Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007657.1 Hibiscus syriacus cultivar Beakdansim tig00025306_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: 98940
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:5918 original size:21 final size:21
Alignment explanation
Indices: 5893--5937 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
5883 TACTATTGCG
5893 TTTTGTTTTGTTTTGTTTTGT
1 TTTTGTTTTGTTTTGTTTTGT
5914 TTTTGTTTTGTTTTGTTTTGT
1 TTTTGTTTTGTTTTGTTTTGT
5935 TTT
1 TTT
5938 ATTTGATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (21 bp):
TTTTGTTTTGTTTTGTTTTGT
Found at i:5946 original size:5 final size:5
Alignment explanation
Indices: 5892--5937 Score: 83
Period size: 5 Copynumber: 9.0 Consensus size: 5
5882 ATACTATTGC
5892 GTTTT GTTTT GTTTT GTTTT GTTTTT GTTTT GTTTT GTTTT GTTTT
1 GTTTT GTTTT GTTTT GTTTT G-TTTT GTTTT GTTTT GTTTT GTTTT
5938 ATTTGATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 35 0.88
6 5 0.12
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
GTTTT
Found at i:6366 original size:33 final size:30
Alignment explanation
Indices: 6286--6368 Score: 76
Period size: 31 Copynumber: 2.6 Consensus size: 30
6276 TTATTTTTAA
*
6286 TTTAAATATATATATATTATTTTATCTAAACT
1 TTTAAA-A-ATATATTTTATTTTATCTAAACT
* * * *
6318 TTTAAAACTACATTTTATTATTATTTTAACT
1 TTTAAAAATATATTTTATT-TTATCTAAACT
6349 TTTCAAAGAATATATTTTAT
1 TTT-AAA-AATATATTTTAT
6369 CTTAATTTAC
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
30 9 0.22
31 13 0.32
32 9 0.22
33 10 0.24
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.53
Consensus pattern (30 bp):
TTTAAAAATATATTTTATTTTATCTAAACT
Found at i:6539 original size:25 final size:26
Alignment explanation
Indices: 6460--6570 Score: 97
Period size: 27 Copynumber: 4.2 Consensus size: 26
6450 CATAAATTAT
6460 ATATTTTTAAATAA--TAATAATAATAAA
1 ATATTTTT-AATAAGTTAAT-AT-ATAAA
6487 ATATTTTTAAATTAAGTTAATA-ATAAA
1 ATATTTTT-AA-TAAGTTAATATATAAA
* *
6514 ATATATTTAATAACTTAATATA-AAA
1 ATATTTTTAATAAGTTAATATATAAA
*
6539 ATATTTTTTA-AAGTTAATATATATATA
1 ATATTTTTAATAAGTTAATATATA-A-A
6566 ATATT
1 ATATT
6571 ATGAATTTAA
Statistics
Matches: 72, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
24 10 0.14
25 21 0.29
26 4 0.06
27 29 0.40
28 3 0.04
29 1 0.01
30 4 0.06
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (26 bp):
ATATTTTTAATAAGTTAATATATAAA
Found at i:6555 original size:24 final size:26
Alignment explanation
Indices: 6477--6561 Score: 88
Period size: 25 Copynumber: 3.3 Consensus size: 26
6467 TAAATAATAA
*
6477 TAATA-ATAAAATATTTTTAAATTAAGT
1 TAATATATAAAATATATTT-AA-TAAGT
*
6504 TAATA-ATAAAATATATTTAATAACT
1 TAATATATAAAATATATTTAATAAGT
* *
6529 TAATATA-AAAATATTTTTTA-AAGT
1 TAATATATAAAATATATTTAATAAGT
6553 TAATATATA
1 TAATATATA
6562 TATAATATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
24 10 0.20
25 21 0.41
26 3 0.06
27 17 0.33
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (26 bp):
TAATATATAAAATATATTTAATAAGT
Found at i:11106 original size:23 final size:21
Alignment explanation
Indices: 11080--11137 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 21
11070 CCCCTGTGGG
11080 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCC-TC-AA
11103 GGGGGAATCGGTT-CCCTCAA
1 GGGGGAATCGGTTCCCCTCAA
*
11123 GGGGG-ATCGATTCCC
1 GGGGGAATCGGTTCCC
11138 TCTGCACCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 6 0.18
20 9 0.27
21 2 0.06
22 3 0.09
23 13 0.39
ACGTcount: A:0.19, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCTCAA
Found at i:17042 original size:65 final size:65
Alignment explanation
Indices: 16904--17067 Score: 199
Period size: 65 Copynumber: 2.5 Consensus size: 65
16894 CCATTGGACC
* * * * *
16904 CTTAGTGCATCGATGCATAAAGTGCATTCAATG-TTTCAAACAAGCCCGAGTGTATCGATGCATG
1 CTTA-TGCATCGATGCATAAAATGCATTCGATGTTTTCAAACAAACACGAGTGCATCGATGCATG
16968 G
65 G
* * *
16969 CTTGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AAATATGAGTGCATCGATGCATG
1 CTTATGCATCGATGCATAAAATGCATTCGATGTTTTCA-AACAAACACGAGTGCATCGATGCATG
17033 G
65 G
*
17034 -TATATGCATCGATGCATATAATGCATTCGATGTT
1 CT-TATGCATCGATGCATAAAATGCATTCGATGTT
17068 CAATTTATTC
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
64 27 0.31
65 57 0.66
66 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (65 bp):
CTTATGCATCGATGCATAAAATGCATTCGATGTTTTCAAACAAACACGAGTGCATCGATGCATGG
Found at i:19196 original size:2 final size:2
Alignment explanation
Indices: 19189--19215 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19179 CTAAACACCC
19189 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
19216 ATAAACCGCC
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:22182 original size:20 final size:17
Alignment explanation
Indices: 22159--22198 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 17
22149 ATTTTTAAAA
22159 TATTAAAATAATTTATTTAT
1 TATTAAAAT--TTTATTT-T
22179 TATTAAAATTTTATTTT
1 TATTAAAATTTTATTTT
22196 TAT
1 TAT
22199 AATTTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 7 0.35
20 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTAAAATTTTATTTT
Found at i:22193 original size:14 final size:14
Alignment explanation
Indices: 22174--22214 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
22164 AAATAATTTA
22174 TTTATTATTAAAAT
1 TTTATTATTAAAAT
* *
22188 TTTATTTTTATAAT
1 TTTATTATTAAAAT
*
22202 TTTATTAATAAAA
1 TTTATTATTAAAA
22215 ATATTAATAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTATTATTAAAAT
Found at i:22319 original size:22 final size:23
Alignment explanation
Indices: 22293--22335 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
22283 AGTGTTATAT
22293 TATA-TTTAAAAATATTTATTAG
1 TATATTTTAAAAATATTTATTAG
* *
22315 TATATTTTAAATATCTTTATT
1 TATATTTTAAAAATATTTATT
22336 TAAATATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
TATATTTTAAAAATATTTATTAG
Found at i:22456 original size:11 final size:11
Alignment explanation
Indices: 22440--22468 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
22430 ATAATATAAA
22440 ATTTATTATAT
1 ATTTATTATAT
22451 ATTTATTATAT
1 ATTTATTATAT
22462 A-TTATTA
1 ATTTATTA
22469 AAATAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTTATTATAT
Found at i:22544 original size:22 final size:23
Alignment explanation
Indices: 22516--22562 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
22506 TTGATTATTT
22516 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
22538 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
22561 TA
1 TA
22563 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:22567 original size:22 final size:22
Alignment explanation
Indices: 22524--22567 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
22514 TTTATTATAA
*
22524 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
22546 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
22568 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:23125 original size:14 final size:14
Alignment explanation
Indices: 23106--23144 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
23096 TAATGGGGAG
23106 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
23120 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
23134 GAATCTCTGCA
1 TAATCCCTGCA
23145 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:24989 original size:443 final size:443
Alignment explanation
Indices: 24163--25049 Score: 1765
Period size: 443 Copynumber: 2.0 Consensus size: 443
24153 ATGTCGTCCA
24163 TAATCAAGGCGAAGATGTAAGGGCTAAGAGCCGACCCCTGGTGGAGTCCGATTTCCACCGGGAAT
1 TAATCAAGGCGAAGATGTAAGGGCTAAGAGCCGACCCCTGGTGGAGTCCGATTTCCACCGGGAAT
24228 GCCTCGGTGTCGCCAACTGTAGTCCTGACGTAAGTAGTAGATCTACAGTACATATCACGAATCGC
66 GCCTCGGTGTCGCCAACTGTAGTCCTGACGTAAGTAGTAGATCTACAGTACATATCACGAATCGC
24293 CCGGATATAAGCAGTTGGTATCCGTCTCGTTTCCAAAGTCTTCCAGATCGTATCGCGAGGAACGC
131 CCGGATATAAGCAGTTGGTATCCGTCTCGTTTCCAAAGTCTTCCAGATCGTATCGCGAGGAACGC
24358 TATCATAAGCCTTCTCAAGGTCAATGAACGCCATGTGAAGATCTCTAGACTTTTCCCTATATTTC
196 TATCATAAGCCTTCTCAAGGTCAATGAACGCCATGTGAAGATCTCTAGACTTTTCCCTATATTTC
24423 TCCATAAGCCGTCGAAGTAGATGAATCGCCTCCGTGGTAGACCTGTTTGGCATAAAGCCAAATTG
261 TCCATAAGCCGTCGAAGTAGATGAATCGCCTCCGTGGTAGACCTGTTTGGCATAAAGCCAAATTG
24488 GTTTTCCGAAACCCTAGTGACTTGTCTCAACCTAGCCTCTATCACCCTTTCCCATAGCTTCATGG
326 GTTTTCCGAAACCCTAGTGACTTGTCTCAACCTAGCCTCTATCACCCTTTCCCATAGCTTCATGG
*
24553 TATGGCTGAGTAGTTTAATACCTCTGTAGTTACCACAACGTTGGGGATCTCCT
391 TATGGCTGAGTAGTTTAATACCTCTGTAGTTACCACAACATTGGGGATCTCCT
24606 TAATCAAGGCGAAGATGTAAGGGCTAAGAGCCGACCCCTGGTGGAGTCCGATTTCCACCGGGAAT
1 TAATCAAGGCGAAGATGTAAGGGCTAAGAGCCGACCCCTGGTGGAGTCCGATTTCCACCGGGAAT
24671 GCCTCGGTGTCGCCAACTGTAGTCCTGACGTAAGTAGTAGATCTACAGTACATATCACGAATCGC
66 GCCTCGGTGTCGCCAACTGTAGTCCTGACGTAAGTAGTAGATCTACAGTACATATCACGAATCGC
24736 CCGGATATAAGCAGTTGGTATCCGTCTCGTTTCCAAAGTCTTCCAGATCGTATCGCGAGGAACGC
131 CCGGATATAAGCAGTTGGTATCCGTCTCGTTTCCAAAGTCTTCCAGATCGTATCGCGAGGAACGC
24801 TATCATAAGCCTTCTCAAGGTCAATGAACGCCATGTGAAGATCTCTAGACTTTTCCCTATATTTC
196 TATCATAAGCCTTCTCAAGGTCAATGAACGCCATGTGAAGATCTCTAGACTTTTCCCTATATTTC
24866 TCCATAAGCCGTCGAAGTAGATGAATCGCCTCCGTGGTAGACCTGTTTGGCATAAAGCCAAATTG
261 TCCATAAGCCGTCGAAGTAGATGAATCGCCTCCGTGGTAGACCTGTTTGGCATAAAGCCAAATTG
24931 GTTTTCCGAAACCCTAGTGACTTGTCTCAACCTAGCCTCTATCACCCTTTCCCATAGCTTCATGG
326 GTTTTCCGAAACCCTAGTGACTTGTCTCAACCTAGCCTCTATCACCCTTTCCCATAGCTTCATGG
24996 TATGGCTGAGTAGTTTAATACCTCTGTAGTTACCACAACATTGGGGATCTCCT
391 TATGGCTGAGTAGTTTAATACCTCTGTAGTTACCACAACATTGGGGATCTCCT
25049 T
1 T
25050 TATTTTTATA
Statistics
Matches: 443, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
443 443 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (443 bp):
TAATCAAGGCGAAGATGTAAGGGCTAAGAGCCGACCCCTGGTGGAGTCCGATTTCCACCGGGAAT
GCCTCGGTGTCGCCAACTGTAGTCCTGACGTAAGTAGTAGATCTACAGTACATATCACGAATCGC
CCGGATATAAGCAGTTGGTATCCGTCTCGTTTCCAAAGTCTTCCAGATCGTATCGCGAGGAACGC
TATCATAAGCCTTCTCAAGGTCAATGAACGCCATGTGAAGATCTCTAGACTTTTCCCTATATTTC
TCCATAAGCCGTCGAAGTAGATGAATCGCCTCCGTGGTAGACCTGTTTGGCATAAAGCCAAATTG
GTTTTCCGAAACCCTAGTGACTTGTCTCAACCTAGCCTCTATCACCCTTTCCCATAGCTTCATGG
TATGGCTGAGTAGTTTAATACCTCTGTAGTTACCACAACATTGGGGATCTCCT
Found at i:28482 original size:13 final size:13
Alignment explanation
Indices: 28445--28484 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
28435 TCGATATTGA
28445 AAAATAAATA-TT
1 AAAATAAATATTT
*
28457 AAAATAATTTATTT
1 AAAATAA-ATATTT
28471 AAAATAAATATTT
1 AAAATAAATATTT
28484 A
1 A
28485 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:29955 original size:3 final size:3
Alignment explanation
Indices: 29947--30072 Score: 200
Period size: 3 Copynumber: 42.3 Consensus size: 3
29937 TTAATATATT
* *
29947 TAA TAA TAA GAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
29995 TGA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
30042 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
30073 GATATGGGTA
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
2 2 0.02
3 112 0.98
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:30702 original size:113 final size:113
Alignment explanation
Indices: 30396--30816 Score: 706
Period size: 113 Copynumber: 3.8 Consensus size: 113
30386 AGAATTATGC
* * * * *
30396 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTTTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
30461 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
30508 AAAAGGTTGAACAAATTC-T-T-ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
30570 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
*
30618 AAAAGGTTGAACAAATTCTTCTCATTTTGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
30683 TATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
30731 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
30796 TATGAACTTTCTCTGGAAAAG
66 TATGAACTTTCTCTGGAAAAG
30817 CTAATCTTTC
Statistics
Matches: 293, Mismatches: 12, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
109 47 0.16
110 55 0.19
111 2 0.01
112 17 0.06
113 172 0.59
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
Found at i:30811 original size:226 final size:222
Alignment explanation
Indices: 30396--30816 Score: 698
Period size: 222 Copynumber: 1.9 Consensus size: 222
30386 AGAATTATGC
* * * *
30396 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTTTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
30461 TATGAACTTCTCCGGAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAATTC
66 TATGAACTTCTCCGGAAAAGATAATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTC
30526 TTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG
131 TTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG
30591 ATGATCCATCAAATGATGGATTCAGGT
196 ATGATCCATCAAATGATGGATTCAGGT
* *
30618 AAAAGGTTGAACAAATTCTTCTCATTTTGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
30683 TATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
66 TATGAAC-TTCTCCGGAAAAGATAATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATT
30748 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
130 C-T-T-ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
30813 AAAG
192 AAAG
30817 CTAATCTTTC
Statistics
Matches: 183, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
222 66 0.36
223 52 0.28
224 1 0.01
225 1 0.01
226 63 0.34
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (222 bp):
AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTCTCCGGAAAAGATAATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTC
TTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG
ATGATCCATCAAATGATGGATTCAGGT
Found at i:31787 original size:165 final size:169
Alignment explanation
Indices: 31485--31873 Score: 608
Period size: 165 Copynumber: 2.3 Consensus size: 169
31475 GTTCTTACCA
* * *
31485 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTCCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCACCTTCCAAAC
* *
31549 TCAATGATTGGTTTTTTGGGTTCATACCAAACCAGATAACTCAAAGAACACTTCCAGAAGATGCT
65 TCAATGATTGGTATTTT-GGTCCATACCAAACCAGATAACTCAAAGAACACTTCCAGAAGATGCT
31614 ATTGGCAAATTCATCTTCTAAACTCAATGATTGTTCTGTCC
129 ATTGGCAAATTCATCTTCTAAACTCAATGATTGTTCTGTCC
* *
31655 AACCAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCACCTTCTAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCACCTTCCAAACT
* * * *
31720 CAATGCTT-G-ATTTT-GTCCA-ATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
66 CAATGATTGGTATTTTGGTCCATACCAAACCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
*
31781 TGGCAAATTCATCTTCTAAATTCAATGATTGTTCTGTCC
131 TGGCAAATTCATCTTCTAAACTCAATGATTGTTCTGTCC
*
31820 AACCAGATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCA
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCA
31874 TTTGTTCTAT
Statistics
Matches: 204, Mismatches: 14, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
165 129 0.63
166 4 0.02
168 4 0.02
169 1 0.00
170 64 0.31
171 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (169 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCACCTTCCAAACT
CAATGATTGGTATTTTGGTCCATACCAAACCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
TGGCAAATTCATCTTCTAAACTCAATGATTGTTCTGTCC
Found at i:31789 original size:83 final size:82
Alignment explanation
Indices: 31485--31874 Score: 575
Period size: 82 Copynumber: 4.7 Consensus size: 82
31475 GTTCTTACCA
* * *
31485 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTCCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAAC
* *
31549 TCAATGATTGGTTTTTTGGGTTC
65 TCAATGATT-G--TTCT--GTCC
* *
31572 ATACCAAACCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAAC
1 A-ACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAAC
31637 TCAATGATTGTTCTGTCC
65 TCAATGATTGTTCTGTCC
* *
31655 AACCAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCACCTTCTAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
* *
31720 CAATGCTTGATTTTGTCC
66 CAATGATTG-TTCTGTCC
* *
31738 AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
31803 CAATGATTGTTCTGTCC
66 CAATGATTGTTCTGTCC
*
31820 AACCAGATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
31875 TTGTTCTATT
Statistics
Matches: 279, Mismatches: 21, Indels: 11
0.90 0.07 0.04
Matches are distributed among these distances:
82 128 0.46
83 80 0.29
85 3 0.01
87 2 0.01
88 64 0.23
89 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (82 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
CAATGATTGTTCTGTCC
Found at i:40336 original size:14 final size:15
Alignment explanation
Indices: 40317--40349 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40307 ATTATTTTTC
40317 AAATTTTA-ATTAAT
1 AAATTTTATATTAAT
*
40331 AAATTTTATCTTAAT
1 AAATTTTATATTAAT
40346 AAAT
1 AAAT
40350 AAAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATTTTATATTAAT
Found at i:41889 original size:17 final size:17
Alignment explanation
Indices: 41864--41898 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
41854 CGGCTTCCAT
*
41864 AATACATTCTCACGAAG
1 AATAAATTCTCACGAAG
41881 AATAAATTCTCACGAAG
1 AATAAATTCTCACGAAG
41898 A
1 A
41899 CATAGAGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (17 bp):
AATAAATTCTCACGAAG
Found at i:42835 original size:13 final size:13
Alignment explanation
Indices: 42798--42837 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
42788 TCGATATTGA
42798 AAAATAAATA-TT
1 AAAATAAATATTT
*
42810 AAAATAATTTATTT
1 AAAATAA-ATATTT
42824 AAAATAAATATTT
1 AAAATAAATATTT
42837 A
1 A
42838 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:44851 original size:17 final size:18
Alignment explanation
Indices: 44822--44856 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
44812 TAAAATAAAT
44822 AAATAAATAATTTATTTA
1 AAATAAATAATTTATTTA
44840 AAATAAAT-ATTTATTTA
1 AAATAAATAATTTATTTA
44857 TTATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATAAATAATTTATTTA
Found at i:44866 original size:17 final size:17
Alignment explanation
Indices: 44823--44874 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
44813 AAAATAAATA
*
44823 AATAAATAATTTATTTAA
1 AATAAAT-ATTTATTTAT
44841 AATAAATATTTATTTAT
1 AATAAATATTTATTTAT
* * *
44858 TATATATATATATTTAT
1 AATAAATATTTATTTAT
44875 GACTATAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 23 0.77
18 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATAAATATTTATTTAT
Found at i:45834 original size:19 final size:19
Alignment explanation
Indices: 45812--45877 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 19
45802 TTTTTTTTTC
45812 CTCTGTTTTTTTTCTCCGT
1 CTCTGTTTTTTTTCTCCGT
* * * *
45831 CTCTCTGTGTTCTCTCTC-T
1 CTCTGTTTTTTTTCTC-CGT
* * *
45850 CTCCGTTTTTTTTTTCTGT
1 CTCTGTTTTTTTTCTCCGT
45869 CTCTGTTTT
1 CTCTGTTTT
45878 CGTCCTCTTT
Statistics
Matches: 33, Mismatches: 12, Indels: 4
0.67 0.24 0.08
Matches are distributed among these distances:
19 32 0.97
20 1 0.03
ACGTcount: A:0.00, C:0.27, G:0.11, T:0.62
Consensus pattern (19 bp):
CTCTGTTTTTTTTCTCCGT
Found at i:46879 original size:17 final size:18
Alignment explanation
Indices: 46850--46884 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
46840 TAAAATAAAT
46850 AAATAAATAATTTATTTA
1 AAATAAATAATTTATTTA
46868 AAATAAAT-ATTTATTTA
1 AAATAAATAATTTATTTA
46885 TTATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATAAATAATTTATTTA
Found at i:46894 original size:17 final size:17
Alignment explanation
Indices: 46851--46902 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
46841 AAAATAAATA
*
46851 AATAAATAATTTATTTAA
1 AATAAAT-ATTTATTTAT
46869 AATAAATATTTATTTAT
1 AATAAATATTTATTTAT
* * *
46886 TATATATATATATTTAT
1 AATAAATATTTATTTAT
46903 GACTATAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 23 0.77
18 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATAAATATTTATTTAT
Found at i:47863 original size:19 final size:19
Alignment explanation
Indices: 47841--47906 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 19
47831 TTTTTTTTTC
47841 CTCTGTTTTTTTTCTCCGT
1 CTCTGTTTTTTTTCTCCGT
* * * *
47860 CTCTCTGTGTTCTCTCTC-T
1 CTCTGTTTTTTTTCTC-CGT
* * *
47879 CTCCGTTTTTTTTTTCTGT
1 CTCTGTTTTTTTTCTCCGT
47898 CTCTGTTTT
1 CTCTGTTTT
47907 CGTCCTCTTT
Statistics
Matches: 33, Mismatches: 12, Indels: 4
0.67 0.24 0.08
Matches are distributed among these distances:
19 32 0.97
20 1 0.03
ACGTcount: A:0.00, C:0.27, G:0.11, T:0.62
Consensus pattern (19 bp):
CTCTGTTTTTTTTCTCCGT
Found at i:48364 original size:3 final size:3
Alignment explanation
Indices: 48356--48458 Score: 161
Period size: 3 Copynumber: 34.3 Consensus size: 3
48346 TTAATATATT
* * *
48356 TAA TAA TAA GAA TAA TAA TGA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
48404 TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
48452 TGA TAA T
1 TAA TAA T
48459 GATATGGGTA
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 92 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:53572 original size:18 final size:18
Alignment explanation
Indices: 53549--53586 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
53539 TTAAGGTTAG
*
53549 GGTTGGTTGAGCAATTTA
1 GGTTGGTTGAACAATTTA
53567 GGTTGGTTGAACAATTTA
1 GGTTGGTTGAACAATTTA
53585 GG
1 GG
53587 GTTTTCATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.34, T:0.37
Consensus pattern (18 bp):
GGTTGGTTGAACAATTTA
Found at i:53846 original size:21 final size:21
Alignment explanation
Indices: 53822--53867 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
53812 AAATCATAGA
53822 ATATAAACACTAATAAAATAT
1 ATATAAACACTAATAAAATAT
* * * *
53843 ATATAATCATTAATAATATTT
1 ATATAAACACTAATAAAATAT
53864 ATAT
1 ATAT
53868 GATAAAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (21 bp):
ATATAAACACTAATAAAATAT
Found at i:60426 original size:58 final size:61
Alignment explanation
Indices: 60325--60459 Score: 154
Period size: 59 Copynumber: 2.3 Consensus size: 61
60315 GGAATATACA
* **
60325 TATAGCTTGGGATG-AAACTTAAACGTTCAAAAGTTTGAGGACTAA-TTTAGAATAA-ATGT
1 TATAGTTTGGGATGAAAACTTAAACGTTCAAAAGTTCAAGGACTAATTTTAGAATAATA-GT
** *
60384 TATAGTTTGGGATGAAAACTT-AGTGTTC-AAAGTTCAAGGACTAATTTTAGAATGATAGT
1 TATAGTTTGGGATGAAAACTTAAACGTTCAAAAGTTCAAGGACTAATTTTAGAATAATAGT
* *
60443 CATATTTTGGGATGAAA
1 TATAGTTTGGGATGAAA
60460 TTTTAATTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
58 14 0.22
59 44 0.68
60 7 0.11
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.34
Consensus pattern (61 bp):
TATAGTTTGGGATGAAAACTTAAACGTTCAAAAGTTCAAGGACTAATTTTAGAATAATAGT
Found at i:62194 original size:27 final size:27
Alignment explanation
Indices: 62164--62221 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
62154 GAAAAGAGTA
62164 AATTACGTA-TTTAGTACCTAAACTATT
1 AATT-CGTATTTTAGTACCTAAACTATT
** *
62191 AATTTTTATTTTAGTACCTAAACTTTT
1 AATTCGTATTTTAGTACCTAAACTATT
62218 AATT
1 AATT
62222 TTTTTCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.48
Consensus pattern (27 bp):
AATTCGTATTTTAGTACCTAAACTATT
Found at i:62222 original size:27 final size:27
Alignment explanation
Indices: 62173--62224 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
62163 AAATTACGTA
62173 TTTAGTACCTAAACTATTAATTTTTAT
1 TTTAGTACCTAAACTATTAATTTTTAT
*
62200 TTTAGTACCTAAACTTTTAATTTTT
1 TTTAGTACCTAAACTATTAATTTTT
62225 TTCAAAATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.54
Consensus pattern (27 bp):
TTTAGTACCTAAACTATTAATTTTTAT
Found at i:70048 original size:37 final size:37
Alignment explanation
Indices: 70006--70113 Score: 130
Period size: 37 Copynumber: 3.2 Consensus size: 37
69996 CCTCTAAAAT
70006 TTTATTTTAGTATAAAAGTAACTTTTGAAGTGTTAAA
1 TTTATTTTAGTATAAAAGTAACTTTTGAAGTGTTAAA
*
70043 TTTA--TT--T-T-----CAAC-TTTGAAGTGTTAAA
1 TTTATTTTAGTATAAAAGTAACTTTTGAAGTGTTAAA
70069 TTTATTTTAGTATAAAAGTAACTTTTGAAGTGTTAAA
1 TTTATTTTAGTATAAAAGTAACTTTTGAAGTGTTAAA
70106 TTTATTTT
1 TTTATTTT
70114 CAACTTTGAA
Statistics
Matches: 58, Mismatches: 2, Indels: 22
0.71 0.02 0.27
Matches are distributed among these distances:
26 18 0.31
27 3 0.05
28 2 0.03
30 1 0.02
31 1 0.02
32 1 0.02
33 1 0.02
35 2 0.03
36 3 0.05
37 26 0.45
ACGTcount: A:0.34, C:0.04, G:0.12, T:0.50
Consensus pattern (37 bp):
TTTATTTTAGTATAAAAGTAACTTTTGAAGTGTTAAA
Found at i:70089 original size:63 final size:63
Alignment explanation
Indices: 70006--70125 Score: 240
Period size: 63 Copynumber: 1.9 Consensus size: 63
69996 CCTCTAAAAT
70006 TTTATTTTAGTATAAAAGTAACTTTTGAAGTGTTAAATTTATTTTCAACTTTGAAGTGTTAAA
1 TTTATTTTAGTATAAAAGTAACTTTTGAAGTGTTAAATTTATTTTCAACTTTGAAGTGTTAAA
70069 TTTATTTTAGTATAAAAGTAACTTTTGAAGTGTTAAATTTATTTTCAACTTTGAAGT
1 TTTATTTTAGTATAAAAGTAACTTTTGAAGTGTTAAATTTATTTTCAACTTTGAAGT
70126 ATTGAAGTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.48
Consensus pattern (63 bp):
TTTATTTTAGTATAAAAGTAACTTTTGAAGTGTTAAATTTATTTTCAACTTTGAAGTGTTAAA
Found at i:71814 original size:3 final size:3
Alignment explanation
Indices: 71802--71839 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
71792 CCATCGGATC
*
71802 ATT A-T ATT ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
71840 TGGTGTTAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:73192 original size:15 final size:16
Alignment explanation
Indices: 73164--73193 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
73154 TAAAATTTTA
73164 TTTATATCTATTAATT
1 TTTATATCTATTAATT
73180 TTTATAT-TATTAAT
1 TTTATATCTATTAAT
73194 ATATGTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTATATCTATTAATT
Found at i:74308 original size:2 final size:2
Alignment explanation
Indices: 74301--74329 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
74291 TATAACCAAT
74301 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
74330 TACATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:74975 original size:16 final size:14
Alignment explanation
Indices: 74954--74992 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
74944 ATTTAATCAC
74954 ATATATCATTTCCATA
1 ATATATC-TTT-CATA
*
74970 ATATATCTTTTATA
1 ATATATCTTTCATA
74984 ATATATCTT
1 ATATATCTT
74993 ATTATCACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.55
15 3 0.14
16 7 0.32
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATATCTTTCATA
Found at i:74984 original size:14 final size:15
Alignment explanation
Indices: 74967--74997 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
74957 TATCATTTCC
74967 ATAATATATCTT-TT
1 ATAATATATCTTATT
74981 ATAATATATCTTATT
1 ATAATATATCTTATT
74996 AT
1 AT
74998 CACCCATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATATATCTTATT
Found at i:79930 original size:20 final size:22
Alignment explanation
Indices: 79905--79958 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
79895 ATGTTTCAAG
*
79905 GGTATCGATACCATCCT-TTA-
1 GGTATCGATACCACCCTCTTAT
*
79925 GGTATCGATACTACCCTCTTAT
1 GGTATCGATACCACCCTCTTAT
*
79947 AGTATCGATACC
1 GGTATCGATACC
79959 TCTTCAACAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 15 0.54
21 3 0.11
22 10 0.36
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (22 bp):
GGTATCGATACCACCCTCTTAT
Found at i:81691 original size:19 final size:19
Alignment explanation
Indices: 81667--81706 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
81657 GACACAACAT
81667 CTTTAGTTAAATAAAATTA
1 CTTTAGTTAAATAAAATTA
81686 CTTTAGTTAAATAAAATTA
1 CTTTAGTTAAATAAAATTA
81705 CT
1 CT
81707 AAAGTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (19 bp):
CTTTAGTTAAATAAAATTA
Found at i:81712 original size:19 final size:19
Alignment explanation
Indices: 81671--81715 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
81661 CAACATCTTT
**
81671 AGTTAAATAAAATTACTTT
1 AGTTAAATAAAATTACTAA
81690 AGTTAAATAAAATTACTAA
1 AGTTAAATAAAATTACTAA
81709 AGTTAAA
1 AGTTAAA
81716 AATCGCAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (19 bp):
AGTTAAATAAAATTACTAA
Found at i:91704 original size:14 final size:14
Alignment explanation
Indices: 91685--91714 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
91675 GAATTACATC
91685 TTCTGGAAAATATT
1 TTCTGGAAAATATT
91699 TTCTGGAAAATATT
1 TTCTGGAAAATATT
91713 TT
1 TT
91715 ATGGTGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (14 bp):
TTCTGGAAAATATT
Found at i:91844 original size:22 final size:23
Alignment explanation
Indices: 91804--91846 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
91794 ATATGATAAA
91804 TAATATTATTTATTATAAAAACT
1 TAATATTATTTATTATAAAAACT
*
91827 TAATATTA-TTATTTTAAAAA
1 TAATATTATTTATTATAAAAA
91847 TATTAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATATTATTTATTATAAAAACT
Found at i:92253 original size:22 final size:23
Alignment explanation
Indices: 92236--92290 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 23
92226 ATTATTATAT
92236 TATATTATTAAAAATATTAATAAA
1 TATATT-TTAAAAATATTAATAAA
* *
92260 TATATTTT-AAAATGTTAATAAT
1 TATATTTTAAAAATATTAATAAA
92282 TAATATTTT
1 T-ATATTTT
92291 TATTAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 13 0.46
23 9 0.32
24 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATAAA
Done.