Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 193 of 193
Found at i:60237436 original size:16 final size:17
Alignment explanation
Indices: 60237415--60237449 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
60237405 CGTGTATTTT
*
60237415 ATAAAAATTTA-AAAAA
1 ATAAAAATTCATAAAAA
60237431 ATAAAAATTCATAAAAA
1 ATAAAAATTCATAAAAA
60237448 AT
1 AT
60237450 TCACTAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAAAATTCATAAAAA
Found at i:60265271 original size:63 final size:63
Alignment explanation
Indices: 60265127--60265290 Score: 188
Period size: 68 Copynumber: 2.7 Consensus size: 63
60265117 TTCTTATTAT
60265127 TTTTATTTATTTATTTA-T-TTTTATG-ATATAAATAAAT--A-TAAAATAATATTAATTTTA
1 TTTTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATTAAAATAATATTAATTTTA
*
60265184 TTTTATTTCATTATTTTTTCATTATTTTATGAATATAAATAAATAAATGTAAAATAATATTAATT
1 TTTTATTT-A-T-TTATTT-ATTATTTTATGAATATAAATAAATAAAT-TAAAATAATATTAATT
*
60265249 TTG
61 TTA
60265252 TTTTA-TTATTTATTTATTA--TTAT-AA-ATAAATAAATAAAT
1 TTTTATTTATTTATTTATTATTTTATGAATATAAATAAATAAAT
60265291 AACAAACCAA
Statistics
Matches: 93, Mismatches: 3, Indels: 20
0.80 0.03 0.17
Matches are distributed among these distances:
57 8 0.09
58 1 0.01
59 15 0.16
60 7 0.08
61 5 0.05
62 1 0.01
63 11 0.12
64 17 0.18
65 1 0.01
66 2 0.02
67 2 0.02
68 23 0.25
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.54
Consensus pattern (63 bp):
TTTTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATTAAAATAATATTAATTTTA
Found at i:60270329 original size:6 final size:6
Alignment explanation
Indices: 60270320--60270374 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
60270310 AAAAATTAAA
* *
60270320 AAAAAG AAAAGAG AGAAA- AAGAA- AAAAAG AAAAAG AAGAGAAG AAAAAG
1 AAAAAG AAAA-AG AAAAAG AAAAAG AAAAAG AAAAAG AA-A-AAG AAAAAG
60270369 AAAAAG
1 AAAAAG
60270375 GGGAGGTCGA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 7 0.17
6 22 0.54
7 7 0.17
8 5 0.12
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:60270329 original size:9 final size:9
Alignment explanation
Indices: 60270298--60270373 Score: 52
Period size: 9 Copynumber: 8.6 Consensus size: 9
60270288 AAGAAATTTA
60270298 AAAAAAAAG
1 AAAAAAAAG
**
60270307 ACAAAAAATT
1 A-AAAAAAAG
60270317 AAAAAAAAG
1 AAAAAAAAG
*
60270326 --AAAAGAG
1 AAAAAAAAG
*
60270333 -AGAAAAAG
1 AAAAAAAAG
60270341 -AAAAAAAG
1 AAAAAAAAG
60270349 AAAAAGAAGAG
1 AAAAA-AA-AG
*
60270360 AAGAAAAAG
1 AAAAAAAAG
60270369 AAAAA
1 AAAAA
60270374 GGGGAGGTCG
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
7 6 0.12
8 12 0.23
9 17 0.33
10 11 0.21
11 6 0.12
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:60270344 original size:23 final size:25
Alignment explanation
Indices: 60270317--60270374 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
60270307 ACAAAAAATT
60270317 AAAAAAAAG-AAAAG-AGAGAA-AA
1 AAAAAAAAGAAAAAGAAGAGAAGAA
60270339 AGAAAAAAAGAAAAAGAAGAGAAGAA
1 A-AAAAAAAGAAAAAGAAGAGAAGAA
60270365 AAAGAAAAAG
1 AAA-AAAAAG
60270375 GGGAGGTCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
22 1 0.03
23 8 0.26
24 5 0.16
25 8 0.26
26 9 0.29
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (25 bp):
AAAAAAAAGAAAAAGAAGAGAAGAA
Found at i:60270350 original size:14 final size:14
Alignment explanation
Indices: 60270299--60270373 Score: 73
Period size: 14 Copynumber: 5.4 Consensus size: 14
60270289 AGAAATTTAA
60270299 AAAAAAAGACAAAA-
1 AAAAAAAGA-AAAAG
**
60270313 AATTAAA-AAAAAG
1 AAAAAAAGAAAAAG
*
60270326 AAAAGAGAGAAAAAG
1 AAAA-AAAGAAAAAG
60270341 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
* *
60270355 AAGAGAAGAAAAAG
1 AAAAAAAGAAAAAG
60270369 AAAAA
1 AAAAA
60270374 GGGGAGGTCG
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
12 4 0.08
13 3 0.06
14 31 0.65
15 10 0.21
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:60271363 original size:50 final size:50
Alignment explanation
Indices: 60271284--60271423 Score: 190
Period size: 50 Copynumber: 2.8 Consensus size: 50
60271274 GATAGAACAA
* * * *
60271284 CAAATCTTTTACCCCTAAAGCGGTAGAGGTGCATATTGAAACTGCAACGG
1 CAAATCTTATACACCTAAAGCTGTAGAGGTGCAGATTGAAACTGCAACGG
* * *
60271334 TAAATCTTATACACCTAAAGCTGTGGAGGTGCAGATTGAAACTGCAATGG
1 CAAATCTTATACACCTAAAGCTGTAGAGGTGCAGATTGAAACTGCAACGG
* * *
60271384 CAAATCTCATACACCTAAAGCTGTAGAGGGGCAGAATGAA
1 CAAATCTTATACACCTAAAGCTGTAGAGGTGCAGATTGAA
60271424 GTTGTAATAG
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 78 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (50 bp):
CAAATCTTATACACCTAAAGCTGTAGAGGTGCAGATTGAAACTGCAACGG
Found at i:60271453 original size:50 final size:50
Alignment explanation
Indices: 60271297--60271442 Score: 157
Period size: 50 Copynumber: 2.9 Consensus size: 50
60271287 ATCTTTTACC
* * * * ** * *
60271297 CCTAAAGCGGTAGAGGTGCATATTGAAACTGCAACGGTAAATCTTATACA
1 CCTAAAGCTGTAGAGGGGCAGAATGAAACTGCAATAGCAAATCTCATACA
* * * *
60271347 CCTAAAGCTGTGGAGGTGCAGATTGAAACTGCAATGGCAAATCTCATACA
1 CCTAAAGCTGTAGAGGGGCAGAATGAAACTGCAATAGCAAATCTCATACA
** *
60271397 CCTAAAGCTGTAGAGGGGCAGAATGAAGTTGTAATAGCAAATCTCA
1 CCTAAAGCTGTAGAGGGGCAGAATGAAACTGCAATAGCAAATCTCA
60271443 GTCATTTAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 83 1.00
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.23
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGGGCAGAATGAAACTGCAATAGCAAATCTCATACA
Found at i:60271693 original size:80 final size:80
Alignment explanation
Indices: 60271549--60272076 Score: 776
Period size: 80 Copynumber: 6.6 Consensus size: 80
60271539 ACCCTAACCT
* * * * * *
60271549 GATCTTTTACCTCAATCATGAGGCAGATTGAAGAAATCTAATCTTTTACCCTAACCAAATGGCAA
1 GATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACTAGAGGGCAA
60271614 GATTGAAGACCATCC
66 GATTGAAGACCATCC
* * * * *
60271629 GATATTTTACCCCGATCATGGGGTAAATTGAAGAAATCTAATCTTTTAACCTAACTAGGGGGCAA
1 GATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACTAGAGGGCAA
60271694 GATTGAAGACCATCC
66 GATTGAAGACCATCC
*
60271709 GATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACAAGAGGGCAA
1 GATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACTAGAGGGCAA
60271774 GATTGAAGACCATCC
66 GATTGAAGACCATCC
*
60271789 GATCTTTTACCTCGATCATGGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACTAGAGGGCAA
1 GATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACTAGAGGGCAA
60271854 GATTGAAGACCATCC
66 GATTGAAGACCATCC
*
60271869 GATCTTTTACCCCGATCAT-GGGTAGATTGAAGAAATCTAATCTTTTACCCTAACTAGAGGGCAA
1 GATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACTAGAGGGCAA
60271933 GATTGAAGACCATCC
66 GATTGAAGACCATCC
* ** * * *
60271948 GATCTTTTACCCCGATTATAAGGCAGATTGAAGAAATTTAATCTTTTACCCTAACCAAAGGGC-A
1 GATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACTAGAGGGCAA
*
60272012 -ATTGAAGACCATCA
66 GATTGAAGACCATCC
* * * * * *
60272026 GATCTCTTACCTCGACCATGAGGTAAATTGAA-ACAATCTAATCTTTTACCC
1 GATCTTTTACCCCGATCATGGGGCAGATTGAAGA-AATCTAATCTTTTACCC
60272077 CTAAAGTTAT
Statistics
Matches: 410, Mismatches: 36, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
77 1 0.00
78 54 0.13
79 78 0.19
80 277 0.68
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.28
Consensus pattern (80 bp):
GATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACTAGAGGGCAA
GATTGAAGACCATCC
Found at i:60276243 original size:9 final size:9
Alignment explanation
Indices: 60276229--60276312 Score: 55
Period size: 9 Copynumber: 9.1 Consensus size: 9
60276219 ATATTTTAAA
60276229 ATTATAATT
1 ATTATAATT
*
60276238 ATTATATTT
1 ATTATAATT
*
60276247 ACTTA-AATG
1 A-TTATAATT
*
60276256 ATT-TATTT
1 ATTATAATT
60276264 ATTAATATATT
1 ATT-ATA-ATT
*
60276275 AATTATGATT
1 -ATTATAATT
* *
60276285 ATAATTATT
1 ATTATAATT
*
60276294 ATAATAATT
1 ATTATAATT
60276303 ATTATAATT
1 ATTATAATT
60276312 A
1 A
60276313 GACTTATAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
8 7 0.12
9 36 0.62
10 8 0.14
11 4 0.07
12 3 0.05
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (9 bp):
ATTATAATT
Found at i:60283397 original size:17 final size:19
Alignment explanation
Indices: 60283375--60283411 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
60283365 CATATATAAT
60283375 ATATAAAT-AA-TTTAAAA
1 ATATAAATAAATTTTAAAA
60283392 ATATAAATAAATTTTAAAA
1 ATATAAATAAATTTTAAAA
60283411 A
1 A
60283412 GTCAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 2 0.11
19 8 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATATAAATAAATTTTAAAA
Found at i:60289063 original size:14 final size:14
Alignment explanation
Indices: 60289044--60289071 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
60289034 TGGGAGTTAG
60289044 GGGTATTTAATTTT
1 GGGTATTTAATTTT
60289058 GGGTATTTAATTTT
1 GGGTATTTAATTTT
60289072 TTTATTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.57
Consensus pattern (14 bp):
GGGTATTTAATTTT
Found at i:60300378 original size:7 final size:6
Alignment explanation
Indices: 60300368--60300428 Score: 61
Period size: 6 Copynumber: 9.7 Consensus size: 6
60300358 TAAAAAATTA
* *
60300368 AAAAAG GAAAAG AGAAAAG AAAAGG AAAAAAG AAAAA- AAAAAG AAAAAAAG
1 AAAAAG AAAAAG A-AAAAG AAAAAG -AAAAAG AAAAAG AAAAAG --AAAAAG
60300419 AAAAAG AAAA
1 AAAAAG AAAA
60300429 GGGGAGGTCG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
5 5 0.11
6 24 0.52
7 11 0.24
8 6 0.13
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:60300390 original size:18 final size:19
Alignment explanation
Indices: 60300369--60300430 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
60300359 AAAAAATTAA
*
60300369 AAAAGGAAAAGAG-AAAAG
1 AAAAGGAAAAAAGAAAAAG
*
60300387 AAAAGGAAAAAAGAAAAAA
1 AAAAGGAAAAAAGAAAAAG
*
60300406 AAAAGAAAAAAAGAAAAAG
1 AAAAGGAAAAAAGAAAAAG
60300425 AAAAGG
1 AAAAGG
60300431 GGAGGTCGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
18 12 0.32
19 26 0.68
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (19 bp):
AAAAGGAAAAAAGAAAAAG
Found at i:60301417 original size:50 final size:50
Alignment explanation
Indices: 60301352--60301516 Score: 213
Period size: 50 Copynumber: 3.3 Consensus size: 50
60301342 TCTTTTACCA
* * * *
60301352 CTAAAGTTGTAGAGGTGTAGATTAAAACTGAAATGGAAAATCTCATACAC
1 CTAAAGCTGTAGAGGTGCAGATTGAAACTGCAATGGAAAATCTCATACAC
* * *
60301402 TTAAAGCTGTGGAGGTGCAGATTGAAACCGCAATGGAAAATCTCATACAC
1 CTAAAGCTGTAGAGGTGCAGATTGAAACTGCAATGGAAAATCTCATACAC
* * * * * *
60301452 CTAAAGCTGTAGAGGGGCAAAATGAAGCTGCAATGGCAAATCTCATTCAC
1 CTAAAGCTGTAGAGGTGCAGATTGAAACTGCAATGGAAAATCTCATACAC
60301502 CTAAAGCTGTAGAGG
1 CTAAAGCTGTAGAGG
60301517 AGAAAATTGA
Statistics
Matches: 99, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 99 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (50 bp):
CTAAAGCTGTAGAGGTGCAGATTGAAACTGCAATGGAAAATCTCATACAC
Found at i:60301715 original size:80 final size:80
Alignment explanation
Indices: 60301585--60302075 Score: 763
Period size: 80 Copynumber: 6.2 Consensus size: 80
60301575 TACAACCTCT
* *
60301585 AATCTTTTACCCTAACCAGATGGCAAGATTAAAGACCATCCGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
60301650 AGATTGAAGAAATCT
66 AGATTGAAGAAATCC
60301665 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
60301730 AGATTGAAGAAATCC
66 AGATTGAAGAAATCC
* *
60301745 AATCTTTTACCCTAACTAGAGGGAAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
* *
60301810 AAATTGAAGAAATCT
66 AGATTGAAGAAATCC
* * * *
60301825 AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCTGATCTTTTACCCCGATTATGGGGT
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
60301890 AGATTGAAGAAATCC
66 AGATTGAAGAAATCC
* * *
60301905 AATCTTTTACCCTAACCAGAAGGCAAGATTGAAGGCCA-CCTAATCTTTTACCCCGATCAT-GGG
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCC-GATCTTTTACCCCGATCATGGGG
60301968 CAGATTGAAGAAATCC
65 CAGATTGAAGAAATCC
* * * *
60301984 AATCTTTTACCCTAACTAAAGGGCAAGATTGAAGACCATCCAATCTTTTACCCCGACCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
* *
60302049 AAATT-AAAATAATCC
66 AGATTGAAGA-AATCC
60302064 AATCTTTTACCC
1 AATCTTTTACCC
60302076 CTAAAGTTAT
Statistics
Matches: 380, Mismatches: 27, Indels: 8
0.92 0.07 0.02
Matches are distributed among these distances:
79 74 0.19
80 306 0.81
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.26
Consensus pattern (80 bp):
AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
AGATTGAAGAAATCC
Found at i:60303815 original size:15 final size:17
Alignment explanation
Indices: 60303785--60303826 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
60303775 AAATATTATT
60303785 TTAATTAAAA-ATTAAA
1 TTAATTAAAAGATTAAA
60303801 -TAATTAAAAGA-TAAA
1 TTAATTAAAAGATTAAA
*
60303816 TTAATTTAAAG
1 TTAATTAAAAG
60303827 GAATAAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (17 bp):
TTAATTAAAAGATTAAA
Found at i:60303834 original size:18 final size:18
Alignment explanation
Indices: 60303802--60303853 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
60303792 AAAATTAAAT
*
60303802 AATTAAAAG-ATAAATTA
1 AATTAAAGGAATAAATTA
* *
60303819 ATTTAAAGGAATAAATGA
1 AATTAAAGGAATAAATTA
* *
60303837 AATTCAAGTAATAAATT
1 AATTAAAGGAATAAATT
60303854 TAAAAGTAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.58, C:0.02, G:0.10, T:0.31
Consensus pattern (18 bp):
AATTAAAGGAATAAATTA
Found at i:60303877 original size:14 final size:13
Alignment explanation
Indices: 60303836--60303880 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
60303826 GGAATAAATG
*
60303836 AAATTCAAGTAAT
1 AAATTAAAGTAAT
60303849 AAATTTAAAAGTAAT
1 AAA-TT-AAAGTAAT
60303864 AAATTAAAGTTAAT
1 AAATTAAAG-TAAT
60303878 AAA
1 AAA
60303881 GAATGTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 7 0.25
14 11 0.39
15 10 0.36
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (13 bp):
AAATTAAAGTAAT
Found at i:60304528 original size:28 final size:27
Alignment explanation
Indices: 60304451--60304530 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 27
60304441 TATTTTAAAA
* * *
60304451 TTAAATTTGATATGAATTTAGATTTAT
1 TTAAATTTGAAATTAATTTAAATTTAT
* * *
60304478 TTAAATTTGAATTTGAGTCTAAATTTATT
1 TTAAATTTGAAATT-AATTTAAATTTA-T
*
60304507 TTAAATTTAAAATTAATTTAAATT
1 TTAAATTTGAAATTAATTTAAATT
60304531 AAAGTCCAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
27 11 0.27
28 17 0.41
29 13 0.32
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.51
Consensus pattern (27 bp):
TTAAATTTGAAATTAATTTAAATTTAT
Found at i:60305169 original size:2 final size:2
Alignment explanation
Indices: 60305162--60305187 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
60305152 TCCAAATGCA
60305162 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
60305188 TTAATGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60306060 original size:30 final size:30
Alignment explanation
Indices: 60306014--60306253 Score: 227
Period size: 30 Copynumber: 8.0 Consensus size: 30
60306004 CCCTAAATTA
* *
60306014 TCTAGAAATTATATTTTGACCCCAAAACTT
1 TCTAAAAATTACATTTTGACCCCAAAACTT
* *
60306044 TCTAAAAATTACATTTTAACCCAAAAACTT
1 TCTAAAAATTACATTTTGACCCCAAAACTT
* * *
60306074 T-TCCAAAATTACATTTTAACCCTAAAACTT
1 TCT-AAAAATTACATTTTGACCCCAAAACTT
* * *
60306104 T-TCCAAAATTACATTTCGACCCTAAAACTT
1 TCT-AAAAATTACATTTTGACCCCAAAACTT
* * * * *
60306134 TTTGAAAATTATATTTTGACCTCGAAACTT
1 TCTAAAAATTACATTTTGACCCCAAAACTT
* *
60306164 TCCAAAAATTACATTTTGACCCCTAAACTT
1 TCTAAAAATTACATTTTGACCCCAAAACTT
* *
60306194 T-TCCAAAATTACATTTTAACCCCAAAACTT
1 TCT-AAAAATTACATTTTGACCCCAAAACTT
* *
60306224 TC-AAAAATTACCATTTTTACCCCCAAACTT
1 TCTAAAAATTA-CATTTTGACCCCAAAACTT
60306254 CCTTAAATCC
Statistics
Matches: 178, Mismatches: 27, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
29 8 0.04
30 169 0.95
31 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.35
Consensus pattern (30 bp):
TCTAAAAATTACATTTTGACCCCAAAACTT
Found at i:60306172 original size:90 final size:90
Alignment explanation
Indices: 60306019--60306245 Score: 291
Period size: 90 Copynumber: 2.5 Consensus size: 90
60306009 AATTATCTAG
*
60306019 AAATTATATTTTGACCCCAAAACTTTCTAAAAATTACATTTTAACCCAAAAACTTTTCCAAAATT
1 AAATTACATTTTGACCCCAAAACTTTCTAAAAATTACATTTTAACCCAAAAACTTTTCCAAAATT
60306084 ACATTTT-AACCCTAAAACTTTTCCA
66 ACATTTTGAACCCT-AAACTTTTCCA
* * * * * * *
60306109 AAATTACATTTCGACCCTAAAACTTTTTGAAAATTATATTTTGACCTC-GAAAC-TTTCCAAAAA
1 AAATTACATTTTGACCCCAAAACTTTCTAAAAATTACATTTTAACC-CAAAAACTTTTCC-AAAA
*
60306172 TTACATTTTGACCCCTAAACTTTTCCA
64 TTACATTTTGAACCCTAAACTTTTCCA
* *
60306199 AAATTACATTTTAACCCCAAAACTTTC-AAAAATTACCATTTTTACCC
1 AAATTACATTTTGACCCCAAAACTTTCTAAAAATTA-CATTTTAACCC
60306246 CCAAACTTCC
Statistics
Matches: 117, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
89 13 0.11
90 98 0.84
91 6 0.05
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.36
Consensus pattern (90 bp):
AAATTACATTTTGACCCCAAAACTTTCTAAAAATTACATTTTAACCCAAAAACTTTTCCAAAATT
ACATTTTGAACCCTAAACTTTTCCA
Found at i:60306246 original size:60 final size:59
Alignment explanation
Indices: 60306019--60306253 Score: 274
Period size: 60 Copynumber: 3.9 Consensus size: 59
60306009 AATTATCTAG
* * * **
60306019 AAATTATATTTTGACCCCAAAACTTTCTAAAAATTACATTTTAACCCAAAAACTTTTCCA
1 AAATTACATTTTAACCCCAAAACTTTC-AAAAATTACATTTTGACCCCTAAACTTTTCCA
* * * **
60306079 AAATTACATTTTAACCCTAAAACTTTTCCAAAATTACATTTCGA-CCCTAAAACTTTTTGA
1 AAATTACATTTTAACCCCAAAAC-TTTCAAAAATTACATTTTGACCCCT-AAACTTTTCCA
* * * *
60306139 AAATTATATTTTGACCTCGAAACTTTCCAAAAATTACATTTTGACCCCTAAACTTTTCCA
1 AAATTACATTTTAACCCCAAAACTTT-CAAAAATTACATTTTGACCCCTAAACTTTTCCA
* *
60306199 AAATTACATTTTAACCCCAAAACTTTCAAAAATTACCATTTTTACCCCCAAACTT
1 AAATTACATTTTAACCCCAAAACTTTCAAAAATTA-CATTTTGACCCCTAAACTT
60306254 CCTTAAATCC
Statistics
Matches: 145, Mismatches: 25, Indels: 10
0.81 0.14 0.06
Matches are distributed among these distances:
59 14 0.10
60 123 0.85
61 8 0.06
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (59 bp):
AAATTACATTTTAACCCCAAAACTTTCAAAAATTACATTTTGACCCCTAAACTTTTCCA
Found at i:60306276 original size:29 final size:30
Alignment explanation
Indices: 60306158--60306278 Score: 101
Period size: 30 Copynumber: 4.1 Consensus size: 30
60306148 TTTGACCTCG
*
60306158 AAACTTTCCAAAAATTA-CA-TTTTGACCCC
1 AAAC-TTCCAAAAATTACCATTTTTAACCCC
60306187 TAAACTTTTCC-AAAATTA-CA-TTTTAACCCC
1 -AAAC--TTCCAAAAATTACCATTTTTAACCCC
* *
60306217 AAAACTTTCAAAAATTACCATTTTTACCCCC
1 -AAACTTCCAAAAATTACCATTTTTAACCCC
** *
60306248 AAACTTCCTTAAA-TCCCATTTTTAACCCC
1 AAACTTCCAAAAATTACCATTTTTAACCCC
60306277 AA
1 AA
60306279 TTTCACCAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
28 3 0.04
29 23 0.29
30 38 0.49
31 14 0.18
ACGTcount: A:0.37, C:0.29, G:0.01, T:0.33
Consensus pattern (30 bp):
AAACTTCCAAAAATTACCATTTTTAACCCC
Found at i:60306658 original size:18 final size:18
Alignment explanation
Indices: 60306635--60306670 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
60306625 GACAATATTT
60306635 TTTAATTTCGCGTTTCGA
1 TTTAATTTCGCGTTTCGA
60306653 TTTAATTTCGCGTTTCGA
1 TTTAATTTCGCGTTTCGA
60306671 AATCTTGCGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (18 bp):
TTTAATTTCGCGTTTCGA
Found at i:60308188 original size:37 final size:38
Alignment explanation
Indices: 60308144--60308249 Score: 153
Period size: 37 Copynumber: 2.8 Consensus size: 38
60308134 ATGATTTTGT
60308144 TATGATTAATGATTAAT-TTGGGTTTAGACAAATGATTA
1 TATGATTAATGATT-ATCTTGGGTTTAGACAAATGATTA
* *
60308182 -ATGATTAATGATTATCTTGGGTTTAGACACATGGTTA
1 TATGATTAATGATTATCTTGGGTTTAGACAAATGATTA
*
60308219 TAGTCATTAATGATTATCTTGGGTTTAGACA
1 TA-TGATTAATGATTATCTTGGGTTTAGACA
60308250 TTTAACTTGC
Statistics
Matches: 62, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
36 2 0.03
37 32 0.52
38 1 0.02
39 27 0.44
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.42
Consensus pattern (38 bp):
TATGATTAATGATTATCTTGGGTTTAGACAAATGATTA
Found at i:60310793 original size:41 final size:42
Alignment explanation
Indices: 60310705--60310793 Score: 119
Period size: 41 Copynumber: 2.1 Consensus size: 42
60310695 TTGAGTCATA
** *
60310705 AGTCTTCCTTTAAATATAATCTCATGCTCGTCCTAAGTCACG
1 AGTCTTCCTTTAAATATAATCTCATGCTAATCCTAAGCCACG
60310747 AGTCTTCCTTT-AATATAATCTCATGCTAAT-CTCAAGCCACG
1 AGTCTTCCTTTAAATATAATCTCATGCTAATCCT-AAGCCACG
*
60310788 CGTCTT
1 AGTCTT
60310794 TCATTTTCGC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
40 2 0.05
41 29 0.69
42 11 0.26
ACGTcount: A:0.26, C:0.27, G:0.11, T:0.36
Consensus pattern (42 bp):
AGTCTTCCTTTAAATATAATCTCATGCTAATCCTAAGCCACG
Found at i:60314930 original size:22 final size:20
Alignment explanation
Indices: 60314899--60314939 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
60314889 ATTCAAAAAT
*
60314899 AAAAAAATAAGAGAATTTTTA
1 AAAAAAATAAAAG-ATTTTTA
60314920 AAAAAACATAAAAGATTTTT
1 AAAAAA-ATAAAAGATTTTT
60314940 CTATAATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (20 bp):
AAAAAAATAAAAGATTTTTA
Found at i:60317412 original size:20 final size:20
Alignment explanation
Indices: 60317375--60317412 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
60317365 TTACATTTTC
*
60317375 TAATAAAAATTATTATTTAA
1 TAATAAAAATTATCATTTAA
60317395 TAAT-AAAATATATCATTT
1 TAATAAAAAT-TATCATTT
60317413 TGTTGCGCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATAAAAATTATCATTTAA
Found at i:60326827 original size:21 final size:22
Alignment explanation
Indices: 60326792--60326836 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
60326782 ATTTTTTTTA
60326792 AAAATTAAAAATATACTA-TAAT
1 AAAATTAAAAATATA-TACTAAT
*
60326814 AAAA-TAAAATTATATACTAAT
1 AAAATTAAAAATATATACTAAT
60326835 AA
1 AA
60326837 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 15 0.71
22 4 0.19
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATTAAAAATATATACTAAT
Found at i:60333312 original size:43 final size:43
Alignment explanation
Indices: 60333265--60333403 Score: 136
Period size: 43 Copynumber: 3.1 Consensus size: 43
60333255 AAAAATACCA
*
60333265 CTAAAGACCATGTTTTTTAGCGGCGTTTGTGGGATAAGCGCCG
1 CTAAAGACCATGTTTTTTAGTGGCGTTTGTGGGATAAGCGCCG
*** * *
60333308 CTAAAGACCATGGCCTGTAGTGGCGTTTGT-GGAAAAGCGCCG
1 CTAAAGACCATGTTTTTTAGTGGCGTTTGTGGGATAAGCGCCG
* * * *
60333350 CTAAAAATCATGTTCTTTAGCGTAGTGGCGTTTGTGAGATAAACGCCG
1 CTAAAGACCATGTT-TTT----TAGTGGCGTTTGTGGGATAAGCGCCG
60333398 CTAAAG
1 CTAAAG
60333404 GCTAAAGACC
Statistics
Matches: 74, Mismatches: 16, Indels: 7
0.76 0.16 0.07
Matches are distributed among these distances:
42 21 0.28
43 26 0.35
47 13 0.18
48 14 0.19
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (43 bp):
CTAAAGACCATGTTTTTTAGTGGCGTTTGTGGGATAAGCGCCG
Found at i:60333436 original size:55 final size:55
Alignment explanation
Indices: 60333349--60333457 Score: 182
Period size: 55 Copynumber: 2.0 Consensus size: 55
60333339 GAAAAGCGCC
* *
60333349 GCTAAAAATCATGTTCTTTAGCGTAGTGGCGTTTGTGAGATAAACGCCGCTAAAG
1 GCTAAAAACCATGTTCTTTAGCGTAATGGCGTTTGTGAGATAAACGCCGCTAAAG
* *
60333404 GCTAAAGACCATGTTCTTTAGCGTAATTGCGTTTGTGAGATAAACGCCGCTAAA
1 GCTAAAAACCATGTTCTTTAGCGTAATGGCGTTTGTGAGATAAACGCCGCTAAA
60333458 AATCATGTTC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (55 bp):
GCTAAAAACCATGTTCTTTAGCGTAATGGCGTTTGTGAGATAAACGCCGCTAAAG
Found at i:60336095 original size:16 final size:16
Alignment explanation
Indices: 60336071--60336106 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
60336061 TTTATTTTAA
*
60336071 ATTTAAATTTTTATAT
1 ATTTAAATTTTTAAAT
*
60336087 ATTTCAATTTTTAAAT
1 ATTTAAATTTTTAAAT
60336103 ATTT
1 ATTT
60336107 GTTAATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTAAATTTTTAAAT
Found at i:60349621 original size:40 final size:40
Alignment explanation
Indices: 60349576--60349659 Score: 150
Period size: 40 Copynumber: 2.1 Consensus size: 40
60349566 TGAACACAGT
*
60349576 AAAATTACAGTTACTTTAAAATATTTGATATATGTATATA
1 AAAATTACAATTACTTTAAAATATTTGATATATGTATATA
*
60349616 AAAATTACAATTATTTTAAAATATTTGATATATGTATATA
1 AAAATTACAATTACTTTAAAATATTTGATATATGTATATA
60349656 AAAA
1 AAAA
60349660 ATATTTATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.42
Consensus pattern (40 bp):
AAAATTACAATTACTTTAAAATATTTGATATATGTATATA
Found at i:60350336 original size:24 final size:24
Alignment explanation
Indices: 60350304--60350351 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
60350294 TACGCTATTT
60350304 ATTTTTATTTTCAATCACCAGTCA
1 ATTTTTATTTTCAATCACCAGTCA
60350328 ATTTTTATTTTCAATCACCAGTCA
1 ATTTTTATTTTCAATCACCAGTCA
60350352 CCACTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.46
Consensus pattern (24 bp):
ATTTTTATTTTCAATCACCAGTCA
Found at i:60352548 original size:7 final size:7
Alignment explanation
Indices: 60352525--60352617 Score: 96
Period size: 7 Copynumber: 13.1 Consensus size: 7
60352515 GTTTTAAAGA
60352525 TTTGGGG
1 TTTGGGG
60352532 TTTTGGGG
1 -TTTGGGG
*
60352540 TTTGAGG
1 TTTGGGG
*
60352547 TTTGGGT
1 TTTGGGG
*
60352554 TTTGAGG
1 TTTGGGG
60352561 TTTGGGG
1 TTTGGGG
60352568 TTTGGGG
1 TTTGGGG
*
60352575 TTTAGGG
1 TTTGGGG
*
60352582 TTTAGGG
1 TTTGGGG
*
60352589 TTTAGGG
1 TTTGGGG
*
60352596 TTTAGGG
1 TTTGGGG
*
60352603 TTTAGGG
1 TTTGGGG
*
60352610 TTTAGGG
1 TTTGGGG
60352617 T
1 T
60352618 CAAAATGTAA
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
7 71 0.91
8 7 0.09
ACGTcount: A:0.09, C:0.00, G:0.46, T:0.45
Consensus pattern (7 bp):
TTTGGGG
Found at i:60352552 original size:14 final size:14
Alignment explanation
Indices: 60352498--60352612 Score: 94
Period size: 14 Copynumber: 8.1 Consensus size: 14
60352488 GGATTGAGGC
60352498 TTGA-GTTTAGGGT
1 TTGAGGTTTAGGGT
* * *
60352511 TTGAGTTTTAAAGAT
1 TTGAGGTTT-AGGGT
* *
60352526 TTGGGGTTTTGGGGT
1 TTGAGG-TTTAGGGT
60352541 TTGAGGTTT-GGGTT
1 TTGAGGTTTAGGG-T
*
60352555 TTGAGGTTTGGGGT
1 TTGAGGTTTAGGGT
*
60352569 TTGGGGTTTAGGGT
1 TTGAGGTTTAGGGT
60352583 TT-AGGGTTTAGGGT
1 TTGA-GGTTTAGGGT
60352597 TT-AGGGTTTAGGGT
1 TTGA-GGTTTAGGGT
60352611 TT
1 TT
60352613 AGGGTCAAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
13 7 0.08
14 57 0.68
15 17 0.20
16 3 0.04
ACGTcount: A:0.12, C:0.00, G:0.42, T:0.46
Consensus pattern (14 bp):
TTGAGGTTTAGGGT
Found at i:60354317 original size:62 final size:59
Alignment explanation
Indices: 60354241--60354380 Score: 217
Period size: 62 Copynumber: 2.3 Consensus size: 59
60354231 ATAGATACCC
* * *
60354241 GGGGCAAAATGGTAATTTTCGGTGAAATCGAGGTTAAAATAGAATTTTAGAAGATTCGGGGG
1 GGGGTAAAATGGTAATTTTCGGTAAAATCGAGGTTAAAACAGAATTTTAGAAGATTC---GG
*
60354303 GGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTTAAAACAGAATTTTAGAAGATTCGG
1 GGGGTAAAATGGTAATTTTCGGTAAAATCGAGGTTAAAACAGAATTTTAGAAGATTCGG
60354362 GGGGTAAAATGGTAATTTT
1 GGGGTAAAATGGTAATTTT
60354381 TGAAAGTTTT
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
59 21 0.28
62 53 0.72
ACGTcount: A:0.35, C:0.05, G:0.30, T:0.30
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTCGGTAAAATCGAGGTTAAAACAGAATTTTAGAAGATTCGG
Found at i:60354401 original size:30 final size:30
Alignment explanation
Indices: 60354362--60354677 Score: 476
Period size: 30 Copynumber: 10.6 Consensus size: 30
60354352 GAAGATTCGG
*
60354362 GGGGT-AAAATGGTAATTTTTG-AAAGTTTT
1 GGGGTCAAAAT-GTAATTTTGGAAAAGTTTT
*
60354391 AGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
* *
60354421 AGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
60354451 GGGGTCAAAATGTAATTTTAGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
60354481 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
60354511 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
* * * * *
60354541 AGGGTTAAAGTATAATTTTTG-AAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
60354570 GGGGTTAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
* *
60354600 GAGGTCAAAATGTAATTTTGGAAACGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
60354630 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
60354660 TGGGTCAAAATGTAATTT
1 GGGGTCAAAATGTAATTT
60354678 CTAGATTGTT
Statistics
Matches: 262, Mismatches: 22, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
29 38 0.15
30 224 0.85
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.38
Consensus pattern (30 bp):
GGGGTCAAAATGTAATTTTGGAAAAGTTTT
Found at i:60354496 original size:119 final size:118
Alignment explanation
Indices: 60354362--60354677 Score: 499
Period size: 119 Copynumber: 2.7 Consensus size: 118
60354352 GAAGATTCGG
* *
60354362 GGGGT-AAAATGGTAATTTTTGAAAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGT
1 GGGGTCAAAAT-GTAATTTTGGAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGT
60354426 CAAAATATAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTAGAAAAGTTTT
65 CAAAATATAATTTTGG-AAAGTTTTGGGGTCAAAATGTAATTTTAGAAAAGTTTT
60354481 GGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGT
1 GGGGTCAAAATGTAATTTTGG-AAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGT
* * * * *
60354546 TAAAGTATAATTTTTGAAAGTTTTGGGGTTAAAATGTAATTTTGGAAAAGTTTT
65 CAAAATATAATTTTGGAAAGTTTTGGGGTCAAAATGTAATTTTAGAAAAGTTTT
* *
60354600 GAGGTCAAAATGTAATTTTGGAAACGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTTGGGT
1 GGGGTCAAAATGTAATTTTGGAAA-GTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGT
*
60354665 CAAAATGTAATTT
65 CAAAATATAATTT
60354678 CTAGATTGTT
Statistics
Matches: 182, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
118 3 0.02
119 119 0.65
120 60 0.33
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.38
Consensus pattern (118 bp):
GGGGTCAAAATGTAATTTTGGAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTAGGGTC
AAAATATAATTTTGGAAAGTTTTGGGGTCAAAATGTAATTTTAGAAAAGTTTT
Found at i:60354501 original size:19 final size:19
Alignment explanation
Indices: 60354477--60354531 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
60354467 TTTAGAAAAG
60354477 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
60354496 TTTT--GG--AAAA-G---
1 TTTTGGGGTCAAAATGTAA
60354507 TTTTGGGGTCAAAATGTAA
1 TTTTGGGGTCAAAATGTAA
60354526 TTTTGG
1 TTTTGG
60354532 AAAAGTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 4 0.14
13 2 0.07
14 1 0.04
15 8 0.29
16 1 0.04
17 2 0.07
19 10 0.36
ACGTcount: A:0.29, C:0.04, G:0.27, T:0.40
Consensus pattern (19 bp):
TTTTGGGGTCAAAATGTAA
Found at i:60355278 original size:23 final size:23
Alignment explanation
Indices: 60355248--60355300 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
60355238 TGAACCCCGC
*
60355248 GCGTCGTCTGCGCGTGTCGTGGT
1 GCGTCGTCGGCGCGTGTCGTGGT
60355271 GCGTCGTCGGCGCGTGTCGTGGT
1 GCGTCGTCGGCGCGTGTCGTGGT
60355294 GCGTCGT
1 GCGTCGT
60355301 TTCATGTCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.00, C:0.26, G:0.45, T:0.28
Consensus pattern (23 bp):
GCGTCGTCGGCGCGTGTCGTGGT
Found at i:60355447 original size:15 final size:15
Alignment explanation
Indices: 60355386--60355448 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
60355376 AAGAGTCGCC
*
60355386 CTTTCCTTTTTC-TT
1 CTTTCCCTTTTCTTT
*
60355400 CTTTCTCTTTTCTTT
1 CTTTCCCTTTTCTTT
*
60355415 -TGTTCTCTATTT-TTT
1 CT-TTCCCT-TTTCTTT
60355430 CTTTCCCTTTTCTTT
1 CTTTCCCTTTTCTTT
60355445 CTTT
1 CTTT
60355449 TGTTTTTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
14 14 0.34
15 23 0.56
16 4 0.10
ACGTcount: A:0.02, C:0.25, G:0.02, T:0.71
Consensus pattern (15 bp):
CTTTCCCTTTTCTTT
Found at i:60356282 original size:20 final size:21
Alignment explanation
Indices: 60356250--60356289 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
60356240 CAGGGCATGG
*
60356250 TGGAGCTTGGTGGTCAGCAGA
1 TGGAGCTTGGTGGCCAGCAGA
60356271 TGGAGC-TGGTGGCCAGCAG
1 TGGAGCTTGGTGGCCAGCAG
60356290 CAGTAGGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.17, C:0.17, G:0.45, T:0.20
Consensus pattern (21 bp):
TGGAGCTTGGTGGCCAGCAGA
Found at i:60356488 original size:6 final size:6
Alignment explanation
Indices: 60356448--60356549 Score: 77
Period size: 6 Copynumber: 17.0 Consensus size: 6
60356438 ACTTTGGACT
* * ** *
60356448 TTTAAA TTTTTAA TTTAATA TTTTAA TTTTTA TTTAAA TTTAAA TTCAAA
1 TTTAAA -TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
60356498 -TTAAA TTTAAATA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA --TAAA
1 TTTAAA TTT-AA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
60356544 TTTAAA
1 TTTAAA
60356550 ATCAATTTTA
Statistics
Matches: 77, Mismatches: 11, Indels: 15
0.75 0.11 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 47 0.61
7 14 0.18
8 4 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:60356513 original size:25 final size:25
Alignment explanation
Indices: 60356485--60356534 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
60356475 TTTTATTTAA
* *
60356485 ATTTAAATTCAAATTAAATTTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
*
60356510 ATTTAAATTTAAAATAAATCTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
60356535 TTAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAAATTCAAAATAAATCTAAAT
Found at i:60356515 original size:42 final size:42
Alignment explanation
Indices: 60356459--60356549 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
60356449 TTAAATTTTT
* * ** *
60356459 AATTT-AATATTTTAATTTTTATTTAAATTTAAATTCAAATTA
1 AATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA-TA
*
60356501 AATTTAAATA-TTTAAATTTAAAATAAATCTAAATTTAAATA
1 AATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAATA
60356542 AATTTAAA
1 AATTTAAA
60356550 ATCAATTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 10 0.24
42 28 0.67
43 4 0.10
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (42 bp):
AATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAATA
Found at i:60356516 original size:31 final size:31
Alignment explanation
Indices: 60356478--60356541 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
60356468 TTTTAATTTT
*
60356478 TATTTAAATTTAAATTCAAAT-TAAATTTAAA
1 TATTTAAATTTAAAAT-AAATCTAAATTTAAA
60356509 TATTTAAATTTAAAATAAATCTAAATTTAAA
1 TATTTAAATTTAAAATAAATCTAAATTTAAA
60356540 TA
1 TA
60356542 AATTTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
TATTTAAATTTAAAATAAATCTAAATTTAAA
Found at i:60356551 original size:17 final size:16
Alignment explanation
Indices: 60356479--60356549 Score: 85
Period size: 17 Copynumber: 4.4 Consensus size: 16
60356469 TTTAATTTTT
60356479 ATTTAAATTTAAATTCAA
1 ATTTAAATTTAAA-T-AA
60356497 A-TTAAATTTAAAT--
1 ATTTAAATTTAAATAA
60356510 ATTTAAATTTAAAATAA
1 ATTTAAATTT-AAATAA
*
60356527 ATCTAAATTTAAATAA
1 ATTTAAATTTAAATAA
60356543 ATTTAAA
1 ATTTAAA
60356550 ATCAATTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
13 1 0.02
14 8 0.17
15 4 0.09
16 13 0.28
17 20 0.43
18 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Done.