Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017330.1 Corchorus olitorius cultivar O-4 contig17363, 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: 74831
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:14639 original size:6 final size:7
Alignment explanation
Indices: 14611--14636 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
14601 GTTTCTGGGT
14611 TTTTTTC
1 TTTTTTC
14618 TTTTTTC
1 TTTTTTC
14625 TTTTTTC
1 TTTTTTC
14632 TTTTT
1 TTTTT
14637 CTTCTTTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:17359 original size:29 final size:30
Alignment explanation
Indices: 17301--17361 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
17291 GTTCTAATTA
* *
17301 ATGTATACATATAAATTATTCAATTTTATT
1 ATGTATAAATATAAATTATTCAATTATATT
*
17331 ATGTATAAATAT-AATTATTTAATTATATT
1 ATGTATAAATATAAATTATTCAATTATATT
17360 AT
1 AT
17362 ATTATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (30 bp):
ATGTATAAATATAAATTATTCAATTATATT
Found at i:18447 original size:2 final size:2
Alignment explanation
Indices: 18440--18469 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18430 ACACCCATAG
18440 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18470 AACTAAAACT
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):
TA
Found at i:18928 original size:26 final size:28
Alignment explanation
Indices: 18893--18944 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
18883 GATTTTGACT
* *
18893 AATTGGTACTAT-ATATTTATGGTTTCA
1 AATTGGTACTATGAAAGTTATGGTTTCA
18920 AATT-GTACTATGAAAGTTATGGTTT
1 AATTGGTACTATGAAAGTTATGGTTT
18945 GATTTATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (28 bp):
AATTGGTACTATGAAAGTTATGGTTTCA
Found at i:20195 original size:37 final size:37
Alignment explanation
Indices: 20140--20210 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
20130 ATCCTATTTG
* *
20140 CATTTTCAATTCCTCTAGCTGAGCAGGAGAAACCAAA
1 CATTCTCAATTCCTCTAGCCGAGCAGGAGAAACCAAA
*
20177 CATTCTCAATTGCTCTAGCCGAGCAGGAGAAACC
1 CATTCTCAATTCCTCTAGCCGAGCAGGAGAAACC
20211 CCTGAACAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (37 bp):
CATTCTCAATTCCTCTAGCCGAGCAGGAGAAACCAAA
Found at i:22243 original size:26 final size:28
Alignment explanation
Indices: 22186--22244 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
22176 AGTGGCTTAA
* *
22186 AGGT-CACTTAATGAAGTTTTCTTTTTT
1 AGGTACACTTAATGAACTTATCTTTTTT
22213 AGGTACACTTAATGAACTTAT-TTTTTT
1 AGGTACACTTAATGAACTTATCTTTTTT
22240 -GGTAC
1 AGGTAC
22245 CAAAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 5 0.17
27 10 0.34
28 14 0.48
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (28 bp):
AGGTACACTTAATGAACTTATCTTTTTT
Found at i:22984 original size:21 final size:21
Alignment explanation
Indices: 22916--22990 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 21
22906 CAGATTATCG
*
22916 AAATTTCATAGATGGGT-ATCA
1 AAATTTCATAGA-AGGTAATCA
* *
22937 AAATTTCAT--AATGTGATTACAA
1 AAATTTCATAGAAGGT-AAT-C-A
22959 AAATTTCATAGAAGGTAATCA
1 AAATTTCATAGAAGGTAATCA
22980 AAATTTCATAG
1 AAATTTCATAG
22991 TGAGATTTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
18 2 0.05
19 1 0.02
20 1 0.02
21 22 0.51
22 11 0.26
23 2 0.05
24 4 0.09
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.33
Consensus pattern (21 bp):
AAATTTCATAGAAGGTAATCA
Found at i:23006 original size:43 final size:42
Alignment explanation
Indices: 22907--23006 Score: 121
Period size: 43 Copynumber: 2.3 Consensus size: 42
22897 TGAACTTTGC
*
22907 AGATTATCGAAATTTCATAGATGGGTATCAAAATTTCATAATG
1 AGATTA-CGAAATTTCATAGATAGGTATCAAAATTTCATAATG
* * *
22950 TGATTACAAAAATTTCATAGA-AGGTAATCAAAATTTCATAGTG
1 AGATTAC-GAAATTTCATAGATAGGT-ATCAAAATTTCATAATG
22993 AGATTTACGAAATT
1 AGA-TTACGAAATT
23007 CTATAGGGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
42 4 0.08
43 40 0.83
44 4 0.08
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (42 bp):
AGATTACGAAATTTCATAGATAGGTATCAAAATTTCATAATG
Found at i:23029 original size:22 final size:22
Alignment explanation
Indices: 23004--23078 Score: 114
Period size: 22 Copynumber: 3.4 Consensus size: 22
22994 GATTTACGAA
*
23004 ATTCTATAGGGAAGTTATCAAC
1 ATTCCATAGGGAAGTTATCAAC
23026 ATTCCATAGGGAAGTTATCAAC
1 ATTCCATAGGGAAGTTATCAAC
* *
23048 ATTCCATAGGGAGGTTATCAAA
1 ATTCCATAGGGAAGTTATCAAC
*
23070 ATTTCATAG
1 ATTCCATAG
23079 TATGGTTATC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (22 bp):
ATTCCATAGGGAAGTTATCAAC
Found at i:23034 original size:44 final size:44
Alignment explanation
Indices: 22976--23079 Score: 122
Period size: 44 Copynumber: 2.4 Consensus size: 44
22966 ATAGAAGGTA
* *
22976 ATCAAAATTTCATAGTGAGATTTA-CGAA-ATTCTATAGGGAAGTT
1 ATCAAAATTTCATAGTGA-AGTTATC-AACATTCCATAGGGAAGTT
* * * *
23020 ATCAACATTCCATAGGGAAGTTATCAACATTCCATAGGGAGGTT
1 ATCAAAATTTCATAGTGAAGTTATCAACATTCCATAGGGAAGTT
23064 ATCAAAATTTCATAGT
1 ATCAAAATTTCATAGT
23080 ATGGTTATCC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
43 6 0.12
44 43 0.88
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (44 bp):
ATCAAAATTTCATAGTGAAGTTATCAACATTCCATAGGGAAGTT
Found at i:23085 original size:22 final size:22
Alignment explanation
Indices: 23060--23101 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
23050 TCCATAGGGA
23060 GGTTATCAAAATTTCATAGTAT
1 GGTTATCAAAATTTCATAGTAT
* *
23082 GGTTATCCAAATTTCGTAGT
1 GGTTATCAAAATTTCATAGT
23102 GTACCAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTAT
Found at i:23087 original size:44 final size:43
Alignment explanation
Indices: 22907--23094 Score: 111
Period size: 44 Copynumber: 4.3 Consensus size: 43
22897 TGAACTTTGC
* * *
22907 AGATTATCGAAATTTCATA--GATGGGTATCAAAATTTCATAATGT
1 AGATTATCAAAATTCCATAGGGA-GGTTATCAAAATTTCAT-A-GT
* * *
22951 -GATTA-CAAAAATTTCATA-GAAGGTAATCAAAATTTCATAGT
1 AGATTATC-AAAATTCCATAGGGAGGTTATCAAAATTTCATAGT
* * * * *
22992 GAGATT-TACGAAATTCTATAGGGAAGTTATCAACATTCCATAG-
1 -AGATTAT-CAAAATTCCATAGGGAGGTTATCAAAATTTCATAGT
* *
23035 GGAAGTTATCAACATTCCATAGGGAGGTTATCAAAATTTCATAGT
1 AG-A-TTATCAAAATTCCATAGGGAGGTTATCAAAATTTCATAGT
* *
23080 ATGGTTATCCAAATT
1 A-GATTATCAAAATT
23095 TCGTAGTGTA
Statistics
Matches: 109, Mismatches: 23, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
41 2 0.02
42 3 0.03
43 43 0.39
44 59 0.54
45 1 0.01
46 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (43 bp):
AGATTATCAAAATTCCATAGGGAGGTTATCAAAATTTCATAGT
Found at i:23245 original size:22 final size:22
Alignment explanation
Indices: 23172--23293 Score: 91
Period size: 22 Copynumber: 5.5 Consensus size: 22
23162 CATATAGAGA
* *
23172 TTATCACAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
* * *
23194 TTATCAAAATTTCATAATATGA
1 TTATCAAAATTTCATAGTGTGG
* * *
23216 TGACCAAAATTTCATGGTGTGG
1 TTATCAAAATTTCATAGTGTGG
* * * *
23238 TTATCAAAGTTTCACAGGACGAGG
1 TTATCAAAATTTCATA-G-TGTGG
* * *
23262 TTATCACAATTTCTTAGTGAGG
1 TTATCAAAATTTCATAGTGTGG
23284 TTATCAAAAT
1 TTATCAAAAT
23294 ATAATATAGC
Statistics
Matches: 74, Mismatches: 24, Indels: 4
0.73 0.24 0.04
Matches are distributed among these distances:
22 57 0.77
23 2 0.03
24 15 0.20
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGG
Found at i:38079 original size:27 final size:26
Alignment explanation
Indices: 38049--38251 Score: 307
Period size: 27 Copynumber: 7.5 Consensus size: 26
38039 TTAAAAAAAG
*
38049 CGATGATACCAATACTCTTACTAATAC
1 CGATGATACCGATACT-TTACTAATAC
*
38076 CGATGATACCAATACTTATACTAATAC
1 CGATGATACCGATACTT-TACTAATAC
38103 CGATGATACCGATACTTATACTAATAC
1 CGATGATACCGATACTT-TACTAATAC
38130 CGATGATACCGATACTTATACTAATAC
1 CGATGATACCGATACTT-TACTAATAC
38157 CGATGATACCGATACTTTTACTAATAC
1 CGATGATACCGATAC-TTTACTAATAC
38184 CGATGATACCGATACTTTTACTAATAC
1 CGATGATACCGATAC-TTTACTAATAC
*
38211 CGATGATACCAATACTTTTACTAATAC
1 CGATGATACCGATAC-TTTACTAATAC
*
38238 CGATGATACTGATA
1 CGATGATACCGATA
38252 ATACCAATAA
Statistics
Matches: 170, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
26 1 0.01
27 167 0.98
28 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.31
Consensus pattern (26 bp):
CGATGATACCGATACTTTACTAATAC
Found at i:38118 original size:54 final size:54
Alignment explanation
Indices: 38049--38251 Score: 343
Period size: 54 Copynumber: 3.8 Consensus size: 54
38039 TTAAAAAAAG
* *
38049 CGATGATACCAATACTCTTACTAATACCGATGATACCAATACTTATACTAATAC
1 CGATGATACCAATACTTTTACTAATACCGATGATACCGATACTTATACTAATAC
* *
38103 CGATGATACCGATACTTATACTAATACCGATGATACCGATACTTATACTAATAC
1 CGATGATACCAATACTTTTACTAATACCGATGATACCGATACTTATACTAATAC
* *
38157 CGATGATACCGATACTTTTACTAATACCGATGATACCGATACTTTTACTAATAC
1 CGATGATACCAATACTTTTACTAATACCGATGATACCGATACTTATACTAATAC
*
38211 CGATGATACCAATACTTTTACTAATACCGATGATACTGATA
1 CGATGATACCAATACTTTTACTAATACCGATGATACCGATA
38252 ATACCAATAA
Statistics
Matches: 141, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 141 1.00
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.31
Consensus pattern (54 bp):
CGATGATACCAATACTTTTACTAATACCGATGATACCGATACTTATACTAATAC
Found at i:38270 original size:27 final size:27
Alignment explanation
Indices: 38265--38327 Score: 101
Period size: 27 Copynumber: 2.3 Consensus size: 27
38255 CCAATAATCC
38265 TAATGATAATACCAAGAATCCTAATGA
1 TAATGATAATACCAAGAATCCTAATGA
*
38292 TAATGATGATGA-CAAGAATCCTAATGA
1 TAATGATAAT-ACCAAGAATCCTAATGA
38319 TAATGATAA
1 TAATGATAA
38328 ACTAGAGGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (27 bp):
TAATGATAATACCAAGAATCCTAATGA
Found at i:38273 original size:21 final size:21
Alignment explanation
Indices: 38247--38295 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
38237 CCGATGATAC
*
38247 TGATAATACCAATAATCCTAA
1 TGATAATACCAAGAATCCTAA
38268 TGATAATACCAAGAATCCTAA
1 TGATAATACCAAGAATCCTAA
38289 TGATAAT
1 TGATAAT
38296 GATGATGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (21 bp):
TGATAATACCAAGAATCCTAA
Found at i:38633 original size:36 final size:36
Alignment explanation
Indices: 38557--38625 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
38547 AAGTAAAAAG
38557 AAAGAATCACAAATTTCTAATAATACAGAAAACAAA
1 AAAGAATCACAAATTTCTAATAATACAGAAAACAAA
38593 AAAGAATCACAAATTTCTAATAATACAGAAAAC
1 AAAGAATCACAAATTTCTAATAATACAGAAAAC
38626 GATAAAGACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.59, C:0.14, G:0.06, T:0.20
Consensus pattern (36 bp):
AAAGAATCACAAATTTCTAATAATACAGAAAACAAA
Found at i:51642 original size:24 final size:25
Alignment explanation
Indices: 51599--51646 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
51589 ATTGGAGTAT
*
51599 TTATTTATCTTGTCTCTTTATTTTA
1 TTATTTATCTTGTCTATTTATTTTA
*
51624 TTATTT-TCTTGTTTATTTATTTT
1 TTATTTATCTTGTCTATTTATTTT
51647 TGTTGTCCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.15, C:0.08, G:0.04, T:0.73
Consensus pattern (25 bp):
TTATTTATCTTGTCTATTTATTTTA
Found at i:52559 original size:22 final size:22
Alignment explanation
Indices: 52531--52584 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
52521 GAACTTATGG
52531 AGAGGTCGAACTCGACCTTCGT
1 AGAGGTCGAACTCGACCTTCGT
*
52553 AGAGGTCGAACTCGACCTTTGT
1 AGAGGTCGAACTCGACCTTCGT
52575 AGAGGTCGAA
1 AGAGGTCGAA
52585 ACAACAACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (22 bp):
AGAGGTCGAACTCGACCTTCGT
Found at i:55232 original size:31 final size:30
Alignment explanation
Indices: 55189--55277 Score: 108
Period size: 29 Copynumber: 3.0 Consensus size: 30
55179 GGACCAGCAT
* *
55189 TAATGTACAATTTGCACCCTGAACTATAAA
1 TAATGGACAATTTGCACCCTCAACTATAAA
* *
55219 TGAATGGATAATTTGCACCCTCAACT-TTAA
1 T-AATGGACAATTTGCACCCTCAACTATAAA
**
55249 TTTTGGACAATTTGCACCCTCAACTATAA
1 TAATGGACAATTTGCACCCTCAACTATAA
55278 TTTACACCGC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 21 0.43
30 7 0.14
31 21 0.43
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (30 bp):
TAATGGACAATTTGCACCCTCAACTATAAA
Found at i:56844 original size:22 final size:22
Alignment explanation
Indices: 56816--56877 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
56806 CTCTGTGTGG
* *
56816 TTATCAAATTTTCTTAATGAA-A
1 TTATCAAAATTTCATAA-GAAGA
*
56838 TTATCAAAATTTCATAAGAAGG
1 TTATCAAAATTTCATAAGAAGA
56860 TTATCAAAAATTTCATAA
1 TTATC-AAAATTTCATAA
56878 TGTCATATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 3 0.09
22 20 0.57
23 12 0.34
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGAAGA
Found at i:56884 original size:31 final size:32
Alignment explanation
Indices: 56835--56899 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
56825 TTTCTTAATG
*
56835 AAATTATCAAAATTTCATA-AGAAGGTTATCAA
1 AAATTATCAAAATGTCATATAG-AGGTTATCAA
* *
56867 AAATT-TCATAATGTCATATTGAGGTTATCAA
1 AAATTATCAAAATGTCATATAGAGGTTATCAA
56898 AA
1 AA
56900 TTTTATGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 23 0.79
32 6 0.21
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (32 bp):
AAATTATCAAAATGTCATATAGAGGTTATCAA
Found at i:57031 original size:90 final size:87
Alignment explanation
Indices: 56880--57260 Score: 272
Period size: 90 Copynumber: 4.3 Consensus size: 87
56870 TTTCATAATG
* * * * * * * *
56880 TCATATTGAGGTTATCAAAATTTTATGGTGTGGTTACCAAAATTTCGTATGGAGGTTATCAAAAT
1 TCATAGTGAGGTTACCAAAATTTAATAGCGAGGTTATCAAAATTTCTTA-GGAGGTTATCAAAAT
* *
56945 TTCATAGGAAGGTTACCAAAATT
65 TTCATAGTAAGGTTATCAAAATT
* * *
56968 TCATAGTGTGGTTACCGAAATTTAATAG-GATCAGGTTATTAAAATTTCTTAGGAAGGTTATCAA
1 TCATAGTGAGGTTACCAAAATTTAATAGCG---AGGTTATCAAAATTTCTTAGG-AGGTTATCAA
**
57032 AATTTCATAGTTCGGTTATCAAAATT
62 AATTTCATAGTAAGGTTATCAAAATT
* * * * * *
57058 TTATAAG-GAGGTTATCAAAATTTCATAGCGAGGTTATCATAATTTCATAAGGAGGTTATTAAAA
1 TCAT-AGTGAGGTTACCAAAATTTAATAGCGAGGTTATCAAAATTTC-TTAGGAGGTTA-TCAAA
* *
57122 ATCTCATAGTATGGTTATCAAAATT
63 ATTTCATAGTAAGGTTATCAAAATT
** * * ** *
57147 TCATAGTTTGATTGCCAAAATTTTGTAG-G-GGTTATCAAAATTT-TATAGTGAGGTTATCGAAA
1 TCATAGTGAGGTTACCAAAATTTAATAGCGAGGTTATCAAAATTTCT-TAG-GAGGTTATCAAAA
* * *
57209 TTTTATACG-GAGATTATCAAAATT
64 TTTCATA-GTAAGGTTATCAAAATT
* * * *
57233 TTATAATGTA-GTTATCAAAATTTTATAG
1 TCATAGTG-AGGTTACCAAAATTTAATAG
57261 TATGGTATTT
Statistics
Matches: 229, Mismatches: 51, Indels: 28
0.74 0.17 0.09
Matches are distributed among these distances:
85 1 0.00
86 42 0.18
87 22 0.10
88 45 0.20
89 49 0.21
90 67 0.29
91 3 0.01
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (87 bp):
TCATAGTGAGGTTACCAAAATTTAATAGCGAGGTTATCAAAATTTCTTAGGAGGTTATCAAAATT
TCATAGTAAGGTTATCAAAATT
Found at i:57116 original size:22 final size:21
Alignment explanation
Indices: 56887--57487 Score: 288
Period size: 22 Copynumber: 28.1 Consensus size: 21
56877 ATGTCATATT
* *
56887 GAGGTTATCAAAATTTTATGG
1 GAGGTTATCAAAATTTCATAG
* * *
56908 TGTGGTTACCAAAATTTCGTATG
1 -GAGGTTATCAAAATTTCATA-G
56931 GAGGTTATCAAAATTTCATAG
1 GAGGTTATCAAAATTTCATAG
*
56952 GAAGGTTACCAAAATTTCATAG
1 G-AGGTTATCAAAATTTCATAG
* * * *
56974 TGTGGTTACCGAAATTTAATAG
1 -GAGGTTATCAAAATTTCATAG
* *
56996 GATCAGGTTATTAAAATTTCTTAG
1 G---AGGTTATCAAAATTTCATAG
57020 GAAGGTTATCAAAATTTCATAG
1 G-AGGTTATCAAAATTTCATAG
** *
57042 TTCGGTTATCAAAATTTTATAAG
1 -GAGGTTATCAAAATTTCAT-AG
57065 GAGGTTATCAAAATTTCATAG
1 GAGGTTATCAAAATTTCATAG
*
57086 CGAGGTTATCATAATTTCATAAG
1 -GAGGTTATCAAAATTTCAT-AG
* *
57109 GAGGTTATTAAAAATCTCATAG
1 GAGGTTA-TCAAAATTTCATAG
*
57131 TATGGTTATCAAAATTTCATAG
1 GA-GGTTATCAAAATTTCATAG
** * ** **
57153 TTTGATTGCCAAAATTTTGTAG
1 -GAGGTTATCAAAATTTCATAG
*
57175 G-GGTTATCAAAATTTTATAG
1 GAGGTTATCAAAATTTCATAG
* *
57195 TGAGGTTATCGAAATTTTATACG
1 -GAGGTTATCAAAATTTCATA-G
* *
57218 GAGATTATCAAAATTTTATAATG
1 GAGGTTATCAAAATTTCAT-A-G
* *
57241 TA-GTTATCAAAATTTTATAG
1 GAGGTTATCAAAATTTCATAG
* **
57261 TATGG-TAT-TTAA---CA-AG
1 GA-GGTTATCAAAATTTCATAG
* *
57277 GATGTTTTCAAAA--T--TAG
1 GAGGTTATCAAAATTTCATAG
* * * *
57294 TGTGGTTACCTAAATTTCATTG
1 -GAGGTTATCAAAATTTCATAG
* *
57316 GAAGGTTATCAAAATTTAATTG
1 G-AGGTTATCAAAATTTCATAG
*
57338 TG-GGGTAGTCAAAATTTCATAG
1 -GAGGTTA-TCAAAATTTCATAG
*
57360 TGAGGTTGTC-----TTCATAG
1 -GAGGTTATCAAAATTTCATAG
* * *
57377 CGTGGTTATCGAAATATCATAGG
1 -GAGGTTATCAAAATTTCATA-G
*
57400 GAGATTAAT-AAAATTTCATAAG
1 GAGGTT-ATCAAAATTTCAT-AG
* *
57422 GAGTTTATCAAAATTTCTTAAG
1 GAGGTTATCAAAATTTCAT-AG
*
57444 G-GGTTATCAAAATTTTATAG
1 GAGGTTATCAAAATTTCATAG
**
57464 TGTTGTTATCAAAATTTCATAG
1 -GAGGTTATCAAAATTTCATAG
57486 GA
1 GA
57488 TTGAATCATC
Statistics
Matches: 446, Mismatches: 90, Indels: 87
0.72 0.14 0.14
Matches are distributed among these distances:
15 1 0.00
16 5 0.01
17 19 0.04
18 8 0.02
20 23 0.05
21 33 0.07
22 309 0.69
23 33 0.07
24 15 0.03
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.38
Consensus pattern (21 bp):
GAGGTTATCAAAATTTCATAG
Found at i:62116 original size:27 final size:27
Alignment explanation
Indices: 62058--62134 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 27
62048 AAGTGAGCCT
* *
62058 AAAATGACCAAAATGCCCTTAGTGTAA
1 AAAATGACCAAAATGCCCCTAGCGTAA
*
62085 AAAATGACCAAAATGCCCCTGGACGT-A
1 AAAATGACCAAAATGCCCCTAG-CGTAA
* *
62112 CAAATGACTAAAATGCCCTCTAG
1 AAAATGACCAAAATGCCC-CTAG
62135 ATGACCCTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 37 0.88
28 5 0.12
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTAGCGTAA
Found at i:64952 original size:21 final size:21
Alignment explanation
Indices: 64920--64961 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
64910 CAAAGAGAAC
64920 CATAATGTTATAGATGTGTTA
1 CATAATGTTATAGATGTGTTA
*
64941 CATATATG-TATATATGTGTTA
1 CATA-ATGTTATAGATGTGTTA
64962 TATTGGCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (21 bp):
CATAATGTTATAGATGTGTTA
Found at i:71723 original size:24 final size:24
Alignment explanation
Indices: 71696--71747 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
71686 TTCCAAGCGT
*
71696 GAATAGAGAAAATAAACATTATAA
1 GAATAGAGAAAATAAACATTACAA
71720 GAATAGAGAAAATAAACATTACAA
1 GAATAGAGAAAATAAACATTACAA
71744 GAAT
1 GAAT
71748 TTTTCTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.62, C:0.06, G:0.13, T:0.19
Consensus pattern (24 bp):
GAATAGAGAAAATAAACATTACAA
Done.