Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019188.1 Corchorus olitorius cultivar O-4 contig19221, 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: 24562
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:611 original size:332 final size:331
Alignment explanation
Indices: 5--814 Score: 1097
Period size: 332 Copynumber: 2.4 Consensus size: 331
1 CCAG
* * * * * *
5 TTTTTTTT-GAATTTATGTCTAATTAAATCTAAACAAAATTCAGATCCTCGTAAAAACAAATACT
1 TTTTTTTTCGAAATTATTTCTAATTAAATCTAAACAAGATTCAGATGCTCATAAAAACAAATCCT
* * * * *
69 TAAATCCAGTGTGGCTGATATTTGGTTAGATGAATATAAATATTCCAAGGAGTCTTTATGCCAAA
66 TAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATACCAAA
* * *
134 AACCATACAAAACTGAGTCGAGGCCTCGAAACGCATTTTTAGCCAAAAACCGTGATAGTTAGTAC
131 AACCATGCAAAACTGAGTCGAGACCCCGAAACGCATTTTTAGCCAAAAACCGTGATAGTTAGTAC
* * * * * *
199 ACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAAGTTTTCCTCAATTTTTTGCCACAAT
196 ACAATTTCAGCTAAAATTTTGCAAAAACTGACCCGAAAAAGTTTTCATCAAATATTTGACACAAT
* * * *
264 AGTTAGAAAAAATATATAATTCAATGCCAAAAAAATTGAAGGGAC-TTTCACGCTTTTAATATCG
261 ACTCAGAAAAAATATAT-ATTCAACGCCAAAAAAATTGAAGGG-CTTTTCACGCTTCTAATATCG
328 TTTTTCCA
324 TTTTTCCA
* * *
336 TTTTTTTTCGAAATTATTTGTAATTAAATCAAAACAAGATTCAGATGCTCATAAAAAGAAATCCT
1 TTTTTTTTCGAAATTATTTCTAATTAAATCTAAACAAGATTCAGATGCTCATAAAAACAAATCCT
* * * *
401 TAAATCAAATGTGACTGAGATTTGGTTAGATGACTATAGATATTTCAAGGAGTCTTTATACGAAA
66 TAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATACCAAA
* * * *
466 AACCATGCAAAACTGAGTCGAGACCCCGGAACGCGTTTTTAGCTAAAAACCGTGATGGTTAGTAC
131 AACCATGCAAAACTGAGTCGAGACCCCGAAACGCATTTTTAGCCAAAAACCGTGATAGTTAGTAC
** *
531 ACAATTTCAGCTAAAATTTTGCAAAAACTGACCCGAAAATTTTTTTATCAAATATTTGACACAAT
196 ACAATTTCAGCTAAAATTTTGCAAAAACTGACCCGAAAAAGTTTTCATCAAATATTTGACACAAT
*
596 ACTCAGAAAAAATATATATTCAACGCCAAAAAAATTGACGGGCTTTTCACGCTTCTAATATCGTT
261 ACTCAGAAAAAATATATATTCAACGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTT
661 TTTCCA
326 TTTCCA
* * *
667 TTTTTTTTCCG-AATTCATTTCTAATTAAATCTAAACAAGATTCAGATGTTCATAAAAATAAAGC
1 TTTTTTTT-CGAAATT-ATTTCTAATTAAATCTAAACAAGATTCAGATGCTCATAAAAACAAATC
* * * * * *
731 C-TAATATCCAATGTGGCTGAGATTTTGTTTGATGAATATTGATATTTCAAGGAGTCTATCTTCC
64 CTTAA-ATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATACC
* *
795 AAAAATCAAGCAAAACTGAG
128 AAAAACCATGCAAAACTGAG
815 CCGTGGTCCC
Statistics
Matches: 418, Mismatches: 56, Indels: 9
0.87 0.12 0.02
Matches are distributed among these distances:
330 1 0.00
331 72 0.17
332 345 0.83
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.32
Consensus pattern (331 bp):
TTTTTTTTCGAAATTATTTCTAATTAAATCTAAACAAGATTCAGATGCTCATAAAAACAAATCCT
TAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATACCAAA
AACCATGCAAAACTGAGTCGAGACCCCGAAACGCATTTTTAGCCAAAAACCGTGATAGTTAGTAC
ACAATTTCAGCTAAAATTTTGCAAAAACTGACCCGAAAAAGTTTTCATCAAATATTTGACACAAT
ACTCAGAAAAAATATATATTCAACGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTT
TTTCCA
Found at i:1179 original size:27 final size:27
Alignment explanation
Indices: 1149--1212 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
1139 TTCAACCCTG
1149 TTTACAATCTTGATATTGAGTGAACAA
1 TTTACAATCTTGATATTGAGTGAACAA
1176 TTTACAATCTTGATATTGAGTGAACAA
1 TTTACAATCTTGATATTGAGTGAACAA
1203 TTTACAATCT
1 TTTACAATCT
1213 ACTGTAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (27 bp):
TTTACAATCTTGATATTGAGTGAACAA
Found at i:3072 original size:60 final size:58
Alignment explanation
Indices: 2985--3146 Score: 202
Period size: 60 Copynumber: 2.7 Consensus size: 58
2975 GCTAATTGCT
* * * **
2985 CAAATAAGGGTCTAATC-TTTACCAAAATGTTCAAATAAGGGCATGATCTTTTAATTTGGT
1 CAAATAAGGGTCTAA-CGTTTGCTAAAATGCTCAAATAAGGGCA--ATCTTTTAATTTGAC
*
3045 CAAATAAGGG-CATAACGTTTGCTAAAATGCTCAAATATGGGTCCAATCTTTTAATTTGAC
1 CAAATAAGGGTC-TAACGTTTGCTAAAATGCTCAAATAAGGG--CAATCTTTTAATTTGAC
3105 CAAATAAGGGTCTAACGTTTGCTAAAATGCTCAAATAAGGGC
1 CAAATAAGGGTCTAACGTTTGCTAAAATGCTCAAATAAGGGC
3147 CTGGTATCGA
Statistics
Matches: 90, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
58 1 0.01
59 2 0.02
60 84 0.93
61 1 0.01
62 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (58 bp):
CAAATAAGGGTCTAACGTTTGCTAAAATGCTCAAATAAGGGCAATCTTTTAATTTGAC
Found at i:3140 original size:31 final size:29
Alignment explanation
Indices: 2981--3145 Score: 106
Period size: 31 Copynumber: 5.5 Consensus size: 29
2971 TCAGGCTAAT
*
2981 TGCTCAAATAAGGGTCTAATCTTTACCAAAA
1 TGCTCAAATAAGGGTCTAA-CTTT-CTAAAA
* * **
3012 TGTTCAAATAAGGG-CATGATCTTT-TAATT
1 TGCTCAAATAAGGGTC-T-AACTTTCTAAAA
*
3041 TGGTCAAATAAGGG-CATAACGTTTGCTAAAA
1 TGCTCAAATAAGGGTC-TAAC-TTT-CTAAAA
* * **
3072 TGCTCAAATATGGGTCCAATCTTT-TAATT
1 TGCTCAAATAAGGGTCTAA-CTTTCTAAAA
3101 TGAC-CAAATAAGGGTCTAACGTTTGCTAAAA
1 TG-CTCAAATAAGGGTCTAAC-TTT-CTAAAA
3132 TGCTCAAATAAGGG
1 TGCTCAAATAAGGG
3146 CCTGGTATCG
Statistics
Matches: 104, Mismatches: 18, Indels: 24
0.71 0.12 0.16
Matches are distributed among these distances:
28 3 0.03
29 42 0.40
30 3 0.03
31 53 0.51
32 3 0.03
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (29 bp):
TGCTCAAATAAGGGTCTAACTTTCTAAAA
Found at i:3267 original size:60 final size:59
Alignment explanation
Indices: 3190--3350 Score: 207
Period size: 60 Copynumber: 2.7 Consensus size: 59
3180 TTACGCCAGG
*
3190 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAATATCAGA
1 CCCTTATTTGAGCATTTT-GATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
* * *
3250 CCCTTATTTGAGTATTTTAGATAACGTTAGG-CATTCATTTGGCCAAATTAAAAGATCGGA
1 CCCTTATTTGAGCATTTT-GATAACGTTAGGCCCTT-ATTTGGCCAAATTAAAAGATCAGA
* * * *
3310 CCCTTATTTTAGCATTTTGACAAACATTAGACCCTTATTTG
1 CCCTTATTTGAGCATTTTGA-TAACGTTAGGCCCTTATTTG
3351 AGCAATTAGC
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
59 5 0.06
60 79 0.91
61 3 0.03
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (59 bp):
CCCTTATTTGAGCATTTTGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
Found at i:6669 original size:35 final size:34
Alignment explanation
Indices: 6630--6695 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
6620 ACCTATATAT
*
6630 AACCTATATAAGTATATACTTAACAAAAAAAAAAA
1 AACCTATATAAGTATATA-ATAACAAAAAAAAAAA
*
6665 AACCTATATAAGTATATAATAACTAAAAAAA
1 AACCTATATAAGTATATAATAACAAAAAAAA
6696 TTGATGAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 11 0.38
35 18 0.62
ACGTcount: A:0.62, C:0.11, G:0.03, T:0.24
Consensus pattern (34 bp):
AACCTATATAAGTATATAATAACAAAAAAAAAAA
Found at i:12235 original size:46 final size:47
Alignment explanation
Indices: 12182--12274 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
12172 AATCTCAGGT
12182 TTCGATTTG-CTAATTATGGAAGAAGTAGAAATATTTAAAGTCAAAA
1 TTCGATTTGCCTAATTATGGAAGAAGTAGAAATATTTAAAGTCAAAA
12228 TTCGATTTGCCTAATTATGGAAGAAGTAGAAATATTTAAAGTCAAAA
1 TTCGATTTGCCTAATTATGGAAGAAGTAGAAATATTTAAAGTCAAAA
12275 GGACAATATA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 9 0.20
47 37 0.80
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (47 bp):
TTCGATTTGCCTAATTATGGAAGAAGTAGAAATATTTAAAGTCAAAA
Found at i:14808 original size:20 final size:22
Alignment explanation
Indices: 14783--14832 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
14773 TCTATGAATT
14783 TTATTTTGATAATTCA-AAA-A
1 TTATTTTGATAATTCATAAAGA
* *
14803 TTATTTTAATAGTTCATAAAGA
1 TTATTTTGATAATTCATAAAGA
14825 -TATTTTGA
1 TTATTTTGA
14833 GAAATAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 14 0.56
21 10 0.40
22 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (22 bp):
TTATTTTGATAATTCATAAAGA
Found at i:15483 original size:80 final size:79
Alignment explanation
Indices: 15380--15532 Score: 261
Period size: 80 Copynumber: 1.9 Consensus size: 79
15370 GCATTCGTTA
15380 TGCAACTCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAAG
1 TGCAACTCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAAG
15445 TCGTCTAAGATCCG
66 TCGTCTAAGATCCG
* * **
15459 TGCAACTCCCCCTCGTTTTTATTTCCCTTCCCAAAATAGGTTTTCCAGCCGACTTATCTTCAAAA
1 TGCAACT-CCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAA
15524 GTCGTCTAA
65 GTCGTCTAA
15533 AAACCGAAAC
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
79 7 0.10
80 62 0.90
ACGTcount: A:0.24, C:0.33, G:0.11, T:0.33
Consensus pattern (79 bp):
TGCAACTCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAAG
TCGTCTAAGATCCG
Found at i:18389 original size:325 final size:326
Alignment explanation
Indices: 17811--18426 Score: 766
Period size: 325 Copynumber: 1.9 Consensus size: 326
17801 TTTTAATTTA
* * *
17811 TTTTTTCATATTTATTCTGAAGTAATTTCTAATTAAATCGAAACAAGATTTATATGCACATAAAA
1 TTTTTTCATATTTATTCCGAAGTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACATAAAA
* *
17876 ACAAACCCTTAAATCCAATGTGCCTAAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTC
66 ACAAACCCTTAAATCCAATGTGCATAAGATTTGAGTAGATGAATAAAGATATTTCAAGGAGTCT-
* *
17941 AACGCCAAGAAAAATGCAAAACAGAACCGTGGCTCTGGAACACGTTTTTAGGCAAAAACCGTGAT
130 AACGCCAAGAAAAATGCAAAACAGAACCGTGGCCCCGGAACACGTTTTTAGGCAAAAACCGTGAT
* * **
18006 AGTTAGTACATGATTTCGGCTAAAATTTTGCAAAACTTGATCCGAAAGATATTTCCTCAATTTTT
195 AGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAGATATTTCCTCAATTTCC
* * *
18071 GGCT-AAAATACTCATGAAAAATATATAATTCGACATCAAAGAGATTAAAAGGCTTCTAATAATA
260 AG-TGAAAATACTAATAAAAAATATATAATTCGACATCAAAGAGATTAAAAGGCTTCTAATAATA
18135 ATG
324 ATG
* * * * *
18138 TTTTTTC-TATTTTTTTCCGAATTAATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAA
1 TTTTTTCATA-TTTATTCCGAAGTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACATAAA
* * * * *
18202 AA-AAATCCTTAAATCTAATGTGGATGAGATTTGGGTAGATGAATAAAGATATTTCAAGGAGTCT
65 AACAAACCCTTAAATCCAATGTGCATAAGATTTGAGTAGATGAATAAAGATATTTCAAGGAGTCT
** ** ** *
18266 -TGGCACAA-AAAATCATGCAAAATTGAGTCG-GGCCCCGGAACGCGTTTTTA-GCAAAAAACCG
130 AACGC-CAAGAAAA--ATGCAAAACAGAACCGTGGCCCCGGAACACGTTTTTAGGC-AAAAACCG
** *
18327 TGAT-GATTAGTACACGATTTTTGCTAAAATTTTGTAAAAATTGA-CCTGAAAGAT-TATTCCTC
191 TGATAG-TTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCC-GAAAGATAT-TTCCTC
18389 AATTTCCAGTGAAAATACTAATAAAAAATATATAATTC
253 AATTTCCAGTGAAAATACTAATAAAAAATATATAATTC
18427 AACACGATAT
Statistics
Matches: 246, Mismatches: 34, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
324 13 0.05
325 109 0.44
326 69 0.28
327 55 0.22
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (326 bp):
TTTTTTCATATTTATTCCGAAGTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACATAAAA
ACAAACCCTTAAATCCAATGTGCATAAGATTTGAGTAGATGAATAAAGATATTTCAAGGAGTCTA
ACGCCAAGAAAAATGCAAAACAGAACCGTGGCCCCGGAACACGTTTTTAGGCAAAAACCGTGATA
GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAGATATTTCCTCAATTTCCA
GTGAAAATACTAATAAAAAATATATAATTCGACATCAAAGAGATTAAAAGGCTTCTAATAATAAT
G
Found at i:20063 original size:647 final size:644
Alignment explanation
Indices: 18941--21123 Score: 2059
Period size: 647 Copynumber: 3.3 Consensus size: 644
18931 CGGTACGCGT
* * * * *
18941 TACACGATTTCAGCTAGAATTTTGCAAAAATTGACT-CGAAAATTATTTCCTCAATTTTAAGTCA
1 TACACGATTTCGGCTAAAATTTTGCAAAAAATGACTGC-AAAATT-TTCCCTCAATTTTAAGCCA
* * * *
19005 GA-ATACTCATAAAAATTATATAATTCAACGTCAAAAAGATTGAA-GGCTTTTTCATGCTTTTAA
64 TATATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGC-TTTTCACGCTTTTAA
* * *
19068 TATCATTTTTCCTATTATTTTCTGAATTAAATTCTAATTAAATCGAAACATGATTCAGATGTTTG
128 TATCATTTTTCATATT-TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGTTTG
*
19133 TTTTACAAATCCTTAAATCGAATGTGCCTGAGATTTGGTTAGATGAATGTAGATATTTCAAGGAG
192 ---T--AAAT-C--AAATC-AATG-G-CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAG
* * * ** * * *
19198 TC-CCGACGCAAAAAGTCATGCAACACTGAACCGGGGTGCCGGAATGCGTTTTTAGCCAAGAACC
246 TCTCAGAC-CAAAAA-TCATGCAAAATTGAACC-GGGCCCCGAAACGCGTTTTTAGCCAA-AAAC
* * * *
19262 GTGATTTCGACTAACGTACACGATTTCGGCT-AATATTTTGCAAAAATT-AACCATAA-ATATTT
307 GTGA--T-GA-TTA-TTACACGATTTCGGCTAAAT-TTTTGCAAAAATTGACCCAAAAGATA-TT
* * * *
19324 TCCCTCAATTTTTGTCTAAAATACTCATAAAATACATATAATTCAACT-CTAAAAAGATTGTAGG
365 T-CCTCAATTTTTGACTAAAATACTCATAAAAAATATATAATTCAA-TGC-AAAAAGATTGAAGG
19388 ACTTTTCACGCTTTTAATATCATTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACA
427 -CTTTTCACGCTTTTAATATCATTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACA
* * * *
19453 AGATTCAGATGCTCGTATAAACAAATCCTTAAATGCAATATGGCTGAGGTTTGATTAGATGAATA
491 AGATTAAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATA
* * * *
19518 TAGATATTCCAAGGAGTCTCGACGCCGAAAATCATGCAAAACTGACTCGGGGCCCTGAAACGCGT
556 TAGATATTTCAAGGAGTCTCGA-GCCAAAAATCATGCAAAATTGAGTCGGGGCCCTGAAACGCGT
* *
19583 TTTCGGCAAAAAACCGTAATGGTTAG
620 TTT-AGCAAAAAACCGTGATGGTTAG
* * *
19609 TACATGATTTCGGCTAAAATTTTGCAAAAAATGACCTGCAATATTTTCCCTCAATTTTCAGCCAT
1 TACACGATTTCGGCTAAAATTTTGCAAAAAATGA-CTGCAAAATTTTCCCTCAATTTTAAGCCAT
* * *
19674 A-ATACTCATAAAAAAATATATAATCCAACGCCAAGAAGATTGAAGGGCTTTTCACG-TTTCAAA
65 ATATACTCAT-AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTT-TAA
* * * * *
19737 TATCGTTTTTCATATTTTTTTCCGAATTAATTTCTAATTAAAACAAAACATGATTCAGATGTTTG
128 TATCATTTTTCATA-TTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGTTTG
* *
19802 T-AA-C-AA-CAATGGCTGAGATTTGGTTAGATGAATATAGATATTTTAAGGAATCTCAGAACCA
192 TAAATCAAATCAATGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCAG-ACCA
* * * *
19863 AAAATTATTCAAAATTGAACCGGGCCCCGTAACGCGTTTTT-GTCAAAAACTGTGATGATTATTA
256 AAAATCATGCAAAATTGAACCGGGCCCCGAAACGCGTTTTTAGCCAAAAAC-GTGATGATTATTA
* * * *
19927 CACGATTTCGGCTAAATTTTTGCAAAAATTGACCCAAAAGATACTTCCTCAATTTTTAACCATAA
320 CACGATTTCGGCTAAATTTTTGCAAAAATTGACCCAAAAGATATTTCCTCAATTTTTGACTAAAA
* *
19992 TATTCATAAAAAATATATAATTCAATGCAAGAAAGATTGAAGAGCTTTTCACGCTTTTAATATCG
385 TACTCATAAAAAATATATAATTCAATGCAA-AAAGATTGAAG-GCTTTTCACGCTTTTAATATCA
* * **
20057 TTTTTCATATTTTTCTGAATGAATTTCTAATTAAATCGAAACAAGATTTAGATGCTTATAAAAAC
448 TTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAAC
* * * * *
20122 AAATCCTTAAATGCAATGTGGCTAAGATTTTATTATATGAATATAGATATTTCAATGAGTGTCGG
513 AAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC-G
* **
20187 TGCCAAAAATCATGCAAAATTGAGTC-GGGCCC-GAAACGCGCTTTTAGCCTAAAACCGTGATGG
577 AGCCAAAAATCATGCAAAATTGAGTCGGGGCCCTGAAACGCG-TTTTAGCAAAAAACCGTGATGG
20250 TTAG
641 TTAG
*
20254 TACACGATTTTGGCTAAAATTTTGCAAAAAATGACATG-AAAATTTTTTCCC-CAATTTTTGGAT
1 TACACGATTTCGGCTAAAATTTTGCAAAAAATGAC-TGCAAAA--TTTTCCCTCAA--TTT---T
* * * * *
20317 AAAATACTCATAATATATACACATATATATATATATATATATTTTAACGCCAAAAAGATTGGAGG
58 --AA-GC-C---ATATATACTCATA-A-A-A-A-ATATATAATTCAACGCCAAAAAGATTGAAGG
** * * * *
20382 ATTTTTTACGCTTTTAATATCATTTTTCATA-TTTTTCAGAATTAATTTTTACTTAAATCGAAAC
111 GCTTTTCACGCTTTTAATATCATTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAAC
* * *
20446 AAGATTCCGATGCTTGTAAAATCAAATTCATAAATTCAATGTGGCTGAGATTTGATTAGATGAAT
176 AAGATTCAGATG-TT-T---GT-AAA-TC--AAA-TCAA--TGGCTGAGATTTGGTTAGATGAAT
* * * * * * *
20511 ATATGGATATCTCAAGGAGTCT-TGGCGCAAAAAATCATGCAAAATTGAGCTGGGGCCGCAAAAC
229 ATA--GATATTTCAAGGAGTCTCAGAC-C-AAAAATCATGCAAAATTGAAC-CGGGCCCCGAAAC
* * * **
20575 GCTTTTTTAGCCAAAAACG-CAT--TT-TTACACGATTTTGGCTAAAAATTT-CTAAAAATTGAC
289 GCGTTTTTAGCCAAAAACGTGATGATTATTACACGATTTCGGCTAAATTTTTGC-AAAAATTGAC
** * * *
20635 CTGAAAGACATTTCCTCAATTTTTGGCTAAAATACTCATTAAAAAAATATATAATTCAACGCCAA
353 CCAAAAGATATTTCCTCAATTTTTGACTAAAATACTCA-T-AAAAAATATATAATTCAATG-CAA
* * * * **
20700 AAAGATTTAAGGGCTTTTGACG-TTTTCAATATCTTTTTTCCTATTTTTTCCAAATTAATTTCTA
415 AAAGATTGAA-GGCTTTTCACGCTTTT-AATATCATTTTTCATA-TTTTTCTGAATTAATTTCTA
* * * *
20764 ATGAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCGTAAATCCAATGTGGTTGAGATT
477 ATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATT
* *
20829 TGATTAGATGAATATAGATATTTCAAGTAGTCTCGGAGCCAAAAATCATGCAAAATTGAGTCGAG
542 TGATTAGATGAATATAGATATTTCAAGGAGTCTC-GAGCCAAAAATCATGCAAAATTGAGTCGGG
* ** *
20894 TCCCTTTAACGCGTTTTTAGCAAAAAACTGTGATGGTTTGTTAG
606 GCCCTGAAACGCG-TTTTAGCAAAAAACCGTGAT-G---GTTAG
* * * * * ** *
20938 TACACAATTTCGACTAAAATTTTGCAAAAATTGAC-ACAAAAGATTTCTCCTCAATTTTTGGCTA
1 TACACGATTTCGGCTAAAATTTTGCAAAAAATGACTGCAAAA-TTTTC-CCTCAATTTTAAGCCA
* * *
21002 -ATATACTCAT-AAAAATATATTATTCAACGCCAAAAAGATTGGAGGGCTTTTTACGCTTTTAAT
64 TATATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAAT
* * * * * *
21065 ATCGTATTTCTTATTTTTTCTAAATTAATTTCTAATGAAATCGAAATAAGATTCAGATG
129 ATCATTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG
21124 CTCATAAAAA
Statistics
Matches: 1258, Mismatches: 179, Indels: 158
0.79 0.11 0.10
Matches are distributed among these distances:
644 4 0.00
645 63 0.05
646 20 0.02
647 236 0.19
648 15 0.01
649 5 0.00
650 2 0.00
651 3 0.00
652 9 0.01
653 17 0.01
654 51 0.04
655 9 0.01
656 6 0.00
657 5 0.00
658 10 0.01
659 1 0.00
660 39 0.03
661 4 0.00
662 49 0.04
663 5 0.00
665 55 0.04
666 40 0.03
667 3 0.00
668 59 0.05
669 104 0.08
670 6 0.00
671 9 0.01
672 3 0.00
674 4 0.00
675 60 0.05
676 35 0.03
677 53 0.04
678 168 0.13
679 22 0.02
680 31 0.02
681 1 0.00
682 7 0.01
683 6 0.00
684 39 0.03
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Consensus pattern (644 bp):
TACACGATTTCGGCTAAAATTTTGCAAAAAATGACTGCAAAATTTTCCCTCAATTTTAAGCCATA
TATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATAT
CATTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGTTTGTAAA
TCAAATCAATGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCAGACCAAAAAT
CATGCAAAATTGAACCGGGCCCCGAAACGCGTTTTTAGCCAAAAACGTGATGATTATTACACGAT
TTCGGCTAAATTTTTGCAAAAATTGACCCAAAAGATATTTCCTCAATTTTTGACTAAAATACTCA
TAAAAAATATATAATTCAATGCAAAAAGATTGAAGGCTTTTCACGCTTTTAATATCATTTTTCAT
ATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTT
AAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGAGCCAAAAA
TCATGCAAAATTGAGTCGGGGCCCTGAAACGCGTTTTAGCAAAAAACCGTGATGGTTAG
Found at i:22624 original size:40 final size:42
Alignment explanation
Indices: 22529--22642 Score: 108
Period size: 40 Copynumber: 2.7 Consensus size: 42
22519 TTAGGAAAGT
* * * *
22529 TTATAAAAATTTTATAGTTAGGTTATCAAAGTTTCTTATGGAGT
1 TTATCAAAATTTTATAGTTAGATTATCAAA--TTCATATGGAGA
* *
22573 TTATCACAATTTTATAGTTA-ATTATCAAA-TCATATGGTGA
1 TTATCAAAATTTTATAGTTAGATTATCAAATTCATATGGAGA
* *
22613 TTATCAAAATTTAATAGGGTAG-TTATCAAA
1 TTATCAAAATTTTATA-GTTAGATTATCAAA
22643 ATTTCATAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
40 22 0.37
41 11 0.19
43 8 0.14
44 18 0.31
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (42 bp):
TTATCAAAATTTTATAGTTAGATTATCAAATTCATATGGAGA
Found at i:23886 original size:58 final size:58
Alignment explanation
Indices: 23811--23927 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
23801 ACGATTTGGC
23811 ACCAGATATCCGAAGGTGTGGAAAGAGCTGCTGTGAAAAATGAAAAAACCATCAAAAA
1 ACCAGATATCCGAAGGTGTGGAAAGAGCTGCTGTGAAAAATGAAAAAACCATCAAAAA
*
23869 ACCAGATATCCGGAGGTGTGGAAAGAGCTGCTGTGAAAAATGAAAAAACCATCAAAAA
1 ACCAGATATCCGAAGGTGTGGAAAGAGCTGCTGTGAAAAATGAAAAAACCATCAAAAA
23927 A
1 A
23928 AAGTTTATTT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.15
Consensus pattern (58 bp):
ACCAGATATCCGAAGGTGTGGAAAGAGCTGCTGTGAAAAATGAAAAAACCATCAAAAA
Done.