Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold423
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: 617052
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 3 of 6
Found at i:235456 original size:18 final size:17
Alignment explanation
Indices: 235418--235456 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
235408 AAAAATATTA
235418 TTTTTTATTTTAATCAAT
1 TTTTTTATTTTAA-CAAT
235436 TTTTTTATCTTTAA-AAT
1 TTTTTTAT-TTTAACAAT
235453 TTTT
1 TTTT
235457 AAAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 8 0.40
19 5 0.25
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTTATTTTAACAAT
Found at i:235505 original size:26 final size:26
Alignment explanation
Indices: 235451--235505 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
235441 TATCTTTAAA
* **
235451 ATTTTTAAAATAATAATAATTAATTT
1 ATTTTTAAAATAAAAATAATTAACAT
235477 ATTTTT-AAATAAAAATAATATAACAT
1 ATTTTTAAAATAAAAATAAT-TAACAT
235503 ATT
1 ATT
235506 AATATCAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTTTTAAAATAAAAATAATTAACAT
Found at i:236582 original size:19 final size:18
Alignment explanation
Indices: 236555--236606 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
236545 AAAATTAGTA
*
236555 ATTTTTATATTTATATTAT
1 ATTTATATATTT-TATTAT
*
236574 ATTTATATATTTT-TAAT
1 ATTTATATATTTTATTAT
236591 ATATTATA-ATTTTATT
1 AT-TTATATATTTTATT
236607 TAAGATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 10 0.36
18 7 0.25
19 11 0.39
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTATATATTTTATTAT
Found at i:236607 original size:30 final size:28
Alignment explanation
Indices: 236555--236622 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 28
236545 AAAATTAGTA
*
236555 ATTTTTATATTTATATTATATTT-ATAT
1 ATTTTTATATTTATATTATATTTAAGAT
*
236582 ATTTTTAATATATTATAATTTTATTTAAGAT
1 ATTTTT-ATAT-TTAT-ATTATATTTAAGAT
236613 ATTTTATATA
1 ATTTT-TATA
236623 AATTTTGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 6 0.18
28 4 0.12
29 4 0.12
30 8 0.24
31 11 0.32
32 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (28 bp):
ATTTTTATATTTATATTATATTTAAGAT
Found at i:236661 original size:16 final size:16
Alignment explanation
Indices: 236616--236661 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
236606 TTAAGATATT
*
236616 TTATATAAATTTTGATA
1 TTATATAAAATTT-ATA
236633 -TAT-TAATAATTTATA
1 TTATATAA-AATTTATA
236648 TTATATAAAATTTA
1 TTATATAAAATTTA
236662 AAAAATTCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 6 0.24
16 16 0.64
17 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
TTATATAAAATTTATA
Found at i:237340 original size:18 final size:18
Alignment explanation
Indices: 237297--237348 Score: 65
Period size: 17 Copynumber: 3.0 Consensus size: 18
237287 GCTTTTTCTA
*
237297 AATA-ATAT-TTATGTTT
1 AATATATATATTATCTTT
237313 AATATATATATATATCTTT
1 AATATATATAT-TATCTTT
237332 AAT-TATATATTATCTTT
1 AATATATATATTATCTTT
237349 TGTTTTAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
16 4 0.12
17 11 0.34
18 8 0.25
19 9 0.28
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (18 bp):
AATATATATATTATCTTT
Found at i:237898 original size:23 final size:22
Alignment explanation
Indices: 237843--237886 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
237833 TGAAACTCAT
*
237843 GATATAATTCACTTTTTGATAA
1 GATATAATTTACTTTTTGATAA
237865 GATATAATTTACTTTTTGATAA
1 GATATAATTTACTTTTTGATAA
237887 ATTATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (22 bp):
GATATAATTTACTTTTTGATAA
Found at i:238094 original size:30 final size:30
Alignment explanation
Indices: 238045--238105 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
238035 ATTCAAGTTC
238045 GAGTTCGGGTCAGTCTTGGGTTTGAGTTCTT
1 GAGTTCGGGTCA-TCTTGGGTTTGAGTTCTT
*
238076 GAGTTCGGGCTC-TCTTGGGTTTGGGTTCTT
1 GAGTTCGGG-TCATCTTGGGTTTGAGTTCTT
238106 TCAAGTTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 17 0.61
31 9 0.32
32 2 0.07
ACGTcount: A:0.07, C:0.15, G:0.36, T:0.43
Consensus pattern (30 bp):
GAGTTCGGGTCATCTTGGGTTTGAGTTCTT
Found at i:238359 original size:26 final size:25
Alignment explanation
Indices: 238291--238359 Score: 65
Period size: 26 Copynumber: 2.8 Consensus size: 25
238281 CATTTATGAT
*
238291 ATAAAAATTA-ATT-CAT-TTTTTA
1 ATAAAAATTATATTGCATATTTTAA
238313 ATAATATAATTATA-TGACATATTTTAA
1 ATAA-A-AATTATATTG-CATATTTTAA
238340 ATAAAAATATATATTGCATA
1 ATAAAAAT-TATATTGCATA
238360 AAATAATTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
22 4 0.11
23 1 0.03
24 6 0.16
25 4 0.11
26 12 0.32
27 11 0.29
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (25 bp):
ATAAAAATTATATTGCATATTTTAA
Found at i:238649 original size:16 final size:16
Alignment explanation
Indices: 238628--238691 Score: 67
Period size: 16 Copynumber: 4.0 Consensus size: 16
238618 TATTAAATAA
238628 TAATTTAATTTGAATT
1 TAATTTAATTTGAATT
* **
238644 TAATTTAATTTTAAAA
1 TAATTTAATTTGAATT
* *
238660 T-ATTATATTTTAAATT
1 TAATT-TAATTTGAATT
238676 TAATTTAATTTGAATT
1 TAATTTAATTTGAATT
238692 GGATAAATAA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
15 3 0.08
16 31 0.84
17 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TAATTTAATTTGAATT
Found at i:241547 original size:15 final size:15
Alignment explanation
Indices: 241483--241559 Score: 52
Period size: 15 Copynumber: 5.1 Consensus size: 15
241473 ATATATTTTG
241483 AATTAT-TAATATATTA
1 AATTATATAA-ATA-TA
*
241499 AATTTTTATAAATATA
1 AA-TTATATAAATATA
* * * *
241515 AAATCTTTAAGTAT-
1 AATTATATAAATATA
241529 AATTATA-AAATGATA
1 AATTATATAAAT-ATA
241544 AATTATATAAATATA
1 AATTATATAAATATA
241559 A
1 A
241560 TATAAATCTA
Statistics
Matches: 47, Mismatches: 9, Indels: 11
0.70 0.13 0.16
Matches are distributed among these distances:
13 3 0.06
14 6 0.13
15 19 0.40
16 10 0.21
17 6 0.13
18 3 0.06
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (15 bp):
AATTATATAAATATA
Found at i:243031 original size:17 final size:17
Alignment explanation
Indices: 243011--243051 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
243001 GTAATTTTCA
243011 TTTTTTTTCGCTTTTTT
1 TTTTTTTTCGCTTTTTT
** *
243028 TTTTCCTTGGCTTTTTT
1 TTTTTTTTCGCTTTTTT
243045 TTTTTTT
1 TTTTTTT
243052 ACTGGATGGA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.80
Consensus pattern (17 bp):
TTTTTTTTCGCTTTTTT
Found at i:245276 original size:12 final size:12
Alignment explanation
Indices: 245259--245286 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
245249 CACCATATAT
245259 ATTATTAAAAAA
1 ATTATTAAAAAA
245271 ATTATTAAAAAA
1 ATTATTAAAAAA
245283 ATTA
1 ATTA
245287 AATATTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
ATTATTAAAAAA
Found at i:246023 original size:12 final size:10
Alignment explanation
Indices: 246005--246092 Score: 53
Period size: 10 Copynumber: 8.9 Consensus size: 10
245995 ATTAATTATT
246005 AATATAT-TAA
1 AATATATAT-A
246015 AATATATATA
1 AATATATATA
246025 AATATATA-A
1 AATATATATA
*
246034 TAATAT-TTTA
1 -AATATATATA
246044 AATATA-ATTA
1 AATATATA-TA
246054 TAATA-A-ATA
1 -AATATATATA
*
246063 AAAATATATA
1 AATATATATA
* *
246073 AACATAACATA
1 AATAT-ATATA
246084 AATATATAT
1 AATATATAT
246093 CTAAAATTTG
Statistics
Matches: 62, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
8 3 0.05
9 10 0.16
10 36 0.58
11 13 0.21
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (10 bp):
AATATATATA
Found at i:246028 original size:20 final size:20
Alignment explanation
Indices: 246005--246090 Score: 72
Period size: 19 Copynumber: 4.3 Consensus size: 20
245995 ATTAATTATT
246005 AATATATTAAAATATATATA
1 AATATATTAAAATATATATA
*
246025 AATATA-TAATAATAT-TTTA
1 AATATATTAA-AATATATATA
* * *
246044 AATATAATTATAATAAATAAA
1 AATAT-ATTAAAATATATATA
*
246065 AATATA-TAAACATA-ACATA
1 AATATATTAAA-ATATATATA
246084 AATATAT
1 AATATAT
246091 ATCTAAAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
19 23 0.44
20 20 0.38
21 9 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
AATATATTAAAATATATATA
Found at i:247403 original size:31 final size:31
Alignment explanation
Indices: 247368--247426 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
247358 TTTGATATGA
247368 TCAAAAAGTTAAAAATC-TAAATTCAAAAAAC
1 TCAAAAA-TTAAAAATCTTAAATTCAAAAAAC
* * *
247399 TCAAATATTAAATATCTTGAATTCAAAA
1 TCAAAAATTAAAAATCTTAAATTCAAAA
247427 TATCTTAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 8 0.33
31 16 0.67
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.29
Consensus pattern (31 bp):
TCAAAAATTAAAAATCTTAAATTCAAAAAAC
Found at i:247710 original size:129 final size:130
Alignment explanation
Indices: 247492--247776 Score: 326
Period size: 129 Copynumber: 2.2 Consensus size: 130
247482 AAATTCACTC
* * *
247492 TACAATTAAATAGAAAGTTAATTGATCACGATATATAAGAGCAAATAAACAAGATATTTAGAAAA
1 TACAATTAAACAGAAAGTTAATTAATCACGATATATAAGAGCAAATAAACAAGAAATTTAGAAAA
** *** * * *
247557 AAATGACATATTTTGTAGTTAAAACGATAATCAAATACTA-AGAAAATTCAAGTAATAAGTCCAC
66 AAATGACATATTTCATAACCAAAACGACAATCAAATACTAGAGAAAA-TCAAGT-ATAAATCAAC
247621 TT
129 TT
* * * * * *
247623 TATAATTAAACAGAAAGTTGATTAATCATGATATAT-A-AGCAAATAGATAGGAAATTTA-AAAA
1 TACAATTAAACAGAAAGTTAATTAATCACGATATATAAGAGCAAATAAACAAGAAATTTAGAAAA
* * *
247685 ACAATGGCATATTTCATAACCAAAACGACAATCAAATATTAGGGAAAATCAAGTATAAATCAACT
66 A-AATGACATATTTCATAACCAAAACGACAATCAAATACTAGAGAAAATCAAGTATAAATCAACT
247750 T
130 T
*
247751 TACAATTAAACAAAAAGTTAATTAAT
1 TACAATTAAACAGAAAGTTAATTAAT
247777 TGATCATAAT
Statistics
Matches: 129, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
128 38 0.29
129 54 0.42
130 6 0.05
131 31 0.24
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.28
Consensus pattern (130 bp):
TACAATTAAACAGAAAGTTAATTAATCACGATATATAAGAGCAAATAAACAAGAAATTTAGAAAA
AAATGACATATTTCATAACCAAAACGACAATCAAATACTAGAGAAAATCAAGTATAAATCAACTT
Found at i:247842 original size:132 final size:127
Alignment explanation
Indices: 247492--247871 Score: 341
Period size: 132 Copynumber: 2.9 Consensus size: 127
247482 AAATTCACTC
* * * ** * * * *
247492 TACAATTAAATAGAAAGTTAATTGATCACGATATATAAGAGCAAATAAACAAGATATTTAGAAAA
1 TACAATTAAACAAAAAGTTAATTAATCATAATACATAA-A-CAAATAGACAGGAAATTTA-AAAA
* * * *
247557 AAATGACATATTTTGTAGTTAAAACGATAATCAAATACTA-AGAAAATTCAAGTAATAAGTCCAC
63 AAATGACATATTTTGTAATTAAAACGATAATCAAATACTAGGGAAAA-TCAAGT-ATAAATCAAC
247621 TT
126 TT
* * * * * * *
247623 TATAATTAAACAGAAAGTTGATTAATCATGATATATAAGCAAATAGATAGGAAATTTAAAAAACA
1 TACAATTAAACAAAAAGTTAATTAATCATAATACATAAACAAATAGACAGGAAATTTAAAAAA-A
* ** ** * *
247688 ATGGCATATTTCATAACCAAAACGACAATCAAATATTAGGGAAAATCAAGTATAAATCAACTT
65 ATGACATATTTTGTAATTAAAACGATAATCAAATACTAGGGAAAATCAAGTATAAATCAACTT
*
247751 TACAATTAAACAAAAAGTTAATTAATTGATCATAATACATAAACAAATGGACA-GAATATTTTAA
1 TACAATTAAACAAAAAGTTAATT-A---ATCATAATACATAAACAAATAGACAGGAA-A-TTTAA
* * * * *
247815 AAATAATGACATATTTTGTAATTAAAACGGTAATTAAATGCTAGGAAAAATCAAGTA
60 AAAAAATGACATATTTTGTAATTAAAACGATAATCAAATACTAGGGAAAATCAAGTA
247872 GTCTTCCCAA
Statistics
Matches: 200, Mismatches: 41, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
128 35 0.17
129 53 0.26
130 5 0.03
131 36 0.18
132 63 0.31
133 8 0.04
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.28
Consensus pattern (127 bp):
TACAATTAAACAAAAAGTTAATTAATCATAATACATAAACAAATAGACAGGAAATTTAAAAAAAA
TGACATATTTTGTAATTAAAACGATAATCAAATACTAGGGAAAATCAAGTATAAATCAACTT
Found at i:248311 original size:16 final size:17
Alignment explanation
Indices: 248290--248328 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
248280 GCTGAACCAG
248290 CAAGAAT-TGAAAAAAT
1 CAAGAATCTGAAAAAAT
*
248306 CAAGAATCTGGAAAAAT
1 CAAGAATCTGAAAAAAT
*
248323 CGAGAA
1 CAAGAA
248329 AACTCTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.56, C:0.10, G:0.18, T:0.15
Consensus pattern (17 bp):
CAAGAATCTGAAAAAAT
Found at i:249471 original size:14 final size:14
Alignment explanation
Indices: 249454--249496 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
249444 TATAATGTTT
249454 TATTTATAAAATTA
1 TATTTATAAAATTA
249468 TATTTA-AAATATTA
1 TATTTATAAA-ATTA
249482 TATATTAATAAAATT
1 TAT-TT-ATAAAATT
249497 TTTATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.12
14 13 0.52
15 2 0.08
16 4 0.16
17 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TATTTATAAAATTA
Found at i:250889 original size:11 final size:11
Alignment explanation
Indices: 250873--251050 Score: 61
Period size: 11 Copynumber: 16.5 Consensus size: 11
250863 TAATAATTTA
250873 TATATTTATAT
1 TATATTTATAT
250884 TATATTATATAT
1 TATATT-TATAT
250896 T-T-TTATATAT
1 TATATT-TATAT
*
250906 TATAATTATATT
1 TATATTTATA-T
*
250918 TAAAGTATTATA-
1 TATA-T-TTATAT
* *
250930 TATAATTA-AA
1 TATATTTATAT
* *
250940 TAAATTT-TAA
1 TATATTTATAT
* *
250950 CATATTAATAAT
1 TATATTTAT-AT
250962 TA-ATATTATA-
1 TATAT-TTATAT
*
250972 TA-ATTT-TTT
1 TATATTTATAT
*
250981 TATATTTTTA-
1 TATATTTATAT
*
250991 TATATTCATAT
1 TATATTTATAT
* *
251002 AATATTTATGT
1 TATATTTATAT
* *
251013 TATTTTTATTT
1 TATATTTATAT
* *
251024 TATGTTTAAAT
1 TATATTTATAT
*
251035 TATATTTTTAT
1 TATATTTATAT
251046 TATAT
1 TATAT
251051 AATTATATTT
Statistics
Matches: 123, Mismatches: 29, Indels: 30
0.68 0.16 0.16
Matches are distributed among these distances:
8 1 0.01
9 5 0.04
10 39 0.32
11 54 0.44
12 19 0.15
14 5 0.04
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (11 bp):
TATATTTATAT
Found at i:251230 original size:18 final size:19
Alignment explanation
Indices: 251194--251233 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
251184 AGATTTAGTA
251194 ATTTCAATATTTATATTAT
1 ATTTCAATATTTATATTAT
*
251213 ATTTCTATATTT-TATTAT
1 ATTTCAATATTTATATTAT
251231 ATT
1 ATT
251234 ATAAATGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTCAATATTTATATTAT
Found at i:251796 original size:19 final size:19
Alignment explanation
Indices: 251773--251816 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
251763 ATTAATTTAA
251773 ATTAAAATAA-ATTTTAAAT
1 ATTAAAA-AATATTTTAAAT
* *
251792 GTTAAAAAATATTTTTAAT
1 ATTAAAAAATATTTTAAAT
251811 ATTAAA
1 ATTAAA
251817 TAAGTAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTAAAAAATATTTTAAAT
Found at i:260874 original size:2 final size:2
Alignment explanation
Indices: 260867--260894 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
260857 TTAGGTTACC
260867 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
260895 AGAATTTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:262017 original size:11 final size:11
Alignment explanation
Indices: 261989--262021 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
261979 ATATAAATTT
*
261989 TAATATTTTTA
1 TAATATTTATA
262000 T-ATATTTATA
1 TAATATTTATA
262010 TAATATTTATA
1 TAATATTTATA
262021 T
1 T
262022 TTTTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TAATATTTATA
Found at i:263644 original size:11 final size:10
Alignment explanation
Indices: 263621--263739 Score: 53
Period size: 10 Copynumber: 12.7 Consensus size: 10
263611 GTTAATAATT
*
263621 TATATATTCA
1 TATATATTTA
263631 TATCATATTTA
1 TAT-ATATTTA
*
263642 TATATTTTTA
1 TATATATTTA
*
263652 TATTATAATTA
1 TA-TATATTTA
*
263663 TATA-ATATA
1 TATATATTTA
263672 -AT-TATTTA
1 TATATATTTA
*
263680 -A-AT-TTTT
1 TATATATTTA
263687 TATATATTTA
1 TATATATTTA
**
263697 -A-A-A-AAA
1 TATATATTTA
263703 TA-ATATTTA
1 TATATATTTA
*
263712 TATACTATTGA
1 TATA-TATTTA
*
263723 TATATATATA
1 TATATATTTA
263733 TATATAT
1 TATATAT
263740 ATTAAACATA
Statistics
Matches: 81, Mismatches: 16, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
6 1 0.01
7 6 0.07
8 11 0.14
9 9 0.11
10 28 0.35
11 26 0.32
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.53
Consensus pattern (10 bp):
TATATATTTA
Found at i:263663 original size:21 final size:21
Alignment explanation
Indices: 263615--263666 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
263605 AATTAAGTTA
263615 ATAATT-TATATATTCATATC
1 ATAATTATATATATTCATATC
* * * *
263635 ATATTTATATATTTTTATATT
1 ATAATTATATATATTCATATC
263656 ATAATTATATA
1 ATAATTATATA
263667 ATATAATTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (21 bp):
ATAATTATATATATTCATATC
Found at i:263968 original size:28 final size:30
Alignment explanation
Indices: 263935--264011 Score: 77
Period size: 32 Copynumber: 2.6 Consensus size: 30
263925 ATTAGAGATC
*
263935 AAATTAATATAATTTTTTATT-A-TCATTT
1 AAATTAATATAATTTTTTATTAATTAATTT
* * *
263963 TAATTAGTCTAATTGATTTTATTAATTAATTT
1 AAATTAATATAATT--TTTTATTAATTAATTT
*
263995 AAATTAAAATAATTTTT
1 AAATTAATATAATTTTT
264012 AAATATTAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
28 11 0.30
30 10 0.27
31 1 0.03
32 15 0.41
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (30 bp):
AAATTAATATAATTTTTTATTAATTAATTT
Found at i:264448 original size:26 final size:26
Alignment explanation
Indices: 264419--264470 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
264409 AATATGAAAA
*
264419 TATAAAAATTAAAAAAAAATTAAATT
1 TATAAAAAATAAAAAAAAATTAAATT
** *
264445 TATAAAAAATAAGTAAAAATTGAATT
1 TATAAAAAATAAAAAAAAATTAAATT
264471 GAATTTTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (26 bp):
TATAAAAAATAAAAAAAAATTAAATT
Found at i:264607 original size:30 final size:32
Alignment explanation
Indices: 264572--264646 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 32
264562 TTACTATACC
*
264572 TAATATTT-ATTTATTT-TTAAATTA-TTTATT
1 TAATATTTAATTT-TTTATAAAATTATTTTATT
264602 TAATATTTAATTTTTTATAAAATTATTTTATT
1 TAATATTTAATTTTTTATAAAATTATTTTATT
264634 TAATTAATTTAAT
1 TAA-T-ATTTAAT
264647 CGATTAAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
30 11 0.28
31 11 0.28
32 9 0.23
33 1 0.03
34 7 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (32 bp):
TAATATTTAATTTTTTATAAAATTATTTTATT
Found at i:264912 original size:1 final size:1
Alignment explanation
Indices: 264906--264935 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
264896 GCAATTCCCT
264906 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
264936 TTCTCCCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:272225 original size:13 final size:13
Alignment explanation
Indices: 272207--272233 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
272197 ATTTTCATGT
272207 TGGGATTTTCGAA
1 TGGGATTTTCGAA
272220 TGGGATTTTCGAA
1 TGGGATTTTCGAA
272233 T
1 T
272234 AAATTAGTAA
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:0.22, C:0.07, G:0.30, T:0.41
Consensus pattern (13 bp):
TGGGATTTTCGAA
Found at i:272283 original size:19 final size:19
Alignment explanation
Indices: 272243--272321 Score: 61
Period size: 19 Copynumber: 4.0 Consensus size: 19
272233 TAAATTAGTA
* *
272243 ATTTATATATTTATATTAT
1 ATTTATATATTTTTAATAT
*
272262 ATTTATATATTTTTAATGT
1 ATTTATATATTTTTAATAT
* *
272281 A-TTATAATTTTATTTAAGAT
1 ATTTAT-ATATT-TTTAATAT
*
272301 ATTTTATATAAATTTTAATAT
1 A-TTTATAT-ATTTTTAATAT
272322 GTTAATAATT
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
18 4 0.09
19 21 0.46
20 7 0.15
21 9 0.20
22 5 0.11
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
ATTTATATATTTTTAATAT
Found at i:274888 original size:25 final size:25
Alignment explanation
Indices: 274841--274896 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
274831 TGTATAAATT
* **
274841 TAAATTTTTTATTATTATATAATAA
1 TAAAATTTTTATTAAAATATAATAA
* *
274866 TAAAATTTTTATTAAAATTTAATTA
1 TAAAATTTTTATTAAAATATAATAA
274891 TAAAAT
1 TAAAAT
274897 ATATAAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TAAAATTTTTATTAAAATATAATAA
Found at i:275695 original size:35 final size:35
Alignment explanation
Indices: 275617--275696 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
275607 AAATTGAATC
* *
275617 TAAAATTCATTAAAAAAATTAAATTTTAAAAATTA
1 TAAAATTAATCAAAAAAATTAAATTTTAAAAATTA
*** * *
275652 TTTTATTAATCAATAAAATTAAATTTTAAATATTA
1 TAAAATTAATCAAAAAAATTAAATTTTAAAAATTA
275687 TAAAATTAAT
1 TAAAATTAAT
275697 TGTACGGATA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (35 bp):
TAAAATTAATCAAAAAAATTAAATTTTAAAAATTA
Found at i:275915 original size:38 final size:38
Alignment explanation
Indices: 275831--275904 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
275821 AAATATATTT
* * *
275831 TTATTAAATATTTATTTTTTATTTTTTATTAAAATTAC
1 TTATTTAATATTTATATTTTATTTTTTATTAAAATTAA
275869 TTATTTAATATTTA-ATTTTA-TTTTTA-TAAAATTAA
1 TTATTTAATATTTATATTTTATTTTTTATTAAAATTAA
275904 T
1 T
275905 ATATATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 9 0.27
36 6 0.18
37 5 0.15
38 13 0.39
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (38 bp):
TTATTTAATATTTATATTTTATTTTTTATTAAAATTAA
Found at i:276599 original size:29 final size:27
Alignment explanation
Indices: 276520--276603 Score: 82
Period size: 29 Copynumber: 3.0 Consensus size: 27
276510 GCCCAAATTC
*
276520 ATAATTA-AGTTAATAATTTATATATTT
1 ATAATTATATTTAA-AATTTATATATTT
** *
276547 AT-ATTATATTTATATGTTTTTATATATT
1 ATAATTATATTTA-AAATTTATATAT-TT
276575 ATAATTATATTTAAAATATTATATATTT
1 ATAATTATATTTAAAAT-TTATATATTT
276603 A
1 A
276604 AATAAATTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
26 4 0.09
27 14 0.31
28 10 0.22
29 17 0.38
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
ATAATTATATTTAAAATTTATATATTT
Found at i:277018 original size:18 final size:19
Alignment explanation
Indices: 276975--277022 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
276965 TATTAGTTAA
276975 TTTAA-ATT-AAAATAATT
1 TTTAATATTAAAAATAATT
276992 TTTAGATATTAAAAAT-ATT
1 TTTA-ATATTAAAAATAATT
277011 TTTAATATTAAA
1 TTTAATATTAAA
277023 TAAATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.14
18 9 0.32
19 10 0.36
20 5 0.18
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TTTAATATTAAAAATAATT
Found at i:277027 original size:20 final size:20
Alignment explanation
Indices: 276971--277028 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 20
276961 ATTTTATTAG
276971 TTAAT-TTAAATTAAAATAATTT
1 TTAATATTAAA-T-AAAT-ATTT
276993 TTAGATATT-AA-AAATATTT
1 TTA-ATATTAAATAAATATTT
277012 TTAATATTAAATAAATA
1 TTAATATTAAATAAATA
277029 ATAAATATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
18 5 0.16
19 9 0.28
20 9 0.28
22 3 0.09
23 4 0.12
24 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
TTAATATTAAATAAATATTT
Found at i:277040 original size:16 final size:16
Alignment explanation
Indices: 277021--277051 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
277011 TTTAATATTA
277021 AATAAATAATAAATAT
1 AATAAATAATAAATAT
*
277037 AATAAATAATTAATA
1 AATAAATAATAAATA
277052 AAAATATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAAATAATAAATAT
Found at i:277640 original size:14 final size:15
Alignment explanation
Indices: 277620--277653 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
277610 AAATAAAGTT
277620 TATATATTTAATTAAA
1 TATAT-TTTAATTAAA
*
277636 TATATTTTTATTAAA
1 TATATTTTAATTAAA
277651 TAT
1 TAT
277654 TTATTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATATTTTAATTAAA
Found at i:277645 original size:16 final size:15
Alignment explanation
Indices: 277620--277677 Score: 62
Period size: 16 Copynumber: 3.7 Consensus size: 15
277610 AAATAAAGTT
277620 TATATATTTAATTAAA
1 TATATATTT-ATTAAA
*
277636 TATATTTTTATTAAA
1 TATATATTTATTAAA
* *
277651 TATTTATTATATTTAA
1 TATATATT-TATTAAA
*
277667 TATTTATTTAT
1 TATATATTTAT
277678 CATTAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 15 0.41
16 22 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATATATTTATTAAA
Found at i:278136 original size:23 final size:23
Alignment explanation
Indices: 278085--278136 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
278075 ATTTCAAATT
*
278085 TTAAA-TTTAAAAATCATTTAAA
1 TTAAATTTTAAAAATCAATTAAA
* *
278107 -AATAATTTTATAAATCAATTAAA
1 TTA-AATTTTAAAAATCAATTAAA
278130 TTAAATT
1 TTAAATT
278137 AATTTAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
21 1 0.04
22 2 0.09
23 19 0.83
24 1 0.04
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
TTAAATTTTAAAAATCAATTAAA
Found at i:279022 original size:16 final size:17
Alignment explanation
Indices: 278997--279052 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 17
278987 TAATAAAATA
*
278997 TATTTTTATTAAATATT
1 TATTTATATTAAATATT
*
279014 TA-TTATATTTAATATT
1 TATTTATATTAAATATT
279030 TATTTATCATTAAA-A-T
1 TATTTAT-ATTAAATATT
279046 TATTTAT
1 TATTTAT
279053 CTAATGTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 22 0.65
17 7 0.21
18 5 0.15
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTTATATTAAATATT
Found at i:279691 original size:19 final size:19
Alignment explanation
Indices: 279672--279739 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 19
279662 GTTAATAATT
279672 TATATATTTATATAGTATT-
1 TATATATTTATATA-TATTA
*
279691 TATATATTTTTATATATTA
1 TATATATTTATATATATTA
*
279710 TATTTATATTTA-AAATATTA
1 TA--TATATTTATATATATTA
279730 TATATATTTA
1 TATATATTTA
279740 AATACATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
18 12 0.28
19 15 0.35
20 9 0.21
21 7 0.16
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (19 bp):
TATATATTTATATATATTA
Found at i:279696 original size:21 final size:20
Alignment explanation
Indices: 279672--279757 Score: 74
Period size: 20 Copynumber: 4.4 Consensus size: 20
279662 GTTAATAATT
279672 TATATATTTATATAGTATTTA
1 TATATATTTATATA-TATTTA
279693 TATAT-TTT-TATATATTATA
1 TATATATTTATATATATT-TA
* *
279712 TTTATATTTA-AAATA-TTA
1 TATATATTTATATATATTTA
* *
279730 TATATATTTAAATACATTT-
1 TATATATTTATATATATTTA
279749 TGATATATT
1 T-ATATATT
279758 AATAAGTTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
18 15 0.28
19 15 0.28
20 19 0.35
21 5 0.09
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (20 bp):
TATATATTTATATATATTTA
Found at i:279703 original size:29 final size:28
Alignment explanation
Indices: 279665--279748 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 28
279655 TAATTGAGTT
*
279665 AATAATTTATATATTTATATAGTATTT-A
1 AATATTTTATATATTTATATA-TATTTAA
* *
279693 TATATTTTTATATATTATATTTATATTTAA
1 AATA-TTTTATATATT-TATATATATTTAA
* * *
279723 AATATTATATATATTTAAATACATTT
1 AATATTTTATATATTTATATATATTT
279749 TGATATATTA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
28 11 0.24
29 25 0.56
30 9 0.20
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (28 bp):
AATATTTTATATATTTATATATATTTAA
Found at i:280146 original size:19 final size:18
Alignment explanation
Indices: 280122--280160 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 18
280112 AATTTGAATT
280122 AAAATAATTTTTAATGTTA
1 AAAAT-ATTTTTAATGTTA
280141 AAAATATTTTTAATGTTA
1 AAAATATTTTTAATGTTA
280159 AA
1 AA
280161 TAAATAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (18 bp):
AAAATATTTTTAATGTTA
Found at i:280178 original size:16 final size:16
Alignment explanation
Indices: 280159--280189 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
280149 TTTAATGTTA
280159 AATAAATAATAGATAT
1 AATAAATAATAGATAT
*
280175 AATAAATAATTGATA
1 AATAAATAATAGATA
280190 AAAATATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (16 bp):
AATAAATAATAGATAT
Found at i:280761 original size:19 final size:20
Alignment explanation
Indices: 280737--280783 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
280727 TATATTTTAA
280737 ATTTAAATAAAA-ATAATTT
1 ATTTAAATAAAATATAATTT
280756 ATTT-AATAAAATATAATTT
1 ATTTAAATAAAATATAATTT
280775 -TATTAAATA
1 AT-TTAAATA
280784 TTTATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.32
19 13 0.52
20 4 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTAAATAAAATATAATTT
Found at i:280794 original size:16 final size:15
Alignment explanation
Indices: 280773--280810 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
280763 AAAATATAAT
280773 TTTATTAAATATTTA
1 TTTATTAAATATTTA
*
280788 TTATATTTAATATTTA
1 TT-TATTAAATATTTA
280804 TTTATTA
1 TTTATTA
280811 TTAAAATTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATTAAATATTTA
Found at i:280796 original size:20 final size:20
Alignment explanation
Indices: 280773--280811 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
280763 AAAATATAAT
*
280773 TTTATTAAATATTTATTATA
1 TTTAATAAATATTTATTATA
**
280793 TTTAATATTTATTTATTAT
1 TTTAATAAATATTTATTAT
280812 TAAAATTACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTAATAAATATTTATTATA
Found at i:280856 original size:31 final size:31
Alignment explanation
Indices: 280791--280866 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
280781 ATATTTATTA
280791 TATTTAATATTT-ATTTATTATTAAAATTACT
1 TATTTAATATTTAATTTATTATTAAAA-TACT
*
280822 TATTTAATATTTAATCTTATTTTTATAAA-A-T
1 TATTTAATATTTAAT-TTATTATTA-AAATACT
280853 TATTT--TATTTAATT
1 TATTTAATATTTAATT
280867 AAATTAAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
28 1 0.02
29 8 0.20
31 18 0.44
32 3 0.07
33 8 0.20
34 3 0.07
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (31 bp):
TATTTAATATTTAATTTATTATTAAAATACT
Found at i:280865 original size:36 final size:38
Alignment explanation
Indices: 280790--280865 Score: 104
Period size: 36 Copynumber: 2.1 Consensus size: 38
280780 AATATTTATT
*
280790 ATATTTAATATTTATTTATTATTAAAATTACTTATTTA
1 ATATTTAATACTTATTTATTATTAAAATTACTTATTTA
*
280828 ATATTTAAT-CTTATTT-TTA-TAAAATTATTTTATTTA
1 ATATTTAATACTTATTTATTATTAAAATTA-CTTATTTA
280864 AT
1 AT
280866 TAAATTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 8 0.23
36 12 0.34
37 6 0.17
38 9 0.26
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (38 bp):
ATATTTAATACTTATTTATTATTAAAATTACTTATTTA
Found at i:282323 original size:87 final size:87
Alignment explanation
Indices: 282176--282350 Score: 280
Period size: 87 Copynumber: 2.0 Consensus size: 87
282166 ATGCTTTGAG
* * * *
282176 GGTGACCAAAACTATTCTTGAAGAGATCAGTTCCAGGGATGATGATAGCCAGAACGTAAATCAGC
1 GGTGAACAAAACTATTCTTGAAGAGATCACTTCCAGCGATGATAATAGCCAGAACGTAAATCAGC
282241 TTCAACGTAAACTAAAGGAGAA
66 TTCAACGTAAACTAAAGGAGAA
*
282263 GGTGAACAAAACTATTCTTGAAGAGATCACTTCCAAGCG-TGATAATAGCCAGAACTTAAATCAG
1 GGTGAACAAAACTATTCTTGAAGAGATCACTTCC-AGCGATGATAATAGCCAGAACGTAAATCAG
*
282327 CTTCAACTTAAACTAAAGGAGAA
65 CTTCAACGTAAACTAAAGGAGAA
282350 G
1 G
282351 CTGTTGGGAA
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
87 78 0.96
88 3 0.04
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.22
Consensus pattern (87 bp):
GGTGAACAAAACTATTCTTGAAGAGATCACTTCCAGCGATGATAATAGCCAGAACGTAAATCAGC
TTCAACGTAAACTAAAGGAGAA
Found at i:286410 original size:143 final size:143
Alignment explanation
Indices: 286149--286436 Score: 522
Period size: 143 Copynumber: 2.0 Consensus size: 143
286139 TAACGTGTTT
286149 AACCTGACATGAATAGCAAGATGTCACAAATGAATCTGATGCTTTTGACTCTTCAGCTGAAAACC
1 AACCTGACATGAATAGCAAGATGTCACAAATGAATCTGATGCTTTTGACTCTTCAGCTGAAAACC
* * **
286214 AGAAGCAGCACGAATCGAGTTCCTACAGCATTTCATGGCCTCAAAGTTGCAGGTAATTTTTCTTC
66 AGAAGCAGCACGAATCGAGTTCCTACAACATTTCATGGCCTCAAAGTTACAGGTAATTTCACTTC
*
286279 TCATATGTGCTTA
131 TCATATATGCTTA
*
286292 AACCTGACATGAATAGCAAGATGTCACAAATGAATCTGATGCTTTTGCCTCTTCAGCTGAAAACC
1 AACCTGACATGAATAGCAAGATGTCACAAATGAATCTGATGCTTTTGACTCTTCAGCTGAAAACC
286357 AGAAGCAGCACGAATCGAGTTCCTACAACATTTCATGGCCTCAAAGTTACAGGTAATTTCACTTC
66 AGAAGCAGCACGAATCGAGTTCCTACAACATTTCATGGCCTCAAAGTTACAGGTAATTTCACTTC
286422 TCATATATGCTTA
131 TCATATATGCTTA
286435 AA
1 AA
286437 TGATTGTACT
Statistics
Matches: 139, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
143 139 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28
Consensus pattern (143 bp):
AACCTGACATGAATAGCAAGATGTCACAAATGAATCTGATGCTTTTGACTCTTCAGCTGAAAACC
AGAAGCAGCACGAATCGAGTTCCTACAACATTTCATGGCCTCAAAGTTACAGGTAATTTCACTTC
TCATATATGCTTA
Found at i:287176 original size:4 final size:4
Alignment explanation
Indices: 287167--287192 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
287157 AATAATGTTG
287167 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
287193 GTTCCCAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:288898 original size:19 final size:18
Alignment explanation
Indices: 288876--288911 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
288866 ATTTACATAT
288876 TTTTAATGTATTATATAAA
1 TTTTAATGTATTA-ATAAA
*
288895 TTTTGATGTATTAATAA
1 TTTTAATGTATTAATAA
288912 TTTATATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (18 bp):
TTTTAATGTATTAATAAA
Found at i:289860 original size:29 final size:25
Alignment explanation
Indices: 289803--289853 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
289793 TATTTTTATT
289803 AATTAAATAATAATCAATAGATCAA
1 AATTAAATAATAATCAATAGATCAA
*
289828 AATTAAATAATAATCGATAGATCAA
1 AATTAAATAATAATCAATAGATCAA
289853 A
1 A
289854 CTAAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (25 bp):
AATTAAATAATAATCAATAGATCAA
Found at i:290039 original size:3 final size:3
Alignment explanation
Indices: 290031--290068 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
290021 TTAATAAGAT
290031 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
290069 TTGGGGGGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:293379 original size:3 final size:3
Alignment explanation
Indices: 293371--293412 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
293361 AAAGCAAAGC
293371 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
293413 TTTTAAGTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:293970 original size:34 final size:34
Alignment explanation
Indices: 293906--294088 Score: 260
Period size: 34 Copynumber: 5.4 Consensus size: 34
293896 CCTATGAGCC
* *
293906 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
293939 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
293973 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
294007 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
294041 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
294075 TGTTGATTAAATGG
1 TGTTGATTAAATGG
294089 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 11 0.08
34 121 0.92
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:294449 original size:19 final size:19
Alignment explanation
Indices: 294393--294455 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
294383 TGGTTGTCGA
**
294393 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
294412 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
294431 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
294450 GTTACT
1 GGTACT
294456 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:298587 original size:34 final size:34
Alignment explanation
Indices: 298521--298705 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
298511 AAGTGGGAGA
* *
298521 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
298554 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
298588 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
298622 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
298656 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
298690 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
298706 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:299096 original size:23 final size:23
Alignment explanation
Indices: 299067--299137 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
299057 TAATTAATAA
299067 AAATTTAAAAATATTTTAT-ATT
1 AAATTTAAAAATATTTTATAATT
*
299089 AATATTT--ATATATTTTATAATT
1 AA-ATTTAAAAATATTTTATAATT
* * *
299111 AAATTTAAAAAAATTTAATGATT
1 AAATTTAAAAATATTTTATAATT
299134 AAAT
1 AAAT
299138 ATCAATTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
21 14 0.35
22 7 0.17
23 19 0.47
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (23 bp):
AAATTTAAAAATATTTTATAATT
Found at i:299102 original size:21 final size:21
Alignment explanation
Indices: 299077--299117 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
299067 AAATTTAAAA
299077 ATATTTTAT-ATTAATATTTAT
1 ATATTTTATAATTAA-ATTTAT
299098 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
299118 AAAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:300435 original size:21 final size:21
Alignment explanation
Indices: 300390--300438 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
300380 ATTTGAATTG
300390 AAATAATTTTTAAATGTTAAA
1 AAATAATTTTTAAATGTTAAA
* *
300411 AAATTATTTTT-AATGTTCAAT
1 AAATAATTTTTAAATGTT-AAA
300432 AAATAAT
1 AAATAAT
300439 AAATATAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (21 bp):
AAATAATTTTTAAATGTTAAA
Found at i:303268 original size:2 final size:2
Alignment explanation
Indices: 303263--303302 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
303253 GATAATCTTC
303263 AT AT 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
303303 TCTAGATATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:303773 original size:22 final size:22
Alignment explanation
Indices: 303745--303791 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
303735 TTATTTCTCT
*
303745 TATTGATGACACAAATCCTAGA
1 TATTGATGACACAAACCCTAGA
*
303767 TATTGATTACACAAACCCTAGA
1 TATTGATGACACAAACCCTAGA
303789 TAT
1 TAT
303792 GATTTTAGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (22 bp):
TATTGATGACACAAACCCTAGA
Found at i:304401 original size:18 final size:18
Alignment explanation
Indices: 304378--304415 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
304368 CTAGGCTGCT
*
304378 CCATTTGCTTCTTTAAGG
1 CCATTTGCTTCTTCAAGG
304396 CCATTTGCTTCTTCAAGG
1 CCATTTGCTTCTTCAAGG
304414 CC
1 CC
304416 CGTTTTCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.29, G:0.16, T:0.39
Consensus pattern (18 bp):
CCATTTGCTTCTTCAAGG
Found at i:304797 original size:16 final size:17
Alignment explanation
Indices: 304773--304810 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
304763 ATTCAAGTTT
*
304773 AATTCATTTAA-AATCA
1 AATTTATTTAATAATCA
*
304789 AATTTATTTAATAATTA
1 AATTTATTTAATAATCA
304806 AATTT
1 AATTT
304811 TAAAATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTATTTAATAATCA
Found at i:306646 original size:29 final size:30
Alignment explanation
Indices: 306604--306679 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
306594 TGAATTAGTT
*
306604 TTTAAATAAATTTTTAT-ATTT-TTATTATA
1 TTTAAATAAATTTTTATCATTTGAT-TTATA
*
306633 TTTAAATAAATTTTTATCATTTGATTTGTA
1 TTTAAATAAATTTTTATCATTTGATTTATA
*
306663 TATAAATAAATTTTTAT
1 TTTAAATAAATTTTTAT
306680 TTCTTATAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 17 0.40
30 24 0.57
31 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (30 bp):
TTTAAATAAATTTTTATCATTTGATTTATA
Found at i:308209 original size:16 final size:16
Alignment explanation
Indices: 308185--308230 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
308175 AAATTATCTT
*
308185 TTCAGTTTTCTTTTTC
1 TTCAATTTTCTTTTTC
308201 TTCAATTTTTCATTTTTC
1 TTCAA-TTTTC-TTTTTC
308219 --CAATTTTCTTTT
1 TTCAATTTTCTTTT
308231 CCACCCTGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 5 0.19
16 7 0.26
17 5 0.19
18 6 0.22
ACGTcount: A:0.13, C:0.17, G:0.02, T:0.67
Consensus pattern (16 bp):
TTCAATTTTCTTTTTC
Found at i:316015 original size:34 final size:34
Alignment explanation
Indices: 315948--316129 Score: 235
Period size: 34 Copynumber: 5.4 Consensus size: 34
315938 ATCATGTTTG
* * *
315948 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
* *
315981 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
* * *
316015 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
316048 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
* * *
316082 TGTTGACTAAATGGGAGATTTGGTAGG-TTGCCAT
1 TGTTGATTAAATGGGTGATTTGGT-GGCTTACCAT
316116 TGTTGATTAAATGG
1 TGTTGATTAAATGG
316130 TGGTTTTTAC
Statistics
Matches: 131, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
33 40 0.31
34 89 0.68
35 2 0.02
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
Found at i:316034 original size:67 final size:67
Alignment explanation
Indices: 315948--316129 Score: 283
Period size: 67 Copynumber: 2.7 Consensus size: 67
315938 ATCATGTTTG
* * * * * *
315948 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
316013 AT
66 AT
316015 TGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 TGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
316080 AT
66 AT
* *
316082 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCATTGTTGATTAAATGG
1 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCATTGTTGATTAAATGG
316130 TGGTTTTTAC
Statistics
Matches: 106, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
67 73 0.69
68 33 0.31
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.41
Consensus pattern (67 bp):
TGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
AT
Found at i:316096 original size:101 final size:100
Alignment explanation
Indices: 315948--316129 Score: 285
Period size: 101 Copynumber: 1.8 Consensus size: 100
315938 ATCATGTTTG
* * *
315948 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGT-GGTTTGC
1 TGTTGATTAAATGGTGATTTAGTAGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGG-TTGC
316012 CATTGTTGACTAAATGGAGATTTGGTAGCTTACCAT
65 CATTGTTGACTAAATGGAGATTTGGTAGCTTACCAT
* *
316048 TGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTAGTAGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
*
316113 CATTGTTGATTAAATGG
65 CATTGTTGACTAAATGG
316130 TGGTTTTTAC
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 12 0.16
101 60 0.81
102 2 0.03
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.41
Consensus pattern (100 bp):
TGTTGATTAAATGGTGATTTAGTAGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
ATTGTTGACTAAATGGAGATTTGGTAGCTTACCAT
Found at i:316490 original size:19 final size:19
Alignment explanation
Indices: 316434--316496 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
316424 TGGTTGTCGA
**
316434 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
316453 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
316472 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
316491 GTTACT
1 GGTACT
316497 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:320631 original size:34 final size:34
Alignment explanation
Indices: 320562--320745 Score: 239
Period size: 34 Copynumber: 5.5 Consensus size: 34
320552 AAGTGGGAGA
* * *
320562 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
* *
320595 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
* * *
320629 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
320662 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
* * *
320696 ATTGTTGACTAAATGGGAGATTTGGTAGG-TTGCC
1 ATTGTTGATTAAATGGGTGATTTGGT-GGCTTACC
320730 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
320746 TGGTTTTTAC
Statistics
Matches: 133, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
33 42 0.32
34 89 0.67
35 2 0.02
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
Found at i:320670 original size:67 final size:67
Alignment explanation
Indices: 320562--320745 Score: 287
Period size: 67 Copynumber: 2.7 Consensus size: 67
320552 AAGTGGGAGA
* * * * * *
320562 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
320627 CC
66 CC
320629 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
1 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
320694 CC
66 CC
* *
320696 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCCATTGTTGATTAAATGG
1 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACCATTGTTGATTAAATGG
320746 TGGTTTTTAC
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
67 75 0.69
68 33 0.31
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.41
Consensus pattern (67 bp):
ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
CC
Found at i:320700 original size:101 final size:100
Alignment explanation
Indices: 320562--320745 Score: 289
Period size: 101 Copynumber: 1.8 Consensus size: 100
320552 AAGTGGGAGA
* * *
320562 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGT-GGTTT
1 ATTGTTGATTAAATGGTGATTTAGTAGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGG-TT
320626 GCCATTGTTGACTAAATGGAGATTTGGTAGCTTACC
65 GCCATTGTTGACTAAATGGAGATTTGGTAGCTTACC
* *
320662 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTAGTAGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
*
320727 GCCATTGTTGATTAAATGG
65 GCCATTGTTGACTAAATGG
320746 TGGTTTTTAC
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 14 0.18
101 60 0.79
102 2 0.03
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.41
Consensus pattern (100 bp):
ATTGTTGATTAAATGGTGATTTAGTAGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTG
CCATTGTTGACTAAATGGAGATTTGGTAGCTTACC
Found at i:321423 original size:5 final size:5
Alignment explanation
Indices: 321413--321456 Score: 58
Period size: 5 Copynumber: 9.4 Consensus size: 5
321403 TTTGTAAGGA
*
321413 TTATT TTATT TTAAT TTATT TTATT TTA-T TTA-T TTA-T TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
321457 TTTGTAGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 12 0.33
5 24 0.67
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:324579 original size:3 final size:3
Alignment explanation
Indices: 324566--324615 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
324556 TTGCACAATT
*
324566 ATA AT- ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
324613 ATA
1 ATA
324616 GTATTTATGT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:326360 original size:2 final size:2
Alignment explanation
Indices: 326348--326387 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
326338 TCTAATTTTC
326348 AT AT A- 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 AT AT A
326388 CTATTAACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:326489 original size:2 final size:2
Alignment explanation
Indices: 326482--326519 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
326472 CCATATGTAC
326482 AT 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
326520 CCATTCATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:326879 original size:3 final size:3
Alignment explanation
Indices: 326871--326898 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
326861 AAAGCAAAGC
326871 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
326899 CTTCCCTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:329627 original size:21 final size:21
Alignment explanation
Indices: 329601--329642 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
329591 TTGCTAGATC
329601 AATTAATCTTGTTATTTACCT
1 AATTAATCTTGTTATTTACCT
329622 AATTAATCTTGTTATTTACCT
1 AATTAATCTTGTTATTTACCT
329643 TAAGTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.52
Consensus pattern (21 bp):
AATTAATCTTGTTATTTACCT
Found at i:336357 original size:18 final size:18
Alignment explanation
Indices: 336336--336371 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
336326 CTCAAAATCA
336336 AGCTCATCCTCAAGGTCG
1 AGCTCATCCTCAAGGTCG
* *
336354 AGCTCGTCCTCAGGGTCG
1 AGCTCATCCTCAAGGTCG
336372 CCACTATAAG
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:0.17, C:0.33, G:0.28, T:0.22
Consensus pattern (18 bp):
AGCTCATCCTCAAGGTCG
Found at i:338340 original size:57 final size:57
Alignment explanation
Indices: 338248--338531 Score: 320
Period size: 57 Copynumber: 5.0 Consensus size: 57
338238 ACTAGCATGT
* * * * *
338248 GGACACGCTTGCCTTGG-GGCGACCTGAGTTGGAGTGACTTGGTGTCACTAACATGC
1 GGACCCGCTCGCCTTGGTGGCGATCTGAGTTGGAGTGACTTGGAGTCACTAATATGC
* * ** *
338304 TGACCCGCTCGTCTTGGTGGCGATCTGAGTCAGAGTGACTTGGCGTCACTAATATGC
1 GGACCCGCTCGCCTTGGTGGCGATCTGAGTTGGAGTGACTTGGAGTCACTAATATGC
* * * * **
338361 AGACCCACTCGCCTTGGTGGCGATCTG-GATTGGAGTGACTTGGCGTCATTGGTATGC
1 GGACCCGCTCGCCTTGGTGGCGATCTGAG-TTGGAGTGACTTGGAGTCACTAATATGC
* * * * * **
338418 GGATCCGCTCACTTTCGTGGCGATCTGGGTTGGAGTGACTTGGAGTCACTGGTATGC
1 GGACCCGCTCGCCTTGGTGGCGATCTGAGTTGGAGTGACTTGGAGTCACTAATATGC
* *
338475 GGACCCGCTCGCCTTGGTGGCGATCTGGGTTGGAGTGACTTAGAGTCACTAATATGC
1 GGACCCGCTCGCCTTGGTGGCGATCTGAGTTGGAGTGACTTGGAGTCACTAATATGC
338532 TGAAGAGAGT
Statistics
Matches: 193, Mismatches: 32, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
56 14 0.07
57 178 0.92
58 1 0.01
ACGTcount: A:0.17, C:0.23, G:0.33, T:0.27
Consensus pattern (57 bp):
GGACCCGCTCGCCTTGGTGGCGATCTGAGTTGGAGTGACTTGGAGTCACTAATATGC
Found at i:345107 original size:2 final size:2
Alignment explanation
Indices: 345100--345135 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
345090 TATCTAAATT
*
345100 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
345136 TAAACACTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:350952 original size:87 final size:89
Alignment explanation
Indices: 350800--350973 Score: 235
Period size: 87 Copynumber: 2.0 Consensus size: 89
350790 ATTAAGGTAT
* **
350800 GTTTAGTGTTAAGTTAAGCCATTGATAGATTTTCAAAGGCAATGTTTGAATGCTCAGAGCAGTAA
1 GTTTAGTATTAAGTTAAGCCATTGATAGATTTTCAAAGGCAATGTTTGAACACTCAGAGCAGTAA
* * *
350865 TTTTTGAATGTTCGTGTCTAAAAC
66 TGTCTGAATGTTCATGTCTAAAAC
* ** **
350889 GTTTAGTATTAAGTTAAG-C-TTGATAGATTTTCGAAGGCAATGTTTGAACACTTTGAGTGGTAA
1 GTTTAGTATTAAGTTAAGCCATTGATAGATTTTCAAAGGCAATGTTTGAACACTCAGAGCAGTAA
350952 TGTCTGAATGTTCATGTCTAAA
66 TGTCTGAATGTTCATGTCTAAA
350974 TGTAAAAGTT
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
87 56 0.76
88 1 0.01
89 17 0.23
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (89 bp):
GTTTAGTATTAAGTTAAGCCATTGATAGATTTTCAAAGGCAATGTTTGAACACTCAGAGCAGTAA
TGTCTGAATGTTCATGTCTAAAAC
Found at i:351751 original size:131 final size:132
Alignment explanation
Indices: 350989--351758 Score: 681
Period size: 131 Copynumber: 5.9 Consensus size: 132
350979 AAGTTCACCT
* * * *
350989 TACAATTAAATAGAAAA-TTGATTGATCATG---ATAGATAAGTAAATAGATAGGATATTTAGAA
1 TACAATTAAATA-AAAAGTTGATTGATCATGAATATATATAAGCAAATAGACAGGACATTTAGAA
* * * * ** * * * *
351050 AAT-ATTAGTATATTTCATAACTAAAATGGTAATTAAATGTTAAGAAAAACCAAGTAATAAGTCC
65 AATGATGA-CATATTTCATAACCAAAACGACAATTAAATGCTAGGAAAAACAAAGTAGTAAGTCC
**
351114 GGTC
129 ATTC
* * * * **
351118 TATAATTATATAAAAATTTGATTGATCAT-AATGTATATAAGCAAATAGACAAAACATTT-GAAA
1 TACAATTAAATAAAAAGTTGATTGATCATGAATATATATAAGCAAATAGACAGGACATTTAG-AA
* ** * * * * * * *
351181 AATGATGGCATATTTCATAATGAAAAGGGCAATTAAATGTTAGGGAAAACCAAGCAGTAAGTTCA
65 AATGATGACATATTTCATAACCAAAACGACAATTAAATGCTAGGAAAAACAAAGTAGTAAGTCCA
351246 TTC
130 TTC
* * * * * *
351249 TAAAATTAAATAAAAAGTTAATTGATCATGATATATATATAAAAAATCAAATATACAAGATATTT
1 TACAATTAAATAAAAAGTTGATTGATCATGA-ATATATAT----AAGCAAATAGACAGGACATTT
* * * ** * ** *
351314 -GAAAAATCATGGCATATTTCGTAATTAAAACGATAATTAAATATTAGGAAAAACAAAGTAATAA
61 AG-AAAATGATGACATATTTCATAACCAAAACGACAATTAAATGCTAGGAAAAACAAAGTAGTAA
*
351378 -TAC-TGCTC
125 GTCCAT--TC
* * * *
351386 TACAATTAAATAGAAAGTTGATTGATCAT-AATATATATAAAGCAAATAAATAGGACATTTGGAA
1 TACAATTAAATAAAAAGTTGATTGATCATGAATATATAT-AAGCAAATAGACAGGACATTTAGAA
* * * * * *
351450 GATGATGATATATTTTATAACCAAAATGACAATTAAATGCTAGGGAAAACAACGTAGTAAGTCCA
65 AATGATGACATATTTCATAACCAAAACGACAATTAAATGCTAGGAAAAACAAAGTAGTAAGTCCA
*
351515 CTC
130 TTC
* * * *
351518 TATAATTAAATATAAAGTTGATTGATCATG---ATATATAAGTAAATAGATAGGACATTTAGAAA
1 TACAATTAAATAAAAAGTTGATTGATCATGAATATATATAAGCAAATAGACAGGACATTTAGAAA
* * *
351580 ATGATGACATATTTCATAACCAAAACGGCAATTAAATGCTAGGAAAAACTACGTAGTAAGTCCAT
66 ATGATGACATATTTCATAACCAAAACGACAATTAAATGCTAGGAAAAACAAAGTAGTAAGTCCAT
351645 TC
131 TC
* *
351647 TACAATTAAATAAAAAGTTAATTGATCATGAA-ATATATAAGCAAATAAACAGGACATTTAGAAA
1 TACAATTAAATAAAAAGTTGATTGATCATGAATATATATAAGCAAATAGACAGGACATTTAGAAA
* *
351711 ATAATGACATATTT-AGTAACCAAAACGACAATTAAATGCTAGGGAAAA
66 ATGATGACATATTTCA-TAACCAAAACGACAATTAAATGCTAGGAAAAA
351759 TAATGACATA
Statistics
Matches: 529, Mismatches: 91, Indels: 40
0.80 0.14 0.06
Matches are distributed among these distances:
128 4 0.01
129 131 0.25
130 8 0.02
131 170 0.32
132 96 0.18
133 10 0.02
135 9 0.02
136 3 0.01
137 98 0.19
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.29
Consensus pattern (132 bp):
TACAATTAAATAAAAAGTTGATTGATCATGAATATATATAAGCAAATAGACAGGACATTTAGAAA
ATGATGACATATTTCATAACCAAAACGACAATTAAATGCTAGGAAAAACAAAGTAGTAAGTCCAT
TC
Found at i:351778 original size:47 final size:47
Alignment explanation
Indices: 351707--351806 Score: 148
Period size: 47 Copynumber: 2.1 Consensus size: 47
351697 AGGACATTTA
351707 GAAAATAATGACATATTTAGTAACCAAAACGACAATTAAATGCTAGG
1 GAAAATAATGACATATTTAGTAACCAAAACGACAATTAAATGCTAGG
* ** *
351754 GAAAATAATGACATATTTCA-TAACCAAGACGGTAATTGAATGCTAGG
1 GAAAATAATGACATATTT-AGTAACCAAAACGACAATTAAATGCTAGG
351801 GAAAAT
1 GAAAAT
351807 CACATAGTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 47 0.98
48 1 0.02
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.24
Consensus pattern (47 bp):
GAAAATAATGACATATTTAGTAACCAAAACGACAATTAAATGCTAGG
Found at i:352023 original size:131 final size:131
Alignment explanation
Indices: 351754--352129 Score: 436
Period size: 131 Copynumber: 2.8 Consensus size: 131
351744 AAATGCTAGG
* * * *
351754 GAAAATAATGACATATTTCATAACCAAGACGGTAATT-GAATGCTAGGGAAAATCACATAGTAAG
1 GAAAA-AATGACATATTTCATAACCAA-ACGGCAATTAG-ATGCTAAGGAAAACCAAATAGTAAG
* * * *
351818 TTCACTCTACGATTAAATAGAAAGTTGATTGATCAT-GATATGTATAAGCAAATAGACATGATAT
63 TTCACTCTACAATTAAATAGAAAGTTGATTGATCATAGATATATATAAGCAAATAGACAAGACAT
351882 TTAAA
128 TT-AA
* *
351887 AAAAAAATGACATATTTCATAACCAAATGGCAATTAGATGCTAAGGAAAACCAAATAGTAAGTTC
1 GAAAAAATGACATATTTCATAACCAAACGGCAATTAGATGCTAAGGAAAACCAAATAGTAAGTTC
*
351952 ACTCTACAATTAAATAGAAAGTTGATTGATTATGAGATATATATAAGCAAATAGACAAGACATTT
66 ACTCTACAATTAAATAGAAAGTTGATTGATCAT-AGATATATATAAGCAAATAGACAAGACATTT
352017 -A
130 AA
* * * ** * ** *
352018 GAAAAACACTGATATATTTCGTAACTAAAACAACAATTAAATG-TTTGGAAAAGCCAAATAATAA
1 GAAAAA-A-TGACATATTTCATAAC-CAAACGGCAATTAGATGCTAAGGAAAA-CCAAATAGTAA
* * *
352082 GTTCACTCTAGAATTAAATAAAAAGTTGATTGATCATATATATATATA
62 GTTCACTCTACAATTAAATAGAAAGTTGATTGATCATAGATATATATA
352130 TATATATATA
Statistics
Matches: 210, Mismatches: 26, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
131 69 0.33
132 23 0.11
133 62 0.30
134 56 0.27
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (131 bp):
GAAAAAATGACATATTTCATAACCAAACGGCAATTAGATGCTAAGGAAAACCAAATAGTAAGTTC
ACTCTACAATTAAATAGAAAGTTGATTGATCATAGATATATATAAGCAAATAGACAAGACATTTA
A
Found at i:352107 original size:134 final size:132
Alignment explanation
Indices: 351755--352129 Score: 414
Period size: 133 Copynumber: 2.8 Consensus size: 132
351745 AATGCTAGGG
* * *** * * * * *
351755 AAAATAATGACATATTTCATAACCAAGACGGTAATTGAATGCTAGGGAAAATCACATAGTAAGTT
1 AAAAAAATGACATATTTCATAA-CAAAACAACAATTAAATGCTAAGGAAAACCAAATAATAAGTT
* * *
351820 CACTCTACG-ATTAAATAGAAAGTTGATTGATCAT-GATATGTATAAGCAAATAGACATGATATT
65 CACTCTA-GAATTAAATAGAAAGTTGATTGATCATAGATATATATAAGCAAATAGACAAGACATT
351883 TAAA
129 TAAA
* *** * *
351887 AAAAAAATGACATATTTCATAACCAAATGGCAATTAGATGCTAAGGAAAACCAAATAGTAAGTTC
1 AAAAAAATGACATATTTCATAACAAAACAACAATTAAATGCTAAGGAAAACCAAATAATAAGTTC
* *
351952 ACTCTACAATTAAATAGAAAGTTGATTGATTATGAGATATATATAAGCAAATAGACAAGACATTT
66 ACTCTAGAATTAAATAGAAAGTTGATTGATCAT-AGATATATATAAGCAAATAGACAAGACATTT
*
352017 AGA
130 AAA
* * * * **
352020 AAAACACTGATATATTTCGTAACTAAAACAACAATTAAATG-TTTGGAAAAGCCAAATAATAAGT
1 AAAAAAATGACATATTTCATAAC-AAAACAACAATTAAATGCTAAGGAAAA-CCAAATAATAAGT
* *
352084 TCACTCTAGAATTAAATAAAAAGTTGATTGATCATATATATATATA
64 TCACTCTAGAATTAAATAGAAAGTTGATTGATCATAGATATATATA
352130 TATATATATA
Statistics
Matches: 206, Mismatches: 32, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
131 64 0.31
132 21 0.10
133 65 0.32
134 56 0.27
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.29
Consensus pattern (132 bp):
AAAAAAATGACATATTTCATAACAAAACAACAATTAAATGCTAAGGAAAACCAAATAATAAGTTC
ACTCTAGAATTAAATAGAAAGTTGATTGATCATAGATATATATAAGCAAATAGACAAGACATTTA
AA
Found at i:352124 original size:2 final size:2
Alignment explanation
Indices: 352117--352149 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
352107 TTGATTGATC
352117 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 A
352150 AGCAAATAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:352153 original size:153 final size:151
Alignment explanation
Indices: 351988--352302 Score: 409
Period size: 153 Copynumber: 2.1 Consensus size: 151
351978 TGATTATGAG
* *
351988 ATATATATAAGCAAATAGACAAGACATTTAGAAAAACACTGAT-ATATTTCGTAACTAAAACAAC
1 ATATATATAAGCAAATAGACAAGACATCTA-AAAAA-AC-GATAATATTTCATAACTAAAACAAC
*** * * * *
352052 AATTAAATGTTTGGAAAAGCCAAATAATAAGTTCACTCTAGAATTAAATAAAAAGTTGATTGATC
63 AATTAAATGTCAAGAAAAACCAAATAATAA-TTCACTCTACAATAAAACAAAAAGTTGATTGATC
352117 AT-ATATATATATATATATATATAT
127 ATGATATATATATATATATATATAT
* * *
352141 ATATATATAAGCAAATAGACAGGACATCTAAAAAAACGATAGCATATTTCATAACTAAAACGATA
1 ATATATATAAGCAAATAGACAAGACATCTAAAAAAACGATA--ATATTTCATAACTAAAACAACA
* * * * *
352206 ATTAAATGTCAAGAAAAACTAAGTAGTAATTCACTTTACAATAAAACAAAATGTTGATTGATCAT
64 ATTAAATGTCAAGAAAAACCAAATAATAATTCACTCTACAATAAAACAAAAAGTTGATTGATCAT
352271 GATATATATATATATATATATAT
129 GATATATATATATATATATATAT
352294 ATATATATA
1 ATATATATA
352303 TATATATATA
Statistics
Matches: 141, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
150 3 0.02
151 2 0.01
152 36 0.26
153 100 0.71
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.31
Consensus pattern (151 bp):
ATATATATAAGCAAATAGACAAGACATCTAAAAAAACGATAATATTTCATAACTAAAACAACAAT
TAAATGTCAAGAAAAACCAAATAATAATTCACTCTACAATAAAACAAAAAGTTGATTGATCATGA
TATATATATATATATATATAT
Found at i:352279 original size:2 final size:2
Alignment explanation
Indices: 352272--352318 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
352262 ATTGATCATG
352272 AT AT AT 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
352314 AT AT A
1 AT AT A
352319 AAAGCAAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:356151 original size:18 final size:19
Alignment explanation
Indices: 356102--356152 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 19
356092 AGCAAATAAG
356102 AAAAATGATTAATAGTATTA
1 AAAAAT-ATTAATAGTATTA
*
356122 AAAATTATTTAA-A-TATTA
1 AAAAATA-TTAATAGTATTA
356140 ATAAAATATTAAT
1 A-AAAATATTAAT
356153 GTGTTATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
18 10 0.38
19 7 0.27
20 9 0.35
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (19 bp):
AAAAATATTAATAGTATTA
Found at i:357369 original size:3 final size:3
Alignment explanation
Indices: 357363--357394 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
357353 ATTATTACCG
357363 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
357395 TGTTTTTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:357986 original size:17 final size:18
Alignment explanation
Indices: 357966--358000 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
357956 TGATATAATT
357966 GATTTAAGT-TTATATTA
1 GATTTAAGTATTATATTA
357983 GATTTAAGTATTATATTA
1 GATTTAAGTATTATATTA
358001 ATATTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.51
Consensus pattern (18 bp):
GATTTAAGTATTATATTA
Found at i:358161 original size:15 final size:15
Alignment explanation
Indices: 358116--358170 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
358106 TTTCATATTA
358116 TAATTTTTAATAAATAT
1 TAATTTTTAAT-AAT-T
358133 TATATTTTT-A-AATT
1 TA-ATTTTTAATAATT
358147 TAATTTTTAATAATT
1 TAATTTTTAATAATT
358162 TAATATTTT
1 TAAT-TTTT
358171 TTTTAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
13 6 0.18
14 4 0.12
15 11 0.32
16 4 0.12
17 3 0.09
18 6 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TAATTTTTAATAATT
Found at i:359000 original size:2 final size:2
Alignment explanation
Indices: 358993--359017 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
358983 CCTTAAGTGG
358993 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 A
359018 AATGAGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:362581 original size:34 final size:34
Alignment explanation
Indices: 362538--362632 Score: 163
Period size: 34 Copynumber: 2.8 Consensus size: 34
362528 GAATATAAAA
362538 TACCTAACACACCTAACATTCTCACCAAATACAT
1 TACCTAACACACCTAACATTCTCACCAAATACAT
362572 TACCTAACACACCTAACATTCTCACCAAATACAT
1 TACCTAACACACCTAACATTCTCACCAAATACAT
* *
362606 CACCTAATACACCTAACATTCTTCACC
1 TACCTAACACACCTAACATTC-TCACC
362633 TAACACACTT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
34 53 0.91
35 5 0.09
ACGTcount: A:0.39, C:0.37, G:0.00, T:0.24
Consensus pattern (34 bp):
TACCTAACACACCTAACATTCTCACCAAATACAT
Found at i:368393 original size:12 final size:13
Alignment explanation
Indices: 368376--368410 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
368366 CCATTTCATA
368376 TTTTTTCTTTTT-
1 TTTTTTCTTTTTC
368388 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
368401 TTTCTTTCTT
1 TTT-TTTCTT
368411 CTTCATCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 3 0.14
14 6 0.29
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:370927 original size:34 final size:34
Alignment explanation
Indices: 370881--370974 Score: 152
Period size: 34 Copynumber: 2.7 Consensus size: 34
370871 AATATAAAAT
*
370881 ACCTAACACACCTAACATTCTCACCAAATACATT
1 ACCTAACACACCTAACATTCTCACCAAATACATC
*
370915 ACTTAACACACCTAACATTCTCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
*
370949 ACCTAACACACATAACATTCTTCACC
1 ACCTAACACACCTAACATTC-TCACC
370975 TAACACACTT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
34 50 0.91
35 5 0.09
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.23
Consensus pattern (34 bp):
ACCTAACACACCTAACATTCTCACCAAATACATC
Found at i:373755 original size:29 final size:29
Alignment explanation
Indices: 373700--373757 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
373690 TTGACATATA
*
373700 TTTAAATATAAATATAAAAATATAAAATT
1 TTTAAATATAAATATAAAAATAAAAAATT
373729 TTTAAATATATAA-A-AAAAATTAAAAAATT
1 TTTAAATATA-AATATAAAAA-TAAAAAATT
373758 AATCATACTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 5 0.19
29 19 0.73
30 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
TTTAAATATAAATATAAAAATAAAAAATT
Found at i:374329 original size:2 final size:2
Alignment explanation
Indices: 374276--374315 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
374266 TCATTCACAA
374276 AT AT 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
374316 TCCTGCTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:375180 original size:14 final size:14
Alignment explanation
Indices: 375141--375185 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
375131 TTAGGGATAT
* *
375141 GTATTTTGACACAG
1 GTATTTTAACACAA
*
375155 GTACTTTAACACAA
1 GTATTTTAACACAA
*
375169 GTATTTTTACACAA
1 GTATTTTAACACAA
375183 GTA
1 GTA
375186 CCTCTGGCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (14 bp):
GTATTTTAACACAA
Found at i:376231 original size:21 final size:21
Alignment explanation
Indices: 376202--376242 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
376192 TTAAATTTTT
*
376202 TAATTGAAATCCATTCTAAAC
1 TAATAGAAATCCATTCTAAAC
**
376223 TAATAGAAATCTTTTCTAAA
1 TAATAGAAATCCATTCTAAA
376243 ATTCAATCAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.37
Consensus pattern (21 bp):
TAATAGAAATCCATTCTAAAC
Found at i:376390 original size:2 final size:2
Alignment explanation
Indices: 376383--376416 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
376373 ATTGCACATT
376383 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
376417 CTCGTGCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:377691 original size:19 final size:18
Alignment explanation
Indices: 377658--377698 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
377648 ACATGATTAT
377658 AATATAATAAAATATACG
1 AATATAATAAAATATACG
*
377676 AATATAATATAAATATATG
1 AATATAATA-AAATATACG
377695 AATA
1 AATA
377699 AATTTACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (18 bp):
AATATAATAAAATATACG
Found at i:377932 original size:22 final size:22
Alignment explanation
Indices: 377902--377948 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
377892 AAAAATTTAA
*
377902 AAATTATTTAAT-ATTAATATTT
1 AAATAATTTAATAATTAA-ATTT
*
377924 AAATAATTTTATAATTAAATTT
1 AAATAATTTAATAATTAAATTT
377946 AAA
1 AAA
377949 AATAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATAATTTAATAATTAAATTT
Found at i:378872 original size:2 final size:2
Alignment explanation
Indices: 378865--378910 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
378855 TGCATTTCTT
* *
378865 TA TA TA TA AA TA TA TA TA TA TA TA TG 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
378907 TA TA
1 TA TA
378911 ATAGACTTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:381127 original size:2 final size:2
Alignment explanation
Indices: 381120--381151 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
381110 TTTGATCATG
381120 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
381152 TATGTTATTT
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:381973 original size:13 final size:13
Alignment explanation
Indices: 381940--381982 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
381930 AAAATAAAAA
381940 AAAATTATC-TTT
1 AAAATTATCTTTT
*
381952 AATAGTTATCTTTT
1 AA-AATTATCTTTT
*
381966 AAAATTATTTTTT
1 AAAATTATCTTTT
381979 AAAA
1 AAAA
381983 AAATTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 2 0.08
13 19 0.73
14 5 0.19
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (13 bp):
AAAATTATCTTTT
Found at i:382265 original size:2 final size:2
Alignment explanation
Indices: 382258--382283 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
382248 TTGGGTTTAA
382258 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
382284 CCTCACGTGT
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:382496 original size:9 final size:9
Alignment explanation
Indices: 382464--382494 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
382454 AAAATTTAAA
382464 TTTTAATAT
1 TTTTAATAT
382473 TTTTAATAT
1 TTTTAATAT
*
382482 TTTTTATAT
1 TTTTAATAT
382491 TTTT
1 TTTT
382495 TAATTTGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTAATAT
Found at i:384311 original size:2 final size:2
Alignment explanation
Indices: 384304--384339 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
384294 TGCATTTCTT
* *
384304 TA TA TA TA AA TA TA TA TA TA TA TG 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
384340 ATAGACTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:386848 original size:36 final size:33
Alignment explanation
Indices: 386808--386884 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 33
386798 ATAAAGTAAT
* *
386808 TAAAATACAATGTAAATATATATTTCAAAATTTATA
1 TAAAATACAAT-T-AATA-ACATATCAAAATTTATA
*
386844 TAAAATA-AATTATTAACATATCAAAATTTATA
1 TAAAATACAATTAATAACATATCAAAATTTATA
386876 T-AAATACAA
1 TAAAATACAA
386885 AATATTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
31 5 0.14
32 18 0.49
33 3 0.08
34 1 0.03
35 3 0.08
36 7 0.19
ACGTcount: A:0.56, C:0.06, G:0.01, T:0.36
Consensus pattern (33 bp):
TAAAATACAATTAATAACATATCAAAATTTATA
Found at i:386885 original size:17 final size:17
Alignment explanation
Indices: 386833--386887 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
386823 ATATATATTT
386833 CAAAATTTATATAAA-A
1 CAAAATTTATATAAATA
*
386849 -TAAA-TTAT-TAACATA
1 CAAAATTTATATAA-ATA
386864 TCAAAATTTATATAAATA
1 -CAAAATTTATATAAATA
386882 CAAAAT
1 CAAAAT
386888 ATTTTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
13 3 0.10
14 5 0.16
15 4 0.13
17 9 0.29
18 7 0.23
19 3 0.10
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (17 bp):
CAAAATTTATATAAATA
Done.