Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold47
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: 2157611
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 149227 characters in sequence are not A, C, G, or T
File 9 of 15
Found at i:1133032 original size:30 final size:28
Alignment explanation
Indices: 1132996--1133108 Score: 99
Period size: 29 Copynumber: 4.0 Consensus size: 28
1132986 AAAATTAAAA
* *
1132996 AATTAAAATCACAAAAAAAATTAATAAATC
1 AATTAAAAT-AC-AAAAAAATAAAAAAATC
*
1133026 AATTAAAAATTCAAAAAAATAAAAAAATC
1 AATT-AAAATACAAAAAAATAAAAAAATC
* *
1133055 AATTAAAAATTC-AAAAAATAAAAAAACC
1 AATT-AAAATACAAAAAAATAAAAAAATC
* *
1133083 AA--AATA-ACAAAAAAACAAAAAAATC
1 AATTAAAATACAAAAAAATAAAAAAATC
1133108 A
1 A
1133109 CAAATTAAAG
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
24 1 0.01
25 18 0.25
28 17 0.23
29 27 0.37
30 5 0.07
31 5 0.07
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.18
Consensus pattern (28 bp):
AATTAAAATACAAAAAAATAAAAAAATC
Found at i:1133033 original size:20 final size:18
Alignment explanation
Indices: 1132988--1133034 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 18
1132978 ATAATAAAAA
1132988 AATTAAAAAATTAAAATC
1 AATTAAAAAATTAAAATC
*
1133006 ACA-AAAAAAATTAATAAATC
1 A-ATTAAAAAATT-A-AAATC
1133026 AATTAAAAA
1 AATTAAAAA
1133035 TTCAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
18 9 0.39
19 3 0.13
20 11 0.48
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.23
Consensus pattern (18 bp):
AATTAAAAAATTAAAATC
Found at i:1133041 original size:29 final size:29
Alignment explanation
Indices: 1133009--1133108 Score: 120
Period size: 29 Copynumber: 3.6 Consensus size: 29
1132999 TAAAATCACA
* *
1133009 AAAAAAATTAATAAATCAATTAAAAATTC
1 AAAAAAATAAAAAAATCAATTAAAAATTC
1133038 AAAAAAATAAAAAAATCAATTAAAAATTC
1 AAAAAAATAAAAAAATCAATTAAAAATTC
* *
1133067 -AAAAAATAAAAAAACCAA--AATAA--C
1 AAAAAAATAAAAAAATCAATTAAAAATTC
*
1133091 AAAAAAACAAAAAAATCA
1 AAAAAAATAAAAAAATCA
1133109 CAAATTAAAG
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.02
25 15 0.23
26 4 0.06
28 17 0.27
29 27 0.42
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (29 bp):
AAAAAAATAAAAAAATCAATTAAAAATTC
Found at i:1133049 original size:8 final size:8
Alignment explanation
Indices: 1133038--1133144 Score: 61
Period size: 8 Copynumber: 12.6 Consensus size: 8
1133028 TTAAAAATTC
1133038 AAAAAAAT
1 AAAAAAAT
1133046 AAAAAAAT
1 AAAAAAAT
1133054 CAATTAAAAATT
1 -AA--AAAAA-T
*
1133066 CAAAAAAT
1 AAAAAAAT
*
1133074 AAAAAAACC
1 AAAAAAA-T
* *
1133083 AAAATAAC
1 AAAAAAAT
*
1133091 AAAAAAAC
1 AAAAAAAT
1133099 AAAAAAAT
1 AAAAAAAT
* * *
1133107 CACAAATT
1 AAAAAAAT
*
1133115 AAAGAAAT
1 AAAAAAAT
**
1133123 CAAAGTAAT
1 -AAAAAAAT
1133132 AAAAAAAT
1 AAAAAAAT
1133140 AAAAA
1 AAAAA
1133145 TTAGAAATCA
Statistics
Matches: 77, Mismatches: 16, Indels: 12
0.73 0.15 0.11
Matches are distributed among these distances:
8 50 0.65
9 20 0.26
11 6 0.08
12 1 0.01
ACGTcount: A:0.76, C:0.08, G:0.02, T:0.14
Consensus pattern (8 bp):
AAAAAAAT
Found at i:1133859 original size:22 final size:20
Alignment explanation
Indices: 1133838--1133877 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1133828 AAAATACATT
*
1133838 TTGTCCAATGTATCGATACA
1 TTGTACAATGTATCGATACA
*
1133858 TTGTAGAATGTATCGATACA
1 TTGTACAATGTATCGATACA
1133878 AGGTCCCTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (20 bp):
TTGTACAATGTATCGATACA
Found at i:1133960 original size:19 final size:21
Alignment explanation
Indices: 1133912--1133966 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
1133902 AATTTCAATA
*
1133912 ATTTGTATCGATACATTCAGT
1 ATTTGTATCGATACATTAAGT
**
1133933 AAATGTATCGATACA-TAAGT
1 ATTTGTATCGATACATTAAGT
1133953 -TTTGTATCGATACA
1 ATTTGTATCGATACA
1133967 ATGTATCGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 12 0.41
20 4 0.14
21 13 0.45
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (21 bp):
ATTTGTATCGATACATTAAGT
Found at i:1134017 original size:21 final size:21
Alignment explanation
Indices: 1133991--1134032 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1133981 GGCTACTGCC
*
1133991 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCAATACATT
*
1134012 AAGGAAGTGTATCAATACATT
1 AAGGAAATGTATCAATACATT
1134033 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCAATACATT
Found at i:1136568 original size:79 final size:78
Alignment explanation
Indices: 1136442--1136640 Score: 214
Period size: 79 Copynumber: 2.6 Consensus size: 78
1136432 CCCCGGTTCC
* * * *
1136442 ATTTCCAAAACATCAATTTTT--C-ATCGAGGATACTCCCATCCCGTTATTTTCGAAGGGATACT
1 ATTTCTAAATCATCAATTTTTCACAATCGGGGATACT-CCAACCCGTTATTTTCGAAGGGATACT
1136504 CCAA-CCTC-AGTTTT
65 CCAATCC-CGA-TTTT
* * * *
1136518 ATTTCTAAAAT-ATTAATTTCTT-ATAATCGGGGATACTCCAACCTCGTTATTTTTGAGGGGATA
1 ATTTCT-AAATCATCAATTT-TTCACAATCGGGGATACTCCAACC-CGTTATTTTCGAAGGGATA
1136581 CTCCAATCCCGATTTT
63 CTCCAATCCCGATTTT
*
1136597 ATTTCTAAATCATCGATTTTTCACAATCGGGGATACTCCAACCC
1 ATTTCTAAATCATCAATTTTTCACAATCGGGGATACTCCAACCC
1136641 CAGTTTTATT
Statistics
Matches: 103, Mismatches: 11, Indels: 16
0.79 0.08 0.12
Matches are distributed among these distances:
76 12 0.12
77 5 0.05
78 12 0.12
79 71 0.69
80 3 0.03
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.36
Consensus pattern (78 bp):
ATTTCTAAATCATCAATTTTTCACAATCGGGGATACTCCAACCCGTTATTTTCGAAGGGATACTC
CAATCCCGATTTT
Found at i:1136637 original size:51 final size:51
Alignment explanation
Indices: 1136574--1136693 Score: 163
Period size: 51 Copynumber: 2.4 Consensus size: 51
1136564 TTATTTTTGA
* * *
1136574 GGGGATACTCCAATCCC-GATTTTATTTCT-AAATCATCGATTTTTCACAATC
1 GGGGATACTCCAACCCCAG-TTTTATTTCTAAAAT-ATCAATTTCTCACAATC
* *
1136625 GGGGATACTCCAACCCCAGTTTTATTTCTAAAATATTAATTTCTCATAATC
1 GGGGATACTCCAACCCCAGTTTTATTTCTAAAATATCAATTTCTCACAATC
1136676 GGGGATACTCCAACCCCA
1 GGGGATACTCCAACCCCA
1136694 TTATTTCCGA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
51 57 0.92
52 5 0.08
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCAGTTTTATTTCTAAAATATCAATTTCTCACAATC
Found at i:1136649 original size:130 final size:130
Alignment explanation
Indices: 1136496--1136771 Score: 480
Period size: 130 Copynumber: 2.1 Consensus size: 130
1136486 TATTTTCGAA
* *
1136496 GGGATACTCCAACCTCAGTTTTATTTCTAAAATATTAATTTCTTATAATCGGGGATACTCCAACC
1 GGGATACTCCAACCCCAGTTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAACC
* * **
1136561 TCGTTATTTTTGAGGGGATACTCCAATCCCGATTTTATTTCTAAATCATCGATTTTTCACAATCG
66 CCATTATTTCCGAGGGGATACTCCAATCCCGATTTTATTTCTAAATCATCGATTTTTCACAATCG
1136626 GGGATACTCCAACCCCAGTTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAACC
1 GGGATACTCCAACCCCAGTTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAACC
*
1136691 CCATTATTTCCGAGGGGATACTCCAATCCCGATTTTATTTCTAAATCATCGATTTTTCATAATCG
66 CCATTATTTCCGAGGGGATACTCCAATCCCGATTTTATTTCTAAATCATCGATTTTTCACAATCG
*
1136756 GAGATACTCCAACCCC
1 GGGATACTCCAACCCC
1136772 GTTATTTTCA
Statistics
Matches: 138, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
130 138 1.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.36
Consensus pattern (130 bp):
GGGATACTCCAACCCCAGTTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAACC
CCATTATTTCCGAGGGGATACTCCAATCCCGATTTTATTTCTAAATCATCGATTTTTCACAATCG
Found at i:1136708 original size:79 final size:78
Alignment explanation
Indices: 1136625--1136830 Score: 261
Period size: 79 Copynumber: 2.6 Consensus size: 78
1136615 TTTCACAATC
* *
1136625 GGGGATACTCCAACCCCAGTTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCC-GTTTTATTTCTAAAATATTAATTTTTCATAATCGGAGATACTCCAAC
*
1136690 CCCATTATTTCCGA
65 CCCATTATTTCCAA
* **
1136704 GGGGATACTCCAATCCCGATTTTATTTCT-AAATCATCGATTTTTCATAATCGGAGATACTCCAA
1 GGGGATACTCCAACCCCG-TTTTATTTCTAAAAT-ATTAATTTTTCATAATCGGAGATACTCCAA
* *
1136768 CCCCGTTATTTTCAA
64 CCCCATTATTTCCAA
* * *
1136783 GGAGATACTCCAACCCCGTTGTTATCTCCAAAATATTAAATTTTTCAT
1 GGGGATACTCCAACCCCGTT-TTATTTCTAAAATATT-AATTTTTCAT
1136831 CGAGAGAGGT
Statistics
Matches: 108, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
78 7 0.06
79 88 0.81
80 13 0.12
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.34
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGTTTTATTTCTAAAATATTAATTTTTCATAATCGGAGATACTCCAACC
CCATTATTTCCAA
Found at i:1137986 original size:41 final size:41
Alignment explanation
Indices: 1137941--1138059 Score: 107
Period size: 41 Copynumber: 3.2 Consensus size: 41
1137931 GAACATTAGT
1137941 AGCAGCTCCAACAGCTTCTAGTAGCGACAGCACCCCAAACC
1 AGCAGCTCCAACAGCTTCTAGTAGCGACAGCACCCCAAACC
* * * *
1137982 AGCAGGTCCAGCAGCTTCCA-T---GA-A-CA--CC-GA-C
1 AGCAGCTCCAACAGCTTCTAGTAGCGACAGCACCCCAAACC
* *
1138013 -GCAGCTCCAACAACTTCTAGTAGCGACAGCACCCGAAACC
1 AGCAGCTCCAACAGCTTCTAGTAGCGACAGCACCCCAAACC
1138053 AGCAGCT
1 AGCAGCT
1138060 TCCACGAACA
Statistics
Matches: 57, Mismatches: 10, Indels: 22
0.64 0.11 0.25
Matches are distributed among these distances:
30 15 0.26
31 2 0.04
32 1 0.02
33 2 0.04
34 2 0.04
35 3 0.05
36 3 0.05
37 2 0.04
38 1 0.02
39 1 0.02
40 2 0.04
41 23 0.40
ACGTcount: A:0.31, C:0.37, G:0.19, T:0.13
Consensus pattern (41 bp):
AGCAGCTCCAACAGCTTCTAGTAGCGACAGCACCCCAAACC
Found at i:1138043 original size:71 final size:72
Alignment explanation
Indices: 1137897--1138059 Score: 222
Period size: 71 Copynumber: 2.3 Consensus size: 72
1137887 CCAACCCACG
* * * *
1137897 AGCACCCAAAACCAGTAGCTCTAGCAGCTTCCACGAACATTAGTAGCAGCTCCAACAGCTTCTAG
1 AGCACCCAAAACCAGCAGCTCCAGCAGCTTCCACGAACATCAGTAGCAGCTCCAACAACTTCTAG
1137962 TAGCGAC
66 TAGCGAC
* * * *
1137969 AGCACCCCAAACCAGCAGGTCCAGCAGCTTCCATGAACA-CCG-ACGCAGCTCCAACAACTTCTA
1 AGCACCCAAAACCAGCAGCTCCAGCAGCTTCCACGAACATCAGTA-GCAGCTCCAACAACTTCTA
1138032 GTAGCGAC
65 GTAGCGAC
*
1138040 AGCACCCGAAACCAGCAGCT
1 AGCACCCAAAACCAGCAGCT
1138060 TCCACGAACA
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
70 1 0.01
71 45 0.56
72 34 0.43
ACGTcount: A:0.32, C:0.36, G:0.18, T:0.14
Consensus pattern (72 bp):
AGCACCCAAAACCAGCAGCTCCAGCAGCTTCCACGAACATCAGTAGCAGCTCCAACAACTTCTAG
TAGCGAC
Found at i:1140003 original size:69 final size:69
Alignment explanation
Indices: 1139913--1140048 Score: 227
Period size: 69 Copynumber: 2.0 Consensus size: 69
1139903 AAAGACATTT
* *
1139913 TGACCTTGAAAACCTTTTATATTCTTCCGAGCTTCTAGCAGGATATAAAAGAGAATAATAAAATT
1 TGACCTTGAAAACCTTTTATATTCCTCCGAGCTTCTAGCAAGATATAAAAGAGAATAATAAAATT
1139978 CACG
66 CACG
* * *
1139982 TGACCTTGAAAACCTTTTATATTCCTCTGGGCTTCTAGCAAGATATAAAAGAGAATAATAAAGTT
1 TGACCTTGAAAACCTTTTATATTCCTCCGAGCTTCTAGCAAGATATAAAAGAGAATAATAAAATT
1140047 CA
66 CA
1140049 TGTGTTCCAC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.31
Consensus pattern (69 bp):
TGACCTTGAAAACCTTTTATATTCCTCCGAGCTTCTAGCAAGATATAAAAGAGAATAATAAAATT
CACG
Found at i:1141434 original size:2 final size:2
Alignment explanation
Indices: 1141427--1141456 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1141417 AATACATGGA
1141427 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1141457 TAATAGAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1141631 original size:31 final size:31
Alignment explanation
Indices: 1141593--1141661 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
1141583 TTTAAAACTC
*
1141593 AAGCTCAATTTAAGATAATATCAAATTATTT
1 AAGCTCAATTTAAGATAAAATCAAATTATTT
*
1141624 AAGCTCAATTTAAGATAAAATTAAATTATTT
1 AAGCTCAATTTAAGATAAAATCAAATTATTT
*
1141655 AAACTCA
1 AAGCTCA
1141662 CTCGATTAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.36
Consensus pattern (31 bp):
AAGCTCAATTTAAGATAAAATCAAATTATTT
Found at i:1142168 original size:34 final size:33
Alignment explanation
Indices: 1142129--1142226 Score: 92
Period size: 34 Copynumber: 2.9 Consensus size: 33
1142119 TGTTATATAA
*
1142129 ATTATTTTTAAATTTATTATACTGTATTTATTAT
1 ATTATTTTTAAATTTATTATA-TATATTTATTAT
* *
1142163 ATTA-TTATAATATTTATTATATTTTATATT-TTAT
1 ATTATTTTTAA-ATTTATTATA-TATAT-TTATTAT
* * *
1142197 ATCATATTTAAAATTATTATATATATTTAT
1 ATTATTTTTAAATTTATTATATATATTTAT
1142227 ACCCTCCTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
32 2 0.04
33 10 0.19
34 34 0.65
35 6 0.12
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (33 bp):
ATTATTTTTAAATTTATTATATATATTTATTAT
Found at i:1142176 original size:20 final size:19
Alignment explanation
Indices: 1142153--1142190 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
1142143 TATTATACTG
1142153 TATTTATTATATTATTATAA
1 TATTTATTATATT-TTATAA
1142173 TATTTATTATATTTTATA
1 TATTTATTATATTTTATA
1142191 TTTTATATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTTATTATATTTTATAA
Found at i:1142203 original size:19 final size:19
Alignment explanation
Indices: 1142156--1142225 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 19
1142146 TATACTGTAT
*
1142156 TTATTATAT-TA-TTATAA
1 TTATTATATATATTTAAAA
* *
1142173 -TATT-TATTATATTTTATA
1 TTATTATA-TATATTTAAAA
1142191 TT-TTATATCATATTTAAAA
1 TTATTATAT-ATATTTAAAA
1142210 TTATTATATATATTTA
1 TTATTATATATATTTA
1142226 TACCCTCCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
15 2 0.05
16 5 0.12
17 2 0.05
18 6 0.15
19 20 0.49
20 6 0.15
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATTATATATATTTAAAA
Found at i:1143061 original size:2 final size:2
Alignment explanation
Indices: 1143054--1143090 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1143044 CATCATTTAA
*
1143054 AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1143091 GATTGTGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1144626 original size:22 final size:20
Alignment explanation
Indices: 1144580--1144648 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
1144570 TACATAAGAC
*
1144580 TTTTTATTATAAAATTTATA
1 TTTTTATAATAAAATTTATA
*
1144600 TTTTTATAATATAATTTTATA
1 TTTTTATAATA-AAATTTATA
*
1144621 TATTTTATAA-AAATAGTTATA
1 T-TTTTATAATAAA-ATTTATA
*
1144642 ATTTTAT
1 TTTTTAT
1144649 TTTACTAGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
20 18 0.44
21 15 0.37
22 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (20 bp):
TTTTTATAATAAAATTTATA
Found at i:1144853 original size:2 final size:2
Alignment explanation
Indices: 1144846--1144871 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1144836 ATTACTCATC
1144846 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1144872 GATGACCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1145144 original size:16 final size:17
Alignment explanation
Indices: 1145125--1145168 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
1145115 AACTAAAATG
1145125 ATTTAAATTCGAAT-TA
1 ATTTAAATTCGAATATA
*
1145141 ATTTAATTTCG-ATATA
1 ATTTAAATTCGAATATA
1145157 A-TTAAATTCGAA
1 ATTTAAATTCGAA
1145169 CAATCAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (17 bp):
ATTTAAATTCGAATATA
Found at i:1147476 original size:2 final size:2
Alignment explanation
Indices: 1147469--1147505 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1147459 ACAATCTGAG
1147469 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1147506 AATTTGTGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1147675 original size:24 final size:25
Alignment explanation
Indices: 1147647--1147716 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 25
1147637 TTGTAAAACG
1147647 AATAATATTAAATATAATT-ATATA
1 AATAATATTAAATATAATTAATATA
* *
1147671 AATAATATAAAAAATAATTAAAATATA
1 AATAATATTAAATATAATT--AATATA
1147698 ATATAATATTAAAATATAA
1 A-ATAATATT-AAATATAA
1147717 ATATTTTGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 17 0.46
27 6 0.16
28 7 0.19
29 7 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
AATAATATTAAATATAATTAATATA
Found at i:1147697 original size:18 final size:17
Alignment explanation
Indices: 1147674--1147717 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1147664 TTATATAAAT
1147674 AATATAAAAAATAATTAA
1 AATATAAAAAAT-ATTAA
*
1147692 AATATAATATAATATTAA
1 AATATAA-AAAATATTAA
1147710 AATATAAA
1 AATATAAA
1147718 TATTTTGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 19 0.79
19 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AATATAAAAAATATTAA
Found at i:1147760 original size:16 final size:15
Alignment explanation
Indices: 1147726--1147769 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1147716 AATATTTTGT
*
1147726 AATTTATATTATATA
1 AATTTATAATATATA
1147741 AA-TTACTAATATATTA
1 AATTTA-TAATATA-TA
1147757 AATTTATAATATA
1 AATTTATAATATA
1147770 AATATTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 3 0.12
15 8 0.32
16 11 0.44
17 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTTATAATATATA
Found at i:1147774 original size:20 final size:21
Alignment explanation
Indices: 1147751--1147792 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1147741 AATTACTAAT
1147751 ATATT-AAAT-TTATAATATAA
1 ATATTAAAATATTAT-ATATAA
1147771 ATATTAAAATATTATATATAA
1 ATATTAAAATATTATATATAA
1147792 A
1 A
1147793 ATATAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 11 0.55
22 4 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATTAAAATATTATATATAA
Found at i:1147781 original size:14 final size:14
Alignment explanation
Indices: 1147736--1147806 Score: 56
Period size: 14 Copynumber: 5.0 Consensus size: 14
1147726 AATTTATATT
* *
1147736 ATATAAATTACTAAT
1 ATATAAA-TATTAAA
*
1147751 ATATTAAAT-TTATA
1 ATA-TAAATATTAAA
1147765 ATATAAATATTAAA
1 ATATAAATATTAAA
*
1147779 ATAT-TATATATAAA
1 ATATAAATAT-TAAA
*
1147793 ATATAAATAATAAA
1 ATATAAATATTAAA
1147807 TATTTGGTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
13 9 0.20
14 25 0.56
15 7 0.16
16 4 0.09
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATAAATATTAAA
Found at i:1147795 original size:28 final size:28
Alignment explanation
Indices: 1147736--1147810 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
1147726 AATTTATATT
* * * *
1147736 ATATAAATTACTAATATATTAAATTTATA
1 ATATAAA-TAATAAAATATTAAATATAAA
* *
1147765 ATATAAATATTAAAATATTATATATAAA
1 ATATAAATAATAAAATATTAAATATAAA
1147793 ATATAAATAAT-AAATATT
1 ATATAAATAATAAAATATT
1147811 TGGTTAAAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
27 7 0.17
28 26 0.65
29 7 0.17
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (28 bp):
ATATAAATAATAAAATATTAAATATAAA
Found at i:1149062 original size:6 final size:5
Alignment explanation
Indices: 1149022--1149103 Score: 53
Period size: 5 Copynumber: 16.4 Consensus size: 5
1149012 AATAATAATA
* * * *
1149022 TAAAT TAAAT TAACT TAAAT TATAA- AAAAT AAAATT TAAAT TATATT
1 TAAAT TAAAT TAAAT TAAAT TA-AAT TAAAT TAAA-T TAAAT TA-AAT
* * *
1149069 TAAA- TAAAT TAAAT T-TAT CAAAT TAAAA TAAAT TA
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TA
1149104 TTTACTTTGA
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
4 8 0.14
5 41 0.69
6 10 0.17
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (5 bp):
TAAAT
Found at i:1149077 original size:21 final size:19
Alignment explanation
Indices: 1149025--1149104 Score: 63
Period size: 20 Copynumber: 4.0 Consensus size: 19
1149015 AATAATATAA
*
1149025 ATTAAATTAACTTAAATTAT
1 ATTAAA-TAAATTAAATTAT
**
1149045 AAAAAATAAAATTTAAATTAT
1 ATTAAAT-AAA-TTAAATTAT
1149066 ATTTAAATAAATTAAATT-T
1 A-TTAAATAAATTAAATTAT
* *
1149085 ATCAAATTAAAATAAATTAT
1 ATTAAA-TAAATTAAATTAT
1149105 TTACTTTGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
18 4 0.08
19 13 0.27
20 14 0.29
21 13 0.27
22 4 0.08
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTAAATAAATTAAATTAT
Found at i:1149077 original size:26 final size:27
Alignment explanation
Indices: 1149010--1149103 Score: 92
Period size: 26 Copynumber: 3.7 Consensus size: 27
1149000 TTTTATTATA
* *
1149010 TAAATAATAATATAAATTAAA-TTAACT
1 TAAATTATAA-ATAAATTAAATTTAAAT
*
1149037 TAAATTATAAA-AAATAAAATTTAAAT
1 TAAATTATAAATAAATTAAATTTAAAT
*
1149063 TATATT-TAAATAAATTAAATTT--AT
1 TAAATTATAAATAAATTAAATTTAAAT
*
1149087 CAAATTA-AAATAAATTA
1 TAAATTATAAATAAATTA
1149104 TTTACTTTGA
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
24 16 0.28
25 11 0.19
26 21 0.37
27 9 0.16
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (27 bp):
TAAATTATAAATAAATTAAATTTAAAT
Found at i:1149715 original size:10 final size:10
Alignment explanation
Indices: 1149686--1149731 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
1149676 TAGATTAAAT
1149686 AAATTAATATA
1 AAATT-ATATA
*
1149697 AATTATATATA
1 AAAT-TATATA
1149708 AAATTATA-A
1 AAATTATATA
1149717 AAA-TATATA
1 AAATTATATA
1149726 AAATTA
1 AAATTA
1149732 ATTTATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
8 4 0.13
9 8 0.27
10 6 0.20
11 11 0.37
12 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
AAATTATATA
Found at i:1150067 original size:40 final size:41
Alignment explanation
Indices: 1150003--1150082 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 41
1149993 AAATTGAATT
*
1150003 AATTTAGATTATTATTTAATTATAAAAA-ATATTTTTATTTA
1 AATTTAGATTATAATTTAATTATAAAAATA-ATTTTTATTTA
1150044 AATTTA-ATTATAATATTAA-TATAAAAATAATTTTTATTT
1 AATTTAGATTATAAT-TTAATTATAAAAATAATTTTTATTT
1150083 TTATTTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
40 25 0.69
41 11 0.31
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (41 bp):
AATTTAGATTATAATTTAATTATAAAAATAATTTTTATTTA
Found at i:1150125 original size:17 final size:17
Alignment explanation
Indices: 1150103--1150139 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
1150093 TAATAAAATA
1150103 AAATTTTAAATCAACTT
1 AAATTTTAAATCAACTT
1150120 AAA-TTTAAATCAACTT
1 AAATTTTAAATCAACTT
1150136 AAAT
1 AAAT
1150140 CTAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.84
17 3 0.16
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTTTAAATCAACTT
Found at i:1150128 original size:16 final size:16
Alignment explanation
Indices: 1150107--1150145 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
1150097 AAAATAAAAT
1150107 TTTAAATCAACTTAAA
1 TTTAAATCAACTTAAA
1150123 TTTAAATCAACTTAAA
1 TTTAAATCAACTTAAA
*
1150139 TCTAAAT
1 TTTAAAT
1150146 AAAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (16 bp):
TTTAAATCAACTTAAA
Found at i:1150657 original size:17 final size:17
Alignment explanation
Indices: 1150578--1150662 Score: 51
Period size: 17 Copynumber: 5.4 Consensus size: 17
1150568 TATTTGATAT
*
1150578 TAATATTATATATTT-AA
1 TAAT-TTATAAATTTAAA
*
1150595 TAA-TTAAAAATTTGAAA
1 TAATTTATAAATTT-AAA
*
1150612 TAATTAATAAA-TT---
1 TAATTTATAAATTTAAA
*
1150625 T-ATTTATAAA-TCAAA
1 TAATTTATAAATTTAAA
1150640 TAATTTATAAATTTAAA
1 TAATTTATAAATTTAAA
*
1150657 TTATTT
1 TAATTT
1150663 TTTAAGTAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
12 9 0.17
13 1 0.02
15 9 0.17
16 9 0.17
17 19 0.37
18 5 0.10
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (17 bp):
TAATTTATAAATTTAAA
Found at i:1151036 original size:22 final size:22
Alignment explanation
Indices: 1151010--1151053 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1151000 TGCAATGCTA
* *
1151010 AATTGCAAAAGAAAAATAAAAG
1 AATTGCAAAAAAAAAAAAAAAG
1151032 AATTGCAAAAAAAAAAAAAAAG
1 AATTGCAAAAAAAAAAAAAAAG
1151054 TCTCCAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.73, C:0.05, G:0.11, T:0.11
Consensus pattern (22 bp):
AATTGCAAAAAAAAAAAAAAAG
Found at i:1151150 original size:5 final size:5
Alignment explanation
Indices: 1151122--1151255 Score: 57
Period size: 5 Copynumber: 27.4 Consensus size: 5
1151112 GATGATTCAT
* * * *
1151122 TTAT- TTATA ATATA TT-TA -TATA TTTTA TTATA TTATA ATATA TTTAAA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA -TTATA
* * * * * *
1151170 ATATT TTATA TGTATA -TATA TTTTA ATATA TT-TA TAAT- TTATA TTTTA
1 TTATA TTATA T-TATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * **
1151218 -TAAA TTTTA AAATA TATATA TTATTA TTATA TTATA TT
1 TTATA TTATA TTATA T-TATA TTA-TA TTATA TTATA TT
1151256 TTATATTTAA
Statistics
Matches: 91, Mismatches: 28, Indels: 21
0.65 0.20 0.15
Matches are distributed among these distances:
3 1 0.01
4 20 0.22
5 54 0.59
6 16 0.18
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:1151189 original size:54 final size:51
Alignment explanation
Indices: 1151131--1151268 Score: 139
Period size: 54 Copynumber: 2.8 Consensus size: 51
1151121 TTTATTTATA
**
1151131 ATATATTTATATATTTTATTATATTATAATATATTTAAAATATTTTATATGTAT
1 ATATATTTATATATTTTATTATATT-T-ATATATTTAAAATATTTTA-AAATAT
*
1151185 ATATATTT-TAATATATTTA-TA-ATTTATAT-TTTATAA-ATTTTAAAATAT
1 ATATATTTAT-ATAT-TTTATTATATTTATATATTTAAAATATTTTAAAATAT
*
1151233 ATATA-TTAT-TATTATATTATATTT-TATATTTAAAAT
1 ATATATTTATATATTTTATTATATTTATATATTTAAAAT
1151269 TATTGGATCT
Statistics
Matches: 72, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
45 3 0.04
46 8 0.11
47 12 0.17
48 10 0.14
49 6 0.08
50 6 0.08
51 4 0.06
52 1 0.01
53 4 0.06
54 14 0.19
55 4 0.06
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (51 bp):
ATATATTTATATATTTTATTATATTTATATATTTAAAATATTTTAAAATAT
Found at i:1151205 original size:26 final size:26
Alignment explanation
Indices: 1151121--1151202 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 26
1151111 AGATGATTCA
* *
1151121 TTTAT-TTATAATATATTTATATATTT
1 TTTATATTATAATATATTTA-AAATAT
1151147 TATTATATTATAATATATTTAAAATAT
1 T-TTATATTATAATATATTTAAAATAT
*
1151174 TTTATATGTAT-ATATATTTTAATATAT
1 TTTATAT-TATAATATA-TTTAAAATAT
1151201 TT
1 TT
1151203 ATAATTTATA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
26 12 0.24
27 23 0.47
28 14 0.29
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (26 bp):
TTTATATTATAATATATTTAAAATAT
Found at i:1151253 original size:34 final size:36
Alignment explanation
Indices: 1151140--1151268 Score: 97
Period size: 36 Copynumber: 3.6 Consensus size: 36
1151130 AATATATTTA
* * * * *
1151140 TATATTTTATTATATTATAATATATTTAAAATATT-T
1 TATATTATA-TATATTTTAAAATATATATAATATTAT
* *
1151176 TATATGTATATATATTTTAATATATTTATAAT-TTA-
1 TATAT-TATATATATTTTAAAATATATATAATATTAT
* *
1151211 TAT-TT-TATAAATTTTAAAATATATATATTATTAT
1 TATATTATATATATTTTAAAATATATATAATATTAT
*
1151245 TATATTATATTTTATATTTAAAAT
1 TATATTATA-TATAT-TTTAAAAT
1151269 TATTGGATCT
Statistics
Matches: 76, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
32 20 0.26
33 4 0.05
34 4 0.05
35 7 0.09
36 27 0.36
37 6 0.08
38 8 0.11
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (36 bp):
TATATTATATATATTTTAAAATATATATAATATTAT
Found at i:1151721 original size:13 final size:13
Alignment explanation
Indices: 1151705--1151755 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
1151695 ATGATTAATT
1151705 ATAATAAATATTA
1 ATAATAAATATTA
*
1151718 ATAATAAATAATA
1 ATAATAAATATTA
*
1151731 ATAATAAA-A-TC
1 ATAATAAATATTA
1151742 ATAATATAATATTA
1 ATAATA-AATATTA
1151756 CGATCGATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
11 7 0.22
12 3 0.09
13 21 0.66
14 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAATAAATATTA
Found at i:1152467 original size:24 final size:25
Alignment explanation
Indices: 1152421--1152467 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
1152411 ATTAACTATA
* * *
1152421 ATAATATTTATTAATTATTATATCT
1 ATAATATTTAATAAATATAATATCT
1152446 ATAAT-TTTAATAAATATAATAT
1 ATAATATTTAATAAATATAATAT
1152468 GATTTAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
ATAATATTTAATAAATATAATATCT
Found at i:1159841 original size:14 final size:15
Alignment explanation
Indices: 1159824--1159855 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1159814 AAAATATAAT
1159824 TTTAAAT-TTAAAAA
1 TTTAAATCTTAAAAA
1159838 TTTAAATCTTAAAAA
1 TTTAAATCTTAAAAA
1159853 TTT
1 TTT
1159856 CATTAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAAATCTTAAAAA
Found at i:1159946 original size:21 final size:20
Alignment explanation
Indices: 1159922--1159967 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
1159912 AATTTAAAAA
1159922 TATTCAATTATATCTTAATTT
1 TATTCAATTATAT-TTAATTT
*
1159943 TATTTTAATTATATTTAATTT
1 TA-TTCAATTATATTTAATTT
1159964 TATT
1 TATT
1159968 TTTAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 2 0.09
21 11 0.48
22 10 0.43
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTCAATTATATTTAATTT
Found at i:1159961 original size:10 final size:10
Alignment explanation
Indices: 1159901--1159968 Score: 57
Period size: 10 Copynumber: 6.7 Consensus size: 10
1159891 GCCATTCAAA
1159901 TATATTTAAT
1 TATATTTAAT
* *
1159911 CA-ATTTAAA
1 TATATTTAAT
* *
1159920 AATATTCAAT
1 TATATTTAAT
1159930 TATATCTTAAT
1 TATAT-TTAAT
*
1159941 TTTATTTTAAT
1 TATA-TTTAAT
1159952 TATATTTAAT
1 TATATTTAAT
*
1159962 TTTATTT
1 TATATTT
1159969 TTAATATATT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
9 7 0.16
10 22 0.49
11 15 0.33
12 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (10 bp):
TATATTTAAT
Found at i:1159968 original size:21 final size:22
Alignment explanation
Indices: 1159927--1159979 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
1159917 AAAAATATTC
1159927 AATTATATCTTAATTTTA-TTTT
1 AATTATAT-TTAATTTTATTTTT
1159949 AATTATATTTAATTTTATTTTT
1 AATTATATTTAATTTTATTTTT
1159971 AA-TATATTT
1 AATTATATTT
1159980 TTATATATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 16 0.53
22 14 0.47
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
AATTATATTTAATTTTATTTTT
Found at i:1161013 original size:31 final size:31
Alignment explanation
Indices: 1160975--1161036 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1160965 ACAAAGTTTC
1160975 ACCTCTTTGAACTCTATGGATCCAAAACCCA
1 ACCTCTTTGAACTCTATGGATCCAAAACCCA
1161006 ACCTCTTTGAACTCTATGGATCCAAAACCCA
1 ACCTCTTTGAACTCTATGGATCCAAAACCCA
1161037 TGAAGTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.32, G:0.10, T:0.26
Consensus pattern (31 bp):
ACCTCTTTGAACTCTATGGATCCAAAACCCA
Found at i:1163145 original size:34 final size:34
Alignment explanation
Indices: 1163081--1163263 Score: 260
Period size: 34 Copynumber: 5.4 Consensus size: 34
1163071 AAATGGAAAC
* *
1163081 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
1163114 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1163148 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
1163182 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1163216 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1163250 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1163264 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 11 0.08
34 121 0.92
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1163626 original size:19 final size:20
Alignment explanation
Indices: 1163568--1163627 Score: 88
Period size: 19 Copynumber: 3.1 Consensus size: 20
1163558 TATTGGTTGT
1163568 CGAGGTACTATTCACGTATA
1 CGAGGTACTATTCACGTATA
*
1163588 -TAGGTACTATTCACGTATA
1 CGAGGTACTATTCACGTATA
*
1163607 CGA-GTACTATTCAAGTATA
1 CGAGGTACTATTCACGTATA
1163626 CG
1 CG
1163628 GTTATTGTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 35 0.97
20 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (20 bp):
CGAGGTACTATTCACGTATA
Found at i:1167765 original size:34 final size:34
Alignment explanation
Indices: 1167699--1167883 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
1167689 AAGTGGGAGA
* *
1167699 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
1167732 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1167766 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
1167800 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1167834 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1167868 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1167884 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1170062 original size:29 final size:29
Alignment explanation
Indices: 1170021--1170088 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 29
1170011 AGTTTTATAC
*
1170021 ATACACATATATA-AAATATTAGTGTGTAT
1 ATACATATATATATAAAT-TTAGTGTGTAT
* *
1170050 ATATATATATATATGTGAATTTAGTGTGTAT
1 ATACATATATATA--TAAATTTAGTGTGTAT
1170081 ATACATAT
1 ATACATAT
1170089 TTTTTACTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 11 0.34
31 18 0.56
32 3 0.09
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (29 bp):
ATACATATATATATAAATTTAGTGTGTAT
Found at i:1170385 original size:25 final size:25
Alignment explanation
Indices: 1170351--1170481 Score: 65
Period size: 25 Copynumber: 4.9 Consensus size: 25
1170341 TTATAATTAT
1170351 ATTTTAAATATTATATATTTATATAA
1 ATTTT-AATATTATATATTTATATAA
1170377 ATTTTAATA-TATTAATAATTTATGATTTATAA
1 ATTTTAATATTA-T-AT-A-TT-T-A--TATAA
* *
1170409 ATTTTAA-AATATATATTTATATTAT
1 ATTTTAATATTATATATTTATA-TAA
*
1170434 ATTTT-ATATT-TAATATTTTATATAT
1 ATTTTAATATTAT-ATA-TTTATATAA
* *
1170459 ATATT-ATATTTATATAATTATAT
1 ATTTTAATA-TTATATATTTATAT
1170482 TTAAAATTAT
Statistics
Matches: 86, Mismatches: 4, Indels: 31
0.71 0.03 0.26
Matches are distributed among these distances:
24 6 0.07
25 33 0.38
26 19 0.22
27 3 0.03
28 4 0.05
29 2 0.02
30 3 0.03
31 2 0.02
32 14 0.16
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (25 bp):
ATTTTAATATTATATATTTATATAA
Found at i:1170435 original size:47 final size:46
Alignment explanation
Indices: 1170325--1170462 Score: 115
Period size: 47 Copynumber: 2.9 Consensus size: 46
1170315 ATATTATATT
*
1170325 TATATATTTTATTATATTATAATTATATTTTAAATATTATATATTTA
1 TATATATTTTATTATATTATAATTATATTTTAAATATTATATA-TAA
* *
1170372 TATAAATTTTAATATATTAATAATTTATGATTTATAAAT-TT-TA-A-AA
1 TATATATTTTATTATATT-ATAA-TTAT-ATTT-TAAATATTATATATAA
* *
1170418 TATATATTTATATTATATTTTATATTTAATATTTTATATA-TATAT
1 TATATATTT-TATTATA--TTATAATT-ATATTTTAAATATTATAT
1170463 TATATTTATA
Statistics
Matches: 73, Mismatches: 7, Indels: 21
0.72 0.07 0.21
Matches are distributed among these distances:
46 14 0.19
47 30 0.41
48 10 0.14
49 8 0.11
50 6 0.08
51 5 0.07
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (46 bp):
TATATATTTTATTATATTATAATTATATTTTAAATATTATATATAA
Found at i:1170442 original size:7 final size:7
Alignment explanation
Indices: 1170318--1170456 Score: 61
Period size: 7 Copynumber: 18.9 Consensus size: 7
1170308 TGAATTTATA
1170318 TTATATT
1 TTATATT
1170325 TATATATT
1 T-TATATT
*
1170333 TTATTATA
1 TTA-TATT
*
1170341 TTATA-A
1 TTATATT
1170347 TTATATT
1 TTATATT
1170354 TTAAATATT
1 TT--ATATT
*
1170363 ATATATT
1 TTATATT
1170370 TATATAAATT
1 T-TAT--ATT
1170380 TTAATATAT
1 TT-ATAT-T
* *
1170389 TAATAAT
1 TTATATT
1170396 TTATGATT
1 TTAT-ATT
*
1170404 TATAAATT
1 T-TATATT
* *
1170412 TTAAAAT
1 TTATATT
*
1170419 ATATA-T
1 TTATATT
1170425 TTATA--
1 TTATATT
1170430 TTATATT
1 TTATATT
1170437 TTATATT
1 TTATATT
*
1170444 TAATATT
1 TTATATT
1170451 TTATAT
1 TTATAT
1170457 ATATATTATA
Statistics
Matches: 103, Mismatches: 15, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
5 5 0.05
6 11 0.11
7 42 0.41
8 28 0.27
9 11 0.11
10 6 0.06
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (7 bp):
TTATATT
Found at i:1170462 original size:32 final size:32
Alignment explanation
Indices: 1170313--1170483 Score: 113
Period size: 32 Copynumber: 5.2 Consensus size: 32
1170303 TGTTGTGAAT
* * *
1170313 TTATATTATATTTATATATTTTATTATATTATAA
1 TTATATTTTATATATATATTATATT-TA-TATAA
*
1170347 TTATATTTTAAATAT-TA-TATATTTATATAA
1 TTATATTTTATATATATATTATATTTATATAA
*
1170377 --AT-TTTAATATATTAATAATTTATGATTTATA-AA
1 TTATATTTTATATA-T-AT-A-TTAT-ATTTATATAA
* * * * *
1170410 TTTTAAAATATATATTTATATTATATTT-TATAT
1 --TTATATTTTATATATATATTATATTTATATAA
1170443 TTAATATTTTATATATATATTATATTTATATAA
1 TT-ATATTTTATATATATATTATATTTATATAA
1170476 TTATATTT
1 TTATATTT
1170484 AAAATTATTC
Statistics
Matches: 105, Mismatches: 17, Indels: 32
0.68 0.11 0.21
Matches are distributed among these distances:
27 7 0.07
28 3 0.03
30 6 0.06
31 5 0.05
32 33 0.31
33 18 0.17
34 23 0.22
35 1 0.01
36 2 0.02
37 2 0.02
38 5 0.05
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (32 bp):
TTATATTTTATATATATATTATATTTATATAA
Found at i:1170915 original size:13 final size:12
Alignment explanation
Indices: 1170897--1170950 Score: 65
Period size: 13 Copynumber: 4.3 Consensus size: 12
1170887 ATGATTAATT
1170897 TAATAAATATTAA
1 TAATAAATATT-A
*
1170910 TAATAAATAATAA
1 TAATAAAT-ATTA
1170923 TAATAAA-ATTA
1 TAATAAATATTA
1170934 TAATATAATATTA
1 TAATA-AATATTA
1170947 TAAT
1 TAAT
1170951 CGTTATTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
11 8 0.22
12 2 0.06
13 24 0.67
14 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TAATAAATATTA
Found at i:1171598 original size:13 final size:13
Alignment explanation
Indices: 1171582--1171606 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1171572 TTTTATCATC
1171582 AATATTTATTATT
1 AATATTTATTATT
1171595 AATATTTATTAT
1 AATATTTATTAT
1171607 AATTAACGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AATATTTATTATT
Found at i:1174286 original size:36 final size:39
Alignment explanation
Indices: 1174245--1174317 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 39
1174235 AAATATGATA
1174245 ATAAAA-AT-ATTTTTATATAAAAATT-ATAA-TAAAATT
1 ATAAAAGATAATTTTTAT-TAAAAATTAATAAGTAAAATT
*
1174281 ATAAAATGATAATTTTTATTAAATATTAATAAGTAAA
1 ATAAAA-GATAATTTTTATTAAAAATTAATAAGTAAA
1174318 TAATTTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
36 6 0.19
38 9 0.29
39 12 0.39
40 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (39 bp):
ATAAAAGATAATTTTTATTAAAAATTAATAAGTAAAATT
Found at i:1174358 original size:14 final size:15
Alignment explanation
Indices: 1174341--1174371 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1174331 TTTTTAAAGT
1174341 AATTTTAAA-TTTAA
1 AATTTTAAACTTTAA
1174355 AATTTTAAACTTTAA
1 AATTTTAAACTTTAA
1174370 AA
1 AA
1174372 AAATTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTTAAACTTTAA
Found at i:1174483 original size:11 final size:10
Alignment explanation
Indices: 1174442--1174517 Score: 50
Period size: 10 Copynumber: 7.7 Consensus size: 10
1174432 GCTATTCAGA
1174442 TATATTTAAT
1 TATATTTAAT
* * *
1174452 AATAGTTAAA
1 TATATTTAAT
*
1174462 AATATTTAAT
1 TATATTTAAT
1174472 TATATCTTAAT
1 TATAT-TTAAT
*
1174483 TTTATTTTAAT
1 TATA-TTTAAT
*
1174494 TTTATTT--T
1 TATATTTAAT
*
1174502 TATTTTTAA-
1 TATATTTAAT
1174511 TATATTT
1 TATATTT
1174518 TTATATATTC
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
8 6 0.12
9 6 0.12
10 22 0.42
11 17 0.33
12 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (10 bp):
TATATTTAAT
Found at i:1174502 original size:17 final size:16
Alignment explanation
Indices: 1174482--1174521 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1174472 TATATCTTAA
*
1174482 TTTTATTTTAATTTTAT
1 TTTTATTTTAA-TATAT
1174499 TTTTATTTTTAATATAT
1 TTTTA-TTTTAATATAT
1174516 TTTTAT
1 TTTTAT
1174522 ATATTCAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 14 0.67
18 6 0.29
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTATTTTAATATAT
Found at i:1175099 original size:12 final size:12
Alignment explanation
Indices: 1175084--1175113 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1175074 TTTATTTTTT
1175084 ATAATTTTTTAA
1 ATAATTTTTTAA
1175096 ATAATTTTTTAA
1 ATAATTTTTTAA
*
1175108 AAAATT
1 ATAATT
1175114 ACTTACTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATAATTTTTTAA
Found at i:1175839 original size:2 final size:2
Alignment explanation
Indices: 1175832--1175865 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1175822 ACATCAACCC
1175832 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1175866 CACTAATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1180008 original size:20 final size:20
Alignment explanation
Indices: 1179983--1180053 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
1179973 TTCTACCTAG
1179983 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
1180003 ATGTATCGATACATGTATAA
1 ATGTATCGATACATTTTTCA
*
1180023 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
1180043 ATGTATCGATA
1 ATGTATCGATA
1180054 TATTCTATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1183369 original size:25 final size:25
Alignment explanation
Indices: 1183298--1183369 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 25
1183288 CGCGACACAC
*
1183298 ATATATAAAATATTAGTGTATATAT
1 ATATATATAATATTAGTGTATATAT
* * * *
1183323 AAATATATGATTTTAGTATATATAT
1 ATATATATAATATTAGTGTATATAT
* *
1183348 ATATATATAATATAAATGTATA
1 ATATATATAATATTAGTGTATA
1183370 AAGATATAAA
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (25 bp):
ATATATATAATATTAGTGTATATAT
Found at i:1185960 original size:18 final size:18
Alignment explanation
Indices: 1185933--1186000 Score: 84
Period size: 18 Copynumber: 3.8 Consensus size: 18
1185923 ATTAGCTTCT
*
1185933 AAAATGAAGGCATAATCC
1 AAAATCAAGGCATAATCC
*
1185951 AAAATCAAGGCACAATCC
1 AAAATCAAGGCATAATCC
*
1185969 AAAATCAAGGCA-CATCC
1 AAAATCAAGGCATAATCC
* *
1185986 AAAACCAAGACATAA
1 AAAATCAAGGCATAA
1186001 AAACATGACC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
17 14 0.33
18 29 0.67
ACGTcount: A:0.53, C:0.24, G:0.12, T:0.12
Consensus pattern (18 bp):
AAAATCAAGGCATAATCC
Found at i:1186886 original size:52 final size:52
Alignment explanation
Indices: 1186808--1186977 Score: 234
Period size: 52 Copynumber: 3.2 Consensus size: 52
1186798 TCTGAAAAGA
* * * * *
1186808 AAATGTATTGATATATTTTTCATTGTATCAATATATTCTGGGTTTTTGACCC
1 AAATGTATCGATATATTTTTTATTGTATCGATATATTTTGAGTTTTTGACCC
*
1186860 AAATGTATCGATATATTTTTTATTGTATCGATATATTTTGAGTTTTTAACCC
1 AAATGTATCGATATATTTTTTATTGTATCGATATATTTTGAGTTTTTGACCC
* *
1186912 AAATATATCGA-ATACTTTTTTTATTGTATCGATATATTTTGAGTTTTTGACTC
1 AAATGTATCGATATA--TTTTTTATTGTATCGATATATTTTGAGTTTTTGACCC
*
1186965 AAATGCATCGATA
1 AAATGTATCGATA
1186978 CATTCTTCAA
Statistics
Matches: 104, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
51 3 0.03
52 56 0.54
53 44 0.42
54 1 0.01
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.48
Consensus pattern (52 bp):
AAATGTATCGATATATTTTTTATTGTATCGATATATTTTGAGTTTTTGACCC
Found at i:1189193 original size:27 final size:27
Alignment explanation
Indices: 1189152--1189229 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
1189142 AAAATATCAA
*
1189152 ATTTTATTCGCGGGGATACTCCAACCCC
1 ATTTT-TTCGAGGGGATACTCCAACCCC
* *
1189180 ATTTTTTCGAGGGGATACTCTAACCTC
1 ATTTTTTCGAGGGGATACTCCAACCCC
* * *
1189207 ATTCTTTCTAGGAGATACTCCAA
1 ATTTTTTCGAGGGGATACTCCAA
1189230 ATCCTTTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 38 0.88
28 5 0.12
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (27 bp):
ATTTTTTCGAGGGGATACTCCAACCCC
Found at i:1192775 original size:30 final size:30
Alignment explanation
Indices: 1192741--1192797 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
1192731 TAAATCAAAA
1192741 TAATCAACCTAAACATAGCTTCAACATGAG
1 TAATCAACCTAAACATAGCTTCAACATGAG
*
1192771 TAATCAACCTAGACATAGCTTCAACAT
1 TAATCAACCTAAACATAGCTTCAACAT
1192798 AACATAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.42, C:0.25, G:0.09, T:0.25
Consensus pattern (30 bp):
TAATCAACCTAAACATAGCTTCAACATGAG
Found at i:1195783 original size:22 final size:22
Alignment explanation
Indices: 1195757--1195798 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1195747 ATTAAAATTT
1195757 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
1195779 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
1195799 ATTTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:1196011 original size:12 final size:12
Alignment explanation
Indices: 1195980--1196022 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
1195970 TGAAAAATCA
* *
1195980 CTTTTTATTTAT
1 CTTTTTTTTTTT
*
1195992 CTTCTTTTTTTT
1 CTTTTTTTTTTT
1196004 CTTTTTTTTTTT
1 CTTTTTTTTTTT
1196016 -TTTTTTT
1 CTTTTTTT
1196023 GAAGCTTGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
11 7 0.26
12 20 0.74
ACGTcount: A:0.05, C:0.09, G:0.00, T:0.86
Consensus pattern (12 bp):
CTTTTTTTTTTT
Found at i:1200566 original size:31 final size:31
Alignment explanation
Indices: 1200528--1200586 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
1200518 CAAAATTTAT
1200528 TTTATTATTAA-AA-TAATTAAATTTAAATAAA
1 TTTATTATTAATAATTAA-T-AATTTAAATAAA
1200559 TTTATTATTAATAATTAATAATTTAAAT
1 TTTATTATTAATAATTAATAATTTAAAT
1200587 CTAATTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
31 20 0.77
32 3 0.12
33 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TTTATTATTAATAATTAATAATTTAAATAAA
Found at i:1202109 original size:17 final size:18
Alignment explanation
Indices: 1202086--1202131 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
1202076 TTTTTATATT
1202086 ATAAAAAATAAAAAT-AA
1 ATAAAAAATAAAAATAAA
* *
1202103 TTAAAAATTAAAAATAAA
1 ATAAAAAATAAAAATAAA
1202121 ATAAAAAATAA
1 ATAAAAAATAA
1202132 CTTTCAATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (18 bp):
ATAAAAAATAAAAATAAA
Found at i:1202884 original size:2 final size:2
Alignment explanation
Indices: 1202879--1202919 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1202869 TTTTTGTGTG
1202879 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1202920 TACTCTAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1205014 original size:20 final size:20
Alignment explanation
Indices: 1204986--1205060 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
1204976 TTTTACCCAG
1204986 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1205006 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
1205026 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
1205046 ATGTATCGATACATT
1 ATGTATCGATACATT
1205061 ATGTCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1205046 original size:40 final size:39
Alignment explanation
Indices: 1204986--1205063 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
1204976 TTTTACCCAG
*
1204986 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* *
1205026 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
1205064 TCTTTTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:1206068 original size:22 final size:21
Alignment explanation
Indices: 1206022--1206069 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
1206012 GTCCAGCATC
1206022 TCATTGAATGTTATCCATTAGT
1 TCATTGAATGTTATCCATTA-T
*
1206044 TCATTGTATGATTATCACATT-T
1 TCATTGAATG-TTATC-CATTAT
1206066 TCAT
1 TCAT
1206070 GTTAAGATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 14 0.61
23 5 0.22
24 4 0.17
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (21 bp):
TCATTGAATGTTATCCATTAT
Found at i:1208905 original size:20 final size:20
Alignment explanation
Indices: 1208867--1208907 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1208857 GGAAGGGTCA
*
1208867 TTTTTTTTATTGATGTTCAT
1 TTTTTTTTATTGATATTCAT
* *
1208887 TTTTTTTTCTTGCTATTCAT
1 TTTTTTTTATTGATATTCAT
1208907 T
1 T
1208908 CCCATTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.10, G:0.07, T:0.71
Consensus pattern (20 bp):
TTTTTTTTATTGATATTCAT
Found at i:1218609 original size:11 final size:11
Alignment explanation
Indices: 1218593--1218648 Score: 60
Period size: 11 Copynumber: 4.8 Consensus size: 11
1218583 TCCTTTACAC
1218593 CAAAAAAAAAA
1 CAAAAAAAAAA
*
1218604 CAAAAATAAAA
1 CAAAAAAAAAA
1218615 CAAAATAAAAAA
1 CAAAA-AAAAAA
1218627 -AACAAAAAAAA
1 CAA-AAAAAAAA
1218638 CCAAGAAAAAA
1 -CAA-AAAAAA
1218649 TAGCCAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
11 23 0.61
12 7 0.18
13 8 0.21
ACGTcount: A:0.84, C:0.11, G:0.02, T:0.04
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:1218619 original size:10 final size:9
Alignment explanation
Indices: 1218594--1218637 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
1218584 CCTTTACACC
1218594 AAAAAAAA-
1 AAAAAAAAT
*
1218602 AACAAAAAT
1 AAAAAAAAT
1218611 AAAACAAAAT
1 AAAA-AAAAT
*
1218621 AAAAAAAAC
1 AAAAAAAAT
1218630 AAAAAAAA
1 AAAAAAAA
1218638 CCAAGAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.23
9 15 0.48
10 9 0.29
ACGTcount: A:0.89, C:0.07, G:0.00, T:0.05
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:1219916 original size:29 final size:29
Alignment explanation
Indices: 1219876--1220744 Score: 1191
Period size: 29 Copynumber: 29.9 Consensus size: 29
1219866 TGTTCATCCC
*
1219876 TTTCAAAACCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1219905 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1219933 TTTCAAAGCCCACAATTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1219962 TTTCAAAGCCCACAAATCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1219991 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
1220020 TTTCAAAGCTCACAAATCAGTGGTACTAT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1220049 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1220078 TTTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1220107 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1220136 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1220164 TTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1220193 TTTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1220222 TTTTAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1220251 TTTCAAAGCCTACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1220280 ATTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1220308 TTTCAAAGCCCACAATTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1220337 TTTCAAAGCCTACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1220366 TTT-AAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1220394 TTTCAAAGCCCACACGAGTCGGTGGCGACTCT
1 TTTCAAAGCCCACA--AGTCAGTGGC-ACTCT
* *
1220426 TTTCAAAGCCCACAAGTTAGTGGCAC-CA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1220454 TTTCAAAGCCCATGCAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCT
*
1220484 TTTCAAAGCCCACAAATCAGTGGCACT-T
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
1220512 TGTTCAAATCCAACAAGTTAGTGGCA-TCC
1 T-TTCAAAGCCCACAAGTCAGTGGCACTCT
*
1220541 TTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1220570 TTTCAAAGCTCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
1220599 TTTTAAAACCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1220628 TTTCAAAGCCCACAAGTCAGTGGCAC-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1220656 TTTCAAAGCCCACAAGTCAAAT-GCACTCT
1 TTTCAAAGCCCACAAGTC-AGTGGCACTCT
**
1220685 TTTCAAAGCCCACACGAGTTGGTGGCAACTCT
1 TTTCAAAGCCCACA--AGTCAGTGGC-ACTCT
*
1220717 TTTCAAAGCCCACACAAGTTAGTGGCAC
1 TTTCAAAG-CC-CACAAGTCAGTGGCAC
1220745 CATTTTTTTT
Statistics
Matches: 749, Mismatches: 70, Indels: 40
0.87 0.08 0.05
Matches are distributed among these distances:
28 177 0.24
29 474 0.63
30 35 0.05
31 16 0.02
32 41 0.05
33 2 0.00
34 4 0.01
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.24
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCT
Found at i:1220108 original size:115 final size:116
Alignment explanation
Indices: 1219874--1220744 Score: 1179
Period size: 115 Copynumber: 7.5 Consensus size: 116
1219864 AATGTTCATC
* *
1219874 CCTTTCAAAACCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCA
* *
1219938 AAGCCCACAATTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACT
66 AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
1219989 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCTCACAAATCAGTGGTACTATTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCA
*
1220054 AAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-
66 AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1220104 CCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTC
1 CC-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTC
* *
1220168 AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACT
65 AAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* * * * *
1220220 CTTTTTAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCTACAAGTCAGTGGCACTCTATTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCA
* *
1220285 AAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAATTCAGTGGCACT
66 AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1220335 CTTTTCAAAGCCTACAAGTCAGTGGCACCCTTTT-AAAGCCCACAAGTCAGTGGCACTCTTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCA
* *
1220399 AAGCCCACACGAGTCGGTGGCGACTCTTTTCAAAGCCCACAAGTTAGTGGCAC-
66 AAGCCCACA--AGTCAGTGGC-ACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1220452 CATTTCAAAGCCCATGCAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAATCAGTGGCACT-TTGT
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTT-T
* * * *
1220515 TCAAATCCAACAAGTTAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACT
63 TCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
1220568 CCTTTCAAAGCTCACAAGTCAGTGGCACTCTTTTTAAAACCCACAAATCAGTGGCACTCTTTTCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCA
*
1220633 AAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAAAT-GCACT
66 AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTC-AGTGGCACT
* ** *
1220683 CTTTTCAAAGCCCACACGAGTTGGTGGCAACTCTTTTCAAAGCCCACACAAGTTAGTGGCAC
1 CCTTTCAAAGCCCACA--AGTCAGTGGC-ACTCTTTTCAAAG-CC-CACAAGTCAGTGGCAC
1220745 CATTTTTTTT
Statistics
Matches: 672, Mismatches: 62, Indels: 39
0.87 0.08 0.05
Matches are distributed among these distances:
114 51 0.08
115 329 0.49
116 157 0.23
117 30 0.04
118 42 0.06
119 49 0.07
120 14 0.02
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (116 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCA
AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:1221360 original size:20 final size:20
Alignment explanation
Indices: 1221310--1221360 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1221300 TTTTACCCAG
* *
1221310 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATGTATCA
* * *
1221330 ATATATTGATACATGTATGA
1 ATGTATCGATACATGTATCA
1221350 ATGTATCGATA
1 ATGTATCGATA
1221361 TATTCTTTAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATGTATCA
Found at i:1221382 original size:40 final size:39
Alignment explanation
Indices: 1221310--1221387 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 39
1221300 TTTTACCCAG
**
1221310 ATGTATCGATACATTTTTCAATATATTGATACATGTATGA
1 ATGTATCGATACATTTTTCAATATATCAATACAT-TATGA
* *
1221350 ATGTATCGATATATTCTTT-AATGTATCAATACATTATG
1 ATGTATCGATACATT-TTTCAATATATCAATACATTATG
1221388 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 4 0.12
40 26 0.79
41 3 0.09
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.44
Consensus pattern (39 bp):
ATGTATCGATACATTTTTCAATATATCAATACATTATGA
Found at i:1224681 original size:2 final size:2
Alignment explanation
Indices: 1224674--1224707 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1224664 AATTCTTTAA
1224674 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1224708 TTTTAAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1224951 original size:2 final size:2
Alignment explanation
Indices: 1224944--1224970 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1224934 ACATGCATAC
1224944 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1224971 AGCTGTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1225666 original size:33 final size:33
Alignment explanation
Indices: 1225579--1225666 Score: 124
Period size: 33 Copynumber: 2.7 Consensus size: 33
1225569 TTAATTGGTG
* *
1225579 ACACCATTTTGC-TTCACTTCTCTAGCTGCTGCA
1 ACACCATTTT-CATTCACTTCTTTAGCTGCCGCA
*
1225612 ACACCATTTTCCTTCACTTCTTTAGCTGCCGCA
1 ACACCATTTTCATTCACTTCTTTAGCTGCCGCA
*
1225645 ACACGATTTTCATTCACTTCTT
1 ACACCATTTTCATTCACTTCTT
1225667 CGACATCTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.02
33 49 0.98
ACGTcount: A:0.19, C:0.33, G:0.09, T:0.39
Consensus pattern (33 bp):
ACACCATTTTCATTCACTTCTTTAGCTGCCGCA
Found at i:1230077 original size:24 final size:24
Alignment explanation
Indices: 1230011--1230077 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 24
1230001 TGAGTAAATT
1230011 TAATATTAATTTTTATATAAATTATA
1 TAAT-TTAATTTTTAT-TAAATTATA
* *
1230037 AAATTTTAA-TTTAATTAAATTATA
1 TAA-TTTAATTTTTATTAAATTATA
1230061 TAATTTAATTTTTATTA
1 TAATTTAATTTTTATTA
1230078 TTAATAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 5 0.14
24 18 0.51
25 5 0.14
26 6 0.17
27 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TAATTTAATTTTTATTAAATTATA
Found at i:1230082 original size:18 final size:17
Alignment explanation
Indices: 1230037--1230095 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 17
1230027 ATAAATTATA
1230037 AAATT-TTAATTTAATT
1 AAATTATTAATTTAATT
1230053 AAATTATATAATTTAATTT
1 AAATTAT-TAATTTAA-TT
** *
1230072 TTATTATTAA-TAAATT
1 AAATTATTAATTTAATT
1230088 AAATTATT
1 AAATTATT
1230096 TATATTAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
16 13 0.37
17 4 0.11
18 11 0.31
19 7 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AAATTATTAATTTAATT
Found at i:1230087 original size:22 final size:22
Alignment explanation
Indices: 1230062--1230103 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1230052 TAAATTATAT
*
1230062 AATTTAATT-TTTATTATTAATA
1 AATTAAATTATTTA-TATTAATA
1230084 AATTAAATTATTTATATTAA
1 AATTAAATTATTTATATTAA
1230104 ATTTATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AATTAAATTATTTATATTAATA
Found at i:1230283 original size:14 final size:14
Alignment explanation
Indices: 1230264--1230294 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1230254 ACATAGTTTA
1230264 TTAATAATATAAAT
1 TTAATAATATAAAT
*
1230278 TTAATAATATAATT
1 TTAATAATATAAAT
1230292 TTA
1 TTA
1230295 TAAAATTAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAATAATATAAAT
Found at i:1230918 original size:19 final size:18
Alignment explanation
Indices: 1230896--1230934 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1230886 AACATCTATT
1230896 ATATATATATATAATTATA
1 ATATATATATATAA-TATA
*
1230915 ATATGTATATATAATATA
1 ATATATATATATAATATA
1230933 AT
1 AT
1230935 CGAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
ATATATATATATAATATA
Found at i:1231580 original size:21 final size:20
Alignment explanation
Indices: 1231556--1231633 Score: 54
Period size: 21 Copynumber: 3.8 Consensus size: 20
1231546 TCGAATAATA
1231556 TCAAAATTTATTACAAATGTT
1 TCAAAA-TTATTACAAATGTT
*
1231577 TC--AATT-GTATCAAATGTTAT
1 TCAAAATTATTA-CAAATG-T-T
*
1231597 TCAAAATTATTATAAATGTT
1 TCAAAATTATTACAAATGTT
**
1231617 ATTTAAATTATTACAAA
1 -TCAAAATTATTACAAA
1231634 AATTATATCA
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
17 2 0.05
18 8 0.18
19 3 0.07
20 4 0.09
21 16 0.36
22 9 0.20
23 2 0.05
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (20 bp):
TCAAAATTATTACAAATGTT
Found at i:1231613 original size:22 final size:21
Alignment explanation
Indices: 1231588--1231629 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
1231578 CAATTGTATC
1231588 AAATGTTATTCAAAATTATTAT
1 AAATGTTATT-AAAATTATTAT
*
1231610 AAATGTTATTTAAATTATTA
1 AAATGTTATTAAAATTATTA
1231630 CAAAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (21 bp):
AAATGTTATTAAAATTATTAT
Found at i:1231639 original size:21 final size:21
Alignment explanation
Indices: 1231600--1231639 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1231590 ATGTTATTCA
* **
1231600 AAATTATTATAAATGTTATTT
1 AAATTATTACAAAAATTATTT
1231621 AAATTATTACAAAAATTAT
1 AAATTATTACAAAAATTAT
1231640 ATCAAATGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (21 bp):
AAATTATTACAAAAATTATTT
Found at i:1231651 original size:21 final size:20
Alignment explanation
Indices: 1231627--1231983 Score: 116
Period size: 21 Copynumber: 16.9 Consensus size: 20
1231617 ATTTAAATTA
1231627 TTACAAAAATTATATCAAATG
1 TTAC-AAAATTATATCAAATG
* *
1231648 TTACTAAAATTCTCTCTAAA-G
1 TTAC-AAAATTATATC-AAATG
** *
1231669 TTATCAATTTTATATTAAGA-G
1 TTA-CAAAATTATATCAA-ATG
* * *
1231690 TTATCAAAATTTTATTAATTG
1 TTA-CAAAATTATATCAAATG
* * *
1231711 TTAGATAAAATATATCAAAGG
1 TTACA-AAATTATATCAAATG
* * *
1231732 CTAAATAAAATTATATCAAAAG
1 -T-TACAAAATTATATCAAATG
* *
1231754 TTACTAAAATTATCTAAAATG
1 TTAC-AAAATTATATCAAATG
* * * *
1231775 TTACTAAAACTATTTAAAATT
1 TTAC-AAAATTATATCAAATG
* *
1231796 TTATCAAAATTATCTAAAATG
1 TTA-CAAAATTATATCAAATG
* *
1231817 TTACCAAAACTATATCAAATA
1 TTA-CAAAATTATATCAAATG
* *
1231838 TTATCGAAATTATATTAAA-G
1 TTA-CAAAATTATATCAAATG
* * *
1231858 ATTGAAAAAATTATATTAAAAG
1 -TT-ACAAAATTATATCAAATG
1231880 TTATCAAAATTATATCAAA-G
1 TTA-CAAAATTATATCAAATG
* *
1231900 TTACCAAAA-TAAACTCAAACG
1 TTA-CAAAATTATA-TCAAATG
* *
1231921 TTACTAAACTTATATTGAAAAT-
1 TTAC-AAAATTATA-T-CAAATG
* *
1231943 TTTCAAAAATTATAT-AAAAG
1 TTAC-AAAATTATATCAAATG
*
1231963 ATTATCAAAATTATATAAAAT
1 -TTA-CAAAATTATATCAAAT
1231984 AAAGATTAAT
Statistics
Matches: 254, Mismatches: 60, Indels: 43
0.71 0.17 0.12
Matches are distributed among these distances:
19 6 0.02
20 20 0.08
21 183 0.72
22 40 0.16
23 5 0.02
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.36
Consensus pattern (20 bp):
TTACAAAATTATATCAAATG
Found at i:1231770 original size:10 final size:10
Alignment explanation
Indices: 1231737--1231815 Score: 56
Period size: 10 Copynumber: 7.6 Consensus size: 10
1231727 AAAGGCTAAA
*
1231737 TAAAATTATA
1 TAAAATTATC
1231747 TCAAAAGTTA-C
1 T-AAAA-TTATC
1231758 TAAAATTATC
1 TAAAATTATC
1231768 TAAAATGT-TAC
1 TAAAAT-TAT-C
* *
1231779 TAAAACTATT
1 TAAAATTATC
1231789 TAAAATTTTATC
1 TAAAA--TTATC
1231801 -AAAATTATC
1 TAAAATTATC
1231810 TAAAAT
1 TAAAAT
1231816 GTTACCAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
9 8 0.15
10 24 0.44
11 17 0.31
12 6 0.11
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.38
Consensus pattern (10 bp):
TAAAATTATC
Found at i:1231783 original size:42 final size:42
Alignment explanation
Indices: 1231738--1231983 Score: 179
Period size: 42 Copynumber: 5.9 Consensus size: 42
1231728 AAGGCTAAAT
* *
1231738 AAAATTATATCAAAAGTTA-CTAAAATTATCTAAAATGTTACT
1 AAAATTATATCAAAAGTTATC-AAAATTATATAAAATGTTACA
* * * * *
1231780 AAAACTAT-TTAAAATTTTATCAAAATTATCTAAAATGTTACC
1 AAAATTATATCAAAA-GTTATCAAAATTATATAAAATGTTACA
* * *
1231822 AAAACTATATCAAATA-TTATCGAAATTATATTAAAGAT-TGA-A
1 AAAATTATATCAAA-AGTTATCAAAATTATA-TAAA-ATGTTACA
* * *
1231864 AAAATTATATTAAAAGTTATCAAAATTATATCAAA-GTTACC
1 AAAATTATATCAAAAGTTATCAAAATTATATAAAATGTTACA
* * * *
1231905 AAAA-TAAACTCAAACGTTA-CTAAACTTATATTGAAAAT-TTTCA
1 AAAATTATA-TCAAAAGTTATC-AAAATTATA-T-AAAATGTTACA
1231948 AAAATTATAT-AAAAGATTATCAAAATTATATAAAAT
1 AAAATTATATCAAAAG-TTATCAAAATTATATAAAAT
1231984 AAAGATTAAT
Statistics
Matches: 162, Mismatches: 25, Indels: 35
0.73 0.11 0.16
Matches are distributed among these distances:
40 7 0.04
41 34 0.21
42 81 0.50
43 33 0.20
44 7 0.04
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.35
Consensus pattern (42 bp):
AAAATTATATCAAAAGTTATCAAAATTATATAAAATGTTACA
Found at i:1231884 original size:84 final size:85
Alignment explanation
Indices: 1231796--1231983 Score: 226
Period size: 84 Copynumber: 2.2 Consensus size: 85
1231786 ATTTAAAATT
* * *
1231796 TTATCAAAATTATCTAAAATGTTACCAAAACTATA-TCAAATATTATCGAAA-TTATATT-AAAG
1 TTATCAAAATTATATAAAATGTTACCAAAA-TAAACTCAAACATTA-CGAAACTTATATTGAAA-
1231858 A-TTGAAAAAATTATATTAAAAG-
63 ATTTGAAAAAATTATA-TAAAAGA
* * *
1231880 TTATCAAAATTATATCAAA-GTTACCAAAATAAACTCAAACGTTACTAAACTTATATTGAAAATT
1 TTATCAAAATTATATAAAATGTTACCAAAATAAACTCAAACATTACGAAACTTATATTGAAAATT
**
1231944 TTCAAAAATTATATAAAAGA
66 TGAAAAAATTATATAAAAGA
1231964 TTATCAAAATTATATAAAAT
1 TTATCAAAATTATATAAAAT
1231984 AAAGATTAAT
Statistics
Matches: 89, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
82 7 0.08
83 32 0.36
84 50 0.56
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.34
Consensus pattern (85 bp):
TTATCAAAATTATATAAAATGTTACCAAAATAAACTCAAACATTACGAAACTTATATTGAAAATT
TGAAAAAATTATATAAAAGA
Found at i:1232578 original size:27 final size:28
Alignment explanation
Indices: 1232548--1232604 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
1232538 TAAGTTATTA
*
1232548 TATTTTT-A-TTATATTCAAATAAATTTT
1 TATTTTTAATTTATATT-AAATAAATCTT
1232575 TATTTTTAATTTATATTAAATAAATCTT
1 TATTTTTAATTTATATTAAATAAATCTT
1232603 TA
1 TA
1232605 AATTAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 7 0.26
28 13 0.48
29 7 0.26
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (28 bp):
TATTTTTAATTTATATTAAATAAATCTT
Found at i:1232680 original size:29 final size:31
Alignment explanation
Indices: 1232649--1232713 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1232639 GTTTAAGTAT
1232649 AAAA-TAAAAAATAAAAATTTTATTTGAATA
1 AAAATTAAAAAATAAAAATTTTATTTGAATA
* *
1232679 AAAATTAAAAATTAAAAA-TTTATTT-AATG
1 AAAATTAAAAAATAAAAATTTTATTTGAATA
1232708 AAAATT
1 AAAATT
1232714 TAAAGATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 9 0.28
30 11 0.34
31 12 0.38
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (31 bp):
AAAATTAAAAAATAAAAATTTTATTTGAATA
Found at i:1232689 original size:30 final size:29
Alignment explanation
Indices: 1232640--1232724 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 29
1232630 TAAGAGATTG
*
1232640 TTTAAGTATAAAA-TAAAAAATAAAAATTTTA
1 TTTAA-TA-AAAATTAAAAATTAAAAA-TTTA
1232671 TTTGAATAAAAATTAAAAATTAAAAATTTA
1 TTT-AATAAAAATTAAAAATTAAAAATTTA
* *
1232701 TTTAATGAAAATTTAAAGATTAAA
1 TTTAAT-AAAAATTAAAAATTAAA
1232725 CCTTATTTGA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
29 3 0.06
30 26 0.54
31 17 0.35
32 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (29 bp):
TTTAATAAAAATTAAAAATTAAAAATTTA
Found at i:1233117 original size:18 final size:18
Alignment explanation
Indices: 1233091--1233139 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
1233081 ATATTTTATT
1233091 TACTATAAATTATAGA-ATA
1 TACTATAAATTATA-ACA-A
1233110 TA-TATAAA-TATAACAA
1 TACTATAAATTATAACAA
1233126 TACTATAAATTATA
1 TACTATAAATTATA
1233140 TTTTTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.15
17 11 0.41
18 10 0.37
19 2 0.07
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (18 bp):
TACTATAAATTATAACAA
Found at i:1234530 original size:20 final size:20
Alignment explanation
Indices: 1234501--1234576 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
1234491 AAAGTACCTA
*
1234501 AATGTATCGATATATTTTTC
1 AATGTATCGATACATTTTTC
* * * *
1234521 AATATATCGATACATGTATG
1 AATGTATCGATACATTTTTC
*
1234541 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTTTTC
1234561 AATGTATCGATACATT
1 AATGTATCGATACATT
1234577 CTGTCTTTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:1238775 original size:19 final size:19
Alignment explanation
Indices: 1238734--1238777 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1238724 AAGGAAGGCC
1238734 ATTC-TTTTTTTTATTGAT
1 ATTCATTTTTTTTATTGAT
* * *
1238752 GTTCATTTTTTTTCTTGCT
1 ATTCATTTTTTTTATTGAT
1238771 ATTCATT
1 ATTCATT
1238778 CCCATTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.14, C:0.11, G:0.07, T:0.68
Consensus pattern (19 bp):
ATTCATTTTTTTTATTGAT
Found at i:1243617 original size:57 final size:57
Alignment explanation
Indices: 1243539--1244014 Score: 360
Period size: 57 Copynumber: 8.4 Consensus size: 57
1243529 ACTGTGACCG
* * * * * * *
1243539 TTTTAAAGTCCACGATTCAGTGGCATTTCTTTTCAAAGTACATAACTCTGTGGCA-TCC
1 TTTTAAAGTCCACAAGTCAGTGGCA--CCCTTTCAAAGCACACAACTCAGTGGCATTCC
* * *
1243597 TTTT-AAGTCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATTCT
1 TTTTAAAGTCCACAAGTCAGTGGCACCCTTTCAAAGCACACAACTCAGTGGCATTCC
* * * * *
1243653 TTTTAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCA-CCC
1 TTTTAAAGTCCACAAGTCAGTGGCACCCTTTCAAAGCACACAACTCAGTGGCATTCC
* * * * * * * *
1243709 TTTCAAAGCCCACAAGTTAGTGGCACTCCTTTTAAAGCCCACAAGTTAGTGGCACTCC
1 TTTTAAAGTCCACAAGTCAGTGGCAC-CCTTTCAAAGCACACAACTCAGTGGCATTCC
* * * * * *
1243767 TTTCAAAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCA-CCC
1 TTTTAAAGTCCACAAGTCAGTGGCAC-CCTTTCAAAGCACACAACTCAGTGGCATTCC
* * * * * * *
1243824 TTTCAAAGCCCATAAGTCAGTGGCACCCTTTCAAAGCCCATAAGTCAGTGGCACTCC
1 TTTTAAAGTCCACAAGTCAGTGGCACCCTTTCAAAGCACACAACTCAGTGGCATTCC
* * * * *
1243881 TTTCAAA-ACGCACAAGTTAGTGGCACTCC-TTCAAAGC-CACAAGTCAGTGGCA-CCC
1 TTTTAAAGTC-CACAAGTCAGTGGCAC-CCTTTCAAAGCACACAACTCAGTGGCATTCC
* * * ** * * *
1243936 TTTCAAAGCCCACAAGTGAGTGGCACTTTTTTCAAAGCCCACAAGTCAGTGGCA-CCC
1 TTTTAAAGTCCACAAGTCAGTGGCAC-CCTTTCAAAGCACACAACTCAGTGGCATTCC
*
1243993 TTTCAAAG-CTCACAAGTCAGTG
1 TTTTAAAGTC-CACAAGTCAGTG
1244015 ACATTCTTTT
Statistics
Matches: 370, Mismatches: 37, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
55 46 0.12
56 82 0.22
57 182 0.49
58 60 0.16
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (57 bp):
TTTTAAAGTCCACAAGTCAGTGGCACCCTTTCAAAGCACACAACTCAGTGGCATTCC
Found at i:1243670 original size:29 final size:28
Alignment explanation
Indices: 1243588--1244063 Score: 548
Period size: 29 Copynumber: 16.8 Consensus size: 28
1243578 ACATAACTCT
* *
1243588 GTGGCATCCTTT-TAAGTCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
*
1243615 GTGGCACCCTTTCAAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* *
1243643 GTGGCATTCTTTTTAAAGCCCACAAGTCA
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCA
1243672 GTGGCA-CCTTTTCAAAGCCCACAAGTCA
1 GTGGCATCC-TTTCAAAGCCCACAAGTCA
* *
1243700 GTGGCACCCTTTCAAAGCCCACAAGTTA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* *
1243728 GTGGCACTCCTTTTAAAGCCCACAAGTTA
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCA
*
1243757 GTGGCACTCCTTTCAAAGCCCACAAGTTA
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCA
1243786 GTGGCACTCCTTTCAAAGCCCACAAGTCA
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCA
* *
1243815 GTGGCACCCTTTCAAAGCCCATAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* *
1243843 GTGGCACCCTTTCAAAGCCCATAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* * *
1243871 GTGGCACTCCTTTCAAAACGCACAAGTTA
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCA
1243900 GTGGCACTCC-TTCAAAG-CCACAAGTCA
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCA
* *
1243927 GTGGCACCCTTTCAAAGCCCACAAGTGA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
**
1243955 GTGGCACTTTTTTCAAAGCCCACAAGTCA
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCA
* *
1243984 GTGGCACCCTTTCAAAGCTCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* * * *
1244012 GTGACATTCTTTTCAAGGACCACAAG-CTA
1 GTGGCA-TCCTTTCAAAGCCCACAAGTC-A
* *
1244041 GTGGTAACTCTTTTCAAAGCCCA
1 GTGG-CA-TCCTTTCAAAGCCCA
1244064 TACGAGTTAG
Statistics
Matches: 393, Mismatches: 44, Indels: 21
0.86 0.10 0.05
Matches are distributed among these distances:
26 2 0.01
27 33 0.08
28 166 0.42
29 178 0.45
30 14 0.04
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (28 bp):
GTGGCATCCTTTCAAAGCCCACAAGTCA
Found at i:1244023 original size:28 final size:28
Alignment explanation
Indices: 1243588--1244014 Score: 590
Period size: 28 Copynumber: 15.1 Consensus size: 28
1243578 ACATAACTCT
* * *
1243588 GTGGCATCCTTT-TAAGTCCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
1243615 GTGGCACCCTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
* * *
1243643 GTGGCATTCTTTTTAAAGCCCACAAGTCA
1 GTGGCA-CCCTTTCAAAGCCCACAAGTCA
*
1243672 GTGGCACCTTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
*
1243700 GTGGCACCCTTTCAAAGCCCACAAGTTA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
* *
1243728 GTGGCACTCCTTTTAAAGCCCACAAGTTA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCA
*
1243757 GTGGCACTCCTTTCAAAGCCCACAAGTTA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCA
1243786 GTGGCACTCCTTTCAAAGCCCACAAGTCA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCA
*
1243815 GTGGCACCCTTTCAAAGCCCATAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
*
1243843 GTGGCACCCTTTCAAAGCCCATAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
* * *
1243871 GTGGCACTCCTTTCAAAACGCACAAGTTA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCA
1243900 GTGGCACTCC-TTCAAAG-CCACAAGTCA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCA
*
1243927 GTGGCACCCTTTCAAAGCCCACAAGTGA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
**
1243955 GTGGCACTTTTTTCAAAGCCCACAAGTCA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCA
*
1243984 GTGGCACCCTTTCAAAGCTCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
1244012 GTG
1 GTG
1244015 ACATTCTTTT
Statistics
Matches: 365, Mismatches: 28, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
26 2 0.01
27 33 0.09
28 170 0.47
29 160 0.44
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.23
Consensus pattern (28 bp):
GTGGCACCCTTTCAAAGCCCACAAGTCA
Found at i:1244025 original size:57 final size:56
Alignment explanation
Indices: 1243588--1244097 Score: 571
Period size: 57 Copynumber: 8.9 Consensus size: 56
1243578 ACATAACTCT
* * * *
1243588 GTGGCATCCTTT-TAAGTCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCA
* * *
1243643 GTGGCATTCTTTTTAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCA
1 GTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCA
* *
1243700 GTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCCTTTT-AAAGCCCACAAGTTA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA--CCTTTTCAAAGCCCACAAGTCA
* *
1243757 GTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACAAGTCA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCA
* * *
1243815 GTGGCACCCTTTCAAAGCCCATAAGTCAGTGGCACCCTTTCAAAGCCCATAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCA
* * * *
1243871 GTGGCACTCCTTTCAAAACGCACAAGTTAGTGGCA-CTCCTTCAAAG-CCACAAGTCA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCT-TTTCAAAGCCCACAAGTCA
* *
1243927 GTGGCACCCTTTCAAAGCCCACAAGTGAGTGGCACTTTTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCA
* * * * *
1243984 GTGGCACCCTTTCAAAGCTCACAAGTCAGTGACATTCTTTTCAAGGACCACAAG-CTA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTC-A
* * * * *
1244041 GTGGTAACTCTTTTCAAAGCCCATACGAGTTAGTGGCAACTATTTTCAAAGCCCACA
1 GTGG-CAC-CCTTTCAAAGCCC--ACAAGTCAGTGGC-AC-CTTTTCAAAGCCCACA
1244098 CAAGTTAGTA
Statistics
Matches: 392, Mismatches: 43, Indels: 33
0.84 0.09 0.07
Matches are distributed among these distances:
55 30 0.08
56 82 0.21
57 189 0.48
58 56 0.14
59 11 0.03
61 10 0.03
62 14 0.04
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.24
Consensus pattern (56 bp):
GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCA
Found at i:1244087 original size:32 final size:32
Alignment explanation
Indices: 1243624--1244106 Score: 147
Period size: 28 Copynumber: 16.7 Consensus size: 32
1243614 AGTGGCACCC
* *
1243624 TTTCAAAG-CC-CACAAGTCAGTGGCATTCT-T
1 TTTCAAAGCCCACACAAGTTAGTGGCA-ACTAT
* *
1243654 TTT-AAAG-CC-CACAAGTCAGTGGC-AC-CT
1 TTTCAAAGCCCACACAAGTTAGTGGCAACTAT
* **
1243681 TTTCAAAG-CC-CACAAGTCAGTGGC-AC-CC
1 TTTCAAAGCCCACACAAGTTAGTGGCAACTAT
*
1243709 TTTCAAAG-CC-CACAAGTTAGTGGC-ACTCCT
1 TTTCAAAGCCCACACAAGTTAGTGGCAACT-AT
**
1243739 TTT-AAAG-CC-CACAAGTTAGTGGC-ACTCC
1 TTTCAAAGCCCACACAAGTTAGTGGCAACTAT
**
1243767 TTTCAAAG-CC-CACAAGTTAGTGGC-ACTCC
1 TTTCAAAGCCCACACAAGTTAGTGGCAACTAT
* **
1243796 TTTCAAAG-CC-CACAAGTCAGTGGC-AC-CC
1 TTTCAAAGCCCACACAAGTTAGTGGCAACTAT
* * **
1243824 TTTCAAAG-CC-CATAAGTCAGTGGC-AC-CC
1 TTTCAAAGCCCACACAAGTTAGTGGCAACTAT
* * **
1243852 TTTCAAAG-CC-CATAAGTCAGTGGC-ACTCC
1 TTTCAAAGCCCACACAAGTTAGTGGCAACTAT
* * *
1243881 TTTCAAA--ACGCACAAGTTAGTGGC-ACT-C
1 TTTCAAAGCCCACACAAGTTAGTGGCAACTAT
* * **
1243909 CTTCAAAG--C-CACAAGTCAGTGGC-AC-CC
1 TTTCAAAGCCCACACAAGTTAGTGGCAACTAT
* *
1243936 TTTCAAAG-CC-CACAAGTGAGTGGC-ACTTT
1 TTTCAAAGCCCACACAAGTTAGTGGCAACTAT
* **
1243965 TTTCAAAG-CC-CACAAGTCAGTGGC-AC-CC
1 TTTCAAAGCCCACACAAGTTAGTGGCAACTAT
* * * * *
1243993 TTTCAAAG--CTCACAAGTCAGTGAC-ATTCT
1 TTTCAAAGCCCACACAAGTTAGTGGCAACTAT
** * * *
1244022 TTTC-AAGGAC-CACAAGCTAGTGGTAACTCT
1 TTTCAAAGCCCACACAAGTTAGTGGCAACTAT
* *
1244052 TTTCAAAGCCCATACGAGTTAGTGGCAACTAT
1 TTTCAAAGCCCACACAAGTTAGTGGCAACTAT
1244084 TTTCAAAGCCCACACAAGTTAGT
1 TTTCAAAGCCCACACAAGTTAGT
1244107 AAGACCTTTT
Statistics
Matches: 399, Mismatches: 36, Indels: 34
0.85 0.08 0.07
Matches are distributed among these distances:
27 29 0.07
28 157 0.39
29 157 0.39
30 16 0.04
31 4 0.01
32 36 0.09
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTTAGTGGCAACTAT
Found at i:1244237 original size:45 final size:48
Alignment explanation
Indices: 1244182--1244272 Score: 125
Period size: 49 Copynumber: 1.9 Consensus size: 48
1244172 ATCGCTAGCA
*
1244182 TTGAATCAGCATATTGG-C-ACCTTT-ATTAGCCCAATGTCGCTGACC
1 TTGAATCAGCACATTGGTCTACCTTTCATTAGCCCAATGTCGCTGACC
* *
1244227 TTGAATCAGCACATTGGTCTACTTTTCCCTTAGCCCAATGTCGCTG
1 TTGAATCAGCACATTGGTCTACCTTT-CATTAGCCCAATGTCGCTG
1244273 GCCTAATTGG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
45 16 0.41
46 1 0.03
47 5 0.13
49 17 0.44
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (48 bp):
TTGAATCAGCACATTGGTCTACCTTTCATTAGCCCAATGTCGCTGACC
Found at i:1249372 original size:29 final size:28
Alignment explanation
Indices: 1249290--1249799 Score: 544
Period size: 29 Copynumber: 17.8 Consensus size: 28
1249280 ACATAACTCT
* *
1249290 GTGGCATCCTTT-TAAGTCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* *
1249317 GTGGCACCCTTTCAAAGCCTACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* *
1249345 GTGGCATTCTTTTTAAAGCCCACAAGTCA
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCA
1249374 GTGGCA-CCTTTTCAAAGCCCACAAGTCA
1 GTGGCATCC-TTTCAAAGCCCACAAGTCA
* *
1249402 GTGGCACCCTTTCAAAGCCCACAAGTTA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* *
1249430 GTGGCACTCCTTTTAAAGCCCACAAGTTA
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCA
*
1249459 GTGGCACTCCTTTCAAAGCCCACAAGTTA
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCA
1249488 GTGGCACTCCTTTCAAAGCCCACAAGTCA
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCA
* *
1249517 GTGGCACCCTTTCAAAGCCCATAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* *
1249545 GTGGCACCCTTTCAAAGCCCATAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* * *
1249573 GTGGCACTCCTTTCAAAACGCACAAGTTA
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCA
1249602 GTGGCACTCC-TTCAAAG-CCACAAGTCA
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCA
* *
1249629 GTGGCACCCTTTCAAAGCCCACAAGTGA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
**
1249657 GTGGCACTTTTTTCAAAGCCCACAAGTCA
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCA
* *
1249686 GTGGCACCCTTTCAAAGCTCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* * * *
1249714 GTGACATTCTTTTCAAGGACCACAAG-CTA
1 GTGGCA-TCCTTTCAAAGCCCACAAGTC-A
* * *
1249743 GTGGTAACTCTTTTCAAAGCCCATACGAGTCA
1 GTGG-CA-TCCTTTCAAAGCCC--ACAAGTCA
**
1249775 GTGGCAACTATTTTCAAAGCCCACA
1 GTGGC-A-TCCTTTCAAAGCCCACA
1249800 CAAGTTAGTA
Statistics
Matches: 417, Mismatches: 50, Indels: 29
0.84 0.10 0.06
Matches are distributed among these distances:
26 2 0.00
27 33 0.08
28 165 0.40
29 177 0.42
30 15 0.04
32 24 0.06
33 1 0.00
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.24
Consensus pattern (28 bp):
GTGGCATCCTTTCAAAGCCCACAAGTCA
Found at i:1249372 original size:57 final size:57
Alignment explanation
Indices: 1249290--1249799 Score: 611
Period size: 57 Copynumber: 8.9 Consensus size: 57
1249280 ACATAACTCT
* * * *
1249290 GTGGCATCCTTT-TAAGTCCACAAGTCAGTGGCAC-CCTTTCAAAGCCTACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCA
* * * *
1249345 GTGGCATTCTTTTTAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCA
1 GTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCA
* * *
1249402 GTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCCTTTTAAAGCCCACAAGTTA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCA
*
1249459 GTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACAAGTCA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCA
* *
1249517 GTGGCACCCTTTCAAAGCCCATAAGTCAGTGGCAC-CCTTTCAAAGCCCATAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCA
* * *
1249573 GTGGCACTCCTTTCAAAACGCACAAGTTAGTGGCACTCC-TTCAAAG-CCACAAGTCA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCA
* **
1249629 GTGGCACCCTTTCAAAGCCCACAAGTGAGTGGCACTTTTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCA
* * * * * *
1249686 GTGGCACCCTTTCAAAGCTCACAAGTCAGTGACATTCTTTTCAAGGACCACAAG-CTA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTC-A
* * * **
1249743 GTGGTAACTCTTTTCAAAGCCCATACGAGTCAGTGGCAACTATTTTCAAAGCCCACA
1 GTGG-CAC-CCTTTCAAAGCCC--ACAAGTCAGTGGC-ACTCCTTTCAAAGCCCACA
1249800 CAAGTTAGTA
Statistics
Matches: 398, Mismatches: 43, Indels: 21
0.86 0.09 0.05
Matches are distributed among these distances:
55 32 0.08
56 81 0.20
57 189 0.47
58 59 0.15
59 11 0.03
61 11 0.03
62 15 0.04
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.24
Consensus pattern (57 bp):
GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCA
Found at i:1249725 original size:28 final size:28
Alignment explanation
Indices: 1249290--1249716 Score: 581
Period size: 28 Copynumber: 15.1 Consensus size: 28
1249280 ACATAACTCT
* * *
1249290 GTGGCATCCTTT-TAAGTCCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
*
1249317 GTGGCACCCTTTCAAAGCCTACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
* * *
1249345 GTGGCATTCTTTTTAAAGCCCACAAGTCA
1 GTGGCA-CCCTTTCAAAGCCCACAAGTCA
*
1249374 GTGGCACCTTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
*
1249402 GTGGCACCCTTTCAAAGCCCACAAGTTA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
* *
1249430 GTGGCACTCCTTTTAAAGCCCACAAGTTA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCA
*
1249459 GTGGCACTCCTTTCAAAGCCCACAAGTTA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCA
1249488 GTGGCACTCCTTTCAAAGCCCACAAGTCA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCA
*
1249517 GTGGCACCCTTTCAAAGCCCATAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
*
1249545 GTGGCACCCTTTCAAAGCCCATAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
* * *
1249573 GTGGCACTCCTTTCAAAACGCACAAGTTA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCA
1249602 GTGGCACTCC-TTCAAAG-CCACAAGTCA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCA
*
1249629 GTGGCACCCTTTCAAAGCCCACAAGTGA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
**
1249657 GTGGCACTTTTTTCAAAGCCCACAAGTCA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCA
*
1249686 GTGGCACCCTTTCAAAGCTCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
1249714 GTG
1 GTG
1249717 ACATTCTTTT
Statistics
Matches: 363, Mismatches: 30, Indels: 13
0.89 0.07 0.03
Matches are distributed among these distances:
26 2 0.01
27 33 0.09
28 169 0.47
29 159 0.44
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.23
Consensus pattern (28 bp):
GTGGCACCCTTTCAAAGCCCACAAGTCA
Found at i:1249939 original size:45 final size:48
Alignment explanation
Indices: 1249884--1249974 Score: 125
Period size: 49 Copynumber: 1.9 Consensus size: 48
1249874 ATCGCTAGCA
*
1249884 TTGAATCAGCATATTGG-C-ACCTTT-ATTAGCCCAATGTCGCTGACC
1 TTGAATCAGCACATTGGTCTACCTTTCATTAGCCCAATGTCGCTGACC
* *
1249929 TTGAATCAGCACATTGGTCTACTTTTCCCTTAGCCCAATGTCGCTG
1 TTGAATCAGCACATTGGTCTACCTTT-CATTAGCCCAATGTCGCTG
1249975 GCCTAATTGG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
45 16 0.41
46 1 0.03
47 5 0.13
49 17 0.44
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (48 bp):
TTGAATCAGCACATTGGTCTACCTTTCATTAGCCCAATGTCGCTGACC
Found at i:1255081 original size:16 final size:17
Alignment explanation
Indices: 1255049--1255081 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1255039 TAATAATTTT
1255049 TTATTTACTGAGCTTATG
1 TTATTTACT-AGCTTATG
1255067 TTATTTACT-GCTTAT
1 TTATTTACTAGCTTAT
1255082 ATATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.55
Consensus pattern (17 bp):
TTATTTACTAGCTTATG
Found at i:1255086 original size:2 final size:2
Alignment explanation
Indices: 1255079--1255117 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1255069 ATTTACTGCT
1255079 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1255118 GAGCGATGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.