Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold24
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: 3006277
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.30
Warning! 383161 characters in sequence are not A, C, G, or T
File 8 of 19
Found at i:1449751 original size:14 final size:14
Alignment explanation
Indices: 1449720--1449775 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
1449710 AATCACTATT
1449720 TAATTA-ATAAA-A
1 TAATTATATAAATA
*
1449732 -AATTATATAAATT
1 TAATTATATAAATA
1449745 TAATTATA-AAATA
1 TAATTATATAAATA
*
1449758 TATATAATATAAA-A
1 TA-ATTATATAAATA
1449772 TAAT
1 TAAT
1449776 AATTTTAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
11 5 0.14
12 5 0.14
13 8 0.22
14 15 0.42
15 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATTATATAAATA
Found at i:1449777 original size:24 final size:22
Alignment explanation
Indices: 1449725--1449777 Score: 54
Period size: 24 Copynumber: 2.4 Consensus size: 22
1449715 CTATTTAATT
**
1449725 AATAA-AAAATTATATAAATTT
1 AATAATAAAATTATATAAATAA
*
1449746 AATTATAAAATATATATAATATAA
1 AATAATAAAAT-TATATAA-ATAA
1449770 AATAATAA
1 AATAATAA
1449778 TTTTAATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 4 0.16
22 5 0.20
23 7 0.28
24 9 0.36
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AATAATAAAATTATATAAATAA
Found at i:1449912 original size:2 final size:2
Alignment explanation
Indices: 1449905--1449931 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1449895 TAGAATCAAC
1449905 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 A
1449932 AAATGGCACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1451377 original size:6 final size:6
Alignment explanation
Indices: 1451367--1451407 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
1451357 AACACGTGTT
* *
1451367 ATATAT ATATAT ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
1451408 AAATGTAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (6 bp):
ATATAC
Found at i:1451805 original size:7 final size:7
Alignment explanation
Indices: 1451793--1451823 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1451783 AAAATTAATA
1451793 AATTTTT
1 AATTTTT
1451800 AATTTTT
1 AATTTTT
1451807 AATTTTT
1 AATTTTT
1451814 AATTTTT
1 AATTTTT
1451821 AAT
1 AAT
1451824 ATTAAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
AATTTTT
Found at i:1453434 original size:90 final size:90
Alignment explanation
Indices: 1453281--1453820 Score: 927
Period size: 90 Copynumber: 6.0 Consensus size: 90
1453271 GCTTCTCCCC
* * * *
1453281 CTTACCATTTGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTTGTCATCCTGTAGTAATC
1 CTTACCATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATC
* *
1453346 TTTCTGGTTCGTGCTCGTTTGGAGG
66 TTTCCGGCTCGTGCTCGTTTGGAGG
1453371 CTTACCATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATC
1 CTTACCATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATC
1453436 TTTCCGGCTCGTGCTCGTTTGGAGG
66 TTTCCGGCTCGTGCTCGTTTGGAGG
1453461 CTTACCATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATC
1 CTTACCATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATC
1453526 TTTCCGGCTCGTGCTCGTTTGGAGG
66 TTTCCGGCTCGTGCTCGTTTGGAGG
1453551 CTTACCATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATC
1 CTTACCATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATC
1453616 TTTCCGGCTCGTGCTCGTTTGGAGG
66 TTTCCGGCTCGTGCTCGTTTGGAGG
*
1453641 CTTACCATTGGGTGGCTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATC
1 CTTACCATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATC
* *
1453706 TGTCCGGCTCGTGCTCGTTTGGATG
66 TTTCCGGCTCGTGCTCGTTTGGAGG
* * *
1453731 CTTACCATCGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCATCCTTTAGCAATC
1 CTTACCATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATC
* * * * *
1453796 TTGCTGGCGCATGCTCGTGTGGAGG
66 TTTCCGGCTCGTGCTCGTTTGGAGG
1453821 AGGCTTCTTC
Statistics
Matches: 430, Mismatches: 20, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 430 1.00
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (90 bp):
CTTACCATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATC
TTTCCGGCTCGTGCTCGTTTGGAGG
Found at i:1453524 original size:180 final size:180
Alignment explanation
Indices: 1453205--1453820 Score: 944
Period size: 180 Copynumber: 3.5 Consensus size: 180
1453195 TCTCCTTTAT
* * * * *
1453205 CATTGTGTTGTTTCTCACCATAAAATGGACTCATGTATGGCTCATCGTCCTTTAGTAATCTTTCC
1 CATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATCTTTCC
*** *
1453270 GGCT--T-CTC------CCCCTTACCATTTGGTGGTTTTTCACCATAGAATGGACTCATGTATGG
66 GGCTCGTGCTCGTTTGGAGGCTTACCATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGG
* * * * *
1453326 CTTGTCATCCTGTAGTAATCTTTCTGGTTCGTGCTCGTTTGGAGGCTTAC
131 CTCGTCGTCCTTTAGTAATCTTTCCGGCTCGTGCTCGTTTGGAGGCTTAC
1453376 CATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATCTTTCC
1 CATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATCTTTCC
1453441 GGCTCGTGCTCGTTTGGAGGCTTACCATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGG
66 GGCTCGTGCTCGTTTGGAGGCTTACCATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGG
1453506 CTCGTCGTCCTTTAGTAATCTTTCCGGCTCGTGCTCGTTTGGAGGCTTAC
131 CTCGTCGTCCTTTAGTAATCTTTCCGGCTCGTGCTCGTTTGGAGGCTTAC
1453556 CATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATCTTTCC
1 CATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATCTTTCC
*
1453621 GGCTCGTGCTCGTTTGGAGGCTTACCATTGGGTGGCTTTTCACCATAGAATGGACTCATGTATGG
66 GGCTCGTGCTCGTTTGGAGGCTTACCATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGG
* *
1453686 CTCGTCGTCCTTTAGTAATCTGTCCGGCTCGTGCTCGTTTGGATGCTTAC
131 CTCGTCGTCCTTTAGTAATCTTTCCGGCTCGTGCTCGTTTGGAGGCTTAC
* * * * *
1453736 CATCGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCATCCTTTAGCAATCTTGCT
1 CATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATCTTTCC
* * *
1453801 GGCGCATGCTCGTGTGGAGG
66 GGCTCGTGCTCGTTTGGAGG
1453821 AGGCTTCTTC
Statistics
Matches: 411, Mismatches: 25, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
171 64 0.16
173 1 0.00
174 3 0.01
180 343 0.83
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (180 bp):
CATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATCTTTCC
GGCTCGTGCTCGTTTGGAGGCTTACCATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGG
CTCGTCGTCCTTTAGTAATCTTTCCGGCTCGTGCTCGTTTGGAGGCTTAC
Found at i:1453691 original size:270 final size:268
Alignment explanation
Indices: 1453205--1453820 Score: 940
Period size: 270 Copynumber: 2.3 Consensus size: 268
1453195 TCTCCTTTAT
* * * * *
1453205 CATTGTGTTGTTTCTCACCATAAAATGGACTCATGTATGGCTCATCGTCCTTTAGTAATCTTTCC
1 CATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATCTTTCC
*** *
1453270 GGCT-T-CTC-----CCCCTTACCATTTGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCT
66 GGCTCTGCTCGTTGGAGGCTTACCATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCT
* * * *
1453328 TGTCATCCTGTAGTAATCTTTCTGGTTCGTGCTCGTTTGGAGGCTTACCATTGGGTGGTTTTTCA
131 CGTCATCCTGTAGTAATCTTTCCGGCTCGTGCTCGTTTGGAGGCTTACCATTGGGTGGCTTTTCA
*
1453393 CCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATCTTTCCGGCTCGTGCTCGTTTGG
196 CCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATCTGTCCGGCTCGTGCTCGTTTGG
1453458 AGGCTTAC
261 AGGCTTAC
1453466 CATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATCTTTCC
1 CATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATCTTTCC
1453531 GGCTCGTGCTCGTTTGGAGGCTTACCATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGG
66 GGCTC-TGCTCG-TTGGAGGCTTACCATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGG
* *
1453596 CTCGTCGTCCTTTAGTAATCTTTCCGGCTCGTGCTCGTTTGGAGGCTTACCATTGGGTGGCTTTT
129 CTCGTCATCCTGTAGTAATCTTTCCGGCTCGTGCTCGTTTGGAGGCTTACCATTGGGTGGCTTTT
1453661 CACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATCTGTCCGGCTCGTGCTCGTTT
194 CACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATCTGTCCGGCTCGTGCTCGTTT
*
1453726 GGATGCTTAC
259 GGAGGCTTAC
* * * * *
1453736 CATCGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCATCCTTTAGCAATCTTGCT
1 CATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATCTTTCC
*
1453801 GGCGCATGCTCGTGTGGAGG
66 GGCTC-TGCTCGT-TGGAGG
1453821 AGGCTTCTTC
Statistics
Matches: 321, Mismatches: 24, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
261 64 0.20
263 1 0.00
264 3 0.01
269 1 0.00
270 252 0.79
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (268 bp):
CATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATCTTTCC
GGCTCTGCTCGTTGGAGGCTTACCATTGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCT
CGTCATCCTGTAGTAATCTTTCCGGCTCGTGCTCGTTTGGAGGCTTACCATTGGGTGGCTTTTCA
CCATAGAATGGACTCATGTATGGCTCGTCGTCCTTTAGTAATCTGTCCGGCTCGTGCTCGTTTGG
AGGCTTAC
Found at i:1453928 original size:105 final size:104
Alignment explanation
Indices: 1453731--1453938 Score: 242
Period size: 105 Copynumber: 2.0 Consensus size: 104
1453721 CGTTTGGATG
* * * * * * *
1453731 CTTACCATCGGGTGGTTTTTCACCATAGAATGGACTCATGTATGGCTCGTCATCCTTTAGCAATC
1 CTTACCATCAGGTGGTTTCTCACCATAGAACGGACTCACGTATGACGCGTCATCCTTTAGCAAAC
*
1453796 TTGCTGGCGCATGCTCGTGTGGAGGAGGCTTCTTCTCCCC
66 TTGCTGGCGCATGCTCGTATGGAGGAGGCTTC-TCTCCCC
* * *
1453836 CTTACCATTAGGTGGTTTCTCACCATAGAACGGACTCACGTATGACGCGTCGT-CTTTCAGTAAA
1 CTTACCATCAGGTGGTTTCTCACCATAGAACGGACTCACGTATGACGCGTCATCCTTT-AGCAAA
* *
1453900 CTTGCTGGCTCATGCT-GATCAT-GCGGAGGCTTCTCTCCC
65 CTTGCTGGCGCATGCTCG-T-ATGGAGGAGGCTTCTCTCCC
1453939 TCACCCTCGG
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
104 11 0.13
105 75 0.86
106 1 0.01
ACGTcount: A:0.18, C:0.27, G:0.24, T:0.31
Consensus pattern (104 bp):
CTTACCATCAGGTGGTTTCTCACCATAGAACGGACTCACGTATGACGCGTCATCCTTTAGCAAAC
TTGCTGGCGCATGCTCGTATGGAGGAGGCTTCTCTCCCC
Found at i:1454898 original size:2 final size:2
Alignment explanation
Indices: 1454843--1454878 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1454833 TATTGAACTA
1454843 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
1454879 CCTATTGAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1456245 original size:116 final size:116
Alignment explanation
Indices: 1456041--1456260 Score: 422
Period size: 116 Copynumber: 1.9 Consensus size: 116
1456031 TGGAAAGTAC
1456041 TTTTCTTTTTATATCCCTTGTTGTATGATATGATTTATTTCCAACAAAAGTTTGAAATTTAGTTT
1 TTTTCTTTTTATATCCCTTGTTGTATGATATGATTTATTTCCAACAAAAGTTTGAAATTTAGTTT
1456106 TCTTATGTGTTGGAGGTGCTGATTCATGAACATGTTCATAAATTGTTCATA
66 TCTTATGTGTTGGAGGTGCTGATTCATGAACATGTTCATAAATTGTTCATA
*
1456157 TTTTCTTTTTATGTCCCTTGTTGTATGATATGATTTATTTCCAACAAAAGTTTGAAATTTAGTTT
1 TTTTCTTTTTATATCCCTTGTTGTATGATATGATTTATTTCCAACAAAAGTTTGAAATTTAGTTT
*
1456222 TCTTATGTGTTGGAGGTGCTGATTCTTGAACATGTTCAT
66 TCTTATGTGTTGGAGGTGCTGATTCATGAACATGTTCAT
1456261 GATGTTCATT
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 102 1.00
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.48
Consensus pattern (116 bp):
TTTTCTTTTTATATCCCTTGTTGTATGATATGATTTATTTCCAACAAAAGTTTGAAATTTAGTTT
TCTTATGTGTTGGAGGTGCTGATTCATGAACATGTTCATAAATTGTTCATA
Found at i:1461941 original size:12 final size:11
Alignment explanation
Indices: 1461914--1461940 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1461904 ATCTTTCTGA
1461914 TTTTTCTTTAT
1 TTTTTCTTTAT
1461925 TTTTTCTTTAT
1 TTTTTCTTTAT
1461936 TTTTT
1 TTTTT
1461941 TATTTTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTCTTTAT
Found at i:1461946 original size:28 final size:29
Alignment explanation
Indices: 1461915--1461984 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 29
1461905 TCTTTCTGAT
1461915 TTTTCTTTATTTTTTCTTTATT-TTTTTA
1 TTTTCTTTATTTTTTCTTTATTATTTTTA
* **
1461943 TTTTCTTAAAATTTTCTTTATTATTTTTA
1 TTTTCTTTATTTTTTCTTTATTATTTTTA
*
1461972 TTAT-TTTATTTTT
1 TTTTCTTTATTTTT
1461985 ATACCCTATG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
28 25 0.74
29 9 0.26
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (29 bp):
TTTTCTTTATTTTTTCTTTATTATTTTTA
Found at i:1468278 original size:29 final size:29
Alignment explanation
Indices: 1468246--1468304 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
1468236 ATTATAAATT
1468246 ATAAATTAAAA-TTAATTAAATAATAAAAA
1 ATAAA-TAAAATTTAATTAAATAATAAAAA
* *
1468275 ATAAATAAAATTTACTTAATTAATAAAAA
1 ATAAATAAAATTTAATTAAATAATAAAAA
1468304 A
1 A
1468305 ATATAGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (29 bp):
ATAAATAAAATTTAATTAAATAATAAAAA
Found at i:1469382 original size:14 final size:14
Alignment explanation
Indices: 1469363--1469389 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1469353 AGGTTGAAGA
1469363 GGACCACAAAATTT
1 GGACCACAAAATTT
1469377 GGACCACAAAATT
1 GGACCACAAAATT
1469390 GGGTTAGAAC
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:0.44, C:0.22, G:0.15, T:0.19
Consensus pattern (14 bp):
GGACCACAAAATTT
Found at i:1473364 original size:2 final size:2
Alignment explanation
Indices: 1473357--1473389 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1473347 TCAATCTTAA
1473357 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
1473390 AAACTAAAAG
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:1474069 original size:22 final size:22
Alignment explanation
Indices: 1474044--1474098 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
1474034 AATATAATAA
1474044 AATATTAAAAATATTTT-TAATT
1 AATATT-AAAATATTTTATAATT
* *
1474066 AATATTTATATATTTTATAATT
1 AATATTAAAATATTTTATAATT
*
1474088 AA-ATTTAAATA
1 AATATTAAAATA
1474099 AAAATATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATATTAAAATATTTTATAATT
Found at i:1474080 original size:21 final size:21
Alignment explanation
Indices: 1474054--1474094 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1474044 AATATTAAAA
1474054 ATATTTT-TAATTAATATTTAT
1 ATATTTTATAATTAA-ATTTAT
1474075 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
1474095 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:1474131 original size:19 final size:18
Alignment explanation
Indices: 1474089--1474134 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
1474079 TTTATAATTA
*
1474089 AATTTAAATAAAAATATT
1 AATTTAAATAAAAATAAT
* *
1474107 ATTTTAATTAATAAATAAT
1 AATTTAAATAA-AAATAAT
1474126 AATTTAAAT
1 AATTTAAAT
1474135 TTATTTAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTTAAATAAAAATAAT
Found at i:1474150 original size:48 final size:48
Alignment explanation
Indices: 1474049--1474149 Score: 127
Period size: 50 Copynumber: 2.1 Consensus size: 48
1474039 AATAAAATAT
** *
1474049 TAAAAATATTTTTAATTAATATTTATATATTTTATAATTAAATTTAAA
1 TAAAAATATTTTTAATTAATAAATATATAATTTATAATTAAATTTAAA
*
1474097 TAAAAATATTATTTTAATTAATAAATA-ATAATTTA-AATT-TATTTAAA
1 TAAAAATA-T-TTTTAATTAATAAATATATAATTTATAATTAAATTTAAA
1474144 TAAAAA
1 TAAAAA
1474150 AATAAATTCT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
47 13 0.28
48 12 0.26
49 8 0.17
50 14 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (48 bp):
TAAAAATATTTTTAATTAATAAATATATAATTTATAATTAAATTTAAA
Found at i:1474155 original size:22 final size:22
Alignment explanation
Indices: 1474090--1474157 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
1474080 TTATAATTAA
* * *
1474090 ATTTAAATAAAAATATTATTTT
1 ATTTAAATAAAAAAATAAATTT
*
1474112 AATT-AATAAATAATAATTTAAATTT
1 ATTTAAATAAA-AA-AA--TAAATTT
1474137 ATTTAAATAAAAAAATAAATT
1 ATTTAAATAAAAAAATAAATT
1474158 CTAACTCAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
21 6 0.17
22 11 0.31
23 1 0.03
24 2 0.06
25 10 0.28
26 6 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTAAATAAAAAAATAAATTT
Found at i:1474314 original size:39 final size:37
Alignment explanation
Indices: 1474271--1474357 Score: 84
Period size: 43 Copynumber: 2.2 Consensus size: 37
1474261 GAAATACGAG
*
1474271 TTTTATTATATTTATTTAGTATTTATAAATAGATATAT
1 TTTTATTATATTTATTTAATATTTATAAATAGAT-TAT
* * *
1474309 CTTTTAAAAATTATATTTTTTTAATATTTTTAAATATATTAT
1 -TTTT----ATTATATTTATTTAATATTTATAAATAGATTAT
1474351 TTTTATT
1 TTTTATT
1474358 TAATTTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
37 3 0.08
39 4 0.10
41 4 0.10
42 3 0.08
43 26 0.65
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (37 bp):
TTTTATTATATTTATTTAATATTTATAAATAGATTAT
Found at i:1474359 original size:28 final size:26
Alignment explanation
Indices: 1474305--1474371 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
1474295 ATAAATAGAT
1474305 ATATCTTTTAAAAATTATATTTTTTTA
1 ATAT-TTTTAAAAATTATATTTTTTTA
1474332 ATATTTTTAAATATATTAT-TTTTATTTA
1 ATATTTTTAAA-A-ATTATATTTT-TTTA
*
1474360 AT-TTTTAAAAAA
1 ATATTTTTAAAAA
1474372 ATTTCTCTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
25 1 0.03
26 8 0.22
27 16 0.44
28 11 0.31
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (26 bp):
ATATTTTTAAAAATTATATTTTTTTA
Found at i:1477662 original size:22 final size:24
Alignment explanation
Indices: 1477634--1477685 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 24
1477624 TTATTTAAAA
1477634 AATATTTAAATTA-TTTTAT-ATT
1 AATATTTAAATTATTTTTATAATT
1477656 AATATTT---TTATTTTTATAATT
1 AATATTTAAATTATTTTTATAATT
1477677 AA-ATTTAAA
1 AATATTTAAA
1477686 AAATTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
19 3 0.12
20 10 0.40
21 5 0.20
22 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
AATATTTAAATTATTTTTATAATT
Found at i:1478637 original size:18 final size:18
Alignment explanation
Indices: 1478580--1478651 Score: 69
Period size: 18 Copynumber: 4.1 Consensus size: 18
1478570 ACGTGGATAT
*
1478580 TAATT-TTTATAATTTGAA
1 TAATTATTT-TAATTTAAA
* * *
1478598 TAATATAATTTGATTCAAA
1 TAAT-TATTTTAATTTAAA
1478617 TAATTATTTTAATTTAAA
1 TAATTATTTTAATTTAAA
1478635 TAATTA-TTT-ATTTAAA
1 TAATTATTTTAATTTAAA
1478651 T
1 T
1478652 TTAACTATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
16 8 0.18
17 3 0.07
18 21 0.47
19 11 0.24
20 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (18 bp):
TAATTATTTTAATTTAAA
Found at i:1478903 original size:11 final size:11
Alignment explanation
Indices: 1478874--1478937 Score: 62
Period size: 11 Copynumber: 6.0 Consensus size: 11
1478864 GTTAAATATG
1478874 ATAATATTAAAT
1 ATAATA-TAAAT
**
1478886 ACGATATAAAT
1 ATAATATAAAT
*
1478897 ATAATATAAAA
1 ATAATATAAAT
1478908 ATAA-A-AAAT
1 ATAATATAAAT
1478917 -TAATATAAAT
1 ATAATATAAAT
*
1478927 ATAAAATAAAT
1 ATAATATAAAT
1478938 TTATGAATGA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
8 3 0.07
9 4 0.10
10 5 0.12
11 26 0.62
12 4 0.10
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:1478922 original size:19 final size:20
Alignment explanation
Indices: 1478893--1478932 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1478883 AATACGATAT
1478893 AAATATAATATAAAAATAAA
1 AAATATAATATAAAAATAAA
*
1478913 AAAT-TAATATAAATATAAA
1 AAATATAATATAAAAATAAA
1478932 A
1 A
1478933 TAAATTTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AAATATAATATAAAAATAAA
Found at i:1479055 original size:19 final size:18
Alignment explanation
Indices: 1479018--1479057 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1479008 ATATAATTAT
* *
1479018 AATACAATAAAATATATA
1 AATACAAAAAAATACATA
1479036 AATACAAAATAAATACATA
1 AATACAAAA-AAATACATA
1479055 AAT
1 AAT
1479058 TATTAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (18 bp):
AATACAAAAAAATACATA
Found at i:1480291 original size:4 final size:4
Alignment explanation
Indices: 1480284--1480308 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1480274 TATATATTTA
1480284 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
1480309 GCATAGACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:1480850 original size:39 final size:39
Alignment explanation
Indices: 1480776--1480851 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 39
1480766 TTATATCTAT
* *
1480776 ATTTAAAAAATTATTTTTAATATTAATATTTATAATTAA
1 ATTTAAAAAAATATTTTTAATATTAATATTAATAATTAA
*
1480815 ATTTAAATAAAATATTTTTATTACTTAA-A-TAATAATT
1 ATTTAAA-AAAATATTTTTAATA-TTAATATTAATAATT
1480852 TATATTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 14 0.44
40 14 0.44
41 4 0.12
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (39 bp):
ATTTAAAAAAATATTTTTAATATTAATATTAATAATTAA
Found at i:1480857 original size:21 final size:22
Alignment explanation
Indices: 1480817--1480858 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1480807 ATAATTAAAT
*
1480817 TTAAATAAAATATTTTTATTAC
1 TTAAATAAAATATTTATATTAC
*
1480839 TTAAATAATA-ATTTATATTA
1 TTAAATAAAATATTTATATTA
1480859 AATCAAATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAAATAAAATATTTATATTAC
Found at i:1481561 original size:18 final size:19
Alignment explanation
Indices: 1481538--1481575 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
1481528 GGATTAAATT
1481538 ATTTATTTAA-ATTTAAAA
1 ATTTATTTAATATTTAAAA
1481556 ATTTATTTAATATTTAAAA
1 ATTTATTTAATATTTAAAA
1481575 A
1 A
1481576 AATTTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTATTTAATATTTAAAA
Found at i:1481582 original size:17 final size:17
Alignment explanation
Indices: 1481542--1481584 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
1481532 TAAATTATTT
*
1481542 ATTTAAATTTAAAAATTT
1 ATTTAAATTTAAAAA-TA
1481560 ATTTAATATTTAAAAA-A
1 ATTTAA-ATTTAAAAATA
1481577 ATTTAAAT
1 ATTTAAAT
1481585 AAATATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 2 0.09
17 6 0.26
18 6 0.26
19 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTAAATTTAAAAATA
Found at i:1482342 original size:23 final size:22
Alignment explanation
Indices: 1482316--1482358 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1482306 ATCAAAAAAA
* *
1482316 TATTTTTATTAAAAATAACTTAG
1 TATTTTCAATAAAAA-AACTTAG
1482339 TATTTTCAATAAAAAAACTT
1 TATTTTCAATAAAAAAACTT
1482359 CATTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (22 bp):
TATTTTCAATAAAAAAACTTAG
Found at i:1482582 original size:25 final size:22
Alignment explanation
Indices: 1482548--1482595 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 22
1482538 ATATATTTTA
1482548 TAATTAAATTTAAATAAAAATATAT
1 TAATTAAATTT--ATAAAAAT-TAT
1482573 TAATTAAATTTATAAAAATTAT
1 TAATTAAATTTATAAAAATTAT
1482595 T
1 T
1482596 TCGAGTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.17
23 8 0.35
25 11 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATTAAATTTATAAAAATTAT
Found at i:1483993 original size:2 final size:2
Alignment explanation
Indices: 1483986--1484062 Score: 84
Period size: 2 Copynumber: 38.5 Consensus size: 2
1483976 GAGGTGGGAC
* *
1483986 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
1484028 TA TG CA TA CA TA CA TA TA TA TA TA TA -A GTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
1484063 TCAAATAATT
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
1 1 0.02
2 59 0.97
3 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1484628 original size:9 final size:9
Alignment explanation
Indices: 1484616--1484656 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
1484606 AATTATATTA
1484616 ATTTTATAT
1 ATTTTATAT
1484625 ATTTTATA-
1 ATTTTATAT
*
1484633 ATTTTATAA
1 ATTTTATAT
1484642 ATGTTTA-AT
1 AT-TTTATAT
1484651 ATTTTA
1 ATTTTA
1484657 ACAAATTAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 12 0.41
9 13 0.45
10 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (9 bp):
ATTTTATAT
Found at i:1484635 original size:26 final size:26
Alignment explanation
Indices: 1484606--1484656 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1484596 TATTAATATA
*
1484606 AATTATATTAAT-TTTATATATTTTAT
1 AATTATATAAATGTTTA-ATATTTTAT
*
1484632 AATTTTATAAATGTTTAATATTTTA
1 AATTATATAAATGTTTAATATTTTA
1484657 ACAAATTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (26 bp):
AATTATATAAATGTTTAATATTTTAT
Found at i:1486619 original size:17 final size:17
Alignment explanation
Indices: 1486597--1486662 Score: 61
Period size: 18 Copynumber: 4.1 Consensus size: 17
1486587 CGAATTATTC
* *
1486597 ATTTAAATTTGAAAATT
1 ATTTAAATTTAAAAAAT
1486614 ATTTAAAATTTAAAAAAT
1 ATTT-AAATTTAAAAAAT
1486632 -TTTAAA--T-AAAAAT
1 ATTTAAATTTAAAAAAT
*
1486645 A-TTAAGTTTAAAAAAT
1 ATTTAAATTTAAAAAAT
1486661 AT
1 AT
1486663 ATTTAGGTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
13 10 0.25
14 1 0.03
15 1 0.03
16 10 0.25
17 7 0.17
18 11 0.28
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
ATTTAAATTTAAAAAAT
Found at i:1486638 original size:16 final size:16
Alignment explanation
Indices: 1486598--1486660 Score: 51
Period size: 16 Copynumber: 4.0 Consensus size: 16
1486588 GAATTATTCA
*
1486598 TTTAAATTTGAAAATTAT
1 TTTAAATTT-AAAA-AAT
*
1486616 TTAAAATTTAAAAAAT
1 TTTAAATTTAAAAAAT
1486632 TTTAAA--T-AAAAAT
1 TTTAAATTTAAAAAAT
* *
1486645 ATTAAGTTTAAAAAAT
1 TTTAAATTTAAAAAAT
1486661 ATATTTAGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
13 10 0.27
14 1 0.03
15 1 0.03
16 13 0.35
17 4 0.11
18 8 0.22
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
TTTAAATTTAAAAAAT
Found at i:1486765 original size:14 final size:14
Alignment explanation
Indices: 1486746--1486812 Score: 68
Period size: 14 Copynumber: 4.9 Consensus size: 14
1486736 TTATTTTTTA
1486746 ATTATATAATATAT
1 ATTATATAATATAT
* *
1486760 ATTATATAATTTTT
1 ATTATATAATATAT
1486774 ATTATAGT-ATATAT
1 ATTATA-TAATATAT
1486788 A-TATATAATACTAT
1 ATTATATAATA-TAT
*
1486802 AATATA-AATAT
1 ATTATATAATAT
1486813 TTAAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
12 1 0.02
13 8 0.18
14 31 0.69
15 5 0.11
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (14 bp):
ATTATATAATATAT
Found at i:1486777 original size:28 final size:28
Alignment explanation
Indices: 1486740--1486796 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 28
1486730 TTCGGTTTAT
1486740 TTTTTAATTATA-TAATATATATTATATAA
1 TTTTTAATTATAGT-ATATATA-TATATAA
1486769 TTTTT-ATTATAGTATATATATATATAA
1 TTTTTAATTATAGTATATATATATATAA
1486796 T
1 T
1486797 ACTATAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 8 0.30
28 13 0.48
29 6 0.22
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTTTAATTATAGTATATATATATATAA
Found at i:1486880 original size:22 final size:21
Alignment explanation
Indices: 1486855--1486901 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
1486845 ATCTAATAAA
1486855 AAATATT-AAATCACTATAGATT
1 AAATATTAAAAT-A-TATAGATT
*
1486877 AAAT-TTAAAATATATATATT
1 AAATATTAAAATATATAGATT
1486897 AAATA
1 AAATA
1486902 AAATAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 11 0.50
21 3 0.14
22 8 0.36
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (21 bp):
AAATATTAAAATATATAGATT
Found at i:1486927 original size:16 final size:16
Alignment explanation
Indices: 1486883--1486928 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 16
1486873 GATTAAATTT
1486883 AAAATATAT-ATATTA
1 AAAATATATAATATTA
1486898 AATAA-A-ATAA-ATTA
1 AA-AATATATAATATTA
1486912 AAAATATATAATATTA
1 AAAATATATAATATTA
1486928 A
1 A
1486929 TAAAATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
13 2 0.08
14 9 0.35
15 8 0.31
16 7 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATATATAATATTA
Found at i:1486933 original size:18 final size:17
Alignment explanation
Indices: 1486883--1486934 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 17
1486873 GATTAAATTT
1486883 AAAATATAT-ATATTAA
1 AAAATATATAATATTAA
*
1486899 ATAA-A-ATAA-ATT-A
1 AAAATATATAATATTAA
1486912 AAAATATATAATATTAA
1 AAAATATATAATATTAA
1486929 TAAAAT
1 -AAAAT
1486935 TAAATAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
13 4 0.14
14 6 0.21
15 6 0.21
16 6 0.21
17 1 0.04
18 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATATATAATATTAA
Found at i:1486942 original size:29 final size:30
Alignment explanation
Indices: 1486874--1486939 Score: 100
Period size: 29 Copynumber: 2.2 Consensus size: 30
1486864 ATCACTATAG
*
1486874 ATTAAATTTAAAATATATATATTAAATAAA
1 ATTAAATTAAAAATATATATATTAAATAAA
1486904 A-TAAATTAAAAATATATAATATT-AATAAA
1 ATTAAATTAAAAATATAT-ATATTAAATAAA
1486933 ATTAAAT
1 ATTAAAT
1486940 AAATTTTAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 22 0.67
30 11 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (30 bp):
ATTAAATTAAAAATATATATATTAAATAAA
Found at i:1487027 original size:15 final size:16
Alignment explanation
Indices: 1486999--1487030 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1486989 ATATTTTTAT
1486999 TTTAAATCAAATTAAA
1 TTTAAATCAAATTAAA
1487015 TTTAAAT-AAATTAAA
1 TTTAAATCAAATTAAA
1487030 T
1 T
1487031 AATATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTAAATCAAATTAAA
Found at i:1488014 original size:2 final size:2
Alignment explanation
Indices: 1488007--1488040 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1487997 GGAATAGGTA
1488007 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
1488041 CATTAAACAT
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):
AT
Found at i:1489059 original size:28 final size:27
Alignment explanation
Indices: 1488996--1489059 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
1488986 ATTGGTTACT
1488996 TTTAATTTCATTATAATTATTTATATA
1 TTTAATTTCATTATAATTATTTATATA
* *
1489023 TTTAAAATTTTA-TATATTTATATATATATA
1 TTT--AATTTCATTATAATTAT-T-TATATA
1489053 TTTAATT
1 TTTAATT
1489060 ATACATCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
27 3 0.10
28 12 0.39
29 7 0.23
30 9 0.29
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTAATTTCATTATAATTATTTATATA
Found at i:1489062 original size:16 final size:16
Alignment explanation
Indices: 1489009--1489062 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
1488999 AATTTCATTA
*
1489009 TAATTATTTATATATT
1 TAATTATATATATATT
1489025 TAAAATT-T-TATATATT
1 T--AATTATATATATATT
1489041 T-A-TATATATATATT
1 TAATTATATATATATT
1489055 TAATTATA
1 TAATTATA
1489063 CATCGAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
12 1 0.03
13 2 0.06
14 9 0.28
15 1 0.03
16 14 0.44
17 1 0.03
18 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TAATTATATATATATT
Found at i:1490070 original size:16 final size:16
Alignment explanation
Indices: 1490011--1490072 Score: 61
Period size: 16 Copynumber: 3.7 Consensus size: 16
1490001 TTGATTTAAA
* *
1490011 TAAATTTAATTTGATT
1 TAAATTTATTTTTATT
*
1490027 TAAATTATTATTTATTAAT
1 TAAA-T-TTATTT-TTATT
*
1490046 TAAAATTATTTTTATT
1 TAAATTTATTTTTATT
1490062 TAAATTTATTT
1 TAAATTTATTT
1490073 AATAAAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
16 18 0.49
17 7 0.19
18 5 0.14
19 7 0.19
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TAAATTTATTTTTATT
Found at i:1490806 original size:26 final size:27
Alignment explanation
Indices: 1490777--1490847 Score: 65
Period size: 33 Copynumber: 2.5 Consensus size: 27
1490767 ATTTATGTAT
*
1490777 TTATAAAATTTAAA-TAAAATATTTTA
1 TTATAAAATTTAAATTAAAAAATTTTA
1490803 TTATTAAATTATAATTTAAATTAAAAAATTTTA
1 TTA-T--A--A-AATTTAAATTAAAAAATTTTA
1490836 TT-TAAAATTTAA
1 TTATAAAATTTAA
1490848 TTCATATAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
26 10 0.27
27 2 0.05
29 2 0.05
31 2 0.05
32 8 0.22
33 13 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TTATAAAATTTAAATTAAAAAATTTTA
Found at i:1490825 original size:20 final size:20
Alignment explanation
Indices: 1490802--1490876 Score: 55
Period size: 21 Copynumber: 3.7 Consensus size: 20
1490792 AAAATATTTT
1490802 ATTATTAAATTATAATTTAA
1 ATTATTAAATTATAATTTAA
** *
1490822 ATTAAAAAATT-TTATTTAA
1 ATTATTAAATTATAATTTAA
* * *
1490841 AAT-TTAATTCATATAAATTAA
1 ATTATTAAAT--TATAATTTAA
1490862 ATTTATTAAATTATA
1 A-TTATTAAATTATA
1490877 TTAAAAACTC
Statistics
Matches: 39, Mismatches: 11, Indels: 9
0.66 0.19 0.15
Matches are distributed among these distances:
18 3 0.08
19 9 0.23
20 10 0.26
21 11 0.28
22 1 0.03
23 5 0.13
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTATTAAATTATAATTTAA
Found at i:1490834 original size:33 final size:30
Alignment explanation
Indices: 1490783--1490849 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 30
1490773 GTATTTATAA
* *
1490783 AATTTAAATAAAATATTTTATTATTAAATTAT
1 AATTTAAATAAAAAATTTTATT-TAAAATT-T
1490815 AATTTAAATTAAAAAATTTTATTTAAAATTT
1 AATTTAAA-TAAAAAATTTTATTTAAAATTT
1490846 AATT
1 AATT
1490850 CATATAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 5 0.16
32 14 0.44
33 13 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTTAAATAAAAAATTTTATTTAAAATTT
Found at i:1492617 original size:15 final size:15
Alignment explanation
Indices: 1492597--1492660 Score: 55
Period size: 15 Copynumber: 4.3 Consensus size: 15
1492587 TGAGATATTT
1492597 ATATTATTTTTTATC
1 ATATTATTTTTTATC
1492612 ATATTATTTATTT-T-
1 ATATTATTT-TTTATC
* *
1492626 ATA-TATATTTTAATT
1 ATATTAT-TTTTTATC
1492641 A-ATTATTTTTTAATC
1 ATATTATTTTTT-ATC
1492656 ATATT
1 ATATT
1492661 TATATCAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
13 5 0.13
14 11 0.28
15 17 0.44
16 6 0.15
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (15 bp):
ATATTATTTTTTATC
Found at i:1494474 original size:17 final size:17
Alignment explanation
Indices: 1494448--1494482 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1494438 TGTAACTTTT
* *
1494448 ATAAATTATAGATAAAA
1 ATAAAATATAAATAAAA
1494465 ATAAAATATAAATAAAA
1 ATAAAATATAAATAAAA
1494482 A
1 A
1494483 AATTATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
ATAAAATATAAATAAAA
Found at i:1497003 original size:2 final size:2
Alignment explanation
Indices: 1496996--1497023 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1496986 ATAAACTTAA
1496996 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
1497024 TGAAACTTTT
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):
AT
Found at i:1498677 original size:18 final size:20
Alignment explanation
Indices: 1498638--1498674 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1498628 ATTTTAAAAT
1498638 ATAATTAATATAATTTTTTA
1 ATAATTAATATAATTTTTTA
*
1498658 ATAATTTATAT-ATTTTT
1 ATAATTAATATAATTTTT
1498675 AATTAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATAATTAATATAATTTTTTA
Found at i:1499079 original size:26 final size:27
Alignment explanation
Indices: 1499032--1499087 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
1499022 TTATTTATCA
1499032 AATATTTCATTTAATAATTTAAATAAT
1 AATATTTCATTTAATAATTTAAATAAT
*
1499059 AATATTT-ATTTAAATAA-TTAATTAAT
1 AATATTTCATTT-AATAATTTAAATAAT
1499085 AAT
1 AAT
1499088 TTTTGTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
AATATTTCATTTAATAATTTAAATAAT
Found at i:1499097 original size:23 final size:25
Alignment explanation
Indices: 1499032--1499107 Score: 66
Period size: 26 Copynumber: 3.0 Consensus size: 25
1499022 TTATTTATCA
* *
1499032 AATATTTCATTTAATAATTTAAATAAT
1 AATATTT-ATGTAATAA-TTAATTAAT
*
1499059 AATATTTATTTAAATAATTAATTAAT
1 AATATTTATGT-AATAATTAATTAAT
* *
1499085 AAT-TTT-TGTAATAAATATTTAAT
1 AATATTTATGTAATAATTAATTAAT
1499108 TTTTTTAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
23 12 0.27
24 2 0.05
25 3 0.07
26 15 0.34
27 12 0.27
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (25 bp):
AATATTTATGTAATAATTAATTAAT
Found at i:1499351 original size:23 final size:23
Alignment explanation
Indices: 1499325--1499372 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1499315 AGTTTCAATC
1499325 AAAAAAAATTTA-ATAAAATTAAA
1 AAAAAAAATTTATAT-AAATTAAA
**
1499348 AAAATTAATTTATATAAATTAAA
1 AAAAAAAATTTATATAAATTAAA
1499371 AA
1 AA
1499373 TCAAAAGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAAAAAATTTATATAAATTAAA
Found at i:1502723 original size:25 final size:25
Alignment explanation
Indices: 1502669--1502725 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
1502659 TATTAATTTT
* *
1502669 TTATTCTTATTAATTTATAATATTA
1 TTATTTTTATTAATTTAGAATATTA
1502694 TTATTTTTATTAATTTAGAATTATTA
1 TTATTTTTATTAATTTAGAA-TATTA
1502720 -TATTTT
1 TTATTTT
1502726 AAAAAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 24 0.83
26 5 0.17
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (25 bp):
TTATTTTTATTAATTTAGAATATTA
Found at i:1502926 original size:24 final size:24
Alignment explanation
Indices: 1502894--1502943 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
1502884 ACACGGAATG
*
1502894 CGCTAAGCAACTGAGCACTTCTTA
1 CGCTAAGCAACTAAGCACTTCTTA
*
1502918 CGCTAAGCACCTAAGCACTTCTTA
1 CGCTAAGCAACTAAGCACTTCTTA
1502942 CG
1 CG
1502944 TGGAGGTGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.28, C:0.32, G:0.16, T:0.24
Consensus pattern (24 bp):
CGCTAAGCAACTAAGCACTTCTTA
Found at i:1503961 original size:27 final size:28
Alignment explanation
Indices: 1503914--1503970 Score: 64
Period size: 27 Copynumber: 2.0 Consensus size: 28
1503904 TAAAAAGATT
*
1503914 AAATATATAAATATAACATCA-ATTTTC
1 AAATATATAAATATAAAATCAGATTTTC
*
1503941 AAATATATGAGAT-TAAAATCAGTATTTTC
1 AAATATAT-AAATATAAAATCAG-ATTTTC
1503970 A
1 A
1503971 TTCATGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 15 0.60
28 3 0.12
29 7 0.28
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (28 bp):
AAATATATAAATATAAAATCAGATTTTC
Found at i:1504234 original size:15 final size:17
Alignment explanation
Indices: 1504163--1504235 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 17
1504153 AATATGATAA
1504163 TTTATATATT-T-ATAT
1 TTTATATATTATAATAT
*
1504178 TTTATTTA-TATAAT-T
1 TTTATATATTATAATAT
*
1504193 TTTATGTATTATAAAAATAT
1 TTTATATATTAT---AATAT
*
1504213 TTAATATATTAT-AT-T
1 TTTATATATTATAATAT
1504228 TTTATATA
1 TTTATATA
1504236 AATTTTAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
14 1 0.02
15 24 0.52
16 7 0.15
19 3 0.07
20 11 0.24
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (17 bp):
TTTATATATTATAATAT
Found at i:1504242 original size:27 final size:27
Alignment explanation
Indices: 1504201--1504317 Score: 81
Period size: 29 Copynumber: 4.0 Consensus size: 27
1504191 TTTTTATGTA
*
1504201 TTATAAAAATATTTAATATATTATATTT
1 TTATATAAAT-TTTAATATATTATATTT
**
1504229 TTATATAAATTTTAATACGTTAATAATTT
1 TTATATAAATTTTAATATATT-AT-ATTT
* **
1504258 ATATTATAAAATTTTAATATATTTATATAA
1 TTA-TAT-AAATTTTAATATA-TTATATTT
* * *
1504288 TTATATTATTTTTATATTTCATTATATTT
1 TTATATAAATTTTA-ATAT-ATTATATTT
1504317 T
1 T
1504318 AAATTTTGAT
Statistics
Matches: 68, Mismatches: 14, Indels: 13
0.72 0.15 0.14
Matches are distributed among these distances:
27 9 0.13
28 17 0.25
29 19 0.28
30 8 0.12
31 13 0.19
32 2 0.03
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (27 bp):
TTATATAAATTTTAATATATTATATTT
Found at i:1504311 original size:16 final size:17
Alignment explanation
Indices: 1504256--1504323 Score: 50
Period size: 17 Copynumber: 3.9 Consensus size: 17
1504246 CGTTAATAAT
* *
1504256 TTATATTATAAAATTTTA
1 TTATATT-TTAAATTTCA
*
1504274 ATATATTTATATAATTAT-A
1 TTATATTT-TA-AATT-TCA
*
1504293 TTAT-TTTTATATTTCA
1 TTATATTTTAAATTTCA
1504309 TTATATTTTAAATTT
1 TTATATTTTAAATTT
1504324 TGATATTATA
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
15 1 0.03
16 8 0.20
17 12 0.30
18 10 0.25
19 8 0.20
20 1 0.03
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATATTTTAAATTTCA
Found at i:1504398 original size:17 final size:18
Alignment explanation
Indices: 1504365--1504402 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1504355 TAAATTATCA
1504365 AATTTTATTATATTTTTT
1 AATTTTATTATATTTTTT
*
1504383 AATTTTTTTA-ATTTTTT
1 AATTTTATTATATTTTTT
1504400 AAT
1 AAT
1504403 ATTAAGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
AATTTTATTATATTTTTT
Found at i:1505188 original size:68 final size:68
Alignment explanation
Indices: 1505100--1505233 Score: 241
Period size: 68 Copynumber: 2.0 Consensus size: 68
1505090 TATGCGTATC
* *
1505100 CGTCGATGCCTTCTTTTGTGTGTTAATGTAGTTTTAAGGTTTTAGACGGAAGCATACATGGTTTC
1 CGTCGATGCCTTCTTTTGTGTGTTAATGTAGTTTTAAGGTTTTAGACGGAAGCATAAATGATTTC
1505165 ATT
66 ATT
*
1505168 CGTCGATGCCTTGTTTTGTGTGTTAATGTAGTTTTAAGGTTTTAGACGGAAGCATAAATGATTTC
1 CGTCGATGCCTTCTTTTGTGTGTTAATGTAGTTTTAAGGTTTTAGACGGAAGCATAAATGATTTC
1505233 A
66 A
1505234 GGTTCCAAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.42
Consensus pattern (68 bp):
CGTCGATGCCTTCTTTTGTGTGTTAATGTAGTTTTAAGGTTTTAGACGGAAGCATAAATGATTTC
ATT
Found at i:1509144 original size:23 final size:23
Alignment explanation
Indices: 1509096--1509145 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1509086 ATGTTGCTTT
* *
1509096 TTTTTAATTTTAGTAAAATTTGA
1 TTTTTAAATTTAGTAAAATATGA
*
1509119 TTTTTAAATTTATTAAATATAT-A
1 TTTTTAAATTTAGTAAA-ATATGA
1509142 TTTT
1 TTTT
1509146 AAAAATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTTAAATTTAGTAAAATATGA
Found at i:1511310 original size:22 final size:22
Alignment explanation
Indices: 1511285--1511330 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1511275 ATATAAAAAA
* *
1511285 AATTTT-TTATTAATATTTATAT
1 AATTTTATAATTAA-ATTTAAAT
1511307 AATTTTATAATTAAATTTAAAT
1 AATTTTATAATTAAATTTAAAT
1511329 AA
1 AA
1511331 AATATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTTTATAATTAAATTTAAAT
Found at i:1512709 original size:18 final size:18
Alignment explanation
Indices: 1512678--1512772 Score: 52
Period size: 20 Copynumber: 5.1 Consensus size: 18
1512668 TATAGAAAAT
1512678 TAAT-TAAA-ATATAATA
1 TAATATAAATATATAATA
1512694 TAATATAAATATATAA-A
1 TAATATAAATATATAATA
* *
1512711 TATTTTTAAATTTATATAATA
1 TA-ATATAAA--TATATAATA
* *
1512732 CTAATTATTAATATATTAAATT
1 -TAA-TATAAATATA-T-AATA
* *
1512754 TTATATAAATATAAAATA
1 TAATATAAATATATAATA
1512772 T
1 T
1512773 TTTAAACATA
Statistics
Matches: 59, Mismatches: 10, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
16 4 0.07
17 7 0.12
18 15 0.25
20 20 0.34
21 4 0.07
22 9 0.15
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATATAAATATATAATA
Found at i:1512766 original size:38 final size:38
Alignment explanation
Indices: 1512684--1512767 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 38
1512674 AAATTAATTA
1512684 AAATATAATATAATATAAATATATAAATATTTTTAAAT
1 AAATATAATATAATATAAATATATAAATATTTTTAAAT
** * * *
1512722 TTATATAATACTAATTATTAATATATTAA-A-TTTTATAT
1 AAATATAATA-TAA-TATAAATATATAAATATTTTTAAAT
1512760 AAATATAA
1 AAATATAA
1512768 AATATTTTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
38 21 0.57
39 4 0.11
40 12 0.32
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (38 bp):
AAATATAATATAATATAAATATATAAATATTTTTAAAT
Found at i:1512828 original size:37 final size:40
Alignment explanation
Indices: 1512740--1512828 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 40
1512730 TACTAATTAT
* * *
1512740 TAATATATTAAATTTTATATAAATATAAAATATTTTAAACA
1 TAATATATT-AATTTGATATAAATATAAAATAATATAAACA
*
1512781 TAAT-TA-TAATTTGATA-AAATATAAAA-AATATAATCA
1 TAATATATTAATTTGATATAAATATAAAATAATATAAACA
1512817 -AATATATTAATT
1 TAATATATTAATT
1512829 GTTAGATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
35 3 0.07
36 9 0.21
37 15 0.36
38 8 0.19
39 1 0.02
40 2 0.05
41 4 0.10
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (40 bp):
TAATATATTAATTTGATATAAATATAAAATAATATAAACA
Found at i:1514259 original size:68 final size:68
Alignment explanation
Indices: 1514130--1514259 Score: 197
Period size: 68 Copynumber: 1.9 Consensus size: 68
1514120 TCATTCCAAG
* * * * *
1514130 TATATTTTTATTTTGATTTTCAATCTACATAAAAAATATTATCTTCTTTGAATATCTATAAATCG
1 TATATATTTATTTTGATTTTCAATCTACATAAAAAATATTACCTTCTTTAAATACCCATAAATCG
1514195 AAA
66 AAA
* *
1514198 TATATATTTGTTTTGATTTTCAATCTATATAAAAAATATTACCTTCTTTAAATACCCATAAA
1 TATATATTTATTTTGATTTTCAATCTACATAAAAAATATTACCTTCTTTAAATACCCATAAA
1514260 GCCCACAACG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 55 1.00
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (68 bp):
TATATATTTATTTTGATTTTCAATCTACATAAAAAATATTACCTTCTTTAAATACCCATAAATCG
AAA
Found at i:1515603 original size:6 final size:6
Alignment explanation
Indices: 1515594--1515622 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1515584 TTGTTCTTGT
1515594 TCTTCC TCTTCC TCTTCC TCTTCC TCTTC
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTC
1515623 TTCACTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCC
Found at i:1517232 original size:2 final size:2
Alignment explanation
Indices: 1517225--1517256 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1517215 AGTTTCGAGA
*
1517225 AT AT AT AT AT AT AT AC 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
1517257 TTAACATGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1517463 original size:30 final size:29
Alignment explanation
Indices: 1517389--1517463 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 29
1517379 GTGGTAATTT
* *
1517389 TTATTTTTTATTTTA-ATAAATTTTTATG
1 TTATTTTTTATTATATATAAATATTTATG
* * *
1517417 TGTATTTTTAAGTATATATATTATATTTATG
1 T-TATTTTTTATTATATATA-AATATTTATG
1517448 TTATTTTTTATTATAT
1 TTATTTTTTATTATAT
1517464 TAGATTTAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
28 1 0.03
29 11 0.30
30 16 0.43
31 9 0.24
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.65
Consensus pattern (29 bp):
TTATTTTTTATTATATATAAATATTTATG
Found at i:1517498 original size:9 final size:8
Alignment explanation
Indices: 1517477--1517521 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
1517467 ATTTAAAATA
1517477 TTATATAT
1 TTATATAT
1517485 TTATATAGT
1 TTATATA-T
1517494 TTATATAAT
1 TTATAT-AT
1517503 TTGATATAT
1 TT-ATATAT
*
1517512 TTATTTAT
1 TTATATAT
1517520 TT
1 TT
1517522 TATTATATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 14 0.42
9 14 0.42
10 5 0.15
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (8 bp):
TTATATAT
Found at i:1517499 original size:17 final size:17
Alignment explanation
Indices: 1517477--1517521 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1517467 ATTTAAAATA
1517477 TTATATATTT-ATATAGT
1 TTATATATTTGATATA-T
1517494 TTATATAATTTGATATAT
1 TTATAT-ATTTGATATAT
*
1517512 TTATTTATTT
1 TTATATATTT
1517522 TATTATATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 10 0.40
18 10 0.40
19 5 0.20
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (17 bp):
TTATATATTTGATATAT
Found at i:1517539 original size:22 final size:21
Alignment explanation
Indices: 1517514--1517556 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1517504 TGATATATTT
* *
1517514 ATTTATTTTATTATATCAGTAA
1 ATTTATATTATAATAT-AGTAA
1517536 ATTTATATTATAATATAGTAA
1 ATTTATATTATAATATAGTAA
1517557 GATATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTTATATTATAATATAGTAA
Found at i:1518045 original size:29 final size:29
Alignment explanation
Indices: 1518013--1518068 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1518003 ATTTTTCTCA
* *
1518013 TTTAATTATTTCAAATGA-TTTTTAATTTT
1 TTTAATTATATAAAAT-ACTTTTTAATTTT
1518042 TTTAATTATATAAAATACTTTTTAATT
1 TTTAATTATATAAAATACTTTTTAATT
1518069 AACCTTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTAATTATATAAAATACTTTTTAATTTT
Found at i:1520430 original size:2 final size:2
Alignment explanation
Indices: 1520423--1520457 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1520413 TCAACTTCCT
1520423 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1520458 TTGAAGATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1526965 original size:29 final size:28
Alignment explanation
Indices: 1526924--1526980 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 28
1526914 AAGAAACATA
*
1526924 GAAAAAAATTGAACTTACACGTATTAGT
1 GAAAAAAATTGAACATACACGTATTAGT
1526952 GAAAAAATATTGAACATACACGTATTAGT
1 GAAAAAA-ATTGAACATACACGTATTAGT
1526981 ATCTAACACA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (28 bp):
GAAAAAAATTGAACATACACGTATTAGT
Found at i:1527993 original size:2 final size:2
Alignment explanation
Indices: 1527986--1528013 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1527976 AGATACATAG
1527986 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
1528014 GATCATTGGT
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):
AT
Found at i:1528333 original size:22 final size:23
Alignment explanation
Indices: 1528298--1528370 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 23
1528288 TGTAAAATTA
1528298 TTATTTAATAATAAAA-ATATTT
1 TTATTTAATAATAAAATATATTT
* * *
1528320 TTATTTGATTATAAAATATATAT
1 TTATTTAATAATAAAATATATTT
**
1528343 AAATATTAAT-ATAAAAT-TATTT
1 TTAT-TTAATAATAAAATATATTT
1528365 TTATTT
1 TTATTT
1528371 TTATTAATTA
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 2 0.05
22 20 0.50
23 14 0.35
24 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (23 bp):
TTATTTAATAATAAAATATATTT
Found at i:1529869 original size:16 final size:17
Alignment explanation
Indices: 1529850--1529884 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1529840 AATAAACTAA
1529850 TTATTTT-ATTATAATT
1 TTATTTTCATTATAATT
1529866 TTATTTTCATTATAATT
1 TTATTTTCATTATAATT
1529883 TT
1 TT
1529885 CTTTCGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATTTTCATTATAATT
Found at i:1530613 original size:18 final size:20
Alignment explanation
Indices: 1530571--1530629 Score: 68
Period size: 18 Copynumber: 3.0 Consensus size: 20
1530561 TATTTGAATA
1530571 TAAATATAATAAAAATAATTT
1 TAAATAT-ATAAAAATAATTT
1530592 TAAATATATAAAAA-AA-TT
1 TAAATATATAAAAATAATTT
* * *
1530610 TAAAAATATTAAAATTATTT
1 TAAATATATAAAAATAATTT
1530630 ATGTCATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 14 0.42
19 3 0.09
20 9 0.27
21 7 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAATATATAAAAATAATTT
Found at i:1530630 original size:19 final size:20
Alignment explanation
Indices: 1530572--1530623 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1530562 ATTTGAATAT
*
1530572 AAATATAATAAAAATAATTT-T
1 AAATAT-ATAAAAA-AATTTAA
1530593 AAATATATAAAAAAATTTAA
1 AAATATATAAAAAAATTTAA
1530613 AAATAT-TAAAA
1 AAATATATAAAA
1530624 TTATTTATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 10 0.34
20 13 0.45
21 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATATATAAAAAAATTTAA
Found at i:1532041 original size:16 final size:16
Alignment explanation
Indices: 1531997--1532043 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
1531987 AATAATTTAA
*
1531997 ATATAATATAAATTTT
1 ATATAATATAAAATTT
*
1532013 TTAATAA-ATTAAAATTT
1 AT-ATAATA-TAAAATTT
1532030 ATATAATATAAAAT
1 ATATAATATAAAAT
1532044 AATAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATAATATAAAATTT
Found at i:1532418 original size:23 final size:25
Alignment explanation
Indices: 1532381--1532429 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 25
1532371 ATATTACATT
1532381 ATTATAAAAATAAAAT-TT-TAAAA
1 ATTATAAAAATAAAATATTATAAAA
1532404 ATTA-AAAAATAAAAATATTATAAAA
1 ATTATAAAAAT-AAAATATTATAAAA
1532429 A
1 A
1532430 CATTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.26
23 9 0.39
24 2 0.09
25 6 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (25 bp):
ATTATAAAAATAAAATATTATAAAA
Found at i:1532952 original size:21 final size:25
Alignment explanation
Indices: 1532930--1532984 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
1532920 AAAAATATTT
1532930 AATTAAATA-TAT-TAA-TTTTTTA
1 AATTAAATAGTATATAATTTTTTTA
* *
1532952 AATTAATTAGTTTATAATTTTTTTA
1 AATTAAATAGTATATAATTTTTTTA
1532977 AATTAAAT
1 AATTAAAT
1532985 TGATCAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.30
23 2 0.07
24 3 0.11
25 14 0.52
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
AATTAAATAGTATATAATTTTTTTA
Found at i:1533506 original size:18 final size:18
Alignment explanation
Indices: 1533465--1533503 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1533455 TTCTTATATA
* *
1533465 AAATTGAATTAATTTTTT
1 AAATTTAATTAATTTATT
1533483 AAATTTAATTAATTTAATT
1 AAATTTAATTAATTT-ATT
1533502 AA
1 AA
1533504 TTTTTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AAATTTAATTAATTTATT
Found at i:1534358 original size:22 final size:22
Alignment explanation
Indices: 1534331--1534428 Score: 63
Period size: 22 Copynumber: 4.5 Consensus size: 22
1534321 ATAATTTATG
1534331 TATTTATATTATATTATAATTA
1 TATTTATATTATATTATAATTA
* * * *
1534353 TATTTAAAATATTTTATATTTA
1 TATTTATATTATATTATAATTA
** * * * *
1534375 TATAAATTTTAAAATAT-TTATA
1 TATTTATATTATATTATAAT-TA
*
1534397 TATTTATATTATATTTTAATTA
1 TATTTATATTATATTATAATTA
* *
1534419 TTTTTTTATT
1 TATTTATATT
1534429 TTATATTCAT
Statistics
Matches: 53, Mismatches: 21, Indels: 4
0.68 0.27 0.05
Matches are distributed among these distances:
21 2 0.04
22 50 0.94
23 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTTATATTATATTATAATTA
Found at i:1534385 original size:27 final size:29
Alignment explanation
Indices: 1534331--1534415 Score: 104
Period size: 28 Copynumber: 2.9 Consensus size: 29
1534321 ATAATTTATG
*
1534331 TATTTATATTATATTATAATTATA-TTTAAAA
1 TATTTATA-TAT-TTAT-ATTAAATTTTAAAA
1534362 TATTT-TATATTTATA-TAAATTTTAAAA
1 TATTTATATATTTATATTAAATTTTAAAA
*
1534389 TATTTATATATTTATATTATATTTTAA
1 TATTTATATATTTATATTAAATTTTAA
1534416 TTATTTTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
26 3 0.06
27 13 0.27
28 14 0.29
29 12 0.24
30 2 0.04
31 5 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TATTTATATATTTATATTAAATTTTAAAA
Found at i:1534398 original size:28 final size:28
Alignment explanation
Indices: 1534339--1534415 Score: 97
Period size: 27 Copynumber: 2.8 Consensus size: 28
1534329 TGTATTTATA
*
1534339 TTATA-TTATAATTATA-TTTAAAATATT
1 TTATATTTAT-ATTAAATTTTAAAATATT
1534366 TTATATTTATA-TAAATTTTAAAATATT
1 TTATATTTATATTAAATTTTAAAATATT
*
1534393 TATATATTTATATTATATTTTAA
1 T-TATATTTATATTAAATTTTAA
1534416 TTATTTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
26 3 0.07
27 18 0.41
28 14 0.32
29 9 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TTATATTTATATTAAATTTTAAAATATT
Found at i:1534428 original size:28 final size:28
Alignment explanation
Indices: 1534339--1534440 Score: 102
Period size: 28 Copynumber: 3.6 Consensus size: 28
1534329 TGTATTTATA
*
1534339 TTATA-TTATAATTATATTTAAAATA-TT
1 TTATATTTAT-ATTATATTTTAAATATTT
*
1534366 TTATATTTATA-TAAATTTTAAAATATTT
1 TTATATTTATATTATATTTT-AAATATTT
* *
1534394 ATATATTTATATTATATTTTAATTATTT
1 TTATATTTATATTATATTTTAAATATTT
*
1534422 TTTTATTTTATATTCATAT
1 TTATA-TTTATATT-ATAT
1534441 CACATCTAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
26 6 0.10
27 11 0.18
28 26 0.42
29 15 0.24
30 4 0.06
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (28 bp):
TTATATTTATATTATATTTTAAATATTT
Found at i:1534812 original size:2 final size:2
Alignment explanation
Indices: 1534805--1534838 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1534795 GTGCATATTT
*
1534805 TA TA TA TA CA 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
1534839 GATCCTTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1535964 original size:18 final size:18
Alignment explanation
Indices: 1535941--1536041 Score: 64
Period size: 18 Copynumber: 5.5 Consensus size: 18
1535931 TAAAATATAA
*
1535941 TAAAAAATATAAACATCAT
1 TAAAATATATAAACAT-AT
*
1535960 TAAAATATATAAATATAT
1 TAAAATATATAAACATAT
*
1535978 TAAAATTTATATAA-ATA-
1 TAAAATATATA-AACATAT
* * *
1535995 TATAATATTTTAAATATAAT
1 TAAAATA-TATAAACAT-AT
* *
1536015 TATAATATATAAAAAT-T
1 TAAAATATATAAACATAT
1536032 TATAAATATA
1 TA-AAATATA
1536042 ATATAAGTAT
Statistics
Matches: 67, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
17 10 0.15
18 26 0.39
19 24 0.36
20 7 0.10
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAATATATAAACATAT
Found at i:1535990 original size:20 final size:18
Alignment explanation
Indices: 1535933--1536041 Score: 89
Period size: 19 Copynumber: 5.9 Consensus size: 18
1535923 TAAAAAATTA
* *
1535933 AAATATAATAAAAAATAT
1 AAATATATTAAAATATAT
*
1535951 AAACATCATTAAAATATAT
1 AAATAT-ATTAAAATATAT
1535970 AAATATATTAAAATTTATAT
1 AAATATATTAAAA--TATAT
* *
1535990 AAATATA-TAATAT-TTT
1 AAATATATTAAAATATAT
*
1536006 AAATATAATTATAATATAT
1 AAATAT-ATTAAAATATAT
*
1536025 AAAAAT-TTATAAATATA
1 AAATATATTA-AAATATA
1536042 ATATAAGTAT
Statistics
Matches: 73, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
16 8 0.11
17 5 0.07
18 22 0.30
19 26 0.36
20 12 0.16
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATATATTAAAATATAT
Found at i:1536011 original size:22 final size:20
Alignment explanation
Indices: 1535965--1536022 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
1535955 ATCATTAAAA
*
1535965 TATATAAATATATTAA-AATT
1 TATATAAATATA-TAATATTT
1535985 TATATAAATATATAATATTT
1 TATATAAATATATAATATTT
*
1536005 TAAATATAAT-TATAATAT
1 TATATA-AATATATAATAT
1536023 ATAAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.09
20 28 0.82
21 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TATATAAATATATAATATTT
Found at i:1536021 original size:27 final size:25
Alignment explanation
Indices: 1535963--1536060 Score: 90
Period size: 28 Copynumber: 3.6 Consensus size: 25
1535953 ACATCATTAA
*
1535963 AATATATAAATATATTAAA-ATTTATAT
1 AATATATAAAT-T-TTAAATA-TAATAT
1535990 AAATATATAATATTTTAAATATAATTAT
1 -AATATATAA-ATTTTAAATATAA-TAT
1536018 AATATATAAAAATTTATAAATATAATAT
1 AATATAT--AAATTT-TAAATATAATAT
1536046 AAGTATATAAATTTT
1 AA-TATATAAATTTT
1536061 TATATCTAAT
Statistics
Matches: 62, Mismatches: 1, Indels: 16
0.78 0.01 0.20
Matches are distributed among these distances:
26 1 0.02
27 20 0.32
28 23 0.37
29 18 0.29
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (25 bp):
AATATATAAATTTTAAATATAATAT
Found at i:1536052 original size:11 final size:11
Alignment explanation
Indices: 1535904--1536052 Score: 53
Period size: 11 Copynumber: 14.5 Consensus size: 11
1535894 ATAATTTTAT
1535904 ATATAATATAA
1 ATATAATATAA
*
1535915 ATAAAATATAA
1 ATATAATATAA
1535926 A-A-AAT-TAA
1 ATATAATATAA
1535934 A-AT-ATAATAA
1 ATATAAT-ATAA
1535944 A-A-AATATAA
1 ATATAATATAA
* *
1535953 ACATCAT-TAA
1 ATATAATATAA
1535963 A-AT-ATATAA
1 ATATAATATAA
*
1535972 ATATATTA-AA
1 ATATAATATAA
*
1535982 AT-TTATATAAA
1 ATATAATAT-AA
1535993 TATATAATATTTTAA
1 -ATATAATA---TAA
1536008 ATATAAT-TATA
1 ATATAATATA-A
1536019 ATAT-ATA-AA
1 ATATAATATAA
*
1536028 A-AT-TTATAA
1 ATATAATATAA
1536037 ATATAATATAA
1 ATATAATATAA
*
1536048 GTATA
1 ATATA
1536053 TAAATTTTTA
Statistics
Matches: 108, Mismatches: 9, Indels: 42
0.68 0.06 0.26
Matches are distributed among these distances:
8 13 0.12
9 22 0.20
10 26 0.24
11 31 0.29
12 2 0.02
13 4 0.04
14 7 0.06
15 2 0.02
16 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (11 bp):
ATATAATATAA
Found at i:1536070 original size:27 final size:26
Alignment explanation
Indices: 1535963--1536062 Score: 87
Period size: 27 Copynumber: 3.6 Consensus size: 26
1535953 ACATCATTAA
* *
1535963 AATATATAAATATATTAAA-ATTTATAT
1 AATATATAAAT-TTTTAAATA-TAATAT
1535990 AA-ATATATAATATTTTAAATATAATTAT
1 AATATATA-AAT-TTTTAAATATAA-TAT
*
1536018 AATATATAAAAATTTATAAATATAATAT
1 AATATAT--AAATTTTTAAATATAATAT
1536046 AAGTATATAAATTTTTA
1 AA-TATATAAATTTTTA
1536063 TATCTAATTC
Statistics
Matches: 62, Mismatches: 4, Indels: 14
0.77 0.05 0.17
Matches are distributed among these distances:
26 5 0.08
27 22 0.35
28 11 0.18
29 20 0.32
30 3 0.05
31 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (26 bp):
AATATATAAATTTTTAAATATAATAT
Found at i:1537131 original size:22 final size:20
Alignment explanation
Indices: 1537094--1537136 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
1537084 CAATTAAAAC
1537094 TTAAAATTAAATAAAATTTA
1 TTAAAATTAAATAAAATTTA
*
1537114 TTAAAATATTAATCAAAATTTA
1 TTAAAAT-TAAAT-AAAATTTA
1537136 T
1 T
1537137 AAATAATAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 4 0.20
22 9 0.45
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAAAATTAAATAAAATTTA
Found at i:1539632 original size:29 final size:29
Alignment explanation
Indices: 1539600--1539663 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
1539590 ATTCATATAT
1539600 TTATA-TTATGTTAAAAATATTTTAT-TGTA
1 TTATATTTAT-TT-AAAATATTTTATATGTA
* *
1539629 TTATAATTTATTTTAAATATTTTATATTTA
1 TTAT-ATTTATTTAAAATATTTTATATGTA
1539659 TTATA
1 TTATA
1539664 AGTTTTTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
29 16 0.53
30 10 0.33
31 4 0.13
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (29 bp):
TTATATTTATTTAAAATATTTTATATGTA
Found at i:1542978 original size:2 final size:2
Alignment explanation
Indices: 1542973--1543017 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1542963 GAGGTGTGTG
1542973 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
1543015 TA T
1 TA T
1543018 CCAATTGGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1545055 original size:21 final size:21
Alignment explanation
Indices: 1545030--1545069 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1545020 TTAATAAAAT
* *
1545030 ATTAAAATTTTAATTTTAATA
1 ATTAAAAATTAAATTTTAATA
1545051 ATTAAAAATTAAATTTTAA
1 ATTAAAAATTAAATTTTAA
1545070 CCATCTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTAAAAATTAAATTTTAATA
Found at i:1546705 original size:28 final size:28
Alignment explanation
Indices: 1546643--1546706 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
1546633 TTGTTATTGT
**
1546643 AAATAATTGAAATGTTTAAAAATATGTTTA
1 AAATAA-T-AAATGTTTAAAAATATGTAGA
*
1546673 AAATAATAAATGTTTAAAGATATG-AGA
1 AAATAATAAATGTTTAAAAATATGTAGA
1546700 ATAATAA
1 A-AATAA
1546707 AATTATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 2 0.07
28 21 0.70
29 1 0.03
30 6 0.20
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (28 bp):
AAATAATAAATGTTTAAAAATATGTAGA
Found at i:1548161 original size:20 final size:18
Alignment explanation
Indices: 1548121--1548163 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1548111 ATAATATTAA
*
1548121 TTATAAAAATATTAAAAT
1 TTATAAAAATATAAAAAT
*
1548139 TTATATAAATATAAAATAT
1 TTATAAAAATATAAAA-AT
1548158 TT-TAAA
1 TTATAAA
1548164 TATAATTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTATAAAAATATAAAAAT
Found at i:1550181 original size:16 final size:16
Alignment explanation
Indices: 1550155--1550200 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
1550145 TTATATGATG
1550155 TTTAAAAATTT-TAAA
1 TTTAAAAATTTATAAA
*
1550170 TATTAAATATTTATAAA
1 T-TTAAAAATTTATAAA
1550187 TTTAAAAATTTATA
1 TTTAAAAATTTATA
1550201 TTTACGCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 1 0.04
16 21 0.78
17 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTAAAAATTTATAAA
Found at i:1551015 original size:157 final size:152
Alignment explanation
Indices: 1550696--1551162 Score: 453
Period size: 157 Copynumber: 3.0 Consensus size: 152
1550686 ATGAACCCGA
* * * *
1550696 AACTTAGCTTAGTTAATTCATGTAGCCAGTTGGTATCCAATAGGTCTGAAGTTTGAATTACAGAA
1 AACTTAGCTTAATTAATTCATGTAGTCAGTTGGTATCCAATAGGTCTAAAGTTTGAATTACAAAA
* * * *
1550761 TTACAACAATTTTCTATCTTTGGACTATGACTT-TCTTTATATATAAAAAGGCATACACAAATAC
66 TTACAACCATTTTCTATC-TTCGACTATGACTTCT-TTTATATATAAAAA---A-A-ACATATAT
1550825 GATGCAAATAAATGAATTATTAAATTTAG
124 GATGCAAATAAATGAATTATTAAATTTAG
*
1550854 -ACTTAGCTTAATTAATTCATGCAGTCAGTTGGTATCCAATAGGTCTAAAGTTTGAATTACAAAA
1 AACTTAGCTTAATTAATTCATGTAGTCAGTTGGTATCCAATAGGTCTAAAGTTTGAATTACAAAA
* * * *
1550918 CTACAACCCTTTTCTATCTTCAGACTACGACTTCTTTTATATATAAAAAAAACATATATGATGTA
66 TTACAACCATTTTCTATCTTC-GACTATGACTTCTTTTATATATAAAAAAAACATATATGATGCA
*
1550983 AATAAATAAATTATTAAATTTAGG
130 AATAAATGAATTATTAAATTTA-G
* * * *
1551007 CTTAACTTAGTTAATTCATGTATTAATTCATGTAGTCAGTTGATA-CCTAATAAGTTTGAAA-TT
1 ---AACTTAG---CTT-A---ATTAATTCATGTAGTCAGTTGGTATCC-AATAGGTCT-AAAGTT
* ** * * * *
1551070 TAAATTACAAAATTGTAATCTTTTTTTATCCTCGAACTATGACTTCTTTTATATAT--AAAAAA-
54 TGAATTACAAAATTACAACCATTTTCTATCTTCG-ACTATGACTTCTTTTATATATAAAAAAAAC
*
1551132 ATATATGATGCAAATAAACGAATTATTAAAT
118 ATATATGATGCAAATAAATGAATTATTAAAT
1551163 CTAAATGAAA
Statistics
Matches: 261, Mismatches: 31, Indels: 31
0.81 0.10 0.10
Matches are distributed among these distances:
152 32 0.12
153 2 0.01
154 1 0.00
156 2 0.01
157 104 0.40
158 1 0.00
160 2 0.01
161 29 0.11
162 6 0.02
163 3 0.01
164 76 0.29
165 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (152 bp):
AACTTAGCTTAATTAATTCATGTAGTCAGTTGGTATCCAATAGGTCTAAAGTTTGAATTACAAAA
TTACAACCATTTTCTATCTTCGACTATGACTTCTTTTATATATAAAAAAAACATATATGATGCAA
ATAAATGAATTATTAAATTTAG
Found at i:1551942 original size:29 final size:30
Alignment explanation
Indices: 1551909--1551965 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
1551899 AAGTCTTTTC
1551909 AATTTATA-TTCAAATAAAT-TTTAACATTT
1 AATTTATACTT-AAATAAATCTTTAACATTT
* *
1551938 AATTTGTACTTAAATAAGTCTTTAACAT
1 AATTTATACTTAAATAAATCTTTAACAT
1551966 AAATAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.46
Consensus pattern (30 bp):
AATTTATACTTAAATAAATCTTTAACATTT
Found at i:1552508 original size:19 final size:19
Alignment explanation
Indices: 1552484--1552521 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1552474 AATTTAGTAA
1552484 TATATATTCGTATTATATT
1 TATATATTCGTATTATATT
**
1552503 TATATATTTTTATTATATT
1 TATATATTCGTATTATATT
1552522 ATGAATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (19 bp):
TATATATTCGTATTATATT
Found at i:1552615 original size:9 final size:10
Alignment explanation
Indices: 1552595--1552634 Score: 57
Period size: 9 Copynumber: 4.1 Consensus size: 10
1552585 TAAATATCAT
1552595 TTTTATATTA
1 TTTTATATTA
1552605 TTTTA-ATTA
1 TTTTATATTA
1552614 TTTTA-ATTA
1 TTTTATATTA
1552623 TATTTATATTA
1 T-TTTATATTA
1552634 T
1 T
1552635 ATAATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 14 0.50
10 9 0.32
11 5 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTATATTA
Found at i:1552616 original size:20 final size:21
Alignment explanation
Indices: 1552542--1552634 Score: 58
Period size: 20 Copynumber: 4.7 Consensus size: 21
1552532 TTAAGTTATT
1552542 TTATATTTATA-TATTTTTTAA
1 TTATATTTATATTA-TTTTTAA
* *
1552563 -TAT-GTTA-ATAATTTTT-A
1 TTATATTTATATTATTTTTAA
* ** *
1552580 TTACATAAATATCATTTTTATA
1 TTATATTTATATTATTTTTA-A
1552602 TTAT-TTTA-ATTA-TTTTAA
1 TTATATTTATATTATTTTTAA
1552620 TTATATTTATATTAT
1 TTATATTTATATTAT
1552635 ATAATTATAT
Statistics
Matches: 52, Mismatches: 11, Indels: 18
0.64 0.14 0.22
Matches are distributed among these distances:
17 1 0.02
18 13 0.25
19 14 0.27
20 18 0.35
21 2 0.04
22 4 0.08
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.61
Consensus pattern (21 bp):
TTATATTTATATTATTTTTAA
Found at i:1552628 original size:19 final size:20
Alignment explanation
Indices: 1552495--1552644 Score: 62
Period size: 19 Copynumber: 7.3 Consensus size: 20
1552485 ATATATTCGT
*
1552495 ATTATATTTATA-TATTTTT
1 ATTATATTTATATTATTTTA
*
1552514 ATTATA-TTATGAATATATTTA
1 ATTATATTTAT-ATTAT-TTTA
*
1552535 AGTTAT-TTTATATTTATATATTT
1 A-TTATATTTATA-TTAT-T-TTA
* * *
1552558 TTTAATATGTTA-ATAATTTTT
1 ATT-ATAT-TTATATTATTTTA
* ** *
1552579 ATTACATAAATATCATTTTTA
1 ATTATATTTATATTA-TTTTA
1552600 TATTAT-TTTA-ATTATTTTA
1 -ATTATATTTATATTATTTTA
*
1552619 ATTATATTTATATTA-TATA
1 ATTATATTTATATTATTTTA
1552638 ATTATAT
1 ATTATAT
1552645 AATATTTAAT
Statistics
Matches: 100, Mismatches: 16, Indels: 30
0.68 0.11 0.21
Matches are distributed among these distances:
18 9 0.09
19 27 0.27
20 16 0.16
21 16 0.16
22 20 0.20
23 7 0.07
24 2 0.02
25 3 0.03
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTATATTTATATTATTTTA
Found at i:1552635 original size:11 final size:11
Alignment explanation
Indices: 1552494--1552652 Score: 67
Period size: 11 Copynumber: 15.0 Consensus size: 11
1552484 TATATATTCG
1552494 TATTATATTTA
1 TATTATATTTA
1552505 TA-TAT-TTT-
1 TATTATATTTA
1552513 TATTATA-TTA
1 TATTATATTTA
*
1552523 TGAATATATTTA
1 T-ATTATATTTA
1552535 -AGTTAT-TTTA
1 TA-TTATATTTA
1552545 TATTTATATATT-
1 TA-TTATAT-TTA
*
1552557 TTTTAATATGTTA
1 TATT-ATAT-TTA
*
1552570 -A-TA-ATTTT
1 TATTATATTTA
* **
1552578 TATTACATAAA
1 TATTATATTTA
* *
1552589 TATCATTTTTA
1 TATTATATTTA
1552600 TATTAT-TTTA
1 TATTATATTTA
1552610 -ATTAT-TTTA
1 TATTATATTTA
1552619 -ATTATATTTA
1 TATTATATTTA
1552629 TATTATATAATTA
1 TATTATAT--TTA
*
1552642 TATAATATTTA
1 TATTATATTTA
1552653 ATATGACTGA
Statistics
Matches: 113, Mismatches: 17, Indels: 36
0.68 0.10 0.22
Matches are distributed among these distances:
8 4 0.04
9 25 0.22
10 20 0.18
11 41 0.36
12 11 0.10
13 12 0.11
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (11 bp):
TATTATATTTA
Found at i:1553060 original size:7 final size:7
Alignment explanation
Indices: 1553048--1553082 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
1553038 TATATATAAA
1553048 TTAATTT
1 TTAATTT
1553055 TTAATTT
1 TTAATTT
1553062 TTAATTT
1 TTAATTT
1553069 TTAATTT
1 TTAATTT
1553076 TTAATTT
1 TTAATTT
1553083 ATACTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTAATTT
Found at i:1553935 original size:15 final size:15
Alignment explanation
Indices: 1553901--1553949 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
1553891 AATATAAACA
*
1553901 AAAAATAAAATTAAATT
1 AAAAATTAAA-TAAA-T
* *
1553918 AAATATTACATAAAT
1 AAAAATTAAATAAAT
1553933 AAAAATTAAATAAAT
1 AAAAATTAAATAAAT
1553948 AA
1 AA
1553950 TAATAAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 16 0.59
16 4 0.15
17 7 0.26
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAATTAAATAAAT
Done.