Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005360.1 Hibiscus syriacus cultivar Beakdansim tig00012172_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: 79837
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:4439 original size:3 final size:3
Alignment explanation
Indices: 4431--4501 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
4421 GGCACCTCAC
4431 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
4479 CCT CCT CCT CCT CCT CCT CCT CC
1 CCT CCT CCT CCT CCT CCT CCT CC
4502 ATTAAAGTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CCT
Found at i:4979 original size:147 final size:147
Alignment explanation
Indices: 4768--5060 Score: 502
Period size: 147 Copynumber: 2.0 Consensus size: 147
4758 TCCTTTTGCT
* *
4768 ATTGCCTGCCACGTTCATACAATGTGCCAAAATGAAGCCCCTATCCTAATTCCAATCTACGTGCC
1 ATTGCCAGCCACGTTCATACAATGTGCCAAAATGAAGCCCCTAGCCTAATTCCAATCTACGTGCC
*
4833 AGCTTACCACCATTATTTCA-TTTTTTCAGCTTACTCGAAA-ACAAGAAA-ACTATAGCAGAACT
66 ACCTTACCACCATTATTTCATTTTTTTCAGCTTACTCGAAAGACAAGAAACA-TATAGCAGAACT
4895 TAAACATACAGTTACATA
130 TAAACATACAGTTACATA
4913 ATTGCCAGCCACGTTCATACAATGTGCCCAAAATGAAGCCCCTAAGCCTAATTCCAATCTACGTG
1 ATTGCCAGCCACGTTCATACAATGTG-CCAAAATGAAGCCCCT-AGCCTAATTCCAATCTACGTG
*
4978 CCACCTTACCACCATTATTTCATTTTTTTTAGCTTACTCGAAAGACAAGAAACATATAGCAGAAC
64 CCACCTTACCACCATTATTTCATTTTTTTCAGCTTACTCGAAAGACAAGAAACATATAGCAGAAC
5043 TTAAACATACAGTTACAT
129 TTAAACATACAGTTACAT
5061 GGAATATGCA
Statistics
Matches: 139, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
145 25 0.18
146 16 0.12
147 41 0.29
148 19 0.14
149 37 0.27
150 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.28
Consensus pattern (147 bp):
ATTGCCAGCCACGTTCATACAATGTGCCAAAATGAAGCCCCTAGCCTAATTCCAATCTACGTGCC
ACCTTACCACCATTATTTCATTTTTTTCAGCTTACTCGAAAGACAAGAAACATATAGCAGAACTT
AAACATACAGTTACATA
Found at i:7071 original size:10 final size:10
Alignment explanation
Indices: 7056--7134 Score: 65
Period size: 10 Copynumber: 7.9 Consensus size: 10
7046 ATGTTCGTTC
7056 GTTTATGTTA
1 GTTTATGTTA
7066 GTTTATGTTA
1 GTTTATGTTA
**
7076 GTTTACATTCA
1 GTTTATGTT-A
*
7087 -TTTATATTA
1 GTTTATGTTA
*
7096 GTTTACGTTCA
1 GTTTATGTT-A
7107 -TTTATGTTA
1 GTTTATGTTA
*
7116 GTTTACGTTCA
1 GTTTATGTT-A
7127 -TTTATGTT
1 GTTTATGTT
7135 CATTCGTTTG
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
9 2 0.04
10 51 0.91
11 3 0.05
ACGTcount: A:0.22, C:0.08, G:0.14, T:0.57
Consensus pattern (10 bp):
GTTTATGTTA
Found at i:7090 original size:20 final size:20
Alignment explanation
Indices: 7067--7134 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
7057 TTTATGTTAG
*
7067 TTTATGTTAGTTTACATTCA
1 TTTATGTTAGTTTACGTTCA
*
7087 TTTATATTAGTTTACGTTCA
1 TTTATGTTAGTTTACGTTCA
7107 TTTATGTTAGTTTACGTTCA
1 TTTATGTTAGTTTACGTTCA
7127 TTTATGTT
1 TTTATGTT
7135 CATTCGTTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.22, C:0.09, G:0.12, T:0.57
Consensus pattern (20 bp):
TTTATGTTAGTTTACGTTCA
Found at i:7154 original size:24 final size:24
Alignment explanation
Indices: 7122--7179 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
7112 GTTAGTTTAC
* *
7122 GTTCATTTATGTTCATTCGTTTGT
1 GTTCGTTTATGTTCATTCATTTGT
* * *
7146 GTTTGTTTACGTTCGTTCATTTGT
1 GTTCGTTTATGTTCATTCATTTGT
7170 GTTCGTTTAT
1 GTTCGTTTAT
7180 CATTTAAACG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.10, C:0.12, G:0.19, T:0.59
Consensus pattern (24 bp):
GTTCGTTTATGTTCATTCATTTGT
Found at i:8154 original size:253 final size:252
Alignment explanation
Indices: 7655--8124 Score: 666
Period size: 253 Copynumber: 1.9 Consensus size: 252
7645 CTATATTTTA
* *
7655 GGTTGCGCCTAAAATGTTATCAGAGTTTAAACTAATGGATCCTTAAATTTTCCCATGATAAGAAA
1 GGTTGCACCTAAAATGTTATCAGAGTTTAAACTAATGGAGCCTTAAATTTTCCCATGATAAGAAA
* * *
7720 ATAAGTTAAAAGATGAAAATGTTATGAATATATATAAGAAATACGGTTGCACCCAATAATTTCAT
66 ATAAGTAAAAAGATGAAAATGTTATGAATATATATAAGAAAGACGATTGCACCCAATAATTTCAT
* * *
7785 GGTTTACTAAGAAATAGGTTATGGTATTTAATGTTAAAATTATTATTAATAAAATAGTTTGCGCC
131 GGTTCACTAAGAAATAGGTTATGGAATGTAATGTTAAAATTATTATTAATAAAATAG-TTGCGCC
**
7850 CAAGAATGTCATGGTTCACTAAAAAGCAAGTTGCAACCTGAAATCTTAATATCTTAAC
195 CAAGAATGTCATAATTCACTAAAAAGCAAGTTGCAACCTGAAATCTTAATATCTTAAC
* * *
7908 GGTTGCACCTAAAATGTTATCAGAGTTTAAGCTGATGGAGCTTTAAATTTTCCCATGATAAG-AA
1 GGTTGCACCTAAAATGTTATCAGAGTTTAAACTAATGGAGCCTTAAATTTTCCCATGATAAGAAA
** *
7972 ATAAGTAAAAAGATGAAAATGTTATGAATATATAT-AGAAAGACGATTGCGTCTAATAATGTT-A
66 ATAAGTAAAAAGATGAAAATGTTATGAATATATATAAGAAAGACGATTGCACCCAATAAT-TTCA
* * *
8035 TGGTTCACTAAGAACA-A-GTTGT-GAACTGTAATGTTAATATTTTTATTAATAAAATAG-TGCG
130 TGGTTCACTAAGAA-ATAGGTTATGGAA-TGTAATGTTAAAATTATTATTAATAAAATAGTTGCG
*
8096 CCCAAGAATGTTATAATTCACTAAGAAAG
193 CCCAAGAATGTCATAATTCACTAA-AAAG
8125 TAGATTCTAT
Statistics
Matches: 193, Mismatches: 20, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
248 25 0.13
249 6 0.03
250 32 0.17
251 34 0.18
252 39 0.20
253 57 0.30
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.33
Consensus pattern (252 bp):
GGTTGCACCTAAAATGTTATCAGAGTTTAAACTAATGGAGCCTTAAATTTTCCCATGATAAGAAA
ATAAGTAAAAAGATGAAAATGTTATGAATATATATAAGAAAGACGATTGCACCCAATAATTTCAT
GGTTCACTAAGAAATAGGTTATGGAATGTAATGTTAAAATTATTATTAATAAAATAGTTGCGCCC
AAGAATGTCATAATTCACTAAAAAGCAAGTTGCAACCTGAAATCTTAATATCTTAAC
Found at i:8202 original size:19 final size:19
Alignment explanation
Indices: 8178--8220 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
8168 ATGTTGCACC
8178 AAGAATGTCATGATTCACT
1 AAGAATGTCATGATTCACT
* * *
8197 AAGAATTTCATGGTTCAGT
1 AAGAATGTCATGATTCACT
8216 AAGAA
1 AAGAA
8221 ATAGGTTGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.30
Consensus pattern (19 bp):
AAGAATGTCATGATTCACT
Found at i:8466 original size:71 final size:72
Alignment explanation
Indices: 8321--8483 Score: 197
Period size: 71 Copynumber: 2.2 Consensus size: 72
8311 TATTATTATT
* *
8321 GATACTTTTAAATATTAAAAAAGTTGAACATAAGATTAAAATTTAAAATATCGATACTTATGCAG
1 GATACTTTTAAA-ATTGAAAAAGTTGAACATAAGATCAAAATTTAAAATATCGATACTTATGCAG
*
8386 TAATGATC
65 TAATAATC
* * *
8394 GATACTTTTAAAATTGAAAAAGTTGATA-A-AAGATCGAAATTTTAAATATCGATACTTATG-TG
1 GATACTTTTAAAATTGAAAAAGTTGA-ACATAAGATCAAAATTTAAAATATCGATACTTATGCAG
*
8456 ATGATAATC
65 -TAATAATC
*
8465 GATACTTTTAGATATTGAA
1 GATACTTTTA-AAATTGAA
8484 CGCGTTGATG
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
70 1 0.01
71 44 0.56
72 21 0.27
73 13 0.16
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (72 bp):
GATACTTTTAAAATTGAAAAAGTTGAACATAAGATCAAAATTTAAAATATCGATACTTATGCAGT
AATAATC
Found at i:8888 original size:99 final size:100
Alignment explanation
Indices: 8753--9054 Score: 421
Period size: 101 Copynumber: 3.0 Consensus size: 100
8743 ACTTTTGCAT
* * * * *
8753 AAAAAGGTGCTACCTATTACGTTATCACGAGCAACATGTTTTATCTTACATTTGAATAATATAAA
1 AAAAAGGTGCTACCTAGTACGTT-T-ATGAGCAACATGTTTTGTCTTACTTTTGTATAATATAAA
*
8818 AGGTTTCATACTTATAACTTAAACGGTTGACATTAAA
64 TGGTTTCATACTTATAACTTAAACGGTTGACATTAAA
*
8855 AAAAAGGCGCTACCTAGTAC-TTTATGAGCAACATGTTTTGTCTTACTTTTGTATAATATAAATG
1 AAAAAGGTGCTACCTAGTACGTTTATGAGCAACATGTTTTGTCTTACTTTTGTATAATATAAATG
*
8919 GTTTCATACTTATAATTTAAACGGTTGACATT-AA
66 GTTTCATACTTATAACTTAAACGGTTGACATTAAA
* * *
8953 AAAAATGTGCTACCTAGTACGTTATTATGAGTAACATGTTTTGTCTTACTTTTGTATAATATAGA
1 AAAAAGGTGCTACCTAGTACG-T-TTATGAGCAACATGTTTTGTCTTACTTTTGTATAATATAAA
* * *
9018 TGATTTCATACTTATAACTTAAACAGATGACA-TAAA
64 TGGTTTCATACTTATAACTTAAACGGTTGACATTAAA
9054 A
1 A
9055 TAGGTGATAC
Statistics
Matches: 180, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
98 20 0.11
99 67 0.37
100 3 0.02
101 72 0.40
102 18 0.10
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (100 bp):
AAAAAGGTGCTACCTAGTACGTTTATGAGCAACATGTTTTGTCTTACTTTTGTATAATATAAATG
GTTTCATACTTATAACTTAAACGGTTGACATTAAA
Found at i:9015 original size:101 final size:101
Alignment explanation
Indices: 8753--9054 Score: 432
Period size: 99 Copynumber: 3.0 Consensus size: 101
8743 ACTTTTGCAT
* * * * * *
8753 AAAAAGGTGCTACCTATTACGTTATCACGAGCAACATGTTTTATCTTACATTTGAATAATATAAA
1 AAAAAGGTGCTACCTAGTACGTTATTATGAGCAACATGTTTTGTCTTACTTTTGTATAATATAAA
*
8818 AGGTTTCATACTTATAACTTAAACGGTTGACATTAAA
66 TGGTTTCATACTTATAACTTAAACGGTTGACATT-AA
*
8855 AAAAAGGCGCTACCTAGTAC--T-TTATGAGCAACATGTTTTGTCTTACTTTTGTATAATATAAA
1 AAAAAGGTGCTACCTAGTACGTTATTATGAGCAACATGTTTTGTCTTACTTTTGTATAATATAAA
*
8917 TGGTTTCATACTTATAATTTAAACGGTTGACATTAA
66 TGGTTTCATACTTATAACTTAAACGGTTGACATTAA
* * *
8953 AAAAATGTGCTACCTAGTACGTTATTATGAGTAACATGTTTTGTCTTACTTTTGTATAATATAGA
1 AAAAAGGTGCTACCTAGTACGTTATTATGAGCAACATGTTTTGTCTTACTTTTGTATAATATAAA
* * *
9018 TGATTTCATACTTATAACTTAAACAGATGACA-TAA
66 TGGTTTCATACTTATAACTTAAACGGTTGACATTAA
9053 AA
1 AA
9055 TAGGTGATAC
Statistics
Matches: 180, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
98 20 0.11
99 68 0.38
100 7 0.04
101 67 0.37
102 18 0.10
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (101 bp):
AAAAAGGTGCTACCTAGTACGTTATTATGAGCAACATGTTTTGTCTTACTTTTGTATAATATAAA
TGGTTTCATACTTATAACTTAAACGGTTGACATTAA
Found at i:13348 original size:20 final size:20
Alignment explanation
Indices: 13319--13361 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
13309 ATTTCACCAC
*
13319 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
13339 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
13359 ATG
1 ATG
13362 GGCTTTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:21561 original size:39 final size:39
Alignment explanation
Indices: 21516--21783 Score: 119
Period size: 39 Copynumber: 7.0 Consensus size: 39
21506 TAGGGAATCA
*
21516 TAACATTCTTGGGCGCAACCATTTTATTAATAAAAATAT
1 TAACATTCTTGGGCACAACCATTTTATTAATAAAAATAT
* ** * * * * *
21555 TAACATTCTAGATCTCAA-CATATTTCTTAGT-GAACTA-
1 TAACATTCTTGGGCACAACCAT-TTTATTAATAAAAATAT
*
21592 TAACATTCTTGGGTGA-AACCCATTTT-TTAATAAAAATAT
1 TAACATTCTTGGG-CACAA-CCATTTTATTAATAAAAATAT
* * ** * * ***
21631 TATCATTAC-AGATCACAACC-TATTTCTTAAT--GAACCG
1 TAACATT-CTTGGGCACAACCAT-TTTATTAATAAAAATAT
*
21668 TGACATTCTTGGGCACAACCATTTTATTAATAAAAATAT
1 TAACATTCTTGGGCACAACCATTTTATTAATAAAAATAT
* ** * * * ***
21707 TAACATTCTAGATCACAA-CATATTACTTAGT--GAACCG
1 TAACATTCTTGGGCACAACCATTTTA-TTAATAAAAATAT
*
21744 TGACATTCTTGGGCACAACCCATTTTATTAATAAAAATAT
1 TAACATTCTTGGGCACAA-CCATTTTATTAATAAAAATAT
21784 ATTCATAACA
Statistics
Matches: 155, Mismatches: 55, Indels: 37
0.63 0.22 0.15
Matches are distributed among these distances:
36 1 0.01
37 56 0.36
38 31 0.20
39 64 0.41
40 3 0.02
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (39 bp):
TAACATTCTTGGGCACAACCATTTTATTAATAAAAATAT
Found at i:21597 original size:76 final size:77
Alignment explanation
Indices: 21501--21783 Score: 387
Period size: 76 Copynumber: 3.7 Consensus size: 77
21491 TGCAACTTGC
* * *
21501 TTTCTTAGGGAATCATAACATTCTTGGGCGCAA-CCATTTTATTAATAAAAATATTAACATTCTA
1 TTTCTTAGTGAACCATAACATTCTTGGGCACAACCCATTTTATTAATAAAAATATTAACATTCTA
*
21565 GATCTCAACATA
66 GATCACAACATA
* * *
21577 TTTCTTAGTGAACTATAACATTCTTGGGTGA-AACCCATTTT-TTAATAAAAATATTATCATTAC
1 TTTCTTAGTGAACCATAACATTCTTGGG-CACAACCCATTTTATTAATAAAAATATTAACATT-C
*
21640 -AGATCACAACCTA
64 TAGATCACAACATA
* * *
21653 TTTCTTAATGAACCGTGACATTCTTGGGCACAA-CCATTTTATTAATAAAAATATTAACATTCTA
1 TTTCTTAGTGAACCATAACATTCTTGGGCACAACCCATTTTATTAATAAAAATATTAACATTCTA
21717 GATCACAACATA
66 GATCACAACATA
* * *
21729 TTACTTAGTGAACCGTGACATTCTTGGGCACAACCCATTTTATTAATAAAAATAT
1 TTTCTTAGTGAACCATAACATTCTTGGGCACAACCCATTTTATTAATAAAAATAT
21784 ATTCATAACA
Statistics
Matches: 183, Mismatches: 17, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
75 9 0.05
76 145 0.79
77 29 0.16
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (77 bp):
TTTCTTAGTGAACCATAACATTCTTGGGCACAACCCATTTTATTAATAAAAATATTAACATTCTA
GATCACAACATA
Found at i:21685 original size:37 final size:37
Alignment explanation
Indices: 21644--21768 Score: 99
Period size: 37 Copynumber: 3.3 Consensus size: 37
21634 CATTACAGAT
21644 CACAACCTATTTCTTAATGAACCGTGACATTCTTGGG
1 CACAACCTATTTCTTAATGAACCGTGACATTCTTGGG
* * *** * * **
21681 CACAACC-ATTTTATTAATAAAAATATTAACATTCTAGAT
1 CACAACCTA-TTTCTTAAT--GAACCGTGACATTCTTGGG
* * *
21720 CACAACATATTACTTAGTGAACCGTGACATTCTTGGG
1 CACAACCTATTTCTTAATGAACCGTGACATTCTTGGG
*
21757 CACAACCCATTT
1 CACAACCTATTT
21769 TATTAATAAA
Statistics
Matches: 60, Mismatches: 24, Indels: 8
0.65 0.26 0.09
Matches are distributed among these distances:
36 1 0.02
37 35 0.58
39 23 0.38
40 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.32
Consensus pattern (37 bp):
CACAACCTATTTCTTAATGAACCGTGACATTCTTGGG
Found at i:33863 original size:13 final size:13
Alignment explanation
Indices: 33845--33870 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33835 ATGCGTTACA
33845 ATCACTTTGACAT
1 ATCACTTTGACAT
33858 ATCACTTTGACAT
1 ATCACTTTGACAT
33871 TATATATAAG
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:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
ATCACTTTGACAT
Found at i:35973 original size:49 final size:49
Alignment explanation
Indices: 35706--35974 Score: 299
Period size: 49 Copynumber: 5.5 Consensus size: 49
35696 GAATACCATG
* *
35706 AGTGGCACCTTTTATGCCGAAAATG-TCCATTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCG-AAATGAACCGTTATGCATTTAACTTTCATT
* * *
35755 AGTGGAACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCCTT
1 AGTGGCACCTTTTATGCCGAAATGAACCGTTATGCATTTAACTTTCATT
** * *
35804 AGTGGCACCTTTTATGTAGAAAT-ACATCGTTATGCATCTAACTTTCATT
1 AGTGGCACCTTTTATGCCGAAATGA-ACCGTTATGCATTTAACTTTCATT
* * ** * * * *
35853 AGTCGCACCTTTTATACCGACGTGCACTGTTATGCTTTTAACTTTTATT
1 AGTGGCACCTTTTATGCCGAAATGAACCGTTATGCATTTAACTTTCATT
* * *
35902 AGTGGCACCTATTATGCGGAAATGAACCGTTATGCATTTAAATTTCATT
1 AGTGGCACCTTTTATGCCGAAATGAACCGTTATGCATTTAACTTTCATT
* * *
35951 GGAGGCACCTTTTATGTCGAAATG
1 AGTGGCACCTTTTATGCCGAAATG
35975 TACCTATGAC
Statistics
Matches: 178, Mismatches: 39, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
48 5 0.03
49 173 0.97
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.38
Consensus pattern (49 bp):
AGTGGCACCTTTTATGCCGAAATGAACCGTTATGCATTTAACTTTCATT
Found at i:38369 original size:21 final size:23
Alignment explanation
Indices: 38343--38510 Score: 112
Period size: 23 Copynumber: 6.8 Consensus size: 23
38333 TAAAATCAAA
38343 ATAATAA-ATAAT-TATAAAAAT
1 ATAATAATATAATATATAAAAAT
38364 ATAATAATATAATATATAAATATAT
1 ATAATAATATAATATATAAA-A-AT
*
38389 ATATATACTATAAGATATATATATATATAT
1 ATA-ATAATAT-A-ATATATA-A-A-A-AT
38419 AATAATAATATAATATATATATAAAT
1 -ATAATAATATAATATATA-A-AAAT
* *
38445 AT-ATATATATATATATATATATAT
1 ATAATA-ATATA-ATATATAAAAAT
* *
38469 ATAAT-ATATATATATATATATAT
1 ATAATAATATA-ATATATAAAAAT
38492 ATAAT-ATATAATACTATAA
1 ATAATAATATAATA-TATAA
38511 TATATACTAC
Statistics
Matches: 128, Mismatches: 5, Indels: 26
0.81 0.03 0.16
Matches are distributed among these distances:
21 7 0.05
22 8 0.06
23 38 0.30
24 9 0.07
25 14 0.11
26 15 0.12
27 2 0.02
28 18 0.14
29 2 0.02
30 12 0.09
31 3 0.02
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (23 bp):
ATAATAATATAATATATAAAAAT
Found at i:38372 original size:8 final size:8
Alignment explanation
Indices: 38342--38527 Score: 103
Period size: 10 Copynumber: 21.0 Consensus size: 8
38332 ATAAAATCAA
38342 AATAATA-
1 AATAATAT
38349 AATAATTAT
1 AATAA-TAT
*
38358 AAAAATAT
1 AATAATAT
38366 AATAATAT
1 AATAATAT
38374 AAT-ATAT
1 AATAATAT
38381 AAATATATAT
1 -AATA-ATAT
*
38391 ATATACTAT
1 A-ATAATAT
38400 AAGATATATAT
1 -A-ATA-ATAT
38411 ATATATATAAT
1 A-ATA-AT-AT
38422 AATAATAT
1 AATAATAT
38430 AAT-ATAT
1 AATAATAT
38437 ATATAAATAT
1 A-AT-AATAT
38447 ATATATATAT
1 A-ATA-ATAT
38457 ATATATATAT
1 A-ATA-ATAT
38467 ATATAATAT
1 A-ATAATAT
38476 -ATATATAT
1 AATA-ATAT
38484 ATATATATAT
1 A-ATA-ATAT
38494 AAT-ATAT
1 AATAATAT
*
38501 AATACTAT
1 AATAATAT
38509 AATATATACT
1 AATA-ATA-T
38519 ACATAATAT
1 A-ATAATAT
38528 GTAATGACCC
Statistics
Matches: 151, Mismatches: 8, Indels: 38
0.77 0.04 0.19
Matches are distributed among these distances:
7 24 0.16
8 36 0.24
9 20 0.13
10 62 0.41
11 9 0.06
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (8 bp):
AATAATAT
Found at i:38388 original size:2 final size:2
Alignment explanation
Indices: 38362--38516 Score: 181
Period size: 2 Copynumber: 82.5 Consensus size: 2
38352 AATTATAAAA
*
38362 AT AT A- AT A- AT AT A- AT AT AT AA AT AT AT AT AT AT ACT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
*
38401 AG AT AT AT AT AT AT AT AT A- AT A- AT A- AT AT A- 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
*
38439 AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
38480 AT AT AT AT AT AT AT A- AT AT AT A- AT ACT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A
38517 CTACATAATA
Statistics
Matches: 134, Mismatches: 5, Indels: 28
0.80 0.03 0.17
Matches are distributed among these distances:
1 12 0.09
2 118 0.88
3 4 0.03
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:39454 original size:22 final size:19
Alignment explanation
Indices: 39402--39473 Score: 72
Period size: 19 Copynumber: 3.6 Consensus size: 19
39392 ATGCAAAAAT
39402 GGTATCGATACCATAGTAG
1 GGTATCGATACCATAGTAG
* *
39421 GGTATCGGTACCATAGTGTG
1 GGTATCGATACCATAGT-AG
*
39441 GAAGTATCGATACCATGGTAG
1 G--GTATCGATACCATAGTAG
*
39462 AGGTATTGATAC
1 -GGTATCGATAC
39474 TGAAGAGCGA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
19 16 0.37
20 11 0.26
21 1 0.02
22 15 0.35
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (19 bp):
GGTATCGATACCATAGTAG
Found at i:39895 original size:58 final size:58
Alignment explanation
Indices: 39799--40201 Score: 553
Period size: 58 Copynumber: 6.9 Consensus size: 58
39789 ACCAAATGGT
* * *
39799 ACTTAGTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTACGGATTTCTGTATTGGGC
1 ACTTTGTGTGCAAAAA-GTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGC
* *
39858 ACTTTGTGTGCAAAAAGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGC
1 ACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGC
* * * *
39916 ACTTTGTGTG-AAAAGGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGAC
1 ACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGC
* *
39973 ACTTTGTGTGCAAAAATATTATGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGC
1 ACTTTGTGTGCAAAAA-GTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGC
** *
40032 ACTTTGTGTGCAAATATCTTAAGAAATTCATA-GAAGTGTATGAATTT-TCGTATTGGGC
1 ACTTTGTGTGCAAA-AAGTTAAGAAATTCATACTAAGTGTATGAATTTCT-GTATTGGGC
* *
40090 ACTCTGTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTT-TCGTATTGGGA
1 ACTTTGTGTGCAAAAA-GTTAAGAAATTCATACTAAGTGTATGAATTTCT-GTATTGGGC
* * *
40149 ACTTTATGTGCAAAAAGATAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
1 ACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTAT
40202 AGGAAATATA
Statistics
Matches: 309, Mismatches: 28, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
57 55 0.18
58 136 0.44
59 117 0.38
60 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (58 bp):
ACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGC
Found at i:40124 original size:117 final size:117
Alignment explanation
Indices: 39799--40201 Score: 580
Period size: 117 Copynumber: 3.5 Consensus size: 117
39789 ACCAAATGGT
* * * *
39799 ACTTAGTGTGCAAAAATGTTAAGAAATTCATACTAAGTGTACGGATTTCTGTATTGGGCACTTTG
1 ACTTTGTGTGC-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTG
* *
39864 TGTGCAAAAA-GATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGC
65 TGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGC
* * *
39916 ACTTTGTGTG-AAAAGGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGACACTTTGT
1 ACTTTGTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGT
* *
39980 GTGCAAAAATATTATGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGC
66 GTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGC
* * * *
40032 ACTTTGTGTGCAAATATCTTAAGAAATTCATA-GAAGTGTATGAATTTTCGTATTGGGCACTCTG
1 ACTTTGTGTGCAAA-ATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTG
*
40096 TGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTT-TCGTATTGGGA
65 TGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCT-GTATTGGGC
* * *
40149 ACTTTATGTGCAAAAAGATAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
1 ACTTTGTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
40202 AGGAAATATA
Statistics
Matches: 254, Mismatches: 27, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
115 57 0.22
116 63 0.25
117 119 0.47
118 15 0.06
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (117 bp):
ACTTTGTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGT
GTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGC
Found at i:42546 original size:40 final size:39
Alignment explanation
Indices: 42423--42570 Score: 126
Period size: 39 Copynumber: 3.8 Consensus size: 39
42413 TTAAAGACAC
* *
42423 CCTTTGTAGGTTTTCA-TCTTAAAC-CTTTTTCTAGAGTGCT
1 CCTTTTTAGGTTTTCACTC-TAAACACTTTTT-TAGAG-CCT
* * *
42463 -CTTTTCAGATTTTCACTCTAAACACTTTTTTAGAGCGT
1 CCTTTTTAGGTTTTCACTCTAAACACTTTTTTAGAGCCT
**
42501 CCTTTTT-GAGTTTTCACTCTAAATGCTTTTTTTAGAGCACT
1 CCTTTTTAG-GTTTTCACTCTAAACAC-TTTTTTAGAGC-CT
* *
42542 -CTTTTTAGGTTTTCCCTCTAACCACTTTT
1 CCTTTTTAGGTTTTCACTCTAAACACTTTT
42571 CAAAAAACTT
Statistics
Matches: 87, Mismatches: 14, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
38 2 0.02
39 45 0.52
40 38 0.44
41 2 0.02
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.48
Consensus pattern (39 bp):
CCTTTTTAGGTTTTCACTCTAAACACTTTTTTAGAGCCT
Found at i:54271 original size:19 final size:20
Alignment explanation
Indices: 54247--54292 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
54237 CAAAATGGAC
*
54247 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
54266 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
54286 TAATTTC
1 CAATTTC
54293 CAGTATAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:58571 original size:20 final size:21
Alignment explanation
Indices: 58551--58597 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
58541 AATATGTAAA
58551 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * *
58572 TTGCGTTGTGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
58593 TCGCA
1 TCGCA
58598 ACGCGAATCT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:58621 original size:20 final size:20
Alignment explanation
Indices: 58593--58659 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
58583 TTTTCCAAAT
* *
58593 TCGCAACGCGAATCTATAAA
1 TCGCAACGCGAATTTGTAAA
* *
58613 TCACAACGCAAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
58633 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
58653 TCGCAAC
1 TCGCAAC
58660 ACATAAGTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:58676 original size:20 final size:20
Alignment explanation
Indices: 58653--58719 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
58643 AATTTGTAAA
58653 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
**
58673 TCGCAATGCGAT-AGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
*
58693 TCGCAACACAAAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
58713 TCGCAAC
1 TCGCAAC
58720 GTGGAATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.03
20 37 0.93
21 2 0.05
ACGTcount: A:0.42, C:0.25, G:0.13, T:0.19
Consensus pattern (20 bp):
TCGCAACACATAAGTCAAAT
Found at i:58677 original size:40 final size:39
Alignment explanation
Indices: 58588--58767 Score: 127
Period size: 40 Copynumber: 4.5 Consensus size: 39
58578 TGTGATTTTC
* * * *
58588 CAAATTCGCAACGCGAATCTATAAATCACAACGCAAATTTGT
1 CAAATTCGCAACGCGAATTTGTAAATCGCAACACAAA---GT
58630 -AAA-TCGCAACGCGAATTTGTAAATCGCAACACATAAGT
1 CAAATTCGCAACGCGAATTTGTAAATCGCAACACA-AAGT
* *
58668 CAAATTCGCAATGCG-A-TAGTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGAATTTGT-AAA-TCGCAACAC-AAAGT
* * ** **
58708 CAAATTCGCAACGTGGAATTT-CAAATTCGCAACTGAATTT
1 CAAATTCGCAACG-CGAATTTGTAAA-TCGCAACACAAAGT
*
58748 CAAATTCGCAACACGAATTT
1 CAAATTCGCAACGCGAATTT
58768 AATTTCGCAA
Statistics
Matches: 113, Mismatches: 16, Indels: 21
0.75 0.11 0.14
Matches are distributed among these distances:
38 5 0.04
39 13 0.12
40 75 0.66
41 18 0.16
42 1 0.01
43 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (39 bp):
CAAATTCGCAACGCGAATTTGTAAATCGCAACACAAAGT
Found at i:58767 original size:20 final size:20
Alignment explanation
Indices: 58687--58779 Score: 100
Period size: 19 Copynumber: 4.7 Consensus size: 20
58677 AATGCGATAG
* **
58687 TCAAATTCGCAACACAAAAG
1 TCAAATTCGCAACACGAATT
**
58707 TCAAATTCGCAACGTGGAATT
1 TCAAATTCGCAAC-ACGAATT
*
58728 TCAAATTCGCAAC-TGAATT
1 TCAAATTCGCAACACGAATT
58747 TCAAATTCGCAACACGAATT
1 TCAAATTCGCAACACGAATT
*
58767 T-AATTTCGCAACA
1 TCAAATTCGCAACA
58780 GGTTTTAGTT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
19 29 0.46
20 19 0.30
21 15 0.24
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.26
Consensus pattern (20 bp):
TCAAATTCGCAACACGAATT
Found at i:58954 original size:14 final size:16
Alignment explanation
Indices: 58935--58971 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
58925 TCCCCATCTC
58935 TAATTTT-TTT-TACA
1 TAATTTTATTTCTACA
*
58949 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
58965 TAATTTT
1 TAATTTT
58972 GCAATGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:61998 original size:18 final size:18
Alignment explanation
Indices: 61975--62010 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
61965 AAGCAAAAGG
*
61975 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
61993 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
62011 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:62417 original size:20 final size:22
Alignment explanation
Indices: 62392--62435 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
62382 ACAACGCTTA
62392 TTTCGCGTTGCG-AA-TTTACC
1 TTTCGCGTTGCGAAAGTTTACC
62412 TTTCGCGTTGCGAAAGTTTACC
1 TTTCGCGTTGCGAAAGTTTACC
62434 TT
1 TT
62436 CAACAGGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 2 0.09
22 8 0.36
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (22 bp):
TTTCGCGTTGCGAAAGTTTACC
Found at i:62516 original size:14 final size:13
Alignment explanation
Indices: 62497--62546 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
62487 AATCAATTAA
62497 ACATTATTGTGGGT
1 ACATTATT-TGGGT
*
62511 ACATTATTT--GA
1 ACATTATTTGGGT
62522 ACATTATTATGGGT
1 ACATTATT-TGGGT
62536 ACATTATTTGG
1 ACATTATTTGG
62547 AAAATAATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 9 0.29
12 1 0.03
13 4 0.13
14 17 0.55
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (13 bp):
ACATTATTTGGGT
Found at i:62524 original size:25 final size:25
Alignment explanation
Indices: 62496--62545 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
62486 AAATCAATTA
*
62496 AACATTATTGTGGGTACATTATTTG
1 AACATTATTATGGGTACATTATTTG
62521 AACATTATTATGGGTACATTATTTG
1 AACATTATTATGGGTACATTATTTG
62546 GAAAATAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (25 bp):
AACATTATTATGGGTACATTATTTG
Found at i:62962 original size:18 final size:18
Alignment explanation
Indices: 62931--62967 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
62921 GTAACTGGAG
*
62931 TTTGAATTTTAATTTCAA
1 TTTGAATTTGAATTTCAA
*
62949 TTTGAGTTTGAATTTCAA
1 TTTGAATTTGAATTTCAA
62967 T
1 T
62968 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (18 bp):
TTTGAATTTGAATTTCAA
Found at i:62974 original size:24 final size:24
Alignment explanation
Indices: 62928--62975 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
62918 TATGTAACTG
* * *
62928 GAGTTTGAATTTTAATTTCAATTT
1 GAGTTTGAATTTCAATATAAATTT
62952 GAGTTTGAATTTCAATATAAATTT
1 GAGTTTGAATTTCAATATAAATTT
62976 CGGCTCCACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.50
Consensus pattern (24 bp):
GAGTTTGAATTTCAATATAAATTT
Found at i:64141 original size:28 final size:28
Alignment explanation
Indices: 64109--64162 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
64099 ATAATTCTTA
*
64109 TTTACACATCAAATTAAACAAATCAACT
1 TTTACAAATCAAATTAAACAAATCAACT
* **
64137 TTTACAAATCAACTTTTACAAATCAA
1 TTTACAAATCAAATTAAACAAATCAA
64163 TTAAATAAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.31
Consensus pattern (28 bp):
TTTACAAATCAAATTAAACAAATCAACT
Found at i:64143 original size:14 final size:14
Alignment explanation
Indices: 64126--64162 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
64116 ATCAAATTAA
64126 ACAAATCAACTTTT
1 ACAAATCAACTTTT
64140 ACAAATCAACTTTT
1 ACAAATCAACTTTT
64154 ACAAATCAA
1 ACAAATCAA
64163 TTAAATAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:65677 original size:42 final size:42
Alignment explanation
Indices: 65596--65694 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 42
65586 GCGGGCGGGA
* * * *
65596 CCTCTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGAAAGGGGCCTCTTGAACGATAGGAGGGG
* *
65638 CTTCTTCG-ATGATGAAAGGGGCCTCTTGAACGATAGGAGGTG
1 CCTCTT-GAATGATGAAAGGGGCCTCTTGAACGATAGGAGGGG
65680 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
65695 TAGGTGCATC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.02
42 46 0.96
43 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.24
Consensus pattern (42 bp):
CCTCTTGAATGATGAAAGGGGCCTCTTGAACGATAGGAGGGG
Found at i:65701 original size:21 final size:21
Alignment explanation
Indices: 65596--65694 Score: 94
Period size: 21 Copynumber: 4.7 Consensus size: 21
65586 GCGGGCGGGA
*
65596 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
65617 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
65638 CTTCTTCG-ATGATGAAAGGGG
1 CCTCTT-GAACGATGAGAGGGG
*
65659 CCTCTTGAACGAT-AGGAGGTG
1 CCTCTTGAACGATGA-GAGGGG
*
65680 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
65695 TAGGTGCATC
Statistics
Matches: 61, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 2 0.03
21 57 0.93
22 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.24
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:67718 original size:14 final size:14
Alignment explanation
Indices: 67701--67739 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
67691 TCATTTTCGC
*
67701 GTTGCGATTTTTGA
1 GTTGCGATTTTGGA
*
67715 GTTGCGATTTTGGT
1 GTTGCGATTTTGGA
67729 GTTGCGATTTT
1 GTTGCGATTTT
67740 CATTTTCGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.10, C:0.08, G:0.31, T:0.51
Consensus pattern (14 bp):
GTTGCGATTTTGGA
Found at i:68139 original size:22 final size:22
Alignment explanation
Indices: 68097--68154 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
68087 GATGGAGATA
68097 GACGGATTTCGCTC-GTGATGGG
1 GACGGATTTCG-TCGGTGATGGG
68119 GACGGATTTCGTCGGAT-ATGGG
1 GACGGATTTCGTCGG-TGATGGG
* *
68141 GTCGGATGTCGTCG
1 GACGGATTTCGTCG
68155 TAGAGAGTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 2 0.06
22 29 0.91
23 1 0.03
ACGTcount: A:0.14, C:0.17, G:0.41, T:0.28
Consensus pattern (22 bp):
GACGGATTTCGTCGGTGATGGG
Found at i:68282 original size:20 final size:20
Alignment explanation
Indices: 68257--68436 Score: 161
Period size: 20 Copynumber: 8.9 Consensus size: 20
68247 TAATATCGTG
*
68257 TTTCGCGTTGAGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
68277 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* * *
68297 TATCGCGTTGCGAATTTAAAA
1 TTTCGCGTTGCGAATTT-GAC
* *
68318 TTCCGAGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
68338 TTTTGTGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
68358 TATCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
68378 -TTCTGTGTTGCG-ATTT-AC
1 TTTC-GCGTTGCGAATTTGAC
* *
68396 AAATTT-GAGTTGCGAATTTCAC
1 ---TTTCGCGTTGCGAATTTGAC
* *
68418 TATCGCATTGCGAATTTGA
1 TTTCGCGTTGCGAATTTGA
68437 GTTATGTGTT
Statistics
Matches: 129, Mismatches: 22, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
18 2 0.02
19 8 0.06
20 96 0.74
21 19 0.15
22 4 0.03
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:68340 original size:61 final size:59
Alignment explanation
Indices: 68263--68434 Score: 195
Period size: 61 Copynumber: 2.8 Consensus size: 59
68253 CGTGTTTCGC
* *
68263 GTTGAGAATTTGACTTTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTAAAATTCCGA
1 GTTGCGAATTTGACTTT-GAGTTGCGAATTTGACTATCGCGTTGCGAATTT-AAATTCCGA
* * * * *
68324 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGAC-TTTGAGTTGCGAATTTGACTATCGCGTTGCGAATTTAAATTCCGA
* *
68384 GTTGCG-ATTT-ACAAATTTGAGTTGCGAATTTCACTATCGCATTGCGAATTT
1 GTTGCGAATTTGAC---TTTGAGTTGCGAATTTGACTATCGCGTTGCGAATTT
68435 GAGTTATGTG
Statistics
Matches: 98, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
58 2 0.02
59 4 0.04
60 44 0.45
61 45 0.46
62 3 0.03
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.40
Consensus pattern (59 bp):
GTTGCGAATTTGACTTTGAGTTGCGAATTTGACTATCGCGTTGCGAATTTAAATTCCGA
Found at i:68420 original size:60 final size:60
Alignment explanation
Indices: 68283--68488 Score: 231
Period size: 60 Copynumber: 3.4 Consensus size: 60
68273 TGACTTTCGC
* * * * *
68283 GTTGCGAATTTGACTATCGCGTTGCGAATTTAAAATTCCGAGTTGCGAATTTGAC--TTTTGT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTT-GAATTCTGTGTTGCG-ATTT-ACAAATTTGA
*
68344 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTTGA
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGAATTCTGTGTTGCGATTTACAAATTTGA
* * * * * *
68404 GTTGCGAATTTCACTATCGCATTGCGAATTTGAGTTATGTGTTGCGATTTACAAATTCGC
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGAATTCTGTGTTGCGATTTACAAATTTGA
68464 GTTGCG-ATTT-ACATATTCGCGTTGC
1 GTTGCGAATTTGAC-TA-TCGCGTTGC
68489 AAAATTGGAG
Statistics
Matches: 128, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
58 4 0.03
59 10 0.08
60 83 0.65
61 31 0.24
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (60 bp):
GTTGCGAATTTGACTATCGCGTTGCGAATTTGAATTCTGTGTTGCGATTTACAAATTTGA
Found at i:68467 original size:20 final size:20
Alignment explanation
Indices: 68444--68488 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
68434 TGAGTTATGT
68444 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
68464 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
68484 GTTGC
1 GTTGC
68489 AAAATTGGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:68508 original size:60 final size:59
Alignment explanation
Indices: 68344--68513 Score: 148
Period size: 60 Copynumber: 2.8 Consensus size: 59
68334 TGACTTTTGT
* * * * * * * *
68344 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTTGA
1 GTTGCGAATTTCACTATCGCATTGCAAATTGGAGTT-AGCGTTGCGATTTACAAATTCGA
* * * *
68404 GTTGCGAATTTCACTATCGCATTGCGAATTTGAGTTATGTGTTGCGATTTACAAATTCGC
1 GTTGCGAATTTCACTATCGCATTGCAAATTGGAGTTA-GCGTTGCGATTTACAAATTCGA
*
68464 GTTGCG-ATTT-ACATATTCGCGTTGCAAAATTGGAGTTCA-CGTTGCGATTT
1 GTTGCGAATTTCAC-TA-TCGCATTGC-AAATTGGAGTT-AGCGTTGCGATTT
68514 TGTTGGTCAT
Statistics
Matches: 95, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
58 2 0.02
59 6 0.06
60 77 0.81
61 9 0.09
62 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (59 bp):
GTTGCGAATTTCACTATCGCATTGCAAATTGGAGTTAGCGTTGCGATTTACAAATTCGA
Found at i:73124 original size:17 final size:17
Alignment explanation
Indices: 73102--73166 Score: 76
Period size: 17 Copynumber: 3.8 Consensus size: 17
73092 AGCCATCCCA
73102 CTGAGTCAACTCGCTGG
1 CTGAGTCAACTCGCTGG
* *
73119 CTGAGTTAACTCGTTGG
1 CTGAGTCAACTCGCTGG
* *
73136 CTGAGTTAACTCGTTGG
1 CTGAGTCAACTCGCTGG
* *
73153 CTAAGCCAACTCGC
1 CTGAGTCAACTCGC
73167 ATTGAGTGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (17 bp):
CTGAGTCAACTCGCTGG
Found at i:76793 original size:38 final size:35
Alignment explanation
Indices: 76719--76853 Score: 191
Period size: 35 Copynumber: 3.8 Consensus size: 35
76709 GATAATGTTG
*
76719 AATATTCCTCTAGTATTGAATGTTGGTAATGACTC
1 AATATTCCACTAGTATTGAATGTTGGTAATGACTC
*
76754 AATATTCCACTAGTATTGAATGTTGGTGGTAATAACTC
1 AATATTCCACTAGTATTGAATG-T--TGGTAATGACTC
76792 AATATTCCACTAGTATTGAATGTTGGTAATGACTC
1 AATATTCCACTAGTATTGAATGTTGGTAATGACTC
* *
76827 AATA-TCTCACTAGTATTGGATATTGGT
1 AATATTC-CACTAGTATTGAATGTTGGT
76854 TATCTCACTA
Statistics
Matches: 91, Mismatches: 5, Indels: 8
0.88 0.05 0.08
Matches are distributed among these distances:
34 2 0.02
35 54 0.59
36 1 0.01
37 1 0.01
38 33 0.36
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (35 bp):
AATATTCCACTAGTATTGAATGTTGGTAATGACTC
Found at i:76857 original size:25 final size:25
Alignment explanation
Indices: 76829--76913 Score: 134
Period size: 25 Copynumber: 3.4 Consensus size: 25
76819 AATGACTCAA
*
76829 TATCTCACTAGTATTGGATATTGGT
1 TATCCCACTAGTATTGGATATTGGT
* *
76854 TATCTCACTACTATTGGATATTGGT
1 TATCCCACTAGTATTGGATATTGGT
*
76879 TATCCCACTAGTATTGGATGTTGGT
1 TATCCCACTAGTATTGGATATTGGT
76904 TATCCCACTA
1 TATCCCACTA
76914 TGTTTAATAG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (25 bp):
TATCCCACTAGTATTGGATATTGGT
Done.