Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000795.1 Hibiscus syriacus cultivar Beakdansim tig00001539_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: 80259
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1264 original size:21 final size:18
Alignment explanation
Indices: 1239--1283 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
1229 GCGTACTTCA
1239 ATTATTGAAAGTTAGAAAAT
1 ATTATT-AAA-TTAGAAAAT
*
1259 AGTTATTAAATTATAAAAT
1 A-TTATTAAATTAGAAAAT
1278 ATTATT
1 ATTATT
1284 TTATTGAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 5 0.22
19 9 0.39
20 4 0.17
21 5 0.22
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (18 bp):
ATTATTAAATTAGAAAAT
Found at i:4931 original size:3 final size:3
Alignment explanation
Indices: 4923--4994 Score: 92
Period size: 3 Copynumber: 23.7 Consensus size: 3
4913 ATATTTATTA
*
4923 AAT AAT AAT AAT -AT ATAT AAT ATAT AAT ATT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
**
4969 AAT TTT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
4995 AACGAAATGA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
2 2 0.03
3 52 0.87
4 6 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:5934 original size:22 final size:22
Alignment explanation
Indices: 5909--5985 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
5899 CATAAAGCTT
5909 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
5931 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
5953 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
5975 TCATCTTTGAA
1 TCATCTTTGAA
5986 GAGTATAGAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:10690 original size:10 final size:10
Alignment explanation
Indices: 10675--10730 Score: 60
Period size: 10 Copynumber: 5.4 Consensus size: 10
10665 TCAATTTTCC
10675 TTTTTTTCTT
1 TTTTTTTCTT
10685 TTTTTTTCTT
1 TTTTTTTCTT
10695 TTTATTTT-TT
1 TTT-TTTTCTT
*
10705 TTCCTTTTTGTT
1 TT--TTTTTCTT
*
10717 TTTTTTTGTT
1 TTTTTTTCTT
10727 TTTT
1 TTTT
10731 CCTTCTTCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
10 29 0.69
11 8 0.19
12 5 0.12
ACGTcount: A:0.02, C:0.07, G:0.04, T:0.88
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:10696 original size:16 final size:16
Alignment explanation
Indices: 10677--10729 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
10667 AATTTTCCTT
*
10677 TTTTTCTTTTTTTTTC
1 TTTTTATTTTTTTTTC
*
10693 TTTTTATTTTTTTTCC
1 TTTTTATTTTTTTTTC
* *
10709 TTTTTGTTTTTTTTTG
1 TTTTTATTTTTTTTTC
10725 TTTTT
1 TTTTT
10730 TCCTTCTTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.02, C:0.08, G:0.04, T:0.87
Consensus pattern (16 bp):
TTTTTATTTTTTTTTC
Found at i:10696 original size:24 final size:24
Alignment explanation
Indices: 10669--10745 Score: 57
Period size: 25 Copynumber: 3.1 Consensus size: 24
10659 CTTGATTCAA
*
10669 TTTTCCTTTTTTTCTTTTTTTTTC
1 TTTTACTTTTTTTCTTTTTTTTTC
*
10693 TTTTTATTTTTTTTCCTTTTTGTTTT-
1 -TTTTACTTTTTTT-CTTTTT-TTTTC
** * * *
10719 TTTTTGTTTTTTCCTTCTTCTTTC
1 TTTTACTTTTTTTCTTTTTTTTTC
10743 TTT
1 TTT
10746 GCTGGATGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
23 3 0.07
24 8 0.19
25 21 0.50
26 6 0.14
27 4 0.10
ACGTcount: A:0.01, C:0.14, G:0.03, T:0.82
Consensus pattern (24 bp):
TTTTACTTTTTTTCTTTTTTTTTC
Found at i:17785 original size:3 final size:3
Alignment explanation
Indices: 17777--17839 Score: 83
Period size: 3 Copynumber: 20.7 Consensus size: 3
17767 ATGTTTATTA
**
17777 AAT AAT AAT AAT -AT ATAT AAT ATAT AAT AAT AAT AAT AAT TTT AAT
1 AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
17823 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
17840 AAGGAAATGA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:18206 original size:31 final size:31
Alignment explanation
Indices: 18170--18246 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
18160 AAGAATTAAA
18170 AGTTTA-GTTACTAAAATGGAGCAAAAACGAT
1 AGTTTATG-TACTAAAATGGAGCAAAAACGAT
18201 AGTTTATGTACTAAAATGGAGCAAAAACGAT
1 AGTTTATGTACTAAAATGGAGCAAAAACGAT
18232 AGTTTATGTACTAAA
1 AGTTTATGTACTAAA
18247 CAAGTTAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
31 44 0.98
32 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (31 bp):
AGTTTATGTACTAAAATGGAGCAAAAACGAT
Found at i:21015 original size:20 final size:19
Alignment explanation
Indices: 20989--21033 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
20979 GATTTATTGA
*
20989 AAAAAAACAAAGATACAAT
1 AAAAAAACAAAAATACAAT
*
21008 ATAAAAAAGAAAAATACAAT
1 A-AAAAAACAAAAATACAAT
21028 AAAAAA
1 AAAAAA
21034 TATCATCGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.78, C:0.07, G:0.04, T:0.11
Consensus pattern (19 bp):
AAAAAAACAAAAATACAAT
Found at i:21447 original size:26 final size:29
Alignment explanation
Indices: 21418--21481 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
21408 CAATTTTAGA
*
21418 AATATAA-AAT-TATAAAA-AATTAAATT
1 AATATAATAATATATAAAATAATTAAAAT
21444 AATATTAAATAATATATAAAATAATTAAAAT
1 AATA-T-AATAATATATAAAATAATTAAAAT
21475 -ATATAAT
1 AATATAAT
21482 TTTCAAAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
26 4 0.12
27 1 0.03
28 5 0.16
29 4 0.12
30 10 0.31
31 8 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
AATATAATAATATATAAAATAATTAAAAT
Found at i:21800 original size:18 final size:17
Alignment explanation
Indices: 21779--21823 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
21769 TGTCAATAAA
21779 ATTAATATTAATATTATT
1 ATTAATATTAAT-TTATT
*
21797 ATTATTATTAATTTATT
1 ATTAATATTAATTTATT
21814 ATTGAATATT
1 ATT-AATATT
21824 TTCATTAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
ATTAATATTAATTTATT
Found at i:22217 original size:29 final size:29
Alignment explanation
Indices: 22167--22236 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
22157 TTAACTTATT
* * *
22167 AAATATATTTTATTCTTGTTTTAACCTAA
1 AAATATATTTTATCCTTATTTTAAACTAA
* *
22196 ATATATATTTTATCCTTATTTTAAATTAA
1 AAATATATTTTATCCTTATTTTAAACTAA
22225 AAATATATTTTA
1 AAATATATTTTA
22237 GTTTTTATCT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.53
Consensus pattern (29 bp):
AAATATATTTTATCCTTATTTTAAACTAA
Found at i:22232 original size:31 final size:29
Alignment explanation
Indices: 22137--22274 Score: 150
Period size: 30 Copynumber: 4.7 Consensus size: 29
22127 ATTTCTTATT
* * *
22137 AAATATATTTTATTTTTATATTAACTTATT
1 AAATATATTTTATTCTTATTTTAACTTA-A
* *
22167 AAATATATTTTATTCTTGTTTTAACCTAA
1 AAATATATTTTATTCTTATTTTAACTTAA
* * *
22196 ATATATATTTTATCCTTATTTTAAATTAA
1 AAATATATTTTATTCTTATTTTAACTTAA
* *
22225 AAATATATTTTAGTTTTTATCTTAACTTAAA
1 AAATATATTTTA-TTCTTATTTTAACTT-AA
*
22256 AAACATATTTTATTCTTAT
1 AAATATATTTTATTCTTAT
22275 CATAACTTTT
Statistics
Matches: 89, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
29 35 0.39
30 41 0.46
31 13 0.15
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.54
Consensus pattern (29 bp):
AAATATATTTTATTCTTATTTTAACTTAA
Found at i:22335 original size:26 final size:25
Alignment explanation
Indices: 22298--22346 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
22288 TTTTGTTATG
* *
22298 ATAATATTTTAAATTTAAGATAAAAT
1 ATAATATATTAAA-TTAAAATAAAAT
22324 ATAATATATTAAATTAAAATAAA
1 ATAATATATTAAATTAAAATAAA
22347 TTTAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (25 bp):
ATAATATATTAAATTAAAATAAAAT
Found at i:22626 original size:20 final size:19
Alignment explanation
Indices: 22581--22629 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
22571 GTGTCACTGG
*
22581 TATAATTTACCTTTTATTT
1 TATAATTTACCTTTAATTT
*
22600 TAAATAATTTATCTTTAAATTT
1 T--ATAATTTACCTTT-AATTT
22622 TATAATTT
1 TATAATTT
22630 TACGTTGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 7 0.28
21 12 0.48
22 5 0.20
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (19 bp):
TATAATTTACCTTTAATTT
Found at i:26674 original size:24 final size:24
Alignment explanation
Indices: 26646--26710 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
26636 TTTGCTTATT
*
26646 TTCATTTACAAAATTTTTTATTAA
1 TTCATTTATAAAATTTTTTATTAA
* * *
26670 TTCATTTATAAACTCTTTTATTAG
1 TTCATTTATAAAATTTTTTATTAA
26694 TTCATTTATTAAAATTT
1 TTCATTTA-TAAAATTT
26711 CATATTTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 28 0.82
25 6 0.18
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (24 bp):
TTCATTTATAAAATTTTTTATTAA
Found at i:26677 original size:12 final size:12
Alignment explanation
Indices: 26662--26705 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
26652 TACAAAATTT
26662 TTTATTAATTCA
1 TTTATTAATTCA
* * *
26674 TTTATAAACTCT
1 TTTATTAATTCA
*
26686 TTTATTAGTTCA
1 TTTATTAATTCA
26698 TTTATTAA
1 TTTATTAA
26706 AATTTCATAT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (12 bp):
TTTATTAATTCA
Found at i:34528 original size:21 final size:21
Alignment explanation
Indices: 34413--34528 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
34403 GCGAAATAAA
**
34413 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
34433 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
34453 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
34474 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
34494 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
34516 AATCGCAACGCGA
1 AATCGCAACGCGA
34529 ATATGAAAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 40 0.57
22 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:34541 original size:20 final size:20
Alignment explanation
Indices: 34516--34688 Score: 222
Period size: 20 Copynumber: 8.6 Consensus size: 20
34506 GATTTTCCAG
* ** *
34516 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
34536 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
34556 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
34576 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* **
34596 AATCGCAATGCGTAGACGTA
1 AATCGCAACGCGTATCCGTA
*
34616 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
34636 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
34657 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
34677 AATCGCAACGCG
1 AATCGCAACGCG
34689 ATTTTTAAAG
Statistics
Matches: 132, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
20 115 0.87
21 17 0.13
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:35110 original size:33 final size:33
Alignment explanation
Indices: 35066--35138 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
35056 ATTTCACTTA
35066 GATTTT-ATTTCGCGTTACGATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTACGATTCTCTCGTTGC
* *
35098 GATTTTCATTTCGCGTTGCTATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTACGATTCTCTCGTTGC
35131 GATTTTCA
1 GATTTTCA
35139 AGTTAGTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 6 0.16
33 32 0.84
ACGTcount: A:0.12, C:0.22, G:0.18, T:0.48
Consensus pattern (33 bp):
GATTTTCATTTCGCGTTACGATTCTCTCGTTGC
Found at i:35244 original size:21 final size:20
Alignment explanation
Indices: 35218--35324 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
35208 TGCAGAAGAG
35218 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
35239 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
35259 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
35281 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
35295 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
35314 TCGCAACGAGA
1 TCGCAACGAGA
35325 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 9 0.13
21 25 0.36
22 10 0.14
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:35298 original size:14 final size:14
Alignment explanation
Indices: 35279--35335 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
35269 GAAAAATGAA
35279 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
35293 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
35312 AATCGCAACGAGAG
1 AATCGCAACGAGAG
35326 AATCGCAACG
1 AATCGCAACG
35336 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:35310 original size:33 final size:33
Alignment explanation
Indices: 35272--35351 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
35262 GCAACGAGAA
35272 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
35305 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
35338 AAACCAAAATCGCA
1 AAATGAAAATCGCA
35352 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:35369 original size:19 final size:19
Alignment explanation
Indices: 35347--35474 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
35337 GAAACCAAAA
*
35347 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
35366 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
35380 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
35399 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
35413 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
35433 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
35453 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
35473 TC
1 TC
35475 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:35388 original size:14 final size:14
Alignment explanation
Indices: 35369--35425 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
35359 TTTCATTTCG
35369 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
35383 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
35402 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
35416 CGTTGCGATT
1 CGTTGCGATT
35426 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:35394 original size:33 final size:33
Alignment explanation
Indices: 35352--35474 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
35342 CAAAATCGCA
35352 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
35385 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
35418 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
35459 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
35475 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:35436 original size:21 final size:21
Alignment explanation
Indices: 35410--35474 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
35400 CGCGTTGCGA
35410 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
35431 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
35451 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
35472 TTC
1 TTC
35475 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:37368 original size:92 final size:93
Alignment explanation
Indices: 37159--37473 Score: 605
Period size: 93 Copynumber: 3.4 Consensus size: 93
37149 TAGATTGCTT
* *
37159 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAATA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
37224 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
37252 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
37317 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
37344 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
37409 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
37437 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
37474 AATACCCTGA
Statistics
Matches: 219, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 92 0.42
93 127 0.58
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:37627 original size:19 final size:19
Alignment explanation
Indices: 37603--37661 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
37593 GCAACGAGAG
37603 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
37622 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
37636 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
37655 AATCGCA
1 AATCGCA
37662 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 11 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.51
ACGTcount: A:0.47, C:0.31, G:0.15, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:37629 original size:33 final size:33
Alignment explanation
Indices: 37571--37661 Score: 137
Period size: 33 Copynumber: 2.7 Consensus size: 33
37561 TAGTTTACTT
* * * *
37571 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAAAA
37605 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
37638 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
37662 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 40 0.75
34 13 0.25
ACGTcount: A:0.46, C:0.29, G:0.16, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAAAA
Found at i:37638 original size:14 final size:14
Alignment explanation
Indices: 37587--37645 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
37577 CACGAAACTT
*
37587 AAAATCGCAACGAG
1 AAAATCGCAACGAC
*
37601 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
37620 AAAATCGCAACGAC
1 AAAATCGCAACGAC
37634 AAAATCGCAACG
1 AAAATCGCAACG
37646 CGAAACCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 22 0.59
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 9 0.24
ACGTcount: A:0.47, C:0.27, G:0.19, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:37679 original size:19 final size:19
Alignment explanation
Indices: 37657--37829 Score: 159
Period size: 19 Copynumber: 9.6 Consensus size: 19
37647 GAAACCAAAA
*
37657 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
37676 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
37690 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
37709 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
37725 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
37742 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
37761 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
37780 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
37799 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
37819 TCGTGTTGCGA
1 TCGCGTTGCGA
37830 AAGTAAACTA
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 17 0.13
16 8 0.06
17 8 0.06
19 81 0.64
20 12 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:37698 original size:14 final size:14
Alignment explanation
Indices: 37679--37735 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
37669 TTTCATTTCG
37679 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
37693 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
37710 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
37726 CGTTGCGATT
1 CGTTGCGATT
37736 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:37787 original size:38 final size:38
Alignment explanation
Indices: 37657--37829 Score: 168
Period size: 33 Copynumber: 4.8 Consensus size: 38
37647 GAAACCAAAA
*
37657 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
37692 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* **
37725 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
37761 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
37799 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
37830 AAGTAAACTA
Statistics
Matches: 115, Mismatches: 15, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 52 0.45
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.38
39 11 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:38304 original size:21 final size:21
Alignment explanation
Indices: 38280--38346 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
38270 TCATTCATCG
38280 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
38301 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
38322 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
38343 AGAG
1 AGAG
38347 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:39770 original size:14 final size:14
Alignment explanation
Indices: 39751--39786 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
39741 ATTGTTTAAT
39751 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
39765 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
39779 TGATTTGT
1 TGATTTGT
39787 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:39923 original size:19 final size:20
Alignment explanation
Indices: 39899--39945 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
39889 GCAACGAGAG
39899 AATCGCAATGC-GAAATGAA
1 AATCGCAATGCGGAAATGAA
39918 AATCGCAATGCGGAAATGAA
1 AATCGCAATGCGGAAATGAA
39938 AATCGCAA
1 AATCGCAA
39946 CGAGAGAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (20 bp):
AATCGCAATGCGGAAATGAA
Found at i:39982 original size:19 final size:19
Alignment explanation
Indices: 39954--40162 Score: 250
Period size: 19 Copynumber: 11.7 Consensus size: 19
39944 AACGAGAGAA
*
39954 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
39973 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
39992 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
40009 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
40026 TCGCATTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
40045 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
40061 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
40078 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
40097 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
40116 TCCGCATTGCGATTTTC--T
1 T-CGCATTGCGATTTTCATT
*
40134 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
40150 TCGCATTGCGATT
1 TCGCATTGCGATT
40163 CTCTCGTTGC
Statistics
Matches: 164, Mismatches: 9, Indels: 34
0.79 0.04 0.16
Matches are distributed among these distances:
14 22 0.13
16 15 0.09
17 14 0.09
18 5 0.03
19 83 0.51
20 25 0.15
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:40161 original size:72 final size:71
Alignment explanation
Indices: 39954--40162 Score: 269
Period size: 72 Copynumber: 2.9 Consensus size: 71
39944 AACGAGAGAA
* ** * * * *
39954 TCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATT-TCCGCA-TTGCGATTCTCTCGTTGCG
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTC-TTGTTGGGATTTTC-ATT-TCGCATTGCG
40017 ATTTTCATT
63 ATTTTCATT
* * * *
40026 TCGCATTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTTGTTGGGATTTTCATTTCGCATTGCGATT
40091 TTCATT
66 TTCATT
40097 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCTTGTTGGGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCTTGTTGGGATTTTCATTTCGCATTGCGAT
40162 T
65 T
40163 CTCTCGTTGC
Statistics
Matches: 119, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
71 37 0.31
72 79 0.66
73 3 0.03
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (71 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTTGTTGGGATTTTCATTTCGCATTGCGATT
TTCATT
Found at i:40184 original size:33 final size:33
Alignment explanation
Indices: 40035--40176 Score: 194
Period size: 33 Copynumber: 4.1 Consensus size: 33
40025 TTCGCATTGG
40035 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
40068 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGC
* * *
40106 GATTTTCATTTCCGCATTGCGATTTTCTTGTTGG
1 GATTTTCATTT-CGCATTGCGATTCTCTCGTTGC
40140 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
40173 GATT
1 GATT
40177 GTAATTTCCG
Statistics
Matches: 95, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
33 44 0.46
34 14 0.15
35 3 0.03
36 7 0.07
37 2 0.02
38 15 0.16
39 10 0.11
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
Found at i:40184 original size:105 final size:103
Alignment explanation
Indices: 39960--40176 Score: 325
Period size: 105 Copynumber: 2.1 Consensus size: 103
39950 AGAATCGCAA
39960 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCA-
40025 TTCGCATTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
65 TTCG-ATTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
*
40065 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCCGCATTGCGAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGA--TTC-TCT-CG--TTGCGAT
40129 TTTC-TT-G-TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
60 TTTCATTCGATTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
40170 TGCGATT
1 TGCGATT
40177 GTAATTTCCG
Statistics
Matches: 105, Mismatches: 1, Indels: 12
0.89 0.01 0.10
Matches are distributed among these distances:
104 10 0.10
105 74 0.70
106 3 0.03
107 3 0.03
108 4 0.04
110 11 0.10
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (103 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TCGATTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:42478 original size:12 final size:12
Alignment explanation
Indices: 42461--42485 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42451 TCTTCGGGGA
42461 CTTTTTCTTCTT
1 CTTTTTCTTCTT
42473 CTTTTTCTTCTT
1 CTTTTTCTTCTT
42485 C
1 C
42486 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:42694 original size:24 final size:24
Alignment explanation
Indices: 42660--42706 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
42650 CTGAAACATC
42660 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
42684 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
42707 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:43427 original size:20 final size:20
Alignment explanation
Indices: 43399--43627 Score: 235
Period size: 20 Copynumber: 11.4 Consensus size: 20
43389 AAATTTCAGT
* * *
43399 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
43419 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
43439 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
43459 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
43479 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
43499 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
43519 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
43539 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
43559 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
43579 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
43599 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
43619 GTTGCGATT
1 GTTGCGATT
43628 CTTGAAAATC
Statistics
Matches: 181, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 180 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:43680 original size:21 final size:20
Alignment explanation
Indices: 43595--43692 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
43585 ATTTATGTGT
* *
43595 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
43615 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
43636 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
43657 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
43678 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
43693 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:43688 original size:42 final size:43
Alignment explanation
Indices: 43595--43693 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
43585 ATTTATGTGT
* *
43595 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
43636 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
43678 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
43694 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:52795 original size:217 final size:220
Alignment explanation
Indices: 52420--52858 Score: 830
Period size: 217 Copynumber: 2.0 Consensus size: 220
52410 TCTCTTATTA
52420 ATAGATTAAGAATAATTTTAAAATATATTATCTTATAATCACTTCAAACTCTTAAAATCAAAAGA
1 ATAGATTAAGAATAATTTTAAAATATATTATCTTATAATCACTTCAAACTCTTAAAATCAAAAGA
**
52485 TACCTTGTCAACGTTGCCTTCATAGAAGTTCTTTTAACGGATTTACATATGAACATGTAATTGGA
66 TACCTCATCAACGTTGCCTTCATAGAAGTTCTTTTAACGGATTTACATATGAACATGTAATTGGA
52550 TGGTCAACAACTAAGCTTAAATTTTCATTCAAAATTTGCATATTATATTTGATCT-AA-A-GAGA
131 TGGTCAACAACTAAGCTTAAATTTTCATTCAAAATTTGCATATTATATTTGATCTAAAGAGGAGA
52612 CCAAATGAGAACACATGTATACACC
196 CCAAATGAGAACACATGTATACACC
*
52637 ATAGATTAAGAATAATTTTAAAATATATTATCTTATAATCACTTCAAACTCTTAAAATCAAAAGG
1 ATAGATTAAGAATAATTTTAAAATATATTATCTTATAATCACTTCAAACTCTTAAAATCAAAAGA
52702 TACCTCATCAACGTTGCCTTCATAGAAGTTCTTTTAACGGATTTACATATGAACATGTAATTGGA
66 TACCTCATCAACGTTGCCTTCATAGAAGTTCTTTTAACGGATTTACATATGAACATGTAATTGGA
52767 TGGTCAACAACTAAGCTTAAATTTTCATTCAAAATTTGCATATTATATTTGATCTAAAGAGGAGA
131 TGGTCAACAACTAAGCTTAAATTTTCATTCAAAATTTGCATATTATATTTGATCTAAAGAGGAGA
52832 CCAAATGAGAACACATGTATACACC
196 CCAAATGAGAACACATGTATACACC
52857 AT
1 AT
52859 CTCTTTCATT
Statistics
Matches: 216, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
217 182 0.84
218 2 0.01
219 1 0.00
220 31 0.14
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (220 bp):
ATAGATTAAGAATAATTTTAAAATATATTATCTTATAATCACTTCAAACTCTTAAAATCAAAAGA
TACCTCATCAACGTTGCCTTCATAGAAGTTCTTTTAACGGATTTACATATGAACATGTAATTGGA
TGGTCAACAACTAAGCTTAAATTTTCATTCAAAATTTGCATATTATATTTGATCTAAAGAGGAGA
CCAAATGAGAACACATGTATACACC
Found at i:56307 original size:5 final size:5
Alignment explanation
Indices: 56294--56323 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
56284 CTTCATTGGT
*
56294 CTCCT CTCCA CTCCA CTCCA CTCCA CTCCA
1 CTCCA CTCCA CTCCA CTCCA CTCCA CTCCA
56324 GTGTGTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.60, G:0.00, T:0.23
Consensus pattern (5 bp):
CTCCA
Found at i:57600 original size:23 final size:23
Alignment explanation
Indices: 57559--57602 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
57549 ATGAGGGATC
*
57559 AAATTGAAATAATTTTAAAATGT
1 AAATTGAAATAATTATAAAATGT
57582 AAATTGAAATTAA-TATAAAAT
1 AAATTGAAA-TAATTATAAAAT
57603 TGGACTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (23 bp):
AAATTGAAATAATTATAAAATGT
Found at i:58029 original size:2 final size:2
Alignment explanation
Indices: 58007--58288 Score: 221
Period size: 2 Copynumber: 144.5 Consensus size: 2
57997 ACATTATTCT
* *
58007 TA TA -A TA TA TG TA CA TA -A TA TA TA TA -A GTA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
*
58046 TA TA TA -A GA -A TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58085 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * ** * * *
58127 TG TA TA CA TA CG TA TGA TG CA TG TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
58169 TA TA TA TA T- TA TA CA TG TA TA TA TA TCA TA TA TG TA TA TA CT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA -TA
* * * * * *
58211 TA TA TA TA TA CA TG T- TA TA CA TG TA TA TA TA TCA TT TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
* **
58253 TA TA TA TA TG TA TA CG T- TA TA TA TA TA -A GTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
58289 GTAATTATGT
Statistics
Matches: 221, Mismatches: 40, Indels: 38
0.74 0.13 0.13
Matches are distributed among these distances:
1 13 0.06
2 199 0.90
3 9 0.04
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (2 bp):
TA
Found at i:58319 original size:22 final size:22
Alignment explanation
Indices: 58294--58377 Score: 91
Period size: 22 Copynumber: 3.8 Consensus size: 22
58284 TATATGTAAT
**
58294 TATGTATGATCAATGATGCATG
1 TATGTATGATGTATGATGCATG
58316 TATG-ATGTATGTATGATGCATG
1 TATGTATG-ATGTATGATGCATG
* *
58338 TATATAT-ATGTATGTATGTATG
1 TATGTATGATGTATG-ATGCATG
58360 TATGTATGTATGTATGAT
1 TATGTATG-ATGTATGAT
58378 CCATACATAC
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
21 10 0.19
22 31 0.60
23 4 0.08
24 7 0.13
ACGTcount: A:0.30, C:0.04, G:0.23, T:0.44
Consensus pattern (22 bp):
TATGTATGATGTATGATGCATG
Found at i:58329 original size:4 final size:4
Alignment explanation
Indices: 58313--58375 Score: 80
Period size: 4 Copynumber: 16.8 Consensus size: 4
58303 TCAATGATGC
* *
58313 ATGT ATG- ATGT ATGT ATG- ATGC ATGT A--T ATAT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
58357 ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATG
58376 ATCCATACAT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 2 0.04
3 6 0.11
4 45 0.85
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.46
Consensus pattern (4 bp):
ATGT
Found at i:58405 original size:45 final size:44
Alignment explanation
Indices: 58313--58405 Score: 114
Period size: 45 Copynumber: 2.1 Consensus size: 44
58303 TCAATGATGC
* ** * * *
58313 ATGTATGATGTATGTATGATGCATGTATATATATGTATGTATGT
1 ATGTATGATGTATGTATGATCCATACATACATATATATGTATAT
*
58357 ATGTATGTATGTATGTATGATCCATACATACATATATATTTATAT
1 ATGTATG-ATGTATGTATGATCCATACATACATATATATGTATAT
58402 ATGT
1 ATGT
58406 CATAATTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 7 0.17
45 34 0.83
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.45
Consensus pattern (44 bp):
ATGTATGATGTATGTATGATCCATACATACATATATATGTATAT
Found at i:58493 original size:33 final size:34
Alignment explanation
Indices: 58419--58518 Score: 100
Period size: 35 Copynumber: 2.9 Consensus size: 34
58409 AATTTATTAA
*
58419 AAAATA-AAAAATATATATGTATATATATTAA-TAT
1 AAAATATATAAAT-TATATGTATATATA-TAAGTAT
* *
58453 --TATATATACACTTATATGTATATATATAAGTAT
1 AAAATATATA-AATTATATGTATATATATAAGTAT
*
58486 AAAATATATAAATAACTATGTATATATATAAGT
1 AAAATATATAAATTA-TATGTATATATATAAGT
58519 TTATGTAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
32 6 0.11
33 19 0.35
34 5 0.09
35 24 0.44
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (34 bp):
AAAATATATAAATTATATGTATATATATAAGTAT
Found at i:68365 original size:12 final size:12
Alignment explanation
Indices: 68340--68397 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
68330 ACGGAGATAT
* *
68340 CAGAAATCAAAA
1 CAGAATTCAGAA
68352 CAGAATTCAGAA
1 CAGAATTCAGAA
* *
68364 CAGAATCCAGAT
1 CAGAATTCAGAA
* *
68376 CAGAAATCAAAA
1 CAGAATTCAGAA
68388 CAGAATTCAG
1 CAGAATTCAG
68398 GTCACGTATC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.53, C:0.19, G:0.14, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:73073 original size:20 final size:21
Alignment explanation
Indices: 73048--73086 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
73038 ATTCGTTGAA
73048 AATTA-TTAAAAAATTAATAT
1 AATTATTTAAAAAATTAATAT
73068 AATTATTTAAAAAATTAAT
1 AATTATTTAAAAAATTAAT
73087 TTGCTAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATTATTTAAAAAATTAATAT
Found at i:78983 original size:21 final size:21
Alignment explanation
Indices: 78957--78999 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
78947 GTTTTTATGG
* *
78957 AAGATTTTATGGCTTCGACAA
1 AAGATTTCATGGCTTCAACAA
78978 AAGATTTCATGGCTTCAACAA
1 AAGATTTCATGGCTTCAACAA
78999 A
1 A
79000 GGCATTGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (21 bp):
AAGATTTCATGGCTTCAACAA
Done.