Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold79
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: 4189514
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 5041 characters in sequence are not A, C, G, or T
File 11 of 26
Found at i:1480192 original size:2 final size:2
Alignment explanation
Indices: 1480187--1480217 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1480177 ACACACACAC
1480187 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 A
1480218 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1480222 original size:2 final size:2
Alignment explanation
Indices: 1480217--1480261 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1480207 ATATATATAT
1480217 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1480259 AG A
1 AG A
1480262 AATTTTAAAT
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1484067 original size:339 final size:336
Alignment explanation
Indices: 1483480--1484124 Score: 1152
Period size: 343 Copynumber: 1.9 Consensus size: 336
1483470 AAAACATAAG
*
1483480 AAAAACTCAAGAGCACCGACATTTAATGAAAGACTATAAAGAAGATCGATATTAGAGTTTTAGAG
1 AAAAACTAAAGAGCACCGACATTTAATGAAAGACTATAAAGAAGATCGATATTAGAGTTTTAGAG
*
1483545 AATACAATTAGAAAAAAGCTAACCTTTCACTCGAAGTAGCATATCATTCAACATTCATAGCATGC
66 AATACAATTAGAAAAAAGCTAACCTTTCACTCGAAGTA-CAGATCATTCAACATTCATAGCATGC
1483610 ATGCCACACAACTACGAATGCTACTTATTGAAAGGTGATTAAATCAGCAAAGTGATGAGAAACAA
130 ATGCCACACAACTACGAATGCTACTTATTGAAAGGTGATTAAATCAGCAAAGTGATGAGAAACAA
1483675 TCTTCATGCCTTCAAACATGATAGAATAGACACACCTACCAATCACTGAAAGTTGACCCTAATAG
195 TCTTCATGCCTTCAAACATGATAGAATAGACACACCTACCAATCACTGAAAGTTGACCC---T--
*
1483740 AATATCAGCAGATTGCAAAGTCTAATTAATATAACAACCAAAATGATTGTAATGAAAAACTCAAG
255 AATATCAGCAGACTGCAAAGTCTAATTAATATAACAACCAAAATGATTGTAATGAAAAACTCAAG
1483805 AATAATGAAAGACTATA
320 AATAATGAAAGACTATA
1483822 AAAAAGCTAAAGAGCACCGACATTTAATGAAAGACTATAAAGAAGATCGATATTAGAGTTTTAGA
1 AAAAA-CTAAAGAGCACCGACATTTAATGAAAGACTATAAAGAAGATCGATATTAGAGTTTTAGA
**
1483887 GAATACAATTAGAAAAAAGCTAACCTTTCGTTCGAAG-A-AGATCATTCAACATTCATAGCATGC
65 GAATACAATTAGAAAAAAGCTAACCTTTCACTCGAAGTACAGATCATTCAACATTCATAGCATGC
*
1483950 ATGCCACATAACTACGAATGCTACTTATTGAAAGGTGATT-AATCAGCAAAGTGATGAGAAACAA
130 ATGCCACACAACTACGAATGCTACTTATTGAAAGGTGATTAAATCAGCAAAGTGATGAGAAACAA
1484014 TCTTCATGCCTTCAAACATGATAGAATAGACACACCTACCAATCACTGAAAGTTGACCCTAATAT
195 TCTTCATGCCTTCAAACATGATAGAATAGACACACCTACCAATCACTGAAAGTTGACCCTAATAT
1484079 CAGCAGACTGCAAAGTCTAATTAATATAACAACCAAAATGATTGTA
260 CAGCAGACTGCAAAGTCTAATTAATATAACAACCAAAATGATTGTA
1484125 GATCACCAGA
Statistics
Matches: 296, Mismatches: 6, Indels: 10
0.95 0.02 0.03
Matches are distributed among these distances:
334 50 0.17
336 1 0.00
339 83 0.28
340 63 0.21
342 6 0.02
343 93 0.31
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (336 bp):
AAAAACTAAAGAGCACCGACATTTAATGAAAGACTATAAAGAAGATCGATATTAGAGTTTTAGAG
AATACAATTAGAAAAAAGCTAACCTTTCACTCGAAGTACAGATCATTCAACATTCATAGCATGCA
TGCCACACAACTACGAATGCTACTTATTGAAAGGTGATTAAATCAGCAAAGTGATGAGAAACAAT
CTTCATGCCTTCAAACATGATAGAATAGACACACCTACCAATCACTGAAAGTTGACCCTAATATC
AGCAGACTGCAAAGTCTAATTAATATAACAACCAAAATGATTGTAATGAAAAACTCAAGAATAAT
GAAAGACTATA
Found at i:1484285 original size:145 final size:140
Alignment explanation
Indices: 1484006--1484295 Score: 535
Period size: 145 Copynumber: 2.0 Consensus size: 140
1483996 CAAAGTGATG
1484006 AGAAACAATCTTCATGCCTTCAAACATGATAGAATAGACACACCTACCAATCACTGAAAGTTGAC
1 AGAAACAATCTTCATGCCTTCAAACATGATAGAATAGACACACCTACCAATCACTGAAAGTTGAC
1484071 CCTAATATCAGCAGACTGCAAAGTCTAATTAATATAACAACCAAAATGATTGTAGATCACCAGAA
66 CCTAATATCAGCAGACTGCAAAGTCTAATTAATATAACAACCAAAATGATTGTAGATCACCAGAA
1484136 TAACAAGAAT
131 TAACAAGAAT
1484146 AGAAACAATCTTCATGCCTTCAAACATGATAGAATAGACACACCTACCAATCACTGAAAGTTGAC
1 AGAAACAATCTTCATGCCTTCAAACATGATAGAATAGACACACCTACCAATCACTGAAAGTTGAC
1484211 CCTAATAGAATATCAGCAGACTGCAAAGTCTAATTAATATAACAACCAAAATGATTGTAGATCAC
66 CC---T--AATATCAGCAGACTGCAAAGTCTAATTAATATAACAACCAAAATGATTGTAGATCAC
1484276 CAGAATAACAAGAAT
126 CAGAATAACAAGAAT
1484291 AGAAA
1 AGAAA
1484296 ACTTGCCACA
Statistics
Matches: 145, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
140 67 0.46
143 1 0.01
145 77 0.53
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.22
Consensus pattern (140 bp):
AGAAACAATCTTCATGCCTTCAAACATGATAGAATAGACACACCTACCAATCACTGAAAGTTGAC
CCTAATATCAGCAGACTGCAAAGTCTAATTAATATAACAACCAAAATGATTGTAGATCACCAGAA
TAACAAGAAT
Found at i:1484596 original size:48 final size:47
Alignment explanation
Indices: 1484533--1484629 Score: 142
Period size: 48 Copynumber: 2.0 Consensus size: 47
1484523 AGTGAATACA
*
1484533 ATAAGAAAAAAAACTAACCTTTCTTCAGAGGTAGTGTATCATCCAACAT
1 ATAAGAAAAAAAACTAAACTTTCTTCAGAGGTAGTGTATCAT--AACAT
* *
1484582 ATAAG-AAAAGAACTAAACTTTCTTTAGAGGTAGTGTATCATAACAT
1 ATAAGAAAAAAAACTAAACTTTCTTCAGAGGTAGTGTATCATAACAT
1484628 AT
1 AT
1484630 GATTAGCATG
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
46 7 0.16
48 33 0.73
49 5 0.11
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.29
Consensus pattern (47 bp):
ATAAGAAAAAAAACTAAACTTTCTTCAGAGGTAGTGTATCATAACAT
Found at i:1487032 original size:213 final size:213
Alignment explanation
Indices: 1486665--1487096 Score: 864
Period size: 213 Copynumber: 2.0 Consensus size: 213
1486655 AATATAAGAG
1486665 AAACTCTTGAGAACTGACTCTAATGAAAGGCTGGATATTAGAGTTTAAGAAAATACAATAACAAA
1 AAACTCTTGAGAACTGACTCTAATGAAAGGCTGGATATTAGAGTTTAAGAAAATACAATAACAAA
1486730 AGAACTAACATTTCTTTTAAAGTAGCGTATCATTCCACATATGATATAGCACACATGCTACTTAA
66 AGAACTAACATTTCTTTTAAAGTAGCGTATCATTCCACATATGATATAGCACACATGCTACTTAA
1486795 ACACAACAGCCAGGACATCATATATACTGTTTCCCCTAAGTGTAAGAAGAATAAGAATGCTACTT
131 ACACAACAGCCAGGACATCATATATACTGTTTCCCCTAAGTGTAAGAAGAATAAGAATGCTACTT
1486860 ATAAAAATAAAGACAATC
196 ATAAAAATAAAGACAATC
1486878 AAACTCTTGAGAACTGACTCTAATGAAAGGCTGGATATTAGAGTTTAAGAAAATACAATAACAAA
1 AAACTCTTGAGAACTGACTCTAATGAAAGGCTGGATATTAGAGTTTAAGAAAATACAATAACAAA
1486943 AGAACTAACATTTCTTTTAAAGTAGCGTATCATTCCACATATGATATAGCACACATGCTACTTAA
66 AGAACTAACATTTCTTTTAAAGTAGCGTATCATTCCACATATGATATAGCACACATGCTACTTAA
1487008 ACACAACAGCCAGGACATCATATATACTGTTTCCCCTAAGTGTAAGAAGAATAAGAATGCTACTT
131 ACACAACAGCCAGGACATCATATATACTGTTTCCCCTAAGTGTAAGAAGAATAAGAATGCTACTT
1487073 ATAAAAATAAAGACAATC
196 ATAAAAATAAAGACAATC
1487091 AAACTC
1 AAACTC
1487097 AAGGCCATAT
Statistics
Matches: 219, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
213 219 1.00
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (213 bp):
AAACTCTTGAGAACTGACTCTAATGAAAGGCTGGATATTAGAGTTTAAGAAAATACAATAACAAA
AGAACTAACATTTCTTTTAAAGTAGCGTATCATTCCACATATGATATAGCACACATGCTACTTAA
ACACAACAGCCAGGACATCATATATACTGTTTCCCCTAAGTGTAAGAAGAATAAGAATGCTACTT
ATAAAAATAAAGACAATC
Found at i:1487403 original size:2 final size:2
Alignment explanation
Indices: 1487396--1487429 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1487386 GGAAATATGT
1487396 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1487430 CCAAAATAAT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1488428 original size:141 final size:144
Alignment explanation
Indices: 1488143--1488428 Score: 382
Period size: 145 Copynumber: 2.0 Consensus size: 144
1488133 CCTCCGTCCA
* *
1488143 TTGAGACATCACCAATGCAAAATTAACAAATCTCTACAAGCAAAACGTTAAATGATATAACTGAT
1 TTGAGACATCACCAACGCAAAATTAACAAATCTCTACAAGCAAAACATTAAATGA-ATAACTGAT
1488208 CTTCCTCGAAAAAATAATTTCTCCATGGAAAATACAAAAAACCCCATCCCATCAAAAAAATCCAA
65 CTTCCTCGAAAAAATAATTTCTCCATGGAAAATACAAAAAACCCCATCCCATCAAAAAAATCCAA
*
1488273 TATACTAACATCTAT
130 AATACTAACATCTAT
* * ** * *
1488288 TTGAGACATCATCAACGCAAAATTAATAAATCTCTAGTAGCAAAACATT-AATG-ATAATTTATC
1 TTGAGACATCACCAACGCAAAATTAACAAATCTCTACAAGCAAAACATTAAATGAATAACTGATC
* * * * * *
1488351 TTTCTCG-AAAAATAGTTTCTCCATGGTAAGTA-TAAAAATCCCATCCCATCAAAAAAAGTCCAA
66 TTCCTCGAAAAAATAATTTCTCCATGGAAAATACAAAAAACCCCATCCCATCAAAAAAA-TCCAA
*
1488414 AATAGTAACATCTAT
130 AATACTAACATCTAT
1488429 GATTGGCCAA
Statistics
Matches: 124, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
140 23 0.19
141 40 0.32
142 14 0.11
144 4 0.03
145 43 0.35
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.27
Consensus pattern (144 bp):
TTGAGACATCACCAACGCAAAATTAACAAATCTCTACAAGCAAAACATTAAATGAATAACTGATC
TTCCTCGAAAAAATAATTTCTCCATGGAAAATACAAAAAACCCCATCCCATCAAAAAAATCCAAA
ATACTAACATCTAT
Found at i:1491156 original size:42 final size:42
Alignment explanation
Indices: 1491087--1491177 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 42
1491077 CCGTTAGCCC
* *
1491087 TTTTCAACCATTAGTCAAGGAGGTCTTACACTTTAATTCCAT
1 TTTTTAACCATTAGTCAAGGAGATCTTACACTTTAATTCCAT
* * **
1491129 TTTTTAACCATTAGTCAAGGAGATCTTATACTTTCATTCTTT
1 TTTTTAACCATTAGTCAAGGAGATCTTACACTTTAATTCCAT
1491171 TTTTTAA
1 TTTTTAA
1491178 TGCTTTTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.45
Consensus pattern (42 bp):
TTTTTAACCATTAGTCAAGGAGATCTTACACTTTAATTCCAT
Found at i:1493619 original size:20 final size:21
Alignment explanation
Indices: 1493582--1493620 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1493572 ATATTCTTAA
**
1493582 TTTATCATAATACCTTTAACC
1 TTTATCATAATAAATTTAACC
1493603 TTTATC-TAATAAATTTAA
1 TTTATCATAATAAATTTAA
1493621 GATATTACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTATCATAATAAATTTAACC
Found at i:1494822 original size:9 final size:9
Alignment explanation
Indices: 1494808--1494849 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
1494798 AAATATAAAA
1494808 TAATTATAT
1 TAATTATAT
1494817 TAATTATAT
1 TAATTATAT
*
1494826 TATATCATAAT
1 TA-ATTAT-AT
1494837 T-ATTATAT
1 TAATTATAT
1494845 TAATT
1 TAATT
1494850 TTATATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
8 3 0.11
9 18 0.64
10 4 0.14
11 3 0.11
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (9 bp):
TAATTATAT
Found at i:1494825 original size:28 final size:29
Alignment explanation
Indices: 1494794--1494854 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
1494784 AATATTTTAA
1494794 ATATAAATAT-AAAATAATTATATTAATT
1 ATATAAATATCAAAATAATTATATTAATT
* * *
1494822 ATAT-TATATCATAATTATTATATTAATT
1 ATATAAATATCAAAATAATTATATTAATT
*
1494850 TTATA
1 ATATA
1494855 TTTTTAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (29 bp):
ATATAAATATCAAAATAATTATATTAATT
Found at i:1494829 original size:25 final size:26
Alignment explanation
Indices: 1494801--1494879 Score: 65
Period size: 28 Copynumber: 3.0 Consensus size: 26
1494791 TAAATATAAA
1494801 TATAAAATAATTATATTAA-TTATAT
1 TATAAAATAATTATATTAATTTATAT
*
1494826 TATATCATAATTATTATATTAATTTTATAT
1 TATA--A-AATAATTATATTAA-TTTATAT
* * *
1494856 TTTTAAATATTTATATT--TTTATAT
1 TATAAAATAATTATATTAATTTATAT
1494880 CATACTTATA
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
24 7 0.16
25 4 0.09
27 11 0.25
28 14 0.32
30 8 0.18
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (26 bp):
TATAAAATAATTATATTAATTTATAT
Found at i:1494853 original size:11 final size:12
Alignment explanation
Indices: 1494810--1494856 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 12
1494800 ATATAAAATA
1494810 ATTATATTAATTAT
1 ATTATATTAA-T-T
1494824 ATTATATCATAATT
1 ATTATAT--TAATT
1494838 ATTATATTAATT
1 ATTATATTAATT
1494850 -TTATATT
1 ATTATATT
1494857 TTTAAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 7 0.23
12 5 0.16
14 15 0.48
15 1 0.03
16 3 0.10
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (12 bp):
ATTATATTAATT
Found at i:1496364 original size:48 final size:48
Alignment explanation
Indices: 1496262--1496367 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 48
1496252 TTCTTAAACT
* * **
1496262 TAAAATTTAATTTAATTATTATATATAATAATTTTTAAATATGTTTTT
1 TAAAATTTAATTTAATTATTATATATAATAATTTTAAAATATATTTAA
*
1496310 TAAAATTTAATTTAATTAATT-TATATAATTATTTTAAAATAATATTTAA
1 TAAAATTTAATTTAATT-ATTATATATAATAATTTTAAAAT-ATATTTAA
1496359 T-AAATTTAA
1 TAAAATTTAA
1496368 AATTTAATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
48 42 0.82
49 9 0.18
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (48 bp):
TAAAATTTAATTTAATTATTATATATAATAATTTTAAAATATATTTAA
Found at i:1498377 original size:21 final size:22
Alignment explanation
Indices: 1498351--1498393 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1498341 TTAAAAAAAA
1498351 TTTAATA-ATTAAATTTAAATT
1 TTTAATATATTAAATTTAAATT
* *
1498372 TTTAATATTTTAATTTTAAATT
1 TTTAATATATTAAATTTAAATT
1498394 AATGATCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTAATATATTAAATTTAAATT
Found at i:1498476 original size:21 final size:21
Alignment explanation
Indices: 1498348--1498465 Score: 65
Period size: 20 Copynumber: 5.8 Consensus size: 21
1498338 TTTTTAAAAA
* *
1498348 AAATTTAATA-ATTAAAT-TT
1 AAATTTATTATATTTAATATT
*
1498367 AAATTT-TTAATATTTTAATTTT
1 AAATTTATT-ATA-TTTAATATT
*
1498389 AAATTAATGATCATATTT-A-ATT
1 AAATT--T-ATTATATTTAATATT
* *
1498411 AAATATA-TATTTTTAATA--
1 AAATTTATTATATTTAATATT
1498429 AACATTTATTATATTTAATATT
1 AA-ATTTATTATATTTAATATT
1498451 AAATTTATT-TATTTA
1 AAATTTATTATATTTA
1498466 CAATTTAAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 27
0.68 0.08 0.24
Matches are distributed among these distances:
18 8 0.11
19 13 0.17
20 19 0.25
21 12 0.16
22 15 0.20
23 1 0.01
24 4 0.05
25 3 0.04
26 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (21 bp):
AAATTTATTATATTTAATATT
Found at i:1502057 original size:7 final size:7
Alignment explanation
Indices: 1502042--1502084 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
1502032 AAAGAAAAAT
1502042 AAATATTA
1 AAAT-TTA
1502050 AAATTTA
1 AAATTTA
1502057 AAATTTA
1 AAATTTA
*
1502064 AAATTATT
1 AAATT-TA
1502072 AAATATTA
1 AAAT-TTA
1502080 AAATT
1 AAATT
1502085 AATTAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
7 16 0.52
8 14 0.45
9 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATTTA
Found at i:1502092 original size:9 final size:9
Alignment explanation
Indices: 1502064--1502112 Score: 59
Period size: 9 Copynumber: 5.7 Consensus size: 9
1502054 TTAAAATTTA
1502064 AAATT-ATT
1 AAATTAATT
1502072 AAA-T-ATT
1 AAATTAATT
1502079 AAAATTAATT
1 -AAATTAATT
1502089 AAATTAATT
1 AAATTAATT
*
1502098 AATTTAATT
1 AAATTAATT
1502107 AAATTA
1 AAATTA
1502113 GAATTCAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
7 4 0.11
8 6 0.17
9 23 0.64
10 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
AAATTAATT
Found at i:1511728 original size:18 final size:18
Alignment explanation
Indices: 1511692--1511729 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1511682 TATAAACATA
*
1511692 AAAAAAAGTTAATTTTTT
1 AAAAAAAGTTAATTATTT
1511710 AAAAAAA-TTAATATATTT
1 AAAAAAAGTTAAT-TATTT
1511728 AA
1 AA
1511730 TTTAATCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
AAAAAAAGTTAATTATTT
Found at i:1512763 original size:13 final size:13
Alignment explanation
Indices: 1512737--1512783 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1512727 GACAATACAC
* *
1512737 ATATATAAATATA
1 ATATAAAAAAATA
1512750 ATATAAAAAAATA
1 ATATAAAAAAATA
1512763 ATATAAACACAAAT-
1 ATATAAA-A-AAATA
1512777 ATATAAA
1 ATATAAA
1512784 TATTTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 18 0.60
14 8 0.27
15 4 0.13
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (13 bp):
ATATAAAAAAATA
Found at i:1514239 original size:44 final size:40
Alignment explanation
Indices: 1514191--1514298 Score: 105
Period size: 44 Copynumber: 2.6 Consensus size: 40
1514181 TTTGGTAATA
*
1514191 ATTTATATTATATAAATTTTAATATATTTATGTATGTATATTAT
1 ATTTATATTATATAAATTTTAATATATTT-T-T-T-AATATTAT
* *
1514235 ATTTATTTTAAATTAAATTTTAAT-TATTTTTTAATATTAT
1 ATTTATATTATA-TAAATTTTAATATATTTTTTAATATTAT
*
1514275 ATTTAAAATTAT-TAAA-TTTAATAT
1 ATTT-ATATTATATAAATTTTAATAT
1514299 TTCTCTTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
38 6 0.11
39 5 0.09
40 11 0.20
41 5 0.09
42 1 0.02
43 1 0.02
44 15 0.27
45 11 0.20
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (40 bp):
ATTTATATTATATAAATTTTAATATATTTTTTAATATTAT
Found at i:1514256 original size:12 final size:12
Alignment explanation
Indices: 1514238--1514286 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
1514228 ATATTATATT
1514238 TATTTTAAATTA
1 TATTTTAAATTA
*
1514250 AATTTT-AATTA
1 TATTTTAAATTA
*
1514261 TTTTTTAATATTA
1 TATTTTAA-ATTA
*
1514274 TATTTAAAATTA
1 TATTTTAAATTA
1514286 T
1 T
1514287 TAAATTTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
11 9 0.30
12 11 0.37
13 10 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTTTAAATTA
Found at i:1514278 original size:24 final size:24
Alignment explanation
Indices: 1514240--1514287 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1514230 ATTATATTTA
*
1514240 TTTTAAATTAAATTT-TAATTATT
1 TTTTAAATTAAATTTAAAATTATT
*
1514263 TTTTAATATTATATTTAAAATTATT
1 TTTTAA-ATTAAATTTAAAATTATT
1514288 AAATTTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 8 0.38
25 7 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTAAATTAAATTTAAAATTATT
Found at i:1517879 original size:2 final size:2
Alignment explanation
Indices: 1517874--1517922 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1517864 CATTACACTT
1517874 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
1517916 TA TA TA T
1 TA TA TA T
1517923 TTCAACTTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1523675 original size:31 final size:33
Alignment explanation
Indices: 1523624--1523686 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 33
1523614 ATCAAGATAC
*
1523624 AATTTCTGTGAAAATTATTTCAAAAATAAAATG
1 AATTTCTGTGAAAATTATTTCAAAAAGAAAATG
*
1523657 AATTT-TGTGAACA-TATTTCAAAAAGAAAAT
1 AATTTCTGTGAAAATTATTTCAAAAAGAAAAT
1523687 TCATTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 16 0.57
32 7 0.25
33 5 0.18
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.35
Consensus pattern (33 bp):
AATTTCTGTGAAAATTATTTCAAAAAGAAAATG
Found at i:1524206 original size:22 final size:22
Alignment explanation
Indices: 1524178--1524221 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1524168 TTATTCTCTT
*
1524178 ATTTTAGATATAATCCAATCAA
1 ATTTTAGATAGAATCCAATCAA
*
1524200 ATTTTAGATAGAATCTAATCAA
1 ATTTTAGATAGAATCCAATCAA
1524222 TCGCAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (22 bp):
ATTTTAGATAGAATCCAATCAA
Found at i:1525231 original size:20 final size:19
Alignment explanation
Indices: 1525184--1525231 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1525174 TTTTTCATAA
1525184 TTAA-TAAATATAAAATTT
1 TTAATTAAATATAAAATTT
* *
1525202 TTTATCAAATAATAAAATTT
1 TTAATTAAAT-ATAAAATTT
1525222 TTAATTAAAT
1 TTAATTAAAT
1525232 TTAATATTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 3 0.12
19 4 0.17
20 17 0.71
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAATTAAATATAAAATTT
Found at i:1526180 original size:2 final size:2
Alignment explanation
Indices: 1526175--1526208 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1526165 AAAAAATTGC
*
1526175 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1526209 TCATGTTCCA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1526429 original size:15 final size:15
Alignment explanation
Indices: 1526409--1526470 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
1526399 TAAAAAAAAT
**
1526409 TTTAAATTTATTTAA
1 TTTAAATTTAAATAA
*
1526424 TTTAAATATAAATAA
1 TTTAAATTTAAATAA
1526439 TTTAAATTTAAATTAA
1 TTTAAATTTAAA-TAA
* *
1526455 ATTAATTTTAAA-AA
1 TTTAAATTTAAATAA
1526469 TT
1 TT
1526471 AATGATTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 3 0.08
15 23 0.59
16 13 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAAATTTAAATAA
Found at i:1526435 original size:21 final size:21
Alignment explanation
Indices: 1526410--1526462 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1526400 AAAAAAAATT
*
1526410 TTAAATTTATTT-AATTTAAA
1 TTAAATTAATTTAAATTTAAA
1526430 TATAAA-TAATTTAAATTTAAA
1 T-TAAATTAATTTAAATTTAAA
1526451 TTAAATTAATTT
1 TTAAATTAATTT
1526463 TAAAAATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAAATTAATTTAAATTTAAA
Found at i:1526446 original size:37 final size:38
Alignment explanation
Indices: 1526405--1526483 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 38
1526395 TCTATAAAAA
* * *
1526405 AAATTTTAAATTTATTTAA-TTTAAATATAAATAATTT
1 AAATTTTAAATTAAATTAATTTTAAAAATAAATAATTT
* *
1526442 AAA-TTTAAATTAAATTAATTTTAAAAATTAATGATTT
1 AAATTTTAAATTAAATTAATTTTAAAAATAAATAATTT
1526479 AAATT
1 AAATT
1526484 AAAAAACTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
36 13 0.37
37 21 0.60
38 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (38 bp):
AAATTTTAAATTAAATTAATTTTAAAAATAAATAATTT
Found at i:1527303 original size:6 final size:6
Alignment explanation
Indices: 1527294--1527318 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1527284 TCCCACCTCT
1527294 TCTTTG TCTTTG TCTTTG TCTTTG T
1 TCTTTG TCTTTG TCTTTG TCTTTG T
1527319 GGGTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (6 bp):
TCTTTG
Found at i:1527448 original size:3 final size:3
Alignment explanation
Indices: 1527440--1527477 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1527430 GATCCAGGGA
1527440 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1527478 ATCAAGGTAC
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:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:1528480 original size:18 final size:17
Alignment explanation
Indices: 1528452--1528494 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1528442 CTTACTACAG
1528452 TTTTTTTTCT-TTCTT-T
1 TTTTTTTTCTCTT-TTAT
*
1528468 TTTTATTTCTCTTTTAT
1 TTTTTTTTCTCTTTTAT
1528485 TTTTTTTTCT
1 TTTTTTTTCT
1528495 TAAGAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTTTCTCTTTTAT
Found at i:1535651 original size:30 final size:32
Alignment explanation
Indices: 1535607--1535666 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
1535597 GTCTATATAT
*
1535607 TTTTAATACTTTTAAATTATACCTAAATAAGC
1 TTTTAATACTTTTAAATTATACCAAAATAAGC
* *
1535639 TTTTAA-A-TTTTAATTTATATCAAAATAA
1 TTTTAATACTTTTAAATTATACCAAAATAA
1535667 ATTTTCATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 18 0.72
31 1 0.04
32 6 0.24
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (32 bp):
TTTTAATACTTTTAAATTATACCAAAATAAGC
Found at i:1535716 original size:22 final size:22
Alignment explanation
Indices: 1535694--1535734 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1535684 TTTATATTTA
1535694 AATAAATT-TTTAAAATAAATT
1 AATAAATTATTTAAAATAAATT
**
1535715 AATATTTTATTTAAAATAAA
1 AATAAATTATTTAAAATAAA
1535735 GATTTATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AATAAATTATTTAAAATAAATT
Found at i:1538019 original size:21 final size:21
Alignment explanation
Indices: 1537995--1538043 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1537985 TATTTATTTG
*
1537995 AATTTAGTAAATTAAATT-TTA
1 AATTTA-TAAATTAAATTAATA
*
1538016 AATTTTATAAATTTAATTAATA
1 AA-TTTATAAATTAAATTAATA
1538038 AATTTA
1 AATTTA
1538044 ACGAGTCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
AATTTATAAATTAAATTAATA
Found at i:1538039 original size:22 final size:22
Alignment explanation
Indices: 1537997--1538042 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1537987 TTTATTTGAA
*
1537997 TTTAGTAAATTAAATTTTAAAT
1 TTTAGTAAATTAAATTATAAAT
*
1538019 TTTA-TAAATTTAATTAATAAAT
1 TTTAGTAAATTAAATT-ATAAAT
1538041 TT
1 TT
1538043 AACGAGTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTAGTAAATTAAATTATAAAT
Found at i:1538578 original size:24 final size:24
Alignment explanation
Indices: 1538540--1538596 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
1538530 AAAATGAATA
1538540 TAATTT-ATTTGTTAT-TATAATTT
1 TAATTTAATTTGTTATGTA-AATTT
* *
1538563 TAATTTAATTTTTTATGTAATTTT
1 TAATTTAATTTGTTATGTAAATTT
*
1538587 TAATTGAATT
1 TAATTTAATT
1538597 GATATTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.21
24 21 0.72
25 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (24 bp):
TAATTTAATTTGTTATGTAAATTT
Found at i:1540542 original size:16 final size:16
Alignment explanation
Indices: 1540483--1540547 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 16
1540473 AATATTTAAA
1540483 ATATTTCAT-ATATAT
1 ATATTTCATAATATAT
* *
1540498 AAATTT--TAATACATT
1 ATATTTCATAATATA-T
*
1540513 AATAATTCATAATATAT
1 -ATATTTCATAATATAT
*
1540530 ATATTTTATAATATAT
1 ATATTTCATAATATAT
1540546 AT
1 AT
1540548 TCATATTTTG
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
13 1 0.03
14 4 0.11
15 6 0.16
16 20 0.53
17 1 0.03
18 6 0.16
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATTTCATAATATAT
Found at i:1541623 original size:16 final size:16
Alignment explanation
Indices: 1541585--1541637 Score: 72
Period size: 16 Copynumber: 3.2 Consensus size: 16
1541575 GAGCATTAAA
*
1541585 ATTTTAGGATTCAAGTC
1 ATTTTAGG-TTCAAATC
1541602 -TCTTTAGGTTCAAATC
1 AT-TTTAGGTTCAAATC
1541618 ATTTTAGGTTCAAATC
1 ATTTTAGGTTCAAATC
1541634 ATTT
1 ATTT
1541638 AAATTAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 26 0.79
17 7 0.21
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.45
Consensus pattern (16 bp):
ATTTTAGGTTCAAATC
Found at i:1545048 original size:2 final size:2
Alignment explanation
Indices: 1545041--1545066 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1545031 AAATGTGGGG
1545041 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
1545067 GTGTGGCTGC
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):
TA
Found at i:1549859 original size:21 final size:20
Alignment explanation
Indices: 1549812--1549865 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
1549802 ATATTTTTAT
*
1549812 ATAA-TTAAATTCAAATAAAA
1 ATAATTTAAATT-ATATAAAA
* *
1549832 ATTATTTTAATTATATAAATA
1 ATAATTTAAATTATATAAA-A
1549853 ATAATTTAAATTA
1 ATAATTTAAATTA
1549866 GATGACACTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAATTTAAATTATATAAAA
Found at i:1556735 original size:3 final size:3
Alignment explanation
Indices: 1556727--1556764 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1556717 GCATAGAAAC
1556727 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1556765 ATTTCTGAAG
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1560813 original size:22 final size:21
Alignment explanation
Indices: 1560764--1560813 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
1560754 ATTTTTATGT
* *
1560764 TTATTTAAATTTAAATTTAAT
1 TTATTTAAATTTAAATTAAAA
*
1560785 TTGATTTAATTTGTAAATTAAAA
1 TT-ATTTAAATT-TAAATTAAAA
1560808 TTATTT
1 TTATTT
1560814 TTTAAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 12 0.50
23 10 0.42
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (21 bp):
TTATTTAAATTTAAATTAAAA
Found at i:1560820 original size:13 final size:13
Alignment explanation
Indices: 1560802--1560826 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1560792 AATTTGTAAA
1560802 TTAAAATTATTTT
1 TTAAAATTATTTT
1560815 TTAAAATTATTT
1 TTAAAATTATTT
1560827 AAAAATATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTAAAATTATTTT
Found at i:1560840 original size:29 final size:30
Alignment explanation
Indices: 1560798--1560883 Score: 81
Period size: 31 Copynumber: 2.9 Consensus size: 30
1560788 ATTTAATTTG
* *
1560798 TAAATTAAAA-TTATTTTTTAAAAT-TATT
1 TAAATAAAAATTTATTTTTTAAAATAAATT
** *
1560826 TAAA-AATATTTTTATATTTTATAAATAAATT
1 TAAATAA-AAATTTATTTTTTA-AAATAAATT
1560857 TAAATAAAAATTTATTTTTT-AAATAAA
1 TAAATAAAAATTTATTTTTTAAAATAAA
1560884 CAAATATTCA
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
27 1 0.02
28 5 0.11
29 16 0.36
30 4 0.09
31 17 0.38
32 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
TAAATAAAAATTTATTTTTTAAAATAAATT
Found at i:1561067 original size:31 final size:29
Alignment explanation
Indices: 1561032--1561090 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
1561022 AAAAATTTTA
* *
1561032 TAATATAAATTGATTTAAATTATTATTTATT
1 TAATAAAAATT-ATTTAAATT-TTAATTATT
*
1561063 TAATAAAAATTATTTTAATTTTAATTAT
1 TAATAAAAATTATTTAAATTTTAATTAT
1561091 AAAATATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.28
30 8 0.32
31 10 0.40
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (29 bp):
TAATAAAAATTATTTAAATTTTAATTATT
Found at i:1561085 original size:21 final size:22
Alignment explanation
Indices: 1561048--1561101 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 22
1561038 AAATTGATTT
*
1561048 AAATTATTATTTATTTAA-TA-A
1 AAATTATT-TTAATTTAATTATA
1561069 AAATTATTTTAATTTTAATTATA
1 AAATTATTTTAA-TTTAATTATA
1561092 AAATATATTT
1 AAAT-TATTT
1561102 ATATTTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.11
21 13 0.46
22 2 0.07
23 5 0.18
24 5 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AAATTATTTTAATTTAATTATA
Found at i:1561174 original size:29 final size:25
Alignment explanation
Indices: 1561137--1561208 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 25
1561127 TTTAATATTT
1561137 TAAATTTAATTATAAAATTATATAAAAA
1 TAAATTTAATT-TAAAA-TA-ATAAAAA
1561165 TAATATTTAACTTTTATAAATAATAAAAA
1 TAA-ATTTAA--TTTA-AAATAATAAAAA
1561194 TAAATTTAATTTAAA
1 TAAATTTAATTTAAA
1561209 TTTTAAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
25 2 0.05
26 4 0.10
28 9 0.22
29 16 0.40
30 4 0.10
31 5 0.12
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (25 bp):
TAAATTTAATTTAAAATAATAAAAA
Found at i:1562173 original size:34 final size:34
Alignment explanation
Indices: 1562094--1562182 Score: 87
Period size: 34 Copynumber: 2.7 Consensus size: 34
1562084 CATACCATAA
* * *
1562094 ATATTTTAATAATTATA-TTAAATTAATATTTAT
1 ATATTTAAATAATTAAATTTAAATAAATATTTAT
*
1562127 ATATTTACATAATTAAATTTAAATAAATATTT-T
1 ATATTTAAATAATTAAATTTAAATAAATATTTAT
* *
1562160 TTTTATTAAATAA-T-AATTTAAAT
1 ATAT-TTAAATAATTAAATTTAAAT
1562183 TGAATTGAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
32 9 0.19
33 18 0.38
34 20 0.43
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (34 bp):
ATATTTAAATAATTAAATTTAAATAAATATTTAT
Found at i:1562333 original size:2 final size:2
Alignment explanation
Indices: 1562326--1562372 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
1562316 TTTAAATCTT
* * * *
1562326 TA TA TA TA TA TA TA TA CA TA CA TA TA CA TA TT 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
1562368 T- TA TA
1 TA TA TA
1562373 ATGGATTACT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1564663 original size:67 final size:67
Alignment explanation
Indices: 1564535--1564671 Score: 195
Period size: 67 Copynumber: 2.0 Consensus size: 67
1564525 TGCTCATTGG
*
1564535 GACCCCAAAAAAATACTGGAGTTTTTTCATTTTTCCAAAAAAAAAAAAAATTCACAAGTTATTGG
1 GACCCCAAAAAAATACCGGAGTTTTTTCATTTTTCC--AAAAAAAAAAAATTCACAAGTTATTGG
1564600 TAAT
64 TAAT
* * * *
1564604 GACCCCAAAAAAAATACCGGAGTTTTTTCATTTTTTC-GAAAAAATAATTTCACAAGTTATTGGT
1 GACCCC-AAAAAAATACCGGAGTTTTTTCATTTTTCCAAAAAAAAAAAATTCACAAGTTATTGGT
1564668 AAT
65 AAT
1564671 G
1 G
1564672 TTTACAGTCG
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
67 28 0.45
69 6 0.10
70 28 0.45
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.32
Consensus pattern (67 bp):
GACCCCAAAAAAATACCGGAGTTTTTTCATTTTTCCAAAAAAAAAAAATTCACAAGTTATTGGTA
AT
Found at i:1565360 original size:11 final size:11
Alignment explanation
Indices: 1565326--1565373 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
1565316 AACATTTTAA
* *
1565326 ATATAATTATA
1 ATATAAATATT
*
1565337 ATATAAAAAATT
1 ATAT-AAATATT
1565349 ATATAAATATT
1 ATATAAATATT
1565360 ATATAAATA-T
1 ATATAAATATT
1565370 ATAT
1 ATAT
1565374 CACACTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 5 0.16
11 19 0.59
12 8 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATATAAATATT
Found at i:1565441 original size:15 final size:15
Alignment explanation
Indices: 1565421--1565458 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1565411 TAGACAGATT
1565421 ATTAAATCTATTTAA
1 ATTAAATCTATTTAA
*
1565436 ATTAAATTTATTTAA
1 ATTAAATCTATTTAA
1565451 ATTTAAAT
1 A-TTAAAT
1565459 AAGCAATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTAAATCTATTTAA
Found at i:1565855 original size:16 final size:16
Alignment explanation
Indices: 1565834--1565868 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1565824 TAAAATATCG
1565834 TATTCATATCTAAAAA
1 TATTCATATCTAAAAA
1565850 TATTCATATCTAAAAA
1 TATTCATATCTAAAAA
1565866 TAT
1 TAT
1565869 ATTGAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (16 bp):
TATTCATATCTAAAAA
Found at i:1566588 original size:22 final size:21
Alignment explanation
Indices: 1566560--1566609 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
1566550 ATTGATTAAG
1566560 ATAATAATTACATAAAAAAATA
1 ATAATAATTA-ATAAAAAAATA
*
1566582 ATAATAA-TAATATAAAAATA
1 ATAATAATTAATAAAAAAATA
*
1566602 AAAATAAT
1 ATAATAAT
1566610 GAAAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 16 0.64
21 2 0.08
22 7 0.28
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (21 bp):
ATAATAATTAATAAAAAAATA
Found at i:1566727 original size:30 final size:29
Alignment explanation
Indices: 1566651--1566731 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 29
1566641 TTTATTATAT
1566651 TCAAATAAA-TCTTTAATTTTTATTTTCAC
1 TCAAATAAACTC-TTAATTTTTATTTTCAC
* * *
1566680 TCAAATGAACCCTTAATTTTTAGTTTTTAC
1 TCAAATAAACTCTTAATTTTTA-TTTTCAC
1566710 -CTAAATAAACTCTTAATTTTTA
1 TC-AAATAAACTCTTAATTTTTA
1566732 ATTTATACTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 19 0.43
30 25 0.57
ACGTcount: A:0.35, C:0.15, G:0.02, T:0.48
Consensus pattern (29 bp):
TCAAATAAACTCTTAATTTTTATTTTCAC
Found at i:1566840 original size:29 final size:28
Alignment explanation
Indices: 1566775--1566843 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 28
1566765 ATTTTATTTT
1566775 ATATAAAAACTTATTTAAATATAAATCAA
1 ATATAAAAACTTATTTAAATATAAA-CAA
* *
1566804 ATGATAAAAGCTTATTTGAATATCATAA-AA
1 AT-ATAAAAACTTATTTAAATAT-A-AACAA
1566834 ATATAAAAAC
1 ATATAAAAAC
1566844 ATACTTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
29 9 0.26
30 22 0.65
31 1 0.03
32 2 0.06
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.32
Consensus pattern (28 bp):
ATATAAAAACTTATTTAAATATAAACAA
Found at i:1567112 original size:34 final size:34
Alignment explanation
Indices: 1567061--1567280 Score: 185
Period size: 34 Copynumber: 6.5 Consensus size: 34
1567051 TGATTATAAG
* *
1567061 TTGTTGGTTAAA-TGGTGATTTAGTAGTTTATCA
1 TTGTTGATTAAATTGGTGATTTAGTAGTTTACCA
* *
1567094 TTATTGATTAAATTGGTGATTTAGTAGTTTGCCA
1 TTGTTGATTAAATTGGTGATTTAGTAGTTTACCA
* * * *
1567128 TTATTGACTAAA-TGAGAGATTTGGTAGTTTACCA
1 TTGTTGATTAAATTG-GTGATTTAGTAGTTTACCA
* ** *
1567162 TTGTTGATTAAATGGGAAATTTAGTAGCTTACCA
1 TTGTTGATTAAATTGGTGATTTAGTAGTTTACCA
* * * * *
1567196 TTGTTGATTAAATGGGTGATTTGGTGGCTTATCA
1 TTGTTGATTAAATTGGTGATTTAGTAGTTTACCA
* * * * * * **
1567230 TTGTTTACTAAATGGGAGATTTGGTAGGTTGTCA
1 TTGTTGATTAAATTGGTGATTTAGTAGTTTACCA
1567264 TTGTTGATTAAA-TGGTG
1 TTGTTGATTAAATTGGTG
1567281 GTTTTTACCA
Statistics
Matches: 155, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
33 15 0.10
34 139 0.90
35 1 0.01
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.43
Consensus pattern (34 bp):
TTGTTGATTAAATTGGTGATTTAGTAGTTTACCA
Found at i:1567157 original size:68 final size:67
Alignment explanation
Indices: 1567061--1567280 Score: 251
Period size: 68 Copynumber: 3.3 Consensus size: 67
1567051 TGATTATAAG
* * * * * *
1567061 TTGTTGGTTAAATGGTGATTTAGTAGTTTATCATTATTGATTAAATTGGTGATTTAGTAGTTTGC
1 TTGTTGATTAAATGGTGATTTGGTAGTTTATCATTGTTGATTAAATGGGAGATTTAGTAGCTTGC
1567126 CA
66 CA
* * * * * *
1567128 TTATTGACTAAATGAGAGATTTGGTAGTTTACCATTGTTGATTAAATGGGAAATTTAGTAGCTTA
1 TTGTTGATTAAATG-GTGATTTGGTAGTTTATCATTGTTGATTAAATGGGAGATTTAGTAGCTTG
1567193 CCA
65 CCA
* * * * * *
1567196 TTGTTGATTAAATGGGTGATTTGGTGGCTTATCATTGTTTACTAAATGGGAGATTTGGTAGGTTG
1 TTGTTGATTAAAT-GGTGATTTGGTAGTTTATCATTGTTGATTAAATGGGAGATTTAGTAGCTTG
*
1567261 TCA
65 CCA
1567264 TTGTTGATTAAATGGTG
1 TTGTTGATTAAATGGTG
1567281 GTTTTTACCA
Statistics
Matches: 126, Mismatches: 25, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
67 15 0.12
68 110 0.87
69 1 0.01
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.43
Consensus pattern (67 bp):
TTGTTGATTAAATGGTGATTTGGTAGTTTATCATTGTTGATTAAATGGGAGATTTAGTAGCTTGC
CA
Found at i:1567240 original size:102 final size:101
Alignment explanation
Indices: 1567061--1567280 Score: 271
Period size: 102 Copynumber: 2.2 Consensus size: 101
1567051 TGATTATAAG
* * * * * *
1567061 TTGTTGGTTAAATGGTGATTTAGTAGTTTATCATTATTGATTAAATTGGTGATTTAGTAGTTTGC
1 TTGTTGATTAAATGGTGATTTAGTAGCTTACCATTATTGATTAAATGGGTGATTTAGTAGCTTAC
*
1567126 CATTATTGACTAAATGAGAGATTTGGTAGTTTACCA
66 CATTATTGACTAAATGAGAGATTTGGTAGGTTACCA
* * *
1567162 TTGTTGATTAAATGG-GAAATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
1 TTGTTGATTAAATGGTG--ATTTAGTAGCTTACCATTATTGATTAAATGGGTGATTTAGTAGCTT
* * * * **
1567226 ATCATTGTTTACTAAATGGGAGATTTGGTAGGTTGTCA
64 ACCATTATTGACTAAATGAGAGATTTGGTAGGTTACCA
1567264 TTGTTGATTAAATGGTG
1 TTGTTGATTAAATGGTG
1567281 GTTTTTACCA
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
100 1 0.01
101 14 0.14
102 84 0.84
103 1 0.01
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.43
Consensus pattern (101 bp):
TTGTTGATTAAATGGTGATTTAGTAGCTTACCATTATTGATTAAATGGGTGATTTAGTAGCTTAC
CATTATTGACTAAATGAGAGATTTGGTAGGTTACCA
Found at i:1567613 original size:19 final size:19
Alignment explanation
Indices: 1567584--1567640 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
1567574 TTGATTGTAG
*
1567584 AGGTACTATTCACGTATAC
1 AGGTGCTATTCACGTATAC
* * *
1567603 ATGTTCTATTCACGTATAT
1 AGGTGCTATTCACGTATAC
*
1567622 GGGTGCTATTCACGTATAC
1 AGGTGCTATTCACGTATAC
1567641 GATTACTGTA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (19 bp):
AGGTGCTATTCACGTATAC
Found at i:1571772 original size:34 final size:35
Alignment explanation
Indices: 1571713--1571931 Score: 254
Period size: 34 Copynumber: 6.5 Consensus size: 35
1571703 AAGTGGGAGA
* *
1571713 ATTGTTGATTAAAT-GG-TGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGATGATTTGGTAGCTTACC
* * *
1571746 ATTGTTGATTAAAT-GGATGATTTAGTAGTTTGCC
1 ATTGTTGATTAAATGGGATGATTTGGTAGCTTACC
*
1571780 ATTGTTGACTAAATGGGA-GATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGATGATTTGGTAGCTTACC
* *
1571814 ATTGTTGATTAAATGGGA-AATTTGATAGCTTACC
1 ATTGTTGATTAAATGGGATGATTTGGTAGCTTACC
* *
1571848 ATTGTTGATTAAATAGG-TGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGATGATTTGGTAGCTTACC
* * * **
1571882 ATTGTTTACTAAATGGGA-GATTTGGTAGGTTGTC
1 ATTGTTGATTAAATGGGATGATTTGGTAGCTTACC
1571916 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1571932 TGATTTTTAC
Statistics
Matches: 161, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
33 16 0.10
34 142 0.88
35 3 0.02
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.41
Consensus pattern (35 bp):
ATTGTTGATTAAATGGGATGATTTGGTAGCTTACC
Found at i:1571893 original size:102 final size:101
Alignment explanation
Indices: 1571713--1571937 Score: 312
Period size: 102 Copynumber: 2.2 Consensus size: 101
1571703 AAGTGGGAGA
* * *
1571713 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGATGATTTAGTAGTTTG
1 ATTGTTGATTAAATGGTGATTTAGTAGCTTACCATTGTTGATTAAATGGATGATTTAGTAGCTTA
1571778 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
* *
1571814 ATTGTTGATTAAATGG-GAAATTT-GATAGCTTACCATTGTTGATTAAATAGG-TGATTTGGTGG
1 ATTGTTGATTAAATGGTG--ATTTAG-TAGCTTACCATTGTTGATTAAAT-GGATGATTTAGTAG
* * **
1571876 CTTACCATTGTTTACTAAATGGGAGATTTGGTAGGTTGTC
62 CTTACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1571916 ATTGTTGATTAAATGGTGATTT
1 ATTGTTGATTAAATGGTGATTT
1571938 TTACTAAACC
Statistics
Matches: 110, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
100 1 0.01
101 21 0.19
102 85 0.77
103 3 0.03
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.42
Consensus pattern (101 bp):
ATTGTTGATTAAATGGTGATTTAGTAGCTTACCATTGTTGATTAAATGGATGATTTAGTAGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:1573048 original size:23 final size:23
Alignment explanation
Indices: 1573018--1573069 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
1573008 ATTTTTAATT
*
1573018 TATATATATTAAAATCATATATA
1 TATATATACTAAAATCATATATA
* *
1573041 TATATATACTCATATCATATATA
1 TATATATACTAAAATCATATATA
1573064 TATATA
1 TATATA
1573070 CTTTATATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (23 bp):
TATATATACTAAAATCATATATA
Found at i:1577545 original size:15 final size:15
Alignment explanation
Indices: 1577521--1577552 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1577511 TTTGTAATAA
1577521 TTTGTGTTATTTTAT
1 TTTGTGTTATTTTAT
*
1577536 TTTGTTTTATTTTAT
1 TTTGTGTTATTTTAT
1577551 TT
1 TT
1577553 CGTATGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (15 bp):
TTTGTGTTATTTTAT
Found at i:1578659 original size:92 final size:92
Alignment explanation
Indices: 1578502--1578679 Score: 347
Period size: 92 Copynumber: 1.9 Consensus size: 92
1578492 TGCAAAGTCT
*
1578502 GATGTAATCCAGATGAAATTTAAGCTTAAGTAACTCAGTTCACGTGGCATCCAGGCTCATCCCTG
1 GATGTAATCCAGATCAAATTTAAGCTTAAGTAACTCAGTTCACGTGGCATCCAGGCTCATCCCTG
1578567 ATATTAGATTCAGATAATTTTAAGTTC
66 ATATTAGATTCAGATAATTTTAAGTTC
1578594 GATGTAATCCAGATCAAATTTAAGCTTAAGTAACTCAGTTCACGTGGCATCCAGGCTCATCCCTG
1 GATGTAATCCAGATCAAATTTAAGCTTAAGTAACTCAGTTCACGTGGCATCCAGGCTCATCCCTG
1578659 ATATTAGATTCAGATAATTTT
66 ATATTAGATTCAGATAATTTT
1578680 TTCTTTCTTC
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 85 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (92 bp):
GATGTAATCCAGATCAAATTTAAGCTTAAGTAACTCAGTTCACGTGGCATCCAGGCTCATCCCTG
ATATTAGATTCAGATAATTTTAAGTTC
Found at i:1584621 original size:7 final size:6
Alignment explanation
Indices: 1584588--1584618 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
1584578 TATCTAAATA
1584588 AAATTT AAATTT AAATTT AAATTTT AAATTT
1 AAATTT AAATTT AAATTT AAA-TTT AAATTT
1584619 TAATGATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:1585835 original size:10 final size:10
Alignment explanation
Indices: 1585796--1585834 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1585786 TTTCAAATCC
*
1585796 ATATAATATA
1 ATATTATATA
*
1585806 ATATGATATA
1 ATATTATATA
*
1585816 ATATTATATT
1 ATATTATATA
1585826 ATATTATAT
1 ATATTATAT
1585835 TTATTCATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (10 bp):
ATATTATATA
Found at i:1585835 original size:15 final size:15
Alignment explanation
Indices: 1585796--1585839 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
1585786 TTTCAAATCC
* *
1585796 ATATAATATAATATG
1 ATATAATATTATATT
1585811 ATATAATATTATATT
1 ATATAATATTATATT
*
1585826 ATATTATATT-TATT
1 ATATAATATTATATT
1585840 CATGAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 4 0.15
15 22 0.85
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATATAATATTATATT
Found at i:1586195 original size:17 final size:16
Alignment explanation
Indices: 1586173--1586227 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
1586163 TATATTAAAT
1586173 TTTAAATTTTAAATATA
1 TTTAAA-TTTAAATATA
*
1586190 TTTAAACATTAAATATA
1 TTTAAA-TTTAAATATA
*
1586207 TATT-CATTTAAA-ATA
1 T-TTAAATTTAAATATA
1586222 TTTAAA
1 TTTAAA
1586228 AATATATTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 2 0.06
15 5 0.16
16 5 0.16
17 17 0.55
18 2 0.06
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAAATTTAAATATA
Found at i:1587901 original size:2 final size:2
Alignment explanation
Indices: 1587894--1587938 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1587884 TTTAAATTCT
*
1587894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC 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
1587936 TA T
1 TA T
1587939 GTATGTGCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1599982 original size:29 final size:27
Alignment explanation
Indices: 1599949--1600011 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
1599939 CTTTTATATT
1599949 AATAATTATATATTTTATAATTAAATTTA
1 AATAATTATATATTTTATAATT-AA-TTA
* * *
1599978 AATAA--AAATATTTTTTAATTTATTA
1 AATAATTATATATTTTATAATTAATTA
1600003 AATAATTAT
1 AATAATTAT
1600012 TTAAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
25 8 0.29
26 1 0.04
27 14 0.50
29 5 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AATAATTATATATTTTATAATTAATTA
Found at i:1600340 original size:3 final size:3
Alignment explanation
Indices: 1600332--1600366 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1600322 CTGATATAAG
1600332 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1600367 TATTGAGGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1600801 original size:21 final size:21
Alignment explanation
Indices: 1600777--1600816 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1600767 AATCTAATAA
1600777 TTTATATATTTATATTATATT
1 TTTATATATTTATATTATATT
*
1600798 TTTATATTTTTATATTATA
1 TTTATATATTTATATTATA
1600817 ATTATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTATATATTTATATTATATT
Found at i:1600806 original size:27 final size:27
Alignment explanation
Indices: 1600771--1600877 Score: 89
Period size: 27 Copynumber: 4.0 Consensus size: 27
1600761 ATGATAAATC
1600771 TAATAATTTATATATTTATATTATATTT
1 TAAT-ATTTATATATTTATATTATATTT
* *
1600799 TTATATTTTTATA-TTATAATTATATTT
1 TAATATTTATATATTTAT-ATTATATTT
* *
1600826 AAAATATTT-T-TATTTATA-TAAATTT
1 -TAATATTTATATATTTATATTATATTT
*
1600851 TAATAAATTA-ATTATTTATATTATATT
1 TAAT-ATTTATA-TATTTATATTATATT
1600878 AATTTTAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
24 3 0.05
25 9 0.14
26 7 0.11
27 30 0.48
28 14 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
TAATATTTATATATTTATATTATATTT
Found at i:1600821 original size:19 final size:19
Alignment explanation
Indices: 1600773--1600825 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
1600763 GATAAATCTA
*
1600773 ATAATTTATATATTTATATT
1 ATAA-TTATATTTTTATATT
*
1600793 ATATTTTTATATTTTTATATT
1 ATA--ATTATATTTTTATATT
1600814 ATAATTATATTT
1 ATAATTATATTT
1600826 AAAATATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 8 0.29
20 3 0.11
21 17 0.61
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATAATTATATTTTTATATT
Found at i:1600890 original size:27 final size:26
Alignment explanation
Indices: 1600775--1600903 Score: 86
Period size: 27 Copynumber: 4.7 Consensus size: 26
1600765 TAAATCTAAT
* *
1600775 AATTTATATATTTATATTATATTTT-TA
1 AATTTTTATA-TTATATTA-ATTTTAAA
*
1600802 TATTTTTATATTATAATT-ATATTTAAA
1 AATTTTTATATTAT-ATTAAT-TTTAAA
*
1600829 ATATTTTTAT-TTATATAAATTTTAATAAA
1 A-ATTTTTATATTATATTAA-TTT--TAAA
1600858 TTAATTATTTATATTATATTAATTTTAAA
1 --AATT-TTTATATTATATTAATTTTAAA
1600887 AATTTTATATATT-TATT
1 AATTTT-TATATTATATT
1600904 TTATATTATA
Statistics
Matches: 83, Mismatches: 6, Indels: 27
0.72 0.05 0.23
Matches are distributed among these distances:
25 2 0.02
26 15 0.18
27 29 0.35
28 9 0.11
29 8 0.10
30 3 0.04
31 9 0.11
32 8 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
AATTTTTATATTATATTAATTTTAAA
Found at i:1600908 original size:33 final size:33
Alignment explanation
Indices: 1600828--1600920 Score: 111
Period size: 32 Copynumber: 2.8 Consensus size: 33
1600818 TTATATTTAA
* *
1600828 AATATTTTTA-TTTATATAAATTTTAATAAATT
1 AATATATTTATTTTATATTAATTTTAATAAATT
*
1600860 AAT-TATTTATATTATATTAATTTTAA-AAATTT
1 AATATATTTATTTTATATTAATTTTAATAAA-TT
*
1600892 TATATATTTATTTTATATTATATTTTAAT
1 AATATATTTATTTTATATTA-ATTTTAAT
1600921 TATTTTGATG
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
31 8 0.16
32 21 0.41
33 15 0.29
34 7 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (33 bp):
AATATATTTATTTTATATTAATTTTAATAAATT
Found at i:1601254 original size:27 final size:26
Alignment explanation
Indices: 1601204--1601256 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
1601194 AAATAAGCGG
1601204 TATTTATATTTTTATTATATTTAAAT
1 TATTTATATTTTTATTATATTTAAAT
1601230 TATTTA-ATTTTTAATTTATATTTAAAT
1 TATTTATATTTTT-A-TTATATTTAAAT
1601257 AAATTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.24
26 7 0.28
27 12 0.48
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TATTTATATTTTTATTATATTTAAAT
Found at i:1605551 original size:30 final size:30
Alignment explanation
Indices: 1605517--1605574 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
1605507 AAATTCAATT
*
1605517 TTGGAAGTATTTTTATTTTTAGAGACGGAA
1 TTGGAAGTATTTTTATTTTCAGAGACGGAA
*
1605547 TTGGAAGTATTTTTATTTTCAGTGACGG
1 TTGGAAGTATTTTTATTTTCAGAGACGG
1605575 TTCTGAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (30 bp):
TTGGAAGTATTTTTATTTTCAGAGACGGAA
Found at i:1606530 original size:35 final size:32
Alignment explanation
Indices: 1606490--1606570 Score: 83
Period size: 35 Copynumber: 2.4 Consensus size: 32
1606480 TTTATTTGTG
*
1606490 TATTTTTTTAT-AATATAATCATATTTTAAATAATT
1 TATTTTTATATAAATATAAT-ATA--TT-AATAATT
*
1606525 TATTTTTATATAAATTTAATATATTAATAATT
1 TATTTTTATATAAATATAATATATTAATAATT
*
1606557 TATTTCATATATAA
1 TATTT-TTATATAA
1606571 TTTAAAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 12 0.29
33 9 0.22
35 13 0.32
36 7 0.17
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (32 bp):
TATTTTTATATAAATATAATATATTAATAATT
Found at i:1606593 original size:33 final size:32
Alignment explanation
Indices: 1606518--1606592 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
1606508 TCATATTTTA
* *
1606518 AATAATTTATTTTTATATAAATTTAATATATT
1 AATAATTTATTTATATATAAATTTAAAATATT
1606550 AATAATTTATTTCATATAT-AATTTAAAATA-T
1 AATAATTTATTT-ATATATAAATTTAAAATATT
1606581 -AT-ATTTATTTAT
1 AATAATTTATTTAT
1606593 TGTGTCATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
28 2 0.05
29 8 0.20
30 2 0.05
31 1 0.03
32 22 0.55
33 5 0.12
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (32 bp):
AATAATTTATTTATATATAAATTTAAAATATT
Found at i:1611318 original size:21 final size:22
Alignment explanation
Indices: 1611294--1611335 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1611284 TGTAAATATT
*
1611294 TTTAA-TTATTAATAAAATTTA
1 TTTAATTTATAAATAAAATTTA
1611315 TTTAATTTATAAATAAAATTT
1 TTTAATTTATAAATAAAATTT
1611336 TAATTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTAATTTATAAATAAAATTTA
Found at i:1611345 original size:20 final size:18
Alignment explanation
Indices: 1611315--1611351 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 18
1611305 ATAAAATTTA
1611315 TTTAATTTATAAATAAAAT
1 TTTAATTTATAAA-AAAAT
1611334 TTTAATTTTATAAAAAAA
1 TTTAA-TTTATAAAAAAA
1611352 CTTATTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTAATTTATAAAAAAAT
Found at i:1611651 original size:20 final size:20
Alignment explanation
Indices: 1611616--1611678 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 20
1611606 ATTATAAAAT
*
1611616 ATATAATTATATATTTTTAAA
1 ATATAA-TAAATATTTTTAAA
*
1611637 ATATAATAAATA--TTTAGAT
1 ATATAATAAATATTTTTA-AA
1611656 ATAATAATAAATATTTTATAAA
1 AT-ATAATAAATATTTT-TAAA
1611678 A
1 A
1611679 ATTAAATACA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
18 4 0.12
19 3 0.09
20 15 0.44
21 6 0.18
22 4 0.12
23 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
ATATAATAAATATTTTTAAA
Found at i:1611675 original size:17 final size:18
Alignment explanation
Indices: 1611639--1611686 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
1611629 TTTTTAAAAT
1611639 ATAATAAATATTTAGATATA
1 ATAATAAATATTT--ATATA
1611659 ATAATAAATATTT-TATA
1 ATAATAAATATTTATATA
*
1611676 AAAATTAAATA
1 ATAA-TAAATA
1611687 CATCTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 7 0.27
18 6 0.23
20 13 0.50
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATAATAAATATTTATATA
Found at i:1611793 original size:2 final size:2
Alignment explanation
Indices: 1611786--1611813 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1611776 GCCAAAAAGA
1611786 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1611814 GGGGGGTGTG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1612424 original size:23 final size:23
Alignment explanation
Indices: 1612395--1612450 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
1612385 AAATTTAAAT
1612395 TTTAAATTTT-A-AATATAACATA
1 TTTAAATTTTCATAATA-AACATA
*
1612417 TATTAAATATTTCATAATAATCATA
1 T-TTAAAT-TTTCATAATAAACATA
1612442 TTTAAATTT
1 TTTAAATTT
1612451 ATTATTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 1 0.03
23 8 0.28
24 9 0.31
25 7 0.24
26 4 0.14
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTAAATTTTCATAATAAACATA
Found at i:1612426 original size:7 final size:7
Alignment explanation
Indices: 1612349--1612427 Score: 51
Period size: 7 Copynumber: 11.4 Consensus size: 7
1612339 CGTAAATATA
1612349 ATTAAAT
1 ATTAAAT
1612356 A-T-AAT
1 ATTAAAT
1612361 ATTAAATT
1 ATTAAA-T
1612369 ATTAAAT
1 ATTAAAT
1612376 ATATAAA-
1 AT-TAAAT
*
1612383 A-AAAAT
1 ATTAAAT
1612389 -TTAAAT
1 ATTAAAT
*
1612395 TTTAAAT
1 ATTAAAT
*
1612402 TTTAAAT
1 ATTAAAT
*
1612409 ATAACATAT
1 ATTA-A-AT
1612418 ATTAAAT
1 ATTAAAT
1612425 ATT
1 ATT
1612428 TCATAATAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
5 7 0.12
6 6 0.10
7 27 0.47
8 13 0.22
9 5 0.09
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (7 bp):
ATTAAAT
Found at i:1612476 original size:20 final size:21
Alignment explanation
Indices: 1612453--1612494 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
1612443 TTAAATTTAT
*
1612453 TATTTTATATTTTA-TTAAAA
1 TATTTTATATTATATTTAAAA
1612473 TATTTTATATTATATTTAAAA
1 TATTTTATATTATATTTAAAA
1612494 T
1 T
1612495 TATTAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATATTATATTTAAAA
Found at i:1612538 original size:29 final size:28
Alignment explanation
Indices: 1612474--1612538 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
1612464 TTATTAAAAT
* *
1612474 ATTTTA-TATTATATTTAAAATTATTAA
1 ATTTTATTTTTATAATTAAAATTATTAA
* * *
1612501 ATATAATTTTTATAATTAAATATTTTTAA
1 ATTTTATTTTTATAATTAAA-ATTATTAA
1612530 ATTTTATTT
1 ATTTTATTT
1612539 GGACTAAATT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
27 4 0.14
28 11 0.38
29 14 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
ATTTTATTTTTATAATTAAAATTATTAA
Found at i:1612942 original size:19 final size:19
Alignment explanation
Indices: 1612883--1612942 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
1612873 AATTTTTTTA
* *
1612883 TATAAAAAGTAAATTTTAT
1 TATAAAAATTAAATATTAT
* * **
1612902 TTTGAAAATTAAAATAAAAT
1 TATAAAAATT-AAATATTAT
1612922 TATAAAAATTAAATATTAT
1 TATAAAAATTAAATATTAT
1612941 TA
1 TA
1612943 AATATTATAT
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (19 bp):
TATAAAAATTAAATATTAT
Found at i:1612974 original size:42 final size:46
Alignment explanation
Indices: 1612928--1613036 Score: 104
Period size: 42 Copynumber: 2.5 Consensus size: 46
1612918 AAATTATAAA
**
1612928 AATTAAATATTATTAAATATTATA-TTTA-AAAAGTATT-AT-ATT
1 AATTAAATATTATTAAATATTATATTTTATAAAAAAATTAATGATT
* * *
1612970 AATTAATTA-AATTAAATTTTTATATTTTATAAAAAAATTAATGATT
1 AATTAAATATTATTAAA-TATTATATTTTATAAAAAAATTAATGATT
* *
1613016 AATAAAAAATTA-TAAATATTA
1 AATTAAATATTATTAAATATTA
1613037 AAATTAAATT
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
41 6 0.12
42 14 0.27
43 4 0.08
44 7 0.14
45 6 0.12
46 13 0.25
47 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (46 bp):
AATTAAATATTATTAAATATTATATTTTATAAAAAAATTAATGATT
Found at i:1613457 original size:21 final size:23
Alignment explanation
Indices: 1613431--1613473 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
1613421 TTAATATGTG
1613431 ATATTTT-AATTTT-TAAAAATA
1 ATATTTTAAATTTTATAAAAATA
1613452 ATATTTTAAATTTTATAAAAAT
1 ATATTTTAAATTTTATAAAAAT
1613474 TAATTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.35
22 6 0.30
23 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATTTTATAAAAATA
Found at i:1613480 original size:21 final size:21
Alignment explanation
Indices: 1613433--1613482 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
1613423 AATATGTGAT
*
1613433 ATTTTAATTTTTAAAAATAATA
1 ATTTAAATTTTTAAAAAT-ATA
*
1613455 TTTTAAATTTTATAAAAAT-TA
1 ATTTAAATTTT-TAAAAATATA
1613476 ATTTAAA
1 ATTTAAA
1613483 ACAACCGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 8 0.33
22 9 0.38
23 7 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTAAATTTTTAAAAATATA
Found at i:1617889 original size:20 final size:19
Alignment explanation
Indices: 1617843--1617892 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 19
1617833 AAATATAAAT
1617843 TATTTAAAAAT-TAATTAA
1 TATTTAAAAATATAATTAA
*
1617861 -ATTT--TAATATAATTATA
1 TATTTAAAAATATAATTA-A
1617878 TATTTAAAAATATAA
1 TATTTAAAAATATAA
1617893 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
15 3 0.12
16 6 0.24
17 5 0.20
18 4 0.16
20 7 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTTAAAAATATAATTAA
Found at i:1617988 original size:24 final size:27
Alignment explanation
Indices: 1617934--1617989 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 27
1617924 TAAAAATTTT
* *
1617934 AAATTTATCATTAAATAAAAATATCAT
1 AAATTTATCATTAAATAAAAATATAAA
*
1617961 AAATTTAT-A-TAATTAAAAA-ATAAA
1 AAATTTATCATTAAATAAAAATATAAA
1617985 AAATT
1 AAATT
1617990 ATTAAATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 8 0.31
25 9 0.35
26 1 0.04
27 8 0.31
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (27 bp):
AAATTTATCATTAAATAAAAATATAAA
Found at i:1618816 original size:84 final size:85
Alignment explanation
Indices: 1618643--1618832 Score: 262
Period size: 84 Copynumber: 2.3 Consensus size: 85
1618633 CTAACTTAAA
* * * *
1618643 AAAT-TTAAAATTTA-AAATATAATTTAGTTAATTTATATAATTTTATTTAAAAAATAATATTTA
1 AAATCTTAATATTTATAAATTTAATTTAATTAATTTATATAA-TTTATTTAAAAAATAATATTCA
**
1618706 ACATATTTAGGTTTAGAATTT
65 ACATATTTAAATTTAGAATTT
1618727 AAATCTTAATATTTATAATATTTAATTTAATTAATTTATATAA-TTATTTAAAAAA-AATATTCA
1 AAATCTTAATATTTATAA-ATTTAATTTAATTAATTTATATAATTTATTTAAAAAATAATATTCA
*
1618790 ACATATTTAAATTTAGAGTTT
65 ACATATTTAAATTTAGAATTT
*
1618811 GAATCTTAATATTTATAAATTT
1 AAATCTTAATATTTATAAATTT
1618833 TTTCTGGTAT
Statistics
Matches: 95, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
83 4 0.04
84 46 0.48
85 21 0.22
86 2 0.02
87 22 0.23
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.48
Consensus pattern (85 bp):
AAATCTTAATATTTATAAATTTAATTTAATTAATTTATATAATTTATTTAAAAAATAATATTCAA
CATATTTAAATTTAGAATTT
Found at i:1619847 original size:15 final size:16
Alignment explanation
Indices: 1619816--1619849 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1619806 ATAAAATATA
*
1619816 TTTTTTATTTTTATTC
1 TTTTTTAATTTTATTC
1619832 TTTTTTAATTTT-TTC
1 TTTTTTAATTTTATTC
1619847 TTT
1 TTT
1619850 AACTAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTAATTTTATTC
Found at i:1620013 original size:16 final size:16
Alignment explanation
Indices: 1619992--1620023 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1619982 AATTAAAATA
*
1619992 TAATTTAATAATAACT
1 TAATTTAACAATAACT
1620008 TAATTTAACAATAACT
1 TAATTTAACAATAACT
1620024 AAAAATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATTTAACAATAACT
Found at i:1620033 original size:21 final size:22
Alignment explanation
Indices: 1620008--1620049 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1619998 AATAATAACT
1620008 TAATT-TAACAAT-AACTAAAAA
1 TAATTCTAA-AATCAACTAAAAA
1620029 TAATTCTAAAATCAACTAAAA
1 TAATTCTAAAATCAACTAAAA
1620050 TTTTATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.29
Consensus pattern (22 bp):
TAATTCTAAAATCAACTAAAAA
Found at i:1620247 original size:33 final size:31
Alignment explanation
Indices: 1620156--1620250 Score: 92
Period size: 28 Copynumber: 3.2 Consensus size: 31
1620146 AATAACCTAA
* *
1620156 AAATACATATATTTTTATTAAATTTT--AA-
1 AAATAAATAAATTTTTATTAAATTTTAAAAT
* * *
1620184 AAATAAATAACTATTT-TTAAA-TATAAAAT
1 AAATAAATAAATTTTTATTAAATTTTAAAAT
1620213 AAATAAATAAATTTTTATTAAATTTTAGAGAAT
1 AAATAAATAAATTTTTATTAAATTTTA-A-AAT
1620246 AAATA
1 AAATA
1620251 TGTTTTATAC
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
26 2 0.04
27 5 0.10
28 14 0.27
29 14 0.27
30 5 0.10
31 3 0.06
32 1 0.02
33 8 0.15
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (31 bp):
AAATAAATAAATTTTTATTAAATTTTAAAAT
Found at i:1620256 original size:29 final size:28
Alignment explanation
Indices: 1620153--1620250 Score: 99
Period size: 29 Copynumber: 3.4 Consensus size: 28
1620143 AATAATAACC
* *
1620153 TAAAAATACATATATTTTTATTAAATTT
1 TAAAAATAAATAAATTTTTATTAAATTT
* * *
1620181 TAAAAATAAATAACTATTT-TTAAATATA
1 TAAAAATAAATAAATTTTTATTAAAT-TT
*
1620209 AAATAAATAAATAAATTTTTATTAAATTT
1 TAA-AAATAAATAAATTTTTATTAAATTT
*
1620238 TAGAGAATAAATA
1 TA-AAAATAAATA
1620251 TGTTTTATAC
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
27 6 0.11
28 18 0.33
29 24 0.44
30 7 0.13
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (28 bp):
TAAAAATAAATAAATTTTTATTAAATTT
Found at i:1620858 original size:16 final size:17
Alignment explanation
Indices: 1620828--1620867 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
1620818 AATTTTTATA
1620828 ATAATAATATATTAAAT
1 ATAATAATATATTAAAT
*
1620845 ATAA-AATATTTTAAAT
1 ATAATAATATATTAAAT
1620861 -TAATAAT
1 ATAATAAT
1620868 TAAATAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 14 0.67
17 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAATAATATATTAAAT
Found at i:1621040 original size:17 final size:17
Alignment explanation
Indices: 1621010--1621044 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1621000 TATAAAGAGA
1621010 ATGATTAAATTAATATT
1 ATGATTAAATTAATATT
1621027 ATGAGTTAAA-TAATATT
1 ATGA-TTAAATTAATATT
1621044 A
1 A
1621045 ATTAAGTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (17 bp):
ATGATTAAATTAATATT
Found at i:1621405 original size:18 final size:19
Alignment explanation
Indices: 1621384--1621428 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1621374 AGATATTCCT
*
1621384 TTAAAAAA-TTTACCTTTC
1 TTAAAAAACTTTACATTTC
*
1621402 TTAAAAAACTTTACATTTT
1 TTAAAAAACTTTACATTTC
1621421 TTAAAAAA
1 TTAAAAAA
1621429 AATCCATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAAAAAACTTTACATTTC
Found at i:1623512 original size:35 final size:35
Alignment explanation
Indices: 1623482--1623550 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
1623472 ATTTAATTAT
* *
1623482 ATAATACAA-AAATT-TAATATAAAATTTTTAAAAA
1 ATAATAAAATAAATTATAA-ATAAAAATTTTAAAAA
1623516 ATAATAAAATAAATTATAAATAAAAATTTTAAAAA
1 ATAATAAAATAAATTATAAATAAAAATTTTAAAAA
1623551 TTTATACCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 8 0.26
35 20 0.65
36 3 0.10
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (35 bp):
ATAATAAAATAAATTATAAATAAAAATTTTAAAAA
Found at i:1625126 original size:15 final size:15
Alignment explanation
Indices: 1625106--1625135 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1625096 TGGACCAGTG
1625106 TTTTTTTC-TTCTTT
1 TTTTTTTCTTTCTTT
1625120 TTTTTTTCTTTCTTT
1 TTTTTTTCTTTCTTT
1625135 T
1 T
1625136 CTCTGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTTTCTTTCTTT
Found at i:1632286 original size:13 final size:13
Alignment explanation
Indices: 1632268--1632355 Score: 63
Period size: 13 Copynumber: 6.5 Consensus size: 13
1632258 ATAATTTTAA
*
1632268 ATATAATATAATT
1 ATATAATATAAAT
1632281 ATATAAT-TAAAT
1 ATATAATATAAAT
*
1632293 AT-TATATATAAAG
1 ATATA-ATATAAAT
*
1632306 ATATTATATAAAAT
1 ATATAATAT-AAAT
*
1632320 ATAATATTATATGAAT
1 AT-ATA--ATATAAAT
*
1632336 ATATAACATAAAT
1 ATATAATATAAAT
*
1632349 AAATAAT
1 ATATAAT
1632356 TATATTAAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
11 2 0.03
12 8 0.14
13 28 0.48
14 6 0.10
15 5 0.09
16 5 0.09
17 4 0.07
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATAATATAAAT
Found at i:1632302 original size:17 final size:16
Alignment explanation
Indices: 1632268--1632331 Score: 62
Period size: 15 Copynumber: 4.1 Consensus size: 16
1632258 ATAATTTTAA
*
1632268 ATATAATATA-ATTAT
1 ATATAATAAATATTAT
*
1632283 ATA-ATTAAATATTAT
1 ATATAATAAATATTAT
*
1632298 ATATAA-AGATATTAT
1 ATATAATAAATATTAT
*
1632313 ATAAAATATAATATTAT
1 ATATAATA-AATATTAT
1632330 AT
1 AT
1632332 GAATATATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
14 4 0.10
15 24 0.62
16 2 0.05
17 9 0.23
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
ATATAATAAATATTAT
Found at i:1632386 original size:30 final size:29
Alignment explanation
Indices: 1632278--1632383 Score: 101
Period size: 30 Copynumber: 3.6 Consensus size: 29
1632268 ATATAATATA
1632278 ATTATAT-AATTAAATATTATATATAAAGAT
1 ATTATATAAATTAAATATTATAT-TAAA-AT
* * *
1632308 ATTATATAAAATATAATATTATATGAATAT
1 ATTATATAAATTA-AATATTATATTAAAAT
* *
1632338 ATAACATAAA-TAAATAATTATATTAAAAT
1 ATTATATAAATTAAAT-ATTATATTAAAAT
1632367 -TTATATAAATTATAATA
1 ATTATATAAATTA-AATA
1632384 ATTTAAATTA
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
28 10 0.16
29 16 0.26
30 20 0.32
31 6 0.10
32 10 0.16
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.42
Consensus pattern (29 bp):
ATTATATAAATTAAATATTATATTAAAAT
Found at i:1633301 original size:42 final size:42
Alignment explanation
Indices: 1633255--1633415 Score: 132
Period size: 42 Copynumber: 3.7 Consensus size: 42
1633245 ATAACTTAAA
1633255 ATTTATTATATTATATATTTAAATAATTTTTTATGTATCAAT
1 ATTTATTATATTATATATTTAAATAATTTTTTATGTATCAAT
* ** * *
1633297 ATTTATT-T-TTATATAAAATTGT-GATTTTTATTTTATTTATAACTTAAA
1 ATTTATTATATTATAT---ATT-TAAATAATT-TTTTATGTAT--C--AAT
1633345 ATTTATTATATTATATATTTAAATAATTTTTTATGTATCAAT
1 ATTTATTATATTATATATTTAAATAATTTTTTATGTATCAAT
* * *
1633387 ATTTATTTTA-TATAAATTTTAATATATTT
1 ATTTATTATATTATATATTTAAATA-ATTT
1633416 ATATATTTAT
Statistics
Matches: 93, Mismatches: 13, Indels: 26
0.70 0.10 0.20
Matches are distributed among these distances:
40 6 0.06
41 13 0.14
42 22 0.24
43 7 0.08
44 11 0.12
46 11 0.12
47 7 0.08
48 9 0.10
49 1 0.01
50 6 0.06
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (42 bp):
ATTTATTATATTATATATTTAAATAATTTTTTATGTATCAAT
Found at i:1633366 original size:23 final size:23
Alignment explanation
Indices: 1633233--1633367 Score: 56
Period size: 23 Copynumber: 6.0 Consensus size: 23
1633223 AATTGTGATT
* *
1633233 TTTATTTTATT-TATAACTTAAAA
1 TTTATTATATTATAT-ATTTAAAA
1633256 TTTATTATATTATATATTTAAATAA
1 TTTATTATATTATATATTT-AA-AA
1633281 TTT-TT-TATGTATCAATATTT---A
1 TTTATTATAT-TAT--ATATTTAAAA
* * **
1633302 TTT-TTATA-TA-AAATTGTGATT
1 TTTATTATATTATATATT-TAAAA
* *
1633323 TTTATTTTATT-TATAACTTAAAA
1 TTTATTATATTATAT-ATTTAAAA
1633346 TTTATTATATTATATATTTAAA
1 TTTATTATATTATATATTTAAA
1633368 TAATTTTTTA
Statistics
Matches: 84, Mismatches: 12, Indels: 32
0.66 0.09 0.25
Matches are distributed among these distances:
17 4 0.05
18 1 0.01
20 2 0.02
21 9 0.11
22 6 0.07
23 36 0.43
24 15 0.18
25 5 0.06
26 6 0.07
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTATTATATTATATATTTAAAA
Found at i:1633417 original size:90 final size:90
Alignment explanation
Indices: 1633219--1633402 Score: 343
Period size: 90 Copynumber: 2.1 Consensus size: 90
1633209 ATTTCTATTA
*
1633219 ATAAAATTGTGATTTTTATTTTATTTATAACTTAAAATTTATTATATTATATATTTAAATAATTT
1 ATAAAATTGTAATTTTTATTTTATTTATAACTTAAAATTTATTATATTATATATTTAAATAATTT
1633284 TTTATGTATCAATATTTATTTTTAT
66 TTTATGTATCAATATTTATTTTTAT
*
1633309 ATAAAATTGTGATTTTTATTTTATTTATAACTTAAAATTTATTATATTATATATTTAAATAATTT
1 ATAAAATTGTAATTTTTATTTTATTTATAACTTAAAATTTATTATATTATATATTTAAATAATTT
1633374 TTTATGTATCAATATTTA-TTTTAT
66 TTTATGTATCAATATTTATTTTTAT
1633398 ATAAA
1 ATAAA
1633403 TTTTAATATA
Statistics
Matches: 94, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
89 11 0.12
90 83 0.88
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (90 bp):
ATAAAATTGTAATTTTTATTTTATTTATAACTTAAAATTTATTATATTATATATTTAAATAATTT
TTTATGTATCAATATTTATTTTTAT
Found at i:1633447 original size:14 final size:16
Alignment explanation
Indices: 1633420--1633453 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
1633410 ATATTTATAT
1633420 ATTTATATTATTTTTA
1 ATTTATATTATTTTTA
1633436 ATTTATA-T-TTTTTA
1 ATTTATATTATTTTTA
1633450 ATTT
1 ATTT
1633454 TTATATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 1 0.06
16 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTATATTATTTTTA
Found at i:1633454 original size:59 final size:61
Alignment explanation
Indices: 1633340--1633487 Score: 146
Period size: 59 Copynumber: 2.5 Consensus size: 61
1633330 TATTTATAAC
* * *
1633340 TTAAAATTTATTATA-TTATATATTTAAATAATTTTTTATGTATCAATATTTA-TTTTATA
1 TTAAATTTTAATATATTTATATATTTAAATAATTTTTAATGTATCAATATTTATTTTTATA
* * * * *
1633399 -TAAATTTTAATATATTTATATATTTATATTATTTTTAATTTAT-ATTTTTTAATTTTTATA
1 TTAAATTTTAATATATTTATATATTTAAATAATTTTTAATGTATCAATATTT-ATTTTTATA
*
1633459 TTAAATTGTT-ATAT-TATATTATATTTAAA
1 TTAAATT-TTAATATATTTA-TATATTTAAA
1633488 ATTATTATAT
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
58 17 0.23
59 25 0.34
60 10 0.14
61 19 0.26
62 2 0.03
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (61 bp):
TTAAATTTTAATATATTTATATATTTAAATAATTTTTAATGTATCAATATTTATTTTTATA
Found at i:1633495 original size:25 final size:25
Alignment explanation
Indices: 1633454--1633512 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
1633444 TTTTTAATTT
*
1633454 TTATA-TT-AAATTGTTATATTATA
1 TTATATTTAAAATTATTATATTATA
*
1633477 TTATATTTAAAATTATTATATTTTA
1 TTATATTTAAAATTATTATATTATA
*
1633502 AT-TATTTAAAA
1 TTATATTTAAAA
1633513 AAATCATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.16
24 11 0.35
25 15 0.48
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTATATTTAAAATTATTATATTATA
Done.