Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008654.1 Hibiscus syriacus cultivar Beakdansim tig00111648_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: 3533819
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 18
Found at i:1422900 original size:9 final size:9
Alignment explanation
Indices: 1422886--1422910 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1422876 AACTCCCTTT
1422886 TTTTTTTCA
1 TTTTTTTCA
1422895 TTTTTTTCA
1 TTTTTTTCA
1422904 TTTTTTT
1 TTTTTTT
1422911 TGTTCATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:1423162 original size:1 final size:1
Alignment explanation
Indices: 1423156--1423206 Score: 57
Period size: 1 Copynumber: 51.0 Consensus size: 1
1423146 GTAAGGTCTC
* * * **
1423156 TTTTTTTTTTTTTTTTTCTTTCTGTTTTTCCTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1423207 CGAAAACCAC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.08, G:0.02, T:0.90
Consensus pattern (1 bp):
T
Found at i:1423570 original size:52 final size:52
Alignment explanation
Indices: 1423508--1423612 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
1423498 GATGGCGACG
1423508 GATACTGTTGATGGCTAGGATTTTAGAAAACTCTAAAATCAATTGGCCTAGA
1 GATACTGTTGATGGCTAGGATTTTAGAAAACTCTAAAATCAATTGGCCTAGA
1423560 GATACTGTTGATGGCTAGGATTTTAGAAAACTCTAAAATCAATTGGCCTAGA
1 GATACTGTTGATGGCTAGGATTTTAGAAAACTCTAAAATCAATTGGCCTAGA
1423612 G
1 G
1423613 TTTCACATTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.30
Consensus pattern (52 bp):
GATACTGTTGATGGCTAGGATTTTAGAAAACTCTAAAATCAATTGGCCTAGA
Found at i:1423764 original size:3 final size:3
Alignment explanation
Indices: 1423713--1423744 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1423703 TAATAATAAA
1423713 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1423745 TAATAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1424371 original size:259 final size:258
Alignment explanation
Indices: 1423902--1424474 Score: 905
Period size: 259 Copynumber: 2.2 Consensus size: 258
1423892 TGAAAAATGT
* * * *
1423902 CCCGAAGGATTTAATCATCATGCTTGAAAGACTTACTGATGACCCAAAGGACTTACTAATTTGGA
1 CCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTGGA
* * *
1423967 AATAGTTTACTAGGTAAGAAACTTTGGAAATTGCTTTCTTACTTTTCAATAATTTCATTTTATGA
66 AATAGTTTACTAAGTAAGAAACTTTGGAAATTACTTTCTTACTTTTCAAAAATTTCATTTTATGA
*
1424032 AAATACTAAATGAGAAACTTTGAAAATTGCTTTATCATTTTTCAAATTATCTTATGAAAGCATCT
131 AAATACTAAATGAAAAACTTTGAAAATTGCTTTATCATTTTTCAAATTATCTTATGAAAGCATCT
*
1424097 TTCCCAAAGGTCTTATAGATGGCCCGAAGGACTTATCATATCGCTCGAAAGACTGGCAGATGA
196 TTCCCAAAGGTCTTATAGATGGCCCGAAGGACTTATCATATCACTCGAAAGACTGGCAGATGA
* *
1424160 CCTGAAAGATTTAATTATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGG
1 CCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAA-TTTGG
*
1424225 AAATAGTTTACTAAGTAAGAAACTTTGGAAATTACTTTCTTACTTTTCAAAAATTTCATTTTTTG
65 AAATAGTTTACTAAGTAAGAAACTTTGGAAATTACTTTCTTACTTTTCAAAAATTTCATTTTATG
*
1424290 AAAATACTAAATGAAAAACTTTGAAAATTGCTTTCTCATTTTTCAAATTAT-TATATGAAAGCAT
130 AAAATACTAAATGAAAAACTTTGAAAATTGCTTTATCATTTTTCAAATTATCT-TATGAAAGCAT
* * * * * *
1424354 CTTTCCCAAATGTCTTATAGATGGCCTGAAGGACTTATCATCTTACTCGACAGACTGTCAGATGA
194 CTTTCCCAAAGGTCTTATAGATGGCCCGAAGGACTTATCATATCACTCGAAAGACTGGCAGATGA
* ** * *
1424419 CCCGAAGGATTTTGTCATCATGCTCGAAAGACTTATTGATGGACCAAAGGACTTAC
1 CCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTAC
1424475 TAAATAAGAA
Statistics
Matches: 287, Mismatches: 26, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
258 54 0.19
259 233 0.81
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (258 bp):
CCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTGGA
AATAGTTTACTAAGTAAGAAACTTTGGAAATTACTTTCTTACTTTTCAAAAATTTCATTTTATGA
AAATACTAAATGAAAAACTTTGAAAATTGCTTTATCATTTTTCAAATTATCTTATGAAAGCATCT
TTCCCAAAGGTCTTATAGATGGCCCGAAGGACTTATCATATCACTCGAAAGACTGGCAGATGA
Found at i:1434069 original size:2 final size:2
Alignment explanation
Indices: 1434062--1434094 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1434052 CTATTAACAA
1434062 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1434095 ACTTAGGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1437044 original size:4 final size:4
Alignment explanation
Indices: 1437035--1438111 Score: 1941
Period size: 4 Copynumber: 271.8 Consensus size: 4
1437025 TCCATTCTTT
1437035 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CAT- CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1437082 CATC CATC CAT- CATC CATC CATC CATC CATC CAT- CATC CATC CA-C
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1437127 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1437175 CATC CAT- CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1437222 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1437270 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
* * * *
1437318 CATC CATC CGTC CGTC CGTC CGTC CATC CATC CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
*
1437366 CATC CATC CATC CATC CATC CGTC CATC CATC CATC CATC CATCC CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CAT-C CATC
1437415 CATC CATC CA-C CATC CATC CATCC CATC CATC CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CAT-C CATC CATC CATC CATC CATC CATC
1437463 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1437511 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1437559 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1437607 CATC CATC CATC CATC CATC CATC CATC CAT- CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1437654 CATC CATC CATC CATCC CATC CATC CATC CATC CATC CATC CATC CATC
1 CATC CATC CATC CAT-C CATC CATC CATC CATC CATC CATC CATC CATC
1437703 CATC CAT- CATC CATC CATC CATC CATC CATC CATC CAT- CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1437749 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1437797 CATC CATC C-TC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1437844 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1437892 CATC CATC CATC CAT- CATC CATC CATC CATC CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1437939 CATC CATC CATC CATC CATC CATC CATCC CATC CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CAT-C CATC CATC CATC CATC CATC
1437988 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
1438036 CATC CATC CATC CATC CATC CATC CATC C--C CATC CATCC CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CAT-C CATC CATC
* *
1438083 CATC CATT CATC CAT- CAT- CATT CATC CAT
1 CATC CATC CATC CATC CATC CATC CATC CAT
1438112 TCATTCATTC
Statistics
Matches: 1047, Mismatches: 7, Indels: 38
0.96 0.01 0.03
Matches are distributed among these distances:
2 2 0.00
3 39 0.04
4 986 0.94
5 20 0.02
ACGTcount: A:0.25, C:0.50, G:0.00, T:0.25
Consensus pattern (4 bp):
CATC
Found at i:1440872 original size:16 final size:17
Alignment explanation
Indices: 1440851--1440882 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1440841 CGATCTTATC
1440851 TGAAAA-TTCAGATATA
1 TGAAAATTTCAGATATA
1440867 TGAAAATTTCAGATAT
1 TGAAAATTTCAGATAT
1440883 CTAAAATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.34
Consensus pattern (17 bp):
TGAAAATTTCAGATATA
Found at i:1440888 original size:16 final size:17
Alignment explanation
Indices: 1440847--1440889 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
1440837 GATCCGATCT
1440847 TATCTGAAAA-TTCAGA
1 TATCTGAAAATTTCAGA
*
1440863 TATATGAAAATTTCAGA
1 TATCTGAAAATTTCAGA
1440880 TATCT-AAAAT
1 TATCTGAAAAT
1440890 AGTGATTCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (17 bp):
TATCTGAAAATTTCAGA
Found at i:1441047 original size:2 final size:2
Alignment explanation
Indices: 1441036--1441065 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1441026 TACCTCTACC
1441036 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1441066 ATTACCCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1448215 original size:16 final size:16
Alignment explanation
Indices: 1448194--1448226 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1448184 AATTCTCTGA
1448194 AATCCCGGTCTAGGGT
1 AATCCCGGTCTAGGGT
1448210 AATCCCGGTCTAGGGT
1 AATCCCGGTCTAGGGT
1448226 A
1 A
1448227 TCAAAATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.30, T:0.24
Consensus pattern (16 bp):
AATCCCGGTCTAGGGT
Found at i:1451073 original size:11 final size:12
Alignment explanation
Indices: 1451052--1451082 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
1451042 TTGGGGCATG
1451052 GTTTAGGGTTTA
1 GTTTAGGGTTTA
1451064 GTTT-GGGTTTA
1 GTTTAGGGTTTA
1451075 GTTTAGGG
1 GTTTAGGG
1451083 CCTAATTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.13, C:0.00, G:0.39, T:0.48
Consensus pattern (12 bp):
GTTTAGGGTTTA
Found at i:1451092 original size:35 final size:35
Alignment explanation
Indices: 1451029--1451105 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
1451019 GTCGAGCCTG
* ** *
1451029 GTTTGGGTTTAATTTGGGGCATGGTTTAGGGTTTA
1 GTTTGGGTTTAATTTAGGGCATAATTTAGGGCTTA
* *
1451064 GTTTGGGTTTAGTTTAGGGCCTAATTTAGGGCTTA
1 GTTTGGGTTTAATTTAGGGCATAATTTAGGGCTTA
*
1451099 ATTTGGG
1 GTTTGGG
1451106 CCCAATTTGT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.16, C:0.05, G:0.35, T:0.44
Consensus pattern (35 bp):
GTTTGGGTTTAATTTAGGGCATAATTTAGGGCTTA
Found at i:1451093 original size:12 final size:12
Alignment explanation
Indices: 1451076--1451113 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1451066 TTGGGTTTAG
1451076 TTTAGGGCCTAA
1 TTTAGGGCCTAA
*
1451088 TTTAGGGCTTAA
1 TTTAGGGCCTAA
*
1451100 TTT-GGGCCCAA
1 TTTAGGGCCTAA
1451111 TTT
1 TTT
1451114 GTAAATGAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (12 bp):
TTTAGGGCCTAA
Found at i:1451770 original size:5 final size:5
Alignment explanation
Indices: 1451760--1451812 Score: 61
Period size: 5 Copynumber: 9.8 Consensus size: 5
1451750 TTTGCATGCA
*
1451760 AAAAT AAAAT AACAT AAAAT AAAAT AAAAT AATAAT AATAAAT AATAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT -A-AAAT AA-AAT
1451809 AAAA
1 AAAA
1451813 ATTAGAAACC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
5 28 0.67
6 9 0.21
7 4 0.10
8 1 0.02
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:1451802 original size:13 final size:13
Alignment explanation
Indices: 1451777--1451814 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1451767 AATAACATAA
1451777 AATAA-AATAAAAT
1 AATAATAAT-AAAT
1451790 AATAATAATAAAT
1 AATAATAATAAAT
1451803 AATAATAA-AAAT
1 AATAATAATAAAT
1451815 TAGAAACCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 4 0.17
13 17 0.71
14 3 0.12
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AATAATAATAAAT
Found at i:1453386 original size:44 final size:46
Alignment explanation
Indices: 1453273--1453768 Score: 139
Period size: 45 Copynumber: 11.0 Consensus size: 46
1453263 TAGGTTGAAG
* *
1453273 AAGG-TTGACTCCTTTTCCCGAGAAAGTAAAAAATGACATCATTAA
1 AAGGATTGACTCCTTTTCGCGAGAAAGTAAAAAATGACATCACTAA
* * *
1453318 AAGGA-TAACACCTCTTT-GCGAGAAAG-AAAAAATGGCATCACTAA
1 AAGGATTGACTCCT-TTTCGCGAGAAAGTAAAAAATGACATCACTAA
* * * * *
1453362 AA-GATTGACTCCTTTTCGCAAGAAATTCAAGAATGA-ACTCAGTAAA
1 AAGGATTGACTCCTTTTCGCGAGAAAGTAAAAAATGACA-TCACT-AA
* * * * * * *
1453408 AAGG--TGACACATCATT-GTGAGAAAGTCAAGAA-GAACAACACTAA
1 AAGGATTGACTCCT-TTTCGCGAGAAAGTAAAAAATG-ACATCACTAA
* * * * * * *
1453452 AAGGA-TGACTCCTCTTCACGAGAAAGTCAAGAATAACAACACTGA
1 AAGGATTGACTCCTTTTCGCGAGAAAGTAAAAAATGACATCACTAA
* * ** * * * * *
1453497 AA-GATTGACTCATTCTCATGAGAAAGTCAAGAAGGAAAACACTAA
1 AAGGATTGACTCCTTTTCGCGAGAAAGTAAAAAATGACATCACTAA
* * * * * * * *
1453542 AA-CATCGACTCCTCTTT-GTGAGAAAATCAAGAATAACAACACTGAA
1 AAGGATTGACTCCT-TTTCGCGAGAAAGTAAAAAATGACATCACT-AA
* ** * * * * *
1453588 AA--ATTGACTCCTCTTCATGAGAAAGTCAAGAATAACAACACTGA
1 AAGGATTGACTCCTTTTCGCGAGAAAGTAAAAAATGACATCACTAA
* * * ** * * * *
1453632 AA-GTTTTACTCCTCTTCATGAGAAATTCAAGAATAACATCACTAA
1 AAGGATTGACTCCTTTTCGCGAGAAAGTAAAAAATGACATCACTAA
* * * * * * * *
1453677 AA-GATCGACTCCTCTTCACGAGAAAGTCAAGAATAACAACACTGA
1 AAGGATTGACTCCTTTTCGCGAGAAAGTAAAAAATGACATCACTAA
* * ** * * *
1453722 AA-GATTTACTCCTCTTCATGAGAAAGTCAAGAATAACATCACTAA
1 AAGGATTGACTCCTTTTCGCGAGAAAGTAAAAAATGACATCACTAA
1453767 AA
1 AA
1453769 AGTTAACTTC
Statistics
Matches: 365, Mismatches: 67, Indels: 38
0.78 0.14 0.08
Matches are distributed among these distances:
43 5 0.01
44 48 0.13
45 295 0.81
46 16 0.04
47 1 0.00
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.22
Consensus pattern (46 bp):
AAGGATTGACTCCTTTTCGCGAGAAAGTAAAAAATGACATCACTAA
Found at i:1453453 original size:45 final size:44
Alignment explanation
Indices: 1453382--1453975 Score: 332
Period size: 45 Copynumber: 13.2 Consensus size: 44
1453372 CCTTTTCGCA
* * * * * *
1453382 AGAAATTCAAGAATGAAC-TCAGTAAAAAGGTGACACATCATTGTG
1 AGAAAGTCAAGAA-GAACAACACTAAAAAGGTGACTCCTC-TTATG
*
1453427 AGAAAGTCAAGAAGAACAACACT-AAAAGGATGACTCCTCTTCACG
1 AGAAAGTCAAGAAGAACAACACTAAAAAGG-TGACTCCTCTT-ATG
* * * * *
1453472 AGAAAGTCAAGAATAACAACACT-GAAAGATTGACTCATTCTCATG
1 AGAAAGTCAAGAAGAACAACACTAAAAAG-GTGACTC-CTCTTATG
*
1453517 AGAAAGTCAAGAAGGAA-AACACTAAAACA--TCGACTCCTCTTTGTG
1 AGAAAGTCAAGAA-GAACAACACTAAAA-AGGT-GACTCCTC-TTATG
* * *
1453562 AGAAAATCAAGAATAACAACACTGAAAAA-TTGACTCCTCTTCATG
1 AGAAAGTCAAGAAGAACAACACT-AAAAAGGTGACTCCTCTT-ATG
* * * *
1453607 AGAAAGTCAAGAATAACAACACT-GAAAGTTTTACTCCTCTTCATG
1 AGAAAGTCAAGAAGAACAACACTAAAAAG-GTGACTCCTCTT-ATG
* * * * *
1453652 AGAAATTCAAGAATAACATCACT-AAAAGATCGACTCCTCTTCACG
1 AGAAAGTCAAGAAGAACAACACTAAAAAGGT-GACTCCTCTT-ATG
* * * *
1453697 AGAAAGTCAAGAATAACAACACT-GAAAGATTTACTCCTCTTCATG
1 AGAAAGTCAAGAAGAACAACACTAAAAAG-GTGACTCCTCTT-ATG
* * * * *
1453742 AGAAAGTCAAGAATAACATCACTAAAAAGTTAACTTCTCCTTATG
1 AGAAAGTCAAGAAGAACAACACTAAAAAGGTGACTCCT-CTTATG
* * ** **
1453787 AGAAAGTCAAGAAGGACAATACTAAAAAATTGACTCCTCTTCGCG
1 AGAAAGTCAAGAAGAACAACACTAAAAAGGTGACTCCTCTT-ATG
* * ** * * *
1453832 AGAAAGTCAAGAATAAAAACA-TTGAAAGATTGATTCATCTTCATG
1 AGAAAGTCAAGAAGAACAACACTAAAAAG-GTGACTCCTCTT-ATG
* * * * * * * * *
1453877 AAAAATTCAATAAGGACAACACT-AAAAGATAAACTCATCCTCACG
1 AGAAAGTCAAGAAGAACAACACTAAAAAGGT-GACTCCT-CTTATG
* * *
1453922 AGAAAGTCAAGAATAACAACACT-GAAAGAGTGACTCCTCTTCACG
1 AGAAAGTCAAGAAGAACAACACTAAAAAG-GTGACTCCTCTT-ATG
1453967 AGAAAGTCA
1 AGAAAGTCA
1453976 CGTTGAGGTT
Statistics
Matches: 440, Mismatches: 82, Indels: 54
0.76 0.14 0.09
Matches are distributed among these distances:
43 3 0.01
44 30 0.07
45 382 0.87
46 24 0.05
47 1 0.00
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (44 bp):
AGAAAGTCAAGAAGAACAACACTAAAAAGGTGACTCCTCTTATG
Found at i:1453476 original size:90 final size:89
Alignment explanation
Indices: 1453356--1453975 Score: 547
Period size: 90 Copynumber: 6.9 Consensus size: 89
1453346 AAAATGGCAT
* * * * * * *
1453356 CACTAAAAGATTGACTCCTTTTCGCAAGAAATTCAAGAATGAAC-TCAGTAAAAAGGTGACACAT
1 CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAT-AACATCACTAAAAAGTTGACTCAT
*
1453420 CATTGTGAGAAAGTCAAGAAGAACAA
65 C-TTATGAGAAAGTCAAGAAGAACAA
* *
1453446 CACTAAAAGGA-TGACTCCTCTTCACGAGAAAGTCAAGAATAACAACACT-GAAAGATTGACTCA
1 CACTAAAA-GATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATCACTAAAAAG-TTGACTCA
*
1453509 TTCTCATGAGAAAGTCAAGAAGGAA-AA
64 -TCTTATGAGAAAGTCAAGAA-GAACAA
* * *** * * *
1453536 CACTAAAACATCGACTCCTCTTTGTGAGAAAATCAAGAATAACAACACTGAAAAA-TTGACTCCT
1 CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATCACT-AAAAAGTTGACTCAT
*
1453600 CTTCATGAGAAAGTCAAGAATAACAA
65 CTT-ATGAGAAAGTCAAGAAGAACAA
* * * * * * *
1453626 CACTGAAAGTTTTACTCCTCTTCATGAGAAATTCAAGAATAACATCACT-AAAAGATCGACTCCT
1 CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATCACTAAAAAG-TTGACTCAT
* *
1453690 CTTCACGAGAAAGTCAAGAATAACAA
65 CTT-ATGAGAAAGTCAAGAAGAACAA
* * * *
1453716 CACTGAAAGATTTACTCCTCTTCATGAGAAAGTCAAGAATAACATCACTAAAAAGTTAACTTC-T
1 CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATCACTAAAAAGTTGAC-TCAT
*
1453780 CCTTATGAGAAAGTCAAGAAGGACAA
65 -CTTATGAGAAAGTCAAGAAGAACAA
* * * * * ** *
1453806 TACTAAAAAATTGACTCCTCTTCGCGAGAAAGTCAAGAATAAAAACA-TTGAAAGATTGATTCAT
1 CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATCACTAAAAAG-TTGACTCAT
* * * *
1453870 CTTCATGAAAAATTCAATAAGGACAA
65 CTT-ATGAGAAAGTCAAGAAGAACAA
** * * * * *
1453896 CACTAAAAGATAAACTCATCCTCACGAGAAAGTCAAGAATAACAACACTGAAAGAG-TGACTCCT
1 CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATCACT-AAAAAGTTGACTCAT
*
1453960 CTTCACGAGAAAGTCA
65 CTT-ATGAGAAAGTCA
1453976 CGTTGAGGTT
Statistics
Matches: 440, Mismatches: 70, Indels: 40
0.80 0.13 0.07
Matches are distributed among these distances:
88 4 0.01
89 23 0.05
90 389 0.88
91 18 0.04
92 6 0.01
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.22
Consensus pattern (89 bp):
CACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATCACTAAAAAGTTGACTCATC
TTATGAGAAAGTCAAGAAGAACAA
Found at i:1453543 original size:135 final size:134
Alignment explanation
Indices: 1453426--1453975 Score: 585
Period size: 135 Copynumber: 4.1 Consensus size: 134
1453416 ACATCATTGT
* *
1453426 GAGAAAGTCAAGAAGAACAACACTAAAAGGA-TGACTCCTCTTCACGAGAAAGTCAAGAATAACA
1 GAGAAAGTCAAGAATAACAACACTAAAA-GATTGACTCCTCTTCATGAGAAAGTCAAGAATAACA
* *
1453490 ACACTGAAAGATTGACTCATTCTCATGAGAAAGTCAAGAAGGAAAACACTAAAACA-TCGACTCC
65 ACACTGAAAGATTAACTC-TCCTCATGAGAAAGTCAAGAAGGAAAACACTAAAA-AGTCGACTCC
* *
1453554 TCTTTGT
128 TCTTCGC
*
1453561 GAGAAAATCAAGAATAACAACACTGAAAA-ATTGACTCCTCTTCATGAGAAAGTCAAGAATAACA
1 GAGAAAGTCAAGAATAACAACACT-AAAAGATTGACTCCTCTTCATGAGAAAGTCAAGAATAACA
* * * * * *
1453625 ACACTGAAAGTTTTACTCCTCTTCATGAGAAATTCAAGAA-TAACATCACT-AAAAGATCGACTC
65 ACACTGAAAGATTAACT-CTCCTCATGAGAAAGTCAAGAAGGAA-AACACTAAAAAG-TCGACTC
*
1453688 CTCTTCAC
127 CTCTTCGC
* * *
1453696 GAGAAAGTCAAGAATAACAACACTGAAAGATTTACTCCTCTTCATGAGAAAGTCAAGAATAACAT
1 GAGAAAGTCAAGAATAACAACACTAAAAGATTGACTCCTCTTCATGAGAAAGTCAAGAATAACAA
* * * * * *
1453761 CACT-AAAAAGTTAACTTCTCCTTATGAGAAAGTCAAGAAGGACAATACTAAAAAATTGACTCCT
66 CACTGAAAGA-TTAAC-TCTCCTCATGAGAAAGTCAAGAAGGAAAACACTAAAAAGTCGACTCCT
1453825 CTTCGC
129 CTTCGC
* * * * * * * * **
1453831 GAGAAAGTCAAGAATAAAAACATTGAAAGATTGATTCATCTTCATGAAAAATTCAATAAGGACAA
1 GAGAAAGTCAAGAATAACAACACTAAAAGATTGACTCCTCTTCATGAGAAAGTCAAGAATAACAA
* * * * *
1453896 CACTAAAAGATAAACTCATCCTCACGAGAAAGTCAAGAA-TAACAACACTGAAAGAGT-GACTCC
66 CACTGAAAGATTAACTC-TCCTCATGAGAAAGTCAAGAAGGAA-AACACT-AAAAAGTCGACTCC
*
1453959 TCTTCAC
128 TCTTCGC
1453966 GAGAAAGTCA
1 GAGAAAGTCA
1453976 CGTTGAGGTT
Statistics
Matches: 349, Mismatches: 51, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
133 1 0.00
134 15 0.04
135 313 0.90
136 20 0.06
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.22
Consensus pattern (134 bp):
GAGAAAGTCAAGAATAACAACACTAAAAGATTGACTCCTCTTCATGAGAAAGTCAAGAATAACAA
CACTGAAAGATTAACTCTCCTCATGAGAAAGTCAAGAAGGAAAACACTAAAAAGTCGACTCCTCT
TCGC
Found at i:1454069 original size:37 final size:37
Alignment explanation
Indices: 1453984--1454081 Score: 99
Period size: 37 Copynumber: 2.6 Consensus size: 37
1453974 CACGTTGAGG
* **
1453984 TTTCTAGAGAAACAATCCTACGAATGACTAAAATGAA
1 TTTCTAGAGAAACAATCCTAAGAATGACTAAAACAAA
* **
1454021 TTAT-TAGAGAAACGATCCTAAGAATGACTCTAACAAA
1 TT-TCTAGAGAAACAATCCTAAGAATGACTAAAACAAA
* * *
1454058 TTTCTACAGAAACCATCATAAGAA
1 TTTCTAGAGAAACAATCCTAAGAA
1454082 GATCTAGAGT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
36 1 0.02
37 48 0.96
38 1 0.02
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.24
Consensus pattern (37 bp):
TTTCTAGAGAAACAATCCTAAGAATGACTAAAACAAA
Found at i:1455433 original size:20 final size:21
Alignment explanation
Indices: 1455408--1455451 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
1455398 ATATGTTCTC
*
1455408 TTTCTTCTTATTTTTTTT-TT
1 TTTCTTCTCATTTTTTTTGTT
1455428 TTTCTTCTCATTTTTTTTGTT
1 TTTCTTCTCATTTTTTTTGTT
1455449 TTT
1 TTT
1455452 GCTCTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.05, C:0.11, G:0.02, T:0.82
Consensus pattern (21 bp):
TTTCTTCTCATTTTTTTTGTT
Found at i:1462875 original size:30 final size:34
Alignment explanation
Indices: 1462839--1462917 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 34
1462829 AAGTTTAATT
1462839 TTTTAATTTAATTACT-TAACTTT-AAA-TTA-C
1 TTTTAATTTAATTACTCTAACTTTCAAATTTATC
* * *
1462869 TTTTAATGTAATCACTCTAACTTTCAAATTTATT
1 TTTTAATTTAATTACTCTAACTTTCAAATTTATC
1462903 TTTTATATTTAATTA
1 TTTTA-ATTTAATTA
1462918 TATATTAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 14 0.36
31 7 0.18
32 3 0.08
33 3 0.08
34 5 0.13
35 7 0.18
ACGTcount: A:0.34, C:0.10, G:0.01, T:0.54
Consensus pattern (34 bp):
TTTTAATTTAATTACTCTAACTTTCAAATTTATC
Found at i:1465279 original size:6 final size:6
Alignment explanation
Indices: 1465268--1465293 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1465258 TTACCGTTTT
1465268 CCGTCC CCGTCC CCGTCC CCGTCC CC
1 CCGTCC CCGTCC CCGTCC CCGTCC CC
1465294 ATATCCGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.69, G:0.15, T:0.15
Consensus pattern (6 bp):
CCGTCC
Found at i:1466958 original size:15 final size:14
Alignment explanation
Indices: 1466938--1467000 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 14
1466928 GGGGATCTTG
1466938 TTAATTTTATTATT
1 TTAATTTTATTATT
*
1466952 ATTAATTTTGTTATT
1 -TTAATTTTATTATT
1466967 TCT-ATTATTATTATTT
1 T-TAATT-TTATTA-TT
1466983 TTATATTTATATTATT
1 TTA-ATTT-TATTATT
1466999 TT
1 TT
1467001 TTATTTATGC
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
14 4 0.10
15 20 0.50
16 8 0.20
17 8 0.20
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (14 bp):
TTAATTTTATTATT
Found at i:1466962 original size:24 final size:24
Alignment explanation
Indices: 1466935--1466998 Score: 80
Period size: 23 Copynumber: 2.7 Consensus size: 24
1466925 CCCGGGGATC
1466935 TTGTTAATTT-TATTATTATTAATT
1 TTGTT-ATTTCTATTATTATTAATT
1466959 TTGTTATTTCTATTATTATT-ATT
1 TTGTTATTTCTATTATTATTAATT
*
1466982 TT-TATATTTATATTATT
1 TTGT-TATTTCTATTATT
1466999 TTTTATTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
22 1 0.03
23 21 0.57
24 15 0.41
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.69
Consensus pattern (24 bp):
TTGTTATTTCTATTATTATTAATT
Found at i:1466995 original size:17 final size:16
Alignment explanation
Indices: 1466975--1467008 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
1466965 TTTCTATTAT
1466975 TATTATTTTTATATTTA
1 TATTATTTTT-TATTTA
1466992 TATTATTTTTTATTTA
1 TATTATTTTTTATTTA
1467008 T
1 T
1467009 GCATACCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTATTTTTTATTTA
Found at i:1467004 original size:24 final size:23
Alignment explanation
Indices: 1466935--1467006 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 23
1466925 CCCGGGGATC
*
1466935 TTGTTAATTTTATTATTATTAATT
1 TTGTT-ATTTTATTATTATTTATT
1466959 TTGTTATTTCTATTATTA-TTATT
1 TTGTTATTT-TATTATTATTTATT
*
1466982 TT-TATATTTATATTATTTTTTATT
1 TTGT-TATTT-TATTATTATTTATT
1467006 T
1 T
1467007 ATGCATACCT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
22 1 0.02
23 22 0.52
24 19 0.45
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (23 bp):
TTGTTATTTTATTATTATTTATT
Found at i:1467469 original size:25 final size:24
Alignment explanation
Indices: 1467418--1467478 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
1467408 GATCTTGTTA
*
1467418 ATTTTATTATTATTAATTATTGTT
1 ATTTTATTATTATTAATTATTATT
*
1467442 ATTTCTATTATTATT-ATTTTTATAT
1 ATTT-TATTATTATTAATTATTAT-T
1467467 ATTTATATTATT
1 ATTT-TATTATT
1467479 TTTTATTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.31
25 22 0.69
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (24 bp):
ATTTTATTATTATTAATTATTATT
Found at i:1468751 original size:108 final size:108
Alignment explanation
Indices: 1468473--1468714 Score: 328
Period size: 108 Copynumber: 2.2 Consensus size: 108
1468463 ATCACACATA
** * * * * *
1468473 AGTCCCCAATAGTTTAGTGCGTTTTTGCATGTTGGTCACCTGCTA-GGACCAAGGT-TGTTATTT
1 AGTCCCCCTTAGTTTAGCGTGTTTTTGCATGTTGATCACATG-TAGGGACCAAAGTAT-TTATTT
* * * *
1468536 ACCCGTTTTCATGCATGTTATGTATTTTTGGGATATTTTTTGTTT
64 ACCCATTTTCATGCATGTTATGTATTTTTGGAATATTTTCTATTT
1468581 AGTCCCCCTTAGTTTAGCGTGTTTTTGCATGTTGATCACATGTAGGGACCAAAGTATTTATTTAC
1 AGTCCCCCTTAGTTTAGCGTGTTTTTGCATGTTGATCACATGTAGGGACCAAAGTATTTATTTAC
1468646 CCATTTTCATGCATGTTATGTATTTTTGGAATATTTTCTATTT
66 CCATTTTCATGCATGTTATGTATTTTTGGAATATTTTCTATTT
*
1468689 AGTCCCCCTT-GTTTAGGCTTGTTTTT
1 AGTCCCCCTTAGTTTA-GCGTGTTTTT
1468715 TATTTTGGTC
Statistics
Matches: 119, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
107 7 0.06
108 111 0.93
109 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.46
Consensus pattern (108 bp):
AGTCCCCCTTAGTTTAGCGTGTTTTTGCATGTTGATCACATGTAGGGACCAAAGTATTTATTTAC
CCATTTTCATGCATGTTATGTATTTTTGGAATATTTTCTATTT
Found at i:1469092 original size:23 final size:23
Alignment explanation
Indices: 1469066--1469114 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1469056 TCTAGTCATA
* *
1469066 TTTGCATTTTG-TTTTATTTTAAT
1 TTTGCATGTTGCTTTTATGTT-AT
1469089 TTTGCATGTTGCTTTTATGTTAT
1 TTTGCATGTTGCTTTTATGTTAT
1469112 TTT
1 TTT
1469115 ATTTTAGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.14, C:0.06, G:0.12, T:0.67
Consensus pattern (23 bp):
TTTGCATGTTGCTTTTATGTTAT
Found at i:1470269 original size:15 final size:15
Alignment explanation
Indices: 1470245--1470278 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1470235 AGATGAGATC
* *
1470245 TTTTAGAATTCATTT
1 TTTTAAAATTAATTT
1470260 TTTTAAAATTAATTT
1 TTTTAAAATTAATTT
1470275 TTTT
1 TTTT
1470279 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (15 bp):
TTTTAAAATTAATTT
Found at i:1480973 original size:46 final size:46
Alignment explanation
Indices: 1480921--1481045 Score: 225
Period size: 46 Copynumber: 2.7 Consensus size: 46
1480911 ATAAACTGAC
*
1480921 AAATAAGCTTACAAGCTTATGGGATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
1480967 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
1481013 AAATAAAGCTTACGAGCTTATGGGA-TAAATGGT
1 AAAT-AAGCTTACGAGCTTATGGGATTAAATGGT
1481046 GAGAAATTTT
Statistics
Matches: 77, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
46 57 0.74
47 20 0.26
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.31
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
Found at i:1483557 original size:20 final size:21
Alignment explanation
Indices: 1483510--1483550 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1483500 TATAGCCCTA
*
1483510 AAAAGCTGTAAGGACCGTTTC
1 AAAAGCTGTAAGGACCATTTC
1483531 AAAAGCTGTAAGGA-CATTTC
1 AAAAGCTGTAAGGACCATTTC
1483551 GACAGCTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (21 bp):
AAAAGCTGTAAGGACCATTTC
Found at i:1487714 original size:21 final size:22
Alignment explanation
Indices: 1487690--1487730 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
1487680 AGAGTCAAAC
1487690 AAACAA-TAAGAAGAA-AAATGA
1 AAACAACT-AGAAGAAGAAATGA
1487711 AAACAACTAGAAGAAGAAAT
1 AAACAACTAGAAGAAGAAAT
1487731 TGGGGCTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.68, C:0.07, G:0.15, T:0.10
Consensus pattern (22 bp):
AAACAACTAGAAGAAGAAATGA
Found at i:1493338 original size:23 final size:22
Alignment explanation
Indices: 1493290--1493338 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1493280 ACGGAATGTC
1493290 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
1493311 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
1493334 AAGGA
1 AAGGA
1493339 AAATTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:1494976 original size:101 final size:102
Alignment explanation
Indices: 1494723--1495000 Score: 522
Period size: 101 Copynumber: 2.7 Consensus size: 102
1494713 GTTGAGGGTC
*
1494723 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACATATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1494788 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAG-ATATGTATATGATTCTTAAGGAATGA
1494826 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1494891 TTGATCCCTAG-TATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGATATGTATATGATTCTTAAGGAATGA
*
1494927 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1494992 TTGATCCCT
66 TTGATCCCT
1495001 GTGAGACACA
Statistics
Matches: 173, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
101 98 0.57
103 75 0.43
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (102 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGATATGTATATGATTCTTAAGGAATGA
Found at i:1495007 original size:22 final size:22
Alignment explanation
Indices: 1494979--1495022 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1494969 GTGAAGTCTG
1494979 GTGAGACACATACTTGATCCCT
1 GTGAGACACATACTTGATCCCT
1495001 GTGAGACACATACTTGATCCCT
1 GTGAGACACATACTTGATCCCT
1495023 AGTATATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (22 bp):
GTGAGACACATACTTGATCCCT
Found at i:1495144 original size:23 final size:23
Alignment explanation
Indices: 1495079--1495136 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
1495069 ATTATTATAT
1495079 GGCACTACGGTGCAACTCTACGC
1 GGCACTACGGTGCAACTCTACGC
*
1495102 TGCACTACGGTGCAACTCTACGC
1 GGCACTACGGTGCAACTCTACGC
1495125 GGCACTACGGTG
1 GGCACTACGGTG
1495137 TAATTCTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.33, G:0.28, T:0.19
Consensus pattern (23 bp):
GGCACTACGGTGCAACTCTACGC
Found at i:1495151 original size:23 final size:23
Alignment explanation
Indices: 1495078--1495153 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
1495068 CATTATTATA
1495078 TGGCACTACGGTGCAACTCTACG
1 TGGCACTACGGTGCAACTCTACG
1495101 CT-GCACTACGGTGCAACTCTACG
1 -TGGCACTACGGTGCAACTCTACG
* * * *
1495124 CGGCACTACGGTGTAATTCTATG
1 TGGCACTACGGTGCAACTCTACG
1495147 TGGCACT
1 TGGCACT
1495154 TCGGCGCATT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 45 0.98
24 1 0.02
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (23 bp):
TGGCACTACGGTGCAACTCTACG
Found at i:1503230 original size:40 final size:40
Alignment explanation
Indices: 1503174--1503253 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
1503164 TCAAAGCACA
* * *
1503174 AAAGAACCCAGCCTTCAAGTTCTGTACGTAGTTATATTTT
1 AAAGAACCCAACCTTCAAATTCTGTACGTAGTTACATTTT
* *
1503214 AAAGAACCCAATCTTCAAATTCTGTATGTAGTTACATTTT
1 AAAGAACCCAACCTTCAAATTCTGTACGTAGTTACATTTT
1503254 TAAGGGAAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (40 bp):
AAAGAACCCAACCTTCAAATTCTGTACGTAGTTACATTTT
Found at i:1504030 original size:87 final size:87
Alignment explanation
Indices: 1503876--1504053 Score: 286
Period size: 87 Copynumber: 2.0 Consensus size: 87
1503866 TAACTTATTA
*
1503876 TATCATTAAGTTTAAACATGTACTCTATAAATATATGACATTTTCTTACATTTAAATATTTACTT
1 TATCATTAAGGTTAAACA-GTACTCTATAAATATATGACATTTTCTTACATTTAAATATTTACTT
**
1503941 AATAATGACAATTTAGTTAGTAG
65 AATAAAAACAATTTAGTTAGTAG
* *
1503964 TATCATTAAGGTTAAACA-TACTCTATAAATATATGATATTTTTGTTACATTTAAATATTTACTT
1 TATCATTAAGGTTAAACAGTACTCTATAAATATATGACA-TTTTCTTACATTTAAATATTTACTT
1504028 AATAAAAACAATTTAGTTAGTAG
65 AATAAAAACAATTTAGTTAGTAG
1504051 TAT
1 TAT
1504054 GTTTCGTTGT
Statistics
Matches: 84, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
86 19 0.23
87 48 0.57
88 17 0.20
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (87 bp):
TATCATTAAGGTTAAACAGTACTCTATAAATATATGACATTTTCTTACATTTAAATATTTACTTA
ATAAAAACAATTTAGTTAGTAG
Found at i:1507808 original size:50 final size:50
Alignment explanation
Indices: 1507703--1507809 Score: 112
Period size: 50 Copynumber: 2.1 Consensus size: 50
1507693 TCACACTCTA
* * * * * *
1507703 ATTTGCCTTTTCATTGCGACTAGGAGGGTTGGTTAGAGCCATATTATCATG
1 ATTTTCCTTTTCATTGAGACTAGGAGGGCTCGATAGAG-CACATTATCATG
1507754 -TTTTCCTTTTCATTGAGACTAGGAGGGCTCGATAG-G-ACATTATCCATCG
1 ATTTTCCTTTTCATTGAGACTAGGAGGGCTCGATAGAGCACATTAT-CAT-G
1507803 ATTTTCC
1 ATTTTCC
1507810 ACATATCATC
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
47 6 0.13
48 3 0.06
49 2 0.04
50 36 0.77
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (50 bp):
ATTTTCCTTTTCATTGAGACTAGGAGGGCTCGATAGAGCACATTATCATG
Found at i:1507932 original size:12 final size:12
Alignment explanation
Indices: 1507904--1507938 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1507894 TTAAATTCCT
*
1507904 TTATCTT-TTTT
1 TTATCTTGTTTC
1507915 TTATCTTGTTTC
1 TTATCTTGTTTC
1507927 TTATCTTGTTTC
1 TTATCTTGTTTC
1507939 CAACATCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.09, C:0.14, G:0.06, T:0.71
Consensus pattern (12 bp):
TTATCTTGTTTC
Found at i:1514526 original size:11 final size:11
Alignment explanation
Indices: 1514481--1514522 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
1514471 TTCCAATTCC
1514481 TTTATCTT-TT
1 TTTATCTTGTT
1514491 ATTTATCTTGTT
1 -TTTATCTTGTT
*
1514503 TTAATCTTGTT
1 TTTATCTTGTT
1514514 TCTTATCTT
1 T-TTATCTT
1514523 TTTCCAGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 19 0.70
12 8 0.30
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (11 bp):
TTTATCTTGTT
Found at i:1515129 original size:15 final size:14
Alignment explanation
Indices: 1515087--1515129 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
1515077 GTTCACCTAT
*
1515087 AACCAAACAACAAC
1 AACCAAACAATAAC
*
1515101 AAGCAAATCAATAAC
1 AACCAAA-CAATAAC
1515116 AACCAAACATATAA
1 AACCAAACA-ATAA
1515130 ATAACAAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.63, C:0.26, G:0.02, T:0.09
Consensus pattern (14 bp):
AACCAAACAATAAC
Found at i:1516078 original size:20 final size:19
Alignment explanation
Indices: 1516053--1516105 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
1516043 AGATTCAATC
*
1516053 AGTATCTATACCAAAGGGA
1 AGTATCAATACCAAAGGGA
*
1516072 GAGTATCAATACCGAAGGGA
1 -AGTATCAATACCAAAGGGA
*
1516092 AGGTATCGATACCA
1 A-GTATCAATACCA
1516106 TTTCAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.19
Consensus pattern (19 bp):
AGTATCAATACCAAAGGGA
Found at i:1516196 original size:22 final size:22
Alignment explanation
Indices: 1516145--1516208 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
1516135 TACCATATCA
**
1516145 TAGTATCAATACCATAGTATTG
1 TAGTATCGGTACCATAGTATTG
1516167 TAGTATCGGTACCATAGTATTG
1 TAGTATCGGTACCATAGTATTG
*
1516189 TAGTATCGGTACCATGGTAT
1 TAGTATCGGTACCATAGTAT
1516209 GGGTATCGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (22 bp):
TAGTATCGGTACCATAGTATTG
Found at i:1516618 original size:55 final size:54
Alignment explanation
Indices: 1516558--1516699 Score: 196
Period size: 55 Copynumber: 2.6 Consensus size: 54
1516548 TAAGCATGCA
* **
1516558 AAAATTAAGAAATCCATACTAAGTGTATGGATTTCGGTATTTCCACTTTGTGTAC
1 AAAATTAAGAAAT-CATACTAAGTGTATGAATTTCGGTATGACCACTTTGTGTAC
* * *
1516613 AAAATTAAAAAATTCATACTAAGTGTATGAATTTCTGTATGAGCACTTTGTGTAC
1 AAAATTAAGAAA-TCATACTAAGTGTATGAATTTCGGTATGACCACTTTGTGTAC
*
1516668 AAAA-TAAGAAATCATACTAAGTGTATTAATTT
1 AAAATTAAGAAATCATACTAAGTGTATGAATTT
1516700 TCGTATAGGA
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
53 20 0.26
54 6 0.08
55 51 0.65
56 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (54 bp):
AAAATTAAGAAATCATACTAAGTGTATGAATTTCGGTATGACCACTTTGTGTAC
Found at i:1517443 original size:68 final size:68
Alignment explanation
Indices: 1516919--1517431 Score: 742
Period size: 68 Copynumber: 7.6 Consensus size: 68
1516909 AAGATAAAAA
* * ** *
1516919 GCCTAACTGTGCATTTGACATAAAAGTACCAATTATGCCAGTTAGGTGAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1516984 GAG
66 GAG
* *
1516987 GCCTAACTGTGCATTTGACAGAAA-GTGTCAATTATGTCAATTAGATGAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1517051 GAG
66 GAG
* * * * *
1517054 GCCTAACTGTGCAGTTGACAGAAAGGTGTCAATTATGCCAATTAGATCAAAGGCTAAATGTCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1517119 GAG
66 GAG
* * * * * *
1517122 TCCTAACTGTACATTTGACAGAAAGGTATTAATTATGCCAGTAAGATGAAAGACT-AGATGCCTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAG-TGCCTT
*
1517186 TAAG
65 TGAG
**
1517190 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGTGAGTTAGATGAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1517255 GAG
66 GAG
* * * *
1517258 ACCTAACTATGCATTTGACAGAAAGGTGTCAATTATGCGAGTTAGATGAAAGGCTAAGTTCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1517323 GAG
66 GAG
* * *
1517326 GCCTAACTATGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCTTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1517391 GAG
66 GAG
*
1517394 GCCTAACTGTGCATTTGGCAGAAAGGTGTCAATTATGC
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGC
1517432 TTGTTATATG
Statistics
Matches: 398, Mismatches: 44, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
67 62 0.16
68 334 0.84
69 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (68 bp):
GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
GAG
Found at i:1518207 original size:25 final size:26
Alignment explanation
Indices: 1518171--1518221 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
1518161 TACATTAAAT
*
1518171 ATTTTGTAATTTAT-TTAAATTAATA
1 ATTTTGTAATTTATCTTAAATGAATA
*
1518196 ATTTTAGT-ATTTTTCTTAAATGAATA
1 ATTTT-GTAATTTATCTTAAATGAATA
1518222 TCATATTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (26 bp):
ATTTTGTAATTTATCTTAAATGAATA
Found at i:1519019 original size:118 final size:118
Alignment explanation
Indices: 1518814--1519416 Score: 658
Period size: 118 Copynumber: 5.2 Consensus size: 118
1518804 AAATACAGAT
* * *
1518814 GATAACATAACCGATTAATTACTGGAAACATTATCAATCATAATAACATATTAGGTAGCGCTTAT
1 GATAACATAACAGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTAT
* * *
1518879 ATAACGTACTAGGTAGCGCCTTTTTAAAGCTGATGGGGCTTTGGAAATCTGAT
66 ATAACGTAATAGGTAGCACCTTTTTAAAGCTGATGGGGCTTTGGAAATCTGAC
* *
1518932 GATAACATAACAGATTAATTACTGGAAACATTATCAAGCATAATAA-ATTATTAGGTAGCACTTA
1 GATAACATAACAGGTTAATTACTGGAAACATTATCAAGCATAATAACA-TATTAGGTAGCGCTTA
* * *
1518996 TATAACGTAATAGGTAGTACCTTTTTAAAGTTGATGGGGCTTTGG-AATCTGAT
65 TATAACGTAATAGGTAGCACCTTTTTAAAGCTGATGGGGCTTTGGAAATCTGAC
* * * * *
1519049 GATAACATAACTGGTTAATTACTAGAAACACTATCAAGGATAAAAACATATTAGGTAGCGCTTAT
1 GATAACATAACAGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTAT
*
1519114 ATAACGTAATAGGTAGCACCTTTTTAAAGCTGATGGAGCTTTTGGAAATCTGAC
66 ATAACGTAATAGGTAGCACCTTTTTAAAGCTGATGGGGC-TTTGGAAATCTGAC
* * * *** * * * **
1519168 GATAACAAAATAGGTTAATTACT-TAATTTTTTAT-TAGTATTATCAACATATTAGGTAATGC--
1 GATAACATAACAGGTTAATTACTGGAA-ACATTATCAAGCATAAT-AACATATTAGGTAGCGCTT
* * * *** * * * * *
1519229 --CT-A--TAAT-GTTACCA-AAGTTT-AAGCTAATAGAGCCTTAGAAATCTGAC
64 ATATAACGTAATAGGTAGCACCTTTTTAAAGCTGATGGGGCTTTGGAAATCTGAC
* * * *
1519276 GATAACATAACTGGTTAATTACTGAAAACATTATCAAGCATAACAACAAATTAGGTAGCGCTTAT
1 GATAACATAACAGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTAT
*
1519341 ATAACGTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGCTTTGGAAATCTGAC
66 ATAACGTAATAGGTAGCACCTTTTTAAAGCTGATGGGGCTTTGGAAATCTGAC
* *
1519394 GATAACAAAATAGGTTAATTACT
1 GATAACATAACAGGTTAATTACT
1519417 TAATTTGTTA
Statistics
Matches: 396, Mismatches: 71, Indels: 36
0.79 0.14 0.07
Matches are distributed among these distances:
108 50 0.13
109 18 0.05
110 3 0.01
111 5 0.01
112 5 0.01
113 1 0.00
114 1 0.00
115 5 0.01
116 4 0.01
117 104 0.26
118 155 0.39
119 45 0.11
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Consensus pattern (118 bp):
GATAACATAACAGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTAT
ATAACGTAATAGGTAGCACCTTTTTAAAGCTGATGGGGCTTTGGAAATCTGAC
Found at i:1519292 original size:108 final size:109
Alignment explanation
Indices: 1519140--1519555 Score: 365
Period size: 108 Copynumber: 3.7 Consensus size: 109
1519130 CACCTTTTTA
* * * * *
1519140 AAGCTGATGGAGCTTTTGGAAATCTGACGATAACAAAATAGGTTAATTACTTAATTTTTTAT-TA
1 AAGCTGATAGAGC-CTTAGAAATCTGACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAA
1519204 GTATTATCAACATATTAGGTAATGCCTATAATGTTACCAAAGTTT
65 GTATTATCAACATATTAGGTAATGCCTATAATGTTACCAAAGTTT
* * * ****
1519249 AAGCTAATAGAGCCTTAGAAATCTGACGATAACATAACT-GGTTAATTACTGAAAACATTATCAA
1 AAGCTGATAGAGCCTTAGAAATCTGACGATAACA-AAATAGGTTAATTACTTAATTTGTTATCAA
* * * ** * * ** **
1519313 GCA-TAACAACAAATTAGGTAGCGCTTATATAACGTAATAGGTAGCGCCTTTTT
65 GTATTATCAACATATTAGGTAATGC--CTATAATGT--TA-CCAAAG----TTT
* * * * *
1519366 AAAGCTGATGGGGCTTTGGAAATCTGACGATAACAAAATAGGTTAATTACTTAATTTGTTAT-TA
1 -AAGCTGATAGAGCCTTAGAAATCTGACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAA
*
1519430 GTATTATCAACATATTAGGTAATGCCTAAAATGTTACCAAAGTTT
65 GTATTATCAACATATTAGGTAATGCCTATAATGTTACCAAAGTTT
* * * ** *
1519475 AAGCTGATAGAGCCTTAGAAATCCGATGATAACATAACCGGTTAATTACTTGATTTGTTATCAAG
1 AAGCTGATAGAGCCTTAGAAATCTGACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAAG
1519540 CT-TTATCAACATATTA
66 -TATTATCAACATATTA
1519556 CAATATATAT
Statistics
Matches: 234, Mismatches: 57, Indels: 32
0.72 0.18 0.10
Matches are distributed among these distances:
108 104 0.44
109 36 0.15
110 8 0.03
112 2 0.01
113 4 0.02
114 2 0.01
116 6 0.03
117 9 0.04
118 63 0.27
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (109 bp):
AAGCTGATAGAGCCTTAGAAATCTGACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAAG
TATTATCAACATATTAGGTAATGCCTATAATGTTACCAAAGTTT
Found at i:1519469 original size:226 final size:226
Alignment explanation
Indices: 1518811--1519524 Score: 875
Period size: 226 Copynumber: 3.1 Consensus size: 226
1518801 AAAAAATACA
* * * *
1518811 GATGATAACATAACCGATTAATTACTGGAAACATTATCAATCATAATAACATATTAGGTAGCGCT
1 GATGATAACATAACCGGTTAATTACTGAAAACATTATCAAGCATAAAAACATATTAGGTAGCGCT
* * *
1518876 TATATAACGTACTAGGTAGCGCCTTTTTAAAGCTGATGGGGCTTTGGAAATCTGATGATAACATA
66 TATATAACGTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGCTTTGGAAATCTGACGATAACAAA
* * * ** * * *
1518941 ACAGATTAATTACTGGAA-ACATTATCAAGCATAAT-AA-ATTATTAGGT-A-GCACTTATATAA
131 ATAGGTTAATTACT-TAATTTATTAT-TAGTATTATCAACA-TATTAGGTAATGC-C-TA-A-AA
* ** ** * * * * *
1519001 CGTAATAGGTAGTACCTTTTTAAAGTTGAT-GGGGCTTTGGAATCT
189 TGT--TA-CCA--A--AGTTT-AAGCTGATAGAGCCTTAGAAATCT
* * *
1519046 GATGATAACATAACTGGTTAATTACT-AGAAACACTATCAAGGATAAAAACATATTAGGTAGCGC
1 GATGATAACATAACCGGTTAATTACTGA-AAACATTATCAAGCATAAAAACATATTAGGTAGCGC
* *
1519110 TTATATAACGTAATAGGTAGCACCTTTTTAAAGCTGATGGAGCTTTTGGAAATCTGACGATAACA
65 TTATATAACGTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGC-TTTGGAAATCTGACGATAACA
* *
1519175 AAATAGGTTAATTACTTAATTTTTTATTAGTATTATCAACATATTAGGTAATGCCTATAATGTTA
129 AAATAGGTTAATTACTTAATTTATTATTAGTATTATCAACATATTAGGTAATGCCTAAAATGTTA
*
1519240 CCAAAGTTTAAGCTAATAGAGCCTTAGAAATCT
194 CCAAAGTTTAAGCTGATAGAGCCTTAGAAATCT
* * * *
1519273 GACGATAACATAACTGGTTAATTACTGAAAACATTATCAAGCATAACAACAAATTAGGTAGCGCT
1 GATGATAACATAACCGGTTAATTACTGAAAACATTATCAAGCATAAAAACATATTAGGTAGCGCT
1519338 TATATAACGTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGCTTTGGAAATCTGACGATAACAAA
66 TATATAACGTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGCTTTGGAAATCTGACGATAACAAA
*
1519403 ATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAATGCCTAAAATGTTACC
131 ATAGGTTAATTACTTAATTTATTATTAGTATTATCAACATATTAGGTAATGCCTAAAATGTTACC
*
1519468 AAAGTTTAAGCTGATAGAGCCTTAGAAATCC
196 AAAGTTTAAGCTGATAGAGCCTTAGAAATCT
1519499 GATGATAACATAACCGGTTAATTACT
1 GATGATAACATAACCGGTTAATTACT
1519525 TGATTTGTTA
Statistics
Matches: 424, Mismatches: 46, Indels: 27
0.85 0.09 0.05
Matches are distributed among these distances:
226 145 0.34
227 112 0.26
228 1 0.00
229 1 0.00
231 1 0.00
232 2 0.00
234 4 0.01
235 104 0.25
236 49 0.12
237 3 0.01
238 2 0.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Consensus pattern (226 bp):
GATGATAACATAACCGGTTAATTACTGAAAACATTATCAAGCATAAAAACATATTAGGTAGCGCT
TATATAACGTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGCTTTGGAAATCTGACGATAACAAA
ATAGGTTAATTACTTAATTTATTATTAGTATTATCAACATATTAGGTAATGCCTAAAATGTTACC
AAAGTTTAAGCTGATAGAGCCTTAGAAATCT
Found at i:1524711 original size:13 final size:13
Alignment explanation
Indices: 1524693--1524723 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1524683 ACCACTCCCA
1524693 TCACCCCTTAAAT
1 TCACCCCTTAAAT
*
1524706 TCACCCCTTAATT
1 TCACCCCTTAAAT
1524719 TCACC
1 TCACC
1524724 ACTTCTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.42, G:0.00, T:0.32
Consensus pattern (13 bp):
TCACCCCTTAAAT
Found at i:1530288 original size:24 final size:26
Alignment explanation
Indices: 1530256--1530313 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
1530246 TAGCAAAAAG
* *
1530256 AAGAAAAAA-TAATAAAAAATAGAGAA
1 AAGAAAAAAGTAA-AAAAGAGAGAGAA
1530282 AAGAAAAAAGTAAAAAAGAGAGAGAA
1 AAGAAAAAAGTAAAAAAGAGAGAGAA
1530308 AAGAAA
1 AAGAAA
1530314 GCAAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 26 0.90
27 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (26 bp):
AAGAAAAAAGTAAAAAAGAGAGAGAA
Found at i:1532509 original size:54 final size:54
Alignment explanation
Indices: 1532411--1532743 Score: 277
Period size: 55 Copynumber: 6.2 Consensus size: 54
1532401 GATTTGTTTT
* * ** * * *
1532411 AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGAT-ATTTTCAAATGAATTTTAAA
1 AGAAACTAAGTC-GATTTTTAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * * *
1532465 AGAAGCTAAGTCGATTTTTGGAAGCTTCTTGATTATTTTTAAATGATTTTTCAA
1 AGAAACTAAGTCGATTTTTAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * *
1532519 AGAAACAAAGT-AATATTTTCATAAGTTTCATGATGATTTTTAAATGAGTTTTCAA
1 AGAAACTAAGTCGAT-TTTT-AGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* *
1532574 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAATTGAGTTTTCAA
1 AGAAACTAAGTC-GATTTTTAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * * * * *
1532629 GGAATCTAA---GATTTTCATG-GGTTTCTTGATG-TTTTCAAAAGAATTTTCAA
1 AGAAACTAAGTCGATTTTTA-GAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * * *
1532679 AGAAATTAAGTCAGATTTTTAGAAGTTTCCTGATGATTTATGAATGGGTTTTCAA
1 AGAAACTAAGTC-GATTTTTAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
1532734 A-AAAGCTAAG
1 AGAAA-CTAAG
1532744 CTTGATTTCC
Statistics
Matches: 221, Mismatches: 45, Indels: 25
0.76 0.15 0.09
Matches are distributed among these distances:
50 21 0.10
51 19 0.09
52 1 0.00
53 19 0.09
54 60 0.27
55 96 0.43
56 3 0.01
57 2 0.01
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.41
Consensus pattern (54 bp):
AGAAACTAAGTCGATTTTTAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
Found at i:1532730 original size:105 final size:104
Alignment explanation
Indices: 1532424--1532781 Score: 328
Period size: 105 Copynumber: 3.3 Consensus size: 104
1532414 AACTAAGCCT
* * * * *
1532424 GATTTTCAGGGGTTTCTTGATATTTTCAAATGAATTTTAAAAGAAGCTAAGTCGATTTTTGGAAG
1 GATTTTCATGGGTTTCTTGATGTTTTCAAATGAATTTTCAAAGAAACTAAGTCGATTTTTAGAAG
* * *
1532489 CTTCTTGATTATTTTTAAATGATTTTTCAAAGAAACAAAGTAA
66 TTTCTTGATGA-TTTTAAATGAGTTTTCAAAGAAAC--A-TAA
* ** * * * *
1532532 TATTTTCATAAGTTTCATGATGATTTTTAAATGAGTTTTCAAAGAAACTAAGTCTGATTTTCAGA
1 GATTTTCATGGGTTTCTTGATG-TTTTCAAATGAATTTTCAAAGAAACTAAGTC-GATTTTTAGA
* * *
1532597 AGTTTCTTGATGATTTTTAATTGAGTTTTCAAGGAATC-TAA
64 AGTTTCTTGATGA-TTTTAAATGAGTTTTCAAAGAAACATAA
* *
1532638 GATTTTCATGGGTTTCTTGATGTTTTCAAAAGAATTTTCAAAGAAATTAAGTCAGATTTTTAGAA
1 GATTTTCATGGGTTTCTTGATGTTTTCAAATGAATTTTCAAAGAAACTAAGTC-GATTTTTAGAA
* * *
1532703 GTTTCCTGATGATTTATGAATGGGTTTTCAAA-AAAGC-TAA
65 GTTTCTTGATGATTT-TAAATGAGTTTTCAAAGAAA-CATAA
* *
1532743 GCTTGATTTCCAAGGGTTTCTTGAT-TATTTCAAATGAAT
1 ----GATTTTCATGGGTTTCTTGATGT-TTTCAAATGAAT
1532782 GTTGATAGAA
Statistics
Matches: 204, Mismatches: 37, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
104 5 0.02
105 64 0.31
106 21 0.10
108 17 0.08
109 57 0.28
110 40 0.20
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (104 bp):
GATTTTCATGGGTTTCTTGATGTTTTCAAATGAATTTTCAAAGAAACTAAGTCGATTTTTAGAAG
TTTCTTGATGATTTTAAATGAGTTTTCAAAGAAACATAA
Found at i:1532732 original size:160 final size:159
Alignment explanation
Indices: 1532411--1532796 Score: 370
Period size: 160 Copynumber: 2.4 Consensus size: 159
1532401 GATTTGTTTT
**
1532411 AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATATTTTCAAATGAATTTTAAAAGAAGCTAAGT
1 AGAAACTAAG-CTGATTTTCAGAAGTTTCTTGATATTTTCAAATGAATTTTAAAAGAAGCTAA--
* * * * *
1532476 CGATTTTTGGAAGCTTCTTGATTATTTTTAAATGATTTTTCAAAGAAACAAAGTAATATTTTCAT
63 CGATTTTTGG-AGCTTCTTGATTATTTTCAAAAGAATTTTCAAAGAAACAAAGTAAGATTTTCAG
*
1532541 AAGTTTCATGATGATTTTTAAATGAGTTTTCAA
127 AAGTTTCATGATGATTTATAAATGAGTTTTCAA
* * * * * *
1532574 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAATTGAGTTTTCAAGGAATCTAA-
1 AGAAACTAAG-CTGATTTTCAGAAGTTTCTTGAT-ATTTTCAAATGAATTTTAAAAGAAGCTAAC
* * ** * *
1532638 GATTTTCATGG-GTTTCTTGA-TGTTTTCAAAAGAATTTTCAAAGAAATTAAGTCAGATTTTTAG
64 GATTTT--TGGAGCTTCTTGATTATTTTCAAAAGAATTTTCAAAGAAACAAAGTAAGATTTTCAG
* * *
1532701 AAGTTTCCTGATGATTTATGAATGGGTTTTCAA
127 AAGTTTCATGATGATTTATAAATGAGTTTTCAA
* * * * *
1532734 A-AAAGCTAAGCTTGATTTCCA-AGGGTTTCTTGAT-TATTTCAAATGAATGTTGATAGAAGCTA
1 AGAAA-CTAAGC-TGATTTTCAGA-AGTTTCTTGATAT-TTTCAAATGAATTTTAAAAGAAGCTA
1532796 A
62 A
1532797 GCCTAATTTT
Statistics
Matches: 182, Mismatches: 34, Indels: 18
0.78 0.15 0.08
Matches are distributed among these distances:
158 1 0.01
159 24 0.13
160 86 0.47
161 14 0.08
163 34 0.19
164 23 0.13
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.40
Consensus pattern (159 bp):
AGAAACTAAGCTGATTTTCAGAAGTTTCTTGATATTTTCAAATGAATTTTAAAAGAAGCTAACGA
TTTTTGGAGCTTCTTGATTATTTTCAAAAGAATTTTCAAAGAAACAAAGTAAGATTTTCAGAAGT
TTCATGATGATTTATAAATGAGTTTTCAA
Found at i:1532819 original size:214 final size:213
Alignment explanation
Indices: 1532424--1532822 Score: 457
Period size: 214 Copynumber: 1.9 Consensus size: 213
1532414 AACTAAGCCT
* * *
1532424 GATTTTCAGGGGTTTCTTGATATTTTCAAATGAATTTTAAAAGAAGCTAAGTCGATTTTTGGAAG
1 GATTTTCAGGGGTTTCTTGATATTTTCAAAAGAATTTTAAAAGAAACTAAGTCGATTTTTAGAAG
* * * * *
1532489 CTTCTTGATTATTTTTAAATGATTTTTCAAAGAAACAAAGTAATATTTTCATAAGTTTCATGATG
66 CTTCCTGATGATTTATAAATGAGTTTTCAAAGAAACAAAGT-ATATTTCCATAAGTTTCATGATG
* * * * *
1532554 ATTTTTAAATGAGTTTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAATT
130 ATTTTCAAATGAATGTTCAAAGAAACTAAGCCTAATTTTCAGAAGTTTCTTGATGATTTTTAATT
1532619 GAGTTTTCAAGGAATCTAA
195 GAGTTTTCAAGGAATCTAA
* * * *
1532638 GATTTTCATGGGTTTCTTGATGTTTTCAAAAGAATTTTCAAAGAAATTAAGTCAGATTTTTAGAA
1 GATTTTCAGGGGTTTCTTGATATTTTCAAAAGAATTTTAAAAGAAACTAAGTC-GATTTTTAGAA
* * * * * *
1532703 GTTTCCTGATGATTTATGAATGGGTTTTCAAA-AAAGCTAAGCT-TGATTTCCA-AGGGTTTCTT
65 GCTTCCTGATGATTTATAAATGAGTTTTCAAAGAAA-CAAAG-TAT-ATTTCCATA-AGTTTCAT
* * * *
1532765 GATTA-TTTCAAATGAATGTTGATAGAAGCTAAGCCTAATTTTCAG-AGATTTCTTGATG
126 GATGATTTTCAAATGAATGTTCAAAGAAACTAAGCCTAATTTTCAGAAG-TTTCTTGATG
1532823 TCTACAAATG
Statistics
Matches: 152, Mismatches: 27, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
213 2 0.01
214 94 0.62
215 55 0.36
216 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.41
Consensus pattern (213 bp):
GATTTTCAGGGGTTTCTTGATATTTTCAAAAGAATTTTAAAAGAAACTAAGTCGATTTTTAGAAG
CTTCCTGATGATTTATAAATGAGTTTTCAAAGAAACAAAGTATATTTCCATAAGTTTCATGATGA
TTTTCAAATGAATGTTCAAAGAAACTAAGCCTAATTTTCAGAAGTTTCTTGATGATTTTTAATTG
AGTTTTCAAGGAATCTAA
Found at i:1534238 original size:20 final size:20
Alignment explanation
Indices: 1534176--1534239 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
1534166 CAATGAAAGG
*
1534176 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAGCTT
* **
1534196 G-TC-TGATGAGAAAGAAG-AA
1 GTTCATAATGAG-AAG-AGCTT
1534215 GTTCATAATGAGAAGAGCTT
1 GTTCATAATGAGAAGAGCTT
1534235 GTTCA
1 GTTCA
1534240 ACCTTTGTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 10
0.65 0.14 0.20
Matches are distributed among these distances:
18 6 0.19
19 8 0.25
20 12 0.38
21 6 0.19
ACGTcount: A:0.39, C:0.09, G:0.25, T:0.27
Consensus pattern (20 bp):
GTTCATAATGAGAAGAGCTT
Found at i:1534977 original size:44 final size:44
Alignment explanation
Indices: 1534871--1534979 Score: 112
Period size: 44 Copynumber: 2.5 Consensus size: 44
1534861 GCCCTATTTA
* * * *
1534871 CTTAAGTCCATCATATAAGGAGATGGATCAGCATCACCATGTTG
1 CTTAATTCCATCATAGAAGGAGATAGATCAGCATCAACATGTTG
* * * ** *
1534915 CTTAATTCTATAACAGAAGGAGATAGATCATTATCAACATTTTG
1 CTTAATTCCATCATAGAAGGAGATAGATCAGCATCAACATGTTG
1534959 -TTCAATTCCATCATAGAAGGA
1 CTT-AATTCCATCATAGAAGGA
1534980 TGTGATTAAC
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
43 2 0.04
44 49 0.96
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (44 bp):
CTTAATTCCATCATAGAAGGAGATAGATCAGCATCAACATGTTG
Found at i:1542255 original size:138 final size:138
Alignment explanation
Indices: 1541748--1542512 Score: 859
Period size: 139 Copynumber: 5.5 Consensus size: 138
1541738 TATTCACGTG
* ** *
1541748 AAAGCGCATTTCAAGGGGGCGCCTTTCC-TTTTTTGTCAGAGAATATATTATAATTACCCTATTA
1 AAAGCGCATTTCAAGGGGGCGCCTTCCCTTTTTTTGTCAGAGAATAGGTTATAATTGCCCTATTA
* * * * * * *
1541812 TGTGTCATGTCCCCTGGTAGGGTACTATTCATGTCAGTACATATAATG-TTGAAGGGGACTCAAT
66 TGTGTCATGTCCCCCGATGGGGCACTATTTATGTCAGTACCTATAATGTTTG-AGGGGACACAAT
1541876 AATGTGGTT
130 AATGTGGTT
* * * *
1541885 AAAGCGCGTTTC-AGGGGGTGCAATTTCCCTTTTTTTGTCAAAGAATAGGTTATAATTGCCCTAT
1 AAAGCGCATTTCAAGGGGGCGC--CTTCCCTTTTTTTGTCAGAGAATAGGTTATAATTGCCCTAT
* * * * **
1541949 TATGTGTCATGTCCCCCGGTGGGGCACTATTTATGTCAATACCTATAATATTTCAGGGGATGCAA
64 TATGTGTCATGTCCCCCGATGGGGCACTATTTATGTCAGTACCTATAATGTTTGAGGGGACACAA
1542014 TAATGTGGTT
129 TAATGTGGTT
** * * *
1542024 AAAGAACGTTT-AAGGGGGGCGCCTTCACTTTTTTTTATCAGAGAATAGGTTATAATTGCCCTAT
1 AAAGCGCATTTCAA-GGGGGCGCCTTC-CCTTTTTTTGTCAGAGAATAGGTTATAATTGCCCTAT
* *
1542088 TATATGTCATGTCCCCC-AGTGGGGCACTATTTATGTTAGTACCTATAATGTTTGAGGGGACACA
64 TATGTGTCATGTCCCCCGA-TGGGGCACTATTTATGTCAGTACCTATAATGTTTGAGGGGACACA
1542152 ATAATGTGGTT
128 ATAATGTGGTT
* * *
1542163 AAAGCGCATTTCAAGGGGG-GCCTTCCCTTTTTTTTATCAAAGAATAGGTTATAATTTCCCTATT
1 AAAGCGCATTTCAAGGGGGCGCCTTCCC-TTTTTTTGTCAGAGAATAGGTTATAATTGCCCTATT
* ** * * * ** *
1542227 ATGTGTCATGTCCCCCTACAGGCCACTATTCATGTCAATACCTATAATGTTTGAGGGGATGCAAC
65 ATGTGTCATGTCCCCCGATGGGGCACTATTTATGTCAGTACCTATAATGTTTGAGGGGACACAAT
1542292 AATGTGGTT
130 AATGTGGTT
* * * * *
1542301 AAAG-GACATTTCATGAGGG-ACCTTCCCTTTTTTTGTTAGAGAATAGGTTATAATTGCCATATT
1 AAAGCG-CATTTCAAGGGGGCGCCTTCCCTTTTTTTGTCAGAGAATAGGTTATAATTGCCCTATT
* * * *
1542364 ATGTGTCATGTCCCCCGATGGGGCACTATTTATGTCAGTAGCTATTATGTTTAAGGGGATGA-AA
65 ATGTGTCATGTCCCCCGATGGGGCACTATTTATGTCAGTACCTATAATGTTTGAGGGGA-CACAA
*
1542428 TAATGTGGCT
129 TAATGTGGTT
* * * * *
1542438 AAAGCGTATTTC-AGGAGTCATGCCTTCCCTTTTTTTGTCAGAGAATATGTTATAATT-TCCTAT
1 AAAGCGCATTTCAAGGGGGC--GCCTTCCCTTTTTTTGTCAGAGAATAGGTTATAATTGCCCTAT
1542501 TATGTGTCATGT
64 TATGTGTCATGT
1542513 GTCCGCTGGT
Statistics
Matches: 531, Mismatches: 80, Indels: 33
0.82 0.12 0.05
Matches are distributed among these distances:
136 10 0.02
137 113 0.21
138 148 0.28
139 249 0.47
140 11 0.02
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.36
Consensus pattern (138 bp):
AAAGCGCATTTCAAGGGGGCGCCTTCCCTTTTTTTGTCAGAGAATAGGTTATAATTGCCCTATTA
TGTGTCATGTCCCCCGATGGGGCACTATTTATGTCAGTACCTATAATGTTTGAGGGGACACAATA
ATGTGGTT
Found at i:1549327 original size:137 final size:136
Alignment explanation
Indices: 1549073--1549850 Score: 482
Period size: 137 Copynumber: 5.6 Consensus size: 136
1549063 ATTTTACCTG
* * * *
1549073 GCCTACTCCATACGTTAGGGCGCTCGATGTAAGATCAGGCCATCCTGCCTACTCCCCTCTGGAAG
1 GCCTACTCCACACGTTAGAGCGCTCG-CGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAAG
* * * ** * **
1549138 AGCTCGGCATGAACTCTGTCTACCCTACCTACCCTACACGTTGAAGTGCTCGGCGTGAATCAGGA
65 CGCTCGGCATGAACTCTGTCTCCCCTGCCTACTATACACGTTAAAGCACTCGGCGTGAATCAGGA
**
1549203 ACACTTT
130 ACACCCT
* * * * *
1549210 GCCTACTCCACATGTTAGAGCGCTCAGCGTAAGATCAAGTCATCATGCCTACTCCCCTTTAGAAG
1 GCCTACTCCACACGTTAGAGCGCTC-GCGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAAG
* ** *
1549275 CGCTCGGCATGCACTCTGTCTCCCCTGCCTACTATTGACGTTAAAGCACTCGGCTTGAATCAGGA
65 CGCTCGGCATGAACTCTGTCTCCCCTGCCTACTATACACGTTAAAGCACTCGGCGTGAATCAGGA
1549340 ACACCCT
130 ACACCCT
* * * * *
1549347 ACCTACTCCACACGTTAGAGCGCTTGGCATAAGATCAGGTCATCCTACCTACTCCTCTCTGGAAG
1 GCCTACTCCACACGTTAGAGCGC-TCGCGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAAG
** * * * * ** * ** * *
1549412 CGCTCAACATGTACTATATCTCCCCTGCCTACTCT-CAACGTCGAAGCGCTCGGTATAATATTAA
65 CGCTCGGCATGAACTCTGTCTCCCCTGCCTACTATAC-ACGTTAAAGCACTCGGCGTGA-A-T-C
* *
1549476 AGCACATCTTATTTTACCCG
126 AGGA-A-C-------ACCCT
* * * * *
1549496 GCCTACTCTATACGTTAGAGCGCTCAGCGTAAGACCATGTCATCCTACCTACTCCCCTCTGGAAG
1 GCCTACTCCACACGTTAGAGCGCTC-GCGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAAG
* * * * * * * *
1549561 CGTTCGACATGTACTCTGTCT-CCCTTCCTACTCT-CAACGTTGAAGCGCTCGGCGAGAAAT-AG
65 CGCTCGGCATGAACTCTGTCTCCCCTGCCTACTATAC-ACGTTAAAGCACTCGGCGTG-AATCAG
* * *
1549623 GAATATCTT
128 GAACACCCT
* * * * * *
1549632 GTCTACTCCACA-GATTAGAGCACCCGGTGTAAGATCAGGTCATCATGCCTACT-CCCTACAGGA
1 GCCTACTCCACACG-TTAGAGCGCTC-GCGTAAGATCAGGTCATCCTGCCTACTCCCCT-CTGGA
** * * * * * * * *
1549695 AGCGCTCAACATGAACTTTGTC-CCTCAT--CTAACTCTTA-ATGGTGAAGCGCTCGGCAG-AAA
63 AGCGCTCGGCATGAACTCTGTCTCC-CCTGCCT-ACT-ATACACGTTAAAGCACTCGGC-GTGAA
* *
1549755 T-ATGAATACCCT
124 TCAGGAACACCCT
* * * * * *
1549767 GCCTACTCCACATGTTAGAGCGCCCACTTAAGATCAGGTCATCCTACCTACTCCCCACTGGAAGC
1 GCCTACTCCACACGTTAGAGCGCTCGCGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
*
1549832 GCTCAGCATGAACTCTGTC
66 GCTCGGCATGAACTCTGTC
1549851 CCCTTCTAAC
Statistics
Matches: 507, Mismatches: 107, Indels: 57
0.76 0.16 0.08
Matches are distributed among these distances:
134 46 0.09
135 42 0.08
136 84 0.17
137 213 0.42
138 3 0.01
139 1 0.00
140 3 0.01
141 1 0.00
142 1 0.00
144 1 0.00
145 3 0.01
147 1 0.00
148 31 0.06
149 77 0.15
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (136 bp):
GCCTACTCCACACGTTAGAGCGCTCGCGTAAGATCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
GCTCGGCATGAACTCTGTCTCCCCTGCCTACTATACACGTTAAAGCACTCGGCGTGAATCAGGAA
CACCCT
Found at i:1549830 original size:134 final size:133
Alignment explanation
Indices: 1549490--1549883 Score: 423
Period size: 136 Copynumber: 2.9 Consensus size: 133
1549480 CATCTTATTT
* * * * * * * *
1549490 TACCCGGCCTACTCTATACGTTAGAGCGCTCAGCGTAAGACCATGTCATCCTACCTACTCCCCTC
1 TACCCTGCCTACTCCACA-GTTAGAGCGCCCA-CTTAAGATCAGGTCATCCTACCTACTCCCCAC
* * * * *
1549555 TGGAAGCGTTCGACATGTACTCTGTCTCCCTTCCT-ACTCTCAACGTTGAAGCGCTCGGCGAGAA
64 TGGAAGCGCTCAACATGAACTCTGTC-CCCTT-CTAACTCTTAACGGTGAAGCGCTCGGCGAGAA
1549619 ATAGGAA
127 ATAGGAA
* * * * ** * * *
1549626 TATCTTGTCTACTCCACAGATTAGAGCACCCGGTGTAAGATCAGGTCATCATGCCTACTCCCTAC
1 TACCCTGCCTACTCCACAG-TTAGAGCGCCCACT-TAAGATCAGGTCATCCTACCTACTCCCCAC
* * * *
1549691 AGGAAGCGCTCAACATGAACTTTGTCCCTCATCTAACTCTTAATGGTGAAGCGCTCGGC-AGAAA
64 TGGAAGCGCTCAACATGAACTCTGTCCC-CTTCTAACTCTTAACGGTGAAGCGCTCGGCGAGAAA
*
1549755 TATGAA
128 TAGGAA
1549761 TACCCTGCCTACTCCACATGTTAGAGCGCCCACTTAAGATCAGGTCATCCTACCTACTCCCCACT
1 TACCCTGCCTACTCCACA-GTTAGAGCGCCCACTTAAGATCAGGTCATCCTACCTACTCCCCACT
* * * *
1549826 GGAAGCGCTCAGCATGAACTCTGTCCCCTTCTAACTCTTAACGTTAAAGTGCTCGGCG
65 GGAAGCGCTCAACATGAACTCTGTCCCCTTCTAACTCTTAACGGTGAAGCGCTCGGCG
1549884 TAATTCTTAA
Statistics
Matches: 208, Mismatches: 44, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
133 25 0.12
134 52 0.25
135 41 0.20
136 90 0.43
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (133 bp):
TACCCTGCCTACTCCACAGTTAGAGCGCCCACTTAAGATCAGGTCATCCTACCTACTCCCCACTG
GAAGCGCTCAACATGAACTCTGTCCCCTTCTAACTCTTAACGGTGAAGCGCTCGGCGAGAAATAG
GAA
Found at i:1553784 original size:128 final size:128
Alignment explanation
Indices: 1553601--1553834 Score: 353
Period size: 128 Copynumber: 1.8 Consensus size: 128
1553591 CCTTTTTTTG
* * * * * *
1553601 TCAGAGAATATGTTATAATTTCCCTATTATGTGTCATATTCATCGGAATGGCACTATTCATGTCA
1 TCAGAGAATAAGCTATAATTGCCCTATTATGTGTCATATTCACCAGAATGACACTATTCATGTCA
*
1553666 GTATCTATCATGTTTGAGGGGACGCAACAATGTGGTTAAAGTGTATTTTAAGGGGGGCGCTTA
66 GTACCTATCATGTTTGAGGGGACGCAACAATGTGGTTAAAGTGTATTTTAAGGGGGGCGCTTA
* *
1553729 TCAGAGAATAAGCTATAATTGCCCTATTATGTGTCAT-GTCTACCAGAATGACACTATTCATTTC
1 TCAGAGAATAAGCTATAATTGCCCTATTATGTGTCATATTC-ACCAGAATGACACTATTCATGTC
* *
1553793 AGTACCTATCATGTTTGAGGGGATGCAATAATGTGGTTAAAG
65 AGTACCTATCATGTTTGAGGGGACGCAACAATGTGGTTAAAG
1553835 CCGTTTCAGG
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
127 2 0.02
128 92 0.98
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (128 bp):
TCAGAGAATAAGCTATAATTGCCCTATTATGTGTCATATTCACCAGAATGACACTATTCATGTCA
GTACCTATCATGTTTGAGGGGACGCAACAATGTGGTTAAAGTGTATTTTAAGGGGGGCGCTTA
Found at i:1554956 original size:21 final size:21
Alignment explanation
Indices: 1554932--1554986 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
1554922 GGTGTCATAA
1554932 AACCCTGTGGGCTGGGCATGT
1 AACCCTGTGGGCTGGGCATGT
* * * * *
1554953 AACCTTGCGGACTTGGTATGT
1 AACCCTGTGGGCTGGGCATGT
*
1554974 ACCCCTGTGGGCT
1 AACCCTGTGGGCT
1554987 ATGAATGTTA
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.25, G:0.33, T:0.27
Consensus pattern (21 bp):
AACCCTGTGGGCTGGGCATGT
Found at i:1555051 original size:42 final size:41
Alignment explanation
Indices: 1554995--1555124 Score: 170
Period size: 42 Copynumber: 3.1 Consensus size: 41
1554985 CTATGAATGT
* * * *
1554995 TACCCTGCGGAGATGACATATGAACTGGTGGGATTGGCATA
1 TACCCTACGAAGATGGCATTTGAACTGGTGGGATTGGCATA
1555036 TACCCTTACGAAGATGGCATTTGAACTGGTGGGATTGGCATA
1 TACCC-TACGAAGATGGCATTTGAACTGGTGGGATTGGCATA
* * * *
1555078 TACCACTGCGAAGATGGCATTTGAACTGGTGGGCTAGGCATG
1 TACC-CTACGAAGATGGCATTTGAACTGGTGGGATTGGCATA
1555120 TACCC
1 TACCC
1555125 CTGTGGCATC
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
41 6 0.08
42 72 0.91
43 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (41 bp):
TACCCTACGAAGATGGCATTTGAACTGGTGGGATTGGCATA
Found at i:1555706 original size:17 final size:17
Alignment explanation
Indices: 1555684--1555719 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1555674 AAACTGAAAC
1555684 ATAAATAT-ATAATTCTA
1 ATAAATATAAT-ATTCTA
1555701 ATAAATATAATATTCTA
1 ATAAATATAATATTCTA
1555718 AT
1 AT
1555720 TATATCAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAATATAATATTCTA
Found at i:1556733 original size:22 final size:21
Alignment explanation
Indices: 1556707--1556760 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1556697 TAATAATAAA
* *
1556707 CACTAAAATGTAATTAGCATAT
1 CACTAAAATAT-ATTACCATAT
*
1556729 CACTAAAAAATATTACCATAT
1 CACTAAAATATATTACCATAT
1556750 CACTAAAATAT
1 CACTAAAATAT
1556761 CTTGAGATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.50, C:0.17, G:0.04, T:0.30
Consensus pattern (21 bp):
CACTAAAATATATTACCATAT
Found at i:1556912 original size:23 final size:21
Alignment explanation
Indices: 1556884--1556925 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
1556874 TAATTATATA
1556884 AATATTATTTTTAATAAAAATTT
1 AATATT-TTTTT-ATAAAAATTT
*
1556907 AATATTTTTTTTTAAAAAT
1 AATATTTTTTTATAAAAAT
1556926 ATTTATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 5 0.28
23 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AATATTTTTTTATAAAAATTT
Found at i:1558499 original size:14 final size:15
Alignment explanation
Indices: 1558480--1558518 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
1558470 AGGTTAGAGA
1558480 TTTAGA-TTAAATCT
1 TTTAGATTTAAATCT
1558494 TTTAGATTTTAAATCT
1 TTTAGA-TTTAAATCT
1558510 TTTA-ATTTA
1 TTTAGATTTA
1558519 GTCTTTAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 10 0.43
15 1 0.04
16 12 0.52
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (15 bp):
TTTAGATTTAAATCT
Found at i:1558571 original size:15 final size:15
Alignment explanation
Indices: 1558551--1558588 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
1558541 AAGCCCCTAG
*
1558551 ATTTTAGGTTCTTTA
1 ATTTTAGGTTCATTA
1558566 ATTTTA-G-TCATTA
1 ATTTTAGGTTCATTA
1558579 ATTTTAGGTT
1 ATTTTAGGTT
1558589 TAGAATTCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
13 11 0.55
14 2 0.10
15 7 0.35
ACGTcount: A:0.24, C:0.05, G:0.13, T:0.58
Consensus pattern (15 bp):
ATTTTAGGTTCATTA
Found at i:1559885 original size:3 final size:3
Alignment explanation
Indices: 1559879--1559923 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
1559869 TTGTAGATAG
1559879 TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1559924 TCCCTTTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1575150 original size:126 final size:126
Alignment explanation
Indices: 1574997--1575249 Score: 497
Period size: 126 Copynumber: 2.0 Consensus size: 126
1574987 ACTTACCAAA
1574997 TGAATCGATAATGTAAAAGACCATATATACTTAATTTAAAAAATCGGTTACCAAAGTCAAAAACA
1 TGAATCGATAATGTAAAAGACCATATATACTTAATTTAAAAAATCGGTTACCAAAGTCAAAAACA
1575062 AATGAGACTATAGACAGTTTACCTATTACTTTCTTATAATACCAGAGAGTCTCCATCCCTT
66 AATGAGACTATAGACAGTTTACCTATTACTTTCTTATAATACCAGAGAGTCTCCATCCCTT
1575123 TGAATCGATAATGTAAAAGACCATATATACTTAATTTAAAAAATCGGTTACCAAAGTCAAAAACA
1 TGAATCGATAATGTAAAAGACCATATATACTTAATTTAAAAAATCGGTTACCAAAGTCAAAAACA
*
1575188 AATGAGACTATAGACAGTTTACCTATTACTTTCTTATAATGCCAGAGAGTCTCCATCCCTT
66 AATGAGACTATAGACAGTTTACCTATTACTTTCTTATAATACCAGAGAGTCTCCATCCCTT
1575249 T
1 T
1575250 TAACTAGTAT
Statistics
Matches: 126, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 126 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.30
Consensus pattern (126 bp):
TGAATCGATAATGTAAAAGACCATATATACTTAATTTAAAAAATCGGTTACCAAAGTCAAAAACA
AATGAGACTATAGACAGTTTACCTATTACTTTCTTATAATACCAGAGAGTCTCCATCCCTT
Found at i:1576514 original size:29 final size:29
Alignment explanation
Indices: 1576480--1576589 Score: 159
Period size: 29 Copynumber: 3.8 Consensus size: 29
1576470 TTAAAACTTT
1576480 TATTTTATTTTTATTTTAACTTAAAAATA
1 TATTTTATTTTTATTTTAACTTAAAAATA
1576509 TATTTTATTTTTATTTTAACTTAAAAATA
1 TATTTTATTTTTATTTTAACTTAAAAATA
*
1576538 TATTTTA-TTTTATCTTTAATTTAAAAATA
1 TATTTTATTTTTAT-TTTAACTTAAAAATA
* * * *
1576567 TTTTTTAATCTTATCTTAACTTA
1 TATTTTATTTTTATTTTAACTTA
1576590 TTAGTCTTAT
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
28 6 0.08
29 63 0.85
30 5 0.07
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (29 bp):
TATTTTATTTTTATTTTAACTTAAAAATA
Found at i:1576623 original size:24 final size:24
Alignment explanation
Indices: 1576543--1576623 Score: 60
Period size: 24 Copynumber: 3.3 Consensus size: 24
1576533 AAATATATTT
*
1576543 TATTTTATCTTTAATTTAAA-AATA
1 TATTTTATC-TTAACTTAAACAATA
* * *
1576567 TTTTTTAATCTTATCTT-AAC-TTA
1 TATTTT-ATCTTAACTTAAACAATA
*
1576590 TTAGTCTTATCTTAACTTAAACAATA
1 -TA-TTTTATCTTAACTTAAACAATA
1576616 TATTTTAT
1 TATTTTAT
1576624 TTTTATCTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
23 4 0.10
24 25 0.60
25 11 0.26
26 2 0.05
ACGTcount: A:0.35, C:0.10, G:0.01, T:0.54
Consensus pattern (24 bp):
TATTTTATCTTAACTTAAACAATA
Found at i:1576788 original size:29 final size:28
Alignment explanation
Indices: 1576725--1576790 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 28
1576715 CTAACATAAC
* * *
1576725 TTAAAAATATATTTTAATCTTATTTTAAT
1 TTAAAAA-ATATTTTAATATAATATTAAT
*
1576754 TT-AAAAATATTTTATTATAATATTAATT
1 TTAAAAAATATTTTAATATAATATTAA-T
1576782 TTAAAAAAT
1 TTAAAAAAT
1576791 GTATGTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
27 16 0.52
28 7 0.23
29 8 0.26
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
TTAAAAAATATTTTAATATAATATTAAT
Found at i:1576959 original size:19 final size:19
Alignment explanation
Indices: 1576935--1576975 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1576925 AAATAAAATA
*
1576935 TATTTTTTAATTTTTCTTT
1 TATTTTTTAATTTTTCTAT
**
1576954 TATTTTTTCTTTTTTCTAT
1 TATTTTTTAATTTTTCTAT
1576973 TAT
1 TAT
1576976 AAACTTTATT
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:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (19 bp):
TATTTTTTAATTTTTCTAT
Found at i:1577808 original size:17 final size:17
Alignment explanation
Indices: 1577786--1577820 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1577776 AAACGAAATA
*
1577786 AAAACTACACAATTAGT
1 AAAACTACAAAATTAGT
*
1577803 AAAACTATAAAATTAGT
1 AAAACTACAAAATTAGT
1577820 A
1 A
1577821 TAGTGGGACG
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:0.57, C:0.11, G:0.06, T:0.26
Consensus pattern (17 bp):
AAAACTACAAAATTAGT
Found at i:1579528 original size:13 final size:15
Alignment explanation
Indices: 1579505--1579574 Score: 69
Period size: 13 Copynumber: 4.8 Consensus size: 15
1579495 CTTTTGTAGT
1579505 TTTATAATTTA-ATA
1 TTTATAATTTATATA
1579519 TTTA-AATTTATTATA
1 TTTATAATTTA-TATA
*
1579534 TTTATTATTT-TAATA
1 TTTATAATTTAT-ATA
1579549 TTT-T-ATTTATATA
1 TTTATAATTTATATA
1579562 TTTATAAATTTAT
1 TTTAT-AATTTAT
1579575 TACTAAAATA
Statistics
Matches: 47, Mismatches: 1, Indels: 14
0.76 0.02 0.23
Matches are distributed among these distances:
13 16 0.34
14 8 0.17
15 13 0.28
16 10 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATAATTTATATA
Found at i:1579563 original size:8 final size:8
Alignment explanation
Indices: 1579505--1579574 Score: 50
Period size: 7 Copynumber: 9.6 Consensus size: 8
1579495 CTTTTGTAGT
1579505 TTTATA-A
1 TTTATATA
1579512 TTTA-ATA
1 TTTATATA
1579519 TTTA-A-A
1 TTTATATA
1579525 TTTATTATA
1 TTTA-TATA
1579534 TTTAT-TA
1 TTTATATA
1579541 TTT-TA-A
1 TTTATATA
1579547 TATT-T-TA
1 T-TTATATA
1579554 TTTATATA
1 TTTATATA
*
1579562 TTTATAAA
1 TTTATATA
1579570 TTTAT
1 TTTAT
1579575 TACTAAAATA
Statistics
Matches: 53, Mismatches: 1, Indels: 17
0.75 0.01 0.24
Matches are distributed among these distances:
6 11 0.21
7 21 0.40
8 16 0.30
9 5 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTTATATA
Found at i:1582668 original size:25 final size:25
Alignment explanation
Indices: 1582640--1582692 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1582630 ACTTCGGGTT
* *
1582640 AGAGAACTAGAGGTAGAAAAAGAAA
1 AGAGAACAAGAGCTAGAAAAAGAAA
* *
1582665 AGAGAACAAGAGCTTGAAATAGAAA
1 AGAGAACAAGAGCTAGAAAAAGAAA
1582690 AGA
1 AGA
1582693 AATCTTGGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.58, C:0.06, G:0.26, T:0.09
Consensus pattern (25 bp):
AGAGAACAAGAGCTAGAAAAAGAAA
Found at i:1586726 original size:22 final size:22
Alignment explanation
Indices: 1586684--1586726 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1586674 GCTTAGACTT
* *
1586684 TCAAATTGTACTAGGATAGAAC
1 TCAAATTGCACTAGGAGAGAAC
1586706 TCAAATTGACACTAGG-GAGAA
1 TCAAATTG-CACTAGGAGAGAA
1586727 GAGAAAAGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (22 bp):
TCAAATTGCACTAGGAGAGAAC
Found at i:1593654 original size:22 final size:22
Alignment explanation
Indices: 1593597--1593657 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
1593587 TCGAAATGGG
**
1593597 GTATCGATACCATAATATAGTA
1 GTATCGATACCATGGTATAGTA
1593619 GTATCGATACCATGGTATAGTA
1 GTATCGATACCATGGTATAGTA
1593641 GTATCGATACCATGGTA
1 GTATCGATACCATGGTA
1593658 GGGGTATCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (22 bp):
GTATCGATACCATGGTATAGTA
Found at i:1593666 original size:20 final size:21
Alignment explanation
Indices: 1593597--1593670 Score: 78
Period size: 22 Copynumber: 3.5 Consensus size: 21
1593587 TCGAAATGGG
** *
1593597 GTATCGATACCATAATATAGTA
1 GTATCGATACCAT-GGATAGGA
*
1593619 GTATCGATACCATGGTATAGTA
1 GTATCGATACCATGG-ATAGGA
*
1593641 GTATCGATACCATGG-TAGGG
1 GTATCGATACCATGGATAGGA
1593661 GTATCGATAC
1 GTATCGATAC
1593671 TGAAGAACCA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 13 0.28
22 34 0.72
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (21 bp):
GTATCGATACCATGGATAGGA
Found at i:1594114 original size:45 final size:45
Alignment explanation
Indices: 1594050--1594140 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
1594040 AAATTTTGTA
* *
1594050 TTGGGCACTTTGTGTGCTAAAATGTTAAGGAATTCATACTAAGTG
1 TTGGGAACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTG
1594095 TTGGGAACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTG
1 TTGGGAACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTG
1594140 T
1 T
1594141 ATGAATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (45 bp):
TTGGGAACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTG
Found at i:1594182 original size:59 final size:59
Alignment explanation
Indices: 1594101--1594387 Score: 314
Period size: 59 Copynumber: 4.9 Consensus size: 59
1594091 AGTGTTGGGA
1594101 ACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGC
1 ACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGC
* ** * * **
1594160 GCTTTGTGTGCTACAAAT-TTAAGAAATTCATACTGTGTGTAAG-ATTTCCGTAATA-TA
1 ACTTTGTGTGCTA-AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGC
* * * ** *
1594217 ACTATGTGTGCTAAAATGTTAAGAAATTCATATTAATTGTATGAATTTATGTATTGGGC
1 ACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGC
* * * * *
1594276 CCTTT-TGTGCTAAAATGTTAAGAAATTTATTCTAAGTGTATAAATTTCCGTATTGGGC
1 ACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGC
* * * * *
1594334 ACTTTTTGTG-TAAACATGTTAAGAAATTCATACTAGGTTTATAAATTTCTGTAT
1 ACTTTGTGTGCTAAA-ATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
1594388 GGGAAATATA
Statistics
Matches: 187, Mismatches: 35, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
56 4 0.02
57 31 0.17
58 73 0.39
59 75 0.40
60 4 0.02
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.40
Consensus pattern (59 bp):
ACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGC
Found at i:1594188 original size:104 final size:104
Alignment explanation
Indices: 1594002--1594193 Score: 298
Period size: 104 Copynumber: 1.8 Consensus size: 104
1593992 ATGGCACTAA
* * *
1594002 GTGTGCTAAAAATGTTAATAAATTCATACTAAGTGTATAAATTTTGTATTGGGCACTTTGTGTGC
1 GTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATAAATTTCGTATTAGGCACTTTGTGTGC
*
1594067 TAAAATGTTAAGGAATTCATACTAAGTGTTGGGAACTTT
66 TAAAATGTTAAGAAATTCATACTAAGTGTTGGGAACTTT
* *
1594106 GTGTGCT-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGCGCTTTGTGTG
1 GTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATAAATTT-CGTATTAGGCACTTTGTGTG
1594170 CTACAAAT-TTAAGAAATTCATACT
65 CTA-AAATGTTAAGAAATTCATACT
1594194 GTGTGTAAGA
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
103 34 0.43
104 42 0.52
105 4 0.05
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (104 bp):
GTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATAAATTTCGTATTAGGCACTTTGTGTGC
TAAAATGTTAAGAAATTCATACTAAGTGTTGGGAACTTT
Found at i:1594197 original size:29 final size:27
Alignment explanation
Indices: 1594164--1594249 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 27
1594154 TTAGGCGCTT
1594164 TGTGTGCTACAAATTTAAGAAATTCATA
1 TGTGTGCTA-AAATTTAAGAAATTCATA
* ** * *
1594192 CTGTGTG-TAAGATTTCCGTAATATAACTA
1 -TGTGTGCTAAAATTTAAGAAAT-TCA-TA
1594221 TGTGTGCTAAAATGTTAAGAAATTCATA
1 TGTGTGCTAAAAT-TTAAGAAATTCATA
1594249 T
1 T
1594250 TAATTGTATG
Statistics
Matches: 43, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
27 9 0.21
28 13 0.30
29 15 0.35
30 6 0.14
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.37
Consensus pattern (27 bp):
TGTGTGCTAAAATTTAAGAAATTCATA
Found at i:1594246 original size:57 final size:59
Alignment explanation
Indices: 1594098--1594368 Score: 266
Period size: 58 Copynumber: 4.6 Consensus size: 59
1594088 CTAAGTGTTG
* *
1594098 GGAACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTA
1 GGAACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTAAGAATTTCCGTAATA
** **
1594157 GGCGCTTTGTGTGCTACAAAT-TTAAGAAATTCATACTGTGTGTAAG-ATTTCCGTAATA
1 GGAACTTTGTGTGCTA-AAATGTTAAGAAATTCATACTAAGTGTAAGAATTTCCGTAATA
* * * * * ** * *
1594215 -TAACTATGTGTGCTAAAATGTTAAGAAATTCATATTAATTGTATGAATTTATGTATTG
1 GGAACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTAAGAATTTCCGTAATA
** * * * *
1594273 GGCCCTTT-TGTGCTAAAATGTTAAGAAATTTATTCTAAGTGTATA-AATTTCCGTATTG
1 GGAACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTA-AGAATTTCCGTAATA
* *
1594331 GGCACTTTTTGTG-TAAACATGTTAAGAAATTCATACTA
1 GGAACTTTGTGTGCTAAA-ATGTTAAGAAATTCATACTA
1594369 GGTTTATAAA
Statistics
Matches: 172, Mismatches: 33, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
56 4 0.02
57 31 0.18
58 72 0.42
59 61 0.35
60 4 0.02
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (59 bp):
GGAACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTAAGAATTTCCGTAATA
Found at i:1594323 original size:116 final size:116
Alignment explanation
Indices: 1594100--1594368 Score: 321
Period size: 116 Copynumber: 2.3 Consensus size: 116
1594090 AAGTGTTGGG
* * *
1594100 AACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGCGCTTT
1 AACTATGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTACGTATTAGGCCCTTT
*
1594165 GTGTGCTACAAATTTAAGAAATTCATACTGTGTGTAAGATTTCCGTAATAT
66 GTGTGCTACAAATTTAAGAAATTCATACTGTGTATAAGATTTCCGTAATAT
* * * *
1594216 AACTATGTGTGCTAAAATGTTAAGAAATTCATATTAATTGTATGAATTTATGTATTGGGCCCTTT
1 AACTATGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTACGTATTAGGCCCTTT
* * * **
1594281 -TGTGCTA-AAATGTTAAGAAATTTATTCTAAGTGTATAA-ATTTCCGTATTGGG
66 GTGTGCTACAAAT-TTAAGAAATTCATACT--GTGTATAAGATTTCCGTAAT-AT
* * *
1594333 CACTTTTTGTG-TAAACATGTTAAGAAATTCATACTA
1 AACTATGTGTGCTAAA-ATGTTAAGAAATTCATACTA
1594369 GGTTTATAAA
Statistics
Matches: 131, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
114 4 0.03
115 21 0.16
116 72 0.55
117 34 0.26
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (116 bp):
AACTATGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTACGTATTAGGCCCTTT
GTGTGCTACAAATTTAAGAAATTCATACTGTGTATAAGATTTCCGTAATAT
Found at i:1594416 original size:174 final size:175
Alignment explanation
Indices: 1594102--1594422 Score: 413
Period size: 174 Copynumber: 1.8 Consensus size: 175
1594092 GTGTTGGGAA
* *
1594102 CTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGCGCTTTGT
1 CTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATAAATTTCCGTATTAGGCACTTTGT
* * * *
1594167 GTGCTACAAATTTAAGAAATTCATACTGTGTGTAAGATTTCCGTAATATAACTATGTGTGCTAAA
66 GTGCTACAAATTTAAGAAATTCATACTGTGTGTAAAATTTCCGTAATAGAAATATATGTGCTAAA
*
1594232 ATGTTAAGAAATTCATATTAATTGTATGAATTTATGTATTGGGCC
131 ATGATAAGAAATTCATATTAATTGTATGAATTTATGTATTGGGCC
* * * *
1594277 CTTT-TGTGCTAAAATGTTAAGAAATTTATTCTAAGTGTATAAATTTCCGTATTGGGCACTTTTT
1 CTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATAAATTTCCGTATTAGGCACTTTGT
* * *
1594341 GTG-TA-AACATGTTAAGAAATTCATACTAG-GTTTATAAATTTCTGT-ATGGGAAATATATGTG
66 GTGCTACAA-AT-TTAAGAAATTCATACT-GTGTGTA-AAATTTCCGTAAT-AGAAATATATGTG
1594402 -TATAAAT-ATAAGAAATTCATA
126 CTA-AAATGATAAGAAATTCATA
1594423 ATAAGGAAAT
Statistics
Matches: 126, Mismatches: 14, Indels: 13
0.82 0.09 0.08
Matches are distributed among these distances:
172 2 0.02
173 4 0.03
174 94 0.75
175 26 0.21
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.40
Consensus pattern (175 bp):
CTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATAAATTTCCGTATTAGGCACTTTGT
GTGCTACAAATTTAAGAAATTCATACTGTGTGTAAAATTTCCGTAATAGAAATATATGTGCTAAA
ATGATAAGAAATTCATATTAATTGTATGAATTTATGTATTGGGCC
Found at i:1599562 original size:59 final size:59
Alignment explanation
Indices: 1599470--1599649 Score: 281
Period size: 59 Copynumber: 3.1 Consensus size: 59
1599460 TGTTTTTCAC
* *
1599470 TGTATGAATTTCCGTATTGGGCACTTTGTGTGCTAAAATGTTAAGAAAATCATACTAAG
1 TGTATGAATTTTCGTATTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAG
* * * * *
1599529 TGTATGAATTTTCATATTAGGCGCTTTTTGTGCTACAATGTTAAGAAATTCATACTAAG
1 TGTATGAATTTTCGTATTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAG
1599588 TGTATGAA-TTTCTGTATTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAG
1 TGTATGAATTTTC-GTATTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAG
1599647 TGT
1 TGT
1599650 TGGGCACTTT
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
58 4 0.04
59 104 0.96
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (59 bp):
TGTATGAATTTTCGTATTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAG
Found at i:1599668 original size:45 final size:45
Alignment explanation
Indices: 1599604--1599694 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
1599594 AATTTCTGTA
1599604 TTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTG
1 TTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTG
1599649 TTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTG
1 TTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTG
1599694 T
1 T
1599695 ATGAATTTCC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (45 bp):
TTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTG
Found at i:1599737 original size:104 final size:105
Alignment explanation
Indices: 1599552--1599875 Score: 400
Period size: 104 Copynumber: 3.0 Consensus size: 105
1599542 ATATTAGGCG
* * *
1599552 CTTTTTGTGCTACAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTTGT
1 CTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGT
1599617 GTGCTAAAATGTTAAGAAATTCATACTAAGTGT-TGGGCA
66 GTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGGGCA
*
1599656 CTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGCACTTTGT
1 CTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGT
* *
1599721 GTGCTACAATGTTAAGAAATTCATACTATGTGTATGAATTTCCGTATTGGCA
66 GTGCTAAAATGTTAAGAAATTCATACTA-----A-G----T--GTATGGGCA
* * * * *
1599773 CTATGTGTGCTAAAATATTAAAAAACACTTCATAATAAGTGTATGAATTT-CGAATTGGGCACTT
1 CTTTGTGTGCTAAAATGTT-AAGAA-A-TTCATACTAAGTGTATGAATTTCCGTATTGGGCACTT
1599837 TGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATG
63 TGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATG
1599876 AATTTCCGTA
Statistics
Matches: 190, Mismatches: 14, Indels: 29
0.82 0.06 0.12
Matches are distributed among these distances:
104 88 0.46
107 4 0.02
109 2 0.01
110 1 0.01
113 1 0.01
114 2 0.01
116 2 0.01
117 22 0.12
118 4 0.02
119 43 0.23
120 21 0.11
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (105 bp):
CTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGT
GTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGGGCA
Found at i:1599744 original size:59 final size:59
Alignment explanation
Indices: 1599649--1599945 Score: 447
Period size: 59 Copynumber: 5.0 Consensus size: 59
1599639 ATACTAAGTG
1599649 TTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTA
1 TTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTA
* * *
1599708 TTAGGCACTTTGTGTGCTACAATGTTAAGAAATTCATACTATGTGTATGAATTTCCGTA
1 TTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTA
* * * * *
1599767 TT-GGCACTATGTGTGCTAAAATATTAAAAAACACTTCATAATAAGTGTATGAATTT-CGAA
1 TTGGGCACTTTGTGTGCTAAAATGTT-AAGAA-A-TTCATACTAAGTGTATGAATTTCCGTA
1599827 TTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTA
1 TTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTA
* *
1599886 TTGGGCACTTTTTGTG-TAAACATGTTAAGAAATTCATACTAGGTGTATGAATTTCCGTA
1 TTGGGCACTTTGTGTGCTAAA-ATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTA
1599945 T
1 T
1599946 GGGAAATATA
Statistics
Matches: 215, Mismatches: 17, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
58 45 0.21
59 119 0.55
60 10 0.05
61 41 0.19
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (59 bp):
TTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTA
Found at i:1599756 original size:163 final size:171
Alignment explanation
Indices: 1599485--1599945 Score: 645
Period size: 163 Copynumber: 2.7 Consensus size: 171
1599475 GAATTTCCGT
* * *
1599485 ATTGGGCACTTTGTGTGCTAAAATGTTAAGAAAATCATACTAAGTGTATGAATTTTCATATTAGG
1 ATTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGG
* * *
1599550 CGCTTTTTGTGCTACAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTT
66 CACTTTTTGTGCTACAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATT-GGCACTAT
* * *
1599615 GTGTGCTAAAATGTT-AAGAA-A-TTCATACT-A-A-G-T-G
130 GTGTGCTAAAATATTAAAAAACACTTCATAATAAGATGATCG
1599649 -TTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGG
1 ATTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGG
* *
1599713 CACTTTGTGTGCTACAATGTTAAGAAATTCATACTATGTGTATGAATTTCCGTATTGGCACTATG
66 CACTTTTTGTGCTACAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGCACTATG
1599778 TGTGCTAAAATATTAAAAAACACTTCATAATAAGTGTATGAATTTCG
131 TGTGCTAAAATATTAAAAAACACTTCATAATAA--G-ATG-A--TCG
*
1599825 AATTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGG
1 -ATTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAG
* *
1599890 GCACTTTTTGTG-TAAACATGTTAAGAAATTCATACTAGGTGTATGAATTTCCGTAT
65 GCACTTTTTGTGCTACA-ATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
1599946 GGGAAATATA
Statistics
Matches: 265, Mismatches: 15, Indels: 20
0.88 0.05 0.07
Matches are distributed among these distances:
162 21 0.08
163 117 0.44
164 1 0.00
165 7 0.03
166 1 0.00
170 1 0.00
171 1 0.00
175 1 0.00
176 1 0.00
177 3 0.01
178 111 0.42
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.38
Consensus pattern (171 bp):
ATTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGG
CACTTTTTGTGCTACAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGCACTATG
TGTGCTAAAATATTAAAAAACACTTCATAATAAGATGATCG
Found at i:1599861 original size:119 final size:117
Alignment explanation
Indices: 1599649--1599940 Score: 435
Period size: 119 Copynumber: 2.5 Consensus size: 117
1599639 ATACTAAGTG
*
1599649 TTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGC
1 TTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTT-CGAATTAGGC
* *
1599714 ACTTTGTGTGCTACAATGTTAAGAAATTCATACTATGTGTATGAATTTCCGTA
65 ACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTA
* * * * *
1599767 TT-GGCACTATGTGTGCTAAAATATTAAAAAACACTTCATAATAAGTGTATGAATTTCGAATTGG
1 TTGGGCACTTTGTGTGCTAAAATGTT-AAGAA-A-TTCATACTAAGTGTATGAATTTCGAATTAG
1599831 GCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTA
63 GCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTA
* *
1599886 TTGGGCACTTTTTGTG-TAAACATGTTAAGAAATTCATACTAGGTGTATGAATTTC
1 TTGGGCACTTTGTGTGCTAAA-ATGTTAAGAAATTCATACTAAGTGTATGAATTTC
1599941 CGTATGGGAA
Statistics
Matches: 155, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
117 42 0.27
118 7 0.05
119 70 0.45
120 36 0.23
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (117 bp):
TTGGGCACTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCGAATTAGGCA
CTTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTA
Found at i:1601492 original size:90 final size:90
Alignment explanation
Indices: 1600846--1601492 Score: 858
Period size: 90 Copynumber: 7.3 Consensus size: 90
1600836 CTAAAACTTT
* * * * * * ** * * *
1600846 TCTCGAGTCTGATCTCACTGGAAGAGTAGAGGAATATATTCACCATATTTCAGAT-TTGGTCTCC
1 TCTCGAGTCTGATCTCCCCGAAAGAGTAGTGGAACAGATTCTTCTTATTTCAGATATTGGCCTTC
1600910 ACAAAAGAGTAGTGAAGCAAATCAA
66 ACAAAAGAGTAGTGAAGCAAATCAA
* * * * *
1600935 TTTCGAGTCTGATATCCAC-AGAAGAGTAGTGGAACATATTCTTCTTATTTCAGATATTGGCATT
1 TCTCGAGTCTGATCTCCCCGA-AAGAGTAGTGGAACAGATTCTTCTTATTTCAGATATTGGCCTT
* *
1600999 CACGAAAGAGTAGTAAAGCAAATCAA
65 CACAAAAGAGTAGTGAAGCAAATCAA
* * *
1601025 TCTCGAGTCTGATCTCCCCAAAAGAGTAGTGGAACATATTCTTTTTATTTCAGATATTGGCCTTC
1 TCTCGAGTCTGATCTCCCCGAAAGAGTAGTGGAACAGATTCTTCTTATTTCAGATATTGGCCTTC
*
1601090 ACGAAAGAGTAGTGAAGCAAATCAA
66 ACAAAAGAGTAGTGAAGCAAATCAA
* * * * *
1601115 --TCGAGTCTGAGCTCCCAGAAAGAGTGGTGGAATAGATTCTTCTTATTTCACATATTGGCCTTC
1 TCTCGAGTCTGATCTCCCCGAAAGAGTAGTGGAACAGATTCTTCTTATTTCAGATATTGGCCTTC
** **
1601178 ATGAAAGAACAGTGAAGCAAATCAA
66 ACAAAAGAGTAGTGAAGCAAATCAA
* *
1601203 TCTCGATTCTGATCT-CCCGAAAGAGTAGTGGAACAGATTCTTCTTATTTCAGATA-TAGCCTTC
1 TCTCGAGTCTGATCTCCCCGAAAGAGTAGTGGAACAGATTCTTCTTATTTCAGATATTGGCCTTC
*
1601266 ATAAAAGAGTAGTGAAGCAAATCAA
66 ACAAAAGAGTAGTGAAGCAAATCAA
*
1601291 TCTCGAGT-TGATCTCCCCGAAAGAGTAGTGGAACAGATTCTTCTTATTTCAAATATTGGCCTTC
1 TCTCGAGTCTGATCTCCCCGAAAGAGTAGTGGAACAGATTCTTCTTATTTCAGATATTGGCCTTC
1601355 ACAAAAGAGTAGTGAAGCAAATCAA
66 ACAAAAGAGTAGTGAAGCAAATCAA
* * ** *
1601380 TCTTGAGTCTGATCTCCCCGAAAGAGTAGTGGAACATATTCTTCTTATTTCAGATATTAACATTC
1 TCTCGAGTCTGATCTCCCCGAAAGAGTAGTGGAACAGATTCTTCTTATTTCAGATATTGGCCTTC
1601445 ACAAAAGAGTAGTGAAGCAAATCAA
66 ACAAAAGAGTAGTGAAGCAAATCAA
* *
1601470 TCTCAAGTCTGATCTCCTCGAAA
1 TCTCGAGTCTGATCTCCCCGAAA
1601493 ATAGAGAAGC
Statistics
Matches: 494, Mismatches: 56, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
87 6 0.01
88 152 0.31
89 117 0.24
90 218 0.44
91 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (90 bp):
TCTCGAGTCTGATCTCCCCGAAAGAGTAGTGGAACAGATTCTTCTTATTTCAGATATTGGCCTTC
ACAAAAGAGTAGTGAAGCAAATCAA
Found at i:1603255 original size:13 final size:15
Alignment explanation
Indices: 1603232--1603309 Score: 76
Period size: 16 Copynumber: 5.3 Consensus size: 15
1603222 TTTTCTTTTT
1603232 TTTATAATTTA-ATA
1 TTTATAATTTATATA
1603246 TTTA-AATTTATTATA
1 TTTATAATTTA-TATA
*
1603261 TTTATTATTT-TAATA
1 TTTATAATTTAT-ATA
1603276 TTT-T-ATTTATATA
1 TTTATAATTTATATA
*
1603289 TTTATATATTTATAAA
1 TTTATA-ATTTATATA
1603305 TTTAT
1 TTTAT
1603310 TAGGAAATAA
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
13 16 0.30
14 8 0.15
15 13 0.24
16 17 0.31
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATAATTTATATA
Found at i:1603264 original size:29 final size:27
Alignment explanation
Indices: 1603232--1603300 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 27
1603222 TTTTCTTTTT
1603232 TTTATAATTTAATATTTAAATTTATTATA
1 TTTATAATTTAATATTT-AATTTA-TATA
* *
1603261 TTTATTATTTTAATATTTTATTTATATA
1 TTTA-TAATTTAATATTTAATTTATATA
1603289 TTTATATATTTA
1 TTTATA-ATTTA
1603301 TAAATTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 2 0.06
28 12 0.34
29 9 0.26
30 12 0.34
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTATAATTTAATATTTAATTTATATA
Found at i:1603275 original size:30 final size:30
Alignment explanation
Indices: 1603234--1603308 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
1603224 TTCTTTTTTT
*
1603234 TATAATTTAATATTTAAATTTATTATATTTA
1 TATATTTTAATATTTAAATTTA-TATATTTA
*
1603265 T-TATTTTAATATTT-TATTTATATATTTA
1 TATATTTTAATATTTAAATTTATATATTTA
1603293 TATATTTATAA-ATTTA
1 TATATTT-TAATATTTA
1603309 TTAGGAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 9 0.23
29 14 0.36
30 15 0.38
31 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
TATATTTTAATATTTAAATTTATATATTTA
Found at i:1603290 original size:8 final size:8
Alignment explanation
Indices: 1603232--1603309 Score: 66
Period size: 8 Copynumber: 10.6 Consensus size: 8
1603222 TTTTCTTTTT
1603232 TTTATA-A
1 TTTATATA
1603239 TTTA-ATA
1 TTTATATA
1603246 TTTA-A-A
1 TTTATATA
1603252 TTTATTATA
1 TTTA-TATA
1603261 TTTAT-TA
1 TTTATATA
1603268 TTT-TA-A
1 TTTATATA
1603274 TATT-T-TA
1 T-TTATATA
1603281 TTTATATA
1 TTTATATA
1603289 TTTATATA
1 TTTATATA
*
1603297 TTTATAAA
1 TTTATATA
1603305 TTTAT
1 TTTAT
1603310 TAGGAAATAA
Statistics
Matches: 61, Mismatches: 1, Indels: 17
0.77 0.01 0.22
Matches are distributed among these distances:
6 11 0.18
7 21 0.34
8 24 0.39
9 5 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTTATATA
Found at i:1603292 original size:20 final size:21
Alignment explanation
Indices: 1603254--1603299 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
1603244 TATTTAAATT
*
1603254 TATTATATTTATTATTTTA-A
1 TATTTTATTTATTATTTTATA
1603274 TATTTTATTTA-TATATTTATA
1 TATTTTATTTATTAT-TTTATA
1603295 TATTT
1 TATTT
1603300 ATAAATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 3 0.13
20 14 0.61
21 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTTTATTTATTATTTTATA
Found at i:1603300 original size:20 final size:19
Alignment explanation
Indices: 1603251--1603301 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 19
1603241 TAATATTTAA
1603251 ATTTATTATATTTA-TTATT
1 ATTTA-TATATTTATTTATT
*
1603270 -TTAATAT-TTTATTTATAT
1 ATTTATATATTTATTTAT-T
1603288 ATTTATATATTTAT
1 ATTTATATATTTAT
1603302 AAATTTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
16 4 0.15
17 7 0.27
18 4 0.15
19 6 0.23
20 5 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTATATATTTATTTATT
Found at i:1612588 original size:7 final size:8
Alignment explanation
Indices: 1612571--1612595 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1612561 GTGATTGGTT
1612571 AAAAGGAA
1 AAAAGGAA
1612579 AAAAGGAA
1 AAAAGGAA
1612587 AAAAGGAA
1 AAAAGGAA
1612595 A
1 A
1612596 TATAATGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AAAAGGAA
Found at i:1613827 original size:15 final size:14
Alignment explanation
Indices: 1613799--1613839 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1613789 TAAGTAACAT
1613799 AAATA-TTTAAAAG
1 AAATATTTTAAAAG
*
1613812 AAAATATTTTATAAG
1 -AAATATTTTAAAAG
1613827 AAATATTTTAAAA
1 AAATATTTTAAAA
1613840 TTTATTAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (14 bp):
AAATATTTTAAAAG
Found at i:1614099 original size:70 final size:70
Alignment explanation
Indices: 1613965--1614123 Score: 187
Period size: 70 Copynumber: 2.3 Consensus size: 70
1613955 ACTATATCCT
* * * * * *
1613965 TAACTTAAAACCCTAAATTTATAATCTTAAACCCTAACCCTATAACCTATATACCCTAACCCTTA
1 TAACTTAAAACTCTAAATTGATAATCCTAAACCCTAACCCTATAACATATAAACCCTAAACCTTA
1614030 ATCTC
66 ATCTC
* * *
1614035 TAACTTAAAAGTCTAAATTGATAATCCTAAACCCTAA-CC-ATGACATAATAAAACCTTAAACCT
1 TAACTTAAAACTCTAAATTGATAATCCTAAACCCTAACCCTATAACAT-AT-AAACCCTAAACCT
*
1614098 TAATCTT
64 TAATCTC
*
1614105 TAACTTAAAACTCTTAATT
1 TAACTTAAAACTCTAAATT
1614124 TAAGGTTTTA
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
68 5 0.07
69 4 0.05
70 66 0.88
ACGTcount: A:0.42, C:0.25, G:0.02, T:0.32
Consensus pattern (70 bp):
TAACTTAAAACTCTAAATTGATAATCCTAAACCCTAACCCTATAACATATAAACCCTAAACCTTA
ATCTC
Found at i:1615486 original size:47 final size:47
Alignment explanation
Indices: 1615415--1615506 Score: 157
Period size: 47 Copynumber: 2.0 Consensus size: 47
1615405 GAGGAATGAT
* *
1615415 GAATGAAAAGCCACATCAGTGGATTGTAATATATCTTCAACAATACG
1 GAATGAAAAGCCACATCAGCGGATTGTAATATAACTTCAACAATACG
*
1615462 GAATGAAAAGCCACATCAGCGGATTGTGATATAACTTCAACAATA
1 GAATGAAAAGCCACATCAGCGGATTGTAATATAACTTCAACAATA
1615507 TGGATTATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (47 bp):
GAATGAAAAGCCACATCAGCGGATTGTAATATAACTTCAACAATACG
Found at i:1617758 original size:82 final size:83
Alignment explanation
Indices: 1617580--1617770 Score: 242
Period size: 82 Copynumber: 2.3 Consensus size: 83
1617570 AATTTAACTT
* * * * *
1617580 TGAAAAACAAAGGATGTGAATAGTATAGATTCTCTGATTTCAATGGAAATTATATCAGTTTATTT
1 TGAAAAACAAATGACGTGAATAGTATAGATTCCCTGATTTC-AT-GAAAATATATCAGTTTATCT
*
1617645 GAGTTAATGTGAAATGTCAA
64 GAGTTAATATGAAATGTCAA
*
1617665 TGAAAAACAAATGACGTGAATAGTATAGATTCCCTGATTCTC-T-AAAATATTTCAGTTTATCTG
1 TGAAAAACAAATGACGTGAATAGTATAGATTCCCTGATT-TCATGAAAATATATCAGTTTATCTG
**
1617728 AGTTGCTATGAAATGTCAA
65 AGTTAATATGAAATGTCAA
* *
1617747 TGACAAGCAAATGACGTGAATAGT
1 TGAAAAACAAATGACGTGAATAGT
1617771 GTAGGTTGTC
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
82 55 0.59
84 1 0.01
85 36 0.38
86 2 0.02
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (83 bp):
TGAAAAACAAATGACGTGAATAGTATAGATTCCCTGATTTCATGAAAATATATCAGTTTATCTGA
GTTAATATGAAATGTCAA
Found at i:1622138 original size:34 final size:34
Alignment explanation
Indices: 1622099--1622169 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
1622089 ATCAAAAGAG
1622099 ACACACTTAGTAAGACAA-AGAAAATATATATTAT
1 ACACACTTAGTAAGACAAGA-AAAATATATATTAT
*
1622133 ACACACTTAGTAAGACAGGAAAAATATATATTAT
1 ACACACTTAGTAAGACAAGAAAAATATATATTAT
1622167 ACA
1 ACA
1622170 AATTTAAAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 34 0.97
35 1 0.03
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.25
Consensus pattern (34 bp):
ACACACTTAGTAAGACAAGAAAAATATATATTAT
Found at i:1624789 original size:34 final size:34
Alignment explanation
Indices: 1624746--1624812 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
1624736 ATGTTTATAT
1624746 GAAAAAGAAAATAACATGAAGCACGGATGAATTG
1 GAAAAAGAAAATAACATGAAGCACGGATGAATTG
*
1624780 GAAAAAGAAAATAATATGAAGCACGGATGAATT
1 GAAAAAGAAAATAACATGAAGCACGGATGAATT
1624813 TATAATCAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.54, C:0.07, G:0.22, T:0.16
Consensus pattern (34 bp):
GAAAAAGAAAATAACATGAAGCACGGATGAATTG
Found at i:1626208 original size:20 final size:20
Alignment explanation
Indices: 1626183--1626230 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
1626173 GCGATTTTTC
1626183 CAAATTCGCAACACAGAAGT
1 CAAATTCGCAACACAGAAGT
1626203 CAAATTCGCAACACAGAAGT
1 CAAATTCGCAACACAGAAGT
1626223 CAAATTCG
1 CAAATTCG
1626231 TAAAGAGCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.44, C:0.25, G:0.15, T:0.17
Consensus pattern (20 bp):
CAAATTCGCAACACAGAAGT
Found at i:1626834 original size:20 final size:20
Alignment explanation
Indices: 1626776--1626835 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
1626766 AAGACTATTT
* * *
1626776 GAAACTTAAATTCGCAACAC
1 GAAACTGAAAATCGCAACGC
* **
1626796 GAAAATGAAAATCATAACGC
1 GAAACTGAAAATCGCAACGC
1626816 GAAACTGAAAATCGCAACGC
1 GAAACTGAAAATCGCAACGC
1626836 CATTTTCATT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.48, C:0.22, G:0.15, T:0.15
Consensus pattern (20 bp):
GAAACTGAAAATCGCAACGC
Found at i:1626850 original size:20 final size:20
Alignment explanation
Indices: 1626827--1626871 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1626817 AAACTGAAAA
1626827 TCGCAACGCCATTTTCATTT
1 TCGCAACGCCATTTTCATTT
*** *
1626847 TCGCGTTGCGATTTTCATTT
1 TCGCAACGCCATTTTCATTT
1626867 TCGCA
1 TCGCA
1626872 TTGCGATTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.16, T:0.42
Consensus pattern (20 bp):
TCGCAACGCCATTTTCATTT
Found at i:1626875 original size:20 final size:20
Alignment explanation
Indices: 1626837--1626881 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1626827 TCGCAACGCC
*
1626837 ATTTTCATTTTCGCGTTGCG
1 ATTTTCATTTTCGCATTGCG
1626857 ATTTTCATTTTCGCATTGCG
1 ATTTTCATTTTCGCATTGCG
1626877 ATTTT
1 ATTTT
1626882 AAGTTTCAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.13, C:0.18, G:0.16, T:0.53
Consensus pattern (20 bp):
ATTTTCATTTTCGCATTGCG
Found at i:1626888 original size:20 final size:20
Alignment explanation
Indices: 1626845--1626888 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1626835 CCATTTTCAT
* * *
1626845 TTTCGCGTTGCGATTTTCAT
1 TTTCGCATTGCGATTTTAAG
1626865 TTTCGCATTGCGATTTTAAG
1 TTTCGCATTGCGATTTTAAG
1626885 TTTC
1 TTTC
1626889 AGAAGCTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.50
Consensus pattern (20 bp):
TTTCGCATTGCGATTTTAAG
Found at i:1628911 original size:21 final size:20
Alignment explanation
Indices: 1628885--1629001 Score: 94
Period size: 21 Copynumber: 5.6 Consensus size: 20
1628875 AGCACCTGTC
1628885 ATCGTTCAAGAGGCCTCTCCT
1 ATCGTTCAAGAGGCC-CTCCT
*
1628906 ATCGTTCAAGAGGCCCAT-AT
1 ATCGTTCAAGAGGCCC-TCCT
* *
1628926 CATCATTCAAGAGGCCCCTCCC
1 -ATCGTTCAAGAGG-CCCTCCT
* *
1628948 ACCGTTCAAGAGGCCC-CTGT
1 ATCGTTCAAGAGGCCCTC-CT
*
1628968 CATCGTTCAAGAGGTCCCTCCC
1 -ATCGTTCAAGAGG-CCCTCCT
*
1628990 ACCGTTCAAGAG
1 ATCGTTCAAGAG
1629002 CCCGATTCAC
Statistics
Matches: 76, Mismatches: 12, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
19 1 0.01
20 5 0.07
21 63 0.83
22 6 0.08
23 1 0.01
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGTTCAAGAGGCCCTCCT
Found at i:1628935 original size:42 final size:41
Alignment explanation
Indices: 1628883--1629001 Score: 166
Period size: 42 Copynumber: 2.8 Consensus size: 41
1628873 GAAGCACCTG
* *
1628883 TCATCGTTCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCATA
1 TCATCGTTCAAGAGGCC-CTCCCACCGTTCAAGAGGCCCATA
* * *
1628925 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGG-CCCTCCCACCGTTCAAGAGGCCCATA
1628967 TCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAG
1 TCATCGTTCAAGAGG-CCCTCCCACCGTTCAAGAG
1629002 CCCGATTCAC
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 67 0.97
43 2 0.03
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.23
Consensus pattern (41 bp):
TCATCGTTCAAGAGGCCCTCCCACCGTTCAAGAGGCCCATA
Done.