Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001180.1 Hibiscus syriacus cultivar Beakdansim tig00002346_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: 41948
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:1593 original size:20 final size:20
Alignment explanation
Indices: 1568--1621 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
1558 AGAATAGTTT
1568 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1588 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
1608 ACTATCGC-ATGCGA
1 ACTATCGCAATGCGA
1622 TTCTCTCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 5 0.16
20 27 0.84
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:1636 original size:14 final size:14
Alignment explanation
Indices: 1617--1669 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 14
1607 GACTATCGCA
1617 TGCGATTCTCTCGT
1 TGCGATTCTCTCGT
*
1631 TGCGATTTTCATTTCGCAT
1 TGCGA--TTC-TCTCG--T
1650 TGCGATTCTCTCGT
1 TGCGATTCTCTCGT
1664 TGCGAT
1 TGCGAT
1670 AGTCATTTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 12 0.38
16 7 0.22
17 7 0.22
19 6 0.19
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.43
Consensus pattern (14 bp):
TGCGATTCTCTCGT
Found at i:1655 original size:33 final size:33
Alignment explanation
Indices: 1612--1689 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
1602 AAAATGACTA
**
1612 TCGCA-TGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCATT
1644 TCGCATTGCGATTCTCTCGTTGCGATAGTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCATT
*
1677 TCCGCGTTGCGAT
1 T-CGCATTGCGAT
1690 AGTCATTTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 5 0.12
33 26 0.63
34 10 0.24
ACGTcount: A:0.13, C:0.26, G:0.22, T:0.40
Consensus pattern (33 bp):
TCGCATTGCGATTCTCTCGTTGCGATAGTCATT
Found at i:1686 original size:20 final size:20
Alignment explanation
Indices: 1661--1754 Score: 170
Period size: 20 Copynumber: 4.7 Consensus size: 20
1651 GCGATTCTCT
1661 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
1681 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1701 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
1721 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1741 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
1755 AATGAATGTC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:3859 original size:3 final size:3
Alignment explanation
Indices: 3851--3886 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
3841 CTTTGGGGAT
* *
3851 TTC TTC TTC TTT TTC TTC TTC TTC TTT TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3887 AGGGTTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:3865 original size:12 final size:13
Alignment explanation
Indices: 3850--3886 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
3840 TCTTTGGGGA
3850 TTTCTTCTTCTT-
1 TTTCTTCTTCTTC
3862 TTTCTTCTTCTTC
1 TTTCTTCTTCTTC
3875 TTT-TTCTTCTTC
1 TTTCTTCTTCTTC
3887 AGGGTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 21 0.88
13 3 0.12
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTCTTCTTCTTC
Found at i:3869 original size:15 final size:15
Alignment explanation
Indices: 3851--3886 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
3841 CTTTGGGGAT
3851 TTCTTCTTCTTTTTC
1 TTCTTCTTCTTTTTC
3866 TTCTTCTTCTTTTTC
1 TTCTTCTTCTTTTTC
3881 TTCTTC
1 TTCTTC
3887 AGGGTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (15 bp):
TTCTTCTTCTTTTTC
Found at i:4089 original size:24 final size:24
Alignment explanation
Indices: 4062--4121 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
4052 CTGAAAAATC
4062 ATCAAAATTCGAGTATTGAACAAG
1 ATCAAAATTCGAGTATTGAACAAG
* * * *
4086 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATTCGAGTATTGAACAAG
*
4110 ATCAAATTTCGA
1 ATCAAAATTCGA
4122 ATACTGACTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTGAACAAG
Found at i:4981 original size:20 final size:20
Alignment explanation
Indices: 4956--5022 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
4946 AAATTCAGTA
4956 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
4976 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
*
4996 TTGCGATAGTCA-AATTCGCG
1 TTGCGATAGTCAGAA-TCTCG
5016 TTGCGAT
1 TTGCGAT
5023 TTACATATTC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 2 0.04
20 43 0.96
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:5032 original size:20 final size:20
Alignment explanation
Indices: 5009--5121 Score: 181
Period size: 20 Copynumber: 5.7 Consensus size: 20
4999 CGATAGTCAA
* *
5009 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
* *
5029 ATTCGCGTTGCAATTTACGT
1 ATTCGCATTGCGATTTACGT
5049 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
5069 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
5089 ATTCGCATTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
5109 ATTCGCATTGCGA
1 ATTCGCATTGCGA
5122 ATTAGGAGAA
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 87 1.00
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:5038 original size:40 final size:40
Alignment explanation
Indices: 4994--5121 Score: 123
Period size: 40 Copynumber: 3.2 Consensus size: 40
4984 GTCAGAATCT
*
4994 CGTTGCGATAGT-CAAATTCGCGTTGCGATTTACATATTCG
1 CGTTGCGAT-GTACAAATTCGCATTGCGATTTACATATTCG
* * ** *
5034 CGTTGCAATTTACGTATTCGCATTGCGATTTACGTATTCG
1 CGTTGCGATGTACAAATTCGCATTGCGATTTACATATTCG
* * ** * *
5074 CATTGCGATTTACGTATTCGCATTACGATTTACGTATTCG
1 CGTTGCGATGTACAAATTCGCATTGCGATTTACATATTCG
*
5114 CATTGCGA
1 CGTTGCGA
5122 ATTAGGAGAA
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
39 1 0.01
40 77 0.99
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (40 bp):
CGTTGCGATGTACAAATTCGCATTGCGATTTACATATTCG
Found at i:5060 original size:60 final size:60
Alignment explanation
Indices: 4996--5121 Score: 164
Period size: 60 Copynumber: 2.1 Consensus size: 60
4986 CAGAATCTCG
* * *
4996 TTGCGATAGT-CAAATTCGCGTTGCGATTTACATATTCGCGTTGCAATTTACGTATTCGCA
1 TTGCGAT-GTACAAATTCGCATTGCGATTTACATATTCGCATTACAATTTACGTATTCGCA
* ** * *
5056 TTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTACGATTTACGTATTCGCA
1 TTGCGATGTACAAATTCGCATTGCGATTTACATATTCGCATTACAATTTACGTATTCGCA
5116 TTGCGA
1 TTGCGA
5122 ATTAGGAGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 1 0.02
60 56 0.98
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (60 bp):
TTGCGATGTACAAATTCGCATTGCGATTTACATATTCGCATTACAATTTACGTATTCGCA
Found at i:5691 original size:25 final size:25
Alignment explanation
Indices: 5657--5704 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
5647 CATCATTGAA
5657 ATTGATGCAGAGGCTGCTGATCGTT
1 ATTGATGCAGAGGCTGCTGATCGTT
5682 ATTGATGCAGAGGCTGCTGATCG
1 ATTGATGCAGAGGCTGCTGATCG
5705 ATTTTTTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (25 bp):
ATTGATGCAGAGGCTGCTGATCGTT
Found at i:9084 original size:27 final size:27
Alignment explanation
Indices: 9053--9133 Score: 162
Period size: 27 Copynumber: 3.0 Consensus size: 27
9043 TTGTATTATG
9053 ATACATATATTAATGATATATCAGCAA
1 ATACATATATTAATGATATATCAGCAA
9080 ATACATATATTAATGATATATCAGCAA
1 ATACATATATTAATGATATATCAGCAA
9107 ATACATATATTAATGATATATCAGCAA
1 ATACATATATTAATGATATATCAGCAA
9134 GTTAAGGGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.33
Consensus pattern (27 bp):
ATACATATATTAATGATATATCAGCAA
Found at i:16290 original size:60 final size:60
Alignment explanation
Indices: 16223--16371 Score: 178
Period size: 60 Copynumber: 2.5 Consensus size: 60
16213 AGTCCTTACG
* * ** *
16223 CTTTTGAATATTTCAATTTCATCCCCAAACTGTGA-CTCTCATTTTAAAT-GAATCCTTAAT
1 CTTTTGAATATTTCAATTTCATCCCCAAACTATGATC-CTCATTCTAAATCG-ATCCCCAAA
*
16283 CTTTTGAATA-TTCTAATTTTATCCCCAAACTATGATCCTCATTCTAAATCGATCCCCAAA
1 CTTTTGAATATTTC-AATTTCATCCCCAAACTATGATCCTCATTCTAAATCGATCCCCAAA
* *
16343 CTTTTGAATCTTTCAATTTCATCTCCAAA
1 CTTTTGAATATTTCAATTTCATCCCCAAA
16372 TTCATTCAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
59 3 0.04
60 68 0.89
61 5 0.07
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.40
Consensus pattern (60 bp):
CTTTTGAATATTTCAATTTCATCCCCAAACTATGATCCTCATTCTAAATCGATCCCCAAA
Found at i:23411 original size:29 final size:29
Alignment explanation
Indices: 23377--23433 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
23367 TCTCAAAAAG
*
23377 TAATATTTATCGAAA-TGTCACTCTTTCAC
1 TAATATTTA-CGAAATTGTCACCCTTTCAC
*
23406 TAATATTTACTAAATTGTCACCCTTTCA
1 TAATATTTACGAAATTGTCACCCTTTCA
23434 TACTACATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (29 bp):
TAATATTTACGAAATTGTCACCCTTTCAC
Found at i:24204 original size:29 final size:29
Alignment explanation
Indices: 24162--24258 Score: 117
Period size: 29 Copynumber: 3.3 Consensus size: 29
24152 ATTCTACAGT
24162 GACCAAGGAGGTCGCCATGCACTCCGGGA
1 GACCAAGGAGGTCGCCATGCACTCCGGGA
* **
24191 GACCAAGGAGGTCGCCATGCACGCC-CAA
1 GACCAAGGAGGTCGCCATGCACTCCGGGA
* *
24219 CGACCAAGGATGTCGCCATGCACTCGGGGCA
1 -GACCAAGGAGGTCGCCATGCACTCCGGG-A
24250 -ACCAAGGAG
1 GACCAAGGAG
24259 CGATGCATGT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
28 1 0.02
29 54 0.96
31 1 0.02
ACGTcount: A:0.27, C:0.32, G:0.32, T:0.09
Consensus pattern (29 bp):
GACCAAGGAGGTCGCCATGCACTCCGGGA
Found at i:24293 original size:23 final size:23
Alignment explanation
Indices: 24263--24339 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 23
24253 AAGGAGCGAT
24263 GCATGTGGGAGATCTCTGCATGG
1 GCATGTGGGAGATCTCTGCATGG
*** *
24286 GCATGTGGGAG--CGGGAGC-TGT
1 GCATGTGGGAGATC-TCTGCATGG
*
24307 GCATG-GGGAGATCTCTACATGG
1 GCATGTGGGAGATCTCTGCATGG
24329 GCATGTGGGAG
1 GCATGTGGGAG
24340 CGGGAGCTGT
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
20 5 0.12
21 9 0.22
22 10 0.25
23 16 0.40
ACGTcount: A:0.18, C:0.16, G:0.44, T:0.22
Consensus pattern (23 bp):
GCATGTGGGAGATCTCTGCATGG
Found at i:24322 original size:43 final size:43
Alignment explanation
Indices: 24262--24355 Score: 170
Period size: 43 Copynumber: 2.2 Consensus size: 43
24252 CAAGGAGCGA
*
24262 TGCATGTGGGAGATCTCTGCATGGGCATGTGGGAGCGGGAGCTG
1 TGCATG-GGGAGATCTCTACATGGGCATGTGGGAGCGGGAGCTG
24306 TGCATGGGGAGATCTCTACATGGGCATGTGGGAGCGGGAGCTG
1 TGCATGGGGAGATCTCTACATGGGCATGTGGGAGCGGGAGCTG
24349 TGCATGG
1 TGCATGG
24356 CCATGCACGT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 43 0.88
44 6 0.12
ACGTcount: A:0.17, C:0.16, G:0.45, T:0.22
Consensus pattern (43 bp):
TGCATGGGGAGATCTCTACATGGGCATGTGGGAGCGGGAGCTG
Found at i:24354 original size:21 final size:21
Alignment explanation
Indices: 24286--24354 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
24276 CTCTGCATGG
24286 GCATGTGGGAGCGGGAGCTGT
1 GCATGTGGGAGCGGGAGCTGT
*** *
24307 GCATG-GGGAGATCTCTA-CATGG
1 GCATGTGGGAG--CGGGAGC-TGT
24329 GCATGTGGGAGCGGGAGCTGT
1 GCATGTGGGAGCGGGAGCTGT
24350 GCATG
1 GCATG
24355 GCCATGCACG
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
20 5 0.14
21 15 0.43
22 10 0.29
23 5 0.14
ACGTcount: A:0.17, C:0.16, G:0.46, T:0.20
Consensus pattern (21 bp):
GCATGTGGGAGCGGGAGCTGT
Found at i:24550 original size:65 final size:65
Alignment explanation
Indices: 24419--24551 Score: 167
Period size: 65 Copynumber: 2.0 Consensus size: 65
24409 GATTCCTGCA
* * * *
24419 CCTGCACCACGACCAAGCTTTAACCCTATCCCTCCTACATGCATTGCATCCATAATTGAGATATT
1 CCTGCACCACGACCAAGCTTTAACCATATCCCTCATACATGCATTGCATCCATAACTGAGAGATT
* * * ** * *
24484 CCTGCATCGCGACCAAGCTTTAACCATATCCCTCATGCATGTGTTGCATCCATAGCTGGGAGATT
1 CCTGCACCACGACCAAGCTTTAACCATATCCCTCATACATGCATTGCATCCATAACTGAGAGATT
24549 CCT
1 CCT
24552 ACATTCGTAG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (65 bp):
CCTGCACCACGACCAAGCTTTAACCATATCCCTCATACATGCATTGCATCCATAACTGAGAGATT
Found at i:24966 original size:21 final size:21
Alignment explanation
Indices: 24937--24980 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
24927 AATCTAGTTA
*
24937 ATTAGTTTGTTAGTATAAATT
1 ATTACTTTGTTAGTATAAATT
* *
24958 ATTACTTTGTTAGTTTAAGTT
1 ATTACTTTGTTAGTATAAATT
24979 AT
1 AT
24981 ATTATATTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.55
Consensus pattern (21 bp):
ATTACTTTGTTAGTATAAATT
Found at i:24981 original size:28 final size:28
Alignment explanation
Indices: 24950--25015 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
24940 AGTTTGTTAG
24950 TATAAATTATTACTTTGTTAGTTTAAGT
1 TATAAATTATTACTTTGTTAGTTTAAGT
* *
24978 TAT-ATTATATTAGTTTGTTAGTTTAAGT
1 TATAAAT-TATTACTTTGTTAGTTTAAGT
*
25006 TATATATTAT
1 TATAAATTAT
25016 ATTATATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.91
29 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.56
Consensus pattern (28 bp):
TATAAATTATTACTTTGTTAGTTTAAGT
Found at i:25073 original size:42 final size:45
Alignment explanation
Indices: 24979--25083 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 45
24969 AGTTTAAGTT
* * *
24979 ATATTATATTAGTTTGTTAGTTTAAGTTATATATTATATTATATAA
1 ATATTA-ATTAGTTTGTTAGTTTAAGTTATATATAATATTAAAAAA
*
25025 A-A--AATTAGTTTATTAGTTTAAGTTAT-TA-AATA-TAAAAAA
1 ATATTAATTAGTTTGTTAGTTTAAGTTATATATAATATTAAAAAA
*
25064 ATATTAATTAATTTGTTAGT
1 ATATTAATTAGTTTGTTAGT
25084 GTCTTTAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
39 6 0.12
40 4 0.08
41 2 0.04
42 35 0.70
43 1 0.02
45 1 0.02
46 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.50
Consensus pattern (45 bp):
ATATTAATTAGTTTGTTAGTTTAAGTTATATATAATATTAAAAAA
Found at i:25524 original size:17 final size:17
Alignment explanation
Indices: 25502--25562 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
25492 GATAATTTCC
25502 GTTTAAAAAAATATTGT
1 GTTTAAAAAAATATTGT
* *
25519 GTTTAAAAATATTTAGTGTT
1 GTTTAAAAA-A-ATATTG-T
*
25539 GTTTAAAAAAAATATTTT
1 GTTT-AAAAAAATATTGT
25557 GTTTAA
1 GTTTAA
25563 TTTATATTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
17 11 0.31
18 6 0.17
19 7 0.20
20 6 0.17
21 5 0.14
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (17 bp):
GTTTAAAAAAATATTGT
Found at i:25824 original size:26 final size:25
Alignment explanation
Indices: 25795--25853 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
25785 AAATTATATT
*
25795 ATTATTAAATCATTAAATATTAAATC
1 ATTATTAAAT-AATAAATATTAAATC
*
25821 ATTAGATT-AATAATAATTATTAAATC
1 ATT--ATTAAATAATAAATATTAAATC
25847 ATTATTA
1 ATTATTA
25854 GTAATTTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
ATTATTAAATAATAAATATTAAATC
Found at i:26837 original size:49 final size:49
Alignment explanation
Indices: 26767--27052 Score: 511
Period size: 49 Copynumber: 5.8 Consensus size: 49
26757 GGCACCCATC
26767 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
26816 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
*
26865 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTTATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
26914 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
* * * *
26963 TATTATTAATAATTAATAATTT-ATTAGTACTGATTAATAATAATGAAAT
1 TATTATTAATATTTAATGATTTGA-TAGTAATGATTAGTAATAATGAAAT
27012 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAAT
27053 TATTAATAAT
Statistics
Matches: 225, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
48 1 0.00
49 223 0.99
50 1 0.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (49 bp):
TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
Found at i:26970 original size:21 final size:21
Alignment explanation
Indices: 26946--27028 Score: 53
Period size: 21 Copynumber: 3.6 Consensus size: 21
26936 GATAGTAATG
*
26946 ATTAGTAA-TAATGAAATTATT
1 ATTAATAATTAAT-AAATTATT
26967 ATTAATAATTAATAATTTATTAGTACT
1 ATTAATAATTAATAA---ATTA-T--T
26994 GATTAATAA-TAATGAAATTATT
1 -ATTAATAATTAAT-AAATTATT
*
27016 ATTAATATTTAAT
1 ATTAATAATTAAT
27029 GATTTGATAG
Statistics
Matches: 50, Mismatches: 2, Indels: 19
0.70 0.03 0.27
Matches are distributed among these distances:
21 16 0.32
22 9 0.18
24 5 0.10
25 5 0.10
27 5 0.10
28 10 0.20
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (21 bp):
ATTAATAATTAATAAATTATT
Found at i:27076 original size:17 final size:18
Alignment explanation
Indices: 27050--27084 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
27040 AATGATTAGT
27050 AATTATTAATAATAATGA
1 AATTATTAATAATAATGA
27068 AATTA-TAATAATAATGA
1 AATTATTAATAATAATGA
27085 TTTACTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (18 bp):
AATTATTAATAATAATGA
Found at i:27284 original size:12 final size:12
Alignment explanation
Indices: 27263--27317 Score: 69
Period size: 12 Copynumber: 4.7 Consensus size: 12
27253 CATAAAAATG
27263 ATTTAATAAT-A
1 ATTTAATAATAA
*
27274 ATTTAAATAAT-G
1 ATTT-AATAATAA
27286 ATTTAATAATAA
1 ATTTAATAATAA
*
27298 ATTTAATAATGA
1 ATTTAATAATAA
27310 ATTTAATA
1 ATTTAATA
27318 TTTAATGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
11 10 0.26
12 29 0.74
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (12 bp):
ATTTAATAATAA
Found at i:27368 original size:26 final size:26
Alignment explanation
Indices: 27339--27501 Score: 224
Period size: 26 Copynumber: 6.3 Consensus size: 26
27329 GATGATTTAG
27339 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
27365 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
*
27391 TAATGATTT-AGTAATAATTATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * * * *
27417 TAATGATTTAATAATATTTA-AATATT
1 TAATGATTTGATAATAATCATTATA-A
27443 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
27469 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
27495 TAATGAT
1 TAATGAT
27502 AATAATGATT
Statistics
Matches: 123, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
25 5 0.04
26 114 0.93
27 4 0.03
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:27406 original size:52 final size:52
Alignment explanation
Indices: 27330--28015 Score: 330
Period size: 52 Copynumber: 13.0 Consensus size: 52
27320 TAATGACTTG
* *
27330 ATGATT-TAGTAATGATTT-GATAATAATCATTATAATAATGATTTGATAATA
1 ATGATTATAATAATGATTTAG-TAATAATCATTATAATAATGATTTAATAATA
* *
27381 ATCATTATAATAATGATTTAGTAATAATTATTATAATAATGATTTAATAATA
1 ATGATTATAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATA
* * * * *
27433 TTTA-AATATTTAATGATTT-GATAATAATCATTATAATAATGATTTAGTAATA
1 ATGATTATA-ATAATGATTTAG-TAATAATCATTATAATAATGATTTAATAATA
* * * * *
27485 ATCATTATAATAATG----A-TAATAATGATT-TAATAATAATAATGATAATA
1 ATGATTATAATAATGATTTAGTAATAATCATTATAATAATGAT-TTAATAATA
* * * * *
27532 ATGATTTAATAGTAATTATTTAGTAATGAT-TTTATAATAATGATTTAATACTA
1 ATGA-TT-ATAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATA
* * * * * *
27585 ATGATT-TAATAATTA-TTACTAATAATTATAGAATAATAACAAATGAGTGTACA-AGT-
1 ATGATTATAATAATGATTTAGTAATAATCAT----T-ATAA-TAATGA-TTTA-ATAATA
* * * * * * * *
27641 GTGGACTACTCGAGT-TTAAATTTA-TACATAGTCAAATT-TATTAATGAATTTAATATTTA
1 AT-GATTA-T--AATAAT-GATTTAGTA-ATAATC--ATTATAATAATG-ATTTAATA-ATA
* *
27700 ATGACTTGATGATTTAGTAATGATTT-GATAATAATCATTATAGTAATGATTTGATAATA
1 ATGA-TT-AT-A---A-TAATGATTTAG-TAATAATCATTATAATAATGATTTAATAATA
* * *
27759 ATCATTATAATAATAATTTAGTAATAATCATTATAATAAT-A-ATAATTTAATA
1 ATGATTATAATAATGATTTAGTAATAATCATTATAATAATGATTTAA--TAATA
* * * * *
27811 ATGATT-T-A-AAT-ATTTAATGATTTAATGATT-TAGTAATGATTTGATAATA
1 ATGATTATAATAATGATTTAGT-A-ATAATCATTATAATAATGATTTAATAATA
* *
27860 ATCATTATAATAATGATTTAATAATAATCATTATAATAATGATTTAATAATA
1 ATGATTATAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATA
* * * * * *
27912 ATAATGATAATAATGATTTAATAATAATAATGATAATAATGATTTAATAGTA
1 ATGATTATAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATA
* * * *
27964 ATTATT-TAGTAATGATTTTA-TAATAATGATTTAATACTAATGATTTAATAAT
1 ATGATTATAATAATGA-TTTAGTAATAATCA-TT-ATAATAATGATTTAATAAT
28016 TATTACTAAT
Statistics
Matches: 488, Mismatches: 84, Indels: 124
0.70 0.12 0.18
Matches are distributed among these distances:
46 9 0.02
47 19 0.04
48 8 0.02
49 36 0.07
50 21 0.04
51 37 0.08
52 202 0.41
53 43 0.09
54 16 0.03
55 4 0.01
56 8 0.02
57 18 0.04
58 11 0.02
59 9 0.02
60 13 0.03
61 12 0.02
62 17 0.03
63 3 0.01
64 2 0.00
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (52 bp):
ATGATTATAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATA
Found at i:27450 original size:78 final size:77
Alignment explanation
Indices: 27339--28015 Score: 327
Period size: 78 Copynumber: 8.5 Consensus size: 77
27329 GATGATTTAG
* *
27339 TAATGATTTGATAATAATCATT-ATAATAATGATTTGATAATAATCATTATAATAATGATTTAGT
1 TAATGATTTAATAATGAT--TTAATAATAATGATTTGATAATAATCATTATAATAATGATTTAGT
27403 AATAATTATTATAA
64 AATAATTATTATAA
*
27417 TAATGATTTAATAAT-ATTTAAATATTTAATGATTTGATAATAATCATTATAATAATGATTTAGT
1 TAATGATTTAATAATGATTT-AATA-ATAATGATTTGATAATAATCATTATAATAATGATTTAGT
*
27481 AATAATCATTATAA
64 AATAATTATTATAA
* * * *
27495 TAATGA--TAATAATGATTTAATAATAAT-A-ATGATAATAATGATTTAATAGTAATTATTTAGT
1 TAATGATTTAATAATGATTTAATAATAATGATTTGATAATAATCA-TT-ATAATAATGATTTAGT
*
27556 AATGATT-TTATAA
64 AATAATTATTATAA
* * * * * ** ** * *
27569 TAATGATTTAATACTAATGATTTAATAATTATTA-CTAATAATTAT-AGAATAATAACAAATGAG
1 TAATGATTT-A-A-TAATGATTTAATAATAATGATTTGATAATAATCATTATAATAATGATTTAG
* * * * ** *
27632 TGTACAAGT-GTGGAC
63 T-AATAATTATTATAA
* * * *
27647 TACTCGAGTTT-A-AAT--TTATACATAGTCAA--ATTT-ATTAATGAATTTAATATTTAATGAC
1 TAAT-GA-TTTAATAATGATT-TA-ATAAT-AATGATTTGA-TAAT-AA--TCAT-TATAAT-A-
* *
27705 TTGATGATTTAGTAATGATT-TGATAA
54 ---ATGATTTAGTAATAATTATTATAA
* * * * * *
27731 TAATCATTATAGTAATGATTTGATAATAATCA-TT-ATAATAATAATTTAGTAATAATCATTATA
1 TAATGATT-TAATAATGATTTAATAATAATGATTTGATAATAATCA-TTA-TAATAATGATT-TA
* *
27794 ATAATAATAATT-TAA
62 GTAATAATTATTATAA
27809 TAATGATTTAAATATTTAATGATTTAATGATTTAGTAATGATTTGATAATAATCATTATAATAAT
1 TAATGATTT--A-A--TAATGATTTAAT-A---A-TAATGATTTGATAATAATCATTATAATAAT
* *
27874 GATTTAATAATAATCATTATAA
56 GATTTAGTAATAATTATTATAA
* * * * * * *
27896 TAATGATTTAATAATAATAATGATAATAATGATTTAATAATAATAATGATAATAATGATTTAATA
1 TAATGATTTAATAATGAT-TTAATAATAATGATTTGATAATAATCATTATAATAATGATTTAGTA
* *
27961 GTAATTATT-TAG
65 ATAATTATTATAA
* *
27973 TAATGATTTTATAATAATGATTTAATACTAATGATTTAATAAT
1 TAATGA--TT-TAATAATGATTTAATAATAATGATTTGATAAT
28016 TATTACTAAT
Statistics
Matches: 460, Mismatches: 81, Indels: 115
0.70 0.12 0.18
Matches are distributed among these distances:
73 13 0.03
74 19 0.04
75 37 0.08
76 14 0.03
77 36 0.08
78 142 0.31
79 45 0.10
80 25 0.05
81 6 0.01
82 25 0.05
83 8 0.02
84 14 0.03
85 17 0.04
86 16 0.03
87 29 0.06
88 5 0.01
89 9 0.02
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (77 bp):
TAATGATTTAATAATGATTTAATAATAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
TAATTATTATAA
Found at i:27503 original size:9 final size:9
Alignment explanation
Indices: 27491--27536 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
27481 AATAATCATT
27491 ATAATAATG
1 ATAATAATG
27500 ATAATAATG
1 ATAATAATG
* *
27509 AT-TTAATA
1 ATAATAATG
27517 ATAATAATG
1 ATAATAATG
27526 ATAATAATG
1 ATAATAATG
27535 AT
1 AT
27537 TTAATAGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
8 6 0.19
9 26 0.81
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (9 bp):
ATAATAATG
Found at i:27520 original size:26 final size:26
Alignment explanation
Indices: 27491--27597 Score: 117
Period size: 26 Copynumber: 4.1 Consensus size: 26
27481 AATAATCATT
27491 ATAATAATGATAATAATGATTTAATA
1 ATAATAATGATAATAATGATTTAATA
27517 ATAATAATGATAATAATGATTTAATA
1 ATAATAATGATAATAATGATTTAATA
* * * * *
27543 GTAATTAT-TTAGTAATGATTTTATA
1 ATAATAATGATAATAATGATTTAATA
* * *
27568 ATAATGATTTAATACTAATGATTTAATA
1 ATAAT-A-ATGATAATAATGATTTAATA
27596 AT
1 AT
27598 TATTACTAAT
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
25 18 0.27
26 32 0.48
27 1 0.01
28 16 0.24
ACGTcount: A:0.48, C:0.01, G:0.08, T:0.43
Consensus pattern (26 bp):
ATAATAATGATAATAATGATTTAATA
Found at i:27534 original size:87 final size:86
Alignment explanation
Indices: 27404--27581 Score: 211
Period size: 87 Copynumber: 2.1 Consensus size: 86
27394 TGATTTAGTA
* * * * *
27404 ATAATTATTATAATAATGATTTAATAATATTTAAATATTTAATGATTTGATAATAATCATTATAA
1 ATAATAATGATAATAATGATTTAATAATATATAAATATATAATGATTTAATAATAATCATT-TAA
27469 TAATGA-TTTAGTAATAATCATT
65 TAATGATTTTA-TAATAATCATT
* *
27491 ATAATAATGATAATAATGATTTAATAATA-AT-AATGATAATAATGATTTAATAGTAATTATTTA
1 ATAATAATGATAATAATGATTTAATAATATATAAAT-AT-ATAATGATTTAATAATAATCATTTA
* *
27554 GTAATGATTTTATAATAATGATT
64 ATAATGATTTTATAATAATCATT
27577 -TAATA
1 ATAATA
27582 CTAATGATTT
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
85 8 0.10
86 21 0.27
87 50 0.63
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.44
Consensus pattern (86 bp):
ATAATAATGATAATAATGATTTAATAATATATAAATATATAATGATTTAATAATAATCATTTAAT
AATGATTTTATAATAATCATT
Found at i:27743 original size:26 final size:26
Alignment explanation
Indices: 27717--28015 Score: 299
Period size: 26 Copynumber: 11.6 Consensus size: 26
27707 GATGATTTAG
* *
27717 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTAATAATAATCATTATAA
*
27743 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
* *
27769 TAATAATTTAGTAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
* *
27795 TAAT-A-ATAATTTAATAATGATT-T-A
1 TAATGATTTAA--TAATAATCATTATAA
* * *
27819 -AAT-ATTTAATGATTTAATGATT-TAG
1 TAATGATTTAAT-A-ATAATCATTATAA
*
27844 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
27870 TAATGATTTAATAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
* *
27896 TAATGATTTAATAATAATAATGATAA
1 TAATGATTTAATAATAATCATTATAA
* *
27922 TAATGATTTAATAATAATAATGATAA
1 TAATGATTTAATAATAATCATTATAA
* * *
27948 TAATGATTTAATAGTAATTATT-TAG
1 TAATGATTTAATAATAATCATTATAA
* * *
27973 TAATGATTTTATAATAATGATTTAATAC
1 TAATGATTTAATAATAATCA-TT-ATAA
28001 TAATGATTTAATAAT
1 TAATGATTTAATAAT
28016 TATTACTAAT
Statistics
Matches: 235, Mismatches: 26, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
22 1 0.00
23 5 0.02
24 15 0.06
25 28 0.12
26 164 0.70
27 6 0.03
28 16 0.07
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (26 bp):
TAATGATTTAATAATAATCATTATAA
Found at i:27793 original size:127 final size:127
Alignment explanation
Indices: 27266--28015 Score: 510
Period size: 127 Copynumber: 5.9 Consensus size: 127
27256 AAAAATGATT
*
27266 TAATAATAATTT-A-AATAATGATT-TAATAAT-A-AATTTAATAATGAATTT-AATATTTAATG
1 TAATAATAATTTAATAATAATCATTATAATAATAATAATTTAATAATG-ATTTAAATATTTAATG
* *
27325 ACTTGATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCATTA
65 ACTTAATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATAATCATTA
* * * *
27388 TAATAATGATTTAGTAAT-A--ATTATTATAATAATGATTTAATAAT-ATTTAAATATTTAATGA
1 TAATAATAATTTAATAATAATCATTATAATAATAATAATTTAATAATGATTTAAATATTTAATGA
* * * *
27449 TTTGATAATAATCATTATAATAATGATTT-AGTAATAATCATTATAATAATGA--TAATAATGAT
66 ----CT--TAATGATT-TAGTAATGATTTGA-TAATAATCATTATAATAATGATTTAATAATAAT
27511 --TTAA
123 CATT-A
* * * * *
27515 TAATAATAA--TGATAATAATGATT-TAATAGTAATTATTTAGTAATGATTTTATAATAATGATT
1 TAATAATAATTTAATAATAATCATTATAATAATAATAATTTAATAATGA--TT-T-A-AAT-ATT
* * * * *** * *
27577 TAAT-AC-TAATGATTTAATAATTA-TT-ACTAATAATTA-TAGAATAAT-AACAAATGAGT-GT
60 TAATGACTTAATGATTTAGTAATGATTTGA-TAATAATCATTATAATAATGATTTAAT-AATAAT
*
27635 ACAAGTGTG
123 -C-A-T-TA
* * * * * * * *
27644 GACTACTCGAGTT--T-A-AAT--TTATACATAGTCA-AATTTATTAATGAATTT-AATATTTAA
1 TAATAAT-AATTTAATAATAATCATTATA-ATAATAATAATTTAATAATG-ATTTAAATATTTAA
* * *
27701 TGACTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTA
63 TGACTTAATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATAATCATTA
*
27766 TAATAATAATTTAGTAATAATCATTATAATAATAATAATTTAATAATGATTTAAATATTTAATGA
1 TAATAATAATTTAATAATAATCATTATAATAATAATAATTTAATAATGATTTAAATATTTAATGA
*
27831 TTTAATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATAATCATTA
66 CTTAATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATAATCATTA
* * * * * *
27893 TAATAATGATTTAATAATAATAATGATAATAATGATTTAATAATAATAATGA-TAATAATGATTT
1 TAATAATAATTTAATAATAATCATTATAATAAT-A-ATAAT-TTAATAATGATTTA-AAT-ATTT
* * * * *
27957 AAT-A-GTAATTATTTAGTAATGATTTTATAATAATGATTTAATACTAATGATTTAATAAT
61 AATGACTTAATGATTTAGTAATGATTTGATAATAATCA-TT-ATAATAATGATTTAATAAT
28016 TATTACTAAT
Statistics
Matches: 495, Mismatches: 71, Indels: 115
0.73 0.10 0.17
Matches are distributed among these distances:
121 13 0.03
122 32 0.06
123 38 0.08
124 40 0.08
125 30 0.06
126 27 0.05
127 154 0.31
128 23 0.05
129 47 0.09
130 52 0.11
131 26 0.05
132 2 0.00
133 4 0.01
134 7 0.01
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (127 bp):
TAATAATAATTTAATAATAATCATTATAATAATAATAATTTAATAATGATTTAAATATTTAATGA
CTTAATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATAATCATTA
Found at i:27827 original size:19 final size:18
Alignment explanation
Indices: 27798--27852 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
27788 ATTATAATAA
*
27798 TAATAATTTAATAATGATT
1 TAATGATTT-ATAATGATT
27817 TAA--ATATT-TAATGATT
1 TAATGAT-TTATAATGATT
27833 TAATGATTTAGTAATGATT
1 TAATGATTTA-TAATGATT
27852 T
1 T
27853 GATAATAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
16 11 0.35
17 4 0.13
18 4 0.13
19 12 0.39
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (18 bp):
TAATGATTTATAATGATT
Found at i:27833 original size:8 final size:8
Alignment explanation
Indices: 27809--27842 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
27799 AATAATTTAA
27809 TAATGATT
1 TAATGATT
27817 TAAAT-ATT
1 T-AATGATT
27825 TAATGATT
1 TAATGATT
27833 TAATGATT
1 TAATGATT
27841 TA
1 TA
27843 GTAATGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 3 0.12
8 18 0.75
9 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (8 bp):
TAATGATT
Found at i:27872 original size:3 final size:3
Alignment explanation
Indices: 27854--27951 Score: 67
Period size: 3 Copynumber: 33.7 Consensus size: 3
27844 TAATGATTTG
* * * * * * *
27854 ATA ATA ATC ATT ATA ATA ATG AT- TTA ATA ATA ATC ATT ATA ATA ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
27901 AT- TTA ATA ATA ATA ATG ATA ATA ATG AT- TTA ATA ATA ATA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
27947 ATA AT
1 ATA AT
27952 GATTTAATAG
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
2 3 0.04
3 70 0.96
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:30577 original size:30 final size:30
Alignment explanation
Indices: 30543--30654 Score: 109
Period size: 30 Copynumber: 4.0 Consensus size: 30
30533 TTCCTTAAAC
30543 AACTAATAAATTATTCTTTAATATAACTTT
1 AACTAATAAATTATTCTTTAATATAACTTT
*
30573 AAC--------TATTCTTTAATATAACGTT
1 AACTAATAAATTATTCTTTAATATAACTTT
* *
30595 AACTAATAAACTATTCTTTAATATAACTTA
1 AACTAATAAATTATTCTTTAATATAACTTT
*
30625 AACTAATAAATGATT-TTTAATTATAA-TTT
1 AACTAATAAATTATTCTTTAA-TATAACTTT
30654 A
1 A
30655 TTACTAAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 19
0.73 0.07 0.21
Matches are distributed among these distances:
22 21 0.31
29 8 0.12
30 38 0.57
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.45
Consensus pattern (30 bp):
AACTAATAAATTATTCTTTAATATAACTTT
Found at i:30579 original size:22 final size:22
Alignment explanation
Indices: 30554--30599 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
30544 ACTAATAAAT
*
30554 TATTCTTTAATATAACTTTAAC
1 TATTCTTTAATATAACGTTAAC
30576 TATTCTTTAATATAACGTTAAC
1 TATTCTTTAATATAACGTTAAC
30598 TA
1 TA
30600 ATAAACTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.13, G:0.02, T:0.48
Consensus pattern (22 bp):
TATTCTTTAATATAACGTTAAC
Found at i:30627 original size:22 final size:22
Alignment explanation
Indices: 30549--30629 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
30539 AAACAACTAA
*
30549 TAAATTATTCTTTAATATAACT
1 TAAACTATTCTTTAATATAACT
*
30571 TTAACTATTCTTTAATATAACGTTAACT
1 TAAACTATTCTTT-A-AT-A---TAACT
30599 AATAAACTATTCTTTAATATAACT
1 --TAAACTATTCTTTAATATAACT
30623 TAAACTA
1 TAAACTA
30630 ATAAATGATT
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
22 18 0.38
23 1 0.02
24 7 0.15
25 1 0.02
27 1 0.02
28 7 0.15
29 1 0.02
30 12 0.25
ACGTcount: A:0.42, C:0.12, G:0.01, T:0.44
Consensus pattern (22 bp):
TAAACTATTCTTTAATATAACT
Found at i:30894 original size:21 final size:21
Alignment explanation
Indices: 30846--30895 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
30836 TTTCTATATG
* *
30846 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAAAAAGA
30867 ATATAACTTAAACTAAAAACGA
1 ATATAACTTAAACTAAAAA-GA
30889 AT-TAACT
1 ATATAACT
30896 AATTTTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.56, C:0.14, G:0.02, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAAAAAGA
Found at i:30965 original size:18 final size:18
Alignment explanation
Indices: 30912--30966 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
30902 TTGTTTTACC
*
30912 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
30930 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
30942 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
30959 CTAATTTA
1 CTAATTTA
30967 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:31025 original size:35 final size:36
Alignment explanation
Indices: 30981--31067 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 36
30971 ATTATTCTTT
30981 TATATAACTTCAACTAATAAACT-ATTTTTTATTATAA
1 TATA-AACTTCAACTAATAAACTAATTTTTTA-TATAA
*
31018 TA-AAACTTAAACTACTAATAAACTAATTTTTTATATAA
1 TATAAACTT---CAACTAATAAACTAATTTTTTATATAA
31056 TATAAA-TTCAAC
1 TATAAACTTCAAC
31068 AACCAAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
35 8 0.19
36 1 0.02
37 2 0.05
38 21 0.49
39 11 0.26
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.41
Consensus pattern (36 bp):
TATAAACTTCAACTAATAAACTAATTTTTTATATAA
Found at i:31117 original size:27 final size:29
Alignment explanation
Indices: 31082--31146 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
31072 AAAATATAAC
*
31082 TTAACTATTTA-ACTAACT-ACAAACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
31109 TTAAATA-TTAGACTAACTAACACACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
31137 TTAATTATTT
1 TTAAATATTT
31147 TTTAATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAATATTTAGACTAACTAACAAACTAA
Found at i:31331 original size:15 final size:15
Alignment explanation
Indices: 31311--31341 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31301 TTCTTCTTTT
31311 CTTTGCTATCTTCTC
1 CTTTGCTATCTTCTC
*
31326 CTTTGCTATTTTCTC
1 CTTTGCTATCTTCTC
31341 C
1 C
31342 CTTTCTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.06, C:0.32, G:0.06, T:0.55
Consensus pattern (15 bp):
CTTTGCTATCTTCTC
Found at i:31606 original size:29 final size:29
Alignment explanation
Indices: 31566--31642 Score: 120
Period size: 29 Copynumber: 2.7 Consensus size: 29
31556 TAAGTCGTTG
31566 GGAT-CCCTTGGCGACCTACAATGTCGCTA
1 GGATGCCC-TGGCGACCTACAATGTCGCTA
*
31595 GGATGCCCTGGCGACCTACAATGTCGCTG
1 GGATGCCCTGGCGACCTACAATGTCGCTA
*
31624 GGATGCCCTGGTGACCTAC
1 GGATGCCCTGGCGACCTAC
31643 CCAACGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 42 0.93
30 3 0.07
ACGTcount: A:0.18, C:0.31, G:0.29, T:0.22
Consensus pattern (29 bp):
GGATGCCCTGGCGACCTACAATGTCGCTA
Found at i:31735 original size:30 final size:28
Alignment explanation
Indices: 31700--31793 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 28
31690 GCCATGCACA
31700 GCCATGCAGAGACTCCAAGCTCGCCCGGAT
1 GCCATGC-GA-ACTCCAAGCTCGCCCGGAT
* *
31730 GCCATGGCGACCTCCAAGGTCGCCCGGAT
1 GCCAT-GCGAACTCCAAGCTCGCCCGGAT
* * *
31759 GCCATGGCGACCTCTAAGGTCGCCCGGAT
1 GCCAT-GCGAACTCCAAGCTCGCCCGGAT
*
31788 GACATG
1 GCCATG
31794 GCGACCTACG
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
28 1 0.02
29 49 0.83
30 7 0.12
31 2 0.03
ACGTcount: A:0.20, C:0.35, G:0.30, T:0.15
Consensus pattern (28 bp):
GCCATGCGAACTCCAAGCTCGCCCGGAT
Found at i:31746 original size:29 final size:29
Alignment explanation
Indices: 31712--31800 Score: 151
Period size: 29 Copynumber: 3.1 Consensus size: 29
31702 CATGCAGAGA
*
31712 CTCCAAGCTCGCCCGGATGCCATGGCGAC
1 CTCCAAGGTCGCCCGGATGCCATGGCGAC
31741 CTCCAAGGTCGCCCGGATGCCATGGCGAC
1 CTCCAAGGTCGCCCGGATGCCATGGCGAC
* *
31770 CTCTAAGGTCGCCCGGATGACATGGCGAC
1 CTCCAAGGTCGCCCGGATGCCATGGCGAC
31799 CT
1 CT
31801 ACGACAACAC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.18, C:0.37, G:0.29, T:0.16
Consensus pattern (29 bp):
CTCCAAGGTCGCCCGGATGCCATGGCGAC
Found at i:34918 original size:20 final size:20
Alignment explanation
Indices: 34862--34908 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
34852 AGTTTTGAAA
34862 TTCGCAACTCGAATTTCTTT
1 TTCGCAACTCGAATTTCTTT
*
34882 TTCGCAACTCAAATTTCTTT
1 TTCGCAACTCGAATTTCTTT
34902 TTCGCAA
1 TTCGCAA
34909 TGCGATTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.23, C:0.26, G:0.09, T:0.43
Consensus pattern (20 bp):
TTCGCAACTCGAATTTCTTT
Found at i:37146 original size:42 final size:42
Alignment explanation
Indices: 37062--37158 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
37052 CCCCCCACTT
* * *
37062 CGAGAGCCATCACCTAATCGAGCTGATTCTACAGCTCGACAC
1 CGAGAGCCATCACCTAATCGAGCTGATTATACACCTCCACAC
* *
37104 CGAGAGCCATCACCTGATCG-GGTCGATTATACACCTCCACAC
1 CGAGAGCCATCACCTAATCGAGCT-GATTATACACCTCCACAC
37146 CGAGAGCCATCAC
1 CGAGAGCCATCAC
37159 ATATTCCATC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
41 2 0.04
42 47 0.96
ACGTcount: A:0.28, C:0.35, G:0.20, T:0.18
Consensus pattern (42 bp):
CGAGAGCCATCACCTAATCGAGCTGATTATACACCTCCACAC
Found at i:37318 original size:21 final size:21
Alignment explanation
Indices: 37275--37327 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
37265 GTTAGGGGAG
*
37275 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
** *
37296 TTGTGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
37317 TTACGTGATGA
1 TTACGTGATGA
37328 CAATGGTGCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.11, G:0.34, T:0.36
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:37390 original size:42 final size:42
Alignment explanation
Indices: 37352--37474 Score: 185
Period size: 42 Copynumber: 3.0 Consensus size: 42
37342 GTGATGAGGT
*
37352 ATGGT-CTTTACGTGGTGAGGTAGATATTTTACGCGATGACA
1 ATGGTGCTCTACGTGGTGAGGTAGATATTTTACGCGATGACA
*
37393 ATGGTGCTCTACGTGGTGAGGTAGATGTTTTACGCGATGACA
1 ATGGTGCTCTACGTGGTGAGGTAGATATTTTACGCGATGACA
* ** *
37435 ATGGTGCTCTATGTGGTGAGGTATCTATTTTACGTGATGA
1 ATGGTGCTCTACGTGGTGAGGTAGATATTTTACGCGATGA
37475 GGTAGACGCT
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 5 0.07
42 69 0.93
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.35
Consensus pattern (42 bp):
ATGGTGCTCTACGTGGTGAGGTAGATATTTTACGCGATGACA
Found at i:37812 original size:21 final size:21
Alignment explanation
Indices: 37783--37847 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
37773 ATTCACCTGT
*
37783 CATCATTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
*
37804 CATCGTTCAAGAGGCCCCTCT
1 CATCGTTCAAGAGGCCCCTCC
37825 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
37846 CA
1 CA
37848 CCATTTAAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.22, C:0.42, G:0.17, T:0.20
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:37857 original size:21 final size:21
Alignment explanation
Indices: 37783--37858 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
37773 ATTCACCTGT
37783 CATCATTCAAGAGGCCCCTCC
1 CATCATTCAAGAGGCCCCTCC
* *
37804 CATCGTTCAAGAGGCCCCTCT
1 CATCATTCAAGAGGCCCCTCC
*
37825 CATCGTTCAAGAGGCCCCTCC
1 CATCATTCAAGAGGCCCCTCC
* *
37846 CACCATTTAAGAG
1 CATCATTCAAGAG
37859 CCTGATTCAC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.24, C:0.38, G:0.17, T:0.21
Consensus pattern (21 bp):
CATCATTCAAGAGGCCCCTCC
Found at i:41450 original size:22 final size:23
Alignment explanation
Indices: 41400--41461 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
41390 CGATTCCCCT
*
41400 AGGGGAAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
41423 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
* *
41445 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
41462 TCTGCCCTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 16 0.44
23 20 0.56
ACGTcount: A:0.21, C:0.26, G:0.31, T:0.23
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Done.