Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold258
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: 5730937
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 25
Found at i:5126977 original size:3 final size:3
Alignment explanation
Indices: 5126969--5127001 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
5126959 CATGTATTTA
5126969 TAT TAT TAT TAT TAT TAT TAT ATAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
5127002 ATCATAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5126984 original size:12 final size:13
Alignment explanation
Indices: 5126969--5127073 Score: 76
Period size: 12 Copynumber: 8.2 Consensus size: 13
5126959 CATGTATTTA
5126969 TATTATTAT-TAT
1 TATTATTATATAT
5126981 TATTATTATATAT
1 TATTATTATATAT
5126994 T-TTATTATATCAT
1 TATTATTATAT-AT
* * *
5127007 AATTTTTAAATAT
1 TATTATTATATAT
*
5127020 T-TTATTATATAA
1 TATTATTATATAT
* * *
5127032 TATTATATTTAAAA
1 TATTAT-TATATAT
5127046 TATT-TTATATAT
1 TATTATTATATAT
5127058 TAATT-TTGATATAT
1 T-ATTATT-ATATAT
5127072 TA
1 TA
5127074 ATAATTCATA
Statistics
Matches: 74, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
12 32 0.43
13 19 0.26
14 23 0.31
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (13 bp):
TATTATTATATAT
Found at i:5127076 original size:29 final size:28
Alignment explanation
Indices: 5126963--5127057 Score: 92
Period size: 26 Copynumber: 3.5 Consensus size: 28
5126953 ATAATCCATG
* *
5126963 TATTTATATTAT-TATTATTAT-TATTATA
1 TATTT-TATTATATAATATTATAT-TTAAA
* *
5126991 TATTTTATTATATCATA--ATTTTTAAA
1 TATTTTATTATATAATATTATATTTAAA
5127017 TATTTTATTATATAATATTATATTTAAAA
1 TATTTTATTATATAATATTATATTT-AAA
5127046 TATTTTA-TATAT
1 TATTTTATTATAT
5127058 TAATTTTGAT
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
26 22 0.39
27 7 0.12
28 18 0.32
29 10 0.18
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (28 bp):
TATTTTATTATATAATATTATATTTAAA
Found at i:5130223 original size:1 final size:1
Alignment explanation
Indices: 5130217--5130250 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
5130207 ACTCAAATTC
* *
5130217 TTTTTTTTTTCTCTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5130251 CCATTTTCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:5130233 original size:13 final size:13
Alignment explanation
Indices: 5130215--5130251 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
5130205 ATACTCAAAT
5130215 TCTTTTTTTTTTC
1 TCTTTTTTTTTTC
5130228 TCTTTTTTTTTT-
1 TCTTTTTTTTTTC
5130240 T-TTTTTTTTTTC
1 TCTTTTTTTTTTC
5130252 CATTTTCCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 12 0.52
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (13 bp):
TCTTTTTTTTTTC
Found at i:5139750 original size:3 final size:3
Alignment explanation
Indices: 5139742--5139793 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
5139732 CTTTTTTCTG
5139742 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5139790 TAT T
1 TAT T
5139794 CTTTGGGTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5140336 original size:20 final size:19
Alignment explanation
Indices: 5140308--5140355 Score: 78
Period size: 20 Copynumber: 2.5 Consensus size: 19
5140298 AGTTATTTTA
*
5140308 TAATAAATTAATTTAATTT
1 TAATAAATTAATTAAATTT
5140327 TAATTAAATTAATTAAATTT
1 TAA-TAAATTAATTAAATTT
5140347 TAATAAATT
1 TAATAAATT
5140356 TTAATAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TAATAAATTAATTAAATTT
Found at i:5140363 original size:10 final size:11
Alignment explanation
Indices: 5140315--5140360 Score: 62
Period size: 11 Copynumber: 4.5 Consensus size: 11
5140305 TTATAATAAA
*
5140315 TTAATTTAATT
1 TTAATTAAATT
5140326 TTAATTAAA--
1 TTAATTAAATT
5140335 TTAATTAAATT
1 TTAATTAAATT
5140346 TTAA-TAAATT
1 TTAATTAAATT
5140356 TTAAT
1 TTAAT
5140361 AAAAAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
9 9 0.29
10 10 0.32
11 12 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TTAATTAAATT
Found at i:5141115 original size:18 final size:18
Alignment explanation
Indices: 5141092--5141142 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
5141082 GGAGCCGAAT
5141092 TTTAAATATATATTTTAA
1 TTTAAATATATATTTTAA
5141110 TTTAAAT-TA-ATATTTAA
1 TTTAAATATATAT-TTTAA
*
5141127 TATTAAAAAT-TATTTT
1 T-TTAAATATATATTTT
5141143 TTATTAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
16 2 0.07
17 8 0.29
18 15 0.54
19 3 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTAAATATATATTTTAA
Found at i:5141176 original size:9 final size:10
Alignment explanation
Indices: 5141158--5141186 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
5141148 AATTATAAAT
5141158 AATAAATTTA
1 AATAAATTTA
5141168 AAT-AATTTA
1 AATAAATTTA
5141177 AATAAATTTA
1 AATAAATTTA
5141187 GTTAAAATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AATAAATTTA
Found at i:5141333 original size:21 final size:18
Alignment explanation
Indices: 5141309--5141356 Score: 51
Period size: 21 Copynumber: 2.5 Consensus size: 18
5141299 GTTTAATATT
5141309 TATTAAAATTATTATATATAA
1 TATTAAAATTATT-TA-AT-A
* *
5141330 TATTATATTTATTTAATA
1 TATTAAAATTATTTAATA
5141348 TATTAAAAT
1 TATTAAAAT
5141357 GATAAATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 8 0.35
19 2 0.09
20 2 0.09
21 11 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TATTAAAATTATTTAATA
Found at i:5141690 original size:13 final size:13
Alignment explanation
Indices: 5141672--5141697 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5141662 TATACTATTA
5141672 AATTTAATATTTT
1 AATTTAATATTTT
5141685 AATTTAATATTTT
1 AATTTAATATTTT
5141698 TAAAATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AATTTAATATTTT
Found at i:5141880 original size:17 final size:17
Alignment explanation
Indices: 5141858--5141897 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5141848 AGTATGCAAA
5141858 TAATTTTTTA-ATATTGT
1 TAATTTTTTATATATT-T
*
5141875 TAATTTTTTATTTATTT
1 TAATTTTTTATATATTT
5141892 TAATTT
1 TAATTT
5141898 AAAAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
TAATTTTTTATATATTT
Found at i:5142022 original size:23 final size:23
Alignment explanation
Indices: 5141996--5142053 Score: 91
Period size: 23 Copynumber: 2.5 Consensus size: 23
5141986 TATCAAAAAA
5141996 AATATTATC-ATAATATCTTGTTC
1 AATATT-TCAATAATATCTTGTTC
5142019 AATATTTCAATAATATCTTGTTC
1 AATATTTCAATAATATCTTGTTC
*
5142042 GATATTTCAATA
1 AATATTTCAATA
5142054 TTGTTTGGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
22 2 0.06
23 31 0.94
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (23 bp):
AATATTTCAATAATATCTTGTTC
Found at i:5142792 original size:29 final size:30
Alignment explanation
Indices: 5142753--5142810 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
5142743 TTTTTTTTAT
5142753 TACTTGAAAATAAAAAATTA-TAAATATTAA
1 TACTTGAAAAT-AAAAATTATTAAATATTAA
* *
5142783 TACTT-AAAATTAAATTTATTAAATATTA
1 TACTTGAAAATAAAAATTATTAAATATTA
5142811 TTTTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.24
29 14 0.56
30 5 0.20
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (30 bp):
TACTTGAAAATAAAAATTATTAAATATTAA
Found at i:5143542 original size:20 final size:21
Alignment explanation
Indices: 5143517--5143607 Score: 73
Period size: 20 Copynumber: 4.2 Consensus size: 21
5143507 AAGTTTATAT
5143517 ATAAATATAAAT-TTTAAAAA
1 ATAAATATAAATATTTAAAAA
*
5143537 ATAAATATTTAATATTTAAAAA
1 ATAAATA-TAAATATTTAAAAA
*
5143559 TTTTAAATATAAA-A--TAAATAA
1 --ATAAATATAAATATTTAAA-AA
5143580 AGTAAATATATAATATTTAAAATA
1 A-TAAATATA-AATATTTAAAA-A
5143604 ATAA
1 ATAA
5143608 TAAATTATTA
Statistics
Matches: 56, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
20 19 0.34
21 8 0.14
22 10 0.18
23 7 0.12
24 12 0.21
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (21 bp):
ATAAATATAAATATTTAAAAA
Found at i:5144566 original size:22 final size:23
Alignment explanation
Indices: 5144540--5144587 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
5144530 AAGTGACAGG
5144540 TTTAAT-ATATAAAA-ATAATTTA
1 TTTAATGATATAAAATATAA-TTA
*
5144562 TTTAATGATGTAAAATATAATTA
1 TTTAATGATATAAAATATAATTA
5144585 TTT
1 TTT
5144588 TTTTTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 13 0.57
24 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (23 bp):
TTTAATGATATAAAATATAATTA
Found at i:5144637 original size:14 final size:15
Alignment explanation
Indices: 5144611--5144639 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5144601 ACAGTAATAT
5144611 TTATAATATATTATA
1 TTATAATATATTATA
5144626 TTATAA-ATATTATA
1 TTATAATATATTATA
5144640 AATTTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATAATATATTATA
Found at i:5147607 original size:21 final size:19
Alignment explanation
Indices: 5147582--5147624 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5147572 TCATATATCT
5147582 TTTGAGACTGGTATGCTTTTC
1 TTTGAGA-TGG-ATGCTTTTC
* *
5147603 TTTGATATTGATGCTTTTC
1 TTTGAGATGGATGCTTTTC
5147622 TTT
1 TTT
5147625 AATATTGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.60
20 2 0.10
21 6 0.30
ACGTcount: A:0.14, C:0.12, G:0.19, T:0.56
Consensus pattern (19 bp):
TTTGAGATGGATGCTTTTC
Found at i:5147618 original size:19 final size:19
Alignment explanation
Indices: 5147594--5147632 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5147584 TGAGACTGGT
*
5147594 ATGCTTTTCTTTGATATTG
1 ATGCTTTTCTTTAATATTG
5147613 ATGCTTTTCTTTAATATTG
1 ATGCTTTTCTTTAATATTG
5147632 A
1 A
5147633 CACCTCTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.10, G:0.13, T:0.56
Consensus pattern (19 bp):
ATGCTTTTCTTTAATATTG
Found at i:5148411 original size:3 final size:3
Alignment explanation
Indices: 5148403--5148438 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
5148393 TTAATTAATT
* *
5148403 TAA TAA TAA TAA TAA TGA TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5148439 GAAGCAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:5150125 original size:61 final size:61
Alignment explanation
Indices: 5150059--5150364 Score: 413
Period size: 61 Copynumber: 5.0 Consensus size: 61
5150049 TAAAACTACT
* *
5150059 ATAATATTTCGATTCATTTTTAACTCAACTTACTATCGAATAATTATTTTCACTAAATAAA
1 ATAATATTTCGATTGATTGTTAACTCAACTTACTATCGAATAATTATTTTCACTAAATAAA
* * * *
5150120 ATAATATTTTGATT-AGCTGTTAACTCAACTTACTATTGAATAATTTTTTTCACTAAATAAA
1 ATAATATTTCGATTGA-TTGTTAACTCAACTTACTATCGAATAATTATTTTCACTAAATAAA
* * *
5150181 ATAATATTTTGATTGGTTGTTAACTCAACTTACTATCGAATAATCATTTT-ACTAAATAAA
1 ATAATATTTCGATTGATTGTTAACTCAACTTACTATCGAATAATTATTTTCACTAAATAAA
** * * *
5150241 A-AATATTTCGATTGGCTGTTAACTTAATTTACTATCGAATAATTTTTTTCACTAAATAAA
1 ATAATATTTCGATTGATTGTTAACTCAACTTACTATCGAATAATTATTTTCACTAAATAAA
* * *
5150301 ATAATATTTCAATTGATTGTTAATTTAACTTACTATCGAATAATCT-TTTTCACTAAATAAA
1 ATAATATTTCGATTGATTGTTAACTCAACTTACTATCGAATAAT-TATTTTCACTAAATAAA
5150362 ATA
1 ATA
5150365 TTTAAAATTA
Statistics
Matches: 219, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
59 42 0.19
60 23 0.11
61 153 0.70
62 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (61 bp):
ATAATATTTCGATTGATTGTTAACTCAACTTACTATCGAATAATTATTTTCACTAAATAAA
Found at i:5150296 original size:120 final size:122
Alignment explanation
Indices: 5150059--5150364 Score: 472
Period size: 120 Copynumber: 2.5 Consensus size: 122
5150049 TAAAACTACT
* * *
5150059 ATAATATTTCGATTCATTTTTAACTCAACTTACTATCGAATAATTATTTTCACTAAATAAAATAA
1 ATAATATTTCGATTGATTGTTAACTCAACTTACTATCGAATAATCATTTTCACTAAATAAAATAA
* *
5150124 TATTTTGATTAGCTGTTAACTCAACTTACTATTGAATAATTTTTTTCACTAAATAAA
66 TATTTCGATTAGCTGTTAACTCAACTTACTATCGAATAATTTTTTTCACTAAATAAA
* *
5150181 ATAATATTTTGATTGGTTGTTAACTCAACTTACTATCGAATAATCATTTT-ACTAAATAAAA-AA
1 ATAATATTTCGATTGATTGTTAACTCAACTTACTATCGAATAATCATTTTCACTAAATAAAATAA
* * *
5150244 TATTTCGATTGGCTGTTAACTTAATTTACTATCGAATAATTTTTTTCACTAAATAAA
66 TATTTCGATTAGCTGTTAACTCAACTTACTATCGAATAATTTTTTTCACTAAATAAA
* * * *
5150301 ATAATATTTCAATTGATTGTTAATTTAACTTACTATCGAATAATCTTTTTCACTAAATAAAATA
1 ATAATATTTCGATTGATTGTTAACTCAACTTACTATCGAATAATCATTTTCACTAAATAAAATA
5150365 TTTAAAATTA
Statistics
Matches: 166, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
120 98 0.59
121 22 0.13
122 46 0.28
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (122 bp):
ATAATATTTCGATTGATTGTTAACTCAACTTACTATCGAATAATCATTTTCACTAAATAAAATAA
TATTTCGATTAGCTGTTAACTCAACTTACTATCGAATAATTTTTTTCACTAAATAAA
Found at i:5160242 original size:19 final size:19
Alignment explanation
Indices: 5160206--5160274 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
5160196 TAATTAAAAA
5160206 ATATTTTAATATTAAATAT
1 ATATTTTAATATTAAATAT
*
5160225 ATCATTTTGATA-TAAATAT
1 AT-ATTTTAATATTAAATAT
5160244 ATA-TTTAATA--AAA-AT
1 ATATTTTAATATTAAATAT
* *
5160259 ATTTTTTAATAATAAA
1 ATATTTTAATATTAAA
5160275 ATAATAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
15 4 0.09
16 10 0.23
17 6 0.14
18 4 0.09
19 11 0.26
20 8 0.19
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (19 bp):
ATATTTTAATATTAAATAT
Found at i:5160416 original size:18 final size:18
Alignment explanation
Indices: 5160370--5160416 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
5160360 AAATAAACAT
*
5160370 TATATATT-TAAACTTAA
1 TATATATTATATACTTAA
*
5160387 T-TAATATAATATACTTAA
1 TAT-ATATTATATACTTAA
5160405 TATATATTATAT
1 TATATATTATAT
5160417 TTTTATGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
16 1 0.04
17 5 0.21
18 17 0.71
19 1 0.04
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (18 bp):
TATATATTATATACTTAA
Found at i:5164631 original size:15 final size:16
Alignment explanation
Indices: 5164611--5164640 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5164601 AATTATCACA
5164611 TAAATAAAA-TAAATT
1 TAAATAAAATTAAATT
5164626 TAAATAAAATTAAAT
1 TAAATAAAATTAAAT
5164641 CAAATCCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAATAAAATTAAATT
Found at i:5165642 original size:19 final size:19
Alignment explanation
Indices: 5165616--5165662 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
5165606 GTATTACTAA
5165616 TAAA-TTAACAATATTTAT
1 TAAATTTAACAATATTTAT
* * *
5165634 TATATTTAAACATTTTTTAT
1 TAAATTT-AACAATATTTAT
5165654 TAAATTTAA
1 TAAATTTAA
5165663 TGCGATGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 3 0.13
19 4 0.17
20 16 0.70
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
TAAATTTAACAATATTTAT
Found at i:5165645 original size:20 final size:20
Alignment explanation
Indices: 5165622--5165662 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5165612 CTAATAAATT
*
5165622 AACAATATTTATTATATTTA
1 AACAATATTTATTAAATTTA
* *
5165642 AACATTTTTTATTAAATTTA
1 AACAATATTTATTAAATTTA
5165662 A
1 A
5165663 TGCGATGAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
AACAATATTTATTAAATTTA
Found at i:5169239 original size:157 final size:157
Alignment explanation
Indices: 5168953--5169250 Score: 485
Period size: 157 Copynumber: 1.9 Consensus size: 157
5168943 ATGCATTTTA
* *
5168953 TGCTTTCTTTGTGATATATTGCATTGATGAATGTTGGTGACATCTTTATATTTCATCAAGTTTTC
1 TGCTTTCATTGTGATATATTGCATTGATGAATATTGGTGACATCTTTATATTTCATCAAGTTTTC
*
5169018 AAATTTTACTGATAAAAGAAGGCAATTGTCCCAAATGGTGCATCCAGACAAGTATAAGAAATATA
66 AAATTTTACTGATAAAAGAAGGCAATTGCCCCAAATGGTGCATCCAGACAAGTATAAGAAATATA
5169083 TTGATTGCTGTGGAATGGACGCGTATT
131 TTGATTGCTGTGGAATGGACGCGTATT
* *
5169110 TGCTTTCATTGTGGTATATTGCATTTATGAATATTGGTGACATCTTTATATTTCATCATA-TTTT
1 TGCTTTCATTGTGATATATTGCATTGATGAATATTGGTGACATCTTTATATTTCATCA-AGTTTT
* *
5169174 CAAATTTTACTGATAAAAGGAGGCAATTGCCCCAAATGGTGCTTCCAGAC-A-TATACAGGAAAT
65 CAAATTTTACTGATAAAAGAAGGCAATTGCCCCAAATGGTGCATCCAGACAAGTATA-A-GAAAT
5169237 ATATTGATTGCTGT
128 ATATTGATTGCTGT
5169251 AAACCCATTC
Statistics
Matches: 131, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
155 4 0.03
156 2 0.02
157 124 0.95
158 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.38
Consensus pattern (157 bp):
TGCTTTCATTGTGATATATTGCATTGATGAATATTGGTGACATCTTTATATTTCATCAAGTTTTC
AAATTTTACTGATAAAAGAAGGCAATTGCCCCAAATGGTGCATCCAGACAAGTATAAGAAATATA
TTGATTGCTGTGGAATGGACGCGTATT
Found at i:5176856 original size:90 final size:92
Alignment explanation
Indices: 5176703--5176887 Score: 295
Period size: 90 Copynumber: 2.0 Consensus size: 92
5176693 TTATGCCTAC
* * * *
5176703 TGGCAATAACACTGAGGAGGGAGGTTGCACTCAACTCTTTTCTGTTATGTCTGTCAAATGATCTA
1 TGGCAATAACACTGAGAAGGGAGATTCCACTCAACTCTTTTCTGTTATGTCTGTCAAAAGATCTA
5176768 TTTAGTGTTGACCTTAAC-TT-GTTAA
66 TTTAGTGTTGACCTTAACTTTAGTTAA
5176793 TGGCAATAACACTGAGAAGGGAGATTCCACTCAACTCTTGTT-TGTTATGTCTGTCAAAAGATCT
1 TGGCAATAACACTGAGAAGGGAGATTCCACTCAACTCTT-TTCTGTTATGTCTGTCAAAAGATCT
*
5176857 ATTTGGTGTTGACCTTAACTTTAGTTAA
65 ATTTAGTGTTGACCTTAACTTTAGTTAA
5176885 TGG
1 TGG
5176888 GTAAAGTCTC
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
90 75 0.86
91 4 0.05
92 8 0.09
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (92 bp):
TGGCAATAACACTGAGAAGGGAGATTCCACTCAACTCTTTTCTGTTATGTCTGTCAAAAGATCTA
TTTAGTGTTGACCTTAACTTTAGTTAA
Found at i:5183083 original size:2 final size:2
Alignment explanation
Indices: 5183071--5183101 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5183061 CCTGTAAGTC
*
5183071 CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
5183102 CTCACCAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:5183649 original size:51 final size:51
Alignment explanation
Indices: 5183573--5183676 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
5183563 CGTCTAACTA
5183573 GACTGTTAGAAACTAAATATAATTAAATATCAAAGGCCGTAATAGCTGGCT
1 GACTGTTAGAAACTAAATATAATTAAATATCAAAGGCCGTAATAGCTGGCT
5183624 GACTGTTAGAAACTAAATATAATTAAATATCAAAGGCCGTAATAGCTGGCT
1 GACTGTTAGAAACTAAATATAATTAAATATCAAAGGCCGTAATAGCTGGCT
5183675 GA
1 GA
5183677 ATGATTTTTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.27
Consensus pattern (51 bp):
GACTGTTAGAAACTAAATATAATTAAATATCAAAGGCCGTAATAGCTGGCT
Found at i:5186016 original size:3 final size:3
Alignment explanation
Indices: 5186008--5186062 Score: 65
Period size: 3 Copynumber: 18.3 Consensus size: 3
5185998 TAAGGTTTAC
* * * *
5186008 ATT ATT ATT ATT ATT GTT ATT GTT ATT GTT ATT ATT ATT ATT ATT TTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
5186056 TTT ATT A
1 ATT ATT A
5186063 AATAAAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:5186734 original size:17 final size:16
Alignment explanation
Indices: 5186712--5186755 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
5186702 CAAGTATTCG
*
5186712 AATCAAATTTTATTTTT
1 AATCAAATTTT-TTTAT
5186729 AATCAATATTTTTTTAT
1 AATCAA-ATTTTTTTAT
5186746 AATACAAATT
1 AAT-CAAATT
5186756 AAAATATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (16 bp):
AATCAAATTTTTTTAT
Found at i:5188499 original size:3 final size:3
Alignment explanation
Indices: 5188453--5188489 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5188443 AGTCTCTTAT
5188453 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5188490 TTTTAATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5189270 original size:18 final size:18
Alignment explanation
Indices: 5189247--5189282 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5189237 AGAAAAAGAA
5189247 AGAAAATTACATTAATGC
1 AGAAAATTACATTAATGC
5189265 AGAAAATTACATTAATGC
1 AGAAAATTACATTAATGC
5189283 GTTAGGCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (18 bp):
AGAAAATTACATTAATGC
Found at i:5189700 original size:2 final size:2
Alignment explanation
Indices: 5189693--5189729 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5189683 TGCTTGGGGT
5189693 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5189730 TTTAGAAACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5191191 original size:12 final size:12
Alignment explanation
Indices: 5191161--5191194 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5191151 GTTTTTTACC
*
5191161 ATATATATATAT
1 ATATATGTATAT
5191173 ATATATGTATAT
1 ATATATGTATAT
*
5191185 GTATATGTAT
1 ATATATGTAT
5191195 GGTGTCGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (12 bp):
ATATATGTATAT
Found at i:5192655 original size:2 final size:2
Alignment explanation
Indices: 5192648--5192703 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
5192638 CATGGAACAT
5192648 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5192690 GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA
5192704 TAACAAGTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5193071 original size:21 final size:23
Alignment explanation
Indices: 5193045--5193086 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
5193035 TTATTTAATA
5193045 AAAAAATTAT-AAT-TTAAAAAT
1 AAAAAATTATAAATATTAAAAAT
5193066 AAAAAATTATAAATATTAAAA
1 AAAAAATTATAAATATTAAAA
5193087 TTTAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
22 3 0.16
23 6 0.32
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAAAATTATAAATATTAAAAAT
Found at i:5194102 original size:14 final size:14
Alignment explanation
Indices: 5194080--5194110 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5194070 TGATTTTACT
*
5194080 ATTATATTATAAAA
1 ATTAAATTATAAAA
5194094 ATTAAATTATAAAA
1 ATTAAATTATAAAA
5194108 ATT
1 ATT
5194111 TTATTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATTAAATTATAAAA
Found at i:5195840 original size:34 final size:34
Alignment explanation
Indices: 5195800--5195912 Score: 136
Period size: 34 Copynumber: 3.3 Consensus size: 34
5195790 AGAATATTTA
*
5195800 TTGATTAAATGGGTGATTTGATGGTTTGTTATTG
1 TTGATTAAATGAGTGATTTGATGGTTTGTTATTG
* * * *
5195834 TTGATTAAATGAATGATTTGATAGTTTATTATTA
1 TTGATTAAATGAGTGATTTGATGGTTTGTTATTG
* * *
5195868 TTGATTAAACGAGTAATTTGATGGTTTGTCATTG
1 TTGATTAAATGAGTGATTTGATGGTTTGTTATTG
* *
5195902 TTAACTAAATG
1 TTGATTAAATG
5195913 GTTAAAAGAT
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (34 bp):
TTGATTAAATGAGTGATTTGATGGTTTGTTATTG
Found at i:5196272 original size:2 final size:2
Alignment explanation
Indices: 5196267--5196291 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5196257 AAAAAAGTTT
5196267 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 T
5196292 TGTTTGGCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5196504 original size:17 final size:18
Alignment explanation
Indices: 5196451--5196506 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 18
5196441 ATAAATATAA
*
5196451 AATATATTAATCACAATTAT
1 AATATATT-A-CACAAATAT
*
5196471 AATATATTA-AAATAATAT
1 AATATATTACACA-AATAT
5196489 AA-ATATTACACAAATAT
1 AATATATTACACAAATAT
5196506 A
1 A
5196507 TAATTTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 14 0.45
18 8 0.26
19 1 0.03
20 8 0.26
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (18 bp):
AATATATTACACAAATAT
Found at i:5200109 original size:13 final size:15
Alignment explanation
Indices: 5200076--5200112 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
5200066 TTACACTCAT
5200076 ATATATTCAATATAA
1 ATATATTCAATATAA
5200091 ATATATTCAATATAA
1 ATATATTCAATATAA
5200106 ATATATT
1 ATATATT
5200113 TAATTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATATTCAATATAA
Found at i:5200447 original size:11 final size:11
Alignment explanation
Indices: 5200431--5200456 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5200421 CAGCCAATTC
5200431 TTTTTTTCTTT
1 TTTTTTTCTTT
5200442 TTTTTTTCTTT
1 TTTTTTTCTTT
5200453 TTTT
1 TTTT
5200457 CCAAAGCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:5204342 original size:45 final size:45
Alignment explanation
Indices: 5204272--5204401 Score: 151
Period size: 45 Copynumber: 2.9 Consensus size: 45
5204262 TCTAATTAGG
* * * *
5204272 TTTTAATTGAGTTTGA--ATAAGTTTATATAAATTTTTA-TATGAA
1 TTTTAATTAAGTTTGAGTTTAACTTTATATAGATTTTTAGT-TGAA
* *
5204315 TTTTAATTAGGTTT-AGGTTTAACTTTATATAGATTTTTAGTTGGA
1 TTTTAATTAAGTTTGA-GTTTAACTTTATATAGATTTTTAGTTGAA
*
5204360 TTTTAATTAAGTTTGAGTTTAAGTTTATATAGATTTTTAGTT
1 TTTTAATTAAGTTTGAGTTTAACTTTATATAGATTTTTAGTT
5204402 TGTATTAAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
42 1 0.01
43 12 0.16
45 59 0.80
46 2 0.03
ACGTcount: A:0.31, C:0.01, G:0.15, T:0.54
Consensus pattern (45 bp):
TTTTAATTAAGTTTGAGTTTAACTTTATATAGATTTTTAGTTGAA
Found at i:5204426 original size:45 final size:45
Alignment explanation
Indices: 5204289--5204431 Score: 128
Period size: 45 Copynumber: 3.2 Consensus size: 45
5204279 TGAGTTTGAA
* * * * * * *
5204289 TAAGTTTATATAAATTTTTA-TATGAATTTTAATTAGGTTTAGGTT
1 TAAGTTTATATAGATTTTTAGT-TGGATATTAAATAAGCTTAAGTT
* * * * *
5204334 TAACTTTATATAGATTTTTAGTTGGATTTTAATTAAGTTTGAGTT
1 TAAGTTTATATAGATTTTTAGTTGGATATTAAATAAGCTTAAGTT
* *
5204379 TAAGTTTATATAGATTTTTAGTTTG-TATTAAATAAGCTTAACTTT
1 TAAGTTTATATAGATTTTTAGTTGGATATTAAATAAGCTTAA-GTT
5204424 TAAGTTTA
1 TAAGTTTA
5204432 ATTTATATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
44 12 0.14
45 70 0.84
46 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.52
Consensus pattern (45 bp):
TAAGTTTATATAGATTTTTAGTTGGATATTAAATAAGCTTAAGTT
Found at i:5204674 original size:25 final size:25
Alignment explanation
Indices: 5204640--5204705 Score: 79
Period size: 20 Copynumber: 2.8 Consensus size: 25
5204630 ACCCTCCCGA
5204640 CCTAATACTTTCCATTATTTTAATC
1 CCTAATACTTTCCATTATTTTAATC
* *
5204665 CCTAATAC--T---TTACTTCAATC
1 CCTAATACTTTCCATTATTTTAATC
5204685 CCTAATACTTTCCATTATTTT
1 CCTAATACTTTCCATTATTTT
5204706 TTTCTTTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 1 0.03
25 13 0.41
ACGTcount: A:0.27, C:0.26, G:0.00, T:0.47
Consensus pattern (25 bp):
CCTAATACTTTCCATTATTTTAATC
Found at i:5205294 original size:29 final size:28
Alignment explanation
Indices: 5205239--5205294 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
5205229 TAAAAGACTA
*
5205239 ACGTACAATAAAAATTAAAAATTTATTT
1 ACGTACAATAAAAATTAAAAACTTATTT
* *
5205267 ACGTATAATAAAAATATAGAAACTTATT
1 ACGTACAATAAAAAT-TAAAAACTTATT
5205295 ATTAGTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (28 bp):
ACGTACAATAAAAATTAAAAACTTATTT
Found at i:5207091 original size:2 final size:2
Alignment explanation
Indices: 5207086--5207125 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5207076 AAAAAGTGTG
*
5207086 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5207126 CAGAGAGCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5220142 original size:25 final size:24
Alignment explanation
Indices: 5220100--5220150 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
5220090 CGTGAAAATA
**
5220100 ATTTTTTAATTAAATAAT-TTATTT
1 ATTTTTTAAAAAAATAATATT-TTT
5220124 ATTTTTTAAAAAAATTAATATTTTT
1 ATTTTTTAAAAAAA-TAATATTTTT
5220149 AT
1 AT
5220151 GTTATCTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 12 0.52
25 9 0.39
26 2 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTTTTTAAAAAAATAATATTTTT
Found at i:5220425 original size:2 final size:2
Alignment explanation
Indices: 5220420--5220455 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5220410 ATATATATAT
5220420 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5220456 GGAGGGAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5221174 original size:2 final size:2
Alignment explanation
Indices: 5221155--5221192 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
5221145 CCCTGCGGTC
* *
5221155 CT CT CG CT CT CG CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5221193 TCCGTAATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.05, T:0.45
Consensus pattern (2 bp):
CT
Found at i:5227557 original size:2 final size:2
Alignment explanation
Indices: 5227550--5227574 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5227540 ATACTAGCAC
5227550 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 A
5227575 GTTCCCAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5230268 original size:6 final size:6
Alignment explanation
Indices: 5230254--5230288 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
5230244 CTCACTTAAA
*
5230254 ACATCT ACATGT ACATGT ACATGT ACATGT ACATG
1 ACATGT ACATGT ACATGT ACATGT ACATGT ACATG
5230289 ATGTAGATCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (6 bp):
ACATGT
Found at i:5233193 original size:47 final size:49
Alignment explanation
Indices: 5233119--5233214 Score: 169
Period size: 47 Copynumber: 2.0 Consensus size: 49
5233109 AAAAGAGTAT
*
5233119 ACGAGCCTGAAACAATGAAGAAAAGCATCAACTT-A-ACACTCATGTGA
1 ACGACCCTGAAACAATGAAGAAAAGCATCAACTTAACACACTCATGTGA
5233166 ACGACCCTGAAACAATGAAGAAAAGCATCAACTTAACACACTCATGTGA
1 ACGACCCTGAAACAATGAAGAAAAGCATCAACTTAACACACTCATGTGA
5233215 GCATTTCCAA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 33 0.72
48 1 0.02
49 12 0.26
ACGTcount: A:0.45, C:0.23, G:0.16, T:0.17
Consensus pattern (49 bp):
ACGACCCTGAAACAATGAAGAAAAGCATCAACTTAACACACTCATGTGA
Found at i:5245309 original size:29 final size:30
Alignment explanation
Indices: 5245250--5245313 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
5245240 AACTTGTACA
* * *
5245250 TAAATAAATTATTAATTTTTATTTTATATT
1 TAAATAAATTATTAACTTTTAATTTAGATT
5245280 TAAATAAATTA-TAACTTTTAATTTAGATT
1 TAAATAAATTATTAACTTTTAATTTAGATT
5245309 TAAAT
1 TAAAT
5245314 TATTTTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (30 bp):
TAAATAAATTATTAACTTTTAATTTAGATT
Found at i:5253201 original size:18 final size:17
Alignment explanation
Indices: 5253175--5253208 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5253165 TATTAACAAA
5253175 ATTAATAAAATAATATAT
1 ATTAATAAAAT-ATATAT
*
5253193 ATTATTAAAATATATA
1 ATTAATAAAATATATA
5253209 AAAAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAATAAAATATATAT
Found at i:5254581 original size:18 final size:20
Alignment explanation
Indices: 5254554--5254599 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
5254544 ATTAAGTTTT
*
5254554 ATATAATAAAA-AT-TATAA
1 ATATATTAAAATATATATAA
*
5254572 ATATATTAAAATTTATATAA
1 ATATATTAAAATATATATAA
5254592 ATATATTA
1 ATATATTA
5254600 TATTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 10 0.42
19 1 0.04
20 13 0.54
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATATTAAAATATATATAA
Found at i:5254608 original size:44 final size:43
Alignment explanation
Indices: 5254514--5254602 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 43
5254504 CATAATCAAA
*
5254514 ATAA-AAAAATTAAAATATAATAAAATATATATTAAGTTTTAT
1 ATAATAAAAATTAAAATATAATAAAATATATATTAAATTTTAT
* *
5254556 ATAATAAAAATTATAAATATATTAAAATTTATA-TAAATATATTAT
1 ATAATAAAAATTA-AAATATAATAAAATATATATTAAAT-T-TTAT
5254601 AT
1 AT
5254603 TTAAAATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
42 4 0.10
43 12 0.30
44 18 0.45
45 6 0.15
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (43 bp):
ATAATAAAAATTAAAATATAATAAAATATATATTAAATTTTAT
Found at i:5254641 original size:17 final size:18
Alignment explanation
Indices: 5254604--5254637 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
5254594 ATATTATATT
5254604 TAAAATATAATTATAAAA
1 TAAAATATAATTATAAAA
5254622 TAAAA-ATAA-TATAAAA
1 TAAAATATAATTATAAAA
5254638 ATAATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAATATAATTATAAAA
Found at i:5255433 original size:6 final size:5
Alignment explanation
Indices: 5255410--5255444 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
5255400 TAGAGTTAAC
* *
5255410 TAAAT TAAAT TTAAT AAAAT TAAAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT
5255445 ACTATAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:5255498 original size:16 final size:17
Alignment explanation
Indices: 5255458--5255504 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
5255448 ATAATTTGAA
*
5255458 TTAATTT-TTAATATTTT
1 TTAATTTATTCATA-TTT
5255475 TTAATTTA-TCATATTT
1 TTAATTTATTCATATTT
*
5255491 TTATTTTATTCATA
1 TTAATTTATTCATA
5255505 AAATTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (17 bp):
TTAATTTATTCATATTT
Found at i:5256876 original size:15 final size:16
Alignment explanation
Indices: 5256856--5256906 Score: 72
Period size: 15 Copynumber: 3.4 Consensus size: 16
5256846 GTTTTTATAT
5256856 TTATATTAT-TTTTTA
1 TTATATTATATTTTTA
*
5256871 TTATATTATATTTTAA
1 TTATATTATATTTTTA
5256887 TTA-ATT-TATTTTTA
1 TTATATTATATTTTTA
5256901 TTATAT
1 TTATAT
5256907 AATCATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 10 0.31
15 14 0.44
16 8 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATATTATATTTTTA
Found at i:5257461 original size:21 final size:21
Alignment explanation
Indices: 5257437--5257479 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5257427 TTTTTGTTTT
5257437 TATACAAA-ATACATAAAAATA
1 TATACAAATATA-ATAAAAATA
* *
5257458 TATATAAATATAATATAAATA
1 TATACAAATATAATAAAAATA
5257479 T
1 T
5257480 TTTAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
TATACAAATATAATAAAAATA
Found at i:5257487 original size:31 final size:33
Alignment explanation
Indices: 5257443--5257530 Score: 83
Period size: 31 Copynumber: 2.8 Consensus size: 33
5257433 TTTTTATACA
* *
5257443 AAATACATAAAAATATATATAAATA-TAA-TAT
1 AAATATATCAAAATATATATAAATATTAATTAT
* * *
5257474 AAATATTTTAAAATTTATAT-AATATTAATTAT
1 AAATATATCAAAATATATATAAATATTAATTAT
* * *
5257506 TAATGTATCAAATTATATATAAATA
1 AAATATATCAAAATATATATAAATA
5257531 AAAAATATCT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
30 4 0.09
31 19 0.43
32 17 0.39
33 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (33 bp):
AAATATATCAAAATATATATAAATATTAATTAT
Found at i:5257568 original size:19 final size:19
Alignment explanation
Indices: 5257544--5257596 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
5257534 AATATCTTGA
*
5257544 ATATAAGATATAATA-AAAT
1 ATATAA-ATATAAAATAAAT
5257563 ATATAAATATAAAATAAAT
1 ATATAAATATAAAATAAAT
*
5257582 ATATAAATATCAAAT
1 ATATAAATATAAAAT
5257597 CTAATCACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.23
19 24 0.77
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (19 bp):
ATATAAATATAAAATAAAT
Found at i:5258108 original size:24 final size:24
Alignment explanation
Indices: 5258056--5258108 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
5258046 TATTCAAATC
5258056 AAATT-AAAATAATAATTTTAAAG
1 AAATTAAAAATAATAATTTTAAAG
* *
5258079 ATATTAAAAATACTTAATTTTAAA-
1 AAATTAAAAATA-ATAATTTTAAAG
5258103 AAATTA
1 AAATTA
5258109 TTCACTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 4 0.16
24 11 0.44
25 10 0.40
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATTAAAAATAATAATTTTAAAG
Found at i:5258889 original size:18 final size:18
Alignment explanation
Indices: 5258833--5258893 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
5258823 TTTGGTCCTC
5258833 AATTTTTAAAATTAAA-AA
1 AATTTTTAAAA-TAAATAA
*
5258851 TAATTTTTTAAAA-ATATTAA
1 -AA-TTTTTAAAATA-AATAA
5258871 AATTTTTAAAATAAATAA
1 AATTTTTAAAATAAATAA
5258889 AATTT
1 AATTT
5258894 ACATATAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
18 19 0.53
19 6 0.17
20 11 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTTTTAAAATAAATAA
Found at i:5259748 original size:18 final size:18
Alignment explanation
Indices: 5259713--5259749 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5259703 TAACACTTGC
**
5259713 TTTTTTTTGTTTTTAATT
1 TTTTTTTTGTTTAGAATT
5259731 TTTTTTTTGTTTAGAATT
1 TTTTTTTTGTTTAGAATT
5259749 T
1 T
5259750 CCGGTGAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (18 bp):
TTTTTTTTGTTTAGAATT
Found at i:5261521 original size:19 final size:19
Alignment explanation
Indices: 5261497--5261534 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5261487 ATTTAAATAT
*
5261497 TTTATT-TATATTATTTTTA
1 TTTATTATA-ATTATATTTA
5261516 TTTATTATAATTATATTTA
1 TTTATTATAATTATATTTA
5261535 AAATATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATTATAATTATATTTA
Found at i:5261606 original size:27 final size:25
Alignment explanation
Indices: 5261574--5261635 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 25
5261564 ATATCAATAA
5261574 TTTATATTAAG-TAAATTTTGATATAT
1 TTTATATTAAGTTAAA-TTT-ATATAT
*
5261600 TTATATATTTATGTTAAATTTATATAT
1 TT-TATA-TTAAGTTAAATTTATATAT
5261627 TTTATATTA
1 TTTATATTA
5261636 TATTTTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
25 3 0.09
26 6 0.19
27 12 0.38
28 7 0.22
29 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (25 bp):
TTTATATTAAGTTAAATTTATATAT
Found at i:5263298 original size:6 final size:6
Alignment explanation
Indices: 5263257--5263298 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
5263247 CATGCCACCA
* *
5263257 ATGGGA ATGGGA ATTGGG- ATGGGC ATGGGC ATGGGC ATGGGC
1 ATGGGC ATGGGC A-TGGGC ATGGGC ATGGGC ATGGGC ATGGGC
5263299 GTGGATATGG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 4 0.12
6 26 0.76
7 4 0.12
ACGTcount: A:0.21, C:0.10, G:0.50, T:0.19
Consensus pattern (6 bp):
ATGGGC
Found at i:5264360 original size:115 final size:115
Alignment explanation
Indices: 5264158--5264388 Score: 428
Period size: 115 Copynumber: 2.0 Consensus size: 115
5264148 ATAGTAGATG
5264158 CCATGGCTGCTCCAATCATTTCATATGATTAGCATCTCCATGGCATGTATGGACTCGAGCATCTG
1 CCATGGCTGCTCCAATCATTTCATATGATTAGCATCTCCATGGCATGTATGGACTCGAGCATCTG
5264223 ACATGAAAAAAAGAACCTGGCTTTCAAAACCCAAGTATTCTTTGCTTCCA
66 ACATGAAAAAAAGAACCTGGCTTTCAAAACCCAAGTATTCTTTGCTTCCA
*
5264273 CCATGGCT-CATCCAATCATTTCATATGATTAGCATCTCCGTGGCATGTATGGACTCGAGCATCT
1 CCATGGCTGC-TCCAATCATTTCATATGATTAGCATCTCCATGGCATGTATGGACTCGAGCATCT
*
5264337 GACATGAAAAAAAGAACCTGGCTTTCAAAACCTAAGTATTCTTTGCTTCCA
65 GACATGAAAAAAAGAACCTGGCTTTCAAAACCCAAGTATTCTTTGCTTCCA
5264388 C
1 C
5264389 TTTGACGGAC
Statistics
Matches: 113, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
114 1 0.01
115 112 0.99
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (115 bp):
CCATGGCTGCTCCAATCATTTCATATGATTAGCATCTCCATGGCATGTATGGACTCGAGCATCTG
ACATGAAAAAAAGAACCTGGCTTTCAAAACCCAAGTATTCTTTGCTTCCA
Found at i:5271292 original size:2 final size:2
Alignment explanation
Indices: 5271285--5271326 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5271275 TACAAATACA
5271285 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5271327 TCCATCATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5271506 original size:69 final size:69
Alignment explanation
Indices: 5271423--5271561 Score: 253
Period size: 69 Copynumber: 2.0 Consensus size: 69
5271413 TTGATTCGAA
*
5271423 ACTCTTACAG-TTTTTTTATTATAAAAAAATACCTCATAAATATGAGTTTGAATAAATAAATATA
1 ACTCTTACAGTTTTTTTTATTAT-AAAAAATACCCCATAAATATGAGTTTGAATAAATAAATATA
5271487 TATCC
65 TATCC
5271492 ACTCTTACAGTTTTTTTTATTATAAAAAATACCCCATAAATATGAGTTTGAATAAATAAATATAT
1 ACTCTTACAGTTTTTTTTATTATAAAAAATACCCCATAAATATGAGTTTGAATAAATAAATATAT
5271557 ATCC
66 ATCC
5271561 A
1 A
5271562 TACATAAATA
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
69 56 0.82
70 12 0.18
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (69 bp):
ACTCTTACAGTTTTTTTTATTATAAAAAATACCCCATAAATATGAGTTTGAATAAATAAATATAT
ATCC
Found at i:5271576 original size:69 final size:70
Alignment explanation
Indices: 5271433--5271579 Score: 228
Period size: 69 Copynumber: 2.1 Consensus size: 70
5271423 ACTCTTACAG
* *
5271433 TTTTTTTATTATAAAAAAATACCTCATAAATATGAGTTTGAATAAATAAATATATATCCACTCTT
1 TTTTTTTATTATAAAAAAATACCCCATAAATATGAGTTTGAATAAATAAATATATATCCACTCAT
*
5271498 ACAGT
66 ACAAT
5271503 TTTTTTTATTAT-AAAAAATACCCCATAAATATGAGTTTGAATAAATAAATATATATCCA-TACA
1 TTTTTTTATTATAAAAAAATACCCCATAAATATGAGTTTGAATAAATAAATATATATCCACT-CA
5271566 TA-AAT
65 TACAAT
*
5271571 ATTTTTTAT
1 TTTTTTTAT
5271580 ATATTTTATA
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
68 11 0.15
69 49 0.68
70 12 0.17
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (70 bp):
TTTTTTTATTATAAAAAAATACCCCATAAATATGAGTTTGAATAAATAAATATATATCCACTCAT
ACAAT
Found at i:5271582 original size:2 final size:2
Alignment explanation
Indices: 5271577--5271635 Score: 93
Period size: 2 Copynumber: 30.0 Consensus size: 2
5271567 AAATATTTTT
* *
5271577 TA TA TA T- TT TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5271618 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
5271636 AAATAACCGA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:5272297 original size:3 final size:3
Alignment explanation
Indices: 5272291--5272316 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5272281 ATGATGATGA
5272291 TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TG
5272317 ATGATGACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:5273461 original size:19 final size:20
Alignment explanation
Indices: 5273426--5273463 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5273416 ATTTTAATTT
*
5273426 TTTATTAATTTATAAATATA
1 TTTATTAATTTAAAAATATA
5273446 TTTATT-ATTTAAAAATAT
1 TTTATTAATTTAAAAATAT
5273464 TAAAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTATTAATTTAAAAATATA
Found at i:5273504 original size:18 final size:18
Alignment explanation
Indices: 5273462--5273504 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
5273452 ATTTAAAAAT
*
5273462 ATTAAAATATTATTTTTT
1 ATTAAAATATTATTTTTA
5273480 ATATAAAAT-TATATTTTTA
1 AT-TAAAATAT-TATTTTTA
5273499 ATTAAA
1 ATTAAA
5273505 TTTTAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTAAAATATTATTTTTA
Found at i:5275375 original size:27 final size:26
Alignment explanation
Indices: 5275313--5275381 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 26
5275303 TGAAGATTTT
*
5275313 TAATATTTATA-AATATTTAATTAAAT
1 TAATATTTATATAA-ATTTAATTAAAC
*
5275339 TAATAATTATATAAATTTAAATTAAAC
1 TAATATTTATATAAATTT-AATTAAAC
* *
5275366 TATTATTTATTTAAAT
1 TAATATTTATATAAAT
5275382 ATTTTTTATA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 14 0.39
27 22 0.61
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (26 bp):
TAATATTTATATAAATTTAATTAAAC
Found at i:5275410 original size:17 final size:18
Alignment explanation
Indices: 5275374--5275415 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
5275364 ACTATTATTT
*
5275374 ATTTAAATATTTTTTATA
1 ATTTAAATATTTTATATA
*
5275392 ATTTAAA-ATTTTATGTA
1 ATTTAAATATTTTATATA
5275409 A-TTAAAT
1 ATTTAAAT
5275416 TTAAAGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 5 0.24
17 9 0.43
18 7 0.33
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTTAAATATTTTATATA
Found at i:5275534 original size:27 final size:24
Alignment explanation
Indices: 5275475--5275536 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 24
5275465 ATTAAGACAC
*
5275475 AATATAAATATAATATGAAAAAAT
1 AATATAAATATAATACGAAAAAAT
5275499 AAT-TAAAATATAATACGATACAAAAAT
1 AATAT-AAATATAATACG--A-AAAAAT
5275526 AATATAAATAT
1 AATATAAATAT
5275537 GACATAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
23 1 0.03
24 14 0.44
26 1 0.03
27 15 0.47
28 1 0.03
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (24 bp):
AATATAAATATAATACGAAAAAAT
Found at i:5279490 original size:53 final size:53
Alignment explanation
Indices: 5279423--5279581 Score: 264
Period size: 53 Copynumber: 3.0 Consensus size: 53
5279413 AGTTGTTACA
**
5279423 TTGGATGAATGATGTGTTAGAGACAGCAATATTTGTTGCCTTGTTAGTGCCGG
1 TTGGATGAATGATGTGTTAGAGACAGCAATATTTGTTGCCTTGTTAGAACCGG
* **
5279476 TTGGATGAATGATGTGTTAGAGACAGCAATATTTGTTGTCTAATTAGAACCGG
1 TTGGATGAATGATGTGTTAGAGACAGCAATATTTGTTGCCTTGTTAGAACCGG
*
5279529 TTGGATGAATGATGTGTTAGAGACAGCAATATTTGTTGCCTTGTTAGACCCGG
1 TTGGATGAATGATGTGTTAGAGACAGCAATATTTGTTGCCTTGTTAGAACCGG
5279582 CCCAGACAAG
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 97 1.00
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.35
Consensus pattern (53 bp):
TTGGATGAATGATGTGTTAGAGACAGCAATATTTGTTGCCTTGTTAGAACCGG
Found at i:5279687 original size:28 final size:29
Alignment explanation
Indices: 5279632--5279688 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
5279622 TCAAATTATT
*
5279632 ATTTAATTATAAAAAATATTTTTATTTAA
1 ATTTAATTATAAAAAATATTGTTATTTAA
5279661 ATTTAATTAT-AAAAATATATGTT-TTTAA
1 ATTTAATTATAAAAAATAT-TGTTATTTAA
5279689 TTTTTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (29 bp):
ATTTAATTATAAAAAATATTGTTATTTAA
Found at i:5279979 original size:2 final size:2
Alignment explanation
Indices: 5279967--5280007 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
5279957 ATATAAACAT
* * *
5279967 TA TA CA TA TA TA TA TA TA TA TA TG TA TA TA TT 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
5280008 TCAAACTCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5281074 original size:2 final size:2
Alignment explanation
Indices: 5281067--5281091 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5281057 ACCGAATTCC
5281067 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 A
5281092 GCTTTGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5284919 original size:3 final size:3
Alignment explanation
Indices: 5284913--5284943 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5284903 CAACATCATC
5284913 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5284944 CAACAACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5285502 original size:2 final size:2
Alignment explanation
Indices: 5285497--5285521 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5285487 TGTCTCTCTC
5285497 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 T
5285522 CTCTGCTACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5285898 original size:6 final size:6
Alignment explanation
Indices: 5285881--5285912 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
5285871 CATGGCCATA
5285881 GGAATGG GGAATG GGAATG GGAATG GGAATG G
1 GGAAT-G GGAATG GGAATG GGAATG GGAATG G
5285913 ATGATATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.31, C:0.00, G:0.53, T:0.16
Consensus pattern (6 bp):
GGAATG
Found at i:5291078 original size:36 final size:33
Alignment explanation
Indices: 5291014--5291098 Score: 86
Period size: 33 Copynumber: 2.5 Consensus size: 33
5291004 AAATTATTTA
*
5291014 AATATAAATAAAAATAAATATTTATTTAAATAT
1 AATATAAATAAAAAAAAATATTTATTTAAATAT
*
5291047 AATA-AAATAATAAAAAAATCATTTACTTTTAAATTTT
1 AATATAAATAA-AAAAAAAT-ATTTA--TTTAAA-TAT
5291084 AAT-TAAA-AAAAAAAA
1 AATATAAATAAAAAAAA
5291099 GGTTATGTAG
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
32 6 0.14
33 11 0.25
34 5 0.11
35 6 0.14
36 8 0.18
37 8 0.18
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (33 bp):
AATATAAATAAAAAAAAATATTTATTTAAATAT
Found at i:5291664 original size:25 final size:24
Alignment explanation
Indices: 5291630--5291676 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
5291620 AACTTATTAG
* *
5291630 ATTTATTTAAATTTTTTTAATTTAA
1 ATTTAATTAAA-TTTGTTAATTTAA
5291655 ATTTAATTAAATTTGTTAATTT
1 ATTTAATTAAATTTGTTAATTT
5291677 GAATATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
ATTTAATTAAATTTGTTAATTTAA
Found at i:5291689 original size:25 final size:25
Alignment explanation
Indices: 5291634--5291690 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
5291624 TATTAGATTT
* *
5291634 ATTTAAATTTTTTTAATTTAAATTT
1 ATTTAAATTTTGTTAATTTAAATTC
* *
5291659 AATTAAA-TTTGTTAATTTGAATATC
1 ATTTAAATTTTGTTAATTTAAAT-TC
5291684 ATTTAAA
1 ATTTAAA
5291691 GATATTAAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (25 bp):
ATTTAAATTTTGTTAATTTAAATTC
Found at i:5292216 original size:27 final size:28
Alignment explanation
Indices: 5292186--5292238 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
5292176 TGTAGATATA
*
5292186 TTACTTTTC-ATAATTA-TTATTTTTTTT
1 TTACTTTTCTAT-ATCATTTATTTTTTTT
5292213 TTACTTTTCTATATCATTTATTTTTT
1 TTACTTTTCTATATCATTTATTTTTT
5292239 AAATGATGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (28 bp):
TTACTTTTCTATATCATTTATTTTTTTT
Found at i:5292236 original size:24 final size:27
Alignment explanation
Indices: 5292186--5292239 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 27
5292176 TGTAGATATA
* *
5292186 TTACTTTTCATAATTATTATTTTTTTT
1 TTACTTTTCATAATTATCATTTATTTT
5292213 TTACTTTTC-T-A-TATCATTTATTTT
1 TTACTTTTCATAATTATCATTTATTTT
5292237 TTA
1 TTA
5292240 AATGATGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 14 0.56
25 1 0.04
26 1 0.04
27 9 0.36
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (27 bp):
TTACTTTTCATAATTATCATTTATTTT
Found at i:5292945 original size:2 final size:2
Alignment explanation
Indices: 5292938--5292973 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5292928 TCTTTAATTG
*
5292938 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
5292974 GAGCCAAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5295709 original size:2 final size:2
Alignment explanation
Indices: 5295692--5295728 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
5295682 TATTATAAAG
*
5295692 TA TA GA TA TA -A 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
5295729 AAAATTGACT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:5298560 original size:26 final size:26
Alignment explanation
Indices: 5298531--5298582 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
5298521 ATAAATGAAC
5298531 TAAAATAACTATTTAATTATAATTAA
1 TAAAATAACTATTTAATTATAATTAA
*
5298557 TAAAATAATTATTTAATTATAATTAA
1 TAAAATAACTATTTAATTATAATTAA
5298583 AGTGATATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
TAAAATAACTATTTAATTATAATTAA
Found at i:5299305 original size:1 final size:1
Alignment explanation
Indices: 5299301--5299335 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
5299291 GAACCCCCAG
5299301 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5299336 CTCCACCTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5301289 original size:16 final size:16
Alignment explanation
Indices: 5301246--5301292 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
5301236 GATTTGACAA
*
5301246 TAAATTT-TTTTGATAT
1 TAAATTTATTTT-TTAT
5301262 TGAAACTTTATTTTTTAT
1 T-AAA-TTTATTTTTTAT
5301280 TAAATTTATTTTT
1 TAAATTTATTTTT
5301293 CATATGCAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 10 0.37
17 6 0.22
18 7 0.26
19 4 0.15
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (16 bp):
TAAATTTATTTTTTAT
Found at i:5302421 original size:16 final size:17
Alignment explanation
Indices: 5302402--5302434 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5302392 TTATATTTTT
5302402 AATT-AATTTTAATAAA
1 AATTAAATTTTAATAAA
*
5302418 AATTAAATTTTATTAAA
1 AATTAAATTTTAATAAA
5302435 TAATATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTAAATTTTAATAAA
Found at i:5303919 original size:12 final size:12
Alignment explanation
Indices: 5303889--5303922 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5303879 CAACATAAAT
5303889 AAAAATAAT-TA
1 AAAAATAATATA
*
5303900 AAATATAATATA
1 AAAAATAATATA
5303912 AAAAATAATAT
1 AAAAATAATAT
5303923 GAATACGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAAATAATATA
Found at i:5304060 original size:33 final size:32
Alignment explanation
Indices: 5304004--5304068 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
5303994 AAATTTTTAA
5304004 TACTTTAAATATATGAAAAATAATATAAAAAT
1 TACTTTAAATATATGAAAAATAATATAAAAAT
*
5304036 TACTTTAAA-ATAATTAAAATATAATATAAAAAT
1 TACTTTAAATAT-ATGAAAA-ATAATATAAAAAT
5304069 AAATATGACA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 2 0.07
32 15 0.50
33 13 0.43
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (32 bp):
TACTTTAAATATATGAAAAATAATATAAAAAT
Found at i:5304074 original size:12 final size:11
Alignment explanation
Indices: 5304010--5304070 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
5304000 TTAATACTTT
5304010 AAAT-ATATGAA
1 AAATAATAT-AA
5304021 AAATAATATAA
1 AAATAATATAA
* *
5304032 AAATTACT-TTA
1 AAA-TAATATAA
5304043 AAATAAT-TAA
1 AAATAATATAA
5304053 AATATAATATAA
1 AA-ATAATATAA
5304065 AAATAA
1 AAATAA
5304071 ATATGACATG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
10 7 0.17
11 23 0.55
12 12 0.29
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (11 bp):
AAATAATATAA
Found at i:5304273 original size:14 final size:15
Alignment explanation
Indices: 5304243--5304276 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
5304233 TATAATTTAA
5304243 ATATTTAATATATTT
1 ATATTTAATATATTT
5304258 ATATTTAATA-ATTT
1 ATATTTAATATATTT
5304272 ATATT
1 ATATT
5304277 ACATATGCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATTTAATATATTT
Found at i:5306524 original size:16 final size:17
Alignment explanation
Indices: 5306505--5306542 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
5306495 TAATATTTTA
5306505 TATATTTATAT-AAATT
1 TATATTTATATAAAATT
*
5306521 TATAATTATATAAAATT
1 TATATTTATATAAAATT
5306538 TATAT
1 TATAT
5306543 CATATTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTTATATAAAATT
Found at i:5306547 original size:16 final size:18
Alignment explanation
Indices: 5306511--5306547 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5306501 TTTATATATT
*
5306511 TATATAAATTTATAATTA
1 TATATAAATTTATAATCA
5306529 TATA-AAATTTAT-ATCA
1 TATATAAATTTATAATCA
5306545 TAT
1 TAT
5306548 TATTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 8 0.44
18 4 0.22
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
TATATAAATTTATAATCA
Found at i:5306778 original size:21 final size:21
Alignment explanation
Indices: 5306728--5306778 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
5306718 TGATAAAAAT
5306728 TTTA-ATAATTTAAATTAATA
1 TTTATATAATTTAAATTAATA
*
5306748 -TTATTTTAATTTAAATTAATA
1 TTTA-TATAATTTAAATTAATA
5306769 TTTATATAAT
1 TTTATATAAT
5306779 AAAAATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 3 0.12
21 20 0.77
22 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTATATAATTTAAATTAATA
Found at i:5307786 original size:14 final size:14
Alignment explanation
Indices: 5307767--5307793 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5307757 AAATCGAGTT
5307767 AAATTATAATTTTA
1 AAATTATAATTTTA
5307781 AAATTATAATTTT
1 AAATTATAATTTT
5307794 TTATTTAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AAATTATAATTTTA
Found at i:5307894 original size:32 final size:31
Alignment explanation
Indices: 5307839--5307919 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 31
5307829 ATAATTAAAA
* * *
5307839 TATAAAAAAAT-ATTTTAATAATATTTATATAT
1 TATAAAATAATAATTTAAAAAATATTT-T-TAT
* *
5307871 TTTAAAATTA-AATTTAAAAAATATTTTTAT
1 TATAAAATAATAATTTAAAAAATATTTTTAT
5307901 TATAAAATAATAATTTAAA
1 TATAAAATAATAATTTAAA
5307920 TTAAATTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
30 11 0.28
31 9 0.22
32 20 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
TATAAAATAATAATTTAAAAAATATTTTTAT
Found at i:5309023 original size:2 final size:2
Alignment explanation
Indices: 5309016--5309059 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
5309006 TTCCAAATTT
* *
5309016 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA -A TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5309057 TA T
1 TA T
5309060 TAAATCCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5318523 original size:2 final size:2
Alignment explanation
Indices: 5318516--5318556 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5318506 AGATTAAGGC
5318516 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
5318557 CCCCCATAAA
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:5319205 original size:137 final size:134
Alignment explanation
Indices: 5318940--5319210 Score: 497
Period size: 137 Copynumber: 2.0 Consensus size: 134
5318930 ATATCAATGG
5318940 ATTATTTAAGGGACTGATGACCTTACTTGACCTAACTAAACACATGAATTTTAAAATAAAATTTA
1 ATTATTTAAGGGACTGATGACCTTACTTGACCTAACTAAACACATGAATTTTAAAATAAAATTTA
*
5319005 CAAAAACAATTTGCATAGGAGCCATTCTCATGAATTAATTAAAAATTAAATTTATATTTCATGTA
66 CAAAAACAATTTGCATAGAAGCCATTCTCATGAATTAATTAAAAATTAAATTTATATTTCATGTA
5319070 GGAT
131 GGAT
5319074 ATTATTTAAGGGACTGATGACCTTACTTGACCTAACTAAACACATGAATTTTAAAATAAAATTTA
1 ATTATTTAAGGGACTGATGACCTTACTTGACCTAACTAAACACATGAATTTTAAAATAAAA--T-
*
5319139 TTACAAAAACAATTTGCATAGAAGCCATTTTCATGAATTAATTAAAAATTAAATTTATATTTCAT
63 TTACAAAAACAATTTGCATAGAAGCCATTCTCATGAATTAATTAAAAATTAAATTTATATTTCAT
5319204 GTAGGAT
128 GTAGGAT
5319211 GTATGTGTAT
Statistics
Matches: 132, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
134 61 0.46
136 1 0.01
137 70 0.53
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (134 bp):
ATTATTTAAGGGACTGATGACCTTACTTGACCTAACTAAACACATGAATTTTAAAATAAAATTTA
CAAAAACAATTTGCATAGAAGCCATTCTCATGAATTAATTAAAAATTAAATTTATATTTCATGTA
GGAT
Found at i:5324077 original size:6 final size:6
Alignment explanation
Indices: 5324068--5324097 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
5324058 TAAAATGAAG
*
5324068 AAAAGA AAAAGA AAAAGA AAAATA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
5324098 TGTTAACTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:5325565 original size:94 final size:94
Alignment explanation
Indices: 5325396--5325581 Score: 300
Period size: 94 Copynumber: 2.0 Consensus size: 94
5325386 GCTGCGTTAT
* *
5325396 GCTGGTGTAATGGTTGATGGTACTGACATTTGAATGACTCAGTCGATTACCGTTTTGTAATCTCT
1 GCTGGTGTAATGGTTGATGGTACTGACATTTGAATGACTCAGTCGATTACCATTTTGTAACCTCT
* *
5325461 AGAGATCTTGTTTTTCTAAATGCAATTAA
66 AGAGACCTTGTTTTTCCAAATGCAATTAA
* * *
5325490 GCTGGTGTAATGGTTTATGTTACTGACATTTGAATGACTCAGTTGATTACCATTTTGTAACCTCT
1 GCTGGTGTAATGGTTGATGGTACTGACATTTGAATGACTCAGTCGATTACCATTTTGTAACCTCT
*
5325555 TGAGACCTTGTTTTTCCAAATGCAATT
66 AGAGACCTTGTTTTTCCAAATGCAATT
5325582 TGTGCTGCGT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
94 84 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (94 bp):
GCTGGTGTAATGGTTGATGGTACTGACATTTGAATGACTCAGTCGATTACCATTTTGTAACCTCT
AGAGACCTTGTTTTTCCAAATGCAATTAA
Found at i:5331516 original size:9 final size:9
Alignment explanation
Indices: 5331502--5331552 Score: 50
Period size: 11 Copynumber: 5.2 Consensus size: 9
5331492 TATGTAATTT
5331502 TAATATATA
1 TAATATATA
5331511 TAATATA-A
1 TAATATATA
5331519 TATATATGATA
1 TA-ATAT-ATA
5331530 TTAATATATA
1 -TAATATATA
5331540 TCTAATATATA
1 --TAATATATA
5331551 TA
1 TA
5331553 CTAAAAATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
8 3 0.08
9 13 0.36
10 4 0.11
11 14 0.39
12 2 0.06
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (9 bp):
TAATATATA
Found at i:5332489 original size:16 final size:18
Alignment explanation
Indices: 5332461--5332496 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
5332451 ATATTTAATA
5332461 TTAAAAATAAAATT-AGT
1 TTAAAAATAAAATTGAGT
5332478 TTAAAAAT-AAATTGAGT
1 TTAAAAATAAAATTGAGT
5332495 TT
1 TT
5332497 TAATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TTAAAAATAAAATTGAGT
Found at i:5332653 original size:36 final size:36
Alignment explanation
Indices: 5332606--5332678 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
5332596 ATATATTATG
* *
5332606 ATAAACATTAAAAGTATTTTAAATTATTTATTTTAA
1 ATAAAAATTAAAAATATTTTAAATTATTTATTTTAA
*
5332642 ATAAAAATTAAAAATATTTTTAATTATTTATTTTAA
1 ATAAAAATTAAAAATATTTTAAATTATTTATTTTAA
5332678 A
1 A
5332679 ATTTAATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (36 bp):
ATAAAAATTAAAAATATTTTAAATTATTTATTTTAA
Done.