Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008873.1 Hibiscus syriacus cultivar Beakdansim tig00112109_pilon, 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: 60568
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:253 original size:3 final size:3
Alignment explanation
Indices: 245--270 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
235 TAAGCTCCCT
245 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
271 TTGTCGTCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:16500 original size:18 final size:18
Alignment explanation
Indices: 16473--16508 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
16463 AATACTCCAT
16473 AAATCTATTGA-AAAAGA
1 AAATCTATTGAGAAAAGA
16490 AAATACTATTGAGAAAAGA
1 AAAT-CTATTGAGAAAAGA
16509 GAAACAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.58, C:0.06, G:0.14, T:0.22
Consensus pattern (18 bp):
AAATCTATTGAGAAAAGA
Found at i:18353 original size:21 final size:21
Alignment explanation
Indices: 18327--18367 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
18317 CTAGCATAGC
18327 CCTTAACAATCTCCTAAGCTT
1 CCTTAACAATCTCCTAAGCTT
18348 CCTTAACAATCTCCTAAGCT
1 CCTTAACAATCTCCTAAGCT
18368 AAAAGCGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (21 bp):
CCTTAACAATCTCCTAAGCTT
Found at i:19516 original size:15 final size:15
Alignment explanation
Indices: 19492--19527 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
19482 ATATTTTTTT
*
19492 ATTTTTTTATTATTA
1 ATTTTATTATTATTA
19507 ATTTTATTATTATTA
1 ATTTTATTATTATTA
19522 ATTTTA
1 ATTTTA
19528 CATATTACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTATTATTATTA
Found at i:19620 original size:37 final size:37
Alignment explanation
Indices: 19577--19676 Score: 182
Period size: 37 Copynumber: 2.7 Consensus size: 37
19567 AGATTACAAA
19577 GGCCCAATCCCGGAGCCCAACAACCCGAAGCCCAATT
1 GGCCCAATCCCGGAGCCCAACAACCCGAAGCCCAATT
* *
19614 GGCCCAATCCCAGAGCCCAACAACTCGAAGCCCAATT
1 GGCCCAATCCCGGAGCCCAACAACCCGAAGCCCAATT
19651 GGCCCAATCCCGGAGCCCAACAACCC
1 GGCCCAATCCCGGAGCCCAACAACCC
19677 ATCAGATTAG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.44, G:0.18, T:0.08
Consensus pattern (37 bp):
GGCCCAATCCCGGAGCCCAACAACCCGAAGCCCAATT
Found at i:19706 original size:25 final size:25
Alignment explanation
Indices: 19677--19751 Score: 141
Period size: 25 Copynumber: 3.0 Consensus size: 25
19667 CCAACAACCC
19677 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
19702 ATCAGATTAGGGTTTCAAACCTTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
19727 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
19752 TCCCCTACTC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:34012 original size:44 final size:45
Alignment explanation
Indices: 33964--34311 Score: 170
Period size: 44 Copynumber: 7.4 Consensus size: 45
33954 TGACCAGATC
* *
33964 TCCTCATCACGTAGGAGCCGTGTCA-ACTTTAAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCACACTTTAAGATGACCAGCCG
* * * * *
34008 TCCTCATCACGTAGGAACCGAGTTATCACCCCTCCTAACGATGGCCAG-AG
1 TCCTCATCACGTAGGAACC--G-TGTCA-CACT-TTAA-GATGACCAGCCG
* * * * * * * *
34058 TTCTTCATCATGTATGAACCATGTCATCTACCCTT-AGACGACCAGACT
1 -TCCTCATCACGTAGGAACCGTGTCA-C-A-CTTTAAGATGACCAGCCG
* *
34106 TCCTCATCACGTAGGAGCCGTGTCA-ACTTTAAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCACACTTTAAGATGACCAGCCG
* * * * *
34150 TCCTCATCACGTAGGAACCGAGTTATCACCCCTCCTAACGATGGCCAG-AG
1 TCCTCATCACGTAGGAACC--G-TGTCA-CACT-TTAA-GATGACCAGCCG
* * * * * * * *
34200 TTCTTCATCATGTATGAACCATGTCATCTACCCTT-AGACGACCAGACT
1 -TCCTCATCACGTAGGAACCGTGTCA-C-A-CTTTAAGATGACCAGCCG
* * *
34248 TCCTCATCACGTAGGAGCCGTGTCA-ACTTTAAGATAATCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCACACTTTAAGATGACCAGCCG
34292 TCCTCATCACGTAGGAACCG
1 TCCTCATCACGTAGGAACCG
34312 AGTTATCACC
Statistics
Matches: 218, Mismatches: 62, Indels: 48
0.66 0.19 0.15
Matches are distributed among these distances:
43 6 0.03
44 74 0.34
46 2 0.01
47 62 0.28
48 12 0.06
49 6 0.03
50 10 0.05
51 46 0.21
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (45 bp):
TCCTCATCACGTAGGAACCGTGTCACACTTTAAGATGACCAGCCG
Found at i:34114 original size:47 final size:46
Alignment explanation
Indices: 34008--34386 Score: 161
Period size: 51 Copynumber: 7.9 Consensus size: 46
33998 TAACCAGCCG
* *
34008 TCCTCATCACGTAGGAACCGA-GTTATCACCCCTCCTA-ACGATGGCCAGAGT
1 TCCTCATCACGTAGGAACC-ATGTCATCA-CCCT--TAGACGA---CCAGACT
* * *
34059 TCTTCATCATGTATGAACCATGTCATCTACCCTTAGACGACCAGACT
1 TCCTCATCACGTAGGAACCATGTCATC-ACCCTTAGACGACCAGACT
* * * ** * *
34106 TCCTCATCACGTAGGAGCCGTGTCA--A-CTTTAAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCATGTCATCACCCTT-AGACGACCAGACT
* *
34150 TCCTCATCACGTAGGAACCGA-GTTATCACCCCTCCTA-ACGATGGCCAGAGT
1 TCCTCATCACGTAGGAACC-ATGTCATCA-CCCT--TAGACGA---CCAGACT
* * *
34201 TCTTCATCATGTATGAACCATGTCATCTACCCTTAGACGACCAGACT
1 TCCTCATCACGTAGGAACCATGTCATC-ACCCTTAGACGACCAGACT
* * * ** * * *
34248 TCCTCATCACGTAGGAGCCGTGTCA--A-CTTTAAGATAATCAGCCG
1 TCCTCATCACGTAGGAACCATGTCATCACCCTT-AGACGACCAGACT
* *
34292 TCCTCATCACGTAGGAACCGA-GTTATCACCCCTCCTA-ACGATGGCCAGAGT
1 TCCTCATCACGTAGGAACC-ATGTCATCA-CCCT--TAGACGA---CCAGACT
* * * *
34343 TCTTCATCATGTATGAACCATGTCATCTACCCTTAGATGACCAG
1 TCCTCATCACGTAGGAACCATGTCATC-ACCCTTAGACGACCAG
34387 GGCTCTTCAT
Statistics
Matches: 242, Mismatches: 55, Indels: 66
0.67 0.15 0.18
Matches are distributed among these distances:
43 6 0.02
44 61 0.25
46 2 0.01
47 56 0.23
48 8 0.03
49 8 0.03
50 16 0.07
51 82 0.34
52 3 0.01
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (46 bp):
TCCTCATCACGTAGGAACCATGTCATCACCCTTAGACGACCAGACT
Found at i:34414 original size:142 final size:142
Alignment explanation
Indices: 33955--34386 Score: 830
Period size: 142 Copynumber: 3.0 Consensus size: 142
33945 AACATCAACT
33955 GACCAGA-TCTCCTCATCACGTAGGAGCCGTGTCAACTTTAAGATAACCAGCCGTCCTCATCACG
1 GACCAGACT-TCCTCATCACGTAGGAGCCGTGTCAACTTTAAGATAACCAGCCGTCCTCATCACG
34019 TAGGAACCGAGTTATCACCCCTCCTAACGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCA
65 TAGGAACCGAGTTATCACCCCTCCTAACGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCA
34084 TCTACCCTTAGAC
130 TCTACCCTTAGAC
34097 GACCAGACTTCCTCATCACGTAGGAGCCGTGTCAACTTTAAGATAACCAGCCGTCCTCATCACGT
1 GACCAGACTTCCTCATCACGTAGGAGCCGTGTCAACTTTAAGATAACCAGCCGTCCTCATCACGT
34162 AGGAACCGAGTTATCACCCCTCCTAACGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCAT
66 AGGAACCGAGTTATCACCCCTCCTAACGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCAT
34227 CTACCCTTAGAC
131 CTACCCTTAGAC
*
34239 GACCAGACTTCCTCATCACGTAGGAGCCGTGTCAACTTTAAGATAATCAGCCGTCCTCATCACGT
1 GACCAGACTTCCTCATCACGTAGGAGCCGTGTCAACTTTAAGATAACCAGCCGTCCTCATCACGT
34304 AGGAACCGAGTTATCACCCCTCCTAACGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCAT
66 AGGAACCGAGTTATCACCCCTCCTAACGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCAT
*
34369 CTACCCTTAGAT
131 CTACCCTTAGAC
34381 GACCAG
1 GACCAG
34387 GGCTCTTCAT
Statistics
Matches: 287, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
142 286 1.00
143 1 0.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.25
Consensus pattern (142 bp):
GACCAGACTTCCTCATCACGTAGGAGCCGTGTCAACTTTAAGATAACCAGCCGTCCTCATCACGT
AGGAACCGAGTTATCACCCCTCCTAACGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCAT
CTACCCTTAGAC
Found at i:34673 original size:3 final size:3
Alignment explanation
Indices: 34660--34692 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
34650 TATATATTTT
34660 TTA TT- TTA TTA TTA TTAA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
34693 ATTTTACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:34683 original size:13 final size:13
Alignment explanation
Indices: 34665--34689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34655 ATTTTTTATT
34665 TTATTATTATTAA
1 TTATTATTATTAA
34678 TTATTATTATTA
1 TTATTATTATTA
34690 TTAATTTTAC
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTATTATTAA
Found at i:34686 original size:16 final size:16
Alignment explanation
Indices: 34665--34695 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
34655 ATTTTTTATT
34665 TTATTATTATTAATTA
1 TTATTATTATTAATTA
34681 TTATTATTATTAATT
1 TTATTATTATTAATT
34696 TTACATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTATTATTAATTA
Found at i:34840 original size:25 final size:25
Alignment explanation
Indices: 34811--34910 Score: 173
Period size: 25 Copynumber: 4.0 Consensus size: 25
34801 CCAACAACCC
34811 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
34836 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
34861 ATTAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
* *
34886 AACAAATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
34911 TCCCCTACTC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 71 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:38638 original size:20 final size:20
Alignment explanation
Indices: 38615--38666 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
38605 AACGCGATCC
38615 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
38635 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
38655 CCAAAATCGCAA
1 CCAGAATCGCAA
38667 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:38683 original size:21 final size:20
Alignment explanation
Indices: 38656--38754 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
38646 AATCAGTTTC
38656 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
38677 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
38698 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
38718 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
38739 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
38755 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:38783 original size:20 final size:20
Alignment explanation
Indices: 38721--38914 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
38711 CGATTTTCCA
* ** *
38721 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
38741 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
38761 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
38781 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
38801 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
38821 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
38841 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
38861 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
38881 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
38902 AAATCGCAACGCG
1 AAATCGCAACGCG
38915 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:38805 original size:60 final size:60
Alignment explanation
Indices: 38721--38914 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
38711 CGATTTTCCA
* ** * *
38721 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
38781 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
38841 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
38902 AAATCGCAACGCG
1 AAATCGCAACGCG
38915 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:39335 original size:33 final size:33
Alignment explanation
Indices: 39296--39366 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
39286 TTCACTTAGA
*
39296 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
39329 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
39362 TTTCA
1 TTTCA
39367 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:39506 original size:14 final size:14
Alignment explanation
Indices: 39487--39541 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
39477 AGAATGACTG
39487 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
39501 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
39520 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
39534 TCGCAACG
1 TCGCAACG
39542 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:39554 original size:33 final size:33
Alignment explanation
Indices: 39487--39557 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
39477 AGAATGACTG
***
39487 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
39520 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
39553 TCGCA
1 TCGCA
39558 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:39575 original size:19 final size:19
Alignment explanation
Indices: 39553--39650 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
39543 GAAACCAAAA
*
39553 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
39572 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
39586 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
39605 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
39619 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
39638 TCGCGTTGCGATT
1 TCGCGTTGCGATT
39651 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:39594 original size:14 final size:14
Alignment explanation
Indices: 39575--39664 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
39565 TTTCATTTCG
39575 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
39589 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
39608 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
39622 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
39639 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
39655 CGTTGCGATT
1 CGTTGCGATT
39665 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:39600 original size:33 final size:33
Alignment explanation
Indices: 39558--39672 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
39548 CAAAATCGCA
39558 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
39591 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
39624 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
39657 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
39673 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:41596 original size:183 final size:185
Alignment explanation
Indices: 41363--41741 Score: 719
Period size: 183 Copynumber: 2.1 Consensus size: 185
41353 TAGATTGCTT
41363 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41428 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
41493 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTG-TTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACA-TGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
41547 AGTAAATTTGTTCGG-TGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41611 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
41676 GTGTATTCTTTAACATGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACATGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
41731 AGTAAATTTAT
1 AGTAAATTTAT
41742 CCATTCAAGT
Statistics
Matches: 191, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
182 9 0.05
183 141 0.74
184 41 0.21
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (185 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACATGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:41695 original size:92 final size:93
Alignment explanation
Indices: 41363--41739 Score: 717
Period size: 93 Copynumber: 4.1 Consensus size: 93
41353 TAGATTGCTT
*
41363 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41428 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
41456 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41520 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
41547 AGTAAATTTGTTCGG-TGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41611 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
41639 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACA-TGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
41703 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
41731 AGTAAATTT
1 AGTAAATTT
41740 ATCCATTCAA
Statistics
Matches: 280, Mismatches: 1, Indels: 7
0.97 0.00 0.02
Matches are distributed among these distances:
90 46 0.16
91 44 0.16
92 93 0.33
93 97 0.35
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:41823 original size:19 final size:18
Alignment explanation
Indices: 41783--41910 Score: 119
Period size: 19 Copynumber: 7.3 Consensus size: 18
41773 TAGTTTACTT
*
41783 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC--AAAA
41803 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAA-CAAAA
*
41822 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAA-CAAAA
*
41841 TCGCAA--CG--ACAGAA
1 TCGCAACGCGAAACAAAA
41855 TCGCAACGCGAAACAAAA
1 TCGCAACGCGAAACAAAA
*
41873 TCGCAA--CG--ACAAGA
1 TCGCAACGCGAAACAAAA
41887 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAA-CAAAA
41906 TCGCA
1 TCGCA
41911 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 8, Indels: 21
0.76 0.07 0.18
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 12 0.13
19 36 0.40
20 12 0.13
21 1 0.01
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (18 bp):
TCGCAACGCGAAACAAAA
Found at i:41858 original size:14 final size:13
Alignment explanation
Indices: 41838--41894 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 13
41828 CGCGAAATGA
41838 AAATCGCAACGAC
1 AAATCGCAACGAC
41851 AGAATCGCAACGCGAAAC
1 A-AATCGCAA--CG--AC
41869 AAAATCGCAACGAC
1 -AAATCGCAACGAC
41883 AAGATCGCAACG
1 AA-ATCGCAACG
41895 CGAAACCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 13
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.08
14 19 0.51
16 4 0.11
18 10 0.27
19 1 0.03
ACGTcount: A:0.46, C:0.28, G:0.19, T:0.07
Consensus pattern (13 bp):
AAATCGCAACGAC
Found at i:41878 original size:32 final size:32
Alignment explanation
Indices: 41819--41910 Score: 141
Period size: 32 Copynumber: 2.8 Consensus size: 32
41809 CGCGAAACCA
**
41819 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
41851 AGAATCGCAACGCGAAA-CAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
41883 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
41911 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
31 1 0.02
32 30 0.54
33 25 0.45
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:41928 original size:19 final size:19
Alignment explanation
Indices: 41906--42040 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
41896 GAAACCAAAA
*
41906 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
41925 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
41941 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
41958 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
41974 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
41991 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
42010 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
42030 TCGTGTTGCGA
1 TCGCGTTGCGA
42041 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:41947 original size:14 final size:14
Alignment explanation
Indices: 41928--41984 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
41918 TTTCATTTCG
41928 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
41942 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
41959 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
41975 CGTTGCGATT
1 CGTTGCGATT
41985 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:41953 original size:33 final size:33
Alignment explanation
Indices: 41911--42003 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
41901 CAAAATCGCA
*
41911 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
41944 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
41977 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
42004 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:43893 original size:38 final size:38
Alignment explanation
Indices: 43850--43922 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
43840 AATTGATTGT
*
43850 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
43888 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
43923 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:43909 original size:19 final size:19
Alignment explanation
Indices: 43845--43909 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
43835 AGTTTAATTG
*
43845 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
43864 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
43882 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
43902 ATTGATTT
1 ATTGATTT
43910 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:43923 original size:14 final size:14
Alignment explanation
Indices: 43904--43939 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
43894 ATTGTTTAAT
43904 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
43918 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
43932 TGATTTGT
1 TGATTTGT
43940 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:44062 original size:19 final size:19
Alignment explanation
Indices: 44046--44147 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
44036 AAAAATGACT
44046 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
44065 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
44084 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
44098 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
44117 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
44137 ATCGCAATGCG
1 ATCGCAATGCG
44148 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:44200 original size:19 final size:19
Alignment explanation
Indices: 44176--44500 Score: 396
Period size: 19 Copynumber: 18.4 Consensus size: 19
44166 GATTATCTCG
44176 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
44195 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
44214 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
44228 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
44247 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
44266 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
44285 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
44304 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
44323 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
44337 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
44356 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
44375 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
44389 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
44408 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
44427 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
44441 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
44461 TTGCGA-TTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
44474 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
44493 TTGCGATT
1 TTGCGATT
44501 GTATTTTCCG
Statistics
Matches: 267, Mismatches: 12, Indels: 54
0.80 0.04 0.16
Matches are distributed among these distances:
13 5 0.02
14 29 0.11
15 1 0.00
16 30 0.11
17 29 0.11
18 2 0.01
19 165 0.62
20 6 0.02
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:44251 original size:71 final size:72
Alignment explanation
Indices: 44176--44500 Score: 380
Period size: 71 Copynumber: 4.6 Consensus size: 72
44166 GATTATCTCG
44176 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
44240 TTTCGCA
66 TTTCGCA
* *
44247 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG-ATTGCGATT
44312 TTCATTTCGCA
62 TTCATTTCGCA
*
44323 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG-ATTGCGATT
*
44381 TTC-TCTCG--
62 TTCATTTCGCA
*
44389 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
44453 TTTCCGCA
66 TTT-CGCA
* *
44461 TTGCGA-TTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
44501 GTATTTTCCG
Statistics
Matches: 226, Mismatches: 11, Indels: 39
0.82 0.04 0.14
Matches are distributed among these distances:
66 37 0.16
68 15 0.07
69 13 0.06
70 2 0.01
71 114 0.50
72 6 0.03
73 6 0.03
74 8 0.04
76 25 0.11
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (72 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
TTTCGCA
Found at i:44419 original size:161 final size:157
Alignment explanation
Indices: 44154--44469 Score: 544
Period size: 161 Copynumber: 2.0 Consensus size: 157
44144 TGCGTTTATA
44154 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
* *
44219 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGT
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
44284 ATTGCGATTTTAATTT-CGCATTGCGATTTTC
127 -TTGCGATTTTAATTTCCGCATTGCGATTTTC
*
44315 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
44380 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
44445 GATTTTCATTTCCGCATTGCGATTT
131 GATTTTAATTTCCGCATTGCGATTT
44470 CATGTTGGGA
Statistics
Matches: 150, Mismatches: 4, Indels: 6
0.94 0.03 0.04
Matches are distributed among these distances:
156 14 0.09
157 13 0.09
158 4 0.03
159 3 0.02
161 116 0.77
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (157 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
GATTTTAATTTCCGCATTGCGATTTTC
Found at i:44445 original size:33 final size:33
Alignment explanation
Indices: 44195--44500 Score: 280
Period size: 33 Copynumber: 8.8 Consensus size: 33
44185 TCATTTCGCA
*
44195 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
44228 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
44264 CATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
44302 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
44337 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
44373 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
44408 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
44441 TTGCGATTTTCATTTCCGCATTGCGATT-TCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
44474 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
44501 GTATTTTCCG
Statistics
Matches: 235, Mismatches: 19, Indels: 39
0.80 0.06 0.13
Matches are distributed among these distances:
31 9 0.04
32 16 0.07
33 93 0.40
34 13 0.06
35 12 0.05
36 11 0.05
37 2 0.01
38 67 0.29
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:44510 original size:52 final size:52
Alignment explanation
Indices: 44154--44469 Score: 542
Period size: 52 Copynumber: 6.0 Consensus size: 52
44144 TGCGTTTATA
*
44154 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
44206 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
44258 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
44315 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
44367 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
44419 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTT
44470 CATGTTGGGA
Statistics
Matches: 253, Mismatches: 5, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
52 182 0.72
53 13 0.05
54 7 0.03
55 8 0.03
57 43 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:47022 original size:24 final size:24
Alignment explanation
Indices: 46988--47034 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
46978 CTGAAACATC
46988 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
47012 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
47035 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:47725 original size:20 final size:20
Alignment explanation
Indices: 47697--48063 Score: 440
Period size: 20 Copynumber: 18.4 Consensus size: 20
47687 AAATTTCAGT
* * * *
47697 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
47717 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
47737 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
47757 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
47777 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
47797 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
47817 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
47837 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
47857 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
47877 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
47897 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
47917 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
47937 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
47957 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
47977 GTTGCGA-TTACGGATACAC
1 GTTGCGATTTACGGATACGC
47996 GTTGCGATTTACGGATA-GC
1 GTTGCGATTTACGGATACGC
* *
48015 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
48035 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
48055 GTTGCGATT
1 GTTGCGATT
48064 ATGGAAAATC
Statistics
Matches: 305, Mismatches: 32, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
19 35 0.11
20 266 0.87
21 4 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:56270 original size:104 final size:106
Alignment explanation
Indices: 56134--56342 Score: 309
Period size: 104 Copynumber: 2.0 Consensus size: 106
56124 TAAAACATAT
56134 ACAGTTTTAATGCCAATAAGCAACCAATTATCAGAATCATC-ATGAGAAAGCAAATGCACCCACC
1 ACAGTTTTAATGCCAATAAGCAACCAATTATCAGAATCATCTATGAGAAAGCAAATGCA-CCACC
* *
56198 CTGG-TAATTTAGGAACTAAAT-GA-ATTTACTTTCAATCAA
65 CTGGCAAATTTAGGAACTAAATAAATATTTACTTTCAATCAA
* **
56237 ACAGTTTTCAGTGCCAATAAGCAACCAATTATCAGAATGGTCTATGAGAAAGCAAATGCACCACC
1 ACAGTTTT-AATGCCAATAAGCAACCAATTATCAGAATCATCTATGAGAAAGCAAATGCACCACC
* *
56302 CTGGCAAATTTGGGAACTAAATAAATATTTCCTTTCAATCA
65 CTGGCAAATTTAGGAACTAAATAAATATTTACTTTCAATCA
56343 TCTATATAGA
Statistics
Matches: 94, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
103 8 0.09
104 39 0.41
105 32 0.34
106 1 0.01
107 14 0.15
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (106 bp):
ACAGTTTTAATGCCAATAAGCAACCAATTATCAGAATCATCTATGAGAAAGCAAATGCACCACCC
TGGCAAATTTAGGAACTAAATAAATATTTACTTTCAATCAA
Done.