Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005034.1 Hibiscus syriacus cultivar Beakdansim tig00011302_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: 177960
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:264 original size:22 final size:21
Alignment explanation
Indices: 239--284 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
229 TGCTGCAACA
239 AAAGCAACAAAA-AGAGAAAAAG
1 AAAG-AACAAAATAGAG-AAAAG
*
261 AAAGAAGAAAATAGAGAAAAG
1 AAAGAACAAAATAGAGAAAAG
282 AAA
1 AAA
285 AAGAATCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.74, C:0.04, G:0.20, T:0.02
Consensus pattern (21 bp):
AAAGAACAAAATAGAGAAAAG
Found at i:284 original size:14 final size:13
Alignment explanation
Indices: 249--289 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
239 AAAGCAACAA
249 AAAG-AGAAAAAG
1 AAAGAAGAAAAAG
261 AAAGAAGAAAATAG
1 AAAGAAGAAAA-AG
275 AGAA-AAGAAAAAG
1 A-AAGAAGAAAAAG
288 AA
1 AA
290 TCCATACATC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 5 0.19
13 9 0.35
14 10 0.38
15 2 0.08
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (13 bp):
AAAGAAGAAAAAG
Found at i:4408 original size:33 final size:35
Alignment explanation
Indices: 4370--4498 Score: 156
Period size: 36 Copynumber: 3.7 Consensus size: 35
4360 ATGTTGATGA
* * *
4370 AATGGTAATGGA-A-GGATGATGTTATTGGCGTGAT
1 AATGGTGATGGATATGG-TGATGATATAGGCGTGAT
4404 -ATGGTGATGGAATATGGTGATGATATAGGCGTGAT
1 AATGGTGATGG-ATATGGTGATGATATAGGCGTGAT
*
4439 AATGGTGATGGACTATGGTGATGATATAGGTGTGAT
1 AATGGTGATGGA-TATGGTGATGATATAGGCGTGAT
*
4475 AATGGAGATGGATTATGGTGATGA
1 AATGGTGATGGA-TATGGTGATGA
4499 AAATAGTATC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
33 9 0.11
34 1 0.01
35 18 0.21
36 56 0.67
ACGTcount: A:0.29, C:0.02, G:0.36, T:0.32
Consensus pattern (35 bp):
AATGGTGATGGATATGGTGATGATATAGGCGTGAT
Found at i:4420 original size:13 final size:11
Alignment explanation
Indices: 4400--4498 Score: 76
Period size: 13 Copynumber: 8.3 Consensus size: 11
4390 GTTATTGGCG
4400 TGATATGGTGA
1 TGATATGGTGA
4411 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
4424 TGATATAGGCG-
1 TGATAT-GGTGA
4435 TGATAATGGTGA
1 TGAT-ATGGTGA
4447 TGGACTATGGTGA
1 T-GA-TATGGTGA
4460 TGATATAGGTG-
1 TGATAT-GGTGA
*
4471 TGATAATGGAGA
1 TGAT-ATGGTGA
4483 TGGATTATGGTGA
1 T-GA-TATGGTGA
4496 TGA
1 TGA
4499 AAATAGTATC
Statistics
Matches: 72, Mismatches: 4, Indels: 23
0.73 0.04 0.23
Matches are distributed among these distances:
11 22 0.31
12 19 0.26
13 29 0.40
14 2 0.03
ACGTcount: A:0.29, C:0.02, G:0.36, T:0.32
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:4456 original size:36 final size:36
Alignment explanation
Indices: 4386--4498 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
4376 AATGGAAGGA
* *
4386 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
4421 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* * *
4457 TGATGATATAGGTGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
4493 TGATGA
1 TGATGA
4499 AAATAGTATC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 55 0.77
ACGTcount: A:0.27, C:0.03, G:0.36, T:0.34
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:4780 original size:19 final size:20
Alignment explanation
Indices: 4733--4783 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
4723 GAAACCCCTT
**
4733 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
4753 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
4772 TGAAGATACATG
1 TGAAAATACATG
4784 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:10474 original size:16 final size:16
Alignment explanation
Indices: 10453--10509 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
10443 CATATAAGGT
10453 AATGAAATAAGAAAAA
1 AATGAAATAAGAAAAA
*
10469 AATGAAA-GA-AAAAA
1 AATGAAATAAGAAAAA
*
10483 AATGAAAT-AGTAAGAA
1 AATGAAATAAG-AAAAA
10499 AATGAAGATAA
1 AATGAA-ATAA
10510 CTTACAACTC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 13 0.38
15 1 0.03
16 17 0.50
17 2 0.06
18 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (16 bp):
AATGAAATAAGAAAAA
Found at i:11338 original size:23 final size:23
Alignment explanation
Indices: 11312--11381 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
11302 AGTCACGTCT
11312 ACACCAGATCCGGAGGTCATGCC
1 ACACCAGATCCGGAGGTCATGCC
* ** * *
11335 ACA-CTGAT--ATA-GTCACGTCT
1 ACACCAGATCCGGAGGTCATG-CC
11355 ACACCAGATCCGGAGGTCATGCC
1 ACACCAGATCCGGAGGTCATGCC
11378 ACAC
1 ACAC
11382 GGTCCCATTA
Statistics
Matches: 32, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 5 0.16
20 5 0.16
21 4 0.12
22 4 0.12
23 9 0.28
24 5 0.16
ACGTcount: A:0.29, C:0.33, G:0.21, T:0.17
Consensus pattern (23 bp):
ACACCAGATCCGGAGGTCATGCC
Found at i:11357 original size:43 final size:43
Alignment explanation
Indices: 11296--11381 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
11286 GAAGTATCAA
11296 TGATATAGTCACGTCTACACCAGATCCGGAGGTCATGCCACAC
1 TGATATAGTCACGTCTACACCAGATCCGGAGGTCATGCCACAC
11339 TGATATAGTCACGTCTACACCAGATCCGGAGGTCATGCCACAC
1 TGATATAGTCACGTCTACACCAGATCCGGAGGTCATGCCACAC
11382 GGTCCCATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (43 bp):
TGATATAGTCACGTCTACACCAGATCCGGAGGTCATGCCACAC
Found at i:15920 original size:11 final size:13
Alignment explanation
Indices: 15888--15917 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
15878 TGGCCAAAGA
15888 TGAAAAGGTATGT
1 TGAAAAGGTATGT
15901 TGAAAAGGTATG-
1 TGAAAAGGTATGT
15913 TGAAA
1 TGAAA
15918 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:21666 original size:12 final size:11
Alignment explanation
Indices: 21616--21680 Score: 69
Period size: 11 Copynumber: 5.6 Consensus size: 11
21606 TTTTTGGCTC
21616 TTTTTTTGTTT
1 TTTTTTTGTTT
*
21627 TTTTTTTGCCTT
1 TTTTTTTG-TTT
21639 TTTTTTTGCCTTT
1 TTTTTTTG--TTT
*
21652 TTTGTTTT-TTG
1 TTT-TTTTGTTT
21663 TTTTTTTGTTT
1 TTTTTTTGTTT
21674 TTTTTTT
1 TTTTTTT
21681 TGAGAAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
10 4 0.09
11 22 0.48
12 10 0.22
13 6 0.13
14 4 0.09
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.85
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:21681 original size:12 final size:12
Alignment explanation
Indices: 21616--21682 Score: 68
Period size: 12 Copynumber: 5.7 Consensus size: 12
21606 TTTTTGGCTC
21616 TTTTTTTG-TTT
1 TTTTTTTGCTTT
*
21627 TTTTTTTGCCTT
1 TTTTTTTGCTTT
21639 TTTTTTTGCCTTT
1 TTTTTTTG-CTTT
*
21652 TTTGTTTT--TTG
1 TTT-TTTTGCTTT
*
21663 TTTTTTTGTTTT
1 TTTTTTTGCTTT
21675 TTTTTTTG
1 TTTTTTTG
21683 AGAAAAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
10 4 0.09
11 13 0.28
12 20 0.43
13 6 0.13
14 4 0.09
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (12 bp):
TTTTTTTGCTTT
Found at i:29004 original size:30 final size:30
Alignment explanation
Indices: 28970--29030 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 30
28960 AAATCGTTTG
28970 GAAAATCTTAAAATT-ACTTTAACTTAATTT
1 GAAAATCTTAAAATTCA-TTTAACTTAATTT
29000 GAAAATCTTAAAATTCATTTAACTTAATTT
1 GAAAATCTTAAAATTCATTTAACTTAATTT
29030 G
1 G
29031 TTATATCGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.43
Consensus pattern (30 bp):
GAAAATCTTAAAATTCATTTAACTTAATTT
Found at i:31480 original size:23 final size:21
Alignment explanation
Indices: 31454--31512 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
31444 TTCCCCTGTG
31454 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCC-TC-AA
*
31477 GGGGGAATCGGTT-CCCTCAG
1 GGGGGAATCGGTTCCCCTCAA
*
31497 GGGGGAATCGATTCCC
1 GGGGGAATCGGTTCCC
31513 TCTGCACCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.39
21 4 0.12
22 3 0.09
23 13 0.39
ACGTcount: A:0.19, C:0.25, G:0.36, T:0.20
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCTCAA
Found at i:31514 original size:20 final size:21
Alignment explanation
Indices: 31430--31512 Score: 87
Period size: 21 Copynumber: 3.9 Consensus size: 21
31420 AACAGAACCC
*
31430 CAGGGGGGTATCGATTCCCCT
1 CAGGGGGGAATCGATTCCCCT
** *
31451 GTGGGGGGAATCGGTTCCCCTT
1 CAGGGGGGAATCGATTCCCC-T
* *
31473 CAAAGGGGGAATCGGTT-CCCT
1 C-AGGGGGGAATCGATTCCCCT
31494 CAGGGGGGAATCGATTCCC
1 CAGGGGGGAATCGATTCCC
31513 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 13 0.26
21 20 0.40
22 4 0.08
23 13 0.26
ACGTcount: A:0.17, C:0.25, G:0.36, T:0.22
Consensus pattern (21 bp):
CAGGGGGGAATCGATTCCCCT
Found at i:35319 original size:21 final size:21
Alignment explanation
Indices: 35279--35320 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
35269 GAGTTTGTTT
**
35279 TCATTTTCAATTTTTGAAACA
1 TCATTTTCAATTTTAAAAACA
*
35300 TCATTTTCTATTTTAAAAACA
1 TCATTTTCAATTTTAAAAACA
35321 ATTTCATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (21 bp):
TCATTTTCAATTTTAAAAACA
Found at i:41696 original size:12 final size:11
Alignment explanation
Indices: 41646--41710 Score: 62
Period size: 10 Copynumber: 5.7 Consensus size: 11
41636 TTTTTGGCTC
41646 TTTTTTTGTTT
1 TTTTTTTGTTT
*
41657 TTTTTTTGCCTT
1 TTTTTTTG-TTT
41669 TTTTTTTGCCTTT
1 TTTTTTTG--TTT
*
41682 TTTGTTTT-TTG
1 TTT-TTTTGTTT
41693 TTTTTTT-TTT
1 TTTTTTTGTTT
41703 TTTTTTTG
1 TTTTTTTG
41711 AGAAAAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
10 13 0.28
11 13 0.28
12 10 0.22
13 6 0.13
14 4 0.09
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.85
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:41707 original size:16 final size:16
Alignment explanation
Indices: 41667--41705 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
41657 TTTTTTTGCC
41667 TTTTTTTTTGCCTTTT
1 TTTTTTTTTGCCTTTT
*
41683 TTGTTTTTTG--TTTT
1 TTTTTTTTTGCCTTTT
41697 TTTTTTTTT
1 TTTTTTTTT
41706 TTTTGAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
16 9 0.43
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (16 bp):
TTTTTTTTTGCCTTTT
Found at i:43259 original size:30 final size:30
Alignment explanation
Indices: 43225--43285 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
43215 AAATCGTTTG
43225 GAAAATCTTAAAATTAC-TTTAACTTAATTT
1 GAAAATCTTAAAA-TACATTTAACTTAATTT
*
43255 GAAAATCTTAAAATCCATTTAACTTAATTT
1 GAAAATCTTAAAATACATTTAACTTAATTT
43285 G
1 G
43286 TTATATCGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (30 bp):
GAAAATCTTAAAATACATTTAACTTAATTT
Found at i:54207 original size:19 final size:20
Alignment explanation
Indices: 54185--54227 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
54175 AGCATGTGTC
54185 TTCATT-AAAATCATGTATT
1 TTCATTAAAAATCATGTATT
54204 TTCATTAAAAATCATGTATT
1 TTCATTAAAAATCATGTATT
54224 TTCA
1 TTCA
54228 AAGGGGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.47
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:57082 original size:24 final size:21
Alignment explanation
Indices: 57047--57089 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
57037 GGCTCATTCT
*
57047 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
57070 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
57090 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:60378 original size:25 final size:24
Alignment explanation
Indices: 60350--60403 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
60340 CTTTACACAT
*
60350 ATATATGTT-TATTTCAAATGTTATA
1 ATATATGTTAT-TTTCAAAT-ATATA
*
60375 ATATA-GTTATTTTCATATATATA
1 ATATATGTTATTTTCAAATATATA
60398 ATATAT
1 ATATAT
60404 ATGGTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 9 0.36
24 10 0.40
25 6 0.24
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.52
Consensus pattern (24 bp):
ATATATGTTATTTTCAAATATATA
Found at i:62839 original size:35 final size:37
Alignment explanation
Indices: 62793--62872 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
62783 TTTGAGAATT
*
62793 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
62828 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
62865 TGGTGATG
1 TGGTGATG
62873 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:67842 original size:11 final size:11
Alignment explanation
Indices: 67828--67883 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
67818 TCTTTTTGAA
67828 TTCTTTTTCTT
1 TTCTTTTTCTT
67839 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
67852 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
67865 TGTCTTTTTC-T
1 T-TCTTTTTCTT
67876 TTCTTTTT
1 TTCTTTTT
67884 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:67852 original size:19 final size:18
Alignment explanation
Indices: 67828--67883 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
67818 TCTTTTTGAA
67828 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
67846 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
67865 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
67883 T
1 T
67884 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:72277 original size:16 final size:17
Alignment explanation
Indices: 72239--72287 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
72229 AAGATAGTGA
72239 AATAAGAAAAAATGAAAG
1 AATAAG-AAAAATGAAAG
*
72257 AATAA-AGAAATGAAATG
1 AATAAGAAAAATGAAA-G
72274 -ATAAGAAAAATGAA
1 AATAAGAAAAATGAA
72288 GATAACTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 13 0.48
17 9 0.33
18 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.14
Consensus pattern (17 bp):
AATAAGAAAAATGAAAG
Found at i:72953 original size:37 final size:35
Alignment explanation
Indices: 72877--72953 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 35
72867 GGAAATTTGG
* * *
72877 TGATGATATAGGCGTGATATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATATGGAGATGGACTACGA
*
72912 TGATGATATAGGCGTGATAATGGAAGATGGATTACGA
1 TGATGATATAGGCGTGAT-ATGG-AGATGGACTACGA
72949 TGATG
1 TGATG
72954 GAAATAGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
35 18 0.50
36 4 0.11
37 14 0.39
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (35 bp):
TGATGATATAGGCGTGATATGGAGATGGACTACGA
Found at i:76719 original size:15 final size:15
Alignment explanation
Indices: 76696--76731 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
76686 ACTAATATTC
* *
76696 TTATCATAATATATA
1 TTATAATAACATATA
76711 TTATAATAACATATA
1 TTATAATAACATATA
76726 TTATAA
1 TTATAA
76732 AGCTAATAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:79330 original size:19 final size:17
Alignment explanation
Indices: 79308--79350 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
79298 TTTCTTTCTT
79308 TTTCTTCTTTTTTGAGTG
1 TTTCTTC-TTTTTGAGTG
*
79326 CTTTCAATCTTTTTGAGTG
1 -TTTC-TTCTTTTTGAGTG
79345 TTTCTT
1 TTTCTT
79351 TTTCCTTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.05
18 4 0.19
19 14 0.67
20 2 0.10
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.63
Consensus pattern (17 bp):
TTTCTTCTTTTTGAGTG
Found at i:80973 original size:15 final size:15
Alignment explanation
Indices: 80950--80985 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
80940 ACTAATATTC
* *
80950 TTATCATAATATATA
1 TTATAATAACATATA
80965 TTATAATAACATATA
1 TTATAATAACATATA
80980 TTATAA
1 TTATAA
80986 AAGCTAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:85984 original size:867 final size:865
Alignment explanation
Indices: 84312--86043 Score: 3320
Period size: 867 Copynumber: 2.0 Consensus size: 865
84302 GAAGGGGGGA
84312 TGATATAGTCACGTCTACACCAGATCCGGAGGTCATGCCACACGGTCCCATTACTAGGTCAAGGG
1 TGATATAGTCACGTCTACACCAGATCCGGAGGTCATGCCACACGGTCCCATTACTAGGTCAAGGG
84377 CCAAACAATTCAGGGAAGTTCTCTTAACTAAGTGTCTTGAAGCTTTTGATTCATTTGATAACTTA
66 CCAAACAATTCAGGGAAGTTCTCTTAACTAAGTGTCTTGAAGCTTTTGATTCATTTGATAACTTA
*
84442 ACACTCTCTTATGTTATGTTATATAATGTTTTAATAGCTAAATAATAACTTAGTATGAACACATC
131 ACACTCTCTTATGTTATGTTATATAATGTTTTAATAGCTAAAGAATAACTTAGTATGAACACATC
84507 TTACACATTGTTATTTTTAATATGTTAAGCATGTTAGGATAGTTTTATTATCATATTAAGCATGA
196 TTACACATTGTTATTTTTAATATGTTAAGCATGTTAGGATAGTTTTATTATCATATTAAGCATGA
84572 TTATTATATACATCAAGGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTCATATTAA
261 TTATTATATACATCAAGGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTCATATTAA
*
84637 CTCTTAGGCTTTATACATTATCTTACACATATTAGGAGATGATTTACTTAGCTCATGACCATTAT
326 CTCTTAGGCTTTATACATTATCTTACACATATTAGGAGATGATGTACTTAGCTCATGACCATTAT
* *
84702 ACTTAGCTCACATTACCATAAACAAACATGGCAGTAAGGTATTTAGCTTGTTTTAGCTCAATATC
391 ACTTAGCTCACATTACCATAAACAAACATGGCAGCAAGGTATTTAGCTCGTTTTAGCTCAATATC
84767 ATGAACTTACCTTGTTTCCTTGCACATATAGGTACAATGGAGTGTGATGCACGTTGAGGTAGCTT
456 ATGAACTTACCTTGTTTCCTTGCACATATAGGTACAATGGAGTGTGATGCACGTTGAGGTAGCTT
*
84832 GGTGAATGATTTGGACGTCATATATAGCTCACAAATAGCTCACAAAGTACAAGGCAGCTCATGGA
521 GGTGAATGATTTGGACGTCATATATAGCTCACAAACAGCTCACAAAGTACAAGGCAGCTCATGGA
* *
84897 ATGCTAAGGGAAGCTCGATTCAGCTGGAGACGCTTCAGGCTAGCTAAACTTAGCTAGTTGGACTA
586 ATGCTAAGGGAAGCTCGATTCAGCTGGAGAAGCTTCAGGCTAGCGAAACTTAGCTAGTTGGACTA
84962 TTTGAAGCTGAGTTGCTAAAAGTGATGACAAAGGTAGCTGAATGTAGCTGAACATGCTGATATGG
651 TTTGAAGCTGAGTTGCTAAAAGTGATGACAAAGGTAGCTGAATGTAGCTGAACATGCTGATATGG
*
85027 AGCTCAAAAGGACTCGGCTAGGAAGATCATTCACAAACAGCCCCATGCTTACTAGCTAGCTCAAC
716 AGCTCAAAAGGACTCAGCTAGGAAGATCATTCACAAACAGCCCCATGCTTACTAGCTAGCTCAAC
* *
85092 ACTCAAGCTAGCTTGGAGGACACATGTACGCCTAAGAAGAAGCACATGACCAGCCATCATCCAAT
781 ACTAAAGCTAGCTTGGAGGACACATGTACGCCTAAGAAAAAGCACATGACCAGCCATCATCCAAT
85157 GCACATGGGTGCACCACAAG
846 GCACATGGGTGCACCACAAG
85177 TGATATAGTCACGTCTACACCAGATCCGGAGGTCATGCCACACGGTCCCATTACTAGGTCAAGGG
1 TGATATAGTCACGTCTACACCAGATCCGGAGGTCATGCCACACGGTCCCATTACTAGGTCAAGGG
*
85242 CGAAACAATTCAGGGAAGTTCTCTTAACTAAGTGTCTTGAAGCTTTTGATTCATTTGATAACTTA
66 CCAAACAATTCAGGGAAGTTCTCTTAACTAAGTGTCTTGAAGCTTTTGATTCATTTGATAACTTA
85307 ACACTCTCTTATGTTATGTTATATAATGTTTTAATAGCTAAAGAATAACTTAGTATGAACACATC
131 ACACTCTCTTATGTTATGTTATATAATGTTTTAATAGCTAAAGAATAACTTAGTATGAACACATC
85372 TTACACATTGTTATTTTTAATATGTTAAGCATGTTAGGATAGTTTTATTATCATATTAAGCATGA
196 TTACACATTGTTATTTTTAATATGTTAAGCATGTTAGGATAGTTTTATTATCATATTAAGCATGA
85437 TTATTATATATACATCAAGGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTCATATT
261 TTA-T-TATATACATCAAGGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTCATATT
85502 AACTCTTAGGCTTTATACATTATCTTACACATATTAGGAGATGATGTACTTAGCTCATGACCATT
324 AACTCTTAGGCTTTATACATTATCTTACACATATTAGGAGATGATGTACTTAGCTCATGACCATT
*
85567 ATACTTAGCTCACATTACCATAAATAAACATGGCAGCAAGGTATTTAGCTCGTTTTAGCTCAATA
389 ATACTTAGCTCACATTACCATAAACAAACATGGCAGCAAGGTATTTAGCTCGTTTTAGCTCAATA
85632 TCATGAACTTACCTTGTTTCCTTGCACATATAGGTACAATGGAGTGTGATGCACGTTGAGGTAGC
454 TCATGAACTTACCTTGTTTCCTTGCACATATAGGTACAATGGAGTGTGATGCACGTTGAGGTAGC
85697 TTGGTGAATGATTTGGACGTCATATATAGCTCACAAACAGCTCACAAAGTACAAGGCAGCTCATG
519 TTGGTGAATGATTTGGACGTCATATATAGCTCACAAACAGCTCACAAAGTACAAGGCAGCTCATG
*
85762 GAATGCTAAGGGAAGCTCGATTCAGCTGGAGAAGCTTCAGGCTAGCGAATCTTAGCTAGTTGGAC
584 GAATGCTAAGGGAAGCTCGATTCAGCTGGAGAAGCTTCAGGCTAGCGAAACTTAGCTAGTTGGAC
85827 TATTTGAAGCTGAGTTGCTAAAAGTGATGACAAAGGTAGCTGAATGTAGCTGAACATGCTGATAT
649 TATTTGAAGCTGAGTTGCTAAAAGTGATGACAAAGGTAGCTGAATGTAGCTGAACATGCTGATAT
*
85892 GGAGCTCAAAAGGACTCAGCTAGGAAGATCATTCACAAACAGCCCCATGCTTGCTAGCTAGCTCA
714 GGAGCTCAAAAGGACTCAGCTAGGAAGATCATTCACAAACAGCCCCATGCTTACTAGCTAGCTCA
85957 ACACTAAAGCTAGCTTGGAGGACACATGTACGCCTAAGAAAAAGCACATGACCAGCCATCATCCA
779 ACACTAAAGCTAGCTTGGAGGACACATGTACGCCTAAGAAAAAGCACATGACCAGCCATCATCCA
86022 ATGCACATGGGTGCACCACAAG
844 ATGCACATGGGTGCACCACAAG
86044 GCTTCCTAGA
Statistics
Matches: 851, Mismatches: 14, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
865 261 0.31
866 1 0.00
867 589 0.69
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (865 bp):
TGATATAGTCACGTCTACACCAGATCCGGAGGTCATGCCACACGGTCCCATTACTAGGTCAAGGG
CCAAACAATTCAGGGAAGTTCTCTTAACTAAGTGTCTTGAAGCTTTTGATTCATTTGATAACTTA
ACACTCTCTTATGTTATGTTATATAATGTTTTAATAGCTAAAGAATAACTTAGTATGAACACATC
TTACACATTGTTATTTTTAATATGTTAAGCATGTTAGGATAGTTTTATTATCATATTAAGCATGA
TTATTATATACATCAAGGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTCATATTAA
CTCTTAGGCTTTATACATTATCTTACACATATTAGGAGATGATGTACTTAGCTCATGACCATTAT
ACTTAGCTCACATTACCATAAACAAACATGGCAGCAAGGTATTTAGCTCGTTTTAGCTCAATATC
ATGAACTTACCTTGTTTCCTTGCACATATAGGTACAATGGAGTGTGATGCACGTTGAGGTAGCTT
GGTGAATGATTTGGACGTCATATATAGCTCACAAACAGCTCACAAAGTACAAGGCAGCTCATGGA
ATGCTAAGGGAAGCTCGATTCAGCTGGAGAAGCTTCAGGCTAGCGAAACTTAGCTAGTTGGACTA
TTTGAAGCTGAGTTGCTAAAAGTGATGACAAAGGTAGCTGAATGTAGCTGAACATGCTGATATGG
AGCTCAAAAGGACTCAGCTAGGAAGATCATTCACAAACAGCCCCATGCTTACTAGCTAGCTCAAC
ACTAAAGCTAGCTTGGAGGACACATGTACGCCTAAGAAAAAGCACATGACCAGCCATCATCCAAT
GCACATGGGTGCACCACAAG
Found at i:91008 original size:13 final size:13
Alignment explanation
Indices: 90986--91015 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
90976 ACTAAACACC
90986 TTTC-ACATACCT
1 TTTCAACATACCT
90998 TTTCAACATACCT
1 TTTCAACATACCT
91011 TTTCA
1 TTTCA
91016 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:93781 original size:18 final size:17
Alignment explanation
Indices: 93760--93801 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 17
93750 TTTTTTTCTT
93760 TTTCTTCTTTTTGAGTG
1 TTTCTTCTTTTTGAGTG
*
93777 CTTTCAATCTTTTTGAGTG
1 -TTTC-TTCTTTTTGAGTG
93796 TTTCTT
1 TTTCTT
93802 TTTCCTTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 8 0.38
19 12 0.57
ACGTcount: A:0.10, C:0.14, G:0.14, T:0.62
Consensus pattern (17 bp):
TTTCTTCTTTTTGAGTG
Found at i:96409 original size:19 final size:20
Alignment explanation
Indices: 96385--96426 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
96375 CGTCCAAGAG
*
96385 CATGTATCTTCAT-TAAAAT
1 CATGTATCTTCATCAAAAAT
*
96404 CATGTATTTTCATCAAAAAT
1 CATGTATCTTCATCAAAAAT
96424 CAT
1 CAT
96427 ATATTTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (20 bp):
CATGTATCTTCATCAAAAAT
Found at i:96424 original size:20 final size:19
Alignment explanation
Indices: 96385--96432 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
96375 CGTCCAAGAG
* *
96385 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATAAAAAT
96404 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCAT-AAAAAT
*
96424 CATATATTT
1 CATGTATTT
96433 ATAAAGGGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATAAAAAT
Found at i:99197 original size:24 final size:24
Alignment explanation
Indices: 99169--99223 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
99159 AAAAAACATA
* *
99169 AAAGAAATTTAAGCACTCCAAAAG
1 AAAGAAATTCAAGCACTCAAAAAG
*
99193 AAAGAAAATTCCAGCACTCAAAAAG
1 AAAG-AAATTCAAGCACTCAAAAAG
99218 -AAGAAA
1 AAAGAAA
99224 AAAACAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 3 0.11
24 7 0.26
25 17 0.63
ACGTcount: A:0.58, C:0.16, G:0.13, T:0.13
Consensus pattern (24 bp):
AAAGAAATTCAAGCACTCAAAAAG
Found at i:100381 original size:35 final size:36
Alignment explanation
Indices: 100334--100401 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
100324 ATTTAGAAGT
*
100334 TGGTGATAATATAGGCGTTAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
100369 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
100402 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:106847 original size:13 final size:13
Alignment explanation
Indices: 106825--106854 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
106815 ACTAAACACC
106825 TTTC-ACATACCT
1 TTTCAACATACCT
106837 TTTCAACATACCT
1 TTTCAACATACCT
106850 TTTCA
1 TTTCA
106855 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:111597 original size:18 final size:20
Alignment explanation
Indices: 111574--111615 Score: 70
Period size: 18 Copynumber: 2.2 Consensus size: 20
111564 GATGTAGGAG
111574 TGTTTTTTTTTCTT-TTT-T
1 TGTTTTTTTTTCTTCTTTAT
111592 TGTTTTTTTTTCTTCTTTAT
1 TGTTTTTTTTTCTTCTTTAT
111612 TGTT
1 TGTT
111616 GCTTTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 14 0.64
19 3 0.14
20 5 0.23
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.83
Consensus pattern (20 bp):
TGTTTTTTTTTCTTCTTTAT
Found at i:111602 original size:21 final size:23
Alignment explanation
Indices: 111576--111624 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
111566 TGTAGGAGTG
*
111576 TTTTTTT-TTCTTT-TT-TTGTT
1 TTTTTTTCTTCTTTATTGTTGCT
111596 TTTTTTTCTTCTTTATTGTTGCT
1 TTTTTTTCTTCTTTATTGTTGCT
111619 TTTTTT
1 TTTTTT
111625 GTTATAGCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 7 0.28
21 6 0.24
22 2 0.08
23 10 0.40
ACGTcount: A:0.02, C:0.08, G:0.06, T:0.84
Consensus pattern (23 bp):
TTTTTTTCTTCTTTATTGTTGCT
Found at i:111851 original size:17 final size:17
Alignment explanation
Indices: 111812--111856 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
111802 AAAATAGAAT
* *
111812 ATGAAAGAAGAAAGGAA
1 ATGATAGAAAAAAGGAA
111829 ATGATA-AAAAAAGGAA
1 ATGATAGAAAAAAGGAA
111845 ATGGATAGAAAA
1 AT-GATAGAAAA
111857 GTTTTTGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 11 0.46
17 9 0.38
18 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.11
Consensus pattern (17 bp):
ATGATAGAAAAAAGGAA
Found at i:112044 original size:35 final size:36
Alignment explanation
Indices: 111996--112063 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
111986 ATTTAGAAGT
111996 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
**
112031 TGGTGATGTTATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
112064 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.28, C:0.03, G:0.37, T:0.32
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:112079 original size:36 final size:35
Alignment explanation
Indices: 111991--112079 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 35
111981 TGGAAATTTA
* **
111991 GAAGTTGGTGATAATATAGGCGTGATATGGTGATG
1 GAAGATGGTGATCTTATAGGCGTGATATGGTGATG
* *
112026 GAATATGGTGATGTTATAGGCGTGATAATGGTGATG
1 GAAGATGGTGATCTTATAGGCGTGAT-ATGGTGATG
*
112062 GACAGATTGT-ATCTTATA
1 GA-AGATGGTGATCTTATA
112080 AAACTATGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
35 22 0.49
36 18 0.40
37 5 0.11
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.34
Consensus pattern (35 bp):
GAAGATGGTGATCTTATAGGCGTGATATGGTGATG
Found at i:113065 original size:35 final size:37
Alignment explanation
Indices: 113019--113093 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
113009 GAATTTTGTT
* *
113019 ATGATATAGGCGTG-TTATGG-TGATGGACTATGGTG
1 ATGATATAGGCGTGATAATGGAAGATGGACTATGGTG
*
113054 ATGATATAGGCGTGATAATGGAAGATGGATTATGGTG
1 ATGATATAGGCGTGATAATGGAAGATGGACTATGGTG
113091 ATG
1 ATG
113094 GAAATAGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 14 0.40
36 5 0.14
37 16 0.46
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.32
Consensus pattern (37 bp):
ATGATATAGGCGTGATAATGGAAGATGGACTATGGTG
Found at i:117006 original size:35 final size:37
Alignment explanation
Indices: 116960--117039 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
116950 TTTGAGAATT
*
116960 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
116995 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
117032 TGGTGATG
1 TGGTGATG
117040 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:118986 original size:8 final size:8
Alignment explanation
Indices: 118973--118999 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
118963 TAAGTAATAT
118973 AATGTATA
1 AATGTATA
118981 AATGTATA
1 AATGTATA
118989 AATGTATA
1 AATGTATA
118997 AAT
1 AAT
119000 ATGTGGTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (8 bp):
AATGTATA
Found at i:123606 original size:24 final size:21
Alignment explanation
Indices: 123571--123613 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
123561 GGCTCATTCT
*
123571 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
123594 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
123614 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:139779 original size:36 final size:36
Alignment explanation
Indices: 139727--139809 Score: 148
Period size: 36 Copynumber: 2.3 Consensus size: 36
139717 GATACTATTT
*
139727 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
139763 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
139799 TCATCACCATA
1 TCATCACCATA
139810 TCACGCCAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:139811 original size:22 final size:23
Alignment explanation
Indices: 139777--139826 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
139767 CACCATAGTC
* *
139777 CATCACCATTATCACGCCTATAT
1 CATCACCATTATCACGCCAATAA
139800 CATCACCA-TATCACGCCAATAA
1 CATCACCATTATCACGCCAATAA
139822 CATCA
1 CATCA
139827 TCCTTCCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.36, C:0.36, G:0.04, T:0.24
Consensus pattern (23 bp):
CATCACCATTATCACGCCAATAA
Found at i:141661 original size:30 final size:30
Alignment explanation
Indices: 141627--141702 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
141617 AAGGAGCTTC
* * *
141627 AACTTAGCCGGAGGAGCTAGCATGTAGTTG
1 AACTTAGCTGGAGGAGCTAGCATATAGCTG
141657 AACTTAGCTGGAGGAGCTAGCATATAGCTG
1 AACTTAGCTGGAGGAGCTAGCATATAGCTG
141687 AACTTAGCTGGAGGAG
1 AACTTAGCTGGAGGAG
141703 AGCTTTGGAC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.29, C:0.16, G:0.33, T:0.22
Consensus pattern (30 bp):
AACTTAGCTGGAGGAGCTAGCATATAGCTG
Found at i:142166 original size:19 final size:20
Alignment explanation
Indices: 142142--142191 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
142132 GGCCAAGAGC
*
142142 ATGTATCTTCATT-AAAATA
1 ATGTATTTTCATTAAAAATA
*
142161 ATGTATTTTCATTAAAAATC
1 ATGTATTTTCATTAAAAATA
142181 ATGTATTTTCA
1 ATGTATTTTCA
142192 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (20 bp):
ATGTATTTTCATTAAAAATA
Found at i:142720 original size:16 final size:16
Alignment explanation
Indices: 142699--142740 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
142689 CCTTTGATAA
**
142699 CATTTCTTTCCCCTTT
1 CATTTCTTTCCAATTT
142715 CATTTCTTAT-CAATTT
1 CATTTCTT-TCCAATTT
142731 CATTTCTTTC
1 CATTTCTTTC
142741 ATTTCTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (16 bp):
CATTTCTTTCCAATTT
Found at i:145508 original size:19 final size:20
Alignment explanation
Indices: 145484--145534 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
145474 GGGCCAAGAG
* *
145484 CATGTATCTTCATTCA-AAT
1 CATGTATTTTCATTAAGAAT
145503 CATGTATTTTCATTAAGAAT
1 CATGTATTTTCATTAAGAAT
145523 CATGTATTTTCA
1 CATGTATTTTCA
145535 AAGGAGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.45
Consensus pattern (20 bp):
CATGTATTTTCATTAAGAAT
Found at i:147655 original size:12 final size:13
Alignment explanation
Indices: 147625--147653 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
147615 GAAAAAAATA
147625 CAAAAG-GAAGTG
1 CAAAAGTGAAGTG
147637 CAAAAGTGAAGTG
1 CAAAAGTGAAGTG
147650 CAAA
1 CAAA
147654 GTCAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.52, C:0.10, G:0.28, T:0.10
Consensus pattern (13 bp):
CAAAAGTGAAGTG
Found at i:149742 original size:7 final size:8
Alignment explanation
Indices: 149728--149791 Score: 76
Period size: 8 Copynumber: 8.0 Consensus size: 8
149718 ATTTTTTTTT
149728 CAAAAAAA
1 CAAAAAAA
149736 CAAAAAAA
1 CAAAAAAA
149744 CAAAAAAA
1 CAAAAAAA
149752 CAAAAAAA
1 CAAAAAAA
**
149760 GGTAAAAAA
1 -CAAAAAAA
**
149769 -AAAAAGG
1 CAAAAAAA
149776 CAAAAAAA
1 CAAAAAAA
149784 CAAAAAAA
1 CAAAAAAA
149792 GAGCCAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
7 4 0.09
8 37 0.79
9 6 0.13
ACGTcount: A:0.83, C:0.09, G:0.06, T:0.02
Consensus pattern (8 bp):
CAAAAAAA
Found at i:149769 original size:13 final size:14
Alignment explanation
Indices: 149748--149788 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
149738 AAAAAACAAA
*
149748 AAAACAAAAAAAGGT
1 AAAA-AAAAAAAGGC
149763 AAAAAAAAAAAGGC
1 AAAAAAAAAAAGGC
149777 AAAAAAACAAAA
1 AAAAAAA-AAAA
149789 AAAGAGCCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.80, C:0.07, G:0.10, T:0.02
Consensus pattern (14 bp):
AAAAAAAAAAAGGC
Found at i:149773 original size:32 final size:33
Alignment explanation
Indices: 149730--149792 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
149720 TTTTTTTTCA
149730 AAAAAACAAAAAAACAAAAAAACAAAAAAAGGT
1 AAAAAACAAAAAAACAAAAAAACAAAAAAAGGT
**
149763 AAAAAA-AAAAAGGCAAAAAAACAAAAAAAG
1 AAAAAACAAAAAAACAAAAAAACAAAAAAAG
149793 AGCCAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 22 0.79
33 6 0.21
ACGTcount: A:0.83, C:0.08, G:0.08, T:0.02
Consensus pattern (33 bp):
AAAAAACAAAAAAACAAAAAAACAAAAAAAGGT
Found at i:149800 original size:19 final size:17
Alignment explanation
Indices: 149728--149802 Score: 61
Period size: 16 Copynumber: 4.4 Consensus size: 17
149718 ATTTTTTTTT
149728 CAAAAAAACAAAAAAA--
1 CAAAAAAA-AAAAAAAGG
149744 CAAAAAAACAAAAAAAGG
1 CAAAAAAA-AAAAAAAGG
*
149762 ---TAAAAAAAAAAAGG
1 CAAAAAAAAAAAAAAGG
149776 CAAAAAAACAAAAAAAGAG
1 CAAAAAAA-AAAAAAAG-G
149795 CCAAAAAA
1 -CAAAAAA
149803 GCCAAAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
14 9 0.18
15 4 0.08
16 16 0.33
17 4 0.08
18 8 0.16
19 1 0.02
20 7 0.14
ACGTcount: A:0.80, C:0.11, G:0.08, T:0.01
Consensus pattern (17 bp):
CAAAAAAAAAAAAAAGG
Found at i:149809 original size:20 final size:20
Alignment explanation
Indices: 149765--149802 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
149755 AAAAAGGTAA
*
149765 AAAAAAAAAGGCAAAAAAAC
1 AAAAAAAAAGCCAAAAAAAC
*
149785 AAAAAAAGAGCCAAAAAA
1 AAAAAAAAAGCCAAAAAA
149803 GCCAAAATTT
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:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGCCAAAAAAAC
Found at i:159922 original size:6 final size:6
Alignment explanation
Indices: 159896--159939 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
159886 AAAAGCAACA
159896 AAAAGAG AAAAAG AAAGAAG AAAAAG AAAAAG -AAAAG AAAAAG A
1 AAAA-AG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
159940 CTCCTACATC
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.14
6 20 0.57
7 10 0.29
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:159925 original size:19 final size:17
Alignment explanation
Indices: 159896--159939 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 17
159886 AAAAGCAACA
159896 AAAAGAGAAAAAGAAAGAAG
1 AAAA-AGAAAAAG-AA-AAG
159916 AAAAAGAAAAAGAAAAG
1 AAAAAGAAAAAGAAAAG
159933 AAAAAGA
1 AAAAAGA
159940 CTCCTACATC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.42
18 2 0.08
19 8 0.33
20 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAGAAAAG
Found at i:159933 original size:11 final size:11
Alignment explanation
Indices: 159904--159939 Score: 54
Period size: 11 Copynumber: 3.1 Consensus size: 11
159894 CAAAAAGAGA
159904 AAAAGAAAGAAG
1 AAAAGAAA-AAG
159916 AAAAAGAAAAAG
1 -AAAAGAAAAAG
159928 AAAAGAAAAAG
1 AAAAGAAAAAG
159939 A
1 A
159940 CTCCTACATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 12 0.52
12 3 0.13
13 8 0.35
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:164866 original size:19 final size:20
Alignment explanation
Indices: 164844--164886 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
164834 AGCATGTGAC
164844 TTCATT-AAAATCATGTATT
1 TTCATTAAAAATCATGTATT
164863 TTCATTAAAAATCATGTATT
1 TTCATTAAAAATCATGTATT
164883 TTCA
1 TTCA
164887 AAGGGGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.47
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:169687 original size:33 final size:34
Alignment explanation
Indices: 169621--169725 Score: 92
Period size: 33 Copynumber: 3.1 Consensus size: 34
169611 GCCTTGTTGA
* * *
169621 TGAATG-AAGGATGAT-TTAATGGTGATGAAATGG
1 TGAATGAAAGGATGATGTTATTGGCG-TGATATGG
169654 T-AATGAAAGGATGATGTTATTGGCGTGATATGG
1 TGAATGAAAGGATGATGTTATTGGCGTGATATGG
* * *
169687 TGAAGGAATATGG-TGATGATATAGGCGTGATAATGG
1 TGAATGAA-A-GGATGATGTTATTGGCGTGAT-ATGG
169723 TGA
1 TGA
169726 TGGACTATGG
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
32 4 0.07
33 18 0.30
34 12 0.20
35 17 0.28
36 9 0.15
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.30
Consensus pattern (34 bp):
TGAATGAAAGGATGATGTTATTGGCGTGATATGG
Found at i:169735 original size:36 final size:36
Alignment explanation
Indices: 169665--169777 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
169655 AATGAAAGGA
* * *
169665 TGATGTTATTGGCGTGAT-ATGGTGAAGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
169700 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
169736 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
169772 TGATGA
1 TGATGA
169778 AAATAGTATC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 55 0.77
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:175449 original size:33 final size:33
Alignment explanation
Indices: 175407--175475 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
175397 GTTGATGAAT
*
175407 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
175440 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
175473 GAA
1 GAA
175476 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:175480 original size:13 final size:12
Alignment explanation
Indices: 175461--175557 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
175451 TTATTGGCGT
175461 GATATGGTGATG
1 GATATGGTGATG
175473 GAATATGGTGAT-
1 G-ATATGGTGATG
*
175485 GATATAG-GA-G
1 GATATGGTGATG
175495 TGATAATGGTGATG
1 -GAT-ATGGTGATG
175509 GACTATGGTGAT-
1 GA-TATGGTGATG
*
175521 GATATAGGCG-T-
1 GATAT-GGTGATG
*
175532 GATAATGGAGATG
1 GAT-ATGGTGATG
175545 GATTATGGTGATG
1 GA-TATGGTGATG
175558 AAAATAGTAT
Statistics
Matches: 68, Mismatches: 5, Indels: 23
0.71 0.05 0.24
Matches are distributed among these distances:
10 2 0.03
11 18 0.26
12 13 0.19
13 32 0.47
14 3 0.04
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:175510 original size:36 final size:36
Alignment explanation
Indices: 175459--175558 Score: 157
Period size: 36 Copynumber: 2.8 Consensus size: 36
175449 TGTTATTGGC
175459 GTGAT-ATGGTGATGGAATATGGTGATGATATAGGA
1 GTGATAATGGTGATGGAATATGGTGATGATATAGGA
* *
175494 GTGATAATGGTGATGGACTATGGTGATGATATAGGC
1 GTGATAATGGTGATGGAATATGGTGATGATATAGGA
* *
175530 GTGATAATGGAGATGGATTATGGTGATGA
1 GTGATAATGGTGATGGAATATGGTGATGA
175559 AAATAGTATC
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 5 0.08
36 55 0.92
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.31
Consensus pattern (36 bp):
GTGATAATGGTGATGGAATATGGTGATGATATAGGA
Done.