Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013553.1 Corchorus olitorius cultivar O-4 contig13586, 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: 75206
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1501 original size:2 final size:2
Alignment explanation
Indices: 1494--1537 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1484 ATTTTAGGTA
*
1494 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1536 AT
1 AT
1538 TGTAGAGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3721 original size:39 final size:39
Alignment explanation
Indices: 3649--3723 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
3639 CGTAACAAGG
* *
3649 CAGACACGATGGTACACGAGATAACACATGAAGACACGA
1 CAGACACGAAGGTACACGAGATAACACAGGAAGACACGA
*
3688 CAGACACGAAGGTACACGAGA-AGACAGAGGAAGACA
1 CAGACACGAAGGTACACGAGATA-ACACAGGAAGACA
3724 GAGGCCTCCG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 1 0.03
39 31 0.97
ACGTcount: A:0.45, C:0.21, G:0.27, T:0.07
Consensus pattern (39 bp):
CAGACACGAAGGTACACGAGATAACACAGGAAGACACGA
Found at i:3789 original size:62 final size:62
Alignment explanation
Indices: 3692--4153 Score: 822
Period size: 62 Copynumber: 7.5 Consensus size: 62
3682 ACACGACAGA
*
3692 CACGAAGGTACACGAGAAGACAGAGGAA-GACAGAGGCCTCCGCAGGAGGCGAGGCCAGCAAG
1 CACGAAGGTACACGAGAAGACAGAGGAAGGA-AGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
* * * *
3754 CACGAAAGTACACGATAAAACAGAGGAAGGAAGAGGCCTCCGCAGGAGGTGAGGCCAGCAGG
1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
*
3816 CACGAAGGTACACGAGAAGACAGAGGAAAGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
*
3878 CACGGAA-GTACACGAGAAGACACAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
1 CAC-GAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
3940 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
4002 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
4064 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
4126 CACGAAGGT-CACGAGAAGACAGAGGAAG
1 CACGAAGGTACACGAGAAGACAGAGGAAG
4154 ACAGACACGA
Statistics
Matches: 384, Mismatches: 13, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
61 22 0.06
62 357 0.93
63 5 0.01
ACGTcount: A:0.35, C:0.23, G:0.39, T:0.04
Consensus pattern (62 bp):
CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
Found at i:4178 original size:34 final size:34
Alignment explanation
Indices: 4126--4248 Score: 221
Period size: 34 Copynumber: 3.6 Consensus size: 34
4116 GGCCAGCAGG
4126 CACGAAGGT-CACGAGAAGACAGAGGAAGACAGA
1 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
*
4159 CACGAAGGTAAACGAGAAGACAGAGGAAGACAGA
1 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
4193 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
1 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
*
4227 CAAGAAGGTACACGAGAAGACA
1 CACGAAGGTACACGAGAAGACA
4249 CAGTGGTGCT
Statistics
Matches: 86, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
33 9 0.10
34 77 0.90
ACGTcount: A:0.48, C:0.17, G:0.32, T:0.03
Consensus pattern (34 bp):
CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
Found at i:4365 original size:2 final size:2
Alignment explanation
Indices: 4360--4391 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4350 ACACACACAC
4360 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4392 GTAGGAAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5146 original size:44 final size:45
Alignment explanation
Indices: 5096--5204 Score: 148
Period size: 45 Copynumber: 2.4 Consensus size: 45
5086 TGAAAACATG
* *
5096 AAGGAGATCAAGGAAAG-TTAGAATCCATGACTGCCAAATGCTTT
1 AAGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTT
* * ** *
5140 AAGGAGATCAAAGAGAGCTTTGGCCCCATGATTGCCAAATGCTTT
1 AAGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTT
5185 AAGGAGATCAAAGAAAGCTT
1 AAGGAGATCAAAGAAAGCTT
5205 TAGCTCCATG
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 15 0.27
45 41 0.73
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.22
Consensus pattern (45 bp):
AAGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTT
Found at i:5176 original size:45 final size:45
Alignment explanation
Indices: 5120--5220 Score: 166
Period size: 45 Copynumber: 2.2 Consensus size: 45
5110 AAGTTAGAAT
* * *
5120 CCATGACTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
1 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAAAGCTTTAGCC
*
5165 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAAAGCTTTAGCT
1 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAAAGCTTTAGCC
5210 CCATGATTGCC
1 CCATGATTGCC
5221 GAGTGCACAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (45 bp):
CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAAAGCTTTAGCC
Found at i:10287 original size:1 final size:1
Alignment explanation
Indices: 10281--10307 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
10271 TTGTTGATTT
10281 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
10308 CCATCCTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19267 original size:81 final size:82
Alignment explanation
Indices: 19128--19283 Score: 226
Period size: 81 Copynumber: 1.9 Consensus size: 82
19118 GTTTGGTAGG
* * * *
19128 ATTGTAGGGAATGAAATAGGTAAAAAAATGAAATAGTAAGGGAAGGAAGGAAAGTTGTTTTCCTT
1 ATTGTAGGGAAAGAAAAAGGTAAAAAAATGAAATAGAAAAGG-AGGAAGGAAAGTTGTTTTCCTT
19193 CTTTTTGTTTAACGAAGA
65 CTTTTTGTTTAACGAAGA
* *
19211 ATTGTATGGAAAGAAAAAGGGTAAGAAAATGAAAT-GAAAAGG-GGAAGGAAAGTTGTTTTCCTT
1 ATTGTAGGGAAAGAAAAA-GGTAAAAAAATGAAATAGAAAAGGAGGAAGGAAAGTTGTTTTCCTT
19274 CTTTTTGTTT
65 CTTTTTGTTT
19284 GGTATATATA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
81 31 0.47
83 20 0.30
84 15 0.23
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.31
Consensus pattern (82 bp):
ATTGTAGGGAAAGAAAAAGGTAAAAAAATGAAATAGAAAAGGAGGAAGGAAAGTTGTTTTCCTTC
TTTTTGTTTAACGAAGA
Found at i:26940 original size:30 final size:29
Alignment explanation
Indices: 26906--26968 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 29
26896 TTTTATCTTA
26906 ACTTTCCCCTTATACTCTCAAATTTTAATG
1 ACTTTCCCCTTATAC-CTCAAATTTTAATG
* *
26936 ACTTTTCTCTTATACCTCAAATTTTAATG
1 ACTTTCCCCTTATACCTCAAATTTTAATG
26965 ACTT
1 ACTT
26969 ATTAACTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.27, C:0.24, G:0.03, T:0.46
Consensus pattern (29 bp):
ACTTTCCCCTTATACCTCAAATTTTAATG
Found at i:37228 original size:15 final size:15
Alignment explanation
Indices: 37198--37238 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
37188 AAAAAAACAT
37198 ATACTATACTATATATA
1 ATACTATA--ATATATA
37215 ATACTATAATATATA
1 ATACTATAATATATA
*
37230 AAACTATAA
1 ATACTATAA
37239 GCTACACGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 15 0.65
17 8 0.35
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (15 bp):
ATACTATAATATATA
Found at i:38231 original size:59 final size:60
Alignment explanation
Indices: 38147--38310 Score: 249
Period size: 59 Copynumber: 2.8 Consensus size: 60
38137 GCTAATTGCT
* *
38147 CAAATAAGGGTCTAACGTTTATCAAAATACTCAAATAAGGGTTTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGTCAAAATACTCAAATAAGGGTTTGATCTTTTAATTTGGC
* ***
38207 CAAATAAGGGCCTAATG-TTGTCAAAATACTCAAATAAGGGCCGGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGTCAAAATACTCAAATAAGGGTTTGATCTTTTAATTTGGC
* *
38266 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTTTG
1 CAAATAAGGGCCTAACGTTTGTCAAAATACTCAAATAAGGGTTTG
38311 GCGTCGAAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
59 54 0.59
60 37 0.41
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.30
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGTCAAAATACTCAAATAAGGGTTTGATCTTTTAATTTGGC
Found at i:38277 original size:29 final size:29
Alignment explanation
Indices: 38191--38277 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
38181 ATAAGGGTTT
*
38191 GATCTTTTAATTTGGCCAAATAAGGGCCT
1 GATCTTTTAATTTGGCCAAATAAGGGCCG
* * * ** *
38220 AATGTTGTCAAAAT-ACTCAAATAAGGGCCG
1 GATCTT-TTAATTTGGC-CAAATAAGGGCCG
38250 GATCTTTTAATTTGGCCAAATAAGGGCC
1 GATCTTTTAATTTGGCCAAATAAGGGCC
38278 TAACGTTTGC
Statistics
Matches: 42, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
29 21 0.50
30 21 0.50
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (29 bp):
GATCTTTTAATTTGGCCAAATAAGGGCCG
Found at i:38467 original size:29 final size:28
Alignment explanation
Indices: 38433--38535 Score: 93
Period size: 29 Copynumber: 3.5 Consensus size: 28
38423 TCAAAATGCT
*
38433 CAAATAAGGGCATGATCTTTTAATTTGGC
1 CAAATAAGGGCCT-ATCTTTTAATTTGGC
**
38462 CAAATAAGGGCCTAT-TGTTTGCCAAAAT-GC
1 CAAATAAGGGCCTATCT-TTT---AATTTGGC
*
38492 TCAAATAAGGGCCCAATCTTTTAATTTGGC
1 -CAAATAAGGG-CCTATCTTTTAATTTGGC
38522 CAAATAAGGGCCTA
1 CAAATAAGGGCCTA
38536 ACGTTTGCCA
Statistics
Matches: 59, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
27 1 0.02
28 8 0.14
29 25 0.42
30 4 0.07
31 13 0.22
32 7 0.12
33 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (28 bp):
CAAATAAGGGCCTATCTTTTAATTTGGC
Found at i:38500 original size:31 final size:31
Alignment explanation
Indices: 38388--38562 Score: 146
Period size: 31 Copynumber: 5.8 Consensus size: 31
38378 TAGGTCCTTA
* *
38388 TTTGCCAAAATGCTCAAACAAGGGTCTAATG
1 TTTGCCAAAATGCTCAAATAAGGGCCTAATG
* * * *
38419 TTTGTCAAAATGCTCAAATAAGGGCATGATC
1 TTTGCCAAAATGCTCAAATAAGGGCCTAATG
* ** *
38450 TTT--TAATTTGGC-CAAATAAGGGCCTATTG
1 TTTGCCAAAAT-GCTCAAATAAGGGCCTAATG
* *
38479 TTTGCCAAAATGCTCAAATAAGGGCCCAATC
1 TTTGCCAAAATGCTCAAATAAGGGCCTAATG
* ** *
38510 TTT--TAATTTGGC-CAAATAAGGGCCTAACG
1 TTTGCCAAAAT-GCTCAAATAAGGGCCTAATG
38539 TTTGCCAAAATGCTCAAATAAGGG
1 TTTGCCAAAATGCTCAAATAAGGG
38563 TTTGGCATCG
Statistics
Matches: 108, Mismatches: 28, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
29 39 0.36
30 8 0.07
31 61 0.56
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (31 bp):
TTTGCCAAAATGCTCAAATAAGGGCCTAATG
Found at i:38500 original size:60 final size:60
Alignment explanation
Indices: 38402--38562 Score: 250
Period size: 60 Copynumber: 2.7 Consensus size: 60
38392 CCAAAATGCT
* * * **
38402 CAAACAAGGGTCTAATGTTTGTCAAAATGCTCAAATAAGGGCATGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCACAATCTTTTAATTTGGC
* *
38462 CAAATAAGGGCCTATTGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGC
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCACAATCTTTTAATTTGGC
*
38522 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGG
38563 TTTGGCATCG
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 92 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (60 bp):
CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCACAATCTTTTAATTTGGC
Found at i:38599 original size:256 final size:255
Alignment explanation
Indices: 38143--38631 Score: 816
Period size: 256 Copynumber: 1.9 Consensus size: 255
38133 AAAGGCTAAT
* **
38143 TGCTCAAATAAGGGTCTAACGTTTATCAAAATACTCAAATAAGGGTTTGATCTTTTAATTTGGCC
1 TGCTCAAACAAGGGTCTAACGTTTATCAAAATACTCAAATAAGGGCATGATCTTTTAATTTGGCC
* **
38208 AAATAAGGGCCTAATGTTGTCAAAATACTCAAATAAGGGCCGGATCTTTTAATTTGGCCAAATAA
66 AAATAAGGGCCTAATGTTGCCAAAATACTCAAATAAGGGCCCAATCTTTTAATTTGGCCAAATAA
* *
38273 GGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTTTGGCGTCGAAAATTATCACCTATCATCGA
131 GGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTTTGGCATCGAAAATTATCACCTATCATCCA
* *
38338 AACTGATGACAGGCCCTTATTTGAGTATTTTCGATAACGTTAGGTCCTTATTTGCCAAAA
196 AACTGACGACAGGCCCTTATTTGAATATTTTCGATAACGTTAGGTCCTTATTTGCCAAAA
* * *
38398 TGCTCAAACAAGGGTCTAATGTTTGTCAAAATGCTCAAATAAGGGCATGATCTTTTAATTTGGCC
1 TGCTCAAACAAGGGTCTAACGTTTATCAAAATACTCAAATAAGGGCATGATCTTTTAATTTGGCC
* *
38463 AAATAAGGGCCTATTGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGCCAAATA
66 AAATAAGGGCCTAATG-TTGCCAAAATACTCAAATAAGGGCCCAATCTTTTAATTTGGCCAAATA
*
38528 AGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTTTGGCATCGAAAATTCTCACCTATCATCC
130 AGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTTTGGCATCGAAAATTATCACCTATCATCC
*
38593 AAACTGACGCCAGGCCCTTATTTGAATATTTTCGATAAC
195 AAACTGACGACAGGCCCTTATTTGAATATTTTCGATAAC
38632 ATTATACCCT
Statistics
Matches: 216, Mismatches: 17, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
255 74 0.34
256 142 0.66
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (255 bp):
TGCTCAAACAAGGGTCTAACGTTTATCAAAATACTCAAATAAGGGCATGATCTTTTAATTTGGCC
AAATAAGGGCCTAATGTTGCCAAAATACTCAAATAAGGGCCCAATCTTTTAATTTGGCCAAATAA
GGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTTTGGCATCGAAAATTATCACCTATCATCCA
AACTGACGACAGGCCCTTATTTGAATATTTTCGATAACGTTAGGTCCTTATTTGCCAAAA
Found at i:38645 original size:31 final size:31
Alignment explanation
Indices: 38607--38678 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
38597 TGACGCCAGG
* *
38607 CCCTTATTTGAATATTTTCGATAACATTATA
1 CCCTTATTTGAACATTTTCGATAACATTAGA
*
38638 CCCTTATTTGAGCATTTTCGATAACATTAGA
1 CCCTTATTTGAACATTTTCGATAACATTAGA
*
38669 CCCTTTTTTG
1 CCCTTATTTG
38679 GTCAAATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.44
Consensus pattern (31 bp):
CCCTTATTTGAACATTTTCGATAACATTAGA
Found at i:42910 original size:14 final size:14
Alignment explanation
Indices: 42867--42910 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
42857 CTACTTATCC
42867 AATCATCTTAATAA
1 AATCATCTTAATAA
* * *
42881 AATTATCTCAAAAA
1 AATCATCTTAATAA
42895 AATCATCTTAATAA
1 AATCATCTTAATAA
42909 AA
1 AA
42911 GCTTTATTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.32
Consensus pattern (14 bp):
AATCATCTTAATAA
Found at i:43239 original size:110 final size:110
Alignment explanation
Indices: 43046--43269 Score: 421
Period size: 110 Copynumber: 2.0 Consensus size: 110
43036 AATGTGACAA
* *
43046 ATATCTACACCTTACTATTAAAGTTATCCCCAAACTGTTGTGTATGCTCAGTATTTGGCTCTTCT
1 ATATCTACACCTTACTATTAAAGTTATCCCCAAACTGCTGTGTATCCTCAGTATTTGGCTCTTCT
43111 CATGCTGACATTTGTCTATAGTTGATTGATTGAGAGAACACCAAT
66 CATGCTGACATTTGTCTATAGTTGATTGATTGAGAGAACACCAAT
*
43156 ATATCTATACCTTACTATTAAAGTTATCCCCAAACTGCTGTGTATCCTCAGTATTTGGCTCTTCT
1 ATATCTACACCTTACTATTAAAGTTATCCCCAAACTGCTGTGTATCCTCAGTATTTGGCTCTTCT
43221 CATGCTGACATTTGTCTATAGTTGATTGATTGAGAGAACACCAAT
66 CATGCTGACATTTGTCTATAGTTGATTGATTGAGAGAACACCAAT
43266 ATAT
1 ATAT
43270 TATTATATAT
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 111 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (110 bp):
ATATCTACACCTTACTATTAAAGTTATCCCCAAACTGCTGTGTATCCTCAGTATTTGGCTCTTCT
CATGCTGACATTTGTCTATAGTTGATTGATTGAGAGAACACCAAT
Found at i:43599 original size:8 final size:7
Alignment explanation
Indices: 43579--43611 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
43569 CTTTTCTTCT
43579 GGAAAAA
1 GGAAAAA
43586 GGAAAAA
1 GGAAAAA
43593 GGAAAAA
1 GGAAAAA
43600 -GAAAAA
1 GGAAAAA
43606 -GAAAAA
1 GGAAAAA
43612 CAAAAAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 12 0.46
7 14 0.54
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
GGAAAAA
Found at i:43610 original size:5 final size:6
Alignment explanation
Indices: 43580--43620 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
43570 TTTTCTTCTG
*
43580 GAAAAA GGAAAAA GGAAAAA GAAAAA GAAAAA CAAAAA GAA
1 GAAAAA -GAAAAA -GAAAAA GAAAAA GAAAAA GAAAAA GAA
43621 GGTTACCCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 19 0.59
7 13 0.41
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:49673 original size:21 final size:21
Alignment explanation
Indices: 49647--49693 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
49637 GTTAGCAATG
*
49647 GGACCTGGTGGACCGGGCGGA
1 GGACCTGGTGGACCGGGAGGA
**
49668 GGACCTGGTGGATGGGGAGGA
1 GGACCTGGTGGACCGGGAGGA
49689 GGACC
1 GGACC
49694 GGGCGGAGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.19, G:0.53, T:0.11
Consensus pattern (21 bp):
GGACCTGGTGGACCGGGAGGA
Found at i:49780 original size:24 final size:24
Alignment explanation
Indices: 49753--49811 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
49743 TTTGGGCCAG
*
49753 GGGGTCCTGGACCCGGAGGTCCCT
1 GGGGTCCTGGACCCGGAGGACCCT
49777 GGGGTCCTGGACCCGGAGGACCCT
1 GGGGTCCTGGACCCGGAGGACCCT
*
49801 GGGGCCCTGGA
1 GGGGTCCTGGA
49812 TTTGGAGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.10, C:0.32, G:0.44, T:0.14
Consensus pattern (24 bp):
GGGGTCCTGGACCCGGAGGACCCT
Found at i:49818 original size:24 final size:23
Alignment explanation
Indices: 49753--49825 Score: 83
Period size: 24 Copynumber: 3.1 Consensus size: 23
49743 TTTGGGCCAG
*
49753 GGGGTCCTGGACCCGGAGGTCCCT
1 GGGGCCCTGGACCCGGAGG-CCCT
*
49777 GGGGTCCTGGACCCGGAGGACCCT
1 GGGGCCCTGGACCCGGAGG-CCCT
***
49801 GGGGCCCTGGATTTGGAGGCCCT
1 GGGGCCCTGGACCCGGAGGCCCT
49824 GG
1 GG
49826 TTTTTGGCCT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 6 0.14
24 38 0.86
ACGTcount: A:0.10, C:0.30, G:0.44, T:0.16
Consensus pattern (23 bp):
GGGGCCCTGGACCCGGAGGCCCT
Found at i:63490 original size:3 final size:3
Alignment explanation
Indices: 63482--63508 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
63472 TCTATATATT
63482 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
63509 CTTAGTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:69010 original size:32 final size:32
Alignment explanation
Indices: 68969--69032 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
68959 GACAGAAGCT
68969 ATGGGTGGAGACACCTTCTAGTATTTGAATTC
1 ATGGGTGGAGACACCTTCTAGTATTTGAATTC
69001 ATGGGTGGAGACACCTTCTAGTATTTGAATTC
1 ATGGGTGGAGACACCTTCTAGTATTTGAATTC
69033 TGTGACATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (32 bp):
ATGGGTGGAGACACCTTCTAGTATTTGAATTC
Found at i:69592 original size:17 final size:18
Alignment explanation
Indices: 69559--69593 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
69549 TTTTTGGCAG
69559 TTTTTTCTAAATGGATAT
1 TTTTTTCTAAATGGATAT
*
69577 TTTTTTTTAAAT-GATAT
1 TTTTTTCTAAATGGATAT
69594 AAATAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.60
Consensus pattern (18 bp):
TTTTTTCTAAATGGATAT
Found at i:71175 original size:2 final size:2
Alignment explanation
Indices: 71168--71210 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
71158 CACTTCAACC
*
71168 AT AT AT AT AGT TT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71210 A
1 A
71211 GTTTATTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.95
3 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:71188 original size:12 final size:11
Alignment explanation
Indices: 71180--71221 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
71170 ATATATAGTT
71180 TATTATATATA
1 TATTATATATA
71191 TA-TATATATA
1 TATTATATATA
*
71201 TATATATATAGTT
1 TAT-TATATA-TA
71214 TATTATAT
1 TATTATAT
71222 TTACCTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 10 0.37
11 2 0.07
12 11 0.41
13 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (11 bp):
TATTATATATA
Done.