Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024237.1 Corchorus olitorius cultivar O-4 contig24270, 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: 18482
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:1474 original size:19 final size:18
Alignment explanation
Indices: 1445--1480 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
1435 TGAAAATAAT
1445 TCTTCAATTGTCTTCAAA
1 TCTTCAATTGTCTTCAAA
1463 TCTTCAAATTGTCTTCAA
1 TCTTC-AATTGTCTTCAA
1481 TAAGTCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (18 bp):
TCTTCAATTGTCTTCAAA
Found at i:3755 original size:21 final size:21
Alignment explanation
Indices: 3725--3779 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
3715 ATTGCCATAG
* *
3725 TTTAGATTTAATTTACTTTGC-
1 TTTATATTTAATTTA-ATTGCT
* *
3746 TTTATTTTTAGTTTAATTGCT
1 TTTATATTTAATTTAATTGCT
3767 TTTATATTTAATT
1 TTTATATTTAATT
3780 GTTTTAATTC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.24, C:0.05, G:0.07, T:0.64
Consensus pattern (21 bp):
TTTATATTTAATTTAATTGCT
Found at i:4676 original size:19 final size:20
Alignment explanation
Indices: 4636--4682 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
4626 ACTAATCATC
*
4636 AAAA-AAAAAAAGAAATC-A
1 AAAATAAAAAAAGAAAACAA
**
4654 AAAATAAAAAAAGAAAAGGA
1 AAAATAAAAAAAGAAAACAA
4674 AAAATAAAA
1 AAAATAAAA
4683 GATAAAGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 4 0.16
19 11 0.44
20 10 0.40
ACGTcount: A:0.83, C:0.02, G:0.09, T:0.06
Consensus pattern (20 bp):
AAAATAAAAAAAGAAAACAA
Found at i:4676 original size:20 final size:19
Alignment explanation
Indices: 4636--4682 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
4626 ACTAATCATC
*
4636 AAAA-AAAAAAAGAAATCA
1 AAAATAAAAAAAGAAAGCA
*
4654 AAAATAAAAAAAGAAAAGGA
1 AAAATAAAAAAAG-AAAGCA
4674 AAAATAAAA
1 AAAATAAAA
4683 GATAAAGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 4 0.16
19 8 0.32
20 13 0.52
ACGTcount: A:0.83, C:0.02, G:0.09, T:0.06
Consensus pattern (19 bp):
AAAATAAAAAAAGAAAGCA
Found at i:5833 original size:35 final size:34
Alignment explanation
Indices: 5769--6593 Score: 389
Period size: 35 Copynumber: 24.8 Consensus size: 34
5759 CAATCTTTCT
* * * *
5769 TTCAGTTAACCCAGCGCGGTCTTTCTTCAGTTTAC
1 TTCAGTTGATCCAGGGCGATCTTT-TTCAGTTTAC
5804 TTCAGTTGATCCAGGGCGATCATTTTTCAGTTTAC
1 TTCAGTTGATCCAGGGCGATC-TTTTTCAGTTTAC
* ** * *
5839 TTCAACTT-ATCCAGATCGATCTTTCTTCAGTTAAT
1 TTC-AGTTGATCCAGGGCGATCTTT-TTCAGTTTAC
** * *
5874 TTCAACTGATCCAAGGTGATC--TTTC----T--
1 TTCAGTTGATCCAGGGCGATCTTTTTCAGTTTAC
* *
5900 TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTAC
1 TTCAGTTGATCCAGGGCGATCTTT-TTCAGTTTAC
*
5935 TTCAGTTGATTCAGGGC-AGTCTTTTTTCAGTTTAC
1 TTCAGTTGATCCAGGGCGA-TC-TTTTTCAGTTTAC
* * *
5970 TTCCAGTTGATCCAGGGTGATCGTTCTTCAGCTTAC
1 TT-CAGTTGATCCAGGGCGATC-TTTTTCAGTTTAC
* * * *
6006 TTCAATTGATCCGGGGCAATCTTTCTTCAG-TTAGT
1 TTCAGTTGATCCAGGGCGATCTTT-TTCAGTTTA-C
**
6041 TTCAACTGATCCAGGGCGATC---TT---TTT--
1 TTCAGTTGATCCAGGGCGATCTTTTTCAGTTTAC
* * *
6067 TTCAGTTGACCCAGAGCGGTCTTTCTTCAGTTTAC
1 TTCAGTTGATCCAGGGCGATCTTT-TTCAGTTTAC
* *
6102 TTCAGTTGATCCAGGGCGATGATTCTTCAGTTTAC
1 TTCAGTTGATCCAGGGCGAT-CTTTTTCAGTTTAC
* * * ** * *
6137 TTCAATTGATCCAGAGCAATCTCTTAACAG-ATAG
1 TTCAGTTGATCCAGGGCGATCT-TTTTCAGTTTAC
** *
6171 TATCAACTGATCCAGGGTGATC--TTTC---TT--
1 T-TCAGTTGATCCAGGGCGATCTTTTTCAGTTTAC
*
6199 TT-AGTTGA-CCTAGGGCGGTCTTTCTTCAGTTTAC
1 TTCAGTTGATCC-AGGGCGATCTTT-TTCAGTTTAC
* * *
6233 TTCAGTTGATCCAAGGCGGTCTTTCTTCCGTTTAC
1 TTCAGTTGATCCAGGGCGATCTTT-TTCAGTTTAC
* * *
6268 TCCAGTTGATCCAGGGCGATCGTTCTTCAGCTTAC
1 TTCAGTTGATCCAGGGCGATC-TTTTTCAGTTTAC
** * * * *
6303 TTCAAATAATCCGGGGCGATCTTTCTTCA-ATTAGT
1 TTCAGTTGATCCAGGGCGATCTTT-TTCAGTTTA-C
**
6338 TTCAACTGATCCAGGGCGATC--TTTC---TT--
1 TTCAGTTGATCCAGGGCGATCTTTTTCAGTTTAC
* * *
6365 TT-AGTTGACCCAGGGCGGTCTTTCATCAGTTTAC
1 TTCAGTTGATCCAGGGCGATCTTT-TTCAGTTTAC
* * *
6399 TTCAGTTGATCTAGGACGATCATTCTTCAGTTTAC
1 TTCAGTTGATCCAGGGCGATC-TTTTTCAGTTTAC
* *
6434 TTCAATTGATTCAGGGCGATC--TTTC----T--
1 TTCAGTTGATCCAGGGCGATCTTTTTCAGTTTAC
* *
6460 TTCAGTTGACCCAGGGCGATATTTCTTCAGTTTAC
1 TTCAGTTGATCCAGGGCGATCTTT-TTCAGTTTAC
* *
6495 TCCAGTTGATCCAGGGCGATCTTTCTTCAG-TTAGT
1 TTCAGTTGATCCAGGGCGATCTTT-TTCAGTTTA-C
* *
6530 TTCAATTGAT-CAGGGGCGATCTTTCTTCAG-TTAGT
1 TTCAGTTGATCCA-GGGCGATCTTT-TTCAGTTTA-C
* **
6565 TTCAATTGATATAGGGCGATCTTTCTTCA
1 TTCAGTTGATCCAGGGCGATCTTT-TTCA
6594 AATTGATCCT
Statistics
Matches: 607, Mismatches: 115, Indels: 136
0.71 0.13 0.16
Matches are distributed among these distances:
25 2 0.00
26 73 0.12
27 3 0.00
28 6 0.01
29 13 0.02
30 5 0.01
31 2 0.00
32 15 0.02
33 7 0.01
34 28 0.05
35 406 0.67
36 46 0.08
37 1 0.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (34 bp):
TTCAGTTGATCCAGGGCGATCTTTTTCAGTTTAC
Found at i:6000 original size:96 final size:95
Alignment explanation
Indices: 5803--6000 Score: 213
Period size: 96 Copynumber: 2.1 Consensus size: 95
5793 CTTCAGTTTA
* *
5803 CTTCAGTTGATCCAGGGCGATCATTTTTCAGTTTACTTCAACTTATCCAGATCGATCTTTCTTCA
1 CTTCAGTTGACCCAGGGCGATCATTTTTCAGTTTACTTCAACTTATCCAGAGCGATCTTTCTTCA
* *
5868 GTTAATTTCAACTGATCCAAGGTGATCTTT
66 GTTAATTCCAACTGATCCAAGGTGATCGTT
* * * * *
5898 CTTTCAGTTGACCCAGGGCGGTC-TTTCTTCAGTTTACTTC-AGTTGATTCAGGGC-AGTCTTTT
1 C-TTCAGTTGACCCAGGGCGATCATTT-TTCAGTTTACTTCAACTT-ATCCAGAGCGA-TCTTTC
* ** *
5960 TTCAGTTTACTTCCAGTTGATCCAGGGTGATCGTT
62 TTCAG-TTAATTCCAACTGATCCAAGGTGATCGTT
5995 CTTCAG
1 CTTCAG
6001 CTTACTTCAA
Statistics
Matches: 85, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
95 8 0.09
96 53 0.62
97 24 0.28
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (95 bp):
CTTCAGTTGACCCAGGGCGATCATTTTTCAGTTTACTTCAACTTATCCAGAGCGATCTTTCTTCA
GTTAATTCCAACTGATCCAAGGTGATCGTT
Found at i:6035 original size:131 final size:131
Alignment explanation
Indices: 5754--6038 Score: 380
Period size: 131 Copynumber: 2.2 Consensus size: 131
5744 TAACCCGGGG
5754 CAGGGCAATCTTTCTTTCAGTTAACCCAGCGCGGTCTTTCTTCAGTTTACTTCAGTTGATCCAGG
1 CAGGGCAATCTTTCTTTCAGTTAACCCAGCGCGGTCTTTCTTCAGTTTACTTCAGTTGATCCAGG
* *
5819 GCGATCATTTTTCAGTTTACTTCAACTTATCCAGATCGATCTTTCTTCAGTTAATTTCAACTGAT
66 GCGATCATTTTTCAGTTTACTTCAACTTATCCAGATCGATCGTTCTTCAGTTAACTTCAACTGAT
5884 C
131 C
* ** * * *
5885 CAAGGTGATCTTTCTTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTACTTCAGTTGATTCAGG
1 CAGGGCAATCTTTCTTTCAGTTAACCCAGCGCGGTCTTTCTTCAGTTTACTTCAGTTGATCCAGG
* * * * *
5950 GC-AGTCTTTTTTCAGTTTACTTCCAGTTGATCCAGGGT-GATCGTTCTTCAGCTT-ACTTCAAT
66 GCGA-TCATTTTTCAGTTTACTTCAACTT-ATCCA-GATCGATCGTTCTTCAG-TTAACTTCAAC
6012 TGATC
127 TGATC
*
6017 CGGGGCAATCTTTC-TTCAGTTA
1 CAGGGCAATCTTTCTTTCAGTTA
6039 GTTTCAACTG
Statistics
Matches: 132, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
130 1 0.01
131 89 0.67
132 38 0.29
133 4 0.03
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.39
Consensus pattern (131 bp):
CAGGGCAATCTTTCTTTCAGTTAACCCAGCGCGGTCTTTCTTCAGTTTACTTCAGTTGATCCAGG
GCGATCATTTTTCAGTTTACTTCAACTTATCCAGATCGATCGTTCTTCAGTTAACTTCAACTGAT
C
Found at i:6046 original size:167 final size:165
Alignment explanation
Indices: 5769--6150 Score: 523
Period size: 167 Copynumber: 2.3 Consensus size: 165
5759 CAATCTTTCT
* * * *
5769 TTCAGTTAACCCAGCGCGGTCTTTCTTCAGTTTACTTCAGTTGATCCAGGGCGATCATTTTTCAG
1 TTCAGTTGATCCAGGGC-GTCTTTCTTCAGTTTACTTCAGTTGATCCAGGGCGATCATTCTTCAG
* * * *
5834 TTTACTTCAACTTATCCAGATCGATCTTTCTTCAGTTAATTTCAACTGATCCAAGGTGATCTTTC
65 CTTACTTCAACTTATCCAGAGCAATCTTTCTTCAGTTAATTTCAACTGATCCAAGGCGATCTTTC
*
5899 TTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTAC
130 TTTCAGTTGACCCAGAGCGGTCTTTCTTCAGTTTAC
* * * *
5935 TTCAGTTGATTCAGGGCAGTCTTTTTTCAGTTTACTTCCAGTTGATCCAGGGTGATCGTTCTTCA
1 TTCAGTTGATCCAGGGC-GTCTTTCTTCAGTTTACTT-CAGTTGATCCAGGGCGATCATTCTTCA
* * * *
6000 GCTTACTTCAA-TTGATCCGGGGCAATCTTTCTTCAGTTAGTTTCAACTGATCCAGGGCGATCTT
64 GCTTACTTCAACTT-ATCCAGAGCAATCTTTCTTCAGTTAATTTCAACTGATCCAAGGCGATCTT
*
6064 TTTTTCAGTTGACCCAGAGCGGTCTTTCTTCAGTTTAC
128 TCTTTCAGTTGACCCAGAGCGGTCTTTCTTCAGTTTAC
** *
6102 TTCAGTTGATCCAGGGCGATGATTCTTCAGTTTACTTCAATTGATCCAG
1 TTCAGTTGATCCAGGGCG-TCTTTCTTCAGTTTACTTCAGTTGATCCAG
6151 AGCAATCTCT
Statistics
Matches: 189, Mismatches: 24, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
166 45 0.24
167 144 0.76
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (165 bp):
TTCAGTTGATCCAGGGCGTCTTTCTTCAGTTTACTTCAGTTGATCCAGGGCGATCATTCTTCAGC
TTACTTCAACTTATCCAGAGCAATCTTTCTTCAGTTAATTTCAACTGATCCAAGGCGATCTTTCT
TTCAGTTGACCCAGAGCGGTCTTTCTTCAGTTTAC
Found at i:6074 original size:96 final size:97
Alignment explanation
Indices: 5973--6553 Score: 431
Period size: 96 Copynumber: 5.9 Consensus size: 97
5963 AGTTTACTTC
* * * * * *
5973 CAGTTGATCCAGGGTGATCGTTCTTCAGCTTACTTCAATTGATCCGGGGCAATCTTTCTTCAG-T
1 CAGTTGACCCAGGGCGATCTTTCTTCAGCTTACTTCAGTTGATCCAGGGCGATCTTTCTTCAGTT
* *
6037 TAGTTTCAACTGATCCAGGGCGATCTTT-TTTT
66 TA-CTTCAATTGATCCAGGGCGATCTTTATTTT
* * * **
6069 CAGTTGACCCAGAGCGGTCTTTCTTCAGTTTACTTCAGTTGATCCAGGGCGATGATTCTTCAGTT
1 CAGTTGACCCAGGGCGATCTTTCTTCAGCTTACTTCAGTTGATCCAGGGCGATCTTTCTTCAGTT
* * *
6134 TACTTCAATTGATCCAGAGCAATCTCTTAACAGATAGTAT
66 TACTTCAATTGATCCAGGGCGATCT-TT-----AT--TTT
** * * *
6174 CAACTGATCCAGGGTGATC--T-TT---CTT--TT-AGTTGA-CCTAGGGCGGTCTTTCTTCAGT
1 CAGTTGACCCAGGGCGATCTTTCTTCAGCTTACTTCAGTTGATCC-AGGGCGATCTTTCTTCAGT
* * * *
6229 TTACTTCAGTTGATCCAAGGCGGTCTTTCTTCCGTTTACT
65 TTACTTCAATTGATCCAGGGCGATC--T-TT--ATTT--T
* * ** * * *
6269 CCAGTTGATCCAGGGCGATCGTTCTTCAGCTTACTTCAAATAATCCGGGGCGATCTTTCTTCA-A
1 -CAGTTGACCCAGGGCGATCTTTCTTCAGCTTACTTCAGTTGATCCAGGGCGATCTTTCTTCAGT
* * *
6333 TTAGTTTCAACTGATCCAGGGCGATCTTTCTTTT
65 TTA-CTTCAATTGATCCAGGGCGATCTTTATTTT
* * * * * *
6367 -AGTTGACCCAGGGCGGTCTTTCATCAGTTTACTTCAGTTGATCTAGGACGATCATTCTTCAGTT
1 CAGTTGACCCAGGGCGATCTTTCTTCAGCTTACTTCAGTTGATCCAGGGCGATCTTTCTTCAGTT
* *
6431 TACTTCAATTGATTCAGGGCGATCTTT-CTTT
66 TACTTCAATTGATCCAGGGCGATCTTTATTTT
* * *
6462 CAGTTGACCCAGGGCGATATTTCTTCAGTTTACTCCAGTTGATCCAGGGCGATCTTTCTTCAG-T
1 CAGTTGACCCAGGGCGATCTTTCTTCAGCTTACTTCAGTTGATCCAGGGCGATCTTTCTTCAGTT
*
6526 TAGTTTCAATTGAT-CAGGGGCGATCTTT
66 TA-CTTCAATTGATCCA-GGGCGATCTTT
6554 CTTCAGTTAG
Statistics
Matches: 379, Mismatches: 75, Indels: 62
0.73 0.15 0.12
Matches are distributed among these distances:
93 1 0.00
95 12 0.03
96 276 0.73
97 10 0.03
98 6 0.02
99 4 0.01
100 3 0.01
102 7 0.02
103 3 0.01
104 5 0.01
105 50 0.13
106 2 0.01
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (97 bp):
CAGTTGACCCAGGGCGATCTTTCTTCAGCTTACTTCAGTTGATCCAGGGCGATCTTTCTTCAGTT
TACTTCAATTGATCCAGGGCGATCTTTATTTT
Found at i:6146 original size:131 final size:132
Alignment explanation
Indices: 5935--6591 Score: 614
Period size: 131 Copynumber: 5.0 Consensus size: 132
5925 TTCAGTTTAC
** * * * *
5935 TTCAGTTGATTCAGGGCAGTCTTTTTTCAGTTTACTTCCAGTTGATCCAGGGTGATCGTTCTTCA
1 TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTACTT-CAGTTGATCCAGGGCGATCTTTCTTCA
* * *
6000 GCTTACTTCAATTGATCCGGGGCAATCTTTCTTCAGTTAGTTTCAACTGATCCAGGGCGATCTTT
65 GTTTACTTCAATTGATCCAGGGCGATCTTTCTTCAGTTAGTTTCAACTGATCCAGGGCGATCTTT
6065 -TT
130 CTT
* **
6067 TTCAGTTGACCCAGAGCGGTCTTTCTTCAGTTTACTTCAGTTGATCCAGGGCGATGATTCTTCAG
1 TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTACTTCAGTTGATCCAGGGCGATCTTTCTTCAG
* * * * *
6132 TTTACTTCAATTGATCCAGAGCAATC--TCTTAACAGATAGTATCAACTGATCCAGGGTGATCTT
66 TTTACTTCAATTGATCCAGGGCGATCTTTCTT--CAGTTAGTTTCAACTGATCCAGGGCGATCTT
6195 TCTT
129 TCTT
* * * *
6199 TT-AGTTGACCTAGGGCGGTCTTTCTTCAGTTTACTTCAGTTGATCCAAGGCGGTCTTTCTTCCG
1 TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTACTTCAGTTGATCCAGGGCGATCTTTCTTCAG
* * * * * * *
6263 TTTACTCCAGTTGATCCAGGGCGATCGTTCTTCAGCTTA-CTTCAAATAATCCGGGGCGATCTTT
66 TTTACTTCAATTGATCCAGGGCGATCTTTCTTCAG-TTAGTTTCAACTGATCCAGGGCGATCTTT
6327 CTT
130 CTT
* * * *
6330 CAATT-AGTTTCAACTGATCCAGGGCGATC--T-TTC---TT--TT-AGTTGACCCAGGGCGGTC
1 ---TTCAG--T----TGACCCAGGGCGGTCTTTCTTCAGTTTACTTCAGTTGATCCAGGGCGATC
* * * * * * * *
6385 TTTCATCAGTTTACTTCAGTTGATCTAGGACGATCATTCTTCAGTTTA-CTTCAATTGATTCAGG
57 TTTCTTCAGTTTACTTCAATTGATCCAGGGCGATCTTTCTTCAG-TTAGTTTCAACTGATCCAGG
6449 GCGATCTTTC-T
121 GCGATCTTTCTT
* * *
6460 TTCAGTTGACCCAGGGCGATATTTCTTCAGTTTACTCCAGTTGATCCAGGGCGATCTTTCTTCAG
1 TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTACTTCAGTTGATCCAGGGCGATCTTTCTTCAG
* * **
6525 -TTAGTTTCAATTGAT-CAGGGGCGATCTTTCTTCAGTTAGTTTCAATTGATATAGGGCGATCTT
66 TTTA-CTTCAATTGATCCA-GGGCGATCTTTCTTCAGTTAGTTTCAACTGATCCAGGGCGATCTT
6588 TCTT
129 TCTT
6592 CAAATTGATC
Statistics
Matches: 434, Mismatches: 62, Indels: 58
0.78 0.11 0.10
Matches are distributed among these distances:
122 13 0.03
124 1 0.00
125 3 0.01
126 1 0.00
127 2 0.00
128 4 0.01
129 4 0.01
130 9 0.02
131 329 0.76
132 41 0.09
133 4 0.01
134 6 0.01
136 1 0.00
137 3 0.01
138 1 0.00
140 12 0.03
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (132 bp):
TTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTACTTCAGTTGATCCAGGGCGATCTTTCTTCAG
TTTACTTCAATTGATCCAGGGCGATCTTTCTTCAGTTAGTTTCAACTGATCCAGGGCGATCTTTC
TT
Found at i:6268 original size:166 final size:165
Alignment explanation
Indices: 6067--6460 Score: 519
Period size: 166 Copynumber: 2.4 Consensus size: 165
6057 CGATCTTTTT
*
6067 TTCAGTTGA-CCCAGAGCGGTCTTTCTTCAGTTTACTTCAGTTGATCCAGGGCGAT-GATTCTTC
1 TTCAGTTGATCCAAG-GCGGTCTTTCTTCAGTTTACTTCAGTTGATCCAGGGCGATCG-TTCTTC
* * * *
6130 AGTTTACTTCAATTGATCCAGAGCAATC-TCTTAACAGA-TAGTATCAACTGATCCAGGGTGATC
64 AGCTTACTTCAAATAATCCAGAGCAATCTTCTT--CA-ATTAGTATCAACTGATCCAGGGCGATC
* *
6193 TTTCTTTTAGTTGACCTAGGGCGGTCTTTCTTCAGTTTAC
126 TTTCTTTTAGTTGACCCAGGGCGGTCTTTCATCAGTTTAC
* *
6233 TTCAGTTGATCCAAGGCGGTCTTTCTTCCGTTTACTCCAGTTGATCCAGGGCGATCGTTCTTCAG
1 TTCAGTTGATCCAAGGCGGTCTTTCTTCAGTTTACTTCAGTTGATCCAGGGCGATCGTTCTTCAG
* * * *
6298 CTTACTTCAAATAATCCGGGGCGATCTTTCTTCAATTAGTTTCAACTGATCCAGGGCGATCTTTC
66 CTTACTTCAAATAATCCAGAGCAATC-TTCTTCAATTAGTATCAACTGATCCAGGGCGATCTTTC
6363 TTTTAGTTGACCCAGGGCGGTCTTTCATCAGTTTAC
130 TTTTAGTTGACCCAGGGCGGTCTTTCATCAGTTTAC
* * * * * *
6399 TTCAGTTGAT-CTAGGACGATCATTCTTCAGTTTACTTCAATTGATTCAGGGCGATCTTTCTT
1 TTCAGTTGATCCAAGG-CGGTCTTTCTTCAGTTTACTTCAGTTGATCCAGGGCGATCGTTCTT
6461 TCAGTTGACC
Statistics
Matches: 201, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
165 5 0.02
166 187 0.93
167 5 0.02
168 4 0.02
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (165 bp):
TTCAGTTGATCCAAGGCGGTCTTTCTTCAGTTTACTTCAGTTGATCCAGGGCGATCGTTCTTCAG
CTTACTTCAAATAATCCAGAGCAATCTTCTTCAATTAGTATCAACTGATCCAGGGCGATCTTTCT
TTTAGTTGACCCAGGGCGGTCTTTCATCAGTTTAC
Found at i:6464 original size:61 final size:60
Alignment explanation
Indices: 6398--6526 Score: 179
Period size: 61 Copynumber: 2.1 Consensus size: 60
6388 CATCAGTTTA
* * * *
6398 CTTCAGTTGATCTAGGACGATCA-TTCTTCAGTTTACTTCAATTGATTCAGGGCGATCTTT
1 CTTCAGTTGACCCAGGACGAT-ATTTCTTCAGTTTACTCCAATTGATCCAGGGCGATCTTT
* *
6458 CTTTCAGTTGACCCAGGGCGATATTTCTTCAGTTTACTCCAGTTGATCCAGGGCGATCTTT
1 C-TTCAGTTGACCCAGGACGATATTTCTTCAGTTTACTCCAATTGATCCAGGGCGATCTTT
6519 CTTCAGTT
1 CTTCAGTT
6527 AGTTTCAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
60 9 0.15
61 52 0.85
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.39
Consensus pattern (60 bp):
CTTCAGTTGACCCAGGACGATATTTCTTCAGTTTACTCCAATTGATCCAGGGCGATCTTT
Found at i:6600 original size:26 final size:26
Alignment explanation
Indices: 6568--6627 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
6558 AGTTAGTTTC
*
6568 AATTGAT-ATAGGGCGATCTTTCTTCA
1 AATTGATCAT-GGGCGATCTATCTTCA
*
6594 AATTGATCCTGGGCGATCTATCTTCA
1 AATTGATCATGGGCGATCTATCTTCA
*
6620 AAGTGATC
1 AATTGATC
6628 CAGTGCGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 29 0.97
27 1 0.03
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (26 bp):
AATTGATCATGGGCGATCTATCTTCA
Found at i:6628 original size:26 final size:26
Alignment explanation
Indices: 6577--6637 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
6567 CAATTGATAT
* *
6577 AGGGCGATCTTTCTTCAAATTGATCC
1 AGGGCGATCTATCTTCAAAGTGATCC
*
6603 TGGGCGATCTATCTTCAAAGTGATCC
1 AGGGCGATCTATCTTCAAAGTGATCC
*
6629 AGTGCGATC
1 AGGGCGATC
6638 AATCAATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (26 bp):
AGGGCGATCTATCTTCAAAGTGATCC
Found at i:6715 original size:51 final size:52
Alignment explanation
Indices: 6612--6718 Score: 126
Period size: 55 Copynumber: 2.0 Consensus size: 52
6602 CTGGGCGATC
* *
6612 TATCTTCAAAGTGATCCAGTGCGATCAATCAATAAAATTTACAATGGTTTAAGTT
1 TATCTTCAAAGTGATCCAGTGCGATCAATC---AAAATTTACAACGATTTAAGTT
** * *
6667 TATCTTCAAAGTGATCTGGTGCGATCAATC-AAGTTTACAGCGATTTAAGTT
1 TATCTTCAAAGTGATCCAGTGCGATCAATCAAAATTTACAACGATTTAAGTT
6718 T
1 T
6719 CCTAAAAGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
51 18 0.39
55 28 0.61
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (52 bp):
TATCTTCAAAGTGATCCAGTGCGATCAATCAAAATTTACAACGATTTAAGTT
Found at i:6756 original size:38 final size:37
Alignment explanation
Indices: 6713--6789 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 37
6703 ACAGCGATTT
* *
6713 AAGTTTCCTAAAAGTGATTCAAGTATGGTCAATCAAGA
1 AAGTTTCCTAAAAGT-AATCAAGTACGGTCAATCAAGA
* * *
6751 AAGTTTCCTAAAGGTAATCCAGTGCGGTCAATCAAGA
1 AAGTTTCCTAAAAGTAATCAAGTACGGTCAATCAAGA
6788 AA
1 AA
6790 ATTCATAGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
37 20 0.59
38 14 0.41
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (37 bp):
AAGTTTCCTAAAAGTAATCAAGTACGGTCAATCAAGA
Found at i:6856 original size:54 final size:54
Alignment explanation
Indices: 6767--6881 Score: 162
Period size: 54 Copynumber: 2.1 Consensus size: 54
6757 CCTAAAGGTA
* * *
6767 ATCCAGTGCGGTCAATCAAGAAAATTCATAGTGGTTTGAGTTT-TCCTTCAAGTG
1 ATCCAGTGCGGTCAATCAAGAAAATTCACAATGGTTTAAGTTTAT-CTTCAAGTG
*
6821 ATCCAGTGCGAG-CAATCAAGAAAATTTACAATGGTTTAAGTTTATCTTCAAGTG
1 ATCCAGTGCG-GTCAATCAAGAAAATTCACAATGGTTTAAGTTTATCTTCAAGTG
6875 ATCCAGT
1 ATCCAGT
6882 ATGGCCAGTC
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
54 53 0.96
55 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (54 bp):
ATCCAGTGCGGTCAATCAAGAAAATTCACAATGGTTTAAGTTTATCTTCAAGTG
Found at i:6973 original size:35 final size:35
Alignment explanation
Indices: 6918--7407 Score: 674
Period size: 35 Copynumber: 14.1 Consensus size: 35
6908 ATTTAGGTTT
* *
6918 ATCTTCAAAGTCGGAA-TCAGATAACTCGGTGTAGC
1 ATCTTCAAAGT-TGAATTCAGATGACTCGGTGTAGC
**
6953 ATCTTCAAAGTTGAATTCAGATGACTTAGTGTAGC
1 ATCTTCAAAGTTGAATTCAGATGACTCGGTGTAGC
*
6988 ATCTTCAAAGTCGGAA-TCAGATGA--C--T-TAGC
1 ATCTTCAAAGT-TGAATTCAGATGACTCGGTGTAGC
*
7018 ATCTTCAAAGTTAGAACT-AGATGACTCGGTGTAGC
1 ATCTTCAAAGTT-GAATTCAGATGACTCGGTGTAGC
*
7053 ATCTTCAAAGTTAAATTCAGATGACTCGGTGTAGC
1 ATCTTCAAAGTTGAATTCAGATGACTCGGTGTAGC
* *
7088 ATGTTCAAAGATGAATTCAGATGACTCGGTGTAGC
1 ATCTTCAAAGTTGAATTCAGATGACTCGGTGTAGC
* *
7123 ATCTCCAAAGTTGAATTCAGATGACTCGGTGTACC
1 ATCTTCAAAGTTGAATTCAGATGACTCGGTGTAGC
7158 ATCTTCAAAGTTGAATTCAGATGACTCGGTGTAGC
1 ATCTTCAAAGTTGAATTCAGATGACTCGGTGTAGC
*
7193 ATCTTCAAAGATGAATTCAGATGACTCGGTGTAGC
1 ATCTTCAAAGTTGAATTCAGATGACTCGGTGTAGC
7228 ATCTTCAAAGTTGAATTCAGATGACTCGGTGTAGC
1 ATCTTCAAAGTTGAATTCAGATGACTCGGTGTAGC
* *
7263 ATCTTCAAAGTTGAATTTAGATGACTTGGTGTAGC
1 ATCTTCAAAGTTGAATTCAGATGACTCGGTGTAGC
**
7298 ATCTTCAAAGTTGAATTCAGATGACTCAATGTAGC
1 ATCTTCAAAGTTGAATTCAGATGACTCGGTGTAGC
* * *
7333 ATCTTCAAAGTTGAATTCAGAGGACTCAGTGTAGT
1 ATCTTCAAAGTTGAATTCAGATGACTCGGTGTAGC
* ** *
7368 ACCTTCGGAGTTAGAA-TCAGATGACTCGGTGTAAC
1 ATCTTCAAAGTT-GAATTCAGATGACTCGGTGTAGC
7403 ATCTT
1 ATCTT
7408 TAAATGATGA
Statistics
Matches: 407, Mismatches: 37, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
30 24 0.06
31 2 0.00
32 1 0.00
34 7 0.02
35 367 0.90
36 6 0.01
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (35 bp):
ATCTTCAAAGTTGAATTCAGATGACTCGGTGTAGC
Found at i:8160 original size:27 final size:27
Alignment explanation
Indices: 8108--8180 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
8098 TAGGTTGGTA
* * *
8108 TTGGACTTGCACTTGGACATTATAGCT
1 TTGGACTTGCATTTGGACCTTATAGCC
* *
8135 TTTGACTTGCATTTGGACCTTTTAGCC
1 TTGGACTTGCATTTGGACCTTATAGCC
* *
8162 TTGGATTTGCTTTTGGACC
1 TTGGACTTGCATTTGGACC
8181 ATAGTGGAGA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.42
Consensus pattern (27 bp):
TTGGACTTGCATTTGGACCTTATAGCC
Found at i:10128 original size:17 final size:18
Alignment explanation
Indices: 10105--10151 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
10095 GGTTGATAGT
10105 GAGGAAGAAGAAGAAATA
1 GAGGAAGAAGAAGAAATA
*
10123 -AGGAAGAAGAAGAAGTA
1 GAGGAAGAAGAAGAAATA
10140 GAGGAAG-AGAAG
1 GAGGAAGAAGAAG
10152 CTTTTTCGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 21 0.78
18 6 0.22
ACGTcount: A:0.57, C:0.00, G:0.38, T:0.04
Consensus pattern (18 bp):
GAGGAAGAAGAAGAAATA
Found at i:14734 original size:27 final size:27
Alignment explanation
Indices: 14696--14770 Score: 123
Period size: 27 Copynumber: 2.8 Consensus size: 27
14686 GACTGTTGCC
*
14696 GCAGTGGATCCTCCCACTTCGACCCCA
1 GCAGTGGATCCTCCCACTTCGACCCAA
*
14723 GCAGTGCATCCTCCCACTTCGACCCAA
1 GCAGTGGATCCTCCCACTTCGACCCAA
*
14750 GCAGTGGATCCTCCAACTTCG
1 GCAGTGGATCCTCCCACTTCG
14771 CCTCGGGTCG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.20, C:0.41, G:0.19, T:0.20
Consensus pattern (27 bp):
GCAGTGGATCCTCCCACTTCGACCCAA
Found at i:15595 original size:17 final size:17
Alignment explanation
Indices: 15573--15607 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
15563 GAAAAAGTGC
15573 ATTCTTGTTGGTACATT
1 ATTCTTGTTGGTACATT
*
15590 ATTCTTGTTGGTATATT
1 ATTCTTGTTGGTACATT
15607 A
1 A
15608 ACATTATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.09, G:0.17, T:0.54
Consensus pattern (17 bp):
ATTCTTGTTGGTACATT
Found at i:16764 original size:6 final size:6
Alignment explanation
Indices: 16755--16789 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
16745 TGACGGTGAT
*
16755 GATGGA GATGGC GATGGC GATGGC GATGGC GATGG
1 GATGGC GATGGC GATGGC GATGGC GATGGC GATGG
16790 TGGTAACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.20, C:0.11, G:0.51, T:0.17
Consensus pattern (6 bp):
GATGGC
Found at i:17198 original size:32 final size:32
Alignment explanation
Indices: 17157--17302 Score: 220
Period size: 32 Copynumber: 4.5 Consensus size: 32
17147 GTGTGAAAAG
* *
17157 AAAATGCCCTTATTTAGCGGCGTCTATAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
* *
17189 AAAACGCCCTTATTTAACGGCGTCTAAAAAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
*
17221 AAAATGCCCTTATTTAGCGGCGTCTAAAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
*
17253 AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
17285 AAAACGCCGCTATATTTA
1 AAAACGCC-CT-TATTTA
17303 ACTGCTTTTT
Statistics
Matches: 103, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
32 95 0.92
33 2 0.02
34 6 0.06
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (32 bp):
AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
Done.