Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1559
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: 258979
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 2 of 3
Found at i:139046 original size:14 final size:14
Alignment explanation
Indices: 139027--139053 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
139017 GTTGAAAGAT
139027 TACATTGTCCAAAC
1 TACATTGTCCAAAC
139041 TACATTGTCCAAA
1 TACATTGTCCAAA
139054 AATATTTTTA
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:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (14 bp):
TACATTGTCCAAAC
Found at i:140694 original size:19 final size:21
Alignment explanation
Indices: 140653--140696 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
140643 TTCTTTCTAT
* *
140653 TTTTCTTAATATTCAAATTTA
1 TTTTCTTAAAATTCAAATATA
140674 TTTT-TTAAAATT-AAATATA
1 TTTTCTTAAAATTCAAATATA
140693 TTTT
1 TTTT
140697 AAAATTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 7 0.33
21 4 0.19
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTCTTAAAATTCAAATATA
Found at i:141427 original size:26 final size:26
Alignment explanation
Indices: 141397--141448 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
141387 AATTATTCAC
141397 TTTTTGAAATAT-A-TATAAATATATAA
1 TTTTT-AAATATAATTAT-AATATATAA
*
141423 TTTTTTAATATAATTATAATATATAA
1 TTTTTAAATATAATTATAATATATAA
141449 AAATATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 5 0.22
26 15 0.65
27 3 0.13
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
TTTTTAAATATAATTATAATATATAA
Found at i:141442 original size:6 final size:7
Alignment explanation
Indices: 141407--141469 Score: 51
Period size: 7 Copynumber: 9.1 Consensus size: 7
141397 TTTTTGAAAT
141407 ATATATAA
1 ATATAT-A
141415 ATATATA
1 ATATATA
* * *
141422 ATTTTTT
1 ATATATA
141429 A-ATATA
1 ATATATA
141435 AT-TATA
1 ATATATA
141441 ATATATAA
1 ATATAT-A
*
141449 AAATATA
1 ATATATA
141456 ATATA-A
1 ATATATA
141462 ATATATA
1 ATATATA
141469 A
1 A
141470 ATGATGAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
6 15 0.35
7 16 0.37
8 12 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATATATA
Found at i:141453 original size:21 final size:21
Alignment explanation
Indices: 141429--141470 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
141419 ATAATTTTTT
141429 AATATAAT-TATAATATATAAA
1 AATATAATATA-AATATATAAA
141450 AATATAATATAAATATATAAA
1 AATATAATATAAATATATAAA
141471 TGATGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AATATAATATAAATATATAAA
Found at i:141732 original size:2 final size:2
Alignment explanation
Indices: 141725--141754 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
141715 TACTTAATTT
141725 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
141755 GGCCAAGTTA
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):
TA
Found at i:142185 original size:2 final size:2
Alignment explanation
Indices: 142178--142215 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
142168 AACTATATGC
*
142178 AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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
142216 CTGTTGAGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:145343 original size:2 final size:2
Alignment explanation
Indices: 145336--145361 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
145326 TTCTTGATTA
145336 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
145362 GGTGTAAACT
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:145656 original size:34 final size:35
Alignment explanation
Indices: 145613--145684 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 35
145603 TGTTCATGTG
145613 AACCATCTCTTGCATTTTTC-TTTCTTAGTATATT
1 AACCATCTCTTGCATTTTTCTTTTCTTAGTATATT
145647 AACCATCTCTTGCATTTTTCTTTTTCTTAGTATATT
1 AACCATCTCTTGCATTTTTC-TTTTCTTAGTATATT
145683 AA
1 AA
145685 TTATTTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 20 0.56
36 16 0.44
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (35 bp):
AACCATCTCTTGCATTTTTCTTTTCTTAGTATATT
Found at i:146383 original size:2 final size:2
Alignment explanation
Indices: 146376--146413 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
146366 ACCAAAGTTT
* *
146376 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
146414 CAAAAATGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:148809 original size:21 final size:22
Alignment explanation
Indices: 148771--148811 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
148761 CAAATGTATT
* *
148771 AAAAATAAATTAATATAATTAA
1 AAAAATAAATCAAGATAATTAA
148793 AAAAATAAA-CAAGATAATT
1 AAAAATAAATCAAGATAATT
148812 TTTTTAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAATAAATCAAGATAATTAA
Found at i:150092 original size:2 final size:2
Alignment explanation
Indices: 150085--150117 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
150075 TTGAAACTTG
150085 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 A
150118 GAATCTAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:155310 original size:13 final size:13
Alignment explanation
Indices: 155270--155310 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
155260 AATATATATC
*
155270 TAAATATAATTAT
1 TAAATATAATTTT
*
155283 AAAATATAATATTT
1 TAAATATAAT-TTT
155297 TAAATATAATTTT
1 TAAATATAATTTT
155310 T
1 T
155311 GAAACCTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TAAATATAATTTT
Found at i:155531 original size:2 final size:2
Alignment explanation
Indices: 155524--155549 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
155514 CTAAACCCAA
155524 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
155550 CAAATAATTA
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:158976 original size:32 final size:33
Alignment explanation
Indices: 158914--158979 Score: 84
Period size: 32 Copynumber: 2.0 Consensus size: 33
158904 GGTATATTAA
158914 AATAAATTAATTAAATATTAATAAAAAATTTATG
1 AATAAATTAA-TAAATATTAATAAAAAATTTATG
158948 AATAAATTAA-AAATA-TAA-AAAATTAATTTATG
1 AATAAATTAATAAATATTAATAAAA--AATTTATG
158980 GATGAATGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
30 4 0.13
31 3 0.10
32 13 0.43
34 10 0.33
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (33 bp):
AATAAATTAATAAATATTAATAAAAAATTTATG
Found at i:159660 original size:8 final size:8
Alignment explanation
Indices: 159639--159704 Score: 55
Period size: 8 Copynumber: 8.2 Consensus size: 8
159629 AATTAAATAA
*
159639 AATATAAT
1 AATATATT
*
159647 ATTATATT
1 AATATATT
159655 AATATATT
1 AATATATT
*
159663 AATATTTT
1 AATATATT
*
159671 AAAAT-TT
1 AATATATT
*
159678 ATATAATATA
1 A-AT-ATATT
159688 AAT-TATT
1 AATATATT
159695 AATATATT
1 AATATATT
159703 AA
1 AA
159705 ATTTATAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
7 9 0.20
8 31 0.67
9 4 0.09
10 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATATATT
Found at i:159674 original size:45 final size:41
Alignment explanation
Indices: 159624--159722 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 41
159614 TAAGATATAA
159624 TTAAAAATTAAATAAAATATAATATTATATTAATATATTAATATT
1 TTAAAAATTAAATAAAATATAA-A-T-TATTAATATATTAA-ATT
* *
159669 TT-AAAATT-TATATAATATAAATTATTAATATATTAAATT
1 TTAAAAATTAAATAAAATATAAATTATTAATATATTAAATT
* *
159708 TATAAATATAAAATA
1 T-TAAAAATTAAATA
159723 TTTTAAATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
39 4 0.09
40 15 0.33
41 5 0.11
42 4 0.09
43 10 0.22
44 6 0.13
45 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (41 bp):
TTAAAAATTAAATAAAATATAAATTATTAATATATTAAATT
Found at i:159701 original size:15 final size:15
Alignment explanation
Indices: 159683--159751 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 15
159673 AATTTATATA
159683 ATATAAATTATTAAT
1 ATATAAATTATTAAT
*
159698 ATATTAAATTTATAAAT
1 ATA-TAAA-TTATTAAT
*
159715 ATA-AAATATTTTAA-
1 ATATAAAT-TATTAAT
159729 ATA-AAATTA-TAAT
1 ATATAAATTATTAAT
159742 ATTATAAATT
1 A-TATAAATT
159752 TAATATAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
12 3 0.07
13 2 0.05
14 10 0.23
15 15 0.34
16 4 0.09
17 10 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATAAATTATTAAT
Found at i:159748 original size:16 final size:16
Alignment explanation
Indices: 159635--159757 Score: 59
Period size: 14 Copynumber: 7.9 Consensus size: 16
159625 TAAAAATTAA
159635 ATAAAA-TATAATATT
1 ATAAAATTATAATATT
*
159650 ATATTAATATATTAATATT
1 ATA-AAAT-TA-TAATATT
* *
159669 TTAAAATT-T-ATATA
1 ATAAAATTATAATATT
159683 ATATAAATTATTAATA-T
1 ATA-AAATTA-TAATATT
*
159700 ATTAAATTTATAA-A-T
1 A-TAAAATTATAATATT
** *
159715 ATAAAA-TATTTTA-A
1 ATAAAATTATAATATT
159729 ATAAAATTATAATATT
1 ATAAAATTATAATATT
159745 AT-AAATT-TAATAT
1 ATAAAATTATAATAT
159758 AAATAAATAA
Statistics
Matches: 82, Mismatches: 14, Indels: 25
0.68 0.12 0.21
Matches are distributed among these distances:
13 3 0.04
14 23 0.28
15 22 0.27
16 7 0.09
17 8 0.10
18 10 0.12
19 9 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAAAATTATAATATT
Found at i:159762 original size:20 final size:20
Alignment explanation
Indices: 159710--159775 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
159700 ATTAAATTTA
*
159710 TAAATATAAAATATTTTAAAT
1 TAAATAT-AAATATTATAAAT
*
159731 AAAAT-TATAATATTATAAAT
1 TAAATATA-AATATTATAAAT
* *
159751 TTAATATAAATA-AATAAAT
1 TAAATATAAATATTATAAAT
159770 TAAATA
1 TAAATA
159776 ATTTTACTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 12 0.32
20 19 0.51
21 6 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAATATAAATATTATAAAT
Found at i:160109 original size:16 final size:15
Alignment explanation
Indices: 160082--160111 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
160072 TATTGATTTG
160082 TTTAATTTAAATAAT
1 TTTAATTTAAATAAT
160097 TTTAATATTAAATAA
1 TTTAAT-TTAAATAA
160112 GTAACAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAATTTAAATAAT
Found at i:165435 original size:31 final size:32
Alignment explanation
Indices: 165400--165463 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
165390 ATAATTATAT
* *
165400 TAAAAAT-ATTATATATTTATATAAATTTTAA
1 TAAAAATAATAATATAATTATATAAATTTTAA
*
165431 T-AAAATAATAATTTAATTATATAAATTTTAA
1 TAAAAATAATAATATAATTATATAAATTTTAA
165462 TA
1 TA
165464 TATTTTTATC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
TAAAAATAATAATATAATTATATAAATTTTAA
Found at i:165465 original size:14 final size:14
Alignment explanation
Indices: 165417--165466 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
165407 ATTATATATT
165417 TATATAAATTTTAA
1 TATATAAATTTTAA
* *
165431 TAAAATAATAATTTAA
1 T-ATATAA-ATTTTAA
165447 TTATATAAATTTTAA
1 -TATATAAATTTTAA
165462 TATAT
1 TATAT
165467 TTTTATCTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 6 0.21
15 11 0.38
16 11 0.38
17 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:165509 original size:5 final size:5
Alignment explanation
Indices: 165493--165548 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
165483 ATTCATTTTT
* * *
165493 TTATA TTTTA TTATA TTTTAA TTATA TTTATA TTAAA TTATA TTATA -TA-A
1 TTATA TTATA TTATA TTAT-A TTATA -TTATA TTATA TTATA TTATA TTATA
165543 TTATA T
1 TTATA T
165549 CATAATCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
3 1 0.02
4 4 0.10
5 27 0.66
6 9 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:165518 original size:11 final size:10
Alignment explanation
Indices: 165487--165540 Score: 63
Period size: 10 Copynumber: 5.2 Consensus size: 10
165477 TGTTATATTC
*
165487 ATTTTTTTAT
1 ATTTTATTAT
165497 ATTTTATTAT
1 ATTTTATTAT
165507 ATTTTAATTAT
1 ATTTT-ATTAT
*
165518 ATTTATATTAA
1 ATTT-TATTAT
*
165529 ATTATATTAT
1 ATTTTATTAT
165539 AT
1 AT
165541 AATTATATCA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 21 0.55
11 16 0.42
12 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTATTAT
Found at i:165525 original size:27 final size:29
Alignment explanation
Indices: 165492--165548 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 29
165482 TATTCATTTT
**
165492 TTTATATTTTATTATATT-T-TAATTATA
1 TTTATATTAAATTATATTATATAATTATA
165519 TTTATATTAAATTATATTATATAATTATA
1 TTTATATTAAATTATATTATATAATTATA
165548 T
1 T
165549 CATAATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 16 0.62
28 1 0.04
29 9 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTATATTAAATTATATTATATAATTATA
Found at i:165539 original size:42 final size:44
Alignment explanation
Indices: 165344--165540 Score: 106
Period size: 42 Copynumber: 4.5 Consensus size: 44
165334 GAGATGAATC
* *
165344 TTATATTTAA-TATATTTATATTTTATTTATATATTTTTAATGTAATATAA
1 TTATATTAAATTATA-TTATATTTTA--T-TATA-TTTTAATCT-ATAT-A
* * * *
165394 TTATATTAAA-AATATTATATATTTATATAAATTTTAAT-AAAATA
1 TTATATTAAATTATATTATAT-TTTAT-TATATTTTAATCTATATA
* * * * * * *
165438 ATA-ATTTAATTATA-TAAATTTTAATATATTTTTATCTCT-TG
1 TTATATTAAATTATATTATATTTTATTATATTTTAATCTATATA
* * *
165479 TTATATT-CATTTTTTTATATTTTATTATATTTTAAT-TATAT-
1 TTATATTAAATTATATTATATTTTATTATATTTTAATCTATATA
165520 TTATATTAAATTATATTATAT
1 TTATATTAAATTATATTATAT
165541 AATTATATCA
Statistics
Matches: 113, Mismatches: 27, Indels: 22
0.70 0.17 0.14
Matches are distributed among these distances:
41 25 0.22
42 36 0.32
43 9 0.08
44 6 0.05
45 3 0.03
47 7 0.06
48 5 0.04
49 6 0.05
50 16 0.14
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.58
Consensus pattern (44 bp):
TTATATTAAATTATATTATATTTTATTATATTTTAATCTATATA
Found at i:165559 original size:29 final size:27
Alignment explanation
Indices: 165502--165560 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
165492 TTTATATTTT
* *
165502 ATTATATTTTAATTATATTTATATTAA
1 ATTATATTTTAATTATATATATATCAA
165529 ATTATATTATATAATTATATCATA-ATCAA
1 ATTATATT-T-TAATTATAT-ATATATCAA
165558 ATT
1 ATT
165561 TAACAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.30
28 1 0.04
29 16 0.59
30 2 0.07
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTATATTTTAATTATATATATATCAA
Found at i:166514 original size:14 final size:14
Alignment explanation
Indices: 166475--166514 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
166465 CAAAACTCTC
166475 ATTTTTTTTTATAA
1 ATTTTTTTTTATAA
*
166489 ATTATTTTTTAT-A
1 ATTTTTTTTTATAA
166502 ATTTTTTTATTAT
1 ATTTTTTT-TTAT
166515 TTTAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
ATTTTTTTTTATAA
Found at i:166742 original size:24 final size:22
Alignment explanation
Indices: 166703--166751 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 22
166693 TTATTTGAAT
*
166703 TATATATATTATGATAT-AATAA
1 TATATATATAATGATATGAA-AA
166725 TATATATATAATGGGATATGAAAA
1 TATATATATAAT--GATATGAAAA
166749 TAT
1 TAT
166752 TTTAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 11 0.48
24 10 0.43
25 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (22 bp):
TATATATATAATGATATGAAAA
Found at i:167467 original size:14 final size:13
Alignment explanation
Indices: 167440--167473 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
167430 TTAAAGAAAG
*
167440 TAAAAAATATATA
1 TAAAAAATAAATA
167453 TAAATAAATAAATA
1 TAAA-AAATAAATA
167467 TAAAAAA
1 TAAAAAA
167474 GCTGAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAAAAATAAATA
Found at i:167712 original size:19 final size:18
Alignment explanation
Indices: 167690--167754 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 18
167680 TATAAATATT
167690 ATTTTTAATTATTTAAAAA
1 ATTTTTAATT-TTTAAAAA
*
167709 A-TTTTAATTTTTATATTAA
1 ATTTTTAATTTTTA-A-AAA
** *
167728 ATTAATAATTTTTTATAAA
1 ATTTTTAA-TTTTTAAAAA
167747 ATTTTTAA
1 ATTTTTAA
167755 GAAATAATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
17 4 0.11
18 9 0.26
19 12 0.34
20 4 0.11
21 6 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTTAATTTTTAAAAA
Found at i:167738 original size:20 final size:19
Alignment explanation
Indices: 167695--167749 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
167685 ATATTATTTT
* * *
167695 TAATTATTTAAAAAATT-T
1 TAATTTTTTATAAAATTAA
*
167713 TAATTTTTATATTAAATTAA
1 TAATTTTT-TATAAAATTAA
167733 TAATTTTTTATAAAATT
1 TAATTTTTTATAAAATT
167750 TTTAAGAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 7 0.23
19 15 0.50
20 8 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATTTTTTATAAAATTAA
Found at i:168045 original size:2 final size:2
Alignment explanation
Indices: 168038--168077 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
168028 CCTTCTAAGC
168038 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
168078 GATTGAAATA
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):
TA
Found at i:170120 original size:32 final size:32
Alignment explanation
Indices: 170062--170123 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
170052 AATAAAATAC
170062 ATATAATATATATATAAATAGATTAAAATTTA
1 ATATAATATATATATAAATAGATTAAAATTTA
*
170094 ATATAAT-TATTATTTAAA-AGATTTAAAATT
1 ATATAATATA-TATATAAATAGA-TTAAAATT
170124 ATAAATTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (32 bp):
ATATAATATATATATAAATAGATTAAAATTTA
Found at i:171698 original size:35 final size:35
Alignment explanation
Indices: 171621--171725 Score: 106
Period size: 35 Copynumber: 2.9 Consensus size: 35
171611 ATAGATTAAA
* *
171621 ATATTAATATATATAATAAATAATTAAAATTTATTTTT
1 ATATTAA-ATA-ATAA-AAATAAATAAAATTTATATTT
171659 ATATTAAATAATAAAATATAAATAAAA-TTATATTT
1 ATATTAAATAATAAAA-ATAAATAAAATTTATATTT
* * *
171694 ATATTGAATAATAAATAA-AAATTATATTTATA
1 ATATTAAATAATAAA-AATAAATAAAATTTATA
171726 CAAAAAATTA
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
34 6 0.10
35 29 0.49
36 14 0.24
37 3 0.05
38 7 0.12
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (35 bp):
ATATTAAATAATAAAAATAAATAAAATTTATATTT
Found at i:171713 original size:92 final size:93
Alignment explanation
Indices: 171608--171786 Score: 229
Period size: 92 Copynumber: 1.9 Consensus size: 93
171598 ACAATTAAGG
* * * * *
171608 ATAATAGATTAAAATATTA-ATATATATAATAAATAATTAAAATTTATTTTTATATTAAATAATA
1 ATAATAGAATAAAA-ATTATATATATACAAAAAATAATTAAAA-TGATGTTTATATTAAATAATA
*
171672 AAATATA-AATAAAATTATATTTATATTGA
64 AAATATATAATAAAAATATATTTATATTGA
* * *
171701 ATAATA-AATAAAAATTATATTTATACAAAAAATTATTAAAATGATGTTTATATTAAATAATGAA
1 ATAATAGAATAAAAATTATATATATACAAAAAATAATTAAAATGATGTTTATATTAAATAATAAA
*
171765 ATATATATTAAAAATATATTTA
66 ATATATAATAAAAATATATTTA
171787 AATTTACATT
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
91 29 0.39
92 39 0.53
93 6 0.08
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (93 bp):
ATAATAGAATAAAAATTATATATATACAAAAAATAATTAAAATGATGTTTATATTAAATAATAAA
ATATATAATAAAAATATATTTATATTGA
Found at i:171808 original size:91 final size:91
Alignment explanation
Indices: 171638--171808 Score: 211
Period size: 91 Copynumber: 1.9 Consensus size: 91
171628 TATATATAAT
* * * *
171638 AAATAATTAAAATTTATTTTTATATTAAATAATAAAATATAAATAAAATTATATTTATATTGAAT
1 AAATAATTAAAATTGATGTTTATATTAAATAATAAAATATAAATAAAAATATATTTAAATTGAAT
*
171703 AATAAATAAAAATTATATTTATACAAA
66 -ATAAACAAAAATTATATTTATACAAA
* * * *
171730 AAATTATTAAAA-TGATGTTTATATTAAATAATGAAATATATATTAAAAATATATTTAAATTTAC
1 AAATAATTAAAATTGATGTTTATATTAAATAATAAAATATA-AATAAAAATATATTTAAATTGA-
*
171794 AT-TAAACAATAATTA
64 ATATAAACAAAAATTA
171809 AAATATTATT
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
91 36 0.54
92 29 0.43
93 2 0.03
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (91 bp):
AAATAATTAAAATTGATGTTTATATTAAATAATAAAATATAAATAAAAATATATTTAAATTGAAT
ATAAACAAAAATTATATTTATACAAA
Found at i:172015 original size:24 final size:23
Alignment explanation
Indices: 171975--172021 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
171965 AATTTCGATG
171975 AAATTAAAAATAATGATAATAATA
1 AAATTAAAAATAATGATAA-AATA
*
171999 AAATT-AAAATCAGTGATAAAATA
1 AAATTAAAAAT-AATGATAAAATA
172022 TGTATTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (23 bp):
AAATTAAAAATAATGATAAAATA
Found at i:173287 original size:17 final size:19
Alignment explanation
Indices: 173244--173293 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
173234 TTAGTTTTCA
*
173244 ATAATTTTATAATTTTATAT
1 ATAATTTAAT-ATTTTATAT
173264 ATAATTTAATATTTTA-AT
1 ATAATTTAATATTTTATAT
*
173282 AT-ATTTATTATT
1 ATAATTTAATATT
173294 AAATTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 9 0.32
18 4 0.14
19 6 0.21
20 9 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATAATTTAATATTTTATAT
Found at i:173362 original size:22 final size:20
Alignment explanation
Indices: 173337--173381 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
173327 TACAAGTAAA
*
173337 ATTTTAATATTTTTATTATAT
1 ATTTTAAAATTTTT-TTATAT
173358 -TATTTAAAATTTTTTTATAT
1 AT-TTTAAAATTTTTTTATAT
173378 ATTT
1 ATTT
173382 AATGATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTTAAAATTTTTTTATAT
Found at i:182571 original size:15 final size:15
Alignment explanation
Indices: 182551--182592 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
182541 CGTACCTAAT
182551 AATATTAATTAAAAA
1 AATATTAATTAAAAA
*
182566 AATATTTA-TAAAAA
1 AATATTAATTAAAAA
*
182580 AAAATATAATTAA
1 AATAT-TAATTAA
182593 TATATTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 10 0.45
15 9 0.41
16 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AATATTAATTAAAAA
Found at i:183221 original size:14 final size:14
Alignment explanation
Indices: 183183--183230 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
183173 TATTTAATAA
* *
183183 AAATATTTTTATTT
1 AAATATTATTATAT
183197 AAAT-TTAATTATAT
1 AAATATT-ATTATAT
*
183211 AAATATTATTATAA
1 AAATATTATTATAT
183225 AAATAT
1 AAATAT
183231 ATTTTATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 2 0.07
14 25 0.86
15 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATATTATTATAT
Found at i:184050 original size:20 final size:19
Alignment explanation
Indices: 184012--184050 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
184002 TTAATTTTTA
* *
184012 TTTATTTATAATTATTTAT
1 TTTATTTATAAATAATTAT
184031 TTTATTTAATAAATAATTAT
1 TTTATTT-ATAAATAATTAT
184051 AAATAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATTTATAAATAATTAT
Found at i:184273 original size:16 final size:16
Alignment explanation
Indices: 184247--184287 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
184237 GTTTTGTTGT
184247 TTTAAATTTAATAAT-A
1 TTTAAA-TTAATAATAA
184263 TTTATAATTAATAATAA
1 TTTA-AATTAATAATAA
184280 TTTAAATT
1 TTTAAATT
184288 TGACTTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTAAATTAATAATAA
Found at i:184813 original size:2 final size:2
Alignment explanation
Indices: 184808--184840 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
184798 AAATTAATTA
184808 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 A
184841 ACTTGAATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:186368 original size:3 final size:3
Alignment explanation
Indices: 186362--186388 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
186352 TTTCTCGAGC
186362 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
186389 GTGTTTAAAT
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):
AAT
Found at i:186711 original size:18 final size:19
Alignment explanation
Indices: 186674--186712 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
186664 ATATTACATA
186674 ATTTAAATTTTTGATAAAAT
1 ATTTAAATTTTT-ATAAAAT
186694 ATTTAAATTTTT-TAAAAT
1 ATTTAAATTTTTATAAAAT
186712 A
1 A
186713 ATTCTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
20 12 0.63
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
ATTTAAATTTTTATAAAAT
Found at i:186997 original size:24 final size:24
Alignment explanation
Indices: 186970--187035 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 24
186960 TTTAATATAT
*
186970 ATTATATTTATATTTAAAATTTTG
1 ATTATATTTATATTTAAAATTGTG
*
186994 ATTA-ATTTAATAATTT-ATATTGTG
1 ATTATATTT-AT-ATTTAAAATTGTG
*
187018 TTTATATTTATATATTAA
1 ATTATATTTATAT-TTAA
187036 CATAAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
23 6 0.18
24 19 0.56
25 9 0.26
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (24 bp):
ATTATATTTATATTTAAAATTGTG
Found at i:189860 original size:7 final size:7
Alignment explanation
Indices: 189848--189888 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
189838 TGATAAGAAT
189848 TATATAA
1 TATATAA
189855 TATATAA
1 TATATAA
189862 -ATATAA
1 TATATAA
*
189868 AAT-TAA
1 TATATAA
*
189874 TATATAT
1 TATATAA
189881 TATATAA
1 TATATAA
189888 T
1 T
189889 TAAAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 11 0.38
7 18 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TATATAA
Found at i:190942 original size:14 final size:14
Alignment explanation
Indices: 190923--190951 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
190913 ATAAAAGTTT
190923 TTTTTTCTCTTTTA
1 TTTTTTCTCTTTTA
190937 TTTTTTCTCTTTTA
1 TTTTTTCTCTTTTA
190951 T
1 T
190952 AATATTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTCTCTTTTA
Found at i:191481 original size:9 final size:9
Alignment explanation
Indices: 191465--191494 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
191455 ATTAGTTTTA
191465 ATTT-TAAT
1 ATTTATAAT
191473 ATTTATAAT
1 ATTTATAAT
191482 ATTTATAAT
1 ATTTATAAT
191491 ATTT
1 ATTT
191495 TTATTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
ATTTATAAT
Found at i:191486 original size:22 final size:21
Alignment explanation
Indices: 191422--191486 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
191412 TAAACTTAAT
*
191422 ATTTTATATAATTAT-ATTTTA
1 ATTTTA-ATATTTATAATTTTA
* * *
191443 AATATAATATTTATTAGTTTTA
1 ATTTTAATATTTA-TAATTTTA
191465 ATTTTAATATTTATAATATTTA
1 ATTTTAATATTTATAAT-TTTA
191487 TAATATTTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
20 6 0.18
21 8 0.24
22 20 0.59
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTTTAATATTTATAATTTTA
Found at i:192261 original size:27 final size:28
Alignment explanation
Indices: 192226--192294 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 28
192216 GATATTGAAC
* *
192226 AAAT-AATTTAATTTAT-GAAAATATTT
1 AAATAAATTTAATTTATAAAAAATAATT
* * *
192252 AATTAAATTTTATTTTTAAAAAATAATT
1 AAATAAATTTAATTTATAAAAAATAATT
192280 AAATAAA-TTAATTTA
1 AAATAAATTTAATTTA
192295 ATTAAACCAA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
26 3 0.09
27 16 0.48
28 14 0.42
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (28 bp):
AAATAAATTTAATTTATAAAAAATAATT
Found at i:196979 original size:24 final size:21
Alignment explanation
Indices: 196922--196979 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
196912 TTTTAGTTCT
196922 TATAATTTTAATTTAATTTTTA
1 TATAA-TTTAATTTAATTTTTA
196944 TATAATTT--TTTAATTTAATTGA
1 TATAATTTAATTTAATTT--TT-A
*
196966 TATTATTTAATTTA
1 TATAATTTAATTTA
196980 TAATATCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 8 0.27
21 5 0.17
22 13 0.43
24 4 0.13
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
TATAATTTAATTTAATTTTTA
Found at i:198583 original size:24 final size:25
Alignment explanation
Indices: 198555--198605 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
198545 TAAGTGTATT
198555 TTAAAATAATA-A-TTTTATATTAAA
1 TTAAAATAATATATTTTTAT-TTAAA
198579 TTAAAATAATATATTTTTATTTAAA
1 TTAAAATAATATATTTTTATTTAAA
198604 TT
1 TT
198606 TAATTATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 11 0.44
25 8 0.32
26 6 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TTAAAATAATATATTTTTATTTAAA
Found at i:198643 original size:22 final size:21
Alignment explanation
Indices: 198600--198639 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
198590 TATTTTTATT
198600 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
198621 TAAATATTAATTA-AAAATA
1 TAAAT-TTAATTATAAAATA
198640 ATATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:198680 original size:144 final size:140
Alignment explanation
Indices: 198523--198805 Score: 444
Period size: 144 Copynumber: 2.0 Consensus size: 140
198513 CTCGGGTCTC
* * * *
198523 AATTTTCTTGTTTCAAGTTAA-TTAAGTGTATTTTAAAATAATAATTTTATATT-AAATTAAAAT
1 AATTTTCTTGTTTCAAGTCAACTCAA-TGTACTTTAAAATAATAATTTTAAATTAAAATTAAAAT
*
198586 AATATATTTTTATTTAAATTTAATTATAAAATATATAAATATTAATTAAAAATAATATTTTAATG
65 AATATATTTTTATTT--A--TAATTATAAAATATATAAATATTAATT-AAAATAATATTTTAATA
*
198651 AGATAAATAATAATTT
125 AAATAAATAATAATTT
198667 AATTTTCTTGTTTCAAGTCAACTCAATGTACTTTAAAATAATAATTTTAAATTAAAATTAAAATA
1 AATTTTCTTGTTTCAAGTCAACTCAATGTACTTTAAAATAATAATTTTAAATTAAAATTAAAATA
198732 ATATATTTTTATTTATAATTATAAAATATATAAATATTAATTAAAATAATATTTTAATAAAATAA
66 ATATATTTTTATTTATAATTATAAAATATATAAATATTAATTAAAATAATATTTTAATAAAATAA
198797 ATAATAATT
131 ATAATAATT
198806 CGCACTTACA
Statistics
Matches: 131, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
140 30 0.23
141 27 0.21
143 1 0.01
144 45 0.34
145 28 0.21
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (140 bp):
AATTTTCTTGTTTCAAGTCAACTCAATGTACTTTAAAATAATAATTTTAAATTAAAATTAAAATA
ATATATTTTTATTTATAATTATAAAATATATAAATATTAATTAAAATAATATTTTAATAAAATAA
ATAATAATTT
Found at i:198733 original size:25 final size:24
Alignment explanation
Indices: 198699--198805 Score: 75
Period size: 25 Copynumber: 4.6 Consensus size: 24
198689 TCAATGTACT
198699 TTAAAATAATAATTTTAAATTAAAA
1 TTAAAATAATAATTTTAAA-TAAAA
** *
198724 TTAAAATAATATATTTTTATTTATAA
1 TTAAAATAATA-A-TTTTAAATAAAA
* * *
198750 TTATAA-AAT-A-TATAAATATTAA
1 TTAAAATAATAATTTTAAATA-AAA
198772 TTAAAATAAT-ATTTT-AATAAAA
1 TTAAAATAATAATTTTAAATAAAA
198794 -T-AAATAATAATT
1 TTAAAATAATAATT
198806 CGCACTTACA
Statistics
Matches: 66, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
20 7 0.11
21 9 0.14
22 10 0.15
23 9 0.14
24 2 0.03
25 14 0.21
26 10 0.15
27 5 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TTAAAATAATAATTTTAAATAAAA
Found at i:198933 original size:22 final size:24
Alignment explanation
Indices: 198890--198933 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
198880 CGGGAAGTTA
*
198890 TTTTTTCAAATAAAAAATAAATAG
1 TTTTTTCAAATAAAAAAGAAATAG
198914 TTTTTT-AAAT-AAAAAGAAAT
1 TTTTTTCAAATAAAAAAGAAAT
198934 TTTTTATAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (24 bp):
TTTTTTCAAATAAAAAAGAAATAG
Found at i:199920 original size:6 final size:7
Alignment explanation
Indices: 199894--199922 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
199884 ATATTTGAAA
199894 AAAATTT
1 AAAATTT
199901 AAAATTT
1 AAAATTT
199908 AAAATTT
1 AAAATTT
199915 -AAATTT
1 AAAATTT
199921 AA
1 AA
199923 GTTCAATTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAAATTT
Found at i:201049 original size:32 final size:33
Alignment explanation
Indices: 200987--201056 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
200977 ATAATTTTGA
200987 ATATAATACAAATGTATTAATGTATCAAAATTT
1 ATATAATACAAATGTATTAATGTATCAAAATTT
*
201020 ATATAATATAAAT-TATTAACATGT-T-AAAATTT
1 ATATAATACAAATGTATT-A-ATGTATCAAAATTT
201052 ATATA
1 ATATA
201057 TATCTAATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
32 16 0.47
33 14 0.41
34 4 0.12
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (33 bp):
ATATAATACAAATGTATTAATGTATCAAAATTT
Found at i:201793 original size:20 final size:18
Alignment explanation
Indices: 201766--201804 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
201756 TGAAATCTAT
201766 ATTTA-TATATAAAATTA
1 ATTTATTATATAAAATTA
201783 ATTTATTATATAAAATTA
1 ATTTATTATATAAAATTA
201801 ATTT
1 ATTT
201805 TTCAAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTATTATATAAAATTA
Found at i:201813 original size:18 final size:18
Alignment explanation
Indices: 201774--201813 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
201764 ATATTTATAT
*
201774 ATAAAATTAATTTATTAT
1 ATAAAATTAATTTATTAA
201792 ATAAAATTAATTT-TTCAA
1 ATAAAATTAATTTATT-AA
201810 ATAA
1 ATAA
201814 TTTGTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAAAATTAATTTATTAA
Found at i:202003 original size:24 final size:24
Alignment explanation
Indices: 201959--202005 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
201949 TTAATATTTA
*
201959 AAAATTTTAAAATATATATTTAAT
1 AAAATTTTAAAATATACATTTAAT
*
201983 AAAATATTTAAAA-ATCCATTTAA
1 AAAAT-TTTAAAATATACATTTAA
202006 CCTTAACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (24 bp):
AAAATTTTAAAATATACATTTAAT
Found at i:202495 original size:20 final size:19
Alignment explanation
Indices: 202441--202498 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 19
202431 CTGTCATTAA
* *
202441 ATCCGTCACAATTTATGAC
1 ATCCGTCACAACTTGTGAC
202460 ATCCTGTCACAACTTGTGAC
1 ATCC-GTCACAACTTGTGAC
202480 ATTCCGTCACAACTTGTGA
1 A-TCCGTCACAACTTGTGA
202499 AGTTTCATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 4 0.11
20 28 0.80
21 3 0.09
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (19 bp):
ATCCGTCACAACTTGTGAC
Found at i:202509 original size:20 final size:20
Alignment explanation
Indices: 202466--202523 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
202456 TGACATCCTG
*
202466 TCACAACTTGTGACATTCCG
1 TCACAACTTGTGACATTCCA
*
202486 TCACAACTTGTGA-AGTTTCA
1 TCACAACTTGTGACA-TTCCA
* *
202506 TCACAATTTGTGATATTC
1 TCACAACTTGTGACATTC
202524 TGTCATAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (20 bp):
TCACAACTTGTGACATTCCA
Found at i:210562 original size:7 final size:7
Alignment explanation
Indices: 210550--210575 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
210540 GATTTTAATT
210550 AATTTAA
1 AATTTAA
210557 AATTTAA
1 AATTTAA
210564 AATTTAA
1 AATTTAA
210571 AATTT
1 AATTT
210576 CCTTTTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
AATTTAA
Found at i:212952 original size:23 final size:24
Alignment explanation
Indices: 212921--212966 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
212911 CACTCATGAT
*
212921 CATCACAGCTAATA-TGATCAAAC
1 CATCACAGCAAATATTGATCAAAC
*
212944 CATCGCAGCAAATATTGATCAAA
1 CATCACAGCAAATATTGATCAAA
212967 TAGATCTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.22
Consensus pattern (24 bp):
CATCACAGCAAATATTGATCAAAC
Found at i:214509 original size:2 final size:2
Alignment explanation
Indices: 214502--214527 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
214492 ACATACATGC
214502 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
214528 TAAACAATAG
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:215598 original size:18 final size:19
Alignment explanation
Indices: 215558--215600 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
215548 TAGATTGAGA
* *
215558 TTATTTTTAAAATTTTATT
1 TTATTATTAAAATTATATT
215577 TTATTATTAAAATTAT-TT
1 TTATTATTAAAATTATATT
215595 TTATTA
1 TTATTA
215601 ATATTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTATTAAAATTATATT
Found at i:216706 original size:16 final size:17
Alignment explanation
Indices: 216671--216703 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
216661 AATTAAATTA
*
216671 AATTTTTTATTTTTATT
1 AATTTTTAATTTTTATT
216688 AATTTTTAATTTTTAT
1 AATTTTTAATTTTTAT
216704 AATATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
AATTTTTAATTTTTATT
Found at i:216821 original size:22 final size:23
Alignment explanation
Indices: 216793--216838 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
216783 TTTGGTTCAA
216793 TTTGATTCAATTTT-ATATAATT
1 TTTGATTCAATTTTGATATAATT
* *
216815 TTTGATTTAATTTTGATTTAATT
1 TTTGATTCAATTTTGATATAATT
216838 T
1 T
216839 CTAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (23 bp):
TTTGATTCAATTTTGATATAATT
Found at i:216828 original size:11 final size:11
Alignment explanation
Indices: 216793--216838 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
216783 TTTGGTTCAA
*
216793 TTTGATTCAAT
1 TTTGATTTAAT
*
216804 TTT-ATATAATT
1 TTTGATTTAA-T
216815 TTTGATTTAAT
1 TTTGATTTAAT
216826 TTTGATTTAAT
1 TTTGATTTAAT
216837 TT
1 TT
216839 CTAAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 4 0.13
11 21 0.70
12 5 0.17
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (11 bp):
TTTGATTTAAT
Found at i:216983 original size:21 final size:19
Alignment explanation
Indices: 216968--217029 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 19
216958 TTTTATCATA
*
216968 ATATATTAAAAATTTATAT
1 ATATATAAAAAATTTATAT
*
216987 ATTTATAAAAAA-TT-TA-
1 ATATATAAAAAATTTATAT
*
217003 ATATATAAATAATTTAT-T
1 ATATATAAAAAATTTATAT
*
217021 TTATATAAA
1 ATATATAAA
217030 TTTTAATTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
16 10 0.29
17 4 0.11
18 11 0.31
19 10 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATATAAAAAATTTATAT
Found at i:217011 original size:16 final size:16
Alignment explanation
Indices: 216966--217018 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
216956 TTTTTTATCA
*
216966 TAATATATTAAAAATT
1 TAATATATAAAAAATT
216982 TATATATTTATAAAAAATT
1 TA-ATA--TATAAAAAATT
*
217001 TAATATATAAATAATT
1 TAATATATAAAAAATT
217017 TA
1 TA
217019 TTTTATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 14 0.44
17 3 0.09
18 3 0.09
19 12 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATATATAAAAAATT
Found at i:217014 original size:20 final size:19
Alignment explanation
Indices: 216975--217014 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
216965 ATAATATATT
**
216975 AAAAATTTATATATTTATA
1 AAAAATTTATATATAAATA
216994 AAAAATTTAATATATAAATA
1 AAAAATTT-ATATATAAATA
217014 A
1 A
217015 TTTATTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATTTATATATAAATA
Found at i:217025 original size:16 final size:16
Alignment explanation
Indices: 216987--217038 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
216977 AAATTTATAT
216987 ATTTATAAAAAATTTA
1 ATTTATAAAAAATTTA
* *
217003 ATATATAAATAATTTA
1 ATTTATAAAAAATTTA
* * *
217019 TTTTATATAAATTTTA
1 ATTTATAAAAAATTTA
217035 ATTT
1 ATTT
217039 GCATTGTGTA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTATAAAAAATTTA
Found at i:221099 original size:2 final size:2
Alignment explanation
Indices: 221092--221124 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
221082 ATTTAAAACA
221092 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 A
221125 CCGTCACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:222846 original size:18 final size:19
Alignment explanation
Indices: 222819--222854 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
222809 TGAATTATTT
*
222819 TATTTTATTTTTA-ATTAA
1 TATTTAATTTTTACATTAA
222837 TATTTAATTTTTACATTA
1 TATTTAATTTTTACATTA
222855 TAAAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTTAATTTTTACATTAA
Found at i:223154 original size:18 final size:19
Alignment explanation
Indices: 223115--223154 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
223105 TTAATATTTC
* *
223115 TAAAATTTATATATTTATA
1 TAAAATTTATATATATAAA
223134 TAAAATTTA-ATATATAAA
1 TAAAATTTATATATATAAA
223152 TAA
1 TAA
223155 TGTATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAAATTTATATATATAAA
Found at i:223678 original size:18 final size:18
Alignment explanation
Indices: 223642--223685 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
223632 TTTAAAAAGT
*
223642 TAAATAAAGTTATAAAAA
1 TAAATAAAGTGATAAAAA
223660 TAAATAAAG-GATAATAAA
1 TAAATAAAGTGATAA-AAA
*
223678 TAATTAAA
1 TAAATAAA
223686 TATTACTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (18 bp):
TAAATAAAGTGATAAAAA
Found at i:223876 original size:28 final size:26
Alignment explanation
Indices: 223831--223885 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
223821 TATCTAATTA
* * *
223831 TTAATTTTAATTTTAATATTTTATAT
1 TTAATTTTAATTATAATAATTAATAT
223857 TTAATTTTACTATTATAATAATTAATAT
1 TTAATTTTA--ATTATAATAATTAATAT
223885 T
1 T
223886 ACTATTACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 9 0.38
28 15 0.62
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
TTAATTTTAATTATAATAATTAATAT
Found at i:225371 original size:17 final size:17
Alignment explanation
Indices: 225351--225390 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
225341 ATTTAAATGA
225351 ATATTAAATATAAATAT
1 ATATTAAATATAAATAT
**
225368 ATATTTGATATAAATAT
1 ATATTAAATATAAATAT
225385 AT-TTAA
1 ATATTAA
225391 TATTTTAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
ATATTAAATATAAATAT
Found at i:225407 original size:18 final size:18
Alignment explanation
Indices: 225385--225422 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
225375 ATATAAATAT
*
225385 ATTTAATAT-TTTAAAAA
1 ATTTTATATATTTAAAAA
225402 ATTTTATATATTTAAAAA
1 ATTTTATATATTTAAAAA
225420 ATT
1 ATT
225423 ATATTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTTATATATTTAAAAA
Found at i:225438 original size:40 final size:41
Alignment explanation
Indices: 225365--225441 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
225355 TAAATATAAA
* * *
225365 TATATATTTGATATAAATATATTTAATATTTTAAAAAATTT
1 TATATATTTGATAAAAATATATTAAATACTTTAAAAAATTT
225406 TATATATTT-A-AAAAATTATATTAAATACTTTAAAAA
1 TATATATTTGATAAAAA-TATATTAAATACTTTAAAAA
225442 TAAAAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 4 0.12
40 19 0.59
41 9 0.28
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (41 bp):
TATATATTTGATAAAAATATATTAAATACTTTAAAAAATTT
Found at i:225673 original size:16 final size:16
Alignment explanation
Indices: 225654--225720 Score: 61
Period size: 18 Copynumber: 4.2 Consensus size: 16
225644 ATAACATATT
225654 TAAAATTTATATAATA
1 TAAAATTTATATAATA
225670 T-AAA-TTAT-TATATA
1 TAAAATTTATATA-ATA
225684 TAAATATTTATATAAATA
1 TAAA-ATTTATAT-AATA
*
225702 TAAAATATTTTA-AATA
1 TAAAAT-TTATATAATA
225718 TAA
1 TAA
225721 TTAAAATATA
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
13 2 0.05
14 8 0.19
15 5 0.12
16 9 0.21
17 6 0.14
18 12 0.28
19 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAATTTATATAATA
Found at i:225678 original size:25 final size:26
Alignment explanation
Indices: 225630--225731 Score: 73
Period size: 27 Copynumber: 3.7 Consensus size: 26
225620 TTAATGCAAT
225630 AAATTTATTAAAATATAACATATTTA
1 AAATTTATTAAAATATAACATATTTA
* *
225656 AAATTTA-TATAATATAAATTATTATATATA
1 AAATTTATTAAAATAT-AA-CA-TAT-T-TA
* *
225686 AATATTTA-TATAAATATAAAATATTTT
1 AA-ATTTATTA-AAATATAACATATTTA
*
225713 AAATATAATTAAAATATAA
1 AAAT-TTATTAAAATATAA
225732 TAAAATATAT
Statistics
Matches: 61, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
25 7 0.11
26 11 0.18
27 14 0.23
28 6 0.10
29 4 0.07
30 5 0.08
31 9 0.15
32 5 0.08
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (26 bp):
AAATTTATTAAAATATAACATATTTA
Found at i:225695 original size:12 final size:13
Alignment explanation
Indices: 225667--225702 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
225657 AATTTATATA
225667 ATATAAATTATTAT
1 ATATAAA-TATTAT
225681 ATATAAATATT-T
1 ATATAAATATTAT
225693 ATATAAATAT
1 ATATAAATAT
225703 AAAATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.50
13 4 0.18
14 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATAAATATTAT
Found at i:225702 original size:20 final size:19
Alignment explanation
Indices: 225679--225747 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
225669 ATAAATTATT
225679 ATATATAAATATTTATATAA
1 ATATA-AAATATTTATATAA
*
225699 ATATAAAATATTTTAAATATA
1 ATATAAAATA-TTTATATA-A
*
225720 AT-TAAAATA-TAATA-AA
1 ATATAAAATATTTATATAA
225736 ATATATAAATAT
1 ATATA-AAATAT
225748 GGTAAGAGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
16 3 0.07
17 3 0.07
18 8 0.20
19 5 0.12
20 19 0.46
21 3 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATAAAATATTTATATAA
Found at i:227313 original size:14 final size:15
Alignment explanation
Indices: 227288--227316 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
227278 AAATTATTAA
227288 AAATTATTTTTATAT
1 AAATTATTTTTATAT
227303 AAATT-TTTTTATAT
1 AAATTATTTTTATAT
227317 TTTTATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AAATTATTTTTATAT
Found at i:228217 original size:20 final size:19
Alignment explanation
Indices: 228173--228222 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
228163 TTTATTAAAT
228173 AAAT-AATAAATCAAATCA
1 AAATAAATAAATCAAATCA
* *
228191 AAATAAATTAAATCAATTTA
1 AAATAAA-TAAATCAAATCA
*
228211 AATTAAATAAAT
1 AAATAAATAAAT
228223 TTACTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.15
19 7 0.26
20 16 0.59
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATAAATAAATCAAATCA
Found at i:228232 original size:15 final size:15
Alignment explanation
Indices: 228145--228225 Score: 67
Period size: 15 Copynumber: 5.4 Consensus size: 15
228135 TTTTATTATT
**
228145 AATTTAAACAAAATA
1 AATTTAAATTAAATA
*
228160 AATTT-TATTAAATA
1 AATTTAAATTAAATA
* *
228174 AATAATAAATCAAATCA
1 AAT-TTAAATTAAAT-A
* *
228191 AA-ATAAATTAAATC
1 AATTTAAATTAAATA
228205 AATTTAAATTAAATA
1 AATTTAAATTAAATA
228220 AATTTA
1 AATTTA
228226 CTTTAAACTT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
14 11 0.21
15 32 0.62
16 6 0.12
17 3 0.06
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (15 bp):
AATTTAAATTAAATA
Found at i:228713 original size:10 final size:10
Alignment explanation
Indices: 228679--228771 Score: 50
Period size: 10 Copynumber: 9.3 Consensus size: 10
228669 TTGATAATAA
* *
228679 AAATTTTTAA
1 AAATTTATAT
228689 AAATTTA-AT
1 AAATTTATAT
*
228698 -ATTTTATAT
1 AAATTTATAT
*
228707 AAATTTAAAT
1 AAATTTATAT
228717 AAATTTATAT
1 AAATTTATAT
*
228727 TAATCTT-TAT
1 AAAT-TTATAT
*
228737 AATATTTTTAT
1 AA-ATTTATAT
*
228748 ATAA-TTAAATT
1 A-AATTTATA-T
*
228759 AAATTTAAAT
1 AAATTTATAT
228769 AAA
1 AAA
228772 ATTTTTATTA
Statistics
Matches: 65, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
8 5 0.08
9 3 0.05
10 40 0.62
11 16 0.25
12 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (10 bp):
AAATTTATAT
Found at i:229522 original size:4 final size:4
Alignment explanation
Indices: 229505--229536 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
229495 ATGACTTTAA
*
229505 TATT TATA TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT
229537 CTCTGCAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TATT
Found at i:229818 original size:5 final size:5
Alignment explanation
Indices: 229810--229937 Score: 61
Period size: 5 Copynumber: 25.4 Consensus size: 5
229800 AAATTACATA
* * **
229810 AATAT AATAT AA-AT AAAAT AATTAA AATAT AATAT AATAT -ATAT TTTA-
1 AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT AATAT AATAT AATAT
* * * *
229858 AATTTT AA-AT AAATAT AAAAT ATTAT AAATAT AATTAT AATAT AATAA
1 AA-TAT AATAT -AATAT AATAT AATAT -AATAT AA-TAT AATAT AATAT
* *
229906 AAAAT ATATATT AATAT AATTT AA-AT -ATAT AA
1 AATAT A-ATA-T AATAT AATAT AATAT AATAT AA
229938 ATTACGAATA
Statistics
Matches: 92, Mismatches: 18, Indels: 26
0.68 0.13 0.19
Matches are distributed among these distances:
3 1 0.01
4 12 0.13
5 56 0.61
6 21 0.23
7 2 0.02
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:229823 original size:11 final size:11
Alignment explanation
Indices: 229807--229934 Score: 83
Period size: 11 Copynumber: 11.8 Consensus size: 11
229797 ATAAAATTAC
229807 ATAAATATAAT
1 ATAAATATAAT
*
229818 ATAAATAAAAT
1 ATAAATATAAT
229829 AATTAAAATATAAT
1 -A-T-AAATATAAT
*
229843 ATAATATATATT
1 ATAA-ATATAAT
*
229855 TTAAAT-T--T
1 ATAAATATAAT
229863 -TAAATA-AAT
1 ATAAATATAAT
*
229872 ATAAA-ATATT
1 ATAAATATAAT
229882 ATAAATATAAT
1 ATAAATATAAT
229893 -TATAATATAAT
1 ATA-AATATAAT
*
229904 A-AAAAATATAT
1 ATAAATATA-AT
*
229915 ATTAATATAAT
1 ATAAATATAAT
*
229926 TTAAATATA
1 ATAAATATA
229935 TAAATTACGA
Statistics
Matches: 92, Mismatches: 11, Indels: 28
0.70 0.08 0.21
Matches are distributed among these distances:
7 5 0.05
8 1 0.01
9 2 0.02
10 19 0.21
11 39 0.42
12 16 0.17
13 2 0.02
14 8 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATAAATATAAT
Found at i:229900 original size:61 final size:59
Alignment explanation
Indices: 229807--229919 Score: 154
Period size: 61 Copynumber: 1.9 Consensus size: 59
229797 ATAAAATTAC
* * * *
229807 ATAAATATAATATAAATAAAATAATTAAAATATAATATAATATATATTTTAAATTTTAA
1 ATAAATATAAAATAAATAAAATAATTAAAATATAATAAAAAATATATATTAAATTTTAA
* *
229866 ATAAATATAAAATATTATAAATATAATTATAATATAATAAAAAATATATATTAA
1 ATAAATATAAAATA-AATAAA-ATAATTAAAATATAATAAAAAATATATATTAA
229920 TATAATTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 13 0.28
60 5 0.11
61 28 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (59 bp):
ATAAATATAAAATAAATAAAATAATTAAAATATAATAAAAAATATATATTAAATTTTAA
Found at i:229924 original size:39 final size:39
Alignment explanation
Indices: 229807--229924 Score: 98
Period size: 39 Copynumber: 2.9 Consensus size: 39
229797 ATAAAATTAC
*
229807 ATAAATATAATATAAATAAAATAAT-TAAAATATAATAT-AAT
1 ATAATTATAATAT-AATAAAA-AATAT-AAAT-TAATATAAAT
* ** * *
229848 ATATATTTTAA-ATTTTAAATAAATATAAAATATTATAAAT
1 ATA-ATTATAATATAATAAA-AAATATAAATTAATATAAAT
*
229888 ATAATTATAATATAATAAAAAATATATATTAATATAA
1 ATAATTATAATATAATAAAAAATATAAATTAATATAA
229925 TTTAAATATA
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
39 26 0.43
40 22 0.37
41 7 0.12
42 5 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (39 bp):
ATAATTATAATATAATAAAAAATATAAATTAATATAAAT
Found at i:230473 original size:31 final size:29
Alignment explanation
Indices: 230437--230510 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 29
230427 AATTTGATCA
230437 AATATATTTTTATTAAGTATTTATTATATTT
1 AATATATTTTTATTAA-TATTTATTAT-TTT
***
230468 AATATAAAATTATT--TATTTATTATTTT
1 AATATATTTTTATTAATATTTATTATTTT
* *
230495 AATTTATTTTAATTAA
1 AATATATTTTTATTAA
230511 ATTAATTGGT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
27 12 0.36
28 10 0.30
31 11 0.33
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (29 bp):
AATATATTTTTATTAATATTTATTATTTT
Found at i:231680 original size:54 final size:54
Alignment explanation
Indices: 231613--231724 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
231603 TTGTTTATTA
*
231613 AATTTTACATAATAAACATACATATTTTATGTAATAAACA-ATAAAATAACTAAT
1 AATTTTACATAATAAACATAAATATTTTATGTAATAAACATA-AAAATAACTAAT
** * *
231667 AATTTTAGGTAATAAACATAAATATTTTATTTAATAAACATAAAAATAGCTAAT
1 AATTTTACATAATAAACATAAATATTTTATGTAATAAACATAAAAATAACTAAT
231721 AATT
1 AATT
231725 AGCTTGTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 51 0.98
55 1 0.02
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.37
Consensus pattern (54 bp):
AATTTTACATAATAAACATAAATATTTTATGTAATAAACATAAAAATAACTAAT
Found at i:231695 original size:22 final size:22
Alignment explanation
Indices: 231668--231710 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
231658 ATAACTAATA
231668 ATTTTAGGTAATAAACATAAAT
1 ATTTTAGGTAATAAACATAAAT
**
231690 ATTTTATTTAATAAACATAAA
1 ATTTTAGGTAATAAACATAAA
231711 AATAGCTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.40
Consensus pattern (22 bp):
ATTTTAGGTAATAAACATAAAT
Found at i:231982 original size:18 final size:18
Alignment explanation
Indices: 231959--232019 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
231949 CTATTATAAT
231959 TATATTTAAAATATTATA
1 TATATTTAAAATATTATA
*
231977 TATATTTATAAAT-TTTTA
1 TATATTTA-AAATATTATA
*
231995 -ATTTTTAAAATATTA-A
1 TATATTTAAAATATTATA
232011 TA-ATTTAAA
1 TATATTTAAA
232020 TTATATAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
16 11 0.31
17 9 0.25
18 12 0.33
19 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TATATTTAAAATATTATA
Found at i:232010 original size:15 final size:16
Alignment explanation
Indices: 231963--232039 Score: 59
Period size: 16 Copynumber: 4.6 Consensus size: 16
231953 TATAATTATA
231963 TTTAAAATATTATATAT
1 TTTAAAATATTA-ATAT
*
231980 ATTTATAAATTTTTAAT-T
1 -TTTA-AAA-TATTAATAT
*
231998 TTTAAAATATTAATAA
1 TTTAAAATATTAATAT
*
232014 TTTAAATTATATAA-AT
1 TTTAAAATAT-TAATAT
*
232030 TTTAATATAT
1 TTTAAAATAT
232040 ATTTAAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
15 6 0.12
16 21 0.44
17 7 0.15
18 5 0.10
19 5 0.10
20 4 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAAAATATTAATAT
Found at i:232033 original size:16 final size:16
Alignment explanation
Indices: 231971--232050 Score: 56
Period size: 16 Copynumber: 4.9 Consensus size: 16
231961 TATTTAAAAT
*
231971 ATTATATATATTTATAA
1 ATTATATAAATTT-TAA
* *
231988 ATT-TTTAATTTTTAA
1 ATTATATAAATTTTAA
* *
232003 AATAT-TAATAATTTAA
1 ATTATATAA-ATTTTAA
232019 ATTATATAAATTTTAA
1 ATTATATAAATTTTAA
*
232035 TATATATTTAAATTTT
1 -AT-TATATAAATTTT
232051 GTATTCATAT
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
15 8 0.16
16 22 0.45
17 8 0.16
18 11 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTATATAAATTTTAA
Found at i:232083 original size:17 final size:17
Alignment explanation
Indices: 231992--232095 Score: 81
Period size: 17 Copynumber: 6.1 Consensus size: 17
231982 TTATAAATTT
*
231992 TTAATTTTTA-A-AATA
1 TTAATTTTTATATTATA
* *
232007 TTAATAATTTAAATTATA
1 TTAAT-TTTTATATTATA
* *
232025 TAAATTTTAATA-TATA
1 TTAATTTTTATATTATA
* *
232041 TTTAAATTTTGTATTCATA
1 -TTAATTTTTATATT-ATA
232060 TTAATTTTTATATT-TA
1 TTAATTTTTATATTATA
232076 TTATATTTTTATATTATA
1 TTA-ATTTTTATATTATA
232094 TT
1 TT
232096 TAAAGTTATG
Statistics
Matches: 69, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
15 5 0.07
16 13 0.19
17 24 0.35
18 24 0.35
19 3 0.04
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (17 bp):
TTAATTTTTATATTATA
Found at i:232390 original size:23 final size:22
Alignment explanation
Indices: 232363--232409 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
232353 TTTAAAAAAT
232363 AAATAAATAAATAATTTTTTATA
1 AAATAAATAAATAATTTTTT-TA
* * *
232386 AAATATATGAGTAATTTTTTTA
1 AAATAAATAAATAATTTTTTTA
232408 AA
1 AA
232410 GGTTGTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (22 bp):
AAATAAATAAATAATTTTTTTA
Found at i:232480 original size:13 final size:14
Alignment explanation
Indices: 232457--232487 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
232447 TCATTTTTTA
232457 TTTATTATTAATAT
1 TTTATTATTAATAT
232471 TTTATT-TTAATAT
1 TTTATTATTAATAT
232484 TTTA
1 TTTA
232488 ATAATTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTATTATTAATAT
Found at i:232947 original size:4 final size:4
Alignment explanation
Indices: 232938--232968 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
232928 TTACAAGTTT
232938 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
232969 TATATAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:233175 original size:21 final size:19
Alignment explanation
Indices: 233135--233220 Score: 67
Period size: 19 Copynumber: 4.7 Consensus size: 19
233125 AAATATTTGA
233135 TATATTTTAAATAATAAAT
1 TATATTTTAAATAATAAAT
233154 TATATTTT---TAATCAAAT
1 TATATTTTAAATAAT-AAAT
* **
233171 TA-ATTAATAAAT--TTTAT
1 TATATT-TTAAATAATAAAT
*
233188 TATTTTTTAAATAATAAAT
1 TATATTTTAAATAATAAAT
*
233207 TATATTTAAAATAA
1 TATATTTTAAATAA
233221 CATAATTTTC
Statistics
Matches: 50, Mismatches: 9, Indels: 16
0.67 0.12 0.21
Matches are distributed among these distances:
16 7 0.14
17 16 0.32
18 3 0.06
19 23 0.46
20 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (19 bp):
TATATTTTAAATAATAAAT
Found at i:233199 original size:29 final size:28
Alignment explanation
Indices: 233086--233199 Score: 79
Period size: 29 Copynumber: 4.0 Consensus size: 28
233076 AGACTATTAT
*
233086 TTAATTAATAAATTTTATTTTATTTAAA
1 TTAATTAATAAATTTTATTTTTTTTAAA
** ** * **
233114 TTTAATT-ATAAA-AATATTTGATATATT
1 -TTAATTAATAAATTTTATTTTTTTTAAA
* * * *
233141 TTAAATAATAAATTATATTTTTAATCAAA
1 TTAATTAATAAATTTTATTTTT-TTTAAA
233170 TTAATTAATAAATTTTATTATTTTTTAAA
1 TTAATTAATAAATTTTATT-TTTTTTAAA
233199 T
1 T
233200 AATAAATTAT
Statistics
Matches: 62, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
26 5 0.08
27 14 0.23
28 11 0.18
29 29 0.47
30 3 0.05
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.54
Consensus pattern (28 bp):
TTAATTAATAAATTTTATTTTTTTTAAA
Found at i:233211 original size:53 final size:56
Alignment explanation
Indices: 233080--233213 Score: 161
Period size: 53 Copynumber: 2.5 Consensus size: 56
233070 TATTTTAGAC
* * * * *
233080 TATTATTTAATTAATAAATTTTA-TTTTATTTAAATTTAATTATAAAAATATTTGA
1 TATTTTTTAAATAATAAATTATATTTTTAATCAAATTTAATTATAAAAATATTTGA
* *
233135 TATATTTTAAATAATAAATTATATTTTTAATCAAA-TTAATTA-ATAAAT-TTT-A
1 TATTTTTTAAATAATAAATTATATTTTTAATCAAATTTAATTATAAAAATATTTGA
233187 TTATTTTTTAAATAATAAATTATATTT
1 -TATTTTTTAAATAATAAATTATATTT
233214 AAAATAACAT
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
52 1 0.01
53 28 0.41
54 5 0.07
55 26 0.38
56 9 0.13
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.54
Consensus pattern (56 bp):
TATTTTTTAAATAATAAATTATATTTTTAATCAAATTTAATTATAAAAATATTTGA
Found at i:234295 original size:14 final size:13
Alignment explanation
Indices: 234278--234316 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
234268 TTAAAATAGT
234278 TATATATTATACAA
1 TATATATTATA-AA
*
234292 TATATAATATAAA
1 TATATATTATAAA
234305 TGATATATTATA
1 T-ATATATTATA
234317 TTATAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 3 0.14
14 19 0.86
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (13 bp):
TATATATTATAAA
Found at i:235283 original size:36 final size:36
Alignment explanation
Indices: 235243--235329 Score: 115
Period size: 36 Copynumber: 2.4 Consensus size: 36
235233 CTCCACCACC
*
235243 TTATAAGTACATA-TCTCC-CCCTCCTCCTCCCCCGGT
1 TTATAAGTACA-AGTCTCCTCCC-CCTCCACCCCCGGT
*
235279 TTATAAGTACAAGTCTCCTCCCCCTCCACCTCCGGT
1 TTATAAGTACAAGTCTCCTCCCCCTCCACCCCCGGT
*
235315 TTACAAGTACAAGTC
1 TTATAAGTACAAGTC
235330 CCCACCACCA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
35 1 0.02
36 42 0.91
37 3 0.07
ACGTcount: A:0.22, C:0.39, G:0.10, T:0.29
Consensus pattern (36 bp):
TTATAAGTACAAGTCTCCTCCCCCTCCACCCCCGGT
Found at i:235344 original size:36 final size:36
Alignment explanation
Indices: 235274--235344 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
235264 TCCTCCTCCC
* * * * *
235274 CCGGTTTATAAGTACAAGTCTCCTCCCCCTCCACCT
1 CCGGTTTACAAGTACAAGTCCCCACCACCACCACCT
235310 CCGGTTTACAAGTACAAGTCCCCACCACCACCACC
1 CCGGTTTACAAGTACAAGTCCCCACCACCACCACC
235345 ACCATCACCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.24, C:0.44, G:0.11, T:0.21
Consensus pattern (36 bp):
CCGGTTTACAAGTACAAGTCCCCACCACCACCACCT
Found at i:235403 original size:57 final size:57
Alignment explanation
Indices: 235298--235455 Score: 250
Period size: 57 Copynumber: 2.8 Consensus size: 57
235288 CAAGTCTCCT
* *
235298 CCCCCTCCACCTCCGGTTTACAAGTACAAG--TCC-CCACCACCACCACCACCATCA
1 CCCCCACCACCTCCTGTTTACAAGTACAAGTCTCCACCACCACCACCACCACCATCA
* *
235352 CCTCCACCACCTCCTGTTTACAAGTACAAGTCTCCACCTCCACCACCACCACCATCA
1 CCCCCACCACCTCCTGTTTACAAGTACAAGTCTCCACCACCACCACCACCACCATCA
*
235409 CCCCCACCACCTCCTGTTTACAAGTACAAGTCTCCACCCCCACCACC
1 CCCCCACCACCTCCTGTTTACAAGTACAAGTCTCCACCACCACCACC
235456 TCCTGTTTAC
Statistics
Matches: 95, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
54 27 0.28
56 3 0.03
57 65 0.68
ACGTcount: A:0.25, C:0.51, G:0.06, T:0.17
Consensus pattern (57 bp):
CCCCCACCACCTCCTGTTTACAAGTACAAGTCTCCACCACCACCACCACCACCATCA
Found at i:235486 original size:42 final size:36
Alignment explanation
Indices: 235407--235491 Score: 161
Period size: 36 Copynumber: 2.4 Consensus size: 36
235397 CCACCACCAT
235407 CACCCCCACCACCTCCTGTTTACAAGTACAAGTCTC
1 CACCCCCACCACCTCCTGTTTACAAGTACAAGTCTC
235443 CACCCCCACCACCTCCTGTTTACAAGTACAAGTCTC
1 CACCCCCACCACCTCCTGTTTACAAGTACAAGTCTC
*
235479 CACCTCCACCACC
1 CACCCCCACCACC
235492 ACCATCACCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.25, C:0.48, G:0.07, T:0.20
Consensus pattern (36 bp):
CACCCCCACCACCTCCTGTTTACAAGTACAAGTCTC
Found at i:235534 original size:60 final size:60
Alignment explanation
Indices: 235463--236265 Score: 859
Period size: 54 Copynumber: 13.5 Consensus size: 60
235453 ACCTCCTGTT
*
235463 TACAAGTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCC
1 TACAATTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCC
* *
235523 TACAAATACAAGTCTCCACCACCACCACCACCATCACCACCTAAG------CCACACCCC
1 TACAATTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCC
* *
235577 TATATTTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAG------CCACACCCC
1 TACAATTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCC
* *
235631 TATATTTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCC
1 TACAATTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCC
*
235691 TACAAGTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAG------CCACACCCC
1 TACAATTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCC
*
235745 TACATTTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAG------CCACACCCC
1 TACAATTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCC
*
235799 TACATTTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCACACCC
1 TACAATTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAG------------CCACACCC
235864 ACACCCC
54 ACACCCC
* *
235871 TACAAGTACAAGTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCCACACCCC
1 TACAATTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCC
* *
235931 TACAAGTACAAGTCTCCACCTCCGCCACCACCATCACCACCTAAG------CCACACCCC
1 TACAATTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCC
* *
235985 TACATTTACAAGTCTCCACCTCCGCCACCACCATCACCACCTAAG------CCACACCCC
1 TACAATTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCC
* *
236039 TACATTTACAAGTCTCCACCTCCGCCACCACCATCACCACCTAAGCCACACCCACACCCACACCC
1 TACAATTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAG------------CCACACCC
236104 ACACCCC
54 ACACCCC
* * *
236111 TACAAATACAAGTCTCCACCGCCGCCACCACCATCACCACCTAAGCCACACCCACACCCC
1 TACAATTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCC
* *
236171 TACAAATACAAGTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCCACATCCACACCC
1 TACAATTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAG-C-CA--CAC--CCACACCC
236236 C
60 C
* *
236237 TACAAATACAAGTCTCCACCGCCACCACC
1 TACAATTACAAGTCTCCACCTCCACCACC
236266 TCCAGTTTAC
Statistics
Matches: 671, Mismatches: 24, Indels: 90
0.85 0.03 0.11
Matches are distributed among these distances:
54 316 0.47
60 210 0.31
61 1 0.00
62 2 0.00
64 3 0.00
66 37 0.06
72 102 0.15
ACGTcount: A:0.31, C:0.51, G:0.05, T:0.13
Consensus pattern (60 bp):
TACAATTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCC
Found at i:235545 original size:93 final size:89
Alignment explanation
Indices: 235355--235548 Score: 232
Period size: 93 Copynumber: 2.1 Consensus size: 89
235345 ACCATCACCT
*
235355 CCACCACCTCCTGTTTACAAGTACAAGTCTCCACCTCCACCACCACCACCATCACCCCCACCACC
1 CCACCACCTCCTGTTTACAAGTACAAGTCTCCACCTCCACCACCACCACCACCACCCCCACCACC
* *
235420 TCCTGTTTACAAGTACAAGTCTCCACCC
66 TCC--TCTACAAATACAAGTCTCCA--C
*
235448 CCACCACCTCCTGTTTACAAGTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACA
1 CCACCACCTCCTGTTTACAAGTACAAGTCTCCACCTCCACCACCACCACCACCACC----CC-CA
235513 CCCACAC-CC-CTACAAATACAAGTCTCCA-
61 -CCAC-CTCCTCTACAAATACAAGTCTCCAC
235541 CCACCACC
1 CCACCACC
235549 ACCACCATCA
Statistics
Matches: 90, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
93 62 0.69
96 17 0.19
97 2 0.02
98 2 0.02
99 6 0.07
100 1 0.01
ACGTcount: A:0.28, C:0.49, G:0.06, T:0.17
Consensus pattern (89 bp):
CCACCACCTCCTGTTTACAAGTACAAGTCTCCACCTCCACCACCACCACCACCACCCCCACCACC
TCCTCTACAAATACAAGTCTCCAC
Found at i:235563 original size:147 final size:143
Alignment explanation
Indices: 235277--235560 Score: 354
Period size: 147 Copynumber: 1.9 Consensus size: 143
235267 TCCTCCCCCG
* * *
235277 GTTTATAAGTACAAGTCTCCTCCCCCTCCACCTCCGGTTTACAAGTACAAGTCCCCACCACCACC
1 GTTTACAAGTACAAGTCTCCACCCCCACCACCTCCGGTTTACAAGTACAAGTCCCCACCACCACC
* * **** *
235342 ACCACCATCACCTCCACCACCTCCTGTTTACAAGTACAAGTCTCCACCTCCACCACCACCACCAT
66 ACCACCATCACCACCACCACCCCCCCCCTACAAATACAAGTCTCCA-C-CCACCACCACCACCAT
235407 CACCCCCACCACCTCCT
129 CA--CCCACCACCTCCT
* * *
235424 GTTTACAAGTACAAGTCTCCACCCCCACCACCTCCTGTTTACAAGTACAAGTCTCCACCTCCACC
1 GTTTACAAGTACAAGTCTCCACCCCCACCACCTCCGGTTTACAAGTACAAGTCCCCACCACCACC
235489 ACCACCATCACCACCTAAGCCACACCCACACCCCTACAAATACAAGTCTCCA-CCACCACCACCA
66 ACCACCATCACCACC--A-CCAC-CCC-C-CCCCTACAAATACAAGTCTCCACCCACCACCACCA
235553 CCATCACC
125 CCATCACC
235561 ACCTAAGCCA
Statistics
Matches: 118, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
147 73 0.62
148 2 0.02
149 1 0.01
150 22 0.19
151 2 0.02
152 1 0.01
153 17 0.14
ACGTcount: A:0.28, C:0.48, G:0.06, T:0.18
Consensus pattern (143 bp):
GTTTACAAGTACAAGTCTCCACCCCCACCACCTCCGGTTTACAAGTACAAGTCCCCACCACCACC
ACCACCATCACCACCACCACCCCCCCCCTACAAATACAAGTCTCCACCCACCACCACCACCATCA
CCCACCACCTCCT
Done.