Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024270.1 Corchorus olitorius cultivar O-4 contig24303, 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: 51825
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:143 original size:27 final size:27
Alignment explanation
Indices: 113--166 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
103 TACACTAAGG
*
113 GCATATTCATGGGCATTTTAGTCATTT
1 GCATATTCAGGGGCATTTTAGTCATTT
* * *
140 GCATGTTCAGGGGTATTTTGGTCATTT
1 GCATATTCAGGGGCATTTTAGTCATTT
167 TAAGTTCACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.13, G:0.24, T:0.44
Consensus pattern (27 bp):
GCATATTCAGGGGCATTTTAGTCATTT
Found at i:2263 original size:24 final size:24
Alignment explanation
Indices: 2231--2280 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
2221 CGGGTTTGGA
2231 AGTTTAGAGAAAGGGGATCAATTT
1 AGTTTAGAGAAAGGGGATCAATTT
2255 AGTTTAGAGAAAGGGGATCAATTT
1 AGTTTAGAGAAAGGGGATCAATTT
2279 AG
1 AG
2281 AGTAGAGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.30, T:0.28
Consensus pattern (24 bp):
AGTTTAGAGAAAGGGGATCAATTT
Found at i:2294 original size:24 final size:24
Alignment explanation
Indices: 2235--2288 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2225 TTTGGAAGTT
**
2235 TAGAGAAAGGGGATCAATTTAGTT
1 TAGAGAAAGGGGATCAATTTAGAG
2259 TAGAGAAAGGGGATCAATTTAGAG
1 TAGAGAAAGGGGATCAATTTAGAG
2283 TAGAGA
1 TAGAGA
2289 TCGGGGTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.04, G:0.31, T:0.24
Consensus pattern (24 bp):
TAGAGAAAGGGGATCAATTTAGAG
Found at i:2952 original size:19 final size:19
Alignment explanation
Indices: 2928--2988 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 19
2918 CGGCCTAGTC
2928 CCTGATTTAAGATTTATTT
1 CCTGATTTAAGATTTATTT
* *
2947 CCTGATTTAATGCAATTTAGTC
1 CCTGATTTAA-G--ATTTATTT
*
2969 CCTGATTTAGGATTTTATTT
1 CCTGATTTAAGA-TTTATTT
2989 ACTCTTGATG
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
19 11 0.33
20 6 0.18
21 1 0.03
22 15 0.45
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (19 bp):
CCTGATTTAAGATTTATTT
Found at i:2972 original size:22 final size:19
Alignment explanation
Indices: 2923--2983 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
2913 TTATGCGGCC
2923 TAGTCCCTGATTTAAGATT
1 TAGTCCCTGATTTAAGATT
* *
2942 TATTTCCTGATTTAATGCAATT
1 TAGTCCCTGATTTAA-G--ATT
*
2964 TAGTCCCTGATTTAGGATT
1 TAGTCCCTGATTTAAGATT
2983 T
1 T
2984 TATTTACTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 17 0.50
20 1 0.03
21 1 0.03
22 15 0.44
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.46
Consensus pattern (19 bp):
TAGTCCCTGATTTAAGATT
Found at i:2973 original size:41 final size:40
Alignment explanation
Indices: 2923--3016 Score: 118
Period size: 40 Copynumber: 2.3 Consensus size: 40
2913 TTATGCGGCC
* *
2923 TAGTCCCTGATTTAAGA-TTTATTTCCTGATTTAATGCAATT
1 TAGTCCCTGATTTAAGATTTTATTTACT--CTTAATGCAATT
* *
2964 TAGTCCCTGATTTAGGATTTTATTTACTCTTGATGCAATT
1 TAGTCCCTGATTTAAGATTTTATTTACTCTTAATGCAATT
*
3004 TAATCCCTGATTT
1 TAGTCCCTGATTT
3017 TAGAAATTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
40 22 0.47
41 16 0.34
42 9 0.19
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (40 bp):
TAGTCCCTGATTTAAGATTTTATTTACTCTTAATGCAATT
Found at i:6634 original size:17 final size:16
Alignment explanation
Indices: 6606--6645 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
6596 CAAGAGACGT
**
6606 TTTTCAAGAAAAATTG
1 TTTTCAAGAAAAAAGG
6622 TTTTCAAGAAAAAAAGG
1 TTTTCAAG-AAAAAAGG
6639 TTTTCAA
1 TTTTCAA
6646 AAATGAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.35
Consensus pattern (16 bp):
TTTTCAAGAAAAAAGG
Found at i:8870 original size:39 final size:39
Alignment explanation
Indices: 8827--8912 Score: 154
Period size: 39 Copynumber: 2.2 Consensus size: 39
8817 AAAAGTACAC
* *
8827 TGGAAGACGGTTTGCTCGAAAATATTTTCAAATGTTGAT
1 TGGAAGACGGTTTGCTAGAAAAAATTTTCAAATGTTGAT
8866 TGGAAGACGGTTTGCTAGAAAAAATTTTCAAATGTTGAT
1 TGGAAGACGGTTTGCTAGAAAAAATTTTCAAATGTTGAT
8905 TGGAAGAC
1 TGGAAGAC
8913 AATCTTATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.34, C:0.09, G:0.24, T:0.33
Consensus pattern (39 bp):
TGGAAGACGGTTTGCTAGAAAAAATTTTCAAATGTTGAT
Found at i:9020 original size:67 final size:67
Alignment explanation
Indices: 8867--9011 Score: 254
Period size: 67 Copynumber: 2.2 Consensus size: 67
8857 AATGTTGATT
* *
8867 GGAAGACGGTTTGCTAGAAAAAATTTTCAAATGTTGATTGGAAGACAATCTTATTAAGGAGTACA
1 GGAAGACGGTTTGCTAGAAAAAATTTTCAAATGTTGACTGGAAGACAATCTTATTAAGGAATACA
8932 CC
66 CC
* *
8934 GGAAGACGGTTTGCTAGAAAGAATTTTGAAATGTTGACTGGAAGACAATCTTATTAAGGAATACA
1 GGAAGACGGTTTGCTAGAAAAAATTTTCAAATGTTGACTGGAAGACAATCTTATTAAGGAATACA
8999 CC
66 CC
9001 GGAAGACGGTT
1 GGAAGACGGTT
9012 ATTTAGAAAT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 74 1.00
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.27
Consensus pattern (67 bp):
GGAAGACGGTTTGCTAGAAAAAATTTTCAAATGTTGACTGGAAGACAATCTTATTAAGGAATACA
CC
Found at i:9346 original size:50 final size:50
Alignment explanation
Indices: 9218--9346 Score: 222
Period size: 50 Copynumber: 2.6 Consensus size: 50
9208 GATGATTTTC
* *
9218 TTAAGATTGAATTGGAAGACAGTTCAAACGATAAGCGGAAGACGGTCCTT
1 TTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACAGTCCTT
*
9268 TTGAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACAGTCCTT
1 TTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACAGTCCTT
*
9318 TTAAGATTGGATTGGAAGACAGTTCAAAG
1 TTAAGATTGAATTGGAAGACAGTTCAAAG
9347 AAGTTGATCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 74 1.00
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.25
Consensus pattern (50 bp):
TTAAGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACAGTCCTT
Found at i:12063 original size:22 final size:19
Alignment explanation
Indices: 12014--12074 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
12004 TTATGTGGCC
12014 TAGTCCCTGATTTAAGATT
1 TAGTCCCTGATTTAAGATT
** *
12033 TTTTTCCTGATTTAATGCAATT
1 TAGTCCCTGATTTAA-G--ATT
*
12055 TAGTCCCTGATTTAGGATT
1 TAGTCCCTGATTTAAGATT
12074 T
1 T
12075 TATTTACTCT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
19 16 0.50
20 1 0.03
21 1 0.03
22 14 0.44
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.48
Consensus pattern (19 bp):
TAGTCCCTGATTTAAGATT
Found at i:19333 original size:22 final size:21
Alignment explanation
Indices: 19281--19334 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
19271 TGCTTATTGA
19281 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
19302 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
19321 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
19335 CACGAATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:22214 original size:41 final size:41
Alignment explanation
Indices: 22112--22399 Score: 235
Period size: 41 Copynumber: 6.8 Consensus size: 41
22102 CCCAAAAACT
* * * *
22112 AAAGTCCCCAAACACATTTATAACACATGGGCGATTCTCTTTCT
1 AAAGTCCCCAAACACATTTATAACACA-GGGC-AATCT-ATACA
* *
22156 AAAGTCCTCAAAAACATTTATAACACAGAGGC-ATCTATACA
1 AAAGTCCCCAAACACATTTATAACACAG-GGCAATCTATACA
* * *
22197 AAAGTCCCCAAACACATTTATAACATAGGAGCAAATCTCTATA
1 AAAGTCCCCAAACACATTTATAACACAGG-GC-AATCTATACA
* *
22240 AAAGTCCTCAAACACATTTATAACACAGAGG-GATCTATACA
1 AAAGTCCCCAAACACATTTATAACACAG-GGCAATCTATACA
* * * *
22281 GAAGTCCCCAAAAACATTTATAACGTA-AGGGCAAT-TTTCTCTA
1 AAAGTCCCCAAACACATTTATAAC--ACAGGGCAATCTAT-AC-A
* * * *
22324 AAAGTCCTCAAACACATTTATAACATAGAGGC-ATCCATACT
1 AAAGTCCCCAAACACATTTATAACACAG-GGCAATCTATACA
* *
22365 AAAGTCCCTAAACACAATTATAACACAAGGGCAAT
1 AAAGTCCCCAAACACATTTATAACAC-AGGGCAAT
22400 TTCTATATGG
Statistics
Matches: 196, Mismatches: 33, Indels: 32
0.75 0.13 0.12
Matches are distributed among these distances:
40 1 0.01
41 87 0.44
42 17 0.09
43 62 0.32
44 29 0.15
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.24
Consensus pattern (41 bp):
AAAGTCCCCAAACACATTTATAACACAGGGCAATCTATACA
Found at i:22252 original size:43 final size:43
Alignment explanation
Indices: 22112--22348 Score: 193
Period size: 43 Copynumber: 5.6 Consensus size: 43
22102 CCCAAAAACT
* * * *
22112 AAAGTCCCCAAACACATTTATAACACATGG-GCGATTCTCTTTCT
1 AAAGTCCCCAAACACATTTATAACACA-GGAGCAAATCTCTAT-A
* * * *
22156 AAAGTCCTCAAAAACATTTATAACACA-GAGGC--ATCTATACA
1 AAAGTCCCCAAACACATTTATAACACAGGA-GCAAATCTCTATA
*
22197 AAAGTCCCCAAACACATTTATAACATAGGAGCAAATCTCTATA
1 AAAGTCCCCAAACACATTTATAACACAGGAGCAAATCTCTATA
* ** * *
22240 AAAGTCCTCAAACACATTTATAACACA-GAG-GGATCTATACA
1 AAAGTCCCCAAACACATTTATAACACAGGAGCAAATCTCTATA
* * * * *
22281 GAAGTCCCCAAAAACATTTATAACGTA-AGG-GCAATTTTCTCTA
1 AAAGTCCCCAAACACATTTATAAC--ACAGGAGCAAATCTCTATA
*
22324 AAAGTCCTCAAACACATTTATAACA
1 AAAGTCCCCAAACACATTTATAACA
22349 TAGAGGCATC
Statistics
Matches: 153, Mismatches: 31, Indels: 21
0.75 0.15 0.10
Matches are distributed among these distances:
41 55 0.36
42 12 0.08
43 59 0.39
44 27 0.18
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (43 bp):
AAAGTCCCCAAACACATTTATAACACAGGAGCAAATCTCTATA
Found at i:22270 original size:84 final size:83
Alignment explanation
Indices: 22112--22406 Score: 376
Period size: 84 Copynumber: 3.5 Consensus size: 83
22102 CCCAAAAACT
* * * * *
22112 AAAGTCCCCAAACACATTTATAACACATGGGCGATTCTCTTTCTAAAGTCCTCAAAAACATTTAT
1 AAAGTCCCCAAACACATTTATAACATA-GGGCAATTCTCTAT-AAAAGTCCTCAAACACATTTAT
22177 AACACAGAGGCATCTATACA
64 AACACAGAGGCATCTATACA
*
22197 AAAGTCCCCAAACACATTTATAACATAGGAGCAAATCTCTATAAAAGTCCTCAAACACATTTATA
1 AAAGTCCCCAAACACATTTATAACATAGG-GCAATTCTCTATAAAAGTCCTCAAACACATTTATA
*
22262 ACACAGAGGGATCTATACA
65 ACACAGAGGCATCTATACA
* * * * *
22281 GAAGTCCCCAAAAACATTTATAACGTAAGGGCAATTTTCTCTAAAAGTCCTCAAACACATTTATA
1 AAAGTCCCCAAACACATTTATAACAT-AGGGCAATTCTCTATAAAAGTCCTCAAACACATTTATA
* * *
22346 ACATAGAGGCATCCATACT
65 ACACAGAGGCATCTATACA
* * *
22365 AAAGTCCCTAAACACAATTATAACACAAGGGCAATT-TCTATA
1 AAAGTCCCCAAACACATTTATAACA-TAGGGCAATTCTCTATA
22407 TGGCAAAGGC
Statistics
Matches: 183, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
83 5 0.03
84 140 0.77
85 38 0.21
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (83 bp):
AAAGTCCCCAAACACATTTATAACATAGGGCAATTCTCTATAAAAGTCCTCAAACACATTTATAA
CACAGAGGCATCTATACA
Found at i:32686 original size:13 final size:12
Alignment explanation
Indices: 32668--32702 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
32658 CAGATAATCG
32668 AAAAAAGAAAAGA
1 AAAAAAGAAAA-A
32681 AAAAAAGAAAAA
1 AAAAAAGAAAAA
32693 AAGAAAAGAA
1 AA-AAAAGAA
32703 GGCAAACCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 3 0.14
13 18 0.86
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:32688 original size:8 final size:8
Alignment explanation
Indices: 32675--32699 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
32665 TCGAAAAAAG
32675 AAAAGAAA
1 AAAAGAAA
32683 AAAAGAAA
1 AAAAGAAA
32691 AAAAGAAA
1 AAAAGAAA
32699 A
1 A
32700 GAAGGCAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:35731 original size:28 final size:27
Alignment explanation
Indices: 35695--35768 Score: 94
Period size: 28 Copynumber: 2.7 Consensus size: 27
35685 GATCAACTAG
35695 GGGGCATTTTGGTCATTTTCAAGATCCA
1 GGGGCATTTTGGTCATTTTCAAG-TCCA
* * * *
35723 GGGGCATTTTAGTCATTTGCACGTCTA
1 GGGGCATTTTGGTCATTTTCAAGTCCA
*
35750 AGGGCATTTTGGTCATTTT
1 GGGGCATTTTGGTCATTTT
35769 AGGGTCACTT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 19 0.49
28 20 0.51
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.39
Consensus pattern (27 bp):
GGGGCATTTTGGTCATTTTCAAGTCCA
Found at i:35764 original size:27 final size:28
Alignment explanation
Indices: 35696--35767 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
35686 ATCAACTAGG
* *
35696 GGGCATTTTGGTCATTTTCAAGATCCAG
1 GGGCATTTTGGTCATTTGCAAGATCCAA
* * *
35724 GGGCATTTTAGTCATTTGCACG-TCTAA
1 GGGCATTTTGGTCATTTGCAAGATCCAA
35751 GGGCATTTTGGTCATTT
1 GGGCATTTTGGTCATTT
35768 TAGGGTCACT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
27 19 0.50
28 19 0.50
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (28 bp):
GGGCATTTTGGTCATTTGCAAGATCCAA
Found at i:36177 original size:20 final size:20
Alignment explanation
Indices: 36154--36194 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
36144 CCTTGTTTAA
36154 TTATTTGCATCCTTGGGCCT
1 TTATTTGCATCCTTGGGCCT
36174 TTATTTGCATCCTTGGGCCT
1 TTATTTGCATCCTTGGGCCT
36194 T
1 T
36195 AGACTTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.46
Consensus pattern (20 bp):
TTATTTGCATCCTTGGGCCT
Found at i:38588 original size:18 final size:18
Alignment explanation
Indices: 38565--38604 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
38555 GGTAAAGAAA
38565 AATTTC-TAGAATTAGTTT
1 AATTTCATAG-ATTAGTTT
*
38583 AATTTCATAGTTTAGTTT
1 AATTTCATAGATTAGTTT
38601 AATT
1 AATT
38605 GTCAATAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.53
Consensus pattern (18 bp):
AATTTCATAGATTAGTTT
Found at i:40504 original size:41 final size:40
Alignment explanation
Indices: 40409--40640 Score: 191
Period size: 41 Copynumber: 5.6 Consensus size: 40
40399 ATAACTAAAG
* * * * *
40409 TCCCCAAACACATTTATAAAACAGGGGCGATTCTCTTCCAAAA
1 TCCCTAAACACATTTATAACACAGAGGC-A-TCT-ATACAAAA
40452 GT-CCTCAAACACATTTATAACACAGAGGCATCTATACAAAA
1 -TCCCT-AAACACATTTATAACACAGAGGCATCTATACAAAA
* * *
40493 CTCCCTAAACACATTTATAACACAGCGGAAATTCTCT-CTAAAA
1 -TCCCTAAACACATTTATAACACAGAGG-CA-TCTATAC-AAAA
* * * *
40536 GCCCTCAAACACATTTATAACATAGAGG-TTATATACAGAAA
1 TCCCT-AAACACATTTATAACACAGAGGCATCTATACA-AAA
* * *
40577 TCCCCAAACACATTTATAACACAGAGGCATCCATACTAAAG
1 TCCCTAAACACATTTATAACACAGAGGCATCTATAC-AAAA
*
40618 TCCCTAAACACAATTATAACACA
1 TCCCTAAACACATTTATAACACA
40641 AGGGCAATTT
Statistics
Matches: 154, Mismatches: 24, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
40 25 0.16
41 63 0.41
42 13 0.08
43 31 0.20
44 22 0.14
ACGTcount: A:0.42, C:0.26, G:0.09, T:0.23
Consensus pattern (40 bp):
TCCCTAAACACATTTATAACACAGAGGCATCTATACAAAA
Found at i:40556 original size:84 final size:84
Alignment explanation
Indices: 40409--40600 Score: 262
Period size: 84 Copynumber: 2.3 Consensus size: 84
40399 ATAACTAAAG
* * ** *
40409 TCCCCAAACACATTTATAAAACAGGGGCGATTCTCTTCCAAAAGTCCTCAAACACATTTATAACA
1 TCCCCAAACACATTTATAACACAGCGGAAATTCTCTTCCAAAAGCCCTCAAACACATTTATAACA
*
40474 CAGAGGCATCTATACA-AAA
66 CAGAGG-ATATATACAGAAA
* *
40493 CTCCCTAAACACATTTATAACACAGCGGAAATTCTC-TCTAAAAGCCCTCAAACACATTTATAAC
1 -TCCCCAAACACATTTATAACACAGCGGAAATTCTCTTCCAAAAGCCCTCAAACACATTTATAAC
* *
40557 ATAGAGGTTATATACAGAAA
65 ACAGAGGATATATACAGAAA
40577 TCCCCAAACACATTTATAACACAG
1 TCCCCAAACACATTTATAACACAG
40601 AGGCATCCAT
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
83 30 0.32
84 35 0.37
85 30 0.32
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.23
Consensus pattern (84 bp):
TCCCCAAACACATTTATAACACAGCGGAAATTCTCTTCCAAAAGCCCTCAAACACATTTATAACA
CAGAGGATATATACAGAAA
Found at i:42390 original size:16 final size:16
Alignment explanation
Indices: 42371--42409 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
42361 AAATTTCTCG
42371 AACCCGAAATGACCCA
1 AACCCGAAATGACCCA
*
42387 AACCCAAAATGACCCA
1 AACCCGAAATGACCCA
42403 AACCCGA
1 AACCCGA
42410 TCAACCCGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.46, C:0.38, G:0.10, T:0.05
Consensus pattern (16 bp):
AACCCGAAATGACCCA
Found at i:43411 original size:2 final size:2
Alignment explanation
Indices: 43399--43463 Score: 78
Period size: 2 Copynumber: 31.0 Consensus size: 2
43389 GAAAGTCTAT
*
43399 TA TA CTA TA TA TA TA TA TA TT TA TA TA TA TA TA CTA TA T- TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
43442 CTA TA TA TA TA GTA TA TA TA TA
1 -TA TA TA TA TA -TA TA TA TA TA
43464 GTAAGTAGAC
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
1 1 0.02
2 47 0.84
3 8 0.14
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:44099 original size:51 final size:51
Alignment explanation
Indices: 44035--44151 Score: 135
Period size: 51 Copynumber: 2.3 Consensus size: 51
44025 GAACTGTAAC
* * * * *
44035 GACCCGAATCCGAAAACCCAAGGTTAAAACCCGAATTTATCCGAACCGCAT
1 GACCCGAAACCGAAAAACCAAGATTAAAACCCGAAATTATCCGAACAGCAT
* * * * * *
44086 GACCCGAACCCGAAAAATCGAGATTCAAACCCGAAATTATCCTAACAGTAT
1 GACCCGAAACCGAAAAACCAAGATTAAAACCCGAAATTATCCGAACAGCAT
44137 GACCCGAAACCGAAA
1 GACCCGAAACCGAAA
44152 GCAACCCAAC
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.40, C:0.30, G:0.15, T:0.15
Consensus pattern (51 bp):
GACCCGAAACCGAAAAACCAAGATTAAAACCCGAAATTATCCGAACAGCAT
Found at i:44189 original size:15 final size:17
Alignment explanation
Indices: 44155--44191 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
44145 ACCGAAAGCA
44155 ACCC-AACCCAGAATTG
1 ACCCGAACCCAGAATTG
44171 ACCCGAACCCA-AA-TG
1 ACCCGAACCCAGAATTG
44186 ACCCGA
1 ACCCGA
44192 CATATGAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
16 6 0.30
17 6 0.30
ACGTcount: A:0.38, C:0.41, G:0.14, T:0.08
Consensus pattern (17 bp):
ACCCGAACCCAGAATTG
Found at i:46116 original size:26 final size:26
Alignment explanation
Indices: 46086--46135 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
46076 CAAATATAGT
46086 AATTATACTTTCCCACAAAAATAAAA
1 AATTATACTTTCCCACAAAAATAAAA
**
46112 AATTATACTTTCCCATTAAAATAA
1 AATTATACTTTCCCACAAAAATAA
46136 CATTCTTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (26 bp):
AATTATACTTTCCCACAAAAATAAAA
Found at i:46539 original size:17 final size:16
Alignment explanation
Indices: 46499--46541 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
46489 CATGTAATCT
*
46499 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
46515 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
46532 TTAGATCACT
1 TT-GATCACT
46542 AGTAATCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 20 0.83
18 1 0.04
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:46549 original size:17 final size:16
Alignment explanation
Indices: 46492--46549 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
46482 ATAAACCCAT
*
46492 GTAATCTTTGATCACCG
1 GTAATC-TTGATCACTG
*
46509 GTGATCTTGCATCACTG
1 GTAATCTTG-ATCACTG
* *
46526 GTGATCTTAGATCACTA
1 GTAATCTT-GATCACTG
46543 GTAATCT
1 GTAATCT
46550 AAGGGGTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
16 3 0.09
17 31 0.89
18 1 0.03
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (16 bp):
GTAATCTTGATCACTG
Found at i:51226 original size:75 final size:76
Alignment explanation
Indices: 51068--51231 Score: 167
Period size: 75 Copynumber: 2.2 Consensus size: 76
51058 CATGTTGCTA
* * *
51068 ATTCGAATTCAAATAATGAGTTTGCTGATGGTGTTAGGCAAAATCTTGAAGTTGATTCACCTGAT
1 ATTCGAATTCAAATAATAAGTTTGCTGATGATGTTAGGCAAAATCTTGAAGCTGATTCACCTGAT
*
51133 CAGATTCCTCTT
66 CAGATT-CTCTG
* * * * *
51145 A-T-GAATTCAAATACTAAGTTTTCTGATGATGATT-TGCAACAA-CTTGAAGCTGATTCACTTT
1 ATTCGAATTCAAATAATAAGTTTGCTGATGATG-TTAGGCAA-AATCTTGAAGCTGATTCACCTG
*
51206 ATCAGGTT-TCTG
64 ATCAGATTCTCTG
*
51218 ATTCGAATTTAAAT
1 ATTCGAATTCAAAT
51232 TTGAGCATCA
Statistics
Matches: 72, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
73 4 0.06
74 1 0.01
75 61 0.85
76 5 0.07
77 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (76 bp):
ATTCGAATTCAAATAATAAGTTTGCTGATGATGTTAGGCAAAATCTTGAAGCTGATTCACCTGAT
CAGATTCTCTG
Done.