1311535 TA
1 TA
1311537 ATATTTTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
13 5 0.14
14 18 0.49
15 5 0.14
16 3 0.08
17 6 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATTTATTATAAAAA
Found at i:1313439 original size:15 final size:14
Alignment explanation
Indices: 1313418--1313451 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1313408 TGATTTTTTT
1313418 ATATTAAATATAAAA
1 ATATTAAATA-AAAA
*
1313433 CTATTAAATAAAAA
1 ATATTAAATAAAAA
1313447 ATATT
1 ATATT
1313452 TTTATTACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (14 bp):
ATATTAAATAAAAA
Found at i:1313670 original size:3 final size:3
Alignment explanation
Indices: 1313662--1313694 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1313652 TAAAAGACCA
1313662 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1313695 GACTTTTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1314265 original size:30 final size:30
Alignment explanation
Indices: 1314175--1314269 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 30
1314165 AACGTGATAT
*
1314175 AAATATTTTAAATTTTA-TATAATATAAATGA
1 AAATATTTTAAATATTATTATAATAT-AAT-A
* * *
1314206 TTAAT-TTATCAATATT-TATATAA-AT-ATA
1 -AAATATTTTAAATATTAT-TATAATATAATA
1314234 AAATATTTTAAATATTATTATAATATAATA
1 AAATATTTTAAATATTATTATAATATAATA
1314264 AAATAT
1 AAATAT
1314270 AAATACATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
27 3 0.06
28 15 0.30
29 5 0.10
30 9 0.18
31 10 0.20
32 8 0.16
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (30 bp):
AAATATTTTAAATATTATTATAATATAATA
Found at i:1314759 original size:15 final size:16
Alignment explanation
Indices: 1314739--1314789 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
1314729 ATTATATATT
1314739 TATATAAATTTTGATA
1 TATATAAATTTTGATA
*
1314755 T-TATAATAATTT-ATA
1 TATATAA-ATTTTGATA
1314770 TTATATAAATTTTGATA
1 -TATATAAATTTTGATA
1314787 TAT
1 TAT
1314790 TCGTATTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 8 0.28
16 13 0.45
17 8 0.28
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (16 bp):
TATATAAATTTTGATA
Found at i:1314765 original size:17 final size:17
Alignment explanation
Indices: 1314738--1314787 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
1314728 TATTATATAT
1314738 TTATATAAATTTTGATA
1 TTATATAAATTTTGATA
1314755 TTATA-ATAA-TTT-ATA
1 TTATATA-AATTTTGATA
1314770 TTATATAAATTTTGATA
1 TTATATAAATTTTGATA
1314787 T
1 T
1314788 ATTCGTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 10 0.34
16 8 0.28
17 11 0.38
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
TTATATAAATTTTGATA
Found at i:1317038 original size:21 final size:21
Alignment explanation
Indices: 1316996--1317039 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1316986 AATATATAGG
**
1316996 ATAAAATAAAAAAATTTAAAA
1 ATAAAATAAAAAAAAGTAAAA
1317017 ATAAAATAAAAAATAAGTAAAA
1 ATAAAATAAAAAA-AAGTAAAA
1317039 A
1 A
1317040 AAATTTATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (21 bp):
ATAAAATAAAAAAAAGTAAAA
Found at i:1317104 original size:33 final size:33
Alignment explanation
Indices: 1317057--1317120 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1317047 TCTTAATTTT
*
1317057 TAATTATAATAAAGATAAATATCATTTTTAATA
1 TAATAATAATAAAGATAAATATCATTTTTAATA
* *
1317090 TAATAATATTAAAGATAAATATTATTTTTAA
1 TAATAATAATAAAGATAAATATCATTTTTAA
1317121 AATTTTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (33 bp):
TAATAATAATAAAGATAAATATCATTTTTAATA
Found at i:1317205 original size:22 final size:22
Alignment explanation
Indices: 1317180--1317231 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
1317170 CTTTTGAAAA
* * *
1317180 TTTTTAATAATAATTTTTTAAT
1 TTTTTAAAAATAATTATTAAAT
1317202 TTTTTAAAAATAATTATTAAAT
1 TTTTTAAAAATAATTATTAAAT
1317224 TTTTTAAA
1 TTTTTAAA
1317232 GTTTATAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTTAAAAATAATTATTAAAT
Found at i:1317726 original size:27 final size:26
Alignment explanation
Indices: 1317696--1317757 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 26
1317686 AAAACTCTAA
1317696 TTTATTATTAT-ATTAAAGTATTAAAAT
1 TTTATTATTATAATTAAA-T-TTAAAAT
*
1317723 TTTA-TATTTATAATTAAATTTAAATT
1 TTTATTA-TTATAATTAAATTTAAAAT
1317749 TTTATTATT
1 TTTATTATT
1317758 TAAAAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 14 0.45
27 11 0.35
28 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (26 bp):
TTTATTATTATAATTAAATTTAAAAT
Found at i:1317758 original size:27 final size:28
Alignment explanation
Indices: 1317696--1317759 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
1317686 AAAACTCTAA
1317696 TTTATTA-TTATATTAAAGTATTAAAAT
1 TTTATTATTTATATTAAAGTATTAAAAT
*
1317723 TTTA-TATTTATAATTAAA-T-TTAAATT
1 TTTATTATTTAT-ATTAAAGTATTAAAAT
1317749 TTTATTATTTA
1 TTTATTATTTA
1317760 AAAAATAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 12 0.36
27 15 0.45
28 6 0.18
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTATTATTTATATTAAAGTATTAAAAT
Found at i:1318007 original size:2 final size:2
Alignment explanation
Indices: 1318000--1318025 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1317990 AAAAGAAAGA
1318000 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
1318026 TTACAATTTT
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:1318110 original size:2 final size:2
Alignment explanation
Indices: 1318103--1318138 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1318093 ATTCATAAGC
1318103 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
1318139 TTCTTATCAA
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:1318329 original size:19 final size:18
Alignment explanation
Indices: 1318305--1318344 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
1318295 ATTTTAAGTA
1318305 ATTTATATATTCATATCAT
1 ATTTATATATT-ATATCAT
*
1318324 ATTTATATATTTTATCAT
1 ATTTATATATTATATCAT
1318342 ATT
1 ATT
1318345 ATTTTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATATATTATATCAT
Found at i:1318333 original size:8 final size:8
Alignment explanation
Indices: 1318305--1318469 Score: 62
Period size: 8 Copynumber: 20.1 Consensus size: 8
1318295 ATTTTAAGTA
1318305 ATTTATAT
1 ATTTATAT
1318313 ATTCATATCAT
1 ATT--TAT-AT
1318324 ATTTATAT
1 ATTTATAT
1318332 ATTT-TAT
1 ATTTATAT
1318339 CA--TAT-T
1 -ATTTATAT
1318345 ATTT-TAT
1 ATTTATAT
*
1318352 ATTTAAAT
1 ATTTATAT
1318360 ATTT-TAT
1 ATTTATAT
1318367 ATTTATAT
1 ATTTATAT
*
1318375 AAATTTTTAT
1 --ATTTATAT
1318385 ACGTTTATA-
1 A--TTTATAT
1318394 ATTTATAT
1 ATTTATAT
* *
1318402 -TATATAA
1 ATTTATAT
*
1318409 ATTTTAAAAT
1 A-TTT-ATAT
*
1318419 ATTTTTAT
1 ATTTATAT
1318427 ATTT-T-T
1 ATTTATAT
*
1318433 ATTATATTTT
1 ATT-TA-TAT
1318443 ATTTATAT
1 ATTTATAT
*
1318451 TTTTATATT
1 ATTTATA-T
1318460 ATATTATAT
1 AT-TTATAT
1318469 A
1 A
1318470 ACATATTTAA
Statistics
Matches: 119, Mismatches: 14, Indels: 47
0.66 0.08 0.26
Matches are distributed among these distances:
5 1 0.01
6 7 0.06
7 29 0.24
8 34 0.29
9 16 0.13
10 27 0.23
11 5 0.04
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (8 bp):
ATTTATAT
Found at i:1318337 original size:28 final size:27
Alignment explanation
Indices: 1318297--1318374 Score: 86
Period size: 28 Copynumber: 2.9 Consensus size: 27
1318287 AGAATGGTAT
* *
1318297 TTTAAGTAATTTATATATTCATATCATA
1 TTTAAATATTTTATATATT-ATATCATA
* * *
1318325 TTTATATATTTTATCATATTATTTTATA
1 TTTAAATATTTTAT-ATATTATATCATA
1318353 TTTAAATATTTTATAT-TTATAT
1 TTTAAATATTTTATATATTATAT
1318375 AAATTTTTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
26 5 0.12
27 2 0.05
28 30 0.71
29 5 0.12
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (27 bp):
TTTAAATATTTTATATATTATATCATA
Found at i:1318393 original size:20 final size:19
Alignment explanation
Indices: 1318355--1318483 Score: 56
Period size: 19 Copynumber: 6.8 Consensus size: 19
1318345 ATTTTATATT
1318355 TAAATATTTTATATTTATA
1 TAAATATTTTATATTTATA
1318374 TAAAT-TTTTATACGTTTATAA
1 TAAATATTTTATA--TTTAT-A
** *
1318395 TTTATATTATATAAATTT-TA
1 TAAATATT-T-TATATTTATA
*
1318415 -AAATATTTTTATATTTTTA
1 TAAATA-TTTTATATTTATA
*
1318434 T-TATA-TTT-TATTTATA
1 TAAATATTTTATATTTATA
*** *
1318450 TTTTTATATTATA-TTATA
1 TAAATATTTTATATTTATA
*
1318468 TAACATATTTAATATT
1 TAA-ATATTTTATATT
1318484 ATCAAATTTA
Statistics
Matches: 81, Mismatches: 15, Indels: 27
0.66 0.12 0.22
Matches are distributed among these distances:
16 8 0.10
17 6 0.07
18 21 0.26
19 23 0.28
20 9 0.11
21 5 0.06
22 5 0.06
23 1 0.01
24 3 0.04
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.60
Consensus pattern (19 bp):
TAAATATTTTATATTTATA
Found at i:1318434 original size:62 final size:61
Alignment explanation
Indices: 1318350--1318479 Score: 144
Period size: 62 Copynumber: 2.1 Consensus size: 61
1318340 ATATTATTTT
1318350 ATATTT-AAATATTTTATATTTA-TATAAATT-TTTATACGTTTATAATTTATATTATATAA-
1 ATATTTAAAATATTTTATATTTATTATAAATTATTTATACGTTTAT-A-TTATATTATATAAC
** **
1318409 AT-TTTAAAATATTTTTATATTTTTATTATATTTTATTTATATTTTTATATTATATTATATAAC
1 ATATTTAAAATA-TTTTATA--TTTATTATAAATTATTTATACGTTTATATTATATTATATAAC
1318472 ATATTTAA
1 ATATTTAA
1318480 TATTATCAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
58 3 0.05
59 7 0.12
60 7 0.12
62 17 0.29
63 9 0.15
64 16 0.27
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (61 bp):
ATATTTAAAATATTTTATATTTATTATAAATTATTTATACGTTTATATTATATTATATAAC
Found at i:1318437 original size:11 final size:11
Alignment explanation
Indices: 1318423--1318456 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1318413 TAAAATATTT
1318423 TTATATTTTTA
1 TTATATTTTTA
1318434 TTATA-TTTTA
1 TTATATTTTTA
1318444 TTTATATTTTTA
1 -TTATATTTTTA
1318456 T
1 T
1318457 ATTATATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 5 0.24
11 11 0.52
12 5 0.24
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATATTTTTA
Found at i:1318466 original size:22 final size:22
Alignment explanation
Indices: 1318417--1318466 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
1318407 AAATTTTAAA
1318417 ATATT-TTTATATTTTTATTAT
1 ATATTATTTATATTTTTATTAT
*
1318438 ATTTTATTTATATTTTTA-TATT
1 ATATTATTTATATTTTTATTA-T
1318460 ATATTAT
1 ATATTAT
1318467 ATAACATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
ATATTATTTATATTTTTATTAT
Found at i:1319482 original size:11 final size:11
Alignment explanation
Indices: 1319463--1319529 Score: 62
Period size: 11 Copynumber: 5.7 Consensus size: 11
1319453 AATATTTTTA
1319463 AAAATTTTGAT
1 AAAATTTTGAT
1319474 AAAATTTTGAT
1 AAAATTTTGAT
**
1319485 ATGATTTTAGAT
1 AAAATTTT-GAT
**
1319497 AAATACTTTAAAT
1 AAA-A-TTTTGAT
1319510 AAAATATTTGAT
1 AAAAT-TTTGAT
1319522 AAAATTTT
1 AAAATTTT
1319530 CATCATTGGA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
11 21 0.48
12 14 0.32
13 6 0.14
14 3 0.07
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.45
Consensus pattern (11 bp):
AAAATTTTGAT
Found at i:1320288 original size:16 final size:17
Alignment explanation
Indices: 1320266--1320303 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1320256 TAAATATTAA
1320266 AATTAAAA-TTTATATT
1 AATTAAAAGTTTATATT
* *
1320282 TATTAAAAGTTTTTATT
1 AATTAAAAGTTTATATT
1320299 AATTA
1 AATTA
1320304 TTGTTGAGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTAAAAGTTTATATT
Found at i:1320553 original size:19 final size:22
Alignment explanation
Indices: 1320507--1320558 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 22
1320497 TTAAAGTAAG
1320507 TTATA-AATATAATATATATAT
1 TTATATAATATAATATATATAT
*
1320528 ATATATAATATAAT-T-TAT-T
1 TTATATAATATAATATATATAT
*
1320547 TTATATATTATA
1 TTATATAATATA
1320559 TAAAAACTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 11 0.41
20 3 0.11
21 5 0.19
22 8 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATATAATATAATATATATAT
Found at i:1321936 original size:2 final size:2
Alignment explanation
Indices: 1321929--1321954 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1321919 AAAATTCTTT
1321929 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
1321955 GTAAGATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1322240 original size:16 final size:17
Alignment explanation
Indices: 1322214--1322255 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
1322204 ATCATTTGTG
*
1322214 ATTTATTTAAAATTATT
1 ATTTATTTAAAAATATT
1322231 ATTT-TTTAAAAATATT
1 ATTTATTTAAAAATATT
*
1322247 -TGTATTTAA
1 ATTTATTTAA
1322256 TTTTTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 2 0.09
16 16 0.73
17 4 0.18
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTATTTAAAAATATT
Found at i:1324949 original size:22 final size:24
Alignment explanation
Indices: 1324900--1324960 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 24
1324890 AAATATAATA
*
1324900 ATTATTAA-AAAATTATTTTATAT
1 ATTATTAATAAAATTATTTTAAAT
1324923 ATTATTAATAAAA-T-TTTTAAAT
1 ATTATTAATAAAATTATTTTAAAT
* * *
1324945 TTTATAAATAATATTA
1 ATTATTAATAAAATTA
1324961 ACAGAATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
22 17 0.55
23 10 0.32
24 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTATTAATAAAATTATTTTAAAT
Found at i:1325516 original size:22 final size:23
Alignment explanation
Indices: 1325474--1325518 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1325464 TTAATAAAAT
*
1325474 AAATTTATAACTATTATTATAAA
1 AAATATATAACTATTATTATAAA
*
1325497 AAATATATAATTA-TATTATAAA
1 AAATATATAACTATTATTATAAA
1325519 TTATAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATATATAACTATTATTATAAA
Found at i:1325523 original size:20 final size:21
Alignment explanation
Indices: 1325472--1325527 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
1325462 AATTAATAAA
*
1325472 ATAAATT-TATAACTATTATT
1 ATAAATTATATAATTATTATT
*
1325492 ATAAAAAATATATAATTA-TATT
1 AT--AAATTATATAATTATTATT
1325514 ATAAATTATA-AATT
1 ATAAATTATATAATT
1325528 TTGTAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 4 0.13
20 9 0.30
22 10 0.33
23 7 0.23
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAAATTATATAATTATTATT
Found at i:1325690 original size:2 final size:2
Alignment explanation
Indices: 1325683--1325722 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1325673 TAATTATAGC
1325683 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
1325723 GCACTGACTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1329085 original size:27 final size:24
Alignment explanation
Indices: 1329057--1329106 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1329047 ATTTTTAAAT
*
1329057 TTTATAAATGAGATTTAATTATCTTA
1 TTTATAAAT-A-ATTTAATAATCTTA
*
1329083 TTTATTAATAATTTAATAATCTTA
1 TTTATAAATAATTTAATAATCTTA
1329107 ATAATGATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.59
25 1 0.05
26 8 0.36
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (24 bp):
TTTATAAATAATTTAATAATCTTA
Found at i:1331203 original size:25 final size:26
Alignment explanation
Indices: 1331164--1331218 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
1331154 TTCTACTTGT
* *
1331164 TTTTTGTTTCCTTTT-TATGTTTCTA
1 TTTTTGTTTCATTTTAAATGTTTCTA
* *
1331189 TTTTTGTTTTATTTTAAATGTTTTTA
1 TTTTTGTTTCATTTTAAATGTTTCTA
1331215 TTTT
1 TTTT
1331219 CTTTGCTACG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.13, C:0.05, G:0.07, T:0.75
Consensus pattern (26 bp):
TTTTTGTTTCATTTTAAATGTTTCTA
Found at i:1333007 original size:71 final size:75
Alignment explanation
Indices: 1332932--1333105 Score: 191
Period size: 75 Copynumber: 2.4 Consensus size: 75
1332922 TTTGCAGAAG
1332932 TTTAAATTTATTTTTTATTTGATTATATA-G-GTTT-AAGTTTTT-AGGGTATAATTT-ATTTTG
1 TTTAAATTTATTTTTTATTTGATTATATATGTGTTTAAAGTTTTTAAGGGTATAATTTAATTTT-
*
1332992 ATTTGTAAAAA
65 ATTTATAAAAA
* * * * *
1333003 TTT-AATTGTGTTTTTTATTAGATGTA-ATATGTGTTTAAATTTTTTAATGGTGTAATTTAATTT
1 TTTAAATT-TATTTTTTATTTGAT-TATATATGTGTTTAAAGTTTTTAAGGGTATAATTTAATTT
1333066 TATTTATAAAAA
64 TATTTATAAAAA
* *
1333078 TTTAAGATTTATTTTTAATTTAATTATA
1 TTTAA-ATTTATTTTTTATTTGATTATA
1333106 AAACTTAAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
70 4 0.05
71 19 0.23
72 3 0.04
73 4 0.05
74 7 0.08
75 25 0.30
76 18 0.22
77 3 0.04
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (75 bp):
TTTAAATTTATTTTTTATTTGATTATATATGTGTTTAAAGTTTTTAAGGGTATAATTTAATTTTA
TTTATAAAAA
Found at i:1333182 original size:15 final size:15
Alignment explanation
Indices: 1333162--1333191 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1333152 TTTGAAGAAG
*
1333162 GAAAGAAGGAAAAAA
1 GAAAGAAAGAAAAAA
1333177 GAAAGAAAGAAAAAA
1 GAAAGAAAGAAAAAA
1333192 ATGAAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
GAAAGAAAGAAAAAA
Found at i:1333288 original size:30 final size:30
Alignment explanation
Indices: 1333252--1333315 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
1333242 TTACCCATGG
* *
1333252 GTCAGGCATAACCCGCGTGTCGACTCGCGA
1 GTCAGGCATAACCCGCATGTCGACTCCCGA
1333282 GTCAGGCATAACCCGCATGTCGACTCCCGA
1 GTCAGGCATAACCCGCATGTCGACTCCCGA
1333312 GTCA
1 GTCA
1333316 ACCTTATTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.22, C:0.34, G:0.27, T:0.17
Consensus pattern (30 bp):
GTCAGGCATAACCCGCATGTCGACTCCCGA
Done.