Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008275.1 Hibiscus syriacus cultivar Beakdansim tig00110933_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1991061
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 8
Found at i:991594 original size:128 final size:127
Alignment explanation
Indices: 991284--991964 Score: 1110
Period size: 128 Copynumber: 5.4 Consensus size: 127
991274 TACTGAAGAG
*
991284 GAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATACCAGTACC
1 GAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACC
*
991349 TATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGA
66 TATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTTGTCAGA
* *
991411 GAATATTTTATCGTTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACC
1 GAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACC
*
991476 TATTATTTCTCAGGGGACTTGAAGGCGCGTCCCCGGAGGCGCGCCTTCCATTATTTTGTCAGA
66 TATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGG-GGCGCGCCTTCCATTATTTTGTCAGA
* *
991539 GAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATTATTACC
1 GAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACC
* * * *
991604 TATTATTTCTCAGGGGACTTGAAGGCGCGTTCACGGGGGAGCGCCTTCTATTATTTTATCAGA
66 TATTATTTCTCAGGGGACTTGAAGGCGCGTTC-CCGGGGCGCGCCTTCCATTATTTTGTCAGA
* *
991667 G-A-A---TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGAACACTATTCATATCATTACC
1 GAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACC
*
991727 TATTATTTCTCATGGGACTTGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCAGA
66 TATTATTTCTCAGGGGACTTGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTTGTCAGA
* *
991790 GAATATGTTATTATTGCCCTATTATGTCACTCATGTCCCTC-GGGACACTATTC--AT-AGTACA
1 GAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACC
991851 TATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGA
66 TATTATTTCTCAGGGGACTTGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTTGTCAGA
*
991914 GAATATGTTATCATTGCCCTATTTTGTCACTCATGTCCCTCGGGGACACTA
1 GAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTA
991965 GATGGATTGC
Statistics
Matches: 516, Mismatches: 29, Indels: 20
0.91 0.05 0.04
Matches are distributed among these distances:
122 1 0.00
123 112 0.22
124 105 0.20
125 12 0.02
126 1 0.00
127 109 0.21
128 173 0.34
129 3 0.01
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (127 bp):
GAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACC
TATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTTGTCAGA
Found at i:991777 original size:251 final size:252
Alignment explanation
Indices: 991284--991964 Score: 1115
Period size: 251 Copynumber: 2.7 Consensus size: 252
991274 TACTGAAGAG
*
991284 GAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATACCAGTACC
1 GAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATA-TAGTACC
991349 TATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAA
65 TATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAA
*
991414 TATTTTATCGTTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTAT
130 TA--TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTAT
*
991479 TATTTCTCAGGGGACTTGAAGGCGCGTCCCCGGAGGCGCGCCTTCCATTATTTTGTCAGA
193 TATTTCTCAGGGGACTTGAAGGCGCGTCCCAGGAGGCGCGCCTTCCATTATTTTGTCAGA
*
991539 GAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATTATTACC
1 GAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATA-TAGTACC
* * *
991604 TATTATTTCTCAGGGGACTTGAAGGCGCGTTCACGGGGGAGCGCCTTCTATTATTTTATCAGAG-
65 TATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGG-GCGCCTTCCATTATTTTGTCAGAGA
* *
991668 A-A-TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGAACACTATTCATATCATTACCTATT
129 ATATTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATT
*
991731 ATTTCTCATGGGACTTGAAGGCGCGTTCCCAGG-GGCGCGCCTTCCATTATTTTGTCAGA
194 ATTTCTCAGGGGACTTGAAGGCGCG-TCCCAGGAGGCGCGCCTTCCATTATTTTGTCAGA
* *
991790 GAATATGTTATTATTGCCCTATTATGTCACTCATGTCCCTC-GGGACACTATTC--ATAGTACAT
1 GAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATAGTACCT
991852 ATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAA
66 ATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGG-GCGCCTTCCATTATTTTGTCAGAGAA
*
991917 TATGTTATCATTGCCCTATTTTGTCACTCATGTCCCTCGGGGACACTA
130 TA--TTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTA
991965 GATGGATTGC
Statistics
Matches: 399, Mismatches: 20, Indels: 17
0.92 0.05 0.04
Matches are distributed among these distances:
247 65 0.16
248 2 0.01
249 1 0.00
250 12 0.03
251 148 0.37
252 47 0.12
254 1 0.00
255 101 0.25
256 22 0.06
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (252 bp):
GAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATAGTACCT
ATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAAT
ATTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTAT
TTCTCAGGGGACTTGAAGGCGCGTCCCAGGAGGCGCGCCTTCCATTATTTTGTCAGA
Found at i:992145 original size:23 final size:23
Alignment explanation
Indices: 992097--992151 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
992087 TGAAGTTTGA
* * *
992097 ATAAATTGGATAAAATGTTATGG
1 ATAAATTGAATAAAATGTGAAGG
992120 ATAAATTGAAT-AAATGTGAAGTG
1 ATAAATTGAATAAAATGTGAAG-G
*
992143 ATAAGTTGA
1 ATAAATTGA
992152 TTGTCACATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.45, C:0.00, G:0.22, T:0.33
Consensus pattern (23 bp):
ATAAATTGAATAAAATGTGAAGG
Found at i:992396 original size:34 final size:33
Alignment explanation
Indices: 992357--992457 Score: 113
Period size: 34 Copynumber: 3.2 Consensus size: 33
992347 TAAGTTGAAA
*
992357 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATA-TATAATTTATAT
*
992391 TTTAATTTTAAATTTTGAATA-AT-A-TTAT-T
1 TTTAATTTTAAATTTCGAATATATAATTTATAT
* *
992420 TTT-ATTTTAAATTTCAAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAAT-ATATAATTTATAT
992453 TTTAA
1 TTTAA
992458 AAACATTTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
28 14 0.25
29 5 0.09
30 6 0.11
31 2 0.04
32 5 0.09
33 4 0.07
34 20 0.36
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (33 bp):
TTTAATTTTAAATTTCGAATATATAATTTATAT
Found at i:992419 original size:28 final size:27
Alignment explanation
Indices: 992388--992458 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 27
992378 CTATAATTTA
**
992388 TATTTTAATTTTAAATTTTGAATAATAT
1 TATTTT-ATTTTAAATTTCAAATAATAT
992416 TATTTTTATTTTAAATTTCAAATAATAT
1 TA-TTTTATTTTAAATTTCAAATAATAT
*
992444 AATTTGTATTTTAAA
1 TATTT-TATTTTAAA
992459 AACATTTATC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 3 0.08
28 31 0.82
29 4 0.11
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.56
Consensus pattern (27 bp):
TATTTTATTTTAAATTTCAAATAATAT
Found at i:993040 original size:42 final size:42
Alignment explanation
Indices: 992977--993085 Score: 182
Period size: 42 Copynumber: 2.6 Consensus size: 42
992967 TATGGTATAA
* *
992977 AACCCTGCGGGCTAGGCATGTAACCTGGCGGGCTAGAAATGT
1 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGAAATGT
* *
993019 AACCCTGCAGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGAAATGT
993061 AACCCTGCGGGCTCGGAATGTAACC
1 AACCCTGCGGGCTCGGAATGTAACC
993086 CTGTGGAGAT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.24, C:0.26, G:0.32, T:0.18
Consensus pattern (42 bp):
AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGAAATGT
Found at i:993086 original size:21 final size:21
Alignment explanation
Indices: 992977--993088 Score: 147
Period size: 21 Copynumber: 5.3 Consensus size: 21
992967 TATGGTATAA
*
992977 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
992998 AA-CCTGGCGGGCTAGAAATGT
1 AACCCT-GCGGGCTAGGAATGT
* *
993019 AACCCTGCAGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
993040 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
993061 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
993082 AACCCTG
1 AACCCTG
993089 TGGAGATGAC
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.08
21 67 0.85
22 6 0.08
ACGTcount: A:0.23, C:0.26, G:0.32, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:993141 original size:21 final size:21
Alignment explanation
Indices: 993098--993142 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
993088 GTGGAGATGA
* *
993098 CATATGAACTGGTGGACTTGG
1 CATATGAACTGGAGGACTGGG
*
993119 CATATGAACTGGAGGGCTGGG
1 CATATGAACTGGAGGACTGGG
993140 CAT
1 CAT
993143 GTACCCCTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.16, G:0.36, T:0.24
Consensus pattern (21 bp):
CATATGAACTGGAGGACTGGG
Found at i:994911 original size:34 final size:31
Alignment explanation
Indices: 994868--994956 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 31
994858 TTAATAATTC
*
994868 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
*
994902 TAAAAAAATAATAATTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* * *
994933 TATAAAATATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
994957 AAAATACTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
31 6 0.12
32 17 0.35
33 2 0.04
34 23 0.48
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:994933 original size:31 final size:33
Alignment explanation
Indices: 994868--994947 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 33
994858 TTAATAATTC
* *
994868 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATATTA-TTTAA
994902 TAAAAAAATAATAATTACATAAATA-TA-TTAA
1 TAAAAAAATAATAATTACATAAATATTATTTAA
*
994933 TATAAAATATAATAA
1 TA-AAAAAATAATAA
994948 CTATTTAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
31 6 0.14
32 11 0.26
33 2 0.05
34 23 0.55
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (33 bp):
TAAAAAAATAATAATTACATAAATATTATTTAA
Found at i:998637 original size:28 final size:29
Alignment explanation
Indices: 998605--998659 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
998595 TAATATAAGT
998605 AATTTATAT-ATTTTCTTTAAAAAATTTA
1 AATTTATATAATTTTCTTTAAAAAATTTA
* *
998633 AATTTATATAATTTTTTTTATAAAATT
1 AATTTATATAATTTTCTTTAAAAAATT
998660 GAAAAGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (29 bp):
AATTTATATAATTTTCTTTAAAAAATTTA
Found at i:999664 original size:18 final size:19
Alignment explanation
Indices: 999641--999678 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
999631 CCCAATAATC
999641 TTATTCC-CTGATAATCTT
1 TTATTCCACTGATAATCTT
999659 TTATTCCTACTGATAATCTT
1 TTATTCC-ACTGATAATCTT
999679 ACATTCCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.24, C:0.21, G:0.05, T:0.50
Consensus pattern (19 bp):
TTATTCCACTGATAATCTT
Found at i:999684 original size:20 final size:20
Alignment explanation
Indices: 999648--999685 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
999638 ATCTTATTCC
**
999648 CTGATAATCTTTTATTCCTA
1 CTGATAATCTTACATTCCTA
999668 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
999686 GTGAATCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45
Consensus pattern (20 bp):
CTGATAATCTTACATTCCTA
Found at i:1001991 original size:22 final size:22
Alignment explanation
Indices: 1001961--1002054 Score: 161
Period size: 22 Copynumber: 4.3 Consensus size: 22
1001951 AATGGAATCA
1001961 TTCAACGCTGAATACTGAACCG
1 TTCAACGCTGAATACTGAACCG
*
1001983 TTCAGCGCTGAATACTGAACCG
1 TTCAACGCTGAATACTGAACCG
*
1002005 TTCAACGCTGAATATTGAACCG
1 TTCAACGCTGAATACTGAACCG
*
1002027 TTCAGCGCTGAATACTGAACCG
1 TTCAACGCTGAATACTGAACCG
1002049 TTCAAC
1 TTCAAC
1002055 ATTCAGCGTG
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 66 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (22 bp):
TTCAACGCTGAATACTGAACCG
Found at i:1002024 original size:44 final size:44
Alignment explanation
Indices: 1001961--1002054 Score: 179
Period size: 44 Copynumber: 2.1 Consensus size: 44
1001951 AATGGAATCA
1001961 TTCAACGCTGAATACTGAACCGTTCAGCGCTGAATACTGAACCG
1 TTCAACGCTGAATACTGAACCGTTCAGCGCTGAATACTGAACCG
*
1002005 TTCAACGCTGAATATTGAACCGTTCAGCGCTGAATACTGAACCG
1 TTCAACGCTGAATACTGAACCGTTCAGCGCTGAATACTGAACCG
1002049 TTCAAC
1 TTCAAC
1002055 ATTCAGCGTG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (44 bp):
TTCAACGCTGAATACTGAACCGTTCAGCGCTGAATACTGAACCG
Found at i:1002245 original size:15 final size:16
Alignment explanation
Indices: 1002209--1002246 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1002199 AGAGACTCTA
*
1002209 AATCATTCGGCATTTG
1 AATCATTCCGCATTTG
*
1002225 AATCATTCCGCGTTT-
1 AATCATTCCGCATTTG
1002240 AATCATT
1 AATCATT
1002247 ATGAAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (16 bp):
AATCATTCCGCATTTG
Found at i:1016925 original size:15 final size:16
Alignment explanation
Indices: 1016907--1016936 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1016897 ATATATGATT
1016907 TAAAA-AAAATATAAA
1 TAAAACAAAATATAAA
1016922 TAAAACAAAATATAA
1 TAAAACAAAATATAA
1016937 GTAATAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (16 bp):
TAAAACAAAATATAAA
Found at i:1028609 original size:26 final size:26
Alignment explanation
Indices: 1028558--1028609 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
1028548 ATTTCTAATT
* *
1028558 TTTTTGAAAAAAATCTAATATTTTAA
1 TTTTTGAAAAAAATATAATATGTTAA
*
1028584 TTTTTGATAAAAATAT-ATCATGTTAA
1 TTTTTGAAAAAAATATAAT-ATGTTAA
1028610 AAAGAAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (26 bp):
TTTTTGAAAAAAATATAATATGTTAA
Found at i:1030768 original size:36 final size:36
Alignment explanation
Indices: 1030677--1030752 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
1030667 CATGCGGGGT
*
1030677 TGACAGAGAAGGAGACGGAGCAGAAGCATTCGGGAC
1 TGACAGAGAAGGAGATGGAGCAGAAGCATTCGGGAC
* *
1030713 TGACAGAGAAGGAGATGGAGCAGAAGCATTTGGGAT
1 TGACAGAGAAGGAGATGGAGCAGAAGCATTCGGGAC
1030749 TGAC
1 TGAC
1030753 GGAAGAGGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.13, G:0.38, T:0.13
Consensus pattern (36 bp):
TGACAGAGAAGGAGATGGAGCAGAAGCATTCGGGAC
Found at i:1037156 original size:20 final size:20
Alignment explanation
Indices: 1037127--1037220 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
1037117 TTTTCCTAAT
*
1037127 TCGCATTGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
** *
1037147 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
1037168 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1037188 GCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1037208 TCGCAACGCGAAT
1 TCGCAATGCGAAT
1037221 CTGACTATCG
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 45 0.74
21 16 0.26
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1037157 original size:41 final size:41
Alignment explanation
Indices: 1037112--1037200 Score: 106
Period size: 41 Copynumber: 2.2 Consensus size: 41
1037102 ACTATAGCAT
* * * * *
1037112 TGCGATTTTCCTAATTCGCATTGCGAATACGTAAATCGCAA
1 TGCGAATTTCCAAAATCGCAATGCGAATACGTAAAGCGCAA
** *
1037153 TGCGAATTTGGAAAATCGCAATGCGATTACGTAAAGCGCAA
1 TGCGAATTTCCAAAATCGCAATGCGAATACGTAAAGCGCAA
1037194 TGCGAAT
1 TGCGAAT
1037201 ACGTAAATCG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (41 bp):
TGCGAATTTCCAAAATCGCAATGCGAATACGTAAAGCGCAA
Found at i:1037230 original size:20 final size:20
Alignment explanation
Indices: 1037207--1037253 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1037197 GAATACGTAA
*
1037207 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGAATCTGACT
*
1037227 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGAATCTGACT
1037247 ATCGCAA
1 ATCGCAA
1037254 TACTGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGAGAATCTGACT
Found at i:1038119 original size:24 final size:24
Alignment explanation
Indices: 1038092--1038145 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1038082 GTTTTTGAAA
1038092 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1038116 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1038140 TTTGAT
1 TTTGAT
1038146 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1040590 original size:20 final size:19
Alignment explanation
Indices: 1040565--1040657 Score: 107
Period size: 20 Copynumber: 4.8 Consensus size: 19
1040555 CAATGCGGAA
1040565 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAA-ATGACT
* *
1040585 ATCGCAACACATAAATGACT
1 ATCGCAACGC-GAAATGACT
1040605 ATCGCAACGCG-AATGACT
1 ATCGCAACGCGAAATGACT
*
1040623 ATTGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
* *
1040643 ACCGCAATGCGAAAT
1 ATCGCAACGCGAAAT
1040658 AAAAATCGCA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
18 16 0.26
19 6 0.10
20 38 0.61
21 2 0.03
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1040630 original size:38 final size:38
Alignment explanation
Indices: 1040565--1040655 Score: 110
Period size: 38 Copynumber: 2.3 Consensus size: 38
1040555 CAATGCGGAA
*
1040565 ATCGCAACGCGAATATGACTATCGCAACACATAAATGACT
1 ATCGCAACGCG-A-ATGACTATCGCAACACAGAAATGACT
* * *
1040605 ATCGCAACGCGAATGACTATTGCAACGCGGAAATGACT
1 ATCGCAACGCGAATGACTATCGCAACACAGAAATGACT
* *
1040643 ACCGCAATGCGAA
1 ATCGCAACGCGAA
1040656 ATAAAAATCG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 33 0.73
39 1 0.02
40 11 0.24
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (38 bp):
ATCGCAACGCGAATGACTATCGCAACACAGAAATGACT
Found at i:1040719 original size:20 final size:20
Alignment explanation
Indices: 1040694--1040748 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
1040684 GCGAAATTAG
* *
1040694 TTTCGCGTTGCGATTTTCAT
1 TTTCGCATTACGATTTTCAT
1040714 TTTCGCATTACGATTTTCAT
1 TTTCGCATTACGATTTTCAT
1040734 TTTCGCATTACGATT
1 TTTCGCATTACGATT
1040749 CACTCGTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.16, C:0.20, G:0.15, T:0.49
Consensus pattern (20 bp):
TTTCGCATTACGATTTTCAT
Found at i:1040781 original size:33 final size:33
Alignment explanation
Indices: 1040724--1040814 Score: 119
Period size: 33 Copynumber: 2.7 Consensus size: 33
1040714 TTTCGCATTA
*
1040724 CGATTTTCATTTTCGCATTACGATTCACTCGTTG
1 CGATTTTCA-TTTCGCATTGCGATTCACTCGTTG
*
1040758 CGATTTTCATTTCGCATTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCATTGCGATTCACTCGTTG
** *
1040791 CGATAGTCATTTCCGCGTTGCGAT
1 CGATTTTCATTT-CGCATTGCGAT
1040815 AGTCTGTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
33 32 0.63
34 19 0.37
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.42
Consensus pattern (33 bp):
CGATTTTCATTTCGCATTGCGATTCACTCGTTG
Found at i:1040938 original size:14 final size:14
Alignment explanation
Indices: 1040919--1040955 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1040909 CATCAATTAA
1040919 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1040933 ACAAATCATCTTTT
1 ACAAATCAACATTT
1040947 ACAAATCAA
1 ACAAATCAA
1040956 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1042926 original size:20 final size:20
Alignment explanation
Indices: 1042901--1042988 Score: 115
Period size: 20 Copynumber: 4.5 Consensus size: 20
1042891 GAAACTTAAA
*
1042901 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1042921 ATCGCAACGCGAAAATAACT
1 ATCGCAACGCGAAAATGACT
*
1042941 ATCGTAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * *
1042961 ATCGTAATGCG-AATTGACT
1 ATCGCAACGCGAAAATGACT
1042980 ATCGCAACG
1 ATCGCAACG
1042989 AGAGAATCGC
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
19 14 0.23
20 46 0.77
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1043056 original size:20 final size:20
Alignment explanation
Indices: 1043031--1043209 Score: 170
Period size: 20 Copynumber: 9.6 Consensus size: 20
1043021 GCGATTCTTT
**
1043031 CATTGCGATAGTCAAATTCG
1 CATTGCGATAGTCATTTTCG
1043051 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
1043071 CATTGCGATAGTCATTTTCT
1 CATTGCGATAGTCATTTTCG
1043091 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
1043111 CGTTGCGAT--T--TTGTT-G
1 CATTGCGATAGTCATT-TTCG
* **
1043127 --TTGTGATTTTCA-TTTCG
1 CATTGCGATAGTCATTTTCG
*
1043144 CATTGCGAT--T--TTCTCG
1 CATTGCGATAGTCATTTTCG
1043160 --TTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
1043178 CGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
1043198 CATTGCGATAGT
1 CATTGCGATAGT
1043210 AAACTATTAT
Statistics
Matches: 134, Mismatches: 10, Indels: 30
0.77 0.06 0.17
Matches are distributed among these distances:
14 13 0.10
16 11 0.08
17 5 0.04
18 6 0.04
19 6 0.04
20 93 0.69
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:1045059 original size:21 final size:21
Alignment explanation
Indices: 1045035--1045089 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
1045025 GAAACTTAAA
*
1045035 ATCGCAACACGAAAAATGACT
1 ATCGCAACGCGAAAAATGACT
**
1045056 ATCGCAACGCG-AATTTGACT
1 ATCGCAACGCGAAAAATGACT
1045076 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1045090 TGAAAATCGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.40, C:0.25, G:0.18, T:0.16
Consensus pattern (21 bp):
ATCGCAACGCGAAAAATGACT
Found at i:1045460 original size:22 final size:22
Alignment explanation
Indices: 1045435--1045483 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1045425 ATTTCGCCGA
1045435 AGATGGAGACTGATATCGTCGG
1 AGATGGAGACTGATATCGTCGG
* *
1045457 AGATGGGGACTGATTTCGTCGG
1 AGATGGAGACTGATATCGTCGG
1045479 AGATG
1 AGATG
1045484 AGGACGGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.39, T:0.24
Consensus pattern (22 bp):
AGATGGAGACTGATATCGTCGG
Found at i:1045488 original size:22 final size:21
Alignment explanation
Indices: 1045423--1045488 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 21
1045413 TGATCGTGAA
* *
1045423 TGATTTCGCCGAAGATGGAGAC
1 TGATTTCGTCGGAGATGG-GAC
*
1045445 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGAT-GGGAC
1045467 TGATTTCGTCGGAGATGAGGAC
1 TGATTTCGTCGGAGATG-GGAC
1045489 GGATGTCGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 35 0.92
23 2 0.05
ACGTcount: A:0.24, C:0.15, G:0.36, T:0.24
Consensus pattern (21 bp):
TGATTTCGTCGGAGATGGGAC
Found at i:1045706 original size:20 final size:20
Alignment explanation
Indices: 1045683--1045792 Score: 103
Period size: 20 Copynumber: 5.5 Consensus size: 20
1045673 CGATAGTCAG
* *
1045683 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
1045703 ATTCGCATTTCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
1045723 ATTCGCTTTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * * **
1045743 AATCGCATTGTGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
* *
1045764 ATTCGCGTTGCAATTTACGT
1 ATTCGCATTGCGATTTACGT
1045784 ATTCGCATT
1 ATTCGCATT
1045793 ACGAATTAGG
Statistics
Matches: 70, Mismatches: 19, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
20 57 0.81
21 13 0.19
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1045727 original size:40 final size:41
Alignment explanation
Indices: 1045683--1045792 Score: 125
Period size: 41 Copynumber: 2.7 Consensus size: 41
1045673 CGATAGTCAG
* **
1045683 ATTCGCGTTGCGATTTACATATTCGCATT-TCGA-TTTACGT
1 ATTCGCGTTGCGATTTACGTATTCGCATTGT-GATTTTACAA
* * * *
1045723 ATTCGCTTTGTGATTTACGTAATCGCATTGTGATTTTCCAA
1 ATTCGCGTTGCGATTTACGTATTCGCATTGTGATTTTACAA
*
1045764 ATTCGCGTTGCAATTTACGTATTCGCATT
1 ATTCGCGTTGCGATTTACGTATTCGCATT
1045793 ACGAATTAGG
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
40 27 0.47
41 30 0.53
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (41 bp):
ATTCGCGTTGCGATTTACGTATTCGCATTGTGATTTTACAA
Found at i:1045810 original size:21 final size:21
Alignment explanation
Indices: 1045793--1045833 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1045783 TATTCGCATT
1045793 ACGAATTAGGAAAATCGCAAC
1 ACGAATTAGGAAAATCGCAAC
* *
1045814 GCGAATTTGGAAAATCGCAA
1 ACGAATTAGGAAAATCGCAA
1045834 TGTGATAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (21 bp):
ACGAATTAGGAAAATCGCAAC
Found at i:1047784 original size:31 final size:30
Alignment explanation
Indices: 1047748--1047812 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
1047738 ATTTAGTGAT
* * *
1047748 AAAATTTGGAGGGATCAATTTAAAATTTTTA
1 AAAATTTAGAAGGAT-AAATTAAAATTTTTA
* *
1047779 AAAATTTAGAAGTATAAATTAAAATTTTTG
1 AAAATTTAGAAGGATAAATTAAAATTTTTA
1047809 AAAA
1 AAAA
1047813 GTTCAATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 17 0.59
31 12 0.41
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (30 bp):
AAAATTTAGAAGGATAAATTAAAATTTTTA
Found at i:1055753 original size:44 final size:44
Alignment explanation
Indices: 1055703--1055792 Score: 137
Period size: 44 Copynumber: 2.0 Consensus size: 44
1055693 GTTTTTGTTA
1055703 TACGAATTTAGATGATCCA-AAATTTCACGATGTTTTGAAAGTCG
1 TACGAATTTAGATGAT-CAGAAATTTCACGATGTTTTGAAAGTCG
***
1055747 TACGAATTTAGATGATCAGAAATTTGTTGATGTTTTGAAAGTCG
1 TACGAATTTAGATGATCAGAAATTTCACGATGTTTTGAAAGTCG
1055791 TA
1 TA
1055793 ACCTATATGA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
43 2 0.05
44 40 0.95
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (44 bp):
TACGAATTTAGATGATCAGAAATTTCACGATGTTTTGAAAGTCG
Found at i:1056860 original size:31 final size:31
Alignment explanation
Indices: 1056801--1056872 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
1056791 GAAGAAGATG
* * * *
1056801 AACAATAAGAATGACGATCGGAAGAATGCCA
1 AACAATGACAATGACGATAGGAACAATGCCA
* *
1056832 AACAGTGACAATGATGATAGGAACAATGCCA
1 AACAATGACAATGACGATAGGAACAATGCCA
1056863 AACAATGACA
1 AACAATGACA
1056873 CCAGTAATCC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.49, C:0.17, G:0.21, T:0.14
Consensus pattern (31 bp):
AACAATGACAATGACGATAGGAACAATGCCA
Found at i:1063288 original size:35 final size:36
Alignment explanation
Indices: 1063249--1063321 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
1063239 TATCATTTAA
1063249 AATGAAGTCATCG-TTGAGGATAAAATTATAGTATT
1 AATGAAGTCATCGTTTGAGGATAAAATTATAGTATT
1063284 AATGAAGTCATCGTTTGAGGATAAAATTATAGTATT
1 AATGAAGTCATCGTTTGAGGATAAAATTATAGTATT
1063320 AA
1 AA
1063322 CAAAATTTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 13 0.35
36 24 0.65
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.34
Consensus pattern (36 bp):
AATGAAGTCATCGTTTGAGGATAAAATTATAGTATT
Found at i:1064242 original size:15 final size:15
Alignment explanation
Indices: 1064222--1064252 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1064212 AACCGGGTAT
1064222 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
*
1064237 CGGGTACGCGATTAC
1 CGGGTACCCGATTAC
1064252 C
1 C
1064253 AGATACCGTA
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:0.19, C:0.32, G:0.29, T:0.19
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:1067056 original size:2 final size:2
Alignment explanation
Indices: 1067049--1067074 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1067039 TCGATGAATG
1067049 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1067075 CCTAATCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1069878 original size:3 final size:3
Alignment explanation
Indices: 1069870--1069913 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
1069860 TGGCAAAAAT
1069870 ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA A
1069914 AAATGTATCA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1075503 original size:27 final size:27
Alignment explanation
Indices: 1075473--1075530 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
1075463 ATAAAACAAG
1075473 AAAAAATA-AAAT-AACAAAATACGTAA
1 AAAAAATACAAATGAACAAAATA-GTAA
* *
1075499 AAAAAATACAAATGAATAAAATATTAA
1 AAAAAATACAAATGAACAAAATAGTAA
1075526 AAAAA
1 AAAAA
1075531 CAAAGACAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 8 0.29
27 12 0.43
28 8 0.29
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.17
Consensus pattern (27 bp):
AAAAAATACAAATGAACAAAATAGTAA
Found at i:1075735 original size:58 final size:57
Alignment explanation
Indices: 1075664--1075772 Score: 130
Period size: 58 Copynumber: 1.9 Consensus size: 57
1075654 ATATACTAAG
* * *
1075664 TAAAACAAATAAAATA-AAGATATACATGATATTAAGAAAAATAATAATAGAAAAAAA
1 TAAAACAAATAAAATATAAGATATACAT-AAATAAAGAAAAATAAAAATAGAAAAAAA
* * * *
1075721 TAAAATAAAGTAAAATATAATATATATATAAATAAATAAAAATAAAAATAGA
1 TAAAACAAA-TAAAATATAAGATATACATAAATAAAGAAAAATAAAAATAGA
1075773 TATAAGAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
57 8 0.19
58 26 0.60
59 9 0.21
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.24
Consensus pattern (57 bp):
TAAAACAAATAAAATATAAGATATACATAAATAAAGAAAAATAAAAATAGAAAAAAA
Found at i:1075784 original size:26 final size:27
Alignment explanation
Indices: 1075702--1075777 Score: 70
Period size: 26 Copynumber: 2.9 Consensus size: 27
1075692 ATATTAAGAA
* * *
1075702 AAATAATAATAGAAAA-AAATA-AAAT
1 AAATAAAAATATAAAATAGATATAAAT
* *
1075727 AAAGT-AAAATATAATATATATATAAAT
1 AAA-TAAAAATATAAAATAGATATAAAT
1075754 AAATAAAAATA-AAAATAGATATAA
1 AAATAAAAATATAAAATAGATATAA
1075778 GAAAATATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
25 11 0.27
26 17 0.41
27 13 0.32
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (27 bp):
AAATAAAAATATAAAATAGATATAAAT
Found at i:1078359 original size:67 final size:65
Alignment explanation
Indices: 1078207--1078426 Score: 203
Period size: 67 Copynumber: 3.3 Consensus size: 65
1078197 AAAGAGATAG
* * ** * *
1078207 AATTCGTTTTAAGGGAAACAACCTCAAAGATATCTGTTGTTTCATGA-AAACGGTCTCAAGGGAA
1 AATTTGTTTTAAGGGAAATAAATTCAAAG--AT-T-TTGTTTCAAGAGAAACTGTCTCAA-GGAA
1078271 -ACAA
61 GACAA
**
1078275 AATTTTGTTTTAAGGGAAATAAATTTTAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGAAGA
1 AA-TTTGTTTTAAGGGAAATAAATTCAAAGA-TTT-TGTTTCAAGAGAAACTGTCTCAAGGAAGA
1078340 CAA
63 CAA
* * *
1078343 AATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAAGGGAAACTATCTCAA-GAGAGAC
1 AATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTTTC-AAGAGAAACTGTCTCAAGGA-AGAC
*
1078407 GA
64 AA
* *
1078409 AATTTGTTTCAAGAGAAA
1 AATTTGTTTTAAGGGAAA
1078427 CTGTCTAAAG
Statistics
Matches: 128, Mismatches: 17, Indels: 16
0.80 0.11 0.10
Matches are distributed among these distances:
65 8 0.06
66 39 0.30
67 40 0.31
68 20 0.16
69 21 0.16
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (65 bp):
AATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAAGGAAGACAA
Found at i:1078438 original size:36 final size:36
Alignment explanation
Indices: 1078374--1078600 Score: 200
Period size: 36 Copynumber: 6.4 Consensus size: 36
1078364 ATTCAAAGAT
*
1078374 TTTGTTTCAAAGGGAAACTATCTCAAGAGAGACGAAA
1 TTTGTTTC-AAGGGAAACTGTCTCAAGAGAGACGAAA
* * **
1078411 TTTGTTTCAAGAGAAACTGTCTAAAGAGAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
* * ** * *
1078447 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGATGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
*** * *
1078484 TTTGTTTCAAATAAAACATAT-TC---A-A-A--TAA
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACGAAA
* *
1078513 TTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
1078549 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
*
1078585 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGGGAAA
1078601 TGTTTTCAAT
Statistics
Matches: 153, Mismatches: 27, Indels: 21
0.76 0.13 0.10
Matches are distributed among these distances:
28 2 0.01
29 17 0.11
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
36 89 0.58
37 40 0.26
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
Found at i:1078466 original size:37 final size:36
Alignment explanation
Indices: 1078387--1078494 Score: 108
Period size: 37 Copynumber: 3.0 Consensus size: 36
1078377 GTTTCAAAGG
* ** * * *
1078387 GAAACTATCTCAAGAGAGACGAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGATAAAATTAGTTCCAAAA
*
1078423 GAAACTGTCTAAAGAGAGATAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGATAAAA-TTAGTTCCAAAA
* * * *
1078460 GAAACTGTCTCAAGGGAGATGAAATTTGTTTCAAA
1 GAAACTGTCTCAAGAGAGATAAAATTAGTTCCAAA
1078495 TAAAACATAT
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
36 29 0.49
37 30 0.51
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGATAAAATTAGTTCCAAAA
Found at i:1078609 original size:101 final size:101
Alignment explanation
Indices: 1078409--1078668 Score: 290
Period size: 101 Copynumber: 2.6 Consensus size: 101
1078399 AGAGAGACGA
* * * * * **
1078409 AATTTGTTTCAAGAGAAACTGTCTAAAGAGAGATAAAACTTAGTTCCAAAAGAAACTGTCTCAAG
1 AATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAG
* * * *
1078474 GGAGATGAAATTTGTTTCAAATAAAACATATTCAAAT
66 AGAGACGAAATTTATTTCAAAGAAAACATATTC-AAT
*
1078511 AATTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAG
1 AATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAG
* * ** *
1078575 AGAGACGAAATTTATTTCAAGGGAAATGTTTTCAAT
66 AGAGACGAAATTTATTTCAAAGAAAACATATTCAAT
* * * *
1078611 -GTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACT
1 AATTTA--TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACT
1078669 ATCTAAAGTG
Statistics
Matches: 134, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
99 4 0.03
100 3 0.02
101 75 0.56
102 52 0.39
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.30
Consensus pattern (101 bp):
AATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAG
AGAGACGAAATTTATTTCAAAGAAAACATATTCAAT
Found at i:1078687 original size:37 final size:37
Alignment explanation
Indices: 1078616--1078687 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
1078606 TCAATGTTTA
* * *
1078616 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTAAAGGGAGACAAAATTT
* * *
1078653 TGTTTCAAGGGAAACTATCTAAAGTGAGATAAAAT
1 TGTTTCAAGAGAAACTATCTAAAGGGAGACAAAAT
1078688 CTTCTTTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTAAAGGGAGACAAAATTT
Found at i:1080251 original size:69 final size:69
Alignment explanation
Indices: 1080147--1080353 Score: 369
Period size: 69 Copynumber: 3.0 Consensus size: 69
1080137 TGTATCTCTC
* * * * *
1080147 TTGATGCTCTATGATATTCGAGTGGAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATAATCTTCGAATGAAGTGGTTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
1080212 TCAT
66 TCAT
1080216 TTGATGCTCTATAATCTTCGAATGAAGTGGTTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATAATCTTCGAATGAAGTGGTTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
1080281 TCAT
66 TCAT
1080285 TTGATGCTCTATAATCTTCGAATGAAGTGGTTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATAATCTTCGAATGAAGTGGTTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
1080350 TCAT
66 TCAT
1080354 AGTTTGAATC
Statistics
Matches: 133, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 133 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (69 bp):
TTGATGCTCTATAATCTTCGAATGAAGTGGTTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
TCAT
Found at i:1083673 original size:11 final size:9
Alignment explanation
Indices: 1083649--1083694 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
1083639 TTAATATAGT
1083649 AAAAAAATA
1 AAAAAAATA
**
1083658 AAAAAGGTA
1 AAAAAAATA
1083667 AAAAAAATTA
1 AAAAAAA-TA
1083677 AAAAGAAATA
1 AAAA-AAATA
1083687 AAAAAAAT
1 AAAAAAAT
1083695 GTGTACATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 16 0.52
10 12 0.39
11 3 0.10
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (9 bp):
AAAAAAATA
Found at i:1083796 original size:15 final size:15
Alignment explanation
Indices: 1083776--1083833 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
1083766 CATGATATTA
1083776 AGAAAAATAAATAAT
1 AGAAAAATAAATAAT
1083791 AGAAAAATAAAATAA-
1 AGAAAAAT-AAATAAT
1083806 AGTAAAAAT--ATAAT
1 AG-AAAAATAAATAAT
* *
1083820 ATATAAATAAATAA
1 AGAAAAATAAATAA
1083834 AACTAAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
13 9 0.25
14 1 0.03
15 14 0.39
16 12 0.33
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.22
Consensus pattern (15 bp):
AGAAAAATAAATAAT
Found at i:1083803 original size:16 final size:16
Alignment explanation
Indices: 1083776--1083835 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
1083766 CATGATATTA
1083776 AGAAAAAT-AAATAAT
1 AGAAAAATAAAATAAT
1083791 AGAAAAATAAAATAA-
1 AGAAAAATAAAATAAT
*
1083806 AGTAAAAATATAATATAT
1 AG-AAAAATAAAATA-AT
1083824 A-AATAAATAAAA
1 AGAA-AAATAAAA
1083836 CTAAAATAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
15 10 0.26
16 19 0.50
17 8 0.21
18 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (16 bp):
AGAAAAATAAAATAAT
Found at i:1083804 original size:5 final size:5
Alignment explanation
Indices: 1083794--1083857 Score: 51
Period size: 5 Copynumber: 12.2 Consensus size: 5
1083784 AAATAATAGA
*
1083794 AAAAT AAAAT AAAGT AAAAAT ATAATAT ATAAAT -AAAT AAAACT AAAAT
1 AAAAT AAAAT AAAAT -AAAAT A-AA-AT A-AAAT AAAAT AAAA-T AAAAT
*
1083843 AGAAT AAAA- AAAAT A
1 AAAAT AAAAT AAAAT A
1083858 TATATAAAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
4 8 0.16
5 22 0.45
6 13 0.27
7 6 0.12
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:1083830 original size:44 final size:41
Alignment explanation
Indices: 1083780--1083863 Score: 105
Period size: 44 Copynumber: 2.0 Consensus size: 41
1083770 ATATTAAGAA
* *
1083780 AAATAAATAATAGAAAAATAAAATAAAGTAAAAATATAATATAT
1 AAATAAATAAAACAAAAATAAAATAAA--AAAAATAT-ATATAT
* *
1083824 AAATAAATAAAACTAAAATAGAATAAAAAAAATATATATA
1 AAATAAATAAAACAAAAATAAAATAAAAAAAATATATATA
1083864 AAACGTATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 5 0.14
42 8 0.22
44 23 0.64
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (41 bp):
AAATAAATAAAACAAAAATAAAATAAAAAAAATATATATAT
Found at i:1083842 original size:15 final size:16
Alignment explanation
Indices: 1083824--1083881 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 16
1083814 TATAATATAT
1083824 AAATA-AATAAAACTA
1 AAATATAATAAAACTA
*
1083839 AAATAGAATAAAA--A
1 AAATATAATAAAACTA
1083853 AAATATATATAAAACGTA
1 AAATATA-ATAAAAC-TA
1083871 TAAATATAATA
1 -AAATATAATA
1083882 TTAAGAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
14 7 0.19
15 11 0.31
16 7 0.19
18 4 0.11
19 7 0.19
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.24
Consensus pattern (16 bp):
AAATATAATAAAACTA
Found at i:1083849 original size:24 final size:24
Alignment explanation
Indices: 1083795--1083850 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
1083785 AATAATAGAA
*
1083795 AAATAAAATAAAGTAAAAATATAAT
1 AAAT-AAATAAAGTAAAAATAAAAT
* *
1083820 ATATAAATAAA-TAAAACTAAAAT
1 AAATAAATAAAGTAAAAATAAAAT
1083843 AGAATAAA
1 A-AATAAA
1083851 AAAAATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 11 0.42
24 12 0.46
25 3 0.12
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (24 bp):
AAATAAATAAAGTAAAAATAAAAT
Found at i:1083862 original size:39 final size:40
Alignment explanation
Indices: 1083782--1083865 Score: 102
Period size: 39 Copynumber: 2.1 Consensus size: 40
1083772 ATTAAGAAAA
*
1083782 ATAAATAATAGAAAAATAAAATAAAGTAAAAATATAATAT
1 ATAAATAATAGAAAAATAAAATAAAGTAAAAAAATAATAT
* *
1083822 ATAAATAA-ATAAAACTAAAATAGAA-TAAAAAAA-ATATAT
1 ATAAATAATAGAAAAATAAAATA-AAGTAAAAAAATA-ATAT
1083861 ATAAA
1 ATAAA
1083866 ACGTATAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
38 1 0.03
39 28 0.72
40 10 0.26
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (40 bp):
ATAAATAATAGAAAAATAAAATAAAGTAAAAAAATAATAT
Found at i:1083897 original size:25 final size:25
Alignment explanation
Indices: 1083869--1083917 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1083859 ATATAAAACG
*
1083869 TATAAATA-TAATATTAAGAAAAATA
1 TATAAATAGTAA-ATGAAGAAAAATA
*
1083894 TATACATAGTAAATGAAGAAAAAT
1 TATAAATAGTAAATGAAGAAAAAT
1083918 TAATACGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (25 bp):
TATAAATAGTAAATGAAGAAAAATA
Found at i:1094394 original size:16 final size:18
Alignment explanation
Indices: 1094373--1094425 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 18
1094363 ATCTATTTTG
1094373 TTACTT-TATA-ATATAA
1 TTACTTATATATATATAA
1094389 TTACTTATATATATAT-A
1 TTACTTATATATATATAA
1094406 -TA-TATATATATATATTAA
1 TTACT-TATATATATA-TAA
1094424 TT
1 TT
1094426 TTTTAATCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
15 1 0.03
16 18 0.58
17 6 0.19
18 5 0.16
19 1 0.03
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (18 bp):
TTACTTATATATATATAA
Found at i:1094401 original size:2 final size:2
Alignment explanation
Indices: 1094394--1094420 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1094384 TATAATTACT
1094394 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1094421 TAATTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1096062 original size:59 final size:59
Alignment explanation
Indices: 1095990--1096124 Score: 195
Period size: 59 Copynumber: 2.3 Consensus size: 59
1095980 GTCGGGTAAC
*
1095990 CATTTTGTAACTTTTAATA-TTCAAGAGACTCAACAAAACA-ACTCTTTATAGTCAGGGGAT
1 CATTTTGTAACTTTTAATAGTTCAAGA-ACTCAACAAAACATA-TC-TTATAGTCAGAGGAT
*
1096050 CATTTTGT-ACTTTTAATAGTTCAAGAACTCAACAAAATATTATCTTATAGTCAGAGGAT
1 CATTTTGTAACTTTTAATAGTTCAAGAACTCAACAAAACA-TATCTTATAGTCAGAGGAT
1096109 CATTTTGTAACTTTTA
1 CATTTTGTAACTTTTA
1096125 TCAAGCGGCT
Statistics
Matches: 69, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
59 44 0.64
60 24 0.35
61 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.38
Consensus pattern (59 bp):
CATTTTGTAACTTTTAATAGTTCAAGAACTCAACAAAACATATCTTATAGTCAGAGGAT
Found at i:1098051 original size:24 final size:24
Alignment explanation
Indices: 1098019--1098066 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1098009 CATCTGTATA
1098019 TTCCATCGTATTTTTTAGCTCGCT
1 TTCCATCGTATTTTTTAGCTCGCT
1098043 TTCCATCGTATTTTTTAGCTCGCT
1 TTCCATCGTATTTTTTAGCTCGCT
1098067 AACTGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.25, G:0.12, T:0.50
Consensus pattern (24 bp):
TTCCATCGTATTTTTTAGCTCGCT
Found at i:1099320 original size:2 final size:2
Alignment explanation
Indices: 1099313--1099341 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1099303 CATAGTATTA
1099313 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1099342 ATTGCACTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1100441 original size:60 final size:60
Alignment explanation
Indices: 1100392--1100529 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 60
1100382 ATTTTGATTT
* * * *
1100392 TTCTAATTTTATCCTCAAAGTATGAATTTCATTCTAAATTATTCCTTAAACATTTGAATA
1 TTCTAATTTCATCCCCAAACTATGAATCTCATTCTAAATTATTCCTTAAACATTTGAATA
* ** ** *
1100452 TTCTAATTTCATCCCCAAACTATGACTCTCATTCTAAA-TGGTCCCCAAACTTTTGAATAA
1 TTCTAATTTCATCCCCAAACTATGAATCTCATTCTAAATTATTCCTTAAACATTTGAAT-A
*
1100512 TTC-AATTTCATCCACAAA
1 TTCTAATTTCATCCCCAAA
1100530 GTCATCCAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 29 0.44
60 37 0.56
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.39
Consensus pattern (60 bp):
TTCTAATTTCATCCCCAAACTATGAATCTCATTCTAAATTATTCCTTAAACATTTGAATA
Found at i:1102145 original size:15 final size:15
Alignment explanation
Indices: 1102122--1102155 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1102112 TCTTCATTTT
* *
1102122 AGAGGATATTTCAAA
1 AGAGAATATTCCAAA
1102137 AGAGAATATTCCAAA
1 AGAGAATATTCCAAA
1102152 AGAG
1 AGAG
1102156 GTTAAAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.09, G:0.21, T:0.21
Consensus pattern (15 bp):
AGAGAATATTCCAAA
Found at i:1118891 original size:52 final size:52
Alignment explanation
Indices: 1118813--1118917 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
1118803 ACTTCTCTTT
1118813 GTTACAAGCTCACCAACAGGGAATTCCAGGGGGTTTCACCACAGATTTCCCA
1 GTTACAAGCTCACCAACAGGGAATTCCAGGGGGTTTCACCACAGATTTCCCA
1118865 GTTACAAGCTCACCAACAGGGAATTCCAGGGGGTTTCACCACAGATTTCCCA
1 GTTACAAGCTCACCAACAGGGAATTCCAGGGGGTTTCACCACAGATTTCCCA
1118917 G
1 G
1118918 GAGCCCCTCC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (52 bp):
GTTACAAGCTCACCAACAGGGAATTCCAGGGGGTTTCACCACAGATTTCCCA
Found at i:1119807 original size:4 final size:4
Alignment explanation
Indices: 1119798--1120109 Score: 528
Period size: 4 Copynumber: 79.2 Consensus size: 4
1119788 GACAGTTTCC
1119798 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1119846 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
1119894 TATG TATG TATG TATG TATG TATG TATG TATG TATG TACG TACG TA--
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1119940 TATG TATG TATG TATG TATG TA-G TATG TATG TATG TATG --TG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1119985 TA-G TATG TATG TATG TATG TATG TATG TATG TATGG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT-G TATG TATG TATG
1120033 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
1120081 TATG TATG CATG CATG CATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
1120110 GACAAAAGAT
Statistics
Matches: 298, Mismatches: 3, Indels: 14
0.95 0.01 0.04
Matches are distributed among these distances:
2 4 0.01
3 6 0.02
4 284 0.95
5 4 0.01
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:1120283 original size:21 final size:21
Alignment explanation
Indices: 1120257--1120313 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1120247 AGCTCATAGT
1120257 CTAATGTCACTCGCTAATGCC
1 CTAATGTCACTCGCTAATGCC
1120278 CTAATGTCACTCGCTAATGCC
1 CTAATGTCACTCGCTAATGCC
*
1120299 CTAATGTCTCTCGCT
1 CTAATGTCACTCGCT
1120314 GATTCCTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.21, C:0.33, G:0.14, T:0.32
Consensus pattern (21 bp):
CTAATGTCACTCGCTAATGCC
Found at i:1127239 original size:14 final size:14
Alignment explanation
Indices: 1127220--1127249 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1127210 TTTAGATTTT
1127220 TTAAAATTACATTA
1 TTAAAATTACATTA
1127234 TTAAAATTACATTA
1 TTAAAATTACATTA
1127248 TT
1 TT
1127250 GATGAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (14 bp):
TTAAAATTACATTA
Found at i:1127765 original size:14 final size:14
Alignment explanation
Indices: 1127729--1127772 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1127719 TATAAAGTGA
1127729 TAGGATTTAGGGTT
1 TAGGATTTAGGGTT
**
1127743 TATAATTTAGGGTT
1 TAGGATTTAGGGTT
* *
1127757 TAGGGTTTAGAGTT
1 TAGGATTTAGGGTT
1127771 TA
1 TA
1127773 TGTGATAGGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (14 bp):
TAGGATTTAGGGTT
Found at i:1127772 original size:21 final size:21
Alignment explanation
Indices: 1127729--1127772 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1127719 TATAAAGTGA
*
1127729 TAGGATTTAGGGTTTATAATT
1 TAGGATTTAGGGTTTAGAATT
* *
1127750 TAGGGTTTAGGGTTTAGAGTT
1 TAGGATTTAGGGTTTAGAATT
1127771 TA
1 TA
1127773 TGTGATAGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (21 bp):
TAGGATTTAGGGTTTAGAATT
Found at i:1127803 original size:34 final size:34
Alignment explanation
Indices: 1127747--1127829 Score: 139
Period size: 34 Copynumber: 2.4 Consensus size: 34
1127737 AGGGTTTATA
1127747 ATTTAGGGTTTAGGGTTTAGAGTTTATGTGATAGG
1 ATTTAGGGTTTA-GGTTTAGAGTTTATGTGATAGG
* *
1127782 ATTTATGGTTTAGGTTTAGAGTTTATGTGATATG
1 ATTTAGGGTTTAGGTTTAGAGTTTATGTGATAGG
1127816 ATTTAGGGTTTAGG
1 ATTTAGGGTTTAGG
1127830 GTTAAGATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 34 0.76
35 11 0.24
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (34 bp):
ATTTAGGGTTTAGGTTTAGAGTTTATGTGATAGG
Found at i:1127945 original size:35 final size:35
Alignment explanation
Indices: 1127897--1128117 Score: 144
Period size: 35 Copynumber: 6.1 Consensus size: 35
1127887 TTCCTTCTAA
*
1127897 TTATGTGACAAGGTTTAGGATTTAGGGTTTATAGT
1 TTATGTGATAAGGTTTAGGATTTAGGGTTTATAGT
*
1127932 TTATGTGATAAGGTTTAGGATTTAGGATTTAGGGTATAGGGT
1 TTATGTGATAAGGTTTAGGATTTAGG-GTT----TATA--GT
* * * * **
1127974 TTATGTGATATGATTTAGGGTTTAGGATTTAGGGT
1 TTATGTGATAAGGTTTAGGATTTAGGGTTTATAGT
* * * *
1128009 TTATGTGATATGATTTAGGATTTAAGGTTTATAAT
1 TTATGTGATAAGGTTTAGGATTTAGGGTTTATAGT
* **
1128044 TTATGTGAT-AGGATTTACGG-TTTATGGTTTACGGT
1 TTATGTGATAAGG-TTTA-GGATTTAGGGTTTATAGT
* * * *
1128079 TTA-GTGTTTAGGATTTATGATTTACGGTTTAGT-GT
1 TTATGTGATAAGG-TTTAGGATTTAGGGTTTA-TAGT
1128114 TTAT
1 TTAT
1128118 AATTTTAAAC
Statistics
Matches: 149, Mismatches: 24, Indels: 25
0.75 0.12 0.13
Matches are distributed among these distances:
34 6 0.04
35 106 0.71
36 4 0.03
37 2 0.01
40 4 0.03
41 2 0.01
42 25 0.17
ACGTcount: A:0.24, C:0.02, G:0.28, T:0.46
Consensus pattern (35 bp):
TTATGTGATAAGGTTTAGGATTTAGGGTTTATAGT
Found at i:1127957 original size:7 final size:7
Alignment explanation
Indices: 1127945--1128102 Score: 50
Period size: 7 Copynumber: 22.6 Consensus size: 7
1127935 TGTGATAAGG
1127945 TTTAGGA
1 TTTAGGA
1127952 TTTAGGA
1 TTTAGGA
*
1127959 TTTAGGG
1 TTTAGGA
* *
1127966 TATAGGG
1 TTTAGGA
1127973 TTTATGTGA
1 TTTA-G-GA
*
1127982 --TATGA
1 TTTAGGA
*
1127987 TTTAGGG
1 TTTAGGA
1127994 TTTAGGA
1 TTTAGGA
*
1128001 TTTAGGG
1 TTTAGGA
1128008 TTTATGTGA
1 TTTA-G-GA
*
1128017 --TATGA
1 TTTAGGA
1128022 TTTAGGA
1 TTTAGGA
1128029 TTTAAGG-
1 TTT-AGGA
**
1128036 TTTATAA
1 TTTAGGA
1128043 TTTATGTGA
1 TTTA-G-GA
1128052 --TAGGA
1 TTTAGGA
1128057 TTTACGG-
1 TTTA-GGA
1128064 TTTATGG-
1 TTTA-GGA
1128071 TTTACGG-
1 TTTA-GGA
1128078 TTTAGTG-
1 TTTAG-GA
1128085 TTTAGGA
1 TTTAGGA
*
1128092 TTTATGA
1 TTTAGGA
1128099 TTTA
1 TTTA
1128103 CGGTTTAGTG
Statistics
Matches: 115, Mismatches: 19, Indels: 34
0.68 0.11 0.20
Matches are distributed among these distances:
5 6 0.05
6 4 0.03
7 95 0.83
8 7 0.06
9 3 0.03
ACGTcount: A:0.25, C:0.01, G:0.27, T:0.47
Consensus pattern (7 bp):
TTTAGGA
Found at i:1127976 original size:42 final size:42
Alignment explanation
Indices: 1127910--1128008 Score: 144
Period size: 42 Copynumber: 2.4 Consensus size: 42
1127900 TGTGACAAGG
* * *
1127910 TTTAGGATTTAGGGTTTATAGTTTATGTGATAAGGTTTAGGA
1 TTTAGGATTTAGGGTATAGAGTTTATGTGATAAGATTTAGGA
* * *
1127952 TTTAGGATTTAGGGTATAGGGTTTATGTGATATGATTTAGGG
1 TTTAGGATTTAGGGTATAGAGTTTATGTGATAAGATTTAGGA
1127994 TTTAGGATTTAGGGT
1 TTTAGGATTTAGGGT
1128009 TTATGTGATA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.44
Consensus pattern (42 bp):
TTTAGGATTTAGGGTATAGAGTTTATGTGATAAGATTTAGGA
Found at i:1127992 original size:21 final size:21
Alignment explanation
Indices: 1127968--1128032 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
1127958 ATTTAGGGTA
1127968 TAGGGTTTATGTGATATGATT
1 TAGGGTTTATGTGATATGATT
1127989 TAGGGTTTA---G----GATT
1 TAGGGTTTATGTGATATGATT
1128003 TAGGGTTTATGTGATATGATT
1 TAGGGTTTATGTGATATGATT
*
1128024 TAGGATTTA
1 TAGGGTTTA
1128033 AGGTTTATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
14 13 0.36
17 1 0.03
18 1 0.03
21 21 0.58
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (21 bp):
TAGGGTTTATGTGATATGATT
Found at i:1128013 original size:28 final size:28
Alignment explanation
Indices: 1127908--1128110 Score: 121
Period size: 28 Copynumber: 7.2 Consensus size: 28
1127898 TATGTGACAA
1127908 GGTTTAGGATTTAGGGTTTAT-AGTTTATG
1 GGTTTAGGATTTAGGGTTTATGA-TTTA-G
* * * * *
1127937 TGATAAGG-TTTAGGATTTAGGATTTAG
1 GGTTTAGGATTTAGGGTTTATGATTTAG
* * * *
1127964 GGTATAGGGTTTA-TGTGATATGATTTAG
1 GGTTTAGGATTTAGGGT-TTATGATTTAG
* *
1127992 GGTTTAGGATTTAGGGTTTATG-TGATAT
1 GGTTTAGGATTTAGGGTTTATGAT-TTAG
* * *
1128020 GATTTAGGATTTAAGGTTTATAATTTA-
1 GGTTTAGGATTTAGGGTTTATGATTTAG
* * * * *
1128047 TGTGATAGGATTTACGGTTTATGGTTTAC
1 GGT-TTAGGATTTAGGGTTTATGATTTAG
* *
1128076 GGTTTAGTG-TTTAGGATTTATGATTTAC
1 GGTTTAG-GATTTAGGGTTTATGATTTAG
1128104 GGTTTAG
1 GGTTTAG
1128111 TGTTTATAAT
Statistics
Matches: 131, Mismatches: 34, Indels: 19
0.71 0.18 0.10
Matches are distributed among these distances:
27 8 0.06
28 111 0.85
29 12 0.09
ACGTcount: A:0.24, C:0.01, G:0.29, T:0.46
Consensus pattern (28 bp):
GGTTTAGGATTTAGGGTTTATGATTTAG
Found at i:1128116 original size:14 final size:13
Alignment explanation
Indices: 1128057--1128116 Score: 68
Period size: 14 Copynumber: 4.3 Consensus size: 13
1128047 TGTGATAGGA
1128057 TTTACGGTTTATGG
1 TTTACGGTTTAT-G
1128071 TTTACGGTTTAGTG
1 TTTACGGTTTA-TG
1128085 TTTA-GGATTTATG
1 TTTACGG-TTTATG
1128098 ATTTACGGTTTAGTG
1 -TTTACGGTTTA-TG
1128113 TTTA
1 TTTA
1128117 TAATTTTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
13 4 0.10
14 32 0.78
15 5 0.12
ACGTcount: A:0.18, C:0.05, G:0.25, T:0.52
Consensus pattern (13 bp):
TTTACGGTTTATG
Found at i:1128122 original size:28 final size:28
Alignment explanation
Indices: 1128064--1128122 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
1128054 GGATTTACGG
* *
1128064 TTTATGGTTTACGGTTTAGTGTTTAGGA
1 TTTATGATTTACGGTTTAGTGTTTAGAA
*
1128092 TTTATGATTTACGGTTTAGTGTTTATAA
1 TTTATGATTTACGGTTTAGTGTTTAGAA
1128120 TTT
1 TTT
1128123 TAAACAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.20, C:0.03, G:0.22, T:0.54
Consensus pattern (28 bp):
TTTATGATTTACGGTTTAGTGTTTAGAA
Found at i:1128956 original size:28 final size:28
Alignment explanation
Indices: 1128924--1128996 Score: 146
Period size: 28 Copynumber: 2.6 Consensus size: 28
1128914 AAAGAAAGTT
1128924 GATCGAAGCATTCCAAAACTGAGGAATC
1 GATCGAAGCATTCCAAAACTGAGGAATC
1128952 GATCGAAGCATTCCAAAACTGAGGAATC
1 GATCGAAGCATTCCAAAACTGAGGAATC
1128980 GATCGAAGCATTCCAAA
1 GATCGAAGCATTCCAAA
1128997 TGCTTGCGTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.18
Consensus pattern (28 bp):
GATCGAAGCATTCCAAAACTGAGGAATC
Found at i:1129096 original size:12 final size:12
Alignment explanation
Indices: 1129079--1129103 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1129069 TCCCCTTTGG
1129079 TGAGTTTGTTTA
1 TGAGTTTGTTTA
1129091 TGAGTTTGTTTA
1 TGAGTTTGTTTA
1129103 T
1 T
1129104 CATTAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (12 bp):
TGAGTTTGTTTA
Found at i:1131518 original size:104 final size:104
Alignment explanation
Indices: 1131338--1131548 Score: 350
Period size: 104 Copynumber: 2.0 Consensus size: 104
1131328 AGACAGATCA
* * *
1131338 CGAGTTAAACAAGGTCGACTCAATCAGTGTTTGATAAATACTCGGATCGAATGGACTCGACTCGA
1 CGAGTTAAACAAGATCGACTCAATCAATGTTCGATAAATACTCGGATCGAATGGACTCGACTCGA
*
1131403 ATTTTTAACGAGCCAAAACAAGCTACTTGACACTCAACT
66 ATTCTTAACGAGCCAAAACAAGCTACTTGACACTCAACT
* *
1131442 CGAGTTAAACAAGATCGACTCGATCAATGTTCGATAAATACTTGGATCGAATGGACTCGACTCGA
1 CGAGTTAAACAAGATCGACTCAATCAATGTTCGATAAATACTCGGATCGAATGGACTCGACTCGA
* *
1131507 ATTCTTAACGAGCCAAAACAAGCTACTTGATACTCGACT
66 ATTCTTAACGAGCCAAAACAAGCTACTTGACACTCAACT
1131546 CGA
1 CGA
1131549 AAAGCTCGTG
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
104 99 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (104 bp):
CGAGTTAAACAAGATCGACTCAATCAATGTTCGATAAATACTCGGATCGAATGGACTCGACTCGA
ATTCTTAACGAGCCAAAACAAGCTACTTGACACTCAACT
Found at i:1134955 original size:20 final size:20
Alignment explanation
Indices: 1134930--1134973 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
1134920 GTAAATTATA
1134930 TTATTCATCACTCAACTATC
1 TTATTCATCACTCAACTATC
1134950 TTATTCATCACTCAACTATC
1 TTATTCATCACTCAACTATC
1134970 TTAT
1 TTAT
1134974 CATTCCTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (20 bp):
TTATTCATCACTCAACTATC
Found at i:1135371 original size:24 final size:23
Alignment explanation
Indices: 1135319--1135371 Score: 54
Period size: 25 Copynumber: 2.2 Consensus size: 23
1135309 TAGATGTGAT
* *
1135319 TTTAAAATAAATAAAAGTTTAAG
1 TTTAAAAAAAATAAAAGGTTAAG
1135342 TATTAAAACAAAATAAAATGGTT-AG
1 T-TTAAAA-AAAATAAAA-GGTTAAG
1135367 TTTAA
1 TTTAA
1135372 GTATTAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 1 0.04
24 10 0.40
25 11 0.44
26 3 0.12
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (23 bp):
TTTAAAAAAAATAAAAGGTTAAG
Found at i:1136318 original size:36 final size:35
Alignment explanation
Indices: 1136261--1136329 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 35
1136251 AGAAGATATA
* * *
1136261 TATAAAATTATATATATATATATAAATAAGAAAACT
1 TATAAAATTATATAGAGATATAAAAATAA-AAAACT
1136297 TATAAAATT-TATAAGAGATATAAAAATAAAAAA
1 TATAAAATTATAT-AGAGATATAAAAATAAAAAA
1136330 TATAACATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 7 0.24
36 22 0.76
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (35 bp):
TATAAAATTATATAGAGATATAAAAATAAAAAACT
Found at i:1138008 original size:14 final size:14
Alignment explanation
Indices: 1137989--1138017 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1137979 GATCCGATAA
1137989 TATATTTATTTATG
1 TATATTTATTTATG
1138003 TATATTTATTTATG
1 TATATTTATTTATG
1138017 T
1 T
1138018 TTTAATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (14 bp):
TATATTTATTTATG
Found at i:1142441 original size:26 final size:26
Alignment explanation
Indices: 1142407--1142457 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
1142397 AACTAAACCC
*
1142407 GTTTTAGCTAAACGTAAGAAACCACG
1 GTTTAAGCTAAACGTAAGAAACCACG
1142433 GTTTAAGCTAAACGTAAGAAACCAC
1 GTTTAAGCTAAACGTAAGAAACCAC
1142458 TAGTGTAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (26 bp):
GTTTAAGCTAAACGTAAGAAACCACG
Found at i:1151698 original size:12 final size:12
Alignment explanation
Indices: 1151681--1151708 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1151671 CCTGACACAC
1151681 ATATTTATATAT
1 ATATTTATATAT
1151693 ATATTTATATAT
1 ATATTTATATAT
1151705 ATAT
1 ATAT
1151709 AAAAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
ATATTTATATAT
Found at i:1155890 original size:23 final size:23
Alignment explanation
Indices: 1155863--1155917 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
1155853 TATTCGTTCG
* * *
1155863 TTTAACGTTCCCGAACATATTTA
1 TTTAACGTTCACAAACATATTCA
*
1155886 TTTAATGTTCACAAACATATTCA
1 TTTAACGTTCACAAACATATTCA
*
1155909 TTCAACGTT
1 TTTAACGTT
1155918 TGCGAGTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (23 bp):
TTTAACGTTCACAAACATATTCA
Found at i:1161958 original size:207 final size:206
Alignment explanation
Indices: 1161562--1161979 Score: 827
Period size: 206 Copynumber: 2.0 Consensus size: 206
1161552 AAACAAACAG
1161562 TTTTTGAAACCCAGAGTTATACTCCTAGTTTTTAGAACCAAAAAAAATCAACGAATTAGAAGCAG
1 TTTTTGAAACCCAGAGTTATACTCCTAGTTTTTAGAACCAAAAAAAATCAACGAATTAGAAGCAG
1161627 AGAATTGGAAGAAATGGGTTTACTATTTTTAGTACTTTGTTTTTGTGCTTTCTTTTCCCTTATCT
66 AGAATTGGAAGAAATGGGTTTACTATTTTTAGTACTTTGTTTTTGTGCTTTCTTTTCCCTTATCT
1161692 GATCTTATTTCATGGTGACTGTTTTAATGAGACATGTCCCAAAGCAAAAGCAATTAGATTTTTTT
131 GATCTTATTTCATGGTGACTGTTTTAATGAGACATGTCCCAAAGCAAAAGCAATTAGATTTTTTT
1161757 CACATTTTAGA
196 CACATTTTAGA
1161768 TTTTTGAAACCCAGAGTTATACTCCTAGTTTTTAGAACCAAAAAAAATCAACGAATTAGAAGCAG
1 TTTTTGAAACCCAGAGTTATACTCCTAGTTTTTAGAACCAAAAAAAATCAACGAATTAGAAGCAG
1161833 AGAATTGGAAGAAATGGGTTTACTATTTTTAGTACTTTGTTTTTGTGCTTTCTTTTCCCTTATCT
66 AGAATTGGAAGAAATGGGTTTACTATTTTTAGTACTTTGTTTTTGTGCTTTCTTTTCCCTTATCT
1161898 GATCTTATTTTCATGGTGACTGTTTTAATGAGACATGTCCCAAAGCAAAAGCAATTAGATTTTTT
131 GATCTTA-TTTCATGGTGACTGTTTTAATGAGACATGTCCCAAAGCAAAAGCAATTAGATTTTTT
1161963 TCACATTTTAGA
195 TCACATTTTAGA
1161975 TTTTT
1 TTTTT
1161980 TTTTAAAACA
Statistics
Matches: 211, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
206 137 0.65
207 74 0.35
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (206 bp):
TTTTTGAAACCCAGAGTTATACTCCTAGTTTTTAGAACCAAAAAAAATCAACGAATTAGAAGCAG
AGAATTGGAAGAAATGGGTTTACTATTTTTAGTACTTTGTTTTTGTGCTTTCTTTTCCCTTATCT
GATCTTATTTCATGGTGACTGTTTTAATGAGACATGTCCCAAAGCAAAAGCAATTAGATTTTTTT
CACATTTTAGA
Found at i:1162777 original size:21 final size:20
Alignment explanation
Indices: 1162752--1162793 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1162742 ATTACATATT
*
1162752 ATTAATATTTTCAATTTAATC
1 ATTAATAGTTT-AATTTAATC
*
1162773 ATTAATAGTTTAATTTTATC
1 ATTAATAGTTTAATTTAATC
1162793 A
1 A
1162794 ATCAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTAATAGTTTAATTTAATC
Found at i:1163934 original size:14 final size:14
Alignment explanation
Indices: 1163915--1163943 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1163905 CGAAATGATC
1163915 TGAAGGTATGTTTT
1 TGAAGGTATGTTTT
1163929 TGAAGGTATGTTTT
1 TGAAGGTATGTTTT
1163943 T
1 T
1163944 ATATCGACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.52
Consensus pattern (14 bp):
TGAAGGTATGTTTT
Found at i:1168034 original size:3 final size:3
Alignment explanation
Indices: 1168026--1168089 Score: 114
Period size: 3 Copynumber: 22.0 Consensus size: 3
1168016 GAGGGCAATC
1168026 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1168073 ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA
1168090 TTAGATCTAC
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.07
3 55 0.93
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1171712 original size:89 final size:89
Alignment explanation
Indices: 1171561--1171741 Score: 362
Period size: 89 Copynumber: 2.0 Consensus size: 89
1171551 AAACAATATC
1171561 TTATAATCAAAAATCATTTGTTTACTTTAATCTAAAAAAGTGATAGCAACCTAAATTTTGCAAAT
1 TTATAATCAAAAATCATTTGTTTACTTTAATCTAAAAAAGTGATAGCAACCTAAATTTTGCAAAT
1171626 AGATGCGGATTAAGGGGTTTGCTT
66 AGATGCGGATTAAGGGGTTTGCTT
1171650 TTATAATCAAAAATCATTTGTTTACTTTAATCTAAAAAAGTGATAGCAACCTAAATTTTGCAAAT
1 TTATAATCAAAAATCATTTGTTTACTTTAATCTAAAAAAGTGATAGCAACCTAAATTTTGCAAAT
1171715 AGATGCGGATTAAGGGGTTTGCTT
66 AGATGCGGATTAAGGGGTTTGCTT
1171739 TTA
1 TTA
1171742 ACTCTTTAGT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 92 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (89 bp):
TTATAATCAAAAATCATTTGTTTACTTTAATCTAAAAAAGTGATAGCAACCTAAATTTTGCAAAT
AGATGCGGATTAAGGGGTTTGCTT
Found at i:1172594 original size:25 final size:27
Alignment explanation
Indices: 1172540--1172596 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
1172530 CAAGCACTGG
*
1172540 CTCGACGACATAATATTTCAAATACTGA
1 CTCGACGACATAATA-TTCAAATACAGA
*
1172568 CTCGACGACATAATA-T-AAATAGAGA
1 CTCGACGACATAATATTCAAATACAGA
1172593 CTCG
1 CTCG
1172597 GTCCATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 11 0.41
26 1 0.04
28 15 0.56
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (27 bp):
CTCGACGACATAATATTCAAATACAGA
Found at i:1180096 original size:18 final size:17
Alignment explanation
Indices: 1180050--1180097 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
1180040 ATGAGACTTT
1180050 TAAAAA-AAATT-ATGA
1 TAAAAATAAATTAATGA
* *
1180065 TCAAAATAATTTAATGA
1 TAAAAATAAATTAATGA
1180082 TAAAAGATAAATTAAT
1 TAAAA-ATAAATTAAT
1180098 ATTTAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 5 0.19
16 4 0.15
17 8 0.31
18 9 0.35
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.31
Consensus pattern (17 bp):
TAAAAATAAATTAATGA
Found at i:1190708 original size:77 final size:77
Alignment explanation
Indices: 1190578--1190727 Score: 255
Period size: 77 Copynumber: 1.9 Consensus size: 77
1190568 GCCAAGGTGA
1190578 GAGTGTCCAACACACCGATACATCTGATATAACATGAATGCTCTATATGTCATCCTAAGCTAATC
1 GAGTGTCCAACACACCGATACATCTGATATAACATGAATGCTCTATATGTCATCCTAAGCTAATC
1190643 TAATTTAGATAG
66 TAATTTAGATAG
* * * *
1190655 GAGTGTCGAACACACCGATATATCTGATATAACATGAATGCTCTATATTTCATCCTAAGTTAATC
1 GAGTGTCCAACACACCGATACATCTGATATAACATGAATGCTCTATATGTCATCCTAAGCTAATC
*
1190720 TACTTTAG
66 TAATTTAG
1190728 GTACAAGTGC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
77 68 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (77 bp):
GAGTGTCCAACACACCGATACATCTGATATAACATGAATGCTCTATATGTCATCCTAAGCTAATC
TAATTTAGATAG
Found at i:1192740 original size:85 final size:85
Alignment explanation
Indices: 1192597--1192768 Score: 344
Period size: 85 Copynumber: 2.0 Consensus size: 85
1192587 TAACTTTATG
1192597 CATATAACAATACTCATAATAAATAATAAGAAAACAAAACAAAATCACTACTTAAGAAACATTAG
1 CATATAACAATACTCATAATAAATAATAAGAAAACAAAACAAAATCACTACTTAAGAAACATTAG
1192662 AAAAATTTCAAGGACTTCCT
66 AAAAATTTCAAGGACTTCCT
1192682 CATATAACAATACTCATAATAAATAATAAGAAAACAAAACAAAATCACTACTTAAGAAACATTAG
1 CATATAACAATACTCATAATAAATAATAAGAAAACAAAACAAAATCACTACTTAAGAAACATTAG
1192747 AAAAATTTCAAGGACTTCCT
66 AAAAATTTCAAGGACTTCCT
1192767 CA
1 CA
1192769 GTTTATCGTT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 87 1.00
ACGTcount: A:0.54, C:0.17, G:0.06, T:0.23
Consensus pattern (85 bp):
CATATAACAATACTCATAATAAATAATAAGAAAACAAAACAAAATCACTACTTAAGAAACATTAG
AAAAATTTCAAGGACTTCCT
Found at i:1209540 original size:3 final size:3
Alignment explanation
Indices: 1209523--1209582 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
1209513 TTTGTAAATT
*
1209523 TAA TAAA TAA T-A TAA TAA T-A TAA T-A TAA TAC TAA T-A TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
1209565 TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
1209583 ATTTAAATGA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
2 8 0.17
3 35 0.76
4 3 0.07
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1209541 original size:8 final size:8
Alignment explanation
Indices: 1209523--1209582 Score: 61
Period size: 8 Copynumber: 7.4 Consensus size: 8
1209513 TTTGTAAATT
1209523 TAATA-AA
1 TAATATAA
1209530 TAATATAA
1 TAATATAA
1209538 TAATATAA
1 TAATATAA
*
1209546 T-ATAATAC
1 TAAT-ATAA
1209554 TAATATAA
1 TAATATAA
*
1209562 TAATTTTAA
1 TAA-TATAA
1209571 TAATAATAA
1 TAAT-ATAA
1209580 TAA
1 TAA
1209583 ATTTAAATGA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
7 7 0.16
8 22 0.50
9 15 0.34
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (8 bp):
TAATATAA
Found at i:1209845 original size:76 final size:76
Alignment explanation
Indices: 1209710--1210345 Score: 1100
Period size: 76 Copynumber: 8.4 Consensus size: 76
1209700 GGAAATGTTT
* * *
1209710 GAAA-ATCAT-CACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCTCCCG
1209773 AAGGCTTTTTG
66 AAGGCTTTTTG
* *
1209784 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCTCCCG
1209849 AAGGCTTTTTG
66 AAGGCTTTTTG
* *
1209860 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAATGATTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCTCCCG
1209925 AAGGCTTTTTG
66 AAGGCTTTTTG
*
1209936 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCTTCCG
1 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCTCCCG
1210001 AAGGCTTTTTTG
66 AAGGC-TTTTTG
*
1210013 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCTTCCG
1 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCTCCCG
1210078 AAGGCTTTTTG
66 AAGGCTTTTTG
* *
1210089 AAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGA-TTGAAAATAT-AAAAAGCTTCCG
1 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCTCCCG
1210152 AAGGCTTTTTG
66 AAGGCTTTTTG
*
1210163 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCTTCCG
1 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCTCCCG
1210228 AAGGCTTTTTG
66 AAGGCTTTTTG
* * *
1210239 AAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTCCTG
1 GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCTCCCG
1210304 AAGGCTTTTTG
66 AAGGCTTTTTG
1210315 GAAACATCATGCACTGAAGGACTTACAGATG
1 GAAACATCATGCACTGAAGGACTTACAGATG
1210346 TGGGAAATAG
Statistics
Matches: 544, Mismatches: 13, Indels: 8
0.96 0.02 0.01
Matches are distributed among these distances:
74 67 0.12
75 25 0.05
76 376 0.69
77 76 0.14
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.23
Consensus pattern (76 bp):
GAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCTCCCG
AAGGCTTTTTG
Found at i:1210876 original size:20 final size:21
Alignment explanation
Indices: 1210851--1210903 Score: 81
Period size: 20 Copynumber: 2.5 Consensus size: 21
1210841 CATAAAGCTT
1210851 TCATCTTTGAAAAGAGAA-TA
1 TCATCTTTGAAAAGAGAACTA
*
1210871 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAA-CTA
1210893 TCATCTTTGAA
1 TCATCTTTGAA
1210904 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 17 0.59
22 12 0.41
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (21 bp):
TCATCTTTGAAAAGAGAACTA
Found at i:1212394 original size:36 final size:35
Alignment explanation
Indices: 1212354--1212422 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 35
1212344 TATTACTTCT
1212354 TATTG-AGATGAGCCTCCAAGAATGCCCAAATATTCA
1 TATTGTAG-TGAGCCTCCAA-AATGCCCAAATATTCA
* * *
1212390 TATTGTTGTGAGCCTTCAAAATGCCCCAATATT
1 TATTGTAGTGAGCCTCCAAAATGCCCAAATATT
1212423 ATTTCTGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 13 0.45
36 15 0.52
37 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (35 bp):
TATTGTAGTGAGCCTCCAAAATGCCCAAATATTCA
Found at i:1215461 original size:18 final size:18
Alignment explanation
Indices: 1215438--1215478 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1215428 TTCCTTCTTC
* *
1215438 TTTTTCCTTTTTGTTTTT
1 TTTTTCCTTTCTATTTTT
1215456 TTTTT-CTTTCTATTTTT
1 TTTTTCCTTTCTATTTTT
1215473 TTTTTC
1 TTTTTC
1215479 TTTGCTGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.83
Consensus pattern (18 bp):
TTTTTCCTTTCTATTTTT
Found at i:1222094 original size:14 final size:14
Alignment explanation
Indices: 1222075--1222148 Score: 55
Period size: 15 Copynumber: 5.1 Consensus size: 14
1222065 TTGGGCTTTG
*
1222075 TAATATTTAATAAA
1 TAATATATAATAAA
1222089 TAATATATAATAATTA
1 TAATATATAATAA--A
1222105 TAATA-ATAATACTAA
1 TAATATATAATA--AA
*
1222120 TAATA-ATAATTTTAA
1 TAATATATAA--TAAA
1222135 TAATA-ATAATAAA
1 TAATATATAATAAA
1222148 T
1 T
1222149 TTAAATGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
13 4 0.08
14 12 0.24
15 27 0.53
16 6 0.12
17 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATATATAATAAA
Found at i:1222101 original size:3 final size:3
Alignment explanation
Indices: 1222082--1222146 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
1222072 TTGTAATATT
* *
1222082 TAA TAAA TAA TATA TAA TAA TTA TAA TAA TAA TAC TAA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
1222129 TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
1222147 ATTTAAATGA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1222151 original size:18 final size:18
Alignment explanation
Indices: 1222117--1222152 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1222107 ATAATAATAC
*
1222117 TAATAATAATAATTTTAA
1 TAATAATAATAAATTTAA
1222135 TAATAATAATAAATTTAA
1 TAATAATAATAAATTTAA
1222153 ATGAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAATAATAAATTTAA
Found at i:1227125 original size:21 final size:21
Alignment explanation
Indices: 1227114--1227176 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
1227104 AAATTTAAGT
*
1227114 ATAT-AAA-ATAAAATTATTA
1 ATATAAAATATAAAAATATTA
* *
1227133 ATATAAAATATAAAAAAATTT
1 ATATAAAATATAAAAATATTA
* *
1227154 ATCTAAAATATATAAAATTTTA
1 ATATAAAATATA-AAAATATTA
1227176 A
1 A
1227177 AATAGTATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
19 4 0.12
20 3 0.09
21 20 0.59
22 7 0.21
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
ATATAAAATATAAAAATATTA
Found at i:1228699 original size:179 final size:184
Alignment explanation
Indices: 1228399--1228764 Score: 679
Period size: 179 Copynumber: 2.0 Consensus size: 184
1228389 TCTGAAGGGT
1228399 TGACACTAAGCAGCAACTGGCTACAAATAGCAGATCTTTTGATTAAGGTACTGTTAACTGATATT
1 TGACACTAAGCAGCAACTGGCTACAAATAGCAGATCTTTTGATTAAGGTACTGTTAACTGATATT
1228464 TAACATTCTTCCCCATTGTGTTTTACTATTTTCTGCAACTGTGTTTCCCTTCTTG-CTGTACAAA
66 TAACATTCTTCCCCATTGTGTTTTACTATTTTCTGCAACTGTGTTTCCCTTCTTGCCTGTACAAA
1228528 CATGGAGTTACAAGC-AG-AAAG-ATGAACTAATTAAGGGTTTTTCC-TGTTTC
131 CATGGAGTTACAAGCAAGAAAAGAATGAACTAATTAAGGGTTTTTCCTTGTTTC
1228578 TGACACTAAGCAGCAACTGGCTACAAATAGCAGATCTTTTGATTAAGGTACTGTTAACTGATATT
1 TGACACTAAGCAGCAACTGGCTACAAATAGCAGATCTTTTGATTAAGGTACTGTTAACTGATATT
1228643 TAACATTCTTCCCCATTGTGTTTTACTATTTTCTGCAACTGTGTTTCCCTTCTTGCTCTGTACAA
66 TAACATTCTTCCCCATTGTGTTTTACTATTTTCTGCAACTGTGTTTCCCTTCTTGC-CTGTACAA
1228708 ACATGGAGTTACAAGCAAGAAAAGAAATGAACTAATTAAGGGTTTTTCCTTGTTTC
130 ACATGGAGTTACAAGCAAGAAAAG-AATGAACTAATTAAGGGTTTTTCCTTGTTTC
1228764 T
1 T
1228765 CCCAGGGAAA
Statistics
Matches: 180, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
179 120 0.67
181 24 0.13
182 2 0.01
183 4 0.02
185 23 0.13
186 7 0.04
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.36
Consensus pattern (184 bp):
TGACACTAAGCAGCAACTGGCTACAAATAGCAGATCTTTTGATTAAGGTACTGTTAACTGATATT
TAACATTCTTCCCCATTGTGTTTTACTATTTTCTGCAACTGTGTTTCCCTTCTTGCCTGTACAAA
CATGGAGTTACAAGCAAGAAAAGAATGAACTAATTAAGGGTTTTTCCTTGTTTC
Found at i:1229066 original size:179 final size:179
Alignment explanation
Indices: 1228766--1229125 Score: 711
Period size: 179 Copynumber: 2.0 Consensus size: 179
1228756 CTTGTTTCTC
1228766 CCAGGGAAACCATGGGGAGGAAGAAAATTACAGTTCAAGGGGAGTTACAACTACACATGGACTGA
1 CCAGGGAAACCATGGGGAGGAAGAAAATTACAGTTCAAGGGGAGTTACAACTACACATGGACTGA
*
1228831 TATTTTTTTCTTCTTGCTATGCTTCTTTTTTACCTGTGGTCCGAACTACTGAAACAATAGATAAC
66 TATTTTTTTCTTCTTGCTATGCTTCTTTTTTACCTGTGGTCCAAACTACTGAAACAATAGATAAC
1228896 AATATTACAACAAAAGAAAAGAAATGGCTGTGACCCACTTCCTTCACTG
131 AATATTACAACAAAAGAAAAGAAATGGCTGTGACCCACTTCCTTCACTG
1228945 CCAGGGAAACCATGGGGAGGAAGAAAATTACAGTTCAAGGGGAGTTACAACTACACATGGACTGA
1 CCAGGGAAACCATGGGGAGGAAGAAAATTACAGTTCAAGGGGAGTTACAACTACACATGGACTGA
1229010 TATTTTTTTCTTCTTGCTATGCTTCTTTTTTACCTGTGGTCCAAACTACTGAAACAATAGATAAC
66 TATTTTTTTCTTCTTGCTATGCTTCTTTTTTACCTGTGGTCCAAACTACTGAAACAATAGATAAC
1229075 AATATTACAACAAAAGAAAAGAAATGGCTGTGACCCACTTCCTTCACTG
131 AATATTACAACAAAAGAAAAGAAATGGCTGTGACCCACTTCCTTCACTG
1229124 CC
1 CC
1229126 TTTTATGTAC
Statistics
Matches: 180, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
179 180 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (179 bp):
CCAGGGAAACCATGGGGAGGAAGAAAATTACAGTTCAAGGGGAGTTACAACTACACATGGACTGA
TATTTTTTTCTTCTTGCTATGCTTCTTTTTTACCTGTGGTCCAAACTACTGAAACAATAGATAAC
AATATTACAACAAAAGAAAAGAAATGGCTGTGACCCACTTCCTTCACTG
Found at i:1233269 original size:30 final size:30
Alignment explanation
Indices: 1233217--1233292 Score: 138
Period size: 30 Copynumber: 2.6 Consensus size: 30
1233207 ATTTGATAAT
1233217 TCTAATTAAATCATTG--TTTTTTTAAATA
1 TCTAATTAAATCATTGTTTTTTTTTAAATA
1233245 TCTAATTAAATCATTGTTTTTTTTTAAATA
1 TCTAATTAAATCATTGTTTTTTTTTAAATA
1233275 TCTAATTAAATCATTGTT
1 TCTAATTAAATCATTGTT
1233293 GAATATGTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 16 0.35
30 30 0.65
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.54
Consensus pattern (30 bp):
TCTAATTAAATCATTGTTTTTTTTTAAATA
Found at i:1233535 original size:22 final size:21
Alignment explanation
Indices: 1233506--1233546 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1233496 AGTATGGAGG
*
1233506 TTGTAAATGATAAATACAGGC
1 TTGTAAATGAAAAATACAGGC
1233527 TTGTGAAATGAAAAATACAG
1 TTGT-AAATGAAAAATACAG
1233547 AACATTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.27
Consensus pattern (21 bp):
TTGTAAATGAAAAATACAGGC
Found at i:1237329 original size:109 final size:105
Alignment explanation
Indices: 1237132--1237345 Score: 383
Period size: 109 Copynumber: 2.0 Consensus size: 105
1237122 AAGGTCCACC
*
1237132 ACTGAAGCAGAGTATCGGGGATTGCAGAAGCTGTTACTGATGTTGTGGCTTCCAGCTTTCTCAAA
1 ACTGAAGCAGAGTATCGGGGATTGCAGAAGCTGTTACTGATGTTGTGGCTTACAGCTTTCTCAAA
1237197 GATATGGGTATAGTGTGCTTTAGTCAGCCTGTCATTTGGA
66 GATATGGGTATAGTGTGCTTTAGTCAGCCTGTCATTTGGA
1237237 ACTGAAGCAGAGTATCGTGGGATTGCAGAAGCTGTTACTGATGTTGTGTGGCTTACAGCTTTGCT
1 ACTGAAGCAGAGTATCG-GGGATTGCAGAAGCTGTTACTGATG-T-TGTGGCTTACAGCTTT-CT
1237302 CAAAGATATGGGTATAGTGTGCTTTAGTCAGCCTGTCATTTGGA
62 CAAAGATATGGGTATAGTGTGCTTTAGTCAGCCTGTCATTTGGA
1237346 GCGACAATAC
Statistics
Matches: 104, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
105 17 0.16
106 25 0.24
107 1 0.01
108 15 0.14
109 46 0.44
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.33
Consensus pattern (105 bp):
ACTGAAGCAGAGTATCGGGGATTGCAGAAGCTGTTACTGATGTTGTGGCTTACAGCTTTCTCAAA
GATATGGGTATAGTGTGCTTTAGTCAGCCTGTCATTTGGA
Found at i:1241779 original size:21 final size:20
Alignment explanation
Indices: 1241755--1241793 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1241745 ATAAATATTA
*
1241755 ATTTCATTCAATAAAATAAAG
1 ATTTAATTCAA-AAAATAAAG
*
1241776 ATTTAATTGAAAAAATAA
1 ATTTAATTCAAAAAATAA
1241794 TTTAGAGGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
ATTTAATTCAAAAAATAAAG
Found at i:1247545 original size:11 final size:11
Alignment explanation
Indices: 1247539--1247565 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1247529 TTTTTCTTTC
1247539 TTCTTTCTTCT
1 TTCTTTCTTCT
1247550 TTCTTTCTTCT
1 TTCTTTCTTCT
1247561 TTCTT
1 TTCTT
1247566 ATTCCTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (11 bp):
TTCTTTCTTCT
Found at i:1247552 original size:18 final size:18
Alignment explanation
Indices: 1247531--1247588 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
1247521 TTTCTCATTT
1247531 TTTCTTTCTTCTTTCTTC
1 TTTCTTTCTTCTTTCTTC
*
1247549 TTTCTTTCTTCTTTCTTA
1 TTTCTTTCTTCTTTCTTC
*
1247567 TTCCTTTCTT-TATTC-TC
1 TTTCTTTCTTCT-TTCTTC
1247584 TTTCT
1 TTTCT
1247589 CTACCCAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 6 0.17
18 29 0.83
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTCTTTCTTCTTTCTTC
Found at i:1249109 original size:17 final size:17
Alignment explanation
Indices: 1249084--1249125 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
1249074 TATATACGTT
*
1249084 TAATTAAATATTAAAAA
1 TAATAAAATATTAAAAA
*
1249101 TAATAAAATATTTAAAA
1 TAATAAAATATTAAAAA
1249118 TAATAAAA
1 TAATAAAA
1249126 ATTTGTTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAATAAAATATTAAAAA
Done.