Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020824.1 Corchorus olitorius cultivar O-4 contig20857, 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: 13623
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:2174 original size:1 final size:1
Alignment explanation
Indices: 2168--2270 Score: 89
Period size: 1 Copynumber: 103.0 Consensus size: 1
2158 GTATACATTG
* * * * * * * *
2168 TTTTTTTGTTTTTTTTTTGTTTTTTGTTTTTTGTTTTTTGTTTTTTGTTTTTTGTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
2233 TTGTTTTTTGTTTTTTGTTTTTTGTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2271 AATATATGGA
Statistics
Matches: 76, Mismatches: 26, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (1 bp):
T
Found at i:2181 original size:7 final size:7
Alignment explanation
Indices: 2165--2269 Score: 187
Period size: 7 Copynumber: 15.3 Consensus size: 7
2155 TATGTATACA
2165 TTGTTTT
1 TTGTTTT
*
2172 TT-TGTT
1 TTGTTTT
2178 TT-TTTT
1 TTGTTTT
2184 TTGTTTT
1 TTGTTTT
2191 TTGTTTT
1 TTGTTTT
2198 TTGTTTT
1 TTGTTTT
2205 TTGTTTT
1 TTGTTTT
2212 TTGTTTT
1 TTGTTTT
2219 TTGTTTT
1 TTGTTTT
2226 TTGTTTT
1 TTGTTTT
2233 TTGTTTT
1 TTGTTTT
2240 TTGTTTT
1 TTGTTTT
2247 TTGTTTT
1 TTGTTTT
2254 TTGTTTT
1 TTGTTTT
2261 TTGTTTT
1 TTGTTTT
2268 TT
1 TT
2270 TAATATATGG
Statistics
Matches: 95, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
6 10 0.11
7 85 0.89
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (7 bp):
TTGTTTT
Found at i:5628 original size:323 final size:323
Alignment explanation
Indices: 4962--13587 Score: 10480
Period size: 321 Copynumber: 26.8 Consensus size: 323
4952 AATCAGACTC
* * * *
4962 CAAATCCTTAGATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* * * *
5027 CTGCCAAAAATCATGCAAAACTGAG-CTGGGC-CCGAAACGCGTTTTTAGCTAAAAACCGTGATG
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
* * * * * * * * *
5090 GTTAGTACATGATTTCGGCTAAAA-ATAAATCAGAAAA--TATTCTC-ATTTTTTTGCAAAATAT
131 GTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTCTCAATTTTTTTCCATAATAC
5151 TTAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTTCACGCTTCTAATATCGTT
196 TTAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGG-TTTTTCACGCTTCTAATATCGTT
* * * * * *
5216 TTTGCA--TTTTTCCCAAATTTATTTATATTTAACTGTAAACAAGATTTAGATGCTCGTAAATA
260 TTTGCATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACAAGATTCAGATTCTCGTAAACA
* *
5278 CAAATTCTTAACTCCATTGTGGCTGAGATTTGGTTCGACGAATATAGATATTTCAAGGAGTCTTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* *
5343 CGGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAGAAACCGTGATA
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
* * * * *
5408 GTTAGTGCACGATTTCGGCTAAAATCTGACTCGGAAAATTTTTTCACAATTTTTTTCCATAGTAC
131 GTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTCTCAATTTTTTTCCATAATAC
* * * *
5473 TTAGAAAATATATATAACTCAACGCCAAAAAAATTGAAGGGTTTTTCACGGTTCTATTATCGTTT
196 TTAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTT
* * * *
5538 TTGCATTTTTTTCCCGAATTTATTTATATTTAACTTTAAACAAGATTCATATTCTCGTAAAAA
261 TTGCATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACAAGATTCAGATTCTCGTAAACA
* * * * *
5601 CAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAAAATAGATATTTCAAGAAGTTTTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAG---TC
* * * * * * *
5666 TTTTTTCGAAAAATCACGCAAAACTGAGTCGGGGCGCCGAAATGCGTTTTTACCCAAAAACCCTG
63 TTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTG
* * * *
5731 ATAGTTAGTACATGATTTCGGCCAAAATCAGAATCGGAAAATTTTTTTTACAATTTTTTTTCCAC
128 ATAGTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTCT-CAA-TTTTTTTCCAT
* *
5796 AATAC-TCGGAAAAATATATAATT------C-----AATTGAAGGGTTTTTCACGCTTCTAATAT
191 AATACTTAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATAT
** * * *
5849 CGTTTTCCCATTTTTTTCCCCGAATTTATTTCTATTTAACACTAAACAAGATTCAGATTGTCGTG
256 CGTTTTTGCATTTTTTT-CCCGAATTTATTTCTATTTAACTCTAAACAAGATTCAGATTCTCGTA
5914 AACA
320 AACA
* * * *
5918 AAAATTCTTAAATCCATTGTGGATGAGATTGGGTTCGAAGAATATAGATATTTCAAGGAGTCTTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* *
5983 CTGCCAAAAATCATGCAAAACTGAGTCGGGGCGCCGAAATGCGTTTTTAGCAAAAAACCGTGATA
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
*
6048 GTTATTACACGATTTCGGCCAAAATCTGAATC-GAAAATTTTTTTCTCAA-TTTTTTCCATAATA
131 GTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAA-TTTTTTCTCAATTTTTTTCCATAATA
* * * * *
6111 -TTCAGAAAAAATATATAATTCAAGGCCAAAATAATTGAAGGGTTTTTTACGCTTTTAATATTGT
195 CTT-AGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGT
* * * * * * * * *
6175 TTTTCCAATTCTTCTACCGAATTTGTTTTTATTTAACTGTAAACAAGATTTAGATACTCGTAAAC
259 TTTTGC-ATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACAAGATTCAGATTCTCGTAAAC
6240 A
323 A
* * *
6241 CAAATTCTTAAATCCATTGTGGATGAGATTTGATTCAATGAATATAGATATTTCAAGGAGTCTTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* * *
6306 CTGCCAAAAATCATGCAAAACTGAACCGGGGCGCCGAAATGCGATTTTAGCAAAAAACCGTGATA
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
* * ** * * *
6371 ATTTGTACACGATTTCGGGGAAAATCTGACTCGGAAAATTTTTTCACTATTTTTTTCCATAATAC
131 GTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTCTCAATTTTTTTCCATAATAC
* * * * * * *
6436 TCAGAAAAAAAATATAATTTAATGCTAAACAAATTGAAGGGTTTTTCATGCTTCTAATATCGTTT
196 TTAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTT
* * *
6501 TTGCA--TTTTTCCCGAATTTATTTCTGTTTAACTTTAAACAAGATTCAGATTCTCGTAAAAA
261 TTGCATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACAAGATTCAGATTCTCGTAAACA
* ** *
6562 CAAATCCCTCGTAAAAACAAATCCTAAAATTCATTGTGGCAAAGATTTGGTTAGATGAATATAGA
1 CAAA----T--T-----C---T--T-AAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGA
* * * * *
6627 TATTTCAAGAAGTGTTTTTGACAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGATTTT
49 TATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTT
* * * *
6692 ATCCAAAAATCGTGATAGTTAGTACACGATTTCGGCCAAAATCTGATTCGAAAAATTTTTTCTCA
114 AGCCAAAAACCGTGATAGTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTCTCA
* * * ** *
6757 ATTTTTTTCCATAATACTCAGAAAAAATATATAATTCTACACCTTAAAAATTGAAGGGTTTTTAA
179 ATTTTTTTCCATAATACTTAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCA
* * * *
6822 CGCTTCTAATATCGTTTTTCCATTTTTTTTCCCGAATTTATTTCTATTCAACTCAAAATATA-AT
244 CGCTTCTAATATCGTTTTTGCA-TTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACA-AGAT
*
6886 TCAGATGCTCGTAAACA
307 TCAGATTCTCGTAAACA
* * *
6903 CAAATTCTTAAATCTATTGTGGATGAGATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* *
6968 CTGCCAAAAATCATGGAAAACTGAGCCGGGGCGCCGAAATGCGATTTTAGCCAAAAACCGTGATA
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
* * * * *
7033 GTTAGTACACGATTTCGGCTAAAATCTGACTCGG-AAATCTTTT-ACACTATTTTTTCCATAATA
131 GTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTCTCAAT-TTTTTTCCATAATA
*
7096 CTCAGAAAAAATATATAATTCAACGCCAAAAAAATTTG-AGGGTTTTTCACGCTTCTAATATCGT
195 CTTAGAAAAAATATATAATTCAACGCCAAAAAAA-TTGAAGGGTTTTTCACGCTTCTAATATCGT
* * *
7160 TTTTGCATTTTTTTCCCGAATTTTATTTCTATTCAACTTTAAACAAGATTCTGATTCTCGTAAAA
259 TTTTGCATTTTTTTCCCGAA-TTTATTTCTATTTAACTCTAAACAAGATTCAGATTCTCGT----
7225 ACAAATCCCTCGTGAAAA
319 --AAA-----C------A
* * * *
7243 CAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGAAGTTTTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* * * * *
7308 CTGCAAAAAATAATGCAAAACTGAGCCGGGGTGCCGAATTGCGTTTTTACCCAAAAACCGTGATA
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
*
7373 ---ACGTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTCTCAATTATTTTTTCCACAA
131 GTTA-GTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTCTCAA-T-TTTTTTCCATAA
* * *
7435 TACTT-GGAAAAATATATAATTCAATGCCAAAAAAATTGAAGGATTTTTCACGCTTCTAATATCG
193 TACTTAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCG
* * * * *
7499 TTTTTCCA-TTTTTTCTCGAATTTATTTGTATTTAACTCTAAACAAGAATCAGATTCACGTAAAC
258 TTTTTGCATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACAAGATTCAGATTCTCGTAAAC
7563 A
323 A
* *** * * * *
7564 CAAATTCATAAATCCATTGTAAATGAGATTTGGTTTGATGAATATAGATATTGCAAGAAGTTTTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* * * * *
7629 CTGCCAAAATTCATGCAAAACTGAGCCGGGGCGCCGAAATGTGATGTTACCCAAAAACCGTGATA
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
*
7694 ---ACGTACACGATTTCGGCCAAAATCTGATTC-GAAAATTTTTT-TAACAATATTTTTT-CATA
131 GTTA-GTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTCT--CAAT-TTTTTTCCATA
* * *
7753 ATACTCAGAAAAAATATATAATTCAACGCCATAAAAAGTGAAGGGGTTTTTCACGCTTCTAATAT
192 ATACTTAGAAAAAATATATAATTCAACGCCAAAAAAATTGAA-GGGTTTTTCACGCTTCTAATAT
* * * * *
7818 CGTTTTTCCATATTTTT-GCGAATTTATTTCTATTTAACTCTCAACATA-ATTCAGATACTCGTA
256 CGTTTTTGCATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACA-AGATTCAGATTCTCGTA
7881 AACA
320 AACA
* ** *
7885 CAAATTCTTAAATCCATTGTGGATGAGATTTGGTTCGATGAATATAGATATTTCAAAAAGTATTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* * * * *
7950 CTGCCAAAAATCATGCAAAACTGAGTCGGGGCGTCGGAATGCGTTTTTAGCAAAAAACCATGATA
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
* * *
8015 GTTAGTACACGATTTCGGCTAAAATCTGACTCGG-AAATTTTTT-TCACTTTTTTTTCCATAATA
131 GTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTCTCA-ATTTTTTTCCATAATA
* *
8078 CTCAGAAAAAATATAAAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTT
195 CTTAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTT
* * * * * *
8143 TTTGCA-TTTTTTCGCGAATTTATTTATAATTAACT-TAAAGAAGATTTAGATGCTCGTAAACA
260 TTTGCATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACAAGATTCAGATTCTCGTAAACA
* **
8205 CAAATTCTTAAATCCATTGTGGCTGGGATTTGGTTCGACAAATATAGATATTTCAAGGAGTCTTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* * *
8270 TTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGTCAAAAACCGTGACA
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
* *
8335 GTTAGTACACGATTTCGGCCAAAATCTGATTCGAAAAATTTTTTCTCAATTTTTTTCCATAATA-
131 GTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTCTCAATTTTTTTCCATAATAC
*
8399 TTCAGAAAAAA-ATTATAATTCAACGCCATAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGT
196 TT-AGAAAAAATA-TATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGT
* * *
8463 TTTTCCATTTTTTCCCCGAATTTATTTCTATTTAACTCTAAACATA-ATTCAGATGCTCGTAAAC
259 TTTTGCATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACA-AGATTCAGATTCTCGTAAAC
8527 A
323 A
* *
8528 CAAATTCTTAAATCCATTGTGGATGAGATTTGGTTCGATGAATATAGATATTTCAAAGAGTCTTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* * *
8593 CTGCCAAAAATCATGCAAAACTGAGCCGGAGCGCCGAAATGAGTTTTTAGCAAAAAACCGTGATA
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
*
8658 ---ACGTACACGATTTCGGCCAAAATCTGAATCGAAAAATTTGTTTCTCAATTTTTTTCCATAAT
131 GTTA-GTACACGATTTCGGCCAAAATCTGAATCGGAAAATTT-TTTCTCAATTTTTTTCCATAAT
** * *
8720 ACTCGGAAAAAATATATTATTTAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGT
194 ACTTAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGT
* * * * * **
8785 TTTTGCA--TTTTTCCTGAATTTATTTCAATTTAACTATAATCAAGATTTAGAAGCTCGTAAACA
259 TTTTGCATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACAAGATTCAGATTCTCGTAAACA
* * *
8848 CAAATTCTTAAATCCATTGTGGCAGAGATTTGGCTCGACGAATATAGATATTTCAAGGAGTCTTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* * * * * *
8913 GTGCTAAAAATCAAGCAAAACTGAGAC-GGGCGCCCAAATGCGATTTTAGCCAAAAACCGTGATA
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
* *
8977 GTTAGTACACGATTTCGGCCAAAATCTGATTC-GAAAATTGTTTTTCTCAATTTACTTTCCATAA
131 GTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAA-T-TTTTTCTCAATTT-TTTTCCATAA
*
9041 TA-TTAAGAAAAAATATATAATTCAACGCCATAAAAATTGAAGGGTTTTTCACGCTTCTAATATC
193 TACTT-AGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATC
* * * * * *
9105 G-TTTTGCCATTTTTTTTCAGAATTTATGTCTATTTAACTCTAAATATA-ATTAAGATTCCCGTA
257 GTTTTTG-CATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACA-AGATTCAGATTCTCGTA
9168 AACA
320 AACA
* * *
9172 CAAATTCTTAAACCCATTGTGGATGAGATTTGGTTCGATAAATATAGATATTTCAAAGG-GTCTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTC-AAGGAGTCTT
* * * * * *
9236 TCTGCAAAAAAATTATGCAAAAACTGAGCCGGGGCACCGCAATACGTTTTTAGCCAAAAAAATCG
65 TCTGC-CAAAAATCATGC-AAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCC--AAAAACCG
* *
9301 TGATACTTAGTACACAATTTCGGCCAAAATCTGAATC-GAAAATTTTTTTCTCAATTTTTTTCCA
126 TGATAGTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAA-TTTTTTCTCAATTTTTTTCCA
* ** * *
9365 TAATAC-TCGAAAAAATATATTTTTCAACGCCAGAAAAATTGAAGGGTTTTTCTCGCTTCTAATA
190 TAATACTTAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATA
* *
9429 TCGTTTTTACATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACATA-ATTCAGATGCTCGT
255 TCGTTTTTGCATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACA-AGATTCAGATTCTCGT
*
9493 TAACA
319 AAACA
* * * * * *
9498 CAAATTCTTAAATCCATTGTTGATGAGATTTGATTCGATGAATATAGATATTTTAAAGAGACTTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* * *
9563 CTTCCAAAAATCATGCAAAAAACTGAGCCGGGGCGCTGAAATGCGTTTTTAGCAAAAAACCGTGA
66 CTGCCAAAAATCATGC--AAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGA
* * * *
9628 TAGTTAGTACCCAATTTCGGCCAAAATCTGAATC-GAAAATTTTTTCTCAATTTTTCTCCAAAAT
129 TAGTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTCTCAATTTTTTTCCATAAT
* * * *
9692 ACTCT-GAAAAAATATATTATTCAACGTCAAAAAAATCGAAGGGTTTTTCATGCTTCTAATATCG
194 ACT-TAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCG
9756 -TTTTGTCA-TTTTTTCCCGAATTTATTTCTATTTAACTCTAAACAAGATTCAGATTCTCGTAAA
258 TTTTTG-CATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACAAGATTCAGATTCTCGTAAA
*
9819 AA
322 CA
* * * * * * *
9821 CAAATCCTTAAATCCTTTGTGACTGAGATTTGGTTCAAGGAAAATAGATATTTCAAGGAGTCTCT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* * * * *
9886 CTTCCAAAAATCATGCAAAAATGAGCCGGGGCGCCGAAATGTGTTTTTAGCAAAAAACCGTGTTA
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
* *
9951 GTTAGTACACGATTTCGGCCAAAATCTGATTCGAAAAATTTTTTCTCAATTTTTTTTCCATAATA
131 GTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTCTCAA-TTTTTTTCCATAATA
* * * * *
10016 -TTCAGAAAAAATTTAAAATTCAACGCCATAGAAATTGAAGGGTTTTTCATGCTTCTAATATCGT
195 CTT-AGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGT
* * * *
10080 TTTTCCATTTTTTTCCCGAATTTATTTCTGTTTAACTCAAAACATA-ATTCAGATGCTCGTAAAC
259 TTTTGCATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACA-AGATTCAGATTCTCGTAAAC
10144 A
323 A
* * *
10145 CAAATTCTTAAATCCATTGTGGATGAGATTTGGTTCAATGAATATAGATATTTCAAAGAGTCTTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* * * *
10210 CTGCCAAAAAT-ATGCAAAACTGAACCGGAGCGCCGAAATGCGATTTTAGCCAAAAACTGTGATA
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
* ** * *
10274 GTTAGTACACGATATCGGCCAAAATCTGAATC-GAATTTTTTTTTTCAA-TTTTTTACATAATAC
131 GTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTCTCAATTTTTTTCCATAATAC
* *
10337 -TAGAAAAAATATATTATTTAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTT
196 TTAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTT
* * * * **
10401 TTGCA-TTTTTTCCCGAATTTATTTCAATTTAACTGTAATCAAGATTTAGAAGCTCGTAAACA
261 TTGCATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACAAGATTCAGATTCTCGTAAACA
* *
10463 CAAATTCTTAAATCCATTGTGGCTGATATTTGGTTCAATGAATATAGATATTTCAAGGAGTCTTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* * * * * *
10528 CTGCCAATAATCATGCAAAACTAAGTCGGGGCGCCGAAATGCGATTTTATCCAAAAACTGTGATA
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
* * * *
10593 GTTAGTACACGATATT-GGCGAAAATCTGAATC-GAAATTTTTTTTTTCAA-TTTTTTCCATAGT
131 GTTAGTACACGAT-TTCGGCCAAAATCTGAATCGGAAA-ATTTTTTCTCAATTTTTTTCCATAAT
* * * *
10655 -CCTCGAAAAAATATATTATTTAACGCCAAAAAAATTGAAGGGTTTTTTCACGCTTCTAATATCG
194 ACTTAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGG-TTTTTCACGCTTCTAATATCG
* * * **
10719 TTTTTGCATTTTTTTCCCGAATTTATTTCTATTTAACTGTAATCAAGATTTAGAAGCTCGTAAAC
258 TTTTTGCATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACAAGATTCAGATTCTCGTAAAC
10784 A
323 A
* * *
10785 CAAATTCTTAAATCCATTGTGGCTAATATTTGGTTCAATGAATATAGATATTTCAAGGAGTCTTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* ** * * * * *
10850 TTGCCAGTAATCATGCAAAACTAAGTCGGGGCGCCGAAATGCGATTTTAGCCAAAAACTGTTATA
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
* * *
10915 GTTAGTACACGATATT-GGTCAAAATCTGAATC-GAAATTTTTTTTTTCAA-TTTTTTCCATAAT
131 GTTAGTACACGAT-TTCGGCCAAAATCTGAATCGGAAA-ATTTTTTCTCAATTTTTTTCCATAAT
* * *
10977 A-TTCGAAAAAATATATTATTCAACGCCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCG-
194 ACTTAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGT
* *
11040 TTTTGTCATTATTTTTCCCTAAATTTATTTCTATTTAACTGTAAACAAGATTCAGATTCTCGTAA
259 TTTTG-CATT-TTTTTCCC-GAATTTATTTCTATTTAACTCTAAACAAGATTCAGATTCTCGTAA
*
11105 AAA
321 ACA
* * * * * *
11108 GAAATCCTTAAATCCATTGTGGCTGAGACTTGATTCAATGAATATAGATATTTCAAGGAGTCTAT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* * * *
11173 CTGCCATAAATCATGCGAAACTAAGCTGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
* * * *
11238 GTTATTACACGATTTCGGCCAAAATTTGATTCGAAAAATTTTTTTCTCAATTTTTTTCCATAATA
131 GTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAA-TTTTTTCTCAATTTTTTTCCATAATA
* * * *
11303 -TTCAGGAAAAATATATAATTCAATGCCATAAAAATTGAAGGGTTTTTCACGCTTATAATATCGT
195 CTT-AGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGT
* * *
11367 TTTT-CCTTTTTTT-CCGAATTTATTTCTATTTAACTGTAAACATA-ATTCAGATGCTCGTAAAC
259 TTTTGCATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACA-AGATTCAGATTCTCGTAAAC
11429 A
323 A
*
11430 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTTTTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAG-TCTT
* * * *
11495 TCTGCCAAAAATCATGCAAAACTGAGTCGAGGCGCTGAAATGCGATTTTAGCCAAAAACCGTGAT
65 TCTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGAT
* * *
11560 AGTTAGTACACGATTTCGACC-AAATCTGATTCGAAAAATTTTTTCTCAATTCTTTTTTCCATAA
130 AGTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTCTCAA-T-TTTTTTCCATAA
* * *
11624 TAC-TA-AAAAAA-ATATAATTCAACGCCATAAAAATTGAAGAGTTTTTCACGCTTGTAATATCG
193 TACTTAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCG
* * * *
11686 TTTTT-CCTTTTTTTTCCGAATTTATTTTTATTTAACTGTAAACATA-ATTCAGATTCTCGTAAA
258 TTTTTGCATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACA-AGATTCAGATTCTCGTAAA
11749 CA
322 CA
* *
11751 CAAATTCTTAAATCCATTGTGGCTGAGATTTGATTCGATGAATATAGATATTTAAAGGAGTCTTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* * * *
11816 CTCCCGAAAATCATGCAATACTGAGCCGGGGCGCCGAAATGCATTTTTAGCCAAAAACCGTGATA
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
*
11881 GTTAGTACACGATTTCAGCCAAAATCTGAATC-GAAAATTTTTTCTCAA-TTTTTTCCATAATA-
131 GTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTCTCAATTTTTTTCCATAATAC
* * * *
11943 TTCAG-AAAAATATATAATTCAACGCCATAATAATTGAAGGGTTTCTCACGCTTCTAATATTGTT
196 TT-AGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTT
** * * * * * **
12007 TTT-CAAATTTTTTAACCAAATTTATGTCTATTTAACTGTAAAGAAGATTTAGAAGCTCGTAAAC
260 TTTGC--ATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACAAGATTCAGATTCTCGTAAAC
12071 A
323 A
12072 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* * ** ** *
12137 CTGCCAAAAATCATGCAAAACTAAGTCGGGGCGCCGAAATGCCATTTTAGCCAAAAATTGTTATA
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
* * * * *
12202 GTTAGTACACAATTTTGGCCAATATCTGAATC-G-AATTTTTTTTTCAA-TTTTTTCCATAATAC
131 GTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTCTCAATTTTTTTCCATAATAC
* * * *
12264 -TCGAAAAAATATATTATTCAACGCCAAAAAAATTGAAGGTTTTTTCACGTTTCTAATATCG-TT
196 TTAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTT
* * * *
12327 TTGTCATTTTTTTCCCCGAATTTATTTATATTTAACTGTAAATAAGATTCAGATTCTCGTAAAAA
261 TTG-CATTTTTTT-CCCGAATTTATTTCTATTTAACTCTAAACAAGATTCAGATTCTCGTAAACA
* * * * * *
12392 GAAATCCTTAAATCCATTGTGGCTGAGACTTGGTTCAAGGAATATAGATATTTCAAGGAGTCTAT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* * *
12457 CTGCCAAAAATCATGCGAAACTAAGCCTGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
* * *
12522 GTTAGTACACGATTTCAGCTAAAATCTGACTCGG-AAATTTTTT-TC-A--------C--AATAC
131 GTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTCTCAATTTTTTTCCATAATAC
* * * *
12574 TCAGAGAAAATATATAATTCAACGCCAAAACAATTGAAGGGTTTTTCACGATTCTAATATCG-TT
196 TTAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTT
* * * *
12638 TTGCATTTTTTTGCCGAATTTATTTCTATTTAACTTTAAA-AGAGATTTAGATTCTCGTAAAAA
261 TTGCATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACA-AGATTCAGATTCTCGTAAACA
* * * * * * * * *
12701 CAAATCCTTAAATCCAATGTGGCTGACATTTGGTTAGATAAATGTAGATATTTTAAAGAGTTTTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* * * *
12766 CTGCCAAAAATCATGCAAAACTGAGCTGGGGCGTCGAAATGCGATTTTAGGCAAAAACCGTGATA
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
* * * * * * *
12831 GTTAATACTCGATTTCGGCCAAAATCTGATTCGAAAAATTTTTACTCAATTTTTTTCCACAAGAC
131 GTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTCTCAATTTTTTTCCATAATAC
* * * *
12896 -TCGTAAAAATATATAATTCAACGCCAAAAAAATTGATGGGTTTTTCACGCTTCTAGTATCGTTT
196 TTAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTT
* * * *
12960 TTACA-TTTTTTCCCTAATTTATGTCTATTTAACTCTAAACAAGATTCAGATTCTCGTGAACA
261 TTGCATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACAAGATTCAGATTCTCGTAAACA
* * * *
13022 CAAATTTTTAAATCCATTGTGGATGAGATTTGGTTCGATGAATATAGATATATCAAGAAGTCTTT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* * * * *
13087 TTGCCAAAAATCATGCAAAACTGAGCCGGGGCGGCAAAATGCGATTTTAGCCAAAATCCGTGATA
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
*** * * * * *
13152 AACA-TACACGATTTCGGCAAAAATAT-AATTC-AAAAATTTATTCTC-ACTTTTTTCCATAATA
131 GTTAGTACACGATTTCGGCCAAAATCTGAA-TCGGAAAATTTTTTCTCAATTTTTTTCCATAATA
* * * *
13213 CTCT-G-AAAAACATATAATTCAATGCCATAAAAATTAAAGGGTTTTTCACGCTTCTAATATCG-
195 CT-TAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGT
*
13275 TTTTGTCATTTTTTTCCCCGAATTTATTTCTATTTAACTCTAAACAAGTTTCAGATTCTCGTAAA
259 TTTTG-CATTTTTTT-CCCGAATTTATTTCTATTTAACTCTAAACAAGATTCAGATTCTCGTAAA
13340 -A
322 CA
* * * * ** * *
13341 GAAATCCTTAAATCCATTATGGCTGAGACTTGGTTAAAGGAATATAGATATTTCAAGGAGTCTAT
1 CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
* * *
13406 CTGCAAAAAATCATGCAAATCTGAGCCGGGGCGCCGAAATGCG-TTTTAGCAAAAAACCGTAGAT
66 CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGT-GAT
* * *
13470 AGTTTAGTACACGATTTCGACCAAAATCTGAATCGAAAAATTTTTACTTCAA--TTTTTCCTATA
130 AG-TTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTC-TCAATTTTTTTCC-ATA
* * *
13533 ATACTCAGAAAAAATAT-TAATTCAAGGCCAAAATAATTGAAGGGTTTTT-ACGCTT
192 ATACTTAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTT
13588 TTGATTTTTT
Statistics
Matches: 7252, Mismatches: 850, Indels: 410
0.85 0.10 0.05
Matches are distributed among these distances:
308 1 0.00
309 183 0.03
310 22 0.00
311 75 0.01
312 17 0.00
313 8 0.00
314 98 0.01
316 125 0.02
317 121 0.02
318 259 0.04
319 373 0.05
320 930 0.13
321 1342 0.19
322 773 0.11
323 1241 0.17
324 575 0.08
325 51 0.01
326 358 0.05
327 59 0.01
328 27 0.00
329 51 0.01
330 1 0.00
332 4 0.00
334 1 0.00
335 2 0.00
337 3 0.00
338 283 0.04
339 22 0.00
340 178 0.02
341 68 0.01
342 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (323 bp):
CAAATTCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
CTGCCAAAAATCATGCAAAACTGAGCCGGGGCGCCGAAATGCGTTTTTAGCCAAAAACCGTGATA
GTTAGTACACGATTTCGGCCAAAATCTGAATCGGAAAATTTTTTCTCAATTTTTTTCCATAATAC
TTAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTT
TTGCATTTTTTTCCCGAATTTATTTCTATTTAACTCTAAACAAGATTCAGATTCTCGTAAACA
Found at i:6574 original size:17 final size:17
Alignment explanation
Indices: 6552--6585 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
6542 GATTCAGATT
6552 CTCGTAAAAACAAATCC
1 CTCGTAAAAACAAATCC
6569 CTCGTAAAAACAAATCC
1 CTCGTAAAAACAAATCC
6586 TAAAATTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.29, G:0.06, T:0.18
Consensus pattern (17 bp):
CTCGTAAAAACAAATCC
Found at i:7242 original size:17 final size:17
Alignment explanation
Indices: 7216--7249 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
7206 GATTCTGATT
7216 CTCGTAAAAACAAATCC
1 CTCGTAAAAACAAATCC
*
7233 CTCGTGAAAACAAATCC
1 CTCGTAAAAACAAATCC
7250 TTAAATCCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.29, G:0.09, T:0.18
Consensus pattern (17 bp):
CTCGTAAAAACAAATCC
Done.