Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007478.1 Corchorus capsularis cultivar CVL-1 contig07499, 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: 77857
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:5017 original size:30 final size:30
Alignment explanation
Indices: 4983--5041 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
4973 TACACTAAAA
4983 AGAGCTTTTGCTTCCGTTTGGAGCTTCTTT
1 AGAGCTTTTGCTTCCGTTTGGAGCTTCTTT
5013 AGAGCTTTTGCTTCCGTTTGGAGCTTCTT
1 AGAGCTTTTGCTTCCGTTTGGAGCTTCTT
5042 CAACGATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (30 bp):
AGAGCTTTTGCTTCCGTTTGGAGCTTCTTT
Found at i:14776 original size:167 final size:165
Alignment explanation
Indices: 14387--14778 Score: 561
Period size: 166 Copynumber: 2.4 Consensus size: 165
14377 TGAGTCATTT
*
14387 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGATAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * * * ** * *
14452 TTAAGTAATCTGTCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTAGCTCATCATCAATCCTTG
65 TTAAGTAATCTGGCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCAAAAGCAAGCCTTG
* *
14517 ATGAAGATCTTTTATTAATTCCACTACTCTATTCAA
130 ATGAAGATCTTTTAGTAATTCCACTACTCTATTAAA
* * * * *
14553 GTCCATTAAGAAATGACCAAAAAGATTACTTATTTAATCCACTCAATAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
14618 TTAAGTAATCTGGCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCTAAAAGCAAGCCTT
65 TTAAGTAATCTGGCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTC-AAAAGCAAGCCTT
*
14683 GGT-AGAGATCTTTTAGTAATTCCACTACTCTATTAAA
129 GATGA-AGATCTTTTAGTAATTCCACTACTCTATTAAA
*
14720 GTCAATTGAGAAATGACTAAAAAGTCTAGTTATTTAATCCCCTCAAGAATCAAAAGTTA
1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTA
14779 ATTTGTCAAG
Statistics
Matches: 198, Mismatches: 25, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
166 106 0.54
167 92 0.46
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (165 bp):
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGGCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCAAAAGCAAGCCTTGA
TGAAGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:14897 original size:3 final size:3
Alignment explanation
Indices: 14891--14929 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
14881 TAGCGTATAT
14891 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
14930 TATATATACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:15568 original size:45 final size:45
Alignment explanation
Indices: 15518--15607 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
15508 GATTACTTCT
*
15518 CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCGGGGTAGGGACCTTTTAGTAATTCCAC
* *
15563 CCAGCTCATCATTAGTTCGGGGTAGGGACCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCGGGGTAGGGACCTTTTAGTAATTCCAC
15608 TACTCTATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.31
Consensus pattern (45 bp):
CCAGCTCATCATTAATCCGGGGTAGGGACCTTTTAGTAATTCCAC
Found at i:20272 original size:27 final size:27
Alignment explanation
Indices: 20233--20302 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 27
20223 TTGATTACCA
* *
20233 ATTACTATGTTTTACTC-TTTGTACTG
1 ATTACCATTTTTTACTCTTTTGTACTG
*
20259 ATTACCATATTTTTACTCTTTTTTACTG
1 ATTACCAT-TTTTTACTCTTTTGTACTG
*
20287 ATTACCATTTCTTACT
1 ATTACCATTTTTTACT
20303 GAATACTACA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 7 0.18
27 15 0.39
28 16 0.42
ACGTcount: A:0.21, C:0.19, G:0.06, T:0.54
Consensus pattern (27 bp):
ATTACCATTTTTTACTCTTTTGTACTG
Found at i:20404 original size:20 final size:21
Alignment explanation
Indices: 20364--20410 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
20354 AATTACCATT
**
20364 TTACTTTTTACTTGATTACCA
1 TTACTTTTTACTTGACAACCA
20385 TTACTTTTTAC-TGACAACCA
1 TTACTTTTTACTTGACAACCA
20405 TTACTT
1 TTACTT
20411 CTTAGCGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.26, C:0.21, G:0.04, T:0.49
Consensus pattern (21 bp):
TTACTTTTTACTTGACAACCA
Found at i:20439 original size:7 final size:7
Alignment explanation
Indices: 20427--20525 Score: 75
Period size: 7 Copynumber: 14.7 Consensus size: 7
20417 GATTACTCTT
20427 TCTTTAC
1 TCTTTAC
20434 TCTTTAC
1 TCTTTAC
20441 TCTTTA-
1 TCTTTAC
20447 TCATTT--
1 TC-TTTAC
*
20453 TTTTTAC
1 TCTTTAC
**
20460 TGATTAC
1 TCTTTAC
20467 TCTTT--
1 TCTTTAC
20472 TCTTTAC
1 TCTTTAC
20479 TCTTTAC
1 TCTTTAC
20486 TCTTTAC
1 TCTTTAC
20493 TCTTTA-
1 TCTTTAC
**
20499 TCATTTTT
1 TC-TTTAC
20507 TCTTTAC
1 TCTTTAC
**
20514 TGATTAC
1 TCTTTAC
20521 TCTTT
1 TCTTT
20526 TACTTTTTGG
Statistics
Matches: 73, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.11
6 5 0.07
7 58 0.79
8 2 0.03
ACGTcount: A:0.15, C:0.21, G:0.02, T:0.62
Consensus pattern (7 bp):
TCTTTAC
Found at i:20460 original size:19 final size:18
Alignment explanation
Indices: 20434--20505 Score: 62
Period size: 19 Copynumber: 4.1 Consensus size: 18
20424 CTTTCTTTAC
20434 TCTTTACTCTTTATCATTT
1 TCTTTACTCTTTATC-TTT
* **
20453 TTTTTACTGATTACTCTTT
1 TCTTTACTCTTTA-TCTTT
20472 TCTTTACTCTTTA-C---
1 TCTTTACTCTTTATCTTT
20486 TCTTTACTCTTTATCATTT
1 TCTTTACTCTTTATC-TTT
20505 T
1 T
20506 TTCTTTACTG
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
14 13 0.32
15 1 0.02
17 1 0.02
19 24 0.59
20 2 0.05
ACGTcount: A:0.15, C:0.21, G:0.01, T:0.62
Consensus pattern (18 bp):
TCTTTACTCTTTATCTTT
Found at i:20483 original size:52 final size:55
Alignment explanation
Indices: 20427--20531 Score: 189
Period size: 52 Copynumber: 2.0 Consensus size: 55
20417 GATTACTCTT
20427 TCTTTACTCTTTACTCTTTATCA-TTTTT-TTTACTGATTACTCTTTT-CTTTAC
1 TCTTTACTCTTTACTCTTTATCATTTTTTCTTTACTGATTACTCTTTTACTTTAC
20479 TCTTTACTCTTTACTCTTTATCATTTTTTCTTTACTGATTACTCTTTTACTTT
1 TCTTTACTCTTTACTCTTTATCATTTTTTCTTTACTGATTACTCTTTTACTTT
20532 TTGGCATTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
52 23 0.46
53 5 0.10
54 18 0.36
55 4 0.08
ACGTcount: A:0.15, C:0.21, G:0.02, T:0.62
Consensus pattern (55 bp):
TCTTTACTCTTTACTCTTTATCATTTTTTCTTTACTGATTACTCTTTTACTTTAC
Found at i:20543 original size:35 final size:35
Alignment explanation
Indices: 20469--20542 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
20459 CTGATTACTC
** *
20469 TTTTCTTTACTCTTTACTCTTTACTCTTTATCATT
1 TTTTCTTTACTGATTACTCTTTACTCTTTAGCATT
* *
20504 TTTTCTTTACTGATTACTCTTTTACTTTTTGGCATT
1 TTTTCTTTACTGATTACTC-TTTACTCTTTAGCATT
20540 TTT
1 TTT
20543 CCTTATTGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
35 17 0.52
36 16 0.48
ACGTcount: A:0.14, C:0.19, G:0.04, T:0.64
Consensus pattern (35 bp):
TTTTCTTTACTGATTACTCTTTACTCTTTAGCATT
Found at i:20619 original size:22 final size:21
Alignment explanation
Indices: 20579--20941 Score: 219
Period size: 21 Copynumber: 17.1 Consensus size: 21
20569 CTTTTCTATT
20579 TTACCTTTT--TTCTTTACTGA
1 TTACCTTTTACTT-TTTACTGA
20599 TTACTCTTTTACTTTTTACTGA
1 TTAC-CTTTTACTTTTTACTGA
* *
20621 TTGCCTTTTTGCTTTTTACTGA
1 TTACC-TTTTACTTTTTACTGA
* *
20643 TTACCTTTTACTTCTTATTGA
1 TTACCTTTTACTTTTTACTGA
* * **
20664 TTAGCTTTTTACTCTTCGCTGA
1 TTA-CCTTTTACTTTTTACTGA
*
20686 TTACCTTTATAC-TCTTACTGA
1 TTACCTTT-TACTTTTTACTGA
* *
20707 TTACCTTTTACTTCTTATTGA
1 TTACCTTTTACTTTTTACTGA
* *
20728 TTACCTTTTACTTTTTGCCGA
1 TTACCTTTTACTTTTTACTGA
* *
20749 TTACTATTTTAC-TCTTACTGA
1 TTAC-CTTTTACTTTTTACTGA
** **
20770 TTACCAGTT-C-GCTTACTGA
1 TTACCTTTTACTTTTTACTGA
** *
20789 TTACCTTTTTGTTTCTTTACTAA
1 TTACC-TTTTACTT-TTTACTGA
*
20812 TTACCAGTTTT-CTCTTTACTGA
1 TTACC--TTTTACTTTTTACTGA
* *
20834 TTGCCTTTTATTCTTTTACTGA
1 TTACCTTTTACT-TTTTACTGA
*
20856 TTACC-TTTACTTCTCTTTACTAA
1 TTACCTTTTAC-T-T-TTTACTGA
*
20879 TTACC-TTTACTTCTTACTGA
1 TTACCTTTTACTTTTTACTGA
* * *
20899 CTACTATTTTAC-TCTTA-TAGA
1 TTAC-CTTTTACTTTTTACT-GA
*
20920 TTACCTTTTAC-TCTTACTGA
1 TTACCTTTTACTTTTTACTGA
20940 TT
1 TT
20942 TTACTGATTA
Statistics
Matches: 270, Mismatches: 52, Indels: 42
0.74 0.14 0.12
Matches are distributed among these distances:
19 14 0.05
20 40 0.15
21 95 0.35
22 86 0.32
23 31 0.11
24 4 0.01
ACGTcount: A:0.18, C:0.21, G:0.07, T:0.53
Consensus pattern (21 bp):
TTACCTTTTACTTTTTACTGA
Found at i:20651 original size:43 final size:43
Alignment explanation
Indices: 20591--20869 Score: 202
Period size: 43 Copynumber: 6.5 Consensus size: 43
20581 ACCTTTTTTC
* *
20591 TTTACTGATTACTCTTTTACTTTTTACTGATTGCCTTTTTGCTT
1 TTTACTGATTAC-CTTTTACTTCTTACTGATTGCCTTTTTACTT
* *
20635 TTTACTGATTACCTTTTACTTCTTATTGATTAG-CTTTTTACTC
1 TTTACTGATTACCTTTTACTTCTTACTGATT-GCCTTTTTACTT
** *
20678 TTCGCTGATTACCTTTATAC-TCTTACTGATTACC-TTTTACTT
1 TTTACTGATTACCTTT-TACTTCTTACTGATTGCCTTTTTACTT
* * * * * *
20720 CTTATTGATTACCTTTTACTTTTTGCCGATT-ACTATTTTAC-T
1 TTTACTGATTACCTTTTACTTCTTACTGATTGCCT-TTTTACTT
* ** * * **
20762 CTTACTGATTACCAGTT-C-GCTTACTGATTACCTTTTTGTTT
1 TTTACTGATTACCTTTTACTTCTTACTGATTGCCTTTTTACTT
* *
20803 CTTTACTAATTACCAGTTTT-C-TCTTTACTGATTGCC-TTTTATTCT
1 -TTTACTGATTACC--TTTTACTTC-TTACTGATTGCCTTTTTACT-T
20848 TTTACTGATTACC-TTTACTTCT
1 TTTACTGATTACCTTTTACTTCT
20870 CTTTACTAAT
Statistics
Matches: 185, Mismatches: 35, Indels: 32
0.73 0.14 0.13
Matches are distributed among these distances:
40 11 0.06
41 11 0.06
42 55 0.30
43 58 0.31
44 38 0.21
45 12 0.06
ACGTcount: A:0.18, C:0.21, G:0.08, T:0.54
Consensus pattern (43 bp):
TTTACTGATTACCTTTTACTTCTTACTGATTGCCTTTTTACTT
Found at i:20887 original size:23 final size:23
Alignment explanation
Indices: 20802--20892 Score: 91
Period size: 22 Copynumber: 4.0 Consensus size: 23
20792 CCTTTTTGTT
*
20802 TCTTTACTAATTACCAGTT-TTC
1 TCTTTACTAATTACCATTTATTC
* * *
20824 TCTTTACTGATTGCCTTTTATTC
1 TCTTTACTAATTACCATTTATTC
*
20847 T-TTTACTGATTACC-TTTACTTC
1 TCTTTACTAATTACCATTTA-TTC
20869 TCTTTACTAATTACC-TTTACTTC
1 TCTTTACTAATTACCATTTA-TTC
20892 T
1 T
20893 TACTGACTAC
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
21 4 0.07
22 31 0.52
23 25 0.42
ACGTcount: A:0.19, C:0.23, G:0.04, T:0.54
Consensus pattern (23 bp):
TCTTTACTAATTACCATTTATTC
Found at i:21041 original size:27 final size:28
Alignment explanation
Indices: 20969--21041 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 28
20959 CATTTTTTTT
*
20969 CTCTTTTTACTAATTACT-CTTTCGTCA
1 CTCTTTTTACTGATTACTGCTTTCGTCA
* *
20996 CTCTTTTTACTGAATACTGTTTTC-T-A
1 CTCTTTTTACTGATTACTGCTTTCGTCA
21022 CTCTTTTTTACTGATTACTG
1 CTC-TTTTTACTGATTACTG
21042 ATTACTAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
26 4 0.10
27 32 0.80
28 4 0.10
ACGTcount: A:0.18, C:0.22, G:0.07, T:0.53
Consensus pattern (28 bp):
CTCTTTTTACTGATTACTGCTTTCGTCA
Found at i:21435 original size:7 final size:7
Alignment explanation
Indices: 21423--21447 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
21413 GCATATGCTA
21423 AATTCCT
1 AATTCCT
21430 AATTCCT
1 AATTCCT
21437 AATTCCT
1 AATTCCT
21444 AATT
1 AATT
21448 GTCTCTAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTCCT
Found at i:24237 original size:15 final size:15
Alignment explanation
Indices: 24217--24249 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
24207 AATCATCACT
24217 AATGCAAACTAATGG
1 AATGCAAACTAATGG
*
24232 AATGCAAATTAATGG
1 AATGCAAACTAATGG
24247 AAT
1 AAT
24250 ATATGATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.24
Consensus pattern (15 bp):
AATGCAAACTAATGG
Found at i:25928 original size:228 final size:228
Alignment explanation
Indices: 25531--25991 Score: 859
Period size: 228 Copynumber: 2.0 Consensus size: 228
25521 CCAGGGCGTT
* *
25531 GCTCTCAGGCCCCAGGTCTCCTGCGCCCATGCTGGTGCTAGTGGCATGTCTCGACTAGCGTTGGC
1 GCTCTCAGGCCCCAAGTCTCCTGCGCCCATGCTGGTGCTAGTGGCATGTCTCGACTAGCGCTGGC
*
25596 CGCCCATGTGGCATGCTTGGCACCCCATGTGGAATGTCTCGCGCTCCATGTACTTCAATGCTATG
66 CGCCCATGTGGCATGCTTGGCACCCCATGTGGAATGCCTCGCGCTCCATGTACTTCAATGCTATG
*
25661 ACTCCTCTTGACATATCTCCTTGCCTTGAAATTCAACTTTGCTCCTTTACTTCAAACTCTTGAAA
131 ACGCCTCTTGACATATCTCCTTGCCTTGAAATTCAACTTTGCTCCTTTACTTCAAACTCTTGAAA
25726 ATCAATCTTATGATGATAAAATTGACTCTTCAA
196 ATCAATCTTATGATGATAAAATTGACTCTTCAA
25759 GCTCTCAGGCCCCAAGTCTCCTGCGCCCATGCTGGTGCTAGTGGCATGTCTCGACTAGCGCTGGC
1 GCTCTCAGGCCCCAAGTCTCCTGCGCCCATGCTGGTGCTAGTGGCATGTCTCGACTAGCGCTGGC
* *
25824 CGCCCATGTGGCATGCTTGGCACCCCATGTGGTATGCCTCGCGCTCCATGTACTTCAGTGCTATG
66 CGCCCATGTGGCATGCTTGGCACCCCATGTGGAATGCCTCGCGCTCCATGTACTTCAATGCTATG
*
25889 ACGCCTCTTGACATATCTCCTTGCCTTGAAATTCAACTTTGCTCCTTTGCTTCAAACTCTTGAAA
131 ACGCCTCTTGACATATCTCCTTGCCTTGAAATTCAACTTTGCTCCTTTACTTCAAACTCTTGAAA
25954 ATCAATCTTATGATGATAAAATTGACTCTTCAA
196 ATCAATCTTATGATGATAAAATTGACTCTTCAA
25987 GCTCT
1 GCTCT
25992 TCAATCACGA
Statistics
Matches: 226, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
228 226 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.31
Consensus pattern (228 bp):
GCTCTCAGGCCCCAAGTCTCCTGCGCCCATGCTGGTGCTAGTGGCATGTCTCGACTAGCGCTGGC
CGCCCATGTGGCATGCTTGGCACCCCATGTGGAATGCCTCGCGCTCCATGTACTTCAATGCTATG
ACGCCTCTTGACATATCTCCTTGCCTTGAAATTCAACTTTGCTCCTTTACTTCAAACTCTTGAAA
ATCAATCTTATGATGATAAAATTGACTCTTCAA
Found at i:27128 original size:15 final size:15
Alignment explanation
Indices: 27108--27137 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
27098 ATTGACTTTA
27108 GTAATTTAAACAATG
1 GTAATTTAAACAATG
27123 GTAATTTAAACAATG
1 GTAATTTAAACAATG
27138 CTTCACCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (15 bp):
GTAATTTAAACAATG
Found at i:29181 original size:16 final size:16
Alignment explanation
Indices: 29160--29230 Score: 81
Period size: 16 Copynumber: 4.4 Consensus size: 16
29150 TCATCTGAGT
*
29160 TCGGGTTATTCGGGTC
1 TCGGGTCATTCGGGTC
* *
29176 TCGGGTCATACGGGTT
1 TCGGGTCATTCGGGTC
**
29192 TTAGGTCATTCGGGT-
1 TCGGGTCATTCGGGTC
29207 TCTGGGTCATTCGGGTC
1 TC-GGGTCATTCGGGTC
29224 TCGGGTC
1 TCGGGTC
29231 TACCGGGTCT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
15 1 0.02
16 42 0.93
17 2 0.04
ACGTcount: A:0.08, C:0.20, G:0.37, T:0.35
Consensus pattern (16 bp):
TCGGGTCATTCGGGTC
Found at i:29518 original size:42 final size:42
Alignment explanation
Indices: 29471--29552 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
29461 TAGATTTTAA
*
29471 TTTTGAATATTAAATACATAATTGATTATCAGGTGAGGTAGG
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
*
29513 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTA
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTA
29553 TGTGTCAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
Found at i:30107 original size:16 final size:16
Alignment explanation
Indices: 30086--30185 Score: 89
Period size: 16 Copynumber: 6.2 Consensus size: 16
30076 TGGGTTATTT
*
30086 GGGTCATACGGGTCTC
1 GGGTCATTCGGGTCTC
*
30102 GGGTCACTCGGGT-TAC
1 GGGTCATTCGGGTCT-C
* *
30118 GGTTCATTCGGGTTTC
1 GGGTCATTCGGGTCTC
*
30134 GGGTTATTCGGGTCTC
1 GGGTCATTCGGGTCTC
*
30150 GAGTCA-TCTGGGT-TGC
1 GGGTCATTC-GGGTCT-C
*
30166 AGGTCATTCGGGTCTC
1 GGGTCATTCGGGTCTC
30182 GGGT
1 GGGT
30186 TGGGCGGGTT
Statistics
Matches: 66, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
15 4 0.06
16 58 0.88
17 4 0.06
ACGTcount: A:0.10, C:0.21, G:0.37, T:0.32
Consensus pattern (16 bp):
GGGTCATTCGGGTCTC
Found at i:30194 original size:48 final size:49
Alignment explanation
Indices: 30094--30203 Score: 129
Period size: 48 Copynumber: 2.3 Consensus size: 49
30084 TTGGGTCATA
* **
30094 CGGGTCTCGGGTCA-CTCGGGTTACGGTTCATTCGGGTTTCGGGTTATT
1 CGGGTCTCGGGTCATCTCGGGTTACGGTTCATTCGGGTCTCGGGTTAGG
* * *
30142 CGGGTCTCGAGTCATCT-GGGTTGCAGG-TCATTCGGGTCTCGGGTTGGG
1 CGGGTCTCGGGTCATCTCGGGTTAC-GGTTCATTCGGGTCTCGGGTTAGG
30190 CGGGT-TCGGGTCAT
1 CGGGTCTCGGGTCAT
30204 TTACTTTATC
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
47 8 0.15
48 41 0.77
49 4 0.08
ACGTcount: A:0.08, C:0.21, G:0.39, T:0.32
Consensus pattern (49 bp):
CGGGTCTCGGGTCATCTCGGGTTACGGTTCATTCGGGTCTCGGGTTAGG
Found at i:35244 original size:3 final size:3
Alignment explanation
Indices: 35236--35293 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
35226 TACATTCTAT
35236 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
35284 TTA TTA TTA T
1 TTA TTA TTA T
35294 ATAATGAATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39450 original size:24 final size:24
Alignment explanation
Indices: 39423--39469 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
39413 CAACTTGACA
*
39423 TTCCGCCAGTAGAATCTGACGATG
1 TTCCGCCAGTAGAATCAGACGATG
*
39447 TTCCGCCTGTAGAATCAGACGAT
1 TTCCGCCAGTAGAATCAGACGAT
39470 ATTTGGGCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (24 bp):
TTCCGCCAGTAGAATCAGACGATG
Found at i:45113 original size:35 final size:35
Alignment explanation
Indices: 45067--45145 Score: 122
Period size: 35 Copynumber: 2.3 Consensus size: 35
45057 CCTTTCTCTC
*
45067 TTTCCGTGATTTAAGCCTCTAAAACTCTCATCTAG
1 TTTCCGCGATTTAAGCCTCTAAAACTCTCATCTAG
* *
45102 TTTCCGCGATTTAAGCCTCTAAATCTCTCATCTGG
1 TTTCCGCGATTTAAGCCTCTAAAACTCTCATCTAG
*
45137 TTTCTGCGA
1 TTTCCGCGA
45146 AAATCTCTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.38
Consensus pattern (35 bp):
TTTCCGCGATTTAAGCCTCTAAAACTCTCATCTAG
Found at i:45432 original size:145 final size:145
Alignment explanation
Indices: 45221--45512 Score: 557
Period size: 145 Copynumber: 2.0 Consensus size: 145
45211 TGTGGCTCAA
45221 AACTCACCGTTTGGTTTTTGAAGAAAACCTGGACCTTTTCATTATTTTTTTCACACTTGGGCCTA
1 AACTCACCGTTTGGTTTTTGAAGAAAACCTGGACCTTTTCATTATTTTTTTCACACTTGGGCCTA
* *
45286 GACCTTTGGGCTTTGATCATATGATGATGATTTGCATTTATAATTTTCAATTAGTATTTTCTTTA
66 GACCTTTGGACTTTGATCATATGATGATGATTTGCATTTATAATTTTCAATTAATATTTTCTTTA
45351 AAGTGAGTTAGCAAT
131 AAGTGAGTTAGCAAT
*
45366 AACTCACCGTTTGGTTTTTGAAGAAAACCTGGACCTTTTCATTATTTTTTTCACACTTGGGTCTA
1 AACTCACCGTTTGGTTTTTGAAGAAAACCTGGACCTTTTCATTATTTTTTTCACACTTGGGCCTA
45431 GACCTTTGGACTTTGATCATATGATGATGATTTGCATTTATAATTTTCAATTAATATTTTCTTTA
66 GACCTTTGGACTTTGATCATATGATGATGATTTGCATTTATAATTTTCAATTAATATTTTCTTTA
45496 AAGTGAGTTAGCAAT
131 AAGTGAGTTAGCAAT
45511 AA
1 AA
45513 ATTAAATTAA
Statistics
Matches: 144, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
145 144 1.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.43
Consensus pattern (145 bp):
AACTCACCGTTTGGTTTTTGAAGAAAACCTGGACCTTTTCATTATTTTTTTCACACTTGGGCCTA
GACCTTTGGACTTTGATCATATGATGATGATTTGCATTTATAATTTTCAATTAATATTTTCTTTA
AAGTGAGTTAGCAAT
Found at i:45610 original size:90 final size:90
Alignment explanation
Indices: 45457--45633 Score: 336
Period size: 90 Copynumber: 2.0 Consensus size: 90
45447 TCATATGATG
45457 ATGATTTGCATTTATAATTTTCAATTAATATTTTCTTTAAAGTGAGTTAGCAATAAATTAAATTA
1 ATGATTTGCATTTATAATTTTCAATTAATATTTTCTTTAAAGTGAGTTAGCAATAAATTAAATTA
45522 ACATACAAAATTTAATGCGAATCAT
66 ACATACAAAATTTAATGCGAATCAT
*
45547 ATGATTTGCATTTATAATTTTCAATTAGTATTTTCTTTAAAGTGAGTTAGCAATAAATTAAATTA
1 ATGATTTGCATTTATAATTTTCAATTAATATTTTCTTTAAAGTGAGTTAGCAATAAATTAAATTA
*
45612 ACATACAAAATTTAATGTGAAT
66 ACATACAAAATTTAATGCGAAT
45634 GAAATTATAT
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 85 1.00
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.42
Consensus pattern (90 bp):
ATGATTTGCATTTATAATTTTCAATTAATATTTTCTTTAAAGTGAGTTAGCAATAAATTAAATTA
ACATACAAAATTTAATGCGAATCAT
Found at i:46798 original size:164 final size:165
Alignment explanation
Indices: 46602--46922 Score: 495
Period size: 166 Copynumber: 2.0 Consensus size: 165
46592 GCAATTATAA
*
46602 AGAGTTTATAATTTTTTTAAATAAACGAAAAATTGAAAAAAG-AAAAAAATAGTAGAGAAAAATA
1 AGAGTTTATAATTTTTATAAATAAACGAAAAATTGAAAAAAGAAAAAAAATAGTAGAGAAAAATA
* * * ** **
46666 GTTAAC-GATTAGTAGAGTACTCTGACAAAAAAAAA-AAAGAGAGAAAGATTGGTGGAGTAGAAT
66 GTCAACGGATTAGTAGAGCACTCTGACAAAAAAAAAGAAA-AAAGAAAGATTAATACAGTAGAAT
46729 TTCTCTAAAAAAATAAATACATTAAAAAATTGATAGT
130 TTCTCT-AAAAAATAAATACATTAAAAAATTGATAGT
* * *
46766 AGAGTTTATGATTTTTATAAATAAATGAAAAATTGAAAAAAGAAAAAAAATAGTAGAGAAAAATT
1 AGAGTTTATAATTTTTATAAATAAACGAAAAATTGAAAAAAGAAAAAAAATAGTAGAGAAAAATA
*
46831 GTCAACGGATTAGTAGAGCACTCTGGCAAAAAAAAAGAAAAAAGAAAGATTAATACAGTAGAATT
66 GTCAACGGATTAGTAGAGCACTCTGACAAAAAAAAAGAAAAAAGAAAGATTAATACAGTAGAATT
46896 TCTCTAAAAAATAAATACATTAAAAAA
131 TCTCTAAAAAATAAATACATTAAAAAA
46923 ATTTATTTTT
Statistics
Matches: 142, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
164 39 0.27
165 48 0.34
166 52 0.37
167 3 0.02
ACGTcount: A:0.55, C:0.06, G:0.15, T:0.25
Consensus pattern (165 bp):
AGAGTTTATAATTTTTATAAATAAACGAAAAATTGAAAAAAGAAAAAAAATAGTAGAGAAAAATA
GTCAACGGATTAGTAGAGCACTCTGACAAAAAAAAAGAAAAAAGAAAGATTAATACAGTAGAATT
TCTCTAAAAAATAAATACATTAAAAAATTGATAGT
Found at i:47223 original size:31 final size:31
Alignment explanation
Indices: 47185--47246 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
47175 TATGTTAGAC
*
47185 AAATAAGGATATAATAGACGTTTCAAAAGTT
1 AAATAAGGATACAATAGACGTTTCAAAAGTT
* *
47216 AAATAAGGGTACAATAGGCGTTTCAAAAGTT
1 AAATAAGGATACAATAGACGTTTCAAAAGTT
47247 TTACAAAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.08, G:0.19, T:0.27
Consensus pattern (31 bp):
AAATAAGGATACAATAGACGTTTCAAAAGTT
Found at i:54006 original size:32 final size:31
Alignment explanation
Indices: 53938--54015 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 31
53928 TTTATGGTTG
* * *
53938 AAAATGCCGTTAAATAGGGACATTTTTTAAA
1 AAAACGCCGCTAAATAGGGACATTTGTTAAA
*
53969 GAAACGCCGCTAAATAGTGG-CACTTTGTTAAA
1 AAAACGCCGCTAAATAG-GGACA-TTTGTTAAA
*
54001 AAAACGCCACTAAAT
1 AAAACGCCGCTAAAT
54016 TGTGACGTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
31 16 0.41
32 23 0.59
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.26
Consensus pattern (31 bp):
AAAACGCCGCTAAATAGGGACATTTGTTAAA
Found at i:54482 original size:2 final size:2
Alignment explanation
Indices: 54475--54506 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
54465 TTATTACTAG
54475 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
54507 ATACATACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:64993 original size:12 final size:12
Alignment explanation
Indices: 64959--64995 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
64949 TGAATGATGA
**
64959 TGAGAACAATAA
1 TGAGAACAATGG
64971 TGAGAACAATGG
1 TGAGAACAATGG
64983 TGAGAACAATGG
1 TGAGAACAATGG
64995 T
1 T
64996 AACAATAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.46, C:0.08, G:0.27, T:0.19
Consensus pattern (12 bp):
TGAGAACAATGG
Found at i:72375 original size:2 final size:2
Alignment explanation
Indices: 72331--72361 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
72321 GAATGGAATA
72331 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
72362 TGATTTCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Done.