Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005507.1 Hibiscus syriacus cultivar Beakdansim tig00012699_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: 115563
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:9448 original size:23 final size:22
Alignment explanation
Indices: 9422--9483 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
9412 TAATAACCAT
* *
9422 ACACGCATATATATCACATATTC
1 ACACACATATATAT-ACAAATTC
*
9445 ACACACATATAATATATAAATTC
1 ACACACATAT-ATATACAAATTC
9468 ACACACATGATATATA
1 ACACACAT-ATATATA
9484 TTTAAATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 28 0.82
24 6 0.18
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (22 bp):
ACACACATATATATACAAATTC
Found at i:9484 original size:25 final size:23
Alignment explanation
Indices: 9441--9490 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
9431 TATATCACAT
9441 ATTCACACACATATAATATATAA
1 ATTCACACACATATAATATATAA
*
9464 ATTCACACACATGATATATATTTAA
1 ATTCACACACAT-ATA-ATATATAA
9489 AT
1 AT
9491 AATATGCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 12 0.50
24 3 0.12
25 9 0.38
ACGTcount: A:0.48, C:0.16, G:0.02, T:0.34
Consensus pattern (23 bp):
ATTCACACACATATAATATATAA
Found at i:10673 original size:46 final size:46
Alignment explanation
Indices: 10617--10731 Score: 144
Period size: 46 Copynumber: 2.5 Consensus size: 46
10607 TTGGTTTCGG
* * * *
10617 TTCGGGTCAATTCTGGTTGGTTTCGGTTCGAATCAACTTTTAGATT
1 TTCGGATCAATTCGGGTTGGTTTCGGTTCAAATCAACCTTTAGATT
* *
10663 TTCGGATCAATTCGGGTTTGTTTTGGTTCAAATCAACCTTTAGATT
1 TTCGGATCAATTCGGGTTGGTTTCGGTTCAAATCAACCTTTAGATT
*
10709 TTC-GAGCTAATTCGGGTT-GTTTC
1 TTCGGATC-AATTCGGGTTGGTTTC
10732 TGTTTAGGTC
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
45 7 0.12
46 53 0.88
ACGTcount: A:0.18, C:0.16, G:0.23, T:0.43
Consensus pattern (46 bp):
TTCGGATCAATTCGGGTTGGTTTCGGTTCAAATCAACCTTTAGATT
Found at i:11099 original size:3 final size:3
Alignment explanation
Indices: 11086--11139 Score: 99
Period size: 3 Copynumber: 17.7 Consensus size: 3
11076 AATTACTAAA
11086 AAT AGAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11132 AAT AAT AA
1 AAT AAT AA
11140 ATTATTATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11253 original size:16 final size:16
Alignment explanation
Indices: 11232--11347 Score: 85
Period size: 16 Copynumber: 7.3 Consensus size: 16
11222 TTTGAGTTGC
11232 TTTCGGTTCGGGTTAT
1 TTTCGGTTCGGGTTAT
* *
11248 TTTCGGTTTGGATT-T
1 TTTCGGTTCGGGTTAT
**
11263 TTTTTGTTCGGGTTGA-
1 TTTCGGTTCGGGTT-AT
* **
11279 TTTCAGTTCGGGTTGC
1 TTTCGGTTCGGGTTAT
11295 TTTCGGTTC-GGTTATT
1 TTTCGGTTCGGGTTA-T
* * *
11311 TTTCAGTTTGGGTTAC
1 TTTCGGTTCGGGTTAT
* *
11327 TTTCGGTTCGAGTTAA
1 TTTCGGTTCGGGTTAT
11343 TTTCG
1 TTTCG
11348 TTTAAACTAT
Statistics
Matches: 76, Mismatches: 19, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
15 15 0.20
16 56 0.74
17 5 0.07
ACGTcount: A:0.09, C:0.12, G:0.28, T:0.52
Consensus pattern (16 bp):
TTTCGGTTCGGGTTAT
Found at i:11315 original size:32 final size:33
Alignment explanation
Indices: 11279--11341 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
11269 TTCGGGTTGA
*
11279 TTTCAGTTCGGGTTGCTTTCGGTTCG-GTTATT
1 TTTCAGTTCGGGTTACTTTCGGTTCGAGTTATT
*
11311 TTTCAGTTTGGGTTACTTTCGGTTCGAGTTA
1 TTTCAGTTCGGGTTACTTTCGGTTCGAGTTA
11342 ATTTCGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.10, C:0.14, G:0.27, T:0.49
Consensus pattern (33 bp):
TTTCAGTTCGGGTTACTTTCGGTTCGAGTTATT
Found at i:16148 original size:44 final size:44
Alignment explanation
Indices: 16086--16186 Score: 175
Period size: 44 Copynumber: 2.3 Consensus size: 44
16076 GAAACAAATA
* *
16086 AAAAATATTATATGATTCATATGGTATATATTTTATTAGTTCTT
1 AAAAATATTATATGATTCACATGGTATATATTTTATTAGTTATT
16130 AAAAATATTATATGATTCACATGGTATATATTTTATTAGTTATT
1 AAAAATATTATATGATTCACATGGTATATATTTTATTAGTTATT
*
16174 AAAAACATTATAT
1 AAAAATATTATAT
16187 TTCCATTACC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.47
Consensus pattern (44 bp):
AAAAATATTATATGATTCACATGGTATATATTTTATTAGTTATT
Found at i:16259 original size:123 final size:122
Alignment explanation
Indices: 16132--16571 Score: 650
Period size: 123 Copynumber: 3.7 Consensus size: 122
16122 TAGTTCTTAA
16132 AAATATTATATGATTCACATGGTATATATTTTATTAGTTATTAAAAACATTATATTTCCATTACC
1 AAATATTATATGATTCACATGGTATATATTTTATTAGTTATTAAAAACATTATATTTCCATTACC
* * *
16197 AACGGCAATGAAACCAAAAG-AACATGGTATATTAAAAATATATTTGATTTTACTTGAT
66 AACGGCAATGAACCCGAAAGCAA-ATGATATATTAAAAA-ATATTTGATTTTACTTGAT
16255 AAATATTATATGATTCACATGGTATATATTTTATTAGTTATTAAAAACATTATATTTCCATTACC
1 AAATATTATATGATTCACATGGTATATATTTTATTAGTTATTAAAAACATTATATTTCCATTACC
*
16320 AACGGCAATGAACCCGAAAGCAAATGATATATTAAAAAATATTTGATTTTACTTGTT
66 AACGGCAATGAACCCGAAAGCAAATGATATATTAAAAAATATTTGATTTTACTTGAT
* * *
16377 AAATATTATATGATTCACATGGTATGTA----GTTA-TTA--AAAAATATTATATTTCCATTACC
1 AAATATTATATGATTCACATGGTATATATTTTATTAGTTATTAAAAACATTATATTTCCATTACC
* *
16435 AACGGCAATGAACCCGAAAGCAAATGATATATTAAAAAAATATTTGATTGTATTTGAT
66 AACGGCAATGAACCCGAAAGCAAATGATATATT-AAAAAATATTTGATTTTACTTGAT
** *
16493 -AA-A-TATATGATTCACATGGTATGCATTTTATTAATTATTAAAAAAACATTATATTTCCATTA
1 AAATATTATATGATTCACATGGTATATATTTTATTAGTTATT--AAAAACATTATATTTCCATTA
16555 CCAACGGCAATGAACCC
64 CCAACGGCAATGAACCC
16572 TAGGGTGTTA
Statistics
Matches: 293, Mismatches: 13, Indels: 23
0.89 0.04 0.07
Matches are distributed among these distances:
113 21 0.07
114 1 0.00
115 57 0.19
116 21 0.07
117 6 0.02
118 6 0.02
122 82 0.28
123 97 0.33
124 2 0.01
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (122 bp):
AAATATTATATGATTCACATGGTATATATTTTATTAGTTATTAAAAACATTATATTTCCATTACC
AACGGCAATGAACCCGAAAGCAAATGATATATTAAAAAATATTTGATTTTACTTGAT
Found at i:16455 original size:115 final size:114
Alignment explanation
Indices: 16165--16571 Score: 482
Period size: 122 Copynumber: 3.4 Consensus size: 114
16155 ATATATTTTA
* * *
16165 TTAGTTATT-AAAAACATTATATTTCCATTACCAACGGCAATGAAACCAAAAG-AACATGGTATA
1 TTAGTTATTAAAAAACATTATATTTCCATTACCAACGGCAATGAACCCGAAAGCAA-ATGATATA
* * *
16228 TTAAAAATATATTTGATTTTACTTGATAAATATTATATGATTCACATGGTATATATT
65 TTAAAAAAATATTTGATTGTACTTGAT-AA-A-TATATGATTCACATGG----TATG
16285 TTA-TTAGTTATTAAAAACATTATATTTCCATTACCAACGGCAATGAACCCGAAAGCAAATGATA
1 TTAGTTA-TTA--AAAAACATTATATTTCCATTACCAACGGCAATGAACCCGAAAGCAAATGATA
* *
16349 TATT-AAAAAATATTTGATTTTACTTGTTAAATATTATATGATTCACATGGTATG
63 TATTAAAAAAATATTTGATTGTACTTGAT-AA-A-TATATGATTCACATGGTATG
*
16403 -TAGTTATTAAAAAATATTATATTTCCATTACCAACGGCAATGAACCCGAAAGCAAATGATATAT
1 TTAGTTATTAAAAAACATTATATTTCCATTACCAACGGCAATGAACCCGAAAGCAAATGATATAT
*
16467 TAAAAAAATATTTGATTGTATTTGATAAATATATGATTCACATGGTATG
66 TAAAAAAATATTTGATTGTACTTGATAAATATATGATTCACATGGTATG
*
16516 CATTTTATTAATTATTAAAAAAACATTATATTTCCATTACCAACGGCAATGAACCC
1 -------TTAGTTATT-AAAAAACATTATATTTCCATTACCAACGGCAATGAACCC
16572 TAGGGTGTTA
Statistics
Matches: 259, Mismatches: 12, Indels: 30
0.86 0.04 0.10
Matches are distributed among these distances:
113 20 0.08
114 1 0.00
115 57 0.22
116 21 0.08
117 5 0.02
118 6 0.02
119 3 0.01
120 5 0.02
121 7 0.03
122 82 0.32
123 50 0.19
124 2 0.01
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.36
Consensus pattern (114 bp):
TTAGTTATTAAAAAACATTATATTTCCATTACCAACGGCAATGAACCCGAAAGCAAATGATATAT
TAAAAAAATATTTGATTGTACTTGATAAATATATGATTCACATGGTATG
Found at i:16611 original size:13 final size:13
Alignment explanation
Indices: 16593--16617 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16583 AAAAACTCGA
16593 AACCGTTAATCGT
1 AACCGTTAATCGT
16606 AACCGTTAATCG
1 AACCGTTAATCG
16618 GTATAACTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (13 bp):
AACCGTTAATCGT
Found at i:16664 original size:31 final size:32
Alignment explanation
Indices: 16629--16688 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
16619 TATAACTATT
* *
16629 ATATTTAACA-TATTAATTAACCGAACCGTTA
1 ATATTAAACAGTATTAATTAACCAAACCGTTA
* *
16660 ATATTAAACAGTTTTGATTAACCAAACCG
1 ATATTAAACAGTATTAATTAACCAAACCG
16689 CTAAAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 9 0.38
32 15 0.62
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (32 bp):
ATATTAAACAGTATTAATTAACCAAACCGTTA
Found at i:17120 original size:50 final size:51
Alignment explanation
Indices: 16987--17181 Score: 259
Period size: 50 Copynumber: 3.8 Consensus size: 51
16977 ATATGTACAT
** ** * *
16987 ACTTACATTGGTGTAAGTATGTGTTAAGCACTACACTTTTTTTTATTGTATTT
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACAC--TTTTTTATTTTATTC
* * *
17040 ACTTACACCGTTGTAAGTATATGTTAAGTGCTATACTTTTTTATTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
*
17091 ACTTACACCGGTGTAA-TATGTGTTAAGTGCTATACTTTTTTATTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
*
17141 ACTTACACCGGTGT-AGTATGTGTTAAGTGCTACATTTTTTT
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTT
17182 TTGTATATTG
Statistics
Matches: 128, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
49 1 0.01
50 70 0.55
51 28 0.22
53 29 0.23
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (51 bp):
ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
Found at i:17150 original size:101 final size:102
Alignment explanation
Indices: 16987--17181 Score: 259
Period size: 101 Copynumber: 1.9 Consensus size: 102
16977 ATATGTACAT
** * *
16987 ACTTACATTGGTGTAAGTATGTGTTAAGCACTACACTTTTTTTTATTGTATTTACTTACACCGTT
1 ACTTACACCGGTGTAAGTATGTGTTAAGCACTACAC-TTTTTTTATTGTATTCACTTACACCGGT
*
17052 GTAAGTATATGTTAAGTGCTATACTTTTTTATTTTATTC
65 GT-AGTATATGTTAAGTGCTACACTTTTTTATTTTATTC
** * *
17091 ACTTACACCGGTGTAA-TATGTGTTAAGTGCTATAC-TTTTTTATTTTATTCACTTACACCGGTG
1 ACTTACACCGGTGTAAGTATGTGTTAAGCACTACACTTTTTTTATTGTATTCACTTACACCGGTG
* *
17154 TAGTATGTGTTAAGTGCTACATTTTTTT
66 TAGTATATGTTAAGTGCTACACTTTTTT
17182 TTGTATATTG
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
100 24 0.30
101 26 0.32
103 16 0.20
104 14 0.17
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (102 bp):
ACTTACACCGGTGTAAGTATGTGTTAAGCACTACACTTTTTTTATTGTATTCACTTACACCGGTG
TAGTATATGTTAAGTGCTACACTTTTTTATTTTATTC
Found at i:22901 original size:21 final size:21
Alignment explanation
Indices: 22871--22939 Score: 129
Period size: 21 Copynumber: 3.3 Consensus size: 21
22861 TAATTTTCAA
*
22871 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
22892 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
22913 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
22934 ACATTG
1 ACATTG
22940 CAATATTAGG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:23867 original size:23 final size:23
Alignment explanation
Indices: 23802--23871 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
23792 CTCCTCAAAA
* *
23802 CCTAAAAATT-CTAAGAGATAAAT
1 CCTAAAAATTAC-AAAAGATAATT
23825 CCTAATAAA-TAC-AAAGATAATT
1 CCTAA-AAATTACAAAAGATAATT
23847 CCTAAAAATTACAAAAGATAATT
1 CCTAAAAATTACAAAAGATAATT
23870 CC
1 CC
23872 GTTTGAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 3 0.07
22 16 0.39
23 18 0.44
24 4 0.10
ACGTcount: A:0.53, C:0.16, G:0.06, T:0.26
Consensus pattern (23 bp):
CCTAAAAATTACAAAAGATAATT
Found at i:25922 original size:60 final size:60
Alignment explanation
Indices: 25786--25922 Score: 141
Period size: 60 Copynumber: 2.3 Consensus size: 60
25776 ATTCTTAGAA
* * * *
25786 AAGGCGCGCTTCATGATCCGCGCTTTACTACCGTGACACCAGCTCAGATAAAACCCTGCG
1 AAGGCGCGCATCATGATCCACACTTTACCACCGTGACACCAGCTCAGATAAAACCCTGCG
* * * * * * *
25846 AAGGCACGAATTATGATCCACACTTTTCCACTGTGGCACCAGCTC-GAATAAAACTCTGCG
1 AAGGCGCGCATCATGATCCACACTTTACCACCGTGACACCAGCTCAG-ATAAAACCCTGCG
* *
25906 AATGCGCGCCTCATGAT
1 AAGGCGCGCATCATGAT
25923 TCACTATTTG
Statistics
Matches: 60, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
59 1 0.02
60 59 0.98
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (60 bp):
AAGGCGCGCATCATGATCCACACTTTACCACCGTGACACCAGCTCAGATAAAACCCTGCG
Found at i:26081 original size:25 final size:25
Alignment explanation
Indices: 26053--26133 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
26043 ATAATTTCAT
*
26053 TTAATTAGATCTATTGTGATTTTAA
1 TTAATTAGATCTAATGTGATTTTAA
* ** *
26078 TTAATTAG-TATAAAATAATTTT-A
1 TTAATTAGATCTAATGTGATTTTAA
* *
26101 TTCAGTTAGATCTACTGTGATTTTAA
1 TT-AATTAGATCTAATGTGATTTTAA
26127 TTAATTA
1 TTAATTA
26134 TTAGAAGAAT
Statistics
Matches: 41, Mismatches: 12, Indels: 6
0.69 0.20 0.10
Matches are distributed among these distances:
23 3 0.07
24 14 0.34
25 21 0.51
26 3 0.07
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (25 bp):
TTAATTAGATCTAATGTGATTTTAA
Found at i:26097 original size:49 final size:49
Alignment explanation
Indices: 26028--26183 Score: 201
Period size: 49 Copynumber: 3.2 Consensus size: 49
26018 TTGCCTAAAC
* * *
26028 ATTAATTAGTA-AAATATAATTTCATTTAATTAGATCTATTGTGATTTTA
1 ATTAATTAGTATAAA-ATAATTTTATTCAATTAGATCTACTGTGATTTTA
*
26077 ATTAATTAGTATAAAATAATTTTATTCAGTTAGATCTACTGTGATTTTA
1 ATTAATTAGTATAAAATAATTTTATTCAATTAGATCTACTGTGATTTTA
* * ** *
26126 ATTAATTA-T-TAGAAGAATTTTATTCAATTAGATCCGCTGTTATTTTA
1 ATTAATTAGTATAAAATAATTTTATTCAATTAGATCTACTGTGATTTTA
26173 ATTAATTAGTA
1 ATTAATTAGTA
26184 AAAGAGATCC
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
47 40 0.43
48 2 0.02
49 49 0.52
50 3 0.03
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (49 bp):
ATTAATTAGTATAAAATAATTTTATTCAATTAGATCTACTGTGATTTTA
Found at i:26535 original size:24 final size:24
Alignment explanation
Indices: 26466--26539 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 24
26456 AGGGCAAAGG
*
26466 AGAAGATAATTTTATTTAATTAGAT
1 AGAATATAATTTTA-TTAATTAGAT
** * *
26491 CCACTATGATTTTAATTAATTAG-T
1 AGAATATAATTTT-ATTAATTAGAT
26515 AGAATATAATTTTATTCAATTAGAT
1 AGAATATAATTTTATT-AATTAGAT
26540 CCATTATCAA
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
23 3 0.08
24 16 0.43
25 17 0.46
26 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (24 bp):
AGAATATAATTTTATTAATTAGAT
Found at i:30153 original size:7 final size:7
Alignment explanation
Indices: 30141--30166 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
30131 ATAATAAAGA
30141 TTTGAAT
1 TTTGAAT
30148 TTTGAAT
1 TTTGAAT
30155 TTTGAAT
1 TTTGAAT
30162 TTTGA
1 TTTGA
30167 TTGTAGCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
TTTGAAT
Found at i:34763 original size:185 final size:185
Alignment explanation
Indices: 34415--34873 Score: 546
Period size: 184 Copynumber: 2.4 Consensus size: 185
34405 ATTTGCCTGT
* * * ** *
34415 CATCCCTTTTTCACCCTGAAACATGCAGTTCAGCATTGAATTCTATAAATAAAACTCTCTGAATT
1 CATCCTTTTTTCACACTAAAACATGCAGTTCAGCAGAGAATTCTATAAATAAAGCTCTCTGAATT
* * * *
34480 CCGAATGAAGGAAAAATAACAAAAACACGGGGGAAAAGATTAACTTTTCACTTCATTAACTTCAA
66 CAGAATTAAGGAAAAATAACAAAAACAAGAGGGAAAAGATTAACTTTTCACTTCATTAACTTCAA
* * *
34545 ATTCTCAACAAAATCACCACTAAAATGACCAC-AAGTACTAAAACAGACGTCTTC
131 ATTCTCAACAAAACCACCACTAAAATCACCACAAAGTACCAAAACAGACGTCTTC
* *
34599 CATCCTTTTTTCACACTAAAACATGCAATTCAGGAGAGAATTCTATAAATAAAGCTCTCTGAATT
1 CATCCTTTTTTCACACTAAAACATGCAGTTCAGCAGAGAATTCTATAAATAAAGCTCTCTGAATT
* * * *
34664 CAGAATTAAGGAAATAATAACAAAAACAAGAGGGAAGAGATTCATTTTTCACTTCGTTAACTTC-
66 CAGAATTAAGGAAA-AATAACAAAAACAAGAGGGAAAAGATTAACTTTTCACTTCATTAACTTCA
* * * * *
34728 AATTTTCCAACAAACCCATCACTAAATTCACCACAAAGTACCAAAACAGATGTCTTC
130 AATTCT-CAACAAAACCACCACTAAAATCACCACAAAGTACCAAAACAGACGTCTTC
* * * *
34785 CATCTCTTTTTTTTTCCCCATACTAAGACAGGCAGTTCAGCAGAGAATTCTACAAATAAAGCTCT
1 CATC-C---TTTTTT---CACACTAAAACATGCAGTTCAGCAGAGAATTCTATAAATAAAGCTCT
* *
34850 TTGAATTCAGAA-TAAGGGAAAATA
59 CTGAATTCAGAATTAAGGAAAAATA
34874 TTCATTTTTT
Statistics
Matches: 233, Mismatches: 32, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
184 74 0.32
185 65 0.28
186 24 0.10
187 1 0.00
190 6 0.03
191 4 0.02
192 7 0.03
193 52 0.22
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (185 bp):
CATCCTTTTTTCACACTAAAACATGCAGTTCAGCAGAGAATTCTATAAATAAAGCTCTCTGAATT
CAGAATTAAGGAAAAATAACAAAAACAAGAGGGAAAAGATTAACTTTTCACTTCATTAACTTCAA
ATTCTCAACAAAACCACCACTAAAATCACCACAAAGTACCAAAACAGACGTCTTC
Found at i:37509 original size:18 final size:17
Alignment explanation
Indices: 37488--37543 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 17
37478 AATAATAAAT
37488 TAATTTAAATAAAATTAA
1 TAATTTAAATAAAA-TAA
* *
37506 TAATTT-ATTAAAAATAT
1 TAATTTAAAT-AAAATAA
37523 TATATTTATAATAAAATAA
1 TA-ATTTA-AATAAAATAA
37542 TA
1 TA
37544 GAAAGTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 6 0.20
18 14 0.47
19 8 0.27
20 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATTTAAATAAAATAA
Found at i:43885 original size:2 final size:2
Alignment explanation
Indices: 43878--43905 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43868 TATTGTATTC
43878 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
43906 GAAAAACCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45386 original size:16 final size:16
Alignment explanation
Indices: 45354--45399 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
45344 TGTTTTCTAA
*
45354 TCGGGTTAAAATTCAGT
1 TCGGGTT-AATTTCAGT
*
45371 TCGGGTTACTTTCAGT
1 TCGGGTTAATTTCAGT
45387 TCGGGTTAATTTC
1 TCGGGTTAATTTC
45400 GATTCAGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 19 0.73
17 7 0.27
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (16 bp):
TCGGGTTAATTTCAGT
Found at i:47038 original size:23 final size:23
Alignment explanation
Indices: 46973--47042 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
46963 TCCTCAAAAA
* *
46973 CCTAAAAATT-CTAAGAGATAAAT
1 CCTAAAAATTAC-AAAAGATAATT
46996 CCTAATAAA-TAC-AAAGATAATT
1 CCTAA-AAATTACAAAAGATAATT
47018 CCTAAAAATTACAAAAGATAATT
1 CCTAAAAATTACAAAAGATAATT
47041 CC
1 CC
47043 GTTTGAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 3 0.07
22 16 0.39
23 18 0.44
24 4 0.10
ACGTcount: A:0.53, C:0.16, G:0.06, T:0.26
Consensus pattern (23 bp):
CCTAAAAATTACAAAAGATAATT
Found at i:47819 original size:4 final size:4
Alignment explanation
Indices: 47810--47844 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
47800 CCAAAATATG
47810 TATT TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TAT
47845 ACATGCATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:54967 original size:18 final size:20
Alignment explanation
Indices: 54938--54974 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
54928 TAAATTTATG
54938 ATAAAGTA-TTTTTGAATAT
1 ATAAAGTATTTTTTGAATAT
54957 ATAAA-TATTTTTTGAATA
1 ATAAAGTATTTTTTGAATA
54975 GAAAAGGCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (20 bp):
ATAAAGTATTTTTTGAATAT
Found at i:57407 original size:2 final size:2
Alignment explanation
Indices: 57396--57431 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
57386 TTAATACAAG
57396 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57432 GCAATTTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:67500 original size:18 final size:18
Alignment explanation
Indices: 67477--67524 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
67467 AAATTGTACT
*
67477 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
*
67495 TATTATA-AATTGTAAAA
1 TATTATATATTTGTAAAA
67512 TATTTATATATTT
1 TA-TTATATATTT
67525 TCTTTGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
18 12 0.48
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:68550 original size:17 final size:17
Alignment explanation
Indices: 68528--68571 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
68518 ATATAAAAAT
68528 AAATATTTAAATTTAAA
1 AAATATTTAAATTTAAA
** **
68545 AAATATAAAAATTTATT
1 AAATATTTAAATTTAAA
68562 AAATATTTAA
1 AAATATTTAA
68572 TCATGATTTA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTTAAATTTAAA
Found at i:68628 original size:16 final size:17
Alignment explanation
Indices: 68607--68649 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
68597 ATATAAAAAT
68607 AAATATTTAAATTTA-A
1 AAATATTTAAATTTATA
** *
68623 AAATATAAAAATTTATT
1 AAATATTTAAATTTATA
68640 AAATATTTAA
1 AAATATTTAA
68650 TCAAGTAATG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATTTAAATTTATA
Found at i:79272 original size:20 final size:20
Alignment explanation
Indices: 79247--79287 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
79237 TTCTATCTCG
79247 CAACTGATTTTGTTGTAAAA
1 CAACTGATTTTGTTGTAAAA
79267 CAACTGATTTTGTTGTAAAA
1 CAACTGATTTTGTTGTAAAA
79287 C
1 C
79288 CTACAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (20 bp):
CAACTGATTTTGTTGTAAAA
Found at i:81671 original size:453 final size:450
Alignment explanation
Indices: 80828--81672 Score: 1140
Period size: 453 Copynumber: 1.9 Consensus size: 450
80818 TTAGATTCTA
* * *
80828 TTGGGTTATGGGGTCCAGCGATCACCCTTACAGATTCTATCGTGTATGGACGCGATATCAGGTGC
1 TTGGGTTAGGGGGTCCAGCGATCACCCTTACAGATTCTATCGTATATGGACGCGATATCAGGCGC
* ** * * * * ** *
80893 GTGACAGCCCAACATGTCGAGGTCCACGTGTGCCTTACGAATCCCCTAGGCCAGCCCGTAACACT
66 GTGACAACCCAACATACCAAGGCCCACGTGTGCCTTACGAAGCCCCTAAGCCAGCCCACAACACG
* *
80958 CTATAGATGCAGGGCTCTGCAATACCGTGGTAACTGTGGGGGTGCCCCATAAGAATCCACCTTGA
131 CTATAGATACAGGGCTCTGCAATACCGTGGTAACTGTGGGGGTGCCCCACAAGAATCCACCTTGA
* * * *
81023 CTTGGGGAAACCAGTGATCACCCGCTACAAAAACGTGAGGTTAAAATGACCCACATTCTTATCAT
196 CTTGGGGAAACCAATGATCACCCGCTACAAAAACATGAGGTTAAAATGACCCACATACTTATCAC
* * * *
81088 CAATTTGTTTTAAGAATGAATGATGAACATTCGCTTCAGAACTTTGTAGTTAAGCGTGCTTGAAC
261 CAATTTGTTTTAAGAAGGAATGATAAACATTCGCTTCAGAACTTTGTAGCTAAACGTGCTTGAAC
* * *
81153 CAGAGTAATTCAAGGATGCGTGACCAATTGGTAAGTTGTTCAAAAAATGAATGACTCGATCCTAA
326 CAGAGTAATCCAAGGATGCGTGACCAATTGGGAAGTTGTTCAAAAAATGAATGACTCAATCCTAA
81218 CAAGTGGTATCAGAGCAGGTTGCAGGTTCGAATCCCCTAGGTGTCGCTAGAGGGTGATTG
391 CAAGTGGTATCAGAGCAGGTTGCAGGTTCGAATCCCCTAGGTGTCGCTAGAGGGTGATTG
* * * *
81278 TTGGGTTAGGGGGTCCATCGATCACCCTTA-GGAATTGTATCGTATATGGGCGCGATATCAGGCG
1 TTGGGTTAGGGGGTCCAGCGATCACCCTTACAG-ATTCTATCGTATATGGACGCGATATCAGGCG
* * * *
81342 TGTGACAACCTATTC-TACCAAGGCCCACGTGTGCCTTGCGAAGCCCCTAAGCCAGCCCACAACA
65 CGTGACAACCCA-ACATACCAAGGCCCACGTGTGCCTTACGAAGCCCCTAAGCCAGCCCACAACA
* * *
81406 CGCTATAGATAC-GAGGCTCTGCAATGCCGTGGTAAACTGTGGAGGGTGCCCTACAATAATCCAC
129 CGCTATAGATACAG-GGCTCTGCAATACCGTGGT-AACTGTGG-GGGTGCCCCACAAGAATCCAC
* * * * * * *
81470 CTTGGCTTGGGGGAAACCAATGATTACCTGCTACAAAGATATGAGGTTAAAATGGCCCACCTACT
191 CTTGACTT-GGGGAAACCAATGATCACCCGCTACAAAAACATGAGGTTAAAATGACCCACATACT
* *
81535 TATCACCAA-TTGATTTTAAGAAGGAATGATAAACATTCGCTTTAGAACTTTGTAGCTAAATGTG
255 TATCACCAATTTG-TTTTAAGAAGGAATGATAAACATTCGCTTCAGAACTTTGTAGCTAAACGTG
* * * **
81599 CTTGAACCAGAGTAATCCAAGGATGGGTGACCCATTGGGAGGTTGTTTGAAAAATGAATGACTCA
319 CTTGAACCAGAGTAATCCAAGGATGCGTGACCAATTGGGAAGTTGTTCAAAAAATGAATGACTCA
81664 ATCCTAACA
384 ATCCTAACA
81673 TATTTTTTTT
Statistics
Matches: 337, Mismatches: 51, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
449 2 0.01
450 132 0.39
451 9 0.03
452 28 0.08
453 166 0.49
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.25
Consensus pattern (450 bp):
TTGGGTTAGGGGGTCCAGCGATCACCCTTACAGATTCTATCGTATATGGACGCGATATCAGGCGC
GTGACAACCCAACATACCAAGGCCCACGTGTGCCTTACGAAGCCCCTAAGCCAGCCCACAACACG
CTATAGATACAGGGCTCTGCAATACCGTGGTAACTGTGGGGGTGCCCCACAAGAATCCACCTTGA
CTTGGGGAAACCAATGATCACCCGCTACAAAAACATGAGGTTAAAATGACCCACATACTTATCAC
CAATTTGTTTTAAGAAGGAATGATAAACATTCGCTTCAGAACTTTGTAGCTAAACGTGCTTGAAC
CAGAGTAATCCAAGGATGCGTGACCAATTGGGAAGTTGTTCAAAAAATGAATGACTCAATCCTAA
CAAGTGGTATCAGAGCAGGTTGCAGGTTCGAATCCCCTAGGTGTCGCTAGAGGGTGATTG
Found at i:85448 original size:2 final size:2
Alignment explanation
Indices: 85441--85477 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
85431 TCAGTAATTC
85441 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
85478 CTCTCTCTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:88790 original size:32 final size:31
Alignment explanation
Indices: 88754--88829 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
88744 CGGGGCCATG
*
88754 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
88786 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
88817 GAGCCTACCTAAG
1 GGGCCTACCTAAG
88830 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:90338 original size:18 final size:18
Alignment explanation
Indices: 90315--90349 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
90305 TTCCATCCGG
*
90315 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
90333 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
90350 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:91636 original size:7 final size:7
Alignment explanation
Indices: 91624--91660 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
91614 GTCAACAGTA
91624 GTCAACG
1 GTCAACG
91631 GTCAACGG
1 GTCAAC-G
91639 GTCAACG
1 GTCAACG
91646 GTCAACG
1 GTCAACG
91653 GTCAACG
1 GTCAACG
91660 G
1 G
91661 GTCGGGTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.27, C:0.27, G:0.32, T:0.14
Consensus pattern (7 bp):
GTCAACG
Found at i:91663 original size:15 final size:14
Alignment explanation
Indices: 91624--91660 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
91614 GTCAACAGTA
91624 GTCAACGGTCAACGG
1 GTCAACGGTCAAC-G
91639 GTCAACGGTCAACG
1 GTCAACGGTCAACG
91653 GTCAACGG
1 GTCAACGG
91661 GTCGGGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.27, C:0.27, G:0.32, T:0.14
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:91670 original size:13 final size:13
Alignment explanation
Indices: 91652--91712 Score: 59
Period size: 13 Copynumber: 4.3 Consensus size: 13
91642 AACGGTCAAC
91652 GGTCAACGGGTCG
1 GGTCAACGGGTCG
91665 GGTCAACGAGTCGAGTCG
1 GGTCAAC--G--G-GTCG
*
91683 GGTAAACGGGTCG
1 GGTCAACGGGTCG
*
91696 GGTAAACGGGTCG
1 GGTCAACGGGTCG
91709 GGTC
1 GGTC
91713 GGGTAAACGG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 27 0.66
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 10 0.24
ACGTcount: A:0.20, C:0.20, G:0.44, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:91684 original size:18 final size:18
Alignment explanation
Indices: 91661--91721 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 18
91651 CGGTCAACGG
*
91661 GTCGGGTCAACGAGTCGA
1 GTCGGGTAAACGAGTCGA
91679 GTCGGGTAAAC--G--G-
1 GTCGGGTAAACGAGTCGA
* *
91692 GTCGGGTAAACGGGTCGG
1 GTCGGGTAAACGAGTCGA
91710 GTCGGGTAAACG
1 GTCGGGTAAACG
91722 GGTTGGGTCG
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 22 0.59
ACGTcount: A:0.21, C:0.18, G:0.44, T:0.16
Consensus pattern (18 bp):
GTCGGGTAAACGAGTCGA
Found at i:91694 original size:31 final size:31
Alignment explanation
Indices: 91656--91730 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
91646 GTCAACGGTC
91656 AACGGGTCGGGTCAACGAGTCGAGTCGGGTA
1 AACGGGTCGGGTCAACGAGTCGAGTCGGGTA
* * *
91687 AACGGGTCGGGTAAACGGGTCGGGTCGGGTA
1 AACGGGTCGGGTCAACGAGTCGAGTCGGGTA
*
91718 AACGGGTTGGGTC
1 AACGGGTCGGGTC
91731 GGGTTGTGAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.20, C:0.17, G:0.45, T:0.17
Consensus pattern (31 bp):
AACGGGTCGGGTCAACGAGTCGAGTCGGGTA
Found at i:91722 original size:18 final size:18
Alignment explanation
Indices: 91689--91734 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
91679 GTCGGGTAAA
91689 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
91707 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
*
91725 TGGGTCGGGT
1 CGGGTCGGGT
91735 TGTGACCGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.13, C:0.15, G:0.52, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:91729 original size:13 final size:13
Alignment explanation
Indices: 91679--91711 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
91669 AACGAGTCGA
91679 GTCGGGTAAACGG
1 GTCGGGTAAACGG
91692 GTCGGGTAAACGG
1 GTCGGGTAAACGG
91705 GTCGGGT
1 GTCGGGT
91712 CGGGTAAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.18, C:0.15, G:0.48, T:0.18
Consensus pattern (13 bp):
GTCGGGTAAACGG
Found at i:91753 original size:9 final size:9
Alignment explanation
Indices: 91739--91784 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
91729 TCGGGTTGTG
91739 ACCGGTCAA
1 ACCGGTCAA
91748 ACCGGTCAAA
1 ACCGGTC-AA
* *
91758 ACAGTTCCAA
1 ACCGGT-CAA
91768 ACCGGTCAA
1 ACCGGTCAA
91777 ACCGGTCA
1 ACCGGTCA
91785 CTTTTCCCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 18 0.58
10 12 0.39
11 1 0.03
ACGTcount: A:0.35, C:0.33, G:0.20, T:0.13
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:102956 original size:38 final size:38
Alignment explanation
Indices: 102905--102979 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
102895 CCAGTAGGCT
102905 ATTTTGGTATTGGTACTCTAGGGAGTATCGATACCCAC
1 ATTTTGGTATTGGTACTCTAGGGAGTATCGATACCCAC
*
102943 ATTTTTGTATTGGTACTCTAGGGAGTATCGATACCCA
1 ATTTTGGTATTGGTACTCTAGGGAGTATCGATACCCA
102980 GGGTCCTAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (38 bp):
ATTTTGGTATTGGTACTCTAGGGAGTATCGATACCCAC
Found at i:113233 original size:2 final size:2
Alignment explanation
Indices: 113216--113268 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
113206 CATTTTCCTC
* *
113216 AT AT AC AT AT AT -T AT AT AC 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 AT
113257 AT AT AT AT AT AT
1 AT AT AT AT AT AT
113269 GCCCTTCATT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.