Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold29
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: 5511024
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 57772 characters in sequence are not A, C, G, or T
File 7 of 34
Found at i:1000263 original size:61 final size:61
Alignment explanation
Indices: 1000165--1000346 Score: 234
Period size: 61 Copynumber: 3.1 Consensus size: 61
1000155 TTAAAGGGCG
* *
1000165 AAAGGAG-AGAGCGTCCTGCTCTTTGAGGACTAAGAAGTGCCAACAACTTGTGTGGGCTTCA
1 AAAGGAGAAG-GCGTCCTGCTCTTTGAGGACTAAGAAGTGCCACCAACTTGTGTGGGCTTTA
** *
1000226 AAAGGAGAAGGCGTCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTATGTGGGCTTTA
1 AAAGGAGAAGGCGTCCTGCTCTTTGAGGACTAAGAAGTGCCACCAACTTGTGTGGGCTTTA
* * *
1000287 AAA-G-GAA----TCCTGCTCTTTGAGGACCAAAAAATGCCACCAACTTGTGTGGGCTTTA
1 AAAGGAGAAGGCGTCCTGCTCTTTGAGGACTAAGAAGTGCCACCAACTTGTGTGGGCTTTA
1000342 AAAGG
1 AAAGG
1000347 CGTCCTACTC
Statistics
Matches: 108, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
55 45 0.42
56 1 0.01
59 3 0.03
60 1 0.01
61 56 0.52
62 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.24
Consensus pattern (61 bp):
AAAGGAGAAGGCGTCCTGCTCTTTGAGGACTAAGAAGTGCCACCAACTTGTGTGGGCTTTA
Found at i:1000323 original size:55 final size:55
Alignment explanation
Indices: 1000178--1000370 Score: 215
Period size: 55 Copynumber: 3.4 Consensus size: 55
1000168 GGAGAGAGCG
* * *
1000178 TCCTGCTCTTTGAGGACTAAGAAGTGCCAACAACTTGTGTGGGCTTCAAAAGGAGAA
1 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA-G-GAA
*** *
1000235 GGCGTCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTATGTGGGCTTTAAAAGGAA
1 ----TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
* * **
1000294 TCCTGCTCTTTGAGGACCAAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
* *
1000349 TCCTACTCTTTAAGGACTAAAA
1 TCCTGCTCTTTGAGGACTAAAA
1000371 GGCGAAAGGA
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
55 66 0.57
59 3 0.03
60 1 0.01
61 46 0.40
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAA
Found at i:1000386 original size:210 final size:212
Alignment explanation
Indices: 1000046--1000562 Score: 750
Period size: 210 Copynumber: 2.4 Consensus size: 212
1000036 ACAAAAAAAA
1000046 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGTGTCCTGCTCTTTGAGGACCAGAAAAGTGC
1 TGCCACCAACTTGTGTGGGCTTTAAAAG-AAAA---GTCCTGCTCTTTGAGGACCA-AAAAGTGC
** * * *
1000111 CATTAACTTGTGTGGGCTTTAAAAGGCATCCTACGCTTTGAGGATTAAAGGGCGAAAGGAGAGAG
61 CACCAACTTGTGTGGGCTTTAAAAGGCATCCTACGCTTTAAGGACTAAAAGGCGAAAGGAGAGAG
*
1000176 CGTCCTGCTCTTTGAGGACTAAGAAGTGCCAACAACTTGTGTGGGCTTCAAAAGGAGAAGGCGTC
126 CGTCCTGCTCTTTGAGGACTAAGAAGTGCCAACAACTTGTGTGGGCTTCAAAAAGAGAAGGCGTC
* *
1000241 CTGCTCTTTGAGGACTGGGAAG
191 CTACTCTTTGAGGACTGGAAAG
* * *
1000263 TGCCACCAACTTATGTGGGCTTTAAAAG-GAA-TCCTGCTCTTTGAGGACCAAAAAATGCCACCA
1 TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGTCCTGCTCTTTGAGGACCAAAAAGTGCCACCA
* *
1000326 ACTTGTGTGGGCTTTAAAAGGCGTCCTACTCTTTAAGGACTAAAAGGCGAAAGGAGAGAGCGTCC
66 ACTTGTGTGGGCTTTAAAAGGCATCCTACGCTTTAAGGACTAAAAGGCGAAAGGAGAGAGCGTCC
* * *
1000391 TGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCGTCCTACT
131 TGCTCTTTGAGGACTAAGAAGTGCCAACAACTTGTGTGGGCTTCAAAAAGAGAAGGCGTCCTACT
1000456 CTTTGAGGACTGGAAAG
196 CTTTGAGGACTGGAAAG
* * * *
1000473 TGCCACCAACCTGTGTGGGCTTTGAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAGGTGCC
1 TGCCACCAACTTGTGTGGGCTTT-AAAAGAAAA---GTCCTGCTCTTTGAGGACCAAAAAGTGCC
*
1000538 ACCAATTTGTGTGGGCTTTAAAAGG
62 ACCAACTTGTGTGGGCTTTAAAAGG
1000563 AAAAGGCATC
Statistics
Matches: 270, Mismatches: 24, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
210 167 0.62
211 24 0.09
212 2 0.01
215 2 0.01
216 48 0.18
217 27 0.10
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (212 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGTCCTGCTCTTTGAGGACCAAAAAGTGCCACCA
ACTTGTGTGGGCTTTAAAAGGCATCCTACGCTTTAAGGACTAAAAGGCGAAAGGAGAGAGCGTCC
TGCTCTTTGAGGACTAAGAAGTGCCAACAACTTGTGTGGGCTTCAAAAAGAGAAGGCGTCCTACT
CTTTGAGGACTGGAAAG
Found at i:1000420 original size:149 final size:153
Alignment explanation
Indices: 1000226--1000501 Score: 409
Period size: 149 Copynumber: 1.8 Consensus size: 153
1000216 GTGGGCTTCA
*
1000226 AAAGGAGAAGGCGTCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTATGTGGGCTTT-AAAA
1 AAAGGAGAAGGCGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTATGTGGGCTTTAAAAA
* *
1000290 G-GAA-TCCTGCTCTTTGAGGACCAAAAAATGCCACCAACTTGTGTGGGCTTT-AAAAGGCGTCC
66 GAGAAGTCCTACTCTTTGAGGACCAAAAAATGCCACCAACCTGTGTGGGCTTTGAAAAGGCGTCC
1000352 TACTCTTTAAGGACTAAAAGGCG
131 TACTCTTTAAGGACTAAAAGGCG
*
1000375 AAAGGAG-AGAGCGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAA
1 AAAGGAGAAG-GCGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTATGTGGGCTTTAAAA
*** *
1000439 AGAGAAGGCGTCCTACTCTTTGAGGACTGGAAAGTGCCACCAACCTGTGTGGGCTTTGAAAAG
65 AGAGAA---GTCCTACTCTTTGAGGACCAAAAAATGCCACCAACCTGTGTGGGCTTTGAAAAG
1000502 AAAAGGCGTC
Statistics
Matches: 111, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
148 2 0.02
149 55 0.50
150 5 0.05
151 3 0.03
155 41 0.37
156 5 0.05
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (153 bp):
AAAGGAGAAGGCGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTATGTGGGCTTTAAAAA
GAGAAGTCCTACTCTTTGAGGACCAAAAAATGCCACCAACCTGTGTGGGCTTTGAAAAGGCGTCC
TACTCTTTAAGGACTAAAAGGCG
Found at i:1000480 original size:61 final size:61
Alignment explanation
Indices: 1000385--1000944 Score: 666
Period size: 61 Copynumber: 9.3 Consensus size: 61
1000375 AAAGGAGAGA
*
1000385 GCGTCCTGCTCTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAG
1 GCGTCCTGCTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAG
* * *
1000446 GCGTCCTACTCTTTGAGGACTGGAAAGTGCCACCAACCTGTGTGGGCTTTGAAAAGAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAG
* * * *
1000507 GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAATTTGTGTGGGCTTTAAAAGGAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAG
* * *
1000568 GCATCCTGCTCTTTGAGGACTGGAAAGTACCACCAACTTGTGTAGGCTTTAAAAAGAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAG
* * * * *
1000629 GCTTCCTGCTCTTTGAGGATTGGAAAGTACCACCAACTTGTGTGGGCTTT-AAAGGAGAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAG
* * *
1000689 GCATCCTGCTCTTTGAGGACT-AAAAGGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAA--GTGCCACCAACTTGTGTGGGCTTTAAAAAG-AAAAG
* * * * *
1000752 GTGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCTGTGTGGGCTTTAAAAGGAAAAA
1 GCGTCCTGCTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAG
* * *
1000814 GCATCCTGCTCTTTGAGGACTGGAAAATGCCACTAACTTGTGTGGGCTTT-----G-AAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAG
* * * * *
1000869 GCATCTTGATCTTTGAGGACT-GAAAGGTGCCACCAACTTGTATGCGCTTT-----G-AAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAG
1000924 GCGTCCTGCTCTTTGAGGACT
1 GCGTCCTGCTCTTTGAGGACT
1000945 AAAGGGTGAA
Statistics
Matches: 440, Mismatches: 51, Indels: 22
0.86 0.10 0.04
Matches are distributed among these distances:
54 4 0.01
55 65 0.15
56 1 0.00
59 3 0.01
60 29 0.07
61 257 0.58
62 27 0.06
63 50 0.11
65 4 0.01
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (61 bp):
GCGTCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAG
Found at i:1000721 original size:183 final size:181
Alignment explanation
Indices: 1000388--1000945 Score: 733
Period size: 183 Copynumber: 3.1 Consensus size: 181
1000378 GGAGAGAGCG
* *
1000388 TCCTGCTCTTTGAGGACTAGG-AAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCGTCC
1 TCCTGCTCTTTGAGGACTAGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATCC
* * *
1000452 TACTCTTTGAGGACTGGAAAGTGCCACCAACCTGTGTGGGCTTTGAAAAGAAAAGGCGTCCTGCT
66 TGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT--AAAG-AAAGGCATCCTGCT
* *
1000517 CTTTGAGGACTAGAAGGTGCCACCAATTTGTGTGGGCTTTAAAAGGAAAAGGCA
128 CTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
* * *
1000571 TCCTGCTCTTTGAGGACT-GGAAAGTACCACCAACTTGTGTAGGCTTTAAAAAGAAAAGGCTTCC
1 TCCTGCTCTTTGAGGACTAGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATCC
* *
1000635 TGCTCTTTGAGGATTGGAAAGTACCACCAACTTGTGTGGGCTTTAAAGGAGAAGGCATCCTGCTC
66 TGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAA-GA-AAGGCATCCTGCTC
* **
1000700 TTTGAGGACTAAAAGGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTG
129 TTTGAGGACTAAAA-GGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCA
* * * *
1000755 TCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACCTGTGTGGGCTTTAAAAGGAAAAAGCATCC
1 TCCTGCTCTTTGAGGACTAGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATCC
* * * *
1000820 TGCTCTTTGAGGACTGGAAAATGCCACTAACTTGTGTGGGCTTT---GAAAGGCATCTTGATCTT
66 TGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAGAAAGGCATCCTGCTCTT
* * * *
1000882 TGAGGACTGAAAGGTGCCACCAACTTGTATGCGCTTT-----G-AAAGGCG
131 TGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1000927 TCCTGCTCTTTGAGGACTA
1 TCCTGCTCTTTGAGGACTA
1000946 AAGGGTGAAA
Statistics
Matches: 337, Mismatches: 32, Indels: 23
0.86 0.08 0.06
Matches are distributed among these distances:
172 25 0.07
179 23 0.07
180 25 0.07
181 6 0.02
182 29 0.09
183 121 0.36
184 29 0.09
185 79 0.23
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (181 bp):
TCCTGCTCTTTGAGGACTAGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATCC
TGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAGAAAGGCATCCTGCTCTT
TGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
Found at i:1002047 original size:8 final size:8
Alignment explanation
Indices: 1002025--1002089 Score: 87
Period size: 8 Copynumber: 7.9 Consensus size: 8
1002015 CTTTTCTCTC
1002025 TTTTCTTTG
1 TTTT-TTTG
1002034 TTTTTTAT-
1 TTTTTT-TG
*
1002042 TTTTTTTA
1 TTTTTTTG
1002050 TTTTTTTG
1 TTTTTTTG
1002058 TTTTTTTG
1 TTTTTTTG
1002066 TTTTTTTG
1 TTTTTTTG
1002074 TTTTTTTTG
1 -TTTTTTTG
1002083 TTTTTTT
1 TTTTTTT
1002090 TAAAAAGTGG
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
7 1 0.02
8 38 0.73
9 13 0.25
ACGTcount: A:0.03, C:0.02, G:0.08, T:0.88
Consensus pattern (8 bp):
TTTTTTTG
Found at i:1002110 original size:1 final size:1
Alignment explanation
Indices: 1002034--1002090 Score: 60
Period size: 1 Copynumber: 57.0 Consensus size: 1
1002024 CTTTTCTTTG
* * * * * *
1002034 TTTTTTATTTTTTTTATTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1002091 AAAAAGTGGG
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.04, C:0.00, G:0.07, T:0.89
Consensus pattern (1 bp):
T
Found at i:1005273 original size:21 final size:21
Alignment explanation
Indices: 1005240--1005280 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1005230 CTAAGTAAAA
1005240 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
1005261 ATAC-TATTAGTATTAATACA
1 ATACGTATT-GTATCAATACA
1005281 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:1005349 original size:20 final size:19
Alignment explanation
Indices: 1005320--1005390 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 19
1005310 ACCCTGAAAA
*
1005320 GTATCAATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
1005340 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
1005359 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
1005380 GTATCGATACA
1 GTATCGATACA
1005391 TGAATAGTGA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 4 0.10
20 34 0.85
21 2 0.05
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:1005473 original size:45 final size:47
Alignment explanation
Indices: 1005385--1005480 Score: 133
Period size: 45 Copynumber: 2.1 Consensus size: 47
1005375 AATATGTATC
* * *
1005385 GATACATGAATAGTGATGAACAGTGATTTTTAACGATACATGAATAGT
1 GATACATGAACAGTGATGAACAGTGA-TTGTAACGATACATGAACAGT
*
1005433 GATACATGAACAGTG-TGAACAGTGA-TGTATCGATACATGAACAGT
1 GATACATGAACAGTGATGAACAGTGATTGTAACGATACATGAACAGT
1005478 GAT
1 GAT
1005481 GAATAGTGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
45 20 0.45
47 10 0.23
48 14 0.32
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.28
Consensus pattern (47 bp):
GATACATGAACAGTGATGAACAGTGATTGTAACGATACATGAACAGT
Found at i:1006116 original size:34 final size:35
Alignment explanation
Indices: 1006053--1006119 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1006043 CTAAGTGATT
1006053 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
1006089 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1006120 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1015990 original size:78 final size:79
Alignment explanation
Indices: 1015796--1015991 Score: 240
Period size: 79 Copynumber: 2.5 Consensus size: 79
1015786 ACGGGGCTAG
* *
1015796 AGTATCCCCGATTATGGAAAATCGATGTTTTAGAAATAAAATCAAGGTTGGAGTATCTCCTCAGA
1 AGTATCCCCGATTATGAAAAATCGATGATTTAGAAATAAAATCAAGGTTGGAGTATCTCCTCAGA
* *
1015861 AATAACAGGGTTGG
66 AATAACAGGGATGA
** * *
1015875 AGTATCCCTAATTAT-AGAAAATC-A-GTATTTTGAAAATAAAATCGAGGTTGGAGTAT-TCCTT
1 AGTATCCCCGATTATGA-AAAATCGATG-ATTTAG-AAATAAAATCAAGGTTGGAGTATCTCC-T
1015936 C-GAAATAACAGGGATGA
62 CAGAAATAACAGGGATGA
*
1015953 AGTATCCCCGATTGTGAAAAATCGATGATTTAGAAATAA
1 AGTATCCCCGATTATGAAAAATCGATGATTTAGAAATAA
1015992 GGCCGGGTTT
Statistics
Matches: 98, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
77 1 0.01
78 46 0.47
79 50 0.51
80 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (79 bp):
AGTATCCCCGATTATGAAAAATCGATGATTTAGAAATAAAATCAAGGTTGGAGTATCTCCTCAGA
AATAACAGGGATGA
Found at i:1016121 original size:130 final size:128
Alignment explanation
Indices: 1015891--1016202 Score: 317
Period size: 130 Copynumber: 2.4 Consensus size: 128
1015881 CCTAATTATA
* * * *
1015891 GAAAATCAGTATTTT-GAAAATAAAATCGAGGTTGGAGTATTCCTTCGAAATAACAGGGATGAAG
1 GAAAATCAGTATTTTAG-AAAT-AAATTGGGGTTGGAGTATCCCCTCGAAATAACAGGGATGAAG
* ** *
1015955 TATCCCCGATTGTGAAAAATCGATGATTTAGAAATAAGGCCGG-GTTTGAAGTATCCTCGATTGT
64 TATCCCCGATTATGAAAAATCGATGATTTAGAAATAAAACCGGAG-TTGAAGTATCCCCGATTGT
1016019 -
128 G
* * * * *
1016019 GAGAAATCAATATTTTAGAAATAAAGTTGGGGTTAGAGTATCCCCTCAGAAATAACGGGGTTGGA
1 GA-AAATCAGTATTTTAGAAATAAA-TTGGGGTTGGAGTATCCCCTC-GAAATAACAGGGATGAA
* * * * ** *
1016084 GTATCCCCGATTATGAGAAATTGGTG-TTTTGAAAATAAAATTGGAGTTGGAGTATCCCCGATTG
63 GTATCCCCGATTATGAAAAATCGATGATTTAG-AAATAAAACCGGAGTTGAAGTATCCCCGATTG
1016148 TG
127 TG
** *
1016150 GAAAATTGGTATTTTAGAAATAAATTGGGGTTGGAGTATCCCCTTGGAAATAA
1 GAAAATCAGTATTTTAGAAATAAATTGGGGTTGGAGTATCCCC-TCGAAATAA
1016203 TGGAATTTGA
Statistics
Matches: 151, Mismatches: 25, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
128 5 0.03
129 61 0.40
130 82 0.54
131 3 0.02
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (128 bp):
GAAAATCAGTATTTTAGAAATAAATTGGGGTTGGAGTATCCCCTCGAAATAACAGGGATGAAGTA
TCCCCGATTATGAAAAATCGATGATTTAGAAATAAAACCGGAGTTGAAGTATCCCCGATTGTG
Found at i:1016141 original size:51 final size:50
Alignment explanation
Indices: 1016078--1016192 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 50
1016068 AAATAACGGG
*
1016078 GTTGGAGTATCCCCGATTAT-GAGAAATTGGTGTTTT-GAAAATAAAATTGGA
1 GTTGGAGTATCCCCGATTATGGA-AAATTGGTATTTTAG-AAAT-AAATTGGA
* *
1016129 GTTGGAGTATCCCCGATTGTGGAAAATTGGTATTTTAGAAATAAATTGGG
1 GTTGGAGTATCCCCGATTATGGAAAATTGGTATTTTAGAAATAAATTGGA
1016179 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
1016193 TTGGAAATAA
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
50 21 0.36
51 35 0.59
52 3 0.05
ACGTcount: A:0.30, C:0.10, G:0.27, T:0.33
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTATGGAAAATTGGTATTTTAGAAATAAATTGGA
Found at i:1022895 original size:28 final size:27
Alignment explanation
Indices: 1022841--1022910 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 27
1022831 AATAAAGCCG
** **
1022841 GGGTTGGAGTATCCCCTCGGAGGTAAC
1 GGGTTGGAGTATCCCCGAGGAAATAAC
*
1022868 AGGGTTGGAGTATCCCCGATGAAATAAC
1 -GGGTTGGAGTATCCCCGAGGAAATAAC
1022896 GAGGTTGGAGTATCC
1 G-GGTTGGAGTATCC
1022911 TCAATTGTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
27 1 0.03
28 35 0.97
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.23
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCGAGGAAATAAC
Found at i:1022902 original size:107 final size:108
Alignment explanation
Indices: 1022765--1022995 Score: 293
Period size: 108 Copynumber: 2.1 Consensus size: 108
1022755 AAAATTGGGA
*** *
1022765 TTGGAGTATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCAATTATGAGAAATCAAT-ATTTTG
1 TTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATGATTTTG
* * * *
1022829 GGAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGTAACAGGG
66 GAAATAAAACCGGAGTTGGAGTATCCCCTCGGAGATAACAGGG
* * *** *
1022872 TTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCAATTGTGAAAAATTGGTGTTTTTG
1 TTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATGATTTTG
* * *
1022937 GAAATAAAATCGTAGTTGGAGTATCCCCTCGGAGATAACGGGG
66 GAAATAAAACCGGAGTTGGAGTATCCCCTCGGAGATAACAGGG
*
1022980 TTGGAGTATCCTCGAT
1 TTGGAGTATCCCCGAT
1022996 TATGAGAAAT
Statistics
Matches: 105, Mismatches: 18, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
107 49 0.47
108 56 0.53
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (108 bp):
TTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATGATTTTG
GAAATAAAACCGGAGTTGGAGTATCCCCTCGGAGATAACAGGG
Found at i:1023000 original size:187 final size:183
Alignment explanation
Indices: 1022748--1023145 Score: 516
Period size: 187 Copynumber: 2.2 Consensus size: 183
1022738 AAATCGATGA
*
1022748 TTAGAAA-AAAATTGG-GATTGGAGTATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCAATTA
1 TTAGAAATAAAATCGGAG-TTGGAGTATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCAATTA
* * * ** *
1022811 TGAGAAATCAATATTTTGGGAATAAAGCC-GGGGTTGGAGTATCCCCTCGGAGGTAACAGGGTTG
65 TGAGAAATCAATATTTTAGAAATAAAGCCGGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTA
* * *
1022875 GAGTATCCCCGATGAAATAAC-GAGGTTGGAGTATCCTCAATTGTGAAAAATTGGTGTTT
130 GAGTATCCCCCATG-AATAACAG-GGTTGGAGTATCCCCAA---TGAAAAATTGATG-TT
* * * * * *
1022934 TTGGAAATAAAATCGTAGTTGGAGTATCCCCTCGGAGATAACGGGGTTGGAGTATCCTCGATTAT
1 TTAGAAATAAAATCGGAGTTGGAGTATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCAATTAT
* * *
1022999 GAGAAATTAATTTTTTAGAAATAAAGCCGGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTAG
66 GAGAAATCAATATTTTAGAAATAAAGCCGGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTAG
* *
1023064 AGTATCCCCCATGATTAACAGGGTTGGAGTATCCCCGATGAAAAATTGATGTT
131 AGTATCCCCCATGAATAACAGGGTTGGAGTATCCCCAATGAAAAATTGATGTT
1023117 TTAGAAATAAAATCGGAGTTGGAGTATCC
1 TTAGAAATAAAATCGGAGTTGGAGTATCC
1023146 ACGATTATAG
Statistics
Matches: 185, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
183 29 0.16
184 12 0.06
186 6 0.03
187 93 0.50
188 45 0.24
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (183 bp):
TTAGAAATAAAATCGGAGTTGGAGTATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCAATTAT
GAGAAATCAATATTTTAGAAATAAAGCCGGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTAG
AGTATCCCCCATGAATAACAGGGTTGGAGTATCCCCAATGAAAAATTGATGTT
Found at i:1023006 original size:80 final size:80
Alignment explanation
Indices: 1022871--1023070 Score: 231
Period size: 80 Copynumber: 2.5 Consensus size: 80
1022861 AGGTAACAGG
*** * * **
1022871 GTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCAATTGTGAAAAATTGGTGTTTTT
1 GTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCTCAATTATGAAAAATTAAT-TTTTT
* * *
1022936 GGAAATAAAATC-GTA
65 AGAAATAAAACCGGGA
* * *
1022951 GTTGGAGTATCCCCTCGGAGATAACGGGGTTGGAGTATCCTCGATTATGAGAAATTAATTTTTTA
1 GTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCTCAATTATGAAAAATTAATTTTTTA
* *
1023016 GAAATAAAGCCGGGG
66 GAAATAAAACCGGGA
* *
1023031 GTTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCC
1 GTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCC
1023071 CCCATGATTA
Statistics
Matches: 101, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
79 14 0.14
80 87 0.86
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (80 bp):
GTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCTCAATTATGAAAAATTAATTTTTTA
GAAATAAAACCGGGA
Found at i:1023093 original size:27 final size:27
Alignment explanation
Indices: 1023029--1023105 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 27
1023019 ATAAAGCCGG
* *
1023029 GGGTTGGAGTATCCCCTCGA-AAATAACG
1 GGGTTGGAGTATCCCC-C-ATGAATAACA
* *
1023057 GGGTTAGAGTATCCCCCATGATTAACA
1 GGGTTGGAGTATCCCCCATGAATAACA
*
1023084 GGGTTGGAGTATCCCCGATGAA
1 GGGTTGGAGTATCCCCCATGAA
1023106 AAATTGATGT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
26 1 0.02
27 25 0.61
28 15 0.37
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCCATGAATAACA
Found at i:1023169 original size:51 final size:51
Alignment explanation
Indices: 1023105--1023202 Score: 130
Period size: 51 Copynumber: 1.9 Consensus size: 51
1023095 TCCCCGATGA
1023105 AAAATTGATGTTTT-AGAAATAAAATCGGAGTT-GGAGTATCCACGATTATAG
1 AAAATTGATGTTTTGA-AAATAAAATCGGAGTTGGGA-TATCCACGATTATAG
* *
1023156 AAAATT-AGTGTTTTGAAAATGAAATCGGAGTTGGGATATCCCCGATT
1 AAAATTGA-TGTTTTGAAAATAAAATCGGAGTTGGGATATCCACGATT
1023203 GCGGAGAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
50 1 0.02
51 37 0.88
52 4 0.10
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (51 bp):
AAAATTGATGTTTTGAAAATAAAATCGGAGTTGGGATATCCACGATTATAG
Found at i:1024964 original size:10 final size:11
Alignment explanation
Indices: 1024938--1024966 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1024928 TGGAATAGTA
1024938 TTTTTTTGTGT
1 TTTTTTTGTGT
1024949 TTTTTTTGT-T
1 TTTTTTTGTGT
1024959 TTTTTTTG
1 TTTTTTTG
1024967 CTAAAGGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (11 bp):
TTTTTTTGTGT
Found at i:1025516 original size:34 final size:33
Alignment explanation
Indices: 1025478--1025543 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 33
1025468 AACTTCCTAG
* *
1025478 ATGTATCAATACAAAGAATAGATGTATCGATACA
1 ATGTACCAATACAAAGAA-AAATGTATCGATACA
* *
1025512 ATGTACCGATACACAGAAAAATGTATCGATAC
1 ATGTACCAATACAAAGAAAAATGTATCGATAC
1025544 GTTTCCTTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 13 0.46
34 15 0.54
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.24
Consensus pattern (33 bp):
ATGTACCAATACAAAGAAAAATGTATCGATACA
Found at i:1025600 original size:19 final size:18
Alignment explanation
Indices: 1025576--1025672 Score: 70
Period size: 19 Copynumber: 5.8 Consensus size: 18
1025566 AGCGATACAT
1025576 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1025595 TGTATCGATAC---C-T-
1 TGTATCGATACAAACTTA
*
1025608 TGTATTGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
1025627 TATATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
1025640 TGTATCGATACAACATTTA
1 TGTATCGATACAA-ACTTA
1025659 TGTATCGATACAAA
1 TGTATCGATACAAA
1025673 TCGCTGAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 25
0.68 0.04 0.27
Matches are distributed among these distances:
13 20 0.32
14 2 0.03
15 1 0.02
16 2 0.03
17 1 0.02
18 3 0.05
19 33 0.53
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1025611 original size:32 final size:32
Alignment explanation
Indices: 1025568--1025670 Score: 161
Period size: 32 Copynumber: 3.2 Consensus size: 32
1025558 AGCTTCCTAG
*
1025568 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
* * *
1025600 CGATACCTTGTATTGATACAACACTTATATAT
1 CGATACATTGTATCGATACAACACTTATGTAT
*
1025632 CGATACATTGTATCGATACAACATTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1025664 CGATACA
1 CGATACA
1025671 AATCGCTGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 63 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:1025751 original size:21 final size:21
Alignment explanation
Indices: 1025727--1025784 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
1025717 ACATTAGTAG
*
1025727 AATGTATTGATACATTCCACA
1 AATGTATCGATACATTCCACA
*
1025748 AATGTATCGATACATTCTACA
1 AATGTATCGATACATTCCACA
1025769 AATGTATCGATACATT
1 AATGTATCGATACATT
1025785 TGGATAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.34
Consensus pattern (21 bp):
AATGTATCGATACATTCCACA
Found at i:1030556 original size:3 final size:3
Alignment explanation
Indices: 1030548--1030588 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
1030538 CGAGTCAACT
*
1030548 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCT TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1030589 TTTGATGGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.29, C:0.34, G:0.00, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:1031917 original size:34 final size:34
Alignment explanation
Indices: 1031845--1031911 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 34
1031835 GGTGTTTGTG
*
1031845 GAAAGAATAAGCACAAAGGAATACAAATGAGCTCT
1 GAAAGAATAAGCACAAAGAAATACAAA-GAGCTCT
1031880 GAAAGAATAA-CAACAAA-AAATACAAA-AGCTCT
1 GAAAGAATAAGC-ACAAAGAAATACAAAGAGCTCT
1031912 TTGAAATGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 6 0.20
34 9 0.30
35 15 0.50
ACGTcount: A:0.57, C:0.15, G:0.15, T:0.13
Consensus pattern (34 bp):
GAAAGAATAAGCACAAAGAAATACAAAGAGCTCT
Found at i:1032279 original size:19 final size:20
Alignment explanation
Indices: 1032251--1032300 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1032241 CTTTTTAAGG
* *
1032251 TGTATGGATACTATG-AACA
1 TGTATCGATACTAAGCAACA
*
1032270 TGTATCGATACTAAGCAATA
1 TGTATCGATACTAAGCAACA
1032290 TGTATCGATAC
1 TGTATCGATAC
1032301 ATCTGGGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
TGTATCGATACTAAGCAACA
Found at i:1035980 original size:11 final size:11
Alignment explanation
Indices: 1035959--1036018 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 11
1035949 ATTAGTTTAA
1035959 AAAAGAAGAGAG
1 AAAA-AAGAGAG
1035971 AAAAAAGAGAAGG
1 AAAAAAGAG-A-G
*
1035984 AAAAGAA-AGAA
1 AAAA-AAGAGAG
1035995 AAAAAAGA-AG
1 AAAAAAGAGAG
*
1036005 AAAATAGAGAG
1 AAAAAAGAGAG
1036016 AAA
1 AAA
1036019 GTTAAAATAC
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
10 10 0.25
11 15 0.38
12 6 0.15
13 7 0.17
14 2 0.05
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (11 bp):
AAAAAAGAGAG
Found at i:1035994 original size:22 final size:22
Alignment explanation
Indices: 1035964--1036018 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1035954 TTTAAAAAAG
* *
1035964 AAGAGAGAAAAAAGAGAAGGAA
1 AAGAGAGAAAAAAAAGAAGAAA
*
1035986 AAGAAAGAAAAAAAAGAAGAAA
1 AAGAGAGAAAAAAAAGAAGAAA
1036008 ATAGAGAGAAA
1 A-AGAGAGAAA
1036019 GTTAAAATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (22 bp):
AAGAGAGAAAAAAAAGAAGAAA
Found at i:1038346 original size:13 final size:13
Alignment explanation
Indices: 1038328--1038357 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1038318 ATACATTATT
1038328 CATTGTATCAATA
1 CATTGTATCAATA
*
1038341 CATTGTATCGATA
1 CATTGTATCAATA
1038354 CATT
1 CATT
1038358 CTGGGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTGTATCAATA
Found at i:1040764 original size:79 final size:77
Alignment explanation
Indices: 1040630--1040852 Score: 229
Period size: 79 Copynumber: 2.8 Consensus size: 77
1040620 TCTTCATCTC
* *
1040630 GGGGATAGTCCAACCCC-AGTTTTATTTCC-AAAACATCCATTTTTCATAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCGA-TTTTA-TTCCTAAAACA-CCATTTTTCACAATCGGGGATACTCCA
*
1040693 ATTCC-ATTATTT-TCGA
63 A--CCTATCATTTCT-GA
* *
1040709 GGGGATACTCTAACCCCGATTTTATTCCTAAAACACCAGTTTTTCACAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTCCTAAAACACCA-TTTTTCACAATCGGGGATACTCCAAC
1040774 CTATCATTTCTGA
65 CTATCATTTCTGA
* * ** * * *
1040787 AGGGATACTCCAACCCTCGGTTTTATTTTTGAAACACCAATTTTCCACAATCGGTGATACTCCAA
1 GGGGATACTCCAACCC-CGATTTTATTCCTAAAACACC-ATTTTTCACAATCGGGGATACTCCAA
1040852 C
64 C
1040853 TCTGATTTTA
Statistics
Matches: 123, Mismatches: 14, Indels: 14
0.81 0.09 0.09
Matches are distributed among these distances:
77 2 0.02
78 29 0.24
79 90 0.73
80 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (77 bp):
GGGGATACTCCAACCCCGATTTTATTCCTAAAACACCATTTTTCACAATCGGGGATACTCCAACC
TATCATTTCTGA
Found at i:1040873 original size:51 final size:52
Alignment explanation
Indices: 1040789--1040904 Score: 155
Period size: 51 Copynumber: 2.2 Consensus size: 52
1040779 ATTTCTGAAG
* ***
1040789 GGATACTCCAACCCTCGGTTTTATTTTTGAAACACCAATTTTCCACAATCG-
1 GGATACTCCAACCCTCGATTTTATTTCCAAAACACCAATTTTCCACAATCGA
* *
1040840 GTGATACTCCAACTCT-GATTTTATTTCCAAAACACCAATTTTTCACAATCGA
1 G-GATACTCCAACCCTCGATTTTATTTCCAAAACACCAATTTTCCACAATCGA
1040892 GGATACTCCAACC
1 GGATACTCCAACC
1040905 TCGTTATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
51 42 0.75
52 14 0.25
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.32
Consensus pattern (52 bp):
GGATACTCCAACCCTCGATTTTATTTCCAAAACACCAATTTTCCACAATCGA
Found at i:1040924 original size:28 final size:28
Alignment explanation
Indices: 1040892--1040963 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
1040882 TCACAATCGA
*
1040892 GGATACTCCAACCTCGTTA-TTTC-ATTGG
1 GGATACTCCAACCTCGCTATTTTCGA--GG
*
1040920 GGATACTCCAACCCCGCTATTTTCGAGG
1 GGATACTCCAACCTCGCTATTTTCGAGG
*
1040948 AGATACTCCAACCTCG
1 GGATACTCCAACCTCG
1040964 GCTTTATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 33 0.87
29 4 0.11
30 1 0.03
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.28
Consensus pattern (28 bp):
GGATACTCCAACCTCGCTATTTTCGAGG
Found at i:1041132 original size:79 final size:78
Alignment explanation
Indices: 1041035--1041217 Score: 208
Period size: 79 Copynumber: 2.3 Consensus size: 78
1041025 TAAAGCATCG
* * *
1041035 ATTTTTCACAATCGGGGATACTCCGACTCC-GTTATTTTCGAA-GGGATACTCCAACCCCGATTT
1 ATTTTCCATAATC-GGGATACTCCAAC-CCAGTTA-TTTCGAAGGGGATACTCCAACCCCGATTT
* *
1041098 TATTTTCAAAATACCA
63 TATTTCCAAAACACCA
* * * *
1041114 ATTTTCTATAATCAGGGATACTCCAACCCAGTTATTTCTAAGGGGATACTCCAACCTCGGTTTTA
1 ATTTTCCATAATC-GGGATACTCCAACCCAGTTATTTCGAAGGGGATACTCCAACCCCGATTTTA
* *
1041179 TTTCCAAAACATCG
65 TTTCCAAAACACCA
1041193 ATTTTCCATAATCGAGGATACTCCA
1 ATTTTCCATAATCG-GGATACTCCA
1041218 GCCCCGTTGT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
78 9 0.10
79 79 0.90
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.33
Consensus pattern (78 bp):
ATTTTCCATAATCGGGATACTCCAACCCAGTTATTTCGAAGGGGATACTCCAACCCCGATTTTAT
TTCCAAAACACCA
Found at i:1046883 original size:49 final size:49
Alignment explanation
Indices: 1046714--1047292 Score: 636
Period size: 49 Copynumber: 11.8 Consensus size: 49
1046704 TGAGAAGAAC
* * * ** *
1046714 GCCAATGTGCTGATTCAAGGCCAACGACATTGGGTTTCAAAGATGATGAAGGC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--AA-A-GATGAAGGT
* * * * *
1046767 GTCAAAATGCTGATTCAAGGCTAGCGATTTTGGACTTAAAGAT-AAGAT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGT
*
1046815 GCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGT
* * *
1046864 GCCAATGTGCTGATTCAAGGCTAGCGACATTGGTAC-TAAAGATGAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGG-ACTTAAAGATGAAGGT
* * *
1046913 GCCAATATGCTGATTCAAGGCCAGCGACATTGGTAC-TAAAGATAAATGT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGG-ACTTAAAGATGAAGGT
* * *
1046962 GCCAATATGCTGATTCAAGGCTAGCGATATTGGTCTTAAAGATAAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGT
* *
1047011 GCCAATATGCTAATTCAAGGCCAGCGATATTGGTCTTAAAGATGAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGT
* * * * *
1047060 GCCAATATGTTGATTCAAGGCCAACGATATTAGTCTTAAAAATGAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGT
* * * *
1047109 GCCAATATGCTGATTCACGGCTAGCGACATTGGACTTAAAGATGACAAAGGC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGGT
* *
1047161 GCCAATATTCTGATTCAAGGCCAACGATATTGGACTT----A--AAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGT
* * * ** *
1047204 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGT
* *
1047253 ACCAATATGCTGATTCAAGGCCAGCGATATTGGATTTAAA
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1047293 AGAAGACGCC
Statistics
Matches: 453, Mismatches: 61, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
43 36 0.08
47 1 0.00
48 43 0.09
49 304 0.67
50 3 0.01
51 2 0.00
52 36 0.08
53 28 0.06
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (49 bp):
GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGT
Found at i:1047217 original size:43 final size:43
Alignment explanation
Indices: 1047155--1047292 Score: 132
Period size: 43 Copynumber: 3.1 Consensus size: 43
1047145 TAAAGATGAC
* *
1047155 AAAGGCGCCAATATTCTGATTCAAGGCCAACGATATTGGACTT
1 AAAGGCGCCAATATGCTGATTCAAGGCCAACGACATTGGACTT
* * * *
1047198 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
1 AAAGGCGCCAATATGCTGATTCAAGGCCAACGACATTGGACTT
* * * *
1047241 AAAGACAAAGGCACCAATATGCTGATTCAAGGCCAGCGATATTGGATTT
1 ------AAAGGCGCCAATATGCTGATTCAAGGCCAACGACATTGGACTT
1047290 AAA
1 AAA
1047293 AGAAGACGCC
Statistics
Matches: 77, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
43 40 0.52
49 37 0.48
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (43 bp):
AAAGGCGCCAATATGCTGATTCAAGGCCAACGACATTGGACTT
Found at i:1047405 original size:33 final size:32
Alignment explanation
Indices: 1047358--1047995 Score: 445
Period size: 33 Copynumber: 19.5 Consensus size: 32
1047348 TTTTGAAGGT
* * *
1047358 TGCCACTGACTTGTGGGCTTAAAAGGAGAAAGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA-AAAGA
** *
1047391 TGCCATAGAGTTGTGGACTTAAAAGGAACAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGGAA-AAGA
* * *
1047424 TGCCACGGAGTTGTGGGCTTTAAAAGGGGAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAA--GGAAAAGA
** * * *
1047459 TGCCACAAAGTCGTGGATTTAAAAGGAAAAAAA
1 TGCCACGGAGTTGTGGACTTAAAAGG-AAAAGA
*
1047492 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGGAA-AAGA
* * *
1047525 TGCCACGGAGTTGTGGGCTTTAAAAGGGGAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAA--GGAAAAGA
* * *
1047560 TGCCACAGAGTCGTCGACTTAAAAGGAAAAAGA
1 TGCCACGGAGTTGTGGACTTAAAAGG-AAAAGA
*
1047593 TGCCACAGAGTTGTGGACTTAAAAGG----G-
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAGA
* * *
1047620 TGCCATGGAGTTATGGACTTAAAAGGAACAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGGAA-AAGA
* * *
1047653 TGCCACGGAGTTGTGGGCTTTAAAAGGGGAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAA--GGAAAAGA
* **
1047688 TGCCACAGAGTCATGGACTTAAAAGGAAAAAGA
1 TGCCACGGAGTTGTGGACTTAAAAGG-AAAAGA
1047721 TGCCACGGAGTTGTGGACTTAAAAGGAATAA-A
1 TGCCACGGAGTTGTGGACTTAAAAGGAA-AAGA
* *
1047753 GTGCCACGGAGTTGTGGACTTAAAATGAACAAGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGAA-AAGA
* * * *
1047787 TGCCACGGAGTGGTGGGCTTTAAAAAGAAAAGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGAAAAGA
* **
1047820 TGCCACGGAGTTGTGGGCTTTGAA-GAAAAGA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAGA
** ** * * *
1047851 TGCCACTAAGTCATGGGCTT---TGGAAAGTGA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAA-AGA
** * **
1047881 TGCCACTAAGTCGTGGACTTTGAA-GAAAAGA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAGA
* * *
1047912 -GCACCACAGAGTTGTGGGCTTTAAAGGAAAAAGA
1 TG--CCACGGAGTTGTGGACTTAAAAGG-AAAAGA
*
1047946 GTGCCACGGAGTTGTGGACTTAAAAAGAAAAAGA
1 -TGCCACGGAGTTGTGGACTT-AAAAGGAAAAGA
*
1047980 TGCCACGGACTTGTGG
1 TGCCACGGAGTTGTGG
1047996 GCTTTTGGAG
Statistics
Matches: 490, Mismatches: 79, Indels: 72
0.76 0.12 0.11
Matches are distributed among these distances:
27 23 0.05
28 1 0.00
29 4 0.01
30 21 0.04
31 24 0.05
32 38 0.08
33 239 0.49
34 73 0.15
35 54 0.11
36 13 0.03
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.20
Consensus pattern (32 bp):
TGCCACGGAGTTGTGGACTTAAAAGGAAAAGA
Found at i:1047508 original size:101 final size:99
Alignment explanation
Indices: 1047370--1047995 Score: 516
Period size: 101 Copynumber: 6.4 Consensus size: 99
1047360 CCACTGACTT
* * *
1047370 GTGGGCTTAAAAGGAGAAAGATGCCATAGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGT
1 GTGGACTTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTTAAAAGGAA-AAGGTGCCACGGAGT
* *
1047435 TGTGGGCTTTAAAAGGGGAA-AGGGTGCCACAAAGTC
65 TGTGGGCTTTAAAA--GGAACAAGGTGCCACAGAGTC
* * *
1047471 GTGGATTTAAAAGGAAAAAAATGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGT
1 GTGGACTTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTTAAAAGGAA-AAGGTGCCACGGAGT
*
1047536 TGTGGGCTTTAAAAGGGGAA-AGGGTGCCACAGAGTC
65 TGTGGGCTTTAAAA--GGAACAAGGTGCCACAGAGTC
* *
1047572 GTCGACTTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTTAAAA-G----GGTGCCATGGAGTT
1 GTGGACTTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTTAAAAGGAAAAGGTGCCACGGAGTT
* * * *
1047632 ATGGAC-TTAAAAGGAACAAGGTGCCACGGAGTT
66 GTGGGCTTTAAAAGGAACAAGGTGCCACAGAGTC
* * * * ** *
1047665 GTGGGCTTTAAAAGGGGAAAGGGTGCCACAGAGTCATGGACTTAAAAGGAAAAAGATGCCACGGA
1 GTGGAC-TTAAAA-GGAAAAAGATGCCACAGAGTTGTGGACTTAAAAGG-AAAAGGTGCCACGGA
* * * * *
1047730 GTTGTGGAC-TTAAAAGGAATAAAGTGCCACGGAGTT
63 GTTGTGGGCTTTAAAAGGAACAAGGTGCCACAGAGTC
* * * * * * *
1047766 GTGGACTTAAAATGAACAAGGTGCCACGGAGTGGTGGGCTTTAAAAAGAAAAGGTGCCACGGAGT
1 GTGGACTTAAAAGGAAAAAGATGCCACAGAGTTGTGGAC-TTAAAAGGAAAAGGTGCCACGGAGT
* *
1047831 TGTGGGCTTT-GAA-GAA-AAGATGCCACTA-AGTC
65 TGTGGGCTTTAAAAGGAACAAGGTGCCAC-AGAGTC
* * * ** * ** ** *
1047863 ATGGGCTT---TGGAAAGTGATGCCACTA-AGTCGTGGACTTTGAA-GAAAAGAGCACCACAGAG
1 GTGGACTTAAAAGGAAAAAGATGCCAC-AGAGTTGTGGACTTAAAAGGAAAAG-GTGCCACGGAG
* * *
1047923 TTGTGGGCTTT-AAAGGAAAAAGAGTGCCACGGAGTT
64 TTGTGGGCTTTAAAAGGAACAAG-GTGCCACAGAGTC
* * *
1047959 GTGGACTTAAAAAGAAAAAGATGCCACGGACTTGTGG
1 GTGGACTTAAAAGGAAAAAGATGCCACAGAGTTGTGG
1047996 GCTTTTGGAG
Statistics
Matches: 428, Mismatches: 75, Indels: 46
0.78 0.14 0.08
Matches are distributed among these distances:
92 10 0.02
93 42 0.10
94 33 0.08
95 48 0.11
96 16 0.04
97 17 0.04
98 3 0.01
99 61 0.14
100 16 0.04
101 182 0.43
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.20
Consensus pattern (99 bp):
GTGGACTTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTTAAAAGGAAAAGGTGCCACGGAGTT
GTGGGCTTTAAAAGGAACAAGGTGCCACAGAGTC
Found at i:1047624 original size:27 final size:27
Alignment explanation
Indices: 1047593--1047645 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1047583 AGGAAAAAGA
*
1047593 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACAGAGTTATGGACTTAAAAGGG
**
1047620 TGCCATGGAGTTATGGACTTAAAAGG
1 TGCCACAGAGTTATGGACTTAAAAGG
1047646 AACAAGGTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.32, T:0.25
Consensus pattern (27 bp):
TGCCACAGAGTTATGGACTTAAAAGGG
Found at i:1047652 original size:128 final size:129
Alignment explanation
Indices: 1047492--1047811 Score: 525
Period size: 128 Copynumber: 2.4 Consensus size: 129
1047482 AGGAAAAAAA
1047492 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGGAAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGGAAA
*
1047557 GGGTGCCACAGAGTCGTCGACTTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTTAAAAGG-G
66 GGGTGCCACAGAGTCATCGACTTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTTAAAAGGAG
* *
1047620 TGCCATGGAGTTATGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGGAAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGGAAA
* *
1047685 GGGTGCCACAGAGTCATGGACTTAAAAGGAAAAAGATGCCACGGAGTTGTGGACTTAAAAGGAAT
66 GGGTGCCACAGAGTCATCGACTTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTTAAAAGG---
1047750 AAAG
128 --AG
* *
1047754 TGCCACGGAGTTGTGGACTTAAAATGAACAAGGTGCCACGGAGTGGTGGGCTTTAAAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAA
1047812 AGAAAAGGTG
Statistics
Matches: 177, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
128 122 0.69
134 55 0.31
ACGTcount: A:0.33, C:0.14, G:0.33, T:0.20
Consensus pattern (129 bp):
TGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGGAAA
GGGTGCCACAGAGTCATCGACTTAAAAGGAAAAAGATGCCACAGAGTTGTGGACTTAAAAGGAG
Found at i:1047966 original size:66 final size:66
Alignment explanation
Indices: 1047358--1048000 Score: 350
Period size: 68 Copynumber: 9.8 Consensus size: 66
1047348 TTTTGAAGGT
* * * ** * * *
1047358 TGCCACTGACTTGTGGGCTTAAAAGGAGAAAGATG-CCATAGAGTTGTGGACTTAAAAGGAACAA
1 TGCCACGGAGTTGTGGACTTAAAAGGA-AAAGA-GACCACGGAGTTGTGGGCTTTAAAGGAAAAA
1047422 G-G
64 GAG
* * * * ** * *
1047424 TGCCACGGAGTTGTGGGCTTTAAAAGGGGAAAGGGTGCCACAAAGTCGT-GGATTTAAAAGGAAA
1 TGCCACGGAGTTGTGGAC-TTAAAA-GGAAAAGAG-ACCACGGAGTTGTGGGCTTT-AAAGGAAA
*
1047488 AA-AA
62 AAGAG
* **
1047492 TGCCACGGAGTTGTGGACTTAAAAGGAACAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGGGAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAA-AAGAG-ACCACGGAGTTGTGGGCTTT-AAAGGAAAA
*
1047556 AGGG
63 AGAG
* * * * *
1047560 TGCCACAGAGTCGTCGACTTAAAAGGAAAA-AGATGCCACAGAGTTGTGGAC-TT------AAAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAGAGA--CCACGGAGTTGTGGGCTTTAAAGGAAAAA
*
1047617 GGG
64 GAG
* * * **
1047620 TGCCATGGAGTTATGGACTTAAAAGGAACAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGGGAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAA-AAGAG-ACCACGGAGTTGTGGGCTTT-AAAGGAAAA
*
1047684 AGGG
63 AGAG
* ** * * *
1047688 TGCCACAGAGTCATGGACTTAAAAGGAAAA-AGATGCCACGGAGTTGTGGACTTAAAAGGAATAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAGAGA--CCACGGAGTTGTGGGCTTTAAAGGAAAAA
1047752 -AG
64 GAG
* * * *
1047754 TGCCACGGAGTTGTGGACTTAAAATGAACAAG-GTGCCACGGAGTGGTGGGCTTTAAA-AAGAAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAA-AAGAG-ACCACGGAGTTGTGGGCTTTAAAGGA-AAA
1047817 AG-G
63 AGAG
* ** ** ** **
1047820 TGCCACGGAGTTGTGGGCTTTGAA-GAAAAGATG-CCACTAAGTCATGGGCTTT---GGAAAGTG
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAGA-GACCACGGAGTTGTGGGCTTTAAAGGAAAAAG
1047880 A-
65 AG
** * ** *
1047881 TGCCACTAAGTCGTGGACTTTGAA-GAAAAGAGCACCACAGAGTTGTGGGCTTTAAAGGAAAAAG
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAGAG-ACCACGGAGTTGTGGGCTTTAAAGGAAAAAG
1047945 AG
65 AG
* *
1047947 TGCCACGGAGTTGTGGACTTAAAAAGAAAA-AGATGCCACGGACTTGTGGGCTTT
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAGAGA--CCACGGAGTTGTGGGCTTT
1048001 TGGAGGTTGT
Statistics
Matches: 448, Mismatches: 85, Indels: 87
0.72 0.14 0.14
Matches are distributed among these distances:
60 44 0.10
61 35 0.08
62 16 0.04
64 18 0.04
65 12 0.03
66 123 0.27
67 76 0.17
68 124 0.28
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.20
Consensus pattern (66 bp):
TGCCACGGAGTTGTGGACTTAAAAGGAAAAGAGACCACGGAGTTGTGGGCTTTAAAGGAAAAAGA
G
Found at i:1049488 original size:33 final size:32
Alignment explanation
Indices: 1049451--1049530 Score: 81
Period size: 33 Copynumber: 2.4 Consensus size: 32
1049441 ATCTGGACCC
* **
1049451 TTTTTGTTGTTGTTTTTTTGTTTGTTTGTTTG
1 TTTTTTTTGTTGTTTTTTTGTGCGTTTGTTTG
* *
1049483 TTTTTTTT-TTCATTTTTTTTGTGCGTTTGTTTT
1 TTTTTTTTGTT--GTTTTTTTGTGCGTTTGTTTG
1049516 TTTTTTATTGTTGTT
1 TTTTTT-TTGTTGTT
1049531 GTTGTTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
31 2 0.05
32 7 0.18
33 25 0.66
34 2 0.05
35 2 0.05
ACGTcount: A:0.03, C:0.03, G:0.16, T:0.79
Consensus pattern (32 bp):
TTTTTTTTGTTGTTTTTTTGTGCGTTTGTTTG
Found at i:1049544 original size:29 final size:30
Alignment explanation
Indices: 1049472--1049544 Score: 69
Period size: 29 Copynumber: 2.4 Consensus size: 30
1049462 GTTTTTTTGT
* *
1049472 TTGTTTGTTTGTTTTTTTTTTCATTTTTTTTG
1 TTGTTT-TTT-TTTTTTTTTTCATTGTTGTTG
** *
1049504 -TGCGTTTGTTTTTTTTTT-ATTGTTGTTG
1 TTGTTTTTTTTTTTTTTTTCATTGTTGTTG
1049532 TTGTTTTTTTTTT
1 TTGTTTTTTTTTT
1049545 GCAGAGGACG
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
28 8 0.25
29 19 0.59
30 2 0.06
31 3 0.09
ACGTcount: A:0.03, C:0.03, G:0.15, T:0.79
Consensus pattern (30 bp):
TTGTTTTTTTTTTTTTTTTCATTGTTGTTG
Found at i:1062542 original size:61 final size:61
Alignment explanation
Indices: 1062467--1062586 Score: 240
Period size: 61 Copynumber: 2.0 Consensus size: 61
1062457 AAGAAGAGTA
1062467 TGAATAACACTCATGAAGGTGCTGGACATGCTGTAAATGCATGAAACATAGCTCAAAATGC
1 TGAATAACACTCATGAAGGTGCTGGACATGCTGTAAATGCATGAAACATAGCTCAAAATGC
1062528 TGAATAACACTCATGAAGGTGCTGGACATGCTGTAAATGCATGAAACATAGCTCAAAAT
1 TGAATAACACTCATGAAGGTGCTGGACATGCTGTAAATGCATGAAACATAGCTCAAAAT
1062587 TCATGAATCA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (61 bp):
TGAATAACACTCATGAAGGTGCTGGACATGCTGTAAATGCATGAAACATAGCTCAAAATGC
Found at i:1062572 original size:28 final size:28
Alignment explanation
Indices: 1062478--1062572 Score: 84
Period size: 28 Copynumber: 3.2 Consensus size: 28
1062468 GAATAACACT
1062478 CATGAAGGTGCTGGACATGCTGTAAATG
1 CATGAAGGTGCTGGACATGCTGTAAATG
** ** *
1062506 CATGAAACATAGCTCAAAATGCTGAATAACACT-
1 CATG-AAGGT-GCTGGACATGCTG--TAA-A-TG
1062539 CATGAAGGTGCTGGACATGCTGTAAATG
1 CATGAAGGTGCTGGACATGCTGTAAATG
1062567 CATGAA
1 CATGAA
1062573 ACATAGCTCA
Statistics
Matches: 50, Mismatches: 10, Indels: 14
0.68 0.14 0.19
Matches are distributed among these distances:
27 1 0.02
28 11 0.22
29 6 0.12
30 10 0.20
31 10 0.20
32 6 0.12
33 5 0.10
34 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (28 bp):
CATGAAGGTGCTGGACATGCTGTAAATG
Found at i:1063523 original size:13 final size:13
Alignment explanation
Indices: 1063505--1063556 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
1063495 AGCTTCATAG
1063505 CGATACATTGTAT
1 CGATACATTGTAT
1063518 CGATACAACACTTATGTAT
1 CGAT---ACA-TT--GTAT
1063537 CGATACATTGTAT
1 CGATACATTGTAT
1063550 CGATACA
1 CGATACA
1063557 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 15 0.45
15 2 0.06
16 6 0.18
17 2 0.06
19 8 0.24
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1063537 original size:19 final size:19
Alignment explanation
Indices: 1063513--1063597 Score: 92
Period size: 19 Copynumber: 4.7 Consensus size: 19
1063503 AGCGATACAT
1063513 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1063532 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1063545 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
* *
1063564 TGTATCGATACAATTACTATT
1 TGTATCGATACAA-CACT-TA
1063585 TGTATCGATACAA
1 TGTATCGATACAA
1063598 ATTGTTGAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
13 9 0.16
14 1 0.02
16 6 0.11
18 1 0.02
19 22 0.39
20 3 0.05
21 14 0.25
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1063546 original size:32 final size:32
Alignment explanation
Indices: 1063505--1063575 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
1063495 AGCTTCATAG
1063505 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1063537 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1063569 CGATACA
1 CGATACA
1063576 ATTACTATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:1073595 original size:79 final size:79
Alignment explanation
Indices: 1073454--1073684 Score: 311
Period size: 79 Copynumber: 2.9 Consensus size: 79
1073444 TTTGGAGATG
* * * * * * *
1073454 ACAACAGGGCTGGAGTATCCCCGATTATGGAAAATCGG-AGTTTTGGAAGTAAAGTCGGGGTTGG
1 ACAACAGGGTTGGAGTATCCCTGATTATAGAAAATTGGTA-TTTTGAAAATAAAATCGGGGTTGG
*
1073518 AGTATCCCCTCGGAA
65 AGTATCCCCTCGAAA
* *
1073533 ACAATAGGGTTGGAGTATCCCTGATTATAGAAAATTGGTATTTTGAAACTAAAATCGGGGTTGGA
1 ACAACAGGGTTGGAGTATCCCTGATTATAGAAAATTGGTATTTTGAAAATAAAATCGGGGTTGGA
*
1073598 GTATCTCCTCGAAA
66 GTATCCCCTCGAAA
* * * *
1073612 ATAACAGGGTTGGAATATCCCTGATTATAGAAAATTGGTGTTTTGAAAATAAAATCGGAGTTGGA
1 ACAACAGGGTTGGAGTATCCCTGATTATAGAAAATTGGTATTTTGAAAATAAAATCGGGGTTGGA
1073677 GTATCCCC
66 GTATCCCC
1073685 GATTGTGAAA
Statistics
Matches: 134, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
79 133 0.99
80 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (79 bp):
ACAACAGGGTTGGAGTATCCCTGATTATAGAAAATTGGTATTTTGAAAATAAAATCGGGGTTGGA
GTATCCCCTCGAAA
Found at i:1073682 original size:51 final size:52
Alignment explanation
Indices: 1073620--1073836 Score: 212
Period size: 51 Copynumber: 4.2 Consensus size: 52
1073610 AAATAACAGG
* * * *
1073620 GTTGGAATATCCCTGATTATAG-AAAATTGGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAGAAAAATTGATGTTTTGAAAATAAAATCAGA
* *
1073671 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGAAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTATAGAAAAATTGATGTTTTGAAAATAAAATCAGA
* ** ** ** *
1073722 GTTGGAGTATCCCCGATTGT-GGTAAATCAATGCTTTTTTAAA-AAAATCAAA
1 GTTGGAGTATCCCCGATTATAGAAAAATTGATG-TTTTGAAAATAAAATCAGA
* ** *
1073773 GTTGGAGTATCCCCGATTA-AGAAAAATTGATGTTTTGGAAATGGAATC-GG
1 GTTGGAGTATCCCCGATTATAGAAAAATTGATGTTTTGAAAATAAAATCAGA
1073823 GATTGGAGTATCCC
1 G-TTGGAGTATCCC
1073837 TAAGATGAAA
Statistics
Matches: 138, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
50 9 0.07
51 122 0.88
52 7 0.05
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATAGAAAAATTGATGTTTTGAAAATAAAATCAGA
Found at i:1076167 original size:20 final size:19
Alignment explanation
Indices: 1076138--1076211 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
1076128 AAAATGCCTG
* *
1076138 AATGTTTCGATACATTGTAA
1 AATGTATCGATACAATG-AA
*
1076158 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-A
* * *
1076178 AATGTATCAATAAAATACAA
1 AATGTATCGATACAAT-GAA
1076198 AATGTATCGATACA
1 AATGTATCGATACA
1076212 TCTGGGTAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.30
Consensus pattern (19 bp):
AATGTATCGATACAATGAA
Found at i:1076249 original size:13 final size:13
Alignment explanation
Indices: 1076231--1076256 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1076221 ACCCAGAATA
1076231 TATCGATACAATG
1 TATCGATACAATG
1076244 TATCGATACAATG
1 TATCGATACAATG
1076257 AATACTGTAT
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):
TATCGATACAATG
Found at i:1076267 original size:20 final size:20
Alignment explanation
Indices: 1076238--1076290 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1076228 ATATATCGAT
1076238 ACAATGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
* *
1076258 ATACTGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
1076278 ACAATGTATCGAT
1 ACAATGTATCGAT
1076291 GCAAATTGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
ACAATGTATCGATACAATGA
Found at i:1076849 original size:1 final size:1
Alignment explanation
Indices: 1076845--1076932 Score: 68
Period size: 1 Copynumber: 88.0 Consensus size: 1
1076835 ATTCTTTTTC
* * * * * * * * *
1076845 AAAAAAACAAAAAAAAACAAAAAAAATAAAAAAATAAAAAACAAAAAACAACAAAAAAACAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
1076910 AAAGAAAAAAAAGAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAA
1076933 GAACCTCCTT
Statistics
Matches: 63, Mismatches: 24, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.86, C:0.08, G:0.03, T:0.02
Consensus pattern (1 bp):
A
Found at i:1076860 original size:10 final size:10
Alignment explanation
Indices: 1076845--1076932 Score: 83
Period size: 10 Copynumber: 8.6 Consensus size: 10
1076835 ATTCTTTTTC
1076845 AAAAAAACAA
1 AAAAAAACAA
1076855 AAAAAAACAA
1 AAAAAAACAA
1076865 AAAAAATA-AA
1 AAAAAA-ACAA
1076875 AAAATAAA-AA
1 AAAA-AAACAA
1076885 ACAAAAAACAA
1 A-AAAAAACAA
1076896 CAAAAAAACAA
1 -AAAAAAACAA
*
1076907 AACAAAGA-AA
1 AA-AAAAACAA
* *
1076917 AAAAAGAGAA
1 AAAAAAACAA
1076927 AAAAAA
1 AAAAAA
1076933 GAACCTCCTT
Statistics
Matches: 69, Mismatches: 2, Indels: 14
0.81 0.02 0.16
Matches are distributed among these distances:
9 5 0.07
10 42 0.61
11 21 0.30
12 1 0.01
ACGTcount: A:0.86, C:0.08, G:0.03, T:0.02
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:1076918 original size:34 final size:34
Alignment explanation
Indices: 1076846--1076919 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
1076836 TTCTTTTTCA
*
1076846 AAAAAACAAAAAAAAACAAAAAAAATAAAAAAAT
1 AAAAAACAAAAAAAAACAAAAAAAATAAAAAAAG
* *
1076880 AAAAAACAAAAAACAACAAAAAAACA-AAACAAAG
1 AAAAAACAAAAAAAAACAAAAAAA-ATAAAAAAAG
1076914 AAAAAA
1 AAAAAA
1076920 AAGAGAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 35 0.97
35 1 0.03
ACGTcount: A:0.86, C:0.09, G:0.01, T:0.03
Consensus pattern (34 bp):
AAAAAACAAAAAAAAACAAAAAAAATAAAAAAAG
Found at i:1077515 original size:55 final size:55
Alignment explanation
Indices: 1077426--1077616 Score: 224
Period size: 55 Copynumber: 3.3 Consensus size: 55
1077416 AATAACAGGA
* * *
1077426 TTTCTAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGTA-T
1 TTTC-AGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACT
* *
1077481 TTTCCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCAGACAAGCTGGTGGCACT
1 TTT-CAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACT
**
1077537 TTTCAGTCCTCAAAGAGCAAAATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCT
1 TTTCAGTCCTCAAAGAGCAGGATGCC-TTT-C----AAAGCCCACACAAGTTGGTGGCA-CT
1077599 TTT-AGTCCTCAAAGAGCA
1 TTTCAGTCCTCAAAGAGCA
1077617 AGACGCTCTC
Statistics
Matches: 118, Mismatches: 9, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
55 68 0.58
56 8 0.07
57 1 0.01
61 36 0.31
62 5 0.04
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (55 bp):
TTTCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACT
Found at i:1077631 original size:61 final size:58
Alignment explanation
Indices: 1077451--1077634 Score: 198
Period size: 61 Copynumber: 3.1 Consensus size: 58
1077441 GAGTAGGACG
* * *
1077451 CCTTTCAAAGCCCACACAAGTTGGTGGTA-TTTTCCAGTCCTCAAAGAGC-AG-G-ATG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAAGAGCCTT
* * *
1077506 CCTTTCAAAGCCCAGACAAGCTGGTGGCACTTTTCAGTCCTCAAAGAGCAAAATGCCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAAGA-GCC--TT
*
1077567 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT-AGTCCTCAAAGAGCAAGACGCTCTCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTTCAGTCCTCAAAGAGCAAGA-GC-CT-T
1077628 CCTTTCA
1 CCTTTCA
1077635 CCCTTTAGTC
Statistics
Matches: 107, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
55 41 0.38
56 5 0.05
58 1 0.01
60 1 0.01
61 53 0.50
62 6 0.06
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (58 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAAGAGCCTT
Found at i:1077703 original size:55 final size:55
Alignment explanation
Indices: 1077641--1077825 Score: 291
Period size: 55 Copynumber: 3.4 Consensus size: 55
1077631 TTCACCCTTT
* * * **
1077641 AGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCTACACAAGTTGGTGGTATTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
1077696 AGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
1077751 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1077806 AGTCCTCGAAA-AGCAGGACG
1 AGTCCTC-AAAGAGCAGGACG
1077826 TGCTCTTTTT
Statistics
Matches: 120, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
55 117 0.98
56 3 0.03
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:1078124 original size:20 final size:19
Alignment explanation
Indices: 1078073--1078147 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
1078063 TTTTCACAAT
*
1078073 TTGTATCGATACGTTATTCA
1 TTGTATCGATACATT-TTCA
* *
1078093 TTGTAACAATACATTGTTCA
1 TTGTATCGATACATT-TTCA
1078113 TTGTATCGATACATTTTGCA
1 TTGTATCGATACATTTT-CA
* *
1078133 ATATATCGATACATT
1 TTGTATCGATACATT
1078148 CAGGCATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 2 0.04
20 44 0.96
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.43
Consensus pattern (19 bp):
TTGTATCGATACATTTTCA
Found at i:1080464 original size:80 final size:79
Alignment explanation
Indices: 1080320--1080473 Score: 191
Period size: 80 Copynumber: 1.9 Consensus size: 79
1080310 CTAACCCCGG
** * * * *
1080320 TTTTATTTCTAAAACATTAATTTTTCATAATCGGAGATACTCTAATCCCGTTATTTCCGAGGGGA
1 TTTTATTTCTAAAACACCAATTTTTCACAATCGGAGATACTCCAACCCCGTTATTTCAGAGGGGA
*
1080385 TACTTCAACTTCAA
66 TACTCCAACTTCAA
* * * **
1080399 TTTTATTTCTTAAAACACCAGTTTTTCACAATTGGGGATACTCCAACCCCGTTATTTCATCGGGG
1 TTTTATTTC-TAAAACACCAATTTTTCACAATCGGAGATACTCCAACCCCGTTATTTCAGAGGGG
1080464 ATACTCCAAC
65 ATACTCCAAC
1080474 CCTGCTATTT
Statistics
Matches: 62, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
79 9 0.15
80 53 0.85
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (79 bp):
TTTTATTTCTAAAACACCAATTTTTCACAATCGGAGATACTCCAACCCCGTTATTTCAGAGGGGA
TACTCCAACTTCAA
Found at i:1080465 original size:28 final size:27
Alignment explanation
Indices: 1080432--1080505 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 27
1080422 TTTCACAATT
*
1080432 GGGGATACTCCAACCCCGTTA-TTTCA
1 GGGGATACTCCAACCCCGCTATTTTCA
*
1080458 TCGGGGATACTCCAACCCTGCTATTTTCGA
1 --GGGGATACTCCAACCCCGCTATTTTC-A
1080488 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1080506 GCTTTATTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
28 36 0.88
29 4 0.10
30 1 0.02
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.24
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGCTATTTTCA
Found at i:1080586 original size:51 final size:51
Alignment explanation
Indices: 1080489--1080606 Score: 141
Period size: 51 Copynumber: 2.3 Consensus size: 51
1080479 TATTTTCGAG
* * * **
1080489 GGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCACAATC-
1 GGGATACTCCAACCCCAGCCTTATTTCCAAAACATCAATTTCTCACAATCA
* *
1080539 GGAGATACTCCAACCCCAGCCTTATTTCTAAAGCATCAAGTTT-TCACAATCA
1 GG-GATACTCCAACCCCAGCCTTATTTCCAAAACATCAA-TTTCTCACAATCA
1080591 GGGATACTCCAACCCC
1 GGGATACTCCAACCCC
1080607 GTTATTTTCG
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
50 2 0.03
51 51 0.88
52 5 0.09
ACGTcount: A:0.30, C:0.31, G:0.13, T:0.27
Consensus pattern (51 bp):
GGGATACTCCAACCCCAGCCTTATTTCCAAAACATCAATTTCTCACAATCA
Found at i:1080625 original size:79 final size:77
Alignment explanation
Indices: 1080542--1080767 Score: 242
Period size: 79 Copynumber: 2.9 Consensus size: 77
1080532 CACAATCGGA
** *
1080542 GATACTCCAACCCCAGCCTTATTTCTAAAGCATCAAGTTTTCACAATCAGGGATACTCCAACCCC
1 GATACTCCAACCCC-GTTTTATTTCTAAA-CATCAAGTTTTCATAATCAGGGATACTCCAACCCC
1080607 GTTATTTTCGAGGG
64 GTTATTTTCGAGGG
* * * *
1080621 GATACTCTAACCTCGATTTTATTT-TCAAA-AT-ACTGATTTTCTATAATCAGGGATACTCCGAC
1 GATACTCCAACCCCG-TTTTATTTCT-AAACATCA-AG-TTTTC-ATAATCAGGGATACTCCAAC
*
1080683 CCTGTTATTTTCGAGGG
61 CCCGTTATTTTCGAGGG
* * * *
1080700 GATACTCCAACCCCGGTTTTATTTCTAGAACATCGATTTTTCATAATCGGGGATACTCCAGCCCC
1 GATACTCCAACCCC-GTTTTATTTCTA-AACATCAAGTTTTCATAATCAGGGATACTCCAACCCC
1080765 GTT
64 GTT
1080768 GTTATCTCCA
Statistics
Matches: 120, Mismatches: 17, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
76 1 0.01
77 3 0.03
78 7 0.06
79 98 0.82
80 9 0.08
81 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (77 bp):
GATACTCCAACCCCGTTTTATTTCTAAACATCAAGTTTTCATAATCAGGGATACTCCAACCCCGT
TATTTTCGAGGG
Found at i:1082149 original size:35 final size:34
Alignment explanation
Indices: 1082124--1082189 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
1082114 AGGAAAGTGT
*
1082124 CCTGC-TTCTTGAGGACAAAGTGAAAAAGAGTATGC
1 CCTGCATT-TTGAGGACAAAG-GAAAAAGAGAATGC
*
1082159 CCTGCATTTTGAGGACAAAGGAAAAAAAGAA
1 CCTGCATTTTGAGGACAAAGGAAAAAGAGAA
1082190 AACGATATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 9 0.32
35 17 0.61
36 2 0.07
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (34 bp):
CCTGCATTTTGAGGACAAAGGAAAAAGAGAATGC
Found at i:1082149 original size:42 final size:40
Alignment explanation
Indices: 1082050--1082593 Score: 263
Period size: 42 Copynumber: 13.3 Consensus size: 40
1082040 TGTCTCTCTT
* * *
1082050 TTTGAGGATAAAGGAAAAGAGAATAA-AATAG-GTCTTGCTC
1 TTTGAGGACAAAGGAAAAAAGAA-AAGAA-AGTGTCCTGCTC
*
1082090 -CTGAAGGACAAAGGAAAAAAGAAAAGGAAAGTGTCCTGCT-
1 TTTG-AGGACAAAGGAAAAAAGAAAA-GAAAGTGTCCTGCTC
* *
1082130 TCTTGAGGACAAAGTG-AAAAAG---AG-TA-TGCCCTGCAT-
1 T-TTGAGGACAAAG-GAAAAAAGAAAAGAAAGTGTCCTGC-TC
*
1082166 TTTGAGGACAAAGGAAAAAAAGAAAACGATA-TGCATCCTGCTC
1 TTTGAGGACAAAGG-AAAAAAGAAAA-GAAAGTG--TCCTGCTC
* * * * *
1082209 TTTGAGGACAAAAGAAAGAGGAAAACAAAGTGCATCTTGCTC
1 TTTGAGGACAAAGGAAAAAAGAAAAGAAAGTG--TCCTGCTC
* * *
1082251 TTTGAGGACAAAAGGGAAAAGAAGGGAATGAAGTGTGTCCTGCTC
1 TTTGAGGAC-AAA-GGAAAA-AA-GAAAAGAA-AGTGTCCTGCTC
* ** *
1082296 TTTGAGGACAAAGGAGAAAAGGAAAAG---GCATCCTACTC
1 TTTGAGGACAAAGGA-AAAAAGAAAAGAAAGTGTCCTGCTC
* *
1082334 TTTGAGGACTAAA-GAAGAAAGAAAAGGAAAGTGTCCTACT-
1 TTTGAGGAC-AAAGGAAAAAAGAAAA-GAAAGTGTCCTGCTC
* *
1082374 TCTTGAGGACAAAGTG---AAA-AAAAG-TA-CGTCCTGCT-
1 T-TTGAGGACAAAG-GAAAAAAGAAAAGAAAGTGTCCTGCTC
**
1082409 TCTCAAGGACAAAGGAAAAAAAGGAAAACGAAATGTGTCCTGCTC
1 T-TTGAGGACAAAGG-AAAAAA-GAAAA-GAAA-GTGTCCTGCTC
* * * *
1082454 TTTGAGGACAAAAGAAAGAGGAAAATAAAGTGCGTCCTGCTC
1 TTTGAGGACAAAGGAAAAAAGAAAAGAAAGT--GTCCTGCTC
* * *
1082496 TTTGAGGACAAAAGAGAAAATAAGGAATGAAGTGTGTCCTGCTC
1 TTTGAGGAC-AAAG-GAAAA-AAGAAAAGAA-AGTGTCCTGCTC
* * * * *
1082540 TTTGAGGACAAAGGAGAGAGGGAAATAAAGTGTGTCCTGCTC
1 TTTGAGGACAAAGGAAAAAAGAAAAGAAA--GTGTCCTGCTC
1082582 TTTGAGGACAAA
1 TTTGAGGACAAA
1082594 AAGGTGCCAC
Statistics
Matches: 394, Mismatches: 58, Indels: 102
0.71 0.10 0.18
Matches are distributed among these distances:
34 2 0.01
35 38 0.10
36 10 0.03
37 10 0.03
38 28 0.07
39 11 0.03
40 30 0.08
41 57 0.14
42 88 0.22
43 36 0.09
44 50 0.13
45 24 0.06
46 7 0.02
47 3 0.01
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.20
Consensus pattern (40 bp):
TTTGAGGACAAAGGAAAAAAGAAAAGAAAGTGTCCTGCTC
Found at i:1082405 original size:35 final size:34
Alignment explanation
Indices: 1082366--1082431 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 34
1082356 AAAGGAAAGT
**
1082366 GTCCTACTTCTTGAGGACAAAGTGAAAAAAAGTAC
1 GTCCTACTTCTCAAGGACAAAG-GAAAAAAAGTAC
*
1082401 GTCCTGCTTCTCAAGGACAAAGGAAAAAAAG
1 GTCCTACTTCTCAAGGACAAAGGAAAAAAAG
1082432 GAAAACGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 9 0.32
35 19 0.68
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (34 bp):
GTCCTACTTCTCAAGGACAAAGGAAAAAAAGTAC
Found at i:1082536 original size:244 final size:244
Alignment explanation
Indices: 1082094--1082556 Score: 743
Period size: 244 Copynumber: 1.9 Consensus size: 244
1082084 TTGCTCCTGA
* * *
1082094 AGGACAAAGGAAAAAAGAAAAGGAAAGTGTCCTGCTTCTTGAGGACAAAGTGAAAAAGAGTATGC
1 AGGACAAAGGAAAAAAGAAAAGGAAAGTGTCCTACTTCTTGAGGACAAAGTGAAAAAAAGTACGC
** *
1082159 CCTGCATTTTGAGGACAAAGGAAAAAAAGAAAACGATATGCATCCTGCTCTTTGAGGACAAAAGA
66 CCTGCATTTCAAGGACAAAGGAAAAAAAGAAAACGAAATGCATCCTGCTCTTTGAGGACAAAAGA
* *
1082224 AAGAGGAAAACAAAGTGCATCTTGCTCTTTGAGGACAAAAGGGAAAAGAAGGGAATGAAGTGTGT
131 AAGAGGAAAACAAAGTGCATCCTGCTCTTTGAGGACAAAAGAGAAAAGAAGGGAATGAAGTGTGT
1082289 CCTGCTCTTTGAGGACAAAGGAGAAAAGGAAAAGGCATCCTACTCTTTG
196 CCTGCTCTTTGAGGACAAAGGAGAAAAGGAAAAGGCATCCTACTCTTTG
*
1082338 AGGACTAAA-GAAGAAAGAAAAGGAAAGTGTCCTACTTCTTGAGGACAAAGTGAAAAAAAGTACG
1 AGGAC-AAAGGAAAAAAGAAAAGGAAAGTGTCCTACTTCTTGAGGACAAAGTGAAAAAAAGTACG
* **
1082402 TCCTGC-TTCTCAAGGACAAAGGAAAAAAAGGAAAACGAAATGTGTCCTGCTCTTTGAGGACAAA
65 CCCTGCATT-TCAAGGACAAAGGAAAAAAA-GAAAACGAAATGCATCCTGCTCTTTGAGGACAAA
* * *
1082466 AGAAAGAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAGAAAATAA-GGAATGAAGTG
128 AGAAAGAGGAAAACAAAGTGCATCCTGCTCTTTGAGGACAAAAGAGAAAAGAAGGGAATGAAGTG
1082530 TGTCCTGCTCTTTGAGGACAAAGGAGA
193 TGTCCTGCTCTTTGAGGACAAAGGAGA
1082557 GAGGGAAATA
Statistics
Matches: 201, Mismatches: 15, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
243 2 0.01
244 117 0.58
245 82 0.41
ACGTcount: A:0.41, C:0.14, G:0.26, T:0.19
Consensus pattern (244 bp):
AGGACAAAGGAAAAAAGAAAAGGAAAGTGTCCTACTTCTTGAGGACAAAGTGAAAAAAAGTACGC
CCTGCATTTCAAGGACAAAGGAAAAAAAGAAAACGAAATGCATCCTGCTCTTTGAGGACAAAAGA
AAGAGGAAAACAAAGTGCATCCTGCTCTTTGAGGACAAAAGAGAAAAGAAGGGAATGAAGTGTGT
CCTGCTCTTTGAGGACAAAGGAGAAAAGGAAAAGGCATCCTACTCTTTG
Found at i:1082539 original size:86 final size:85
Alignment explanation
Indices: 1082201--1082594 Score: 369
Period size: 86 Copynumber: 4.7 Consensus size: 85
1082191 ACGATATGCA
* * *
1082201 TCCTGCTCTTTGAGGACAAAAGAAAGAGGAAAACAAAGTGCATCTTGCTCTTTGAGGACAAAAGG
1 TCCTGCTCTTTGAGGACAAAAGAAAGAGGAAAA-AAAGTGCGTCCTGCTCTTTGAGGACAAAAGA
*
1082266 GAAAAGAAGGGAATGAAGTGTG
65 GAAAA-AAAGGAATGAAGTGTG
* * *
1082288 TCCTGCTCTTTGAGGACAAAGGAGAAA-AGG---AAAAG-GCATCCTACTCTTTGAGGACTAAAG
1 TCCTGCTCTTTGAGGACAAA--AGAAAGAGGAAAAAAAGTGCGTCCTGCTCTTTGAGGACAAAAG
1082348 AAGAAAGAAAAGG-A--AA--GTG
64 -AGAAA-AAAAGGAATGAAGTGTG
* * * **
1082367 TCCTACT-TCTTGAGGAC-----AAAG-TGAAAAAAAGTACGTCCTGCT-TCTCAAGGAC-AAAG
1 TCCTGCTCT-TTGAGGACAAAAGAAAGAGGAAAAAAAGTGCGTCCTGCTCT-TTGAGGACAAAAG
* *
1082423 -GAAAAAAAGGAAAACGAAATGTG
64 AGAAAAAAAGG--AATGAAGTGTG
1082446 TCCTGCTCTTTGAGGACAAAAGAAAGAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGA
1 TCCTGCTCTTTGAGGACAAAAGAAAGAGGAAAA-AAAGTGCGTCCTGCTCTTTGAGGACAAAAGA
*
1082511 GAAAATAAGGAATGAAGTGTG
65 GAAAAAAAGGAATGAAGTGTG
* * * *
1082532 TCCTGCTCTTTGAGGACAAAGGAGAGAGGGAAATAAAGTGTGTCCTGCTCTTTGAGGACAAAA
1 TCCTGCTCTTTGAGGACAAAAGAAAGA-GGAAAAAAAGTGCGTCCTGCTCTTTGAGGACAAAA
1082595 AGGTGCCACC
Statistics
Matches: 253, Mismatches: 24, Indels: 61
0.75 0.07 0.18
Matches are distributed among these distances:
72 10 0.04
73 4 0.02
75 11 0.04
76 13 0.05
77 2 0.01
78 1 0.00
79 34 0.13
80 1 0.00
81 2 0.01
83 23 0.09
84 16 0.06
85 7 0.03
86 82 0.32
87 30 0.12
88 12 0.05
89 5 0.02
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.20
Consensus pattern (85 bp):
TCCTGCTCTTTGAGGACAAAAGAAAGAGGAAAAAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAG
AAAAAAAGGAATGAAGTGTG
Found at i:1082675 original size:61 final size:60
Alignment explanation
Indices: 1082573--1083334 Score: 662
Period size: 61 Copynumber: 12.4 Consensus size: 60
1082563 AATAAAGTGT
* *
1082573 GTCCTGCTCTTTGAGGAC-AAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAAGAAAGGC
1 GTCCTGCTCTTTGAGGACTAGAAA-GTGCCACCAACTTGTGTGGGCTTT-AAAAAGAAAGGC
* * * *
1082634 ATCATGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAA-GC
1 GTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTT--AAAAAGAAAGGC
* * * * * * *
1082695 ATCCTGCTCTTTGAGGACTGGAAAATGCCACTAACTTGTGTAGGCTTTGAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAG-AAAGGC
* * * * * * * * *
1082756 GTCTTACTTTTTGAAGACT-GAAAAATGCCACCAACTTGTGTCGGCTTTGAAAGGAAAAAGC
1 GTCCTGCTCTTTGAGGACTAG-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAAG-AAAGGC
* * * * * * * * *
1082817 ATCCTACTCTTTGAAGACT-GAAAAATGCCACCAACATGTGTGGGCTTTGAAAGGAAAATGT
1 GTCCTGCTCTTTGAGGACTAG-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAAG-AAAGGC
* * *
1082878 GTCCTGCTCTTTGAGGACT-GAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACTAG-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAAG-AAAGGC
* * *
1082939 ATCTTGCTCTTTGAGGATTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAAGGC
1 GTCCTGCTCTTTGAGGACTAG-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAAG----AAAGGC
* * * ** ** * *
1083004 GTCATGCTCTTTAAGGACTGGAGGGTGCCACCAACTCATGTGGGCTTT-GAAGGAGAAGGC
1 GTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGA-AAGGC
*
1083064 GTCCTGCATCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAAGGC
1 GTCCTGC-TCTTTGAGGACTAGAAA-GTGCCACCAACTTGTGTGGGCTTT-AAA--AAGAAAGGC
* * * * * *
1083128 GTCCTGCTCTTTGAGGACTA-AAGGGTGCCATCAACTCGTGTGGGCTTT-GAAGGAGAAGGT
1 GTCCTGCTCTTTGAGGACTAGAA-AGTGCCACCAACTTGTGTGGGCTTTAAAAAGA-AAGGC
* * * *
1083188 ATCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAG-AAAGGC
* * * *
1083249 GTCCTTCTCTTTGAGGACAAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAATGC
1 GTCCTGCTCTTTGAGGACTAG-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAAG-AAAGGC
1083311 GTCCTGCTCTTTGAGGACT-GAAAG
1 GTCCTGCTCTTTGAGGACTAGAAAG
1083335 GGCTAAAAGA
Statistics
Matches: 591, Mismatches: 88, Indels: 45
0.82 0.12 0.06
Matches are distributed among these distances:
59 6 0.01
60 64 0.11
61 323 0.55
62 97 0.16
63 41 0.07
64 35 0.06
65 25 0.04
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (60 bp):
GTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAGGC
Found at i:1082791 original size:122 final size:121
Alignment explanation
Indices: 1082574--1083333 Score: 852
Period size: 122 Copynumber: 6.2 Consensus size: 121
1082564 ATAAAGTGTG
* * *
1082574 TCCTGCTCTTTGAGGAC--AAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAA-AAGAAAGGCAT
1 TCCTGCTCTTTGAGGACTGAAAAA--TGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGGCGT
* *
1082636 CATGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCA
63 CCTGCTCTTTGAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTTG-AAAGAGAAAGCA
* * * * *
1082696 TCCTGCTCTTTGAGGACTGGAAAATGCCACTAACTTGTGTAGGCTTTGAAAGGAAAAGGCGTCTT
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCT
* * * * * *
1082761 ACTTTTTGAAGACTGAAAAATGCCACCAACTTGTGTCGGCTTTGAAAGGAAAAAGCA
66 GCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAA-GAGAAAGCA
* * * * * *
1082818 TCCTACTCTTTGAAGACTGAAAAATGCCACCAACATGTGTGGGCTTTGAAAGGAAAATGTGTCCT
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCT
*
1082883 GCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG-GAAAAGGCA
66 GCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGAG-AAA-GCA
* * * *
1082940 TCTTGCTCTTTGAGGATTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAAATGCCACCAACTTGTGTGGGCTTT-AAAAG--GAAAAGGCG
* * * ** ** * * *
1083005 TCATGCTCTTTAAGGACTGGAGGGTGCCACCAACTCATGTGGGCTTTGAAGGAGAAGGCG
62 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGAGAAAGCA
*
1083065 TCCTGCATCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAAGGCG
1 TCCTGC-TCTTTGAGGACTGAAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGG--AAAAGGCG
* * * * * *
1083129 TCCTGCTCTTTGAGGACT-AAAGGGTGCCATCAACTCGTGTGGGCTTTGAAGGAGAAGGTA
62 TCCTGCTCTTTGAGGACTGAAA-AGTGCCACCAACTTGTGTGGGCTTTGAAAGAGAAAGCA
*
1083189 TCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCT
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCT
* * *
1083254 TCTCTTTGAGGACAAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAA-AGAAAATGCG
66 GCTCTTTGAGGAC-TGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGAG-AAA-GCA
1083312 TCCTGCTCTTTGAGGACTGAAA
1 TCCTGCTCTTTGAGGACTGAAA
1083334 GGGCTAAAAG
Statistics
Matches: 544, Mismatches: 72, Indels: 43
0.83 0.11 0.07
Matches are distributed among these distances:
121 33 0.06
122 236 0.43
123 96 0.18
124 85 0.16
125 31 0.06
126 62 0.11
127 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (121 bp):
TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCT
GCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGAGAAAGCA
Found at i:1082906 original size:183 final size:184
Alignment explanation
Indices: 1082573--1083333 Score: 846
Period size: 183 Copynumber: 4.1 Consensus size: 184
1082563 AATAAAGTGT
*
1082573 GTCCTGCTCTTTGAGGAC-AAAAAGGTGCCACCAACTCGTGTGGGCTTT-AAA-AAAGAAAGGCA
1 GTCCTGCTCTTTGAGGACTGAAAA-GTGCCACCAACTCGTGTGGGCTTTGAAAGAAA-AAAGGCA
* ** *
1082635 TCATGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAA-GAGAAA-GCAT
64 TCATGCTCTTTGAAGACTGA-AAAATGCCACCAACTTGTGTGGGCTTTG-AAAGGA-AAAGGCGT
* * *
1082697 CCTGCTCTTTGAGGACTGGAAAATGCCACTAACTTGTGTAGGCTTTGAAAGGAAAAGGC
126 CCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGC
* * * * * * * *
1082756 GTCTTACTTTTTGAAGACTGAAAAATGCCACCAACTTGTGTCGGCTTTGAAAGGAAAAA-GCATC
1 GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGAAAAAAGGCATC
* * * * *
1082820 CTACTCTTTGAAGACTGAAAAATGCCACCAACATGTGTGGGCTTTGAAAGGAAAATGTGTCCTGC
66 ATGCTCTTTGAAGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTCCTGC
1082885 TCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGC
131 TCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGC
* * * * *
1082939 ATCTTGCTCTTTGAGGATTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAAAGGC
1 GTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTCGTGTGGGCTTT-GAAAG-AAAAAAGGC
* * *** ** *
1083004 GTCATGCTCTTT-AAGGACTGGAGGGTGCCACCAACTCATGTGGGCTTTG-AAGGAGAAGGCGTC
63 ATCATGCTCTTTGAA-GACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTC
* *
1083067 CTGCATCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAAGGC
127 CTGC-TCTTTGAGGACTGAAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGG--AAAAGGC
* * * * *
1083128 GTCCTGCTCTTTGAGGACT-AAAGGGTGCCATCAACTCGTGTGGGCTTTG-AAG-GAGAAGGTAT
1 GTCCTGCTCTTTGAGGACTGAAA-AGTGCCACCAACTCGTGTGGGCTTTGAAAGAAAAAAGGCAT
* * * * *
1083190 CCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTT
65 CATGCTCTTTGAAGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTCCTG
* * * *
1083255 CTCTTTGAGGACAAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAATGC
130 CTCTTTGAGGAC-TGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGC
1083311 GTCCTGCTCTTTGAGGACTGAAA
1 GTCCTGCTCTTTGAGGACTGAAA
1083334 GGGCTAAAAG
Statistics
Matches: 486, Mismatches: 71, Indels: 41
0.81 0.12 0.07
Matches are distributed among these distances:
182 6 0.01
183 177 0.36
184 93 0.19
185 51 0.10
186 33 0.07
187 81 0.17
188 22 0.05
189 23 0.05
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (184 bp):
GTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGAAAAAAGGCATC
ATGCTCTTTGAAGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTCCTGC
TCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGC
Found at i:1089740 original size:51 final size:51
Alignment explanation
Indices: 1089679--1089909 Score: 170
Period size: 51 Copynumber: 4.5 Consensus size: 51
1089669 AAATAACAGG
* * * *
1089679 GTTGGAGTATCCCTGATTAT-AGAGAATTGGTGTTTT-GAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTAGTATTTTAG-AAATAAAATCGGA
*
1089730 GTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTAGAAATAAAATCGGA
** ** * * *
1089781 GTTGGAGTATCCCCGATTGCGGTAAATCGATGCTTTTTTA-AAA-AAAATCAGA
1 GTTGGAGTATCCCCGATTATGAAAAAT-TA-G-TATTTTAGAAATAAAATCGGA
* * * * * * *
1089833 GTTGGAATATCCCCGATTAAGAAAAATT-GATGTTTTGGAAATGGAACTGGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAG-TATTTTAGAAAT-AAAATCGGA
*
1089885 -TTGGAGTATCCCCGA-GATGAAAAAT
1 GTTGGAGTATCCCCGATTATGAAAAAT
1089910 CTAGAAATTT
Statistics
Matches: 145, Mismatches: 27, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
49 6 0.04
50 11 0.08
51 80 0.55
52 38 0.26
53 4 0.03
54 6 0.04
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTAGAAATAAAATCGGA
Found at i:1089742 original size:79 final size:79
Alignment explanation
Indices: 1089513--1089743 Score: 304
Period size: 79 Copynumber: 2.9 Consensus size: 79
1089503 TTTGGAGATG
* * * * * * *
1089513 ACAACGGGGCTGGAGTATCTCC-GATTATAGAAAATCGGTGTTTTGGAAGTAAAGTTGGGGTTGG
1 ACAACAGGGTTGGAGTATC-CCTGATTATAGAAAATCGGTGTTTTGAAAATAAAATCGGAGTTGG
* *
1089577 AGTATCCACTCGGAA
65 AGTATCCCCTCGAAA
* *
1089592 ACAACAGGGTTGGAGTATCCCTGATTATAGAAAATCGGTATTTTGAAACTAAAATC-GAGGTTGG
1 ACAACAGGGTTGGAGTATCCCTGATTATAGAAAATCGGTGTTTTGAAAATAAAATCGGA-GTTGG
1089656 AGTATCCCCTCGAAA
65 AGTATCCCCTCGAAA
* * *
1089671 ATAACAGGGTTGGAGTATCCCTGATTATAGAGAATTGGTGTTTTGAAAATAAAATCGGAGTTGGA
1 ACAACAGGGTTGGAGTATCCCTGATTATAGAAAATCGGTGTTTTGAAAATAAAATCGGAGTTGGA
1089736 GTATCCCC
66 GTATCCCC
1089744 GATTGTGAAA
Statistics
Matches: 134, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
78 3 0.02
79 129 0.96
80 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (79 bp):
ACAACAGGGTTGGAGTATCCCTGATTATAGAAAATCGGTGTTTTGAAAATAAAATCGGAGTTGGA
GTATCCCCTCGAAA
Found at i:1089844 original size:103 final size:104
Alignment explanation
Indices: 1089711--1089899 Score: 249
Period size: 103 Copynumber: 1.8 Consensus size: 104
1089701 AGAATTGGTG
* * **
1089711 TTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTGTGAAAAATT-AGTATTTTAGAAAT-AA
1 TTTTGAAAATAAAATCAGAGTTGGAATATCCCCGATTAAGAAAAATTGA-TATTTTAGAAATGAA
1089774 AATCGGAGTTGGAGTATCCCCGATTGCGGTAAATCGATGCT
65 AATCGGA-TTGGAGTATCCCCGATTGCGGTAAATCGATGCT
* * * *
1089815 TTTTTAAAA-AAAATCAGAGTTGGAATATCCCCGATTAAGAAAAATTGATGTTTTGGAAATGGAA
1 TTTTGAAAATAAAATCAGAGTTGGAATATCCCCGATTAAGAAAAATTGATATTTTAGAAATGAAA
* *
1089879 CTGGGATTGGAGTATCCCCGA
66 ATCGGATTGGAGTATCCCCGA
1089900 GATGAAAAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
103 58 0.79
104 15 0.21
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (104 bp):
TTTTGAAAATAAAATCAGAGTTGGAATATCCCCGATTAAGAAAAATTGATATTTTAGAAATGAAA
ATCGGATTGGAGTATCCCCGATTGCGGTAAATCGATGCT
Found at i:1092245 original size:13 final size:13
Alignment explanation
Indices: 1092226--1092256 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1092216 ATACAATGAG
1092226 CAATGTATCGATA
1 CAATGTATCGATA
*
1092239 GAATGTATCGATA
1 CAATGTATCGATA
1092252 CAATG
1 CAATG
1092257 CAAAATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1092265 original size:20 final size:19
Alignment explanation
Indices: 1092187--1092274 Score: 71
Period size: 20 Copynumber: 4.8 Consensus size: 19
1092177 AAAATGCCTG
* *
1092187 AATGTATCGAAACATTGTAA
1 AATGTATCGATACAATG-AA
*
1092207 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-A
1092227 AATGTATCGAT---A-G--
1 AATGTATCGATACAATGAA
1092240 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AA
*
1092260 AATGTATCAATACAA
1 AATGTATCGATACAA
1092275 ATTGTGAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
13 11 0.20
16 2 0.04
17 2 0.04
19 1 0.02
20 40 0.71
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.27
Consensus pattern (19 bp):
AATGTATCGATACAATGAA
Found at i:1092868 original size:10 final size:9
Alignment explanation
Indices: 1092849--1092919 Score: 83
Period size: 9 Copynumber: 7.9 Consensus size: 9
1092839 CATTCTTTTT
1092849 AAAAAAAAC
1 AAAAAAAAC
1092858 AAAAAATAAC
1 AAAAAA-AAC
1092868 AAAAAAAAC
1 AAAAAAAAC
1092877 AAAAAAAA-
1 AAAAAAAAC
* *
1092885 TAAAATAAC
1 AAAAAAAAC
*
1092894 -AGAAAAAC
1 AAAAAAAAC
1092902 AAAAAACAAC
1 AAAAAA-AAC
1092912 AAAAAAAA
1 AAAAAAAA
1092920 ACAACACAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
8 12 0.23
9 23 0.43
10 18 0.34
ACGTcount: A:0.85, C:0.10, G:0.01, T:0.04
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:1092880 original size:26 final size:26
Alignment explanation
Indices: 1092851--1092915 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
1092841 TTCTTTTTAA
1092851 AAAAAACAA-AAAATAACAAAAAAAAC
1 AAAAAACAACAAAATAAC-AAAAAAAC
* *
1092877 AAAAAA-AATAAAATAACAGAAAAAC
1 AAAAAACAACAAAATAACAAAAAAAC
1092902 AAAAAACAACAAAA
1 AAAAAACAACAAAA
1092916 AAAAACAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 15 0.43
26 20 0.57
ACGTcount: A:0.83, C:0.11, G:0.02, T:0.05
Consensus pattern (26 bp):
AAAAAACAACAAAATAACAAAAAAAC
Found at i:1092906 original size:31 final size:32
Alignment explanation
Indices: 1092868--1092950 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 32
1092858 AAAAAATAAC
1092868 AAAAAAAACAAAAAAAATAAA-ATA-ACAGAAA
1 AAAAAAAACAAAAAAAATAAACA-ACACAGAAA
1092899 AACAAAAAACAACAAAAAA-AAACAACACAG-AA
1 AA-AAAAAACAA-AAAAAATAAACAACACAGAAA
* *
1092931 AAAAAAGAGAAAAAAAATAA
1 AAAAAAAACAAAAAAAATAA
1092951 CCTGCTTAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
30 6 0.13
31 11 0.24
32 17 0.38
33 11 0.24
ACGTcount: A:0.82, C:0.10, G:0.05, T:0.04
Consensus pattern (32 bp):
AAAAAAAACAAAAAAAATAAACAACACAGAAA
Found at i:1092916 original size:33 final size:32
Alignment explanation
Indices: 1092870--1092933 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
1092860 AAAATAACAA
1092870 AAAAAACAAAAAAAATAAA-ATA-ACAGAAAAAC
1 AAAAAACAAAAAAAA-AAACA-ACACAGAAAAAC
1092902 AAAAAACAACAAAAAAAAACAACACAGAAAAA
1 AAAAAACAA-AAAAAAAAACAACACAGAAAAA
1092934 AAAGAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.81, C:0.12, G:0.03, T:0.03
Consensus pattern (32 bp):
AAAAAACAAAAAAAAAAACAACACAGAAAAAC
Found at i:1092922 original size:10 final size:10
Alignment explanation
Indices: 1092849--1092923 Score: 71
Period size: 10 Copynumber: 7.1 Consensus size: 10
1092839 CATTCTTTTT
1092849 AAAAAAAACA
1 AAAAAAAACA
*
1092859 AAAAATAAC-
1 AAAAAAAACA
1092868 AAAAAAAACAA
1 AAAAAAAAC-A
*
1092879 AAAAAATAAAA
1 AAAAAA-AACA
1092890 TAACAGAAAAACA
1 -AA-A-AAAAACA
*
1092903 AAAAACAACA
1 AAAAAAAACA
1092913 AAAAAAAACA
1 AAAAAAAACA
1092923 A
1 A
1092924 CACAGAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
9 8 0.15
10 24 0.45
11 8 0.15
12 6 0.11
13 4 0.08
14 3 0.06
ACGTcount: A:0.84, C:0.11, G:0.01, T:0.04
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:1092933 original size:18 final size:17
Alignment explanation
Indices: 1092849--1092936 Score: 69
Period size: 17 Copynumber: 5.2 Consensus size: 17
1092839 CATTCTTTTT
1092849 AAAAAAAACA-A-AAAA
1 AAAAAAAACACAGAAAA
*
1092864 TAACAAAAAAAACA-AAAA
1 -AA-AAAAAACACAGAAAA
1092882 AAATAAAATA-ACAGAAAA
1 AAA-AAAA-ACACAGAAAA
* *
1092900 ACAAAAAACA-ACAAAA
1 AAAAAAAACACAGAAAA
*
1092916 AAAAACAACACAGAAAA
1 AAAAAAAACACAGAAAA
1092933 AAAA
1 AAAA
1092937 GAGAAAAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
16 17 0.29
17 30 0.51
18 12 0.20
ACGTcount: A:0.83, C:0.11, G:0.02, T:0.03
Consensus pattern (17 bp):
AAAAAAAACACAGAAAA
Found at i:1094005 original size:55 final size:55
Alignment explanation
Indices: 1093917--1094692 Score: 355
Period size: 55 Copynumber: 13.3 Consensus size: 55
1093907 TCCTTTCACT
* * * *
1093917 TTTC-AGTCCTTAAAAAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCAA
1 TTTCTAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCAC
* *
1093971 TTTCTAGTCCTCAAAGAGTAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTCTAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCAC
* * * * * *
1094026 TTTCCAGTCCTCAAAGAGCAGGATGCTTTTCAAAGCCCATACAAGCTGGTGGCAC
1 TTTCTAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCAC
*
1094081 TTT-TCAGTCCTCAAAGAGTAGAACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
1 TTTCT-AGTCCTCAAAGAGTAGGACGCC-TTT-C----AAAGCCCACACAAGTTGGTGGCAC
* * * * * * * ** **
1094142 CTTCTAGTCCTTAAAGAGTAAGACGCTCTCCCCTTTCACCTTTTAGTCCTCAAAGAGCAGGATGC
1 TTTCTAGTCCTCAAAGAGTAGGACG------CCTTTCA-----AAGCCCACACA-AGTTGGTGGC
1094207 -C
54 AC
* * * * * ** * * * * * * ** *
1094208 TTTCAAAGCCCACACA-AGTTGGTGGCACCTTC-TAGTCCTCAAAGAGTAAGACGCTCTCCCC
1 TTTC-TAGTCCTCAAAGAGTAGGACGC-CTTTCAAAGCCCACACA-AGT-TG--G-T-GGCAC
* *
1094269 TTTCACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTT---C---TAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-C
* * * *
1094331 TTTC-AGTTCTCAAAAAGCT-GGACGCCTTTCAAAGCCTACACAAGTTGGTGGCAT
1 TTTCTAGTCCTCAAAGAG-TAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCAC
* * * *
1094385 TTTTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTCTAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCAC
* * * * * *
1094440 TTTCCAATCCTCAAAGAGCAGGACACCTTTCAAAGCCCACATAAGTTGGTGGCAT
1 TTTCTAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCAC
* * * * ** *
1094495 TTTCCAGTCCTCAAAGAGCAGGATGCTTTCTCCTTTTAAAGAGCACCCAAGTTGGTGGCAAC
1 TTTCTAGTCCTCAAAGAGTAGGA------CGCCTTTCAAAGCCCACACAAGTTGGTGGC-AC
* * * * *
1094557 -TTCCAGTCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCTACACAAGTTGGTGACACC
1 TTTCTAGTCCTCAAAGAGTAGGA--C--GC-CTTT-CAAAGCCCACACAAGTTGGTGGCA-C
* *
1094618 TTT-TAGTCCTTAAAGAGTAGGACGCCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
1 TTTCTAGTCCTCAAAGAGTAGGACG-C----C-TTTCAAAGCCCACACAAGTTGGTGGCAC
*
1094678 TTTTTAGTCCTCAAA
1 TTTCTAGTCCTCAAA
1094693 AAACAAGACG
Statistics
Matches: 560, Mismatches: 103, Indels: 111
0.72 0.13 0.14
Matches are distributed among these distances:
54 7 0.01
55 287 0.51
56 5 0.01
57 3 0.01
58 2 0.00
59 4 0.01
60 12 0.02
61 164 0.29
62 12 0.02
63 1 0.00
64 1 0.00
65 2 0.00
66 33 0.06
67 27 0.05
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (55 bp):
TTTCTAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCAC
Found at i:1094177 original size:61 final size:62
Alignment explanation
Indices: 1094051--1094177 Score: 145
Period size: 61 Copynumber: 2.1 Consensus size: 62
1094041 GAGCAGGATG
* * **
1094051 CTTTTCAAAGCCCATACAAGCTGGTGGCACTTTTCAGTCCTCAAAGAGTAGAACGCCTTTTC
1 CTTTTCAAAGCCCACACAAGCTGGTGGCACTTCTCAGTCCTCAAAGAGTAGAACGCCTTCCC
* *
1094113 CTTTT-AAAGCCCACACAAGTTGGTGGCACCTTCT-AGTCCTTAAAGAGTA-AGACG-CTCTCCC
1 CTTTTCAAAGCCCACACAAGCTGGTGGCA-CTTCTCAGTCCTCAAAGAGTAGA-ACGCCT-TCCC
1094174 CTTT
1 CTTT
1094178 CACCTTTTAG
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
60 3 0.05
61 44 0.79
62 9 0.16
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.29
Consensus pattern (62 bp):
CTTTTCAAAGCCCACACAAGCTGGTGGCACTTCTCAGTCCTCAAAGAGTAGAACGCCTTCCC
Found at i:1094355 original size:94 final size:94
Alignment explanation
Indices: 1094112--1094332 Score: 424
Period size: 94 Copynumber: 2.4 Consensus size: 94
1094102 AACGCCTTTT
* *
1094112 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTTAAAGAGTAAGACGCTCTCCCCTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAAGACGCTCTCCCCTT
1094177 TCACCTTTTAGTCCTCAAAGAGCAGGATG
66 TCACCTTTTAGTCCTCAAAGAGCAGGATG
1094206 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAAGACGCTCTCCCCTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAAGACGCTCTCCCCTT
1094271 TCACCTTTTAGTCCTCAAAGAGCAGGATG
66 TCACCTTTTAGTCCTCAAAGAGCAGGATG
1094300 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTT
1094333 TCAGTTCTCA
Statistics
Matches: 125, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 125 1.00
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.26
Consensus pattern (94 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAAGACGCTCTCCCCTT
TCACCTTTTAGTCCTCAAAGAGCAGGATG
Found at i:1094417 original size:110 final size:111
Alignment explanation
Indices: 1094276--1094694 Score: 412
Period size: 110 Copynumber: 3.6 Consensus size: 111
1094266 CCCTTTCACC
*
1094276 TTTTAGTCCTCAAAGAGCAGGATG-CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTTC
1 TTTTAGTCCTCAAAGAGCAGGATGTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
* *
1094340 TCAAAAAGCTGGACGCCTTTCAAAGCCTACACAAGTTGGTGGCATT
66 TCAAAAAGCAGGACACCTTTCAAAGCCTACACAAGTTGGTGGCATT
* *
1094386 TTTTAGTCCTCAAAGAGCAGGATG-CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAATC
1 TTTTAGTCCTCAAAGAGCAGGATGTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTC
* * *
1094449 CTCAAAGAGCAGGACACCTTTCAAAGCCCACATAAGTTGGTGGCATT
65 CTCAAAAAGCAGGACACCTTTCAAAGCCTACACAAGTTGGTGGCATT
** * ** * * *
1094496 TTCCAGTCCTCAAAGAGCAGGATGCTTTCTCCTTTTAAAGAGCACCCAAGTTGGTGGCAACTTCC
1 TTTTAGTCCTCAAAGAGCAGGATG-----TCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * **
1094561 AGTCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCTACACAAGTTGGTGACACC
61 AGTCCTCAAAAAGCAGGA--C--AC-CTTT-CAAAGCCTACACAAGTTGGTGGCATT
* * * * * * *
1094618 TTTTAGTCCTTAAAGAGTAGGACGCCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 TTTTAGTCCTCAAAGAGCAGGA-----TGTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1094683 AGTCCTCAAAAA
61 AGTCCTCAAAAA
1094695 ACAAGACGCC
Statistics
Matches: 251, Mismatches: 39, Indels: 26
0.79 0.12 0.08
Matches are distributed among these distances:
109 3 0.01
110 120 0.48
116 43 0.17
117 2 0.01
118 1 0.00
120 1 0.00
121 4 0.02
122 76 0.30
127 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (111 bp):
TTTTAGTCCTCAAAGAGCAGGATGTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
TCAAAAAGCAGGACACCTTTCAAAGCCTACACAAGTTGGTGGCATT
Found at i:1094683 original size:61 final size:60
Alignment explanation
Indices: 1094275--1094692 Score: 366
Period size: 55 Copynumber: 7.3 Consensus size: 60
1094265 CCCCTTTCAC
1094275 CTTTT-AGTCCTCAAAGAGCAGGATGC----C-TTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGATGCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * * *
1094329 CCTTTCAGTTCTCAAAAAGCTGGACGC----C-TTTCAAAGCCTACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGATGCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1094384 TTTTTTAGTCCTCAAAGAGCAGGATGC----C-TTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGATGCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
1094439 -TTTTCCAATCCTCAAAGAGCAGGA--C---ACCTTTCAAAGCCCACATAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGATGCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
** *
1094494 -TTTTCCAGTCCTCAAAGAGCAGGATGCTTTCTCCTTTT-AAAGAGCACCCAAGTTGGTGGCAA
1 CTTTT-CAGTCCTCAAAGAGCAGGATGCTTT-T-CTTTTCAAAGCCCACACAAGTTGGTGGC-A
* * * *
1094556 C-TTCCAGTCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCTACACAAGTTGGTGACA
1 CTTTTCAGTCCTCAAAGAGCAGGATGCTTT-TCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
1094616 CCTTTT-AGTCCTTAAAGAGTAGGACGCCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
1 -CTTTTCAGTCCTCAAAGAGCAGGATG-CTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
*
1094677 CTTTTTAGTCCTCAAA
1 CTTTTCAGTCCTCAAA
1094693 AAACAAGACG
Statistics
Matches: 306, Mismatches: 40, Indels: 29
0.82 0.11 0.08
Matches are distributed among these distances:
53 1 0.00
54 9 0.03
55 157 0.51
57 1 0.00
60 10 0.03
61 115 0.38
62 13 0.04
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.28
Consensus pattern (60 bp):
CTTTTCAGTCCTCAAAGAGCAGGATGCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:1094704 original size:61 final size:62
Alignment explanation
Indices: 1094467--1094692 Score: 241
Period size: 61 Copynumber: 3.7 Consensus size: 62
1094457 GCAGGACACC
* *
1094467 TTTCAAAGCCCACATAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGCTTTCTCCT
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCTTTCTCCT
** * * *
1094529 TTT-AAAGAGCACCCAAGTTGGTGGCAAC-TTCCAGTCCTCAAAGAGCAGGATGCTTTCT-CT
1 TTTCAAAGCCCACACAAGTTGGTGGC-ACTTTTCAGTCCTCAAAGAGCAGGACGCTTTCTCCT
* * * * *
1094589 TTGCAAAGCCTACACAAGTTGGTGACACCTTTT-AGTCCTTAAAGAGTAGGACGCCTTT-T-CT
1 TTTCAAAGCCCACACAAGTTGGTGGCA-CTTTTCAGTCCTCAAAGAGCAGGACG-CTTTCTCCT
* *
1094650 TTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAA
1 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAA
1094693 AAACAAGACG
Statistics
Matches: 137, Mismatches: 20, Indels: 15
0.80 0.12 0.09
Matches are distributed among these distances:
60 10 0.07
61 115 0.84
62 12 0.09
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (62 bp):
TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCTTTCTCCT
Found at i:1094821 original size:42 final size:42
Alignment explanation
Indices: 1094705--1094870 Score: 194
Period size: 42 Copynumber: 3.9 Consensus size: 42
1094695 ACAAGACGCC
* *
1094705 ATTTTCCTTTTCTCCTTTT-TCCTCAAAGAGCAGGACACACTTC
1 ATTTTCCTTTT-T-CTTTTGTCCTCAAAGAGCAGGACGCACTTT
*
1094748 ATTCTCTTCTTTTCTCTTTTGTCCTCAAAGAGCAGGACGCACTTT
1 ATT-T-TCCTTTT-TCTTTTGTCCTCAAAGAGCAGGACGCACTTT
*
1094793 ATTTTCCTCTTTCTTTTGTCCTCAAAGAGCAGGACGCA-TTT
1 ATTTTCCTTTTTCTTTTGTCCTCAAAGAGCAGGACGCACTTT
* *
1094834 CGTTTTCCTTTTTCCTTTGTCCTCGAAA-AGCAGGACG
1 -ATTTTCCTTTTTCTTTTGTCCTC-AAAGAGCAGGACG
1094871 TACTCTTTCT
Statistics
Matches: 110, Mismatches: 8, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
41 3 0.03
42 56 0.51
43 11 0.10
44 7 0.06
45 33 0.30
ACGTcount: A:0.19, C:0.27, G:0.14, T:0.40
Consensus pattern (42 bp):
ATTTTCCTTTTTCTTTTGTCCTCAAAGAGCAGGACGCACTTT
Found at i:1094824 original size:87 final size:84
Alignment explanation
Indices: 1094705--1094870 Score: 210
Period size: 87 Copynumber: 1.9 Consensus size: 84
1094695 ACAAGACGCC
* * *
1094705 ATTTTCCTTTTCTCCTTTTTCCTCAAAGAGCAGGACACACTTCATTCTCTTCTTTTCTCTTTTGT
1 ATTTTCCTTTTCT-CTTTGTCCTCAAAGAGCAGGACACACTTCATT-T-TCCTTTT-TCCTTTGT
1094770 CCTC-AAAGAGCAGGACGCACTTT
62 CCTCGAAA-AGCAGGACGCACTTT
* * *
1094793 ATTTTCCTCTTTCT-TTTGTCCTCAAAGAGCAGGACGCATTTCGTTTTCCTTTTTCCTTTGTCCT
1 ATTTTCCT-TTTCTCTTTGTCCTCAAAGAGCAGGACACACTTCATTTTCCTTTTTCCTTTGTCCT
1094857 CGAAAAGCAGGACG
65 CGAAAAGCAGGACG
1094871 TACTCTTTCT
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
84 20 0.29
85 9 0.13
86 1 0.01
87 27 0.39
88 8 0.11
89 5 0.07
ACGTcount: A:0.19, C:0.27, G:0.14, T:0.40
Consensus pattern (84 bp):
ATTTTCCTTTTCTCTTTGTCCTCAAAGAGCAGGACACACTTCATTTTCCTTTTTCCTTTGTCCTC
GAAAAGCAGGACGCACTTT
Found at i:1095599 original size:20 final size:20
Alignment explanation
Indices: 1095570--1095622 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1095560 TTTTCACAAT
1095570 TTGTATCGATACATTATTCA
1 TTGTATCGATACATTATTCA
* *
1095590 TTGTAACGATACATTGTTCA
1 TTGTATCGATACATTATTCA
1095610 TTGTATCGATACA
1 TTGTATCGATACA
1095623 ATGTATCGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACATTATTCA
Found at i:1095649 original size:13 final size:13
Alignment explanation
Indices: 1095608--1095650 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
1095598 ATACATTGTT
1095608 CATTGTATCGATA
1 CATTGTATCGATA
*
1095621 CAATGTATCGATA
1 CATTGTATCGATA
*
1095634 CATTGTATCAATA
1 CATTGTATCGATA
1095647 CATT
1 CATT
1095651 CTGGGTTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1098246 original size:79 final size:77
Alignment explanation
Indices: 1098001--1098295 Score: 349
Period size: 78 Copynumber: 3.8 Consensus size: 77
1097991 TTCATCTCGA
1098001 GGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGATACTCTAATCCC
1 GGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGATACTCTAATCCC
1098066 GTTATTTCCGAG
66 GTTATTTCCGAG
1098078 GGAATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGATACTCTAATCC
1 GG-ATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGATACTCTAATCC
* *
1098143 TGTTATTTTCGAG
65 CGTTATTTCCGAG
* * * * * * * * *
1098156 AGGATACTCCAACTCCGATTTTATTCCTAAAGC-CCTATTTTTTCACAATTTGGGATACTCTAAC
1 -GGATACTCCAACCCCGGTTTTATTTCTAAAACATC-AATTTTTCATAA-TCGGGATACTCTAAT
**
1098220 CCCGGCATTTCCGAAG
63 CCCGTTATTTCCG-AG
* * * * * *
1098236 GGATACTCCAACCCCCTGTTTTATTTTTGAAACACCAATTTTCCACAATCGAGGATACTC
1 GGATACTCCAA-CCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCG-GGATACTC
1098296 CAACTCTGAT
Statistics
Matches: 185, Mismatches: 25, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
77 3 0.02
78 109 0.59
79 37 0.20
80 34 0.18
81 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.34
Consensus pattern (77 bp):
GGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGATACTCTAATCCC
GTTATTTCCGAG
Found at i:1098451 original size:51 final size:51
Alignment explanation
Indices: 1098393--1098510 Score: 137
Period size: 51 Copynumber: 2.3 Consensus size: 51
1098383 CTATTTTCGA
* * * * * *
1098393 GGGGATACTCAAACCTCGGCTTTATTTCCAAAATATTAATTTCTCACAATC
1 GGGGATACTCCAACCCCAGCCTTATTTCCAAAACATCAATTTCTCACAATC
* * * *
1098444 GGGGATACTCCAACCCCAGCCTTATTTCTAAAGCATCGATTTTTCACAATC
1 GGGGATACTCCAACCCCAGCCTTATTTCCAAAACATCAATTTCTCACAATC
*
1098495 AGGGATACTCCAACCC
1 GGGGATACTCCAACCC
1098511 TGTTATTTTC
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (51 bp):
GGGGATACTCCAACCCCAGCCTTATTTCCAAAACATCAATTTCTCACAATC
Found at i:1098527 original size:79 final size:78
Alignment explanation
Indices: 1098444--1098661 Score: 237
Period size: 79 Copynumber: 2.8 Consensus size: 78
1098434 TCTCACAATC
** *
1098444 GGGGATACTCCAACCCCAGCCTTATTTCTAAAGCATCGATTTTTCACAATCAGGGATACTCCAAC
1 GGGGATACTCCAACCCCAGTTTTATTTCTAAA-CATCGATTTTTCATAATCAGGGATACTCCAAC
1098509 CCTGTTATTT-TCGA
65 CCTGTTATTTCT-GA
* * *
1098523 GGGGATACTCTAACCCCAATTTTATTT-TCAAA-ATACTGA-TTTTCTATAATTAGGGATACTCC
1 GGGGATACTCCAACCCCAGTTTTATTTCT-AAACAT-C-GATTTTTC-ATAATCAGGGATACTCC
* *
1098585 GACCTTGTTATTTCTGA
62 AACCCTGTTATTTCTGA
* * * *
1098602 GGGGATACTCCAACCCTAGTTTTATTTCCAGAACACCGATTTTTCATAATCGGGGATACT
1 GGGGATACTCCAACCCCAGTTTTATTTCTA-AACATCGATTTTTCATAATCAGGGATACT
1098662 TCAGCCCCAT
Statistics
Matches: 115, Mismatches: 15, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
77 2 0.02
78 7 0.06
79 96 0.83
80 9 0.08
81 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (78 bp):
GGGGATACTCCAACCCCAGTTTTATTTCTAAACATCGATTTTTCATAATCAGGGATACTCCAACC
CTGTTATTTCTGA
Found at i:1107152 original size:39 final size:39
Alignment explanation
Indices: 1107077--1107167 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 39
1107067 TTTTCTTTCT
1107077 CCCTTAATTAAAGTAATTTTAACAAATTCGTACATTCTCC
1 CCCTTAATTAAAGTAATTTTAACAAATTCG-ACATTCTCC
* *
1107117 CCCTTAA-TAAGGTAATTTTAGCAAATTTACG-CATTCTCC
1 CCCTTAATTAAAGTAATTTTAACAAA-TT-CGACATTCTCC
* *
1107156 CCTTTTATTAAA
1 CCCTTAATTAAA
1107168 AAAAATCTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
39 29 0.67
40 12 0.28
41 2 0.05
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (39 bp):
CCCTTAATTAAAGTAATTTTAACAAATTCGACATTCTCC
Found at i:1109020 original size:13 final size:13
Alignment explanation
Indices: 1109002--1109039 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1108992 ATAATCCCCC
1109002 TGTATCGATACAG
1 TGTATCGATACAG
*
1109015 TGTATCGATACAT
1 TGTATCGATACAG
1109028 TGTATCGATACA
1 TGTATCGATACA
1109040 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1111130 original size:15 final size:15
Alignment explanation
Indices: 1111110--1111140 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1111100 ATTTCGTTTG
*
1111110 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1111125 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1111140 G
1 G
1111141 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1114321 original size:52 final size:52
Alignment explanation
Indices: 1114254--1114391 Score: 213
Period size: 52 Copynumber: 2.7 Consensus size: 52
1114244 AATTTATCTG
1114254 CATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTA
1 CATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTA
* * *
1114306 CATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCCTG
1 CATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTA
*** *
1114358 CATGTATCGATACAAAGATTAGTGTATCGATACA
1 CATGTATCGATACATTTAATAGTGTATCGATACA
1114392 ATGTATCGAT
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 77 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (52 bp):
CATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTA
Found at i:1114398 original size:13 final size:13
Alignment explanation
Indices: 1114380--1114438 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
1114370 CAAAGATTAG
1114380 TGTATCGATACAA
1 TGTATCGATACAA
1114393 TGTATCGATAC-A
1 TGTATCGATACAA
1114405 TG--T-GAGT--AA
1 TGTATCGA-TACAA
1114414 TGTATCGATACAA
1 TGTATCGATACAA
1114427 TGTATCGATACA
1 TGTATCGATACA
1114439 TGTGAGTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
9 5 0.13
10 2 0.05
11 2 0.05
12 5 0.13
13 25 0.64
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1114423 original size:34 final size:34
Alignment explanation
Indices: 1114380--1114459 Score: 160
Period size: 34 Copynumber: 2.4 Consensus size: 34
1114370 CAAAGATTAG
1114380 TGTATCGATACAATGTATCGATACATGTGAGTAA
1 TGTATCGATACAATGTATCGATACATGTGAGTAA
1114414 TGTATCGATACAATGTATCGATACATGTGAGTAA
1 TGTATCGATACAATGTATCGATACATGTGAGTAA
1114448 TGTATCGATACA
1 TGTATCGATACA
1114460 TTTTTTTTGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (34 bp):
TGTATCGATACAATGTATCGATACATGTGAGTAA
Found at i:1114521 original size:13 final size:13
Alignment explanation
Indices: 1114503--1114527 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1114493 CAAAAAAATA
1114503 TGTATCGATACAT
1 TGTATCGATACAT
1114516 TGTATCGATACA
1 TGTATCGATACA
1114528 ACATTTTATG
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:1114523 original size:33 final size:33
Alignment explanation
Indices: 1114481--1114547 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1114471 AGTAGCTTAA
1114481 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1114514 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1114547 A
1 A
1114548 GATCATTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1118844 original size:13 final size:13
Alignment explanation
Indices: 1118826--1118851 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1118816 CAACTTTATG
1118826 TGTATCGATACAT
1 TGTATCGATACAT
1118839 TGTATCGATACAT
1 TGTATCGATACAT
1118852 ACTTTGTGTA
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:1118865 original size:32 final size:33
Alignment explanation
Indices: 1118806--1118869 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
1118796 TACAGGCCAA
1118806 TGTATCGATACAACTTTATGTGTATCGATACAT
1 TGTATCGATACAACTTTATGTGTATCGATACAT
1118839 TGTATCGATACATAC-TT-TGTGTATCGATACA
1 TGTATCGATACA-ACTTTATGTGTATCGATACA
1118870 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 14 0.47
33 14 0.47
34 2 0.07
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAACTTTATGTGTATCGATACAT
Found at i:1119327 original size:13 final size:13
Alignment explanation
Indices: 1119309--1119335 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1119299 ACATTATGCT
1119309 TTGTATCGATACA
1 TTGTATCGATACA
1119322 TTGTATCGATACA
1 TTGTATCGATACA
1119335 T
1 T
1119336 GCACAATTGT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1124207 original size:34 final size:35
Alignment explanation
Indices: 1124169--1124235 Score: 93
Period size: 37 Copynumber: 1.9 Consensus size: 35
1124159 CCTTACAACA
*
1124169 CTATC-TTT-AAAGGCTAAGATGGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
1124203 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1124236 AATCACTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 5 0.17
36 11 0.38
37 13 0.45
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:1124711 original size:13 final size:13
Alignment explanation
Indices: 1124693--1124718 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1124683 CAATTTTTTG
1124693 TGTATCGATACAT
1 TGTATCGATACAT
1124706 TGTATCGATACAT
1 TGTATCGATACAT
1124719 ACTTTGTGTA
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:1124730 original size:32 final size:33
Alignment explanation
Indices: 1124673--1124736 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1124663 TACAAGCCAA
**
1124673 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1124706 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1124737 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1125417 original size:39 final size:39
Alignment explanation
Indices: 1125342--1125422 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
1125332 TTTTATTTCT
1125342 CCCTTAATCAAAATAATTTTAACAAATTCGTACATTCTCC
1 CCCTTAATCAAAATAATTTTAACAAATTCG-ACATTCTCC
* *
1125382 CCCTTAAT-AAGATAATTTTAGCAAATTTACG-CATTCTCC
1 CCCTTAATCAAAATAATTTTAACAAA-TT-CGACATTCTCC
1125421 CC
1 CC
1125423 TTTTATTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
39 25 0.68
40 10 0.27
41 2 0.05
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.35
Consensus pattern (39 bp):
CCCTTAATCAAAATAATTTTAACAAATTCGACATTCTCC
Found at i:1126870 original size:23 final size:24
Alignment explanation
Indices: 1126825--1126871 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1126815 CAAAGAATTG
*
1126825 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
1126849 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
1126872 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:1127905 original size:84 final size:84
Alignment explanation
Indices: 1127750--1127914 Score: 201
Period size: 84 Copynumber: 2.0 Consensus size: 84
1127740 CATTTTCCAC
* * * *
1127750 TTGCAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTCTTTTTAAAAGAATTATTTTCTAAAC
1 TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
1127815 TCATTGATTTACTTTCATT
66 TCATTGATTTACTTTCATT
* *
1127834 TTGCAACTC-TTTCATATTCTTCTCTAATTCACTTAATTTC-TTTT-CAAGAATATCATTCTCTA
1 TTGCAACTCATTTC-TATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAAT-T-ATTCTCTA
* * *
1127896 CACTTATTGATTTATTTTC
63 AACTCATTGATTTACTTTC
1127915 TTCTTTGAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
82 6 0.09
83 9 0.13
84 54 0.78
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.52
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:1129985 original size:13 final size:13
Alignment explanation
Indices: 1129967--1129992 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1129957 CAATTTTTTG
1129967 TGTATCGATACAT
1 TGTATCGATACAT
1129980 TGTATCGATACAT
1 TGTATCGATACAT
1129993 ACTTTGTGTA
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:1130004 original size:32 final size:33
Alignment explanation
Indices: 1129947--1130010 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1129937 TACAAGCCAA
**
1129947 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1129980 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1130011 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1133623 original size:33 final size:33
Alignment explanation
Indices: 1133586--1133652 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
1133576 CGAGAGTTGA
* * *
1133586 TCACTTCACTTTCGCAGCACAT-GAGTGAGCACT
1 TCACTTCACTCTCACAACACATGGA-TGAGCACT
1133619 TCACTTCACTCTCACAACACATGGATGAGCACT
1 TCACTTCACTCTCACAACACATGGATGAGCACT
1133652 T
1 T
1133653 TAGTGCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (33 bp):
TCACTTCACTCTCACAACACATGGATGAGCACT
Found at i:1133963 original size:17 final size:17
Alignment explanation
Indices: 1133941--1134002 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
1133931 AAAGGGAAAG
1133941 AATTTTTTTTGAAAATA
1 AATTTTTTTTGAAAATA
* * **
1133958 AATTTTTTATCAAAGGGGA
1 AATTTTTTTTGAAA--ATA
1133977 GAATTTTTTTTGAAAATA
1 -AATTTTTTTTGAAAATA
1133995 AATTTTTT
1 AATTTTTT
1134003 ATCAAGAGGG
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
17 20 0.59
18 1 0.03
19 1 0.03
20 12 0.35
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.50
Consensus pattern (17 bp):
AATTTTTTTTGAAAATA
Found at i:1133985 original size:38 final size:37
Alignment explanation
Indices: 1133939--1134023 Score: 145
Period size: 37 Copynumber: 2.3 Consensus size: 37
1133929 AAAAAGGGAA
1133939 AGAATTTTTTTTGAAAATAAATTTTTTATCAA-AGGGG
1 AGAATTTTTTTTGAAAATAAATTTTTTATCAAGA-GGG
1133976 AGAATTTTTTTTGAAAATAAATTTTTTATCAAGAGGG
1 AGAATTTTTTTTGAAAATAAATTTTTTATCAAGAGGG
*
1134013 AGAAATTTTTT
1 AGAATTTTTTT
1134024 AAACGAGAGC
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
37 45 0.98
38 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.15, T:0.45
Consensus pattern (37 bp):
AGAATTTTTTTTGAAAATAAATTTTTTATCAAGAGGG
Done.