Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009098.1 Corchorus capsularis cultivar CVL-1 contig09119, 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: 45216
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:435 original size:16 final size:16
Alignment explanation
Indices: 414--447 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
404 AAGCATAAGC
414 TTATGGTTCTCATTGA
1 TTATGGTTCTCATTGA
430 TTATGGTTCTCATTGA
1 TTATGGTTCTCATTGA
446 TT
1 TT
448 CTGTATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.53
Consensus pattern (16 bp):
TTATGGTTCTCATTGA
Found at i:10800 original size:21 final size:21
Alignment explanation
Indices: 10776--10816 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
10766 AAAAAGCAAT
* *
10776 TAAATAAAAGTAAAGTAAAAC
1 TAAATAAAACTAAACTAAAAC
*
10797 TAAATTAAACTAAACTAAAA
1 TAAATAAAACTAAACTAAAA
10817 GGGTGATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.22
Consensus pattern (21 bp):
TAAATAAAACTAAACTAAAAC
Found at i:12931 original size:16 final size:16
Alignment explanation
Indices: 12910--12943 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
12900 GGACTTCAAT
*
12910 GCAGTAAAGAGCATGA
1 GCAGTAAAGAGCACGA
12926 GCAGTAAAGAGCACGA
1 GCAGTAAAGAGCACGA
12942 GC
1 GC
12944 CTGGTATGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.32, T:0.09
Consensus pattern (16 bp):
GCAGTAAAGAGCACGA
Found at i:14393 original size:48 final size:48
Alignment explanation
Indices: 14322--15385 Score: 643
Period size: 48 Copynumber: 22.2 Consensus size: 48
14312 AATTACCTTG
* * *
14322 GCCGAGAATGTTGGTGTTCGGCCTTATTGCCCGACACGAGGACTTACT
1 GCCGAGAATGATGGCGTTCGGCCTTATTGCCCGACACGGGGACTTACT
* *
14370 GCCGA-AGATGATGGCGTTCGGCCTTATTGCCCGACATGGGGACTTATT
1 GCCGAGA-ATGATGGCGTTCGGCCTTATTGCCCGACACGGGGACTTACT
* * * *
14418 GCCGA-AGATGTTGGCGTTCGGCCTCATTGCCCGACACGGGTAGTTACT
1 GCCGAGA-ATGATGGCGTTCGGCCTTATTGCCCGACACGGGGACTTACT
* * * * * * *
14466 GCCGA-AATTGATGGTGATCGGCTTTATTGCTCGACATGAGGACTTATT
1 GCCGAGAA-TGATGGCGTTCGGCCTTATTGCCCGACACGGGGACTTACT
* ** * * * *
14514 GCCGAGAATGATGTCACTCGGCCTTATTGCCCAACACGTGGATTTATT
1 GCCGAGAATGATGGCGTTCGGCCTTATTGCCCGACACGGGGACTTACT
* * * ** *** *
14562 GCTGAGAATACAGGGCACTCGGCCTTATTGCCCGACATAAAGGACTTATT
1 GCCGAGAAT-GATGGCGTTCGGCCTTATTGCCCGACA-CGGGGACTTACT
* *
14612 GCCGAGAATAACAT-GCGCTCGGCCTTATTGCCCGACACGGGGACTTACT
1 GCCGAGAAT--GATGGCGTTCGGCCTTATTGCCCGACACGGGGACTTACT
* * * * * *
14661 GCCGA-AGATGATGGTGATAGGCC-T-TT-CCTGACACGAGGACTTATT
1 GCCGAGA-ATGATGGCGTTCGGCCTTATTGCCCGACACGGGGACTTACT
* * ** * *
14706 GCTGAGAATGATGTCACTCGGCCTTATTGCCCAACACGGGTACTTACT
1 GCCGAGAATGATGGCGTTCGGCCTTATTGCCCGACACGGGGACTTACT
* * ** * * *
14754 GCCGAGAATAATGGGCGTTTGGTTTTATTGCCCAACACAGGGGATTTATT
1 GCCGAGAATGAT-GGCGTTCGGCCTTATTGCCCGACAC-GGGGACTTACT
* * * * * *
14804 GCTGAGAATAACGTGCGTTCGACTTTATTGCCCGACACGGGGACTTATT
1 GCCGAGAATGATG-GCGTTCGGCCTTATTGCCCGACACGGGGACTTACT
** * * *
14853 GCCGAGAATGATTTCATTCGGCCTTATTACCCCGACTA-GAGGACTTACT
1 GCCGAGAATGATGGCGTTCGGCCTTATT-GCCCGAC-ACGGGGACTTACT
* * *
14902 GCAGAGAATGA------T-AG--TTA---CCCAACCA-GGGGACTTACT
1 GCCGAGAATGATGGCGTTCGGCCTTATTGCCCGA-CACGGGGACTTACT
* ** * *
14938 GCCGAGAATGATGTCACTCGGCCTTATTGCCCAAGACGGGGACTTACT
1 GCCGAGAATGATGGCGTTCGGCCTTATTGCCCGACACGGGGACTTACT
* * * * *
14986 ACCGATAATAAAGGGCGCTT-GACCTTATTGCCCGACACGGGGACTTACT
1 GCCGAGAAT-GATGGCG-TTCGGCCTTATTGCCCGACACGGGGACTTACT
* * * * *
15035 CCCGAGAATGATGTCATTCGGCCTTATTGCCCGAGACGGGGACTTACA
1 GCCGAGAATGATGGCGTTCGGCCTTATTGCCCGACACGGGGACTTACT
* * * * * *
15083 ACCGAGAATGATGTCATTCGGCTTTATTGCCTGACTA-GGGGAGTTACT
1 GCCGAGAATGATGGCGTTCGGCCTTATTGCCCGAC-ACGGGGACTTACT
* * *
15131 GTCGATAATGATGGCGCTCGGCCTTATTGCCCGACACGGGGACTTACT
1 GCCGAGAATGATGGCGTTCGGCCTTATTGCCCGACACGGGGACTTACT
* * * ** *
15179 GCCGA-AAGTTATGGCGCTCGACCTTATTGCTTGAC-CAGGGGACTTATT
1 GCCGAGAA-TGATGGCGTTCGGCCTTATTGCCCGACAC-GGGGACTTACT
* * * * ** ** * *
15227 GCCAAGGATGAAGGCGTTCGTCGGTCTTACGGCCCGTTATGGGGACCTAC-
1 GCCGAGAATGATGGCG-T--TCGGCCTTATTGCCCGACACGGGGACTTACT
* ** * **
15277 GACCGAGAATGATGACCCTCGACCTTATTGCCTAACACGGGGACTTACT
1 G-CCGAGAATGATGGCGTTCGGCCTTATTGCCCGACACGGGGACTTACT
* * * * * * *
15326 GCCAAGAATGATGTCGATCGGCCTTACTGTCCAACAAGGGGACTTACT
1 GCCGAGAATGATGGCGTTCGGCCTTATTGCCCGACACGGGGACTTACT
*
15374 GCCGAGAGTGAT
1 GCCGAGAATGAT
15386 CCCAAGGGAG
Statistics
Matches: 786, Mismatches: 185, Indels: 90
0.74 0.17 0.08
Matches are distributed among these distances:
36 25 0.03
37 1 0.00
40 3 0.00
42 2 0.00
43 2 0.00
45 34 0.04
46 4 0.01
47 14 0.02
48 448 0.57
49 143 0.18
50 79 0.10
51 31 0.04
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (48 bp):
GCCGAGAATGATGGCGTTCGGCCTTATTGCCCGACACGGGGACTTACT
Found at i:15338 original size:195 final size:193
Alignment explanation
Indices: 14926--15378 Score: 473
Period size: 195 Copynumber: 2.3 Consensus size: 193
14916 TTACCCAACC
* * *
14926 AGGGGACTTACTGCCGAGAATGATGTCACTCGGCCTTATTGCCCAAGACGGGGACTTACTACCGA
1 AGGGGACTTACTGCCGAGAATGATGTCGCTCGGCCTTATTGCCCAACACGGGGACTTACTGCCGA
* * * *
14991 TAATAAAGGGCGCTTGACCTTATTGCCCGACACGGGGACTTACTCCCGAGAATGATGTCATTCGG
66 TAATAAAGGGCGCTCGACCTTATTGCCCGACACGGGGACTTACTCCCAAGAATGAAGGCATTCGG
** * * * * * *
15056 CCTTATTGCCCGAGACGGGGACTTACAACCGAGAATGATGTCATTCGGCTTTATTGCCTGACT
131 CCTTACGGCCCGAGACGGGGACCTACAACCGAGAATGATGACACTCGACCTTATTGCCTAACT
* * * * *
15119 AGGGGAGTTACTGTCGATAATGATGGCGCTCGGCCTTATTGCCCGACACGGGGACTTACTGCCGA
1 AGGGGACTTACTGCCGAGAATGATGTCGCTCGGCCTTATTGCCCAACACGGGGACTTACTGCCGA
* * ** * * * *
15184 -AAGT-TATGGCGCTCGACCTTATTGCTTGAC-CAGGGGACTTATTGCCAAGGATGAAGGCGTTC
66 TAA-TAAAGGGCGCTCGACCTTATTGCCCGACAC-GGGGACTTACTCCCAAGAATGAAGGC-AT-
* ** * * *
15246 GTCGGTCTTACGGCCCGTTATGGGGACCTACGACCGAGAATGATGACCCTCGACCTTATTGCCTA
127 -TCGGCCTTACGGCCCGAGACGGGGACCTACAACCGAGAATGATGACACTCGACCTTATTGCCTA
15311 AC-
191 ACT
* * * * *
15313 ACGGGGACTTACTGCCAAGAATGATGTCGATCGGCCTTACTGTCCAACAAGGGGACTTACTGCCG
1 A-GGGGACTTACTGCCGAGAATGATGTCGCTCGGCCTTATTGCCCAACACGGGGACTTACTGCCG
15378 A
65 A
15379 GAGTGATCCC
Statistics
Matches: 210, Mismatches: 44, Indels: 10
0.80 0.17 0.04
Matches are distributed among these distances:
191 1 0.00
192 43 0.20
193 59 0.28
194 1 0.00
195 106 0.50
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.24
Consensus pattern (193 bp):
AGGGGACTTACTGCCGAGAATGATGTCGCTCGGCCTTATTGCCCAACACGGGGACTTACTGCCGA
TAATAAAGGGCGCTCGACCTTATTGCCCGACACGGGGACTTACTCCCAAGAATGAAGGCATTCGG
CCTTACGGCCCGAGACGGGGACCTACAACCGAGAATGATGACACTCGACCTTATTGCCTAACT
Found at i:18326 original size:2 final size:2
Alignment explanation
Indices: 18319--18346 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18309 CAAACATAGC
18319 AT 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
18347 TAAACCTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18562 original size:21 final size:21
Alignment explanation
Indices: 18519--18562 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
18509 TATATAGGGG
*
18519 TTGCTAAATACCGTCTTAGTT
1 TTGCTAAATACCGTCCTAGTT
*
18540 TTGCTAAATACCGTCCTATTT
1 TTGCTAAATACCGTCCTAGTT
18561 TT
1 TT
18563 TATACTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.45
Consensus pattern (21 bp):
TTGCTAAATACCGTCCTAGTT
Found at i:18595 original size:31 final size:31
Alignment explanation
Indices: 18557--18635 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
18547 ATACCGTCCT
* * *
18557 ATTTTTTATACTTTTGCCCTTTACCCTTTGC
1 ATTTTTTACACTTTTACCATTTACCCTTTGC
18588 ATTTTTTACACTTTTACCATTTACCCTTTGC
1 ATTTTTTACACTTTTACCATTTACCCTTTGC
18619 ATTTTTTACACTTTTAC
1 ATTTTTTACACTTTTAC
18636 ACTGAGTCTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.18, C:0.24, G:0.04, T:0.54
Consensus pattern (31 bp):
ATTTTTTACACTTTTACCATTTACCCTTTGC
Found at i:18601 original size:16 final size:16
Alignment explanation
Indices: 18576--18632 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
18566 ACTTTTGCCC
*
18576 TTTACCCTTTGCATTT
1 TTTACACTTTGCATTT
* ***
18592 TTTACACTTT-TACCA
1 TTTACACTTTGCATTT
*
18607 TTTACCCTTTGCATTT
1 TTTACACTTTGCATTT
18623 TTTACACTTT
1 TTTACACTTT
18633 TACACTGAGT
Statistics
Matches: 29, Mismatches: 11, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
15 10 0.34
16 19 0.66
ACGTcount: A:0.18, C:0.25, G:0.04, T:0.54
Consensus pattern (16 bp):
TTTACACTTTGCATTT
Found at i:20639 original size:22 final size:22
Alignment explanation
Indices: 20528--20713 Score: 137
Period size: 22 Copynumber: 8.6 Consensus size: 22
20518 CTCCAACGTA
* *
20528 GAAATATTGATAACCTCATTAT
1 GAAATTTTGATAACCTCACTAT
* * * *
20550 GAAACTTCGATAGCCTCTCTAT
1 GAAATTTTGATAACCTCACTAT
* *
20572 GAAA-TTTGATAACCACACTGT
1 GAAATTTTGATAACCTCACTAT
* ***
20593 GAAATTTTGACAACGAAACTAT
1 GAAATTTTGATAACCTCACTAT
* *
20615 GAAATTTTGATAACCTCAGTGT
1 GAAATTTTGATAACCTCACTAT
* *
20637 GAAATTTTGATAATCTCCCTAT
1 GAAATTTTGATAACCTCACTAT
* * *
20659 -AAA-ATTGGTAACCT-ATTAT
1 GAAATTTTGATAACCTCACTAT
* * *
20678 GAAAATTTTGATAATCACACCAT
1 G-AAATTTTGATAACCTCACTAT
20701 GAAATTTTGATAA
1 GAAATTTTGATAA
20714 TGTACCTCCT
Statistics
Matches: 123, Mismatches: 36, Indels: 10
0.73 0.21 0.06
Matches are distributed among these distances:
19 3 0.02
20 8 0.07
21 22 0.18
22 86 0.70
23 4 0.03
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (22 bp):
GAAATTTTGATAACCTCACTAT
Found at i:20787 original size:22 final size:22
Alignment explanation
Indices: 20755--20970 Score: 87
Period size: 22 Copynumber: 9.3 Consensus size: 22
20745 GACTCTATAT
*
20755 AATTCTGATAACCTCTCCATAA
1 AATTTTGATAACCTCTCCATAA
* *
20777 AATTTTCATAACCTC-CCTATGA
1 AATTTTGATAACCTCTCC-ATAA
* * * *
20799 AATTTTGTTAATCTCTCTAGAAA
1 AATTTTGATAACCTCTCCA-TAA
20822 AATTTTGATAACCTCCCTCCCTATATTGA
1 AATTTTGATAACCT--CT-CC-ATA---A
* * *
20851 AATTTTGTTAATAACCACACTATAA
1 AATTTTG---ATAACCTCTCCATAA
* * ** *
20876 AATTTCGATAACCTTTGTATGA
1 AATTTTGATAACCTCTCCATAA
* * *
20898 AATTTTGTTAACCCCTCTA-AGA
1 AATTTTGATAACCTCTCCATA-A
* *
20920 AATTTTGATAACCTCTTTCATGA
1 AATTTTGATAACCTC-TCCATAA
*
20943 AATTTTGATAACCTC-CCTATAT
1 AATTTTGATAACCTCTCC-ATAA
20965 AATTTT
1 AATTTT
20971 CCTTTGATTG
Statistics
Matches: 141, Mismatches: 36, Indels: 34
0.67 0.17 0.16
Matches are distributed among these distances:
21 3 0.02
22 75 0.53
23 32 0.23
25 9 0.06
26 2 0.01
27 1 0.01
28 3 0.02
29 9 0.06
30 1 0.01
32 6 0.04
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.39
Consensus pattern (22 bp):
AATTTTGATAACCTCTCCATAA
Found at i:20945 original size:23 final size:22
Alignment explanation
Indices: 20875--20957 Score: 96
Period size: 22 Copynumber: 3.7 Consensus size: 22
20865 CCACACTATA
*
20875 AAATTTCGATAACCT-TTGTATG
1 AAATTTTGATAACCTCTT-TATG
* * * *
20897 AAATTTTGTTAACCCCTCTAAG
1 AAATTTTGATAACCTCTTTATG
20919 AAATTTTGATAACCTCTTTCATG
1 AAATTTTGATAACCTCTTT-ATG
20942 AAATTTTGATAACCTC
1 AAATTTTGATAACCTC
20958 CCTATATAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
22 31 0.62
23 19 0.38
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACCTCTTTATG
Found at i:20969 original size:45 final size:43
Alignment explanation
Indices: 20861--20970 Score: 116
Period size: 45 Copynumber: 2.5 Consensus size: 43
20851 AATTTTGTTA
* *
20861 ATAACCACACTATAAAATTTCGATAACCTTTGTATGAAATTTTG
1 ATAACC-CCCTATAAAATTTTGATAACCTTTGTATGAAATTTTG
*
20905 TTAACCCCTCTA-AGAAATTTTGATAACCTCTT-TCATGAAATTTTG
1 ATAACCCC-CTATA-AAATTTTGATAACCT-TTGT-ATGAAATTTTG
*
20950 ATAACCTCCCTATATAATTTT
1 ATAACC-CCCTATAAAATTTT
20971 CCTTTGATTG
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
43 2 0.04
44 23 0.42
45 27 0.49
46 3 0.05
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (43 bp):
ATAACCCCCTATAAAATTTTGATAACCTTTGTATGAAATTTTG
Found at i:24460 original size:2 final size:2
Alignment explanation
Indices: 24453--24495 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
24443 TTAAGCCGTT
*
24453 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA 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 TA
24495 T
1 T
24496 CTTTTTGGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:27385 original size:17 final size:17
Alignment explanation
Indices: 27360--27398 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
27350 GTAGATGCAG
*
27360 CCTATCATCTCATACTA
1 CCTAGCATCTCATACTA
27377 CCTAGCATCTCATACTA
1 CCTAGCATCTCATACTA
27394 CCTAG
1 CCTAG
27399 GTACTATGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.36, G:0.05, T:0.31
Consensus pattern (17 bp):
CCTAGCATCTCATACTA
Found at i:28557 original size:19 final size:19
Alignment explanation
Indices: 28533--28569 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
28523 AGACGCATTC
28533 ATAACTTTGTTCTGTATAT
1 ATAACTTTGTTCTGTATAT
28552 ATAACTTTGTTCTGTATA
1 ATAACTTTGTTCTGTATA
28570 ATATGCACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (19 bp):
ATAACTTTGTTCTGTATAT
Found at i:35350 original size:2 final size:2
Alignment explanation
Indices: 35343--35371 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35333 CTTCCCCAAC
35343 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35372 CATTAATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39603 original size:127 final size:127
Alignment explanation
Indices: 39377--39633 Score: 505
Period size: 127 Copynumber: 2.0 Consensus size: 127
39367 GTATTGGTAA
*
39377 CATCATGCTATTTCTTCATACATGCGCGTAATCTAGTCATGAGACTGATCAAGATAGTTTTTAGG
1 CATCATGCTATTTCTTCATACATGCGCGTAATCTAGTCATGAGACTGATCAAGACAGTTTTTAGG
39442 TTAATTAGCCATTTGGTTTTGACTTTAAGTAATACCAGTGAATCAAAATTAGATATCTACAC
66 TTAATTAGCCATTTGGTTTTGACTTTAAGTAATACCAGTGAATCAAAATTAGATATCTACAC
39504 CATCATGCTATTTCTTCATACATGCGCGTAATCTAGTCATGAGACTGATCAAGACAGTTTTTAGG
1 CATCATGCTATTTCTTCATACATGCGCGTAATCTAGTCATGAGACTGATCAAGACAGTTTTTAGG
39569 TTAATTAGCCATTTGGTTTTGACTTTAAGTAATACCAGTGAATCAAAATTAGATATCTACAC
66 TTAATTAGCCATTTGGTTTTGACTTTAAGTAATACCAGTGAATCAAAATTAGATATCTACAC
39631 CAT
1 CAT
39634 AGAAACATTC
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 129 1.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Consensus pattern (127 bp):
CATCATGCTATTTCTTCATACATGCGCGTAATCTAGTCATGAGACTGATCAAGACAGTTTTTAGG
TTAATTAGCCATTTGGTTTTGACTTTAAGTAATACCAGTGAATCAAAATTAGATATCTACAC
Found at i:43070 original size:10 final size:10
Alignment explanation
Indices: 43055--43103 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
43045 AACCGACTAA
43055 TCGGTTTTGG
1 TCGGTTTTGG
*
43065 TCGGTTTGCGG
1 TCGGTTT-TGG
*
43076 TCGGTTTCGG
1 TCGGTTTTGG
*
43086 TCGGTTTT-A
1 TCGGTTTTGG
43095 TCGGTTTTG
1 TCGGTTTTG
43104 ATTTATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.24
10 17 0.50
11 9 0.26
ACGTcount: A:0.02, C:0.14, G:0.37, T:0.47
Consensus pattern (10 bp):
TCGGTTTTGG
Found at i:43079 original size:11 final size:10
Alignment explanation
Indices: 43055--43092 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
43045 AACCGACTAA
*
43055 TCGGTTTTGG
1 TCGGTTTCGG
43065 TCGGTTTGCGG
1 TCGGTTT-CGG
43076 TCGGTTTCGG
1 TCGGTTTCGG
43086 TCGGTTT
1 TCGGTTT
43093 TATCGGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.00, C:0.16, G:0.39, T:0.45
Consensus pattern (10 bp):
TCGGTTTCGG
Found at i:43722 original size:6 final size:6
Alignment explanation
Indices: 43711--43743 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
43701 GTCATTATAA
43711 TATCTT TATCTT TATCTT TATCTT TATCTT TAT
1 TATCTT TATCTT TATCTT TATCTT TATCTT TAT
43744 ATTATATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (6 bp):
TATCTT
Found at i:44652 original size:6 final size:6
Alignment explanation
Indices: 44641--44668 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
44631 CGGATATTTA
44641 CAATAC CAATAC CAATAC CAATAC CAAT
1 CAATAC CAATAC CAATAC CAATAC CAAT
44669 TTTATCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (6 bp):
CAATAC
Found at i:45117 original size:20 final size:19
Alignment explanation
Indices: 45070--45118 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
45060 TACTAAAATG
* *
45070 TTACTTCTTTATAGCATTA
1 TTACTTTTTTATACCATTA
*
45089 TTATGTTTTTTATAACCATTA
1 TTA-CTTTTTTAT-ACCATTA
45110 TTACTTTTT
1 TTACTTTTT
45119 CAGTAACCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.12
20 12 0.50
21 9 0.38
ACGTcount: A:0.24, C:0.12, G:0.04, T:0.59
Consensus pattern (19 bp):
TTACTTTTTTATACCATTA
Found at i:45125 original size:21 final size:21
Alignment explanation
Indices: 45084--45126 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
45074 TTCTTTATAG
* *
45084 CATTATTATGTTTTTTATAAC
1 CATTATTATCTTTTTCATAAC
45105 CATTATTA-CTTTTTCAGTAAC
1 CATTATTATCTTTTTCA-TAAC
45126 C
1 C
45127 TTAGATAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.28, C:0.16, G:0.05, T:0.51
Consensus pattern (21 bp):
CATTATTATCTTTTTCATAAC
Done.