Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006555.1 Hibiscus syriacus cultivar Beakdansim tig00016024_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: 78314
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:571 original size:21 final size:22
Alignment explanation
Indices: 541--582 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
531 CCAATTTAAA
* *
541 CAATATTAATTAATTAAATAAT
1 CAATATTAATAAATCAAATAAT
563 CAAT-TTAATAAATCAAATAA
1 CAATATTAATAAATCAAATAA
583 ATTAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (22 bp):
CAATATTAATAAATCAAATAAT
Found at i:697 original size:23 final size:26
Alignment explanation
Indices: 653--701 Score: 77
Period size: 23 Copynumber: 2.0 Consensus size: 26
643 CTTAACTTTC
653 TTCTCTTTCTCTTCTTTCTTCCTATT
1 TTCTCTTTCTCTTCTTTCTTCCTATT
679 TTCTC-TTCT-TTCTTT-TTCCTATT
1 TTCTCTTTCTCTTCTTTCTTCCTATT
702 CTTTATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.35
24 6 0.26
25 4 0.17
26 5 0.22
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (26 bp):
TTCTCTTTCTCTTCTTTCTTCCTATT
Found at i:710 original size:20 final size:23
Alignment explanation
Indices: 664--710 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 23
654 TCTCTTTCTC
*
664 TTCTTTCTTCCTATTTTCTCTTCT
1 TTCTTTCTTCCTA-TTTCTCTTAT
688 TTCTTT-TTCCTA-TTCT-TTAT
1 TTCTTTCTTCCTATTTCTCTTAT
708 TTC
1 TTC
711 ACTCCCGGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 6 0.27
21 4 0.18
23 6 0.27
24 6 0.27
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.68
Consensus pattern (23 bp):
TTCTTTCTTCCTATTTCTCTTAT
Found at i:1315 original size:2 final size:2
Alignment explanation
Indices: 1308--1334 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1298 AAATATCATC
1308 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1335 TTAAATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2387 original size:16 final size:17
Alignment explanation
Indices: 2351--2384 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2341 TTCACAAGCT
2351 TATTATTAATTTAAAAAA
1 TATTATTAATTT-AAAAA
*
2369 TATTTTTAATTTAAAA
1 TATTATTAATTTAAAA
2385 TATGAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTATTAATTTAAAAA
Found at i:2403 original size:28 final size:28
Alignment explanation
Indices: 2364--2489 Score: 91
Period size: 28 Copynumber: 4.4 Consensus size: 28
2354 TATTAATTTA
2364 AAAAATATTTTTAATTTAAAATATGAAT
1 AAAAATATTTTTAATTTAAAATATGAAT
* *
2392 AAAAATATTTTTAA-GTAAAGATA-AAAT
1 AAAAATATTTTTAATTTAAA-ATATGAAT
* *
2419 AAAAATTATATTTTTTAATTTAAAATAAGAGT
1 -AAAA--ATA-TTTTTAATTTAAAATATGAAT
*
2451 AAAATATATATTTTTATATT-AAAT-T-AAT
1 AAAA-ATAT-TTTTAAT-TTAAAATATGAAT
2479 AATAAATATTT
1 AA-AAATATTT
2490 AAATATATTT
Statistics
Matches: 80, Mismatches: 8, Indels: 21
0.73 0.07 0.19
Matches are distributed among these distances:
27 9 0.11
28 29 0.36
29 3 0.04
30 17 0.21
31 16 0.20
32 6 0.08
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (28 bp):
AAAAATATTTTTAATTTAAAATATGAAT
Found at i:2461 original size:32 final size:31
Alignment explanation
Indices: 2362--2465 Score: 105
Period size: 28 Copynumber: 3.5 Consensus size: 31
2352 ATTATTAATT
*
2362 TAAAAA-ATA-TTTTTAATTTAAAATATGAA
1 TAAAAATATATTTTTTAATTTAAAATAAGAA
*
2391 T-AAAA-ATA-TTTTTAA-GTAAAGATAA-AA
1 TAAAAATATATTTTTTAATTTAAA-ATAAGAA
*
2418 TAAAAATTATATTTTTTAATTTAAAATAAGAG
1 TAAAAA-TATATTTTTTAATTTAAAATAAGAA
2450 TAAAATATATATTTTT
1 TAAAA-ATATATTTTT
2466 ATATTAAATT
Statistics
Matches: 63, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
27 7 0.11
28 21 0.33
29 1 0.02
30 3 0.05
31 11 0.17
32 19 0.30
33 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (31 bp):
TAAAAATATATTTTTTAATTTAAAATAAGAA
Found at i:2610 original size:27 final size:25
Alignment explanation
Indices: 2567--2616 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
2557 TTTTTACATT
2567 AAAATAAAAAATTAATAAATTAAGA
1 AAAATAAAAAATTAATAAATTAAGA
*
2592 AAAATACAAATAATTAATAAGTTAA
1 AAAATA-AAA-AATTAATAAATTAA
2617 AACAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.27
26 3 0.14
27 13 0.59
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (25 bp):
AAAATAAAAAATTAATAAATTAAGA
Found at i:2631 original size:27 final size:27
Alignment explanation
Indices: 2567--2633 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
2557 TTTTTACATT
2567 AAAAT-AAAA-AATTAATAAATTAAGA
1 AAAATAAAAATAATTAATAAATTAAGA
* *
2592 AAAATACAAATAATTAATAAGTTAA-A
1 AAAATAAAAATAATTAATAAATTAAGA
2618 ACAAA-AAAATATAATT
1 A-AAATAAAA-ATAATT
2634 TTAAAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
25 5 0.14
26 8 0.23
27 22 0.63
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (27 bp):
AAAATAAAAATAATTAATAAATTAAGA
Found at i:12569 original size:97 final size:99
Alignment explanation
Indices: 12435--12630 Score: 378
Period size: 97 Copynumber: 2.0 Consensus size: 99
12425 TAGTAATTCG
12435 TATTATTCATTTTTTTGTAATTAAAAAAACATTTGGACATTTTATTTTTAATTTCAAATCAAATA
1 TATTATTCATTTTTTTGTAATTAAAAAAACATTTGGACATTTTATTTTTAATTTCAAATCAAATA
12500 ATAAATTAATCTTTAAAACCAATTCAATTGGATC
66 ATAAATTAATCTTTAAAACCAATTCAATTGGATC
12534 TATTATTCA-TTTTTTGTAATT-AAAAAACATTTGGACATTTTATTTTTAATTTCAAATCAAATA
1 TATTATTCATTTTTTTGTAATTAAAAAAACATTTGGACATTTTATTTTTAATTTCAAATCAAATA
12597 ATAAATTAATCTTTAAAACCAATTCAATTGGATC
66 ATAAATTAATCTTTAAAACCAATTCAATTGGATC
12631 GCAACACAAA
Statistics
Matches: 97, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
97 76 0.78
98 12 0.12
99 9 0.09
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.44
Consensus pattern (99 bp):
TATTATTCATTTTTTTGTAATTAAAAAAACATTTGGACATTTTATTTTTAATTTCAAATCAAATA
ATAAATTAATCTTTAAAACCAATTCAATTGGATC
Found at i:19927 original size:48 final size:48
Alignment explanation
Indices: 19871--19963 Score: 186
Period size: 48 Copynumber: 1.9 Consensus size: 48
19861 TGGTGACACA
19871 TGTCACCACCTATTTGAAGAAAATAGTAATTGTTGTTGGGAAGATATG
1 TGTCACCACCTATTTGAAGAAAATAGTAATTGTTGTTGGGAAGATATG
19919 TGTCACCACCTATTTGAAGAAAATAGTAATTGTTGTTGGGAAGAT
1 TGTCACCACCTATTTGAAGAAAATAGTAATTGTTGTTGGGAAGAT
19964 TCGAATCAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (48 bp):
TGTCACCACCTATTTGAAGAAAATAGTAATTGTTGTTGGGAAGATATG
Found at i:20535 original size:24 final size:24
Alignment explanation
Indices: 20481--20536 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
20471 TCTAACTATC
20481 ATAAATAAAAAATTCAAAATTAATA
1 ATAAA-AAAAAATTCAAAATTAATA
* *
20506 ACAAAAAAAAATTCAAAATTTATA
1 ATAAAAAAAAATTCAAAATTAATA
*
20530 TTAAAAA
1 ATAAAAA
20537 GTTGTAATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (24 bp):
ATAAAAAAAAATTCAAAATTAATA
Found at i:25763 original size:35 final size:38
Alignment explanation
Indices: 25716--25785 Score: 110
Period size: 35 Copynumber: 1.9 Consensus size: 38
25706 TCCTAGTAAG
*
25716 TCCTACTTCAAAA-GATCAT-AAA-AAACATGATCGAA
1 TCCTACTCCAAAAGGATCATAAAAGAAACATGATCGAA
25751 TCCTACTCCAAAAGGATCATAAAAGAAACATGATC
1 TCCTACTCCAAAAGGATCATAAAAGAAACATGATC
25786 ACCCCTTTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
35 12 0.39
36 6 0.19
37 3 0.10
38 10 0.32
ACGTcount: A:0.47, C:0.21, G:0.10, T:0.21
Consensus pattern (38 bp):
TCCTACTCCAAAAGGATCATAAAAGAAACATGATCGAA
Found at i:37516 original size:23 final size:23
Alignment explanation
Indices: 37489--37561 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
37479 TTCTTCCATT
37489 AGGTTTATGGGGTTTTTTAAATG
1 AGGTTTATGGGGTTTTTTAAATG
* ** * *
37512 AGGTTCAT-GTCTATGTCTT--ATT
1 AGGTTTATGGGGT-T-TTTTAAATG
37534 AGGTTTATGGGGTTTTTTAAATG
1 AGGTTTATGGGGTTTTTTAAATG
37557 AGGTT
1 AGGTT
37562 CATGTCTATG
Statistics
Matches: 35, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
21 3 0.09
22 12 0.34
23 17 0.49
24 3 0.09
ACGTcount: A:0.21, C:0.04, G:0.27, T:0.48
Consensus pattern (23 bp):
AGGTTTATGGGGTTTTTTAAATG
Found at i:37536 original size:45 final size:45
Alignment explanation
Indices: 37486--37578 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
37476 TTTTTCTTCC
37486 ATTAGGTTTATGGGGTTTTTTAAATGAGGTTCATGTCTATGTCTT
1 ATTAGGTTTATGGGGTTTTTTAAATGAGGTTCATGTCTATGTCTT
37531 ATTAGGTTTATGGGGTTTTTTAAATGAGGTTCATGTCTATGTCTT
1 ATTAGGTTTATGGGGTTTTTTAAATGAGGTTCATGTCTATGTCTT
37576 ATT
1 ATT
37579 TTGTATGTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.20, C:0.06, G:0.24, T:0.49
Consensus pattern (45 bp):
ATTAGGTTTATGGGGTTTTTTAAATGAGGTTCATGTCTATGTCTT
Found at i:40010 original size:19 final size:20
Alignment explanation
Indices: 39986--40036 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
39976 AATGACCAAT
39986 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
40005 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
40025 AAAATCGCAACG
1 AAAATCGCAACG
40037 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:40030 original size:20 final size:20
Alignment explanation
Indices: 39986--40303 Score: 147
Period size: 20 Copynumber: 15.6 Consensus size: 20
39976 AATGACCAAT
* *
39986 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
40005 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
40025 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
40045 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
40065 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
40086 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
40109 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
40129 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* *
40149 AAAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
40169 ATAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
40189 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
40212 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
40232 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
40252 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
40272 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
*
40292 AGAATCGCAACG
1 AAAATCGCAACG
40304 TTGAAAATAA
Statistics
Matches: 243, Mismatches: 44, Indels: 23
0.78 0.14 0.07
Matches are distributed among these distances:
19 17 0.07
20 183 0.75
21 14 0.06
23 29 0.12
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:40161 original size:40 final size:40
Alignment explanation
Indices: 40111--40301 Score: 240
Period size: 40 Copynumber: 4.7 Consensus size: 40
40101 TTTAGAAGAA
* * *
40111 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAA
1 AATCGCAATGCGATTGATAGAATCGCAATGCGACTGAGAG
* * *
40151 AATCGCAATGCGATTTATATAATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGATAGAATCGCAATGCGACTGAGAG
* *
40191 AGTCGCAACGCGATTTAGA-AGAAAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGA-TT-GATAG--AATCGCAATGCGACTGAGAG
* *
40234 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGATAGAATCGCAATGCGACTGAGAG
*
40274 AATCGCAATGCGATTTATAGAATCGCAA
1 AATCGCAATGCGATTGATAGAATCGCAA
40302 CGTTGAAAAT
Statistics
Matches: 131, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
40 92 0.70
41 5 0.04
42 4 0.03
43 30 0.23
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (40 bp):
AATCGCAATGCGATTGATAGAATCGCAATGCGACTGAGAG
Found at i:40219 original size:83 final size:83
Alignment explanation
Indices: 40131--40290 Score: 230
Period size: 83 Copynumber: 1.9 Consensus size: 83
40121 CGATTGATAG
* * * * * * * *
40131 AATCGCAATGCGATTGATAAAATCGCAATGCGATTTATATAATCGCAATGCGATTGAGAGAGTCG
1 AATCGCAATGCGACTGAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCG
40196 CAACGCGATTTAGAAGAA
66 CAACGCGATTTAGAAGAA
*
40214 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCG
1 AATCGCAATGCGACTGAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCG
*
40279 CAATGCGATTTA
66 CAACGCGATTTA
40291 TAGAATCGCA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
83 67 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.21
Consensus pattern (83 bp):
AATCGCAATGCGACTGAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCG
CAACGCGATTTAGAAGAA
Found at i:40224 original size:103 final size:103
Alignment explanation
Indices: 40090--40303 Score: 320
Period size: 103 Copynumber: 2.1 Consensus size: 103
40080 GCTTCCAAGT
* * * *
40090 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAAAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAAAATC
* * * * *
40155 GCAATGCGATTTATATAATCGCAATGCGATTGAGAGAG
66 GCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
*
40193 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAAAATC
* *
40258 GCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAA
66 GCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
40296 TCGCAACG
1 TCGCAACG
40304 TTGAAAATAA
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
103 99 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (103 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAAAATC
GCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
Found at i:40361 original size:6 final size:6
Alignment explanation
Indices: 40350--40392 Score: 58
Period size: 5 Copynumber: 7.8 Consensus size: 6
40340 AGTATCCGCG
40350 CGACCA CGACCA CGACCA CGA-CA CGA-CA CGACC- CGACC- CGACC
1 CGACCA CGACCA CGACCA CGACCA CGACCA CGACCA CGACCA CGACC
40393 CGAGACGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 20 0.56
6 16 0.44
ACGTcount: A:0.30, C:0.51, G:0.19, T:0.00
Consensus pattern (6 bp):
CGACCA
Found at i:41109 original size:5 final size:5
Alignment explanation
Indices: 41075--41107 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
41065 CGCCACCGTC
*
41075 TCGGG TCGGG TCGGG TCGGG TCGGG TCGTG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG
41108 TGGTAATACG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.21, G:0.55, T:0.24
Consensus pattern (5 bp):
TCGGG
Found at i:41280 original size:20 final size:22
Alignment explanation
Indices: 41251--41306 Score: 89
Period size: 20 Copynumber: 2.6 Consensus size: 22
41241 ATTGTAGACT
*
41251 ATCGCATTGCGATTCTTGG-A-
1 ATCGCGTTGCGATTCTTGGAAG
41271 ATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTCTTGGAAG
41293 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
41307 TTCTTTTGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 18 0.55
21 1 0.03
22 14 0.42
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.34
Consensus pattern (22 bp):
ATCGCGTTGCGATTCTTGGAAG
Found at i:41360 original size:20 final size:20
Alignment explanation
Indices: 41270--41757 Score: 212
Period size: 20 Copynumber: 23.9 Consensus size: 20
41260 CGATTCTTGG
**
41270 AATCGCGTTGCGATTCTTGGA
1 AATCGCGTTGCGATT-TTCTA
41291 AGATCGCGTTGCGATTTTCT-
1 A-ATCGCGTTGCGATTTTCTA
* * *
41311 -TTTGACCGTTGCGATTTTCTT
1 AATCG--CGTTGCGATTTTCTA
** **
41332 TTTAACGTTGCGATTTTCTA
1 AATCGCGTTGCGATTTTCTA
* *
41352 AATCGCGTTGCGATTCTCTC
1 AATCGCGTTGCGATTTTCTA
* * *
41372 AATCGCATTGCGATTCTATA
1 AATCGCGTTGCGATTTTCTA
* * *
41392 AATCGCATTGCGATTCTCTC
1 AATCGCGTTGCGATTTTCTA
* * * *
41412 AGTCGCATTGCGATTCTCTC
1 AATCGCGTTGCGATTTTCTA
* * *
41432 AGTCGCATTGTGATTTTCTTCTA
1 AATCGCGTTGCGA--TT-TTCTA
* *
41455 AATCGCGTTGCGATTCTCTC
1 AATCGCGTTGCGATTTTCTA
* * *
41475 AATCGCATTGCGATTCTATA
1 AATCGCGTTGCGATTTTCTA
* * *
41495 AATCGCATTGCGATTCTCTC
1 AATCGCGTTGCGATTTTCTA
* * * *
41515 AGTCGCATTGCGATTCTCTC
1 AATCGCGTTGCGATTTTCTA
* *
41535 AGTCGCATTGCGATTTTCTTCTA
1 AATCGCGTTGCGA--TT-TTCTA
* * *
41558 AATCGCGTTGCGACTCTCTC
1 AATCGCGTTGCGATTTTCTA
* * * *
41578 AATCGCATTGCGATTCTATC
1 AATCGCGTTGCGATTTTCTA
* * * *
41598 AATCGCATTGCGATTCTATC
1 AATCGCGTTGCGATTTTCTA
*
41618 AATCGCATTGCGATTTTCTTCTA
1 AATCGCGTTGCGA--TT-TTCTA
** **
41641 AATCGCGTTGCGAACTTGGA
1 AATCGCGTTGCGATTTTCTA
*
41661 AGCTCGCGTTGCGATTTTCT-
1 A-ATCGCGTTGCGATTTTCTA
* * *
41681 -TTTGACCGTTGCGATTTTCTT
1 AATCG--CGTTGCGATTTTCTA
** ** *
41702 TTTAACGTTACGATTTTCTA
1 AATCGCGTTGCGATTTTCTA
*
41722 AATCGCGTTGCGATTTT-GA
1 AATCGCGTTGCGATTTTCTA
*
41741 TATCGCGTTGCGATTTT
1 AATCGCGTTGCGATTTT
41758 ATTGGTCATT
Statistics
Matches: 379, Mismatches: 69, Indels: 40
0.78 0.14 0.08
Matches are distributed among these distances:
18 4 0.01
19 17 0.04
20 274 0.72
21 19 0.05
22 24 0.06
23 41 0.11
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
AATCGCGTTGCGATTTTCTA
Found at i:41471 original size:83 final size:82
Alignment explanation
Indices: 41339--41653 Score: 336
Period size: 83 Copynumber: 3.8 Consensus size: 82
41329 CTTTTTAACG
* * * * * *
41339 TTGCGATTTTCTAAATCGCGTTGCGA--TTCTCTCAATCGCATTGCGATTCTATAAATCGCATTG
1 TTGCGATTCTCTCAGTCGCATTGCGATTTTCTCTAAATCGCATTGCGATTCTCTAAATCGCATTG
*
41402 CGATTCTCTCAGTCGCA
66 CGATTCTCTCAATCGCA
* * *
41419 TTGCGATTCTCTCAGTCGCATTGTGATTTTCTTCTAAATCGCGTTGCGATTCTCTCAATCGCATT
1 TTGCGATTCTCTCAGTCGCATTGCGATTTTC-TCTAAATCGCATTGCGATTCTCTAAATCGCATT
* *
41484 GCGATTCTATAAATCGCA
65 GCGATTCTCTCAATCGCA
* * *
41502 TTGCGATTCTCTCAGTCGCATTGCGA--TTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCG
1 TTGCGATTCTCTCAGTCGCATTGCGATTTTCTCTAAATCGCATTGCGA--TTC-TCTAAATCGCA
*
41565 TTGCGACTCTCTCAATCGCA
63 TTGCGATTCTCTCAATCGCA
* * * * *
41585 TTGCGATTCTATCAATCGCATTGCGA--TTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCG
1 TTGCGATTCTCTCAGTCGCATTGCGATTTTCTCTAAATCGCATTGCGA--TTC-TCTAAATCGCA
41648 TTGCGA
63 TTGCGA
41654 ACTTGGAAGC
Statistics
Matches: 204, Mismatches: 25, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
80 35 0.17
81 3 0.01
82 6 0.03
83 160 0.78
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.37
Consensus pattern (82 bp):
TTGCGATTCTCTCAGTCGCATTGCGATTTTCTCTAAATCGCATTGCGATTCTCTAAATCGCATTG
CGATTCTCTCAATCGCA
Found at i:41478 original size:103 final size:103
Alignment explanation
Indices: 41347--41632 Score: 527
Period size: 103 Copynumber: 2.8 Consensus size: 103
41337 CGTTGCGATT
41347 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTC
1 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTC
*
41412 AGTCGCATTGCGATTCTCTCAGTCGCATTGTGATTTTC
66 AGTCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTC
41450 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTC
1 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTC
41515 AGTCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTC
66 AGTCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTC
* * *
41553 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTATC
1 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTC
*
41618 AATCGCATTGCGATT
66 AGTCGCATTGCGATT
41633 TTCTTCTAAA
Statistics
Matches: 178, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 178 1.00
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (103 bp):
TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTC
AGTCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTC
Found at i:41500 original size:123 final size:122
Alignment explanation
Indices: 41337--41632 Score: 398
Period size: 123 Copynumber: 2.4 Consensus size: 122
41327 TTCTTTTTAA
* * * *
41337 CGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTG
1 CGTTGCGATTCTCTCAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTATAAATCGCATTG
* * * *
41402 CGATTCTCTCAGTCGCATTGCGA-TTC-TCTCAGTCGCATTGTGATTTTCTTCTAAATCG
66 CGATTCTCTCAGTCGCATTGCGATTTCTTCTAAATCGCATTGCGA--CTC-TCTAAATCG
* * * *
41460 CGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTG
1 CGTTGCGATTCTCTCAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTATAAATCGCATTG
* *
41525 CGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCG
66 CGATTCTCTCAGTCGCATTGCGA-TTTCTTCTAAATCGCATTGCGACTCTCTAAATCG
* *
41583 CATTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCATTGCGATT
1 CGTTGCGATTCTCTCAATCGCATTGCGATTCTATCAATCGCATTGCGATT
41633 TTCTTCTAAA
Statistics
Matches: 153, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
123 135 0.88
124 2 0.01
125 3 0.02
126 13 0.08
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.37
Consensus pattern (122 bp):
CGTTGCGATTCTCTCAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTATAAATCGCATTG
CGATTCTCTCAGTCGCATTGCGATTTCTTCTAAATCGCATTGCGACTCTCTAAATCG
Found at i:44626 original size:18 final size:19
Alignment explanation
Indices: 44603--44639 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
44593 ATGATATCAT
44603 GTGTGTTGCGTTT-CCATG
1 GTGTGTTGCGTTTACCATG
*
44621 GTGTGTTGGGTTTACCATG
1 GTGTGTTGCGTTTACCATG
44640 TCATCTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.08, C:0.14, G:0.35, T:0.43
Consensus pattern (19 bp):
GTGTGTTGCGTTTACCATG
Found at i:54218 original size:6 final size:6
Alignment explanation
Indices: 54207--54617 Score: 242
Period size: 6 Copynumber: 67.2 Consensus size: 6
54197 GAAAGTGAGA
* *
54207 GAGATG GAGATG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGAAG GAGA--
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAG--G GAGAGG
* * **
54255 GAGAGA GAGAGG GAGA-G AAGGAGG GAGAGG GAGAGG GAGAAA GAGAGG
1 GAGAGG GAGAGG GAGAGG GA-GAGG GAGAGG GAGAGG GAGAGG GAGAGG
* ** * * *
54303 GGGAGG GAGAAA GAGAGG GGGAGG GAGAGG AAGAGA GAGAGG GAGAGAG
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAG-G
* *
54352 G-GAGG GAGAGG GAGAGAAG GAGAGAG GAAGAGG GAGA-- GAGATGG AGATAGA
1 GAGAGG GAGAGG GAGAG--G GAGAG-G G-AGAGG GAGAGG GAGA-GG -GAGAGG
* * *
54403 GAGAGG AAGAGGG AGAGAGG GAGAAG GAGA-- GAGAGA GAGAGG GAGAGG
1 GAGAGG GAGA-GG -GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG
*
54451 GAG-GG AGAGAGG GAGAGAG AGAGAGG GAG-GG AGAGAGA GAGAGAG G-GAGG
1 GAGAGG -GAGAGG GAGAG-G -GAGAGG GAGAGG -GAGAGG GAGAG-G GAGAGG
* * * *
54501 GAGAGG GGGAGA GAGAGG G-GATAG G-GAGG GAGAGG G-GATAG G-GAGG
1 GAGAGG GAGAGG GAGAGG GAGA-GG GAGAGG GAGAGG GAGA-GG GAGAGG
* * * *
54547 GAGAGA GAGAGT GTGAGA GAGAGG GAGGGAGG GAGAGGGG GAGAGG GAGAGAG
1 GAGAGG GAGAGG GAGAGG GAGAGG GA--GAGG GAGA--GG GAGAGG GAGAG-G
* *
54600 G-GAGA GAGAGA GAGAGG G
1 GAGAGG GAGAGG GAGAGG G
54618 CTAAGAAGTA
Statistics
Matches: 322, Mismatches: 46, Indels: 74
0.73 0.10 0.17
Matches are distributed among these distances:
4 12 0.04
5 19 0.06
6 231 0.72
7 22 0.07
8 38 0.12
ACGTcount: A:0.38, C:0.00, G:0.60, T:0.02
Consensus pattern (6 bp):
GAGAGG
Found at i:54222 original size:24 final size:23
Alignment explanation
Indices: 54187--54610 Score: 195
Period size: 22 Copynumber: 18.5 Consensus size: 23
54177 ATAGAGAGGG
54187 GGGAG-GGAGAGAAAGTGAGAGAGA
1 GGGAGAGG-GAGAAAG-GAGAGAGA
* * *
54211 TGGAGATGGAG-AGGGAGAGGGAGA
1 GGGAGAGGGAGAAAGGAGA--GAGA
54235 GGGAGAGGGAGAGAAGGAGAGAGA
1 GGGAGAGGGAGA-AAGGAGAGAGA
* *
54259 GAGAGAGGGAGAGAAGGAGGGAGA
1 GGGAGAGGGAGA-AAGGAGAGAGA
54283 GGGAGAGGGAG-AA--AGAGAG-
1 GGGAGAGGGAGAAAGGAGAGAGA
* *
54302 GGG-GAGGGAGAAAGAGAGGGGGA
1 GGGAGAGGGAGAAAG-GAGAGAGA
* * *
54325 GGGAGAGGAAGAGAGAGAGGGAGA
1 GGGAGAGGGAGAAAG-GAGAGAGA
*
54349 GAGG-GAGGGAG-AGGGAGAGA-A
1 G-GGAGAGGGAGAAAGGAGAGAGA
* *
54370 GGAGAGAGGAAG-AGGGAGAGAGA
1 GG-GAGAGGGAGAAAGGAGAGAGA
* ** *
54393 TGGAGATAGAGAGAGGA-AGAG-
1 GGGAGAGGGAGAAAGGAGAGAGA
54414 GGAGAGAGGGAG-AAGGAGAGAGA
1 GG-GAGAGGGAGAAAGGAGAGAGA
* *
54437 GAGAGAGGGAG-AGGGAGGGAGAGA
1 GGGAGAGGGAGAAAGGA--GAGAGA
* * *
54461 GGGAGAGAGAGAGAGG-GAGGGA
1 GGGAGAGGGAGAAAGGAGAGAGA
* * * *
54483 GAGAGAGAGAG-AGGGAGGGAGA
1 GGGAGAGGGAGAAAGGAGAGAGA
* * ** * *
54505 GGGGGAGAGAGAGGGGATAGGGA
1 GGGAGAGGGAGAAAGGAGAGAGA
* *
54528 GGGAGAGGG-GATAGGGAGGGAGA
1 GGGAGAGGGAGA-AAGGAGAGAGA
* *
54551 GAGAGAGTGTGAGAGAGAGG-GAGGGA
1 GGGAGAG-G-GAGA-A-AGGAGAGAGA
* *
54577 GGGAGAGGGGGAGAGG-GAGAGA
1 GGGAGAGGGAGAAAGGAGAGAGA
*
54599 GGGAGAGAGAGA
1 GGGAGAGGGAGA
54611 GAGAGGGCTA
Statistics
Matches: 306, Mismatches: 65, Indels: 60
0.71 0.15 0.14
Matches are distributed among these distances:
18 7 0.02
19 5 0.02
20 6 0.02
21 10 0.03
22 112 0.37
23 39 0.13
24 99 0.32
25 7 0.02
26 19 0.06
27 2 0.01
ACGTcount: A:0.38, C:0.00, G:0.60, T:0.02
Consensus pattern (23 bp):
GGGAGAGGGAGAAAGGAGAGAGA
Found at i:54228 original size:18 final size:17
Alignment explanation
Indices: 54207--54617 Score: 257
Period size: 16 Copynumber: 24.7 Consensus size: 17
54197 GAAAGTGAGA
*
54207 GAGATGGAGATGGAGAGG
1 GAGA-GGAGAGGGAGAGG
54225 GAGAGGGAGAGGGAGAGG
1 GAGA-GGAGAGGGAGAGG
*
54243 GAGA-GA-A-GGAGAGA
1 GAGAGGAGAGGGAGAGG
54257 GAGA-GAGAGGGAGAGAAG
1 GAGAGGAGAGGGAGAG--G
54275 GAG-GGAGAGGGAGAGG
1 GAGAGGAGAGGGAGAGG
* *
54291 GAGAAAGAGAGGGGGAGG
1 GAG-AGGAGAGGGAGAGG
* *
54309 GAGAAAGAGAGGGGGAGG
1 GAG-AGGAGAGGGAGAGG
*
54327 GAGAGGAAGAGAGAGAGG
1 GAGAGG-AGAGGGAGAGG
*
54345 GAGAGAGGGAGGGAGAGG
1 GAGAG-GAGAGGGAGAGG
54363 GAGA-GA-AGGAGAGAGG
1 GAGAGGAGAGG-GAGAGG
* * *
54379 AAGAGG-GAGAGAGATG
1 GAGAGGAGAGGGAGAGG
*
54395 GAGATAGAGAGAGGA-AGAG
1 GAGA-GGAGAG-GGAGAG-G
*
54414 G-GA-GAGAGGGAGAAG
1 GAGAGGAGAGGGAGAGG
*
54429 GAGA-GAGAGAGAGAGG
1 GAGAGGAGAGGGAGAGG
54445 GAGAGG-GAGGGAGAGAG
1 GAGAGGAGAGGGAGAG-G
*
54462 G-GA-GAGAGAGAGAGG
1 GAGAGGAGAGGGAGAGG
*
54477 GAG-GGAGA--GAGAGA
1 GAGAGGAGAGGGAGAGG
54491 GAGAGG-GAGGGAGAGG
1 GAGAGGAGAGGGAGAGG
* *
54507 GGGAGAGAGAGGGGATAGG
1 GAGAG-GAGA-GGGAGAGG
*
54526 GAG-GGAGAGGGGATAGG
1 GAGAGGAGA-GGGAGAGG
*
54543 GAG-GGAGAGAGAGAGTG
1 GAGAGGAGAGGGAGAG-G
54560 TGAGA-GAGA-GG-GAGG
1 -GAGAGGAGAGGGAGAGG
*
54575 GAG-GGAGAGGGGGAGAG
1 GAGAGGAGAGGGAGAG-G
*
54592 G-GA-GAGAGGGAGAGA
1 GAGAGGAGAGGGAGAGG
54607 GAGA-GAGAGGG
1 GAGAGGAGAGGG
54618 CTAAGAAGTA
Statistics
Matches: 321, Mismatches: 34, Indels: 78
0.74 0.08 0.18
Matches are distributed among these distances:
14 29 0.09
15 19 0.06
16 115 0.36
17 35 0.11
18 109 0.34
19 14 0.04
ACGTcount: A:0.38, C:0.00, G:0.60, T:0.02
Consensus pattern (17 bp):
GAGAGGAGAGGGAGAGG
Found at i:54798 original size:70 final size:69
Alignment explanation
Indices: 54684--54821 Score: 195
Period size: 70 Copynumber: 2.0 Consensus size: 69
54674 AAAAGTGCTC
*
54684 TATTTTACCTGAGTGAAAGGGATCATCGATTTCTCCTTTACCAATCACCATTACCTGCAAAAGCC
1 TATTTTACCTGAGTGAAAGGGATCATCGATTTCTCCTTCACCAAT-ACCATTACCTGCAAAAGCC
54749 TGAGT
65 TGAGT
* * * * * * *
54754 TATTTTACCTTAGTGAAAGGGGTTATCGCTTTCTCCTTCGCCAATATCATTACCTGCAAAAGTCT
1 TATTTTACCTGAGTGAAAGGGATCATCGATTTCTCCTTCACCAATACCATTACCTGCAAAAGCCT
54819 GAG
66 GAG
54822 CAGAGCAGAT
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
69 21 0.35
70 39 0.65
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (69 bp):
TATTTTACCTGAGTGAAAGGGATCATCGATTTCTCCTTCACCAATACCATTACCTGCAAAAGCCT
GAGT
Found at i:56224 original size:35 final size:35
Alignment explanation
Indices: 56131--56226 Score: 138
Period size: 35 Copynumber: 2.7 Consensus size: 35
56121 AACACAGTCA
* * *
56131 TCAATTACATTTTAAACCCCAAAATCCAAAATATT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
*
56166 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
* *
56201 TCAATTACATGCTCAACCCCAAATTC
1 TCAATTACATTCTAAACCCCAAATTC
56227 ATAGTCCATT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.42, C:0.27, G:0.01, T:0.30
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAATACT
Found at i:56563 original size:148 final size:148
Alignment explanation
Indices: 56387--56674 Score: 479
Period size: 148 Copynumber: 1.9 Consensus size: 148
56377 CTCAATTTAG
* * *
56387 TTTATAAAATAGTTGACTCGAATTTTTTTCGATTTGAGTTTATAAAATTTAAATGAAGTCGAATT
1 TTTATAAAATAGTTGACTCAAATTTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCAAATT
* * * *
56452 GAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTATAATATTATTT
66 GAATTGAATTTTCAAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATAATATTT
*
56517 GATTCTAATTCAGTTCAA
131 GATCCTAATTCAGTTCAA
56535 TTTATAAAATAGTTGACT-AAATTTTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCAAAT
1 TTTATAAAATAGTTGACTCAAA-TTTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCAAAT
*
56599 TGAATTGAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATAATATT
65 TGAATTGAATTTTCAAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATAATATT
56664 TGATCCTAATT
130 TGATCCTAATT
56675 TAAATAGTTT
Statistics
Matches: 130, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
147 2 0.02
148 128 0.98
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (148 bp):
TTTATAAAATAGTTGACTCAAATTTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCAAATT
GAATTGAATTTTCAAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATAATATTT
GATCCTAATTCAGTTCAA
Found at i:57208 original size:35 final size:35
Alignment explanation
Indices: 57169--57248 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
57159 GGGGTTGGGC
* *
57169 ATGTAATTGAAGTATTTTGGAATTTGAGGTTTAGA
1 ATGTAATTGAAGCATTTTAGAATTTGAGGTTTAGA
*
57204 ATGTAATTGAAGCATTTTAGAATTTGGGGTTTAGA
1 ATGTAATTGAAGCATTTTAGAATTTGAGGTTTAGA
57239 ATGTAATTGA
1 ATGTAATTGA
57249 TTATTGTGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.33, C:0.01, G:0.25, T:0.41
Consensus pattern (35 bp):
ATGTAATTGAAGCATTTTAGAATTTGAGGTTTAGA
Found at i:57943 original size:18 final size:19
Alignment explanation
Indices: 57920--57960 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
57910 TTTAAGACGA
57920 TAAAAA-CATATATATTTG
1 TAAAAATCATATATATTTG
* *
57938 TAAAAATCTTATTTATTTG
1 TAAAAATCATATATATTTG
57957 TAAA
1 TAAA
57961 TCTATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (19 bp):
TAAAAATCATATATATTTG
Found at i:57982 original size:2 final size:2
Alignment explanation
Indices: 57975--58003 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
57965 TTTTATTGAT
57975 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
58004 TACAATGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58649 original size:27 final size:27
Alignment explanation
Indices: 58601--58652 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
58591 ATTATATATA
* *
58601 TATTTTTTTGTTAATATGAATAATACT
1 TATTTTTTTATCAATATGAATAATACT
58628 TATTTTTTTATCAATCAT-AATAATA
1 TATTTTTTTATCAAT-ATGAATAATA
58653 TTTGTTTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.54
Consensus pattern (27 bp):
TATTTTTTTATCAATATGAATAATACT
Found at i:59597 original size:27 final size:27
Alignment explanation
Indices: 59544--59599 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
59534 TATTTTTGCA
* *
59544 CGTCCCCTCTTGCTCCCCGTTGCATGT
1 CGTCCCCTCCTGCTCCCCGCTGCATGT
* *
59571 CGTCCCCTCCTGCTCCTCGCTGTATGT
1 CGTCCCCTCCTGCTCCCCGCTGCATGT
59598 CG
1 CG
59600 CTGCAGCTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.04, C:0.45, G:0.20, T:0.32
Consensus pattern (27 bp):
CGTCCCCTCCTGCTCCCCGCTGCATGT
Found at i:59815 original size:26 final size:26
Alignment explanation
Indices: 59768--59825 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
59758 ACATAAAAGA
* *
59768 AAGAAAGGGAGAAGAGATTGCAGCCG
1 AAGAAAGGGAGAAGAGAGTGCACCCG
* *
59794 AAGAAAGGGAGAATATAGTGCACCCG
1 AAGAAAGGGAGAAGAGAGTGCACCCG
59820 -AGAAAG
1 AAGAAAG
59826 AAAGAAAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 6 0.21
26 22 0.79
ACGTcount: A:0.45, C:0.12, G:0.34, T:0.09
Consensus pattern (26 bp):
AAGAAAGGGAGAAGAGAGTGCACCCG
Found at i:60351 original size:15 final size:16
Alignment explanation
Indices: 60323--60356 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
60313 AAAATTTACT
60323 TTATAAGTTTATTATA
1 TTATAAGTTTATTATA
60339 TTATAAG-TTATTATA
1 TTATAAGTTTATTATA
60354 TTA
1 TTA
60357 AATTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATAAGTTTATTATA
Found at i:62448 original size:17 final size:17
Alignment explanation
Indices: 62393--62453 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
62383 ACAATATAAA
*
62393 TTAAACAAAATATTTTT
1 TTAAACACAATATTTTT
* *
62410 TTAAAACAACACTAAATATTT
1 TT-AAAC-ACA--ATATTTTT
62431 TTAAACACAATATTTTT
1 TTAAACACAATATTTTT
62448 TTAAAC
1 TTAAAC
62454 GGAAATTATC
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
17 14 0.40
18 4 0.11
19 5 0.14
20 4 0.11
21 8 0.23
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAACACAATATTTTT
Found at i:62920 original size:44 final size:50
Alignment explanation
Indices: 62862--62969 Score: 129
Period size: 50 Copynumber: 2.3 Consensus size: 50
62852 GTTTAAAGAC
* *
62862 ACTAACAAATTAATTAAAT-ATTTTTT-T-T-ATAT-TTA-ATAACTTAA
1 ACTAACAAACTAATTAAATAATTTTTTATATAATATAATATATAACTTAA
* *
62906 ACTAAGAAACTAATTAACTAATTTTTTATATAATATAATATATAACTTAA
1 ACTAACAAACTAATTAAATAATTTTTTATATAATATAATATATAACTTAA
*
62956 ACTAACAAGCTAAT
1 ACTAACAAACTAAT
62970 AATTTATACT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
44 16 0.31
45 7 0.13
46 1 0.02
47 1 0.02
48 4 0.08
49 2 0.04
50 21 0.40
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (50 bp):
ACTAACAAACTAATTAAATAATTTTTTATATAATATAATATATAACTTAA
Found at i:62980 original size:21 final size:21
Alignment explanation
Indices: 62947--62995 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
62937 AATATAATAT
*
62947 ATAACTTAAACTAACAAGCTA
1 ATAACTTAAACTAACAAACTA
* *
62968 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
62989 ATTAACT
1 A-TAACT
62996 AAATTTTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:75817 original size:31 final size:31
Alignment explanation
Indices: 75779--75839 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
75769 ATGCCGTGCT
*
75779 TTACTTCAATTTTGCAATTTAGTTGATAAGA
1 TTACTTCAATTTTACAATTTAGTTGATAAGA
75810 TTACTTCAATTTTACAATTTAGTTGATAAG
1 TTACTTCAATTTTACAATTTAGTTGATAAG
75840 CTTTGCATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (31 bp):
TTACTTCAATTTTACAATTTAGTTGATAAGA
Done.