Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007123.1 Corchorus capsularis cultivar CVL-1 contig07144, 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: 20582
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Found at i:116 original size:13 final size:13
Alignment explanation
Indices: 84--117 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
74 GTTTTTTCTT
84 AAATTATTTTTTA
1 AAATTATTTTTTA
**
97 AGGTTATTTTTTA
1 AAATTATTTTTTA
110 AAATTATT
1 AAATTATT
118 AGTTTTAATA
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (13 bp):
AAATTATTTTTTA
Found at i:280 original size:21 final size:21
Alignment explanation
Indices: 254--298 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
244 TAATACTGGA
254 TTGCTAAAT-ACCGCCCCATTT
1 TTGCT-AATCACCGCCCCATTT
*
275 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
296 TTG
1 TTG
299 ACGCTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.18, C:0.33, G:0.11, T:0.38
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:567 original size:32 final size:32
Alignment explanation
Indices: 514--662 Score: 147
Period size: 32 Copynumber: 4.6 Consensus size: 32
504 CCGTGGCGAA
* ** *
514 GCCGCCCCACTTGGGAAGCTTCGCCATGGCAA
1 GCCGCCCCACTGGGGCGGCTTCGCCATGGCAG
*
546 GCCGCCCTCA-TGGGGCGGCTTCACCATGGGCAG
1 GCCGCCC-CACTGGGGCGGCTTCGCCAT-GGCAG
* * *
579 GCCGCCCCACTGGGGCGGCTTAGACAGGGCAG
1 GCCGCCCCACTGGGGCGGCTTCGCCATGGCAG
* ** *
611 GCCGTCCCGGTGGGGCGGCTTCGCCACGGCAG
1 GCCGCCCCACTGGGGCGGCTTCGCCATGGCAG
* *
643 GCTGCCCCAGTGGGGCGGCT
1 GCCGCCCCACTGGGGCGGCT
663 CGGCTATTTT
Statistics
Matches: 96, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
32 70 0.73
33 26 0.27
ACGTcount: A:0.12, C:0.36, G:0.38, T:0.13
Consensus pattern (32 bp):
GCCGCCCCACTGGGGCGGCTTCGCCATGGCAG
Found at i:842 original size:32 final size:33
Alignment explanation
Indices: 733--846 Score: 103
Period size: 33 Copynumber: 3.5 Consensus size: 33
723 CCGGTGCCGT
* *
733 CCCCCTGGGGCGG--CTGAGCCATGGCCAAG-CCG
1 CCCCCTGGGGCGGCACT-A-CCATGGACAGGACCG
* *
765 CCCTCCTGGGGCGACACTACCATGGCCAGGA-CG
1 CCC-CCTGGGGCGGCACTACCATGGACAGGACCG
* *
798 CCTCCCTGGGGCGGCCCTACCATGGATA-GACCG
1 CC-CCCTGGGGCGGCACTACCATGGACAGGACCG
831 CCCCCTGGGGCGGCAC
1 CCCCCTGGGGCGGCAC
847 CGGTACTAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
32 18 0.26
33 47 0.68
34 2 0.03
35 2 0.03
ACGTcount: A:0.14, C:0.41, G:0.33, T:0.11
Consensus pattern (33 bp):
CCCCCTGGGGCGGCACTACCATGGACAGGACCG
Found at i:959 original size:32 final size:32
Alignment explanation
Indices: 908--1050 Score: 216
Period size: 32 Copynumber: 4.4 Consensus size: 32
898 AAAAAGCCTT
* *
908 GCCGCCCTAGTGGGGCGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
940 GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
* *
972 GCCGTCCTAGTGGGGCGGCTAGCCATGGCAGA
1 GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
*
1004 GCCGTCCTAGTGGGGA-GGCTCCGCCGTGGCAGA
1 GCCGTCCTAGT-GGGACGGCT-AGCCGTGGCAGA
1037 GCCGTCCTAGTGGG
1 GCCGTCCTAGTGGG
1051 TAGGCTCCGC
Statistics
Matches: 102, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
32 78 0.76
33 24 0.24
ACGTcount: A:0.13, C:0.29, G:0.42, T:0.15
Consensus pattern (32 bp):
GCCGTCCTAGTGGGACGGCTAGCCGTGGCAGA
Found at i:3415 original size:28 final size:27
Alignment explanation
Indices: 3384--3484 Score: 100
Period size: 28 Copynumber: 3.7 Consensus size: 27
3374 AGGGTCATCC
3384 AGGGGCATTTTGGTCATTTTCACATCAT
1 AGGGGCATTTTGGTCATTTTCACAT-AT
3412 AGGGGCATTTTGGTCATTCTTGCAC-TA-
1 AGGGGCATTTTGGTCATT-TT-CACATAT
* * * *
3439 A-GGGTATTTTGGTCATTTGCATATTT
1 AGGGGCATTTTGGTCATTTTCACATAT
* *
3465 AGGGACATTTTGGTAATTTT
1 AGGGGCATTTTGGTCATTTT
3485 TAGTACACCT
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
24 2 0.03
25 2 0.03
26 16 0.27
27 15 0.25
28 19 0.32
29 3 0.05
30 3 0.05
ACGTcount: A:0.21, C:0.13, G:0.24, T:0.43
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTCACATAT
Found at i:7759 original size:27 final size:26
Alignment explanation
Indices: 7721--7849 Score: 147
Period size: 27 Copynumber: 4.9 Consensus size: 26
7711 GTAATCAGTA
7721 ATCAGTAAAAAGAGTAAGAAAAGAGCC
1 ATCAGTAAAAAGAGTAAGAAAAGAG-C
* *
7748 ATCAGTAAAAAGAGTAAG-AAACAGT
1 ATCAGTAAAAAGAGTAAGAAAAGAGC
*
7773 ATTCAGTAAAAAGAATAAGAAAAGAGTC
1 A-TCAGTAAAAAGAGTAAGAAAAGAG-C
* *
7801 ATCAGTAAAAAGAGTAGGAAATA-A-T
1 ATCAGTAAAAAGAGTAAGAAA-AGAGC
7826 ATTCAGTAAAAAGAGTAAGAAAAG
1 A-TCAGTAAAAAGAGTAAGAAAAG
7850 TGCGATAGTA
Statistics
Matches: 87, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
25 3 0.03
26 40 0.46
27 42 0.48
28 2 0.02
ACGTcount: A:0.57, C:0.07, G:0.20, T:0.16
Consensus pattern (26 bp):
ATCAGTAAAAAGAGTAAGAAAAGAGC
Found at i:7778 original size:26 final size:25
Alignment explanation
Indices: 7716--7847 Score: 138
Period size: 26 Copynumber: 5.0 Consensus size: 25
7706 AATTAGTAAT
7716 CAGTAATCAGTAAAAAGAGTAAGAAAA
1 CAGT-ATCAGTAAAAAGAGTAAG-AAA
* *
7743 GAGCCATCAGTAAAAAGAGTAAGAAA
1 CAG-TATCAGTAAAAAGAGTAAGAAA
*
7769 CAGTATTCAGTAAAAAGAATAAGAAAA
1 CAGTA-TCAGTAAAAAGAGTAAG-AAA
* *
7796 GAGTCATCAGTAAAAAGAGTAGGAAA
1 CAGT-ATCAGTAAAAAGAGTAAGAAA
* *
7822 TAATATTCAGTAAAAAGAGTAAGAAA
1 CAGTA-TCAGTAAAAAGAGTAAGAAA
7848 AGTGCGATAG
Statistics
Matches: 89, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
25 2 0.02
26 45 0.51
27 41 0.46
28 1 0.01
ACGTcount: A:0.56, C:0.08, G:0.20, T:0.17
Consensus pattern (25 bp):
CAGTATCAGTAAAAAGAGTAAGAAA
Found at i:7779 original size:53 final size:53
Alignment explanation
Indices: 7716--7849 Score: 214
Period size: 53 Copynumber: 2.5 Consensus size: 53
7706 AATTAGTAAT
*
7716 CAGTAATCAGTAAAAAGAGTAAGAAAAGAGCCATCAGTAAAAAGAGTAAGAAA
1 CAGTATTCAGTAAAAAGAGTAAGAAAAGAGCCATCAGTAAAAAGAGTAAGAAA
* * *
7769 CAGTATTCAGTAAAAAGAATAAGAAAAGAGTCATCAGTAAAAAGAGTAGGAAA
1 CAGTATTCAGTAAAAAGAGTAAGAAAAGAGCCATCAGTAAAAAGAGTAAGAAA
* *
7822 TAATATTCAGTAAAAAGAGTAAGAAAAG
1 CAGTATTCAGTAAAAAGAGTAAGAAAAG
7850 TGCGATAGTA
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 74 1.00
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.16
Consensus pattern (53 bp):
CAGTATTCAGTAAAAAGAGTAAGAAAAGAGCCATCAGTAAAAAGAGTAAGAAA
Found at i:7938 original size:7 final size:7
Alignment explanation
Indices: 7928--8065 Score: 63
Period size: 7 Copynumber: 19.7 Consensus size: 7
7918 AAAGGCAATC
7928 AGTAAAG
1 AGTAAAG
7935 AGTAAA-
1 AGTAAAG
*
7941 ATGGTAAAA
1 A--GTAAAG
*
7950 AGTAATG
1 AGTAAAG
**
7957 -GTAATC
1 AGTAAAG
*
7963 AGTAAAC
1 AGTAAAG
*
7970 AGTAAAAT
1 AGT-AAAG
7978 AGTAAAG
1 AGTAAAG
*
7985 AGTAAAA
1 AGTAAAG
**
7992 AGTAATC
1 AGTAAAG
7999 AGTAAAG
1 AGTAAAG
8006 AG-AAATG
1 AGTAAA-G
8013 -GTAAAG
1 AGTAAAG
8019 AGTAATAG
1 AGTAA-AG
**
8027 AGTAATC
1 AGTAAAG
*
8034 AGTGAAG
1 AGTAAAG
*
8041 A-AAAATG
1 AGTAAA-G
8048 -GTAAAG
1 AGTAAAG
8054 AGTAAAG
1 AGTAAAG
8061 AGTAA
1 AGTAA
8066 TCAGTAAAGG
Statistics
Matches: 100, Mismatches: 19, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
6 14 0.14
7 67 0.67
8 18 0.18
9 1 0.01
ACGTcount: A:0.54, C:0.03, G:0.23, T:0.20
Consensus pattern (7 bp):
AGTAAAG
Found at i:7965 original size:35 final size:35
Alignment explanation
Indices: 7924--8101 Score: 220
Period size: 35 Copynumber: 5.1 Consensus size: 35
7914 TTGAAAAGGC
* *
7924 AATCAGTAAAGAGTAAAATGGTAAAAAGTAATG-GT
1 AATCAGTAAAGAG-AAAATGGTAAAGAGTAAAGAGT
* * *
7959 AATCAGTAAACAGTAAAATAGTAAAGAGTAAAAAGT
1 AATCAGTAAAGAG-AAAATGGTAAAGAGTAAAGAGT
7995 AATCAGTAAAGAG-AAATGGTAAAGAGTAATAGAGT
1 AATCAGTAAAGAGAAAATGGTAAAGAGTAA-AGAGT
*
8030 AATCAGTGAAGA-AAAATGGTAAAGAGTAAAGAGT
1 AATCAGTAAAGAGAAAATGGTAAAGAGTAAAGAGT
* *
8064 AATCAGTAAAG-GAAAAATGGTAAAGAATGAAGAGT
1 AATCAGTAAAGAG-AAAATGGTAAAGAGTAAAGAGT
8099 AAT
1 AAT
8102 TAGCAAAATG
Statistics
Matches: 126, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
34 30 0.24
35 82 0.65
36 14 0.11
ACGTcount: A:0.54, C:0.03, G:0.23, T:0.20
Consensus pattern (35 bp):
AATCAGTAAAGAGAAAATGGTAAAGAGTAAAGAGT
Found at i:7983 original size:15 final size:14
Alignment explanation
Indices: 7963--8004 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
7953 AATGGTAATC
7963 AGTAAACAGTAAAA
1 AGTAAACAGTAAAA
*
7977 TAGTAAAGAGTAAAA
1 -AGTAAACAGTAAAA
*
7992 AGTAATCAGTAAA
1 AGTAAACAGTAAA
8005 GAGAAATGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.60, C:0.05, G:0.17, T:0.19
Consensus pattern (14 bp):
AGTAAACAGTAAAA
Found at i:8052 original size:69 final size:69
Alignment explanation
Indices: 7924--8089 Score: 219
Period size: 69 Copynumber: 2.4 Consensus size: 69
7914 TTGAAAAGGC
* *
7924 AATCAGTAAAGAGTAAAATGGTAAAAAGTAATGGTAATCAGTAAACAGTAAAATAGTAAAGAGTA
1 AATCAGTAAAGAG--AAATGGTAAAGAGTAATGGTAATCAGTAAACAGAAAAATAGTAAAGAGTA
7989 AAAAGT
64 AAAAGT
* *
7995 AATCAGTAAAGAGAAATGGTAAAGAGTAATAGAGTAATCAGT-GA-AGAAAAATGGTAAAGAGTA
1 AATCAGTAAAGAGAAATGGTAAAGAGTAAT-G-GTAATCAGTAAACAGAAAAATAGTAAAGAGTA
*
8058 AAGAGT
64 AAAAGT
*
8064 AATCAGTAAAGGAAAAATGGTAAAGA
1 AATCAGTAAA-GAGAAATGGTAAAGA
8090 ATGAAGAGTA
Statistics
Matches: 86, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
69 48 0.56
70 16 0.19
71 22 0.26
ACGTcount: A:0.54, C:0.04, G:0.23, T:0.19
Consensus pattern (69 bp):
AATCAGTAAAGAGAAATGGTAAAGAGTAATGGTAATCAGTAAACAGAAAAATAGTAAAGAGTAAA
AAGT
Found at i:8121 original size:69 final size:70
Alignment explanation
Indices: 7924--8214 Score: 204
Period size: 69 Copynumber: 4.0 Consensus size: 70
7914 TTGAAAAGGC
* *
7924 AATCAGTAAAGAGTAAAATGGTAAA-AAGTAAT-G-GTAATCAGTAAACAGTAAAAT-AGTAAAG
1 AATCAGTAAAGA--AAAATGGTAAAGAA-TAATAGAGTAATCAGT-CA-AGAAAAATGAGTAAAG
*
7985 AGTAAAAAGT
61 AGTAAAGAGT
* * *
7995 AATCAGTAAAGAGAAATGGTAAAGAGTAATAGAGTAATCAGTGAAGAAAAATG-GTAAAGAGTAA
1 AATCAGTAAAGAAAAATGGTAAAGAATAATAGAGTAATCAGTCAAGAAAAATGAGTAAAGAGTAA
8059 AGAGT
66 AGAGT
* * ***
8064 AATCAGTAAAGGAAAAATGGTAAAGAATGA-AGAGTAATTAG-CAA-AATGGTAGAGTAAAGAGT
1 AATCAGTAAA-GAAAAATGGTAAAGAATAATAGAGTAATCAGTCAAGAAAAAT-GAGTAAAGAGT
*
8126 AAAGTAAAGAG
64 AAAG---AG-T
* * * * *
8137 AGATCAGTAAAAAAAAATGGTAAAGAGTAAAGTAAAAAGTAATCAGTAAAGAAAATATG-GTAAT
1 A-ATCAGTAAAGAAAAATGGTAAAGAAT-AA-T--AGAGTAATCAGTCAAGAAAA-ATGAGTAAA
*
8201 CAGTAAAGAGT
60 GAGTAAAGAGT
8212 AAT
1 AAT
8215 AGTGATCAGT
Statistics
Matches: 174, Mismatches: 26, Indels: 37
0.73 0.11 0.16
Matches are distributed among these distances:
67 3 0.02
68 3 0.02
69 69 0.40
70 19 0.11
71 21 0.12
72 2 0.01
73 16 0.09
74 12 0.07
75 1 0.01
76 2 0.01
78 9 0.05
79 13 0.07
80 3 0.02
81 1 0.01
ACGTcount: A:0.54, C:0.03, G:0.23, T:0.20
Consensus pattern (70 bp):
AATCAGTAAAGAAAAATGGTAAAGAATAATAGAGTAATCAGTCAAGAAAAATGAGTAAAGAGTAA
AGAGT
Found at i:8160 original size:39 final size:40
Alignment explanation
Indices: 8117--8411 Score: 149
Period size: 44 Copynumber: 7.1 Consensus size: 40
8107 AAATGGTAGA
*
8117 GTAAAGAGTAAAGTAAAGAG-AGATCAGTAAA-AAAAAATG
1 GTAAAGAGTAAAGTAAAAAGTA-ATCAGTAAAGAAAAAATG
*
8156 GTAAAGAGTAAAGTAAAAAGTAATCAGTAAAGAAAATATG
1 GTAAAGAGTAAAGTAAAAAGTAATCAGTAAAGAAAAAATG
** * * **
8196 GTAATCAGTAAAG-AGTAATAGTGATCAGT-AAGAAGTAATG
1 GTAAAGAGTAAAGTA--AAAAGTAATCAGTAAAGAAAAAATG
** *
8236 GTAATCAGTAAAAAGTAAAAAGGTAATCAATAAA-AAGTAAAATG
1 GTAAAGAGT--AAAGTAAAAA-GTAATCAGTAAAGAA--AAAATG
** * *
8280 GTAATCAGTAAAAAGT-AAAGGTAATCAGTGAAA-AGTAAAATG
1 GTAAAGAGT--AAAGTAAAAAGTAATCAGT-AAAGA-AAAAATG
* * *
8322 GTAATTAGA-AAAGAGTAAAAGGGTAATCAGTAAA-AAGTGAAATG
1 GTAA--AGAGTAA-AGTAAAA-AGTAATCAGTAAAGAA--AAAATG
** * *
8366 GTAATTAGTAAAAAGTAAAGAGTAATCAGTAAAGAAAAAATA
1 GTAAAGAGT--AAAGTAAAAAGTAATCAGTAAAGAAAAAATG
8408 GTAA
1 GTAA
8412 GAAGTTAGAA
Statistics
Matches: 203, Mismatches: 29, Indels: 45
0.73 0.10 0.16
Matches are distributed among these distances:
39 29 0.14
40 36 0.18
41 16 0.08
42 43 0.21
43 29 0.14
44 48 0.24
45 2 0.01
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (40 bp):
GTAAAGAGTAAAGTAAAAAGTAATCAGTAAAGAAAAAATG
Found at i:8263 original size:22 final size:22
Alignment explanation
Indices: 8165--8398 Score: 222
Period size: 22 Copynumber: 11.0 Consensus size: 22
8155 GGTAAAGAGT
8165 AAAGTAAAAA-GTAATCAGT--
1 AAAGTAAAAAGGTAATCAGTAA
8184 AAAG-AAAATATGGTAATCAGTAA
1 AAAGTAAAA-A-GGTAATCAGTAA
* * *
8207 AGAGT-AATA-GTGATCAGTAA
1 AAAGTAAAAAGGTAATCAGTAA
* *
8227 GAAGT--AATGGTAATCAGTAA
1 AAAGTAAAAAGGTAATCAGTAA
*
8247 AAAGTAAAAAGGTAATCAATAA
1 AAAGTAAAAAGGTAATCAGTAA
*
8269 AAAGTAAAATGGTAATCAGTAA
1 AAAGTAAAAAGGTAATCAGTAA
*
8291 AAAGT--AAAGGTAATCAGTGA
1 AAAGTAAAAAGGTAATCAGTAA
* *
8311 AAAGTAAAATGGTAATTAG-AA
1 AAAGTAAAAAGGTAATCAGTAA
*
8332 AAGAGTAAAAGGGTAATCAGTAA
1 AA-AGTAAAAAGGTAATCAGTAA
* * *
8355 AAAGTGAAATGGTAATTAGTAA
1 AAAGTAAAAAGGTAATCAGTAA
*
8377 AAAGTAAAGA-GTAATCAGTAA
1 AAAGTAAAAAGGTAATCAGTAA
8398 A
1 A
8399 GAAAAAATAG
Statistics
Matches: 175, Mismatches: 27, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
18 4 0.02
19 6 0.03
20 45 0.26
21 23 0.13
22 88 0.50
23 9 0.05
ACGTcount: A:0.54, C:0.04, G:0.21, T:0.22
Consensus pattern (22 bp):
AAAGTAAAAAGGTAATCAGTAA
Found at i:8296 original size:64 final size:64
Alignment explanation
Indices: 8219--8398 Score: 229
Period size: 64 Copynumber: 2.8 Consensus size: 64
8209 AGTAATAGTG
* *
8219 ATCAGTAAGAAGTAATGGTAATCAGTAAAAAGTAAAAAGGTAATCAATAAAAAGTAAAATGGTA
1 ATCAGTAAAAAGTAATGGTAATCAGTAAAAAGTAAAAAGGTAATCAATAAAAAGTAAAAGGGTA
* * * * *
8283 ATCAGTAAAAAGTAAAGGTAATCAGTGAAAAGTAAAATGGTAATTAGA-AAAGAGTAAAAGGGTA
1 ATCAGTAAAAAGTAATGGTAATCAGTAAAAAGTAAAAAGGTAATCA-ATAAAAAGTAAAAGGGTA
* * *
8347 ATCAGTAAAAAGTGAAATGGTAATTAGTAAAAAGTAAAGA-GTAATCAGTAAA
1 ATCAGTAAAAAGT--AATGGTAATCAGTAAAAAGTAAAAAGGTAATCAATAAA
8399 GAAAAAATAG
Statistics
Matches: 98, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
64 68 0.69
65 10 0.10
66 20 0.20
ACGTcount: A:0.54, C:0.04, G:0.21, T:0.22
Consensus pattern (64 bp):
ATCAGTAAAAAGTAATGGTAATCAGTAAAAAGTAAAAAGGTAATCAATAAAAAGTAAAAGGGTA
Found at i:8492 original size:64 final size:63
Alignment explanation
Indices: 8381--8506 Score: 150
Period size: 64 Copynumber: 2.0 Consensus size: 63
8371 TAGTAAAAAG
* * *
8381 TAAAGAGTAATCAGTAAAGAAAAAATAGTAAGAAGTTAGAAGAAATCAGTAAAATGGTAAAGGA
1 TAAAGAGTAATCAGTAAAGAAAAAATAGTAAGAAGTTAAAACAAATCAGTAAAA-AGTAAAGGA
* *
8445 TAAAGAGTAATCAGTAAAG-GAAAATGGT-AGAGAG-TAAAACATTAATCAGTAAAAAGTAAAGG
1 TAAAGAGTAATCAGTAAAGAAAAAATAGTAAGA-AGTTAAAACA--AATCAGTAAAAAGTAAAGG
8507 CAATCAGTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
62 8 0.15
63 16 0.30
64 30 0.56
ACGTcount: A:0.55, C:0.04, G:0.22, T:0.19
Consensus pattern (63 bp):
TAAAGAGTAATCAGTAAAGAAAAAATAGTAAGAAGTTAAAACAAATCAGTAAAAAGTAAAGGA
Found at i:8496 original size:42 final size:42
Alignment explanation
Indices: 8457--8581 Score: 135
Period size: 42 Copynumber: 3.0 Consensus size: 42
8447 AAGAGTAATC
* * *
8457 AGTAAAGGAAAAT-GGTAGAGAGTAAAACATTAATCAGTAAAA
1 AGTAAAGG-AAATCAGTAAAGAATAAAACATTAATCAGTAAAA
* * *
8499 AGTAAAGGCAATCAGTAAAGAATAAAATATTAATCAGTAAAG
1 AGTAAAGGAAATCAGTAAAGAATAAAACATTAATCAGTAAAA
* * * *
8541 AGTAAAGAGTAATCAGTAAAGAGTAAAATAATAATCAGTAA
1 AGTAAAG-GAAATCAGTAAAGAATAAAACATTAATCAGTAA
8582 GTGGTAATTA
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
41 3 0.04
42 39 0.54
43 30 0.42
ACGTcount: A:0.55, C:0.06, G:0.18, T:0.21
Consensus pattern (42 bp):
AGTAAAGGAAATCAGTAAAGAATAAAACATTAATCAGTAAAA
Found at i:8536 original size:22 final size:22
Alignment explanation
Indices: 8508--8581 Score: 105
Period size: 22 Copynumber: 3.4 Consensus size: 22
8498 AAGTAAAGGC
* *
8508 AATCAGTAAAGAATAAAATATT
1 AATCAGTAAAGAGTAAAATAAT
* *
8530 AATCAGTAAAGAGT-AAAGAGT
1 AATCAGTAAAGAGTAAAATAAT
8551 AATCAGTAAAGAGTAAAATAAT
1 AATCAGTAAAGAGTAAAATAAT
8573 AATCAGTAA
1 AATCAGTAA
8582 GTGGTAATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.41
22 27 0.59
ACGTcount: A:0.57, C:0.05, G:0.15, T:0.23
Consensus pattern (22 bp):
AATCAGTAAAGAGTAAAATAAT
Found at i:8546 original size:7 final size:7
Alignment explanation
Indices: 8534--8567 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
8524 AATATTAATC
8534 AGTAAAG
1 AGTAAAG
8541 AGTAAAG
1 AGTAAAG
**
8548 AGTAATC
1 AGTAAAG
8555 AGTAAAG
1 AGTAAAG
8562 AGTAAA
1 AGTAAA
8568 ATAATAATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.18
Consensus pattern (7 bp):
AGTAAAG
Found at i:8609 original size:21 final size:22
Alignment explanation
Indices: 8585--8625 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
8575 TCAGTAAGTG
* *
8585 GTAATTAGT-AAGCGTAAAATA
1 GTAATCAGTAAAGAGTAAAATA
8606 GTAATCAGTAAAGAGTAAAA
1 GTAATCAGTAAAGAGTAAAA
8626 GGTGATCAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.51, C:0.05, G:0.20, T:0.24
Consensus pattern (22 bp):
GTAATCAGTAAAGAGTAAAATA
Found at i:8611 original size:35 final size:36
Alignment explanation
Indices: 8549--8616 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
8539 AGAGTAAAGA
8549 GTAATCAGTAAAGAGTAAAATAATAATCAGTAAGTG
1 GTAATCAGTAAAGAGTAAAATAATAATCAGTAAGTG
* * *
8585 GTAATTAGT-AAGCGTAAAATAGTAATCAGTAA
1 GTAATCAGTAAAGAGTAAAATAATAATCAGTAA
8617 AGAGTAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 21 0.72
36 8 0.28
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (36 bp):
GTAATCAGTAAAGAGTAAAATAATAATCAGTAAGTG
Found at i:15259 original size:17 final size:17
Alignment explanation
Indices: 15237--15269 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
15227 CAAAACTTGA
*
15237 CTTTCAAGTTAGATTAC
1 CTTTCAAGTTAAATTAC
15254 CTTTCAAGTTAAATTA
1 CTTTCAAGTTAAATTA
15270 TTTACCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42
Consensus pattern (17 bp):
CTTTCAAGTTAAATTAC
Found at i:15455 original size:3 final size:3
Alignment explanation
Indices: 15442--15483 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
15432 AATCATATAT
15442 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
15484 ACAATACATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17359 original size:34 final size:34
Alignment explanation
Indices: 17316--17385 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
17306 TTACGCCATA
17316 TAAGCTTATACTTCCATGTCATCTTGATCCACCT
1 TAAGCTTATACTTCCATGTCATCTTGATCCACCT
17350 TAAGCTTATACTTCCATGTCATCTTGATCCACCT
1 TAAGCTTATACTTCCATGTCATCTTGATCCACCT
17384 TA
1 TA
17386 CTTTGTCTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.24, C:0.29, G:0.09, T:0.39
Consensus pattern (34 bp):
TAAGCTTATACTTCCATGTCATCTTGATCCACCT
Found at i:19245 original size:21 final size:21
Alignment explanation
Indices: 19220--19259 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
19210 TTTGCCTTTC
19220 TTCAACAATCTAAAAGCTAAA
1 TTCAACAATCTAAAAGCTAAA
19241 TTCAACAATCTAAAAGCTA
1 TTCAACAATCTAAAAGCTA
19260 TATTGTAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.20, G:0.05, T:0.25
Consensus pattern (21 bp):
TTCAACAATCTAAAAGCTAAA
Done.