Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012824.1 Corchorus olitorius cultivar O-4 contig12857, 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: 60606
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1213 original size:22 final size:23
Alignment explanation
Indices: 1181--1223 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1171 CACCCTGATT
1181 CTCATAAAAACAGTAT-AAAGGC
1 CTCATAAAAACAGTATGAAAGGC
*
1203 CTCATAGAAACAGTATGAAAG
1 CTCATAAAAACAGTATGAAAG
1224 CTTGTATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (23 bp):
CTCATAAAAACAGTATGAAAGGC
Found at i:3817 original size:2 final size:2
Alignment explanation
Indices: 3810--3844 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3800 ACTTTTGTCA
3810 AT AT 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 AT AT A
3845 ACAGTACTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10591 original size:42 final size:42
Alignment explanation
Indices: 10513--10593 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
10503 TATCACCTTG
*
10513 ATTGACTTTGTATTTCTCTGTTGTTTTTTCCCCTGCTTGATT
1 ATTGACTTTGTATTTCTCTGTTGTTTTTTCCACTGCTTGATT
* **
10555 ATTGACTTCT-TATTTCTCTTTTGTTTTTTTGACTGCTTG
1 ATTGACTT-TGTATTTCTCTGTTGTTTTTTCCACTGCTTG
10594 GTTGAAGTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.97
43 1 0.03
ACGTcount: A:0.10, C:0.17, G:0.14, T:0.59
Consensus pattern (42 bp):
ATTGACTTTGTATTTCTCTGTTGTTTTTTCCACTGCTTGATT
Found at i:20287 original size:2 final size:2
Alignment explanation
Indices: 20280--20309 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20270 ATTTTACCTA
20280 AT 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 AT
20310 TTGATAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23113 original size:14 final size:14
Alignment explanation
Indices: 23094--23121 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
23084 TGAGCATTGG
23094 ATTTTATGTTATGA
1 ATTTTATGTTATGA
23108 ATTTTATGTTATGA
1 ATTTTATGTTATGA
23122 GACACTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (14 bp):
ATTTTATGTTATGA
Found at i:23632 original size:19 final size:19
Alignment explanation
Indices: 23589--23629 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
23579 GAGTCATTTT
*
23589 TAAATAAAAATATAATATA
1 TAAATAAAATTATAATATA
*
23608 TAAATAAAATTTTAATAT-
1 TAAATAAAATTATAATATA
23626 TAAA
1 TAAA
23630 ATATAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATTATAATATA
Found at i:29203 original size:19 final size:19
Alignment explanation
Indices: 29179--29260 Score: 87
Period size: 19 Copynumber: 4.3 Consensus size: 19
29169 GATAATAGCA
*
29179 AAATAGTAAATAAATTGAT
1 AAATAGTAAATAAATAGAT
*
29198 AAATAGTAAATAAATAAAT
1 AAATAGTAAATAAATAGAT
* *
29217 AAATAAATAGATAAATAG-T
1 AAAT-AGTAAATAAATAGAT
*
29236 AAATGAATAAAT-AATAGAT
1 AAAT-AGTAAATAAATAGAT
29255 AAATAG
1 AAATAG
29261 CTCTAATTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
18 6 0.11
19 37 0.70
20 10 0.19
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (19 bp):
AAATAGTAAATAAATAGAT
Found at i:29211 original size:4 final size:4
Alignment explanation
Indices: 29185--29259 Score: 66
Period size: 4 Copynumber: 19.5 Consensus size: 4
29175 AGCAAAATAG
** * *
29185 TAAA TAAA TTGA TAAA T-AG TAAA TAAA TAAA TAAA TAAA TAGA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * *
29232 T-AG TAAA TGAA TAAA T-AA TAGA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
29260 GCTCTAATTT
Statistics
Matches: 54, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
3 7 0.13
4 47 0.87
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:29223 original size:31 final size:31
Alignment explanation
Indices: 29121--29259 Score: 58
Period size: 31 Copynumber: 4.5 Consensus size: 31
29111 AGATAAGTGT
* * * *
29121 ATAATTAAATGAAGAAATAAAT-AATAGGTAA
1 ATAAATAAATAAATAAATAGATAAATA-GTAA
* *
29152 ATAAA-AAA-AGATAAATAGAT-AATAGCAAAA
1 ATAAATAAATAAATAAATAGATAAATAG--TAA
** *
29182 TAGTAAATAAATTGATAAATAG-TAAATAAATAA
1 -A-TAAATAAATAAATAAATAGATAAAT-AGTAA
* *
29215 ATAAATAAATAGATAAATAG-TAAATGAATAA
1 ATAAATAAATAAATAAATAGATAAAT-AGTAA
*
29246 AT-AATAGATAAATA
1 ATAAATAAATAAATA
29260 GCTCTAATTT
Statistics
Matches: 87, Mismatches: 13, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
28 1 0.01
29 12 0.14
30 15 0.17
31 35 0.40
32 5 0.06
33 6 0.07
34 12 0.14
35 1 0.01
ACGTcount: A:0.64, C:0.01, G:0.10, T:0.25
Consensus pattern (31 bp):
ATAAATAAATAAATAAATAGATAAATAGTAA
Found at i:29258 original size:26 final size:27
Alignment explanation
Indices: 29162--29260 Score: 104
Period size: 26 Copynumber: 3.9 Consensus size: 27
29152 ATAAAAAAAG
*
29162 ATAAATAGAT-AATAGCA-AAATAGTAA
1 ATAAATAAATAAATAG-ATAAATAGTAA
**
29188 ATAAATTGATAAATAG-T-AA-A-TAA
1 ATAAATAAATAAATAGATAAATAGTAA
29211 ATAAATAAATAAATAGATAAATAGTAA
1 ATAAATAAATAAATAGATAAATAGTAA
*
29238 ATGAATAAAT-AATAGATAAATAG
1 ATAAATAAATAAATAGATAAATAG
29261 CTCTAATTTA
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
23 17 0.27
24 2 0.03
25 4 0.06
26 23 0.37
27 17 0.27
ACGTcount: A:0.63, C:0.01, G:0.10, T:0.26
Consensus pattern (27 bp):
ATAAATAAATAAATAGATAAATAGTAA
Found at i:29259 original size:15 final size:15
Alignment explanation
Indices: 29135--29259 Score: 78
Period size: 15 Copynumber: 8.3 Consensus size: 15
29125 TTAAATGAAG
**
29135 AAATAAATAATAGGT
1 AAATAAATAATAAAT
29150 AAATAAA-AA-AAGAT
1 AAATAAATAATAA-AT
* *
29164 AAATAGATAATAGCA-
1 AAATAAATAATA-AAT
*
29179 AAAT-AGTAAATAAAT
1 AAATAAAT-AATAAAT
** *
29194 TGATAAATAGTAAAT
1 AAATAAATAATAAAT
29209 AAATAAATAAATAAAT
1 AAATAAAT-AATAAAT
* *
29225 AGATAAATAGTAAAT
1 AAATAAATAATAAAT
* *
29240 GAATAAATAATAGAT
1 AAATAAATAATAAAT
29255 AAATA
1 AAATA
29260 GCTCTAATTT
Statistics
Matches: 81, Mismatches: 21, Indels: 16
0.69 0.18 0.14
Matches are distributed among these distances:
13 1 0.01
14 11 0.14
15 52 0.64
16 17 0.21
ACGTcount: A:0.65, C:0.01, G:0.10, T:0.25
Consensus pattern (15 bp):
AAATAAATAATAAAT
Found at i:29260 original size:8 final size:8
Alignment explanation
Indices: 29143--29248 Score: 73
Period size: 8 Copynumber: 13.5 Consensus size: 8
29133 AGAAATAAAT
*
29143 AATAGGTA
1 AATAGATA
29151 AATA-A-A
1 AATAGATA
*
29157 AAAAGATA
1 AATAGATA
29165 AATAGAT-
1 AATAGATA
29172 AATAGCA-A
1 AATAG-ATA
29180 AATAGTAAATA
1 AATAG---ATA
*
29191 AATTGATA
1 AATAGATA
29199 AATAG-TA
1 AATAGATA
*
29206 AATAAATA
1 AATAGATA
*
29214 AATAAATA
1 AATAGATA
29222 AATAGATA
1 AATAGATA
29230 AATAG-TA
1 AATAGATA
29237 AAT-GAATA
1 AATAG-ATA
29245 AATA
1 AATA
29249 ATAGATAAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 21
0.73 0.07 0.19
Matches are distributed among these distances:
6 5 0.06
7 17 0.22
8 51 0.65
10 1 0.01
11 5 0.06
ACGTcount: A:0.64, C:0.01, G:0.10, T:0.25
Consensus pattern (8 bp):
AATAGATA
Found at i:29630 original size:10 final size:10
Alignment explanation
Indices: 29615--29644 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
29605 TGGCTCTGGC
29615 TCTAATTAAA
1 TCTAATTAAA
*
29625 TCTAATTAAC
1 TCTAATTAAA
29635 TCTAATTAAA
1 TCTAATTAAA
29645 ATATAATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (10 bp):
TCTAATTAAA
Found at i:31009 original size:55 final size:54
Alignment explanation
Indices: 30950--31136 Score: 209
Period size: 53 Copynumber: 3.5 Consensus size: 54
30940 TTGAGATCAT
* *
30950 CTCTGATCATTGAAAACTTATTGGATTGACCGCACTTGATCGTTTGAAAAATCGA
1 CTCTGATCATTGAAAACTTCTTGGA-TGACCGCACTTGATCATTTGAAAAATCGA
* * *** *
31005 CTCTGATCATTTAAAACTTTCTGGGATGACCGCA-TTGGATCATTTG-GGGATCAA
1 CTCTGATCATTGAAAAC-TTCTTGGATGACCGCACTT-GATCATTTGAAAAATCGA
* * * *
31059 CTCTGATCATTGAAAACTTCTAGGACGACCGCACTCGATCATTT-AAAAACCGA
1 CTCTGATCATTGAAAACTTCTTGGATGACCGCACTTGATCATTTGAAAAATCGA
*
31112 CTCTGAACATTGAAAACTTCTTGGA
1 CTCTGATCATTGAAAACTTCTTGGA
31137 ACAACCGCAC
Statistics
Matches: 109, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
53 48 0.44
54 23 0.21
55 32 0.29
56 6 0.06
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (54 bp):
CTCTGATCATTGAAAACTTCTTGGATGACCGCACTTGATCATTTGAAAAATCGA
Found at i:31181 original size:54 final size:54
Alignment explanation
Indices: 30944--31319 Score: 308
Period size: 54 Copynumber: 6.7 Consensus size: 54
30934 ACCACTTTGA
* * ** * * **
30944 GATCATCTCTGATCATTGAAAACTTATTGGATTGACCGCACTTGATCGTTTGAAA
1 GATCAACTCTGATCATTGAAAACTTCTTGGAACGACCGCACTAGATCATTTG-GG
* * * * * * *
30999 AATCGACTCTGATCATTTAAAACTT-TCTGGGATGACCGCATTGGATCATTTGGG
1 GATCAACTCTGATCATTGAAAACTTCT-TGGAACGACCGCACTAGATCATTTGGG
* * ***
31053 GATCAACTCTGATCATTGAAAACTTCTAGG-ACGACCGCACTCGATCATTTAAA
1 GATCAACTCTGATCATTGAAAACTTCTTGGAACGACCGCACTAGATCATTTGGG
* * * * * *
31106 AACCGACTCTGAACATTGAAAACTTCTTGGAACAACCGCACTAGATTATTTGGG
1 GATCAACTCTGATCATTGAAAACTTCTTGGAACGACCGCACTAGATCATTTGGG
* *
31160 GCTCAACTTTGATCACTGAAAAGATCACTGAAAACTTCTTGGAACGACCGCACTAGATCATTTGG
1 GATCAAC-----T--CT-----GATCATTGAAAACTTCTTGGAACGACCGCACTAGATCATTTGG
31225 G
54 G
* * *
31226 GATCAACTCTAATCATTGAAAACTTCTTAGAACGACCGCACTGGATCATTTGGG
1 GATCAACTCTGATCATTGAAAACTTCTTGGAACGACCGCACTAGATCATTTGGG
*
31280 GATCAACTCTGATCATTGAAAACTTC-TGTGAATGACCGCA
1 GATCAACTCTGATCATTGAAAACTTCTTG-GAACGACCGCA
31320 TAAGGTCATC
Statistics
Matches: 257, Mismatches: 48, Indels: 33
0.76 0.14 0.10
Matches are distributed among these distances:
53 43 0.17
54 120 0.47
55 42 0.16
59 3 0.01
61 3 0.01
66 46 0.18
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.29
Consensus pattern (54 bp):
GATCAACTCTGATCATTGAAAACTTCTTGGAACGACCGCACTAGATCATTTGGG
Found at i:31300 original size:120 final size:119
Alignment explanation
Indices: 31063--31301 Score: 309
Period size: 120 Copynumber: 2.0 Consensus size: 119
31053 GATCAACTCT
* * *
31063 GATCATTGAAAACTTCTAGGACGACCGCACTCGATCATTTAAAAACCGACTCTGAACATTGAAAA
1 GATCACTGAAAACTTCTAGGACGACCGCACTAGATCATTTAAAAACCAACTCTGAACATTGAAAA
* * * *
31128 CTTCTTGGAACAACCGCACTAGATTATTTGGGGCTCAACTTTGATCACTGAAAA
66 CTTCTTAGAACAACCGCACTAGATCATTTGGGGATCAACTCTGATCACTGAAAA
* **** *
31182 GATCACTGAAAACTTCTTGGAACGACCGCACTAGATCATTTGGGGATCAACTCT-AATCATTGAA
1 GATCACTGAAAACTTCTAGG-ACGACCGCACTAGATCATTTAAAAACCAACTCTGAA-CATTGAA
* * *
31246 AACTTCTTAGAACGACCGCACTGGATCATTTGGGGATCAACTCTGATCATTGAAAA
64 AACTTCTTAGAACAACCGCACTAGATCATTTGGGGATCAACTCTGATCACTGAAAA
31302 CTTCTGTGAA
Statistics
Matches: 102, Mismatches: 16, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
119 20 0.20
120 82 0.80
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.26
Consensus pattern (119 bp):
GATCACTGAAAACTTCTAGGACGACCGCACTAGATCATTTAAAAACCAACTCTGAACATTGAAAA
CTTCTTAGAACAACCGCACTAGATCATTTGGGGATCAACTCTGATCACTGAAAA
Found at i:31338 original size:54 final size:51
Alignment explanation
Indices: 31182--31395 Score: 164
Period size: 54 Copynumber: 4.0 Consensus size: 51
31172 TCACTGAAAA
* * **
31182 GATCACTGAAAACTTCTTGGAACGACCGCACTAGATCATTTGGGGATCAACTCT
1 GATCATTGAAAACTTCTT-GAACGACCGCA-TAGGTCATTT-CTGATCAACTCT
* **
31236 AATCATTGAAAACTTCTTAGAACGACCGCACT-GGATCATTTGGGGATCAACTCT
1 GATCATTGAAAACTTCTT-GAACGACCGCA-TAGG-TCATTT-CTGATCAACTCT
* *
31290 GATCATTGAAAACTTCTGTGAATGACCGCATAAGGTCATCTTCTGATCAACAT-A
1 GATCATTGAAAACTTCT-TGAACGACCGCAT-AGGTCAT-TTCTGATCAAC-TCT
** *
31344 GATC-TCTGAAAACTTCTATGAACGACCGCGCAGGGTCATTTTCTGGTCAACT
1 GATCAT-TGAAAACTTCT-TGAACGACCGCATA-GGTCA-TTTCTGATCAACT
31396 TAGATCTCTG
Statistics
Matches: 137, Mismatches: 14, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
53 5 0.04
54 125 0.91
55 7 0.05
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (51 bp):
GATCATTGAAAACTTCTTGAACGACCGCATAGGTCATTTCTGATCAACTCT
Found at i:31400 original size:54 final size:54
Alignment explanation
Indices: 31296--31409 Score: 156
Period size: 54 Copynumber: 2.1 Consensus size: 54
31286 CTCTGATCAT
* * *
31296 TGAAAACTTCTGTGAATGACCGCATAAGGTCATCTTCTGATCAACATAGATCTC
1 TGAAAACTTCTATGAACGACCGCACAAGGTCATCTTCTGATCAACATAGATCTC
* * * * *
31350 TGAAAACTTCTATGAACGACCGCGCAGGGTCATTTTCTGGTCAACTTAGATCTC
1 TGAAAACTTCTATGAACGACCGCACAAGGTCATCTTCTGATCAACATAGATCTC
31404 TGAAAA
1 TGAAAA
31410 TTTAGAAAGA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (54 bp):
TGAAAACTTCTATGAACGACCGCACAAGGTCATCTTCTGATCAACATAGATCTC
Found at i:31988 original size:22 final size:21
Alignment explanation
Indices: 31958--31998 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
31948 TTAATAAGCA
31958 AAGAATATATATATATATAAG
1 AAGAATATATATATATATAAG
31979 AAGACATATATATATATATA
1 AAGA-ATATATATATATATA
31999 TAAGAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.34
Consensus pattern (21 bp):
AAGAATATATATATATATAAG
Found at i:31989 original size:24 final size:24
Alignment explanation
Indices: 31962--32011 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
31952 TAAGCAAAGA
*
31962 ATATATATATATATAAGAAGACAT
1 ATATATATATATATAAGAAAACAT
31986 ATATATATATATATAAGAAAACAT
1 ATATATATATATATAAGAAAACAT
32010 AT
1 AT
32012 GTACAGAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (24 bp):
ATATATATATATATAAGAAAACAT
Found at i:34241 original size:29 final size:28
Alignment explanation
Indices: 34209--34264 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
34199 TCCAAATTGC
*
34209 AAGTTCAAAGGGCAAAATGTCCAAAATTA
1 AAGTTCAAAGGGCAAAACGT-CAAAATTA
* **
34238 AAGTTTAGGGGGCAAAACGTCAAAATT
1 AAGTTCAAAGGGCAAAACGTCAAAATT
34265 GTACAAGTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.21
Consensus pattern (28 bp):
AAGTTCAAAGGGCAAAACGTCAAAATTA
Found at i:36154 original size:192 final size:192
Alignment explanation
Indices: 35845--36217 Score: 728
Period size: 192 Copynumber: 1.9 Consensus size: 192
35835 GAATCACTGC
35845 AGAAAAGAATGAGAAGGTTGCTTCAAGGGGTATGCCTAATTGCTTAGCTTGTGGTTCTGAAGCCA
1 AGAAAAGAATGAGAAGGTTGCTTCAAGGGGTATGCCTAATTGCTTAGCTTGTGGTTCTGAAGCCA
*
35910 TTTTGGGAATGTGAAAAGCTACCTGTTTTGTCATCTTCAGCCCCTAAAAAGGCCAATCCAAAAGT
66 TTTTGGGAATGTGAAAAGCTACATGTTTTGTCATCTTCAGCCCCTAAAAAGGCCAATCCAAAAGT
*
35975 TTAACGACAGTAATTGGCTATCGCAGAAGACAGTTAATCAATAGATTGAATCACTGCAGAAA
131 ATAACGACAGTAATTGGCTATCGCAGAAGACAGTTAATCAATAGATTGAATCACTGCAGAAA
36037 AGAAAAGAATGAGAAGGTTGCTTCAAGGGGTATGCCTAATTGCTTAGCTTGTGGTTCTGAAGCCA
1 AGAAAAGAATGAGAAGGTTGCTTCAAGGGGTATGCCTAATTGCTTAGCTTGTGGTTCTGAAGCCA
36102 TTTTGGGAATGTGAAAAGCTACATGTTTTGTCATCTTCAGCCCCTAAAAAGGCCAATCCAAAAGT
66 TTTTGGGAATGTGAAAAGCTACATGTTTTGTCATCTTCAGCCCCTAAAAAGGCCAATCCAAAAGT
36167 ATAACGACAGTAATTGGCTATCGCAGAAGACAGTTAATCAATAGATTGAAT
131 ATAACGACAGTAATTGGCTATCGCAGAAGACAGTTAATCAATAGATTGAAT
36218 GGTTTCGAGT
Statistics
Matches: 179, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
192 179 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.27
Consensus pattern (192 bp):
AGAAAAGAATGAGAAGGTTGCTTCAAGGGGTATGCCTAATTGCTTAGCTTGTGGTTCTGAAGCCA
TTTTGGGAATGTGAAAAGCTACATGTTTTGTCATCTTCAGCCCCTAAAAAGGCCAATCCAAAAGT
ATAACGACAGTAATTGGCTATCGCAGAAGACAGTTAATCAATAGATTGAATCACTGCAGAAA
Found at i:45146 original size:7 final size:7
Alignment explanation
Indices: 45136--45165 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
45126 TGCATTTAGA
45136 TTAGTTT
1 TTAGTTT
45143 TTAGTTT
1 TTAGTTT
45150 TTAGTTT
1 TTAGTTT
45157 TTAGTTT
1 TTAGTTT
45164 TT
1 TT
45166 TGCATGAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.73
Consensus pattern (7 bp):
TTAGTTT
Found at i:48391 original size:22 final size:22
Alignment explanation
Indices: 48349--48393 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
48339 CAAACTAAGA
48349 AAAACAAACTAGAAAACGGATG
1 AAAACAAACTAGAAAACGGATG
48371 AAAACAAACTAGAAAACGGATG
1 AAAACAAACTAGAAAACGGATG
48393 A
1 A
48394 TGCTTCGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.60, C:0.13, G:0.18, T:0.09
Consensus pattern (22 bp):
AAAACAAACTAGAAAACGGATG
Found at i:51427 original size:2 final size:2
Alignment explanation
Indices: 51420--51453 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
51410 TACCACTTTA
51420 AT AT AT 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 AT AT AT
51454 TTTAAGATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53065 original size:132 final size:131
Alignment explanation
Indices: 52926--53181 Score: 399
Period size: 132 Copynumber: 1.9 Consensus size: 131
52916 AAACTTTTTT
* * * *
52926 AAAAATTCTAATATATCTAAGTTTTTTAATTAAATTTGTAAAATGGTAAAAATAAAATAAG-TAT
1 AAAAATTCTAATACATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAAT-AGTTAT
* * *
52990 AAGGATATTATATTTAATTAAATAAAAAATAGAGTTTTTAGTTG-AGTAAAACTATAAAAGTATA
65 AAGGATATTAGATTTAATGAAAT-AAAAATAAAGTTTTTAGTTGTA-TAAAACTATAAAAGTATA
53054 TTTA
128 TTTA
*
53058 AAAAATTCTAATACATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATA
1 AAAAATTCTAATACATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATA
53123 AGGATATTAGATTTAATGAAATAAAAATAAAGTTTTTAGTTGTATAAAACTATAAAAGT
66 AGGATATTAGATTTAATGAAATAAAAATAAAGTTTTTAGTTGTATAAAACTATAAAAGT
53182 TTAAACAATG
Statistics
Matches: 114, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
131 36 0.32
132 78 0.68
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (131 bp):
AAAAATTCTAATACATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATA
AGGATATTAGATTTAATGAAATAAAAATAAAGTTTTTAGTTGTATAAAACTATAAAAGTATATTT
A
Found at i:60603 original size:25 final size:24
Alignment explanation
Indices: 60552--60606 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 24
60542 GTCAGCCTTG
*
60552 AATTT-TTTAATGTTTTATTCTTA
1 AATTTATTTAATGTTTTATTATTA
*
60575 AATTTATTTAATGTCTTTATTATTC
1 AATTTATTTAATGT-TTTATTATTA
60600 AATTTAT
1 AATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.18
24 8 0.29
25 15 0.54
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (24 bp):
AATTTATTTAATGTTTTATTATTA
Done.