Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1894
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: 17372
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Found at i:2976 original size:27 final size:27
Alignment explanation
Indices: 2946--3024 Score: 68
Period size: 32 Copynumber: 2.7 Consensus size: 27
2936 AATAATCGTG
*
2946 TTTAAGATATTATATATTTATATAAAT
1 TTTAACATATTATATATTTATATAAAT
* *
2973 TTTAATACATTAATAATTTATATTATATAAAT
1 TTT-A-ACA-T-ATTATATAT-TTATATAAAT
3005 TATTAACATATTTATATATT
1 T-TTAACATA-TTATATATT
3025 CTTATTATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
27 3 0.08
28 1 0.03
29 4 0.10
30 8 0.20
31 10 0.25
32 12 0.30
33 2 0.05
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (27 bp):
TTTAACATATTATATATTTATATAAAT
Found at i:3498 original size:12 final size:12
Alignment explanation
Indices: 3463--3500 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3453 TAAATTTAAT
3463 TATAAAAAAT-A
1 TATAAAAAATAA
* *
3474 TATAAATATTAA
1 TATAAAAAATAA
3486 TATAAAAAATAA
1 TATAAAAAATAA
3498 TAT
1 TAT
3501 TTTAATATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TATAAAAAATAA
Found at i:3500 original size:24 final size:23
Alignment explanation
Indices: 3453--3496 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
3443 TATTTTTATT
3453 TAAATTTAATTATAAAAAATATA
1 TAAATTTAATTATAAAAAATATA
3476 TAAATATTAA-TATAAAAAATA
1 TAAAT-TTAATTATAAAAAATA
3497 ATATTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAATTTAATTATAAAAAATATA
Found at i:4603 original size:19 final size:18
Alignment explanation
Indices: 4581--4680 Score: 67
Period size: 19 Copynumber: 5.1 Consensus size: 18
4571 TAATAATATT
4581 ATATTATATAAATATATAA
1 ATATTAT-TAAATATATAA
*
4600 ATATT-TTAAATTTATATA
1 ATATTATTAAATATATA-A
4618 ATATCGTATTAAAATTAATATAAA
1 ATAT--TATT-AAA-T-ATAT-AA
* * *
4642 ATATCATAAAAAATATAA
1 ATATTATTAAATATATAA
*
4660 ATATAATTTAAATATATAA
1 ATATTA-TTAAATATATAA
4679 AT
1 AT
4681 TACAAGATTT
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
17 9 0.14
18 13 0.20
19 21 0.33
20 1 0.02
21 5 0.08
22 5 0.08
23 1 0.02
24 8 0.12
25 1 0.02
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (18 bp):
ATATTATTAAATATATAA
Found at i:5291 original size:3 final size:3
Alignment explanation
Indices: 5283--5319 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5273 CTTTTCAACC
5283 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5320 ATAAATTTAC
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5590 original size:3 final size:3
Alignment explanation
Indices: 5582--5653 Score: 137
Period size: 3 Copynumber: 24.3 Consensus size: 3
5572 TTGCTCTCTC
5582 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5630 ATT ATT ATT ATT ATT ATT A-T ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
5654 ATTCTCCAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 66 0.97
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5761 original size:12 final size:12
Alignment explanation
Indices: 5741--5787 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
5731 AAACTACTCA
*
5741 CTTTCCCTTCCC
1 CTTTCCCTTTCC
* *
5753 CTTTTCCTTTTC
1 CTTTCCCTTTCC
5765 CTTTCCCTTTCC
1 CTTTCCCTTTCC
5777 CTTT-CCTTTCC
1 CTTTCCCTTTCC
5788 ACTACTTCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 7 0.23
12 23 0.77
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (12 bp):
CTTTCCCTTTCC
Found at i:5767 original size:18 final size:17
Alignment explanation
Indices: 5741--5784 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
5731 AAACTACTCA
*
5741 CTTTCCCTTCCCCTTTTC
1 CTTTTCCTTCCCC-TTTC
*
5759 CTTTTCCTTTCCCTTTC
1 CTTTTCCTTCCCCTTTC
*
5776 CCTTTCCTT
1 CTTTTCCTT
5785 TCCACTACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (17 bp):
CTTTTCCTTCCCCTTTC
Found at i:5972 original size:15 final size:15
Alignment explanation
Indices: 5952--6004 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
5942 ACATAATTTT
5952 ATTTATTAAATTAAA
1 ATTTATTAAATTAAA
5967 ATTTA-TAATATT--A
1 ATTTATTAA-ATTAAA
*
5980 ATATATTAAA-TATAA
1 ATTTATTAAATTA-AA
5995 ATTTATTAAA
1 ATTTATTAAA
6005 AAAAACATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
12 1 0.03
13 6 0.19
14 6 0.19
15 18 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTATTAAATTAAA
Found at i:6851 original size:38 final size:36
Alignment explanation
Indices: 6782--6855 Score: 87
Period size: 38 Copynumber: 2.0 Consensus size: 36
6772 ATACGATTAC
*
6782 AAAATATAATATGTATAAAATTATCAAAATATTAAAT
1 AAAATAAAATATGTATAAAATTATCAAAATA-TAAAT
* *
6819 AAAATAAATATATTTATAAAATTTAT-ATAATATAAAT
1 AAAATAAA-ATATGTATAAAA-TTATCAAAATATAAAT
6856 TATTAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 12 0.38
38 16 0.50
39 4 0.12
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (36 bp):
AAAATAAAATATGTATAAAATTATCAAAATATAAAT
Found at i:6854 original size:16 final size:17
Alignment explanation
Indices: 6833--6926 Score: 62
Period size: 16 Copynumber: 5.9 Consensus size: 17
6823 TAAATATATT
6833 TATAAAAT-TTATATAA
1 TATAAAATATTATATAA
*
6849 TATAAATTATTA-AT-A
1 TATAAAATATTATATAA
*
6864 TATTAAAAT-TAATATAAA
1 TA-TAAAATATTATAT-AA
*
6882 TATAAAATATTTTA-AA
1 TATAAAATATTATATAA
* *
6898 TAT-AATTATAATAT-A
1 TATAAAATATTATATAA
6913 -ATAAAATA-TATATA
1 TATAAAATATTATATA
6927 CATAAAATTT
Statistics
Matches: 59, Mismatches: 10, Indels: 19
0.67 0.11 0.22
Matches are distributed among these distances:
14 6 0.10
15 17 0.29
16 21 0.36
17 9 0.15
18 6 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TATAAAATATTATATAA
Found at i:6878 original size:49 final size:46
Alignment explanation
Indices: 6816--6937 Score: 140
Period size: 49 Copynumber: 2.6 Consensus size: 46
6806 CAAAATATTA
* *
6816 AATAAAATAAATATATTTATAAAATTTATATAATATAAATTATTAATAT
1 AATAAAATTAATATATATATAAAATTTATA-AATAT-AATTA-TAATAT
* * *
6865 ATTAAAATTAATATAAATATAAAATATTTTAAATATAATTATAATAT
1 AATAAAATTAATATATATATAAAAT-TTATAAATATAATTATAATAT
*
6912 AATAAAA-T-ATATATACATAAAATTTA
1 AATAAAATTAATATATATATAAAATTTA
6938 AATCTACAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
44 2 0.03
45 13 0.21
46 1 0.02
47 12 0.19
48 5 0.08
49 26 0.41
50 4 0.06
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (46 bp):
AATAAAATTAATATATATATAAAATTTATAAATATAATTATAATAT
Found at i:6887 original size:17 final size:17
Alignment explanation
Indices: 6817--6902 Score: 65
Period size: 17 Copynumber: 5.2 Consensus size: 17
6807 AAAATATTAA
* **
6817 ATAAAATAAATATATTT
1 ATAAAATTAATATAAAT
*
6834 ATAAAATTTATAT-AAT
1 ATAAAATTAATATAAAT
6850 AT-AAATT-AT-TAATAT
1 ATAAAATTAATATAA-AT
6865 ATTAAAATTAATATAAAT
1 A-TAAAATTAATATAAAT
* *
6883 ATAAAA-TATTTTAAAT
1 ATAAAATTAATATAAAT
6899 ATAA
1 ATAA
6903 TTATAATATA
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
13 1 0.02
14 3 0.05
15 8 0.14
16 16 0.28
17 21 0.37
18 5 0.09
19 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAAATTAATATAAAT
Found at i:6890 original size:27 final size:28
Alignment explanation
Indices: 6843--6923 Score: 87
Period size: 27 Copynumber: 2.9 Consensus size: 28
6833 TATAAAATTT
*
6843 ATATAATATAAAT-TATTAATATATTAAA
1 ATATAATATAAATATA-AAATATATTAAA
*
6871 AT-TAATATAAATATAAAATAT-TTTAA
1 ATATAATATAAATATAAAATATATTAAA
6897 ATATAATTATAATATAATAAAATATAT
1 ATATAA-TATAA-AT-ATAAAATATAT
6924 ATACATAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
26 6 0.13
27 18 0.40
28 9 0.20
29 2 0.04
30 9 0.20
31 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
ATATAATATAAATATAAAATATATTAAA
Found at i:7447 original size:19 final size:20
Alignment explanation
Indices: 7425--7463 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
7415 TATTAATTGA
7425 ATAA-AAAAATATAATTTTT
1 ATAATAAAAATATAATTTTT
*
7444 ATAATTAAAATTATAATTTT
1 ATAA-TAAAAATATAATTTT
7464 GTAATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
21 13 0.76
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAATAAAAATATAATTTTT
Found at i:8420 original size:14 final size:14
Alignment explanation
Indices: 8402--8450 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
8392 TATAATTTTA
8402 AAAATATATAAATT
1 AAAATATATAAATT
*
8416 GAAATACT-TAAATT
1 AAAATA-TATAAATT
*
8430 AATAATATAAAAATT
1 AA-AATATATAAATT
8445 AAAATA
1 AAAATA
8451 CTCTATAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (14 bp):
AAAATATATAAATT
Found at i:8727 original size:19 final size:17
Alignment explanation
Indices: 8705--8747 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
8695 CAATATATAT
8705 ATTTGTCATTAAAATAATA
1 ATTT-TCATTAAAA-AATA
* *
8724 ATTTTGATTTAAAAATA
1 ATTTTCATTAAAAAATA
8741 ATTTTCA
1 ATTTTCA
8748 AATTAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 10 0.48
18 7 0.33
19 4 0.19
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (17 bp):
ATTTTCATTAAAAAATA
Found at i:9439 original size:22 final size:22
Alignment explanation
Indices: 9414--9477 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 22
9404 AAAAAAATAT
9414 ATTTAATAATTTTA-AAATTTTA
1 ATTTAA-AATTTTATAAATTTTA
* *
9436 ATTTTAAATTTTATAAATTTTT
1 ATTTAAAATTTTATAAATTTTA
*
9458 ATTCATAAA--TTATAAATTTT
1 ATTTA-AAATTTTATAAATTTT
9478 TTTATATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 18 0.50
22 15 0.42
23 3 0.08
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTAAAATTTTATAAATTTTA
Found at i:9522 original size:38 final size:38
Alignment explanation
Indices: 9479--9593 Score: 103
Period size: 38 Copynumber: 3.0 Consensus size: 38
9469 ATAAATTTTT
* *
9479 TTATATATAAAAATATAATAATATTAGATAT-AATATAA
1 TTATATATAAAAATA-AATAAAATAAGATATAAATATAA
*
9517 TTATATA-AAAAATAATTAAAATAAGATATAAAATATAA
1 TTATATATAAAAATAAATAAAATAAGATAT-AAATATAA
* *
9555 TATAATATTTAAAAATGATATAAATATAA-A-ATAAATATA
1 T-T-ATATATAAAAAT-AAATAAA-ATAAGATATAAATATA
9594 TAATATGTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
36 12 0.19
37 7 0.11
38 15 0.23
39 1 0.02
40 11 0.17
41 8 0.12
42 6 0.09
43 4 0.06
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (38 bp):
TTATATATAAAAATAAATAAAATAAGATATAAATATAA
Found at i:9567 original size:19 final size:19
Alignment explanation
Indices: 9545--9665 Score: 86
Period size: 18 Copynumber: 6.8 Consensus size: 19
9535 AAATAAGATA
9545 TAAAATATAATATAATATT
1 TAAAATATAATATAATATT
* *
9564 TAAAA-ATGATATAA-ATA
1 TAAAATATAATATAATATT
*
9581 TAAAATAAATATATAATATGT
1 TAAAATATA-ATATAATAT-T
*
9602 TAAAATTTATAA-A-AATAAT
1 TAAAA--TATAATATAATATT
9621 T-AAA-AT-AT-T-ATA--
1 TAAAATATAATATAATATT
9633 TAAAATATAATATAATATT
1 TAAAATATAATATAATATT
9652 TAAAA-ATAATATAA
1 TAAAATATAATATAA
9666 AAATAAATTA
Statistics
Matches: 80, Mismatches: 7, Indels: 31
0.68 0.06 0.26
Matches are distributed among these distances:
12 1 0.01
13 3 0.04
14 6 0.08
15 4 0.05
16 1 0.01
17 10 0.12
18 21 0.26
19 18 0.22
20 6 0.08
21 6 0.08
22 1 0.01
23 3 0.04
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
TAAAATATAATATAATATT
Found at i:9575 original size:30 final size:29
Alignment explanation
Indices: 9483--9673 Score: 128
Period size: 29 Copynumber: 6.5 Consensus size: 29
9473 ATTTTTTTAT
* * *
9483 ATATAAAA-ATATAATAATA-TTAGATATA
1 ATATAAAATATA-AATAATATTTAAAAATG
* * * *
9511 ATATAATTATATAAAAAATAATTAAAATAAG
1 ATATAA-AATATAAATAATATTTAAAA-ATG
9542 ATATAAAATATAATATAATATTTAAAAATG
1 ATATAAAATATAA-ATAATATTTAAAAATG
* *
9572 ATAT-AAATATAAAATAA-ATATATAATATG
1 ATATAAAATAT-AAATAATATTTA-AAAATG
* *
9601 -T-TAAAATTTATAAA-AATAATTAAAATATT
1 ATATAAAA--TATAAATAATATTTAAAA-ATG
*
9630 ATATAAAATATAATATAATATTTAAAAATA
1 ATATAAAATATAA-ATAATATTTAAAAATG
9660 ATATAAAA-ATAAAT
1 ATATAAAATATAAAT
9674 TAAATATATA
Statistics
Matches: 129, Mismatches: 18, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
27 1 0.01
28 20 0.16
29 39 0.30
30 36 0.28
31 33 0.26
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (29 bp):
ATATAAAATATAAATAATATTTAAAAATG
Found at i:9582 original size:36 final size:37
Alignment explanation
Indices: 9537--9635 Score: 110
Period size: 38 Copynumber: 2.6 Consensus size: 37
9527 AATAATTAAA
9537 ATAAGATATAAAATATAATATAATAT-TTAAAAATGAT
1 ATAA-ATATAAAATATAATATAATATGTTAAAAATGAT
* * *
9574 ATAAATATAAAATAAATATATAATATGTTAAAATTTAT
1 ATAAATATAAAATATA-ATATAATATGTTAAAAATGAT
* *
9612 AAAAATAATTAAAATATTATATAA
1 ATAAAT-A-TAAAATATAATATAA
9636 AATATAATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
36 11 0.21
37 13 0.25
38 14 0.27
39 7 0.13
40 7 0.13
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (37 bp):
ATAAATATAAAATATAATATAATATGTTAAAAATGAT
Found at i:9615 original size:47 final size:46
Alignment explanation
Indices: 9533--9697 Score: 162
Period size: 47 Copynumber: 3.6 Consensus size: 46
9523 AAAAAATAAT
* * * *
9533 TAAAATAAGATATAAAATATAATATAATATTTAAAAATGATATAAATA
1 TAAAATAA-ATATATAATATATTAAAAT-TTTAAAAATAATATAAATA
*
9581 TAAAATAAATATATAATATGTTAAAATTTATAAAAATAAT-TAAAATA
1 TAAAATAAATATATAATATATTAAAATTT-TAAAAATAATAT-AAATA
* * * *
9628 TTATATAAA-ATAT-A-ATA-TAATA-TTTAAAAATAATATAAAAA
1 TAAAATAAATATATAATATATTAAAATTTTAAAAATAATATAAATA
*
9669 TAAATTAAATATATAATATATTAAAATTT
1 TAAAATAAATATATAATATATTAAAATTT
9698 ATATAACATA
Statistics
Matches: 95, Mismatches: 14, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
41 20 0.21
42 7 0.07
43 5 0.05
44 5 0.05
45 5 0.05
46 9 0.09
47 36 0.38
48 8 0.08
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (46 bp):
TAAAATAAATATATAATATATTAAAATTTTAAAAATAATATAAATA
Found at i:9634 original size:88 final size:87
Alignment explanation
Indices: 9483--9734 Score: 312
Period size: 88 Copynumber: 2.8 Consensus size: 87
9473 ATTTTTTTAT
* * * *
9483 ATATAAAAATATAAT-AATAT-TAGATATAATATAATTATATAAAAAATAATTAAAATAAGATAT
1 ATATAAAAATAAAATAAATATATA-ATATATTAAAATT-TAT-AAAAATAATTAAAAT-ATATAT
*
9546 AAAATATAATATAATATTTAAAAATG
62 AAAATATAATATAATATTTAAAAATA
* *
9572 ATATAAATATAAAATAAATATATAATATGTTAAAATTTATAAAAATAATTAAAATATTATATAAA
1 ATATAAAAATAAAATAAATATATAATATATTAAAATTTATAAAAATAATTAAAATA-TATATAAA
9637 ATATAATATAATATTTAAAAATA
65 ATATAATATAATATTTAAAAATA
* *
9660 ATATAAAAATAAATTAAATATATAATATATTAAAATTTATATAACATAAATTATTAAATATAT-T
1 ATATAAAAATAAAATAAATATATAATATATTAAAATTTATA-AAAAT-AATTA--AAATATATAT
*
9724 AAAATTTAATA
62 AAAATATAATA
9735 AAAATATATA
Statistics
Matches: 144, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
87 1 0.01
88 82 0.57
89 20 0.14
90 31 0.22
91 5 0.03
92 5 0.03
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (87 bp):
ATATAAAAATAAAATAAATATATAATATATTAAAATTTATAAAAATAATTAAAATATATATAAAA
TATAATATAATATTTAAAAATA
Found at i:9665 original size:52 final size:54
Alignment explanation
Indices: 9572--9688 Score: 154
Period size: 52 Copynumber: 2.2 Consensus size: 54
9562 TTTAAAAATG
*
9572 ATATA-AATATAAAATAAATATATAATATGTTAAAATTTATAAAAAT-AATTAA
1 ATATATAATATAAAATAAATATATAATATGTTAAAATATATAAAAATAAATTAA
* *
9624 A-ATATTATATAAAATATA-ATATAATAT-TTAAAAATAATATAAAAATAAATTAA
1 ATATATAATATAAAATAAATATATAATATGTT-AAAAT-ATATAAAAATAAATTAA
9677 ATATATAATATA
1 ATATATAATATA
9689 TTAAAATTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
50 2 0.04
51 17 0.30
52 21 0.38
53 7 0.12
54 9 0.16
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (54 bp):
ATATATAATATAAAATAAATATATAATATGTTAAAATATATAAAAATAAATTAA
Found at i:9680 original size:30 final size:30
Alignment explanation
Indices: 9481--9680 Score: 127
Period size: 30 Copynumber: 6.7 Consensus size: 30
9471 AAATTTTTTT
*
9481 ATATATAAAAATATAAT-AATA-TTAGATATA
1 ATATAT-AAAATATAATAAATATTTA-AAATA
** * *
9511 ATATA-ATTATATAAAAAATAATTAAAATA
1 ATATATAAAATATAATAAATATTTAAAATA
*
9540 AGATATAAAATATAATATAATATTT-AAA-A
1 ATATATAAAATATAATA-AATATTTAAAATA
* *
9569 ATGATATAAATATAAAATAAATA--TATAAT-
1 AT-ATATAAA-ATATAATAAATATTTAAAATA
* *
9598 ATGT-TAAAATTTATAA-AAATAATTAAAATA
1 ATATATAAAA--TATAATAAATATTTAAAATA
*
9628 TTATATAAAATATAATATAATATTTAAAAATA
1 ATATATAAAATATAATA-AATATTT-AAAATA
9660 ATATA-AAAATA-AATTAAATAT
1 ATATATAAAATATAA-TAAATAT
9681 ATAATATATT
Statistics
Matches: 133, Mismatches: 19, Indels: 36
0.71 0.10 0.19
Matches are distributed among these distances:
26 1 0.01
27 9 0.07
28 13 0.10
29 28 0.21
30 40 0.30
31 32 0.24
32 10 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (30 bp):
ATATATAAAATATAATAAATATTTAAAATA
Found at i:9695 original size:37 final size:35
Alignment explanation
Indices: 9615--9737 Score: 104
Period size: 37 Copynumber: 3.7 Consensus size: 35
9605 AATTTATAAA
9615 AATA-ATTAAAATATTATATAAAAT--A-TA-ATAT
1 AATATATTAAAATA-TATATAAAATAAATTATATAT
9646 AATAT-TTAAAA-ATAATATAAAAATAAATTAAATATAT
1 AATATATTAAAATAT-ATAT-AAAATAAATT--ATATAT
* *
9683 AATATATTAAAATTTATATAACATAAATTAT-TA-
1 AATATATTAAAATATATATAAAATAAATTATATAT
*
9716 AATATATTAAAATTTA-ATAAAA
1 AATATATTAAAATATATATAAAA
9738 ATATATAATT
Statistics
Matches: 78, Mismatches: 3, Indels: 21
0.76 0.03 0.21
Matches are distributed among these distances:
29 1 0.01
30 5 0.06
31 15 0.19
32 5 0.06
33 17 0.22
34 3 0.04
35 2 0.03
36 1 0.01
37 18 0.23
38 10 0.13
39 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (35 bp):
AATATATTAAAATATATATAAAATAAATTATATAT
Found at i:9736 original size:19 final size:19
Alignment explanation
Indices: 9595--9741 Score: 52
Period size: 19 Copynumber: 7.4 Consensus size: 19
9585 ATAAATATAT
*
9595 AATATGTTAAAATTT-ATA
1 AATATATTAAAATTTAATA
*
9613 AAAATAATTAAAATATTATATAA
1 AATAT-ATTAAAAT-TTA-AT-A
*
9636 AATATAATATAATATTTAA-A
1 AATAT-AT-TAAAATTTAATA
* *
9656 AATA-ATATAAAAATAAATTA
1 AATATAT-TAAAATTTAA-TA
*
9676 AATATA-TAATATATTAA-A
1 AATATATTAAAAT-TTAATA
* * * *
9694 ATTTATATAACATAAATTATTA
1 A-ATATATTA-A-AATTTAATA
9716 AATATATTAAAATTTAATA
1 AATATATTAAAATTTAATA
*
9735 AAAATAT
1 AATATAT
9742 ATAATTTTTT
Statistics
Matches: 94, Mismatches: 20, Indels: 29
0.66 0.14 0.20
Matches are distributed among these distances:
18 16 0.17
19 28 0.30
20 17 0.18
21 11 0.12
22 6 0.06
23 11 0.12
24 5 0.05
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.39
Consensus pattern (19 bp):
AATATATTAAAATTTAATA
Found at i:9881 original size:11 final size:10
Alignment explanation
Indices: 9865--9898 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
9855 GCAAAGAGAG
9865 TTTTTCTTTT
1 TTTTTCTTTT
9875 CTTTTTCATTTT
1 -TTTTTC-TTTT
9887 TTTTTCTTTT
1 TTTTTCTTTT
9897 TT
1 TT
9899 GTTTATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.27
11 12 0.55
12 4 0.18
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:16831 original size:39 final size:39
Alignment explanation
Indices: 16782--16865 Score: 132
Period size: 39 Copynumber: 2.2 Consensus size: 39
16772 AGCTGATATT
16782 TTTGTACTCATGTATGAAAACGTAAGTTTTGATGATTTA
1 TTTGTACTCATGTATGAAAACGTAAGTTTTGATGATTTA
* * *
16821 TTTGTACTCATGTCTGAAAACGTAGGTTTTGATTATTTA
1 TTTGTACTCATGTATGAAAACGTAAGTTTTGATGATTTA
*
16860 TCTGTA
1 TTTGTA
16866 TACTTCATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.27, C:0.10, G:0.18, T:0.45
Consensus pattern (39 bp):
TTTGTACTCATGTATGAAAACGTAAGTTTTGATGATTTA
Found at i:17276 original size:2 final size:2
Alignment explanation
Indices: 17269--17307 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
17259 CATCATCATC
17269 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17308 CCGTCCCCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.