Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold13
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: 2744999
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.26
Warning! 506982 characters in sequence are not A, C, G, or T
File 6 of 15
Found at i:1230398 original size:13 final size:13
Alignment explanation
Indices: 1230380--1230405 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1230370 ATTAAGGAAA
1230380 TGTATCGATACAT
1 TGTATCGATACAT
1230393 TGTATCGATACAT
1 TGTATCGATACAT
1230406 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1232787 original size:51 final size:50
Alignment explanation
Indices: 1232724--1233060 Score: 331
Period size: 51 Copynumber: 6.6 Consensus size: 50
1232714 TTAAGTTTCT
* * *
1232724 CAATTGTTCATAATCGGGGATACTCCAACCCCGGCTTTATTTCCAAAATAT
1 CAATT-TTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACAC
**
1232775 TGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTA-TTCCTAAAACAC
1 CAATTT-TCATAATCGGGGATACTCCAACCCCGGTTTTATTTCC-AAAACAC
* * * * * ***
1232826 TAATTTTCCACAATTGGGGATACTCCAACTCCGATTTTATTTTTGAAACAC
1 CAATTTT-CATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACAC
* * * * *
1232877 CAATTTTCCACAGTTGGGGATACTCTAACCCCGGTTTTATTTTCAAAACAC
1 CAATTTT-CATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACAC
* * *
1232928 CAATTTTCTATAATCAGGGGATACTCCAACTCTGATTTTATTTCCAAAAACAC
1 CAATTTTC-ATAATC-GGGGATACTCCAACCCCGGTTTTATTTCC-AAAACAC
* ** *
1232981 CAATTTTTCAT-CTCGGGGATACTCCAACCCCGGTTTTATTTTTAAAACAT
1 CAA-TTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACAC
*
1233031 CAATTTT--TCATCGGGGATACTCCAACCCCG
1 CAATTTTCATAATCGGGGATACTCCAACCCCG
1233061 TTATTTTCGA
Statistics
Matches: 241, Mismatches: 36, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
47 1 0.00
48 20 0.08
49 4 0.02
50 16 0.07
51 155 0.64
52 28 0.12
53 12 0.05
54 5 0.02
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (50 bp):
CAATTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACAC
Found at i:1233190 original size:76 final size:76
Alignment explanation
Indices: 1232995--1233179 Score: 316
Period size: 76 Copynumber: 2.4 Consensus size: 76
1232985 TTTTCATCTC
* *
1232995 GGGGATACTCCAACCCCGGTTTTATTTTTAAAACATCAATTTTTCATCGGGGATACTCCAACCCC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCC
*
1233060 GTTATTTTCGA
66 GTTATTTCCGA
*
1233071 GGGGATACTCCAACCTCGATTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCC
1233136 GTTATTTCCGA
66 GTTATTTCCGA
* *
1233147 GGGGATACTCCAACCCCGACTTTATATCTAAAA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAA
1233180 ATATTGTTTT
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 102 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (76 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCC
GTTATTTCCGA
Found at i:1233275 original size:51 final size:50
Alignment explanation
Indices: 1233200--1233299 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 50
1233190 TTTCATAATC
* * *
1233200 CCGATTTATTTCTAAAATACCAATTTTTCACAATCG-GAGATACTCCAACT
1 CCGATTTATTTCCAAAACACCAATTTCTCACAATCGAG-GATACTCCAACT
1233250 CCGATTTTATTTCCAAAACACCAATTTCTCACAATCGAGGATACTCCAAC
1 CCGA-TTTATTTCCAAAACACCAATTTCTCACAATCGAGGATACTCCAAC
1233300 CCCGCTATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
50 4 0.09
51 40 0.89
52 1 0.02
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (50 bp):
CCGATTTATTTCCAAAACACCAATTTCTCACAATCGAGGATACTCCAACT
Found at i:1240244 original size:13 final size:13
Alignment explanation
Indices: 1240226--1240251 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1240216 CAATTTTTTG
1240226 TGTATCGATACAT
1 TGTATCGATACAT
1240239 TGTATCGATACAT
1 TGTATCGATACAT
1240252 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1241355 original size:13 final size:13
Alignment explanation
Indices: 1241337--1241375 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1241327 ATAATCACCT
*
1241337 TGTATCGATACAG
1 TGTATCGATACAA
1241350 TGTATCGATACAA
1 TGTATCGATACAA
1241363 TGTATCGATACAA
1 TGTATCGATACAA
1241376 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1241386 original size:20 final size:20
Alignment explanation
Indices: 1241361--1241439 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
1241351 GTATCGATAC
1241361 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1241381 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
1241406 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
1241426 CATGTATCGATACA
1 AATGTATCGATACA
1241440 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1241593 original size:8 final size:8
Alignment explanation
Indices: 1241580--1241608 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1241570 CATTCAACAT
1241580 AAAATCAC
1 AAAATCAC
1241588 AAAATCAC
1 AAAATCAC
1241596 AAAATCAC
1 AAAATCAC
1241604 AAAAT
1 AAAAT
1241609 TTAATCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.66, C:0.21, G:0.00, T:0.14
Consensus pattern (8 bp):
AAAATCAC
Found at i:1243487 original size:15 final size:15
Alignment explanation
Indices: 1243467--1243497 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1243457 ATTTCGTTTG
*
1243467 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1243482 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1243497 G
1 G
1243498 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1245330 original size:21 final size:21
Alignment explanation
Indices: 1245301--1245345 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1245291 AAGTTTTCAT
*
1245301 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1245321 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1245343 TTT
1 TTT
1245346 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1247581 original size:13 final size:13
Alignment explanation
Indices: 1247563--1247588 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1247553 CAATTTTTTG
1247563 TGTATCGATACAT
1 TGTATCGATACAT
1247576 TGTATCGATACAT
1 TGTATCGATACAT
1247589 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1248048 original size:61 final size:61
Alignment explanation
Indices: 1247971--1248719 Score: 973
Period size: 61 Copynumber: 12.3 Consensus size: 61
1247961 GATCCTAACA
* * **
1247971 AGCAGGACACCTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGCACCTTTAGTCCTCAAAG
1 AGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAG
* * * *
1248032 AACAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTAGTCCTCAAAG
1 AGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAG
* * ** *
1248093 AGCAGGACACTTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTCCAATCCTCAAAG
1 AGCAGGACGC-CTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAG
* * *
1248155 AGTAGGACACCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTAGTCCTCAAAG
1 AGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAG
* * * * *
1248216 AGCACGACACC-TTTTCCTTTTAAAGCCCACACAAGTTGGTGTCACCTTTAGTCCTCAAAA
1 AGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAG
* *
1248276 AGCAGGAC-ACATTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
1 AGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-AGTCCTCAAAG
*
1248337 AGCAGGACG-C-----C-TTTTAAATCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAG
1 AGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACC-TTTAGTCCTCAAAG
* *** * *
1248392 AGCAAGACATTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAATCCTCAAAG
1 AGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACC-TTTAGTCCTCAAAG
* * *
1248454 AGCAGGACGCC-TTTTCCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTAGTCCTTAAAG
1 AGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAG
* *
1248514 AGCAGGACGCC-TTTTCTTTTTAAAGCCCACAAAAGTTGGTGGCACCTTTTAGTCCTTAAAG
1 AGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACC-TTTAGTCCTCAAAG
* *
1248575 AGCAGGACACC-TTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTAGTCCTCAAAG
1 AGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAG
* *
1248635 AGCAGGACGCTTTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAG
1 AGCAGGACGC--CTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTTAGTCCTCAAAG
* *
1248699 TGCAGGACGCCTTTTCCTTTT
1 AGCAGGACGCCTTTTTCTTTT
1248720 CTCCTTAGTC
Statistics
Matches: 614, Mismatches: 57, Indels: 33
0.87 0.08 0.05
Matches are distributed among these distances:
55 46 0.07
56 4 0.01
59 1 0.00
60 165 0.27
61 230 0.37
62 112 0.18
63 33 0.05
64 23 0.04
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (61 bp):
AGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAG
Found at i:1248330 original size:121 final size:121
Alignment explanation
Indices: 1247971--1248719 Score: 1003
Period size: 121 Copynumber: 6.2 Consensus size: 121
1247961 GATCCTAACA
* ** *
1247971 AGCAGGACACCTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGCACCTTTAGTCCTCAAAGAACA
1 AGCAGGACACCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCA
* *
1248036 GGATGC-CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC-TTTAGTCCTCAAAG
65 GGA--CACTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAG
* * ** * *
1248093 AGCAGGACACTTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTCCAATCCTCAAAGAGT
1 AGCAGGACAC--CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGC
*
1248158 AGGACACCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACC-TTTAGTCCTCAAAG
64 AGGACA-CTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAG
* * *
1248216 AGCACGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGTCACCTTTAGTCCTCAAAAAGCAG
1 AGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAG
* *
1248281 GACACATTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
66 GACACTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAG
* *
1248337 AGCAGG--A-C---GCCTTTTAAATCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCA
1 AGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTTAGTCCTCAAAGAGCA
* * * *
1248396 AGACATTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAATCCTCAAAG
65 GGACA-CTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAG
* * *
1248454 AGCAGGACGCCTTTTCCTTTTAAAGCCCACACGAGTTGGTGGCACCTTTAGTCCTTAAAGAGCAG
1 AGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAG
* * * *
1248519 GACGCCTTTTCTTTTTAAAGCCCACAAAAGTTGGTGGCACCTTTTAGTCCTTAAAG
66 GACACTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAG
* *
1248575 AGCAGGACACCTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAG
1 AGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAG
* *
1248640 GACGCTTTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAG
66 GACAC---TTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAG
* *
1248699 TGCAGGACGCCTTTTCCTTTT
1 AGCAGGACACCTTTTCCTTTT
1248720 CTCCTTAGTC
Statistics
Matches: 554, Mismatches: 57, Indels: 30
0.86 0.09 0.05
Matches are distributed among these distances:
115 29 0.05
116 21 0.04
117 53 0.10
118 1 0.00
119 1 0.00
120 36 0.06
121 183 0.33
122 30 0.05
123 127 0.23
124 73 0.13
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (121 bp):
AGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAG
GACACTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAG
Found at i:1248788 original size:55 final size:55
Alignment explanation
Indices: 1248725--1248917 Score: 208
Period size: 55 Copynumber: 3.4 Consensus size: 55
1248715 CTTTTCTCCT
*
1248725 TAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACGAGTTGGTAGCATTTTCC
1 TAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACGAGTTGGTAGCA-CTTCC
* * * *
1248781 TA-TCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTCT
1 TAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACGAGTTGGTAGCACTTCC
* * * * * * *
1248835 TAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGACCACTCCAGTTGGTGGCACTCCC
1 TAGTCCTCAAAGAGCAGGA---C---ACCTTTCAAAGCCCACACGAGTTGGTAGCACTTCC
1248896 TAGTCCTCAAAGAGCAGGACAC
1 TAGTCCTCAAAGAGCAGGACAC
1248918 TCTCTCCTTT
Statistics
Matches: 116, Mismatches: 14, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
54 5 0.04
55 60 0.52
56 2 0.02
58 2 0.02
61 47 0.41
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (55 bp):
TAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACGAGTTGGTAGCACTTCC
Found at i:1248926 original size:61 final size:60
Alignment explanation
Indices: 1248801--1248929 Score: 161
Period size: 61 Copynumber: 2.1 Consensus size: 60
1248791 GAGTAGGACG
* * * * *
1248801 CCTTTCAAAGCCCACACGAGTTGGTGGCACTTCTTAGTCCTCAAAGAGCAGGATGCCTTTT
1 CCTTTCAAAGACCACACCAGTTGGTGGCACTCCCTAGTCCTCAAAGAGCAGGA-GCCTTCT
* *
1248862 CCTTTTAAAGACCACTCCAGTTGGTGGCACTCCCTAGTCCTCAAAGAGCAGGA-CACTCTCT
1 CCTTTCAAAGACCACACCAGTTGGTGGCACTCCCTAGTCCTCAAAGAGCAGGAGC-CT-TCT
1248923 CCTTTCA
1 CCTTTCA
1248930 CCCATTAGTC
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
59 1 0.02
60 2 0.03
61 55 0.95
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (60 bp):
CCTTTCAAAGACCACACCAGTTGGTGGCACTCCCTAGTCCTCAAAGAGCAGGAGCCTTCT
Found at i:1248983 original size:155 final size:160
Alignment explanation
Indices: 1248783--1249569 Score: 823
Period size: 155 Copynumber: 4.8 Consensus size: 160
1248773 CATTTTCCTA
* * *
1248783 TCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTCTTAGTCCTCAAAGA
1 TCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGA
* * * *
1248848 GCAGGATGCCTTTTCCTTTTAAAGACCACTCCAGTTGGTGGCACTCCCTAGTCCTCAAAGAGCAG
66 GCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTCTCTAGTCCTCAAAGAGCAG
1248913 GACACTCTCTC-C-TT-T-CACCCATT-AG
131 GACACTCTCTCACATTGTGCACCCATTCAG
* * * *
1248938 TCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACATAAGTTAGTGGCACTTCTCAGCCCTCAAAGA
1 TCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGA
* * *
1249003 GCAGGATGCCTTTTCCTTTTAAAGACCACTCCAA-TTGGTGGCACTCCCTAGTCCTCAAAGAGCA
66 GCAGGATGCCTTTTCCTTTTAAAGCCCAC-ACAAGTTGGTGGCACTCTCTAGTCCTCAAAGAGCA
* * ****
1249067 GGACACCTCTTAAAGCCCACATAAGTTGGTGGCATTTTCCAG
130 GGACA-CTC-T----CTCACAT-TG-TGCACCCA--TT-CAG
* **
1249109 TCCTCAAAAAGCAGGACGCCTTTCAAAGCTTACACAAGTTGGTGGCACTTC-CAAGTCCTCAAAG
1 TCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCTC-AGTCCTCAAAG
* * *
1249173 AGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTTAGTCCTCAAAGAGCA
65 AGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTCTCTAGTCCTCAAAGAGCA
* * * * ***
1249237 AGACGCCTTTCAAAGCCCACACGAGTTGGTGGCA-TTTTTCAG
130 GGAC-AC--T-----CTCTCAC-A-TT-GT-GCACCCATTCAG
* *
1249279 TCCTTAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTCTCAGTCCTCAAAGA
1 TCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGA
*
1249344 GCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCTAGTCCTCAAAGAGTA
66 GCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTC-TCTAGTCCTCAAAGAGCA
* * *
1249408 GGACGCTCTCT--C-TTCT-CACCC-TTTAG
130 GGACACTCTCTCACATTGTGCACCCATTCAG
1249434 TCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-TCAGTCCTCAAAG
1 TCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTCTCAGTCCTCAAAG
* * * *
1249498 AGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTGTAGTCCTCAAAGAGC
65 AGCAGGATGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACTCTCTAGTCCTCAAAGAGC
1249563 AGGACAC
129 AGGACAC
1249570 ACTTTATTTT
Statistics
Matches: 532, Mismatches: 63, Indels: 73
0.80 0.09 0.11
Matches are distributed among these distances:
155 205 0.39
156 53 0.10
157 2 0.00
158 2 0.00
161 3 0.01
162 1 0.00
163 3 0.01
166 1 0.00
167 2 0.00
168 1 0.00
169 2 0.00
170 130 0.24
171 116 0.22
172 5 0.01
173 2 0.00
174 3 0.01
177 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (160 bp):
TCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGA
GCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTCTCTAGTCCTCAAAGAGCAG
GACACTCTCTCACATTGTGCACCCATTCAG
Found at i:1249111 original size:55 final size:53
Alignment explanation
Indices: 1249020--1249413 Score: 369
Period size: 55 Copynumber: 7.0 Consensus size: 53
1249010 GCCTTTTCCT
* * * *
1249020 TTTAAAGACCACTCCAA-TTGGTGGCACTCCCTAGTCCTCAAAGAGCAGGACACC
1 TTTAAAGCCCAC-ACAAGTTGGTGGCACTTCC-AGTCCTCAAAGAGCAGGACGCC
* * *
1249074 TCTTAAAGCCCACATAAGTTGGTGGCATTTTCCAGTCCTCAAAAAGCAGGACGCC
1 T-TTAAAGCCCACACAAGTTGGTGGCA-CTTCCAGTCCTCAAAGAGCAGGACGCC
**
1249129 TTTCAAAGCTTACACAAGTTGGTGGCACTTCCAAGTCCTCAAAGAGCAGGACGCCTTCTCC
1 TTT-AAAGCCCACACAAGTTGGTGGCACTTCC-AGTCCTCAAAGAGCAGGACG------CC
* *
1249190 TTTTAAAGCCCACACAAGTTGGTGGCACCTT-TAGTCCTCAAAGAGCAAGACGCC
1 -TTTAAAGCCCACACAAGTTGGTGGCA-CTTCCAGTCCTCAAAGAGCAGGACGCC
* * * *
1249244 TTTCAAAGCCCACACGAGTTGGTGGCATTTTTCAGTCCTTAAAGAGCAGGACGCC
1 TTT-AAAGCCCACACAAGTTGGTGGCA-CTTCCAGTCCTCAAAGAGCAGGACGCC
* *
1249299 TTTCAAAGCCCACACGAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTTTTCC
1 TTT-AAAGCCCACACAAGTTGGTGGCACTTC-CAGTCCTCAAAGAGCAGGA---C---GCC
* *
1249360 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGGACGC
1 -TTTAAAGCCCACACAAGTTGGTGGCA-CTTCCAGTCCTCAAAGAGCAGGACGC
1249414 TCTCTCTTCT
Statistics
Matches: 286, Mismatches: 30, Indels: 47
0.79 0.08 0.13
Matches are distributed among these distances:
53 3 0.01
54 37 0.13
55 145 0.51
56 3 0.01
58 2 0.01
60 19 0.07
61 64 0.22
62 13 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (53 bp):
TTTAAAGCCCACACAAGTTGGTGGCACTTCCAGTCCTCAAAGAGCAGGACGCC
Found at i:1249196 original size:116 final size:113
Alignment explanation
Indices: 1248935--1249421 Score: 441
Period size: 116 Copynumber: 4.3 Consensus size: 113
1248925 TTTCACCCAT
* * * *
1248935 TAGTCCTCAAAGAGCAGGACGCC-T-T-TTAAAGCCCACATAAGTTAGTGGCACTTCTCAGCCCT
1 TAGTCCTCAAAGAGCAGGACGCCTTCTCTTAAAGCCCACACAAGTTGGTGGCATTTC-CAGTCCT
* * * *
1248997 CAAAGAGCAGGATGCCTTTTCCTTTTAAAGACCACTCCAA-TTGGTGGCA-CTCCC
65 CAAAGAGCAGGACGCC-TTT-C----AAAGCCCAC-ACAAGTTGGTGGCACCTTCC
* *
1249051 TAGTCCTCAAAGAGCAGGAC-AC--CTCTTAAAGCCCACATAAGTTGGTGGCATTTTCCAGTCCT
1 TAGTCCTCAAAGAGCAGGACGCCTTCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTCCAGTCCT
* **
1249113 CAAAAAGCAGGACGCCTTTCAAAGCTTACACAAGTTGGTGGCA-CTTCC
65 CAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCC
*
1249161 AAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT--AG
1 TAGTCCTCAAAGAGCAGGACGCCTTCT-C--TTAAAGCCCACACAAGTTGGTGGCA--TTTCCAG
* * ** *
1249224 TCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACGAGTTGGTGGCATTTTTC
61 TCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCC
* * *
1249277 -AGTCCTTAAAGAGCAGGACGCCTT-TC--AAAGCCCACACGAGTTGGTGGCACTTCTCAGTCCT
1 TAGTCCTCAAAGAGCAGGACGCCTTCTCTTAAAGCCCACACAAGTTGGTGGCATTTC-CAGTCCT
*
1249338 CAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C
65 CAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAGTTGGTGGCACCTTCC
*
1249392 TAGTCCTCAAAGAGTAGGACG-CTCTCTCTT
1 TAGTCCTCAAAGAGCAGGACGCCT-TCTCTT
1249422 CTCACCCTTT
Statistics
Matches: 313, Mismatches: 32, Indels: 49
0.79 0.08 0.12
Matches are distributed among these distances:
107 2 0.01
109 25 0.08
110 58 0.19
111 4 0.01
112 1 0.00
113 3 0.01
114 3 0.01
115 75 0.24
116 134 0.43
117 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (113 bp):
TAGTCCTCAAAGAGCAGGACGCCTTCTCTTAAAGCCCACACAAGTTGGTGGCATTTCCAGTCCTC
AAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCC
Found at i:1249299 original size:170 final size:170
Alignment explanation
Indices: 1248936--1249567 Score: 786
Period size: 170 Copynumber: 3.8 Consensus size: 170
1248926 TTCACCCATT
* * * *
1248936 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACATAAGTTAGTGGCACTTCTCAGCCCTCAAA
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAA
* * * *
1249001 GAGCAGGATGCCTTTTCCTTTTAAAGACCACTCCAA-TTGGTGGCA-CTCCCTAGTCCTCAAAGA
66 GAGCAGGACGCCTTTTCCTTTTAAAGCCCAC-ACAAGTTGGTGGCACCT-TCTAGTCCTCAAAGA
* * *
1249064 GCAGGACACCTCTT-AAAGCCCACATAAGTTGGTGGCATTTTCC
129 GCAGGACGCCT-TTCAAAGCCCACA-CAGTTGGTGGCATTTTTC
* **
1249107 AGTCCTCAAAAAGCAGGACGCCTTTCAAAGCTTACACAAGTTGGTGGCACTTC-CAAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCTC-AGTCCTCAA
*
1249171 AGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-TAGTCCTCAAAGAG
65 AGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAG
*
1249235 CAAGACGCCTTTCAAAGCCCACACGAGTTGGTGGCATTTTTC
130 CAGGACGCCTTTCAAAGCCCACAC-AGTTGGTGGCATTTTTC
* *
1249277 AGTCCTTAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTCTCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAA
* *
1249342 GAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGT
66 GAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGC
* ** *
1249407 AGGACGCTCTCTC--TTCTCAC-C---------C---TTT-
131 AGGACGC-CTTTCAAAGCCCACACAGTTGGTGGCATTTTTC
1249432 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-TCAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTCTCAGTCCTCAA
* * *
1249496 AGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTGTAGTCCTCAAAGA
65 AGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGA
1249561 GCAGGAC
129 GCAGGAC
1249568 ACACTTTATT
Statistics
Matches: 415, Mismatches: 36, Indels: 35
0.85 0.07 0.07
Matches are distributed among these distances:
155 79 0.19
156 51 0.12
159 1 0.00
169 3 0.01
170 161 0.39
171 114 0.27
172 6 0.01
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (170 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAA
GAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGC
AGGACGCCTTTCAAAGCCCACACAGTTGGTGGCATTTTTC
Found at i:1249492 original size:55 final size:57
Alignment explanation
Indices: 1249427--1249567 Score: 198
Period size: 62 Copynumber: 2.4 Consensus size: 57
1249417 CTCTTCTCAC
1249427 CCTTTAGTCCTCAAAGAGCAGGACG-C-C-TTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1249481 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTT-AGTCCTCAAAGAGCAGGACGCC----TCTTTTCAAAGCCCACACAAGTTGGTGGCA
*
1249543 CTTTGTAGTCCTCAAAGAGCAGGAC
1 CCTT-TAGTCCTCAAAGAGCAGGAC
1249568 ACACTTTATT
Statistics
Matches: 77, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
54 5 0.06
55 20 0.26
56 1 0.01
61 1 0.01
62 49 0.64
63 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (57 bp):
CCTTTAGTCCTCAAAGAGCAGGACGCCTCTTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:1249647 original size:43 final size:43
Alignment explanation
Indices: 1249550--1249729 Score: 174
Period size: 42 Copynumber: 4.1 Consensus size: 43
1249540 GCACTTTGTA
*
1249550 GTCCTCAAAGAGCAGGACACACTTT-ATTTTCCTCTTTCT--TTT
1 GTCCTCAAAGAGCAAGACACA-TTTCATTTTCCT-TTTCTCCTTT
* *
1249592 GTCCTCAAAGAGCAAGACGCATTTCGTTTTCCTTTTCTCCTTT
1 GTCCTCAAAGAGCAAGACACATTTCATTTTCCTTTTCTCCTTT
* *
1249635 GTCCTCAAAGAGCAAGACGC-TCTT--TGTTTCCTTCTTTTCCCTTTT
1 GTCCTCAAAGAGCAAGACACAT-TTCAT-TTTCCTT-TTCT-CC-TTT
* *
1249680 AGTCCTCAAAGAGCAGGACACATTTCATTTTCCTTTTTTCCTTT
1 -GTCCTCAAAGAGCAAGACACATTTCATTTTCCTTTTCTCCTTT
*
1249724 TTCCTC
1 GTCCTC
1249730 GAAAAACAGG
Statistics
Matches: 119, Mismatches: 7, Indels: 23
0.80 0.05 0.15
Matches are distributed among these distances:
41 9 0.08
42 34 0.29
43 33 0.28
44 5 0.04
45 5 0.04
46 24 0.20
47 8 0.07
48 1 0.01
ACGTcount: A:0.19, C:0.28, G:0.12, T:0.41
Consensus pattern (43 bp):
GTCCTCAAAGAGCAAGACACATTTCATTTTCCTTTTCTCCTTT
Found at i:1249704 original size:89 final size:85
Alignment explanation
Indices: 1249550--1249729 Score: 227
Period size: 89 Copynumber: 2.1 Consensus size: 85
1249540 GCACTTTGTA
* * *
1249550 GTCCTCAAAGAGCAGGACACACTTTATTTTCCTCTTTCTTTTGTCCTCAAAGAGCAAGACGCATT
1 GTCCTCAAAGAGCAAGACACACTTTAGTTTCCTCTTTCTTTTGTCCTCAAAGAGCAAGACACATT
*
1249615 TCGTTTTCCTTTTCTCCTTT
66 TCATTTTCCTTTTCTCCTTT
* * *
1249635 GTCCTCAAAGAGCAAGACGCTCTTT-GTTTCCTTCTTTTCCCTTTTAGTCCTCAAAGAGCAGGAC
1 GTCCTCAAAGAGCAAGACACACTTTAGTTTCC-TC-TTT--CTTTT-GTCCTCAAAGAGCAAGAC
*
1249699 ACATTTCATTTTCCTTTTTTCCTTT
61 ACATTTCATTTTCCTTTTCTCCTTT
*
1249724 TTCCTC
1 GTCCTC
1249730 GAAAAACAGG
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
84 5 0.06
85 24 0.30
86 3 0.04
88 5 0.06
89 44 0.54
ACGTcount: A:0.19, C:0.28, G:0.12, T:0.41
Consensus pattern (85 bp):
GTCCTCAAAGAGCAAGACACACTTTAGTTTCCTCTTTCTTTTGTCCTCAAAGAGCAAGACACATT
TCATTTTCCTTTTCTCCTTT
Found at i:1250301 original size:14 final size:14
Alignment explanation
Indices: 1250282--1250310 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1250272 GGGACGAATT
1250282 CATTTCCCATCGTC
1 CATTTCCCATCGTC
1250296 CATTTCCCATCGTC
1 CATTTCCCATCGTC
1250310 C
1 C
1250311 TTAGTCGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.45, G:0.07, T:0.34
Consensus pattern (14 bp):
CATTTCCCATCGTC
Found at i:1250496 original size:32 final size:32
Alignment explanation
Indices: 1250455--1250527 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
1250445 ACAAACAGAA
**
1250455 AATGTATCGATACATAAGTGTTGTATTGATAC
1 AATGTATCGATACATAAGTGTTGTATCAATAC
*
1250487 AATGTATCGATACATAAGTTTTGTATCAATAC
1 AATGTATCGATACATAAGTGTTGTATCAATAC
1250519 AATGTATCG
1 AATGTATCG
1250528 CTACGAAGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCAATAC
Found at i:1250513 original size:19 final size:18
Alignment explanation
Indices: 1250457--1250519 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 18
1250447 AAACAGAAAA
1250457 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
*
1250476 TGTATTGATAC--AA---
1 TGTATCGATACATAAGTT
1250489 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
*
1250508 TGTATCAATACA
1 TGTATCGATACA
1250520 ATGTATCGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
13 10 0.29
15 2 0.06
17 2 0.06
19 21 0.60
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:1252986 original size:51 final size:50
Alignment explanation
Indices: 1252896--1253176 Score: 264
Period size: 51 Copynumber: 5.6 Consensus size: 50
1252886 TTAAGTTTCT
* * ** * *
1252896 CAATTGTTCATAATCGGAGATACTCCAACCCCGGCTTTATTTCCAAAATAT
1 CAATT-TTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
** ***
1252947 TGATTTCTCATAATCGGGGATACTCCAACTCCGATTTTATTTTTGAAACAC
1 CAATTT-TCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
* * *
1252998 CAATTTTCCACAATCGGGGATACTCCAAC-CCCAGTTTTATTTTCAAAACAC
1 CAATTTT-CATAATCGGGGATACTCCAACTCCGA-TTTTATTTCCAAAACAC
* *
1253049 CAATTTTCTATAATCAGGGATACTCCAACTCTGATTTTATTTCCAAAAACAC
1 CAATTTTC-ATAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAACAC
* * * * * *
1253101 CAATTTTTCAT-CTCGGGGATACTCCAGCCCCGGTTTTATTTCTAAAACAT
1 CAA-TTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
*
1253151 CAATTTT--TCATCGGGGATACTCCAAC
1 CAATTTTCATAATCGGGGATACTCCAAC
1253177 CCCGTTATTT
Statistics
Matches: 190, Mismatches: 32, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
47 1 0.01
48 15 0.08
49 4 0.02
50 15 0.08
51 136 0.72
52 14 0.07
53 5 0.03
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (50 bp):
CAATTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
Found at i:1253072 original size:102 final size:105
Alignment explanation
Indices: 1252907--1253176 Score: 310
Period size: 102 Copynumber: 2.7 Consensus size: 105
1252897 AATTGTTCAT
* * * * ** *
1252907 AATCGGAGATACTCCAACCCCGGCTTTATTTCCAAAATATTGA-TTTCTCATAATCGGGGATACT
1 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACATCAATTTTCTCATAATCAGGGATACT
***
1252971 CCAACTCCGATTTTATTT-TTGAAACACCAATTTTCCA-C
66 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTCCATC
* *
1253009 AATCGGGGATACTCCAACCCCAGTTTTATTTTCAAAACACCAATTTTCT-ATAATCAGGGATACT
1 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACATCAATTTTCTCATAATCAGGGATACT
* *
1253073 CCAACTCTGATTTTATTTCCAAAAACACCAATTTTTCATC
66 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTCCATC
* *
1253113 --TCGGGGATACTCCAGCCCCGGTTTTA-TTTCTAAAACATCAATTTT-TC---ATCGGGGATAC
1 AATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACATCAATTTTCTCATAATCAGGGATAC
1253171 TCCAAC
65 TCCAAC
1253177 CCCGTTATTT
Statistics
Matches: 145, Mismatches: 18, Indels: 13
0.82 0.10 0.07
Matches are distributed among these distances:
99 16 0.11
101 5 0.03
102 103 0.71
103 20 0.14
104 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.33
Consensus pattern (105 bp):
AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACATCAATTTTCTCATAATCAGGGATACT
CCAACTCCGATTTTATTTCCAAAAACACCAATTTTCCATC
Found at i:1253246 original size:76 final size:76
Alignment explanation
Indices: 1253116--1253299 Score: 287
Period size: 76 Copynumber: 2.4 Consensus size: 76
1253106 TTTCATCTCG
* *
1253116 GGGATACTCCAGCCCCGGTTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCCG
1 GGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCAGGGATACTCCAACCCCG
1253181 TTATTTTCGAA
66 TTATTTTCGAA
* * *
1253192 GGGTTACTCCAACCTCGGTTTTATTTCTAAAACATTAATTTTTCATCAGGGATACTCCAACCCCG
1 GGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCAGGGATACTCCAACCCCG
*
1253257 TTATTTTCGAG
66 TTATTTTCGAA
** *
1253268 GGGATACTCCAACCCCGACTTTATATCTAAAA
1 GGGATACTCCAACCCCGGTTTTATTTCTAAAA
1253300 ATATTGTTTT
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 97 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.33
Consensus pattern (76 bp):
GGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCAGGGATACTCCAACCCCG
TTATTTTCGAA
Found at i:1253373 original size:51 final size:51
Alignment explanation
Indices: 1253267--1253438 Score: 209
Period size: 51 Copynumber: 3.4 Consensus size: 51
1253257 TTATTTTCGA
* * **** *
1253267 GGGGATACTCCAACCCCGACTTTATATCTAAAAATATTGTTTTTTTATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCT-AAAATACCAATTTTTCATAATC
* *
1253319 GGGGGTACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCATAATC
** * * *
1253370 GGGGATACTCCAACTACGATTTTATTTCCAAAACACCAATTTCTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCATAATC
1253421 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1253439 CTATTTTCGC
Statistics
Matches: 102, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
51 76 0.75
52 26 0.25
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCATAATC
Found at i:1255973 original size:122 final size:122
Alignment explanation
Indices: 1255751--1255995 Score: 454
Period size: 122 Copynumber: 2.0 Consensus size: 122
1255741 AGGAACCCAC
1255751 TATTAGACACTCCTAGATCTATGAAATCTCTAAACATCACTCTTGAAATCAATTTTGAGGCATCT
1 TATTAGACACTCCTAGATCTATGAAATCTCTAAACATCACTCTTGAAATCAATTTTGAGGCATCT
* * *
1255816 GAATTCCTCGACATAATGGCACCAAAACTCGAAGAAACCCAAAAACATTTGATAGAT
66 GAATTCCTCAACATAATGGCACCAAAACTCAAAGAAACCCAAAAACACTTGATAGAT
*
1255873 TATTAGACACTCCTAGATCTATGGAATCTCTAAACATCACTCTTGAAATCAATTTTGAGGCATCT
1 TATTAGACACTCCTAGATCTATGAAATCTCTAAACATCACTCTTGAAATCAATTTTGAGGCATCT
1255938 GAATTCCTCAACATAATGGCACCAAAACTCAAAGAAACCCAAAAACACTTGATAGAT
66 GAATTCCTCAACATAATGGCACCAAAACTCAAAGAAACCCAAAAACACTTGATAGAT
1255995 T
1 T
1255996 TGATAATTCA
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
122 119 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (122 bp):
TATTAGACACTCCTAGATCTATGAAATCTCTAAACATCACTCTTGAAATCAATTTTGAGGCATCT
GAATTCCTCAACATAATGGCACCAAAACTCAAAGAAACCCAAAAACACTTGATAGAT
Found at i:1257884 original size:26 final size:26
Alignment explanation
Indices: 1257855--1257904 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
1257845 AATGGTGGTT
1257855 GAATTCAACATATGCAAGATTAAGTA
1 GAATTCAACATATGCAAGATTAAGTA
1257881 GAATTCAACATATGCAAGATTAAG
1 GAATTCAACATATGCAAGATTAAG
1257905 CAAGATTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (26 bp):
GAATTCAACATATGCAAGATTAAGTA
Found at i:1257912 original size:26 final size:26
Alignment explanation
Indices: 1257855--1257920 Score: 98
Period size: 26 Copynumber: 2.5 Consensus size: 26
1257845 AATGGTGGTT
*
1257855 GAATTCAACATATGCAAGATTAAGTA
1 GAATTCAACATATGCAAGATTAAGAA
1257881 GAATTCAACATATGCAAGATTAAGCAA
1 GAATTCAACATATGCAAGATTAAG-AA
1257908 G-ATTCAAACATAT
1 GAATTC-AACATAT
1257921 AGTCATACTA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
26 28 0.76
27 9 0.24
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.26
Consensus pattern (26 bp):
GAATTCAACATATGCAAGATTAAGAA
Found at i:1258207 original size:16 final size:16
Alignment explanation
Indices: 1258186--1258218 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1258176 GAAATGACTC
1258186 TTGTGCCTCTAATGAA
1 TTGTGCCTCTAATGAA
1258202 TTGTGCCTCTAATGAA
1 TTGTGCCTCTAATGAA
1258218 T
1 T
1258219 AGTTAAGCGT
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:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (16 bp):
TTGTGCCTCTAATGAA
Found at i:1259826 original size:39 final size:42
Alignment explanation
Indices: 1259766--1259844 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 42
1259756 ACAATTACAT
1259766 AACATAAATATGATACT-AAAAATAA-ATAAACATAATATTA
1 AACATAAATATGATACTAAAAAATAATATAAACATAATATTA
* *
1259806 AACAT-AATATGATA-TGAAAAAATAATATGAATATAATAT
1 AACATAAATATGATACT-AAAAAATAATATAAACATAATAT
1259845 AAATATATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
38 1 0.03
39 9 0.26
40 13 0.38
41 11 0.32
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (42 bp):
AACATAAATATGATACTAAAAAATAATATAAACATAATATTA
Found at i:1259843 original size:11 final size:11
Alignment explanation
Indices: 1259764--1259851 Score: 51
Period size: 11 Copynumber: 8.3 Consensus size: 11
1259754 ATACAATTAC
*
1259764 ATAACATAAAT
1 ATAATATAAAT
* *
1259775 ATGATACTAAAA
1 ATAATA-TAAAT
*
1259787 ATAA-ATAAAC
1 ATAATATAAAT
*
1259797 ATAATATTAAAC
1 ATAATA-TAAAT
*
1259809 ATAATAT-GAT
1 ATAATATAAAT
*
1259819 ATGA-A-AAA-
1 ATAATATAAAT
*
1259827 ATAATATGAAT
1 ATAATATAAAT
1259838 ATAATATAAAT
1 ATAATATAAAT
1259849 ATA
1 ATA
1259852 TGTATTTATT
Statistics
Matches: 58, Mismatches: 12, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
8 3 0.05
9 3 0.05
10 14 0.24
11 20 0.34
12 18 0.31
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:1259939 original size:18 final size:17
Alignment explanation
Indices: 1259901--1259943 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1259891 GTCCAAATTT
*
1259901 ATATAAATATATATAAT
1 ATATAAATATATATAAA
1259918 ATATTAAATATA-ATTAAA
1 ATA-TAAATATATA-TAAA
1259936 ATATAAAT
1 ATATAAAT
1259944 GAATAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAAATATATATAAA
Found at i:1260374 original size:20 final size:20
Alignment explanation
Indices: 1260335--1260385 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1260325 CGATACATTA
**
1260335 TATCGATACAT-GTTAATTG
1 TATCGATACATGGACAATTG
1260354 TATCGATACATGGACAATTG
1 TATCGATACATGGACAATTG
*
1260374 TATTGATACATG
1 TATCGATACATG
1260386 AGATTGGCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (20 bp):
TATCGATACATGGACAATTG
Found at i:1266960 original size:50 final size:50
Alignment explanation
Indices: 1266883--1267038 Score: 267
Period size: 50 Copynumber: 3.1 Consensus size: 50
1266873 ACTTAGAGTT
* *
1266883 AACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGATGAAGAATAGTC
1 AACAATTACGGCCACCTCTCTCAATTGTCAAAGGTTGGTGAAGAATAGTC
* *
1266933 AACAATTATGGCCACCTCTCTCAATTGTCAAAGGTTGGTGAAGAATAATC
1 AACAATTACGGCCACCTCTCTCAATTGTCAAAGGTTGGTGAAGAATAGTC
*
1266983 AACAATTACGACCACCTCTCTCAATTGTCAAAGGTTGGTGAAGAATAGTC
1 AACAATTACGGCCACCTCTCTCAATTGTCAAAGGTTGGTGAAGAATAGTC
1267033 AACAAT
1 AACAAT
1267039 GGCAACACCT
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 99 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (50 bp):
AACAATTACGGCCACCTCTCTCAATTGTCAAAGGTTGGTGAAGAATAGTC
Found at i:1268081 original size:25 final size:25
Alignment explanation
Indices: 1268052--1268100 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1268042 AATGATGATA
*
1268052 ATAAAGTGAATTATAATAAAAAATC
1 ATAAAATGAATTATAATAAAAAATC
** *
1268077 ATAAAATTTATTATATTAAAAAAT
1 ATAAAATGAATTATAATAAAAAAT
1268101 ATATATAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
ATAAAATGAATTATAATAAAAAATC
Found at i:1268127 original size:45 final size:45
Alignment explanation
Indices: 1268064--1268191 Score: 129
Period size: 45 Copynumber: 2.8 Consensus size: 45
1268054 AAAGTGAATT
*
1268064 ATAATAAAAAATCA-TAAAATTTA-TTATATTAAAAAATATATATA
1 ATAATTAAAAATCATTAAAATTTATTTATATTAAAAAATAT-TATA
* * * *
1268108 ATAATTAAAAATTATTAAAATCATATTTACATT-AAAAATATTTTA
1 ATAATTAAAAATCATTAAAAT-TTATTTATATTAAAAAATATTATA
* *
1268153 A-AGTTAAATAATGATTAAAATTATATTTATATTAAAAAA
1 ATAATTAAA-AATCATTAAAATT-TATTTATATTAAAAAA
1268192 CAAATTAACC
Statistics
Matches: 69, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
44 18 0.26
45 30 0.43
46 15 0.22
47 6 0.09
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (45 bp):
ATAATTAAAAATCATTAAAATTTATTTATATTAAAAAATATTATA
Found at i:1269422 original size:3 final size:3
Alignment explanation
Indices: 1269414--1269460 Score: 85
Period size: 3 Copynumber: 15.3 Consensus size: 3
1269404 CAAAGGCTAT
1269414 TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1269460 T
1 T
1269461 CATTTTCTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1269586 original size:20 final size:22
Alignment explanation
Indices: 1269563--1269604 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
1269553 TTTTAAAAAA
1269563 TAAAAAAA-GTGGATA-ATTTT
1 TAAAAAAATGTGGATAGATTTT
*
1269583 TAAAAAAATTTGGATAGATTTT
1 TAAAAAAATGTGGATAGATTTT
1269605 AAGAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 6 0.32
22 5 0.26
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (22 bp):
TAAAAAAATGTGGATAGATTTT
Found at i:1269588 original size:21 final size:22
Alignment explanation
Indices: 1269564--1269604 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1269554 TTTAAAAAAT
1269564 AAAAAAAGTGGATA-ATTTTTA
1 AAAAAAAGTGGATAGATTTTTA
**
1269585 AAAAAATTTGGATAGATTTT
1 AAAAAAAGTGGATAGATTTT
1269605 AAGAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.37
Consensus pattern (22 bp):
AAAAAAAGTGGATAGATTTTTA
Found at i:1269973 original size:2 final size:2
Alignment explanation
Indices: 1269960--1269989 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1269950 ATTATGTATT
*
1269960 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1269990 GTCCCAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1270321 original size:16 final size:17
Alignment explanation
Indices: 1270300--1270335 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1270290 TTTATTGACT
*
1270300 TTTTAAATTT-AAATTA
1 TTTTAAATTTGAAATAA
1270316 TTTTAAATTTGAAATAA
1 TTTTAAATTTGAAATAA
1270333 TTT
1 TTT
1270336 GAATTTAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTTAAATTTGAAATAA
Found at i:1276344 original size:31 final size:32
Alignment explanation
Indices: 1276289--1276353 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 32
1276279 TGTTAAATTA
** * *
1276289 AATTATTTTAAATAT-AATTTTTTTATTTTTT
1 AATTATTTTAAATATAAAAATTTTAATTATTT
*
1276320 AATTATTTTAAATTTAAAAATTTTAATTATTT
1 AATTATTTTAAATATAAAAATTTTAATTATTT
1276352 AA
1 AA
1276354 AAATATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
AATTATTTTAAATATAAAAATTTTAATTATTT
Found at i:1276348 original size:24 final size:26
Alignment explanation
Indices: 1276316--1276366 Score: 79
Period size: 24 Copynumber: 2.0 Consensus size: 26
1276306 TTTTTTTATT
*
1276316 TTTTAATTATTT-TAAAT-TTAAAAA
1 TTTTAATTATTTAAAAATATTAAAAA
1276340 TTTTAATTATTTAAAAATATTAAAAA
1 TTTTAATTATTTAAAAATATTAAAAA
1276366 T
1 T
1276367 ATTTTATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 12 0.50
25 4 0.17
26 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTTAATTATTTAAAAATATTAAAAA
Found at i:1276398 original size:22 final size:22
Alignment explanation
Indices: 1276369--1276426 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
1276359 TTAAAAATAT
* *
1276369 TTTATATTTGAGTTA-TTTAAA
1 TTTATATTTAAATTATTTTAAA
1276390 TTTACTATTTAAATTATTTTAAA
1 TTTA-TATTTAAATTATTTTAAA
*
1276413 TATT-TTTTTAAATT
1 T-TTATATTTAAATT
1276427 TAAATTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 4 0.13
22 18 0.58
23 7 0.23
24 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (22 bp):
TTTATATTTAAATTATTTTAAA
Found at i:1276899 original size:27 final size:27
Alignment explanation
Indices: 1276869--1276998 Score: 102
Period size: 28 Copynumber: 4.6 Consensus size: 27
1276859 ATTTATAGAT
*
1276869 TTTTTAATTAAATTTTTACACATAAAA
1 TTTTTAATTAAATTTTTACACATACAA
* * *
1276896 TTTTTAATTAAAATTTTAACACATGCAT
1 TTTTTAATT-AAATTTTTACACATACAA
* * *
1276924 TTTTTAATTTAAATTTGTACATATGACTA
1 TTTTTAA-TTAAATTTTTACACAT-ACAA
* *
1276953 TTTTT-ATTAGATTTCCTTCACACATGGC-A
1 TTTTTAATTAAATTT--TT-ACACAT-ACAA
1276982 TTTTTAATTAAATTTTT
1 TTTTTAATTAAATTTTT
1276999 TCTAACCAAA
Statistics
Matches: 81, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
27 16 0.20
28 35 0.43
29 15 0.19
30 15 0.19
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.51
Consensus pattern (27 bp):
TTTTTAATTAAATTTTTACACATACAA
Found at i:1278253 original size:20 final size:20
Alignment explanation
Indices: 1278228--1278374 Score: 105
Period size: 20 Copynumber: 6.8 Consensus size: 20
1278218 TTTTACCAAG
1278228 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
1278248 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
1278268 ATGTATCGATACATTTTGTCTTTTTTACCCA
1 ATGTATCGATACA--------TTTTT---CA
*
1278299 GATGTATGGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
* * *
1278320 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
1278340 ATGTATTGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
*
1278360 ATATATCGATACATT
1 ATGTATCGATACATT
1278375 CTGTCTTTTT
Statistics
Matches: 98, Mismatches: 17, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
20 75 0.77
21 2 0.02
24 5 0.05
28 3 0.03
31 1 0.01
32 12 0.12
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1278283 original size:40 final size:40
Alignment explanation
Indices: 1278228--1278373 Score: 157
Period size: 40 Copynumber: 3.9 Consensus size: 40
1278218 TTTTACCAAG
1278228 ATGTATCGATACATTTTTCAATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCAATGTATCGATACATGTATGA
** **
1278268 ATGTATCGATACATTTTGTC--T-T-T-TTTAC--CCA-G-
1 ATGTATCGATACATTTT-TCAATGTATCGATACATGTATGA
*
1278300 ATGTATGGATACATTTTTCAATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCAATGTATCGATACATGTATGA
* *
1278340 ATGTATTGATACATTTTTCAATATATCGATACAT
1 ATGTATCGATACATTTTTCAATGTATCGATACAT
1278374 TCTGTCTTTT
Statistics
Matches: 85, Mismatches: 11, Indels: 20
0.73 0.09 0.17
Matches are distributed among these distances:
31 2 0.02
32 16 0.19
33 2 0.02
34 2 0.02
35 1 0.01
36 6 0.07
37 1 0.01
38 2 0.02
39 2 0.02
40 49 0.58
41 2 0.02
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (40 bp):
ATGTATCGATACATTTTTCAATGTATCGATACATGTATGA
Found at i:1278334 original size:72 final size:72
Alignment explanation
Indices: 1278217--1278356 Score: 253
Period size: 72 Copynumber: 1.9 Consensus size: 72
1278207 AAAAGTCACA
1278217 TTTTTACCAAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
1 TTTTTACCAAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
1278282 TTTGTCT
66 TTTGTCT
* * *
1278289 TTTTTACCCAGATGTATGGATACATTTTTCAATGTATCGATACATGTATGAATGTATTGATACAT
1 TTTTTACCAAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
1278354 TTT
66 TTT
1278357 TCAATATATC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (72 bp):
TTTTTACCAAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
TTTGTCT
Found at i:1278677 original size:39 final size:39
Alignment explanation
Indices: 1278623--1278698 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
1278613 TTGTATTCCC
1278623 CTCACCATCACACTTTAGAGTTGGATTAGACATCAATCT
1 CTCACCATCACACTTTAGAGTTGGATTAGACATCAATCT
*
1278662 CTCACCATCACACTTTAGAGTTGGATTAGCCATCAAT
1 CTCACCATCACACTTTAGAGTTGGATTAGACATCAAT
1278699 ATATCCCATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.30
Consensus pattern (39 bp):
CTCACCATCACACTTTAGAGTTGGATTAGACATCAATCT
Found at i:1292290 original size:1 final size:1
Alignment explanation
Indices: 1292284--1292367 Score: 51
Period size: 1 Copynumber: 84.0 Consensus size: 1
1292274 CCTTCGTACC
** ** * * * ** * *
1292284 AAAAAAAATTAAAAAAAAACCAAGAAAAAAAACAAAAAAAAGAAAAAACCAAAAGAAAAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
1292349 AAAAAAAACAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAA
1292368 GGGGTCCAGA
Statistics
Matches: 63, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.85, C:0.10, G:0.04, T:0.02
Consensus pattern (1 bp):
A
Found at i:1292311 original size:12 final size:11
Alignment explanation
Indices: 1292284--1292367 Score: 66
Period size: 11 Copynumber: 7.7 Consensus size: 11
1292274 CCTTCGTACC
**
1292284 AAAAAAAATTA
1 AAAAAAAAACA
*
1292295 AAAAAAAACCA
1 AAAAAAAAACA
1292306 AGAAAAAAAAC-
1 A-AAAAAAAACA
*
1292317 -AAAAAAAAGA
1 AAAAAAAAACA
**
1292327 AAAAACCAA-A
1 AAAAAAAAACA
*
1292337 AGAAAAAAACA
1 AAAAAAAAACA
1292348 AAAAAAAAACA
1 AAAAAAAAACA
1292359 AACAAAAAA
1 AA-AAAAAA
1292368 GGGGTCCAGA
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
9 8 0.14
10 7 0.12
11 29 0.50
12 14 0.24
ACGTcount: A:0.85, C:0.10, G:0.04, T:0.02
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:1292311 original size:13 final size:12
Alignment explanation
Indices: 1292294--1292367 Score: 60
Period size: 13 Copynumber: 5.7 Consensus size: 12
1292284 AAAAAAAATT
1292294 AAAAAAAAACCA
1 AAAAAAAAACCA
*
1292306 AGAAAAAAAACAAAAA
1 A-AAAAAAAAC---CA
1292322 AAAGAAAAAACCA
1 AAA-AAAAAACCA
*
1292335 AAAGAAAAAAACA
1 AAA-AAAAAACCA
1292348 AAAAAAAAA-CA
1 AAAAAAAAACCA
1292359 AACAAAAAA
1 AA-AAAAAA
1292368 GGGGTCCAGA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
11 4 0.08
12 13 0.25
13 25 0.47
15 2 0.04
16 9 0.17
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACCA
Found at i:1292320 original size:18 final size:17
Alignment explanation
Indices: 1292294--1292367 Score: 60
Period size: 17 Copynumber: 4.2 Consensus size: 17
1292284 AAAAAAAATT
**
1292294 AAAAAAAAACCAAGAAA
1 AAAAAAAAAAAAAGAAA
1292311 AAAAACAAAAAAAAGAAA
1 AAAAA-AAAAAAAAGAAA
*
1292329 AAACCAAAAGAAAAAA-ACA
1 AAA--AAAA-AAAAAAGAAA
* *
1292348 AAAAAAAAACAAACAAA
1 AAAAAAAAAAAAAGAAA
1292365 AAA
1 AAA
1292368 GGGGTCCAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
16 5 0.11
17 14 0.30
18 13 0.28
19 7 0.15
20 8 0.17
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAGAAA
Found at i:1292321 original size:31 final size:30
Alignment explanation
Indices: 1292294--1292356 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
1292284 AAAAAAAATT
*
1292294 AAAAAAAAACCAAGA-AAAAAAACAAAAAA
1 AAAAAAAAACCAAAAGAAAAAAACAAAAAA
*
1292323 AAGAAAAAACCAAAAGAAAAAAACAAAAAA
1 AAAAAAAAACCAAAAGAAAAAAACAAAAAA
1292353 AAAA
1 AAAA
1292357 CAAACAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 13 0.43
30 17 0.57
ACGTcount: A:0.86, C:0.10, G:0.05, T:0.00
Consensus pattern (30 bp):
AAAAAAAAACCAAAAGAAAAAAACAAAAAA
Found at i:1292361 original size:29 final size:27
Alignment explanation
Indices: 1292294--1292367 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 27
1292284 AAAAAAAATT
*
1292294 AAAAAAAAACCAAGAAAAAAAACAAAAA
1 AAAAAAAAACCAAAAAAAAAAAC-AAAA
1292322 AAAGAAAAAACCAAAAGAAAAAAACAAAA
1 AAA-AAAAAACCAAAA-AAAAAAACAAAA
1292351 AAAAAACAAA-CAAAAAA
1 AAAAAA-AAACCAAAAAA
1292368 GGGGTCCAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
27 2 0.05
28 11 0.26
29 21 0.50
30 8 0.19
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (27 bp):
AAAAAAAAACCAAAAAAAAAAACAAAA
Found at i:1292368 original size:30 final size:30
Alignment explanation
Indices: 1292283--1292366 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 30
1292273 TCCTTCGTAC
*
1292283 CAAAAAAAATTAAAAAA-AAACCAAGAAAAAAAA
1 CAAAAAAAA-GAAAAAACAAA--AAG-AAAAAAA
*
1292316 CAAAAAAAAGAAAAAACCAAAAGAAAAAAA
1 CAAAAAAAAGAAAAAACAAAAAGAAAAAAA
*
1292346 CAAAAAAAA-AACAAACAAAAA
1 CAAAAAAAAGAAAAAACAAAAA
1292367 AGGGGTCCAG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 10 0.22
30 16 0.35
31 3 0.07
32 6 0.13
33 11 0.24
ACGTcount: A:0.83, C:0.11, G:0.04, T:0.02
Consensus pattern (30 bp):
CAAAAAAAAGAAAAAACAAAAAGAAAAAAA
Found at i:1293649 original size:28 final size:28
Alignment explanation
Indices: 1293634--1293999 Score: 455
Period size: 28 Copynumber: 12.9 Consensus size: 28
1293624 CCAATAGGTT
*
1293634 AGTGGCATCCTTTCAACGCCCACAAGTC
1 AGTGGCATCCTTTCAAAGCCCACAAGTC
* * * *
1293662 AGTGGCATCTTTTCGAAGCCCATAAGTT
1 AGTGGCATCCTTTCAAAGCCCACAAGTC
*
1293690 AGTGGAATCCTTTCAAAGCCCACAAGTC
1 AGTGGCATCCTTTCAAAGCCCACAAGTC
* * *
1293718 AGCGGCACCCTTTCAAAGCCCATAAGTC
1 AGTGGCATCCTTTCAAAGCCCACAAGTC
1293746 AGTGGCATCCTTTCAAAGCCCACAAGTC
1 AGTGGCATCCTTTCAAAGCCCACAAGTC
* *
1293774 AGTGGCACCCTTTCAAAGTCCACAAGTC
1 AGTGGCATCCTTTCAAAGCCCACAAGTC
*
1293802 AGTGGCATCCTTTCAAAGCCCACAAGTT
1 AGTGGCATCCTTTCAAAGCCCACAAGTC
*
1293830 AGTGGCAT-CTCTTCAAAGACCACAAGTC
1 AGTGGCATCCT-TTCAAAGCCCACAAGTC
* *
1293858 AGTGGCACCCTTTCAAAGCCAACAAGTC
1 AGTGGCATCCTTTCAAAGCCCACAAGTC
* *
1293886 AGTGGCACCCTTTCAAAGCCCACACAAATC
1 AGTGGCATCCTTTCAAAG-CC-CACAAGTC
* *
1293916 AGTGGCACCCTTCCAAAGCCCACAAGTC
1 AGTGGCATCCTTTCAAAGCCCACAAGTC
* *
1293944 AGTGGCACCCTTTCAATGCCCACACAAGTC
1 AGTGGCATCCTTTCAAAG-CC-CACAAGTC
* *
1293974 GGTGGCAACTCTTTTCAAAGCCCACA
1 AGTGGC-A-TCCTTTCAAAGCCCACA
1294000 CAAGTTAGTG
Statistics
Matches: 293, Mismatches: 37, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
27 2 0.01
28 232 0.79
29 8 0.03
30 40 0.14
31 3 0.01
32 8 0.03
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (28 bp):
AGTGGCATCCTTTCAAAGCCCACAAGTC
Found at i:1298311 original size:11 final size:11
Alignment explanation
Indices: 1298292--1298326 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1298282 TTTTAGTAAA
1298292 TTAATAATTAT
1 TTAATAATTAT
*
1298303 TTGATAATTAT
1 TTAATAATTAT
1298314 TTAATAA-TAT
1 TTAATAATTAT
1298324 TTA
1 TTA
1298327 TATGAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (11 bp):
TTAATAATTAT
Found at i:1303322 original size:7 final size:7
Alignment explanation
Indices: 1303295--1303342 Score: 73
Period size: 7 Copynumber: 7.1 Consensus size: 7
1303285 AATAAGAGAG
1303295 AGAAAG-
1 AGAAAGA
1303301 AGAAA-A
1 AGAAAGA
*
1303307 AGAAGGA
1 AGAAAGA
1303314 AGAAAGA
1 AGAAAGA
1303321 AGAAAGA
1 AGAAAGA
1303328 AGAAAGA
1 AGAAAGA
1303335 AGAAAGA
1 AGAAAGA
1303342 A
1 A
1303343 AGTAAAAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
6 9 0.24
7 29 0.76
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (7 bp):
AGAAAGA
Found at i:1303343 original size:11 final size:11
Alignment explanation
Indices: 1303295--1303344 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
1303285 AATAAGAGAG
*
1303295 AGAAAGAGAAAA
1 AGAAAGA-AGAA
*
1303307 AGAAGGAAGAA
1 AGAAAGAAGAA
1303318 AG-AAGAA-AGA
1 AGAAAGAAGA-A
1303328 AGAAAGAAGAA
1 AGAAAGAAGAA
1303339 AGAAAG
1 AGAAAG
1303345 TAAAAAACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
9 1 0.03
10 7 0.22
11 17 0.53
12 7 0.22
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (11 bp):
AGAAAGAAGAA
Found at i:1308874 original size:20 final size:20
Alignment explanation
Indices: 1308849--1308898 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1308839 CAGATATATT
1308849 GATACATTCTTCAATGTATC
1 GATACATTCTTCAATGTATC
* *
1308869 GATACATGT-ATGAATGTATC
1 GATACAT-TCTTCAATGTATC
*
1308889 AATACATTCT
1 GATACATTCT
1308899 GTCTTTTTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
19 1 0.04
20 22 0.92
21 1 0.04
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (20 bp):
GATACATTCTTCAATGTATC
Found at i:1319781 original size:61 final size:62
Alignment explanation
Indices: 1319652--1320255 Score: 743
Period size: 61 Copynumber: 10.1 Consensus size: 62
1319642 GAGCAGGATG
* * * * * *
1319652 CCTTTCAAAGCCCACACAAGCTAGTGGCACTTTTCTAGTCCTCAAAGAGTAGGACACCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
1319714 CCTTTTAAAGTCCACACAAGTTGGTGGCACCTTTC-AGTCTTCAAAGAACAGGACACCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
*
1319775 CTTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCTAGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
1319836 CTTTTTAAAGCCCACACAAGTTGGTGGCA--TTTCCTAGTCCTCGAAGAGCA-TACG------
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-CTAGTCCTCAAAGAGCAGGACGCCTTTT
* * **
1319890 CCTTTTAAAGCCCGCACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGTTTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
*
1319952 CCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCTAGTCTTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* *
1320013 CCTTTTAAAGCCCACACAAGTTGGTGGCA--TTTCCTAGTCCTCAAAGAGTAGGA------TG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-CTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
1320068 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AATCCTCGAAGAGCAGGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * **
1320129 CCTTTTAAAGCCCACACAAGCTGGTGGCA-CTTTC-AGTCCTCAAAGAACAGGACGTATTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* *
1320189 CCTTTTAAAGCCCACAGAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
1320250 CCTTTT
1 CCTTTT
1320256 CTCCTTTACC
Statistics
Matches: 474, Mismatches: 45, Indels: 47
0.84 0.08 0.08
Matches are distributed among these distances:
54 27 0.06
55 61 0.13
56 7 0.01
57 3 0.01
60 61 0.13
61 256 0.54
62 59 0.12
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.29
Consensus pattern (62 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:1319972 original size:177 final size:177
Alignment explanation
Indices: 1319627--1320249 Score: 816
Period size: 177 Copynumber: 3.5 Consensus size: 177
1319617 CTCATTTCAC
* * *
1319627 CCTT-TAGTCCTCAAAGAGCAGGATGCC-TTT-C----AAAGCCCACACAAGCTAGTGGCACTTT
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-TTT
* * * * *
1319685 TCTAGTCCTCAAAGAGTAGGACACCTTTTCCTTTTAAAGTCCACACAAGTTGGTGGCACCTTTCA
65 CCTAGTCCTCAAAGAGCAGG--A-C---GCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCA
* * * *
1319750 GTCTTCAAAGAACAGGACACCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA
124 GTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
*
1319804 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCATTTC
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTC
* * *
1319869 CTAGTCCTCGAAGAGCA-TACGCCTTTTAAAGCCCGCACAAGTTGGTGGCACTTTTCTAGTCCTC
66 CTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTC
**
1319933 AAAGAGCAGGACGTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
130 AAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
*
1319981 CCTTCTAGTCTTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTC
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTC
* * * *
1320046 CTAGTCCTCAAAGAGTAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAATCCTCG
66 CTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCA
* *
1320111 AAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGCTGGTGGCA
131 AAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * ** *
1320158 CTTTC-AGTCCTCAAAGAACAGGACGTATTTTCCTTTTAAAGCCCACAGAAGTTGGTGGCACTTT
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-TTT
*
1320222 TC-AGTCCTCAAAGAGCAGGACGCCTTTT
65 CCTAGTCCTCAAAGAGCAGGACGCCTTTT
1320250 CCTTTTCTCC
Statistics
Matches: 396, Mismatches: 40, Indels: 21
0.87 0.09 0.05
Matches are distributed among these distances:
176 106 0.27
177 188 0.47
178 58 0.15
179 4 0.01
180 1 0.00
183 18 0.05
184 21 0.05
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (177 bp):
CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTC
CTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCA
AAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:1320408 original size:42 final size:41
Alignment explanation
Indices: 1320288--1320525 Score: 183
Period size: 41 Copynumber: 5.6 Consensus size: 41
1320278 ACGCCTTTTC
* *
1320288 CTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTCATTT
1 CTTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTT
* *
1320329 CCTTCTTTTTCCTTCTAGTTCTCAAAGAGCAGGACACATTTTATTCT
1 -C-T-TTTTTCCTT-T-GTCCTCAAAGAGCAGGACACATTTCATT-T
* * *
1320376 CTTTTTTCCTTTGTCCTCAAAAAGCATGACACATTTAATTT
1 CTTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTT
* * * * * ** *
1320417 CCTTTTTCCTTTCT-CTCCAAAGGGTATGATGCATTTTATTT
1 CTTTTTTCCTTTGTCCT-CAAAGAGCAGGACACATTTCATTT
* * * *
1320458 CCTTTTTTCCTTAGTCCCCAAGGAGCAGGACCCATTTCA-TT
1 -CTTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTT
* **
1320499 CTCCTTTTCCTTAATCCTCAAAGAGCA
1 CT-TTTTTCCTTTGTCCTCAAAGAGCA
1320526 AGATGCCCCA
Statistics
Matches: 156, Mismatches: 31, Indels: 19
0.76 0.15 0.09
Matches are distributed among these distances:
40 4 0.03
41 53 0.34
42 50 0.32
43 3 0.02
44 18 0.12
45 2 0.01
46 25 0.16
47 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.41
Consensus pattern (41 bp):
CTTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTT
Found at i:1320468 original size:83 final size:85
Alignment explanation
Indices: 1320284--1320510 Score: 230
Period size: 83 Copynumber: 2.7 Consensus size: 85
1320274 CAGGACGCCT
* * *
1320284 TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCCTTCTTTTTCC-TTCTAGT
1 TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTT-C--CTTTTTCCTTTCTA-C
1320348 TCTCAAAGAGCAGGACACATTTTA
62 TCTCAAAGAGCAGGACACATTTTA
* * *
1320372 -TTCTCTTTTTTCCTTTGTCCTCAAAAAGCATGACACATTTAATTTCCTTTTTCCTTTCT-CTC-
1 TTTC-CTTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTTTTCCTTTCTACTCT
* * * **
1320434 CAAAGGGTATGATGCATTTTA
65 CAAAGAGCAGGACACATTTTA
* * * *
1320455 TTTCCTTTTTTCCTTAGTCCCCAAGGAGCAGGACCCATTTCATTCTCC-TTTTCCTT
1 TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCATT-TCCTTTTTCCTT
1320511 AATCCTCAAA
Statistics
Matches: 117, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
83 57 0.49
84 8 0.07
85 8 0.07
86 4 0.03
87 4 0.03
88 36 0.31
ACGTcount: A:0.19, C:0.26, G:0.11, T:0.43
Consensus pattern (85 bp):
TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTTTTCCTTTCTACTCTC
AAAGAGCAGGACACATTTTA
Found at i:1323644 original size:79 final size:80
Alignment explanation
Indices: 1323468--1323673 Score: 274
Period size: 79 Copynumber: 2.6 Consensus size: 80
1323458 TCATTCATGT
* * * * *
1323468 TTTTATTTCCAAAATACCAATTTTTTATAATC-GGGATACTCCAA-CCTCATTATTTCCGAGGGG
1 TTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAACCCTCATTATTTCCAAAGGG
* *
1323531 ATACTCCAACCCCTA
66 ATACTCCAAACCCGA
* *
1323546 TTTTATTTTTCAAAACACCAATTTTTCATAATCGGGGATACTCCAACCCT-GTTATTTCCAAAGG
1 TTTTATTTCT-AAAACACCAATTTTTCATAATCGGGGATACTCCAACCCTCATTATTTCCAAAGG
*
1323610 GATACTCCAAACCCGG
65 GATACTCCAAACCCGA
* *
1323626 TTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCTACCC
1 TTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAACCC
1323674 CGGTTTTAGT
Statistics
Matches: 112, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
78 8 0.07
79 56 0.50
80 45 0.40
81 3 0.03
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.34
Consensus pattern (80 bp):
TTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAACCCTCATTATTTCCAAAGGG
ATACTCCAAACCCGA
Found at i:1323724 original size:49 final size:50
Alignment explanation
Indices: 1323607--1323724 Score: 141
Period size: 51 Copynumber: 2.4 Consensus size: 50
1323597 TTATTTCCAA
* *
1323607 AGGGATACTCCAAACCCGGTTTTATTTCTAAAACACCAATTTTTCACAATC
1 AGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAA-TTTCCACAATC
* * * * *
1323658 GGGGATACTCCTACCCCGGTTTTAGTTTC-AAAACATCGA-TTCCACCATC
1 AGGGATACTCCAACCCCGGTTTTA-TTTCTAAAACACCAATTTCCACAATC
1323707 AGGGATACTCCAACCCCG
1 AGGGATACTCCAACCCCG
1323725 TTATTTTTCG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
49 24 0.42
51 29 0.51
52 4 0.07
ACGTcount: A:0.29, C:0.30, G:0.14, T:0.27
Consensus pattern (50 bp):
AGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTCCACAATC
Found at i:1323767 original size:129 final size:128
Alignment explanation
Indices: 1323527--1323883 Score: 400
Period size: 129 Copynumber: 2.7 Consensus size: 128
1323517 TTATTTCCGA
* * * *
1323527 GGGGATACTCCAACCCCTATTTTATTTTTCAAAACACCAATTTTTCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCAATTTTA-TTTCCAAAACACCAA-TTTCCACAATC-GGGATACTCCAA
* * *
1323592 CCCTGTTA-TTTCCAAAGGGATACTCCAAACCC-GGTTTTATTTCTAAAACACCAATTTTTCACA
63 CCCCGTTATTTTTC-GAGGGATACTCC-AACCCTGGTTTTATTTCTAAAACACCAATTTTTCACA
1323655 ATC
126 ATC
* ** * * *
1323658 GGGGATACTCCTACCCCGGTTTTAGTTT-CAAAACATCGA-TTCCACCATCAGGGATACTCCAAC
1 GGGGATACTCCAACCCCAATTTTA-TTTCCAAAACACCAATTTCCACAATC-GGGATACTCCAAC
* *
1323721 CCCGTTATTTTTCGAGGGGATACTCCAACCCTGGTTTTATTTCTAAAACACTACTTTTTCACAAT
64 CCCGTTATTTTTCGA-GGGATACTCCAACCCTGGTTTTATTTCTAAAACACCAATTTTTCACAAT
1323786 C
128 C
* *
1323787 GGGGATACTCCAACTCCAATTTTATTTCCAAAACACCAATTTTTCACAATCGAGGATACTCCAAC
1 GGGGATACTCCAACCCCAATTTTATTTCCAAAACACCAA-TTTCCACAATCG-GGATACTCCAAC
* * *
1323852 CCCATTATTTAATCGA-GGATACTCTAACCCTG
64 CCCGTTATTT-TTCGAGGGATACTCCAACCCTG
1323884 TTATTTTCGA
Statistics
Matches: 192, Mismatches: 26, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
128 35 0.18
129 75 0.39
130 25 0.13
131 53 0.28
132 4 0.02
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (128 bp):
GGGGATACTCCAACCCCAATTTTATTTCCAAAACACCAATTTCCACAATCGGGATACTCCAACCC
CGTTATTTTTCGAGGGATACTCCAACCCTGGTTTTATTTCTAAAACACCAATTTTTCACAATC
Found at i:1323800 original size:51 final size:50
Alignment explanation
Indices: 1323736--1323853 Score: 164
Period size: 51 Copynumber: 2.3 Consensus size: 50
1323726 TATTTTTCGA
** * * *
1323736 GGGGATACTCCAACCCTGGTTTTATTTCTAAAACACTACTTTTTCACAATC
1 GGGGATACTCCAACCC-AATTTTATTTCCAAAACACCAATTTTTCACAATC
1323787 GGGGATACTCCAACTCCAATTTTATTTCCAAAACACCAATTTTTCACAATC
1 GGGGATACTCCAAC-CCAATTTTATTTCCAAAACACCAATTTTTCACAATC
*
1323838 GAGGATACTCCAACCC
1 GGGGATACTCCAACCC
1323854 CATTATTTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
50 2 0.03
51 56 0.93
52 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.31
Consensus pattern (50 bp):
GGGGATACTCCAACCCAATTTTATTTCCAAAACACCAATTTTTCACAATC
Found at i:1323809 original size:78 final size:77
Alignment explanation
Indices: 1323658--1323809 Score: 173
Period size: 78 Copynumber: 1.9 Consensus size: 77
1323648 TTTCACAATC
* *
1323658 GGGGATACTCCTACCCCGGTTTTAGTTTCAAAACATCGATTCCACCATCAGGGATACTCCAACCC
1 GGGGATACTCCAACCCCGGTTTTAGTTTCAAAACATCGATTCCACAATCAGGGATACTCCAACCC
*
1323723 CGTTATTTTTCGA
66 CG-AATTTTTCGA
* ** * *
1323736 GGGGATACTCCAACCCTGGTTTTA-TTTCTAAAACACTACTTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGGTTTTAGTTTC-AAAACA-T-CGATTCCACAATCAGGGATACTCCAA
*
1323800 CTCC-AATTTT
63 CCCCGAATTTT
1323810 ATTTCCAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
77 4 0.06
78 33 0.53
79 1 0.02
80 24 0.39
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.32
Consensus pattern (77 bp):
GGGGATACTCCAACCCCGGTTTTAGTTTCAAAACATCGATTCCACAATCAGGGATACTCCAACCC
CGAATTTTTCGA
Found at i:1323866 original size:28 final size:28
Alignment explanation
Indices: 1323834--1323907 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
1323824 AATTTTTCAC
1323834 AATCGAGGATACTCCAACCCCATTATTT
1 AATCGAGGATACTCCAACCCCATTATTT
* **
1323862 AATCGAGGATACTCTAACCCTGTTATTT
1 AATCGAGGATACTCCAACCCCATTATTT
1323890 --TCGAGGGGATACTCCAAC
1 AATCGA--GGATACTCCAAC
1323908 TCTGGCTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
26 4 0.10
28 36 0.90
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (28 bp):
AATCGAGGATACTCCAACCCCATTATTT
Found at i:1324120 original size:79 final size:78
Alignment explanation
Indices: 1323862--1324122 Score: 265
Period size: 79 Copynumber: 3.3 Consensus size: 78
1323852 CCCATTATTT
* * * * * *
1323862 AATCGAGGATACTCTAACCCTGTTATTTTCGAGGGGATACTCCAACTCTGGCTTTATTTCTAAAA
1 AATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTTCAACCCCGGCTTTATTTCT-AAA
* ** *
1323927 TATTGATTTCTCAC
65 CACCGATTTTTCAC
* * * * * * *
1323941 AATCGGGGATATTCCAACCTCGTTATTTTTGCGGGGATAC-TCTGACCACGGCCTTATTTCTAAA
1 AATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTTC-AACCCCGGCTTTATTTCTAAA
*
1324005 GCACCGATTTTCCAC
65 -CACCGATTTTTCAC
**
1324020 AATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTTCAACCCCGATTTTATTT-TCAGA
1 AATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTTCAACCCCGGCTTTATTTCT-A-A
*
1324084 ACACCGATTTTTCAT
64 ACACCGATTTTTCAC
*
1324099 AATCGGGGATACTCCAGCCCCGTT
1 AATCGGGGATACTCCAACCCCGTT
1324123 GTTATCCCCA
Statistics
Matches: 147, Mismatches: 30, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
78 5 0.03
79 138 0.94
80 4 0.03
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (78 bp):
AATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTTCAACCCCGGCTTTATTTCTAAAC
ACCGATTTTTCAC
Found at i:1325780 original size:21 final size:21
Alignment explanation
Indices: 1325754--1325812 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
1325744 TCAACGTGGT
1325754 CTTGTATCGATACATTTCGAA
1 CTTGTATCGATACATTTCGAA
* **
1325775 CTTGTATCGATACATTCACTTA
1 CTTGTATCGATACATT-TCGAA
1325797 -TTGTATCGATACATTT
1 CTTGTATCGATACATTT
1325813 TATAGAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
CTTGTATCGATACATTTCGAA
Found at i:1326599 original size:32 final size:32
Alignment explanation
Indices: 1326573--1326935 Score: 275
Period size: 32 Copynumber: 11.9 Consensus size: 32
1326563 TGCCATTGAT
*
1326573 TTGTGTGGGCTTTTGAGAGGGTTGCCACCGAC
1 TTGTGTGGGCTTTAGAGAGGGTTGCCACCGAC
* * * * *
1326605 TTGTGTAGGCTTTCAAAGAAAGGATGCTACCGAC
1 TTGTGTGGGCTTT-AGAG-AGGGTTGCCACCGAC
* *
1326639 TTGTGTGGGCTTT-GAAAGGGTTGCCATCGAC
1 TTGTGTGGGCTTTAGAGAGGGTTGCCACCGAC
1326670 TTGTGTGGGCTTTAGAGAGGGTTGCCACCGAC
1 TTGTGTGGGCTTTAGAGAGGGTTGCCACCGAC
*
1326702 TTGTGTGGGCTTTAGAGAGGGTTGCCACCAAC
1 TTGTGTGGGCTTTAGAGAGGGTTGCCACCGAC
* * * **
1326734 TTGTGTAGGCTTTTTGAGAAGGTTGCCACTAAC
1 TTGTGTGGGC-TTTAGAGAGGGTTGCCACCGAC
* * * *
1326767 -T-TATGGGCTTTA-AGAGGGGATGCCAACAAC
1 TTGTGTGGGCTTTAGAGA-GGGTTGCCACCGAC
** *
1326797 -T-TGTGCACTTTAGAGAGGG-TGCCACTGAC
1 TTGTGTGGGCTTTAGAGAGGGTTGCCACCGAC
* * **
1326826 -T-TGTGGACTTTA-AAAGGG-TGCCA-TTAC
1 TTGTGTGGGCTTTAGAGAGGGTTGCCACCGAC
* *
1326853 GT-TGTGGGCTTT-GAGAGGG-TGCCACCAAC
1 TTGTGTGGGCTTTAGAGAGGGTTGCCACCGAC
*
1326882 -T-TGTGGGCTTT-GAGAAAGGTTGCCACCGAC
1 TTGTGTGGGCTTTAGAG-AGGGTTGCCACCGAC
1326912 -T-TGTGGGCTTT-GAGAGGG-TGCCAC
1 TTGTGTGGGCTTTAGAGAGGGTTGCCAC
1326936 TAACTTATGG
Statistics
Matches: 277, Mismatches: 43, Indels: 26
0.80 0.12 0.08
Matches are distributed among these distances:
27 3 0.01
28 50 0.18
29 29 0.10
30 48 0.17
31 32 0.12
32 70 0.25
33 21 0.08
34 24 0.09
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (32 bp):
TTGTGTGGGCTTTAGAGAGGGTTGCCACCGAC
Found at i:1326750 original size:97 final size:92
Alignment explanation
Indices: 1326576--1326934 Score: 307
Period size: 97 Copynumber: 3.9 Consensus size: 92
1326566 CATTGATTTG
* * * * *
1326576 TGTGGGCTTTTGAGAGGGTTGCCACCGACTTGTGTAGGCTTTCAAAGAAAGGATGCTACCGACTT
1 TGTGGGCTTTAGAGAGGGTTGCCACCAACTTGTG--GGCTTT-AGAGAAAGGTTGCCACCGACTT
1326641 GTGTGGGCTTTGAAAGGGTTGCCATCGACTT
63 GTGT-GGCTTTGAAAGGGTTGCCATCGACTT
* * *
1326672 GTGTGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAG-AGGGTTGCCACCAACTT
1 -TGTGGGCTTTAGAGAGGGTTGCCACCAAC-T-TGTGGGCTTTAGAGAAAGGTTGCCACCGACTT
*
1326736 GTGTAGGCTTTTTGAGAA-GGTTGCCA-CTAAC-T
63 GTGT-GGC--TTTGA-AAGGGTTGCCATC-GACTT
* * * ** * *
1326768 TATGGGCTTTA-AGAGGGGATGCCAACAACTTGTGCACTTTAGAG--AGGGTGCCACTGACTTGT
1 TGTGGGCTTTAGAGA-GGGTTGCCACCAACTTGTGGGCTTTAGAGAAAGGTTGCCACCGACTTGT
* * * *
1326830 G-GACTTTAAAAGGG-TGCCAT-TACGT
65 GTGGCTTTGAAAGGGTTGCCATCGACTT
1326855 TGTGGGCTTT-GAGAGGG-TGCCACCAACTTGTGGGCTTT-GAGAAAGGTTGCCACCGACTTGTG
1 TGTGGGCTTTAGAGAGGGTTGCCACCAACTTGTGGGCTTTAGAGAAAGGTTGCCACCGACTTGTG
*
1326917 -GGCTTTGAGAGGG-TGCCA
66 TGGCTTTGAAAGGGTTGCCA
1326935 CTAACTTATG
Statistics
Matches: 219, Mismatches: 30, Indels: 37
0.77 0.10 0.13
Matches are distributed among these distances:
84 3 0.01
85 18 0.08
86 37 0.17
87 20 0.09
88 6 0.03
90 2 0.01
92 15 0.07
93 12 0.05
94 4 0.02
95 41 0.19
96 5 0.02
97 49 0.22
98 3 0.01
99 4 0.02
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (92 bp):
TGTGGGCTTTAGAGAGGGTTGCCACCAACTTGTGGGCTTTAGAGAAAGGTTGCCACCGACTTGTG
TGGCTTTGAAAGGGTTGCCATCGACTT
Found at i:1326857 original size:28 final size:28
Alignment explanation
Indices: 1326642--1327107 Score: 319
Period size: 28 Copynumber: 15.9 Consensus size: 28
1326632 TACCGACTTG
* *
1326642 TGTGGGCTTTGAAAGGGTTGCCA-TCGACTT
1 TGTGGGCTTTAAAAGGG-TGCCACT-AAC-T
* **
1326672 GTGTGGGCTTTAGAGAGGGTTGCCACCGACTT
1 -TGTGGGCTTTA-AAAGGG-TGCCACTAAC-T
* *
1326704 GTGTGGGCTTTAGAGAGGGTTGCCACCAACT
1 -TGTGGGCTTTA-AAAGGG-TGCCACTAACT
* *
1326735 TGTGTAGGCTTTTTGAGAAGGTTGCCACTAACT
1 TGTG--GGC--TTT-AAAAGGGTGCCACTAACT
* *
1326768 TATGGGCTTTAAGAGGGGATGCCAAC-AACT
1 TGTGGGCTTTAA-AAGGG-TGCC-ACTAACT
** * *
1326798 TGTGCACTTTAGAGAGGGTGCCACTGACT
1 TGTGGGCTTTA-AAAGGGTGCCACTAACT
* *
1326827 TGTGGACTTTAAAAGGGTGCCA-TTACGT
1 TGTGGGCTTTAAAAGGGTGCCACTAAC-T
* * *
1326855 TGTGGGCTTTGAGAGGGTGCCACCAACT
1 TGTGGGCTTTAAAAGGGTGCCACTAACT
* **
1326883 TGTGGGCTTTGAGAAAGGTTGCCACCGACT
1 TGTGGGCTTT-A-AAAGGGTGCCACTAACT
* *
1326913 TGTGGGCTTTGAGAGGGTGCCACTAACT
1 TGTGGGCTTTAAAAGGGTGCCACTAACT
* * * *
1326941 TATGGGCTTTGAAAGGGTGCTACTGACT
1 TGTGGGCTTTAAAAGGGTGCCACTAACT
*
1326969 CGTGGGCTTTAAAA-GGTGCCACTAACT
1 TGTGGGCTTTAAAAGGGTGCCACTAACT
* ** *
1326996 TATAAGCTTTAAAAGGGTGCCATTAACT
1 TGTGGGCTTTAAAAGGGTGCCACTAACT
* *
1327024 TGTGAGCTTTAAAAGGGTGCCACTGACT
1 TGTGGGCTTTAAAAGGGTGCCACTAACT
*
1327052 TGTGCGGGCTTGTGAAAAGGGTGCTACTAACT
1 TGT--GGGCTT-T-AAAAGGGTGCCACTAACT
* *
1327084 CGTGGGCTTTGAAAGGGTGCCACT
1 TGTGGGCTTTAAAAGGGTGCCACT
1327108 GTTTATGGGC
Statistics
Matches: 355, Mismatches: 59, Indels: 45
0.77 0.13 0.10
Matches are distributed among these distances:
27 24 0.07
28 143 0.40
29 26 0.07
30 58 0.16
31 18 0.05
32 66 0.19
33 13 0.04
34 6 0.02
35 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTAAAAGGGTGCCACTAACT
Found at i:1326914 original size:115 final size:114
Alignment explanation
Indices: 1326644--1327129 Score: 403
Period size: 115 Copynumber: 4.1 Consensus size: 114
1326634 CCGACTTGTG
* * * *
1326644 TGGGCTTTGAAAGGGTTGCCATCGACTTGTGTGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTG
1 TGGGCTTTGAAAAGGTTGCCATCAAC-T-TGTGGACTTTAGAGAGGG-TGCCACTGAC-T-TGTG
* * * *
1326709 GGCTTTAGAGAGGGTTGCCACCAACTTGTGTAGGCTTTTTGAGAAGGTTGCCACTAACTTA
61 GGCTTTA-AAAGGG-TGCCACTAACTCGTG--GGC--TTTGA-AAGGGTGCCACTAACTTA
* * * * *
1326770 TGGGCTTT-AAGAGGGGATGCCAACAACTTGTGCACTTTAGAGAGGGTGCCACTGACTTGTGGAC
1 TGGGCTTTGAA-A-AGGTTGCCATCAACTTGTGGACTTTAGAGAGGGTGCCACTGACTTGTGGGC
* * * * *
1326834 TTTAAAAGGGTGCCA-TTACGTTGTGGGCTTTGAGAGGGTGCCACCAACTTG
64 TTTAAAAGGGTGCCACTAAC-TCGTGGGCTTTGAAAGGGTGCCACTAACTTA
* * * * *
1326885 TGGGCTTTGAGAAAGGTTGCCACCGACTTGTGGGCTTT-GAGAGGGTGCCACTAACTTATGGGCT
1 TGGGCTTTGA-AAAGGTTGCCATCAACTTGTGGACTTTAGAGAGGGTGCCACTGACTTGTGGGCT
* * * *
1326949 TTGAAAGGGTGCTACTGACTCGTGGGCTTT-AAAAGGTGCCACTAACTTA
65 TTAAAAGGGTGCCACTAACTCGTGGGCTTTGAAAGGGTGCCACTAACTTA
** * * *
1326998 TAAGCTTT-AAAAGGGTGCCATTAACTTGT-GAGCTTTA-AAAGGGTGCCACTGACTTGTGCGGG
1 TGGGCTTTGAAAAGGTTGCCATCAACTTGTGGA-CTTTAGAGAGGGTGCCACTGACTTGT--GGG
* **
1327060 CTTGTGAAAAGGGTGCTACTAACTCGTGGGCTTTGAAAGGGTGCCACT-GTTTA
63 CTT-T-AAAAGGGTGCCACTAACTCGTGGGCTTTGAAAGGGTGCCACTAACTTA
*
1327113 TGGGCTTTGAGAAGGTT
1 TGGGCTTTGAAAAGGTT
1327130 ACTTTACTGG
Statistics
Matches: 296, Mismatches: 50, Indels: 38
0.77 0.13 0.10
Matches are distributed among these distances:
110 1 0.00
111 37 0.12
112 1 0.00
113 27 0.09
114 46 0.16
115 79 0.27
116 25 0.08
117 1 0.00
118 3 0.01
119 2 0.01
120 10 0.03
121 5 0.02
122 10 0.03
123 1 0.00
124 9 0.03
125 18 0.06
126 10 0.03
127 11 0.04
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (114 bp):
TGGGCTTTGAAAAGGTTGCCATCAACTTGTGGACTTTAGAGAGGGTGCCACTGACTTGTGGGCTT
TAAAAGGGTGCCACTAACTCGTGGGCTTTGAAAGGGTGCCACTAACTTA
Found at i:1328743 original size:32 final size:33
Alignment explanation
Indices: 1328707--1328772 Score: 125
Period size: 32 Copynumber: 2.0 Consensus size: 33
1328697 GTATCCCCGA
1328707 GAAGAAAAATTTAATATTTTTGGAA-AAAAATG
1 GAAGAAAAATTTAATATTTTTGGAATAAAAATG
1328739 GAAGAAAAATTTAATATTTTTGGAATAAAAATG
1 GAAGAAAAATTTAATATTTTTGGAATAAAAATG
1328772 G
1 G
1328773 GGTTGGAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 25 0.76
33 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.32
Consensus pattern (33 bp):
GAAGAAAAATTTAATATTTTTGGAATAAAAATG
Found at i:1329152 original size:232 final size:231
Alignment explanation
Indices: 1328742--1329266 Score: 584
Period size: 232 Copynumber: 2.3 Consensus size: 231
1328732 AAAAATGGAA
* * * *
1328742 GAAAAATTTAATATTTTTGGAATAAAAATGGGGTTGGAGTATTCCCTTAGAAATAACGGGATTAG
1 GAAAAATTTAATA-TTTTGAAATAAAAACGGGGTTGGAGTATCCCCTCAGAAATAACGGGA-TAG
* * * *
1328807 AGTACCCTGAAAAAAATTTAATACTTTGGAAATAAAAACGGAGTTAGAGTATCCCCCTTAGAATT
64 AGTACCCAGAAAAAAATTTAACACTTTGGAAATAAAAACAGAGTTAGAGTATCCCCCTCAGAATT
* * * * *
1328872 GATAGGGTTGGAATATCTCAAGATGAAAAATTTGGCATTTTAGAAATAAAAACGGGGTTAGAGTG
129 AATAGGCTTGGAATATCCCAAGATGAAAAATTTGGAATTTTAGAAATAAAAACGGGGTTAGAGTA
* * * *
1328937 T-CCC-CTAAGAATTGATGGGGTTAGAGTATCCCTAAGAT
194 TGCCCTCGAA-AA-TAACGGGGTTAGAGTATCCCCAAGAT
1328975 -AAAAATTTAATATTTTGAAAATAAAAACGGGGTTGGAGTATCCCCTCAGAAATAACGGG-TAGT
1 GAAAAATTTAATATTTTG-AAATAAAAACGGGGTTGGAGTATCCCCTCAGAAATAACGGGATAG-
* * * * *
1329038 A-TCCCCGAGATAAAAAATTTAACATTTTGGAAATAAAAGCA-AGGTTGGAGTAT-CCCCTCGGA
64 AGTACCC-AGA-AAAAAATTTAACACTTTGGAAATAAAAACAGA-GTTAGAGTATCCCCCTCAGA
* * * *
1329100 ATTAATGAGGCTT-GAGTATCCCCAAGAT-AAAAATTT-TAATAATTTGGAAATAAAAATGGGGT
126 ATTAAT-AGGCTTGGAATAT-CCCAAGATGAAAAATTTGGAAT--TTTAGAAATAAAAACGGGGT
*
1329162 TGGAGTATGCCCTCGAAAATAACGGGGTTAGAGTATCCCCAAGAT
187 TAGAGTATGCCCTCGAAAATAACGGGGTTAGAGTATCCCCAAGAT
* * *
1329207 GAAAAATTTAATGTTTTGGAAATAAAAGCGGGGTTGGAGTATCCCCTCGGAAATAACGGG
1 GAAAAATTTAATATTTT-GAAATAAAAACGGGGTTGGAGTATCCCCTCAGAAATAACGGG
1329267 GTTGGAATAT
Statistics
Matches: 249, Mismatches: 30, Indels: 26
0.82 0.10 0.09
Matches are distributed among these distances:
230 9 0.04
231 34 0.14
232 143 0.57
233 59 0.24
234 4 0.02
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.27
Consensus pattern (231 bp):
GAAAAATTTAATATTTTGAAATAAAAACGGGGTTGGAGTATCCCCTCAGAAATAACGGGATAGAG
TACCCAGAAAAAAATTTAACACTTTGGAAATAAAAACAGAGTTAGAGTATCCCCCTCAGAATTAA
TAGGCTTGGAATATCCCAAGATGAAAAATTTGGAATTTTAGAAATAAAAACGGGGTTAGAGTATG
CCCTCGAAAATAACGGGGTTAGAGTATCCCCAAGAT
Found at i:1329246 original size:158 final size:153
Alignment explanation
Indices: 1328742--1329284 Score: 508
Period size: 154 Copynumber: 3.5 Consensus size: 153
1328732 AAAAATGGAA
* ** * ** * * *
1328742 GAAAAATTTAATATTTTTGG-AATAAAAATGGGGTTGGAGTATTCCCTTAGAAATAACGGGATTA
1 GAAAAATTTAACA-TTTTGGAAATAAAAGCGGGGTTGGAGTATCCCCTCGGAATTAATGGGGTTA
* * * * * * *
1328806 GAGTA--CCC-TGAAAAAAATTTAATACTTTGGAAATAAAAACGGAGTTAGAGTATCCCCCTTAG
65 GAGTATCCCCAAGATAAAAATTTAATAATTTGAAAATAAAAACGGGGTTGGAGTAT-CCCCTCAG
* * *
1328868 AATTGATA-GGGTTGGAATAT-CTCAAGAT
129 AAAT-A-ACGGG-T--AGTATCCCCAAGAT
** * * * * ** *
1328896 GAAAAATTTGGCATTTTAGAAATAAAAACGGGGTTAGAGTGTCCCCTAAGAATTGATGGGGTTAG
1 GAAAAATTTAACATTTTGGAAATAAAAGCGGGGTTGGAGTATCCCCTCGGAATTAATGGGGTTAG
* *
1328961 AGTATCCCTAAGATAAAAATTTAATATTTTGAAAATAAAAACGGGGTTGGAGTATCCCCTCAGAA
66 AGTATCCCCAAGATAAAAATTTAATAATTTGAAAATAAAAACGGGGTTGGAGTATCCCCTCAGAA
*
1329026 ATAACGGGTAGTATCCCCGAGAT
131 ATAACGGGTAGTATCCCCAAGAT
* ** *
1329049 AAAAAATTTAACATTTTGGAAATAAAAGCAAGGTTGGAGTATCCCCTCGGAATTAATGAGGCTT-
1 GAAAAATTTAACATTTTGGAAATAAAAGCGGGGTTGGAGTATCCCCTCGGAATTAATG-GGGTTA
* * *
1329113 GAGTATCCCCAAGATAAAAATTTTAATAATTTGGAAATAAAAATGGGGTTGGAGTATGCCCTC-G
65 GAGTATCCCCAAGATAAAAA-TTTAATAATTTGAAAATAAAAACGGGGTTGGAGTATCCCCTCAG
1329177 AAAATAACGGGGTTAGAGTATCCCCAAGAT
129 -AAATAAC-GGG-T--AGTATCCCCAAGAT
** * * *
1329207 GAAAAATTTAATGTTTTGGAAATAAAAGCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGG
1 GAAAAATTTAACATTTTGGAAATAAAAGCGGGGTTGGAGTATCCCCTCGGAATTAATGGGGTTAG
*
1329272 AATATCCCCAAGA
66 AGTATCCCCAAGA
1329285 CGAAAAATCG
Statistics
Matches: 322, Mismatches: 53, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
152 4 0.01
153 77 0.24
154 101 0.31
155 7 0.02
156 13 0.04
157 43 0.13
158 77 0.24
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (153 bp):
GAAAAATTTAACATTTTGGAAATAAAAGCGGGGTTGGAGTATCCCCTCGGAATTAATGGGGTTAG
AGTATCCCCAAGATAAAAATTTAATAATTTGAAAATAAAAACGGGGTTGGAGTATCCCCTCAGAA
ATAACGGGTAGTATCCCCAAGAT
Found at i:1329307 original size:79 final size:78
Alignment explanation
Indices: 1328742--1329292 Score: 503
Period size: 79 Copynumber: 7.1 Consensus size: 78
1328732 AAAAATGGAA
* * ** *
1328742 GAAAAATTTAATATTTTTGG-AATAAAAATGGGGTTGGAGTATTCCCTTAGAAATAACGGGATTA
1 GAAAAATTTAATA-TTTTGGAAATAAAAACGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTT-
*
1328806 GAGTA--CCC-TGA-
64 GAGTATCCCCAAGAT
* * * * ** * * **
1328817 AAAAAATTTAATACTTTGGAAATAAAAACGGAGTTAGAGTATCCCCCTTAGAATTGATAGGGTTG
1 GAAAAATTTAATATTTTGGAAATAAAAACGGGGTTGGAGTAT-CCCCTCGGAAATAACGGGGTT-
* *
1328882 GAATAT-CTCAAGAT
64 GAGTATCCCCAAGAT
*** * * * ** * * *
1328896 GAAAAATTTGGCATTTTAGAAATAAAAACGGGGTTAGAGTGTCCCCTAAGAATTGATGGGGTTAG
1 GAAAAATTTAATATTTTGGAAATAAAAACGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTT-G
*
1328961 AGTATCCCTAAGAT
65 AGTATCCCCAAGAT
* *
1328975 -AAAAATTTAATATTTTGAAAATAAAAACGGGGTTGGAGTATCCCCTCAGAAATAAC-GGG-T-A
1 GAAAAATTTAATATTTTGGAAATAAAAACGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGA
*
1329036 GTATCCCCGAGAT
66 GTATCCCCAAGAT
* * * ** * * *
1329049 AAAAAATTTAACATTTTGGAAATAAAAGCAAGGTTGGAGTATCCCCTCGGAATTAATGAGGCTTG
1 GAAAAATTTAATATTTTGGAAATAAAAACGGGGTTGGAGTATCCCCTCGGAAATAACG-GGGTTG
1329114 AGTATCCCCAAGAT
65 AGTATCCCCAAGAT
* * * *
1329128 -AAAAATTTTAATAATTTGGAAATAAAAATGGGGTTGGAGTATGCCCTCGAAAATAACGGGGTTA
1 GAAAAA-TTTAATATTTTGGAAATAAAAACGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTT-
1329192 GAGTATCCCCAAGAT
64 GAGTATCCCCAAGAT
* *
1329207 GAAAAATTTAATGTTTTGGAAATAAAAGCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGG
1 GAAAAATTTAATATTTTGGAAATAAAAACGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTT-G
* *
1329272 AATATCCCCAAGAC
65 AGTATCCCCAAGAT
1329286 GAAAAAT
1 GAAAAAT
1329293 CGATATTTTT
Statistics
Matches: 390, Mismatches: 72, Indels: 24
0.80 0.15 0.05
Matches are distributed among these distances:
74 17 0.04
75 79 0.20
76 20 0.05
77 7 0.02
78 81 0.21
79 181 0.46
80 5 0.01
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (78 bp):
GAAAAATTTAATATTTTGGAAATAAAAACGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGA
GTATCCCCAAGAT
Found at i:1331701 original size:22 final size:20
Alignment explanation
Indices: 1331649--1331704 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
1331639 AAAAACCTAG
1331649 AATGTATCGATACAATGAGA
1 AATGTATCGATACAATGAGA
* * *
1331669 AATATATCGATACAATTATA
1 AATGTATCGATACAATGAGA
1331689 AGCATGTATCGATACA
1 A--ATGTATCGATACA
1331705 TTTACTTATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 18 0.60
22 12 0.40
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:1331717 original size:20 final size:20
Alignment explanation
Indices: 1331692--1331732 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1331682 AATTATAAGC
*
1331692 ATGTATCGATACATTTACTT
1 ATGTATCAATACATTTACTT
*
1331712 ATGTATCAATACATTTCCTT
1 ATGTATCAATACATTTACTT
1331732 A
1 A
1331733 ACAGTATGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (20 bp):
ATGTATCAATACATTTACTT
Found at i:1332597 original size:35 final size:35
Alignment explanation
Indices: 1332531--1332631 Score: 114
Period size: 35 Copynumber: 2.9 Consensus size: 35
1332521 AATGAAATAG
* * * *
1332531 GTCCTGCTCCTTAAAGATAAA-TGAAAGAGGAGTAT
1 GTCCTGCTCCTTGAAGACAAAGGGAAA-AGGAGTAC
*
1332566 GTCCTGCTCCTTGAGGACAAAGGGAAAAGGAGTAC
1 GTCCTGCTCCTTGAAGACAAAGGGAAAAGGAGTAC
* * *
1332601 GTCTTGCTCTTTGAAGACAAAGGAAAAAGGA
1 GTCCTGCTCCTTGAAGACAAAGGGAAAAGGA
1332632 AATGAAGCAC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 52 0.93
36 4 0.07
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.22
Consensus pattern (35 bp):
GTCCTGCTCCTTGAAGACAAAGGGAAAAGGAGTAC
Found at i:1332786 original size:63 final size:61
Alignment explanation
Indices: 1332682--1332829 Score: 215
Period size: 63 Copynumber: 2.4 Consensus size: 61
1332672 AAGAAATGCG
**
1332682 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAATAAAAAAAGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTAATGTGGGCTTT-AAA-AAAAAAAGGCA
* * *
1332745 TCTTGCTCTTTAAGGACTAAAAGGTGCCACCAACTAATGTGGGCTTTAAAAGAAAAAGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTAATGTGGGCTTTAAAAAAAAAAGGCA
* *
1332806 TCCTACTCTTCGAGGACTAAAAGG
1 TCCTGCTCTTTGAGGACTAAAAGG
1332830 CTAAAAGGGG
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
61 30 0.39
62 3 0.04
63 43 0.57
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.25
Consensus pattern (61 bp):
TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTAATGTGGGCTTTAAAAAAAAAAGGCA
Found at i:1337639 original size:32 final size:32
Alignment explanation
Indices: 1337584--1337684 Score: 166
Period size: 32 Copynumber: 3.1 Consensus size: 32
1337574 TTCAACGATT
1337584 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
*
1337617 TTTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
1337649 TGTATCGATACATAAGTTTTGTATTGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1337681 TGTA
1 TGTA
1337685 AGCTACTGCC
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 52 0.81
33 12 0.19
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1337643 original size:19 final size:18
Alignment explanation
Indices: 1337582--1337679 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
1337572 ATTTCAACGA
1337582 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
1337601 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1337617 -TT-TATCGATACATAAG
1 TTTGTATCGATACATAAG
1337633 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1337649 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
1337665 TTTTGTATTGATACA
1 -TTTGTATCGATACA
1337680 ATGTAAGCTA
Statistics
Matches: 65, Mismatches: 1, Indels: 26
0.71 0.01 0.28
Matches are distributed among these distances:
13 20 0.31
14 2 0.03
15 4 0.06
17 4 0.06
18 2 0.03
19 21 0.32
20 12 0.18
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1337800 original size:52 final size:52
Alignment explanation
Indices: 1337755--1337883 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
1337745 CACTGATCTT
*
1337755 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATTGATACACTATAAAA
* * *
1337807 TGTATCGATACATACAGGCAAATTTGCGCAGATGTATTGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATTGATACACTATAAAA
1337859 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1337884 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATTGATACACTATAAAA
Found at i:1346675 original size:28 final size:28
Alignment explanation
Indices: 1346594--1346675 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
1346584 TTTTGGAGAT
*
1346594 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
1346622 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
1346650 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
1346676 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:1346818 original size:51 final size:51
Alignment explanation
Indices: 1346658--1346828 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
1346648 GAAATAACGA
* * *
1346658 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
1346710 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
1346763 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
1346814 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1346829 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:1346874 original size:27 final size:28
Alignment explanation
Indices: 1346811--1346886 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
1346801 AAAATAAAGT
*
1346811 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
1346839 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
1346866 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1346887 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1349374 original size:13 final size:13
Alignment explanation
Indices: 1349356--1349381 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1349346 ACAAAGATCC
1349356 ATGTATCGATACA
1 ATGTATCGATACA
1349369 ATGTATCGATACA
1 ATGTATCGATACA
1349382 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1349377 original size:33 final size:33
Alignment explanation
Indices: 1349335--1349401 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1349325 AAAATTTCCA
***
1349335 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1349368 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1349401 A
1 A
1349402 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1349445 original size:19 final size:18
Alignment explanation
Indices: 1349421--1349488 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1349411 CAGTAGCCAA
1349421 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1349440 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1349455 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1349472 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1349489 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1349461 original size:13 final size:13
Alignment explanation
Indices: 1349443--1349467 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1349433 ACAATACTTA
1349443 TGTATCGATACAT
1 TGTATCGATACAT
1349456 TGTATCGATACA
1 TGTATCGATACA
1349468 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1349465 original size:32 final size:32
Alignment explanation
Indices: 1349424--1349486 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1349414 TAGCCAATTA
*
1349424 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1349456 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1349487 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1349550 original size:21 final size:21
Alignment explanation
Indices: 1349524--1349601 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
1349514 GTTGGGACCC
*
1349524 TGTATCAATACATTTGTAGAA
1 TGTATCGATACATTTGTAGAA
1349545 TGTATCGATACATTTGT-GAA
1 TGTATCGATACATTTGTAGAA
* *
1349565 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTA-GAA
1349586 TGTATCGATACATTTG
1 TGTATCGATACATTTG
1349602 GAATTTTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
19 3 0.06
20 15 0.30
21 30 0.60
22 2 0.04
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTGTAGAA
Found at i:1355921 original size:21 final size:20
Alignment explanation
Indices: 1355894--1355979 Score: 70
Period size: 23 Copynumber: 4.2 Consensus size: 20
1355884 CGTCCTCCCC
1355894 CAAAAAAAAAC--CAAATAAA
1 CAAAAAAAAACAACAAA-AAA
* *
1355913 CAAAAAAAAAGAAGAAAAAAA
1 CAAAAAAAAACAA-CAAAAAA
1355934 CAAAAATAAATACAAACAAAAAA
1 CAAAAA-AAA-AC-AACAAAAAA
*
1355957 CAAAAAACAAAGAA-AAAAAA
1 CAAAAAA-AAACAACAAAAAA
1355977 CAA
1 CAA
1355980 CAACAACAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
19 10 0.18
20 9 0.16
21 11 0.20
22 8 0.15
23 15 0.27
24 2 0.04
ACGTcount: A:0.81, C:0.12, G:0.03, T:0.03
Consensus pattern (20 bp):
CAAAAAAAAACAACAAAAAA
Found at i:1355941 original size:31 final size:31
Alignment explanation
Indices: 1355894--1355979 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
1355884 CGTCCTCCCC
*
1355894 CAAAAAAAAAC-CAAATAAACAAA-AAAAAA
1 CAAAAAAAAACAAAAATAAACAAACAAAAAA
*
1355923 GAAGAAAAAAACAAAAATAAATACAAACAAAAAA
1 CAA-AAAAAAACAAAAAT-AA-ACAAACAAAAAA
*
1355957 CAAAAAACAAAGAAAAA-AAACAA
1 CAAAAAA-AAACAAAAATAAACAA
1355980 CAACAACAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
29 2 0.04
30 8 0.17
31 8 0.17
32 4 0.09
33 9 0.19
34 16 0.34
ACGTcount: A:0.81, C:0.12, G:0.03, T:0.03
Consensus pattern (31 bp):
CAAAAAAAAACAAAAATAAACAAACAAAAAA
Found at i:1355956 original size:18 final size:17
Alignment explanation
Indices: 1355894--1355976 Score: 67
Period size: 19 Copynumber: 4.5 Consensus size: 17
1355884 CGTCCTCCCC
*
1355894 CAAAAAAAAACCAAATAAA
1 CAAAAAAAAA--AAACAAA
* *
1355913 CAAAAAAAAAGAAGAAA
1 CAAAAAAAAAAAACAAA
*
1355930 AAAACAAAAATAAATACAAA
1 CAAA-AAAAA-AAA-ACAAA
1355950 CAAAAAACAAAAAACAAA
1 CAAAAAA-AAAAAACAAA
*
1355968 GAAAAAAAA
1 CAAAAAAAA
1355977 CAACAACAAC
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
17 10 0.19
18 16 0.30
19 18 0.34
20 9 0.17
ACGTcount: A:0.82, C:0.11, G:0.04, T:0.04
Consensus pattern (17 bp):
CAAAAAAAAAAAACAAA
Found at i:1355981 original size:23 final size:21
Alignment explanation
Indices: 1355910--1355982 Score: 83
Period size: 23 Copynumber: 3.3 Consensus size: 21
1355900 AAAACCAAAT
*
1355910 AAACAAAAAAAAAGAAGAAAA
1 AAACAAAAAAAAAGAAAAAAA
* *
1355931 AAACAAAAATAAATACAAACAAA
1 AAACAAAAA-AAA-AGAAAAAAA
1355954 AAACAAAAAACAAAGAAAAAAA
1 AAACAAAAAA-AAAGAAAAAAA
1355976 ACAACAA
1 A-AACAA
1355983 CAACAACCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
21 9 0.21
22 12 0.28
23 22 0.51
ACGTcount: A:0.82, C:0.11, G:0.04, T:0.03
Consensus pattern (21 bp):
AAACAAAAAAAAAGAAAAAAA
Found at i:1357476 original size:29 final size:30
Alignment explanation
Indices: 1357433--1357522 Score: 116
Period size: 29 Copynumber: 3.1 Consensus size: 30
1357423 TTCCTCACCC
1357433 TTCAAAAGCCCACAAGTCAGTGGCATCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTT
* * *
1357463 TTC-AAAGCCCACAAATCAGTGGCAAC--C
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTT
1357490 TTCAAAAGCCCACAAGTTC-GTGGCATCTTT
1 TTCAAAAGCCCACAAG-TCAGTGGCATCTTT
1357520 TTC
1 TTC
1357523 CTTTTAAGCC
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
27 3 0.06
28 18 0.36
29 23 0.46
30 6 0.12
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.26
Consensus pattern (30 bp):
TTCAAAAGCCCACAAGTCAGTGGCATCTTT
Found at i:1357572 original size:32 final size:32
Alignment explanation
Indices: 1357495--1357638 Score: 144
Period size: 33 Copynumber: 4.3 Consensus size: 32
1357485 CAACCTTCAA
* * * *
1357495 AAGCCCACAAGTTCGTGGCATCTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTT-TTTTT
* *
1357528 AAGCCCATAACTCCGTGGTACCTTTTTTTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTTTTTT
* *
1357560 AAGTCCACAACTCCGTGGCACTCCTTTTCTTTTGT
1 AAGCCCACAACTCCGTGGCA--CCTTTT-TTTTTT
* *
1357595 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCAC-CTTTTT-TTTTT
1357629 AAGCCCACAA
1 AAGCCCACAA
1357639 GTTAGTGGCA
Statistics
Matches: 92, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
32 21 0.23
33 24 0.26
34 24 0.26
35 23 0.25
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (32 bp):
AAGCCCACAACTCCGTGGCACCTTTTTTTTTT
Found at i:1357586 original size:34 final size:35
Alignment explanation
Indices: 1357495--1357655 Score: 158
Period size: 34 Copynumber: 4.8 Consensus size: 35
1357485 CAACCTTCAA
* *
1357495 AAGCCCACAAGTTCGTGGCA-T-CTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCACTCCTTTTTCCTTTT
* * *
1357528 AAGCCCATAACTCCGTGGTA--CCTTTTT-TTTTT
1 AAGCCCACAACTCCGTGGCACTCCTTTTTCCTTTT
* *
1357560 AAGTCCACAACTCCGTGGCACTCC-TTTTCTTTTGT
1 AAGCCCACAACTCCGTGGCACTCCTTTTTCCTTT-T
*
1357595 AAGCCCACAACTCTGTGGCACT-CTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCACTCCTTTTTCCTTTT
* **
1357629 AAGCCCACAAGTTAGTGGCAC-CCTTTT
1 AAGCCCACAACTCCGTGGCACTCCTTTT
1357656 CAAAAGCCCA
Statistics
Matches: 107, Mismatches: 14, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
32 21 0.20
33 26 0.24
34 31 0.29
35 29 0.27
ACGTcount: A:0.19, C:0.29, G:0.14, T:0.37
Consensus pattern (35 bp):
AAGCCCACAACTCCGTGGCACTCCTTTTTCCTTTT
Found at i:1357613 original size:35 final size:34
Alignment explanation
Indices: 1357495--1357656 Score: 147
Period size: 35 Copynumber: 4.9 Consensus size: 34
1357485 CAACCTTCAA
* *
1357495 AAGCCCACAAGT-TCGTGGCA-TCTTTTTCCTTTT
1 AAGCCCACAACTCT-GTGGCACTCCTTTTCCTTTT
* * * **
1357528 AAGCCCATAACTCCGTGGTA--CCTTTTTTTTTT
1 AAGCCCACAACTCTGTGGCACTCCTTTTCCTTTT
* * *
1357560 AAGTCCACAACTCCGTGGCACTCCTTTTCTTTTGT
1 AAGCCCACAACTCTGTGGCACTCCTTTTCCTTT-T
*
1357595 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT
1 AAGCCCACAACTCTGTGGCACTCCTTTTCCTTTT
*
1357629 AAGCCCACAAGT-TAGTGGCAC-CCTTTTC
1 AAGCCCACAACTCT-GTGGCACTCCTTTTC
1357657 AAAAGCCCAC
Statistics
Matches: 107, Mismatches: 17, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
32 26 0.24
33 22 0.21
34 29 0.27
35 30 0.28
ACGTcount: A:0.19, C:0.30, G:0.14, T:0.37
Consensus pattern (34 bp):
AAGCCCACAACTCTGTGGCACTCCTTTTCCTTTT
Found at i:1357664 original size:30 final size:28
Alignment explanation
Indices: 1357629--1357699 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 28
1357619 TTTTCCTTTT
* *
1357629 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTTAGCGGCAACC--TTCAA
*
1357659 AAGCCCACAAGTCAGCGGCAACCTTCAA
1 AAGCCCACAAGTTAGCGGCAACCTTCAA
*
1357687 AAGCACACAAGTT
1 AAGCCCACAAGTT
1357700 GGTGACATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
28 16 0.44
30 20 0.56
ACGTcount: A:0.35, C:0.31, G:0.17, T:0.17
Consensus pattern (28 bp):
AAGCCCACAAGTTAGCGGCAACCTTCAA
Found at i:1357842 original size:43 final size:43
Alignment explanation
Indices: 1357715--1357844 Score: 197
Period size: 43 Copynumber: 3.0 Consensus size: 43
1357705 CATCTTCTTC
* * * * *
1357715 TAAGTCCAATGTCGCTGGCCTAGAATCAGCACATTGGCATCAT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
*
1357758 TAAGACCAATATCGCTGGCCTTGATTCAGCACATTGGCACCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
*
1357801 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
1357844 T
1 T
1357845 GTCTTTGAGA
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 79 1.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (43 bp):
TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
Found at i:1358091 original size:48 final size:49
Alignment explanation
Indices: 1357948--1358299 Score: 219
Period size: 52 Copynumber: 7.0 Consensus size: 49
1357938 ATCTTTTTTC
* * **
1357948 TCATCTTTAA-ACCCAATGTCGCTGGCCTTGAATCAACATATTGGTGCCTTT
1 TCATCTTTAAGA-CCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T
* * * * * *
1357999 GTCACCTTTAAGTCCAATATTGTTAGCCTTCAATCAGCATATTGGCACCT
1 -TCATCTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT
* * * *
1358049 TTATC-TT-AGTACTAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT
1 TCATCTTTAAG-ACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT
* *
1358097 TCATCTTTAAGACCAATATCGTTGGCCTTGAATCAGCATATTGGCGCCTT
1 TCATCTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-T
* * * * ** * *
1358147 CATCATCTTTAAAACCCAATGTTGATTGGCCTTGTCTCAACACATTGGCA--T
1 --TCATCTTTAAGA-CCAATATCG-CTGGCCTTGAATCAGCATATTGGCACCT
* * * * * * * * * *
1358198 TCTTCTTCAAGTCTAATGTTGCTGGCCATGAATCAGCACATTGTCATTCTT
1 TCATCTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCA--CCT
* * *
1358249 CTCATCTTTAAGCCCAATATCACTGGTCTTGAATCAGCATATTGGCACCT
1 -TCATCTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT
1358299 T
1 T
1358300 TATCACTCTT
Statistics
Matches: 229, Mismatches: 57, Indels: 31
0.72 0.18 0.10
Matches are distributed among these distances:
47 21 0.09
48 44 0.19
49 46 0.20
50 6 0.03
51 2 0.01
52 83 0.36
53 7 0.03
54 20 0.09
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (49 bp):
TCATCTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT
Found at i:1358133 original size:97 final size:99
Alignment explanation
Indices: 1357962--1358146 Score: 257
Period size: 97 Copynumber: 1.9 Consensus size: 99
1357952 CTTTAAACCC
* ** * *
1357962 AATGTCGCTGGCCTTGAATCAACATATTGGTGCCTTTGTCACCTTTAAGTCCAATATTGTTAGCC
1 AATGTCGCTGGCCTTGAATCAACACATTGGCACC-TTGTCACCTTTAAGACCAATATCGTTAGCC
1358027 TTCAATCAGCATATTGGCACCTTTATCTTAGTACT
65 TTCAATCAGCATATTGGCACCTTTATCTTAGTACT
* * *
1358062 AATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T-TCATCTTTAAGACCAATATCGTTGGCCT
1 AATGTCGCTGGCCTTGAATCAACACATTGGCACCTTGTCACCTTTAAGACCAATATCGTTAGCCT
* *
1358125 TGAATCAGCATATTGGCGCCTT
66 TCAATCAGCATATTGGCACCTT
1358147 CATCATCTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
97 44 0.59
98 1 0.01
100 30 0.40
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (99 bp):
AATGTCGCTGGCCTTGAATCAACACATTGGCACCTTGTCACCTTTAAGACCAATATCGTTAGCCT
TCAATCAGCATATTGGCACCTTTATCTTAGTACT
Found at i:1358137 original size:149 final size:151
Alignment explanation
Indices: 1357946--1358310 Score: 384
Period size: 149 Copynumber: 2.4 Consensus size: 151
1357936 TTATCTTTTT
* * * **
1357946 TCTCATCTTTAA-ACCCAATGTCGCTGGCCTTGAATCAACATATTGGTGCCTTTGTCACCTTT-A
1 TCTCATCTTTAAGA-CCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCATCACCTTTAA
** * *
1358009 AGTCCAATATTG-TTAGCCTTCAATCAGCATATTGGCACCTT-TATCTT-AGTACTAATGTCGCT
65 AACCCAATATTGATTAGCCTTCAATCAACACATTGGCA--TTCT-TCTTAAGT-CTAATGTCGCT
*
1358071 GGCCTTGAATCAGCACATTGGCA-CC
126 GGCCATGAATCAGCACATTGGCATCC
* *
1358096 T-TCATCTTTAAGACCAATATCGTTGGCCTTGAATCAGCATATTGGCGCCTTCATCATCTTTAAA
1 TCTCATCTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCATCACCTTTAAA
* * *** *
1358160 ACCCAATGTTGATTGGCCTTGTCTCAACACATTGGCATTCTTCTTCAAGTCTAATGTTGCTGGCC
66 ACCCAATATTGATTAGCCTTCAATCAACACATTGGCATTCTTCTT-AAGTCTAATGTCGCTGGCC
* *
1358225 ATGAATCAGCACATTGTCATTCT
130 ATGAATCAGCACATTGGCA-TCC
* * * * *
1358248 TCTCATCTTTAAGCCCAATATCACTGGTCTTGAATCAGCATATTGGCACCTTTATCACTCTTT
1 TCTCATCTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCATCAC-CTTT
1358311 TCATCCTCAT
Statistics
Matches: 178, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
149 57 0.32
150 44 0.25
151 22 0.12
152 2 0.01
153 49 0.28
154 4 0.02
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.35
Consensus pattern (151 bp):
TCTCATCTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCATCACCTTTAAA
ACCCAATATTGATTAGCCTTCAATCAACACATTGGCATTCTTCTTAAGTCTAATGTCGCTGGCCA
TGAATCAGCACATTGGCATCC
Found at i:1358982 original size:13 final size:13
Alignment explanation
Indices: 1358964--1359020 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1358954 CATAAAGTGT
1358964 TGTATCGATACAA
1 TGTATCGATACAA
1358977 TGTATCGATACATAA
1 TGTATCGATAC--AA
1358992 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1359009 TGTATCGATACA
1 TGTATCGATACA
1359021 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1358999 original size:32 final size:32
Alignment explanation
Indices: 1358944--1359044 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
1358934 TTCAACGATT
1358944 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
1358977 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
1359009 TGTATCGATACATAAGTTTTGTATTGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1359041 TGTA
1 TGTA
1359045 AGCTACTGCC
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 53 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1359001 original size:19 final size:18
Alignment explanation
Indices: 1358942--1359039 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
1358932 ATTTCAACGA
1358942 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
1358961 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1358977 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1358993 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1359009 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
1359025 TTTTGTATTGATACA
1 -TTTGTATCGATACA
1359040 ATGTAAGCTA
Statistics
Matches: 65, Mismatches: 1, Indels: 26
0.71 0.01 0.28
Matches are distributed among these distances:
13 22 0.34
15 4 0.06
17 4 0.06
19 23 0.35
20 12 0.18
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1359100 original size:13 final size:13
Alignment explanation
Indices: 1359082--1359106 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1359072 ATTACTCAAA
1359082 TGTATCGATACAT
1 TGTATCGATACAT
1359095 TGTATCGATACA
1 TGTATCGATACA
1359107 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1359173 original size:52 final size:52
Alignment explanation
Indices: 1359115--1359243 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
1359105 CACTGATCTT
* *
1359115 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTACCGATACGCTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTACCGATACACTATAAAA
* * *
1359167 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTACCGATACACTATAAAA
1359219 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1359244 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTACCGATACACTATAAAA
Found at i:1364248 original size:79 final size:78
Alignment explanation
Indices: 1363830--1364271 Score: 355
Period size: 78 Copynumber: 5.7 Consensus size: 78
1363820 AAAGTGGCAA
* ** * *
1363830 GGTTGGAGTGTCCCTTCG-AAAT-ACGGGGTTTAAGTATCCTCGAGATGAAAATTTTAATATTTT
1 GGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAGATGAAAAATTTAATA-TTT
**
1363893 TGG-AATAAAAAAG
65 TGGAAATAAAACGG
* * ** *
1363906 GGTTGTAGTATCCCTTCAAAAATAACAAGGTTGGAGTA-CCTTC--GA-GAAAAATTTAATATTT
1 GGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCC-CCGAGATGAAAAATTTAATATTT
*
1363967 TGGAAAAAAAAACGG
65 TGG-AAATAAAACGG
* * * * * * * * **
1363982 GGTTGAAGTATCCTTTTTG-AATTGATGGGGTTGGAATAT-CCCAAGATGAAAAATTTAGCATTT
1 GGTTGGAGTATCC-CTTCGAAAATAACGGGGTTGGAGTATCCCCGAGATGAAAAATTTAATATTT
**
1364045 TGGAAATAAAAGCAA
65 TGGAAATAAAA-CGG
* * * * * * ** *
1364060 GGTTGGAGTATCCCTTAGGAATTGATGGGGTTAGAGTATCCCTAAGATAAAAAATTTAATATTTT
1 GGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAGATGAAAAATTTAATATTTT
*
1364125 GGAAATAAAATGG
66 GGAAATAAAACGG
* * *
1364138 GGTTGGAGTATCCCCTC-AGAAATAACTGGGTTGGAGTATCCCCGAGATGAAAATTTTAATATTT
1 GGTTGGAGTATCCCTTCGA-AAATAACGGGGTTGGAGTATCCCCGAGATGAAAAATTTAATATTT
*
1364202 TGGAAACAAAAGCGG
65 TGGAAATAAAA-CGG
* * ** *
1364217 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAATATCTTCGAGACGAAAAAT
1 GGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAGATGAAAAAT
1364272 CGATATTTTT
Statistics
Matches: 291, Mismatches: 59, Indels: 29
0.77 0.16 0.08
Matches are distributed among these distances:
74 6 0.02
75 13 0.04
76 50 0.17
77 20 0.07
78 121 0.42
79 80 0.27
80 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (78 bp):
GGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAGATGAAAAATTTAATATTTT
GGAAATAAAACGG
Done.