Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013638.1 Corchorus capsularis cultivar CVL-1 contig13659, 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: 146201
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:18696 original size:2 final size:2
Alignment explanation
Indices: 18689--18713 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18679 TTACATAAAC
18689 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
18714 ATGGGTAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:27538 original size:19 final size:18
Alignment explanation
Indices: 27514--27560 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
27504 CTGACGTGGC
*
27514 AATGCCACGTCGGACAAAA
1 AATGCCACATCGGAC-AAA
* *
27533 AATGCCACATTGGACCAA
1 AATGCCACATCGGACAAA
27551 AATGCCACAT
1 AATGCCACAT
27561 GGTAAGGTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.40, C:0.28, G:0.17, T:0.15
Consensus pattern (18 bp):
AATGCCACATCGGACAAA
Found at i:39557 original size:12 final size:12
Alignment explanation
Indices: 39540--39564 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39530 CAACCTTAAC
39540 ACACACACACAT
1 ACACACACACAT
39552 ACACACACACAT
1 ACACACACACAT
39564 A
1 A
39565 TATATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.40, G:0.00, T:0.08
Consensus pattern (12 bp):
ACACACACACAT
Found at i:40055 original size:15 final size:15
Alignment explanation
Indices: 40035--40065 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40025 TCATTAATCA
40035 ATAATCAGAGATTAC
1 ATAATCAGAGATTAC
40050 ATAATCAGAGATTAC
1 ATAATCAGAGATTAC
40065 A
1 A
40066 AACGTCGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (15 bp):
ATAATCAGAGATTAC
Found at i:40219 original size:20 final size:20
Alignment explanation
Indices: 40196--40238 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
40186 TAAATTACAA
40196 AGAA-AACTCACAATTCCGTG
1 AGAATAACTCAC-ATTCCGTG
40216 AGAATAACTCACATTCCGTG
1 AGAATAACTCACATTCCGTG
40236 AGA
1 AGA
40239 GTAGAACCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (20 bp):
AGAATAACTCACATTCCGTG
Found at i:40359 original size:15 final size:15
Alignment explanation
Indices: 40339--40367 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40329 TCATTAATCA
40339 ATAATCAGAGATTAC
1 ATAATCAGAGATTAC
40354 ATAATCAGAGATTA
1 ATAATCAGAGATTA
40368 TAAACACCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (15 bp):
ATAATCAGAGATTAC
Found at i:41506 original size:22 final size:20
Alignment explanation
Indices: 41471--41514 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
41461 GTAAGGGCTC
41471 TAAAACACAATTTAAATAAAT
1 TAAAACACAATTT-AATAAAT
* *
41492 TAAAATACATATTTAGTAAAT
1 TAAAACACA-ATTTAATAAAT
41513 TA
1 TA
41515 TGATATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (20 bp):
TAAAACACAATTTAATAAAT
Found at i:43783 original size:1 final size:1
Alignment explanation
Indices: 43779--43806 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
43769 TATTTTTCTT
43779 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
43807 CCCCATGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:47857 original size:61 final size:61
Alignment explanation
Indices: 47762--47996 Score: 355
Period size: 61 Copynumber: 3.9 Consensus size: 61
47752 TATTTTGTTA
* * *
47762 GGAAGTTTCAAACGTACACCTACTATTCCCGCCAAACTATATATAAAATGAACGGATGCTG
1 GGAAGTTTCAAACGTACACCTGCTATTCCCGCCAATCTACATATAAAATGAACGGATGCTG
* * ** *
47823 GGAAGTTTCAAACGTACATCTGCTATTCCCGCCAATCTACATACAAAATGAATAGATG-TCA
1 GGAAGTTTCAAACGTACACCTGCTATTCCCGCCAATCTACATATAAAATGAACGGATGCT-G
* * *
47884 GGAAGTTTCAAACGTACACTTGCTATTCCCTCCAATCTACATATAAAATGAACGGATGCCG
1 GGAAGTTTCAAACGTACACCTGCTATTCCCGCCAATCTACATATAAAATGAACGGATGCTG
47945 GGAAGTTTCAAACGTACACCTGCTATTCCCGCCAATCTACATATAAAATGAA
1 GGAAGTTTCAAACGTACACCTGCTATTCCCGCCAATCTACATATAAAATGAA
47997 TCCGTTCTAT
Statistics
Matches: 154, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
60 1 0.01
61 153 0.99
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (61 bp):
GGAAGTTTCAAACGTACACCTGCTATTCCCGCCAATCTACATATAAAATGAACGGATGCTG
Found at i:47978 original size:122 final size:122
Alignment explanation
Indices: 47761--47997 Score: 402
Period size: 122 Copynumber: 1.9 Consensus size: 122
47751 GTATTTTGTT
* *
47761 AGGAAGTTTCAAACGTACACCTACTATTCCCGCCAAACTATATATAAAATGAACGGATGCTGGGA
1 AGGAAGTTTCAAACGTACACCTACTATTCCCGCCAAACTACATATAAAATGAACGGATGCCGGGA
*
47826 AGTTTCAAACGTACATCTGCTATTCCCGCCAATCTACATACAAAATGAATAGATGTC
66 AGTTTCAAACGTACACCTGCTATTCCCGCCAATCTACATACAAAATGAATAGATGTC
* * * *
47883 AGGAAGTTTCAAACGTACACTTGCTATTCCCTCCAATCTACATATAAAATGAACGGATGCCGGGA
1 AGGAAGTTTCAAACGTACACCTACTATTCCCGCCAAACTACATATAAAATGAACGGATGCCGGGA
*
47948 AGTTTCAAACGTACACCTGCTATTCCCGCCAATCTACATATAAAATGAAT
66 AGTTTCAAACGTACACCTGCTATTCCCGCCAATCTACATACAAAATGAAT
47998 CCGTTCTATC
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
122 107 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (122 bp):
AGGAAGTTTCAAACGTACACCTACTATTCCCGCCAAACTACATATAAAATGAACGGATGCCGGGA
AGTTTCAAACGTACACCTGCTATTCCCGCCAATCTACATACAAAATGAATAGATGTC
Found at i:49118 original size:44 final size:40
Alignment explanation
Indices: 49031--49119 Score: 99
Period size: 44 Copynumber: 2.1 Consensus size: 40
49021 AGGTATAGAA
* * *
49031 TATGATATGATGGAAAATGATGGAATTAGGAAAGAAACAT
1 TATGATATGATGAAAAATGATGAAATTAGGAAAGAAAAAT
49071 TATGATGATGATGAAAAATGTATGAAATTTTAGGAGAA-AAAAAT
1 TATGAT-ATGATGAAAAATG-ATGAAA--TTAGGA-AAGAAAAAT
49115 TATGA
1 TATGA
49120 AAGAAATGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
40 6 0.15
41 12 0.29
42 5 0.12
44 16 0.39
45 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.22, T:0.28
Consensus pattern (40 bp):
TATGATATGATGAAAAATGATGAAATTAGGAAAGAAAAAT
Found at i:49404 original size:3 final size:3
Alignment explanation
Indices: 49358--49389 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
49348 AACAATCTCC
49358 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
49390 CTTAATACTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:59397 original size:95 final size:98
Alignment explanation
Indices: 59255--59491 Score: 318
Period size: 95 Copynumber: 2.4 Consensus size: 98
59245 TATCGCTAAA
* * *
59255 AAAAACTTCATCTCCAATCGCAGAGCCGTTATGTCTAACCAATATTTGCTGCCACATGTAACTCT
1 AAAAAGTTCATCTTCGATCGCAGAGCCGTTATGTCTAACCAATATTTGCTGCCACATGTAACTCT
59320 GTTCCCT-A-A-TAAGATCCTATTATTGTCGGT
66 GTTCCCTAATATTAAGATCCTATTATTGTCGGT
* *
59350 AAAAAGTTCATCTTTGATCGCAGAGCCGTTATGTCTAACCAATATTTGCTGCCATATGTAACTCT
1 AAAAAGTTCATCTTCGATCGCAGAGCCGTTATGTCTAACCAATATTTGCTGCCACATGTAACTCT
59415 GTTCCCTAATAGTTGGTTTTTAAGATCCTATTATTGTCGGT
66 GTTCCCTAATA--------TTAAGATCCTATTATTGTCGGT
*
59456 AAAAAGTTCATCTTCGATCGAAGAGCCGTTAATGTC
1 AAAAAGTTCATCTTCGATCGCAGAGCCGTT-ATGTC
59492 CAACAAATTC
Statistics
Matches: 123, Mismatches: 7, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
95 67 0.54
96 1 0.01
97 1 0.01
106 49 0.40
107 5 0.04
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.35
Consensus pattern (98 bp):
AAAAAGTTCATCTTCGATCGCAGAGCCGTTATGTCTAACCAATATTTGCTGCCACATGTAACTCT
GTTCCCTAATATTAAGATCCTATTATTGTCGGT
Found at i:64764 original size:2 final size:2
Alignment explanation
Indices: 64757--64782 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
64747 AAATTTCCTC
64757 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
64783 GTAATAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66733 original size:17 final size:17
Alignment explanation
Indices: 66711--66747 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
66701 CTTGGATAAC
66711 ATGAAGAAAAGTTGTCA
1 ATGAAGAAAAGTTGTCA
66728 ATGAAGAAAAGTTGTCA
1 ATGAAGAAAAGTTGTCA
66745 ATG
1 ATG
66748 GATCCAAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.24
Consensus pattern (17 bp):
ATGAAGAAAAGTTGTCA
Found at i:67278 original size:7 final size:7
Alignment explanation
Indices: 67263--67293 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
67253 ATGATAGAGA
67263 GAGTAAG
1 GAGTAAG
*
67270 GACTAAG
1 GAGTAAG
67277 GAGTAAG
1 GAGTAAG
67284 GAGTAAG
1 GAGTAAG
67291 GAG
1 GAG
67294 GAGGAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.42, C:0.03, G:0.42, T:0.13
Consensus pattern (7 bp):
GAGTAAG
Found at i:83310 original size:16 final size:17
Alignment explanation
Indices: 83289--83320 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
83279 GGATTAATTC
83289 TAATTAATTAA-GTAAA
1 TAATTAATTAATGTAAA
83305 TAATTAATTAATGTAA
1 TAATTAATTAATGTAA
83321 TGTAATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
TAATTAATTAATGTAAA
Found at i:87272 original size:118 final size:118
Alignment explanation
Indices: 87064--87301 Score: 449
Period size: 118 Copynumber: 2.0 Consensus size: 118
87054 AAATCCCACC
* *
87064 ATGATGTGAAGTCCTGAGTTTGTGTTACGAGTTGATTCGGATACAAACTCAGTTTTTAAAAGATT
1 ATGATGTGAAGTCCTGAGTTTGTGTTAAGAGTTGATTCAGATACAAACTCAGTTTTTAAAAGATT
87129 AAAAACTACTCATTTGAAAATAAACCACCAATGATATATATAATAATTAATTT
66 AAAAACTACTCATTTGAAAATAAACCACCAATGATATATATAATAATTAATTT
*
87182 ATGATGTGAAGTCCTGAGTTTGTGTTAAGAGTTGATTTAGATACAAACTCAGTTTTTAAAAGATT
1 ATGATGTGAAGTCCTGAGTTTGTGTTAAGAGTTGATTCAGATACAAACTCAGTTTTTAAAAGATT
87247 AAAAACTACTCATTTGAAAATAAACCACCAATGATATATATAATAATTAATTT
66 AAAAACTACTCATTTGAAAATAAACCACCAATGATATATATAATAATTAATTT
87300 AT
1 AT
87302 CATTTAAAAA
Statistics
Matches: 117, Mismatches: 3, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
118 117 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (118 bp):
ATGATGTGAAGTCCTGAGTTTGTGTTAAGAGTTGATTCAGATACAAACTCAGTTTTTAAAAGATT
AAAAACTACTCATTTGAAAATAAACCACCAATGATATATATAATAATTAATTT
Found at i:92042 original size:13 final size:13
Alignment explanation
Indices: 92024--92049 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
92014 GAAATTACTA
92024 GTTAACAAAACAT
1 GTTAACAAAACAT
92037 GTTAACAAAACAT
1 GTTAACAAAACAT
92050 TAGCAAAATA
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:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (13 bp):
GTTAACAAAACAT
Found at i:93696 original size:17 final size:18
Alignment explanation
Indices: 93676--93710 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
93666 TTAATTTAGG
*
93676 ATTTTCTTTAA-AATTTT
1 ATTTTCTTCAATAATTTT
93693 ATTTTCTTCAATAATTTT
1 ATTTTCTTCAATAATTTT
93711 CCATTTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTCTTCAATAATTTT
Found at i:98097 original size:166 final size:163
Alignment explanation
Indices: 97630--98111 Score: 567
Period size: 166 Copynumber: 2.9 Consensus size: 163
97620 TGAGTCATTT
* *
97630 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTTAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTATTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACA-
* * * *
97695 TTTAA-TAATCTGCCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTAGTTTATCATCAATCCTT
64 TTTAAGTAATCTG-CAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTA-CTCATCATCAATCCTT
* * *
97759 GAT-GTGGATCTTTTATTAATTCCACTACTCTATTCAA
127 GGTAG-GGATCTTTTAGTAATTCCACTACTCTATTAAA
* *
97796 GTCCATTGAGAAATAACCAAAAAGATTACTTT-TTTAATCCCCTCAAGAATCAAAAGTTAGGACA
1 GTCAATTGAGAAATGACCAAAAAG-TTA-TTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACA
* * * ** * *
97860 -TTAAGTAATCTGCAAAGTAGGAAAAAACGAAAAAAATAAGTTTTCTAACTTCAAAAGCAAGCCT
64 TTTAAGTAATCTGC-AAGTAGGAAAAGACGAAAAAAATTAGTTCTCT-AC-TCATCATCAATCCT
*
97924 TGGTAGGGGTCTTTTAGTAATTCCACTACTCTATTAAA
126 TGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * * *
97962 GTCAATTGAGAAATGATCAAAAAGTCTATTTATTTAATCACCTCAAGAATCAAAAGTTGGGGCAT
1 GTCAATTGAGAAATGACCAAAAAGT-TATTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * **
98027 TTAAGTAATCGGTCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTCACTCCTCATTAATCCGGG
65 TTAAGTAATCTG-CAAGTAGGAAAAGACGAAAAAAATTAGTTCTCT-ACTCATCATCAATCCTTG
98092 GTAGGGATCTTTTAGTAATT
128 GTAGGGATCTTTTAGTAATT
98112 TTCATATGTT
Statistics
Matches: 266, Mismatches: 40, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
164 5 0.02
165 38 0.14
166 177 0.67
167 45 0.17
168 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (163 bp):
GTCAATTGAGAAATGACCAAAAAGTTATTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTACTCATCATCAATCCTTGGTA
GGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:98147 original size:2 final size:2
Alignment explanation
Indices: 98140--98172 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
98130 TAATATGTAG
98140 TA 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 TA T
98173 TATTAAAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:102732 original size:24 final size:24
Alignment explanation
Indices: 102676--102729 Score: 63
Period size: 29 Copynumber: 2.0 Consensus size: 24
102666 CCAAAAAGTA
102676 TTAGTATTTAATTAATGTAATGTTTTTT
1 TTAGTATTTAATTAATGTAATG----TT
102704 TTAGTAGTTTAATTAATGTAATGTT
1 TTAGTA-TTTAATTAATGTAATGTT
102729 T
1 T
102730 AGTCAGGGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 3 0.12
28 6 0.24
29 16 0.64
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (24 bp):
TTAGTATTTAATTAATGTAATGTT
Found at i:105171 original size:57 final size:57
Alignment explanation
Indices: 105101--105216 Score: 214
Period size: 57 Copynumber: 2.0 Consensus size: 57
105091 TTATTGAATC
* *
105101 AATGAAAATTTACAAACAATCTGGCTTACTATACAATTTTGTTTACAAAATATCCTT
1 AATGAAAATTTACAAACAAACTGGCTTACTATACAATTTTGTTCACAAAATATCCTT
105158 AATGAAAATTTACAAACAAACTGGCTTACTATACAATTTTGTTCACAAAATATCCTT
1 AATGAAAATTTACAAACAAACTGGCTTACTATACAATTTTGTTCACAAAATATCCTT
105215 AA
1 AA
105217 AAAAAAGGTA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.34
Consensus pattern (57 bp):
AATGAAAATTTACAAACAAACTGGCTTACTATACAATTTTGTTCACAAAATATCCTT
Found at i:105977 original size:16 final size:17
Alignment explanation
Indices: 105956--105989 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
105946 CGGCCATTTC
105956 TTTT-GGCGTGCTTAAT
1 TTTTGGGCGTGCTTAAT
105972 TTTTGGGCGTGCTTAAT
1 TTTTGGGCGTGCTTAAT
105989 T
1 T
105990 ACCACATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.12, C:0.12, G:0.26, T:0.50
Consensus pattern (17 bp):
TTTTGGGCGTGCTTAAT
Found at i:108437 original size:22 final size:22
Alignment explanation
Indices: 108412--108453 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
108402 ATATATGTAC
*
108412 ATATAATAATATTAATATTAAT
1 ATATAATAATAATAATATTAAT
* *
108434 ATATATTAATAATATTATTA
1 ATATAATAATAATAATATTA
108454 TTATTATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATAATAATAATAATATTAAT
Found at i:108448 original size:19 final size:18
Alignment explanation
Indices: 108424--108459 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
108414 ATAATAATAT
108424 TAATATTAATATATATTAA
1 TAATATTAATAT-TATTAA
*
108443 TAATATTATTATTATTA
1 TAATATTAATATTATTA
108460 TTAAAATGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATATTAATATTATTAA
Found at i:108458 original size:9 final size:9
Alignment explanation
Indices: 108415--108463 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
108405 TATGTACATA
*
108415 TAATAATAT
1 TAATATTAT
*
108424 TAATATTAA
1 TAATATTAT
*
108433 TATATATTAA
1 TA-ATATTAT
108443 TAATATTAT
1 TAATATTAT
*
108452 TATTATTAT
1 TAATATTAT
108461 TAA
1 TAA
108464 AATGTCAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
9 25 0.74
10 9 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TAATATTAT
Found at i:117338 original size:49 final size:49
Alignment explanation
Indices: 117261--117356 Score: 147
Period size: 49 Copynumber: 2.0 Consensus size: 49
117251 AGTGCATTCT
* **
117261 TTTACTTTTCCTTGCACATTTTTCTCAATTTTTACAACAAAATTGAATC
1 TTTAATTTTCCTTGCACATTTTAATCAATTTTTACAACAAAATTGAATC
* *
117310 TTTAATTTTCCTTGCACCTTTTAATCAATTTTTATAACAAAATTGAA
1 TTTAATTTTCCTTGCACATTTTAATCAATTTTTACAACAAAATTGAA
117357 AACTAACAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.31, C:0.18, G:0.04, T:0.47
Consensus pattern (49 bp):
TTTAATTTTCCTTGCACATTTTAATCAATTTTTACAACAAAATTGAATC
Found at i:117930 original size:265 final size:265
Alignment explanation
Indices: 117453--117944 Score: 815
Period size: 265 Copynumber: 1.9 Consensus size: 265
117443 TCAACAACCT
* *
117453 CAACCTCATCATCATCAGAAATGGCTACCTCATTACCTATAACAAATTTACTTCATTACTGATCA
1 CAACCTCAACATCATCAGAAATGGCTACCTCATTACCTATAACAAATTTACTTCATTACCGATCA
* * *
117518 GAAGGGATGCAAACGCGAAGACTAACTTTTTGCTCCAAAAAATGATAAACTAATAGTGCATTTAC
66 GAAGGGATGCAAACGCGAAGACTAACTGTTTGCTCCAAAAAAGGATAAACTAATAGTGCACTTAC
* *
117583 CAGCATCCTCTTCATCCATGGGGTCCTCCCAATATTGCTTGACCCTCTTCTCTTCTTTCCTATCT
131 CAGCATCCTCTTCATCCATGGGGTCCTCCCAACATTGCTTGACCCTCTTCTCTTCTTTCCCATCT
* *
117648 TCGCGGTCCTTGTCCGAGAAGGATCTCATAGGGTTGTTTTTGGCTTGATTAGCAACCTCTTCATC
196 TCACGGTCCTCGTCCGAGAAGGATCTCATAGGGTTGTTTTTGGCTTGATTAGCAACCTCTTCATC
117713 ATCAG
261 ATCAG
* *
117718 CAACCTCAACCTCATTAGAAAT-GCGTACCTCATTACCTATAACAAATTTACTTCATTACCGATC
1 CAACCTCAACATCATCAGAAATGGC-TACCTCATTACCTATAACAAATTTACTTCATTACCGATC
*
117782 AGAAGGGATGCAAACGCGAAGACTAACTGTTTGCTCCAAAAAAGGATAAACTAATAGTGTACTTA
65 AGAAGGGATGCAAACGCGAAGACTAACTGTTTGCTCCAAAAAAGGATAAACTAATAGTGCACTTA
* * * *
117847 CTAGCATCCTCTTCATCCGTGGGGTCCTCCCAGCATTGCTTGACTCTCTTCTCTTCTTTCCCATC
130 CCAGCATCCTCTTCATCCATGGGGTCCTCCCAACATTGCTTGACCCTCTTCTCTTCTTTCCCATC
*
117912 TTCATGGTCCTCGTCCGAGAAGGATCTCATAGG
195 TTCACGGTCCTCGTCCGAGAAGGATCTCATAGG
117945 ATACTCCTTC
Statistics
Matches: 209, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
264 2 0.01
265 207 0.99
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (265 bp):
CAACCTCAACATCATCAGAAATGGCTACCTCATTACCTATAACAAATTTACTTCATTACCGATCA
GAAGGGATGCAAACGCGAAGACTAACTGTTTGCTCCAAAAAAGGATAAACTAATAGTGCACTTAC
CAGCATCCTCTTCATCCATGGGGTCCTCCCAACATTGCTTGACCCTCTTCTCTTCTTTCCCATCT
TCACGGTCCTCGTCCGAGAAGGATCTCATAGGGTTGTTTTTGGCTTGATTAGCAACCTCTTCATC
ATCAG
Found at i:118600 original size:27 final size:27
Alignment explanation
Indices: 118559--118613 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
118549 AATTTTATAA
* *
118559 TGAAATTGAACAGAGATGATAGATTCT
1 TGAAATTAAAAAGAGATGATAGATTCT
*
118586 TGAAATTAAAAAGAGGTGATAGATTCT
1 TGAAATTAAAAAGAGATGATAGATTCT
118613 T
1 T
118614 CAAAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.31
Consensus pattern (27 bp):
TGAAATTAAAAAGAGATGATAGATTCT
Found at i:118623 original size:27 final size:27
Alignment explanation
Indices: 118570--118624 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
118560 GAAATTGAAC
* **
118570 AGAGATGATAGATTCTTGAAATTAAAA
1 AGAGATGATAGATTCTTCAAAAAAAAA
*
118597 AGAGGTGATAGATTCTTCAAAAAAAAA
1 AGAGATGATAGATTCTTCAAAAAAAAA
118624 A
1 A
118625 TTCTCCCATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.25
Consensus pattern (27 bp):
AGAGATGATAGATTCTTCAAAAAAAAA
Found at i:120647 original size:2 final size:2
Alignment explanation
Indices: 120635--120679 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
120625 CCGGTGTATC
*
120635 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
120675 AT AT A
1 AT AT A
120680 AAATTTGGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:123056 original size:16 final size:16
Alignment explanation
Indices: 123032--123067 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
123022 CACCAAAATC
*
123032 ATTTTTCAGATTCAGT
1 ATTTATCAGATTCAGT
123048 ATTTATCAGATTCAGT
1 ATTTATCAGATTCAGT
123064 ATTT
1 ATTT
123068 GTTTATCTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (16 bp):
ATTTATCAGATTCAGT
Found at i:124089 original size:2 final size:2
Alignment explanation
Indices: 124082--124107 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
124072 GGAATACGAA
124082 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
124108 CCATTTTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:133651 original size:249 final size:249
Alignment explanation
Indices: 133213--133712 Score: 1000
Period size: 249 Copynumber: 2.0 Consensus size: 249
133203 AACTTCATCA
133213 AGTTTTTCACCAGCTAGCCACTGTGTTTTTTCAGTTGGCCTTTTTCTCTTATCTCATGGTTGTTG
1 AGTTTTTCACCAGCTAGCCACTGTGTTTTTTCAGTTGGCCTTTTTCTCTTATCTCATGGTTGTTG
133278 CTTTCTAGTCAACTTCCAAGTCACATTCATTATTATTAATCTATTATGCATATGCTTTTAAAATA
66 CTTTCTAGTCAACTTCCAAGTCACATTCATTATTATTAATCTATTATGCATATGCTTTTAAAATA
133343 TTATTACTACTTCAATAATATTTATTCCTGTACTTAGTTTAACAATTTGTCAGCTGATAATTATA
131 TTATTACTACTTCAATAATATTTATTCCTGTACTTAGTTTAACAATTTGTCAGCTGATAATTATA
133408 ATTTATTTCTTACCTACAATATTCTTCAAGTTCATTTAACAAAATTGAAAAACG
196 ATTTATTTCTTACCTACAATATTCTTCAAGTTCATTTAACAAAATTGAAAAACG
133462 AGTTTTTCACCAGCTAGCCACTGTGTTTTTTCAGTTGGCCTTTTTCTCTTATCTCATGGTTGTTG
1 AGTTTTTCACCAGCTAGCCACTGTGTTTTTTCAGTTGGCCTTTTTCTCTTATCTCATGGTTGTTG
133527 CTTTCTAGTCAACTTCCAAGTCACATTCATTATTATTAATCTATTATGCATATGCTTTTAAAATA
66 CTTTCTAGTCAACTTCCAAGTCACATTCATTATTATTAATCTATTATGCATATGCTTTTAAAATA
133592 TTATTACTACTTCAATAATATTTATTCCTGTACTTAGTTTAACAATTTGTCAGCTGATAATTATA
131 TTATTACTACTTCAATAATATTTATTCCTGTACTTAGTTTAACAATTTGTCAGCTGATAATTATA
133657 ATTTATTTCTTACCTACAATATTCTTCAAGTTCATTTAACAAAATTGAAAAACG
196 ATTTATTTCTTACCTACAATATTCTTCAAGTTCATTTAACAAAATTGAAAAACG
133711 AG
1 AG
133713 AGAGGGGGAA
Statistics
Matches: 251, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
249 251 1.00
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.44
Consensus pattern (249 bp):
AGTTTTTCACCAGCTAGCCACTGTGTTTTTTCAGTTGGCCTTTTTCTCTTATCTCATGGTTGTTG
CTTTCTAGTCAACTTCCAAGTCACATTCATTATTATTAATCTATTATGCATATGCTTTTAAAATA
TTATTACTACTTCAATAATATTTATTCCTGTACTTAGTTTAACAATTTGTCAGCTGATAATTATA
ATTTATTTCTTACCTACAATATTCTTCAAGTTCATTTAACAAAATTGAAAAACG
Done.