Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014350.1 Corchorus capsularis cultivar CVL-1 contig14371, 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: 11389
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Found at i:1020 original size:43 final size:43
Alignment explanation
Indices: 957--1304 Score: 224
Period size: 43 Copynumber: 7.8 Consensus size: 43
947 TCCACAGTAA
957 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGAATGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGAATGTAATCAAC
* **
1000 AAGAGTAAAATAGTAGTCAGTAAAAAGT-A-AATAGTAATCAGT
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAT-GTAATCAAC
* * * * * **
1042 AAGAGTAAAAAAAAAAGTAATAAGTAAGAAGTAA-AAGGAAATCAGT
1 AAGAGT----AAAATAGTAATCAGTAAAAAGTAAGAATGTAATCAAC
* * * *
1088 AAGAGTAAAA-AGGTGATCAGTAAAGAGTAA-AAAGCTAATCAGC
1 AAGAGTAAAATA-GTAATCAGTAAAAAGTAAGAATG-TAATCAAC
* * * *
1131 AAGAAGTAAAA-AGATAATCAGTAAAACGCAAAAAGGTAATCAGTA-
1 AAG-AGTAAAATAG-TAATCAGTAAAAAGTAAGAATGTAATCA--AC
* * * * *
1176 AAAACTAAAAGAGTAATCAGTAAAAAAGGAGCAGAAAATAGTAATCAGTAA
1 AAGAGTAAAATAGTAATCAGT-AAAAAGTA--AG--AAT-GTAATCA--AC
* * *
1227 AAGAGTAAAATGGTAATCACTAAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGAATGTAATCAAC
*
1270 AAGAGTAAAATAGTAATCAGTACAAAGTAAAGAAT
1 AAGAGTAAAATAGTAATCAGTAAAAAGT-AAGAAT
1305 AATAAGTGAA
Statistics
Matches: 243, Mismatches: 40, Indels: 43
0.75 0.12 0.13
Matches are distributed among these distances:
41 4 0.02
42 35 0.14
43 63 0.26
44 46 0.19
45 20 0.08
46 34 0.14
47 4 0.02
48 2 0.01
49 2 0.01
50 17 0.07
51 16 0.07
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.18
Consensus pattern (43 bp):
AAGAGTAAAATAGTAATCAGTAAAAAGTAAGAATGTAATCAAC
Found at i:1033 original size:21 final size:22
Alignment explanation
Indices: 951--1300 Score: 222
Period size: 22 Copynumber: 15.6 Consensus size: 22
941 GGGGTTTCCA
951 CAGTAAAAGAGTAAAATAGTAAT
1 CAGTAAAA-AGTAAAATAGTAAT
974 CAGTAAAAAGTAAGAAT-GTAAT
1 CAGTAAAAAGTAA-AATAGTAAT
* *
996 CA--ACAAGAGTAAAATAGTAGT
1 CAGTA-AAAAGTAAAATAGTAAT
1017 CAGTAAAAAGT-AAATAGTAAT
1 CAGTAAAAAGTAAAATAGTAAT
** *
1038 CAGTAAGAGTAAAAAAAAAAGTAAT
1 CAGTAA-A--AAGTAAAATAGTAAT
* * * *
1063 AAGTAAGAAGTAAAA-GGAAAT
1 CAGTAAAAAGTAAAATAGTAAT
* *
1084 CAGT-AAGAGTAAAA-AGGTGAT
1 CAGTAAAAAGTAAAATA-GTAAT
*
1105 CAGTAAAGAGTAAAA-AGCTAAT
1 CAGTAAAAAGTAAAATAG-TAAT
* *
1127 CAGCAAGAAGTAAAA-AGATAAT
1 CAGTAAAAAGTAAAATAG-TAAT
* *
1149 CAGTAAAACGCAAAA-AGGTAAT
1 CAGTAAAAAGTAAAATA-GTAAT
* *
1171 CAGTAAAAACTAAAAGAGTAAT
1 CAGTAAAAAGTAAAATAGTAAT
*
1193 CAGTAAAAAAGGAGCAGAAAATAGTAAT
1 CAGT--AAAA--AG--TAAAATAGTAAT
*
1221 CAGTAAAAGAGTAAAATGGTAAT
1 CAGTAAAA-AGTAAAATAGTAAT
* *
1244 CACTAAAAAGTAAGAA-GGTAAT
1 CAGTAAAAAGTAA-AATAGTAAT
*
1266 CA--ACAAGAGTAAAATAGTAAT
1 CAGTA-AAAAGTAAAATAGTAAT
*
1287 CAGTACAAAGTAAA
1 CAGTAAAAAGTAAA
1301 GAATAATAAG
Statistics
Matches: 261, Mismatches: 41, Indels: 51
0.74 0.12 0.14
Matches are distributed among these distances:
20 15 0.06
21 57 0.22
22 113 0.43
23 34 0.13
24 6 0.02
25 17 0.07
26 5 0.02
28 14 0.05
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.18
Consensus pattern (22 bp):
CAGTAAAAAGTAAAATAGTAAT
Found at i:1067 original size:25 final size:27
Alignment explanation
Indices: 1018--1082 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 27
1008 AATAGTAGTC
* *
1018 AGTAAAAAGTAAATAGTAATCAGTAAG-
1 AGTAAAAAG-AAAAAGTAATAAGTAAGA
1045 AGTAAAAA-AAAAAGTAATAAGTAAGA
1 AGTAAAAAGAAAAAGTAATAAGTAAGA
*
1071 AGTAAAAGGAAA
1 AGTAAAAAGAAA
1083 TCAGTAAGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 15 0.45
26 7 0.21
27 11 0.33
ACGTcount: A:0.63, C:0.02, G:0.18, T:0.17
Consensus pattern (27 bp):
AGTAAAAAGAAAAAGTAATAAGTAAGA
Found at i:1199 original size:15 final size:15
Alignment explanation
Indices: 1181--1234 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
1171 CAGTAAAAAC
1181 TAAAAGAGTAATCAG
1 TAAAAGAGTAATCAG
* * *
1196 TAAAAAAG-GAGCAG
1 TAAAAGAGTAATCAG
*
1210 -AAAATAGTAATCAG
1 TAAAAGAGTAATCAG
1224 TAAAAGAGTAA
1 TAAAAGAGTAA
1235 AATGGTAATC
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 6 0.20
14 8 0.27
15 16 0.53
ACGTcount: A:0.57, C:0.06, G:0.20, T:0.17
Consensus pattern (15 bp):
TAAAAGAGTAATCAG
Found at i:2861 original size:28 final size:27
Alignment explanation
Indices: 2830--2929 Score: 98
Period size: 28 Copynumber: 3.7 Consensus size: 27
2820 AAGGTCATCC
2830 AGGGGCATTTTGGTCATTTTCACATCAT
1 AGGGGCATTTTGGTCATTTTCACAT-AT
*
2858 AGGGGCATTTTGGTCATTCTT-GCATA-
1 AGGGGCATTTTGGTCATT-TTCACATAT
* * * *
2884 A-GGGTATTTTGGTCATTTGCATATTT
1 AGGGGCATTTTGGTCATTTTCACATAT
* *
2910 AGGGACATTTTGGTAATTTT
1 AGGGGCATTTTGGTCATTTT
2930 TAGTACACCT
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
24 1 0.02
25 17 0.29
26 2 0.03
27 15 0.26
28 21 0.36
29 2 0.03
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.43
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTCACATAT
Found at i:3050 original size:33 final size:33
Alignment explanation
Indices: 3013--3081 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
3003 TGATGTGTAC
*
3013 TTTTGGCATTTTTTGCATCTTAACATTCTTGCA
1 TTTTGGCATTTTTTGCATCTCAACATTCTTGCA
* *
3046 TTTTGTCATTTTTTGCATCTCAATATTCTTGCA
1 TTTTGGCATTTTTTGCATCTCAACATTCTTGCA
3079 TTT
1 TTT
3082 CAGTCACATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.17, C:0.17, G:0.10, T:0.55
Consensus pattern (33 bp):
TTTTGGCATTTTTTGCATCTCAACATTCTTGCA
Found at i:7384 original size:23 final size:22
Alignment explanation
Indices: 7356--7679 Score: 134
Period size: 22 Copynumber: 15.0 Consensus size: 22
7346 GTAGTCAGTA
*
7356 AGAAGTAAAGGTAATTAGTAAAG
1 AGAA-TAAAGGTAATCAGTAAAG
*
7379 AGAAGTAAAGGTAATCATTAAA-
1 AGAA-TAAAGGTAATCAGTAAAG
*
7401 A-AATAAAAGGCAATCAGTAAAG
1 AGAAT-AAAGGTAATCAGTAAAG
*
7423 AGAA-AAATGGTAATTAGTAAAG
1 AGAATAAA-GGTAATCAGTAAAG
* *
7445 AAACAAAAAGGTAATCAGT-AAG
1 AGA-ATAAAGGTAATCAGTAAAG
* *
7467 CG-A-AATGGTAATCAGTAAA-
1 AGAATAAAGGTAATCAGTAAAG
* * * *
7486 AGTAA-AATA-ATAATCGGCAAAA
1 AG-AATAA-AGGTAATCAGTAAAG
*
7508 AGTAA-AAA-GTAATCAAT-AAG
1 AG-AATAAAGGTAATCAGTAAAG
* *
7528 A-AGTAAAAGGTAAACAGT-AAG
1 AGAAT-AAAGGTAATCAGTAAAG
* *
7549 AGTATAAAGGTAATCAGTGAAG
1 AGAATAAAGGTAATCAGTAAAG
*
7571 AGTAA-AAAGCTAATC-G-ATAAG
1 AG-AATAAAGGTAATCAGTA-AAG
* *
7592 A-AGTAAAAGGTAATCAGTAAAA
1 AGAAT-AAAGGTAATCAGTAAAG
* *
7614 AGCAA-AAAGGGCAATCAGTAAAA
1 AG-AATAAA-GGTAATCAGTAAAG
*
7637 AGTA-AAAGAGTAATCAGTAAAG
1 AGAATAAAG-GTAATCAGTAAAG
7659 AGTAA-AATA-GTAATCAGTAAA
1 AG-AATAA-AGGTAATCAGTAAA
7680 TCAGTAATTA
Statistics
Matches: 234, Mismatches: 39, Indels: 57
0.71 0.12 0.17
Matches are distributed among these distances:
18 1 0.00
19 14 0.06
20 10 0.04
21 75 0.32
22 77 0.33
23 52 0.22
24 5 0.02
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.19
Consensus pattern (22 bp):
AGAATAAAGGTAATCAGTAAAG
Found at i:7420 original size:44 final size:45
Alignment explanation
Indices: 7362--7659 Score: 143
Period size: 43 Copynumber: 6.9 Consensus size: 45
7352 AGTAAGAAGT
* * *
7362 AAAGGTAATTAGTAAAGAGAAGTAAA-GGTAATCATTAAA-AAA-TA
1 AAAGGTAATCAGTAAAGAGAA--AAATGGTAATCAGTAAAGAAACAA
* *
7406 AAAGGCAATCAGTAAAGAGAAAAATGGTAATTAGTAAAGAAACAA
1 AAAGGTAATCAGTAAAGAGAAAAATGGTAATCAGTAAAGAAACAA
* *
7451 AAAGGTAATCAGT-AAGCG--AAATGGTAATCAGTAAAAGTAA-AA
1 AAAGGTAATCAGTAAAGAGAAAAATGGTAATCAGT-AAAGAAACAA
* * * * * **
7493 TAA--TAATCGGCAAAAAGTAAAAA--GTAATCAAT-AAG-AAGTA
1 AAAGGTAATCAGTAAAGAG-AAAAATGGTAATCAGTAAAGAAACAA
* * * **
7533 AAAGGTAAACAGT-AAGAGTATAAA-GGTAATCAGTGAAG-AGTAA
1 AAAGGTAATCAGTAAAGAG-AAAAATGGTAATCAGTAAAGAAACAA
* * *
7576 AAAGCTAATC-G-ATAAGAAGTAAAA-GGTAATCAGTAAA-AAGCAA
1 AAAGGTAATCAGTA-AAG-AGAAAAATGGTAATCAGTAAAGAAACAA
* * *
7619 AAAGGGCAATCAGTAAAAAGTAAAA-GAGTAATCAGTAAAGA
1 AAA-GGTAATCAGTAAAGAGAAAAATG-GTAATCAGTAAAGA
7660 GTAAAATAGT
Statistics
Matches: 197, Mismatches: 35, Indels: 42
0.72 0.13 0.15
Matches are distributed among these distances:
39 2 0.01
40 12 0.06
41 12 0.06
42 42 0.21
43 55 0.28
44 44 0.22
45 28 0.14
46 2 0.01
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.18
Consensus pattern (45 bp):
AAAGGTAATCAGTAAAGAGAAAAATGGTAATCAGTAAAGAAACAA
Found at i:7571 original size:22 final size:20
Alignment explanation
Indices: 7307--7678 Score: 210
Period size: 21 Copynumber: 17.4 Consensus size: 20
7297 TAATCAGTAA
7307 AATCAGTAAGAGTAAAAGGT
1 AATCAGTAAGAGTAAAAGGT
* * *
7327 CATCAATAAGAGTAAAATAGT
1 AATCAGTAAGAGTAAAA-GGT
*
7348 AGTCAGTAAGAAGT-AAAGGT
1 AATCAGTAAG-AGTAAAAGGT
* *
7368 AATTAGTAAAGAGAAGTAAAGGT
1 AATCAGT-AAGAGTA--AAAGGT
* * * *
7391 AATCATTAAAAAATAAAAGGC
1 AATCAGT-AAGAGTAAAAGGT
*
7412 AATCAGTAAAGAGAAAAATGGT
1 AATCAGT-AAGAGTAAAA-GGT
* **
7434 AATTAGTAAAGAAACAAAAAGGT
1 AATCAGT-AAG--AGTAAAAGGT
* *
7457 AATCAGTAAGCG-AAATGGT
1 AATCAGTAAGAGTAAAAGGT
* **
7476 AATCAGTAAAAGTAAAATAAT
1 AATCAGTAAGAGTAAAA-GGT
* * * *
7497 AATCGGCAAAAAGTAAAAAGT
1 AATCAG-TAAGAGTAAAAGGT
*
7518 AATCAATAAGAAGTAAAAGGT
1 AATCAGTAAG-AGTAAAAGGT
*
7539 AAACAGTAAGAGTATAAAGGT
1 AATCAGTAAGAGTA-AAAGGT
*
7560 AATCAGTGAAGAGTAAAAAGCT
1 AATCAGT-AAGAGT-AAAAGGT
7582 AATC-GATAAGAAGTAAAAGGT
1 AATCAG-TAAG-AGTAAAAGGT
* * *
7603 AATCAGTAAAAAGCAAAAAGGGC
1 AATCAGT-AAGAG-TAAAA-GGT
*
7626 AATCAGTAAAAAGTAAAAGAGT
1 AATCAGT-AAGAGTAAAAG-GT
*
7648 AATCAGTAAAGAGTAAAATAGT
1 AATCAGT-AAGAGTAAAA-GGT
7670 AATCAGTAA
1 AATCAGTAA
7679 ATCAGTAATT
Statistics
Matches: 276, Mismatches: 52, Indels: 47
0.74 0.14 0.13
Matches are distributed among these distances:
19 16 0.06
20 33 0.12
21 95 0.34
22 85 0.31
23 41 0.15
24 6 0.02
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCAGTAAGAGTAAAAGGT
Found at i:7648 original size:15 final size:15
Alignment explanation
Indices: 7630--7671 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
7620 AAGGGCAATC
7630 AGTAAAAAGTAAAAG
1 AGTAAAAAGTAAAAG
**
7645 AGTAATCAGT-AAAG
1 AGTAAAAAGTAAAAG
7659 AGTAAAATAGTAA
1 AGTAAAA-AGTAA
7672 TCAGTAAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
14 9 0.43
15 11 0.52
16 1 0.05
ACGTcount: A:0.60, C:0.02, G:0.19, T:0.19
Consensus pattern (15 bp):
AGTAAAAAGTAAAAG
Found at i:7731 original size:55 final size:55
Alignment explanation
Indices: 7664--7982 Score: 489
Period size: 55 Copynumber: 5.8 Consensus size: 55
7654 TAAAGAGTAA
* *
7664 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTCTAGGT
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGT
* *
7719 AATAGTAATCAGTAAATCAGTAATTAAGT-AAAAGAGATTAATTAGAGTTAAGGT
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGT
* * *
7773 AATAGTAATCAGTAAATCAATAATTAAGT-AAAAGAGATTAATCAGAGACAACGT
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGT
* * *
7827 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAGGAGATTAATCAGAGACAACGT
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGT
*
7882 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAGGAGATTAATCAGAGTCAAGGT
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGT
* * * *
7937 AATAGTAATCAGTAAATCAGTAATCAGGTAAAAAGATAGTAATCAG
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAG
7983 TAAAATTGAT
Statistics
Matches: 245, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
54 98 0.40
55 147 0.60
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.26
Consensus pattern (55 bp):
AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGT
Found at i:7837 original size:163 final size:164
Alignment explanation
Indices: 7664--7982 Score: 516
Period size: 163 Copynumber: 1.9 Consensus size: 164
7654 TAAAGAGTAA
* * *
7664 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTCTAGGTAATAGTAATC
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGACAACGTAATAGTAATC
* *
7729 AGTAAATCAGTAATTAAGTAAAA-GAGATTAATTAGAGTTAAGGTAATAGTAATCAGTAAATCAA
66 AGTAAATCAGTAATTAAGTAAAAGGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAA
*
7793 TAATTAAGTAAAAGAGAT-TAATCAGAGACAACGT
131 TAATCAAGTAAAA-AGATATAATCAGAGACAACGT
* *
7827 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAGGAGATTAATCAGAGACAACGTAATAGTAATC
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGACAACGTAATAGTAATC
*
7892 AGTAAATCAGTAATTAAGTAAAAGGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAG
66 AGTAAATCAGTAATTAAGTAAAAGGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAA
*
7957 TAATCAGGTAAAAAGATAGTAATCAG
131 TAATCAAGTAAAAAGATA-TAATCAG
7983 TAAAATTGAT
Statistics
Matches: 143, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
163 87 0.61
164 49 0.34
165 7 0.05
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.26
Consensus pattern (164 bp):
AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGACAACGTAATAGTAATC
AGTAAATCAGTAATTAAGTAAAAGGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAA
TAATCAAGTAAAAAGATATAATCAGAGACAACGT
Found at i:7871 original size:26 final size:26
Alignment explanation
Indices: 7841--7927 Score: 72
Period size: 26 Copynumber: 3.2 Consensus size: 26
7831 GTAATCAGTA
7841 AATCAGTAATTAAGTAAAAGGAGATT
1 AATCAGTAATTAAGTAAAAGGAGATT
* * *
7867 AATCAG-AGA-CAACGTAATAGTA-ATCAGT
1 AATCAGTA-ATTAA-GTAAAAGGAGAT---T
7895 AAATCAGTAATTAAGTAAAAGGAGATT
1 -AATCAGTAATTAAGTAAAAGGAGATT
7922 AATCAG
1 AATCAG
7928 AGTCAAGGTA
Statistics
Matches: 46, Mismatches: 6, Indels: 18
0.66 0.09 0.26
Matches are distributed among these distances:
25 5 0.11
26 20 0.43
27 1 0.02
28 1 0.02
29 14 0.30
30 5 0.11
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.24
Consensus pattern (26 bp):
AATCAGTAATTAAGTAAAAGGAGATT
Found at i:8290 original size:22 final size:21
Alignment explanation
Indices: 8261--8380 Score: 97
Period size: 21 Copynumber: 5.8 Consensus size: 21
8251 AGGTATCTGA
* *
8261 AAGGGTAAAATGGTAATTAGT
1 AAGGGTAAAATAGTAATCAGT
8282 AAGGAGTAAAATAGTAATCAGT
1 AAGG-GTAAAATAGTAATCAGT
** * **
8304 AAAAAGTAAGAA-GGTAATCAAC
1 -AAGGGTAA-AATAGTAATCAGT
* *
8326 AAGAGTAAAATAGTAGTCAGT
1 AAGGGTAAAATAGTAATCAGT
8347 AA----AAAATAGTAATCAGT
1 AAGGGTAAAATAGTAATCAGT
8364 AAGGGTAAAATAGTAAT
1 AAGGGTAAAATAGTAAT
8381 ACGTAAAAGG
Statistics
Matches: 78, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
17 16 0.21
20 2 0.03
21 30 0.38
22 26 0.33
23 4 0.05
ACGTcount: A:0.52, C:0.04, G:0.22, T:0.23
Consensus pattern (21 bp):
AAGGGTAAAATAGTAATCAGT
Found at i:8354 original size:17 final size:17
Alignment explanation
Indices: 8332--8365 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
8322 CAACAAGAGT
*
8332 AAAATAGTAGTCAGTAA
1 AAAATAGTAATCAGTAA
8349 AAAATAGTAATCAGTAA
1 AAAATAGTAATCAGTAA
8366 GGGTAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (17 bp):
AAAATAGTAATCAGTAA
Found at i:8399 original size:21 final size:21
Alignment explanation
Indices: 8383--8510 Score: 132
Period size: 21 Copynumber: 6.0 Consensus size: 21
8373 ATAGTAATAC
* *
8383 GTAAAAGGAAATCAGT-AAGA
1 GTAAAAGGTAATCAGTAAAAA
* *
8403 GTAAAAAGGTGATCAGTAAAGA
1 GT-AAAAGGTAATCAGTAAAAA
* * *
8425 GTAAAAAGCTAATCAGCAAGAA
1 GT-AAAAGGTAATCAGTAAAAA
8447 GTAAAAGGTAATCAGTAAAAA
1 GTAAAAGGTAATCAGTAAAAA
** *
8468 GCGAAAGGAAATCAGTAAAAA
1 GTAAAAGGTAATCAGTAAAAA
8489 GTAAAAGAGTAATCAGTAAAAA
1 GTAAAAG-GTAATCAGTAAAAA
8511 AAAAGAGCAG
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
20 2 0.02
21 51 0.57
22 36 0.40
ACGTcount: A:0.55, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
GTAAAAGGTAATCAGTAAAAA
Found at i:8501 original size:43 final size:44
Alignment explanation
Indices: 8385--8510 Score: 134
Period size: 43 Copynumber: 2.9 Consensus size: 44
8375 AGTAATACGT
* * *
8385 AAAAGGAAATCAGT-AAGAGTAAAA-AGGTGATCAGTAAAGAGTA
1 AAAAGGAAATCAGTAAAAAGTAAAAGA-GTAATCAGTAAAAAGTA
** * * *
8428 AAAAGCTAATCAGCAAGAAGTAAAAG-GTAATCAGTAAAAAG-C
1 AAAAGGAAATCAGTAAAAAGTAAAAGAGTAATCAGTAAAAAGTA
*
8470 GAAAGGAAATCAGTAAAAAGTAAAAGAGTAATCAGTAAAAA
1 AAAAGGAAATCAGTAAAAAGTAAAAGAGTAATCAGTAAAAA
8511 AAAAGAGCAG
Statistics
Matches: 67, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
42 21 0.31
43 38 0.57
44 8 0.12
ACGTcount: A:0.56, C:0.07, G:0.21, T:0.15
Consensus pattern (44 bp):
AAAAGGAAATCAGTAAAAAGTAAAAGAGTAATCAGTAAAAAGTA
Found at i:10001 original size:13 final size:14
Alignment explanation
Indices: 9978--10006 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
9968 ACTTCTACTC
9978 AATGCATGAATGCA
1 AATGCATGAATGCA
9992 AATG-ATGAATGCA
1 AATGCATGAATGCA
10005 AA
1 AA
10007 GTCCAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21
Consensus pattern (14 bp):
AATGCATGAATGCA
Done.