Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 11 of 32
Found at i:1326700 original size:15 final size:15
Alignment explanation
Indices: 1326632--1326700 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
1326622 ATTTTTATAT
*
1326632 AAAAAATTATAATTA
1 AAAAAATTATAAATA
1326647 AGTAAAAATTATAAATA
1 A--AAAAATTATAAATA
**
1326664 TTAAAATT-TAAATA
1 AAAAAATTATAAATA
** *
1326678 ATTTAAATTATAATTA
1 A-AAAAATTATAAATA
1326694 AAAAAAT
1 AAAAAAT
1326701 ATTATTCAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
14 6 0.14
15 17 0.40
16 6 0.14
17 13 0.31
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (15 bp):
AAAAAATTATAAATA
Found at i:1326728 original size:11 final size:12
Alignment explanation
Indices: 1326696--1326728 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1326686 TATAATTAAA
1326696 AAAATATTATTC
1 AAAATATTATTC
1326708 AAAATA-TATT-
1 AAAATATTATTC
1326718 AAAATATTATT
1 AAAATATTATT
1326729 TTTTATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 6 0.30
11 8 0.40
12 6 0.30
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (12 bp):
AAAATATTATTC
Found at i:1326737 original size:20 final size:22
Alignment explanation
Indices: 1326712--1326763 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 22
1326702 TTATTCAAAA
1326712 TATATTAAAATAT-TAT-TTTT
1 TATATTAAAATATATATATTTT
* *
1326732 TATATTAATATTTATATATTTT
1 TATATTAAAATATATATATTTT
1326754 TATAATTAAA
1 TAT-ATTAAA
1326764 TTTAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 11 0.42
21 3 0.12
22 7 0.27
23 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TATATTAAAATATATATATTTT
Found at i:1326753 original size:22 final size:20
Alignment explanation
Indices: 1326712--1326767 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 20
1326702 TTATTCAAAA
*
1326712 TATATTAAA-ATATTATTTTT
1 TATATTAAATTTA-TATTTTT
1326732 TATATTAATATTTATATATTTT
1 TATATTAA-ATTTATAT-TTTT
1326754 TATAATTAAATTTA
1 TAT-ATTAAATTTA
1326768 AATAAAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 8 0.26
21 4 0.13
22 14 0.45
23 5 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATATTAAATTTATATTTTT
Found at i:1326891 original size:16 final size:16
Alignment explanation
Indices: 1326872--1326903 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1326862 AATTAATTTT
1326872 TTTAAAAAAAAATTAA
1 TTTAAAAAAAAATTAA
*
1326888 TTTAAAAAAACATTAA
1 TTTAAAAAAAAATTAA
1326904 ACTATATCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
TTTAAAAAAAAATTAA
Found at i:1327512 original size:19 final size:20
Alignment explanation
Indices: 1327481--1327520 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
1327471 TTTTATTATT
1327481 TAAATTTATTTATA-AAATA
1 TAAATTTATTTATATAAATA
1327500 TAAATATTA-TTATATAAATA
1 TAAAT-TTATTTATATAAATA
1327520 T
1 T
1327521 TTTTTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAATTTATTTATATAAATA
Found at i:1328545 original size:14 final size:14
Alignment explanation
Indices: 1328526--1328552 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1328516 TGAATAGTGC
1328526 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
1328540 AAGAAAAAAAGAA
1 AAGAAAAAAAGAA
1328553 TTTTATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:1330292 original size:18 final size:18
Alignment explanation
Indices: 1330269--1330322 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 18
1330259 CTTGAGTTGA
1330269 ATTTTATTATATTTAAAT
1 ATTTTATTATATTTAAAT
*
1330287 ATTTTATTA-ATTAAAAT
1 ATTTTATTATATTTAAAT
*
1330304 AATATT-TT-TATTTAAAT
1 -ATTTTATTATATTTAAAT
1330321 AT
1 AT
1330323 AATTATAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 2 0.06
17 16 0.52
18 13 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTATTATATTTAAAT
Found at i:1330429 original size:11 final size:11
Alignment explanation
Indices: 1330395--1330432 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1330385 TAAATTATTG
*
1330395 AATTGAATT-A
1 AATTTAATTAA
1330405 AATTTAAATTAA
1 AATTT-AATTAA
1330417 AATTTAATTAA
1 AATTTAATTAA
1330428 AATTT
1 AATTT
1330433 TTTAAATTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 4 0.16
11 15 0.60
12 6 0.24
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (11 bp):
AATTTAATTAA
Found at i:1331857 original size:2 final size:2
Alignment explanation
Indices: 1331852--1331882 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1331842 CCTTTTTTTA
1331852 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 A
1331883 AGAGAAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1332104 original size:2 final size:2
Alignment explanation
Indices: 1332097--1332136 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
1332087 TAGGTTGGTT
1332097 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
1332137 GTTGATAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1332608 original size:37 final size:37
Alignment explanation
Indices: 1332543--1332654 Score: 163
Period size: 37 Copynumber: 3.0 Consensus size: 37
1332533 GATTACCCCT
1332543 ATAATTTTTGTTTCATGCAAATGAGTTTTAATTGGTAC
1 ATAATTTTTGTTTCATGCAAATG-GTTTTAATTGGTAC
* *
1332581 ATAATTTTT-TTTCTTGCAAATTGGTTTTAATTGGTAT
1 ATAATTTTTGTTTCATGCAAA-TGGTTTTAATTGGTAC
*
1332618 ATAATTTTTGTTCCATGCAAATGGATTTTAATTGGTA
1 ATAATTTTTGTTTCATGCAAATGG-TTTTAATTGGTA
1332655 TGTAATTTAA
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
37 35 0.52
38 32 0.48
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (37 bp):
ATAATTTTTGTTTCATGCAAATGGTTTTAATTGGTAC
Found at i:1332647 original size:38 final size:38
Alignment explanation
Indices: 1332542--1332662 Score: 167
Period size: 38 Copynumber: 3.2 Consensus size: 38
1332532 TGATTACCCC
1332542 TATAATTTTTGTTTCATGCAAAT-GAGTTTTAATTGGTA
1 TATAATTTTTGTTTCATGCAAATGGA-TTTTAATTGGTA
* *
1332580 CATAATTTTT-TTTCTTGCAAATTGG-TTTTAATTGGTA
1 TATAATTTTTGTTTCATGCAAA-TGGATTTTAATTGGTA
*
1332617 TATAATTTTTGTTCCATGCAAATGGATTTTAATTGGTA
1 TATAATTTTTGTTTCATGCAAATGGATTTTAATTGGTA
*
1332655 TGTAATTT
1 TATAATTT
1332663 AATTGGAAAC
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
37 34 0.47
38 38 0.52
39 1 0.01
ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51
Consensus pattern (38 bp):
TATAATTTTTGTTTCATGCAAATGGATTTTAATTGGTA
Found at i:1333012 original size:19 final size:19
Alignment explanation
Indices: 1332990--1333038 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1332980 ATTAATATCT
1332990 TTTTTATATTTTTATCATA
1 TTTTTATATTTTTATCATA
* * **
1333009 TTTTAATTTTTTTATTTTA
1 TTTTTATATTTTTATCATA
1333028 TATTTTATATT
1 T-TTTTATATT
1333039 ATATCTAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTATATTTTTATCATA
Found at i:1333035 original size:12 final size:12
Alignment explanation
Indices: 1332972--1333042 Score: 55
Period size: 11 Copynumber: 6.2 Consensus size: 12
1332962 ATTTTGATAA
1332972 ATTTATATATTAAT
1 ATTT-TATATT-AT
1332986 ATCTTT-T-TTAT
1 AT-TTTATATTAT
*
1332997 ATTTT-TATCAT
1 ATTTTATATTAT
1333008 ATTTTA-ATT-T
1 ATTTTATATTAT
*
1333018 -TTTTATTTTAT
1 ATTTTATATTAT
1333029 ATTTTATATTAT
1 ATTTTATATTAT
1333041 AT
1 AT
1333043 CTAAAATTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
9 5 0.11
10 7 0.15
11 15 0.32
12 14 0.30
13 1 0.02
14 3 0.06
15 2 0.04
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTTTATATTAT
Found at i:1336427 original size:15 final size:15
Alignment explanation
Indices: 1336409--1336466 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
1336399 ATTTTAATTT
1336409 TTTAATAATTATTAA
1 TTTAATAATTATTAA
1336424 TTT-ATAAATT-TTAA
1 TTTAAT-AATTATTAA
*
1336438 TTTAA-ATTTAATTAA
1 TTTAATAATT-ATTAA
1336453 TTTATATAATTATT
1 TTTA-ATAATTATT
1336467 TTTAAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
13 3 0.09
14 9 0.26
15 16 0.46
16 4 0.11
17 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTAATAATTATTAA
Found at i:1336470 original size:29 final size:28
Alignment explanation
Indices: 1336409--1336481 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
1336399 ATTTTAATTT
* *
1336409 TTTAATAATTATTAATTTATAAATTTTAA
1 TTTAAAAATAATTAATTTATAAATTTT-A
**
1336438 TTTAAATTTAATTAATTTATATAATTATT-
1 TTTAAAAATAATTAATTTATA-AATT-TTA
1336467 TTTAAAAATAATTAA
1 TTTAAAAATAATTAA
1336482 AATAAATTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 30 0.83
30 4 0.11
31 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TTTAAAAATAATTAATTTATAAATTTTA
Found at i:1338712 original size:15 final size:16
Alignment explanation
Indices: 1338692--1338743 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 16
1338682 TAATTAAGTA
1338692 AAAATTATAAAT-ATT
1 AAAATTATAAATAATT
1338707 AAAATT-TAAATAATT
1 AAAATTATAAATAATT
* *
1338722 TAAATTATAATTAA--
1 AAAATTATAAATAATT
1338736 AAAATTAT
1 AAAATTAT
1338744 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
14 12 0.38
15 14 0.44
16 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAATTATAAATAATT
Found at i:1338751 original size:26 final size:25
Alignment explanation
Indices: 1338719--1338767 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1338709 AATTTAAATA
*
1338719 ATTTAAATTATAATTAAAAAATTATT
1 ATTTAAAATAT-ATTAAAAAATTATT
*
1338745 ATTTAAAATATATTAAAATATTA
1 ATTTAAAATATATTAAAAAATTA
1338768 CTTTTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTTAAAATATATTAAAAAATTATT
Found at i:1344371 original size:12 final size:12
Alignment explanation
Indices: 1344350--1344385 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1344340 TGATGGTGAA
*
1344350 AAGAAGGACGAG
1 AAGAAAGACGAG
1344362 AAGAAAGACGAG
1 AAGAAAGACGAG
1344374 AAGAAAGACGAG
1 AAGAAAGACGAG
1344386 GCCAAGCCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.56, C:0.08, G:0.36, T:0.00
Consensus pattern (12 bp):
AAGAAAGACGAG
Found at i:1344869 original size:2 final size:2
Alignment explanation
Indices: 1344862--1344891 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1344852 TTCCTTTTTA
*
1344862 AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1344892 GAAAAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1345603 original size:37 final size:38
Alignment explanation
Indices: 1345538--1345611 Score: 116
Period size: 37 Copynumber: 2.0 Consensus size: 38
1345528 GATTACCCCT
1345538 ATAATTTTTGTTTCATGCAAATGAGTTTTAATTGGTAC
1 ATAATTTTTGTTTCATGCAAATGAGTTTTAATTGGTAC
*
1345576 ATAATTTTT-TTTCTTGCAAAT-AGGTTTTAATTGGTA
1 ATAATTTTTGTTTCATGCAAATGA-GTTTTAATTGGTA
1345612 ATGTGGTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 1 0.03
37 24 0.71
38 9 0.26
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (38 bp):
ATAATTTTTGTTTCATGCAAATGAGTTTTAATTGGTAC
Found at i:1345954 original size:30 final size:32
Alignment explanation
Indices: 1345915--1345993 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
1345905 TGATAAATTT
* *
1345915 ATATATTAATATTTT-A-TTTATATTTTTATC
1 ATATTTTAATATTTTAATTTTATATTTATATC
* *
1345945 ATATTTTAATTTTTTAATTTTATATTTATATT
1 ATATTTTAATATTTTAATTTTATATTTATATC
1345977 ATATTTTAA-ATTATTAA
1 ATATTTTAATATT-TTAA
1345994 ATCTTAAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 13 0.32
31 3 0.07
32 25 0.61
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (32 bp):
ATATTTTAATATTTTAATTTTATATTTATATC
Found at i:1346279 original size:10 final size:11
Alignment explanation
Indices: 1346264--1346306 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
1346254 AGTTTGATAA
1346264 TTTATT-TATT
1 TTTATTATATT
1346274 TTTATTATATT
1 TTTATTATATT
**
1346285 AATATTATATT
1 TTTATTATATT
*
1346296 TATATTATATT
1 TTTATTATATT
1346307 CGTATTAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 6 0.21
11 23 0.79
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTATTATATT
Found at i:1346313 original size:11 final size:11
Alignment explanation
Indices: 1346276--1346306 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1346266 TATTTATTTT
1346276 TATTATATTAA
1 TATTATATTAA
*
1346287 TATTATATTTA
1 TATTATATTAA
1346298 TATTATATT
1 TATTATATT
1346307 CGTATTAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTATATTAA
Found at i:1346313 original size:22 final size:22
Alignment explanation
Indices: 1346266--1346306 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1346256 TTTGATAATT
*
1346266 TATT-TATTTTTATTATATTAA
1 TATTATATTTATATTATATTAA
1346287 TATTATATTTATATTATATT
1 TATTATATTTATATTATATT
1346307 CGTATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTATATTTATATTATATTAA
Found at i:1346862 original size:108 final size:101
Alignment explanation
Indices: 1346794--1346987 Score: 302
Period size: 100 Copynumber: 1.9 Consensus size: 101
1346784 CAATTTTCTT
* *
1346794 TTTTTTTTTTTAAAAAAAAAGTCATTTTTGTTGTTCCAAAAGTATAAAGAAAATAGTTTTTAACT
1 TTTTCTTTTTTAAAAAAAAAGTCATTTTTGTTGTTCCAAAAGTATAATGAAAATAGTTTTTAACT
* *
1346859 TTTTTACCTAACAAAAAGTTGGAAAAACTTTAACAA
66 TTTTTACCCAACAAAAAATTGGAAAAACTTTAACAA
*
1346895 TTTTCTTTTTT-CAAAAAAAGTCATTTTTGTTGTTCCAAAAGTATAATGAAAATAGTTTTTTTAA
1 TTTTCTTTTTTAAAAAAAAAGTCATTTTTGTTGTTCCAAAAGTATAATGAAAATAG--TTTTTAA
1346959 CTTTTTTACCCAAC-AAAAATCTGGAAAAA
64 CTTTTTTACCCAACAAAAAAT-TGGAAAAA
1346988 TCGAAAATTT
Statistics
Matches: 85, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
100 42 0.49
101 15 0.18
102 28 0.33
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (101 bp):
TTTTCTTTTTTAAAAAAAAAGTCATTTTTGTTGTTCCAAAAGTATAATGAAAATAGTTTTTAACT
TTTTTACCCAACAAAAAATTGGAAAAACTTTAACAA
Found at i:1348187 original size:20 final size:20
Alignment explanation
Indices: 1348162--1348222 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
1348152 CAAATTCATA
1348162 TATATTTATATTTAATTATT
1 TATATTTATATTTAATTATT
1348182 TATATTTAT-TTTCAATTAATT
1 TATATTTATATTT-AATT-ATT
* *
1348203 T-TATTTTTATTTAATAATT
1 TATATTTATATTTAATTATT
1348222 T
1 T
1348223 TAAAAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
19 7 0.19
20 22 0.61
21 7 0.19
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
TATATTTATATTTAATTATT
Found at i:1348216 original size:16 final size:17
Alignment explanation
Indices: 1348177--1348218 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
1348167 TTATATTTAA
1348177 TTATTT-ATATTTATTT
1 TTATTTAATATTTATTT
* *
1348193 TCAATTAAT-TTTATTT
1 TTATTTAATATTTATTT
1348209 TTATTTAATA
1 TTATTTAATA
1348219 ATTTTAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTTAATATTTATTT
Found at i:1349008 original size:16 final size:16
Alignment explanation
Indices: 1348983--1349013 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1348973 ATAACATTAT
*
1348983 TAATTGAATAAAAAAA
1 TAATTAAATAAAAAAA
1348999 TAATTAAATAAAAAA
1 TAATTAAATAAAAAA
1349014 TTTTAAAATA
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:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
TAATTAAATAAAAAAA
Found at i:1349865 original size:11 final size:10
Alignment explanation
Indices: 1349845--1349873 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
1349835 AAGATTGAAT
1349845 TAAATATATA
1 TAAATATATA
1349855 TAAAT-TATA
1 TAAATATATA
1349864 TAAATATATA
1 TAAATATATA
1349874 ATATTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TAAATATATA
Found at i:1351056 original size:14 final size:14
Alignment explanation
Indices: 1351039--1351071 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1351029 TTTTTTATTT
1351039 AAAT-TTAATTATAA
1 AAATATTAA-TATAA
1351053 AAATATTAATATAA
1 AAATATTAATATAA
1351067 AAATA
1 AAATA
1351072 ATTTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATATTAATATAA
Found at i:1352237 original size:15 final size:15
Alignment explanation
Indices: 1352213--1352243 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1352203 AAATCTTAGC
1352213 TTTTTCTTTTGTTTT
1 TTTTTCTTTTGTTTT
*
1352228 TTTTTTTTTTGTTTT
1 TTTTTCTTTTGTTTT
1352243 T
1 T
1352244 CCCCATACGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.03, G:0.06, T:0.90
Consensus pattern (15 bp):
TTTTTCTTTTGTTTT
Found at i:1352705 original size:17 final size:16
Alignment explanation
Indices: 1352683--1352717 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1352673 ACGATGTTAA
1352683 AATTATATTATTTAATT
1 AATTATA-TATTTAATT
*
1352700 AATTATATATTTTATT
1 AATTATATATTTAATT
1352716 AA
1 AA
1352718 ATATTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTATATATTTAATT
Found at i:1353400 original size:17 final size:16
Alignment explanation
Indices: 1353369--1353418 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
1353359 AATTTTAAAA
1353369 TATTTTTAT-TTATAT
1 TATTTTTATATTATAT
1353384 TATTTTTCATATTATAT
1 TATTTTT-ATATTATAT
*
1353401 CATATTTTATATTATAT
1 TAT-TTTTATATTATAT
1353418 T
1 T
1353419 TTAATTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 7 0.23
16 2 0.07
17 17 0.57
18 4 0.13
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTTTTATATTATAT
Found at i:1353410 original size:12 final size:12
Alignment explanation
Indices: 1353395--1353435 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
1353385 ATTTTTCATA
*
1353395 TTATATCATATT
1 TTATATTATATT
1353407 TTATATTATATT
1 TTATATTATATT
1353419 TTA-ATTAT-TT
1 TTATATTATATT
1353429 TTATATT
1 TTATATT
1353436 GTATAACCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 5 0.19
11 8 0.30
12 14 0.52
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATATTATATT
Found at i:1353417 original size:22 final size:22
Alignment explanation
Indices: 1353392--1353435 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1353382 ATTATTTTTC
1353392 ATATTAT-ATCATATTTTATATT
1 ATATTATAATCAT-TTTTATATT
* *
1353414 ATATTTTAATTATTTTTATATT
1 ATATTATAATCATTTTTATATT
1353436 GTATAACCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
ATATTATAATCATTTTTATATT
Found at i:1355537 original size:15 final size:14
Alignment explanation
Indices: 1355490--1355541 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
1355480 ATTATTATAT
1355490 TAAAATATATATAAA
1 TAAAAT-TATATAAA
* *
1355505 TATAAAATATTTTAAA
1 TA-AAATTA-TATAAA
1355521 TAAAATTATGATAAA
1 TAAAATTAT-ATAAA
1355536 TAAAAT
1 TAAAAT
1355542 AATTCACGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 19 0.63
16 10 0.33
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (14 bp):
TAAAATTATATAAA
Found at i:1360244 original size:2 final size:2
Alignment explanation
Indices: 1360237--1360268 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1360227 TTTTTGTGAC
1360237 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
1360269 CATTGGCATT
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:1362485 original size:25 final size:25
Alignment explanation
Indices: 1362445--1362495 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1362435 AATATTTTAT
1362445 AAATATTTATTATTTAA-AATAATA
1 AAATATTTATTATTTAATAATAATA
* *
1362469 AAATATATTATTTTTTAATATTAATA
1 AAATAT-TTATTATTTAATAATAATA
1362495 A
1 A
1362496 TTTATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 6 0.26
25 10 0.43
26 7 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AAATATTTATTATTTAATAATAATA
Found at i:1362493 original size:26 final size:24
Alignment explanation
Indices: 1362445--1362520 Score: 72
Period size: 23 Copynumber: 3.3 Consensus size: 24
1362435 AATATTTTAT
1362445 AAATATTTATTATTTAAAATAATA
1 AAATATTTATTATTTAAAATAATA
* *
1362469 AAATATATTATT-TTT-TAATATTA
1 AAATAT-TTATTATTTAAAATAATA
*
1362492 ATA-ATTTATTA-TTAAAAT-ATA
1 AAATATTTATTATTTAAAATAATA
1362513 AATATATT
1 AA-ATATT
1362521 AATGTTTAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
21 10 0.24
22 6 0.15
23 11 0.27
24 9 0.22
25 5 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AAATATTTATTATTTAAAATAATA
Found at i:1362534 original size:46 final size:46
Alignment explanation
Indices: 1362449--1362536 Score: 119
Period size: 46 Copynumber: 1.9 Consensus size: 46
1362439 TTTTATAAAT
*
1362449 ATTTATTATTTAAAATAATAAAATATATTATTTTTTAATATTAATA
1 ATTTATTATTTAAAATAATAAAATATATTATTTTATAATATTAATA
1362495 ATTTATTA-TTAAAAT-AT-AAATATATTAATGTTTAATAATATT
1 ATTTATTATTTAAAATAATAAAATATATT-AT-TTT-ATAATATT
1362537 CAAAAATATT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
43 9 0.24
44 4 0.11
45 10 0.26
46 15 0.39
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (46 bp):
ATTTATTATTTAAAATAATAAAATATATTATTTTATAATATTAATA
Found at i:1362601 original size:22 final size:22
Alignment explanation
Indices: 1362550--1362623 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
1362540 AAATATTTAA
* *
1362550 AATTAAAATATTTTATACTTTTT
1 AATTAAAAT-TTTAATATTTTTT
*
1362573 ATTTTAAAATTTTAATATTTTTT
1 A-ATTAAAATTTTAATATTTTTT
*
1362596 AATTAAAA-TTAAATAATTTTTT
1 AATTAAAATTTTAAT-ATTTTTT
*
1362618 TATTAA
1 AATTAA
1362624 CATAATAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
21 5 0.12
22 18 0.42
23 13 0.30
24 7 0.16
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (22 bp):
AATTAAAATTTTAATATTTTTT
Found at i:1362630 original size:20 final size:21
Alignment explanation
Indices: 1362584--1362632 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
1362574 TTTTAAAATT
1362584 TTAAT-ATTTTTTAATTAAAA
1 TTAATAATTTTTTAATTAAAA
* *
1362604 TTAAATAATTTTTTTATTAACA
1 TT-AATAATTTTTTAATTAAAA
1362626 -TAATAAT
1 TTAATAAT
1362633 ATATTGTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 8 0.32
21 4 0.16
22 13 0.52
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAATAATTTTTTAATTAAAA
Found at i:1363847 original size:20 final size:20
Alignment explanation
Indices: 1363795--1363848 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1363785 ATCTCGTATG
1363795 ATTATATTTTAT-TTTAAAA
1 ATTATATTTTATATTTAAAA
*
1363814 ATT-TTTTTATATATTTAAAA
1 ATTATATTT-TATATTTAAAA
*
1363834 ATTATATTTCATATT
1 ATTATATTTTATATT
1363849 AAATATGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 4 0.14
19 6 0.21
20 15 0.52
21 4 0.14
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTATATTTTATATTTAAAA
Found at i:1364303 original size:34 final size:35
Alignment explanation
Indices: 1364242--1364344 Score: 163
Period size: 35 Copynumber: 3.0 Consensus size: 35
1364232 CGTCAACACT
*
1364242 TATTTTCACTAATAAAATATTGGTAATGATTCTGA
1 TATTTTCACTAATAAAATATTGGTAATGATGCTGA
*
1364277 TATTTTCACCAATAAAA-ATTGGTAATGATGCTGA
1 TATTTTCACTAATAAAATATTGGTAATGATGCTGA
* *
1364311 CATTTTCAATAATAAAATATTGGTAATGATGCTG
1 TATTTTCACTAATAAAATATTGGTAATGATGCTG
1364345 GATGCTGATA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
34 30 0.48
35 32 0.52
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.39
Consensus pattern (35 bp):
TATTTTCACTAATAAAATATTGGTAATGATGCTGA
Found at i:1366380 original size:18 final size:19
Alignment explanation
Indices: 1366346--1366396 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1366336 GTAAGAGAAA
*
1366346 ATATTTATGTATTTTTA-TT
1 ATATTTATAT-TTTTTAGTT
1366365 ATATTTATATTTTTTATGTT
1 ATATTTATATTTTTTA-GTT
*
1366385 ATAATTATATTT
1 ATATTTATATTT
1366397 AAGATTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 6 0.21
19 9 0.32
20 13 0.46
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
ATATTTATATTTTTTAGTT
Found at i:1367055 original size:21 final size:20
Alignment explanation
Indices: 1367012--1367058 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
1367002 AACTAAAATT
* *
1367012 AAATTTTATTATATATATTA
1 AAATTTTATTATACATATGA
*
1367032 AAATTTTATTTTTACATATGA
1 AAATTTTA-TTATACATATGA
1367053 AAATTT
1 AAATTT
1367059 GATCTATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
AAATTTTATTATACATATGA
Found at i:1368101 original size:21 final size:20
Alignment explanation
Indices: 1368062--1368102 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1368052 ATTAAAAAAT
1368062 TATTTTTATATTAATATTTA
1 TATTTTTATATTAATATTTA
1368082 TATTTTGTATAATTAA-ATTTA
1 TATTTT-TAT-ATTAATATTTA
1368103 AAATAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 8 0.42
22 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TATTTTTATATTAATATTTA
Found at i:1368487 original size:3 final size:3
Alignment explanation
Indices: 1368481--1368507 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1368471 ATAGTAGTAG
1368481 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1368508 GATTAGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1370217 original size:14 final size:13
Alignment explanation
Indices: 1370191--1370229 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
1370181 CATCCTTATT
1370191 AATTAATTTATTAA
1 AATTAA-TTATTAA
1370205 ACATTAATTATTAA
1 A-ATTAATTATTAA
*
1370219 AATTAAATATT
1 AATTAATTATT
1370230 TGAAAGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 9 0.39
14 9 0.39
15 5 0.22
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTAATTATTAA
Found at i:1373730 original size:19 final size:20
Alignment explanation
Indices: 1373689--1373730 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
1373679 TCATTTATCT
* **
1373689 AAAATTTATATTTAAAATTA
1 AAAATTAATATTTAAAAAAA
1373709 AAAATTAAT-TTTAAAAAAA
1 AAAATTAATATTTAAAAAAA
1373728 AAA
1 AAA
1373731 TTTGGAGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATTAATATTTAAAAAAA
Found at i:1374608 original size:2 final size:2
Alignment explanation
Indices: 1374601--1374651 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
1374591 TTGTCATTCA
* * *
1374601 AT AT AT AT AT AT AT GT AT AT AT AT AT AT GT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1374643 AT AT AT AT A
1 AT AT AT AT A
1374652 AAAGGTTGGA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1376309 original size:21 final size:21
Alignment explanation
Indices: 1376275--1376319 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1376265 TTGATAGTGA
1376275 TTAATTAATTAAATATAA-AT
1 TTAATTAATTAAATATAATAT
* *
1376295 TTAATTGAGTTAAATTTAATAT
1 TTAATT-AATTAAATATAATAT
1376317 TTA
1 TTA
1376320 TAATTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 10 0.48
22 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
TTAATTAATTAAATATAATAT
Found at i:1376959 original size:2 final size:2
Alignment explanation
Indices: 1376954--1376985 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1376944 ATATATATAT
1376954 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1376986 TTAATAGCGG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1378334 original size:3 final size:3
Alignment explanation
Indices: 1378326--1378353 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1378316 CAAGTCAATA
1378326 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1378354 GGCCAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1381089 original size:10 final size:10
Alignment explanation
Indices: 1381074--1381103 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1381064 GTAAATTGTT
1381074 TTTATATATA
1 TTTATATATA
1381084 TTTATATATA
1 TTTATATATA
*
1381094 TATATATATA
1 TTTATATATA
1381104 CAAATTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TTTATATATA
Found at i:1384419 original size:14 final size:14
Alignment explanation
Indices: 1384400--1384431 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1384390 CTCTAAGACA
1384400 TGATTTACTTAACT
1 TGATTTACTTAACT
1384414 TGATTTACTTAACT
1 TGATTTACTTAACT
1384428 TGAT
1 TGAT
1384432 CCCTGAGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.50
Consensus pattern (14 bp):
TGATTTACTTAACT
Found at i:1389234 original size:15 final size:15
Alignment explanation
Indices: 1389214--1389242 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1389204 TTGAGATCTC
1389214 ATTTATTATTTTTTT
1 ATTTATTATTTTTTT
1389229 ATTTATTATTTTTT
1 ATTTATTATTTTTT
1389243 AATATACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
ATTTATTATTTTTTT
Found at i:1389646 original size:64 final size:65
Alignment explanation
Indices: 1389535--1389656 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 65
1389525 ACTATTATAG
* * *
1389535 ATATTATAAATATTATTATGATTAATTATGATAAATATTAAAGATAAAA-AATTAAAAATTATTA
1 ATATAATAAATATTATTATGATTAATTATAATAAATATGAAAGATAAAATAATTAAAAATTATTA
* * *
1389599 ATATAATAAATATTATTTTGATTACTTATAATAAATATCGATA-ATAAAATAATTAAAA
1 ATATAATAAATATTATTATGATTAATTATAATAAATAT-GAAAGATAAAATAATTAAAA
1389657 CTGTAAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 40 0.80
65 10 0.20
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (65 bp):
ATATAATAAATATTATTATGATTAATTATAATAAATATGAAAGATAAAATAATTAAAAATTATTA
Found at i:1392537 original size:2 final size:2
Alignment explanation
Indices: 1392530--1392564 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1392520 ATAAAGTTTC
1392530 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 A
1392565 AAGGTTGTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1393366 original size:98 final size:98
Alignment explanation
Indices: 1393247--1393441 Score: 363
Period size: 98 Copynumber: 2.0 Consensus size: 98
1393237 GTTTAAAATT
* *
1393247 TGATATTCAAGTCATATAAATTTTTTTATATAAAAATATTTATTTTTTATTTTAAAACTCATAAA
1 TGATATTCAAGTCATATAAATTCTTTTATATAAAAATATTTATTTTTTATTCTAAAACTCATAAA
1393312 ATTTGAATCCAATCATTGTATTCTAATCCTATA
66 ATTTGAATCCAATCATTGTATTCTAATCCTATA
*
1393345 TGATATTCAAGTTATATAAATTCTTTTATATAAAAATATTTATTTTTTATTCTAAAACTCATAAA
1 TGATATTCAAGTCATATAAATTCTTTTATATAAAAATATTTATTTTTTATTCTAAAACTCATAAA
1393410 ATTTGAATCCAATCATTGTATTCTAATCCTAT
66 ATTTGAATCCAATCATTGTATTCTAATCCTAT
1393442 CGCGTATATA
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (98 bp):
TGATATTCAAGTCATATAAATTCTTTTATATAAAAATATTTATTTTTTATTCTAAAACTCATAAA
ATTTGAATCCAATCATTGTATTCTAATCCTATA
Found at i:1394598 original size:2 final size:2
Alignment explanation
Indices: 1394593--1394627 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1394583 ATATATATAT
1394593 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1394628 CACGCACACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1394896 original size:18 final size:17
Alignment explanation
Indices: 1394847--1394909 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 17
1394837 TATTTTAATA
1394847 TTTATATAATA-AAAATT
1 TTTATA-AATATAAAATT
* * *
1394864 ATTA-AAATTTTAAATT
1 TTTATAAATATAAAATT
*
1394880 TTATATAAATATAAAATA
1 TT-TATAAATATAAAATT
1394898 TTT-TAAATATAA
1 TTTATAAATATAA
1394910 TTATAATATA
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
15 3 0.08
16 16 0.44
17 6 0.17
18 11 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTATAAATATAAAATT
Found at i:1394958 original size:27 final size:26
Alignment explanation
Indices: 1394859--1394959 Score: 80
Period size: 27 Copynumber: 3.7 Consensus size: 26
1394849 TATATAATAA
1394859 AAATTATTAAAATTT-TAAAT-TTTAT
1 AAATTA-TAAAATTTATAAATATTTAT
* *
1394884 ATAAATATAAAATATTTTAAATATAATTAT
1 A-AATTATAAAAT-TTATAAATAT--TTAT
* *
1394914 AATATAATAAAATATATAAATATTTCAT
1 AA-ATTATAAAATTTATAAATATTT-AT
*
1394942 AAATTATTAAATTTATAA
1 AAATTATAAAATTTATAA
1394960 TAATAAATCA
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
25 7 0.12
26 6 0.10
27 20 0.33
28 5 0.08
29 9 0.15
30 13 0.22
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (26 bp):
AAATTATAAAATTTATAAATATTTAT
Found at i:1394959 original size:39 final size:36
Alignment explanation
Indices: 1394855--1394962 Score: 93
Period size: 38 Copynumber: 2.9 Consensus size: 36
1394845 TATTTATATA
1394855 ATAAAA-ATTATTAAAATT-TTAAATTT-T-ATATAAAT
1 ATAAAATATT-TT-AAATTATTAAATTTATAATA-AAAT
1394890 ATAAAATATTTTAAATATAATTATAA--TATAATAAAAT
1 ATAAAATATTTTAAAT-T-ATTA-AATTTATAATAAAAT
1394927 ATATAAATATTTCATAAATTATTAAATTTATAATAA
1 ATA-AAATATTT--TAAATTATTAAATTTATAATAA
1394963 TAAATCATCC
Statistics
Matches: 61, Mismatches: 0, Indels: 20
0.75 0.00 0.25
Matches are distributed among these distances:
34 4 0.07
35 9 0.15
36 4 0.07
37 13 0.21
38 17 0.28
39 9 0.15
40 5 0.08
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.44
Consensus pattern (36 bp):
ATAAAATATTTTAAATTATTAAATTTATAATAAAAT
Found at i:1395578 original size:2 final size:2
Alignment explanation
Indices: 1395571--1395599 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1395561 TGGGTATGTT
1395571 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1395600 TGCTCAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1395952 original size:50 final size:49
Alignment explanation
Indices: 1395877--1395976 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 49
1395867 TGTTTTTGGC
*
1395877 CATAGTCAGAAAGGAAGATACTGAGAGCCTAAGCACGTCATGAATTTGAA
1 CATAGTCAGAAAGGAAGATACTGAGAGCCTAAGCACGTCAGGAA-TTGAA
1395927 CATAGTCAGAAAGGAAGATACTGAGAGCCTAAGCACGTCAGGAATTGAA
1 CATAGTCAGAAAGGAAGATACTGAGAGCCTAAGCACGTCAGGAATTGAA
1395976 C
1 C
1395977 TTGTCAAAAG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 6 0.12
50 43 0.88
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (49 bp):
CATAGTCAGAAAGGAAGATACTGAGAGCCTAAGCACGTCAGGAATTGAA
Found at i:1397205 original size:10 final size:10
Alignment explanation
Indices: 1397190--1397361 Score: 50
Period size: 11 Copynumber: 17.8 Consensus size: 10
1397180 AGCTAATTCA
1397190 TATATTTTAT
1 TATATTTTAT
1397200 TATA-TTTA-
1 TATATTTTAT
1397208 TATA-TTT-T
1 TATATTTTAT
* *
1397216 TATGTATTA-
1 TATATTTTAT
1397225 TA-ATTTTAT
1 TATATTTTAT
**
1397234 T-TAAATTAT
1 TATATTTTAT
1397243 TATATATTTA-
1 TATAT-TTTAT
*
1397253 TATAAATTT-T
1 TAT-ATTTTAT
* *
1397263 TATAATTTAA
1 TATATTTTAT
1397273 TA-ATTTATAAT
1 TATATTT-T-AT
**
1397284 ATATATTAAAT
1 -TATATTTTAT
1397295 TA-ATTTTA-
1 TATATTTTAT
*
1397303 -ATATATTA-
1 TATATTTTAT
1397311 TATATTTATAT
1 TATATTT-TAT
*
1397322 TATATTCGTAT
1 TATATT-TTAT
*
1397333 TATTTTTATAT
1 TATATTT-TAT
1397344 TATATTTTAAT
1 TATATTTT-AT
1397355 T-TATTTT
1 TATATTTT
1397362 TTAAGTCACA
Statistics
Matches: 119, Mismatches: 22, Indels: 42
0.65 0.12 0.23
Matches are distributed among these distances:
7 1 0.01
8 19 0.16
9 32 0.27
10 29 0.24
11 33 0.28
12 2 0.02
13 3 0.03
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (10 bp):
TATATTTTAT
Found at i:1397218 original size:16 final size:17
Alignment explanation
Indices: 1397189--1397343 Score: 52
Period size: 18 Copynumber: 8.8 Consensus size: 17
1397179 AAGCTAATTC
1397189 ATATA-TTTTATTATATTT
1 ATATATTTTTA-TATA-TT
*
1397207 ATATATTTTTATGTATT
1 ATATATTTTTATATATT
* *
1397224 ATAATTTTATTTAAATTATT
1 AT-ATATT-TTTATA-TATT
* *
1397244 ATATATTTATATAAATTT
1 ATATATTTTTATATA-TT
* * *
1397262 TTATAATTTAATA-ATT
1 ATATATTTTTATATATT
*
1397278 -TATA---ATATATATT
1 ATATATTTTTATATATT
* *
1397291 AAATTAATTTTAATATATT
1 ATA-T-ATTTTTATATATT
*
1397310 ATATATTTATATTATATT
1 ATATATTTTTA-TATATT
*
1397328 CGTATTATTTTTATAT
1 -ATA-TATTTTTATAT
1397344 TATATTTTAA
Statistics
Matches: 100, Mismatches: 22, Indels: 29
0.66 0.15 0.19
Matches are distributed among these distances:
12 3 0.03
13 3 0.03
14 1 0.01
15 5 0.05
16 3 0.03
17 11 0.11
18 34 0.34
19 27 0.27
20 13 0.13
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (17 bp):
ATATATTTTTATATATT
Found at i:1397245 original size:20 final size:20
Alignment explanation
Indices: 1397220--1397270 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1397210 TATTTTTATG
*
1397220 TATTATAATTTTATTTAAAT
1 TATTATAATTTTATATAAAT
1397240 TATTAT-ATATTTATATAAAT
1 TATTATAAT-TTTATATAAAT
*
1397260 TTTTATAATTT
1 TATTATAATTT
1397271 AATAATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 2 0.07
20 23 0.85
21 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTATAATTTTATATAAAT
Found at i:1397343 original size:22 final size:24
Alignment explanation
Indices: 1397306--1397349 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
1397296 AATTTTAATA
1397306 TATTATATATTTATATTATATTCG
1 TATTATATATTTATATTATATTCG
1397330 TATTAT-T-TTTATATTATATT
1 TATTATATATTTATATTATATT
1397350 TTAATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.65
23 1 0.05
24 6 0.30
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (24 bp):
TATTATATATTTATATTATATTCG
Found at i:1399136 original size:11 final size:11
Alignment explanation
Indices: 1399120--1399157 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1399110 TTATTTTATT
1399120 AAATTAAATTA
1 AAATTAAATTA
1399131 AAATTAAA-T-
1 AAATTAAATTA
*
1399140 AAATTAATTTA
1 AAATTAAATTA
1399151 AAATTAA
1 AAATTAA
1399158 TATAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
9 7 0.29
10 2 0.08
11 15 0.62
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AAATTAAATTA
Found at i:1399142 original size:20 final size:21
Alignment explanation
Indices: 1399119--1399162 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
1399109 TTTATTTTAT
1399119 TAAATTAAATTAAAATTAA-A
1 TAAATTAAATTAAAATTAATA
*
1399139 TAAATTAATTTAAAATTAATA
1 TAAATTAAATTAAAATTAATA
1399160 TAA
1 TAA
1399163 TTTTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAATTAAATTAAAATTAATA
Found at i:1399261 original size:20 final size:20
Alignment explanation
Indices: 1399233--1399270 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1399223 GATGAGTTAT
1399233 CTAAATTTTCAAT-CTTAAGA
1 CTAAATTTT-AATACTTAAGA
*
1399253 CTAAGTTTTAATACTTAA
1 CTAAATTTTAATACTTAA
1399271 AACTCAACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.42
Consensus pattern (20 bp):
CTAAATTTTAATACTTAAGA
Found at i:1399515 original size:129 final size:130
Alignment explanation
Indices: 1399375--1399643 Score: 477
Period size: 136 Copynumber: 2.0 Consensus size: 130
1399365 TTCACTTCAA
1399375 TTATGTAATTAAAGGCATTTAATTCG-AAAAAATAAAAAGAATAAAAAGAAAAATAAAATATAAT
1 TTATGTAATTAAAGGCATTTAATTCGAAAAAAATAAAAAGAATAAAAAGAAAAATAAAATATAAT
1399439 GTAGTATTTATCGTTAATATTAAATTTATGTTAATTATAAAAATTACATATATTAATTATTTACT
66 GTAGTATTTATCGTTAATATTAAATTTATGTTAATTATAAAAATTACATATATTAATTATTTACT
1399504 TTATGTAATTAAAGGCATTTAATTCGAAAAAATAAAAAATAAAAAGAATAAAAAGAAAAATAAAA
1 TTATGTAATTAAAGGCATTTAATTCG-----A-AAAAAATAAAAAGAATAAAAAGAAAAATAAAA
1399569 TATAATGTAGTATTTATCGTTAATATTAAATTTATGTTAATTATAAAAATTACATATATTAATTA
60 TATAATGTAGTATTTATCGTTAATATTAAATTTATGTTAATTATAAAAATTACATATATTAATTA
1399634 TTTACT
125 TTTACT
1399640 TTAT
1 TTAT
1399644 TAACGTTTGG
Statistics
Matches: 133, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
129 26 0.20
136 107 0.80
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (130 bp):
TTATGTAATTAAAGGCATTTAATTCGAAAAAAATAAAAAGAATAAAAAGAAAAATAAAATATAAT
GTAGTATTTATCGTTAATATTAAATTTATGTTAATTATAAAAATTACATATATTAATTATTTACT
Found at i:1401371 original size:21 final size:21
Alignment explanation
Indices: 1401346--1401387 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1401336 TGTCTTATCT
* *
1401346 TATAATTCATCTAATATTTTA
1 TATAATTCATATAATAATTTA
*
1401367 TATAATTTATATAATAATTTA
1 TATAATTCATATAATAATTTA
1401388 ATTTTAACCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (21 bp):
TATAATTCATATAATAATTTA
Found at i:1401463 original size:15 final size:15
Alignment explanation
Indices: 1401439--1401469 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1401429 GCCATATTTG
*
1401439 ACAATTTAACATCTA
1 ACAATCTAACATCTA
1401454 ACAATCTAACATCTA
1 ACAATCTAACATCTA
1401469 A
1 A
1401470 TGAGTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (15 bp):
ACAATCTAACATCTA
Found at i:1407918 original size:11 final size:12
Alignment explanation
Indices: 1407879--1407924 Score: 58
Period size: 13 Copynumber: 3.7 Consensus size: 12
1407869 TGACATATTT
1407879 TTTAATATTTTA
1 TTTAATATTTTA
1407891 TTATAATATTATATA
1 TT-TAATATT-T-TA
1407906 TTTAAT-TTTTA
1 TTTAATATTTTA
1407917 TTTAATAT
1 TTTAATAT
1407925 AAATAAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 8 0.27
12 4 0.13
13 9 0.30
14 5 0.17
15 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTAATATTTTA
Found at i:1407970 original size:39 final size:39
Alignment explanation
Indices: 1407921--1407997 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
1407911 TTTTTATTTA
1407921 ATATAAATAAAAACAACACATTATATGATTATAAAATAT
1 ATATAAATAAAAACAACACATTATATGATTATAAAATAT
* * *
1407960 ATATAAATAAAAATAATATATTATATGATTATAAAATA
1 ATATAAATAAAAACAACACATTATATGATTATAAAATA
1407998 AATTAAACCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.34
Consensus pattern (39 bp):
ATATAAATAAAAACAACACATTATATGATTATAAAATAT
Found at i:1411296 original size:22 final size:22
Alignment explanation
Indices: 1411266--1411308 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1411256 TTAAAAGCAA
* * *
1411266 AAATTAAAAGTTAAAGATTTAC
1 AAATAAAAAATTAAAAATTTAC
1411288 AAATAAAAAATTAAAAATTTA
1 AAATAAAAAATTAAAAATTTA
1411309 TATTAGTTGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (22 bp):
AAATAAAAAATTAAAAATTTAC
Found at i:1413334 original size:4 final size:4
Alignment explanation
Indices: 1413325--1413349 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1413315 TGATAAATGA
1413325 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
1413350 GGAGCCAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1419368 original size:15 final size:15
Alignment explanation
Indices: 1419350--1419384 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1419340 TCTCTCCTGC
1419350 GCTTCCCTCTCTCTT
1 GCTTCCCTCTCTCTT
*
1419365 GCTTCCCTTTCTCTT
1 GCTTCCCTCTCTCTT
1419380 GCTTC
1 GCTTC
1419385 TGCAGCAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.43, G:0.09, T:0.49
Consensus pattern (15 bp):
GCTTCCCTCTCTCTT
Found at i:1424380 original size:14 final size:14
Alignment explanation
Indices: 1424360--1424402 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
1424350 TATAAAAGAT
1424360 TAAATTTTAAAAAA
1 TAAATTTTAAAAAA
*
1424374 TATATTTTTTAAAAAA
1 TA-A-ATTTTAAAAAA
*
1424390 TAAATTATAAAAA
1 TAAATTTTAAAAA
1424403 TAATATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 10 0.42
15 2 0.08
16 12 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATTTTAAAAAA
Found at i:1424624 original size:20 final size:18
Alignment explanation
Indices: 1424599--1424642 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
1424589 TGTGACTTCA
*
1424599 ATTATTTACTTAACAAAATT
1 ATTATTTACATAA-AAAA-T
1424619 ATTATTTTACATAAAAAAT
1 ATTA-TTTACATAAAAAAT
1424638 ATTAT
1 ATTAT
1424643 AATTAATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 1 0.05
19 5 0.23
20 8 0.36
21 8 0.36
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTATTTACATAAAAAAT
Found at i:1425079 original size:32 final size:33
Alignment explanation
Indices: 1425043--1425113 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
1425033 ATATTATAAT
*
1425043 TATATTTAA-AATATT-TTTTATATAAATTTTAA
1 TATATTTAATAAT-TTATATTATATAAATTTTAA
*
1425075 TATA-TTAATAATTTATATTATATAATTTTTAA
1 TATATTTAATAATTTATATTATATAAATTTTAA
*
1425107 AATATTT
1 TATATTT
1425114 GTATACTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
31 6 0.18
32 25 0.76
33 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
TATATTTAATAATTTATATTATATAAATTTTAA
Found at i:1425647 original size:18 final size:18
Alignment explanation
Indices: 1425621--1425676 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
1425611 TATAATTGAT
*
1425621 AATATATAAAAATAAATA
1 AATAAATAAAAATAAATA
* *
1425639 AATAAATAAATATGAATA
1 AATAAATAAAAATAAATA
*
1425657 TAA-AAATAAAGGATAAATA
1 -AATAAATAAA-AATAAATA
1425676 A
1 A
1425677 TTAATATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
18 23 0.74
19 8 0.26
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (18 bp):
AATAAATAAAAATAAATA
Found at i:1426578 original size:11 final size:11
Alignment explanation
Indices: 1426562--1426589 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1426552 ATGATAAATT
1426562 TTAAAATTAAA
1 TTAAAATTAAA
1426573 TTAAAATTAAA
1 TTAAAATTAAA
1426584 TTAAAA
1 TTAAAA
1426590 AAACACCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TTAAAATTAAA
Found at i:1427055 original size:11 final size:11
Alignment explanation
Indices: 1427039--1427072 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1427029 TATGATTTTG
*
1427039 AAAATAAATTT
1 AAAATAAATTA
1427050 AAAATAAATTA
1 AAAATAAATTA
*
1427061 AAAAAAAATTA
1 AAAATAAATTA
1427072 A
1 A
1427073 GGTTGCTGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAATAAATTA
Found at i:1427498 original size:147 final size:148
Alignment explanation
Indices: 1427303--1427592 Score: 381
Period size: 149 Copynumber: 2.0 Consensus size: 148
1427293 CCCAAATACA
* * *
1427303 TTTTTGACAATTAAGCTGTAAAATCTATTTTTTTAGATTTTATTTCCATATAAAGAAGGGTTTCT
1 TTTTTGACAATTAAGCTATAAAATCTA-TTTTTTAGATTTCATTTCCATATAAAGAAGAGTTTCT
* * * * * **
1427368 AAATAAA-TAA-AATAGAGGATAAACACTAAAATTCAACTCTTATTAAAAATGAATTTCATTTAA
65 AAATAAATTAATAATA-AAGAGAAACACTAAAATTCAACTCTTA-TAAAAATAAAATCCACGTAA
1427431 TATTTTAATAAAATCATTTTT
128 TATTTTAATAAAATCATTTTT
* *
1427452 TTTTTGACAAATT-AGCTATAAAATCTA-TTTTTAGATTTCATTTCCATTTAAAGAATAGTTTCT
1 TTTTTGAC-AATTAAGCTATAAAATCTATTTTTTAGATTTCATTTCCATATAAAGAAGAGTTTCT
*
1427515 AAATAAATTAATTAATAAAGAGAAATACTAAAATTCAACTCTTATAAAAATAAAATCCACGTAAT
65 AAATAAATTAA-TAATAAAGAGAAACACTAAAATTCAACTCTTATAAAAATAAAATCCACGTAAT
*
1427580 ATTTTAGTAAAAT
129 ATTTTAATAAAAT
1427593 TATAAATAAT
Statistics
Matches: 123, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
147 39 0.32
148 31 0.25
149 45 0.37
150 8 0.07
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.40
Consensus pattern (148 bp):
TTTTTGACAATTAAGCTATAAAATCTATTTTTTAGATTTCATTTCCATATAAAGAAGAGTTTCTA
AATAAATTAATAATAAAGAGAAACACTAAAATTCAACTCTTATAAAAATAAAATCCACGTAATAT
TTTAATAAAATCATTTTT
Found at i:1428313 original size:23 final size:22
Alignment explanation
Indices: 1428272--1428318 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
1428262 TTATATTATT
**
1428272 TAAATTTAAAATATGATATCTAA
1 TAAATTTAAAATAAAATAT-TAA
1428295 TAAATTTAAAATAAAATATTAA
1 TAAATTTAAAATAAAATATTAA
1428317 TA
1 TA
1428319 TTTTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAATTTAAAATAAAATATTAA
Found at i:1430659 original size:2 final size:2
Alignment explanation
Indices: 1430652--1430678 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1430642 GTACATAGGT
1430652 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1430679 GCACACACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1430800 original size:22 final size:21
Alignment explanation
Indices: 1430775--1430824 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
1430765 ATATTTTTTA
1430775 TTATTAA-TAAAAATTTATTAAT
1 TTATTAAGTAAAAA-TT-TTAAT
*
1430797 TTA-TAAGTAATAATTTTAAT
1 TTATTAAGTAAAAATTTTAAT
1430817 TTCATTAA
1 TT-ATTAA
1430825 ATATATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 7 0.29
21 6 0.25
22 11 0.46
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
TTATTAAGTAAAAATTTTAAT
Found at i:1434755 original size:2 final size:2
Alignment explanation
Indices: 1434748--1434777 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1434738 AGTTGTGAGT
1434748 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1434778 TGACCACTGA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1436262 original size:2 final size:2
Alignment explanation
Indices: 1436257--1436291 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1436247 AATAATTTAA
1436257 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1436292 TGCTAAGAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1438928 original size:25 final size:25
Alignment explanation
Indices: 1438883--1438933 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
1438873 AATTTTTTAA
*
1438883 TATTTTTATTTAAATATATTA-ATT
1 TATTTTAATTTAAATATATTATATT
1438907 TATTTTAATTTTAAAT-TAATTATATT
1 TATTTTAA-TTTAAATAT-ATTATATT
1438933 T
1 T
1438934 TAAAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 8 0.35
25 11 0.48
26 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TATTTTAATTTAAATATATTATATT
Found at i:1439266 original size:16 final size:15
Alignment explanation
Indices: 1439247--1439280 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1439237 TATCTTACGT
1439247 TTAAAGTAAAATTAAA
1 TTAAAGTAAAA-TAAA
*
1439263 TTAAATTAAAATAAA
1 TTAAAGTAAAATAAA
1439278 TTA
1 TTA
1439281 CTCATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (15 bp):
TTAAAGTAAAATAAA
Found at i:1439505 original size:2 final size:2
Alignment explanation
Indices: 1439500--1439532 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1439490 GCATATATGC
*
1439500 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1439533 AAAGAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1440996 original size:26 final size:25
Alignment explanation
Indices: 1440967--1441027 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
1440957 AAAATAAATT
1440967 ATTAACATGTAAAAATTTATTAAAAA
1 ATTAACATGTAAAAATTT-TTAAAAA
* *
1440993 ATTATA-ATTTTTAAAATTTTTAAAAA
1 ATTA-ACA-TGTAAAAATTTTTAAAAA
*
1441019 AGTAACATG
1 ATTAACATG
1441028 AACACATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
25 2 0.07
26 16 0.57
27 10 0.36
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.39
Consensus pattern (25 bp):
ATTAACATGTAAAAATTTTTAAAAA
Found at i:1441512 original size:17 final size:17
Alignment explanation
Indices: 1441467--1441596 Score: 70
Period size: 16 Copynumber: 7.4 Consensus size: 17
1441457 ATTAAAACAT
1441467 AATATA-AAAATAATATA
1 AATATATAAAATAA-ATA
*
1441484 CACATAATATAAAATACATA
1 -A-AT-ATATAAAATAAATA
*
1441504 AATATATAAAATATATA
1 AATATATAAAATAAATA
1441521 TAA-A-ATAAAATAAATTA
1 -AATATATAAAATAAA-TA
* *
1441538 ATATATAAAAAATTATATA
1 A-ATATATAAAA-TAAATA
* * **
1441557 AAAATATAATAT-TTTA
1 AATATATAAAATAAATA
*
1441573 AATATAAAAAATAATATA
1 AATATATAAAATAA-ATA
1441591 AATATA
1 AATATA
1441597 AACATATAAT
Statistics
Matches: 87, Mismatches: 14, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
16 22 0.25
17 18 0.21
18 21 0.24
19 11 0.13
20 9 0.10
21 6 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
AATATATAAAATAAATA
Found at i:1441515 original size:59 final size:59
Alignment explanation
Indices: 1441428--1441542 Score: 137
Period size: 59 Copynumber: 1.9 Consensus size: 59
1441418 CAAACAAAAA
** *
1441428 ATAATATAAATACGATATTTATAAAAAATAT-TA-AAACATAATATAAAAATAATATACAC
1 ATAATATAAATACGATAAATATAAAAAATATATATAAA-ATAAAAT-AAAATAATATACAC
* *
1441487 ATAATATAAAATAC-ATAAATATATAAAATATATATAAAATAAAATAAATTAATATA
1 ATAATAT-AAATACGATAAATATAAAAAATATATATAAAATAAAATAAAATAATATA
1441543 TAAAAAATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
59 31 0.65
60 14 0.29
61 3 0.06
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (59 bp):
ATAATATAAATACGATAAATATAAAAAATATATATAAAATAAAATAAAATAATATACAC
Found at i:1441528 original size:24 final size:24
Alignment explanation
Indices: 1441501--1441605 Score: 78
Period size: 24 Copynumber: 4.5 Consensus size: 24
1441491 TATAAAATAC
1441501 ATAAATATATAAAATATATATAAA
1 ATAAATATATAAAATATATATAAA
*
1441525 AT-AA-A-ATAAATTAATATATAAA
1 ATAAATATATAAAAT-ATATATAAA
* **
1441547 A-AATTATATAAAA-ATATAATATT
1 ATAAATATATAAAATATAT-ATAAA
* *
1441570 TTAAATATAAAAAATA-ATATAAA
1 ATAAATATATAAAATATATATAAA
*
1441593 TATAAACATATAA
1 -ATAAATATATAA
1441606 TTTTTTCCCC
Statistics
Matches: 60, Mismatches: 13, Indels: 16
0.67 0.15 0.18
Matches are distributed among these distances:
21 6 0.10
22 16 0.27
23 9 0.15
24 28 0.47
25 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAAATATATAAAATATATATAAA
Found at i:1441541 original size:33 final size:33
Alignment explanation
Indices: 1441487--1441607 Score: 118
Period size: 33 Copynumber: 3.5 Consensus size: 33
1441477 TAATATACAC
* * * *
1441487 ATAATATAAAATACATAAATATATAAAATATAT
1 ATAAAATAAAATAAATTAATATATAAAAAATAT
1441520 ATAAAATAAAATAAATTAATATATAAAAAATTAT
1 ATAAAATAAAATAAATTAATATATAAAAAA-TAT
* **
1441554 ATAAAAATATAATATTTTAA-ATATAAAAAATAAT
1 AT-AAAATAAAATAAATTAATATATAAAAAAT-AT
1441588 ATAAATATAAACATATAATT
1 ATAAA-ATAAA-ATA-AATT
1441608 TTTTCCCCTC
Statistics
Matches: 72, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
33 30 0.42
34 23 0.32
35 17 0.24
36 2 0.03
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (33 bp):
ATAAAATAAAATAAATTAATATATAAAAAATAT
Found at i:1441562 original size:22 final size:22
Alignment explanation
Indices: 1441423--1441564 Score: 92
Period size: 24 Copynumber: 6.0 Consensus size: 22
1441413 TTAAACAAAC
1441423 AAAAAATAATATAAATACGATATTTAT
1 AAAAAATAATATAAA-A--ATA--TAT
1441450 AAAAAAT-AT-TAAAACATA-AT
1 AAAAAATAATATAAAA-ATATAT
* *
1441470 ATAAAAATAATATACACATAATAT
1 A-AAAAATAATATAAAAAT-ATAT
1441494 AAAATACATAAATATATAAAATATAT
1 AAAA-A-AT-AATATA-AAAATATAT
* *
1441520 ATAAAATAAAATAAATTAATATAT
1 AAAAAATAATATAAA--AATATAT
*
1441544 AAAAAATTATATAAAAATATA
1 AAAAAATAATATAAAAATATA
1441565 ATATTTTAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 27
0.72 0.08 0.21
Matches are distributed among these distances:
20 3 0.03
21 6 0.06
22 12 0.13
23 15 0.16
24 26 0.28
25 7 0.07
26 15 0.16
27 10 0.11
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.30
Consensus pattern (22 bp):
AAAAAATAATATAAAAATATAT
Found at i:1441578 original size:34 final size:34
Alignment explanation
Indices: 1441492--1441607 Score: 119
Period size: 35 Copynumber: 3.4 Consensus size: 34
1441482 TACACATAAT
* *
1441492 ATAAAATACA-TAAATATATAAAA-TATATATAAA
1 ATAAAATAAATTAAATATAAAAAATTATATA-AAA
1441525 ATAAAATAAATTAATATATAAAAAATTATATAAAA
1 ATAAAATAAATTAA-ATATAAAAAATTATATAAAA
* ** * *
1441560 ATATAATATTTTAAATATAAAAAATAATATAAAT
1 ATAAAATAAATTAAATATAAAAAATTATATAAAA
1441594 ATAAACATATAATT
1 ATAAA-ATA-AATT
1441608 TTTTCCCCTC
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
33 9 0.13
34 25 0.37
35 26 0.38
36 8 0.12
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (34 bp):
ATAAAATAAATTAAATATAAAAAATTATATAAAA
Found at i:1441582 original size:155 final size:157
Alignment explanation
Indices: 1441290--1441594 Score: 356
Period size: 155 Copynumber: 2.0 Consensus size: 157
1441280 GAGATCAATA
*
1441290 TATATAAAAATTTAACACATAATACGAAAAATAACATATAACATAATATAAATACATGAAAATAT
1 TATATAAAAATTTAAAACATAATACGAAAAATAACATATAACATAATATAAATACATGAAAATAT
* ** * * * * ** **
1441355 AAAAATATAGATAATCGAATACTTAATATGTTAAAATTTATATAAATTTATTTTACTTTTAAACA
66 AAAAATATAGAAAATAAAATAATTAATATATAAAAAATTATATAAAAATATAATACTTTTAAACA
1441420 AACAAAAAATAATATAAATACGATATT
131 AACAAAAAATAATATAAATACGATATT
*
1441447 TATA-AAAAATATTAAAACATAATA-TAAAAAT-A-ATATACACATAATATAAAATACAT-AAAT
1 TATATAAAAAT-TTAAAACATAATACGAAAAATAACATATA-ACATAATAT-AAATACATGAAA-
*
1441507 ATATAAAATATATATAAAATAAAATAAATTAATATATAAAAAATTATATAAAAATATAATA-TTT
62 ATATAAAA-ATATAGAAAATAAAAT-AATTAATATATAAAAAATTATATAAAAATATAATACTTT
* *
1441571 T-AA-ATATAAAAAATAATATAAATA
125 TAAACAAACAAAAAATAATATAAATA
1441595 TAAACATATA
Statistics
Matches: 126, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
154 5 0.04
155 32 0.25
156 30 0.24
157 32 0.25
158 27 0.21
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.32
Consensus pattern (157 bp):
TATATAAAAATTTAAAACATAATACGAAAAATAACATATAACATAATATAAATACATGAAAATAT
AAAAATATAGAAAATAAAATAATTAATATATAAAAAATTATATAAAAATATAATACTTTTAAACA
AACAAAAAATAATATAAATACGATATT
Found at i:1441892 original size:17 final size:15
Alignment explanation
Indices: 1441870--1441925 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
1441860 TTTTTCACTA
1441870 ATAATATAAATATATTT
1 ATAATATAAATA-A-TT
1441887 ATAATATAAATAATT
1 ATAATATAAATAATT
* *
1441902 AAAATATAAAAAATT
1 ATAATATAAATAATT
*
1441917 AGAATATAA
1 ATAATATAA
1441926 TTATACCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
15 23 0.64
16 1 0.03
17 12 0.33
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (15 bp):
ATAATATAAATAATT
Found at i:1443331 original size:15 final size:15
Alignment explanation
Indices: 1443311--1443341 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1443301 ATGGGAACTC
1443311 TGGAATGTACGGTGG
1 TGGAATGTACGGTGG
*
1443326 TGGAATGTATGGTGG
1 TGGAATGTACGGTGG
1443341 T
1 T
1443342 CTTGGTGGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.03, G:0.45, T:0.32
Consensus pattern (15 bp):
TGGAATGTACGGTGG
Found at i:1448258 original size:11 final size:10
Alignment explanation
Indices: 1448241--1448287 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
1448231 TTAAATAAAA
1448241 ATATTAAATT
1 ATATTAAATT
1448251 ATATTTAAATT
1 ATA-TTAAATT
*
1448262 AAATTAAATT
1 ATATTAAATT
*
1448272 TTATTAAATT
1 ATATTAAATT
1448282 A-ATTAA
1 ATATTAA
1448288 TAATTAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
9 5 0.16
10 18 0.56
11 9 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
ATATTAAATT
Found at i:1448269 original size:21 final size:19
Alignment explanation
Indices: 1448243--1448287 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
1448233 AAATAAAAAT
1448243 ATTAAATTATATTTAAATTAA
1 ATTAAATTATA-TTAAATT-A
*
1448264 ATTAAATTTTATTAAATTA
1 ATTAAATTATATTAAATTA
1448283 ATTAA
1 ATTAA
1448288 TAATTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 7 0.30
21 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTAAATTATATTAAATTA
Found at i:1448271 original size:40 final size:44
Alignment explanation
Indices: 1448192--1448274 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 44
1448182 TTTTATTATT
*
1448192 TAAATAATATTATAATATTTTTAATATTATAATTAAAATTTAAA
1 TAAATAATATTATAATATATTTAATATTATAATTAAAATTTAAA
*
1448236 TAAA-AATATTA-AATTATATTTAA-ATTA-AATTAAATTTTA
1 TAAATAATATTATAA-TATATTTAATATTATAATTAAAATTTA
1448275 TTAAATTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
41 11 0.31
42 6 0.17
43 15 0.42
44 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (44 bp):
TAAATAATATTATAATATATTTAATATTATAATTAAAATTTAAA
Found at i:1448471 original size:19 final size:19
Alignment explanation
Indices: 1448426--1448473 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1448416 ATAATATTTT
* *
1448426 AATTTTTAAATTTTTTGAT
1 AATTTTTTAATTTTTTGAA
* *
1448445 AATATTTTAATTTTTTTAA
1 AATTTTTTAATTTTTTGAA
1448464 AATTTTTTAA
1 AATTTTTTAA
1448474 AAGTTTAACC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
AATTTTTTAATTTTTTGAA
Found at i:1450092 original size:26 final size:26
Alignment explanation
Indices: 1450056--1450109 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1450046 AGACCGTTCG
1450056 TTTATTGAGGGTACTCTGTTAGGACA
1 TTTATTGAGGGTACTCTGTTAGGACA
1450082 TTTATTGAGGGTACTCTGTTAGGACA
1 TTTATTGAGGGTACTCTGTTAGGACA
1450108 TT
1 TT
1450110 ATAAGAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.41
Consensus pattern (26 bp):
TTTATTGAGGGTACTCTGTTAGGACA
Found at i:1456986 original size:20 final size:20
Alignment explanation
Indices: 1456961--1457000 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1456951 TCTGCTAAGT
1456961 TAGTATTTTCTGGATTCTAC
1 TAGTATTTTCTGGATTCTAC
1456981 TAGTATTTTCTGGATTCTAC
1 TAGTATTTTCTGGATTCTAC
1457001 CATACAATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.50
Consensus pattern (20 bp):
TAGTATTTTCTGGATTCTAC
Found at i:1457463 original size:26 final size:26
Alignment explanation
Indices: 1457434--1457489 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
1457424 GATAACATAG
1457434 TTATTCATTAGGTGAGCTGTTATTAC
1 TTATTCATTAGGTGAGCTGTTATTAC
*
1457460 TTATTTATTAGGTGAGCTGTTATTAC
1 TTATTCATTAGGTGAGCTGTTATTAC
1457486 TTAT
1 TTAT
1457490 CTATAGGGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.23, C:0.09, G:0.18, T:0.50
Consensus pattern (26 bp):
TTATTCATTAGGTGAGCTGTTATTAC
Found at i:1458501 original size:3 final size:3
Alignment explanation
Indices: 1458495--1458530 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1458485 ATCATGTGCG
1458495 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1458531 TGTAAAATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1459833 original size:21 final size:22
Alignment explanation
Indices: 1459792--1459848 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
1459782 ATAATTAAAT
* *
1459792 TTAAATAAAAATATTTTAATTA
1 TTAAATAAAAATATCTGAATTA
1459814 TTAAAT-AAAATATCTGAATTAA
1 TTAAATAAAAATATCTGAATT-A
1459836 TTCAAATTAAAAA
1 TT-AAA-TAAAAA
1459849 AAAATTCCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 12 0.41
22 9 0.31
23 3 0.10
24 1 0.03
25 4 0.14
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (22 bp):
TTAAATAAAAATATCTGAATTA
Found at i:1463174 original size:2 final size:2
Alignment explanation
Indices: 1463167--1463201 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1463157 TATGCTGTGC
1463167 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 A
1463202 AAACTTTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1463249 original size:2 final size:2
Alignment explanation
Indices: 1463242--1463276 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1463232 AATTTTTGTC
1463242 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1463277 CTTCTTTAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1464903 original size:29 final size:29
Alignment explanation
Indices: 1464845--1464903 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
1464835 ATAAGTCTTA
* **
1464845 AAAATAAATATAAATAATTTTTTATTAAT
1 AAAATAAATATAAATAATTTATTAAAAAT
*
1464874 AAAATAAA-ATATTATAATTTATTAAAAAT
1 AAAATAAATATA-AATAATTTATTAAAAAT
1464903 A
1 A
1464904 TATAAGTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
AAAATAAATATAAATAATTTATTAAAAAT
Done.