Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012374.1 Corchorus olitorius cultivar O-4 contig12407, 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: 15745
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:4637 original size:53 final size:53
Alignment explanation
Indices: 4577--4686 Score: 184
Period size: 53 Copynumber: 2.1 Consensus size: 53
4567 TCTTTAAATC
*
4577 CAATAGTTCATTGCATTTCGTATTATTTGGTATATGTGCTTATTTAATAGGTT
1 CAATAGTTCATTGCATTTCGTATTATTTGGTATATATGCTTATTTAATAGGTT
* * *
4630 CAATAGTTCATTGCATTTTGTATTGTTTGGTATGTATGCTTATTTAATAGGTT
1 CAATAGTTCATTGCATTTCGTATTATTTGGTATATATGCTTATTTAATAGGTT
4683 CAAT
1 CAAT
4687 TGAATAAACA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.25, C:0.09, G:0.17, T:0.49
Consensus pattern (53 bp):
CAATAGTTCATTGCATTTCGTATTATTTGGTATATATGCTTATTTAATAGGTT
Found at i:12712 original size:41 final size:41
Alignment explanation
Indices: 12665--12746 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
12655 ACTTGATCCT
12665 CCTAATAATTAAGGTAAAAAATTAAATACAGGTTTAGCCCC
1 CCTAATAATTAAGGTAAAAAATTAAATACAGGTTTAGCCCC
* *
12706 CCTAATAATTAAGGTAACAAATTAAATCCAGGTTTAGCCCC
1 CCTAATAATTAAGGTAAAAAATTAAATACAGGTTTAGCCCC
12747 TAATTATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (41 bp):
CCTAATAATTAAGGTAAAAAATTAAATACAGGTTTAGCCCC
Found at i:13781 original size:324 final size:320
Alignment explanation
Indices: 13382--15741 Score: 2223
Period size: 324 Copynumber: 7.2 Consensus size: 320
13372 TTTTGCAAAA
* * *
13382 TTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTGGCTAAAAACGCG-TTCTAGAGCCCCGG
1 TTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTC-GGGGCCCTGG
* * *
13446 CTCAA-TTTTGCATGATTTTTGAC-TCAAAGACTCCTTGAAATATCAATATTCATCGAACCAAAT
65 AT-AAGTTTTGCATGATTTTTGGCGT-AAAGACTCCTTGAAATATCAATATTCATCTAACCAAAT
* * * * * *
13509 CTCTGCCACATTGGATATAAGGATTTGTTTTTACGGGCATCTGAATCTTGATCCTATTTAATTAG
128 CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
* * *
13574 AAATTAATTCGG-GAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCATCAATCTTTTTTG
193 AAATAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCATCAAT-TTTTTGG
* *
13638 AGTGGAATTATATATTTTTTTTCTGAGTATTGTGGCAAAAAAATTGAGAAATAACTTTTTGGGTC
257 CGTTGAATTATATA--TTTTTTCTGAGTATTGTGGC-AAAAAATTGAGAAA-AACTTTTTGGGTC
13703 AGT
318 AGT
* ** * * *
13706 TTTTAGCTGAAATTGTGTACTAACTATCACGATTTTGGGCTAAAAACGCGTTTCGGGGCCCTGGA
1 TTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCTGGA
** * *
13771 TAAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTC
66 TAAGTTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCAATATTCATCTAACCAAATCTC
* ** * * *
13836 AGCCACATTGAATTTATTGATTTGTTTTAACGAGCATCTTAATCATGTTTCGATTTAATTAGAAA
131 AGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
* * * * *
13901 TTAATTCAGAAAAATAT-GAAAAACGATATTAAAAGCGTGAAAAGTCTCCA--AATTTTTTCGCG
196 TAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAG-C-CCATCAATTTTTTGGCG
** * * * * *** *
13963 TTGAATTATATATAATATATGGGTATCGTGGTTGAAAATTGAAGAAAAA-TATTTCGGGTCTATT
259 TTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTG-AGAAAAACT-TTTTGGGTC-A--
14027 TTTGT
319 ---GT
* * *
14032 AAAATTTTAGCCGAAATC--GT--GAACCATCACGGTCTTTTGGCTAAAAATGCG-TTCTGAGGC
1 ----TTTTAGCCGAAATCATGTACTAACCATCACGGT-TTTTGGCTAAAAACGCGTTTC-GGGGC
* * * * *
14092 CAC-GGGTCAGTTTTGCATGATTTTTGGCGTAAAGACTCCTTAAAATATAAATATTCATCAAACC
60 C-CTGGATAAGTTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCAATATTCATCTAACC
* * *
14156 AAATCTCAGCCACATTCGATTTAAAGATTTGTTTTTACGAGTATGCATCTGAATCTTGTTTCCAT
124 AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTAC--G-A-GCATCTGAATCTTGTTTCGAT
* * ** * * * *
14221 TTGATTAGAAATTAATTCTAAAAAAAAAATCGAAAAATGATAATAGAAGCGTGAAAA--ACATTG
185 TTAATTAGAAATAAATTC--GGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCA-T-
* * *
14284 CAATCTTTTTGGCGTTGGAA-TATATATTTTTTATGAGTATTTTGGCAAAAAATTGAGAAAAAAT
246 CAAT-TTTTTGGCGTT-GAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAACT
14348 TTTTCGGGTCAGT
309 TTTT-GGGTCAGT
* * * * *
14361 TTTTAGCCGAAAATCATGTAC---CCATTATAGCTTTTTGGCTAAAAACGCGTTTCGGGG-CGTC
1 TTTTAGCCG-AAATCATGTACTAACCATCA-CGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCTG
* * * * * *
14422 GACTCAGTTTTGCATGGTTTTTGACATAAAGACTCCTTGAAAAATCTATATTCATCTAACCAAAT
64 GA-TAAGTTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCAATATTCATCTAACCAAAT
* * *
14487 CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAAATAA
128 CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
* * * *
14552 AAATAAATTCGGAAAAAAGAATATGAAAAAAGATATTAGAAGCATGAAAA-ACCATTCAATTTTT
193 AAATAAATTCGG-AAAAA-AAT-GGAAAAACGATATTAGAAGCGTGAAAAGCCCA-TCAATTTTT
* * * * * *
14616 CTGGCGTTGAATTACATATTTTTTCTGAGTATTGTGGGAAAAAACTGAGGGAAAACGTTTCGGGT
254 -TGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA-GAAAAACTTTTTGGGT
14681 CAGTTTTTGT
317 CA------GT
* * *
14691 AAAATTTTAGCCGAAATCATCTACTAACCATAACGGTTTTTGGGCTAAAAACGCGTTTTGGGG-C
1 ----TTTTAGCCGAAATCATGTACTAACCATCACGGTTTTT-GGCTAAAAACGCGTTTCGGGGCC
* ** ** * *
14755 CTCGACTCCGTTTTGCA-GGGTTTTGGCCATAAAGACTCCTTGAAATATCGATATTCATCTAACC
61 CTGGA-TAAGTTTTGCATGATTTTTGG-CGTAAAGACTCCTTGAAATATCAATATTCATCTAACC
* *
14819 AAATCTCAGCCATAATT-TATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTA
124 AAATCTCAGCCA-CATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTA
* * **
14883 ATTAAAAATAAATTCGGAAAAAAATATGAAAAACGATATTAGAAGCGTGAAAA-ATCATTCAATT
188 ATTAGAAATAAATTCGGAAAAAAAT-GGAAAAACGATATTAGAAGCGTGAAAAGCCCA-TCAATT
** * * * *
14947 GTTTTGGCGTTGAATTATATATTTCATCTGAGTATTATGACAAATAATTGAAGAAAAAAATTTTT
251 -TTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTG-AG-AAAAACTTTTT
15012 GGGTCAGTTTTT
313 GGGTCAG----T
* * * * *
15024 TCAAAACTTTAGCCGAAATCGTTTACT---CATCACTGTTTTAGGCTAAAAACGCGTTCCGGGGC
1 T------TTTAGCCGAAATCATGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGG-
* * * * *
15086 CCCT-GCTATGTTTTGCATGACATTTTGGCGTAAAGACTCCTTGAAAAATCGATATTCATCTAAC
59 CCCTGGATAAGTTTTGCATGA-TTTTTGGCGTAAAGACTCCTTGAAATATCAATATTCATCTAAC
* *
15150 CAAATCTCAGTCATAATT-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
123 CAAATCTCAGCCA-CATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
* * * *
15214 AATTAAAAATAAATTCGGAAAAAAATGAAAAAACGATATTAAAAGCGTGAAAAGCCCGTCAATCT
187 AATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCATCAA--T
* *
15279 TTTTTTGCGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAACTTTTTCG
250 TTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAACTTTTT-G
15344 GGTCAGT
314 GGTCAGT
* * * *
15351 TTTTAGCCGAAATCATGTACTAACCGTCACGGTTTTTAGCTAAAAACGCGTTCCGGAGTCCC--G
1 TTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGG-GGCCCTGG
*
15414 ACTCAA-TTTTGCATGATTTTTGGC-TCAAAGACTCCTTGAAATATCAATATTCATCGAACCAAA
65 A-T-AAGTTTTGCATGATTTTTGGCGT-AAAGACTCCTTGAAATATCAATATTCATCTAACCAAA
* *
15477 TCTCAGCCACATTGAATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
127 TCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
* *
15542 GAAATAAATTCGGAAAAAAAATGAAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATTTTTTT
192 GAAATAAATTCGG-AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCATCAA--TTTTT
* * * ****
15607 TTGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTATTCAACTC
254 TGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG-AAAAACTTTTTGGGTC
15672 AGT
318 AGT
* * ** *
15675 TTTTAACCGAAATC--GT-GT-A-CA-CA--GTTTTTGGCTAAAAACGCGTTTCACGGCCCTGGC
1 TTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCTGGA
*
15732 TCAGTTTTGC
66 TAAGTTTTGC
15742 GTAA
Statistics
Matches: 1709, Mismatches: 225, Indels: 212
0.80 0.10 0.10
Matches are distributed among these distances:
315 5 0.00
316 28 0.02
317 1 0.00
318 2 0.00
319 2 0.00
320 18 0.01
321 38 0.02
322 11 0.01
323 174 0.10
324 422 0.25
325 43 0.03
326 25 0.01
327 217 0.13
328 10 0.01
329 5 0.00
330 27 0.02
331 100 0.06
332 177 0.10
333 30 0.02
334 124 0.07
335 95 0.06
336 152 0.09
337 3 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (320 bp):
TTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCTGGA
TAAGTTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCAATATTCATCTAACCAAATCTC
AGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
TAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCATCAATTTTTTGGCGTT
GAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAACTTTTTGGGTCAGT
Found at i:15238 original size:990 final size:973
Alignment explanation
Indices: 13382--15688 Score: 2719
Period size: 990 Copynumber: 2.3 Consensus size: 973
13372 TTTTGCAAAA
* * * * * *
13382 TTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCTAGAGCCCCGGC
1 TTTTAGCCGAAATCATGTAC--ACCATCAAGCTTTTTGGCTAAAAACGCGTT-TCGGGGCCCGAC
13447 TCAATTTTGCATGATTTTTGACTCAAAGACTCCTTGAAATATCAATATTCATCGAACCAAATCTC
63 TCAATTTTGCATGATTTTTGACTCAAAGACTCCTTGAAATATCAATATTCATCGAACCAAATCTC
* * * * *
13512 TGCCACATTGGATATAAGGATTTGTTTTTACGGGCATCTGAATCTTGATCCTATTTAATTAGAAA
128 AGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
* * * * *
13577 TTAATTCGG-GAAAAAT-GGAAAAACGATATTAGAAGCGTGAAAAGCCCATCAATCTTTTTTGAG
193 TAAATTCGGAAAAAAATATGAAAAAAGATATTAGAAGCGTGAAAA-ACCATCAAT-TTTTTTGAG
* * *
13640 TGGAATTATATATTTTTTTTCTGAGTATTGTGGCAAAAAAATTGA-GAAATAACTTTTTGGGTCA
256 TTGAATTATATA--TTTTTTCTGAGTATTGTGG-AAAAAAATTGAGGAAATAACGTTTCGGGTCA
* ** * * * *
13704 GTTTTTAGCTGAAATTGTGTACTAACTATCACGATTTTGGGCTAAAAACGCGTTTCGGGGCCCTG
318 GTTTTTAGCCGAAATCATCTACTAACCATAACGATTTTGGGCTAAAAACGCGTTTCGGGGCCCTC
* * ** * *
13769 GATAAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATC
383 GATAAGTTTTGCATGAGTTTTGGCATAAAGACTCCTTGAAATATCGATATTCATCTAACCAAATC
* ** * *
13834 TCAGCCACATTGAATTTATTGATTTGTTTTAACGAGCATCTTAATCATGTTTCGATTTAATTAGA
448 TCAGCCAAATTGAATTTAAGGATTTGTTTTAACGAGCATCTGAATCATGTTTCGATTTAATTAAA
* * *
13899 AATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCTCCAAATTTTTTCGCGT
513 AATAAATTCAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAATCTCCAAATTTTTTCGCGT
* * *** *
13964 TGAATTATATATAATATATGGGTATCGTGGTTGAAAATTGAAGAAAAATATTTCGGGTCTATTTT
578 TGAATTATATATAATATATGAGTATCATGGACAAAAATTGAAGAAAAAAATTTCGGGTCTATTTT
* * * *
14029 TGTAAAATTTTAGCCGAAATCGTGAACCATCACGGTCTTTTGGCTAAAAATGCGTTCTGAGGCCA
643 TGTAAAACTTTAGCCGAAATCGTGAACCATCACGGTCTTTAGGCTAAAAACGCGTTCCGAGGCCA
* *
14094 CGGGTCAGTTTTGCATGATTTTTGGCGTAAAGACTCCTTAAAATATAAATATTCATCAAACCAAA
708 CGGCTCAGTTTTGCATGAATTTTGGCGTAAAGACTCCTTAAAATATAAATATTCATCAAACCAAA
* *
14159 TCTCAGCCACATTCGATTTAAAGATTTGTTTTTACGAGTATGCATCTGAATCTTGTTTCCATTTG
773 TCTCAGCCAAATTCGATTTAAAGATTTGTTTTTAC-AGTATGCATCTGAATCTTGTTTCCATTTA
* * * * **
14224 ATTAGAAATTAATTCTAAAAAAAAAATCG-AAAAATGATAATAGAAGCGTGAAAAA-CATTGCAA
837 ATTAAAAATAAATTCT-AAAAAAAAAT-GAAAAAACGATAATAAAAGCGTGAAAAACCCGT-CAA
* *
14287 TC-TTTTTGGCGTTGGAA-TATATATTTTTTATGAGTATTTTGGCAAAAAATTGAGAAAAAATTT
899 TCTTTTTTGGCGTT-GAATTATATAATTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAATTT
14350 TTCGGGTCAGT
963 TTCGGGTCAGT
* *
14361 TTTTAGCCGAAAATCATGTAC-CCATTATAGCTTTTTGGCTAAAAACGCGTTTCGGGGCGTCGAC
1 TTTTAGCCG-AAATCATGTACACCATCA-AGCTTTTTGGCTAAAAACGCGTTTCGGGGC-CCGAC
* * * * *
14425 TCAGTTTTGCATGGTTTTTGACAT-AAAGACTCCTTGAAAAATCTATATTCATCTAACCAAATCT
63 TCAATTTTGCATGATTTTTGAC-TCAAAGACTCCTTGAAATATCAATATTCATCGAACCAAATCT
* * * *
14489 CAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAAATAAAA
127 CAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
* *
14554 ATAAATTCGGAAAAAAGAATATGAAAAAAGATATTAGAAGCATGAAAAACCATTCAATTTTTCTG
192 ATAAATTCGG-AAAAA-AATATGAAAAAAGATATTAGAAGCGTGAAAAACCA-TCAATTTTT-TT
* * * * *
14619 GCGTTGAATTACATATTTTTTCTGAGTATTGTGGGAAAAAACTGAGGGAA-AACGTTTCGGGTCA
253 GAGTTGAATTATATATTTTTTCTGAGTATTGTGGAAAAAAATTGAGGAAATAACGTTTCGGGTCA
*
14683 GTTTTTGTAAAATTTTAGCCGAAATCATCTACTAACCATAACGGTTTTTGGGCTAAAAACGCGTT
318 ------GT----TTTTAGCCGAAATCATCTACTAACCATAAC-GATTTTGGGCTAAAAACGCGTT
* ** *
14748 TTGGGG-CCTCGACTCCGTTTTGCA-GGGTTTTGGCCATAAAGACTCCTTGAAATATCGATATTC
372 TCGGGGCCCTCGA-TAAGTTTTGCATGAGTTTTGG-CATAAAGACTCCTTGAAATATCGATATTC
* * *
14811 ATCTAACCAAATCTCAGCCATAATT-TATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
435 ATCTAACCAAATCTCAGCCA-AATTGAATTTAAGGATTTGTTTTAACGAGCATCTGAATCATGTT
*
14875 TCGATTTAATTAAAAATAAATTCGGAAAAAAATATGAAAAACGATATTAGAAGCGTGAAAAATCA
499 TCGATTTAATTAAAAATAAATTC--AAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAATC-
* * * * *
14940 TTC-AATTGTTTTGGCGTTGAATTATATAT-TTCATCTGAGTATTAT-GACAAATAATTGAAGAA
561 TCCAAATT-TTTTCGCGTTGAATTATATATAAT-ATATGAGTATCATGGACAAA-AATTGAAGAA
* ** *
15002 AAAAATTTTTGGGTC-AGTTTTT-TCAAAACTTTAGCCGAAATCGTTTACTCATCACTGT-TTTA
623 AAAAA-TTTCGGGTCTA-TTTTTGT-AAAACTTTAGCCGAAATCGTGAAC-CATCACGGTCTTTA
* * *
15064 GGCTAAAAACGCGTTCCGGGGCCCCTGCT-ATGTTTTGCATGACATTTTGGCGTAAAGACTCCTT
684 GGCTAAAAACGCGTTCCGAGGCCACGGCTCA-GTTTTGCATGA-ATTTTGGCGTAAAGACTCCTT
** * * *
15128 GAAAA-ATCGATATTCATCTAACCAAATCTCAGTCATAATT-GATTTAAGGATTTGTTTTTAC-G
747 -AAAATATAAATATTCATCAAACCAAATCTCAGCCA-AATTCGATTTAAAGATTTGTTTTTACAG
* **
15190 -A-GCATCTGAATCTTGTTTCGATTTAATTAAAAATAAATTC-GGAAAAAAATGAAAAAACGATA
810 TATGCATCTGAATCTTGTTTCCATTTAATTAAAAATAAATTCTAAAAAAAAATGAAAAAACGATA
* * * *
15252 TTAAAAGCGTGAAAAGCCCGTCAATCTTTTTTTGCGTTGAATTATATAATTTTTCTGAGTATTGT
875 ATAAAAGCGTGAAAAACCCGTCAATCTTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTGT
*
15317 GGCAAAAAATTGAGAAAAACTTTTTCGGGTCAGT
940 GGCAAAAAATTGAGAAAAAATTTTTCGGGTCAGT
* * * * * *
15351 TTTTAGCCGAAATCATGTACTAACCGTCACGGTTTTTAGCTAAAAACGCGTTCCGGAGTCCCGAC
1 TTTTAGCCGAAATCATGTAC--ACCATCAAGCTTTTTGGCTAAAAACGCGTTTCGG-GGCCCGAC
*
15416 TCAATTTTGCATGATTTTTGGCTCAAAGACTCCTTGAAATATCAATATTCATCGAACCAAATCTC
63 TCAATTTTGCATGATTTTTGACTCAAAGACTCCTTGAAATATCAATATTCATCGAACCAAATCTC
*
15481 AGCCACATTGAATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
128 AGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
* *
15546 TAAATTCGGAAAAAAA-ATGAAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATTTTTTTTTG
193 TAAATTCGGAAAAAAATATGAAAAAA-GATATTAGAAGCGTGAAAA-ACCATCAA--TTTTTTTG
* * * ***
15610 TGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA-GAAAAAAC-TATTCAACTCA
254 AGTTGAATTATATATTTTTTCTGAGTATTGTGGAAAAAAATTGAGGAAATAACGT-TTCGGGTCA
*
15673 GTTTTTAACCGAAATC
318 GTTTTTAGCCGAAATC
15689 GTGTACACAG
Statistics
Matches: 1128, Mismatches: 146, Indels: 107
0.82 0.11 0.08
Matches are distributed among these distances:
977 9 0.01
978 146 0.13
979 31 0.03
980 49 0.04
981 10 0.01
982 42 0.04
984 2 0.00
985 2 0.00
988 10 0.01
989 113 0.10
990 266 0.24
991 196 0.17
992 51 0.05
993 49 0.04
994 71 0.06
995 74 0.07
996 7 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (973 bp):
TTTTAGCCGAAATCATGTACACCATCAAGCTTTTTGGCTAAAAACGCGTTTCGGGGCCCGACTCA
ATTTTGCATGATTTTTGACTCAAAGACTCCTTGAAATATCAATATTCATCGAACCAAATCTCAGC
CACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAA
ATTCGGAAAAAAATATGAAAAAAGATATTAGAAGCGTGAAAAACCATCAATTTTTTTGAGTTGAA
TTATATATTTTTTCTGAGTATTGTGGAAAAAAATTGAGGAAATAACGTTTCGGGTCAGTTTTTAG
CCGAAATCATCTACTAACCATAACGATTTTGGGCTAAAAACGCGTTTCGGGGCCCTCGATAAGTT
TTGCATGAGTTTTGGCATAAAGACTCCTTGAAATATCGATATTCATCTAACCAAATCTCAGCCAA
ATTGAATTTAAGGATTTGTTTTAACGAGCATCTGAATCATGTTTCGATTTAATTAAAAATAAATT
CAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAATCTCCAAATTTTTTCGCGTTGAATTAT
ATATAATATATGAGTATCATGGACAAAAATTGAAGAAAAAAATTTCGGGTCTATTTTTGTAAAAC
TTTAGCCGAAATCGTGAACCATCACGGTCTTTAGGCTAAAAACGCGTTCCGAGGCCACGGCTCAG
TTTTGCATGAATTTTGGCGTAAAGACTCCTTAAAATATAAATATTCATCAAACCAAATCTCAGCC
AAATTCGATTTAAAGATTTGTTTTTACAGTATGCATCTGAATCTTGTTTCCATTTAATTAAAAAT
AAATTCTAAAAAAAAATGAAAAAACGATAATAAAAGCGTGAAAAACCCGTCAATCTTTTTTGGCG
TTGAATTATATAATTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAATTTTTCGGGTCAGT
Found at i:15533 original size:655 final size:642
Alignment explanation
Indices: 13381--15720 Score: 2497
Period size: 655 Copynumber: 3.6 Consensus size: 642
13371 TTTTTGCAAA
** *
13381 ATTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCTAGA-GCCCCG
1 ATTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGGCCACG
* *
13445 GCTCAATTTTGCATGATTTTTGACTCAAAGACTCCTTGAAATATCAATATTCATCGAACCAAATC
66 ACTCAATTTTGCATGATTTTTGGCTCAAAGACTCCTTGAAATATCAATATTCATCGAACCAAATC
* * * * *
13510 TCTGCCACATTGGATATAAGGATTTGTTTTTACGGGCATCTGAATCTTGATCCTATTTAATTAGA
131 TCAGCCACATT-GATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* * * * *
13575 AATTAATTCGG-GAAAAAT-GGAAAAACGATATTAGAAGCGTGAAAAGCCCA-TCAATCTTTTTT
195 AATAAATTCGGAAAAAAATATGAAAAACGATATTAGAAGCGTGAAAA-ACCATTCAATCTTTTTG
* * * *
13637 GAGTGGAATTATATATTTTTTTTCTGAGTATTGTGGCAAAAAAATTGAGAAATAACTTTTTGGGT
259 GCGTTGAATTATATA--TTTTTTCTGAGTATTGTGGC-AAAAAATTGAGAAAAAAATTTTTGGGT
* * *
13702 CAGTTTTTAGCTGAAATTGTGTACTAACTATCAC-GATTTTGGGCTAAAAACGCGTTTCGGGG-C
321 CAGTTTTTAGCCGAAATCGTGTACT--C-ATCACTGATTTTAGGCTAAAAACGCGTTTCGGGGCC
* ** * *
13765 CCTGGATAAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCA
383 CCT-GCT-AGTTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAAAATCTATATTCATCTAACCA
** * * *
13830 AATCTCAGCCACATTGAATTTATTGATTTGTTTTAACGAGCATCTTAATCATGTTTCGATTTAAT
446 AATCTCAGCCACATTG-ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAT
* * * * * *
13895 TAGAAATTAATTCAGAAAAATATG-AAAAACGATATTAAAAGCGTGAAAAG-TCTCCAAATTTTT
510 TAAAAATAAATTCGGAAAAAAATGAAAAAACGATATTAAAAGCGTGAAAAGCCCT-CAATTTTTT
* * * * * ***
13958 TCGCGTTGAATTATAT-ATAATATATGGGTATCGTGGTTGAAAATTGAAGAAAAA-TATTTCGGG
574 TCGCGTTGAATTATATAAT-TTTTCTGAGTATTGTGGCAAAAAATTG-AGAAAAACTATTTCGGG
14021 TCTATTTTTGT
637 TC-A----TGT
* * *
14032 AAAATTTTAGCCGAAATC--GT--GAACCATCACGGTCTTTTGGCTAAAAATGCGTT-CTGAGGC
1 ---ATTTTAGCCGAAATCATGTACTAACCATCACGGT-TTTTGGCTAAAAACGCGTTCCGGAGGC
** * * * *
14092 CACGGGTCAGTTTTGCATGATTTTTGGCGT-AAAGACTCCTTAAAATATAAATATTCATCAAACC
62 CACGACTCAATTTTGCATGATTTTTGGC-TCAAAGACTCCTTGAAATATCAATATTCATCGAACC
* * *
14156 AAATCTCAGCCACATTCGATTTAAAGATTTGTTTTTACGAGTATGCATCTGAATCTTGTTTCCAT
126 AAATCTCAGCCACATT-GATATAAGGATTTGTTTTTAC--G-A-GCATCTGAATCTTGTTTCGAT
* * ** * * *
14221 TTGATTAGAAATTAATTCTAAAAAAAAAATCGAAAAATGATAATAGAAGCGTGAAAAA-CATTGC
186 TTAATTAGAAATAAATTCGGAAAAAAATAT-GAAAAACGATATTAGAAGCGTGAAAAACCATT-C
* *
14285 AATCTTTTTGGCGTTGGAA-TATATATTTTTTATGAGTATTTTGGCAAAAAATTGAG-AAAAAAT
249 AATCTTTTTGGCGTT-GAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAT
* * * * *
14348 TTTTCGGGTCAGTTTTTAGCCGAAAATCATGTACCCATTA-TAGCTTTTTGGCTAAAAACGCGTT
313 TTTT-GGGTCAGTTTTTAGCCG-AAATCGTGTACTCATCACT-GATTTTAGGCTAAAAACGCGTT
** * * *
14412 TCGGGGCGTC-GACTCAGTTTTGCATGGTTTTTGACATAAAGACTCCTTGAAAAATCTATATTCA
375 TCGGGGCCCCTG-CT-AGTTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAAAATCTATATTCA
*
14476 TCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTC
438 TCTAACCAAATCTCAGCCACATT-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTC
* * * *
14541 GATTTAAATAAAAATAAATTCGGAAAAAAGAATATGAAAAAA-GATATTAGAAGCATGAAAAACC
502 GATTTAATTAAAAATAAATTCGG--AAAA-AA-ATGAAAAAACGATATTAAAAGCGTGAAAAGCC
* * * * * * * *
14605 ATTCAATTTTTCTGGCGTTGAATTACATATTTTTTCTGAGTATTGTGGGAAAAAACTGAGGGAAA
563 -CTCAATTTTTTTCGCGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATTGA-GAAAA
*
14670 AC-GTTTCGGGTCAGTTTTTGT
626 ACTATTTCGGGTCA-----TGT
* * **
14691 AAAATTTTAGCCGAAATCATCTACTAACCATAACGGTTTTTGGGCTAAAAACGCGTTTTGG-GGC
1 ---ATTTTAGCCGAAATCATGTACTAACCATCACGGTTTTT-GGCTAAAAACGCGTTCCGGAGGC
* ** ** * *
14755 CTCGACTCCGTTTTGCA-GGGTTTTGGC-CATAAAGACTCCTTGAAATATCGATATTCATCTAAC
62 CACGACTCAATTTTGCATGATTTTTGGCTC--AAAGACTCCTTGAAATATCAATATTCATCGAAC
* * *
14818 CAAATCTCAGCCATAATTTATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTA
125 CAAATCTCAGCCA-CATTGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTA
* *
14883 ATTAAAAATAAATTCGGAAAAAAATATGAAAAACGATATTAGAAGCGTGAAAAATCATTCAAT-T
189 ATTAGAAATAAATTCGGAAAAAAATATGAAAAACGATATTAGAAGCGTGAAAAACCATTCAATCT
** * * *
14947 GTTTTGGCGTTGAATTATATATTTCATCTGAGTATTATGACAAATAATTGAAGAAAAAAATTTTT
254 -TTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTG-AGAAAAAAATTTTT
*
15012 GGGTCAGTTTTTTCAAAACTTTAGCCGAAATCGTTTACTCATCACTG-TTTTAGGCTAAAAACGC
317 GGGTCAG----TT------TTTAGCCGAAATCGTGTACTCATCACTGATTTTAGGCTAAAAACGC
* * *
15076 GTTCCGGGGCCCCTGCTATGTTTTGCATGACATTTTGGCGTAAAGACTCCTTGAAAAATCGATAT
372 GTTTCGGGGCCCCTGCTA-GTTTTGCATGA-TTTTTGGCGTAAAGACTCCTTGAAAAATCTATAT
* *
15141 TCATCTAACCAAATCTCAGTCATAATTGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
435 TCATCTAACCAAATCTCAGCCA-CATTGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
15206 TTCGATTTAATTAAAAATAAATTCGGAAAAAAATGAAAAAACGATATTAAAAGCGTGAAAAGCCC
499 TTCGATTTAATTAAAAATAAATTCGGAAAAAAATGAAAAAACGATATTAAAAGCGTGAAAAGCCC
*
15271 GTCAATCTTTTTTTGCGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAA
564 -TCAAT-TTTTTTCGCGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAA
*
15336 CTTTTTCGGGTCA-GT
627 CTATTTCGGGTCATGT
* * *
15351 -TTTTAGCCGAAATCATGTACTAACCGTCACGGTTTTTAGCTAAAAACGCGTTCCGGAGTCC-CG
1 ATTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGGCCACG
15414 ACTCAATTTTGCATGATTTTTGGCTCAAAGACTCCTTGAAATATCAATATTCATCGAACCAAATC
66 ACTCAATTTTGCATGATTTTTGGCTCAAAGACTCCTTGAAATATCAATATTCATCGAACCAAATC
15479 TCAGCCACATTGAATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
131 TCAGCCACATTG-ATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* ** *
15544 AATAAATTCGGAAAAAAA-ATGAAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATTTTTTTT
195 AATAAATTCGGAAAAAAATATG-AAAAACGATATTAGAAGCGTGAAAAACCATTCAA-TCTTTTT
* * * * ****
15608 TGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTATTCAACTCA
258 GGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTTGGGTCA
* *
15673 GTTTTTAACCGAAATCGTGTA--CA-CA--G-TTTTTGGCTAAAAACGCGTTTC
323 GTTTTTAGCCGAAATCGTGTACTCATCACTGATTTTAGGCTAAAAACGCGTTTC
15721 ACGGCCCTGG
Statistics
Matches: 1428, Mismatches: 186, Indels: 158
0.81 0.10 0.09
Matches are distributed among these distances:
640 21 0.01
642 2 0.00
643 2 0.00
645 16 0.01
650 14 0.01
651 111 0.08
652 3 0.00
653 5 0.00
654 176 0.12
655 250 0.18
656 126 0.09
657 8 0.01
658 133 0.09
659 143 0.10
660 16 0.01
661 2 0.00
662 12 0.01
663 104 0.07
664 13 0.01
665 32 0.02
666 61 0.04
667 38 0.03
668 128 0.09
669 12 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (642 bp):
ATTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGGCCACG
ACTCAATTTTGCATGATTTTTGGCTCAAAGACTCCTTGAAATATCAATATTCATCGAACCAAATC
TCAGCCACATTGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
ATAAATTCGGAAAAAAATATGAAAAACGATATTAGAAGCGTGAAAAACCATTCAATCTTTTTGGC
GTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTTGGGTCAGTT
TTTAGCCGAAATCGTGTACTCATCACTGATTTTAGGCTAAAAACGCGTTTCGGGGCCCCTGCTAG
TTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAAAATCTATATTCATCTAACCAAATCTCAGCC
ACATTGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAAT
TCGGAAAAAAATGAAAAAACGATATTAAAAGCGTGAAAAGCCCTCAATTTTTTTCGCGTTGAATT
ATATAATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAACTATTTCGGGTCATGT
Done.