Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012613.1 Corchorus capsularis cultivar CVL-1 contig12634, 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: 20025
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Found at i:1579 original size:225 final size:224
Alignment explanation
Indices: 1160--1583 Score: 627
Period size: 225 Copynumber: 1.9 Consensus size: 224
1150 AATTGTGAAG
* * * *
1160 TTGATGTTTTAGGCCTTGAAGAAAGCTTTCAAATGAGCTCTACTAACTCCAAAATACGTTATCTG
1 TTGATATTGTAGGCCTTGAAGAAAGCTTTCAAATGAACTCTACTAACTCCAAAATACGTCATCTG
* *
1225 AGCATTGGTTACACAAATAACGCATTCAGAGTGATCATTTTCTCAAGAACAACGTTCTGTGCACA
66 AGCATTGGTTACACAAAAAACGCATTCAAAGTGATCATTTTCTCAAGAACAA---TCTGTGCACA
*
1290 AACTTGCAAAATCGTGAAGAACAAGTTTTAGGTTTTGAAGAAAGTTTTCTTTGACAAACCCACTT
128 AACGTGCAAAATCGTGAAGAACAAGTTTTAGGTTTTGAAGAAAGTTTTCTTTGACAAACCCACTT
1355 TTCATGAGCTTACTCACCCTGAAACACAACAT
193 TTCATGAGCTTACTCACCCTGAAACACAACAT
* * * *
1387 TTGATATTGTAGGCTTTGAAGATTAAGCTTTCAAATGAACTCTACTAACTTCGAATTACGTCATC
1 TTGATATTGTAGGCCTTGAAGA--AAGCTTTCAAATGAACTCTACTAACTCCAAAATACGTCATC
* **
1452 TGTGTGTTGGTTACACAAAAAAACGCATTCAAAGTGATCATTTTCTCAAGAACAA-C-GTGCACA
64 TGAGCATTGGTTACAC-AAAAAACGCATTCAAAGTGATCATTTTCTCAAGAACAATCTGTGCACA
* * *
1515 AACGTGCAAAATCGTGGAGATCAAGTTTTAGGTTTTGAAGAAAGTTTTCTTTGACAAGCCCACTT
128 AACGTGCAAAATCGTGAAGAACAAGTTTTAGGTTTTGAAGAAAGTTTTCTTTGACAAACCCACTT
1580 TTCA
193 TTCA
1584 ACAGTATGTA
Statistics
Matches: 177, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
225 72 0.41
226 1 0.01
227 19 0.11
229 49 0.28
230 36 0.20
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (224 bp):
TTGATATTGTAGGCCTTGAAGAAAGCTTTCAAATGAACTCTACTAACTCCAAAATACGTCATCTG
AGCATTGGTTACACAAAAAACGCATTCAAAGTGATCATTTTCTCAAGAACAATCTGTGCACAAAC
GTGCAAAATCGTGAAGAACAAGTTTTAGGTTTTGAAGAAAGTTTTCTTTGACAAACCCACTTTTC
ATGAGCTTACTCACCCTGAAACACAACAT
Found at i:1929 original size:22 final size:21
Alignment explanation
Indices: 1860--1949 Score: 67
Period size: 22 Copynumber: 4.2 Consensus size: 21
1850 AATAACCTTT
* * *
1860 CTATGAAAATTTGATAACCAGA
1 CTAT-AAATTTTGATAATCACA
** *
1882 CTATGAAATTTTGATAATTTCC
1 CTAT-AAATTTTGATAATCACA
1904 CTATAAGATTTTGATAATCACA
1 CTATAA-ATTTTGATAATCACA
*
1926 CTATATAA--TTGCTAATCACA
1 CTATA-AATTTTGATAATCACA
1946 CTAT
1 CTAT
1950 GAAAATTATA
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 15 0.27
21 2 0.04
22 38 0.68
23 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.37
Consensus pattern (21 bp):
CTATAAATTTTGATAATCACA
Found at i:1961 original size:20 final size:20
Alignment explanation
Indices: 1914--1961 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1904 CTATAAGATT
*
1914 TTGATAATCACACTATATAA
1 TTGATAATCACACTATAAAA
*
1934 TTGCTAATCACACTATGAAAA
1 TTGATAATCACACTAT-AAAA
1955 TT-ATAAT
1 TTGATAAT
1962 AACCACACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (20 bp):
TTGATAATCACACTATAAAA
Found at i:2225 original size:22 final size:22
Alignment explanation
Indices: 2200--2340 Score: 90
Period size: 22 Copynumber: 6.4 Consensus size: 22
2190 ACCTCCCTAG
**
2200 GAAATTTTGATAATCTTTTTAT
1 GAAATTTTGATAATCTTAATAT
* * * **
2222 GAAAATTAGGT-ATCCTTTGTAT
1 GAAATTTTGATAAT-CTTAATAT
2244 GAAATTTTGATAA-C-TACACTAT
1 GAAATTTTGATAATCTTA-A-TAT
* *
2266 GAAGTTTTGATAATCTTCATAT
1 GAAATTTTGATAATCTTAATAT
* ** *
2288 GAAATTTTGGTAATCACACTAT
1 GAAATTTTGATAATCTTAATAT
* *
2310 GAAATTTTGATAACCTTCATAT
1 GAAATTTTGATAATCTTAATAT
*
2332 GTAATTTTG
1 GAAATTTTG
2341 GTTTGATTGT
Statistics
Matches: 89, Mismatches: 24, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
20 1 0.01
21 3 0.03
22 81 0.91
23 3 0.03
24 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (22 bp):
GAAATTTTGATAATCTTAATAT
Found at i:2341 original size:44 final size:44
Alignment explanation
Indices: 2241--2342 Score: 152
Period size: 44 Copynumber: 2.3 Consensus size: 44
2231 GTATCCTTTG
* * *
2241 TATGAAATTTTGATAACTACACTATGAAGTTTTGATAATCTTCA
1 TATGAAATTTTGGTAACTACACTATGAAATTTTGATAACCTTCA
2285 TATGAAATTTTGGTAA-TCACACTATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGGTAACT-ACACTATGAAATTTTGATAACCTTCA
*
2329 TATGTAATTTTGGT
1 TATGAAATTTTGGT
2343 TTGATTGTCA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
43 1 0.02
44 52 0.98
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (44 bp):
TATGAAATTTTGGTAACTACACTATGAAATTTTGATAACCTTCA
Found at i:2546 original size:29 final size:30
Alignment explanation
Indices: 2512--2569 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
2502 ATTAACAGTC
* *
2512 AAATAAGCTCATGAACTA-CAATTGTGGCT
1 AAATAAACCCATGAACTACCAATTGTGGCT
*
2541 AAATAAACCCATGAACTACCAATTTTGGC
1 AAATAAACCCATGAACTACCAATTGTGGC
2570 AAAAATTACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.26
Consensus pattern (30 bp):
AAATAAACCCATGAACTACCAATTGTGGCT
Found at i:2907 original size:29 final size:30
Alignment explanation
Indices: 2858--2914 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
2848 TTGATCTGGT
* *
2858 CAAAATTGCTAGTTCAGGGGCTTGTTTGGC
1 CAAAATTGCAAGTTCAGGGGCTTATTTGGC
*
2888 CAAAATTG-AAGTTCATGGGCTTATTTG
1 CAAAATTGCAAGTTCAGGGGCTTATTTG
2915 ACCATTGGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.35
Consensus pattern (30 bp):
CAAAATTGCAAGTTCAGGGGCTTATTTGGC
Found at i:4010 original size:5 final size:5
Alignment explanation
Indices: 4000--4025 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3990 TATATAGTAG
4000 TAAGA TAAGA TAAGA TAAGA TAAGA T
1 TAAGA TAAGA TAAGA TAAGA TAAGA T
4026 TTGTTAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (5 bp):
TAAGA
Found at i:5036 original size:16 final size:16
Alignment explanation
Indices: 4997--5036 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
4987 TTTTTTATCA
*
4997 AATAATCATTTTCATT
1 AATAATTATTTTCATT
5013 AATAATTATTTTCATT
1 AATAATTATTTTCATT
*
5029 AATCATTA
1 AATAATTA
5037 CAAACATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (16 bp):
AATAATTATTTTCATT
Found at i:8818 original size:2 final size:2
Alignment explanation
Indices: 8811--8845 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
8801 GTGTAATACA
8811 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8846 CCATTCTCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13302 original size:99 final size:89
Alignment explanation
Indices: 13140--13329 Score: 238
Period size: 99 Copynumber: 2.0 Consensus size: 89
13130 CATACTTGGA
* *
13140 TTTTCTTAAAAATTGGAGATTTGACTTCGTACGTAATTGTTATATGAATTCATGACATGAGTAAG
1 TTTTCTTAAAAATTGAAGATTTGACTTAGTACGTAATTGTTATATGAATTCATGACATGAGTAAG
*
13205 ACATTATTTTTTTTAA-CGTTAACT
66 ACATTA-TTTTTTTAACCGATAACT
*
13229 TTTTCTTAAAAATTGAAGATTTGACTAGTTAGTACGTAATTGTTATATATATGAATTGATCCTGA
1 TTTTCTTAAAAATTGAAGATTTGAC---TTAGTACGTAATTG---T-TATATGAA-T--TCATGA
13294 CATGAGTAAGACATTATTTTTTTAACCGATAACT
56 CATGAGTAAGACATTATTTTTTTAACCGATAACT
13328 TT
1 TT
13330 ATCCTTTACA
Statistics
Matches: 86, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
89 24 0.28
92 13 0.15
95 1 0.01
96 8 0.09
97 1 0.01
98 9 0.10
99 30 0.35
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (89 bp):
TTTTCTTAAAAATTGAAGATTTGACTTAGTACGTAATTGTTATATGAATTCATGACATGAGTAAG
ACATTATTTTTTTAACCGATAACT
Found at i:16803 original size:2 final size:2
Alignment explanation
Indices: 16796--16839 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
16786 TTCTAAATTA
*
16796 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
16839 A
1 A
16840 AAAGTACGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16912 original size:31 final size:31
Alignment explanation
Indices: 16864--16929 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 31
16854 GGGAAACTTT
* * *
16864 ATATTTTCCGATTGTACCCTTATTTTTAAAAC
1 ATATTTTCCAATTGTACCCTT-TTTTAAAAAA
16896 ATATTTT-CAATTGTACCCTTTTTTAAAAAA
1 ATATTTTCCAATTGTACCCTTTTTTAAAAAA
16926 ATAT
1 ATAT
16930 ATTAAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 12 0.39
31 12 0.39
32 7 0.23
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.47
Consensus pattern (31 bp):
ATATTTTCCAATTGTACCCTTTTTTAAAAAA
Found at i:17288 original size:22 final size:22
Alignment explanation
Indices: 17068--17313 Score: 132
Period size: 22 Copynumber: 11.3 Consensus size: 22
17058 TAAATGTCTC
* *
17068 AATTTCATAAGGA-G-TACCAA
1 AATTTCATAAAGAGGTTATCAA
* * *
17088 AATTTGATAGA-AGGTTATC-T
1 AATTTCATAAAGAGGTTATCAA
* * * *
17108 AATTTCATAGAGTGATTATCGA
1 AATTTCATAAAGAGGTTATCAA
*
17130 AATTTCATAGAGATCGGATTATCAA
1 AATTTCATAAAGA--GG-TTATCAA
*
17155 AATTT-ATAGGAAGA--TTATAAA
1 AATTTCATA--AAGAGGTTATCAA
** **
17176 AATTTCATAGTGTTGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
*
17198 AATTTCA-AAGCGAGGTTATCAA
1 AATTTCATAA-AGAGGTTATCAA
* * * * *
17220 AATTACATAATGTGATTATCAG
1 AATTTCATAAAGAGGTTATCAA
** *
17242 AATTTCATAAAG-GGACAACAA
1 AATTTCATAAAGAGGTTATCAA
*
17263 AATTTTATAAAGAGGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
*
17285 AATTTCACAAAGAGGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
*
17307 ATTTTCA
1 AATTTCA
17314 AAATGTATTT
Statistics
Matches: 170, Mismatches: 41, Indels: 28
0.71 0.17 0.12
Matches are distributed among these distances:
19 1 0.01
20 20 0.12
21 36 0.21
22 93 0.55
23 2 0.01
24 4 0.02
25 11 0.06
26 3 0.02
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (22 bp):
AATTTCATAAAGAGGTTATCAA
Found at i:17309 original size:43 final size:43
Alignment explanation
Indices: 17190--17311 Score: 113
Period size: 43 Copynumber: 2.8 Consensus size: 43
17180 TCATAGTGTT
* ** * *
17190 GTTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGTG
1 GTTATCAAAATTTCAAA-AGAGGTTATCAAAATTTTATAAAGAG
* * ** *
17234 ATTATCAGAATTTCATAAAG-GGACAACAAAATTTTATAAAGAG
1 GTTATCAAAATTTCA-AAAGAGGTTATCAAAATTTTATAAAGAG
17277 GTTATCAAAATTTCACAAAGAGGTTATC-AAATTTT
1 GTTATCAAAATTTCA-AAAGAGGTTATCAAAATTTT
17312 CAAAATGTAT
Statistics
Matches: 60, Mismatches: 16, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
43 40 0.67
44 18 0.30
45 2 0.03
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (43 bp):
GTTATCAAAATTTCAAAAGAGGTTATCAAAATTTTATAAAGAG
Found at i:17481 original size:22 final size:22
Alignment explanation
Indices: 17434--17521 Score: 76
Period size: 22 Copynumber: 4.0 Consensus size: 22
17424 AATTCATAAT
*
17434 ATTTCATTA-GGAGGTTA-CTAAT
1 ATTTCA-TAGGGAGGTTATC-AAA
17456 ATTTCATAGGGAGGTTATCAAA
1 ATTTCATAGGGAGGTTATCAAA
* *
17478 ATTTTATAGTGTA-GTTATCAAA
1 ATTTCATAG-GGAGGTTATCAAA
* *
17500 ATTTCATATGAAGGTTAT-AAA
1 ATTTCATAGGGAGGTTATCAAA
17521 A
1 A
17522 GTCTCAATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
21 8 0.14
22 45 0.80
23 3 0.05
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.39
Consensus pattern (22 bp):
ATTTCATAGGGAGGTTATCAAA
Found at i:17770 original size:22 final size:22
Alignment explanation
Indices: 17720--17771 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
17710 GGGGTCAAAA
17720 AAAATTT-ATAAAAAGGTTATC
1 AAAATTTCATAAAAAGGTTATC
*
17741 AAAATTTCATAAAGAGGTTATC
1 AAAATTTCATAAAAAGGTTATC
*
17763 AAATTTTCA
1 AAAATTTCA
17772 AAATGTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.35
Consensus pattern (22 bp):
AAAATTTCATAAAAAGGTTATC
Found at i:17985 original size:44 final size:44
Alignment explanation
Indices: 17937--18032 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
17927 ATTTAGTTTT
* **
17937 CAAAATTTTATAA-GAGGGTAATCAAAATTTCATAGGGAGATTAA
1 CAAAATTTCATAATGA-GGTAATCAAAAAATCATAGGGAGATTAA
* * *
17981 CAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGAGGTTAT
1 CAAAATTTCATAATGAGGTAATCAAAAAATCATAGGGAGATTAA
18025 CAAAATTT
1 CAAAATTT
18033 GTAGTTATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 43 0.96
45 2 0.04
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30
Consensus pattern (44 bp):
CAAAATTTCATAATGAGGTAATCAAAAAATCATAGGGAGATTAA
Found at i:18092 original size:23 final size:22
Alignment explanation
Indices: 17957--18331 Score: 170
Period size: 22 Copynumber: 17.0 Consensus size: 22
17947 TAAGAGGGTA
*
17957 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
17979 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
18001 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* ** *
18023 ATCAAAATTT-GTAGTTA--TA
1 ATCAAAATTTCATAGGGAGGTT
* * * *
18042 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATAGGGAGGTT
*
18064 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* * *
18087 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGGGAG-GTT
**
18110 ATCAAAATTTCATAACGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * * *
18132 ATCACAATTTTATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * * * *
18154 ATTAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
*
18176 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATAGGGAGGTT
* * * ** * *
18198 TTTAAATTTTCATAACGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * *
18220 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * **
18242 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
**
18265 ATCAAAATTTCATATTGAGGTCT
1 ATCAAAATTTCATAGGGAGGT-T
* * *
18288 -TCGAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
18309 AAT-AAAATTTCATAAGAAGGTT
1 -ATCAAAATTTCATAGGGAGGTT
18331 A
1 A
18332 AAAAAATATA
Statistics
Matches: 254, Mismatches: 86, Indels: 27
0.69 0.23 0.07
Matches are distributed among these distances:
19 10 0.04
20 3 0.01
21 7 0.03
22 176 0.69
23 58 0.23
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:18864 original size:23 final size:21
Alignment explanation
Indices: 18768--18879 Score: 68
Period size: 22 Copynumber: 5.2 Consensus size: 21
18758 ACTTAATAAC
*
18768 TTTTTAATTAATCTTATAAGA
1 TTTTTAAATAATCTTATAAGA
* * *
18789 TTTTTTTATTAAGCTTAGT--GTA
1 -TTTTTAAATAATCTTA-TAAG-A
* *
18811 TTTTTTAGTAA-CTTATAAGA
1 TTTTTAAATAATCTTATAAGA
*
18831 TTTCTTTAATAACTCTTATAAGA
1 TTT-TTAAATAA-TCTTATAAGA
* *
18854 TTTTTAAAATAATCTTTTAAAA
1 TTTTT-AAATAATCTTATAAGA
18876 TTTT
1 TTTT
18880 AGTAGCTATT
Statistics
Matches: 75, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
19 1 0.01
20 8 0.11
21 19 0.25
22 29 0.39
23 18 0.24
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (21 bp):
TTTTTAAATAATCTTATAAGA
Found at i:19203 original size:31 final size:31
Alignment explanation
Indices: 19168--19284 Score: 180
Period size: 31 Copynumber: 3.8 Consensus size: 31
19158 GGCGCGTCAC
* *
19168 GTGTCACTTTTTGGTATACATGGTGTGACAT
1 GTGTCACTTTTTGGTATACGTGGCGTGACAT
19199 GTGTCACTTTTTGGTATACGTGGCGTGACAT
1 GTGTCACTTTTTGGTATACGTGGCGTGACAT
*
19230 GTGTCACTTTTTGGTACACGTGGCGTGACAT
1 GTGTCACTTTTTGGTATACGTGGCGTGACAT
* * *
19261 GTATCACTTTTTTGTACACGTGGC
1 GTGTCACTTTTTGGTATACGTGGC
19285 ATGCCACGTC
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 81 1.00
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.39
Consensus pattern (31 bp):
GTGTCACTTTTTGGTATACGTGGCGTGACAT
Found at i:19282 original size:62 final size:62
Alignment explanation
Indices: 19140--19284 Score: 182
Period size: 62 Copynumber: 2.3 Consensus size: 62
19130 ATGTCACATG
** * * * * * * *
19140 TCACTTTTTGAAACACGCGGCGCGTCACGTGTCACTTTTTGGTATACATGGTGTGACATGTG
1 TCACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACACATGGCGTGACATGTA
* *
19202 TCACTTTTTGGTATACGTGGCGTGACATGTGTCACTTTTTGGTACACGTGGCGTGACATGTA
1 TCACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACACATGGCGTGACATGTA
*
19264 TCACTTTTTTGTACACGTGGC
1 TCACTTTTTGGTACACGTGGC
19285 ATGCCACGTC
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
62 70 1.00
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.37
Consensus pattern (62 bp):
TCACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACACATGGCGTGACATGTA
Done.