Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010114.1 Corchorus capsularis cultivar CVL-1 contig10135, 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: 42011
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Found at i:45 original size:2 final size:2
Alignment explanation
Indices: 38--73 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
28 AACAATTTTC
*
38 AT AT AT AT AT AT AT AT AC 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 AT AT
74 GCTACTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1147 original size:16 final size:17
Alignment explanation
Indices: 1123--1156 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1113 GAGGACTAGC
*
1123 TGAGGTGGCA-AAGGAG
1 TGAGCTGGCACAAGGAG
1139 TGAGCTGGCACAAGGAG
1 TGAGCTGGCACAAGGAG
1156 T
1 T
1157 TTGTTGAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.29, C:0.12, G:0.44, T:0.15
Consensus pattern (17 bp):
TGAGCTGGCACAAGGAG
Found at i:4772 original size:48 final size:48
Alignment explanation
Indices: 4698--5341 Score: 502
Period size: 48 Copynumber: 13.3 Consensus size: 48
4688 CTGAATACAA
* * * *
4698 ATCACCACCTCCTCCTTATGTCTACAAGTCACCTCCACCGCCATCTCC
1 ATCACCTCCTCCTCCTTACGTTTACAAGTCACCTCCACCACCATCTCC
* * * * * * *
4746 TTCACCACCTCCACCATACGTTTACAAAT-ACCCACCACCACCATCACC
1 ATCACCTCCTCCTCCTTACGTTTACAAGTCA-CCTCCACCACCATCTCC
* * * * *
4794 ATCACCTCCTCCTCCCTATGTCTATAAATCACCACCTCCACCTCCACCATCTCC
1 ATCACCTCCTCCTCCTTACGTTTACAAGT---CACCTCCA---CCACCATCTCC
* * *
4848 ATCACCTCCTCCTCCCTACGTTTACAAGTCCCCTCCACCACCGTCTCC
1 ATCACCTCCTCCTCCTTACGTTTACAAGTCACCTCCACCACCATCTCC
* * *
4896 ATCACCTCCCCCTCCTTACGTTTACAAGTCCCCTCCACCACCATCGCC
1 ATCACCTCCTCCTCCTTACGTTTACAAGTCACCTCCACCACCATCTCC
* * * * * *
4944 GTCACCTCCTCCTCCTTACATTTACAAATCACCCCCACCACCTTCACC
1 ATCACCTCCTCCTCCTTACGTTTACAAGTCACCTCCACCACCATCTCC
* * * * * * * *
4992 ATCACCACCTCCACCATATGTTTACAAGTCACCTCCTCCTCCCTCACC
1 ATCACCTCCTCCTCCTTACGTTTACAAGTCACCTCCACCACCATCTCC
* * * * * *
5040 ACCACCTCCACCTCCCTACGTCTATAAATCACCTCCACCACCATCTCC
1 ATCACCTCCTCCTCCTTACGTTTACAAGTCACCTCCACCACCATCTCC
* * * * * * * * *
5088 GTCACCACCTCCACCATATGTTTACAAGTCACCACCTCCTCCCTCTCC
1 ATCACCTCCTCCTCCTTACGTTTACAAGTCACCTCCACCACCATCTCC
* * * * *
5136 ATCACCTCC-CCGCCTTACGTCTACAAGTCCCCACCCCCACCATCTCC
1 ATCACCTCCTCCTCCTTACGTTTACAAGTCACCTCCACCACCATCTCC
* * * * * * *
5183 ATCACCTCCCCCACCTTACGTCTACAAGTCCCCACCCCCACCTTCTCC
1 ATCACCTCCTCCTCCTTACGTTTACAAGTCACCTCCACCACCATCTCC
* * * * *
5231 ATCACCTCCTCCTCCCTATGTTTACAAATCTCCTCCACCACCGTCTCC
1 ATCACCTCCTCCTCCTTACGTTTACAAGTCACCTCCACCACCATCTCC
* * * * * * * *
5279 GTCCCCTCCACCTCCATAC-TACTACAAGTCACCTCCACCTCCTTCACC
1 ATCACCTCCTCCTCCTTACGT-TTACAAGTCACCTCCACCACCATCTCC
*
5327 ATCGCCTCCTCCTCC
1 ATCACCTCCTCCTCC
5342 ATATTACTAC
Statistics
Matches: 476, Mismatches: 110, Indels: 20
0.79 0.18 0.03
Matches are distributed among these distances:
47 41 0.09
48 387 0.81
51 12 0.03
52 1 0.00
54 35 0.07
ACGTcount: A:0.21, C:0.51, G:0.04, T:0.24
Consensus pattern (48 bp):
ATCACCTCCTCCTCCTTACGTTTACAAGTCACCTCCACCACCATCTCC
Found at i:4997 original size:15 final size:15
Alignment explanation
Indices: 4979--5008 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4969 AAATCACCCC
*
4979 CACCACCTTCACCAT
1 CACCACCTCCACCAT
4994 CACCACCTCCACCAT
1 CACCACCTCCACCAT
5009 ATGTTTACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.57, G:0.00, T:0.17
Consensus pattern (15 bp):
CACCACCTCCACCAT
Found at i:5220 original size:27 final size:27
Alignment explanation
Indices: 5143--5226 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 27
5133 TCCATCACCT
*
5143 CCCCGCCTTACGTCTACAAGTCCCCAC
1 CCCCACCTTACGTCTACAAGTCCCCAC
* * *
5170 CCCCACC--A--TCT-CCA-TCACCTC
1 CCCCACCTTACGTCTACAAGTCCCCAC
5191 CCCCACCTTACGTCTACAAGTCCCCAC
1 CCCCACCTTACGTCTACAAGTCCCCAC
5218 CCCCACCTT
1 CCCCACCTT
5227 CTCCATCACC
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
21 12 0.27
22 2 0.05
23 4 0.09
25 4 0.09
26 2 0.05
27 20 0.45
ACGTcount: A:0.19, C:0.56, G:0.06, T:0.19
Consensus pattern (27 bp):
CCCCACCTTACGTCTACAAGTCCCCAC
Found at i:7058 original size:12 final size:11
Alignment explanation
Indices: 7041--7079 Score: 51
Period size: 12 Copynumber: 3.3 Consensus size: 11
7031 TTGGCTAGGG
7041 TTTTTTCTTTTC
1 TTTTTT-TTTTC
7053 TTTTTTTTTCTC
1 TTTTTTTTT-TC
7065 TTTCTTTTTTTC
1 TTT-TTTTTTTC
7077 TTT
1 TTT
7080 CGTTTCTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.12
12 16 0.64
13 6 0.24
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:7061 original size:15 final size:16
Alignment explanation
Indices: 7041--7075 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
7031 TTGGCTAGGG
7041 TTTTTTCT-TTTCTTT
1 TTTTTTCTCTTTCTTT
7056 TTTTTTCTCTTTCTTT
1 TTTTTTCTCTTTCTTT
7072 TTTT
1 TTTT
7076 CTTTCGTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTTCTCTTTCTTT
Found at i:7066 original size:17 final size:15
Alignment explanation
Indices: 7041--7087 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
7031 TTGGCTAGGG
7041 TTTTTTCTTTTCTTTT
1 TTTTTTC-TTTCTTTT
7057 TTTTTCTCTTTCTTTT
1 TTTTT-TCTTTCTTTT
7073 TTTCTTTCGTTTCTT
1 TTT-TTTC-TTTCTT
7088 CATCTCCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 18 0.64
17 10 0.36
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (15 bp):
TTTTTTCTTTCTTTT
Found at i:13368 original size:1 final size:1
Alignment explanation
Indices: 13362--13400 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
13352 CTCTATTGGC
* * *
13362 AAAAAAAAAAAAAGAAAAAAAAAGAAAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13401 CAAACTCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.92, C:0.03, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:13381 original size:10 final size:10
Alignment explanation
Indices: 13362--13394 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
13352 CTCTATTGGC
13362 AAAA-AAAAA
1 AAAAGAAAAA
13371 AAAAGAAAAA
1 AAAAGAAAAA
13381 AAAAGAAAAA
1 AAAAGAAAAA
13391 AAAA
1 AAAA
13395 ACAAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.17
10 19 0.83
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:14675 original size:11 final size:10
Alignment explanation
Indices: 14652--14683 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
14642 CCCGTTGTGC
14652 AAAAATAAAA
1 AAAAATAAAA
14662 AAAAATAAATA
1 AAAAATAAA-A
14673 AAAAATAAAA
1 AAAAATAAAA
14683 A
1 A
14684 CCAACCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:15502 original size:48 final size:48
Alignment explanation
Indices: 15438--15736 Score: 260
Period size: 48 Copynumber: 6.1 Consensus size: 48
15428 GGCACCTCTA
* * * *
15438 CCTTACATCTATAAGTCTCCTCCTCCACCATCTCCCTCACCCCCTCCT
1 CCTTATATCTACAAGTCTCCACCTCCACCATCTCCCTCACCTCCTCCT
* * * *
15486 CCTTATGTCTACAAGTCTCCACCTCCACCATCTCCATCACCTCCACCC
1 CCTTATATCTACAAGTCTCCACCTCCACCATCTCCCTCACCTCCTCCT
* * * * * *
15534 CCATACATTTACAAATCTCCACCTCCACCATC-CCCATCACCTCCACCG
1 CCTTATATCTACAAGTCTCCACCTCCACCATCTCCC-TCACCTCCTCCT
* * * * *
15582 CCTTATATCTACAAGTCCCCACCACCAACTTCTCCCTCACCTCCTCCC
1 CCTTATATCTACAAGTCTCCACCTCCACCATCTCCCTCACCTCCTCCT
* * * *
15630 CCTTACATCTACAAGTCTCCACCCCCACCCCCACCATCTCCATCACCACCTCCT
1 CCTTATATCTACAAGTCT------CCACCTCCACCATCTCCCTCACCTCCTCCT
* * * * *
15684 CCCTATGTTTACAAGTCCCCACCACCACCATC-CCCATCACCTCCTCCT
1 CCTTATATCTACAAGTCTCCACCTCCACCATCTCCC-TCACCTCCTCCT
15732 CCTTA
1 CCTTA
15737 CGTTTATAAG
Statistics
Matches: 200, Mismatches: 42, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
47 4 0.02
48 156 0.78
49 3 0.01
54 37 0.19
ACGTcount: A:0.21, C:0.52, G:0.03, T:0.24
Consensus pattern (48 bp):
CCTTATATCTACAAGTCTCCACCTCCACCATCTCCCTCACCTCCTCCT
Found at i:15529 original size:24 final size:24
Alignment explanation
Indices: 15502--15580 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
15492 GTCTACAAGT
15502 CTCCACCTCCACCATCTCCATCAC
1 CTCCACCTCCACCATCTCCATCAC
* * * * * *
15526 CTCCACCCCCATACATTTACA-AAT
1 CTCCACCTCCA-CCATCTCCATCAC
*
15550 CTCCACCTCCACCATCCCCATCAC
1 CTCCACCTCCACCATCTCCATCAC
15574 CTCCACC
1 CTCCACC
15581 GCCTTATATC
Statistics
Matches: 40, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
23 5 0.12
24 29 0.73
25 6 0.15
ACGTcount: A:0.24, C:0.56, G:0.00, T:0.20
Consensus pattern (24 bp):
CTCCACCTCCACCATCTCCATCAC
Found at i:15553 original size:96 final size:96
Alignment explanation
Indices: 15441--15727 Score: 306
Period size: 96 Copynumber: 2.9 Consensus size: 96
15431 ACCTCTACCT
* * * * *
15441 TACATCTATAAGTCTCCTCCTCCACCATCTCCCTCACCCCCTCCTCCTTATGTCTACAAGTCTCC
1 TACATCTACAAATCTCCACCTCCACCATCTCCCTCACCACCTCCTCCTTATGTCTACAAGTCCCC
*
15506 ACCTCCACCATCTCCATCACCTCCACCCCCA
66 ACCACCACCATCTCCATCACCTCCACCCCCA
* * * * *
15537 TACATTTACAAATCTCCACCTCCACCATC-CCCATCACCTCCACCGCCTTATATCTACAAGTCCC
1 TACATCTACAAATCTCCACCTCCACCATCTCCC-TCACCACCTCCTCCTTATGTCTACAAGTCCC
* * * * *
15601 CACCACCAACTTCTCCCTCACCTCCTCCCCCT
65 CACCACCACCATCTCCATCACCTCCACCCCCA
* * * * *
15633 TACATCTACAAGTCTCCACCCCCACCCCCACCATCTCCATCACCACCTCCTCCCTATGTTTACAA
1 TACATCTACAAATCT------CCACCTCCACCATCTCCCTCACCACCTCCTCCTTATGTCTACAA
*
15698 GTCCCCACCACCACCATCCCCATCACCTCC
60 GTCCCCACCACCACCATCTCCATCACCTCC
15728 TCCTCCTTAC
Statistics
Matches: 154, Mismatches: 29, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
95 3 0.02
96 90 0.58
102 59 0.38
103 2 0.01
ACGTcount: A:0.22, C:0.52, G:0.03, T:0.23
Consensus pattern (96 bp):
TACATCTACAAATCTCCACCTCCACCATCTCCCTCACCACCTCCTCCTTATGTCTACAAGTCCCC
ACCACCACCATCTCCATCACCTCCACCCCCA
Found at i:15760 original size:54 final size:52
Alignment explanation
Indices: 15462--16347 Score: 186
Period size: 48 Copynumber: 17.8 Consensus size: 52
15452 GTCTCCTCCT
* * * * *
15462 CCACCATCTCCC-TCACCCCCTCCTCCTTATGTCTACAAGT----CTCCACCT
1 CCACCATC-CCCATCACCTCCTCCTCCTTACGTTTACAAGTCCCACCCCACCA
* * * * * * * *
15510 CCACCATCTCCATCACCTCCACCCCCATACATTTACAAAT----CTCCACCT
1 CCACCATCCCCATCACCTCCTCCTCCTTACGTTTACAAGTCCCACCCCACCA
* * ** *
15558 CCACCATCCCCATCACCTCCACCGCCTTATATCTACAAGT----CCCCACCA
1 CCACCATCCCCATCACCTCCTCCTCCTTACGTTTACAAGTCCCACCCCACCA
* * * * * *
15606 CCAACTTCTCCC-TCACCTCCTCCCCCTTACATCTACAAGTCTCCACCCCCACCC
1 CCACCATC-CCCATCACCTCCTCCTCCTTACGTTTACAAGTC-CCA-CCCCACCA
* * * *
15660 CCACCATCTCCATCACCACCTCCTCCCTATGTTTACAAGT----CCCCACCA
1 CCACCATCCCCATCACCTCCTCCTCCTTACGTTTACAAGTCCCACCCCACCA
*
15708 CCACCATCCCCATCACCTCCTCCTCCTTACGTTTATAAGTCACCACCACCACCATA
1 CCACCATCCCCATCACCTCCTCCTCCTTACGTTTACAAGTC-CCACC-CCACC--A
* * * * * * * * * *** ** *** *
15764 TGTCTACAAGTCTCCACCTCCACCTTCTCCCTCACCTCCCCCATATGTTTACAAGTCTCCA
1 ---CCACCA-TCCCCATCACCTCCTCCT-CCTTACGT-TTACA-A-G-TCCCACCCCACCA
* * * **
15825 CCACCGCCATCTCCATCACCACCTCCTCCCTATATTTACAAGT----CCCCACCA
1 CCA---CCATCCCCATCACCTCCTCCTCCTTACGTTTACAAGTCCCACCCCACCA
* * *
15876 CCACCATCCCCATCACCTCCTCCTCCTTACCTTTATAAGT----CGCCACCA
1 CCACCATCCCCATCACCTCCTCCTCCTTACGTTTACAAGTCCCACCCCACCA
* * * * * * *
15924 CCACCATCACCATCACCACCTCCACCCTATGTTTACAAAT----CTCCACCA
1 CCACCATCCCCATCACCTCCTCCTCCTTACGTTTACAAGTCCCACCCCACCA
* * * * * *
15972 CCACCTTCTCCATCACCTCCACCACCTTACGTTTACAAGTCCC-CACCTCCA
1 CCACCATCCCCATCACCTCCTCCTCCTTACGTTTACAAGTCCCACCCCACCA
* ** * * * * * *
16023 GCTTC-TCCCC-TCGCCCCCTCCCCCTTACGTCTACAAGT----CTCCACCT
1 CCACCATCCCCATCACCTCCTCCTCCTTACGTTTACAAGTCCCACCCCACCA
* * * * *
16069 CCACCTTCTCCC-TCGCC-CCTCCCCCTTACGTCTACAAGT----CTCCACC-
1 CCACCATC-CCCATCACCTCCTCCTCCTTACGTTTACAAGTCCCACCCCACCA
* * * * *
16115 CCACCATCTCCTTCACCTCCTCCTCCTTATGTCTACAAGT--CA--CTACCA
1 CCACCATCCCCATCACCTCCTCCTCCTTACGTTTACAAGTCCCACCCCACCA
* * * * *
16163 CCACCATCTCCC-TCACCTCCACCACCTTATGTCTATAAGT--CA-CCC-CCA
1 CCACCATC-CCCATCACCTCCTCCTCCTTACGTTTACAAGTCCCACCCCACCA
* * * *
16211 CCACCATCCCCATCACCTCCACCACCTTATGTTTACAAGT----CCCCTCCA
1 CCACCATCCCCATCACCTCCTCCTCCTTACGTTTACAAGTCCCACCCCACCA
* * * * * *
16259 CCTCCATCTCCTTCACCTCCACCTCCTTACATGTACAAGTCTCCA--CCA-C-
1 CCACCATCCCCATCACCTCCTCCTCCTTACGTTTACAAGTC-CCACCCCACCA
* * *
16308 CC-CCATCACCATCACCTCCTCCACCTTATGTTTACAAGTC
1 CCACCATCCCCATCACCTCCTCCTCCTTACGTTTACAAGTC
16348 TCCTCCCCCA
Statistics
Matches: 648, Mismatches: 141, Indels: 98
0.73 0.16 0.11
Matches are distributed among these distances:
45 2 0.00
46 18 0.03
47 63 0.10
48 406 0.63
49 31 0.05
50 5 0.01
51 17 0.03
53 4 0.01
54 40 0.06
55 1 0.00
56 2 0.00
57 1 0.00
58 4 0.01
59 8 0.01
60 28 0.04
61 9 0.01
62 1 0.00
63 4 0.01
64 3 0.00
65 1 0.00
ACGTcount: A:0.21, C:0.50, G:0.04, T:0.24
Consensus pattern (52 bp):
CCACCATCCCCATCACCTCCTCCTCCTTACGTTTACAAGTCCCACCCCACCA
Found at i:15799 original size:48 final size:48
Alignment explanation
Indices: 15747--16359 Score: 538
Period size: 48 Copynumber: 12.9 Consensus size: 48
15737 CGTTTATAAG
* * * * * *
15747 TCACCACCACCACCATATGTCTACAAGTCTCCACCTCCACCTTCTCCC
1 TCACCTCCTCCACCTTATGTTTACAAGTCTCCACCACCACCATCTCCC
* * *
15795 TCACCT-C-CC-CCATATGTTTACAAGTCTCCACCACCGCCATCTCCA
1 TCACCTCCTCCACCTTATGTTTACAAGTCTCCACCACCACCATCTCCC
* * * * *
15840 TCACCACCTCCTCCCTATATTTACAAGTCCCCACCACCACCATC-CCC
1 TCACCTCCTCCACCTTATGTTTACAAGTCTCCACCACCACCATCTCCC
* ** * * * *
15887 ATCACCTCCTCCTCCTTACCTTTATAAGTCGCCACCACCACCATCACCA
1 -TCACCTCCTCCACCTTATGTTTACAAGTCTCCACCACCACCATCTCCC
* * * * *
15936 TCACCACCTCCACCCTATGTTTACAAATCTCCACCACCACCTTCTCCA
1 TCACCTCCTCCACCTTATGTTTACAAGTCTCCACCACCACCATCTCCC
* * * * * *
15984 TCACCTCCACCACCTTACGTTTACAAGTCCCCACCTCCAGCTTCTCCCC
1 TCACCTCCTCCACCTTATGTTTACAAGTCTCCACCACCACCATCT-CCC
* * * * * * *
16033 TCGCCCCCTCCCCCTTACGTCTACAAGTCTCCACCTCCACCTTCTCCC
1 TCACCTCCTCCACCTTATGTTTACAAGTCTCCACCACCACCATCTCCC
* * * * *
16081 TCGCC-CCTCCCCCTTACGTCTACAAGTCTCCACC-CCACCATCTCCT
1 TCACCTCCTCCACCTTATGTTTACAAGTCTCCACCACCACCATCTCCC
* * * *
16127 TCACCTCCTCCTCCTTATGTCTACAAGTCACTACCACCACCATCTCCC
1 TCACCTCCTCCACCTTATGTTTACAAGTCTCCACCACCACCATCTCCC
* * * * *
16175 TCACCTCCACCACCTTATGTCTATAAGTCACCCCCACCACCATC-CCC
1 TCACCTCCTCCACCTTATGTTTACAAGTCTCCACCACCACCATCTCCC
* * * * *
16222 ATCACCTCCACCACCTTATGTTTACAAGTCCCCTCCACCTCCATCTCCT
1 -TCACCTCCTCCACCTTATGTTTACAAGTCTCCACCACCACCATCTCCC
* * ** * * * *
16271 TCACCTCCACCTCCTTACATGTACAAGTCTCCACCACCCCCATCACCA
1 TCACCTCCTCCACCTTATGTTTACAAGTCTCCACCACCACCATCTCCC
* *
16319 TCACCTCCTCCACCTTATGTTTACAAGTCTCCTCCCCCACC
1 TCACCTCCTCCACCTTATGTTTACAAGTCTCCACCACCACC
16360 TGCATATTAT
Statistics
Matches: 474, Mismatches: 81, Indels: 20
0.82 0.14 0.03
Matches are distributed among these distances:
45 36 0.08
46 17 0.04
47 62 0.13
48 315 0.66
49 44 0.09
ACGTcount: A:0.21, C:0.50, G:0.05, T:0.24
Consensus pattern (48 bp):
TCACCTCCTCCACCTTATGTTTACAAGTCTCCACCACCACCATCTCCC
Found at i:16277 original size:15 final size:15
Alignment explanation
Indices: 16257--16286 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16247 AAGTCCCCTC
*
16257 CACCTCCATCTCCTT
1 CACCTCCACCTCCTT
16272 CACCTCCACCTCCTT
1 CACCTCCACCTCCTT
16287 ACATGTACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.57, G:0.00, T:0.30
Consensus pattern (15 bp):
CACCTCCACCTCCTT
Found at i:16280 original size:287 final size:286
Alignment explanation
Indices: 15765--16305 Score: 744
Period size: 287 Copynumber: 1.9 Consensus size: 286
15755 ACCACCATAT
* *
15765 GTCTACAAGTCTCCACCTCCACCTTCTCCCTCACCTCCCCCATATGTTTACAAGTCTCCACCACC
1 GTCTACAAGTCTCCACCTCCACCTTCTCCCTCACCTCCCCCATACGTCTACAAGTCTCCACCACC
* * *
15830 GCCATCTCCATCACCACCTCCTCCCTATATTTACAAGTCCCCACCACCACCATCCCCATCACCTC
66 ACCATCTCCATCACCACCTCCTCCCTATATCTACAAGTCACCACCACCACCATCCCCATCACCTC
* * * * *
15895 CTCCTCCTTACCTTTATAAGTCGCCACCACCACCATCACCATCACCACCTCCACCCTATGTTTAC
131 CACCACCTTACCTCTATAAGTCACCACCACCACCATCACCATCACCACCACCACCCTATGTTTAC
* * * *
15960 AAATCTCCACCACCACCTTCTCCATCACCTCCACCACCTTACGTTTACAAGTCCCCACCTCCAGC
196 AAATCCCCACCACCACCATCTCCATCACCTCCACCACCTTACATGTACAAGTCCCCACCTCCAGC
16025 TTCTCCCCTCGCCCCCTCCCCCTTAC
261 TTCTCCCCTCGCCCCCTCCCCCTTAC
* *
16051 GTCTACAAGTCTCCACCTCCACCTTCTCCCTCGCCCCTCCCCCTTACGTCTACAAGTCTCCACC-
1 GTCTACAAGTCTCCACCTCCACCTTCTCCCT--CACCTCCCCCATACGTCTACAAGTCTCCACCA
* * * * *
16115 CCACCATCTCCTTCACCTCCTCCTCCTTATGTCTACAAGTCACTACCACCACCATCTCCC-TCAC
64 CCACCATCTCCATCACCACCTCCTCCCTATATCTACAAGTCACCACCACCACCATC-CCCATCAC
** * * * *
16179 CTCCACCACCTTATGTCTATAAGTCACCCCCACCACCATCCCCATCACCTCCACCACCTTATGTT
128 CTCCACCACCTTACCTCTATAAGTCACCACCACCACCATCACCATCACCACCACCACCCTATGTT
* * * * * *
16244 TACAAGTCCCCTCCACCTCCATCTCCTTCACCTCCACCTCCTTACATGTACAAGTCTCCACC
193 TACAAATCCCCACCACCACCATCTCCATCACCTCCACCACCTTACATGTACAAGTCCCCACC
16306 ACCCCCATCA
Statistics
Matches: 219, Mismatches: 33, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
286 31 0.14
287 158 0.72
288 30 0.14
ACGTcount: A:0.21, C:0.50, G:0.05, T:0.25
Consensus pattern (286 bp):
GTCTACAAGTCTCCACCTCCACCTTCTCCCTCACCTCCCCCATACGTCTACAAGTCTCCACCACC
ACCATCTCCATCACCACCTCCTCCCTATATCTACAAGTCACCACCACCACCATCCCCATCACCTC
CACCACCTTACCTCTATAAGTCACCACCACCACCATCACCATCACCACCACCACCCTATGTTTAC
AAATCCCCACCACCACCATCTCCATCACCTCCACCACCTTACATGTACAAGTCCCCACCTCCAGC
TTCTCCCCTCGCCCCCTCCCCCTTAC
Found at i:20072 original size:26 final size:26
Alignment explanation
Indices: 20043--20098 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
20033 ATTTTAATAT
*
20043 TTAAATT-TTATTTTTTATTAAAAAAA
1 TTAAATTATTATTTTAT-TTAAAAAAA
*
20069 TT-AATTATTATTTTATTTCAAAAAA
1 TTAAATTATTATTTTATTTAAAAAAA
20094 -TAAAT
1 TTAAAT
20099 ATTGGCGGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 1 0.04
25 15 0.58
26 10 0.38
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TTAAATTATTATTTTATTTAAAAAAA
Found at i:20101 original size:24 final size:26
Alignment explanation
Indices: 20043--20101 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
20033 ATTTTAATAT
* *
20043 TTAAATTTTATTTTTTATTAAAAAAA
1 TTAAATATTATTTTATATTAAAAAAA
* *
20069 TTAATTATTATTTTAT-TTCAAAAAA
1 TTAAATATTATTTTATATTAAAAAAA
20094 -TAAATATT
1 TTAAATATT
20102 GGCGGGATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 7 0.25
25 8 0.29
26 13 0.46
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
TTAAATATTATTTTATATTAAAAAAA
Found at i:21292 original size:48 final size:48
Alignment explanation
Indices: 21240--21359 Score: 134
Period size: 48 Copynumber: 2.5 Consensus size: 48
21230 CAAGTCACCT
* *
21240 CCACCGCCATCTCATTCA-CTACCTCCACCATACATTTACAAATCCCCA
1 CCACCACCATCTCAATCACCT-CCTCCACCATACATTTACAAATCCCCA
** * * * * *
21288 CCACCACCATCAAAATCACCTCCTCCTCCCTACGTTTACAAGTCCCCT
1 CCACCACCATCTCAATCACCTCCTCCACCATACATTTACAAATCCCCA
*
21336 CCACCACCATCTCCATCACCTCCT
1 CCACCACCATCTCAATCACCTCCT
21360 TATGTTTACA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
48 57 0.97
49 2 0.03
ACGTcount: A:0.26, C:0.49, G:0.03, T:0.23
Consensus pattern (48 bp):
CCACCACCATCTCAATCACCTCCTCCACCATACATTTACAAATCCCCA
Found at i:21404 original size:48 final size:48
Alignment explanation
Indices: 21302--21529 Score: 180
Period size: 48 Copynumber: 4.9 Consensus size: 48
21292 CACCATCAAA
* * * * * *
21302 ATCACCTCCTCCTCCCTACGTTTACAAGTCCCCTCCACCACCATCTCC
1 ATCACCTCCACCTCCCTATGTCTACAAATCCCCTCCTCCACCGTCTCC
* * * * *
21350 ATCACCT---CCT---TATGTTTACAAGTCCCCTCCTCCTCCCTCTCG
1 ATCACCTCCACCTCCCTATGTCTACAAATCCCCTCCTCCACCGTCTCC
* * * * *
21392 ATCCCCTCCACCTCCCTACGTCTATAAATCACCTCCCCCACCGTCTCC
1 ATCACCTCCACCTCCCTATGTCTACAAATCCCCTCCTCCACCGTCTCC
* * * *
21440 ATCACCTCCACCACCGTATGTCTACAAGTCCCCACCTCCACCGTCTCC
1 ATCACCTCCACCTCCCTATGTCTACAAATCCCCTCCTCCACCGTCTCC
** * * * *
21488 AAAACCTCCTCCTCCCTATGTTTACAAATCTCCTCCACCACC
1 ATCACCTCCACCTCCCTATGTCTACAAATCCCCTCCTCCACC
21530 AACCCAATCC
Statistics
Matches: 140, Mismatches: 34, Indels: 12
0.75 0.18 0.06
Matches are distributed among these distances:
42 33 0.24
45 6 0.04
48 101 0.72
ACGTcount: A:0.20, C:0.50, G:0.05, T:0.25
Consensus pattern (48 bp):
ATCACCTCCACCTCCCTATGTCTACAAATCCCCTCCTCCACCGTCTCC
Found at i:21544 original size:96 final size:94
Alignment explanation
Indices: 21305--21574 Score: 235
Period size: 96 Copynumber: 2.9 Consensus size: 94
21295 CATCAAAATC
* * * * * *
21305 ACCTCCTCCTCCCTACGTTTACAAGTCCCCTCCACCACCA-TC-T-CCAT-CACCTCCTTATGTT
1 ACCTCCTCCTCCCTACGTTTACAAATCACCTCCACCACCACCCATCCCCTCCACCTCCATATGTC
* * * **
21366 TACAAGTCCCCTCCTCCTCCCTCTCGATC
66 TACAAGTCCCCACCTCCACCCTCTCCAAA
* * * * * * * * *
21395 CCCTCCACCTCCCTACGTCTATAAATCACCTCCCCCACCGTCTCCATCACCTCCACCACCGTATG
1 ACCTCCTCCTCCCTACGTTTACAAATCACCTCCACCACC-AC-CCATCCCCTCCACCTCCATATG
*
21460 TCTACAAGTCCCCACCTCCACCGTCTCCAAA
64 TCTACAAGTCCCCACCTCCACCCTCTCCAAA
* *
21491 ACCTCCTCCTCCCTATGTTTACAAATCTCCTCCACCACCAACCCAATCCCCTCCACCTCCATACT
1 ACCTCCTCCTCCCTACGTTTACAAATCACCTCCACCACC-ACCC-ATCCCCTCCACCTCCATA-T
* *
21556 -ACTACAAGTCACCACCTCC
63 GTCTACAAGTCCCCACCTCC
21575 TCCTCCACGT
Statistics
Matches: 138, Mismatches: 34, Indels: 10
0.76 0.19 0.05
Matches are distributed among these distances:
90 32 0.23
93 1 0.01
94 1 0.01
95 4 0.03
96 99 0.72
97 1 0.01
ACGTcount: A:0.21, C:0.50, G:0.05, T:0.24
Consensus pattern (94 bp):
ACCTCCTCCTCCCTACGTTTACAAATCACCTCCACCACCACCCATCCCCTCCACCTCCATATGTC
TACAAGTCCCCACCTCCACCCTCTCCAAA
Found at i:23372 original size:28 final size:28
Alignment explanation
Indices: 23302--23373 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
23292 CTAGGACGTC
* *
23302 TCCCTCTGGTGTATAAGGCGGAAATTCG
1 TCCCTCTGATGTATCAGGCGGAAATTCG
* *
23330 TCCCTCTGATGTATCAGGCGTTAAA-TCT
1 TCCCTCTGATGTATCAGGCG-GAAATTCG
23358 TCCCTCTGATGTATCA
1 TCCCTCTGATGTATCA
23374 CATGGCATGC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 36 0.92
29 3 0.08
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (28 bp):
TCCCTCTGATGTATCAGGCGGAAATTCG
Found at i:25918 original size:156 final size:156
Alignment explanation
Indices: 25571--26103 Score: 670
Period size: 156 Copynumber: 3.4 Consensus size: 156
25561 CTAGGCTTCA
* * * * * *
25571 CACCTCAAACTGTCCTTAAATGAAAAACTTGCATAAGTTTTTCA-CCTTGAGTCTGATTGAGCTG
1 CACCCCAAACTGTCCTTAACTGAAAAACATGCATAAGTTTTTCATCC-TAAGTCTGTTTGAGATG
*** * * * * *
25635 AAACTTTGCCA--AGGGACTTAGATT-CTCTTCACAAGACTATGGAAAAAA--CT--CTAAAACC
65 AAACTCCACCAGTA-GG-CTTAGATTATTC-CCATAAAACTATGGAAAAAATTCTAAGTAAAACC
* * * * *
25693 GAGCTCCCCT-TGATGGTGAACTTGGTTTCT
127 AAACT-CCCTATCATAGTGAAGTTGGTTTCT
* * * * * *
25723 CTCCCTAAACTGTCCTTAAATAAAAAACTTGTATAAGTTTTTCATCCTAAGTCTGTTTGAGATGA
1 CACCCCAAACTGTCCTTAACTGAAAAACATGCATAAGTTTTTCATCCTAAGTCTGTTTGAGATGA
25788 AACTCCACCAGTAGGCTTAGATTATTCCCATAAAACTATGGAAAAAATTCTAAGTAAAACCAAAC
66 AACTCCACCAGTAGGCTTAGATTATTCCCATAAAACTATGGAAAAAATTCTAAGTAAAACCAAAC
25853 TCCCTATCATAGTGAAGTTGGTTTCT
131 TCCCTATCATAGTGAAGTTGGTTTCT
*
25879 CACCCCAAACTGTCCTTAACTGAAAAACATACATAAGTTTTTCATCCTAAGTCTGTTTGAGATGA
1 CACCCCAAACTGTCCTTAACTGAAAAACATGCATAAGTTTTTCATCCTAAGTCTGTTTGAGATGA
* * *
25944 AACTCCACTAGTAGGCTTAGATTATTCCCATAAAACTATGGAAAAAATTCTAAGTAAAATCGAAC
66 AACTCCACCAGTAGGCTTAGATTATTCCCATAAAACTATGGAAAAAATTCTAAGTAAAACCAAAC
26009 TCCCTATCATAGTGAAGTTGGTTTCT
131 TCCCTATCATAGTGAAGTTGGTTTCT
* **
26035 CACCCCAAACTATATTTAACTGAAAAACATGCATAAGTTTTTCATCCTAAGTCTGTTTGAGATGA
1 CACCCCAAACTGTCCTTAACTGAAAAACATGCATAAGTTTTTCATCCTAAGTCTGTTTGAGATGA
26100 AACT
66 AACT
26104 TAGCCAAGAT
Statistics
Matches: 337, Mismatches: 35, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
152 86 0.26
153 6 0.02
154 3 0.01
155 4 0.01
156 238 0.71
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (156 bp):
CACCCCAAACTGTCCTTAACTGAAAAACATGCATAAGTTTTTCATCCTAAGTCTGTTTGAGATGA
AACTCCACCAGTAGGCTTAGATTATTCCCATAAAACTATGGAAAAAATTCTAAGTAAAACCAAAC
TCCCTATCATAGTGAAGTTGGTTTCT
Found at i:30794 original size:48 final size:48
Alignment explanation
Indices: 30742--30862 Score: 118
Period size: 48 Copynumber: 2.5 Consensus size: 48
30732 CTCCACGACG
* *
30742 TCCTTACGTCTACAAGTCTCCACCAACACCATCTCCATCACCTCCTCC
1 TCCTTACGTCTACAAGTCTCCACCAACACCATCCCCATCACCTCCACC
* * * * * ** *
30790 TCCTTATGTTTATAAATCTCCTCCCCCGCCATCCCCATCACCTCCACC
1 TCCTTACGTCTACAAGTCTCCACCAACACCATCCCCATCACCTCCACC
* *
30838 TCCATAC-TACTACAAGTCACCACCA
1 TCCTTACGT-CTACAAGTCTCCACCA
30863 CCTCCTTCAC
Statistics
Matches: 54, Mismatches: 18, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
47 1 0.02
48 53 0.98
ACGTcount: A:0.24, C:0.46, G:0.04, T:0.26
Consensus pattern (48 bp):
TCCTTACGTCTACAAGTCTCCACCAACACCATCCCCATCACCTCCACC
Found at i:40289 original size:14 final size:14
Alignment explanation
Indices: 40270--40298 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40260 GAGCTAAATA
40270 TGGCCAATGGTTTC
1 TGGCCAATGGTTTC
40284 TGGCCAATGGTTTC
1 TGGCCAATGGTTTC
40298 T
1 T
40299 CCATACAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.28, T:0.38
Consensus pattern (14 bp):
TGGCCAATGGTTTC
Found at i:41244 original size:283 final size:281
Alignment explanation
Indices: 40736--41299 Score: 1056
Period size: 283 Copynumber: 2.0 Consensus size: 281
40726 TTCATGGACT
*
40736 TTGACAACCATGAAGAAGAGAAGAAAAGACTATCCAAGGGACAGAGGAAAGCACAACGCAAGGCT
1 TTGACAACCATGAAGAAGAGAAGAAAAGACTATCCAAGGGACAGAAGAAAGCACAACGCAAGGCT
*
40801 GAAAAAGATGCTAGAAAAAGGATTTTTTACTGTTATTTCTGCAACAAAGGAGGATTATCTGAAGG
66 GAAAAAGATGCCAGAAAAAGGATTTTTTACTGTTATTTCTGCAACAAAGGAGGATTATCTGAAGG
40866 TGGTATCTTGGAGCATAATGACAAATGTCACAAACATTTCAAATTTTCGTGCAAAGTCTGCAACA
131 TGGTATCTTGGAGCATAATGACAAATGTCACAAACATTTCAAATTTTCGTGCAAAGTCTGCAACA
40931 ACAAGTTTAAGACTCTGGAAGACCTCCATCAGCACCAGTACATTAAACGTAAATCGTCAATCTTC
196 ACAAGTTTAAGACTCTGGAAGACCTCCATCAGCACCA--ACATTAAACGTAAATCGTCAATCTTC
*
40996 AAGAAGGTACTTGTTCTTTTCTG
259 AAGAAGGTACCTGTTCTTTTCTG
*
41019 TTGACAACCATGAAGAAGAGAAGAAAAGACTATCCAAGGGACGGAAGAAAGCACAACGCAAGGCT
1 TTGACAACCATGAAGAAGAGAAGAAAAGACTATCCAAGGGACAGAAGAAAGCACAACGCAAGGCT
41084 GAAAAAGATGCCAGAAAAAGGATTTTTTACTGTTATTTCTGCAACAAAGGAGGATTATCTGAAGG
66 GAAAAAGATGCCAGAAAAAGGATTTTTTACTGTTATTTCTGCAACAAAGGAGGATTATCTGAAGG
*
41149 TGGTATCTTGGAGTATAATGACAAATGTCACAAACATTTCAAATTTTCGTGCAAAGTCTGCAACA
131 TGGTATCTTGGAGCATAATGACAAATGTCACAAACATTTCAAATTTTCGTGCAAAGTCTGCAACA
*
41214 ACAAGTTTAAGACTCTGGAAGACTTCCATCAGCACCAACATTAAACGTAAATCGTCAATCTTCAA
196 ACAAGTTTAAGACTCTGGAAGACCTCCATCAGCACCAACATTAAACGTAAATCGTCAATCTTCAA
41279 GAAGGTACCTGTTCTTTTCTG
261 GAAGGTACCTGTTCTTTTCTG
41300 CTTAGTTTTT
Statistics
Matches: 275, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
281 48 0.17
283 227 0.83
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (281 bp):
TTGACAACCATGAAGAAGAGAAGAAAAGACTATCCAAGGGACAGAAGAAAGCACAACGCAAGGCT
GAAAAAGATGCCAGAAAAAGGATTTTTTACTGTTATTTCTGCAACAAAGGAGGATTATCTGAAGG
TGGTATCTTGGAGCATAATGACAAATGTCACAAACATTTCAAATTTTCGTGCAAAGTCTGCAACA
ACAAGTTTAAGACTCTGGAAGACCTCCATCAGCACCAACATTAAACGTAAATCGTCAATCTTCAA
GAAGGTACCTGTTCTTTTCTG
Found at i:41993 original size:2 final size:2
Alignment explanation
Indices: 41986--42011 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41976 TAGTTAAGGA
41986 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
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.