Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 134 of 150
Found at i:40235566 original size:114 final size:114
Alignment explanation
Indices: 40235311--40235542 Score: 360
Period size: 114 Copynumber: 2.0 Consensus size: 114
40235301 TGTAATTTTT
* * *
40235311 TTGTATGAATATTGTAATTTTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTA
1 TTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTA
* **** *
40235376 ATATTGTAATTTTGTATGAATATTATAATTTTTTTATGAATATTGTAATG
66 ATATTGTAATTTTGTATGAATATTATAATGTGGGGAT-AATATTGTAATA
40235426 TTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAA-TTTTTTGTATGAATATTGTA
1 TTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTA
40235490 ATATTGTAATTTTGTATGAATATTATAATGTGGGGAT-ATATTGTAATA
66 ATATTGTAATTTTGTATGAATATTATAATGTGGGGATAATATTGTAATA
40235538 TTGTA
1 TTGTA
40235543 ATTTTTTATA
Statistics
Matches: 108, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
112 15 0.14
114 52 0.48
115 41 0.38
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.52
Consensus pattern (114 bp):
TTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTA
ATATTGTAATTTTGTATGAATATTATAATGTGGGGATAATATTGTAATA
Found at i:40235653 original size:27 final size:27
Alignment explanation
Indices: 40235618--40235678 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
40235608 ATGTTTTGTT
40235618 CACCATTGGCGCCTCCCAAACAGGCAC
1 CACCATTGGCGCCTCCCAAACAGGCAC
**
40235645 CACCATTGGCGCCTCCCAAGTAGGCAC
1 CACCATTGGCGCCTCCCAAACAGGCAC
40235672 CACCATT
1 CACCATT
40235679 AGCACCTTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.25, C:0.43, G:0.18, T:0.15
Consensus pattern (27 bp):
CACCATTGGCGCCTCCCAAACAGGCAC
Found at i:40235696 original size:27 final size:27
Alignment explanation
Indices: 40235618--40235685 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
40235608 ATGTTTTGTT
* * **
40235618 CACCATTGGCGCCTCCCAAACAGGCAC
1 CACCATTAGCACCTCCCAAGTAGGCAC
* *
40235645 CACCATTGGCGCCTCCCAAGTAGGCAC
1 CACCATTAGCACCTCCCAAGTAGGCAC
40235672 CACCATTAGCACCT
1 CACCATTAGCACCT
40235686 TCCAGATAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.25, C:0.43, G:0.18, T:0.15
Consensus pattern (27 bp):
CACCATTAGCACCTCCCAAGTAGGCAC
Found at i:40238484 original size:15 final size:15
Alignment explanation
Indices: 40238460--40238489 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40238450 TTCTCAATTT
40238460 TAAAAAGAAAAGAAA
1 TAAAAAGAAAAGAAA
*
40238475 TAAAAGGAAAAGAAA
1 TAAAAAGAAAAGAAA
40238490 AATAATTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (15 bp):
TAAAAAGAAAAGAAA
Found at i:40244792 original size:9 final size:9
Alignment explanation
Indices: 40244780--40244810 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40244770 ATTAAATGAA
40244780 TCGAGTTAT
1 TCGAGTTAT
*
40244789 TCGAGTTAA
1 TCGAGTTAT
40244798 TCGAGTTAT
1 TCGAGTTAT
40244807 TCGA
1 TCGA
40244811 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:40252994 original size:16 final size:16
Alignment explanation
Indices: 40252955--40252996 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
40252945 TTTACCAAAT
40252955 TAATATTTAGATATTA
1 TAATATTTAGATATTA
40252971 CTAA-ATTTAGATATT-
1 -TAATATTTAGATATTA
40252986 TAGATATTTAG
1 TA-ATATTTAG
40252997 TTCACTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 2 0.09
15 1 0.04
16 17 0.74
17 3 0.13
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (16 bp):
TAATATTTAGATATTA
Found at i:40256969 original size:26 final size:26
Alignment explanation
Indices: 40256933--40256987 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
40256923 GGATGGGGCG
40256933 GTTCCTAGGCAAAAGGTGAGATACTT
1 GTTCCTAGGCAAAAGGTGAGATACTT
40256959 GTTCCTAGGCAAAAGGTGAGATACTT
1 GTTCCTAGGCAAAAGGTGAGATACTT
40256985 GTT
1 GTT
40256988 TAAGGAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (26 bp):
GTTCCTAGGCAAAAGGTGAGATACTT
Found at i:40261648 original size:2 final size:2
Alignment explanation
Indices: 40261635--40261676 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
40261625 TTTAAAGAGG
*
40261635 AT AT AG AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
40261677 TGGATATTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40266551 original size:29 final size:29
Alignment explanation
Indices: 40266474--40266552 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 29
40266464 TAAATTAAAC
** **
40266474 TTTTTCCCCATTTTGATACCTAAACTTTT
1 TTTTTCCCCAAATTGATACCTAAACTACT
* * * *
40266503 TTTTTGTCGC-AAGTGGTACCTAAACTACT
1 TTTTT-CCCCAAATTGATACCTAAACTACT
40266532 TTTTTCCCCAAATTGATACCT
1 TTTTTCCCCAAATTGATACCT
40266553 CCGTTAGTCA
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
28 2 0.06
29 32 0.89
30 2 0.06
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.44
Consensus pattern (29 bp):
TTTTTCCCCAAATTGATACCTAAACTACT
Found at i:40274349 original size:9 final size:9
Alignment explanation
Indices: 40274337--40274384 Score: 55
Period size: 8 Copynumber: 5.3 Consensus size: 9
40274327 TAAAAAAATT
40274337 AATTATTAA
1 AATTATTAA
40274346 AATTATTAA
1 AATTATTAA
40274355 AATTGATATAA
1 AATT-AT-TAA
*
40274366 ATTTA-TAA
1 AATTATTAA
40274374 AATTA-TAA
1 AATTATTAA
40274382 AAT
1 AAT
40274385 AATAATAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
8 13 0.37
9 13 0.37
10 3 0.09
11 6 0.17
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (9 bp):
AATTATTAA
Found at i:40274392 original size:27 final size:26
Alignment explanation
Indices: 40274343--40274459 Score: 96
Period size: 27 Copynumber: 4.3 Consensus size: 26
40274333 AATTAATTAT
40274343 TAAAATTATTAAAAT-TGATATAAATTTA
1 TAAAATTA-TAAAATAT-A-ATAAATTTA
*
40274371 TAAAATTATAAAATAATAAT-AACTTA
1 TAAAATTATAAAAT-ATAATAAATTTA
*
40274397 TAAATATTATAAAATATAAAAAATTTA
1 TAAA-ATTATAAAATATAATAAATTTA
* * *
40274424 GTAAATTTTAATAAATTATAA-AAAATTA
1 -TAAA-ATT-ATAAAATATAATAAATTTA
40274452 TAAAATTA
1 TAAAATTA
40274460 ATTTTATAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
25 1 0.01
26 15 0.20
27 27 0.36
28 22 0.29
29 11 0.14
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (26 bp):
TAAAATTATAAAATATAATAAATTTA
Found at i:40274484 original size:22 final size:23
Alignment explanation
Indices: 40274439--40274507 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
40274429 TTTTAATAAA
40274439 TTATAAAAA-ATTATAAAATTAATT
1 TTATAAAAACATTATAAAA--AATT
40274463 TTATAAAAACA-TATAAAAAA-T
1 TTATAAAAACATTATAAAAAATT
40274484 TTA-AAAAACGATTCATAAAAAATT
1 TTATAAAAAC-ATT-ATAAAAAATT
40274508 ATTGAAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
20 6 0.15
21 5 0.12
22 3 0.08
23 8 0.20
24 17 0.43
25 1 0.03
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.33
Consensus pattern (23 bp):
TTATAAAAACATTATAAAAAATT
Found at i:40274565 original size:9 final size:9
Alignment explanation
Indices: 40274337--40274568 Score: 89
Period size: 10 Copynumber: 24.0 Consensus size: 9
40274327 TAAAAAAATT
*
40274337 AATTATTAA
1 AATTATAAA
*
40274346 AATTATTAA
1 AATTATAAA
*
40274355 AATTGATATA
1 AATT-ATAAA
40274365 AATT-TATAA
1 AATTATA-AA
40274374 AATTAT-AA
1 AATTATAAA
*
40274382 AATAATAATA
1 AATTATAA-A
*
40274392 ACTTATAAA
1 AATTATAAA
*
40274401 TATTAT-AA
1 AATTATAAA
40274409 AA-TATAAAA
1 AATTAT-AAA
*
40274418 AATT-TAGTA
1 AATTATA-AA
*
40274427 AATTTTAATA
1 AATTATAA-A
40274437 AATTATAAAA
1 AATTAT-AAA
40274447 AATTATAAAA
1 AATTAT-AAA
40274457 TTAATTTTATAAA
1 --AA--TTATAAA
*
40274470 AACATATAAAA
1 AA-TTAT-AAA
*
40274481 AATTTAAAAA
1 AA-TTATAAA
40274491 ACGATTCATAAAA
1 A--ATT-AT-AAA
*
40274504 AATTATTGAA
1 AATTA-TAAA
40274514 AATTAT-AA
1 AATTATAAA
* *
40274522 AATGATTAA
1 AATTATAAA
* *
40274531 AAGTATTAA
1 AATTATAAA
40274540 AATTAATAAA
1 AATT-ATAAA
40274550 AATTTATAAA
1 AA-TTATAAA
40274560 AATTATAAA
1 AATTATAAA
40274569 CAAAATCATA
Statistics
Matches: 174, Mismatches: 24, Indels: 50
0.70 0.10 0.20
Matches are distributed among these distances:
7 3 0.02
8 20 0.11
9 54 0.31
10 63 0.36
11 19 0.11
12 4 0.02
13 7 0.04
14 4 0.02
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (9 bp):
AATTATAAA
Found at i:40281246 original size:24 final size:24
Alignment explanation
Indices: 40281214--40281269 Score: 96
Period size: 23 Copynumber: 2.4 Consensus size: 24
40281204 TATATTAAAT
40281214 ATATATATTTTTATTTTTAAACAA
1 ATATATATTTTTATTTTTAAACAA
*
40281238 ATATATA-TTTTATTTTTAATCAA
1 ATATATATTTTTATTTTTAAACAA
40281261 ATATATATT
1 ATATATATT
40281270 ATATATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 22 0.73
24 8 0.27
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (24 bp):
ATATATATTTTTATTTTTAAACAA
Found at i:40281811 original size:22 final size:22
Alignment explanation
Indices: 40281786--40281827 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
40281776 TATCTAAACA
40281786 ATAACAGTAAAATAGTAGCATT
1 ATAACAGTAAAATAGTAGCATT
* *
40281808 ATAATAGTGAAATAGTAGCA
1 ATAACAGTAAAATAGTAGCA
40281828 AAATAAGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (22 bp):
ATAACAGTAAAATAGTAGCATT
Found at i:40281833 original size:22 final size:22
Alignment explanation
Indices: 40281785--40281833 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
40281775 ATATCTAAAC
*
40281785 AATAACAGTAAAATAGTAGCAT
1 AATAACAGTAAAATAGTAGCAA
* * *
40281807 TATAATAGTGAAATAGTAGCAA
1 AATAACAGTAAAATAGTAGCAA
40281829 AATAA
1 AATAA
40281834 GAAGAAAACA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.06, G:0.14, T:0.24
Consensus pattern (22 bp):
AATAACAGTAAAATAGTAGCAA
Found at i:40283338 original size:16 final size:16
Alignment explanation
Indices: 40283316--40283362 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
40283306 CACTGGAATA
40283316 GAATAGAGTTGTAATG
1 GAATAGAGTTGTAATG
* *
40283332 TAATAGAGATGTAATG
1 GAATAGAGTTGTAATG
40283348 GAATA-ACGTTGTAAT
1 GAATAGA-GTTGTAAT
40283363 CAGTAATCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 1 0.04
16 25 0.96
ACGTcount: A:0.40, C:0.02, G:0.26, T:0.32
Consensus pattern (16 bp):
GAATAGAGTTGTAATG
Found at i:40283956 original size:3 final size:3
Alignment explanation
Indices: 40283948--40283985 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
40283938 TCTGACTCCA
*
40283948 TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
40283986 AAATTTTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:40294309 original size:13 final size:12
Alignment explanation
Indices: 40294286--40294312 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40294276 TAAAATAAAG
40294286 TAAAGAAAAAAA
1 TAAAGAAAAAAA
40294298 TAAAGAAAAAAA
1 TAAAGAAAAAAA
40294310 TAA
1 TAA
40294313 CAAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.11
Consensus pattern (12 bp):
TAAAGAAAAAAA
Found at i:40300186 original size:37 final size:37
Alignment explanation
Indices: 40300144--40300447 Score: 405
Period size: 37 Copynumber: 8.0 Consensus size: 37
40300134 GGTAGTTTTA
*
40300144 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
40300181 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
40300218 GTTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
40300255 GTTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
40300292 GTTACACTTATCTGATCAAGTGACAAAGTGATAAGT-
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
40300328 GCTAAACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAA---GT-G
*
40300369 CTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT-
1 -----GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
40300410 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
40300447 G
1 G
40300448 TAGCCTAGCT
Statistics
Matches: 245, Mismatches: 11, Indels: 22
0.88 0.04 0.08
Matches are distributed among these distances:
36 66 0.27
37 143 0.58
39 2 0.01
43 2 0.01
46 32 0.13
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:40300437 original size:82 final size:81
Alignment explanation
Indices: 40300294--40300489 Score: 324
Period size: 82 Copynumber: 2.4 Consensus size: 81
40300284 GATAAGTGGT
40300294 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTAAACTTATCTGATCAAGAGACAAAGTGA
1 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTAAACTTATCTGATCAAGAGACAAAGTGA
*
40300359 TAAGTGGTAGCTTTAGC
66 TAAGTGGTAGC-CTAGC
* * *
40300376 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTACACTTATCTGATCAAGTGGCAAAGTGA
1 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTAAACTTATCTGATCAAGAGACAAAGTGA
40300441 TAAGTGGTAGCCTAGC
66 TAAGTGGTAGCCTAGC
*
40300457 TACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 TACACTTATCTGATCAAGTGACAAAGTGATAAGTG
40300490 ATCATACGTA
Statistics
Matches: 109, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
79 12 0.11
80 5 0.05
81 19 0.17
82 73 0.67
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.28
Consensus pattern (81 bp):
TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTAAACTTATCTGATCAAGAGACAAAGTGA
TAAGTGGTAGCCTAGC
Found at i:40303929 original size:19 final size:19
Alignment explanation
Indices: 40303905--40303961 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
40303895 TAATCCTACT
40303905 TAAATTCCTAAAAGATAAA
1 TAAATTCCTAAAAGATAAA
** *
40303924 TAAATTTAATTAAAGATAAAA
1 TAAA-TTCCTAAAAGAT-AAA
*
40303945 TAAAATCCTAAAA-ATAA
1 TAAATTCCTAAAAGATAA
40303962 TCCTTAATAA
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
18 2 0.07
19 6 0.21
20 14 0.48
21 7 0.24
ACGTcount: A:0.61, C:0.07, G:0.04, T:0.28
Consensus pattern (19 bp):
TAAATTCCTAAAAGATAAA
Found at i:40304642 original size:18 final size:18
Alignment explanation
Indices: 40304619--40304653 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
40304609 ACTCTGTAAT
40304619 TAGTTTAAATTTAATTTC
1 TAGTTTAAATTTAATTTC
40304637 TAGTTTAAATTTAATTT
1 TAGTTTAAATTTAATTT
40304654 TTAAATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (18 bp):
TAGTTTAAATTTAATTTC
Found at i:40304684 original size:23 final size:23
Alignment explanation
Indices: 40304658--40304732 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 23
40304648 TAATTTTTAA
*
40304658 ATTTTGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
* *
40304681 ATTTAGAATTGTTTAGCGATAAT
1 ATTTAGAATTATTTAGTGATAAT
*
40304704 ATTTAGTATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
40304727 ATTTAG
1 ATTTAG
40304733 GAAAAATCTA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.35, C:0.01, G:0.15, T:0.49
Consensus pattern (23 bp):
ATTTAGAATTATTTAGTGATAAT
Found at i:40304685 original size:13 final size:13
Alignment explanation
Indices: 40304667--40304732 Score: 63
Period size: 13 Copynumber: 5.5 Consensus size: 13
40304657 AATTTTGAAT
40304667 TATTTAGTGATAA
1 TATTTAGTGATAA
*
40304680 TATTTA--GA-AT
1 TATTTAGTGATAA
* *
40304690 TGTTTAGCGATAA
1 TATTTAGTGATAA
40304703 TATTTAGT-AT--
1 TATTTAGTGATAA
40304713 TATTTAGTGATAA
1 TATTTAGTGATAA
40304726 TATTTAG
1 TATTTAG
40304733 GAAAAATCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
10 14 0.33
11 4 0.10
12 4 0.10
13 20 0.48
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:40305040 original size:25 final size:28
Alignment explanation
Indices: 40304975--40305032 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
40304965 ATCTATTTTC
40304975 AAAGCATAATTTTCTTTATTATTAACTA
1 AAAGCATAATTTTCTTTATTATTAACTA
40305003 AAAGCATAATTTTCTTTATTATTAACTA
1 AAAGCATAATTTTCTTTATTATTAACTA
40305031 AA
1 AA
40305033 CTCTTTTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.45
Consensus pattern (28 bp):
AAAGCATAATTTTCTTTATTATTAACTA
Found at i:40307110 original size:2 final size:2
Alignment explanation
Indices: 40307103--40307139 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
40307093 TTCAATTTTC
40307103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40307140 GCAAACATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40309860 original size:8 final size:8
Alignment explanation
Indices: 40309847--40309880 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
40309837 TATCACATTT
40309847 TTTTTATA
1 TTTTTATA
40309855 TTTTTATA
1 TTTTTATA
40309863 TTTTTATTA
1 TTTTTA-TA
40309872 TATTTTATA
1 T-TTTTATA
40309881 GGACATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 14 0.58
9 5 0.21
10 5 0.21
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTATA
Found at i:40315915 original size:23 final size:23
Alignment explanation
Indices: 40315872--40315916 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
40315862 TATGGTAGTG
**
40315872 ATTATAAATAATGTTCTTTTTTA
1 ATTATAAATAATGTTAATTTTTA
40315895 ATTATAAATAAT-TGTAATTTTT
1 ATTATAAATAATGT-TAATTTTT
40315917 CATATGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (23 bp):
ATTATAAATAATGTTAATTTTTA
Found at i:40317536 original size:3 final size:3
Alignment explanation
Indices: 40317523--40317601 Score: 70
Period size: 3 Copynumber: 26.3 Consensus size: 3
40317513 TGTATTTTGG
** *
40317523 TTA TT- TTA TTA TTA AAA TATA TTA TTA TTA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
40317568 GTA TTA TTA TCA ATA TTA TTG TTA TTA TTG TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
40317602 ATTTCCATTT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
2 2 0.03
3 54 0.93
4 2 0.03
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:40317564 original size:18 final size:18
Alignment explanation
Indices: 40317543--40317595 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
40317533 ATTAAAATAT
40317543 ATTATTATTATTATTATC
1 ATTATTATTATTATTATC
*
40317561 ATTATTAGTATTATTATC
1 ATTATTATTATTATTATC
* *
40317579 AATATTATTGTTATTAT
1 ATTATTATTATTATTAT
40317596 TGTTATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (18 bp):
ATTATTATTATTATTATC
Found at i:40317843 original size:18 final size:18
Alignment explanation
Indices: 40317817--40317868 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
40317807 CATATCTTTG
*
40317817 ATTTATATATATATACTT
1 ATTTTTATATATATACTT
*
40317835 ATTTTTATATATACA-TT
1 ATTTTTATATATATACTT
*
40317852 ATAATTTATATATATAC
1 AT-TTTTATATATATAC
40317869 ATATATTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 4 0.14
18 24 0.86
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTTATATATATACTT
Found at i:40317933 original size:18 final size:18
Alignment explanation
Indices: 40317910--40317945 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40317900 TTTTAAATTT
*
40317910 TTTATAAGTATATATATA
1 TTTATAAGTACATATATA
*
40317928 TTTATACGTACATATATA
1 TTTATAAGTACATATATA
40317946 CTTACATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.47
Consensus pattern (18 bp):
TTTATAAGTACATATATA
Found at i:40318509 original size:35 final size:35
Alignment explanation
Indices: 40318463--40318534 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
40318453 GAAGGTCGTA
*
40318463 CTCTAACTTACTGGGTTTTAATTTTCACGATGAAT
1 CTCTAACTTACTGGGTTTCAATTTTCACGATGAAT
40318498 CTCTAACTTACTGGGTTTCAATTTTCACGATGAAT
1 CTCTAACTTACTGGGTTTCAATTTTCACGATGAAT
40318533 CT
1 CT
40318535 AAATACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (35 bp):
CTCTAACTTACTGGGTTTCAATTTTCACGATGAAT
Found at i:40320427 original size:16 final size:17
Alignment explanation
Indices: 40320392--40320433 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
40320382 ATTATATTTT
40320392 TAAAAATACTAATTACTA
1 TAAAAA-ACTAATTACTA
*
40320410 TAAAAAACT-ATTAGTA
1 TAAAAAACTAATTACTA
40320426 TAATAAAA
1 TAA-AAAA
40320434 ATAAATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 9 0.41
17 7 0.32
18 6 0.27
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (17 bp):
TAAAAAACTAATTACTA
Found at i:40326636 original size:24 final size:24
Alignment explanation
Indices: 40326609--40326654 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
40326599 TTATAAAAGA
* *
40326609 AAAAGAAAGAAAGAGAAATAATGT
1 AAAAGAAAAAAAAAGAAATAATGT
*
40326633 AAAAGAAAAAAAAAGAATTAAT
1 AAAAGAAAAAAAAAGAAATAAT
40326655 TTTTTTAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (24 bp):
AAAAGAAAAAAAAAGAAATAATGT
Found at i:40329412 original size:21 final size:21
Alignment explanation
Indices: 40329386--40329428 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
40329376 CTAAGGATAT
*
40329386 ATGGTCTCGGGTAATACCAGC
1 ATGGTCTCGGATAATACCAGC
*
40329407 ATGGTCTCGGATGATACCAGC
1 ATGGTCTCGGATAATACCAGC
40329428 A
1 A
40329429 GACTAGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (21 bp):
ATGGTCTCGGATAATACCAGC
Found at i:40330655 original size:26 final size:26
Alignment explanation
Indices: 40330601--40330681 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 26
40330591 ACATTTAAAA
*
40330601 AATATATTTTTATACTTTTTAAATAAATTT
1 AATA-ATTTTTA-A-TTTTAAAAT-AATTT
40330631 AATAATTTTTAATTTTAAAATAATTT
1 AATAATTTTTAATTTTAAAATAATTT
40330657 -ATAATTTTTTAAATTTTAAAA-AATT
1 AATAA-TTTTT-AATTTTAAAATAATT
40330682 AATTAAATGT
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
25 4 0.08
26 14 0.29
27 18 0.38
28 1 0.02
29 7 0.15
30 4 0.08
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (26 bp):
AATAATTTTTAATTTTAAAATAATTT
Found at i:40331103 original size:7 final size:7
Alignment explanation
Indices: 40331091--40331131 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
40331081 CTCAGAATGA
40331091 AAAAAAT
1 AAAAAAT
40331098 AAAAAAT
1 AAAAAAT
40331105 AAAAAAT
1 AAAAAAT
40331112 AAAAAAT
1 AAAAAAT
40331119 AAAAAAT
1 AAAAAAT
40331126 AAAAAA
1 AAAAAA
40331132 ACAAATATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:40338451 original size:29 final size:29
Alignment explanation
Indices: 40338402--40338457 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
40338392 ATAGAGACTT
*
40338402 GATTAAATTAGTCCATCTACTATTAAATG
1 GATTAAATTAGTCCATCTACTACTAAATG
* * *
40338431 GATTAATTTAGTCCTTGTACTACTAAA
1 GATTAAATTAGTCCATCTACTACTAAA
40338458 AAAGAATCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (29 bp):
GATTAAATTAGTCCATCTACTACTAAATG
Found at i:40339914 original size:24 final size:25
Alignment explanation
Indices: 40339868--40339914 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
40339858 ATATTTTTTA
40339868 ATTTCTTTTCAATTTTTTGAGAAAC
1 ATTTCTTTTCAATTTTTTGAGAAAC
*
40339893 ATTTGTTTT-AATGTTTTT-AGAA
1 ATTTCTTTTCAAT-TTTTTGAGAA
40339915 TTTTTGATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.55
Consensus pattern (25 bp):
ATTTCTTTTCAATTTTTTGAGAAAC
Found at i:40342266 original size:21 final size:22
Alignment explanation
Indices: 40342209--40342267 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 22
40342199 TTTTAAAAAA
40342209 ATATAAATAAATAAATATGTACAT
1 ATATAAATAAA-AAATA-GTACAT
* *
40342233 A-A-AAACAACAAATA-TACAT
1 ATATAAATAAAAAATAGTACAT
40342252 ATATAAATAAAAAATA
1 ATATAAATAAAAAATA
40342268 ATTACAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
19 6 0.21
20 1 0.03
21 15 0.52
22 5 0.17
23 1 0.03
24 1 0.03
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.25
Consensus pattern (22 bp):
ATATAAATAAAAAATAGTACAT
Found at i:40344080 original size:45 final size:45
Alignment explanation
Indices: 40344030--40344125 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
40344020 GTAACGATAG
** *
40344030 CAGTAACAATAACAGTATTCAACACACAAAGTGTTGAATCTGTAA
1 CAGTAACAATAACAGTATTCAACACACAAAGTGTCAAATCGGTAA
** *
40344075 CAGTAACGGTAACAGTATTCGACACACAAAGTGTCAAATCGGTAA
1 CAGTAACAATAACAGTATTCAACACACAAAGTGTCAAATCGGTAA
40344120 CAGTAA
1 CAGTAA
40344126 TAGTAGTTGG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.22
Consensus pattern (45 bp):
CAGTAACAATAACAGTATTCAACACACAAAGTGTCAAATCGGTAA
Found at i:40347473 original size:109 final size:109
Alignment explanation
Indices: 40347291--40347583 Score: 457
Period size: 109 Copynumber: 2.7 Consensus size: 109
40347281 ATATTTGTCA
* * * * **
40347291 ATTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGCACG-TTCCTCGAATTCCCAAACG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTTCAAACG
* * *
40347353 CAAAGCATTGCCTTATTTTGAAATTTTTGAAAGGATATTTAGCT
66 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTTAGCT
*
40347397 ATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTTCAAACG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTTCAAACG
40347462 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTTAGCT
66 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTTAGCT
40347506 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTTCAAACG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTTCAAACG
* *
40347571 CGAAATATTGCCT
66 CAAAACATTGCCT
40347584 CAATCAAAAA
Statistics
Matches: 171, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
106 13 0.08
108 26 0.15
109 132 0.77
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (109 bp):
ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTTCAAACG
CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTTAGCT
Found at i:40347667 original size:20 final size:20
Alignment explanation
Indices: 40347628--40347668 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
40347618 ATTTATATGC
*
40347628 ATAATGGAATAATAATCATG
1 ATAATGGAATAATAAACATG
40347648 ATAATGTGAATAA-AAACATG
1 ATAATG-GAATAATAAACATG
40347668 A
1 A
40347669 ACAAAAACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.27
Consensus pattern (20 bp):
ATAATGGAATAATAAACATG
Found at i:40348090 original size:2 final size:2
Alignment explanation
Indices: 40348023--40348071 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
40348013 AACATGAAAA
* **
40348023 AT AT AT GT AT AT AT GC AT -T AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40348063 AT AT AT AT A
1 AT AT AT AT A
40348072 AGTAAATATG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:40348187 original size:3 final size:3
Alignment explanation
Indices: 40348179--40348228 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
40348169 ATATAAAAGC
40348179 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40348227 AA
1 AA
40348229 CAACAACAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40352662 original size:32 final size:33
Alignment explanation
Indices: 40352617--40352711 Score: 95
Period size: 32 Copynumber: 2.9 Consensus size: 33
40352607 TCTTTAATTT
* * *
40352617 TTATGATTGTTTTATTATAAAATATATTATT-A
1 TTATTATTATTTTATTATAAAATAAATTATTGA
**
40352649 TTATTATTATTTTATTATATTATAAATTAAATTGA
1 TTATTATTATTTTATTATAAAATAAATT--ATTGA
* *
40352684 TTA-TATTATTATATTATGAAATAAATTA
1 TTATTATTATTTTATTATAAAATAAATTA
40352712 AGAAAAGACA
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
32 24 0.47
34 23 0.45
35 4 0.08
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (33 bp):
TTATTATTATTTTATTATAAAATAAATTATTGA
Found at i:40352677 original size:29 final size:30
Alignment explanation
Indices: 40352654--40352710 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
40352644 TATTATTATT
*
40352654 ATTATTTTATTATATTAT-AAATTAAATTG
1 ATTATATTATTATATTATGAAATTAAATTG
40352683 ATTATATTATTATATTATGAAA-TAAATT
1 ATTATATTATTATATTATGAAATTAAATT
40352711 AAGAAAAGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (30 bp):
ATTATATTATTATATTATGAAATTAAATTG
Found at i:40352691 original size:37 final size:37
Alignment explanation
Indices: 40352629--40352700 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
40352619 ATGATTGTTT
* *
40352629 TATTATAAAATATATTATTATTATTATTATTTTATTA
1 TATTATAAAATAAATTATTATTATTATTATATTATTA
*
40352666 TATTATAAATTAAATTGATTA-TATTATTATATTAT
1 TATTATAAAATAAATT-ATTATTATTATTATATTAT
40352701 GAAATAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 27 0.87
38 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (37 bp):
TATTATAAAATAAATTATTATTATTATTATATTATTA
Found at i:40354214 original size:38 final size:38
Alignment explanation
Indices: 40354112--40354244 Score: 117
Period size: 38 Copynumber: 3.4 Consensus size: 38
40354102 GACGTCGAGT
* * * * *
40354112 CGATGAGACACTAGGTGTCACTATTTTACTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA--ACTTTACTTCAGCTAG-TC
* * *
40354153 CGATGAGATACTGGGTATC-ACTTTACTTCAGCTAGGC
1 CGATGAGACACTGGGTGTCAACTTTACTTCAGCTAGTC
* *
40354190 CGATGAGACACTGGGTGTCAACTTTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTTTACTTC-AGCTAGTC
*
40354228 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
40354245 CCAATCTGGT
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
37 17 0.22
38 39 0.51
39 4 0.05
41 16 0.21
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.29
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCAACTTTACTTCAGCTAGTC
Found at i:40359207 original size:16 final size:16
Alignment explanation
Indices: 40359175--40359208 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40359165 AATATATCTC
*
40359175 AAAGAAAAGAGAGAAA
1 AAAGAAAAGAAAGAAA
*
40359191 AAAGAAAAGAAATAAA
1 AAAGAAAAGAAAGAAA
40359207 AA
1 AA
40359209 TAAAGAACAT
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:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (16 bp):
AAAGAAAAGAAAGAAA
Found at i:40360409 original size:41 final size:41
Alignment explanation
Indices: 40360358--40360445 Score: 160
Period size: 41 Copynumber: 2.2 Consensus size: 41
40360348 TAATCAAAAC
40360358 ATGA-ATATAACACATAAGTAATCATATTAAATCTTGAAAT
1 ATGACATATAACACATAAGTAATCATATTAAATCTTGAAAT
*
40360398 ATGACATATAACACATAATTAATCATATTAAATCTTGAAAT
1 ATGACATATAACACATAAGTAATCATATTAAATCTTGAAAT
40360439 ATGACAT
1 ATGACAT
40360446 GTGACTTATC
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 4 0.09
41 42 0.91
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (41 bp):
ATGACATATAACACATAAGTAATCATATTAAATCTTGAAAT
Found at i:40364377 original size:27 final size:27
Alignment explanation
Indices: 40364347--40364401 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
40364337 AATATAATAT
*
40364347 AATTA-TAAAATAATTAAATTTTACTTA
1 AATTATTAAAAT-ATTAAATTTTAATTA
* *
40364374 AATTATTAACATATTTAATTTTAATTA
1 AATTATTAAAATATTAAATTTTAATTA
40364401 A
1 A
40364402 TTTTATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (27 bp):
AATTATTAAAATATTAAATTTTAATTA
Found at i:40366883 original size:26 final size:26
Alignment explanation
Indices: 40366806--40366897 Score: 93
Period size: 26 Copynumber: 3.6 Consensus size: 26
40366796 AAGCTCATGT
* *
40366806 GAGCCATGTAAT-GGGAAGC-TCCGGA
1 GAGCCAT-TAATCGGGAAGCTTACGAA
* *
40366831 GAGCCATTAA-CGAGAAGCTTACAAA
1 GAGCCATTAATCGGGAAGCTTACGAA
*
40366856 GAGCCTTTAATCGGGAAGCTTACGAA
1 GAGCCATTAATCGGGAAGCTTACGAA
40366882 GAGCCA-TATATCGGGA
1 GAGCCATTA-ATCGGGA
40366898 CGCTCATAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
24 9 0.16
25 21 0.38
26 25 0.45
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.18
Consensus pattern (26 bp):
GAGCCATTAATCGGGAAGCTTACGAA
Found at i:40370005 original size:32 final size:31
Alignment explanation
Indices: 40369968--40370029 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
40369958 GGCCTATTTT
40369968 TATTTTAAAAAT-TTTAAAAAAATTAAAAAAAG
1 TATTTTAAAAATATTT--AAAAATTAAAAAAAG
*
40370000 TATTTTAAAAATATTTTAAAATTAAAAAAA
1 TATTTTAAAAATATTTAAAAATTAAAAAAA
40370030 TTAAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 13 0.46
32 12 0.43
33 3 0.11
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (31 bp):
TATTTTAAAAATATTTAAAAATTAAAAAAAG
Found at i:40370009 original size:12 final size:11
Alignment explanation
Indices: 40369968--40370020 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
40369958 GGCCTATTTT
40369968 TATTTT-AAAA
1 TATTTTAAAAA
40369978 -ATTTTAAAAA
1 TATTTTAAAAA
* **
40369988 AATTAAAAAAA
1 TATTTTAAAAA
40369999 GTATTTTAAAAA
1 -TATTTTAAAAA
40370011 TATTTTAAAA
1 TATTTTAAAA
40370021 TTAAAAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
9 5 0.14
10 4 0.11
11 18 0.51
12 8 0.23
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:40370053 original size:44 final size:40
Alignment explanation
Indices: 40369981--40370113 Score: 196
Period size: 44 Copynumber: 3.2 Consensus size: 40
40369971 TTTAAAAATT
40369981 TTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
40370021 TTAAAAAAATTAAAAAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAAATT----AAAAAAAGTATTTTAAAAATATTTTAAAA
* * *
40370065 TTAAAAAAATT-TAAAAAGTATGTAAAAAATATTTTAAAA
1 TTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
40370104 TTAAAAAAAT
1 TTAAAAAAAT
40370114 AAATATATTT
Statistics
Matches: 86, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
39 35 0.41
40 11 0.13
44 40 0.47
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (40 bp):
TTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
Found at i:40370093 original size:39 final size:39
Alignment explanation
Indices: 40370038--40370113 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
40370028 AATTAAAAAA
* *
40370038 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTT
1 AAAAAGTATGTAAAAAATATTTTAAAATTAAAAAAATTT
40370077 AAAAAGTATGTAAAAAATATTTTAAAATTAAAAAAAT
1 AAAAAGTATGTAAAAAATATTTTAAAATTAAAAAAAT
40370114 AAATATATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (39 bp):
AAAAAGTATGTAAAAAATATTTTAAAATTAAAAAAATTT
Found at i:40370369 original size:15 final size:15
Alignment explanation
Indices: 40370349--40370400 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
40370339 ACTACAAAAC
40370349 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
40370364 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
40370383 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
40370398 ATT
1 ATT
40370401 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:40370508 original size:22 final size:22
Alignment explanation
Indices: 40370480--40370523 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40370470 TGTTAAATAA
40370480 TTTATTAAAATAATAAATTATT
1 TTTATTAAAATAATAAATTATT
* * *
40370502 TTTATTATATTAATAATTTATT
1 TTTATTAAAATAATAAATTATT
40370524 ATATGACTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTATTAAAATAATAAATTATT
Found at i:40374403 original size:30 final size:31
Alignment explanation
Indices: 40374338--40374404 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
40374328 TTGTATTGGG
* * **
40374338 ACTAAAATTGATCAATTCAAAAAGTACAATG
1 ACTAAAATTGACCAATTCAAAAAGTAAAAAA
40374369 ACTAAAATTGACCAATT-AAAAA-TAAAAAAA
1 ACTAAAATTGACCAATTCAAAAAGT-AAAAAA
40374399 ACTAAA
1 ACTAAA
40374405 TCTATAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 1 0.03
30 14 0.45
31 16 0.52
ACGTcount: A:0.60, C:0.12, G:0.06, T:0.22
Consensus pattern (31 bp):
ACTAAAATTGACCAATTCAAAAAGTAAAAAA
Found at i:40377790 original size:2 final size:2
Alignment explanation
Indices: 40377783--40377824 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
40377773 CTACTAGTGT
*
40377783 AG AG AG AG AG AG AG AC AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
40377825 TTATTGTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40379169 original size:11 final size:12
Alignment explanation
Indices: 40379152--40379180 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
40379142 AATATTAAAA
40379152 ATAAAAAATTTT
1 ATAAAAAATTTT
40379164 -TAAAAAATTTT
1 ATAAAAAATTTT
40379175 ATAAAA
1 ATAAAA
40379181 TAAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATAAAAAATTTT
Found at i:40389025 original size:16 final size:16
Alignment explanation
Indices: 40388991--40389041 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
40388981 CAAAAACACG
40388991 AATA-AAAAAATAATT
1 AATATAAAAAATAATT
*
40389006 -ATATTAAAAATAATT
1 AATATAAAAAATAATT
*
40389021 AATATAAAAAATATTT
1 AATATAAAAAATAATT
40389037 AATAT
1 AATAT
40389042 GGATATAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 3 0.10
15 10 0.32
16 18 0.58
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATATAAAAAATAATT
Found at i:40390543 original size:25 final size:26
Alignment explanation
Indices: 40390502--40390563 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
40390492 ATTGAATCTA
*
40390502 AATTTTAAAAAATAAAA-AT-AAAAT
1 AATTTTTAAAAATAAAAGATAAAAAT
*
40390526 AATTTCTTAAAATTAAAAGTATAAAAAT
1 AATTT-TTAAAAATAAAAG-ATAAAAAT
40390554 AATTTTTAAA
1 AATTTTTAAA
40390564 TATACACATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 5 0.16
25 10 0.31
27 7 0.22
28 10 0.31
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (26 bp):
AATTTTTAAAAATAAAAGATAAAAAT
Found at i:40391910 original size:13 final size:13
Alignment explanation
Indices: 40391892--40391916 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40391882 CAATATATTT
40391892 ATTAATTAAAAAC
1 ATTAATTAAAAAC
40391905 ATTAATTAAAAA
1 ATTAATTAAAAA
40391917 TATAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:40392251 original size:14 final size:14
Alignment explanation
Indices: 40392232--40392258 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40392222 TTAAATTTGA
40392232 AATTTAATTTTTAT
1 AATTTAATTTTTAT
40392246 AATTTAATTTTTA
1 AATTTAATTTTTA
40392259 AAATAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AATTTAATTTTTAT
Found at i:40392822 original size:29 final size:30
Alignment explanation
Indices: 40392767--40392824 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
40392757 ACTTGGATTT
* *
40392767 TTAAAATTGAAAAGTAGAGTGACTAAATTC
1 TTAAAAATGAAAAGTAGAGAGACTAAATTC
* *
40392797 TTAAAAAT-AAAAGTAGGGAGATTAAATT
1 TTAAAAATGAAAAGTAGAGAGACTAAATT
40392825 TCAAATTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.17, T:0.29
Consensus pattern (30 bp):
TTAAAAATGAAAAGTAGAGAGACTAAATTC
Found at i:40394410 original size:13 final size:13
Alignment explanation
Indices: 40394394--40394420 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40394384 TTTTTACAAC
40394394 GTTTTTTTTTTTG
1 GTTTTTTTTTTTG
40394407 GTTTTTTTTTTTG
1 GTTTTTTTTTTTG
40394420 G
1 G
40394421 GGGGGTGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (13 bp):
GTTTTTTTTTTTG
Found at i:40403229 original size:14 final size:14
Alignment explanation
Indices: 40403207--40403239 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
40403197 AAATTACTCA
*
40403207 TTTAAATTTTTAAT
1 TTTATATTTTTAAT
40403221 TTTATATTTTTAAT
1 TTTATATTTTTAAT
40403235 TTTAT
1 TTTAT
40403240 TTTATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATATTTTTAAT
Found at i:40407001 original size:27 final size:27
Alignment explanation
Indices: 40406953--40407010 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
40406943 AAACCCGGTG
* *
40406953 CAGCAGCAGCCACTCCAGGGTTAAACC
1 CAGCAGCAGCAACACCAGGGTTAAACC
* *
40406980 CAGCAGCAGCAACACCATGGTTGAACC
1 CAGCAGCAGCAACACCAGGGTTAAACC
40407007 CAGC
1 CAGC
40407011 TCCAGCAGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.36, G:0.22, T:0.10
Consensus pattern (27 bp):
CAGCAGCAGCAACACCAGGGTTAAACC
Found at i:40407948 original size:3 final size:3
Alignment explanation
Indices: 40407942--40407976 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
40407932 CTCGTCATCT
40407942 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
40407977 TTCTTCAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
TCC
Found at i:40408009 original size:30 final size:30
Alignment explanation
Indices: 40407975--40408032 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
40407965 CTCCTCCTCC
*
40407975 TCTTCTTCAAATTCCTCTTCTACTTCTACT
1 TCTTCTTCAAATTCCTCTTCCACTTCTACT
* *
40408005 TCTTCTTCGATTTCCTCTTCCACTTCTA
1 TCTTCTTCAAATTCCTCTTCCACTTCTA
40408033 GTATTTGCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.14, C:0.34, G:0.02, T:0.50
Consensus pattern (30 bp):
TCTTCTTCAAATTCCTCTTCCACTTCTACT
Found at i:40411020 original size:15 final size:15
Alignment explanation
Indices: 40411002--40411057 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
40410992 TAACACATGA
*
40411002 AATAATATGTACGGT
1 AATAAAATGTACGGT
* *
40411017 AATAAAATGTA-TGA
1 AATAAAATGTACGGT
* *
40411031 AATAATATGTATGGT
1 AATAAAATGTACGGT
40411046 AATAAAATGTAC
1 AATAAAATGTAC
40411058 AAAAACATTA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
14 11 0.34
15 21 0.66
ACGTcount: A:0.48, C:0.04, G:0.16, T:0.32
Consensus pattern (15 bp):
AATAAAATGTACGGT
Found at i:40411032 original size:29 final size:29
Alignment explanation
Indices: 40410998--40411056 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
40410988 ATAATAACAC
40410998 ATGAAATAATATGTACGGTAATAAAATGT
1 ATGAAATAATATGTACGGTAATAAAATGT
*
40411027 ATGAAATAATATGTATGGTAATAAAATGT
1 ATGAAATAATATGTACGGTAATAAAATGT
40411056 A
1 A
40411057 CAAAAACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.49, C:0.02, G:0.17, T:0.32
Consensus pattern (29 bp):
ATGAAATAATATGTACGGTAATAAAATGT
Found at i:40411040 original size:14 final size:14
Alignment explanation
Indices: 40410998--40411043 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
40410988 ATAATAACAC
40410998 ATGAAATAATATGT
1 ATGAAATAATATGT
* * *
40411012 ACGGTAATAAAATGT
1 A-TGAAATAATATGT
40411027 ATGAAATAATATGT
1 ATGAAATAATATGT
40411041 ATG
1 ATG
40411044 GTAATAAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.48, C:0.02, G:0.17, T:0.33
Consensus pattern (14 bp):
ATGAAATAATATGT
Found at i:40424991 original size:2 final size:2
Alignment explanation
Indices: 40424984--40425015 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40424974 CTTCACTTAC
40424984 AT AT AT 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 AT AT AT
40425016 GTGTGAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40430351 original size:14 final size:15
Alignment explanation
Indices: 40430329--40430405 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
40430319 CAATCAAACA
40430329 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
40430343 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
40430358 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
40430378 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
40430392 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
40430406 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:40430370 original size:20 final size:20
Alignment explanation
Indices: 40430345--40430384 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40430335 AATATTTTCC
*
40430345 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
40430365 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
40430385 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:40430390 original size:34 final size:35
Alignment explanation
Indices: 40430333--40430399 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
40430323 CAAACACCAG
*
40430333 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
40430368 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
40430400 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:40430452 original size:8 final size:8
Alignment explanation
Indices: 40430439--40430504 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 8
40430429 GTTAAAGTAT
40430439 ATATTATA
1 ATATTATA
40430447 ATATTATA
1 ATATTATA
40430455 ATATTAT-
1 ATATTATA
* *
40430462 TTCTTA-A
1 ATATTATA
*
40430469 TTATTA-A
1 ATATTATA
40430476 ATATATATA
1 ATAT-TATA
40430485 TCATATTAT-
1 --ATATTATA
40430494 ATATTATA
1 ATATTATA
40430502 ATA
1 ATA
40430505 AGTAAATATA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
7 20 0.42
8 20 0.42
9 1 0.02
10 3 0.06
11 4 0.08
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (8 bp):
ATATTATA
Found at i:40430545 original size:13 final size:13
Alignment explanation
Indices: 40430522--40430558 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
40430512 ATAATAAATA
40430522 AAAGCAACAAAAAG
1 AAAG-AACAAAAAG
40430536 AAAGAACAAAAAG
1 AAAGAACAAAAAG
40430549 AAAG-ACAAAA
1 AAAGAACAAAA
40430559 GGTTAAACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 6 0.26
13 13 0.57
14 4 0.17
ACGTcount: A:0.76, C:0.11, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAGAACAAAAAG
Found at i:40430556 original size:12 final size:12
Alignment explanation
Indices: 40430528--40430600 Score: 55
Period size: 12 Copynumber: 6.1 Consensus size: 12
40430518 AATAAAAGCA
40430528 ACAAAAAGAAAG
1 ACAAAAAGAAAG
40430540 AACAAAAAGAAAG
1 -ACAAAAAGAAAG
* *
40430553 ACAAAAGGTTAA-
1 ACAAAAAG-AAAG
*
40430565 ACGAAATAGAAAG
1 AC-AAAAAGAAAG
40430578 --AAAAAGAAAG
1 ACAAAAAGAAAG
40430588 A-AAAAGAGAAAG
1 ACAAAA-AGAAAG
40430600 A
1 A
40430601 GAAAGAAGGA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
10 9 0.18
11 4 0.08
12 18 0.37
13 18 0.37
ACGTcount: A:0.71, C:0.05, G:0.19, T:0.04
Consensus pattern (12 bp):
ACAAAAAGAAAG
Found at i:40430585 original size:10 final size:10
Alignment explanation
Indices: 40430543--40430607 Score: 53
Period size: 10 Copynumber: 6.2 Consensus size: 10
40430533 AAGAAAGAAC
40430543 AAAAAGAAAG
1 AAAAAGAAAG
40430553 ACAAAAGGTTAAACG
1 A-AAAA-G--AAA-G
*
40430568 AAATAGAAAG
1 AAAAAGAAAG
40430578 AAAAAGAAAG
1 AAAAAGAAAG
40430588 AAAAAG--AG
1 AAAAAGAAAG
*
40430596 AAAGAGAAAG
1 AAAAAGAAAG
40430606 AA
1 AA
40430608 GGAAAGGAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
8 7 0.16
10 21 0.47
11 7 0.16
12 1 0.02
13 1 0.02
14 6 0.13
15 2 0.04
ACGTcount: A:0.71, C:0.03, G:0.22, T:0.05
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:40430600 original size:22 final size:21
Alignment explanation
Indices: 40430572--40430621 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
40430562 TAAACGAAAT
40430572 AGAAAGAAAAAGAAAGAAAAAG
1 AGAAAGAAAAAG-AAGAAAAAG
* * *
40430594 AGAAAGAGAAAGAAGGAAAGG
1 AGAAAGAAAAAGAAGAAAAAG
40430615 AGAAAGA
1 AGAAAGA
40430622 TACAAAGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (21 bp):
AGAAAGAAAAAGAAGAAAAAG
Found at i:40431562 original size:40 final size:39
Alignment explanation
Indices: 40431440--40431577 Score: 111
Period size: 40 Copynumber: 3.5 Consensus size: 39
40431430 CTTCGAGTCT
* * * *
40431440 ATGAGACACTAGGTGTCAATTTACTACTTCTGATTAATTCG
1 ATGAGACACTGGGTGTCAAATTATTACTTC-GATT-ATCCG
* * * * *
40431481 ATAAGGCACTGGGTG-CCAA-T-TTACTTCGGTTTAACCG
1 ATGAGACACTGGGTGTCAAATTATTACTTC-GATTATCCG
*
40431518 ATGAGACACTGGGTGTCAAATTATTACTTCGAATTATCCA
1 ATGAGACACTGGGTGTCAAATTATTACTTCG-ATTATCCG
* *
40431558 ATGAGGCACTGGGTGCCAAA
1 ATGAGACACTGGGTGTCAAA
40431578 CTAGTATGTT
Statistics
Matches: 75, Mismatches: 18, Indels: 9
0.74 0.18 0.09
Matches are distributed among these distances:
37 16 0.21
38 12 0.16
39 3 0.04
40 32 0.43
41 12 0.16
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (39 bp):
ATGAGACACTGGGTGTCAAATTATTACTTCGATTATCCG
Found at i:40440059 original size:24 final size:24
Alignment explanation
Indices: 40440032--40440082 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
40440022 CATACTTTAA
40440032 ATTGGGATAATTTAATCCATCTCC
1 ATTGGGATAATTTAATCCATCTCC
40440056 ATTGGGATAATTTAATCCATCTCC
1 ATTGGGATAATTTAATCCATCTCC
40440080 ATT
1 ATT
40440083 TATAATGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (24 bp):
ATTGGGATAATTTAATCCATCTCC
Found at i:40444230 original size:18 final size:18
Alignment explanation
Indices: 40444207--40444241 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40444197 TTACATATAA
40444207 AAATAATAATTGTATTTG
1 AAATAATAATTGTATTTG
* *
40444225 AAATAATTATTTTATTT
1 AAATAATAATTGTATTT
40444242 TATAATATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
AAATAATAATTGTATTTG
Found at i:40445387 original size:16 final size:16
Alignment explanation
Indices: 40445362--40445401 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
40445352 GAAATTTTAT
*
40445362 ATTTTCCACCC-TTCA
1 ATTTTTCACCCTTTCA
40445377 AGTTTTTCACCCTTTCA
1 A-TTTTTCACCCTTTCA
40445394 ATTTTTCA
1 ATTTTTCA
40445402 TATTTCTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 16 0.73
17 5 0.23
ACGTcount: A:0.20, C:0.30, G:0.03, T:0.47
Consensus pattern (16 bp):
ATTTTTCACCCTTTCA
Found at i:40447262 original size:50 final size:50
Alignment explanation
Indices: 40447182--40447424 Score: 233
Period size: 50 Copynumber: 4.9 Consensus size: 50
40447172 CATTTGGGTA
*
40447182 AAGAAGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGAT
1 AAGAAGTCTCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGAT
* * *
40447232 AAGAGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAAGTCTCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGAT
* * * ** * * * *
40447282 GAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCAATAT
1 AAGAAGTCTCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGAT
* * * * *
40447332 GAGAACTCTCATGTAAGACCATATCTGGGATATGACATTGGCAGTAC-A-A-
1 AAGAAGTCTCATGTAAGACCATGTCTGGGACATGGCATTGGCA-T-CGAGAT
* * * *
40447381 AA-AACATCTCATGTCAGACCATGTCTGGGACATGACTTTGGCAT
1 AAGAA-GTCTCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
40447425 GTTATTATCA
Statistics
Matches: 164, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
48 3 0.02
49 34 0.21
50 125 0.76
51 1 0.01
52 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (50 bp):
AAGAAGTCTCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGAT
Found at i:40457594 original size:29 final size:29
Alignment explanation
Indices: 40457552--40457611 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
40457542 TTTAGTTGGG
40457552 ATCCAACATCTAAATCTAATCACAAGTGC
1 ATCCAACATCTAAATCTAATCACAAGTGC
40457581 ATCCAACATCTAAATCTAATCACAAGTGC
1 ATCCAACATCTAAATCTAATCACAAGTGC
40457610 AT
1 AT
40457612 TATTGTTTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.42, C:0.27, G:0.07, T:0.25
Consensus pattern (29 bp):
ATCCAACATCTAAATCTAATCACAAGTGC
Found at i:40460861 original size:14 final size:15
Alignment explanation
Indices: 40460844--40460872 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40460834 TGGTTTCCAA
40460844 AATAAATT-GAATTT
1 AATAAATTCGAATTT
40460858 AATAAATTCGAATTT
1 AATAAATTCGAATTT
40460873 GTAAAAGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.41
Consensus pattern (15 bp):
AATAAATTCGAATTT
Found at i:40464102 original size:3 final size:3
Alignment explanation
Indices: 40464094--40464139 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
40464084 AAATTGAGAA
40464094 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
40464140 GTAGGGACTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:40467642 original size:19 final size:19
Alignment explanation
Indices: 40467615--40467661 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
40467605 TTAAAAAAAC
40467615 AAAAA-ATTTTATA-TTCAG
1 AAAAATATTTTA-ACTTCAG
40467633 AAAAATATTTTAACTTCAG
1 AAAAATATTTTAACTTCAG
*
40467652 -ATAATATTTT
1 AAAAATATTTT
40467662 CATCGAAAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (19 bp):
AAAAATATTTTAACTTCAG
Found at i:40467902 original size:2 final size:2
Alignment explanation
Indices: 40467895--40467927 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
40467885 AAATAAATAA
40467895 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40467928 GTACATGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40469550 original size:50 final size:50
Alignment explanation
Indices: 40469456--40470059 Score: 317
Period size: 50 Copynumber: 12.1 Consensus size: 50
40469446 AATTTGTTTA
* * * * * * *
40469456 ACTGCAATGTCAGGGAAACAAGATTCGCTGTCGTGACTTTAATCTATTCT
1 ACTGCACTGCCAGGGAAATAAGATTCGCCGTTGTGGCTTCAATCTATTCT
* * *
40469506 ACTGCACCGCCAGGGAGATAAGATTCGCCGTTATGGCTTCAATCTATT-T
1 ACTGCACTGCCAGGGAAATAAGATTCGCCGTTGTGGCTTCAATCTATTCT
* * * * * * * * * * *
40469555 AATTGCAATGTC-GAGAAACAAGATCCGCCATCGTAGCTTCAATCTGTTCA
1 -ACTGCACTGCCAGGGAAATAAGATTCGCCGTTGTGGCTTCAATCTATTCT
* * * *
40469605 ACTACACTGCCA-AGAAAGTAAGATTTGCCGTTGTGGCTTCAATCT-TTTT
1 ACTGCACTGCCAGGGAAA-TAAGATTCGCCGTTGTGGCTTCAATCTATTCT
* * * * * * * *
40469654 AATTGCAATGTCGGGGAAACAAGATTCACCGTCGTGGCTTCAATCTATTCC
1 -ACTGCACTGCCAGGGAAATAAGATTCGCCGTTGTGGCTTCAATCTATTCT
* * * *
40469705 ACTACACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCT-TTTT
1 ACTGCACTGCCAGGGAAATAAGATTCGCCGTTGTGGCTTCAATCTATTCT
* * * * ** * * * *
40469754 AATTGCAATGTCGGGGAAACCAGATCCGCCATTGTAGCTTCAATCTATTCC
1 -ACTGCACTGCCAGGGAAATAAGATTCGCCGTTGTGGCTTCAATCTATTCT
* * *
40469805 ACTGCACCGCCA-GGAAAGTAAGATTCGCTGTTGTGGCTTCAATCT-TTTT
1 ACTGCACTGCCAGGGAAA-TAAGATTCGCCGTTGTGGCTTCAATCTATTCT
* * * ** * * * * *
40469854 CATTGCAATGCCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCC
1 -ACTGCACTGCCAGGGAAATAAGATTCGCCGTTGTGGCTTCAATCTATTCT
* * * * * * **
40469905 ACTGCACCGCTAAGGAAGTAAGATTCACCGTTGTGGCTTCAATAT-TTAA
1 ACTGCACTGCCAGGGAAATAAGATTCGCCGTTGTGGCTTCAATCTATTCT
* * * * * * * * * *
40469954 ATTGCAATGTCGGGGAAACT-AGATCCGCCATCGTAGCTTCAATCTGTTCC
1 ACTGCACTGCCAGGGAAA-TAAGATTCGCCGTTGTGGCTTCAATCTATTCT
* * * * * * *
40470004 ACTGTACCGCCAGGGAAGTAAGATTCGCCGCTGTGGCTTTATTCTATTCC
1 ACTGCACTGCCAGGGAAATAAGATTCGCCGTTGTGGCTTCAATCTATTCT
40470054 ACTGCA
1 ACTGCA
40470060 ACGTCAAGGA
Statistics
Matches: 391, Mismatches: 147, Indels: 32
0.69 0.26 0.06
Matches are distributed among these distances:
49 83 0.21
50 293 0.75
51 15 0.04
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (50 bp):
ACTGCACTGCCAGGGAAATAAGATTCGCCGTTGTGGCTTCAATCTATTCT
Found at i:40469728 original size:100 final size:100
Alignment explanation
Indices: 40469442--40470042 Score: 780
Period size: 100 Copynumber: 6.0 Consensus size: 100
40469432 GGATTATTTT
* * * ** *
40469442 CTTCAAT-TTGTTTAACTGCAATGTCAGGGAAACAAGATTCGCTGTCGT-GACTTTAATCTATTC
1 CTTCAATCTT-TTTAATTGCAATGTCGGGGAAACAAGATCCGCCATCGTAG-CTTCAATCTATTC
* *
40469505 TACTGCACCGCCAGGG-AGATAAGATTCGCCGTTATGG
64 CACTGCACCGCCAGGGAAG-TAAGATTCGCCGTTGTGG
* * * *
40469542 CTTCAATCTATTTAATTGCAATGTC-GAGAAACAAGATCCGCCATCGTAGCTTCAATCTGTTCAA
1 CTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGATCCGCCATCGTAGCTTCAATCTATTCCA
* * * * *
40469606 CTACACTGCCAAGAAAGTAAGATTTGCCGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
* * * *
40469641 CTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGATTCACCGTCGTGGCTTCAATCTATTCCA
1 CTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGATCCGCCATCGTAGCTTCAATCTATTCCA
*
40469706 CTACACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
* *
40469741 CTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATCCGCCATTGTAGCTTCAATCTATTCCA
1 CTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGATCCGCCATCGTAGCTTCAATCTATTCCA
* *
40469806 CTGCACCGCCAGGAAAGTAAGATTCGCTGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
* * * * *
40469841 CTTCAATCTTTTTCATTGCAATGCCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGATCCGCCATCGTAGCTTCAATCTATTCCA
* * *
40469906 CTGCACCGCTAAGGAAGTAAGATTCACCGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
* * * *
40469941 CTTCAAT-ATTTAAATTGCAATGTCGGGGAAACTAGATCCGCCATCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGATCCGCCATCGTAGCTTCAATCTATTCCA
* *
40470005 CTGTACCGCCAGGGAAGTAAGATTCGCCGCTGTGG
66 CTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
40470040 CTT
1 CTT
40470043 TATTCTATTC
Statistics
Matches: 440, Mismatches: 57, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
99 164 0.37
100 275 0.62
101 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (100 bp):
CTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGATCCGCCATCGTAGCTTCAATCTATTCCA
CTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
Found at i:40470176 original size:88 final size:88
Alignment explanation
Indices: 40470067--40470254 Score: 259
Period size: 88 Copynumber: 2.1 Consensus size: 88
40470057 GCAACGTCAA
* * * * * *
40470067 GGAGATAAGACTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCCATTTT
1 GGAGATAAGGCTGGTATCTTCGATCTACTTCGCTGCCAATACAGAAAGACAAGATCTGCCATTTT
* * *
40470132 CAACCTACTCTATTGCTGCTCAT
66 CAACCTACTCTACTGCTACTCAG
* * * *
40470155 GGAGACAAGGCTGGTATCTTCGATCTACTTCGCTGCCAATGCATAAAGACAAGATCTGCTATTTT
1 GGAGATAAGGCTGGTATCTTCGATCTACTTCGCTGCCAATACAGAAAGACAAGATCTGCCATTTT
40470220 CAACCTACTCTACTGCTACTCAG
66 CAACCTACTCTACTGCTACTCAG
40470243 GGAGATAAGGCT
1 GGAGATAAGGCT
40470255 TTATGGTTTC
Statistics
Matches: 86, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (88 bp):
GGAGATAAGGCTGGTATCTTCGATCTACTTCGCTGCCAATACAGAAAGACAAGATCTGCCATTTT
CAACCTACTCTACTGCTACTCAG
Found at i:40471520 original size:17 final size:17
Alignment explanation
Indices: 40471498--40471535 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
40471488 ACTTTTTTCA
**
40471498 TTTTCATTTTTTCATTT
1 TTTTCATTTCATCATTT
40471515 TTTTCATTTCATCATTT
1 TTTTCATTTCATCATTT
40471532 TTTT
1 TTTT
40471536 ACGACTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTCATTTCATCATTT
Found at i:40478947 original size:5 final size:5
Alignment explanation
Indices: 40478939--40478978 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
40478929 CCAATAAAGG
* *
40478939 ATAAA ATAAA ATAAA ATAAA GTAAC ATAAA ATAAA A-AAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
40478979 CGAGTCAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:40479108 original size:2 final size:2
Alignment explanation
Indices: 40479103--40479144 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
40479093 AAAAATTTAT
40479103 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40479145 ATGCACATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40479338 original size:36 final size:35
Alignment explanation
Indices: 40479292--40479389 Score: 87
Period size: 36 Copynumber: 2.9 Consensus size: 35
40479282 TACAAAATAT
* **
40479292 AAAAAATGTATAAATATAATATATAGATAAACTATG
1 AAAATATGTATAAATATAA-ATATAGATAAAAAATG
** *
40479328 AAAATATGTATGTATATAAATATATATAAAAAATG
1 AAAATATGTATAAATATAAATATAGATAAAAAATG
* *
40479363 -AAATA--TATATATATAAATA-AAATAAAA
1 AAAATATGTATAAATATAAATATAGATAAAA
40479390 TATATGTATA
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
31 7 0.13
32 13 0.24
34 5 0.09
35 13 0.24
36 16 0.30
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.32
Consensus pattern (35 bp):
AAAATATGTATAAATATAAATATAGATAAAAAATG
Found at i:40479374 original size:24 final size:24
Alignment explanation
Indices: 40479341--40479448 Score: 89
Period size: 24 Copynumber: 4.5 Consensus size: 24
40479331 ATATGTATGT
*
40479341 ATATAAATATATATAAAAAATGAA
1 ATATATATATATATAAAAAATGAA
*
40479365 ATATATATATATA-AATAAAATAAA
1 ATATATATATATATAA-AAAATGAA
* * *
40479389 ATATATGTATATATAATATA-GAA
1 ATATATATATATATAAAAAATGAA
*
40479412 A-ATATATATGCAT-TATAAAATGTAA
1 ATATATATAT--ATATAAAAAATG-AA
*
40479437 ATGTATATATAT
1 ATATATATATAT
40479449 TCATGTATAT
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
22 7 0.11
23 9 0.14
24 38 0.58
25 5 0.08
26 7 0.11
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (24 bp):
ATATATATATATATAAAAAATGAA
Found at i:40484425 original size:79 final size:80
Alignment explanation
Indices: 40484313--40484470 Score: 176
Period size: 79 Copynumber: 2.0 Consensus size: 80
40484303 AAATTCATGC
* * * * ** * *
40484313 TTATATATATATATATATTATAAATTGATATATAATAACGGCCTTTCCATAACATGCAAAATTTT
1 TTATATATAAATATATATTATAAATAGACATATAACAACAACCTGTCCATAACATACAAAATTTT
40484378 AAC-AGACAAATAGAA
66 -ACTAGACAAATAGAA
* * * *
40484393 TTAT-TATAAATATATATTATAGATAGGCATATAACAACAATCTGTCCATAATATACAAAATTTT
1 TTATATATAAATATATATTATAAATAGACATATAACAACAACCTGTCCATAACATACAAAATTTT
*
40484457 ACTAGATAAATAGA
66 ACTAGACAAATAGA
40484471 GTTTTAAATT
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
78 2 0.03
79 58 0.91
80 4 0.06
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.35
Consensus pattern (80 bp):
TTATATATAAATATATATTATAAATAGACATATAACAACAACCTGTCCATAACATACAAAATTTT
ACTAGACAAATAGAA
Found at i:40485359 original size:22 final size:21
Alignment explanation
Indices: 40485334--40485376 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
40485324 TTGTATAATA
40485334 ACATATT-TAGTCCTCAATACTT
1 ACATATTCTA-TCCTCAA-ACTT
40485356 ACATATTCTATCCTCAAACTT
1 ACATATTCTATCCTCAAACTT
40485377 GTTAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 14 0.70
23 2 0.10
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.40
Consensus pattern (21 bp):
ACATATTCTATCCTCAAACTT
Found at i:40486822 original size:31 final size:31
Alignment explanation
Indices: 40486784--40486861 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
40486774 AAGAATAACA
40486784 TGATTTGTTTAATTACGTACAACCATTATTT
1 TGATTTGTTTAATTACGTACAACCATTATTT
40486815 TGATTTGTTTAATTACGTACAACCATTATTT
1 TGATTTGTTTAATTACGTACAACCATTATTT
*
40486846 TGATTTTTTTTAATTA
1 TGA-TTTGTTTAATTA
40486862 GATGGATTGA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 34 0.76
32 11 0.24
ACGTcount: A:0.28, C:0.10, G:0.09, T:0.53
Consensus pattern (31 bp):
TGATTTGTTTAATTACGTACAACCATTATTT
Found at i:40487099 original size:16 final size:17
Alignment explanation
Indices: 40487080--40487115 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
40487070 TAATTATATA
40487080 ATTTC-AAATTTAAAAT
1 ATTTCAAAATTTAAAAT
*
40487096 ATTTCAAAATTTAAATT
1 ATTTCAAAATTTAAAAT
40487113 ATT
1 ATT
40487116 AACATTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTCAAAATTTAAAAT
Found at i:40490099 original size:3 final size:3
Alignment explanation
Indices: 40490091--40490131 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
40490081 CGCCCAATTA
*
40490091 TCT TCT TCT TCT TCT TCT TAT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
40490132 ATTTTTCTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:40491313 original size:7 final size:7
Alignment explanation
Indices: 40491301--40491341 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
40491291 GATAAGACTG
40491301 TTAGTGA
1 TTAGTGA
40491308 TTAGTGA
1 TTAGTGA
40491315 TTAGTGA
1 TTAGTGA
40491322 TTAGTGA
1 TTAGTGA
*
40491329 TTAGTTA
1 TTAGTGA
40491336 TTAGTG
1 TTAGTG
40491342 GGGGAGTGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (7 bp):
TTAGTGA
Found at i:40491375 original size:5 final size:5
Alignment explanation
Indices: 40491365--40491397 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
40491355 TATGTATAGT
40491365 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
40491398 TTCCCCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:40492560 original size:26 final size:26
Alignment explanation
Indices: 40492531--40492580 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
40492521 TAGGGGATAG
*
40492531 GATTCTGTATGTCTA-AACTGTTATTT
1 GATTCTG-ATATCTATAACTGTTATTT
*
40492557 GATTCTGATATCTATTACTGTTAT
1 GATTCTGATATCTATAACTGTTAT
40492581 GGACTTAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.50
Consensus pattern (26 bp):
GATTCTGATATCTATAACTGTTATTT
Found at i:40494546 original size:33 final size:33
Alignment explanation
Indices: 40494509--40494576 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
40494499 GTACACAAGG
40494509 ACGTATCATCAAAATTAACGGAGTACGAAACAT
1 ACGTATCATCAAAATTAACGGAGTACGAAACAT
*
40494542 ACGTATCATCAAAATTAACGGAGTACGGAACAT
1 ACGTATCATCAAAATTAACGGAGTACGAAACAT
40494575 AC
1 AC
40494577 CTGGACAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (33 bp):
ACGTATCATCAAAATTAACGGAGTACGAAACAT
Found at i:40502380 original size:22 final size:22
Alignment explanation
Indices: 40502328--40502382 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
40502318 AACAGTTCAG
*
40502328 ACAAGATGCAAAACATATCAGAT
1 ACAA-ATGCAGAACATATCAGAT
**
40502351 ACGGATGCAGAACATATCAGA-
1 ACAAATGCAGAACATATCAGAT
40502372 ATCAAATGCAG
1 A-CAAATGCAG
40502383 TTTCCTACCC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 1 0.04
22 23 0.88
23 2 0.08
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.16
Consensus pattern (22 bp):
ACAAATGCAGAACATATCAGAT
Found at i:40508224 original size:31 final size:31
Alignment explanation
Indices: 40508187--40508245 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
40508177 GAAAGTAATC
40508187 ACTGAACTAATCAAAAGTTTACATTTAAGTA
1 ACTGAACTAATCAAAAGTTTACATTTAAGTA
* *
40508218 ACTGAACTAATCAAAATTTTTCATTTAA
1 ACTGAACTAATCAAAAGTTTACATTTAA
40508246 ATCATTGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.36
Consensus pattern (31 bp):
ACTGAACTAATCAAAAGTTTACATTTAAGTA
Found at i:40510395 original size:21 final size:21
Alignment explanation
Indices: 40510371--40510411 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
40510361 GAGTTGATTT
40510371 TTAGTGACTCGTGACACGAGA
1 TTAGTGACTCGTGACACGAGA
40510392 TTAGTGACTCGTGACACGAG
1 TTAGTGACTCGTGACACGAG
40510412 CTCAGTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (21 bp):
TTAGTGACTCGTGACACGAGA
Found at i:40512231 original size:85 final size:85
Alignment explanation
Indices: 40512072--40512231 Score: 230
Period size: 85 Copynumber: 1.9 Consensus size: 85
40512062 GGGTGACTCG
* *
40512072 TTTCACGAGCAGCCAAGGCATCGCGAAATGCCTCACCACCTTGTGAAGTGACATGCCTCACCACT
1 TTTCACGAGCAGCCAAGGCATAGCGAAATGCCTCACCACCTTGCGAAGTGACATGCCTCACCACT
**
40512137 TCATGGGATCGCTTGATCCA
66 TCACAGGATCGCTTGATCCA
* * * * * *
40512157 TTTCACGAGCAGTCAGGGCCTAGCGAAATGCCTCACCAGCTTGCGAAGTGTCATGCCTCATCACT
1 TTTCACGAGCAGCCAAGGCATAGCGAAATGCCTCACCACCTTGCGAAGTGACATGCCTCACCACT
40512222 TCACAGGATC
66 TCACAGGATC
40512232 ACTTCGCCCA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
85 65 1.00
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.23
Consensus pattern (85 bp):
TTTCACGAGCAGCCAAGGCATAGCGAAATGCCTCACCACCTTGCGAAGTGACATGCCTCACCACT
TCACAGGATCGCTTGATCCA
Found at i:40515423 original size:21 final size:21
Alignment explanation
Indices: 40515355--40515555 Score: 96
Period size: 21 Copynumber: 9.5 Consensus size: 21
40515345 AAGCTCGAAG
* *
40515355 GCTGAACAGAAGCTCATGAGA
1 GCTGAACGGAAGCTCATAAGA
* * * * * *
40515376 ACTAAACAGAAACCCATAAGG
1 GCTGAACGGAAGCTCATAAGA
* *
40515397 GTTGAACGGAAGCTCGTAAGA
1 GCTGAACGGAAGCTCATAAGA
* * * *
40515418 GCTGAACAGAAACCCCATAAGG
1 GCTGAAC-GGAAGCTCATAAGA
* *
40515440 GTTGAACGGAAGCTCGTAAGA
1 GCTGAACGGAAGCTCATAAGA
* * * *
40515461 GCTGAACAGAAACCCATAAGG
1 GCTGAACGGAAGCTCATAAGA
* * * *
40515482 GTTAAACAGAAGCTCAAAAGA
1 GCTGAACGGAAGCTCATAAGA
* * *
40515503 GCTGAATGGAAACTCATATGA
1 GCTGAACGGAAGCTCATAAGA
* * * * *
40515524 GTTAAACAGAAGCTCGTGAGA
1 GCTGAACGGAAGCTCATAAGA
*
40515545 GCTAAACGGAA
1 GCTGAACGGAA
40515556 AGTAAACACG
Statistics
Matches: 124, Mismatches: 55, Indels: 2
0.69 0.30 0.01
Matches are distributed among these distances:
21 109 0.88
22 15 0.12
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.15
Consensus pattern (21 bp):
GCTGAACGGAAGCTCATAAGA
Found at i:40515426 original size:42 final size:42
Alignment explanation
Indices: 40515357--40515556 Score: 229
Period size: 42 Copynumber: 4.7 Consensus size: 42
40515347 GCTCGAAGGC
* * * *
40515357 TGAACAGAAGCTCATGAGAACTAAACAGAAACCCATAAGGGT
1 TGAACAGAAGCTCGTAAGAGCTGAACAGAAACCCATAAGGGT
*
40515399 TGAACGGAAGCTCGTAAGAGCTGAACAGAAACCCCATAAGGGT
1 TGAACAGAAGCTCGTAAGAGCTGAACAGAAA-CCCATAAGGGT
*
40515442 TGAACGGAAGCTCGTAAGAGCTGAACAGAAACCCATAAGGGT
1 TGAACAGAAGCTCGTAAGAGCTGAACAGAAACCCATAAGGGT
* ** ** * * *
40515484 TAAACAGAAGCTCAAAAGAGCTGAATGGAAACTCATATGAGT
1 TGAACAGAAGCTCGTAAGAGCTGAACAGAAACCCATAAGGGT
* * * *
40515526 TAAACAGAAGCTCGTGAGAGCTAAACGGAAA
1 TGAACAGAAGCTCGTAAGAGCTGAACAGAAA
40515557 GTAAACACGA
Statistics
Matches: 138, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
42 96 0.70
43 42 0.30
ACGTcount: A:0.42, C:0.18, G:0.25, T:0.15
Consensus pattern (42 bp):
TGAACAGAAGCTCGTAAGAGCTGAACAGAAACCCATAAGGGT
Found at i:40515515 original size:85 final size:84
Alignment explanation
Indices: 40515357--40515556 Score: 247
Period size: 85 Copynumber: 2.4 Consensus size: 84
40515347 GCTCGAAGGC
* * * * **
40515357 TGAACAGAAGCTCATGAGAACTAAACAGAAACCCATAAGGGTTGAACGGAAGCTCGTAAGAGCTG
1 TGAACAGAAGCTCGTGAGAGCTAAACAGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTG
*
40515422 AACAGAAACCCCATAAGGGT
66 AACAGAAA-CCCATAAGAGT
* * *
40515442 TGAACGGAAGCTCGTAAGAGCTGAACAGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTG
1 TGAACAGAAGCTCGTGAGAGCTAAACAGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTG
** * *
40515507 AATGGAAACTCATATGAGT
66 AACAGAAACCCATAAGAGT
* *
40515526 TAAACAGAAGCTCGTGAGAGCTAAACGGAAA
1 TGAACAGAAGCTCGTGAGAGCTAAACAGAAA
40515557 GTAAACACGA
Statistics
Matches: 96, Mismatches: 19, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
84 34 0.35
85 62 0.65
ACGTcount: A:0.42, C:0.18, G:0.25, T:0.15
Consensus pattern (84 bp):
TGAACAGAAGCTCGTGAGAGCTAAACAGAAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTG
AACAGAAACCCATAAGAGT
Done.