Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008878.1 Corchorus capsularis cultivar CVL-1 contig08899, 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: 35906
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:1910 original size:23 final size:22
Alignment explanation
Indices: 1884--1934 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1874 GAAATTTTAT
*
1884 TAACCAACACTATGAGATGTTGA
1 TAACCAACA-TATGAGATATTGA
** *
1907 TAACCTCCATATGATATATTGA
1 TAACCAACATATGAGATATTGA
1929 TAACCA
1 TAACCA
1935 CGTTATGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (22 bp):
TAACCAACATATGAGATATTGA
Found at i:1998 original size:22 final size:22
Alignment explanation
Indices: 1973--2041 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
1963 GAATTGTTAG
*
1973 TAATCACACTTTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
1995 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* * *
2017 TAACCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
2039 TAA
1 TAA
2042 ATCTTCCTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:2106 original size:45 final size:45
Alignment explanation
Indices: 1986--2108 Score: 121
Period size: 45 Copynumber: 2.8 Consensus size: 45
1976 TCACACTTTG
* * *
1986 AAATTTTGAT-AATC-ACACTATGAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAATCTTC-CTATGAAATT-TGATAAACCTCCCTATA
2030 AAATTTTGATAAATCTTCCTAT-AAAGTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATGAAA-TTTGATAAACCTCCCTATA
* * *
2075 AAATTTTGCTAACT-TTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTCCTATGAAAT-TTGATAA
2109 CTACAAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
44 24 0.36
45 42 0.63
46 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (45 bp):
AAATTTTGATAAATCTTCCTATGAAATTTGATAAACCTCCCTATA
Found at i:2224 original size:22 final size:21
Alignment explanation
Indices: 1984--2277 Score: 142
Period size: 22 Copynumber: 13.6 Consensus size: 21
1974 AATCACACTT
* *
1984 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAA-CTCTCTA
* *
2006 TGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAA-CTCTCTA
*
2028 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGATAACTC-T-CTA
* *
2051 T-AAAGTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AA-CTCTCTA
* * *
2073 TAAAATTTTGCTAACTTTCTTA
1 TGAAATTTTGATAACTCTC-TA
*
2095 TGAAATCTTGATAA----CTA
1 TGAAATTTTGATAACTCTCTA
* * *
2112 -CAAATTTTAATAACTTCCCTA
1 TGAAATTTTGATAAC-TCTCTA
**
2133 TGATTTTTTGATAAC-CTCATTA
1 TGAAATTTTGATAACTCTC--TA
* *
2155 TG-AATGTTTGTTAATCTCCCTA
1 TGAAAT-TTTGATAA-CTCTCTA
2177 TGAAATTTTGAT--CTACATACTA
1 TGAAATTTTGATAACT-C-T-CTA
*
2199 TGAAATTTTGATAACTCTCTTG
1 TGAAATTTTGATAACTCTC-TA
* **
2221 TGAAATTTTGAAAACTAAACTA
1 TGAAATTTTGATAACT-CTCTA
2243 TGAAATTTTGATAAC-CTTCATA
1 TGAAATTTTGATAACTC-TC-TA
2265 TGAAATTTTGATA
1 TGAAATTTTGATA
2278 TCCTCCCTGA
Statistics
Matches: 206, Mismatches: 39, Indels: 54
0.69 0.13 0.18
Matches are distributed among these distances:
16 10 0.05
17 2 0.01
18 1 0.00
19 2 0.01
20 3 0.01
21 11 0.05
22 151 0.73
23 20 0.10
24 6 0.03
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (21 bp):
TGAAATTTTGATAACTCTCTA
Found at i:2312 original size:20 final size:19
Alignment explanation
Indices: 2267--2315 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
2257 CCTTCATATG
2267 AAATTTTGATATCCTCCCT
1 AAATTTTGATATCCTCCCT
* *
2286 GAATTTTGATATCCTCCTT
1 AAATTTTGATATCCTCCCT
2305 AAAATTTTGAT
1 -AAATTTTGAT
2316 TAATTCATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (19 bp):
AAATTTTGATATCCTCCCT
Found at i:2510 original size:66 final size:66
Alignment explanation
Indices: 2421--2568 Score: 165
Period size: 66 Copynumber: 2.2 Consensus size: 66
2411 AATCACATTT
* * * * * * **
2421 TGAAAATTTGATAA-CCTCTTTATGAAATTTTGATAACCTC-TTTATAAAATTTTGTTGACCCCA
1 TGAAATTTTGATAATCC-CATTATGAAATTATGATAACCTCGCTT-TAAAATTTTGATAACAACA
2484 CTA
64 CTA
* * *
2487 TGAAATTTTTATAATCCCATTATGTAATTATGATAACCTCGCTTTGAAATTTTGATAACAACACT
1 TGAAATTTTGATAATCCCATTATGAAATTATGATAACCTCGCTTTAAAATTTTGATAACAACACT
2552 A
66 A
2553 TGAAATTTTGATAATC
1 TGAAATTTTGATAATC
2569 TTTCTATAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
66 64 0.94
67 4 0.06
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (66 bp):
TGAAATTTTGATAATCCCATTATGAAATTATGATAACCTCGCTTTAAAATTTTGATAACAACACT
A
Found at i:2559 original size:88 final size:88
Alignment explanation
Indices: 2393--2562 Score: 218
Period size: 88 Copynumber: 1.9 Consensus size: 88
2383 CCCAGAAATA
* * *
2393 CCACTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAAC
1 CCACTATGAAATTTTTATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAAC
** **
2458 CTCTTTATAAAATTTTGTTGACC
66 AACACTATAAAATTTTGTTGACC
* *
2481 CCACTATGAAATTTTTATAATCCCATTATG-TAATTATGATAACCTCGCTT-TGAAATTTTGATA
1 CCACTATGAAATTTTTATAATCACATTATGAAAATT-TGATAACCTC-CTTATGAAATTTTGATA
*
2544 ACAACACTATGAAATTTTG
64 ACAACACTATAAAATTTTG
2563 ATAATCTTTC
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 4 0.06
88 64 0.91
89 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.41
Consensus pattern (88 bp):
CCACTATGAAATTTTTATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAAC
AACACTATAAAATTTTGTTGACC
Found at i:2575 original size:22 final size:22
Alignment explanation
Indices: 2396--2667 Score: 139
Period size: 22 Copynumber: 12.5 Consensus size: 22
2386 AGAAATACCA
*
2396 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATCTC-T
* * *
2419 -TTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCTCT
* *
2440 TTATGAAATTTTGATAACCTCT
1 CTATGAAATTTTGATAATCTCT
* * * * * * *
2462 TTATAAAATTTTGTTGACCCCA
1 CTATGAAATTTTGATAATCTCT
* *
2484 CTATGAAATTTTTATAATCCCAT
1 CTATGAAATTTTGATAATCTC-T
* * * *
2507 -TATGTAATTATGATAACCTCG
1 CTATGAAATTTTGATAATCTCT
* * *
2528 CTTTGAAATTTTGATAA-CAACA
1 CTATGAAATTTTGATAATC-TCT
*
2550 CTATGAAATTTTGATAATCTTT
1 CTATGAAATTTTGATAATCTCT
*
2572 CTAT-AAATTTTGATGATTCGATCT
1 CTATGAAATTTTGAT-AATC--TCT
* *
2596 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATCTCT
* *
2618 CTATGAGA-TTTGATAACCT-T
1 CTATGAAATTTTGATAATCTCT
* * *
2638 CTATCAAATTTTGGTACTC-CT
1 CTATGAAATTTTGATAATCTCT
2659 -TATGAAATT
1 CTATGAAATT
2668 AAGACTTTTA
Statistics
Matches: 189, Mismatches: 48, Indels: 27
0.72 0.18 0.10
Matches are distributed among these distances:
20 15 0.08
21 32 0.17
22 123 0.65
23 1 0.01
24 9 0.05
25 9 0.05
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCTCT
Found at i:2702 original size:22 final size:21
Alignment explanation
Indices: 2673--2728 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
2663 AAATTAAGAC
2673 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* * *
2694 TTTTGATAACCACGCTATAAAA
1 TTTTGATAACCTC-ATATGAAA
2716 TTTTGATAACCTC
1 TTTTGATAACCTC
2729 CCCATGAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 5 0.17
22 24 0.83
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:2738 original size:22 final size:22
Alignment explanation
Indices: 2688--2738 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2678 TAACCTTCAT
* *
2688 ATGAAATTTTGATAACCACGCT
1 ATGAAATTTTGATAACCACCCC
* *
2710 ATAAAATTTTGATAACCTCCCC
1 ATGAAATTTTGATAACCACCCC
2732 ATGAAAT
1 ATGAAAT
2739 ATTTAATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACCCC
Found at i:2920 original size:22 final size:22
Alignment explanation
Indices: 2892--3042 Score: 153
Period size: 22 Copynumber: 6.9 Consensus size: 22
2882 TAACTTGATC
2892 CTATGAAATTTTGGTAACCATA
1 CTATGAAATTTTGGTAACCATA
*
2914 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCATA
* *
2936 CAATGGAATTTTGGTAACCATA
1 CTATGAAATTTTGGTAACCATA
* *
2958 CTCTGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCATA
* * *
2980 CTATGGAATTTTGATAACC-TC
1 CTATGAAATTTTGGTAACCATA
** * **
3001 CTCCGAAATTATAATAACCAT-
1 CTATGAAATTTTGGTAACCATA
*
3022 CTTATGAAATTTTGATAACCA
1 C-TATGAAATTTTGGTAACCA
3043 CATAGAGACA
Statistics
Matches: 105, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
21 15 0.14
22 90 0.86
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.34
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCATA
Found at i:2948 original size:44 final size:44
Alignment explanation
Indices: 2898--2998 Score: 175
Period size: 44 Copynumber: 2.3 Consensus size: 44
2888 GATCCTATGA
2898 AATTTTGGTAACCATACTATGAAATTTTGGTAACCACACAATGG
1 AATTTTGGTAACCATACTATGAAATTTTGGTAACCACACAATGG
* *
2942 AATTTTGGTAACCATACTCTGAAATTTTGGTAACCACACTATGG
1 AATTTTGGTAACCATACTATGAAATTTTGGTAACCACACAATGG
*
2986 AATTTTGATAACC
1 AATTTTGGTAACC
2999 TCCTCCGAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (44 bp):
AATTTTGGTAACCATACTATGAAATTTTGGTAACCACACAATGG
Found at i:3457 original size:32 final size:31
Alignment explanation
Indices: 3421--3486 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 31
3411 TTAGTAATGG
*
3421 CAATTTCGAAATATGTTTTAAAGAA-AATGGTA
1 CAATTT-GAAATATGTTTTAAA-AATAAGGGTA
*
3453 CAA-TTGGAATATGTTTTAAAAATAAGGGTA
1 CAATTTGAAATATGTTTTAAAAATAAGGGTA
3483 CAAT
1 CAAT
3487 CGGAAAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
29 2 0.07
30 23 0.77
31 2 0.07
32 3 0.10
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (31 bp):
CAATTTGAAATATGTTTTAAAAATAAGGGTA
Found at i:3464 original size:30 final size:30
Alignment explanation
Indices: 3430--3491 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
3420 GCAATTTCGA
* *
3430 AATATGTTTTAAAGAA-AATGGTACAATTGG
1 AATATGTTTTAAA-AATAAGGGTACAATCGG
3460 AATATGTTTTAAAAATAAGGGTACAATCGG
1 AATATGTTTTAAAAATAAGGGTACAATCGG
3490 AA
1 AA
3492 AACATAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.31
Consensus pattern (30 bp):
AATATGTTTTAAAAATAAGGGTACAATCGG
Found at i:5931 original size:29 final size:30
Alignment explanation
Indices: 5899--5961 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
5889 ATGTTTTGTC
* *
5899 CCCTAAACT-TCAATTTTGGACATTTTACT
1 CCCTAAACTCTCAAGTTTGGACACTTTACT
* *
5928 CCCTAAACTCTTAAGTTTGGACGCTTTACT
1 CCCTAAACTCTCAAGTTTGGACACTTTACT
5958 CCCT
1 CCCT
5962 TTCAACAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 9 0.31
30 20 0.69
ACGTcount: A:0.24, C:0.29, G:0.10, T:0.38
Consensus pattern (30 bp):
CCCTAAACTCTCAAGTTTGGACACTTTACT
Found at i:11906 original size:81 final size:81
Alignment explanation
Indices: 11785--11992 Score: 299
Period size: 81 Copynumber: 2.6 Consensus size: 81
11775 TACTGGAGTT
* * * *
11785 TTTTCCTTTTGGGGCTCTTGCCATGATCATGAGGTGCCGACTTGTATCCAAAGAAGTCATCATTC
1 TTTTCCTTTTAGGGCTCTTGCCATGACCATGAGGTACCGACTTGTATCCAAAGAAGTCATCATCC
*
11850 TCATCATACATAAATG
66 TCATCATACAGAAATG
* *
11866 TTTTCCTTTTAGGGCTCTTGCCATGACCATTAGGTACCGACTTGTATCCAAAGAAGTCATCGTCC
1 TTTTCCTTTTAGGGCTCTTGCCATGACCATGAGGTACCGACTTGTATCCAAAGAAGTCATCATCC
* *
11931 TCTTCGTACAGAAATG
66 TCATCATACAGAAATG
* * * *
11947 TTTTCCTTTTAGGGCTCTTGCCATGATCACGAGGTGCAGACTTGTA
1 TTTTCCTTTTAGGGCTCTTGCCATGACCATGAGGTACCGACTTGTA
11993 CCCCCAGATG
Statistics
Matches: 113, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 113 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.35
Consensus pattern (81 bp):
TTTTCCTTTTAGGGCTCTTGCCATGACCATGAGGTACCGACTTGTATCCAAAGAAGTCATCATCC
TCATCATACAGAAATG
Found at i:24406 original size:157 final size:157
Alignment explanation
Indices: 24120--24409 Score: 553
Period size: 157 Copynumber: 1.8 Consensus size: 157
24110 TGCTACCTGC
*
24120 GGGAGATATATCATGGGATAAAATAATCTAAGTCTTTCCCATACCCAGGGAAGGCCGCCCTATGA
1 GGGAGATATATCATGGGATAAAATAATCTAAGTCTTTCCCATACCCAGGGAAGGCCACCCTATGA
24185 CTATCATAGTCATAAGATGCAATATCCTCATCCCTTGCACTGAGGAGGCAGAGAGTAAGAGAGTA
66 CTATCATAGTCATAAGATGCAATATCCTCATCCCTTGCACTGAGGAGGCAGAGAGTAAGAGAGTA
24250 TCAGCAATGCTACCTGACCATGCAGGT
131 TCAGCAATGCTACCTGACCATGCAGGT
*
24277 GGGAGATATATCATGGGATAAAATAATCTAAGTCTTTCCCATACCTAGGGAAGGCCACCCTATGA
1 GGGAGATATATCATGGGATAAAATAATCTAAGTCTTTCCCATACCCAGGGAAGGCCACCCTATGA
*
24342 CTATCATAGTCATAAGATGCAATCTCCTCATCCCTTGCACTGAGGAGGCAGAGAGTAAGAGAGTA
66 CTATCATAGTCATAAGATGCAATATCCTCATCCCTTGCACTGAGGAGGCAGAGAGTAAGAGAGTA
24407 TCA
131 TCA
24410 ATGACTATCA
Statistics
Matches: 130, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
157 130 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.23
Consensus pattern (157 bp):
GGGAGATATATCATGGGATAAAATAATCTAAGTCTTTCCCATACCCAGGGAAGGCCACCCTATGA
CTATCATAGTCATAAGATGCAATATCCTCATCCCTTGCACTGAGGAGGCAGAGAGTAAGAGAGTA
TCAGCAATGCTACCTGACCATGCAGGT
Found at i:24455 original size:72 final size:72
Alignment explanation
Indices: 24338--24481 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
24328 AGGCCACCCT
24338 ATGACTATCATAGTCATAAGATGCAATCTCCTCATCCCTTGCACTGAGGAGGCAGAGAGTAAGAG
1 ATGACTATCATAGTCATAAGATGCAATCTCCTCATCCCTTGCACTGAGGAGGCAGAGAGTAAGAG
24403 AGTATCA
66 AGTATCA
24410 ATGACTATCATAGTCATAAGATGCAATCTCCTCATCCCTTGCACTGAGGAGGCAGAGAGTAAGAG
1 ATGACTATCATAGTCATAAGATGCAATCTCCTCATCCCTTGCACTGAGGAGGCAGAGAGTAAGAG
24475 AGTATCA
66 AGTATCA
24482 GTAAGTGAAA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (72 bp):
ATGACTATCATAGTCATAAGATGCAATCTCCTCATCCCTTGCACTGAGGAGGCAGAGAGTAAGAG
AGTATCA
Found at i:25533 original size:20 final size:20
Alignment explanation
Indices: 25508--25546 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
25498 AGAAGAGTTC
25508 GCCTTCCTCAGCAAGTAAAT
1 GCCTTCCTCAGCAAGTAAAT
25528 GCCTTCCTCAGCAAGTAAA
1 GCCTTCCTCAGCAAGTAAA
25547 GCCCACCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (20 bp):
GCCTTCCTCAGCAAGTAAAT
Found at i:29800 original size:231 final size:230
Alignment explanation
Indices: 29397--29824 Score: 732
Period size: 231 Copynumber: 1.9 Consensus size: 230
29387 GCTGGCCCGT
*
29397 CCAAATAAATTTGCCATGTGGACAGAAAATGCCACGTGTGTTGGCCCAAATAAACAGTAAAATGC
1 CCAAATAAATTTGCCACGTGGACAGAAAATGCCACGTGTGTTGGCCCAAATAAACAGTAAAATGC
** *
29462 TAATTTAAAGTTTTTCTTTTTCGGAGAGGGGTTGTTCTCTTGTTCGCAAAGATCTAGGAGCAACA
66 TAATTTAAAGTTTTTCTTTTTCCAAGAGGGGTTGTTCTCTTGTTCGCAAAGATCCAGGAGCAACA
*
29527 CAATCAAAGAGGTTGAAGAGTTCCATGATTTTATTCTGCATTATAGTTCATGTAAGACCAATTTG
131 CAATCAAAGAGATTGAAGAGTTCCATGATTTTATTCTGCATTATAGTTCATGTAAGACCAATTTG
29592 TCAAAAAAAAAAAAAAAAACCCCACGTGTGCTGGC
196 TCAAAAAAAAAAAAAAAAACCCCACGTGTGCTGGC
* *
29627 CCAAATAAATTTGCCACGTGGACAGAAAATGCCACGTGTGTTGGCCTAAATAAACAGTAACATGC
1 CCAAATAAATTTGCCACGTGGACAGAAAATGCCACGTGTGTTGGCCCAAATAAACAGTAAAATGC
* * *
29692 TAATTTAAGGTATTTTCTTTTTCCAAGAGGGGTTGTTCTCTTGTTCGCAACGATCCAGGAGCAAT
66 TAATTTAAAGT-TTTTCTTTTTCCAAGAGGGGTTGTTCTCTTGTTCGCAAAGATCCAGGAGCAAC
*
29757 ACAATCAGAGAGATTGAAGAGTTCCATGATTTTACTT-TGCATTATAGTTCATGTAAGACCAATT
130 ACAATCAAAGAGATTGAAGAGTTCCATGATTTTA-TTCTGCATTATAGTTCATGTAAGACCAATT
29821 TGTC
194 TGTC
29825 TGTAGGTCTT
Statistics
Matches: 185, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
230 72 0.39
231 111 0.60
232 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (230 bp):
CCAAATAAATTTGCCACGTGGACAGAAAATGCCACGTGTGTTGGCCCAAATAAACAGTAAAATGC
TAATTTAAAGTTTTTCTTTTTCCAAGAGGGGTTGTTCTCTTGTTCGCAAAGATCCAGGAGCAACA
CAATCAAAGAGATTGAAGAGTTCCATGATTTTATTCTGCATTATAGTTCATGTAAGACCAATTTG
TCAAAAAAAAAAAAAAAAACCCCACGTGTGCTGGC
Found at i:35885 original size:2 final size:2
Alignment explanation
Indices: 35878--35906 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35868 AATTTCGTTT
35878 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
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
Done.