Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014576.1 Corchorus olitorius cultivar O-4 contig14609, 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: 151068
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:765 original size:44 final size:45
Alignment explanation
Indices: 715--822 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 45
705 GGAAACGTGC
* * *
715 AGGAGATCAAGGAAAG-TTAGAATCCATGACTGCCAAGTGCTTTA
1 AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTTA
* * ** * *
759 AGGAGATCAAAGAGAGCTTTGGCCCCATGATTGTCAAATGCTTTA
1 AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTTA
*
804 AGGAGATCAAAGAGAGCTT
1 AGGAGATCAAAGAAAGCTT
823 TGGCTCCATG
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 14 0.26
45 40 0.74
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (45 bp):
AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTTA
Found at i:801 original size:45 final size:45
Alignment explanation
Indices: 738--838 Score: 166
Period size: 45 Copynumber: 2.2 Consensus size: 45
728 AAGTTAGAAT
* *
738 CCATGACTGCCAAGTGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
1 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
* *
783 CCATGATTGTCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCT
1 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
828 CCATGATTGCC
1 CCATGATTGCC
839 GAGCGCACAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.26
Consensus pattern (45 bp):
CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
Found at i:957 original size:3 final size:3
Alignment explanation
Indices: 949--975 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
939 AAAGAGAGAG
949 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
976 AGAAAACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:6615 original size:1 final size:1
Alignment explanation
Indices: 6609--6649 Score: 82
Period size: 1 Copynumber: 41.0 Consensus size: 1
6599 TCGCTATCGG
6609 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6650 CCCTACCATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:17189 original size:18 final size:17
Alignment explanation
Indices: 17168--17202 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
17158 TCTAAACCTC
17168 AATAAATATATAAATATA
1 AATAAATATA-AAATATA
17186 AATAAATATAAAATATA
1 AATAAATATAAAATATA
17203 TATAGTTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATAAATATAAAATATA
Found at i:19861 original size:30 final size:30
Alignment explanation
Indices: 19827--19887 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
19817 TTAGTAAGAT
19827 ATTAAAATTTGAGAATATAAGAGGAAAGTC
1 ATTAAAATTTGAGAATATAAGAGGAAAGTC
**
19857 ATTAAAATTTGAGGGTATAAGAGGAAAGTC
1 ATTAAAATTTGAGAATATAAGAGGAAAGTC
19887 A
1 A
19888 AGATAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.23, T:0.26
Consensus pattern (30 bp):
ATTAAAATTTGAGAATATAAGAGGAAAGTC
Found at i:20681 original size:66 final size:66
Alignment explanation
Indices: 20606--20736 Score: 174
Period size: 66 Copynumber: 2.0 Consensus size: 66
20596 TTGGTATCCC
* * * **
20606 ATCCAGTACTAATTCGGATCCGA-TCCGCGTTGTGCATTTGGTTATGATGGGTGAGTCCCCCAAC
1 ATCCAGTACTAATCCGGATCCGACT-CGCGTCGCGCACCTGGTTATGATGGGTGAGTCCCCCAAC
20670 AT
65 AT
* * *
20672 ATCCGGTACTAATCCGGATCCGACTCGCGTCGCGCACCTGGTTATGGTGGGTGAGTCTCCCAACA
1 ATCCAGTACTAATCCGGATCCGACTCGCGTCGCGCACCTGGTTATGATGGGTGAGTCCCCCAACA
20737 GGACAACTGC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 55 0.98
67 1 0.02
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.27
Consensus pattern (66 bp):
ATCCAGTACTAATCCGGATCCGACTCGCGTCGCGCACCTGGTTATGATGGGTGAGTCCCCCAACA
T
Found at i:22316 original size:30 final size:31
Alignment explanation
Indices: 22280--22343 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
22270 TTCTTGCAAC
22280 TTTAATTAGCTTG-TC-AAATTATGTCCTTGA
1 TTTAATT-GCTTGTTCAAAATTATGTCCTTGA
**
22310 TTTAATTTTTTGTTCAAAAATTATGTCCTTGA
1 TTTAATTGCTTGTTC-AAAATTATGTCCTTGA
22342 TT
1 TT
22344 ACCATATCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 3 0.10
30 9 0.31
32 17 0.59
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.52
Consensus pattern (31 bp):
TTTAATTGCTTGTTCAAAATTATGTCCTTGA
Found at i:23842 original size:3 final size:3
Alignment explanation
Indices: 23836--23880 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
23826 TATTATCACC
* * *
23836 GTT GTT GTT GTT GTT GTT ATT GTC GTT GTT GTT ATT GTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
23881 CTTCTTGTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.04, C:0.02, G:0.29, T:0.64
Consensus pattern (3 bp):
GTT
Found at i:23889 original size:15 final size:15
Alignment explanation
Indices: 23840--23880 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
23830 ATCACCGTTG
23840 TTGTTGTTGTTGTTA
1 TTGTTGTTGTTGTTA
*
23855 TTGTCGTTGTTGTTA
1 TTGTTGTTGTTGTTA
23870 TTGTTGTTGTT
1 TTGTTGTTGTT
23881 CTTCTTGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.05, C:0.02, G:0.27, T:0.66
Consensus pattern (15 bp):
TTGTTGTTGTTGTTA
Found at i:30099 original size:162 final size:162
Alignment explanation
Indices: 29812--30237 Score: 550
Period size: 162 Copynumber: 2.6 Consensus size: 162
29802 TAGATTAGAC
* * * *
29812 AATAACTAACTGAATTACCATGAACACACATGTTGGGTTGAGTGGAATGAGCTCAATACCCCTTA
1 AATAACTAACAGAATTACCA--AAAACACATGTTGGGTTTAGTGGAATGAGCTCAATGCCCCTTA
* * * * *
29877 AGCAAGTTCTCGAATTCGAGTCTTGTAAAGGAGAACTTCCCCTATATGGGGTCTGACACGGCTTG
64 AGCAAGGTCTCGAATTCGAGTCTTGTAAAGGAGAGCTTCCCCCATATAGGGTCAGACACGGCTTG
** * *
29942 ACTCTGGACTAGTCAGGGCCCAATGTGATTATCG
129 ACTCCAGACTACTCAGGGCCCAATGTGATTACCG
* * *
29976 AATAACTAACAGAATTACCAAAAACACATGTTGGGTTTAGTGGAATGGGTTCAATGCCCCTTAAA
1 AATAACTAACAGAATTACCAAAAACACATGTTGGGTTTAGTGGAATGAGCTCAATGCCCCTTAAG
* *
30041 CAAGGTCTCGAATTCGAGTCTTGTAAAGGAGAGCTTCCCCCATTTAGGGTCAGACACGGGTTGAC
66 CAAGGTCTCGAATTCGAGTCTTGTAAAGGAGAGCTTCCCCCATATAGGGTCAGACACGGCTTGAC
*
30106 TCCAGACTACTCAGGGCCCAATGTGGTTACCG
131 TCCAGACTACTCAGGGCCCAATGTGATTACCG
* * * * * * *
30138 GAT-ACTAACAAAATTACCACAAACACATGTTGTGTTT-GATGGAGTGAGCTCAATGTCCCTTGA
1 AATAACTAACAGAATTACCAAAAACACATGTTGGGTTTAG-TGGAATGAGCTCAATGCCCCTTAA
* * *
30201 GCAAGGTCTCGAATTTGAGTCTTGTGAAGGAAAGCTT
65 GCAAGGTCTCGAATTCGAGTCTTGTAAAGGAGAGCTT
30238 TCAACTTCCT
Statistics
Matches: 229, Mismatches: 32, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
160 1 0.00
161 83 0.36
162 126 0.55
164 19 0.08
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (162 bp):
AATAACTAACAGAATTACCAAAAACACATGTTGGGTTTAGTGGAATGAGCTCAATGCCCCTTAAG
CAAGGTCTCGAATTCGAGTCTTGTAAAGGAGAGCTTCCCCCATATAGGGTCAGACACGGCTTGAC
TCCAGACTACTCAGGGCCCAATGTGATTACCG
Found at i:31027 original size:29 final size:31
Alignment explanation
Indices: 30965--31032 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 31
30955 GAATCAGGGT
*
30965 AAAATGTCTTGAATTTGGAAGTTCAATGGGC
1 AAAATGTCTTGAATTTGGAAATTCAATGGGC
*
30996 AAAATGTCTT-TATTT-GAAATTC-ATGAGGC
1 AAAATGTCTTGAATTTGGAAATTCAATG-GGC
31025 AAAATGTC
1 AAAATGTC
31033 CATGACAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 3 0.09
29 17 0.50
30 4 0.12
31 10 0.29
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.34
Consensus pattern (31 bp):
AAAATGTCTTGAATTTGGAAATTCAATGGGC
Found at i:41516 original size:13 final size:13
Alignment explanation
Indices: 41498--41536 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
41488 TCACTGCCTG
*
41498 CCTCTGCCTCTGC
1 CCTCTGACTCTGC
*
41511 CCTCTGTCTCTGC
1 CCTCTGACTCTGC
41524 CCTCTGACTCTGC
1 CCTCTGACTCTGC
41537 TTCCTATTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.03, C:0.49, G:0.15, T:0.33
Consensus pattern (13 bp):
CCTCTGACTCTGC
Found at i:63939 original size:22 final size:22
Alignment explanation
Indices: 63914--63965 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
63904 TATCTTAGAT
63914 ATAAT-ATATATTATTAAATAAA
1 ATAATAATATATT-TTAAATAAA
*
63936 ATAATAAATATATTTTAAATAAT
1 ATAAT-AATATATTTTAAATAAA
63959 A-AATAAT
1 ATAATAAT
63966 GAGTTCAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 3 0.11
22 8 0.30
23 9 0.33
24 7 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAATAATATATTTTAAATAAA
Found at i:64278 original size:30 final size:30
Alignment explanation
Indices: 64242--64303 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
64232 ATTTTTATCT
*
64242 TGACTTTCCTCTTATATCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
*
64272 TGACTTTTCTCTTATACCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
64302 TG
1 TG
64304 GCTTATTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.23, G:0.05, T:0.47
Consensus pattern (30 bp):
TGACTTTCCTCTTATACCCTCAAATTTTAA
Found at i:65590 original size:30 final size:29
Alignment explanation
Indices: 65555--65631 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
65545 ATGTGAAAAT
*
65555 GGCTTATTTGGTCTTTTTTAAGAGTTTATG
1 GGCTTATTTGGTCTTTTTT-AGAGTTCATG
**
65585 GGCTTATTTGG-CTGTAATTAGAGTTCATG
1 GGCTTATTTGGTCT-TTTTTAGAGTTCATG
*
65614 GGCTTATTTGGTCATTTT
1 GGCTTATTTGGTCTTTTT
65632 ATGTAAGTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 24 0.62
30 15 0.38
ACGTcount: A:0.17, C:0.09, G:0.25, T:0.49
Consensus pattern (29 bp):
GGCTTATTTGGTCTTTTTTAGAGTTCATG
Found at i:69610 original size:18 final size:18
Alignment explanation
Indices: 69584--69618 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
69574 AGACATGTGT
*
69584 CTTTTATAATCATATCTA
1 CTTTAATAATCATATCTA
69602 CTTTAATAATCATATCT
1 CTTTAATAATCATATCT
69619 CTTAAGTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (18 bp):
CTTTAATAATCATATCTA
Found at i:72069 original size:9 final size:9
Alignment explanation
Indices: 72055--72079 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
72045 GGAGTGGAAA
72055 AAAAAAACC
1 AAAAAAACC
72064 AAAAAAACC
1 AAAAAAACC
72073 AAAAAAA
1 AAAAAAA
72080 TCATTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAACC
Found at i:79269 original size:19 final size:19
Alignment explanation
Indices: 79245--79303 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 19
79235 CTGTTTAGTA
79245 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
79264 ACTGTACAGATTG-GATTAGAT
1 ACTGTACAGA-TGAGATT--AT
*
79285 ACTGTAAAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
79304 TAGAGCAACG
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 16 0.46
20 4 0.11
21 15 0.43
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.32
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAT
Found at i:79378 original size:19 final size:19
Alignment explanation
Indices: 79350--79386 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
79340 TGTGGACCCA
*
79350 AAACGATGATGAAACAGTC
1 AAACGATGATAAAACAGTC
*
79369 AAACGGTGATAAAACAGT
1 AAACGATGATAAAACAGT
79387 TACAGATAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.14, G:0.22, T:0.16
Consensus pattern (19 bp):
AAACGATGATAAAACAGTC
Found at i:88350 original size:17 final size:16
Alignment explanation
Indices: 88296--88346 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
88286 GATCACTCCC
*
88296 AGATCACTAGTGATCTA
1 AGATCACCAGTGATC-A
88313 AGATCACCAGTGATGCA
1 AGATCACCAGTGAT-CA
*
88330 AGATCACCGGTGATCA
1 AGATCACCAGTGATCA
88346 A
1 A
88347 AGATTACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Found at i:92457 original size:16 final size:17
Alignment explanation
Indices: 92412--92464 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
92402 CGTTTGATAT
*
92412 CGTTTTCGTTTTT-TTG
1 CGTTTTTGTTTTTGTTG
** *
92428 TTTTTTTGTTTTTGTTT
1 CGTTTTTGTTTTTGTTG
92445 CGTTTTTG-TTTTGTTG
1 CGTTTTTGTTTTTGTTG
92461 CGTT
1 CGTT
92465 GTCAATTTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
16 21 0.72
17 8 0.28
ACGTcount: A:0.00, C:0.08, G:0.19, T:0.74
Consensus pattern (17 bp):
CGTTTTTGTTTTTGTTG
Found at i:96239 original size:18 final size:18
Alignment explanation
Indices: 96216--96252 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
96206 TTCCCGCCAA
96216 AACAACAGCAGCAACAAC
1 AACAACAGCAGCAACAAC
**
96234 AACAACAGCCTCAACAAC
1 AACAACAGCAGCAACAAC
96252 A
1 A
96253 CCAAACTCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.35, G:0.08, T:0.03
Consensus pattern (18 bp):
AACAACAGCAGCAACAAC
Found at i:113253 original size:31 final size:31
Alignment explanation
Indices: 113218--113304 Score: 111
Period size: 31 Copynumber: 2.8 Consensus size: 31
113208 GTTTTGTTTC
* * *
113218 ATGAATTTCCAAACTCAAGACAATTTATTCT
1 ATGAACTTCCAAATTCAAGACAATTTATCCT
* * *
113249 ATGAACTTACAAATTCAAGACATTTTGTCCT
1 ATGAACTTCCAAATTCAAGACAATTTATCCT
*
113280 ATGAACTTCCAAATTCAAAACAATT
1 ATGAACTTCCAAATTCAAGACAATT
113305 AGCATTCTGA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (31 bp):
ATGAACTTCCAAATTCAAGACAATTTATCCT
Found at i:116039 original size:246 final size:246
Alignment explanation
Indices: 115598--116057 Score: 715
Period size: 246 Copynumber: 1.9 Consensus size: 246
115588 TGATGGGCGT
* * * * *
115598 CTAATTTGGGGTCTAATCGTGTCTGACTCTATATGGTGGTAACTTTGTCAATGTATGATTCCACA
1 CTAATTCGGGGTCTAATCGTGTCAGACCCTATATGGTGGCAACTTTATCAATGTATGATTCCACA
* * *
115663 ATTCACAGTACTTGAATCTGAGACCTGACTTAAGAGACATTGAGTTCCTTCCACTCAACCCAACA
66 ATTCACAGTACTTGAATCTGAGACCTAACTTAAAAGACATTGAGCTCCTTCCACTCAACCCAACA
* * * * *
115728 ATTGTTGATATTATTAATCTTTCAATTAACACAAAACAAAAAGAATGGCAGGTATATACATATAG
131 AGTGTTGATATTAATAACCTTTCAATTAACACAAAACAAAAAGAATGGCAGATATAGACATATAG
115793 TAGACCTCATCTATGTTATGGTATCCATCCAGTAATCACACTGAACATTGA
196 TAGACCTCATCTATGTTATGGTATCCATCCAGTAATCACACTGAACATTGA
**
115844 CTAATTCGGGGTCTAATCGTGTCAGACCCTATATGGTGGCAACTTTATCAATGTATGATTCCGTA
1 CTAATTCGGGGTCTAATCGTGTCAGACCCTATATGGTGGCAACTTTATCAATGTATGATTCCACA
* * *
115909 ATTCATAGTACTTGAA-CTCGAGACCTAATTTAAAAGACGTTGAGCTCCTTCCACTCAACCCAAC
66 ATTCACAGTACTTGAATCT-GAGACCTAACTTAAAAGACATTGAGCTCCTTCCACTCAACCCAAC
* *
115973 AAGTGTTGATATTAATAACCTTTCCATTAACACAAAACAAACAGAATGGCAGATATAGACATATA
130 AAGTGTTGATATTAATAACCTTTCAATTAACACAAAACAAAAAGAATGGCAGATATAGACATATA
*
116038 GTGGACCTCATCTATGTTAT
195 GTAGACCTCATCTATGTTAT
116058 TATGGTAATT
Statistics
Matches: 192, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
245 2 0.01
246 190 0.99
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (246 bp):
CTAATTCGGGGTCTAATCGTGTCAGACCCTATATGGTGGCAACTTTATCAATGTATGATTCCACA
ATTCACAGTACTTGAATCTGAGACCTAACTTAAAAGACATTGAGCTCCTTCCACTCAACCCAACA
AGTGTTGATATTAATAACCTTTCAATTAACACAAAACAAAAAGAATGGCAGATATAGACATATAG
TAGACCTCATCTATGTTATGGTATCCATCCAGTAATCACACTGAACATTGA
Found at i:119425 original size:19 final size:20
Alignment explanation
Indices: 119375--119432 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
119365 GCTGCTCTAA
* *
119375 TAATCTCATTTGTATAGTACC
1 TAATCTCATCTGTACAGTA-C
* *
119396 TAATATAATCTGTACAGT-C
1 TAATCTCATCTGTACAGTAC
119415 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
119433 TGCTAAACCG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 17 0.55
21 14 0.45
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTAC
Found at i:150083 original size:333 final size:333
Alignment explanation
Indices: 149006--150713 Score: 2355
Period size: 336 Copynumber: 5.1 Consensus size: 333
148996 GTGCATAAGT
* * * * *
149006 TTTTTAATGATTTTTGGCCCCGAGAATCCTTGAGACATCTATAGTCATCTAACCAAATCTCAG-C
1 TTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCC
* * **
149070 AAAGTTGGATTTAAGGATTTGGTTTTATGAACATCAGAATCATGTTTCGATTTAATT-AGAAATT
66 AAA-TTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGTTTCGATTT-ATTCAGAAATT
* * *
149134 AATTCGGAAACATATTGAAAAATCGATATTAGAAGCTTGAAAAATCCTTCAATCTTTTTGCCATT
129 AATTCGGAAACATATAGGAAAATCGATATTAGAAGCTTGAAAAACCCTTCAATCTTTTTGCCATT
* *
149199 GAATTATACATATTC----AGTGTTTTGGCCAAAGATAGTGGAAAATATCTTTCGGGTCAATTTT
194 GAATTATACATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAA-AACTTTCGGGTCAATTTT
* * * *
149260 TCCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTTTTTTCGCTACAAACGCG-T
258 TGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAG------TTTTTGGCTAAAAACGCGTT
*
149324 TCTGGGGTCCCGGCTCAG
317 TC-GGGGCCCCGGCTCAG
*
149342 ATTTT-AATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCCCAGC
1 -TTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGC
*
149406 CAAATTGGATTTAAGGATTTGATTTTACGGGCATCAAAATCATGTTTCGATTTATTCAGAAATTA
65 CAAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGTTTCGATTTATTCAGAAATTA
* * * * * * * *
149471 ATTC-GAAAGGATATAGGAAAATCAATATTCGAAGCGTGAAAAGCCGTTCAAACTTTTTG-GAGT
130 ATTCGGAAA-CATATAGGAAAATCGATATTAGAAGCTTGAAAAACCCTTCAATCTTTTTGCCA-T
* * *
149534 TCAATTATATATATATATTCTATAAGTGTTTTGGCCAAAGATAGTGG-AAAAACTTTCGGGTCAA
193 T-GA--AT-TATACATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAAAACTTTCGGGTCAA
* * * * * *
149598 TTTTTGCAAAATTTTAGCTGAAATGGTGTAATTACCATCACAGTTTTTGGCTACAAACACG-TTC
254 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTTC
*
149662 TGGGGCCCCAGCTCAG
319 -GGGGCCCCGGCTCAG
*
149678 TTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCACAGCC
1 TTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCC
* *
149743 AAATTGGATTTAAGGATTTGATTTTACAGGCATCAGAATCATGTTTCTATTTATTCAGAAATTAA
66 AAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGTTTCGATTTATTCAGAAATTAA
* * * * * * *
149808 TTCGGAAAGATATAGGAAAATCGATACTCGAAGCGTGAAAAACCCTTCAAACTTTTTGGCGTTGA
131 TTCGGAAACATATAGGAAAATCGATATTAGAAGCTTGAAAAACCCTTCAATCTTTTTGCCATTGA
* * *
149873 ATTATATATATTCTATAAGTGCTTTGGCCAAAGATTGTGGAAAAAACTTTCCGGTCAATTTTTGC
196 ATTATACATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAAAACTTTCGGGTCAATTTTTGC
* * *
149938 AAAATTTTAGCTGAAAATGGTGTACTAA-CATCACAGTTTTTGACTAAAAACGCGTTTCGGGGCC
261 AAAATTTTAGCCG-AAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGCC
*
150002 CCGGCTTAG
325 CCGGCTCAG
150011 TTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCC
1 TTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCC
* *
150076 GAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGTTTCTATTTATTCAGAAATTAA
66 AAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGTTTCGATTTATTCAGAAATTAA
* * *
150141 TTCGGAAACATATTGGACAATCGATATTAGAAGCTTGAAAAACCATTCAATCTTTTTGCCATTGA
131 TTCGGAAACATATAGGAAAATCGATATTAGAAGCTTGAAAAACCCTTCAATCTTTTTGCCATTGA
* *
150206 ATTATACATATTCTATAAGTGTTTTGGCAAAAGATTGTGGAAAAAACTTTCGGGTAAATTTTTGC
196 ATTATACATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAAAACTTTCGGGTCAATTTTTGC
* *
150271 AAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTTTTGGCTAAAAACGCGTTCCGGGG
261 AAAATTTTAGCCGAAATCGTGTACTAACCATCACAG---TTTTTGGCTAAAAACGCGTTTCGGGG
150336 CCCCGGCTCAG
323 CCCCGGCTCAG
* * *
150347 TGTTCAAAGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAATCAAATCTCAGCC
1 TTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCC
* * * * *
150412 AAATTGAATTTAAGGATCTGATTTTACGAGCATCAAAATCATGTTTCGATTTAATCAGAAATTAA
66 AAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGTTTCGATTTATTCAGAAATTAA
150477 TTCGGAAACATATAGGAAAATCGATATTAGAAGCTTGAAAAACCCTTCAATCTTTTTGCCATTGA
131 TTCGGAAACATATAGGAAAATCGATATTAGAAGCTTGAAAAACCCTTCAATCTTTTTGCCATTGA
* * *
150542 ATTATACATATTCTATAAGTGTTTTGGCCAAACATTGT-GAAAAATATATTTCGGGTCATTTTTT
196 ATTATACATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAAA-A-CTTTCGGGTCAATTTTT
* * * * *
150606 ACAAAATTTTAGCCGAAATCGTTTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGTC
259 GCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGC
*
150671 CCCAGCTCAG
324 CCCGGCTCAG
*
150681 TTTTTAATGATTTTTGGCCCCGAGACTCCTTGA
1 TTTTCAATGATTTTTGGCCCCGAGACTCCTTGA
150714 TATAAGCGTG
Statistics
Matches: 1241, Mismatches: 106, Indels: 51
0.89 0.08 0.04
Matches are distributed among these distances:
332 48 0.04
333 336 0.27
334 80 0.06
335 19 0.02
336 609 0.49
337 61 0.05
339 2 0.00
340 10 0.01
342 50 0.04
343 3 0.00
344 23 0.02
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (333 bp):
TTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCC
AAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGTTTCGATTTATTCAGAAATTAA
TTCGGAAACATATAGGAAAATCGATATTAGAAGCTTGAAAAACCCTTCAATCTTTTTGCCATTGA
ATTATACATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAAAACTTTCGGGTCAATTTTTGC
AAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGCCC
CGGCTCAG
Found at i:150316 original size:669 final size:666
Alignment explanation
Indices: 149006--150713 Score: 2411
Period size: 669 Copynumber: 2.5 Consensus size: 666
148996 GTGCATAAGT
* * * * *
149006 TTTTTAATGATTTTTGGCCCCGAGAATCCTTGAGACATCTATAGTCATCTAACCAAATCTCAG-C
1 TTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCC
* * *
149070 AAAGTTGGATTTAAGGATTTGGTTTTATGAACATCAGAATCATGTTTCGATTTAATT-AGAAATT
66 AAA-TTGGATTTAAGGATTTGATTTTACGAGCATCAGAATCATGTTTCGATTT-ATTCAGAAATT
* * *
149134 AATTCGGAAACATATTGAAAAATCGATATTAGAAGCTTGAAAAATCCTTCAATCTTTTTGCCATT
129 AATTCGGAAACATATAGGAAAATCGATATTAGAAGCTTGAAAAACCCTTCAATCTTTTTGCCATT
* *
149199 GAATTATACATATTC----AGTGTTTTGGCCAAAGATAGTGGAAAATATCTTTCGGGTCAATTTT
194 GAATTATACATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAA-AACTTTCGGGTCAATTTT
* *
149260 TCCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTTTTTTCGCTACAAACGCG-T
258 TACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG------TTTTT-GCTAAAAACGCGTT
*
149324 TCTGGGGTCCCGGCTCAGATTTTAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCA
316 TC-GGGGCCCCGGCTCAG-TTTTAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCA
149389 TCTAACCAAATCCCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAAAATCATGTTTC
379 TCTAACCAAATCCCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAAAATCATGTTTC
* * * *
149454 GATTTATTCAGAAATTAATTCGAAAGGATATAGGAAAATCAATATTCGAAGCGTGAAAAGCCGTT
444 GATTTATTCAGAAATTAATTCGAAAGCATATAGGAAAATCAATATTAGAAGCGTGAAAAACCATT
* * *
149519 CAAACTTTTTGGAGTTCAATTATATATATATATTCTATAAGTGTTTTGGCCAAAGATAGTGGAAA
509 CAAACTTTTTGCAGTTCAA-TATATATACATATTCTATAAGTGTTTTGGCAAAAGATAGTGGAAA
* * * *
149584 AACTTTCGGGTCAATTTTTGCAAAATTTTAGCTGAAATGGTGTAATTACCATCACAGTTTTTGGC
573 AACTTTCGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGC
* *
149649 TACAAACACGTTCTGGGGCCCCAGCTCAG
638 TAAAAACACGTTCCGGGGCCCCAGCTCAG
*
149678 TTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCACAGCC
1 TTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCC
*
149743 AAATTGGATTTAAGGATTTGATTTTAC-AGGCATCAGAATCATGTTTCTATTTATTCAGAAATTA
66 AAATTGGATTTAAGGATTTGATTTTACGA-GCATCAGAATCATGTTTCGATTTATTCAGAAATTA
* * * * * * *
149807 ATTCGGAAAGATATAGGAAAATCGATACTCGAAGCGTGAAAAACCCTTCAAACTTTTTGGCGTTG
130 ATTCGGAAACATATAGGAAAATCGATATTAGAAGCTTGAAAAACCCTTCAATCTTTTTGCCATTG
* * * *
149872 AATTATATATATTCTATAAGTGCTTTGGCCAAAGATTGTGGAAAAAACTTTCCGGTCAATTTTTG
195 AATTATACATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAAAACTTTCGGGTCAATTTTTA
* * *
149937 CAAAATTTTAGCTGAAAATGGTGTACTAA-CATCACAGTTTTTGACTAAAAACGCGTTTCGGGGC
260 CAAAATTTTAGCCG-AAATCGTGTACTAACCATCACGGTTTTTG-CTAAAAACGCGTTTCGGGGC
*
150001 CCCGGCTTAGTTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCA
323 CCCGGCTCAGTTTT-AATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCA
* * * *
150066 AATCTCAGCCGAATTGGATTTAAGGATTTGATTTTACGGGCATCAGAATCATGTTTCTATTTATT
387 AATCCCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAAAATCATGTTTCGATTTATT
* * * * *
150131 CAGAAATTAATTCGGAAA-CATATTGGACAATCGATATTAGAAGCTTGAAAAACCATTCAATCTT
452 CAGAAATTAATTC-GAAAGCATATAGGAAAATCAATATTAGAAGCGTGAAAAACCATTCAAACTT
* *
150195 TTTGCCA-TT-GA-AT-TATACATATTCTATAAGTGTTTTGGCAAAAGATTGTGGAAAAAACTTT
516 TTTG-CAGTTCAATATATATACATATTCTATAAGTGTTTTGGCAAAAGATAGTGG-AAAAACTTT
150256 CGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTTTTGGCTAA
579 CGGGTAAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAG---TTTTTGGCTAA
* *
150321 AAACGCGTTCCGGGGCCCCGGCTCAG
641 AAACACGTTCCGGGGCCCCAGCTCAG
* * *
150347 TGTTCAAAGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAATCAAATCTCAGCC
1 TTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCC
* * * *
150412 AAATTGAATTTAAGGATCTGATTTTACGAGCATCAAAATCATGTTTCGATTTAATCAGAAATTAA
66 AAATTGGATTTAAGGATTTGATTTTACGAGCATCAGAATCATGTTTCGATTTATTCAGAAATTAA
150477 TTCGGAAACATATAGGAAAATCGATATTAGAAGCTTGAAAAACCCTTCAATCTTTTTGCCATTGA
131 TTCGGAAACATATAGGAAAATCGATATTAGAAGCTTGAAAAACCCTTCAATCTTTTTGCCATTGA
* * *
150542 ATTATACATATTCTATAAGTGTTTTGGCCAAACATTGT-GAAAAATATATTTCGGGTCATTTTTT
196 ATTATACATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAAA-A-CTTTCGGGTCAATTTTT
* * *
150606 ACAAAATTTTAGCCGAAATCGTTTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGTC
259 ACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTT-GCTAAAAACGCGTTTCGGGGC
*
150671 CCCAGCTCAGTTTTTAATGATTTTTGGCCCCGAGACTCCTTGA
323 CCCGGCTCAG-TTTTAATGATTTTTGGCCCCGAGACTCCTTGA
150714 TATAAGCGTG
Statistics
Matches: 924, Mismatches: 89, Indels: 48
0.87 0.08 0.05
Matches are distributed among these distances:
665 35 0.04
666 58 0.06
668 12 0.01
669 453 0.49
670 102 0.11
671 9 0.01
672 176 0.19
673 4 0.00
675 37 0.04
676 38 0.04
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (666 bp):
TTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAGCC
AAATTGGATTTAAGGATTTGATTTTACGAGCATCAGAATCATGTTTCGATTTATTCAGAAATTAA
TTCGGAAACATATAGGAAAATCGATATTAGAAGCTTGAAAAACCCTTCAATCTTTTTGCCATTGA
ATTATACATATTCTATAAGTGTTTTGGCCAAAGATTGTGGAAAAAACTTTCGGGTCAATTTTTAC
AAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGCTAAAAACGCGTTTCGGGGCCCC
GGCTCAGTTTTAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACCAAATC
CCAGCCAAATTGGATTTAAGGATTTGATTTTACGGGCATCAAAATCATGTTTCGATTTATTCAGA
AATTAATTCGAAAGCATATAGGAAAATCAATATTAGAAGCGTGAAAAACCATTCAAACTTTTTGC
AGTTCAATATATATACATATTCTATAAGTGTTTTGGCAAAAGATAGTGGAAAAACTTTCGGGTAA
ATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAAACACGTTC
CGGGGCCCCAGCTCAG
Done.