Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold273
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: 1282806
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 9
Found at i:154360 original size:18 final size:18
Alignment explanation
Indices: 154334--154377 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
154324 TAAAAGGCAG
*
154334 CTCATCTATGATTATCAT
1 CTCAACTATGATTATCAT
154352 CTCAACTATGATTATCAT
1 CTCAACTATGATTATCAT
154370 CTCAACTA
1 CTCAACTA
154378 CACCTTTCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.39
Consensus pattern (18 bp):
CTCAACTATGATTATCAT
Found at i:154893 original size:19 final size:20
Alignment explanation
Indices: 154869--154908 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
154859 TTTAAAAATG
154869 TGTAAAATTA-ATTTTTCAT
1 TGTAAAATTATATTTTTCAT
*
154888 TGTAAAATTATCTTTTTCAT
1 TGTAAAATTATATTTTTCAT
154908 T
1 T
154909 AATTAATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (20 bp):
TGTAAAATTATATTTTTCAT
Found at i:156042 original size:30 final size:30
Alignment explanation
Indices: 155998--156058 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
155988 TCTACTTCTA
*
155998 GTTGCTGATCTACTTCTGGTTACTATTACT
1 GTTGCTGATATACTTCTGGTTACTATTACT
* * **
156028 GTTGTTGATATACTTTTGGTTGTTATTACT
1 GTTGCTGATATACTTCTGGTTACTATTACT
156058 G
1 G
156059 ATCTGCTTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.16, C:0.13, G:0.20, T:0.51
Consensus pattern (30 bp):
GTTGCTGATATACTTCTGGTTACTATTACT
Found at i:156060 original size:24 final size:24
Alignment explanation
Indices: 156033--156097 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
156023 TTACTGTTGT
* * *
156033 TGATATACTTTTGGTTGTTATTAC
1 TGATCTACTTCTGGTTGTCATTAC
*
156057 TGATCTGCTTCTGGTTGTCATTAC
1 TGATCTACTTCTGGTTGTCATTAC
*
156081 TGATCTACTTCTAGTTG
1 TGATCTACTTCTGGTTG
156098 CTGTTGTTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.17, C:0.15, G:0.18, T:0.49
Consensus pattern (24 bp):
TGATCTACTTCTGGTTGTCATTAC
Found at i:156894 original size:22 final size:23
Alignment explanation
Indices: 156864--156906 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
156854 CTAAGATAAT
*
156864 TATACAAAGGAAATAGAGGTTCA
1 TATACAAAGGAAATAAAGGTTCA
156887 TATA-AAAGGAAATAAAGGTT
1 TATACAAAGGAAATAAAGGTT
156907 TTTTATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.51, C:0.05, G:0.21, T:0.23
Consensus pattern (23 bp):
TATACAAAGGAAATAAAGGTTCA
Found at i:162651 original size:143 final size:143
Alignment explanation
Indices: 162095--162644 Score: 616
Period size: 144 Copynumber: 3.8 Consensus size: 143
162085 TGTAAATTTC
* * * * * * * *
162095 AAAAATCTAATTTCGTACATTAATGGACAACCGAAACGACATGAAAA-GTTTTGAAGATTTCTAC
1 AAAAAT-TCATTTTGTACCTTAATGGAGAACCGAAAAGATACGAAAACGTTTTGAAGATTTCTAT
* *
162159 ACCCCTACAGAAAA-CTATAGGAATATTAGAAATCTT-GAAAATTAAGATAATAATTTTTATTTA
65 A-CCCTACAAAAAATC-ATAGGAATATTAGAAATCTTAAAAAATTAAGATAATAATTTTTATTTA
*
162222 ATTTTTAA-TTTCTAA
128 ATTTTTAATTTTATAA
* * * *
162237 AAAAATTCATCTCGTGCCTTAATGGAGAACCGAAAAGATACGAAAAC-TTTTAAAGATTTCTATA
1 AAAAATTCATTTTGTACCTTAATGGAGAACCGAAAAGATACGAAAACGTTTTGAAGATTTCTATA
* ** *
162301 CTCTTATGAAAAATCATAGGAATATTAGAAATCTTGAAAAAA-TAGGATAATAATTTTTATTTAA
66 C-CCTACAAAAAATCATAGGAATATTAGAAATCTT-AAAAAATTAAGATAATAATTTTTATTTAA
*
162365 TTTTTAATTTCTAAAA
129 TTTTTAATTT-TATAA
* ** * *
162381 AAAAAATCATTTTGTACCTTAACAGAGAACCGAAAAGATCCGAAAAAGTTTTGAAGATTTCTATA
1 AAAAATTCATTTTGTACCTTAATGGAGAACCGAAAAGATACGAAAACGTTTTGAAGATTTCTATA
* * *
162446 CCC-A-AACGAAAACCATAGGAATATTAGAAATCTTGAAAAATTAAGATAATAGTTTTTATTTAA
66 CCCTACAA--AAAATCATAGGAATATTAGAAATCTTAAAAAATTAAGATAATAATTTTTATTTAA
* *
162509 TTTTAAATTTTTTAA
129 TTTTTAATTTTATAA
* * * *
162524 GAAAATTTATTTTGTACCTTGATGGAGAACCAAAAAGATAC-AAAACGTTTTGAAGATTTCTATA
1 AAAAATTCATTTTGTACCTTAATGGAGAACCGAAAAGATACGAAAACGTTTTGAAGATTTCTATA
* *
162588 TCCCTACAAAAAATCATAAGAATATTA-AAAGTTTTAAAAAATTAAGATAATAATTTT
66 -CCCTACAAAAAATCATAGGAATATTAGAAA-TCTTAAAAAATTAAGATAATAATTTT
162645 CGTTTAAAGA
Statistics
Matches: 343, Mismatches: 50, Indels: 29
0.81 0.12 0.07
Matches are distributed among these distances:
140 1 0.00
141 74 0.22
142 61 0.18
143 90 0.26
144 98 0.29
145 19 0.06
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (143 bp):
AAAAATTCATTTTGTACCTTAATGGAGAACCGAAAAGATACGAAAACGTTTTGAAGATTTCTATA
CCCTACAAAAAATCATAGGAATATTAGAAATCTTAAAAAATTAAGATAATAATTTTTATTTAATT
TTTAATTTTATAA
Found at i:163429 original size:20 final size:20
Alignment explanation
Indices: 163401--163438 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
163391 ACTGCCAAAG
163401 AAATATATCAATACATTAAT
1 AAATATATCAATACATTAAT
* *
163421 AAATGTATCGATACATTA
1 AAATATATCAATACATTA
163439 TGTATCGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (20 bp):
AAATATATCAATACATTAAT
Found at i:163443 original size:15 final size:15
Alignment explanation
Indices: 163423--163451 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
163413 ACATTAATAA
163423 ATGTATCGATACATT
1 ATGTATCGATACATT
163438 ATGTATCGATACAT
1 ATGTATCGATACAT
163452 GTAGGCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (15 bp):
ATGTATCGATACATT
Found at i:165730 original size:84 final size:85
Alignment explanation
Indices: 165588--165748 Score: 288
Period size: 84 Copynumber: 1.9 Consensus size: 85
165578 TTATTCATCA
* *
165588 GGGATACTCCAAACCTCATTCCTCCGAAGGGATACTCCAACCCTGCTCTTAAACTTGTCAAGATT
1 GGGATACTCCAAACCCCATTCCTCCGAAGGGATACTCCAACCCTGCTCCTAAACTTGTCAAGATT
165653 TGAATCTTGTTTCATTGTCG
66 TGAATCTTGTTTCATTGTCG
*
165673 GGGATACTCC-AACCCCATTCCTCCGAGGGGATACTCCAACCCTGCTCCTAAACTTGTCAAGATT
1 GGGATACTCCAAACCCCATTCCTCCGAAGGGATACTCCAACCCTGCTCCTAAACTTGTCAAGATT
165737 TGAATCTTGTTT
66 TGAATCTTGTTT
165749 TTGCCCAAAA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
84 63 0.86
85 10 0.14
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (85 bp):
GGGATACTCCAAACCCCATTCCTCCGAAGGGATACTCCAACCCTGCTCCTAAACTTGTCAAGATT
TGAATCTTGTTTCATTGTCG
Found at i:167021 original size:167 final size:163
Alignment explanation
Indices: 166511--167030 Score: 444
Period size: 167 Copynumber: 3.2 Consensus size: 163
166501 ATTTATCTCA
* * * * * *
166511 TATTAAATTACTTTTCAAAAATTTATTCATTTTCATATGTTTTTGAATTTTTCCTTAAAATTTCT
1 TATTAAATCAGTTTTGAAAAATTCATTCATTTTCATA-GTTTTTGATTTTTTCCTTGAAATTTCT
* * * * **
166576 CTATTTTCC-AAAACAGAGTTTTCTACTT-CAT-AATTTTTTAAAGGGG--TTTC-TTGGTTTTT
65 -TTTTTTCCAAAAACA-AGTTTTCTA-TTCCATAAATATTTTCAGGGGGATTTTCTTTGGTTTAA
* * * * *
166635 AATTTTTAAAATTCATCAAATATTACTATTTAACTCA
127 AATTTTTAAAATACATCTAATATTGCTATTGAACTCC
* * * *
166672 TATTAAATCAGTTTT-AAAAGA-TCAATTTATTTTCATAAATTTTGGATTTTTTCCTTTGAAATC
1 TATTAAATCAGTTTTGAAAA-ATTC-ATTCATTTTCAT-AGTTTTTGATTTTTTCC-TTGAAATT
* * * * * * * *
166735 CCTTTTTTTTCAAAAAACCGAGTTGTCTAATCCATAAATATTTTCAGGAGAATTTTGTTTGGTTT
62 TC-TTTTTTTCCAAAAA-CAAGTTTTCTATTCCATAAATATTTTCAGGGGGATTTTCTTTGGTTT
* * * * *
166800 AAAATTTTTAAAATATATCTAATAATGTTATGGAATTCC
125 AAAATTTTTAAAATACATCTAATATTGCTATTGAACTCC
**
166839 TATTAAGCCAGTTTTGAAAAATTCATTCATTTTCATGAGTTTTTGATTTTTTCCTTGAAATTTCT
1 TATTAAATCAGTTTTGAAAAATTCATTCATTTTCAT-AGTTTTTGATTTTTTCCTTGAAATTTCT
* * *
166904 TTTTTTCCCGAAAAACTAAATTTTCTATTCCATAAATATTTTCGGGGGGATTTTCTTTGGTCTAA
65 TTTTTT-CC-AAAAAC-AAGTTTTCTATTCCATAAATATTTTCAGGGGGATTTTCTTTGGTTTAA
* * *
166969 AATTATTAAAATGCATCTAATATTGCCATTGAACTCC
127 AATTTTTAAAATACATCTAATATTGCTATTGAACTCC
* * * *
167006 CATTAATTTAGTTTTGAGAAATTCA
1 TATTAAATCAGTTTTGAAAAATTCA
167031 AGTTATTTTT
Statistics
Matches: 278, Mismatches: 64, Indels: 28
0.75 0.17 0.08
Matches are distributed among these distances:
160 5 0.02
161 38 0.14
162 15 0.05
163 16 0.06
164 11 0.04
165 7 0.03
166 13 0.05
167 167 0.60
168 6 0.02
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.47
Consensus pattern (163 bp):
TATTAAATCAGTTTTGAAAAATTCATTCATTTTCATAGTTTTTGATTTTTTCCTTGAAATTTCTT
TTTTTCCAAAAACAAGTTTTCTATTCCATAAATATTTTCAGGGGGATTTTCTTTGGTTTAAAATT
TTTAAAATACATCTAATATTGCTATTGAACTCC
Found at i:168422 original size:20 final size:19
Alignment explanation
Indices: 168370--168430 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
168360 AAAAAAAAAA
168370 ATTCCAAATGTATCGATAC
1 ATTCCAAATGTATCGATAC
**
168389 ATTTGTAGAATGTATCGATAC
1 A-TTCCA-AATGTATCGATAC
*
168410 ATTCACAAATGTATCCATAC
1 ATTC-CAAATGTATCGATAC
168430 A
1 A
168431 GGGTCCCAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 18 0.53
21 15 0.44
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (19 bp):
ATTCCAAATGTATCGATAC
Found at i:168559 original size:13 final size:13
Alignment explanation
Indices: 168541--168566 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
168531 CATTTTTCTG
168541 TGTATCGATACAT
1 TGTATCGATACAT
168554 TGTATCGATACAT
1 TGTATCGATACAT
168567 GGATCTTTGT
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:168563 original size:33 final size:33
Alignment explanation
Indices: 168521--168587 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
168511 GCCAAGGAAA
***
168521 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
168554 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
168587 T
1 T
168588 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:169040 original size:13 final size:13
Alignment explanation
Indices: 169022--169046 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
169012 CATAAAATGT
169022 TGTATCGATACAA
1 TGTATCGATACAA
169035 TGTATCGATACA
1 TGTATCGATACA
169047 TATTTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:169062 original size:32 final size:33
Alignment explanation
Indices: 169002--169067 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
168992 TTCAACGATT
169002 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
** *
169035 TGTATCGATACAT-ATTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
169067 T
1 T
169068 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:169126 original size:13 final size:13
Alignment explanation
Indices: 169108--169132 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
169098 ATTACTCAAA
169108 TGTATCGATACAT
1 TGTATCGATACAT
169121 TGTATCGATACA
1 TGTATCGATACA
169133 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:169184 original size:52 final size:53
Alignment explanation
Indices: 169121--169256 Score: 181
Period size: 52 Copynumber: 2.6 Consensus size: 53
169111 ATCGATACAT
*
169121 TGTATCGATACACTGATC-T-TTGTATCGATACACACAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATCATAATGTATCGATACACACAGGCAAATTTGCCCAGA
* ** *
169173 TGTATCGATACA-TTTCATAATGTATCGATACATGCAGGTAAATTTGCCCAGA
1 TGTATCGATACACTATCATAATGTATCGATACACACAGGCAAATTTGCCCAGA
*
169225 TGTATCGATACACTATTA-AATGTATCGATACA
1 TGTATCGATACACTATCATAATGTATCGATACA
169257 TGCAAGCAAC
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
50 2 0.03
51 2 0.03
52 67 0.91
53 3 0.04
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (53 bp):
TGTATCGATACACTATCATAATGTATCGATACACACAGGCAAATTTGCCCAGA
Found at i:169257 original size:52 final size:52
Alignment explanation
Indices: 169141--169265 Score: 182
Period size: 52 Copynumber: 2.4 Consensus size: 52
169131 CACTGATCTT
**
169141 TGTATCGATACACACAGGCAAATTTGCCCAGATGTATCGATACATTTCATAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTTCATAA
*
169193 TGTATCGATACATGCAGGTAAATTTGCCCAGATGTATCGATACACTATT-A-AA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACA-T-TTCATAA
*
169245 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
169266 CTTTTCATAT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
52 62 0.94
53 2 0.03
54 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTTCATAA
Found at i:174756 original size:52 final size:53
Alignment explanation
Indices: 174674--174840 Score: 168
Period size: 52 Copynumber: 3.2 Consensus size: 53
174664 TTTCCGAGGG
* *
174674 GATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTTTTCCACAATCGGA
1 GATACTCCAACTCCGGTTTTATTTC-CAAAAACACCAATTTTTCCACAATCGGA
* * ** *
174726 GATACTCCAA-TCCTGGTTTTATTTTC-AAAACGCCAA-TTTTCCTTTAATCGGG
1 GATACTCCAACTCC-GGTTTTATTTCCAAAAACACCAATTTTTCC-ACAATCGGA
* *
174778 GATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC-GA
1 GATACTCCAACTCCGGTTTTATTTCCAAAAACACCAATTTTTCCACAATCGGA
174829 GGATACTCCAAC
1 -GATACTCCAAC
174841 CTCGTTATTT
Statistics
Matches: 94, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
51 10 0.11
52 66 0.70
53 13 0.14
54 5 0.05
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.33
Consensus pattern (53 bp):
GATACTCCAACTCCGGTTTTATTTCCAAAAACACCAATTTTTCCACAATCGGA
Found at i:174860 original size:28 final size:28
Alignment explanation
Indices: 174824--174900 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
174814 ATTTTTCACA
* * *
174824 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
174852 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
174880 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
174901 ACTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:174967 original size:107 final size:107
Alignment explanation
Indices: 174775--174979 Score: 261
Period size: 107 Copynumber: 1.9 Consensus size: 107
174765 TCCTTTAATC
* * *
174775 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
174840 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CCCCGTTATTT-ATCGGGGATACTCCAACCCCGTTACTTCCGA
* *** * * *
174883 GGGGATACTCCAACCCCGACTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
174947 CCCCGTTATTT-TCGAAGGGATACTCCAATCCCG
66 CCCCGTTATTTATCG--GGGATACTCCAACCCCG
174980 ATTTTTTTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
105 3 0.04
107 58 0.70
108 22 0.27
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.29
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTATCGGGGATACTCCAACCCCGTTACTTCCGA
Found at i:175003 original size:79 final size:79
Alignment explanation
Indices: 174854--175056 Score: 230
Period size: 79 Copynumber: 2.6 Consensus size: 79
174844 GTTATTTCAT
* * *
174854 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
* * *
174919 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * ** *
174933 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAAT-A
174997 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* * *
175012 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGAAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGG-GATACTCCAACCC
175057 TGTTATTATC
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
78 7 0.07
79 97 0.93
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:176888 original size:160 final size:155
Alignment explanation
Indices: 176316--176944 Score: 744
Period size: 155 Copynumber: 4.0 Consensus size: 155
176306 ATGTTTATCA
* * * * * *
176316 TTTTTAATCTTTTATATTCTTATGGGCATCCATAAGGATGTAAAAGATTTAAAAAACATTTCGTA
1 TTTTTTATCTTTTATATTCCTATGGACATCCATAGGGATATAAAAGATTTCAAAAACATTTCGTA
* * *
176381 T-CTTTCCGGGCTTCCATTAGCA-TACAAAATGGCATTTTCGAAAGTAAATAAACTTAAATTGAA
66 TCCTTT-CGAGCTTCCATTAG-AGTACAAAATAGCATTTTCGAAAGTAAATAAAATTAAATTGAA
* *
176444 CTAAAACTTTCAGGATAAATTTTAATT
129 TTAAAATTTTCAGGATAAATTTTAATT
* ** *
176471 TTTTTTATCTTTTATATTCCTATGGGCATCTGTAGGGATATAAAAGATTTCAAAAATATTTCGTA
1 TTTTTTATCTTTTATATTCCTATGGACATCCATAGGGATATAAAAGATTTCAAAAACATTTCGTA
* * * *
176536 TCCTTTCAAGCTTCCATTAGGGTACGAAATAACATTTTCGAAAGTAAATAAAATTAAATTGAATT
66 TCCTTTCGAGCTTCCATTAGAGTACAAAATAGCATTTTCGAAAGTAAATAAAATTAAATTGAATT
*
176601 AAAATTTTCAAGATAAATTTTAATT
131 AAAATTTTCAGGATAAATTTTAATT
* * * *
176626 TTTTTTATATTTTATATTCCTATGGACATCCGTAGGGGTATAAAAGATTTCAAAAATATTTCGTA
1 TTTTTTATCTTTTATATTCCTATGGACATCCATAGGGATATAAAAGATTTCAAAAACATTTCGTA
* * * * *
176691 TCCTTTCGAGCTTCCATTAGGGTACGAAATAGTATTTTTGAATA-TAAATAAAATTCAATTGAAT
66 TCCTTTCGAGCTTCCATTAGAGTACAAAATAGCATTTTCGAA-AGTAAATAAAATTAAATTGAAT
* *
176755 TAATATTTTCAGGATAAATTCTCATTATT
130 TAAAATTTTCAGGATAAATT-T--TAATT
** * * *
176784 TTTTTCTAATCTTTTATATTTTTATGAACATCCACAGGGGTATAAAAGATTTCAAAAACATTTCG
1 TTTTT-T-ATCTTTTATATTCCTATGGACATCCATAGGGATATAAAAGATTTCAAAAACATTTCG
* * * * *
176849 TATCCTTTCGGGCTTCCATTAGAGTACAAAATGGTATTTTCGAAAATAAATAAAATTAAGTTGAA
64 TATCCTTTCGAGCTTCCATTAGAGTACAAAATAGCATTTTCGAAAGTAAATAAAATTAAATTGAA
* * * *
176914 TTAATACTTTTGA-GAAAAATTTTAATC
129 TTAA-AATTTTCAGGATAAATTTTAATT
176941 TTTT
1 TTTT
176945 ATATTCCTAT
Statistics
Matches: 414, Mismatches: 50, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
155 267 0.64
156 6 0.01
157 7 0.02
158 9 0.02
159 3 0.01
160 117 0.28
161 5 0.01
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (155 bp):
TTTTTTATCTTTTATATTCCTATGGACATCCATAGGGATATAAAAGATTTCAAAAACATTTCGTA
TCCTTTCGAGCTTCCATTAGAGTACAAAATAGCATTTTCGAAAGTAAATAAAATTAAATTGAATT
AAAATTTTCAGGATAAATTTTAATT
Found at i:176901 original size:315 final size:310
Alignment explanation
Indices: 176316--176944 Score: 760
Period size: 315 Copynumber: 2.0 Consensus size: 310
176306 ATGTTTATCA
* * * *
176316 TTTTTAATCTTTTATATTCTTATGGGCATCCATAAGGATGTAAAAGATTTAAAAAACATTTCGTA
1 TTTTTAATATTTTATATTCCTATGGACATCCATAAGGATATAAAAGATTTAAAAAACATTTCGTA
* * *
176381 TCTTTCCGGGCTTCCATTAGCATACAAAATGGCATTTTCGAAAGTAAATAAACTTAAATTGAACT
66 TCTTTCCGAGCTTCCATTAGCATACAAAATAGCATTTTCGAAAGTAAATAAAATTAAATTGAACT
** ***
176446 AAAACTTTCAGGATAAATTTTAATTTTTTTTATCTTTTATATTCCTATGGGCATCTGTAGGGATA
131 AAAACTTTCAGGATAAATTTTAATTTTTTTTATCTTTTATATTCCTATGAACATCCACAGGGATA
* * *
176511 TAAAAGATTTCAAAAATATTTCGTATCCTTTCAAGCTTCCATTAGGGTACGAAATAACATTTTCG
196 TAAAAGATTTCAAAAACATTTCGTATCCTTTCAAGCTTCCATTAGAGTACAAAATAACATTTTCG
* * *
176576 AAAGTAAATAAAATTAAATTGAATTAA-AATTTTCAAGATAAATTTTAATT
261 AAAATAAATAAAATTAAATTGAATTAATAATTTT-AAGAAAAATTTTAATC
* * * * * *
176626 TTTTTTATATTTTATATTCCTATGGACATCCGTAGGGGTATAAAAGATTTCAAAAATATTTCGTA
1 TTTTTAATATTTTATATTCCTATGGACATCCATAAGGATATAAAAGATTTAAAAAACATTTCGTA
** * * * *
176691 TCCTTT-CGAGCTTCCATTAGGGTACGAAATAGTATTTTTGAATA-TAAATAAAATTCAATTGAA
66 T-CTTTCCGAGCTTCCATTAGCATACAAAATAGCATTTTCGAA-AGTAAATAAAATTAAATTGAA
* * * * **
176754 TTAATATTTTCAGGATAAATTCTCATTATTTTTTTCTAATCTTTTATATTTTTATGAACATCCAC
129 CTAAAACTTTCAGGATAAATT-T--TAATTTTTTT-T-ATCTTTTATATTCCTATGAACATCCAC
* ** ***
176819 AGGGGTATAAAAGATTTCAAAAACATTTCGTATCCTTTCGGGCTTCCATTAGAGTACAAAATGGT
189 AGGGATATAAAAGATTTCAAAAACATTTCGTATCCTTTCAAGCTTCCATTAGAGTACAAAATAAC
* * *
176884 ATTTTCGAAAATAAATAAAATTAAGTTGAATTAATACTTTTGAGAAAAATTTTAATC
254 ATTTTCGAAAATAAATAAAATTAAATTGAATTAATAATTTTAAGAAAAATTTTAATC
176941 TTTT
1 TTTT
176945 ATATTCCTAT
Statistics
Matches: 266, Mismatches: 45, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
310 120 0.45
311 6 0.02
313 9 0.03
314 1 0.00
315 125 0.47
316 5 0.02
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (310 bp):
TTTTTAATATTTTATATTCCTATGGACATCCATAAGGATATAAAAGATTTAAAAAACATTTCGTA
TCTTTCCGAGCTTCCATTAGCATACAAAATAGCATTTTCGAAAGTAAATAAAATTAAATTGAACT
AAAACTTTCAGGATAAATTTTAATTTTTTTTATCTTTTATATTCCTATGAACATCCACAGGGATA
TAAAAGATTTCAAAAACATTTCGTATCCTTTCAAGCTTCCATTAGAGTACAAAATAACATTTTCG
AAAATAAATAAAATTAAATTGAATTAATAATTTTAAGAAAAATTTTAATC
Found at i:178904 original size:22 final size:22
Alignment explanation
Indices: 178870--178923 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
178860 TTTGACTTAG
178870 TTTTTCTTT-TTTTATTCTCTC
1 TTTTTCTTTCTTTTATTCTCTC
* *
178891 TTTTTCTTTCTTTTTTTCTTTC
1 TTTTTCTTTCTTTTATTCTCTC
178913 TCTTTT-TTTCT
1 T-TTTTCTTTCT
178924 CTAAGTTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 9 0.31
22 16 0.55
23 4 0.14
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTCTTTCTTTTATTCTCTC
Found at i:178906 original size:12 final size:12
Alignment explanation
Indices: 178872--178920 Score: 62
Period size: 12 Copynumber: 3.9 Consensus size: 12
178862 TGACTTAGTT
*
178872 TTTCTTTTTTTA
1 TTTCTTTTTTTC
*
178884 TTCTCTCTTTTTC
1 TT-TCTTTTTTTC
178897 TTTCTTTTTTTC
1 TTTCTTTTTTTC
178909 TTTCTCTTTTTT
1 TTTCT-TTTTTT
178921 TCTCTAAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 16 0.50
13 16 0.50
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTCTTTTTTTC
Found at i:178923 original size:26 final size:25
Alignment explanation
Indices: 178872--178919 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
178862 TGACTTAGTT
178872 TTTCTTTTTTTATTCTCTCTTTTTC
1 TTTCTTTTTTTATTCTCTCTTTTTC
*
178897 TTTCTTTTTTTCTT-TCTCTTTTT
1 TTTCTTTTTTTATTCTCTCTTTTT
178920 TTCTCTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (25 bp):
TTTCTTTTTTTATTCTCTCTTTTTC
Found at i:180047 original size:15 final size:15
Alignment explanation
Indices: 179979--180056 Score: 57
Period size: 15 Copynumber: 4.9 Consensus size: 15
179969 TCTGATCTTC
* *
179979 CTTTTTTATTTTCTT
1 CTTTTTTCTTTTTTT
* *
179994 ATTTTTTATTTTCATTT
1 CTTTTTTCTTTT--TTT
* *
180011 CATTTTGTGCTTTTTTAA
1 C-TTTT-TTCTTTTTT-T
180029 CTTTTTTCTTTTTTT
1 CTTTTTTCTTTTTTT
180044 CTTTTTTCTTTTT
1 CTTTTTTCTTTTT
180057 AAGGAATTTC
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
15 24 0.48
16 8 0.16
17 8 0.16
18 5 0.10
19 5 0.10
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.77
Consensus pattern (15 bp):
CTTTTTTCTTTTTTT
Found at i:182029 original size:27 final size:28
Alignment explanation
Indices: 181969--182123 Score: 159
Period size: 28 Copynumber: 5.6 Consensus size: 28
181959 GTGTAGGGAC
*
181969 CTTTTCAAAGCCCACATGTCAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
181997 CCTTTCAAAG-CCATAAGTTAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* * * * *
182024 CATTTCAAAACCCATAAGTTAGTGGTAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
182052 TTTTTTAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* * * **
182080 CTTTTCAAAGTCAACAAGTCAATGGCGC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
182108 CTTTTCAAAGCCCACA
1 CTTTTCAAAGCCCACA
182124 TAAGTTGGTG
Statistics
Matches: 103, Mismatches: 23, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
27 22 0.21
28 81 0.79
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCAT
Found at i:182150 original size:31 final size:31
Alignment explanation
Indices: 182112--182200 Score: 90
Period size: 31 Copynumber: 2.9 Consensus size: 31
182102 TGGCGCCTTT
182112 TCAAAGCCCACATAAGTTGGTGGCACCCTAA-
1 TCAAAGCCCACATAAGTTGGTGGCACCC-AAG
* * * * *
182143 TCAAAGCCCGCATGAGTTGGTAGCGCTCAAG
1 TCAAAGCCCACATAAGTTGGTGGCACCCAAG
** *
182174 TCAGGGCCCACACAAGTTGGTGGCACC
1 TCAAAGCCCACATAAGTTGGTGGCACC
182201 TATGTCCGAG
Statistics
Matches: 44, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
30 2 0.05
31 42 0.95
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.18
Consensus pattern (31 bp):
TCAAAGCCCACATAAGTTGGTGGCACCCAAG
Found at i:182609 original size:12 final size:14
Alignment explanation
Indices: 182589--182621 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
182579 CCAACGGGGT
*
182589 TTAAAAAAATAAAA
1 TTAAAAAATTAAAA
182603 -TAAAAAATTAAAA
1 TTAAAAAATTAAAA
182616 TTAAAA
1 TTAAAA
182622 GATAGGGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
TTAAAAAATTAAAA
Found at i:196725 original size:19 final size:20
Alignment explanation
Indices: 196701--196752 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
196691 AAAATCCCAG
*
196701 ATGTATCGATACAATGA-TA
1 ATGTATCGATACAATCATTA
*
196720 ATGTATCGATACATTCATTA
1 ATGTATCGATACAATCATTA
196740 ATGTATCGATACA
1 ATGTATCGATACA
196753 TTTCTTTGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATCATTA
Found at i:196743 original size:20 final size:19
Alignment explanation
Indices: 196701--196754 Score: 81
Period size: 20 Copynumber: 2.8 Consensus size: 19
196691 AAAATCCCAG
* *
196701 ATGTATCGATACAATGATA
1 ATGTATCGATACATTCATA
196720 ATGTATCGATACATTCATTA
1 ATGTATCGATACATTCA-TA
196740 ATGTATCGATACATT
1 ATGTATCGATACATT
196755 TCTTTGGTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (19 bp):
ATGTATCGATACATTCATA
Found at i:196796 original size:13 final size:13
Alignment explanation
Indices: 196780--196805 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
196770 AGGGTTGCTT
196780 TGTATCGATACAA
1 TGTATCGATACAA
196793 TGTATCGATACAA
1 TGTATCGATACAA
196806 AACTTATGTA
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):
TGTATCGATACAA
Found at i:201507 original size:25 final size:27
Alignment explanation
Indices: 201446--201518 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 27
201436 CAAGAAATGG
** *
201446 TTGTCAAGAAAT-TATCATCAAGAACTT
1 TTGTCAAGAAATGT-TTGTCAAAAACTT
*
201473 TTGTCGAG-AATGTTTGTCAAAAAC-T
1 TTGTCAAGAAATGTTTGTCAAAAACTT
*
201498 TTGTCAAGAAATTTTTGTCAA
1 TTGTCAAGAAATGTTTGTCAA
201519 TATGACCCCT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
25 8 0.21
26 22 0.58
27 8 0.21
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (27 bp):
TTGTCAAGAAATGTTTGTCAAAAACTT
Found at i:201516 original size:14 final size:14
Alignment explanation
Indices: 201435--201518 Score: 59
Period size: 14 Copynumber: 6.3 Consensus size: 14
201425 TTGCCATTTA
**
201435 TCAAGAAATGGTTG
1 TCAAGAAATTTTTG
* **
201449 TCAAGAAATTATCA
1 TCAAGAAATTTTTG
*
201463 TCAAG-AACTTTTG
1 TCAAGAAATTTTTG
* *
201476 TCGAG-AATGTTTG
1 TCAAGAAATTTTTG
*
201489 TCAA-AAA-CTTTG
1 TCAAGAAATTTTTG
201501 TCAAGAAATTTTTG
1 TCAAGAAATTTTTG
201515 TCAA
1 TCAA
201519 TATGACCCCT
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
12 8 0.15
13 22 0.42
14 23 0.43
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (14 bp):
TCAAGAAATTTTTG
Found at i:201636 original size:28 final size:29
Alignment explanation
Indices: 201526--201941 Score: 340
Period size: 28 Copynumber: 14.7 Consensus size: 29
201516 CAATATGACC
* * *
201526 CCTTTTCAAAGCGCACATGTTAGTGGCAC
1 CCTTTTCAAAGCCCACATGTCAGTGGCAT
* * *
201555 CCTTTACAAAGTCCACATGTTAGTGGCAT
1 CCTTTTCAAAGCCCACATGTCAGTGGCAT
** * *
201584 CCTAGTCAAAGCCCACAAGTTAGTGGCA-
1 CCTTTTCAAAGCCCACATGTCAGTGGCAT
201612 CCTTTTCAAAGCCCACATGTCAGTGGCAT
1 CCTTTTCAAAGCCCACATGTCAGTGGCAT
** ** * *
201641 CCTAATCAAAGCCTGCAAGTCAGTGGTA-
1 CCTTTTCAAAGCCCACATGTCAGTGGCAT
* *
201669 CCTTTTCAAAGCCCACATTTAAGCT-GCA-
1 CCTTTTCAAAGCCCACATGTCAG-TGGCAT
* * *
201697 -CTTTTGCAAAGGCCATAAGTCAGTGGCAT
1 CCTTTT-CAAAGCCCACATGTCAGTGGCAT
*
201726 CC-TTTCAAAGCCCACATGTTAGTGGCA-
1 CCTTTTCAAAGCCCACATGTCAGTGGCAT
* * *
201753 -CTTAGTCAAAGCCCACAAGTTAGTGGCA-
1 CCTT-TTCAAAGCCCACATGTCAGTGGCAT
* *
201781 CATTTTCAAAGCCCACATGTTAGTGGCAT
1 CCTTTTCAAAGCCCACATGTCAGTGGCAT
* * *
201810 CC-TTTCAAAGCCCATAAGTCAGTGACAT
1 CCTTTTCAAAGCCCACATGTCAGTGGCAT
*
201838 CC-TTTCAAAGCCCACATGTCAGTGGTA-
1 CCTTTTCAAAGCCCACATGTCAGTGGCAT
* * *
201865 CCTTTTTAAAGCCCACAAGTTAGTGGCA-
1 CCTTTTCAAAGCCCACATGTCAGTGGCAT
* * *
201893 -CTCTTTCAAATCTCATATGTCAGTGGCAT
1 CCT-TTTCAAAGCCCACATGTCAGTGGCAT
* *
201922 CC-TTTCAAAACCCATATGTC
1 CCTTTTCAAAGCCCACATGTC
201942 GTAACGTGCG
Statistics
Matches: 311, Mismatches: 62, Indels: 29
0.77 0.15 0.07
Matches are distributed among these distances:
26 1 0.00
27 11 0.04
28 220 0.71
29 77 0.25
30 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (29 bp):
CCTTTTCAAAGCCCACATGTCAGTGGCAT
Found at i:201791 original size:84 final size:84
Alignment explanation
Indices: 201526--201935 Score: 384
Period size: 84 Copynumber: 4.8 Consensus size: 84
201516 CAATATGACC
* * * * * * *
201526 CCTTTTCAAAGCGCACATGTTAGTGGCACCCTTTACAAAGTCCACATGTTAGTGGCATCCTAGTC
1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTT-CAAAGCCCACATGTCAGTGGCA-CCTTGTC
201591 AAAGCCCACAAGTTAGTGGCA
64 AAAGCCCACAAGTTAGTGGCA
* * ** * * *
201612 CCTTTTCAAAGCCCACATGTCAGTGGCATCCTAATCAAAGCCTGCAAGTCAGTGGTACCTTTTCA
1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCCT-TTCAAAGCCCACATGTCAGTGGCACCTTGTCA
*
201677 AAGCCCAC-ATTTAAGCT-GCA
65 AAGCCCACAAGTT-AG-TGGCA
* * *
201697 -CTTTTGCAAAGGCCATAAGTCAGTGGCATCCTTTCAAAGCCCACATGTTAGTGGCA-CTTAGTC
1 CCTTTT-CAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACATGTCAGTGGCACCTT-GTC
201760 AAAGCCCACAAGTTAGTGGCA
64 AAAGCCCACAAGTTAGTGGCA
* * * * * *
201781 CATTTTCAAAGCCCACATGTTAGTGGCATCCTTTCAAAGCCCATAAGTCAGTGACATCCTT-TCA
1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACATGTCAGTGGCA-CCTTGTCA
* * *
201845 AAGCCCACATGTCAGTGGTA
65 AAGCCCACAAGTTAGTGGCA
* * * * *
201865 CCTTTTTAAAGCCCACAAGTTAGTGGCA-CTCTTTCAAATCTCATATGTCAGTGGCATCCTT-TC
1 CCTTTTCAAAGCCCACAAGTCAGTGGCATC-CTTTCAAAGCCCACATGTCAGTGGCA-CCTTGTC
*
201928 AAAACCCA
64 AAAGCCCA
201936 TATGTCGTAA
Statistics
Matches: 269, Mismatches: 44, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
83 5 0.02
84 165 0.61
85 49 0.18
86 49 0.18
87 1 0.00
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (84 bp):
CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACATGTCAGTGGCACCTTGTCAA
AGCCCACAAGTTAGTGGCA
Found at i:205117 original size:52 final size:52
Alignment explanation
Indices: 205032--205156 Score: 205
Period size: 52 Copynumber: 2.4 Consensus size: 52
205022 ATATGAAAAG
*
205032 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGACAAAT
1 TTGCTTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGACAAAT
* * **
205084 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGTAAAT
1 TTGCTTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGACAAAT
205136 TTGCTTGCATGTATCGATACA
1 TTGCTTGCATGTATCGATACA
205157 AAGATCAATG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (52 bp):
TTGCTTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGACAAAT
Found at i:205167 original size:52 final size:51
Alignment explanation
Indices: 205032--205176 Score: 193
Period size: 52 Copynumber: 2.8 Consensus size: 51
205022 ATATGAAAAG
*
205032 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGACAAAT
1 TTGCTTGCATGTATCGATACA-TTAATAATGTATCGATACATCTGGACAAAT
* * **
205084 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGTAAAT
1 TTGCTTGCATGTATCGATACA-TTAATAATGTATCGATACATCTGGACAAAT
*
205136 TTGCTTGCATGTATCGATACA-AAGATCAATGTATCGATACA
1 TTGCTTGCATGTATCGATACATTA-AT-AATGTATCGATACA
205177 ATGTATCGAT
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 81 0.98
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (51 bp):
TTGCTTGCATGTATCGATACATTAATAATGTATCGATACATCTGGACAAAT
Found at i:205180 original size:13 final size:13
Alignment explanation
Indices: 205162--205189 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
205152 ATACAAAGAT
205162 CAATGTATCGATA
1 CAATGTATCGATA
205175 CAATGTATCGATA
1 CAATGTATCGATA
205188 CA
1 CA
205190 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:205257 original size:20 final size:20
Alignment explanation
Indices: 205228--205285 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
205218 ACAGTAGCTT
205228 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
205247 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
205267 CTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
205286 TCATTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:205584 original size:28 final size:27
Alignment explanation
Indices: 205551--205988 Score: 313
Period size: 28 Copynumber: 15.6 Consensus size: 27
205541 GTCATTGGTA
* *
205551 ACTTTTTAAAGCCCACAAGTCATTGGC
1 ACTTTTCAAAGCCCACAAGTCAGTGGC
* * * *
205578 ACATTTTCAAAGCCCATAAATTAGTGGA
1 AC-TTTTCAAAGCCCACAAGTCAGTGGC
*
205606 ACCTTTTCAAAGCCCACATGTCAGTGGC
1 A-CTTTTCAAAGCCCACAAGTCAGTGGC
* * * *
205634 ATCTTGGTT-AAAGCTCGCAAGTAAGTGGT
1 A-CTT--TTCAAAGCCCACAAGTCAGTGGC
* * *
205663 ACCTTTTCAAAGCCCACATGTAAGTTGC
1 A-CTTTTCAAAGCCCACAAGTCAGTGGC
* * *
205691 ATCCTTTCAAAGCCCATAAGTCAGTGAC
1 A-CTTTTCAAAGCCCACAAGTCAGTGGC
* * *
205719 ATCCTTTCAAAGCCCATAAGTCAGTGAC
1 A-CTTTTCAAAGCCCACAAGTCAGTGGC
*
205747 ATCCTTTT-AAAGCCCACATGTCAGTGGC
1 A--CTTTTCAAAGCCCACAAGTCAGTGGC
* * *
205775 ACTTAGTCAAAGCCCACATGTTAGTGGC
1 ACTT-TTCAAAGCCCACAAGTCAGTGGC
* * * *
205803 ATCCTTTCAAAGCCTACAAATCAATGGC
1 A-CTTTTCAAAGCCCACAAGTCAGTGGC
* * *
205831 ATCCTTTCAAAGCCCACAAGTCAATGAC
1 A-CTTTTCAAAGCCCACAAGTCAGTGGC
*** * * *
205859 ACCTTTTCAAAGTGTACATGTTAATGGC
1 A-CTTTTCAAAGCCCACAAGTCAGTGGC
*
205887 ATCCTTTCAAAGCCCACAAGTCAGTGGC
1 A-CTTTTCAAAGCCCACAAGTCAGTGGC
* *
205915 ATCCTTTCAAAGCCCACAAGTTAGTGGC
1 A-CTTTTCAAAGCCCACAAGTCAGTGGC
* * *
205943 ATCTTTTCAAAGTCAACAAGTCAATGGC
1 A-CTTTTCAAAGCCCACAAGTCAGTGGC
205971 ACCTTTTCAAAGCCCACA
1 A-CTTTTCAAAGCCCACA
205989 CAAGTTGGTG
Statistics
Matches: 330, Mismatches: 72, Indels: 17
0.79 0.17 0.04
Matches are distributed among these distances:
26 3 0.01
27 5 0.02
28 294 0.89
29 26 0.08
30 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (27 bp):
ACTTTTCAAAGCCCACAAGTCAGTGGC
Found at i:205787 original size:84 final size:84
Alignment explanation
Indices: 205558--205988 Score: 388
Period size: 84 Copynumber: 5.1 Consensus size: 84
205548 GTAACTTTTT
* * * * * *
205558 AAAGCCCACAAGTCATTGGCA-CATTTTCAAAGCCCATAAATTAGTGGAACCTTTTCAAAGCCCA
1 AAAGCCCACAAGTCAGTGGCATC-CTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCA
* * *
205622 CATGTCAGTGGCAT-CTTGGTT
65 CAAGTCAATGGCATCCTT--TC
* * * * * * *
205643 AAAGCTCGCAAGTAAGTGGTA-CCTTTTCAAAGCCCACATGTAAGTTGCATCC-TTTCAAAGCCC
1 AAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCC
* * *
205706 ATAAGTCAGTGACATCCTTTC
64 ACAAGTCAATGGCATCCTTTC
* * * * *
205727 AAAGCCCATAAGTCAGTGACATCCTTTTAAAGCCCACATGTCAGTGGCA-CTTAGTCAAAGCCCA
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTT-TTCAAAGCCCA
* * *
205791 CATGTTAGTGGCATCCTTTC
65 CAAGTCAATGGCATCCTTTC
* * * * * ***
205811 AAAGCCTACAAATCAATGGCATCCTTTCAAAGCCCACAAGTCAATGACACCTTTTCAAAGTGTAC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCAC
* *
205876 ATGTTAATGGCATCCTTTC
66 AAGTCAATGGCATCCTTTC
* * * *
205895 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGTCAAC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCAC
205960 AAGTCAATGGCA-CCTTTTC
66 AAGTCAATGGCATCC-TTTC
205979 AAAGCCCACA
1 AAAGCCCACA
205989 CAAGTTGGTG
Statistics
Matches: 283, Mismatches: 55, Indels: 17
0.80 0.15 0.05
Matches are distributed among these distances:
82 1 0.00
83 3 0.01
84 210 0.74
85 64 0.23
86 5 0.02
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (84 bp):
AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCAC
AAGTCAATGGCATCCTTTC
Found at i:206015 original size:31 final size:31
Alignment explanation
Indices: 205977--206065 Score: 106
Period size: 31 Copynumber: 2.9 Consensus size: 31
205967 TGGCACCTTT
*
205977 TCAAAGCCCACACAAGTTGGTGGCACCCTAG
1 TCAAAGCCCACACAAGTTGGTGGCACCCGAG
** * * *
206008 TCAAAGCCCGTACGAGTTGGCGGCACTCGAG
1 TCAAAGCCCACACAAGTTGGTGGCACCCGAG
* *
206039 TCAAGGCCCACACAAGTTAGTGGCACC
1 TCAAAGCCCACACAAGTTGGTGGCACC
206066 TATGTCCGAG
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.27, C:0.31, G:0.26, T:0.16
Consensus pattern (31 bp):
TCAAAGCCCACACAAGTTGGTGGCACCCGAG
Found at i:206367 original size:20 final size:20
Alignment explanation
Indices: 206342--206381 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
206332 ATTTGGGGAC
*
206342 AAACATTACTTGATTCGATT
1 AAACATCACTTGATTCGATT
*
206362 AAACATCACTTGATTTGATT
1 AAACATCACTTGATTCGATT
206382 TTTATTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (20 bp):
AAACATCACTTGATTCGATT
Found at i:207059 original size:20 final size:20
Alignment explanation
Indices: 207006--207061 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
206996 ATCAATCCAT
* * *
207006 TGTATCGATACATGTATGAA
1 TGTATCGATACATTTTTCAA
207026 TGTATCGATACATTTTTCAA
1 TGTATCGATACATTTTTCAA
207046 TGTATCGATACATTTT
1 TGTATCGATACATTTT
207062 GTTTTTTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTTTTCAA
Found at i:211271 original size:20 final size:21
Alignment explanation
Indices: 211246--211298 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
211236 ATCGATACAT
*
211246 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGCA-AAGAA
*
211266 TGTATCGATACTTGCAAAGAA
1 TGTATCGATACATGCAAAGAA
211287 TGTATCGATACA
1 TGTATCGATACA
211299 GGTGCTTGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGCAAAGAA
Found at i:211364 original size:19 final size:20
Alignment explanation
Indices: 211340--211393 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
211330 CTTAATTGTT
*
211340 TGTATCGATACATTGA-AGA
1 TGTATCGATACATTGACAAA
211359 TGTATCGATACA-TGACCAAA
1 TGTATCGATACATTGA-CAAA
*
211379 TGTATTGATACATTG
1 TGTATCGATACATTG
211394 GCTTGTAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 3 0.10
19 12 0.40
20 13 0.43
21 2 0.07
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATTGACAAA
Found at i:217276 original size:13 final size:13
Alignment explanation
Indices: 217257--217295 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
217247 ACAGCATTCT
217257 CTGTATCGATACA
1 CTGTATCGATACA
*
217270 TTGTATCGATACA
1 CTGTATCGATACA
217283 CTGTATCGATACA
1 CTGTATCGATACA
217296 AAGGGTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:219879 original size:19 final size:20
Alignment explanation
Indices: 219855--219908 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
219845 CTTAACTGTT
*
219855 TGTATCGATACATTGA-AGA
1 TGTATCGATACATTGACAAA
219874 TGTATCGATACA-TGACCAAA
1 TGTATCGATACATTGA-CAAA
*
219894 TGTATTGATACATTG
1 TGTATCGATACATTG
219909 GCTTGTAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 3 0.10
19 12 0.40
20 13 0.43
21 2 0.07
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATTGACAAA
Found at i:221710 original size:12 final size:12
Alignment explanation
Indices: 221693--221719 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
221683 ACAATTTCCT
221693 CATGTATCGATA
1 CATGTATCGATA
221705 CATGTATCGATA
1 CATGTATCGATA
221717 CAT
1 CAT
221720 TGTCCCATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (12 bp):
CATGTATCGATA
Found at i:221715 original size:33 final size:32
Alignment explanation
Indices: 221673--221738 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 32
221663 GTTACAAGCA
*
221673 ATGTATCGATACAATT-TCCTCATGTATCGATAC
1 ATGTATCGATAC-ATTGTCC-CATGTATCAATAC
221706 ATGTATCGATACATTGTCCCATGTATCAATAC
1 ATGTATCGATACATTGTCCCATGTATCAATAC
221738 A
1 A
221739 AATACCTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (32 bp):
ATGTATCGATACATTGTCCCATGTATCAATAC
Found at i:222282 original size:13 final size:13
Alignment explanation
Indices: 222264--222288 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
222254 TTTAAAATTC
222264 TCCCCCTTTGTCT
1 TCCCCCTTTGTCT
222277 TCCCCCTTTGTC
1 TCCCCCTTTGTC
222289 ATATAATAAA
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:0.00, C:0.48, G:0.08, T:0.44
Consensus pattern (13 bp):
TCCCCCTTTGTCT
Found at i:231032 original size:21 final size:21
Alignment explanation
Indices: 231006--231144 Score: 103
Period size: 20 Copynumber: 6.7 Consensus size: 21
230996 GTTACAAGCA
231006 ATGTATCGATACAATT-TCCTC
1 ATGTATCGATACAATTGTCC-C
231027 ATGTATCGATAC-ATTGTCCC
1 ATGTATCGATACAATTGTCCC
* **
231047 ATGTATCGATACAAATAGTGAC
1 ATGTATCGATAC-AATTGTCCC
* * * * *
231069 AGGGTAGCTACTGCCAA---TCTC
1 A-TGTATCGA-T-ACAATTGTCCC
*
231090 ATGTATCGATACAGTTGT-CC
1 ATGTATCGATACAATTGTCCC
231110 ATGTATCGATACAATTGT-CC
1 ATGTATCGATACAATTGTCCC
231130 ATGTATCGATACAAT
1 ATGTATCGATACAAT
231145 GTATCGATAC
Statistics
Matches: 93, Mismatches: 16, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
18 2 0.02
19 1 0.01
20 56 0.60
21 19 0.20
22 6 0.06
23 5 0.05
24 3 0.03
25 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACAATTGTCCC
Found at i:231148 original size:13 final size:13
Alignment explanation
Indices: 231130--231156 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
231120 ACAATTGTCC
231130 ATGTATCGATACA
1 ATGTATCGATACA
231143 ATGTATCGATACA
1 ATGTATCGATACA
231156 A
1 A
231157 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:231854 original size:38 final size:37
Alignment explanation
Indices: 231787--231871 Score: 93
Period size: 38 Copynumber: 2.3 Consensus size: 37
231777 TTTAAAACAT
* * *
231787 AATATAAAAATAATATACAGATAACATGAATATATGT-A
1 AATATAAAAATAACATACAAATAAAATGAAT-TAT-TAA
*
231825 CATATAAAAATATACATA-AAATAAAATGAATTATTAA
1 AATATAAAAATA-ACATACAAATAAAATGAATTATTAA
231862 AATATAAAAA
1 AATATAAAAA
231872 ATTTATATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
36 1 0.03
37 13 0.32
38 22 0.55
39 4 0.10
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (37 bp):
AATATAAAAATAACATACAAATAAAATGAATTATTAA
Found at i:232545 original size:22 final size:23
Alignment explanation
Indices: 232520--232567 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
232510 ATTCATAAGC
*
232520 AAACTCATT-CATAAATCATTTA
1 AAACTCATTAAATAAATCATTTA
*
232542 AAACTCATTAAATAAATTATTTA
1 AAACTCATTAAATAAATCATTTA
232565 AAA
1 AAA
232568 TTTATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (23 bp):
AAACTCATTAAATAAATCATTTA
Found at i:234382 original size:13 final size:13
Alignment explanation
Indices: 234364--234412 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
234354 CATGGGACAA
234364 TGTATCGATACAT
1 TGTATCGATACAT
234377 TGTATCGATACA-
1 TGTATCGATACAT
*
234389 TG-A-GGA-A-AT
1 TGTATCGATACAT
234398 TGTATCGATACAT
1 TGTATCGATACAT
234411 TG
1 TG
234413 CTTGTAACGG
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
8 1 0.03
9 3 0.10
10 3 0.10
11 3 0.10
12 3 0.10
13 16 0.55
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:234407 original size:34 final size:33
Alignment explanation
Indices: 234343--234412 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 33
234333 CTATCACTAT
*
234343 TTGTATTGATACATGGGACAATGTATCGATACA
1 TTGTATCGATACATGGGACAATGTATCGATACA
234376 TTGTATCGATACATGAGGA-AATTGTATCGATACA
1 TTGTATCGATACATG-GGACAA-TGTATCGATACA
234410 TTG
1 TTG
234413 CTTGTAACGG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 16 0.47
34 18 0.53
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATGGGACAATGTATCGATACA
Found at i:235326 original size:22 final size:24
Alignment explanation
Indices: 235296--235344 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
235286 TTTGGTTCGT
* *
235296 AAAGGGAAAAAAGGAAGA-AAA-A
1 AAAGAGAAAAAAGAAAGACAAAGA
235318 AAAGAGAAAAAAGAAAGACAAAGA
1 AAAGAGAAAAAAGAAAGACAAAGA
235342 AAA
1 AAA
235345 AATTTTTGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 16 0.70
23 3 0.13
24 4 0.17
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (24 bp):
AAAGAGAAAAAAGAAAGACAAAGA
Found at i:240938 original size:90 final size:89
Alignment explanation
Indices: 240775--241013 Score: 303
Period size: 90 Copynumber: 2.7 Consensus size: 89
240765 AATCCTTATA
* *
240775 ATCTTTC-TTTTTTTCTATGAAAAAGAATATGATTCTTAGATATAATTTATGCATTAGTCTAATT
1 ATCTTTCTTTTTTTTCTAT-AAAAA-AATCTGATTCTTAGATATAATTAATGCATTAGTCTAA-T
240839 CTTGTAGTCTGACATTTACAATCAATC
63 CTTGTAGTCTGACATTTACAATCAATC
* *
240866 ATTCTTTCTTTTTTTTCTATAAAAAAATCCGATTCTCAGATATAA-TAATGCATTAGTCTAATCT
1 A-TCTTTCTTTTTTTTCTATAAAAAAATCTGATTCTTAGATATAATTAATGCATTAGTCTAATCT
*
240930 T-TACAGTCTGACATTTACAATCAGTC
65 TGT--AGTCTGACATTTACAATCAATC
* * *
240956 A----ACTTTTTTTTCTATAAAAAAATCTGATTCTTAGATATAATTCATGCTTTAGTCTAAT
1 ATCTTTCTTTTTTTTCTATAAAAAAATCTGATTCTTAGATATAATTAATGCATTAGTCTAAT
241014 TTTTCTAATC
Statistics
Matches: 133, Mismatches: 10, Indels: 15
0.84 0.06 0.09
Matches are distributed among these distances:
85 36 0.27
86 15 0.11
88 1 0.01
89 4 0.03
90 37 0.28
91 18 0.14
92 11 0.08
93 11 0.08
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (89 bp):
ATCTTTCTTTTTTTTCTATAAAAAAATCTGATTCTTAGATATAATTAATGCATTAGTCTAATCTT
GTAGTCTGACATTTACAATCAATC
Found at i:241105 original size:249 final size:254
Alignment explanation
Indices: 240778--241249 Score: 661
Period size: 249 Copynumber: 1.9 Consensus size: 254
240768 CCTTATAATC
* * * ** * * *
240778 TTTCTTTTTTTCTATGAAAAAGAATATGATTCTTAGATATAATTTATGCATTAGTCTAATTCTTG
1 TTTCTTTTTTTCTATAAAAAAGAATATGATTCTCAAATATAATCCACGCATTAGTATAATCCTTG
* * *
240843 TAGTCTGACATTTACAATCAATC-ATTCTTTCTTTTTTTTC-TATAAAAA-AATCCGATTCTCAG
66 TAGTCTAACATTTACAATCAATCAACT-TTTCTTTTTTTACATA-AAAAATAATCCGATTCTCAG
* * *
240905 ATATAA-TAATGCATTAGTCTAATCTTTACAGTCTGACATTTACAATCAGTCAAC-TTT-TTTTT
129 ATATAATTAATGCATTAATCTAATATTTACAGTCTGACATTTACAATCAATCAACTTTTCTTTTT
*
240967 CTATAAAAAAATCTGATTCTTAGATATAATTCATGCTTTAGTCTAATTTTTCTAATCAACT
194 CTATAAAAAAATCTGATTCTCAGATATAATTCATGCTTTAGTCTAATTTTTCTAATCAACT
*
241028 TTTCTTTTTTT-TATAAAAAAGAATTTGATTCTCAAATATAATCCACGCATTAGTATAATCCTTG
1 TTTCTTTTTTTCTATAAAAAAGAATATGATTCTCAAATATAATCCACGCATTAGTATAATCCTTG
* * * *
241092 TAGTTTAACATTTACAATCAATTAACTTTTCTTTTTTTACATAAAAAATAATCTGATTTTCAGAT
66 TAGTCTAACATTTACAATCAATCAACTTTTCTTTTTTTACATAAAAAATAATCCGATTCTCAGAT
* * *
241157 ATAATTCATGCATTAATCTAATATTTGCAGTTTGACATTTACAATCAATCAACTTTTCTTTTTCT
131 ATAATTAATGCATTAATCTAATATTTACAGTCTGACATTTACAATCAATCAACTTTTCTTTTTCT
*
241222 ATAAAAAAGTCTGATTCTCAGATATAAT
196 ATAAAAAAATCTGATTCTCAGATATAAT
241250 CACATTTATT
Statistics
Matches: 192, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
249 81 0.42
250 33 0.17
251 42 0.22
252 3 0.02
253 33 0.17
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.44
Consensus pattern (254 bp):
TTTCTTTTTTTCTATAAAAAAGAATATGATTCTCAAATATAATCCACGCATTAGTATAATCCTTG
TAGTCTAACATTTACAATCAATCAACTTTTCTTTTTTTACATAAAAAATAATCCGATTCTCAGAT
ATAATTAATGCATTAATCTAATATTTACAGTCTGACATTTACAATCAATCAACTTTTCTTTTTCT
ATAAAAAAATCTGATTCTCAGATATAATTCATGCTTTAGTCTAATTTTTCTAATCAACT
Found at i:241159 original size:92 final size:89
Alignment explanation
Indices: 241020--241250 Score: 284
Period size: 92 Copynumber: 2.6 Consensus size: 89
241010 TAATTTTTCT
* * *
241020 AATCAACTTTTCTTTTTTTTATAAAAAAGAATTTGATTCTCAAATATAATCCACGCATTAGTATA
1 AATCAACTTTTC-TTTTTTTATAAAAAA-AATCTGATTCTCAGATATAATCCACGCATTAATATA
* *
241085 ATCCTTGTAGTTTAACATTTACAATC
64 ATACTTGCAGTTTAACATTTACAATC
* * * * *
241111 AATTAACTTTTCTTTTTTTACATAAAAAATAATCTGATTTTCAGATATAATTCATGCATTAATCT
1 AATCAACTTTTCTTTTTTT--ATAAAAAA-AATCTGATTCTCAGATATAATCCACGCATTAATAT
* *
241176 AATATTTGCAGTTTGACATTTACAATC
63 AATACTTGCAGTTTAACATTTACAATC
* *
241203 AATCAACTTTTCTTTTTCTAT-AAAAAAGTCTGATTCTCAGATATAATC
1 AATCAACTTTTCTTTTTTTATAAAAAAAATCTGATTCTCAGATATAATC
241251 ACATTTATTT
Statistics
Matches: 120, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
88 19 0.16
89 5 0.04
90 9 0.08
91 11 0.09
92 76 0.63
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.43
Consensus pattern (89 bp):
AATCAACTTTTCTTTTTTTATAAAAAAAATCTGATTCTCAGATATAATCCACGCATTAATATAAT
ACTTGCAGTTTAACATTTACAATC
Found at i:241753 original size:14 final size:15
Alignment explanation
Indices: 241722--241773 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
241712 ATGATTTTTT
* *
241722 AATATATTTATAAAA
1 AATATTTTTCTAAAA
*
241737 AA-ATTTATTTTAAAA
1 AATATTT-TTCTAAAA
241752 AATATTTTTCTAAAA
1 AATATTTTTCTAAAA
241767 ATATATT
1 A-ATATT
241774 CACGAAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 3 0.10
15 19 0.61
16 9 0.29
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTTTCTAAAA
Found at i:244605 original size:13 final size:13
Alignment explanation
Indices: 244587--244612 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
244577 TATATGGTCC
244587 ACACTCATCCATA
1 ACACTCATCCATA
244600 ACACTCATCCATA
1 ACACTCATCCATA
244613 GGATGATGTA
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:0.38, G:0.00, T:0.23
Consensus pattern (13 bp):
ACACTCATCCATA
Found at i:244994 original size:58 final size:59
Alignment explanation
Indices: 244902--245018 Score: 173
Period size: 58 Copynumber: 2.0 Consensus size: 59
244892 AAATGGCATC
* * * * *
244902 AATGAGAAGATTATCTTTTGAATTTAAAAAATAAATTTTCTAAATGACATCAGTGAGAT
1 AATGAGAAGAATATCTTTTAAACTTAAAAAATAAATTTTCTAAATAACATCAATGAGAT
*
244961 AATGAGAAGAATAT-TTTTAAACTTAAAAGATAAATTTTCTAAATAACATCAATGAGAT
1 AATGAGAAGAATATCTTTTAAACTTAAAAAATAAATTTTCTAAATAACATCAATGAGAT
245019 TAAGTTAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
58 39 0.75
59 13 0.25
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (59 bp):
AATGAGAAGAATATCTTTTAAACTTAAAAAATAAATTTTCTAAATAACATCAATGAGAT
Found at i:248847 original size:18 final size:18
Alignment explanation
Indices: 248824--248862 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
248814 ATTTAAGTTT
*
248824 AATTAG-ATTTTATTTTAA
1 AATTAGAATTTGA-TTTAA
248842 AATTAGAATTTGATTTAA
1 AATTAGAATTTGATTTAA
248860 AAT
1 AAT
248863 AAAATTAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (18 bp):
AATTAGAATTTGATTTAA
Found at i:248865 original size:23 final size:21
Alignment explanation
Indices: 248839--248881 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 21
248829 GATTTTATTT
248839 TAAAATTAGAATTTGATTTAAAA
1 TAAAATTAGAA-TT-ATTTAAAA
248862 TAAAATTAGAATTATTTAAA
1 TAAAATTAGAATTATTTAAA
248882 TTTATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.35
22 2 0.10
23 11 0.55
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
TAAAATTAGAATTATTTAAAA
Found at i:250069 original size:13 final size:13
Alignment explanation
Indices: 250051--250091 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
250041 TATTTATTTA
*
250051 AATTTATTTTTTT
1 AATTTAATTTTTT
*
250064 AATTTAATATTTT
1 AATTTAATTTTTT
*
250077 AATTCAATTTTTT
1 AATTTAATTTTTT
250090 AA
1 AA
250092 AAATATCAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (13 bp):
AATTTAATTTTTT
Found at i:250790 original size:24 final size:24
Alignment explanation
Indices: 250763--250808 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
250753 TTTATATTTT
*
250763 ATTTAATATAA-TATAATATAATAA
1 ATTT-ATATAATTATAAAATAATAA
250787 ATTTATATAATTATAAAATAAT
1 ATTTATATAATTATAAAATAAT
250809 TGATTAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATTTATATAATTATAAAATAATAA
Found at i:251137 original size:16 final size:16
Alignment explanation
Indices: 251103--251137 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
251093 CAATTCAAAG
* *
251103 TTTAAATTATTTTGTA
1 TTTAAATTATTTGGCA
251119 TTTAAATTATTTGGCA
1 TTTAAATTATTTGGCA
251135 TTT
1 TTT
251138 TAGTCGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.60
Consensus pattern (16 bp):
TTTAAATTATTTGGCA
Found at i:251244 original size:19 final size:20
Alignment explanation
Indices: 251208--251247 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
251198 TACTTAAATC
251208 ATTTAAATTTGATTATTTTA
1 ATTTAAATTTGATTATTTTA
251228 ATTT-AATTT-ATTAATTTTA
1 ATTTAAATTTGATT-ATTTTA
251247 A
1 A
251248 AATCAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.16
19 12 0.63
20 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (20 bp):
ATTTAAATTTGATTATTTTA
Found at i:251360 original size:2 final size:2
Alignment explanation
Indices: 251353--251390 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
251343 GTGAATTATC
251353 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
251391 TTGTAAAGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:251606 original size:32 final size:33
Alignment explanation
Indices: 251570--251636 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
251560 TAAGTATAAT
* **
251570 AAAATATAATAAT-AACTATTTATTCAAAATCA
1 AAAATATAATAATAAAATATTTATAAAAAATCA
251602 AAAATATAATAATAAAATATTTATAAAAAATCA
1 AAAATATAATAATAAAATATTTATAAAAAATCA
251635 AA
1 AA
251637 TTAGTTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (33 bp):
AAAATATAATAATAAAATATTTATAAAAAATCA
Found at i:252474 original size:31 final size:30
Alignment explanation
Indices: 252437--252498 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
252427 AAAATGCACC
*
252437 TAAT-TTTTTATTCAATTTTTTTTTAAAT-T
1 TAATATTTTTATTCAA-ATTTTTTTAAATAT
*
252466 TAATATTTTTATTTAAATTTTTTTAAATAT
1 TAATATTTTTATTCAAATTTTTTTAAATAT
252496 TAA
1 TAA
252499 AATAAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 15 0.52
30 14 0.48
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (30 bp):
TAATATTTTTATTCAAATTTTTTTAAATAT
Found at i:252506 original size:22 final size:19
Alignment explanation
Indices: 252479--252523 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
252469 TATTTTTATT
252479 TAAATTTTTTTAAATATTAAAA
1 TAAA-TTTTTTAAAT-TT-AAA
252501 TAAA-TTTTTAAATTTAAA
1 TAAATTTTTTAAATTTAAA
252519 TAAAT
1 TAAAT
252524 AACTTAACTC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 7 0.32
19 2 0.09
20 9 0.41
22 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAATTTTTTAAATTTAAA
Found at i:252519 original size:18 final size:20
Alignment explanation
Indices: 252485--252523 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
252475 TATTTAAATT
252485 TTTTTAAATATTAAAATAAA
1 TTTTTAAATATTAAAATAAA
252505 TTTTTAAAT-TT-AAATAAA
1 TTTTTAAATATTAAAATAAA
252523 T
1 T
252524 AACTTAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
19 2 0.11
20 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTTAAATATTAAAATAAA
Found at i:255407 original size:7 final size:7
Alignment explanation
Indices: 255395--255426 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
255385 TAAACTGCAC
255395 ATTTTTT
1 ATTTTTT
255402 ATTTTTT
1 ATTTTTT
255409 ATTTTTT
1 ATTTTTT
255416 ATTTTTT
1 ATTTTTT
255423 -TTTT
1 ATTTT
255427 AAAAAAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.16
7 21 0.84
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
ATTTTTT
Found at i:256579 original size:2 final size:2
Alignment explanation
Indices: 256572--256617 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
256562 GACCATCAGA
256572 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
256614 AT AT
1 AT AT
256618 TACAACTCTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:256786 original size:17 final size:17
Alignment explanation
Indices: 256756--256802 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
256746 TTAGTAGTTA
* *
256756 TTTAG-TTAAATTTAGT
1 TTTAGTTTAATTTTAAT
256772 TTTAGTTTAATTTTAAT
1 TTTAGTTTAATTTTAAT
* *
256789 TTTAATTTTATTTT
1 TTTAGTTTAATTTT
256803 GTAATATTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 5 0.19
17 21 0.81
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (17 bp):
TTTAGTTTAATTTTAAT
Found at i:264796 original size:15 final size:15
Alignment explanation
Indices: 264778--264831 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
264768 CTTCTTCTCT
*
264778 CCTCCTCCTGTCATC
1 CCTCCTCCTATCATC
*
264793 CCTCCTCTCTCTATTATC
1 CCT-C-CTC-CTATCATC
*
264811 TCTCCTCCTATCATC
1 CCTCCTCCTATCATC
264826 CCTCCT
1 CCTCCT
264832 ATCTCTACTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 15 0.48
16 4 0.13
17 4 0.13
18 8 0.26
ACGTcount: A:0.09, C:0.50, G:0.02, T:0.39
Consensus pattern (15 bp):
CCTCCTCCTATCATC
Found at i:264815 original size:18 final size:18
Alignment explanation
Indices: 264794--264855 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
264784 CCTGTCATCC
264794 CTCCTCTCTCTATTATCT
1 CTCCTCTCTCTATTATCT
* *
264812 CT-C-CTC-CTATCATCC
1 CTCCTCTCTCTATTATCT
* *
264827 CTCCTATCTCTACTATCT
1 CTCCTCTCTCTATTATCT
*
264845 CTCCTGTCTCT
1 CTCCTCTCTCT
264856 CCTCCTATCA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
15 9 0.26
16 4 0.12
17 3 0.09
18 18 0.53
ACGTcount: A:0.11, C:0.44, G:0.02, T:0.44
Consensus pattern (18 bp):
CTCCTCTCTCTATTATCT
Found at i:264825 original size:33 final size:33
Alignment explanation
Indices: 264779--264849 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
264769 TTCTTCTCTC
* * *
264779 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCT
264812 CTCCTCCTATCATCCCTCCTATCTCTACTATCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCT
264845 CTCCT
1 CTCCT
264850 GTCTCTCCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.46, G:0.01, T:0.41
Consensus pattern (33 bp):
CTCCTCCTATCATCCCTCCTATCTCTACTATCT
Found at i:264829 original size:12 final size:11
Alignment explanation
Indices: 264807--264878 Score: 53
Period size: 12 Copynumber: 6.5 Consensus size: 11
264797 CTCTCTCTAT
264807 TATCTCTCCTCC
1 TATCTC-CCTCC
264819 TATCATCCCTCC
1 TATC-TCCCTCC
*
264831 TATCT--CTAC
1 TATCTCCCTCC
264840 TATCT--CTCC
1 TATCTCCCTCC
*
264849 TGTCTCTCCTCC
1 TATCTC-CCTCC
264861 TATCATCCCTCC
1 TATC-TCCCTCC
*
264873 TCTCTC
1 TATCTC
264879 TTCTTTCTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
9 15 0.30
11 3 0.06
12 28 0.56
13 4 0.08
ACGTcount: A:0.11, C:0.47, G:0.01, T:0.40
Consensus pattern (11 bp):
TATCTCCCTCC
Found at i:264855 original size:42 final size:42
Alignment explanation
Indices: 264809--264888 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
264799 CTCTCTATTA
264809 TCTCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTG
1 TCTCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTG
* * *
264851 TCTCTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 TCTCTCCTCCTATCATCCCTCCTATCTCTACTATCTCT
264889 TTGAGGGCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.09, C:0.46, G:0.01, T:0.44
Consensus pattern (42 bp):
TCTCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTG
Found at i:268072 original size:17 final size:17
Alignment explanation
Indices: 268052--268088 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
268042 TATTATTTAA
268052 TTAAATTTAATTTTAGT
1 TTAAATTTAATTTTAGT
* *
268069 TTAATTTTAATTTTATT
1 TTAAATTTAATTTTAGT
268086 TTA
1 TTA
268089 CAATCTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TTAAATTTAATTTTAGT
Found at i:268075 original size:11 final size:11
Alignment explanation
Indices: 268046--268088 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
268036 TAAAATTATT
*
268046 ATTTAA-TTAA
1 ATTTAATTTTA
268056 ATTTAATTTTA
1 ATTTAATTTTA
*
268067 GTTTAATTTTA
1 ATTTAATTTTA
*
268078 ATTTTATTTTA
1 ATTTAATTTTA
268089 CAATCTTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 6 0.21
11 22 0.79
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
ATTTAATTTTA
Found at i:269114 original size:28 final size:27
Alignment explanation
Indices: 269057--269128 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 27
269047 ATTATTTAAG
* *
269057 TAAAAATTATAAATT--ATAAATAAATA
1 TAAAAATTA-AAATTAAAAAAATAAAAA
269083 TAAAAATTAATAATTAAAAAAATAAAAA
1 TAAAAATTAA-AATTAAAAAAATAAAAA
*
269111 TAAATATTAAAATTAAAA
1 TAAAAATTAAAATTAAAA
269129 TTTTATATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
25 1 0.03
26 13 0.32
27 8 0.20
28 18 0.45
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (27 bp):
TAAAAATTAAAATTAAAAAAATAAAAA
Found at i:269610 original size:16 final size:16
Alignment explanation
Indices: 269567--269610 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
269557 TAATATAATA
*
269567 TTATAATTATAAAATT
1 TTATAATTATTAAATT
*
269583 TTATAATT-TTAATTT
1 TTATAATTATTAAATT
*
269598 TTTTAATTATTAA
1 TTATAATTATTAA
269611 CAATCATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATAATTATTAAATT
Found at i:271496 original size:15 final size:17
Alignment explanation
Indices: 271460--271492 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
271450 ATATATGTAT
271460 ATTATATACAATAAAAA
1 ATTATATACAATAAAAA
*
271477 ATTATATACATTAAAA
1 ATTATATACAATAAAA
271493 TTATGTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (17 bp):
ATTATATACAATAAAAA
Found at i:272158 original size:2 final size:2
Alignment explanation
Indices: 272151--272184 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
272141 GCAATTTCAA
*
272151 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
272185 AAAAAACGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:279457 original size:13 final size:13
Alignment explanation
Indices: 279439--279463 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
279429 TTTCACCATG
279439 TATCGATACAATA
1 TATCGATACAATA
279452 TATCGATACAAT
1 TATCGATACAAT
279464 GTCCCATGTA
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:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:279471 original size:33 final size:33
Alignment explanation
Indices: 279413--279480 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
279403 GCCGTTGGGC
* *
279413 ACAATATATCGATACTTTTCACCATGTATCGAT
1 ACAATATATCGATACATGTCACCATGTATCGAT
*
279446 ACAATATATCGATACAATGTC-CCATGTATTGAT
1 ACAATATATCGATAC-ATGTCACCATGTATCGAT
279479 AC
1 AC
279481 TTTTTACTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 28 0.90
34 3 0.10
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (33 bp):
ACAATATATCGATACATGTCACCATGTATCGAT
Found at i:279527 original size:42 final size:42
Alignment explanation
Indices: 279468--279564 Score: 176
Period size: 42 Copynumber: 2.3 Consensus size: 42
279458 TACAATGTCC
* *
279468 CATGTATTGATACTTTTTACTTAGGGTAGCTACTGCCAGTTT
1 CATGTATCGATACTTTTTACTTAGAGTAGCTACTGCCAGTTT
279510 CATGTATCGATACTTTTTACTTAGAGTAGCTACTGCCAGTTT
1 CATGTATCGATACTTTTTACTTAGAGTAGCTACTGCCAGTTT
279552 CATGTATCGATAC
1 CATGTATCGATAC
279565 AATTGAGTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.40
Consensus pattern (42 bp):
CATGTATCGATACTTTTTACTTAGAGTAGCTACTGCCAGTTT
Found at i:281753 original size:20 final size:20
Alignment explanation
Indices: 281730--281775 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
281720 GCCGGTTGCA
281730 ACCTGGGTGTGCC-GATCGCG
1 ACCTGGGTGTGCCAG-TCGCG
*
281750 ACCTGGGTGTGCCAGTTGCG
1 ACCTGGGTGTGCCAGTCGCG
281770 ACCTGG
1 ACCTGG
281776 AAGGGGCTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.11, C:0.28, G:0.39, T:0.22
Consensus pattern (20 bp):
ACCTGGGTGTGCCAGTCGCG
Found at i:291645 original size:52 final size:52
Alignment explanation
Indices: 291497--291625 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
291487 CGAAATATGA
*
291497 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
* *
291549 AAATTTGCTTGTATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
*
291601 AAATTTGCCTGCATATATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
291626 AAGATCAGTG
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:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Found at i:291652 original size:13 final size:13
Alignment explanation
Indices: 291634--291658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
291624 CAAAGATCAG
291634 TGTATCGATACAA
1 TGTATCGATACAA
291647 TGTATCGATACA
1 TGTATCGATACA
291659 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:291744 original size:32 final size:32
Alignment explanation
Indices: 291703--291806 Score: 136
Period size: 32 Copynumber: 3.2 Consensus size: 32
291693 AGCTTCGTAG
291703 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* * *
291735 CGATACATTGTATCGATATAACACTTAGGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* * **
291767 CGATATATTATATCGATACAGTACTTTATGTAT
1 CGATACATTGTATCGATACAAAAC-TTATGTAT
291800 CGATACA
1 CGATACA
291807 AATCGTTGAA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
32 48 0.79
33 13 0.21
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:292806 original size:43 final size:43
Alignment explanation
Indices: 292745--293160 Score: 445
Period size: 43 Copynumber: 9.1 Consensus size: 43
292735 TAAAGGTGGA
* *
292745 AAAGGTGCCAATATGCTGATTCAAGGCTAGCAATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
292788 AAAGGTGCCAATGTGCTGATTCAAAGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
292831 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
292880 GAAGGTGCCAATATGCTGATTCAAGGCTAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
292923 AAAGATGAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGACTT
1 -AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
292972 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * *
293015 AAAGATGAAGGTGCCAATATGTTGATTCAAGGCCAACGATATTAGACTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
293064 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
293107 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAACTATATTGGACTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
293156 AAAGG
1 AAAGG
293161 AAGATGCCAC
Statistics
Matches: 314, Mismatches: 35, Indels: 48
0.79 0.09 0.12
Matches are distributed among these distances:
43 152 0.48
44 2 0.01
45 3 0.01
46 2 0.01
47 4 0.01
48 3 0.01
49 148 0.47
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:292885 original size:92 final size:92
Alignment explanation
Indices: 292693--293160 Score: 765
Period size: 92 Copynumber: 5.1 Consensus size: 92
292683 TAAAGATGGA
* * *
292693 AAAGGTGCCAATATGCTAATTCAAGGCCAGCTATATTGGACTTAAAGGTGGAAAAGGTGCCAATA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATA
* * *
292758 TGCTGATTCAAGGCTAGCAATATTGGACTT
63 TGCTGATTCAAGGCCAACGATATTGGACTT
* *
292788 AAAGGTGCCAATGTGCTGATTCAAAGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
292853 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAACGATATTGGACTT
* * *
292880 GAAGGTGCCAATATGCTGATTCAAGGCTAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
292945 TGATTCAAGGCCAACGATATTGGACTT
66 TGATTCAAGGCCAACGATATTGGACTT
* *
292972 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
293037 TGATTCAAGGCCAACGATATTAGACTT
66 TGATTCAAGGCCAACGATATTGGACTT
293064 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
293129 TGATTCAAGGCCAACTATATTGGACTT
66 TGATTCAAGGCCAACGATATTGGACTT
293156 AAAGG
1 AAAGG
293161 AAGATGCCAC
Statistics
Matches: 350, Mismatches: 23, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
92 305 0.87
94 1 0.00
95 44 0.13
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (92 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAACGATATTGGACTT
Found at i:292905 original size:21 final size:21
Alignment explanation
Indices: 292838--292905 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
292828 CTTAAAGATG
292838 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
*
292859 AA-G-GCCAGCGATAT--TGGACTTG
1 AAGGTGCCA---ATATGCT-GA-TTC
292881 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
292902 AAGG
1 AAGG
292906 CTAGCTACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 18
0.64 0.04 0.32
Matches are distributed among these distances:
19 4 0.11
20 2 0.06
21 14 0.39
22 10 0.28
23 2 0.06
24 4 0.11
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (21 bp):
AAGGTGCCAATATGCTGATTC
Found at i:293089 original size:21 final size:21
Alignment explanation
Indices: 293022--293089 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
293012 CTTAAAGATG
293022 AAGGTGCCAATATGTTGATTC
1 AAGGTGCCAATATGTTGATTC
* * *
293043 AA-G-GCCAACGATATTAGACTTA
1 AAGGTGCCAA-TATGTT-GA-TTC
*
293065 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGTTGATTC
293086 AAGG
1 AAGG
293090 CCAGCTACAT
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
19 5 0.14
20 5 0.14
21 10 0.29
22 6 0.17
23 4 0.11
24 5 0.14
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (21 bp):
AAGGTGCCAATATGTTGATTC
Found at i:293242 original size:32 final size:31
Alignment explanation
Indices: 293165--293314 Score: 178
Period size: 32 Copynumber: 4.7 Consensus size: 31
293155 TAAAGGAAGA
* * *
293165 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGT
1 TGCCACCGACTTGTGTGGGCTTTAG-AG-GGGT
293198 TGCCACCGACTTGTGTGGGCTTTAGAGGGGAT
1 TGCCACCGACTTGTGTGGGCTTTAGAGGGG-T
* * *
293230 TGCCACCAACTTGTGTGAGCTTTTGAGAAGGG-
1 TGCCACCGACTTGTGTGGGC-TTT-AGAGGGGT
293262 TGCCACCGACTTGTGTGGGCTTT-GAGGGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGA-GGGGT
293293 TGCCACCGACTTGTGTGGGCTT
1 TGCCACCGACTTGTGTGGGCTT
293315 AGAAGGAAAA
Statistics
Matches: 103, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
29 2 0.02
30 3 0.03
31 27 0.26
32 39 0.38
33 26 0.25
34 6 0.06
ACGTcount: A:0.16, C:0.20, G:0.35, T:0.29
Consensus pattern (31 bp):
TGCCACCGACTTGTGTGGGCTTTAGAGGGGT
Found at i:293280 original size:64 final size:64
Alignment explanation
Indices: 293165--293314 Score: 248
Period size: 64 Copynumber: 2.3 Consensus size: 64
293155 TAAAGGAAGA
*
293165 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAGGGGAT
1 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGGTGCCACCGACTTGTGTGGGCTTT-GAGGGGAT
* *
293230 TGCCACCAACTTGTGTGAGCTTTTG-AGAAGGGTGCCACCGACTTGTGTGGGCTTTGAGGGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGGTGCCACCGACTTGTGTGGGCTTTGAGGGGAT
*
293293 TGCCACCGACTTGTGTGGGCTT
1 TGCCACCAACTTGTGTGGGCTT
293315 AGAAGGAAAA
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
63 27 0.34
64 29 0.36
65 24 0.30
ACGTcount: A:0.16, C:0.20, G:0.35, T:0.29
Consensus pattern (64 bp):
TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGGTGCCACCGACTTGTGTGGGCTTTGAGGGGAT
Found at i:293342 original size:35 final size:38
Alignment explanation
Indices: 293293--293479 Score: 99
Period size: 33 Copynumber: 5.4 Consensus size: 38
293283 TTGAGGGGGT
* * * *
293293 TGCCACCGACTTGTGTGGGCTT-AGAA-GGAAAAAGA-
1 TGCCACAGAGTTGTGTGGACTTAAAAAGGGAAAAAGAG
293328 TGCCACAGAG-T-TGTGGACTTAAAAAGGGAAAAAGAG
1 TGCCACAGAGTTGTGTGGACTTAAAAAGGGAAAAAGAG
* *
293364 TGCCACGGAGTTGTG-GG-CTTTGAAAA--G---AAG-G
1 TGCCACAGAGTTGTGTGGAC-TTAAAAAGGGAAAAAGAG
* * *
293395 TGCCATAGAG-T-CGTGGACTT-AAAA-GGAACAAG-G
1 TGCCACAGAGTTGTGTGGACTTAAAAAGGGAAAAAGAG
** *
293428 TGCCATGGAG-T-TGTGGACTTTAAAAGGGAAAAAAGAG
1 TGCCACAGAGTTGTGTGGACTTAAAAAGGG-AAAAAGAG
*
293465 TGCCACGGAGTTGTG
1 TGCCACAGAGTTGTG
293480 GCCTTTGAAA
Statistics
Matches: 121, Mismatches: 13, Indels: 32
0.73 0.08 0.19
Matches are distributed among these distances:
29 5 0.04
30 6 0.05
31 10 0.08
32 3 0.02
33 30 0.25
34 8 0.07
35 20 0.17
36 15 0.12
37 19 0.16
38 3 0.02
39 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.20
Consensus pattern (38 bp):
TGCCACAGAGTTGTGTGGACTTAAAAAGGGAAAAAGAG
Found at i:293391 original size:64 final size:62
Alignment explanation
Indices: 293328--294155 Score: 271
Period size: 61 Copynumber: 12.8 Consensus size: 62
293318 AGGAAAAAGA
* *
293328 TGCCACAGAGTTGTGGACTTAAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAA
1 TGCCACAGAGTCGTGGACTT-AAAA-GGAAAAAG-GTGCCACGGAGTTGTGGACTTT-AAAAGAA
293393 GG
62 -G
* * *
293395 TGCCATAGAGTCGTGGACTTAAAAGGAACAAGGTGCCATGGAGTTGTGGACTTTAAAAGGGAAAA
1 TGCCACAGAGTCGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAA--G----
293460 AAGAG
60 -A-AG
* * * ** * * *
293465 TGCCACGGAGTTGTGGCCTTTGAA--AAGAAGGTGCCACGGAGTCGCGGACTTTAAAAGGAAGG
1 TGCCACAGAGTCGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAA-GAA-G
* * *
293527 TGCCACAGAGTCATGGACTTAAAAGGAAGAAGATGCCAC-GAGGTTGTGGACTTTAAAAGGGAAA
1 TGCCACAGAGTCGTGGACTTAAAAGGAAAAAGGTGCCACGGA-GTTGTGGACTTTAAAA--G---
293591 AAAGAG
60 --A-AG
** * **
293597 TGCCACAGAGTCGTGGACTT-TGA-GACAAAA-G-GCCACTGAGTCATGGACTTTGAGACAA-AA
1 TGCCACAGAGTCGTGGACTTAAAAGGA-AAAAGGTGCCACGGAGTTGTGGACTTT-A-A-AAGAA
293657 G
62 G
* * *
293658 ATGCCACTGAGTCGTGGACTTTGAAGAAAAGGAAAAAGAG-GCCACGGAGGTGTGGGC-TTAAAA
1 -TGCCACAGAGTCGTGGAC-TT----AAAAGGAAAAAG-GTGCCACGGAGTTGTGGACTTTAAAA
293721 GGAAAAAAGGG
59 -G----AA--G
* *
293732 TGCCACGGAGTCGTGGACTTAAAA-G-----GGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAA
1 TGCCACAGAGTCGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTTT-AAAAG----A
293791 GAG
61 -AG
* * * * * * *
293794 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCATGGAGTTGTGGACTTAGAAGGAAAAA
1 TGCCACAGAGTCGTGGAC-TTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTT--TA--AAAGA
293859 GAG
61 -AG
* * * * *
293862 TGCCACGGAGTTGTGGGCTTAAAA-G-----GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAG
1 TGCCACAGAGTCGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTT--TA--AAAGA-
293921 AG
61 AG
* * * * * * *
293923 TGCCACGGAGTTGTGGGCTT-AAACG-----GGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAG
1 TGCCACAGAGTCGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTT--TA--AAAGA-
293982 AG
61 AG
* * * * * * *
293984 TGCCACGGAGTTGTGGGCTTAGAAGGAAAAAAAGTGCCACGGAGTTGTGGGC-TTAAAAG-GG
1 TGCCACAGAGTCGTGGACTTAAAAGG-AAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGAAG
* * * * * *
294045 TGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TTAAACG-GG
1 TGCCACAGAGTCGTGGACTTAAAAGGAAAAAG-GTGCCACGGAGTTGTGGACTTTAAAAGAAG
* * * *
294106 TGCCACGGAATTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGG
1 TGCCACAGAGTCGTGGACTTAAAAGGAAAAAG-GTGCCACGGAGTTGTGG
294156 GCTTAGAAGG
Statistics
Matches: 634, Mismatches: 61, Indels: 138
0.76 0.07 0.17
Matches are distributed among these distances:
60 8 0.01
61 217 0.34
62 75 0.12
63 25 0.04
64 52 0.08
65 11 0.02
66 7 0.01
67 44 0.07
68 82 0.13
69 29 0.05
70 57 0.09
71 2 0.00
72 7 0.01
73 17 0.03
74 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.34, T:0.19
Consensus pattern (62 bp):
TGCCACAGAGTCGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGAAG
Found at i:293491 original size:101 final size:100
Alignment explanation
Indices: 293307--294319 Score: 406
Period size: 95 Copynumber: 10.4 Consensus size: 100
293297 ACCGACTTGT
* *
293307 GTGGGCTTAGAAGGAAAAAGATGCCACAGAGTTGTGGACTTAAAAAGGGAAAAAGAGTGCCACGG
1 GTGGACTTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTTAAAAAGGGAAAAAGAGTGCCACGG
* *
293372 AGTTGTGGGCTTTGAAAAGAAGGTGCCATAGAGTC
66 AGTTGTGGCCTTTGAAAAGAAGGTGCCACAGAGTC
* * ** *
293407 GTGGACTTAAAAGGAACAAGGTGCCATGGAGTTGTGGACTTTAAAAGGGAAAAAAGAGTGCCACG
1 GTGGACTTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTTAAAAAGGG-AAAAAGAGTGCCACG
*
293472 GAGTTGTGGCCTTTGAAAAGAAGGTGCCACGGAGTC
65 GAGTTGTGGCCTTTGAAAAGAAGGTGCCACAGAGTC
* * ** *
293508 GCGGACTTTAAAAGG---AAGGTGCCACAGAGTCATGGACTT-AAAA-GGAAGAAGA-TGCCAC-
1 GTGGAC-TTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTTAAAAAGGGAAAAAGAGTGCCACG
*
293566 GAGGTTGTGGACTTT-AAAAGGGAAAAAAGAGTGCCACAGAGTC
65 GA-GTTGTGGCCTTTGAAAA--G----AAG-GTGCCACAGAGTC
** * ** * *
293609 GTGGACTT-TGA-GACAAAAG--GCCACTGAGTCATGGACTT----TGAGACAAAAGA-TGCCAC
1 GTGGACTTAAAAGGA-AAAAGATGCCACAGAGTTGTGGACTTAAAAAGGGA-AAAAGAGTGCCAC
* * * *
293665 TGAGTCGTGGACTTTGAAGAAAAGGAAAAAGAG-GCCACGGAGGT-
64 GGAGTTGTGGCCTTT---GAAAA-G---AAG-GTGCCACAGA-GTC
* * * *
293709 GTGGGCTTAAAAGGAAAAAAGGGTGCCACGGAGTCGTGGACTT-AAAA--G-----G-GTGCCAC
1 GTGGACTTAAAAGG-AAAAA-GATGCCACAGAGTTGTGGACTTAAAAAGGGAAAAAGAGTGCCAC
* * *
293765 GGAGTTGTGGGCTTTGAAAAGAAAAAGAGTGCCACGGAGTT
64 GGAGTTGTGGCCTTTGAAAAG---AAG-GTGCCACAGAGTC
* * * ** *
293806 GTGGGCTTTAAAAAGAAAAAGGTGCCATGGAGTTGTGGACTT-AGAA-GGAAAAAGAGTGCCACG
1 GTGGAC-TTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTTAAAAAGGGAAAAAGAGTGCCACG
* * *
293869 GAGTTGTGGGC-TT-AAAAG--GGTGCCACGGAGTT
65 GAGTTGTGGCCTTTGAAAAGAAGGTGCCACAGAGTC
* * * * *
293901 GTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT--AAA-CG-----G-GTGCCACA
1 GTGGACTTAAAAGGAAAAAGA-TGCCACAGAGTTGTGGACTTAAAAAGGGAAAAAGAGTGCCACG
* * * * *
293957 GAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTT
65 GAGTTGTGGCCTTTGAA--AAGAAG-GTGCCACAGAGTC
* * * * *
293996 GTGGGCTTAGAAGGAAAAAAAGTGCCACGGAGTTGTGGGCTT-AAAA--G-----G-GTGCCACG
1 GTGGACTTAAAAGGAAAAAGA-TGCCACAGAGTTGTGGACTTAAAAAGGGAAAAAGAGTGCCACG
* * * * *
294052 GAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTT
65 GAGTTGTGGCCTTTGAA--AAGAAG-GTGCCACAGAGTC
* * * * *
294091 GTGGGCTTAAACGG-----G-TGCCACGGAATTGTGGACTT-AGAA-GGAAAAAGAGTGCCACGG
1 GTGGACTTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTTAAAAAGGGAAAAAGAGTGCCACGG
* * * ** * *
294148 AGTTGTGGGCTTAGAAGGAAAAAGAGTGCCATGGTGTT
66 AGTTGTGGCCTTTGAA--AAGAAG-GTGCCACAGAGTC
* *
294186 GTGGGCTTAAAAGG-----G-TGCCACAGAGTTGTGGACTT-AGAA-GGAAAAAGAGTGCCACGG
1 GTGGACTTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTTAAAAAGGGAAAAAGAGTGCCACGG
* * * *
294243 AGTTGTGGGC-TT-AAACG--GGTGCCACGGAGTT
66 AGTTGTGGCCTTTGAAAAGAAGGTGCCACAGAGTC
* * *
294274 GTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAA
1 GTGGACTTAAAAGGAAAAAGA-TGCCACAGAGTTGTGGACTTAAAA
294320 TGGTGCCACA
Statistics
Matches: 770, Mismatches: 77, Indels: 136
0.78 0.08 0.14
Matches are distributed among these distances:
88 61 0.08
89 4 0.01
90 2 0.00
91 1 0.00
92 2 0.00
93 3 0.00
94 24 0.03
95 292 0.38
96 47 0.06
97 27 0.04
98 14 0.02
99 43 0.06
100 100 0.13
101 86 0.11
102 21 0.03
103 25 0.03
105 17 0.02
106 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.35, T:0.19
Consensus pattern (100 bp):
GTGGACTTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTTAAAAAGGGAAAAAGAGTGCCACGG
AGTTGTGGCCTTTGAAAAGAAGGTGCCACAGAGTC
Found at i:293549 original size:30 final size:31
Alignment explanation
Indices: 293482--293555 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
293472 GAGTTGTGGC
* *
293482 CTTTGAAAA-GAAGGTGCCACGGAGTCGCGGA
1 CTTT-AAAAGGAAGGTGCCACAGAGTCACGGA
*
293513 CTTTAAAAGGAAGGTGCCACAGAGTCATGGA
1 CTTTAAAAGGAAGGTGCCACAGAGTCACGGA
293544 C-TTAAAAGGAAG
1 CTTTAAAAGGAAG
293556 AAGATGCCAC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 15 0.38
31 24 0.62
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.18
Consensus pattern (31 bp):
CTTTAAAAGGAAGGTGCCACAGAGTCACGGA
Found at i:293669 original size:32 final size:32
Alignment explanation
Indices: 293590--293681 Score: 143
Period size: 30 Copynumber: 2.9 Consensus size: 32
293580 TAAAAGGGAA
*
293590 AAAAGAGTGCCACAGAGTCGTGGACTTTGAGAC
1 AAAAGA-TGCCACTGAGTCGTGGACTTTGAGAC
*
293623 AAAAG--GCCACTGAGTCATGGACTTTGAGAC
1 AAAAGATGCCACTGAGTCGTGGACTTTGAGAC
293653 AAAAGATGCCACTGAGTCGTGGACTTTGA
1 AAAAGATGCCACTGAGTCGTGGACTTTGA
293682 AGAAAAGGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
30 28 0.52
32 21 0.39
33 5 0.09
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (32 bp):
AAAAGATGCCACTGAGTCGTGGACTTTGAGAC
Found at i:293763 original size:232 final size:232
Alignment explanation
Indices: 293312--293847 Score: 561
Period size: 232 Copynumber: 2.3 Consensus size: 232
293302 CTTGTGTGGG
* *
293312 CTTAGAAGGAAAAAGATGCCAC-AGAGTTGTGGACTTAAAAAGGGAAAAAGAGTGCCACGGAGTT
1 CTTAAAAGGAAAAAGATGCCACGAGAGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTT
* * * * *
293376 GTGGGCTTTGAAAAGAAGGTGCCATAGAGTCGTGGACTTAAAAGGAACAAGGTGCCATGGAGTTG
66 GTGGACTTTGAAAAGAAGGTGCCATAGAGTCATGGACTTAAAAGGAAAAAGATGCCATGGAGTCG
* * *
293441 TGGACTTTAAAAGGGAAAAAAGAGTGCCACGGAGTTGTGGCCTTTGAAAAGAAGGTGCCACGGAG
131 TGGACTTTAAAAAGGAAAAAAGAGTGCCACGGAGGTGTGGCCTTGGAAAAGAAGGTGCCACGGAG
293506 TCGCGGACTTTAAAAGGAAGGTGCCACAGAGTCATGGA
196 TCGCGGACTTTAAAAGG-AGGTGCCACAGAGTCATGGA
* *
293544 CTTAAAAGGAAGAAGATGCCACGAG-GTTGTGGACTTTAAAAGGGAAAAAAGAGTGCCACAGAGT
1 CTTAAAAGGAAAAAGATGCCACGAGAGTTGTGGACTTTAAAAGGG-AAAAAGAGTGCCACGGAGT
* **
293608 CGTGGACTTTGAGACAA-AA-G-GCCACT-GAGTCATGGACTT-TGA-GACAAAAGATGCCACT-
65 TGTGGACTTTGA-A-AAGAAGGTGCCA-TAGAGTCATGGACTTAAAAGGA-AAAAGATGCCA-TG
*
293666 GAGTCGTGGACTTTGAAGAAAAGG-AAAAAGAG-GCCACGGAGGTGTGGGCTTAAAAGGAAAA-A
125 GAGTCGTGGACTTT--A-AAAAGGAAAAAAGAGTGCCACGGAGGTGTGGCCTT----GGAAAAGA
* * ** *
293728 AGGGTGCCACGGAGTCGTGGAC-TTAAAA-G-GGTGCCACGGAGTTGTGGG
183 A-GGTGCCACGGAGTCGCGGACTTTAAAAGGAGGTGCCACAGAGTCATGGA
* * *
293776 CTTTGAAAA-GAAAAAGAGTGCCACG-GAGTTGTGGGCTTTAAAA-AGAAAAAG-GTGCCATGGA
1 C-TT-AAAAGGAAAAAGA-TGCCACGAGAGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGA
293837 GTTGTGGACTT
63 GTTGTGGACTT
293848 AGAAGGAAAA
Statistics
Matches: 258, Mismatches: 27, Indels: 39
0.80 0.08 0.12
Matches are distributed among these distances:
230 2 0.01
231 41 0.16
232 94 0.36
233 52 0.20
234 35 0.14
235 10 0.04
236 24 0.09
ACGTcount: A:0.35, C:0.14, G:0.33, T:0.19
Consensus pattern (232 bp):
CTTAAAAGGAAAAAGATGCCACGAGAGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTT
GTGGACTTTGAAAAGAAGGTGCCATAGAGTCATGGACTTAAAAGGAAAAAGATGCCATGGAGTCG
TGGACTTTAAAAAGGAAAAAAGAGTGCCACGGAGGTGTGGCCTTGGAAAAGAAGGTGCCACGGAG
TCGCGGACTTTAAAAGGAGGTGCCACAGAGTCATGGA
Found at i:293903 original size:95 final size:95
Alignment explanation
Indices: 293690--294316 Score: 480
Period size: 95 Copynumber: 6.7 Consensus size: 95
293680 GAAGAAAAGG
* *
293690 AAAAAGAG-GCCACGGAGGTGTGGGCTTAAAAGGAAAAAAGGGTGCCACGGAGTCGTGGACTT--
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGG-AAAAA-GGTGCCACGGAGTTGTGGACTTAG
*
293752 -----AAAAGGGTGCCACGGAGTTGTGGGCTTT
64 AAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT
* *
293780 GAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCATGGAGTTGTGGA
1 ------AAAAAGAGTGCCACGGAGTTGTGGGC-TTAAAAGGAAAAAGGTGCCACGGAGTTGTGGA
293845 CTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
59 CTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* * * *
293882 -AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTA-A
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAG-GTGCCACGGAGTTGTGGACTTAGA
* * *
293945 ACG-----G-GTGCCACAGAGTTGTGGACTT
65 AGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* * *
293970 AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAAAGTGCCACGGAGTTGTGGG
1 ------AAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGG-AAAAAGGTGCCACGGAGTTGTGGA
* *
294035 CTT-------AAAAGGGTGCCACGGAGTTGTGGACTT
59 CTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* *
294065 AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT-AAACG-----GGTGCCACGGAATTGTGGAC
1 ------AAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGAC
294124 TTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
60 TTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* * *
294160 AGAAGGAAAAAGAGTGCCATGGTGTTGTGGGCTTAAAA-G-----GGTGCCACAGAGTTGTGGAC
1 ------AAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGAC
294219 TTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
60 TTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* * * * *
294255 -AAACGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTA
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAG-GTGCCACGGAGTTGTGGACTTA
294317 AAATGGTGCC
Statistics
Matches: 456, Mismatches: 37, Indels: 77
0.80 0.06 0.14
Matches are distributed among these distances:
88 63 0.14
89 2 0.00
94 20 0.04
95 281 0.62
96 36 0.08
97 21 0.05
98 7 0.02
102 2 0.00
103 24 0.05
ACGTcount: A:0.31, C:0.13, G:0.37, T:0.19
Consensus pattern (95 bp):
AAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTTAGAA
GGAAAAAGAGTGCCACGGAGTTGTGGGCTT
Found at i:293921 original size:61 final size:61
Alignment explanation
Indices: 293821--294375 Score: 609
Period size: 61 Copynumber: 9.0 Consensus size: 61
293811 CTTTAAAAAG
* *
293821 AAAAAGGTGCCATGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
293882 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* *
293943 AAACGGGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* * * *
294004 AGAAGGAAAAAAAGTGCCACGGAGTTGTGGGCTT-------AAAAGGGTGCCACGGAGTTGTGGA
1 AAAAGG-------GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGG
294062 CTT
59 CTT
* * * * *
294065 AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTA-AACG-----G-GTGCCACGGAATTGTGGA
1 -------AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGG
294123 CTT
59 CTT
* * * *
294126 AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCATGGTGTTGTGGG
1 -------AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGG
294191 CTT
59 CTT
*
294194 AAAAGGGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
*
294255 AAACGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* * * *
294316 AAAATGGTGCCACAGAGTTGTGGACTTAAAAGG-AAAAGAGTGCCACGTAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
294376 TGCAGAAAAG
Statistics
Matches: 438, Mismatches: 30, Indels: 53
0.84 0.06 0.10
Matches are distributed among these distances:
60 26 0.06
61 367 0.84
62 4 0.01
67 1 0.00
68 40 0.09
ACGTcount: A:0.30, C:0.13, G:0.36, T:0.20
Consensus pattern (61 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
Found at i:294005 original size:156 final size:156
Alignment explanation
Indices: 293793--294316 Score: 933
Period size: 156 Copynumber: 3.4 Consensus size: 156
293783 AAGAAAAAGA
* * * * *
293793 GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAG-GTGCCATGGAGTTGTGGACTTAGAAGGAAA
1 GTGCCACGGAGTTGTGGAC-TTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAA
293857 AAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGA
65 AAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGA
293922 GTGCCACGGAGTTGTGGGCTTAAACGG
130 GTGCCACGGAGTTGTGGGCTTAAACGG
*
293949 GTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAA
1 GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAA
*
294014 AAAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAG
66 AGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAG
294079 TGCCACGGAGTTGTGGGCTTAAACGG
131 TGCCACGGAGTTGTGGGCTTAAACGG
*
294105 GTGCCACGGAATTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAA
1 GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAA
* * *
294170 AGAGTGCCATGGTGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGACTTAGAAGGAAAAAGAG
66 AGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAG
294235 TGCCACGGAGTTGTGGGCTTAAACGG
131 TGCCACGGAGTTGTGGGCTTAAACGG
294261 GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTA
1 GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTA
294317 AAATGGTGCC
Statistics
Matches: 353, Mismatches: 14, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
155 12 0.03
156 341 0.97
ACGTcount: A:0.30, C:0.13, G:0.37, T:0.20
Consensus pattern (156 bp):
GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAA
AGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAG
TGCCACGGAGTTGTGGGCTTAAACGG
Found at i:295723 original size:14 final size:15
Alignment explanation
Indices: 295704--295754 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
295694 CCTTTGCACC
*
295704 TTTTTTGTTTTGTTT
1 TTTTTTGTTTTGATT
295719 TTTTTGTGTTTTG-TT
1 TTTTT-TGTTTTGATT
295734 TTTTTT-TTTTGACTT
1 TTTTTTGTTTTGA-TT
295749 TTTTTT
1 TTTTTT
295755 TACTTTTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.15
14 1 0.03
15 20 0.61
16 7 0.21
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.84
Consensus pattern (15 bp):
TTTTTTGTTTTGATT
Found at i:295723 original size:16 final size:16
Alignment explanation
Indices: 295704--295741 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
295694 CCTTTGCACC
295704 TTTTTTGTTTTGTTTT
1 TTTTTTGTTTTGTTTT
*
295720 TTTTGTGTTTTGTTTT
1 TTTTTTGTTTTGTTTT
295736 TTTTTT
1 TTTTTT
295742 TTGACTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (16 bp):
TTTTTTGTTTTGTTTT
Found at i:295732 original size:21 final size:20
Alignment explanation
Indices: 295706--295744 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
295696 TTTGCACCTT
295706 TTTTGTTTTGTTTTTTTTGTG
1 TTTTGTTTT-TTTTTTTTGTG
295727 TTTTGTTTTTTTTTTTTG
1 TTTTGTTTTTTTTTTTTG
295745 ACTTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (20 bp):
TTTTGTTTTTTTTTTTTGTG
Found at i:302814 original size:52 final size:52
Alignment explanation
Indices: 302666--302794 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
302656 CGAAATATGA
302666 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
302718 AAATTTGCTTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
302770 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
302795 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:302821 original size:13 final size:13
Alignment explanation
Indices: 302803--302827 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
302793 CAAAGATCAG
302803 TGTATCGATACAA
1 TGTATCGATACAA
302816 TGTATCGATACA
1 TGTATCGATACA
302828 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:302894 original size:19 final size:18
Alignment explanation
Indices: 302870--302967 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
302860 TAACTTACAT
302870 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
302889 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
302902 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
302921 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
302934 TGTATTGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
302954 TGTATCGATACAAA
1 TGTATCGATACAAA
302968 TCATTGAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.38
20 12 0.19
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Done.