Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003968.1 Hibiscus syriacus cultivar Beakdansim tig00008596_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: 74376
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:614 original size:24 final size:24
Alignment explanation
Indices: 587--641 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
577 TAAAACTATA
587 TATAA-ATGAATATATAATATAATT
1 TATAATAT-AATATATAATATAATT
* * *
611 TATAATATAATATGTATTATAAAT
1 TATAATATAATATATAATATAATT
*
635 AATAATA
1 TATAATA
642 ACGGTTTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
TATAATATAATATATAATATAATT
Found at i:1238 original size:2 final size:2
Alignment explanation
Indices: 1231--1255 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1221 ATATGTCTAC
1231 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
1256 AAAAGCATAA
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:10625 original size:129 final size:133
Alignment explanation
Indices: 10480--10718 Score: 389
Period size: 130 Copynumber: 1.8 Consensus size: 133
10470 ATACAATAAA
* * *
10480 TTTAAACTTAAATCAATACTAATTAATTAAAAAATTTATAT-AATTTTTTATTTTATAGCTATAT
1 TTTAAACCTAAATCAATACTAATTAATTAAAAAATTTATATAAAATTTTTATTTTATAACTATAT
10544 ATTATTTAAATTAATT-GTAAACT-TTTTTTT-AA-TAAAAAATATATATATATATATAACATAT
66 ATTATTTAAATTAATTAG-AAACTGTTTTTTTGAATTAAAAAATATATATATATATATAACATAT
10605 GACT
130 GACT
* *
10609 TTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTTTTATTTTATAATTATAT
1 TTTAAACCTAAATCAATACTAATTAATTAAAAAATTTATATAAAATTTTTATTTTATAACTATAT
10674 ATTATTTAAATTAATTAGAAACTGTTTTTTTGAATTAAAAAATAT
66 ATTATTTAAATTAATTAGAAACTGTTTTTTTGAATTAAAAAATAT
10719 TTAATTTTTA
Statistics
Matches: 100, Mismatches: 5, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
129 39 0.39
130 41 0.41
131 8 0.08
132 2 0.02
133 10 0.10
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.47
Consensus pattern (133 bp):
TTTAAACCTAAATCAATACTAATTAATTAAAAAATTTATATAAAATTTTTATTTTATAACTATAT
ATTATTTAAATTAATTAGAAACTGTTTTTTTGAATTAAAAAATATATATATATATATAACATATG
ACT
Found at i:15092 original size:21 final size:21
Alignment explanation
Indices: 15062--15109 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
15052 TATTTCATCA
*
15062 AAAGGATAAGTCCTTTAATCG
1 AAAGGTTAAGTCCTTTAATCG
*
15083 AAAGGTTAAGTCCTTTCATCG
1 AAAGGTTAAGTCCTTTAATCG
15104 AAAGGT
1 AAAGGT
15110 CTTAACCCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (21 bp):
AAAGGTTAAGTCCTTTAATCG
Found at i:18334 original size:16 final size:17
Alignment explanation
Indices: 18313--18352 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
18303 AAATATCTTC
18313 AAAAAATA-ATTTTAAG
1 AAAAAATATATTTTAAG
*
18329 AAAAAATATTTTTTAAG
1 AAAAAATATATTTTAAG
18346 ACAAAAA
1 A-AAAAA
18353 CTGGTCTGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 8 0.38
18 5 0.24
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (17 bp):
AAAAAATATATTTTAAG
Found at i:19094 original size:12 final size:10
Alignment explanation
Indices: 19053--19093 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
19043 TTTATCACAC
19053 CAAATTCTCT
1 CAAATTCTCT
19063 CAAATTCTCT
1 CAAATTCTCT
19073 -AAATTTCTCT
1 CAAA-TTCTCT
*
19083 CAAATACTCT
1 CAAATTCTCT
19093 C
1 C
19094 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:19142 original size:13 final size:14
Alignment explanation
Indices: 19114--19142 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19104 ATATTTTATA
19114 ATGTTTTTACTATT
1 ATGTTTTTACTATT
19128 ATGTTTTTACT-TT
1 ATGTTTTTACTATT
19141 AT
1 AT
19143 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (14 bp):
ATGTTTTTACTATT
Found at i:19411 original size:111 final size:111
Alignment explanation
Indices: 19217--19438 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
19207 TGAAAATCAT
*
19217 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
* *
19282 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
*
19328 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
19393 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
19439 TTTTTGTAAT
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:20987 original size:21 final size:18
Alignment explanation
Indices: 20949--20983 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
20939 GCAGCCACCG
20949 CAGCCATATATGATGCCA
1 CAGCCATATATGATGCCA
20967 CAGCCATATATGATGCC
1 CAGCCATATATGATGCC
20984 GCCATCACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (18 bp):
CAGCCATATATGATGCCA
Found at i:23420 original size:21 final size:21
Alignment explanation
Indices: 23378--23420 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
23368 TTTCTGGGCT
* * *
23378 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
23399 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
23420 A
1 A
23421 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:24150 original size:149 final size:150
Alignment explanation
Indices: 23961--24268 Score: 555
Period size: 150 Copynumber: 2.1 Consensus size: 150
23951 GGGTAGAGGG
* *
23961 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* * *
24025 TACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
24090 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
24110 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
24175 TACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
24240 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
24260 TCTACGCGG
1 TCTACGCGG
24269 CACTTTGGTG
Statistics
Matches: 152, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
149 51 0.34
150 101 0.66
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:30365 original size:21 final size:21
Alignment explanation
Indices: 30323--30365 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
30313 TTTCTGGGCT
* * *
30323 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
30344 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
30365 A
1 A
30366 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:31095 original size:149 final size:150
Alignment explanation
Indices: 30906--31221 Score: 555
Period size: 150 Copynumber: 2.1 Consensus size: 150
30896 GGGTAGAGGG
* *
30906 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* * *
30970 TACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
31035 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
31055 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
31120 TACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
31185 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
31205 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
31222 TGCATTTATA
Statistics
Matches: 159, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
149 52 0.33
150 107 0.67
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:32528 original size:50 final size:50
Alignment explanation
Indices: 32451--32574 Score: 133
Period size: 50 Copynumber: 2.5 Consensus size: 50
32441 CTACGTGGCG
** * * * * *
32451 TATAGCGCGGATC-GGGGGTGCGCTATACCCACGTGGCGCCAGATCACCG
1 TATAGCGCGGGGCAGGGGGCGCACTATACCCACGTGACGCCAAATCACCA
* * *
32500 TATATCGCGGGGCAGGGGGCGCACTATACCCACGTGACGCCAAATTAGCA
1 TATAGCGCGGGGCAGGGGGCGCACTATACCCACGTGACGCCAAATCACCA
* *
32550 TATAGCGCGGTGCAGGAGGCGCACT
1 TATAGCGCGGGGCAGGGGGCGCACT
32575 TTTCTGCTAA
Statistics
Matches: 61, Mismatches: 13, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
49 10 0.16
50 51 0.84
ACGTcount: A:0.22, C:0.28, G:0.34, T:0.16
Consensus pattern (50 bp):
TATAGCGCGGGGCAGGGGGCGCACTATACCCACGTGACGCCAAATCACCA
Found at i:37161 original size:3 final size:3
Alignment explanation
Indices: 37153--37222 Score: 86
Period size: 3 Copynumber: 23.3 Consensus size: 3
37143 ATATTAATTA
* * * * * *
37153 ATT ATT ATT ATT ATT ATA ATT ATA ATT ATA ATA ATA ATA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
37201 ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
37223 AATATATTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:37757 original size:11 final size:10
Alignment explanation
Indices: 37742--37785 Score: 56
Period size: 9 Copynumber: 4.5 Consensus size: 10
37732 ACAACCATTC
37742 AGAAAAGAAA
1 AGAAAAGAAA
37752 CAGAAAAG-AA
1 -AGAAAAGAAA
37762 AGAAAAGAAA
1 AGAAAAGAAA
*
37772 AG-AAAGAAG
1 AGAAAAGAAA
37781 AGAAA
1 AGAAA
37786 CTTATTGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 15 0.50
10 8 0.27
11 7 0.23
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (10 bp):
AGAAAAGAAA
Found at i:37761 original size:5 final size:5
Alignment explanation
Indices: 37742--37785 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
37732 ACAACCATTC
*
37742 AGAAA AGAAA CAGAAA AG-AA AGAAA AGAAA AG-AA AGAAG AGAAA
1 AGAAA AGAAA -AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
37786 CTTATTGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 8 0.24
5 21 0.62
6 5 0.15
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:37772 original size:14 final size:14
Alignment explanation
Indices: 37745--37785 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
37735 ACCATTCAGA
37745 AAAGAAACAGAAAAG
1 AAAGAAA-AGAAAAG
37760 AAAGAAAAGAAAAG
1 AAAGAAAAGAAAAG
*
37774 AAAGAAGAGAAA
1 AAAGAAAAGAAA
37786 CTTATTGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAAAG
Found at i:39332 original size:6 final size:7
Alignment explanation
Indices: 39311--39335 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39301 TGTCTCCATT
39311 AATTAAA
1 AATTAAA
39318 AATTAAA
1 AATTAAA
39325 AATTAAA
1 AATTAAA
39332 AATT
1 AATT
39336 TATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATTAAA
Found at i:51270 original size:83 final size:84
Alignment explanation
Indices: 51162--51442 Score: 415
Period size: 83 Copynumber: 3.3 Consensus size: 84
51152 CAAACATTAA
51162 TTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
1 TTGGAAGATGAATTTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
51226 G-CAGAACCAATCATTGAAT
65 GACAGAACCAATCATTGAAT
* * *
51245 TGGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGG-TTGG
1 TTGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
51309 ACAGAACCAATCATTGAAT
66 ACAGAACCAATCATTGAAT
* *
51328 TTGGAAGATGAATTGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 TTGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT-G
51393 TAAGAACTACAGAACCAATCATTGAAT
65 ---G----ACAGAACCAATCATTGAAT
51420 TTGGAAGATGAATTTGCTCATAG
1 TTGGAAGATGAATTTGCTCATAG
51443 TAGAAATAAG
Statistics
Matches: 177, Mismatches: 10, Indels: 13
0.88 0.05 0.06
Matches are distributed among these distances:
82 4 0.02
83 128 0.72
84 3 0.02
85 1 0.01
88 1 0.01
92 40 0.23
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (84 bp):
TTGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
ACAGAACCAATCATTGAAT
Found at i:51659 original size:114 final size:115
Alignment explanation
Indices: 51346--51649 Score: 576
Period size: 114 Copynumber: 2.7 Consensus size: 115
51336 TGAATTGGCT
*
51346 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAGAACTACAGAACCAA
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAACTACAGAACCAA
51411 TCATT-GAATTTGGAAGATGAATTTGCTCATAGTAGAAATAAGGAAACTC
66 TCATTGGAATTTGGAAGATGAATTTGCTCATAGTAGAAATAAGGAAACTC
51460 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAACTACAGAACCAA
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAACTACAGAACCAA
*
51525 TCA-TGGAATTTGGAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTC
66 TCATTGGAATTTGGAAGATGAATTTGCTCATAGTAGAAATAAGGAAACTC
51574 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAACTACAGAACCAA
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAACTACAGAACCAA
51639 TCATTGGAATT
66 TCATTGGAATT
51650 AAAAGATGAA
Statistics
Matches: 186, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
113 1 0.01
114 178 0.96
115 7 0.04
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.33
Consensus pattern (115 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAACTACAGAACCAA
TCATTGGAATTTGGAAGATGAATTTGCTCATAGTAGAAATAAGGAAACTC
Found at i:52544 original size:112 final size:111
Alignment explanation
Indices: 52368--53313 Score: 1558
Period size: 112 Copynumber: 8.5 Consensus size: 111
52358 TGGATTGACA
52368 TTTT-CAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * *
52432 AGAATTTGTTCAACCTTTTGTCTGAATTCATTACTTGATGGATTATT
66 AGAATTTGTTCAACCTTTT-ACTGAATCCATCACTTGATGGATCATC
*
52479 TTTTTCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
52544 AGAATTTGTTCAACCTTTTACATGAATCCATCATTTGATGGATCATC
66 AGAATTTGTTCAACCTTTTAC-TGAATCCATCACTTGATGGATCATC
* *
52591 TTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
52656 AGAATTTGTTCAACCTTTTACATGAATCCATCATTTGATGGATCATC
66 AGAATTTGTTCAACCTTTTAC-TGAATCCATCACTTGATGGATCATC
52703 TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
52768 AGAATTTGTTCAACCTTTTACCTGAATCCATCACTTGATGGATCATC
66 AGAATTTGTTCAACCTTTTA-CTGAATCCATCACTTGATGGATCATC
52815 TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
52880 AGAATTTGTTCAACCTTTTACCTGAATCCATCACTTGATGGATCATC
66 AGAATTTGTTCAACCTTTTA-CTGAATCCATCACTTGATGGATCATC
52927 TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* *
52992 AGAATTTGTTCAACCTTTTACCTGAATCCATCATTTAATGGATCATC
66 AGAATTTGTTCAACCTTTTA-CTGAATCCATCACTTGATGGATCATC
*
53039 TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAACGAAGAAGAAGTTCATAATGAGA
1 TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
** * *
53104 AGAA-TTCATCAACCTTTTGTCTGAATTCATCACTTGATGGATCATC
66 AGAATTTGTTCAACCTTTT-ACTGAATCCATCACTTGATGGATCATC
53150 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AGAAAGTTCATAATGA
1 TTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG-AAGTTCATAATGA
** * * *
53214 GAAGAGCTTGTTCAACCTTTTACATGAATTCATCAATTGATGGATCAAC
64 GAAGAATTTGTTCAACCTTTTAC-TGAATCCATCACTTGATGGATCATC
*
53263 ATTTT-CAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGA
1 -TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
53314 CAACTTTTTC
Statistics
Matches: 796, Mismatches: 29, Indels: 19
0.94 0.03 0.02
Matches are distributed among these distances:
111 52 0.07
112 697 0.88
113 43 0.05
114 4 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (111 bp):
TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAATTTGTTCAACCTTTTACTGAATCCATCACTTGATGGATCATC
Found at i:53330 original size:55 final size:55
Alignment explanation
Indices: 53259--53377 Score: 220
Period size: 55 Copynumber: 2.2 Consensus size: 55
53249 ATTGATGGAT
* *
53259 CAACATTTTCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGA
1 CAACTTTTTCAAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGA
53314 CAACTTTTTCAAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGA
1 CAACTTTTTCAAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGA
53369 CAACTTTTT
1 CAACTTTTT
53378 GCATAATCCT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 62 1.00
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (55 bp):
CAACTTTTTCAAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGA
Found at i:53712 original size:3 final size:3
Alignment explanation
Indices: 53704--53770 Score: 107
Period size: 3 Copynumber: 22.3 Consensus size: 3
53694 ATATTAATTA
* * *
53704 ATT ATT ATT ATT ATT ATA ATT ATA ATT ATA ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
53752 ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
53771 AATATATTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:54300 original size:11 final size:11
Alignment explanation
Indices: 54284--54320 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
54274 AACAACCATT
54284 CAGAAAAGAAA
1 CAGAAAAGAAA
54295 CAGAAAAG-AA
1 CAGAAAAGAAA
54305 -AGAAAAGAAA
1 CAGAAAAGAAA
*
54315 AAGAAA
1 CAGAAA
54321 GAAGAGAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 7 0.29
10 4 0.17
11 13 0.54
ACGTcount: A:0.76, C:0.05, G:0.19, T:0.00
Consensus pattern (11 bp):
CAGAAAAGAAA
Found at i:54308 original size:15 final size:15
Alignment explanation
Indices: 54288--54329 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
54278 ACCATTCAGA
54288 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
54303 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
54318 AAAGAAGAGAAA
1 AAAGAAAAGAAA
54330 CTTACTGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:54310 original size:20 final size:20
Alignment explanation
Indices: 54285--54329 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
54275 ACAACCATTC
*
54285 AGAAAAGAAACAGAAAAGAA-
1 AGAAAAGAAAAAG-AAAGAAG
54305 AGAAAAGAAAAAGAAAGAAG
1 AGAAAAGAAAAAGAAAGAAG
54325 AGAAA
1 AGAAA
54330 CTTACTGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (20 bp):
AGAAAAGAAAAAGAAAGAAG
Found at i:60222 original size:2 final size:2
Alignment explanation
Indices: 60215--60270 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
60205 TTTTTACATA
60215 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
60257 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
60271 GGCTGTCCCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64004 original size:10 final size:8
Alignment explanation
Indices: 63979--64036 Score: 64
Period size: 8 Copynumber: 6.9 Consensus size: 8
63969 TTTAGGTCTA
63979 TTTTATTT
1 TTTTATTT
63987 TTTTATTT
1 TTTTATTT
63995 TATGTTATTT
1 T-T-TTATTT
*
64005 TTCCTA-TT
1 TT-TTATTT
64013 TTTTATTT
1 TTTTATTT
64021 TTTTATTGT
1 TTTTATT-T
64030 TTTTATT
1 TTTTATT
64037 AAGTTTATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
7 2 0.05
8 22 0.51
9 12 0.28
10 7 0.16
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.79
Consensus pattern (8 bp):
TTTTATTT
Found at i:67543 original size:2 final size:2
Alignment explanation
Indices: 67536--67581 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
67526 ATCCTTTCGA
67536 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
67578 AT AT
1 AT AT
67582 CCCTTGTTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67842 original size:8 final size:8
Alignment explanation
Indices: 67829--67972 Score: 163
Period size: 8 Copynumber: 18.5 Consensus size: 8
67819 GAGGAAGAAT
67829 AAAAAAAG
1 AAAAAAAG
67837 AAAAAAAG
1 AAAAAAAG
67845 AAAAAAA-
1 AAAAAAAG
67852 AAAAAAA-
1 AAAAAAAG
67859 AAAAAAAG
1 AAAAAAAG
67867 -AAAAAAG
1 AAAAAAAG
67874 AAAAAAAG
1 AAAAAAAG
67882 AAAAAAAG
1 AAAAAAAG
67890 AAAAAAAG
1 AAAAAAAG
*
67898 GAAAAAAG
1 AAAAAAAG
*
67906 AAGAAAAG
1 AAAAAAAG
*
67914 AAGAAAAG
1 AAAAAAAG
*
67922 AAGAAAAG
1 AAAAAAAG
*
67930 AAGAAAA-
1 AAAAAAAG
*
67937 ATAAAAAG
1 AAAAAAAG
**
67945 AAAAAATT
1 AAAAAAAG
67953 AAAAAATA-
1 AAAAAA-AG
*
67961 AAAGAAAG
1 AAAAAAAG
67969 AAAA
1 AAAA
67973 CTGATCAAAT
Statistics
Matches: 120, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
7 27 0.22
8 93 0.77
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:67904 original size:1 final size:1
Alignment explanation
Indices: 67829--67896 Score: 82
Period size: 1 Copynumber: 68.0 Consensus size: 1
67819 GAGGAAGAAT
* * * * * *
67829 AAAAAAAGAAAAAAAGAAAAAAAAAAAAAAAAAAAAAGAAAAAAGAAAAAAAGAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
67894 AAA
1 AAA
67897 GGAAAAAAGA
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:67955 original size:14 final size:15
Alignment explanation
Indices: 67822--67957 Score: 70
Period size: 15 Copynumber: 9.0 Consensus size: 15
67812 ACACAGAGAG
*
67822 GAAGAATAA-AAAAA
1 GAAGAAAAATAAAAA
*
67836 GAA-AAAAAGAAAAA
1 GAAGAAAAATAAAAA
*
67850 -AA-AAAAAAAAAAA
1 GAAGAAAAATAAAAA
*
67863 AAAGAAAAA-AGAAAA
1 GAAGAAAAATA-AAAA
* *
67878 AAAGAAAAAAAGAAAA
1 GAAGAAAAATA-AAAA
* *
67894 AAAGGAAAAAAGAAGAAAA
1 GAA-G-AAAAA-TA-AAAA
67913 GAAGAAAAGA-AGAAAA
1 GAAGAAAA-ATA-AAAA
67929 GAAGAAAAATAAAAA
1 GAAGAAAAATAAAAA
*
67944 GAA-AAAATTAAAAA
1 GAAGAAAAATAAAAA
67958 ATAAAAGAAA
Statistics
Matches: 108, Mismatches: 4, Indels: 20
0.82 0.03 0.15
Matches are distributed among these distances:
13 16 0.15
14 21 0.19
15 26 0.24
16 24 0.22
17 5 0.05
18 7 0.06
19 9 0.08
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (15 bp):
GAAGAAAAATAAAAA
Found at i:67963 original size:14 final size:13
Alignment explanation
Indices: 67831--67957 Score: 61
Period size: 13 Copynumber: 9.4 Consensus size: 13
67821 GGAAGAATAA
67831 AAAAAGAAAAAA-
1 AAAAAGAAAAAAT
67843 AGAAAA-AAAAAA-
1 A-AAAAGAAAAAAT
*
67855 AAAAA-AAAAAAGA
1 AAAAAGAAAAAA-T
67868 AAAAAGAAAAAA-
1 AAAAAGAAAAAAT
67880 AGAAAA-AAAGAAA-
1 A-AAAAGAAA-AAAT
* *
67893 AAAAGGAAAAAAGA
1 AAAAAGAAAAAA-T
*
67907 AGAAAAGAAGAAAAGA
1 A-AAAAGAA-AAAA-T
67923 AGAAAAGAAGAAAAAT
1 A-AAAAG-A-AAAAAT
67939 AAAAAGAAAAAATT
1 AAAAAGAAAAAA-T
67953 AAAAA
1 AAAAA
67958 ATAAAAGAAA
Statistics
Matches: 98, Mismatches: 3, Indels: 26
0.77 0.02 0.20
Matches are distributed among these distances:
11 10 0.10
12 18 0.18
13 25 0.26
14 14 0.14
15 11 0.11
16 14 0.14
17 5 0.05
18 1 0.01
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.02
Consensus pattern (13 bp):
AAAAAGAAAAAAT
Found at i:68651 original size:28 final size:28
Alignment explanation
Indices: 68608--68682 Score: 132
Period size: 28 Copynumber: 2.7 Consensus size: 28
68598 TCAAGAAGCC
*
68608 AACCTAAAACACATTACCTCCCTAAATT
1 AACCTGAAACACATTACCTCCCTAAATT
*
68636 AACCTGAAACATATTACCTCCCTAAATT
1 AACCTGAAACACATTACCTCCCTAAATT
68664 AACCTGAAACACATTACCT
1 AACCTGAAACACATTACCT
68683 TCCCAAGTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.41, C:0.31, G:0.03, T:0.25
Consensus pattern (28 bp):
AACCTGAAACACATTACCTCCCTAAATT
Found at i:70583 original size:193 final size:192
Alignment explanation
Indices: 70225--70633 Score: 569
Period size: 193 Copynumber: 2.1 Consensus size: 192
70215 AATCAAGCAA
* * * * *
70225 GATGA-TAAGTCATTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAAATGAGTTTTTAG
1 GATGAGTAAGTCCTTCGAGCCATCCATAAAACCTTCGGGCAGGATGTTCTCAAATGAGTTTTAAG
* * * * * *
70289 AAATTAAGCCTGATTTTTAGGGGTTTCTTGGTGATTATTTTCAAAGTTTTTAAAAGGAAGCTAAG
66 AAACTAAGCCTAAGTTTTAGGGGTTTCTTGATGATTATTCTCAAAGTTTTTAAAAGGAAACTAAG
* * *
70354 CCTAATTTTTAGGGGTTCCTTGATGACAACTAAGAAACTAGGCTTGATTTTCAATGGTTTCTT
131 CCTAATTTTTAGGGCTTCCTT-ATGACAACTAAGAAACTAAGCTTGATTTTCAAGGGTTTCTT
* *
70417 GATGAGTAAGTCCTTCGAGCCATTCATAAAACCTTCGGGTAGGATGTTCTCAAATGAGTTTTAAG
1 GATGAGTAAGTCCTTCGAGCCATCCATAAAACCTTCGGGCAGGATGTTCTCAAATGAGTTTTAAG
70482 AAACTAAGCCTAAGTTTTAGGGGTTTCTTGATGATTA-TCTCAAAAGAGTTTTTTAAAAGGAAAC
66 AAACTAAGCCTAAGTTTTAGGGGTTTCTTGATGATTATTCTC--AA-AG-TTTTTAAAAGGAAAC
70546 TAAGCCTAATTTTTAGGGACTT-C-T-TGACAACTAAGAAACTAAGCTTGATTTTCAAGGGTTTC
127 TAAGCCTAATTTTTAGGG-CTTCCTTATGACAACTAAGAAACTAAGCTTGATTTTCAAGGGTTTC
70608 TT
191 TT
70610 GATGAGTAAGTCCTTCTG-GCCATC
1 GATGAGTAAGTCCTTC-GAGCCATC
70634 AGTAAGTCTT
Statistics
Matches: 193, Mismatches: 17, Indels: 13
0.87 0.08 0.06
Matches are distributed among these distances:
192 8 0.04
193 144 0.75
194 3 0.02
195 3 0.02
196 33 0.17
197 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (192 bp):
GATGAGTAAGTCCTTCGAGCCATCCATAAAACCTTCGGGCAGGATGTTCTCAAATGAGTTTTAAG
AAACTAAGCCTAAGTTTTAGGGGTTTCTTGATGATTATTCTCAAAGTTTTTAAAAGGAAACTAAG
CCTAATTTTTAGGGCTTCCTTATGACAACTAAGAAACTAAGCTTGATTTTCAAGGGTTTCTT
Found at i:70969 original size:54 final size:56
Alignment explanation
Indices: 70872--70987 Score: 137
Period size: 54 Copynumber: 2.1 Consensus size: 56
70862 AAAGATTTTT
* * * *** *
70872 AGAAACTAAGCTTAATTTTTAGGGGTTTCTTGATGTTTTTAAATAAAT-TTTTGAA
1 AGAAGCTAAGCCTAATTTTTAAGGGTTTCTTGATAACTGTAAATAAATCTTTTGAA
* *
70927 AGAAGCTAAGCCTAA-TTTTAAGGGTTTCTTGATAACTGTAAATGAATCTTTTTAA
1 AGAAGCTAAGCCTAATTTTTAAGGGTTTCTTGATAACTGTAAATAAATCTTTTGAA
70982 AGAAGC
1 AGAAGC
70988 AAAATTTTCC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 26 0.51
55 25 0.49
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (56 bp):
AGAAGCTAAGCCTAATTTTTAAGGGTTTCTTGATAACTGTAAATAAATCTTTTGAA
Found at i:70984 original size:55 final size:54
Alignment explanation
Indices: 70807--70987 Score: 134
Period size: 55 Copynumber: 3.2 Consensus size: 54
70797 TCCGAAGAAA
* * * *
70807 TTTTAAACGAAGCTAAGCCTAATTTATACGGG-TTCATTGATGACAACTGAAAACGAAAGAT
1 TTTTAAA-GAAGCTAAGCCTAATTT-TAAGGGTTTC-TTGAT---AACTGTAAATG-AA-TT
* * * *** * *
70868 TTTT--AGAAACTAAGCTTAATTTTTAGGGGTTTCTTGATGTTTTTAAATAAATT
1 TTTTAAAGAAGCTAAGCCTAA-TTTTAAGGGTTTCTTGATAACTGTAAATGAATT
*
70921 TTTGAAAGAAGCTAAGCCTAATTTTAAGGGTTTCTTGATAACTGTAAATGAATCT
1 TTTTAAAGAAGCTAAGCCTAATTTTAAGGGTTTCTTGATAACTGTAAATGAAT-T
70976 TTTTAAAGAAGC
1 TTTTAAAGAAGC
70988 AAAATTTTCC
Statistics
Matches: 94, Mismatches: 21, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
53 4 0.04
54 28 0.30
55 29 0.31
58 22 0.23
59 7 0.07
61 4 0.04
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.37
Consensus pattern (54 bp):
TTTTAAAGAAGCTAAGCCTAATTTTAAGGGTTTCTTGATAACTGTAAATGAATT
Found at i:71985 original size:91 final size:91
Alignment explanation
Indices: 71867--72226 Score: 506
Period size: 91 Copynumber: 4.0 Consensus size: 91
71857 TGAGGGATTG
* *
71867 ACATTTCCGATGGAGAGTTCATAATGAGATA-AACTCATCCAACGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATAGAGAGTTCATAATGAGA-AGAACTCATCCAACGAGGGAGAAGAAGTTCATAAT
*
71931 GAGAAGAACTTGTTCAACCTTGGCTCA
65 GAGAAGAACTTGTTCAACATTGGCTCA
* * * *
71958 ACATTTCCAATAGAGAGTTCATAATGAGAAAAAGTCATCCAACGAGGGAGGATAAGTTCATAATG
1 ACATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATG
* *
72023 TGAAGAACTTGTTCAACCTTGGCTCA
66 AGAAGAACTTGTTCAACATTGGCTCA
* *
72049 ACATTTCCAGTAGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTTATAATG
1 ACATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATG
* *
72114 AGAAGAACTTGTTCAATATTGACTCA
66 AGAAGAACTTGTTCAACATTGGCTCA
* * * * * * *
72140 ATATTTCCAGTGGAGAGTTTATAATGAGAAGGACTCATCCAACAATGGAGAAGAAGTTCATAATG
1 ACATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATG
* *
72205 ATAAGAACTTATTCAACATTGG
66 AGAAGAACTTGTTCAACATTGG
72227 TTTGATTCCA
Statistics
Matches: 241, Mismatches: 27, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
90 1 0.00
91 240 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (91 bp):
ACATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAACATTGGCTCA
Found at i:72348 original size:117 final size:117
Alignment explanation
Indices: 72137--72637 Score: 602
Period size: 117 Copynumber: 4.3 Consensus size: 117
72127 CAATATTGAC
* * * * *
72137 TCAATATTTCCAGTGGAGAGTTTATAATGAGAAGGACTCATCCAACAATGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAAGGGAGAAGAAGTTCATA
* * * *
72202 ATGATAAGAACTTATTCAACATTGGTTTGATTCCATCAAAGAATGAGGTGGA
66 ATGAGAAGAACTTGTTCAACCTTTGTTTGATTCCATCAAAGAATGAGGTGGA
* * * *
72254 TCAACATTTCTAGTGGAGAGTTCATAATGAGAATAACTCATTCGATAAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAAGGGAGAAGAAGTTCATA
* * *
72319 ATGAGAATAACTTGTTCAACCTTTGTTTGATTCCATCACAGAAGGAGGTGGA
66 ATGAGAAGAACTTGTTCAACCTTTGTTTGATTCCATCAAAGAATGAGGTGGA
* * * *
72371 TCAACATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAATAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAAGGGAGAAGAAGTTCATA
** *
72436 AT--G-AGAACTTGTTTCAACCTTTGTTCAATACCATCACAA-AATGAGGTGGA
66 ATGAGAAGAACTTG-TTCAACCTTTGTTTGATTCCATCA-AAGAATGAGGTGGA
* *
72486 TCAATATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAAGGGAGAAGAAGTTCATA
* * * * *
72551 GTGAGAAGAACTTGTTCAACC-TTG-GTGATTCCATCACATAATGAAGTGGA
66 ATGAGAAGAACTTGTTCAACCTTTGTTTGATTCCATCAAAGAATGAGGTGGA
* * ** * *
72601 -CTGATATCACCAGCGAAGAGTTCATAATGAGAAGAAC
1 TC-AACATTTCCAGTGGAGAGTTCATAATGAGAAGAAC
72638 ACGTCCGATT
Statistics
Matches: 331, Mismatches: 46, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
114 9 0.03
115 142 0.43
116 4 0.01
117 168 0.51
118 8 0.02
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.27
Consensus pattern (117 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTGTTTGATTCCATCAAAGAATGAGGTGGA
Found at i:72550 original size:232 final size:230
Alignment explanation
Indices: 72137--72588 Score: 620
Period size: 232 Copynumber: 1.9 Consensus size: 230
72127 CAATATTGAC
* * * * * *
72137 TCAATATTTCCAGTGGAGAGTTTATAATGAGAAGGACTCATCCAACAATGGAGAAGAAGTTCATA
1 TCAACATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTCATA
** * *
72202 ATGATAAGAACTTATTCAACATTGGTTTGATTCCATCAAAGAATGAGGTGGATCAACATTTCTAG
66 ATG--AAGAACTTATTCAACATTGGTTCAATACCATCAAAGAATGAGGTGGATCAACATTTCCAG
* * * *
72267 TGGAGAGTTCATAATGAGAATAACTCATTCGATAAGGGAGAAGAAGTTCATAATGAGAATAACTT
129 TGGAGAGTTCATAATGAGAAGAACTCATCCGACAAGGGAGAAGAAGTTCATAATGAGAAGAACTT
*
72332 GTTCAACCTTTGTTTGATTCCATCACAGAAGGAGGTGGA
194 GTTCAACC-TTG-GTGATTCCATCACAGAAGGAGGTGGA
* * *
72371 TCAACATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAATAAGTTCATA
1 TCAACATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTCATA
* * * *
72436 ATG-AGAACTTGTTTCAACCTTTGTTCAATACCATCACAA-AATGAGGTGGATCAATATTTCCAG
66 ATGAAGAACTT-ATTCAACATTGGTTCAATACCATCA-AAGAATGAGGTGGATCAACATTTCCAG
* *
72499 TGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCATAGTGAGAAGAACTT
129 TGGAGAGTTCATAATGAGAAGAACTCATCCGACAAGGGAGAAGAAGTTCATAATGAGAAGAACTT
72564 GTTCAACCTTGGTGATTCCATCACA
194 GTTCAACCTTGGTGATTCCATCACA
72589 TAATGAAGTG
Statistics
Matches: 192, Mismatches: 24, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
230 13 0.07
231 10 0.05
232 108 0.56
233 2 0.01
234 59 0.31
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.27
Consensus pattern (230 bp):
TCAACATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTCATA
ATGAAGAACTTATTCAACATTGGTTCAATACCATCAAAGAATGAGGTGGATCAACATTTCCAGTG
GAGAGTTCATAATGAGAAGAACTCATCCGACAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACCTTGGTGATTCCATCACAGAAGGAGGTGGA
Found at i:74007 original size:20 final size:20
Alignment explanation
Indices: 73957--73999 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 20
73947 TTTTTTTTTA
73957 TTTTATGTTGTTTTTCCTGTTT
1 TTTTAT-TT-TTTTTCCTGTTT
73979 TTTTATTTTTTTTCCTGTTT
1 TTTTATTTTTTTTCCTGTTT
73999 T
1 T
74000 ATTTTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.05, C:0.09, G:0.09, T:0.77
Consensus pattern (20 bp):
TTTTATTTTTTTTCCTGTTT
Done.