Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013144.1 Corchorus olitorius cultivar O-4 contig13177, 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: 45800
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:2078 original size:21 final size:21
Alignment explanation
Indices: 2032--2078 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
2022 TTTGCATATT
2032 TAATT-TTAATTTTAATTTTA
1 TAATTATTAATTTTAATTTTA
* *
2052 TTATTATTATTTTTAA-TTTA
1 TAATTATTAATTTTAATTTTA
2072 TGAATTA
1 T-AATTA
2079 ATTTTTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TAATTATTAATTTTAATTTTA
Found at i:5660 original size:19 final size:18
Alignment explanation
Indices: 5636--5671 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5626 TGAAGACTTA
5636 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
5655 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
5672 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:5678 original size:30 final size:30
Alignment explanation
Indices: 5624--5683 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
5614 GAAGTTCGTG
* *
5624 TTTGAAGACTTATTGAAGACAATTTGAAGA
1 TTTGAAGACTCATTGAAGACAATTTCAAGA
*
5654 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA
5684 GCAAGAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (30 bp):
TTTGAAGACTCATTGAAGACAATTTCAAGA
Found at i:8064 original size:19 final size:18
Alignment explanation
Indices: 8040--8075 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
8030 TGAAGACTTA
8040 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
8059 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
8076 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:8082 original size:30 final size:30
Alignment explanation
Indices: 8028--8087 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
8018 GAAGTTCGTG
* *
8028 TTTGAAGACTTATTGAAGACAATTTGAAGA
1 TTTGAAGACTCATTGAAGACAATTTCAAGA
*
8058 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA
8088 GCAAGAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (30 bp):
TTTGAAGACTCATTGAAGACAATTTCAAGA
Found at i:12449 original size:25 final size:28
Alignment explanation
Indices: 12403--12455 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
12393 TTTCAAATGC
12403 AATCTAAATTACTGAAAGGTGAA-TTAACT
1 AATCTAAATTAC--AAAGGTGAACTTAACT
12432 AATCTAAATTA-AAA-GTGAACTTAA
1 AATCTAAATTACAAAGGTGAACTTAA
12456 AATGACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
25 5 0.22
26 7 0.30
29 11 0.48
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.30
Consensus pattern (28 bp):
AATCTAAATTACAAAGGTGAACTTAACT
Found at i:12529 original size:27 final size:27
Alignment explanation
Indices: 12454--12532 Score: 122
Period size: 27 Copynumber: 2.9 Consensus size: 27
12444 AAGTGAACTT
* *
12454 AAAATGACCAAAATGTCTCTGAATGTG
1 AAAATGACCAAAATGTCCCTGGATGTG
12481 AAAATGACCAAAATGTCCCTGGATGTG
1 AAAATGACCAAAATGTCCCTGGATGTG
* *
12508 CAAATGACCAAAATGCCCCTGGATG
1 AAAATGACCAAAATGTCCCTGGATG
12533 ACCCTAATGC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AAAATGACCAAAATGTCCCTGGATGTG
Found at i:12545 original size:27 final size:27
Alignment explanation
Indices: 12455--12546 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 27
12445 AGTGAACTTA
* * * ***
12455 AAATGACCAAAATGTCTCTGAATGTGA
1 AAATGACCAAAATGCCCCTGGATGCCC
* **
12482 AAATGACCAAAATGTCCCTGGATGTGC
1 AAATGACCAAAATGCCCCTGGATGCCC
12509 AAATGACCAAAATGCCCCTGGATGACCC
1 AAATGACCAAAATGCCCCTGGATG-CCC
*
12537 TAATG-CCAAA
1 AAATGACCAAA
12547 TAAGAAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
27 52 0.91
28 5 0.09
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGATGCCC
Found at i:16309 original size:11 final size:11
Alignment explanation
Indices: 16293--16331 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
16283 TATTTAAGAA
16293 GTAAATTTATT
1 GTAAATTTATT
16304 GTAAATTTATT
1 GTAAATTTATT
** *
16315 GTTTATTTATG
1 GTAAATTTATT
16326 GTAAAT
1 GTAAAT
16332 GACAGATAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (11 bp):
GTAAATTTATT
Found at i:22443 original size:14 final size:14
Alignment explanation
Indices: 22424--22450 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22414 TTAAAATTTA
22424 AAATTAAATGTTTT
1 AAATTAAATGTTTT
22438 AAATTAAATGTTT
1 AAATTAAATGTTT
22451 AGGATTTATT
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:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
AAATTAAATGTTTT
Found at i:26477 original size:23 final size:23
Alignment explanation
Indices: 26447--26493 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
26437 TTTGAAACAT
*
26447 AGTATGCTTCACATACAGAGTTG
1 AGTATGCTTCACAGACAGAGTTG
26470 AGTATGCTTCACAGACAGAGTTG
1 AGTATGCTTCACAGACAGAGTTG
26493 A
1 A
26494 ATCGATGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (23 bp):
AGTATGCTTCACAGACAGAGTTG
Found at i:28098 original size:32 final size:32
Alignment explanation
Indices: 28062--28155 Score: 87
Period size: 32 Copynumber: 3.2 Consensus size: 32
28052 TAGACACCCG
28062 ATTTTGAGTTTAGAGTATTTAATCTTCTTTTT
1 ATTTTGAGTTTAGAGTATTTAATCTTCTTTTT
* * * *
28094 ATTTTAAGTGTCGA--A---ACAT-TT-TATTT
1 ATTTTGAGTTTAGAGTATTTA-ATCTTCTTTTT
28120 -TTTTGAGTTTAGAGTATTTAATCTTCTTTTT
1 ATTTTGAGTTTAGAGTATTTAATCTTCTTTTT
28151 ATTTT
1 ATTTT
28156 AAGTGTCGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 18
0.63 0.11 0.25
Matches are distributed among these distances:
25 10 0.22
26 4 0.09
27 4 0.09
28 2 0.04
29 2 0.04
30 4 0.09
31 4 0.09
32 15 0.33
ACGTcount: A:0.23, C:0.06, G:0.12, T:0.59
Consensus pattern (32 bp):
ATTTTGAGTTTAGAGTATTTAATCTTCTTTTT
Found at i:28127 original size:57 final size:57
Alignment explanation
Indices: 28063--28178 Score: 232
Period size: 57 Copynumber: 2.0 Consensus size: 57
28053 AGACACCCGA
28063 TTTTGAGTTTAGAGTATTTAATCTTCTTTTTATTTTAAGTGTCGAAACATTTTATTT
1 TTTTGAGTTTAGAGTATTTAATCTTCTTTTTATTTTAAGTGTCGAAACATTTTATTT
28120 TTTTGAGTTTAGAGTATTTAATCTTCTTTTTATTTTAAGTGTCGAAACATTTTATTT
1 TTTTGAGTTTAGAGTATTTAATCTTCTTTTTATTTTAAGTGTCGAAACATTTTATTT
28177 TT
1 TT
28179 GGTGGAGACT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.24, C:0.07, G:0.12, T:0.57
Consensus pattern (57 bp):
TTTTGAGTTTAGAGTATTTAATCTTCTTTTTATTTTAAGTGTCGAAACATTTTATTT
Found at i:28241 original size:18 final size:19
Alignment explanation
Indices: 28202--28241 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
28192 GTGCTCCCGT
28202 TGTGATGCTCCCACTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
28223 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
28241 T
1 T
28242 TCTAACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Found at i:29509 original size:18 final size:19
Alignment explanation
Indices: 29486--29525 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
29476 AATGGTCAGA
29486 ATTG-AATGGGAGCATCAC
1 ATTGAAATGGGAGCATCAC
29504 ATTGAAAAATGGGAGCATCAC
1 ATTG--AAATGGGAGCATCAC
29525 A
1 A
29526 ATGGGAGCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (19 bp):
ATTGAAATGGGAGCATCAC
Found at i:33641 original size:35 final size:34
Alignment explanation
Indices: 33572--33665 Score: 100
Period size: 35 Copynumber: 2.7 Consensus size: 34
33562 ATCAGGTCAA
* *
33572 AGTTTTTAAATTGGGAAAGTTCCCACGAGTTTTT
1 AGTTTTCAAATTGGGAAAGTTCCCACAAGTTTTT
*
33606 ACGTTTTCAAATTGGGAAAGTTCCTATCAAG-TTTT
1 A-GTTTTCAAATTGGGAAAGTTCCCA-CAAGTTTTT
* * *
33641 AATTTTGAATTTAGGGAAAGTTCCC
1 AGTTTTCAAATT-GGGAAAGTTCCC
33666 GTCATTTTCG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
34 9 0.18
35 38 0.76
36 3 0.06
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (34 bp):
AGTTTTCAAATTGGGAAAGTTCCCACAAGTTTTT
Found at i:38480 original size:75 final size:75
Alignment explanation
Indices: 38355--38503 Score: 228
Period size: 75 Copynumber: 2.0 Consensus size: 75
38345 TCTGGACTGG
* * *
38355 GAGCAAAGGAATGATGAATTTTAATTAAAAATTGTTTCAAAATCAATTTTAGTCAAAGCAATGGT
1 GAGCAAAGGAAAGATGAATTTTAATCAAAAATTGTTTCAAAATCAATTTTAGTCAAAACAATGGT
*
38420 TTCGAGGTGT
66 TTCAAGGTGT
* *
38430 GAGCAAAGGAAAGATGAGTTTTAATCAAAAGA-TGTTTCAAAATCAGTTTTAGTCAAAACAATGG
1 GAGCAAAGGAAAGATGAATTTTAATCAAAA-ATTGTTTCAAAATCAATTTTAGTCAAAACAATGG
38494 TTTCAAGGTG
65 TTTCAAGGTG
38504 ACTGAATCTA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
75 66 0.99
76 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.31
Consensus pattern (75 bp):
GAGCAAAGGAAAGATGAATTTTAATCAAAAATTGTTTCAAAATCAATTTTAGTCAAAACAATGGT
TTCAAGGTGT
Found at i:38938 original size:15 final size:16
Alignment explanation
Indices: 38913--38942 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
38903 AACAGAGAGA
38913 AAAAGAGAAAAAAAGT
1 AAAAGAGAAAAAAAGT
38929 AAAA-AGAAAAAAAG
1 AAAAGAGAAAAAAAG
38943 CACTTGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (16 bp):
AAAAGAGAAAAAAAGT
Found at i:39752 original size:22 final size:22
Alignment explanation
Indices: 39724--39786 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 22
39714 AAGTGCATAA
39724 AAAAATGATGAAAATGAAAATG
1 AAAAATGATGAAAATGAAAATG
**
39746 AAAAATGAAAAAAATG-AAATG
1 AAAAATGATGAAAATGAAAATG
39767 AAAAA--ATGAAAA--AAAATG
1 AAAAATGATGAAAATGAAAATG
39785 AA
1 AA
39787 GAAAAGAAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 7 0.19
19 5 0.14
21 10 0.28
22 14 0.39
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (22 bp):
AAAAATGATGAAAATGAAAATG
Found at i:39770 original size:13 final size:14
Alignment explanation
Indices: 39748--39777 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
39738 TGAAAATGAA
39748 AAATGAAAAAAATG
1 AAATGAAAAAAATG
39762 AAATG-AAAAAATG
1 AAATGAAAAAAATG
39775 AAA
1 AAA
39778 AAAAATGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (14 bp):
AAATGAAAAAAATG
Found at i:40122 original size:50 final size:50
Alignment explanation
Indices: 40066--40164 Score: 162
Period size: 50 Copynumber: 2.0 Consensus size: 50
40056 AAGTTTCATA
** *
40066 ATAAGATTGCATTCCATTTGTGAGTCTGATATCAAAATTCGATTTTCAAG
1 ATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTTCAAG
*
40116 ATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
1 ATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTTCAA
40165 AGGGCATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36
Consensus pattern (50 bp):
ATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTTCAAG
Found at i:40544 original size:16 final size:19
Alignment explanation
Indices: 40509--40547 Score: 57
Period size: 16 Copynumber: 2.2 Consensus size: 19
40499 CAAAGACAAA
40509 TCAAGAAGAGCAGAAGGAT
1 TCAAGAAGAGCAGAAGGAT
40528 TCAAGAA-AGCA-AA-GAT
1 TCAAGAAGAGCAGAAGGAT
40544 TCAA
1 TCAA
40548 AGTAACAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 2 0.10
18 4 0.20
19 7 0.35
ACGTcount: A:0.51, C:0.13, G:0.23, T:0.13
Consensus pattern (19 bp):
TCAAGAAGAGCAGAAGGAT
Found at i:40827 original size:127 final size:126
Alignment explanation
Indices: 40572--40851 Score: 479
Period size: 127 Copynumber: 2.2 Consensus size: 126
40562 AGCTTCAATC
* *
40572 ACAACATCAGACTCAGAGTTAGTTTTCAAGTTATCAAAGTTGACCACTGATCGGTCTTCTCTCAG
1 ACAACATCAGACTCAGAGTTAATTTTCAAGTTATCAAAGTTGACCACTGACCGGTCTTCTCTCAG
* * *
40637 CAGTTATCAACGTTGATCGCAAACTGATCCCCTTTCATCATCAATCAAGAAGTTTTTAGTT
66 CAGTTATCAAAGTTGATCACAAACTGATCCCCTTTCATCATCAATCAAGAAGTTTTCAGTT
* *
40698 ACAACATCAGACTCAGAGTTATTTTTCAAGTTATCAAAGTTGACCGCTGACCGGTCTTCTCTCAG
1 ACAACATCAGACTCAGAGTTAATTTTCAAGTTATCAAAGTTGACCACTGACCGGTCTTCTCTCAG
40763 CAAGTTATCAAAGTTGATCACAAACTGATCCCCTTTCATCATCAATCAAGAAGTTTTCAGTT
66 C-AGTTATCAAAGTTGATCACAAACTGATCCCCTTTCATCATCAATCAAGAAGTTTTCAGTT
*
40825 ACAACATCAGATTCAGAGTTAATTTTC
1 ACAACATCAGACTCAGAGTTAATTTTC
40852 CAAAGGTATT
Statistics
Matches: 145, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
126 63 0.43
127 82 0.57
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (126 bp):
ACAACATCAGACTCAGAGTTAATTTTCAAGTTATCAAAGTTGACCACTGACCGGTCTTCTCTCAG
CAGTTATCAAAGTTGATCACAAACTGATCCCCTTTCATCATCAATCAAGAAGTTTTCAGTT
Found at i:41051 original size:68 final size:68
Alignment explanation
Indices: 40961--41534 Score: 793
Period size: 68 Copynumber: 8.5 Consensus size: 68
40951 AGACCCGTTA
* *
40961 AGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTCTCGCAAGCCAAACTCGTTTCCATACGAGCCAG
1 AGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAGTCAG
*
41026 TTA
66 TTT
**
41029 AGCCTTGGTTCCATCCAAGCAGCAAAGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAGTCAG
1 AGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAGTCAG
41094 TTT
66 TTT
** * *
41097 AGCCTTGGTTCCATCCAAAAAGCAGGGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAGCCAA
1 AGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAGTCAG
*
41162 TTA
66 TTT
41165 AGCCTTGGTTCCATCCAAGCAGCAGGGGCTTT-TCCACAAGCCAAACTCGTTTCCATACGAGTCA
1 AGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTCT-CACAAGCCAAACTCGTTTCCATACGAGTCA
*
41229 CTTT
65 GTTT
* *** * * *
41233 AG-CTTCGGTTCCATCCGAA--TGCTTTGACTTT-TC-CAAGCCAAATTCGTTTCCATATGAGTC
1 AGCCTT-GGTTCCATCC-AAGCAGCAGGGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAGTC
41293 AGTTT
64 AGTTT
* * *
41298 AGCCTTGGTTCCATCCAAGAAGAAGAGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAGTCAG
1 AGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAGTCAG
41363 TTT
66 TTT
*
41366 AGCCTTGGTTCCATCCAAGCAGCAGGGGCTTT-TCCACAGGCCAAACTCGTTTCCATACGAGTCA
1 AGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTCT-CACAAGCCAAACTCGTTTCCATACGAGTCA
41430 GTTT
65 GTTT
* * * *
41434 AGCCTTGGTTCCATCCAAGAAGCAGAGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAGCCAA
1 AGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAGTCAG
*
41499 TTA
66 TTT
* *
41502 AACCTTGGTTCCATCCAAGCATCCAGGGGCTTT
1 AGCCTTGGTTCCATCCAAGCA-GCAGGGGCTTT
41535 TCCATAAGCC
Statistics
Matches: 448, Mismatches: 47, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
64 2 0.00
65 41 0.09
66 10 0.02
67 15 0.03
68 368 0.82
69 12 0.03
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (68 bp):
AGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTCTCACAAGCCAAACTCGTTTCCATACGAGTCAG
TTT
Found at i:41476 original size:269 final size:269
Alignment explanation
Indices: 40997--41494 Score: 831
Period size: 269 Copynumber: 1.9 Consensus size: 269
40987 GGCTTTCTCG
*
40997 CAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTGGTTCCATCCAAGCAGCAAAGGCTTTC
1 CAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTGGTTCCATCCAAGAAGCAAAGGCTTTC
41062 TCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAAAAGCAGGGGCT
66 TCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAAAAGCAGGGGCT
* *
41127 TTCTCACAAGCCAAACTCGTTTCCATACGAGCCAATTAAGCCTTGGTTCCATCCAAGCAGCAGGG
131 TTCTCACAAGCCAAACTCGTTTCCATACGAGCCAATTAAGCCTTGGTTCCATCCAAGAAGCAGAG
41192 GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCACTTTAGCTTCGGTTCCATCCGAATGCTT
196 GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCACTTTAGCTTCGGTTCCATCCGAATGCTT
41257 TGACTTTTC
261 TGACTTTTC
* * * *
41266 CAAGCCAAATTCGTTTCCATATGAGTCAGTTTAGCCTTGGTTCCATCCAAGAAG-AAGAGGCTTT
1 CAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTGGTTCCATCCAAGAAGCAA-AGGCTTT
**
41330 CTCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAGCAGGGGC
65 CTCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAAAAGCAGGGGC
* * * *
41395 TTT-TCCACAGGCCAAACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAGAAGCAG
130 TTTCT-CACAAGCCAAACTCGTTTCCATACGAGCCAATTAAGCCTTGGTTCCATCCAAGAAGCAG
41459 AGGC-TTTCTCACAAGCCAAACTCGTTTCCATACGAG
194 AGGCTTTTC-CACAAGCCAAACTCGTTTCCATACGAG
41495 CCAATTAAAC
Statistics
Matches: 213, Mismatches: 13, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
268 7 0.03
269 206 0.97
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.27
Consensus pattern (269 bp):
CAAGCCAAACTCGTTTCCATACGAGCCAGTTAAGCCTTGGTTCCATCCAAGAAGCAAAGGCTTTC
TCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAGCCTTGGTTCCATCCAAAAAGCAGGGGCT
TTCTCACAAGCCAAACTCGTTTCCATACGAGCCAATTAAGCCTTGGTTCCATCCAAGAAGCAGAG
GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCACTTTAGCTTCGGTTCCATCCGAATGCTT
TGACTTTTC
Found at i:41572 original size:21 final size:21
Alignment explanation
Indices: 41548--41612 Score: 58
Period size: 28 Copynumber: 2.8 Consensus size: 21
41538 ATAAGCCACG
41548 TTCCATATAAATTAAGCTTAC
1 TTCCATATAAATTAAGCTTAC
*
41569 TTCCAAGTAGGCTCAAATTTAAGCTTAT
1 TTCC-A-TA---T-AAA-TTAAGCTTAC
41597 TTCCATATAAATTAAG
1 TTCCATATAAATTAAG
41613 TTTTAAATCC
Statistics
Matches: 36, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
21 9 0.25
22 4 0.11
23 3 0.08
26 3 0.08
27 4 0.11
28 13 0.36
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (21 bp):
TTCCATATAAATTAAGCTTAC
Found at i:41671 original size:35 final size:37
Alignment explanation
Indices: 41632--41708 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 37
41622 CTCAGGGTAC
41632 CTTTCA-A-CTATCAAAGTTGACTGGAAACAGGTCAT
1 CTTTCACAGCTATCAAAGTTGACTGGAAACAGGTCAT
*
41667 CTTTCAGCAGTTATCAAAGTTGACTGGAAACAGGTCAT
1 CTTTCA-CAGCTATCAAAGTTGACTGGAAACAGGTCAT
41705 CTTT
1 CTTT
41709 TCTCAGTGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
35 6 0.16
37 1 0.03
38 31 0.82
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Consensus pattern (37 bp):
CTTTCACAGCTATCAAAGTTGACTGGAAACAGGTCAT
Found at i:41790 original size:36 final size:32
Alignment explanation
Indices: 41718--41791 Score: 87
Period size: 35 Copynumber: 2.2 Consensus size: 32
41708 TTCTCAGTGT
*
41718 TAGTTTCAACCTCAGACATGTCTTTATCTTTC
1 TAGTTTCAACCTCAGACAGGTCTTTATCTTTC
*
41750 -AGTTTCAGACCTCAGAACAGGTCTTCTTTTCTTTC
1 TAGTTTCA-ACCTCAG-ACAGGTC-T-TTATCTTTC
41785 TAGTTTC
1 TAGTTTC
41792 GAATAAATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 7 0.20
32 7 0.20
33 6 0.17
34 1 0.03
35 8 0.23
36 6 0.17
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.43
Consensus pattern (32 bp):
TAGTTTCAACCTCAGACAGGTCTTTATCTTTC
Found at i:44550 original size:24 final size:22
Alignment explanation
Indices: 44497--44563 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 22
44487 ATGTGTTGAT
*
44497 CTTTTTTTTGTTGGGCTTTTATT
1 CTTTTTTTTGTTGGG-TTTTATG
*
44520 TTCTTTTTTTGTTTGGGTTTTATAG
1 CT-TTTTTTTG-TTGGGTTTTAT-G
*
44545 CTTTTTATTG-TGGGTTTTA
1 CTTTTTTTTGTTGGGTTTTA
44564 AATTTCCGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
22 9 0.24
23 1 0.03
24 21 0.57
25 6 0.16
ACGTcount: A:0.07, C:0.06, G:0.19, T:0.67
Consensus pattern (22 bp):
CTTTTTTTTGTTGGGTTTTATG
Found at i:45185 original size:33 final size:33
Alignment explanation
Indices: 45134--45273 Score: 145
Period size: 33 Copynumber: 4.1 Consensus size: 33
45124 AAGAATTTCA
45134 TTAAGTTTTTAATTGGGAAAGTTCCCACCAGTT
1 TTAAGTTTTTAATTGGGAAAGTTCCCACCAGTT
* * * *
45167 TTAAATTTTTAATCGGGAAAGTCCCCACCGGTT
1 TTAAGTTTTTAATTGGGAAAGTTCCCACCAGTT
** *
45200 TTAAGTTTTTAAAAATTGGGAAAGTTCCCATTAACTT
1 TTAAGTTTTT---AATTGGGAAAGTTCCCA-CCAGTT
* *
45237 TTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTT
1 TTAAGTTTT-TAATTGGGAAAGTTCCCA-CCAGTT
45272 TT
1 TT
45274 TTTGCAAAAT
Statistics
Matches: 88, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
33 38 0.43
35 24 0.27
36 15 0.17
37 11 0.12
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.39
Consensus pattern (33 bp):
TTAAGTTTTTAATTGGGAAAGTTCCCACCAGTT
Found at i:45257 original size:35 final size:37
Alignment explanation
Indices: 45198--45266 Score: 115
Period size: 35 Copynumber: 1.9 Consensus size: 37
45188 TCCCCACCGG
45198 TTTTAAGTTTTTAAAAATTGGGAAAGTTCCCATTAAC
1 TTTTAAGTTTTTAAAAATTGGGAAAGTTCCCATTAAC
*
45235 TTTTAAG-TTTT-CAAATTGGGAAAGTTCCCATT
1 TTTTAAGTTTTTAAAAATTGGGAAAGTTCCCATT
45267 CAGTTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 20 0.65
36 4 0.13
37 7 0.23
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (37 bp):
TTTTAAGTTTTTAAAAATTGGGAAAGTTCCCATTAAC
Done.