Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013405.1 Corchorus olitorius cultivar O-4 contig13438, 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: 133168
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:11 original size:2 final size:2
Alignment explanation
Indices: 5--54 Score: 91
Period size: 2 Copynumber: 24.5 Consensus size: 2
1 TCTG
5 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
47 CT CAT CT C
1 CT C-T CT C
55 ATTAGGTGCT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 45 0.96
3 2 0.04
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:181 original size:12 final size:12
Alignment explanation
Indices: 164--207 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
154 TTAGTTCCTT
164 AAATTTTATACA
1 AAATTTTATACA
* *
176 AAATTTTATTTGCT
1 AAATTTTA--TACA
190 AAATTTTATACA
1 AAATTTTATACA
202 AAATTT
1 AAATTT
208 ACTTTACCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 16 0.62
14 10 0.38
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (12 bp):
AAATTTTATACA
Found at i:219 original size:26 final size:26
Alignment explanation
Indices: 164--220 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
154 TTAGTTCCTT
* *
164 AAATTTTATACAAAATTTTATTTGCT
1 AAATTTTATACAAAATTTTATTTACC
190 AAATTTTATACAAAA-TTTACTTTACC
1 AAATTTTATACAAAATTTTA-TTTACC
216 AAATT
1 AAATT
221 GTCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.46
Consensus pattern (26 bp):
AAATTTTATACAAAATTTTATTTACC
Found at i:12133 original size:91 final size:91
Alignment explanation
Indices: 11937--12122 Score: 363
Period size: 91 Copynumber: 2.0 Consensus size: 91
11927 TCTTCTCTTC
11937 TCTTTCCTTCCAAGACCTCTGATATTCCAAGTCAATATCTTCATAAATAACGAGAAACAAGCCGC
1 TCTTTCCTTCCAAGACCTCTGATATTCCAAGTCAATATCTTCATAAATAACGAGAAACAAGCCGC
12002 ATCAGGACAATCGAGATTGTACTCAA
66 ATCAGGACAATCGAGATTGTACTCAA
12028 TCTTTCCTTCCAAGACCTCTGATATTCCAAGTCAATATCTTCATAAATAACGAGAAACAAGCCGC
1 TCTTTCCTTCCAAGACCTCTGATATTCCAAGTCAATATCTTCATAAATAACGAGAAACAAGCCGC
*
12093 ATCAGGACAATTGAGATTGTACTCAA
66 ATCAGGACAATCGAGATTGTACTCAA
12119 TCTT
1 TCTT
12123 CCTCTTCAAG
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 94 1.00
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (91 bp):
TCTTTCCTTCCAAGACCTCTGATATTCCAAGTCAATATCTTCATAAATAACGAGAAACAAGCCGC
ATCAGGACAATCGAGATTGTACTCAA
Found at i:13466 original size:18 final size:17
Alignment explanation
Indices: 13445--13490 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
13435 ATTGGATGGG
13445 TGATGAATGATGGAGGAA
1 TGATGAATGATGGAGG-A
*
13463 TGATGAATGAT-GATGA
1 TGATGAATGATGGAGGA
13479 TGATG-ATGATGG
1 TGATGAATGATGG
13491 CATGATGACG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 5 0.19
16 7 0.27
17 3 0.12
18 11 0.42
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.28
Consensus pattern (17 bp):
TGATGAATGATGGAGGA
Found at i:15535 original size:2 final size:2
Alignment explanation
Indices: 15528--15558 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15518 CCGCCCTGAC
15528 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
15559 TTAACGTGAG
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:18030 original size:3 final size:3
Alignment explanation
Indices: 18024--18061 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
18014 TCACGGTGGT
18024 GGC GGC GGC GGC GGC GGC GGC GGC GGC GGC GGC GGC GG
1 GGC GGC GGC GGC GGC GGC GGC GGC GGC GGC GGC GGC GG
18062 GGTTTATGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.68, T:0.00
Consensus pattern (3 bp):
GGC
Found at i:18841 original size:3 final size:3
Alignment explanation
Indices: 18833--18867 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
18823 AAGGCAACAA
18833 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
18868 AGATTAGCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:24727 original size:2 final size:2
Alignment explanation
Indices: 24720--24750 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
24710 TCCCATATTG
24720 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24751 GGCATAGATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25261 original size:21 final size:21
Alignment explanation
Indices: 25220--25263 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
25210 GCATGCGTTA
*
25220 TCGCTTCCTTTCGTCACGCTT
1 TCGCTTCCTTTCATCACGCTT
*
25241 TCGCTT-CTTTCATCTCAGCTT
1 TCGCTTCCTTTCATCAC-GCTT
25262 TC
1 TC
25264 ATACAGCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.07, C:0.36, G:0.11, T:0.45
Consensus pattern (21 bp):
TCGCTTCCTTTCATCACGCTT
Found at i:26559 original size:2 final size:2
Alignment explanation
Indices: 26552--26579 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
26542 TTCAATATCA
26552 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
26580 TGAAATTCAA
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:39257 original size:28 final size:28
Alignment explanation
Indices: 39193--39284 Score: 107
Period size: 27 Copynumber: 3.4 Consensus size: 28
39183 GTACTTGGAG
* **
39193 TGACCAAAATGCCCCCGGATGTGC-AAA
1 TGACCAAAATGCCCCTGGACATGCAAAA
39220 TGACCAAAATGCCCCTGGACATGCAAAA
1 TGACCAAAATGCCCCTGGACATGCAAAA
* * *
39248 TGGCCGAAATGCCCCTGGACATTC-AAA
1 TGACCAAAATGCCCCTGGACATGCAAAA
*
39275 TGACTAAAAT
1 TGACCAAAAT
39285 AAGAAGTAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
27 31 0.56
28 24 0.44
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (28 bp):
TGACCAAAATGCCCCTGGACATGCAAAA
Found at i:53320 original size:29 final size:29
Alignment explanation
Indices: 53287--53344 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
53277 GTAGTCATTG
53287 GTCCTTTTTAATGTTTAAGTTGGTCCCAT
1 GTCCTTTTTAATGTTTAAGTTGGTCCCAT
53316 GTCCTTTTTAATGTTTAAGTTGGTCCCAT
1 GTCCTTTTTAATGTTTAAGTTGGTCCCAT
53345 ATTTGCTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.48
Consensus pattern (29 bp):
GTCCTTTTTAATGTTTAAGTTGGTCCCAT
Found at i:55710 original size:41 final size:41
Alignment explanation
Indices: 55622--55716 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 41
55612 TGTTTCCGTG
* * *
55622 TTCAATATGGTCCCTAATTTAGGATTCTATTTAATATTCGA
1 TTCAATTTGGTCCCTAATTTAGGATTCTAGTCAATATTCGA
* * * * *
55663 TACAATTTAGTCCCTGATTTAGGATTCTAGTCACTATTTGA
1 TTCAATTTGGTCCCTAATTTAGGATTCTAGTCAATATTCGA
55704 TTCAATTTGGTCC
1 TTCAATTTGGTCC
55717 ATATTTTTCT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (41 bp):
TTCAATTTGGTCCCTAATTTAGGATTCTAGTCAATATTCGA
Found at i:56396 original size:18 final size:18
Alignment explanation
Indices: 56356--56396 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
56346 GTTAAAATTG
* *
56356 GAAAAATGGTAAAAATGA
1 GAAAAATGGAAAAAATCA
*
56374 AAAAAATGGAAAAAATCA
1 GAAAAATGGAAAAAATCA
56392 GAAAA
1 GAAAA
56397 TTAAAAGATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.02, G:0.17, T:0.12
Consensus pattern (18 bp):
GAAAAATGGAAAAAATCA
Found at i:59193 original size:349 final size:349
Alignment explanation
Indices: 58554--59252 Score: 1326
Period size: 349 Copynumber: 2.0 Consensus size: 349
58544 CTCTACAGGA
*
58554 TTGAAGAAATCCTAAGTATGTTCAAACTAGAACAATAAAGCTAAATTCTCAAAAGAACTCTCTTT
1 TTGAAGAAATCCTAAGTATGTTCAAACTAGAACAATAAAGATAAATTCTCAAAAGAACTCTCTTT
*
58619 GATTGGAAAACTTAACTTGTGTTTACAAGAGAGATATGAAACCCTTATATAGTAGTAAGGGAGGT
66 GATTGGAAAACTTAACTTGTGTTTACAAGAGAGATATGAAACCCTTATATAGTAGTAAGGGACGT
*
58684 CCTAACCGTAATCCTAAAAGCATATGGGCGGCTATAAAGGCTTACAAGCCAAAAATAAAGACAAG
131 CCTAACCGTAATCCTAAAAGCATATGGGCGGCTATAAAGCCTTACAAGCCAAAAATAAAGACAAG
58749 GAAAACTAGTCCAAGTCCAACTAGGAAAAATAAATAACAAAGCATAATTAAACAAGGATTGGACT
196 GAAAACTAGTCCAAGTCCAACTAGGAAAAATAAATAACAAAGCATAATTAAACAAGGATTGGACT
*
58814 TAGTCAAACAAGGCCCAATCCTAATGTCATCAAAACATAAAAATAAGCTAATCTAAGATAGAATA
261 TAGTCAAACAAGGCCCAAACCTAATGTCATCAAAACATAAAAATAAGCTAATCTAAGATAGAATA
58879 AAGCCTCATAAGGCCAATTAGACT
326 AAGCCTCATAAGGCCAATTAGACT
*
58903 TTGAAGAAATTCTAAGTATGTTCAAACTAGAACAATAAAGATAAATTCTCAAAAGAACTCTCTTT
1 TTGAAGAAATCCTAAGTATGTTCAAACTAGAACAATAAAGATAAATTCTCAAAAGAACTCTCTTT
*
58968 GATTGGAAAACTTAACTTGTGTTTACAAGAGAGATATGGAACCCTTATATAGTAGTAAGGGACGT
66 GATTGGAAAACTTAACTTGTGTTTACAAGAGAGATATGAAACCCTTATATAGTAGTAAGGGACGT
*
59033 CCTAACCGTAATCCTAAAAGCATATGGGTGGCTATAAAGCCTTACAAGCCAAAAATAAAGACAAG
131 CCTAACCGTAATCCTAAAAGCATATGGGCGGCTATAAAGCCTTACAAGCCAAAAATAAAGACAAG
59098 GAAAACTAGTCCAAGTCCAACTAGGAAAAATAAATAACAAAGCATAATTAAACAAGGATTGGACT
196 GAAAACTAGTCCAAGTCCAACTAGGAAAAATAAATAACAAAGCATAATTAAACAAGGATTGGACT
*
59163 TAGTCAAACAAGGCCCAAACCTAATGTCATCAAAACATAAAAATAAGCTAATCTAAGATAGGATA
261 TAGTCAAACAAGGCCCAAACCTAATGTCATCAAAACATAAAAATAAGCTAATCTAAGATAGAATA
59228 AAGCCTCATAAGGCCAATTAGACT
326 AAGCCTCATAAGGCCAATTAGACT
59252 T
1 T
59253 AAACAAGACC
Statistics
Matches: 342, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
349 342 1.00
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.23
Consensus pattern (349 bp):
TTGAAGAAATCCTAAGTATGTTCAAACTAGAACAATAAAGATAAATTCTCAAAAGAACTCTCTTT
GATTGGAAAACTTAACTTGTGTTTACAAGAGAGATATGAAACCCTTATATAGTAGTAAGGGACGT
CCTAACCGTAATCCTAAAAGCATATGGGCGGCTATAAAGCCTTACAAGCCAAAAATAAAGACAAG
GAAAACTAGTCCAAGTCCAACTAGGAAAAATAAATAACAAAGCATAATTAAACAAGGATTGGACT
TAGTCAAACAAGGCCCAAACCTAATGTCATCAAAACATAAAAATAAGCTAATCTAAGATAGAATA
AAGCCTCATAAGGCCAATTAGACT
Found at i:62128 original size:2 final size:2
Alignment explanation
Indices: 62121--62174 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
62111 CACAACAAAT
62121 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
62163 AC AC AC AC AC AC
1 AC AC AC AC AC AC
62175 TTGTTTACCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:67603 original size:13 final size:13
Alignment explanation
Indices: 67587--67612 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
67577 TTCTAATTTC
67587 TAATTCTTTTTTG
1 TAATTCTTTTTTG
67600 TAATTCTTTTTTG
1 TAATTCTTTTTTG
67613 GTGTTTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (13 bp):
TAATTCTTTTTTG
Found at i:75936 original size:40 final size:40
Alignment explanation
Indices: 75861--76561 Score: 317
Period size: 40 Copynumber: 16.4 Consensus size: 40
75851 CTTCCTAACT
* ** * *
75861 GGAAGGTGTTGTCTACTTTACCCAATTTGTCCTTCCCCAAC
1 GGAAGGTGTTGTTTAAATT-CCCAATTTGCCCTTCCCCATC
75902 GGAAGGTGTTGTTTAAATTCCCAATTTGCCCTTCCCCATC
1 GGAAGGTGTTGTTTAAATTCCCAATTTGCCCTTCCCCATC
* *
75942 AGAAGGTGTTGTTTAAATTCCCAATTTGCCCTTCCTCATC
1 GGAAGGTGTTGTTTAAATTCCCAATTTGCCCTTCCCCATC
* * * *
75982 GGAAGGTGTTGTTTAAGTCTGCTTTACCCAATTTGTCATTCCTCATC
1 GGAAGGTGTTGTTTAA------ATT-CCCAATTTGCCCTTCCCCATC
* * * * *
76029 GAAAGGTGTTGTTTAAGTCTGCTTTACCCAATTTTCTCTTCCTCATC
1 GGAAGGTGTTGTTTAA------ATT-CCCAATTTGCCCTTCCCCATC
* * *
76076 GAAAGGTGTTGTTTAAGTCTACTTTACCCAATTTTCCCTTCCCCACC
1 GGAAGGTGTTGTTTAA----A--TT-CCCAATTTGCCCTTCCCCATC
* * **
76123 GGAATGTGTTGTTTAAATTCCCAATTTGCCTTTCCTTATC
1 GGAAGGTGTTGTTTAAATTCCCAATTTGCCCTTCCCCATC
* * * * *
76163 GGAAGGTATTGTTTAAGTCTGCTTTACCCAATTTGCCATTTCTCATC
1 GGAAGGTGTTGTTTAA------ATT-CCCAATTTGCCCTTCCCCATC
* * * *
76210 GGAAGGTGTTGTTTAAGTCTGCTGTACCCAATTTGCCATTTCTCATC
1 GGAAGGTGTTGTTTAA-----AT-T-CCCAATTTGCCCTTCCCCATC
** * **
76257 GGAAGGTGTTGTCCAGAGTTGTCTACTTTTCCCAATTTGCCCCTCCCCGCC
1 GGAAGGTG-T-T-----G-T-T-TA-AATTCCCAATTTGCCCTTCCCCATC
** * * **
76308 GGAAGGTGTTGTTTAGTTTACCAGTTTGCCCTTCCTAATC
1 GGAAGGTGTTGTTTAAATTCCCAATTTGCCCTTCCCCATC
* * ** *
76348 GGAAAGTGTTGTTTAGATTCCCTGTTTGCCCTTCCCCACC
1 GGAAGGTGTTGTTTAAATTCCCAATTTGCCCTTCCCCATC
** * * *
76388 GGAAGGTGTTGTTTAGTTTACCAATTTGCCCTT-CCTAAC
1 GGAAGGTGTTGTTTAAATTCCCAATTTGCCCTTCCCCATC
* * * * * * *
76427 TAGAAGGTATTGTTTACATTCCCAGTTTGCCCTACCCTACC
1 -GGAAGGTGTTGTTTAAATTCCCAATTTGCCCTTCCCCATC
* * * *
76468 GAAAAGTGTTGTTTAAATTCCCAATTTGCCCTT-CCTAAC
1 GGAAGGTGTTGTTTAAATTCCCAATTTGCCCTTCCCCATC
* * * * **
76507 TGGAATGTGTTGTTTGAATTCCCAGTCTGCCCTTCCTTATC
1 -GGAAGGTGTTGTTTAAATTCCCAATTTGCCCTTCCCCATC
76548 GGAAGGTGTTGTTT
1 GGAAGGTGTTGTTT
76562 CTATTTCCTT
Statistics
Matches: 531, Mismatches: 97, Indels: 65
0.77 0.14 0.09
Matches are distributed among these distances:
39 9 0.02
40 273 0.51
41 29 0.05
42 1 0.00
43 2 0.00
44 1 0.00
45 1 0.00
46 5 0.01
47 176 0.33
48 1 0.00
49 2 0.00
50 1 0.00
51 23 0.04
52 1 0.00
53 1 0.00
54 1 0.00
55 1 0.00
56 1 0.00
57 2 0.00
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (40 bp):
GGAAGGTGTTGTTTAAATTCCCAATTTGCCCTTCCCCATC
Found at i:75987 original size:80 final size:80
Alignment explanation
Indices: 75861--76561 Score: 389
Period size: 80 Copynumber: 8.2 Consensus size: 80
75851 CTTCCTAACT
* * * * *
75861 GGAAGGTGTTGTCTACTTTACCCAATTTGTCCTTCCCCAACGGAAGGTGTTGTTTAAATTCCCAA
1 GGAAGGTGTTGTTTAATTT-CCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCAA
75926 TTTGCCCTTCCCCATC
65 TTTGCCCTTCCCCATC
* * *
75942 AGAAGGTGTTGTTTAAATTCCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTGCTTT
1 GGAAGGTGTTGTTTAATTTCCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTTTAA------ATT
* * *
76007 ACCCAATTTGTCATTCCTCATC
60 -CCCAATTTGCCCTTCCCCATC
* * * *
76029 GAAAGGTGTTGTTTAAGTCTGCTTTACCCAATTTTCTCTTCCTCATCGAAAGGTGTTGTTTAAGT
1 GGAAGGTGTTGTTTAA------TTT-CCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTTTAA--
* *
76094 CTACTTTACCCAATTTTCCCTTCCCCACC
57 --A--TT-CCCAATTTGCCCTTCCCCATC
* * * * * *
76123 GGAATGTGTTGTTTAAATTCCCAATTTGCCTTTCCTTATCGGAAGGTATTGTTTAAGTCTGCTTT
1 GGAAGGTGTTGTTTAATTTCCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTTTAA------ATT
* * *
76188 ACCCAATTTGCCATTTCTCATC
60 -CCCAATTTGCCCTTCCCCATC
* *
76210 GGAAGGTGTTGTTTAAGTCTGCTGTACCCAATTTGCCATTTCTCATCGGAAGGTGTTGTCCAGAG
1 GGAAGGTGTTGTTTAA---T--T-T-CCCAATTTGCCCTTCCTCATCGGAAGGTG-T-T-----G
** * **
76275 TTGTCTACTTTTCCCAATTTGCCCCTCCCCGCC
52 -T-T-TA-AATTCCCAATTTGCCCTTCCCCATC
* * * * * * **
76308 GGAAGGTGTTGTTTAGTTTACCAGTTTGCCCTTCCTAATCGGAAAGTGTTGTTTAGATTCCCTGT
1 GGAAGGTGTTGTTTAATTTCCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCAAT
*
76373 TTGCCCTTCCCCACC
66 TTGCCCTTCCCCATC
* * * * * * *
76388 GGAAGGTGTTGTTTAGTTTACCAATTTGCCCTTCCT-AACTAGAAGGTATTGTTTACATTCCCAG
1 GGAAGGTGTTGTTTAATTTCCCAATTTGCCCTTCCTCATC-GGAAGGTGTTGTTTAAATTCCCAA
* * *
76452 TTTGCCCTACCCTACC
65 TTTGCCCTTCCCCATC
* * * * * * *
76468 GAAAAGTGTTGTTTAAATTCCCAATTTGCCCTTCCT-AACTGGAATGTGTTGTTTGAATTCCCAG
1 GGAAGGTGTTGTTTAATTTCCCAATTTGCCCTTCCTCATC-GGAAGGTGTTGTTTAAATTCCCAA
* **
76532 TCTGCCCTTCCTTATC
65 TTTGCCCTTCCCCATC
76548 GGAAGGTGTTGTTT
1 GGAAGGTGTTGTTT
76562 CTATTTCCTT
Statistics
Matches: 488, Mismatches: 95, Indels: 75
0.74 0.14 0.11
Matches are distributed among these distances:
79 2 0.00
80 199 0.41
81 17 0.03
82 1 0.00
83 1 0.00
84 1 0.00
86 2 0.00
87 97 0.20
88 2 0.00
89 2 0.00
90 1 0.00
91 23 0.05
92 3 0.01
93 4 0.01
94 92 0.19
95 2 0.00
96 1 0.00
98 30 0.06
99 3 0.01
101 1 0.00
102 1 0.00
103 1 0.00
104 2 0.00
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (80 bp):
GGAAGGTGTTGTTTAATTTCCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCAAT
TTGCCCTTCCCCATC
Found at i:76035 original size:47 final size:47
Alignment explanation
Indices: 75961--76268 Score: 389
Period size: 47 Copynumber: 6.7 Consensus size: 47
75951 TGTTTAAATT
*
75961 CCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTGCTTTA
1 CCCAATTTGCCATTCCTCATCGGAAGGTGTTGTTTAAGTCTGCTTTA
* *
76008 CCCAATTTGTCATTCCTCATCGAAAGGTGTTGTTTAAGTCTGCTTTA
1 CCCAATTTGCCATTCCTCATCGGAAGGTGTTGTTTAAGTCTGCTTTA
* * *
76055 CCCAATTTTCTC-TTCCTCATCGAAAGGTGTTGTTTAAGTCTACTTTA
1 CCCAATTTGC-CATTCCTCATCGGAAGGTGTTGTTTAAGTCTGCTTTA
* * * * * *
76102 CCCAATTTTCCCTTCCCCACCGGAATGTGTTGTTTAA------ATT-
1 CCCAATTTGCCATTCCTCATCGGAAGGTGTTGTTTAAGTCTGCTTTA
* * *
76142 CCCAATTTGCCTTTCCTTATCGGAAGGTATTGTTTAAGTCTGCTTTA
1 CCCAATTTGCCATTCCTCATCGGAAGGTGTTGTTTAAGTCTGCTTTA
* *
76189 CCCAATTTGCCATTTCTCATCGGAAGGTGTTGTTTAAGTCTGCTGTA
1 CCCAATTTGCCATTCCTCATCGGAAGGTGTTGTTTAAGTCTGCTTTA
*
76236 CCCAATTTGCCATTTCTCATCGGAAGGTGTTGT
1 CCCAATTTGCCATTCCTCATCGGAAGGTGTTGT
76269 CCAGAGTTGT
Statistics
Matches: 228, Mismatches: 24, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
40 30 0.13
41 2 0.01
46 3 0.01
47 192 0.84
48 1 0.00
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (47 bp):
CCCAATTTGCCATTCCTCATCGGAAGGTGTTGTTTAAGTCTGCTTTA
Found at i:76177 original size:181 final size:183
Alignment explanation
Indices: 75921--76362 Score: 611
Period size: 181 Copynumber: 2.4 Consensus size: 183
75911 TGTTTAAATT
* * *
75921 CCCAATTTGCCCTTCCCCATCAGAAGGTGTTGTTTAAATTCCCAATTTGCCCTTCCTCATCGGAA
1 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCCAATTTGCCCTTCCTAATCGGAA
*
75986 GGTGTTGTTTAAGTCTGCTTTACCCAATTTGTCATTCCTCATCGAAAGGTGTTGTTTAAGTCTGC
66 GGTGTTGTTTAAGTCTGCTTTACCCAATTTGCCATTCCTCATCGAAAGGTGTTGTTTAAGTCTGC
* * **
76051 TTTACCCAATTTTCTC-TTCCTCATCGAAAGGTGTTGTTTA-A-GTCTACTTTA
131 TGTACCCAATTTGC-CATTCCTCATCGAAAGGTGTTGTCCAGATGTCTACTTTA
* * * *
76102 CCCAATTTTCCCTTCCCCACCGGAATGTGTTGTTTAAATTCCCAATTTGCCTTTCCTTATCGGAA
1 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCCAATTTGCCCTTCCTAATCGGAA
* * *
76167 GGTATTGTTTAAGTCTGCTTTACCCAATTTGCCATTTCTCATCGGAAGGTGTTGTTTAAGTCTGC
66 GGTGTTGTTTAAGTCTGCTTTACCCAATTTGCCATTCCTCATCGAAAGGTGTTGTTTAAGTCTGC
* * *
76232 TGTACCCAATTTGCCATTTCTCATCGGAAGGTGTTGTCCAGAGTTGTCTACTTTT
131 TGTACCCAATTTGCCATTCCTCATCGAAAGGTGTTGTCCAGA--TGTCTACTTTA
* * ** * *
76287 CCCAATTTGCCCCTCCCCGCCGGAAGGTGTTGTTTAGTTTACCAGTTTGCCCTTCCTAATCGGAA
1 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCCAATTTGCCCTTCCTAATCGGAA
*
76352 AGTGTTGTTTA
66 GGTGTTGTTTA
76363 GATTCCCTGT
Statistics
Matches: 227, Mismatches: 29, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
180 1 0.00
181 152 0.67
182 1 0.00
185 73 0.32
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (183 bp):
CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCCAATTTGCCCTTCCTAATCGGAA
GGTGTTGTTTAAGTCTGCTTTACCCAATTTGCCATTCCTCATCGAAAGGTGTTGTTTAAGTCTGC
TGTACCCAATTTGCCATTCCTCATCGAAAGGTGTTGTCCAGATGTCTACTTTA
Found at i:76260 original size:134 final size:134
Alignment explanation
Indices: 76008--76268 Score: 362
Period size: 134 Copynumber: 1.9 Consensus size: 134
75998 GTCTGCTTTA
* * *
76008 CCCAATTTGTCATTCCTCATCGAAAGGTGTTGTTTAAGTCTGCTTTACCCAATTTTCTCTTCCTC
1 CCCAATTTGCCATTCCTCATCGAAAGGTATTGTTTAAGTCTGCTTTACCCAATTTGCTCTTCCTC
* * * *
76073 ATCGAAAGGTGTTGTTTAAGTCTACTTTACCCAATTTTCCCTTCCCCACCGGAATGTGTTGTTTA
66 ATCGAAAGGTGTTGTTTAAGTCTACTGTACCCAATTTGCCATTCCCCACCGGAAGGTGTTGTTTA
76138 AATT
131 AATT
* * * *
76142 CCCAATTTGCCTTTCCTTATCGGAAGGTATTGTTTAAGTCTGCTTTACCCAATTTGC-CATTTCT
1 CCCAATTTGCCATTCCTCATCGAAAGGTATTGTTTAAGTCTGCTTTACCCAATTTGCTC-TTCCT
* * * * *
76206 CATCGGAAGGTGTTGTTTAAGTCTGCTGTACCCAATTTGCCATTTCTCATCGGAAGGTGTTGT
65 CATCGAAAGGTGTTGTTTAAGTCTACTGTACCCAATTTGCCATTCCCCACCGGAAGGTGTTGT
76269 CCAGAGTTGT
Statistics
Matches: 110, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
133 1 0.01
134 109 0.99
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (134 bp):
CCCAATTTGCCATTCCTCATCGAAAGGTATTGTTTAAGTCTGCTTTACCCAATTTGCTCTTCCTC
ATCGAAAGGTGTTGTTTAAGTCTACTGTACCCAATTTGCCATTCCCCACCGGAAGGTGTTGTTTA
AATT
Found at i:85006 original size:13 final size:13
Alignment explanation
Indices: 84988--85012 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
84978 TTTTATTCTT
84988 TTGAAAAATTTTC
1 TTGAAAAATTTTC
85001 TTGAAAAATTTT
1 TTGAAAAATTTT
85013 GAAAAATCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
TTGAAAAATTTTC
Found at i:85436 original size:16 final size:16
Alignment explanation
Indices: 85415--85447 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
85405 AAGGAATAGG
85415 TAATCAATAAAAGCAA
1 TAATCAATAAAAGCAA
*
85431 TAATCAATCAAAGCAA
1 TAATCAATAAAAGCAA
85447 T
1 T
85448 GCAAGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.15, G:0.06, T:0.21
Consensus pattern (16 bp):
TAATCAATAAAAGCAA
Found at i:87886 original size:11 final size:10
Alignment explanation
Indices: 87870--87902 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
87860 GGTTATATCG
87870 AAAAATATAAA
1 AAAAATA-AAA
87881 AAAAATAAAA
1 AAAAATAAAA
87891 AAAAATAAAA
1 AAAAATAAAA
87901 AA
1 AA
87903 TGTTTTGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 15 0.68
11 7 0.32
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:95104 original size:23 final size:23
Alignment explanation
Indices: 95078--95124 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
95068 GACAAGCCTA
95078 TGATTGCTCTGTTTCGACTTGTT
1 TGATTGCTCTGTTTCGACTTGTT
95101 TGATTGCTCTGTTTCGACTTGTT
1 TGATTGCTCTGTTTCGACTTGTT
95124 T
1 T
95125 TTTTTTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.09, C:0.17, G:0.21, T:0.53
Consensus pattern (23 bp):
TGATTGCTCTGTTTCGACTTGTT
Found at i:102456 original size:29 final size:28
Alignment explanation
Indices: 102351--102476 Score: 130
Period size: 27 Copynumber: 4.5 Consensus size: 28
102341 TTGAAGTGAC
*
102351 CCAAAATGCACCCCTGGACGTGC-AAATGA
1 CCAAAATG--CCCCTGGACATGCAAAATGA
* **
102380 CGAAAATGCCCCTGGAGGTGC-AAATGA
1 CCAAAATGCCCCTGGACATGCAAAATGA
*
102407 CCAAAATACCCCTGGACATGCAAAAATGA
1 CCAAAATGCCCCTGGACATGC-AAAATGA
* **
102436 CCAAAATGCCCTTGGTTATGCAAAATGA
1 CCAAAATGCCCCTGGACATGCAAAATGA
*
102464 TCAAAATGCCCCT
1 CCAAAATGCCCCT
102477 TTAAGTGACC
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
27 35 0.42
28 18 0.22
29 30 0.36
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (28 bp):
CCAAAATGCCCCTGGACATGCAAAATGA
Found at i:102458 original size:56 final size:55
Alignment explanation
Indices: 102351--102476 Score: 137
Period size: 56 Copynumber: 2.2 Consensus size: 55
102341 TTGAAGTGAC
* * *
102351 CCAAAATGCACCCCTGGACGTGCAAATGACGAAAATGCCCCTGGAGGTGC-AAATGA
1 CCAAAAT--ACCCCTGGACATGCAAATGACCAAAATGCCCCTGGAGATGCAAAATGA
* **
102407 CCAAAATACCCCTGGACATGCAAAAATGACCAAAATGCCCTTGGTTATGCAAAATGA
1 CCAAAATACCCCTGGACATGC--AAATGACCAAAATGCCCCTGGAGATGCAAAATGA
* *
102464 TCAAAATGCCCCT
1 CCAAAATACCCCT
102477 TTAAGTGACC
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
54 13 0.22
56 29 0.49
57 17 0.29
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (55 bp):
CCAAAATACCCCTGGACATGCAAATGACCAAAATGCCCCTGGAGATGCAAAATGA
Found at i:102477 original size:29 final size:30
Alignment explanation
Indices: 102351--102477 Score: 108
Period size: 29 Copynumber: 4.5 Consensus size: 30
102341 TTGAAGTGAC
* *
102351 CCAAAATGCACCCCTGGACGTGC--AAATGA
1 CCAAAATGC-CCCTTGGACATGCAAAAATGA
* **
102380 CGAAAATGCCCC-TGGAGGTGC--AAATGA
1 CCAAAATGCCCCTTGGACATGCAAAAATGA
*
102407 CCAAAATACCCC-TGGACATGCAAAAATGA
1 CCAAAATGCCCCTTGGACATGCAAAAATGA
**
102436 CCAAAATG-CCCTTGGTTATGC-AAAATGA
1 CCAAAATGCCCCTTGGACATGCAAAAATGA
*
102464 TCAAAATGCCCCTT
1 CCAAAATGCCCCTT
102478 TAAGTGACCG
Statistics
Matches: 84, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
27 31 0.37
28 20 0.24
29 33 0.39
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (30 bp):
CCAAAATGCCCCTTGGACATGCAAAAATGA
Found at i:105074 original size:24 final size:22
Alignment explanation
Indices: 105047--105106 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
105037 AGGCATTTGG
105047 TTGGGCCATTTTTTTAACCTTTAC
1 TTGGGCCATTTTTTT--CCTTTAC
* *
105071 TTGGGCAATTTTATTTTCTTTAC
1 TTGGGCCATTTT-TTTCCTTTAC
*
105094 TTGGTCCATTTTT
1 TTGGGCCATTTTT
105107 ATTTACTTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 1 0.03
23 16 0.52
24 11 0.35
25 3 0.10
ACGTcount: A:0.15, C:0.17, G:0.13, T:0.55
Consensus pattern (22 bp):
TTGGGCCATTTTTTTCCTTTAC
Found at i:105104 original size:23 final size:24
Alignment explanation
Indices: 105065--105110 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
105055 TTTTTTTAAC
105065 CTTTACTTGGGCAA-TTTTATTTT
1 CTTTACTTGGGCAATTTTTATTTT
* *
105088 CTTTACTTGGTCCATTTTTATTT
1 CTTTACTTGGGCAATTTTTATTT
105111 ACTTGGTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.15, C:0.15, G:0.11, T:0.59
Consensus pattern (24 bp):
CTTTACTTGGGCAATTTTTATTTT
Found at i:105111 original size:19 final size:20
Alignment explanation
Indices: 105084--105131 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 20
105074 GGCAATTTTA
*
105084 TTTTCTTTACTTGGTCCAT-
1 TTTTATTTACTTGGTCCATC
105103 TTTTATTTACTTGGTCCATC
1 TTTTATTTACTTGGTCCATC
105123 TCTTTATTT
1 T-TTTATTT
105132 CCATGGGGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 18 0.69
20 1 0.04
21 7 0.27
ACGTcount: A:0.12, C:0.19, G:0.08, T:0.60
Consensus pattern (20 bp):
TTTTATTTACTTGGTCCATC
Found at i:120626 original size:39 final size:38
Alignment explanation
Indices: 120541--120943 Score: 330
Period size: 39 Copynumber: 10.5 Consensus size: 38
120531 TCTCTATCGT
*** * *
120541 AGTAAACCTGCTTAGGTCCCATTCA-AAGTTGCCATTTA
1 AGTAAACCTGCTTAGGTCTTGTTTAGAA-TTTCCATTTA
120579 AGTAAACCTGCTTAGGTCTATGTTTAGAATTTCCATTTA
1 AGTAAACCTGCTTAGGTCT-TGTTTAGAATTTCCATTTA
*
120618 AGTAAACCTGCTCAGGTCTATGTTTAGAATTTCCATTTA
1 AGTAAACCTGCTTAGGTCT-TGTTTAGAATTTCCATTTA
120657 AGTAAACCTGCTTAGGTCTATGTTTAGAATTT-CATTTA
1 AGTAAACCTGCTTAGGTCT-TGTTTAGAATTTCCATTTA
* *
120695 AGTAAACCTGCTTAGGTCTTCATTTAGAAGTTT-CGTTTA
1 AGTAAACCTGCTTAGGTCTT-GTTTAGAA-TTTCCATTTA
* *
120734 AATCAAACCTGCTTAGGTCCTTGTGTAGAATTTCC-----
1 AGT-AAACCTGCTTAGGT-CTTGTTTAGAATTTCCATTTA
* * ** *
120769 A-TAAACCTGCATAGG-CGTCTGCTTAGAGCTT-CGTTTA
1 AGTAAACCTGCTTAGGTC-T-TGTTTAGAATTTCCATTTA
*
120806 A-TCAAACCTGCTTAGGTCCTTTCTTTAGAACTTT-CATTTA
1 AGT-AAACCTGCTTAGGT-C-TTGTTTAGAA-TTTCCATTTA
* * * *
120846 ATTAAACCTGCTTAGGTCCTTATTTAGAATTTTCGTTTA
1 AGTAAACCTGCTTAGGT-CTTGTTTAGAATTTCCATTTA
* * *
120885 A-TCAAACCTGCTTAGGTCCTTATTTAAAATTTCCGTTTAA
1 AGT-AAACCTGCTTAGGT-CTTGTTTAGAATTTCCATTT-A
*
120925 AGCAAACCTGCTTAGGTCT
1 AGTAAACCTGCTTAGGTCT
120944 CCGTTCCGTT
Statistics
Matches: 313, Mismatches: 29, Indels: 45
0.81 0.07 0.12
Matches are distributed among these distances:
31 1 0.00
32 2 0.01
33 20 0.06
34 1 0.00
35 1 0.00
37 3 0.01
38 66 0.21
39 150 0.48
40 65 0.21
41 4 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (38 bp):
AGTAAACCTGCTTAGGTCTTGTTTAGAATTTCCATTTA
Found at i:120672 original size:78 final size:76
Alignment explanation
Indices: 120582--120943 Score: 370
Period size: 78 Copynumber: 4.7 Consensus size: 76
120572 CCATTTAAGT
* *
120582 AAACCTGCTTAGGT-CTATGTTTAGAATTTCCATTTAAGTAAACCTGCTCAGGTCTATGTTTAGA
1 AAACCTGCTTAGGTCCT-TGTTTAGAATTTCCATTTAAGTAAACCTGCTTAGGTCT-TATTTAGA
*
120646 ATTTCCATTTAAGT-
64 ATTT-CGTTTAA-TC
120660 AAACCTGCTTAGGT-CTATGTTTAGAATTT-CATTTAAGTAAACCTGCTTAGGTCTTCATTTAGA
1 AAACCTGCTTAGGTCCT-TGTTTAGAATTTCCATTTAAGTAAACCTGCTTAGGTCTT-ATTTAGA
120723 AGTTTCGTTTAAATC
64 A-TTTCGTTT-AATC
* * **
120738 AAACCTGCTTAGGTCCTTGTGTAGAATTTCC-----A-TAAACCTGCATAGG-CGTCTGCTTAGA
1 AAACCTGCTTAGGTCCTTGTTTAGAATTTCCATTTAAGTAAACCTGCTTAGGTC-T-TATTTAGA
**
120796 GCTTCGTTTAATC
64 ATTTCGTTTAATC
* *
120809 AAACCTGCTTAGGTCCTTTCTTTAGAACTTT-CATTTAATTAAACCTGCTTAGGTCCTTATTTAG
1 AAACCTGCTTAGGTCC-TTGTTTAGAA-TTTCCATTTAAGTAAACCTGCTTAGGT-CTTATTTAG
120873 AATTTTCGTTTAATC
63 AA-TTTCGTTTAATC
* * * *
120888 AAACCTGCTTAGGTCCTTATTTAAAATTTCCGTTTAAAGCAAACCTGCTTAGGTCT
1 AAACCTGCTTAGGTCCTTGTTTAGAATTTCCATTT-AAGTAAACCTGCTTAGGTCT
120944 CCGTTCCGTT
Statistics
Matches: 242, Mismatches: 21, Indels: 42
0.79 0.07 0.14
Matches are distributed among these distances:
71 20 0.08
72 17 0.07
73 22 0.09
74 2 0.01
76 1 0.00
77 40 0.17
78 92 0.38
79 47 0.19
80 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (76 bp):
AAACCTGCTTAGGTCCTTGTTTAGAATTTCCATTTAAGTAAACCTGCTTAGGTCTTATTTAGAAT
TTCGTTTAATC
Found at i:120853 original size:111 final size:111
Alignment explanation
Indices: 120573--120877 Score: 325
Period size: 111 Copynumber: 2.7 Consensus size: 111
120563 TCAAAGTTGC
* * * *
120573 CATTTAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCCATTTAAGTAAACCTGCTCAGGT-CT
1 CATTTAAGTAAACCTGCTTAGGTCTTTCTTTAGAATTT-CATTTAATTAAACCTGCTTAGGTCCT
* * *
120637 ATGTTTAGAATTTCCATTTAAGTAAACCTGCTTAGGTCTATGTTTAGAATTT
65 -TGTTTAGAATTTCC---T-AGTAAACCTGCATAGGTCTATGCTTAGAACTT
* *
120689 CATTTAAGTAAACCTGCTTAGGTC-TTCATTTAGAAGTTTCGTTTAAATCAAACCTGCTTAGGTC
1 CATTTAAGTAAACCTGCTTAGGTCTTTC-TTTAGAA-TTTCATTT-AATTAAACCTGCTTAGGTC
* * *
120753 CTTGTGTAGAATTTCC-A-TAAACCTGCATAGG-CGTCTGCTTAGAGCTT
63 CTTGTTTAGAATTTCCTAGTAAACCTGCATAGGTC-TATGCTTAGAACTT
*
120800 CGTTTAA-TCAAACCTGCTTAGGTCCTTTCTTTAGAACTTTCATTTAATTAAACCTGCTTAGGTC
1 CATTTAAGT-AAACCTGCTTAGGT-CTTTCTTTAGAA-TTTCATTTAATTAAACCTGCTTAGGTC
*
120864 CTTATTTAGAATTT
63 CTTGTTTAGAATTT
120878 TCGTTTAATC
Statistics
Matches: 163, Mismatches: 18, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
110 2 0.01
111 73 0.45
112 16 0.10
113 3 0.02
115 1 0.01
116 35 0.21
117 31 0.19
118 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (111 bp):
CATTTAAGTAAACCTGCTTAGGTCTTTCTTTAGAATTTCATTTAATTAAACCTGCTTAGGTCCTT
GTTTAGAATTTCCTAGTAAACCTGCATAGGTCTATGCTTAGAACTT
Found at i:121913 original size:23 final size:24
Alignment explanation
Indices: 121869--121934 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
121859 AGGCATTTGG
121869 TTGGGCCATTTT-TTTAACCTTTAC
1 TTGGGCCATTTTATTT-ACCTTTAC
*
121893 TTGGGCCATTTTATTT-TCTTTAC
1 TTGGGCCATTTTATTTACCTTTAC
* *
121916 ATGGTCCATTTTTATTTAC
1 TTGGGCCA-TTTTATTTAC
121935 TTGGTCCATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 12 0.34
24 20 0.57
25 3 0.09
ACGTcount: A:0.17, C:0.18, G:0.12, T:0.53
Consensus pattern (24 bp):
TTGGGCCATTTTATTTACCTTTAC
Found at i:121933 original size:19 final size:19
Alignment explanation
Indices: 121906--121945 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
121896 GGCCATTTTA
*
121906 TTTTCTTTACATGGTCCAT
1 TTTTATTTACATGGTCCAT
*
121925 TTTTATTTACTTGGTCCAT
1 TTTTATTTACATGGTCCAT
121944 TT
1 TT
121946 ACTTGGTCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.57
Consensus pattern (19 bp):
TTTTATTTACATGGTCCAT
Found at i:121947 original size:13 final size:13
Alignment explanation
Indices: 121929--121956 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
121919 GTCCATTTTT
121929 ATTTACTTGGTCC
1 ATTTACTTGGTCC
121942 ATTTACTTGGTCC
1 ATTTACTTGGTCC
121955 AT
1 AT
121957 CTCTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.18, C:0.21, G:0.14, T:0.46
Consensus pattern (13 bp):
ATTTACTTGGTCC
Found at i:124429 original size:23 final size:23
Alignment explanation
Indices: 124384--124429 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
124374 TTTCGGCGTG
* *
124384 TTCAATTTGGTCCCTCAATTTTA
1 TTCAATTGGGTCCCTCAAGTTTA
124407 TTCAATTGGGTCCC-CAACGTTTA
1 TTCAATTGGGTCCCTCAA-GTTTA
124430 AGATTGGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (23 bp):
TTCAATTGGGTCCCTCAAGTTTA
Found at i:126223 original size:30 final size:31
Alignment explanation
Indices: 126189--126252 Score: 94
Period size: 34 Copynumber: 2.0 Consensus size: 31
126179 GGCAATTGCA
126189 AGTCCTAG-CAATTAGATAGTGATTATCTAG
1 AGTCCTAGACAATTAGATAGTGATTATCTAG
126219 AGTCCTAGCAAACAATTAGATAGTGATTATCTAG
1 AGTCCTAG---ACAATTAGATAGTGATTATCTAG
126253 TTGCGTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 8 0.27
34 22 0.73
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (31 bp):
AGTCCTAGACAATTAGATAGTGATTATCTAG
Found at i:127497 original size:16 final size:16
Alignment explanation
Indices: 127476--127507 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
127466 AGGAATAGGC
127476 AATCAATCAAAACAAT
1 AATCAATCAAAACAAT
*
127492 AATCAATCAAAGCAAT
1 AATCAATCAAAACAAT
127508 GCAAGAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.19, G:0.03, T:0.19
Consensus pattern (16 bp):
AATCAATCAAAACAAT
Found at i:132069 original size:26 final size:27
Alignment explanation
Indices: 132029--132099 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 27
132019 GGTCATCTAG
** *
132029 GGGCATTTTGGTCATTTTTACACT-AA
1 GGGCATTTTCATCATTTTCACACTCAA
* * * *
132055 GGGCATTTTCATCATTTGCAGATTCAG
1 GGGCATTTTCATCATTTTCACACTCAA
132082 GGGCATTTTCATCATTTT
1 GGGCATTTTCATCATTTT
132100 AGATCCACTT
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
26 18 0.50
27 18 0.50
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.42
Consensus pattern (27 bp):
GGGCATTTTCATCATTTTCACACTCAA
Done.