Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009072.1 Hibiscus syriacus cultivar Beakdansim tig00112503_pilon, whole genome shotgun sequence
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: 2600608
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 13
Found at i:948212 original size:248 final size:249
Alignment explanation
Indices: 947354--948457 Score: 1495
Period size: 248 Copynumber: 4.4 Consensus size: 249
947344 TTATTGACAA
* * * * *
947354 ATAGCCCTTCTTGCCTTGAGCTATGTTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* *** * * * * *
947419 GAAGGTATTTTGG-ACACATATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCGTCG
66 GAAGGT-CTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCC-TTG
* * * * * * * * *
947483 AAGCTGAG-TGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGT
129 GAGCTGAGCT-TAGTCAAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTAT
* * * * * * ** *
947547 GCTGCAAATGATATG-CCTTGTAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTAG
193 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAG
*
947603 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTT
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
*
947668 GAAGGGTCTTTGGTTGGCAGATAACCCTTCTCGACTT-AGTTATGCTGCAAATGATATGCCTTGG
66 GAA-GGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGG
* * * * *
947732 AGCTGAGCGTT-GTCGAACTCGAAGGTCTTTTAGTGACAAATAACCTTTCTAGCCTTGAGTTATA
130 AGCTGAGC-TTAGTCAAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
* *
947796 CTGTAAATGATGTTCCCTCGAAGCTGAGTGTAATAGAACTCGGGGGGTCTTTGGCAG
194 CTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC-GGGGGTCTTTGGCAG
* * * * *
947853 ATAGGCCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGTTGAGCGTATTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
** * *
947918 GAATATCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATTATATGTCTTGGA
66 GAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGA
* *
947983 GCTGAGCTTAGTCAAACTCGAAGGTTTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTT
131 GCTGAGCTTAGTCAAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
*
948048 GTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTC-GGGGTCTTTGGCAG
196 GTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAG
* * * * *
948101 ATAGCCCTTCTCGACTTAAGCTATGATGCAAATGATGTTCCTTGAAGCTAAGCATAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
*
948166 GAAGGTCTTTGGTTGGAAGATAACCCTTCTCA-ACTTAAGTTATGCTGCAAATGATATGCCTTGG
66 GAAGGTCTTTGGTTGGCAGATAACCCTTCT-AGACTTAAGTTATGCTGCAAATGATATGCCTTGG
* *
948230 AGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGACAGATAACCCTTTTAGCCTTGAGTTATGC
130 AGCTGAGCTTAGTCAAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
948295 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAG
195 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAG
* * *
948350 ATAGGCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTGGAGCTGAGCATAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* *
948415 GAAGGTCTTT-GTTGGCAGATAACCCTTCTAGCCTTGAGTTATG
66 GAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
948458 TTGCGGATAG
Statistics
Matches: 756, Mismatches: 88, Indels: 23
0.87 0.10 0.03
Matches are distributed among these distances:
247 1 0.00
248 316 0.42
249 227 0.30
250 212 0.28
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (249 bp):
ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
GAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGA
GCTGAGCTTAGTCAAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
GTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAG
Found at i:948300 original size:498 final size:498
Alignment explanation
Indices: 947354--948457 Score: 1560
Period size: 498 Copynumber: 2.2 Consensus size: 498
947344 TTATTGACAA
* * * *
947354 ATAGCCCTTCTTGCCTTGAGCTATGT-TGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACT
1 ATAGGCCTTCTTGACTTAAGCTAT-TCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACT
*** * *
947418 CGAAGGTAT-TTTGG-ACACATATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCGT
65 CGAA--TATCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCGT
* * * *
947481 CGAAGCTGAGTGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTG
128 CGAAGCTGAGTGTAGTCAAACTCAAAGGTCTTTTGGTGACAGACAACCCTTCTAGACTTAAGTTA
*** * *
947546 TGCTGCAAATGATATGCCTTGTAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTAGATAGCCCT
193 TGCTGCAAATGATATGCCTCAAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCT
* * * * *
947611 TCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGGTC
258 TCTCGACTTAAGCTATGATGCAAATGATGTGCCTTGAAGCTAAGCATAGTCGAACTCGAAGGGTC
* *
947676 TTTGGTTGGCAGATAACCCTTCTCGACTTAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCG
323 TTTGGTTGGAAGATAACCCTTCTCAACTTAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCG
* *
947741 TTGTCGAACTCGAAGGTCTTTTAGTGACAAATAACCTTTCTAGCCTTGAGTTATACTGTAAATGA
388 TAGTCAAACTCGAAGGTCTTTTAGTGACAAATAACCTTTCTAGCCTTGAGTTATACTGTAAATGA
*
947806 TGTTCCCTCGAAGCTGAGTGTAATAGAACTCGGGGGGTCTTTGGCAG
453 TGTGCCCTCGAAGCTGAGTGTAATAGAACTC-GGGGGTCTTTGGCAG
* *
947853 ATAGGCCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGTTGAGCGTATTCGAACTC
1 ATAGGCCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * * *
947918 GAATATCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATTATATGTC-TTGG
66 GAATATCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCGTCGA
* * * * *
947982 AGCTGAGCT-TAGTCAAACTCGAAGGTTTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
131 AGCTGAG-TGTAGTCAAACTCAAAGGTCTTTTGGTGACAGACAACCCTTCTAGACTTAAGTTATG
* * * * *
948046 TTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCG-GGGTCTTTGGCAGATAGCCCTT
195 CTGCAAATGATATG-CCTCAAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTT
*
948110 CTCGACTTAAGCTATGATGCAAATGATGTTCCTTGAAGCTAAGCATAGTCGAACTCGAA-GGTCT
259 CTCGACTTAAGCTATGATGCAAATGATGTGCCTTGAAGCTAAGCATAGTCGAACTCGAAGGGTCT
948174 TTGGTTGGAAGATAACCCTTCTCAACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCG
324 TTGGTTGGAAGATAACCCTTCTCAACTT-AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCG
* * *
948239 TAGTCAAACTCGAAGGTCTTTTGGTGACAGATAACCCTTT-TAGCCTTGAGTTATGCTGTAAATG
388 TAGTCAAACTCGAAGGTCTTTTAGTGACAAATAA-CCTTTCTAGCCTTGAGTTATACTGTAAATG
*
948303 ATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAG
452 ATGTGCCCTCGAAGCTGAGTGTAATAGAACTCGGGGGTCTTTGGCAG
* * * *
948350 ATAGGCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTGGAGCTGAGCATAGTCGAACTC
1 ATAGGCCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
**
948415 GAAGGTCTTT-GTTGGCAGATAACCCTTCTAGCCTTGAGTTATG
66 GAATATCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATG
948458 TTGCGGATAG
Statistics
Matches: 537, Mismatches: 61, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
496 31 0.06
497 116 0.22
498 264 0.49
499 126 0.23
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (498 bp):
ATAGGCCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
GAATATCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCGTCGA
AGCTGAGTGTAGTCAAACTCAAAGGTCTTTTGGTGACAGACAACCCTTCTAGACTTAAGTTATGC
TGCAAATGATATGCCTCAAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCT
CGACTTAAGCTATGATGCAAATGATGTGCCTTGAAGCTAAGCATAGTCGAACTCGAAGGGTCTTT
GGTTGGAAGATAACCCTTCTCAACTTAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
TCAAACTCGAAGGTCTTTTAGTGACAAATAACCTTTCTAGCCTTGAGTTATACTGTAAATGATGT
GCCCTCGAAGCTGAGTGTAATAGAACTCGGGGGTCTTTGGCAG
Found at i:953832 original size:11 final size:11
Alignment explanation
Indices: 953816--953849 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
953806 AGAGACCAAA
953816 AATAAATAAAT
1 AATAAATAAAT
953827 AATAAATTAAAT
1 AATAAA-TAAAT
*
953839 AAAAAATAAAT
1 AATAAATAAAT
953850 TAAATTAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:953839 original size:16 final size:16
Alignment explanation
Indices: 953818--953854 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
953808 AGACCAAAAA
*
953818 TAAATAAATAATAAAT
1 TAAATAAAAAATAAAT
953834 TAAATAAAAAATAAAT
1 TAAATAAAAAATAAAT
953850 TAAAT
1 TAAAT
953855 TAAGCTAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAATAAAAAATAAAT
Found at i:954883 original size:5 final size:5
Alignment explanation
Indices: 954873--954934 Score: 52
Period size: 5 Copynumber: 11.8 Consensus size: 5
954863 GACCTTAACA
* * * *
954873 AAAAT AAAAT AAAAT AAATT AAATT AAATT AGATTAAT AAAAT GAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-A--AAT AAAAT AAAAT
*
954921 GAAAT AAAAT AAAA
1 AAAAT AAAAT AAAA
954935 AAATAAATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
5 45 0.90
6 1 0.02
7 1 0.02
8 3 0.06
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (5 bp):
AAAAT
Found at i:954900 original size:15 final size:14
Alignment explanation
Indices: 954874--954933 Score: 59
Period size: 15 Copynumber: 4.2 Consensus size: 14
954864 ACCTTAACAA
*
954874 AAATAAAATAAAAT
1 AAATTAAATAAAAT
*
954888 AAATTAAATTAAATT
1 AAATTAAA-TAAAAT
*
954903 AGATT-AATAAAAT
1 AAATTAAATAAAAT
*
954916 GAAATGAAATAAAAT
1 -AAATTAAATAAAAT
954931 AAA
1 AAA
954934 AAAATAAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 5 0.14
14 15 0.41
15 17 0.46
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (14 bp):
AAATTAAATAAAAT
Found at i:955188 original size:35 final size:35
Alignment explanation
Indices: 955019--955314 Score: 186
Period size: 37 Copynumber: 8.2 Consensus size: 35
955009 TTTAAAAACG
*
955019 TTTTCAAAACTATATATCATATAATTTTCAAAAATGA
1 TTTT-AAAACTATATATTATATAATTTTC-AAAATGA
* *
955056 TTTTAAAA--ATACTA-TATA-AGTTTTCCAAAATGT
1 TTTTAAAACTATA-TATTATATAATTTT-CAAAATGA
** * *
955089 TTTTTTAACTATTTATTATATAAATTTTCAAAAAATGTTT
1 TTTTAAAACTATATATTATAT-AATTTTC--AAAATG--A
955129 TTTTAAAAACTATATA-T-TAT-ATTTTCAAAATGA
1 TTTT-AAAACTATATATTATATAATTTTCAAAATGA
*
955162 TTTCAAAACTATATATTATATAATTTTCAAAAT-A
1 TTTTAAAACTATATATTATATAATTTTCAAAATGA
* *
955196 TTTTTAAAACTTATGTATTGTATATAAGTTTTCAAAAACGA
1 -TTTTAAAAC-TATATA-T-TATATAA-TTTTC-AAAATGA
* *
955237 TTTAAAAACTATATAATATAT-A-TTTCAAAAACT-A
1 TTTTAAAACTATATATTATATAATTTTC-AAAA-TGA
**
955271 TTTTTTGAAAACTATATATTATAT--TTTTCAAAAACA
1 --TTTT-AAAACTATATATTATATAATTTTCAAAATGA
955307 TTTTAAAA
1 TTTTAAAA
955315 AATTATACTA
Statistics
Matches: 209, Mismatches: 22, Indels: 60
0.72 0.08 0.21
Matches are distributed among these distances:
32 11 0.05
33 25 0.12
34 27 0.13
35 33 0.16
36 19 0.09
37 41 0.20
38 13 0.06
39 13 0.06
40 18 0.09
41 9 0.04
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (35 bp):
TTTTAAAACTATATATTATATAATTTTCAAAATGA
Found at i:958256 original size:23 final size:25
Alignment explanation
Indices: 958202--958250 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
958192 TGTTAAAAAT
958202 ATAAA-AAAATTTAATAGAGTGAAC
1 ATAAATAAAATTTAATAGAGTGAAC
*
958226 ATAAATAAAATTTCA-AGA-TGAAC
1 ATAAATAAAATTTAATAGAGTGAAC
958249 AT
1 AT
958251 CGATAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 7 0.30
24 8 0.35
25 8 0.35
ACGTcount: A:0.57, C:0.06, G:0.10, T:0.27
Consensus pattern (25 bp):
ATAAATAAAATTTAATAGAGTGAAC
Found at i:959707 original size:23 final size:22
Alignment explanation
Indices: 959681--959724 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
959671 AAAAAATTAT
959681 CTAAAACACTATAAT-TTTTTTAC
1 CTAAAACA-T-TAATATTTTTTAC
959704 CTAAAACATTAATATTTTTTA
1 CTAAAACATTAATATTTTTTA
959725 ATATTTTCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 8 0.40
23 8 0.40
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (22 bp):
CTAAAACATTAATATTTTTTAC
Found at i:959721 original size:21 final size:23
Alignment explanation
Indices: 959681--959722 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
959671 AAAAAATTAT
*
959681 CTAAAACACTATAATTTTTTTAC
1 CTAAAACACTATAATATTTTTAC
959704 CTAAAACA-T-TAATATTTTT
1 CTAAAACACTATAATATTTTT
959723 TAATATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 1 0.06
23 8 0.44
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.45
Consensus pattern (23 bp):
CTAAAACACTATAATATTTTTAC
Found at i:959773 original size:22 final size:22
Alignment explanation
Indices: 959748--959789 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
959738 AATATCAAAC
*
959748 AATAACAAAATCGATAGAAAAA
1 AATAACAAAACCGATAGAAAAA
*
959770 AATAATAAAACCGATAGAAA
1 AATAACAAAACCGATAGAAA
959790 TAATAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.10, G:0.10, T:0.14
Consensus pattern (22 bp):
AATAACAAAACCGATAGAAAAA
Found at i:964066 original size:23 final size:23
Alignment explanation
Indices: 964005--964072 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
963995 CATTTTATAT
* *
964005 GGCACTTCGGTACAATTCTACGT
1 GGCACTTCGGTACATTTCTACGC
* * *
964028 GGCACTACGGTTCATTTCTATGC
1 GGCACTTCGGTACATTTCTACGC
* *
964051 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTACATTTCTACG
964073 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTACATTTCTACGC
Found at i:967968 original size:23 final size:23
Alignment explanation
Indices: 967934--968002 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
967924 CATTATTATA
967934 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
967957 TGGCACTCCGGTGTAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
967980 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTCTACG
968003 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.29
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:971194 original size:24 final size:24
Alignment explanation
Indices: 971161--971229 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
971151 TAATGCATCG
971161 ATGTATAAGGAGTGCATCGATGCAC
1 ATGT-TAAGGAGTGCATCGATGCAC
*
971186 ATGTTAAGG-GATGCATCGATACAC
1 ATGTTAAGGAG-TGCATCGATGCAC
*
971210 -TG-T-A-GAATGCATCGATGCAC
1 ATGTTAAGGAGTGCATCGATGCAC
971230 TTCAAGGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 13 0.33
21 1 0.03
22 1 0.03
23 3 0.08
24 17 0.44
25 4 0.10
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (24 bp):
ATGTTAAGGAGTGCATCGATGCAC
Found at i:971452 original size:17 final size:17
Alignment explanation
Indices: 971430--971462 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
971420 GCCAAGGTGA
971430 GTGCATATTATTATATT
1 GTGCATATTATTATATT
971447 GTGCATATTATTATAT
1 GTGCATATTATTATAT
971463 AAAAATTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (17 bp):
GTGCATATTATTATATT
Found at i:972403 original size:23 final size:23
Alignment explanation
Indices: 972350--972414 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
972340 TTTATATGGC
* * *
972350 ACTTCGGTACAATTCTACGTGGC
1 ACTTCGGTACATTTCTACGCGGA
* *
972373 ACTACGGTTCATTTCTACGCGGA
1 ACTTCGGTACATTTCTACGCGGA
* *
972396 ACTTCGGTGCATTTATACG
1 ACTTCGGTACATTTCTACG
972415 AGCTGTGGTG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (23 bp):
ACTTCGGTACATTTCTACGCGGA
Found at i:975328 original size:21 final size:21
Alignment explanation
Indices: 975299--975360 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
975289 CTCTTTAGTA
* *
975299 TCACTGCCGGCATCTTTCTTC
1 TCACCGCCGTCATCTTTCTTC
* * *
975320 TCCCCGCCGTCTTTTTTCTTC
1 TCACCGCCGTCATCTTTCTTC
* *
975341 TCACCGTCGTCGTCTTTCTT
1 TCACCGCCGTCATCTTTCTT
975361 AGGCGGAACC
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.05, C:0.39, G:0.13, T:0.44
Consensus pattern (21 bp):
TCACCGCCGTCATCTTTCTTC
Found at i:979433 original size:33 final size:33
Alignment explanation
Indices: 979391--979456 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
979381 ATATTTTCAC
979391 CCTTTTCTTCTAGATAATTCGTGATTTAGTGGT
1 CCTTTTCTTCTAGATAATTCGTGATTTAGTGGT
979424 CCTTTTCTTCTAGATAATTCGTGATTTAGTGGT
1 CCTTTTCTTCTAGATAATTCGTGATTTAGTGGT
979457 TTACTTTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.48
Consensus pattern (33 bp):
CCTTTTCTTCTAGATAATTCGTGATTTAGTGGT
Found at i:981201 original size:2 final size:2
Alignment explanation
Indices: 981196--981231 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
981186 TATCTTTTTT
981196 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
981232 CATCTTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:982909 original size:209 final size:208
Alignment explanation
Indices: 982549--982965 Score: 816
Period size: 209 Copynumber: 2.0 Consensus size: 208
982539 TGTTATCTGC
982549 AGCAAAGCACAAGAGACAAGGGACCACTTGTTCTTACAGTGCCCCTTGGATGTTTCTTTATGGGA
1 AGCAAAGCACAAGAGACAAGGGACCACTTGTTCTTACAGTGCCCCTTGGATGTTTCTTTATGGGA
982614 TTCCATTTTGTTCCTTAACGGGTTGAGGAGTACCACTTTGTCATGGGGATATGTTATCATGGGCT
66 TTCCATTTTGTTCCTTAACGGGTTGAGGAGTACCACTTTGTCATGGGGATATGTTATCATGGGCT
*
982679 TGTGGTGCTTGGAACGGTAAGTCCCTTCTCACAACTATTTTGAAGTTAGTTTGGGTGTGCAAATA
131 TGTGGTGCTTGGAAAGGTAAGTCCCTTCTCACAACTATTTTGAAGTTAGTTT-GGTGTGCAAATA
982744 TATATACCCTGTGG
195 TATATACCCTGTGG
982758 AGCAAAGCACAAGAGACAAGGGACCACTTGTTCTTACAGTGCCCCTTGGATGTTTCTTTATGGGA
1 AGCAAAGCACAAGAGACAAGGGACCACTTGTTCTTACAGTGCCCCTTGGATGTTTCTTTATGGGA
982823 TTCCATTTTGTTCCTTAACGGGTTGAGGAGTACCACTTTGTCATGGGGATATGTTATCATGGGCT
66 TTCCATTTTGTTCCTTAACGGGTTGAGGAGTACCACTTTGTCATGGGGATATGTTATCATGGGCT
982888 TGTGGTGCTTGGAAAGGTAAGTCCCTTCTCACAACTATTTTGAAGTTAGTTTGGTGTGCAAATAT
131 TGTGGTGCTTGGAAAGGTAAGTCCCTTCTCACAACTATTTTGAAGTTAGTTTGGTGTGCAAATAT
982953 ATATACCCTGTGG
196 ATATACCCTGTGG
982966 GAGGAAAGAA
Statistics
Matches: 207, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
208 26 0.13
209 181 0.87
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (208 bp):
AGCAAAGCACAAGAGACAAGGGACCACTTGTTCTTACAGTGCCCCTTGGATGTTTCTTTATGGGA
TTCCATTTTGTTCCTTAACGGGTTGAGGAGTACCACTTTGTCATGGGGATATGTTATCATGGGCT
TGTGGTGCTTGGAAAGGTAAGTCCCTTCTCACAACTATTTTGAAGTTAGTTTGGTGTGCAAATAT
ATATACCCTGTGG
Found at i:986549 original size:2 final size:2
Alignment explanation
Indices: 986542--986567 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
986532 ACTACTTACC
986542 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
986568 TAATGATGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:991298 original size:18 final size:18
Alignment explanation
Indices: 991277--991313 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
991267 CCGTTGACAT
991277 GACCCATTGACCCGACCC
1 GACCCATTGACCCGACCC
*
991295 GACCCGTTGACCCGACCC
1 GACCCATTGACCCGACCC
991313 G
1 G
991314 TTAACCGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.49, G:0.22, T:0.11
Consensus pattern (18 bp):
GACCCATTGACCCGACCC
Found at i:991306 original size:13 final size:13
Alignment explanation
Indices: 991290--991315 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
991280 CCATTGACCC
991290 GACCCGACCCGTT
1 GACCCGACCCGTT
991303 GACCCGACCCGTT
1 GACCCGACCCGTT
991316 AACCGTTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.46, G:0.23, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:991312 original size:31 final size:31
Alignment explanation
Indices: 991254--991312 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
991244 GTCACAACCC
*
991254 GACCCGACCCGACCCGTTGACATGACCCATT
1 GACCCGACCCGACCCGTTGACACGACCCATT
*
991285 GACCCGACCCGACCCGTTGACCCGACCC
1 GACCCGACCCGACCCGTTGACACGACCC
991313 GTTAACCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.20, C:0.47, G:0.20, T:0.12
Consensus pattern (31 bp):
GACCCGACCCGACCCGTTGACACGACCCATT
Found at i:995477 original size:22 final size:22
Alignment explanation
Indices: 995452--995501 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
995442 TAATTTAATT
*
995452 TATTAATGATATAACTTTATAA
1 TATTAATAATATAACTTTATAA
* * *
995474 TATTTATAATTTAATTTTATAA
1 TATTAATAATATAACTTTATAA
995496 -ATTAAT
1 TATTAAT
995502 TGATTTTATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
TATTAATAATATAACTTTATAA
Found at i:995524 original size:13 final size:13
Alignment explanation
Indices: 995470--995525 Score: 51
Period size: 13 Copynumber: 4.0 Consensus size: 13
995460 ATATAACTTT
995470 ATAATATTTATAA
1 ATAATATTTATAA
*
995483 TTTAAT-TTTATAA
1 -ATAATATTTATAA
995496 ATTAATTGATTTTATAA
1 A-TAA-T-A-TTTATAA
995513 ATAATATTTATAA
1 ATAATATTTATAA
995526 TGTATTTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
13 17 0.49
14 6 0.17
15 1 0.03
16 3 0.09
17 8 0.23
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (13 bp):
ATAATATTTATAA
Found at i:997080 original size:21 final size:22
Alignment explanation
Indices: 997056--997096 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
997046 ACAAACGTCG
*
997056 TAATTGTCAA-ATAAATAAACT
1 TAATTATCAATATAAATAAACT
*
997077 TAATTATCAATTTAAATAAA
1 TAATTATCAATATAAATAAA
997097 TAAAATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (22 bp):
TAATTATCAATATAAATAAACT
Found at i:999668 original size:73 final size:73
Alignment explanation
Indices: 999549--999696 Score: 262
Period size: 73 Copynumber: 2.0 Consensus size: 73
999539 TGACACAAAT
* *
999549 AATTTTAGAGTGGTTCAACTTTCTCAATAAAGTTTACATCCACTACCTTGGCTT-TCACACTAAG
1 AATTTTAGAGTGATTCAACTTTCTCAATAAAGTTTACATACACTACCTTGGCTTCT-ACACTAAG
999613 GATTTCAAC
65 GATTTCAAC
999622 AATTTTAGAGTGATTCAACTTTCTCAATAAAGTTTACATACACTACCTTGGCTTCTACACTAAGG
1 AATTTTAGAGTGATTCAACTTTCTCAATAAAGTTTACATACACTACCTTGGCTTCTACACTAAGG
999687 ATTTCAAC
66 ATTTCAAC
999695 AA
1 AA
999697 ATTCACTAAT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
73 71 0.99
74 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (73 bp):
AATTTTAGAGTGATTCAACTTTCTCAATAAAGTTTACATACACTACCTTGGCTTCTACACTAAGG
ATTTCAAC
Found at i:1000366 original size:17 final size:17
Alignment explanation
Indices: 1000327--1000367 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1000317 TACTACTGTT
*
1000327 AAAAGTAGTATCGGTACT
1 AAAA-TAGTATCGGTACC
*
1000345 GAAATAGTATCGGTACC
1 AAAATAGTATCGGTACC
1000362 AAAATA
1 AAAATA
1000368 ACATTATGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (17 bp):
AAAATAGTATCGGTACC
Found at i:1002787 original size:16 final size:16
Alignment explanation
Indices: 1002761--1002798 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1002751 ATAATAAGGG
*
1002761 GAAAAATAAAATAAAT
1 GAAAAATAAAAGAAAT
1002777 -AAAATATAAAAGAAAT
1 GAAAA-ATAAAAGAAAT
1002793 GAAAAA
1 GAAAAA
1002799 AAGGCTAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
15 4 0.21
16 11 0.58
17 4 0.21
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (16 bp):
GAAAAATAAAAGAAAT
Found at i:1003789 original size:12 final size:12
Alignment explanation
Indices: 1003774--1003799 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1003764 AAATAATAAT
1003774 AATAATACAATA
1 AATAATACAATA
1003786 AATAATACAATA
1 AATAATACAATA
1003798 AA
1 AA
1003800 ATATTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AATAATACAATA
Found at i:1004823 original size:106 final size:106
Alignment explanation
Indices: 1004693--1005141 Score: 641
Period size: 106 Copynumber: 4.2 Consensus size: 106
1004683 AGTATTGTTC
* * ***
1004693 CGAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCAGGAAATTGTTTATTGAC
1 CGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGAC
* ** ** *
1004757 AACCAGCCGTCATTTCGTTATGAAGTTGAACTTGTGTTGTCT
65 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
1004799 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
*
1004864 ACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
1004905 GGAGTCCAATATCCTTCG-TCGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGAC
*
1004969 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
65 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
1005011 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1005076 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
1005117 AGAGTCCAATATCATTCGCTATGAA
1 CGAGTCCAATATCCTTCGCTGTGAA
1005142 ATTGGGAAGT
Statistics
Matches: 313, Mismatches: 27, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
105 1 0.00
106 310 0.99
107 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:1004937 original size:212 final size:212
Alignment explanation
Indices: 1004694--1005346 Score: 813
Period size: 212 Copynumber: 3.2 Consensus size: 212
1004684 GTATTGTTCC
* * *
1004694 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCAG-GAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCT-AAAACAGAGAAATTGTTTATTGACA
* * **
1004758 ACCAGCCGTCATTTCGTTATGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGA
65 ACCAGCCGTCACTTCGTCATGAAGTTGAACTTGCATTGTCTCGAGTCCAATATCCTTCGCTGTGA
* *
1004823 AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGTGGTCCCTTCGTCGTGAAG
130 AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
*
1004888 TTGAACTTGCGTTGTCTG
195 TTGAACTTGCGTTGTCTA
** * *
1004906 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTAAAACAGAGAAATTGTTTATTGACAA
* * * *
1004971 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAA
66 CCAGCCGTCACTTCGTCATGAAGTTGAACTTGCATTGTCTCGAGTCCAATATCCTTCGCTGTGAA
* *
1005036 GTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACTACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1005101 TGAACTTGCGTTGTCTA
196 TGAACTTGCGTTGTCTA
* *
1005118 GAGTCCAATATCATTCG-C-T--A--TGAAATT-G----------G-GAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTAAAACAGAGAAATTGTTTATTGACAA
* * * * *
1005165 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAA
66 CCAGCCGTCACTTCGTCATGAAGTTGAACTTGCATTGTCTCGAGTCCAATATCCTTCGCTGTGAA
* * * *
1005230 GTTGAAATTGGCTTTGAAATTGAGAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* *
1005295 TGAACTTGCATTGTCTG
196 TGAACTTGCGTTGTCTA
* * *
1005312 GAGTGGCACGATATCCTCCGTCGTGGAGTTGAAAT
1 GAGT--C-CAATATCCTTCGTCGTGAAGTTGAAAT
1005347 CGCGGATGGC
Statistics
Matches: 398, Mismatches: 33, Indels: 29
0.87 0.07 0.06
Matches are distributed among these distances:
194 160 0.40
195 1 0.00
196 1 0.00
197 9 0.02
198 1 0.00
199 1 0.00
201 1 0.00
203 6 0.02
205 1 0.00
206 7 0.02
208 1 0.00
210 1 0.00
211 4 0.01
212 204 0.51
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (212 bp):
GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTAAAACAGAGAAATTGTTTATTGACAA
CCAGCCGTCACTTCGTCATGAAGTTGAACTTGCATTGTCTCGAGTCCAATATCCTTCGCTGTGAA
GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
TGAACTTGCGTTGTCTA
Found at i:1005199 original size:88 final size:88
Alignment explanation
Indices: 1005050--1005229 Score: 324
Period size: 88 Copynumber: 2.0 Consensus size: 88
1005040 AAATTGGCTC
*
1005050 TGAAATTGGGAAGTTGTTTATTGACTACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1005115 CTAGAGTCCAATATCATTCGCTA
66 CTAGAGTCCAATATCATTCGCTA
1005138 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* * *
1005203 CTTGAGTCCAATATCCTTCGCTG
66 CTAGAGTCCAATATCATTCGCTA
1005226 TGAA
1 TGAA
1005230 GTTGAAATTG
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (88 bp):
TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTAGAGTCCAATATCATTCGCTA
Found at i:1005282 original size:194 final size:194
Alignment explanation
Indices: 1004946--1005315 Score: 650
Period size: 194 Copynumber: 1.9 Consensus size: 194
1004936 ATTGGCTCTA
*
1004946 AAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
1 AAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
* * *
1005011 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACT
66 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTATTGACA
*
1005076 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCATTCGCTATG
131 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTAGAGTCCAATATCATTCGCTATG
* *
1005140 AAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
1 AAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
* *
1005205 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAGTTATTTATTGACA
66 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTATTGACA
*
1005270 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGT
131 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTAGAGT
1005316 GGCACGATAT
Statistics
Matches: 166, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
194 166 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (194 bp):
AAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTATTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTAGAGTCCAATATCATTCGCTATG
Found at i:1006886 original size:22 final size:22
Alignment explanation
Indices: 1006861--1006904 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1006851 CATTTTTGTC
*
1006861 CATTTGATGCTCAATGGTTTGA
1 CATTTGATGCTCAAAGGTTTGA
*
1006883 CATTTGATGTTCAAAGGTTTGA
1 CATTTGATGCTCAAAGGTTTGA
1006905 TGGGGTAGCT
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:0.25, C:0.11, G:0.23, T:0.41
Consensus pattern (22 bp):
CATTTGATGCTCAAAGGTTTGA
Found at i:1007557 original size:7 final size:7
Alignment explanation
Indices: 1007547--1007616 Score: 61
Period size: 7 Copynumber: 9.7 Consensus size: 7
1007537 TCTTTTGTTT
1007547 TTTTTCC
1 TTTTTCC
1007554 TTTTTCC
1 TTTTTCC
**
1007561 TTTTTTGTT
1 -TTTTT-CC
1007570 TTTTTCC
1 TTTTTCC
1007577 TTTTTTCC
1 -TTTTTCC
*
1007585 TTTTTTC
1 TTTTTCC
*
1007592 TTTTTTC
1 TTTTTCC
*
1007599 -TTTTCT
1 TTTTTCC
1007605 TTTTTCC
1 TTTTTCC
1007612 TTTTT
1 TTTTT
1007617 TGCTTCTTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
6 4 0.08
7 30 0.59
8 17 0.33
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.80
Consensus pattern (7 bp):
TTTTTCC
Found at i:1007557 original size:8 final size:8
Alignment explanation
Indices: 1007546--1007617 Score: 84
Period size: 8 Copynumber: 9.8 Consensus size: 8
1007536 TTCTTTTGTT
1007546 TTTTTTCC
1 TTTTTTCC
1007554 -TTTTTCC
1 TTTTTTCC
**
1007561 TTTTTTGT
1 TTTTTTCC
1007569 TTTTTTCC
1 TTTTTTCC
1007577 TTTTTTCC
1 TTTTTTCC
1007585 TTTTTT-C
1 TTTTTTCC
1007592 TTTTTT-C
1 TTTTTTCC
1007599 --TTTT-C
1 TTTTTTCC
1007604 TTTTTTCC
1 TTTTTTCC
1007612 TTTTTT
1 TTTTTT
1007618 GCTTCTTATT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
5 5 0.09
7 19 0.34
8 32 0.57
ACGTcount: A:0.00, C:0.18, G:0.01, T:0.81
Consensus pattern (8 bp):
TTTTTTCC
Found at i:1007564 original size:16 final size:15
Alignment explanation
Indices: 1007546--1007616 Score: 85
Period size: 15 Copynumber: 4.9 Consensus size: 15
1007536 TTCTTTTGTT
1007546 TTTTTTCCTTTTTCC
1 TTTTTTCCTTTTTCC
**
1007561 TTTTTTGTTTTTTTCC
1 TTTTTT-CCTTTTTCC
*
1007577 TTTTTTCCTTTTTTC
1 TTTTTTCCTTTTTCC
1007592 TTTTTT-C-TTTT-C
1 TTTTTTCCTTTTTCC
1007604 TTTTTTCCTTTTT
1 TTTTTTCCTTTTT
1007617 TGCTTCTTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
12 7 0.15
13 5 0.10
14 5 0.10
15 18 0.38
16 13 0.27
ACGTcount: A:0.00, C:0.18, G:0.01, T:0.80
Consensus pattern (15 bp):
TTTTTTCCTTTTTCC
Found at i:1007570 original size:24 final size:24
Alignment explanation
Indices: 1007539--1007618 Score: 99
Period size: 24 Copynumber: 3.2 Consensus size: 24
1007529 TTGTTCTTTC
1007539 TTTTGTTTTTTTTCCTTTTTCCTT
1 TTTTGTTTTTTTTCCTTTTTCCTT
1007563 TTTTG-TTTTTTTCCTTTTTTCCTTT
1 TTTTGTTTTTTTTCC-TTTTTCC-TT
* *
1007588 TTTCTTTTTTCTTTTCTTTTTTCCTT
1 TTT-TGTTTT-TTTTCCTTTTTCCTT
1007614 TTTTG
1 TTTTG
1007619 CTTCTTATTG
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
23 9 0.19
24 12 0.25
25 6 0.12
26 6 0.12
27 10 0.21
28 5 0.10
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (24 bp):
TTTTGTTTTTTTTCCTTTTTCCTT
Found at i:1010667 original size:16 final size:16
Alignment explanation
Indices: 1010641--1010678 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1010631 ATAATAAGGG
*
1010641 GAAAAATAAAATAAAT
1 GAAAAATAAAAGAAAT
1010657 -AAAATATAAAAGAAAT
1 GAAAA-ATAAAAGAAAT
1010673 GAAAAA
1 GAAAAA
1010679 AAGGCTAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
15 4 0.21
16 11 0.58
17 4 0.21
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (16 bp):
GAAAAATAAAAGAAAT
Found at i:1011893 original size:17 final size:16
Alignment explanation
Indices: 1011871--1011909 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
1011861 CCTATAAAAG
*
1011871 AAATAATAATAATAATA
1 AAATAATAAT-ACAATA
1011888 AAATAAATAATACAATA
1 AAAT-AATAATACAATA
1011905 AAATA
1 AAATA
1011910 TTTTTATAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 13 0.65
18 6 0.30
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATAATAATACAATA
Found at i:1012953 original size:2 final size:2
Alignment explanation
Indices: 1012946--1012995 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1012936 ATAACATCCT
1012946 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
1012988 TA TA TA TA
1 TA TA TA TA
1012996 CTTTTAAGAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1016697 original size:21 final size:21
Alignment explanation
Indices: 1016643--1016699 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
1016633 TTCTGGTAGA
*
1016643 TCGCTACCTAAAATGTTAATT
1 TCGCTAACTAAAATGTTAATT
**
1016664 T-TTTAACTGAAAATGTTAATT
1 TCGCTAACT-AAAATGTTAATT
1016685 TCGCTAACTAAAATG
1 TCGCTAACTAAAATG
1016700 AATATTTCCG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 4 0.14
21 20 0.69
22 5 0.17
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.39
Consensus pattern (21 bp):
TCGCTAACTAAAATGTTAATT
Found at i:1016780 original size:46 final size:46
Alignment explanation
Indices: 1016707--1016798 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
1016697 ATGAATATTT
* * *
1016707 CCGATATTAACATTTCCGGTAGTAAAAATAACATTTTAAGTAGCGC
1 CCGATATAAACATTTCCAGTAGAAAAAATAACATTTTAAGTAGCGC
* * *
1016753 CCGATATAAATATTTCCAGTAGAAAAAATAATATTTTAGGTAGCGC
1 CCGATATAAACATTTCCAGTAGAAAAAATAACATTTTAAGTAGCGC
1016799 TCTACCAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (46 bp):
CCGATATAAACATTTCCAGTAGAAAAAATAACATTTTAAGTAGCGC
Found at i:1020286 original size:12 final size:12
Alignment explanation
Indices: 1020255--1020289 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1020245 AAATTTAAAA
* *
1020255 TTATAATATATT
1 TTATAATTTTTT
1020267 TTATAATTTTTT
1 TTATAATTTTTT
1020279 TTATAATTTTT
1 TTATAATTTTT
1020290 ATTAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATAATTTTTT
Found at i:1023410 original size:58 final size:58
Alignment explanation
Indices: 1022930--1023383 Score: 755
Period size: 58 Copynumber: 7.8 Consensus size: 58
1022920 CATATTTCCC
*
1022930 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTACACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
* * *
1022988 ATACGGAAATTCATAAACTTAGTATGAATTTCTTAACTTTTTGCAGACATAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
* *
1023046 ATACGGAAATTCATACACATAGTATGTATTTCTTAACTTTTTGCACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
* * *
1023104 ATACGGAAATTTATACACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCGA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
* * *
1023162 ATTCGGAAATTCATACGCATAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
* *
1023220 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACTTTTTACACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
* *
1023278 ATACGGAAATTCATACACTTATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCTA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
*
1023336 ATACAGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACAC
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACAC
1023384 TTAGTGTCAT
Statistics
Matches: 365, Mismatches: 31, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 365 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (58 bp):
ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
Found at i:1025321 original size:19 final size:18
Alignment explanation
Indices: 1025282--1025323 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
1025272 AATAATATAC
1025282 ATATTAAATAATTAACCTA
1 ATATTAAATAATTAA-CTA
1025301 ATATTCAAACTAATTAA-TA
1 ATATT-AAA-TAATTAACTA
1025320 ATAT
1 ATAT
1025324 ATAATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 11 0.52
20 3 0.14
21 7 0.33
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATTAAATAATTAACTA
Found at i:1027279 original size:22 final size:22
Alignment explanation
Indices: 1027221--1027289 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
1027211 ATTATATGGA
1027221 TATTTTATTCATT-TATTTTATT
1 TATTTTATT-ATTATATTTTATT
*
1027243 TGATTTT-TTACTATATTTTA-T
1 T-ATTTTATTATTATATTTTATT
*
1027264 TATTATTATTATTATATATTTCTT
1 TATT-TTATTATTATAT-TTTATT
1027288 TA
1 TA
1027290 ATATTTTACT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
20 3 0.08
21 6 0.16
22 18 0.47
23 8 0.21
24 3 0.08
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.68
Consensus pattern (22 bp):
TATTTTATTATTATATTTTATT
Found at i:1027294 original size:24 final size:24
Alignment explanation
Indices: 1027254--1027303 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1027244 GATTTTTTAC
*
1027254 TATATTTTATTATTATTATTA-TTA
1 TATATTTTATTAATATT-TTACTTA
1027278 TATATTTCT-TTAATATTTTACTTA
1 TATATTT-TATTAATATTTTACTTA
1027302 TA
1 TA
1027304 AGTCTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 3 0.13
24 19 0.83
25 1 0.04
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (24 bp):
TATATTTTATTAATATTTTACTTA
Found at i:1030323 original size:8 final size:8
Alignment explanation
Indices: 1030310--1030348 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1030300 GAACATTTCA
*
1030310 TGCATTCT
1 TGCATTTT
1030318 TGCA-TTT
1 TGCATTTT
1030325 TGCATTTT
1 TGCATTTT
*
1030333 TGCCTTTT
1 TGCATTTT
1030341 TGCATTTT
1 TGCATTTT
1030349 CATCTACAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:1031544 original size:18 final size:17
Alignment explanation
Indices: 1031530--1031590 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 17
1031520 AATAAAAAGG
1031530 GCAAAAAGAAAAAAAAA
1 GCAAAAAGAAAAAAAAA
*
1031547 GCAAAAA-AAAAAGCAAA
1 GCAAAAAGAAAAA-AAAA
*
1031564 --AAAAAG-AACAAAAA
1 GCAAAAAGAAAAAAAAA
*
1031578 GAAAAAAGAAAAA
1 GCAAAAAGAAAAA
1031591 GGGACAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
14 3 0.09
15 8 0.23
16 11 0.31
17 13 0.37
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (17 bp):
GCAAAAAGAAAAAAAAA
Found at i:1031555 original size:12 final size:12
Alignment explanation
Indices: 1031538--1031583 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
1031528 GGGCAAAAAG
1031538 AAAAAAAAAGCA
1 AAAAAAAAAGCA
1031550 AAAAAAAAAGCA
1 AAAAAAAAAGCA
1031562 AAAAAAAGAA-CA
1 AAAAAAA-AAGCA
1031574 AAAAGAAAAA
1 AAAA-AAAAA
1031584 AGAAAAAGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 27 0.84
13 5 0.16
ACGTcount: A:0.85, C:0.07, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGCA
Found at i:1031556 original size:13 final size:13
Alignment explanation
Indices: 1031538--1031590 Score: 67
Period size: 13 Copynumber: 4.2 Consensus size: 13
1031528 GGGCAAAAAG
1031538 AAAAAAAAAGC-A
1 AAAAAAAAAGCAA
1031550 AAAAAAAAAGCAA
1 AAAAAAAAAGCAA
*
1031563 AAAAAAGAA-CAA
1 AAAAAAAAAGCAA
1031575 AAAGAAAAAAG-AA
1 AAA-AAAAAAGCAA
1031588 AAA
1 AAA
1031591 GGGACAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
12 17 0.47
13 19 0.53
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGCAA
Found at i:1031589 original size:12 final size:11
Alignment explanation
Indices: 1031532--1031590 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 11
1031522 TAAAAAGGGC
1031532 AAAAAG-AAAA
1 AAAAAGAAAAA
1031542 AAAAAGCAAAAA
1 AAAAAG-AAAAA
1031554 AAAAAGCAAAAA
1 AAAAAG-AAAAA
*
1031566 AAAGAACAAAAAGA
1 AAA-AA-GAAAA-A
1031580 AAAAAGAAAAA
1 AAAAAGAAAAA
1031591 GGGACAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
10 6 0.14
11 1 0.02
12 23 0.55
13 8 0.19
14 4 0.10
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:1031600 original size:32 final size:32
Alignment explanation
Indices: 1031523--1031600 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 32
1031513 TAATCAGAAT
*
1031523 AAAAAGGG-CAAAAAGAAAAAAAAAGCAAAAA
1 AAAAAGGGACAAAAAGAAAAAAAAAGAAAAAA
** * *
1031554 AAAAAGCAAAAAAAAG-AACAAAAAGAAAAAA
1 AAAAAGGGACAAAAAGAAAAAAAAAGAAAAAA
1031585 GAAAAAGGGACAAAAA
1 -AAAAAGGGACAAAAA
1031601 ACACATGCAA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
31 19 0.51
32 18 0.49
ACGTcount: A:0.78, C:0.06, G:0.15, T:0.00
Consensus pattern (32 bp):
AAAAAGGGACAAAAAGAAAAAAAAAGAAAAAA
Found at i:1032215 original size:21 final size:21
Alignment explanation
Indices: 1032191--1032230 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1032181 TACCCCATCA
1032191 AACC-TTTGAGCATCAAATGTC
1 AACCATTT-AGCATCAAATGTC
1032212 AACCATTTAGCATCAAATG
1 AACCATTTAGCATCAAATG
1032231 AACAAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (21 bp):
AACCATTTAGCATCAAATGTC
Found at i:1033291 original size:36 final size:36
Alignment explanation
Indices: 1033183--1033306 Score: 160
Period size: 36 Copynumber: 3.4 Consensus size: 36
1033173 ATTGAAAACA
* * *
1033183 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
* *
1033219 TTTCCCTTGGAACTAAGTTTT-GTCTCTCTTAAGACAG
1 TTTCCCTTGAAAC-AA-TTTTCGTCTCTCTTGAGACAG
* *
1033256 TTTCTCTTGAAACAATTTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
1033292 TTTCCCTTGAAACAA
1 TTTCCCTTGAAACAA
1033307 AACCTTTGAA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 4 0.05
36 41 0.55
37 27 0.36
38 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGACAG
Found at i:1033400 original size:67 final size:68
Alignment explanation
Indices: 1033282--1033438 Score: 198
Period size: 68 Copynumber: 2.4 Consensus size: 68
1033272 TTTCGTCTAT
* **
1033282 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTTCCCTAAAACA-AATTTT-TT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTTCCCTAAAACATAATTTTGTT
1033343 CTCC
66 -TCC
* *
1033347 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTA-TTTCCCTTAAAACATAATTTTGT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTTCCC-TAAAACATAATTTTGT
1033411 TTCC
65 TTCC
* *
1033415 CTTGAGACCGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
1033439 ACAGATATCT
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
65 17 0.22
66 8 0.10
67 22 0.28
68 30 0.38
69 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTTCCCTAAAACATAATTTTGTT
TCC
Found at i:1034210 original size:105 final size:105
Alignment explanation
Indices: 1034080--1034796 Score: 1072
Period size: 105 Copynumber: 7.0 Consensus size: 105
1034070 GCACTCGAGG
* * ** *
1034080 CAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
*
1034145 AGCCAATTTCAACTTCAC-ACGAAGGATATTGTACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
1034185 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAAC-ACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* * *
1034249 GCCAATTTCAACTTCATAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
1034289 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGT---CAAC-ACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* * *
1034350 ACCAATTTCAACTT--CAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
1034388 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCCAAC-ACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT-CAACAACAACTTCTCAATTTCAG
*
1034452 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* **
1034493 CAACGCAAGTTCAACTTCACGACGAAGGGA-C-CTGCTTGTCAACAACAACTTCCCAATCGCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1034556 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
1034596 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAGCAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1034661 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
1034701 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** *
1034761 TTCAATTTCAACTTCACGAC-AGAGGATATTGGACTC
66 GCCAATTTCAACTTCACAACGA-AGGATATTGGACTC
1034797 TGAACAATGC
Statistics
Matches: 572, Mismatches: 27, Indels: 31
0.91 0.04 0.05
Matches are distributed among these distances:
99 64 0.11
100 36 0.06
101 31 0.05
102 9 0.02
103 160 0.28
104 64 0.11
105 208 0.36
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:1034672 original size:208 final size:209
Alignment explanation
Indices: 1034080--1034796 Score: 1077
Period size: 208 Copynumber: 3.5 Consensus size: 209
1034070 GCACTCGAGG
* * * *
1034080 CAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCACTGCTTGTCAAC-AACAACTTCTCAATTTCAG
*
1034145 AGCCAATTTCAACTTCAC-ACGAAGGATATTGTACTCCAGACAACGCAAGTTCAACTTCACGACG
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* * *
1034209 AAGGGACCGCTGCCTGTCAACACAACTTCTCAATTTCAGAGCCAATTTCAACTTCATAATGAAGG
130 AAGGGACCGCTGCTTGTCAACACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
1034274 ATATTGGACTTCAGA
195 ATATTGGACTTCAGA
* *
1034289 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGT---CAAC-ACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCACTGCTTGTCAACAACAACTTCTCAATTTCAGA
* * *
1034350 ACCAATTTCAACTT--CAATGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1034413 AGGGACCGCTGCTTGTCCAACACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
131 AGGGACCGCTGCTTGT-CAACACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
1034478 ATATTGGACTTCAGA
195 ATATTGGACTTCAGA
* **
1034493 CAACGCAAGTTCAACTTCACGACGAAGGGA-C-CTGCTTGTCAACAACAACTTCCCAATCGCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCACTGCTTGTCAACAACAACTTCTCAATTTCAGA
1034556 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * *
1034621 AGGGACCGCTGCTTGTCAGCAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGG
131 AGGGACCGCTGCTTGTCAAC-ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
*
1034686 ATATTGGACTCCAGA
195 ATATTGGACTTCAGA
*
1034701 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCACTGCTTGTCAACAACAACTTCTCAATTTCAGA
** *
1034761 TTCAATTTCAACTTCACGAC-AGAGGATATTGGACTC
66 GCCAATTTCAACTTCACAACGA-AGGATATTGGACTC
1034797 TGAACAATGC
Statistics
Matches: 466, Mismatches: 30, Indels: 28
0.89 0.06 0.05
Matches are distributed among these distances:
202 8 0.02
203 60 0.13
204 121 0.26
205 42 0.09
206 28 0.06
207 4 0.01
208 151 0.32
209 38 0.08
210 14 0.03
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (209 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCACTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
AGGGACCGCTGCTTGTCAACACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
TATTGGACTTCAGA
Found at i:1037998 original size:59 final size:58
Alignment explanation
Indices: 1037884--1037998 Score: 140
Period size: 59 Copynumber: 2.0 Consensus size: 58
1037874 TCAGATGATG
* * * * *
1037884 ATTTTGTAACTTTTAATAGTTGAGGACTCAATAAAATAGCACCCTACAGTCGGGGATT
1 ATTTTGTAACTTTTAATAGTGGAGGACTCAACAAAACAACACCCTACAATCGGGGATT
* * * *
1037942 ATTTTGTAACTTTTGATAGTCGGAGGACTCAACAAAGCAACACCCTATAATTGGGGA
1 ATTTTGTAACTTTTAATAGT-GGAGGACTCAACAAAACAACACCCTACAATCGGGGA
1037999 ACCATTTGTA
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
58 19 0.40
59 28 0.60
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (58 bp):
ATTTTGTAACTTTTAATAGTGGAGGACTCAACAAAACAACACCCTACAATCGGGGATT
Found at i:1038853 original size:18 final size:17
Alignment explanation
Indices: 1038819--1038853 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1038809 TATTTGATAA
*
1038819 ATTAAAAAATAATTATT
1 ATTAAAAAATAAGTATT
1038836 ATTAAAAAAGTAAGTATT
1 ATTAAAAAA-TAAGTATT
1038854 TTATTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (17 bp):
ATTAAAAAATAAGTATT
Found at i:1040659 original size:90 final size:90
Alignment explanation
Indices: 1040506--1040688 Score: 366
Period size: 90 Copynumber: 2.0 Consensus size: 90
1040496 GAGAGGAGTA
1040506 AAGCGAGGTTAGCTGGAGAAGAACTTAGTTGGGAGCCTATGACCTTCCCGCCATTGCATGACACC
1 AAGCGAGGTTAGCTGGAGAAGAACTTAGTTGGGAGCCTATGACCTTCCCGCCATTGCATGACACC
1040571 TTTATGTTTGGAGGACATATGTTTC
66 TTTATGTTTGGAGGACATATGTTTC
1040596 AAGCGAGGTTAGCTGGAGAAGAACTTAGTTGGGAGCCTATGACCTTCCCGCCATTGCATGACACC
1 AAGCGAGGTTAGCTGGAGAAGAACTTAGTTGGGAGCCTATGACCTTCCCGCCATTGCATGACACC
1040661 TTTATGTTTGGAGGACATATGTTTC
66 TTTATGTTTGGAGGACATATGTTTC
1040686 AAG
1 AAG
1040689 GGAGTCAGCA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 93 1.00
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (90 bp):
AAGCGAGGTTAGCTGGAGAAGAACTTAGTTGGGAGCCTATGACCTTCCCGCCATTGCATGACACC
TTTATGTTTGGAGGACATATGTTTC
Found at i:1048715 original size:11 final size:10
Alignment explanation
Indices: 1048699--1048786 Score: 54
Period size: 11 Copynumber: 8.3 Consensus size: 10
1048689 AACAGGGGGG
1048699 AAGAAAAACAA
1 AAGAAAAA-AA
*
1048710 AAGAAAATACA
1 AAGAAAA-AAA
**
1048721 AA-AAAGGAA
1 AAGAAAAAAA
1048730 AA-AAAAAAA
1 AAGAAAAAAA
*
1048739 AGGAAAAAAA
1 AAGAAAAAAA
*
1048749 AGGAAAAAAATAA
1 A--AGAAAAA-AA
1048762 AAGAAAAACAA
1 AAGAAAAA-AA
1048773 AAGAATAAAAA
1 AAGAA-AAAAA
1048784 AAG
1 AAG
1048787 GGTTCAAGAT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
9 9 0.15
10 11 0.18
11 28 0.47
12 9 0.15
13 3 0.05
ACGTcount: A:0.81, C:0.03, G:0.12, T:0.03
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:1048733 original size:10 final size:10
Alignment explanation
Indices: 1048732--1048758 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1048722 AAAAGGAAAA
1048732 AAAAAAAAGG
1 AAAAAAAAGG
1048742 AAAAAAAAGG
1 AAAAAAAAGG
1048752 AAAAAAA
1 AAAAAAA
1048759 TAAAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGG
Found at i:1048737 original size:14 final size:14
Alignment explanation
Indices: 1048697--1048749 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
1048687 GAAACAGGGG
*
1048697 GGAAGAAAAACAAAA
1 GGAA-AAAAAAAAAA
*
1048712 -GAAAATACAAAAAA
1 GGAAAA-AAAAAAAA
1048726 GGAAAAAAAAAAAA
1 GGAAAAAAAAAAAA
1048740 GGAAAAAAAA
1 GGAAAAAAAA
1048750 GGAAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
13 2 0.06
14 26 0.79
15 5 0.15
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (14 bp):
GGAAAAAAAAAAAA
Found at i:1048747 original size:24 final size:23
Alignment explanation
Indices: 1048720--1048785 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 23
1048710 AAGAAAATAC
1048720 AAAAAAGGAAAAAAAAAAAAGGAA
1 AAAAAAGGAAAAAAAAAAAA-GAA
*
1048744 AAAAAAGGAAAAAAATAAAAGAA
1 AAAAAAGGAAAAAAAAAAAAGAA
* *
1048767 AAACAAAAGAATAAAAAAA
1 AAA-AAAGGAAAAAAAAAA
1048786 GGGTTCAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.16
24 31 0.84
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.03
Consensus pattern (23 bp):
AAAAAAGGAAAAAAAAAAAAGAA
Found at i:1048763 original size:14 final size:13
Alignment explanation
Indices: 1048697--1048774 Score: 58
Period size: 14 Copynumber: 5.8 Consensus size: 13
1048687 GAAACAGGGG
1048697 GGAAGAAAAACAAAA
1 GGAA-AAAAA-AAAA
1048712 -GAAAATACAAAAAA
1 GGAAAA-A-AAAAAA
1048726 GGAAAAAAAAAAAA
1 GG-AAAAAAAAAAA
1048740 GG---AAAAAAAA
1 GGAAAAAAAAAAA
1048750 GGAAAAAAATAAAA
1 GGAAAAAAA-AAAA
1048764 -GAAAAACAAAA
1 GGAAAAA-AAAA
1048775 GAATAAAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 20
0.73 0.00 0.27
Matches are distributed among these distances:
10 10 0.19
13 14 0.26
14 22 0.41
15 4 0.07
16 4 0.07
ACGTcount: A:0.79, C:0.04, G:0.14, T:0.03
Consensus pattern (13 bp):
GGAAAAAAAAAAA
Found at i:1048768 original size:19 final size:18
Alignment explanation
Indices: 1048728--1048785 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 18
1048718 ACAAAAAAGG
**
1048728 AAAAAA-AAAAAAGGAAA
1 AAAAAACAAAAAAATAAA
**
1048745 AAAAAGGAAAAAAATAAA
1 AAAAAACAAAAAAATAAA
*
1048763 AGAAAAACAAAAGAATAAA
1 A-AAAAACAAAAAAATAAA
1048782 AAAA
1 AAAA
1048786 GGGTTCAAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
17 5 0.15
18 13 0.39
19 15 0.45
ACGTcount: A:0.84, C:0.02, G:0.10, T:0.03
Consensus pattern (18 bp):
AAAAAACAAAAAAATAAA
Found at i:1050200 original size:64 final size:64
Alignment explanation
Indices: 1050132--1050292 Score: 178
Period size: 64 Copynumber: 2.5 Consensus size: 64
1050122 ATTTTTCAAG
* * * * *
1050132 GTGTATCGATGCACATGAAGTATATCGATGTACTCCTTTAAAATAAAAACATCGAATGCCATAA
1 GTGTATCGATGCACAAGAAGTACATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATAA
* * * * ** **
1050196 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATTAAAACATCGAAGGTGATTT
1 GTGTATCGATGCACAAGAAGTACATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATAA
* * *
1050260 GTGTACCGATGCACAAGTAGTGCATCGATGCAC
1 GTGTATCGATGCACAAGAAGTACATCGATGCAC
1050293 ACGTTATGGA
Statistics
Matches: 83, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 83 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (64 bp):
GTGTATCGATGCACAAGAAGTACATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATAA
Found at i:1052255 original size:2 final size:2
Alignment explanation
Indices: 1052248--1052289 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
1052238 TATTTAAATA
* * *
1052248 AT AT AT AT AT AT AT AT AT -T AT AC AA AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1052289 A
1 A
1052290 CGCTGAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1055362 original size:3 final size:3
Alignment explanation
Indices: 1055356--1055388 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1055346 TATGTAACAT
*
1055356 TAA TAA TAA TAT TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1055389 TTTAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1055371 original size:6 final size:6
Alignment explanation
Indices: 1055344--1055402 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
1055334 CTGTAAAAAA
* * * * *
1055344 AATATGT AACATT AATAAT AATATT AATAAT AATAAT AATA-T AATTTT
1 AATAT-T AATATT AATATT AATATT AATATT AATATT AATATT AATATT
1055392 AATA-T AATATT
1 AATATT AATATT
1055403 TATAATCCGG
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
5 9 0.21
6 30 0.70
7 4 0.09
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (6 bp):
AATATT
Found at i:1055794 original size:55 final size:55
Alignment explanation
Indices: 1055691--1055884 Score: 277
Period size: 55 Copynumber: 3.5 Consensus size: 55
1055681 TCCCTCTTTT
* * *
1055691 TTCAGGGAGTAT-AGAACTCAAAC-ATCTTCAACACTCGTGTCTGT-TCCCTATTCC
1 TTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGTGTCT-TCTCCCTATTCC
*
1055745 TTCAGAGAGTATAAGACTTGAACAATCTTCAACAATCGTGTCTTCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTTCTCCCTATTCC
* * * *
1055800 TTTAGAGAGTATAAGACTCGAACAATCTTCAACTATCATGTCTGCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTTCTCCCTATTCC
1055855 TTCAGAGAGTATAAGACTCGAACAATCTTC
1 TTCAGAGAGTATAAGACTCGAACAATCTTC
1055885 TTCTTATGGG
Statistics
Matches: 127, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
54 18 0.14
55 109 0.86
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.31
Consensus pattern (55 bp):
TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTTCTCCCTATTCC
Found at i:1055902 original size:55 final size:55
Alignment explanation
Indices: 1055735--1056050 Score: 233
Period size: 55 Copynumber: 5.8 Consensus size: 55
1055725 TCGTGTCTGT
* ** * *
1055735 TCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAAC-AAT-CGTGTCTTC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTTCTAATGGGT-TC-GC
* **
1055790 TCCCTATTCCTTTAGAGAGTATAAGACTCGAACAATCTTCAACTATCAT--G-TCTGC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTTCTA--ATGGGTTC-GC
*
1055845 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTTCTTATGGGTTCGC
1 TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTTCTAATGGGTTCGC
* * * * * * *
1055900 TCCCTCTTTCTTCAGAGAGTAT-AGAACTTGAA-TATCTTCTTCAAACGGGTTTGC
1 TCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCTTCTAATGGGTTCGC
* * * * * * *
1055954 TCCCTCTTTC-TCTAGGGAGTATAAAACTCGGAC-ATCTTCTTCAAACGGGTTCGC
1 TCCCTATTCCTTC-AGAGAGTATAAGACTCGAACAATCTTCTTCTAATGGGTTCGC
* * *
1056008 TCCCTCTTTC-TCTAGGGAGTAT-AGAACTCGAAC-ATCTTCTTCT
1 TCCCTATTCCTTC-AGAGAGTATAAG-ACTCGAACAATCTTCTTCT
1056051 GCTTCACTAC
Statistics
Matches: 227, Mismatches: 23, Indels: 23
0.83 0.08 0.08
Matches are distributed among these distances:
53 5 0.02
54 100 0.44
55 116 0.51
56 3 0.01
57 1 0.00
58 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (55 bp):
TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTTCTAATGGGTTCGC
Found at i:1055917 original size:110 final size:107
Alignment explanation
Indices: 1055669--1056046 Score: 361
Period size: 110 Copynumber: 3.5 Consensus size: 107
1055659 AGTATTTTGC
* * * *
1055669 CAATGGGTTCGTTCCCTCTTTTTTCAGGGAGTATAGAACTCAAACATCTTCAACACTCGTGTCTG
1 CAATGGGTTCGCTCCCTCTTTCTTCAGAGAGTATAGAACTCGAACATCTTCAACA-TCGTGTCTG
* * **
1055734 TTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAA
65 CTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTT
* * * * * *
1055777 CAAT-CGTGTCTTCTCCCTATTCCTTTAGAGAGTATA-AGACTCGAACAATCTTCAACTATCATG
1 CAATGGGT-TC-GCTCCCTCTTTCTTCAGAGAGTATAGA-ACTCGAAC-ATCTTCAAC-ATCGTG
1055840 TCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTT
61 TCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTT
* * * ** * * *
1055887 CTTATGGGTTCGCTCCCTCTTTCTTCAGAGAGTATAGAACTTGAATATCTTCTTCAAACGGGTTT
1 C-AATGGGTTCGCTCCCTCTTTCTTCAGAGAGTATAGAACTCGAACATCTTCAAC-ATCGTGTCT
* * * * *
1055952 GCTCCCTCTTTC-TCTAGGGAGTATAAAACTCGGAC-ATCTTCTT
64 GCTCCCTATTCCTTC-AGAGAGTATAAGACTCGAACAATCTTCTT
* *
1055995 CAAACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATAGAACTCGAACATCTTC
1 C-AATGGGTTCGCTCCCTCTTTCTTC-AGAGAGTATAGAACTCGAACATCTTC
1056047 TTCTGCTTCA
Statistics
Matches: 220, Mismatches: 40, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
107 4 0.02
108 60 0.27
109 64 0.29
110 84 0.38
111 6 0.03
112 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (107 bp):
CAATGGGTTCGCTCCCTCTTTCTTCAGAGAGTATAGAACTCGAACATCTTCAACATCGTGTCTGC
TCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCTT
Found at i:1055958 original size:54 final size:54
Alignment explanation
Indices: 1055858--1056049 Score: 253
Period size: 54 Copynumber: 3.5 Consensus size: 54
1055848 CTATTCCTTC
** *
1055858 AGAGAGTATA-AGACTCGAACAATCTTCTTCTTATGGGTTCGCTCCCTCTTTCT-T
1 AGAGAGTATAGA-ACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* * *
1055912 CAGAGAGTATAGAACTTGAATATCTTCTTCAAACGGGTTTGCTCCCTCTTTCTCT
1 -AGAGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* * *
1055967 AGGGAGTATAAAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGAGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
*
1056021 AGGGAGTATAGAACTCGAACATCTTCTTC
1 AGAGAGTATAGAACTCGAACATCTTCTTC
1056050 TGCTTCACTA
Statistics
Matches: 121, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
54 103 0.85
55 17 0.14
56 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (54 bp):
AGAGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
Found at i:1070146 original size:3 final size:3
Alignment explanation
Indices: 1070140--1070172 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1070130 TATGTAACAT
*
1070140 TAA TAA TAA TAT TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1070173 TTTAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1070155 original size:6 final size:6
Alignment explanation
Indices: 1070127--1070186 Score: 52
Period size: 6 Copynumber: 10.2 Consensus size: 6
1070117 TGTAAAAAAA
* * * * *
1070127 TAATAT GTAACAT TAATAA TAATAT TAATAA TAATAA TAATA- TAATTT
1 TAATAT -TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT
1070175 TAATA- TAATAT T
1 TAATAT TAATAT T
1070187 TATAATCCGG
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
5 9 0.20
6 30 0.68
7 5 0.11
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (6 bp):
TAATAT
Found at i:1076371 original size:10 final size:11
Alignment explanation
Indices: 1076340--1076375 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
1076330 AAACCAGTTC
1076340 AACCGCGGTTG
1 AACCGCGGTTG
1076351 AACCGCGGTTG
1 AACCGCGGTTG
1076362 AACC-CGGTTG
1 AACCGCGGTTG
1076372 AACC
1 AACC
1076376 AGTGAACCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.22, C:0.31, G:0.31, T:0.17
Consensus pattern (11 bp):
AACCGCGGTTG
Found at i:1081531 original size:21 final size:20
Alignment explanation
Indices: 1081502--1081540 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1081492 CTTTAAAAAA
1081502 TAATATTATAAATATATTTTG
1 TAATATTAT-AATATATTTTG
* *
1081523 TAATTTTATATTATATTT
1 TAATATTATAATATATTT
1081541 GATTTATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TAATATTATAATATATTTTG
Found at i:1082520 original size:24 final size:24
Alignment explanation
Indices: 1082468--1082523 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
1082458 TGAACGTTCG
*
1082468 GTTATGTTCGTTTATATGCATTTA
1 GTTATGTTCGTTTATATGCATTCA
* *
1082492 GTTATGTTCGTTTATGTGCGTTCA
1 GTTATGTTCGTTTATATGCATTCA
*
1082516 TTTATGTT
1 GTTATGTT
1082524 TAACCTAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.16, C:0.09, G:0.20, T:0.55
Consensus pattern (24 bp):
GTTATGTTCGTTTATATGCATTCA
Found at i:1083965 original size:16 final size:16
Alignment explanation
Indices: 1083940--1084004 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
1083930 CCAACGTTTA
1083940 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
1083956 TGTTCATTTATATTCG
1 TGTTCGTTTATGTTCG
*
1083972 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
1083988 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1084004 T
1 T
1084005 TTATTTATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.09, C:0.11, G:0.22, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1084095 original size:16 final size:16
Alignment explanation
Indices: 1084074--1084105 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1084064 AAAAAAAATT
1084074 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1084090 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1084106 CTTATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.12, G:0.25, T:0.56
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1084414 original size:2 final size:2
Alignment explanation
Indices: 1084407--1084432 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1084397 TTAGATATTC
1084407 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
1084433 CAATTGCTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1085629 original size:2 final size:2
Alignment explanation
Indices: 1085622--1085657 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1085612 TATACAAAGG
1085622 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1085658 GCGCTTGGCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1087343 original size:51 final size:51
Alignment explanation
Indices: 1087267--1087378 Score: 170
Period size: 51 Copynumber: 2.2 Consensus size: 51
1087257 TAGGGGTATA
* ** * *
1087267 GCGCGGTGCAGGGGTCGCGTCTTTGCTTTAAGTCTGACACAATTATGCAAG
1 GCGCGGTGCAGAGACCGCGCCTTTGCTTTAACTCTGACACAATTATGCAAG
*
1087318 GCGCGGTGCAGAGACCGCGCCTTTGCTTTAACTCTGAGACAATTATGCAAG
1 GCGCGGTGCAGAGACCGCGCCTTTGCTTTAACTCTGACACAATTATGCAAG
1087369 GCGCGGTGCA
1 GCGCGGTGCA
1087379 TTGGTCGCGA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.24
Consensus pattern (51 bp):
GCGCGGTGCAGAGACCGCGCCTTTGCTTTAACTCTGACACAATTATGCAAG
Found at i:1089036 original size:2 final size:2
Alignment explanation
Indices: 1089029--1089054 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1089019 TTAGATATTC
1089029 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
1089055 CAATTGCTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1090249 original size:2 final size:2
Alignment explanation
Indices: 1090242--1090273 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1090232 TATACAAAGG
1090242 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1090274 GCGCTTGGCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1091957 original size:51 final size:51
Alignment explanation
Indices: 1091881--1091992 Score: 170
Period size: 51 Copynumber: 2.2 Consensus size: 51
1091871 TAGGGGTATA
* ** * *
1091881 GCGCGGTGCAGGGGTCGCGTCTTTGCTTTAAGTCTGACACAATTATGCAAG
1 GCGCGGTGCAGAGACCGCGCCTTTGCTTTAACTCTGACACAATTATGCAAG
*
1091932 GCGCGGTGCAGAGACCGCGCCTTTGCTTTAACTCTGAGACAATTATGCAAG
1 GCGCGGTGCAGAGACCGCGCCTTTGCTTTAACTCTGACACAATTATGCAAG
1091983 GCGCGGTGCA
1 GCGCGGTGCA
1091993 TTGGTCGCGA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.24
Consensus pattern (51 bp):
GCGCGGTGCAGAGACCGCGCCTTTGCTTTAACTCTGACACAATTATGCAAG
Found at i:1098050 original size:17 final size:17
Alignment explanation
Indices: 1098030--1098094 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 17
1098020 ATTAATTAAA
1098030 TAAAATAATAAAATAAT
1 TAAAATAATAAAATAAT
* *
1098047 TAAAACAATTAAATAA-
1 TAAAATAATAAAATAAT
*
1098063 -AATACTAATAAAAT-AT
1 TAA-AATAATAAAATAAT
*
1098079 TAAAAAAAATAAAATA
1 T-AAAATAATAAAATA
1098095 TACCTTAAGT
Statistics
Matches: 36, Mismatches: 7, Indels: 9
0.69 0.13 0.17
Matches are distributed among these distances:
15 3 0.08
16 8 0.22
17 23 0.64
18 2 0.06
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAATAATAAAATAAT
Found at i:1098057 original size:30 final size:32
Alignment explanation
Indices: 1098023--1098083 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
1098013 CAAAAAAATT
1098023 AATTAAAT-AAA-A-TAATAAAATAATTAAAAC
1 AATTAAATAAAATACTAATAAAAT-ATTAAAAC
1098053 AATTAAATAAAATACTAATAAAATATTAAAA
1 AATTAAATAAAATACTAATAAAATATTAAAA
1098084 AAAATAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 8 0.29
31 3 0.11
32 8 0.29
33 9 0.32
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (32 bp):
AATTAAATAAAATACTAATAAAATATTAAAAC
Found at i:1099956 original size:59 final size:60
Alignment explanation
Indices: 1099834--1099961 Score: 140
Period size: 59 Copynumber: 2.2 Consensus size: 60
1099824 AACATAATGA
* * ** * *
1099834 ATAGTCG-GTGACCATTTTATAACTTTTATTAATCGATTGACTCAACAAAGTAATTTATT
1 ATAGTCGAGAGACCATTTTATAACTTTTAATAATCGAAAGACTCAACAAAATAATTCATT
*
1099893 ATAGTCGAGAGACCATTTTATAACTTTTAAT-ATC-AAAGAACTTAACAAAATAATATCA-T
1 ATAGTCGAGAGACCATTTTATAACTTTTAATAATCGAAAG-ACTCAACAAAATAAT-TCATT
1099952 ATAGTC-AGAG
1 ATAGTCGAGAG
1099962 TATCATTTAT
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
58 6 0.10
59 30 0.51
60 23 0.39
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (60 bp):
ATAGTCGAGAGACCATTTTATAACTTTTAATAATCGAAAGACTCAACAAAATAATTCATT
Found at i:1110088 original size:37 final size:37
Alignment explanation
Indices: 1110033--1110104 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
1110023 AGAGTCGATG
* *
1110033 GTTTACCTATGTCTTTCGGGACATATGGGCAGTTATA
1 GTTTACCTATGTCTTTCGGAACATATGGACAGTTATA
1110070 GTTTACCTATGT-TCTTCGGAACATATGGACAGTTA
1 GTTTACCTATGTCT-TTCGGAACATATGGACAGTTA
1110105 CATAGGTCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 1 0.03
37 31 0.97
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.38
Consensus pattern (37 bp):
GTTTACCTATGTCTTTCGGAACATATGGACAGTTATA
Found at i:1120096 original size:25 final size:27
Alignment explanation
Indices: 1120063--1120132 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 27
1120053 TGACAATAAT
* *
1120063 AATACATATGAATATTTA-AT-GTATA
1 AATAAATATGAATATTTATATACTATA
* *
1120088 AATAAATATATAAT-TTTATATACTATC
1 AATAAATAT-GAATATTTATATACTATA
1120115 AATAAAT-TGAATATTTAT
1 AATAAATATGAATATTTAT
1120133 CCAAAAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
25 15 0.42
26 11 0.31
27 10 0.28
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (27 bp):
AATAAATATGAATATTTATATACTATA
Found at i:1121031 original size:18 final size:18
Alignment explanation
Indices: 1120997--1121035 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
1120987 TTAGAGTCGA
1120997 ATATAAATAATAATAAATT
1 ATATAAATAAT-ATAAATT
1121016 ATATAATATAAT-TAAATT
1 ATATAA-ATAATATAAATT
1121034 AT
1 AT
1121036 TAAGTAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 6 0.32
20 5 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATAAATAATATAAATT
Found at i:1123416 original size:30 final size:30
Alignment explanation
Indices: 1123382--1123444 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
1123372 TTATTTCATT
*
1123382 TAAATA-AATAATATAACTTTAAAAATTAAA
1 TAAATATAATAAAAT-ACTTTAAAAATTAAA
** *
1123412 TAAATATTTTAAAATATTTTAAAAATTAAA
1 TAAATATAATAAAATACTTTAAAAATTAAA
1123442 TAA
1 TAA
1123445 TATTATTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (30 bp):
TAAATATAATAAAATACTTTAAAAATTAAA
Found at i:1129783 original size:18 final size:18
Alignment explanation
Indices: 1129756--1129803 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1129746 GCAATATAAT
* *
1129756 TTAAATAATATAAATTAA
1 TTAAAAAATATAAACTAA
*
1129774 TTAAAAAATA-AAACTGA
1 TTAAAAAATATAAACTAA
1129791 TTAAAATAATATA
1 TTAAAA-AATATA
1129804 TATTGATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 11 0.44
18 13 0.52
19 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
TTAAAAAATATAAACTAA
Found at i:1134089 original size:55 final size:55
Alignment explanation
Indices: 1134028--1134317 Score: 372
Period size: 55 Copynumber: 5.3 Consensus size: 55
1134018 TTCTTTCAAG
* * *
1134028 GAGTATAAGACTCGAACAATCTTCAACAAATGGGTCCGCTCTCTATTCCTTGAAA
1 GAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGA
* * * *
1134083 GAGTATAGGACTTGAATAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTGAGA
1 GAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGA
* *
1134138 GAGTATAGGACTCAAACAATCTTCATA-AAACGGGTCCGCTCTCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCA-ACAAACGGGTCCGCTCTCTATTCCTTCAGA
* *
1134193 GAGTAT-AGAACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATTCCATCAGA
1 GAGTATAAG-ACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGA
* ** * *
1134248 GAGTAT-AGAACTCGAACAATCTTCAACAAACGAGTTTGCTCCCTATTCCATCAGA
1 GAGTATAAG-ACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGA
1134303 GAGTAT-AGAACTCGA
1 GAGTATAAG-ACTCGA
1134318 TCTTCATAAA
Statistics
Matches: 216, Mismatches: 16, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
54 2 0.01
55 213 0.99
56 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.26
Consensus pattern (55 bp):
GAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGA
Found at i:1135668 original size:7 final size:7
Alignment explanation
Indices: 1135656--1135786 Score: 120
Period size: 7 Copynumber: 19.7 Consensus size: 7
1135646 TTTTCTCTAT
1135656 TTTTTCA
1 TTTTTCA
1135663 TTTTTCA
1 TTTTTCA
1135670 TTTTTCA
1 TTTTTCA
1135677 TTTTTC-
1 TTTTTCA
*
1135683 TCTTTCA
1 TTTTTCA
1135690 TTTTTCA
1 TTTTTCA
1135697 TTTTTCA
1 TTTTTCA
1135704 TTTTTTTCA
1 --TTTTTCA
1135713 TTTTTCA
1 TTTTTCA
1135720 -TTTT--
1 TTTTTCA
*
1135724 TTTCTCA
1 TTTTTCA
1135731 TTTTTCA
1 TTTTTCA
*
1135738 TTTTT-T
1 TTTTTCA
*
1135744 TTTTTCC
1 TTTTTCA
1135751 TTTTT-A
1 TTTTTCA
1135757 TTTTT--
1 TTTTTCA
1135762 TTTTT-A
1 TTTTTCA
*
1135768 TTTTTTTA
1 -TTTTTCA
1135776 TTTTT-A
1 TTTTTCA
1135782 TTTTT
1 TTTTT
1135787 TCATCAGGCG
Statistics
Matches: 107, Mismatches: 7, Indels: 21
0.79 0.05 0.16
Matches are distributed among these distances:
5 8 0.07
6 25 0.23
7 66 0.62
8 1 0.01
9 7 0.07
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTCA
Found at i:1135691 original size:27 final size:23
Alignment explanation
Indices: 1135655--1135724 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 23
1135645 TTTTTCTCTA
1135655 TTTTTTCATTTTTCATTTTTCATTT
1 TTTTTTCATTTTTCATTTTTCA--T
1135680 TTCTCTTTCATTTTTCATTTTTCAT
1 TT-T-TTTCATTTTTCATTTTTCAT
1135705 TTTTTTCATTTTTCATTTTT
1 TTTTTTCATTTTTCATTTTT
1135725 TTCTCATTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
23 17 0.40
24 1 0.02
25 5 0.12
26 1 0.02
27 19 0.44
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTTTCATTTTTCATTTTTCAT
Found at i:1135699 original size:34 final size:32
Alignment explanation
Indices: 1135640--1135772 Score: 132
Period size: 34 Copynumber: 4.1 Consensus size: 32
1135630 TGAACCCTTC
*
1135640 TTTT-ATTTTTCTCTATTTTTTCATTTTTCAT
1 TTTTCATTTTTCTCTTTTTTTTCATTTTTCAT
1135671 TTTTCATTTTTCTCTTTCATTTTTCATTTTTCATTT
1 TTTTCATTTTTCTCTTT--TTTTTCATTTTTCA--T
*
1135707 TTTTCATTTTTCAT-TTTTTTCTCATTTTTCAT
1 TTTTCATTTTTC-TCTTTTTTTTCATTTTTCAT
* * *
1135739 TTTT-TTTTTTC-CTTTTTATTT-TTTTTTTAT
1 TTTTCATTTTTCTCTTTTT-TTTCATTTTTCAT
1135769 TTTT
1 TTTT
1135773 TTATTTTTAT
Statistics
Matches: 88, Mismatches: 6, Indels: 17
0.79 0.05 0.15
Matches are distributed among these distances:
30 16 0.18
31 12 0.14
32 16 0.18
34 27 0.31
36 16 0.18
37 1 0.01
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.77
Consensus pattern (32 bp):
TTTTCATTTTTCTCTTTTTTTTCATTTTTCAT
Found at i:1135731 original size:27 final size:26
Alignment explanation
Indices: 1135663--1135787 Score: 77
Period size: 27 Copynumber: 4.8 Consensus size: 26
1135653 TATTTTTTCA
1135663 TTTTTCATTTTTCATTTTTCTCTTTCA--
1 TTTTTCATTTTTCA-TTTT-T-TTTCATT
1135690 TTTTTCATTTTTCA-TTTTTTTCATT
1 TTTTTCATTTTTCATTTTTTTTCATT
* *
1135715 TTTCATT-TTTTTCTCATTTTTCATTT-TTT
1 TTT--TTCATTTT-TCATTTTT--TTTCATT
* *
1135744 TTTTTCCTTTTT-ATTTTTTTTTTATT
1 TTTTTCATTTTTCA-TTTTTTTTCATT
1135770 TTTTT-ATTTTT-ATTTTTT
1 TTTTTCATTTTTCATTTTTT
1135788 CATCAGGCGA
Statistics
Matches: 82, Mismatches: 5, Indels: 25
0.73 0.04 0.22
Matches are distributed among these distances:
23 5 0.06
24 7 0.09
25 15 0.18
26 12 0.15
27 27 0.33
28 8 0.10
29 5 0.06
30 3 0.04
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTTCATTTTTCATTTTTTTTCATT
Found at i:1135748 original size:25 final size:24
Alignment explanation
Indices: 1135706--1135787 Score: 66
Period size: 25 Copynumber: 3.5 Consensus size: 24
1135696 ATTTTTCATT
**
1135706 TTTTTCATTTTTCATTTTTTTCTCA
1 TTTTT-ATTTTTTTTTTTTTTCTCA
1135731 TTTTTCA---TTTTTTTTTTTC-C-
1 TTTTT-ATTTTTTTTTTTTTTCTCA
* *
1135751 TTTTTATTTTTTTTTTATTTTTTTA
1 TTTTTATTTTTTTTTT-TTTTCTCA
1135776 TTTTTATTTTTT
1 TTTTTATTTTTT
1135788 CATCAGGCGA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
19 1 0.02
20 5 0.11
21 1 0.02
22 17 0.36
23 4 0.09
25 19 0.40
ACGTcount: A:0.10, C:0.09, G:0.00, T:0.82
Consensus pattern (24 bp):
TTTTTATTTTTTTTTTTTTTCTCA
Found at i:1135760 original size:18 final size:19
Alignment explanation
Indices: 1135663--1135786 Score: 119
Period size: 20 Copynumber: 6.3 Consensus size: 19
1135653 TATTTTTTCA
1135663 TTTTTCATTTTTCATTTTT
1 TTTTTCATTTTTCATTTTT
*
1135682 CTCTTTCATTTTTCATTTTTCATT
1 -TTTTTCATTTTTCA--TTT--TT
1135706 TTTTTCATTTTTCA-TTTT
1 TTTTTCATTTTTCATTTTT
*
1135724 TTTCTCATTTTTCATTTTTT
1 TTTTTCATTTTTCA-TTTTT
*
1135744 TTTTTCCTTTTT-ATTTTT
1 TTTTTCATTTTTCATTTTT
*
1135762 TTTTT-ATTTTTTTATTTTT
1 TTTTTCA-TTTTTCATTTTT
1135781 ATTTTT
1 -TTTTT
1135787 TCATCAGGCG
Statistics
Matches: 89, Mismatches: 6, Indels: 18
0.79 0.05 0.16
Matches are distributed among these distances:
18 30 0.34
19 7 0.08
20 34 0.38
22 3 0.03
23 13 0.15
24 2 0.02
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTCATTTTTCATTTTT
Found at i:1135762 original size:61 final size:59
Alignment explanation
Indices: 1135663--1135787 Score: 146
Period size: 61 Copynumber: 2.1 Consensus size: 59
1135653 TATTTTTTCA
1135663 TTTTTCATTTTTCATTTTTCTCTTTCATTTTTCA-TTTTTCATTTTTTTCATTTTTCATTT
1 TTTTTCATTTTTCATTTTTCTCTTTCATTTTTCATTTTTTCATTTTTTT-ATTTTT-ATTT
* * * *
1135723 TTTTCTCATTTTTCATTTTTTTTTTTCCTTTTT-ATTTTTTTTTTATTTTTTTATTTTTATTT
1 TTTT-TCATTTTTCATTTTTCTCTTTCATTTTTCA---TTTTTTCATTTTTTTATTTTTATTT
1135785 TTT
1 TTT
1135788 CATCAGGCGA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
60 5 0.09
61 25 0.45
62 7 0.12
63 6 0.11
64 13 0.23
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.78
Consensus pattern (59 bp):
TTTTTCATTTTTCATTTTTCTCTTTCATTTTTCATTTTTTCATTTTTTTATTTTTATTT
Found at i:1146169 original size:22 final size:22
Alignment explanation
Indices: 1146144--1146188 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1146134 ATGTTTTGTT
1146144 ATTTTAAATAAAA-ATAAAATTA
1 ATTTTAAATAAAACA-AAAATTA
*
1146166 ATTTTAATTAAAACAAAAATTA
1 ATTTTAAATAAAACAAAAATTA
1146188 A
1 A
1146189 GGTCTGCGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
ATTTTAAATAAAACAAAAATTA
Found at i:1151112 original size:20 final size:21
Alignment explanation
Indices: 1151062--1151118 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
1151052 ACATAGATTT
*
1151062 TGTCCCGAAGGACCACATATA
1 TGTCCCGAAGGACCACATAGA
1151083 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
1151104 TGT-CCGAAGGACCAC
1 TGTCCCGAAGGACCAC
1151119 TCCTTAAGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 12 0.34
21 23 0.66
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.16
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAGA
Found at i:1153505 original size:23 final size:22
Alignment explanation
Indices: 1153453--1153505 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
1153443 TCTGGGATTA
* **
1153453 ATTTTTTTATTTGATTTTTTTT
1 ATTTTTTTAATTGATTTTTTGG
*
1153475 AGTGTTTTTAATTGATTTTTTGGG
1 A-TTTTTTTAATTGATTTTTT-GG
1153499 ATTTTTT
1 ATTTTTT
1153506 GTTTTTTTGG
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 1 0.04
23 22 0.92
24 1 0.04
ACGTcount: A:0.15, C:0.00, G:0.13, T:0.72
Consensus pattern (22 bp):
ATTTTTTTAATTGATTTTTTGG
Found at i:1153746 original size:3 final size:3
Alignment explanation
Indices: 1153738--1153799 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
1153728 TAATATGTAA
1153738 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1153786 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
1153800 AATGGTTTCG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1156070 original size:5 final size:5
Alignment explanation
Indices: 1156060--1156084 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1156050 GGAATGACCG
1156060 AAACA AAACA AAACA AAACA AAACA
1 AAACA AAACA AAACA AAACA AAACA
1156085 GAGTGTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACA
Found at i:1156242 original size:13 final size:13
Alignment explanation
Indices: 1156224--1156248 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1156214 ACTTCAGGTG
1156224 AAAACCTAATCCT
1 AAAACCTAATCCT
1156237 AAAACCTAATCC
1 AAAACCTAATCC
1156249 CACTTTTGTT
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:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAACCTAATCCT
Found at i:1163095 original size:21 final size:21
Alignment explanation
Indices: 1163071--1163118 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
1163061 TATTTTATTA
1163071 ATGAATATGGAAAACATTACT
1 ATGAATATGGAAAACATTACT
1163092 ATGAATATGGAAAACATTACT
1 ATGAATATGGAAAACATTACT
1163113 ATGAAT
1 ATGAAT
1163119 GAAAAGAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.29
Consensus pattern (21 bp):
ATGAATATGGAAAACATTACT
Found at i:1168341 original size:19 final size:20
Alignment explanation
Indices: 1168325--1168372 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
1168315 GTTTTCTTTG
*
1168325 TTATTTTTCTCTTTCTTCTT
1 TTATTTTTCTCTTTCTTATT
1168345 TTA-TTTTCTCTTT-TTATT
1 TTATTTTTCTCTTTCTTATT
1168363 TTATTTTTCT
1 TTATTTTTCT
1168373 TTCTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.27
19 16 0.62
20 3 0.12
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (20 bp):
TTATTTTTCTCTTTCTTATT
Found at i:1168388 original size:18 final size:19
Alignment explanation
Indices: 1168329--1168387 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 19
1168319 TCTTTGTTAT
*
1168329 TTTTCTCTTTCTTCTTTTA
1 TTTTCTCTTTCTTATTTTA
1168348 TTTTCTCTTT-TTATTTTA
1 TTTTCTCTTTCTTATTTTA
* *
1168366 TTTT-TCTTTCTTTTTTTC
1 TTTTCTCTTTCTTATTTTA
1168384 TTTT
1 TTTT
1168388 TTATATATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
17 5 0.14
18 21 0.58
19 10 0.28
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTCTCTTTCTTATTTTA
Found at i:1168396 original size:29 final size:33
Alignment explanation
Indices: 1168348--1168413 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 33
1168338 TCTTCTTTTA
* *
1168348 TTTTCTCTTTTTATTTTA-TTTTTC-TTTCTTT
1 TTTTCTCTTTTTATTATATTTTTTCTTTTATTT
1168379 TTTTCT-TTTTTA-TATATTTTTTCTTTTATTT
1 TTTTCTCTTTTTATTATATTTTTTCTTTTATTT
1168410 TTTT
1 TTTT
1168414 GTCCTGAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 3 0.10
30 12 0.39
31 16 0.52
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (33 bp):
TTTTCTCTTTTTATTATATTTTTTCTTTTATTT
Found at i:1170453 original size:15 final size:15
Alignment explanation
Indices: 1170420--1170468 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
1170410 GTATAATAAA
*
1170420 TTCTACCCAAACATACT
1 TTCTACCC--ACATGCT
*
1170437 TTCTACTCACATGCT
1 TTCTACCCACATGCT
1170452 TTCTACCCACATGCT
1 TTCTACCCACATGCT
1170467 TT
1 TT
1170469 GTTATTCACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 22 0.76
17 7 0.24
ACGTcount: A:0.24, C:0.35, G:0.04, T:0.37
Consensus pattern (15 bp):
TTCTACCCACATGCT
Found at i:1171500 original size:5 final size:5
Alignment explanation
Indices: 1171490--1171534 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
1171480 TTGTCTTTGC
* *
1171490 ATTTA ATTTA ATTTA ATTTA ATTAA AGTTCAA ATTTA ATTTA ATT
1 ATTTA ATTTA ATTTA ATTTA ATTTA A-TT-TA ATTTA ATTTA ATT
1171535 CAATATCCCC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
5 29 0.81
6 4 0.11
7 3 0.08
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (5 bp):
ATTTA
Found at i:1176902 original size:12 final size:12
Alignment explanation
Indices: 1176885--1176909 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1176875 ACTATTCATA
1176885 TGAATAGTAACC
1 TGAATAGTAACC
1176897 TGAATAGTAACC
1 TGAATAGTAACC
1176909 T
1 T
1176910 CGCAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (12 bp):
TGAATAGTAACC
Done.