Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012051.1 Corchorus olitorius cultivar O-4 contig12084, 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: 102432
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1940 original size:2 final size:2
Alignment explanation
Indices: 1933--1966 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1923 GATATGAATT
1933 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
1967 ATTTGAGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4239 original size:39 final size:39
Alignment explanation
Indices: 4184--4259 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
4174 TGACATAGTT
*
4184 TGCTTTGGTTTCTCCTTGGGAGAACCAGTTCCTGAAGTC
1 TGCTTTGGTTTATCCTTGGGAGAACCAGTTCCTGAAGTC
*
4223 TGCTTTGGTTTATCCTTGGGAGAACTAGTTCCTGAAG
1 TGCTTTGGTTTATCCTTGGGAGAACCAGTTCCTGAAG
4260 CATGATCATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (39 bp):
TGCTTTGGTTTATCCTTGGGAGAACCAGTTCCTGAAGTC
Found at i:11655 original size:3 final size:3
Alignment explanation
Indices: 11647--11685 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
11637 GTTTGAAGCA
11647 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
11686 GTAGACGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:43792 original size:6 final size:6
Alignment explanation
Indices: 43782--43820 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
43772 GGATAGCGGC
* *
43782 AGGGAC AGGGAA AGGGAA AGGGAC AGGGAA AGGGAA AGG
1 AGGGAA AGGGAA AGGGAA AGGGAA AGGGAA AGGGAA AGG
43821 CTGGTCCGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.44, C:0.05, G:0.51, T:0.00
Consensus pattern (6 bp):
AGGGAA
Found at i:43805 original size:18 final size:18
Alignment explanation
Indices: 43782--43820 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
43772 GGATAGCGGC
43782 AGGGACAGGGAAAGGGAA
1 AGGGACAGGGAAAGGGAA
43800 AGGGACAGGGAAAGGGAA
1 AGGGACAGGGAAAGGGAA
43818 AGG
1 AGG
43821 CTGGTCCGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.05, G:0.51, T:0.00
Consensus pattern (18 bp):
AGGGACAGGGAAAGGGAA
Found at i:47066 original size:21 final size:21
Alignment explanation
Indices: 47040--47081 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
47030 TGTTGCGTTT
*
47040 GCAGACAGTGATAATTTCAAA
1 GCAGACAGTGATAATTCCAAA
*
47061 GCAGACAGTGATTATTCCAAA
1 GCAGACAGTGATAATTCCAAA
47082 CCTGGCAACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (21 bp):
GCAGACAGTGATAATTCCAAA
Found at i:61251 original size:2 final size:2
Alignment explanation
Indices: 61244--61284 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
61234 GATTCTCATA
61244 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
61285 AATGTAGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:73294 original size:16 final size:16
Alignment explanation
Indices: 73269--73299 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
73259 ACAGTTTTTT
*
73269 TTTTTTTTTTTTTCTG
1 TTTTTGTTTTTTTCTG
73285 TTTTTGTTTTTTTCT
1 TTTTTGTTTTTTTCT
73300 CATTTCGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.87
Consensus pattern (16 bp):
TTTTTGTTTTTTTCTG
Found at i:76284 original size:16 final size:17
Alignment explanation
Indices: 76252--76284 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
76242 ACACTTTCAC
*
76252 CTCTCCTCTTTCTTTCT
1 CTCTCCTCTTCCTTTCT
76269 CTCTCC-CTTCCTTTCT
1 CTCTCCTCTTCCTTTCT
76285 AATTTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (17 bp):
CTCTCCTCTTCCTTTCT
Found at i:98115 original size:28 final size:28
Alignment explanation
Indices: 98080--98137 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
98070 GAGTCTTGTT
98080 AAGATCTTCGGACCTGTCTGTCATTAAA
1 AAGATCTTCGGACCTGTCTGTCATTAAA
98108 AAGATCTTCGGACCTGTCTGTCATTAAA
1 AAGATCTTCGGACCTGTCTGTCATTAAA
98136 AA
1 AA
98138 AAACAAGCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (28 bp):
AAGATCTTCGGACCTGTCTGTCATTAAA
Found at i:100323 original size:662 final size:659
Alignment explanation
Indices: 99022--101091 Score: 2761
Period size: 662 Copynumber: 3.1 Consensus size: 659
99012 ATCATGAACA
* * * * * *
99022 TAAAAACAAAAT-ATTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCAAGG
1 TAAAAAC-AAATCCTTAAGTCCAACGTGGCTGAGATTTGGTTAGATGAATATATATGTTTCAAGG
* * * * * * *
99086 AGTCTGGGCGCTAAAAATCAAGCAAAACTGAG-TCGGTCCTCGGAACGCGTTTTTAGTCAAAAAC
65 AGTTTGGGCGCCAAAAATCAAGCAAAACTGAGCTGGGGCCCCGGAACGCGTTTTTGGCCAAAAAC
* ***
99150 CGTGATGATTAGTACACGATTTCATCTAAA-ATTTTGCAAAAAAATGACCCGAAAAATTTTTCCT
130 CGTGATGGTTAGTACACGATTTTGGCTAAACA--TTGC-AAAAAATGACCCGAAAAATTTTTCCT
* * * * * * *
99214 CAATTTTTGACCACAATTCTCATAAAT-ATATATATAATTCAACGCCAAAAAGATTG-AAGGAAT
192 CAATTTTTGCCCACAATACTCAT--ATGAAATATGTAACTCAATGCCAAAAAGATTGAAAGG-CT
* * * * * **
99277 TTTCAAGTATATAATATCGTTTTTTGC-ATTTTTTTATGAATTAATTTCTAATTAAATTGAAATA
254 TTTCAAGCATCTAATATCG-CTTTTCCTATTTTTTTCTGAATTAATTTCTAATTAAA-T-CCA-A
* * ** * * ** * * *
99341 AGATTCAAATGCTCG-AAAAGAAAATCCTTAAATACAACATAGCTGAGATTTGGTTAGATGAATA
315 ACA-TCAGATGCTCGTAAAATCAAATCCTTAATTCCAATGTGGCCGAGATTTAGTTAGATGAATA
* * * * * * * * *
99405 TATATGTTTCAAGGAGTTTGGGCACCAAAAATCAAGCTAAACTGAGATGGAGT-CCC-GAAAGGT
379 TAGATATTTCAAGGAGTCTGGGCGCTAAAAATGAAGCAAAACTGAG-TCG-GTCCCCGGAACGG-
* * ** ** * * *
99468 GTTTTTAGACAAAAACCGTGATGGTTAGTATATAATTTCGGCTAAAATTTTGCGAAAAAA-CATC
441 GTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCATCTAAAATTTTGCAAAAAAATGACC
* **
99532 CGAAAATTTTTTCTCAATTTTTGACCACAATTCTCATAAAAATATATATAATTCAGTGCCAAAAA
506 CGAAAAATTTTTCTCAATTTTTGACCACAATTCTCAT-AAAATATATATAATTCAACGCCAAAAA
* * * * * * * *
99597 TATTGAATGGCTTTTCGAGCATCTAATATCGTTTTTCCATTTTTCTT-GAATTAATTTGTAATTA
570 GATTGAAGGGATTTTCAAGAATCTAATATCGTTTTTACATTTTTTTTCGAATTAATTTCTAATTA
*
99661 AATCGAAACAAGATTCAAATGCTTG
635 AATCGAAACAAGATTCAAATGCTCG
* *
99686 TAAAAACAAATCCTTAAGTCCAACGTGACTGAGATTTGGTTAGATGAATATATATGTTTCAAGGG
1 TAAAAACAAATCCTTAAGTCCAACGTGGCTGAGATTTGGTTAGATGAATATATATGTTTCAAGGA
** * *
99751 GTTTGGATGCCAAAAATCAAGCTAAACTGAGCTGGGGCCCCGAAACGCGTTTTTGGCCAAAAACC
66 GTTTGGGCGCCAAAAATCAAGCAAAACTGAGCTGGGGCCCCGGAACGCGTTTTTGGCCAAAAACC
* *
99816 GTGACGGTTAGTACACGGTTTTGGCTAAACATTGCAAAAAATGACCCGAAAAATTTTTCCTCAAT
131 GTGATGGTTAGTACACGATTTTGGCTAAACATTGCAAAAAATGACCCGAAAAATTTTTCCTCAAT
99881 TTTTGCCCACAATACTCATATGAAATATGTAACTCAATGCCAAAAAGATTGAAAGGCTTTTCAAG
196 TTTTGCCCACAATACTCATATGAAATATGTAACTCAATGCCAAAAAGATTGAAAGGCTTTTCAAG
*
99946 CATCTAATATCGCTTTTCCTATTTTTTTCTGAATTAATTTCTGATTAAATCCAAACATCAGATGC
261 CATCTAATATCGCTTTTCCTATTTTTTTCTGAATTAATTTCTAATTAAATCCAAACATCAGATGC
100011 TCGTAAAATCAAATCCTTAATTCCAATGTGGCCGAGATTTAGTTAGATGAATATAGATATTTCAA
326 TCGTAAAATCAAATCCTTAATTCCAATGTGGCCGAGATTTAGTTAGATGAATATAGATATTTCAA
*
100076 GGTGTCTGGGCGCTAAAAATGAAGCAAAACTGAGTCGGTCCCCGGAACGGGTTTTTAGCCAAAAA
391 GGAGTCTGGGCGCTAAAAATGAAGCAAAACTGAGTCGGTCCCCGGAACGGGTTTTTAGCCAAAAA
* *
100141 CCGTGATGGTTTGTGCACGATTTCATCTAAAATTTTGCAAAAAAATGACCCGAAAAATTTTTCGT
456 CCGTGATGGTTAGTACACGATTTCATCTAAAATTTTGCAAAAAAATGACCCGAAAAATTTTTC-T
*
100206 CAATTTTTGACCACAATTCTCATAAAGATATATATAATTCAACACCAAAAAGATTGAAGGGATTT
520 CAATTTTTGACCACAATTCTCATAAA-ATATATATAATTCAACGCCAAAAAGATTGAAGGGATTT
*
100271 TCAAGAATCTAATATCGTTTTTACATTTTTTTTCAAAATTAATTTCTAATTAAATCGAAACAAGA
584 TCAAGAATCTAATATCGTTTTTACATTTTTTTTC-GAATTAATTTCTAATTAAATCGAAACAAGA
100336 TTCAAATGCTCG
648 TTCAAATGCTCG
* * * *
100348 TAAAAACAGATCCTTAAGTCCAACGTGGCTGAGATTTAGTTAGATGAATATTTATGTTTCAAGGG
1 TAAAAACAAATCCTTAAGTCCAACGTGGCTGAGATTTGGTTAGATGAATATATATGTTTCAAGGA
*
100413 GTTTGGGCGCCAAAAATCAAGCAAAACTGAGCTGGGGCTCCGGAACGCGTTTTTGGCCAAAAACC
66 GTTTGGGCGCCAAAAATCAAGCAAAACTGAGCTGGGGCCCCGGAACGCGTTTTTGGCCAAAAACC
*
100478 GTGATTGTTAGTACACGATTTTGGCTAAACATTGCAAAAAATGACCCGAAAAATTTTTCCTCAAT
131 GTGATGGTTAGTACACGATTTTGGCTAAACATTGCAAAAAATGACCCGAAAAATTTTTCCTCAAT
*
100543 TTTTGCCCACAATACTCATATGAAATATGTAACTC-ATCGCCAAAAAGATTGAAAGACTTTTCAA
196 TTTTGCCCACAATACTCATATGAAATATGTAACTCAAT-GCCAAAAAGATTGAAAGGCTTTTCAA
*
100607 GCATCTAATATCGCTTTTCCTATTTTTTTCTG-ATCTAATTTCTTATTAAATCCAAACATCAGAT
260 GCATCTAATATCGCTTTTCCTATTTTTTTCTGAAT-TAATTTCTAATTAAATCCAAACATCAGAT
100671 GCTCGTAAAATCAAATCCTTAATTCCAATGTGGCCGAGA-TTAGGTTAGATGAATATAGATATTT
324 GCTCGTAAAATCAAATCCTTAATTCCAATGTGGCCGAGATTTA-GTTAGATGAATATAGATATTT
* ** *
100735 CAAAGAGTCTGGGCGCTAAAAATGAAGCAAAACTGAGTCGGTCCCCGGAACACGTTTATAGCCAA
388 CAAGGAGTCTGGGCGCTAAAAATGAAGCAAAACTGAGTCGGTCCCCGGAACGGGTTTTTAGCCAA
*
100800 AAACCGTGATTGTTAGTACACGATTTCATCTAAAATTTTGCAAAAAAATGACCCG-AAAATTGTT
453 AAACCGTGATGGTTAGTACACGATTTCATCTAAAATTTTGCAAAAAAATGACCCGAAAAATT-TT
* * *
100864 TCCTTAAATTTTGACCACAATTCTCATTAAAATATATAAAATTCAACGCCAAAAAGATTGAAGGG
517 T-CTCAATTTTTGACCACAATTCTCA-TAAAATATATATAATTCAACGCCAAAAAGATTGAAGGG
* * * *
100929 ATTTTCAAGTATATAATATCGTTTTTTTCAGTTTTTTTCTGAATTAATTTCTAATTAAATCGAAA
580 ATTTTCAAGAATCTAATATCG-TTTTTACATTTTTTTTC-GAATTAATTTCTAATTAAATCGAAA
100994 CAAGATTCAAATGCTCG
643 CAAGATTCAAATGCTCG
* * * *
101011 -AAAAGA-AAATCCTTAAATACAACATGGCTGAGCTTTGGTTAGATGAATATATATGTTTCAAGG
1 TAAAA-ACAAATCCTTAAGTCCAACGTGGCTGAGATTTGGTTAGATGAATATATATGTTTCAAGG
* *
101074 AGTTTGGCCACCAAAAAT
65 AGTTTGGGCGCCAAAAAT
101092 ACATGATTTA
Statistics
Matches: 1256, Mismatches: 128, Indels: 46
0.88 0.09 0.03
Matches are distributed among these distances:
657 2 0.00
658 66 0.05
659 103 0.08
660 86 0.07
661 21 0.02
662 728 0.58
663 117 0.09
664 82 0.07
665 50 0.04
666 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (659 bp):
TAAAAACAAATCCTTAAGTCCAACGTGGCTGAGATTTGGTTAGATGAATATATATGTTTCAAGGA
GTTTGGGCGCCAAAAATCAAGCAAAACTGAGCTGGGGCCCCGGAACGCGTTTTTGGCCAAAAACC
GTGATGGTTAGTACACGATTTTGGCTAAACATTGCAAAAAATGACCCGAAAAATTTTTCCTCAAT
TTTTGCCCACAATACTCATATGAAATATGTAACTCAATGCCAAAAAGATTGAAAGGCTTTTCAAG
CATCTAATATCGCTTTTCCTATTTTTTTCTGAATTAATTTCTAATTAAATCCAAACATCAGATGC
TCGTAAAATCAAATCCTTAATTCCAATGTGGCCGAGATTTAGTTAGATGAATATAGATATTTCAA
GGAGTCTGGGCGCTAAAAATGAAGCAAAACTGAGTCGGTCCCCGGAACGGGTTTTTAGCCAAAAA
CCGTGATGGTTAGTACACGATTTCATCTAAAATTTTGCAAAAAAATGACCCGAAAAATTTTTCTC
AATTTTTGACCACAATTCTCATAAAATATATATAATTCAACGCCAAAAAGATTGAAGGGATTTTC
AAGAATCTAATATCGTTTTTACATTTTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTC
AAATGCTCG
Found at i:100325 original size:330 final size:331
Alignment explanation
Indices: 99022--101091 Score: 2353
Period size: 330 Copynumber: 6.2 Consensus size: 331
99012 ATCATGAACA
* * * * *
99022 TAAAAACAAAAT-ATTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCAAGG
1 TAAAAAC-AAATCCTTAAATCCAACGTGGCTGAGATTTGGTTAGATGAATATATATGTTTCAAGG
* * *
99086 AGTCTGGGCGCTAAAAATCAAGCAAAACTGAG-TCGGTCCTCGGAACGCGTTTTTAGTCAAAAAC
65 AGTCTGGGCGCCAAAAATCAAGCAAAACTGAGCTCGGTCCCCGGAACGCGTTTTTAGCCAAAAAC
* *
99150 CGTGATGATTAGTACACGATTTCATCTAAAATTTTGCAAAAAAATGACCCGAAAAATTTTTCCTC
130 CGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAAAATGACCCGAAAAATTTTTCCTC
* *
99215 AATTTTTGACCACAATTCTCATAAATATATATATAATTCAACGCCAAAAAGATTGAAGGAATTTT
195 AATTTTTGACCACAATTCTCATAAAGATATATATAATTCAACGCCAAAAAGATTGAAGGGATTTT
* * * *
99280 CAAGTATATAATATCGTTTTTTGCATTTTTTTAT-GAATTAATTTCTAATTAAATTGAAATAAGA
260 CAAGCATCTAATATCG-TTTTT-CATTTTTTT-TCGAATTAATTTCTAATTAAATCGAAA-CA-A
99344 TTCAAATGCTCG
320 TTCAAATGCTCG
* * *
99356 -AAAAGA-AAATCCTTAAATACAACATAGCTGAGATTTGGTTAGATGAATATATATGTTTCAAGG
1 TAAAA-ACAAATCCTTAAATCCAACGTGGCTGAGATTTGGTTAGATGAATATATATGTTTCAAGG
* * * * * * * * *
99419 AGTTTGGGCACCAAAAATCAAGCTAAACTGAGATGGAGT-CCCGAAAGGTGTTTTTAGACAAAAA
65 AGTCTGGGCGCCAAAAATCAAGCAAAACTGAGCTCG-GTCCCCGGAACGCGTTTTTAGCCAAAAA
* ** * * * * *
99483 CCGTGATGGTTAGTATATAATTTCGGCTAAAATTTTGCGAAAAAA-CATCCG-AAAATTTTTTCT
129 CCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAAAATGACCCGAAAAATTTTTCCT
* ** * * *
99546 CAATTTTTGACCACAATTCTCATAAAAATATATATAATTCAGTGCCAAAAATATTGAATGGCTTT
194 CAATTTTTGACCACAATTCTCATAAAGATATATATAATTCAACGCCAAAAAGATTGAAGGGATTT
* * *
99611 TCGAGCATCTAATATCGTTTTTCCATTTTTCTT-GAATTAATTTGTAATTAAATCGAAACAAGAT
259 TCAAGCATCTAATATCGTTTTT-CATTTTTTTTCGAATTAATTTCTAATTAAATCGAAAC-A-AT
*
99675 TCAAATGCTTG
321 TCAAATGCTCG
* * *
99686 TAAAAACAAATCCTTAAGTCCAACGTGACTGAGATTTGGTTAGATGAATATATATGTTTCAAGGG
1 TAAAAACAAATCCTTAAATCCAACGTGGCTGAGATTTGGTTAGATGAATATATATGTTTCAAGGA
* ** * * * * *
99751 GTTTGGATGCCAAAAATCAAGCTAAACTGAGCTGGGGCCCCGAAACGCGTTTTTGGCCAAAAACC
66 GTCTGGGCGCCAAAAATCAAGCAAAACTGAGCTCGGTCCCCGGAACGCGTTTTTAGCCAAAAACC
* * **
99816 GTGACGGTTAGTACACGGTTTTGGCTAAACA--TTGC-AAAAAATGACCCGAAAAATTTTTCCTC
131 GTGATGGTTAGTACACGATTTCAGCTAAA-ATTTTGCAAAAAAATGACCCGAAAAATTTTTCCTC
* * * * * * * * *
99878 AATTTTTGCCCACAATACTCAT-ATGAAATATGTAACTCAATGCCAAAAAGATTGAAAGGCTTTT
195 AATTTTTGACCACAATTCTCATAAAGATATATATAATTCAACGCCAAAAAGATTGAAGGGATTTT
* * * *
99942 CAAGCATCTAATATCGCTTTTCCTATTTTTTTCTGAATTAATTTCTGATTAAATCCAAAC-A-TC
260 CAAGCATCTAATATCGTTTTTCAT-TTTTTTTC-GAATTAATTTCTAATTAAATCGAAACAATTC
*
100005 AGATGCTCG
323 AAATGCTCG
* * * * * * * *
100014 TAAAATCAAATCCTTAATTCCAATGTGGCCGAGATTTAGTTAGATGAATATAGATATTTCAAGGT
1 TAAAAACAAATCCTTAAATCCAACGTGGCTGAGATTTGGTTAGATGAATATATATGTTTCAAGGA
* * *
100079 GTCTGGGCGCTAAAAATGAAGCAAAACTGAG-TCGGTCCCCGGAACGGGTTTTTAGCCAAAAACC
66 GTCTGGGCGCCAAAAATCAAGCAAAACTGAGCTCGGTCCCCGGAACGCGTTTTTAGCCAAAAACC
* * * *
100143 GTGATGGTTTGTGCACGATTTCATCTAAAATTTTGCAAAAAAATGACCCGAAAAATTTTTCGTCA
131 GTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAAAATGACCCGAAAAATTTTTCCTCA
*
100208 ATTTTTGACCACAATTCTCATAAAGATATATATAATTCAACACCAAAAAGATTGAAGGGATTTTC
196 ATTTTTGACCACAATTCTCATAAAGATATATATAATTCAACGCCAAAAAGATTGAAGGGATTTTC
* *
100273 AAGAATCTAATATCGTTTTTACATTTTTTTTCAAAATTAATTTCTAATTAAATCGAAACAAGATT
261 AAGCATCTAATATCGTTTTT-CATTTTTTTTC-GAATTAATTTCTAATTAAATCGAAAC-A-ATT
100338 CAAATGCTCG
322 CAAATGCTCG
* * * * *
100348 TAAAAACAGATCCTTAAGTCCAACGTGGCTGAGATTTAGTTAGATGAATATTTATGTTTCAAGGG
1 TAAAAACAAATCCTTAAATCCAACGTGGCTGAGATTTGGTTAGATGAATATATATGTTTCAAGGA
* * * * *
100413 GTTTGGGCGCCAAAAATCAAGCAAAACTGAGCTGGGGCTCCGGAACGCGTTTTTGGCCAAAAACC
66 GTCTGGGCGCCAAAAATCAAGCAAAACTGAGCTCGGTCCCCGGAACGCGTTTTTAGCCAAAAACC
* **
100478 GTGATTGTTAGTACACGATTTTGGCTAAACA--TTGC-AAAAAATGACCCGAAAAATTTTTCCTC
131 GTGATGGTTAGTACACGATTTCAGCTAAA-ATTTTGCAAAAAAATGACCCGAAAAATTTTTCCTC
* * * * * * * *
100540 AATTTTTGCCCACAATACTCAT-ATGAAATATGTAACTCATCGCCAAAAAGATTGAA-AGACTTT
195 AATTTTTGACCACAATTCTCATAAAGATATATATAATTCAACGCCAAAAAGATTGAAGGGA-TTT
* * * *
100603 TCAAGCATCTAATATCGCTTTTCCTATTTTTTTCTG-ATCTAATTTCTTATTAAATCCAAAC-A-
259 TCAAGCATCTAATATCGTTTTTCAT-TTTTTTTC-GAAT-TAATTTCTAATTAAATCGAAACAAT
*
100665 TCAGATGCTCG
321 TCAAATGCTCG
* * * * * * * *
100676 TAAAATCAAATCCTTAATTCCAATGTGGCCGAGATTAGGTTAGATGAATATAGATATTTCAAAGA
1 TAAAAACAAATCCTTAAATCCAACGTGGCTGAGATTTGGTTAGATGAATATATATGTTTCAAGGA
* * * *
100741 GTCTGGGCGCTAAAAATGAAGCAAAACTGAG-TCGGTCCCCGGAACACGTTTATAGCCAAAAACC
66 GTCTGGGCGCCAAAAATCAAGCAAAACTGAGCTCGGTCCCCGGAACGCGTTTTTAGCCAAAAACC
* * *
100805 GTGATTGTTAGTACACGATTTCATCTAAAATTTTGCAAAAAAATGACCCG-AAAATTGTTTCCTT
131 GTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAAAATGACCCGAAAAATT-TTTCCTC
* *
100869 AAATTTTGACCACAATTCTCATTAAA-ATATATAAAATTCAACGCCAAAAAGATTGAAGGGATTT
195 AATTTTTGACCACAATTCTCA-TAAAGATATATATAATTCAACGCCAAAAAGATTGAAGGGATTT
* * *
100933 TCAAGTATATAATATCGTTTTTTTCAGTTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAG
259 TCAAGCATCTAATATCG--TTTTTCATTTTTTTTC-GAATTAATTTCTAATTAAATCGAAAC-A-
100998 ATTCAAATGCTCG
319 ATTCAAATGCTCG
* * *
101011 -AAAAGA-AAATCCTTAAATACAACATGGCTGAGCTTTGGTTAGATGAATATATATGTTTCAAGG
1 TAAAA-ACAAATCCTTAAATCCAACGTGGCTGAGATTTGGTTAGATGAATATATATGTTTCAAGG
* * *
101074 AGTTTGGCCACCAAAAAT
65 AGTCTGGGCGCCAAAAAT
101092 ACATGATTTA
Statistics
Matches: 1461, Mismatches: 232, Indels: 86
0.82 0.13 0.05
Matches are distributed among these distances:
326 2 0.00
327 103 0.07
328 195 0.13
329 93 0.06
330 236 0.16
331 219 0.15
332 197 0.13
333 127 0.09
334 225 0.15
335 63 0.04
336 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (331 bp):
TAAAAACAAATCCTTAAATCCAACGTGGCTGAGATTTGGTTAGATGAATATATATGTTTCAAGGA
GTCTGGGCGCCAAAAATCAAGCAAAACTGAGCTCGGTCCCCGGAACGCGTTTTTAGCCAAAAACC
GTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAAAATGACCCGAAAAATTTTTCCTCA
ATTTTTGACCACAATTCTCATAAAGATATATATAATTCAACGCCAAAAAGATTGAAGGGATTTTC
AAGCATCTAATATCGTTTTTCATTTTTTTTCGAATTAATTTCTAATTAAATCGAAACAATTCAAA
TGCTCG
Found at i:101343 original size:273 final size:275
Alignment explanation
Indices: 100829--101364 Score: 733
Period size: 273 Copynumber: 2.0 Consensus size: 275
100819 ACGATTTCAT
* * * * * *
100829 CTAAAATTTTGCAAAAAAATGACCCGAAAATTGTTTCCTTAAATTTTGACCACAATTCTCATTAA
1 CTAAAATTTTGCAAAAAAATCAACCGAAAAATGTTTCCTCAAATTTTGACCACAATTATCATAAA
* *
100894 AATATATAAAATTCAACGCCAAAAAGATTGAAGGGATTTTCAAGTATATAATATCGTTTTTTTCA
66 AATATATAAAATTCAACGCCAAAAAGATTGAAGGGATTTTCAAGCATATAATATCGTTTTTTCCA
* *
100959 GTTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGAAAAGAAAATCCT
131 GTTTTTTCCTGAATTAATTTCTAATTAAATCGAAACAAGATTAAAATGCTCGAAAAGAAAATCCT
*
101024 TAAATACAACATGGCTGAGCTTTGGTTAGATGAATATATATGTTTCAAGGAGTTTGGCCACCAAA
196 TAAATACAACATGGCTGAGATTTGGTTAGATGAATATATATGTTTCAAGGAGTTTGGCCACCAAA
101089 AATACATGATTTAGG
261 AATACATGATTTAGG
* * *
101104 CTAAAATTTTGCGAAAAAA-CAACCGAAAAGAT-TTTCCTCAATTTTTTGACCATAATTATCATA
1 CTAAAATTTTGCAAAAAAATCAACCGAAAA-ATGTTTCCTCAA-ATTTTGACCACAATTATCATA
* * * * * * *
101167 AAAATATATATAATTTAATGCCAAAAATATTGAAGGGCTTTTCGAGCATCTAATATCG-TTTTTC
64 AAAATATATAAAATTCAACGCCAAAAAGATTGAAGGGATTTTCAAGCATATAATATCGTTTTTTC
* *
101231 CA-TTTTTTCCTGAATTAGTTTCTAA-TAAATCGAAATAAGATTAAAATGCTCGTAAAA-ACAAA
129 CAGTTTTTTCCTGAATTAATTTCTAATTAAATCGAAACAAGATTAAAATGCTCG-AAAAGA-AAA
* * * * * *
101293 TCCTTAAGTCCAACGTGGCTGAGATTTGGTTAGATGAATATATATGTTTCAAGGGGTTTGGGCGC
192 TCCTTAAATACAACATGGCTGAGATTTGGTTAGATGAATATATATGTTTCAAGGAGTTTGGCCAC
101358 CAAAAAT
257 CAAAAAT
101365 CAAGCAAAAC
Statistics
Matches: 228, Mismatches: 29, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
272 26 0.11
273 93 0.41
274 23 0.10
275 86 0.38
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (275 bp):
CTAAAATTTTGCAAAAAAATCAACCGAAAAATGTTTCCTCAAATTTTGACCACAATTATCATAAA
AATATATAAAATTCAACGCCAAAAAGATTGAAGGGATTTTCAAGCATATAATATCGTTTTTTCCA
GTTTTTTCCTGAATTAATTTCTAATTAAATCGAAACAAGATTAAAATGCTCGAAAAGAAAATCCT
TAAATACAACATGGCTGAGATTTGGTTAGATGAATATATATGTTTCAAGGAGTTTGGCCACCAAA
AATACATGATTTAGG
Found at i:101653 original size:603 final size:603
Alignment explanation
Indices: 100581--101679 Score: 1412
Period size: 603 Copynumber: 1.8 Consensus size: 603
100571 GTAACTCATC
*
100581 GCCAAAAAGATTGAAAGACTTTTCAAGCATCTAATATCGCTTTTCCTATTTTTTTCTGATCTAAT
1 GCCAAAAAGATTGAAAGACTTTTCAAGCATCTAATATCGCTTTTCCTATTTTTTCCTGATCTAAT
* * * * * * *
100646 TTCTTATTAAATCCAAACATCAGATGCTCGTAAAATCAAATCCTTAATTCCAATGTGGCCGAGAT
66 TTCTTAATAAATCAAAACATAAAATGCTCGTAAAAACAAATCCTTAAGTCCAACGTGGCCGAGAT
* *
100711 TAGGTTAGATGAATATAGATATTTCAAAGAGTCTGGGCGCTAAAAATGAAGCAAAACTGAGTCGG
131 TAGGTTAGATGAATATAGATATTTCAAAGAGTCTGGGCGCCAAAAATCAAGCAAAACTGAGTCGG
* * *
100776 TCCCCGGAACACGTTTATAGCCAAAAACCGTGATTGTTAGTACACGATTTCATCTAAAATTTTGC
196 GCCCCGGAACACGTTTATAGCCAAAAACCGTGATTGATAGTACACGATTTCAGCTAAAA-TTTGC
* * * * * *
100841 AAAAAAATGACCCGAAAATTGTTTCCTTAAATTTTGACCACAATTCTCATTAAAATATATAAAAT
260 AAAAAAATGAACAGAAAATTGTTTCCTCAAATTTTGACCACAATACACATTAAAATATAT-AAAC
* * **
100906 TCAACGCCAAAAAGATTGAAGGGATTTTCAAGTATATAATATCGTTTTTTTCAGTTTTTTTCTGA
324 TCAACGCCAAAAAGATTGAAAGGATTTTCAAGCATATAATATCGTTTTCCTCAGTTTTTTTCTGA
*
100971 ATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGAAAAGAAAATCCTTAAATACAACAT
389 ATTAATTTCTAATTAAATCCAAACAAGATTCAAATGCTCGAAAAGAAAATCCTTAAATACAACAT
* * * *
101036 GGCTGAGCTTTGGTTAGATGAATATATATGTTTCAAGGAGTTTGGCCACCAAAAATACATGATTT
454 GGCCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTTGGCCACCAAAAATACATGATTT
101101 AGGCTAAAATTTTGCGAAAAAACAACCGAAAAGATTTTCCTCAATTTTTTGACCATAATTATCAT
519 AGGCTAAAATTTTGCGAAAAAACAACCGAAAAGATTTTCCTCAATTTTTTGACCATAATTATCAT
101166 AAAAATATATATAATTTAAT
584 AAAAATATATATAATTTAAT
* * * * * *
101186 GCCAAAAATATTGAAGGGCTTTTCGAGCATCTAATATCGTTTTTCC-ATTTTTTCCTGAAT-TAG
1 GCCAAAAAGATTGAAAGACTTTTCAAGCATCTAATATCGCTTTTCCTATTTTTTCCTG-ATCTAA
* *
101249 TTTC-TAATAAATCGAAATAAGATTAAAATGCTCGTAAAAACAAATCCTTAAGTCCAACGTGGCT
65 TTTCTTAATAAATC--AA-AACA-TAAAATGCTCGTAAAAACAAATCCTTAAGTCCAACGTGGCC
* * * * * *
101313 GAGATTTGGTTAGATGAATATATATGTTTCAAGGGGTTTGGGCGCCAAAAATCAAGCAAAACTGA
126 GAGATTAGGTTAGATGAATATAGATATTTCAAAGAGTCTGGGCGCCAAAAATCAAGCAAAACTGA
* * * * **
101378 GCTGGGGCCCCGGAACGCGTTTTTGGCCAAAAACCGTGA-TGAT-GTACACGATTTTGGCTAAAC
191 G-TCGGGCCCCGGAACACGTTTATAGCCAAAAACCGTGATTGATAGTACACGATTTCAGCTAAA-
* * * *
101441 A-TTGC-AAAAAATGAACAGAAAAATT-TTTCCTCAATTTTTGCCCAGAATACACATATGAAATA
254 ATTTGCAAAAAAATGAACAG-AAAATTGTTTCCTCAAATTTTGACCACAATACACAT-TAAAATA
* * *
101503 TGT-AACTCAACGCCAAAAAGATTGAAAGGCTTTTCAAGCATCTAATATCGCTTTTCCT-A-TTT
317 TATAAACTCAACGCCAAAAAGATTGAAAGGATTTTCAAGCATATAATATCG-TTTTCCTCAGTTT
* * **
101565 TTTTCTGAATTAATTTCTGATTAAATCCAAACATA-ATTCAGATGCTCGTAAAATCAAATCCTTA
381 TTTTCTGAATTAATTTCTAATTAAATCCAAACA-AGATTCAAATGCTCG-AAAAGAAAATCCTTA
* * ** *
101629 ATTCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATATTTTAAGGAGT
444 AATACAACATGGCCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT
101680 CTGGGCGCTA
Statistics
Matches: 418, Mismatches: 64, Indels: 26
0.82 0.13 0.05
Matches are distributed among these distances:
602 46 0.11
603 107 0.26
604 55 0.13
605 62 0.15
606 19 0.05
607 97 0.23
608 32 0.08
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32
Consensus pattern (603 bp):
GCCAAAAAGATTGAAAGACTTTTCAAGCATCTAATATCGCTTTTCCTATTTTTTCCTGATCTAAT
TTCTTAATAAATCAAAACATAAAATGCTCGTAAAAACAAATCCTTAAGTCCAACGTGGCCGAGAT
TAGGTTAGATGAATATAGATATTTCAAAGAGTCTGGGCGCCAAAAATCAAGCAAAACTGAGTCGG
GCCCCGGAACACGTTTATAGCCAAAAACCGTGATTGATAGTACACGATTTCAGCTAAAATTTGCA
AAAAAATGAACAGAAAATTGTTTCCTCAAATTTTGACCACAATACACATTAAAATATATAAACTC
AACGCCAAAAAGATTGAAAGGATTTTCAAGCATATAATATCGTTTTCCTCAGTTTTTTTCTGAAT
TAATTTCTAATTAAATCCAAACAAGATTCAAATGCTCGAAAAGAAAATCCTTAAATACAACATGG
CCGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTTGGCCACCAAAAATACATGATTTAG
GCTAAAATTTTGCGAAAAAACAACCGAAAAGATTTTCCTCAATTTTTTGACCATAATTATCATAA
AAATATATATAATTTAAT
Found at i:101739 original size:330 final size:331
Alignment explanation
Indices: 101186--101814 Score: 874
Period size: 330 Copynumber: 1.9 Consensus size: 331
101176 ATAATTTAAT
* * * * *
101186 GCCAAAAATATTGAAGGGCTTTTCGAGCATCTAATATCGTTTTTCCATTTTTTCCTGAATTAGTT
1 GCCAAAAAGATTGAAAGGCTTTTCAAGCATCTAATATCGCTTTTCCATTTTTTCCTGAATTAATT
* * *
101251 TCTAATAAATCGAAATAAGATTAAAATGCTCGTAAAAACAAATCCTTAAGTCCAACGTGGCTGAG
66 TCTAATAAATCCAAACAAGATTAAAATGCTCGTAAAAACAAATCCTTAAGTCCAACGTGGCCGAG
* * * *
101316 ATTTGGTTAGATGAATATATATGTTTCAAGGGGTTTGGGCGCCAAAAATCAAGCAAAACTGAGCT
131 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGCCAAAAATCAAGCAAAACTGAGCT
* * * **
101381 GGGGCCCCGGAACGCGTTTTTGGCCAAAAACCGTGA-TGAT-GTACACGATTTTGGCTAAACA-T
196 CGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATTGATAGTACACGATTTCAGCTAAA-ATT
*
101443 TGC-AAAAAATGAACAGAAAAATTTTTCCTCAATTTTTGCCCAGAATACACATATGAAATATGTA
260 TGCAAAAAAATGAACAGAAAAATTTTTCCTCAAATTTTGCCCAGAATACACATATGAAATATGTA
101507 ACTCAAC
325 ACTCAAC
*
101514 GCCAAAAAGATTGAAAGGCTTTTCAAGCATCTAATATCGCTTTTCCTATTTTTTTCTGAATTAAT
1 GCCAAAAAGATTGAAAGGCTTTTCAAGCATCTAATATCGCTTTTCC-ATTTTTTCCTGAATTAAT
* * * * * *
101579 TTCTGATTAAATCCAAACATA-ATTCAGATGCTCGTAAAATCAAATCCTTAATTCCAATGTGGCC
65 TTCT-AATAAATCCAAACA-AGATTAAAATGCTCGTAAAAACAAATCCTTAAGTCCAACGTGGCC
* *
101643 GAGATTTGGTTAGATGAATATAGATATTTTAAGGAGTCTGGGCGCTAAAAATCAAGCAAAACTGA
128 GAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGCCAAAAATCAAGCAAAACTGA
* * *
101708 G-TCGGTCCCCGAAACGCGTTTTTAAGCCAAAAACCGTGATTGTTAGTACACGATTTCATCTAAA
193 GCTCGGGCCCCGAAACGCGTTTTT-AGCCAAAAACCGTGATTGATAGTACACGATTTCAGCTAAA
* *
101772 ATTTTGCAAAAAAATGACCCGAAAAATTTTTCCTCAAATTTTG
257 A-TTTGCAAAAAAATGAACAGAAAAATTTTTCCTCAAATTTTG
101815 ACCATAATTC
Statistics
Matches: 260, Mismatches: 32, Indels: 12
0.86 0.11 0.04
Matches are distributed among these distances:
328 42 0.16
329 39 0.15
330 122 0.47
331 5 0.02
332 16 0.06
333 4 0.02
334 32 0.12
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (331 bp):
GCCAAAAAGATTGAAAGGCTTTTCAAGCATCTAATATCGCTTTTCCATTTTTTCCTGAATTAATT
TCTAATAAATCCAAACAAGATTAAAATGCTCGTAAAAACAAATCCTTAAGTCCAACGTGGCCGAG
ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGCCAAAAATCAAGCAAAACTGAGCT
CGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATTGATAGTACACGATTTCAGCTAAAATTT
GCAAAAAAATGAACAGAAAAATTTTTCCTCAAATTTTGCCCAGAATACACATATGAAATATGTAA
CTCAAC
Found at i:102024 original size:158 final size:160
Alignment explanation
Indices: 101727--102049 Score: 440
Period size: 158 Copynumber: 2.0 Consensus size: 160
101717 CGAAACGCGT
* *
101727 TTTTAAGCCAAAAACCGTGATTGTTAGTACACGATTTCATCTAAAATTTTGCAAAAAAATGACCC
1 TTTTAAGCCAAAAACCGTGATTGTTAATACACGATTTCAGCTAAAATTTTGCAAAAAAAT-ACCC
*
101792 GAAAAATTTTTCCTCAAATTTTGACCATAATTCTCAAAAAAATATATATAATTCAACGCAAAAAG
65 GAAAAATTTTTCCTCAAATTTTGACCACAATTCTCAAAAAAATATATATAATTCAACGCAAAAAG
* *
101857 GATTTAAGGGATTTTCAAGTATATAATATCA
130 GATTGAAGGGATTTTCAAGCATATAATATCA
* * * *
101888 TTTT-AGCCAAAAACCGTG-TTGGTTAATACATGATTTCGGCTAAAATTTTGCGAAAAAACT-TC
1 TTTTAAGCCAAAAACCGTGATT-GTTAATACACGATTTCAGCTAAAATTTTGC-AAAAAAATACC
* *
101950 CGAAAAATTTTTCCTC-AATTTTGACCACAATTCTCATAAAAATATATATAATTCAGCGCCAAAA
64 CGAAAAATTTTTCCTCAAATTTTGACCACAATTCTCAAAAAAATATATATAATTCAACG-CAAAA
* * * *
102014 A-GATTGAAGGGCTTTTCGAGCATCTAATATCG
128 AGGATTGAAGGGATTTTCAAGCATATAATATCA
102046 TTTT
1 TTTT
102050 TCCATTTTTC
Statistics
Matches: 144, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
158 68 0.47
159 25 0.17
160 40 0.28
161 11 0.08
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (160 bp):
TTTTAAGCCAAAAACCGTGATTGTTAATACACGATTTCAGCTAAAATTTTGCAAAAAAATACCCG
AAAAATTTTTCCTCAAATTTTGACCACAATTCTCAAAAAAATATATATAATTCAACGCAAAAAGG
ATTGAAGGGATTTTCAAGCATATAATATCA
Done.