Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167874.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_142, 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: 66706
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:2186 original size:21 final size:21
Alignment explanation
Indices: 2161--2203 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2151 TAATGTCCTA
*
2161 AAAGAGCTTAA-AGAGTTACGT
1 AAAGAGCATAAGAG-GTTACGT
2182 AAAGAGCATAAGAGGTTACGT
1 AAAGAGCATAAGAGGTTACGT
2203 A
1 A
2204 TACAGGTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (21 bp):
AAAGAGCATAAGAGGTTACGT
Found at i:9938 original size:48 final size:47
Alignment explanation
Indices: 9843--9958 Score: 169
Period size: 47 Copynumber: 2.4 Consensus size: 47
9833 AAAAAAGAGG
* *
9843 AAAAGGTCAAATTGAAAACCCGAAAGGGCAATTTGAACCATATAAAA
1 AAAAGGTCAAATTGAAAACCCAAAAAGGCAATTTGAACCATATAAAA
* * *
9890 AAAAAGTCAAATTGAAAACCCAAAAAGGCGATTTGAACTATATAAAAA
1 AAAAGGTCAAATTGAAAACCCAAAAAGGCAATTTGAACCATAT-AAAA
*
9938 AAAAGGTCCAATTGAAAACCC
1 AAAAGGTCAAATTGAAAACCC
9959 GATAGGGTGG
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
47 38 0.62
48 23 0.38
ACGTcount: A:0.53, C:0.16, G:0.15, T:0.17
Consensus pattern (47 bp):
AAAAGGTCAAATTGAAAACCCAAAAAGGCAATTTGAACCATATAAAA
Found at i:10932 original size:89 final size:89
Alignment explanation
Indices: 10781--11154 Score: 352
Period size: 89 Copynumber: 4.2 Consensus size: 89
10771 ATCATTTCTT
* * * * * * *
10781 ATGATTCGTGGTTTTGT-CTCGATCATTTATTCTTGACCGTAACTTGGTCTTGGTCACTTTATTT
1 ATGATTCGTGGTTTTGTCCTCAATCATTCATTTTTGACC-TGACTCGATCCTGGTCACTTTATTT
* * *
10845 CGACTCGTGGTTTTGTC-CTGATTAC
65 CGACTCGTGGTTTCGTCTCAG-TCAC
* * *
10870 ATGATTCATGGTTTTGTCCT-GATCATTCATTTTTGACCTGAACTCGATCCTGGTCGCTTTATTT
1 ATGATTCGTGGTTTTGTCCTCAATCATTCATTTTTGACCTG-ACTCGATCCTGGTCACTTTATTT
* * * *
10934 TGACTCATGGTTTC--ATCGGTCAC
65 CGACTCGTGGTTTCGTCTCAGTCAC
* * *
10957 ATGATTCGTAGTTTTAT-CTCAAT-ATTTCATTTTCT-ACCTCGACTCGATCCTGGTCATTTTAT
1 ATGATTCGTGGTTTTGTCCTCAATCA-TTCATTTT-TGACCT-GACTCGATCCTGGTCACTTTAT
* *
11019 TTCGACTTGTGGTTTTGTCTCAGTCAC
63 TTCGACTCGTGGTTTCGTCTCAGTCAC
* * * * *
11046 ATGATTCATGGTTTTGTCC-CAATCATTCATTTTTGACCTTGATTCGATCCCGTTCGCTTTATTT
1 ATGATTCGTGGTTTTGTCCTCAATCATTCATTTTTGACC-TGACTCGATCCTGGTCACTTTATTT
* *
11110 TGACTTGTGGTTTCGTCTCAGTCAC
65 CGACTCGTGGTTTCGTCTCAGTCAC
*
11135 ATGATTCGTGATTTTGTCCT
1 ATGATTCGTGGTTTTGTCCT
11155 AATTATTTAT
Statistics
Matches: 233, Mismatches: 38, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
86 3 0.01
87 62 0.27
88 6 0.03
89 157 0.67
90 5 0.02
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.45
Consensus pattern (89 bp):
ATGATTCGTGGTTTTGTCCTCAATCATTCATTTTTGACCTGACTCGATCCTGGTCACTTTATTTC
GACTCGTGGTTTCGTCTCAGTCAC
Found at i:11565 original size:3 final size:3
Alignment explanation
Indices: 11557--11607 Score: 93
Period size: 3 Copynumber: 16.7 Consensus size: 3
11547 CATGTTATAT
11557 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
11606 TT
1 TT
11608 TTCATTTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12091 original size:21 final size:21
Alignment explanation
Indices: 12047--12094 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
12037 CATTTGAGAA
* * * *
12047 TTTTTTTGGATTTTTTTTGTT
1 TTTTTTTAGATTTTTCTAGGT
12068 TTTTTTTAGATTTTTCTAGGT
1 TTTTTTTAGATTTTTCTAGGT
12089 TTTTTT
1 TTTTTT
12095 AGGTTTCTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.08, C:0.02, G:0.12, T:0.77
Consensus pattern (21 bp):
TTTTTTTAGATTTTTCTAGGT
Found at i:12194 original size:19 final size:19
Alignment explanation
Indices: 12172--12208 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
12162 TCCAGTGAAG
12172 TTTCCAG-AATCCAGTGGGC
1 TTTCCAGAAAT-CAGTGGGC
12191 TTTCCAGAAATCAGTGGG
1 TTTCCAGAAATCAGTGGG
12209 TTCTCTAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (19 bp):
TTTCCAGAAATCAGTGGGC
Found at i:12643 original size:33 final size:34
Alignment explanation
Indices: 12571--12634 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
12561 TTAAAAAGGG
*
12571 AAAAAATTATTCTATCTTTTTCAAAAAAAAAAGA
1 AAAAAATTAATCTATCTTTTTCAAAAAAAAAAGA
*
12605 AAAAAATTAATCTATC-TTTTCTAAAAAAAA
1 AAAAAATTAATCTATCTTTTTCAAAAAAAAA
12635 TTCTAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 13 0.46
34 15 0.54
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (34 bp):
AAAAAATTAATCTATCTTTTTCAAAAAAAAAAGA
Found at i:13361 original size:41 final size:41
Alignment explanation
Indices: 13304--13388 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
13294 AATACTAGCA
*
13304 TACGAAACTATTTCTACCCACTTGGTAAAGTAGTTAATTAT
1 TACGAAACCATTTCTACCCACTTGGTAAAGTAGTTAATTAT
13345 TACGAAACCATTTCTACCCACTTGGTAAAGTAGTTAATTAT
1 TACGAAACCATTTCTACCCACTTGGTAAAGTAGTTAATTAT
13386 TAC
1 TAC
13389 AAAGATAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (41 bp):
TACGAAACCATTTCTACCCACTTGGTAAAGTAGTTAATTAT
Found at i:34284 original size:35 final size:35
Alignment explanation
Indices: 34235--34340 Score: 128
Period size: 35 Copynumber: 3.1 Consensus size: 35
34225 AAGTGACAAG
34235 TTAATTTGACGTATAGATTAATAATATTGAATAGA
1 TTAATTTGACGTATAGATTAATAATATTGAATAGA
*** *
34270 TTAATTTTTTGTATAGA-T-ATAATTATTGTATAGA
1 TTAATTTGACGTATAGATTAATAA-TATTGAATAGA
*
34304 TATAATTTGACGTATAGATTAATAATA-TGAAAAGA
1 T-TAATTTGACGTATAGATTAATAATATTGAATAGA
34339 TT
1 TT
34341 CAACTGTAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
33 4 0.07
34 13 0.22
35 34 0.59
36 3 0.05
37 4 0.07
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.43
Consensus pattern (35 bp):
TTAATTTGACGTATAGATTAATAATATTGAATAGA
Found at i:34287 original size:17 final size:17
Alignment explanation
Indices: 34245--34326 Score: 78
Period size: 17 Copynumber: 4.7 Consensus size: 17
34235 TTAATTTGAC
*
34245 GTATAGATTAATAATATT
1 GTATAGATTAAT-TTATT
* *
34263 GAATAGATTAATTTTTT
1 GTATAGATTAATTTATT
34280 GTATAGATATAA-TTATT
1 GTATAGAT-TAATTTATT
*
34297 GTATAGATATAATTTGA-C
1 GTATAGAT-TAATTT-ATT
34315 GTATAGATTAAT
1 GTATAGATTAAT
34327 AATATGAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
17 30 0.55
18 24 0.44
19 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.13, T:0.45
Consensus pattern (17 bp):
GTATAGATTAATTTATT
Found at i:34726 original size:20 final size:20
Alignment explanation
Indices: 34701--34742 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
34691 AACTATTAGT
34701 TCAAAATTTAGCTCATCTAA
1 TCAAAATTTAGCTCATCTAA
34721 TCAAAATTTAGCTCATCTAA
1 TCAAAATTTAGCTCATCTAA
34741 TC
1 TC
34743 TATGTAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (20 bp):
TCAAAATTTAGCTCATCTAA
Found at i:37968 original size:4 final size:4
Alignment explanation
Indices: 37959--38045 Score: 61
Period size: 4 Copynumber: 21.2 Consensus size: 4
37949 ATTTACAAAT
* * *
37959 ATAA ATAA ATAA ATAA ACAA TTAA ACAA ATAA AT-A A-AA ATATA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA-A ATAA
* * * *
38006 ATAA AGAA ATAA TTTAA TAGAA ATAA ATGA ATAAA ATAA A
1 ATAA ATAA ATAA -ATAA -ATAA ATAA ATAA AT-AA ATAA A
38046 AAAAGTACTA
Statistics
Matches: 64, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
3 4 0.06
4 47 0.73
5 13 0.20
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:38006 original size:15 final size:15
Alignment explanation
Indices: 37986--38041 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
37976 CAATTAAACA
37986 AATAAATAAAAATAT
1 AATAAATAAAAATAT
38001 AATAAATAAAGAA-AT
1 AATAAATAAA-AATAT
* *
38016 AATTTAATAGAAATA-
1 AA-TAAATAAAAATAT
*
38031 AATGAATAAAA
1 AATAAATAAAA
38042 TAAAAAAAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
14 7 0.21
15 18 0.53
16 9 0.26
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (15 bp):
AATAAATAAAAATAT
Found at i:38044 original size:39 final size:38
Alignment explanation
Indices: 37955--38050 Score: 95
Period size: 39 Copynumber: 2.4 Consensus size: 38
37945 ATGTATTTAC
*
37955 AAATATAAATAAATAAATAAACAATTAAACAAATAAATAA
1 AAATA-AAATAAATAAAGAAACAATTAAACAAATAAAT-A
* * *
37995 AAATATAATAAATAAAGAAATAATTTAATAGAAATAAAT-
1 AAATAAAATAAATAAAGAAACAA-TTAA-ACAAATAAATA
* *
38034 GAATAAAATAAAAAAAG
1 AAATAAAATAAATAAAG
38051 TACTAGAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
39 29 0.62
40 9 0.19
41 9 0.19
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (38 bp):
AAATAAAATAAATAAAGAAACAATTAAACAAATAAATA
Found at i:39526 original size:76 final size:76
Alignment explanation
Indices: 39433--39579 Score: 197
Period size: 76 Copynumber: 1.9 Consensus size: 76
39423 TTGGAATCTT
* ** *
39433 TTAGAAACTTATACAATA-TTCTTCAAAAACGATCAATTTGATTGATGGTTGTAGCCTGTAGGTA
1 TTAGAAACTTATACAATAGTT-TTCAAAAACGATCAATATGATTGATGGTCATAGCCTGTAAGTA
*
39497 TCACAGTGAATC
65 GCACAGTGAATC
* * * *
39509 TTAGAAACTTATGCAATAGTTTTCGAAAAGGATCAGTATGATTGATGGTCATAGCCTGTAAGTAG
1 TTAGAAACTTATACAATAGTTTTCAAAAACGATCAATATGATTGATGGTCATAGCCTGTAAGTAG
39574 CACAGT
66 CACAGT
39580 TAACCTCCCC
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 59 0.97
77 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.33
Consensus pattern (76 bp):
TTAGAAACTTATACAATAGTTTTCAAAAACGATCAATATGATTGATGGTCATAGCCTGTAAGTAG
CACAGTGAATC
Found at i:43256 original size:66 final size:66
Alignment explanation
Indices: 43144--43281 Score: 240
Period size: 66 Copynumber: 2.1 Consensus size: 66
43134 TACATATTCC
* *
43144 CTAAACTGAAGCGTGTGAGACGAGCTAGCTAGGGTTGAAAGGCTTTCAAAGTCTTTGGCAGATAT
1 CTAAACTGAAGCGTGTGAGACGAGCTAGCCAGGGTTGAAAGACTTTCAAAGTCTTTGGCAGATAT
43209 T
66 T
* *
43210 CTAAACTGAAGCGTGTGAGACGAGCTAGCCAGGGTTGTAAGACTTTCAAAGTCTTTGGTAGATAT
1 CTAAACTGAAGCGTGTGAGACGAGCTAGCCAGGGTTGAAAGACTTTCAAAGTCTTTGGCAGATAT
43275 T
66 T
43276 CTAAAC
1 CTAAAC
43282 AGTAGTTGCA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (66 bp):
CTAAACTGAAGCGTGTGAGACGAGCTAGCCAGGGTTGAAAGACTTTCAAAGTCTTTGGCAGATAT
T
Found at i:44310 original size:42 final size:42
Alignment explanation
Indices: 44240--44325 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 42
44230 ACTTAACATA
* * *
44240 TTTTAAATTTAAAATTTTTATACTAAAAATTTTATTTTTTTAT
1 TTTTAAATTTAAAATTTTTATACAAAAAATATT-TTTTTTAAT
*
44283 TTTTAAA-TTATAATTTTTTATA-AAAAAATATTTTTTTTAAT
1 TTTTAAATTTA-AAATTTTTATACAAAAAATATTTTTTTTAAT
44324 TT
1 TT
44326 AAATGAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
41 10 0.26
42 11 0.29
43 17 0.45
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (42 bp):
TTTTAAATTTAAAATTTTTATACAAAAAATATTTTTTTTAAT
Found at i:54169 original size:12 final size:12
Alignment explanation
Indices: 54152--54176 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54142 TATGTAATAA
54152 ATATAAATATAG
1 ATATAAATATAG
54164 ATATAAATATAG
1 ATATAAATATAG
54176 A
1 A
54177 GATTGGACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATATAAATATAG
Found at i:56394 original size:20 final size:21
Alignment explanation
Indices: 56357--56395 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
56347 TGTAGACACC
56357 CAATTGGGTCCAGGCCCAAGT
1 CAATTGGGTCCAGGCCCAAGT
*
56378 CAATTGGG-CCTGGCCCAA
1 CAATTGGGTCCAGGCCCAA
56396 ATGGGTAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.23, C:0.31, G:0.28, T:0.18
Consensus pattern (21 bp):
CAATTGGGTCCAGGCCCAAGT
Found at i:56478 original size:11 final size:12
Alignment explanation
Indices: 56439--56478 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
56429 TTACTATTTT
56439 TTTTTCTTTCCT-
1 TTTTT-TTTCCTC
56451 TTTTTTTTCCTC
1 TTTTTTTTCCTC
*
56463 TTTTTTTTCTTC
1 TTTTTTTTCCTC
56475 TTTT
1 TTTT
56479 GTATTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 6 0.23
12 20 0.77
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTTTCCTC
Found at i:56491 original size:3 final size:3
Alignment explanation
Indices: 56480--56616 Score: 55
Period size: 3 Copynumber: 42.0 Consensus size: 3
56470 TCTTCTTTTG
* *
56480 TAT TTT TAT TATT TAT TAT TAT TAT TAT GTAT TAA TA- TAT GTAT ATAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT -TAT TAT TAT TAT -TAT -TAT
* * * * * *
56528 CTATT TAT CTTT TTT TCT CTGT TAA TAT TTT TAT GTAT TA- TAT GTAT
1 -TA-T TAT -TAT TAT TAT -TAT TAT TAT TAT TAT -TAT TAT TAT -TAT
56575 ATAGT TAT ATATT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT
1 -TA-T TAT -TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
56617 CTTTTTTTGT
Statistics
Matches: 106, Mismatches: 14, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
2 6 0.06
3 63 0.59
4 34 0.32
5 3 0.03
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:56499 original size:16 final size:16
Alignment explanation
Indices: 56480--56513 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56470 TCTTCTTTTG
* *
56480 TATTTTTATTATTTAT
1 TATTATTATTATGTAT
56496 TATTATTATTATGTAT
1 TATTATTATTATGTAT
56512 TA
1 TA
56514 ATATATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TATTATTATTATGTAT
Found at i:56596 original size:14 final size:14
Alignment explanation
Indices: 56552--56614 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
56542 TTCTCTGTTA
56552 ATATTT-TTATGTATT
1 ATATTTATTAT-TA-T
*
56567 ATATGTATATAGTTAT
1 ATATTTAT-TA-TTAT
56583 ATATTTATTATTAT
1 ATATTTATTATTAT
56597 -TATTATATTATTAT
1 ATATT-TATTATTAT
56611 -TATT
1 ATATT
56615 ATCTTTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
13 4 0.10
14 17 0.40
15 7 0.17
16 9 0.21
17 4 0.10
18 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (14 bp):
ATATTTATTATTAT
Found at i:56615 original size:14 final size:14
Alignment explanation
Indices: 56579--56616 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
56569 ATGTATATAG
56579 TTATATATT-TATTA
1 TTAT-TATTATATTA
56593 TTATTATTATATTA
1 TTATTATTATATTA
56607 TTATTATTAT
1 TTATTATTAT
56617 CTTTTTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTATTATTATATTA
Found at i:57058 original size:14 final size:14
Alignment explanation
Indices: 57039--57076 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
57029 TCAGAAGAAA
57039 TTTTTTGGGATTTT
1 TTTTTTGGGATTTT
57053 TTTTTTGGGATTTT
1 TTTTTTGGGATTTT
*
57067 TTTTCTGGGA
1 TTTTTTGGGA
57077 ATTTCTGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.08, C:0.03, G:0.24, T:0.66
Consensus pattern (14 bp):
TTTTTTGGGATTTT
Found at i:57681 original size:4 final size:4
Alignment explanation
Indices: 57624--57665 Score: 59
Period size: 4 Copynumber: 10.5 Consensus size: 4
57614 TTTGATTTGT
*
57624 TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTATT TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TT
57666 AGATTAGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 28 0.82
5 3 0.09
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:57692 original size:34 final size:32
Alignment explanation
Indices: 57623--57694 Score: 90
Period size: 34 Copynumber: 2.2 Consensus size: 32
57613 TTTTGATTTG
* * *
57623 TTTTATTTATTTATTTATTTATTTATTATTAT
1 TTTTATTTATTGATTGATTTATTTAATATTAT
*
57655 TTTTATTTATTAGATTAGATTTATTTAATATTCT
1 TTTTATTTATT-GATT-GATTTATTTAATATTAT
57689 TTTTAT
1 TTTTAT
57695 CTTTATTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 11 0.32
33 3 0.09
34 20 0.59
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.69
Consensus pattern (32 bp):
TTTTATTTATTGATTGATTTATTTAATATTAT
Found at i:57705 original size:11 final size:10
Alignment explanation
Indices: 57689--57753 Score: 55
Period size: 11 Copynumber: 6.4 Consensus size: 10
57679 TTAATATTCT
57689 TTTTATCTTTA
1 TTTTAT-TTTA
57700 TTTTATTTTTA
1 TTTTA-TTTTA
57711 TTTT-TTTTA
1 TTTTATTTTA
57720 CTTTTA-TTT-
1 -TTTTATTTTA
*
57729 TTTTATTTTT
1 TTTTATTTTA
*
57739 TTATTATTCTA
1 TT-TTATTTTA
57750 TTTT
1 TTTT
57754 CTTTAAATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
8 5 0.11
9 8 0.17
10 11 0.24
11 21 0.46
12 1 0.02
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:57712 original size:26 final size:24
Alignment explanation
Indices: 57674--57742 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 24
57664 TTAGATTAGA
*
57674 TTTATTTAATATTCTTTTTATCTTTAT
1 TTTATTT-TTATT-TTTTTATCTTT-T
57701 TTTATTTTTATTTTTTT-TACTTTT
1 TTTATTTTTATTTTTTTAT-CTTTT
*
57725 ATT-TTTTTATTTTTTTAT
1 TTTATTTTTATTTTTTTAT
57743 TATTCTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
23 13 0.34
24 5 0.13
25 9 0.24
26 4 0.11
27 7 0.18
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTATTTTTATTTTTTTATCTTTT
Found at i:57718 original size:15 final size:15
Alignment explanation
Indices: 57688--57738 Score: 68
Period size: 14 Copynumber: 3.3 Consensus size: 15
57678 TTTAATATTC
57688 TTTTTATCTTTATTTTA
1 TTTTTAT-TTT-TTTTA
57705 TTTTTATTTTTTTTA
1 TTTTTATTTTTTTTA
*
57720 CTTTTA-TTTTTTTA
1 TTTTTATTTTTTTTA
57734 TTTTT
1 TTTTT
57739 TTATTATTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
14 12 0.38
15 10 0.31
16 3 0.09
17 7 0.22
ACGTcount: A:0.14, C:0.04, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTATTTTTTTTA
Found at i:57726 original size:21 final size:21
Alignment explanation
Indices: 57696--57743 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
57686 TCTTTTTATC
57696 TTTATTTTATTTTTAT-TTTT
1 TTTATTTTATTTTTATATTTT
*
57716 TTTACTTTTATTTTTTTATTTT
1 TTTA-TTTTATTTTTATATTTT
57738 TTTATT
1 TTTATT
57744 ATTCTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 4 0.16
21 13 0.52
22 8 0.32
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTATTTTATTTTTATATTTT
Found at i:57740 original size:16 final size:16
Alignment explanation
Indices: 57602--57758 Score: 70
Period size: 16 Copynumber: 9.5 Consensus size: 16
57592 CTCCAGGTTT
*
57602 TTTTTTTGATTTTTTGA
1 TTTTTTT-ATTTTTTTA
*
57619 TTTGTTTTATTTATTTA
1 TTT-TTTTATTTTTTTA
* *
57636 TTTATTTA-TTTATTA
1 TTTTTTTATTTTTTTA
**
57651 TTATTTTTATTTATTAGA
1 TT-TTTTTATTT-TTTTA
** **
57669 TTAGATTTA-TTTAATA
1 TT-TTTTTATTTTTTTA
57685 TTCTTTTTATCTTTATTT-
1 TT-TTTTTAT-TTT-TTTA
*
57703 TATTTTTATTTTTTT-
1 TTTTTTTATTTTTTTA
**
57718 TACTTTTATTTTTTTA
1 TTTTTTTATTTTTTTA
* *
57734 TTTTTTTATTATTCTA
1 TTTTTTTATTTTTTTA
57750 TTTTCTTTA
1 TTTT-TTTA
57759 AATAAAAAAT
Statistics
Matches: 107, Mismatches: 24, Indels: 18
0.72 0.16 0.12
Matches are distributed among these distances:
15 24 0.22
16 37 0.35
17 28 0.26
18 17 0.16
19 1 0.01
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTTTTATTTTTTTA
Found at i:58073 original size:114 final size:116
Alignment explanation
Indices: 57803--58117 Score: 440
Period size: 114 Copynumber: 2.7 Consensus size: 116
57793 ATTTTTAGGG
* * *
57803 AAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAATATTTCCCAAAAAAAAATTTTTAGGGAAAA
1 AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAATTT--CAAAAAAAAATTTTCAGGGAAAA
* *
57868 GTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCATAAAAAATAAATTTTTGAGG
64 GTTGAAAGTATCAATTTTCCCT--AAATAAATTTCA-AAAAAATAAATTTTTGAGA
* *
57924 AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAAATTTCAAAAAAAAATTTTGA-GGAAAAGT
1 AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAATTTCAAAAAAAAATTTTCAGGGAAAAGT
57988 TGAAAGTATCAATTTTCCCT-AATAAATTTTC-AAAAAATAAATTTTTGAGA
66 TGAAAGTATCAATTTTCCCTAAATAAA-TTTCAAAAAAATAAATTTTTGAGA
* * * * *
58038 AAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAATTTTC-GAAAAATATTTTCAGGGAAAAGT
1 AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAATTTCAAAAAAAAATTTTCAGGGAAAAGT
58102 TGAAAGTATCAATTTT
66 TGAAAGTATCAATTTT
58118 TCCTGCACAA
Statistics
Matches: 179, Mismatches: 13, Indels: 11
0.88 0.06 0.05
Matches are distributed among these distances:
113 11 0.06
114 79 0.44
115 6 0.03
116 4 0.02
118 27 0.15
119 15 0.08
121 37 0.21
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (116 bp):
AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAATTTCAAAAAAAAATTTTCAGGGAAAAGT
TGAAAGTATCAATTTTCCCTAAATAAATTTCAAAAAAATAAATTTTTGAGA
Found at i:58134 original size:60 final size:58
Alignment explanation
Indices: 57785--58117 Score: 317
Period size: 58 Copynumber: 5.7 Consensus size: 58
57775 TTCCAAAAAA
* * * * *
57785 AAAAAAACATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAATATTTCCC
1 AAAAAAATA-TTTTAGGGAAAAGTTGAAAGTATCAATTTTCC-TCAAAATAAAAATTT-TC
* *
57846 AAAAAAAAATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT--AAA-TTTC
1 AAAAAAATA-TTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCA-AAATAAAAATTTTC
* *
57903 ATAAAAAATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAAA-TTTC
1 A-AAAAAAT--ATTTTAG-GGAAAAGTTGAAAGTATCAATTTTCC-TCAAAATAAAAATTTTC
* *
57965 AAAAAAAAATTTT-GAGGAAAAGTTGAAAGTATCAATTTTCC-C-TAAT--AAATTTTC
1 AAAAAAATATTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTCAAAATAAAAATTTTC
* * * * *
58019 AAAAAATAAATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAATTTTC
1 AAAAAA-ATATTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTCAAAATAAAAATTTTC
*
58079 -GAAAAATATTTTCAGGGAAAAGTTGAAAGTATCAATTTT
1 AAAAAAATATTTT-AGGGAAAAGTTGAAAGTATCAATTTT
58118 TCCTGCACAA
Statistics
Matches: 240, Mismatches: 16, Indels: 35
0.82 0.05 0.12
Matches are distributed among these distances:
53 3 0.01
54 10 0.04
55 10 0.04
56 27 0.11
57 3 0.01
58 68 0.28
59 17 0.07
60 41 0.17
61 53 0.22
62 8 0.03
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (58 bp):
AAAAAAATATTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAAAATAAAAATTTTC
Found at i:61998 original size:10 final size:10
Alignment explanation
Indices: 61983--62045 Score: 60
Period size: 10 Copynumber: 6.3 Consensus size: 10
61973 ACAATGGATG
61983 AAAAATGAAA
1 AAAAATGAAA
61993 AAAAATGATGAA
1 AAAAATGA--AA
*
62005 AAAAA--AGA
1 AAAAATGAAA
62013 AAAAATGAGAA
1 AAAAATGA-AA
*
62024 AAAAAAGAAA
1 AAAAATGAAA
62034 AAAAA-GAAA
1 AAAAATGAAA
62043 AAA
1 AAA
62046 TGAGAAAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
8 6 0.13
9 7 0.16
10 17 0.38
11 8 0.18
12 7 0.16
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (10 bp):
AAAAATGAAA
Found at i:62002 original size:20 final size:20
Alignment explanation
Indices: 61979--62036 Score: 84
Period size: 19 Copynumber: 3.0 Consensus size: 20
61969 ATCAACAATG
*
61979 GATGAAAAATGAA-AAAAAAT
1 GATGAAAAA-AAAGAAAAAAT
61999 GATGAAAAAAAAGAAAAAAT
1 GATGAAAAAAAAGAAAAAAT
62019 GA-GAAAAAAAAGAAAAAA
1 GATGAAAAAAAAGAAAAAA
62037 AAGAAAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 18 0.50
20 18 0.50
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.09
Consensus pattern (20 bp):
GATGAAAAAAAAGAAAAAAT
Found at i:62015 original size:19 final size:19
Alignment explanation
Indices: 61979--62035 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 19
61969 ATCAACAATG
61979 GATGAAAAATGAAA-AAAAAT
1 GATGAAAAA--AAAGAAAAAT
61999 GATGAAAAAAAAGAAAAAAT
1 GATGAAAAAAAAG-AAAAAT
62019 GA-GAAAAAAAAGAAAAA
1 GATGAAAAAAAAGAAAAA
62036 AAAGAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.23
19 10 0.29
20 17 0.49
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (19 bp):
GATGAAAAAAAAGAAAAAT
Found at i:62025 original size:28 final size:28
Alignment explanation
Indices: 62002--62055 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
61992 AAAAAATGAT
*
62002 GAAAAAAAAGAAAAAATGAGAAAAAAAA
1 GAAAAAAAAGAAAAAATGAGAAAATAAA
62030 GAAAAAAAAGAAAAAATGAGAAAATA
1 GAAAAAAAAGAAAAAATGAGAAAATA
62056 TTCAAATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.06
Consensus pattern (28 bp):
GAAAAAAAAGAAAAAATGAGAAAATAAA
Found at i:62037 original size:20 final size:20
Alignment explanation
Indices: 61991--62045 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
61981 TGAAAAATGA
61991 AAAAAAATGATGAAAAAAAAG
1 AAAAAAATGA-GAAAAAAAAG
62012 -AAAAAATGAGAAAAAAAAG
1 AAAAAAATGAGAAAAAAAAG
62031 AAAAAAA--AGAAAAAA
1 AAAAAAATGAGAAAAAA
62046 TGAGAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.24
19 10 0.30
20 15 0.45
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (20 bp):
AAAAAAATGAGAAAAAAAAG
Found at i:62051 original size:10 final size:10
Alignment explanation
Indices: 61983--62053 Score: 76
Period size: 9 Copynumber: 7.3 Consensus size: 10
61973 ACAATGGATG
*
61983 AAAAATGAAA
1 AAAAATGAGA
61993 AAAAATGATGA
1 AAAAATGA-GA
*
62004 AAAAA-AAGA
1 AAAAATGAGA
62013 AAAAATGAGA
1 AAAAATGAGA
*
62023 AAAAA-AAGA
1 AAAAATGAGA
*
62032 AAAAA-AAGA
1 AAAAATGAGA
62041 AAAAATGAGA
1 AAAAATGAGA
62051 AAA
1 AAA
62054 TATTCAAATT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
9 24 0.45
10 23 0.43
11 6 0.11
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (10 bp):
AAAAATGAGA
Found at i:62053 original size:19 final size:19
Alignment explanation
Indices: 61992--62045 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
61982 GAAAAATGAA
61992 AAAAAATGATGAAAAAAAAG
1 AAAAAATGA-GAAAAAAAAG
62012 AAAAAATGAGAAAAAAAAG
1 AAAAAATGAGAAAAAAAAG
*
62031 AAAAAA-AAGAAAAAA
1 AAAAAATGAGAAAAAA
62046 TGAGAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
18 8 0.24
19 16 0.48
20 9 0.27
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (19 bp):
AAAAAATGAGAAAAAAAAG
Found at i:63322 original size:41 final size:41
Alignment explanation
Indices: 63248--63458 Score: 302
Period size: 41 Copynumber: 5.1 Consensus size: 41
63238 TGATTGGTCA
63248 AGGAGCAATTTACTTTCTCAAAGTTCCGT--TGCCTCTGTTTAG
1 AGGAGCAATTTACTTT-TCAAAG-T-CGTGGTGCCTCTGTTTAG
63290 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
63331 AGGAGCAATTTACTTTCCCAAAGTCGTGGTGCCTCTGTTGAG
1 AGGAGCAATTTACTTT-TCAAAGTCGTGGTGCCTCTGTTTAG
* *
63373 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTGAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
63414 AGGAGCAATTTATTTTTCCAAGTCGTGGTG-CTCTGTTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTG-TTTAG
63455 AGGA
1 AGGA
63459 ACTTCGACAA
Statistics
Matches: 159, Mismatches: 6, Indels: 9
0.91 0.03 0.05
Matches are distributed among these distances:
39 3 0.02
40 6 0.04
41 95 0.60
42 55 0.35
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:63364 original size:83 final size:83
Alignment explanation
Indices: 63248--63458 Score: 313
Period size: 83 Copynumber: 2.6 Consensus size: 83
63238 TGATTGGTCA
* *
63248 AGGAGCAATTTACTTTCTCAAAGTTCCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAA
1 AGGAGCAATTTACTTTCCCAAAG-T-CGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAA
*
63311 GTCGTGGTGCCTCTGTTTAG
64 GTCGTGGTGCCTCTGTTGAG
*
63331 AGGAGCAATTTACTTTCCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTACTTTCCAAAGT
1 AGGAGCAATTTACTTTCCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGT
63396 CGTGGTGCCTCTGTTGAG
66 CGTGGTGCCTCTGTTGAG
* *
63414 AGGAGCAATTTATTTTTCC-AAGTCGTGGTG-CTCTGTTTTAGAGGA
1 AGGAGCAATTTACTTTCCCAAAGTCGTGGTGCCTCTG-TTTAGAGGA
63459 ACTTCGACAA
Statistics
Matches: 118, Mismatches: 7, Indels: 7
0.89 0.05 0.05
Matches are distributed among these distances:
81 8 0.07
82 20 0.17
83 90 0.76
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (83 bp):
AGGAGCAATTTACTTTCCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGT
CGTGGTGCCTCTGTTGAG
Found at i:63473 original size:1 final size:1
Alignment explanation
Indices: 63467--63580 Score: 138
Period size: 1 Copynumber: 114.0 Consensus size: 1
63457 GAACTTCGAC
* * *
63467 AAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* ** * * * *
63532 AAAAAAAAAAAGAAAAAAAATCAAAAACAAACAACAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
63581 TGAAAATGTT
Statistics
Matches: 94, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 94 1.00
ACGTcount: A:0.91, C:0.07, G:0.01, T:0.01
Consensus pattern (1 bp):
A
Found at i:63521 original size:39 final size:39
Alignment explanation
Indices: 63467--63580 Score: 167
Period size: 39 Copynumber: 2.9 Consensus size: 39
63457 GAACTTCGAC
63467 AAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAACAAAA-A
1 AAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAA-AAAAGA
63506 AAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAGA
* * * *
63545 AAAAAAATCAAAAACAAACAACAAAAAAACAAAAAA
1 AAAAAAA-AAAAAAAAAACAAAAAAAAAAAAAAAAA
63581 TGAAAATGTT
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
38 4 0.06
39 41 0.59
40 24 0.35
ACGTcount: A:0.91, C:0.07, G:0.01, T:0.01
Consensus pattern (39 bp):
AAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAGA
Found at i:63532 original size:43 final size:43
Alignment explanation
Indices: 63467--63580 Score: 158
Period size: 43 Copynumber: 2.7 Consensus size: 43
63457 GAACTTCGAC
*
63467 AAAAAAAAAAAAAA-AAACAAAAAAAAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAACAAAAAAAA
*
63509 AAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAACAAAAAAAA
** * * *
63552 TCAAAAACAAACAACAAAAAAACAAAAAA
1 AAAAAAAAAAAAAACAAAAAAAAAAAAAA
63581 TGAAAATGTT
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
42 14 0.22
43 50 0.78
ACGTcount: A:0.91, C:0.07, G:0.01, T:0.01
Consensus pattern (43 bp):
AAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAACAAAAAAAA
Found at i:63792 original size:12 final size:13
Alignment explanation
Indices: 63777--63805 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
63767 TCTTTCCGCT
63777 TTTTTTTTTC-TC
1 TTTTTTTTTCTTC
63789 TTTTTTTTTCTTC
1 TTTTTTTTTCTTC
63802 TTTT
1 TTTT
63806 GTATTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTTTCTTC
Found at i:64930 original size:5 final size:5
Alignment explanation
Indices: 64908--65056 Score: 68
Period size: 5 Copynumber: 29.8 Consensus size: 5
64898 CCGCTCCAGG
*
64908 TTTT- TTTT- TTTTT TTTTA TTTTA -TTTA -TTTA TTTTA -TTTA -TTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* *
64952 TTATTA TTTT- TATTTA TTAGATTA GGTTTA TTTAATA TTCT- TTTTA TCTTTA
1 TT-TTA TTTTA T-TTTA TT---TTA -TTTTA TTT--TA TTTTA TTTTA T-TTTA
* * *
65004 TTTTA TTTTTA TTTT- TTTTA TTTT- CTTT- TTTTA TTTTT TTATTA TTCTA
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TTTTA
65053 TTTT
1 TTTT
65057 CTTTAAATAA
Statistics
Matches: 116, Mismatches: 11, Indels: 35
0.72 0.07 0.22
Matches are distributed among these distances:
4 38 0.33
5 47 0.41
6 23 0.20
7 4 0.03
8 3 0.03
9 1 0.01
ACGTcount: A:0.18, C:0.03, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:64934 original size:9 final size:9
Alignment explanation
Indices: 64921--65055 Score: 61
Period size: 9 Copynumber: 14.9 Consensus size: 9
64911 TTTTTTTTTT
64921 TTTTATTT-
1 TTTTATTTA
64929 TATTTATTTA
1 T-TTTATTTA
64939 TTTTATTTA
1 TTTTATTTA
64948 -TTTATTATTA
1 TTTTA-T-TTA
64958 TTTTTATTTA
1 -TTTTATTTA
**
64968 TTAGA-TTA
1 TTTTATTTA
*
64976 GGTTTATTTAA
1 -TTTTATTT-A
*
64987 TATTCTTTTTA
1 T-TT-TATTTA
64998 TCTTTATTT-
1 T-TTTATTTA
*
65007 TATT-TTTA
1 TTTTATTTA
*
65015 TTTTTTTTA
1 TTTTATTTA
*
65024 TTTTCTTT-
1 TTTTATTTA
65032 TTTTATTT-
1 TTTTATTTA
65040 TTTTA-TTA
1 TTTTATTTA
*
65048 TTCTATTT
1 TTTTATTT
65056 TCTTTAAATA
Statistics
Matches: 98, Mismatches: 14, Indels: 29
0.70 0.10 0.21
Matches are distributed among these distances:
7 5 0.05
8 29 0.30
9 35 0.36
10 13 0.13
11 8 0.08
12 8 0.08
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (9 bp):
TTTTATTTA
Found at i:64985 original size:4 final size:4
Alignment explanation
Indices: 64922--64969 Score: 53
Period size: 4 Copynumber: 11.5 Consensus size: 4
64912 TTTTTTTTTT
*
64922 TTTA TTTTA TTTA TTTA TTTTA TTTA TTTA -TTA TTATT TTTA TTTA TT
1 TTTA -TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TT
64970 AGATTAGGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
3 3 0.08
4 24 0.63
5 11 0.29
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:65009 original size:11 final size:10
Alignment explanation
Indices: 64993--65056 Score: 53
Period size: 11 Copynumber: 6.4 Consensus size: 10
64983 TTAATATTCT
64993 TTTTATCTTTA
1 TTTTAT-TTTA
65004 TTTTATTTTTA
1 TTTTA-TTTTA
65015 TTTT-TTTTA
1 TTTTATTTTA
*
65024 TTTT-CTTT-
1 TTTTATTTTA
*
65032 TTTTATTTTT
1 TTTTATTTTA
*
65042 TTATTATTCTA
1 TT-TTATTTTA
65053 TTTT
1 TTTT
65057 CTTTAAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
8 4 0.09
9 15 0.33
10 4 0.09
11 21 0.47
12 1 0.02
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:65056 original size:13 final size:12
Alignment explanation
Indices: 64982--65056 Score: 52
Period size: 11 Copynumber: 6.2 Consensus size: 12
64972 ATTAGGTTTA
*
64982 TTTAATATTCTT
1 TTTATTATTCTT
64994 TTTATCTTTATT-TT
1 TTTA---TTATTCTT
*
65008 ATTT-TTATTTTT
1 -TTTATTATTCTT
65020 TTTATT-TTCTT
1 TTTATTATTCTT
65031 TTT-TTATT-TT
1 TTTATTATTCTT
65041 TTTATTATTCTAT
1 TTTATTATTCT-T
65054 TTT
1 TTT
65057 CTTTAAATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 19
0.71 0.03 0.26
Matches are distributed among these distances:
10 7 0.14
11 22 0.43
12 9 0.18
13 4 0.08
14 2 0.04
15 7 0.14
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTATTATTCTT
Found at i:65228 original size:57 final size:57
Alignment explanation
Indices: 65073--65534 Score: 420
Period size: 57 Copynumber: 7.9 Consensus size: 57
65063 ATAAAAATCA
*
65073 AAATTTCCAAAAAAAAAAAT-TTTT-AGGGAAAAGTTGAAAGTATCAATTTTCTTAAAAAT
1 AAATTT-CAAAAAAAAAAATATTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCT--AAAT
**
65132 AAAATTTC--AAAAAAGGAT-TTTTG-GGAAAAGTTGAAAGTATCAATTTTCCT-AAT
1 -AAATTTCAAAAAAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTAAAT
**
65185 AAATTTCCAAAAAAAAAAATATTTTTTGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
1 AAATTT-CAAAAAAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTCC-T--AAAT
* *
65246 AAATTTCATAAAAAATAA-ATTTTGAGG-AAAGTTGAAAGTATCAATTTTCCTTAAAAAT
1 AAATTTCAAAAAAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTCC-T--AAAT
*
65304 AAAAAATTCAAAAAAAAATAA-ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT
1 --AAATTTCAAAAAAAAA-AATA-TTTTGAGGAAAAGTTGAAAGTATCAATTTTCC-T--AAAT
** *
65367 CAAAATTTCAAAAAAAAAGGT-TTTTGGGGAAAAGTTGAAAGTATCAATTTTCCCT-AAT
1 --AAATTTCAAAAAAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTT-CCTAAAT
*
65425 AAATTTTCAAAAAAATAAAT-TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATT
1 AAA-TTTCAAAAAAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT--AAA-T
*
65485 AAAATTTTC-----AAAAAATATTTTCAGGGAAAAGTTGAAAGTATCAATTTTCC
1 -AAA-TTTCAAAAAAAAAAATATTTTGA-GGAAAAGTTGAAAGTATCAATTTTCC
65535 CTGCACAAGA
Statistics
Matches: 351, Mismatches: 26, Indels: 52
0.82 0.06 0.12
Matches are distributed among these distances:
52 6 0.02
53 4 0.01
55 8 0.02
56 42 0.12
57 85 0.24
58 60 0.17
59 10 0.03
60 30 0.09
61 50 0.14
62 10 0.03
63 46 0.13
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (57 bp):
AAATTTCAAAAAAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTAAAT
Found at i:65500 original size:239 final size:232
Alignment explanation
Indices: 65064--65534 Score: 668
Period size: 239 Copynumber: 2.0 Consensus size: 232
65054 TTTCTTTAAA
* * *
65064 TAAAAATCAAAATTTCCAAAAAAAAAAATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCTTAAA
1 TAAAAATAAAAAATTCAAAAAAAAAAAATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCTTAAA
65129 AATAAAATTTCAAAAAAGGATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTAATAAATTTCCA
66 AATAAAATTTCAAAAAAGGATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTAATAAATTTCCA
**
65194 AAAAAAAAAATATTTTTTGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCATAAAA
131 AAAAAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCA-AAAA
*
65259 AATAAATTTTGA-GG-AAAGTTGAAAGTATCAATTTTCCT
195 AAT--ATTTTCAGGGAAAAGTTGAAAGTATCAATTTTCCT
65297 TAAAAATAAAAAATTCAAAAAAAAATAAATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTT
1 TAAAAATAAAAAATTCAAAAAAAAA-AAATTTTTAG-GGAAAAGTTGAAAGTATCAATTTT-CTT
*
65361 GAAAATCAAAATTTCAAAAAAAAAGG-TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCCTAAT
63 AAAAAT-AAAATTTC---AAAAAAGGATTTTT-GGGAAAAGTTGAAAGTATCAATTTT-CCTAAT
* * *
65425 AAATTTTCAAAAAAATAAAT-TTTTGAGGAAAAGTTGAAAGTATCAATTTTCC-TCGAAATTAAA
122 AAATTTCCAAAAAAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAA-T-AA
65488 ATTTTC-AAAAAATATTTTCAGGGAAAAGTTGAAAGTATCAATTTTCC
185 A-TTTCAAAAAAATATTTTCAGGGAAAAGTTGAAAGTATCAATTTTCC
65535 CTGCACAAGA
Statistics
Matches: 214, Mismatches: 10, Indels: 22
0.87 0.04 0.09
Matches are distributed among these distances:
233 23 0.11
234 32 0.15
235 8 0.04
236 8 0.04
237 6 0.03
238 12 0.06
239 94 0.44
240 27 0.13
241 4 0.02
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (232 bp):
TAAAAATAAAAAATTCAAAAAAAAAAAATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCTTAAA
AATAAAATTTCAAAAAAGGATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTAATAAATTTCCA
AAAAAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCAAAAAA
ATATTTTCAGGGAAAAGTTGAAAGTATCAATTTTCCT
Found at i:66421 original size:17 final size:17
Alignment explanation
Indices: 66401--66435 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
66391 ATTTTATTCA
66401 TTATTCATT-ATTAATTT
1 TTATTCATTCATT-ATTT
66418 TTATTCATTCATTATTT
1 TTATTCATTCATTATTT
66435 T
1 T
66436 AAGTTCTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATTCATTCATTATTT
Done.