Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015949.1 Corchorus capsularis cultivar CVL-1 contig15970, 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: 21844
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:1435 original size:21 final size:21
Alignment explanation
Indices: 1409--1476 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 21
1399 ATCAAAGAAG
1409 AAGAAAAACTGGGCCTAAAAA
1 AAGAAAAACTGGGCCTAAAAA
* *
1430 AAG--AAAGTGGTCGC-AAAAA
1 AAGAAAAACTGGGC-CTAAAAA
1449 GGAA-AAAAACTGGGCCTAAAAA
1 --AAGAAAAACTGGGCCTAAAAA
1471 AAGAAA
1 AAGAAA
1477 GAGGTCGCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
19 12 0.33
20 3 0.08
21 9 0.25
22 12 0.33
ACGTcount: A:0.57, C:0.12, G:0.22, T:0.09
Consensus pattern (21 bp):
AAGAAAAACTGGGCCTAAAAA
Found at i:1466 original size:41 final size:41
Alignment explanation
Indices: 1401--1495 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 41
1391 AAATTCTCAT
* *
1401 CAAAGAAGAAGAAAAACTGGGCCTAAAAAAAGAAAGTGGTCG
1 CAAAAAAGAA-AAAAACTGGGCCTAAAAAAAGAAAGAGGTCG
*
1443 CAAAAAGGAAAAAAACTGGGCCTAAAAAAAGAAAGAGGTCG
1 CAAAAAAGAAAAAAACTGGGCCTAAAAAAAGAAAGAGGTCG
1484 CAAAAAAGAAAA
1 CAAAAAAGAAAA
1496 TAAAAAGAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 41 0.84
42 8 0.16
ACGTcount: A:0.58, C:0.12, G:0.23, T:0.07
Consensus pattern (41 bp):
CAAAAAAGAAAAAAACTGGGCCTAAAAAAAGAAAGAGGTCG
Found at i:1940 original size:12 final size:12
Alignment explanation
Indices: 1906--1952 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
1896 CATCAAATAA
1906 TTCAAATCAAAG
1 TTCAAATCAAAG
* *
1918 TTCGAACCAAAG
1 TTCAAATCAAAG
*
1930 TTTAAATCAAAG
1 TTCAAATCAAAG
1942 TTCAAATCAAA
1 TTCAAATCAAA
1953 AGTGAATCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.26
Consensus pattern (12 bp):
TTCAAATCAAAG
Found at i:2259 original size:19 final size:19
Alignment explanation
Indices: 2213--2259 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
2203 TTCTTATAAA
* * *
2213 CAAAAAAGATTGTTTTTGT
1 CAAAAAAAAGTGTTTTTCT
2232 -AAAAGAAAAGTGTTTTTCT
1 CAAAA-AAAAGTGTTTTTCT
2251 CAAAAAAAA
1 CAAAAAAAA
2260 AAAGGTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 4 0.17
19 15 0.65
20 4 0.17
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (19 bp):
CAAAAAAAAGTGTTTTTCT
Found at i:2351 original size:19 final size:18
Alignment explanation
Indices: 2319--2371 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
2309 TAGTGAAATA
*
2319 AAAAAAAATAGTTTTT-GC
1 AAAAAAAA-GGTTTTTCGC
*
2337 AAAAGAAAAGTGTTTTTCTC
1 AAAA-AAAAG-GTTTTTCGC
2357 AAAAAAAAGGTTTTT
1 AAAAAAAAGGTTTTT
2372 AGAGAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 10 0.33
19 15 0.50
20 5 0.17
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (18 bp):
AAAAAAAAGGTTTTTCGC
Found at i:2430 original size:16 final size:16
Alignment explanation
Indices: 2411--2456 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
2401 AAGCAAGCGC
2411 ATGAAAAAAAGAGAAA
1 ATGAAAAAAAGAGAAA
2427 ATG-AAAAAAGAAGAAA
1 ATGAAAAAAAG-AGAAA
2443 A--AAGAAAAAGAGAA
1 ATGAA-AAAAAGAGAA
2457 GCTCTAGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (16 bp):
ATGAAAAAAAGAGAAA
Found at i:2456 original size:18 final size:18
Alignment explanation
Indices: 2414--2457 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
2404 CAAGCGCATG
*
2414 AAAAA-AAGAGAAAATGA
1 AAAAAGAAGAGAAAAAGA
2431 AAAAAGAAGA-AAAAAGA
1 AAAAAGAAGAGAAAAAGA
2448 AAAAGAGAAG
1 AAAA-AGAAG
2458 CTCTAGGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.02
Consensus pattern (18 bp):
AAAAAGAAGAGAAAAAGA
Found at i:3512 original size:70 final size:70
Alignment explanation
Indices: 3329--3667 Score: 486
Period size: 71 Copynumber: 4.8 Consensus size: 70
3319 AACACTTTGA
* * * * *
3329 CTTTTCCACAAGTCAAACTCGTTTCCATACGAGTCAGTTCAAACATCGGTTCCATTC-GAGCATT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAG-GCATT
3393 CAGGGG
65 CAGGGG
* *
3399 CTTTTTTCACAAGCCAAACTTGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAGGCATT
1 C-TTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAGGCATT
*
3464 CAAGGG
65 CAGGGG
* * *
3470 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGTTTTGGTTCCATCCAAGCA-TC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAGGCATTC
3534 TAGGGG
66 -AGGGG
* * *
3540 CTTTTTCCACAAGCCAAACTCATTCCCATACGAATCAGTTCAAGCTTTGGTTCCATCCAGGCATT
1 C-TTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAGGCATT
3605 CAGGGG
65 CAGGGG
*
3611 CTTTTCCACAAG-CAAACTCGTTTCCATACGAGTCAGTTCAAGCGTTGGTTCCATCCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCA
3668 AGCAAGATGG
Statistics
Matches: 240, Mismatches: 24, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
69 43 0.18
70 73 0.30
71 121 0.50
72 3 0.01
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (70 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAGGCATTC
AGGGG
Found at i:3583 original size:141 final size:140
Alignment explanation
Indices: 3329--3671 Score: 526
Period size: 141 Copynumber: 2.4 Consensus size: 140
3319 AACACTTTGA
* * * *
3329 CTTTTCCACAAGTCAAACTCGTTTCCATACGAGTCAGTTCAAACATCGGTTCCATTCGAGCATTC
1 CTTTTCCACAAG-CAAACTCGTTTCCATACGAGTCAGTTCAAGCATTGGTTCCATCCAAGCATTC
* ** * *
3394 AGGGGCTTTTTTCACAAGCCAAACTTGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAG
65 AGGGGCTTTTTCCACAAGCCAAACTCATTCCCATACGAATCAGTTCAAGCTTTGGTTCCATCCAG
3459 GCATTCAAGGG
130 GCATTCAAGGG
* **
3470 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGTTTTGGTTCCATCCAAGCA-TC
1 CTTTTCCACAAG-CAAACTCGTTTCCATACGAGTCAGTTCAAGCATTGGTTCCATCCAAGCATTC
3534 TAGGGGCTTTTTCCACAAGCCAAACTCATTCCCATACGAATCAGTTCAAGCTTTGGTTCCATCCA
65 -AGGGGCTTTTTCCACAAGCCAAACTCATTCCCATACGAATCAGTTCAAGCTTTGGTTCCATCCA
*
3599 GGCATTCAGGGG
129 GGCATTCAAGGG
*
3611 CTTTTCCACAAGCAAACTCGTTTCCATACGAGTCAGTTCAAGCGTTGGTTCCATCCAAGCA
1 CTTTTCCACAAGCAAACTCGTTTCCATACGAGTCAGTTCAAGCATTGGTTCCATCCAAGCA
3672 AGATGGACTT
Statistics
Matches: 184, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
140 49 0.27
141 135 0.73
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (140 bp):
CTTTTCCACAAGCAAACTCGTTTCCATACGAGTCAGTTCAAGCATTGGTTCCATCCAAGCATTCA
GGGGCTTTTTCCACAAGCCAAACTCATTCCCATACGAATCAGTTCAAGCTTTGGTTCCATCCAGG
CATTCAAGGG
Found at i:3877 original size:8 final size:8
Alignment explanation
Indices: 3864--3944 Score: 66
Period size: 8 Copynumber: 10.9 Consensus size: 8
3854 GTTGGTCAAT
3864 TTCAATCC
1 TTCAATCC
*
3872 TTCAATAC
1 TTCAATCC
3880 TTCAAT--
1 TTCAATCC
*
3886 TTCAATTC
1 TTCAATCC
3894 TTCAATCC
1 TTCAATCC
3902 TTCAAT--
1 TTCAATCC
* *
3908 ATCAATTC
1 TTCAATCC
*
3916 TTCAA--A
1 TTCAATCC
3922 TTCAATCC
1 TTCAATCC
*
3930 TTCAATGC
1 TTCAATCC
3938 TTCAATC
1 TTCAATC
3945 TCAAATTACA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
6 16 0.27
8 43 0.73
ACGTcount: A:0.31, C:0.27, G:0.01, T:0.41
Consensus pattern (8 bp):
TTCAATCC
Found at i:3884 original size:22 final size:22
Alignment explanation
Indices: 3859--4071 Score: 165
Period size: 22 Copynumber: 9.9 Consensus size: 22
3849 TGACAGTTGG
*
3859 TCAATTTCAATCCTTCAATACT
1 TCAATTTCAATTCTTCAATACT
*
3881 TCAATTTCAATTCTTCAATCCT
1 TCAATTTCAATTCTTCAATACT
*
3903 TCAATATCAATTCTTCAA-A-T
1 TCAATTTCAATTCTTCAATACT
*
3923 TCAATCCTTCAATGCTTCAAT-C-
1 TCAAT--TTCAATTCTTCAATACT
* * *
3945 TCAAATTACAAATGC--CAATGCT
1 TC-AATTTC-AATTCTTCAATACT
**
3967 TCAATTTCGCTTCTTCAATACT
1 TCAATTTCAATTCTTCAATACT
* * *
3989 TCAATTTCCATTTTTCAATTCT
1 TCAATTTCAATTCTTCAATACT
*
4011 TCAATTTCAATAT-TTCAATGCT
1 TCAATTTCAAT-TCTTCAATACT
* *
4033 TCAGTTTCAA-T-TTCAATGCT
1 TCAATTTCAATTCTTCAATACT
* *
4053 TCAAGTTCAATCCTTCAAT
1 TCAATTTCAATTCTTCAAT
4072 TCAATGCTTC
Statistics
Matches: 156, Mismatches: 22, Indels: 26
0.76 0.11 0.13
Matches are distributed among these distances:
20 30 0.19
21 8 0.05
22 114 0.73
23 4 0.03
ACGTcount: A:0.30, C:0.24, G:0.04, T:0.42
Consensus pattern (22 bp):
TCAATTTCAATTCTTCAATACT
Found at i:3889 original size:14 final size:14
Alignment explanation
Indices: 3872--4086 Score: 74
Period size: 14 Copynumber: 15.1 Consensus size: 14
3862 ATTTCAATCC
3872 TTCAATACTTCAAT
1 TTCAATACTTCAAT
*
3886 TTCAATTCTTCAAT
1 TTCAATACTTCAAT
3900 CCTTCAATA--TCAATT
1 --TTCAATACTTCAA-T
3915 CTTCAA-A-TTCAAT
1 -TTCAATACTTCAAT
*
3928 CCTTCAATGCTTCAAT
1 --TTCAATACTTCAAT
*
3944 CTCAA-A-TTACAAAT
1 TTCAATACTT-C-AAT
** *
3958 GCCAATGCTTCAAT
1 TTCAATACTTCAAT
** *
3972 TTCGCTTCTTCAAT
1 TTCAATACTTCAAT
*
3986 ACTTCAAT--TTCCATTT
1 --TTCAATACTT-CA-AT
*
4002 TTCAATTCTTCAAT
1 TTCAATACTTCAAT
*
4016 TTCAATATTTCAAT
1 TTCAATACTTCAAT
*
4030 GCTTCAGT--TTCAAT
1 --TTCAATACTTCAAT
* *
4044 TTCAATGCTTCAAG
1 TTCAATACTTCAAT
*
4058 TTCAATCCTTCAA-
1 TTCAATACTTCAAT
*
4071 TTCAATGCTTCAAT
1 TTCAATACTTCAAT
4085 TT
1 TT
4087 ATCTTTCTTC
Statistics
Matches: 155, Mismatches: 24, Indels: 44
0.70 0.11 0.20
Matches are distributed among these distances:
12 7 0.05
13 15 0.10
14 101 0.65
15 6 0.04
16 26 0.17
ACGTcount: A:0.30, C:0.24, G:0.04, T:0.42
Consensus pattern (14 bp):
TTCAATACTTCAAT
Found at i:3899 original size:36 final size:35
Alignment explanation
Indices: 3859--4149 Score: 126
Period size: 36 Copynumber: 8.2 Consensus size: 35
3849 TGACAGTTGG
*
3859 TCAATTTCAATCCTTCAATACTTCAATTTCAATTCT
1 TCAATTTCAAT-CTTCAATACTTCAATTTCAATGCT
* * * *
3895 TCAATCCTTCAAT-ATCAATTCTTCAAATTCAATCCT
1 TCAAT--TTCAATCTTCAATACTTCAATTTCAATGCT
**
3931 TCAATGCTTCAATC-TCAA-A-TTACAAATGCCAATGCT
1 TCAAT--TTCAATCTTCAATACTT-C-AATTTCAATGCT
** *
3967 TCAATTTCGCTTCTTCAATACTTCAATTTCCA---T
1 TCAATTTC-AATCTTCAATACTTCAATTTCAATGCT
4000 T---TTTCAATTCTTCAAT--TTCAATATTTCAATGCT
1 TCAATTTCAA-TCTTCAATACTTC-A-ATTTCAATGCT
* * * *
4033 TCAGTTTCAAT-TTCAATGCTTCAAGTTCAATCCT
1 TCAATTTCAATCTTCAATACTTCAATTTCAATGCT
* ** *
4067 TCAA-TTCAATGCTTCAAT-TTATCTTTCTTCAATTCT
1 TCAATTTCAAT-CTTCAATACT-TCAAT-TTCAATGCT
* *
4103 TCAATCATCCAATGCTTCAATTCTTCAATAATTCAATGCT
1 TCAAT--TTCAAT-CTTCAATACTTCAAT--TTCAATGCT
4143 TCAATTT
1 TCAATTT
4150 ACTTCAATGA
Statistics
Matches: 193, Mismatches: 33, Indels: 56
0.68 0.12 0.20
Matches are distributed among these distances:
28 3 0.02
29 1 0.01
30 18 0.09
33 10 0.05
34 24 0.12
35 13 0.07
36 83 0.43
37 2 0.01
38 9 0.05
39 16 0.08
40 14 0.07
ACGTcount: A:0.30, C:0.24, G:0.04, T:0.43
Consensus pattern (35 bp):
TCAATTTCAATCTTCAATACTTCAATTTCAATGCT
Found at i:3990 original size:8 final size:7
Alignment explanation
Indices: 3978--4147 Score: 66
Period size: 8 Copynumber: 23.1 Consensus size: 7
3968 CAATTTCGCT
3978 TCTTCAA
1 TCTTCAA
3985 TACTTCAA
1 T-CTTCAA
*
3993 T-TTCCAT
1 TCTT-CAA
*
4000 TTTTCAA
1 TCTTCAA
4007 TTCTTCAA
1 -TCTTCAA
4015 T-TTCAA
1 TCTTCAA
*
4021 TATTTCAA
1 T-CTTCAA
*
4029 TGCTTCAG
1 T-CTTCAA
4037 T-TTCAA
1 TCTTCAA
4043 T-TTCAA
1 TCTTCAA
4049 TGCTTCAA
1 T-CTTCAA
*
4057 -GTTCAA
1 TCTTCAA
4063 TCCTTCAA
1 T-CTTCAA
4071 --TTCAA
1 TCTTCAA
4076 TGCTTCAA
1 T-CTTCAA
* **
4084 TTTATCTT
1 TCT-TCAA
4092 TCTTCAA
1 TCTTCAA
4099 TTCTTCAA
1 -TCTTCAA
*
4107 TCATCCAA
1 TC-TTCAA
4115 TGCTTCAA
1 T-CTTCAA
4123 TTCTTCAA
1 -TCTTCAA
*
4131 TAATTCAA
1 T-CTTCAA
4139 TGCTTCAA
1 T-CTTCAA
4147 T
1 T
4148 TTACTTCAAT
Statistics
Matches: 124, Mismatches: 20, Indels: 37
0.69 0.11 0.20
Matches are distributed among these distances:
5 5 0.04
6 24 0.19
7 13 0.10
8 80 0.65
9 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.45
Consensus pattern (7 bp):
TCTTCAA
Found at i:4055 original size:28 final size:28
Alignment explanation
Indices: 4002--4147 Score: 102
Period size: 28 Copynumber: 5.0 Consensus size: 28
3992 ATTTCCATTT
**
4002 TTCAATTCTTCAATTTCAATATTTCAATG
1 TTCAA-TCTTCAATTTCAATGCTTCAATG
*
4031 CTTCAGT-TTCAATTTCAATGCTTCAA-G
1 -TTCAATCTTCAATTTCAATGCTTCAATG
*
4058 TTCAATCCTTCAA-TTCAATGCTTCAATT
1 TTCAAT-CTTCAATTTCAATGCTTCAATG
** *
4086 TATCTTTCTTCAATTCTTCAAT-CATCCAATG
1 T-TCAATCTTCAA-T-TTCAATGC-TTCAATG
4117 CTTCAATTCTTCAATAATTCAATGCTTCAAT
1 -TTCAA-TCTTCAAT--TTCAATGCTTCAAT
4148 TTACTTCAAT
Statistics
Matches: 91, Mismatches: 13, Indels: 22
0.72 0.10 0.17
Matches are distributed among these distances:
26 5 0.05
27 14 0.15
28 29 0.32
29 4 0.04
30 5 0.05
31 14 0.15
32 19 0.21
33 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.05, T:0.44
Consensus pattern (28 bp):
TTCAATCTTCAATTTCAATGCTTCAATG
Found at i:4123 original size:24 final size:24
Alignment explanation
Indices: 4093--4163 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
4083 ATTTATCTTT
*
4093 CTTCAATTCTTCAATCATCCAATG
1 CTTCAATTCTTCAATAATCCAATG
*
4117 CTTCAATTCTTCAATAATTCAATG
1 CTTCAATTCTTCAATAATCCAATG
*
4141 CTTCAATTTACTTCAATGATCCA
1 CTTCAA-TT-CTTCAATAATCCA
4164 GGGTGATCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 28 0.68
25 2 0.05
26 11 0.27
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.39
Consensus pattern (24 bp):
CTTCAATTCTTCAATAATCCAATG
Found at i:4260 original size:13 final size:14
Alignment explanation
Indices: 4244--4277 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
4234 ATTCTTCAGC
4244 ACTTCAA-TTCAAT
1 ACTTCAATTTCAAT
4257 ACTTCAATTTCAAT
1 ACTTCAATTTCAAT
*
4271 TCTTCAA
1 ACTTCAA
4278 ATTCCAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (14 bp):
ACTTCAATTTCAAT
Found at i:4306 original size:36 final size:36
Alignment explanation
Indices: 4222--4386 Score: 129
Period size: 36 Copynumber: 4.4 Consensus size: 36
4212 CAATGCCCCA
*
4222 GTTTCAATTTCAATTCTTCAGCACTT-C-AAT-TCAAT
1 GTTTCAATTTCAATTCTTCA--AATTCCAAATGTCAAT
** *
4257 ACTTCAATTTCAATTCTTCAAATTCCAAATGCCAAT
1 GTTTCAATTTCAATTCTTCAAATTCCAAATGTCAAT
* * *
4293 GTTTCAATTTCAATCCTTCAATGTTTCAATTTCAATATTTCAAT
1 GTTTCAATTTCAATTCTTC-A------AATTCCAA-ATGTCAAT
* * *
4337 GCTTCAAATCCAATTCTTCAAATTCCAAATGTCAAT
1 GTTTCAATTTCAATTCTTCAAATTCCAAATGTCAAT
4373 GTTTCAATTTCAAT
1 GTTTCAATTTCAAT
4387 ATATCAATGC
Statistics
Matches: 100, Mismatches: 19, Indels: 21
0.71 0.14 0.15
Matches are distributed among these distances:
33 3 0.03
34 1 0.01
35 21 0.21
36 38 0.38
37 8 0.08
43 8 0.08
44 21 0.21
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (36 bp):
GTTTCAATTTCAATTCTTCAAATTCCAAATGTCAAT
Found at i:4314 original size:22 final size:22
Alignment explanation
Indices: 4289--4357 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
4279 TTCCAAATGC
*
4289 CAATGTTTCAATTTCAATCCTT
1 CAATGTTTCAATTTCAATACTT
*
4311 CAATGTTTCAATTTCAATATTT
1 CAATGTTTCAATTTCAATACTT
* * * *
4333 CAATGCTTCAAATCCAATTCTT
1 CAATGTTTCAATTTCAATACTT
4355 CAA
1 CAA
4358 ATTCCAAATG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.32, C:0.22, G:0.04, T:0.42
Consensus pattern (22 bp):
CAATGTTTCAATTTCAATACTT
Found at i:4326 original size:14 final size:14
Alignment explanation
Indices: 4299--4394 Score: 54
Period size: 14 Copynumber: 6.6 Consensus size: 14
4289 CAATGTTTCA
4299 ATTTCAATCCTTCAAT
1 ATTTCAAT--TTCAAT
*
4315 GTTTCAATTTCAAT
1 ATTTCAATTTCAAT
4329 ATTTCAATGCTTCAA-
1 ATTTCAAT--TTCAAT
*
4344 A-TCCAATTCTTCAA-
1 ATTTCAA-T-TTCAAT
* *
4358 ATTCCAAATGTCAAT
1 ATTTC-AATTTCAAT
*
4373 GTTTCAATTTCAAT
1 ATTTCAATTTCAAT
*
4387 ATATCAAT
1 ATTTCAAT
4395 GCTTCAATTT
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
14 42 0.65
15 9 0.14
16 14 0.22
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (14 bp):
ATTTCAATTTCAAT
Found at i:4335 original size:58 final size:58
Alignment explanation
Indices: 4259--4393 Score: 138
Period size: 58 Copynumber: 2.3 Consensus size: 58
4249 AATTCAATAC
* *
4259 TTCAATTTCAAT-TCTTCAAAT-TCCAAATGCCAATGT-TTC-AATTTC-AATCCTTCAATGT
1 TTCAATTTCAATAT-TTCAAATCTCCAAAT-CCAAT-TCTTCAAATTCCAAAT--GTCAATGT
*
4317 TTCAATTTCAATATTTC-AATGCTTCAAATCCAATTCTTCAAATTCCAAATGTCAATGT
1 TTCAATTTCAATATTTCAAAT-CTCCAAATCCAATTCTTCAAATTCCAAATGTCAATGT
*
4375 TTCAATTTCAATATATCAA
1 TTCAATTTCAATATTTCAA
4394 TGCTTCAATT
Statistics
Matches: 66, Mismatches: 4, Indels: 13
0.80 0.05 0.16
Matches are distributed among these distances:
57 4 0.06
58 46 0.70
59 13 0.20
60 3 0.05
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (58 bp):
TTCAATTTCAATATTTCAAATCTCCAAATCCAATTCTTCAAATTCCAAATGTCAATGT
Found at i:4352 original size:80 final size:80
Alignment explanation
Indices: 4251--4442 Score: 262
Period size: 80 Copynumber: 2.4 Consensus size: 80
4241 AGCACTTCAA
* *
4251 TTCAATACTTCAATTTCAATTCTTCAAATTCCAAATGCCAATGTTTCAATTTCAATCCT-TCAAT
1 TTCAATGCTTCAATTTCAATTCTTCAAATTCCAAATGCCAATGTTTCAATTTCAAT-ATATCAAT
*
4315 GTTTCAATTTCAATAT-
65 GCTTCAATTTCAAT-TC
* * *
4331 TTCAATGCTTCAAATCCAATTCTTCAAATTCCAAATGTCAATGTTTCAATTTCAATATATCAATG
1 TTCAATGCTTCAATTTCAATTCTTCAAATTCCAAATGCCAATGTTTCAATTTCAATATATCAATG
*
4396 CTTCAATTTCGATTC
66 CTTCAATTTCAATTC
* *
4411 TTCCATTGCTTCAATTTCAATTCTTCGAATTC
1 TT-CAATGCTTCAATTTCAATTCTTCAAATTC
4443 AGTGTTTCAA
Statistics
Matches: 98, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
79 2 0.02
80 71 0.72
81 25 0.26
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.42
Consensus pattern (80 bp):
TTCAATGCTTCAATTTCAATTCTTCAAATTCCAAATGCCAATGTTTCAATTTCAATATATCAATG
CTTCAATTTCAATTC
Found at i:4378 original size:22 final size:23
Alignment explanation
Indices: 4347--4401 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
4337 GCTTCAAATC
* *
4347 CAATTCTTCAAATTCCAA-ATGT
1 CAATGCTTCAAATTCCAATATAT
* *
4369 CAATGTTTC-AATTTCAATATAT
1 CAATGCTTCAAATTCCAATATAT
4391 CAATGCTTCAA
1 CAATGCTTCAA
4402 TTTCGATTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 7 0.27
22 18 0.69
23 1 0.04
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.38
Consensus pattern (23 bp):
CAATGCTTCAAATTCCAATATAT
Found at i:4402 original size:22 final size:22
Alignment explanation
Indices: 4368--4433 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
4358 ATTCCAAATG
*
4368 TCAATGTTTCAATTTCAATAT-A
1 TCAATGCTTCAATTTCAAT-TCA
* *
4390 TCAATGCTTCAATTTCGATTCT
1 TCAATGCTTCAATTTCAATTCA
*
4412 TCCATTGCTTCAATTTCAATTC
1 T-CAATGCTTCAATTTCAATTC
4434 TTCGAATTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 1 0.03
22 18 0.49
23 18 0.49
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.45
Consensus pattern (22 bp):
TCAATGCTTCAATTTCAATTCA
Found at i:4871 original size:30 final size:30
Alignment explanation
Indices: 4827--4907 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 30
4817 AGCTTGCATT
4827 TTGCATAC-TGCATTACTTCAATTTTAACA
1 TTGCATACATGCATTACTTCAATTTTAACA
4856 TTGCATACATGCATTAGCATTACTTCAATTTTAACA
1 TTGCAT--A--CA-T-GCATTACTTCAATTTTAACA
*
4892 TTGTATACATGCATTA
1 TTGCATACATGCATTA
4908 AGATATCATA
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
29 6 0.14
30 6 0.14
31 2 0.05
32 2 0.05
33 1 0.02
34 1 0.02
35 1 0.02
36 25 0.57
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.41
Consensus pattern (30 bp):
TTGCATACATGCATTACTTCAATTTTAACA
Found at i:4876 original size:36 final size:36
Alignment explanation
Indices: 4836--4907 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
4826 TTTGCATACT
4836 GCATTACTTCAATTTTAACATTGCATACATGCATTA
1 GCATTACTTCAATTTTAACATTGCATACATGCATTA
*
4872 GCATTACTTCAATTTTAACATTGTATACATGCATTA
1 GCATTACTTCAATTTTAACATTGCATACATGCATTA
4908 AGATATCATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.40
Consensus pattern (36 bp):
GCATTACTTCAATTTTAACATTGCATACATGCATTA
Found at i:10115 original size:27 final size:27
Alignment explanation
Indices: 10084--10156 Score: 94
Period size: 26 Copynumber: 2.7 Consensus size: 27
10074 AAGTGGACTT
*
10084 AAAATGACCAAAATGCCCCTGAATGTG
1 AAAATGACCAAAATGCCCCTGAATGTA
* * * *
10111 CAAATGACCAGAATG-CCCTTAGTGTA
1 AAAATGACCAAAATGCCCCTGAATGTA
10137 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
10157 ATATGACCCT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 21 0.55
27 17 0.45
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATGTA
Found at i:11161 original size:22 final size:22
Alignment explanation
Indices: 11136--11187 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
11126 AGAGACGGAG
11136 AGAGACACACATACACAGAGAT
1 AGAGACACACATACACAGAGAT
** * *
11158 AGAGGGAGAGATACACAGAGAT
1 AGAGACACACATACACAGAGAT
*
11180 ATAGACAC
1 AGAGACAC
11188 GCAGAGGGGC
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.17, G:0.25, T:0.10
Consensus pattern (22 bp):
AGAGACACACATACACAGAGAT
Found at i:21462 original size:85 final size:87
Alignment explanation
Indices: 21355--21583 Score: 347
Period size: 85 Copynumber: 2.7 Consensus size: 87
21345 AAATTGTTAA
*
21355 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAG-T
1 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAA
*
21419 AATAAATTAATAATAAA-AT-T
66 AATAAATAAATAATAAAGATAT
* * * * *
21439 GAATAGTAATCAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAGGA
1 -AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
*
21504 AAATAAATAAATTATAAAGATAT
65 AAATAAATAAATAATAAAGATAT
*
21527 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATAT
1 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATAT
21584 AAAAAAGGAA
Statistics
Matches: 128, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
85 58 0.45
86 15 0.12
87 54 0.42
88 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (87 bp):
AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAA
AATAAATAAATAATAAAGATAT
Done.