Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167935.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_198, 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: 52463
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:879 original size:23 final size:23
Alignment explanation
Indices: 852--895 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
842 AGATGAGATT
* *
852 TAAGCCTAGTTTAGATGGCACTA
1 TAAGCCCAGATTAGATGGCACTA
*
875 TAAGCCCAGATTAGCTGGCAC
1 TAAGCCCAGATTAGATGGCAC
896 CCAAATGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (23 bp):
TAAGCCCAGATTAGATGGCACTA
Found at i:968 original size:23 final size:23
Alignment explanation
Indices: 910--969 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
900 ATGATATTTA
*
910 TTTAAGCCTAGATCA-CTAGCAC
1 TTTAAGCCTAGATTAGCTAGCAC
* * * *
932 -CTAAGCCCAAATTAGCTATCAC
1 TTTAAGCCTAGATTAGCTAGCAC
954 TTTAAGCCTAGATTAG
1 TTTAAGCCTAGATTAG
970 TTGACACACT
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
21 10 0.36
22 6 0.21
23 12 0.43
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.28
Consensus pattern (23 bp):
TTTAAGCCTAGATTAGCTAGCAC
Found at i:1132 original size:23 final size:23
Alignment explanation
Indices: 1097--1164 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 23
1087 CCAACTAATA
*
1097 TTTAAGCAC-AGATTAGCTGGCAC
1 TTTAAGC-CTAGATTAGTTGGCAC
* **
1120 TTTAAGCCTAGATTTGTTGATAC
1 TTTAAGCCTAGATTAGTTGGCAC
*
1143 -TTAAGCCTAAATTAGTTGGCAC
1 TTTAAGCCTAGATTAGTTGGCAC
1165 CTAAATACGG
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
22 19 0.53
23 17 0.47
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (23 bp):
TTTAAGCCTAGATTAGTTGGCAC
Found at i:2435 original size:35 final size:35
Alignment explanation
Indices: 2317--2471 Score: 102
Period size: 35 Copynumber: 4.4 Consensus size: 35
2307 TTTAGTGGTC
* * *
2317 TTTATTTTCTGACTTATGAG-TTCGT-CCTGATCATC
1 TTTATTTTCTGACTTATG-GCTTCATCCCAG-TCATT
* * * * * * *
2352 CTTATTTTCTTAGTTGTGACTTCATCTCAGTCATC
1 TTTATTTTCTGACTTATGGCTTCATCCCAGTCATT
* * *
2387 GTTA-TTCCTTGACTTATGGCTT-AGTCTCAGTCATT
1 TTTATTTTC-TGACTTATGGCTTCA-TCCCAGTCATT
* * *
2422 TTTATTTTCTGACTTGTGGTTTCATCCCAGTCGTT
1 TTTATTTTCTGACTTATGGCTTCATCCCAGTCATT
2457 TTTATTTTCTGACTT
1 TTTATTTTCTGACTT
2472 GCAACTTTGT
Statistics
Matches: 93, Mismatches: 21, Indels: 12
0.74 0.17 0.10
Matches are distributed among these distances:
34 4 0.04
35 83 0.89
36 6 0.06
ACGTcount: A:0.15, C:0.20, G:0.14, T:0.50
Consensus pattern (35 bp):
TTTATTTTCTGACTTATGGCTTCATCCCAGTCATT
Found at i:2470 original size:70 final size:69
Alignment explanation
Indices: 2264--2471 Score: 177
Period size: 70 Copynumber: 3.0 Consensus size: 69
2254 CTCGACTTGC
** * * * *
2264 GGCTTAGTCCCAGTCATTTTTATTTTCTAACTTGCAGTTTCCTTTTAGTGGTCTTTATTTTCTGA
1 GGCTTAGT-CCAGTCATTTTTATTTTCTAACTTGTGGTTTCATCTCAGTCGTCTTTATTTTCTGA
2329 CTTAT
65 CTTAT
* * ** * * ** * * *
2334 GAG-TTCGTCCTGATCATCCTTATTTTCTTAGTTGTGACTTCATCTCAGTCATCGTTA-TTCCTT
1 G-GCTTAGTCCAG-TCATTTTTATTTTCTAACTTGTGGTTTCATCTCAGTCGTCTTTATTTTC-T
2397 GACTTAT
63 GACTTAT
* * *
2404 GGCTTAGTCTCAGTCATTTTTATTTTCTGACTTGTGGTTTCATCCCAGTCGTTTTTATTTTCTGA
1 GGCTTAGTC-CAGTCATTTTTATTTTCTAACTTGTGGTTTCATCTCAGTCGTCTTTATTTTCTGA
2469 CTT
65 CTT
2472 GCAACTTTGT
Statistics
Matches: 102, Mismatches: 30, Indels: 12
0.71 0.21 0.08
Matches are distributed among these distances:
69 7 0.07
70 89 0.87
71 6 0.06
ACGTcount: A:0.15, C:0.20, G:0.15, T:0.50
Consensus pattern (69 bp):
GGCTTAGTCCAGTCATTTTTATTTTCTAACTTGTGGTTTCATCTCAGTCGTCTTTATTTTCTGAC
TTAT
Found at i:2491 original size:140 final size:139
Alignment explanation
Indices: 2230--2502 Score: 305
Period size: 140 Copynumber: 2.0 Consensus size: 139
2220 TTGACTTACA
* * *
2230 ACTTCGTCTCAATCATCTTTATCCCTCGACTTGCGGCTTAGTCCCAGTCATTTTTATTTTCTAAC
1 ACTTCATCTCAATCATCGTTATCCCTCGACTTACGGCTTAGTCCCAGTCATTTTTATTTTCTAAC
* *** * ** *
2295 TTGCAGTTTCCTTTTAGTGGTCTTTATTTTCTGACTTATGAGTTCGTCCTGATCATCCTTATTTT
66 TTGCAGTTTCATCCCAGTCGTCTTTATTTTCTGACTTACAACTTCGTCCTGATCATCCTTA-TTT
2360 CTTAGTTGTG
130 CTTAGTTGTG
* * * * * *
2370 ACTTCATCTCAGTCATCGTTATTCCTTGACTTATGGCTTAGTCTCAGTCATTTTTATTTTCTGAC
1 ACTTCATCTCAATCATCGTTATCCCTCGACTTACGGCTTAGTCCCAGTCATTTTTATTTTCTAAC
** * * * * *
2435 TTGTGGTTTCATCCCAGTCGTTTTTATTTTCTGACTTGCAACTTTGT-CTTAGTCATCTTTATTT
66 TTGCAGTTTCATCCCAGTCGTCTTTATTTTCTGACTTACAACTTCGTCCTGA-TCATCCTTATTT
2499 CTTA
130 CTTA
2503 ATTTGCAGTT
Statistics
Matches: 108, Mismatches: 24, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
139 10 0.09
140 98 0.91
ACGTcount: A:0.16, C:0.22, G:0.14, T:0.48
Consensus pattern (139 bp):
ACTTCATCTCAATCATCGTTATCCCTCGACTTACGGCTTAGTCCCAGTCATTTTTATTTTCTAAC
TTGCAGTTTCATCCCAGTCGTCTTTATTTTCTGACTTACAACTTCGTCCTGATCATCCTTATTTC
TTAGTTGTG
Found at i:2679 original size:6 final size:6
Alignment explanation
Indices: 2668--2733 Score: 64
Period size: 6 Copynumber: 10.7 Consensus size: 6
2658 TCTTAAAAAC
* *
2668 AAACAA AAACAA AACCAA AAACAAA AAATCAA AAACCAA AAA-ATA AAACCA
1 AAACAA AAACAA AAACAA AAAC-AA AAA-CAA AAA-CAA AAACA-A AAACAA
2719 AAACAA AAA-AA AAAC
1 AAACAA AAACAA AAAC
2734 TTTTGAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
5 6 0.12
6 27 0.54
7 16 0.32
8 1 0.02
ACGTcount: A:0.79, C:0.18, G:0.00, T:0.03
Consensus pattern (6 bp):
AAACAA
Found at i:2700 original size:14 final size:14
Alignment explanation
Indices: 2678--2721 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2668 AAACAAAAAC
*
2678 AAAACCAAAAACAA
1 AAAATCAAAAACAA
2692 AAAATCAAAAACCAA
1 AAAATCAAAAA-CAA
*
2707 AAAAT-AAAACCAA
1 AAAATCAAAAACAA
2720 AA
1 AA
2722 CAAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 5 0.19
14 14 0.52
15 8 0.30
ACGTcount: A:0.77, C:0.18, G:0.00, T:0.05
Consensus pattern (14 bp):
AAAATCAAAAACAA
Found at i:5205 original size:10 final size:10
Alignment explanation
Indices: 5181--5209 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5171 ATATTTTATC
5181 AATTAAAAT-
1 AATTAAAATA
5190 AATTAAAATA
1 AATTAAAATA
5200 AATTAAAATA
1 AATTAAAATA
5210 TAAAAGCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AATTAAAATA
Found at i:6297 original size:21 final size:19
Alignment explanation
Indices: 6274--6318 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 19
6264 CTTTTTTTAT
6274 AAAATAAAATAAAAATTAACTA
1 AAAAT-AAATAAAAA-TAA-TA
6296 AAAATAAATAAAAATAATA
1 AAAATAAATAAAAATAATA
6315 AAAA
1 AAAA
6319 ATGATAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.26
20 3 0.13
21 9 0.39
22 5 0.22
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (19 bp):
AAAATAAATAAAAATAATA
Found at i:7188 original size:2 final size:2
Alignment explanation
Indices: 7181--7213 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
7171 AGTTTAGTAG
7181 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7214 TCATATGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7533 original size:17 final size:18
Alignment explanation
Indices: 7513--7570 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 18
7503 TATATTTTTA
7513 AAATTAATATTA-AAATT
1 AAATTAATATTATAAATT
* *
7530 AAATAAAATATTTTATTAATT
1 AAAT-TAATA--TTATAAATT
7551 AAA-TAATATTATAAATT
1 AAATTAATATTATAAATT
7568 AAA
1 AAA
7571 CTTGAACTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 15 0.45
18 4 0.12
19 4 0.12
20 3 0.09
21 7 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATTAATATTATAAATT
Found at i:7568 original size:21 final size:20
Alignment explanation
Indices: 7517--7570 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 20
7507 TTTTTAAAAT
7517 TAATATTA-AAATTAAATAA
1 TAATATTATAAATTAAATAA
* *
7536 -AATATT-T-TATTAATTAAA
1 TAATATTATAAATTAAAT-AA
7554 TAATATTATAAATTAAA
1 TAATATTATAAATTAAA
7571 CTTGAACTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
17 6 0.23
18 8 0.31
19 6 0.23
20 1 0.04
21 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAATATTATAAATTAAATAA
Found at i:9157 original size:2 final size:2
Alignment explanation
Indices: 9145--9176 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
9135 AAAGAGATTC
9145 AT AT A- AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9177 CAAGTTAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:14322 original size:3 final size:3
Alignment explanation
Indices: 14314--14351 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
14304 TATCGTTTTA
14314 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
14352 GGTAATACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20898 original size:26 final size:26
Alignment explanation
Indices: 20869--20930 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
20859 CACATCACTT
*
20869 GCATATGCATTATGAAAAAAACATTC
1 GCATTTGCATTATGAAAAAAACATTC
* **
20895 GCATTTACATTATGAAAAAGGCATTC
1 GCATTTGCATTATGAAAAAAACATTC
20921 GCATTTGCAT
1 GCATTTGCAT
20931 CACTTACATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.31
Consensus pattern (26 bp):
GCATTTGCATTATGAAAAAAACATTC
Found at i:21600 original size:23 final size:23
Alignment explanation
Indices: 21531--21623 Score: 75
Period size: 23 Copynumber: 4.1 Consensus size: 23
21521 AAGTCCAATC
* * *
21531 TAGTTGGCA-TCTAGGCCTAGAT
1 TAGTTGGCACTTTAAGCCTAAAT
* * **
21553 TAATTGGCAC-TTAAGCCCATCT
1 TAGTTGGCACTTTAAGCCTAAAT
21575 TAGTTGGCACTTTAAGCCTAAAT
1 TAGTTGGCACTTTAAGCCTAAAT
* *
21598 TAGTTGGTAGTTTAAG-CTCAAAT
1 TAGTTGGCACTTTAAGCCT-AAAT
21621 TAG
1 TAG
21624 CTAGAACCTA
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
22 26 0.46
23 30 0.54
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (23 bp):
TAGTTGGCACTTTAAGCCTAAAT
Found at i:21927 original size:22 final size:22
Alignment explanation
Indices: 21902--21946 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
21892 AAGACATTTG
* *
21902 GGCATGATCTCTAAGACTTCTA
1 GGCATAATCTCTAAGACCTCTA
* *
21924 GGCATAATTTGTAAGACCTCTA
1 GGCATAATCTCTAAGACCTCTA
21946 G
1 G
21947 ATAAAATATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (22 bp):
GGCATAATCTCTAAGACCTCTA
Found at i:22038 original size:126 final size:124
Alignment explanation
Indices: 21822--22165 Score: 388
Period size: 126 Copynumber: 2.8 Consensus size: 124
21812 AACCTCCAAG
* * ** *
21822 CAAAATATTTTAAAATTTTAAAGTTTCAACCCCTTGGGTACAAAGAGCATTTAAAGATGTCGAGA
1 CAAAATATTTTAAAATTTTAAAGTTTCAACGCCTT-GATATGAAGAGCATTTAAAGATATCGAGA
* * * * * * *
21887 TTTGTAAGACATTTGGGCATGATCTCTAAGACTTCTAGGCATAATTTGTAAGACCTCTAGA
65 TTTGTAAGACCTTTAGGCATAATCTCTAAGACTTCTAGGCACAATCTATAAGACCACT-GA
* * * *
21948 TAAAATATTTTAAAATTTCAAAGTTTCAATGCCTCTGATATGAGGAGCATTTAAAGATATCGAGA
1 CAAAATATTTTAAAATTTTAAAGTTTCAACGCCT-TGATATGAAGAGCATTTAAAGATATCGAGA
* * * *
22013 TTTGTAAGACCTCTAGACATAATCTCTAAGACTTCTAGGCACAATCTATAAGATCACTGG
65 TTTGTAAGACCTTTAGGCATAATCTCTAAGACTTCTAGGCACAATCTATAAGACCACTGA
* * * *
22073 CAAAATATTTTAAATTTTTAAAGATTT-AACGCGTTTGATATGATA-AGCATTCAAAGATATTGA
1 CAAAATATTTTAAAATTTTAAAG-TTTCAACGC-CTTGATATGA-AGAGCATTTAAAGATATCGA
*
22136 GATTTGTAAGA-CTTTCGGCATAATCTCTAA
63 GATTTGTAAGACCTTTAGGCATAATCTCTAA
22166 AACCTCCGGA
Statistics
Matches: 183, Mismatches: 31, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
124 16 0.09
125 60 0.33
126 106 0.58
127 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (124 bp):
CAAAATATTTTAAAATTTTAAAGTTTCAACGCCTTGATATGAAGAGCATTTAAAGATATCGAGAT
TTGTAAGACCTTTAGGCATAATCTCTAAGACTTCTAGGCACAATCTATAAGACCACTGA
Found at i:22049 original size:22 final size:22
Alignment explanation
Indices: 22017--22065 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
22007 TCGAGATTTG
* *
22017 TAAGACCTCTAGACATAATCTC
1 TAAGACCTCTAGACACAATCTA
* *
22039 TAAGACTTCTAGGCACAATCTA
1 TAAGACCTCTAGACACAATCTA
22061 TAAGA
1 TAAGA
22066 TCACTGGCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (22 bp):
TAAGACCTCTAGACACAATCTA
Found at i:22201 original size:22 final size:22
Alignment explanation
Indices: 22152--22215 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
22142 TAAGACTTTC
*
22152 GGCATAATCTCTAAAACCTCCG
1 GGCATAATCTTTAAAACCTCCG
* * * *
22174 GACATAATCTTTAAGATCTTCG
1 GGCATAATCTTTAAAACCTCCG
22196 GGCATAA-CTTTCAAAACCTC
1 GGCATAATCTTT-AAAACCTC
22216 TAGGAAAAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 4 0.12
22 28 0.88
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (22 bp):
GGCATAATCTTTAAAACCTCCG
Found at i:23081 original size:21 final size:22
Alignment explanation
Indices: 23055--23096 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
23045 TTATTTATTG
* *
23055 AATT-AAATAAAAATGAAAAAA
1 AATTAAAAGAAAAAGGAAAAAA
23076 AATTAAAAGAAAAAGGAAAAA
1 AATTAAAAGAAAAAGGAAAAA
23097 TATGGCTGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (22 bp):
AATTAAAAGAAAAAGGAAAAAA
Found at i:24227 original size:22 final size:22
Alignment explanation
Indices: 24163--24228 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
24153 TAGGTTCAGT
* *
24163 AGGAAGAAAAGGAAAAGAATAAG
1 AGGAA-AAAAGAAAAAGAAAAAG
* *
24186 A-TAAAGAAAGAAGACA-AAAAAG
1 AGGAAA-AAAGAA-AAAGAAAAAG
24208 AGGAAAAAAGAAAAAGAAAAA
1 AGGAAAAAAGAAAAAGAAAAA
24229 AAAAAGTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
21 3 0.09
22 24 0.73
23 6 0.18
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.03
Consensus pattern (22 bp):
AGGAAAAAAGAAAAAGAAAAAG
Found at i:24230 original size:25 final size:27
Alignment explanation
Indices: 24188--24240 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 27
24178 AGAATAAGAT
* *
24188 AAAGAAAGAAGACAAAAAAGAG-GAAA
1 AAAGAAAGAAGAAAAAAAAAAGTGAAA
24214 AAAGAAA-AAGAAAAAAAAAAGTGAAA
1 AAAGAAAGAAGAAAAAAAAAAGTGAAA
24240 A
1 A
24241 GAATGATGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (27 bp):
AAAGAAAGAAGAAAAAAAAAAGTGAAA
Found at i:28141 original size:19 final size:19
Alignment explanation
Indices: 28053--28148 Score: 77
Period size: 19 Copynumber: 5.1 Consensus size: 19
28043 TTGAGGTCTC
*
28053 GATTTTGGGTTAGGGTTTG
1 GATTTAGGGTTAGGGTTTG
* * * *
28072 GGTTTAGGTTTAAGGTTTA
1 GATTTAGGGTTAGGGTTTG
* * *
28091 AAGTTTAGGGCTAGGCTTT-
1 GA-TTTAGGGTTAGGGTTTG
* *
28110 GACTTATGGTTAGGGTTTG
1 GATTTAGGGTTAGGGTTTG
*
28129 GATTTAGGGTTAGGTTTTG
1 GATTTAGGGTTAGGGTTTG
28148 G
1 G
28149 GGTCTCGATT
Statistics
Matches: 56, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
18 12 0.21
19 32 0.57
20 12 0.21
ACGTcount: A:0.17, C:0.03, G:0.36, T:0.44
Consensus pattern (19 bp):
GATTTAGGGTTAGGGTTTG
Found at i:29463 original size:56 final size:55
Alignment explanation
Indices: 29245--29672 Score: 320
Period size: 56 Copynumber: 7.6 Consensus size: 55
29235 TAAAGGAAAA
* * * * *
29245 TTTGAAATTATTTTTATTTATTTTAGAAAATTTGATACTTCAATTTTTTCCCTTAAACA
1 TTTGAAATTA-TTTT-TTTATTTAAGAAAAATTGATACTTCAAATTTTT-CCTCAAA-T
* * * * *
29304 TTTGAAATCATTATATTTTATTTAAGGAAAAATTAATATTTTAATTTTTTCCTCAAAT
1 TTTGAAATTATT-T-TTTTATTTAA-GAAAAATTGATACTTCAAATTTTTCCTCAAAT
** * * * *
29362 TTCAAAATTATTCTTTTTA---AGGAAAAATTAATACTTTAACTTTTTCCTCAAAT
1 TTTGAAATTATT-TTTTTATTTAAGAAAAATTGATACTTCAAATTTTTCCTCAAAT
* * *
29415 TTTGAAATTATTTTTTTATTTAATGTAAAATTGATACTTCAAAATTTTCGTCAAAT
1 TTTGAAATTATTTTTTTATTTAA-GAAAAATTGATACTTCAAATTTTTCCTCAAAT
** * * *
29471 TTCAAAATTATTTTTTTATTTAATGAAAAATTGATACTTTAACTTTTTTCTCAAAAT
1 TTTGAAATTATTTTTTTATTTAA-GAAAAATTGATACTTCAAATTTTTCCTC-AAAT
* *
29528 TTT-AAATTA-TTTTTTATTTAA-AGAAAATTAATACTTCAACTTTTT-CTCAAAACATTT
1 TTTGAAATTATTTTTTTATTTAAGA-AAAATTGATACTTCAAATTTTTCCTC--AA-A--T
* * *
29585 TTTGAAA-TA-TTTTCTATTTAAGGAAAATTGATATTTC-AATTTTTCCTCAAACATT
1 TTTGAAATTATTTTTTTATTTAAGAAAAATTGATACTTCAAATTTTTCCTC-AA-A-T
29640 TCTTGAAA-TATTTTTTTATTTAAAGAAAAATTG
1 T-TTGAAATTATTTTTTTATTT-AAGAAAAATTG
29673 GTATTCTAAA
Statistics
Matches: 308, Mismatches: 42, Indels: 39
0.79 0.11 0.10
Matches are distributed among these distances:
52 6 0.02
53 44 0.14
54 24 0.08
55 17 0.06
56 95 0.31
57 52 0.17
58 25 0.08
59 24 0.08
60 21 0.07
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.49
Consensus pattern (55 bp):
TTTGAAATTATTTTTTTATTTAAGAAAAATTGATACTTCAAATTTTTCCTCAAAT
Found at i:29535 original size:112 final size:110
Alignment explanation
Indices: 29249--29668 Score: 342
Period size: 109 Copynumber: 3.7 Consensus size: 110
29239 GGAAAATTTG
* * * * * *
29249 AAATTATTTTTATTTATTTTAGAAAATTTGATACTTCAA-TTTTTTCCCTTAAACATTTGAAATC
1 AAATTA-TTTT-TTTATTTAAGAAAAATTGATACTTTAACTTTTTT--CTCAAA-ATTTTAAATT
* * * **
29313 ATTATATTTTATTTAAGGAAAAATTAATATTTTAATTTTTTCCTCAAATTTCA
61 ATT-T-TTTTATTTAAAG-AAAATTAATACTTCAAAATTTTCCTCAAATTTCA
* * *
29366 AAATTATTCTTTTTA---AGGAAAAATTAATACTTTAACTTTTTCCTC-AAATTTTGAAATTATT
1 AAATTATT-TTTTTATTTAAGAAAAATTGATACTTTAACTTTTTTCTCAAAATTTT-AAATTATT
* * *
29427 TTTTTATTTAATGTAAAATTGATACTTCAAAATTTTCGTCAAATTTCA
64 TTTTTATTTAAAG-AAAATTAATACTTCAAAATTTTCCTCAAATTTCA
29475 AAATTATTTTTTTATTTAATGAAAAATTGATACTTTAACTTTTTTCTCAAAATTTTAAATTA-TT
1 AAATTATTTTTTTATTTAA-GAAAAATTGATACTTTAACTTTTTTCTCAAAATTTTAAATTATTT
* * **
29539 TTTTATTTAAAGAAAATTAATACTTC-AACTTTTTCTCAAAACATTTTTTG
65 TTTTATTTAAAGAAAATTAATACTTCAAAATTTTCCTC--AA-A--TTTCA
* * *
29589 AAA-TA-TTTTCTATTTAAGGAAAATTGATA-TTTCAA-TTTTTCCTCAAACATTTCTTGAAA-T
1 AAATTATTTTTTTATTTAAGAAAAATTGATACTTT-AACTTTTTTCTCAAA-A-TT-TT-AAATT
29649 ATTTTTTTATTTAAAGAAAA
61 ATTTTTTTATTTAAAGAAAA
29669 ATTGGTATTC
Statistics
Matches: 254, Mismatches: 30, Indels: 41
0.78 0.09 0.13
Matches are distributed among these distances:
108 6 0.02
109 55 0.22
110 32 0.13
111 39 0.15
112 48 0.19
113 28 0.11
114 32 0.13
116 6 0.02
117 8 0.03
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (110 bp):
AAATTATTTTTTTATTTAAGAAAAATTGATACTTTAACTTTTTTCTCAAAATTTTAAATTATTTT
TTTATTTAAAGAAAATTAATACTTCAAAATTTTCCTCAAATTTCA
Found at i:30875 original size:46 final size:42
Alignment explanation
Indices: 30811--30894 Score: 98
Period size: 46 Copynumber: 1.9 Consensus size: 42
30801 AAAGAAAAAT
*
30811 ATAAATAAATAAATAAATAATCAA-GACAAAACATAAAATTGG
1 ATAAATAAATAAATAAATAAT-AATAACAAAACATAAAATTGG
*
30853 ATAAATAAAATAAAAGTAAAATAATAATAATAAAACATAAAA
1 ATAAAT-AAAT-AAA-T-AAATAATAATAACAAAACATAAAA
30895 AAAGGTATAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
42 6 0.17
43 4 0.11
44 3 0.09
45 3 0.09
46 19 0.54
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (42 bp):
ATAAATAAATAAATAAATAATAATAACAAAACATAAAATTGG
Found at i:31697 original size:32 final size:32
Alignment explanation
Indices: 31563--31806 Score: 100
Period size: 32 Copynumber: 7.1 Consensus size: 32
31553 GACTAATCCA
* *
31563 AAGTAAAAAATGAGGACTTAGTCTAAG-TCTAT
1 AAGTAAAAAATGATGACTTGGTCTAAGCT-TAT
* * *
31595 AAGTCGAAAATGATGATGACGACTTGATCTGAA-CCTAT
1 AAGT--AAAA--A--ATGATGACTTGGTCT-AAGCTTAT
* * * * * *
31633 AAGTCAAAATTGATGATTTGGTTTGACCTTAT
1 AAGTAAAAAATGATGACTTGGTCTAAGCTTAT
*
31665 AAGTAAAAAATGATGACTTGGTCTAAGTTTAT
1 AAGTAAAAAATGATGACTTGGTCTAAGCTTAT
** *
31697 AAGTTAAAATGAA-GATGACTTAATCTGAGCTTAT
1 AAG-TAAAA--AATGATGACTTGGTCTAAGCTTAT
*
31731 AAGTTAAAATGAAGATGATTACTTGGTCTAAG-TCTAT
1 AAG-T-AAA--AA-ATGATGACTTGGTCTAAGCT-TAT
* *
31768 AATTCAAAATTGAGATGATGACTTGGTCTGAGCTTAT
1 AAGT-AAAA---A-ATGATGACTTGGTCTAAGCTTAT
31805 AA
1 AA
31807 ATCAAAATGA
Statistics
Matches: 159, Mismatches: 31, Indels: 39
0.69 0.14 0.17
Matches are distributed among these distances:
31 1 0.01
32 46 0.29
33 5 0.03
34 28 0.18
35 6 0.04
36 10 0.06
37 41 0.26
38 20 0.13
39 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (32 bp):
AAGTAAAAAATGATGACTTGGTCTAAGCTTAT
Found at i:31731 original size:34 final size:34
Alignment explanation
Indices: 31660--31748 Score: 112
Period size: 34 Copynumber: 2.7 Consensus size: 34
31650 TTGGTTTGAC
**
31660 CTTATAAG-TAAAA--AATGATGACTTGGTCTAAG
1 CTTATAAGTTAAAATGAA-GATGACTTAATCTAAG
* *
31692 TTTATAAGTTAAAATGAAGATGACTTAATCTGAG
1 CTTATAAGTTAAAATGAAGATGACTTAATCTAAG
31726 CTTATAAGTTAAAATGAAGATGA
1 CTTATAAGTTAAAATGAAGATGA
31749 TTACTTGGTC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
32 7 0.14
33 5 0.10
34 35 0.71
35 2 0.04
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.33
Consensus pattern (34 bp):
CTTATAAGTTAAAATGAAGATGACTTAATCTAAG
Found at i:31784 original size:37 final size:36
Alignment explanation
Indices: 31674--31843 Score: 141
Period size: 37 Copynumber: 4.7 Consensus size: 36
31664 TAAGTAAAAA
* * * *
31674 ATGATGACTTGGTCTAAGTTTATAAGTTAAAATGAAG
1 ATGATTACTTGGTCTAAG-CTATAAATCAAAATGAAG
** * * *
31711 ATG---ACTTAATCTGAGCTTATAAGTTAAAATGAAG
1 ATGATTACTTGGTCTAAGC-TATAAATCAAAATGAAG
*
31745 ATGATTACTTGGTCTAAGTCTATAATTCAAAATTG-AG
1 ATGATTACTTGGTCTAAG-CTATAAATCAAAA-TGAAG
* *
31782 ATGATGACTTGGTCTGAGCTTATAAATCAAAATGAAG
1 ATGATTACTTGGTCTAAGC-TATAAATCAAAATGAAG
*
31819 ATGATTACTTGGTTTAAGCCTATAA
1 ATGATTACTTGGTCTAAG-CTATAA
31844 GTCGAAATAA
Statistics
Matches: 109, Mismatches: 15, Indels: 18
0.77 0.11 0.13
Matches are distributed among these distances:
34 29 0.27
36 3 0.03
37 73 0.67
38 4 0.04
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (36 bp):
ATGATTACTTGGTCTAAGCTATAAATCAAAATGAAG
Found at i:31820 original size:74 final size:71
Alignment explanation
Indices: 31674--31845 Score: 229
Period size: 74 Copynumber: 2.4 Consensus size: 71
31664 TAAGTAAAAA
* * * *
31674 ATGATGACTTGGTCTAAGTTTATAAGTTAAAATGAAGATGACTTAATCTGAGCTTATAAGTTAAA
1 ATGATTACTTGGTCTAAGTCTATAAGTTAAAATGAAGATGACTTAATCTGAGCTTATAAATCAAA
31739 ATGAAG
66 ATGAAG
**
31745 ATGATTACTTGGTCTAAGTCTATAA-TTCAAAATTGAGATGATGACTTGGTCTGAGCTTATAAAT
1 ATGATTACTTGGTCTAAGTCTATAAGTT-AAAA-TGA-A-GATGACTTAATCTGAGCTTATAAAT
31809 CAAAATGAAG
62 CAAAATGAAG
* *
31819 ATGATTACTTGGTTTAAGCCTATAAGT
1 ATGATTACTTGGTCTAAGTCTATAAGT
31846 CGAAATAAGA
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
70 2 0.02
71 27 0.31
72 3 0.03
73 1 0.01
74 54 0.61
75 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (71 bp):
ATGATTACTTGGTCTAAGTCTATAAGTTAAAATGAAGATGACTTAATCTGAGCTTATAAATCAAA
ATGAAG
Found at i:32874 original size:22 final size:21
Alignment explanation
Indices: 32845--32895 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
32835 GATTTAAGTC
32845 TTTC-TTTTC-CTCCTTTTTATT
1 TTTCATTTTCTCT-CTTTTT-TT
*
32866 TTTCATTTTTTCTCTTTTTTT
1 TTTCATTTTCTCTCTTTTTTT
32887 TTTCATTTT
1 TTTCATTTT
32896 TTTTTCACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 15 0.56
22 10 0.37
23 2 0.07
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTCATTTTCTCTCTTTTTTT
Found at i:32898 original size:22 final size:22
Alignment explanation
Indices: 32857--32897 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
32847 TCTTTTCCTC
32857 CTTTTTATTTTTCATTTTTTCT
1 CTTTTTATTTTTCATTTTTTCT
32879 CTTTTT-TTTTTCATTTTTT
1 CTTTTTATTTTTCATTTTTT
32898 TTTCACTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.80
Consensus pattern (22 bp):
CTTTTTATTTTTCATTTTTTCT
Found at i:32900 original size:11 final size:11
Alignment explanation
Indices: 32859--32902 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
32849 TTTTCCTCCT
32859 TTTTATTTTTCA
1 TTTT-TTTTTCA
* *
32871 -TTTTTTCTCT
1 TTTTTTTTTCA
32881 TTTTTTTTTCA
1 TTTTTTTTTCA
32892 TTTTTTTTTCA
1 TTTTTTTTTCA
32903 CTTCATTCCC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 5 0.19
11 22 0.81
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTTTTCA
Found at i:38223 original size:55 final size:54
Alignment explanation
Indices: 38076--38500 Score: 291
Period size: 57 Copynumber: 7.6 Consensus size: 54
38066 ATTTGAAATC
* * * *
38076 ATTATTTTTTATTTAAGAAAAAACTAATACTTT-AACTTTTTCCTCAAATTTTGAA
1 ATTATTTTTTATTTAAG-AAAAATTGATA-TTTCAACTTTTTTCTCAATTTTTGAA
* *
38131 ATTATTCTTTTTATTTAAAGGAAAATTTGATACTTCAACTTTTTTCTCAATTTTTGAA
1 ATTA-T-TTTTTATTT-AA-GAAAAATTGATATTTCAACTTTTTTCTCAATTTTTGAA
* * **
38189 ATTATTTTTTATTTAAGGAAAAATTAATATTTCAA-TTTTTTCCTCAAATTTCAAA
1 ATTATTTTTTATTTAA-GAAAAATTGATATTTCAACTTTTTT-CTCAATTTTTGAA
* * * *
38244 ATTAATTTTTATTTATGAAAATTTTGATACTTT-AAC-TTTTTCTTAAATTTTT-AA
1 ATTATTTTTTATTTAAGAAAA-ATTGATA-TTTCAACTTTTTTC-TCAATTTTTGAA
**
38298 ATTCCTTTTTATTTTAA-AAAAATTGATATTTCAAC-TTTTTCTCAAAATATTTTTTGAA
1 ATTATTTTTTA-TTTAAGAAAAATTGATATTTCAACTTTTTTCTC---A-A-TTTTTGAA
* * * *
38356 A-TATTTTCTATTTCAAG-AAAATTGATATTTTAA-TTTTTCCTTAAAACTTTTTTTTGAA
1 ATTATTTTTTATTT-AAGAAAAATTGATATTTCAACTTTTTTC-T-CAA----TTTTTGAA
**
38414 A-T-TTTTTTATTTAAGAAAAATTGATATTTCAACTTTTTGTCAAACATTTCTTGAA
1 ATTATTTTTTATTTAAGAAAAATTGATATTTCAACTTTTT-TCTCA-ATTT-TTGAA
*
38469 A-TATTTTTTTATTTAAAGAAAAATTGGTATTT
1 ATTA-TTTTTTATTT-AAGAAAAATTGATATTT
38501 TAAAAATTTC
Statistics
Matches: 301, Mismatches: 35, Indels: 65
0.75 0.09 0.16
Matches are distributed among these distances:
52 4 0.01
53 15 0.05
54 30 0.10
55 77 0.26
56 21 0.07
57 81 0.27
58 71 0.24
59 2 0.01
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (54 bp):
ATTATTTTTTATTTAAGAAAAATTGATATTTCAACTTTTTTCTCAATTTTTGAA
Found at i:38534 original size:114 final size:112
Alignment explanation
Indices: 38303--38535 Score: 258
Period size: 114 Copynumber: 2.1 Consensus size: 112
38293 TTTAAATTCC
* *
38303 TTTTTATTTTAAAAAAATTGATATTTCAACTTTTTCTCAAAATATTTTTTGAAATATTTTCTATT
1 TTTTTATTTTAAAAAAATTGATATTTCAACTTTTTCTCAAAACATTTCTTGAAATATTTTCTATT
* ** * ***
38368 TCAAGAAAATTGATATTTTAATTTTTCCTTAAAACTTTTTTTTGAAATT
66 TAAAGAAAATTGATATTTTAAAATTTCATT-AAAC-TTTTGGGGAAATT
* *
38417 TTTTTA-TTTAAGAAAAATTGATATTTCAACTTTTTGTC-AAACATTTCTTGAAATATTTTTTTA
1 TTTTTATTTTAA-AAAAATTGATATTTCAACTTTTTCTCAAAACATTTCTTGAAATA-TTTTCTA
* *
38480 TTTAAAGAAAAATTGGTATTTTAAAAATTTCATT-AA-TTTTGGGGAAAATA
64 TTTAAAG-AAAATTGATATTTT-AAAATTTCATTAAACTTTTGGGG-AAATT
38530 TTTTTA
1 TTTTTA
38536 GTTATTTTTC
Statistics
Matches: 101, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
112 5 0.05
113 30 0.30
114 45 0.45
115 13 0.13
116 8 0.08
ACGTcount: A:0.36, C:0.06, G:0.07, T:0.51
Consensus pattern (112 bp):
TTTTTATTTTAAAAAAATTGATATTTCAACTTTTTCTCAAAACATTTCTTGAAATATTTTCTATT
TAAAGAAAATTGATATTTTAAAATTTCATTAAACTTTTGGGGAAATT
Found at i:39669 original size:3 final size:3
Alignment explanation
Indices: 39661--39721 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
39651 ATAAAATAAA
39661 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT
1 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT
39709 AGT AGT AGT AGT A
1 AGT AGT AGT AGT A
39722 ATAATAATAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.34, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
AGT
Found at i:39726 original size:3 final size:3
Alignment explanation
Indices: 39720--39749 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
39710 GTAGTAGTAG
*
39720 TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39750 AAGTAAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:42825 original size:18 final size:18
Alignment explanation
Indices: 42802--42855 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
42792 TTATCATTCA
*
42802 AATAATATAATATTATGT
1 AATAATATAATATTATGC
42820 AATAATATAATATATCATGC
1 AATAATATAATAT-T-ATGC
42840 AATTAATATAA-ATTAT
1 AA-TAATATAATATTAT
42856 TATACAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 15 0.47
19 2 0.06
20 7 0.22
21 8 0.25
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (18 bp):
AATAATATAATATTATGC
Found at i:42846 original size:21 final size:20
Alignment explanation
Indices: 42793--42902 Score: 86
Period size: 21 Copynumber: 5.5 Consensus size: 20
42783 AAACTAAAAT
* *
42793 TATCATTCAAATAATAT-AA
1 TATCATGCAATTAATATAAA
* *
42812 TATTATGTAA-TAATATAATA
1 TATCATGCAATTAATATAA-A
42832 TATCATGCAATTAATATAAA
1 TATCATGCAATTAATATAAA
* *
42852 TTATTATACAATT-ATAATAAA
1 -TATCATGCAATTAAT-ATAAA
42873 GTATCATGCAATTAAT-TAACA
1 -TATCATGCAATTAATATAA-A
42894 -ATCATGCAA
1 TATCATGCAA
42903 AAAAATATAT
Statistics
Matches: 74, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
18 6 0.08
19 17 0.23
20 15 0.20
21 34 0.46
22 2 0.03
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (20 bp):
TATCATGCAATTAATATAAA
Found at i:42868 original size:39 final size:41
Alignment explanation
Indices: 42793--42888 Score: 110
Period size: 39 Copynumber: 2.4 Consensus size: 41
42783 AAACTAAAAT
* * *
42793 TATCATTCAAATAATATAATATTATGTAATAATATAAT-A-
1 TATCATGCAATTAATATAATATTATGTAACAATATAATAAG
42832 TATCATGCAATTAATATAA-ATTAT-TATACAATTATAATAAAG
1 TATCATGCAATTAATATAATATTATGTA-ACAA-TATAAT-AAG
42874 TATCATGCAATTAAT
1 TATCATGCAATTAAT
42889 TAACAATCAT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
37 2 0.04
38 8 0.16
39 23 0.47
41 1 0.02
42 15 0.31
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (41 bp):
TATCATGCAATTAATATAATATTATGTAACAATATAATAAG
Found at i:44144 original size:6 final size:6
Alignment explanation
Indices: 44078--44144 Score: 80
Period size: 6 Copynumber: 11.0 Consensus size: 6
44068 AACTAAAACC
* * * * *
44078 AAAATC AAAATT AAAACT AAAATT AAAACCT AAAATT AAAACT AAAATC
1 AAAATT AAAATT AAAATT AAAATT AAAA-TT AAAATT AAAATT AAAATT
44127 AAAATT AAAATT AAAATT
1 AAAATT AAAATT AAAATT
44145 TTTGGGCTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
6 46 0.90
7 5 0.10
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (6 bp):
AAAATT
Found at i:44144 original size:12 final size:12
Alignment explanation
Indices: 44066--44142 Score: 93
Period size: 12 Copynumber: 6.3 Consensus size: 12
44056 CAAAATAATA
**
44066 AAAACTAAAACC
1 AAAACTAAAATT
44078 AAAA-TCAAAATT
1 AAAACT-AAAATT
44090 AAAACTAAAATT
1 AAAACTAAAATT
44102 AAAACCTAAAATT
1 AAAA-CTAAAATT
*
44115 AAAACTAAAATC
1 AAAACTAAAATT
*
44127 AAAATTAAAATT
1 AAAACTAAAATT
44139 AAAA
1 AAAA
44143 TTTTTGGGCT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
11 1 0.02
12 43 0.75
13 13 0.23
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAACTAAAATT
Found at i:44572 original size:18 final size:17
Alignment explanation
Indices: 44549--44590 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
44539 TTAAATTCAA
44549 AAGAATTACAATATGTGC
1 AAGAATTACAAT-TGTGC
* *
44567 AAGAATTTCAATTTTGC
1 AAGAATTACAATTGTGC
44584 AAGAATT
1 AAGAATT
44591 TATAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (17 bp):
AAGAATTACAATTGTGC
Found at i:44640 original size:35 final size:34
Alignment explanation
Indices: 44595--44665 Score: 97
Period size: 35 Copynumber: 2.1 Consensus size: 34
44585 AGAATTTATA
44595 AATTTTTAAGAATTTAAAGATTAGCAAAAATTTC
1 AATTTTTAAGAATTTAAAGATTAGCAAAAATTTC
** * *
44629 AATTTTGTAAGAATTTTCAGATTGGCAAGAATTTC
1 AATTTT-TAAGAATTTAAAGATTAGCAAAAATTTC
44664 AA
1 AA
44666 ATTCACAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 6 0.19
35 26 0.81
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (34 bp):
AATTTTTAAGAATTTAAAGATTAGCAAAAATTTC
Found at i:44646 original size:18 final size:17
Alignment explanation
Indices: 44549--44679 Score: 77
Period size: 18 Copynumber: 7.5 Consensus size: 17
44539 TTAAATTCAA
* *
44549 AAGAATTACAATATGTGC
1 AAGAATTTCAAT-TTTGC
44567 AAGAATTTCAATTTTGC
1 AAGAATTTCAATTTTGC
* *
44584 AAGAATTTATAAATTTT-T
1 AAGAA-TT-TCAATTTTGC
* * *
44602 AAGAATTTAAAGATTAGC
1 AAGAATTTCAA-TTTTGC
* *
44620 AAAAATTTCAATTTTGT
1 AAGAATTTCAATTTTGC
*
44637 AAGAATTTTCAGA-TTGGC
1 AAGAA-TTTCA-ATTTTGC
* **
44655 AAGAATTTCAAATTCAC
1 AAGAATTTCAATTTTGC
44672 AAGAATTT
1 AAGAATTT
44680 TTAGATTGGC
Statistics
Matches: 89, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
16 5 0.06
17 36 0.40
18 40 0.45
19 8 0.09
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (17 bp):
AAGAATTTCAATTTTGC
Found at i:45026 original size:18 final size:17
Alignment explanation
Indices: 44982--45032 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
44972 TATTCGTAAG
* *
44982 AATTGAAGATTCAAAAA
1 AATTTAAGATTCACAAA
*
44999 AATTTTAGATTCACAAA
1 AATTTAAGATTCACAAA
*
45016 AATTTAAAGATTTACAA
1 AATTT-AAGATTCACAA
45033 GGTTTTCAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 19 0.68
18 9 0.32
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (17 bp):
AATTTAAGATTCACAAA
Found at i:46523 original size:22 final size:21
Alignment explanation
Indices: 46480--46518 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
46470 TTTTTTCCTC
*
46480 TTTTTTTCATTTTATTTTGCA
1 TTTTTTGCATTTTATTTTGCA
46501 TTTTTTGCATTTT-TTTTG
1 TTTTTTGCATTTTATTTTG
46519 TGCATCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.08, G:0.08, T:0.74
Consensus pattern (21 bp):
TTTTTTGCATTTTATTTTGCA
Found at i:51438 original size:21 final size:20
Alignment explanation
Indices: 51393--51478 Score: 95
Period size: 21 Copynumber: 4.2 Consensus size: 20
51383 ATCATAGAAA
**
51393 TAATATAAATATCACACAA-
1 TAATATAAATATCATGCAAT
*
51412 TAATATAATATATTATGCAAT
1 TAATATAA-ATATCATGCAAT
51433 TAATATAAATAATCATGCAAT
1 TAATATAAAT-ATCATGCAAT
51454 T-ATAATAAAGTATCATGCAAT
1 TAAT-ATAAA-TATCATGCAAT
51475 TAAT
1 TAAT
51479 TAACAATCAC
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
19 8 0.14
20 12 0.21
21 34 0.60
22 3 0.05
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (20 bp):
TAATATAAATATCATGCAAT
Found at i:51673 original size:19 final size:19
Alignment explanation
Indices: 51629--51665 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
51619 AATAAAAACA
51629 AAAAAAATCAAAACCAAAG
1 AAAAAAATCAAAACCAAAG
*
51648 AAAAAAATCAAAATCAAA
1 AAAAAAATCAAAACCAAA
51666 ATAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.76, C:0.14, G:0.03, T:0.08
Consensus pattern (19 bp):
AAAAAAATCAAAACCAAAG
Found at i:51676 original size:25 final size:25
Alignment explanation
Indices: 51632--51679 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
51622 AAAAACAAAA
* *
51632 AAAATCAAAACCAAAGAAAAAAATC
1 AAAATCAAAACAAAAAAAAAAAATC
*
51657 AAAATCAAAATAAAAAAAAAAAA
1 AAAATCAAAACAAAAAAAAAAAA
51680 AGAAAATGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.79, C:0.10, G:0.02, T:0.08
Consensus pattern (25 bp):
AAAATCAAAACAAAAAAAAAAAATC
Found at i:51679 original size:19 final size:21
Alignment explanation
Indices: 51617--51680 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 21
51607 ACAGAGAAAG
51617 AAAATAAAAACAAAAAAAATC
1 AAAATAAAAACAAAAAAAATC
* *
51638 AAAACCAAAGAAAAAAATCAAAATC
1 AAAA-TAAA-AACAAAA--AAAATC
51663 AAAATAAAAA-AAAAAAAA
1 AAAATAAAAACAAAAAAAA
51681 GAAAATGGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
20 4 0.11
21 4 0.11
22 7 0.19
23 8 0.22
24 3 0.08
25 10 0.28
ACGTcount: A:0.81, C:0.09, G:0.02, T:0.08
Consensus pattern (21 bp):
AAAATAAAAACAAAAAAAATC
Done.