Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008124.1 Corchorus capsularis cultivar CVL-1 contig08145, 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: 56483
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:164 original size:88 final size:87
Alignment explanation
Indices: 18--181 Score: 222
Period size: 88 Copynumber: 1.9 Consensus size: 87
8 GGCAAACCAG
* * * * *
18 TACTAGTAATGGAATCAAGCCCAAATCGTAATGGTTAAATCCCAAATCATGTACGGTGAAACTGT
1 TACTAATAATGGAATCAAACCCAAAGCGTAATGATCAAATCCCAAATCATGTACGGTGAAACTGT
83 AAAGCATGATTCCCTAAACCCC
66 AAAGCATGATTCCCTAAACCCC
* * * *
105 TACTAATAATGGGATCAAACCGCAAAGCGTAATGATCAAA-CTCTAAATCATGTATGGTGAAATT
1 TACTAATAATGGAATCAAACC-CAAAGCGTAATGATCAAATC-CCAAATCATGTACGGTGAAACT
169 GTAAAGCATGATT
64 GTAAAGCATGATT
182 AGGCAATCCC
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
87 19 0.29
88 47 0.71
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (87 bp):
TACTAATAATGGAATCAAACCCAAAGCGTAATGATCAAATCCCAAATCATGTACGGTGAAACTGT
AAAGCATGATTCCCTAAACCCC
Found at i:239 original size:22 final size:21
Alignment explanation
Indices: 209--283 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
199 TAATGGGATT
209 AAACCCCAAATCTTAATGGTC
1 AAACCCCAAATCTTAATGGTC
** ** *
230 AAAGCCCC-AATCATCGATTATG
1 AAA-CCCCAAATC-TTAATGGTC
*
252 AAACCCGAAATCTTAATGGTC
1 AAACCCCAAATCTTAATGGTC
273 AAACCCCAAAT
1 AAACCCCAAAT
284 ATGAAAGTCA
Statistics
Matches: 39, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
21 24 0.62
22 15 0.38
ACGTcount: A:0.40, C:0.28, G:0.11, T:0.21
Consensus pattern (21 bp):
AAACCCCAAATCTTAATGGTC
Found at i:459 original size:2 final size:2
Alignment explanation
Indices: 452--479 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
442 CTTAATGAAC
452 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
480 GATTTATCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:735 original size:88 final size:87
Alignment explanation
Indices: 550--737 Score: 236
Period size: 87 Copynumber: 2.1 Consensus size: 87
540 TTTAAACTCT
* * *
550 TACTAGTAATGGGATCAAATCCCAAATCATAATGGTCAAAACCCAAATCATGTATAGTGAATTTG
1 TACTAGTAATGGGATCAAATCCCAAAACATAATAGTCAAAACCCAAATCATGTATAGTGAATGTG
615 AAAGCATGATTAGGCAAACCCC
66 AAAGCATGATTAGGCAAACCCC
* * * * *
637 TACTAATAATGGGATCAAA-CCGCAAAACGTAATAGTTAAACCCCAAATCATGTATGGTGATACT
1 TACTAGTAATGGGATCAAATCC-CAAAACATAATAGTCAAAACCCAAATCATGTATAGTGA-A-T
***
701 GT-AAAGCATGATTAGGCAAATTGC
63 GTGAAAGCATGATTAGGCAAACCCC
725 TACTAGTAATGGG
1 TACTAGTAATGGG
738 GCTAAATAAT
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
86 2 0.02
87 50 0.58
88 32 0.37
89 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (87 bp):
TACTAGTAATGGGATCAAATCCCAAAACATAATAGTCAAAACCCAAATCATGTATAGTGAATGTG
AAAGCATGATTAGGCAAACCCC
Found at i:856 original size:28 final size:30
Alignment explanation
Indices: 791--866 Score: 97
Period size: 28 Copynumber: 2.6 Consensus size: 30
781 TAATACCCAA
791 AAAT-ATCCCTTAAGTTTTTCGTTTGGGACG
1 AAATAATCCCTTAAGTTTTTC-TTTGGGACG
*
821 AAATAATCCCTTATGTTTTT-TTT-GGAC-
1 AAATAATCCCTTAAGTTTTTCTTTGGGACG
848 AAATTAATCCCTTAAGTTT
1 AAA-TAATCCCTTAAGTTT
867 AAAAAAAGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 3 0.07
28 18 0.43
29 3 0.07
30 4 0.10
31 14 0.33
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (30 bp):
AAATAATCCCTTAAGTTTTTCTTTGGGACG
Found at i:2190 original size:41 final size:41
Alignment explanation
Indices: 2145--2227 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
2135 CGTGGTAATC
*
2145 CTTTTCTTTTGGGTGCCAAGAAAGATATTTGTGCGTCGAAT
1 CTTTTCTTTTGGGTGCCAAGAAAGAGATTTGTGCGTCGAAT
2186 CTTTTCTTTTGGGTGCCAAGAAAGAGATTTGTGCGTCGAAT
1 CTTTTCTTTTGGGTGCCAAGAAAGAGATTTGTGCGTCGAAT
2227 C
1 C
2228 AACCACTTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (41 bp):
CTTTTCTTTTGGGTGCCAAGAAAGAGATTTGTGCGTCGAAT
Found at i:11187 original size:21 final size:21
Alignment explanation
Indices: 11163--11219 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
11153 AGTCATCAGG
* *
11163 ATGCGGGCTGGGGGCTGTGGC
1 ATGCGGGCTGGGCGCTGAGGC
11184 ATGC-GGCATGGGCGCTGAGGC
1 ATGCGGGC-TGGGCGCTGAGGC
* *
11205 TTGCGGCCTGGGCGC
1 ATGCGGGCTGGGCGC
11220 CCAGCGGCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 3 0.10
21 25 0.83
22 2 0.07
ACGTcount: A:0.07, C:0.25, G:0.51, T:0.18
Consensus pattern (21 bp):
ATGCGGGCTGGGCGCTGAGGC
Found at i:28550 original size:9 final size:9
Alignment explanation
Indices: 28539--28573 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
28529 CAATTAATGT
*
28539 TAACATTTT
1 TAACATTTA
28548 TAACATTTA
1 TAACATTTA
*
28557 AAACATTTA
1 TAACATTTA
28566 TAACATTT
1 TAACATTT
28574 GTATTTGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (9 bp):
TAACATTTA
Found at i:29384 original size:33 final size:33
Alignment explanation
Indices: 29333--29408 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
29323 ACAACCGCCT
* * *
29333 TCCTGGGGTGGTATGAGCCATGGTTTGCCACCC
1 TCCTGGGGCGGCAAGAGCCATGGTTTGCCACCC
* *
29366 TCCTGGGGCGGCAAGAGCCATGGTTTGCCGCTC
1 TCCTGGGGCGGCAAGAGCCATGGTTTGCCACCC
*
29399 TCCTAGGGCG
1 TCCTGGGGCG
29409 ACAGGGTCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.12, C:0.29, G:0.36, T:0.24
Consensus pattern (33 bp):
TCCTGGGGCGGCAAGAGCCATGGTTTGCCACCC
Found at i:29637 original size:21 final size:21
Alignment explanation
Indices: 29611--29654 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29601 CAAAACTGGA
29611 TTGCTAAAT-ACCGCCCCATTT
1 TTGCT-AATCACCGCCCCATTT
*
29632 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
29653 TT
1 TT
29655 CACGCTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.34, G:0.09, T:0.39
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:29888 original size:32 final size:34
Alignment explanation
Indices: 29852--29914 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
29842 CGCCCCAAGA
29852 GGGCGGCTT-ACCA-TAGGCAGGCCGCCCCACTT
1 GGGCGGCTTCACCATTAGGCAGGCCGCCCCACTT
*
29884 GGGCGGCTTCACCATTGGGCAGGCCGCCCCA
1 GGGCGGCTTCACCATTAGGCAGGCCGCCCCA
29915 GTGGGGAGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 9 0.32
33 4 0.14
34 15 0.54
ACGTcount: A:0.14, C:0.38, G:0.33, T:0.14
Consensus pattern (34 bp):
GGGCGGCTTCACCATTAGGCAGGCCGCCCCACTT
Found at i:30029 original size:21 final size:21
Alignment explanation
Indices: 30005--30048 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
29995 CAAAAGTGTA
*
30005 AAAAGTGGGACGGTATTTAGC
1 AAAAGTAGGACGGTATTTAGC
30026 AAAAGTAGGACGGTATTTAGC
1 AAAAGTAGGACGGTATTTAGC
30047 AA
1 AA
30049 CCCCCTTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.09, G:0.30, T:0.23
Consensus pattern (21 bp):
AAAAGTAGGACGGTATTTAGC
Found at i:34897 original size:2 final size:2
Alignment explanation
Indices: 34890--34920 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
34880 TCACATAGAC
34890 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34921 TCCAGTCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35649 original size:41 final size:40
Alignment explanation
Indices: 35604--35752 Score: 167
Period size: 41 Copynumber: 3.7 Consensus size: 40
35594 ACCCAATAGC
35604 CAAAGTCCTCAAACACATTCATAACACAGAGGCATCTATAT
1 CAAAGTCCTCAAACACATT-ATAACACAGAGGCATCTATAT
* * * * *
35645 CAAAGTCCACAAACACAATTATAACACAGGGGCAACTCTCT
1 CAAAGTCCTCAAACAC-ATTATAACACAGAGGCATCTATAT
* * *
35686 CAAAGTCCTCAAGCACATTTTTAACACAGAGGCATCTATAC
1 CAAAGTCCTCAAACACA-TTATAACACAGAGGCATCTATAT
*
35727 CAAAGTCC-CTAAACACA-TGTAACACA
1 CAAAGTCCTC-AAACACATTATAACACA
35753 AGGGCAATTT
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
39 8 0.09
40 2 0.02
41 77 0.86
42 3 0.03
ACGTcount: A:0.41, C:0.28, G:0.11, T:0.20
Consensus pattern (40 bp):
CAAAGTCCTCAAACACATTATAACACAGAGGCATCTATAT
Found at i:35691 original size:82 final size:80
Alignment explanation
Indices: 35604--35759 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 80
35594 ACCCAATAGC
*
35604 CAAAGTCCTCAAACACATTCATAACACAGAGGCATCTATATCAAAGTCCAC-AAACACAATTATA
1 CAAAGTCCTCAAACACATTCATAACACAGAGGCATCTATACCAAAGTCC-CTAAACAC-A-TATA
*
35668 ACACAGGGGCAACTCTCT
63 ACACAAGGGCAACTCTCT
* ** *
35686 CAAAGTCCTCAAGCACATTTTTAACACAGAGGCATCTATACCAAAGTCCCTAAACACATGTAACA
1 CAAAGTCCTCAAACACATTCATAACACAGAGGCATCTATACCAAAGTCCCTAAACACATATAACA
35751 CAAGGGCAA
66 CAAGGGCAA
35760 TTTTCTTTAC
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
80 14 0.21
81 2 0.03
82 51 0.76
ACGTcount: A:0.41, C:0.28, G:0.12, T:0.19
Consensus pattern (80 bp):
CAAAGTCCTCAAACACATTCATAACACAGAGGCATCTATACCAAAGTCCCTAAACACATATAACA
CAAGGGCAACTCTCT
Found at i:38815 original size:22 final size:22
Alignment explanation
Indices: 38790--39012 Score: 127
Period size: 22 Copynumber: 10.1 Consensus size: 22
38780 AATCATATTG
*
38790 TGAAAATTTGATAACCTCATTA
1 TGAAAATTTGATAACCTCACTA
* *
38812 TG-AAATTTCGATAACCTCCCTG
1 TGAAAATTT-GATAACCTCACTA
* * * *
38834 CGAAATTTTGATAACCACACTG
1 TGAAAATTTGATAACCTCACTA
* * *
38856 TGAAATTTTGATAAGCACACTA
1 TGAAAATTTGATAACCTCACTA
* *
38878 TGAAAATTTTGATAATCTTC-TTA
1 TGAAAA-TTTGATAA-CCTCACTA
* * * *
38901 TGAAATTTTGGTAATCACACTA
1 TGAAAATTTGATAACCTCACTA
* *
38923 T-AAAA-TTGGTAACCGCACTA
1 TGAAAATTTGATAACCTCACTA
*
38943 TCAAAATTTTGATAACCTC-CTCA
1 TGAAAA-TTTGATAACCTCACT-A
* *
38966 T-AAAATCTTGATAACCACACAA
1 TGAAAAT-TTGATAACCTCACTA
* *
38988 TG-AAATTTCAATAACCTCCCTA
1 TGAAAATTT-GATAACCTCACTA
39010 TGA
1 TGA
39013 GAATGAAACT
Statistics
Matches: 155, Mismatches: 32, Indels: 27
0.72 0.15 0.13
Matches are distributed among these distances:
20 14 0.09
21 17 0.11
22 91 0.59
23 32 0.21
24 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCACTA
Found at i:38858 original size:66 final size:66
Alignment explanation
Indices: 38769--38962 Score: 185
Period size: 66 Copynumber: 2.9 Consensus size: 66
38759 CTCCAACATA
* * * * * * *
38769 GAAATATTGATAATCATATTGTGAAAATTTGATAACCTCATTATGAAATTTCGATAACCTCCCTG
1 GAAATTTTGATAATCACACTGTGAAAATTTGATAACCACACTATGAAATTTTGATAACCTCCCTA
38834 C
66 C
* * * * * *
38835 GAAATTTTGATAACCACACTGTGAAATTTTGATAAGCACACTATGAAAATTTTGATAATCTTCTT
1 GAAATTTTGATAATCACACTGTGAAAATTTGATAACCACACTATG-AAATTTTGATAACCTCCCT
*
38900 AT
65 AC
* * * * *
38902 GAAATTTTGGTAATCACACTAT-AAAA-TTGGTAACCGCACTATCAAAATTTTGATAACCTCC
1 GAAATTTTGATAATCACACTGTGAAAATTTGATAACCACACTAT-GAAATTTTGATAACCTCC
38963 TCATAAAATC
Statistics
Matches: 102, Mismatches: 24, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
65 28 0.27
66 40 0.39
67 34 0.33
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (66 bp):
GAAATTTTGATAATCACACTGTGAAAATTTGATAACCACACTATGAAATTTTGATAACCTCCCTA
C
Found at i:38933 original size:20 final size:21
Alignment explanation
Indices: 38908--38950 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
38898 TTATGAAATT
*
38908 TTGGTAATCACACTAT-AAAA
1 TTGGTAACCACACTATCAAAA
*
38928 TTGGTAACCGCACTATCAAAA
1 TTGGTAACCACACTATCAAAA
38949 TT
1 TT
38951 TTGATAACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.30
Consensus pattern (21 bp):
TTGGTAACCACACTATCAAAA
Found at i:38985 original size:65 final size:65
Alignment explanation
Indices: 38836--38994 Score: 165
Period size: 65 Copynumber: 2.4 Consensus size: 65
38826 CCTCCCTGCG
* * * * * * *
38836 AAATTTTGATAACCACACTGTGAAATTTTGATAAGCACACTATGAAAATTTTGATAATCTTCTTA
1 AAATTTTGATAACCACACTAT-AAA-ATTGATAACCACACTATCAAAATTTTGATAACCTCCTCA
*
38901 TG
64 TA
* * * *
38903 AAATTTTGGTAATCACACTATAAAATTGGTAACCGCACTATCAAAATTTTGATAACCTCCTCATA
1 AAATTTTGATAACCACACTATAAAATTGATAACCACACTATCAAAATTTTGATAACCTCCTCATA
* * *
38968 AAATCTTGATAACCACACAATGAAATT
1 AAATTTTGATAACCACACTATAAAATT
38995 TCAATAACCT
Statistics
Matches: 75, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
65 54 0.72
66 3 0.04
67 18 0.24
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (65 bp):
AAATTTTGATAACCACACTATAAAATTGATAACCACACTATCAAAATTTTGATAACCTCCTCATA
Found at i:39223 original size:22 final size:22
Alignment explanation
Indices: 39148--39350 Score: 136
Period size: 22 Copynumber: 9.4 Consensus size: 22
39138 CCTCCCTATA
*
39148 AAATTTTGTTAACC-T--TATG
1 AAATTTTGATAACCTTCATATG
* * *
39167 AAATTTTGATAAGC-ACACTATA
1 AAATTTTGATAACCTTCA-TATG
**
39189 AAATTTCAATAACCTTCATATG
1 AAATTTTGATAACCTTCATATG
* * * *
39211 AAATTTTGTTAACCTCCCTAAG
1 AAATTTTGATAACCTTCATATG
*
39233 AAATTTTGATAACCTT-TTGATG
1 AAATTTTGATAACCTTCAT-ATG
39255 AAATTTTGATAA-CTGT-ACTATG
1 AAATTTTGATAACCT-TCA-TATG
*
39277 AAGTTTTGATAACCTTCATAT-
1 AAATTTTGATAACCTTCATATG
* *
39298 AAATTTTGGTAACCAT-ACTATG
1 AAATTTTGATAACCTTCA-TATG
* *
39320 AAATTTTGATAACTTTCCTAATG
1 AAATTTTGATAACCTTCAT-ATG
*
39343 TAATTTTG
1 AAATTTTG
39351 GTTTGATTGT
Statistics
Matches: 142, Mismatches: 29, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
19 12 0.08
20 1 0.01
21 19 0.13
22 94 0.66
23 16 0.11
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCTTCATATG
Found at i:39317 original size:43 final size:43
Alignment explanation
Indices: 39143--39350 Score: 176
Period size: 44 Copynumber: 4.8 Consensus size: 43
39133 ATCCCCCTCC
* *
39143 CTATAAAATTTTGTTAACC-T--TATGAAATTTTGATAAGCAC-A
1 CTATGAAATTTTGATAACCTTCATATGAAATTTTGATAA-C-CTA
* ** * *
39184 CTATAAAATTTCAATAACCTTCATATGAAATTTTGTTAACCTCC
1 CTATGAAATTTTGATAACCTTCATATGAAATTTTGATAACCT-A
* * *
39228 CTAAGAAATTTTGATAACCTT-TTGATGAAATTTTGATAACTGTA
1 CTATGAAATTTTGATAACCTTCAT-ATGAAATTTTGATAAC-CTA
* *
39272 CTATGAAGTTTTGATAACCTTCATAT-AAATTTTGGTAACCATA
1 CTATGAAATTTTGATAACCTTCATATGAAATTTTGATAACC-TA
* * *
39315 CTATGAAATTTTGATAACTTTCCTAATGTAATTTTG
1 CTATGAAATTTTGATAACCTTCAT-ATGAAATTTTG
39351 GTTTGATTGT
Statistics
Matches: 134, Mismatches: 22, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
41 16 0.12
42 2 0.01
43 37 0.28
44 70 0.52
45 9 0.07
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (43 bp):
CTATGAAATTTTGATAACCTTCATATGAAATTTTGATAACCTA
Found at i:51188 original size:391 final size:391
Alignment explanation
Indices: 50467--51246 Score: 1533
Period size: 391 Copynumber: 2.0 Consensus size: 391
50457 CTCTTTTGTT
50467 TTCTATTTTTATTATTTTATTAAGTTTAGCCCCAAGTTAAAATTTTATTTTTATTTTAAGGGTAA
1 TTCTATTTTTATTATTTTATTAAGTTTAGCCCCAAGTTAAAATTTTATTTTTATTTTAAGGGTAA
*
50532 ATTTCAAAATTAATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAACTAATTTCACTAA
66 ATTTCAAAATTAATAATTTATTGCTATAGGGTTTTAGAAATAAAATACAAAACTAATTTCACTAA
50597 GTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGATAAATTCCATAATTAATAATATTGTT
131 GTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGATAAATTCCATAATTAATAATATTGTT
50662 ATAGGGTTTTAGAAATAAAATATATAATTAATTCACTAAGTGTAGTCCAAAATAAAATTAAAATT
196 ATAGGGTTTTAGAAATAAAATATATAATTAATTCACTAAGTGTAGTCCAAAATAAAATTAAAATT
50727 TTATTTTAAGGGTTAGAAAAATTAAAATTTATAAATGGTGTATTAGAACCAATAAGATGTTAACA
261 TTATTTTAAGGGTTAGAAAAATTAAAATTTATAAATGGTGTATTAGAACCAATAAGATGTTAACA
50792 TGTCGCCTGACGTATGATAGACACATCAGGAGGGAACATTGTGTGTGGCAAAATGGAGAGGCGTT
326 TGTCGCCTGACGTATGATAGACACATCAGGAGGGAACATTGTGTGTGGCAAAATGGAGAGGCGTT
50857 G
391 G
*
50858 TTCTATTTTTATTATTTTATTAAGTTTAGCTCCAAGTTAAAATTTTATTTTTATTTTAAGGGTAA
1 TTCTATTTTTATTATTTTATTAAGTTTAGCCCCAAGTTAAAATTTTATTTTTATTTTAAGGGTAA
50923 ATTTCAAAATTAATAATTTATTGCTATAGGGTTTTAGAAATAAAATACAAAACTAATTTCACTAA
66 ATTTCAAAATTAATAATTTATTGCTATAGGGTTTTAGAAATAAAATACAAAACTAATTTCACTAA
*
50988 GTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATTAATAATATTGTT
131 GTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGATAAATTCCATAATTAATAATATTGTT
51053 ATAGGGTTTTAGAAATAAAATATATAATTAATTCACTAAGTGTAGTCCAAAATAAAATTAAAATT
196 ATAGGGTTTTAGAAATAAAATATATAATTAATTCACTAAGTGTAGTCCAAAATAAAATTAAAATT
51118 TTATTTTAAGGGTTAGAAAAATTAAAATTTATAAATGGTGTATTAGAACCAATAAGATGTTAACA
261 TTATTTTAAGGGTTAGAAAAATTAAAATTTATAAATGGTGTATTAGAACCAATAAGATGTTAACA
51183 TGTCGCCTGACGTATGATAGACACATCAGGAGGGAACATTGTGTGTGGCAAAATGGAGAGGCGT
326 TGTCGCCTGACGTATGATAGACACATCAGGAGGGAACATTGTGTGTGGCAAAATGGAGAGGCGT
51247 GTAGCAAAGT
Statistics
Matches: 386, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
391 386 1.00
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.38
Consensus pattern (391 bp):
TTCTATTTTTATTATTTTATTAAGTTTAGCCCCAAGTTAAAATTTTATTTTTATTTTAAGGGTAA
ATTTCAAAATTAATAATTTATTGCTATAGGGTTTTAGAAATAAAATACAAAACTAATTTCACTAA
GTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGATAAATTCCATAATTAATAATATTGTT
ATAGGGTTTTAGAAATAAAATATATAATTAATTCACTAAGTGTAGTCCAAAATAAAATTAAAATT
TTATTTTAAGGGTTAGAAAAATTAAAATTTATAAATGGTGTATTAGAACCAATAAGATGTTAACA
TGTCGCCTGACGTATGATAGACACATCAGGAGGGAACATTGTGTGTGGCAAAATGGAGAGGCGTT
G
Found at i:52134 original size:6 final size:6
Alignment explanation
Indices: 52117--52147 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
52107 TTGAATAGAG
52117 TTCTTT TT-TTT TTCTTT TTCTTT TTCTTT TT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TT
52148 TGAGGGGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TTCTTT
Done.