Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 4 of 150
Found at i:1076014 original size:27 final size:27
Alignment explanation
Indices: 1075943--1076018 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
1075933 GGAGTGGGTG
* * * *
1075943 CCGCCTATGGGGATGGCATCACCGATG
1 CCGCCTATGGGGAAGGCGTGACCGATA
*
1075970 CCGCCTATGGGGAAGGCGTGACCGGTA
1 CCGCCTATGGGGAAGGCGTGACCGATA
*
1075997 CCGCCTATGGGAAAGGCGTGAC
1 CCGCCTATGGGGAAGGCGTGAC
1076019 TAGTGCCGCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.20, C:0.28, G:0.37, T:0.16
Consensus pattern (27 bp):
CCGCCTATGGGGAAGGCGTGACCGATA
Found at i:1076027 original size:27 final size:27
Alignment explanation
Indices: 1075940--1076029 Score: 92
Period size: 27 Copynumber: 3.3 Consensus size: 27
1075930 GGGGGAGTGG
* * * *
1075940 GTGCCGCCTATGGGGATGGCATCACC-
1 GTGCCGCCTATGGGAAAGGCGTGACCA
* *
1075966 GATGCCGCCTATGGGGAAGGCGTGACCG
1 G-TGCCGCCTATGGGAAAGGCGTGACCA
* *
1075994 GTACCGCCTATGGGAAAGGCGTGACTA
1 GTGCCGCCTATGGGAAAGGCGTGACCA
1076021 GTGCCGCCT
1 GTGCCGCCT
1076030 CTTCCATAGG
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
26 1 0.02
27 52 0.96
28 1 0.02
ACGTcount: A:0.18, C:0.28, G:0.37, T:0.18
Consensus pattern (27 bp):
GTGCCGCCTATGGGAAAGGCGTGACCA
Found at i:1081403 original size:12 final size:12
Alignment explanation
Indices: 1081386--1081435 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
1081376 TACCTCTTCT
1081386 TCCTCATCATCC
1 TCCTCATCATCC
*
1081398 TCCTCATCATCA
1 TCCTCATCATCC
* *
1081410 TCTTCGTCATCC
1 TCCTCATCATCC
* *
1081422 TCATCCTCATCC
1 TCCTCATCATCC
1081434 TC
1 TC
1081436 TACCCCATCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.16, C:0.46, G:0.02, T:0.36
Consensus pattern (12 bp):
TCCTCATCATCC
Found at i:1081409 original size:15 final size:15
Alignment explanation
Indices: 1081389--1081429 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1081379 CTCTTCTTCC
1081389 TCATCATCCTCCTCA
1 TCATCATCCTCCTCA
* *
1081404 TCATCATCTTCGTCA
1 TCATCATCCTCCTCA
*
1081419 TCCTCATCCTC
1 TCATCATCCTC
1081430 ATCCTCTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.17, C:0.44, G:0.02, T:0.37
Consensus pattern (15 bp):
TCATCATCCTCCTCA
Found at i:1081801 original size:15 final size:15
Alignment explanation
Indices: 1081781--1081817 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1081771 CTGGATCATA
1081781 TTCATCATCATCCTC
1 TTCATCATCATCCTC
* *
1081796 TTCATCTTCCTCCTC
1 TTCATCATCATCCTC
1081811 TTCATCA
1 TTCATCA
1081818 GACTCCGGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.16, C:0.41, G:0.00, T:0.43
Consensus pattern (15 bp):
TTCATCATCATCCTC
Found at i:1083208 original size:24 final size:24
Alignment explanation
Indices: 1083161--1083213 Score: 81
Period size: 26 Copynumber: 2.2 Consensus size: 24
1083151 AAAAAATAAC
1083161 CAAAATATTATAATTTTTTTATTTA
1 CAAAATATTATAA-TTTTTTATTTA
1083186 TCAAAATATTATAA-TTTTTATTTA
1 -CAAAATATTATAATTTTTTATTTA
1083210 CAAA
1 CAAA
1083214 TATAAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 4 0.15
24 10 0.37
26 13 0.48
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (24 bp):
CAAAATATTATAATTTTTTATTTA
Found at i:1083309 original size:27 final size:27
Alignment explanation
Indices: 1083278--1083344 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
1083268 TGCCAAGGTG
*
1083278 ATTGGCGGCACCAAAGGTGTCAAAGCC
1 ATTGGCGGCACCAAAGGTGCCAAAGCC
* *
1083305 ATTGGCGGCACCAAATGTGCCAAAGCT
1 ATTGGCGGCACCAAAGGTGCCAAAGCC
1083332 ATTGGCGGCACCA
1 ATTGGCGGCACCA
1083345 GTGCTATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAGCC
Found at i:1083415 original size:23 final size:24
Alignment explanation
Indices: 1083389--1083447 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 24
1083379 AGAAGGAGAG
*
1083389 GGAAAGAAAGAA-AGAAAGAAAAA
1 GGAAAGAAAGAAGAGAAAAAAAAA
*
1083412 GGAAAG-GAGAAGAGAAAAAAAAA
1 GGAAAGAAAGAAGAGAAAAAAAAA
*
1083435 AGAAAG-AAGAAGA
1 GGAAAGAAAGAAGA
1083448 AGAGGAAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 4 0.13
23 27 0.87
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (24 bp):
GGAAAGAAAGAAGAGAAAAAAAAA
Found at i:1083455 original size:16 final size:16
Alignment explanation
Indices: 1083434--1083486 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
1083424 AGAAAAAAAA
1083434 AAGAAAGAAGAAGAAG
1 AAGAAAGAAGAAGAAG
* *
1083450 AGGAAAGGAGAAG-AG
1 AAGAAAGAAGAAGAAG
*
1083465 AAAAAACGAAGAAGAAG
1 AAGAAA-GAAGAAGAAG
1083482 AAGAA
1 AAGAA
1083487 GAGGGAAGGA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 6 0.21
16 17 0.59
17 6 0.21
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (16 bp):
AAGAAAGAAGAAGAAG
Found at i:1083503 original size:35 final size:39
Alignment explanation
Indices: 1083395--1083512 Score: 151
Period size: 38 Copynumber: 3.2 Consensus size: 39
1083385 AGAGGGAAAG
1083395 AAAGAAAGAAAGAA-AA-AGGAAAGGAGAAGAGAAAAAAA
1 AAAGAAAG-AAGAAGAAGAGGAAAGGAGAAGAGAAAAAAA
*
1083433 AAAGAAAGAAGAAGAAGAGGAAAGGAGAAGAGAAAAAAC
1 AAAGAAAGAAGAAGAAGAGGAAAGGAGAAGAGAAAAAAA
* *
1083472 GAAG-AAGAAGAAGAAGAGGGAA-G-GAAG-G-AAAAAA
1 AAAGAAAGAAGAAGAAGAGGAAAGGAGAAGAGAAAAAAA
1083506 AAAGAAA
1 AAAGAAA
1083513 AAAAGGTAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
34 8 0.11
35 3 0.04
36 4 0.06
37 6 0.08
38 27 0.38
39 24 0.33
ACGTcount: A:0.69, C:0.01, G:0.31, T:0.00
Consensus pattern (39 bp):
AAAGAAAGAAGAAGAAGAGGAAAGGAGAAGAGAAAAAAA
Found at i:1083548 original size:17 final size:19
Alignment explanation
Indices: 1083519--1083555 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1083509 GAAAAAAAGG
1083519 TAATTTTTATTATAA-ATT
1 TAATTTTTATTATAATATT
1083537 TAATTTTT-TTATAATATT
1 TAATTTTTATTATAATATT
1083555 T
1 T
1083556 GTGTGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TAATTTTTATTATAATATT
Found at i:1084258 original size:62 final size:65
Alignment explanation
Indices: 1084127--1084258 Score: 200
Period size: 65 Copynumber: 2.1 Consensus size: 65
1084117 AAGGAAAGGG
1084127 TTTTTTTCGGGTTTTTTACCAAAATATTACAAAAAAAATAAAAAAAATACCAAAATATTATAAAC
1 TTTTTTTCGGGTTTTTTACCAAAATATTACAAAAAAAATAAAAAAAATACCAAAATATTATAAAC
* * * *
1084192 TTTTTTTCGGGTTTTTTACTAAATTATTA-TAAAAAAAT-AAAAATA-ACCAAAATATTAT-AAC
1 TTTTTTTCGGGTTTTTTACCAAAATATTACAAAAAAAATAAAAAAAATACCAAAATATTATAAAC
1084253 TTTTTT
1 TTTTTT
1084259 ATTTACCAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
61 9 0.14
62 13 0.21
63 6 0.10
64 8 0.13
65 27 0.43
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (65 bp):
TTTTTTTCGGGTTTTTTACCAAAATATTACAAAAAAAATAAAAAAAATACCAAAATATTATAAAC
Found at i:1084270 original size:26 final size:27
Alignment explanation
Indices: 1084237--1084299 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
1084227 AATAAAAATA
*
1084237 ACCAAAATATTAT-AACTTTTTTATTT
1 ACCAAAATATTATAAAATTTTTTATTT
1084263 ACCAAAATATTATAAAATTTTTTATTT
1 ACCAAAATATTATAAAATTTTTTATTT
1084290 ACCAAAATAT
1 ACCAAAATAT
1084300 ACCAAAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 13 0.37
27 22 0.63
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (27 bp):
ACCAAAATATTATAAAATTTTTTATTT
Found at i:1084381 original size:27 final size:27
Alignment explanation
Indices: 1084338--1084400 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
1084328 AAAAAACCTA
*
1084338 TGGCGGCACCAAAGGTGCCAAAGTGAT
1 TGGCGGCACCAAAGGTGCCAAAGAGAT
* *
1084365 TGGCGGCACCGATGGTGCCAAAGAGAT
1 TGGCGGCACCAAAGGTGCCAAAGAGAT
1084392 TGGCGGCAC
1 TGGCGGCAC
1084401 AGGACTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.25, C:0.24, G:0.37, T:0.14
Consensus pattern (27 bp):
TGGCGGCACCAAAGGTGCCAAAGAGAT
Found at i:1084797 original size:16 final size:15
Alignment explanation
Indices: 1084772--1084801 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1084762 GTACTGAAAT
1084772 AATATAAAATAATAA
1 AATATAAAATAATAA
1084787 AATATTAAAATAATA
1 AATA-TAAAATAATA
1084802 TATTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AATATAAAATAATAA
Found at i:1087642 original size:16 final size:15
Alignment explanation
Indices: 1087621--1087650 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1087611 AATAAAAATA
1087621 TATTATTTTCATATTT
1 TATTATTTT-ATATTT
1087637 TATTATTTTATATT
1 TATTATTTTATATT
1087651 ATTTCAGTAC
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:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTTATATTT
Found at i:1088058 original size:27 final size:27
Alignment explanation
Indices: 1088017--1088077 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
1088007 TTAGTCATGC
* *
1088017 GCCGCCAATCTCTTTGGCACCATCGGT
1 GCCGCCAATCACTTTGACACCATCGGT
* *
1088044 GCCGCCAATCACTTTGACACCTTTGGT
1 GCCGCCAATCACTTTGACACCATCGGT
1088071 GCCGCCA
1 GCCGCCA
1088078 TAAGTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.16, C:0.38, G:0.21, T:0.25
Consensus pattern (27 bp):
GCCGCCAATCACTTTGACACCATCGGT
Found at i:1088178 original size:27 final size:28
Alignment explanation
Indices: 1088117--1088181 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
1088107 TATTTTTGGT
****
1088117 ATATTTTGGTAAATAAAATTTTTTTATA
1 ATATTTTGGTAAATAAAATAAAGTTATA
1088145 ATATTTTGGTAAATAAAA-AAAGTTATA
1 ATATTTTGGTAAATAAAATAAAGTTATA
1088172 ATATTTTGGT
1 ATATTTTGGT
1088182 TATTTTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
27 15 0.45
28 18 0.55
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.48
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAATAAAGTTATA
Found at i:1088926 original size:3 final size:3
Alignment explanation
Indices: 1088920--1089017 Score: 57
Period size: 3 Copynumber: 34.3 Consensus size: 3
1088910 CCTCCTTTCC
* * *
1088920 TCT TCT TCT TCT TCT TCT TCT T-T TTT TC- TCT TCT CCT T-T CCT T-T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * *
1088964 CCT T-T CCT TCT TTT TCTT TCT T-T T-T TCT TCT CCTT TCC TCT TCT
1 TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TC-T TCT TCT TCT
1089008 TCT TCT TCT T
1 TCT TCT TCT T
1089018 TCTTTTTTTT
Statistics
Matches: 72, Mismatches: 15, Indels: 16
0.70 0.15 0.16
Matches are distributed among these distances:
2 11 0.15
3 56 0.78
4 5 0.07
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:1088956 original size:41 final size:40
Alignment explanation
Indices: 1088896--1089088 Score: 188
Period size: 41 Copynumber: 4.8 Consensus size: 40
1088886 TACCTTTTTT
*
1088896 TTCTT-TTTTTTT-TC-CCTCCTTTCCTCTTCTTCTTCTTC
1 TTCTTCTTTTTTTCTCTTCTCCTTTCCT-TTCTTCTTCTTC
*
1088934 TTCTTCTTTTTTTCTCTTCTCCTTTCCTTTCCTT-TCCTTC
1 TTCTTCTTTTTTTCTCTTCTCCTTTCCTTT-CTTCTTCTTC
* *
1088974 TTTTTCTTTCTTTTTTCTTCTCCTTTCCTCTTCTTCTTCTTC
1 TTCTTCTTT-TTTTCTCTTCTCCTTTCCT-TTCTTCTTCTTC
*
1089016 TTTCTTTTTTTTTTTCTCTTCTCCTTTCCTTT-TTCTTTCTTTCC
1 -TTC-TTCTTTTTTTCTCTTCTCCTTTCCTTTCTTC-TTC-TT-C
*
1089060 TT-TTCTTTCTTTC-C-TCTCCTTT-CTTTCTT
1 TTCTTCTTTTTTTCTCTTCTCCTTTCCTTTCTT
1089089 TCTTTCTTTC
Statistics
Matches: 132, Mismatches: 10, Indels: 25
0.79 0.06 0.15
Matches are distributed among these distances:
38 9 0.07
39 17 0.13
40 18 0.14
41 46 0.35
42 12 0.09
43 24 0.18
44 6 0.05
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (40 bp):
TTCTTCTTTTTTTCTCTTCTCCTTTCCTTTCTTCTTCTTC
Found at i:1088961 original size:5 final size:5
Alignment explanation
Indices: 1088953--1089099 Score: 53
Period size: 5 Copynumber: 29.6 Consensus size: 5
1088943 TTTTCTCTTC
* * * *
1088953 TCCTT TCCTT TCCTT TCC-T TCTTT TTCTT TCTTTT TTCTT CTCCTT TCCTCT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TC-CTT TCCTT -TCCTT TCCT-T
* ** *
1089005 TCTTCTT CTTCTT T-CTT T--TT TTTTT TCTCTT CTCCTT TCCTTT TTCTT
1 TC--CTT -TCCTT TCCTT TCCTT TCCTT TC-CTT -TCCTT TCC-TT TCCTT
* *
1089053 T-CTT TCCTT TTCTT T-CTT TCCTC TCCTT T-CTT T-CTT T-CTT T-CTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
1089097 TCC
1 TCC
1089100 CTCTCCTTCT
Statistics
Matches: 112, Mismatches: 15, Indels: 30
0.71 0.10 0.19
Matches are distributed among these distances:
3 3 0.03
4 31 0.28
5 50 0.45
6 22 0.20
7 3 0.03
8 3 0.03
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (5 bp):
TCCTT
Found at i:1089037 original size:63 final size:62
Alignment explanation
Indices: 1088951--1089095 Score: 147
Period size: 63 Copynumber: 2.4 Consensus size: 62
1088941 TTTTTTCTCT
* * * *
1088951 TCTCCTTTCCTTTCCTTTCCTTCT-TTTTCTTTCTTTTTTC-TTC--TCCTTTCCTCTTC-TTCT
1 TCTCCTTT-CTTT-CTTTCTTTCTCTTCTCTTTCCTTTTTCTTTCTTTCCTTTCCT-TTCTTTCC
* * * *
1089011 TCTTCTTTCTTTTTTTTTTTCTCTTCTCCTTTCCTTTTTCTTTCTTTCCTTTTCTTTCTTTCC
1 TCTCCTTTCTTTCTTTCTTTCTCTTCT-CTTTCCTTTTTCTTTCTTTCCTTTCCTTTCTTTCC
1089074 TCTCCTTTCTTTCTTTCTTTCT
1 TCTCCTTTCTTTCTTTCTTTCT
1089096 TTCCCTCTCC
Statistics
Matches: 68, Mismatches: 11, Indels: 9
0.77 0.12 0.10
Matches are distributed among these distances:
58 7 0.10
59 7 0.10
60 18 0.26
61 3 0.04
62 3 0.04
63 30 0.44
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (62 bp):
TCTCCTTTCTTTCTTTCTTTCTCTTCTCTTTCCTTTTTCTTTCTTTCCTTTCCTTTCTTTCC
Found at i:1089054 original size:85 final size:81
Alignment explanation
Indices: 1088888--1089071 Score: 269
Period size: 82 Copynumber: 2.2 Consensus size: 81
1088878 ATAAAAATTA
* *
1088888 CCTTTTTTTTCTTTTTTTTTTCCCTCCTTTCCTCTTCTTCTTCTTCTTCTTCTTTTTTTCTCTTC
1 CCTTCTTTTTCTTTCTTTTTTCCCTCCTTTCCTCTTCTTCTTCTTCTTCTTCTTTTTTTCTCTTC
1088953 TCCTTTCCTTTCCTTT
66 TCCTTTCCTTTCCTTT
* *
1088969 CCTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTCTTCTTCTTCTTCTTTCTTTTTTTTTTTCTC
1 CCTTCTTTTTCTTTCTTTTTTC-CCTCCTTTCCTCTTCTTCTTCTTC-TTC-TTCTTTTTTTCTC
*
1089034 TTCTCCTTTCCTTTTTCTTT
63 TTCTCCTTTCC-TTTCCTTT
* *
1089054 CTTTCCTTTTCTTTCTTT
1 CCTTCTTTTTCTTTCTTT
1089072 CCTCTCCTTT
Statistics
Matches: 92, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
81 20 0.22
82 23 0.25
83 3 0.03
84 23 0.25
85 23 0.25
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (81 bp):
CCTTCTTTTTCTTTCTTTTTTCCCTCCTTTCCTCTTCTTCTTCTTCTTCTTCTTTTTTTCTCTTC
TCCTTTCCTTTCCTTT
Found at i:1089094 original size:36 final size:37
Alignment explanation
Indices: 1088955--1089094 Score: 114
Period size: 36 Copynumber: 3.8 Consensus size: 37
1088945 TTCTCTTCTC
* *
1088955 CTTTCCTTTCCTTTCCTTCTTTTTCTTT-C-TTT-TTT
1 CTTTCCTCTCCTTTCCTT-TCTTTCTTTCCTTTTCTTT
* *
1088990 CTTCTCCTTTCCTCTTCTTCTTC-TTCTTT-CTTTT-TTT
1 CTT-TCCTCTCCT-TTCCT-TTCTTTCTTTCCTTTTCTTT
*
1089027 TTTTCTCTTCTCCTTTCCTTTTTCTTTCTTTCCTTTTCTTT
1 CTTTC-C-TCTCCTTTCC--TTTCTTTCTTTCCTTTTCTTT
1089068 CTTTCCTCTCCTTT-CTTTCTTTCTTTC
1 CTTTCCTCTCCTTTCCTTTCTTTCTTTC
1089095 TTTCCCTCTC
Statistics
Matches: 88, Mismatches: 6, Indels: 21
0.77 0.05 0.18
Matches are distributed among these distances:
35 3 0.03
36 30 0.34
37 17 0.19
38 10 0.11
39 15 0.17
40 6 0.07
41 7 0.08
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (37 bp):
CTTTCCTCTCCTTTCCTTTCTTTCTTTCCTTTTCTTT
Found at i:1089096 original size:85 final size:83
Alignment explanation
Indices: 1088905--1089082 Score: 235
Period size: 85 Copynumber: 2.2 Consensus size: 83
1088895 TTTCTTTTTT
1088905 TTTTCC-CTCCTTT-C-C-TCTTCTTCTTCTTCTTCTTCTTTTTTTCTCTTCTCCTTTCCTTTCC
1 TTTTCCTCTCCTTTCCTCTTCTTCTTCTTCTTCTTCTTCTTTTTTTCTCTTCTCCTTTCCTTTCC
*
1088966 TTTCCTTCTTTTTCTTTC
66 TTTCCTTCCTTTTCTTTC
*
1088984 TTTTTTCTTCTCCTTTCCTCTTCTTCTTCTTCTTTCTT-TT-TTTTTTTCTCTTCTCCTTTCCTT
1 --TTTTCCTCTCCTTTCCTCTTCTTCTTCTTC-TTCTTCTTCTTTTTTTCTCTTCTCCTTTCC-T
* *
1089047 TTTCTTTCTTTCCTTTTCTTTC
62 TTCCTTTCCTTCCTTTTCTTTC
1089069 -TTTCCTCTCCTTTC
1 TTTTCCTCTCCTTTC
1089083 TTTCTTTCTT
Statistics
Matches: 86, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
81 5 0.06
82 20 0.23
83 1 0.01
84 22 0.26
85 33 0.38
86 5 0.06
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (83 bp):
TTTTCCTCTCCTTTCCTCTTCTTCTTCTTCTTCTTCTTCTTTTTTTCTCTTCTCCTTTCCTTTCC
TTTCCTTCCTTTTCTTTC
Found at i:1089097 original size:79 final size:81
Alignment explanation
Indices: 1088888--1089098 Score: 242
Period size: 82 Copynumber: 2.6 Consensus size: 81
1088878 ATAAAAATTA
* *
1088888 CCTTTTTTTTCTTTT-TTT-TTTCC-CTCCTTTCCTCTTCTTC-TTC-TTCTTCTTCTTTTTTTC
1 CCTTTCTTTCCTTTTCTTTCTTTCCTCTCCTTTCCTCTTCTTCTTTCTTTCTTCTTCTTTTTTTC
1088948 TCTTCTCCTTTCCTTT
66 TCTTCTCCTTTCCTTT
* * *
1088964 CCTTTCCTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTCTTCTTCTTCTTCTTTCTT-TT-TTT
1 CCTTTCTTTCCTTTTCTTTC---TTTCCTCTCCTTTCCTCTTCTTC-T-TTCTTTCTTCTTCTTT
1089027 TTTTCTCTTCTCCTTTCCTTTT
61 TTTTCTCTTCTCCTTTCC-TTT
*
1089049 TCTTTCTTTCCTTTTCTTTCTTTCCTCTCCTTT-CT-TTCTTTCTTTCTTTC
1 CCTTTCTTTCCTTTTCTTTCTTTCCTCTCCTTTCCTCTTC-TTCTTTCTTTC
1089099 CCTCTCCTTC
Statistics
Matches: 114, Mismatches: 9, Indels: 21
0.79 0.06 0.15
Matches are distributed among these distances:
76 11 0.10
77 3 0.03
79 7 0.06
80 4 0.04
81 9 0.08
82 29 0.25
84 21 0.18
85 25 0.22
86 5 0.04
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (81 bp):
CCTTTCTTTCCTTTTCTTTCTTTCCTCTCCTTTCCTCTTCTTCTTTCTTTCTTCTTCTTTTTTTC
TCTTCTCCTTTCCTTT
Found at i:1089504 original size:2 final size:2
Alignment explanation
Indices: 1089497--1089528 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1089487 AATTAATTGT
1089497 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1089529 TAAAGAGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1095455 original size:18 final size:20
Alignment explanation
Indices: 1095414--1095457 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1095404 AATATAATCA
*
1095414 TATCATATTTATAAATACAT
1 TATCATAATTATAAATACAT
1095434 TATCATAATT-TAAATA-AT
1 TATCATAATTATAAATACAT
1095452 TATCAT
1 TATCAT
1095458 TTATTGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 6 0.26
20 9 0.39
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (20 bp):
TATCATAATTATAAATACAT
Found at i:1102690 original size:26 final size:26
Alignment explanation
Indices: 1102642--1102691 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1102632 TGGTAATGTA
*
1102642 TTAAATATTTTTTTCCATTAAATTTG
1 TTAAATATTTTTTTCCATAAAATTTG
*
1102668 TTAAATTTTTTTTTCTCA-AAAATT
1 TTAAATATTTTTTTC-CATAAAATT
1102692 GTTGGATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (26 bp):
TTAAATATTTTTTTCCATAAAATTTG
Found at i:1104502 original size:31 final size:31
Alignment explanation
Indices: 1104467--1104532 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 31
1104457 ATTTACTTAA
1104467 ATGTATACAAT-TGAATTAAAAGT-AAAGTTTC
1 ATGTATA-AATCTGAATTAAAA-TCAAAGTTTC
*
1104498 ATGTATAAATCTGAATTACAATCAAAGTTTC
1 ATGTATAAATCTGAATTAAAATCAAAGTTTC
1104529 ATGT
1 ATGT
1104533 GTATAATTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (31 bp):
ATGTATAAATCTGAATTAAAATCAAAGTTTC
Found at i:1114477 original size:156 final size:158
Alignment explanation
Indices: 1114164--1114477 Score: 436
Period size: 159 Copynumber: 2.0 Consensus size: 158
1114154 CTCCAGCACC
* *
1114164 GGCACCGGCTCCACCACCGGCTGGCTTAAATGGAAGTTCTAGCAGTAGTGTTAGCTTGGTTAGCA
1 GGCACCGGCTCCACCACCGGCTGGCTTAAATGGAAGTTCTAGCAGTAGTGTCAGCCTGGTTAGCA
* * *
1114229 GTGGTTGTAGCAGCAGCAGCAGCAGCAGCAGTGTATTTTCGAGCTTATTTACATCCACTACTGTA
66 GTGGTTGTAGCAGCAGCAGCAGCAGCAG-AGTGTATTTGCAAGCTTATTTACATCCACGACTGTA
* *
1114294 TCTGCGAGCATACACCCTCCTCAACCTCT
130 TCTGCAAGCATACAACCTCCTCAACCTCT
* * * *
1114323 GGCACCGGCTCCACCACTGGTTGGCTTAAATGGAAGTTGTAGCGGTAGTGTCAGCCTGGTTAGCA
1 GGCACCGGCTCCACCACCGGCTGGCTTAAATGGAAGTTCTAGCAGTAGTGTCAGCCTGGTTAGCA
* * * * * *
1114388 GTGG-TGCTAGCAGCAGTAGCAGTAG-TG-GTGTATTTGCAAGCTTATTTGCCTCCTCGACTGTA
66 GTGGTTG-TAGCAGCAGCAGCAGCAGCAGAGTGTATTTGCAAGCTTATTTACATCCACGACTGTA
1114450 TCTGCAAGCATACAACCTCCTCAACCTC
130 TCTGCAAGCATACAACCTCCTCAACCTC
1114478 CGGCTTTAAC
Statistics
Matches: 137, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
156 55 0.40
158 3 0.02
159 79 0.58
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (158 bp):
GGCACCGGCTCCACCACCGGCTGGCTTAAATGGAAGTTCTAGCAGTAGTGTCAGCCTGGTTAGCA
GTGGTTGTAGCAGCAGCAGCAGCAGCAGAGTGTATTTGCAAGCTTATTTACATCCACGACTGTAT
CTGCAAGCATACAACCTCCTCAACCTCT
Found at i:1121797 original size:156 final size:153
Alignment explanation
Indices: 1121487--1121790 Score: 382
Period size: 156 Copynumber: 2.0 Consensus size: 153
1121477 TTAAAGGAGG
* * * * *
1121487 AGGTTGAGGAGGTTGTATGCTTGCAGATACAGTTGAGGAGGCAAATAAACTTGCAAATACACCAC
1 AGGTTGAGGAGGTCGAATGCTTGCAGATACAGTCGAGGAGGCAAATAAACTCGAAAATACACCAC
* **
1121552 TGCTGCTGCTATTGCTAGCACCACTGCTAACCAGGCTGATGCAACCGCTACAACTTCCATTTAAG
66 TGCTGCTGCTA-T-CTA-CACCACTGCTAACCAAGCTGACACAACCGCTACAACTTCCATTTAAG
1121617 CCAGCCGATGGTGGAGCTGGTGCCGT
128 CCAGCCGATGGTGGAGCTGGTGCCGT
* * *
1121643 AGGTTGAGGAGGTCGAATGCTTGCAGATACAGTCGAGGAGGTAAATAAGCTCGAAAATACACCGC
1 AGGTTGAGGAGGTCGAATGCTTGCAGATACAGTCGAGGAGGCAAATAAACTCGAAAATACACCAC
* * ** *
1121708 TGCTGCTGCTA-C-A-ACCACTGCTAATCAAGCTGACACTAGTGCTACAACTTCCATTTAAGCTA
66 TGCTGCTGCTATCTACACCACTGCTAACCAAGCTGACACAACCGCTACAACTTCCATTTAAGCCA
* *
1121770 GCTGGA-GGTGGAGCCGGTGCC
131 GC-CGATGGTGGAGCTGGTGCC
1121791 AGTGCCGGAG
Statistics
Matches: 129, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
150 57 0.44
151 2 0.02
152 1 0.01
153 1 0.01
156 68 0.53
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (153 bp):
AGGTTGAGGAGGTCGAATGCTTGCAGATACAGTCGAGGAGGCAAATAAACTCGAAAATACACCAC
TGCTGCTGCTATCTACACCACTGCTAACCAAGCTGACACAACCGCTACAACTTCCATTTAAGCCA
GCCGATGGTGGAGCTGGTGCCGT
Found at i:1121807 original size:12 final size:12
Alignment explanation
Indices: 1121792--1121827 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1121782 GCCGGTGCCA
*
1121792 GTGCCGGAGCTG
1 GTGCTGGAGCTG
1121804 GTGCTGGAGCTG
1 GTGCTGGAGCTG
1121816 GTGCTGGAGCTG
1 GTGCTGGAGCTG
1121828 CAGCTTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.08, C:0.19, G:0.50, T:0.22
Consensus pattern (12 bp):
GTGCTGGAGCTG
Found at i:1126540 original size:17 final size:18
Alignment explanation
Indices: 1126518--1126552 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1126508 ACAAAAACCC
1126518 AAAATCCAAAAT-GAAAA
1 AAAATCCAAAATCGAAAA
*
1126535 AAAATCGAAAATCGAAAA
1 AAAATCCAAAATCGAAAA
1126553 CCGAATCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.69, C:0.11, G:0.09, T:0.11
Consensus pattern (18 bp):
AAAATCCAAAATCGAAAA
Found at i:1130458 original size:83 final size:72
Alignment explanation
Indices: 1130281--1130466 Score: 237
Period size: 83 Copynumber: 2.4 Consensus size: 72
1130271 GCATAGTGCA
*
1130281 CTAAAGATCGATAAAAATTGACCATTGGACACACCCACATAAATACATGCATGCATACATATATA
1 CTAAAGATCGAT-AAAATTGACCATTGGACACACCCACAAAAATACATGCATGCATACATATATA
1130346 TACGCGCG
65 TACGCGCG
1130354 CTAAAGATCGATAAAAGTTGACCATTGGACACACACACACAAAAATGCATGCATGCATGCATACA
1 CTAAAGATCGATAAAA-TTGACCATTGGACACAC-C-CACAAAAAT--A--CATGCATGCATACA
1130419 TATATATACCCACGCGCG
59 TATATAT----ACGCGCG
*
1130437 CTAAAGATTGATAGAAATTGACCATTGGAC
1 CTAAAGATCGATA-AAATTGACCATTGGAC
1130467 CTCATTTGGC
Statistics
Matches: 99, Mismatches: 2, Indels: 14
0.86 0.02 0.12
Matches are distributed among these distances:
72 4 0.04
73 29 0.29
74 1 0.01
75 8 0.08
77 1 0.01
79 21 0.21
83 32 0.32
84 3 0.03
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.22
Consensus pattern (72 bp):
CTAAAGATCGATAAAATTGACCATTGGACACACCCACAAAAATACATGCATGCATACATATATAT
ACGCGCG
Found at i:1132955 original size:24 final size:24
Alignment explanation
Indices: 1132910--1132955 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1132900 ATATGAGAAG
**
1132910 AGAGAAAAATAAAAGGGAAAAAGA
1 AGAGAAAAATAAAAGAAAAAAAGA
1132934 AGAGAAAAAT-AAAGAAATAAAA
1 AGAGAAAAATAAAAGAAA-AAAA
1132956 AAAAATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.07
Consensus pattern (24 bp):
AGAGAAAAATAAAAGAAAAAAAGA
Found at i:1134822 original size:2 final size:2
Alignment explanation
Indices: 1134817--1134847 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1134807 TCCCGTGTGT
1134817 TA TA 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 TA TA T
1134848 TGAACCTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1137597 original size:19 final size:20
Alignment explanation
Indices: 1137552--1137607 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 20
1137542 TTTTCACCAA
*
1137552 AAAATTTCTAAATTA-TTATT
1 AAAATTT-TAAATAATTTATT
*
1137572 AAGATTTTAAATAATTTA-T
1 AAAATTTTAAATAATTTATT
*
1137591 AAAATTTAAAATTAATT
1 AAAATTTTAAA-TAATT
1137608 GAATCTTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (20 bp):
AAAATTTTAAATAATTTATT
Found at i:1150413 original size:2 final size:2
Alignment explanation
Indices: 1150406--1150440 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1150396 AATGCATGAA
1150406 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1150441 CACCTCGGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1155065 original size:10 final size:10
Alignment explanation
Indices: 1155050--1155075 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1155040 GTCTAAATAG
1155050 GTATATGTAT
1 GTATATGTAT
1155060 GTATATGTAT
1 GTATATGTAT
1155070 GTATAT
1 GTATAT
1155076 TTGTCCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (10 bp):
GTATATGTAT
Found at i:1164362 original size:27 final size:28
Alignment explanation
Indices: 1164323--1164377 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
1164313 TACAGGTAGC
*
1164323 TAAAAAACATTTACTAATAGTTAAGTGA
1 TAAAAAACATTTACTAATAATTAAGTGA
*
1164351 TAAAAAA-ATTTACTAATAATTGAGTGA
1 TAAAAAACATTTACTAATAATTAAGTGA
1164378 CTATGAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.33
Consensus pattern (28 bp):
TAAAAAACATTTACTAATAATTAAGTGA
Found at i:1169882 original size:14 final size:15
Alignment explanation
Indices: 1169856--1169884 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1169846 TATAAAAACT
1169856 ATAAAATATTCAAAA
1 ATAAAATATTCAAAA
1169871 ATAAAA-ATTCAAAA
1 ATAAAATATTCAAAA
1169885 TTCAAAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (15 bp):
ATAAAATATTCAAAA
Found at i:1169905 original size:21 final size:20
Alignment explanation
Indices: 1169849--1169918 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 20
1169839 TAAATAATAT
*
1169849 AAAAACTATAAAATATTCAAA
1 AAAAAATATAAAA-ATTCAAA
*
1169870 AATAAAA-ATTCAAAATTCAAA
1 AA-AAAATA-TAAAAATTCAAA
*
1169891 GAAAAATTATAAAAAGTTCATAA
1 -AAAAAATATAAAAA-TTCA-AA
1169914 AAAAA
1 AAAAA
1169919 GAAAAGAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
21 18 0.46
22 19 0.49
23 2 0.05
ACGTcount: A:0.67, C:0.07, G:0.03, T:0.23
Consensus pattern (20 bp):
AAAAAATATAAAAATTCAAA
Found at i:1170363 original size:21 final size:21
Alignment explanation
Indices: 1170339--1170386 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
1170329 TTTAAAATTA
1170339 ATTTTTCATTTTTGGTCCTTG
1 ATTTTTCATTTTTGGTCCTTG
1170360 ATTTTTCATTTTTGGTCCTTG
1 ATTTTTCATTTTTGGTCCTTG
1170381 ATTTTT
1 ATTTTT
1170387 AGAATTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.10, C:0.12, G:0.12, T:0.65
Consensus pattern (21 bp):
ATTTTTCATTTTTGGTCCTTG
Found at i:1182094 original size:263 final size:262
Alignment explanation
Indices: 1181619--1182406 Score: 1188
Period size: 263 Copynumber: 3.0 Consensus size: 262
1181609 ATATAATTAC
* *
1181619 ATTGGATATGTATATTCAGCTGTGAGAATGCATACATTTATTTATATATATGTGTGATGCAATGC
1 ATTGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGATGCAATGC
* * *
1181684 TGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCAGGCTTATTTCCTAGCAGGTG
66 TGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCCATCTCCATGCTTGTTTCCTAGCAGGTG
* *
1181749 TTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTTCTTTGGACTGA
131 TTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCTGTTTTCTTTGGACCGA
* * *
1181814 GTTCGGCGGTAAATCGGAACTCTTTGTTACCTTGAAAAAAAATATTATTACATTGACAAATGTTT
196 TTTCGGCGATGAATCGGAACTCTTTGTTACCTTGAAAAAAAATATTATTACATTGACAAATG-TT
1181879 TAA
260 TAA
* *
1181882 ATTGGATATGTAGATTCAGCTGTGAGAATGCATACGTTTATTTATAGATGTGTGTGATGCAATGC
1 ATTGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGATGCAATGC
*
1181947 TGTTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCCATCTCCATGCTTGTTTCCTAGCAGGTG
66 TGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCCATCTCCATGCTTGTTTCCTAGCAGGTG
* * * *
1182012 TTGTTGTACTTTAGTTTCTTAAAGTGCTATCCTTATTCTCCCTAATCCTGTTTTCTTTGGACCGA
131 TTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCTGTTTTCTTTGGACCGA
* *
1182077 TTTCGGCGATGAATCGGAACTCTTTGTTACCTTGAAAAAGAATATTATTACATTGACAAATG-CT
196 TTTCGGCGATGAATCGGAACTCTTTGTTACCTTGAAAAAAAATATTATTACATTGACAAATGTTT
1182141 --
261 AA
*
1182141 -TT--ATA---CG-TTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGTGATGCAAT
1 ATTGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTATATA--TGTGTGTGATGCAAT
* *
1182199 GTTGCTATGTTATTAGTGTTGATTGAATCATTAGCCCCCCATCTCCATGCTTGTTTCCTAGCAGG
64 GCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCCATCTCCATGCTTGTTTCCTAGCAGG
*
1182264 TGGTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAAT-CTGGTTTTCTTTGGAC
129 TGTTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCT-GTTTTCTTTGGAC
* * ** *
1182328 CGATTTCGACAATGAATTAGAATTCTTTGTTACCTT--AAAAAAATATTATTACATTGACAAATG
193 CGATTTCGGCGATGAATCGGAACTCTTTGTTACCTTGAAAAAAAATATTATTACATTGACAAATG
1182391 CTTTAA
258 -TTTAA
1182397 ATTGGATATG
1 ATTGGATATG
1182407 CTTGTTTTTT
Statistics
Matches: 476, Mismatches: 37, Indels: 26
0.88 0.07 0.05
Matches are distributed among these distances:
252 58 0.12
253 3 0.01
254 165 0.35
256 3 0.01
257 2 0.00
258 2 0.00
259 3 0.01
261 1 0.00
263 239 0.50
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (262 bp):
ATTGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGATGCAATGC
TGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCCATCTCCATGCTTGTTTCCTAGCAGGTG
TTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCTGTTTTCTTTGGACCGA
TTTCGGCGATGAATCGGAACTCTTTGTTACCTTGAAAAAAAATATTATTACATTGACAAATGTTT
AA
Found at i:1182289 original size:254 final size:250
Alignment explanation
Indices: 1181896--1182395 Score: 804
Period size: 254 Copynumber: 2.0 Consensus size: 250
1181886 GATATGTAGA
* * *
1181896 TTCAGCTGTGAGAATGCATACGTTTATTTATAGATGTGTGTGATGCAATGCTGTTATGTTCTTAG
1 TTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGATGCAATGCTGCTATGTTCTTAG
1181961 TGTTGATTGAATCATTAGCCCCCCATCTCCATGCTTGTTTCCTAGCAGGTGTTGTTGTACTTTAG
66 TGTTGATTGAATCATTAGCCCCCCATCTCCATGCTTGTTTCCTAGCAGGTGTTGTTGTACTTTAG
* * * * *
1182026 TTTCTTAAAGTGCTATCCTTATTCTCCCTAATCCTGTTTTCTTTGGACCGATTTCGGCGATGAAT
131 TCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTTCTTTGGACCGATTTCGGCGATGAAT
1182091 CGGAACTCTTTGTTACCTTGAAAAAGAATATTATTACATTGACAAATGCTTTATACG
196 CGGAACTCTTTGTTACCTTGAAAAA-AATATTATTACATTGACAAATGCTTTATA-G
* *
1182148 TTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGTGATGCAATGTTGCTATGTTATT
1 TTCAGCTGTGAGAATGCATACATTTATTTATATA--TGTGTGTGATGCAATGCTGCTATGTTCTT
*
1182213 AGTGTTGATTGAATCATTAGCCCCCCATCTCCATGCTTGTTTCCTAGCAGGTGGTGTTGTACTTT
64 AGTGTTGATTGAATCATTAGCCCCCCATCTCCATGCTTGTTTCCTAGCAGGTGTTGTTGTACTTT
* * *
1182278 AGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCTGGTTTTCTTTGGACCGATTTCGACAATGA
129 AGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTTCTTTGGACCGATTTCGGCGATGA
** *
1182343 ATTAGAATTCTTTGTTACCTT-AAAAAAATATTATTACATTGACAAATGCTTTA
194 ATCGGAACTCTTTGTTACCTTGAAAAAAATATTATTACATTGACAAATGCTTTA
1182396 AATTGGATAT
Statistics
Matches: 229, Mismatches: 17, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
252 59 0.26
253 5 0.02
254 165 0.72
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (250 bp):
TTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGATGCAATGCTGCTATGTTCTTAG
TGTTGATTGAATCATTAGCCCCCCATCTCCATGCTTGTTTCCTAGCAGGTGTTGTTGTACTTTAG
TCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTTCTTTGGACCGATTTCGGCGATGAAT
CGGAACTCTTTGTTACCTTGAAAAAAATATTATTACATTGACAAATGCTTTATAG
Found at i:1191186 original size:70 final size:70
Alignment explanation
Indices: 1191073--1191212 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
1191063 CAACCGGAGA
1191073 GCGAAGACAACCCCTTGGGTACTCTAGCAATGACATGCCTCACCGTATTTATGGCGTATCGGTTT
1 GCGAAGACAACCCCTTGGGTACTCTAGCAATGACATGCCTCACCGTATTTATGGCGTATCGGTTT
1191138 TACAT
66 TACAT
1191143 GCGAAGACAACCCCTTGGGTACTCTAGCAATGACATGCCTCACCGTATTTATGGCGTATCGGTTT
1 GCGAAGACAACCCCTTGGGTACTCTAGCAATGACATGCCTCACCGTATTTATGGCGTATCGGTTT
1191208 TACAT
66 TACAT
1191213 TCCGATTTAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (70 bp):
GCGAAGACAACCCCTTGGGTACTCTAGCAATGACATGCCTCACCGTATTTATGGCGTATCGGTTT
TACAT
Found at i:1191806 original size:263 final size:262
Alignment explanation
Indices: 1191300--1192494 Score: 1843
Period size: 263 Copynumber: 4.6 Consensus size: 262
1191290 TGATCCTAAA
* * *
1191300 CAGGTGTTGTTGTACATTAGTCTCTTAAAGTGCTA-CCCTATTCCCCCGAA-TCTGGTTTTCTTT
1 CAGGTGTTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAATTC-GGTTTTCTTT
* * *
1191363 GGACCGATTTCGGTGATGAATTGGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGACA
65 GGACCGATTTCGGCGATGAATCGAAACTCTTTGTTACCTTGAAAA-AAATATTATTACATTGACA
* *
1191428 AATGCTTTAAATTGGATATGTAGATTCAGCTATGAGAATGCATACATTTATTTATATATGTGTGT
129 AATGCTTTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGT
1191493 GATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTC
194 GATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTC
1191558 CTAG
259 CTAG
*
1191562 CAGGTGGTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAATTCGGTTTT-TTTG
1 CAGGTGTTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAATTCGGTTTTCTTTG
* * *
1191626 GACCGATTTTGGCGATGAATCGAAACTCTTTGTTACCTTGAAAAAAGTATTATTACATTGACAAT
66 GACCGATTTCGGCGATGAATCGAAACTCTTTGTTACCTTGAAAAAAATATTATTACATTGACAAA
* * * *
1191691 TGCTTTAAAATGGATATGTACATTCAGCTGTTAGAATGCATATATTTATTTTTATAAGTGTGTGT
131 TGCTTTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATAT-A-TGTGTGT
* *
1191756 GATGCAGTGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTA
194 GATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTC
1191821 CTAG
259 CTAG
* *
1191825 CAGATG-T--TGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAA-TCTGGTTTTCTTC
1 CAGGTGTTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAATTC-GGTTTTCTTT
*
1191886 GGACCGATTTCGGGGATGAATC-AGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGAC
65 GGACCGATTTCGGCGATGAATCGA-AACTCTTTGTTACCTTGAAAA-AAATATTATTACATTGAC
*
1191950 AAATGCTTTAAATTGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTG
128 AAATGCTTTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTG
*
1192015 TGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTT
193 TGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTT
1192080 CCTAG
258 CCTAG
* * * * * *
1192085 CAGGTGTTGGTGTACTTTAGTTTCTTAAAGTGCTATCCCCATTCGCCCTAATCCTGTTTCCTTTG
1 CAGGTGTTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAATTCGGTTTTCTTTG
*
1192150 GACCGATTTCGGCGATGAATCGGAACTCTTTGTTACCTTGAAAAAGAATATTATTACATTGACAA
66 GACCGATTTCGGCGATGAATCGAAACTCTTTGTTACCTTGAAAAA-AATATTATTACATTGACAA
* * *
1192215 ATGCTTTAAATTGGATATATACGTTCAGCTGTGAGAATGCATACATTTATTTATATATGCGTGTG
130 ATGCTTTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTG
* * * *
1192280 ATGCAATGTTGCTATGTTATTAGTGTTGATTGAATCATTAGCCCCTCATCTCCAAGCTTGTTTCC
195 ATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTCC
1192345 TAG
260 TAG
* * *
1192348 CAGGTGTTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTTCTTTG
1 CAGGTGTTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAATTCGGTTTTCTTTG
* * * *
1192413 GACCGATTTCGACAATGAAT-TAGAATTCTTTGTTACCTT-AAAAAAATATTATTACATTGACAA
66 GACCGATTTCGGCGATGAATCGA-AACTCTTTGTTACCTTGAAAAAAATATTATTACATTGACAA
1192476 ATGCTTTAAATTGGATATG
130 ATGCTTTAAATTGGATATG
1192495 CTTGTTTTTT
Statistics
Matches: 854, Mismatches: 64, Indels: 31
0.90 0.07 0.03
Matches are distributed among these distances:
259 2 0.00
260 126 0.15
261 150 0.18
262 153 0.18
263 420 0.49
264 3 0.00
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.39
Consensus pattern (262 bp):
CAGGTGTTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAATTCGGTTTTCTTTG
GACCGATTTCGGCGATGAATCGAAACTCTTTGTTACCTTGAAAAAAATATTATTACATTGACAAA
TGCTTTAAATTGGATATGTACATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGA
TGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTCCT
AG
Found at i:1192319 original size:523 final size:524
Alignment explanation
Indices: 1191307--1192494 Score: 1956
Period size: 523 Copynumber: 2.3 Consensus size: 524
1191297 AAACAGGTGT
*
1191307 TGTTGTACATTAGTCTCTTAAAGTGCTA-CCCTATTCCCCCGAATCTGGTTTTCTTTGGACCGAT
1 TGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCTGGTTTTCTTTGGACCGAT
* *
1191371 TTCGGTGATGAATTGGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGACAAATGCTTT
66 TTCGGCGATGAATTAGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGACAAATGCTTT
1191436 AAATTGGATATGTAGATTCAGCTATGAGAATGCATACATTTATTTATATATGTGTGTGATGCAAT
131 AAATTGGATATGTAGATTCAGCTATGAGAATGCATACATTTATTTATATATGTGTGTGATGCAAT
*
1191501 GCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTCCTAGCAGG
196 GCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGG
* * *
1191566 TGGTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAATTCGGTTTTTTTGGACCG
261 TGGTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCCATTCCCCCTAATCCGGTTTCTTTGGACCG
* * *
1191631 ATTTTGGCGATGAATCGAAACTCTTTGTTACCTTGAAAAAAGTATTATTACATTGACAATTGCTT
326 ATTTCGGCGATGAATCGAAACTCTTTGTTACCTTGAAAAAAATATTATTACATTGACAAATGCTT
* * * * *
1191696 TAAAATGGATATGTACATTCAGCTGTTAGAATGCATATATTTATTTTTATAAGTGTGTGTGATGC
391 TAAAATGGATATATACATTCAGCTGTGAGAATGCATACATTTATTTATATAAGTGCGTGTGATGC
* * * *
1191761 AGTGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTACTAGC
456 AATGCTGCTATGTTATTAGTGTTGATTGAATCATTAGCCCCTCATCTCCAAGCTTGTTTACTAGC
1191826 A-GA
521 AGGA
* *
1191829 TGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAATCTGGTTTTCTTCGGACCGAT
1 TGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCTGGTTTTCTTTGGACCGAT
* *
1191894 TTCGGGGATGAATCAGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGACAAATGCTTT
66 TTCGGCGATGAATTAGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGACAAATGCTTT
*
1191959 AAATTGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGATGCAAT
131 AAATTGGATATGTAGATTCAGCTATGAGAATGCATACATTTATTTATATATGTGTGTGATGCAAT
1192024 GCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGG
196 GCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGG
* * * *
1192089 TGTTGGTGTACTTTAGTTTCTTAAAGTGCTATCCCCATTCGCCCTAATCCTGTTTCCTTTGGACC
261 TGGTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCCATTCCCCCTAATCCGGTTT-CTTTGGACC
*
1192154 GATTTCGGCGATGAATCGGAACTCTTTGTTACCTTGAAAAAGAATATTATTACATTGACAAATGC
325 GATTTCGGCGATGAATCGAAACTCTTTGTTACCTTGAAAAA-AATATTATTACATTGACAAATGC
* *
1192219 TTTAAATTGGATATATACGTTCAGCTGTGAGAATGCATACATTTATTTATAT-A-TGCGTGTGAT
389 TTTAAAATGGATATATACATTCAGCTGTGAGAATGCATACATTTATTTATATAAGTGCGTGTGAT
* *
1192282 GCAATGTTGCTATGTTATTAGTGTTGATTGAATCATTAGCCCCTCATCTCCAAGCTTGTTTCCTA
454 GCAATGCTGCTATGTTATTAGTGTTGATTGAATCATTAGCCCCTCATCTCCAAGCTTGTTTACTA
*
1192347 GCAGGTGT
519 GCA-G-GA
*
1192355 TGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCCGGTTTTCTTTGGACCGAT
1 TGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCTGGTTTTCTTTGGACCGAT
* * *
1192420 TTCGACAATGAATTAGAATTCTTTGTTACCTT-AAAA-AAATATTATTACATTGACAAATGCTTT
66 TTCGGCGATGAATTAGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGACAAATGCTTT
1192483 AAATTGGATATG
131 AAATTGGATATG
1192495 CTTGTTTTTT
Statistics
Matches: 619, Mismatches: 41, Indels: 10
0.92 0.06 0.01
Matches are distributed among these distances:
522 27 0.04
523 344 0.56
524 87 0.14
525 71 0.11
526 90 0.15
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.39
Consensus pattern (524 bp):
TGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCTGGTTTTCTTTGGACCGAT
TTCGGCGATGAATTAGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGACAAATGCTTT
AAATTGGATATGTAGATTCAGCTATGAGAATGCATACATTTATTTATATATGTGTGTGATGCAAT
GCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGG
TGGTGGTGTACTTTAGTCTCTTAAAGTGCTATCCCCATTCCCCCTAATCCGGTTTCTTTGGACCG
ATTTCGGCGATGAATCGAAACTCTTTGTTACCTTGAAAAAAATATTATTACATTGACAAATGCTT
TAAAATGGATATATACATTCAGCTGTGAGAATGCATACATTTATTTATATAAGTGCGTGTGATGC
AATGCTGCTATGTTATTAGTGTTGATTGAATCATTAGCCCCTCATCTCCAAGCTTGTTTACTAGC
AGGA
Found at i:1197430 original size:39 final size:39
Alignment explanation
Indices: 1197387--1197465 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
1197377 ACGCTGAAAT
1197387 AGGGTACGAGGCATTACCAGAACACATACACTTGTAAAC
1 AGGGTACGAGGCATTACCAGAACACATACACTTGTAAAC
1197426 AGGGTACGAGGCATTACCAGAACACATACACTTGTAAAC
1 AGGGTACGAGGCATTACCAGAACACATACACTTGTAAAC
1197465 A
1 A
1197466 TATTAAACCG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (39 bp):
AGGGTACGAGGCATTACCAGAACACATACACTTGTAAAC
Found at i:1198248 original size:51 final size:51
Alignment explanation
Indices: 1198189--1198292 Score: 145
Period size: 51 Copynumber: 2.0 Consensus size: 51
1198179 TCGGTGACAA
* * * * *
1198189 TAACAGTAACAGTATTTGGCGCACAAACTGTTGAATCGGTAACAGTAACAG
1 TAACAGTAACAGTATTCGACACACAAACTATCGAATCGGTAACAGTAACAG
* *
1198240 TAACAGTAATAGTATTCGACACACAAAGTATCGAATCGGTAACAGTAACAG
1 TAACAGTAACAGTATTCGACACACAAACTATCGAATCGGTAACAGTAACAG
1198291 TA
1 TA
1198293 GTCAGCACGT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.23
Consensus pattern (51 bp):
TAACAGTAACAGTATTCGACACACAAACTATCGAATCGGTAACAGTAACAG
Found at i:1198282 original size:45 final size:46
Alignment explanation
Indices: 1198090--1198292 Score: 162
Period size: 45 Copynumber: 4.4 Consensus size: 46
1198080 TAATCAGTAA
* * * *
1198090 CGGTAGCAGTAACAGTAACAGTATTCAACACACAAAGT-GCTGAAT
1 CGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTATCGGAAT
* * * * * * *
1198135 CTGTAATAGTAACGGTAATAGAATTCGACACACAAAGT-GCCGAAT
1 CGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTATCGGAAT
* * * * *
1198180 CGGTGACAATAACAGTAACAGTATTTGGCGCACAAACTGTTGAATCGGTAA-
1 CGGTAACAGTAACAGTAACAGTATTCGACACACAAA--G-T--ATCGG-AAT
* *
1198231 CAGTAACAGTAACAGTAATAGTATTCGACACACAAAGTATC-GAAT
1 CGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTATCGGAAT
1198276 CGGTAACAGTAACAGTA
1 CGGTAACAGTAACAGTA
1198293 GTCAGCACGT
Statistics
Matches: 122, Mismatches: 28, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
44 2 0.02
45 80 0.66
46 3 0.02
47 1 0.01
48 2 0.02
49 1 0.01
51 31 0.25
52 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (46 bp):
CGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTATCGGAAT
Found at i:1201375 original size:73 final size:73
Alignment explanation
Indices: 1201258--1201419 Score: 236
Period size: 73 Copynumber: 2.2 Consensus size: 73
1201248 ATTTCATCCT
* * *
1201258 TTTATATTTGTTTTATCTATTTATTTATTTATTTGTTATTCTTTTA-CTTTTCAAACATTTAAAT
1 TTTATATTTGTTTTATCTATCTATTTATTTATTTATTATTCTTTTACCTTTT-AAACACTTAAAT
* *
1201322 TTGATATTA
65 TTAATATCA
* **
1201331 TTTAAATTTGTTTTATCTATCTATTTATTTATTTATTATTCTTTTACCTTTTAAATGCTTAAATT
1 TTTATATTTGTTTTATCTATCTATTTATTTATTTATTATTCTTTTACCTTTTAAACACTTAAATT
1201396 TAATATCA
66 TAATATCA
1201404 TTTATATTTGTTTTAT
1 TTTATATTTGTTTTAT
1201420 TTATTTTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
73 74 0.94
74 5 0.06
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.62
Consensus pattern (73 bp):
TTTATATTTGTTTTATCTATCTATTTATTTATTTATTATTCTTTTACCTTTTAAACACTTAAATT
TAATATCA
Found at i:1201654 original size:13 final size:12
Alignment explanation
Indices: 1201623--1201671 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
1201613 GAGTATGACT
1201623 TTTTTATTTTATC
1 TTTTTA-TTTATC
*
1201636 TTTTTATTTATT
1 TTTTTATTTATC
*
1201648 TTCTTTATTAATC
1 TT-TTTATTTATC
*
1201661 TATTTATTTAT
1 TTTTTATTTAT
1201672 TTATGTCATT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 15 0.50
13 15 0.50
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTATTTATC
Found at i:1202072 original size:32 final size:32
Alignment explanation
Indices: 1202030--1202095 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
1202020 GTGTCCTAAT
1202030 TTACGAGACATGATCCTTCATTCTCGATTAAC
1 TTACGAGACATGATCCTTCATTCTCGATTAAC
* *
1202062 TTACGGGACATGATCCTTCATTCTTGATTAAC
1 TTACGAGACATGATCCTTCATTCTCGATTAAC
1202094 TT
1 TT
1202096 GAAATAAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.38
Consensus pattern (32 bp):
TTACGAGACATGATCCTTCATTCTCGATTAAC
Found at i:1205462 original size:5 final size:5
Alignment explanation
Indices: 1205454--1205493 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
1205444 TTATTTTATT
1205454 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1205494 TTAAATAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:1206166 original size:33 final size:32
Alignment explanation
Indices: 1206108--1206172 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
1206098 TAGAGTGTGA
1206108 ATTAAATTAGAAAAGTAAATAAATTTAGATAGG
1 ATTAAATTAG-AAAGTAAATAAATTTAGATAGG
*
1206141 ATTAAATTAG-AATTAAAGTATAATTTAGATAG
1 ATTAAATTAGAAAGTAAA-TA-AATTTAGATAG
1206173 AAATTCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 6 0.21
32 2 0.07
33 21 0.72
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (32 bp):
ATTAAATTAGAAAGTAAATAAATTTAGATAGG
Found at i:1206887 original size:21 final size:21
Alignment explanation
Indices: 1206813--1206923 Score: 107
Period size: 23 Copynumber: 5.1 Consensus size: 21
1206803 CGGCTTTGCC
*
1206813 TATCAGGCACTTTATGTGTTG
1 TATCAGGCACTTTATGTGTCG
*
1206834 TACATCAGACACTTTATGTGTCG
1 T--ATCAGGCACTTTATGTGTCG
1206857 TATCTCAGGCACTTTATGTGTCG
1 TA--TCAGGCACTTTATGTGTCG
* ** *
1206880 TATCAGGCACCTCGTGTGTCA
1 TATCAGGCACTTTATGTGTCG
* *
1206901 TTTCAGGCA-TTTATATGTCG
1 TATCAGGCACTTTATGTGTCG
1206921 TAT
1 TAT
1206924 ACTGATCAGG
Statistics
Matches: 72, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
20 8 0.11
21 25 0.35
23 39 0.54
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.39
Consensus pattern (21 bp):
TATCAGGCACTTTATGTGTCG
Found at i:1209577 original size:9 final size:9
Alignment explanation
Indices: 1209548--1209584 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
1209538 TGAGTTTTCG
1209548 AATTCGAAT
1 AATTCGAAT
*
1209557 AACTCGAAT
1 AATTCGAAT
1209566 AATTCGAAT
1 AATTCGAAT
*
1209575 AATTCAAAT
1 AATTCGAAT
1209584 A
1 A
1209585 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:1209966 original size:17 final size:18
Alignment explanation
Indices: 1209939--1209999 Score: 72
Period size: 17 Copynumber: 3.4 Consensus size: 18
1209929 CTCCCCCCAA
1209939 TTTACTTTCCCTCAAACT
1 TTTACTTTCCCTCAAACT
*
1209957 TTTA-TTTCCC-AAAACTT
1 TTTACTTTCCCTCAAAC-T
*
1209974 TTTATTTTCCCTCTAAACT
1 TTTACTTTCCCTC-AAACT
1209993 TTTACTT
1 TTTACTT
1210000 CTCACCCTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
16 4 0.11
17 11 0.31
18 10 0.28
19 7 0.19
20 4 0.11
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTACTTTCCCTCAAACT
Found at i:1210622 original size:5 final size:5
Alignment explanation
Indices: 1210612--1210639 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1210602 GAAATTTTTT
1210612 GATTC GATTC GATTC GATTC GATTC GAT
1 GATTC GATTC GATTC GATTC GATTC GAT
1210640 CGAATGCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (5 bp):
GATTC
Found at i:1211337 original size:23 final size:23
Alignment explanation
Indices: 1211305--1211401 Score: 140
Period size: 23 Copynumber: 4.2 Consensus size: 23
1211295 TAAGTGTCAT
* *
1211305 ACTGATATGTAGTCGAAGCTACC
1 ACTGAAATGTAGCCGAAGCTACC
*
1211328 ACTGAAATGTAGCCGTAGCTACC
1 ACTGAAATGTAGCCGAAGCTACC
*
1211351 ACTGAAATGTAGCTGAAGCTACC
1 ACTGAAATGTAGCCGAAGCTACC
* *
1211374 GCTGAAATGTAGCCGAAACTACC
1 ACTGAAATGTAGCCGAAGCTACC
1211397 ACTGA
1 ACTGA
1211402 TCAATAACAC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 65 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.22
Consensus pattern (23 bp):
ACTGAAATGTAGCCGAAGCTACC
Found at i:1217746 original size:32 final size:32
Alignment explanation
Indices: 1217681--1217746 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
1217671 TTTTTTTAAA
* **
1217681 TTTCGAATAAATCAAATCAAGTTATTCGGTTT
1 TTTCGAATAAATCAAATCAAGTAATTCAATTT
*
1217713 TTTCGAATTAACTCAAAT-AAGTAATTCAATTT
1 TTTCGAA-TAAATCAAATCAAGTAATTCAATTT
1217745 TT
1 TT
1217747 CGAGTTCGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 20 0.69
33 9 0.31
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (32 bp):
TTTCGAATAAATCAAATCAAGTAATTCAATTT
Found at i:1220908 original size:9 final size:9
Alignment explanation
Indices: 1220894--1221075 Score: 57
Period size: 9 Copynumber: 19.2 Consensus size: 9
1220884 TTTCGGTACA
1220894 ATAATTTTT
1 ATAATTTTT
1220903 ATAATTTTTTT
1 ATAA--TTTTT
*
1220914 ATAAATTTT
1 ATAATTTTT
*
1220923 ATATTTATTT
1 ATAATT-TTT
* *
1220933 ACATTTTTT
1 ATAATTTTT
*
1220942 AGAATTTTCTT
1 ATAA-TTT-TT
* *
1220953 ATGA-CTTT
1 ATAATTTTT
*
1220961 ATAAAATTTT
1 AT-AATTTTT
1220971 ATAATATTTT
1 ATAAT-TTTT
*
1220981 CCT-ATATTTT
1 -ATAAT-TTTT
*
1220991 ATATTTTTT
1 ATAATTTTT
*
1221000 ACGAATTTTAT
1 A-TAATTTT-T
1221011 ATAA-TTTT
1 ATAATTTTT
*
1221019 ACAATTTTT
1 ATAATTTTT
*
1221028 ATATTTTATT
1 ATAATTT-TT
* *
1221038 A-AAATTTA
1 ATAATTTTT
*
1221046 ATAGTTTTT
1 ATAATTTTT
*
1221055 ATAACTTTT
1 ATAATTTTT
*
1221064 ATTGATTTTT
1 A-TAATTTTT
1221074 AT
1 AT
1221076 TTTTTATTCT
Statistics
Matches: 126, Mismatches: 31, Indels: 32
0.67 0.16 0.17
Matches are distributed among these distances:
8 10 0.08
9 55 0.44
10 45 0.36
11 16 0.13
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.60
Consensus pattern (9 bp):
ATAATTTTT
Found at i:1221007 original size:18 final size:17
Alignment explanation
Indices: 1220986--1221065 Score: 70
Period size: 18 Copynumber: 4.4 Consensus size: 17
1220976 ATTTTCCTAT
1220986 ATTTTATATTTTTTACGA
1 ATTTTATATTTTTTAC-A
*
1221004 ATTTTATATAATTTTACA
1 ATTTTATAT-TTTTTACA
*
1221022 ATTTTTATATTTTATTAAA
1 A-TTTTATATTTT-TTACA
* * *
1221041 ATTTAATAGTTTTTATA
1 ATTTTATATTTTTTACA
1221058 ACTTTTAT
1 A-TTTTAT
1221066 TGATTTTTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
17 5 0.10
18 27 0.53
19 19 0.37
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.60
Consensus pattern (17 bp):
ATTTTATATTTTTTACA
Found at i:1221018 original size:19 final size:17
Alignment explanation
Indices: 1220965--1221035 Score: 72
Period size: 18 Copynumber: 3.9 Consensus size: 17
1220955 GACTTTATAA
*
1220965 AATTTTATAATATTTTCC
1 AATTTTAT-ATATTTTAC
*
1220983 TATATTTTATATTTTTTAC
1 -A-ATTTTATATATTTTAC
1221002 GAATTTTATATAATTTTAC
1 -AATTTTATAT-ATTTTAC
1221021 AATTTT-TATATTTTA
1 AATTTTATATATTTTA
1221036 TTAAAATTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
16 6 0.13
17 3 0.07
18 15 0.33
19 15 0.33
20 7 0.15
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (17 bp):
AATTTTATATATTTTAC
Found at i:1221043 original size:19 final size:18
Alignment explanation
Indices: 1220987--1221044 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
1220977 TTTTCCTATA
*
1220987 TTTTATATTTTTTACGAA-
1 TTTTATATTTTTTA-AAAT
* *
1221005 TTTTATATAATTTTACAAT
1 TTTTATAT-TTTTTAAAAT
1221024 TTTTATATTTTATTAAAAT
1 TTTTATATTTT-TTAAAAT
1221043 TT
1 TT
1221045 AATAGTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 12 0.36
19 21 0.64
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTATATTTTTTAAAAT
Found at i:1221044 original size:37 final size:38
Alignment explanation
Indices: 1220958--1221044 Score: 101
Period size: 37 Copynumber: 2.3 Consensus size: 38
1220948 TTCTTATGAC
* *
1220958 TTTA-TAAAATTTTATAATATTTTCCTATATTTTATAT
1 TTTATTAAAATTTTATAATATTTTACAATATTTTATAT
*
1220995 TTT-TTACGAATTTTAT-ATAATTTTACAAT-TTTTATAT
1 TTTATTA-AAATTTTATAAT-ATTTTACAATATTTTATAT
1221032 TTTATTAAAATTT
1 TTTATTAAAATTT
1221045 AATAGTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
37 23 0.55
38 19 0.45
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (38 bp):
TTTATTAAAATTTTATAATATTTTACAATATTTTATAT
Found at i:1221460 original size:46 final size:45
Alignment explanation
Indices: 1221385--1221483 Score: 137
Period size: 46 Copynumber: 2.2 Consensus size: 45
1221375 CTTGAACTTT
* *
1221385 TTTTTTTTATTTTTATGTTGGGTTTTATTTAGATTTTGGGCCAGA
1 TTTTATTTATTTTTATGTTGGGTTCTATTTAGATTTTGGGCCAGA
* *
1221430 TTTTATTTATTTATT-TGGTTGGGTTCTATTTAGATTTTGGGGCAGG
1 TTTTATTTATTT-TTAT-GTTGGGTTCTATTTAGATTTTGGGCCAGA
1221476 TTTTATTT
1 TTTTATTT
1221484 TGGGCGTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
45 12 0.25
46 36 0.75
ACGTcount: A:0.15, C:0.04, G:0.21, T:0.60
Consensus pattern (45 bp):
TTTTATTTATTTTTATGTTGGGTTCTATTTAGATTTTGGGCCAGA
Found at i:1225328 original size:13 final size:13
Alignment explanation
Indices: 1225310--1225337 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1225300 ACAAAATTGG
1225310 AAAGATGATAAAT
1 AAAGATGATAAAT
1225323 AAAGATGATAAAT
1 AAAGATGATAAAT
1225336 AA
1 AA
1225338 TAAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (13 bp):
AAAGATGATAAAT
Found at i:1230654 original size:7 final size:8
Alignment explanation
Indices: 1230637--1230669 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
1230627 TAAAATACTT
1230637 TTTTAAAA
1 TTTTAAAA
1230645 TTTT-AAA
1 TTTTAAAA
1230652 TTTTAAAA
1 TTTTAAAA
1230660 TTTTTAAAA
1 -TTTTAAAA
1230669 T
1 T
1230670 ACTTTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.30
8 8 0.35
9 8 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
TTTTAAAA
Found at i:1234089 original size:164 final size:164
Alignment explanation
Indices: 1233793--1234095 Score: 471
Period size: 164 Copynumber: 1.8 Consensus size: 164
1233783 AAGTAGTTAG
* * *
1233793 GCACATCAACTCCAATAGCCTTTAGTTAAGCCCTAATATCCCTCATTTCCATGATGGCATTAAAT
1 GCACATCAACTCCAATAGCCTTTAGTTAAGCCCTAATATCCATCATTTCCATGATGACATTAAAC
* * ** * * *
1233858 TAGTGAACTTCATTGATGGTATTTTTCTCATTATGGTATTATCTAGGGTTTTATCTGAAGGTTCA
66 TAGTGAACTTCATTGATGATATTTTTCTCATTATGGTACTATCTAGAATTTCATATGAAGATTCA
1233923 AATTATTCATCAATGGCGTCTTGTTAAATAAAGT
131 AATTATTCATCAATGGCGTCTTGTTAAATAAAGT
* * *
1233957 GCACGTCAACTTCAATAGCCTTTAGTTAAGCCGTAATATCCATCATTTCCATGATGACATTAAAC
1 GCACATCAACTCCAATAGCCTTTAGTTAAGCCCTAATATCCATCATTTCCATGATGACATTAAAC
*
1234022 TAGTGAACTTCATTGATGATATTTTTCTCATTATGGTGCTATCTAGAATTTCATATGAAGATTCA
66 TAGTGAACTTCATTGATGATATTTTTCTCATTATGGTACTATCTAGAATTTCATATGAAGATTCA
*
1234087 AATTGTTCA
131 AATTATTCA
1234096 ACATTCAATA
Statistics
Matches: 124, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
164 124 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (164 bp):
GCACATCAACTCCAATAGCCTTTAGTTAAGCCCTAATATCCATCATTTCCATGATGACATTAAAC
TAGTGAACTTCATTGATGATATTTTTCTCATTATGGTACTATCTAGAATTTCATATGAAGATTCA
AATTATTCATCAATGGCGTCTTGTTAAATAAAGT
Found at i:1234653 original size:16 final size:16
Alignment explanation
Indices: 1234623--1234653 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1234613 AAAAATTATA
*
1234623 AAAATATTCAAAAAAT
1 AAAATATTAAAAAAAT
1234639 AAAATATTAAAAAAA
1 AAAATATTAAAAAAA
1234654 GATAAAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATATTAAAAAAAT
Found at i:1240285 original size:77 final size:77
Alignment explanation
Indices: 1240173--1240482 Score: 487
Period size: 77 Copynumber: 4.0 Consensus size: 77
1240163 TGATCGGGGG
* * *
1240173 AATTGGGAATTAGGGTTTTTTATTTGAAGTTCAATTTGTGTAATTATATTGACCAAAGGAATAGC
1 AATTGAGAATTAGGGTTTTTGA-TTGGAGTTCAATTTGTGTAATTATATTGACCAAAGGAATAGC
1240238 CTTTGATAAGGAT
65 CTTTGATAAGGAT
* *
1240251 AACTGAGAATTAGGGTTTTTGATTGGAGTTCAATTTGTGTAGTTATATTGACCAAAGGAATAGCC
1 AATTGAGAATTAGGGTTTTTGATTGGAGTTCAATTTGTGTAATTATATTGACCAAAGGAATAGCC
1240316 TTTGATAAGGAT
66 TTTGATAAGGAT
* *
1240328 ATTTGAGAATTAGGGTTTTTAATTGGAGTTCAATTTGTGTAATTATATTGACCAAAGGAATAGCC
1 AATTGAGAATTAGGGTTTTTGATTGGAGTTCAATTTGTGTAATTATATTGACCAAAGGAATAGCC
*
1240393 TTTGATCAGGAT
66 TTTGATAAGGAT
* * * *
1240405 AATTGGGAATTAGGGTTTTTGATTTGTGTTCAATTTGTGT-ATTTTAATTGACCAAAGGAATAGC
1 AATTGAGAATTAGGGTTTTTGATTGGAGTTCAATTTGTGTAATTAT-ATTGACCAAAGGAATAGC
1240469 CTTTGATAAGGAT
65 CTTTGATAAGGAT
1240482 A
1 A
1240483 GACTTTAAAG
Statistics
Matches: 214, Mismatches: 17, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
76 4 0.02
77 191 0.89
78 19 0.09
ACGTcount: A:0.31, C:0.07, G:0.23, T:0.39
Consensus pattern (77 bp):
AATTGAGAATTAGGGTTTTTGATTGGAGTTCAATTTGTGTAATTATATTGACCAAAGGAATAGCC
TTTGATAAGGAT
Found at i:1245864 original size:2 final size:2
Alignment explanation
Indices: 1245857--1245885 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1245847 GTGTTGATGT
1245857 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1245886 CTTATTCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1247841 original size:23 final size:23
Alignment explanation
Indices: 1247798--1247841 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1247788 TGAAGTTTTA
*
1247798 AAAGAAATGTCACACGTTATACT
1 AAAGAAATGTCACACCTTATACT
1247821 AAAGAAATGTCA-ACCTCTATA
1 AAAGAAATGTCACACCT-TATA
1247842 TCAGCATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.25
Consensus pattern (23 bp):
AAAGAAATGTCACACCTTATACT
Found at i:1248384 original size:24 final size:25
Alignment explanation
Indices: 1248357--1248403 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
1248347 TTAATATACT
*
1248357 ATTTGGTACATGA-TTTTTTTTTCA
1 ATTTGATACATGAGTTTTTTTTTCA
**
1248381 ATTTGATATTTGAGTTTTTTTTT
1 ATTTGATACATGAGTTTTTTTTT
1248404 TATTCTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.19, C:0.04, G:0.13, T:0.64
Consensus pattern (25 bp):
ATTTGATACATGAGTTTTTTTTTCA
Found at i:1257211 original size:3 final size:3
Alignment explanation
Indices: 1257203--1257300 Score: 128
Period size: 3 Copynumber: 32.7 Consensus size: 3
1257193 TAGCAATAGG
1257203 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
1257251 AAT AAT AAT AGT AACT CAA- AAA AAT AAT TAT AAT -AT AAT TAT AAT
1 AAT AAT AAT AAT AA-T -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1257296 AAT AA
1 AAT AA
1257301 CATGAAAAAT
Statistics
Matches: 84, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
2 4 0.05
3 77 0.92
4 1 0.01
5 2 0.02
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1258797 original size:100 final size:100
Alignment explanation
Indices: 1258624--1259384 Score: 1215
Period size: 100 Copynumber: 7.6 Consensus size: 100
1258614 TTTGCTCTAC
* * * *
1258624 TGCAATGTCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGTACCG-TCAGGGA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCT-AAGGA
* *
1258688 AGTAAGATCCACCGTTGTGGCTTCAATCTTTTTAAT
65 AGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
* * * * * * * *
1258724 TGCAATGTCAGGAAAACTAGATCCGCCGTCGTAGCTTTAATCTATTCCATTGCACTGCTAAGAAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAA
* *
1258789 GTAAGATCCGTCGTTGTGGCTTCAATCTTTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
* *
1258824 TACAATATCAGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAA
*
1258889 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
*
1258924 TGCAATATCAGGGAAACCAGATCCGCCGTAGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAA
*
1258989 GTAAGATCCGCCGTTGTGGCTTTAATCTTTTTTAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
*
1259024 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTACTAAGG-A
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAA
1259088 GATAAGATCCGCCGTTGTGGCTTCAAGT-TTTTTTAT
66 G-TAAGATCCGCCGTTGTGGCTTCAA-TCTTTTTTAT
1259124 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGG-A
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAA
* *
1259188 GATAAGATCCGTCGTTGTGGCTTCAAGCTTTTTTAT
66 G-TAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
*
1259224 TGCAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAA
1259289 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
* *
1259324 TGCAATATCAGGGAAACCAGATCCGCCGTCATAGCTTCAATCTGTTCCATTGTACTGCTAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAA
1259385 TAAGATAGAA
Statistics
Matches: 615, Mismatches: 41, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
99 2 0.00
100 609 0.99
101 4 0.01
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (100 bp):
TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGTACTGCTAAGGAA
GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
Found at i:1259679 original size:44 final size:44
Alignment explanation
Indices: 1259622--1259947 Score: 327
Period size: 44 Copynumber: 7.3 Consensus size: 44
1259612 AGATCTGTAC
* * *
1259622 TCTTCGATATACTTCACGCCAATACATGAAGACAAGATCTACTT
1 TCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
* * *** *
1259666 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAATATCTGCTT
1 TCTTCGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTT
* * *
1259711 TCCTCGATCTACTTCACGCCAATACATGAAGACAAGATCTCCTT
1 TCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
* ** * *
1259755 TCTTCGATCTACTTCACCACCAGTATGTGAAGACAAGATTTGCTA
1 TCTTCGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGCTT
* *
1259800 TCTTTGATCTACTTCACGCCAGTACATGAAAACAAGATCTGCTT
1 TCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
* * *
1259844 TCTTCGATCTACTT--CGCCACTAGTATGGGAAGACAAGATATG-TT
1 TCTTCGATCTACTTCACGCCAGTA-CAT--GAAGACAAGATCTGCTT
* * * *
1259888 ATCTTTGATCTACTTCACGCCAGTACATGAAGATAATATCTACTT
1 -TCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
1259933 T-TTCCGATCTACTTC
1 TCTT-CGATCTACTTC
1259948 GCCACCAGTA
Statistics
Matches: 226, Mismatches: 46, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
42 7 0.03
43 4 0.02
44 108 0.48
45 98 0.43
46 2 0.01
47 7 0.03
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (44 bp):
TCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
Found at i:1259718 original size:45 final size:44
Alignment explanation
Indices: 1259648--1259971 Score: 310
Period size: 45 Copynumber: 7.3 Consensus size: 44
1259638 CGCCAATACA
*
1259648 TGAAGACAAGATCTACTTTCTTCGATCTACTTCGCCACCAGTATG
1 TGAAGACAAGATCTGCTTTCTTCGATCTACTTC-CCACCAGTATG
* * * * * * **
1259693 GGAAGACAATATCTGCTTTCCTCGATCTACTTCACGCCAATACA
1 TGAAGACAAGATCTGCTTTCTTCGATCTACTTCCCACCAGTATG
*
1259737 TGAAGACAAGATCTCCTTTCTTCGATCTACTTCACCACCAGTATG
1 TGAAGACAAGATCTGCTTTCTTCGATCTACTTC-CCACCAGTATG
* * * * * **
1259782 TGAAGACAAGATTTGCTATCTTTGATCTACTTCACGCCAGTACA
1 TGAAGACAAGATCTGCTTTCTTCGATCTACTTCCCACCAGTATG
* *
1259826 TGAAAACAAGATCTGCTTTCTTCGATCTACTTCGCCACTAGTATG
1 TGAAGACAAGATCTGCTTTCTTCGATCTACTTC-CCACCAGTATG
* * * * * **
1259871 GGAAGACAAGATATG-TTATCTTTGATCTACTTCACGCCAGTACA
1 TGAAGACAAGATCTGCTT-TCTTCGATCTACTTCCCACCAGTATG
* * *
1259915 TGAAGATAATATCTACTTT-TTCCGATCTACTTCGCCACCAGTATG
1 TGAAGACAAGATCTGCTTTCTT-CGATCTACTTC-CCACCAGTATG
*
1259960 GGAAGACAAGAT
1 TGAAGACAAGAT
1259972 TTACTGCTAC
Statistics
Matches: 216, Mismatches: 57, Indels: 12
0.76 0.20 0.04
Matches are distributed among these distances:
43 2 0.01
44 100 0.46
45 114 0.53
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.31
Consensus pattern (44 bp):
TGAAGACAAGATCTGCTTTCTTCGATCTACTTCCCACCAGTATG
Found at i:1259765 original size:89 final size:89
Alignment explanation
Indices: 1259622--1259971 Score: 506
Period size: 89 Copynumber: 3.9 Consensus size: 89
1259612 AGATCTGTAC
*
1259622 TCTTCGATATACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCGCCACC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCGCCACC
* *
1259687 AGTATGGGAAGACAATATCTGCTT
66 AGTATGGGAAGACAAGATATGCTT
* * *
1259711 TCCTCGATCTACTTCACGCCAATACATGAAGACAAGATCTCCTTTCTTCGATCTACTTCACCACC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCGCCACC
* * *
1259776 AGTATGTGAAGACAAGATTTGCTA
66 AGTATGGGAAGACAAGATATGCTT
* * * * *
1259800 TCTTTGATCTACTTCACGCCAGTACATGAAAACAAGATCTGCTTTCTTCGATCTACTTCGCCACT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCGCCACC
1259865 AGTATGGGAAGACAAGATATG-TT
66 AGTATGGGAAGACAAGATATGCTT
* * * *
1259888 ATCTTTGATCTACTTCACGCCAGTACATGAAGATAATATCTACTTT-TTCCGATCTACTTCGCCA
1 -TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTT-CGATCTACTTCGCCA
1259952 CCAGTATGGGAAGACAAGAT
64 CCAGTATGGGAAGACAAGAT
1259972 TTACTGCTAC
Statistics
Matches: 236, Mismatches: 23, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
88 3 0.01
89 233 0.99
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (89 bp):
TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCGCCACC
AGTATGGGAAGACAAGATATGCTT
Found at i:1263885 original size:39 final size:39
Alignment explanation
Indices: 1263838--1263924 Score: 174
Period size: 39 Copynumber: 2.2 Consensus size: 39
1263828 TTATACAAAT
1263838 ATTAAATGCTTTAAAAGTTATACCCAAATACAAATAGTC
1 ATTAAATGCTTTAAAAGTTATACCCAAATACAAATAGTC
1263877 ATTAAATGCTTTAAAAGTTATACCCAAATACAAATAGTC
1 ATTAAATGCTTTAAAAGTTATACCCAAATACAAATAGTC
1263916 ATTAAATGC
1 ATTAAATGC
1263925 CATTGGACCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (39 bp):
ATTAAATGCTTTAAAAGTTATACCCAAATACAAATAGTC
Found at i:1270350 original size:85 final size:84
Alignment explanation
Indices: 1270208--1270384 Score: 266
Period size: 85 Copynumber: 2.1 Consensus size: 84
1270198 GACATATCTA
* * *
1270208 TTGATAGACTGAGGAGGATGGGACTTGTAAAACAGTTCATCCGGTGGGTTGAGAGTCGTAAAGTG
1 TTGATAGACTGAGGAGAATGGGACTTGTAAAACAATTCATCCGATGGGTTGAGAGTCGTAAAGTG
*
1270273 AGGGTTTGAAGTAAAAGAG
66 AGAGTTTGAAGTAAAAGAG
* * * *
1270292 TTGATGGATTGAGGAGAATGGGGACTTGTAAGACAATTCATTCGATGGGTTGAGAGTCGTAAAGT
1 TTGATAGACTGAGGAGAAT-GGGACTTGTAAAACAATTCATCCGATGGGTTGAGAGTCGTAAAGT
1270357 GAGAGTTTGAAGTAAAAGAG
65 GAGAGTTTGAAGTAAAAGAG
1270377 TTGA-AGAC
1 TTGATAGAC
1270385 AAGGATAGGA
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
84 18 0.22
85 64 0.78
ACGTcount: A:0.32, C:0.07, G:0.34, T:0.26
Consensus pattern (84 bp):
TTGATAGACTGAGGAGAATGGGACTTGTAAAACAATTCATCCGATGGGTTGAGAGTCGTAAAGTG
AGAGTTTGAAGTAAAAGAG
Found at i:1273631 original size:2 final size:2
Alignment explanation
Indices: 1273577--1273612 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1273567 AAATGCATAA
1273577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1273613 AGGTATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1273637 original size:24 final size:24
Alignment explanation
Indices: 1273592--1273637 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1273582 TATATATATA
* * *
1273592 TATATATATATATATAATATAAGG
1 TATATAAAAATATATAAGATAAGG
*
1273616 TATATAAAAATATATAGGATAA
1 TATATAAAAATATATAAGATAA
1273638 AAAGATAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (24 bp):
TATATAAAAATATATAAGATAAGG
Found at i:1273718 original size:2 final size:2
Alignment explanation
Indices: 1273711--1273740 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1273701 AAGCTTAAGA
1273711 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1273741 GCTAGTAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1275467 original size:44 final size:44
Alignment explanation
Indices: 1275415--1275627 Score: 122
Period size: 44 Copynumber: 4.8 Consensus size: 44
1275405 CCACTGTAAC
* ** *
1275415 CTTAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTG
1 CTTAGGGAGATAAAATCCACCATCTTCAATCTACTCCACTACTG
* **** * *
1275459 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTATTG
1 CTTAGGGAGATAAAATCCACCATCTTCAATCTACTCCACTACTG
** * * *** * * **
1275503 CCCAGGGAGATAGAAT-TACTGGCTTCAATGTACTCCACTGCAAC
1 CTTAGGGAGATAAAATCCACCATCTTCAATCTACTCCACTAC-TG
* * ** *
1275547 CTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTG
1 CTTAGGGAGATAAAATCCACCATCTTCAATCTACTCCACTACTG
* ****
1275591 CTTAGGGAGATAAGATCTGTAATCTTCAATCTACTCC
1 CTTAGGGAGATAAAATCCACCATCTTCAATCTACTCC
1275628 GCTGCTGCCC
Statistics
Matches: 117, Mismatches: 50, Indels: 4
0.68 0.29 0.02
Matches are distributed among these distances:
43 16 0.14
44 85 0.73
45 16 0.14
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.30
Consensus pattern (44 bp):
CTTAGGGAGATAAAATCCACCATCTTCAATCTACTCCACTACTG
Found at i:1275554 original size:132 final size:132
Alignment explanation
Indices: 1275356--1276149 Score: 960
Period size: 132 Copynumber: 6.0 Consensus size: 132
1275346 ATTTTTTCTG
* **
1275356 TCTATTCCACTGTTGCCCCA-GG-AGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTTA
1 TCTATTCCACTGCTG-CCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACA
* *
1275419 GGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCT
64 GGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCT
1275484 TCAA
129 TCAA
** * *
1275488 TCTATTCCACTATTGCCCAGGG-AGATAGAATTACTGGCTTCAATGTACTCCACTGCAACCTCAG
1 TCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAG
* *
1275552 GGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTT
65 GGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTT
1275617 CAA
130 CAA
* * * * *
1275620 TCTACTCCGCTGCTGCCCAGGGAAGTAGAATTTCTGGCTTCAATGTACTCCACTGCAACCACAGA
1 TCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGG
** * * * * *
1275685 GAGGTAAAATCTGCCGTCTTCGATCTGCTTCGCTATCTA-TGC--AGGAAGGCAAGATCTAAAAT
66 GAGGTAAAATCCACCATCTTTGATCTGC-TC-C-A-CTACTGCTTAGGGAGACAAGATCTGAAAT
*
1275747 CTTCAG
127 CTTCAA
*
1275753 TCTATTCCACTGCTGCCCAGGG-AGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAG
1 TCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAG
* * * *
1275817 GGAGGTAAAATCCACCATTTTTTATTTGCTCCACTACTGCTTAGGGAGACAAGGTCTGAAATCTT
65 GGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTT
*
1275882 TAA
130 CAA
* * * *
1275885 TCTGTTCTACTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCATTGTAACCAC-GA
1 TCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAG-
* ** * * * * * * * **
1275949 GTAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGTCT-ATGTAGGAAGGCAAGATCTGCTATC
65 GGAGGTAAAATCCACCATCTTTGATCTGCTCCACT-ACTGCT-TAGGGAGACAAGATCTGAAATC
1276013 TTCAA
128 TTCAA
*
1276018 TCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCAC-GA
1 TCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAG-
** *
1276082 GGAGGTAAAATCCGTCATTTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTT
65 GGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTT
1276147 CAA
130 CAA
1276150 CCTGCTCCAC
Statistics
Matches: 568, Mismatches: 79, Indels: 30
0.84 0.12 0.04
Matches are distributed among these distances:
129 3 0.01
130 4 0.01
131 6 0.01
132 333 0.59
133 214 0.38
134 1 0.00
135 4 0.01
136 3 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (132 bp):
TCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGG
GAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTC
AA
Found at i:1275642 original size:44 final size:44
Alignment explanation
Indices: 1275443--1275642 Score: 136
Period size: 44 Copynumber: 4.5 Consensus size: 44
1275433 ACCATCTTTG
* **
1275443 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
1 ATCTACTCCACTACTGCCCAGGGAGATAAGATCTGTAATCTTCA
* * * *
1275487 ATCTATTCCACTATTGCCCAGGGAGAT-AGA-AT-TACTGGCTTCA
1 ATCTACTCCACTACTGCCCAGGGAGATAAGATCTGTAAT--CTTCA
* * ** * * **** **
1275530 ATGTACTCCACTGCAACCTCAGGGAGGTAAAATCCACCATCTTTG
1 ATCTACTCCACTACTGCC-CAGGGAGATAAGATCTGTAATCTTCA
* **
1275575 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCA
1 ATCTACTCCACTACTGCCCAGGGAGATAAGATCTGTAATCTTCA
* *
1275619 ATCTACTCCGCTGCTGCCCAGGGA
1 ATCTACTCCACTACTGCCCAGGGA
1275643 AGTAGAATTT
Statistics
Matches: 108, Mismatches: 42, Indels: 12
0.67 0.26 0.07
Matches are distributed among these distances:
41 3 0.03
42 1 0.01
43 20 0.19
44 66 0.61
45 17 0.16
47 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (44 bp):
ATCTACTCCACTACTGCCCAGGGAGATAAGATCTGTAATCTTCA
Found at i:1275794 original size:265 final size:265
Alignment explanation
Indices: 1275356--1276161 Score: 1090
Period size: 265 Copynumber: 3.0 Consensus size: 265
1275346 ATTTTTTCTG
* * **
1275356 TCTATTCCACTGTTGCCCCA-GG-AGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTTA
1 TCTACTCCACTGCTG-CCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACA
* ** * * ** *
1275419 GGGAGGTAAAATCCACCATCTTTGATCTGC-TC-C-A-CTACTGCTTAGGGAGATAAGATCTGTA
64 GAGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTATCTA-TGC--AGGAAGGCAAGATCTGAA
** *
1275480 ATCTTCAATCTATTCCACTATTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGCA
126 ATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTA
* *
1275545 ACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
191 ACCTCAGGGAGGTAAAATCCACCATTTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTG
*
1275610 TAATCTTCAA
256 AAATCTTCAA
* * *
1275620 TCTACTCCGCTGCTGCCCAGGGAAGTAGAATTTCTGGCTTCAATGTACTCCACTGCAACCACAGA
1 TCTACTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGA
* *
1275685 GAGGTAAAATCTGCCGTCTTCGATCTGCTTCGCTATCTATGCAGGAAGGCAAGATCTAAAATCTT
66 GAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTATCTATGCAGGAAGGCAAGATCTGAAATCTT
*
1275750 CAGTCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTC
131 CAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTC
* * *
1275815 AGGGAGGTAAAATCCACCATTTTTTATTTGCTCCACTACTGCTTAGGGAGACAAGGTCTGAAATC
196 AGGGAGGTAAAATCCACCATTTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATC
*
1275880 TTTAA
261 TTCAA
** * * *
1275885 TCTGTTCTACTGCTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCATTGTAACCAC-GA
1 TCTACTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGA
* * **
1275949 GTAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGTCTATGTAGGAAGGCAAGATCTGCTATCT
66 G-AGGTAAAATCTGCCATCTTCGATCTGCTTCGCTATCTATGCAGGAAGGCAAGATCTGAAATCT
*
1276014 TCAATCTATTCCGCTGCTGCCCAGGGA-AGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
130 TCAATCTATTCCACTGCTGCCCAGGGAGA-TAGAATTACTGGCTTCAATGTACTCCACTGTAACC
* **
1276078 AC-GAGGAGGTAAAATCCGTCATTTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAA
194 TCAG-GGAGGTAAAATCCACCATTTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAA
1276142 ATCTTCAA
258 ATCTTCAA
* *
1276150 CCTGCTCCACTG
1 TCTACTCCACTG
1276162 TCTCCGAGGG
Statistics
Matches: 479, Mismatches: 54, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
263 4 0.01
264 78 0.16
265 389 0.81
266 1 0.00
267 4 0.01
268 3 0.01
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (265 bp):
TCTACTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGA
GAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTATCTATGCAGGAAGGCAAGATCTGAAATCTT
CAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTC
AGGGAGGTAAAATCCACCATTTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATC
TTCAA
Found at i:1276137 original size:397 final size:397
Alignment explanation
Indices: 1275355--1276148 Score: 1077
Period size: 397 Copynumber: 2.0 Consensus size: 397
1275345 GATTTTTTCT
* *
1275355 GTCTATTCCACTGTTGCCCCAGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTTAG
1 GTCTATTCCACTGCTGCCCCAGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAG
* *
1275420 GGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTT
66 GGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTT
* *
1275485 CAATCTATTCCACTATTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGCAACCTC
131 CAATCTATTCCACTACTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGCAACCAC
* * * *
1275550 AGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATC
196 AGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGATTAGGAAGACAAGATCTGTAATC
*
1275615 TTCAATCTACTCCGCTGCTGCCCAGGGAAGTAGAATTTCTGGCTTCAATGTACTCCACTGCAACC
261 TTCAATCTACTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACC
* * *
1275680 ACAGAGAGGTAAAATCTGCCGTCTTCGATCTGCTTCGCTATCTATGCAGGAAGGCAAGATCTAAA
326 ACAGAGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTATCTATGCAGGAAGACAAGATCTAAA
1275745 ATCTTCA
391 ATCTTCA
1275752 GTCTATTCCACTGCTG-CCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCA
1 GTCTATTCCACTGCTGCCCCA-GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCA
* * * *
1275816 GGGAGGTAAAATCCACCATTTTTTATTTGCTCCACTACTGCTTAGGGAGACAAGGTCTGAAATCT
65 GGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCT
* * * * * * *
1275881 TTAATCTGTTCTACTGCTGTCCAGGGA-AGTAGAATTACTGGCTTCAATGTACTCCATTGTAACC
130 TCAATCTATTCCACTACTGCCCAGGGAGA-TAGAATTACTGGCTTCAATGTACTCCACTGCAACC
* ** * * * *
1275945 AC-GAGTAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGTCT-ATGTAGGAAGGCAAGATCTG
194 ACAG-GGAGGTAAAATCCACCATCTTCGATCTGCTCCACT-ACTGAT-TAGGAAGACAAGATCTG
*
1276008 CT-ATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACT
256 -TAATCTTCAATCTACTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACT
* * * * *
1276072 GTAACCAC-GAGGAGGTAAAATCCGTCATTTTTGATCTGC-TC-C-A-CTACTGCTTAGGGAGAC
320 GCAACCACAGA-GAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTATCTA-TGC--AGGAAGAC
*
1276132 AAGATCTGAAATCTTCA
381 AAGATCTAAAATCTTCA
1276149 ACCTGCTCCA
Statistics
Matches: 348, Mismatches: 39, Indels: 20
0.86 0.10 0.05
Matches are distributed among these distances:
394 3 0.01
395 4 0.01
396 7 0.02
397 227 0.65
398 106 0.30
399 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (397 bp):
GTCTATTCCACTGCTGCCCCAGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAG
GGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTT
CAATCTATTCCACTACTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGCAACCAC
AGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGATTAGGAAGACAAGATCTGTAATC
TTCAATCTACTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACC
ACAGAGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTATCTATGCAGGAAGACAAGATCTAAA
ATCTTCA
Found at i:1276256 original size:220 final size:220
Alignment explanation
Indices: 1275966--1276446 Score: 809
Period size: 220 Copynumber: 2.2 Consensus size: 220
1275956 AAATCTGCCA
* * * ***
1275966 TCTTCGATCTGCTTCGCTGTCTATGTAGGAAGGCAAGATCTGCTATCTTCAATCTATTCCGCTGC
1 TCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTAAAATCTTCAATCTATTCCGCTGC
*
1276031 TGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCCG
66 TGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAAGGAGGTAAAATCCG
* * * *
1276096 TCATTTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAACCTGCTCCACT
131 CCATCTTCGATCTACTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAACCTGCTCCACT
1276161 GTCTCCGAGGGAGGCGAGGTTGATG
196 GTCTCCGAGGGAGGCGAGGTTGATG
*
1276186 TCTTCGATCTGCTTCACTGTCGATGCAGGAAGACAAGATCTAAAATCTTCAATCTATTCCGCTGC
1 TCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTAAAATCTTCAATCTATTCCGCTGC
* *
1276251 TGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAAGGAGGTAAAATCGG
66 TGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAAGGAGGTAAAATCCG
* *
1276316 CCATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTGCTCCACT
131 CCATCTTCGATCTACTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAACCTGCTCCACT
*
1276381 GTCTCCGAGGGAGGCGAGGTTGGTG
196 GTCTCCGAGGGAGGCGAGGTTGATG
1276406 TCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCT
1 TCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCT
1276447 GTTATCATCG
Statistics
Matches: 243, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
220 243 1.00
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (220 bp):
TCTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTAAAATCTTCAATCTATTCCGCTGC
TGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAAGGAGGTAAAATCCG
CCATCTTCGATCTACTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAACCTGCTCCACT
GTCTCCGAGGGAGGCGAGGTTGATG
Found at i:1277712 original size:20 final size:20
Alignment explanation
Indices: 1277673--1277709 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
1277663 GCCTCTCCAT
1277673 TTTTACTTTTTCATTTTTCA
1 TTTTACTTTTTCATTTTTCA
1277693 TTTTAC-TTTTCATTTTT
1 TTTTACTTTTTCATTTTT
1277710 TCACATCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTACTTTTTCATTTTTCA
Found at i:1282619 original size:2 final size:2
Alignment explanation
Indices: 1282579--1282603 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1282569 AAATGCATAA
1282579 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 A
1282604 AAATATAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1285402 original size:15 final size:15
Alignment explanation
Indices: 1285382--1285414 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1285372 GCAAATTATT
1285382 ATAAATTCAGTAAAC
1 ATAAATTCAGTAAAC
1285397 ATAAATTCAGTAAAC
1 ATAAATTCAGTAAAC
1285412 ATA
1 ATA
1285415 TTTGATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (15 bp):
ATAAATTCAGTAAAC
Found at i:1302496 original size:62 final size:62
Alignment explanation
Indices: 1302369--1302500 Score: 142
Period size: 62 Copynumber: 2.1 Consensus size: 62
1302359 TGTGTGTCTG
* * * * * * *
1302369 GGCCGTGTAACTTATTGTTTGTGGTATAAAGCCACACAGCTAGGGATATGTATGTGTGCCTA
1 GGCCGTGTAACTCACTGTTTGTGGTATAAAGCCACACAGCTAGGGACATGGACGTGTACCCA
* * *
1302431 GGCCGTGTATCTCACTGTTTGTGGTATTAAA-CCACAC-GGTCAGGGACATGGGCGTGTACCCA
1 GGCCGTGTAACTCACTGTTTGTGGTA-TAAAGCCACACAGCT-AGGGACATGGACGTGTACCCA
1302493 GGCCGTGT
1 GGCCGTGT
1302501 GGGTCACATG
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
61 2 0.03
62 52 0.90
63 4 0.07
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (62 bp):
GGCCGTGTAACTCACTGTTTGTGGTATAAAGCCACACAGCTAGGGACATGGACGTGTACCCA
Found at i:1309872 original size:25 final size:25
Alignment explanation
Indices: 1309821--1309877 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 25
1309811 ATTAAGTTTT
1309821 CAAAAAAGTGTAAACATCATATCTACC
1 CAAAAAAGTGTAAACATCATA-CTA-C
*
1309848 CAAAAAAGTGTAAAGATCATA-TAC
1 CAAAAAAGTGTAAACATCATACTAC
1309872 CAAAAA
1 CAAAAA
1309878 TGGGTTAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 7 0.24
25 2 0.07
27 20 0.69
ACGTcount: A:0.54, C:0.18, G:0.09, T:0.19
Consensus pattern (25 bp):
CAAAAAAGTGTAAACATCATACTAC
Found at i:1313432 original size:31 final size:31
Alignment explanation
Indices: 1313359--1313450 Score: 80
Period size: 31 Copynumber: 3.0 Consensus size: 31
1313349 TTGGTATACT
* *
1313359 GTACTTATA-TTTAGTTTTAGTGTTCAATTTG
1 GTACTTA-AGTTTAATTTTAATGTTCAATTTG
* *
1313390 GTA-TCTGAGTTTAATTTTAATGTTCAGTTTG
1 GTACT-TAAGTTTAATTTTAATGTTCAATTTG
* * * *
1313421 GTACTTAAGTTTGACTTCAATATTCAATTT
1 GTACTTAAGTTTAATTTTAATGTTCAATTT
1313451 AATTTTTGAT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
30 2 0.04
31 45 0.94
32 1 0.02
ACGTcount: A:0.25, C:0.09, G:0.15, T:0.51
Consensus pattern (31 bp):
GTACTTAAGTTTAATTTTAATGTTCAATTTG
Found at i:1314510 original size:14 final size:15
Alignment explanation
Indices: 1314491--1314519 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1314481 CAACCAACAA
1314491 TTTTAATTTT-AATT
1 TTTTAATTTTCAATT
1314505 TTTTAATTTTCAATT
1 TTTTAATTTTCAATT
1314520 ACGTATGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTAATTTTCAATT
Found at i:1316826 original size:29 final size:30
Alignment explanation
Indices: 1316794--1316862 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
1316784 TAGGGATCCT
* * *
1316794 ATCAAATTAGTCTC-TTTAGTACTAA-AATA
1 ATCAAATTAGTC-CATATACTACTAACAAGA
**
1316823 ATCAGTTTAGTCCATATACTACTAACAAGA
1 ATCAAATTAGTCCATATACTACTAACAAGA
1316853 ATCAAATTAG
1 ATCAAATTAG
1316863 GCCAAATTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
28 1 0.03
29 19 0.61
30 11 0.35
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (30 bp):
ATCAAATTAGTCCATATACTACTAACAAGA
Found at i:1321405 original size:28 final size:27
Alignment explanation
Indices: 1321374--1321439 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 27
1321364 CCCAAAAATC
1321374 TTTTAAAATTTTTCATTA-AGCTCCCAATT
1 TTTTAAAATTTTT-ATTAGA-C-CCCAATT
*
1321403 TTTTGAAAATATTTATTAGACCCCAA-T
1 TTTT-AAAATTTTTATTAGACCCCAATT
1321430 TTTTAAAATT
1 TTTTAAAATT
1321440 CGCATTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
26 5 0.15
27 5 0.15
28 5 0.15
29 9 0.27
30 9 0.27
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.47
Consensus pattern (27 bp):
TTTTAAAATTTTTATTAGACCCCAATT
Found at i:1326885 original size:9 final size:9
Alignment explanation
Indices: 1326871--1326915 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
1326861 AATTATTTTT
1326871 TAAAAAATA
1 TAAAAAATA
1326880 TAAAAAA-A
1 TAAAAAATA
1326888 TCAAAAAA-A
1 T-AAAAAATA
*
1326897 TAAAAAGTA
1 TAAAAAATA
1326906 TAAAAAATA
1 TAAAAAATA
1326915 T
1 T
1326916 TTTTAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 7 0.22
9 25 0.78
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (9 bp):
TAAAAAATA
Found at i:1326910 original size:17 final size:17
Alignment explanation
Indices: 1326871--1326915 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1326861 AATTATTTTT
1326871 TAAAAAATATAAAAAAA
1 TAAAAAATATAAAAAAA
*
1326888 TCAAAAAA-ATAAAAAGTA
1 T-AAAAAATATAAAAA-AA
1326906 TAAAAAATAT
1 TAAAAAATAT
1326916 TTTTAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (17 bp):
TAAAAAATATAAAAAAA
Found at i:1331836 original size:14 final size:15
Alignment explanation
Indices: 1331808--1331836 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1331798 TCACTGCTAC
1331808 AAAGGAGAGGAAAGA
1 AAAGGAGAGGAAAGA
1331823 AAAGGAGA-GAAAGA
1 AAAGGAGAGGAAAGA
1331837 GACGACAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (15 bp):
AAAGGAGAGGAAAGA
Found at i:1331890 original size:5 final size:5
Alignment explanation
Indices: 1331880--1331912 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
1331870 CATATACAGC
*
1331880 AAGAA AAGAA AAGAA AAGAA AGGAA AAGAA AAG
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAG
1331913 GAGGGAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:1339302 original size:14 final size:14
Alignment explanation
Indices: 1339283--1339317 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1339273 GACGGGATTG
1339283 TTGGAAAAATAGGT
1 TTGGAAAAATAGGT
1339297 TTGGAAAAATAGGT
1 TTGGAAAAATAGGT
1339311 TTGGAAA
1 TTGGAAA
1339318 CGCAGCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (14 bp):
TTGGAAAAATAGGT
Found at i:1341573 original size:26 final size:27
Alignment explanation
Indices: 1341513--1341583 Score: 99
Period size: 26 Copynumber: 2.7 Consensus size: 27
1341503 TCATTAATCA
*
1341513 GGAAGCTCACAAAGAGCTAATTTAACG
1 GGAAGCTCACAAAGAGCTAATGTAACG
* *
1341540 GGAAGCTCACGAAGAGC-CATGTAACG
1 GGAAGCTCACAAAGAGCTAATGTAACG
*
1341566 GGACGCTCACAAAGAGCT
1 GGAAGCTCACAAAGAGCT
1341584 GTGGTATGTC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
26 22 0.58
27 16 0.42
ACGTcount: A:0.37, C:0.23, G:0.27, T:0.14
Consensus pattern (27 bp):
GGAAGCTCACAAAGAGCTAATGTAACG
Found at i:1342882 original size:14 final size:14
Alignment explanation
Indices: 1342863--1342893 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1342853 GGAATTGTTT
*
1342863 TAATCTAAATTTAC
1 TAATCTAAATTAAC
1342877 TAATCTAAATTAAC
1 TAATCTAAATTAAC
1342891 TAA
1 TAA
1342894 GAACCCGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:1344614 original size:5 final size:5
Alignment explanation
Indices: 1344604--1344645 Score: 56
Period size: 5 Copynumber: 9.2 Consensus size: 5
1344594 TATAGATATA
1344604 CTTTT CTTTT CTTTT CTTTT C-TTT C-TTT C-TTT CTTTT -TTTT C
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT C
1344646 AACATGAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 16 0.46
5 19 0.54
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
CTTTT
Found at i:1344617 original size:10 final size:10
Alignment explanation
Indices: 1344604--1344645 Score: 56
Period size: 9 Copynumber: 4.6 Consensus size: 10
1344594 TATAGATATA
1344604 CTTTTCTTTT
1 CTTTTCTTTT
1344614 CTTTTCTTTT
1 CTTTTCTTTT
1344624 C-TTTC-TTT
1 CTTTTCTTTT
1344632 C-TTTCTTTT
1 CTTTTCTTTT
1344641 -TTTTC
1 CTTTTC
1344646 AACATGAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.27
9 11 0.37
10 11 0.37
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
CTTTTCTTTT
Found at i:1345635 original size:6 final size:6
Alignment explanation
Indices: 1345617--1345677 Score: 90
Period size: 6 Copynumber: 10.5 Consensus size: 6
1345607 TAAATAGAAG
* *
1345617 AAAATA ACAATA AACATA AAAATA AAAATA AAAATA AAAATA AAAAT-
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
1345664 AAAAT- AAAATA AAA
1 AAAATA AAAATA AAA
1345678 CAAAATAGAC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
5 10 0.20
6 40 0.80
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:1349923 original size:36 final size:36
Alignment explanation
Indices: 1349883--1349953 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
1349873 ACCACTTTTA
* * * * *
1349883 AATATTACAACTATATCATTATGTCGAATCACTTAC
1 AATATTACAAATACATCAATAGGCCGAATCACTTAC
1349919 AATATTACAAATACATCAATAGGCCGAATCACTTA
1 AATATTACAAATACATCAATAGGCCGAATCACTTA
1349954 TAAGTTTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (36 bp):
AATATTACAAATACATCAATAGGCCGAATCACTTAC
Found at i:1354605 original size:14 final size:14
Alignment explanation
Indices: 1354586--1354616 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1354576 GGAATTATTT
*
1354586 TAATCTAAATTTAC
1 TAATCTAAATTAAC
1354600 TAATCTAAATTAAC
1 TAATCTAAATTAAC
1354614 TAA
1 TAA
1354617 GAACCCGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:1362215 original size:26 final size:27
Alignment explanation
Indices: 1362150--1362217 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 27
1362140 ATTAATCAGG
* *
1362150 AAGCTCACAAAGAGCCAATTTAATGGA
1 AAGCTCACAAAGAGCCAATGTAACGGA
** *
1362177 AAGCTCATGAAGAGCC-ATGTAACGGG
1 AAGCTCACAAAGAGCCAATGTAACGGA
*
1362203 ACGCTCACAAAGAGC
1 AAGCTCACAAAGAGC
1362218 TGTGGTATGT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
26 19 0.58
27 14 0.42
ACGTcount: A:0.40, C:0.22, G:0.24, T:0.15
Consensus pattern (27 bp):
AAGCTCACAAAGAGCCAATGTAACGGA
Found at i:1366459 original size:17 final size:15
Alignment explanation
Indices: 1366427--1366455 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1366417 TGATAAAATT
1366427 AAATATTATTTTTTA
1 AAATATTATTTTTTA
1366442 AAATATTATTTTTT
1 AAATATTATTTTTT
1366456 TTAATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AAATATTATTTTTTA
Found at i:1366932 original size:2 final size:2
Alignment explanation
Indices: 1366925--1366949 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1366915 TACACTACAA
1366925 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 A
1366950 AAGTACATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1376298 original size:67 final size:66
Alignment explanation
Indices: 1376169--1376299 Score: 174
Period size: 67 Copynumber: 2.0 Consensus size: 66
1376159 AAATAATTTT
* * * *
1376169 AAATAATATCAAATAAATTAATGTTTTTGGTGAGTTTAATTTGGGAATTCAAAAAAAAGATAATC
1 AAATAATATAAAATAAATAAATGTTTTTGGTAAGTTGAATTTGGGAATTCAAAAAAAAGATAATC
1376234 A
66 A
* * *
1376235 AAATAATATAAAATAAATCAAAT-TTTTTGGTCAAGTTGAATTTGGGGATTCAACAAAACGATAA
1 AAATAATATAAAATAAAT-AAATGTTTTTGGT-AAGTTGAATTTGGGAATTCAAAAAAAAGATAA
1376299 T
64 T
1376300 AGACCGAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
66 25 0.45
67 31 0.55
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.34
Consensus pattern (66 bp):
AAATAATATAAAATAAATAAATGTTTTTGGTAAGTTGAATTTGGGAATTCAAAAAAAAGATAATC
A
Found at i:1381984 original size:18 final size:18
Alignment explanation
Indices: 1381950--1381995 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
1381940 TCCAAGTCAG
*
1381950 ATAAAAAAAATTAAAATAA
1 ATAAATAAAATTAAAAT-A
*
1381969 ATAACTAAAA-TAAAATA
1 ATAAATAAAATTAAAATA
1381986 ATAAATAAAA
1 ATAAATAAAA
1381996 AATTAAGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.42
18 6 0.25
19 8 0.33
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (18 bp):
ATAAATAAAATTAAAATA
Found at i:1381996 original size:18 final size:20
Alignment explanation
Indices: 1381950--1382001 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
1381940 TCCAAGTCAG
1381950 ATAAA-AAAAATTAAAATAA
1 ATAAATAAAAATTAAAATAA
*
1381969 ATAACT-AAAA-TAAAAT-A
1 ATAAATAAAAATTAAAATAA
1381986 ATAAATAAAAAATTAA
1 ATAAAT-AAAAATTAA
1382002 GGAAGCAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 6 0.22
18 6 0.22
19 12 0.44
20 3 0.11
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (20 bp):
ATAAATAAAAATTAAAATAA
Done.