Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002374.1 Hibiscus syriacus cultivar Beakdansim tig00004849_pilon, 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: 60651
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:7438 original size:17 final size:18
Alignment explanation
Indices: 7405--7438 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
7395 TCCAACAAAC
*
7405 TACATATAAAAATAATTT
1 TACATATAAAAACAATTT
7423 TACATAT-AAAACAATT
1 TACATATAAAAACAATT
7439 AAACACAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (18 bp):
TACATATAAAAACAATTT
Found at i:7530 original size:24 final size:25
Alignment explanation
Indices: 7488--7534 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
7478 GTATATAACT
7488 TTATATATTATCAATAAATCAAATGA
1 TTATATATTATCAATAAAT-AAATGA
7514 TTATATATTAT-AA-AAATAAAT
1 TTATATATTATCAATAAATAAAT
7535 TTAATAGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
24 4 0.19
25 2 0.10
26 11 0.52
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (25 bp):
TTATATATTATCAATAAATAAATGA
Found at i:8220 original size:25 final size:27
Alignment explanation
Indices: 8176--8234 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 27
8166 CAATAATAGT
* ** *
8176 AAAATATATATTAAATTATTTTTATAA
1 AAAATATATAATAAATTATTAATAGAA
8203 AAAATATA-AATAAA-TATTAATAGAA
1 AAAATATATAATAAATTATTAATAGAA
8228 AAAATAT
1 AAAATAT
8235 TTTTTCTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 15 0.54
26 5 0.18
27 8 0.29
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (27 bp):
AAAATATATAATAAATTATTAATAGAA
Found at i:25328 original size:2 final size:2
Alignment explanation
Indices: 25316--25373 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
25306 CAACTCGTGA
25316 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25357 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
25374 CCCAGGAGGG
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29591 original size:60 final size:60
Alignment explanation
Indices: 29481--29594 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
29471 GTATAAGATA
* ** *
29481 TTGCTTTGTTGAATCCCTCGACTATTAAAAGTTACAAAATGGTCCCTCAACTATAGAGAG
1 TTGCTTTGTTGAATCCCTCAACTATTAAAAGTTACAAAATAATCACTCAACTATAGAGAG
* * *
29541 TTGCTTTGTTGAGTCTCTCAACTATTAAAAGTTACAAAATAATCATTCAACTAT
1 TTGCTTTGTTGAATCCCTCAACTATTAAAAGTTACAAAATAATCACTCAACTAT
29595 TCATTATGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.35
Consensus pattern (60 bp):
TTGCTTTGTTGAATCCCTCAACTATTAAAAGTTACAAAATAATCACTCAACTATAGAGAG
Found at i:31189 original size:13 final size:13
Alignment explanation
Indices: 31171--31205 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
31161 ATTGTTTTTT
31171 TAATATTTAAATA
1 TAATATTTAAATA
31184 TAATATTTTAAATA
1 TAATA-TTTAAATA
31198 T-ATATTTA
1 TAATATTTA
31206 TTGAGTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.19
13 8 0.38
14 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TAATATTTAAATA
Found at i:31193 original size:14 final size:14
Alignment explanation
Indices: 31171--31204 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
31161 ATTGTTTTTT
31171 TAATA-TTTAAATA
1 TAATATTTTAAATA
31184 TAATATTTTAAATA
1 TAATATTTTAAATA
31198 T-ATATTT
1 TAATATTT
31205 ATTGAGTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATATTTTAAATA
Found at i:31390 original size:21 final size:20
Alignment explanation
Indices: 31304--31461 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
31294 AAATGACCAA
**
31304 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
31323 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
31343 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
31363 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
31384 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
31405 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
31425 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
31446 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
31462 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:31493 original size:20 final size:20
Alignment explanation
Indices: 31428--31637 Score: 192
Period size: 20 Copynumber: 10.5 Consensus size: 20
31418 CGATTTTCCA
* ** *
31428 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
31448 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
31468 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
31488 ATATCGCAACACGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
31508 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
31528 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
31548 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
31568 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
31588 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
31608 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
31628 AAATCACAAC
1 AAATCGCAAC
31638 ACTGAAATTT
Statistics
Matches: 156, Mismatches: 28, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 152 0.97
21 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:32357 original size:24 final size:24
Alignment explanation
Indices: 32318--32364 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
32308 AAATTTGGTC
32318 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
32342 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
32365 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:34933 original size:19 final size:19
Alignment explanation
Indices: 34893--34986 Score: 135
Period size: 19 Copynumber: 5.2 Consensus size: 19
34883 GATTCTCTCG
34893 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
34913 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
34932 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
34946 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
34965 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
34984 TTG
1 TTG
34987 TGATAGTCAA
Statistics
Matches: 67, Mismatches: 2, Indels: 11
0.84 0.03 0.14
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 32 0.48
20 15 0.22
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:34941 original size:53 final size:52
Alignment explanation
Indices: 34874--34986 Score: 217
Period size: 53 Copynumber: 2.2 Consensus size: 52
34864 GAAATGAAAA
34874 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
34927 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
34979 TCGCATTG
1 TCGCATTG
34987 TGATAGTCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 26 0.43
53 34 0.57
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:35123 original size:19 final size:19
Alignment explanation
Indices: 35049--35236 Score: 199
Period size: 19 Copynumber: 10.6 Consensus size: 19
35039 CCATTACATT
35049 TCGCAATGCGGAAATGAAAA
1 TCGCAATGC-GAAATGAAAA
*
35069 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
35083 TCGCAATGCGAAATGAAAAA
1 TCGCAATGCGAAATG-AAAA
35103 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
35122 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
35136 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
35155 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
35174 TCGCAATGCAAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
35193 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
*
35207 TCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAA
*
35226 TCGCATTGCGA
1 TCGCAATGCGA
35237 TTCTCTCGTT
Statistics
Matches: 142, Mismatches: 10, Indels: 33
0.77 0.05 0.18
Matches are distributed among these distances:
14 30 0.21
15 3 0.02
16 6 0.04
17 4 0.03
18 4 0.03
19 71 0.50
20 24 0.17
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:35130 original size:53 final size:52
Alignment explanation
Indices: 35049--35179 Score: 244
Period size: 53 Copynumber: 2.5 Consensus size: 52
35039 CCATTACATT
35049 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG-AAAA
35103 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
35155 TCGCAATGCGAAATGAAAATCGCAA
1 TCGCAATGCGAAATGAAAATCGCAA
35180 TGCAAAATGA
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 29 0.38
53 39 0.51
54 9 0.12
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (52 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
Found at i:35191 original size:71 final size:72
Alignment explanation
Indices: 35081--35236 Score: 278
Period size: 71 Copynumber: 2.2 Consensus size: 72
35071 GCAACGAGAG
*
35081 AATCGCAATGCGAAATGAAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAAATCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCG
35146 AAATGAA
66 AAATGAA
35153 AATCGCAATGCGAAATG-AAAATCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAAATCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCG
*
35217 AAATTAA
66 AAATGAA
*
35224 AATCGCATTGCGA
1 AATCGCAATGCGA
35237 TTCTCTCGTT
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
71 64 0.79
72 17 0.21
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAAATCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCG
AAATGAA
Found at i:35209 original size:52 final size:52
Alignment explanation
Indices: 35049--35230 Score: 219
Period size: 52 Copynumber: 3.5 Consensus size: 52
35039 CCATTACATT
* *
35049 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGAAATGCGAAACG-AAAA
* *
35103 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGAAATGCGAAACGAAAA
* *
35155 TCGCAATGCGAAATGAAAATCGCAATGCA-A-AAT-GAAAAT-CGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACG-AGAGAATCG-AAATGCGAAACGA-A-AA
*
35207 TCGCAATGCGAAATTAAAATCGCA
1 TCGCAATGCGAAATGAAAATCGCA
35231 TTGCGATTCT
Statistics
Matches: 119, Mismatches: 5, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
50 7 0.06
51 7 0.06
52 56 0.47
53 40 0.34
54 9 0.08
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGAAATGCGAAACGAAAA
Found at i:35268 original size:20 final size:19
Alignment explanation
Indices: 35245--35291 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
35235 GATTCTCTCG
35245 TTGCGATTGTAATTTCCACA
1 TTGCGATTGTAATTT-CACA
* * *
35265 TTGCGATTTTCATTTCGCA
1 TTGCGATTGTAATTTCACA
35284 TTGCGATT
1 TTGCGATT
35292 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (19 bp):
TTGCGATTGTAATTTCACA
Found at i:35287 original size:19 final size:19
Alignment explanation
Indices: 35263--35342 Score: 116
Period size: 19 Copynumber: 4.5 Consensus size: 19
35253 GTAATTTCCA
35263 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
35282 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
35298 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
35315 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
35334 CATTGCGAT
1 CATTGCGAT
35343 AGTCAATTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.11
16 7 0.13
17 7 0.13
19 34 0.63
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:35293 original size:53 final size:52
Alignment explanation
Indices: 35226--35342 Score: 198
Period size: 53 Copynumber: 2.2 Consensus size: 52
35216 GAAATTAAAA
35226 TCGCATTGCGATTCTCTCGTTGCGATTGTAATTTCCACATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTGTAATTT-CACATTGCGATTTTCATT
* * *
35279 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTGTAATTTCACATTGCGATTTTCATT
35331 TCGCATTGCGAT
1 TCGCATTGCGAT
35343 AGTCAATTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 29 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTGTAATTTCACATTGCGATTTTCATT
Found at i:35476 original size:13 final size:14
Alignment explanation
Indices: 35449--35484 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
35439 CATCAATTAC
35449 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
35463 ACAAATCATC-TTT
1 ACAAATCAACTTTT
35476 ACAAATCAA
1 ACAAATCAA
35485 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:37482 original size:14 final size:14
Alignment explanation
Indices: 37463--37519 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
37453 GCGAAATGAA
*
37463 AATCGCAACGACAG
1 AATCGCAACGAAAG
37477 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
37494 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
37510 AATCGCAACG
1 AATCGCAACG
37520 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:37490 original size:33 final size:33
Alignment explanation
Indices: 37444--37536 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
37434 GCGAAACCAA
*
37444 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
37477 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
37510 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
37537 TGCGATTTTA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:37501 original size:19 final size:19
Alignment explanation
Indices: 37407--37541 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
37397 TAGTTTACTT
* *
37407 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
37427 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
37446 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
37465 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
37479 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
37498 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
37512 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
37531 TCGCAATGCGA
1 TCGCAACGCGA
37542 TTTTATGTAT
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:37578 original size:20 final size:20
Alignment explanation
Indices: 37555--37705 Score: 187
Period size: 20 Copynumber: 7.5 Consensus size: 20
37545 TATGTATTAT
37555 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
37575 CGTTGCGATATACGGATACG
1 CGTTGCGATTTACGGATACG
* **
37595 CATTGCGATTTACCCATACG
1 CGTTGCGATTTACGGATACG
*
37615 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACG
37635 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* *
37655 CGTTGCGATTTATGTG-TTCG
1 CGTTGCGATTTACG-GATACG
* ** *
37675 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGGATACG
37695 CGTTGCGATTT
1 CGTTGCGATTT
37706 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
20 112 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:37699 original size:60 final size:60
Alignment explanation
Indices: 37532--37705 Score: 204
Period size: 60 Copynumber: 2.9 Consensus size: 60
37522 AAATGAAAAT
* ** *
37532 CGCAATGCGATTTTATGTATTATCGTTGCGATTTACGGATACGCGTTGCGATATACGGATA
1 CGCATTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATA
*** * *
37593 CGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATA
1 CGCATTGCGATTTATGTATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATA
* * * ** *
37653 CGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 CGCATTGCGATTTATGTATTCGCGTTGCGATTTACGGATACGCGTTGCGATTT
37706 TGGAAAATCG
Statistics
Matches: 93, Mismatches: 20, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
60 84 0.90
61 9 0.10
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (60 bp):
CGCATTGCGATTTATGTATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATA
Found at i:37722 original size:21 final size:21
Alignment explanation
Indices: 37692--37774 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
37682 ATTTTCATAT
*
37692 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
37713 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
37734 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
37755 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
37775 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:37765 original size:42 final size:43
Alignment explanation
Indices: 37672--37770 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
37662 ATTTATGTGT
* *
37672 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
37713 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
37755 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
37771 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:40935 original size:32 final size:33
Alignment explanation
Indices: 40894--40958 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
40884 CCTCCATTAT
40894 TTGATAAGTTTGT-CCCCAACACAAAACCTTAC
1 TTGATAAGTTTGTCCCCCAACACAAAACCTTAC
40926 TTGATAAGTTTGTCCCCCAACACAAAACCTTAC
1 TTGATAAGTTTGTCCCCCAACACAAAACCTTAC
40959 GTACGTCCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.34, C:0.29, G:0.09, T:0.28
Consensus pattern (33 bp):
TTGATAAGTTTGTCCCCCAACACAAAACCTTAC
Found at i:41792 original size:2 final size:2
Alignment explanation
Indices: 41787--41811 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41777 AAGTTAAATC
41787 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
41812 ACCACAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46484 original size:17 final size:18
Alignment explanation
Indices: 46462--46495 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
46452 TTTATTGTAA
46462 TTTTTACAAA-TTCTTTC
1 TTTTTACAAATTTCTTTC
*
46479 TTTTTATAAATTTCTTT
1 TTTTTACAAATTTCTTT
46496 AATTTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTACAAATTTCTTTC
Found at i:46568 original size:25 final size:25
Alignment explanation
Indices: 46534--46582 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
46524 TATCTTAACC
*
46534 GATTTCTACTAAGGAAGGAAAAAAA
1 GATTTCTACTAAAGAAGGAAAAAAA
*
46559 GATTTCTACTAAAGAAGGGAAAAA
1 GATTTCTACTAAAGAAGGAAAAAA
46583 GAGAATTCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.51, C:0.08, G:0.20, T:0.20
Consensus pattern (25 bp):
GATTTCTACTAAAGAAGGAAAAAAA
Found at i:49286 original size:39 final size:39
Alignment explanation
Indices: 49232--49308 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 39
49222 GATTTTCTTT
* * *
49232 TTGGCCCTGGGAAATTACAGGAATCTTCAGATATTCTCC
1 TTGGCCCAGAGAAATTACAAGAATCTTCAGATATTCTCC
* * *
49271 TTGGCCCAGAGAAATTACAAGAATTTTCATATTTTCTC
1 TTGGCCCAGAGAAATTACAAGAATCTTCAGATATTCTC
49309 TTTGCTCCTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.34
Consensus pattern (39 bp):
TTGGCCCAGAGAAATTACAAGAATCTTCAGATATTCTCC
Found at i:49332 original size:39 final size:39
Alignment explanation
Indices: 49301--49384 Score: 132
Period size: 39 Copynumber: 2.2 Consensus size: 39
49291 GAATTTTCAT
* * * *
49301 ATTTTCTCTTTGCTCCTGAGACATCATAAGAATCCTCTG
1 ATTTTCGCTTTGCCCCTAAAACATCATAAGAATCCTCTG
49340 ATTTTCGCTTTGCCCCTAAAACATCATAAGAATCCTCTG
1 ATTTTCGCTTTGCCCCTAAAACATCATAAGAATCCTCTG
49379 ATTTTC
1 ATTTTC
49385 TCATTGGCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.38
Consensus pattern (39 bp):
ATTTTCGCTTTGCCCCTAAAACATCATAAGAATCCTCTG
Found at i:52719 original size:17 final size:17
Alignment explanation
Indices: 52697--52735 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
52687 AGTCGAGCTA
*
52697 GAAGAGGCAGTTAGGCG
1 GAAGAGGCAGTAAGGCG
52714 GAAGAGGCAGTAAGGCG
1 GAAGAGGCAGTAAGGCG
52731 GAAGA
1 GAAGA
52736 AGATTCTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.36, C:0.10, G:0.46, T:0.08
Consensus pattern (17 bp):
GAAGAGGCAGTAAGGCG
Done.