Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1856
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: 140810
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Found at i:912 original size:20 final size:21
Alignment explanation
Indices: 874--915 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
864 AATAAACTTG
* *
874 AAAATATTACACATGATTTAA
1 AAAATAATACAAATGATTTAA
895 AAAATAATACAAAT-ATTTAA
1 AAAATAATACAAATGATTTAA
915 A
1 A
916 TATCATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (21 bp):
AAAATAATACAAATGATTTAA
Found at i:1371 original size:19 final size:20
Alignment explanation
Indices: 1334--1374 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1324 AAAAAAATAT
1334 ATTAAAGATTATATTATTAA
1 ATTAAAGATTATATTATTAA
1354 ATTAAA-ATTAT-TTGATTAA
1 ATTAAAGATTATATT-ATTAA
1373 AT
1 AT
1375 ATTCAACTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 2 0.10
19 12 0.60
20 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
ATTAAAGATTATATTATTAA
Found at i:2813 original size:13 final size:13
Alignment explanation
Indices: 2783--2845 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 13
2773 CTGTAGATTT
2783 TTAAAAAAA-TTA
1 TTAAAAAAACTTA
**
2795 ACAAAAAAACTTA
1 TTAAAAAAACTTA
2808 TTAAAAATATACTTA
1 TTAAAAA-A-ACTTA
*
2823 TTATAAAAAATTATA
1 TTA-AAAAAACT-TA
2838 TTAAAAAA
1 TTAAAAAA
2846 CATATTTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
12 7 0.17
13 8 0.20
14 8 0.20
15 14 0.34
16 4 0.10
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (13 bp):
TTAAAAAAACTTA
Found at i:3570 original size:31 final size:31
Alignment explanation
Indices: 3532--3590 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3522 TTGTGTTTAT
*
3532 TTTTTAATA-AATAATAATAATATAATTATTA
1 TTTTTAATACAAAAATAAT-ATATAATTATTA
*
3563 TTTTTAATACAAAAATAATATTTAATTA
1 TTTTTAATACAAAAATAATATATAATTA
3591 ACTTTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (31 bp):
TTTTTAATACAAAAATAATATATAATTATTA
Found at i:3820 original size:127 final size:129
Alignment explanation
Indices: 3640--3894 Score: 367
Period size: 128 Copynumber: 2.0 Consensus size: 129
3630 AAAATTAAAT
*
3640 TAAAAAAAGTTTATTATTATTATTATTTAATAAAATTAAAAATAATATTTAATTAAGTTAAAA-A
1 TAAAAAAAGTTTATTATTATAATTATTTAATAAAATTAAAAATAATATTTAATTAAGTTAAAACA
*
3704 ATTACATTAACAAATTAAAATATTAATTATATAT-TTTATAAAAATAAAAGTATTAAATAAAAAA
66 ATTACATTAACAAATTAAAATATTAATTAT-TATGTTTATAAAAATAAAAATATTAAATAAAAAA
* *
3768 TAAAAAAGGTTTTTTTATTATAATT-TTTAATAAAA-T-AAAATAAATATTTAATTAAGTTAAAA
1 TAAAAAAAG-TTTATTATTATAATTATTTAATAAAATTAAAAAT-AATATTTAATTAAGTTAAAA
* * * * *
3830 CATTTACATTAACAAATTAAAATATTAATTATTATGTTTTTTAAAATAAAAATTTTAAATTAAAA
64 CAATTACATTAACAAATTAAAATATTAATTATTATGTTTATAAAAATAAAAATATTAAATAAAAA
3895 TTTTATTATT
Statistics
Matches: 114, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
126 5 0.04
127 24 0.21
128 72 0.63
129 13 0.11
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (129 bp):
TAAAAAAAGTTTATTATTATAATTATTTAATAAAATTAAAAATAATATTTAATTAAGTTAAAACA
ATTACATTAACAAATTAAAATATTAATTATTATGTTTATAAAAATAAAAATATTAAATAAAAAA
Found at i:7630 original size:24 final size:23
Alignment explanation
Indices: 7603--7672 Score: 68
Period size: 25 Copynumber: 2.9 Consensus size: 23
7593 AATTAATATT
7603 TAAATTTATATAATAAAATAAAAA
1 TAAATTTATA-AATAAAATAAAAA
* * *
7627 TAAATTTCATAAAAATAAATTAAAT
1 TAAATTT-ATAAATA-AAATAAAAA
* *
7652 TAATTTTAAAAATAAAATAAA
1 TAAATTTATAAATAAAATAAA
7673 TTAGATTTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
23 6 0.16
24 15 0.41
25 16 0.43
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (23 bp):
TAAATTTATAAATAAAATAAAAA
Found at i:7664 original size:22 final size:23
Alignment explanation
Indices: 7636--7680 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
7626 ATAAATTTCA
*
7636 TAAAAATAAATTAAATTA-ATTT
1 TAAAAATAAAATAAATTAGATTT
7658 TAAAAATAAAATAAATTAGATTT
1 TAAAAATAAAATAAATTAGATTT
7681 AAATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
TAAAAATAAAATAAATTAGATTT
Found at i:8139 original size:39 final size:43
Alignment explanation
Indices: 8081--8166 Score: 108
Period size: 41 Copynumber: 2.1 Consensus size: 43
8071 TAAACCCTTT
*
8081 TTAATTTAATTTTTATTTAAAAATAATT-AATATT-TATTTTA
1 TTAATATAATTTTTATTTAAAAATAATTAAATATTATATTTTA
** *
8122 TTAATATAA-TTTT-TTTAAAGTTAATTAAATATTATTTTTTA
1 TTAATATAATTTTTATTTAAAAATAATTAAATATTATATTTTA
8163 TTAA
1 TTAA
8167 AAATAATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
39 11 0.28
40 10 0.26
41 18 0.46
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (43 bp):
TTAATATAATTTTTATTTAAAAATAATTAAATATTATATTTTA
Found at i:9854 original size:2 final size:2
Alignment explanation
Indices: 9794--9845 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
9784 AAACATATTG
9794 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
9836 AT AT AT AT AT
1 AT AT AT AT AT
9846 GAGATATATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11746 original size:21 final size:21
Alignment explanation
Indices: 11721--11766 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
11711 TTTGTTTGTA
11721 TATTTATTT-T-TATCATGATTT
1 TATTTATTTATCTATC-T-ATTT
11742 TATTTATTTATCTATCTATTT
1 TATTTATTTATCTATCTATTT
11763 TATT
1 TATT
11767 GTGTTTGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 17 0.74
22 2 0.09
23 4 0.17
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (21 bp):
TATTTATTTATCTATCTATTT
Found at i:14434 original size:2 final size:2
Alignment explanation
Indices: 14427--14462 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
14417 ACTTACATTT
14427 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14463 AAGATAAAGG
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16994 original size:2 final size:2
Alignment explanation
Indices: 16989--17019 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16979 TTTTTTCATG
16989 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 T
17020 GGATGAGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18251 original size:2 final size:2
Alignment explanation
Indices: 18244--18291 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
18234 CATTTCGTAC
18244 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
*
18286 AC AT AT
1 AT AT AT
18292 GTGGAACTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21449 original size:7 final size:7
Alignment explanation
Indices: 21430--21476 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
21420 CAATATCATT
21430 TTTAATA
1 TTTAATA
21437 -TTAATA
1 TTTAATA
21443 TTTAATAAA
1 TTTAAT--A
*
21452 TTTAAAA
1 TTTAATA
*
21459 TTTAAAA
1 TTTAATA
21466 TTTAATA
1 TTTAATA
21473 TTTA
1 TTTA
21477 TAACCCCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 6 0.17
7 23 0.66
9 6 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (7 bp):
TTTAATA
Found at i:21678 original size:3 final size:3
Alignment explanation
Indices: 21670--21725 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
21660 ACCAAAAGAC
21670 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
21718 AAT AAT AA
1 AAT AAT AA
21726 ATTAAAAAGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:21874 original size:2 final size:2
Alignment explanation
Indices: 21867--21918 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
21857 TCTTTCATGA
21867 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
21909 AT AT AT AT AT
1 AT AT AT AT AT
21919 TAAGATTACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22215 original size:4 final size:4
Alignment explanation
Indices: 22206--22234 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
22196 AGCTAGTTCT
22206 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
22235 ACATGGCTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:23540 original size:2 final size:2
Alignment explanation
Indices: 23533--23562 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23523 TTTCTTACCC
23533 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
23563 TAACTAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26198 original size:18 final size:18
Alignment explanation
Indices: 26168--26216 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
26158 CGTAATTATG
26168 AAAAAATAAAAA-TAATT
1 AAAAAATAAAAATTAATT
*
26185 AAAAAATTAGAAATTAATTT
1 AAAAAA-TAAAAATTAA-TT
26205 AAACAAATAAAA
1 AAA-AAATAAAA
26217 TAAGTGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 6 0.23
18 5 0.19
19 3 0.12
20 9 0.35
21 3 0.12
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (18 bp):
AAAAAATAAAAATTAATT
Found at i:26217 original size:19 final size:17
Alignment explanation
Indices: 26168--26217 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 17
26158 CGTAATTATG
*
26168 AAAAAATAAAAATAATT
1 AAAAAATAAAATTAATT
26185 AAAAAATTAGAAATTAATTT
1 AAAAAA-TA-AAATTAA-TT
26205 AAACAAATAAAAT
1 AAA-AAATAAAAT
26218 AAGTGAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 6 0.21
18 2 0.07
19 10 0.36
20 7 0.25
21 3 0.11
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
AAAAAATAAAATTAATT
Found at i:28708 original size:11 final size:10
Alignment explanation
Indices: 28677--28713 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
28667 AAAATTAATT
28677 TAAAAACAAA
1 TAAAAACAAA
28687 TAAAAACAAA
1 TAAAAACAAA
*
28697 TAAAATCTAAA
1 TAAAAAC-AAA
28708 TAAAAA
1 TAAAAA
28714 TATTTAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (10 bp):
TAAAAACAAA
Found at i:37083 original size:38 final size:37
Alignment explanation
Indices: 37041--37175 Score: 128
Period size: 38 Copynumber: 3.6 Consensus size: 37
37031 GTTCAATTTG
* * *
37041 GAATTCTCTAGCCGCCAATCACTATCCAATTCCAAATT
1 GAATTCTCTAACCGTCAATCAC-AGCCAATTCCAAATT
* * * *
37079 GAATTCTCTAGCTGGCAGCTGC-CAGCCAATTCCAAATT
1 GAATTCTCTAACCGTCA-AT-CACAGCCAATTCCAAATT
** * *
37117 GAATTCTCTAACCGTCAGCCGCCAGCCAATTTCAAATT
1 GAATTCTCTAACCGTCAATC-ACAGCCAATTCCAAATT
37155 GAATTCTCTAACCGTCAATCA
1 GAATTCTCTAACCGTCAATCA
37176 ATTCAATTTG
Statistics
Matches: 80, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
36 1 0.01
38 76 0.95
39 2 0.03
40 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.27
Consensus pattern (37 bp):
GAATTCTCTAACCGTCAATCACAGCCAATTCCAAATT
Found at i:41835 original size:76 final size:76
Alignment explanation
Indices: 41721--41867 Score: 222
Period size: 76 Copynumber: 1.9 Consensus size: 76
41711 CTCTAGTCGC
* * * * *
41721 CAGCCACCATCAAATTCCAAATTGAATTTTCTAGCCGTCAGCTGCCAGCCAATTCCAAATTGAAT
1 CAGCCACCAGCAAATTCCAAATTGAATTCTCTAACCGTCAGCCGCCAACCAATTCCAAATTGAAT
41786 TCTCTAGCTAT
66 TCTCTAGCTAT
* * *
41797 CAGCCACCAGCCAATTCCAAATTGAATTCTCTAACCGTCAGCCGCCAACTAATTTCAAATTGAAT
1 CAGCCACCAGCAAATTCCAAATTGAATTCTCTAACCGTCAGCCGCCAACCAATTCCAAATTGAAT
41862 TCTCTA
66 TCTCTA
41868 ACCATCAACC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
76 63 1.00
ACGTcount: A:0.31, C:0.30, G:0.11, T:0.28
Consensus pattern (76 bp):
CAGCCACCAGCAAATTCCAAATTGAATTCTCTAACCGTCAGCCGCCAACCAATTCCAAATTGAAT
TCTCTAGCTAT
Found at i:41870 original size:38 final size:38
Alignment explanation
Indices: 41706--41867 Score: 198
Period size: 38 Copynumber: 4.3 Consensus size: 38
41696 GTTTAATTTG
* * * *
41706 GAATTCTCTAGTCGCCAGCCACCATCAAATTCCAAATT
1 GAATTCTCTAGCCGTCAGCCACCAGCCAATTCCAAATT
* **
41744 GAATTTTCTAGCCGTCAGCTGCCAGCCAATTCCAAATT
1 GAATTCTCTAGCCGTCAGCCACCAGCCAATTCCAAATT
**
41782 GAATTCTCTAGCTATCAGCCACCAGCCAATTCCAAATT
1 GAATTCTCTAGCCGTCAGCCACCAGCCAATTCCAAATT
* * * * *
41820 GAATTCTCTAACCGTCAGCCGCCAACTAATTTCAAATT
1 GAATTCTCTAGCCGTCAGCCACCAGCCAATTCCAAATT
41858 GAATTCTCTA
1 GAATTCTCTA
41868 ACCATCAACC
Statistics
Matches: 105, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 105 1.00
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.28
Consensus pattern (38 bp):
GAATTCTCTAGCCGTCAGCCACCAGCCAATTCCAAATT
Found at i:43748 original size:2 final size:2
Alignment explanation
Indices: 43741--43767 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43731 AGACTTTAAT
43741 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 T
43768 GTGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43772 original size:2 final size:2
Alignment explanation
Indices: 43767--43797 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
43757 TATATATATA
43767 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
43798 TTTGTCCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:45631 original size:13 final size:14
Alignment explanation
Indices: 45607--45635 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
45597 ATTTATATAG
45607 TGTATCTATATTTT
1 TGTATCTATATTTT
45621 TGTATCT-TATTTT
1 TGTATCTATATTTT
45634 TG
1 TG
45636 AACACTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.66
Consensus pattern (14 bp):
TGTATCTATATTTT
Found at i:47327 original size:14 final size:13
Alignment explanation
Indices: 47302--47326 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47292 AGGCAATAAT
47302 TTTTATAATTTTC
1 TTTTATAATTTTC
47315 TTTTATAATTTT
1 TTTTATAATTTT
47327 TTCATATGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTATAATTTTC
Found at i:47768 original size:9 final size:9
Alignment explanation
Indices: 47754--47782 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
47744 TTTTTATCAA
47754 TTATTTATT
1 TTATTTATT
47763 TTATTTATT
1 TTATTTATT
47772 TTATTT-TT
1 TTATTTATT
47780 TTA
1 TTA
47783 AATATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTATTTATT
Found at i:49611 original size:2 final size:2
Alignment explanation
Indices: 49604--49629 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
49594 AAAAAGATTC
49604 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
49630 GTAAAGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57110 original size:14 final size:14
Alignment explanation
Indices: 57088--57130 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
57078 TTTTATCATG
*
57088 TATTCATATTATAT
1 TATTTATATTATAT
*
57102 TATTTATATCATAT
1 TATTTATATTATAT
*
57116 TTTTTATATTATAT
1 TATTTATATTATAT
57130 T
1 T
57131 CATGTTGCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTTATATTATAT
Found at i:57115 original size:19 final size:19
Alignment explanation
Indices: 57091--57129 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
57081 TATCATGTAT
57091 TCATATTATATTAT-TTATA
1 TCATATT-TATTATATTATA
*
57110 TCATATTTTTTATATTATA
1 TCATATTTATTATATTATA
57129 T
1 T
57130 TCATGTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TCATATTTATTATATTATA
Found at i:57116 original size:25 final size:25
Alignment explanation
Indices: 57065--57116 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
57055 TATATTAGAG
57065 TCATATTTATATATTTTATCATGTAT
1 TCATATTTATATATTTTATCA-GTAT
57091 TCATA-TTATATTATTTATATCA-TAT
1 TCATATTTATA-TATTT-TATCAGTAT
57116 T
1 T
57117 TTTTATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 9 0.38
26 10 0.42
27 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.58
Consensus pattern (25 bp):
TCATATTTATATATTTTATCAGTAT
Found at i:66185 original size:2 final size:2
Alignment explanation
Indices: 66178--66210 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
66168 AATAGATGTG
*
66178 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
66211 AAGGAAGGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:69563 original size:12 final size:12
Alignment explanation
Indices: 69510--69567 Score: 57
Period size: 12 Copynumber: 4.7 Consensus size: 12
69500 TCATCTCATA
69510 TTTT-TATTATT
1 TTTTATATTATT
69521 TTTTATATCGTATAT
1 TTTTATAT--TAT-T
*
69536 TTTTATATTATA
1 TTTTATATTATT
69548 TTTTA-ATTACTT
1 TTTTATATTA-TT
69560 TTTTATAT
1 TTTTATAT
69568 CGTGTCGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
11 8 0.21
12 14 0.36
13 5 0.13
14 3 0.08
15 9 0.23
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATATTATT
Found at i:70972 original size:2 final size:2
Alignment explanation
Indices: 70965--70992 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
70955 GACTGTAATC
70965 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
70993 GTTTTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74224 original size:21 final size:21
Alignment explanation
Indices: 74209--74264 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
74199 TTTTTTCAGA
74209 TTTAGAAGCTTATTTTACATC
1 TTTAGAAGCTTATTTTACATC
*
74230 TTTAGAAGCTTAGTTTACATC
1 TTTAGAAGCTTATTTTACATC
74251 TTTAGAAGCTTATT
1 TTTAGAAGCTTATT
74265 CAAGATCCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (21 bp):
TTTAGAAGCTTATTTTACATC
Found at i:77000 original size:72 final size:72
Alignment explanation
Indices: 76768--76992 Score: 441
Period size: 72 Copynumber: 3.1 Consensus size: 72
76758 TTTGATTTCT
76768 TTGGATTTATCTAATAATAATTTACAAGGCCATATCCCTGATTCATTTGGTAACTTGGTTAGTTT
1 TTGGATTTATCTAATAATAATTTACAAGGCCATATCCCTGATTCATTTGGTAACTTGGTTAGTTT
76833 GGAATTC
66 GGAATTC
76840 TTGGATTTATCTAATAATAATTTACAAGGCCATATCCCTGATTCATTTGGTAACTTGGTTAGTTT
1 TTGGATTTATCTAATAATAATTTACAAGGCCATATCCCTGATTCATTTGGTAACTTGGTTAGTTT
76905 GGAATTC
66 GGAATTC
*
76912 TTGGATTTATCTAATAATAATTTACAAGGCCATATCCCTTATTCATTTGGTAACTTGGTTAGTTT
1 TTGGATTTATCTAATAATAATTTACAAGGCCATATCCCTGATTCATTTGGTAACTTGGTTAGTTT
76977 GGAATTC
66 GGAATTC
76984 TTGGATTTA
1 TTGGATTTA
76993 CGCAATAACA
Statistics
Matches: 152, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 152 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (72 bp):
TTGGATTTATCTAATAATAATTTACAAGGCCATATCCCTGATTCATTTGGTAACTTGGTTAGTTT
GGAATTC
Found at i:79793 original size:22 final size:23
Alignment explanation
Indices: 79742--79793 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
79732 GAAACACAAA
*
79742 ATGAACACAACATAAAAAATAAT
1 ATGAATACAACATAAAAAATAAT
* *
79765 -TAAAATACAGCAT-AAAAATAAT
1 AT-GAATACAACATAAAAAATAAT
79787 ATGAATA
1 ATGAATA
79794 TAATACAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.63, C:0.10, G:0.06, T:0.21
Consensus pattern (23 bp):
ATGAATACAACATAAAAAATAAT
Found at i:80650 original size:58 final size:59
Alignment explanation
Indices: 80571--80683 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 59
80561 CAATTTTTTT
* * *
80571 AATTAAATCATTATAACAAATTATG-AAAAAATGTCACGAATTGAGATATGATACATTA
1 AATTAAATCATTATAAAAAATTATGTAAAAAATGTCACGAATGGAGATACGATACATTA
* * *
80629 AATTAAATTATTA-AGAAAAATTATGTAAAATATGTCATGAATGGAGATACGATAC
1 AATTAAATCATTATA-AAAAATTATGTAAAAAATGTCACGAATGGAGATACGATAC
80684 GAATATGACA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 1 0.02
58 21 0.45
59 25 0.53
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (59 bp):
AATTAAATCATTATAAAAAATTATGTAAAAAATGTCACGAATGGAGATACGATACATTA
Found at i:81470 original size:4 final size:4
Alignment explanation
Indices: 81426--81489 Score: 62
Period size: 4 Copynumber: 16.2 Consensus size: 4
81416 TACAAATATT
* * *
81426 TTTC TTT- TTTC CTCC TTTCC TTTT TTTC TTT- TTTC -TTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC TTTC
81472 TTTC TTTC TTTC TCTTC T
1 TTTC TTTC TTTC T-TTC T
81490 GCCAAAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
3 9 0.18
4 32 0.65
5 8 0.16
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:83737 original size:37 final size:38
Alignment explanation
Indices: 83667--83768 Score: 109
Period size: 37 Copynumber: 2.7 Consensus size: 38
83657 ATACCACTGA
* *
83667 ATAAGAATAGTGGTTTTTGTTCCAACCCGTGCCAC-CG
1 ATAAGAATAGTGGTTTTTGTTCCAACCCATGCCACTAG
* **
83704 GTAAGAATAGTGGTTTTTGTTATGAA-CCATGCCACTAG
1 ATAAGAATAGTGGTTTTTGTT-CCAACCCATGCCACTAG
* * *
83742 ATTAGAATAGTAGTTTTTGTTCTAACC
1 ATAAGAATAGTGGTTTTTGTTCCAACC
83769 TATACCACAA
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
37 30 0.58
38 22 0.42
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (38 bp):
ATAAGAATAGTGGTTTTTGTTCCAACCCATGCCACTAG
Found at i:84457 original size:31 final size:31
Alignment explanation
Indices: 84416--84496 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
84406 ATAAAAGAAT
*
84416 ATTAATAAAAA-TATTATTAAAACTATATTTA
1 ATTAATAAAAATTA-TATTAAAAATATATTTA
* *
84447 ATTATTAAAAATTATGTTAAAAATATATTTTA
1 ATTAATAAAAATTATATTAAAAATATA-TTTA
** *
84479 AAAAATAAAAATAATATT
1 ATTAATAAAAATTATATT
84497 GGTAGATCTA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
31 21 0.52
32 19 0.47
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (31 bp):
ATTAATAAAAATTATATTAAAAATATATTTA
Found at i:85048 original size:20 final size:21
Alignment explanation
Indices: 85014--85059 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
85004 TTTTATTTTT
85014 AAATATAATTATAAAAAATCA
1 AAATATAATTATAAAAAATCA
*
85035 AAAT-TAATTGTAAAAAATCA
1 AAATATAATTATAAAAAATCA
85055 AAATA
1 AAATA
85060 ACTGAAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.28
Consensus pattern (21 bp):
AAATATAATTATAAAAAATCA
Found at i:85379 original size:9 final size:8
Alignment explanation
Indices: 85365--85389 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
85355 ATATACAGAC
85365 AAAAAAAT
1 AAAAAAAT
85373 AAAAAAAT
1 AAAAAAAT
85381 AAAAAAAT
1 AAAAAAAT
85389 A
1 A
85390 TTAATAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:85396 original size:22 final size:22
Alignment explanation
Indices: 85370--85415 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
85360 CAGACAAAAA
85370 AATAAAAAAATAAAAAAATATT
1 AATAAAAAAATAAAAAAATATT
** * *
85392 AATAAATGAATGAAATAATATT
1 AATAAAAAAATAAAAAAATATT
85414 AA
1 AA
85416 AATAAATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (22 bp):
AATAAAAAAATAAAAAAATATT
Found at i:99087 original size:72 final size:72
Alignment explanation
Indices: 98970--99109 Score: 253
Period size: 72 Copynumber: 1.9 Consensus size: 72
98960 AACTTAGCCG
* *
98970 TATTTAAGCAATGACTTTGGGGCTCTTCCCTGACCTCTATCATCCTTCTATTTCTTCACTTTAAA
1 TATTTAAGCAATGACTTTGGGGCTCTTCCCTGACCTCCATCATCCTTCTATTTCATCACTTTAAA
99035 CTGTCTC
66 CTGTCTC
*
99042 TATTTAAGCAATGATTTTGGGGCTCTTCCCTGACCTCCATCATCCTTCTATTTCATCACTTTAAA
1 TATTTAAGCAATGACTTTGGGGCTCTTCCCTGACCTCCATCATCCTTCTATTTCATCACTTTAAA
99107 CTG
66 CTG
99110 CGATCAAGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.21, C:0.27, G:0.11, T:0.41
Consensus pattern (72 bp):
TATTTAAGCAATGACTTTGGGGCTCTTCCCTGACCTCCATCATCCTTCTATTTCATCACTTTAAA
CTGTCTC
Found at i:105350 original size:14 final size:15
Alignment explanation
Indices: 105322--105350 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
105312 AATTATGACA
105322 TAATAAATATATTTT
1 TAATAAATATATTTT
105337 TAATAAAT-TATTTT
1 TAATAAATATATTTT
105351 ATAGTCGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATAAATATATTTT
Found at i:105897 original size:11 final size:12
Alignment explanation
Indices: 105881--105909 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
105871 GTGATTTTTC
105881 ATTTTG-ATATG
1 ATTTTGAATATG
105892 ATTTTGAATATG
1 ATTTTGAATATG
105904 ATTTTG
1 ATTTTG
105910 TTAAAGTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (12 bp):
ATTTTGAATATG
Found at i:106180 original size:31 final size:31
Alignment explanation
Indices: 106144--106236 Score: 116
Period size: 31 Copynumber: 3.0 Consensus size: 31
106134 CTGGTTTCAA
* *
106144 ACCGTGTCACAGGTTAAGAATAGTGGTTTTT
1 ACCGTGCCACAGGATAAGAATAGTGGTTTTT
**
106175 ACCGTGCCACCA-GATAAGAATAGTATTTTTT
1 ACCGTGCCA-CAGGATAAGAATAGTGGTTTTT
* *
106206 ACTGTGCCACCGGATAAGAATAGTGGTTTTT
1 ACCGTGCCACAGGATAAGAATAGTGGTTTTT
106237 GTTCCAACTA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
30 1 0.02
31 49 0.94
32 2 0.04
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (31 bp):
ACCGTGCCACAGGATAAGAATAGTGGTTTTT
Found at i:107952 original size:22 final size:22
Alignment explanation
Indices: 107925--107970 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
107915 ACACAAAAAA
107925 AATAAAACAAT-AAATAACTATT
1 AATAAAACAATGAAATAA-TATT
**
107947 AATAAATGAATGAAATAATATT
1 AATAAAACAATGAAATAATATT
107969 AA
1 AA
107971 AATATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (22 bp):
AATAAAACAATGAAATAATATT
Found at i:108034 original size:22 final size:23
Alignment explanation
Indices: 108009--108054 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
107999 ATTTGAATAA
*
108009 TAAATTATCT-TTGAATGAATTT
1 TAAATTATCTCTTAAATGAATTT
108031 TAAATTATCTCTTAAATGAATTT
1 TAAATTATCTCTTAAATGAATTT
108054 T
1 T
108055 GTAAACGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (23 bp):
TAAATTATCTCTTAAATGAATTT
Found at i:109117 original size:25 final size:24
Alignment explanation
Indices: 109077--109129 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
109067 ATTTAGATAT
*
109077 TTTTATATTTATTATTTAT-ATTA
1 TTTTATATTCATTATTTATAATTA
*
109100 TTTTATATATCATATATTTTTAATTA
1 TTTTATAT-TCAT-TATTTATAATTA
109126 TTTT
1 TTTT
109130 TTCATATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.32
24 3 0.12
25 6 0.24
26 8 0.32
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTTATATTCATTATTTATAATTA
Found at i:114717 original size:21 final size:21
Alignment explanation
Indices: 114702--114757 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
114692 TTTTTTCAGA
114702 TTTAGAAGCTTATTTTACATC
1 TTTAGAAGCTTATTTTACATC
*
114723 TTTAGAAGCTTAGTTTACATC
1 TTTAGAAGCTTATTTTACATC
114744 TTTAGAAGCTTATT
1 TTTAGAAGCTTATT
114758 CAAGATCCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (21 bp):
TTTAGAAGCTTATTTTACATC
Found at i:123722 original size:4 final size:4
Alignment explanation
Indices: 123713--123738 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
123703 TCTAAGCAGG
123713 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
123739 TAAGATTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:123929 original size:24 final size:22
Alignment explanation
Indices: 123902--123950 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
123892 TCTTTTTAAA
123902 ATAAATTATACGATTTTTATATAT
1 ATAAATT-T-CGATTTTTATATAT
* *
123926 ATAAATTTTGATTTTTTTATAT
1 ATAAATTTCGATTTTTATATAT
123948 ATA
1 ATA
123951 TATAACGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 15 0.65
23 1 0.04
24 7 0.30
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (22 bp):
ATAAATTTCGATTTTTATATAT
Found at i:123966 original size:24 final size:24
Alignment explanation
Indices: 123914--123969 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
123904 AAATTATACG
**
123914 ATTTTTATATATATAAATTTTGAT
1 ATTTTTATATATATAAACGTTGAT
*
123938 TTTTTTATATATATATAACGTT-AT
1 ATTTTTATATATATA-AACGTTGAT
123962 ATTTTTAT
1 ATTTTTAT
123970 TATTTTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (24 bp):
ATTTTTATATATATAAACGTTGAT
Found at i:125272 original size:28 final size:28
Alignment explanation
Indices: 125241--125301 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
125231 TTTTTTACAA
125241 ACAAA-AATAACCACCATATTTGACAAAT
1 ACAAAGAA-AACCACCATATTTGACAAAT
*
125269 ACAAAGGAAACCACCATATTTGACAAAT
1 ACAAAGAAAACCACCATATTTGACAAAT
125297 ACAAA
1 ACAAA
125302 TGGTGGCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.54, C:0.21, G:0.07, T:0.18
Consensus pattern (28 bp):
ACAAAGAAAACCACCATATTTGACAAAT
Found at i:129851 original size:28 final size:28
Alignment explanation
Indices: 129820--129881 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
129810 TTTTTTACAA
129820 ACAAA-AATAACCACCATATTTGACAAAT
1 ACAAAGAA-AACCACCATATTTGACAAAT
*
129848 ACAAAGGAAACCACCATATTTGACAAAT
1 ACAAAGAAAACCACCATATTTGACAAAT
129876 ACAAAG
1 ACAAAG
129882 GGTGGCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.53, C:0.21, G:0.08, T:0.18
Consensus pattern (28 bp):
ACAAAGAAAACCACCATATTTGACAAAT
Found at i:129882 original size:28 final size:28
Alignment explanation
Indices: 129828--129882 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
129818 AAACAAAAAT
129828 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
129856 AACCACCATATTTGACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
129883 GTGGCATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:131293 original size:2 final size:2
Alignment explanation
Indices: 131286--131311 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
131276 GACTCTAAAC
131286 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
131312 GTTCTTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:132273 original size:8 final size:8
Alignment explanation
Indices: 132260--132291 Score: 50
Period size: 7 Copynumber: 4.2 Consensus size: 8
132250 GTGTTCAAAG
132260 AAAAAAAT
1 AAAAAAAT
132268 -AAAAAAT
1 AAAAAAAT
132275 -AAAAAAT
1 AAAAAAAT
132282 AAAAAAAT
1 AAAAAAAT
132290 AA
1 AA
132292 TTTTTCGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 14 0.61
8 9 0.39
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:132278 original size:6 final size:7
Alignment explanation
Indices: 132261--132287 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
132251 TGTTCAAAGA
132261 AAAAAAT
1 AAAAAAT
132268 AAAAAAT
1 AAAAAAT
132275 AAAAAAT
1 AAAAAAT
132282 AAAAAA
1 AAAAAA
132288 ATAATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:132885 original size:10 final size:10
Alignment explanation
Indices: 132870--132901 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
132860 GAGTCTAATC
132870 GTATATATAT
1 GTATATATAT
132880 GTATATATAT
1 GTATATATAT
*
132890 ATATATATAT
1 GTATATATAT
132900 GT
1 GT
132902 GTGTGTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (10 bp):
GTATATATAT
Found at i:133095 original size:14 final size:14
Alignment explanation
Indices: 133076--133103 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
133066 GTCGATGGAA
133076 ACTTAATTAACTGG
1 ACTTAATTAACTGG
133090 ACTTAATTAACTGG
1 ACTTAATTAACTGG
133104 TGGTAATCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
ACTTAATTAACTGG
Done.