Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008165.1 Hibiscus syriacus cultivar Beakdansim tig00110745_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2894944
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 11
Found at i:1074731 original size:21 final size:20
Alignment explanation
Indices: 1074699--1074751 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
1074689 TTTTTCCTCT
1074699 TTTTTTTCTTTTATTTTTCTA
1 TTTTTTT-TTTTATTTTTCTA
* * *
1074720 TTTTTTTGTTTTCTTTTTTTC
1 TTTTTTT-TTTTATTTTTCTA
1074741 TTTTTTTTTTT
1 TTTTTTTTTTT
1074752 CTTTCTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.04, C:0.08, G:0.02, T:0.87
Consensus pattern (20 bp):
TTTTTTTTTTTATTTTTCTA
Found at i:1074775 original size:24 final size:24
Alignment explanation
Indices: 1074729--1074775 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1074719 ATTTTTTTGT
* * * *
1074729 TTTCTTTTTTTCTTTTTTTTTTTC
1 TTTCTTTTTTTATATTATATTTTC
1074753 TTTCTTTTTTTATATTATATTTT
1 TTTCTTTTTTTATATTATATTTT
1074776 TTAGCTCTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTCTTTTTTTATATTATATTTTC
Found at i:1074777 original size:1 final size:1
Alignment explanation
Indices: 1074698--1074763 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
1074688 TTTTTTCCTC
* * * * * * * * *
1074698 TTTTTTTTCTTTTATTTTTCTATTTTTTTGTTTTCTTTTTTTCTTTTTTTTTTTCTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1074763 T
1 T
1074764 ATATTATATT
Statistics
Matches: 47, Mismatches: 18, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.03, C:0.09, G:0.02, T:0.86
Consensus pattern (1 bp):
T
Found at i:1077745 original size:43 final size:46
Alignment explanation
Indices: 1077623--1077747 Score: 141
Period size: 47 Copynumber: 2.8 Consensus size: 46
1077613 TATAAAATCT
*
1077623 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
1077668 CTTACTATTTAAATTCCATAAGATCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
1077715 TTTGCCA-TT-ATT-CATAAGCTCGTAAACTTATTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
1077748 GCATACTTAC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
43 19 0.28
44 3 0.04
45 9 0.13
46 2 0.03
47 35 0.51
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1082220 original size:54 final size:54
Alignment explanation
Indices: 1082138--1082739 Score: 693
Period size: 54 Copynumber: 11.1 Consensus size: 54
1082128 TTTGTACCTA
* * *
1082138 AGTGCCGATATGGTCATTCATAAACTCATTATGAATTCCATGGGTTTCACACAT
1 AGTGCCGATACGGTCATTCATAAACTCATTATGAATTTCATGGGTTGCACACAT
* *
1082192 AGTGCCGATACGGCCATTCATAAACTCATTATGAATTTAATGGGTTGCACACAT
1 AGTGCCGATACGGTCATTCATAAACTCATTATGAATTTCATGGGTTGCACACAT
** * * *
1082246 AGTGCATATACGATCATTCATAAACTTCATTATGAA-TTCTATGGGTTGCAAATAT
1 AGTGCCGATACGGTCATTCATAAAC-TCATTATGAATTTC-ATGGGTTGCACACAT
* * * * * * * *
1082301 AGTGTCTATACGATCATTAATAAACTTATTATAAATTTCGTGGGTTGCACATAT
1 AGTGCCGATACGGTCATTCATAAACTCATTATGAATTTCATGGGTTGCACACAT
* * *
1082355 AGTGTCGATACGATCATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACAT
1 AGTGCCGATACGGTCATTCATAAACTCATTATGAATTTCAT-GGGTTGCACACAT
* *
1082410 AGTGCCGATACGGTCATTCATAAACTCATTATGAATTCCATGGGTTACACACAT
1 AGTGCCGATACGGTCATTCATAAACTCATTATGAATTTCATGGGTTGCACACAT
* * * * * * *
1082464 AGTCCCGATACAGTCATTCATAAACTCATAATAAATTTCGTGGATTGCATACAT
1 AGTGCCGATACGGTCATTCATAAACTCATTATGAATTTCATGGGTTGCACACAT
* * * * *
1082518 AGTGTCGATACGGTCATTTATAAACTCTTTATGAATTCCTTGGGTTGCACACAT
1 AGTGCCGATACGGTCATTCATAAACTCATTATGAATTTCATGGGTTGCACACAT
* * * * *
1082572 AGTGTCGATATGGTCATTCATAAACTCATTATGAATTTTATAGGTTGCACACAC
1 AGTGCCGATACGGTCATTCATAAACTCATTATGAATTTCATGGGTTGCACACAT
** * * * * * *
1082626 AGTGATGAAACGGTCATTCATAAACTCATTATAAATTACGTGGGTTTCATACAT
1 AGTGCCGATACGGTCATTCATAAACTCATTATGAATTTCATGGGTTGCACACAT
** * **
1082680 AGTGTTGATAGGGTCATTCATAAACTCATTATGAATTTTGTGGGTTGCACACAT
1 AGTGCCGATACGGTCATTCATAAACTCATTATGAATTTCATGGGTTGCACACAT
1082734 AGTGCC
1 AGTGCC
1082740 ACTATAAAAG
Statistics
Matches: 465, Mismatches: 79, Indels: 8
0.84 0.14 0.01
Matches are distributed among these distances:
54 368 0.79
55 97 0.21
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (54 bp):
AGTGCCGATACGGTCATTCATAAACTCATTATGAATTTCATGGGTTGCACACAT
Found at i:1084182 original size:199 final size:202
Alignment explanation
Indices: 1083842--1084242 Score: 765
Period size: 199 Copynumber: 2.0 Consensus size: 202
1083832 AAGACCATAA
1083842 ACCCCTCCATTCTTCCATTTTTACTAATAAGTCTTAAACACCATCTCCAAATTAAATCCTTGTAA
1 ACCCCTCCATTCTTCCATTTTTACTAATAAGTCTTAAACACCATCTCCAAATTAAATCCTTGTAA
1083907 TTTTCAATTTATTCAAAATAACCCACTAAATTTTAAATTATTTCACTATAGATACTAACCTGATG
66 TTTTCAATTTATTCAAAATAACCCACTAAATTTTAAATTATTTCACTATAGATACTAACCTGATG
1083972 TTTGGGTATTACAATTGTCATATGTTAGCCTTA-CC-CATCTCTTTCACCGCTTAC-CCACCAAT
131 TTTGGGTATTACAATTGTCATATGTTAGCCTTACCCACATCTCTTTCACCGCTTACTCCACCAAT
1084034 TTCCCCC
196 TTCCCCC
1084041 ACCCCTCCATTCTTCCATTTTTACTAATAAGTCTTAAACACCATCTCCAAATTAAATCCTTGTAA
1 ACCCCTCCATTCTTCCATTTTTACTAATAAGTCTTAAACACCATCTCCAAATTAAATCCTTGTAA
1084106 TTTTC-ATTTATTCAAAATAACCCACTAAATTTTAAATTATTTCACTATAGATACTAACCTGATG
66 TTTTCAATTTATTCAAAATAACCCACTAAATTTTAAATTATTTCACTATAGATACTAACCTGATG
1084170 TTTGGGGTATTACAATTGTCATATGTTAGCCTTACCCACATCTCTTTCACCGCTTACTCCACCAA
131 TTT-GGGTATTACAATTGTCATATGTTAGCCTTACCCACATCTCTTTCACCGCTTACTCCACCAA
1084235 TTTCCCCC
195 TTTCCCCC
1084243 CAAATTCCAA
Statistics
Matches: 198, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
198 62 0.31
199 100 0.51
200 2 0.01
201 19 0.10
202 15 0.08
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.37
Consensus pattern (202 bp):
ACCCCTCCATTCTTCCATTTTTACTAATAAGTCTTAAACACCATCTCCAAATTAAATCCTTGTAA
TTTTCAATTTATTCAAAATAACCCACTAAATTTTAAATTATTTCACTATAGATACTAACCTGATG
TTTGGGTATTACAATTGTCATATGTTAGCCTTACCCACATCTCTTTCACCGCTTACTCCACCAAT
TTCCCCC
Found at i:1089770 original size:31 final size:31
Alignment explanation
Indices: 1089732--1089802 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
1089722 ATGAGTCAGC
* *
1089732 CTCACTTGCTTTCCTT-CTCCACATTGATTAT
1 CTCACTTGCCTTCCTTCCT-CACATTGATTAG
* *
1089763 CTCACTTGCCTTGCTTCCTCACGTTGATTAG
1 CTCACTTGCCTTCCTTCCTCACATTGATTAG
1089794 CTCTACTTG
1 CTC-ACTTG
1089803 TCTACGTGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 27 0.79
32 7 0.21
ACGTcount: A:0.14, C:0.32, G:0.11, T:0.42
Consensus pattern (31 bp):
CTCACTTGCCTTCCTTCCTCACATTGATTAG
Found at i:1094703 original size:15 final size:16
Alignment explanation
Indices: 1094685--1094716 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1094675 TTTGAAGTAT
1094685 AATGTAT-TGATTAAA
1 AATGTATGTGATTAAA
1094700 AATGTATGTGATTAAA
1 AATGTATGTGATTAAA
1094716 A
1 A
1094717 CAAAGTTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.38
Consensus pattern (16 bp):
AATGTATGTGATTAAA
Found at i:1101238 original size:21 final size:21
Alignment explanation
Indices: 1101209--1101280 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
1101199 TATCTCAGGC
* *
1101209 TTTCGAAACTTCCCTTAGGGG
1 TTTCAAAACATCCCTTAGGGG
*
1101230 TTTCAAAACCTCCCTTAGGGG
1 TTTCAAAACATCCCTTAGGGG
* ** *
1101251 TTTTAAAACATCGATTAGGGT
1 TTTCAAAACATCCCTTAGGGG
1101272 TTTCAAAAC
1 TTTCAAAAC
1101281 CTTTGAGAAG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (21 bp):
TTTCAAAACATCCCTTAGGGG
Found at i:1115215 original size:39 final size:39
Alignment explanation
Indices: 1115172--1115251 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
1115162 TCTCATGATT
* *
1115172 TATCAAA-ACCATGATAAACAACATCATACGTAATAGTCA
1 TATCAAAGA-CATGATAAACAACATCATACATAACAGTCA
*
1115211 TATCAAAGATATGATAAACAACATCATACATAACAGTCA
1 TATCAAAGACATGATAAACAACATCATACATAACAGTCA
1115250 TA
1 TA
1115252 CATATTCGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 36 0.97
40 1 0.03
ACGTcount: A:0.50, C:0.19, G:0.07, T:0.24
Consensus pattern (39 bp):
TATCAAAGACATGATAAACAACATCATACATAACAGTCA
Found at i:1115421 original size:18 final size:18
Alignment explanation
Indices: 1115383--1115447 Score: 67
Period size: 19 Copynumber: 3.5 Consensus size: 18
1115373 TCATAATCAA
* *
1115383 AACTTGTTTCCAGACTCAT
1 AACTTATTT-CAGATTCAT
*
1115402 AACTTATTTCGGATTCAT
1 AACTTATTTCAGATTCAT
*
1115420 AACTTAATTTCATATTCAT
1 AACTT-ATTTCAGATTCAT
*
1115439 AGCTTATTT
1 AACTTATTT
1115448 TTAATTTCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
18 16 0.41
19 23 0.59
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (18 bp):
AACTTATTTCAGATTCAT
Found at i:1120153 original size:243 final size:243
Alignment explanation
Indices: 1119725--1120214 Score: 962
Period size: 243 Copynumber: 2.0 Consensus size: 243
1119715 CACTGGTGCA
1119725 TCCCATATGAGACACCGGGTCTTGTAAATATTGGATCTTAACAATCCTAATAAATATGCCTTTAA
1 TCCCATATGAGACACCGGGTCTTGTAAATATTGGATCTTAACAATCCTAATAAATATGCCTTTAA
*
1119790 TTCTCTAGGCTCAATTAAAGCCACTCAATACAAGGCTATAGGAAAAAAACAGTACCTAGTAACAT
66 TTCTCTAGGCTCAATTAAAGCCACTCAATACAAGGCTATAGAAAAAAAACAGTACCTAGTAACAT
1119855 CTCTTTTTTATATCTTACATCTAAATCTATAGGTAATACATATAATTCTTCTAGAAACATATCAA
131 CTCTTTTTTATATCTTACATCTAAATCTATAGGTAATACATATAATTCTTCTAGAAACATATCAA
1119920 TACTCTCAATTAGTTGGAATATCTTCTAACCTAACTGACACACATATC
196 TACTCTCAATTAGTTGGAATATCTTCTAACCTAACTGACACACATATC
1119968 TCCCATATGAGACACCGGGTCTTGTAAATATTGGATCTTAACAATCCTAATAAATATGCCTTTAA
1 TCCCATATGAGACACCGGGTCTTGTAAATATTGGATCTTAACAATCCTAATAAATATGCCTTTAA
1120033 TTCTCTAGGCTCAATTAAAGCCACTCAATACAAGGCTATAGAAAAAAAACAGTACCTAGTAACAT
66 TTCTCTAGGCTCAATTAAAGCCACTCAATACAAGGCTATAGAAAAAAAACAGTACCTAGTAACAT
1120098 CTCTTTTTTATATCTTACATCTAAATCTATAGGTAATACATATAATTCTTCTAGAAACATATCAA
131 CTCTTTTTTATATCTTACATCTAAATCTATAGGTAATACATATAATTCTTCTAGAAACATATCAA
*
1120163 TACTCTCAATTAGTTGGAATATCTTCTAACCTAACTGACACGCATATC
196 TACTCTCAATTAGTTGGAATATCTTCTAACCTAACTGACACACATATC
1120211 TCCC
1 TCCC
1120215 GTATACCCTT
Statistics
Matches: 245, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
243 245 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.32
Consensus pattern (243 bp):
TCCCATATGAGACACCGGGTCTTGTAAATATTGGATCTTAACAATCCTAATAAATATGCCTTTAA
TTCTCTAGGCTCAATTAAAGCCACTCAATACAAGGCTATAGAAAAAAAACAGTACCTAGTAACAT
CTCTTTTTTATATCTTACATCTAAATCTATAGGTAATACATATAATTCTTCTAGAAACATATCAA
TACTCTCAATTAGTTGGAATATCTTCTAACCTAACTGACACACATATC
Found at i:1120521 original size:53 final size:53
Alignment explanation
Indices: 1120459--1120563 Score: 167
Period size: 53 Copynumber: 2.0 Consensus size: 53
1120449 TGACGAGTTA
1120459 ACCTTAATTGGTGATAACT-ATTGCTACAATTGTACTACTTACTTGACAAGTCG
1 ACCTTAATTGGTGATAACTGA-TGCTACAATTGTACTACTTACTTGACAAGTCG
* * *
1120512 ACCTTAATTGGTGATAACTGATGCTACAGTTGTACTCCTTACTTGACTAGTC
1 ACCTTAATTGGTGATAACTGATGCTACAATTGTACTACTTACTTGACAAGTC
1120564 TCCGCTTTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
53 47 0.98
54 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (53 bp):
ACCTTAATTGGTGATAACTGATGCTACAATTGTACTACTTACTTGACAAGTCG
Found at i:1121059 original size:12 final size:12
Alignment explanation
Indices: 1121042--1121077 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
1121032 ATCTTGAACC
1121042 CTTTTTTATTTT
1 CTTTTTTATTTT
1121054 CTTTTTCT-TTTT
1 CTTTTT-TATTTT
1121066 CTTTTTTATTTT
1 CTTTTTTATTTT
1121078 TCATTCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 1 0.05
12 20 0.91
13 1 0.05
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (12 bp):
CTTTTTTATTTT
Found at i:1121072 original size:19 final size:19
Alignment explanation
Indices: 1121050--1121089 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1121040 CCCTTTTTTA
* * *
1121050 TTTTCTTTTTCTTTTTCTT
1 TTTTATTTTTCATTCTCTT
1121069 TTTTATTTTTCATTCTCTT
1 TTTTATTTTTCATTCTCTT
1121088 TT
1 TT
1121090 CTTTTGAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTATTTTTCATTCTCTT
Found at i:1121074 original size:24 final size:24
Alignment explanation
Indices: 1121042--1121094 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1121032 ATCTTGAACC
* *
1121042 CTTTTTTA-TTTTCTTTTTCTTTTT
1 CTTTTTTATTTTTCATTCTC-TTTT
1121066 CTTTTTTATTTTTCATTCTCTTTT
1 CTTTTTTATTTTTCATTCTCTTTT
1121090 CTTTT
1 CTTTT
1121095 GAATTTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (24 bp):
CTTTTTTATTTTTCATTCTCTTTT
Found at i:1126805 original size:90 final size:90
Alignment explanation
Indices: 1126694--1126871 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 90
1126684 TAATCCCGAA
* * * *
1126694 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGAT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1126759 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
*
1126784 TATTAAATTTTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
* *
1126849 TAGTGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
1126872 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
TAGGGTAACTTGGATATAAAAGGAT
Found at i:1133636 original size:90 final size:90
Alignment explanation
Indices: 1133525--1133702 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
1133515 AAGTATCGAA
* * * * *
1133525 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCACTGATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACACTAATATGAC
*
1133590 TAGGGTAACTTGGATATAAAAGGAT
66 AAGGGTAACTTGGATATAAAAGGAT
*
1133615 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACACTAATATGAC
*
1133680 AAGGGTAACTTGGCTATAAAAGG
66 AAGGGTAACTTGGATATAAAAGG
1133703 GTGTGTTAGG
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.36
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACACTAATATGAC
AAGGGTAACTTGGATATAAAAGGAT
Found at i:1137938 original size:21 final size:23
Alignment explanation
Indices: 1137894--1137939 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
1137884 CAACATACTT
1137894 TTCTTTATGTACATTTTCCATTA
1 TTCTTTATGTACATTTTCCATTA
1137917 TTCTTTA-GTA-ATTATT-CATTA
1 TTCTTTATGTACATT-TTCCATTA
1137938 TT
1 TT
1137940 TTCATTTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 10 0.45
22 5 0.23
23 7 0.32
ACGTcount: A:0.24, C:0.13, G:0.04, T:0.59
Consensus pattern (23 bp):
TTCTTTATGTACATTTTCCATTA
Found at i:1138002 original size:45 final size:45
Alignment explanation
Indices: 1137939--1138076 Score: 152
Period size: 45 Copynumber: 3.1 Consensus size: 45
1137929 TATTCATTAT
* * * * * *
1137939 TTTCATTTAGGGCATCCTTACATGCCTCTAATGCACCGTTATGCA
1 TTTCAATTATGGCATCCTTTCATGCCTTTAATGAACCATTATGCA
* * *
1137984 TTT-TATTAATGGCATCCTTTCATGCCTTTAATGTACCATTATGTA
1 TTTCAATT-ATGGCATCCTTTCATGCCTTTAATGAACCATTATGCA
* * *
1138029 TTTCAATTATGGAATCCTTTCATACCTTTAATGAACTATTATGCA
1 TTTCAATTATGGCATCCTTTCATGCCTTTAATGAACCATTATGCA
1138074 TTT
1 TTT
1138077 AGTATTTTAT
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
44 2 0.03
45 72 0.94
46 3 0.04
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (45 bp):
TTTCAATTATGGCATCCTTTCATGCCTTTAATGAACCATTATGCA
Found at i:1138251 original size:54 final size:54
Alignment explanation
Indices: 1138193--1138552 Score: 399
Period size: 54 Copynumber: 6.7 Consensus size: 54
1138183 AATATTTATT
* *
1138193 AACATACGATGAATTCTGTGGGTTGCACACATAGTGCCGAAACGGTTGTTCATC
1 AACATATGATGAATTCTGTGGATTGCACACATAGTGCCGAAACGGTTGTTCATC
* * * * * **
1138247 AACATATGATTATTTCTATGGGTTGTACACATAGTGTTGAAACGGTTGTTCATC
1 AACATATGATGAATTCTGTGGATTGCACACATAGTGCCGAAACGGTTGTTCATC
* * * *
1138301 AACATATGATGAAATCCGTGGATAGCACACAAAGTGCCGAAACGGTTGTTCATC
1 AACATATGATGAATTCTGTGGATTGCACACATAGTGCCGAAACGGTTGTTCATC
* * * *
1138355 AACATATGATGAATTCAT-TGAAATGCACACATAGTGCCGAAACGATTGTTCACC
1 AACATATGATGAATTC-TGTGGATTGCACACATAGTGCCGAAACGGTTGTTCATC
* * * * * *
1138409 GACATATGATGAATT-TCGTGAAATGTACACATAGTACCGAAA-GGTTGTTCATA
1 AACATATGATGAATTCT-GTGGATTGCACACATAGTGCCGAAACGGTTGTTCATC
* * *
1138462 AATATATGATGAATTTTGTGGGTTGCACACATAGTGCC-AAACGGTTGTTCATC
1 AACATATGATGAATTCTGTGGATTGCACACATAGTGCCGAAACGGTTGTTCATC
*
1138515 AACATATGATGAATTTCT-TGAAATT-CACACATAGTGCC
1 AACATATGATGAA-TTCTGTG-GATTGCACACATAGTGCC
1138553 TATTAGTTAA
Statistics
Matches: 255, Mismatches: 44, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
52 4 0.02
53 74 0.29
54 177 0.69
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (54 bp):
AACATATGATGAATTCTGTGGATTGCACACATAGTGCCGAAACGGTTGTTCATC
Found at i:1138305 original size:27 final size:27
Alignment explanation
Indices: 1138275--1138367 Score: 75
Period size: 27 Copynumber: 3.5 Consensus size: 27
1138265 TGGGTTGTAC
*
1138275 ACATAGTGTTGAAACGGTTGTTCATCA
1 ACATAGTGATGAAACGGTTGTTCATCA
* * * *
1138302 ACATA-TGATGAAATCCGTGGAT-AGCA
1 ACATAGTGATGAAA-CGGTTGTTCATCA
* **
1138328 CACAAAGTGCCGAAACGGTTGTTCATCA
1 -ACATAGTGATGAAACGGTTGTTCATCA
1138356 ACATA-TGATGAA
1 ACATAGTGATGAA
1138368 TTCATTGAAA
Statistics
Matches: 47, Mismatches: 15, Indels: 9
0.66 0.21 0.13
Matches are distributed among these distances:
26 15 0.32
27 23 0.49
28 9 0.19
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (27 bp):
ACATAGTGATGAAACGGTTGTTCATCA
Found at i:1138935 original size:22 final size:22
Alignment explanation
Indices: 1138889--1138935 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1138879 TCAGTACCCC
*
1138889 TACTATGGTATCGATACTACTA
1 TACTATGGTATCGATACTACCA
* *
1138911 TACTGTGGTATCGATACTCCCA
1 TACTATGGTATCGATACTACCA
1138933 TAC
1 TAC
1138936 AGTATAGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (22 bp):
TACTATGGTATCGATACTACCA
Found at i:1141020 original size:30 final size:30
Alignment explanation
Indices: 1140986--1141044 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
1140976 TTTTGGTCCC
* **
1140986 TAAACTTTTTAAAGTTTATACTTTAGTCAT
1 TAAACTTTTCAAAACTTATACTTTAGTCAT
*
1141016 TAAACTTTTCAAAACTTATATTTTAGTCA
1 TAAACTTTTCAAAACTTATACTTTAGTCA
1141045 CTAAGTGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (30 bp):
TAAACTTTTCAAAACTTATACTTTAGTCAT
Found at i:1144975 original size:17 final size:17
Alignment explanation
Indices: 1144953--1145004 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1144943 GCATTAAAAA
1144953 AAGCATGATGTTCATTT
1 AAGCATGATGTTCATTT
*
1144970 AAGCATGCAT-TGCATTT
1 AAGCATG-ATGTTCATTT
*
1144987 TAGCAT-ATAGTTCATTT
1 AAGCATGAT-GTTCATTT
1145004 A
1 A
1145005 GGAAAGTAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 2 0.07
17 24 0.86
18 2 0.07
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.40
Consensus pattern (17 bp):
AAGCATGATGTTCATTT
Found at i:1145082 original size:17 final size:17
Alignment explanation
Indices: 1145027--1145114 Score: 70
Period size: 17 Copynumber: 5.2 Consensus size: 17
1145017 ATTTATGCAT
*
1145027 CTAGTTCATTAAATAAA
1 CTAGTTCATTAATTAAA
* *
1145044 CTACTTCATTAA-TAATG
1 CTAGTTCATTAATTAA-A
*
1145061 TTAGTTCATTAATTAAA
1 CTAGTTCATTAATTAAA
* * *
1145078 CTAGTTAAATCATTAAA
1 CTAGTTCATTAATTAAA
** *
1145095 CTAGTGAATTAATCAAA
1 CTAGTTCATTAATTAAA
1145112 CTA
1 CTA
1145115 ACTCATAATT
Statistics
Matches: 56, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
16 3 0.05
17 50 0.89
18 3 0.05
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:1147288 original size:15 final size:15
Alignment explanation
Indices: 1147268--1147296 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1147258 TAACTCAGTT
1147268 GGATCCATTCGATAA
1 GGATCCATTCGATAA
1147283 GGATCCATTCGATA
1 GGATCCATTCGATA
1147297 TGGAGCCAAA
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:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (15 bp):
GGATCCATTCGATAA
Found at i:1150198 original size:48 final size:48
Alignment explanation
Indices: 1150048--1150198 Score: 198
Period size: 48 Copynumber: 3.1 Consensus size: 48
1150038 CATATAGTAC
* * *
1150048 TCATACGAAAATTCAA-TATATGTATTAAACAAAATTGATCGATAACCA
1 TCATACAAAAATGCAACT-TATGCATTAAACAAAATTGATCGATAACCA
* * * *
1150096 TCATACGAAAATGTAACTTATGCATTAAACAAAATAGATTGATAACCA
1 TCATACAAAAATGCAACTTATGCATTAAACAAAATTGATCGATAACCA
*
1150144 TTATACAAAAATGCAACTTAT-CATTAAACCAAAATTGATCGATAACCA
1 TCATACAAAAATGCAACTTATGCATTAAA-CAAAATTGATCGATAACCA
1150192 TCATACA
1 TCATACA
1150199 TCATACACAA
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
47 7 0.08
48 82 0.91
49 1 0.01
ACGTcount: A:0.48, C:0.17, G:0.08, T:0.28
Consensus pattern (48 bp):
TCATACAAAAATGCAACTTATGCATTAAACAAAATTGATCGATAACCA
Found at i:1150622 original size:32 final size:32
Alignment explanation
Indices: 1150581--1150644 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
1150571 CTCAGGAGTT
*
1150581 TGATTATGATCTACACAAGCATCCATAATCAC
1 TGATTATGATATACACAAGCATCCATAATCAC
*
1150613 TGATTATGATATATACAAGCATCCATAATCAC
1 TGATTATGATATACACAAGCATCCATAATCAC
1150645 ACACATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (32 bp):
TGATTATGATATACACAAGCATCCATAATCAC
Found at i:1150898 original size:20 final size:20
Alignment explanation
Indices: 1150873--1150918 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1150863 TATTACGGTG
*
1150873 TCGATACCTTTCTTTTGGTA
1 TCGATACCTTCCTTTTGGTA
1150893 TCGATACCTTCCTTTTGGTA
1 TCGATACCTTCCTTTTGGTA
1150913 TCGATA
1 TCGATA
1150919 ATTCTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.22, G:0.15, T:0.46
Consensus pattern (20 bp):
TCGATACCTTCCTTTTGGTA
Found at i:1157443 original size:20 final size:20
Alignment explanation
Indices: 1157418--1157478 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
1157408 TGATGCTAGA
1157418 AAGTTTGGGGATTGAATTAT
1 AAGTTTGGGGATTGAATTAT
*** *
1157438 AAGTTT-TCAAATG--TTA-
1 AAGTTTGGGGATTGAATTAT
1157454 AAGTTTGGGGATTGAATTAT
1 AAGTTTGGGGATTGAATTAT
1157474 AAGTT
1 AAGTT
1157479 CGCAAATGTT
Statistics
Matches: 29, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
16 6 0.21
17 6 0.21
19 6 0.21
20 11 0.38
ACGTcount: A:0.33, C:0.02, G:0.25, T:0.41
Consensus pattern (20 bp):
AAGTTTGGGGATTGAATTAT
Found at i:1157457 original size:36 final size:36
Alignment explanation
Indices: 1157417--1157495 Score: 140
Period size: 36 Copynumber: 2.2 Consensus size: 36
1157407 ATGATGCTAG
**
1157417 AAAGTTTGGGGATTGAATTATAAGTTTTCAAATGTT
1 AAAGTTTGGGGATTGAATTATAAGTTCGCAAATGTT
1157453 AAAGTTTGGGGATTGAATTATAAGTTCGCAAATGTT
1 AAAGTTTGGGGATTGAATTATAAGTTCGCAAATGTT
1157489 AAAGTTT
1 AAAGTTT
1157496 TAGATTGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.39
Consensus pattern (36 bp):
AAAGTTTGGGGATTGAATTATAAGTTCGCAAATGTT
Found at i:1159407 original size:4 final size:5
Alignment explanation
Indices: 1159383--1159415 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1159373 AACGGTCAAC
*
1159383 GGTCG GGTCG GGTCG GGTC- GGTCG GGTTG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
1159416 AGACCGGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.18, G:0.58, T:0.24
Consensus pattern (5 bp):
GGTCG
Found at i:1159407 original size:14 final size:15
Alignment explanation
Indices: 1159383--1159415 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1159373 AACGGTCAAC
1159383 GGTCGGGTCGGGTCG
1 GGTCGGGTCGGGTCG
*
1159398 GGTC-GGTCGGGTTG
1 GGTCGGGTCGGGTCG
1159412 GGTC
1 GGTC
1159416 AGACCGGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.00, C:0.18, G:0.58, T:0.24
Consensus pattern (15 bp):
GGTCGGGTCGGGTCG
Found at i:1159423 original size:19 final size:19
Alignment explanation
Indices: 1159382--1159424 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1159372 CAACGGTCAA
* **
1159382 CGGTCGGGTCGGGTCGGGT
1 CGGTCGGGTCGGGTCAGAC
*
1159401 CGGTCGGGTTGGGTCAGAC
1 CGGTCGGGTCGGGTCAGAC
1159420 CGGTC
1 CGGTC
1159425 AAACCGGTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.05, C:0.23, G:0.51, T:0.21
Consensus pattern (19 bp):
CGGTCGGGTCGGGTCAGAC
Found at i:1159424 original size:9 final size:9
Alignment explanation
Indices: 1159412--1159490 Score: 61
Period size: 9 Copynumber: 8.3 Consensus size: 9
1159402 GGTCGGGTTG
*
1159412 GGTCAGACC
1 GGTCAAACC
1159421 GGTCAAACC
1 GGTCAAACC
*
1159430 GGTTCGAACC
1 GG-TCAAACC
1159440 GGTCGAAACC
1 GGTC-AAACC
*
1159450 AGTCAAACC
1 GGTCAAACC
1159459 GGTCAGAA-C
1 GGTCA-AACC
*
1159468 GGTTGAAAACC
1 GG-T-CAAACC
*
1159479 GGTCAAATC
1 GGTCAAACC
1159488 GGT
1 GGT
1159491 TTCCATGCCT
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
9 31 0.55
10 21 0.38
11 4 0.07
ACGTcount: A:0.30, C:0.27, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1159458 original size:29 final size:30
Alignment explanation
Indices: 1159422--1159491 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
1159412 GGTCAGACCG
1159422 GTCAAACCGGTTC-GAACCGGTCG-AAACCA
1 GTCAAACCGGTTCAGAA-CGGTCGAAAACCA
* *
1159451 GTCAAACCGG-TCAGAACGGTTGAAAACCG
1 GTCAAACCGGTTCAGAACGGTCGAAAACCA
*
1159480 GTCAAATCGGTT
1 GTCAAACCGGTT
1159492 TCCATGCCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 7 0.20
29 27 0.77
30 1 0.03
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.17
Consensus pattern (30 bp):
GTCAAACCGGTTCAGAACGGTCGAAAACCA
Found at i:1166663 original size:19 final size:19
Alignment explanation
Indices: 1166617--1166675 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
1166607 TCGGGTCGGG
*
1166617 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGGT
*
1166636 TCAGGCCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
1166655 TC-GAACCGGTCGAAACCGGT
1 TCAG-ACCGGTC-AAACCGGT
1166675 T
1 T
1166676 GAAAACCAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
18 1 0.03
19 25 0.71
20 9 0.26
ACGTcount: A:0.25, C:0.31, G:0.27, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:1175001 original size:21 final size:22
Alignment explanation
Indices: 1174972--1175012 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1174962 GTTTCGACTG
*
1174972 AGTTCAAATAATTA-AAGATAT
1 AGTTAAAATAATTACAAGATAT
1174993 AGTTAAAATAATTACAAGAT
1 AGTTAAAATAATTACAAGAT
1175013 TGGAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.32
Consensus pattern (22 bp):
AGTTAAAATAATTACAAGATAT
Found at i:1184852 original size:28 final size:28
Alignment explanation
Indices: 1184820--1184874 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
1184810 ATGTATCTAG
* * *
1184820 TATTAGAAACTAGATATCAAATACCATA
1 TATTAGAAAATAGAAATCAAAAACCATA
1184848 TATTAGAAAATAGAAATCAAAAACCAT
1 TATTAGAAAATAGAAATCAAAAACCAT
1184875 GTTTTTAATT
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:0.55, C:0.13, G:0.07, T:0.25
Consensus pattern (28 bp):
TATTAGAAAATAGAAATCAAAAACCATA
Found at i:1193032 original size:20 final size:20
Alignment explanation
Indices: 1193007--1193060 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1192997 GTAAACAGTG
1193007 AGGGTATCGGTACCTGTAAA
1 AGGGTATCGGTACCTGTAAA
* **
1193027 AGGGTATCAGTACCTGTAGC
1 AGGGTATCGGTACCTGTAAA
1193047 AGGGTATCGGTACC
1 AGGGTATCGGTACC
1193061 CCTGTAGCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (20 bp):
AGGGTATCGGTACCTGTAAA
Found at i:1193577 original size:45 final size:45
Alignment explanation
Indices: 1193518--1193722 Score: 315
Period size: 45 Copynumber: 4.6 Consensus size: 45
1193508 CATTTCTTAT
* * *
1193518 CAATCTACTTACCATTTATCCCATAAGCTCGTAAGCTTAGTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* *
1193563 CAATATAGTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
1193608 CAATATACTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTATAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT-TAC
*
1193653 CAATATACTTATCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* *
1193698 CAATACACTTTCCATTT-TTCCATAA
1 CAATATACTTACCATTTATTCCATAA
1193723 CCATATACCA
Statistics
Matches: 147, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
44 34 0.23
45 86 0.59
46 27 0.18
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (45 bp):
CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
Found at i:1194999 original size:14 final size:14
Alignment explanation
Indices: 1194980--1195015 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1194970 TGACCAACAG
*
1194980 AATCTGTTTTGCAC
1 AATCTGCTTTGCAC
*
1194994 AATCTGCTTTGCAG
1 AATCTGCTTTGCAC
1195008 AATCTGCT
1 AATCTGCT
1195016 GTCCGTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (14 bp):
AATCTGCTTTGCAC
Found at i:1197907 original size:33 final size:32
Alignment explanation
Indices: 1197868--1197956 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 32
1197858 ATCGTCTCTC
1197868 ATTTTTTCTCTTTTTCTTTTATTTTCTTTTTCT
1 ATTTTTT-TCTTTTTCTTTTATTTTCTTTTTCT
* *
1197901 ATTTTTTTC---TAC-TTTGTTTTCTTTTTCT
1 ATTTTTTTCTTTTTCTTTTATTTTCTTTTTCT
* *
1197929 -TTTTATTCTTTTTCTATTTTTTTTCTTT
1 ATTTTTTTCTTTTTCT-TTTATTTTCTTT
1197957 CTTATAATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
27 7 0.15
28 15 0.33
29 2 0.04
30 2 0.04
32 13 0.28
33 7 0.15
ACGTcount: A:0.07, C:0.13, G:0.01, T:0.79
Consensus pattern (32 bp):
ATTTTTTTCTTTTTCTTTTATTTTCTTTTTCT
Found at i:1197949 original size:9 final size:10
Alignment explanation
Indices: 1197894--1197951 Score: 64
Period size: 10 Copynumber: 5.5 Consensus size: 10
1197884 TTTTATTTTC
1197894 TTTTTCTATT
1 TTTTTCTATT
1197904 TTTTTCTACTT
1 TTTTTCTA-TT
1197915 TGTTTTCT-TT
1 T-TTTTCTATT
*
1197925 TTCTTTTTATT
1 TT-TTTCTATT
1197936 CTTTTTCTATT
1 -TTTTTCTATT
1197947 TTTTT
1 TTTTT
1197952 TCTTTCTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
9 1 0.02
10 20 0.49
11 12 0.29
12 8 0.20
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTTTCTATT
Found at i:1200246 original size:14 final size:14
Alignment explanation
Indices: 1200227--1200257 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1200217 AATAGTACCA
1200227 TGAACAGTGAATAG
1 TGAACAGTGAATAG
*
1200241 TGAACATTGAATAG
1 TGAACAGTGAATAG
1200255 TGA
1 TGA
1200258 GGGTATCGAT
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:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (14 bp):
TGAACAGTGAATAG
Found at i:1200256 original size:21 final size:19
Alignment explanation
Indices: 1200215--1200257 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
1200205 ATTCTTTTTA
*
1200215 TGAATAGTACCATGAACAG
1 TGAATAGTAACATGAACAG
*
1200234 TGAATAGTGAACATTGAATAG
1 TGAATAGT-AACA-TGAACAG
1200255 TGA
1 TGA
1200258 GGGTATCGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 3 0.15
21 9 0.45
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (19 bp):
TGAATAGTAACATGAACAG
Found at i:1200808 original size:45 final size:45
Alignment explanation
Indices: 1200749--1200953 Score: 306
Period size: 45 Copynumber: 4.6 Consensus size: 45
1200739 CATTTCTTAT
* * *
1200749 CAATCTACTTACCATTTATCCCATAAGCTCGTAAGCTTAGTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* * *
1200794 CAATATAGTTACCATTTGTTCAATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
*
1200839 CAATATACTTACCA-TTATTCCATAAGCTCGTAAGCGTATTTATAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT-TAC
1200884 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* *
1200929 CAATACACTTGCCATTT-TTCCATAA
1 CAATATACTTACCATTTATTCCATAA
1200954 CCATATACCA
Statistics
Matches: 145, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
44 32 0.22
45 87 0.60
46 26 0.18
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (45 bp):
CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
Found at i:1210648 original size:93 final size:93
Alignment explanation
Indices: 1210543--1210727 Score: 370
Period size: 93 Copynumber: 2.0 Consensus size: 93
1210533 CTTAAATTTT
1210543 TTATCTAGATATTAAGTAAGTTTTTTTAATTAAGCTAATGTGATTATAAAGTAGTATTTATTCTA
1 TTATCTAGATATTAAGTAAGTTTTTTTAATTAAGCTAATGTGATTATAAAGTAGTATTTATTCTA
1210608 AATACTCTCAACAATTTGATAATGAATC
66 AATACTCTCAACAATTTGATAATGAATC
1210636 TTATCTAGATATTAAGTAAGTTTTTTTAATTAAGCTAATGTGATTATAAAGTAGTATTTATTCTA
1 TTATCTAGATATTAAGTAAGTTTTTTTAATTAAGCTAATGTGATTATAAAGTAGTATTTATTCTA
1210701 AATACTCTCAACAATTTGATAATGAAT
66 AATACTCTCAACAATTTGATAATGAAT
1210728 GGTCAATCAC
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (93 bp):
TTATCTAGATATTAAGTAAGTTTTTTTAATTAAGCTAATGTGATTATAAAGTAGTATTTATTCTA
AATACTCTCAACAATTTGATAATGAATC
Found at i:1211476 original size:81 final size:82
Alignment explanation
Indices: 1211381--1211530 Score: 221
Period size: 81 Copynumber: 1.8 Consensus size: 82
1211371 ACTTTAGCGG
* * * *
1211381 CGTTTCTTAAACAAACGCCGCTATAGAGTAGTACTATAGCGGCATTTTTATATAAACGCTGCAAT
1 CGTTTCTTAAACAAACGCCACAACAGAGTAGTACTATAGCGGCATTTTTATACAAACGCTGCAAT
1211446 AGGTACATATGTAATGA
66 AGGTACATATGTAATGA
* * * *
1211463 CGTTT-TTCAACAAACGCCACAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACTCTGCAAT
1 CGTTTCTTAAACAAACGCCACAACAGAGTAGTACTATAGCGGCATTTTTATACAAACGCTGCAAT
1211527 AGGT
66 AGGT
1211531 CCATCTATAG
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
81 55 0.92
82 5 0.08
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (82 bp):
CGTTTCTTAAACAAACGCCACAACAGAGTAGTACTATAGCGGCATTTTTATACAAACGCTGCAAT
AGGTACATATGTAATGA
Found at i:1211509 original size:41 final size:41
Alignment explanation
Indices: 1211370--1211721 Score: 167
Period size: 41 Copynumber: 8.5 Consensus size: 41
1211360 CACAAAATGA
* *
1211370 TACTTTAGCGGCGTTTCTTAAACAAACGCCGCTATAGAGTAG
1 TACTTTAGCGGCGTTT-TTATACAAACGCCGCAATAGAGTAG
* * * * *
1211412 TACTATAGCGGCATTTTTATATAAACGCTGCAATAG-GTACA
1 TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGTA-G
* ** * * *
1211453 TA-TGTAATGACGTTTTTCA-ACAAACGCCACAACAGAGTAG
1 TACTTTAGCGGCGTTTTT-ATACAAACGCCGCAATAGAGTAG
* *
1211493 TACTTTAGCGGCGTTTTTATACAAACTCTGCAATAG-GTCCA-
1 TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGT--AG
* * * * * * *
1211534 T-CTATAGTGGCATTTTTTTCTGACAAACGCCGCAAAAGATTTG
1 TACTTTAGCGGC--GTTTTTAT-ACAAACGCCGCAATAGAGTAG
* * * * **
1211577 TACTTTAGCGGCGATTTTATAAAAATGCCACAATAGAGTTC
1 TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGTAG
* * * * * * * * * *
1211618 TCCTATAGTGGCTTTTTTTCTAATAAACGCTGCAACATATTAG
1 TACTTTAGCGGC-GTTTTTAT-ACAAACGCCGCAATAGAGTAG
* * * * * *
1211661 AACTTTAGCGGCGTTTTTACACAAACGTCGCAAAAAAATATG
1 TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGTA-G
1211703 TACTTTAGCGGCGTTTTTA
1 TACTTTAGCGGCGTTTTTA
1211722 AACGCCGCTA
Statistics
Matches: 220, Mismatches: 74, Indels: 32
0.67 0.23 0.10
Matches are distributed among these distances:
40 38 0.17
41 84 0.38
42 55 0.25
43 34 0.15
44 9 0.04
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (41 bp):
TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGTAG
Found at i:1211550 original size:81 final size:82
Alignment explanation
Indices: 1211390--1211686 Score: 258
Period size: 84 Copynumber: 3.6 Consensus size: 82
1211380 GCGTTTCTTA
* * * * * * *
1211390 AACAAACGCCGCTATAGAGTAGTACTATAGCGGCATTTTTATATAAACGCTGCAATAGGTACATA
1 AACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACTCTGCAATAGGTACATC
* * * *
1211455 TGTAATGACGTTTTTC-
66 TATAGTGGCATTTTTCT
* *
1211471 AACAAACGCCACAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACTCTGCAATAGGTCCATC
1 AACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACTCTGCAATAGGTACATC
1211536 TATAGTGGCATTTTTTTCT
66 TATAGTGGCA--TTTTTCT
* * * * * * ** *
1211555 GACAAACGCCGCAAAAGATTTGTACTTTAGCGGCGATTTTATA-AAAATGCCACAATAGAGTTC-
1 AACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACT-CTGCAATAG-GTACA
*
1211618 TCCTATAGTGGCTTTTTTTCT
64 T-CTATAGTGGC-ATTTTTCT
* * * * * *
1211639 AATAAACGCTGCAACATATTAGAACTTTAGCGGCGTTTTTACACAAAC
1 AACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAAC
1211687 GTCGCAAAAA
Statistics
Matches: 174, Mismatches: 34, Indels: 12
0.79 0.15 0.05
Matches are distributed among these distances:
81 62 0.36
83 10 0.06
84 86 0.49
85 16 0.09
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (82 bp):
AACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACTCTGCAATAGGTACATC
TATAGTGGCATTTTTCT
Found at i:1216429 original size:43 final size:43
Alignment explanation
Indices: 1216382--1216652 Score: 416
Period size: 43 Copynumber: 6.3 Consensus size: 43
1216372 ACCAGATCTT
* *
1216382 TTGCGGTGTTTGTGGGAAAAACGCCGCTAAATCTCAAGACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTA
* *
1216425 TTGCGGCATTTGTGGAAAAAACGCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTA
*
1216468 TTGCGGCGTTTGTGGGAAAAATGCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTA
* *
1216511 TTGCGGCGTTTTTGGGAAAAATGCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTA
* * *
1216554 TTGCGGCATTTGTGGGAAAAACGCCACTAAATATCAACACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTA
* * * *
1216597 TTGCGGTGTTTGTTGGACAAACGCCGCTAAATATCAACACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTA
1216640 TTGCGGCGTTTGT
1 TTGCGGCGTTTGT
1216653 AACCCCGCTA
Statistics
Matches: 209, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 209 1.00
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (43 bp):
TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTA
Found at i:1217935 original size:12 final size:12
Alignment explanation
Indices: 1217918--1217953 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1217908 AGAGTAGAAA
1217918 GAAGGAAAAGAG
1 GAAGGAAAAGAG
1217930 GAAGGAAAAGAG
1 GAAGGAAAAGAG
*
1217942 AAAGAGAAAAGA
1 GAAG-GAAAAGA
1217954 AAATGGATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 15 0.68
13 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (12 bp):
GAAGGAAAAGAG
Found at i:1222707 original size:21 final size:21
Alignment explanation
Indices: 1222681--1222721 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1222671 GACCGTTACA
1222681 CTGGGGGGGAATCGGTACCCC
1 CTGGGGGGGAATCGGTACCCC
1222702 CTGGGGGGGAATCGGTACCC
1 CTGGGGGGGAATCGGTACCC
1222722 TTTGGACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.15, C:0.27, G:0.44, T:0.15
Consensus pattern (21 bp):
CTGGGGGGGAATCGGTACCCC
Found at i:1223010 original size:19 final size:20
Alignment explanation
Indices: 1222986--1223025 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1222976 AATTTAATCG
*
1222986 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
1223005 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
1223025 A
1 A
1223026 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:1224261 original size:19 final size:20
Alignment explanation
Indices: 1224218--1224265 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1224208 TCTAAATCTT
*
1224218 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1224238 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1224257 TTTTCAAAA
1 TTTTCAAAA
1224266 GAAAATTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1224978 original size:21 final size:21
Alignment explanation
Indices: 1224944--1224984 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1224934 TTTAAGATTC
1224944 CCCAGAGGGAACAGATTCCCT
1 CCCAGAGGGAACAGATTCCCT
* *
1224965 CCCAGGGGGTACAGATTCCC
1 CCCAGAGGGAACAGATTCCC
1224985 CGGGAACAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.34, G:0.27, T:0.15
Consensus pattern (21 bp):
CCCAGAGGGAACAGATTCCCT
Found at i:1225961 original size:20 final size:20
Alignment explanation
Indices: 1225917--1225961 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1225907 CAGCAAGAGG
*
1225917 GTATCGATACCAAAGGTTTA
1 GTATCGATACCAAAGGGTTA
* *
1225937 TTATCGATACTAAAGGGTTA
1 GTATCGATACCAAAGGGTTA
1225957 GTATC
1 GTATC
1225962 TGTACCTTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (20 bp):
GTATCGATACCAAAGGGTTA
Found at i:1228180 original size:2 final size:2
Alignment explanation
Indices: 1228071--1228164 Score: 93
Period size: 2 Copynumber: 47.0 Consensus size: 2
1228061 TTTAAACAAC
1228071 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
* * * * * *
1228113 TA TG TA TA TA TA TG TG TA TA TG T- TA CA CA TA TA TCA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
*
1228155 TA CA TA TA TA
1 TA TA TA TA TA
1228165 CACATAAGTA
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
1 2 0.03
2 73 0.92
3 4 0.05
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1228531 original size:20 final size:20
Alignment explanation
Indices: 1228508--1228547 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1228498 AATTTGGCAA
*
1228508 CAAAAATTTCCAAAACAAAT
1 CAAAAATTTCCAAAAAAAAT
* *
1228528 CAAAATTTTTCAAAAAAAAT
1 CAAAAATTTCCAAAAAAAAT
1228548 AATATTTCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (20 bp):
CAAAAATTTCCAAAAAAAAT
Found at i:1229018 original size:16 final size:16
Alignment explanation
Indices: 1228997--1229031 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1228987 TCAATTGCAT
1228997 GTCAGGTTCATAACAG
1 GTCAGGTTCATAACAG
* *
1229013 GTCAGGTTGATAATAG
1 GTCAGGTTCATAACAG
1229029 GTC
1 GTC
1229032 GGGTAATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (16 bp):
GTCAGGTTCATAACAG
Found at i:1229992 original size:18 final size:18
Alignment explanation
Indices: 1229971--1230012 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1229961 TAATACTATA
1229971 AATAACATTATT-TATATT
1 AATAA-ATTATTATATATT
*
1229989 AATAATTTATTATATATT
1 AATAAATTATTATATATT
*
1230007 ATTAAA
1 AATAAA
1230013 ATAAAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
AATAAATTATTATATATT
Found at i:1230036 original size:30 final size:29
Alignment explanation
Indices: 1229999--1230097 Score: 102
Period size: 27 Copynumber: 3.6 Consensus size: 29
1229989 AATAATTTAT
1229999 TATATATTATTAAAATAAAAATATTATTA
1 TATATATTATTAAAATAAAAATATTATTA
* *
1230028 TCATATATTATTATAAT-ATAAT-TTATTA
1 T-ATATATTATTAAAATAAAAATATTATTA
* *
1230056 TAT-TATTA-TAATATGAAAAATA-TAATA
1 TATATATTATTAAAAT-AAAAATATTATTA
1230083 T-TATATTATTAAAAT
1 TATATATTATTAAAAT
1230098 TATTAATAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
25 4 0.07
26 6 0.11
27 16 0.28
28 12 0.21
29 5 0.09
30 14 0.25
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (29 bp):
TATATATTATTAAAATAAAAATATTATTA
Found at i:1230065 original size:18 final size:18
Alignment explanation
Indices: 1230001--1230069 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 18
1229991 TAATTTATTA
* *
1230001 TATATTATTAAAATA-AA
1 TATATTATTATAATATAT
* *
1230018 AATATTATTATCATATAT
1 TATATTATTATAATATAT
* *
1230036 TAT-TATAATATAATTTAT
1 TATAT-TATTATAATATAT
1230054 TATATTATTATAATAT
1 TATATTATTATAATAT
1230070 GAAAAATATA
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
17 13 0.33
18 25 0.64
19 1 0.03
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATTATTATAATATAT
Found at i:1230084 original size:22 final size:22
Alignment explanation
Indices: 1230054--1230105 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1230044 TATAATTTAT
*
1230054 TATATTATTATAATATGAAAAA
1 TATAATATTATAATATGAAAAA
* * *
1230076 TATAATATTATATTATTAAAAT
1 TATAATATTATAATATGAAAAA
1230098 TATTAATA
1 TA-TAATA
1230106 AATATATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TATAATATTATAATATGAAAAA
Found at i:1230963 original size:31 final size:31
Alignment explanation
Indices: 1230886--1230963 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
1230876 TAAAAAAACA
*
1230886 TAAGTTTTGATCACTAACATTATTATTTTAT
1 TAAGTTTTGATCACTTACATTATTATTTTAT
* * *
1230917 TAAGTTTTGGTCACTTACGTTATTGTTTTAT
1 TAAGTTTTGATCACTTACATTATTATTTTAT
1230948 TAAGTTTTGATCACTT
1 TAAGTTTTGATCACTT
1230964 GGACGTTGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.53
Consensus pattern (31 bp):
TAAGTTTTGATCACTTACATTATTATTTTAT
Found at i:1237965 original size:45 final size:45
Alignment explanation
Indices: 1237914--1238019 Score: 160
Period size: 45 Copynumber: 2.4 Consensus size: 45
1237904 GACCAATCTG
* *
1237914 AAAGATTGACTCCTCTTTGCGAGAAAGTCAA-GAAGGACAACACTA
1 AAAGATTGACTCCTCTTTACGAGAAAATCAAGGAA-GACAACACTA
*
1237959 AAAGATTTACTCCTCTTTACGAGAAAATCAAGGAAGACAACACTA
1 AAAGATTGACTCCTCTTTACGAGAAAATCAAGGAAGACAACACTA
*
1238004 AAATATTGACTCCTCT
1 AAAGATTGACTCCTCT
1238020 GCATAAGGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
45 52 0.95
46 3 0.05
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.24
Consensus pattern (45 bp):
AAAGATTGACTCCTCTTTACGAGAAAATCAAGGAAGACAACACTA
Found at i:1238032 original size:45 final size:46
Alignment explanation
Indices: 1237914--1238035 Score: 115
Period size: 45 Copynumber: 2.7 Consensus size: 46
1237904 GACCAATCTG
*** *
1237914 AAAGATTGACTCCTCTTTGCGA-GAAAGTCAA-GAAGGACAACACTA
1 AAAGATTGACTCCTCTGCACAAGGAAA-TCAAGGAAGGACAACACTA
* ** * *
1237959 AAAGATTTACTCCTCTTTACGAGAAAATCAAGGAA-GACAACACTA
1 AAAGATTGACTCCTCTGCACAAGGAAATCAAGGAAGGACAACACTA
* *
1238004 AAATATTGACTCCTCTGCATAAGGAAATCAAG
1 AAAGATTGACTCCTCTGCACAAGGAAATCAAG
1238036 AATACCAAAG
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
45 59 0.91
46 6 0.09
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (46 bp):
AAAGATTGACTCCTCTGCACAAGGAAATCAAGGAAGGACAACACTA
Found at i:1238051 original size:38 final size:38
Alignment explanation
Indices: 1238008--1238260 Score: 233
Period size: 38 Copynumber: 6.9 Consensus size: 38
1237998 ACACTAAAAT
* * * *
1238008 ATTGACTCCTCTGCATAAGGAAATCAAGAATACCAAAG
1 ATTGACTTCTCTTCATGAGGAAATCAAGAATAACAAAG
1238046 ATTGACTTCTCTTCATGA-GAAAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCATGAGGAAA-TCAAGAATAACAAAG
* *
1238084 ATTGACTTCTCTTCACT-AGGAAGTCAATAATAACAAAG
1 ATTGACTTCTCTTCA-TGAGGAAATCAAGAATAACAAAG
*
1238122 ATTGACTTCTCTTCATGAGG-----AAG--T--CAATG
1 ATTGACTTCTCTTCATGAGGAAATCAAGAATAACAAAG
* ** * * *
1238151 ATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAAG
1 ATTGACTTCTCTTCATGAGGAAATCAAGAATAACAAAG
* * *
1238189 ATTGCCTTCTCTTCATGAGGAAGTCAAGAATAACATAG
1 ATTGACTTCTCTTCATGAGGAAATCAAGAATAACAAAG
** *
1238227 ATTGACTTCTCTTCACAAGG-AGTCAAGAATAACA
1 ATTGACTTCTCTTCATGAGGAAATCAAGAATAACA
1238261 TTGAAAATTG
Statistics
Matches: 179, Mismatches: 23, Indels: 27
0.78 0.10 0.12
Matches are distributed among these distances:
29 21 0.12
31 1 0.01
33 2 0.01
34 2 0.01
36 1 0.01
37 19 0.11
38 129 0.72
39 4 0.02
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (38 bp):
ATTGACTTCTCTTCATGAGGAAATCAAGAATAACAAAG
Found at i:1238170 original size:29 final size:29
Alignment explanation
Indices: 1238121--1238176 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1238111 TAATAACAAA
* *
1238121 GATTGACTTCTCTTCATGAGGAAGTCAAT
1 GATTGACTCCTCTTCACGAGGAAGTCAAT
* *
1238150 GATTGACTCCTCTTCGCGAGGGAGTCA
1 GATTGACTCCTCTTCACGAGGAAGTCA
1238177 GGAATAACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (29 bp):
GATTGACTCCTCTTCACGAGGAAGTCAAT
Found at i:1238191 original size:67 final size:67
Alignment explanation
Indices: 1238083--1238215 Score: 203
Period size: 67 Copynumber: 2.0 Consensus size: 67
1238073 GAATAACAAA
* * *
1238083 GATTGACTTCTCTTCACTAGGAAGTCAATAATAACAAAGATTGACTTCTCTTCATGAGGAAGTCA
1 GATTGACTCCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCATGAGGAAGTCA
1238148 AT
66 AT
* * * *
1238150 GATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAAGATTGCCTTCTCTTCATGAGGAAGTCA
1 GATTGACTCCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCATGAGGAAGTCA
1238215 A
66 A
1238216 GAATAACATA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (67 bp):
GATTGACTCCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCATGAGGAAGTCA
AT
Found at i:1238966 original size:42 final size:40
Alignment explanation
Indices: 1238891--1238994 Score: 145
Period size: 42 Copynumber: 2.5 Consensus size: 40
1238881 ACCCGAAGGT
*
1238891 CTTACGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTACGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
* *
1238931 CTTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGA
1 CTTAC-GATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGA
*
1238973 CTTACTGATGGCCCGAAAGACT
1 CTTAC-GATGGCCCGAAGGACT
1238995 AACCAATTTG
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 5 0.09
41 15 0.27
42 35 0.64
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (40 bp):
CTTACGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
Found at i:1239223 original size:260 final size:255
Alignment explanation
Indices: 1238743--1239374 Score: 1027
Period size: 260 Copynumber: 2.5 Consensus size: 255
1238733 ATCTTATAGT
1238743 CCAATTT-GGGAAATAGTTTACTA-GTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAAT
1 CCAATTTGGGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAAT
* *
1238806 TTCATTTTCTGAAAATATTAAACGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAATTCATG
66 TTCATTTTATGAAAA-ATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAATTCATG
*
1238871 AAAACATCTTACCCGAAGGTCTTACGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTAC
130 AAAACATCCTACCCGAAGGTCTTACGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTAC
1238936 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTAA
195 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTAA
1238997 CCAATTTGGGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAAT
1 CCAATTTGGGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAAT
* * * *
1239062 TTCATTTTATGAAAAGATTTAAATGAGGAACTTTGGAAATCGCTTTCTCATTTTTTAAATTTTAT
66 TTCATTTTATGAAAA-A-TTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAATTCA-
1239127 GTGAAAACATCCTACCCGAAGGTCTTACGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGAC
128 -TGAAAACATCCTACCCGAAGGTCTTAC-GATGGCCCGAAGGACTTATCATCTTGCTCGAAAGAC
* * ** * *
1239192 TTACAGATGACCTGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGCTTGAAGGACTTA
191 TTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTAA
* *
1239257 CCAATTTGGGGAAATAGTTTACTGGGTAAGAAAATTTGGAAATCGCTTTCTTACTTTTCAAAAAT
1 CCAATTTGGGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAAT
*
1239322 TTCATTTTCA-GAAAAAAATAAATGAGAAACTTTGGAAATCGCTTTCTCATTTT
66 TTCATTTT-ATG-AAAAATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTT
1239375 CAGACAACTT
Statistics
Matches: 352, Mismatches: 18, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
254 7 0.02
255 16 0.05
256 55 0.16
257 41 0.12
259 60 0.17
260 168 0.48
261 5 0.01
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (255 bp):
CCAATTTGGGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAAT
TTCATTTTATGAAAAATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAATTCATGA
AAACATCCTACCCGAAGGTCTTACGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACA
GATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTAA
Found at i:1256530 original size:3 final size:3
Alignment explanation
Indices: 1256512--1256553 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
1256502 ATGTAAATTT
* *
1256512 TAA TAA -AA TAAA TAA TAA TTA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1256554 ATGATATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1257913 original size:28 final size:30
Alignment explanation
Indices: 1257882--1257948 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
1257872 TTTAAGCAAG
*
1257882 TAAAGTATT-TT-TTCTCAAAATAAGTACT
1 TAAAGTATTATTCTGCTCAAAATAAGTACT
* *
1257910 TAAAGT-TTATTCTGGTCAAAATAGGTACT
1 TAAAGTATTATTCTGCTCAAAATAAGTACT
1257939 TAAAAGTATT
1 T-AAAGTATT
1257949 CAATTTTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 2 0.06
28 8 0.25
29 15 0.47
30 5 0.16
31 2 0.06
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (30 bp):
TAAAGTATTATTCTGCTCAAAATAAGTACT
Found at i:1258442 original size:10 final size:10
Alignment explanation
Indices: 1258427--1258494 Score: 55
Period size: 10 Copynumber: 6.1 Consensus size: 10
1258417 CATTTAAACG
1258427 ATAAACGAAC
1 ATAAACGAAC
1258437 ATAAACGAAAGC
1 ATAAACG-AA-C
1258449 AATAAACGAAC
1 -ATAAACGAAC
* *
1258460 ACAAACGAAAGAAT
1 ATAAAC----GAAC
1258474 ATAAACGAAC
1 ATAAACGAAC
1258484 ATAAACGAAC
1 ATAAACGAAC
1258494 A
1 A
1258495 ATACAAACAC
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
10 26 0.55
11 3 0.06
12 3 0.06
13 7 0.15
14 8 0.17
ACGTcount: A:0.62, C:0.18, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1258457 original size:23 final size:24
Alignment explanation
Indices: 1258427--1258492 Score: 107
Period size: 23 Copynumber: 2.8 Consensus size: 24
1258417 CATTTAAACG
*
1258427 ATAAACGAACATAAACGAAAGCA-
1 ATAAACGAACATAAACGAAAGAAT
*
1258450 ATAAACGAACACAAACGAAAGAAT
1 ATAAACGAACATAAACGAAAGAAT
1258474 ATAAACGAACATAAACGAA
1 ATAAACGAACATAAACGAA
1258493 CAATACAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
23 21 0.54
24 18 0.46
ACGTcount: A:0.62, C:0.17, G:0.12, T:0.09
Consensus pattern (24 bp):
ATAAACGAACATAAACGAAAGAAT
Found at i:1258502 original size:23 final size:23
Alignment explanation
Indices: 1258429--1258502 Score: 89
Period size: 23 Copynumber: 3.2 Consensus size: 23
1258419 TTTAAACGAT
1258429 AAACGAACATAAACGAAAGCAAT-
1 AAACGAACATAAACGAAA-CAATA
* *
1258452 AAACGAACACAAACGAAAGAATA
1 AAACGAACATAAACGAAACAATA
1258475 TAAACGAACATAAACG-AACAATA
1 -AAACGAACATAAACGAAACAATA
1258498 CAAAC
1 -AAAC
1258503 ACAAAAAACA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
22 3 0.07
23 27 0.61
24 14 0.32
ACGTcount: A:0.62, C:0.19, G:0.11, T:0.08
Consensus pattern (23 bp):
AAACGAACATAAACGAAACAATA
Found at i:1258776 original size:14 final size:14
Alignment explanation
Indices: 1258757--1258818 Score: 71
Period size: 14 Copynumber: 4.7 Consensus size: 14
1258747 GCCCTCTGTT
1258757 CGAACATAAATGAA
1 CGAACATAAATGAA
*
1258771 CGAACATAACCT-AA
1 CGAACATAA-ATGAA
1258785 CGAACATAAATGAA
1 CGAACATAAATGAA
1258799 C--A-A-AAATGAA
1 CGAACATAAATGAA
1258809 CGAACATAAA
1 CGAACATAAA
1258819 CAAACATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
10 8 0.20
11 1 0.03
12 2 0.05
13 2 0.05
14 26 0.65
15 1 0.03
ACGTcount: A:0.58, C:0.18, G:0.11, T:0.13
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:1274463 original size:35 final size:33
Alignment explanation
Indices: 1274398--1274466 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
1274388 ATAATATTTA
* * *
1274398 TTATAACAATGAAATTTTGTTACTATAATTAAC
1 TTATAACAATAAAATTTTGTCACAATAATTAAC
*
1274431 TTATCACAATAAAATATTTGTCACAATCAATTAAC
1 TTATAACAATAAAAT-TTTGTCACAAT-AATTAAC
1274466 T
1 T
1274467 ATTTCATCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 13 0.43
34 9 0.30
35 8 0.27
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.39
Consensus pattern (33 bp):
TTATAACAATAAAATTTTGTCACAATAATTAAC
Found at i:1275069 original size:200 final size:197
Alignment explanation
Indices: 1274777--1275153 Score: 520
Period size: 200 Copynumber: 1.9 Consensus size: 197
1274767 TTATAAGTTT
* *
1274777 TTATTATGACTAAATAATTTTTTACAATTTGTTATAGTGAAACAATATTATTTGTCACAAAGTTT
1 TTATTATGACTAAATAATTTTTTACAATTTGTTATAGTGAAACAACATTACTTGTCACAAAGTTT
* * * **
1274842 TATAATGAGAAATTAATATTTGTTATAAAATGTTAATTTGATTAAATAAATTTGTTACAATTTTT
66 TATAATGAGAAATTAATATTTGTTATAAAATATTAATTTGATTAAATAAATTTGTCAAAAGATTT
* *
1274907 TATTTTGACAAAATATTATGACTAAATAAATTTGACATAACTTTTTAATTTGATTAAATTTAATG
131 TATTCTGACAAAATATTATGACTAAATAAATTTAACATAACTTTTTAATTTGATTAAATTTAATG
1274972 TG
196 TG
* * * * **
1274974 TTATTGTGACTAAATCATTTTATTACAATTTGTTATTGTGAAAGAACATTACTTGTCACAATTTT
1 TTATTATGACTAAATAATTTT-TTACAATTTGTTATAGTGAAACAACATTACTTGTCACAA--AG
* * * * *
1275039 TTTTATATTGAGGAGTTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTGTCAAAAGA
63 TTTTATAATGAGAAATTAATATTTGTTATAAAATATTAATTTGATTAAATAAATTTGTCAAAAGA
* * *
1275104 TTTTATTCTGATAAAATATTTTGACTAAATAAATTTAACATAATTTTTTA
128 TTTTATTCTGACAAAATATTATGACTAAATAAATTTAACATAACTTTTTA
1275154 TTTCAACTAA
Statistics
Matches: 154, Mismatches: 23, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
197 19 0.12
198 35 0.23
200 100 0.65
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (197 bp):
TTATTATGACTAAATAATTTTTTACAATTTGTTATAGTGAAACAACATTACTTGTCACAAAGTTT
TATAATGAGAAATTAATATTTGTTATAAAATATTAATTTGATTAAATAAATTTGTCAAAAGATTT
TATTCTGACAAAATATTATGACTAAATAAATTTAACATAACTTTTTAATTTGATTAAATTTAATG
TG
Found at i:1275258 original size:22 final size:22
Alignment explanation
Indices: 1275233--1275275 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1275223 ATTTTATTTA
*
1275233 AATTTGTTATTATAACTAAAAT
1 AATTTGTTATGATAACTAAAAT
1275255 AATTTGTTATGATAACTAAAA
1 AATTTGTTATGATAACTAAAA
1275276 ATATATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (22 bp):
AATTTGTTATGATAACTAAAAT
Found at i:1277969 original size:36 final size:36
Alignment explanation
Indices: 1277918--1278240 Score: 520
Period size: 36 Copynumber: 8.9 Consensus size: 36
1277908 TTTGTGATTT
*
1277918 CATCGGCACTTCCGATTCAAGTCGAATGGAAGGAAG
1 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
*
1277954 CATTGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
1 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
* * *
1277990 TAACGGCACTTCCGATTCAAGTTGAACGGAAGGAAG
1 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
*
1278026 CAACGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
1 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
* *
1278062 CATCGGCATTTCCGATTCAAGTCGAACGGAAGAAAG
1 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
1278098 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
1 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
* *
1278134 CATCGGCACTTTCTGATTCAAGACGAACGGAAGGAAG
1 CATCGGCAC-TTCCGATTCAAGTCGAACGGAAGGAAG
* *
1278171 CATCGACACTTCCGATTCAAGTCGAACGGAATGAAG
1 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
*
1278207 CATCGGCACTTCCGATTCAAGTCGAATGGAAGGA
1 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGA
1278241 GGCAATTCAT
Statistics
Matches: 264, Mismatches: 22, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
36 231 0.88
37 33 0.12
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.19
Consensus pattern (36 bp):
CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
Found at i:1278264 original size:109 final size:107
Alignment explanation
Indices: 1277932--1278265 Score: 415
Period size: 109 Copynumber: 3.1 Consensus size: 107
1277922 GGCACTTCCG
* * * * *
1277932 ATTCAAGTCGAATGGAAGGAAGCATTGGCACTTCCGATTCAAGTCGAACGGAAGGAAGTAACGGC
1 ATTCAAGACGAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTCGAACGGAA-GAAGCATCGGC
* * *
1277997 ACTTCCGATTCAAGTTGAACGGAAGGAAGCAACGGCAC--TTCC
65 ACTTCCGATTCAAGTCGAACGGAAGGAAGCAA-TGCACTTTTTC
* *
1278039 GATTCAAGTCGAACGGAAGGAAGCATCGGCATTTCCGATTCAAGTCGAACGGAAGAAAGCATCGG
1 -ATTCAAGACGAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTCGAACGGAAG-AAGCATCGG
* *
1278104 CACTTCCGATTCAAGTCGAACGGAAGGAAGC-ATCGGCACTTTCTG
64 CACTTCCGATTCAAGTCGAACGGAAGGAAGCAAT--GCACTTTTTC
*
1278149 ATTCAAGACGAACGGAAGGAAGCATCGACACTTCCGATTCAAGTCGAACGGAATGAAGCATCGGC
1 ATTCAAGACGAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTCGAACGGAA-GAAGCATCGGC
* * *
1278214 ACTTCCGATTCAAGTCGAATGGAAGGAGGCAATTCATCTTTTTTC
65 ACTTCCGATTCAAGTCGAACGGAAGGAAGCAATGCA-C-TTTTTC
1278259 A-TCAAGA
1 ATTCAAGA
1278266 AGGTTGAGAA
Statistics
Matches: 199, Mismatches: 18, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
107 2 0.01
108 93 0.47
109 95 0.48
110 9 0.05
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (107 bp):
ATTCAAGACGAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTCGAACGGAAGAAGCATCGGCA
CTTCCGATTCAAGTCGAACGGAAGGAAGCAATGCACTTTTTC
Found at i:1281098 original size:138 final size:138
Alignment explanation
Indices: 1280949--1281211 Score: 334
Period size: 138 Copynumber: 1.9 Consensus size: 138
1280939 GTTACAAAAC
* * * * *
1280949 TTGTCACTATATAACATTGTTG-CGCCACAAAATAGGGAGAAATATTTCTGATAGTATATGTTTT
1 TTGTCACTATATAACATTGTTGACACCAAAAAATAAGGAGAAATAGTT-TGATAATATAT-TTTT
*
1281013 CATAATGATTAAAATATATAACTACA-ATAATAATTAATTAC-AAAAAACTTAAATTTTATTAAT
64 CATAATGATTAAAATATATAACTACACA-AATAATTAATTACAAAAAAAATTAAATTTTATTAAT
1281076 TACAATATATT
128 TACAATATATT
* * * ** * *
1281087 TTGTTACTATATATCATTTTTGACATTAAAAAATAAGGAGAAGTGGTTTGATAATATATTTTTCA
1 TTGTCACTATATAACATTGTTGACACCAAAAAATAAGGAGAAATAGTTTGATAATATATTTTTCA
* * *
1281152 TAATGATTAAAATATATAAGTACACAAATAATTTATTACAAAAAAAATTGAATTTTATTA
66 TAATGATTAAAATATATAACTACACAAATAATTAATTACAAAAAAAATTAAATTTTATTA
1281212 TTTTATGTGA
Statistics
Matches: 106, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
137 41 0.39
138 48 0.45
139 17 0.16
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (138 bp):
TTGTCACTATATAACATTGTTGACACCAAAAAATAAGGAGAAATAGTTTGATAATATATTTTTCA
TAATGATTAAAATATATAACTACACAAATAATTAATTACAAAAAAAATTAAATTTTATTAATTAC
AATATATT
Found at i:1289093 original size:466 final size:467
Alignment explanation
Indices: 1288409--1289342 Score: 1834
Period size: 466 Copynumber: 2.0 Consensus size: 467
1288399 CCCATCTTCC
1288409 TGCTAATCGTTCCAAAAATGAGTTCTGCCATCATAAAAGTGGAACCCAAATAACTCTACCAGACA
1 TGCTAATCGTTCCAAAAATGAGTTCTGCCATCATAAAAGTGGAACCCAAATAACTCTACCAGACA
1288474 AAAAGCCATTTGTAACACCCATATCCCGTATATGTTTCCGTATACAAATACAAATGTCACATTAC
66 AAAAGCCATTTGTAACACCCATATCCCGTATATGTTTCCGTATACAAATACAAATGTCACATTAC
1288539 TTTAAAAAATGTTTATTCATTTTTTTGTAAAGTCTTTAAAATTTTGTTGCAAACTTAATTTCCAC
131 TTTAAAAAATGTTTATTCATTTTTTTGTAAAGTCTTTAAAATTTTGTTGCAAACTTAATTTCCAC
*
1288604 ATAAATAAATGTAATAAATAAGTATTCATTAAGACCTATAACAAAATATCATGTTAAATTTAATT
196 ATAAATAAACGTAATAAATAAGTATTCATTAAGACCTATAACAAAATATCATGTTAAATTTAATT
*
1288669 ACATGCCAAACAAGTTTCCAAAATGATTTTTAGTGTCCTAATGTTACTGGTGAGCCAACCTTAGT
261 ACATGCCAAACAAGTTTCCAAAATGATTTTTAGTGTCCTAATGTTACTGGTAAGCCAACCTTAGT
1288734 GGATGATATATGCTGCTACAGCTATACTCCTTACTTGATTTTTCTATGTTGTTAACTACACGTGG
326 GGATGATATATGCTGCTACAGCTATACTCCTTACTTGATTTTTCTATGTTGTTAACTACACGTGG
1288799 AAACACACACGTTAAATGTTACTTAGTGAGTCATAATATTGTAAGTAACCCTTATGTATACATAA
391 AAACACACACGTTAAATGTTACTTAGTGAGTCATAATATTGTAAGTAACCCTTATGTATACATAA
1288864 GTATATTTTATT
456 GTATATTTTATT
*
1288876 TGCTAA-CGTTCCAGAAATGAGTTCTGCCATCATAAAAGTGGAACCCAAATAACTCTACCAGACA
1 TGCTAATCGTTCCAAAAATGAGTTCTGCCATCATAAAAGTGGAACCCAAATAACTCTACCAGACA
1288940 AAAAGCCATTTGTAACACCCATATCCCGTATATGTTTCCGTATACAAATACAAATGTCACATTAC
66 AAAAGCCATTTGTAACACCCATATCCCGTATATGTTTCCGTATACAAATACAAATGTCACATTAC
1289005 TTTAAAAAATGTTTATTCATTTTTTTGTAAAGTCTTTAAAATTTTGTTGCAAACTTAATTTCCAC
131 TTTAAAAAATGTTTATTCATTTTTTTGTAAAGTCTTTAAAATTTTGTTGCAAACTTAATTTCCAC
1289070 ATAAATAAACGTAATAAATAAGTATTCATTAAGACCTATAACAAAATATCATGTTAAATTTAATT
196 ATAAATAAACGTAATAAATAAGTATTCATTAAGACCTATAACAAAATATCATGTTAAATTTAATT
1289135 ACATGCCAAACAAGTTTCCAAAATGATTTTTAGTGTCCTAATGTTACTGGTAAGCCAACCTTAGT
261 ACATGCCAAACAAGTTTCCAAAATGATTTTTAGTGTCCTAATGTTACTGGTAAGCCAACCTTAGT
1289200 GGATGATATATGCTGCTACAGCTATACTCCTTACTTGATTTTTCTATGTTGTTAACTACACGTGG
326 GGATGATATATGCTGCTACAGCTATACTCCTTACTTGATTTTTCTATGTTGTTAACTACACGTGG
1289265 AAACACACACGTTAAATGTTACTTAGTGAGTCATAATATTGTAAGTAACCCTTATGTATACATAA
391 AAACACACACGTTAAATGTTACTTAGTGAGTCATAATATTGTAAGTAACCCTTATGTATACATAA
1289330 GTATATTTTATT
456 GTATATTTTATT
1289342 T
1 T
1289343 ACAATTATCA
Statistics
Matches: 464, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
466 458 0.99
467 6 0.01
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (467 bp):
TGCTAATCGTTCCAAAAATGAGTTCTGCCATCATAAAAGTGGAACCCAAATAACTCTACCAGACA
AAAAGCCATTTGTAACACCCATATCCCGTATATGTTTCCGTATACAAATACAAATGTCACATTAC
TTTAAAAAATGTTTATTCATTTTTTTGTAAAGTCTTTAAAATTTTGTTGCAAACTTAATTTCCAC
ATAAATAAACGTAATAAATAAGTATTCATTAAGACCTATAACAAAATATCATGTTAAATTTAATT
ACATGCCAAACAAGTTTCCAAAATGATTTTTAGTGTCCTAATGTTACTGGTAAGCCAACCTTAGT
GGATGATATATGCTGCTACAGCTATACTCCTTACTTGATTTTTCTATGTTGTTAACTACACGTGG
AAACACACACGTTAAATGTTACTTAGTGAGTCATAATATTGTAAGTAACCCTTATGTATACATAA
GTATATTTTATT
Found at i:1289482 original size:45 final size:45
Alignment explanation
Indices: 1289404--1289783 Score: 498
Period size: 45 Copynumber: 8.4 Consensus size: 45
1289394 ATTCATATTT
* * *
1289404 ATAATGCA-CCATTATGCATTTTCAACTATAACATACCTTTATGTTG
1 ATAATGCACCCA-TATGCA-TTTCAACTATAGCATACTTTTCTGTTG
* * *
1289450 ATAATGCACCCATATACATTTCAACTATAACATACTTTTCCGTTG
1 ATAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTG
* *
1289495 ATAATGCACCGATATCCATTT-AAGCTATAGCATACTTTTCTGTTG
1 ATAATGCACCCATATGCATTTCAA-CTATAGCATACTTTTCTGTTG
* * *
1289540 ATGATGCACCCATATGTATTTCAACTATAGTATACTTTTCTGTTG
1 ATAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTG
*
1289585 ATAATGCACCCATATGCATTTCAACTATAGTATACTTTTCTGTTG
1 ATAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTG
* * *
1289630 ATAATGCACCCATATGCATTACAACTATAGTATACTTTTTTGTTG
1 ATAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTG
* * * *
1289675 TTAATGCACCCATATGCATTTCAACTATA-TATACCTTTCTATTG
1 ATAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTG
* * *
1289719 ATAATGCACCCATATGCATTTCAACTATGGCAT-CTTTTTATGCTG
1 ATAATGCACCCATATGCATTTCAACTATAGCATAC-TTTTCTGTTG
1289764 ATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATT
1289784 AATATTTTCG
Statistics
Matches: 300, Mismatches: 29, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
44 42 0.14
45 240 0.80
46 15 0.05
47 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.39
Consensus pattern (45 bp):
ATAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTG
Found at i:1296542 original size:45 final size:45
Alignment explanation
Indices: 1296458--1296659 Score: 244
Period size: 45 Copynumber: 4.4 Consensus size: 45
1296448 ATTCATATTT
1296458 ATAATGCA-CCATTATGCATTTTTCAACTATAACATACTTTTATGTTG
1 ATAATGCACCCA-TATGCA--TTTCAACTATAACATACTTTTATGTTG
* *
1296505 ATAATGCACCTATATGCATTTCAACTATAACCTACTTTTATGTTG
1 ATAATGCACCCATATGCATTTCAACTATAACATACTTTTATGTTG
** * *
1296550 ATAATGCACCCATATGCATTTCAACTATAGTATACATTTCTGTTG
1 ATAATGCACCCATATGCATTTCAACTATAACATACTTTTATGTTG
* * ** * * **
1296595 ATAATGCACCCATATACATTTCAATTATGGCATCCTTTCATGCCG
1 ATAATGCACCCATATGCATTTCAACTATAACATACTTTTATGTTG
1296640 ATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATT
1296660 ATTATTTTCA
Statistics
Matches: 135, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
45 119 0.88
47 14 0.10
48 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (45 bp):
ATAATGCACCCATATGCATTTCAACTATAACATACTTTTATGTTG
Found at i:1299046 original size:137 final size:137
Alignment explanation
Indices: 1298800--1299060 Score: 425
Period size: 137 Copynumber: 1.9 Consensus size: 137
1298790 GGATTGAAAA
* * *
1298800 CAATTACCTTAACGCTCATCGTGACACTCTCATGCTTAGATTATCAACGAACGCCGTCCAAACTT
1 CAATTACCTTAACGCTCATCGTGACACTCTCATGCTTAGATTATCAACAAAAGCCATCCAAACTT
1298865 TCTCGGAAGAAGACTTTCCTTTCAACTTTTCTCTCTCTACGACTCTATCTCTCTCACTCATCTTT
66 TCTCGGAAGAAGACTTTCCTTTCAACTTTTCTCTCTCTACGACTCTATCTCTCTCACTCATCTTT
1298930 TTTTATC
131 TTTTATC
* * * * **
1298937 CAATT-CCTTTAACGCTCGTCGTGACACTCTCCTGGTTAGATTATCAACAAAAGTCATCCAATTT
1 CAATTACC-TTAACGCTCATCGTGACACTCTCATGCTTAGATTATCAACAAAAGCCATCCAAACT
1299001 TTCTCGGAAGAAGACTTTCCTTTCAACTTTTCTCTCTCTACGACTCTATCTCTCTCACTC
65 TTCTCGGAAGAAGACTTTCCTTTCAACTTTTCTCTCTCTACGACTCTATCTCTCTCACTC
1299061 CAAGAGTTAC
Statistics
Matches: 114, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
136 2 0.02
137 112 0.98
ACGTcount: A:0.23, C:0.30, G:0.10, T:0.36
Consensus pattern (137 bp):
CAATTACCTTAACGCTCATCGTGACACTCTCATGCTTAGATTATCAACAAAAGCCATCCAAACTT
TCTCGGAAGAAGACTTTCCTTTCAACTTTTCTCTCTCTACGACTCTATCTCTCTCACTCATCTTT
TTTTATC
Found at i:1303295 original size:16 final size:15
Alignment explanation
Indices: 1303276--1303328 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
1303266 AAAAATCAAT
1303276 TACCCGAAGATCCGGG
1 TACCCGAA-ATCCGGG
* *
1303292 TACCCGACACTTCGGG
1 TACCCGA-AATCCGGG
*
1303308 TACCCGAAAACCCGGG
1 TACCCG-AAATCCGGG
1303324 TACCC
1 TACCC
1303329 AGATTTACAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 28 0.93
17 2 0.07
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.13
Consensus pattern (15 bp):
TACCCGAAATCCGGG
Found at i:1312123 original size:20 final size:21
Alignment explanation
Indices: 1312098--1312179 Score: 71
Period size: 20 Copynumber: 3.9 Consensus size: 21
1312088 TTTTGGTGCA
*
1312098 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAACCGATTCCCCCCAT
**
1312118 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCAT
1312139 GAAGGGGAACCGATTCCCCCACA-
1 G-A-GGGAACCGATTCCCCC-CAT
* *
1312162 G-GGGAATCGATACCCCCC
1 GAGGGAACCGATTCCCCCC
1312180 TGGGGTTCTG
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
19 1 0.02
20 24 0.47
21 8 0.16
22 1 0.02
23 17 0.33
ACGTcount: A:0.24, C:0.35, G:0.26, T:0.15
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAT
Found at i:1319482 original size:51 final size:50
Alignment explanation
Indices: 1319366--1319513 Score: 161
Period size: 51 Copynumber: 2.9 Consensus size: 50
1319356 AAGGTACGGT
* * * **
1319366 CCATGCACCGCGCCTTATGTGATGTGGCTCCACGTGGGGTAAGGCGGGGC
1 CCATGCACCGCGCCTTATGTGATGTGGCTCTATGTTGGGTAAGGCGCAGC
* ** *
1319416 CCATGTACCATGCCTTACGCTGATGTGGCTCTATGTTGGGTAAGGCGCAGC
1 CCATGCACCGCGCCTTATG-TGATGTGGCTCTATGTTGGGTAAGGCGCAGC
** **
1319467 CCATGCACCGCGCCTTATGATGACATGGCGATATGTTGGGTAAGGCG
1 CCATGCACCGCGCCTTATG-TGATGTGGCTCTATGTTGGGTAAGGCG
1319514 TGGTTCATGG
Statistics
Matches: 79, Mismatches: 18, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
50 15 0.19
51 64 0.81
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.24
Consensus pattern (50 bp):
CCATGCACCGCGCCTTATGTGATGTGGCTCTATGTTGGGTAAGGCGCAGC
Found at i:1319614 original size:41 final size:41
Alignment explanation
Indices: 1319504--1319616 Score: 145
Period size: 41 Copynumber: 2.8 Consensus size: 41
1319494 GCGATATGTT
* * * * *
1319504 GGGTAAGGCGTGGTTCATGGGCCGCACCTTCTGTCACGTAG
1 GGGTATGGCGCGGTACATGGGCCGCGCCTTCTGCCACGTAG
*
1319545 GGGTATGGCGCGGTACATGGGTCGCGCCTTCTGCCACGTAG
1 GGGTATGGCGCGGTACATGGGCCGCGCCTTCTGCCACGTAG
* * *
1319586 GGGTATGGTGCGGTGCATGGGCCACGCCTTC
1 GGGTATGGCGCGGTACATGGGCCGCGCCTTC
1319617 CTATAATTAT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.12, C:0.26, G:0.39, T:0.23
Consensus pattern (41 bp):
GGGTATGGCGCGGTACATGGGCCGCGCCTTCTGCCACGTAG
Found at i:1323602 original size:3 final size:3
Alignment explanation
Indices: 1323540--1323585 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
1323530 CTCCTCACTG
* * *
1323540 TCA TCA TCA TTA CCA CCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1323586 TGTTGTTGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:1327166 original size:21 final size:22
Alignment explanation
Indices: 1327134--1327174 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1327124 GTCCCTGGCA
1327134 CGGGGACGGTA-CGGGGACGGC
1 CGGGGACGGTACCGGGGACGGC
1327155 CGGGGTAC-GTACCGGGGACG
1 CGGGG-ACGGTACCGGGGACG
1327175 TGCCACGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.15, C:0.24, G:0.54, T:0.07
Consensus pattern (22 bp):
CGGGGACGGTACCGGGGACGGC
Found at i:1327979 original size:12 final size:12
Alignment explanation
Indices: 1327962--1327989 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1327952 TTTTCTGTCC
1327962 CCGTCCCCGTAT
1 CCGTCCCCGTAT
1327974 CCGTCCCCGTAT
1 CCGTCCCCGTAT
1327986 CCGT
1 CCGT
1327990 ATCAGTGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.50, G:0.18, T:0.25
Consensus pattern (12 bp):
CCGTCCCCGTAT
Found at i:1327989 original size:18 final size:18
Alignment explanation
Indices: 1327958--1327992 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1327948 ACCGTTTTCT
*
1327958 GTCCCCGTCCCCGTATCC
1 GTCCCCGTACCCGTATCC
*
1327976 GTCCCCGTATCCGTATC
1 GTCCCCGTACCCGTATC
1327993 AGTGCAACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.49, G:0.17, T:0.26
Consensus pattern (18 bp):
GTCCCCGTACCCGTATCC
Found at i:1335619 original size:5 final size:5
Alignment explanation
Indices: 1335609--1336037 Score: 159
Period size: 5 Copynumber: 86.2 Consensus size: 5
1335599 CTCTTTATAG
* *
1335609 TATTA TA-T- TATTA TATT- TA-TA TAATA TATGTCA TA-TA TATTTC
1 TATTA TATTA TATTA TATTA TATTA TATTA TAT-T-A TATTA TA-TTA
* *
1335652 TATTA TA-TA T-TGTA TAGTA TA-TA TATTA TAATA TATGT- TA-TA TAGTTA
1 TATTA TATTA TAT-TA TATTA TATTA TATTA TATTA TAT-TA TATTA TA-TTA
* * *
1335700 T-TATA TAGTA TATTA TATAA TA-TA -ATTA TATTA TA-TA TATTA TATAA
1 TAT-TA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
* *
1335747 TA-TA -ATTA TATTA TA-TA TAATA TATAAA TATTA TATTA TA-TA GTA-TA
1 TATTA TATTA TATTA TATTA TATTA TAT-TA TATTA TATTA TATTA -TATTA
* ** *
1335794 TATATA TAGTA TA-TA T-TTA TATTTA TATTA TGGTA TATTTA TATAA
1 TAT-TA TATTA TATTA TATTA TA-TTA TATTA TATTA TA-TTA TATTA
* *
1335840 TATATA GTATTA T-TTA TA-TA TAGTA -ACTTA TATTA T-TATA TAGTA
1 TAT-TA -TATTA TATTA TATTA TATTA TA-TTA TATTA TAT-TA TATTA
*
1335885 TA-TA CTATAA TATTA TATTA TATATA TATATA TATTA TA-TA GTA-TA
1 TATTA -TATTA TATTA TATTA TAT-TA TAT-TA TATTA TATTA -TATTA
* *
1335931 TATGTA GTA-TA TATTA TAGTGTA TATTT TATTA TATATA TAGTA TA-TA
1 TAT-TA -TATTA TATTA TA-T-TA TATTA TATTA TAT-TA TATTA TATTA
* * *
1335979 TTTTA TAGTA TAATA TA-TA GTATTA TATGGTA TATTACA TATGT- TATT-
1 TATTA TATTA TATTA TATTA -TATTA TAT--TA TATT--A TAT-TA TATTA
1336027 TATTA TATTA T
1 TATTA TATTA T
1336038 TAACATTAAT
Statistics
Matches: 331, Mismatches: 33, Indels: 120
0.68 0.07 0.25
Matches are distributed among these distances:
3 6 0.02
4 71 0.21
5 181 0.55
6 51 0.15
7 21 0.06
8 1 0.00
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (5 bp):
TATTA
Found at i:1335637 original size:2 final size:2
Alignment explanation
Indices: 1335612--1336006 Score: 204
Period size: 2 Copynumber: 208.5 Consensus size: 2
1335602 TTTATAGTAT
* * * *
1335612 TA TA T- TA T- TA TA TT TA TA TA -A TA TA TG TCA TA TA TA TT TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
* *
1335652 TA T- TA TA TA T- TG TA TA GTA TA TA TA T- TA TA -A TA TA TG T-
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
1335690 TA TA TA GT- TA T- TA TA TA GTA TA T- TA TA TA -A TA TA -A T- TA
1 TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
1335728 TA T- TA TA TA TA T- TA TA TA -A TA TA -A T- TA TA T- 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
*
1335764 TA -A TA TA TA AA TA T- TA TA T- TA TA TA GTA TA TA TA TA TA GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA
* * * *
1335805 TA TA TT TA TA TT TA TA T- TA TGG TA TA TT TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
*
1335846 GTA T- TA TT TA TA TA TA GTA -A CT- TA TA T- TA T- TA TA TA GTA
1 -TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA TA -TA
1335885 TA TA CTA TA -A TA T- TA TA T- TA TA TA TA TA TA TA TA T- TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
1335924 TA GTA TA TA TG TA GTA TA TA T- TA TA GTG TA TA T- TT TA T- TA
1 TA -TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
*
1335964 TA TA TA TA GTA TA TA T- TT TA TA GTA TA -A TA TA TA GTA T- TA
1 TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA
1336004 TA T
1 TA T
1336007 GGTATATTAC
Statistics
Matches: 308, Mismatches: 27, Indels: 116
0.68 0.06 0.26
Matches are distributed among these distances:
1 40 0.13
2 238 0.77
3 30 0.10
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1338751 original size:22 final size:22
Alignment explanation
Indices: 1338726--1338768 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1338716 ATTTCGATTT
1338726 ATAAATCTATATTACTATATAA
1 ATAAATCTATATTACTATATAA
*
1338748 ATAAATCTATATTTCTATATA
1 ATAAATCTATATTACTATATA
1338769 GCATTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAAATCTATATTACTATATAA
Found at i:1338786 original size:18 final size:18
Alignment explanation
Indices: 1338763--1338801 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1338753 TCTATATTTC
*
1338763 TATATAGCATTATTAAGA
1 TATATAACATTATTAAGA
*
1338781 TATATAATATTATTAAGA
1 TATATAACATTATTAAGA
1338799 TAT
1 TAT
1338802 TATTATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (18 bp):
TATATAACATTATTAAGA
Found at i:1338809 original size:26 final size:25
Alignment explanation
Indices: 1338780--1338876 Score: 65
Period size: 26 Copynumber: 3.8 Consensus size: 25
1338770 CATTATTAAG
1338780 ATATATAATATTATTAAGATATTATT
1 ATATATAATATTATTAA-ATATTATT
** *
1338806 ATATATTTTAATT-TTATAATATTCTT
1 ATATATAAT-ATTATTA-AATATTATT
*
1338832 ATA-ATATATATTATTTACATATTATT
1 ATATATA-ATATTA-TTAAATATTATT
* *
1338858 ATTTA-AATAATATTTAAAT
1 ATATATAATATTA-TTAAAT
1338877 TAAATGATAT
Statistics
Matches: 55, Mismatches: 10, Indels: 13
0.71 0.13 0.17
Matches are distributed among these distances:
25 16 0.29
26 31 0.56
27 8 0.15
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (25 bp):
ATATATAATATTATTAAATATTATT
Found at i:1338859 original size:14 final size:15
Alignment explanation
Indices: 1338835--1338871 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1338825 TATTCTTATA
1338835 ATATATATTATTTAC
1 ATATATATTATTTAC
*
1338850 ATAT-TATTATTTAA
1 ATATATATTATTTAC
1338864 ATA-ATATT
1 ATATATATT
1338872 TAAATTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (15 bp):
ATATATATTATTTAC
Found at i:1338923 original size:22 final size:22
Alignment explanation
Indices: 1338895--1338938 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1338885 ATTGAAAGAT
1338895 TTAAAGTATTATTTATAATTTA
1 TTAAAGTATTATTTATAATTTA
1338917 TTAAAGTATTATTTATAATTTA
1 TTAAAGTATTATTTATAATTTA
1338939 ATAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
TTAAAGTATTATTTATAATTTA
Found at i:1345364 original size:2 final size:2
Alignment explanation
Indices: 1345330--1345625 Score: 122
Period size: 2 Copynumber: 161.5 Consensus size: 2
1345320 TTTATAGTAT
* * * *
1345330 TA TA T- TA T- TA TA TT TA TG TA -A TA TA TG TCA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
* * * *
1345370 TA T- TA TA TA T- TG TA TA GTA TC TA TA T- TA TA GTT TT 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
* *
1345411 T- TA AA TA T- TT TA TA -A TA T- TA TA T- TA TA TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
*
1345449 TA T- TA TA -A TA T- TA TA T- TA TA T- TA TA AA TA GTA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* *
1345486 TA TA TA -A TA TA TA -A TA TA TA T- TA T- TG TG TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1345523 T- TA TA TA TA TA -A TA TA TA T- TT TA TA GTA TA -A TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* *
1345561 TA T- TA TA TGG TA TA T- TA CA TA TA T- TA TA T- TA T- TA TA T-
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1345598 TA TA AA TA GTA TA TA T- TA TA TA -A TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA T
1345626 TGTTTATGCT
Statistics
Matches: 225, Mismatches: 26, Indels: 86
0.67 0.08 0.26
Matches are distributed among these distances:
1 35 0.16
2 177 0.79
3 13 0.06
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1345408 original size:23 final size:22
Alignment explanation
Indices: 1345360--1345530 Score: 85
Period size: 23 Copynumber: 7.9 Consensus size: 22
1345350 ATATATGTCA
*
1345360 TATATATTTATATTATATATTG
1 TATATATCTATATTATATATTG
*
1345382 TATAGTATCTATATTATAGT-TTT
1 TATA-TATCTATATTATA-TATTG
1345405 TATATAT-TA-A--ATAT-TT-
1 TATATATCTATATTATATATTG
*
1345421 TATAATAT-TATATTATATATAG
1 TAT-ATATCTATATTATATATTG
* * *
1345443 TATATATATTATAATATTATATTA
1 TATATAT-CTATATTA-TATATTG
** * *
1345467 TAT-TATAAATAGTATATATTA
1 TATATATCTATATTATATATTG
*
1345488 TATA-ATATATAATATATATTATTG
1 TATATATCTAT-AT-TATA-TATTG
*
1345512 TGTATAT-TATATTATATAT
1 TATATATCTATATTATATAT
1345531 ATAATATATA
Statistics
Matches: 120, Mismatches: 13, Indels: 33
0.72 0.08 0.20
Matches are distributed among these distances:
16 3 0.03
17 9 0.08
18 4 0.03
20 5 0.04
21 25 0.21
22 20 0.17
23 33 0.28
24 19 0.16
25 2 0.02
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.54
Consensus pattern (22 bp):
TATATATCTATATTATATATTG
Found at i:1345435 original size:5 final size:5
Alignment explanation
Indices: 1345415--1345623 Score: 109
Period size: 5 Copynumber: 41.8 Consensus size: 5
1345405 TATATATTAA
* * *
1345415 ATATT TTATA ATATT ATATT ATA-T ATAGT ATA-T ATATT ATA-- ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
* *
1345461 ATATT ATATT ATA-A ATAGTAT ATATT ATATA ATA-T ATAATAT ATATT
1 ATATT ATATT ATATT ATA-T-T ATATT ATATT ATATT AT-AT-T ATATT
* * * * *
1345508 ATTGTGT ATATT ATATT ATA-T ATATA ATATAT ATTTT ATAGT ATAAT
1 A-TAT-T ATATT ATATT ATATT ATATT ATAT-T ATATT ATATT ATATT
*
1345555 ATA-T ATTATT ATATGGT ATATT ACA-T ATATT ATA-T -TATT ATATT
1 ATATT A-TATT ATAT--T ATATT ATATT ATATT ATATT ATATT ATATT
* *
1345599 ATA-A ATAGTAT ATATT ATATA ATAT
1 ATATT ATA-T-T ATATT ATATT ATAT
1345624 ATTGTTTATG
Statistics
Matches: 159, Mismatches: 21, Indels: 48
0.70 0.09 0.21
Matches are distributed among these distances:
3 5 0.03
4 27 0.17
5 98 0.62
6 13 0.08
7 16 0.10
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (5 bp):
ATATT
Found at i:1349182 original size:21 final size:21
Alignment explanation
Indices: 1349157--1349196 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1349147 AAGACTTTAT
1349157 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
1349178 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
1349197 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:1353038 original size:23 final size:22
Alignment explanation
Indices: 1353007--1353083 Score: 75
Period size: 23 Copynumber: 3.5 Consensus size: 22
1352997 ACACTAGACA
1353007 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
* * * *
1353030 ATGCATCGATACA-CCATGAAG
1 GTGCATCGATGCATCCTTGAAT
* *
1353051 GTGCACCAATGCATTCCTTGAAT
1 GTGCATCGATGCA-TCCTTGAAT
1353074 GTGCATCGAT
1 GTGCATCGAT
1353084 TCACTCTATT
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
21 15 0.38
23 25 0.62
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:1353070 original size:44 final size:43
Alignment explanation
Indices: 1352987--1353083 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 43
1352977 TTAGTGCATA
* * *
1352987 ATGCATCGATACACTAGACAGTGCATCGATGCATCCCTTGAAT
1 ATGCATCGATACACCAGACAGTGCACCAATGCATCCCTTGAAT
*
1353030 ATGCATCGATACACCATGA-AGGTGCACCAATGCATTCCTTGAAT
1 ATGCATCGATACACCA-GACA-GTGCACCAATGCATCCCTTGAAT
*
1353074 GTGCATCGAT
1 ATGCATCGAT
1353084 TCACTCTATT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
43 16 0.34
44 31 0.66
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.26
Consensus pattern (43 bp):
ATGCATCGATACACCAGACAGTGCACCAATGCATCCCTTGAAT
Found at i:1355980 original size:21 final size:21
Alignment explanation
Indices: 1355954--1356002 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
1355944 TAGTGTACCA
1355954 ATGCACCTTGGCTATGCATCG
1 ATGCACCTTGGCTATGCATCG
1355975 ATGCACCTTGGCTATGCATCG
1 ATGCACCTTGGCTATGCATCG
1355996 ATGCACC
1 ATGCACC
1356003 ATACGCTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.31, G:0.22, T:0.27
Consensus pattern (21 bp):
ATGCACCTTGGCTATGCATCG
Found at i:1357656 original size:18 final size:17
Alignment explanation
Indices: 1357630--1357663 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1357620 ATGCTATTTT
1357630 GGTACCGATACTCATAGG
1 GGTACCGATACT-ATAGG
*
1357648 GGTATCGATACTATAG
1 GGTACCGATACTATAG
1357664 AAAGAGTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (17 bp):
GGTACCGATACTATAGG
Found at i:1358097 original size:22 final size:22
Alignment explanation
Indices: 1358072--1358142 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
1358062 GAGAGAATGT
* * *
1358072 ACTTTCGTATCAGTGTTGTGGC
1 ACTTTAGTATTAGTGCTGTGGC
1358094 ACTTTAGTATTAGTGCTGTGGC
1 ACTTTAGTATTAGTGCTGTGGC
**
1358116 ACTTTAGTATTAGTGCTAAGGC
1 ACTTTAGTATTAGTGCTGTGGC
1358138 ACTTT
1 ACTTT
1358143 CGTTATTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (22 bp):
ACTTTAGTATTAGTGCTGTGGC
Found at i:1363123 original size:185 final size:185
Alignment explanation
Indices: 1362805--1363175 Score: 733
Period size: 185 Copynumber: 2.0 Consensus size: 185
1362795 ACCATTTTTA
1362805 ACATTCGAGATGATAAAAGACTTAGAATTTTCAATTCTTGAATAAACACTTGAAGACTAAATTAT
1 ACATTCGAGATGATAAAAGACTTAGAATTTTCAATTCTTGAATAAACACTTGAAGACTAAATTAT
1362870 TGGAAATAATGCATACAATTAGACCAAATGAAATGATCAAAATACTCTCAAGCTCTAAAATAATT
66 TGGAAATAATGCATACAATTAGACCAAATGAAATGATCAAAATACTCTCAAGCTCTAAAATAATT
1362935 AAAATAACCACGAGTGCTGAAATGGTTTAAATACCCTCGCATTTTAATATAAGTG
131 AAAATAACCACGAGTGCTGAAATGGTTTAAATACCCTCGCATTTTAATATAAGTG
1362990 ACATTCGAGATGATAAAAGACTTAGAATTTTCAATTCTTGAATAAACACTTGAAGACTAAATTAT
1 ACATTCGAGATGATAAAAGACTTAGAATTTTCAATTCTTGAATAAACACTTGAAGACTAAATTAT
*
1363055 TGGAAATAATGCATACAATTAGACCAAATGAAATGATCAAAATACTCTCAAGCTCTAAAATGATT
66 TGGAAATAATGCATACAATTAGACCAAATGAAATGATCAAAATACTCTCAAGCTCTAAAATAATT
1363120 AAAATAACCACGAGTGCTGAAATGGTTTAAATACCCTCGCATTTTAATATAAGTG
131 AAAATAACCACGAGTGCTGAAATGGTTTAAATACCCTCGCATTTTAATATAAGTG
1363175 A
1 A
1363176 ATGTCCTTAG
Statistics
Matches: 185, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 185 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (185 bp):
ACATTCGAGATGATAAAAGACTTAGAATTTTCAATTCTTGAATAAACACTTGAAGACTAAATTAT
TGGAAATAATGCATACAATTAGACCAAATGAAATGATCAAAATACTCTCAAGCTCTAAAATAATT
AAAATAACCACGAGTGCTGAAATGGTTTAAATACCCTCGCATTTTAATATAAGTG
Found at i:1364238 original size:44 final size:45
Alignment explanation
Indices: 1364157--1364242 Score: 115
Period size: 44 Copynumber: 1.9 Consensus size: 45
1364147 TGGCTCATTT
* *
1364157 GCTTTGGGCTTAGGGTAAGTCCTTATACCCCTCAGGTGGCTCCTAC
1 GCTTTGGGCTTAGGGTAAGTCCTTATAACCCTAAGGT-GCTCCTAC
1364203 GCTTT-GGC-TAGGGTAAGTCCTTATAGACCC-AAGGTGCTCC
1 GCTTTGGGCTTAGGGTAAGTCCTTATA-ACCCTAAGGTGCTCC
1364243 CTTAGGTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
43 5 0.14
44 21 0.57
45 6 0.16
46 5 0.14
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (45 bp):
GCTTTGGGCTTAGGGTAAGTCCTTATAACCCTAAGGTGCTCCTAC
Found at i:1368994 original size:12 final size:12
Alignment explanation
Indices: 1368977--1369019 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
1368967 ATATTTTTTA
1368977 AAAAAAATATTT
1 AAAAAAATATTT
1368989 AAAAAAAATATTT
1 -AAAAAAATATTT
* *
1369002 TAAAAATTATATT
1 AAAAAAATAT-TT
1369015 AAAAA
1 AAAAA
1369020 TATTATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAAAAATATTT
Found at i:1369014 original size:14 final size:14
Alignment explanation
Indices: 1368972--1369007 Score: 65
Period size: 13 Copynumber: 2.6 Consensus size: 14
1368962 AATTTATATT
1368972 TTTTAAAAAAAATA
1 TTTTAAAAAAAATA
1368986 -TTTAAAAAAAATA
1 TTTTAAAAAAAATA
1368999 TTTTAAAAA
1 TTTTAAAAA
1369008 TTATATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTTAAAAAAAATA
Found at i:1371803 original size:24 final size:24
Alignment explanation
Indices: 1371788--1371848 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
1371778 GAAATCACTC
1371788 TAACATGCTTGCATGAACAAAACA
1 TAACATGCTTGCATGAACAAAACA
1371812 TAACATGCTTGCATGAACAAAACA
1 TAACATGCTTGCATGAACAAAACA
*
1371836 TAACATGCATGCA
1 TAACATGCTTGCA
1371849 CATTTAATGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.44, C:0.21, G:0.13, T:0.21
Consensus pattern (24 bp):
TAACATGCTTGCATGAACAAAACA
Found at i:1386082 original size:46 final size:45
Alignment explanation
Indices: 1385946--1386082 Score: 229
Period size: 45 Copynumber: 3.0 Consensus size: 45
1385936 GTAACCATGC
* *
1385946 AAATAAGCTTATGAGTTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1385991 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
1386036 AAATAAGCTTACGAGCTTATGGGATTAAATGGTTAGTATATTGGTA
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATATTGGTA
1386082 A
1 A
1386083 GAAATGTTAT
Statistics
Matches: 87, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
45 63 0.72
46 24 0.28
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.34
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Done.