Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008712.1 Corchorus capsularis cultivar CVL-1 contig08733, 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: 15446
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Found at i:2310 original size:20 final size:21
Alignment explanation
Indices: 2268--2310 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
2258 TGGGTAATTA
*
2268 TTGACTAATAAAAATGTAATC
1 TTGACTAATAAAAATGCAATC
2289 TTGAC-AATAAAAAT-CAAGTC
1 TTGACTAATAAAAATGCAA-TC
2309 TT
1 TT
2311 TAGCCTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 13 0.65
21 5 0.25
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.33
Consensus pattern (21 bp):
TTGACTAATAAAAATGCAATC
Found at i:3368 original size:37 final size:37
Alignment explanation
Indices: 3300--3655 Score: 206
Period size: 37 Copynumber: 9.4 Consensus size: 37
3290 TACCCCAATA
* *
3300 AATTAAGAGTC-AAATAATAGTAACCAATAATTAAGT
1 AATTAAGAGTCAAAATAATAGTAATCAGTAATTAAGT
* *
3336 AATTAAGAGTCAAAATGATAGTAACCAGTAATTAAGT
1 AATTAAGAGTCAAAATAATAGTAATCAGTAATTAAGT
* *
3373 AATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGA-T
1 AATTAAGAGTCAAAATAATAGTAATCAGT--AATTAAGT
* * *
3411 AATTAAGAGTCAAAAAGAAATAGTAATCAGTAAAT-CGAT
1 AATTAAGAGTC-AAAA-TAATAGTAATCAGTAATTAAG-T
** * *
3450 AATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGT
1 AATTAAGAGTCAAAATAATAGTAATCAGTAATTAAGT
* * * *
3487 AATT-A-AG-CAAAAAAAGAGATTAACCAGTAAAATTGA-T
1 AATTAAGAGTCAAAATAATAG--TAATCAGT--AATTAAGT
* * * * * *
3524 AATTAAGAGTCAAAGTAATAATAGTCGGCAAAATTGA-T
1 AATTAAGAGTCAAAATAATAGTAATCAG--TAATTAAGT
* * * * *
3562 AATTAAGGGTCAAGATAAGAGATTAATCAGTAAAGTCAGT
1 AATTAAGAGTCAAAATAATAG--TAATCAGT-AATTAAGT
* * *
3602 AATTAAAGAGTCAAGGTAAAAATAGTAATCAGTAAATCAGT
1 AATT-AAGAGTCAA---AATAATAGTAATCAGTAATTAAGT
*
3643 AATTAAGAATCAA
1 AATTAAGAGTCAA
3656 GGGATTAATC
Statistics
Matches: 250, Mismatches: 45, Indels: 46
0.73 0.13 0.13
Matches are distributed among these distances:
34 7 0.03
35 2 0.01
36 19 0.08
37 76 0.30
38 50 0.20
39 26 0.10
40 38 0.15
41 19 0.08
42 8 0.03
44 5 0.02
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.26
Consensus pattern (37 bp):
AATTAAGAGTCAAAATAATAGTAATCAGTAATTAAGT
Found at i:3488 original size:151 final size:151
Alignment explanation
Indices: 3300--3655 Score: 411
Period size: 151 Copynumber: 2.3 Consensus size: 151
3290 TACCCCAATA
* * * * * * *
3300 AATTAAGAGTCAA-ATAATAGTAACCAATAATTAAGTAATTAAGAGTCAAAATGATAGTAACCAG
1 AATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGA-TCAAAAAGAGAGTAACCAG
* *
3364 T-AATTAAGTAATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGTCAA-A-A
65 TAAATTAA-TAATTAAGAGTCAAAGTAATAATAATCAGCAAAATTGATAATTAAGAGTCAAGATA
3426 AGAAATAGTAATCAGTAAA-TC-GAT
129 AGAAAT--TAATCAGTAAAGTCAG-T
* *
3450 AATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGCA-AAAAAAGAGATTAACCAG
1 AATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAG-ATCAAAAAGAGAGTAACCAG
* * * *
3514 TAAAATTGATAATTAAGAGTCAAAGTAATAATAGTCGGCAAAATTGATAATTAAGGGTCAAGATA
65 T-AAATTAATAATTAAGAGTCAAAGTAATAATAATCAGCAAAATTGATAATTAAGAGTCAAGATA
*
3579 AGAGATTAATCAGTAAAGTCAGT
129 AGAAATTAATCAGTAAAGTCAGT
3602 AATTAAAGAGTCAAGGTAAAAATAGTAATCAGTAAATCAGTAATTAAGAATCAA
1 AATT-AAGAGTCAAGGT---AATAGTAATCAGTAAATCAGTAATTAAG-ATCAA
3656 GGGATTAATC
Statistics
Matches: 175, Mismatches: 18, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
150 28 0.16
151 83 0.47
152 14 0.08
153 19 0.11
156 29 0.17
157 2 0.01
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.26
Consensus pattern (151 bp):
AATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGATCAAAAAGAGAGTAACCAGT
AAATTAATAATTAAGAGTCAAAGTAATAATAATCAGCAAAATTGATAATTAAGAGTCAAGATAAG
AAATTAATCAGTAAAGTCAGT
Found at i:3834 original size:44 final size:44
Alignment explanation
Indices: 3784--3938 Score: 161
Period size: 44 Copynumber: 3.5 Consensus size: 44
3774 ATCAAATGGT
* * *
3784 AAGAGTAGAAAGGGTATTTAGAGTGAAAAATGGTATTAAGTAAA
1 AAGAGTAAAAATGGTATTAAGAGTGAAAAATGGTATTAAGTAAA
* * * *
3828 AAGAGTAAAAATGGTA--AAAAGAGACAAAATGGTATCATCGTAAA
1 AAGAGTAAAAATGGTATTAAGAGTGA-AAAATGGTATTA-AGTAAA
* * **
3872 AAGAGTAAAAATGATATTAAGAGTAAAAAAAATGGTATTAAGTATT
1 AAGAGTAAAAATGGTATTAAGAGT--GAAAAATGGTATTAAGTAAA
3918 AAGAGTAAAAATGGTATTAAG
1 AAGAGTAAAAATGGTATTAAG
3939 TAAAGAGTAA
Statistics
Matches: 89, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
42 5 0.06
43 11 0.12
44 34 0.38
46 27 0.30
47 11 0.12
48 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.22, T:0.24
Consensus pattern (44 bp):
AAGAGTAAAAATGGTATTAAGAGTGAAAAATGGTATTAAGTAAA
Found at i:3846 original size:18 final size:18
Alignment explanation
Indices: 3823--3861 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3813 ATGGTATTAA
3823 GTAAAAAGAGTA-AAAATG
1 GTAAAAAGAG-ACAAAATG
3841 GTAAAAAGAGACAAAATG
1 GTAAAAAGAGACAAAATG
3859 GTA
1 GTA
3862 TCATCGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.59, C:0.03, G:0.23, T:0.15
Consensus pattern (18 bp):
GTAAAAAGAGACAAAATG
Found at i:3917 original size:28 final size:27
Alignment explanation
Indices: 3886--3959 Score: 102
Period size: 25 Copynumber: 2.8 Consensus size: 27
3876 GTAAAAATGA
3886 TATTAAGAGTAAAAAAAATGGTATTAAG
1 TATTAAGAGT-AAAAAAATGGTATTAAG
3914 TATTAAGAGT--AAAAATGGTATTAAG
1 TATTAAGAGTAAAAAAATGGTATTAAG
3939 TA--AAGAGTAAGAAAAATGGTA
1 TATTAAGAGTAA-AAAAATGGTA
3960 ATTAGCAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.14
25 17 0.40
26 10 0.23
28 10 0.23
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (27 bp):
TATTAAGAGTAAAAAAATGGTATTAAG
Found at i:8851 original size:15 final size:16
Alignment explanation
Indices: 8804--8877 Score: 50
Period size: 16 Copynumber: 4.8 Consensus size: 16
8794 ATTTCCCGAA
*
8804 AAAAGAAAAAAGAAAG
1 AAAAGGAAAAAGAAAG
* *
8820 ATAAATG-AAAAG--TG
1 A-AAAGGAAAAAGAAAG
8834 AAAAGGAAAAA-AAAG
1 AAAAGGAAAAAGAAAG
*
8849 AAAAAGAAGAAAGAAA-
1 AAAAGGAA-AAAGAAAG
8865 AAAAGAGAAAAAG
1 AAAAG-GAAAAAG
8878 CAACGATGGT
Statistics
Matches: 44, Mismatches: 7, Indels: 14
0.68 0.11 0.22
Matches are distributed among these distances:
13 4 0.09
14 6 0.14
15 8 0.18
16 17 0.39
17 9 0.20
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (16 bp):
AAAAGGAAAAAGAAAG
Found at i:8939 original size:43 final size:43
Alignment explanation
Indices: 8883--9021 Score: 181
Period size: 43 Copynumber: 3.2 Consensus size: 43
8873 AAAAGCAACG
8883 ATGGTTTTAAAAAAGAGTCATGGTTCTCAAAAGGTTTTGATAAA
1 ATGGTTTTAAAAAAGAGTCATGGTT-TCAAAAGGTTTTGATAAA
* *
8927 ATGGTTTT-AAAAAGACTCATGGTTTTCAAAAGTTTTTGATAAA
1 ATGGTTTTAAAAAAGAGTCATGG-TTTCAAAAGGTTTTGATAAA
* * * *
8970 ACGGTTTTTCAAAAAGAGTCATAGTTTAAAAAGGTTTTGATAAA
1 ATGG-TTTTAAAAAAGAGTCATGGTTTCAAAAGGTTTTGATAAA
*
9014 ATGATTTT
1 ATGGTTTT
9022 CCAAAGTTGT
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
43 37 0.45
44 34 0.41
45 12 0.14
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.37
Consensus pattern (43 bp):
ATGGTTTTAAAAAAGAGTCATGGTTTCAAAAGGTTTTGATAAA
Found at i:9592 original size:18 final size:19
Alignment explanation
Indices: 9569--9606 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
9559 CAAAGTAGAG
*
9569 AAGGAAAAAA-AAAGGAAA
1 AAGGAAAAAAGAAAAGAAA
9587 AAGGAAAAAAGAAAAGAAA
1 AAGGAAAAAAGAAAAGAAA
9606 A
1 A
9607 GAAAAACCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (19 bp):
AAGGAAAAAAGAAAAGAAA
Found at i:10241 original size:6 final size:6
Alignment explanation
Indices: 10230--10317 Score: 76
Period size: 6 Copynumber: 14.8 Consensus size: 6
10220 AAAATGAAAT
* *
10230 AAAAAG AAAAAG AAAAAG AAAAAG AAAGAA- ATAAAAA AAAAAG AAAGAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA-AAG A-AAAAG AAAAAG AAA-AAG
* * *
10280 AAAAAG -AAAAG AGAGAG AAAATG --AAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
10318 AGAGAATGAA
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
4 3 0.05
5 5 0.08
6 48 0.73
7 10 0.15
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:10264 original size:32 final size:32
Alignment explanation
Indices: 10217--10288 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
10207 GAGTGCATGT
* *
10217 AAAAA-AATGAAATAAAAAGAAAAAGAAA-AAG
1 AAAAAGAAAGAAATAAAAA-AAAAAGAAAGAAA
10248 AAAAAGAAAGAAATAAAAAAAAAAGAAAGAAA
1 AAAAAGAAAGAAATAAAAAAAAAAGAAAGAAA
10280 AAAAAGAAA
1 AAAAAGAAA
10289 AGAGAGAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
31 14 0.38
32 23 0.62
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.04
Consensus pattern (32 bp):
AAAAAGAAAGAAATAAAAAAAAAAGAAAGAAA
Found at i:10290 original size:49 final size:50
Alignment explanation
Indices: 10217--10332 Score: 139
Period size: 49 Copynumber: 2.3 Consensus size: 50
10207 GAGTGCATGT
10217 AAAAA-AATGAAATAAAAAGAAAAAGAAAAAGAAAAAGAAAGAAATAA-AAA
1 AAAAAGAATGAAA-AAAAAGAAAAAGAAAAAGAAAAAGAAAGAAA-AAGAAA
* * * *
10267 AAAAAGAAAGAAAAAAAAG-AAAAGAGAGAGAAAATGAAAGAAAAAGAAA
1 AAAAAGAATGAAAAAAAAGAAAAAGAAAAAGAAAAAGAAAGAAAAAGAAA
* *
10316 AAAGAGAATGAAGAAAA
1 AAAAAGAATGAAAAAAA
10333 GAAGCTCTAG
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
48 2 0.04
49 38 0.67
50 11 0.19
51 6 0.11
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.04
Consensus pattern (50 bp):
AAAAAGAATGAAAAAAAAGAAAAAGAAAAAGAAAAAGAAAGAAAAAGAAA
Found at i:10300 original size:20 final size:19
Alignment explanation
Indices: 10230--10315 Score: 104
Period size: 19 Copynumber: 4.5 Consensus size: 19
10220 AAAATGAAAT
*
10230 AAAAAGAAA-AAGAAAAAG
1 AAAAAGAAAGAAAAAAAAG
10248 AAAAAGAAAGAAATAAAAA-
1 AAAAAGAAAGAAA-AAAAAG
10267 AAAAAGAAAGAAAAAAAAG
1 AAAAAGAAAGAAAAAAAAG
* *
10286 AAAAGAGAGAGAAAATGAAAG
1 AAAA-AGAAAGAAAA-AAAAG
10307 AAAAAGAAA
1 AAAAAGAAA
10316 AAAGAGAATG
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
18 14 0.24
19 19 0.32
20 18 0.31
21 8 0.14
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (19 bp):
AAAAAGAAAGAAAAAAAAG
Found at i:10310 original size:10 final size:10
Alignment explanation
Indices: 10219--10315 Score: 96
Period size: 10 Copynumber: 9.9 Consensus size: 10
10209 GTGCATGTAA
*
10219 AAAAATGAAAT
1 AAAAA-GAAAG
10230 AAAAAGAAA-
1 AAAAAGAAAG
*
10239 AAGAA-AAAG
1 AAAAAGAAAG
10248 AAAAAGAAAG
1 AAAAAGAAAG
10258 AAATAA-AAA-
1 AAA-AAGAAAG
10267 AAAAAGAAAG
1 AAAAAGAAAG
10277 AAAAA-AAAG
1 AAAAAGAAAG
*
10286 AAAAGAGAGAG
1 AAAA-AGAAAG
*
10297 AAAATGAAAG
1 AAAAAGAAAG
10307 AAAAAGAAA
1 AAAAAGAAA
10316 AAAGAGAATG
Statistics
Matches: 73, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
8 5 0.07
9 22 0.30
10 32 0.44
11 14 0.19
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.04
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:10318 original size:37 final size:37
Alignment explanation
Indices: 10220--10318 Score: 119
Period size: 38 Copynumber: 2.6 Consensus size: 37
10210 TGCATGTAAA
*
10220 AAAATGAAATAAAAAGAAAAAGAAAAAGAAAAAGAAAG
1 AAAATGAAAAAAAAAGAAAAA-AAAAAGAAAAAGAAAG
* *
10258 -AAATAAAAAAAAAAGAAAGAAAAAAAAGAAAAGAGAGAG
1 AAAATGAAAAAAAAAG-AA-AAAAAAAAGAAAA-AGAAAG
*
10297 AAAATGAAAGAAAAAGAAAAAA
1 AAAATGAAAAAAAAAGAAAAAA
10319 GAGAATGAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
37 13 0.25
38 16 0.31
39 10 0.19
40 13 0.25
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (37 bp):
AAAATGAAAAAAAAAGAAAAAAAAAAGAAAAAGAAAG
Found at i:10320 original size:43 final size:42
Alignment explanation
Indices: 10220--10334 Score: 109
Period size: 37 Copynumber: 2.9 Consensus size: 42
10210 TGCATGTAAA
*
10220 AAAATGAAATAAAAAG-AAAAAG--AAAAAGAAAA-AGAAAG
1 AAAATGAAAAAAAAAGAAAAAAGAAAAAAAGAAAAGAGAAAG
* * *
10258 -AAATAAAAAAAAAAG-AAAGA-AAAAAAAGAAAAGAGAGAG
1 AAAATGAAAAAAAAAGAAAAAAGAAAAAAAGAAAAGAGAAAG
* **
10297 AAAATGAAAGAAAAAGAAAAAAGAGAATGAAGAAAAGA
1 AAAATGAAAAAAAAAGAAAAAAGA-AAAAAAGAAAAGA
10335 AGCTCTAGGG
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
37 17 0.28
38 10 0.16
39 5 0.08
40 13 0.21
41 4 0.07
42 1 0.02
43 11 0.18
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.04
Consensus pattern (42 bp):
AAAATGAAAAAAAAAGAAAAAAGAAAAAAAGAAAAGAGAAAG
Found at i:10667 original size:51 final size:51
Alignment explanation
Indices: 10603--10701 Score: 137
Period size: 51 Copynumber: 1.9 Consensus size: 51
10593 GAAGTTTTAT
*
10603 AATAAGATCGCATTCCATTTACGAGTTC-AATATCAAAATTCGATTTTCTAA
1 AATAAGATCGCATTCCATTTACGAG-TCAAAGATCAAAATTCGATTTTCTAA
* ** *
10654 AATAAGATTGCATTCCATTTGTGAGTCAAAGATCAAAATTCGCTTTTC
1 AATAAGATCGCATTCCATTTACGAGTCAAAGATCAAAATTCGATTTTC
10702 AAAGGGCATT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 2 0.05
51 40 0.95
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (51 bp):
AATAAGATCGCATTCCATTTACGAGTCAAAGATCAAAATTCGATTTTCTAA
Found at i:11489 original size:70 final size:70
Alignment explanation
Indices: 11315--11722 Score: 529
Period size: 70 Copynumber: 5.9 Consensus size: 70
11305 AATGCTTCGA
* * * *
11315 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAGTTCGAGCTTTGATTCCATCCAAGCATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATTC
*
11380 ---GA
66 AAGGG
* *
11382 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATTC
*
11447 GAGGG
66 AAGGG
* * *
11452 CTTTACCACGAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTCGGGTTCCATCCAAGCATT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTT-TGGTTCCATCCAAGCATT
*
11517 CAAGAG
65 CAAGGG
* * * * *
11523 CTTTTCCACTAGCCAAACTCATTTCCATACGAGTCAGATT-TAGCCTTGGTTCCATCCAAGCAGT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAG-TTCAAGCTTTGGTTCCATCCAAGCATT
*
11587 CAGGGG
65 CAAGGG
* * *
11593 CTTTTCCACAAGCCAAACTCGGTTCCATACGAGGT-TGTTTAAGCTTTGGTTCCATCCAAGCATT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGA-GTCAGTTCAAGCTTTGGTTCCATCCAAGCATT
*
11657 TAAGGG
65 CAAGGG
* * *
11663 CTTTTCCACAAGCCAAACTCGTTTCCATTCGAGTCAATTCAAGCATTGGTTCCATCCAAG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAG
11723 AAGCATGGGT
Statistics
Matches: 299, Mismatches: 34, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
67 63 0.21
69 4 0.01
70 169 0.57
71 61 0.20
72 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.30
Consensus pattern (70 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATTC
AAGGG
Found at i:11554 original size:141 final size:140
Alignment explanation
Indices: 11328--11722 Score: 525
Period size: 141 Copynumber: 2.8 Consensus size: 140
11318 TTCCATAAGT
* *
11328 CAAACTCGTTTCCATACGAGTCAGTTCGAGCTTTGATTCCATCCAAGCATTC--GA-CTTTTCCA
1 CAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATTCAAGAGCTTTTCCA
* * *
11390 -TAAGTCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATTC-GAGGGC
66 CT-AGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCATTGGTTCCATCCAAGCAGTCAG-GGGC
*
11453 TTTACCACGAGC
129 TTTACCACAAGC
*
11465 CAAACTCGTTTCCATACGAGTCAGTTCAAGCTTCGGGTTCCATCCAAGCATTCAAGAGCTTTTCC
1 CAAACTCGTTTCCATACGAGTCAGTTCAAGCTT-TGGTTCCATCCAAGCATTCAAGAGCTTTTCC
* * *
11530 ACTAGCCAAACTCATTTCCATACGAGTCAGATT-TAGCCTTGGTTCCATCCAAGCAGTCAGGGGC
65 ACTAGCCAAACTCGTTTCCATACGAGTCAG-TTCAAGCATTGGTTCCATCCAAGCAGTCAGGGGC
*
11594 TTTTCCACAAGC
129 TTTACCACAAGC
* * * * *
11606 CAAACTCGGTTCCATACGAGGT-TGTTTAAGCTTTGGTTCCATCCAAGCATTTAAGGGCTTTTCC
1 CAAACTCGTTTCCATACGA-GTCAGTTCAAGCTTTGGTTCCATCCAAGCATTCAAGAGCTTTTCC
* * *
11670 ACAAGCCAAACTCGTTTCCATTCGAGTCAATTCAAGCATTGGTTCCATCCAAG
65 ACTAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCATTGGTTCCATCCAAG
11723 AAGCATGGGT
Statistics
Matches: 227, Mismatches: 22, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
137 32 0.14
138 17 0.07
139 2 0.01
140 74 0.33
141 96 0.42
142 6 0.03
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (140 bp):
CAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATTCAAGAGCTTTTCCA
CTAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCATTGGTTCCATCCAAGCAGTCAGGGGCTT
TACCACAAGC
Found at i:11679 original size:211 final size:207
Alignment explanation
Indices: 11315--11722 Score: 554
Period size: 211 Copynumber: 2.0 Consensus size: 207
11305 AATGCTTCGA
* * * *
11315 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAGTTCGAGCTTTGATTCCATCCAAGCATTC
1 CTTTTCCATAAGCCAAACTCATTTCCATACGAGTCAGTTCGAGCCTTGATTCCATCCAAGCAGTC
* * *
11380 GACTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCAT
66 GACTTTTCCACAAGCCAAACTCGGTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCAT
* * *
11445 TCGAGGGCTTTACCACGAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGC-TTCGGGTTCCATC
131 TCAAGGGCTTTACCACAAGCCAAACTCGTTTCCATACGAGTCAATTCAAGCATT--GGTTCCATC
11509 CAAGCATTCAAGAG
194 CAAGCATTCAAGAG
* *
11523 CTTTTCCACT-AGCCAAACTCATTTCCATACGAGTCAGATT-TAGCCTTGGTTCCATCCAAGCAG
1 CTTTTCCA-TAAGCCAAACTCATTTCCATACGAGTCAG-TTCGAGCCTTGATTCCATCCAAGCAG
* * *
11586 TCAGGGGCTTTTCCACAAGCCAAACTCGGTTCCATACGAGGT-TGTTTAAGCTTTGGTTCCATCC
64 TC---GACTTTTCCACAAGCCAAACTCGGTTCCATACGA-GTCAGTTCAAGCTTTGGTTCCATCC
* * *
11650 AAGCATTTAAGGGCTTTTCCACAAGCCAAACTCGTTTCCATTCGAGTCAATTCAAGCATTGGTTC
125 AAGCATTCAAGGGCTTTACCACAAGCCAAACTCGTTTCCATACGAGTCAATTCAAGCATTGGTTC
11715 CATCCAAG
190 CATCCAAG
11723 AAGCATGGGT
Statistics
Matches: 175, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
208 54 0.31
209 3 0.02
210 13 0.07
211 101 0.58
212 4 0.02
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.30
Consensus pattern (207 bp):
CTTTTCCATAAGCCAAACTCATTTCCATACGAGTCAGTTCGAGCCTTGATTCCATCCAAGCAGTC
GACTTTTCCACAAGCCAAACTCGGTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCAT
TCAAGGGCTTTACCACAAGCCAAACTCGTTTCCATACGAGTCAATTCAAGCATTGGTTCCATCCA
AGCATTCAAGAG
Found at i:12554 original size:14 final size:14
Alignment explanation
Indices: 12535--12568 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
12525 GCATATTAAC
12535 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
12549 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
*
12563 ATTAGT
1 TTTAGT
12569 ATCATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50
Consensus pattern (14 bp):
TTTAGTCCATTTAG
Found at i:12745 original size:20 final size:20
Alignment explanation
Indices: 12707--12747 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
12697 ATAAATACAA
*
12707 GACATTTGATTTACGAATTG
1 GACATTTGATTTACAAATTG
*
12727 GACATTTGATTTGCAAATTG
1 GACATTTGATTTACAAATTG
12747 G
1 G
12748 TGCTCTTTTT
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:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (20 bp):
GACATTTGATTTACAAATTG
Found at i:14900 original size:20 final size:21
Alignment explanation
Indices: 14858--14900 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
14848 TGGGTAAATA
*
14858 TTGACTAATAAAAATGTAATC
1 TTGACTAATAAAAATGCAATC
14879 TTGAC-AATAAAAAT-CAAGTC
1 TTGACTAATAAAAATGCAA-TC
14899 TT
1 TT
14901 TAGCCTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 13 0.65
21 5 0.25
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.33
Consensus pattern (21 bp):
TTGACTAATAAAAATGCAATC
Done.