Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012710.1 Corchorus capsularis cultivar CVL-1 contig12731, 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: 110903
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1273 original size:43 final size:43
Alignment explanation
Indices: 1211--1742 Score: 674
Period size: 43 Copynumber: 12.3 Consensus size: 43
1201 ACGATCAATA
* * *
1211 CTACACCAAGTCATGTGATTCACCGAATCTAACTTTGAAGATG
1 CTACACCGAGTCATCTGATTCACCGAATCCAACTTTGAAGATG
* * *
1254 CTACACTGAATCATCTGATTCACTGAATCCAACTTTGAAGATG
1 CTACACCGAGTCATCTGATTCACCGAATCCAACTTTGAAGATG
* * *
1297 CTACACCGAGTCATCTGATTCACCGAATCTAACCTTAAAGATG
1 CTACACCGAGTCATCTGATTCACCGAATCCAACTTTGAAGATG
*
1340 CTACACCGAGTCATCTGATTCACCG-ATCCAATTTTGAAGAATG
1 CTACACCGAGTCATCTGATTCACCGAATCCAACTTTGAAG-ATG
* * * * *
1383 CTGCCCCAAGTCATCTGATTCACCAAATCCAATTTTGAAGATG
1 CTACACCGAGTCATCTGATTCACCGAATCCAACTTTGAAGATG
** * *
1426 CTACTAAAGAGTCATCTGATTCACTGAATCCAACTTTAAAAGATG
1 CTAC-ACCGAGTCATCTGATTCACCGAATCCAACTTT-GAAGATG
*
1471 CTACCACCGAGTCATCTGATTCACCGAATCCAATTTTGAAGATG
1 CTA-CACCGAGTCATCTGATTCACCGAATCCAACTTTGAAGATG
* * * *
1515 CTGC-CCAAGTCATCTGATTCACGGAATCCAATTTTGAAGATG
1 CTACACCGAGTCATCTGATTCACCGAATCCAACTTTGAAGATG
* *
1557 CTACACCGAGTCATTTGATTCACTGAATCCAACTTTGAAGATG
1 CTACACCGAGTCATCTGATTCACCGAATCCAACTTTGAAGATG
*
1600 CTACACCGAGTCATCTGATTCACCAAATCCAACTTTGAAGATTG
1 CTACACCGAGTCATCTGATTCACCGAATCCAACTTTGAAGA-TG
**
1644 -TACACCGAGTCATCTGATTCACCGAATCCATTTTTGAAGATG
1 CTACACCGAGTCATCTGATTCACCGAATCCAACTTTGAAGATG
* * * * *
1686 CTGCACCGAGCCATCTCATTCACTGAATCCAATTTTGAAGATG
1 CTACACCGAGTCATCTGATTCACCGAATCCAACTTTGAAGATG
* *
1729 CTGCACCAAGTCAT
1 CTACACCGAGTCAT
1743 ATGAAGAGAT
Statistics
Matches: 426, Mismatches: 55, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
42 51 0.12
43 288 0.68
44 49 0.12
45 37 0.09
46 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.28
Consensus pattern (43 bp):
CTACACCGAGTCATCTGATTCACCGAATCCAACTTTGAAGATG
Found at i:2381 original size:21 final size:21
Alignment explanation
Indices: 2357--2396 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2347 ACAACTCACC
*
2357 TGGGTGATCAGACAAACCACA
1 TGGGTCATCAGACAAACCACA
*
2378 TGGGTCTTCAGACAAACCA
1 TGGGTCATCAGACAAACCA
2397 TGTGGGCACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (21 bp):
TGGGTCATCAGACAAACCACA
Found at i:4392 original size:29 final size:29
Alignment explanation
Indices: 4356--4437 Score: 164
Period size: 29 Copynumber: 2.8 Consensus size: 29
4346 CATAACAAAA
4356 TGCATCGGGAATATTCTTACTTGACAATT
1 TGCATCGGGAATATTCTTACTTGACAATT
4385 TGCATCGGGAATATTCTTACTTGACAATT
1 TGCATCGGGAATATTCTTACTTGACAATT
4414 TGCATCGGGAATATTCTTACTTGA
1 TGCATCGGGAATATTCTTACTTGA
4438 AGATTCGAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (29 bp):
TGCATCGGGAATATTCTTACTTGACAATT
Found at i:7836 original size:12 final size:13
Alignment explanation
Indices: 7797--7830 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
7787 AATCTCAATC
7797 TAAAGCAAATTAA
1 TAAAGCAAATTAA
7810 TAAAG-AAATTAA
1 TAAAGCAAATTAA
7822 TAAAGCAAA
1 TAAAGCAAA
7831 CAATAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.65, C:0.06, G:0.09, T:0.21
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:14431 original size:38 final size:38
Alignment explanation
Indices: 14388--14462 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 38
14378 AATAAAAATT
* * *
14388 AAAAGGCAGAAACAGAAAAA-TAAAAATATATTTTTTTA
1 AAAAGG-AAAAACAGAAAAAGGAAAAATAAATTTTTTTA
* *
14426 AAAAGGAAAAACGGAAAAAGGAAAATTAAATTTTTTT
1 AAAAGGAAAAACAGAAAAAGGAAAAATAAATTTTTTT
14463 TAAAGAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 11 0.35
38 20 0.65
ACGTcount: A:0.57, C:0.04, G:0.13, T:0.25
Consensus pattern (38 bp):
AAAAGGAAAAACAGAAAAAGGAAAAATAAATTTTTTTA
Found at i:14443 original size:37 final size:37
Alignment explanation
Indices: 14386--14480 Score: 95
Period size: 37 Copynumber: 2.5 Consensus size: 37
14376 TAAATAAAAA
* * * *
14386 TTAAAAGGCAGAAACAGAAAAA-TAAAAATATATTTTT
1 TTAAAAGG-AAAAACGGAAAAAGGAAAAATAAATTTTT
*
14423 TTAAAAAGGAAAAACGGAAAAAGGAAAATTAAATTTTT
1 TT-AAAAGGAAAAACGGAAAAAGGAAAAATAAATTTTT
*
14461 TTTAAA-GAAAAATCGGAAAA
1 TTAAAAGGAAAAA-CGGAAAA
14481 CCCAATAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
36 6 0.12
37 23 0.47
38 20 0.41
ACGTcount: A:0.58, C:0.04, G:0.14, T:0.24
Consensus pattern (37 bp):
TTAAAAGGAAAAACGGAAAAAGGAAAAATAAATTTTT
Found at i:21536 original size:29 final size:29
Alignment explanation
Indices: 21477--21545 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
21467 ACGAGAAACA
* * * *
21477 GTACCGACGCG-CTAAAGACGTCAACGTT
1 GTACGGACGCGCCAAAAAACGTCAACGCT
21505 GTACGGACGCGCCAAAAAACGTCAACGCT
1 GTACGGACGCGCCAAAAAACGTCAACGCT
21534 GTACGGACGCGC
1 GTACGGACGCGC
21546 TGAAGCTGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 10 0.28
29 26 0.72
ACGTcount: A:0.29, C:0.30, G:0.28, T:0.13
Consensus pattern (29 bp):
GTACGGACGCGCCAAAAAACGTCAACGCT
Found at i:26482 original size:35 final size:35
Alignment explanation
Indices: 26436--26512 Score: 136
Period size: 35 Copynumber: 2.2 Consensus size: 35
26426 GAATATTTTC
*
26436 TAAGATGATAGAGAATTGTGTGGGATTAGGTTACA
1 TAAGGTGATAGAGAATTGTGTGGGATTAGGTTACA
*
26471 TAAGGTGATAGAGAATTGTGTGGGATTGGGTTACA
1 TAAGGTGATAGAGAATTGTGTGGGATTAGGTTACA
26506 TAAGGTG
1 TAAGGTG
26513 GCTATTTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.31
Consensus pattern (35 bp):
TAAGGTGATAGAGAATTGTGTGGGATTAGGTTACA
Found at i:27092 original size:11 final size:11
Alignment explanation
Indices: 27076--27105 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
27066 GGTCTTTAAT
*
27076 TCTTCAAATTA
1 TCTTCAAATAA
27087 TCTTCAAATAA
1 TCTTCAAATAA
27098 TCTTCAAA
1 TCTTCAAA
27106 CACGAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAA
Found at i:28714 original size:5 final size:5
Alignment explanation
Indices: 28704--28764 Score: 77
Period size: 5 Copynumber: 11.6 Consensus size: 5
28694 CATGTTCTTT
* *
28704 TTTTC TTTTC TTTTC TTTTA TTTTA TTTTC TTTTC TTTTC TTGTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -T-TTTC TTTTC
28756 TTTTTC TTT
1 -TTTTC TTT
28765 CTTCTTTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
5 40 0.78
6 7 0.14
7 4 0.08
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:28769 original size:7 final size:6
Alignment explanation
Indices: 28703--28772 Score: 51
Period size: 5 Copynumber: 11.7 Consensus size: 6
28693 CCATGTTCTT
*
28703 TTTTTC -TTTTC -TTTTC TTTTAT- TTTATTT TCTTTTC -TTTTC TTGTTTC
1 TTTTTC TTTTTC TTTTTC TTTT-TC TTT-TTC T-TTTTC TTTTTC TT-TTTC
28751 -TTTTC TTTTTC TTTCTTC TTTT
1 TTTTTC TTTTTC TTT-TTC TTTT
28773 ATATGAGTTG
Statistics
Matches: 54, Mismatches: 1, Indels: 18
0.74 0.01 0.25
Matches are distributed among these distances:
5 19 0.35
6 18 0.33
7 15 0.28
8 2 0.04
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:29483 original size:14 final size:15
Alignment explanation
Indices: 29464--29493 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
29454 ATTCAATTTC
29464 TTTTCTTC-TTCTTT
1 TTTTCTTCATTCTTT
29478 TTTTCTTCATTCTTT
1 TTTTCTTCATTCTTT
29493 T
1 T
29494 CACTTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTCTTCATTCTTT
Found at i:30797 original size:28 final size:28
Alignment explanation
Indices: 30764--30830 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
30754 GCGCCAGGCT
* *
30764 GTTGACAG-CTTCAGCGCGCCCGTACAGC
1 GTTGAC-GTCTTCAACGCGCCCGTACAAC
* *
30792 GTTGACGTCTTTAACGCGTCCGTACAAC
1 GTTGACGTCTTCAACGCGCCCGTACAAC
30820 GTTGACGTCTT
1 GTTGACGTCTT
30831 TAGCGCGTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 1 0.03
28 33 0.97
ACGTcount: A:0.18, C:0.30, G:0.25, T:0.27
Consensus pattern (28 bp):
GTTGACGTCTTCAACGCGCCCGTACAAC
Found at i:30831 original size:28 final size:28
Alignment explanation
Indices: 30778--30840 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
30768 ACAGCTTCAG
* *
30778 CGCGCCCGTACAGCGTTGACGTCTTTAA
1 CGCGTCCGTACAACGTTGACGTCTTTAA
*
30806 CGCGTCCGTACAACGTTGACGTCTTTAG
1 CGCGTCCGTACAACGTTGACGTCTTTAA
30834 CGCGTCC
1 CGCGTCC
30841 ATACTGTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.16, C:0.33, G:0.25, T:0.25
Consensus pattern (28 bp):
CGCGTCCGTACAACGTTGACGTCTTTAA
Found at i:33432 original size:33 final size:32
Alignment explanation
Indices: 33395--33501 Score: 117
Period size: 33 Copynumber: 3.2 Consensus size: 32
33385 CGCCAAGCGA
* *
33395 TGGCCGGTTG-TGGCCGGACATGTCCATGTCGCG
1 TGGCCGG-TGATGGCCGGGCATCTCCA-GTCGCG
*
33428 TGGCCGGTGATGGCCGGGCATCTCCGAGTCACG
1 TGGCCGGTGATGGCCGGGCATCTCC-AGTCGCG
* * *
33461 TGGCCGGTGTTGGCCGGGCTTCTCCAAGTCGCA
1 TGGCCGGTGATGGCCGGGCATCTCC-AGTCGCG
33494 TGGCCGGT
1 TGGCCGGT
33502 CACTCGCGCC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
32 2 0.03
33 61 0.95
34 1 0.02
ACGTcount: A:0.09, C:0.29, G:0.39, T:0.22
Consensus pattern (32 bp):
TGGCCGGTGATGGCCGGGCATCTCCAGTCGCG
Found at i:38872 original size:10 final size:10
Alignment explanation
Indices: 38857--38885 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
38847 TGGTCGAAAA
38857 TTTATTTTAT
1 TTTATTTTAT
38867 TTTATTTTA-
1 TTTATTTTAT
38876 TTTATTTTAT
1 TTTATTTTAT
38886 ATGTTTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTTAT
Found at i:38879 original size:4 final size:5
Alignment explanation
Indices: 38857--38885 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
38847 TGGTCGAAAA
38857 TTTAT TTTAT TTTAT TTTA- TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
38886 ATGTTTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:39984 original size:33 final size:33
Alignment explanation
Indices: 39947--40053 Score: 92
Period size: 33 Copynumber: 3.2 Consensus size: 33
39937 CGCCAAGCGA
*
39947 TGGCCGGCTG-TGGCCGGACATGTCC-ATGTCGCG
1 TGGCCGG-TGATGGCCGGACATCTCCGA-GTCGCG
** *
39980 TGGCCGGTGATGGAGGGGCATCTCCGAGTCGCG
1 TGGCCGGTGATGGCCGGACATCTCCGAGTCGCG
* * * * * *
40013 TGGCCGGTGTTGGCCGGGCTTCTTCAAGTCGCA
1 TGGCCGGTGATGGCCGGACATCTCCGAGTCGCG
40046 TGGCCGGT
1 TGGCCGGT
40054 CACTCGCGCC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
32 2 0.03
33 58 0.95
34 1 0.02
ACGTcount: A:0.09, C:0.27, G:0.41, T:0.22
Consensus pattern (33 bp):
TGGCCGGTGATGGCCGGACATCTCCGAGTCGCG
Found at i:49193 original size:21 final size:21
Alignment explanation
Indices: 49160--49208 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
49150 AAGAATTGTA
**
49160 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
49180 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
49201 GCATTCCT
1 GC-TTCCT
49209 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:55084 original size:28 final size:28
Alignment explanation
Indices: 55053--55113 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
55043 AAAGCTTCAA
**
55053 CGCGTCCATACAGTGTTGACGTCTTTAG
1 CGCGTCCATACAACGTTGACGTCTTTAG
*
55081 CGCGTCCGTACAACGTTGACGTCTTTAG
1 CGCGTCCATACAACGTTGACGTCTTTAG
*
55109 TGCGT
1 CGCGT
55114 TCGTACTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.31
Consensus pattern (28 bp):
CGCGTCCATACAACGTTGACGTCTTTAG
Found at i:58829 original size:17 final size:17
Alignment explanation
Indices: 58799--58832 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
58789 AGTACTAAAT
58799 CTTAAATAAATTTTCAA
1 CTTAAATAAATTTTCAA
* *
58816 CTTAATTAATTTTTCAA
1 CTTAAATAAATTTTCAA
58833 GAGAATGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (17 bp):
CTTAAATAAATTTTCAA
Found at i:60042 original size:13 final size:13
Alignment explanation
Indices: 60024--60051 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
60014 CCTCAAAATA
60024 AATATATAGTAAT
1 AATATATAGTAAT
60037 AATATATAGTAAT
1 AATATATAGTAAT
60050 AA
1 AA
60052 GAGGAGGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (13 bp):
AATATATAGTAAT
Found at i:60869 original size:2 final size:2
Alignment explanation
Indices: 60862--60887 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
60852 ATAAGTAATA
60862 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
60888 CTCCGGGCTA
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:64756 original size:8 final size:8
Alignment explanation
Indices: 64743--64767 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
64733 GCTGCTGGTT
64743 TGGATGTC
1 TGGATGTC
64751 TGGATGTC
1 TGGATGTC
64759 TGGATGTC
1 TGGATGTC
64767 T
1 T
64768 AGAAGATGAC
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:0.12, C:0.12, G:0.36, T:0.40
Consensus pattern (8 bp):
TGGATGTC
Found at i:65027 original size:20 final size:20
Alignment explanation
Indices: 65004--65047 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
64994 AGTTTTTTTC
65004 TTAGCATTAGGGTTTTAGTT
1 TTAGCATTAGGGTTTTAGTT
65024 TTAGCATTAGGGTTTTAGTT
1 TTAGCATTAGGGTTTTAGTT
65044 TTAG
1 TTAG
65048 TATAAATAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.05, G:0.25, T:0.50
Consensus pattern (20 bp):
TTAGCATTAGGGTTTTAGTT
Found at i:67176 original size:136 final size:136
Alignment explanation
Indices: 66932--67340 Score: 800
Period size: 136 Copynumber: 3.0 Consensus size: 136
66922 TCAACAGCAA
66932 CAGCATGTCATTGAAGTACCATCTTTTCACAACAAAGTCTATTGTTATTTCCCTAAATTAAAGCT
1 CAGCATGTCATTGAAGTACCATCTTTTCACAACAAAGTCTATTGTTATTTCCCTAAATTAAAGCT
*
66997 TGAAAGCTTCATTGTTTTTTTGAATAAACTCCAATCCCTGATTATTAGAATTAAACTTTTAAACT
66 TGAAAGCTTCATTGTTTTCTTGAATAAACTCCAATCCCTGATTATTAGAATTAAACTTTTAAACT
67062 GAACCT
131 GAACCT
67068 CAGCATGTCATTGAAGTACCATCTTTTCACAACAAAGTCTATTGTTATTTCCCTAAATTAAAGCT
1 CAGCATGTCATTGAAGTACCATCTTTTCACAACAAAGTCTATTGTTATTTCCCTAAATTAAAGCT
*
67133 TGAAAGCTTCATTGATTTCTTGAATAAACTCCAATCCCTGATTATTAGAATTAAACTTTTAAACT
66 TGAAAGCTTCATTGTTTTCTTGAATAAACTCCAATCCCTGATTATTAGAATTAAACTTTTAAACT
67198 GAACCT
131 GAACCT
67204 CAGCATGTCATTGAAGTACCATCTTTTCACAACAAAGTCTATTGTTATTTCCCTAAATTAAAGCT
1 CAGCATGTCATTGAAGTACCATCTTTTCACAACAAAGTCTATTGTTATTTCCCTAAATTAAAGCT
67269 TGAAAGCTTCATTGTTTTCTTGAATAAACTCCAATCCCTGATTATTAGAATTAAACTTTTAAACT
66 TGAAAGCTTCATTGTTTTCTTGAATAAACTCCAATCCCTGATTATTAGAATTAAACTTTTAAACT
67334 GAACCT
131 GAACCT
67340 C
1 C
67341 CGCTACCTAA
Statistics
Matches: 270, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 270 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (136 bp):
CAGCATGTCATTGAAGTACCATCTTTTCACAACAAAGTCTATTGTTATTTCCCTAAATTAAAGCT
TGAAAGCTTCATTGTTTTCTTGAATAAACTCCAATCCCTGATTATTAGAATTAAACTTTTAAACT
GAACCT
Found at i:68952 original size:13 final size:14
Alignment explanation
Indices: 68927--68955 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
68917 TCTCTAAAAA
68927 CTTCTCTCTTTCCT
1 CTTCTCTCTTTCCT
68941 CTTCTC-CTTTCCT
1 CTTCTCTCTTTCCT
68954 CT
1 CT
68956 GTCCTAGTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (14 bp):
CTTCTCTCTTTCCT
Found at i:73879 original size:13 final size:14
Alignment explanation
Indices: 73854--73882 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
73844 TCTCTAAAAA
73854 CTTCTCTCTTTCCT
1 CTTCTCTCTTTCCT
73868 CTTCTC-CTTTCCT
1 CTTCTCTCTTTCCT
73881 CT
1 CT
73883 GTCCTAGTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (14 bp):
CTTCTCTCTTTCCT
Found at i:76412 original size:21 final size:21
Alignment explanation
Indices: 76388--76800 Score: 455
Period size: 21 Copynumber: 19.9 Consensus size: 21
76378 TATTTCATCT
76388 CCAAAGTTTGATAGTCAAACC
1 CCAAAGTTTGATAGTCAAACC
*
76409 CCAAA-TTTCGATAGTCAACCC
1 CCAAAGTTT-GATAGTCAAACC
*
76430 CCAAAGTTTGATAGTCAATCC
1 CCAAAGTTTGATAGTCAAACC
* * *
76451 CCAACGTTTGATGGTCAATCC
1 CCAAAGTTTGATAGTCAAACC
*
76472 CCAAA-TTTGATGGTCAAACC
1 CCAAAGTTTGATAGTCAAACC
* * *
76492 CTAAATTTTGATGGTCAAACCC
1 CCAAAGTTTGATAGTCAAA-CC
*
76514 CCAAAGTTCGATAGTCAAACC
1 CCAAAGTTTGATAGTCAAACC
* *
76535 CTAAA-TTTGATAGGCAAACC
1 CCAAAGTTTGATAGTCAAACC
* *
76555 TCAAAGTTTGATGGTCAAACC
1 CCAAAGTTTGATAGTCAAACC
* *
76576 CCAAACTTCGATAGTC-AACC
1 CCAAAGTTTGATAGTCAAACC
* *
76596 TCCAAAGTTCGATAGTCAATCC
1 -CCAAAGTTTGATAGTCAAACC
*
76618 CCAAA-TTTGATAGTCAATCC
1 CCAAAGTTTGATAGTCAAACC
* *
76638 CCAAATTTTGATGGTCAAACC
1 CCAAAGTTTGATAGTCAAACC
**
76659 CCAAA-TTTGATTTTCAAACC
1 CCAAAGTTTGATAGTCAAACC
*
76679 CCAAAGTTTGATGGT-AAATCC
1 CCAAAGTTTGATAGTCAAA-CC
** *
76700 CCAAAGTTTGACGGCCAAACC
1 CCAAAGTTTGATAGTCAAACC
76721 CCAAAGTTTGATAGTCAAACC
1 CCAAAGTTTGATAGTCAAACC
* *
76742 CCAAAATTTGATTGTC-AACC
1 CCAAAGTTTGATAGTCAAACC
* *
76762 CCAAAGTTTGATTGTCAAATC
1 CCAAAGTTTGATAGTCAAACC
76783 CCAAAGTTTGATAGTCAA
1 CCAAAGTTTGATAGTCAA
76801 CACATTAAAC
Statistics
Matches: 339, Mismatches: 41, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
20 100 0.29
21 213 0.63
22 26 0.08
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (21 bp):
CCAAAGTTTGATAGTCAAACC
Found at i:76488 original size:83 final size:82
Alignment explanation
Indices: 76388--76800 Score: 472
Period size: 83 Copynumber: 5.0 Consensus size: 82
76378 TATTTCATCT
*
76388 CCAAAGTTTGATAGTCAAACCCCAAATTTCGATAGTCAACCCCCAAAGTTTGATAGTCAATCCCC
1 CCAAAGTTTGATGGTCAAACCCCAAATTT-GATAGTCAACCCCCAAAGTTTGATAGTCAATCCCC
*
76453 AACGTTTGATGGTCAATCC
65 AA-GTTTGATGGTCAAACC
* * * *
76472 CCAAA-TTTGATGGTCAAACCCTAAATTTTGATGGTCAAACCCCCAAAGTTCGATAGTCAAACCC
1 CCAAAGTTTGATGGTCAAACCCCAAA-TTTGATAGTC-AACCCCCAAAGTTTGATAGTCAATCCC
* *
76536 TAAATTTGATAGG-CAAACC
64 CAAGTTTGAT-GGTCAAACC
* * * *
76555 TCAAAGTTTGATGGTCAAACCCCAAACTTCGATAGTCAACCTCCAAAGTTCGATAGTCAATCCCC
1 CCAAAGTTTGATGGTCAAACCCCAAA-TTTGATAGTCAACCCCCAAAGTTTGATAGTCAATCCCC
* * *
76620 AAATTTGATAGTCAATCC
65 AAGTTTGATGGTCAAACC
* ** * * *
76638 CCAAATTTTGATGGTCAAACCCCAAATTTGATTTTCAAACCCCAAAGTTTGATGGTAAATCCCCA
1 CCAAAGTTTGATGGTCAAACCCCAAATTTGATAGTCAACCCCCAAAGTTTGATAGTCAATCCCC-
* *
76703 AAGTTTGACGGCCAAACC
65 AAGTTTGATGGTCAAACC
* * *
76721 CCAAAGTTTGATAGTCAAACCCCAAAATTTGATTGTCAA-CCCCAAAGTTTGATTGTCAAATCCC
1 CCAAAGTTTGATGGTCAAACCCC-AAATTTGATAGTCAACCCCCAAAGTTTGATAGTC-AATCCC
* *
76785 AAAGTTTGATAGTCAA
64 CAAGTTTGATGGTCAA
76801 CACATTAAAC
Statistics
Matches: 279, Mismatches: 42, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
82 31 0.11
83 164 0.59
84 84 0.30
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (82 bp):
CCAAAGTTTGATGGTCAAACCCCAAATTTGATAGTCAACCCCCAAAGTTTGATAGTCAATCCCCA
AGTTTGATGGTCAAACC
Found at i:76502 original size:41 final size:41
Alignment explanation
Indices: 76388--76800 Score: 456
Period size: 41 Copynumber: 9.9 Consensus size: 41
76378 TATTTCATCT
*
76388 CCAAAGTTTGATAGTCAAACCCCAAATTTCGATAGTCAACCC
1 CCAAAGTTTGATAGTCAAACCCCAAATTT-GATAGTCAAACC
* * * *
76430 CCAAAGTTTGATAGTCAATCCCCAACGTTTGATGGTCAATCC
1 CCAAAGTTTGATAGTCAAACCCCAA-ATTTGATAGTCAAACC
* * *
76472 CCAAA-TTTGATGGTCAAACCCTAAATTTTGATGGTCAAACCC
1 CCAAAGTTTGATAGTCAAACCCCAAA-TTTGATAGTCAAA-CC
* * *
76514 CCAAAGTTCGATAGTCAAACCCTAAATTTGATAGGCAAACC
1 CCAAAGTTTGATAGTCAAACCCCAAATTTGATAGTCAAACC
* * *
76555 TCAAAGTTTGATGGTCAAACCCCAAACTTCGATAGTC-AACC
1 CCAAAGTTTGATAGTCAAACCCCAAA-TTTGATAGTCAAACC
* * *
76596 TCCAAAGTTCGATAGTCAATCCCCAAATTTGATAGTCAATCC
1 -CCAAAGTTTGATAGTCAAACCCCAAATTTGATAGTCAAACC
* * **
76638 CCAAATTTTGATGGTCAAACCCCAAATTTGATTTTCAAACC
1 CCAAAGTTTGATAGTCAAACCCCAAATTTGATAGTCAAACC
* ** *
76679 CCAAAGTTTGATGGT-AAATCCCCAAAGTTTGACGGCCAAACC
1 CCAAAGTTTGATAGTCAAA-CCCCAAA-TTTGATAGTCAAACC
*
76721 CCAAAGTTTGATAGTCAAACCCCAAAATTTGATTGTC-AACC
1 CCAAAGTTTGATAGTCAAACCCC-AAATTTGATAGTCAAACC
* *
76762 CCAAAGTTTGATTGTCAAATCCCAAAGTTTGATAGTCAA
1 CCAAAGTTTGATAGTCAAACCCCAAA-TTTGATAGTCAA
76801 CACATTAAAC
Statistics
Matches: 314, Mismatches: 44, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
40 6 0.02
41 154 0.49
42 127 0.40
43 27 0.09
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (41 bp):
CCAAAGTTTGATAGTCAAACCCCAAATTTGATAGTCAAACC
Found at i:77741 original size:16 final size:16
Alignment explanation
Indices: 77720--77752 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
77710 TATAATGAAC
77720 TTAATATTCAACATAT
1 TTAATATTCAACATAT
*
77736 TTAATATTCAATATAT
1 TTAATATTCAACATAT
77752 T
1 T
77753 GAATGACTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAATATTCAACATAT
Found at i:79812 original size:16 final size:16
Alignment explanation
Indices: 79793--79827 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
79783 ATATATCTAT
79793 ATATATATATAAT-ATA
1 ATATATA-ATAATAATA
79809 ATATATAATAATAATA
1 ATATATAATAATAATA
79825 ATA
1 ATA
79828 ATAGTCATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATATAATAATAATA
Found at i:79827 original size:21 final size:20
Alignment explanation
Indices: 79779--79824 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
79769 AGGGGACAAA
*
79779 AATAATATATCTATATATAT
1 AATAATATATATATATATAT
79799 ATATAATATA-ATATATA-AT
1 A-ATAATATATATATATATAT
79818 AATAATA
1 AATAATA
79825 ATAATAGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.25
19 3 0.12
20 7 0.29
21 8 0.33
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AATAATATATATATATATAT
Found at i:79828 original size:12 final size:13
Alignment explanation
Indices: 79779--79830 Score: 56
Period size: 12 Copynumber: 4.1 Consensus size: 13
79769 AGGGGACAAA
*
79779 AATAATATAT-CT
1 AATAATATATAAT
79791 ATATATATATATAAT
1 A-ATA-ATATATAAT
79806 -ATAATATATAAT
1 AATAATATATAAT
79818 AATAATA-ATAAT
1 AATAATATATAAT
79830 A
1 A
79831 GTCATTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
12 16 0.46
13 12 0.34
14 6 0.17
15 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
AATAATATATAAT
Found at i:82212 original size:75 final size:76
Alignment explanation
Indices: 82106--82259 Score: 249
Period size: 75 Copynumber: 2.0 Consensus size: 76
82096 AAAATAATAA
*
82106 TGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTCAGGAGATAGTTTAAGAAATAAA-AT
1 TGAGAATATTTTCAAAATCTTGCCAAATTGTGGGAGATTCAGGAGATAGTTTAAGAAATAAATA-
82170 AATAATAAAG-T
65 AATAATAAAGAT
* * *
82181 TGAGAATATTTTCAAAATCTTGCCAAATTGTGGGAGGTTTAGGAGATATTTTAAGAAATAAATAA
1 TGAGAATATTTTCAAAATCTTGCCAAATTGTGGGAGATTCAGGAGATAGTTTAAGAAATAAATAA
82246 ATAATAAAGAT
66 ATAATAAAGAT
82257 TGA
1 TGA
82260 ACAGTAATGA
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
75 68 0.93
76 5 0.07
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.32
Consensus pattern (76 bp):
TGAGAATATTTTCAAAATCTTGCCAAATTGTGGGAGATTCAGGAGATAGTTTAAGAAATAAATAA
ATAATAAAGAT
Found at i:87203 original size:26 final size:26
Alignment explanation
Indices: 87170--87230 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
87160 CCATCGAGAG
*
87170 AAAGAAAAGAAAAGAAAAGAA-TTGAA
1 AAAGAAAAGAAAA-AAAAGAAGCTGAA
* *
87196 AAAGAAAAGGAAACAAAGAAGCTGAA
1 AAAGAAAAGAAAAAAAAGAAGCTGAA
87222 AAAGTAAAA
1 AAAG-AAAA
87231 AATGAAGGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 6 0.20
26 20 0.67
27 4 0.13
ACGTcount: A:0.70, C:0.03, G:0.20, T:0.07
Consensus pattern (26 bp):
AAAGAAAAGAAAAAAAAGAAGCTGAA
Found at i:88688 original size:35 final size:35
Alignment explanation
Indices: 88643--89177 Score: 713
Period size: 35 Copynumber: 15.4 Consensus size: 35
88633 TGCATTTTGA
* *
88643 TTGACCCAGGGCGGTCTTGCTTCAGTTTATTTCAA
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* *
88678 TTGACCCAGGGTGGTCTTGCTTCAGTTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* **
88713 TTGACCCATGATGGTCTTTCTTCAGTTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* *
88748 TTGACCTAGGGCAGTCTTTCTTCAGTTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
88783 TTGA-CCAGGGCGGTCTTTCTTCAGTTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* *
88817 TTGACCCAGGGTGGTATTTCTTCAGTTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* *
88852 TTGACCCAAGGCGGTCTTTCTTTAGTTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
*
88887 TTGACCCATGGCGGTCTTTCTTCAGTTTA-TTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * *
88921 TTGACCTAGAGCGGTCTTTCTTAAGTTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
88956 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* *
88991 TTGATCCAGGGAGGTCTTTCTTCAGTTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
*
89026 TTGA-CCAGGGCGGTCTTTCTTCAGTTTATTTCAA
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * ** * * *
89060 TCGATCCAGGGCAATCATTCTTTAGTTTATTTAAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * **
89095 TTGACCCAAGGTGGTCTTTCTTCAACTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* *
89130 TTGA-CCGGGGCGGTCATTT-TTCAGTGTA-TTCAG
1 TTGACCCAGGGCGGTC-TTTCTTCAGTTTATTTCAG
*
89163 TTGACCCATGGCGGT
1 TTGACCCAGGGCGGT
89178 GTTTTCATAG
Statistics
Matches: 438, Mismatches: 57, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
33 9 0.02
34 115 0.26
35 314 0.72
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (35 bp):
TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
Found at i:88837 original size:104 final size:105
Alignment explanation
Indices: 88643--89177 Score: 713
Period size: 104 Copynumber: 5.1 Consensus size: 105
88633 TGCATTTTGA
* * * *
88643 TTGACCCAGGGCGGTCTTGCTTCAGTTTATTTCAATTGACCCAGGGTGGTCTTGCTTCAGTTTAT
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTAT
* **
88708 TTCAGTTGACCCATGATGGTCTTTCTTCAGTTTATTTCAG
66 TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* *
88748 TTGACCTAGGGCAGTCTTTCTTCAGTTTATTTCAGTTGA-CCAGGGCGGTCTTTCTTCAGTTTAT
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTAT
* *
88812 TTCAGTTGACCCAGGGTGGTATTTCTTCAGTTTATTTCAG
66 TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * *
88852 TTGACCCAAGGCGGTCTTTCTTTAGTTTATTTCAGTTGACCCATGGCGGTCTTTCTTCAGTTTA-
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTAT
* * *
88916 TTCAGTTGACCTAGAGCGGTCTTTCTTAAGTTTATTTCAG
66 TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* *
88956 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGAGGTCTTTCTTCAGTTTAT
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTAT
*
89021 TTCAGTTGA-CCAGGGCGGTCTTTCTTCAGTTTATTTCAA
66 TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * ** * * * * * **
89060 TCGATCCAGGGCAATCATTCTTTAGTTTATTTAAGTTGACCCAAGGTGGTCTTTCTTCAACTTAT
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTAT
* *
89125 TTCAGTTGA-CCGGGGCGGTCATTT-TTCAGTGTA-TTCAG
66 TTCAGTTGACCCAGGGCGGTC-TTTCTTCAGTTTATTTCAG
*
89163 TTGACCCATGGCGGT
1 TTGACCCAGGGCGGT
89178 GTTTTCATAG
Statistics
Matches: 379, Mismatches: 48, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
103 14 0.04
104 295 0.78
105 70 0.18
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (105 bp):
TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTAT
TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
Found at i:88904 original size:139 final size:140
Alignment explanation
Indices: 88643--89177 Score: 731
Period size: 139 Copynumber: 3.9 Consensus size: 140
88633 TGCATTTTGA
* * *
88643 TTGACCCAGGGCGGTCTTGCTTCAGTTTATTTCAATTGACCCAGGGTGGTCTTGCTTCAGTTTAT
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTAT
* ** * *
88708 TTCAGTTGACCCATGATGGTCTTTCTTCAGTTTATTTCAGTTGACCTAGGGCAGTCTTTCTTCAG
66 TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAG
88773 TTTATTTCAG
131 TTTATTTCAG
*
88783 TTGA-CCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTATTTCTTCAGTTTAT
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTAT
* * *
88847 TTCAGTTGACCCAAGGCGGTCTTTCTTTAGTTTATTTCAGTTGACCCATGGCGGTCTTTCTTCAG
66 TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAG
88912 TTTA-TTCAG
131 TTTATTTCAG
* * * *
88921 TTGACCTAGAGCGGTCTTTCTTAAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTAT
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTAT
* *
88986 TTCAGTTGATCCAGGGAGGTCTTTCTTCAGTTTATTTCAGTTGA-CCAGGGCGGTCTTTCTTCAG
66 TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAG
*
89050 TTTATTTCAA
131 TTTATTTCAG
* * ** * * * * **
89060 TCGATCCAGGGCAATCATTCTTTAGTTTATTTAAGTTGACCCAAGGTGGTCTTTCTTCAACTTAT
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTAT
* * *
89125 TTCAGTTGA-CCGGGGCGGTCATTT-TTCAGTGTA-TTCAGTTGACCCATGGCGGT
66 TTCAGTTGACCCAGGGCGGTC-TTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGT
89178 GTTTTCATAG
Statistics
Matches: 352, Mismatches: 39, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
137 9 0.03
138 58 0.16
139 281 0.80
140 4 0.01
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (140 bp):
TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTAT
TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAG
TTTATTTCAG
Found at i:89281 original size:35 final size:35
Alignment explanation
Indices: 89242--89652 Score: 619
Period size: 35 Copynumber: 11.7 Consensus size: 35
89232 TCTTTTCATG
* *
89242 GAAGTTTTCAGAGTTCAGAGCTGATCTCATTTCAA
1 GAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAA
* *
89277 GAAGTTTTCAGAGGTAAGAGTTGATCTCATTCCAA
1 GAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAA
* * * * *
89312 GAAGTTTCCA-ATGATCAGAATTGATTTCATTGCAA
1 GAAGTTTTCAGA-GGTCAGAGTTGATCTCATTTCAA
* * *
89347 GAAGTTTTCAGAGATCAGAATTGATCTCATTGCAA
1 GAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAA
89382 GAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAA
1 GAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAA
*
89417 GAAGTTTTCAGAGGTCAGAGTTGATCTCATATCAA
1 GAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAA
89452 GAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAA
1 GAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAA
*
89487 GAAGTTTTCAGAGGTCAGAGTAGATCTCATTTCAA
1 GAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAA
*
89522 GAAGTTTTCAGAGGTCAGAGTTGATCTCATTCCAA
1 GAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAA
*
89557 GAAGTTTTCAGAGGTCAGAGTTGATCTCATTCCAA
1 GAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAA
*
89592 GAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAG
1 GAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAA
* *
89627 GAAGTTTTC-GATGATTAGAGTTGATC
1 GAAGTTTTCAGA-GGTCAGAGTTGATC
89653 CAGTGCGGCT
Statistics
Matches: 349, Mismatches: 24, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
34 3 0.01
35 345 0.99
36 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (35 bp):
GAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAA
Found at i:90902 original size:75 final size:75
Alignment explanation
Indices: 90802--90943 Score: 214
Period size: 75 Copynumber: 1.9 Consensus size: 75
90792 TAATAATGAG
* * *
90802 AATATTTTCTAAATCTTGTCAAATTGTGGTAGATTCAGGAGATAGTTTAAGAAATAAA-ATAATA
1 AATATTTTCTAAATCTTGCCAAATTGTGGGAGATTCAGGAGATAGTTTAAAAAATAAATA-AATA
90866 ATAGAGTTGAT
65 ATAGAGTTGAT
* * *
90877 AATATTTTCTAAATCTTGCCAAATTGTGGGAGGTTTAGGAGATATTTTAAAAAATAAATAAATAA
1 AATATTTTCTAAATCTTGCCAAATTGTGGGAGATTCAGGAGATAGTTTAAAAAATAAATAAATAA
90942 TA
66 TA
90944 AAGATTGAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
75 59 0.98
76 1 0.02
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (75 bp):
AATATTTTCTAAATCTTGCCAAATTGTGGGAGATTCAGGAGATAGTTTAAAAAATAAATAAATAA
TAGAGTTGAT
Found at i:93582 original size:17 final size:16
Alignment explanation
Indices: 93559--93747 Score: 90
Period size: 17 Copynumber: 12.6 Consensus size: 16
93549 ATAATATTTA
93559 GAAATTATATATGTAAT
1 GAAATTATATAT-TAAT
* *
93576 CAAATTATA-ATT-AG
1 GAAATTATATATTAAT
*
93590 GAAA-TA-ATATTTAT
1 GAAATTATATATTAAT
93604 -AAATTATATATGTAAT
1 GAAATTATATAT-TAAT
93620 GAAATTATA-ATTACAT
1 GAAATTATATATTA-AT
*
93636 --AA-TA-ATATTTA-
1 GAAATTATATATTAAT
* * *
93647 GAGATTCTAAATGTAAT
1 GAAATTATATAT-TAAT
93664 GAAATTATA-ATTAA-
1 GAAATTATATATTAAT
* *
93678 GAAAATA-ATATTTA-
1 GAAATTATATATTAAT
* * *
93692 GACATTCTAAATGTAAT
1 GAAATTATATAT-TAAT
93709 GAAATTATAT-TTAA-
1 GAAATTATATATTAAT
93723 -AAATTATATATGTAAT
1 GAAATTATATAT-TAAT
93739 GAAATTATA
1 GAAATTATA
93748 ATGAATATAT
Statistics
Matches: 128, Mismatches: 22, Indels: 44
0.66 0.11 0.23
Matches are distributed among these distances:
12 3 0.02
13 24 0.19
14 25 0.20
15 22 0.17
16 16 0.12
17 38 0.30
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (16 bp):
GAAATTATATATTAAT
Found at i:93597 original size:44 final size:43
Alignment explanation
Indices: 93533--93731 Score: 236
Period size: 44 Copynumber: 4.5 Consensus size: 43
93523 AAATGGTCAA
* * *
93533 AAATTATAATGAGAATATAATATTTAGAAATTATATATGTAATC
1 AAATTATAATTAGAA-ATAATATTTAGAAATTATAAATGTAATG
* *
93577 AAATTATAATTAGGAAATAATATTTATAAATTATATATGTAATG
1 AAATTATAATTA-GAAATAATATTTAGAAATTATAAATGTAATG
* * *
93621 AAATTATAATTACATAATAATATTTAGAGATTCTAAATGTAATG
1 AAATTATAATTAGA-AATAATATTTAGAAATTATAAATGTAATG
* *
93665 AAATTATAATTAAGAAAATAATATTTAGACATTCTAAATGTAATG
1 AAATTATAATT-AG-AAATAATATTTAGAAATTATAAATGTAATG
* * *
93710 AAATTATATTTAAAAATTATAT
1 AAATTATAATTAGAAATAATAT
93732 ATGTAATGAA
Statistics
Matches: 138, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
43 9 0.07
44 86 0.62
45 42 0.30
46 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (43 bp):
AAATTATAATTAGAAATAATATTTAGAAATTATAAATGTAATG
Found at i:93644 original size:88 final size:89
Alignment explanation
Indices: 93549--93717 Score: 250
Period size: 89 Copynumber: 1.9 Consensus size: 89
93539 TAATGAGAAT
* * * *
93549 ATAATATTTAGAAATTATATATGTAATCAAATTATAATT-AGGAAATAATATTTATAAATTATAT
1 ATAATATTTAGAAATTATAAATGTAATCAAATTATAATTAAGAAAATAATATTTAGAAATTATAA
93613 ATGTAATGAAATTATAATTACATA
66 ATGTAATGAAATTATAATTACATA
* * * * *
93637 ATAATATTTAGAGATTCTAAATGTAATGAAATTATAATTAAGAAAATAATATTTAGACATTCTAA
1 ATAATATTTAGAAATTATAAATGTAATCAAATTATAATTAAGAAAATAATATTTAGAAATTATAA
93702 ATGTAATGAAATTATA
66 ATGTAATGAAATTATA
93718 TTTAAAAATT
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
88 35 0.49
89 36 0.51
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (89 bp):
ATAATATTTAGAAATTATAAATGTAATCAAATTATAATTAAGAAAATAATATTTAGAAATTATAA
ATGTAATGAAATTATAATTACATA
Found at i:93721 original size:30 final size:30
Alignment explanation
Indices: 93665--93747 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 30
93655 AAATGTAATG
* *
93665 AAATTAT-AAT-TAA-GAAAATAATATTTAG
1 AAATTATAAATGTAATG-AAATTATATTTAA
* *
93693 ACATTCTAAATGTAATGAAATTATATTTAA
1 AAATTATAAATGTAATGAAATTATATTTAA
*
93723 AAATTATATATGTAATGAAATTATA
1 AAATTATAAATGTAATGAAATTATA
93748 ATGAATATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
28 5 0.11
29 3 0.07
30 36 0.80
31 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (30 bp):
AAATTATAAATGTAATGAAATTATATTTAA
Found at i:93747 original size:15 final size:15
Alignment explanation
Indices: 93702--93747 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
93692 GACATTCTAA
93702 ATGTAATGAAATTAT
1 ATGTAATGAAATTAT
*
93717 ATTTAA--AAATTATAT
1 ATGTAATGAAA-T-TAT
93732 ATGTAATGAAATTAT
1 ATGTAATGAAATTAT
93747 A
1 A
93748 ATGAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
13 3 0.12
14 1 0.04
15 17 0.68
16 1 0.04
17 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (15 bp):
ATGTAATGAAATTAT
Found at i:93800 original size:44 final size:44
Alignment explanation
Indices: 93715--93808 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
93705 TAATGAAATT
* *
93715 ATATTTAAAAATTATATATGTAATGAAATTATAATGAATATATA
1 ATATTTAAAAATTATATATGTAATAAAATTATAATGAATATAAA
* * * *
93759 ATATTTAGAAATTATATATGTAATAAATATTTTTAT-TATATAAA
1 ATATTTAAAAATTATATATGTAATAAA-ATTATAATGAATATAAA
93803 ATATTT
1 ATATTT
93809 TTATTATATA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 37 0.86
45 6 0.14
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (44 bp):
ATATTTAAAAATTATATATGTAATAAAATTATAATGAATATAAA
Found at i:93826 original size:20 final size:18
Alignment explanation
Indices: 93783--93824 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
93773 TATATGTAAT
93783 AAATATTTTTATTATATA
1 AAATATTTTTATTATATA
93801 AAATATTTTTATTATATA
1 AAATATTTTTATTATATA
93819 AAATAT
1 AAATAT
93825 ATATATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AAATATTTTTATTATATA
Found at i:94315 original size:2 final size:2
Alignment explanation
Indices: 94308--94342 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
94298 TGAATCACTC
94308 AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
94343 TAATTTTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:94497 original size:11 final size:11
Alignment explanation
Indices: 94481--94523 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
94471 TATACTATAT
94481 CTAATTAATAG
1 CTAATTAATAG
*
94492 CTAATTAATAT
1 CTAATTAATAG
94503 CTAATTAATAG
1 CTAATTAATAG
*
94514 TTAATTAATA
1 CTAATTAATA
94524 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:94505 original size:22 final size:22
Alignment explanation
Indices: 94477--94523 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
94467 CCATTATACT
94477 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
94499 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
94521 ATA
1 ATA
94524 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:96831 original size:11 final size:11
Alignment explanation
Indices: 96817--96842 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
96807 ATAGAGTTCC
96817 TAAGAAGAAAA
1 TAAGAAGAAAA
96828 TAAGAAGAAAA
1 TAAGAAGAAAA
96839 TAAG
1 TAAG
96843 GCTAACCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (11 bp):
TAAGAAGAAAA
Found at i:102594 original size:43 final size:42
Alignment explanation
Indices: 102532--102634 Score: 127
Period size: 42 Copynumber: 2.4 Consensus size: 42
102522 ATCGAAACAA
* *
102532 ATAATTC-TCATATATAAAGCAAAAAATTCTACTCCATTTCAAG
1 ATAATTCATCA-AAATAAAGC-AAAAATTCTACTCCATCTCAAG
* * * *
102575 GTAATTCATCAAAATAAAGCTAATATTCTACTCCATCTCTAG
1 ATAATTCATCAAAATAAAGCAAAAATTCTACTCCATCTCAAG
102617 ATAATTCATCAAAATAAA
1 ATAATTCATCAAAATAAA
102635 ACTAATATTA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 35 0.67
43 14 0.27
44 3 0.06
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (42 bp):
ATAATTCATCAAAATAAAGCAAAAATTCTACTCCATCTCAAG
Found at i:102622 original size:42 final size:42
Alignment explanation
Indices: 102557--102643 Score: 138
Period size: 42 Copynumber: 2.1 Consensus size: 42
102547 AAAGCAAAAA
* * *
102557 ATTCTACTCCATTTCAAGGTAATTCATCAAAATAAAGCTAAT
1 ATTCTACTCCATCTCAAGATAATTCATCAAAATAAAACTAAT
*
102599 ATTCTACTCCATCTCTAGATAATTCATCAAAATAAAACTAAT
1 ATTCTACTCCATCTCAAGATAATTCATCAAAATAAAACTAAT
102641 ATT
1 ATT
102644 AATTGTTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (42 bp):
ATTCTACTCCATCTCAAGATAATTCATCAAAATAAAACTAAT
Found at i:104809 original size:42 final size:43
Alignment explanation
Indices: 104752--104851 Score: 130
Period size: 45 Copynumber: 2.3 Consensus size: 43
104742 TCGCATATAC
* * *
104752 AAAGCAAATAATTCTA-CTCCATCTCTAGGTAATTCATCAAAAT
1 AAAGCTAAT-ATTCTACCTCCATCTCTAGATAATTCATAAAAAT
*
104795 AAAGGTAATATTCTACTCCTCCATCTCTAGATAATTCATAAAAAT
1 AAAGCTAATATTCTA--CCTCCATCTCTAGATAATTCATAAAAAT
104840 AAAGCTAATATT
1 AAAGCTAATATT
104852 AATTGTTTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 6 0.12
43 7 0.14
45 36 0.73
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (43 bp):
AAAGCTAATATTCTACCTCCATCTCTAGATAATTCATAAAAAT
Found at i:108253 original size:28 final size:28
Alignment explanation
Indices: 108221--108275 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
108211 TCACTTCCTA
*
108221 CAAGTTACGTGCATCAATCACAGCACTG
1 CAAGTAACGTGCATCAATCACAGCACTG
108249 CAAGTAACGTGCATCAATCACAGCACT
1 CAAGTAACGTGCATCAATCACAGCACT
108276 CACACGCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.29, G:0.16, T:0.20
Consensus pattern (28 bp):
CAAGTAACGTGCATCAATCACAGCACTG
Done.