Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009401.1 Corchorus capsularis cultivar CVL-1 contig09422, 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: 27525
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2202 original size:12 final size:13
Alignment explanation
Indices: 2161--2205 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
2151 AATTATTGTT
2161 TGCTTTATTAATC
1 TGCTTTATTAATC
*
2174 TGCTTTATTAATT
1 TGCTTTATTAATC
2187 TGCTTTA-TAATC
1 TGCTTTATTAATC
2199 TGCTTTA
1 TGCTTTA
2206 GATTTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:5786 original size:14 final size:13
Alignment explanation
Indices: 5742--5790 Score: 55
Period size: 14 Copynumber: 3.7 Consensus size: 13
5732 TAAGAGACAT
*
5742 TTTTCAAAAATTG
1 TTTTCAAAAATAG
5755 TTTTCAGAAAA-AG
1 TTTTCA-AAAATAG
*
5768 GTTTCAAAAATGAG
1 TTTTCAAAAAT-AG
5782 TTTTCAAAA
1 TTTTCAAAA
5791 TGTTTTTGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 4 0.13
13 12 0.40
14 14 0.47
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (13 bp):
TTTTCAAAAATAG
Found at i:7961 original size:8 final size:8
Alignment explanation
Indices: 7913--8034 Score: 88
Period size: 8 Copynumber: 15.2 Consensus size: 8
7903 CACGATCTCT
7913 TTCTTCAA
1 TTCTTCAA
**
7921 TAATTCAA
1 TTCTTCAA
*
7929 TGCTTCAA
1 TTCTTCAA
*
7937 CTCTTCAA
1 TTCTTCAA
* *
7945 TTATCCAA
1 TTCTTCAA
7953 TTCTTCAA
1 TTCTTCAA
7961 TTAC-TCAA
1 TT-CTTCAA
7969 TTAC-TC-A
1 TT-CTTCAA
7976 TTGCTTCAA
1 TT-CTTCAA
*
7985 CTCTTCAA
1 TTCTTCAA
*
7993 TTCTTCTA
1 TTCTTCAA
* *
8001 TTATTCCA
1 TTCTTCAA
*
8009 TTATTCAA
1 TTCTTCAA
8017 TTCTTCAA
1 TTCTTCAA
*
8025 TGCTTCAA
1 TTCTTCAA
8033 TT
1 TT
8035 TATTTCAGAA
Statistics
Matches: 90, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
7 4 0.04
8 83 0.92
9 3 0.03
ACGTcount: A:0.28, C:0.25, G:0.02, T:0.45
Consensus pattern (8 bp):
TTCTTCAA
Found at i:8017 original size:48 final size:48
Alignment explanation
Indices: 7924--8032 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 48
7914 TCTTCAATAA
*
7924 TTCAATGCTTCAACTCTTCAATTATCCAATTCTTCAATTACTCAATTAC
1 TTCAATGCTTCAACTCTTCAATTATCCAATTATTCAATTACTCAATT-C
* * * * * *
7973 -TCATTGCTTCAACTCTTCAATTCTTCTATTATTCCATTATTCAATTC
1 TTCAATGCTTCAACTCTTCAATTATCCAATTATTCAATTACTCAATTC
8020 TTCAATGCTTCAA
1 TTCAATGCTTCAA
8033 TTTATTTCAG
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
47 1 0.02
48 50 0.98
ACGTcount: A:0.28, C:0.26, G:0.03, T:0.44
Consensus pattern (48 bp):
TTCAATGCTTCAACTCTTCAATTATCCAATTATTCAATTACTCAATTC
Found at i:8083 original size:8 final size:8
Alignment explanation
Indices: 8069--8351 Score: 133
Period size: 8 Copynumber: 34.2 Consensus size: 8
8059 CTTTCTTTCT
8069 TTCTTCAA
1 TTCTTCAA
*
8077 TTATTCAA
1 TTCTTCAA
*
8085 TGCTTCAA
1 TTCTTCAA
*
8093 CTCTTCAA
1 TTCTTCAA
*
8101 TTATTCAA
1 TTCTTCAA
*
8109 TGCTTCAAA
1 TTCTTC-AA
8118 TTCTTCAA
1 TTCTTCAA
* *
8126 TTATCCAA
1 TTCTTCAA
*
8134 TGCTTCAA
1 TTCTTCAA
8142 TTCTTCAA
1 TTCTTCAA
*
8150 TTATTCAA
1 TTCTTCAA
*
8158 TTTATTTCAGAA
1 -TT-CTTC--AA
*
8170 TGATC-TC-T
1 T--TCTTCAA
8178 TTCTTCAA
1 TTCTTCAA
8186 TTCTTCAA
1 TTCTTCAA
* *
8194 TGCTTCATT
1 TTCTTCA-A
*
8203 TTATTTCAGCA
1 TT-CTTCA--A
*
8214 TGATC-TC-T
1 T--TCTTCAA
8222 TTCTTCAA
1 TTCTTCAA
*
8230 TTATTCAA
1 TTCTTCAA
*
8238 TGCTTCAA
1 TTCTTCAA
*
8246 CTCTTCAA
1 TTCTTCAA
* *
8254 TTATCCAA
1 TTCTTCAA
* *
8262 TGCTTTAA
1 TTCTTCAA
*
8270 TTCTTCGA
1 TTCTTCAA
*
8278 TTATTCAA
1 TTCTTCAA
*
8286 TGCTTCAA
1 TTCTTCAA
*
8294 CTCTTCAA
1 TTCTTCAA
* *
8302 TTATCCAA
1 TTCTTCAA
*
8310 TTCTTTAA
1 TTCTTCAA
*
8318 TGCTTCAA
1 TTCTTCAA
*
8326 TTCTTAAA
1 TTCTTCAA
8334 TTCTTCAA
1 TTCTTCAA
*
8342 TGCTTCAA
1 TTCTTCAA
8350 TT
1 TT
8352 TATTTCAAAA
Statistics
Matches: 195, Mismatches: 64, Indels: 32
0.67 0.22 0.11
Matches are distributed among these distances:
6 4 0.02
7 4 0.02
8 160 0.82
9 10 0.05
10 7 0.04
11 6 0.03
12 2 0.01
13 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.46
Consensus pattern (8 bp):
TTCTTCAA
Found at i:8102 original size:24 final size:24
Alignment explanation
Indices: 8069--8158 Score: 153
Period size: 24 Copynumber: 3.7 Consensus size: 24
8059 CTTTCTTTCT
8069 TTCTTCAATTATTCAATGCTTCAA
1 TTCTTCAATTATTCAATGCTTCAA
*
8093 CTCTTCAATTATTCAATGCTTCAAA
1 TTCTTCAATTATTCAATGCTTC-AA
*
8118 TTCTTCAATTATCCAATGCTTCAA
1 TTCTTCAATTATTCAATGCTTCAA
8142 TTCTTCAATTATTCAAT
1 TTCTTCAATTATTCAAT
8159 TTATTTCAGA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
24 39 0.64
25 22 0.36
ACGTcount: A:0.30, C:0.22, G:0.03, T:0.44
Consensus pattern (24 bp):
TTCTTCAATTATTCAATGCTTCAA
Found at i:8190 original size:44 final size:44
Alignment explanation
Indices: 8136--8245 Score: 166
Period size: 44 Copynumber: 2.5 Consensus size: 44
8126 TTATCCAATG
*
8136 CTTCAATTCTTCAATTATTCAATTTATTTCAGAATGATCTCTTT
1 CTTCAATTCTTCAATGATTCAATTTATTTCAGAATGATCTCTTT
* * *
8180 CTTCAATTCTTCAATGCTTCATTTTATTTCAGCATGATCTCTTT
1 CTTCAATTCTTCAATGATTCAATTTATTTCAGAATGATCTCTTT
* *
8224 CTTCAATTATTCAATGCTTCAA
1 CTTCAATTCTTCAATGATTCAA
8246 CTCTTCAATT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 60 1.00
ACGTcount: A:0.25, C:0.21, G:0.05, T:0.48
Consensus pattern (44 bp):
CTTCAATTCTTCAATGATTCAATTTATTTCAGAATGATCTCTTT
Found at i:8390 original size:8 final size:8
Alignment explanation
Indices: 8377--8417 Score: 64
Period size: 8 Copynumber: 5.1 Consensus size: 8
8367 GGGGTGGTCT
8377 TTCTTCAA
1 TTCTTCAA
8385 TTCTTCAA
1 TTCTTCAA
*
8393 TGCTTCAA
1 TTCTTCAA
*
8401 TTCATCAA
1 TTCTTCAA
8409 TTCTTCAA
1 TTCTTCAA
8417 T
1 T
8418 GCATCAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.02, T:0.46
Consensus pattern (8 bp):
TTCTTCAA
Found at i:8409 original size:24 final size:24
Alignment explanation
Indices: 8381--8426 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
8371 TGGTCTTTCT
*
8381 TCAATTCTTCAATGCTTCAATTCA
1 TCAATTCTTCAATGCATCAATTCA
8405 TCAATTCTTCAATGCATCAATT
1 TCAATTCTTCAATGCATCAATT
8427 TATTTCAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.24, G:0.04, T:0.41
Consensus pattern (24 bp):
TCAATTCTTCAATGCATCAATTCA
Found at i:8426 original size:16 final size:16
Alignment explanation
Indices: 8377--8426 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
8367 GGGGTGGTCT
*
8377 TTCTTCAATTCTTCAA
1 TTCTTCAATTCATCAA
*
8393 TGCTTCAATTCATCAA
1 TTCTTCAATTCATCAA
*
8409 TTCTTCAATGCATCAA
1 TTCTTCAATTCATCAA
8425 TT
1 TT
8427 TATTTCAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.28, C:0.24, G:0.04, T:0.44
Consensus pattern (16 bp):
TTCTTCAATTCATCAA
Found at i:8458 original size:44 final size:44
Alignment explanation
Indices: 8409--8537 Score: 122
Period size: 44 Copynumber: 3.2 Consensus size: 44
8399 AATTCATCAA
*
8409 TTCTTCAATGCATCAATTTATTTCAGAATGATCGGGGGTAGTCT
1 TTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTAGTCT
* *
8453 TTCTTCAATTCTTCAA-TTA-TTC--AATG--C----GTCA---A
1 TTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGT-AGTCT
*
8485 TTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTGGTCT
1 TTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTAGTCT
8529 TTCTTCAAT
1 TTCTTCAAT
8538 TATTCAATGC
Statistics
Matches: 65, Mismatches: 6, Indels: 28
0.66 0.06 0.28
Matches are distributed among these distances:
32 15 0.23
33 3 0.05
34 5 0.08
35 1 0.02
36 4 0.06
38 2 0.03
40 4 0.06
42 5 0.08
43 3 0.05
44 23 0.35
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (44 bp):
TTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTAGTCT
Found at i:8466 original size:8 final size:8
Alignment explanation
Indices: 8453--8502 Score: 64
Period size: 8 Copynumber: 6.2 Consensus size: 8
8443 GGGGTAGTCT
8453 TTCTTCAA
1 TTCTTCAA
8461 TTCTTCAA
1 TTCTTCAA
*
8469 TTATTCAA
1 TTCTTCAA
* *
8477 TGCGTCAA
1 TTCTTCAA
8485 TTCTTCAA
1 TTCTTCAA
*
8493 TGCTTCAA
1 TTCTTCAA
8501 TT
1 TT
8503 TATTTCAGAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.26, C:0.22, G:0.06, T:0.46
Consensus pattern (8 bp):
TTCTTCAA
Found at i:8485 original size:76 final size:75
Alignment explanation
Indices: 8332--8690 Score: 518
Period size: 76 Copynumber: 4.8 Consensus size: 75
8322 TCAATTCTTA
* **
8332 AATTCTTCAATGCTTCAATTTATTTCAAAATGATC-GGGGTGGTCTTTCTTCAATTCTTCAATGC
1 AATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGT-GTCTTTCTTCAATTCTTCAATTA
*
8396 TTCAATTCATC
65 TTCAATGCATC
*
8407 AATTCTTCAATGCATCAATTTATTTCAGAATGATCGGGGGTAGTCTTTCTTCAATTCTTCAATTA
1 AATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGT-GTCTTTCTTCAATTCTTCAATTA
*
8472 TTCAATGCGTC
65 TTCAATGCATC
* **
8483 AATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTGGTCTTTCTTCAATTATTCAATGC
1 AATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGT-GTCTTTCTTCAATTCTTCAATTA
*
8548 TTCAATTCATC
65 TTCAATGCATC
*
8559 AATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTG---GTC-T---TTCTTCAATTAT
1 AATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTGTCTTTCTTCAATTCTTCAATTAT
*
8617 TCAATGCTTC
66 TCAATGCATC
8627 AATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTGATCTTTCTTCAATTCTTCAATT
1 AATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTG-TCTTTCTTCAATTCTTCAATT
8691 TAGTTCAGAA
Statistics
Matches: 254, Mismatches: 21, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
68 59 0.23
71 1 0.00
72 4 0.02
73 1 0.00
75 34 0.13
76 155 0.61
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.42
Consensus pattern (75 bp):
AATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTGTCTTTCTTCAATTCTTCAATTAT
TCAATGCATC
Found at i:8560 original size:24 final size:24
Alignment explanation
Indices: 8533--8578 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
8523 TGGTCTTTCT
8533 TCAATTATTCAATGCTTCAATTCA
1 TCAATTATTCAATGCTTCAATTCA
*
8557 TCAATTCTTCAATGCTTCAATT
1 TCAATTATTCAATGCTTCAATT
8579 TATTTCAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.43
Consensus pattern (24 bp):
TCAATTATTCAATGCTTCAATTCA
Found at i:8578 original size:16 final size:16
Alignment explanation
Indices: 8531--8577 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
8521 GGTGGTCTTT
*
8531 CTTCAATTATTCAATG
1 CTTCAATTCTTCAATG
* *
8547 CTTCAATTCATCAATT
1 CTTCAATTCTTCAATG
*
8563 CTTCAATGCTTCAAT
1 CTTCAATTCTTCAAT
8578 TTATTTCAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.04, T:0.43
Consensus pattern (16 bp):
CTTCAATTCTTCAATG
Found at i:8578 original size:152 final size:144
Alignment explanation
Indices: 8332--8689 Score: 583
Period size: 144 Copynumber: 2.4 Consensus size: 144
8322 TCAATTCTTA
*
8332 AATTCTTCAATGCTTCAATTTATTTCAAAATGATC-GGGGTGGTCTTTCTTCAATTCTTCAATGC
1 AATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTGGTCTTTCTTCAATTCTTCAATGC
*
8396 TTCAATTCATCAATTCTTCAATGCATCAATTTATTTCAGAATGATCGGGGGTAGTCTTTCTTCAA
66 TTCAATTCATCAATTCTTCAATGCATCAATTTATTTCAGAATGATCGGGGGT-G---GTC-T---
8461 TTCTTCAATTATTCAATGCGTC
123 TTCTTCAATTATTCAATGCGTC
*
8483 AATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTGGTCTTTCTTCAATTATTCAATGC
1 AATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTGGTCTTTCTTCAATTCTTCAATGC
*
8548 TTCAATTCATCAATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTGGTCTTTCTTCAA
66 TTCAATTCATCAATTCTTCAATGCATCAATTTATTTCAGAATGATCGGGGGTGGTCTTTCTTCAA
*
8613 TTATTCAATGCTTC
131 TTATTCAATGCGTC
*
8627 AATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTGATCTTTCTTCAATTCTTCAAT
1 AATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTGGTCTTTCTTCAATTCTTCAAT
8690 TTAGTTCAGA
Statistics
Matches: 199, Mismatches: 7, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
144 82 0.41
147 1 0.01
148 2 0.01
151 35 0.18
152 79 0.40
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.42
Consensus pattern (144 bp):
AATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTGGTCTTTCTTCAATTCTTCAATGC
TTCAATTCATCAATTCTTCAATGCATCAATTTATTTCAGAATGATCGGGGGTGGTCTTTCTTCAA
TTATTCAATGCGTC
Found at i:8621 original size:8 final size:8
Alignment explanation
Indices: 8605--8646 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
8595 GGGGTGGTCT
8605 TTCTTCAA
1 TTCTTCAA
*
8613 TTATTCAA
1 TTCTTCAA
*
8621 TGCTTCAA
1 TTCTTCAA
8629 TTCTTCAA
1 TTCTTCAA
*
8637 TGCTTCAA
1 TTCTTCAA
8645 TT
1 TT
8647 TATTTCAGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.48
Consensus pattern (8 bp):
TTCTTCAA
Found at i:8628 original size:16 final size:16
Alignment explanation
Indices: 8607--8646 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
8597 GGTGGTCTTT
8607 CTTCAATTATTCAATG
1 CTTCAATTATTCAATG
*
8623 CTTCAATTCTTCAATG
1 CTTCAATTATTCAATG
8639 CTTCAATT
1 CTTCAATT
8647 TATTTCAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.45
Consensus pattern (16 bp):
CTTCAATTATTCAATG
Found at i:8649 original size:68 final size:68
Alignment explanation
Indices: 8548--8689 Score: 248
Period size: 68 Copynumber: 2.1 Consensus size: 68
8538 TATTCAATGC
* *
8548 TTCAATTCATCAATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTGGTCTTTCTTCAA
1 TTCAATGCATCAATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTGATCTTTCTTCAA
8613 TTA
66 TTA
*
8616 TTCAATGCTTCAATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTGATCTTTCTTCAA
1 TTCAATGCATCAATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTGATCTTTCTTCAA
*
8681 TTC
66 TTA
8684 TTCAAT
1 TTCAAT
8690 TTAGTTCAGA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (68 bp):
TTCAATGCATCAATTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTGATCTTTCTTCAA
TTA
Found at i:8679 original size:36 final size:37
Alignment explanation
Indices: 8639--8769 Score: 113
Period size: 36 Copynumber: 3.4 Consensus size: 37
8629 TTCTTCAATG
8639 CTTCAATTTA-TTTCAGAATGATCGGGGGTGATCTTT
1 CTTCAATTTATTTTCAGAATGATCGGGGGTGATCTTT
** * *
8675 CTTCAATTCTTCAATTTAGTTCAGAACAATCGGGGGTGGTCTTA
1 CTTCAA-T-TT--A-TT--TTCAGAATGATCGGGGGTGATCTTT
* * *
8719 CTTCAGTTTA-TTTCAGAATGATCAGGGGTGATCGTT
1 CTTCAATTTATTTTCAGAATGATCGGGGGTGATCTTT
*
8755 CTTCAATTTAGTTTC
1 CTTCAATTTATTTTC
8770 TACAATTTAT
Statistics
Matches: 74, Mismatches: 12, Indels: 17
0.72 0.12 0.17
Matches are distributed among these distances:
36 34 0.46
37 5 0.07
38 3 0.04
40 2 0.03
42 3 0.04
43 1 0.01
44 26 0.35
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (37 bp):
CTTCAATTTATTTTCAGAATGATCGGGGGTGATCTTT
Found at i:8692 original size:44 final size:43
Alignment explanation
Indices: 8629--8762 Score: 138
Period size: 44 Copynumber: 3.2 Consensus size: 43
8619 AATGCTTCAA
*
8629 TTCTTCAATGCTTCAATTTATTTCAGAATGATCGGGGGTGATC
1 TTCTTCAATTCTTCAATTTATTTCAGAATGATCGGGGGTGATC
* **
8672 TTTCTTCAATTCTTCAATTTAGTTCAGAACAATCGGGGGTG---
1 -TTCTTCAATTCTTCAATTTATTTCAGAATGATCGGGGGTGATC
* * *
8713 GTCTT--A--CTTCAGTTTATTTCAGAATGATCAGGGGTGATC
1 TTCTTCAATTCTTCAATTTATTTCAGAATGATCGGGGGTGATC
8752 GTTCTTCAATT
1 -TTCTTCAATT
8763 TAGTTTCTAC
Statistics
Matches: 71, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
36 25 0.35
38 1 0.01
40 8 0.11
42 1 0.01
44 36 0.51
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.40
Consensus pattern (43 bp):
TTCTTCAATTCTTCAATTTATTTCAGAATGATCGGGGGTGATC
Found at i:10480 original size:48 final size:49
Alignment explanation
Indices: 10428--10520 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
10418 TTTTATCACA
*
10428 TTTGAAAGA-ATATTGCC-CTGTGTTATATGTGTTTAAGGACTTTGTATG
1 TTTGAAAGAGA-ATTGCCAATGTGTTATATGTGTTTAAGGACTTTGTATG
* **
10476 TTTGAAAGAGAGTTGCCAATGTGTTATATGTGTTTTGGGACTTTG
1 TTTGAAAGAGAATTGCCAATGTGTTATATGTGTTTAAGGACTTTG
10521 GCTATTGGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
48 14 0.36
49 25 0.64
ACGTcount: A:0.24, C:0.08, G:0.26, T:0.43
Consensus pattern (49 bp):
TTTGAAAGAGAATTGCCAATGTGTTATATGTGTTTAAGGACTTTGTATG
Found at i:18671 original size:4 final size:4
Alignment explanation
Indices: 18662--18695 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
18652 CACCTTTTAC
18662 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
18696 CATATGCAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:18886 original size:22 final size:22
Alignment explanation
Indices: 18861--18909 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
18851 CCCTTTAAAT
*
18861 AGAATCTTGGGTTCAAATCTAG
1 AGAATCTCGGGTTCAAATCTAG
18883 AGAATCTCGGGTTCAAATCTAG
1 AGAATCTCGGGTTCAAATCTAG
*
18905 TGAAT
1 AGAAT
18910 GGAGAAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (22 bp):
AGAATCTCGGGTTCAAATCTAG
Found at i:21394 original size:29 final size:29
Alignment explanation
Indices: 21362--21458 Score: 86
Period size: 29 Copynumber: 3.1 Consensus size: 29
21352 CGTGAAGAAG
* * *
21362 AAAGAAAAGAAACAGAAGAGAGAGAAAAA
1 AAAGAAAAGAAAAAGAAGAAAAAGAAAAA
* *
21391 AAAGGAAATAAAAAGAAGAAAAAGAAAAA
1 AAAGAAAAGAAAAAGAAGAAAAAGAAAAA
*
21420 ATAAGGAAAAAGAAAATGAAAAAGAAAAAGAAAAA
1 A-AA-G-AAAAG-AAA--AAGAAGAAAAAGAAAAA
21455 AAAG
1 AAAG
21459 CCACGTCAGA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
29 25 0.46
30 2 0.04
31 1 0.02
32 3 0.06
33 4 0.07
34 2 0.04
35 17 0.31
ACGTcount: A:0.76, C:0.01, G:0.20, T:0.03
Consensus pattern (29 bp):
AAAGAAAAGAAAAAGAAGAAAAAGAAAAA
Found at i:21417 original size:6 final size:6
Alignment explanation
Indices: 21356--21454 Score: 71
Period size: 6 Copynumber: 16.3 Consensus size: 6
21346 AAAGTTCGTG
* * *
21356 AAGAAGA AAG-AA AAGAAA CAGAAGA GAGAGAA AA-AAA AGGAAA TAA-AAA
1 AAGAA-A AAGAAA AAGAAA AAGAA-A AAGA-AA AAGAAA AAGAAA -AAGAAA
* * *
21405 GAAGAAA AAGAAA AA-ATA AGGAAA AAGAAA ATGAAA AAGAAA AAGAAA
1 -AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
21453 AA
1 AA
21455 AAAGCCACGT
Statistics
Matches: 73, Mismatches: 12, Indels: 15
0.73 0.12 0.15
Matches are distributed among these distances:
5 10 0.14
6 49 0.67
7 13 0.18
8 1 0.01
ACGTcount: A:0.76, C:0.01, G:0.20, T:0.03
Consensus pattern (6 bp):
AAGAAA
Done.