Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 205 of 210
Found at i:60481539 original size:45 final size:46
Alignment explanation
Indices: 60481355--60481692 Score: 560
Period size: 46 Copynumber: 7.5 Consensus size: 46
60481345 TGATCAGTGA
*
60481355 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGATACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
60481401 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
60481447 CAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
60481493 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
* *
60481538 CAAGTGACAAAGTGATAAGTGGTATCTTTAGCTACTCTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
* *
60481584 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTATACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
60481629 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
60481674 C-AGGGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
60481693 ATCATACGTA
Statistics
Matches: 278, Mismatches: 13, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
43 12 0.04
44 5 0.02
45 104 0.37
46 157 0.56
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.29
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:60481569 original size:91 final size:91
Alignment explanation
Indices: 60481355--60481692 Score: 574
Period size: 91 Copynumber: 3.7 Consensus size: 91
60481345 TGATCAGTGA
*
60481355 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGATACACTTATCTGATCAAGTGACAAAGTGATAAG
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
*
60481420 TGGTAGCTTTAGCTACACTTATCTGAT
66 TGGTAGC-CTAGCTACACTTATCTGAT
*
60481447 CAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
60481512 TGGTAGCCTAGCTACACTTATCTGAT
66 TGGTAGCCTAGCTACACTTATCTGAT
* *
60481538 CAAGTGACAAAGTGATAAGTGGTATCTTTAGCTACTCTTATCTGATCAAGTGACAAAGTGATAAG
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
*
60481603 TGGTAGCCTAGCTATACTTATCTGAT
66 TGGTAGCCTAGCTACACTTATCTGAT
* *
60481629 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGATC-AGGGAC-AAGTGATAAG
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
60481691 TG
66 TG
60481693 ATCATACGTA
Statistics
Matches: 235, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
88 12 0.05
89 5 0.02
90 18 0.08
91 130 0.55
92 70 0.30
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.29
Consensus pattern (91 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
TGGTAGCCTAGCTACACTTATCTGAT
Found at i:60491504 original size:23 final size:24
Alignment explanation
Indices: 60491440--60491508 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 24
60491430 AGTTAAAAAA
60491440 TATATCAAATTCGTATTGATGACT
1 TATATCAAATTCGTATTGATGACT
* * *
60491464 TA-AT--ATTTGGT-TTTATGA-T
1 TATATCAAATTCGTATTGATGACT
60491483 TATATCAAATTCGTATTGATGACT
1 TATATCAAATTCGTATTGATGACT
60491507 TA
1 TA
60491509 ATAGAGGTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
19 3 0.09
20 8 0.24
21 5 0.15
22 5 0.15
23 8 0.24
24 5 0.15
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (24 bp):
TATATCAAATTCGTATTGATGACT
Found at i:60492899 original size:10 final size:10
Alignment explanation
Indices: 60492886--60492910 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
60492876 AAAATAATTT
60492886 AAATTTTAAA
1 AAATTTTAAA
60492896 AAATTTTAAA
1 AAATTTTAAA
60492906 AAATT
1 AAATT
60492911 AAATCGACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AAATTTTAAA
Found at i:60493042 original size:9 final size:9
Alignment explanation
Indices: 60492922--60493086 Score: 68
Period size: 9 Copynumber: 17.4 Consensus size: 9
60492912 AATCGACAAA
60492922 AAAAATTAT
1 AAAAATTAT
*
60492931 AAAAA-AAT
1 AAAAATTAT
* *
60492939 AAATATTGT
1 AAAAATTAT
*
60492948 AGAAA-TAT
1 AAAAATTAT
*
60492956 AAAAATTCT
1 AAAAATTAT
60492965 AATAAATTAT
1 AA-AAATTAT
60492975 -AAAATTAAT
1 AAAAATT-AT
*
60492984 AAAACATATTT
1 AAAA-AT-TAT
60492995 AAAATATT-T
1 AAAA-ATTAT
**
60493004 GAAATTTTAT
1 -AAAAATTAT
*
60493014 AAAAATTCTT
1 AAAAATT-AT
*
60493024 AAAAGCTTAT
1 AAAA-ATTAT
60493034 AAAAATTAT
1 AAAAATTAT
*
60493043 AAAAAAAATAT
1 --AAAAATTAT
* *
60493054 TAAAGTTGAT
1 AAAAATT-AT
*
60493064 ACAAATTTAT
1 A-AAAATTAT
60493074 AAAAATTAT
1 AAAAATTAT
60493083 AAAA
1 AAAA
60493087 GAACATAAAA
Statistics
Matches: 114, Mismatches: 27, Indels: 30
0.67 0.16 0.18
Matches are distributed among these distances:
8 17 0.15
9 43 0.38
10 29 0.25
11 24 0.21
12 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:60493047 original size:20 final size:20
Alignment explanation
Indices: 60493010--60493047 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
60493000 ATTTGAAATT
* *
60493010 TTATAAAAATTCTTAAAAGC
1 TTATAAAAATTATAAAAAGC
60493030 TTATAAAAATTATAAAAA
1 TTATAAAAATTATAAAAA
60493048 AAATATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (20 bp):
TTATAAAAATTATAAAAAGC
Found at i:60493686 original size:10 final size:10
Alignment explanation
Indices: 60493673--60493697 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
60493663 TTTTAATATT
60493673 TTATATTTTA
1 TTATATTTTA
60493683 TTATATTTTA
1 TTATATTTTA
60493693 TTATA
1 TTATA
60493698 AGTTTCTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATATTTTA
Found at i:60493731 original size:30 final size:27
Alignment explanation
Indices: 60493660--60493789 Score: 76
Period size: 28 Copynumber: 4.6 Consensus size: 27
60493650 GGTTTAAATG
60493660 ATTTTTTAATA-TTTTATATTTTATTAT
1 ATTTTTTAA-AGTTTTATATTTTATTAT
60493687 ATTTTATTATAAGTTTCTATGATTTT-TTAT
1 ATTTT-TTA-AAGTTT-TAT-ATTTTATTAT
60493717 AAATTTTTTAAAG-TTTATATCTATT-TTA-
1 --ATTTTTTAAAGTTTTATAT-T-TTATTAT
* *
60493745 ATATTCTTAAA-TATTTATATTTTTATGAT
1 AT-TTTTTAAAGT-TTTATA-TTTTATTAT
60493774 -TTTTTTATAAGTTTTA
1 ATTTTTTA-AAGTTTTA
60493790 AAGAAATTTT
Statistics
Matches: 83, Mismatches: 3, Indels: 33
0.70 0.03 0.28
Matches are distributed among these distances:
26 2 0.02
27 21 0.25
28 24 0.29
29 13 0.16
30 10 0.12
31 8 0.10
32 5 0.06
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (27 bp):
ATTTTTTAAAGTTTTATATTTTATTAT
Found at i:60493827 original size:9 final size:8
Alignment explanation
Indices: 60493806--60493913 Score: 54
Period size: 9 Copynumber: 11.8 Consensus size: 8
60493796 TTTTATATGT
60493806 TTTTATAAA
1 TTTT-TAAA
*
60493815 ATTTTAAA
1 TTTTTAAA
60493823 TATTTTAAATA
1 T-TTTT-AA-A
60493834 TGTTTTATTAA
1 T-TTTTA--AA
*
60493845 TTTTTATA
1 TTTTTAAA
60493853 TTTTTATAA
1 TTTTTA-AA
60493862 TTTTTATAA
1 TTTTTA-AA
60493871 TTTTTATAATA
1 -TTTT-TAA-A
*
60493882 TTTTTATTA
1 TTTTTA-AA
*
60493891 TTTATAAA
1 TTTTTAAA
60493899 TTTTTAAGA
1 TTTTTAA-A
60493908 TTTTTA
1 TTTTTA
60493914 TGGGAAAATA
Statistics
Matches: 79, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
8 18 0.23
9 32 0.41
10 17 0.22
11 11 0.14
12 1 0.01
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (8 bp):
TTTTTAAA
Found at i:60493862 original size:17 final size:17
Alignment explanation
Indices: 60493831--60493914 Score: 89
Period size: 18 Copynumber: 4.6 Consensus size: 17
60493821 AATATTTTAA
60493831 ATATGTTTTATTAATTTTT
1 ATAT-TTTTA-TAATTTTT
60493850 ATATTTTTATAATTTTT
1 ATATTTTTATAATTTTT
60493867 ATAATTTTTATAATATTTT
1 AT-ATTTTTATAAT-TTTT
60493886 -TATTATTTATAAATTTTT
1 ATATT-TTTAT-AATTTTT
*
60493904 AAGATTTTTAT
1 -ATATTTTTAT
60493915 GGGAAAATAT
Statistics
Matches: 58, Mismatches: 1, Indels: 12
0.82 0.01 0.17
Matches are distributed among these distances:
17 13 0.22
18 26 0.45
19 16 0.28
20 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
ATATTTTTATAATTTTT
Found at i:60493903 original size:37 final size:35
Alignment explanation
Indices: 60493836--60493914 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 35
60493826 TTTAAATATG
60493836 TTTTATTAATTTTTATATTTTTATAATTTTTATA-AT
1 TTTTA-TAATTTTTATATTTTTATAATTTTTA-AGAT
60493872 TTTTATAATATTTT-TATTATTTATAAATTTTTAAGAT
1 TTTTATAAT-TTTTATATT-TTTAT-AATTTTTAAGAT
60493909 TTTTAT
1 TTTTAT
60493915 GGGAAAATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
35 8 0.21
36 15 0.38
37 16 0.41
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (35 bp):
TTTTATAATTTTTATATTTTTATAATTTTTAAGAT
Found at i:60499806 original size:19 final size:19
Alignment explanation
Indices: 60499782--60499818 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
60499772 TTTTTTATAT
60499782 TTTTAAATTACATTATTAC
1 TTTTAAATTACATTATTAC
* *
60499801 TTTTAATTTATATTATTA
1 TTTTAAATTACATTATTA
60499819 ACCTTAAGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAAATTACATTATTAC
Found at i:60499952 original size:42 final size:42
Alignment explanation
Indices: 60499872--60499955 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
60499862 AGCTTGATTC
* *
60499872 CAAAAATTAGTAAATGAGCTTAATTGAGCTCTAGCTCGAGTA
1 CAAAAATTAGTAAACGAGCTTAATTGAGCTCTAACTCGAGTA
*
60499914 CAAAAATTAGTAAGCGAGCTTAATTGAGCT-TGAACTCGAGTA
1 CAAAAATTAGTAAACGAGCTTAATTGAGCTCT-AACTCGAGTA
60499956 GCTCGATTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 1 0.03
42 37 0.97
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (42 bp):
CAAAAATTAGTAAACGAGCTTAATTGAGCTCTAACTCGAGTA
Found at i:60507699 original size:2 final size:2
Alignment explanation
Indices: 60507692--60507725 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
60507682 TAGATTGTTG
60507692 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60507726 TTTGTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:60508215 original size:108 final size:108
Alignment explanation
Indices: 60508026--60508350 Score: 571
Period size: 108 Copynumber: 3.0 Consensus size: 108
60508016 AAGGGAAAAG
*
60508026 TTTTAAATTAAGGCAATATTTCACGTTTGGAAAATTCGAGAAAATGTGCCCTAACGTGCTGGGTT
1 TTTTAAATTAAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAATGTGCCCTAACGTGCTGGGTT
60508091 TCGATTTCTCGTTCGACTAAATAGCCAAATATCCTTTTTAAAC
66 TCGATTTCTCGTTCGACTAAATAGCCAAATATCCTTTTTAAAC
60508134 TTTTAAATTAAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAATGTGCCCTAACGTGCTGGGTT
1 TTTTAAATTAAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAATGTGCCCTAACGTGCTGGGTT
60508199 TCGATTTCTCGTTCGACTAAATAGCCAAATATCCTTTTTAAAC
66 TCGATTTCTCGTTCGACTAAATAGCCAAATATCCTTTTTAAAC
* * * * *
60508242 TTTTAAAATAAGGCAATACTTCGCGTTTGGAAAA-TCAAGGAAACGTGCCCTAACGTGCTGGGTT
1 TTTTAAATTAAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAATGTGCCCTAACGTGCTGGGTT
* *
60508306 TCGATTTCTCGTTCGACTAAATAGCCAAATATCCTCTTAAAAC
66 TCGATTTCTCGTTCGACTAAATAGCCAAATATCCTTTTTAAAC
60508349 TT
1 TT
60508351 CAAAGTATGG
Statistics
Matches: 209, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
107 70 0.33
108 139 0.67
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (108 bp):
TTTTAAATTAAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAATGTGCCCTAACGTGCTGGGTT
TCGATTTCTCGTTCGACTAAATAGCCAAATATCCTTTTTAAAC
Found at i:60509299 original size:9 final size:9
Alignment explanation
Indices: 60509285--60509312 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
60509275 TTTTGTTACA
60509285 ACAATTAAT
1 ACAATTAAT
60509294 ACAATTAAT
1 ACAATTAAT
60509303 ACAATTAAT
1 ACAATTAAT
60509312 A
1 A
60509313 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:60509334 original size:68 final size:68
Alignment explanation
Indices: 60509255--60509464 Score: 379
Period size: 68 Copynumber: 3.1 Consensus size: 68
60509245 ATAAAATTTG
*
60509255 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
60509320 AAA
66 AAA
60509323 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
60509388 AAA
66 AAA
*
60509391 TTTACTAATCAAATGTTGGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
60509454 AAT
66 AAA
60509457 TTTACTAA
1 TTTACTAA
60509465 CAATTAATTT
Statistics
Matches: 139, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
66 27 0.19
67 1 0.01
68 111 0.80
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.40
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:60509365 original size:9 final size:9
Alignment explanation
Indices: 60509353--60509380 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
60509343 TTTTATTACA
60509353 ACAATTAAT
1 ACAATTAAT
60509362 ACAATTAAT
1 ACAATTAAT
60509371 ACAATTAAT
1 ACAATTAAT
60509380 A
1 A
60509381 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:60509474 original size:16 final size:16
Alignment explanation
Indices: 60509453--60509494 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
60509443 AATAATTTGA
*
60509453 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
60509469 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
60509485 TAGTTTTAAT
1 TAATTTTAAT
60509495 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:60509528 original size:23 final size:23
Alignment explanation
Indices: 60509470--60509528 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 23
60509460 ACTAACAATT
* * * *
60509470 AATTTTAA-TAACAATTAGTTTT
1 AATTTTAATTAAAAAATAATTTA
60509492 AATTTT-ATTAAAAAATAATTTA
1 AATTTTAATTAAAAAATAATTTA
60509514 AATTTTAATTAAAAA
1 AATTTTAATTAAAAA
60509529 CGGGCCGGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 1 0.03
22 22 0.71
23 8 0.26
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
AATTTTAATTAAAAAATAATTTA
Found at i:60510240 original size:17 final size:17
Alignment explanation
Indices: 60510206--60510240 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
60510196 ATATTTTTAA
*
60510206 AATAATTTTTTATTTTT
1 AATAATTTTTTATGTTT
*
60510223 AATAATTTTTTGTGTTT
1 AATAATTTTTTATGTTT
60510240 A
1 A
60510241 TTAAAAATGG
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:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (17 bp):
AATAATTTTTTATGTTT
Found at i:60513657 original size:2 final size:2
Alignment explanation
Indices: 60513650--60513687 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
60513640 TCAAAAAGTG
60513650 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
60513688 GAAATTAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60514727 original size:106 final size:107
Alignment explanation
Indices: 60514503--60514812 Score: 507
Period size: 106 Copynumber: 2.9 Consensus size: 107
60514493 TAAATTAATA
* *
60514503 CAATATTTTGCGTTTGGAAAATTCGAGAAAATGTGCCCTAACGTGCTGGTTTTCGATTTCTCGTT
1 CAATATTTCGCGTTTGGAAAATTCGAGAAAATGTGCCCTAACGTGCTGGGTTTCGA-TTCTCGTT
*
60514568 CGACTAAATAGCCAAATATCCTTTTTAAACTTTTAAATTAAGG
65 CGACTAAATAGCCAAATATCCTTTTTAAACTTTTAAAATAAGG
60514611 CAATATTTCGCGTTTGGAAAATTCGAGAAAATGTGCCCTAACGTGCTGGGTTTCGA-TCTCGTTC
1 CAATATTTCGCGTTTGGAAAATTCGAGAAAATGTGCCCTAACGTGCTGGGTTTCGATTCTCGTTC
*
60514675 GACTAAATAGCCAAATATTCTTTTTAAACTTTTAAAATAAGG
66 GACTAAATAGCCAAATATCCTTTTTAAACTTTTAAAATAAGG
* * *
60514717 CAATACTTCGCGTTTGGAAAA-TCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTT
1 CAATATTTCGCGTTTGGAAAATTCGAGAAAATGTGCCCTAACGTGCTGGGTTTCGA-TTCTCGTT
* *
60514781 CGACTAAATAGCCAAATATCCTCTTAAAACTT
65 CGACTAAATAGCCAAATATCCTTTTTAAACTT
60514813 CAAAGTATGG
Statistics
Matches: 190, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
105 32 0.17
106 68 0.36
107 36 0.19
108 54 0.28
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (107 bp):
CAATATTTCGCGTTTGGAAAATTCGAGAAAATGTGCCCTAACGTGCTGGGTTTCGATTCTCGTTC
GACTAAATAGCCAAATATCCTTTTTAAACTTTTAAAATAAGG
Found at i:60519610 original size:96 final size:97
Alignment explanation
Indices: 60519495--60519683 Score: 308
Period size: 96 Copynumber: 2.0 Consensus size: 97
60519485 CTCATTTTGT
* * * *
60519495 ATTTTAGCAAAATTTGCTATCTTAATTAATCTATTCATTTCGAGCTTTGTTCTCAATAAATTTTC
1 ATTTTAGCAAAATTTGCTATCTTAATTAATCTATTCATTGCAAGCATTGTTCTCAATAAAATTTC
*
60519560 ATCGTATCCATTGTGATAATCTTTTTCATCTC
66 ATCGTATCCATTGTAATAATCTTTTTCATCTC
*
60519592 ATTTTAGC-AAATTTGCTATCTTGATTAATCTATTCATTGCAAGCATTGTTCTCAATAAAATTTC
1 ATTTTAGCAAAATTTGCTATCTTAATTAATCTATTCATTGCAAGCATTGTTCTCAATAAAATTTC
*
60519656 ATCTTATCCATTGTAATAATCTTTTTCA
66 ATCGTATCCATTGTAATAATCTTTTTCA
60519684 AGCATTTTTT
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
96 77 0.91
97 8 0.09
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.47
Consensus pattern (97 bp):
ATTTTAGCAAAATTTGCTATCTTAATTAATCTATTCATTGCAAGCATTGTTCTCAATAAAATTTC
ATCGTATCCATTGTAATAATCTTTTTCATCTC
Found at i:60520737 original size:132 final size:132
Alignment explanation
Indices: 60520491--60520802 Score: 525
Period size: 132 Copynumber: 2.4 Consensus size: 132
60520481 CAATGTAGCT
* **
60520491 GATTGAAGATTTCAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGTGGATTTTA
1 GATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCAGATTTTA
* * *
60520556 CCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGAA
66 CCTCCCTGTGGTTACAGTGGAGTACATAGAAGCCAGAAACTCTACTTCCCTGGACAACAGTGGAA
60520621 TA
131 TA
*
60520623 GATTGAAGATTACAGATCTTATCTCCCTAAGTAATAGTGGAGCAGATCGAAGATGGCAGATTTTA
1 GATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCAGATTTTA
*
60520688 CCTCCCTGTGGTTACAGTGGAGTACATAGAAGCCAGAAACTCTATTTCCCTGGACAACAGTGGAA
66 CCTCCCTGTGGTTACAGTGGAGTACATAGAAGCCAGAAACTCTACTTCCCTGGACAACAGTGGAA
60520753 TA
131 TA
* * *
60520755 GATTGAAGATTACAGGTCTTATCTCCCAAAGCAGTAGTGGAGCAGATC
1 GATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATC
60520803 ATATTAAGTC
Statistics
Matches: 168, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 168 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (132 bp):
GATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCAGATTTTA
CCTCCCTGTGGTTACAGTGGAGTACATAGAAGCCAGAAACTCTACTTCCCTGGACAACAGTGGAA
TA
Found at i:60522617 original size:2 final size:2
Alignment explanation
Indices: 60522610--60522647 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
60522600 TAGATTGTTG
* *
60522610 TA TA TA TA TT TT TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60522648 TTTGTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (2 bp):
TA
Found at i:60523140 original size:108 final size:108
Alignment explanation
Indices: 60522951--60523275 Score: 589
Period size: 108 Copynumber: 3.0 Consensus size: 108
60522941 AAGGGAAAAG
60522951 TTTTAAATTAAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAATGTGCCCTAACGTGCTGGGTT
1 TTTTAAATTAAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAATGTGCCCTAACGTGCTGGGTT
60523016 TCGATTTCTCGTTCGACTAAATAGCCAAATATCCTTTTTAAAC
66 TCGATTTCTCGTTCGACTAAATAGCCAAATATCCTTTTTAAAC
60523059 TTTTAAATTAAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAATGTGCCCTAACGTGCTGGGTT
1 TTTTAAATTAAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAATGTGCCCTAACGTGCTGGGTT
60523124 TCGATTTCTCGTTCGACTAAATAGCCAAATATCCTTTTTAAAC
66 TCGATTTCTCGTTCGACTAAATAGCCAAATATCCTTTTTAAAC
* * * *
60523167 TTTTAAAATAAGGCAATACTTCGCGTTTGGAAAA-TCGAGGAAACGTGCCCTAACGTGCTGGGTT
1 TTTTAAATTAAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAATGTGCCCTAACGTGCTGGGTT
* *
60523231 TCGATTTCTCGTTCGACTAAATAGCCAAATATCCTCTTAAAAC
66 TCGATTTCTCGTTCGACTAAATAGCCAAATATCCTTTTTAAAC
60523274 TT
1 TT
60523276 CAAAGTATGG
Statistics
Matches: 211, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
107 71 0.34
108 140 0.66
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (108 bp):
TTTTAAATTAAGGCAATATTTCGCGTTTGGAAAATTCGAGAAAATGTGCCCTAACGTGCTGGGTT
TCGATTTCTCGTTCGACTAAATAGCCAAATATCCTTTTTAAAC
Found at i:60524315 original size:1 final size:1
Alignment explanation
Indices: 60524309--60524334 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
60524299 GAACTAAACT
60524309 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
60524335 CCTTGACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:60526346 original size:42 final size:40
Alignment explanation
Indices: 60526294--60526386 Score: 95
Period size: 36 Copynumber: 2.4 Consensus size: 40
60526284 GGGTTCGAGC
* *
60526294 TCGAGTTCAAGCTTGAGTACAAAAATTAGTAAATGAGCTTAA
1 TCGAGCTC-AGCTT-AGTACAAAAATTAGTAAACGAGCTTAA
*
60526336 TCGAGCTCA----AGTACAAAAATTAGTCAACGAGCTTAA
1 TCGAGCTCAGCTTAGTACAAAAATTAGTAAACGAGCTTAA
*
60526372 TCAAGCTCGAGCTTA
1 TCGAGCTC-AGCTTA
60526387 AAAATAGATG
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
36 32 0.76
37 1 0.02
41 2 0.05
42 7 0.17
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (40 bp):
TCGAGCTCAGCTTAGTACAAAAATTAGTAAACGAGCTTAA
Found at i:60526391 original size:36 final size:36
Alignment explanation
Indices: 60526300--60526379 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
60526290 GAGCTCGAGT
** *
60526300 TCAAGCTTGAGTACAAAAATTAGTAAATGAGCTTAA
1 TCAAGCTCAAGTACAAAAATTAGTAAACGAGCTTAA
* *
60526336 TCGAGCTCAAGTACAAAAATTAGTCAACGAGCTTAA
1 TCAAGCTCAAGTACAAAAATTAGTAAACGAGCTTAA
60526372 TCAAGCTC
1 TCAAGCTC
60526380 GAGCTTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.25
Consensus pattern (36 bp):
TCAAGCTCAAGTACAAAAATTAGTAAACGAGCTTAA
Found at i:60532327 original size:15 final size:14
Alignment explanation
Indices: 60532297--60532334 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
60532287 TCGGAAAAGT
60532297 AAATCATTTTTTAA
1 AAATCATTTTTTAA
* *
60532311 AAATTATTTTTTGA
1 AAATCATTTTTTAA
60532325 AAATCATTTT
1 AAATCATTTT
60532335 CAGTAAAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (14 bp):
AAATCATTTTTTAA
Found at i:60533256 original size:55 final size:55
Alignment explanation
Indices: 60533195--60533306 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
60533185 AAATACTCAC
60533195 GACTAATTAATTTAGGGATTCATACATTTAATGTTTCTAAATACCTAACATTTTG
1 GACTAATTAATTTAGGGATTCATACATTTAATGTTTCTAAATACCTAACATTTTG
60533250 GACTAATTAATTTAGGGATTCATACATTTAATGTTTCTAAATACCTAACATTTTG
1 GACTAATTAATTTAGGGATTCATACATTTAATGTTTCTAAATACCTAACATTTTG
60533305 GA
1 GA
60533307 TACACCTAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (55 bp):
GACTAATTAATTTAGGGATTCATACATTTAATGTTTCTAAATACCTAACATTTTG
Found at i:60535342 original size:42 final size:42
Alignment explanation
Indices: 60535290--60535378 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
60535280 GCTCGAGCTC
* * *
60535290 AAGCTTGAGCTTGAGTACAAAAATTAGTAAATGAGCTTAATT
1 AAGCTCGAGCTCGAGTACAAAAATTAGTAAACGAGCTTAATT
*
60535332 AAGCTCGAGCTCGAGTACAAAAATTAGTAAGCGAGCTTAATT
1 AAGCTCGAGCTCGAGTACAAAAATTAGTAAACGAGCTTAATT
*
60535374 GAGCT
1 AAGCT
60535379 TGAAATCGAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.27
Consensus pattern (42 bp):
AAGCTCGAGCTCGAGTACAAAAATTAGTAAACGAGCTTAATT
Found at i:60535388 original size:42 final size:42
Alignment explanation
Indices: 60535302--60535390 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
60535292 GCTTGAGCTT
* **
60535302 GAGTACAAAAATTAGTAAATGAGCTTAATTAAGCTCGAGCTC
1 GAGTACAAAAATTAGTAAACGAGCTTAATTAAGCTCGAAATC
* * *
60535344 GAGTACAAAAATTAGTAAGCGAGCTTAATTGAGCTTGAAATC
1 GAGTACAAAAATTAGTAAACGAGCTTAATTAAGCTCGAAATC
60535386 GAGTA
1 GAGTA
60535391 GCTCGATTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26
Consensus pattern (42 bp):
GAGTACAAAAATTAGTAAACGAGCTTAATTAAGCTCGAAATC
Found at i:60543126 original size:6 final size:6
Alignment explanation
Indices: 60543115--60543178 Score: 85
Period size: 6 Copynumber: 10.5 Consensus size: 6
60543105 TAACATGAAG
* *
60543115 AAAATA AAAATAAA AAAATA AAAATA AAAAT- AAAATA TATATA AAAATA
1 AAAATA AAAAT--A AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
60543164 AAAATA AAAATA AAA
1 AAAATA AAAATA AAA
60543179 TTGGGTTGCC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
5 5 0.10
6 40 0.78
8 6 0.12
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:60543169 original size:29 final size:27
Alignment explanation
Indices: 60543115--60543179 Score: 105
Period size: 29 Copynumber: 2.4 Consensus size: 27
60543105 TAACATGAAG
60543115 AAAATAAAA-ATAAAAAAATAAAAATA
1 AAAATAAAATATAAAAAAATAAAAATA
60543141 AAAATAAAATATATATAAAAATAAAAATA
1 AAAATAAAATATA-A-AAAAATAAAAATA
60543170 AAAATAAAAT
1 AAAATAAAAT
60543180 TGGGTTGCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
26 9 0.25
27 3 0.08
28 1 0.03
29 23 0.64
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (27 bp):
AAAATAAAATATAAAAAAATAAAAATA
Found at i:60549850 original size:166 final size:167
Alignment explanation
Indices: 60549647--60549973 Score: 471
Period size: 167 Copynumber: 2.0 Consensus size: 167
60549637 TAAATTACTA
* * **
60549647 TCCTAGAATATAAAATGACAAAAATATCGTCATAATAATGTTCCTTATTTTAT-AAAAAT-GGGT
1 TCCTAAAATATAAAATGACAAAAATATCGTCATAATAATATTCCTTATTTTATAAAAAATAGATT
* * * * **
60549710 TTTCTGTAATTTCCCAATTAAGTTAGAACTCGATTGTCTCAATTGATGAGTGATA-CTAGTTCAG
66 TTTC-ATAATTTCCCAACTAAGTTAGAACTCGATTATCTCAATTGATGAGCGATATC-AACTCAG
*
60549774 CCAATCCTAAATATTAGTATAGATTAAATTAACTTTTTG
129 CCAATCCTAAATATCAGTATAGATTAAATTAACTTTTTG
60549813 TCCTAAAATATAAAATGACAAAAATATCGTCATAATAATATTCCTTATTTTATAAAAAATAGATT
1 TCCTAAAATATAAAATGACAAAAATATCGTCATAATAATATTCCTTATTTTATAAAAAATAGATT
** * * *
60549878 TTTCATAATTTTTCAACTAAGTTAGAACTCGGTTATCTCAATTGATGAGCGATATCAACTCTGTC
66 TTTCATAATTTCCCAACTAAGTTAGAACTCGATTATCTCAATTGATGAGCGATATCAACTCAGCC
60549943 AATCCTAAATATCAGTATAGATTAAATTAAC
131 AATCCTAAATATCAGTATAGATTAAATTAAC
60549974 GTTCTACCCT
Statistics
Matches: 142, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
166 51 0.36
167 84 0.59
168 7 0.05
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.37
Consensus pattern (167 bp):
TCCTAAAATATAAAATGACAAAAATATCGTCATAATAATATTCCTTATTTTATAAAAAATAGATT
TTTCATAATTTCCCAACTAAGTTAGAACTCGATTATCTCAATTGATGAGCGATATCAACTCAGCC
AATCCTAAATATCAGTATAGATTAAATTAACTTTTTG
Found at i:60552677 original size:2 final size:2
Alignment explanation
Indices: 60552670--60552699 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
60552660 ATTAATTTAT
60552670 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
60552700 AGTAATTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60554268 original size:2 final size:2
Alignment explanation
Indices: 60554261--60554290 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
60554251 GCAAATTTGA
60554261 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
60554291 TAAGAAATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60556524 original size:2 final size:2
Alignment explanation
Indices: 60556517--60556555 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
60556507 AGATGAAAAC
* * *
60556517 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60556556 GGAGTCAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (2 bp):
TA
Found at i:60569219 original size:21 final size:21
Alignment explanation
Indices: 60569190--60569243 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
60569180 ATGATATTGA
60569190 AATGATATTTATATTTATGAT
1 AATGATATTTATATTTATGAT
* * *
60569211 AATGTTATTTATCTTTGTGAT
1 AATGATATTTATATTTATGAT
* *
60569232 AATTAAATTTAT
1 AATGATATTTAT
60569244 CTAGCCATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (21 bp):
AATGATATTTATATTTATGAT
Found at i:60583365 original size:84 final size:85
Alignment explanation
Indices: 60583206--60583380 Score: 334
Period size: 84 Copynumber: 2.1 Consensus size: 85
60583196 CATAAAAGTG
*
60583206 ATATACTTACATAATACATAACTTACATAATTTAAATTTTTAATACATAACTTACATAACTTATT
1 ATATATTTACATAATACATAACTTACATAATTTAAATTTTTAATACATAACTTACATAACTTATT
60583271 AATATTTATATATAGTTTTA
66 AATATTTATATATAGTTTTA
60583291 ATATATTTACATAATACATAACTTACATAATTTAAA-TTTTAATACATAACTTACATAACTTATT
1 ATATATTTACATAATACATAACTTACATAATTTAAATTTTTAATACATAACTTACATAACTTATT
60583355 AATATTTATATATAGTTTTA
66 AATATTTATATATAGTTTTA
60583375 ATATAT
1 ATATAT
60583381 ATTTTTTAAA
Statistics
Matches: 89, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
84 54 0.61
85 35 0.39
ACGTcount: A:0.44, C:0.10, G:0.01, T:0.45
Consensus pattern (85 bp):
ATATATTTACATAATACATAACTTACATAATTTAAATTTTTAATACATAACTTACATAACTTATT
AATATTTATATATAGTTTTA
Found at i:60583400 original size:20 final size:21
Alignment explanation
Indices: 60583375--60583414 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
60583365 TATAGTTTTA
60583375 ATATATA-TTTTTTAAAATTT
1 ATATATATTTTTTTAAAATTT
60583395 ATATATATTTTTTTAAAATT
1 ATATATATTTTTTTAAAATT
60583415 GATACATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATATTTTTTTAAAATTT
Found at i:60583435 original size:9 final size:9
Alignment explanation
Indices: 60583421--60583897 Score: 419
Period size: 9 Copynumber: 55.4 Consensus size: 9
60583411 AATTGATACA
60583421 TTACATAAC
1 TTACATAAC
60583430 TTACATAACC
1 TTACATAA-C
60583440 TACATACATAAAC
1 T---TACAT-AAC
60583453 TTACATAA-
1 TTACATAAC
60583461 -TACATAAC
1 TTACATAAC
60583469 TTACATAAC
1 TTACATAAC
*
60583478 TT--A-AAT
1 TTACATAAC
*
60583484 TTATCA-ATC
1 TTA-CATAAC
*
60583493 ATATCATAAC
1 TTA-CATAAC
60583503 TTACAT-AC
1 TTACATAAC
* * *
60583511 ATAAAT-AT
1 TTACATAAC
60583519 TTATCAT-A-
1 TTA-CATAAC
60583527 -T-CATAAC
1 TTACATAAC
60583534 TTACATAAC
1 TTACATAAC
**
60583543 CCACATAAC
1 TTACATAAC
60583552 TTACATAAC
1 TTACATAAC
60583561 TTACATAATAAC
1 TTAC---ATAAC
*
60583573 TTACACAA-
1 TTACATAAC
60583581 -TACATAAC
1 TTACATAAC
*
60583589 CTACATAAC
1 TTACATAAC
*
60583598 TTATATAAC
1 TTACATAAC
60583607 TTACATAAC
1 TTACATAAC
60583616 TTAACATAAC
1 TT-ACATAAC
60583626 TTACATAA-
1 TTACATAAC
60583634 -TACATAAC
1 TTACATAAC
60583642 TTACATAAC
1 TTACATAAC
*
60583651 CTACATAA-
1 TTACATAAC
60583659 -TACATAAC
1 TTACATAAC
60583667 TTACATAAC
1 TTACATAAC
60583676 TTACATAAC
1 TTACATAAC
60583685 TTACATAA-
1 TTACATAAC
*
60583693 -TACACAAC
1 TTACATAAC
60583701 TTACATAAC
1 TTACATAAC
60583710 TTACATAAC
1 TTACATAAC
60583719 TTACATAA-
1 TTACATAAC
60583727 -TACATAAC
1 TTACATAAC
60583735 TTACATAAC
1 TTACATAAC
*
60583744 TTACAT-TC
1 TTACATAAC
*
60583752 -TACACAAC
1 TTACATAAC
60583760 TTACATAAC
1 TTACATAAC
*
60583769 CTACATAA-
1 TTACATAAC
60583777 -TACATAAC
1 TTACATAAC
60583785 TTACATAAC
1 TTACATAAC
60583794 TTACATAA-
1 TTACATAAC
*
60583802 -TACACAAC
1 TTACATAAC
60583810 TTACATAAC
1 TTACATAAC
60583819 TTACATAA-
1 TTACATAAC
60583827 -TACATAAC
1 TTACATAAC
60583835 TTACATAAC
1 TTACATAAC
*
60583844 TTATATAA-
1 TTACATAAC
60583852 -TACATAAC
1 TTACATAAC
*
60583860 TTACATAAT
1 TTACATAAC
*
60583869 TTACTTAA-
1 TTACATAAC
60583877 -TACATAAC
1 TTACATAAC
*
60583885 TTACATAAT
1 TTACATAAC
60583894 TTAC
1 TTAC
60583898 TTAATACATA
Statistics
Matches: 390, Mismatches: 36, Indels: 84
0.76 0.07 0.16
Matches are distributed among these distances:
5 3 0.01
6 5 0.01
7 78 0.20
8 12 0.03
9 254 0.65
10 20 0.05
12 9 0.02
13 7 0.02
14 2 0.01
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.32
Consensus pattern (9 bp):
TTACATAAC
Found at i:60583528 original size:31 final size:31
Alignment explanation
Indices: 60583433--60583540 Score: 107
Period size: 31 Copynumber: 3.4 Consensus size: 31
60583423 ACATAACTTA
* *
60583433 CATAACCTACATACAT-AA-ACTTA-CATAAT
1 CATAACTTACATACATAAATATTTATCAT-AT
*
60583462 ACATAACTTACATAACTTAAAT-TTATCAATCATAT
1 -CATAACTTACAT-ACATAAATATT-T--ATCATAT
60583497 CATAACTTACATACATAAATATTTATCATAT
1 CATAACTTACATACATAAATATTTATCATAT
60583528 CATAACTTACATA
1 CATAACTTACATA
60583541 ACCCACATAA
Statistics
Matches: 66, Mismatches: 4, Indels: 15
0.78 0.05 0.18
Matches are distributed among these distances:
30 11 0.17
31 23 0.35
32 3 0.05
33 9 0.14
34 14 0.21
35 3 0.05
36 3 0.05
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.34
Consensus pattern (31 bp):
CATAACTTACATACATAAATATTTATCATAT
Found at i:60583611 original size:34 final size:34
Alignment explanation
Indices: 60583421--60583893 Score: 376
Period size: 34 Copynumber: 13.8 Consensus size: 34
60583411 AATTGATACA
*
60583421 TTACATAACTTACATAACCTAC---ATACATAAAC
1 TTACATAACTTACATAACTTACATAATACAT-AAC
* *
60583453 TTACATAA--TACATAACTTACAT-A-ACTTAAAT
1 TTACATAACTTACATAACTTACATAATACAT-AAC
* * *
60583484 TTATCA-ATCATATCATAACTTACATACATAAATATTTATC
1 TTA-CATAACTTA-CATAACTTACATA-ATACATA---A-C
* **
60583524 ATATCATAACTTACATAACCCACATAACTTACATAAC
1 TTA-CATAACTTACATAACTTACATAA--TACATAAC
* * *
60583561 TTACATAA-TAACTTACACAATACATAACCTACATAAC
1 TTACATAACTTACATA-AC-TTACATAA--TACATAAC
*
60583598 TTATATAACTTACATAACTTAACATAACTTACATAA-
1 TTACATAACTTACATAACTT-ACATAA--TACATAAC
*
60583634 -TACATAACTTACATAACCTACATAATACATAAC
1 TTACATAACTTACATAACTTACATAATACATAAC
*
60583667 TTACATAACTTACATAACTTACATAATACACAAC
1 TTACATAACTTACATAACTTACATAATACATAAC
60583701 TTACATAACTTACATAACTTACATAATACATAAC
1 TTACATAACTTACATAACTTACATAATACATAAC
* *
60583735 TTACATAACTTACAT-TC-TACACAACTTACATAAC
1 TTACATAACTTACATAACTTACATAA--TACATAAC
*
60583769 CTACATAA--TACATAACTTACATAACTTACATAA-
1 TTACATAACTTACATAACTTACATAA--TACATAAC
*
60583802 -TACACAACTTACATAACTTACATAATACATAAC
1 TTACATAACTTACATAACTTACATAATACATAAC
* *
60583835 TTACATAACTTATATAA--TACATAACTTACATAAT
1 TTACATAACTTACATAACTTACATAA--TACATAAC
*
60583869 TTACTTAA--TACATAACTTACATAAT
1 TTACATAACTTACATAACTTACATAAT
60583894 TTACTTAATA
Statistics
Matches: 367, Mismatches: 40, Indels: 68
0.77 0.08 0.14
Matches are distributed among these distances:
30 11 0.03
31 10 0.03
32 56 0.15
33 4 0.01
34 178 0.49
35 22 0.06
36 10 0.03
37 43 0.12
38 6 0.02
39 2 0.01
40 16 0.04
41 9 0.02
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (34 bp):
TTACATAACTTACATAACTTACATAATACATAAC
Found at i:60583655 original size:25 final size:25
Alignment explanation
Indices: 60583422--60583908 Score: 350
Period size: 25 Copynumber: 19.0 Consensus size: 25
60583412 ATTGATACAT
60583422 TACATAACTTACATAACCTACAT-AC
1 TACATAACTTACATAA-CTACATAAC
*
60583447 -ATA-AACTTACATAA-TACATAAC
1 TACATAACTTACATAACTACATAAC
** *
60583469 TTACATAACTTA-A-ATTTATCA-ATC
1 -TACATAACTTACATAACTA-CATAAC
*
60583493 ATATCATAACTTACAT-ACATAAATATTTATC
1 -TA-CATAACTTACATAAC-TACATA---A-C
*
60583524 ATATCATAACTTACATAACCCACATAAC
1 -TA-CATAACTTACATAA-CTACATAAC
*
60583552 TTACATAACTTACATAA-TAACTTACAC
1 -TACATAACTTACATAACT-ACATA-AC
* *
60583579 AATACATAACCTACATAACTTATATAAC
1 --TACATAACTTACATAAC-TACATAAC
60583607 TTACATAACTTAACATAACTTACATAA-
1 -TACATAACTT-ACATAAC-TACATAAC
60583634 TACATAACTTACATAACCTACATAA-
1 TACATAACTTACATAA-CTACATAAC
60583659 TACATAACTTACATAACTTACATAAC
1 TACATAACTTACATAAC-TACATAAC
*
60583685 TTACATAA--TACACAACTTACATAAC
1 -TACATAACTTACATAAC-TACATAAC
60583710 TTACATAACTTACATAA-TACATAAC
1 -TACATAACTTACATAACTACATAAC
* *
60583735 TTACATAACTTACAT-TCTACACAAC
1 -TACATAACTTACATAACTACATAAC
*
60583760 TTACATAACCTACATAA-TACATAAC
1 -TACATAACTTACATAACTACATAAC
*
60583785 TTACATAACTTACATAA-TACACAAC
1 -TACATAACTTACATAACTACATAAC
60583810 TTACATAACTTACATAA-TACATAAC
1 -TACATAACTTACATAACTACATAAC
*
60583835 TTACATAACTTATATAA-TACATAAC
1 -TACATAACTTACATAACTACATAAC
* *
60583860 TTACATAATTTACTTAA-TACATAAC
1 -TACATAACTTACATAACTACATAAC
* *
60583885 TTACATAATTTACTTAA-TACATAA
1 -TACATAACTTACATAACTACATAA
60583909 ATATATATCA
Statistics
Matches: 396, Mismatches: 35, Indels: 62
0.80 0.07 0.13
Matches are distributed among these distances:
21 5 0.01
22 2 0.01
23 12 0.03
24 12 0.03
25 245 0.62
26 17 0.04
27 41 0.10
28 34 0.09
29 4 0.01
30 1 0.00
31 17 0.04
32 5 0.01
33 1 0.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (25 bp):
TACATAACTTACATAACTACATAAC
Found at i:60583878 original size:50 final size:50
Alignment explanation
Indices: 60583421--60583942 Score: 460
Period size: 50 Copynumber: 10.2 Consensus size: 50
60583411 AATTGATACA
* *
60583421 TTACATAACTTACAT-A-ACCT-ACATACATAAACTTACATAATACATAAC
1 TTACATAACTTACATAATACATAACTTACAT-AACTTACATAATACATAAC
* * * * *
60583469 TTACATAACTTAAAT-TTATCA-ATCATATCATAACTTACATACATAAATATTTATC
1 TTACATAACTTACATAATA-CATAACTTA-CATAACTTACATA-ATACATA---A-C
* * *
60583524 ATATCATAACTTACATAACCCACATAACTTACATAACTTACATAATAACTTACAC
1 TTA-CATAACTTACATAA--TACATAACTTACATAACTTACATAAT-ACATA-AC
* * *
60583579 AATACATAACCTACATAACTTATATAACTTACATAACTTAACATAACTTACATAA-
1 -TTACATAACTTACATAA--TACATAACTTACATAACTT-ACATAA--TACATAAC
60583634 -TACATAACTTACATAACCTACATAA--TACATAACTTACATAACTTACATAAC
1 TTACATAACTTACATAA--TACATAACTTACATAACTTACATAA--TACATAAC
*
60583685 TTACATAA--TACACAACTTACATAACTTACATAACTTACATAATACATAAC
1 TTACATAACTTACATAA--TACATAACTTACATAACTTACATAATACATAAC
** * *
60583735 TTACATAACTTACATTCTACACAACTTACATAACCTACATAATACATAAC
1 TTACATAACTTACATAATACATAACTTACATAACTTACATAATACATAAC
*
60583785 TTACATAACTTACATAATACACAACTTACATAACTTACATAATACATAAC
1 TTACATAACTTACATAATACATAACTTACATAACTTACATAATACATAAC
* * *
60583835 TTACATAACTTATATAATACATAACTTACATAATTTACTTAATACATAAC
1 TTACATAACTTACATAATACATAACTTACATAACTTACATAATACATAAC
* * * * * *
60583885 TTACATAATTTACTTAATACATAA-ATATATATCATATCAT-AT-CATAAC
1 TTACATAACTTACATAATACATAACTTACATAACTTA-CATAATACATAAC
60583933 TTACATAACT
1 TTACATAACT
60583943 CATTTATACT
Statistics
Matches: 402, Mismatches: 46, Indels: 52
0.80 0.09 0.10
Matches are distributed among these distances:
48 29 0.07
49 10 0.02
50 207 0.51
51 19 0.05
52 27 0.07
53 22 0.05
54 1 0.00
55 35 0.09
56 22 0.05
57 6 0.01
58 19 0.05
59 5 0.01
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (50 bp):
TTACATAACTTACATAATACATAACTTACATAACTTACATAATACATAAC
Found at i:60583908 original size:16 final size:16
Alignment explanation
Indices: 60583443--60583893 Score: 308
Period size: 16 Copynumber: 27.1 Consensus size: 16
60583433 CATAACCTAC
60583443 ATACATAAACTTACATA
1 ATACAT-AACTTACATA
60583460 ATACATAACTTACAT-
1 ATACATAACTTACATA
* * *
60583475 A-ACTTAAATTTATCAATC
1 ATACAT-AACTTA-C-ATA
60583493 ATATCATAACTTACATA
1 ATA-CATAACTTACATA
* *
60583510 CATAAAT-ATTTATCAT-
1 -ATACATAACTTA-CATA
60583526 AT-CATAACTTACATA
1 ATACATAACTTACATA
*
60583541 ACCCACATAACTTACATA
1 A--TACATAACTTACATA
*
60583559 ACTTACATAATAACTTACACA
1 A--TAC---ATAACTTACATA
*
60583580 ATACATAACCTACATA
1 ATACATAACTTACATA
*
60583596 ACTTATATAACTTACATA
1 A--TACATAACTTACATA
60583614 ACTTAACATAACTTACATA
1 A--T-ACATAACTTACATA
60583633 ATACATAACTTACAT-
1 ATACATAACTTACATA
60583648 A-AC----C-TACATA
1 ATACATAACTTACATA
60583658 ATACATAACTTACATA
1 ATACATAACTTACATA
60583674 ACTTACATAACTTACATA
1 A--TACATAACTTACATA
*
60583692 ATACACAACTTACATA
1 ATACATAACTTACATA
60583708 ACTTACATAACTTACATA
1 A--TACATAACTTACATA
60583726 ATACATAACTTACATA
1 ATACATAACTTACATA
* *
60583742 ACTTACAT-TC-TACACA
1 A--TACATAACTTACATA
*
60583758 ACTTACATAACCTACATA
1 A--TACATAACTTACATA
60583776 ATACATAACTTACATA
1 ATACATAACTTACATA
*
60583792 ACTTACATAA--TACACA
1 A--TACATAACTTACATA
60583808 ACTTACATAACTTACATA
1 A--TACATAACTTACATA
60583826 ATACATAACTTACATA
1 ATACATAACTTACATA
*
60583842 ACTTATATAA--TACATA
1 A--TACATAACTTACATA
* *
60583858 ACTTACATAATTTACTTA
1 A--TACATAACTTACATA
60583876 ATACATAACTTACATA
1 ATACATAACTTACATA
60583892 AT
1 AT
60583894 TTACTTAATA
Statistics
Matches: 360, Mismatches: 32, Indels: 85
0.75 0.07 0.18
Matches are distributed among these distances:
9 5 0.01
10 2 0.01
11 2 0.01
14 10 0.03
15 15 0.04
16 165 0.46
17 18 0.05
18 106 0.29
19 23 0.06
20 2 0.01
21 12 0.03
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (16 bp):
ATACATAACTTACATA
Found at i:60589818 original size:43 final size:43
Alignment explanation
Indices: 60589757--60589854 Score: 135
Period size: 43 Copynumber: 2.3 Consensus size: 43
60589747 CAAAATTTGT
* *
60589757 GGCGTTTATGATGAAAGCGCCGCTAAAAGTCATGATCTATAGC
1 GGCGTTTGTGATGAAAGCGCCACTAAAAGTCATGATCTATAGC
*
60589800 GGCGTTTGTGA-GAAAAGCGCCATTAAAAGTCATGATCTATAGC
1 GGCGTTTGTGATG-AAAGCGCCACTAAAAGTCATGATCTATAGC
* *
60589843 AGCATTTGTGAT
1 GGCGTTTGTGAT
60589855 TGAAGCTGTA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
42 1 0.02
43 47 0.98
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (43 bp):
GGCGTTTGTGATGAAAGCGCCACTAAAAGTCATGATCTATAGC
Found at i:60591391 original size:56 final size:50
Alignment explanation
Indices: 60591173--60591421 Score: 327
Period size: 50 Copynumber: 4.8 Consensus size: 50
60591163 GATAATAACA
* ** * *
60591173 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
60591224 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
60591274 TGCCAATGCCATGACCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
60591324 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATC-T-CGG
*
60591379 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
60591422 TTACCCAAAT
Statistics
Matches: 175, Mismatches: 17, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
50 96 0.55
51 33 0.19
53 3 0.02
54 1 0.01
55 2 0.01
56 40 0.23
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:60591537 original size:13 final size:13
Alignment explanation
Indices: 60591516--60591547 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
60591506 GCTTGGATCA
*
60591516 TCATCAAATAAAT
1 TCATAAAATAAAT
60591529 TCATAAAATAAAT
1 TCATAAAATAAAT
60591542 TCATAA
1 TCATAA
60591548 TTGTTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:60598517 original size:56 final size:50
Alignment explanation
Indices: 60598299--60598547 Score: 300
Period size: 50 Copynumber: 4.8 Consensus size: 50
60598289 GATAATAACA
* ** * * *
60598299 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * * *
60598350 TACCCATGCCATCTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
60598400 TGCCAATGCCATGACCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
60598450 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATC-T-CGG
*
60598505 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
60598548 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
50 93 0.55
51 31 0.18
53 3 0.02
54 1 0.01
55 2 0.01
56 40 0.24
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:60598663 original size:13 final size:13
Alignment explanation
Indices: 60598642--60598673 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
60598632 GCTTGGATCA
*
60598642 TCATCAAATAAAT
1 TCATAAAATAAAT
60598655 TCATAAAATAAAT
1 TCATAAAATAAAT
60598668 TCATAA
1 TCATAA
60598674 TTTCTTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:60599357 original size:43 final size:43
Alignment explanation
Indices: 60599299--60599443 Score: 184
Period size: 43 Copynumber: 3.4 Consensus size: 43
60599289 AAACGCCACT
* *
60599299 AAAGTCATGATCTATAGCGGCGTTTGTGAGAGAAGCGTCGCTA
1 AAAGTCATGATCTATAGCGGCGTTTGTGAGAAAAGCGCCGCTA
* *
60599342 AAAGTCATGATCTATAACAGCGTTTGTGAGAAAAGCGCCGCTA
1 AAAGTCATGATCTATAGCGGCGTTTGTGAGAAAAGCGCCGCTA
* * * * *
60599385 AAGGTCGTGATCTATAGCGGCGTTTGTGATAAAAGTGCAGCTA
1 AAAGTCATGATCTATAGCGGCGTTTGTGAGAAAAGCGCCGCTA
* *
60599428 AAGGTCGTGA-CTATAG
1 AAAGTCATGATCTATAG
60599444 GCGCCGCTAA
Statistics
Matches: 91, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 6 0.07
43 85 0.93
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (43 bp):
AAAGTCATGATCTATAGCGGCGTTTGTGAGAAAAGCGCCGCTA
Found at i:60608875 original size:34 final size:34
Alignment explanation
Indices: 60608809--60608875 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
60608799 AGCTAGAGAT
* *
60608809 GCATCAAATAAATACTGAATATGAAGAGGGATAA
1 GCATCAAATAAATACTAAATATGAAAAGGGATAA
* *
60608843 GCATCAAATAGATACTAAATATGAAAATGGATA
1 GCATCAAATAAATACTAAATATGAAAAGGGATA
60608876 GGGAACTAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.51, C:0.09, G:0.18, T:0.22
Consensus pattern (34 bp):
GCATCAAATAAATACTAAATATGAAAAGGGATAA
Found at i:60611919 original size:2 final size:2
Alignment explanation
Indices: 60611912--60611950 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
60611902 CGGATAGGTA
60611912 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
60611951 AATTTAACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60622091 original size:17 final size:17
Alignment explanation
Indices: 60622069--60622103 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
60622059 TAATTGTTAA
60622069 ATTGGTAAAAACAATTT
1 ATTGGTAAAAACAATTT
*
60622086 ATTGGTGAAAACAATTT
1 ATTGGTAAAAACAATTT
60622103 A
1 A
60622104 GTGACATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (17 bp):
ATTGGTAAAAACAATTT
Found at i:60630754 original size:9 final size:9
Alignment explanation
Indices: 60630740--60630824 Score: 116
Period size: 9 Copynumber: 9.4 Consensus size: 9
60630730 TTTGGTTAAA
60630740 AATTAACCG
1 AATTAACCG
60630749 AATTAACCG
1 AATTAACCG
*
60630758 AATTACCCG
1 AATTAACCG
60630767 AATTAACCG
1 AATTAACCG
* *
60630776 GATTACCCG
1 AATTAACCG
60630785 AATTAACCG
1 AATTAACCG
* *
60630794 GATTACCCG
1 AATTAACCG
*
60630803 AATTACCCG
1 AATTAACCG
60630812 AATTAACCG
1 AATTAACCG
60630821 AATT
1 AATT
60630825 GAATCACTAC
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 66 1.00
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:60630875 original size:6 final size:6
Alignment explanation
Indices: 60630864--60630892 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
60630854 ACTTTTAGAC
60630864 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
60630893 AATTTTTTTT
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:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:60640512 original size:18 final size:18
Alignment explanation
Indices: 60640474--60640512 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
60640464 ACACTACTAT
* * *
60640474 ATTATTTGAGTTATTTGA
1 ATTATTCGAGTTACTTAA
60640492 ATTATTCGAGTTACTTAA
1 ATTATTCGAGTTACTTAA
60640510 ATT
1 ATT
60640513 GTAAAATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51
Consensus pattern (18 bp):
ATTATTCGAGTTACTTAA
Found at i:60651877 original size:3 final size:3
Alignment explanation
Indices: 60651862--60651949 Score: 56
Period size: 3 Copynumber: 29.0 Consensus size: 3
60651852 TGAATGAATA
* * *
60651862 AAT AAT TAT AAT AAT AAT GAGAT AAGT AAT AAC AAT AA- ATAC AAT AAT
1 AAT AAT AAT AAT AAT AAT -A-AT AA-T AAT AAT AAT AAT A-AT AAT AAT
* * * *
60651910 AGT AAT AAC ATT AA- AA- AAT AAT AAT AAT AAT AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
60651950 GATATTGTTA
Statistics
Matches: 66, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
2 5 0.08
3 53 0.80
4 6 0.09
5 2 0.03
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:60651898 original size:24 final size:23
Alignment explanation
Indices: 60651854--60651899 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
60651844 AAATTGTATG
* *
60651854 AATGAATAAATAATTATAATAAT
1 AATGAATAAATAATAACAATAAT
*
60651877 AATGAGATAAGTAATAACAATAA
1 AATGA-ATAAATAATAACAATAA
60651900 ATACAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.61, C:0.02, G:0.09, T:0.28
Consensus pattern (23 bp):
AATGAATAAATAATAACAATAAT
Found at i:60660038 original size:18 final size:18
Alignment explanation
Indices: 60659996--60660042 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
60659986 CACTTATATT
*
60659996 ATTTTTTTATTTTTTTAA
1 ATTTTTATATTTTTTTAA
*
60660014 ATATTTATATTGTTTTT-A
1 ATTTTTATATT-TTTTTAA
60660032 ATTTTTA-ATTT
1 ATTTTTATATTT
60660043 AATTTTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 1 0.04
17 3 0.12
18 16 0.64
19 5 0.20
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (18 bp):
ATTTTTATATTTTTTTAA
Found at i:60660428 original size:2 final size:2
Alignment explanation
Indices: 60660421--60660449 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
60660411 AATAAACATA
60660421 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 A
60660450 GATGAATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:60661723 original size:20 final size:20
Alignment explanation
Indices: 60661695--60661732 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
60661685 CAGTATACCA
*
60661695 AATATTTTTTTAATTATATG
1 AATAATTTTTTAATTATATG
60661715 AATAATTTTTTAATTATA
1 AATAATTTTTTAATTATA
60661733 ATTATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
AATAATTTTTTAATTATATG
Found at i:60677974 original size:19 final size:19
Alignment explanation
Indices: 60677936--60677976 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
60677926 GATTTTTTCC
*
60677936 TTTTAAATTTTAAATCTTT
1 TTTTAAATTTTAAATATTT
**
60677955 TTTTAAATTTTATTTATTT
1 TTTTAAATTTTAAATATTT
60677974 TTT
1 TTT
60677977 CTCTGTCTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTAAATTTTAAATATTT
Found at i:60679102 original size:18 final size:18
Alignment explanation
Indices: 60679079--60679116 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
60679069 ACAGGTTCAA
60679079 CAACAGCACCAGCAACAG
1 CAACAGCACCAGCAACAG
*
60679097 CAACAGCACCAGCACCAG
1 CAACAGCACCAGCAACAG
60679115 CA
1 CA
60679117 CCAGATTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.42, G:0.16, T:0.00
Consensus pattern (18 bp):
CAACAGCACCAGCAACAG
Found at i:60679117 original size:6 final size:6
Alignment explanation
Indices: 60679082--60679120 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
60679072 GGTTCAACAA
* *
60679082 CAGCAC CAGCAA CAGCAA CAGCAC CAGCAC CAGCAC CAG
1 CAGCAC CAGCAC CAGCAC CAGCAC CAGCAC CAGCAC CAG
60679121 ATTCAGACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.38, C:0.44, G:0.18, T:0.00
Consensus pattern (6 bp):
CAGCAC
Found at i:60684263 original size:13 final size:13
Alignment explanation
Indices: 60684245--60684283 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
60684235 TGCAGTTGAA
60684245 AAATACTTTTCAG
1 AAATACTTTTCAG
*
60684258 AAATACTTTTGA-
1 AAATACTTTTCAG
60684270 AAAGTACTTTTCAG
1 AAA-TACTTTTCAG
60684284 TGGAGAAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 3 0.14
13 19 0.86
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (13 bp):
AAATACTTTTCAG
Found at i:60684513 original size:15 final size:15
Alignment explanation
Indices: 60684495--60684546 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
60684485 TAAATATAAT
60684495 AATAATTTATATTTA
1 AATAATTTATATTTA
60684510 AATAATTTA-ATTTA
1 AATAATTTATATTTA
* *
60684524 ATGACAAATTATATTTA
1 A--ATAATTTATATTTA
60684541 AATAAT
1 AATAAT
60684547 CTAATATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 6 0.20
15 12 0.40
16 6 0.20
17 6 0.20
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (15 bp):
AATAATTTATATTTA
Found at i:60690262 original size:35 final size:35
Alignment explanation
Indices: 60690200--60690285 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
60690190 TTTTATTTGT
*
60690200 TTTA-ATTATATAATTAATGATATTTAAA-TATAA
1 TTTATATTATATAATTAATGATAATTAAATTATAA
*
60690233 TTTATATTATATGAATTTATGATAATTAAATTATAA
1 TTTATATTATAT-AATTAATGATAATTAAATTATAA
* *
60690269 -TGATATTATATTATTAA
1 TTTATATTATATAATTAA
60690286 ATAAATCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 4 0.09
34 11 0.24
35 25 0.56
36 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (35 bp):
TTTATATTATATAATTAATGATAATTAAATTATAA
Found at i:60690271 original size:25 final size:23
Alignment explanation
Indices: 60690227--60690287 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
60690217 TGATATTTAA
*
60690227 ATATAATTTATATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
60690251 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
60690276 ATATTATTAAAT
1 ATATAATTAAAT
60690288 AAATCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:60699968 original size:26 final size:26
Alignment explanation
Indices: 60699932--60699981 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
60699922 TCACGTGTTG
* *
60699932 TTCTTTTAGACTCAGTGGGATAATTT
1 TTCTTTCAGACTCAGCGGGATAATTT
60699958 TTCTTTCAGACTCAGCGGGATAAT
1 TTCTTTCAGACTCAGCGGGATAAT
60699982 ATAGGAGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (26 bp):
TTCTTTCAGACTCAGCGGGATAATTT
Found at i:60702705 original size:28 final size:28
Alignment explanation
Indices: 60702674--60702739 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
60702664 ATAAAAAATA
**
60702674 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAAAATTTTTTTATTT
60702702 ACCAAAATATTATAAAATTTTTTTATTT
1 ACCAAAATATTATAAAATTTTTTTATTT
60702730 ACCAAAATAT
1 ACCAAAATAT
60702740 ACAAAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (28 bp):
ACCAAAATATTATAAAATTTTTTTATTT
Found at i:60703438 original size:19 final size:19
Alignment explanation
Indices: 60703414--60703472 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 19
60703404 TCTAATTAAG
60703414 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
* * *
60703433 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTAATT
*
60703451 TAATAACTTTATTTTAATT
1 TAATAACTCTATTTTAATT
60703470 TAA
1 TAA
60703473 AAAAATTAAG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
18 15 0.47
19 17 0.53
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATAACTCTATTTTAATT
Found at i:60703443 original size:18 final size:17
Alignment explanation
Indices: 60703422--60703472 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
60703412 AGTAATAACT
60703422 CTATTTTAATTTAATAAA
1 CTATTTTAATTTAAT-AA
* *
60703440 CTATTCTCATTTAATAA
1 CTATTTTAATTTAATAA
60703457 CTTTATTTTAATTTAA
1 C--TATTTTAATTTAA
60703473 AAAAATTAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 3 0.11
18 13 0.48
19 11 0.41
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (17 bp):
CTATTTTAATTTAATAA
Found at i:60703545 original size:18 final size:19
Alignment explanation
Indices: 60703485--60703540 Score: 78
Period size: 18 Copynumber: 3.0 Consensus size: 19
60703475 AAATTAAGTT
60703485 AATTAAAATAGAGTTATTA
1 AATTAAAATAGAGTTATTA
* * *
60703504 AATGAGAATAG-TTTATTA
1 AATTAAAATAGAGTTATTA
60703522 AATTAAAATAGAGTTATTA
1 AATTAAAATAGAGTTATTA
60703541 CTTAATTAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (19 bp):
AATTAAAATAGAGTTATTA
Found at i:60704238 original size:27 final size:27
Alignment explanation
Indices: 60704185--60704276 Score: 166
Period size: 27 Copynumber: 3.4 Consensus size: 27
60704175 ATTTTTTGGT
60704185 ATATTTTGGTAAATAAAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAA-TTATA
60704213 ATATTTTGGTAAATAAAAAAAATTATA
1 ATATTTTGGTAAATAAAAAAAATTATA
*
60704240 ATATTTTGGTAAATAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAATTATA
60704267 ATATTTTGGT
1 ATATTTTGGT
60704277 TATTTTTTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
27 41 0.65
28 22 0.35
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAATTATA
Found at i:60704617 original size:23 final size:23
Alignment explanation
Indices: 60704589--60704644 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
60704579 AAAATTGAAG
60704589 TTCGAGTTAAACGAATTGAGTTA
1 TTCGAGTTAAACGAATTGAGTTA
60704612 TTCGAGTTAAACGAATTGAGTTA
1 TTCGAGTTAAACGAATTGAGTTA
60704635 TTCGAGTTAA
1 TTCGAGTTAA
60704645 TCGAGTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (23 bp):
TTCGAGTTAAACGAATTGAGTTA
Found at i:60704731 original size:9 final size:9
Alignment explanation
Indices: 60704712--60704748 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
60704702 TGAGTTTTCA
*
60704712 AATTTGAAT
1 AATTCGAAT
*
60704721 AACTCGAAT
1 AATTCGAAT
60704730 AATTCGAAT
1 AATTCGAAT
60704739 AATTCGAAT
1 AATTCGAAT
60704748 A
1 A
60704749 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:60705031 original size:11 final size:11
Alignment explanation
Indices: 60705016--60705121 Score: 92
Period size: 11 Copynumber: 9.4 Consensus size: 11
60705006 AATAAAAATA
60705016 AAAAAGTATTTT
1 AAAAA-TATTTT
60705028 AAAAATATTTT
1 AAAAATATTTT
60705039 AAAAATATTTT
1 AAAAATATTTT
* * *
60705050 AAAATTAAAAATTA
1 -AAA--AATATTTT
60705064 AAAAAGTATTTT
1 AAAAA-TATTTT
60705076 AAAAATATTTT
1 AAAAATATTTT
**
60705087 --AAA-ATTAA
1 AAAAATATTTT
60705095 AAAAATTATTTT
1 AAAAA-TATTTT
60705107 AAAAATATTTT
1 AAAAATATTTT
60705118 AAAA
1 AAAA
60705122 TTAAAAAATA
Statistics
Matches: 76, Mismatches: 10, Indels: 17
0.74 0.10 0.17
Matches are distributed among these distances:
8 3 0.04
9 3 0.04
10 3 0.04
11 35 0.46
12 24 0.32
13 3 0.04
14 5 0.07
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:60705066 original size:48 final size:46
Alignment explanation
Indices: 60704998--60705090 Score: 168
Period size: 48 Copynumber: 2.0 Consensus size: 46
60704988 ATCAAAAATT
60704998 TATTTTAAAATAAAAATAAAAAAGTATTTTAAAAATATTTTAAAAA
1 TATTTTAAAATAAAAATAAAAAAGTATTTTAAAAATATTTTAAAAA
60705044 TATTTTAAAATTAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAA
1 TATTTTAAAA-TAAAAA-TAAAAAAGTATTTTAAAAATATTTTAAAA
60705091 TTAAAAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 10 0.22
47 6 0.13
48 29 0.64
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (46 bp):
TATTTTAAAATAAAAATAAAAAAGTATTTTAAAAATATTTTAAAAA
Found at i:60705130 original size:30 final size:30
Alignment explanation
Indices: 60705057--60705130 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 30
60705047 TTTAAAATTA
*
60705057 AAAATTAAAAAAGTATTTTAAAAATATTTT
1 AAAATTAAAAAATTATTTTAAAAATATTTT
60705087 AAAATTAAAAAAATTATTTTAAAAATATTTT
1 AAAATT-AAAAAATTATTTTAAAAATATTTT
60705118 AAAATTAAAAAAT
1 AAAATTAAAAAAT
60705131 AAATATATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
30 13 0.31
31 29 0.69
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (30 bp):
AAAATTAAAAAATTATTTTAAAAATATTTT
Found at i:60705571 original size:21 final size:21
Alignment explanation
Indices: 60705542--60705581 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
60705532 TCCCTCAAAC
60705542 TTTTATCCCCCAAAACTTTTTA
1 TTTTAT-CCCCAAAACTTTTTA
*
60705564 TTTT-TCCCCTAAACTTTT
1 TTTTATCCCCAAAACTTTT
60705582 ACTTCTCACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 1 0.06
22 4 0.24
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTATCCCCAAAACTTTTTA
Found at i:60712172 original size:25 final size:25
Alignment explanation
Indices: 60712112--60712173 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
60712102 CTCAAGTCGT
* * *
60712112 AAGAGCTTACCGTTATTCAGCTCAG
1 AAGAGCTTACTGATATTAAGCTCAG
*
60712137 AAGAGCTTACTGATATTAAGCTCGG
1 AAGAGCTTACTGATATTAAGCTCAG
*
60712162 ATGAGCTTACTG
1 AAGAGCTTACTG
60712174 TTTATTACTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (25 bp):
AAGAGCTTACTGATATTAAGCTCAG
Found at i:60715937 original size:9 final size:9
Alignment explanation
Indices: 60715884--60715921 Score: 76
Period size: 9 Copynumber: 4.2 Consensus size: 9
60715874 TGGCTCCAAC
60715884 AGAGTTGAA
1 AGAGTTGAA
60715893 AGAGTTGAA
1 AGAGTTGAA
60715902 AGAGTTGAA
1 AGAGTTGAA
60715911 AGAGTTGAA
1 AGAGTTGAA
60715920 AG
1 AG
60715922 CTCAGTTGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.34, T:0.21
Consensus pattern (9 bp):
AGAGTTGAA
Found at i:60724239 original size:6 final size:6
Alignment explanation
Indices: 60724218--60724269 Score: 54
Period size: 6 Copynumber: 8.5 Consensus size: 6
60724208 ATGTACCCTG
*
60724218 TAAAAA T-AAAA T-AAAA TAAAAA TAAAATA GTAAAAA TAAATAA TAATAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAA-A -TAAAAA TAAA-AA TAAAAA
60724267 TAA
1 TAA
60724270 TAGGAAAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
5 10 0.24
6 19 0.46
7 7 0.17
8 5 0.12
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (6 bp):
TAAAAA
Found at i:60724239 original size:16 final size:16
Alignment explanation
Indices: 60724218--60724271 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
60724208 ATGTACCCTG
60724218 TAAAAATAAAATAAAA
1 TAAAAATAAAATAAAA
*
60724234 TAAAAATAAAAT--AG
1 TAAAAATAAAATAAAA
60724248 TAAAAAT-AAATAATAA
1 TAAAAATAAAATAA-AA
*
60724264 TAATAATA
1 TAAAAATA
60724272 GGAAAATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 4 0.13
14 8 0.26
16 19 0.61
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (16 bp):
TAAAAATAAAATAAAA
Found at i:60724254 original size:25 final size:26
Alignment explanation
Indices: 60724225--60724291 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 26
60724215 CTGTAAAAAT
*
60724225 AAAATAAAATAAAAATAA-AATAGTA
1 AAAATAAAATAAAAATAATAATAGGA
*
60724250 AAAAT-AAATAATAATAATAATAGGA
1 AAAATAAAATAAAAATAATAATAGGA
* *
60724275 AAATTAAAATTAAAATA
1 AAAATAAAATAAAAATA
60724292 TTTTTTTTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 11 0.31
25 15 0.43
26 9 0.26
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (26 bp):
AAAATAAAATAAAAATAATAATAGGA
Found at i:60730902 original size:46 final size:46
Alignment explanation
Indices: 60730799--60730960 Score: 251
Period size: 46 Copynumber: 3.6 Consensus size: 46
60730789 TACGTATGAT
* *
60730799 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGA-CTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
60730842 CACTTATCACTTTGTTACTTGATCAGATAAGTATAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
60730888 CACTTATCACTTTGTCACCTT-ATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCA-CTTGATCAGATAAGTGTAGCTAAAGCTAC
60730934 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
60730961 AGTACTCAAA
Statistics
Matches: 108, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
43 10 0.09
44 4 0.04
45 24 0.22
46 67 0.62
47 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:60731053 original size:19 final size:19
Alignment explanation
Indices: 60731029--60731073 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
60731019 TTTTATTCTC
60731029 ATTTCATCAATAAA-TATAT
1 ATTTCATC-ATAAATTATAT
60731048 ATTTCATCATAAATTATAT
1 ATTTCATCATAAATTATAT
*
60731067 AATTCAT
1 ATTTCAT
60731074 GAAATTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTTCATCATAAATTATAT
Found at i:60735831 original size:46 final size:45
Alignment explanation
Indices: 60735735--60735850 Score: 155
Period size: 46 Copynumber: 2.6 Consensus size: 45
60735725 TACGTATGAT
* * * *
60735735 CACTTATCAC-TTGTC-CCTGATTAGATAAGTGTAGTTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGTAAAGCTAC
* *
60735778 CATTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG-TAAAGCTAC
60735824 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
60735851 AGTACTCAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
43 9 0.15
44 4 0.06
45 17 0.27
46 32 0.52
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (45 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGTAAAGCTAC
Found at i:60740467 original size:3 final size:3
Alignment explanation
Indices: 60740459--60740488 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
60740449 ATTATTTAGT
60740459 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
60740489 GTTTTTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:60740696 original size:22 final size:22
Alignment explanation
Indices: 60740662--60740703 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
60740652 ACTTACATAT
* *
60740662 ATATATATTTTTATATATTAAA
1 ATATATATATTTATACATTAAA
*
60740684 ATATGTATATTTATACATTA
1 ATATATATATTTATACATTA
60740704 TATATTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATATATATTTATACATTAAA
Found at i:60740950 original size:21 final size:20
Alignment explanation
Indices: 60740917--60740964 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
60740907 TCGTTTTTGT
*
60740917 TCATATTTTTTATTCACATCA
1 TCATATTTATTATTC-CATCA
*
60740938 TCATGTTTATTATTCCATCA
1 TCATATTTATTATTCCATCA
60740958 TGCATAT
1 T-CATAT
60740965 AAATATCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.27, C:0.19, G:0.04, T:0.50
Consensus pattern (20 bp):
TCATATTTATTATTCCATCA
Found at i:60741392 original size:109 final size:109
Alignment explanation
Indices: 60741016--60741539 Score: 784
Period size: 110 Copynumber: 4.8 Consensus size: 109
60741006 TTTCTAATTG
* * * *
60741016 AGGCAATATTTAGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
60741081 CGTTCAACCAAATGGCTAAATATCCTTTTAAAAGATTTCAAAATA
66 CGTTCAACCAAATGGCTAAATATCCTTTTAAAA-ATTTCAAAATA
* *
60741126 AGGCAATGTTTTGCGTTTGGAAATTCAAGAAAACGTGCCCTAAGGTGTTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* * * *
60741191 CGTTCAACCAAATGACTTAATATCCTTTTAAAAAATTTTAAGATA
66 CGTTCAACCAAATGGCTAAATATCCTTTT-AAAAATTTCAAAATA
* *
60741236 AGGCAATGTTTTGCGTTTGGAAACTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* *
60741301 CGTTCAACCAAATGGCTTAATATCCTTTTCAAAATTTCAAAATA
66 CGTTCAACCAAATGGCTAAATATCCTTTTAAAAATTTCAAAATA
* * *
60741345 TGGCAATGTTTTGCGTTTAGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* *
60741410 CGTTCAACCAAATAGCTAAATATCCTTTCAAAAATTTCAAAATA
66 CGTTCAACCAAATGGCTAAATATCCTTTTAAAAATTTCAAAATA
* * *
60741454 AGGCAATGTTTTGCGTTTGGAAATTCGAG-GAATGTGCCCTAAGGTGCTGGGTTTCGA--TTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* * *
60741516 CGTTTAACCAAATTGCCAAATATC
66 CGTTCAACCAAATGGCTAAATATC
60741540 GTCTTGAATT
Statistics
Matches: 379, Mismatches: 34, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
106 26 0.07
108 24 0.06
109 141 0.37
110 184 0.49
111 4 0.01
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (109 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTCAACCAAATGGCTAAATATCCTTTTAAAAATTTCAAAATA
Found at i:60741422 original size:219 final size:219
Alignment explanation
Indices: 60741016--60741539 Score: 797
Period size: 219 Copynumber: 2.4 Consensus size: 219
60741006 TTTCTAATTG
* * *
60741016 AGGCAATATTTAGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTTTCGATTTTTCT
*
60741081 CGTTCAACCAAATGGCTAAATATCCTTTTAAAAGATTTCAAAATAAGGCAATGTTTTGCGTTTGG
66 CGTTCAACCAAATGGCTAAATATCCTTTTAAAAGATTTCAAAATAAGGCAATGTTTTGCGTTTAG
* * *
60741146 AAATTCAAGAAAACGTGCCCTAAGGTGTTGGGTGTCGATTTTTCTCGTTCAACCAAAT-GACTTA
131 AAATTCAAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAG-CTAA
* *
60741210 ATATCCTTTTAAAAAATTTTAAGATA
195 ATATCC-TTTAAAAAATTTCAAAATA
* * *
60741236 AGGCAATGTTTTGCGTTTGGAAACTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTTTCGATTTTTCT
* * *
60741301 CGTTCAACCAAATGGCTTAATATCCTTTTCAAA-ATTTCAAAATATGGCAATGTTTTGCGTTTAG
66 CGTTCAACCAAATGGCTAAATATCCTTTTAAAAGATTTCAAAATAAGGCAATGTTTTGCGTTTAG
*
60741365 AAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAGCTAAA
131 AAATTCAAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAGCTAAA
*
60741430 TATCCTTTCAAAAATTTCAAAATA
196 TATCCTTTAAAAAATTTCAAAATA
* *
60741454 AGGCAATGTTTTGCGTTTGGAAATTCGAG-GAATGTGCCCTAAGGTGCTGGGTTTCGA--TTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTTTCGATTTTTCT
* * *
60741516 CGTTTAACCAAATTGCCAAATATC
66 CGTTCAACCAAATGGCTAAATATC
60741540 GTCTTGAATT
Statistics
Matches: 277, Mismatches: 26, Indels: 7
0.89 0.08 0.02
Matches are distributed among these distances:
215 25 0.09
217 24 0.09
218 44 0.16
219 93 0.34
220 91 0.33
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (219 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTTTCGATTTTTCT
CGTTCAACCAAATGGCTAAATATCCTTTTAAAAGATTTCAAAATAAGGCAATGTTTTGCGTTTAG
AAATTCAAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATAGCTAAA
TATCCTTTAAAAAATTTCAAAATA
Found at i:60744049 original size:27 final size:27
Alignment explanation
Indices: 60744011--60744073 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
60744001 TTTTAGTCTT
* **
60744011 GTGCCGCCAATGGGATTGGCACCACCG
1 GTGCCGCCAATGAGAAAGGCACCACCG
* *
60744038 GTGCCGCCAATGAGAAAGGCATCATCG
1 GTGCCGCCAATGAGAAAGGCACCACCG
60744065 GTGCCGCCA
1 GTGCCGCCA
60744074 TTCCATTACC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.22, C:0.32, G:0.32, T:0.14
Consensus pattern (27 bp):
GTGCCGCCAATGAGAAAGGCACCACCG
Found at i:60749215 original size:11 final size:11
Alignment explanation
Indices: 60749199--60749228 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
60749189 TATAGGCAAA
60749199 TTAATTTTGTT
1 TTAATTTTGTT
60749210 TTAATTTTGTT
1 TTAATTTTGTT
60749221 TTAATTTT
1 TTAATTTT
60749229 AAGAGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (11 bp):
TTAATTTTGTT
Found at i:60762072 original size:29 final size:30
Alignment explanation
Indices: 60762040--60762097 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 30
60762030 GATGAAAATG
60762040 TAACAAAACCTAGCAAATATTGTT-AAACC
1 TAACAAAACCTAGCAAATATTGTTGAAACC
60762069 TAACAAAACCTAGCAAATATTGTTGAAAC
1 TAACAAAACCTAGCAAATATTGTTGAAAC
60762098 TTGGAACAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.48, C:0.19, G:0.09, T:0.24
Consensus pattern (30 bp):
TAACAAAACCTAGCAAATATTGTTGAAACC
Found at i:60762312 original size:14 final size:14
Alignment explanation
Indices: 60762293--60762319 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
60762283 ACAAGCAAAC
60762293 TGTTATGAACCAAG
1 TGTTATGAACCAAG
60762307 TGTTATGAACCAA
1 TGTTATGAACCAA
60762320 TTAAAACCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (14 bp):
TGTTATGAACCAAG
Found at i:60769945 original size:25 final size:25
Alignment explanation
Indices: 60769889--60769947 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
60769879 CTCAAGTCAT
* *
60769889 AAGAGCTTACAGTTATTCAGCTCGG
1 AAGAGCTTACAGATATTAAGCTCGG
* *
60769914 AAAAGCTTACTGATATTAAGCTCGG
1 AAGAGCTTACAGATATTAAGCTCGG
*
60769939 ATGAGCTTA
1 AAGAGCTTA
60769948 ATGTTTATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (25 bp):
AAGAGCTTACAGATATTAAGCTCGG
Found at i:60788062 original size:13 final size:13
Alignment explanation
Indices: 60788044--60788071 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
60788034 AAGATAATTA
60788044 TTCAATTACTTTG
1 TTCAATTACTTTG
60788057 TTCAATTACTTTG
1 TTCAATTACTTTG
60788070 TT
1 TT
60788072 TTATTGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (13 bp):
TTCAATTACTTTG
Found at i:60801175 original size:15 final size:15
Alignment explanation
Indices: 60801150--60801184 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
60801140 GACTCTATTT
*
60801150 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
60801164 TAATTAATATTAAGA
1 TAATTAATATTAAGA
60801179 TAATTA
1 TAATTA
60801185 TTAAAGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:60805907 original size:25 final size:25
Alignment explanation
Indices: 60805847--60805909 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
60805837 ACCTATCCTC
* * **
60805847 GATGATCTTACTGTTATTCTGCTCG
1 GATGAGCTTACTGATATTAAGCTCG
* * *
60805872 AAAGAGTTTACTGATATTAAGCTCG
1 GATGAGCTTACTGATATTAAGCTCG
60805897 GATGAGCTTACTG
1 GATGAGCTTACTG
60805910 TTTATCGCTC
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (25 bp):
GATGAGCTTACTGATATTAAGCTCG
Found at i:60808156 original size:18 final size:18
Alignment explanation
Indices: 60808103--60808157 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
60808093 AAATCAAAAG
60808103 AGTTTATTTAAAAGTTCT
1 AGTTTATTTAAAAGTTCT
** * ** *
60808121 TTTTTTTTTTGAATTTCT
1 AGTTTATTTAAAAGTTCT
60808139 AGTTTATTTAAAAGTTCT
1 AGTTTATTTAAAAGTTCT
60808157 A
1 A
60808158 TTATAATTTA
Statistics
Matches: 25, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.27, C:0.05, G:0.09, T:0.58
Consensus pattern (18 bp):
AGTTTATTTAAAAGTTCT
Found at i:60817812 original size:13 final size:14
Alignment explanation
Indices: 60817789--60817817 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
60817779 ACAATAATGA
60817789 TATAGTAATAATAT
1 TATAGTAATAATAT
60817803 TATA-TAATAATAT
1 TATAGTAATAATAT
60817816 TA
1 TA
60817818 ATGATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
TATAGTAATAATAT
Found at i:60818806 original size:16 final size:16
Alignment explanation
Indices: 60818785--60818825 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
60818775 TTCGCTGTAT
60818785 TGGAATAGATGCGTAA
1 TGGAATAGATGCGTAA
60818801 TGGAATAGATGCGTAA
1 TGGAATAGATGCGTAA
60818817 TGGAATAGA
1 TGGAATAGA
60818826 GGCGCAATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.39, C:0.05, G:0.32, T:0.24
Consensus pattern (16 bp):
TGGAATAGATGCGTAA
Found at i:60818898 original size:44 final size:46
Alignment explanation
Indices: 60818815--60818903 Score: 146
Period size: 44 Copynumber: 2.0 Consensus size: 46
60818805 ATAGATGCGT
*
60818815 AATGGAATAGAGGCGCAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGCAATAGGTAATTCTTGTGTTTGGTTGAATGG
*
60818861 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATG
1 AATGGAATAGAGGCGCAATAGGTAATTCTTGTGTTTGGTTGAATG
60818904 TAATAGAGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 20 0.49
45 3 0.07
46 18 0.44
ACGTcount: A:0.27, C:0.06, G:0.31, T:0.36
Consensus pattern (46 bp):
AATGGAATAGAGGCGCAATAGGTAATTCTTGTGTTTGGTTGAATGG
Found at i:60818903 original size:39 final size:44
Alignment explanation
Indices: 60818815--60818920 Score: 123
Period size: 39 Copynumber: 2.5 Consensus size: 44
60818805 ATAGATGCGT
* *
60818815 AATGGAATAGAGGCGCAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--ATGG
60818861 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T-G
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
* *
60818900 AATGTAATAGAGGTGTAATAG
1 AATGGAATAGAGGCGTAATAG
60818921 CATAAGAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
39 18 0.33
40 2 0.04
43 1 0.02
44 13 0.24
45 3 0.05
46 18 0.33
ACGTcount: A:0.29, C:0.05, G:0.31, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
Found at i:60818964 original size:15 final size:15
Alignment explanation
Indices: 60818944--60818979 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
60818934 GCTAAAATGA
60818944 CTAGAATACCCTTAG
1 CTAGAATACCCTTAG
60818959 CTAGAATACCCTTAG
1 CTAGAATACCCTTAG
60818974 C-AGAAT
1 CTAGAAT
60818980 TTTTTTAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (15 bp):
CTAGAATACCCTTAG
Found at i:60819133 original size:18 final size:17
Alignment explanation
Indices: 60819081--60819133 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
60819071 TTATTATTAA
60819081 ATATAATTTAATAAAAAT
1 ATATAATTTAAT-AAAAT
60819099 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
*
60819116 ATATGAATTTACTAAAAT
1 ATAT-AATTTAATAAAAT
60819134 CATAATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 9 0.27
18 24 0.73
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:60821552 original size:35 final size:35
Alignment explanation
Indices: 60821506--60821577 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
60821496 GTTACATGGT
60821506 ACTTTTGCCTCAACTAAACCTATATCCAAAACCAC
1 ACTTTTGCCTCAACTAAACCTATATCCAAAACCAC
60821541 ACTTTTGCCTCAACTAAACCTATATCCAAAACCAC
1 ACTTTTGCCTCAACTAAACCTATATCCAAAACCAC
60821576 AC
1 AC
60821578 ATTAGAATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.35, G:0.03, T:0.25
Consensus pattern (35 bp):
ACTTTTGCCTCAACTAAACCTATATCCAAAACCAC
Found at i:60826820 original size:6 final size:6
Alignment explanation
Indices: 60826809--60826838 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
60826799 ATTGTTTTCT
60826809 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
60826839 AATTAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:60828054 original size:5 final size:5
Alignment explanation
Indices: 60828046--60828102 Score: 50
Period size: 5 Copynumber: 11.6 Consensus size: 5
60828036 TTTATATATA
*
60828046 ATAAT ATAAT ATAAT ATAAT A-ACAT ACTTAT -TAAT -TAAGT A-AAT
1 ATAAT ATAAT ATAAT ATAAT ATA-AT A-TAAT ATAAT ATAA-T ATAAT
60828090 ATAAT ATAAT ATA
1 ATAAT ATAAT ATA
60828103 CAACTTTTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 9 0.20
5 33 0.75
6 2 0.05
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:60828096 original size:34 final size:32
Alignment explanation
Indices: 60828053--60828124 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 32
60828043 ATAATAATAT
60828053 AATATAATATAATA-ACATACTTATT-AATTAAGTA
1 AATATAATATAATATACA-ACTT-TTAAATTAA--A
60828087 AATATAATATAATATACAACTTTTAAATTAAA
1 AATATAATATAATATACAACTTTTAAATTAAA
60828119 AATATA
1 AATATA
60828125 TTAGATTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
32 7 0.19
33 2 0.06
34 24 0.67
35 3 0.08
ACGTcount: A:0.56, C:0.06, G:0.01, T:0.38
Consensus pattern (32 bp):
AATATAATATAATATACAACTTTTAAATTAAA
Found at i:60836954 original size:40 final size:40
Alignment explanation
Indices: 60836904--60836997 Score: 152
Period size: 40 Copynumber: 2.4 Consensus size: 40
60836894 GTTTGGATAA
*
60836904 AAAACGCCGCTAAAGATCGAGCATTAGTGGCACTTTTTGG
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCACTTTTTGG
* * *
60836944 AAAACGCCGCTAAAGGTCGAGTATTAGCGGCGCTTTTTGG
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCACTTTTTGG
60836984 AAAACGCCGCTAAA
1 AAAACGCCGCTAAA
60836998 AACAACCATT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (40 bp):
AAAACGCCGCTAAAGATCGAGCATTAGCGGCACTTTTTGG
Found at i:60837172 original size:14 final size:14
Alignment explanation
Indices: 60837146--60837186 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
60837136 CAAGTAATTA
60837146 TATGGATTTAAGGAT
1 TATGGA-TTAAGGAT
60837161 TATGGATTAAGGAT
1 TATGGATTAAGGAT
*
60837175 TATGGTTTAAGG
1 TATGGATTAAGG
60837187 GTTGGGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (14 bp):
TATGGATTAAGGAT
Found at i:60840707 original size:43 final size:43
Alignment explanation
Indices: 60840646--60840730 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
60840636 CAATGATGTA
* *
60840646 CAAGATTTCTTTGATTAAGTAAATGTATTATATCTTTTATTAT
1 CAAGATTTCTTTGATTAAGAAAATGCATTATATCTTTTATTAT
* *
60840689 CAAGATTTAC-TTGATTAAGAAAATGCATTGTATGTTTTATTA
1 CAAGATTT-CTTTGATTAAGAAAATGCATTATATCTTTTATTA
60840731 CCTTGCATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 36 0.97
44 1 0.03
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (43 bp):
CAAGATTTCTTTGATTAAGAAAATGCATTATATCTTTTATTAT
Done.