Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018151.1 Corchorus olitorius cultivar O-4 contig18184, 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: 129614
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:618 original size:324 final size:314
Alignment explanation
Indices: 35--830 Score: 852
Period size: 318 Copynumber: 2.5 Consensus size: 314
25 ATCTAATAGA
* * * * *
35 GTTTTTAAGAGCATCTGAATCTTGTTTC-ACTTTAATAAGATA-TAATTCTGAAAATATAG-AAA
1 GTTTTTACGAGCATCTGAATCTTGTTTCGA-TTTAATTAGAAATTAATTCTGAAAAAATGGAAAA
* * * * *
97 AACAATATT---GCATGAAAAACCCTTCAGTCTTGTTGGCATTGAATTATATATTTTTTCTGAAT
65 AACGATATTAAAGCATG-AAAAGCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTCTGAAT
* * * * * * * *
159 ATTGTGGCATAAAATTGAGGGAAAATTTTTCGGGTCAGTTTTTAACCGATATCTTGTATTAACCA
128 ATTGTGGCAAAAAATTGAGGAAAAATTTTACAGGTCAGTTTTTAACCGAAATCGTATACTAACCA
* * * * * **
224 TCTTATGTTTTTTGGCTAAAAATGCGTTCTGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGT
193 TC-TACGGTTTTTGGCTAAAAACGCGTTCTAGAGCCCCGACTCAGTTTTGCATGATTTTTGAAGT
* ** * * * *
289 AAAGACTCCTTGAAATATCTATATTCATCTAATGAAATCTCAACCATATGGGATTTAAGTATTT
257 AAAGACTCCTTG--A-A---ATATTCATCGAACCAAATCTCAACCACATGAGATATAAGAATTT
* *
353 GTTTTTACGAGCATCTGAATCTTGTTTCGTTTTAATTAGAAATTAATTCGGAAAAAAATGGAAAA
1 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCTG-AAAAAATGGAAAA
* * * *
418 AACGATATTAGAAGCATGAGAATGCCTTCAATATTTTTGGCGTTGAATTATATATTTTTGTGAGT
65 AACGATATTA-AAGCATGA-AAAGCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTCTGAAT
*
483 ATTGTGGCAAAAAAAATTGAGGAAAAATTTTACAGGTCAGTTTTTAGCCGAAATCGTATACTAAC
128 ATTGTGGC--AAAAAATTGAGGAAAAATTTTACAGGTCAGTTTTTAACCGAAATCGTATACTAAC
* * * *
548 TATC-ACGGTTTTTGGCTAAAAACGCGTT-TCAGAGTCCCGACTCAGTTTTGTATTATTTTTGAA
191 CATCTACGGTTTTTGGCTAAAAACGCGTTCT-AGAGCCCCGACTCAGTTTTGCATGATTTTTGAA
* *
611 GTAAAGACTCCTTGAAATATTCATCGAACCAAATCTCAGCCACATTAGATATAAGAATTT
255 GTAAAGACTCCTTGAAATATTCATCGAACCAAATCTCAACCACATGAGATATAAGAATTT
* * *
671 GTTTTTACAAGCACCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAATGGAAAAA
1 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAATGGAAAAA
* * * * *
736 TCGATATTAAAAGCATGAAAAGTCTTTTAATCTTTTTGGCGTCGAATTATATATTTTTCCTCAAT
66 ACGATATT-AAAGCATGAAAAG-CCTTCAATCTTTTTGGCGTTGAATTATATATTTTT-CTGAAT
* * *
801 ATTATGACAAAAAATTGGGAGAAAAATTTT
128 ATTGTGGCAAAAAATTGAG-GAAAAATTTT
831 TCGAATCAGT
Statistics
Matches: 400, Mismatches: 62, Indels: 33
0.81 0.13 0.07
Matches are distributed among these distances:
316 13 0.03
317 70 0.17
318 128 0.32
319 7 0.02
320 7 0.02
321 12 0.03
322 1 0.00
323 1 0.00
324 79 0.20
325 33 0.08
326 49 0.12
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (314 bp):
GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAATGGAAAAA
ACGATATTAAAGCATGAAAAGCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTCTGAATATT
GTGGCAAAAAATTGAGGAAAAATTTTACAGGTCAGTTTTTAACCGAAATCGTATACTAACCATCT
ACGGTTTTTGGCTAAAAACGCGTTCTAGAGCCCCGACTCAGTTTTGCATGATTTTTGAAGTAAAG
ACTCCTTGAAATATTCATCGAACCAAATCTCAACCACATGAGATATAAGAATTT
Found at i:14891 original size:1 final size:1
Alignment explanation
Indices: 14887--14919 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
14877 TTCTAAGCCC
14887 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
14920 GGTGCCCACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19880 original size:19 final size:21
Alignment explanation
Indices: 19842--19892 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
19832 TAATAATTTC
*
19842 ATTTGTACAGTAGTTAATCTA
1 ATTTGTATAGTAGTTAATCTA
*
19863 ATTTGTATAGT-G-TAATCTC
1 ATTTGTATAGTAGTTAATCTA
*
19882 ATCTGTATAGT
1 ATTTGTATAGT
19893 TACTAAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 16 0.59
20 1 0.04
21 10 0.37
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (21 bp):
ATTTGTATAGTAGTTAATCTA
Found at i:34245 original size:42 final size:42
Alignment explanation
Indices: 34199--34282 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
34189 AGAATGCCAC
* * *
34199 CATCATCATCATGAGGAGGACTCC-CAGACTGAGCACCACCAT
1 CATCATCATCATGAGGAGCACGCCAAAGA-TGAGCACCACCAT
* *
34241 CATCATGATGATGAGGAGCACGCCAAAGATGAGCACCACCAT
1 CATCATCATCATGAGGAGCACGCCAAAGATGAGCACCACCAT
34283 GCTCATGAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 33 0.92
43 3 0.08
ACGTcount: A:0.33, C:0.30, G:0.21, T:0.15
Consensus pattern (42 bp):
CATCATCATCATGAGGAGCACGCCAAAGATGAGCACCACCAT
Found at i:40564 original size:19 final size:19
Alignment explanation
Indices: 40530--40576 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 19
40520 TTTTTTTCTT
40530 TTTCTGTTTTCAAATTGC-ACC
1 TTTCT-TTTTCAAATT-CTA-C
40551 TTTCTTTTTC-AATTCTAC
1 TTTCTTTTTCAAATTCTAC
40569 TTTCTTTT
1 TTTCTTTT
40577 CCAGTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.40
19 5 0.20
20 5 0.20
21 5 0.20
ACGTcount: A:0.15, C:0.21, G:0.04, T:0.60
Consensus pattern (19 bp):
TTTCTTTTTCAAATTCTAC
Found at i:40584 original size:18 final size:18
Alignment explanation
Indices: 40550--40584 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40540 CAAATTGCAC
*
40550 CTTTCTTTTTCAATTCTA
1 CTTTCTTTTCCAATTCTA
*
40568 CTTTCTTTTCCAGTTCT
1 CTTTCTTTTCCAATTCT
40585 TTTTGGTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.26, G:0.03, T:0.60
Consensus pattern (18 bp):
CTTTCTTTTCCAATTCTA
Found at i:40972 original size:18 final size:18
Alignment explanation
Indices: 40949--40985 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
40939 TGAGATGCTT
40949 AGGTTGTGTTTGGTTAGG
1 AGGTTGTGTTTGGTTAGG
40967 AGGTTGTGTTTGGTTAGG
1 AGGTTGTGTTTGGTTAGG
40985 A
1 A
40986 AATGTTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (18 bp):
AGGTTGTGTTTGGTTAGG
Found at i:41265 original size:17 final size:17
Alignment explanation
Indices: 41243--41287 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
41233 ATAATTTAAG
41243 AAACATTACTAGTAATA
1 AAACATTACTAGTAATA
**
41260 AAACATTACTAGTTCTA
1 AAACATTACTAGTAATA
*
41277 AATCATTACTA
1 AAACATTACTA
41288 ATCATGTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (17 bp):
AAACATTACTAGTAATA
Found at i:56358 original size:21 final size:23
Alignment explanation
Indices: 56334--56377 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
56324 ATTAATACTA
*
56334 AAGAGTCTTAA-T-AATTTGATT
1 AAGAGTATTAACTAAATTTGATT
*
56355 AAGATTATTAACTAAATTTGATT
1 AAGAGTATTAACTAAATTTGATT
56378 CAACTAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 1 0.05
23 9 0.47
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (23 bp):
AAGAGTATTAACTAAATTTGATT
Found at i:79406 original size:1 final size:1
Alignment explanation
Indices: 79400--79425 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
79390 CCTTGTGCCC
79400 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
79426 CCTTTTTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:90770 original size:24 final size:24
Alignment explanation
Indices: 90743--90802 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
90733 TTATCCCCTG
90743 ATCACCCATCTAGGGGGTAATCCA
1 ATCACCCATCTAGGGGGTAATCCA
** * *
90767 ATCACTTATCTAGGGGGTGATCCG
1 ATCACCCATCTAGGGGGTAATCCA
90791 ATCACCCATCTA
1 ATCACCCATCTA
90803 AATCCAAGTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (24 bp):
ATCACCCATCTAGGGGGTAATCCA
Found at i:95156 original size:24 final size:25
Alignment explanation
Indices: 95119--95166 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
95109 GCTTTATATA
95119 ATAATAATATAGATTATA-ATAGATG
1 ATAATAATATAGA-TATACATAGATG
95144 ATAAT-ATATAGATATACATAGAT
1 ATAATAATATAGATATACATAGAT
95167 AGTATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.18
24 13 0.59
25 5 0.23
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.35
Consensus pattern (25 bp):
ATAATAATATAGATATACATAGATG
Found at i:96267 original size:21 final size:22
Alignment explanation
Indices: 96235--96279 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
96225 CGTATACGAG
96235 TTTGTCCTA-TTTTATGTGGAT
1 TTTGTCCTATTTTTATGTGGAT
*
96256 TTTGTGCC-ATTTTTATGTGTAT
1 TTTGT-CCTATTTTTATGTGGAT
96278 TT
1 TT
96280 GATTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.13, C:0.09, G:0.18, T:0.60
Consensus pattern (22 bp):
TTTGTCCTATTTTTATGTGGAT
Found at i:104414 original size:6 final size:6
Alignment explanation
Indices: 104405--104445 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
104395 TCATCATCAT
* * *
104405 CAACAG CAACAG CAACAG CAGCAG CAGCAG CAGCAG CAACA
1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACA
104446 TCAGGCAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.44, C:0.34, G:0.22, T:0.00
Consensus pattern (6 bp):
CAACAG
Found at i:104422 original size:12 final size:12
Alignment explanation
Indices: 104405--104445 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
104395 TCATCATCAT
*
104405 CAACAGCAACAG
1 CAACAGCAGCAG
104417 CAACAGCAGCAG
1 CAACAGCAGCAG
*
104429 CAGCAGCAGCAG
1 CAACAGCAGCAG
104441 CAACA
1 CAACA
104446 TCAGGCAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.44, C:0.34, G:0.22, T:0.00
Consensus pattern (12 bp):
CAACAGCAGCAG
Found at i:104428 original size:3 final size:3
Alignment explanation
Indices: 104408--104442 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
104398 TCATCATCAA
* *
104408 CAG CAA CAG CAA CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
104443 ACATCAGGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.40, C:0.34, G:0.26, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:107339 original size:2 final size:2
Alignment explanation
Indices: 107332--107371 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
107322 GTAATAGTAG
107332 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
107372 GTTTTCATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:122608 original size:63 final size:63
Alignment explanation
Indices: 122524--122658 Score: 245
Period size: 63 Copynumber: 2.1 Consensus size: 63
122514 AAAACTTTAC
*
122524 ATTTGGAACTGTAGTTTCTGAATTGGGATTTCCAGAATTGAAAGGCAAATTGGAGCTTTCATT
1 ATTTGGAACTGTAATTTCTGAATTGGGATTTCCAGAATTGAAAGGCAAATTGGAGCTTTCATT
122587 ATTTGGAACTG-AATTTACTGAATTGGGATTTCCAGAATTGAAAGGCAAATTGGAGCTTTCATT
1 ATTTGGAACTGTAATTT-CTGAATTGGGATTTCCAGAATTGAAAGGCAAATTGGAGCTTTCATT
122650 ATTTGGAAC
1 ATTTGGAAC
122659 ATGATCACCA
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
62 4 0.06
63 66 0.94
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (63 bp):
ATTTGGAACTGTAATTTCTGAATTGGGATTTCCAGAATTGAAAGGCAAATTGGAGCTTTCATT
Found at i:125843 original size:178 final size:178
Alignment explanation
Indices: 125544--125875 Score: 488
Period size: 178 Copynumber: 1.9 Consensus size: 178
125534 TCCGATACTA
* * *
125544 CTTGAAAAATCTATATTCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACG
1 CTTGAAAAATCTATATTCATCTAACCAAATCTCAACCACATCGAATTTAAGGATTTGATTTTACG
* *
125609 AGCATCTGAATTTTGTTTCAATTTAATTAGAAATAAATTCGGAAAAAAAGGAAAAAC-ACTACTA
66 AGCATCTGAATCTTGTTTCAATTTAATTAGAAATAAATTCGGAAAAAAAGGAAAAACGA-TAATA
125673 GAAGCGTGAAAAACCCTACAATTTTGCATGATTTTTGGCAGAAAAACTC
130 GAAGCGTGAAAAACCCTACAATTTTGCATGATTTTTGGCAGAAAAACTC
* *****
125722 CTTGAAATATCTATATTCATCTAACCAAATCTCAGTTGTATCGAATTTAAGGATTTGATTTTACG
1 CTTGAAAAATCTATATTCATCTAACCAAATCTCAACCACATCGAATTTAAGGATTTGATTTTACG
* * * **
125787 AGCATTTGAATCTTGTTTCGATTTAATTATATTTAAATTC-GAAAAAAATGGAAAAACGATAATA
66 AGCATCTGAATCTTGTTTCAATTTAATTAGAAATAAATTCGGAAAAAAA-GGAAAAACGATAATA
125851 GAAGCGTGAAAAACCCTACAATTTT
130 GAAGCGTGAAAAACCCTACAATTTT
125876 TTTTTTGGCG
Statistics
Matches: 136, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
177 8 0.06
178 127 0.93
179 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.33
Consensus pattern (178 bp):
CTTGAAAAATCTATATTCATCTAACCAAATCTCAACCACATCGAATTTAAGGATTTGATTTTACG
AGCATCTGAATCTTGTTTCAATTTAATTAGAAATAAATTCGGAAAAAAAGGAAAAACGATAATAG
AAGCGTGAAAAACCCTACAATTTTGCATGATTTTTGGCAGAAAAACTC
Found at i:127051 original size:653 final size:654
Alignment explanation
Indices: 125694--129614 Score: 4525
Period size: 649 Copynumber: 6.0 Consensus size: 654
125684 AACCCTACAA
* **
125694 TTTTGCATGATTTTTGGCAGAAAAACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGTT
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * * * * * * ***
125759 GTATCGAATTTAAGGATTTGATTTTACGAGCATTTGAATCTTGTTTCGATTTAATTATATTTAAA
66 GCATTGGATTTGAGGATTTGATTTTACAAGCATTTGAATCTTGTTTCGATTTAATAAGAAACAAA
* * * * * *
125824 TTCGAAAAAAATGGAAAAACGATAATAGAAGCGTGAAAAACCCTACAATTTTTTTTTTGGCGTTG
131 TTCGGAAAAAATGGGAAAACGATATTAGAAGCGTAAAAAACCCTACAA-TTTTTTATTGTCGTTG
* * * * * * * * *
125889 AACTATATATATTTTCTAAGTATTGTGGCAAAAAAATTGAGGAAAAACCTTCCGTGTCAGTTTTT
195 AATTATATATTTTTTCTGAGTATTGTGG-TAAAAAATTGAGGAATAACTTTTCGGGTTAGTTTTT
* * * *
125954 -CTAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGATTTTGGC-AAAAA-GCTCG-CCTCG
259 GC-AAAATTTTAGCCGAAATCGTGTACTATCCATCATAGTTTTTGGCTAAAAACG-T-GTTC-CG
* ** * * * * *
126015 AGG-CCCCGGCTTTGTTTTGCATGATTTTTGGCAGAAAGACTCC-TTGAAATATCTATAATCATC
320 -GGACCCCGACTCAGTTTGGCATGATTTTTGGTAGATAGACTCCTTTG-AATATCTATATTCATG
* * ** *
126078 TAACCAAATCTCAGCCACATTGGA-CTTAAGGATTTGCATTTACGAGCATCTGAATTTTGTTTCG
383 TAATCAAATCTCAGCCATATTGGATC-TAAGGATTTGTTTTTACGAGCATCTAAATTTTGTTTCG
* * * * *
126142 ATTTAATT-CAGATTAAATTCGG---GAA--AAAATCGATATTAGAAGCGTG-AAAACTCTTC-A
447 ATTTAATTACA-AATAAATTCGGAATAAAGGAAAAACAATATTAGAAGCGTGAAAAACCCTTCAA
* * *
126199 ATTTTTTTGGCGTTGAACTATATATTTTTTCTGATTATTGTGGCAAAAAATTAAGAAAAAATTTT
511 ATTTTTTTGGCGTT-AACTATACATTTTTTCTGAGTATTGTGGCAAAAAATTATGAAAAAATTTT
* * *
126264 TCGGGTCAATTTTTAGCCGAAATAGTGTACTAACCATCACAATTTTTGGCT-AAAAATGAGTTTC
575 TCGGCTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAAATGAGTTTC
126328 GAGGCCCCGGCTCAG
640 GAGGCCCCGGCTCAG
* *
126343 TTTTGCATGATTTTTGGCGGAAAGATTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
126408 GCATTGGATTTGAGGATTTGATTTTACAAGCATTTGAATCTTGTTTCGATTTAATAAGAAACAAA
66 GCATTGGATTTGAGGATTTGATTTTACAAGCATTTGAATCTTGTTTCGATTTAATAAGAAACAAA
*
126473 TTCGGGAAAACAATAGGGAAAACGATATTAGAAGCGTAAAAAACCCTAC-ATTTATTTATTGTCT
131 TTC-GGAAAA-AAT-GGGAAAACGATATTAGAAGCGTAAAAAACCCTACAATTT-TTTATTGTCG
126537 TTGAATTATATA-TTTTTCTGAGTATTGTGGTAAAAAATTGAGGAATAACTTTTCGGGTTAGTTT
192 TTGAATTATATATTTTTTCTGAGTATTGTGGTAAAAAATTGAGGAATAACTTTTCGGGTTAGTTT
* *
126601 TTGCAAAATTTTAGCCGAAATCGT-AACTATCTATCATAGTTTTTGGCTAAAAACGTGTTCCGGG
257 TTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCATAGTTTTTGGCTAAAAACGTGTTCCGGG
126665 ACCCCGACTCAGTTTGGCATGATTTTTGGTAGATAGACTCCTTTGAATATCTATATTCATGTAAT
322 ACCCCGACTCAGTTTGGCATGATTTTTGGTAGATAGACTCCTTTGAATATCTATATTCATGTAAT
**
126730 CAAATCTCAGCTGTATTGGATCTAAGGATTTGTTTTTACGAGCATCTAAATTTTGTTTCGATTTA
387 CAAATCTCAGCCATATTGGATCTAAGGATTTGTTTTTACGAGCATCTAAATTTTGTTTCGATTTA
*
126795 ATTACAAATAAATTCGGAATAAAGGAAAAACAATATTAGAAGCATGAAAAACCCTTCAAATTTTT
452 ATTACAAATAAATTCGGAATAAAGGAAAAACAATATTAGAAGCGTGAAAAACCCTTCAAATTTTT
* * *
126860 TTGGCGAT-ACTATACATTTTTTCTCAGTATTATGGCAAAAAATTATGAAAAAATTTTTCGGCTC
517 TTGGCGTTAACTATACATTTTTTCTGAGTATTGTGGCAAAAAATTATGAAAAAATTTTTCGGCTC
* *
126924 AA-TTTTAGCCGAAATTGTGTACTAACCATCACGATTTTTGGGTAAAAAATGAGTTTCGAGGCCC
582 AATTTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAAATGAGTTTCGAGGCCC
*
126988 CTGCTCAG
647 CGGCTCAG
* *
126996 TTTTGCATGAATTTTGGCGGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * *
127061 GTATTGGATATGAGGATTTGATTTTACAAGCATTTGAATCTTGTTTCGGTTTAATAAGAAACAAA
66 GCATTGGATTTGAGGATTTGATTTTACAAGCATTTGAATCTTGTTTCGATTTAATAAGAAACAAA
*
127126 TTCGGGAAAACAAAAT-GGAAAACGATATTAGAAGCGTAAAAAACCCTACAATTTTTTATTGTCT
131 TTC-GG--AA-AAAATGGGAAAACGATATTAGAAGCGTAAAAAACCCTACAATTTTTTATTGTCG
*
127190 TTGAATTATATATTTTTTCTGAGTATTGTGGTAAAAAATTGAGGAATACCTTTTCGGGTTAGTTT
192 TTGAATTATATATTTTTTCTGAGTATTGTGGTAAAAAATTGAGGAATAACTTTTCGGGTTAGTTT
* * *
127255 TTGCAAAATTTTAGCCGAAATCGTGTACTATCTATCATAGTTTTTGTCTAAAAACGTGTTCCGGA
257 TTGCAAAATTTTAGCCGAAATCGTGTACTATCCATCATAGTTTTTGGCTAAAAACGTGTTCCGGG
* *
127320 ACCCCGACTCAGTTTGGCATGATTTTTGCTAGATAGACTTCTTTGAATATCTATATTCATGTAAT
322 ACCCCGACTCAGTTTGGCATGATTTTTGGTAGATAGACTCCTTTGAATATCTATATTCATGTAAT
127385 CAAATCTCAGCCATATTGGATCTAAGGATTTGTTTTTACGAGCATCTAAATTTTGTTTCGATTTA
387 CAAATCTCAGCCATATTGGATCTAAGGATTTGTTTTTACGAGCATCTAAATTTTGTTTCGATTTA
* *
127450 ATTACAAATAAATTCAGAATAAAGGAAAAACAATATTAGAAGCGTGAAAAACCCTTCAATTTTTT
452 ATTACAAATAAATTCGGAATAAAGGAAAAACAATATTAGAAGCGTGAAAAACCCTTCAAATTTTT
*
127515 TTGGCGTTGAACTATACATTTTTTCTGAGTATTGTGGCAAAAAATTATGAAAAAAATTTTCGGCT
517 TTGGCGTT-AACTATACATTTTTTCTGAGTATTGTGGCAAAAAATTATGAAAAAATTTTTCGGCT
* * * *
127580 CAATTTTTAGCTGAAATCGTGTACGT---CA-C-GGTTTTTTTGCTAAAAAATGAGTTTCGAGGC
581 CAATTTTTAGCCGAAATCGTGTAC-TAACCATCACGATTTTTGGCTAAAAAATGAGTTTCGAGGC
127640 CCCGGCTCAG
645 CCCGGCTCAG
* * **
127650 TTTTGCATGATTTTTGGCAGAAAAAATCCTTGAAATATCTATATTCATCTAACCAAATCTCAGTT
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * * * * * ***
127715 G-TTTCGAATTTAAGGATTTGATTTTACGAGCATTTGAATCTTGTTTCGATTTAATTATATTTAA
66 GCATT-GGATTTGAGGATTTGATTTTACAAGCATTTGAATCTTGTTTCGATTTAATAAGAAACAA
* * * * * * *
127779 ATTCGAAAAAAATGGAAAAACGATATTAGTAGCGT-GAAAACCCTTCAA-ATTTT-TTGGCGTTG
130 ATTCGGAAAAAATGGGAAAACGATATTAGAAGCGTAAAAAACCCTACAATTTTTTATTGTCGTTG
* * * * * * * * *
127841 AACTATATATATTTTCTAAGTATTGTGGCAAAAAAATTGAGGAAAAACCTTCCGTGTCAGTTTTT
195 AATTATATATTTTTTCTGAGTATTGTGG-TAAAAAATTGAGGAATAACTTTTCGGGTTAGTTTTT
* * * * ***
127906 -CTAAAATTCTAGCCGAAATCGTGTACTAACCATCACAGATTTTGGC-AAAAA-GCTCACCTCGA
259 GC-AAAATTTTAGCCGAAATCGTGTACTATCCATCATAGTTTTTGGCTAAAAACG-TGTTC-CG-
* ** * * ** *
127968 GG-CCCCGGCTTTGTTTTGCATGATTTTTGGTAGAAAGACTCCTTAAAATATCTATATTCATCTA
320 GGACCCCGACTCAGTTTGGCATGATTTTTGGTAGATAGACTCCTTTGAATATCTATATTCATGTA
* * * *
128032 ACCAAATCTCAGCCACATTGGA-CTTAAGGATTTGTTTTTACGAGCATCTTAATTTTGTTTCTAT
385 ATCAAATCTCAGCCATATTGGATC-TAAGGATTTGTTTTTACGAGCATCTAAATTTTGTTTCGAT
* * * * *
128096 TTAATT-CAGATTAAATTCGG---GAA--AAAATCGATATTAGAAGCGTG-AAAACTCTTCAAAT
449 TTAATTACA-AATAAATTCGGAATAAAGGAAAAACAATATTAGAAGCGTGAAAAACCCTTCAAAT
* * * * *
128154 TTTTTTGGCGTTGAACTATATATTTTTTCTGAGTATTATGGCAAACAATTAAGAAAAAATTCTTC
513 TTTTTTGGCGTT-AACTATACATTTTTTCTGAGTATTGTGGCAAAAAATTATGAAAAAATTTTTC
* * ** * * *
128219 GGGTCAATTTTTAGCCGAAGTCGTGTACGTTTCCATCACGATTATTGG-GAAAAAACGAGTTTCG
577 GGCTCAATTTTTAGCCGAAATCGTGTAC-TAACCATCACGATTTTTGGCTAAAAAATGAGTTTCG
128283 AGGCCCCGGCTCAG
641 AGGCCCCGGCTCAG
* * *
128297 TTTTGCATGATTTTTGGCGGAAAGACTCCTTGATATATCTGTATTCATCTAACCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
128362 GCATTGGATTTGAGGATTTGATTTTACAAGCATTTGAATCTTGTTTCGATTTAATAAGAAACAAA
66 GCATTGGATTTGAGGATTTGATTTTACAAGCATTTGAATCTTGTTTCGATTTAATAAGAAACAAA
** *
128427 TTCGGGGAAAAAAAAGGAAAACGATATTAGAAGCGTAAAAAACCCTACAATTTTTTATTGTCTTT
131 TTC--GGAAAAAATGGGAAAACGATATTAGAAGCGTAAAAAACCCTACAATTTTTTATTGTCGTT
* *
128492 GAATTATATATTTTTTCTTGAGTATTGTGGTAAAAAATTAAGGAATAACTTTTCGAGTTAGTTTT
194 GAATTATATATTTTTTC-TGAGTATTGTGGTAAAAAATTGAGGAATAACTTTTCGGGTTAGTTTT
*
128557 TGCAAAATTTTAGCCGAAATCGTGTACTATCCATTATAGTTTTTGGCTAAAAACGTGTTCCGGGA
258 TGCAAAATTTTAGCCGAAATCGTGTACTATCCATCATAGTTTTTGGCTAAAAACGTGTTCCGGGA
128622 CCCCGACTCAGTTTGGCATGATTTTTGGTAGATAGACTCCTTTGAATATCTATATTCATGTAATC
323 CCCCGACTCAGTTTGGCATGATTTTTGGTAGATAGACTCCTTTGAATATCTATATTCATGTAATC
128687 AAATCTCAGCCATATTGGATCTAAGGATTTGTTTTTACGAGCATCTAAATTTTGTTTCGATTTAA
388 AAATCTCAGCCATATTGGATCTAAGGATTTGTTTTTACGAGCATCTAAATTTTGTTTCGATTTAA
* *
128752 TTACAAATAAATTTGGAATAAAGGAAAAACAATATTAGAAGCGTGAAAAACCCTTCAATTTTTTT
453 TTACAAATAAATTCGGAATAAAGGAAAAACAATATTAGAAGCGTGAAAAACCCTTCAAATTTTTT
* * **
128817 TGGCATTGAACTATACATTTTTTCTGAGTATTGTGGAAAAAAATTATGAAAAAAAAAATTTCGGC
518 TGGCGTT-AACTATACATTTTTTCTGAGTATTGTGGCAAAAAATTATG--AAAAAATTTTTCGGC
* *
128882 TCAATTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAAACGAGTTTCGAGG
580 TCAATTTTTAGCCGAAATCGTGTACTAACCATCAC-GATTTTTGGCTAAAAAATGAGTTTCGAGG
*
128947 CCCCGTCTCAG
644 CCCCGGCTCAG
* * *
128958 TTTTGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTATATTCATCGAACCAAATTTCAGCC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * * * * ** * * *
129023 ACAATGGATTT-ACTGATTT-TTTCTTACAAGC-TTCTAAAT-TTGTTTCGGCTTAATTATAAAT
66 GCATTGGATTTGA-GGATTTGATT-TTACAAGCATT-TGAATCTTGTTTCGATTTAATAAGAAAC
* * * * * *
129084 AAATTCAGAAAAAAT-GGAAAACGATATTGGAAGCGTGAAAAATCCTTCAAATTTTT-TTGT-GT
128 AAATTCGGAAAAAATGGGAAAACGATATTAGAAGCGTAAAAAACCCTACAATTTTTTATTGTCGT
** * * * *
129146 TGAATTATATATTTTTTTCTGAGTATTGTGACAGAAAATTCG-GAAAAAAAATAATTTC-GG---
193 TGAATTATATA-TTTTTTCTGAGTATTGTGGTAAAAAATT-GAG-GAATAACT--TTTCGGGTTA
** * ** ** *
129206 G----T-C-ACTTTTTAGCCGAAAATCGTGTA-TGTTAATCACGGTTTTTAGGCTAAAAACGCGT
253 GTTTTTGCAAAATTTTAGCCG-AAATCGTGTACTATCCATCATAGTTTTT-GGCTAAAAACGTG-
* * ** * * * * *
129264 TTCGGGGA-CCCGGCTCAGTTTTACATGATTTTTTGCAGGA-AGCCTCC-TTGAAATAACTGTAT
315 TTCCGGGACCCCGACTCAGTTTGGCATGATTTTTGGTA-GATAGACTCCTTTG-AATATCTATAT
* * * * * * * *
129326 TCATCG-AACCAAATCTCAGCCACAATGGATTTAAGGATATGTTTTTACGAGCATCTGAGTTTAG
378 TCAT-GTAATCAAATCTCAGCCATATTGGATCTAAGGATTTGTTTTTACGAGCATCTAAATTTTG
* * * * * *
129390 TTTTGATTTAATTAGAAATAAATTCAGAAAAAAAAAATTGGAAAAACGATATTGGAAGCGTGAAA
442 TTTCGATTTAATTACAAATAAATTC-G---GAATAAA--GGAAAAACAATATTAGAAGCGTGAAA
* * *** * * * *
129455 CACCTTTC-AATTTTTTTTAAGTTGAA-T-TAGATATTTTTATGAGTATTGTGACAATAAATT-T
501 AACCCTTCAAATTTTTTTGGCGTT-AACTATACAT-TTTTTCTGAGTATTGTGGCAAAAAATTAT
* * * * *
129516 -AGAAAATATTTTCGTG-TCACTTTTGAGCCGAAATCGTGTAATAACAATCACGATTTTTGGGCT
564 GAAAAAAT-TTTTCG-GCTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGATTTTT-GGCT
** * * * *
129579 -AAAAATGCCTTTCGGGGACTCGGCTTAG
626 AAAAAATGAGTTTCGAGGCCCCGGCTCAG
129607 TTTTGCAT
1 TTTTGCAT
Statistics
Matches: 2831, Mismatches: 350, Indels: 182
0.84 0.10 0.05
Matches are distributed among these distances:
643 98 0.03
644 19 0.01
646 4 0.00
647 146 0.05
648 217 0.08
649 582 0.21
650 106 0.04
651 52 0.02
652 292 0.10
653 337 0.12
654 252 0.09
655 315 0.11
656 20 0.01
657 111 0.04
658 88 0.03
659 9 0.00
660 70 0.02
661 113 0.04
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (654 bp):
TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
GCATTGGATTTGAGGATTTGATTTTACAAGCATTTGAATCTTGTTTCGATTTAATAAGAAACAAA
TTCGGAAAAAATGGGAAAACGATATTAGAAGCGTAAAAAACCCTACAATTTTTTATTGTCGTTGA
ATTATATATTTTTTCTGAGTATTGTGGTAAAAAATTGAGGAATAACTTTTCGGGTTAGTTTTTGC
AAAATTTTAGCCGAAATCGTGTACTATCCATCATAGTTTTTGGCTAAAAACGTGTTCCGGGACCC
CGACTCAGTTTGGCATGATTTTTGGTAGATAGACTCCTTTGAATATCTATATTCATGTAATCAAA
TCTCAGCCATATTGGATCTAAGGATTTGTTTTTACGAGCATCTAAATTTTGTTTCGATTTAATTA
CAAATAAATTCGGAATAAAGGAAAAACAATATTAGAAGCGTGAAAAACCCTTCAAATTTTTTTGG
CGTTAACTATACATTTTTTCTGAGTATTGTGGCAAAAAATTATGAAAAAATTTTTCGGCTCAATT
TTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAAATGAGTTTCGAGGCCCCGGC
TCAG
Done.