Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold175
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: 1254584
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 8 of 8
Found at i:1088937 original size:51 final size:51
Alignment explanation
Indices: 1088875--1089043 Score: 266
Period size: 51 Copynumber: 3.3 Consensus size: 51
1088865 TTATTTCTGA
* *
1088875 GGGGATACTCCAACCCCAATTTTATTTCTAAAATATCAATTTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCACAATC
*
1088926 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCTACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCACAATC
* * * * *
1088977 GGGGATACTCCAACTCTGATTTTATTTCTAAAACACCAATTTTTCACAATT
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCACAATC
1089028 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
1089044 TGTTATTTCC
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 108 1.00
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCACAATC
Found at i:1089112 original size:79 final size:79
Alignment explanation
Indices: 1088977--1089129 Score: 209
Period size: 79 Copynumber: 1.9 Consensus size: 79
1088967 TTCTACAATC
* * * **
1088977 GGGGATACTCCAACTCTGATTTTATTTCTAAAACACCAATTTTTCACAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAATCAGGGATACTCCAAC
*
1089042 CCTGTTATTTCCGA
66 CCCGTTATTTCCGA
** *
1089056 GGGGATAC-CTCAACCCCGATTTTATTTCTGGAACACCAATTTTCCATAATCAGGGATACTCCAA
1 GGGGATACTC-CAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAATCAGGGATACTCCAA
1089120 CCCCGTTATT
65 CCCCGTTATT
1089130 ATCTCCAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
78 1 0.02
79 63 0.98
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.32
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAATCAGGGATACTCCAAC
CCCGTTATTTCCGA
Found at i:1091198 original size:4 final size:4
Alignment explanation
Indices: 1091189--1091219 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1091179 TTTTGAGGTG
*
1091189 TTTA TTTA TTTA TTTA TTTA TTAA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1091220 GTGTTGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:1101528 original size:18 final size:19
Alignment explanation
Indices: 1101502--1101537 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1101492 ATTCTTTTTT
1101502 AAAAAAAAACAAA-AAAAC
1 AAAAAAAAACAAAGAAAAC
*
1101520 AAAACAAAACAAAGAAAA
1 AAAAAAAAACAAAGAAAA
1101538 AAGAGAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (19 bp):
AAAAAAAAACAAAGAAAAC
Found at i:1102629 original size:55 final size:55
Alignment explanation
Indices: 1102536--1102930 Score: 542
Period size: 55 Copynumber: 7.0 Consensus size: 55
1102526 GACACCTTTT
* **
1102536 CCTTTCAAAGCCCACACAGGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACG
*
1102591 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACG
* *
1102646 TCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACG
*
1102701 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACG
* *
1102756 CCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCTTT
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGA--C--G
*
1102815 CTCTTTGCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACACCTTT
1 C-CTTT-CAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGG--A-C--G
* *
1102877 CCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT-AATCCTCAAAGAGCAGGA
1 CC-TTTCAAAGCCCACACAAGTTGGTGGCA-TTTTTCAGTCCTCAAAGAGCAGGA
1102931 AGCACTTTAT
Statistics
Matches: 314, Mismatches: 14, Indels: 20
0.90 0.04 0.06
Matches are distributed among these distances:
55 206 0.66
56 2 0.01
57 1 0.00
59 4 0.01
60 2 0.01
61 85 0.27
62 13 0.04
63 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACG
Found at i:1102678 original size:27 final size:27
Alignment explanation
Indices: 1102648--1102788 Score: 75
Period size: 27 Copynumber: 5.1 Consensus size: 27
1102638 GCAGGACGTC
1102648 TTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTAAAGCCCACACAAGTTGGTGGCA
** * * * ** ** *
1102675 TTTTTCAGTCCTCAAAGAGCAGGACGCC
1 TTTTAAAGCCCACACA-AGTTGGTGGCA
1102703 TTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTAAAGCCCACACAAGTTGGTGGCA
** * * * ** ** *
1102730 TTTTTCAGTCCTCAAAGAGCAGGACGCC
1 TTTTAAAGCCCACACA-AGTTGGTGGCA
*
1102758 TCTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTAAAGCCCACACAAGTTGGTGGCA
1102785 TTTT
1 TTTT
1102789 CCAGTCCTCA
Statistics
Matches: 70, Mismatches: 42, Indels: 4
0.60 0.36 0.03
Matches are distributed among these distances:
27 37 0.53
28 33 0.47
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (27 bp):
TTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:1102706 original size:28 final size:28
Alignment explanation
Indices: 1102675--1102758 Score: 71
Period size: 28 Copynumber: 3.0 Consensus size: 28
1102665 GTTGGTGGCA
1102675 TTTTTCAGTCCTCAAAGAGCAGGACGCC
1 TTTTTCAGTCCTCAAAGAGCAGGACGCC
** * * * ** ** *
1102703 TTTTAAAGCCCACACA-AGTTGGTGGCA
1 TTTTTCAGTCCTCAAAGAGCAGGACGCC
1102730 TTTTTCAGTCCTCAAAGAGCAGGACGCC
1 TTTTTCAGTCCTCAAAGAGCAGGACGCC
1102758 T
1 T
1102759 CTTAAAGCCC
Statistics
Matches: 35, Mismatches: 20, Indels: 2
0.61 0.35 0.04
Matches are distributed among these distances:
27 17 0.49
28 18 0.51
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (28 bp):
TTTTTCAGTCCTCAAAGAGCAGGACGCC
Found at i:1103002 original size:41 final size:42
Alignment explanation
Indices: 1102914--1102996 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
1102904 GCACTTTTTA
*
1102914 ATCCTCAAAGAGCAGGAAGCACTTTATTTTCCTCTTTCTTTC
1 ATCCTCAAAGAGCAGGAAGCACTTTATTTCCCTCTTTCTTTC
* * * * *
1102956 ATCCTCAAAGAGCAGGACGTATTTTGTTTCCCTTTTTCTTT
1 ATCCTCAAAGAGCAGGAAGCACTTTATTTCCCTCTTTCTTT
1102997 GTCCTCGAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (42 bp):
ATCCTCAAAGAGCAGGAAGCACTTTATTTCCCTCTTTCTTTC
Found at i:1103793 original size:19 final size:21
Alignment explanation
Indices: 1103750--1103801 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
1103740 TTCAATGATT
*
1103750 TGTATCGATACATTCAGTAAA
1 TGTATCGATACATTAAGTAAA
1103771 TGTATCGATACA-TAAGT-AA
1 TGTATCGATACATTAAGTAAA
1103790 TGTATCGATACA
1 TGTATCGATACA
1103802 GTGTATCGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 14 0.47
20 4 0.13
21 12 0.40
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (21 bp):
TGTATCGATACATTAAGTAAA
Found at i:1103872 original size:13 final size:13
Alignment explanation
Indices: 1103854--1103913 Score: 76
Period size: 13 Copynumber: 5.0 Consensus size: 13
1103844 ATTTATAGAA
1103854 TGTATCGATACAT
1 TGTATCGATACAT
1103867 TGTATCGATACAT
1 TGTATCGATACAT
*
1103880 T-TAT--AGA-A-
1 TGTATCGATACAT
1103888 TGTATCGATACAT
1 TGTATCGATACAT
1103901 TGTATCGATACAT
1 TGTATCGATACAT
1103914 CGATCTTTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
8 1 0.03
9 4 0.10
10 2 0.05
11 2 0.05
12 4 0.10
13 27 0.68
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1103876 original size:34 final size:34
Alignment explanation
Indices: 1103833--1103913 Score: 162
Period size: 34 Copynumber: 2.4 Consensus size: 34
1103823 GCCAAGGAAA
1103833 TGTATCGATACATTTATAGAATGTATCGATACAT
1 TGTATCGATACATTTATAGAATGTATCGATACAT
1103867 TGTATCGATACATTTATAGAATGTATCGATACAT
1 TGTATCGATACATTTATAGAATGTATCGATACAT
1103901 TGTATCGATACAT
1 TGTATCGATACAT
1103914 CGATCTTTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (34 bp):
TGTATCGATACATTTATAGAATGTATCGATACAT
Found at i:1106021 original size:51 final size:51
Alignment explanation
Indices: 1105941--1106109 Score: 164
Period size: 51 Copynumber: 3.3 Consensus size: 51
1105931 ATTTTTCATC
* * * *
1105941 TCGGGGATACTCCAA-TCCCAGTTTCATTTCCAAAACATCAA-TTTCTCTTAA
1 TCGGGGATACTCCAACTCCGA-TTTTATTTCCAAAACACCAATTTTC-CATAA
* * *
1105992 TCGGGGATACTCTAACTCCGATTTTATTTCTAAAACACCCATTTTCCATAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCATAA
** * * * *
1106043 TCGATGATACTCCAACTCCGATTTTATTTCCAGAATACTGACTTTT-CATAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC-CAATTTTCCATAA
*
1106094 TCAGGGATACTCCAAC
1 TCGGGGATACTCCAAC
1106110 CCCGTTATTT
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
51 84 0.88
52 12 0.12
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.34
Consensus pattern (51 bp):
TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCATAA
Found at i:1106189 original size:76 final size:76
Alignment explanation
Indices: 1106093--1106381 Score: 415
Period size: 76 Copynumber: 3.8 Consensus size: 76
1106083 ACTTTTCATA
* * *
1106093 ATCAGGGATACTCCAACCCCGTTATTTCTGAGGGGGCACTCCAACCTCGGTTTTATTTATAAAAC
1 ATCAGGGATACTCCAACCCCGTTATTTCTGAGGGGACACTCCAACCCCGGTTTTATTTCTAAAAC
*
1106158 ATCAATTTTTT
66 ATCAATTTTTC
* *
1106169 ATCAGGGATACTCCAGCCCCGTTATTTCTGAGGGGACACTCCAACCCCGATTTTATTTCTAAAAC
1 ATCAGGGATACTCCAACCCCGTTATTTCTGAGGGGACACTCCAACCCCGGTTTTATTTCTAAAAC
1106234 ATCAATTTTTC
66 ATCAATTTTTC
* * *
1106245 ATCGGGGATACTCCAACCCCGTTATTT-TCGAGGGGACTCTCCAACCCCGGTTTTGTTTCTAAAA
1 ATCAGGGATACTCCAACCCCGTTATTTCT-GAGGGGACACTCCAACCCCGGTTTTATTTCTAAAA
1106309 CATCAATTTTTC
65 CATCAATTTTTC
* * * * *
1106321 ATCGGGGATACTCCAACCCTGTTATTT-T--TGGGATACTCCAACCCCGGTTTTATATCTAAAA
1 ATCAGGGATACTCCAACCCCGTTATTTCTGAGGGGACACTCCAACCCCGGTTTTATTTCTAAAA
1106382 ATATTGTTTT
Statistics
Matches: 195, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
73 28 0.14
75 1 0.01
76 166 0.85
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (76 bp):
ATCAGGGATACTCCAACCCCGTTATTTCTGAGGGGACACTCCAACCCCGGTTTTATTTCTAAAAC
ATCAATTTTTC
Found at i:1106437 original size:28 final size:28
Alignment explanation
Indices: 1106398--1106452 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
1106388 TTTTTTCATA
*
1106398 ATCGGGGGTACTCTAACCCCGTTATTTC
1 ATCGGGGATACTCTAACCCCGTTATTTC
**
1106426 ATCGGGGATACTCTAGTCCCGTTATTT
1 ATCGGGGATACTCTAACCCCGTTATTT
1106453 TCGAGGGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (28 bp):
ATCGGGGATACTCTAACCCCGTTATTTC
Found at i:1106460 original size:28 final size:28
Alignment explanation
Indices: 1106415--1106496 Score: 119
Period size: 28 Copynumber: 2.9 Consensus size: 28
1106405 GTACTCTAAC
*** *
1106415 CCCGTTATTTCATCGGGGATACTCTAGT
1 CCCGTTATTTCCGAGGGGATACTCCAGT
*
1106443 CCCGTTATTTTCGAGGGGATACTCCAGT
1 CCCGTTATTTCCGAGGGGATACTCCAGT
1106471 CCCGTTATTTCCGAGGGGATACTCCA
1 CCCGTTATTTCCGAGGGGATACTCCA
1106497 ACCTCGATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.18, C:0.27, G:0.23, T:0.32
Consensus pattern (28 bp):
CCCGTTATTTCCGAGGGGATACTCCAGT
Found at i:1106545 original size:51 final size:50
Alignment explanation
Indices: 1106485--1106652 Score: 232
Period size: 51 Copynumber: 3.3 Consensus size: 50
1106475 TTATTTCCGA
1106485 GGGGATACTCCAACCTCGATTTTATTTCTAAAATACCAATTTTCCACAATC
1 GGGGATACTCCAACCTCGATTTTATTTCTAAAATACCAATTTT-CACAATC
*
1106536 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCTCGATTTTATTTCTAAAATACCAA-TTTTCACAATC
* * *
1106587 GGGGATACTTCAA-CTCTGATTTTATTTCTAAACCAT-CAAATTTTCACAATT
1 GGGGATACTCCAACCTC-GATTTTATTTCTAAA--ATACCAATTTTCACAATC
*
1106638 GGAGATACTCCAACC
1 GGGGATACTCCAACC
1106653 CTGTTATTTC
Statistics
Matches: 105, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
50 2 0.02
51 93 0.89
52 8 0.08
53 2 0.02
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (50 bp):
GGGGATACTCCAACCTCGATTTTATTTCTAAAATACCAATTTTCACAATC
Found at i:1107789 original size:20 final size:20
Alignment explanation
Indices: 1107764--1107801 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1107754 CTGCCAAGGA
1107764 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
*
1107784 AATGTATCTATACATTAT
1 AATGTATCGATACATTAT
1107802 ATCGATGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (20 bp):
AATGTATCGATACATTATTC
Found at i:1109944 original size:13 final size:13
Alignment explanation
Indices: 1109926--1109951 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1109916 TCGAGCAAGT
1109926 ATGTATCGATACA
1 ATGTATCGATACA
1109939 ATGTATCGATACA
1 ATGTATCGATACA
1109952 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1112199 original size:21 final size:21
Alignment explanation
Indices: 1112166--1112210 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1112156 TTGCAAGTTG
*
1112166 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1112188 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1112208 AAA
1 AAA
1112211 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1116097 original size:13 final size:13
Alignment explanation
Indices: 1116079--1116103 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1116069 CATGTTTCTG
1116079 TGTATCGATACAT
1 TGTATCGATACAT
1116092 TGTATCGATACA
1 TGTATCGATACA
1116104 GGGTGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1116267 original size:20 final size:20
Alignment explanation
Indices: 1116224--1116269 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1116214 AAATCTTTTG
1116224 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1116245 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1116265 CAAAA
1 CAAAA
1116270 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1118666 original size:13 final size:13
Alignment explanation
Indices: 1118648--1118673 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1118638 TACAGCAAGT
1118648 ATGTATCGATACA
1 ATGTATCGATACA
1118661 ATGTATCGATACA
1 ATGTATCGATACA
1118674 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1123570 original size:18 final size:18
Alignment explanation
Indices: 1123549--1123622 Score: 51
Period size: 18 Copynumber: 4.2 Consensus size: 18
1123539 AAATCCTGTT
1123549 AAAGTCAACCCAAAAGTC
1 AAAGTCAACCCAAAAGTC
* ***
1123567 AAAGTAAATAGAAAA-TC
1 AAAGTCAACCCAAAAGTC
* ** *
1123584 AAAATCAACTAAAAACTC
1 AAAGTCAACCCAAAAGTC
* *
1123602 AAAGTTAAACCAAAAGTC
1 AAAGTCAACCCAAAAGTC
1123620 AAA
1 AAA
1123623 AATAGACATT
Statistics
Matches: 40, Mismatches: 15, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
17 12 0.30
18 28 0.70
ACGTcount: A:0.59, C:0.18, G:0.08, T:0.15
Consensus pattern (18 bp):
AAAGTCAACCCAAAAGTC
Found at i:1124766 original size:13 final size:14
Alignment explanation
Indices: 1124723--1124766 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
1124713 TAAAAATATT
1124723 AAAAATATATTTTA
1 AAAAATATATTTTA
* *
1124737 AAAATACATACTTTA
1 AAAA-ATATATTTTA
1124752 AAAAATAT-TTTTA
1 AAAAATATATTTTA
1124765 AA
1 AA
1124767 TTTCAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
13 6 0.24
14 7 0.28
15 12 0.48
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (14 bp):
AAAAATATATTTTA
Found at i:1125837 original size:45 final size:45
Alignment explanation
Indices: 1125773--1125871 Score: 180
Period size: 45 Copynumber: 2.2 Consensus size: 45
1125763 AATGTTTCAG
* *
1125773 CATTTCATTATTTCACATGACATCACCATAGACAAACCCTACTTC
1 CATTTCATTATTTCACATGACACCACCATAGACAAAACCTACTTC
1125818 CATTTCATTATTTCACATGACACCACCATAGACAAAACCTACTTC
1 CATTTCATTATTTCACATGACACCACCATAGACAAAACCTACTTC
1125863 CATTTCATT
1 CATTTCATT
1125872 TTTTTCACTC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.32
Consensus pattern (45 bp):
CATTTCATTATTTCACATGACACCACCATAGACAAAACCTACTTC
Found at i:1127092 original size:15 final size:12
Alignment explanation
Indices: 1127059--1127084 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1127049 TGGCAGAATG
1127059 TTATAATATGAT
1 TTATAATATGAT
1127071 TTATAATATGAT
1 TTATAATATGAT
1127083 TT
1 TT
1127085 CATATAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (12 bp):
TTATAATATGAT
Found at i:1130945 original size:373 final size:372
Alignment explanation
Indices: 1130088--1131193 Score: 1613
Period size: 373 Copynumber: 3.0 Consensus size: 372
1130078 AATGATAGGG
* *
1130088 GAGGATTCTCTTTGAATGCTTTTGGGTAGTGAGGATGATAGCTGTTTCACTTAGAAGTGCCAAAA
1 GAGGTTTCTCTTTGAATGCTTTTGGGTAGTGAGGATGATAGCTGTTTCACTTAGAGGTGCC-AAA
*
1130153 TACTTGACTTCTGTCATTTGTATGGTTGGTTATATAGATTTCAGAATTTGTATTGCACCTATATC
65 TACTTGACTTCTGTCATTTGTATGGTT-GTTATATAGATTTCAGAATTTATATTGCACCTATATC
* *
1130218 ATAAAATATGAATACTAATGAAGAGATACCTACGGAATTATTGAGTTTTGTGTGTCTAAAGTCTA
129 ATAAAATATGAATACTAATGAAGAGATACCTACTGACTTATTGAGTTTTGTGTGTCTAAAGTCTA
* ** *
1130283 TAAGATATA---T-G---TGTTTCACTTCTAATGTTGCTATTTTCATTATAAGATAATGCTTATA
194 TAATATATATCTTAGTAATGTTTTGCTTCTAATGTTGCTATTTTCATTATAAGATAATGCTCATA
* ** *
1130341 ATCAATAAATTTTGGCTTCC-TT-TTTT-TTTTTGGTGGGGGGGGGGGGGGGGTTTGCTGGGAGT
259 ATCAATAAA-TTTGGCCTCCTTTCTTTTCTTTTTTTTGGGGGGGGGGGGGGGG--TGTTGGGAGT
1130403 GCCTTAAAATTTTCTCATTAAAAGTCTACTTCTCATATTCTCAACCAATGAT
321 GCCTTAAAATTTTCTCATTAAAAGTCTACTTCTCATATTCTCAACCAATGAT
* *
1130455 AGGGAAGGTTTCTCTTTGAATGCTTTTGGGTAGTGAAGATGATAGCTGTTTCA-AT-G-GGTGCC
1 ---G-AGGTTTCTCTTTGAATGCTTTTGGGTAGTGAGGATGATAGCTGTTTCACTTAGAGGTGCC
1130517 AAAGTACTTGACTTCTGTCATTTGTATGGTTGTT-TATAGATTTCAGAATTTATATTGCACCTAT
62 AAA-TACTTGACTTCTGTCATTTGTATGGTTGTTATATAGATTTCAGAATTTATATTGCACCTAT
*
1130581 ATCATAAAATATGAATACTGATGAAGAGATACCTACTGACTTATTGAG-TTTGTGTGTCTAAAGT
126 ATCATAAAATATGAATACTAATGAAGAGATACCTACTGACTTATTGAGTTTTGTGTGTCTAAAGT
* * *
1130645 CTATAATATATATCTTAGTATATGTTTTGCTTCTAATGTTGCTATTTTTATTATGAGATAGTGCT
191 CTATAATATATATCTTAGTA-ATGTTTTGCTTCTAATGTTGCTATTTTCATTATAAGATAATGCT
* *
1130710 CATAATCAATGAATTTGGCCCCCTTTCTTTTCATTTTTTTTGGGGGGGGGGGGGGGGTGTTGGGA
255 CATAATCAATAAATTTGGCCTCCTTTCTTTTC-TTTTTTTTGGGGGGGGGGGGGGGGTGTTGGGA
* * * *
1130775 GTGCCTTCAAATTTTCTCATTAAAAGTCTACTTCTCATGTTCTCAGCCAGTGAT
319 GTGCCTTAAAATTTTCTCATTAAAAGTCTACTTCTCATATTCTCAACCAATGAT
*
1130829 -AGGTTTCTCTTTGAATGCTTTTGGTTAGTGAGGATGATAGCTGTTTCACTTAGAGGTGCCAAAT
1 GAGGTTTCTCTTTGAATGCTTTTGGGTAGTGAGGATGATAGCTGTTTCACTTAGAGGTGCCAAAT
1130893 ACTTGACTTCTGTCATTTGTATGGTTGTTTATATAGATTTCAGAATTTATATTGCACCTATATCA
66 ACTTGACTTCTGTCATTTGTATGGTTG-TTATATAGATTTCAGAATTTATATTGCACCTATATCA
*
1130958 TAAAATATGAATATTAATGAAGAGATACCTACTGACTTATTGAGTTTTGTGTGTGTCTAAAGTCT
130 TAAAATATGAATACTAATGAAGAGATACCTACTGACTTATTGAG-TTT-TGTGTGTCTAAAGTCT
*
1131023 ATAATATATATCTTACTACATGTTTTGCTTCTAATGTTGCTATTTTCATTATAAGATAATGCTCA
193 ATAATATATATCTTAGTA-ATGTTTTGCTTCTAATGTTGCTATTTTCATTATAAGATAATGCTCA
* * *
1131088 TACTCAATAAAGTTGGCCTCCTTTCTTTTC----TTTGGGGTTGGGGGGGGGGGGGTGTTGGGAG
257 TAATCAATAAATTTGGCCTCCTTTCTTTTCTTTTTTTTGGG--GGGGGGGGGGGGGTGTTGGGAG
* *
1131149 TGCCTTAAAATTTTCTCAGTAAAAGTCTACTTCTCATAGTCTCAA
320 TGCCTTAAAATTTTCTCATTAAAAGTCTACTTCTCATATTCTCAA
1131194 GAGTTTTGTC
Statistics
Matches: 667, Mismatches: 45, Indels: 45
0.88 0.06 0.06
Matches are distributed among these distances:
365 27 0.04
366 74 0.11
367 6 0.01
368 33 0.05
369 48 0.07
370 3 0.00
371 81 0.12
372 19 0.03
373 189 0.28
374 61 0.09
375 2 0.00
376 124 0.19
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (372 bp):
GAGGTTTCTCTTTGAATGCTTTTGGGTAGTGAGGATGATAGCTGTTTCACTTAGAGGTGCCAAAT
ACTTGACTTCTGTCATTTGTATGGTTGTTATATAGATTTCAGAATTTATATTGCACCTATATCAT
AAAATATGAATACTAATGAAGAGATACCTACTGACTTATTGAGTTTTGTGTGTCTAAAGTCTATA
ATATATATCTTAGTAATGTTTTGCTTCTAATGTTGCTATTTTCATTATAAGATAATGCTCATAAT
CAATAAATTTGGCCTCCTTTCTTTTCTTTTTTTTGGGGGGGGGGGGGGGGTGTTGGGAGTGCCTT
AAAATTTTCTCATTAAAAGTCTACTTCTCATATTCTCAACCAATGAT
Found at i:1133289 original size:23 final size:23
Alignment explanation
Indices: 1133260--1133303 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1133250 TACAGGTATC
1133260 CTACTCTCAATCTTTTTTCTTTA
1 CTACTCTCAATCTTTTTTCTTTA
1133283 CTACTCTCAATCTTTTTTCTT
1 CTACTCTCAATCTTTTTTCTT
1133304 GCTCCATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.57
Consensus pattern (23 bp):
CTACTCTCAATCTTTTTTCTTTA
Found at i:1141314 original size:19 final size:19
Alignment explanation
Indices: 1141286--1141322 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1141276 TGTTATTTTA
* *
1141286 TTTATTTTTAAATAATAAT
1 TTTATATTTAAAAAATAAT
1141305 TTTATATTTAAAAAATAA
1 TTTATATTTAAAAAATAA
1141323 ATAAAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTATATTTAAAAAATAAT
Found at i:1146627 original size:16 final size:16
Alignment explanation
Indices: 1146597--1146626 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1146587 CTTTTCCTTC
1146597 TTTTTGTTCTTTTTTG
1 TTTTTGTTCTTTTTTG
1146613 TTTTTGTT-TTTTTT
1 TTTTTGTTCTTTTTT
1146627 TTGAATGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.87
Consensus pattern (16 bp):
TTTTTGTTCTTTTTTG
Found at i:1148025 original size:19 final size:19
Alignment explanation
Indices: 1148001--1148038 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1147991 ATTCGTTCTT
1148001 TTTGGGCATCTCATTATGA
1 TTTGGGCATCTCATTATGA
1148020 TTTGGGCATCTCATTATGA
1 TTTGGGCATCTCATTATGA
1148039 CATCCACTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (19 bp):
TTTGGGCATCTCATTATGA
Found at i:1164192 original size:15 final size:15
Alignment explanation
Indices: 1164174--1164202 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1164164 TCGGGTTGCA
1164174 GGTGCTGAAAAGCAT
1 GGTGCTGAAAAGCAT
1164189 GGTGCTGAAAAGCA
1 GGTGCTGAAAAGCA
1164203 GCACGATAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.14, G:0.34, T:0.17
Consensus pattern (15 bp):
GGTGCTGAAAAGCAT
Found at i:1166289 original size:2 final size:2
Alignment explanation
Indices: 1166276--1166338 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
1166266 TGAAATCATG
*
1166276 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1166318 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
1166339 TTGCTTCTGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1166989 original size:2 final size:2
Alignment explanation
Indices: 1166984--1167023 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1166974 GCATGGGTGA
1166984 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1167024 TTTGAAAGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1167654 original size:19 final size:20
Alignment explanation
Indices: 1167615--1167657 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1167605 TATAATTAAA
*
1167615 TTTAAATAAAAATATATTAT
1 TTTAAATAAAAATATACTAT
*
1167635 TTTAATTAAAAAT-TACTAT
1 TTTAAATAAAAATATACTAT
1167654 TTTA
1 TTTA
1167658 GACCAAGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAAATAAAAATATACTAT
Found at i:1168193 original size:2 final size:2
Alignment explanation
Indices: 1168186--1168219 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1168176 AATGTGAGAG
*
1168186 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1168220 ACACTCATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1168903 original size:18 final size:17
Alignment explanation
Indices: 1168880--1168925 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
1168870 CTATTTCAGT
1168880 AATTAATTTAATAAATAA
1 AATTAATTTAATAAA-AA
* *
1168898 AATTAATTTAGTCAAAA
1 AATTAATTTAATAAAAA
*
1168915 AATCAATTTAA
1 AATTAATTTAA
1168926 ATTAATGGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (17 bp):
AATTAATTTAATAAAAA
Found at i:1170483 original size:16 final size:16
Alignment explanation
Indices: 1170462--1170494 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1170452 TAATTAGGAT
1170462 TGTTATACCCCAAAGA
1 TGTTATACCCCAAAGA
1170478 TGTTATACCCCAAAGA
1 TGTTATACCCCAAAGA
1170494 T
1 T
1170495 ATCGATCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.27
Consensus pattern (16 bp):
TGTTATACCCCAAAGA
Found at i:1175349 original size:42 final size:42
Alignment explanation
Indices: 1175215--1175729 Score: 351
Period size: 42 Copynumber: 12.2 Consensus size: 42
1175205 TAATGAAATG
* * * * * * * * *
1175215 AAGAAGTCCCCCGGGTTTAAGCTGACAGGCAGACAAAAGGTG
1 AAGAAGTCTCTCGGGTCTGAGCCGACGGGCAGACGAAAGATA
* * * * * *
1175257 AAGAAGTCTC-CTGGGTTTAAGCCGATGGGTAGACGAAAGGTG
1 AAGAAGTCTCTC-GGGTCTGAGCCGACGGGCAGACGAAAGATA
*
1175299 AAGAAGTCTCTCGGGTCTGAGCCGATGGGCAGACGAAAGATA
1 AAGAAGTCTCTCGGGTCTGAGCCGACGGGCAGACGAAAGATA
* * *
1175341 AAGAAGTCTCTCGAGTCTGAGCCGACGAGCAGA-TAAAGGATA
1 AAGAAGTCTCTCGGGTCTGAGCCGACGGGCAGACGAAA-GATA
* * * * * * **
1175383 AAGAAGTCTCTCGAGTCTGAGCTGGCGAGTAGGCGATTGATA
1 AAGAAGTCTCTCGGGTCTGAGCCGACGGGCAGACGAAAGATA
* * * * *
1175425 GAGGAAGTCTCTTGGGAT-TGAGCCAACGAGCAGACAAAAGATA
1 -AAGAAGTCTCTCGGG-TCTGAGCCGACGGGCAGACGAAAGATA
* * * * * **
1175468 AAGAAGTCTCCCGAGTCTGAACCAACGGGTAGACGATTGATAA
1 AAGAAGTCTCTCGGGTCTGAGCCGACGGGCAGACGAAAGAT-A
* * * *
1175511 AAAAAGTCTCCCAGGACTGAGCCGACGGGCAGACGAAAGATA
1 AAGAAGTCTCTCGGGTCTGAGCCGACGGGCAGACGAAAGATA
* * * * ** *
1175553 AATAAGTCTATTGAGTCTGAGTTGACGGGCAGACGAAAGATG
1 AAGAAGTCTCTCGGGTCTGAGCCGACGGGCAGACGAAAGATA
* ** *
1175595 TAGAAGTCT-TCTGGGTCTGAG-CGAACGGGCAGATAAAAGGTA
1 AAGAAGTCTCTC-GGGTCTGAGCCG-ACGGGCAGACGAAAGATA
*
1175637 AAGAAGTCTC-CTAGGTCTGAGCCGACGGGCAGACGAAAGATGA
1 AAGAAGTCTCTC-GGGTCTGAGCCGACGGGCAGACGAAAGAT-A
* * * * * *
1175680 AA-AAGTCTCCCAGGTTTGAGCTGACGGGTAGACGAAAGATG
1 AAGAAGTCTCTCGGGTCTGAGCCGACGGGCAGACGAAAGATA
1175721 AAGAAGTCT
1 AAGAAGTCT
1175730 GGAATAAGAT
Statistics
Matches: 378, Mismatches: 80, Indels: 30
0.77 0.16 0.06
Matches are distributed among these distances:
41 9 0.02
42 298 0.79
43 70 0.19
44 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.31, T:0.18
Consensus pattern (42 bp):
AAGAAGTCTCTCGGGTCTGAGCCGACGGGCAGACGAAAGATA
Found at i:1175505 original size:85 final size:85
Alignment explanation
Indices: 1175357--1175561 Score: 230
Period size: 85 Copynumber: 2.4 Consensus size: 85
1175347 TCTCTCGAGT
* * * * *** *
1175357 CTGAGCCGACGAGCAGATAAAGGATAAAGAAGTCTCTCGAGTCTGAGCTGGCGAGTAGGCGATTG
1 CTGAGCCGACGAGCAGACAAAAGATAAAGAAGTCTCCCGAGTCTGAACCAACGAGTAGACGATTG
* ** ***
1175422 ATAGAGGAAGTCTCTTGGGA
66 ATAAAAAAAGTCTCCCAGGA
* * *
1175442 TTGAGCCAACGAGCAGACAAAAGATAAAGAAGTCTCCCGAGTCTGAACCAACGGGTAGACGATTG
1 CTGAGCCGACGAGCAGACAAAAGATAAAGAAGTCTCCCGAGTCTGAACCAACGAGTAGACGATTG
1175507 ATAAAAAAAGTCTCCCAGGA
66 ATAAAAAAAGTCTCCCAGGA
* * *
1175527 CTGAGCCGACGGGCAGACGAAAGATAAATAAGTCT
1 CTGAGCCGACGAGCAGACAAAAGATAAAGAAGTCT
1175562 ATTGAGTCTG
Statistics
Matches: 98, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
85 98 1.00
ACGTcount: A:0.35, C:0.19, G:0.29, T:0.17
Consensus pattern (85 bp):
CTGAGCCGACGAGCAGACAAAAGATAAAGAAGTCTCCCGAGTCTGAACCAACGAGTAGACGATTG
ATAAAAAAAGTCTCCCAGGA
Found at i:1177537 original size:79 final size:79
Alignment explanation
Indices: 1177375--1177550 Score: 203
Period size: 79 Copynumber: 2.2 Consensus size: 79
1177365 GAGATAAAGA
* * * * * * *
1177375 CGGGGTTAGAGTATCTCCTCAGAAATAACGGGGCTGGAGTATCCCTGATTGTGGAAAATCAGTGT
1 CGGGGTTGGAGTATCCCCTCAAAAATAACAGGGCTGGAGTATCCCCGATTATGAAAAATCAGTGT
* *
1177440 TCTAGAATTAATAC
66 TCTAGAAATAAAAC
*
1177454 CGGGGTTGGAGTATCCCCTCAAAAATAACAGGGTTGGAGTATCCCCGATTATGAAAAATC-GATG
1 CGGGGTTGGAGTATCCCCTCAAAAATAACAGGGCTGGAGTATCCCCGATTATGAAAAATCAG-TG
* *
1177518 TT-TTGAAAATAAAAT
65 TTCTAG-AAATAAAAC
*
1177533 CGGGGTTGGAATATCCCC
1 CGGGGTTGGAGTATCCCC
1177551 GATGGTGAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
78 3 0.04
79 79 0.96
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.27
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCAAAAATAACAGGGCTGGAGTATCCCCGATTATGAAAAATCAGTGT
TCTAGAAATAAAAC
Found at i:1177548 original size:51 final size:51
Alignment explanation
Indices: 1177484--1177601 Score: 173
Period size: 51 Copynumber: 2.3 Consensus size: 51
1177474 AAAAATAACA
*
1177484 GGGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGAAAATAAAATCG
1 GGGTTGGAGTATCCCCGATGATGAAAAATCGATGTTTTGAAAATAAAATCG
* * * * * *
1177535 GGGTTGGAATATCCCCGATGGTGAAAAATTGTTGTTTTGGAAATAAAATTG
1 GGGTTGGAGTATCCCCGATGATGAAAAATCGATGTTTTGAAAATAAAATCG
1177586 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
1177602 TCGAAAATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.31
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCGATGATGAAAAATCGATGTTTTGAAAATAAAATCG
Found at i:1177633 original size:78 final size:78
Alignment explanation
Indices: 1177535--1178019 Score: 503
Period size: 79 Copynumber: 6.2 Consensus size: 78
1177525 AATAAAATCG
* * * *
1177535 GGGTTGGAATATCCCCGATGGTGAAAAATTGTTGTTTTGGAAATAAAATTGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTTTGGAAATAAAATTGGGGTTGGAGTATCC
* *
1177600 CCTCGAAAATAAT
66 CCTCAAAAATAAC
* * * * *
1177613 AGGTTAGAGTATCCTCGATGGTGGAAAATTGATGTTTTGGAAATAAAATT-GGGTTAGAGTATCC
1 GGGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTTTGGAAATAAAATTGGGGTTGGAGTATCC
*
1177677 CCTCGAAAATAAC
66 CCTCAAAAATAAC
* * ** * ** *
1177690 GGGTTGGAGTATCCTCTATTGTGGAAAATCAATGTTTTGAAAATAAAACAGGGGTTGAAGTATCC
1 GGGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTTTGGAAATAAAATTGGGGTTGGAGTATCC
1177755 CCTCAAAAATAAC
66 CCTCAAAAATAAC
* **
1177768 GGGATTGGAGTA-CCTCGATTGTGTAAAATTGATG-TTTGGAAAATAAAAATCAGGGTTGGAGTA
1 GGG-TTGGAGTATCCTCGATTGTGAAAAATTGATGTTTTGG-AAAT-AAAATTGGGGTTGGAGTA
1177831 TCCCCTCAAAAATAAC
63 TCCCCTCAAAAATAAC
** * * * * *
1177847 GGGGTAAGAGTAT-CTCCGATTAT-AGAAGATTGGTGTTTTGGAAATGAAATTGGGGTTAGAGTA
1 -GGGTTGGAGTATCCT-CGATTGTGA-AAAATTGATGTTTTGGAAATAAAATTGGGGTTGGAGTA
**
1177910 TCCCCTCGTAAATAAC
63 TCCCCTCAAAAATAAC
* * * * * *
1177926 GGGGTTGAAGTATCCCCGATTGTGAAAAATCGATGCTTTGGAAATAAAATCGAGGTTGGAGTATC
1 -GGGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTTTGGAAATAAAATTGGGGTTGGAGTATC
* *
1177991 CTCTCAAAAATAATA
65 CCCTCAAAAATAA-C
1178006 GGGTTGGAGTATCC
1 GGGTTGGAGTATCC
1178020 CCTCGAAAAT
Statistics
Matches: 336, Mismatches: 59, Indels: 23
0.80 0.14 0.06
Matches are distributed among these distances:
77 70 0.21
78 93 0.28
79 145 0.43
80 23 0.07
81 5 0.01
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (78 bp):
GGGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTTTGGAAATAAAATTGGGGTTGGAGTATCC
CCTCAAAAATAAC
Found at i:1178012 original size:28 final size:28
Alignment explanation
Indices: 1177979--1178048 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
1177969 ATAAAATCGA
* *
1177979 GGTTGGAGTATCCTCTCAAAAATAATAG
1 GGTTGGAGTATCCCCTCAAAAATAACAG
* *
1178007 GGTTGGAGTATCCCCTCGAAAATAACGG
1 GGTTGGAGTATCCCCTCAAAAATAACAG
*
1178035 GGTTAGAGTATCCC
1 GGTTGGAGTATCCC
1178049 GATTGTGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (28 bp):
GGTTGGAGTATCCCCTCAAAAATAACAG
Found at i:1178109 original size:106 final size:107
Alignment explanation
Indices: 1177899--1178100 Score: 286
Period size: 106 Copynumber: 1.9 Consensus size: 107
1177889 AATGAAATTG
*
1177899 GGGTTAGAGTATCCCCTCGTAAATAACGGGGTTGAAGTATCCCCGATTGTGAAAAATCGATGCTT
1 GGGTTAGAGTATCCCCTCGAAAATAACGGGGTTGAAGTATCCCCGATTGTGAAAAATCGATGCTT
*
1177964 TGGAAATAAAATCGAGGTTGGAGTATCCTCTCAAAAATAATA
66 TGGAAATAAAATCGAGGTTAGAGTATCCTCTCAAAAATAATA
* * *
1178006 GGGTTGGAGTATCCCCTCGAAAATAACGGGGTT-AGAGTAT-CCCGATTGTGAAAAATTTG-TGT
1 GGGTTAGAGTATCCCCTCGAAAATAACGGGGTTGA-AGTATCCCCGATTGTGAAAAA-TCGATGC
* *
1178068 TTTGGAAATAAGA-CTGGGGTTAGAGTATCCTCT
64 TTTGGAAATAAAATC-GAGGTTAGAGTATCCTCT
1178101 TGGAAATAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
105 1 0.01
106 46 0.54
107 38 0.45
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.29
Consensus pattern (107 bp):
GGGTTAGAGTATCCCCTCGAAAATAACGGGGTTGAAGTATCCCCGATTGTGAAAAATCGATGCTT
TGGAAATAAAATCGAGGTTAGAGTATCCTCTCAAAAATAATA
Found at i:1180558 original size:50 final size:49
Alignment explanation
Indices: 1180406--1180566 Score: 214
Period size: 50 Copynumber: 3.2 Consensus size: 49
1180396 GAAATGATTA
* * * *
1180406 AAAATGCCTGAATGTATCGATACATTGAGGAATGTATCTATACATCTGGGT
1 AAAAT-CCAGAATGTATCGATACAATGA-AAATGTATCGATACATCTGGGT
* * * *
1180457 AAAACCCCGAATGTATCGATATAATGAAAATGTATCGATACATCTAGGT
1 AAAATCCAGAATGTATCGATACAATGAAAATGTATCGATACATCTGGGT
*
1180506 AAAATTCAGAATGTATCGATACAATGAACAATGTATCGATACATCTGGGT
1 AAAATCCAGAATGTATCGATACAATGAA-AATGTATCGATACATCTGGGT
1180556 AAAATCCAGAA
1 AAAATCCAGAA
1180567 ATTTTGAATT
Statistics
Matches: 96, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
49 43 0.45
50 49 0.51
51 4 0.04
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (49 bp):
AAAATCCAGAATGTATCGATACAATGAAAATGTATCGATACATCTGGGT
Found at i:1182178 original size:13 final size:13
Alignment explanation
Indices: 1182160--1182185 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1182150 CAATTTTTGG
1182160 TGTATCGATACAT
1 TGTATCGATACAT
1182173 TGTATCGATACAT
1 TGTATCGATACAT
1182186 ACTTGATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1182201 original size:32 final size:33
Alignment explanation
Indices: 1182140--1182203 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1182130 TACAAGCCAA
** *
1182140 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGATGTATCGATACAT
1182173 TGTATCGATAC-ATACTTGATGTATCGATACA
1 TGTATCGATACAATACTTGATGTATCGATACA
1182204 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGATGTATCGATACAT
Found at i:1184751 original size:13 final size:13
Alignment explanation
Indices: 1184733--1184770 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
1184723 ATAAACCCCC
1184733 TGTATCGATACAA
1 TGTATCGATACAA
1184746 TGTATCGATACAA
1 TGTATCGATACAA
1184759 TGTATCGATACA
1 TGTATCGATACA
1184771 TTGAATTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1185470 original size:13 final size:13
Alignment explanation
Indices: 1185452--1185477 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1185442 TACACAAAGT
1185452 ATGTATCGATACA
1 ATGTATCGATACA
1185465 ATGTATCGATACA
1 ATGTATCGATACA
1185478 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1185475 original size:32 final size:33
Alignment explanation
Indices: 1185434--1185497 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1185424 TAGCCAAACT
**
1185434 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1185466 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1185498 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1188534 original size:15 final size:15
Alignment explanation
Indices: 1188514--1188544 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1188504 TAAAAATGTC
*
1188514 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1188529 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1188544 C
1 C
1188545 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1190618 original size:13 final size:13
Alignment explanation
Indices: 1190600--1190637 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1190590 CATTTTACTT
1190600 TGTATCGATACAA
1 TGTATCGATACAA
*
1190613 TGTATCGATACAC
1 TGTATCGATACAA
1190626 TGTATCGATACA
1 TGTATCGATACA
1190638 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1190792 original size:20 final size:20
Alignment explanation
Indices: 1190749--1190794 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1190739 AAATCTTTTG
1190749 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1190770 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1190790 CAAAA
1 CAAAA
1190795 CCAACATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1191922 original size:13 final size:13
Alignment explanation
Indices: 1191904--1191929 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1191894 TACACAAAGT
1191904 ATGTATCGATACA
1 ATGTATCGATACA
1191917 ATGTATCGATACA
1 ATGTATCGATACA
1191930 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1199007 original size:13 final size:13
Alignment explanation
Indices: 1198989--1199014 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1198979 TACACAAAGT
1198989 ATGTATCGATACA
1 ATGTATCGATACA
1199002 ATGTATCGATACA
1 ATGTATCGATACA
1199015 CCAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1199129 original size:20 final size:19
Alignment explanation
Indices: 1199076--1199130 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
1199066 TTTCAAATGC
1199076 ATGTATCGATACATCAGAA
1 ATGTATCGATACATCAGAA
** *
1199095 AAATAACAAGATACATCAGAA
1 ATGTATC--GATACATCAGAA
1199116 ATTGTATCGATACAT
1 A-TGTATCGATACAT
1199131 TCACACGGGA
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
19 4 0.15
20 7 0.26
21 13 0.48
22 3 0.11
ACGTcount: A:0.47, C:0.15, G:0.13, T:0.25
Consensus pattern (19 bp):
ATGTATCGATACATCAGAA
Found at i:1204740 original size:13 final size:13
Alignment explanation
Indices: 1204722--1204747 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1204712 TACACCAAGT
1204722 ATGTATCGATACA
1 ATGTATCGATACA
1204735 ATGTATCGATACA
1 ATGTATCGATACA
1204748 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1204744 original size:32 final size:33
Alignment explanation
Indices: 1204703--1204767 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1204693 GTAGCCAAAC
* **
1204703 ATGTATCGATACACCAAGTA-TGTATCGATACA
1 ATGTATCGATACACAAAAAATTGTATCGATACA
1204735 ATGTATCGATACACAAAAAATTGTATCGATACA
1 ATGTATCGATACACAAAAAATTGTATCGATACA
1204768 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACACAAAAAATTGTATCGATACA
Found at i:1206984 original size:22 final size:22
Alignment explanation
Indices: 1206957--1207012 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
1206947 TTACAAGTTG
1206957 AAATAAAGAACTTGGCTAATG-A
1 AAATAAAGAACTTGGCTAA-GAA
* *
1206979 AAATAATGAA-TTAGCTAAGAA
1 AAATAAAGAACTTGGCTAAGAA
1207000 AAATAAA-AACTTG
1 AAATAAAGAACTTG
1207013 CATGATTCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 3 0.11
21 16 0.57
22 9 0.32
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.23
Consensus pattern (22 bp):
AAATAAAGAACTTGGCTAAGAA
Found at i:1208822 original size:15 final size:15
Alignment explanation
Indices: 1208802--1208832 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1208792 TAAAAATGTC
*
1208802 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1208817 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1208832 C
1 C
1208833 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1210907 original size:13 final size:13
Alignment explanation
Indices: 1210889--1210926 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1210879 CATTTTACTT
1210889 TGTATCGATACAA
1 TGTATCGATACAA
*
1210902 TGTATCGATACAC
1 TGTATCGATACAA
1210915 TGTATCGATACA
1 TGTATCGATACA
1210927 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1211081 original size:20 final size:20
Alignment explanation
Indices: 1211038--1211083 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1211028 AAATCTTTTG
1211038 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1211059 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1211079 CAAAA
1 CAAAA
1211084 CCAACATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1212211 original size:13 final size:13
Alignment explanation
Indices: 1212193--1212218 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1212183 TACACAAAGT
1212193 ATGTATCGATACA
1 ATGTATCGATACA
1212206 ATGTATCGATACA
1 ATGTATCGATACA
1212219 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1219296 original size:13 final size:13
Alignment explanation
Indices: 1219278--1219303 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1219268 TACACAAAGT
1219278 ATGTATCGATACA
1 ATGTATCGATACA
1219291 ATGTATCGATACA
1 ATGTATCGATACA
1219304 CCAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1219418 original size:20 final size:19
Alignment explanation
Indices: 1219365--1219419 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
1219355 TTTCAAATGC
1219365 ATGTATCGATACATCAGAA
1 ATGTATCGATACATCAGAA
** *
1219384 AAATAACAAGATACATCAGAA
1 ATGTATC--GATACATCAGAA
1219405 ATTGTATCGATACAT
1 A-TGTATCGATACAT
1219420 TCACACGGGA
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
19 4 0.15
20 7 0.26
21 13 0.48
22 3 0.11
ACGTcount: A:0.47, C:0.15, G:0.13, T:0.25
Consensus pattern (19 bp):
ATGTATCGATACATCAGAA
Found at i:1225030 original size:13 final size:13
Alignment explanation
Indices: 1225012--1225037 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1225002 TACACCAAGT
1225012 ATGTATCGATACA
1 ATGTATCGATACA
1225025 ATGTATCGATACA
1 ATGTATCGATACA
1225038 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1225034 original size:32 final size:33
Alignment explanation
Indices: 1224993--1225057 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1224983 GTAGCCAAAC
* **
1224993 ATGTATCGATACACCAAGTA-TGTATCGATACA
1 ATGTATCGATACACAAAAAATTGTATCGATACA
1225025 ATGTATCGATACACAAAAAATTGTATCGATACA
1 ATGTATCGATACACAAAAAATTGTATCGATACA
1225058 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACACAAAAAATTGTATCGATACA
Found at i:1227274 original size:22 final size:22
Alignment explanation
Indices: 1227247--1227302 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
1227237 TTACAAGTTG
1227247 AAATAAAGAACTTGGCTAATG-A
1 AAATAAAGAACTTGGCTAA-GAA
* *
1227269 AAATAATGAA-TTAGCTAAGAA
1 AAATAAAGAACTTGGCTAAGAA
1227290 AAATAAA-AACTTG
1 AAATAAAGAACTTG
1227303 CATGATTCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 3 0.11
21 16 0.57
22 9 0.32
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.23
Consensus pattern (22 bp):
AAATAAAGAACTTGGCTAAGAA
Found at i:1231196 original size:13 final size:14
Alignment explanation
Indices: 1231178--1231216 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
1231168 CATTTACTTT
1231178 TGTATCGATACA-A
1 TGTATCGATACACA
*
1231191 TGTATCGATACACC
1 TGTATCGATACACA
1231205 TGTATCGATACA
1 TGTATCGATACA
1231217 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (14 bp):
TGTATCGATACACA
Found at i:1231371 original size:20 final size:20
Alignment explanation
Indices: 1231328--1231373 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1231318 AAATCTTTTG
1231328 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1231349 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1231369 CAAAA
1 CAAAA
1231374 CCAACATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1232501 original size:13 final size:13
Alignment explanation
Indices: 1232483--1232508 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1232473 TACACAAAGT
1232483 ATGTATCGATACA
1 ATGTATCGATACA
1232496 ATGTATCGATACA
1 ATGTATCGATACA
1232509 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1232506 original size:32 final size:33
Alignment explanation
Indices: 1232465--1232531 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 33
1232455 TAGCCAAACT
**
1232465 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
*
1232497 TGTATCGATACACAAAAAATTGTATTGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1232530 TG
1 TG
1232532 GCTTGTAACG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 17 0.55
33 14 0.45
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1239582 original size:13 final size:13
Alignment explanation
Indices: 1239564--1239589 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1239554 TACACAAAGT
1239564 ATGTATCGATACA
1 ATGTATCGATACA
1239577 ATGTATCGATACA
1 ATGTATCGATACA
1239590 CCAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1239704 original size:20 final size:19
Alignment explanation
Indices: 1239651--1239705 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
1239641 TTTCAAATGC
1239651 ATGTATCGATACATCAGAA
1 ATGTATCGATACATCAGAA
** *
1239670 AAATAACAAGATACATCAGAA
1 ATGTATC--GATACATCAGAA
1239691 ATTGTATCGATACAT
1 A-TGTATCGATACAT
1239706 TCACACGGGA
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
19 4 0.15
20 7 0.26
21 13 0.48
22 3 0.11
ACGTcount: A:0.47, C:0.15, G:0.13, T:0.25
Consensus pattern (19 bp):
ATGTATCGATACATCAGAA
Found at i:1245315 original size:13 final size:13
Alignment explanation
Indices: 1245297--1245322 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1245287 TACACCAAGT
1245297 ATGTATCGATACA
1 ATGTATCGATACA
1245310 ATGTATCGATACA
1 ATGTATCGATACA
1245323 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1245319 original size:32 final size:33
Alignment explanation
Indices: 1245278--1245342 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1245268 GTAGCCAAAC
* **
1245278 ATGTATCGATACACCAAGTA-TGTATCGATACA
1 ATGTATCGATACACAAAAAATTGTATCGATACA
1245310 ATGTATCGATACACAAAAAATTGTATCGATACA
1 ATGTATCGATACACAAAAAATTGTATCGATACA
1245343 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACACAAAAAATTGTATCGATACA
Found at i:1247559 original size:22 final size:22
Alignment explanation
Indices: 1247532--1247587 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
1247522 TTACAAGTTG
1247532 AAATAAAGAACTTGGCTAATG-A
1 AAATAAAGAACTTGGCTAA-GAA
* *
1247554 AAATAATGAA-TTAGCTAAGAA
1 AAATAAAGAACTTGGCTAAGAA
1247575 AAATAAA-AACTTG
1 AAATAAAGAACTTG
1247588 CATGATTCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 3 0.11
21 16 0.57
22 9 0.32
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.23
Consensus pattern (22 bp):
AAATAAAGAACTTGGCTAAGAA
Found at i:1251494 original size:20 final size:20
Alignment explanation
Indices: 1251469--1251535 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
1251459 GGAAATTCAA
1251469 TGTATCGATACATTTTTCTT
1 TGTATCGATACATTTTTCTT
1251489 TGTATCGATACA-------T
1 TGTATCGATACATTTTTCTT
1251502 TGTATCGATACATTTTTCTT
1 TGTATCGATACATTTTTCTT
1251522 TGTATCGATACATT
1 TGTATCGATACATT
1251536 GTATCGATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 13 0.32
20 27 0.68
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.49
Consensus pattern (20 bp):
TGTATCGATACATTTTTCTT
Found at i:1251506 original size:13 final size:13
Alignment explanation
Indices: 1251488--1251546 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
1251478 ACATTTTTCT
1251488 TTGTATCGATACA
1 TTGTATCGATACA
1251501 TTGTATCGATACA
1 TTGTATCGATACA
*
1251514 TT-T-T---T-CT
1 TTGTATCGATACA
1251521 TTGTATCGATACA
1 TTGTATCGATACA
1251534 TTGTATCGATACA
1 TTGTATCGATACA
1251547 GGGTGATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
7 3 0.08
8 2 0.05
9 1 0.03
11 1 0.03
12 2 0.05
13 29 0.76
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1251511 original size:33 final size:33
Alignment explanation
Indices: 1251469--1251546 Score: 156
Period size: 33 Copynumber: 2.4 Consensus size: 33
1251459 GGAAATTCAA
1251469 TGTATCGATACATTTTTCTTTGTATCGATACAT
1 TGTATCGATACATTTTTCTTTGTATCGATACAT
1251502 TGTATCGATACATTTTTCTTTGTATCGATACAT
1 TGTATCGATACATTTTTCTTTGTATCGATACAT
1251535 TGTATCGATACA
1 TGTATCGATACA
1251547 GGGTGATTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (33 bp):
TGTATCGATACATTTTTCTTTGTATCGATACAT
Found at i:1254128 original size:13 final size:13
Alignment explanation
Indices: 1254110--1254135 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1254100 TACACCAAGT
1254110 ATGTATCGATACA
1 ATGTATCGATACA
1254123 ATGTATCGATACA
1 ATGTATCGATACA
1254136 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1254132 original size:32 final size:33
Alignment explanation
Indices: 1254091--1254155 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1254081 GTAGCCAAAC
* **
1254091 ATGTATCGATACACCAAGTA-TGTATCGATACA
1 ATGTATCGATACACAAAAAATTGTATCGATACA
1254123 ATGTATCGATACACAAAAAATTGTATCGATACA
1 ATGTATCGATACACAAAAAATTGTATCGATACA
1254156 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACACAAAAAATTGTATCGATACA
Done.