Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007219.1 Hibiscus syriacus cultivar Beakdansim tig00019093_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: 168015
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2404 original size:20 final size:21
Alignment explanation
Indices: 2387--2434 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
2377 CAATATATAT
2387 TATTTTAAATTTA-AATATGA
1 TATTTTAAATTTATAATATGA
*
2407 TATTTTAAGTTTATAATATTGA
1 TATTTTAAATTTATAATA-TGA
*
2429 TTTTTT
1 TATTTT
2435 GTATTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.50
21 4 0.17
22 8 0.33
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (21 bp):
TATTTTAAATTTATAATATGA
Found at i:2448 original size:13 final size:13
Alignment explanation
Indices: 2432--2473 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
2422 ATATTGATTT
2432 TTTGTATTTTTTA
1 TTTGTATTTTTTA
2445 TTTGT-TTTTTT-
1 TTTGTATTTTTTA
2456 TTTGTCATTCTTTTA
1 TTTGT-ATT-TTTTA
2471 TTT
1 TTT
2474 AATTTTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 5 0.20
12 6 0.24
13 7 0.28
14 4 0.16
15 3 0.12
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTGTATTTTTTA
Found at i:2479 original size:26 final size:24
Alignment explanation
Indices: 2429--2479 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
2419 ATAATATTGA
**
2429 TTTTTTGTATTTTTTATTTGTTTT
1 TTTTTTGTATTTTTTATTTAATTT
2453 TTTTTTGTCATTCTTTTATTTAATTT
1 TTTTTTGT-ATT-TTTTATTTAATTT
2479 T
1 T
2480 ATTATTGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 8 0.35
25 3 0.13
26 12 0.52
ACGTcount: A:0.12, C:0.04, G:0.06, T:0.78
Consensus pattern (24 bp):
TTTTTTGTATTTTTTATTTAATTT
Found at i:2487 original size:27 final size:24
Alignment explanation
Indices: 2433--2487 Score: 56
Period size: 27 Copynumber: 2.2 Consensus size: 24
2423 TATTGATTTT
* * *
2433 TTGTATTTTTTATTTGTTTTTTTT
1 TTGTATTTTTTATTTATTTTATTA
2457 TTGTCATTCTTTTATTTAATTTTATTA
1 TTGT-ATT-TTTTATTT-ATTTTATTA
2484 TTGT
1 TTGT
2488 TGATCTAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 4 0.16
25 3 0.12
26 8 0.32
27 10 0.40
ACGTcount: A:0.15, C:0.04, G:0.07, T:0.75
Consensus pattern (24 bp):
TTGTATTTTTTATTTATTTTATTA
Found at i:7142 original size:136 final size:136
Alignment explanation
Indices: 6897--7245 Score: 524
Period size: 136 Copynumber: 2.6 Consensus size: 136
6887 TTGTTAGATT
* * * *
6897 GAACAAGTTCTTCGCATTATGAACTTCTTCTCTC-TTTT-GGATGAGTTTTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
* * ** * *
6960 CTTCACTGAAAATGTTGATCCCTCAAGCGAGGCGTCCCTGACTCGAAATG-CTGTGAATCGAGTG
66 CTCCATTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGACTCGAAATGTC-ATGAATCGAGTG
7024 ATAGGTC
130 ATAGGTC
7031 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
* * * *
7096 CTCCATTGGAAATGTCAATTCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGA
66 CTCCATTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGACTCGAAATGTCATGAATCGAGTGA
7161 TAGGTC
131 TAGGTC
* *
7167 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
7232 CTCCATTGAAAATG
66 CTCCATTGAAAATG
7246 CTGATCCACC
Statistics
Matches: 195, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
134 31 0.16
135 4 0.02
136 159 0.82
137 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGACTCGAAATGTCATGAATCGAGTGA
TAGGTC
Found at i:8243 original size:11 final size:11
Alignment explanation
Indices: 8219--8276 Score: 71
Period size: 11 Copynumber: 5.1 Consensus size: 11
8209 TCCTTCTTCA
*
8219 TTTTTCTTTCT
1 TTTTTTTTTCT
*
8230 TTTTTTTTCTTT
1 TTTTTTTT-TCT
8242 TTTTTTTCTTCT
1 TTTTTTT-TTCT
*
8254 TTTTTTTTTCA
1 TTTTTTTTTCT
8265 TTTTTTTTTCT
1 TTTTTTTTTCT
8276 T
1 T
8277 CAAGCATAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
11 21 0.52
12 18 0.45
13 1 0.03
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:8257 original size:25 final size:26
Alignment explanation
Indices: 8219--8277 Score: 95
Period size: 25 Copynumber: 2.3 Consensus size: 26
8209 TCCTTCTTCA
*
8219 TTTTTCTT-TCTTTTTTTTTCTTTTT
1 TTTTTCTTCTCTTTTTTTTTCATTTT
8244 TTTTTCTTCT-TTTTTTTTTCATTTT
1 TTTTTCTTCTCTTTTTTTTTCATTTT
8269 TTTTTCTTC
1 TTTTTCTTC
8278 AAGCATAGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 31 0.97
26 1 0.03
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.85
Consensus pattern (26 bp):
TTTTTCTTCTCTTTTTTTTTCATTTT
Found at i:8278 original size:14 final size:13
Alignment explanation
Indices: 8219--8278 Score: 61
Period size: 14 Copynumber: 4.5 Consensus size: 13
8209 TCCTTCTTCA
*
8219 TTTTTCTTTCTTTT
1 TTTTTCATT-TTTT
8233 TTTTTC--TTTTT
1 TTTTTCATTTTTT
*
8244 TTTTTCTTCTTTTT
1 TTTTTCAT-TTTTT
8258 TTTTTCATTTTTT
1 TTTTTCATTTTTT
8271 TTTCTTCA
1 TTT-TTCA
8279 AGCATAGTAC
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
11 10 0.24
12 1 0.02
13 8 0.20
14 22 0.54
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTCATTTTTT
Found at i:28508 original size:20 final size:21
Alignment explanation
Indices: 28483--28575 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
28473 TTTTCCCAAT
*
28483 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* * **
28503 TCGCAACGTGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
28524 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
28544 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
28565 TCGCAATGCGA
1 TCGCAATGCGA
28576 TACTTACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:28528 original size:41 final size:41
Alignment explanation
Indices: 28483--28575 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
28473 TTTTCCCAAT
*
28483 TCGCAATGCGAATAAGTAAATCGCAACGTGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
28524 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
28565 TCGCAATGCGA
1 TCGCAATGCGA
28576 TACTTACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:28588 original size:41 final size:41
Alignment explanation
Indices: 28502--28636 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
28492 GAATAAGTAA
* ** *
28502 ATCGCAACGTGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
28543 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
28584 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
28625 TTCGCAACGCGA
1 ATCGCAACGCGA
28637 TACTGACTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 5 0.06
41 73 0.91
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:28589 original size:20 final size:20
Alignment explanation
Indices: 28564--28657 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
28554 AATTGGGAAA
*
28564 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
28584 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
28605 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
28625 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
28645 TTCGCAACGCGAT
1 ATCGCAACGCGAT
28658 TTACATAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:28873 original size:22 final size:22
Alignment explanation
Indices: 28845--28888 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
28835 CACTCTCTCA
*
28845 CCCATCTCTGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
28867 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
28889 TATCTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:29177 original size:20 final size:20
Alignment explanation
Indices: 29152--29189 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29142 CGATTCTCTC
29152 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
29172 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
29190 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:30528 original size:18 final size:18
Alignment explanation
Indices: 30507--30551 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
30497 TCCACTTCGG
* *
30507 GAGCCATCACCTCGCCCA
1 GAGCCATCACCCCACCCA
* *
30525 GAGCTATCACCCCACCTA
1 GAGCCATCACCCCACCCA
30543 GAGCCATCA
1 GAGCCATCA
30552 TCTGATCGAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:31098 original size:14 final size:14
Alignment explanation
Indices: 31079--31136 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
31069 ATGCGAAATG
31079 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
31093 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
31109 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
31125 AAAATCGCAACG
1 AAAATCGCAACG
31137 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:31121 original size:32 final size:33
Alignment explanation
Indices: 31063--31153 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
31053 GGAAATGGCT
*
31063 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
31096 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
31128 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
31154 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:31147 original size:19 final size:19
Alignment explanation
Indices: 31025--31158 Score: 92
Period size: 19 Copynumber: 7.6 Consensus size: 19
31015 TAGTTTACTT
* **
31025 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
31044 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
31064 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
31083 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
31097 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
31115 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
31129 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
31148 TCGCAATGCGA
1 TCGCAACGCGA
31159 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 35 0.38
20 17 0.18
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:31189 original size:14 final size:14
Alignment explanation
Indices: 31170--31227 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
31160 TTGTGTTTCG
31170 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
* *
31184 CGTTGCAATTTCATTT
1 CGTTGCGATTT--TGT
31200 CGTGTTGCGATTTTGT
1 C--GTTGCGATTTTGT
31216 CGTTGCGATTTT
1 CGTTGCGATTTT
31228 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 21 0.58
16 6 0.17
18 9 0.25
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:31207 original size:32 final size:33
Alignment explanation
Indices: 31165--31243 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
31155 GCGATTTGTG
31165 TTTCGCGTTGCGATTTTGTCGTTGC-AATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGAATTTCA
* *
31197 TTTCGTGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGAATTTCA
*
31230 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
31244 AGCCATTTCC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 24 0.57
33 18 0.43
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGAATTTCA
Found at i:31242 original size:19 final size:19
Alignment explanation
Indices: 31216--31282 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
31206 GCGATTTTGT
**
31216 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
31235 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
31255 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
31274 CGTTGCGAT
1 CGTTGCGAT
31283 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:31262 original size:20 final size:19
Alignment explanation
Indices: 31228--31282 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
31218 TTGCGATTTT
*
31228 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
31247 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
31267 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
31283 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:33278 original size:19 final size:19
Alignment explanation
Indices: 33254--33388 Score: 182
Period size: 19 Copynumber: 7.6 Consensus size: 19
33244 AAAACAGACT
* *
33254 ATCGCAACGCGAAATGGAA
1 ATCGCAATGCGAAATGAAA
33273 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
33292 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
33311 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
33325 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
33344 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
33363 ATCGCAA--CG--A-GAAA
1 ATCGCAATGCGAAATGAAA
33377 ATCGCAATGCGA
1 ATCGCAATGCGA
33389 TTTTCATTTC
Statistics
Matches: 106, Mismatches: 2, Indels: 18
0.84 0.02 0.14
Matches are distributed among these distances:
14 22 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 1 0.01
19 73 0.69
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:33377 original size:33 final size:36
Alignment explanation
Indices: 33254--33388 Score: 151
Period size: 33 Copynumber: 3.8 Consensus size: 36
33244 AAAACAGACT
*
33254 ATCGCAACGCGAAATGGAAATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG-AATGAAAATCGCAATGCGAAATGAAA
33292 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAA
1 ATCGCAA-GCG-AATGAAAATCGCAATGCGAAATGAAA
33325 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG-AATGAAAATCGCAATGCGAAATGAAA
33363 ATCGCAA-CG-A-GAAAATCGCAATGCGA
1 ATCGCAAGCGAATGAAAATCGCAATGCGA
33389 TTTTCATTTC
Statistics
Matches: 90, Mismatches: 2, Indels: 15
0.84 0.02 0.14
Matches are distributed among these distances:
33 46 0.51
34 2 0.02
35 2 0.02
36 4 0.04
37 1 0.01
38 35 0.39
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (36 bp):
ATCGCAAGCGAATGAAAATCGCAATGCGAAATGAAA
Found at i:33401 original size:52 final size:52
Alignment explanation
Indices: 33271--33388 Score: 236
Period size: 52 Copynumber: 2.3 Consensus size: 52
33261 CGCGAAATGG
33271 AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA
1 AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA
33323 AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA
1 AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA
33375 AAATCGCAATGCGA
1 AAATCGCAATGCGA
33389 TTTTCATTTC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (52 bp):
AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA
Found at i:33464 original size:20 final size:20
Alignment explanation
Indices: 33407--33464 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
33397 TCGCATTGCA
* *
33407 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
*
33427 ATTTTCGCGTTGCGATAGCT
1 ATTTTCGCGTTGCGATAGCC
*
33447 ATTTTCGTGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
33465 TCAAATGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:34551 original size:24 final size:24
Alignment explanation
Indices: 34524--34577 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
34514 GTATTCAAAA
* *
34524 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
34548 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
34572 TTTGAT
1 TTTGAT
34578 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:37083 original size:19 final size:19
Alignment explanation
Indices: 37061--37191 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
37051 GGAAATTACT
37061 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
37080 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
37094 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
37113 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
37127 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
37146 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
37160 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
37179 ATCGCAACGCGAA
1 ATCGCAATGCGAA
37192 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:37103 original size:33 final size:33
Alignment explanation
Indices: 37061--37187 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
37051 GGAAATTACT
37061 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
37094 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
37126 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
37160 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
37188 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:37168 original size:66 final size:66
Alignment explanation
Indices: 37062--37194 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
37052 GAAATTACTA
*
37062 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
37127 T
66 T
*
37128 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
37193 T
66 T
37194 T
1 T
37195 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:37209 original size:19 final size:20
Alignment explanation
Indices: 37187--37229 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
37177 AAATCGCAAC
37187 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
37206 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
37226 GCGA
1 GCGA
37230 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:37214 original size:14 final size:14
Alignment explanation
Indices: 37215--37248 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
37205 TGCGATTTTC
37215 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
37229 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
37243 ATTTTC
1 ATTTTC
37249 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:37390 original size:14 final size:14
Alignment explanation
Indices: 37371--37407 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
37361 CATCAATTAA
37371 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
37385 ACAAATCACCTTTT
1 ACAAATCAACTTTT
37399 ACAAATCAA
1 ACAAATCAA
37408 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:38738 original size:21 final size:21
Alignment explanation
Indices: 38672--38738 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
38662 GTGAATCGGG
*
38672 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
38692 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
38714 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
38735 CTCT
1 CTCT
38739 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:38757 original size:42 final size:41
Alignment explanation
Indices: 38672--38794 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
38662 GTGAATCGGG
* * * * *
38672 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
38714 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
38756 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
38795 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:40908 original size:19 final size:19
Alignment explanation
Indices: 40791--40955 Score: 152
Period size: 19 Copynumber: 9.1 Consensus size: 19
40781 TCTTTTGGTT
*
40791 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
40810 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
40830 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
40848 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
40864 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
40882 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
40897 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
40916 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
40935 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
40954 GA
1 GA
40956 TTTTGGTTTC
Statistics
Matches: 121, Mismatches: 13, Indels: 24
0.77 0.08 0.15
Matches are distributed among these distances:
14 19 0.16
15 3 0.02
16 2 0.02
17 1 0.01
18 4 0.03
19 63 0.52
20 27 0.22
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:40928 original size:38 final size:36
Alignment explanation
Indices: 40791--40955 Score: 153
Period size: 33 Copynumber: 4.6 Consensus size: 36
40781 TCTTTTGGTT
*
40791 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCG--AA-GAGAATCGCAACGC
**
40830 GGAAATGACTATCGCAA--CG-AGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAGAGAATCGCAACGC
** * *
40864 GAAATGACTATCGCGAC-C--AGACAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAGAGAATCGCAACGC
*
40897 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGCG-AA-GAGAATCGCAACGC
*
40935 GAAATGAAAATCGCAATGCGA
1 GAAATGAAAATCGCAACGCGA
40956 TTTTGGTTTC
Statistics
Matches: 109, Mismatches: 10, Indels: 15
0.81 0.07 0.11
Matches are distributed among these distances:
33 43 0.39
34 16 0.15
35 1 0.01
37 2 0.02
38 33 0.30
40 14 0.13
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (36 bp):
GAAATGAAAATCGCAACGCGAAGAGAATCGCAACGC
Found at i:40984 original size:19 final size:19
Alignment explanation
Indices: 40951--41031 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
40941 AAAATCGCAA
**
40951 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
40970 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
40989 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
41003 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
41023 TGCGATTTT
1 TGCGATTTT
41032 CATTCTCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 23 0.46
20 11 0.22
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:41623 original size:41 final size:41
Alignment explanation
Indices: 41571--41648 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
41561 CGAAAGTCAG
* * *
41571 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
*
41612 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
41649 CCCAATTTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:41645 original size:20 final size:20
Alignment explanation
Indices: 41552--41645 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
41542 TGCTATGTAA
* *
41552 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTAAGT
*
41572 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
* ** * *
41592 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTAAGT
*
41613 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
*
41633 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
41646 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:41664 original size:41 final size:41
Alignment explanation
Indices: 41571--41666 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 41
41561 CGAAAGTCAG
* * * **
41571 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCAAT
*
41612 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT--CAAT
41655 T-T-GCGTTGCGAT
1 TATCGCGTTGCGAT
41667 TTACTTATTC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 42 0.91
42 1 0.02
43 3 0.07
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.39
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCAAT
Found at i:42376 original size:22 final size:22
Alignment explanation
Indices: 42348--42399 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
42338 AAAATTAAAA
42348 ACCGGGTATCGGGTACCCGATT
1 ACCGGGTATCGGGTACCCGATT
42370 ACCGGGTATCGGGTACCCGATT
1 ACCGGGTATCGGGTACCCGATT
42392 ACCGGGTA
1 ACCGGGTA
42400 CCCGTAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.19, C:0.27, G:0.33, T:0.21
Consensus pattern (22 bp):
ACCGGGTATCGGGTACCCGATT
Found at i:54040 original size:19 final size:19
Alignment explanation
Indices: 54016--54053 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
54006 TGATGTTGTG
54016 ACTGGGTTGACCGGTCTGA
1 ACTGGGTTGACCGGTCTGA
54035 ACTGGGTTGACCGGTCTGA
1 ACTGGGTTGACCGGTCTGA
54054 CCCAACCCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.21, G:0.37, T:0.26
Consensus pattern (19 bp):
ACTGGGTTGACCGGTCTGA
Found at i:54078 original size:17 final size:17
Alignment explanation
Indices: 54052--54101 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
54042 TGACCGGTCT
* *
54052 GACCCAACCCGTTGACT
1 GACCCGACCCGTTGACC
*
54069 GACTCGACCCGTTGACC
1 GACCCGACCCGTTGACC
54086 GACCCGACCCGTTGAC
1 GACCCGACCCGTTGAC
54102 ATTTTGGGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.20, C:0.42, G:0.22, T:0.16
Consensus pattern (17 bp):
GACCCGACCCGTTGACC
Found at i:54142 original size:29 final size:29
Alignment explanation
Indices: 54098--54257 Score: 216
Period size: 29 Copynumber: 5.6 Consensus size: 29
54088 CCCGACCCGT
*
54098 TGACATTTTGGGAATTAATTTGAAAAATG
1 TGACATTTTGGGAATTATTTTGAAAAATG
*
54127 TGACATTTTGGAAATTATTTT-AAAAATG
1 TGACATTTTGGGAATTATTTTGAAAAATG
* * *
54155 TGACATTTTGGG-ATTTTTTTTAAAAAAG
1 TGACATTTTGGGAATTATTTTGAAAAATG
54183 TGACATTTTGGGAATTATTTTGAAAAATG
1 TGACATTTTGGGAATTATTTTGAAAAATG
* * *
54212 TGACATTCTGGGAATTATTTTAAAAAAAAG
1 TGACATTTTGGGAATTATTTT-GAAAAATG
*
54242 TGACATTTTGGAAATT
1 TGACATTTTGGGAATT
54258 TTTGAATGTG
Statistics
Matches: 115, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
27 7 0.06
28 36 0.31
29 52 0.45
30 20 0.17
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.41
Consensus pattern (29 bp):
TGACATTTTGGGAATTATTTTGAAAAATG
Found at i:54151 original size:28 final size:28
Alignment explanation
Indices: 54098--54257 Score: 212
Period size: 28 Copynumber: 5.6 Consensus size: 28
54088 CCCGACCCGT
*
54098 TGACATTTTGGGAATTAATTTGAAAAATG
1 TGACATTTTGGGAATT-ATTTTAAAAATG
*
54127 TGACATTTTGGAAATTATTTTAAAAATG
1 TGACATTTTGGGAATTATTTTAAAAATG
* * *
54155 TGACATTTTGGGATTTTTTTTAAAAAAG
1 TGACATTTTGGGAATTATTTTAAAAATG
54183 TGACATTTTGGGAATTATTTTGAAAAATG
1 TGACATTTTGGGAATTATTTT-AAAAATG
* *
54212 TGACATTCTGGGAATTATTTTAAAAAAAAG
1 TGACATTTTGGGAATTATTTT--AAAAATG
*
54242 TGACATTTTGGAAATT
1 TGACATTTTGGGAATT
54258 TTTGAATGTG
Statistics
Matches: 115, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
28 54 0.47
29 41 0.36
30 20 0.17
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.41
Consensus pattern (28 bp):
TGACATTTTGGGAATTATTTTAAAAATG
Found at i:54261 original size:57 final size:56
Alignment explanation
Indices: 54098--54263 Score: 217
Period size: 57 Copynumber: 2.9 Consensus size: 56
54088 CCCGACCCGT
* * * *
54098 TGACATTTTGGGAATTAATTTGAAAAATGTGACATTTTGGAAATTATTTTAAAAATG
1 TGACATTTTGGGAATTATTTTAAAAAAAGTGACATTTTGGAAATT-TTTGAAAAATG
* * *
54155 TGACATTTTGGG-ATTTTTTTTAAAAAAGTGACATTTTGGGAATTATTTTGAAAAATG
1 TGACATTTTGGGAATTATTTTAAAAAAAGTGACATTTT-GGAAAT-TTTTGAAAAATG
*
54212 TGACATTCTGGGAATTATTTTAAAAAAAAGTGACATTTTGGAAATTTTTGAA
1 TGACATTTTGGGAATTATTTT-AAAAAAAGTGACATTTTGGAAATTTTTGAA
54264 TGTGGACTAT
Statistics
Matches: 95, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
56 21 0.22
57 45 0.47
58 13 0.14
59 16 0.17
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.41
Consensus pattern (56 bp):
TGACATTTTGGGAATTATTTTAAAAAAAGTGACATTTTGGAAATTTTTGAAAAATG
Found at i:55206 original size:63 final size:63
Alignment explanation
Indices: 55138--55261 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 63
55128 CTAATGTGAC
* *
55138 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGATAGGCCCTGCA-GCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTACGGCCCTGAGATCTA-TCTCGGATAGGCCCT-CAGGCCCTAAGATGTGT
* * *
55201 TCTTAGGTAGGCCCTACGGCCCTGAGATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCTACGGCCCTGAGATCTATCTCGGATAGGCCCTCAGGCCCTAAGATGT
55262 TCCCTTAGGA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
62 2 0.04
63 51 0.94
64 1 0.02
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCCTACGGCCCTGAGATCTATCTCGGATAGGCCCTCAGGCCCTAAGATGTGT
Found at i:55253 original size:31 final size:32
Alignment explanation
Indices: 55138--55259 Score: 94
Period size: 31 Copynumber: 3.9 Consensus size: 32
55128 CTAATGTGAC
* *
55138 TCTTAGGTAGGCTCTGC-GGCCCTGAGATC-A
1 TCTTAGGTAGGCCCTGCAGGCCCTAAGATCTA
* * *
55168 T-TCTCGGATAGGCCCTGCA-GCCCTAAGATGTGT
1 TCT-TAGG-TAGGCCCTGCAGGCCCTAAGATCT-A
* *
55201 TCTTAGGTAGGCCCTAC-GGCCCTGAGATCTA
1 TCTTAGGTAGGCCCTGCAGGCCCTAAGATCTA
* *
55232 TCTTGGGTAGGCTCT-CAGGCCCTAAGAT
1 TCTTAGGTAGGCCCTGCAGGCCCTAAGAT
55260 GTTCCCTTAG
Statistics
Matches: 71, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
29 1 0.01
30 5 0.07
31 41 0.58
32 19 0.27
33 4 0.06
34 1 0.01
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (32 bp):
TCTTAGGTAGGCCCTGCAGGCCCTAAGATCTA
Found at i:55330 original size:25 final size:25
Alignment explanation
Indices: 55278--55330 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
55268 AGGATAACTC
*
55278 TTTTATGAGATTTACTGCAGTATAA
1 TTTTATGAGATTTACTGCACTATAA
* *
55303 TTTTATGAGATTTACTGGACTATGA
1 TTTTATGAGATTTACTGCACTATAA
55328 TTT
1 TTT
55331 GTTTAGTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (25 bp):
TTTTATGAGATTTACTGCACTATAA
Found at i:56453 original size:188 final size:192
Alignment explanation
Indices: 56082--56464 Score: 729
Period size: 188 Copynumber: 2.0 Consensus size: 192
56072 CCCGATCGAT
56082 GAGATTTGAGTAGATTCCCCACCTCCGACAAGTGATTCTGCTCCTAGACCCCGACAAATTTACCT
1 GAGATTTGAGTAGATTCCCCACCTCCGACAAGTGATTCTGCTCCTAGACCCCGACAAATTTACCT
*
56147 CCTACTGCTGGGATTGGCATGACTACACCGATCAGGGGAGCAACCGATAGTGAGCCTGATTCTAC
66 CCTACTGCTGGGATTGGCATGACTACACCGATCAGGGGAGCAACCGATAGTGAGCATGATTCTAC
56212 CAGAGTTGCATTTGATGAGAATTTTGGTAGACAATTTTTACAGTTGATTCAAGGAGCGGTCA
131 CAGAGTTGCATTTGATGAGAATTTTGGTAGACAATTTTTACAGTTGATTCAAGGAGCGGTCA
56274 GAGATTTGAGTA-ATTCCCCACCTCCGACAAGTGATTCTGCTCCTAGACCCCGACAAATTTACCT
1 GAGATTTGAGTAGATTCCCCACCTCCGACAAGTGATTCTGCTCCTAGACCCCGACAAATTTACCT
56338 CCTACTGCT-GGATTGGCATGACTACACCGATCAGGGG-GCAACCGATAGTGAG-ATGATTCTAC
66 CCTACTGCTGGGATTGGCATGACTACACCGATCAGGGGAGCAACCGATAGTGAGCATGATTCTAC
56400 CAGAGTTGCATTTGATGAGAATTTTGGTAGACAATTTTTACAGTTGATTCAAGGAGCGGTCA
131 CAGAGTTGCATTTGATGAGAATTTTGGTAGACAATTTTTACAGTTGATTCAAGGAGCGGTCA
56462 GAG
1 GAG
56465 CTACTGGTGC
Statistics
Matches: 190, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
188 74 0.39
189 15 0.08
190 28 0.15
191 61 0.32
192 12 0.06
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Consensus pattern (192 bp):
GAGATTTGAGTAGATTCCCCACCTCCGACAAGTGATTCTGCTCCTAGACCCCGACAAATTTACCT
CCTACTGCTGGGATTGGCATGACTACACCGATCAGGGGAGCAACCGATAGTGAGCATGATTCTAC
CAGAGTTGCATTTGATGAGAATTTTGGTAGACAATTTTTACAGTTGATTCAAGGAGCGGTCA
Found at i:62483 original size:21 final size:22
Alignment explanation
Indices: 62433--62505 Score: 87
Period size: 21 Copynumber: 3.3 Consensus size: 22
62423 GAGTCGAGGG
*
62433 TTCTACGCGGTCCTTT-GGGACAA
1 TTCTATGCGGT-CTTTCGGGAC-A
62456 TTCTATGCGGTCTTTCGGGACA
1 TTCTATGCGGTCTTTCGGGACA
* *
62478 -TCTATGTGGTCATTCGGGACA
1 TTCTATGCGGTCTTTCGGGACA
62499 TTCTATG
1 TTCTATG
62506 TGGCACTTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
21 19 0.42
22 11 0.24
23 15 0.33
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (22 bp):
TTCTATGCGGTCTTTCGGGACA
Found at i:62787 original size:23 final size:23
Alignment explanation
Indices: 62738--62788 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
62728 TGATTAAGGT
* *
62738 ATGTTATGAATGTATATAACTGT
1 ATGTTATGAAAGTATATAACTGC
* *
62761 ATGTTATGAAAGTATGTTACTGC
1 ATGTTATGAAAGTATATAACTGC
62784 ATGTT
1 ATGTT
62789 TCATTAGTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (23 bp):
ATGTTATGAAAGTATATAACTGC
Found at i:66857 original size:24 final size:22
Alignment explanation
Indices: 66823--66868 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
66813 TATTAATTAT
*
66823 TTTTAATAATATAATATTCTTA
1 TTTTAATAATATAATAATCTTA
*
66845 TTTTAATAAAATATAGTAATCTTA
1 TTTTAAT--AATATAATAATCTTA
66869 CTATTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
24 13 0.65
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTTAATAATATAATAATCTTA
Found at i:66981 original size:23 final size:24
Alignment explanation
Indices: 66937--66990 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
66927 ATATTTCATA
*
66937 ATTATTATAATGTTTAAAATG-AT
1 ATTATTAAAATGTTTAAAATGAAT
*
66960 ATTATTAAAAT-TTTAATGATGAAT
1 ATTATTAAAATGTTTAA-AATGAAT
*
66984 AATATTA
1 ATTATTA
66991 TTTTATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 5 0.19
23 13 0.50
24 8 0.31
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (24 bp):
ATTATTAAAATGTTTAAAATGAAT
Found at i:67024 original size:19 final size:21
Alignment explanation
Indices: 66983--67030 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
66973 TAATGATGAA
* *
66983 TAATATTATTTTATATATCTT
1 TAATATTAATATATATATCTT
67004 TAATATTAATATA-ATAT-TT
1 TAATATTAATATATATATCTT
*
67023 TAGTATTA
1 TAATATTA
67031 TTTTTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.38
20 4 0.17
21 11 0.46
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TAATATTAATATATATATCTT
Found at i:67081 original size:22 final size:22
Alignment explanation
Indices: 67030--67081 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
67020 TTTTAGTATT
*
67030 ATTTTTAAAAAATAATTATTAA
1 ATTTTTAAAAAATAATTAATAA
* * *
67052 AATATTAAAAATATATTTAAT-A
1 ATTTTTAAAAA-ATAATTAATAA
67074 ATTTTTAA
1 ATTTTTAA
67082 TTTTATGATA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTTTTAAAAAATAATTAATAA
Found at i:72047 original size:21 final size:21
Alignment explanation
Indices: 72017--72060 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
72007 AATATAAATT
*
72017 GTGTAGCGATGCACTGCTACA
1 GTGTACCGATGCACTGCTACA
*
72038 GTGTACCGATTCACTGCTACA
1 GTGTACCGATGCACTGCTACA
72059 GT
1 GT
72061 AACTTCAGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (21 bp):
GTGTACCGATGCACTGCTACA
Found at i:72806 original size:31 final size:31
Alignment explanation
Indices: 72771--72881 Score: 195
Period size: 31 Copynumber: 3.6 Consensus size: 31
72761 CCATAGATTT
*
72771 CGAAGAACCTAGGTAAACAATCCATATGTCC
1 CGAAGAACATAGGTAAACAATCCATATGTCC
*
72802 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAATCCATATGTCC
*
72833 CGAAGAACATAGGTAAACAATCCATATATCC
1 CGAAGAACATAGGTAAACAATCCATATGTCC
72864 CGAAGAACATAGGTAAAC
1 CGAAGAACATAGGTAAAC
72882 CCTCGACCCT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.18
Consensus pattern (31 bp):
CGAAGAACATAGGTAAACAATCCATATGTCC
Found at i:73965 original size:3 final size:3
Alignment explanation
Indices: 73915--73951 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
73905 ATGAAAAAGT
* *
73915 ATA ATA ATA ATA ATA ATT ATA ATA AGA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
73952 AGCAAATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:74456 original size:134 final size:132
Alignment explanation
Indices: 74154--74725 Score: 585
Period size: 134 Copynumber: 4.2 Consensus size: 132
74144 GTAAACGTTA
* *
74154 ATTCATTCCACTGTTCATAAGGGAAGATTGAATCGAGACAGACTTGTTCCACTGCTACTCAGGGA
1 ATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAG-CAGACTTGTTCCACTGCTACTCAGGGA
* * * * **
74219 AGATCAAATTCGAAAAGAAAGAGGGATATGTTCCGCTACTTCTTGAGGGAAATTTAGATCTAAAA
65 AGATCAAATT-G-GAA-AAAGAGGGATATGTTCCGCTACTTCTTGAGGGAAAATCAAATCTGGAA
74284 ATGATT-
127 ATG-TTG
* * * * * *
74290 ATTCATTACACTGTTCTTTAGGGAAGATTGAATCTACGCAGACTTGCTCTACTACTACTCAGGGA
1 ATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGA-GCAGACTTGTTCCACTGCTACTCAGGGA
* * ** * *
74355 AGATCAAATATGGAAAAAGATGGATTTGTTATGTTGCTTCTTGAGGGAAAATCAAATCTGGAAAT
65 AGATCAAAT-TGGAAAAAGAGGGATATGTTCCGCTACTTCTTGAGGGAAAATCAAATCTGGAAAT
74420 GTTG
129 GTTG
* * * * *
74424 ATTCATTCCACTATTCTTCACGGAATATTGAATTGAGGCA-AGCTTGTTCCATTGCTACTCAGGG
1 ATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGA-GCAGA-CTTGTTCCACTGCTACTCAGGG
* * * * * **
74488 AAAATCAAATCTAGAAAAAGAGGGATTTGTTTCGCTACTTCTTGAGGGAAAAT-AATATTTGGGG
64 AAGATCAAAT-TGGAAAAAGAGGGATATGTTCCGCTACTTCTTGAGGGAAAATCAA-ATCTGGAA
**
74552 ACATTG
127 ATGTTG
* *
74558 ATTTATTCCACTGTTCTTCAGGGAAGATTGAATCGAGAATGACTTGTTCCACTGCTACTCAGGGA
1 ATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGCA-GACTTGTTCCACTGCTACTCAGGGA
* * * * * *
74623 AGATCAAATTTGGAAAGAGAGGGGATATGTTCCGTTATTTCTTCAGGGAAAATCAGATCTAGG-G
65 AGATCAAA-TTGGAAAAAGA-GGGATATGTTCCGCTACTTCTTGAGGGAAAATCAAATCT-GGAA
74687 ATGTTG
127 ATGTTG
* *
74693 ATTCATTCCACTGTTCTTTAGGGGAGATTGAAT
1 ATTCATTCCACTGTTCTTCAGGGAAGATTGAAT
74726 TGAGTTTGAT
Statistics
Matches: 359, Mismatches: 66, Indels: 23
0.80 0.15 0.05
Matches are distributed among these distances:
133 7 0.02
134 212 0.59
135 69 0.19
136 69 0.19
137 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (132 bp):
ATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGCAGACTTGTTCCACTGCTACTCAGGGAA
GATCAAATTGGAAAAAGAGGGATATGTTCCGCTACTTCTTGAGGGAAAATCAAATCTGGAAATGT
TG
Found at i:75998 original size:13 final size:13
Alignment explanation
Indices: 75967--76040 Score: 71
Period size: 13 Copynumber: 5.7 Consensus size: 13
75957 TTGAACCCCC
*
75967 TTTTTGTTTATTCT
1 TTTTTCTTT-TTCT
*
75981 CTTTTCTTTTTCT
1 TTTTTCTTTTTCT
*
75994 TTTTTCTTTCT-T
1 TTTTTCTTTTTCT
*
76006 TTTTTC-TTTTAT
1 TTTTTCTTTTTCT
*
76018 TTTTTCATTTTCT
1 TTTTTCTTTTTCT
76031 TTATTTCTTT
1 TT-TTTCTTT
76041 AGGAGATGTA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
11 3 0.06
12 14 0.28
13 20 0.40
14 13 0.26
ACGTcount: A:0.05, C:0.14, G:0.01, T:0.80
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:76005 original size:17 final size:17
Alignment explanation
Indices: 75983--76040 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
75973 TTTATTCTCT
75983 TTTCTTTTTCTTTTTTC
1 TTTCTTTTTCTTTTTTC
*
76000 TTTCTTTTTTTCTTTTATTT
1 TTTC--TTTTTCTTTT-TTC
*
76020 TTTCATTTTCTTTATTTC
1 TTTCTTTTTCTTT-TTTC
76038 TTT
1 TTT
76041 AGGAGATGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 4 0.12
18 13 0.38
19 11 0.32
20 6 0.18
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTCTTTTTCTTTTTTC
Found at i:76008 original size:12 final size:13
Alignment explanation
Indices: 75982--76023 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 13
75972 GTTTATTCTC
* *
75982 TTTTCTTTTTCTT
1 TTTTCTTTCTATT
75995 TTTTCTTTCT-TT
1 TTTTCTTTCTATT
76007 TTTTCTTT-TATT
1 TTTTCTTTCTATT
76019 TTTTC
1 TTTTC
76024 ATTTTCTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 1 0.04
12 17 0.63
13 9 0.33
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTTTCTATT
Found at i:78539 original size:175 final size:175
Alignment explanation
Indices: 78233--78585 Score: 608
Period size: 175 Copynumber: 2.0 Consensus size: 175
78223 TGCCCTTAAC
78233 AATCATCATCGCATAAACTTATATTTTTTTATGCATCATGTCATGAAATAGTATTACAGGCTCTC
1 AATCATCATCGCATAAACTTATATTTTTTTATGCATCATGTCATGAAATAGTATTACAGGCTCTC
78298 TGGTGGTTCCATTGCATTCTTTAACCAAATGTCATCACCTTGTAGCAAACCATGCCCACATGGTG
66 --GTGGTTCCATTGCATTCTTTAACCAAATGTCATCACCTTGTAGCAAACCATGCCCACATGGTG
78363 ACAAAGTAGTCTTTTCCATATCTTCTGGATTCATCTTTATTTGATTATA
129 ACAAAGTAGTCTTTTCCATATC-T-TGGATTCATCTTTATTTGATTATA
78412 AATCAT-ATCGACATAAACTTATA-TTTTTTATGCATCATGTCATG-AATAGTATTACCATGGCT
1 AATCATCATCG-CATAAACTTATATTTTTTTATGCATCATGTCATGAAATAGTATTA-CA-GGCT
78474 CTC-TGGTTCCATTGCATTC-TTAACCAAATGTCATCACCTTGTAGCAAACCATGCCCACATGGT
63 CTCGTGGTTCCATTGCATTCTTTAACCAAATGTCATCACCTTGTAGCAAACCATGCCCACATGGT
78537 GACAAAGTAGTCTTTTCCATATCTTGGATTCATCTTTATTTGATTATA
128 GACAAAGTAGTCTTTTCCATATCTTGGATTCATCTTTATTTGATTATA
78585 A
1 A
78586 CCCGAAAAGA
Statistics
Matches: 171, Mismatches: 0, Indels: 12
0.93 0.00 0.07
Matches are distributed among these distances:
173 25 0.15
174 1 0.01
175 67 0.39
176 16 0.09
177 10 0.06
178 27 0.16
179 25 0.15
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.38
Consensus pattern (175 bp):
AATCATCATCGCATAAACTTATATTTTTTTATGCATCATGTCATGAAATAGTATTACAGGCTCTC
GTGGTTCCATTGCATTCTTTAACCAAATGTCATCACCTTGTAGCAAACCATGCCCACATGGTGAC
AAAGTAGTCTTTTCCATATCTTGGATTCATCTTTATTTGATTATA
Found at i:85960 original size:15 final size:16
Alignment explanation
Indices: 85940--85976 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
85930 GATTAGAATA
85940 AAATAAACAAAAGAT-
1 AAATAAACAAAAGATG
*
85955 AAATAAACGAAAGATG
1 AAATAAACAAAAGATG
85971 AAATAA
1 AAATAA
85977 GATAATAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (16 bp):
AAATAAACAAAAGATG
Found at i:90246 original size:11 final size:10
Alignment explanation
Indices: 90232--90276 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
90222 AAATTTTGGC
*
90232 TTTTTTGGCT
1 TTTTTTGCCT
90242 TTTTTTG--T
1 TTTTTTGCCT
90250 TTTTTTGCCT
1 TTTTTTGCCT
90260 TCTTTTTGCCT
1 T-TTTTTGCCT
90271 TTTTTT
1 TTTTTT
90277 TGTTTCTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.25
10 14 0.44
11 10 0.31
ACGTcount: A:0.00, C:0.13, G:0.11, T:0.76
Consensus pattern (10 bp):
TTTTTTGCCT
Found at i:90247 original size:19 final size:20
Alignment explanation
Indices: 90225--90275 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
90215 TTTTTTGAAA
*
90225 TTTTGGCTTTTTTGGCTT-T
1 TTTTGGCTTTTTTGCCTTCT
*
90244 TTTT-GTTTTTTTGCCTTCT
1 TTTTGGCTTTTTTGCCTTCT
*
90263 TTTTGCCTTTTTT
1 TTTTGGCTTTTTT
90276 TTGTTTCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 11 0.42
19 9 0.35
20 6 0.23
ACGTcount: A:0.00, C:0.14, G:0.14, T:0.73
Consensus pattern (20 bp):
TTTTGGCTTTTTTGCCTTCT
Found at i:90266 original size:21 final size:20
Alignment explanation
Indices: 90240--90296 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
90230 GCTTTTTTGG
90240 CTTTTTTTGTTTTTTTGCCTT
1 CTTTTTTTGTTTTTTTG-CTT
* *
90261 CTTTTTGCCT-TTTTTTTGTTT
1 CTTTTT--TTGTTTTTTTGCTT
90282 C-TTTTTTGTTTTTTT
1 CTTTTTTTGTTTTTTT
90297 TTTTTGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
18 1 0.03
19 7 0.23
20 4 0.13
21 9 0.30
22 8 0.27
23 1 0.03
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.79
Consensus pattern (20 bp):
CTTTTTTTGTTTTTTTGCTT
Found at i:90277 original size:11 final size:11
Alignment explanation
Indices: 90249--90278 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
90239 GCTTTTTTTG
90249 TTTTTTTGCCT
1 TTTTTTTGCCT
*
90260 TCTTTTTGCCT
1 TTTTTTTGCCT
90271 TTTTTTTG
1 TTTTTTTG
90279 TTTCTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.10, T:0.73
Consensus pattern (11 bp):
TTTTTTTGCCT
Found at i:90297 original size:21 final size:22
Alignment explanation
Indices: 90240--90298 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
90230 GCTTTTTTGG
*
90240 CTTTTTT-TGTTTTTTTGCCTT
1 CTTTTTTGTTTTTTTTTGCCTT
* *
90261 C-TTTTTGCCTTTTTTTTG-TTT
1 CTTTTTTG-TTTTTTTTTGCCTT
90282 CTTTTTTGTTTTTTTTT
1 CTTTTTTGTTTTTTTTT
90299 TTTGAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 5 0.16
21 12 0.39
22 14 0.45
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (22 bp):
CTTTTTTGTTTTTTTTTGCCTT
Found at i:90299 original size:11 final size:11
Alignment explanation
Indices: 90270--90299 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
90260 TCTTTTTGCC
90270 TTTTTTTTGTT
1 TTTTTTTTGTT
*
90281 TCTTTTTTGTT
1 TTTTTTTTGTT
90292 TTTTTTTT
1 TTTTTTTT
90300 TTGAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:90674 original size:15 final size:16
Alignment explanation
Indices: 90654--90690 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
90644 GATTAGAATA
90654 AAATAAACAAAAGAT-
1 AAATAAACAAAAGATG
*
90669 AAATAAACGAAAGATG
1 AAATAAACAAAAGATG
90685 AAATAA
1 AAATAA
90691 GATAATAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (16 bp):
AAATAAACAAAAGATG
Found at i:102498 original size:131 final size:131
Alignment explanation
Indices: 102254--102607 Score: 451
Period size: 131 Copynumber: 2.7 Consensus size: 131
102244 ATAATTTTAA
* * * * *
102254 GAGAGAAAACGATAATATCTAATTATTTTCAATTGAGAATAAATTACATATCATGCCTTAAAACA
1 GAGAGAAAACGATAATATCTAA-TATTTTCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * *
102319 -ATCATTTATTACCCCAATTGAAATGAAGAGATATCACTATTTCGTCTT-AAAATTCAATATTGA
65 TA-CATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAAAATCAATATTGA
*
102382 TTC
129 CTC
** * *
102385 GATTGAAGATGATAATATCTAATGATTTTCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAAT-ATTTTCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
*
102450 TACATTTATTACTCCGATCGAAATGAAGAGATATCACTATTCCGTCTTAAAAAATCAATATTGAC
65 TACATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAAAATCAATATTGAC
102515 TC
130 TC
* ** * * * *
102517 GAGAGAAAACGGTAATATCTTCTTTTTTCCAATCGAGAATAAATGATCTCTCATTCCCTAAAGCA
1 GAGAGAAAACGATAATATCTAATATTTT-CAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
*
102582 TTCATTTATTACTCCAATCGAAATGA
65 TACATTTATTACTCCAATCGAAATGA
102608 TTAGATATTA
Statistics
Matches: 191, Mismatches: 28, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
130 1 0.01
131 100 0.52
132 90 0.47
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCTAATATTTTCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAT
ACATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAAAATCAATATTGACT
C
Found at i:103260 original size:28 final size:27
Alignment explanation
Indices: 103228--103295 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 27
103218 ACAAAGAATA
103228 AAAATAAATAAAACATG-GGGACTAAATT
1 AAAATAAATAAAA-ATGAGGGAC-AAATT
* *
103256 AAAATAAACTAAAATTGTATGGACAAATT
1 AAAATAAA-TAAAAATG-AGGGACAAATT
103285 AAAATAAATAA
1 AAAATAAATAA
103296 GAAAATGGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 13 0.37
29 18 0.51
30 4 0.11
ACGTcount: A:0.60, C:0.06, G:0.10, T:0.24
Consensus pattern (27 bp):
AAAATAAATAAAAATGAGGGACAAATT
Found at i:103816 original size:122 final size:122
Alignment explanation
Indices: 103594--103832 Score: 462
Period size: 122 Copynumber: 2.0 Consensus size: 122
103584 GACCGCCGTA
103594 CACGGCAATCAAAACCCCCCAAAATAACCCAAGAGCCTCCTTAAACCTAGATCTATACCCCTAGG
1 CACGGCAATCAAAACCCCCCAAAATAACCCAAGAGCCTCCTTAAACCTAGATCTATACCCCTAGG
103659 CTAAAATCGCCTAAAAACCTATAAATGCCTCAAAACGAGCCCCGACCTTTCAGTTCT
66 CTAAAATCGCCTAAAAACCTATAAATGCCTCAAAACGAGCCCCGACCTTTCAGTTCT
103716 CACGTGCAATCAAAACCCCCCAAAATAA-CCAAGAGCCTCCTTAAACCTAGATCTATACCCCTAG
1 CACG-GCAATCAAAACCCCCCAAAATAACCCAAGAGCCTCCTTAAACCTAGATCTATACCCCTAG
103780 GCTAAAATCGCCTAAAAACCTATAAATGCCTCAAAACGAGCCCCGACCTTTCA
65 GCTAAAATCGCCTAAAAACCTATAAATGCCTCAAAACGAGCCCCGACCTTTCA
103833 CTCAGAGCCC
Statistics
Matches: 116, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
122 93 0.80
123 23 0.20
ACGTcount: A:0.37, C:0.34, G:0.10, T:0.18
Consensus pattern (122 bp):
CACGGCAATCAAAACCCCCCAAAATAACCCAAGAGCCTCCTTAAACCTAGATCTATACCCCTAGG
CTAAAATCGCCTAAAAACCTATAAATGCCTCAAAACGAGCCCCGACCTTTCAGTTCT
Found at i:103852 original size:68 final size:68
Alignment explanation
Indices: 103773--103900 Score: 256
Period size: 68 Copynumber: 1.9 Consensus size: 68
103763 TAGATCTATA
103773 CCCCTAGGCTAAAATCGCCTAAAAACCTATAAATGCCTCAAAACGAGCCCCGACCTTTCACTCAG
1 CCCCTAGGCTAAAATCGCCTAAAAACCTATAAATGCCTCAAAACGAGCCCCGACCTTTCACTCAG
103838 AGC
66 AGC
103841 CCCCTAGGCTAAAATCGCCTAAAAACCTATAAATGCCTCAAAACGAGCCCCGACCTTTCA
1 CCCCTAGGCTAAAATCGCCTAAAAACCTATAAATGCCTCAAAACGAGCCCCGACCTTTCA
103901 GTTCTCACGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 60 1.00
ACGTcount: A:0.34, C:0.35, G:0.12, T:0.18
Consensus pattern (68 bp):
CCCCTAGGCTAAAATCGCCTAAAAACCTATAAATGCCTCAAAACGAGCCCCGACCTTTCACTCAG
AGC
Found at i:108137 original size:3 final size:3
Alignment explanation
Indices: 108129--108168 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
108119 TCCCGACATT
*
108129 TTA TTA TTA TTA TTA TTA TTAA TTA TAA TTA TTTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA -TTA TTA TT
108169 GTTGTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 27 0.82
4 6 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:108143 original size:9 final size:9
Alignment explanation
Indices: 108129--108168 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
108119 TCCCGACATT
108129 TTATTATTA
1 TTATTATTA
108138 TTATTATTA
1 TTATTATTA
*
108147 TTAATTATAA
1 TT-ATTATTA
108157 TTATTTATTA
1 TTA-TTATTA
108167 TT
1 TT
108169 GTTGTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
9 12 0.44
10 15 0.56
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTATTATTA
Found at i:110291 original size:131 final size:130
Alignment explanation
Indices: 110091--110457 Score: 405
Period size: 131 Copynumber: 2.8 Consensus size: 130
110081 CGATAACGAG
* * * * * * *
110091 AATAGTAATATATTTTCATTTCAGTTGGAGTAATAAATGACTGCTCTAAGGCATGAGAGGTCGTT
1 AATAGTAATATCTCTCCATTTCA-TTGGAGTAATAAATGACTGTTTTAATGCATGAGAGGTCATT
* * * * *
110156 TATTCTCTATTGGAAATAATTTGATACTGTCATTTTCTCTCGAATTAATA-TCAATTTTCAAGAT
65 TATTCTCTATTGGAAATAATTAGATATTATCATTTTCACTCGAATCAATATTCAATTTT-AAGAT
*
110220 GG
129 GA
* * * *
110222 AATAGTGATATCTCTCCATTTCGATTGGAGCAATAAATGACTATTTTAATGTATGAGAGGTCATT
1 AATAGTAATATCTCTCCATTTC-ATTGGAGTAATAAATGACTGTTTTAATGCATGAGAGGTCATT
* * * * * *
110287 TATTCTCGATTGGAAATCATTAGATATTATCGTTTTCACTTGAATCGATATTGAATTTTAAGATG
65 TATTCTCTATTGGAAATAATTAGATATTATCATTTTCACTCGAATCAATATTCAATTTTAAGATG
110352 A
130 A
** * * * * *
110353 AATAGTAATATCTCTTTATTTCAATTGGGGTAATAAATGATTGTTTCAATGCACGAAAGGTCATT
1 AATAGTAATATCTCTCCATTTC-ATTGGAGTAATAAATGACTGTTTTAATGCATGAGAGGTCATT
110418 TATTCT-TGATTGGAAATAATTAGATATTATCATTTTCACT
65 TATTCTCT-ATTGGAAATAATTAGATATTATCATTTTCACT
110458 ATTTAAATTA
Statistics
Matches: 195, Mismatches: 38, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
131 187 0.96
132 8 0.04
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.40
Consensus pattern (130 bp):
AATAGTAATATCTCTCCATTTCATTGGAGTAATAAATGACTGTTTTAATGCATGAGAGGTCATTT
ATTCTCTATTGGAAATAATTAGATATTATCATTTTCACTCGAATCAATATTCAATTTTAAGATGA
Found at i:129191 original size:15 final size:15
Alignment explanation
Indices: 129171--129200 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
129161 ATAAGAATTC
129171 ATAATGTTGTACCCT
1 ATAATGTTGTACCCT
129186 ATAATGTTGTACCCT
1 ATAATGTTGTACCCT
129201 CACGTGTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (15 bp):
ATAATGTTGTACCCT
Found at i:129642 original size:25 final size:25
Alignment explanation
Indices: 129614--129672 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
129604 AAAGCTTTGG
*
129614 TGATTAAAATGATATATTTCTTTAA
1 TGATTAAAATGATATATATCTTTAA
129639 TGATTAAAATGATATATATCTTTAA
1 TGATTAAAATGATATATATCTTTAA
*
129664 TGATGAAAA
1 TGATTAAAA
129673 CATCAACAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.42
Consensus pattern (25 bp):
TGATTAAAATGATATATATCTTTAA
Found at i:130948 original size:122 final size:121
Alignment explanation
Indices: 130732--130950 Score: 271
Period size: 122 Copynumber: 1.8 Consensus size: 121
130722 TAGTGGTGTT
* ***** *
130732 TTTATATAAACACCGCTAAAGACTATATATTAGTGGCATTTTTATGCAAATGTTGCTATAGACTC
1 TTTATACAAACACCGCTAAAGACTATATATTAGTGGCATTTTTATGCAAACACAACTAAAGACTC
* * *
130797 GTACATTAATGGTGTTTTTTGAATAAACGCCGTAATTTCTCAGCACATTAGCGGCG
66 GTACATTAATGATATTTTTTGAACAAACGCCGTAATTTCTCAGCACATTAGCGGCG
* *
130853 TTTATACAAACACCGCTAAAGACT-TGTACTTTAGTGGTATTTTTATGCAAACACAACTAAAGAC
1 TTTATACAAACACCGCTAAAGACTATATA--TTAGTGGCATTTTTATGCAAACACAACTAAAGAC
* *
130917 TCGTACTTTAGTGATATTTTTT-ATACAAACGCCG
64 TCGTACATTAATGATATTTTTTGA-ACAAACGCCG
130951 CTAAAGATTC
Statistics
Matches: 81, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
120 3 0.04
121 24 0.30
122 54 0.67
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (121 bp):
TTTATACAAACACCGCTAAAGACTATATATTAGTGGCATTTTTATGCAAACACAACTAAAGACTC
GTACATTAATGATATTTTTTGAACAAACGCCGTAATTTCTCAGCACATTAGCGGCG
Found at i:130952 original size:83 final size:83
Alignment explanation
Indices: 130853--131005 Score: 202
Period size: 83 Copynumber: 1.8 Consensus size: 83
130843 ATTAGCGGCG
* *
130853 TTTATACAAACACCGCTAAAGACTT-GTACTTTAGTGGTATTTTTATG-CAAACACAACTAAAGA
1 TTTATACAAACACCGCTAAAGA-TTCATACTTTAGTGGCATTTTTA-GACAAACACAACTAAAGA
130916 CTCGTACTTTAGTGATATTT
64 CTCGTACTTTAGTGATATTT
* * * * * *
130936 TTTATACAAACGCCGCTAAAGATTCATTCTTTAGTGGCGTTTTTAGATAAACACCACTATAGACT
1 TTTATACAAACACCGCTAAAGATTCATACTTTAGTGGCATTTTTAGACAAACACAACTAAAGACT
131001 CGTAC
66 CGTAC
131006 ATTGAAAGCT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
82 3 0.05
83 57 0.95
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (83 bp):
TTTATACAAACACCGCTAAAGATTCATACTTTAGTGGCATTTTTAGACAAACACAACTAAAGACT
CGTACTTTAGTGATATTT
Found at i:130955 original size:42 final size:41
Alignment explanation
Indices: 130853--131005 Score: 153
Period size: 41 Copynumber: 3.7 Consensus size: 41
130843 ATTAGCGGCG
* *
130853 TTTATACAAACACCGCTAAAGACTTGTACTTTAGTGGTATT
1 TTTATACAAACACCGCTAAAGACTCGTACTTTAGTGATATT
* **
130894 TTTATGCAAACACAACTAAAGACTCGTACTTTAGTGATATTT
1 TTTATACAAACACCGCTAAAGACTCGTACTTTAGTGATA-TT
* * * * ***
130936 TTTATACAAACGCCGCTAAAGATTCATTCTTTAGTGGCGTT
1 TTTATACAAACACCGCTAAAGACTCGTACTTTAGTGATATT
* * * *
130977 TTTAGATAAACACCACTATAGACTCGTAC
1 TTTATACAAACACCGCTAAAGACTCGTAC
131006 ATTGAAAGCT
Statistics
Matches: 88, Mismatches: 23, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
41 57 0.65
42 31 0.35
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (41 bp):
TTTATACAAACACCGCTAAAGACTCGTACTTTAGTGATATT
Found at i:138788 original size:11 final size:11
Alignment explanation
Indices: 138769--138802 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
138759 GTTTATATAG
*
138769 ACTTAATTATC
1 ACTTTATTATC
138780 ACTTTATTATC
1 ACTTTATTATC
138791 ACTTTATTATC
1 ACTTTATTATC
138802 A
1 A
138803 TAAGAAGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (11 bp):
ACTTTATTATC
Found at i:146651 original size:2 final size:2
Alignment explanation
Indices: 146644--146683 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
146634 CTCTTTTTCA
146644 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
146684 GTAAACATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:146700 original size:16 final size:16
Alignment explanation
Indices: 146681--146714 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
146671 TATATATATA
146681 TATGTAAACATAAAAT
1 TATGTAAACATAAAAT
* *
146697 TATGTACATATAAAAT
1 TATGTAAACATAAAAT
146713 TA
1 TA
146715 CATTTATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (16 bp):
TATGTAAACATAAAAT
Found at i:149550 original size:21 final size:22
Alignment explanation
Indices: 149500--149551 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
149490 GAGTAGCTCG
* *
149500 TTAATTTTTTTTATAATTTTTA
1 TTAATTTATTTTATAAATTTTA
*
149522 GTAA-TTATTTTA-AAATTTTA
1 TTAATTTATTTTATAAATTTTA
149542 TTAATTTATT
1 TTAATTTATT
149552 AATATATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 10 0.40
21 12 0.48
22 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTAATTTATTTTATAAATTTTA
Found at i:150576 original size:26 final size:24
Alignment explanation
Indices: 150512--150576 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 24
150502 ATCATTTTAA
150512 TTAAAATAT-TAATTATTAAAATAT
1 TTAAAATATAT-ATTATTAAAATAT
*
150536 TTAAAATATAT-TTATTAATAT-T
1 TTAAAATATATATTATTAAAATAT
150558 TCTAATAATATAATATTAT
1 T-TAA-AATAT-ATATTAT
150577 ATTTTTAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
22 2 0.06
23 12 0.34
24 14 0.40
25 3 0.09
26 4 0.11
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
TTAAAATATATATTATTAAAATAT
Found at i:150578 original size:22 final size:23
Alignment explanation
Indices: 150548--150594 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
150538 AAAATATATT
150548 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
150571 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
150593 TA
1 TA
150595 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:150608 original size:32 final size:32
Alignment explanation
Indices: 150542--150621 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
150532 ATATTTAAAA
* *
150542 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
150574 TATATTT-TTAATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT--AT
*
150606 TATATTATAATAATAT
1 TATATT-TATTAATAT
150622 AAGATATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 13 0.32
31 6 0.15
32 15 0.38
33 1 0.03
34 5 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATAATAT
Found at i:150617 original size:53 final size:53
Alignment explanation
Indices: 150560--150661 Score: 131
Period size: 53 Copynumber: 1.9 Consensus size: 53
150550 TTAATATTTC
*
150560 TAATAATAT-A-ATATTATATTTTTAATATTATAATAA-A-ATAATCAATTATATTA
1 TAATAATATAAGATATTA-ATTTTT--TATT-TAATAATATATAATAAATTATATTA
150613 TAATAATATAAGATATTAATTTTTTATTTAATAATATATAATAAATTAT
1 TAATAATATAAGATATTAATTTTTTATTTAATAATATATAATAAATTAT
150662 TAATAAAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
51 6 0.14
52 5 0.11
53 20 0.45
54 7 0.16
55 6 0.14
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (53 bp):
TAATAATATAAGATATTAATTTTTTATTTAATAATATATAATAAATTATATTA
Found at i:150735 original size:19 final size:18
Alignment explanation
Indices: 150711--150779 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
150701 ATATTATTAA
150711 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
150730 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
150748 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
150770 ATT-TTAATAA
1 ATTATTAATAA
150780 ATATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:150783 original size:34 final size:35
Alignment explanation
Indices: 150745--150824 Score: 87
Period size: 35 Copynumber: 2.3 Consensus size: 35
150735 TTATATATTT
*
150745 AATATTAATATAATA-AT-CTAA-TAATATTTTAATA
1 AATA-TAATATAAAATATACTAATTAATATTTTAA-A
* *
150779 AATAT-ATTTAAAATATACTAATTAATATTTTTAA
1 AATATAATATAAAATATACTAATTAATATTTTAAA
150813 AATATAATATAA
1 AATATAATATAA
150825 CTATTACTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
32 6 0.16
33 3 0.08
34 14 0.37
35 15 0.39
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (35 bp):
AATATAATATAAAATATACTAATTAATATTTTAAA
Found at i:150793 original size:23 final size:23
Alignment explanation
Indices: 150746--150818 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
150736 TATATATTTA
*
150746 ATATTAATATAATA-ATCTAATAAT
1 ATATTAATA-AATATATTTAA-AAT
*
150770 ATTTTAATAAATATATTTAAAAT
1 ATATTAATAAATATATTTAAAAT
* * *
150793 ATACTAATTAATATTTTTAAAAT
1 ATATTAATAAATATATTTAAAAT
150816 ATA
1 ATA
150819 ATATAACTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 29 0.69
24 13 0.31
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATTAATAAATATATTTAAAAT
Found at i:150876 original size:33 final size:31
Alignment explanation
Indices: 150857--150927 Score: 92
Period size: 33 Copynumber: 2.3 Consensus size: 31
150847 ATATAATTTA
150857 TAATATTTTTATTTCAATAAAATATACCAATAT
1 TAATATTTTTATTT-AATAAAATATA-CAATAT
*
150890 TAATATTTTTATTTAATAAAATTATA-AA-AA
1 TAATATTTTTATTTAATAAAA-TATACAATAT
150920 TAATATTT
1 TAATATTT
150928 AATAATAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
30 9 0.25
31 2 0.06
32 7 0.19
33 18 0.50
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (31 bp):
TAATATTTTTATTTAATAAAATATACAATAT
Found at i:151377 original size:60 final size:60
Alignment explanation
Indices: 151278--151429 Score: 189
Period size: 60 Copynumber: 2.5 Consensus size: 60
151268 TTTTAAAGTG
* *
151278 GTCCCTAAACTTTTGAATATTT-TAATTTCATCCTCAAACTATGACTCGCCTTCTAAATTA
1 GTCCCTAAACTTTTGAAT-TTTCAAATTTCATCATCAAACTATGACTCGCCTTCTAAATTA
* * * * * *
151338 TTCCTTAAACTTTTGAATTTTCAAATTTCATCATTAAACTATGACTCTCTTTCTAAATTG
1 GTCCCTAAACTTTTGAATTTTCAAATTTCATCATCAAACTATGACTCGCCTTCTAAATTA
* * *
151398 GTCCCCAAACTTTTGAATATTCCAATTTCATC
1 GTCCCTAAACTTTTGAATTTTCAAATTTCATC
151430 CCCAAATTAT
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
59 3 0.04
60 75 0.96
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.42
Consensus pattern (60 bp):
GTCCCTAAACTTTTGAATTTTCAAATTTCATCATCAAACTATGACTCGCCTTCTAAATTA
Found at i:153453 original size:20 final size:20
Alignment explanation
Indices: 153428--153474 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
153418 CATTTGGTTA
153428 TTTTCCCCTGAGTTAGATTC
1 TTTTCCCCTGAGTTAGATTC
153448 TTTTCCCCTGAGTTAGATTC
1 TTTTCCCCTGAGTTAGATTC
153468 TTTTCCC
1 TTTTCCC
153475 AATAAGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.13, C:0.28, G:0.13, T:0.47
Consensus pattern (20 bp):
TTTTCCCCTGAGTTAGATTC
Found at i:156036 original size:11 final size:11
Alignment explanation
Indices: 156020--156058 Score: 51
Period size: 11 Copynumber: 3.3 Consensus size: 11
156010 TTTATCTTTT
156020 AAATTTTATAA
1 AAATTTTATAA
156031 AAATTTTATATA
1 AAATTTTATA-A
156043 TAAATTTTATTAA
1 -AAATTTTA-TAA
156056 AAA
1 AAA
156059 GTATATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 10 0.40
12 4 0.16
13 9 0.36
14 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AAATTTTATAA
Found at i:156042 original size:13 final size:13
Alignment explanation
Indices: 156026--156058 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
156016 TTTTAAATTT
156026 TATAAAAATTTTA
1 TATAAAAATTTTA
*
156039 TATATAAATTTTA
1 TATAAAAATTTTA
156052 T-TAAAAA
1 TATAAAAA
156059 GTATATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TATAAAAATTTTA
Found at i:156613 original size:44 final size:43
Alignment explanation
Indices: 156479--156682 Score: 178
Period size: 44 Copynumber: 4.7 Consensus size: 43
156469 TAATCTTATT
* ** *
156479 TTTTTATC-TTTATAATAGAGGTCCTTAATTTTTTTAATCCCAC
1 TTTTTA-CATTTATAATTGAGACCCTTAATTTTTTCAATCCCAC
* * *
156522 CTTTTACATTTATAATTGAGACTCTTAA-TTTTTCAATCCCGC
1 TTTTTACATTTATAATTGAGACCCTTAATTTTTTCAATCCCAC
* ** *
156564 TTTTTATATTTATAATTGATTCCCTTAATTTTTTTCAATCTCAC
1 TTTTTACATTTATAATTGAGACCCTTAA-TTTTTTCAATCCCAC
* * * ** *
156608 TTTTTACCTTTATGATTGAGACCCCTAATTTTTTCAATCATATT
1 TTTTTACATTTATAATTGAGACCCTTAATTTTTTCAATCCCA-C
* * * *
156652 TTTTTACTTTTATAATTTAGGCCCATAATTT
1 TTTTTACATTTATAATTGAGACCCTTAATTT
156683 CATCATTTTT
Statistics
Matches: 129, Mismatches: 28, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
42 36 0.28
43 33 0.26
44 60 0.47
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.51
Consensus pattern (43 bp):
TTTTTACATTTATAATTGAGACCCTTAATTTTTTCAATCCCAC
Found at i:156654 original size:86 final size:85
Alignment explanation
Indices: 156479--156682 Score: 205
Period size: 86 Copynumber: 2.4 Consensus size: 85
156469 TAATCTTATT
* *
156479 TTTTTATCTTTATAATAGAGGTCCTTAATTTTTTTAATCCCACCTTTTACATTTATAATTGAGAC
1 TTTTTATATTTATAATTGAGGTCCTTAATTTTTTTAATCCCACCTTTTACATTTATAATTGAGAC
* * * *
156544 TCTTAATTTTTCAATCCCGC
66 CCCTAATTTTTCAATCCAGA
* * * * *
156564 TTTTTATATTTATAATTGA-TTCCCTTAATTTTTTTCAATCTCACTTTTTACCTTTATGATTGAG
1 TTTTTATATTTATAATTGAGGT-CCTTAATTTTTTT-AATCCCACCTTTTACATTTATAATTGAG
*
156628 ACCCCTAATTTTTTCAAT-CATA
64 ACCCCTAA-TTTTTCAATCCAGA
* * * *
156650 TTTTTTTACTTTTATAATTTAGGCCCATAATTT
1 TTTTTATA--TTTATAATTGAGGTCCTTAATTT
156683 CATCATTTTT
Statistics
Matches: 96, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
84 1 0.01
85 30 0.31
86 38 0.40
87 9 0.09
88 18 0.19
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.51
Consensus pattern (85 bp):
TTTTTATATTTATAATTGAGGTCCTTAATTTTTTTAATCCCACCTTTTACATTTATAATTGAGAC
CCCTAATTTTTCAATCCAGA
Found at i:157374 original size:22 final size:22
Alignment explanation
Indices: 157346--157399 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
157336 GGTGGTTGTA
157346 CGGTCGA-ACAATGTTGGGTGTT
1 CGGTCGATACAATGTT-GGTGTT
*
157368 CGGTCGATTGACGATGTTGGTGTT
1 CGGTCGA-T-ACAATGTTGGTGTT
157392 CGGTCGAT
1 CGGTCGAT
157400 TGACGGCGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 7 0.25
23 1 0.04
24 13 0.46
25 7 0.25
ACGTcount: A:0.15, C:0.15, G:0.37, T:0.33
Consensus pattern (22 bp):
CGGTCGATACAATGTTGGTGTT
Found at i:157392 original size:24 final size:24
Alignment explanation
Indices: 157356--157413 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
157346 CGGTCGAACA
157356 ATGTTGGGTGTTCGGTCGATTGACG
1 ATGTT-GGTGTTCGGTCGATTGACG
157381 ATGTTGGTGTTCGGTCGATTGACG
1 ATGTTGGTGTTCGGTCGATTGACG
**
157405 GCGTTGGTG
1 ATGTTGGTG
157414 GCGGCTGACG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.10, C:0.12, G:0.41, T:0.36
Consensus pattern (24 bp):
ATGTTGGTGTTCGGTCGATTGACG
Found at i:158580 original size:3 final size:3
Alignment explanation
Indices: 158572--158596 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
158562 ATACCCCCAC
158572 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
158597 GTTATCAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:159801 original size:126 final size:127
Alignment explanation
Indices: 159609--159860 Score: 416
Period size: 126 Copynumber: 2.0 Consensus size: 127
159599 AAACAAACAA
*
159609 CTTCGAGAATATGTTCATGAACATAGGCATAATTAAACATGTCTATGAAAAAATAAAAATCCGTT
1 CTTCGAGAATATGTTCATGAACATAAGCATAATTAAACATGTCTATGAAAAAATAAAAATCCGTT
* *
159674 TATGTTAGGAATTTGTAAGCGAAAAAATTAATAAAATCGATATCAACGTAGAATGATACATC
66 TATGTTAGGAATTTGTAAGCGAAAAAAATAATAAAATCGATATCAACATAGAATGATACATC
* **
159736 CTTCGAGAATATGTTCA-GAACATAAGTATAATTAAACATGTCTATGAAAAAATAAAAATTTGTT
1 CTTCGAGAATATGTTCATGAACATAAGCATAATTAAACATGTCTATGAAAAAATAAAAATCCGTT
* * *
159800 TATGTTAGGAATTTGTAAGCGAAAAAAATAATCAAATTGATATCAATATAGAATGATACAT
66 TATGTTAGGAATTTGTAAGCGAAAAAAATAATAAAATCGATATCAACATAGAATGATACAT
159861 GCACAAGAGA
Statistics
Matches: 116, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
126 99 0.85
127 17 0.15
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (127 bp):
CTTCGAGAATATGTTCATGAACATAAGCATAATTAAACATGTCTATGAAAAAATAAAAATCCGTT
TATGTTAGGAATTTGTAAGCGAAAAAAATAATAAAATCGATATCAACATAGAATGATACATC
Done.