Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011449.1 Corchorus capsularis cultivar CVL-1 contig11470, whole genome shotgun sequence
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: 91961
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1670 original size:156 final size:155
Alignment explanation
Indices: 1386--1676 Score: 376
Period size: 156 Copynumber: 1.9 Consensus size: 155
1376 TAAACTGGAC
* * * * *
1386 TTCTCACCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAG
1 TTCTCACCTCAAACTATCCTTAAATAAAAAACTAGCATAAGTTTTTCATTCTAAATCTCAATGAA
* * *
1451 CTAAAACTTTTCCAAGGGACTTAGATTCTCTCCATGAGACTATGGAAAAAATTCTAAGTAAAACC
66 CT-AAACTTTTCCAAGGGACTTAGATTATCCCCATAAGACTATGGAAAAAATTCTAAGTAAAACC
1516 AAACTCCCCTTGATGGTGAACTAGGT
130 AAACTCCCCTTGATGGTGAACTAGGT
* *
1542 TTCTCCCCTTAAACTATCCTTAAATAAAAAACTAGCATAAGTTTTTCATTCTAAATC-CAATGAA
1 TTCTCACCTCAAACTATCCTTAAATAAAAAACTAGCATAAGTTTTTCATTCTAAATCTCAATG-A
*
1606 ACT-GA-TTTTCCACCAGTAGG-CTTAGATTATCCCCATAA-AGCTATGGAAAAAATTCTAAGTA
65 ACTAAACTTTTCCA--AG--GGACTTAGATTATCCCCATAAGA-CTATGGAAAAAATTCTAAGTA
*
1667 AAACCGAACT
125 AAACCAAACT
1677 GTCTAACATA
Statistics
Matches: 117, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
153 7 0.06
154 1 0.01
155 7 0.06
156 100 0.85
157 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.30
Consensus pattern (155 bp):
TTCTCACCTCAAACTATCCTTAAATAAAAAACTAGCATAAGTTTTTCATTCTAAATCTCAATGAA
CTAAACTTTTCCAAGGGACTTAGATTATCCCCATAAGACTATGGAAAAAATTCTAAGTAAAACCA
AACTCCCCTTGATGGTGAACTAGGT
Found at i:1699 original size:156 final size:154
Alignment explanation
Indices: 1386--1746 Score: 367
Period size: 156 Copynumber: 2.3 Consensus size: 154
1376 TAAACTGGAC
* * * *
1386 TTCTCACCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAG
1 TTCTCCCCT-AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAATCTCAATGAA
* * *
1451 CTAAAACTTTTCCAAGGGACTTAGATTCTCTCCATGAGACTATGGAAAAAATTCTAAGTAAAACC
65 CT-AAACTTTTCCAAGGGACTTAGATTATCCCCATAAGACTATGGAAAAAATTCTAAGTAAAACC
** * *
1516 AAACTCCCCTTGATGGTGAACTAGGT
129 AAACTCCCCTACATAGAGAACTAGGT
* *
1542 TTCTCCCCTTAAACTATCCTTAAATAAAAAACTAGCATAAGTTTTTCATTCTAAATC-CAATGAA
1 TTCTCCCC-TAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAATCTCAATG-A
*
1606 ACT-GA-TTTTCCACCAGTAGG-CTTAGATTATCCCCATAA-AGCTATGGAAAAAATTCTAAGTA
64 ACTAAACTTTTCCA--AG--GGACTTAGATTATCCCCATAAGA-CTATGGAAAAAATTCTAAGTA
* ** * *
1667 AAACCGAACT-GTCTAACATAGAGAAGTTGGT
124 AAACCAAACTCCCCT-ACATAGAGAACTAGGT
* * *
1698 TTGACACCCC-AAATTGTCCTTAACTGAAAAACTAGCATAAGTTTTTCAT
1 TT--CTCCCCTAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCAT
1747 CTTAAGTCTG
Statistics
Matches: 171, Mismatches: 24, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
153 7 0.04
154 1 0.01
155 9 0.05
156 146 0.85
157 3 0.02
158 5 0.03
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.30
Consensus pattern (154 bp):
TTCTCCCCTAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAATCTCAATGAAC
TAAACTTTTCCAAGGGACTTAGATTATCCCCATAAGACTATGGAAAAAATTCTAAGTAAAACCAA
ACTCCCCTACATAGAGAACTAGGT
Found at i:3280 original size:22 final size:23
Alignment explanation
Indices: 3248--3292 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
3238 GTTTTGGCAG
*
3248 TACAATTTTTAGAAC-TAAAAAT
1 TACAATATTTAGAACTTAAAAAT
3270 TACAATATTTAGAACTTAAAAAT
1 TACAATATTTAGAACTTAAAAAT
3293 AAGTAGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (23 bp):
TACAATATTTAGAACTTAAAAAT
Found at i:5575 original size:6 final size:7
Alignment explanation
Indices: 5559--5588 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
5549 TTAGAATAGC
5559 AAAATTA
1 AAAATTA
5566 AAAATTA
1 AAAATTA
5573 AAAATTA
1 AAAATTA
5580 AAAA-TA
1 AAAATTA
5586 AAA
1 AAA
5589 CTAACGTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAATTA
Found at i:11957 original size:17 final size:17
Alignment explanation
Indices: 11932--11974 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
11922 GAAATCGAAA
*
11932 GAGAAAGAGACTGAGAT-
1 GAGAGAGAGAC-GAGATC
*
11949 GAGAGAGAGACGGGATC
1 GAGAGAGAGACGAGATC
11966 GAGAGAGAG
1 GAGAGAGAG
11975 GCGCAAGGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.42, C:0.07, G:0.44, T:0.07
Consensus pattern (17 bp):
GAGAGAGAGACGAGATC
Found at i:16257 original size:32 final size:32
Alignment explanation
Indices: 16216--16276 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
16206 AGCAATCATC
16216 ATTTTCCATTTTACTGATAATTAATGGCATAA
1 ATTTTCCATTTTACTGATAATTAATGGCATAA
16248 ATTTTCCATTTTACTGATAATTAATGGCA
1 ATTTTCCATTTTACTGATAATTAATGGCA
16277 AGAATGCCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (32 bp):
ATTTTCCATTTTACTGATAATTAATGGCATAA
Found at i:16599 original size:31 final size:31
Alignment explanation
Indices: 16564--16640 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
16554 CTTTTTGGCA
* *
16564 CACGTGGCATGTCACATGTTACTTTTTTATC
1 CACGTGACATGTCACATGTTACTTTTTGATC
* * **
16595 CACGTGACCTGCCATGTGTTACTTTTTGATC
1 CACGTGACATGTCACATGTTACTTTTTGATC
*
16626 CACGTGCCATGTCAC
1 CACGTGACATGTCAC
16641 GTCGGACACC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.36
Consensus pattern (31 bp):
CACGTGACATGTCACATGTTACTTTTTGATC
Found at i:17947 original size:2 final size:2
Alignment explanation
Indices: 17942--17976 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
17932 TACTAGTGTG
17942 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 T
17977 GCCTATACGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21258 original size:4 final size:4
Alignment explanation
Indices: 21249--21276 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
21239 CGAACTTCTT
21249 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
21277 ACACTAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:28945 original size:2 final size:2
Alignment explanation
Indices: 28938--28984 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
28928 GTATAGTGAG
*
28938 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
28981 TA TA
1 TA TA
28985 CATGATATGA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:31986 original size:27 final size:27
Alignment explanation
Indices: 31956--32009 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
31946 AATTCTTTTA
31956 AGAAAATTCAGTTAAGAAATGAAATTT
1 AGAAAATTCAGTTAAGAAATGAAATTT
31983 AGAAAATTCAGTTAAGAAATGAAATTT
1 AGAAAATTCAGTTAAGAAATGAAATTT
32010 TGTTGTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.52, C:0.04, G:0.15, T:0.30
Consensus pattern (27 bp):
AGAAAATTCAGTTAAGAAATGAAATTT
Found at i:32002 original size:13 final size:14
Alignment explanation
Indices: 31953--32001 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
31943 ATAAATTCTT
31953 TTAAGAAAATTCAG
1 TTAAGAAAATTCAG
** *
31967 TTAAG-AAATGAAA
1 TTAAGAAAATTCAG
*
31980 TTTAGAAAATTCAG
1 TTAAGAAAATTCAG
31994 TTAAGAAA
1 TTAAGAAA
32002 TGAAATTTTG
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.29
Consensus pattern (14 bp):
TTAAGAAAATTCAG
Found at i:32327 original size:11 final size:11
Alignment explanation
Indices: 32313--32350 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
32303 ATTCATAACA
32313 AATTTATAATT
1 AATTTATAATT
32324 AATTTATAATT
1 AATTTATAATT
32335 -ATTTGATAATT
1 AATTT-ATAATT
*
32346 TATTT
1 AATTT
32351 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:32522 original size:2 final size:2
Alignment explanation
Indices: 32515--32544 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
32505 AGTAGGTTTA
32515 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
32545 CAATTAATCT
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:43005 original size:1 final size:1
Alignment explanation
Indices: 43001--43034 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
42991 AAAATATGAC
* *
43001 TTTTTTTTTCTTTTTTTTTTTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
43035 GATCGAGATC
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:43015 original size:10 final size:10
Alignment explanation
Indices: 43000--43034 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
42990 AAAAATATGA
43000 CTTTTTTTTT
1 CTTTTTTTTT
43010 CTTTTTTTTT
1 CTTTTTTTTT
*
43020 TTTTTTTTTT
1 CTTTTTTTTT
43030 CTTTT
1 CTTTT
43035 GATCGAGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:50696 original size:2 final size:2
Alignment explanation
Indices: 50689--50715 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
50679 ACATTCCCCC
50689 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
50716 GCTCGATATG
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:51697 original size:21 final size:20
Alignment explanation
Indices: 51667--51711 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
51657 AGAGTCCTAA
*
51667 ATTCAATTC-ATTACTCATAG
1 ATTCAATTCAAATACTCA-AG
51687 ATTCAAATTCAAATACTCAAG
1 ATTC-AATTCAAATACTCAAG
51708 ATTC
1 ATTC
51712 TCCAATAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 11 0.50
22 7 0.32
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.36
Consensus pattern (20 bp):
ATTCAATTCAAATACTCAAG
Found at i:52624 original size:31 final size:31
Alignment explanation
Indices: 52583--52648 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
52573 AACTTTATAT
*
52583 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
* *
52614 TTTCCAATTGTACCCTTTTTTTTAAAATATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
52645 TTTC
1 TTTC
52649 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.27, C:0.18, G:0.05, T:0.50
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATA
Found at i:52998 original size:44 final size:43
Alignment explanation
Indices: 52929--53089 Score: 135
Period size: 44 Copynumber: 3.6 Consensus size: 43
52919 GTCTCTATGT
* ** *
52929 GGTTATCAAAATTTCATAAGATGGTTATTATAATTCCATGAG-GA
1 GGTTATCAAAATTTCAT-AGGTGGTTACCAAAATTCCAT-AGTGA
* * *
52973 GGTTATCAAAATTCCATAGTGTGGTTACCAAAATTGCATAGTGT
1 GGTTATCAAAATTTCATAG-GTGGTTACCAAAATTCCATAGTGA
* * *
53017 GGTTACCAAAATTTCATAGAGTGGTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATAG-GTGGTTACCAAAATTCCATA-G-TGA
* * *
53063 TGTTATTAAAATTTCTTAGGTTGGTTA
1 GGTTATCAAAATTTCATAGG-TGGTTA
53090 TTGAAATTTC
Statistics
Matches: 95, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
43 4 0.04
44 67 0.71
45 2 0.02
46 22 0.23
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.37
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAGGTGGTTACCAAAATTCCATAGTGA
Found at i:53073 original size:24 final size:22
Alignment explanation
Indices: 52928--53111 Score: 108
Period size: 22 Copynumber: 8.3 Consensus size: 22
52918 TGTCTCTATG
* * *
52928 TGGTTATCAAAATTTCATAAGA
1 TGGTTATTAAAATTTCATAGGT
* *
52950 TGGTTATTATAATTCCATGAGG-
1 TGGTTATTAAAATTTCAT-AGGT
* * *
52972 AGGTTATCAAAATTCCATA-GT
1 TGGTTATTAAAATTTCATAGGT
** *
52993 GTGGTTACCAAAATTGCATA-GT
1 -TGGTTATTAAAATTTCATAGGT
**
53015 GTGGTTACCAAAATTTCATAGAG-
1 -TGGTTATTAAAATTTCATAG-GT
**
53038 TGGTTACCAAAATTTCATAGGAT
1 TGGTTATTAAAATTTCATAGG-T
*
53061 CAT-GTTATTAAAATTTCTTAGGT
1 --TGGTTATTAAAATTTCATAGGT
* *
53084 TGGTTATTGAAATTTCATAGGG
1 TGGTTATTAAAATTTCATAGGT
53106 TGGTTA
1 TGGTTA
53112 ATTATCACAA
Statistics
Matches: 135, Mismatches: 17, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
20 1 0.01
21 3 0.02
22 110 0.81
23 3 0.02
24 17 0.13
25 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAGGT
Found at i:53200 original size:22 final size:22
Alignment explanation
Indices: 53150--53271 Score: 79
Period size: 22 Copynumber: 5.5 Consensus size: 22
53140 AAAAAGATTC
* *
53150 CAAAATGTCATAGCGAGGTTATA
1 CAAAATTTCATAGTGAGGTTA-A
* *
53173 C-GAATTTCATAGTGTGGTTAA
1 CAAAATTTCATAGTGAGGTTAA
*
53194 CAAAATTTCATTAG-AAGGTT-A
1 CAAAATTTCA-TAGTGAGGTTAA
* * * * *
53215 CTAATACTTCATCGGGAGGTTAT
1 C-AAAATTTCATAGTGAGGTTAA
* * *
53238 CAAAATTTTATAGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAA
53260 CAAAATTTCATA
1 CAAAATTTCATA
53272 TAGGAAGGTT
Statistics
Matches: 75, Mismatches: 19, Indels: 11
0.71 0.18 0.10
Matches are distributed among these distances:
21 6 0.08
22 64 0.85
23 5 0.07
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAA
Found at i:53362 original size:22 final size:22
Alignment explanation
Indices: 53293--53564 Score: 111
Period size: 22 Copynumber: 12.5 Consensus size: 22
53283 TAAAAGTCTC
* *
53293 AATTTCATA-AG-GAGTACCAA
1 AATTTCATAGAGTGATTATCAA
*
53313 AATTTAATAGAAG-G-TTATC-A
1 AATTTCATAG-AGTGATTATCAA
* *
53333 AATCTCATAGAGTGATTATCGA
1 AATTTCATAGAGTGATTATCAA
* *
53355 AATTTCATAAATATAGGATTATCAA
1 AATTTCATAGA-GT--GATTATCAA
*
53380 AATTT-ATATGA-AGATTATCAA
1 AATTTCATA-GAGTGATTATCAA
* *
53401 AATTTCATAGTGTTG-TTACCAA
1 AATTTCATAGAG-TGATTATCAA
* * *
53423 AATTTCA-AGGCGGGTTTATCAA
1 AATTTCATA-GAGTGATTATCAA
*
53445 AATTACATA-ATGTGATTATCAA
1 AATTTCATAGA-GTGATTATCAA
* * * *
53467 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAGAGTGATTATCAA
* *
53489 AATTTTATAAAGATG-TTATCAA
1 AATTTCATAGAG-TGATTATCAA
* * * *
53511 ATTTTCATAAAGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
** *
53533 TTTTTCA-AAATGTGATTA-CAAA
1 AATTTCATAGA-GTGATTATC-AA
53555 AATTTCATAG
1 AATTTCATAG
53565 TGGTATTTCT
Statistics
Matches: 190, Mismatches: 40, Indels: 41
0.70 0.15 0.15
Matches are distributed among these distances:
19 2 0.01
20 18 0.09
21 30 0.16
22 117 0.62
23 6 0.03
24 3 0.02
25 14 0.07
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
AATTTCATAGAGTGATTATCAA
Found at i:53675 original size:19 final size:19
Alignment explanation
Indices: 53645--53708 Score: 101
Period size: 19 Copynumber: 3.3 Consensus size: 19
53635 TGATGGAGTA
53645 ATCAAAATTTCAGGGAGGAT
1 ATCAAAA-TTCAGGGAGGAT
*
53665 ACCAAAATTCAGGGAGGAT
1 ATCAAAATTCAGGGAGGAT
*
53684 ATCAAAATTCAGTGAGGAT
1 ATCAAAATTCAGGGAGGAT
53703 ATCAAA
1 ATCAAA
53709 CTTTCATACG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 35 0.85
20 6 0.15
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (19 bp):
ATCAAAATTCAGGGAGGAT
Found at i:53840 original size:45 final size:45
Alignment explanation
Indices: 53675--54151 Score: 192
Period size: 44 Copynumber: 10.9 Consensus size: 45
53665 ACCAAAATTC
* * *
53675 AGGGAGGA-TATCAAAA-TTC--AGTGAGGATATCAAACTTTCAT
1 AGGGAAGATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCAT
* * * * * *
53716 A-CGAAGGTTATCAAATTTTCATAGTTTA-GTTTTCAAAACTTCAT
1 AGGGAAGATTATCAAAATTTCATAG-TGAGGTTATCAAAATTTCAT
* * * ** *
53760 A-AGAGGGTTATCAAAATTTCATAGT-ATATAGATCAAAATTTCAT
1 AGGGAAGATTATCAAAATTTCATAGTGAGGT-TATCAAAATTTCAT
* * * **
53804 AGGGTAGATTAACAAAATTTCATAATGAGGTTATCAAAAAATCAT
1 AGGGAAGATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCAT
* *
53849 AGGG-AGCTTATCAAAATTT--T--T-A-GTTATCAAGATTTCAT
1 AGGGAAGATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCAT
* * * * * *
53887 AAGAAAG-TTATCAAAATTTTATAGGGAGGTTTATTAAAATTTTAT
1 AGGGAAGATTATCAAAATTTCATAGTGAGG-TTATCAAAATTTCAT
* **
53932 A-GGAAGATTTATCAAAATTTTCATAGCGAGGTTATCTCAATTTCAT
1 AGGGAAGA-TTATCAAAA-TTTCATAGTGAGGTTATCAAAATTTCAT
* * * * * *
53978 AGTG-TGATTATCAAAATTTTAAAGTGTGATTA-CTAACAA-TTCAT
1 AGGGAAGATTATCAAAATTTCATAGTGAGGTTATC-AA-AATTTCAT
* * * * * * ** * * *
54022 ATGG-AGGTTTTTAAATTTTTATAAAGTGGTTATCAATATATCAT
1 AGGGAAGATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCAT
* * * * * *
54066 ATGG-AGGTTATCAACATCTCACAGTAGTTGGTTATCAAAATTTCAT
1 AGGGAAGATTATCAAAATTTCATAGT-G-AGGTTATCAAAATTTCAT
* *
54112 TGGGAAG-TTATCAAAATTTCATATTGAGGTCT-TCAAAATT
1 AGGGAAGATTATCAAAATTTCATAGTGAGGT-TATCAAAATT
54152 CCTTTAACAA
Statistics
Matches: 322, Mismatches: 85, Indels: 55
0.70 0.18 0.12
Matches are distributed among these distances:
38 27 0.08
39 3 0.01
40 5 0.02
41 8 0.02
42 5 0.02
43 5 0.02
44 135 0.42
45 63 0.20
46 57 0.18
47 14 0.04
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.37
Consensus pattern (45 bp):
AGGGAAGATTATCAAAATTTCATAGTGAGGTTATCAAAATTTCAT
Found at i:53848 original size:22 final size:22
Alignment explanation
Indices: 53823--53864 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
53813 TAACAAAATT
* *
53823 TCATAATGAGGTTATCAAAAAA
1 TCATAAGGAGCTTATCAAAAAA
*
53845 TCATAGGGAGCTTATCAAAA
1 TCATAAGGAGCTTATCAAAA
53865 TTTTTAGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (22 bp):
TCATAAGGAGCTTATCAAAAAA
Found at i:53925 original size:23 final size:23
Alignment explanation
Indices: 53894--53998 Score: 97
Period size: 23 Copynumber: 4.6 Consensus size: 23
53884 CATAAGAAAG
53894 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* * *
53917 TTATTAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
*
53940 TTATCAAAATTTTCATAGCGAGG-
1 TTATCAAAATTTT-ATAGGGAGGT
** * * * *
53963 TTATCTCAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAGGGAGGT
53985 TTATCAAAATTTTA
1 TTATCAAAATTTTA
53999 AAGTGTGATT
Statistics
Matches: 65, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
21 1 0.02
22 16 0.25
23 42 0.65
24 6 0.09
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:53974 original size:46 final size:45
Alignment explanation
Indices: 53894--53998 Score: 117
Period size: 46 Copynumber: 2.3 Consensus size: 45
53884 CATAAGAAAG
* *
53894 TTATCAAAATTTTATAGGGAGGTTTATTAAAATTTTATAG-GAAGA
1 TTATCAAAATTTTATAGCGAGGTTTATTAAAATTTCATAGTG-AGA
* *
53939 TTTATCAAAATTTTCATAGCGAGG-TTATCT-CAATTTCATAGTGTGA
1 -TTATCAAAATTTT-ATAGCGAGGTTTAT-TAAAATTTCATAGTGAGA
53985 TTATCAAAATTTTA
1 TTATCAAAATTTTA
53999 AAGTGTGATT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
44 1 0.02
45 13 0.25
46 28 0.54
47 10 0.19
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (45 bp):
TTATCAAAATTTTATAGCGAGGTTTATTAAAATTTCATAGTGAGA
Found at i:56821 original size:54 final size:54
Alignment explanation
Indices: 56754--56936 Score: 217
Period size: 54 Copynumber: 3.3 Consensus size: 54
56744 ACACTAATTT
* *
56754 TATGCAT-TAATAGCTCAATTGCTTCAATTACATAACCTTTTACATGCAATTATA
1 TATGCATCT-ATAGCTCAATTGCTTCAATTACACAACCTTTTACAAGCAATTATA
*
56808 TATGCATCTATAGCTCAATTGCTTCAATCT-CAGAACCTTTTACAAGCAATTATA
1 TATGCATCTATAGCTCAATTGCTTCAAT-TACACAACCTTTTACAAGCAATTATA
* * * *
56862 TCTGCATGATCTATAGCTCAATTGCTTCACTTACACAACCCTTTTACAAGTAACTATA
1 TATGC---ATCTATAGCTCAATTGCTTCAATTACACAA-CCTTTTACAAGCAATTATA
* *
56920 TCTGCATTTATAGCTCA
1 TATGCATCTATAGCTCA
56937 CATGCATACC
Statistics
Matches: 114, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
54 52 0.46
55 13 0.11
56 1 0.01
57 26 0.23
58 22 0.19
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (54 bp):
TATGCATCTATAGCTCAATTGCTTCAATTACACAACCTTTTACAAGCAATTATA
Found at i:56976 original size:26 final size:26
Alignment explanation
Indices: 56947--56998 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
56937 CATGCATACC
56947 AAATATAAATCTCAATTCATTTATAA
1 AAATATAAATCTCAATTCATTTATAA
56973 AAATATAAATCTCAATTCATTTATAA
1 AAATATAAATCTCAATTCATTTATAA
56999 GTACAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (26 bp):
AAATATAAATCTCAATTCATTTATAA
Found at i:57014 original size:26 final size:26
Alignment explanation
Indices: 56953--57008 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
56943 TACCAAATAT
* *
56953 AAATCTCAATTCATTTATAAAAATAT
1 AAATCTCAATTCATTTATAAAAACAA
**
56979 AAATCTCAATTCATTTATAAGTACAA
1 AAATCTCAATTCATTTATAAAAACAA
57005 AAAT
1 AAAT
57009 TACAATGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (26 bp):
AAATCTCAATTCATTTATAAAAACAA
Found at i:57583 original size:32 final size:32
Alignment explanation
Indices: 57544--57613 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
57534 TTAATATTTT
*
57544 ATTAATTTATCGATTAATTAATAACTTTTTAA
1 ATTAATTTATCGATTAATTAATAACTTTCTAA
57576 ATTAATTTATCGATTAATTAATAACTTTCTAA
1 ATTAATTTATCGATTAATTAATAACTTTCTAA
57608 ATTAAT
1 ATTAAT
57614 GATAATAGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (32 bp):
ATTAATTTATCGATTAATTAATAACTTTCTAA
Found at i:62065 original size:31 final size:31
Alignment explanation
Indices: 62030--62088 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
62020 CCACGTGTAC
*
62030 CAAAAAGTGACGCGTGCCATGCCACATGTTT
1 CAAAAAGTGACACGTGCCATGCCACATGTTT
* * *
62061 CAAAATGTGACATGTGGCATGCCACATG
1 CAAAAAGTGACACGTGCCATGCCACATG
62089 CACAAAATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (31 bp):
CAAAAAGTGACACGTGCCATGCCACATGTTT
Found at i:63205 original size:67 final size:67
Alignment explanation
Indices: 63097--63270 Score: 278
Period size: 67 Copynumber: 2.6 Consensus size: 67
63087 TATGCTTCAA
* ** *
63097 GATTTGTTTCAAGGGTCGAATGACTTGATCTTGAACTTGATGATAATTTGAGAGTTTGATTTGAT
1 GATTTGATTCAAGGGTCGAATGACTTGATCTTGAACTTGATGATAATTTGAGAACTTGATTTCAT
63162 TT
66 TT
* *
63164 GATTTGATTCAAGGGTCGAACGACTTGATCTTGAACTTGATGGTAATTTGAGAACTTGATTTCAT
1 GATTTGATTCAAGGGTCGAATGACTTGATCTTGAACTTGATGATAATTTGAGAACTTGATTTCAT
63229 TT
66 TT
*
63231 GATTTGATTCAAGGGTCGAATGACTTGGTCTTGAA-TTGAT
1 GATTTGATTCAAGGGTCGAATGACTTGATCTTGAACTTGAT
63271 AATTTAATTC
Statistics
Matches: 99, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
66 5 0.05
67 94 0.95
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (67 bp):
GATTTGATTCAAGGGTCGAATGACTTGATCTTGAACTTGATGATAATTTGAGAACTTGATTTCAT
TT
Found at i:63281 original size:40 final size:40
Alignment explanation
Indices: 63232--63311 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 40
63222 ATTTCATTTG
* * *
63232 ATTTGATTCAAGGGTC-GAATGACTTGGTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTG-ACGACTTGATCTTGAATTGATA
63272 ATTTAATTCAAGGGTCTTGACGACTTGATCTTGAATTGAT
1 ATTTAATTCAAGGGTC-TGACGACTTGATCTTGAATTGAT
63312 GACTTGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
40 15 0.43
41 19 0.54
42 1 0.03
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.39
Consensus pattern (40 bp):
ATTTAATTCAAGGGTCTGACGACTTGATCTTGAATTGATA
Found at i:63329 original size:94 final size:96
Alignment explanation
Indices: 63227--63405 Score: 247
Period size: 99 Copynumber: 1.9 Consensus size: 96
63217 ACTTGATTTC
* *
63227 ATTTGATTTGATTCAAGGGTC-GAATGACTTGGTCTTGAA-T-TGATAATTTAATTCAAGGGTCT
1 ATTTGATTTGATTCAAGGGTCTG-ATGACTTGATCTCGAATTATGATAATTTAATTCAAGGGTCT
63289 TGACGACTTGATCTTGAATTGATGACTTGGGA
65 TGACGACTTGATCTTGAATTGATGACTTGGGA
* *
63321 ATTTGATTTGATTCGAGGGTCTTTGATGACTTGATCTCGAATTGATGATAATTTGATTCAAGGGT
1 ATTTGATTTGATTCAAGGGTC--TGATGACTTGATCTCGAATT-ATGATAATTTAATTCAAGGGT
**
63386 CTTGGTGACTTGATCTTGAA
63 CTTGACGACTTGATCTTGAA
63406 CAAACAAAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
94 20 0.27
96 14 0.19
97 2 0.03
99 37 0.51
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.40
Consensus pattern (96 bp):
ATTTGATTTGATTCAAGGGTCTGATGACTTGATCTCGAATTATGATAATTTAATTCAAGGGTCTT
GACGACTTGATCTTGAATTGATGACTTGGGA
Found at i:63570 original size:26 final size:26
Alignment explanation
Indices: 63517--63571 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
63507 TGGATCTTCT
**
63517 TTCAATAATTTCCCAATAACTGGGTC
1 TTCAATAATTTCCCAATAACTGAATC
*
63543 TTCAATAA-TTCTCCAATAATTGAATC
1 TTCAATAATTTC-CCAATAACTGAATC
63569 TTC
1 TTC
63572 TTTGAAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (26 bp):
TTCAATAATTTCCCAATAACTGAATC
Found at i:64099 original size:17 final size:17
Alignment explanation
Indices: 64077--64119 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
64067 AAATTTGTAG
64077 GAAATTTCTGATTGGCC
1 GAAATTTCTGATTGGCC
*
64094 GAAATTTTTGATTGGCC
1 GAAATTTCTGATTGGCC
64111 GAAATTTCT
1 GAAATTTCT
64120 TGCTCTACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.40
Consensus pattern (17 bp):
GAAATTTCTGATTGGCC
Found at i:70864 original size:96 final size:99
Alignment explanation
Indices: 70597--70880 Score: 466
Period size: 96 Copynumber: 2.9 Consensus size: 99
70587 TTAATTGATA
*
70597 AATAAAATTACATATTAAACCTTAAAACTTAAAAATAGAAAAGGATATTTTAGATATTTCATGTC
1 AATAAAATTACATATTAAACCTTAAAACTTAAAAATAGAAAAGGATATTTTAGATATTTCAGGTC
*
70662 AAGGTTTTTGAAATTTAGACTTATATAATATAAT
66 AAGGTTTTTGAAGTTTAGACTTATATAATATAAT
* * * *
70696 AATAAAATTACATATTAAACTTTAAAACTTTAAAATAGAAAAGGATATTTTAGATATTTGAGGTT
1 AATAAAATTACATATTAAACCTTAAAACTTAAAAATAGAAAAGGATATTTTAGATATTTCAGGTC
*
70761 AATGTTTTTGAAGTTTAGACTTATAT-A-AT-AT
66 AAGGTTTTTGAAGTTTAGACTTATATAATATAAT
*
70792 AATAAAATTACATATTAAACCTTAAAACTTAAAAATAGAAAATGATATTTTAGATATTTCAGGTC
1 AATAAAATTACATATTAAACCTTAAAACTTAAAAATAGAAAAGGATATTTTAGATATTTCAGGTC
*
70857 AAGGTTTTTGAAGTTTAGATTTAT
66 AAGGTTTTTGAAGTTTAGACTTAT
70881 CTATATCTAT
Statistics
Matches: 171, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
96 84 0.49
97 2 0.01
98 1 0.01
99 84 0.49
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.39
Consensus pattern (99 bp):
AATAAAATTACATATTAAACCTTAAAACTTAAAAATAGAAAAGGATATTTTAGATATTTCAGGTC
AAGGTTTTTGAAGTTTAGACTTATATAATATAAT
Found at i:71002 original size:32 final size:32
Alignment explanation
Indices: 70929--71003 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 32
70919 ACTTTTATGT
*
70929 TTTCTAATTGTACCCTTATTTTTAAAATATTA
1 TTTCTAATTGTACCCTTATTTTTAAAACATTA
*
70961 TTTCCAATTGTACCCTT-TTCTTTAAAACA-TA
1 TTTCTAATTGTACCCTTATT-TTTAAAACATTA
70992 TTTCTAAATTGT
1 TTTCT-AATTGT
71004 CATTACTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 8 0.21
32 30 0.79
ACGTcount: A:0.29, C:0.16, G:0.04, T:0.51
Consensus pattern (32 bp):
TTTCTAATTGTACCCTTATTTTTAAAACATTA
Found at i:71157 original size:38 final size:35
Alignment explanation
Indices: 71094--71170 Score: 109
Period size: 38 Copynumber: 2.1 Consensus size: 35
71084 AATTTGGCTT
71094 TTTGTTTCCAACATCCTATTTAATTTTGCCTTTTGTC
1 TTTGTTTCCAACATCCTATTTAATTTTG-C-TTTGTC
* *
71131 TTTGTTTCCAATCGTTCTATTTAATTTTGCTTTGTC
1 TTTGTTTCCAA-CATCCTATTTAATTTTGCTTTGTC
71167 TTTG
1 TTTG
71171 GTCTTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 10 0.27
37 12 0.32
38 15 0.41
ACGTcount: A:0.14, C:0.18, G:0.10, T:0.57
Consensus pattern (35 bp):
TTTGTTTCCAACATCCTATTTAATTTTGCTTTGTC
Found at i:71334 original size:19 final size:20
Alignment explanation
Indices: 71307--71344 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
71297 TACTATTATT
71307 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
71327 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
71345 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:71538 original size:22 final size:22
Alignment explanation
Indices: 71510--71649 Score: 93
Period size: 22 Copynumber: 6.3 Consensus size: 22
71500 TGTCTCTATG
71510 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
71532 TGGTTATTATAATTTCATGAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
71554 AGGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
71576 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* * * * *
71598 TCAGGTTATTAAAATCTCTTAGGT
1 T--GGTTATCAAAATTTCATAAGA
** * *
71622 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAAGA
71644 TGGTTA
1 TGGTTA
71650 ATTATCACAA
Statistics
Matches: 92, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
21 2 0.02
22 72 0.78
23 1 0.01
24 17 0.18
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:71710 original size:22 final size:22
Alignment explanation
Indices: 71685--71743 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
71675 ATCAAAGAGA
*
71685 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGCGAGG
* *
71707 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGCGAGG
*
71729 TTAACAAAATTTCAT
1 TTATCAAAATTTCAT
71744 TAAATATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGG
Found at i:71775 original size:22 final size:22
Alignment explanation
Indices: 71749--71814 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
71739 TTCATTAAAT
*
71749 ATTTTATGGGGAGGTTATCAAA
1 ATTTTATAGGGAGGTTATCAAA
* *
71771 ATTTTATAGTGTGGTTATCAAA
1 ATTTTATAGGGAGGTTATCAAA
* * *
71793 ATTTCATATGAAGGTTAT-AAA
1 ATTTTATAGGGAGGTTATCAAA
71814 A
1 A
71815 GTCTCAATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
21 4 0.11
22 32 0.89
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (22 bp):
ATTTTATAGGGAGGTTATCAAA
Found at i:71946 original size:22 final size:22
Alignment explanation
Indices: 71875--72003 Score: 75
Period size: 22 Copynumber: 5.8 Consensus size: 22
71865 CATAAAGTGA
* *
71875 TTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGTGAT--G
* *
71899 ATTATCAAAATTT-ATAG-AAAG
1 -TTATCAAAATTTCATAGTGATG
* *
71920 ATTATCAGAATTTCATAGTGTTG
1 -TTATCAAAATTTCATAGTGATG
* * *
71943 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGATG
* * *
71965 TTATCAAAATTACATAAT-CTG
1 TTATCAAAATTTCATAGTGATG
*
71986 ATTATCAGAATTTCATAG
1 -TTATCAAAATTTCATAG
72004 AGGGGTCAAC
Statistics
Matches: 80, Mismatches: 21, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
21 14 0.17
22 49 0.61
23 2 0.03
24 4 0.05
25 11 0.14
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGATG
Found at i:72038 original size:22 final size:22
Alignment explanation
Indices: 72012--72068 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
72002 AGAGGGGTCA
*
72012 ACAAAATTTTATAAA-GAGCTT
1 ACAAAATTTTATAAATGAGATT
*
72033 ATCAAATTTTTA-AAATGAGATT
1 A-CAAAATTTTATAAATGAGATT
72055 ACAAAAATTTTATA
1 AC-AAAATTTTATA
72069 GTGGTATTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 5 0.17
22 23 0.79
23 1 0.03
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (22 bp):
ACAAAATTTTATAAATGAGATT
Found at i:72175 original size:20 final size:20
Alignment explanation
Indices: 72150--72205 Score: 78
Period size: 19 Copynumber: 2.8 Consensus size: 20
72140 TTATGGAGTA
72150 ATCAAAATTTCAATGAGGAT
1 ATCAAAATTTCAATGAGGAT
**
72170 ATCAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCAATGAGGAT
72189 ATCAAAATTTCATATGA
1 ATCAAAATTTCA-ATGA
72206 AGGTTATGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 17 0.57
20 11 0.37
21 2 0.07
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.29
Consensus pattern (20 bp):
ATCAAAATTTCAATGAGGAT
Found at i:72302 original size:22 final size:22
Alignment explanation
Indices: 72188--72305 Score: 80
Period size: 22 Copynumber: 5.4 Consensus size: 22
72178 TCAGGGAGGA
*
72188 TATCAAAATTTCAT-ATGAAGGT
1 TATCAAAATTTCATAAT-AAAGT
* * * **
72210 TATGAAAAATTCATAGTTTAGT
1 TATCAAAATTTCATAATAAAGT
* * *
72232 TTTCAAAATTTCACAAGAGAA-T
1 TATCAAAATTTCATAATA-AAGT
* *
72254 TATCAAAATTTCATAGT-ATGT
1 TATCAAAATTTCATAATAAAGT
*
72275 AGATCAAAATTTCATAATAAAGT
1 -TATCAAAATTTCATAATAAAGT
72298 TATCAAAA
1 TATCAAAA
72306 AATCATAGAG
Statistics
Matches: 68, Mismatches: 23, Indels: 10
0.67 0.23 0.10
Matches are distributed among these distances:
20 1 0.01
21 1 0.01
22 61 0.90
23 5 0.07
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAATAAAGT
Found at i:72312 original size:44 final size:43
Alignment explanation
Indices: 72188--72313 Score: 123
Period size: 44 Copynumber: 2.9 Consensus size: 43
72178 TCAGGGAGGA
* *
72188 TATCAAAATTTCAT-ATGAAGGTTATGAAAAATTCATAGTTTAG
1 TATCAAAATTTCATAAT-AAAGTTATCAAAAATTCATAGTTTAG
* * * *
72231 TTTTCAAAATTTCACAAGAGAA-TTATCAAAATTTCATAGTATGTAG
1 -TATCAAAATTTCATAATA-AAGTTATCAAAAATTCATAGT-T-TAG
*
72277 -ATCAAAATTTCATAATAAAGTTATCAAAAAATCATAG
1 TATCAAAATTTCATAATAAAGTTATCAAAAATTCATAG
72314 AGAGGTTATC
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
43 2 0.03
44 58 0.88
45 3 0.05
46 3 0.05
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (43 bp):
TATCAAAATTTCATAATAAAGTTATCAAAAATTCATAGTTTAG
Found at i:72348 original size:60 final size:61
Alignment explanation
Indices: 72277--72415 Score: 163
Period size: 60 Copynumber: 2.2 Consensus size: 61
72267 TAGTATGTAG
*
72277 ATCAAAATTTCATAATAAAGTTATCAAAAAATCATAGAGAGG-TTATCAAAATTTGTAGTT
1 ATCAAAATTTCATAAGAAAGTTATCAAAAAATCATAGAGAGGTTTATCAAAATTTGTAGTT
* * ** * * *
72337 ATCAAGATTTCATAAGAAAGTTCTCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAAGATTT
1 ATCAAAATTTCATAAGAAAGTTATCAAAAAATCATAGAGAGGTTTATCAAAA-TTTGT-AG--TT
72402 ATCAAAATTTCATA
1 ATCAAAATTTCATA
72416 GCGATGTACA
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
60 35 0.54
61 9 0.14
62 4 0.06
63 2 0.03
65 15 0.23
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.36
Consensus pattern (61 bp):
ATCAAAATTTCATAAGAAAGTTATCAAAAAATCATAGAGAGGTTTATCAAAATTTGTAGTT
Found at i:72404 original size:20 final size:21
Alignment explanation
Indices: 72360--72416 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
72350 AAGAAAGTTC
*
72360 TCAAAATTTTATAGGGAGGTTTA
1 TCAAAATTTTATA--GAGATTTA
72383 TCAAAATTTTATA-AGATTTA
1 TCAAAATTTTATAGAGATTTA
*
72403 TCAAAATTTCATAG
1 TCAAAATTTTATAG
72417 CGATGTACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 18 0.58
23 13 0.42
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (21 bp):
TCAAAATTTTATAGAGATTTA
Found at i:72669 original size:22 final size:22
Alignment explanation
Indices: 72638--72691 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
72628 AAGGTTTTCG
* * * *
72638 AAATTCCATAGTATCGTTATTA
1 AAATTTCATAGGAACGTTATCA
*
72660 AAATTTCATAGGAAGGTTATCA
1 AAATTTCATAGGAACGTTATCA
72682 AAATTTCATA
1 AAATTTCATA
72692 ATGGGATCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (22 bp):
AAATTTCATAGGAACGTTATCA
Found at i:72826 original size:6 final size:6
Alignment explanation
Indices: 72815--72857 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
72805 AAACTAGTAT
*
72815 AAGATA AAGATA AAGATA AAGATA AAGATA AAGTTA AAGATA A
1 AAGATA AAGATA AAGATA AAGATA AAGATA AAGATA AAGATA A
72858 TGTTTCTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (6 bp):
AAGATA
Found at i:78730 original size:14 final size:14
Alignment explanation
Indices: 78711--78737 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
78701 GTTATCCATC
78711 AAAAAAAAAACATG
1 AAAAAAAAAACATG
78725 AAAAAAAAAACAT
1 AAAAAAAAAACAT
78738 CGAGAAGGGA
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:0.81, C:0.07, G:0.04, T:0.07
Consensus pattern (14 bp):
AAAAAAAAAACATG
Found at i:85043 original size:21 final size:20
Alignment explanation
Indices: 85001--85044 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
84991 TCTTGTAATC
*
85001 TAAAATTACTAAAAAAGTTA
1 TAAAATTACTAAAAAAGCTA
* *
85021 TAAAAGTTATTAAAATAGCTA
1 TAAAA-TTACTAAAAAAGCTA
85042 TAA
1 TAA
85045 TGTTTTCCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
TAAAATTACTAAAAAAGCTA
Found at i:86734 original size:12 final size:13
Alignment explanation
Indices: 86717--86757 Score: 59
Period size: 12 Copynumber: 3.3 Consensus size: 13
86707 TCATGCACCC
86717 AAAACATTTATA-
1 AAAACATTTATAT
86729 AAAACATTT-TAT
1 AAAACATTTATAT
*
86741 AAATCATTTATAT
1 AAAACATTTATAT
86754 AAAA
1 AAAA
86758 ACGGTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 2 0.08
12 17 0.68
13 6 0.24
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAACATTTATAT
Found at i:86944 original size:13 final size:13
Alignment explanation
Indices: 86926--86950 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
86916 AAACATTAAT
86926 ATCAAAATCATAG
1 ATCAAAATCATAG
86939 ATCAAAATCATA
1 ATCAAAATCATA
86951 AACCAGAGTA
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:0.56, C:0.16, G:0.04, T:0.24
Consensus pattern (13 bp):
ATCAAAATCATAG
Found at i:87865 original size:6 final size:6
Alignment explanation
Indices: 87856--87896 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
87846 ATTTTCCTAA
* *
87856 TTTCCT TTTCCT TTTTCA TTT-CT TTT-CT TTTCCT TTTCCT T
1 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT T
87897 GCTTGGGCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
5 9 0.29
6 22 0.71
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTCCT
Found at i:88421 original size:20 final size:21
Alignment explanation
Indices: 88396--88435 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
88386 AAACACTTAC
88396 CTCTCTT-TA-AACCAATGAAT
1 CTCTCTTATATAACC-ATGAAT
88416 CTCTCTTATATAACCATGAA
1 CTCTCTTATATAACCATGAA
88436 ATTTAACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (21 bp):
CTCTCTTATATAACCATGAAT
Found at i:89988 original size:3 final size:3
Alignment explanation
Indices: 89974--90028 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
89964 TCAACAAATT
*
89974 TTA TTC TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
90022 TTA TTA T
1 TTA TTA T
90029 ATTTTTATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:90036 original size:8 final size:8
Alignment explanation
Indices: 89984--90038 Score: 65
Period size: 9 Copynumber: 6.4 Consensus size: 8
89974 TTATTCTTAT
89984 TATTATTA
1 TATTATTA
89992 TTATTATTA
1 -TATTATTA
90001 TTATTATTA
1 -TATTATTA
90010 TTATTATTA
1 -TATTATTA
90019 TTATTATTA
1 -TATTATTA
*
90028 TATTTTTA
1 TATTATTA
90036 TAT
1 TAT
90039 CACACCGCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
8 10 0.22
9 35 0.78
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TATTATTA
Found at i:90343 original size:21 final size:21
Alignment explanation
Indices: 90317--90383 Score: 125
Period size: 21 Copynumber: 3.2 Consensus size: 21
90307 CTCTACCAAA
90317 CTAATGAATGATCAATGTGAT
1 CTAATGAATGATCAATGTGAT
*
90338 CTAATGAATGATCAATGCGAT
1 CTAATGAATGATCAATGTGAT
90359 CTAATGAATGATCAATGTGAT
1 CTAATGAATGATCAATGTGAT
90380 CTAA
1 CTAA
90384 AATAACATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (21 bp):
CTAATGAATGATCAATGTGAT
Done.