Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold63
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: 2211945
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 524 characters in sequence are not A, C, G, or T
File 7 of 16
Found at i:1050658 original size:21 final size:20
Alignment explanation
Indices: 1050634--1050676 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1050624 ATGTTTTAAG
1050634 TAAATATAAACAAATA-ATTTT
1 TAAATA-AAA-AAATATATTTT
*
1050655 TAAATAAAATAATATATTTT
1 TAAATAAAAAAATATATTTT
1050675 TA
1 TA
1050677 TTTAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 10 0.50
21 6 0.30
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAATAAAAAAATATATTTT
Found at i:1051066 original size:12 final size:12
Alignment explanation
Indices: 1051032--1051083 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
1051022 AGATTTAAGC
*
1051032 ATTTAAATTTAAT
1 ATTT-AATTTTAT
* *
1051045 ATTCATTTTTAT
1 ATTTAATTTTAT
1051057 ATTTAATTTT-T
1 ATTTAATTTTAT
*
1051068 ATTTATTTTTAT
1 ATTTAATTTTAT
1051080 ATTT
1 ATTT
1051084 TATCTTTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
11 10 0.31
12 19 0.59
13 3 0.09
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTTAATTTTAT
Found at i:1051086 original size:13 final size:12
Alignment explanation
Indices: 1051043--1051083 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1051033 TTTAAATTTA
*
1051043 ATATTCATTTTT
1 ATATTTATTTTT
*
1051055 ATATTTAATTTT
1 ATATTTATTTTT
1051067 -TATTTATTTTT
1 ATATTTATTTTT
1051078 ATATTT
1 ATATTT
1051084 TATCTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (12 bp):
ATATTTATTTTT
Found at i:1051091 original size:23 final size:23
Alignment explanation
Indices: 1051044--1051091 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1051034 TTAAATTTAA
*
1051044 TATTCATTTTTATATTTAATTTT
1 TATTCATTTTTATATTTAATCTT
* *
1051067 TATTTATTTTTATATTTTATCTT
1 TATTCATTTTTATATTTAATCTT
1051090 TA
1 TA
1051092 AAAAATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (23 bp):
TATTCATTTTTATATTTAATCTT
Found at i:1051444 original size:21 final size:21
Alignment explanation
Indices: 1051401--1051444 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1051391 ACTCGTATCC
* * **
1051401 ATATTTAAAATAATTTTTTAA
1 ATATATAAAAAAATTTTAAAA
1051422 ATATATAAAAAAATTTTAAAA
1 ATATATAAAAAAATTTTAAAA
1051443 AT
1 AT
1051445 TAAAACATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATATAAAAAAATTTTAAAA
Found at i:1056530 original size:16 final size:17
Alignment explanation
Indices: 1056498--1056530 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1056488 TGACAACAAA
*
1056498 TTAAATATCATAAATTT
1 TTAAATATCAAAAATTT
1056515 TTAAATAT-AAAAATTT
1 TTAAATATCAAAAATTT
1056531 AAATTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAAATATCAAAAATTT
Found at i:1056669 original size:19 final size:19
Alignment explanation
Indices: 1056647--1056694 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
1056637 ATAAATTTTT
*
1056647 TAAAATATATATAATTAAA
1 TAAAATATAAATAATTAAA
*
1056666 TAAAA-ATTAAATACTTAAA
1 TAAAATA-TAAATAATTAAA
1056685 T-AAATATAAA
1 TAAAATATAAA
1056695 ATCTAGATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATATAAATAATTAAA
Found at i:1056980 original size:13 final size:13
Alignment explanation
Indices: 1056962--1057019 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 13
1056952 CTAAATTAAA
1056962 ATTAAATTTAATT
1 ATTAAATTTAATT
*
1056975 ATTAAA-TTATTTT
1 ATTAAATTTA-ATT
1056988 ATTTTAATATTTAATT
1 A--TTAA-ATTTAATT
*
1057004 TTTAAATTTAATT
1 ATTAAATTTAATT
1057017 ATT
1 ATT
1057020 TACGTTATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
12 3 0.08
13 19 0.53
14 4 0.11
15 4 0.11
16 3 0.08
17 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTAAATTTAATT
Found at i:1057018 original size:29 final size:28
Alignment explanation
Indices: 1056963--1057020 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
1056953 TAAATTAAAA
*
1056963 TTAAATTTAATTATTAAATTATTTTATT
1 TTAAATTTAATTATTAAATTATATTATT
*
1056991 TTAATATTTAATTTTTAAATT-TAATTATT
1 TTAA-ATTTAATTATTAAATTAT-ATTATT
1057020 T
1 T
1057021 ACGTTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
TTAAATTTAATTATTAAATTATATTATT
Found at i:1057020 original size:8 final size:8
Alignment explanation
Indices: 1056967--1057021 Score: 50
Period size: 8 Copynumber: 7.6 Consensus size: 8
1056957 TTAAAATTAA
1056967 ATTTAATT
1 ATTTAATT
*
1056975 ATTAAATT
1 ATTTAATT
*
1056983 ATTTTA-T
1 ATTTAATT
1056990 -TTTAA-T
1 ATTTAATT
1056996 ATTTAATT
1 ATTTAATT
1057004 -TTTAA--
1 ATTTAATT
1057009 ATTTAATT
1 ATTTAATT
1057017 ATTTA
1 ATTTA
1057022 CGTTATAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
6 10 0.26
7 11 0.29
8 17 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATTTAATT
Found at i:1057556 original size:18 final size:20
Alignment explanation
Indices: 1057509--1057556 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1057499 TATTTTTATT
1057509 TAAA-TTTAATTATAAAAAA
1 TAAATTTTAATTATAAAAAA
*
1057528 TATAATATTAA-TAT-AAAAA
1 TA-AATTTTAATTATAAAAAA
1057547 TAAATTTTAA
1 TAAATTTTAA
1057557 AAAATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 7 0.28
19 9 0.36
20 5 0.20
21 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATTTTAATTATAAAAAA
Found at i:1062415 original size:2 final size:2
Alignment explanation
Indices: 1062408--1062439 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1062398 ACAAAAACTA
1062408 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
1062440 TAAGAGGGAG
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:1062995 original size:32 final size:32
Alignment explanation
Indices: 1062959--1063036 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
1062949 CGATTCAGAT
*
1062959 ATTTAATAATAAAAAAATA-ATTTTATATTAAA
1 ATTTAATAATAAAAAAATATA-TATATATTAAA
* * *
1062991 ATTTAATTATAAATATATATATATATATTAAA
1 ATTTAATAATAAAAAAATATATATATATTAAA
1063023 ATTTTAAATAATAA
1 A-TTT-AATAATAA
1063037 TTTAAATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
32 27 0.71
33 4 0.11
34 7 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
ATTTAATAATAAAAAAATATATATATATTAAA
Found at i:1063443 original size:21 final size:22
Alignment explanation
Indices: 1063390--1063443 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
1063380 AAAAATTTAA
1063390 TATATAAAT-AATTATATAATT
1 TATATAAATAAATTATATAATT
* ** *
1063411 TAAATATTTAAATT-TATTATT
1 TATATAAATAAATTATATAATT
1063432 TATATAAATAAA
1 TATATAAATAAA
1063444 ACGGATTCAA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATATAAATAAATTATATAATT
Found at i:1063814 original size:21 final size:20
Alignment explanation
Indices: 1063790--1063828 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1063780 TTTGAATTTA
*
1063790 ATTTAATTTAAAAATTAAATT
1 ATTT-ATTTAAAAAATAAATT
*
1063811 ATTTTTTTAAAAAATAAA
1 ATTTATTTAAAAAATAAA
1063829 AAATTATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTTATTTAAAAAATAAATT
Found at i:1063838 original size:21 final size:20
Alignment explanation
Indices: 1063796--1063840 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1063786 TTTAATTTAA
* **
1063796 TTTAAAAATTAAATTATTTT
1 TTTAAAAAATAAAAAATTTT
1063816 TTTAAAAAATAAAAAATTATT
1 TTTAAAAAATAAAAAATT-TT
1063837 TTTA
1 TTTA
1063841 TATTAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAAAAAATAAAAAATTTT
Found at i:1064500 original size:7 final size:7
Alignment explanation
Indices: 1064461--1064516 Score: 60
Period size: 8 Copynumber: 7.7 Consensus size: 7
1064451 GTTATCATTG
1064461 AATATAA
1 AATATAA
1064468 AATAATAA
1 AAT-ATAA
*
1064476 AACATAA
1 AATATAA
*
1064483 AACTATTA
1 AA-TATAA
1064491 AATATAA
1 AATATAA
1064498 AATAATAA
1 AAT-ATAA
1064506 AATA-AA
1 AATATAA
1064512 AATAT
1 AATAT
1064517 TTTTAATGTC
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
6 6 0.15
7 17 0.41
8 18 0.44
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.27
Consensus pattern (7 bp):
AATATAA
Found at i:1064508 original size:15 final size:15
Alignment explanation
Indices: 1064461--1064515 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
1064451 GTTATCATTG
1064461 AATATAAAATAATAA
1 AATATAAAATAATAA
* *
1064476 AACATAAAACT-ATTA
1 AATATAAAA-TAATAA
1064491 AATATAAAATAATAA
1 AATATAAAATAATAA
1064506 AATA-AAAATA
1 AATATAAAATA
1064516 TTTTTAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
14 7 0.21
15 26 0.76
16 1 0.03
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (15 bp):
AATATAAAATAATAA
Found at i:1064956 original size:6 final size:6
Alignment explanation
Indices: 1064939--1065005 Score: 57
Period size: 6 Copynumber: 10.8 Consensus size: 6
1064929 GAGTATTAAA
* *
1064939 TAAATT TAAAATT TAAATT TAAATT TAAATT T-GATT T-GATT TAAAAATT
1 TAAATT T-AAATT TAAATT TAAATT TAAATT TAAATT TAAATT T--AAATT
*
1064988 TAAATT TATTATT TAAAT
1 TAAATT TA-AATT TAAAT
1065006 GTATTAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
5 9 0.17
6 28 0.54
7 11 0.21
8 4 0.08
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:1064957 original size:13 final size:13
Alignment explanation
Indices: 1064939--1065005 Score: 61
Period size: 13 Copynumber: 5.4 Consensus size: 13
1064929 GAGTATTAAA
1064939 TAAATTTAAAATT
1 TAAATTTAAAATT
1064952 TAAATTT-AAATT
1 TAAATTTAAAATT
*
1064964 TAAATTT--GATT
1 TAAATTTAAAATT
*
1064975 T-GATTTAAAAATT
1 TAAATTT-AAAATT
**
1064988 TAAATTTATTATT
1 TAAATTTAAAATT
1065001 TAAAT
1 TAAAT
1065006 GTATTAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
10 4 0.09
11 4 0.09
12 12 0.27
13 20 0.45
14 4 0.09
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (13 bp):
TAAATTTAAAATT
Found at i:1065053 original size:22 final size:23
Alignment explanation
Indices: 1065027--1065091 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 23
1065017 GTTAAAAAAT
1065027 ATTTTTATATTAATATTTAT-AA
1 ATTTTTATATTAATATTTATAAA
1065049 ATTTTTATAATT-ATATTTAATAAA
1 ATTTTTAT-ATTAATATTT-ATAAA
* * *
1065073 AATATTATTTTAATATTTA
1 ATTTTTATATTAATATTTA
1065092 AATAATGACT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
22 14 0.39
23 8 0.22
24 14 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATTTTTATATTAATATTTATAAA
Found at i:1065748 original size:4 final size:4
Alignment explanation
Indices: 1065717--1065782 Score: 91
Period size: 4 Copynumber: 17.0 Consensus size: 4
1065707 CTAATAAAAT
* * *
1065717 TAAA TCAA TAAA -GAA TAAA TAAG T-AA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1065763 TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA
1065783 GACTCACAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
3 4 0.07
4 50 0.93
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:1067303 original size:3 final size:3
Alignment explanation
Indices: 1067290--1067327 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
1067280 TGTTTGGTAG
1067290 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1067328 GTTAAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1076394 original size:16 final size:16
Alignment explanation
Indices: 1076304--1076433 Score: 72
Period size: 16 Copynumber: 8.1 Consensus size: 16
1076294 TAAACGTGAT
1076304 AATATAAAATA-ATAAA
1 AATATAAAATATAT-AA
*
1076320 AATATAAAATAAATAAA
1 AATATAAAATATAT-AA
* * *
1076337 AATTTTAAAATCTATAT
1 AA-TATAAAATATATAA
* * *
1076354 CATATGAATTAT-TAA
1 AATATAAAATATATAA
*
1076369 TATAATAAAATATATAA
1 AAT-ATAAAATATATAA
*
1076386 AATATAAAATATTTTAA
1 AATATAAAATA-TATAA
* *
1076403 AA-AT-AATTATGATAT
1 AATATAAAATAT-ATAA
1076418 AA-ATAAAATATATAA
1 AATATAAAATATATAA
1076433 A
1 A
1076434 TTAATAAATT
Statistics
Matches: 87, Mismatches: 20, Indels: 15
0.71 0.16 0.12
Matches are distributed among these distances:
14 1 0.01
15 18 0.21
16 39 0.45
17 20 0.23
18 9 0.10
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (16 bp):
AATATAAAATATATAA
Found at i:1080129 original size:14 final size:14
Alignment explanation
Indices: 1080110--1080151 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1080100 ACTATTTCAT
1080110 ATAATATTAAA-ATA
1 ATAATA-TAAATATA
1080124 ATAATATAAATATA
1 ATAATATAAATATA
*
1080138 ATATAAATAAATAT
1 ATA-ATATAAATAT
1080152 TTTAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 4 0.16
14 12 0.48
15 9 0.36
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATAATATAAATATA
Found at i:1080180 original size:20 final size:20
Alignment explanation
Indices: 1080157--1080195 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1080147 AATATTTTAA
*
1080157 ATTTTATATA-AATATAAAAT
1 ATTTTAAATATAAT-TAAAAT
1080177 ATTTTAAATATAATTAAAA
1 ATTTTAAATATAATTAAAA
1080196 GATATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTTAAATATAATTAAAAT
Found at i:1080188 original size:24 final size:23
Alignment explanation
Indices: 1080130--1080188 Score: 64
Period size: 27 Copynumber: 2.3 Consensus size: 23
1080120 AATAATAATA
1080130 TAAATATAATATAAATAAATATTT
1 TAAATAT-ATATAAATAAATATTT
*
1080154 TAAATTTTATATAAATATAAAATATTT
1 TAAA-TATATAT-AA-AT-AAATATTT
1080181 TAAATATA
1 TAAATATA
1080189 ATTAAAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 8 0.28
25 4 0.14
26 5 0.17
27 12 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAATATATATAAATAAATATTT
Found at i:1080788 original size:5 final size:5
Alignment explanation
Indices: 1080776--1080855 Score: 50
Period size: 5 Copynumber: 17.6 Consensus size: 5
1080766 AATATTTTAA
* * * *
1080776 AATA- AATAT AATAT -TTAT TAT-T AATAT AATAA AAT-T TATAT AA-AT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
* *
1080821 ATTTT AA-AT AA-A- AATAT AATAT AATAT AATAT AAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AAT
1080856 TTATAAATAA
Statistics
Matches: 58, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
3 2 0.03
4 20 0.34
5 36 0.62
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AATAT
Found at i:1080789 original size:27 final size:27
Alignment explanation
Indices: 1080758--1080842 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 27
1080748 ATATTTTATA
1080758 AATATTTTAATATTTTAAAATAAATAT
1 AATATTTTAATATTTTAAAATAAATAT
* * *
1080785 AATA-TTTATTATTAATATAATAAA-AT
1 AATATTTTAATATT-TTAAAATAAATAT
* * * *
1080811 -TTATATAAATATTTTAAATAAAAATAT
1 AATATTTTAATATTTTAAA-ATAAATAT
1080838 AATAT
1 AATAT
1080843 AATATAATAT
Statistics
Matches: 42, Mismatches: 11, Indels: 9
0.68 0.18 0.15
Matches are distributed among these distances:
25 5 0.12
26 20 0.48
27 14 0.33
28 3 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
AATATTTTAATATTTTAAAATAAATAT
Found at i:1080792 original size:18 final size:19
Alignment explanation
Indices: 1080740--1080791 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1080730 AAAAATAATT
*
1080740 TAAAAATAATATTTTATAAA
1 TAAATATAATATTTTA-AAA
* *
1080760 T-ATTTTAATATTTTAAAA
1 TAAATATAATATTTTAAAA
1080778 TAAATATAATATTT
1 TAAATATAATATTT
1080792 ATTATTAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 4 0.15
19 21 0.81
20 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TAAATATAATATTTTAAAA
Found at i:1080809 original size:32 final size:32
Alignment explanation
Indices: 1080760--1080824 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
1080750 ATTTTATAAA
**
1080760 TATTTTAATATTTTAAAATAAATAT-AATATT
1 TATTTTAATATAATAAAATAAATATAAATATT
**
1080791 TATTATTAATATAATAAAATTTATATAAATATT
1 TATT-TTAATATAATAAAATAAATATAAATATT
1080824 T
1 T
1080825 TAAATAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 4 0.14
32 17 0.61
33 7 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TATTTTAATATAATAAAATAAATATAAATATT
Found at i:1080812 original size:21 final size:20
Alignment explanation
Indices: 1080744--1080822 Score: 58
Period size: 19 Copynumber: 4.0 Consensus size: 20
1080734 ATAATTTAAA
*
1080744 AATAATATTT-TATAAATAT
1 AATAAAATTTATATAAATAT
** *
1080763 TTTAATATTT-TA-AAATA-
1 AATAAAATTTATATAAATAT
*
1080780 AATATAATATTTATTATTAATAT
1 AATA-AA-ATTTA-TATAAATAT
1080803 AATAAAATTTATATAAATAT
1 AATAAAATTTATATAAATAT
1080823 TTTAAATAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
17 2 0.04
18 6 0.13
19 14 0.30
20 8 0.17
21 7 0.15
22 6 0.13
23 4 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATAAAATTTATATAAATAT
Found at i:1080851 original size:15 final size:15
Alignment explanation
Indices: 1080776--1080855 Score: 50
Period size: 13 Copynumber: 5.9 Consensus size: 15
1080766 AATATTTTAA
1080776 AATA-AATATAATAT
1 AATATAATATAATAT
* *
1080790 -TTATTAT-TAATAT
1 AATATAATATAATAT
* *
1080803 AATAAAAT-TTATAT
1 AATATAATATAATAT
* *
1080817 AA-ATATTTTAA-AT
1 AATATAATATAATAT
1080830 AA-A-AATATAATAT
1 AATATAATATAATAT
1080843 AATATAATATAAT
1 AATATAATATAAT
1080856 TTATAAATAA
Statistics
Matches: 49, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
12 5 0.10
13 20 0.41
14 16 0.33
15 8 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATAATATAATAT
Found at i:1081407 original size:21 final size:21
Alignment explanation
Indices: 1081369--1081422 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
1081359 CTTTTATCTC
* *
1081369 ATTTAAATATTTTGTTATATAG
1 ATTTAAA-ATTATATTATATAG
*
1081391 -TTTGAAAATTATATTATTTAG
1 ATTT-AAAATTATATTATATAG
1081412 ATTTAAAATTA
1 ATTTAAAATTA
1081423 ATATCGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (21 bp):
ATTTAAAATTATATTATATAG
Found at i:1083694 original size:30 final size:28
Alignment explanation
Indices: 1083646--1083706 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 28
1083636 TCGAGCTTTG
1083646 ATAAGATTTTTATAAATTTAATAAAAAA
1 ATAAGATTTTTATAAATTTAATAAAAAA
* * *
1083674 ATAATATTTTTATTTAAATTTAATTATAAA
1 ATAAGATTTTTA--TAAATTTAATAAAAAA
1083704 ATA
1 ATA
1083707 TATAAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 11 0.39
30 17 0.61
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
ATAAGATTTTTATAAATTTAATAAAAAA
Found at i:1083719 original size:22 final size:19
Alignment explanation
Indices: 1083688--1083729 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
1083678 TATTTTTATT
1083688 TAAATTTAATTATAAAATATA
1 TAAATTTAA-TATAAAA-ATA
1083709 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
1083729 T
1 T
1083730 TTTAATAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATTTAATATAAAAATA
Found at i:1084787 original size:13 final size:14
Alignment explanation
Indices: 1084769--1084801 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1084759 TGATTTTTTT
1084769 AATAATTT-ATATA
1 AATAATTTAATATA
1084782 AATAATTTAATATA
1 AATAATTTAATATA
1084796 ATATAA
1 A-ATAA
1084802 AATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 6 0.33
15 4 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATAATTTAATATA
Found at i:1085465 original size:28 final size:28
Alignment explanation
Indices: 1085420--1085479 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1085410 TTTACTTGAG
* * * * *
1085420 ATTTGATTTTTGATTTTATTAAATATTA
1 ATTTAATTTTTAAATTTATCAAATAATA
1085448 ATTTAATTTTTAAATTTATCAAATAATA
1 ATTTAATTTTTAAATTTATCAAATAATA
1085476 ATTT
1 ATTT
1085480 TTTAAAATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (28 bp):
ATTTAATTTTTAAATTTATCAAATAATA
Found at i:1088779 original size:8 final size:8
Alignment explanation
Indices: 1088763--1088852 Score: 69
Period size: 8 Copynumber: 11.0 Consensus size: 8
1088753 ATAAAATATG
*
1088763 ATATTAAT
1 ATATAAAT
1088771 ATATAAAT
1 ATATAAAT
1088779 ATATAAAT
1 ATATAAAT
*
1088787 CAATATTAAT
1 --ATATAAAT
1088797 ATATAAAT
1 ATATAAAT
1088805 ATATTAAA-
1 ATA-TAAAT
* *
1088813 ATTTATAT
1 ATATAAAT
1088821 A-ATAAAT
1 ATATAAAT
*
1088828 -TATTAAT
1 ATATAAAT
1088835 ATATTAAAAT
1 ATA-T-AAAT
1088845 ATATAAAT
1 ATATAAAT
1088853 TTTTAATTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
7 12 0.18
8 34 0.52
9 6 0.09
10 13 0.20
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (8 bp):
ATATAAAT
Found at i:1088853 original size:38 final size:34
Alignment explanation
Indices: 1088763--1088854 Score: 103
Period size: 38 Copynumber: 2.5 Consensus size: 34
1088753 ATAAAATATG
* * *
1088763 ATATTAATATATAAATATATAAATCAATATTAAT
1 ATATAAATATATAAATTTATAAATAAATATTAAT
1088797 ATATAAATATATTAAAATTTATATAATAAATTATTAAT
1 ATATAAATATA-T-AAATTTATA-AATAAA-TATTAAT
1088835 ATATTAAAATATATAAATTT
1 ATA-T-AAATATATAAATTT
1088855 TTAATTTTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
34 10 0.20
35 1 0.02
36 8 0.16
37 5 0.10
38 16 0.33
39 2 0.04
40 7 0.14
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (34 bp):
ATATAAATATATAAATTTATAAATAAATATTAAT
Found at i:1089264 original size:3 final size:3
Alignment explanation
Indices: 1089256--1089297 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
1089246 GAGTGCATCA
*
1089256 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAGT GAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AA
1089298 ACCCAAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.94
4 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1090846 original size:9 final size:9
Alignment explanation
Indices: 1090834--1090916 Score: 61
Period size: 9 Copynumber: 9.4 Consensus size: 9
1090824 AATAATTAAA
1090834 AAATAATAT
1 AAATAATAT
1090843 AAAT--TAT
1 AAATAATAT
1090850 -AAT-ATAT
1 AAATAATAT
1090857 AAAT-ATAT
1 AAATAATAT
*
1090865 AAATAATTT
1 AAATAATAT
1090874 AAATATATAT
1 AAATA-ATAT
1090884 AATATAA-AT
1 AA-ATAATAT
*
1090893 ATAATAAATTT
1 A-AAT-AATAT
*
1090904 AAATAAAAT
1 AAATAATAT
1090913 AAAT
1 AAAT
1090917 TATTCACAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
6 3 0.05
7 6 0.10
8 11 0.18
9 24 0.39
10 12 0.20
11 5 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
AAATAATAT
Found at i:1090853 original size:15 final size:14
Alignment explanation
Indices: 1090824--1090914 Score: 73
Period size: 15 Copynumber: 6.4 Consensus size: 14
1090814 ATCTAAAAAA
1090824 AATAAT-TAAA-A-
1 AATAATATAAATAT
1090835 AATAATATAAATTAT
1 AATAATATAAA-TAT
1090850 AAT-ATATAAATATAT
1 AATAATAT-AA-ATAT
*
1090865 AAATAATTTAAATAT
1 -AATAATATAAATAT
1090880 ATATAATATAAATAT
1 A-ATAATATAAATAT
* *
1090895 AATAAATTTAAATAA
1 AAT-AATATAAATAT
1090910 AATAA
1 AATAA
1090915 ATTATTCACA
Statistics
Matches: 66, Mismatches: 4, Indels: 17
0.76 0.05 0.20
Matches are distributed among these distances:
11 6 0.09
12 4 0.06
14 10 0.15
15 37 0.56
16 6 0.09
17 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATAATATAAATAT
Found at i:1090903 original size:30 final size:27
Alignment explanation
Indices: 1090823--1090916 Score: 81
Period size: 27 Copynumber: 3.5 Consensus size: 27
1090813 AATCTAAAAA
*
1090823 AAATA-AT-TAAA-AAATAATATAAATT
1 AAATATATATAAATAAATAA-ATAATTT
* *
1090848 ATA-ATATATAAATATATAAATAATTT
1 AAATATATATAAATAAATAAATAATTT
1090874 AAATATATATAATATAAATATAATAAATTT
1 AAATATATATAA-ATAAATA-AAT-AATTT
*
1090904 AAATA-AAATAAAT
1 AAATATATATAAAT
1090917 TATTCACAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
24 1 0.02
25 4 0.07
26 12 0.21
27 13 0.23
28 8 0.14
29 8 0.14
30 10 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
AAATATATATAAATAAATAAATAATTT
Found at i:1090909 original size:24 final size:24
Alignment explanation
Indices: 1090834--1090916 Score: 84
Period size: 24 Copynumber: 3.5 Consensus size: 24
1090824 AATAATTAAA
1090834 AAATAATATAAAT-T-ATAATATAT
1 AAATAATATAAATATAATAA-ATAT
*
1090857 AAAT-ATATAAATA-ATTTAAATAT
1 AAATAATATAAATATA-ATAAATAT
* *
1090880 ATATAATATAAATATAATAAATTT
1 AAATAATATAAATATAATAAATAT
*
1090904 AAATAAAATAAAT
1 AAATAATATAAAT
1090917 TATTCACAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
22 8 0.16
23 11 0.22
24 29 0.59
25 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
AAATAATATAAATATAATAAATAT
Found at i:1090971 original size:16 final size:16
Alignment explanation
Indices: 1090842--1090960 Score: 58
Period size: 15 Copynumber: 7.4 Consensus size: 16
1090832 AAAAATAATA
1090842 TAAAT-TATAATATA-
1 TAAATATATAATATAT
1090856 TAAATATATAA-ATAATT
1 TAAATATATAATAT-A-T
1090873 TAAATATAT-ATA-AT
1 TAAATATATAATATAT
1090887 ATAAATATAATAA-AT-T
1 -TAAATAT-ATAATATAT
*
1090903 TAAATAAAATAA-ATTAT
1 TAAAT-ATATAATA-TAT
* *
1090920 TCACAA-ATTAAAATTTAT
1 T-A-AATA-TATAATATAT
*
1090938 AAAATATATAATATAT
1 TAAATATATAATATAT
1090954 TAAATAT
1 TAAATAT
1090961 TATCATAATT
Statistics
Matches: 80, Mismatches: 8, Indels: 32
0.67 0.07 0.27
Matches are distributed among these distances:
14 8 0.10
15 24 0.30
16 23 0.29
17 16 0.20
18 7 0.09
19 2 0.03
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATATATAATATAT
Found at i:1093400 original size:22 final size:19
Alignment explanation
Indices: 1093375--1093414 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
1093365 ATGAAATAAA
1093375 TAAAAATATAATATGAATATTT
1 TAAAAAT-T-ATAT-AATATTT
1093397 TAAAAATTATATAATATT
1 TAAAAATTATATAATATT
1093415 AAATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 4 0.22
21 1 0.06
22 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TAAAAATTATATAATATTT
Found at i:1093436 original size:16 final size:15
Alignment explanation
Indices: 1093397--1093460 Score: 69
Period size: 15 Copynumber: 4.2 Consensus size: 15
1093387 ATGAATATTT
*
1093397 TAAAAATTATATAATA
1 TAAAAATTTTA-AATA
*
1093413 T-TAAATTTTAATATA
1 TAAAAATTTTAA-ATA
1093428 TAAAAA-TTTAAATA
1 TAAAAATTTTAAATA
1093442 TAAAATATTTTAAATA
1 TAAAA-ATTTTAAATA
1093458 TAA
1 TAA
1093461 TTATAATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
14 9 0.22
15 17 0.41
16 15 0.37
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAAAATTTTAAATA
Found at i:1093478 original size:59 final size:54
Alignment explanation
Indices: 1093369--1093489 Score: 129
Period size: 59 Copynumber: 2.2 Consensus size: 54
1093359 TTTGATATGA
* * *
1093369 AATAAATAAAAATATAATATGAATATTTTAAAAATTATATAATATTAAATTT-T
1 AATATATAAAAATATAATATAAATATTTTAAAAATTATATAATATAAAATTTAT
* *
1093422 AATATATAAAAATTTAAATATAAAATATTTTAAATATAATTATAATATTATAAAATTTAT
1 AATATATAAAAATAT-AATAT-AAATATTTT-AA-A-AATTAT-ATAATATAAAATTTAT
1093482 AA-ATATAA
1 AATATATAA
1093490 TATAAATGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
53 13 0.23
54 5 0.09
55 8 0.14
56 2 0.04
57 1 0.02
58 6 0.11
59 18 0.32
60 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (54 bp):
AATATATAAAAATATAATATAAATATTTTAAAAATTATATAATATAAAATTTAT
Found at i:1094887 original size:14 final size:14
Alignment explanation
Indices: 1094868--1094896 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1094858 CAGAAATATT
1094868 TAATCAAATAATTA
1 TAATCAAATAATTA
1094882 TAATCAAATAATTA
1 TAATCAAATAATTA
1094896 T
1 T
1094897 CTTATTTATT
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:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (14 bp):
TAATCAAATAATTA
Found at i:1095957 original size:22 final size:21
Alignment explanation
Indices: 1095906--1095958 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1095896 TCTTATTAAC
1095906 TTAATTTTTTAAGTCTAAAAT
1 TTAATTTTTTAAGTCTAAAAT
*
1095927 TTAGTTTTTTATA-TCTAAAAT
1 TTAATTTTTTA-AGTCTAAAAT
1095948 TTAATCTTTTT
1 TTAAT-TTTTT
1095959 TTAATTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (21 bp):
TTAATTTTTTAAGTCTAAAAT
Found at i:1097540 original size:16 final size:18
Alignment explanation
Indices: 1097519--1097552 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1097509 GATTATAATG
1097519 ATTTAAA-AA-ATAAAAA
1 ATTTAAATAACATAAAAA
1097535 ATTTAAATAACATAAAAA
1 ATTTAAATAACATAAAAA
1097553 TATAAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
ATTTAAATAACATAAAAA
Found at i:1101468 original size:41 final size:41
Alignment explanation
Indices: 1101407--1101490 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
1101397 TATCAAATAC
* *
1101407 ATACCTATATCAACATTCAGCTAAGATTTGAGGAACACAGA
1 ATACCTATATCAACACTCAGCTAAGATTCGAGGAACACAGA
1101448 ATACCTATATCAACACTCAGCTAAGATTCGAGGAACACAGA
1 ATACCTATATCAACACTCAGCTAAGATTCGAGGAACACAGA
1101489 AT
1 AT
1101491 TTTTGTATCC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (41 bp):
ATACCTATATCAACACTCAGCTAAGATTCGAGGAACACAGA
Found at i:1103781 original size:65 final size:65
Alignment explanation
Indices: 1103677--1103812 Score: 254
Period size: 65 Copynumber: 2.1 Consensus size: 65
1103667 CAAATTTTGA
*
1103677 AATGAAAATGCCAATGGTGAGAGTTGTAAAATGCTCTAACTTACTGACTGCAAGAACTAGCTCTT
1 AATGAAAATGCCAATGGTGAGAGTTGTAAAATGCTCTAACTTACTGACTGCAAGAACTAGCTCTC
*
1103742 AATGAAAATGCCAATGGTGAGAGTTGTATAATGCTCTAACTTACTGACTGCAAGAACTAGCTCTC
1 AATGAAAATGCCAATGGTGAGAGTTGTAAAATGCTCTAACTTACTGACTGCAAGAACTAGCTCTC
1103807 AATGAA
1 AATGAA
1103813 TCACAAACCC
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 69 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (65 bp):
AATGAAAATGCCAATGGTGAGAGTTGTAAAATGCTCTAACTTACTGACTGCAAGAACTAGCTCTC
Found at i:1104932 original size:5 final size:5
Alignment explanation
Indices: 1104922--1104961 Score: 62
Period size: 5 Copynumber: 7.6 Consensus size: 5
1104912 AGAAGAACCA
1104922 AATCG AATCG AATCG AATCG AATCG AATCGG AATTCG AAT
1 AATCG AATCG AATCG AATCG AATCG AATC-G AA-TCG AAT
1104962 TGCTTGGGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 25 0.76
6 6 0.18
7 2 0.06
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (5 bp):
AATCG
Found at i:1107372 original size:21 final size:20
Alignment explanation
Indices: 1107346--1107398 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
1107336 GACACATATC
* *
1107346 TTAAAAATATATTTAAATAA
1 TTAAAAATATAATTAAAAAA
*
1107366 TTTAAAATATTAATTAAAAAA
1 TTAAAAATA-TAATTAAAAAA
*
1107387 TAAAAAATATAA
1 TTAAAAATATAA
1107399 CAGATTCTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TTAAAAATATAATTAAAAAA
Found at i:1107392 original size:20 final size:20
Alignment explanation
Indices: 1107347--1107398 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
1107337 ACACATATCT
* *
1107347 TAAAAATATATTTAAATAAT
1 TAAAAATATAATTAAATAAA
*
1107367 TTAAAATATTAATTAAA-AAA
1 TAAAAATA-TAATTAAATAAA
1107387 TAAAAAATATAA
1 T-AAAAATATAA
1107399 CAGATTCTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAAAATATAATTAAATAAA
Found at i:1107875 original size:2 final size:2
Alignment explanation
Indices: 1107870--1107910 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1107860 TCTCTCTCTC
1107870 TA TA TA 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 TA TA TA T
1107911 GGATTTATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1113206 original size:21 final size:21
Alignment explanation
Indices: 1113180--1113222 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1113170 TTATAGTGTA
1113180 CAAAGTTGTCCAGTTGTTGGT
1 CAAAGTTGTCCAGTTGTTGGT
*
1113201 CAAAGTTGTCCTGTTGTTGGT
1 CAAAGTTGTCCAGTTGTTGGT
1113222 C
1 C
1113223 GTGTTCTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.16, G:0.28, T:0.40
Consensus pattern (21 bp):
CAAAGTTGTCCAGTTGTTGGT
Found at i:1117428 original size:24 final size:25
Alignment explanation
Indices: 1117401--1117447 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1117391 AATGCCTTAA
1117401 TTTTTATTATTT-TATTTAAATATT
1 TTTTTATTATTTATATTTAAATATT
*
1117425 TTTTTATTTTTTATATTTAAATA
1 TTTTTATTATTTATATTTAAATA
1117448 ATAAAACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTTTATTATTTATATTTAAATATT
Found at i:1117560 original size:29 final size:28
Alignment explanation
Indices: 1117505--1117570 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 28
1117495 GTAAAATTTT
*
1117505 AATTAAAAATTTATTTAAATATAATAAA
1 AATTAAAAATTTATTTAAAAATAATAAA
*
1117533 AATATAAAAATTTATTTAAAAA-ATATAAT
1 AAT-TAAAAATTTATTTAAAAATA-ATAAA
1117562 AATTAAAAA
1 AATTAAAAA
1117571 AATTTTAACC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 10 0.29
29 24 0.71
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
AATTAAAAATTTATTTAAAAATAATAAA
Found at i:1118957 original size:18 final size:20
Alignment explanation
Indices: 1118936--1118973 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
1118926 AATAATTTCA
1118936 TTTAAA-ATAATT-TAATAT
1 TTTAAATATAATTATAATAT
1118954 TTTAAATATAATTATAATAT
1 TTTAAATATAATTATAATAT
1118974 AAAAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 6 0.33
20 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAAATATAATTATAATAT
Found at i:1119376 original size:20 final size:19
Alignment explanation
Indices: 1119351--1119399 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
1119341 AAAAAATTAA
1119351 ATATTAAAAAAATATTTTTT
1 ATATTAAAAAAATA-TTTTT
**
1119371 ATATTAATATTAATATTTTT
1 ATATTAA-AAAAATATTTTT
1119391 ATAATTAAA
1 AT-ATTAAA
1119400 TTTAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATTAAAAAAATATTTTT
Found at i:1119597 original size:30 final size:29
Alignment explanation
Indices: 1119552--1119607 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1119542 TAATAATTAT
1119552 ATTTAAAAGATAAAAAATTATTTTTAAAA
1 ATTTAAAAGATAAAAAATTATTTTTAAAA
*
1119581 ATTTTAAAGATAAAAAATTATTTTTAA
1 ATTTAAAAGATAAAAAATTATTTTTAA
1119608 TAATCATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (29 bp):
ATTTAAAAGATAAAAAATTATTTTTAAAA
Found at i:1119637 original size:13 final size:12
Alignment explanation
Indices: 1119594--1119642 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
1119584 TTAAAGATAA
1119594 AAAATTATTTTT
1 AAAATTATTTTT
*
1119606 AATAATCATATTTT
1 AA-AATTAT-TTTT
1119620 AAAATTATGTTTT
1 AAAATTAT-TTTT
1119633 AAAA-TATTTT
1 AAAATTATTTT
1119643 AAAGATGATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
11 3 0.09
12 5 0.16
13 18 0.56
14 6 0.19
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (12 bp):
AAAATTATTTTT
Found at i:1120180 original size:23 final size:22
Alignment explanation
Indices: 1120112--1120176 Score: 53
Period size: 23 Copynumber: 2.8 Consensus size: 22
1120102 TTTTCATGTT
1120112 ATAAATAACATTTTATTTATAATA
1 ATAAAT-A-ATTTTATTTATAATA
* *
1120136 AT-AAT-ATTATATTAAACGTAATA
1 ATAAATAATTTTATT-TA--TAATA
1120159 ATAAATAATTTTATTTAT
1 ATAAATAATTTTATTTAT
1120177 TAATTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
20 7 0.22
21 1 0.03
22 1 0.03
23 10 0.31
24 6 0.19
25 7 0.22
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (22 bp):
ATAAATAATTTTATTTATAATA
Found at i:1120394 original size:13 final size:13
Alignment explanation
Indices: 1120378--1120402 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1120368 TTATTCTTTT
1120378 ATTTTTTTCATTA
1 ATTTTTTTCATTA
1120391 ATTTTTTTCATT
1 ATTTTTTTCATT
1120403 CAAAAAGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTTTTCATTA
Found at i:1121508 original size:35 final size:35
Alignment explanation
Indices: 1121472--1121539 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
1121462 ATGTATATTA
*
1121472 AAATA-TATATTTTTTAA-TGTTATAAATATTTTTT
1 AAATATTATATTTATTAATTGTTATAAA-ATTTTTT
* *
1121506 AAATATTTTATTTATTAATTTTTATAAAATTTTT
1 AAATATTATATTTATTAATTGTTATAAAATTTTT
1121540 ATCGTATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 5 0.17
35 16 0.55
36 8 0.28
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (35 bp):
AAATATTATATTTATTAATTGTTATAAAATTTTTT
Found at i:1122457 original size:26 final size:25
Alignment explanation
Indices: 1122428--1122478 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
1122418 AATTTTTATA
1122428 TAATTTTAAATTATTATTTA-TAAAAT
1 TAATTTTAAA-T-TTATTTATTAAAAT
*
1122454 TAATTTTTAATTTATTTATTAAAAT
1 TAATTTTAAATTTATTTATTAAAAT
1122479 GACTTTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 7 0.30
25 7 0.30
26 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TAATTTTAAATTTATTTATTAAAAT
Found at i:1122509 original size:22 final size:22
Alignment explanation
Indices: 1122484--1122525 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1122474 AAAATGACTT
*
1122484 TAATTATT-TATATTTTTAAACA
1 TAATT-TTGTATATATTTAAACA
1122506 TAATTTTGTATATATTTAAA
1 TAATTTTGTATATATTTAAA
1122526 GAAGACCGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TAATTTTGTATATATTTAAACA
Found at i:1122829 original size:17 final size:17
Alignment explanation
Indices: 1122786--1122847 Score: 81
Period size: 17 Copynumber: 3.5 Consensus size: 17
1122776 TTTAATATGT
1122786 TTATATATTTATATTTATA
1 TTATAT-TTTATA-TTATA
*
1122805 TTAT-TTTTGTATTATA
1 TTATATTTTATATTATA
1122821 TTATATTTTATATTATA
1 TTATATTTTATATTATA
1122838 TTATAATTTT
1 TTAT-ATTTT
1122848 TGATATCATA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
16 9 0.23
17 20 0.51
18 6 0.15
19 4 0.10
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (17 bp):
TTATATTTTATATTATA
Found at i:1122839 original size:22 final size:23
Alignment explanation
Indices: 1122756--1122842 Score: 64
Period size: 22 Copynumber: 4.1 Consensus size: 23
1122746 ATGTTTAAAG
* *
1122756 TATTATATATTTATATAAAATT-
1 TATTATATATTTATATTATATTA
*
1122778 TA--ATATGTTTATA-TAT-TTA
1 TATTATATATTTATATTATATTA
* *
1122797 TATT-TATA-TTATTTTTGTATTA
1 TATTATATATTTA-TATTATATTA
1122819 TATTATAT-TTTATATTATATTA
1 TATTATATATTTATATTATATTA
1122841 TA
1 TA
1122843 ATTTTTGATA
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
18 2 0.04
19 6 0.12
20 14 0.29
21 2 0.04
22 19 0.39
23 6 0.12
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TATTATATATTTATATTATATTA
Found at i:1124027 original size:17 final size:16
Alignment explanation
Indices: 1124007--1124048 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
1123997 AATTTTATAA
1124007 ATAT-TAAAACTCAAT
1 ATATATAAAACTCAAT
*
1124022 ATATATACGAACTCAAT
1 ATATATA-AAACTCAAT
1124039 ATATATAAAA
1 ATATATAAAA
1124049 AAATAATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 4 0.17
16 4 0.17
17 15 0.65
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (16 bp):
ATATATAAAACTCAAT
Found at i:1124121 original size:24 final size:23
Alignment explanation
Indices: 1124080--1124134 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
1124070 TATATGATAT
*
1124080 AATATGAATACACGAATATATCAA
1 AATATAAATACACGAATA-ATCAA
* * *
1124104 AATATAAATAGACTAATAATTAA
1 AATATAAATACACGAATAATCAA
*
1124127 CATATAAA
1 AATATAAA
1124135 AATTTATATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.58, C:0.09, G:0.05, T:0.27
Consensus pattern (23 bp):
AATATAAATACACGAATAATCAA
Found at i:1124656 original size:26 final size:25
Alignment explanation
Indices: 1124626--1124681 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 25
1124616 TTTTTTAAAT
1124626 TTTAAACACAATA-AAAAATAAATATA
1 TTTAAACA-AATATAAAAAT-AATATA
*
1124652 TTT-AATAAATATAAAAATAATATA
1 TTTAAACAAATATAAAAATAATATA
1124676 TTTAAA
1 TTTAAA
1124682 TATATTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 13 0.48
25 11 0.41
26 3 0.11
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (25 bp):
TTTAAACAAATATAAAAATAATATA
Found at i:1124681 original size:21 final size:21
Alignment explanation
Indices: 1124635--1124705 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 21
1124625 TTTTAAACAC
1124635 AATA-AAAAATAAATATATTTAATA
1 AATATAAAAAT-AATATA-TT--TA
1124659 AATATAAAAATAATATATTTA
1 AATATAAAAATAATATATTTA
** *
1124680 AATATATTAATACTATATATTA
1 AATATAAAAATAATATAT-TTA
1124702 AATA
1 AATA
1124706 CACGTTATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
21 17 0.40
22 7 0.17
23 2 0.05
24 10 0.24
25 6 0.14
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (21 bp):
AATATAAAAATAATATATTTA
Found at i:1125525 original size:20 final size:20
Alignment explanation
Indices: 1125500--1125545 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1125490 AAGAATTGAA
*
1125500 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
**
1125520 GAGGGATACTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
1125540 GAGGGA
1 GAGGGA
1125546 GCCTCTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.50, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:1125687 original size:27 final size:27
Alignment explanation
Indices: 1125622--1125692 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
1125612 AAACAAGCCT
* *
1125622 CCATATTTGACAAATACAAAGGAAACAA
1 CCATTTTTGACAAACACAAA-GAAACAA
*
1125650 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACAA
1125677 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
1125693 AATAGGTGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.48, C:0.23, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACAA
Found at i:1130094 original size:20 final size:20
Alignment explanation
Indices: 1130069--1130107 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1130059 AAGAATTGAA
1130069 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAT
**
1130089 GAGGGATACTTGAGAGGGA
1 GAGGGATACAAGAGAGGGA
1130108 GGAAAGAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.46, T:0.13
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAT
Found at i:1130416 original size:18 final size:18
Alignment explanation
Indices: 1130393--1130429 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1130383 TGAACTCCCT
1130393 AACTTCAGTCTTCTTCTC
1 AACTTCAGTCTTCTTCTC
1130411 AACTTCAGTCTTCTTCTC
1 AACTTCAGTCTTCTTCTC
1130429 A
1 A
1130430 GGGTTAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.19, C:0.32, G:0.05, T:0.43
Consensus pattern (18 bp):
AACTTCAGTCTTCTTCTC
Found at i:1133469 original size:22 final size:23
Alignment explanation
Indices: 1133414--1133481 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 23
1133404 GTTTGAGATA
* *
1133414 TTAAGTGAGTTAAATTCAAATATT
1 TTAA-TGAGTTTAATTCAAGTATT
1133438 TTAAT-A-TTTAATTCAAGTA-T
1 TTAATGAGTTTAATTCAAGTATT
* *
1133458 TTCATGAGTTTAATT-AAGTTTT
1 TTAATGAGTTTAATTCAAGTATT
1133480 TT
1 TT
1133482 TACTATTGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 5 0.14
21 16 0.43
22 11 0.30
23 1 0.03
24 4 0.11
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.50
Consensus pattern (23 bp):
TTAATGAGTTTAATTCAAGTATT
Found at i:1133863 original size:18 final size:19
Alignment explanation
Indices: 1133840--1133884 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
1133830 ATCATACGAA
1133840 TTTAATTAAATTT-TTATT
1 TTTAATTAAATTTATTATT
*
1133858 TTTAA-TATATTTATTATT
1 TTTAATTAAATTTATTATT
1133876 TTTAATTAA
1 TTTAATTAA
1133885 TATTGAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 6 0.26
18 15 0.65
19 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTAATTAAATTTATTATT
Found at i:1133949 original size:19 final size:20
Alignment explanation
Indices: 1133912--1133950 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1133902 CAAATTTTGG
*
1133912 TTGAATTCAAATATTTAAAT
1 TTGAAATCAAATATTTAAAT
1133932 TTGAAATCAAAT-TTTAAAT
1 TTGAAATCAAATATTTAAAT
1133951 AATTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (20 bp):
TTGAAATCAAATATTTAAAT
Found at i:1143798 original size:15 final size:15
Alignment explanation
Indices: 1143778--1143810 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1143768 TTATTCATGT
*
1143778 CTTGTTTGTATTATC
1 CTTGTTTGTATCATC
1143793 CTTGTTTGTATCATC
1 CTTGTTTGTATCATC
1143808 CTT
1 CTT
1143811 CTAATATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.18, G:0.12, T:0.58
Consensus pattern (15 bp):
CTTGTTTGTATCATC
Found at i:1145402 original size:33 final size:33
Alignment explanation
Indices: 1145359--1145464 Score: 176
Period size: 33 Copynumber: 3.2 Consensus size: 33
1145349 TCTAACAGAA
* *
1145359 GAAGGCTCACTTGAACGAAAACTGCTTGACCGT
1 GAAGGTTCACTTGGACGAAAACTGCTTGACCGT
*
1145392 GAAGGTTCACTTGGATGAAAACTGCTTGACCGT
1 GAAGGTTCACTTGGACGAAAACTGCTTGACCGT
*
1145425 GAAGGTTCACTTGGACGAAAACTGCTTGACCAT
1 GAAGGTTCACTTGGACGAAAACTGCTTGACCGT
1145458 GAAGGTT
1 GAAGGTT
1145465 TTGAGTTGCT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 68 1.00
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (33 bp):
GAAGGTTCACTTGGACGAAAACTGCTTGACCGT
Found at i:1151241 original size:20 final size:21
Alignment explanation
Indices: 1151185--1151242 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
1151175 ATTCATATAT
*
1151185 TAATAACGATTGATATCGATAA
1 TAATAACGA-TGTTATCGATAA
*
1151207 TAAAAACGATCGTTATC-ATAA
1 TAATAACGAT-GTTATCGATAA
1151228 -AATAACGACTGTTAT
1 TAATAACGA-TGTTAT
1151243 TTTATGACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 12 0.39
21 6 0.19
22 13 0.42
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (21 bp):
TAATAACGATGTTATCGATAA
Found at i:1156588 original size:33 final size:33
Alignment explanation
Indices: 1156546--1156611 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1156536 TACATAAAGA
*
1156546 ACATAGATGAGCCCATGCACTAGAAATAACATC
1 ACATAGATGAGCCCATGCACTAGAAAGAACATC
*
1156579 ACATAGATGAGCCTATGCACTAGAAAGAACATC
1 ACATAGATGAGCCCATGCACTAGAAAGAACATC
1156612 GATTTGCAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.18
Consensus pattern (33 bp):
ACATAGATGAGCCCATGCACTAGAAAGAACATC
Found at i:1158530 original size:15 final size:17
Alignment explanation
Indices: 1158500--1158544 Score: 58
Period size: 15 Copynumber: 2.7 Consensus size: 17
1158490 TATTATATTT
*
1158500 ATATTTAATAAATTTTTA
1 ATATTT-ATAATTTTTTA
1158518 AT-TTT-TAATTTTTTA
1 ATATTTATAATTTTTTA
1158533 ATATTTATAATT
1 ATATTTATAATT
1158545 GATATTGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 11 0.46
16 3 0.12
17 8 0.33
18 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTTATAATTTTTTA
Found at i:1158563 original size:52 final size:54
Alignment explanation
Indices: 1158456--1158570 Score: 146
Period size: 52 Copynumber: 2.1 Consensus size: 54
1158446 GTATATATTT
* * *
1158456 ATATTTATATTTTAAATTTTTTGAATGATTATATTATTATATTTATATTTAATAA
1 ATATTTA-ATTTTAAATTTTTTGAATGATTATATAATTATATTGATAATTAATAA
* *
1158511 ATTTTTAATTTTTAATTTTTT-AAT-ATT-TATAATTGATATTGATAATTAATAA
1 ATATTTAATTTTAAATTTTTTGAATGATTATATAATT-ATATTGATAATTAATAA
1158563 ATATTTAA
1 ATATTTAA
1158571 ATATAAATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
51 6 0.11
52 25 0.47
53 3 0.06
54 13 0.25
55 6 0.11
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.57
Consensus pattern (54 bp):
ATATTTAATTTTAAATTTTTTGAATGATTATATAATTATATTGATAATTAATAA
Found at i:1159593 original size:30 final size:31
Alignment explanation
Indices: 1159538--1159595 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
1159528 AAATTATAAA
***
1159538 TATTAATATAAAAATAATTTTTAAAAATTTT
1 TATTAATATAAAAATAATAAATAAAAATTTT
1159569 TATTAAT-TAAAAATAATAAATAAAAAT
1 TATTAATATAAAAATAATAAATAAAAAT
1159596 AATATGAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 17 0.71
31 7 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
TATTAATATAAAAATAATAAATAAAAATTTT
Found at i:1160208 original size:22 final size:22
Alignment explanation
Indices: 1160169--1160217 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1160159 AAAAAAAATT
*
1160169 TATATAAAATTAATTATAAAAA
1 TATAAAAAATTAATTATAAAAA
*
1160191 TATAAAAATATTAA-TATAAAAT
1 TATAAAAA-ATTAATTATAAAAA
1160213 TATAA
1 TATAA
1160218 TTATAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TATAAAAAATTAATTATAAAAA
Found at i:1160208 original size:34 final size:35
Alignment explanation
Indices: 1160156--1160223 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 35
1160146 TTATTTATAT
*
1160156 AATAAAAAAAATTTATATAAAA-T-TAATTATAAA
1 AATAAAAAAAATTAATATAAAATTATAATTATAAA
*
1160189 AATATAAAAATATTAATATAAAATTATAATTATAA
1 AATA-AAAAAAATTAATATAAAATTATAATTATAA
1160224 TTTTTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 4 0.13
34 16 0.53
35 1 0.03
36 9 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (35 bp):
AATAAAAAAAATTAATATAAAATTATAATTATAAA
Found at i:1160615 original size:11 final size:11
Alignment explanation
Indices: 1160601--1160629 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1160591 TATGACTCAT
1160601 TTATTTAAAAC
1 TTATTTAAAAC
1160612 TTATTTAAAAC
1 TTATTTAAAAC
1160623 TTATTTA
1 TTATTTA
1160630 TTAATTGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (11 bp):
TTATTTAAAAC
Found at i:1163475 original size:28 final size:26
Alignment explanation
Indices: 1163416--1163476 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
1163406 AAAACAATGG
*
1163416 AAAAG-TTTTCAACAAGGGGGAGTAA
1 AAAAGATTTTCAACAAGGGGGAGAAA
*
1163441 AGAAGATTTTCCAACAAGGGGGAGCAAA
1 AAAAGATTTT-CAACAAGGGGGAG-AAA
1163469 AAAAGATT
1 AAAAGATT
1163477 AAGGCACAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 4 0.13
26 4 0.13
27 13 0.43
28 9 0.30
ACGTcount: A:0.46, C:0.10, G:0.26, T:0.18
Consensus pattern (26 bp):
AAAAGATTTTCAACAAGGGGGAGAAA
Found at i:1168954 original size:15 final size:15
Alignment explanation
Indices: 1168934--1168963 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1168924 ATAATTTATC
1168934 TCACCTAGGAGGCTA
1 TCACCTAGGAGGCTA
1168949 TCACCTAGGAGGCTA
1 TCACCTAGGAGGCTA
1168964 GAACTTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (15 bp):
TCACCTAGGAGGCTA
Found at i:1170126 original size:14 final size:15
Alignment explanation
Indices: 1170087--1170134 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
1170077 TTATATAAAA
1170087 TAAAATTTAGTAAGTATT
1 TAAAATTTA-TAA-T-TT
1170105 TAAAATTTA-AATTT
1 TAAAATTTATAATTT
*
1170119 TAATATTTATAATTT
1 TAAAATTTATAATTT
1170134 T
1 T
1170135 TTTATTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.36
15 7 0.25
16 2 0.07
18 9 0.32
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (15 bp):
TAAAATTTATAATTT
Found at i:1174795 original size:14 final size:14
Alignment explanation
Indices: 1174772--1174824 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
1174762 TATATAATGT
*
1174772 ATATTTAAATATAA
1 ATATTAAAATATAA
1174786 ATATTAAAATATAA
1 ATATTAAAATATAA
* * *
1174800 TTTTTAAAATTTTAA
1 ATATTAAAA-TATAA
1174815 ATATATAAAA
1 ATAT-TAAAA
1174825 ATTTTTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
14 20 0.65
15 6 0.19
16 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATTAAAATATAA
Found at i:1174853 original size:25 final size:26
Alignment explanation
Indices: 1174784--1174845 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 26
1174774 ATTTAAATAT
1174784 AAATATTAAA-ATAT---AATTTTTA
1 AAATATTAAATATATAAAAATTTTTA
*
1174806 AAATTTTAAATATATAAAAATTTTTA
1 AAATATTAAATATATAAAAATTTTTA
1174832 AAA-ATTAAATATAT
1 AAATATTAAATATAT
1174846 TTATATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 9 0.26
23 4 0.12
25 10 0.29
26 11 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AAATATTAAATATATAAAAATTTTTA
Found at i:1175860 original size:27 final size:27
Alignment explanation
Indices: 1175823--1175911 Score: 126
Period size: 26 Copynumber: 3.3 Consensus size: 27
1175813 AAAAGTCACA
*
1175823 TTTTTTATTTGTCAAAAATAATAGTTT
1 TTTTTTATTTGTAAAAAATAATAGTTT
*
1175850 TTTTTTATTTGTAAAAAATAATA-ATT
1 TTTTTTATTTGTAAAAAATAATAGTTT
*
1175876 TTTTTTATTTGTAAAAAATGATAGTTT
1 TTTTTTATTTGTAAAAAATAATAGTTT
*
1175903 GTTGTTTAT
1 -TTTTTTAT
1175912 CAAAATTGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
26 24 0.44
27 24 0.44
28 7 0.13
ACGTcount: A:0.34, C:0.01, G:0.09, T:0.56
Consensus pattern (27 bp):
TTTTTTATTTGTAAAAAATAATAGTTT
Found at i:1180126 original size:28 final size:27
Alignment explanation
Indices: 1180089--1180192 Score: 117
Period size: 28 Copynumber: 4.0 Consensus size: 27
1180079 ACAAAAGCCA
*
1180089 TCTTTTTTGTTTGTCAAAAATGGTGGT
1 TCTTTTTTGTTTGTAAAAAATGGTGGT
* *
1180116 TCCTTTTTTGTTTGTAAAAAATGATAGT
1 T-CTTTTTTGTTTGTAAAAAATGGTGGT
1180144 TC-TTTTTGTTTGTAAAAAATGGTGG-
1 TCTTTTTTGTTTGTAAAAAATGGTGGT
* * *
1180169 -C-TTGTTGTTTGTTAAAATTGGTGG
1 TCTTTTTTGTTTGTAAAAAATGGTGG
1180193 CTAATTTTTA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
24 21 0.31
26 21 0.31
27 2 0.03
28 24 0.35
ACGTcount: A:0.22, C:0.06, G:0.22, T:0.50
Consensus pattern (27 bp):
TCTTTTTTGTTTGTAAAAAATGGTGGT
Found at i:1180176 original size:24 final size:24
Alignment explanation
Indices: 1180092--1180194 Score: 98
Period size: 24 Copynumber: 4.0 Consensus size: 24
1180082 AAAGCCATCT
*
1180092 TTTTTGTTTGTCAAAAATGGTGGTTCC
1 TTTTTGTTTGTAAAAAATGGTGG---C
* *
1180119 TTTTTTGTTTGTAAAAAATGATAGTTC
1 -TTTTTGTTTGTAAAAAATGGT-G-GC
1180146 TTTTTGTTTGTAAAAAATGGTGGC
1 TTTTTGTTTGTAAAAAATGGTGGC
* * *
1180170 TTGTTGTTTGTTAAAATTGGTGGC
1 TTTTTGTTTGTAAAAAATGGTGGC
1180194 T
1 T
1180195 AATTTTTATT
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
24 23 0.35
25 1 0.02
26 20 0.31
27 1 0.02
28 19 0.29
29 1 0.02
ACGTcount: A:0.22, C:0.06, G:0.22, T:0.50
Consensus pattern (24 bp):
TTTTTGTTTGTAAAAAATGGTGGC
Found at i:1185492 original size:16 final size:16
Alignment explanation
Indices: 1185471--1185501 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1185461 TAAAATTATC
1185471 TAAAATATTAAAAAAG
1 TAAAATATTAAAAAAG
1185487 TAAAATATTAAAAAA
1 TAAAATATTAAAAAA
1185502 TATTCTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
TAAAATATTAAAAAAG
Found at i:1186651 original size:148 final size:148
Alignment explanation
Indices: 1186227--1186647 Score: 709
Period size: 148 Copynumber: 2.9 Consensus size: 148
1186217 TTAAAGAAGT
* * ** * *
1186227 CTATGTAATGCTTTAAACATGGTATTTCAAAAGAGACACAGACCATAGATGAAAATATATGCATA
1 CTATGTAATGCTTTAAACATGGTATTTCAAAGGAAACACAGACCACGGACGAAAATATATTCATA
*
1186292 ACCTATGATACAATGAATGAGAAGACTAGAGTAGCTTCAATAAAGAAGACAAGAAAGCCAAGAAT
66 ACCTATGATACAATGAATGATAAGACTAGAGTAGCTTCAATAAAGAAGACAAGAAAGCCAAGAAT
1186357 TAATTCCTTAAAGTATGC
131 TAATTCCTTAAAGTATGC
1186375 CTATGTAATGCTTTAAACATGGTATTTCAAAGGAAACACAGACCACGGACGAAAATATATTCATA
1 CTATGTAATGCTTTAAACATGGTATTTCAAAGGAAACACAGACCACGGACGAAAATATATTCATA
*
1186440 ACCTATGATACAATGAATGATAAGGCTAGAGTAGCTTCAATAAAGAAGACAAGAAAGCCAAGAAT
66 ACCTATGATACAATGAATGATAAGACTAGAGTAGCTTCAATAAAGAAGACAAGAAAGCCAAGAAT
1186505 TAATTCCTTAAAGTATGC
131 TAATTCCTTAAAGTATGC
*
1186523 CTATGTAATGCTTTAAACATGGTATTTCAAAGGAAACAC-GACCACGGGCGAAAATATATTCATA
1 CTATGTAATGCTTTAAACATGGTATTTCAAAGGAAACACAGACCACGGACGAAAATATATTCATA
* ** * *
1186587 ACCTATGATACAATGAATGATAAGACTAGAGTAGCCTCAATGCAGAAAACAAGAGAGCCAA
66 ACCTATGATACAATGAATGATAAGACTAGAGTAGCTTCAATAAAGAAGACAAGAAAGCCAA
1186648 AGAAACTAGT
Statistics
Matches: 258, Mismatches: 15, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
147 79 0.31
148 179 0.69
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (148 bp):
CTATGTAATGCTTTAAACATGGTATTTCAAAGGAAACACAGACCACGGACGAAAATATATTCATA
ACCTATGATACAATGAATGATAAGACTAGAGTAGCTTCAATAAAGAAGACAAGAAAGCCAAGAAT
TAATTCCTTAAAGTATGC
Found at i:1189697 original size:14 final size:13
Alignment explanation
Indices: 1189597--1189698 Score: 56
Period size: 12 Copynumber: 8.2 Consensus size: 13
1189587 TAAATAATTA
1189597 TTTAAATT-TAAT
1 TTTAAATTATAAT
*
1189609 TATAAA-TATTAA-
1 TTTAAATTA-TAAT
* *
1189621 TATAAA-TATATT
1 TTTAAATTATAAT
*
1189633 TTTAATATTATTAT
1 TTTAA-ATTATAAT
* *
1189647 TTTAAATAATAAA
1 TTTAAATTATAAT
1189660 TTT-AATT-TAA-
1 TTTAAATTATAAT
* *
1189670 TTTAAATAAAAATT
1 TTTAAATTATAA-T
1189684 TTTAAATTATAAT
1 TTTAAATTATAAT
1189697 TT
1 TT
1189699 CATCATAAAT
Statistics
Matches: 68, Mismatches: 13, Indels: 17
0.69 0.13 0.17
Matches are distributed among these distances:
10 3 0.04
11 9 0.13
12 22 0.32
13 15 0.22
14 19 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTAAATTATAAT
Found at i:1190446 original size:127 final size:127
Alignment explanation
Indices: 1190220--1190473 Score: 436
Period size: 127 Copynumber: 2.0 Consensus size: 127
1190210 CAAGTTTGAT
* * *
1190220 CTAAAATATAAAATTCAAATTTTGCTCAAATGCATCAATATTTGTAAATAAATAATCAAGCTTGT
1 CTAAAATATAAAATTAAAATTTTACTCAAATGCATCAATATTTATAAATAAATAATCAAGCTTGT
* * *
1190285 TTAAGCTTATTTATATTATATATATTATGTATTTAAAATATATTTTTTCTAAATTTAATCAA
66 TTAAGCTTACTTATATTATAGATACTATGTATTTAAAATATATTTTTTCTAAATTTAATCAA
* *
1190347 CTAAAATATAAGATTAAAATTTTACTCAAATGTATCAATATTTATAAATAAATAATCAAGCTTGT
1 CTAAAATATAAAATTAAAATTTTACTCAAATGCATCAATATTTATAAATAAATAATCAAGCTTGT
1190412 TTAAGCTTACTTATATTATAGATACTATGTATTTAAAATATATTTTTTCTAAATTTAATCAA
66 TTAAGCTTACTTATATTATAGATACTATGTATTTAAAATATATTTTTTCTAAATTTAATCAA
1190474 GAGTAATTTA
Statistics
Matches: 119, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
127 119 1.00
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (127 bp):
CTAAAATATAAAATTAAAATTTTACTCAAATGCATCAATATTTATAAATAAATAATCAAGCTTGT
TTAAGCTTACTTATATTATAGATACTATGTATTTAAAATATATTTTTTCTAAATTTAATCAA
Found at i:1190571 original size:14 final size:14
Alignment explanation
Indices: 1190531--1190587 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
1190521 TTTTTTAATA
*
1190531 TTTATATTATA-AT
1 TTTATATAATATAT
*
1190544 ATTATATATATATAT
1 TTTATATA-ATATAT
*
1190559 TTTATATAATATAA
1 TTTATATAATATAT
*
1190573 ATTATATAATATAT
1 TTTATATAATATAT
1190587 T
1 T
1190588 AACTATAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
13 6 0.17
14 20 0.57
15 9 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTATATAATATAT
Found at i:1190578 original size:25 final size:27
Alignment explanation
Indices: 1190528--1190612 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 27
1190518 TATTTTTTTA
*
1190528 ATATTTATATTATAATATTATATATAT
1 ATATTTATATTATAATATAATATATAT
1190555 ATATTT-TA-TATAATATAA-ATTATAT
1 ATATTTATATTATAATATAATA-TATAT
* *
1190580 AATATATTA-ACTATAAAAATAATATATTAT
1 -ATAT-TTATATTAT-AATATAATATA-TAT
1190610 ATA
1 ATA
1190613 ATAAAAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
24 1 0.02
25 14 0.29
26 6 0.12
27 9 0.19
28 3 0.06
29 11 0.23
30 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATTTATATTATAATATAATATATAT
Found at i:1190715 original size:13 final size:14
Alignment explanation
Indices: 1190699--1190755 Score: 57
Period size: 13 Copynumber: 4.1 Consensus size: 14
1190689 TTTTTTAAAA
1190699 AAATTT-ATTTTTT
1 AAATTTAATTTTTT
1190712 AAATTTAATATTTTT
1 AAATTTAAT-TTTTT
1190727 --ATTTAAATTTTTT
1 AAATTT-AATTTTTT
* *
1190740 AAAATTATTTTTTT
1 AAATTTAATTTTTT
1190754 AA
1 AA
1190756 GTTTTTGTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 15 0.41
14 14 0.38
15 8 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AAATTTAATTTTTT
Found at i:1190740 original size:22 final size:23
Alignment explanation
Indices: 1190715--1190761 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1190705 ATTTTTTAAA
*
1190715 TTTAATATT-TTTATTTAAATTT
1 TTTAAAATTATTTATTTAAATTT
* *
1190737 TTTAAAATTATTTTTTTAAGTTT
1 TTTAAAATTATTTATTTAAATTT
1190760 TT
1 TT
1190762 GTCTAGTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
TTTAAAATTATTTATTTAAATTT
Found at i:1190873 original size:21 final size:21
Alignment explanation
Indices: 1190838--1190878 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1190828 GAACAATAAA
* *
1190838 TAAATGACTTTTAAACAATTT
1 TAAATGACTTATAAAAAATTT
*
1190859 TAAATGAGTTATAAAAAATT
1 TAAATGACTTATAAAAAATT
1190879 CTTTCATCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (21 bp):
TAAATGACTTATAAAAAATTT
Found at i:1191959 original size:6 final size:6
Alignment explanation
Indices: 1191925--1191973 Score: 55
Period size: 6 Copynumber: 7.7 Consensus size: 6
1191915 ATATTTATGG
1191925 TTAAA- TTATAAT TTAAAATT TTAAAAT TTAAAT TTAAAT TTAAAT TTAA
1 TTAAAT TTA-AAT TT-AAA-T TT-AAAT TTAAAT TTAAAT TTAAAT TTAA
1191974 CTTGATTTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
5 3 0.08
6 22 0.55
7 7 0.17
8 8 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
TTAAAT
Found at i:1192088 original size:21 final size:21
Alignment explanation
Indices: 1192022--1192080 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
1192012 TATTAAATTA
1192022 TAAAAAATA-ATTTTTAT-AT
1 TAAAAAATATATTTTTATAAT
**
1192041 TAATATTTATATATTTTTATAAT
1 TAA-A-AAATATATTTTTATAAT
1192064 TAAAAAATAT-TTTTTAT
1 TAAAAAATATATTTTTAT
1192081 TATATAAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
19 3 0.09
20 8 0.25
21 7 0.22
22 9 0.28
23 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TAAAAAATATATTTTTATAAT
Found at i:1199573 original size:11 final size:11
Alignment explanation
Indices: 1199557--1199630 Score: 53
Period size: 11 Copynumber: 6.6 Consensus size: 11
1199547 GTAGAATTAA
1199557 TATTTTATAAT
1 TATTTTATAAT
*
1199568 TATTTTATATT
1 TATTTTATAAT
*
1199579 TATATATT-TTAT
1 TAT-T-TTATAAT
*
1199591 TATATTATAAT
1 TATTTTATAAT
*
1199602 TATATTTA-AAA
1 TAT-TTTATAAT
**
1199613 TATTTTATTTT
1 TATTTTATAAT
1199624 TATTTTA
1 TATTTTA
1199631 ATTTTAATAT
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
10 6 0.12
11 31 0.65
12 9 0.19
13 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTTATAAT
Found at i:1199897 original size:20 final size:21
Alignment explanation
Indices: 1199872--1199942 Score: 74
Period size: 22 Copynumber: 3.4 Consensus size: 21
1199862 GCAATCAGGT
*
1199872 ATATATTTATATATA-AACAC
1 ATATATTTATATATATAACAA
* *
1199892 ATATATATATATATATAATAA
1 ATATATTTATATATATAACAA
*
1199913 AGTATATTTATATGTATATA-AA
1 A-TATATTTATATATATA-ACAA
1199935 ATATATTT
1 ATATATTT
1199943 TATTAAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
20 14 0.33
21 11 0.26
22 17 0.40
23 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (21 bp):
ATATATTTATATATATAACAA
Found at i:1199992 original size:20 final size:19
Alignment explanation
Indices: 1199955--1200049 Score: 56
Period size: 20 Copynumber: 5.1 Consensus size: 19
1199945 TTAAAAAATT
* *
1199955 TTATAATAAATTATAAATAA
1 TTAT-ATAAAATAAAAATAA
1199975 TTATATACAAATAAAAAT-A
1 TTATATA-AAATAAAAATAA
* *
1199994 TTA-ATAAATTTAAAATAA
1 TTATATAAAATAAAAATAA
* * *
1200012 -TATATATTAATATATATCAA
1 TTATATA-AAATAAAAAT-AA
1200032 -TAT-TAAAATAAAAATAA
1 TTATATAAAATAAAAATAA
1200049 T
1 T
1200050 GTATTTATGA
Statistics
Matches: 57, Mismatches: 12, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
17 12 0.21
18 14 0.25
19 14 0.25
20 17 0.30
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
TTATATAAAATAAAAATAA
Found at i:1200012 original size:14 final size:15
Alignment explanation
Indices: 1199995--1200047 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 15
1199985 ATAAAAATAT
1199995 TAATAAAT-TTAAAA
1 TAATAAATATTAAAA
* *
1200009 TAATATATATTAATA
1 TAATAAATATTAAAA
*
1200024 TATATCAATATTAAAA
1 TA-ATAAATATTAAAA
1200040 TAA-AAATA
1 TAATAAATA
1200048 ATGTATTTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
14 11 0.35
15 8 0.26
16 12 0.39
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
TAATAAATATTAAAA
Found at i:1200883 original size:38 final size:38
Alignment explanation
Indices: 1200817--1200949 Score: 185
Period size: 38 Copynumber: 3.5 Consensus size: 38
1200807 TCAAAAAGAG
* * *
1200817 TTCAATTTGGAATTCTCTAGCCACCAGCCACCGGCCAAT
1 TTCAAATT-GAATTCTCTAGCCATCAGCCGCCGGCCAAT
* * * *
1200856 TCCAAATTGAATTCTCTAGTCGTCAGCCGCCGGTCAAT
1 TTCAAATTGAATTCTCTAGCCATCAGCCGCCGGCCAAT
*
1200894 TTCAAATTGAATTCTCTAGCCATCAGCCGCCAGCCAAT
1 TTCAAATTGAATTCTCTAGCCATCAGCCGCCGGCCAAT
1200932 TTCAAATTGAATTCTCTA
1 TTCAAATTGAATTCTCTA
1200950 ACCGTCAACT
Statistics
Matches: 82, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
38 76 0.93
39 6 0.07
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.29
Consensus pattern (38 bp):
TTCAAATTGAATTCTCTAGCCATCAGCCGCCGGCCAAT
Found at i:1206546 original size:29 final size:30
Alignment explanation
Indices: 1206469--1206546 Score: 68
Period size: 29 Copynumber: 2.6 Consensus size: 30
1206459 TTTTTTATTA
* *
1206469 ATTTTAACTAATTTTTTTATCAAAATAATAGT
1 ATTTTAA-TAATTTATTTA-CAAAATAATAAT
* ** * *
1206501 AATTCGATAAATAATTTA-AAAATAATAAT
1 ATTTTAATAATTTATTTACAAAATAATAAT
1206530 ATTTTAATAATTTATTT
1 ATTTTAATAATTTATTT
1206547 TTATTTTAAT
Statistics
Matches: 34, Mismatches: 12, Indels: 3
0.69 0.24 0.06
Matches are distributed among these distances:
29 22 0.65
31 8 0.24
32 4 0.12
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (30 bp):
ATTTTAATAATTTATTTACAAAATAATAAT
Found at i:1208948 original size:25 final size:25
Alignment explanation
Indices: 1208894--1208948 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1208884 TAAAGTAAGT
1208894 AAAATATGGTAAAATATTATATAAA
1 AAAATATGGTAAAATATTATATAAA
* **
1208919 TAAATATTTTAAAAT-TTATATAATA
1 AAAATATGGTAAAATATTATATAA-A
1208944 AAAAT
1 AAAAT
1208949 TATTAATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
AAAATATGGTAAAATATTATATAAA
Found at i:1208954 original size:24 final size:25
Alignment explanation
Indices: 1208903--1208961 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
1208893 TAAAATATGG
*
1208903 TAAAATATTATATAAATAAATATTT
1 TAAAATATTATATAAATAAAAATTT
1208928 TAAAAT-TTATAT-AATAAAAATTAT
1 TAAAATATTATATAAATAAAAATT-T
*
1208952 TAATATATTA
1 TAAAATATTA
1208962 AATTTTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 9 0.30
24 12 0.40
25 9 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TAAAATATTATATAAATAAAAATTT
Done.