Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 112 of 427
Found at i:29606663 original size:14 final size:15
Alignment explanation
Indices: 29606614--29606663 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
29606604 CGTATCTTGG
* *
29606614 TTTCTTTCTCCTGGA
1 TTTCTTTATTCTGGA
*
29606629 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
29606644 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
29606658 TTTCTT
1 TTTCTT
29606664 ATTATCTTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 8 0.27
15 22 0.73
ACGTcount: A:0.08, C:0.20, G:0.12, T:0.60
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:29609105 original size:46 final size:46
Alignment explanation
Indices: 29609048--29609217 Score: 175
Period size: 46 Copynumber: 3.7 Consensus size: 46
29609038 TTGAGCATCC
* *
29609048 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTAT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCAT
* * * * *
29609094 GAAATCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCAT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ACGCAT
* * **
29609139 CCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCC
1 --GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCAT
*
29609187 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
29609218 GGGCGGGTTA
Statistics
Matches: 101, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
43 6 0.06
45 6 0.06
46 54 0.53
47 25 0.25
48 5 0.05
50 5 0.05
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCAT
Found at i:29609201 original size:93 final size:93
Alignment explanation
Indices: 29609042--29609212 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
29609032 CGATGGTTGA
* * *
29609042 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTATGAAATCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCACGAAATCGTTGAGT
29609107 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * **
29609135 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCACGAAATCGTTGAGT
29609200 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
29609213 ACTTAGGGCG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCACGAAATCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:29621620 original size:21 final size:22
Alignment explanation
Indices: 29621580--29621625 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
29621570 ATTTAATTAA
*
29621580 TTTTAAAAATTTTAAAAATACT
1 TTTTAAAAATTTTAAAAATAAT
*
29621602 TTTTAAAAATTTT-ATAATAAT
1 TTTTAAAAATTTTAAAAATAAT
29621623 TTT
1 TTT
29621626 AATAACTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTAAAAATTTTAAAAATAAT
Found at i:29622924 original size:10 final size:10
Alignment explanation
Indices: 29622906--29622954 Score: 71
Period size: 10 Copynumber: 4.9 Consensus size: 10
29622896 AATTTTAGCT
29622906 TTTATCTTTA
1 TTTATCTTTA
*
29622916 TTTAACTTTA
1 TTTATCTTTA
*
29622926 TTTATCCTTA
1 TTTATCTTTA
29622936 TTTATCTTTA
1 TTTATCTTTA
*
29622946 TTTGTCTTT
1 TTTATCTTT
29622955 TAGAATTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.18, C:0.12, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:29624528 original size:21 final size:22
Alignment explanation
Indices: 29624494--29624535 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
29624484 TGTGAAGAGG
**
29624494 GGCACACGGTCGTGT-GACTAA
1 GGCACACGCCCGTGTGGACTAA
29624515 GGCACACGCCCGTGTGGACTA
1 GGCACACGCCCGTGTGGACTA
29624536 GGGATATGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.21, C:0.29, G:0.33, T:0.17
Consensus pattern (22 bp):
GGCACACGCCCGTGTGGACTAA
Found at i:29625389 original size:24 final size:24
Alignment explanation
Indices: 29625355--29625401 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
29625345 TAACCCATTA
**
29625355 TAGAATAAAAAACATTATCAGAAC
1 TAGAATAAAAAACAGAATCAGAAC
*
29625379 TAGAATCAAAAACAGAATCAGAA
1 TAGAATAAAAAACAGAATCAGAA
29625402 TCAGGTGACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.60, C:0.13, G:0.11, T:0.17
Consensus pattern (24 bp):
TAGAATAAAAAACAGAATCAGAAC
Found at i:29625400 original size:6 final size:6
Alignment explanation
Indices: 29625371--29625458 Score: 65
Period size: 6 Copynumber: 14.3 Consensus size: 6
29625361 AAAAAACATT
* * *
29625371 ATCAGA A-CTAGA ATCAAA AACAGA ATCAGA ATCAG- GTGACAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* *
29625420 ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
29625459 GTGAATGCAA
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
5 4 0.06
6 51 0.80
7 7 0.11
8 2 0.03
ACGTcount: A:0.50, C:0.16, G:0.17, T:0.17
Consensus pattern (6 bp):
ATCAGA
Found at i:29625415 original size:31 final size:31
Alignment explanation
Indices: 29625380--29625458 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
29625370 TATCAGAACT
* *
29625380 AGAATCAAAAACAGAATCAGAATCAGGTGAC
1 AGAATCAAAATCAGAATCAGAATCAGGTAAC
* *
29625411 AGAATCAGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGAATCAGGTAAC
29625442 AGAATCAAAATCAGAAT
1 AGAATCAAAATCAGAAT
29625459 GTGAATGCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.51, C:0.15, G:0.18, T:0.16
Consensus pattern (31 bp):
AGAATCAAAATCAGAATCAGAATCAGGTAAC
Found at i:29625444 original size:25 final size:23
Alignment explanation
Indices: 29625389--29625455 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 23
29625379 TAGAATCAAA
29625389 AACAGAATCAGAATCAGGTGACAG
1 AACAGAATCAGAATCA-GTGACAG
29625413 AATCAGAATCAGAATCAGT-ATCAGG
1 AA-CAGAATCAGAATCAGTGA-CA-G
*
29625438 TAACAGAATCAAAATCAG
1 -AACAGAATCAGAATCAG
29625456 AATGTGAATG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 1 0.03
24 6 0.16
25 29 0.76
26 2 0.05
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.16
Consensus pattern (23 bp):
AACAGAATCAGAATCAGTGACAG
Found at i:29625896 original size:27 final size:27
Alignment explanation
Indices: 29625866--29626061 Score: 275
Period size: 27 Copynumber: 7.3 Consensus size: 27
29625856 GGGGCAAACT
* * *
29625866 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
29625893 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
29625920 AGTATTTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
29625947 AGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
29625974 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
29626001 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
29626028 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
29626055 GATAATT
1 GGTAATT
29626062 TCACAAATTA
Statistics
Matches: 153, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 153 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:29625990 original size:81 final size:81
Alignment explanation
Indices: 29625870--29626061 Score: 305
Period size: 81 Copynumber: 2.4 Consensus size: 81
29625860 CAAACTGGTA
* * * *
29625870 ATTT-TACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTTAGTATTTCTACCCT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCT
*
29625934 ACAGGGGTATTTCAGT
66 ACAAGGGTATTTCAGT
29625950 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCT
*
29626015 ACAAGGGTATTTCGGT
66 ACAAGGGTATTTCAGT
* *
29626031 AATTCTACCCTACAAGGGTATTTCGATAATT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATT
29626062 TCACAAATTA
Statistics
Matches: 103, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
80 4 0.04
81 99 0.96
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.35
Consensus pattern (81 bp):
ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCT
ACAAGGGTATTTCAGT
Found at i:29626104 original size:81 final size:81
Alignment explanation
Indices: 29625866--29626115 Score: 236
Period size: 81 Copynumber: 3.1 Consensus size: 81
29625856 GGGGCAAACT
* * * * ** * *
29625866 GGTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTTAGTATTTCTAC
1 GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACAATACAGGGGTATTTCAGTAATTCTAC
**
29625931 CCTACAGGGGTATTTC
66 CAAACAGGGGTATTTC
* * * **
29625947 AGTATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTAC
1 GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACAATACAGGGGTATTTCAGTAATTCTAC
** *
29626012 CCTACAAGGGTATTTC
66 CAAACAGGGGTATTTC
* ** * *
29626028 GGTAATTCTACCCTACAAGGGTATTTCGATAATT-TCACAA-ATTAGGGGTATTTTGGTACTTTT
1 GGTAATTCTACCCTACAAGGGTATTTCGATAATTCT-ACAATA-CAGGGGTATTTCAGTAATTCT
*
29626091 A-CAAACCAGGGGTATTTT
64 ACCAAA-CAGGGGTATTTC
29626109 GGTAATT
1 GGTAATT
29626116 TTATTGATCG
Statistics
Matches: 144, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
80 4 0.03
81 140 0.97
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (81 bp):
GGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACAATACAGGGGTATTTCAGTAATTCTAC
CAAACAGGGGTATTTC
Found at i:29626117 original size:27 final size:27
Alignment explanation
Indices: 29626046--29626171 Score: 92
Period size: 27 Copynumber: 4.7 Consensus size: 27
29626036 TACCCTACAA
* * * **
29626046 GGGTATTTCGATAATTTCACAAATTAG
1 GGGTATTTTGGTAATTTTACAAACCAG
*
29626073 GGGTATTTTGGTACTTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
*** *
29626100 GGGTATTTTGGTAATTTTATTGATC-G
1 GGGTATTTTGGTAATTTTACAAACCAG
** *
29626126 AGGGTATTTTGGTAATTTTGTAAACCAA
1 -GGGTATTTTGGTAATTTTACAAACCAG
* **
29626154 GAGTATTTCAGTAATTTT
1 GGGTATTTTGGTAATTTT
29626172 GTAAATCGAG
Statistics
Matches: 78, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
26 1 0.01
27 77 0.99
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAG
Found at i:29626131 original size:54 final size:54
Alignment explanation
Indices: 29626073--29626185 Score: 136
Period size: 54 Copynumber: 2.1 Consensus size: 54
29626063 CACAAATTAG
* * * ** **
29626073 GGGTATTTTGGTACTTTTACAAACCAGGGGTATTTTGGTAATTTTATTGATCGA
1 GGGTATTTTGGTAATTTTACAAACCAAGAGTATTTCAGTAATTTTATAAATCGA
** *
29626127 GGGTATTTTGGTAATTTTGTAAACCAAGAGTATTTCAGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTACAAACCAAGAGTATTTCAGTAATTTTATAAATCGA
29626181 GGGTA
1 GGGTA
29626186 AAATGGTAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.41
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAACCAAGAGTATTTCAGTAATTTTATAAATCGA
Found at i:29626439 original size:27 final size:27
Alignment explanation
Indices: 29626164--29626428 Score: 386
Period size: 27 Copynumber: 9.8 Consensus size: 27
29626154 GAGTATTTCA
*
29626164 GTAATTTTGTAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
29626191 GTAATTATGTAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* *
29626218 ATAATTCTGTATATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* * **
29626245 GTAATTCTGTAAATCGATGGTAAGACA
1 GTAATTCTGTAAATCGAGGGTAAAATG
29626272 GTAATTCTGTAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
29626299 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* *
29626326 GTAATTCTATAAATTGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* * *
29626353 GTTATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
**
29626380 GTAATTCTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAATG
29626407 GTAATTCTGTAAATCGAGGGTA
1 GTAATTCTGTAAATCGAGGGTA
29626429 CTTTGGTAAT
Statistics
Matches: 214, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 214 1.00
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAATG
Found at i:29628447 original size:6 final size:6
Alignment explanation
Indices: 29628418--29628505 Score: 65
Period size: 6 Copynumber: 14.3 Consensus size: 6
29628408 AAGAAACATT
* * *
29628418 ATCAGA A-CTAGA ATCAAA AACAGA ATCAGA ATCAG- GTGACAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* *
29628467 ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
29628506 GTGAATGCAA
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
5 4 0.06
6 51 0.80
7 7 0.11
8 2 0.03
ACGTcount: A:0.50, C:0.16, G:0.17, T:0.17
Consensus pattern (6 bp):
ATCAGA
Found at i:29628462 original size:31 final size:31
Alignment explanation
Indices: 29628427--29628505 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
29628417 TATCAGAACT
* *
29628427 AGAATCAAAAACAGAATCAGAATCAGGTGAC
1 AGAATCAAAATCAGAATCAGAATCAGGTAAC
* *
29628458 AGAATCAGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGAATCAGGTAAC
29628489 AGAATCAAAATCAGAAT
1 AGAATCAAAATCAGAAT
29628506 GTGAATGCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.51, C:0.15, G:0.18, T:0.16
Consensus pattern (31 bp):
AGAATCAAAATCAGAATCAGAATCAGGTAAC
Found at i:29628491 original size:25 final size:23
Alignment explanation
Indices: 29628436--29628502 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 23
29628426 TAGAATCAAA
29628436 AACAGAATCAGAATCAGGTGACAG
1 AACAGAATCAGAATCA-GTGACAG
29628460 AATCAGAATCAGAATCAGT-ATCAGG
1 AA-CAGAATCAGAATCAGTGA-CA-G
*
29628485 TAACAGAATCAAAATCAG
1 -AACAGAATCAGAATCAG
29628503 AATGTGAATG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 1 0.03
24 6 0.16
25 29 0.76
26 2 0.05
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.16
Consensus pattern (23 bp):
AACAGAATCAGAATCAGTGACAG
Found at i:29628943 original size:27 final size:27
Alignment explanation
Indices: 29628913--29629080 Score: 239
Period size: 27 Copynumber: 6.3 Consensus size: 27
29628903 GGGGCAAACT
* * *
29628913 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
29628940 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
29628967 AGTATTTCTACCCTACAAGGG-ATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
29628993 GGTAATTCTACCCTATAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
*
29629020 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
29629047 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
29629074 GGTAATT
1 GGTAATT
29629081 TCACAAATTA
Statistics
Matches: 123, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 22 0.18
27 101 0.82
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:29629007 original size:53 final size:54
Alignment explanation
Indices: 29628917--29629082 Score: 246
Period size: 53 Copynumber: 3.1 Consensus size: 54
29628907 CAAACTGGTA
* *
29628917 ATTT-TACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCAGT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGT
* *
29628970 ATTTCTACCCTACAAGGG-ATTTCGGTAATTCTACCCTATAGGGGTATTTTAGT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGT
* * *
29629023 AATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGGT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGT
29629077 AATTTC
1 -ATTTC
29629083 ACAAATTAGG
Statistics
Matches: 100, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
53 53 0.53
54 43 0.43
55 4 0.04
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (54 bp):
ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGT
Found at i:29629096 original size:54 final size:52
Alignment explanation
Indices: 29628926--29629107 Score: 176
Period size: 54 Copynumber: 3.4 Consensus size: 52
29628916 AATTTTACCC
*
29628926 CACA-AGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCAGT-ATTTCTA
1 CACATAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTTC-A
* * *
29628977 CCCTACA-AGGG-ATTTCGGTAATTCTACCCTATAGGGGTATTTTAGTAATTCTACC
1 --C-ACATAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATT-T-CA
* *
29629032 CTACA-AGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGGTAATTTCA
1 C-ACATAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTTCA
* *
29629084 CAAATTAGGGGTATTTTGGTAATT
1 CACA-TA-GGGTATTTCGGTAATT
29629108 TTACAAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
51 2 0.02
52 2 0.02
53 44 0.40
54 60 0.55
55 1 0.01
56 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (52 bp):
CACATAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTTCA
Found at i:29629123 original size:81 final size:80
Alignment explanation
Indices: 29628941--29629134 Score: 223
Period size: 81 Copynumber: 2.4 Consensus size: 80
29628931 GGGTATCTCG
** * * **
29628941 GTAATTCTACCCTACAGGGGTATTTCAGTATTTCTACCCTACAAGGGATTTCGGTAATTCTACCC
1 GTAATTCTACCAAACAGGGGTATTTCGGTAATTCTACCCTACAAGGGATTTCGGTAATTCTACAA
29629006 TATAGGGGTATTTTA
66 TATAGGGGTATTTTA
** *
29629021 GTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGGTAATT-TCAC
1 GTAATTCTACCAAACAGGGGTATTTCGGTAATTCTACCCTACAAGGG-ATTTCGGTAATTCT-AC
*
29629085 AA-ATTAGGGGTATTTTG
64 AATA-TAGGGGTATTTTA
* *
29629102 GTAATTTTA-CAAACCAGGGGTATTTTGGTAATT
1 GTAATTCTACCAAA-CAGGGGTATTTCGGTAATT
29629135 TTATTGATCG
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
80 48 0.48
81 51 0.52
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (80 bp):
GTAATTCTACCAAACAGGGGTATTTCGGTAATTCTACCCTACAAGGGATTTCGGTAATTCTACAA
TATAGGGGTATTTTA
Found at i:29629153 original size:27 final size:27
Alignment explanation
Indices: 29629065--29629137 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
29629055 TACCCTACAA
* * **
29629065 GGGTATTTCGGTAATTTCACAAATTAG
1 GGGTATTTTGGTAATTTTACAAACCAG
29629092 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
29629119 GGGTATTTTGGTAATTTTA
1 GGGTATTTTGGTAATTTTA
29629138 TTGATCGAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAG
Found at i:29629430 original size:27 final size:27
Alignment explanation
Indices: 29629182--29629419 Score: 350
Period size: 27 Copynumber: 8.8 Consensus size: 27
29629172 TAGTATTTCA
*
29629182 GTAATTTTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
29629209 ATACTTCTGTAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
29629236 GTAATTCTGTAAATCGAGGGTAAGACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
29629263 GTAATTCTGTAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
29629290 GTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
** *
29629317 GTAATTCCATAAATTGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
29629344 GTTATTCTATAAATCGAGGGTAAAGCG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
29629371 GTAATTCTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
29629398 GTAATTCTGTAAATCGAGGGTA
1 GTAATTCTGTAAATCGAGGGTA
29629420 CTTTGGTAAT
Statistics
Matches: 189, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 189 1.00
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.28
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:29629442 original size:81 final size:79
Alignment explanation
Indices: 29629182--29629446 Score: 314
Period size: 81 Copynumber: 3.3 Consensus size: 79
29629172 TAGTATTTCA
* * *
29629182 GTAATTTTGTAAATCGAGGGTAAAACGATACTTCTGTAAATCGAGGGTAAAATGGTAATTCTGTA
1 GTAA-TTT-TAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTA
*
29629247 AATCGAGGGTAAGACG
64 AATCGAGGGTAAAACG
* * **
29629263 GTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGGTAATTCCATA
1 GTAATT-T-TAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTA
*
29629328 AATTGAGGGTAAAACG
64 AATCGAGGGTAAAACG
* * *
29629344 GTTATTCTATAAATCGAGGGTAAAGCGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTA
1 GTAATT-T-TAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTA
****
29629409 AATCGAGGGTACTTTG
64 AATCGAGGGTAAAACG
29629425 GTAATTTTACAAGTCGAGGGTA
1 GTAATTTTA-AA-TCGAGGGTA
29629447 TTTTAGTAAT
Statistics
Matches: 158, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
79 2 0.01
80 5 0.03
81 151 0.96
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (79 bp):
GTAATTTTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAA
TCGAGGGTAAAACG
Found at i:29633526 original size:21 final size:22
Alignment explanation
Indices: 29633485--29633526 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
29633475 TCGTGTGACT
*
29633485 AAGGCACATGCCGGTGTGGACC
1 AAGGCACATGCCGGTGGGGACC
29633507 AAGG-ACATGACC-GTGGGGAC
1 AAGGCACATG-CCGGTGGGGAC
29633527 AGGCCATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.26, C:0.24, G:0.38, T:0.12
Consensus pattern (22 bp):
AAGGCACATGCCGGTGGGGACC
Found at i:29634253 original size:3 final size:3
Alignment explanation
Indices: 29634231--29634292 Score: 94
Period size: 3 Copynumber: 21.3 Consensus size: 3
29634221 ACGTGCCTTC
29634231 AAT AATT AA- AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29634275 AAT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT A
29634293 CTAAACTAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
2 6 0.11
3 46 0.84
4 3 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29637317 original size:34 final size:34
Alignment explanation
Indices: 29637279--29637347 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 34
29637269 TGACGATGAG
*
29637279 ATCGTGAAGTTTAAT-GTTTATGACACTATTAGTC
1 ATCGTCAAGTTT-ATCGTTTATGACACTATTAGTC
*
29637313 ATCGTCAAGTTTATCGTTTATGACGCTATTAGTC
1 ATCGTCAAGTTTATCGTTTATGACACTATTAGTC
29637347 A
1 A
29637348 CCTGAATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 2 0.06
34 30 0.94
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (34 bp):
ATCGTCAAGTTTATCGTTTATGACACTATTAGTC
Found at i:29637845 original size:13 final size:14
Alignment explanation
Indices: 29637827--29637875 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
29637817 CAACCTAAAT
29637827 TTTATTTTTATTA-
1 TTTATTTTTATTAC
* *
29637840 TTTATTATT-TTAT
1 TTTATTTTTATTAC
29637853 TTTATTATTTATTAC
1 TTTATT-TTTATTAC
29637868 TTTATTTT
1 TTTATTTT
29637876 GTTTGAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 3 0.10
13 14 0.47
14 4 0.13
15 9 0.30
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATTTTTATTAC
Found at i:29637853 original size:8 final size:7
Alignment explanation
Indices: 29637827--29637873 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
29637817 CAACCTAAAT
29637827 TTTATT-
1 TTTATTA
29637833 TTTATTA
1 TTTATTA
29637840 TTTATTA
1 TTTATTA
29637847 -TT-TTA
1 TTTATTA
29637852 TTTTATTA
1 -TTTATTA
29637860 TTTATTA
1 TTTATTA
29637867 CTTTATT
1 -TTTATT
29637874 TTGTTTGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
5 3 0.08
6 8 0.22
7 16 0.44
8 9 0.25
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTATTA
Found at i:29637857 original size:20 final size:20
Alignment explanation
Indices: 29637825--29637875 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
29637815 AACAACCTAA
29637825 ATTTTATTTTTATTATTTATT
1 ATTTTA-TTTTATTATTTATT
29637846 ATTTTATTTTATTATTTATT
1 ATTTTATTTTATTATTTATT
*
29637866 ACTTTATTTT
1 ATTTTATTTT
29637876 GTTTGAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 23 0.79
21 6 0.21
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (20 bp):
ATTTTATTTTATTATTTATT
Found at i:29639121 original size:13 final size:13
Alignment explanation
Indices: 29639103--29639129 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29639093 ATCCTTAAGC
29639103 AAAAAAAGAAAAG
1 AAAAAAAGAAAAG
29639116 AAAAAAAGAAAAG
1 AAAAAAAGAAAAG
29639129 A
1 A
29639130 GATGTATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:29640761 original size:2 final size:2
Alignment explanation
Indices: 29640715--29640742 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29640705 ATTATTCCAC
29640715 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
29640743 CTAAGCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29643544 original size:47 final size:44
Alignment explanation
Indices: 29643432--29643559 Score: 134
Period size: 47 Copynumber: 2.8 Consensus size: 44
29643422 GGGTTACTGT
*
29643432 GAGCTAGTGTAAGACATGTCTGGGACATGCACCGGCCACATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATC-G-CACATTATGA
*
29643478 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG-ACATTGA-GA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGCACATT-ATGA
* *
29643523 CGAGTGCTAGTGTAATACATGTCTGGGATATGCATCG
1 -GA--GCTAGTGTAAGACATGTCTGGGACATGCATCG
29643560 GCCTCGAAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 12
0.81 0.06 0.14
Matches are distributed among these distances:
45 7 0.10
46 22 0.31
47 28 0.39
48 14 0.20
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (44 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGCACATTATGA
Found at i:29650978 original size:46 final size:46
Alignment explanation
Indices: 29650843--29651052 Score: 157
Period size: 46 Copynumber: 4.6 Consensus size: 46
29650833 GTTATTGTGA
* * * * *
29650843 GCTAGTGTAAGA-CATGTCTGGGACATGCATCAGCGAC-ATTATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGCATCGGC-TCGA-GACGAGT
* * * *
29650889 GCCAGTGTAAGATCATGTCTGGGACATGGCATCGGTATTGAGACGAGT
1 GCTAGTGTAAGACCATGTCTGGGACAT-GCATCGG-CTCGAGACGAGT
* **
29650937 GCTAGTGTAAGA-CATGTTTGATACATGCATCGGCCTCGAGACGTAAGT
1 GCTAGTGTAAGACCATGTCTGGGACATGCATCGG-CTCGAGACG--AGT
*
29650985 --TAGTGTAAGA-CATGTCTGGGACATGCATCGGCTACGAGA--TGT
1 GCTAGTGTAAGACCATGTCTGGGACATGCATCGGCT-CGAGACGAGT
* *
29651027 GCCAGTGTAAGACCATGTTTGGGACA
1 GCTAGTGTAAGACCATGTCTGGGACA
29651053 CGGCATCAAC
Statistics
Matches: 133, Mismatches: 21, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
42 2 0.02
44 9 0.07
45 14 0.11
46 58 0.44
47 25 0.19
48 24 0.18
49 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (46 bp):
GCTAGTGTAAGACCATGTCTGGGACATGCATCGGCTCGAGACGAGT
Found at i:29653941 original size:40 final size:40
Alignment explanation
Indices: 29653886--29654118 Score: 299
Period size: 40 Copynumber: 5.6 Consensus size: 40
29653876 TATTCGAATG
*
29653886 ATATCCGGGCTAAGTCTCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
29653926 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
29653966 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGATTTGTGCTAATGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT--A-----G----TGACT
*
29654017 ACATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
29654057 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
29654097 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
29654119 TACTTGGGTT
Statistics
Matches: 174, Mismatches: 7, Indels: 25
0.84 0.03 0.12
Matches are distributed among these distances:
39 14 0.08
40 117 0.67
41 2 0.01
42 1 0.01
44 1 0.01
47 1 0.01
49 1 0.01
51 37 0.21
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:29654026 original size:51 final size:51
Alignment explanation
Indices: 29653950--29654051 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
29653940 TCCCGAAGGC
* *
29653950 ATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG
1 ATTTGTGCTAATGACTACATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG
29654001 ATTTGTGCTAATGACTACATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG
1 ATTTGTGCTAATGACTACATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG
29654052 TGACTATATC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (51 bp):
ATTTGTGCTAATGACTACATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG
Found at i:29654065 original size:91 final size:91
Alignment explanation
Indices: 29653910--29654088 Score: 331
Period size: 91 Copynumber: 2.0 Consensus size: 91
29653900 TCTCGAAGGC
* *
29653910 ATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGG
1 ATTTGTGCTAATGACTACATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGG
*
29653975 CTAAGTCCCGAAGGCATTTGTGCTAG
66 CTAAGACCCGAAGGCATTTGTGCTAG
29654001 ATTTGTGCTAATGACTACATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGG
1 ATTTGTGCTAATGACTACATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGG
29654066 CTAAGACCCGAAGGCATTTGTGC
66 CTAAGACCCGAAGGCATTTGTGC
29654089 GAGTTGCTAT
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (91 bp):
ATTTGTGCTAATGACTACATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGG
CTAAGACCCGAAGGCATTTGTGCTAG
Found at i:29656037 original size:56 final size:56
Alignment explanation
Indices: 29655977--29656085 Score: 164
Period size: 56 Copynumber: 1.9 Consensus size: 56
29655967 TCCCAGATAG
* * *
29655977 GGTCTTACTCGCACACATACATCGGAGTCACATATCGATGTCAATGTATAAAACGT
1 GGTCTTACTCGCACACATACATCAGAGTCACATATCGATGCCAACGTATAAAACGT
* * *
29656033 GGTCTTACTCGCACATATATATCAGAGTCATATATCGATGCCAACGTATAAAA
1 GGTCTTACTCGCACACATACATCAGAGTCACATATCGATGCCAACGTATAAAA
29656086 TTCCCTTGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 47 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (56 bp):
GGTCTTACTCGCACACATACATCAGAGTCACATATCGATGCCAACGTATAAAACGT
Found at i:29656624 original size:26 final size:26
Alignment explanation
Indices: 29656590--29656644 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
29656580 GTTAATCTAA
29656590 AACATATATTTCATATTTCATCAACT
1 AACATATATTTCATATTTCATCAACT
29656616 AACATATATTTCATATTTCATCAACT
1 AACATATATTTCATATTTCATCAACT
29656642 AAC
1 AAC
29656645 TTCACAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (26 bp):
AACATATATTTCATATTTCATCAACT
Found at i:29658440 original size:75 final size:75
Alignment explanation
Indices: 29658317--29658471 Score: 265
Period size: 75 Copynumber: 2.1 Consensus size: 75
29658307 GAGATAGGGC
*
29658317 CACACGGTTGTGTGCCCCAGCTATGTGGAAGTGTCTAGGCCATGTGAGAGGCCAACACGCCCATG
1 CACACGGCTGTGTGCCCCAGCTATGTGGAAGTGTCTAGGCCATGTGAGAGGCCAACACGCCCATG
29658382 TGAAAGGAGG
66 TGAAAGGAGG
* * * *
29658392 CACACGGCTGTGTGCCCCGGCTGTGTGGAAGTGTCTAGGCTATGTGAGAGGGCAACACGCCCATG
1 CACACGGCTGTGTGCCCCAGCTATGTGGAAGTGTCTAGGCCATGTGAGAGGCCAACACGCCCATG
29658457 TGAAAGGAGG
66 TGAAAGGAGG
29658467 CACAC
1 CACAC
29658472 AGCCGTGTTG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.23, C:0.25, G:0.34, T:0.18
Consensus pattern (75 bp):
CACACGGCTGTGTGCCCCAGCTATGTGGAAGTGTCTAGGCCATGTGAGAGGCCAACACGCCCATG
TGAAAGGAGG
Found at i:29667385 original size:18 final size:18
Alignment explanation
Indices: 29667362--29667397 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29667352 AAGATGGCTA
29667362 GAGTTGATAAAGGATTAT
1 GAGTTGATAAAGGATTAT
* *
29667380 GAGTTGATGAATGATTAT
1 GAGTTGATAAAGGATTAT
29667398 CACCCGGGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.28, T:0.36
Consensus pattern (18 bp):
GAGTTGATAAAGGATTAT
Found at i:29669865 original size:26 final size:25
Alignment explanation
Indices: 29669828--29669879 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
29669818 AAAATGGTCA
*
29669828 TTTTTCCTAATTTTAAGTTGTTGAG
1 TTTTTCCCAATTTTAAGTTGTTGAG
29669853 TTTTTGCCCAATTTTAAGTTGTTGAG
1 TTTTT-CCCAATTTTAAGTTGTTGAG
29669879 T
1 T
29669880 ATCTAGATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.19, C:0.10, G:0.17, T:0.54
Consensus pattern (25 bp):
TTTTTCCCAATTTTAAGTTGTTGAG
Found at i:29670409 original size:95 final size:96
Alignment explanation
Indices: 29670196--29670463 Score: 255
Period size: 95 Copynumber: 2.8 Consensus size: 96
29670186 GTTTGTGTGC
* * * * * * * * *
29670196 TAGTGTAAGGCATGACTGGGACAT-GCATCAGCCATATTATGAGAGCCAGTGTAAGACCATGTCT
1 TAGTGTAAGACATGTCTGGGACATGGCATC-GACTTAATGTAAGAGCCAATGTAAGACGATGTCT
* * ** * *
29670260 GAGACATGGCATCAGCATTGAGACGAT---AGC
65 GGGACATGGCATCGGCACGGACACG-TGGGAGT
* * **
29670290 TAGTGTAAGACATGTTTGGTACATGG-ATCGACCTCTTGGTGT-A-AGCCAATGTAAGAC-ATGT
1 TAGTGTAAGACATGTCTGGGACATGGCATCGA---CTTAATGTAAGAGCCAATGTAAGACGATGT
*
29670351 TTGGGACATGGCATCGGCACGGACACGTGGGAGT
63 CTGGGACATGGCATCGGCACGGACACGTGGGAGT
29670385 TAGTGTAAGACATGTCTGGGACATGGCATCGACTTAATGTAAGAGCCAATGTAAGACGATGTCTG
1 TAGTGTAAGACATGTCTGGGACATGGCATCGACTTAATGTAAGAGCCAATGTAAGACGATGTCTG
29670450 GGACATGGCATCGG
66 GGACATGGCATCGG
29670464 TATTATGTCT
Statistics
Matches: 141, Mismatches: 22, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
92 1 0.01
93 32 0.23
94 37 0.26
95 42 0.30
96 29 0.21
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (96 bp):
TAGTGTAAGACATGTCTGGGACATGGCATCGACTTAATGTAAGAGCCAATGTAAGACGATGTCTG
GGACATGGCATCGGCACGGACACGTGGGAGT
Found at i:29671586 original size:21 final size:22
Alignment explanation
Indices: 29671546--29671586 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
29671536 TTGAATTGTT
**
29671546 CACACGGGCGCATTGCCCCTCC
1 CACACGGGCGCAGCGCCCCTCC
29671568 CACACGGGCG-AGCGCCCCT
1 CACACGGGCGCAGCGCCCCT
29671587 GTGTCTAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.15, C:0.49, G:0.27, T:0.10
Consensus pattern (22 bp):
CACACGGGCGCAGCGCCCCTCC
Found at i:29674600 original size:26 final size:26
Alignment explanation
Indices: 29674574--29674637 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
29674564 TCTTTTTTAT
*
29674574 TTAT-TTATTTTATTCAT-TTTAACTA
1 TTATATTATTATATT-ATATTTAACTA
29674599 TTATATTATTATATTATATTTAA-TAA
1 TTATATTATTATATTATATTTAACT-A
29674625 TTATAATTATTAT
1 TTAT-ATTATTAT
29674638 TTCTTAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
25 7 0.21
26 19 0.56
27 8 0.24
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATATTATTATATTATATTTAACTA
Found at i:29674896 original size:15 final size:15
Alignment explanation
Indices: 29674876--29674906 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29674866 CTCACTTAAA
29674876 TTCGTAAATATTTAT
1 TTCGTAAATATTTAT
29674891 TTCGTAAATATTTAT
1 TTCGTAAATATTTAT
29674906 T
1 T
29674907 AGAAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (15 bp):
TTCGTAAATATTTAT
Found at i:29674914 original size:13 final size:15
Alignment explanation
Indices: 29674879--29674917 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
29674869 ACTTAAATTC
*
29674879 GTAAATATTTATTTC
1 GTAAATATTTATTTA
29674894 GTAAATATTTA-TTA
1 GTAAATATTTATTTA
29674908 G-AAATATTTA
1 GTAAATATTTA
29674918 CGAATCTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.39
14 3 0.13
15 11 0.48
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (15 bp):
GTAAATATTTATTTA
Found at i:29681800 original size:16 final size:17
Alignment explanation
Indices: 29681768--29681804 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
29681758 AAACCCTAAT
*
29681768 TTTCCCTCTTTTTTTTC
1 TTTCCCTCTTTTCTTTC
29681785 TTTCCCT-TTTTCTTTC
1 TTTCCCTCTTTTCTTTC
29681801 TTTC
1 TTTC
29681805 TTTCCCTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTCCCTCTTTTCTTTC
Found at i:29681898 original size:13 final size:14
Alignment explanation
Indices: 29681879--29681919 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
29681869 TCATTTTAAC
29681879 AATTATATTATTAT
1 AATTATATTATTAT
*
29681893 -ATTATATT-TAAT
1 AATTATATTATTAT
29681905 AATTATAATTATTAT
1 AATTAT-ATTATTAT
29681920 TTCTTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 3 0.14
13 13 0.59
14 3 0.14
15 3 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATTATATTATTAT
Found at i:29683786 original size:18 final size:20
Alignment explanation
Indices: 29683763--29683809 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
29683753 AGTTGAATTG
29683763 GTATCGATAAAAAT-TA-AA
1 GTATCGATAAAAATGTACAA
* *
29683781 GTATCGATATAATTGTACAA
1 GTATCGATAAAAATGTACAA
29683801 GTATCGATA
1 GTATCGATA
29683810 CATTTTGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 12 0.48
19 2 0.08
20 11 0.44
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.32
Consensus pattern (20 bp):
GTATCGATAAAAATGTACAA
Found at i:29692001 original size:34 final size:34
Alignment explanation
Indices: 29691954--29692018 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
29691944 ACTGCTATTG
*
29691954 ATACTATGATGGGCTTAGGCCCTAATGCATACTA
1 ATACTATGATGGGCTAAGGCCCTAATGCATACTA
* * *
29691988 ATACTGTGTTGGGCTAAGGCCCTACTGCATA
1 ATACTATGATGGGCTAAGGCCCTAATGCATA
29692019 TTTGATACTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (34 bp):
ATACTATGATGGGCTAAGGCCCTAATGCATACTA
Found at i:29693720 original size:30 final size:30
Alignment explanation
Indices: 29693684--29693844 Score: 231
Period size: 30 Copynumber: 5.5 Consensus size: 30
29693674 GACAAGATTG
* * * * *
29693684 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
29693714 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
29693742 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
29693772 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
29693802 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
29693831 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
29693845 GATTCACTAT
Statistics
Matches: 122, Mismatches: 5, Indels: 9
0.90 0.04 0.07
Matches are distributed among these distances:
27 2 0.02
28 22 0.18
29 20 0.16
30 76 0.62
31 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:29693775 original size:58 final size:58
Alignment explanation
Indices: 29693684--29693844 Score: 227
Period size: 58 Copynumber: 2.8 Consensus size: 58
29693674 GACAAGATTG
* * * * * *
29693684 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAG-CTGAATTATATA
29693742 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTG--AATTATATA
29693802 GCACTAAGTGTGCGAGCTGAAAA-TATATAGCACTAAGTGTGCG
1 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCG
29693845 GATTCACTAT
Statistics
Matches: 94, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
57 2 0.02
58 41 0.44
59 20 0.21
60 31 0.33
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAATTATATA
Found at i:29696500 original size:43 final size:43
Alignment explanation
Indices: 29696452--29696640 Score: 270
Period size: 43 Copynumber: 4.4 Consensus size: 43
29696442 TTATTTTAAA
**
29696452 AAACGCCGCTAAAGGCCATGACCTTTGGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGCCGCGACCTTTGGCGGCGCTTTTCCCAC
* * *
29696495 AAACGCTGCTAAAGGTCGCGGCCTTTGGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGCCGCGACCTTTGGCGGCGCTTTTCCCAC
* * * *
29696538 AAACGCTGCTAAAGGTCGCGGCCTTTGGCGGCGCTTTTCCTAC
1 AAACGCCGCTAAAGGCCGCGACCTTTGGCGGCGCTTTTCCCAC
* * *
29696581 AAACGCCGCTAAAAGCCGCGACCTTTAGCGGCACTTTTCCCAC
1 AAACGCCGCTAAAGGCCGCGACCTTTGGCGGCGCTTTTCCCAC
29696624 AAACGCCGCTAAAGGCC
1 AAACGCCGCTAAAGGCC
29696641 ATGAAATTTT
Statistics
Matches: 132, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 132 1.00
ACGTcount: A:0.21, C:0.34, G:0.24, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGGCCGCGACCTTTGGCGGCGCTTTTCCCAC
Found at i:29696949 original size:19 final size:19
Alignment explanation
Indices: 29696904--29696950 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
29696894 TAAATATTAA
*
29696904 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
29696923 AATTAAAACT-AAAATAAAT
1 AA-TAAAAATAAAAATAAAG
29696942 AATAAAAAT
1 AATAAAAAT
29696951 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 6 0.26
19 11 0.48
20 6 0.26
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:29696951 original size:25 final size:24
Alignment explanation
Indices: 29696894--29696980 Score: 70
Period size: 25 Copynumber: 3.6 Consensus size: 24
29696884 CTCAAGTTAT
*
29696894 TAAATATTAAAATAAAAATAAAAA
1 TAAAAATTAAAATAAAAATAAAAA
*
29696918 TATAGAATTAAAACT-AAAATAAATAA
1 TA-AAAATTAAAA-TAAAAATAAA-AA
* * * *
29696944 TAAAAATTAGATTAAATATAAAGA
1 TAAAAATTAAAATAAAAATAAAAA
*
29696968 TATAAA-TAAAATA
1 TAAAAATTAAAATA
29696981 CAGCAAGTCT
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
23 5 0.10
24 9 0.18
25 30 0.61
26 5 0.10
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (24 bp):
TAAAAATTAAAATAAAAATAAAAA
Found at i:29701133 original size:49 final size:46
Alignment explanation
Indices: 29701045--29701141 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 46
29701035 CTTCAAATAC
* *
29701045 TAGTTAACTCCTAAACCTTAAACCCTAAACCGTACATCTTAAACCA
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATACATCTTAAACCA
*
29701091 TAGTTAACTCATAAACCTGCTTAAACCCTAAACCATATATCTTAAACCA
1 TAGTTAACTCATAAA-C--CTTAAACCCTAAACCATACATCTTAAACCA
29701140 TA
1 TA
29701142 AACCTTAAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
46 14 0.31
47 1 0.02
49 30 0.67
ACGTcount: A:0.40, C:0.28, G:0.04, T:0.28
Consensus pattern (46 bp):
TAGTTAACTCATAAACCTTAAACCCTAAACCATACATCTTAAACCA
Found at i:29701138 original size:14 final size:14
Alignment explanation
Indices: 29701112--29701156 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
29701102 TAAACCTGCT
*
29701112 TAAACCCTAAACCA
1 TAAACCTTAAACCA
* *
29701126 TATATCTTAAACCA
1 TAAACCTTAAACCA
*
29701140 TAAACCTTAAACTA
1 TAAACCTTAAACCA
29701154 TAA
1 TAA
29701157 TGATAATTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAACCTTAAACCA
Found at i:29701433 original size:41 final size:41
Alignment explanation
Indices: 29701314--29701409 Score: 176
Period size: 41 Copynumber: 2.4 Consensus size: 41
29701304 GTTATATGAC
29701314 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCCCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCCCTGGT
*
29701355 TTTTAGCGGCGTTTTACCAAAAGCACCGCTAATGCCCTGG-
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCCCTGGT
29701395 TTTTAGCGGCGTTTT
1 TTTTAGCGGCGTTTT
29701410 TTGATAAAAC
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 15 0.28
41 39 0.72
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCCCTGGT
Found at i:29708638 original size:18 final size:19
Alignment explanation
Indices: 29708615--29708653 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
29708605 TTCTCTGACG
29708615 CTGTTCCTCC-GTCTTTTT
1 CTGTTCCTCCGGTCTTTTT
*
29708633 CTGTTCCTCCGGTTTTTTT
1 CTGTTCCTCCGGTCTTTTT
29708652 CT
1 CT
29708654 TTTCTTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.00, C:0.31, G:0.13, T:0.56
Consensus pattern (19 bp):
CTGTTCCTCCGGTCTTTTT
Found at i:29709704 original size:34 final size:33
Alignment explanation
Indices: 29709657--29709736 Score: 97
Period size: 34 Copynumber: 2.4 Consensus size: 33
29709647 GCATGACTGC
*
29709657 TACTGATACTGTGATGGGCTAAAACCCTAATGCA
1 TACTGATATTGTGATGGG-TAAAACCCTAATGCA
** * *
29709691 TACTGATATTGTGATGGGTAAGGCCTTACTGCA
1 TACTGATATTGTGATGGGTAAAACCCTAATGCA
29709724 TATCTGATATTGT
1 TA-CTGATATTGT
29709737 ACTGAGATGG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 13 0.32
34 27 0.68
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.34
Consensus pattern (33 bp):
TACTGATATTGTGATGGGTAAAACCCTAATGCA
Found at i:29713176 original size:42 final size:42
Alignment explanation
Indices: 29713117--29713200 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
29713107 GAAAGTAAAT
29713117 TATGTAAGTCACAATTCTTTTTCTCAAAATCATTATATACTA
1 TATGTAAGTCACAATTCTTTTTCTCAAAATCATTATATACTA
29713159 TATGTAAGTCACAATTCTTTTTCTCAAAATCATTATATACTA
1 TATGTAAGTCACAATTCTTTTTCTCAAAATCATTATATACTA
29713201 ACTTATATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.43
Consensus pattern (42 bp):
TATGTAAGTCACAATTCTTTTTCTCAAAATCATTATATACTA
Found at i:29713501 original size:110 final size:110
Alignment explanation
Indices: 29713378--29713598 Score: 370
Period size: 110 Copynumber: 2.0 Consensus size: 110
29713368 AGAATTTACC
* * * *
29713378 TTTGGTTCCTCGATGGCCATAAGGCAAATTTTGGCTACTTCATCATCATCATTATCAGATGAATC
1 TTTGGTTCATCGATGGCCATAAGGAAAATATTGGCTACTTCATCATCATCATTATCAGATAAATC
* * *
29713443 TTCATCACTCTAAGTAGCAATATGAGCCTTGAGTTTTTGTTTGTT
66 CTCATCACTCCAAGTAGCAACATGAGCCTTGAGTTTTTGTTTGTT
29713488 TTTGGTTCATCGATGGCCATAAGGAAAATATTGGCTACTTCATCATCATCATTATCAGATAAATC
1 TTTGGTTCATCGATGGCCATAAGGAAAATATTGGCTACTTCATCATCATCATTATCAGATAAATC
*
29713553 CTCGTCACTCCAAGTAGCAACATGAGCCTTGAGTTTTTGTTTGTT
66 CTCATCACTCCAAGTAGCAACATGAGCCTTGAGTTTTTGTTTGTT
29713598 T
1 T
29713599 GACCTCTTTT
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 103 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (110 bp):
TTTGGTTCATCGATGGCCATAAGGAAAATATTGGCTACTTCATCATCATCATTATCAGATAAATC
CTCATCACTCCAAGTAGCAACATGAGCCTTGAGTTTTTGTTTGTT
Found at i:29717616 original size:29 final size:26
Alignment explanation
Indices: 29717579--29717660 Score: 67
Period size: 29 Copynumber: 2.9 Consensus size: 26
29717569 CGAGCTAAAT
29717579 TGATAAATTTTGTAAATATTAAAAATAA
1 TGAT-AATTTTGTAAATATTAAAAA-AA
* *
29717607 TTTATTAATTTTTTAGAAT-TTAAATTAAAA
1 -TGA-TAATTTTGTA-AATATTAAA--AAAA
29717637 TGATAATTTTTGTAAATATTAAAA
1 TGATAA-TTTTGTAAATATTAAAA
29717661 TTTTTATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
27 1 0.02
28 6 0.14
29 28 0.65
30 6 0.14
31 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (26 bp):
TGATAATTTTGTAAATATTAAAAAAA
Found at i:29717915 original size:13 final size:14
Alignment explanation
Indices: 29717899--29717933 Score: 63
Period size: 13 Copynumber: 2.6 Consensus size: 14
29717889 TACTTATCAT
29717899 TTAAAAAATGTAA-
1 TTAAAAAATGTAAC
29717912 TTAAAAAATGTAAC
1 TTAAAAAATGTAAC
29717926 TTAAAAAA
1 TTAAAAAA
29717934 ATATTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.29
Consensus pattern (14 bp):
TTAAAAAATGTAAC
Found at i:29718363 original size:27 final size:25
Alignment explanation
Indices: 29718317--29718366 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
29718307 TATAGATATG
* *
29718317 TAAAAAAATTTGTTTTGAAATTTTT
1 TAAAAAAATTTCTTTAGAAATTTTT
29718342 TAAATAAATATTTCTTTAGAAATTT
1 TAAA-AAA-ATTTCTTTAGAAATTT
29718367 ATCATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 3 0.14
27 14 0.67
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (25 bp):
TAAAAAAATTTCTTTAGAAATTTTT
Found at i:29725239 original size:39 final size:39
Alignment explanation
Indices: 29725185--29725265 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
29725175 ATATTTCACT
*
29725185 CACATGGAAGTTCAAATACAAGACCCTAAGGTAAGCTAA
1 CACATGGAAGTTCAAACACAAGACCCTAAGGTAAGCTAA
29725224 CACATGGAAGTTCAAACACAAGACCCTAAGGTAAGCTAA
1 CACATGGAAGTTCAAACACAAGACCCTAAGGTAAGCTAA
29725263 CAC
1 CAC
29725266 CATACCAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.16
Consensus pattern (39 bp):
CACATGGAAGTTCAAACACAAGACCCTAAGGTAAGCTAA
Found at i:29727763 original size:34 final size:34
Alignment explanation
Indices: 29727724--29727789 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
29727714 TTCTCAACTT
* * *
29727724 AGCGTAAAGTTGTTTCTTTCACAGAATCTAAAGA
1 AGCGTAAAGCTATTTCTCTCACAGAATCTAAAGA
*
29727758 AGCGTAAAGCTATTTCTCTCTCAGAATCTAAA
1 AGCGTAAAGCTATTTCTCTCACAGAATCTAAA
29727790 AAACTACTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (34 bp):
AGCGTAAAGCTATTTCTCTCACAGAATCTAAAGA
Found at i:29730505 original size:16 final size:18
Alignment explanation
Indices: 29730473--29730505 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
29730463 TAATCCCAAC
29730473 TCCCTACTAACAACTGAA
1 TCCCTACTAACAACTGAA
29730491 TCCC-ACTAA-AACTGA
1 TCCCTACTAACAACTGA
29730506 CACCTGATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.39, C:0.33, G:0.06, T:0.21
Consensus pattern (18 bp):
TCCCTACTAACAACTGAA
Found at i:29733511 original size:2 final size:2
Alignment explanation
Indices: 29733504--29733544 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
29733494 ATTCTACAAC
29733504 AT AT 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 AT AT A
29733545 AGGTCCTTAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29735925 original size:51 final size:51
Alignment explanation
Indices: 29735849--29735950 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
29735839 CCATATCTGG
29735849 GAAAATACTGCATCTCACCACCACCATAATGCCCATACCGAGGGTGAATAA
1 GAAAATACTGCATCTCACCACCACCATAATGCCCATACCGAGGGTGAATAA
* *
29735900 GAAAATACTGCATCTCACCACCACCATCATGCCCATACTGAGGGTGAATAA
1 GAAAATACTGCATCTCACCACCACCATAATGCCCATACCGAGGGTGAATAA
29735951 AATATTTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.36, C:0.29, G:0.16, T:0.19
Consensus pattern (51 bp):
GAAAATACTGCATCTCACCACCACCATAATGCCCATACCGAGGGTGAATAA
Found at i:29737873 original size:83 final size:84
Alignment explanation
Indices: 29737758--29737933 Score: 279
Period size: 83 Copynumber: 2.1 Consensus size: 84
29737748 CCAGTGTTCT
*
29737758 TGGTGT-TTCTTTCCATTGATTTTTCTTGGCATGTTTCTTGGCTTTCTAAGGCAA-CTTTAGTTG
1 TGGTGTCTTCTTTCCATTGATTTTTCTTGGCATGTTTCTTGGCTTTCTAAAG-AAGCTTTAGTTG
*
29737821 GTGC-TTGGTGGCTCAAAGA
65 GTGCTTTAGTGGCTCAAAGA
29737840 TGGTGTCTTCTTTCCATTGATATTTT-TTGGCATGTTTCTTGGCTTTCTAAAGAAGCTTTAGTTG
1 TGGTGTCTTCTTTCCATTGAT-TTTTCTTGGCATGTTTCTTGGCTTTCTAAAGAAGCTTTAGTTG
29737904 GTGCTTTAGTGGCTCAAAGA
65 GTGCTTTAGTGGCTCAAAGA
*
29737924 TGATGTCTTC
1 TGGTGTCTTC
29737934 GTAGGAGCTT
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
82 8 0.09
83 52 0.60
84 27 0.31
ACGTcount: A:0.16, C:0.15, G:0.23, T:0.45
Consensus pattern (84 bp):
TGGTGTCTTCTTTCCATTGATTTTTCTTGGCATGTTTCTTGGCTTTCTAAAGAAGCTTTAGTTGG
TGCTTTAGTGGCTCAAAGA
Found at i:29741980 original size:43 final size:43
Alignment explanation
Indices: 29741919--29742005 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
29741909 CCTATGTTTT
29741919 TGGCTTAGCGGACATTTGTTGTCCCCTGCTTTCAACCAAACAA
1 TGGCTTAGCGGACATTTGTTGTCCCCTGCTTTCAACCAAACAA
29741962 TGGCTTAGCGGACATTTGTTGTCCCCTGCTTTCAACCAAACAA
1 TGGCTTAGCGGACATTTGTTGTCCCCTGCTTTCAACCAAACAA
29742005 T
1 T
29742006 CTTCTATGCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (43 bp):
TGGCTTAGCGGACATTTGTTGTCCCCTGCTTTCAACCAAACAA
Found at i:29742606 original size:26 final size:26
Alignment explanation
Indices: 29742575--29742633 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
29742565 TTATCCCAAC
*
29742575 AAAATTTTGACA-ATTTTACCCCTAGT
1 AAAATTTTGA-AGATTTTACCACTAGT
* *
29742601 AAAATTTTGAAGATTTTGCCACTGGT
1 AAAATTTTGAAGATTTTACCACTAGT
29742627 AAAATTT
1 AAAATTT
29742634 CGAGAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 1 0.03
26 28 0.97
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.39
Consensus pattern (26 bp):
AAAATTTTGAAGATTTTACCACTAGT
Found at i:29744011 original size:11 final size:11
Alignment explanation
Indices: 29743995--29744019 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29743985 TAGAATATAA
29743995 ATGATTATTTT
1 ATGATTATTTT
29744006 ATGATTATTTT
1 ATGATTATTTT
29744017 ATG
1 ATG
29744020 GTTCATGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (11 bp):
ATGATTATTTT
Found at i:29745286 original size:45 final size:44
Alignment explanation
Indices: 29745201--29745286 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 44
29745191 TATGTAATCT
*
29745201 GAACTCATTGAGTTGTGTCTGAGTTCATGATATATGTGACATCC
1 GAACTCATTGAGTTGTGTCTGAGTTCATGATATATATGACATCC
* *
29745245 GAACTCATTGAGTTGTGGTCTGAGTTCGTGATATGTATGACA
1 GAACTCATTGAGTTGT-GTCTGAGTTCATGATATATATGACA
29745287 CATGTTTTGG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 16 0.42
45 22 0.58
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (44 bp):
GAACTCATTGAGTTGTGTCTGAGTTCATGATATATATGACATCC
Found at i:29757552 original size:19 final size:19
Alignment explanation
Indices: 29757528--29757567 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
29757518 TGTGTTATCA
*
29757528 TAAATTCATAGGCATAACT
1 TAAATTCATAGACATAACT
**
29757547 TAAATTTGTAGACATAACT
1 TAAATTCATAGACATAACT
29757566 TA
1 TA
29757568 CACATTTTCA
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:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (19 bp):
TAAATTCATAGACATAACT
Found at i:29761771 original size:40 final size:39
Alignment explanation
Indices: 29761606--29761789 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
29761596 AAATTGAATG
* * *
29761606 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
29761646 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
29761686 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
29761726 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
29761765 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
29761790 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:29761814 original size:80 final size:81
Alignment explanation
Indices: 29761646--29761834 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
29761636 GCTGGAAATT
* * * *
29761646 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
29761711 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
29761727 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
29761790 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
29761806 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
29761835 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:29764793 original size:40 final size:40
Alignment explanation
Indices: 29764681--29764833 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
29764671 GGATATAGCG
* * * * ***
29764681 ACTCGCTCAAAAGCCTTCGGGACATAGCCCGGTTATAATA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA
* * *
29764721 GCTCGCACAAATGCCTTCGGGACTTAACCCGGATTTGGGA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA
* **
29764761 ACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTC
1 ACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATATGGGA
*
29764801 ACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
29764834 CATCATTCGA
Statistics
Matches: 92, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 3 0.03
40 78 0.85
41 11 0.12
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA
Found at i:29772781 original size:40 final size:41
Alignment explanation
Indices: 29772737--29772840 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 41
29772727 TTATAATAGC
* *
29772737 TCGCACAAATGCCTTCGGGACTTAACCCGGATTTGG-GAAT
1 TCGCACAAATGCCTTCGGGACTTAACCCGGATATGGTCAAT
* ** *
29772777 TCGCACAAATGCCTTC-AGATCTTAGTCCGGATATGGTCACT
1 TCGCACAAATGCCTTCGGGA-CTTAACCCGGATATGGTCAAT
*
29772818 TAGCACAAA-GCCTTCGGGACTTA
1 TCGCACAAATGCCTTCGGGACTTA
29772841 GCTCGGACAT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
39 2 0.04
40 39 0.74
41 12 0.23
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (41 bp):
TCGCACAAATGCCTTCGGGACTTAACCCGGATATGGTCAAT
Found at i:29778493 original size:48 final size:48
Alignment explanation
Indices: 29778412--29778788 Score: 286
Period size: 48 Copynumber: 7.9 Consensus size: 48
29778402 ATTTGGGTGA
* * * *
29778412 TATGTGCGCTAGTGTAAGATCAAGTCTGGGACATAGCATCGGCCACAT
1 TATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAT
* * * ***
29778460 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGTATCGGCGTTGA-
1 TATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CACAT
* * ***
29778508 TAGGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGA-
1 TATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CACAT
* * **
29778556 TAGGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG-CATTT
1 TATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAT
* *
29778603 GTATGTGCGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCACAT
1 -TATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAT
* * * * * * * *
29778652 TGTGAGAGCCAATGCAAGACCATGTTTGGGACACGCCATCGG---CAT
1 TATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAT
* * *
29778697 TGA-GATAAGAGCTAGTGTAAGATCATG-CTAGGGACATGGCATCAGCCTCGA-
1 T-ATG-T--GAGCTAGTGTAAGACCATGTCT-GGGACATGGCATCGGCCAC-AT
* ** *
29778748 TATGTGAGCCAGTGTAAGACCATGTCCAGGACATGACATCG
1 TATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCG
29778789 ATAATTTACC
Statistics
Matches: 267, Mismatches: 47, Indels: 30
0.78 0.14 0.09
Matches are distributed among these distances:
45 5 0.02
47 1 0.00
48 250 0.94
49 5 0.02
50 2 0.01
51 3 0.01
52 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (48 bp):
TATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAT
Found at i:29778573 original size:96 final size:97
Alignment explanation
Indices: 29778409--29778788 Score: 396
Period size: 96 Copynumber: 3.9 Consensus size: 97
29778399 GACATTTGGG
* * * *
29778409 TGATATGTGCGCTAGTGTAAGATCAAGTCTGGGACATAGCATCGGCCACATTATGAGAGCCAGTG
1 TGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTAGGAGAGCCAGTG
*
29778474 TAAGACCATGTCTGGGACATGGTATCGGC-GT
66 TAAGACCATGTCTGGGACATGGCATCGGCAGT
* *** * * *
29778505 TGATAGGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGA-TAGGTGCGCTAGT
1 TGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CACATTAGGAGAGCCAGT
*
29778569 GTAAGACCATGTCTGGGACATGGCATCGGCATT
65 GTAAGACCATGTCTGGGACATGGCATCGGCAGT
* *
29778602 TG-TATGTGCGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCACATT-GTGAGAGCCAAT
1 TGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTAG-GAGAGCCAGT
* * * *
29778665 GCAAGACCATGTTTGGGACACGCCATCGGCA-T
65 GTAAGACCATGTCTGGGACATGGCATCGGCAGT
* ** * * * * * *
29778697 TGAGATAAGAGCTAGTGTAAGATCATG-CTAGGGACATGGCATCAGCCTCGA-TATGTGAGCCAG
1 TGATATGTGCGCTAGTGTAAGACCATGTCT-GGGACATGGCATCGGCCAC-ATTAGGAGAGCCAG
** *
29778760 TGTAAGACCATGTCCAGGACATGACATCG
64 TGTAAGACCATGTCTGGGACATGGCATCG
29778789 ATAATTTACC
Statistics
Matches: 233, Mismatches: 43, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
95 6 0.03
96 222 0.95
97 5 0.02
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.24
Consensus pattern (97 bp):
TGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTAGGAGAGCCAGTG
TAAGACCATGTCTGGGACATGGCATCGGCAGT
Found at i:29778671 original size:144 final size:144
Alignment explanation
Indices: 29778409--29778788 Score: 399
Period size: 144 Copynumber: 2.6 Consensus size: 144
29778399 GACATTTGGG
* * * *
29778409 TGATATGTGCGCTAGTGTAAGATCAAGTCTGGGACATAGCATCGGCCACAT-TATGAGAGCCAGT
1 TGATATGTGCGCTAGTGTAAGATCATGTCTGGGACATGGCATCGG-CACTTGTATGTGAGCCAGT
* *** * * * * *
29778473 GTAAGACCATGTCTGGGACATGGTATCGGCGTTGATAGGTGCGCTAGTGTAAGACCATGTCTGGG
65 GTAAGACCATGTCTGGGACATGGCATCGGCGCACATAGGAGAGCCAATGCAAGACCATGTCTGGG
* * *
29778538 ACATGGCATCGGCGT
130 ACACGCCATCGGCAT
* * * * *
29778553 TGATAGGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTTGTATGTGCGCTAGTG
1 TGATATGTGCGCTAGTGTAAGATCATGTCTGGGACATGGCATCGGCACTTGTATGTGAGCCAGTG
* * *
29778618 TAAGACCATGTTTGGGACATGGCATCGGC-CACATTGTGAGAGCCAATGCAAGACCATGTTTGGG
66 TAAGACCATGTCTGGGACATGGCATCGGCGCACATAG-GAGAGCCAATGCAAGACCATGTCTGGG
29778682 ACACGCCATCGGCAT
130 ACACGCCATCGGCAT
* ** * * *
29778697 TGAGATAAGAGCTAGTGTAAGATCATG-CTAGGGACATGGCATCAGC-CTCGATATGTGAGCCAG
1 TGATATGTGCGCTAGTGTAAGATCATGTCT-GGGACATGGCATCGGCACTTG-TATGTGAGCCAG
** *
29778760 TGTAAGACCATGTCCAGGACATGACATCG
64 TGTAAGACCATGTCTGGGACATGGCATCG
29778789 ATAATTTACC
Statistics
Matches: 193, Mismatches: 39, Indels: 8
0.80 0.16 0.03
Matches are distributed among these distances:
143 10 0.05
144 183 0.95
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.24
Consensus pattern (144 bp):
TGATATGTGCGCTAGTGTAAGATCATGTCTGGGACATGGCATCGGCACTTGTATGTGAGCCAGTG
TAAGACCATGTCTGGGACATGGCATCGGCGCACATAGGAGAGCCAATGCAAGACCATGTCTGGGA
CACGCCATCGGCAT
Found at i:29784565 original size:46 final size:46
Alignment explanation
Indices: 29784507--29784687 Score: 224
Period size: 46 Copynumber: 3.9 Consensus size: 46
29784497 TAGGATGGTT
*
29784507 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
29784553 GAGCGTCTGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
* *
29784599 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
29784646 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29784688 GCGGGTTACA
Statistics
Matches: 114, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 70 0.61
47 32 0.28
48 2 0.02
50 4 0.04
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (46 bp):
GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:29784668 original size:93 final size:93
Alignment explanation
Indices: 29784509--29784679 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
29784499 GGATGGTTGA
* * *
29784509 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCTGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
29784574 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
29784602 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
29784667 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
29784680 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:29788767 original size:48 final size:48
Alignment explanation
Indices: 29788694--29788882 Score: 198
Period size: 48 Copynumber: 3.9 Consensus size: 48
29788684 CATTTGGGTT
* * * *
29788694 ATATGTGCGCTAGTGTAAGAACATGTCTGGGACATGGCATCGGCGTTG
1 ATATGTGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCATTG
* * * *
29788742 ATATGTGTGCTAGTGTAAGACCATGTTTGGGACATGGCATCGACATTG
1 ATATGTGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCATTG
* *** * * * **
29788790 AGACAAGAGCTACTGTAAGACCATGTCTAGAACATGGCATCGGCCTCA
1 ATATGTGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCATTG
* * *
29788838 ATATGTGAGCCAATGTAAGACCCTGTCTAGGACATGGCATCGGCA
1 ATATGTGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCA
29788883 ATTTACCCTC
Statistics
Matches: 114, Mismatches: 27, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 114 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (48 bp):
ATATGTGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCATTG
Found at i:29788871 original size:96 final size:96
Alignment explanation
Indices: 29788702--29788879 Score: 239
Period size: 96 Copynumber: 1.9 Consensus size: 96
29788692 TTATATGTGC
* * * * ** * * *
29788702 GCTAGTGTAAGAACATGTCTGGGACATGGCATCGGCGTTGATATGTGTGCTAGTGTAAGACCATG
1 GCTACTGTAAGAACATGTCTAGAACATGGCATCGGCCTCAATATGTGAGCCAATGTAAGACCATG
* *
29788767 TTTGGGACATGGCATCGACATTGAGACAAGA
66 TCTAGGACATGGCATCGACATTGAGACAAGA
* *
29788798 GCTACTGTAAGACCATGTCTAGAACATGGCATCGGCCTCAATATGTGAGCCAATGTAAGACCCTG
1 GCTACTGTAAGAACATGTCTAGAACATGGCATCGGCCTCAATATGTGAGCCAATGTAAGACCATG
29788863 TCTAGGACATGGCATCG
66 TCTAGGACATGGCATCG
29788880 GCAATTTACC
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
96 69 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (96 bp):
GCTACTGTAAGAACATGTCTAGAACATGGCATCGGCCTCAATATGTGAGCCAATGTAAGACCATG
TCTAGGACATGGCATCGACATTGAGACAAGA
Found at i:29792744 original size:20 final size:21
Alignment explanation
Indices: 29792719--29792758 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
29792709 CACTTGAAAT
29792719 AGGGC-ACACACCCGTGTGAA
1 AGGGCAACACACCCGTGTGAA
* *
29792739 AGGGCAATACGCCCGTGTGA
1 AGGGCAACACACCCGTGTGA
29792759 TCATTATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.28, G:0.33, T:0.12
Consensus pattern (21 bp):
AGGGCAACACACCCGTGTGAA
Found at i:29794278 original size:48 final size:48
Alignment explanation
Indices: 29793918--29794331 Score: 237
Period size: 46 Copynumber: 8.8 Consensus size: 48
29793908 GGGTATAATA
* *
29793918 CCGATGCCATGTCCCAGACATGTTCTTACACT-G-GCTCATCCATCAA-G
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCAT-C-TCAATG
* * * **
29793965 TCAATGCCATGTCCCAAACATGGTCTTACACT-G-ACT-ATCGAAATCGGGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCAAT----G
* * * **
29794014 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCACATATCCGTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACT--CATCTCAATG
* * * * *
29794064 TCGATGCCATGTCCCGGACGTGATCTTACA-TTGACAC-C-TCT-ATACGTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAG-CACTCATCTCA-A--TG
* *
29794112 CCTATGCCATGTCCCAGACATGGTCTTACACT-G-ACTCATCTC-GTAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCAAT-G
* *
29794158 CCGAT-CCATGTCCCAGACAT-GTCTTACAC-AGGC-TTACATCTCGA-G
1 CCGATGCCATGTCCCAGACATGGTCTTACACTA-GCACT-CATCTCAATG
* *
29794203 ACCGATG-CATGTCCCAAACAT-GTCTTACACTAGCACTCGTCTCAATG
1 -CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCAATG
* * * *
29794250 CCGATGCCATGTCCCGGACATGGTCTTACACTGGCTCTCA--TAATATGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCA-AT-G
* *
29794298 CCGATG-CATGTCCCAAACAT-GTCTTACAGTAGCA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCA
29794332 TAAAATTAAC
Statistics
Matches: 285, Mismatches: 49, Indels: 67
0.71 0.12 0.17
Matches are distributed among these distances:
44 11 0.04
45 20 0.07
46 71 0.25
47 62 0.22
48 53 0.19
49 34 0.12
50 29 0.10
51 2 0.01
54 3 0.01
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.26
Consensus pattern (48 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCAATG
Found at i:29794303 original size:94 final size:94
Alignment explanation
Indices: 29793918--29794331 Score: 316
Period size: 94 Copynumber: 4.4 Consensus size: 94
29793908 GGGTATAATA
* * * ** * *
29793918 CCGATGCCATGTCCCAGACATGTTCTTACACT-G-GCTCATCCATCAAGTCAATGCCATGTCCCA
1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCACTCAT-C-TCGTGCCGATGCCATGTCCCA
* * * *
29793981 AACATGGTCTTACACTGACTATCGAAATCGGGG
64 GACATGGTCTTACACTGACTCTC-ATATC-AGG
* * *
29794014 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCACATATCCGTGTCGATGCCATGTCCC
1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCACT--CATCT-CGTGCCGATGCCATGTCCC
* * * * *
29794079 GGACGTGATCTTACATTGACACCTC-TAT-ACGTG
63 AGACATGGTCTTACACTGAC-TCTCATATCA-G-G
* *
29794112 CCTATGCCATGTCCCAGACATGGTCTTACACT-G-ACTCATCTCGTAGCCGAT-CCATGTCCCAG
1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCACTCATCTCGT-GCCGATGCCATGTCCCAG
* * * *
29794174 ACAT-GTCTTACACAGGCT-TACATCTCGAGA
65 ACATGGTCTTACACTGACTCT-CATATC-AGG
* * *
29794204 CCGATG-CATGTCCCAAACAT-GTCTTACACTAGCACTCGTCTCAATGCCGATGCCATGTCCCGG
1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCACTCATCTC-GTGCCGATGCCATGTCCCAG
*
29794267 ACATGGTCTTACACTGGCTCTCATAAT-ATGG
65 ACATGGTCTTACACTGACTCTCAT-ATCA-GG
*
29794298 CCGATG-CATGTCCCAAACAT-GTCTTACAGTAGCA
1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCA
29794332 TAAAATTAAC
Statistics
Matches: 258, Mismatches: 39, Indels: 44
0.76 0.11 0.13
Matches are distributed among these distances:
90 11 0.04
91 15 0.06
92 30 0.12
93 33 0.13
94 60 0.23
95 2 0.01
96 32 0.12
97 3 0.01
98 36 0.14
99 31 0.12
100 5 0.02
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.26
Consensus pattern (94 bp):
CCGATGCCATGTCCCAAACATGGTCTTACACTAGCACTCATCTCGTGCCGATGCCATGTCCCAGA
CATGGTCTTACACTGACTCTCATATCAGG
Found at i:29796051 original size:14 final size:14
Alignment explanation
Indices: 29796034--29796066 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
29796024 TCTGAATTGG
29796034 TACATCTGCATACA
1 TACATCTGCATACA
*
29796048 TACATTTGCATACA
1 TACATCTGCATACA
29796062 TACAT
1 TACAT
29796067 GCATATGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.33
Consensus pattern (14 bp):
TACATCTGCATACA
Found at i:29796065 original size:18 final size:18
Alignment explanation
Indices: 29796042--29796077 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29796032 GGTACATCTG
*
29796042 CATACATACATTTGCATA
1 CATACATACATATGCATA
*
29796060 CATACATGCATATGCATA
1 CATACATACATATGCATA
29796078 AACTATTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.31
Consensus pattern (18 bp):
CATACATACATATGCATA
Found at i:29796435 original size:92 final size:92
Alignment explanation
Indices: 29796272--29796454 Score: 224
Period size: 92 Copynumber: 2.0 Consensus size: 92
29796262 GTCGCGTATT
* * * *
29796272 ATTGACTGAACTGGCAGTTTTACTACAACCTAACGGTATAGCAGTTCACCGCATTGCACTATACC
1 ATTGACTGAACTGACAGTTTTACTACAACCTAACGGTATAGCAATTCACCACATTGCACCATACC
*
29796337 GCATGTACGTTAGCTACGCTACGTACC
66 ACATGTACGTTAGCTACGCTACGTACC
* ** * * * *
29796364 ATTGACTGAACTGACAGTTTTACTGCAACCTATTGGTTTAGCAAATT-ATCATATTGTACCATAC
1 ATTGACTGAACTGACAGTTTTACTACAACCTAACGGTATAGC-AATTCACCACATTGCACCATAC
* *
29796428 CATATGTACGTTAGCTACGTTACGTAC
65 CACATGTACGTTAGCTACGCTACGTAC
29796455 TACCATCTAA
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
92 73 0.96
93 3 0.04
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (92 bp):
ATTGACTGAACTGACAGTTTTACTACAACCTAACGGTATAGCAATTCACCACATTGCACCATACC
ACATGTACGTTAGCTACGCTACGTACC
Found at i:29798336 original size:46 final size:46
Alignment explanation
Indices: 29798286--29798454 Score: 184
Period size: 46 Copynumber: 3.7 Consensus size: 46
29798276 TGAGCATCCG
29798286 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
* * *
29798332 AACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCCA
* * * *
29798379 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
* *
29798425 AGCTCGTTGATTTGAGTCCGAGTTCACTTA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTA
29798455 GGGGTGGGTT
Statistics
Matches: 103, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 56 0.54
47 28 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
Found at i:29798440 original size:93 final size:93
Alignment explanation
Indices: 29798279--29798449 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
29798269 GGATGGTTGA
* *
29798279 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCAAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAACTCGTTGAGT
29798344 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
29798372 GCATCC-AAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAT
1 GCATCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAACTCGTTGAG
29798436 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
29798450 ACTTAGGGGT
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:29800847 original size:12 final size:11
Alignment explanation
Indices: 29800822--29800868 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
29800812 CTAATTTAAC
29800822 ATAAAATCAAA
1 ATAAAATCAAA
29800833 ATAAAATCAAAA
1 ATAAAATC-AAA
29800845 ATAAAAT--AA
1 ATAAAATCAAA
29800854 ATAAAAAT-AAA
1 AT-AAAATCAAA
29800865 ATAA
1 ATAA
29800869 GATTTTCTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
9 4 0.12
10 7 0.21
11 12 0.36
12 10 0.30
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (11 bp):
ATAAAATCAAA
Found at i:29800850 original size:6 final size:5
Alignment explanation
Indices: 29800822--29800868 Score: 51
Period size: 5 Copynumber: 8.8 Consensus size: 5
29800812 CTAATTTAAC
29800822 ATAAA ATCAAA ATAAA ATCAAAA ATAAA AT-AA ATAAAA ATAAA ATAA
1 ATAAA AT-AAA ATAAA AT--AAA ATAAA ATAAA AT-AAA ATAAA ATAA
29800869 GATTTTCTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
4 4 0.11
5 19 0.51
6 9 0.24
7 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:29804242 original size:47 final size:46
Alignment explanation
Indices: 29804169--29804439 Score: 178
Period size: 47 Copynumber: 5.8 Consensus size: 46
29804159 ATTTTTTTGT
*
29804169 GAGCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCCACATTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCACA-TATGA
* * *
29804215 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CATTGAGACGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACATGGCATCGGCCA--CATATGA
* * * * * *
29804263 GAGCTAGTGTAAGACATGTCTAGGACAT-GCATCAGCCTCGAGACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCAC-ATATG-A
* * * * *
29804310 -AGCCAGTGTAAGACTTGTCTAGGACAT-GCATTGGCTACGAGATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCAC-ATATGA
* ** * * ***
29804355 TAGTTAGTGTAAGACCATGTCTGGGACATCGTATCGAG-TTGATAT-A
1 GAGCCAGTGTAAGA-CATGTCTGGGACATGGCATCG-GCCACATATGA
*
29804401 TGAGCCAGTGTAAGACCATATCTGGGACATGGCATCGGC
1 -GAGCCAGTGTAAGA-CATGTCTGGGACATGGCATCGGC
29804440 ACCTTACCCA
Statistics
Matches: 181, Mismatches: 31, Indels: 25
0.76 0.13 0.11
Matches are distributed among these distances:
45 1 0.01
46 74 0.41
47 76 0.42
48 28 0.15
49 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCACATATGA
Found at i:29804318 original size:46 final size:46
Alignment explanation
Indices: 29804169--29804383 Score: 202
Period size: 46 Copynumber: 4.6 Consensus size: 46
29804159 ATTTTTTTGT
* * * * *
29804169 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGA
1 GAGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGA-GACGA
* * *
29804215 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGA
1 GAGCCAGTGTAAGA-CATGTCTAGGACAT-GCATCGGCCTCGAGACGA
* *
29804263 GAGCTAGTGTAAGACATGTCTAGGACATGCATCAGCCTCGAGACGTA
1 GAGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGACG-A
* * *
29804310 -AGCCAGTGTAAGACTTGTCTAGGACATGCATTGG-CTACGAGATGA
1 GAGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCT-CGAGACGA
* ** *
29804355 TAGTTAGTGTAAGACCATGTCTGGGACAT
1 GAGCCAGTGTAAGA-CATGTCTAGGACAT
29804384 CGTATCGAGT
Statistics
Matches: 142, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
45 3 0.02
46 74 0.52
47 40 0.28
48 24 0.17
49 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.23
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGACGA
Found at i:29804429 original size:140 final size:140
Alignment explanation
Indices: 29804174--29804436 Score: 318
Period size: 140 Copynumber: 1.9 Consensus size: 140
29804164 TTTGTGAGCT
* *
29804174 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTAGGACATGCATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTCTGG
* * *
29804239 GACATGGCATCGGCATTGAGACGAGAGCTAGTGTAAGACATGTCTAGGACAT-GCATCAGCCTCG
66 GACATCGCATCGG-ATTGAGACGAGAGCCAGTGTAAGACATATCTAGGACATGGCATCAGCCTCG
29804303 AGACGTAAGCC
130 AGACGTAAGCC
* * * * **
29804314 AGTGTAAGACTTGTCTAGGACATGCATTGGCTACGA-GATGATAGTTAGTGTAAGACCATGTCTG
1 AGTGTAAGACATGTCTAGGACATGCATCGGCCAC-ATGATGAGAGCCAGTGTAAGACCATGTCTG
* * * *
29804378 GGACATCGTATC-GAGTTGATA-TATGAGCCAGTGTAAGACCATATCTGGGACATGGCATC
65 GGACATCGCATCGGA-TTGAGACGA-GAGCCAGTGTAAGA-CATATCTAGGACATGGCATC
29804437 GGCACCTTAC
Statistics
Matches: 103, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
138 2 0.02
139 19 0.18
140 76 0.74
141 6 0.06
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (140 bp):
AGTGTAAGACATGTCTAGGACATGCATCGGCCACATGATGAGAGCCAGTGTAAGACCATGTCTGG
GACATCGCATCGGATTGAGACGAGAGCCAGTGTAAGACATATCTAGGACATGGCATCAGCCTCGA
GACGTAAGCC
Found at i:29808025 original size:18 final size:18
Alignment explanation
Indices: 29808002--29808037 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29807992 CGTGTGGACC
29808002 TGTGGACCTACACAGGCA
1 TGTGGACCTACACAGGCA
29808020 TGTGGACCTACACAGGCA
1 TGTGGACCTACACAGGCA
29808038 GTCCACACGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (18 bp):
TGTGGACCTACACAGGCA
Found at i:29813750 original size:28 final size:29
Alignment explanation
Indices: 29813685--29813756 Score: 121
Period size: 28 Copynumber: 2.5 Consensus size: 29
29813675 ATAGTGAATC
29813685 CGCACACTTAGTGCTATATATATTCAACT
1 CGCACACTTAGTGCTATATATATTCAACT
29813714 CGCACACTTAGTGCTATATA-A-TCAAACT
1 CGCACACTTAGTGCTATATATATTC-AACT
29813742 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29813757 GTACAATTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 2 0.05
28 20 0.48
29 20 0.48
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATATTCAACT
Found at i:29814208 original size:2 final size:2
Alignment explanation
Indices: 29814201--29814228 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29814191 CGAATGTATG
29814201 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
29814229 CAATGTCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29821571 original size:28 final size:29
Alignment explanation
Indices: 29821508--29821577 Score: 117
Period size: 28 Copynumber: 2.4 Consensus size: 29
29821498 AGTGAATCCA
29821508 CACACTTAGTGCTATATATATTCAACTCG
1 CACACTTAGTGCTATATATATTCAACTCG
29821537 CACACTTAGTGCTATATA-A-TCAAACTCG
1 CACACTTAGTGCTATATATATTC-AACTCG
29821565 CACACTTAGTGCT
1 CACACTTAGTGCT
29821578 GTACAATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 2 0.05
28 20 0.50
29 18 0.45
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.31
Consensus pattern (29 bp):
CACACTTAGTGCTATATATATTCAACTCG
Found at i:29821599 original size:30 final size:28
Alignment explanation
Indices: 29821508--29821606 Score: 101
Period size: 28 Copynumber: 3.4 Consensus size: 28
29821498 AGTGAATCCA
* *
29821508 CACACTTAGTGCTATATATATTCAACTCG
1 CACACTTAGTGCTATAAAT-TTAAACTCG
*
29821537 CACACTTAGTGCTATATAA-TCAAACTCG
1 CACACTTAGTGCTATA-AATTTAAACTCG
* *
29821565 CACACTTAGTGCTGTACAATTTTAAACCCG
1 CACACTTAGTGCTATA-AA-TTTAAACTCG
*
29821595 CACACTCAGTGC
1 CACACTTAGTGC
29821607 CAATCTTGTC
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 24 0.41
29 16 0.27
30 19 0.32
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.29
Consensus pattern (28 bp):
CACACTTAGTGCTATAAATTTAAACTCG
Found at i:29828463 original size:29 final size:28
Alignment explanation
Indices: 29828388--29828464 Score: 66
Period size: 29 Copynumber: 2.7 Consensus size: 28
29828378 CAACGGATTG
** * *
29828388 TCATGCATACAGATTTATAGAGGAAGAT
1 TCATGCATACAGATCCATAGAGGAAAAC
* * *
29828416 TCATGAATAC-GAACTCATATATGGAAAAC
1 TCATGCATACAGATC-CATAGA-GGAAAAC
29828445 TCATGCATACAGATCCATAG
1 TCATGCATACAGATCCATAG
29828465 GTGAATACTT
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
27 2 0.06
28 13 0.36
29 18 0.50
30 3 0.08
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (28 bp):
TCATGCATACAGATCCATAGAGGAAAAC
Found at i:29828741 original size:2 final size:2
Alignment explanation
Indices: 29828736--29828803 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
29828726 CATAGATATA
29828736 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
29828778 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
29828804 CATATATCTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:29833868 original size:46 final size:48
Alignment explanation
Indices: 29833764--29833892 Score: 155
Period size: 46 Copynumber: 2.8 Consensus size: 48
29833754 TGTAACCCGC
*
29833764 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA--CCTAGTTACAT
* *
29833814 CC---A-CGAACTCGGACTCAACTCAACGAGTTCGGA-C-A-TTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTT-ACAT
29833856 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
29833893 TGCCCAAATA
Statistics
Matches: 70, Mismatches: 4, Indels: 14
0.80 0.05 0.16
Matches are distributed among these distances:
41 2 0.03
42 6 0.09
43 1 0.01
45 1 0.01
46 57 0.81
47 1 0.01
50 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.20
Consensus pattern (48 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTTACAT
Found at i:29836276 original size:14 final size:14
Alignment explanation
Indices: 29836257--29836317 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
29836247 CAAAGATAAC
29836257 AAGAAAACCGAATA
1 AAGAAAACCGAATA
* *
29836271 AAG-AAATCAAGATA
1 AAGAAAACCGA-ATA
* *
29836285 GAGAAACCCGAATA
1 AAGAAAACCGAATA
*
29836299 AAGAAATCCAGAATA
1 AAGAAAACC-GAATA
29836314 AAGA
1 AAGA
29836318 GATCCAGGAT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
13 5 0.14
14 18 0.50
15 13 0.36
ACGTcount: A:0.61, C:0.13, G:0.16, T:0.10
Consensus pattern (14 bp):
AAGAAAACCGAATA
Found at i:29836314 original size:15 final size:15
Alignment explanation
Indices: 29836257--29836334 Score: 81
Period size: 15 Copynumber: 5.4 Consensus size: 15
29836247 CAAAGATAAC
*
29836257 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
*
29836271 AAGAAATCAAG-ATA
1 AAGAAATCCAGAATA
* *
29836285 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
29836299 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
29836314 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
29836329 AAGAAA
1 AAGAAA
29836335 CCCAAGATAC
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
13 2 0.04
14 23 0.45
15 26 0.51
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:29836343 original size:15 final size:15
Alignment explanation
Indices: 29836268--29836343 Score: 59
Period size: 15 Copynumber: 5.2 Consensus size: 15
29836258 AGAAAACCGA
*
29836268 ATAAAGAAA-TCAAG
1 ATAAAGAAACCCAAG
* *
29836282 ATAGAGAAACCCGA-
1 ATAAAGAAACCCAAG
*
29836296 ATAAAGAAATCC-AG
1 ATAAAGAAACCCAAG
* * *
29836310 AATAAAGAGATCCAGG
1 -ATAAAGAAACCCAAG
29836326 ATAAAGAAACCCAAG
1 ATAAAGAAACCCAAG
29836341 ATA
1 ATA
29836344 CGATACTATG
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
13 1 0.02
14 18 0.38
15 28 0.58
16 1 0.02
ACGTcount: A:0.57, C:0.14, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAACCCAAG
Found at i:29849843 original size:23 final size:24
Alignment explanation
Indices: 29849794--29849844 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 24
29849784 TAGTTTTCTC
*
29849794 TTAATTTTTAATTTTATTCAATTAA
1 TTAATTTTT-ATTTAATTCAATTAA
29849819 TTAATTTTT-TTTAATTC-ATTGAA
1 TTAATTTTTATTTAATTCAATT-AA
29849842 TTA
1 TTA
29849845 TTAATATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 3 0.12
23 12 0.50
25 9 0.38
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (24 bp):
TTAATTTTTATTTAATTCAATTAA
Found at i:29849843 original size:27 final size:28
Alignment explanation
Indices: 29849798--29849859 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 28
29849788 TTTCTCTTAA
*
29849798 TTTTTAATTTTATTCAATTAATTAAT-TT
1 TTTTTAATTTCATTCAATT-ATTAATATT
*
29849826 TTTTTAA-TTCATTGAATTATTAATATT
1 TTTTTAATTTCATTCAATTATTAATATT
29849853 TTTTTAA
1 TTTTTAA
29849860 AATCTTCTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 6 0.19
27 18 0.58
28 7 0.23
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTTTAATTTCATTCAATTATTAATATT
Found at i:29855894 original size:20 final size:20
Alignment explanation
Indices: 29855869--29855927 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
29855859 GTATAAACTA
* *
29855869 TAATTCATCCATATCAATAG
1 TAATTCATCCATTTCAACAG
*
29855889 TAATTCATTCATTTCAACAG
1 TAATTCATCCATTTCAACAG
29855909 TAATTCATCCATTTCAACA
1 TAATTCATCCATTTCAACA
29855928 TATCTCATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.37
Consensus pattern (20 bp):
TAATTCATCCATTTCAACAG
Found at i:29856642 original size:18 final size:19
Alignment explanation
Indices: 29856603--29856643 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
29856593 GGGAGGTATG
*
29856603 ATAAAATAATGAGTATGGGA
1 ATAAAATAATGAG-AAGGGA
29856623 ATAAAATAATGA-AAGGGA
1 ATAAAATAATGAGAAGGGA
29856641 ATA
1 ATA
29856644 TGATGAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
20 12 0.60
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (19 bp):
ATAAAATAATGAGAAGGGA
Found at i:29859714 original size:49 final size:49
Alignment explanation
Indices: 29859637--29859850 Score: 347
Period size: 49 Copynumber: 4.4 Consensus size: 49
29859627 ATCAAGATTC
* * *
29859637 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
* * *
29859686 GCGAAAATGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
* *
29859735 GTGAAAGTATATATATATGTGATAAGGCCTAATGGCCGATGTGGTGAAT
1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
*
29859784 GTGAAAGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
29859833 GTGAAAGTGTATATATAT
1 GTGAAAGTGTATATATAT
29859851 ATGTGGTAAA
Statistics
Matches: 152, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 152 1.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (49 bp):
GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
Found at i:29862172 original size:40 final size:40
Alignment explanation
Indices: 29862116--29862333 Score: 271
Period size: 40 Copynumber: 5.5 Consensus size: 40
29862106 TGGATGATAA
* * *
29862116 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
*
29862156 TCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
29862196 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
29862236 CCGGGCTTAGTCCCAAAGGCAATTGTGCTAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
29862276 CCGGGCTATGTCCCGAAGGCATTCGAGTGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
29862316 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
29862334 TACTTGGCTT
Statistics
Matches: 156, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
39 16 0.10
40 140 0.90
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Done.