Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold328
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: 54420
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Found at i:3131 original size:18 final size:17
Alignment explanation
Indices: 3087--3132 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
3077 AAATCATTTG
*
3087 TTAACAA-TATTAATTT
1 TTAACAATTATTAATTC
3103 TTAA-AATTTATTAAATTC
1 TTAACAA-TTATT-AATTC
3121 TTAACAATTATT
1 TTAACAATTATT
3133 TTTAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
15 2 0.08
16 4 0.16
17 4 0.16
18 13 0.52
19 2 0.08
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAACAATTATTAATTC
Found at i:9735 original size:26 final size:25
Alignment explanation
Indices: 9679--9758 Score: 151
Period size: 25 Copynumber: 3.2 Consensus size: 25
9669 TGAAATTCCC
9679 ATCATGGAACATTTACCTAACCATT
1 ATCATGGAACATTTACCTAACCATT
9704 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAA-CCATT
9730 ATCATGGAACATTTACCTAACCATT
1 ATCATGGAACATTTACCTAACCATT
9755 ATCA
1 ATCA
9759 ATTTGTATCA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
25 29 0.54
26 25 0.46
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.31
Consensus pattern (25 bp):
ATCATGGAACATTTACCTAACCATT
Found at i:16736 original size:26 final size:26
Alignment explanation
Indices: 16706--16779 Score: 132
Period size: 26 Copynumber: 2.9 Consensus size: 26
16696 CCCATAATGG
16706 AACATTTACCTAACCCATTATCATGA
1 AACATTTACCTAACCCATTATCATGA
*
16732 AACATTTACCTAACCCATTATCATGG
1 AACATTTACCTAACCCATTATCATGA
16758 AACATTTACCTAA-CCATTATCA
1 AACATTTACCTAACCCATTATCA
16780 ATTTGTATCA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 9 0.19
26 38 0.81
ACGTcount: A:0.38, C:0.27, G:0.04, T:0.31
Consensus pattern (26 bp):
AACATTTACCTAACCCATTATCATGA
Found at i:18092 original size:18 final size:18
Alignment explanation
Indices: 18063--18118 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
18053 TTTTGTTTCT
18063 TTATTAAATATTATTATTA
1 TTATT-AATATTATTATTA
* **
18082 TT-TCTAATATTGTTAAGA
1 TTAT-TAATATTATTATTA
18100 TTATTAATATTATTATTA
1 TTATTAATATTATTATTA
18118 T
1 T
18119 CTTTTTTATA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (18 bp):
TTATTAATATTATTATTA
Found at i:18280 original size:28 final size:29
Alignment explanation
Indices: 18214--18268 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
18204 TTTCATGTTG
* *
18214 TTATTATTAGTAGTATACTATTATATTTA
1 TTATTAATATTAGTATACTATTATATTTA
*
18243 TTATTAATATTAGTATA-TATTTTATT
1 TTATTAATATTAGTATACTATTATATT
18269 ATGTATGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (29 bp):
TTATTAATATTAGTATACTATTATATTTA
Found at i:18430 original size:13 final size:13
Alignment explanation
Indices: 18412--18442 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
18402 TTATATAGCC
*
18412 TTATTTTAGTATT
1 TTATTTTAATATT
18425 TTATTTTAATATT
1 TTATTTTAATATT
18438 TTATT
1 TTATT
18443 ATTTGTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (13 bp):
TTATTTTAATATT
Found at i:18622 original size:21 final size:23
Alignment explanation
Indices: 18597--18655 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
18587 ATATTATTGT
*
18597 TATATTTATTATATA-GTA-GTG
1 TATATTTATTATATATCTATGTG
18618 TATATTT-TTAT-TATCTATGTG
1 TATATTTATTATATATCTATGTG
*
18639 TATATATATTTATATAT
1 TATATTTA-TTATATAT
18656 ATAGTATGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 2 0.06
20 6 0.19
21 16 0.52
23 4 0.13
24 3 0.10
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (23 bp):
TATATTTATTATATATCTATGTG
Found at i:18627 original size:23 final size:25
Alignment explanation
Indices: 18597--18661 Score: 84
Period size: 23 Copynumber: 2.7 Consensus size: 25
18587 ATATTATTGT
18597 TATATTTATTATATAGTAGTGTATA
1 TATATTTATTATATAGTAGTGTATA
*
18622 T-T-TTTATTATCTA-T-GTGTATA
1 TATATTTATTATATAGTAGTGTATA
18643 TATATTTATATATATAGTA
1 TATATTTAT-TATATAGTA
18662 TGATTTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
21 8 0.24
22 2 0.06
23 15 0.45
24 6 0.18
25 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (25 bp):
TATATTTATTATATAGTAGTGTATA
Found at i:18685 original size:18 final size:19
Alignment explanation
Indices: 18664--18703 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
18654 ATATAGTATG
18664 ATTTTTAAT-TACTTTATT
1 ATTTTTAATATACTTTATT
* *
18682 ATTTTTATTATATTTTATT
1 ATTTTTAATATACTTTATT
18701 ATT
1 ATT
18704 CTTTTTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTTTTAATATACTTTATT
Found at i:18708 original size:22 final size:22
Alignment explanation
Indices: 18677--18728 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
18667 TTTAATTACT
18677 TTATTATTTTTATTATATTTTA
1 TTATTATTTTTATTATATTTTA
* * *
18699 TTATTCTTTTTTTTGTATTTTA
1 TTATTATTTTTATTATATTTTA
*
18721 ATATTATT
1 TTATTATT
18729 ACTATTATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (22 bp):
TTATTATTTTTATTATATTTTA
Found at i:18740 original size:134 final size:131
Alignment explanation
Indices: 18466--18742 Score: 285
Period size: 134 Copynumber: 2.1 Consensus size: 131
18456 TTGTTACTAT
* *
18466 TATTAATATTATATAATAGTGTATACTTTTTATCATATATGTGTATATATATATTTGTACATAAT
1 TATTATTATTATATAATAGTGTATACTTTTTATCATATATGTGTATATATATATTTATACATAAT
* * * *
18531 CTTATTTTCATTACTTTATTTCAATATTTTTGTTGTATTTGTTTTTTCGTATTTCAATATTATTG
66 ATGATTTTAATTACTTTATTTCAATATTTTTGTTGTATTTGTTTTTTCGTATTTCAATATTATTA
*
18596 T
131 C
* * * *
18597 TA-TATTTATTATATAGTAGTGTATA-TTTTTATTATCTATGTGTATATATAT-TTATATATATA
1 TATTA-TTATTATATAATAGTGTATACTTTTTATCATATATGTGTATATATATATT-TATACATA
* *** * * *
18659 GTATGATTTTTAATTACTTTATTATTTTTATTATATT-TTATTATTCT-TTTTTTTGTATTTTAA
64 ATATGA-TTTTAATTACTTTATT-TCAATATT-T-TTGTT-GTATT-TGTTTTTTCGTATTTCAA
18722 TATTATTAC
123 TATTATTAC
18731 TATTATTATTAT
1 TATTATTATTAT
18743 TGTAGCGACG
Statistics
Matches: 119, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
129 2 0.02
130 35 0.29
131 35 0.29
132 5 0.04
133 3 0.03
134 36 0.30
135 3 0.03
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.60
Consensus pattern (131 bp):
TATTATTATTATATAATAGTGTATACTTTTTATCATATATGTGTATATATATATTTATACATAAT
ATGATTTTAATTACTTTATTTCAATATTTTTGTTGTATTTGTTTTTTCGTATTTCAATATTATTA
C
Found at i:19901 original size:18 final size:19
Alignment explanation
Indices: 19878--19920 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
19868 ACATATATGT
19878 ATAATAAT-GATGAAAAT-A
1 ATAATAATAG-TGAAAATAA
19896 ATAATAATAGTGAAAATAA
1 ATAATAATAGTGAAAATAA
19915 ATAATA
1 ATAATA
19921 TAATAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (19 bp):
ATAATAATAGTGAAAATAA
Found at i:19928 original size:15 final size:17
Alignment explanation
Indices: 19892--19932 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
19882 TAATGATGAA
19892 AATAAT-AATAATAGTG
1 AATAATAAATAATAGTG
19908 AA-AATAAATAATA-T-
1 AATAATAAATAATAGTG
19922 AATAATAAATA
1 AATAATAAATA
19933 TAATAGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 2 0.09
15 12 0.52
16 9 0.39
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (17 bp):
AATAATAAATAATAGTG
Found at i:20105 original size:26 final size:26
Alignment explanation
Indices: 20045--20109 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
20035 TACGAAGAAG
* *
20045 TATATATAATATAATAATAATATTAA
1 TATAAATAATATAAAAATAATATTAA
*
20071 AATACAATAAT-TAAAAATAATATTATA
1 TATA-AATAATATAAAAATAATATTA-A
20098 TATAAAT-ATATA
1 TATAAATAATATA
20110 CAATATTCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
25 2 0.06
26 21 0.66
27 9 0.28
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
TATAAATAATATAAAAATAATATTAA
Found at i:20674 original size:20 final size:19
Alignment explanation
Indices: 20651--20696 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
20641 AGGAAGAGGA
*
20651 GGGAGAGAAAAGAGGGAGCG
1 GGGAGAGAAAAGAGGG-GAG
* *
20671 GGGAAAGAAGAGAGGGGAG
1 GGGAGAGAAAAGAGGGGAG
20690 GGGAGAG
1 GGGAGAG
20697 CTCCGGCCAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.39, C:0.02, G:0.59, T:0.00
Consensus pattern (19 bp):
GGGAGAGAAAAGAGGGGAG
Found at i:21269 original size:22 final size:22
Alignment explanation
Indices: 21239--21296 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
21229 TACGAGGACT
*
21239 GTGGAGGTATGGGACTGTTGTA
1 GTGGGGGTATGGGACTGTTGTA
*
21261 GTGGGGGTATGGGGCTGTTGTA
1 GTGGGGGTATGGGACTGTTGTA
21283 GTGGGGGTATGGGA
1 GTGGGGGTATGGGA
21297 TTGCTTCATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.14, C:0.03, G:0.53, T:0.29
Consensus pattern (22 bp):
GTGGGGGTATGGGACTGTTGTA
Found at i:21577 original size:16 final size:16
Alignment explanation
Indices: 21556--21587 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21546 ATATTTTTGT
21556 TATATGTATGTATATA
1 TATATGTATGTATATA
*
21572 TATATGTATTTATATA
1 TATATGTATGTATATA
21588 ATAGTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (16 bp):
TATATGTATGTATATA
Found at i:21757 original size:27 final size:27
Alignment explanation
Indices: 21695--21758 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
21685 ATTGAATATT
*
21695 ATTATTATTATTATTACTATTGTCATA
1 ATTATTATTATTATTACTATTATCATA
* * * *
21722 TTTAGTATTATTTTTACT-TTCATTATA
1 ATTATTATTATTATTACTATT-ATCATA
21749 ATTATTATTA
1 ATTATTATTA
21759 CTGATCTTCG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
26 2 0.07
27 27 0.93
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.59
Consensus pattern (27 bp):
ATTATTATTATTATTACTATTATCATA
Found at i:21962 original size:23 final size:24
Alignment explanation
Indices: 21936--21985 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
21926 TTATATGTAG
*
21936 TATGTACATA-TTTTCAATACTAT
1 TATGTAAATACTTTTCAATACTAT
* *
21959 TATGTAAATACTTTTCATTCCTAT
1 TATGTAAATACTTTTCAATACTAT
21983 TAT
1 TAT
21986 TACGGATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.50
Consensus pattern (24 bp):
TATGTAAATACTTTTCAATACTAT
Found at i:25440 original size:11 final size:11
Alignment explanation
Indices: 25424--25474 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
25414 TCTTTCGAAA
25424 TTTCTTTTTTC
1 TTTCTTTTTTC
*
25435 TTTCTTTTTTG
1 TTTCTTTTTTC
*
25446 TTT-TTTTAT-
1 TTTCTTTTTTC
*
25455 TTTATTTTTTC
1 TTTCTTTTTTC
*
25466 TCTCTTTTT
1 TTTCTTTTT
25475 ATATACATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 10 0.30
11 20 0.61
ACGTcount: A:0.04, C:0.12, G:0.02, T:0.82
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:26079 original size:17 final size:17
Alignment explanation
Indices: 26039--26081 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
26029 ATTTTAGTCC
*
26039 TTTTTGATTTTATTTAT
1 TTTTTTATTTTATTTAT
*
26056 TTATTTATTTTATTT-T
1 TTTTTTATTTTATTTAT
26072 TGTTTTTATT
1 T-TTTTTATT
26082 AAATATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (17 bp):
TTTTTTATTTTATTTAT
Found at i:26112 original size:3 final size:3
Alignment explanation
Indices: 26106--26224 Score: 66
Period size: 3 Copynumber: 39.0 Consensus size: 3
26096 TCATTTCTAA
* ** *
26106 TAT TAT TAA TAT TAT TAT GTA- TAT TAT TAT TGC TAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
26151 T-C TAGT TAT TAA CA- TAT TAT TAT TTT TAAT GTAT TAT TAT TACT AAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT T-AT -TAT TAT TAT TA-T TAT
*
26198 TAT TAT TAT T-T CTAG TAT TAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT
26225 ATATAACATT
Statistics
Matches: 87, Mismatches: 19, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
2 5 0.06
3 72 0.83
4 9 0.10
5 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:26345 original size:22 final size:21
Alignment explanation
Indices: 26306--26368 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 21
26296 TTTTCTTTTA
26306 ATATTTTATATATTATTATGTAC
1 ATATTTTA-ATA-TATTATGTAC
*
26329 ATATTTTAATATCATTA-GT-T
1 ATATTTTAATAT-ATTATGTAC
26349 ATATATTT-ATATATTATGTA
1 ATAT-TTTAATATATTATGTA
26369 TATTTCTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
19 4 0.11
20 10 0.29
21 6 0.17
22 7 0.20
23 8 0.23
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.56
Consensus pattern (21 bp):
ATATTTTAATATATTATGTAC
Found at i:26643 original size:25 final size:24
Alignment explanation
Indices: 26538--26648 Score: 91
Period size: 25 Copynumber: 4.5 Consensus size: 24
26528 ATATATTCTT
** *
26538 TACTATTCCATGTATATATTTTTA
1 TACTATTTTATGTATATATTTTAA
* *
26562 TA-TCATCTTATGTATAAATTCTTGAA
1 TACT-ATTTTATGTATATATT-TT-AA
* *
26588 TACTATGTTATATATATACTTTTAA
1 TACTATTTTATGTATATA-TTTTAA
26613 TACTATTTTATGTATATATTATT-A
1 TACTATTTTATGTATATATT-TTAA
26637 TATCTATTTTAT
1 TA-CTATTTTAT
26649 CCCTATTATA
Statistics
Matches: 70, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
23 1 0.01
24 19 0.27
25 31 0.44
26 16 0.23
27 3 0.04
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.54
Consensus pattern (24 bp):
TACTATTTTATGTATATATTTTAA
Found at i:26838 original size:20 final size:20
Alignment explanation
Indices: 26810--26847 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
26800 ATACAACTTT
26810 TTATCATTATTATTATATAA
1 TTATCATTATTATTATATAA
*
26830 TTATTATTATTATTATAT
1 TTATCATTATTATTATAT
26848 TAGTATATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATCATTATTATTATATAA
Found at i:26848 original size:14 final size:14
Alignment explanation
Indices: 26815--26873 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
26805 ACTTTTTATC
*
26815 ATTATTATTATATA
1 ATTATTATTATATT
26829 ATTATTATTATTATT
1 ATTATTATTA-TATT
*
26844 A-TATTAGTATATGT
1 ATTATTATTATAT-T
26858 -TTATTATGTAT-TT
1 ATTATTAT-TATATT
26871 ATT
1 ATT
26874 TTAATATTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
13 4 0.11
14 26 0.70
15 7 0.19
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (14 bp):
ATTATTATTATATT
Found at i:27074 original size:28 final size:28
Alignment explanation
Indices: 27032--27091 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
27022 TATATTGTTA
27032 TTTTCTATTATTATTA-TAAATACATTAT
1 TTTTCTATTATTATTAGT-AATACATTAT
*
27060 TTTTCTTATTA-TATTAGTAGTACATTAT
1 TTTTC-TATTATTATTAGTAATACATTAT
27088 TTTT
1 TTTT
27092 ATTTTCTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (28 bp):
TTTTCTATTATTATTAGTAATACATTAT
Found at i:33745 original size:72 final size:72
Alignment explanation
Indices: 33628--33836 Score: 312
Period size: 72 Copynumber: 2.9 Consensus size: 72
33618 CCAGATACTT
**
33628 CAAAGATGATAACTCCCCTATAGACAATGGAA-AAGTACCATTTAATTGATTTTCTGAAACATCA
1 CAAAGATGATAACTCCCCTATAGACAATGGAATTTG-ACCATTTAATTGATTTTCTGAAACATCA
*
33692 AATAACTC
65 AAGAACTC
*
33700 CAAAGATGATAACTCCCCTATCGACAATGGAATTTGACCATTTAATTGATTTTCTGAAACATCAA
1 CAAAGATGATAACTCCCCTATAGACAATGGAATTTGACCATTTAATTGATTTTCTGAAACATCAA
33765 AGAACTC
66 AGAACTC
* * * * * *
33772 CAAAGATGATAACTGCCCTATAGACAAGGGAATTTGGCCGTTTAGTTGATTTTCTGAAAGATCAA
1 CAAAGATGATAACTCCCCTATAGACAATGGAATTTGACCATTTAATTGATTTTCTGAAACATCAA
33837 GGTAGGTAGC
Statistics
Matches: 125, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
72 124 0.99
73 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (72 bp):
CAAAGATGATAACTCCCCTATAGACAATGGAATTTGACCATTTAATTGATTTTCTGAAACATCAA
AGAACTC
Found at i:35116 original size:26 final size:26
Alignment explanation
Indices: 35079--35135 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
35069 TTTAGGTCTT
*
35079 AAAAGCTGAAGGAGAAAAAAAGAAAG
1 AAAAGCTAAAGGAGAAAAAAAGAAAG
* *
35105 AAAAGCTAAAGGAGATAAAAAGAAGG
1 AAAAGCTAAAGGAGAAAAAAAGAAAG
35131 AAAAG
1 AAAAG
35136 AAGATGGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.65, C:0.04, G:0.26, T:0.05
Consensus pattern (26 bp):
AAAAGCTAAAGGAGAAAAAAAGAAAG
Found at i:37201 original size:3 final size:3
Alignment explanation
Indices: 37193--37249 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
37183 ATTGAAGTAA
37193 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
37241 AAT AAT AAT
1 AAT AAT AAT
37250 GTAACACCCC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:39956 original size:26 final size:26
Alignment explanation
Indices: 39894--40037 Score: 224
Period size: 26 Copynumber: 5.7 Consensus size: 26
39884 TGAAATGCCC
*
39894 ATCATGGAACATTTACCTAAACC---
1 ATCATGGAACATTTACCTAATCCATT
*
39917 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAATCCATT
*
39943 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAATCCATT
39969 ATCATGGAACATTTACCTAA-CCATT
1 ATCATGGAACATTTACCTAATCCATT
*
39994 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAATCCATT
40020 ATCATGGAACATTTACCT
1 ATCATGGAACATTTACCT
40038 TTATCAATTT
Statistics
Matches: 111, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
23 22 0.20
25 24 0.22
26 65 0.59
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAATCCATT
Found at i:40010 original size:51 final size:52
Alignment explanation
Indices: 39894--40037 Score: 242
Period size: 51 Copynumber: 2.8 Consensus size: 52
39884 TGAAATGCCC
* *
39894 ATCATGGAACATTTACCTAAACC---ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
39943 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAA-CCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
39994 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCT
40038 TTATCAATTT
Statistics
Matches: 90, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
49 21 0.23
51 49 0.54
52 20 0.22
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.33
Consensus pattern (52 bp):
ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
Found at i:40019 original size:77 final size:75
Alignment explanation
Indices: 39894--40037 Score: 227
Period size: 77 Copynumber: 1.9 Consensus size: 75
39884 TGAAATGCCC
*
39894 ATCATGGAACATTTACCTAAACCATCATGGAACATTTACCTAACCCATTATCATGGAATATTTAC
1 ATCATGGAACATTTACCTAAACCATCATGGAACATTTACCTAACCCATTATCATGGAACATTTAC
39959 CTAATCCATT
66 CTAATCCATT
* *
39969 ATCATGGAACATTTACCT-AACCATTATCATGGAATATTTACCTAATCCATTATCATGGAACATT
1 ATCATGGAACATTTACCTAAACC---ATCATGGAACATTTACCTAACCCATTATCATGGAACATT
40033 TACCT
63 TACCT
40038 TTATCAATTT
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
74 4 0.06
75 18 0.29
77 41 0.65
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.33
Consensus pattern (75 bp):
ATCATGGAACATTTACCTAAACCATCATGGAACATTTACCTAACCCATTATCATGGAACATTTAC
CTAATCCATT
Found at i:46992 original size:25 final size:25
Alignment explanation
Indices: 46963--47067 Score: 201
Period size: 25 Copynumber: 4.2 Consensus size: 25
46953 CATGAAATCC
46963 ATCATGGAACATTTACCTAACCATT
1 ATCATGGAACATTTACCTAACCATT
46988 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAA-CCATT
47014 ATCATGGAACATTTACCTAACCATT
1 ATCATGGAACATTTACCTAACCATT
47039 ATCATGGAACATTTACCTAACCATT
1 ATCATGGAACATTTACCTAACCATT
47064 ATCA
1 ATCA
47068 ATGTATCAAT
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
25 54 0.68
26 25 0.32
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.31
Consensus pattern (25 bp):
ATCATGGAACATTTACCTAACCATT
Found at i:47023 original size:51 final size:50
Alignment explanation
Indices: 46963--47067 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 50
46953 CATGAAATCC
46963 ATCATGGAACATTTACCTAACCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCATTATCATGGAACATTTACCTAA-CCATT
47014 ATCATGGAACATTTACCTAACCATTATCATGGAACATTTACCTAACCATT
1 ATCATGGAACATTTACCTAACCATTATCATGGAACATTTACCTAACCATT
47064 ATCA
1 ATCA
47068 ATGTATCAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 9 0.17
51 45 0.83
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.31
Consensus pattern (50 bp):
ATCATGGAACATTTACCTAACCATTATCATGGAACATTTACCTAACCATT
Found at i:53940 original size:25 final size:26
Alignment explanation
Indices: 53886--53993 Score: 166
Period size: 26 Copynumber: 4.2 Consensus size: 26
53876 ATGAAGTCCC
*
53886 ATCATGCGAACACTTACCTAACCCATT
1 ATCATG-GAACATTTACCTAACCCATT
53913 ATCATGGAACATTTACCT-ACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
53938 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
53964 ATCATAGAACATTTACCTAA-CCATT
1 ATCATGGAACATTTACCTAACCCATT
53989 ATCAT
1 ATCAT
53994 TTTTATCAAT
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
25 34 0.45
26 36 0.47
27 6 0.08
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:53955 original size:51 final size:51
Alignment explanation
Indices: 53894--53993 Score: 173
Period size: 51 Copynumber: 2.0 Consensus size: 51
53884 CCATCATGCG
* *
53894 AACACTTACCTAACCCATTATCATGGAACATTTACCTACCCATTATCATGA
1 AACACTTACCTAACCCATTATCATAGAACATTTACCTAACCATTATCATGA
*
53945 AACATTTACCTAACCCATTATCATAGAACATTTACCTAACCATTATCAT
1 AACACTTACCTAACCCATTATCATAGAACATTTACCTAACCATTATCAT
53994 TTTTATCAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.31
Consensus pattern (51 bp):
AACACTTACCTAACCCATTATCATAGAACATTTACCTAACCATTATCATGA
Found at i:54144 original size:80 final size:85
Alignment explanation
Indices: 54027--54190 Score: 261
Period size: 82 Copynumber: 2.0 Consensus size: 85
54017 ATGGATATCA
54027 AGTGCACATTTTGTCTACAACAACATGATGGCTGCCACTT-ACTGTAAAAT-GG-AGTTTGTCAT
1 AGTGCACATTTTGTCTACAACAACATGATGGCTGCCACTTCA-TGTAAAATGGGAAGTTTGTCAT
54089 GCAAAT-CTCTTATTTTGCAC
65 GCAAATCCTCTTATTTTGCAC
54109 AGTGCACA-TTTGTCTAC-ACAACA-GATGGCTGGCCACTTCATGTAAAATGGGAAGTTTGTCAT
1 AGTGCACATTTTGTCTACAACAACATGATGGCT-GCCACTTCATGTAAAATGGGAAGTTTGTCAT
54171 GCAAATCCTCTTATTTTGCA
65 GCAAATCCTCTTATTTTGCA
54191 TCACTATTTA
Statistics
Matches: 77, Mismatches: 0, Indels: 9
0.90 0.00 0.10
Matches are distributed among these distances:
79 7 0.09
80 21 0.27
81 12 0.16
82 24 0.31
83 13 0.17
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (85 bp):
AGTGCACATTTTGTCTACAACAACATGATGGCTGCCACTTCATGTAAAATGGGAAGTTTGTCATG
CAAATCCTCTTATTTTGCAC
Done.