Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016655.1 Corchorus olitorius cultivar O-4 contig16688, 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: 107576
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:805 original size:35 final size:35
Alignment explanation
Indices: 763--894 Score: 212
Period size: 35 Copynumber: 3.7 Consensus size: 35
753 TGAGTCCATA
763 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT
**
798 TTGAAGATGCTACACCGAGTCATCT-GAGTTCATTT
1 TTGAAGATGCTACACCGAGTCATCTGGA-TTCAACT
*
833 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT
868 TTCGAAGATGCTACACCGAGTCATCTG
1 TT-GAAGATGCTACACCGAGTCATCTG
895 AGAAGATGGT
Statistics
Matches: 89, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
34 2 0.02
35 62 0.70
36 25 0.28
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (35 bp):
TTGAAGATGCTACACCGAGTCATCTGGATTCAACT
Found at i:845 original size:70 final size:71
Alignment explanation
Indices: 763--896 Score: 252
Period size: 70 Copynumber: 1.9 Consensus size: 71
753 TGAGTCCATA
*
763 TTGAAGATGCTACACCGAGTCATCTGGATTCAACTTT-GAAGATGCTACACCGAGTCATCTGAGT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACTTTCGAAGATGCTACACCGAGTCATCTGAGT
827 TCATTT
66 TCATTT
833 TTGAAGATGCTACACCGAGTCATCTGAATTCAACTTTCGAAGATGCTACACCGAGTCATCTGAG
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAACTTTCGAAGATGCTACACCGAGTCATCTGAG
897 AAGATGGTAA
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
70 36 0.58
71 26 0.42
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (71 bp):
TTGAAGATGCTACACCGAGTCATCTGAATTCAACTTTCGAAGATGCTACACCGAGTCATCTGAGT
TCATTT
Found at i:1031 original size:50 final size:50
Alignment explanation
Indices: 978--1566 Score: 1036
Period size: 50 Copynumber: 11.8 Consensus size: 50
968 GGTTTGAACT
* *
978 GACTCGTATGGAAACGAGTTTGGCTTATGGAAAAGCAC-ATGTTGATAATT
1 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGC-CTATGTTGATAATC
*
1028 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATT
1 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATC
1078 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATC
1 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATC
1128 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATC
1 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATC
* *
1178 GACTCATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTGTTGATAATC
1 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATC
*
1228 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGTCTATGTTGATAATC
1 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATC
*
1278 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATG
1 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATC
*
1328 GACTTGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATC
1 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATC
*
1378 GAATCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATC
1 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATC
*
1428 GACTCGTATGGAAACGAGTTTGGCTTGTGAAAAAGCCTATGTTGATAATC
1 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATC
* *
1478 GACTCGTATGGAAACGAGTTTAGCCTGTGGAAAAGCCTATGTTGATAATC
1 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATC
* *
1528 GACTCGTATGGAAACGAGTTTGACTTATGGAAAAGCCTA
1 GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
1567 AACCTTCGGA
Statistics
Matches: 516, Mismatches: 22, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
49 1 0.00
50 515 1.00
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (50 bp):
GACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATC
Found at i:2233 original size:50 final size:50
Alignment explanation
Indices: 2169--2316 Score: 215
Period size: 50 Copynumber: 3.0 Consensus size: 50
2159 TTAAATGCCC
* * * *
2169 TTTGAAAAGTGAATTTTGATCTTGGACTCACAACTGGAATGCAATCTTAT
1 TTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTAT
* *
2219 TTTGAAAAGCGAATTTTAATCTTGAACTCACAAATGGAAAGCAATTTTAT
1 TTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTAT
* * *
2269 TTTGAAAAGCAAATTTTGATCTTGAACTCATAAATGGAAAGAAATCTT
1 TTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTT
2317 GTTATAAAAC
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 87 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (50 bp):
TTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTAT
Found at i:2917 original size:6 final size:6
Alignment explanation
Indices: 2906--2957 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
2896 ATCAACTATC
**
2906 TTTTGA TTTTGA -TTTGA -TTTGAA TTTTTGA TTTTGA TTTTTT TTTTGA
1 TTTTGA TTTTGA TTTTGA TTTTG-A -TTTTGA TTTTGA TTTTGA TTTTGA
2954 TTTT
1 TTTT
2958 TTTTATTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 9 0.23
6 25 0.64
7 1 0.03
8 4 0.10
ACGTcount: A:0.15, C:0.00, G:0.13, T:0.71
Consensus pattern (6 bp):
TTTTGA
Found at i:2936 original size:13 final size:13
Alignment explanation
Indices: 2918--2977 Score: 50
Period size: 14 Copynumber: 4.5 Consensus size: 13
2908 TTGATTTTGA
2918 TTTGATTTGAATT
1 TTTGATTTGAATT
2931 TTTGATTTTG-ATT
1 TTTGA-TTTGAATT
** *
2944 TTTTTTTTGATTTT
1 TTTGATTTGA-ATT
*
2958 TTTTATTTGAATT
1 TTTGATTTGAATT
2971 TCTTGAT
1 T-TTGAT
2978 GGAGGGGACT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
12 4 0.11
13 14 0.38
14 19 0.51
ACGTcount: A:0.17, C:0.02, G:0.12, T:0.70
Consensus pattern (13 bp):
TTTGATTTGAATT
Found at i:2951 original size:12 final size:12
Alignment explanation
Indices: 2936--2961 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2926 GAATTTTTGA
2936 TTTTGATTTTTT
1 TTTTGATTTTTT
2948 TTTTGATTTTTT
1 TTTTGATTTTTT
2960 TT
1 TT
2962 ATTTGAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (12 bp):
TTTTGATTTTTT
Found at i:3380 original size:22 final size:21
Alignment explanation
Indices: 3340--3383 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
3330 TCCAAGTGCC
3340 TTTATTTTCCTTTTTTCATTT
1 TTTATTTTCCTTTTTTCATTT
3361 TTTATTTT-CTTCATTTTCATTT
1 TTTATTTTCCTT--TTTTCATTT
3383 T
1 T
3384 CATTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 3 0.14
21 8 0.38
22 10 0.48
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTATTTTCCTTTTTTCATTT
Found at i:3382 original size:15 final size:15
Alignment explanation
Indices: 3343--3384 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
3333 AAGTGCCTTT
*
3343 ATTTTCCTTTT-TTC
1 ATTTTCATTTTCTTC
*
3357 ATTTTTTATTTTCTTC
1 A-TTTTCATTTTCTTC
3373 ATTTTCATTTTC
1 ATTTTCATTTTC
3385 ATTTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 1 0.04
15 18 0.78
16 4 0.17
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTCATTTTCTTC
Found at i:7154 original size:41 final size:41
Alignment explanation
Indices: 7104--7264 Score: 223
Period size: 41 Copynumber: 3.9 Consensus size: 41
7094 CAAATTGAGC
* * * *
7104 CAAACAGTAATTAGAATCCTAAATCAAGGACAAAATTGTAT
1 CAAATAGTAAATAGAATCCTAAATTAGGGACAAAATTGTAT
* * *
7145 CAAATAGTAAGTAGAATCCTAAATTAGGGGCCAAATTGTAT
1 CAAATAGTAAATAGAATCCTAAATTAGGGACAAAATTGTAT
* *
7186 CAAATAGTAAATAGAATCCTTAATTAGGGACTAAATTGTAT
1 CAAATAGTAAATAGAATCCTAAATTAGGGACAAAATTGTAT
* *
7227 CAAATAGTAAATAGAATCCTAAATTAGGGGCCAAATTG
1 CAAATAGTAAATAGAATCCTAAATTAGGGACAAAATTG
7265 AACACGGAAA
Statistics
Matches: 107, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 107 1.00
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (41 bp):
CAAATAGTAAATAGAATCCTAAATTAGGGACAAAATTGTAT
Found at i:7230 original size:82 final size:82
Alignment explanation
Indices: 7104--7264 Score: 259
Period size: 82 Copynumber: 2.0 Consensus size: 82
7094 CAAATTGAGC
* *
7104 CAAACAGTAATTAGAATCCTAAATCAAGGACAAAATTGTATCAAATAGTAAGTAGAATCCTAAAT
1 CAAACAGTAAATAGAATCCTAAATCAAGGACAAAATTGTATCAAATAGTAAATAGAATCCTAAAT
7169 TAGGGGCCAAATTGTAT
66 TAGGGGCCAAATTGTAT
* * * * *
7186 CAAATAGTAAATAGAATCCTTAATTAGGGACTAAATTGTATCAAATAGTAAATAGAATCCTAAAT
1 CAAACAGTAAATAGAATCCTAAATCAAGGACAAAATTGTATCAAATAGTAAATAGAATCCTAAAT
7251 TAGGGGCCAAATTG
66 TAGGGGCCAAATTG
7265 AACACGGAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 72 1.00
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (82 bp):
CAAACAGTAAATAGAATCCTAAATCAAGGACAAAATTGTATCAAATAGTAAATAGAATCCTAAAT
TAGGGGCCAAATTGTAT
Found at i:18928 original size:23 final size:23
Alignment explanation
Indices: 18898--18943 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
18888 CAGATGAAAC
18898 AATACTAGCTCTTCCGGAGCCTT
1 AATACTAGCTCTTCCGGAGCCTT
*
18921 AATACTAGCTCTTCTGGAGCCTT
1 AATACTAGCTCTTCCGGAGCCTT
18944 CAATCAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (23 bp):
AATACTAGCTCTTCCGGAGCCTT
Found at i:31734 original size:27 final size:27
Alignment explanation
Indices: 31693--31757 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
31683 CCTGAGTGCA
*
31693 CAAATGACCAAAATGCCTCTAAATATG
1 CAAATGACCAAAATGCCCCTAAATATG
** * * *
31720 CAAATGACCTGAATGCCCCTGAGTGTG
1 CAAATGACCAAAATGCCCCTAAATATG
31747 CAAATGACCAA
1 CAAATGACCAA
31758 TTAAGAAACA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (27 bp):
CAAATGACCAAAATGCCCCTAAATATG
Found at i:32789 original size:33 final size:34
Alignment explanation
Indices: 32738--32812 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
32728 ATAATTTTTA
* *
32738 ATGATAAAAGAAAGGTAGAAGGAGGAGATTATGC
1 ATGATAAAAGAAAGGTAGAAGAAGGAGATCATGC
32772 ATGATAAAA-AAAGGTAGAAGAAGGAGATCATGC
1 ATGATAAAAGAAAGGTAGAAGAAGGAGATCATGC
*
32805 ATGCTAAA
1 ATGATAAA
32813 TAAACTTTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 29 0.76
34 9 0.24
ACGTcount: A:0.49, C:0.05, G:0.28, T:0.17
Consensus pattern (34 bp):
ATGATAAAAGAAAGGTAGAAGAAGGAGATCATGC
Found at i:32877 original size:31 final size:31
Alignment explanation
Indices: 32842--32901 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
32832 TATCTAACCT
*
32842 TAGACTTGTATGATTCAACTTTCAATCTCCG
1 TAGACTTGTATGATTAAACTTTCAATCTCCG
32873 TAGACTTGTATGATTAAACTTTCAATCTC
1 TAGACTTGTATGATTAAACTTTCAATCTC
32902 GATCTTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (31 bp):
TAGACTTGTATGATTAAACTTTCAATCTCCG
Found at i:33486 original size:2 final size:2
Alignment explanation
Indices: 33479--33516 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
33469 TAACATACCC
* *
33479 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33517 TGATTAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:33494 original size:10 final size:10
Alignment explanation
Indices: 33478--33516 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
33468 CTAACATACC
33478 CATATATATA
1 CATATATATA
*
33488 TATATATATA
1 CATATATATA
33498 CATATATATA
1 CATATATATA
33508 CATATATAT
1 CATATATAT
33517 TGATTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (10 bp):
CATATATATA
Found at i:38335 original size:19 final size:18
Alignment explanation
Indices: 38311--38346 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
38301 TGAAGACTTA
38311 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
38330 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
38347 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:38353 original size:30 final size:30
Alignment explanation
Indices: 38299--38358 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
38289 TAAGTTCGTG
* *
38299 TTTGAAGACTTATTGAAGACAATTTGAAGA
1 TTTGAAGACTCATTGAAGACAATTTCAAGA
*
38329 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA
38359 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:39893 original size:13 final size:13
Alignment explanation
Indices: 39875--39918 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
39865 GGGGAGATTG
39875 TTTACTATTTTCT
1 TTTACTATTTTCT
*
39888 TTTACTTTTTTCT
1 TTTACTATTTTCT
*
39901 TTT-CTATATTCGT
1 TTTACTATTTTC-T
39914 TTTAC
1 TTTAC
39919 ACTTGATCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 6 0.23
13 19 0.73
14 1 0.04
ACGTcount: A:0.14, C:0.16, G:0.02, T:0.68
Consensus pattern (13 bp):
TTTACTATTTTCT
Found at i:45799 original size:21 final size:22
Alignment explanation
Indices: 45756--45833 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 22
45746 TTAAGGAGAA
*
45756 AATTTGTCGACTAAAGAGAAGC
1 AATTAGTCGACTAAAGAGAAGC
45778 AATTAGTCGACTAAAG-GAAGC
1 AATTAGTCGACTAAAGAGAAGC
*
45799 AAAACTA-TCGACTAAAGAGAGGAGC
1 --AATTAGTCGACTAAAGAGA--AGC
45824 AATT-GTCGAC
1 AATTAGTCGAC
45834 AAGGATTCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
21 5 0.11
22 25 0.53
23 14 0.30
25 3 0.06
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.19
Consensus pattern (22 bp):
AATTAGTCGACTAAAGAGAAGC
Found at i:47506 original size:17 final size:17
Alignment explanation
Indices: 47486--47519 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
47476 GGTAATTAAA
*
47486 AAAAAAATTGTTTTCAT
1 AAAAAAAGTGTTTTCAT
*
47503 AAAAGAAGTGTTTTCAT
1 AAAAAAAGTGTTTTCAT
47520 GATAGAGGAG
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:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (17 bp):
AAAAAAAGTGTTTTCAT
Found at i:48366 original size:19 final size:18
Alignment explanation
Indices: 48342--48377 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
48332 TGAAGACTTA
48342 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
48361 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
48378 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:48384 original size:30 final size:30
Alignment explanation
Indices: 48330--48389 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
48320 GAAGTTCGTG
* *
48330 TTTGAAGACTTATTGAAGACAATTTGAAGA
1 TTTGAAGACTCATTGAAGACAATTTCAAGA
*
48360 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA
48390 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:50032 original size:30 final size:31
Alignment explanation
Indices: 49990--50070 Score: 82
Period size: 30 Copynumber: 2.7 Consensus size: 31
49980 TTGAGAAGTT
*
49990 TGGTAA-GATTGTGAAAGTTGA-GAAAAAGAA
1 TGGTAAGGTTTGTGAAAGTTGAGGAAAAAG-A
* *
50020 TGGT-AGGTTTGTGAGAA-TTGAGGAAGATGA
1 TGGTAAGGTTTGTGA-AAGTTGAGGAAAAAGA
50050 TGGTAAGGTTTG-GAAAGTTGA
1 TGGTAAGGTTTGTGAAAGTTGA
50071 AAAGAAAATG
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
29 3 0.07
30 26 0.60
31 14 0.33
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.28
Consensus pattern (31 bp):
TGGTAAGGTTTGTGAAAGTTGAGGAAAAAGA
Found at i:61166 original size:5 final size:5
Alignment explanation
Indices: 61158--61187 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
61148 ACTTCCCTCC
*
61158 CCTTT CCTTT CCTTT TCTTT CCTTT CCTTT
1 CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT
61188 AAAAACTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (5 bp):
CCTTT
Found at i:61179 original size:15 final size:15
Alignment explanation
Indices: 61159--61187 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
61149 CTTCCCTCCC
61159 CTTTCCTTTCCTTTT
1 CTTTCCTTTCCTTTT
61174 CTTTCCTTTCCTTT
1 CTTTCCTTTCCTTT
61188 AAAAACTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (15 bp):
CTTTCCTTTCCTTTT
Found at i:68172 original size:17 final size:18
Alignment explanation
Indices: 68146--68180 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
68136 GGTTATTTAT
68146 TAATTATTTTA-ATATTA
1 TAATTATTTTATATATTA
*
68163 TAATTTTTTTATATATTA
1 TAATTATTTTATATATTA
68181 CATTTTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TAATTATTTTATATATTA
Found at i:68332 original size:13 final size:13
Alignment explanation
Indices: 68314--68340 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
68304 AAATATAATA
68314 AATATGATTTATG
1 AATATGATTTATG
68327 AATATGATTTATG
1 AATATGATTTATG
68340 A
1 A
68341 GGTTATAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (13 bp):
AATATGATTTATG
Found at i:70972 original size:20 final size:21
Alignment explanation
Indices: 70947--71005 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 21
70937 AACATAAACC
*
70947 ACATAA-TCCTTTTCTAAGAA
1 ACATAACTCCATTTCTAAGAA
*
70967 ACATAAACCTCCATTTCTGAGAA
1 ACAT-AA-CTCCATTTCTAAGAA
70990 ACATAAACCTCCATTT
1 ACAT-AA-CTCCATTT
71006 TAGATACTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 4 0.12
21 2 0.06
23 28 0.82
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.31
Consensus pattern (21 bp):
ACATAACTCCATTTCTAAGAA
Found at i:70983 original size:23 final size:23
Alignment explanation
Indices: 70957--71005 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
70947 ACATAATCCT
70957 TTTCTAAGAAACATAAACCTCCA
1 TTTCTAAGAAACATAAACCTCCA
*
70980 TTTCTGAGAAACATAAACCTCCA
1 TTTCTAAGAAACATAAACCTCCA
71003 TTT
1 TTT
71006 TAGATACTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (23 bp):
TTTCTAAGAAACATAAACCTCCA
Found at i:76051 original size:20 final size:20
Alignment explanation
Indices: 76026--76066 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
76016 ATCAATCAAG
**
76026 ATTCAAGAACAGTCATAGCC
1 ATTCAAGAACAACCATAGCC
76046 ATTCAAGAACAACCATAGCC
1 ATTCAAGAACAACCATAGCC
76066 A
1 A
76067 CTGACCTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.27, G:0.12, T:0.17
Consensus pattern (20 bp):
ATTCAAGAACAACCATAGCC
Found at i:80454 original size:40 final size:40
Alignment explanation
Indices: 80367--80511 Score: 229
Period size: 40 Copynumber: 3.6 Consensus size: 40
80357 TCGTAAGAAA
* *
80367 AAAAGATTTGGGTCGGAAAAGTTGTATAGAATTTTGTAAGG
1 AAAAGATTTGGGCCCGAAAAGTTGTATAGAA-TTTGTAAGG
80408 AAAAGATTTGGGCCCGAAAAGTTGTATAGAATTTGTAAGG
1 AAAAGATTTGGGCCCGAAAAGTTGTATAGAATTTGTAAGG
*
80448 AAAAGATTTAGGCCCGAAAAGTTGTATAGAATTTGTAAGG
1 AAAAGATTTGGGCCCGAAAAGTTGTATAGAATTTGTAAGG
*
80488 AAAAGATTT-GGCCTTGAAAAGTTG
1 AAAAGATTTGGGCC-CGAAAAGTTG
80512 CATACCCCCA
Statistics
Matches: 99, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
39 4 0.04
40 66 0.67
41 29 0.29
ACGTcount: A:0.38, C:0.06, G:0.27, T:0.29
Consensus pattern (40 bp):
AAAAGATTTGGGCCCGAAAAGTTGTATAGAATTTGTAAGG
Found at i:81752 original size:59 final size:58
Alignment explanation
Indices: 81625--81755 Score: 147
Period size: 59 Copynumber: 2.2 Consensus size: 58
81615 TGTCGGCTTT
* * *
81625 CCTTCTCTTCTCTTTCCTTCCCTCATCGCTGCTACCAATAAAATCCCATCATCGATGAC
1 CCTTCTCTTCTCTTTCCTTCCCACATCACTGCTACCAATAAAA-CCCATCATCGATAAC
* * * * *
81684 CCTTGTCTTCTCTTTCCTTCCCACATCACTGTTACCACTAAAA-CCATGTCGTTGATAAC
1 CCTTCTCTTCTCTTTCCTTCCCACATCACTGCTACCAATAAAACCCA--TCATCGATAAC
*
81743 CTTTCTCTTCTCT
1 CCTTCTCTTCTCT
81756 ACCTTCTTCT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
57 3 0.05
59 57 0.95
ACGTcount: A:0.19, C:0.37, G:0.07, T:0.37
Consensus pattern (58 bp):
CCTTCTCTTCTCTTTCCTTCCCACATCACTGCTACCAATAAAACCCATCATCGATAAC
Found at i:81966 original size:18 final size:18
Alignment explanation
Indices: 81945--81989 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
81935 AAGTCTAATC
81945 CCCCAAATTAACCTAAAA
1 CCCCAAATTAACCTAAAA
81963 CCCCAAATTAACCTAAAA
1 CCCCAAATTAACCTAAAA
81981 CCCCAAATT
1 CCCCAAATT
81990 TTCCTTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.47, C:0.36, G:0.00, T:0.18
Consensus pattern (18 bp):
CCCCAAATTAACCTAAAA
Found at i:86342 original size:12 final size:11
Alignment explanation
Indices: 86324--86350 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
86314 TTGTTGTTGG
86324 GTTTTTTTTTT
1 GTTTTTTTTTT
86335 GTTTTTTTTTT
1 GTTTTTTTTTT
86346 GTTTT
1 GTTTT
86351 AAATTCTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (11 bp):
GTTTTTTTTTT
Found at i:92002 original size:12 final size:12
Alignment explanation
Indices: 91985--92012 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
91975 TTTTTACTAA
91985 CCTAGACTAAAT
1 CCTAGACTAAAT
91997 CCTAGACTAAAT
1 CCTAGACTAAAT
92009 CCTA
1 CCTA
92013 ACAAATATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.29, G:0.07, T:0.25
Consensus pattern (12 bp):
CCTAGACTAAAT
Found at i:100832 original size:16 final size:16
Alignment explanation
Indices: 100811--100841 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
100801 TATATATAAA
100811 TAATAAATAACAGTAC
1 TAATAAATAACAGTAC
*
100827 TAATAAATAATAGTA
1 TAATAAATAACAGTA
100842 TTAAAAAGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (16 bp):
TAATAAATAACAGTAC
Found at i:101253 original size:26 final size:26
Alignment explanation
Indices: 101215--101270 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
101205 TGCAGGTTCA
* * *
101215 CATCTTTCCCATTATCCACACGCTGC
1 CATCTTTCACATTATCCACACACTAC
101241 CATCTTTCACATTATCCACACACTAC
1 CATCTTTCACATTATCCACACACTAC
101267 CATC
1 CATC
101271 CATCCATACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.25, C:0.41, G:0.04, T:0.30
Consensus pattern (26 bp):
CATCTTTCACATTATCCACACACTAC
Found at i:103856 original size:2 final size:2
Alignment explanation
Indices: 103851--103890 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
103841 TTGATAATTG
103851 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
103891 ATCGGTTGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:104114 original size:13 final size:14
Alignment explanation
Indices: 104086--104126 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
104076 CCAAGTGGGG
* *
104086 TAGTAATAATTAAC
1 TAGTAGTAACTAAC
104100 TAGTAGTAA-TAAC
1 TAGTAGTAACTAAC
104113 TAGTAGTAACTAAC
1 TAGTAGTAACTAAC
104127 ATTCATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (14 bp):
TAGTAGTAACTAAC
Found at i:106694 original size:3 final size:3
Alignment explanation
Indices: 106666--106710 Score: 54
Period size: 3 Copynumber: 13.7 Consensus size: 3
106656 TTCATAGGCC
106666 AAT AATT AAT ATAT ATAT ATAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AA-T AAT A-AT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT AA
106711 AATTGCACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 26 0.65
4 14 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:106789 original size:3 final size:3
Alignment explanation
Indices: 106777--106823 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
106767 ATTATACTTG
*
106777 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
106824 CAAGCAGGGC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:107064 original size:45 final size:45
Alignment explanation
Indices: 107005--107119 Score: 187
Period size: 45 Copynumber: 2.6 Consensus size: 45
106995 AGTGCATTAC
*
107005 CTAA-ATTCTACTGATCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTGATCCATCTCTAGGTAATTCATCAAAACAAAG
*
107049 CTAATATTCAACTGATCCATCTCTAGGTAATTCATCAAAACAAAG
1 CTAATATTCTACTGATCCATCTCTAGGTAATTCATCAAAACAAAG
**
107094 CTAATATTCTACTCTTCCATCTCTAG
1 CTAATATTCTACTGATCCATCTCTAG
107120 ATATAAATTA
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
44 4 0.06
45 61 0.94
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (45 bp):
CTAATATTCTACTGATCCATCTCTAGGTAATTCATCAAAACAAAG
Done.