Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002938.1 Hibiscus syriacus cultivar Beakdansim tig00006068_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: 117371
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1300 original size:19 final size:19
Alignment explanation
Indices: 1276--1364 Score: 79
Period size: 19 Copynumber: 4.4 Consensus size: 19
1266 TTATTTTGGA
1276 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
1295 TTTTTCACTATCGCAACAACAC
1 TTTTTCACTATCG---CAACAC
* *
1317 GTTTTCAAACTCTCGCAACAC
1 TTTTTC--ACTATCGCAACAC
* * *
1338 ATTTTAACTATCGTAACAC
1 TTTTTCACTATCGCAACAC
1357 ATTTTTCA
1 -TTTTTCA
1365 AAATCGCGTT
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
19 24 0.43
20 5 0.09
21 10 0.18
22 11 0.20
24 6 0.11
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:13001 original size:97 final size:97
Alignment explanation
Indices: 12829--13020 Score: 253
Period size: 97 Copynumber: 2.0 Consensus size: 97
12819 AGAGTATAAT
* * * ** *
12829 GTAAGATCTTTTGATAGTACTCTAGGAGTAGAACCACCCTGTTCCATATTTGGTCTTCGAATATT
1 GTAAGATCTTTTGAGAGTACTCTAGCAGTAGAACCACCCGGTTCCATATTTCATCTTCGAAGATT
* * *
12894 GTGATTAGGACACAGATTCTATGCTGTCTAGA
66 GCGATCAGGACACAGATCCTATGCTGTCTAGA
* *
12926 GTAAGAT-TTTCTGAGAGTACTCTAGCAGTAGAACCACCCGGTTTCATCTTTCATC-TCTGAAGA
1 GTAAGATCTTT-TGAGAGTACTCTAGCAGTAGAACCACCCGGTTCCATATTTCATCTTC-GAAGA
12989 TTGCGATCAGGACACAGATCCTATGCTGTCTA
64 TTGCGATCAGGACACAGATCCTATGCTGTCTA
13021 TAGCACCCAT
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
96 5 0.06
97 77 0.94
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (97 bp):
GTAAGATCTTTTGAGAGTACTCTAGCAGTAGAACCACCCGGTTCCATATTTCATCTTCGAAGATT
GCGATCAGGACACAGATCCTATGCTGTCTAGA
Found at i:14856 original size:68 final size:68
Alignment explanation
Indices: 14656--14858 Score: 316
Period size: 68 Copynumber: 3.0 Consensus size: 68
14646 ATTATGTATT
* * * *
14656 TAGTTATATAACTATTCAAGTGGTTATGATAAACATTACGTTTTAATTTTTAAATTTGATTAATA
1 TAGTTATATAACTATTCATGTGATTATGATAAATATTACGTTTTAATTTTTAAATTTGATTAATT
14721 ATC
66 ATC
* * *
14724 CAGTTATATAACTATTCATGTGATTATGATAAATAATACGATTTAATTTTTAAATTTGATTAATT
1 TAGTTATATAACTATTCATGTGATTATGATAAATATTACGTTTTAATTTTTAAATTTGATTAATT
14789 ATC
66 ATC
* * *
14792 TAGTTATATAACTATTCATGTGATAATGATATATATTACGTTTTAATTTTTTAATTTGATTAATT
1 TAGTTATATAACTATTCATGTGATTATGATAAATATTACGTTTTAATTTTTAAATTTGATTAATT
14857 AT
66 AT
14859 GATTATGATG
Statistics
Matches: 122, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 122 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (68 bp):
TAGTTATATAACTATTCATGTGATTATGATAAATATTACGTTTTAATTTTTAAATTTGATTAATT
ATC
Found at i:16374 original size:19 final size:20
Alignment explanation
Indices: 16350--16391 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
16340 TTTTATCACA
*
16350 CTAAATTT-TCTCAAATTCT
1 CTAAATTTCTCTCAAATACT
16369 CTAAATTTCTCTCAAATACT
1 CTAAATTTCTCTCAAATACT
16389 CTA
1 CTA
16392 TCTTTTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (20 bp):
CTAAATTTCTCTCAAATACT
Found at i:16721 original size:112 final size:112
Alignment explanation
Indices: 16515--16855 Score: 515
Period size: 112 Copynumber: 3.0 Consensus size: 112
16505 TGGAAATCAT
* * *
16515 ATATCTCTACACTTTGCTGATACGTTAACATTTTAACATTTTAATTT-AATTTAAATTATCAGTA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACATTTTAATTTAAATTTAAATTATTAGTA
* *
16579 ATATTTAGTTGATTTATTTAATGCATGATTATTATATTAAGAATTAA
66 ATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* *
16626 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAAATTTAAATTATTAGTA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACATTTTAATTTAAATTTAAATTATTAGTA
*
16691 ATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATCAA
66 ATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
16738 ATATATCGACACTTTGCTGATACGATAACATTTTAACATTTTAACGTTTTAATTTAATTTAAATT
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACATTTTAA---TTT-A---AATTTAAATT
*
16803 ATTAGT-ATAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
59 ATTAGTAATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
16856 TTTTTGTAAT
Statistics
Matches: 210, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
111 44 0.21
112 101 0.48
115 3 0.01
116 1 0.00
118 45 0.21
119 16 0.08
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.45
Consensus pattern (112 bp):
ATATCTCGACACTTTGCTGATACGATAACATTTTAACATTTTAATTTAAATTTAAATTATTAGTA
ATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:24142 original size:14 final size:15
Alignment explanation
Indices: 24125--24162 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
24115 AATCATAAAC
24125 AAATAATATT-TTTT
1 AAATAATATTATTTT
24139 AAATAGATATTATTTT
1 AAATA-ATATTATTTT
24155 ATAATAAT
1 A-AATAAT
24163 TTCTATTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.24
15 5 0.24
16 7 0.33
17 4 0.19
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
AAATAATATTATTTT
Found at i:26273 original size:28 final size:29
Alignment explanation
Indices: 26218--26287 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
26208 AATCTGTTTG
*
26218 TATTTATAATTAGGACCCCTAATTTTTTA
1 TATTTATAATTAAGACCCCTAATTTTTTA
* *
26247 TATTTATAATTAAGCCCCCT-GTTTTTTA
1 TATTTATAATTAAGACCCCTAATTTTTTA
26275 TAATTTCATAATT
1 T-ATTT-ATAATT
26288 TTTTTAGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.22
29 22 0.61
30 6 0.17
ACGTcount: A:0.30, C:0.14, G:0.06, T:0.50
Consensus pattern (29 bp):
TATTTATAATTAAGACCCCTAATTTTTTA
Found at i:26420 original size:109 final size:115
Alignment explanation
Indices: 26236--26461 Score: 304
Period size: 109 Copynumber: 2.0 Consensus size: 115
26226 ATTAGGACCC
** *
26236 CTAATTTTTTATATTTATAATTAAGCCCCCTGTTTTTTATAATTTCATAATTTTTTTAGTTTTGA
1 CTAATTTTTTATATTTATAATTAAGCCCCCTGTTTTTTATAATTTCATAAAATGTTTAGTTTTGA
*
26301 CCCT-CTTTTTCATTTATCTTA-T-T-ATTCAATTTTGAATTAAATTTAA
66 CCCTCCTTTTCCATTTATCTTATTATCATTCAATTTTGAATTAAATTTAA
**
26347 CTAA-TTTTTATATTTATAATT-AGGGCCCTAG-TTTTTATAATTTCATAAAATGTTTAGTTTTG
1 CTAATTTTTTATATTTATAATTAAGCCCCCT-GTTTTTTATAATTTCATAAAATGTTTAGTTTTG
* *
26409 ACCCTCCTTTTCCATTTCTCTTATTAACTCATTTAATTTTGAATTAAATTTAA
65 ACCCTCCTTTTCCATTTATCTTATT-A-TCATTCAATTTTGAATTAAATTTAA
26462 TCATGTTTTT
Statistics
Matches: 100, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
109 39 0.39
110 33 0.33
111 5 0.05
114 1 0.01
115 22 0.22
ACGTcount: A:0.28, C:0.13, G:0.06, T:0.53
Consensus pattern (115 bp):
CTAATTTTTTATATTTATAATTAAGCCCCCTGTTTTTTATAATTTCATAAAATGTTTAGTTTTGA
CCCTCCTTTTCCATTTATCTTATTATCATTCAATTTTGAATTAAATTTAA
Found at i:26942 original size:19 final size:19
Alignment explanation
Indices: 26918--26954 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
26908 CAAATGCAAT
26918 GCATATATTATGTGAATGC
1 GCATATATTATGTGAATGC
26937 GCATATATTATGTGAATG
1 GCATATATTATGTGAATG
26955 TTTGAAGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (19 bp):
GCATATATTATGTGAATGC
Found at i:35627 original size:20 final size:18
Alignment explanation
Indices: 35571--35630 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 18
35561 ACTCTAATTC
35571 TATATATTCTTTTATATTTT
1 TATATATTC--TTATATTTT
*
35591 TATATATTATATAATATTGGTT
1 TATATATTCT-T-ATATT--TT
35613 TATATATTCTTATATTTT
1 TATATATTCTTATATTTT
35631 ACCATAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
18 3 0.09
19 1 0.03
20 18 0.53
21 1 0.03
22 11 0.32
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (18 bp):
TATATATTCTTATATTTT
Found at i:35654 original size:22 final size:22
Alignment explanation
Indices: 35626--35675 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
35616 ATATTCTTAT
35626 ATTTTACCATAAATTAAAAGTA
1 ATTTTACCATAAATTAAAAGTA
35648 ATTTTACCATAAATTAAAAGTA
1 ATTTTACCATAAATTAAAAGTA
35670 ATTTTA
1 ATTTTA
35676 AATCTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (22 bp):
ATTTTACCATAAATTAAAAGTA
Found at i:46441 original size:2 final size:2
Alignment explanation
Indices: 46434--46482 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
46424 TAAACAATAA
46434 AT 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 AT
46476 AT AT AT A
1 AT AT AT A
46483 ACTATAATCC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:47632 original size:27 final size:27
Alignment explanation
Indices: 47579--47634 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
47569 CTAGAGATTT
* *
47579 TAAATTAAATCATCCCAGGTTTGTATA
1 TAAATAAAATCATCCCAGGTTTCTATA
*
47606 TAAATAAAATTATCCCA-GTGTTCTATA
1 TAAATAAAATCATCCCAGGT-TTCTATA
47633 TA
1 TA
47635 TCCAAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (27 bp):
TAAATAAAATCATCCCAGGTTTCTATA
Found at i:47948 original size:2 final size:2
Alignment explanation
Indices: 47941--47967 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47931 TTTTATTGTT
47941 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 T
47968 TTTTTGCGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48605 original size:13 final size:13
Alignment explanation
Indices: 48587--48612 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48577 TACCCATCAT
48587 CAACAAAAAAAGA
1 CAACAAAAAAAGA
48600 CAACAAAAAAAGA
1 CAACAAAAAAAGA
48613 ACCGAGAGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.15, G:0.08, T:0.00
Consensus pattern (13 bp):
CAACAAAAAAAGA
Found at i:52412 original size:185 final size:184
Alignment explanation
Indices: 52095--52486 Score: 601
Period size: 185 Copynumber: 2.1 Consensus size: 184
52085 ATTAAATTTT
* *
52095 AAATTTTAAATATATTATATATAACATATGAGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
* * *
52160 TTTAAGATCCAATAACTTTTAAATCTAAATCAATATTAATTAATTTAAAAAATTATATAAAATTT
66 TGTAAGATACAATAACTTTTAAACCTAAATCAATATTAATTAATTTAAAAAATTATATAAAATTT
* *
52225 TTATTTTATAATTATATATTATTTAAATTAATTGTAAAATGTTTTTTTAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAAAT-TTTTTTGAATTAAA
* *
52280 AAATATTAAATATATTATATATAACATATG-GACTAAGCCCAAATCATTTAAAACTCAATTAATA
1 AAATATTAAATATATTATATATAACATATGAG-CTAAGCCCAAACCATTTAAAACCCAATTAATA
* * *
52344 ATGTAAGATATAATAACTTTTAAACCTAAATCATTATTAATTAA-TTAAAAAATTTATCTAAAAT
65 ATGTAAGATACAATAACTTTTAAACCTAAATCAATATTAATTAATTTAAAAAA-TTATATAAAAT
*
52408 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
129 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAAATTTTTTTGAATTAAA
* *
52464 AAATATTTAAT-TTTTATATATAA
1 AAATATTAAATATATTATATATAA
52487 ATTAAAAATT
Statistics
Matches: 190, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
183 11 0.06
184 32 0.17
185 147 0.77
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (184 bp):
AAATATTAAATATATTATATATAACATATGAGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
TGTAAGATACAATAACTTTTAAACCTAAATCAATATTAATTAATTTAAAAAATTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAAATTTTTTTGAATTAAA
Found at i:67446 original size:9 final size:9
Alignment explanation
Indices: 67432--67465 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
67422 TAGAAGGGAA
67432 AAATAAAAT
1 AAATAAAAT
67441 AAATAAAAT
1 AAATAAAAT
67450 AAAT-AAAT
1 AAATAAAAT
67458 AAGATAAA
1 AA-ATAAA
67466 GAAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:67455 original size:13 final size:13
Alignment explanation
Indices: 67431--67476 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
67421 GTAGAAGGGA
67431 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
67445 AAAATAAATAAAT
1 AAAATAAATAAAT
* * *
67458 AAGATAAAGAAAA
1 AAAATAAATAAAT
67471 AAAATA
1 AAAATA
67477 GTAAAGTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 23 0.82
14 5 0.18
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.17
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:67524 original size:2 final size:2
Alignment explanation
Indices: 67517--67543 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
67507 GAAAAAGGAA
67517 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
67544 CATCAAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:67936 original size:2 final size:2
Alignment explanation
Indices: 67929--67953 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
67919 TATTAAAGAA
67929 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
67954 ATAATAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:67984 original size:17 final size:18
Alignment explanation
Indices: 67951--67986 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
67941 ATATATATAT
*
67951 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
67969 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
67986 A
1 A
67987 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:68395 original size:37 final size:36
Alignment explanation
Indices: 68345--68482 Score: 172
Period size: 37 Copynumber: 3.8 Consensus size: 36
68335 GTGCTTGTGG
* * * * *
68345 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AAATCT
* *
68382 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAAT-CT
*
68419 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
68453 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
68483 GGACGAAAAG
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
34 28 0.31
35 4 0.04
36 4 0.04
37 53 0.60
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
Found at i:68456 original size:34 final size:35
Alignment explanation
Indices: 68379--68479 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
68369 TTAGTAGAAC
68379 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
68417 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
68450 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
68480 GTAGGACGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 1 0.02
34 33 0.53
37 27 0.44
38 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:69326 original size:105 final size:105
Alignment explanation
Indices: 69025--70071 Score: 1531
Period size: 105 Copynumber: 10.0 Consensus size: 105
69015 CATTGTTCCA
* * * ** *
69025 AGTCCAATATCCTCCGTCGTGAAGCTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
* * * * *
69089 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** *
69131 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
69191 AGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
69231 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
* *
69296 AGCGATCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
69336 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
69396 AGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
69436 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
69501 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
69541 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
69606 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
69646 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATGGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGG-AAGTTG-TTGTTGACAA
*
69711 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
69753 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAG
* *
69818 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** * * *
69859 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
69924 AGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
69964 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTAGCTCTGAGATTGGAAAGTTGTTATTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
70029 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
70069 AGT
1 AGT
70072 GCCACGATAT
Statistics
Matches: 862, Mismatches: 66, Indels: 27
0.90 0.07 0.03
Matches are distributed among these distances:
100 171 0.20
101 7 0.01
102 8 0.01
103 1 0.00
104 10 0.01
105 426 0.49
106 144 0.17
107 95 0.11
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:69378 original size:205 final size:206
Alignment explanation
Indices: 69025--70071 Score: 1515
Period size: 205 Copynumber: 5.0 Consensus size: 206
69015 CATTGTTCCA
* * * * ** *
69025 AGTCCAATATCCTCCGTCGTGAAGCTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAAC
* * *
69090 CAGCCG-TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
65 CAG-CGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
** *
69154 GTTGAAATTGAATCTGAA-TGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTTGTGAAGTTGAAC
129 GTTGAAATTGGCTCTGAATTGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
69218 TTGCGTTGTCTGG
194 TTGCGTTGTCTGG
* ** *
69231 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACC
* *
69296 AGCGATCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
69361 TGAAATTGGCTCTGAA-TGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTTGTGAAGTTGAACTT
131 TGAAATTGGCTCTGAATTGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
69425 GCGTTGTCTGG
196 GCGTTGTCTGG
* * *
69436 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACC
* *
69501 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* * *
69566 TGAAATTGGCTATGAGATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
131 TGAAATTGGCTCTGA-ATT--GAAATT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
69631 ACTTGCGTTGTCTGG
192 ACTTGCGTTGTCTGG
* * * *
69646 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATGGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGG-AAGTTG-TTGTTGACAA
* *
69711 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCATTGTGAA
64 CCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* *
69776 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTCGTGAAGT
129 GTTGAAATTGGCTCTG-AATTGA-AA--T-TTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGT
*
69841 TGAACTTGCATTGTCTGG
189 TGAACTTGCGTTGTCTGG
** * **
69859 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACC
69924 AGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* *
69989 TGAAATTAGCTCTGAGATTGGAAAGTTGTTATTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
131 TGAAATTGGCTCTGA-ATT-GAAA-TT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
*
70054 ACTTGCGTTGTCTCG
192 ACTTGCGTTGTCTGG
70069 AGT
1 AGT
70072 GCCACGATAT
Statistics
Matches: 770, Mismatches: 55, Indels: 28
0.90 0.06 0.03
Matches are distributed among these distances:
204 2 0.00
205 279 0.36
206 46 0.06
207 1 0.00
209 6 0.01
210 148 0.19
211 95 0.12
212 95 0.12
213 97 0.13
214 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (206 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACC
AGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
TGAAATTGGCTCTGAATTGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
GCGTTGTCTGG
Found at i:69913 original size:423 final size:413
Alignment explanation
Indices: 69025--70071 Score: 1539
Period size: 423 Copynumber: 2.5 Consensus size: 413
69015 CATTGTTCCA
* *** *
69025 AGTCCAATATCC-TCCGTCGTGAAGCTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCC-T-GTGAAGTTGAAATTGGCTCT-GAAATTGGAAGTTG-TTGTTGACAA
* * * * *
69089 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
62 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
** * *
69154 GTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGCAGCGGTCCCTTCGTTGTGAAGTT
127 GTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
* * **
69214 GAACTTGCGTTGTCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGA
192 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* * *
69279 AGTTGTTGTTGACAAACAGCGATCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAAT
257 AATGGTTATTGACAAACAGCGATCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAAT
* * *
69344 ATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCG
322 ATCCTTCACTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAACCAGCCGTCCCTTCG
* *
69409 TTGTGAAGTTGAACTTGCGTTGTCTGG
387 TCGTGAAGTTGAACTTGCATTGTCTGG
* *
69436 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTC-CTGTGAAGTTGAAATTGGCTCTGAAATTGG-AAGTTGTTGTTGACAAGC
*
69501 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
64 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* *
69566 TGAAATTGGCTATGAGATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
129 TGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
69631 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA
194 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG-AA
* * *
69696 ATGGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
258 ATGG-TTATTGACAAACAGCGATCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAAT
*
69761 ATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTC
322 ATCCTTCACTGTGAAGTTGAAATTGGCTCTG-AA-TGA-AA--T-TTTGTTGACAACCAGCCGTC
69826 CCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
381 CCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
*
69859 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTC-CTGTGAAGTTGAAATTGGCTCTGAAATTG-GAAGTTGTTGTTGACAAGC
*
69924 AGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
64 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* * *
69989 TGAAATTAGCTCTGAGATTGGAAAGTTGTTATTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
129 TGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
*
70054 ACTTGCGTTGTCTCGAGT
194 ACTTGCGTTGTCTGGAGT
70072 GCCACGATAT
Statistics
Matches: 572, Mismatches: 47, Indels: 22
0.89 0.07 0.03
Matches are distributed among these distances:
410 87 0.15
411 37 0.06
412 4 0.01
414 5 0.01
415 93 0.16
416 4 0.01
417 85 0.15
418 2 0.00
419 3 0.01
420 2 0.00
422 1 0.00
423 248 0.43
424 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (413 bp):
AGTCCAATATCCTTCCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAGTTGTTGTTGACAAGCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
AAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
TTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATG
GTTATTGACAAACAGCGATCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCC
TTCACTGTGAAGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAACCAGCCGTCCCTTCGTCGT
GAAGTTGAACTTGCATTGTCTGG
Found at i:70827 original size:36 final size:35
Alignment explanation
Indices: 70778--71018 Score: 176
Period size: 36 Copynumber: 6.9 Consensus size: 35
70768 GATTTTGTGT
* *
70778 TTCAAGAGTAACTGTCTCAAGATAGACGAAAATTGA
1 TTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTGA
70814 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT-A
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTGA
* * * *
70849 GTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGT
1 -TT-CAAGAGAAACTGTCTCAAGAGAGAC-AAAATTGA
* * ** *
70887 TTCAA-AGAAAACATAT-TC---A-A-A-TATTTTGT
1 TTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATTGA
* * * *
70916 TTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTGA
* *
70952 TTCAAGAGAAACTATCTCAAGAGAGACAAAATTTA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTGA
*
70987 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTCAAGAGAAACTGTCTCAAGAGAGACAAAA
71019 CTCTTCTAGT
Statistics
Matches: 166, Mismatches: 22, Indels: 34
0.75 0.10 0.15
Matches are distributed among these distances:
28 2 0.01
29 17 0.10
30 1 0.01
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 12 0.07
36 97 0.58
37 29 0.17
38 3 0.02
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (35 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTGA
Found at i:71944 original size:22 final size:22
Alignment explanation
Indices: 71919--71969 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
71909 TTGTGTTTGG
*
71919 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTAGCATTTGATGC
*
71941 TCAAAGGTTTAGTATTTGATGC
1 TCAAAGGTTTAGCATTTGATGC
71963 TCAAAGG
1 TCAAAGG
71970 ATTGATGGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTAGCATTTGATGC
Found at i:72623 original size:20 final size:20
Alignment explanation
Indices: 72577--72622 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
72567 TTTTTGTCCC
*
72577 CTTTTTTATTTTTGTTTTTT
1 CTTTTTTATTATTGTTTTTT
*
72597 CTTTTTTGTTATTG-TTTTT
1 CTTTTTTATTATTGTTTTTT
72616 CTTTTTT
1 CTTTTTT
72623 TTGCTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.04, C:0.07, G:0.07, T:0.83
Consensus pattern (20 bp):
CTTTTTTATTATTGTTTTTT
Found at i:72633 original size:19 final size:18
Alignment explanation
Indices: 72592--72641 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
72582 TTATTTTTGT
*
72592 TTTTTCTTTTTTGTTATTG
1 TTTTTCTTTTTT-TTATTC
*
72611 TTTTTCTTTTTTTTGCTTC
1 TTTTTCTTTTTTTT-ATTC
72630 -TTTTCTTTTTTT
1 TTTTTCTTTTTTT
72642 CTTTTTGCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.02, C:0.10, G:0.06, T:0.82
Consensus pattern (18 bp):
TTTTTCTTTTTTTTATTC
Found at i:75671 original size:9 final size:9
Alignment explanation
Indices: 75657--75690 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
75647 TAGAAGGGAA
75657 AAATAAAAT
1 AAATAAAAT
75666 AAATAAAAT
1 AAATAAAAT
75675 AAAT-AAAT
1 AAATAAAAT
75683 AAGATAAA
1 AA-ATAAA
75691 GAAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:75680 original size:13 final size:13
Alignment explanation
Indices: 75656--75701 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
75646 GTAGAAGGGA
75656 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
75670 AAAATAAATAAAT
1 AAAATAAATAAAT
* * *
75683 AAGATAAAGAAAA
1 AAAATAAATAAAT
75696 AAAATA
1 AAAATA
75702 GTAAAGTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 23 0.82
14 5 0.18
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.17
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:75749 original size:2 final size:2
Alignment explanation
Indices: 75742--75766 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
75732 GAAAAAGGAA
75742 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
75767 CATCAAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:76156 original size:2 final size:2
Alignment explanation
Indices: 76149--76179 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
76139 TATTAAAGAA
76149 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
76180 ATAATAACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:76210 original size:17 final size:18
Alignment explanation
Indices: 76177--76212 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
76167 ATATATATAT
*
76177 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
76195 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
76212 A
1 A
76213 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:76623 original size:37 final size:36
Alignment explanation
Indices: 76573--76710 Score: 172
Period size: 37 Copynumber: 3.8 Consensus size: 36
76563 GTGCTTGTGG
* * * * *
76573 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AAATCT
* *
76610 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAAT-CT
*
76647 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
76681 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
76711 GGACGAAAAG
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
34 28 0.31
35 4 0.04
36 4 0.04
37 53 0.60
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
Found at i:76684 original size:34 final size:35
Alignment explanation
Indices: 76607--76707 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
76597 TTAGTAGAAC
76607 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
76645 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
76678 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
76708 GTAGGACGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 1 0.02
34 33 0.53
37 27 0.44
38 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:78010 original size:2 final size:2
Alignment explanation
Indices: 78003--78035 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
77993 CGAATAGTAC
78003 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 T
78036 TGTTTGATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:79814 original size:43 final size:42
Alignment explanation
Indices: 79748--80099 Score: 184
Period size: 43 Copynumber: 8.2 Consensus size: 42
79738 TGAGAACAAA
*
79748 AAACGCCGCAATAGGTCAATATCTATTA-CGACGTTTTTTTGAAC
1 AAACGCCGCAA-AGGTCAATATCTA-TAGCGACG-TTTTTGGAAC
* * *
79792 AAACGCCGCAAAGGTCGATATCTATAGCGGCGTTTTTGGAAT
1 AAACGCCGCAAAGGTCAATATCTATAGCGACGTTTTTGGAAC
* * * * *
79834 AAACGCCGCAAAAAGATGT-GATA--TATAGCGGCGTTTCTAGAAA
1 AAACGCCGC--AAAG--GTCAATATCTATAGCGACGTTTTTGGAAC
* * * * *
79877 AAACGCCGCAAAAGGTC-AGACCTATAACGGCGTTTTTGAACAC
1 AAACGCCGC-AAAGGTCAATATCTATAGCGACGTTTTTGGA-AC
* ** * * * *
79920 AAACGCCGCAAAAGAGAAGACCTATA-CTGGCGTTTTTAGAAC
1 AAACGCCGCAAAGGTCAATATCTATAGC-GACGTTTTTGGAAC
* * * *
79962 AAACGCCGTAAAAGGTC-AGACCTATAGCGGCGTTTTTGGACAC
1 AAACGCCG-CAAAGGTCAATATCTATAGCGACGTTTTTGGA-AC
* * * * *
80005 AAACGCCGCAAAATGTC-ATACCTATAACGGCGTTTTTGAACAC
1 AAACGCCGC-AAAGGTCAATATCTATAGCGACGTTTTTGGA-AC
* * *
80048 AAACGCCGCAAAAAGTC-ATA-CATATAGCGGCGTTTTTTGATAC
1 AAACGCCGC-AAAGGTCAATATC-TATAGCGACGTTTTTGGA-AC
80091 AAACGCCGC
1 AAACGCCGC
80100 TAATTACCTT
Statistics
Matches: 259, Mismatches: 33, Indels: 33
0.80 0.10 0.10
Matches are distributed among these distances:
40 4 0.02
42 74 0.29
43 160 0.62
44 15 0.06
45 4 0.02
46 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (42 bp):
AAACGCCGCAAAGGTCAATATCTATAGCGACGTTTTTGGAAC
Found at i:79909 original size:85 final size:83
Alignment explanation
Indices: 79783--80099 Score: 320
Period size: 85 Copynumber: 3.7 Consensus size: 83
79773 TTACGACGTT
* * * * *
79783 TTTTTGAACAAACGCCGC-AAAGGTCGATATCTATAGCGGCGTTTTTGGA-ATAAACGCCGCAAA
1 TTTTAGAAAAAACGCCGCAAAAGGTC-AGACCTATAGCGGCGTTTTTGGACACAAACGCCGC-AA
79846 AAGATGTGATATATAGCGGCG
64 AAGATGTGATATATA-CGGCG
* *
79867 TTTCTAGAAAAAACGCCGCAAAAGGTCAGACCTATAACGGCGTTTTTGAACACAAACGCCGCAAA
1 TTT-TAGAAAAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAACGCCGCAAA
* **
79932 AGA-GAAGACCTATACTGGCG
65 AGATG-TGATATATAC-GGCG
* *
79952 TTTTTAGAACAAACGCCGTAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAACGCCGC-AA
1 -TTTTAGAAAAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAACGCCGCAAA
*
80016 A-ATGTCATACCTATAACGGCG
65 AGATGTGATA--TAT-ACGGCG
* * * * * *
80037 TTTTTGAACACAAACGCCGCAAAAAGTCATACATATAGCGGCGTTTTTTGATACAAACGCCGC
1 TTTTAGAA-A-AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAACGCCGC
80100 TAATTACCTT
Statistics
Matches: 195, Mismatches: 26, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
83 2 0.01
84 16 0.08
85 109 0.56
86 68 0.35
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (83 bp):
TTTTAGAAAAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAACGCCGCAAAA
GATGTGATATATACGGCG
Found at i:79925 original size:128 final size:127
Alignment explanation
Indices: 79745--80099 Score: 380
Period size: 128 Copynumber: 2.8 Consensus size: 127
79735 GTTTGAGAAC
* * * * *
79745 AAAAAACGCCGCAATAGGTCAATATCTATTACGACGTTTTTTTG-A-ACAAACGCCGCAAAGGTC
1 AAAAAACGCCGCAAAAGGTC-ATACCTATAACGGCG--TTTTTGAACACAAACGCCGCAAAAGTC
* * ** *
79808 GATATCTATAGCGGCGTTTTTGGAATAAACGCCGCAAAAAGATGTGATATATAGCGGCGTTTCTA
63 GATA-CTATAGCGGCGTTTTTAGAACAAACGCCGCAAAAAGATCAGACATATAGCGGCGTTTCTA
79873 G
127 G
* *
79874 AAAAAACGCCGCAAAAGGTCAGACCTATAACGGCGTTTTTGAACACAAACGCCGCAAAAG-AGAA
1 AAAAAACGCCGCAAAAGGTCATACCTATAACGGCGTTTTTGAACACAAACGCCGCAAAAGTCG-A
* * * * * *
79938 GACCTATA-CTGGCGTTTTTAGAACAAACGCCG-TAAAAGGTCAGACCTATAGCGGCGTTTTTGG
65 TA-CTATAGC-GGCGTTTTTAGAACAAACGCCGCAAAAAGATCAGACATATAGCGGCGTTTCTAG
* *
80001 ACACAAACGCCGCAAAATGTCATACCTATAACGGCGTTTTTGAACACAAACGCCGCAAAAAGTC-
1 A-AAAAACGCCGCAAAAGGTCATACCTATAACGGCGTTTTTGAACACAAACGCCGC-AAAAGTCG
*
80065 ATACATATAGCGGCGTTTTTTGATACAAACGCCGC
64 ATAC-TATAGCGGCGTTTTTAGA-ACAAACGCCGC
80100 TAATTACCTT
Statistics
Matches: 190, Mismatches: 25, Indels: 21
0.81 0.11 0.09
Matches are distributed among these distances:
126 6 0.03
127 28 0.15
128 121 0.64
129 35 0.18
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.23
Consensus pattern (127 bp):
AAAAAACGCCGCAAAAGGTCATACCTATAACGGCGTTTTTGAACACAAACGCCGCAAAAGTCGAT
ACTATAGCGGCGTTTTTAGAACAAACGCCGCAAAAAGATCAGACATATAGCGGCGTTTCTAG
Found at i:83992 original size:41 final size:41
Alignment explanation
Indices: 83925--84449 Score: 532
Period size: 41 Copynumber: 12.6 Consensus size: 41
83915 TTGTAAACTT
* * * * *
83925 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACGAGTCTTTA
* *
83968 GCGGCGTTTGAATAGAAACGCCACTAAAGTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * *
84009 GCGGCGTTTGTATAAAAATGTCAATAAAGTATGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* *
84050 GCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * * * *
84091 GCGACGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACGAGTCTTTA
* * * *
84134 ACGGCGTTTGAATAAAAATGCCACTAAAGTACGCGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * **
84175 GCGGAGTTTGTATAAAAACGCAACTAAAGTATAAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * *
84216 ACGACGTTTGTATAAAAACGCCACTAAATTATGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * * *
84257 GCGACGTTTGTAAACACAAACGCCACTATAGTAC-ATGTGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACGA-GTCTTTA
** * * *
84300 ATGGCGTTTGTATAAAAACGCCACTAAAGTACAATTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * *
84341 GCGGCGTTTTTATAAAAATGCCACTAAATTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * *
84382 GCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTT
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
84423 GCGGCGTTTGT-TGAAAAAACGCCACTA
1 GCGGCGTTTGTAT--AAAAACGCCACTA
84450 TTGATGAACC
Statistics
Matches: 397, Mismatches: 77, Indels: 17
0.81 0.16 0.03
Matches are distributed among these distances:
40 1 0.00
41 306 0.77
42 19 0.05
43 71 0.18
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
Found at i:84149 original size:125 final size:123
Alignment explanation
Indices: 83942--84433 Score: 378
Period size: 125 Copynumber: 4.0 Consensus size: 123
83932 TTGTAAACAC
* * * * * * * *
83942 AAACGCCACTATAGTACAAGTGTATAGCGGCGTTTG-AATAGAAACGCCACTAAAGTACGAGTCT
1 AAACGCAACTAAAGTACAAGTCTTTAACGACGTTTGTAA-AAAAACGCCACTAAAGTACAAGTCT
* * * * * *
84006 TTAGCGGCGTTTGTATAAAAATGTCAATAAAGTATGAGTCTTTAGCGGCGTTTGTATAA
65 ATAACGGCGTTTGAATAAAAATGCCAATAAAGTACGAGTCTTTAGCGGAGTTTGTATAA
* * * * * * *
84065 AAATGCCACTAAATTACGAGTCTTTAGCGACGTTTGTAAACACAAACGCCACTATAGTACAAGTG
1 AAACGCAACTAAAGTACAAGTCTTTAACGACGTTTGTAAA-A-AAACGCCACTAAAGTACAAGTC
* *
84130 TATAACGGCGTTTGAATAAAAATGCCACTAAAGTACGCGTCTTTAGCGGAGTTTGTATAA
64 TATAACGGCGTTTGAATAAAAATGCCAATAAAGTACGAGTCTTTAGCGGAGTTTGTATAA
* * * ** *
84190 AAACGCAACTAAAGTATAAGTCTTTAACGACGTTTGTATAAAAACGCCACTAAATTATGAGTCTT
1 AAACGCAACTAAAGTACAAGTCTTTAACGACGTTTGTAAAAAAACGCCACTAAAGTACAAGTCTA
* * * * * * * ** *
84255 TAGCGACGTTTGTAA-ACACAAACGCCACTATAGTAC-ATGTGTATAATGGCGTTTGTATAA
66 TAACGGCGTTTG-AATA-A-AAATGCCAATAAAGTACGA-GTCTTTAGCGGAGTTTGTATAA
* * * * * * * * * * *
84315 AAACGCCACTAAAGTACAATTCTATAGCGGCGTTTTTATAAAAATGCCACTAAATTACGAGTCTT
1 AAACGCAACTAAAGTACAAGTCTTTAACGACGTTTGTAAAAAAACGCCACTAAAGTACAAGTCTA
* * * * * * * *
84380 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTTGCGGCGTTTGT
66 TAACGGCGTTTGAATAAAAATGCCAATAAAGTACGAGTCTTTAGCGGAGTTTGT
84434 TGAAAAAACG
Statistics
Matches: 300, Mismatches: 60, Indels: 18
0.79 0.16 0.05
Matches are distributed among these distances:
123 87 0.29
124 9 0.03
125 204 0.68
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (123 bp):
AAACGCAACTAAAGTACAAGTCTTTAACGACGTTTGTAAAAAAACGCCACTAAAGTACAAGTCTA
TAACGGCGTTTGAATAAAAATGCCAATAAAGTACGAGTCTTTAGCGGAGTTTGTATAA
Found at i:84205 original size:166 final size:166
Alignment explanation
Indices: 83929--84450 Score: 762
Period size: 166 Copynumber: 3.2 Consensus size: 166
83919 AAACTTGCGG
* *
83929 CGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGGCGTTTGAATAGAAACGCCACTA
1 CGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAACGCCACTA
83994 AAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGTCAA-TAAAGTATGAGTCTTTAGCGGCGTT
66 AAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATG-CAACTAAAGTATGAGTCTTTAGCGGCGTT
*
84058 TGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGA
130 TGTATAAAAACGCCACTAAATTACGAGTCTTTAGCGA
*
84095 CGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATGCCACTA
1 CGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAACGCCACTA
* * * * * *
84160 AAGTACGCGTCTTTAGCGGAGTTTGTATAAAAACGCAACTAAAGTATAAGTCTTTAACGACGTTT
66 AAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGCAACTAAAGTATGAGTCTTTAGCGGCGTTT
*
84225 GTATAAAAACGCCACTAAATTATGAGTCTTTAGCGA
131 GTATAAAAACGCCACTAAATTACGAGTCTTTAGCGA
* * *
84261 CGTTTGTAAACACAAACGCCACTATAGTACATGTGTATAATGGCGTTTGTATAAAAACGCCACTA
1 CGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAACGCCACTA
* * * * * * *
84326 AAGTACAATTCTATAGCGGCGTTTTTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGCGTTT
66 AAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGCAACTAAAGTATGAGTCTTTAGCGGCGTTT
* * * * *
84391 GTATAAAAACGCCACTAAAGTACTACTCTTTTGCGG
131 GTATAAAAACGCCACTAAATTACGAGTCTTTAGCGA
*
84427 CGTTTGTTGAA-A-AAACGCCACTAT
1 CGTTTG-TAAACACAAACGCCACTAT
84451 TGATGAACCT
Statistics
Matches: 319, Mismatches: 35, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
165 15 0.05
166 301 0.94
167 3 0.01
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (166 bp):
CGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAACGCCACTA
AAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGCAACTAAAGTATGAGTCTTTAGCGGCGTTT
GTATAAAAACGCCACTAAATTACGAGTCTTTAGCGA
Found at i:86096 original size:13 final size:15
Alignment explanation
Indices: 86078--86110 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
86068 ACAGCTTACC
86078 GGAAAAC-TCC-ATG
1 GGAAAACATCCAATG
86091 GGAAAACATCCAATG
1 GGAAAACATCCAATG
86106 GGAAA
1 GGAAA
86111 GATGAAGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 3 0.17
15 8 0.44
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.12
Consensus pattern (15 bp):
GGAAAACATCCAATG
Found at i:87867 original size:31 final size:30
Alignment explanation
Indices: 87809--87869 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
87799 TGTCAAATAT
* * **
87809 TAACAAATAGTTTGATTTATATTATTTAAA
1 TAACAAATAATTTGATTGATAAAATTTAAA
87839 TAACTAAATAATTTGATTGATAAAATTTAAA
1 TAAC-AAATAATTTGATTGATAAAATTTAAA
87870 GAGAGATGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.43
Consensus pattern (30 bp):
TAACAAATAATTTGATTGATAAAATTTAAA
Found at i:90197 original size:27 final size:28
Alignment explanation
Indices: 90147--90202 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 28
90137 AAATGAAAAG
90147 AAGAAACAATTAAATGATTATACAAATA
1 AAGAAACAATTAAATGATTATACAAATA
*
90175 AAGAAACGATT-AATGATTATACAAATA
1 AAGAAACAATTAAATGATTATACAAATA
90202 A
1 A
90203 TTTACCTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.59, C:0.07, G:0.09, T:0.25
Consensus pattern (28 bp):
AAGAAACAATTAAATGATTATACAAATA
Found at i:90737 original size:2 final size:2
Alignment explanation
Indices: 90699--90726 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
90689 TTATATTTGA
90699 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
90727 TGAATATATA
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:92097 original size:25 final size:23
Alignment explanation
Indices: 92065--92139 Score: 77
Period size: 25 Copynumber: 3.3 Consensus size: 23
92055 TTTAAATGAA
*
92065 AATA-AAAAAAATTAAATTAAGTT
1 AATATAAAAATATT-AATTAAGTT
92088 AATAGTAAAATATATTTAA-TAAGTT
1 AATA-TAAAA-ATA-TTAATTAAGTT
92113 AATATAAAAATATT--TTAAGTT
1 AATATAAAAATATTAATTAAGTT
92134 AATATA
1 AATATA
92140 TATAATTATA
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
21 12 0.26
22 2 0.04
23 7 0.15
24 5 0.11
25 14 0.30
26 4 0.09
27 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.37
Consensus pattern (23 bp):
AATATAAAAATATTAATTAAGTT
Found at i:92151 original size:25 final size:22
Alignment explanation
Indices: 92081--92139 Score: 84
Period size: 21 Copynumber: 2.6 Consensus size: 22
92071 AAAAATTAAA
92081 TTAAGTTAATAGTAAAATATATT
1 TTAAGTTAATA-TAAAATATATT
92104 TAATAAGTTAATATAAAA-ATATT
1 T--TAAGTTAATATAAAATATATT
92127 TTAAGTTAATATA
1 TTAAGTTAATATA
92140 TATAATTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 12 0.35
23 7 0.21
24 5 0.15
25 10 0.29
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (22 bp):
TTAAGTTAATATAAAATATATT
Found at i:92931 original size:31 final size:31
Alignment explanation
Indices: 92890--92957 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
92880 AGGTGACCAC
* **
92890 ATCTTAATTAAATGAAAATGAAAGTGA-TCAT
1 ATCTTAATTAAATAAAAACAAAAGTGACT-AT
*
92921 ATCTTGATTAAATAAAAACAAAAGTGACTAT
1 ATCTTAATTAAATAAAAACAAAAGTGACTAT
92952 ATCTTA
1 ATCTTA
92958 TGTTTTTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.32
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACAAAAGTGACTAT
Found at i:93684 original size:8 final size:8
Alignment explanation
Indices: 93671--93703 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
93661 AGGGACGGAA
93671 CAGATGAG
1 CAGATGAG
93679 CAGATGAG
1 CAGATGAG
93687 CAGATGAG
1 CAGATGAG
93695 CAGATGAG
1 CAGATGAG
93703 C
1 C
93704 CCCCTATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.36, T:0.12
Consensus pattern (8 bp):
CAGATGAG
Found at i:97225 original size:6 final size:6
Alignment explanation
Indices: 97214--97248 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
97204 ACATGCCAAC
* *
97214 AATGGG AATGGG AATGGG AATGTG AATGGG CATGG
1 AATGGG AATGGG AATGGG AATGGG AATGGG AATGG
97249 ATCTGGGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.03, G:0.46, T:0.20
Consensus pattern (6 bp):
AATGGG
Found at i:98604 original size:30 final size:30
Alignment explanation
Indices: 98568--98625 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
98558 CAATCACCCC
*
98568 CCAACCAAGAGAAGCCGACATCTCCATCAA
1 CCAACCAAGAGAAGCCGACATATCCATCAA
*
98598 CCAACCAAGAGAAGCCGATATATCCATC
1 CCAACCAAGAGAAGCCGACATATCCATC
98626 TACAGGTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.34, G:0.14, T:0.12
Consensus pattern (30 bp):
CCAACCAAGAGAAGCCGACATATCCATCAA
Found at i:102928 original size:30 final size:30
Alignment explanation
Indices: 102894--102998 Score: 192
Period size: 30 Copynumber: 3.5 Consensus size: 30
102884 AATTCTTATC
102894 ATTTCCATTTTGGTCCTTAACATATAGATA
1 ATTTCCATTTTGGTCCTTAACATATAGATA
102924 ATTTCCATTTTGGTCCTTAACATATAGATA
1 ATTTCCATTTTGGTCCTTAACATATAGATA
* *
102954 ATTTCCATTTCGGTCCTTAACATATAGAGA
1 ATTTCCATTTTGGTCCTTAACATATAGATA
102984 ATTTCCATTTTGGTC
1 ATTTCCATTTTGGTC
102999 TTTTTTTTAA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.43
Consensus pattern (30 bp):
ATTTCCATTTTGGTCCTTAACATATAGATA
Found at i:105830 original size:17 final size:17
Alignment explanation
Indices: 105808--105840 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
105798 AAACTAGAAC
105808 TTTGTTTTAAATTAAAT
1 TTTGTTTTAAATTAAAT
105825 TTTGTTTTAAATTAAA
1 TTTGTTTTAAATTAAA
105841 CTCTTGCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (17 bp):
TTTGTTTTAAATTAAAT
Found at i:109784 original size:20 final size:20
Alignment explanation
Indices: 109721--109786 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
109711 GTTGCAACCG
* *
109721 ATTTTTCATATACAAACCAG
1 ATTTTTCATATAGAAACCAA
* * **
109741 ATTTTT-TTAGGTTGAAACTTA
1 ATTTTTCATA--TAGAAACCAA
109762 ATTTTTCATATAGAAACCAA
1 ATTTTTCATATAGAAACCAA
109782 ATTTT
1 ATTTT
109787 AAGTTGCAAC
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
19 2 0.06
20 18 0.55
21 11 0.33
22 2 0.06
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (20 bp):
ATTTTTCATATAGAAACCAA
Found at i:112699 original size:2 final size:2
Alignment explanation
Indices: 112694--112721 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
112684 AACTCAACCA
112694 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
112722 AATTAAAGAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:113187 original size:2 final size:2
Alignment explanation
Indices: 113180--113268 Score: 61
Period size: 2 Copynumber: 49.0 Consensus size: 2
113170 TCGGGCCGGG
* *
113180 TA TA TA TA TA TA TA T- TA AA TA TA TA AA TA T- TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
113219 TT TT TA -A T- TT TA -A TT TA T- TA -A TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
113255 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
113269 ATTATTTTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
1 9 0.13
2 61 0.87
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:114199 original size:14 final size:14
Alignment explanation
Indices: 114171--114210 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
114161 TTTTTTTTGT
114171 GTTTGTGTT-GTTC
1 GTTTGTGTTCGTTC
*
114184 GTTTATGTTCGTTC
1 GTTTGTGTTCGTTC
*
114198 GTTCGTGTTCGTT
1 GTTTGTGTTCGTT
114211 TATTATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.03, C:0.12, G:0.28, T:0.57
Consensus pattern (14 bp):
GTTTGTGTTCGTTC
Found at i:114255 original size:31 final size:31
Alignment explanation
Indices: 114220--114300 Score: 144
Period size: 31 Copynumber: 2.6 Consensus size: 31
114210 TTATTATTTA
*
114220 AATGAACGAACATGAACAATCTATATTCCTT
1 AATGAACGAACATGAACAAGCTATATTCCTT
*
114251 AATGAACGAACATGAACAAGCTATATTCTTT
1 AATGAACGAACATGAACAAGCTATATTCCTT
114282 AATGAACGAACATGAACAA
1 AATGAACGAACATGAACAA
114301 AAAAAATTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.25
Consensus pattern (31 bp):
AATGAACGAACATGAACAAGCTATATTCCTT
Found at i:116619 original size:35 final size:35
Alignment explanation
Indices: 116573--116648 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
116563 CAAATAGTCC
* * *
116573 TCAATTTCATTCTAAACCCCAATTTTCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
116608 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
116643 TCAATT
1 TCAATT
116649 AAATTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:117262 original size:126 final size:128
Alignment explanation
Indices: 117042--117285 Score: 375
Period size: 126 Copynumber: 1.9 Consensus size: 128
117032 ATTATTTATA
* ** *
117042 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAAT-AA-TAATCATTTAACCAGGATCTGACATGTA
* *
117107 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGTT
64 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGTT
117172 ATCAATTTGGTCCTAAATTAAATAAAATTTAAT-A-AATCATTTAACCAGGATCTGACATGTATT
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAATAATCATTTAACCAGGATCTGACATGTATT
* * *
117235 AACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 AACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
117286 GAAGAAATTA
Statistics
Matches: 105, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
126 72 0.69
128 1 0.01
130 32 0.30
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (128 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAATAATCATTTAACCAGGATCTGACATGTATT
AACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGTT
Done.