Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3078.1
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: 163959
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.27
Warning! 16409 characters in sequence are not A, C, G, or T
Found at i:1251 original size:27 final size:26
Alignment explanation
Indices: 1203--1254 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
1193 GCGAGGCTGC
*
1203 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
1229 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
1255 TTACAGTGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:1941 original size:27 final size:27
Alignment explanation
Indices: 1911--2272 Score: 447
Period size: 27 Copynumber: 13.4 Consensus size: 27
1901 ATCGATAGTC
* *
1911 CTACCCTACAGGGGTATTTTAGTATTT
1 CTACCCTACAGGGGTATTTCAGTAATT
* **
1938 CTACCCTACAAGGGTATTTTGGTAATT
1 CTACCCTACAGGGGTATTTCAGTAATT
* *
1965 CTACCCTAGAGGGGCATTTCAGTAATT
1 CTACCCTACAGGGGTATTTCAGTAATT
1992 CTACCCTACAGGGGTATTTCAGTAATT
1 CTACCCTACAGGGGTATTTCAGTAATT
* * * * *
2019 CAACCTTATAGAGGTATTTTAGTAATT
1 CTACCCTACAGGGGTATTTCAGTAATT
* * *
2046 CTACCTTACAAGGGTATTTCGGTAATT
1 CTACCCTACAGGGGTATTTCAGTAATT
*
2073 CTACCTTACAGGGGGTATTT-AGTAATT
1 CTACCCTACA-GGGGTATTTCAGTAATT
* *
2100 CTACCCTATAGGGGTATTTCGGTAATT
1 CTACCCTACAGGGGTATTTCAGTAATT
* * *
2127 CTACCTTATAAGGGTATTTCAGTAATT
1 CTACCCTACAGGGGTATTTCAGTAATT
2154 CTACCCTACAGGGGTATTTCAGTAATT
1 CTACCCTACAGGGGTATTTCAGTAATT
* * *
2181 CTACCTTACAGGGGTATTTTAATAATT
1 CTACCCTACAGGGGTATTTCAGTAATT
*
2208 CTACCCTACAGGGGTATTTCGGTAATT
1 CTACCCTACAGGGGTATTTCAGTAATT
* * *
2235 CTACCTTACAGGGGTATTTTAGTAATG
1 CTACCCTACAGGGGTATTTCAGTAATT
*
2262 CTAGCCTACAG
1 CTACCCTACAG
2273 ATATGAGATT
Statistics
Matches: 288, Mismatches: 45, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
26 9 0.03
27 271 0.94
28 8 0.03
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (27 bp):
CTACCCTACAGGGGTATTTCAGTAATT
Found at i:1994 original size:54 final size:54
Alignment explanation
Indices: 1911--2272 Score: 510
Period size: 54 Copynumber: 6.7 Consensus size: 54
1901 ATCGATAGTC
* * * *
1911 CTACCCTACAGGGGTATTTTAGTATTTCTACCCTACAAGGGTATTTTGGTAATT
1 CTACCTTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGGTAATT
* * * * *
1965 CTACCCTAGAGGGGCATTTCAGTAATTCTACCCTACAGGGGTATTTCAGTAATT
1 CTACCTTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGGTAATT
* * * * *
2019 CAACCTTATAGAGGTATTTTAGTAATTCTACCTTACAAGGGTATTTCGGTAATT
1 CTACCTTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGGTAATT
*
2073 CTACCTTACAGGGGGTA-TTTAGTAATTCTACCCTATAGGGGTATTTCGGTAATT
1 CTACCTTACA-GGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGGTAATT
* * * *
2127 CTACCTTATAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAGTAATT
1 CTACCTTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGGTAATT
*
2181 CTACCTTACAGGGGTATTTTAATAATTCTACCCTACAGGGGTATTTCGGTAATT
1 CTACCTTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGGTAATT
* *
2235 CTACCTTACAGGGGTATTTTAGTAATGCTAGCCTACAG
1 CTACCTTACAGGGGTATTTTAGTAATTCTACCCTACAG
2273 ATATGAGATT
Statistics
Matches: 271, Mismatches: 35, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
53 5 0.02
54 261 0.96
55 5 0.02
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (54 bp):
CTACCTTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGGTAATT
Found at i:11176 original size:18 final size:18
Alignment explanation
Indices: 11153--11189 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
11143 AAAATGAACA
11153 AGTCCCTATAGATGTCAT
1 AGTCCCTATAGATGTCAT
11171 AGTCCCTATAGATGTCAT
1 AGTCCCTATAGATGTCAT
11189 A
1 A
11190 CTTTCAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (18 bp):
AGTCCCTATAGATGTCAT
Found at i:11829 original size:43 final size:43
Alignment explanation
Indices: 11766--11853 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
11756 GGTAGGACGT
*
11766 ACAAGACCAGCACTCGGATCACATAATCACATAACACATACTA
1 ACAAGACCAGCACTCAGATCACATAATCACATAACACATACTA
11809 ACAAGACCAGCACTCAGATCACATAATCACATAACACATACTA
1 ACAAGACCAGCACTCAGATCACATAATCACATAACACATACTA
11852 AC
1 AC
11854 CCTAGTAACA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.45, C:0.31, G:0.08, T:0.16
Consensus pattern (43 bp):
ACAAGACCAGCACTCAGATCACATAATCACATAACACATACTA
Found at i:11988 original size:31 final size:31
Alignment explanation
Indices: 11950--12043 Score: 188
Period size: 31 Copynumber: 3.0 Consensus size: 31
11940 TAGAGTTATA
11950 CTCATTCACATAATTAAACATACAATTCATG
1 CTCATTCACATAATTAAACATACAATTCATG
11981 CTCATTCACATAATTAAACATACAATTCATG
1 CTCATTCACATAATTAAACATACAATTCATG
12012 CTCATTCACATAATTAAACATACAATTCATG
1 CTCATTCACATAATTAAACATACAATTCATG
12043 C
1 C
12044 AATATTAAAG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.41, C:0.23, G:0.03, T:0.32
Consensus pattern (31 bp):
CTCATTCACATAATTAAACATACAATTCATG
Found at i:14133 original size:35 final size:35
Alignment explanation
Indices: 14066--14254 Score: 236
Period size: 35 Copynumber: 5.3 Consensus size: 35
14056 CAAACCACCC
* * *
14066 AAACACACCAGATGCTCATAAAAGAGCCAATCCAAAC-
1 AAACACGCCA-ATGCTCAT--AAGAGCTAATCCAACCG
*
14103 ATAACACGCCAATGCTCATAAGAGCTAATCCAACTG
1 A-AACACGCCAATGCTCATAAGAGCTAATCCAACCG
* * * *
14139 TAACATGCCAATCCTCATAAGAGCTAATCCAACCA
1 AAACACGCCAATGCTCATAAGAGCTAATCCAACCG
*
14174 AAACACGCCAATTCTCATAAGAGCTAATCCAACCG
1 AAACACGCCAATGCTCATAAGAGCTAATCCAACCG
* *
14209 AAACATGCCAATGCTCATAAGAGCTAATCTAACCG
1 AAACACGCCAATGCTCATAAGAGCTAATCCAACCG
14244 AAACACGCCAA
1 AAACACGCCAA
14255 ATAGAGAGTA
Statistics
Matches: 133, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
35 116 0.87
37 9 0.07
38 8 0.06
ACGTcount: A:0.42, C:0.30, G:0.12, T:0.16
Consensus pattern (35 bp):
AAACACGCCAATGCTCATAAGAGCTAATCCAACCG
Found at i:18327 original size:47 final size:46
Alignment explanation
Indices: 18264--18363 Score: 114
Period size: 47 Copynumber: 2.2 Consensus size: 46
18254 GTCTTAAATA
* * *
18264 TGTCTTAAGTCTATTAATGCATG-T-TAATTAGTATATCATTTTAATG
1 TGTCTTAAGTCTATTAAT--ATGTTATAATAAGTACATCATTTTAACG
* *
18310 TGTCTTAAGTTTAATTAATATGTTATAATAAGTACATCTTTTTAACG
1 TGTCTTAAGTCT-ATTAATATGTTATAATAAGTACATCATTTTAACG
18357 TGTCTTA
1 TGTCTTA
18364 GATTAAGATA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
45 3 0.07
46 12 0.26
47 31 0.67
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (46 bp):
TGTCTTAAGTCTATTAATATGTTATAATAAGTACATCATTTTAACG
Found at i:27068 original size:27 final size:27
Alignment explanation
Indices: 27038--27285 Score: 291
Period size: 27 Copynumber: 9.2 Consensus size: 27
27028 ATTACCAAAG
* *
27038 TACCCTCAATTTACTGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
27065 TACCCTCGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
* **
27092 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
27119 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
27146 TACCATCGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
** * *
27173 TACCCTTAATTTACAGAATTACCGTTG
1 TACCCTCGATTTACAGAATTACTGTTT
*
27200 TACTCTCGATTTACAGAATTA-TCGTTT
1 TACCCTCGATTTACAGAATTACT-GTTT
* *
27227 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
27254 TACCCTCGATTTATAAAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
27281 TACCC
1 TACCC
27286 CTAGGGTGTT
Statistics
Matches: 188, Mismatches: 31, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
27 188 1.00
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:30993 original size:50 final size:49
Alignment explanation
Indices: 30875--31064 Score: 193
Period size: 50 Copynumber: 3.8 Consensus size: 49
30865 CTGGTACGCA
* **
30875 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATCC-GTACACG
* *
30924 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTCATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATC-CGTACACG
* * * * ** * * *
30974 TAGTAGCCTGCACTTAGTACAACACACGTGATCAAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCTAA-CCATC-CGTACACG
* *
31025 TAGTAGCCTGCACTTAGTACTACACATGCGACCTCACCAT
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCAT
31065 AGATCATTCG
Statistics
Matches: 115, Mismatches: 23, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
49 31 0.27
50 46 0.40
51 38 0.33
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATCCGTACACG
Found at i:31048 original size:101 final size:99
Alignment explanation
Indices: 30875--31064 Score: 272
Period size: 101 Copynumber: 1.9 Consensus size: 99
30865 CTGGTACGCA
* * * *
30875 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACAACACACGCGACAAATTATCCGGTACACATAGTAGCCTGCACTTA
*
30940 GTACTACACACGTGACCTAACCATCTCATACACG
66 GTACTACACACGCGACCTAACCATCTCATACACG
* * *
30974 TAGTAGCCTGCACTTAGTACAACACACGTGATCAAAGTTATCGGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACAACACACGCGA-CAAA-TTATCCGGTACACATAGTAGCCTGCACT
* *
31039 TAGTACTACACATGCGACCTCACCAT
64 TAGTACTACACACGCGACCTAACCAT
31065 AGATCATTCG
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 28 0.35
100 3 0.04
101 48 0.61
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACAACACACGCGACAAATTATCCGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCTAACCATCTCATACACG
Found at i:35834 original size:27 final size:26
Alignment explanation
Indices: 35786--35837 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
35776 GCGAGGCTAC
*
35786 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
35812 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
35838 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:36529 original size:27 final size:27
Alignment explanation
Indices: 36499--36660 Score: 234
Period size: 27 Copynumber: 6.0 Consensus size: 27
36489 ATCGGTAGTC
* * *
36499 CTACCCTATAGGGGTATTTTAATAATT
1 CTACCCTACAGGGGTATTTCAGTAATT
*
36526 CTACCCTACAGGGGTATTTCGGTAATT
1 CTACCCTACAGGGGTATTTCAGTAATT
* *
36553 CTACCTTACAGGGGTATTTTAGTAATT
1 CTACCCTACAGGGGTATTTCAGTAATT
* *
36580 CTACCCTACAGGGTTATTTCGGTAATT
1 CTACCCTACAGGGGTATTTCAGTAATT
*
36607 CTACCCTATAGGGGTATTTCAGTAATT
1 CTACCCTACAGGGGTATTTCAGTAATT
*
36634 CTACCCTACAGGGGTATTTCAATAATT
1 CTACCCTACAGGGGTATTTCAGTAATT
36661 TTGTCAATCG
Statistics
Matches: 119, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 119 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (27 bp):
CTACCCTACAGGGGTATTTCAGTAATT
Found at i:36660 original size:54 final size:54
Alignment explanation
Indices: 36490--36653 Score: 265
Period size: 54 Copynumber: 3.0 Consensus size: 54
36480 CATGGGTAAA
* * *
36490 TCGGTAGTCCTACCCTATAGGGGTATTTTAATAATTCTACCCTACAGGGGTATT
1 TCGGTAATTCTACCCTATAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATT
* * *
36544 TCGGTAATTCTACCTTACAGGGGTATTTTAGTAATTCTACCCTACAGGGTTATT
1 TCGGTAATTCTACCCTATAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATT
*
36598 TCGGTAATTCTACCCTATAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATT
1 TCGGTAATTCTACCCTATAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATT
36652 TC
1 TC
36654 AATAATTTTG
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 100 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (54 bp):
TCGGTAATTCTACCCTATAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATT
Found at i:36675 original size:27 final size:27
Alignment explanation
Indices: 36645--36879 Score: 108
Period size: 27 Copynumber: 8.7 Consensus size: 27
36635 TACCCTACAG
* *
36645 GGGTATTTCAATAATTTTGTCAATCGA
1 GGGTATTTCAGTAATTTTGACAATCGA
*** * * *
36672 GGGTAAAACGGTAATTCTGTA-AATCGG
1 GGGTATTTCAGTAATTTTG-ACAATCGA
*
36699 GGGTACTTT-GGTAATTTT-ACAAGTCGA
1 GGGTA-TTTCAGTAATTTTGACAA-TCGA
* * * *
36726 GAGTATTTCAGTAATTTTAAAAATTGA
1 GGGTATTTCAGTAATTTTGACAATCGA
*
36753 GGGTATTTCAGTAATTTTG-CAAACTGA
1 GGGTATTTCAGTAATTTTGACAATC-GA
* * *
36780 GGGTATTTCGGTAA-TTTCACAAAT-TA
1 GGGTATTTCAGTAATTTTGAC-AATCGA
** * *
36806 GGGGTATTTTGGTAATTTT-ACAAACCAA
1 -GGGTATTTCAGTAATTTTGAC-AATCGA
** * *
36834 GGGTATTTTTGTAATTTT-ACAAACTA
1 GGGTATTTCAGTAATTTTGACAATCGA
*
36860 GGGGTATTTTAGTAATTTTG
1 -GGGTATTTCAGTAATTTTG
36880 TAAACCAAGG
Statistics
Matches: 161, Mismatches: 33, Indels: 27
0.73 0.15 0.12
Matches are distributed among these distances:
25 1 0.01
26 15 0.09
27 136 0.84
28 9 0.06
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.39
Consensus pattern (27 bp):
GGGTATTTCAGTAATTTTGACAATCGA
Found at i:36684 original size:81 final size:81
Alignment explanation
Indices: 36521--36689 Score: 198
Period size: 81 Copynumber: 2.1 Consensus size: 81
36511 GGTATTTTAA
* * * * **
36521 TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCTTACAGGGGTATTTTAGTAATTCTACCC
1 TAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAATAATTCTACAA
***
36586 TACAGGGTTATTTCGG
66 TACAGGGTTAAAACGG
* * *
36602 TAATTCTACCCTATAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAATAATTTTGTCA
1 TAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAATAATTCT-ACA
36667 AT-CGAGGG-TAAAACGG
65 ATAC-AGGGTTAAAACGG
36683 TAATTCT
1 TAATTCT
36690 GTAAATCGGG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
81 68 0.92
82 6 0.08
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (81 bp):
TAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCAATAATTCTACAA
TACAGGGTTAAAACGG
Found at i:36884 original size:27 final size:27
Alignment explanation
Indices: 36698--36931 Score: 186
Period size: 27 Copynumber: 8.7 Consensus size: 27
36688 CTGTAAATCG
* * *
36698 GGGGTACTTTGGTAATTTTAC-AAGTC
1 GGGGTATTTTGGTAATTTTACAAACTA
* ** * *
36724 GAGAGTATTTCAGTAATTTTA-AAAATT
1 G-GGGTATTTTGGTAATTTTACAAACTA
** *
36751 GAGGGTATTTCAGTAATTTTGCAAACT-
1 G-GGGTATTTTGGTAATTTTACAAACTA
* * *
36778 GAGGGTATTTCGGTAATTTCACAAATTA
1 G-GGGTATTTTGGTAATTTTACAAACTA
*
36806 GGGGTATTTTGGTAATTTTACAAACCA
1 GGGGTATTTTGGTAATTTTACAAACTA
* *
36833 AGGGTATTTTTGTAATTTTACAAACTA
1 GGGGTATTTTGGTAATTTTACAAACTA
* ** *
36860 GGGGTATTTTAGTAATTTTGTAAACCA
1 GGGGTATTTTGGTAATTTTACAAACTA
* * * *
36887 AGGGCATTTTGATAATTTTACAAACCA
1 GGGGTATTTTGGTAATTTTACAAACTA
*
36914 GGGGTATTTTGGTGATTT
1 GGGGTATTTTGGTAATTT
36932 GGTAAACTAA
Statistics
Matches: 169, Mismatches: 35, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
26 1 0.01
27 163 0.96
28 5 0.03
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (27 bp):
GGGGTATTTTGGTAATTTTACAAACTA
Found at i:36885 original size:54 final size:54
Alignment explanation
Indices: 36736--36923 Score: 218
Period size: 54 Copynumber: 3.5 Consensus size: 54
36726 GAGTATTTCA
* * * ** **
36736 GTAATTTTA-AAAATTGAGGGTATTTCAGTAATTTTGCAAACTGAGGGTATTTCG
1 GTAATTTTACAAACTAG-GGGTATTTTAGTAATTTTGCAAACCAAGGGTATTTTT
* * * *
36790 GTAATTTCACAAATTAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTT
1 GTAATTTTACAAACTAGGGGTATTTTAGTAATTTTGCAAACCAAGGGTATTTTT
* *
36844 GTAATTTTACAAACTAGGGGTATTTTAGTAATTTTGTAAACCAAGGGCA-TTTT
1 GTAATTTTACAAACTAGGGGTATTTTAGTAATTTTGCAAACCAAGGGTATTTTT
*
36897 GATAATTTTACAAACCAGGGGTATTTT
1 G-TAATTTTACAAACTAGGGGTATTTT
36924 GGTGATTTGG
Statistics
Matches: 115, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
53 5 0.04
54 105 0.91
55 5 0.04
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (54 bp):
GTAATTTTACAAACTAGGGGTATTTTAGTAATTTTGCAAACCAAGGGTATTTTT
Found at i:38169 original size:15 final size:15
Alignment explanation
Indices: 38140--38178 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
38130 AACAGAGAAG
38140 CCAAGAATAAAGAAAT
1 CCAAG-ATAAAGAAAT
38156 CCAAGATAAAGAAAT
1 CCAAGATAAAGAAAT
*
38171 CCATGATA
1 CCAAGATA
38179 CGAGAATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.15
Consensus pattern (15 bp):
CCAAGATAAAGAAAT
Found at i:41014 original size:50 final size:49
Alignment explanation
Indices: 40896--41071 Score: 235
Period size: 50 Copynumber: 3.5 Consensus size: 49
40886 CTGGTACATA
* *
40896 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
** * *
40945 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCGGTACACG
* * * *
40995 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCCGGTACACG
41046 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
41072 TGCGACCTCA
Statistics
Matches: 111, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
49 31 0.28
50 45 0.41
51 35 0.32
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
Found at i:41079 original size:101 final size:99
Alignment explanation
Indices: 40896--41079 Score: 278
Period size: 101 Copynumber: 1.8 Consensus size: 99
40886 CTGGTACATA
* *
40896 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
*
40961 GTACTACACACGTGACCTAACCATCTGATACACG
66 GTACTACACACGCGACCTAACCATCTGATACACG
* * * *
40995 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCCGGTACACATAGTAGCCTGCACT
*
41060 TAGTACTACACATGCGACCT
64 TAGTACTACACACGCGACCT
41080 CACAATAGAT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
99 29 0.39
100 3 0.04
101 43 0.57
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCTAACCATCTGATACACG
Found at i:62073 original size:17 final size:17
Alignment explanation
Indices: 62050--62092 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
62040 TGAAGTGTTT
62050 TTTGAAAACCCTACTT-
1 TTTGAAAACCCTACTTA
*
62066 TATTGAAAACCCTTCTTA
1 T-TTGAAAACCCTACTTA
62084 TTTGAAAAC
1 TTTGAAAAC
62093 TTGAGTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 22 0.92
18 1 0.04
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (17 bp):
TTTGAAAACCCTACTTA
Found at i:63495 original size:27 final size:27
Alignment explanation
Indices: 63465--63543 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 27
63455 TCATTCTACC
63465 CTACAGGGGTATTTCGATAATTTTACA
1 CTACAGGGGTATTTCGATAATTTTACA
* * *
63492 CTACAAGGGTAATCCGATAATTTTACA
1 CTACAGGGGTATTTCGATAATTTTACA
* * *
63519 -AATC-GGGGTATTTTGGTAATTTTAC
1 CTA-CAGGGGTATTTCGATAATTTTAC
63544 GAACTGAGGT
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
26 17 0.40
27 25 0.60
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (27 bp):
CTACAGGGGTATTTCGATAATTTTACA
Found at i:67212 original size:20 final size:20
Alignment explanation
Indices: 67181--67238 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
67171 AAAGCATCAA
* *
67181 AGTGCA-AATAGGTCACTAG
1 AGTGCATAATAGGGCACCAG
67200 AGTGCATAATAGGGCACCAG
1 AGTGCATAATAGGGCACCAG
* *
67220 AGTACATTATAGGGGCACC
1 AGTGCATAATA-GGGCACC
67239 GTAGTTCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.18
20 20 0.61
21 7 0.21
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (20 bp):
AGTGCATAATAGGGCACCAG
Found at i:69204 original size:29 final size:28
Alignment explanation
Indices: 69172--69227 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
69162 TTTAAGGACT
*
69172 AAATTGTGAAAAATGTAAAAGTTTAGGGA
1 AAATTGTGAAAAATG-AAAAGTTGAGGGA
*
69201 AAATTGTGAATAATGAAAAGTTGAGGG
1 AAATTGTGAAAAATGAAAAGTTGAGGG
69228 TCATATGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.46, C:0.00, G:0.27, T:0.27
Consensus pattern (28 bp):
AAATTGTGAAAAATGAAAAGTTGAGGGA
Found at i:71222 original size:4 final size:4
Alignment explanation
Indices: 71213--71257 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
71203 TTACTACCAA
71213 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
71258 TTTTTTTAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:73856 original size:37 final size:37
Alignment explanation
Indices: 73806--73884 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
73796 TTATTACGAA
* * *
73806 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
73843 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
73880 GTCTT
1 GTCTT
73885 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:74081 original size:47 final size:47
Alignment explanation
Indices: 74003--74413 Score: 750
Period size: 47 Copynumber: 8.7 Consensus size: 47
73993 CCCTTCGGGA
* * * * * *
74003 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
74050 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
74097 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
74144 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
74191 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
74238 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
74285 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
74332 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
74379 CTTATCACATATATACACTTTCACATTCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
74414 AGAATCCTAA
Statistics
Matches: 354, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 354 1.00
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:75575 original size:18 final size:18
Alignment explanation
Indices: 75552--75593 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
75542 CATATGCATT
75552 TTTAATCACATCAAGCAA
1 TTTAATCACATCAAGCAA
75570 TTTAATCACATCAAGCAA
1 TTTAATCACATCAAGCAA
75588 TTTAAT
1 TTTAAT
75594 ACAATTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (18 bp):
TTTAATCACATCAAGCAA
Found at i:76922 original size:16 final size:16
Alignment explanation
Indices: 76897--76939 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
76887 ACAGCCAAAC
76897 TTTCAGCTTTTCGGCA
1 TTTCAGCTTTTCGGCA
* *
76913 TTTCAACTTTTCGGTA
1 TTTCAGCTTTTCGGCA
76929 TTTCAGCTTTT
1 TTTCAGCTTTT
76940 GCCGATCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.51
Consensus pattern (16 bp):
TTTCAGCTTTTCGGCA
Found at i:83052 original size:17 final size:18
Alignment explanation
Indices: 83030--83063 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
83020 TCACATTGAA
83030 GTGTTTT-AGTGAAAACC
1 GTGTTTTCAGTGAAAACC
*
83047 GTGTTTTCATTGAAAAC
1 GTGTTTTCAGTGAAAAC
83064 ACTTCTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (18 bp):
GTGTTTTCAGTGAAAACC
Found at i:84174 original size:29 final size:29
Alignment explanation
Indices: 84104--84215 Score: 138
Period size: 29 Copynumber: 3.9 Consensus size: 29
84094 ACCCCTACAT
* *
84104 ACATACATATGTCCCACTT-GGCCCAA-TC
1 ACATTCATATGGCCCA-TTAGGCCCAATTC
* *
84132 TCATTTATATGGCCCATTAGGCCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAATTC
* *
84161 ACATTCATATGGCCCATCAGGCGCAATTC
1 ACATTCATATGGCCCATTAGGCCCAATTC
*
84190 ATATTCATATGGCCCATTAGGCCCAA
1 ACATTCATATGGCCCATTAGGCCCAA
84216 ATCATCTTTA
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
27 2 0.03
28 19 0.27
29 50 0.70
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.28
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAATTC
Found at i:94454 original size:45 final size:45
Alignment explanation
Indices: 94390--94649 Score: 429
Period size: 45 Copynumber: 5.8 Consensus size: 45
94380 TATCGTACGG
94390 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
*
94435 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATGATGCCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
*
94480 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATGATGCCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
94525 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* *
94570 TACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* *
94615 TGA-TA-TCGGG-CTTCGAGCCTAGCAGGC-AAAATGCC
1 T-ACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCC
94650 AATGGATGAA
Statistics
Matches: 209, Mismatches: 5, Indels: 5
0.95 0.02 0.02
Matches are distributed among these distances:
42 7 0.03
43 17 0.08
44 5 0.02
45 179 0.86
46 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.25
Consensus pattern (45 bp):
TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
Found at i:96896 original size:33 final size:33
Alignment explanation
Indices: 96859--96924 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
96849 AATTTTAGTG
*
96859 TTTTAGGGAATACATCGTAATTAAATTAAAACA
1 TTTTAGAGAATACATCGTAATTAAATTAAAACA
96892 TTTTAGAGAATACATCGTAATTAAATTAAAACA
1 TTTTAGAGAATACATCGTAATTAAATTAAAACA
96925 ACGCAACAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (33 bp):
TTTTAGAGAATACATCGTAATTAAATTAAAACA
Found at i:97655 original size:49 final size:49
Alignment explanation
Indices: 97599--97729 Score: 199
Period size: 49 Copynumber: 2.7 Consensus size: 49
97589 GTGTGGTTGA
* *
97599 GCCACCAGATATTGCAGATTTATTGCCACATACAGAATAATGTGGACAT
1 GCCACCAGAAAATGCAGATTTATTGCCACATACAGAATAATGTGGACAT
* *
97648 GCTACCAGAAAATGCAAATTTATTGCCACATACAGAATAATGTGGACAT
1 GCCACCAGAAAATGCAGATTTATTGCCACATACAGAATAATGTGGACAT
* * *
97697 GCCACTAGAAAATGTAGATTTATTGCCAGATAC
1 GCCACCAGAAAATGCAGATTTATTGCCACATAC
97730 TTCCTCCATA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 73 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (49 bp):
GCCACCAGAAAATGCAGATTTATTGCCACATACAGAATAATGTGGACAT
Found at i:98492 original size:27 final size:27
Alignment explanation
Indices: 98462--98521 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
98452 TGNGTGGTAG
* *
98462 AGCCACCAG-AACAGATATTTGTGGCAT
1 AGCCACCAGAAACAGATA-ATGTGGCAA
98489 AGCCACCAGAAACAGATAATGTGGCAA
1 AGCCACCAGAAACAGATAATGTGGCAA
98516 AGCCAC
1 AGCCAC
98522 TTAACAGAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (27 bp):
AGCCACCAGAAACAGATAATGTGGCAA
Found at i:98708 original size:22 final size:21
Alignment explanation
Indices: 98680--98744 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
98670 GCAAATACGT
98680 TTGGCACACAACCATAATCAGG
1 TTGGCACA-AACCATAATCAGG
* *
98702 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACA-AACCATAAT-CAGG
*
98724 TTGACACAAAGCCATAATCAG
1 TTGGCACAAA-CCATAATCAG
98745 AAGGCTTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 3 0.09
22 29 0.85
23 2 0.06
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (21 bp):
TTGGCACAAACCATAATCAGG
Found at i:101516 original size:22 final size:22
Alignment explanation
Indices: 101491--101536 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
101481 TGCGATATCC
101491 CAGATATGGTCTTATATGTTAT
1 CAGATATGGTCTTATATGTTAT
101513 CAGATATGGTCTTATATGTTAT
1 CAGATATGGTCTTATATGTTAT
101535 CA
1 CA
101537 CAATGCCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.43
Consensus pattern (22 bp):
CAGATATGGTCTTATATGTTAT
Found at i:104443 original size:29 final size:29
Alignment explanation
Indices: 104401--104459 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
104391 ATCTATCAAC
104401 AACCTCTTATTTTCTACCATAAATTTCTA
1 AACCTCTTATTTTCTACCATAAATTTCTA
* *
104430 AACCTTTTATTTTCTACCATTAATTTCTA
1 AACCTCTTATTTTCTACCATAAATTTCTA
104459 A
1 A
104460 CATTCAGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.00, T:0.47
Consensus pattern (29 bp):
AACCTCTTATTTTCTACCATAAATTTCTA
Found at i:108223 original size:40 final size:40
Alignment explanation
Indices: 108162--108396 Score: 276
Period size: 40 Copynumber: 5.8 Consensus size: 40
108152 GAGCATTTGA
108162 ATATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTTG
* * * *
108202 CTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAG-TG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTG
* **
108241 ATTTTATCCGGGCTAAGACCCGAAGGCAATTACGCGAGTTG
1 A-TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTG
* * *
108282 ATATATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTCG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTG
* * *
108322 ATATATATCCGGGCTAAGACCCGAAGGCAATTATACAAGTTG
1 --ATATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTG
* * *
108364 ATATGTCCGGGTTAAGACCCGAAGGCAAATGTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTGTG
108397 TTTGCGGCTA
Statistics
Matches: 162, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
39 2 0.01
40 120 0.74
41 6 0.04
42 34 0.21
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.23
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTG
Found at i:108363 original size:82 final size:81
Alignment explanation
Indices: 108162--108396 Score: 321
Period size: 80 Copynumber: 2.9 Consensus size: 81
108152 GAGCATTTGA
* * *
108162 ATATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAG
1 ATATATCCGGGCTAAGACCCGAAGGCAATT-ATGCGAGTTGATATATCCGGGTTAAGACCCGAAG
*
108226 GCAATTGTGCTAGTGAT
65 GCAATTGTGCGAGTGAT
* * * *
108243 -TTTATCCGGGCTAAGACCCGAAGGCAATTACGCGAGTTGATATATCCGGGCTAAGACCCGCAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGTTAAGACCCGAAGG
*
108307 CATTTGTGCGAGTCGAT
66 CAATTGTGCGAGT-GAT
* * *
108324 ATATATCCGGGCTAAGACCCGAAGGCAATTATACAAGTTGATATGTCCGGGTTAAGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGTTAAGACCCGAAGG
*
108389 CAAATGTG
66 CAATTGTG
108397 TTTGCGGCTA
Statistics
Matches: 133, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
80 64 0.48
81 6 0.05
82 63 0.47
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.23
Consensus pattern (81 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGTTAAGACCCGAAGG
CAATTGTGCGAGTGAT
Found at i:118812 original size:40 final size:39
Alignment explanation
Indices: 118757--118887 Score: 147
Period size: 40 Copynumber: 3.3 Consensus size: 39
118747 NNNNNNNNNN
*
118757 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTG-TTA
* * *
118797 TATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGTTA
** * * *
118837 TGCCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGT-GTTA
118877 TATCC-GGCTAA
1 TATCCGGGCTAA
118888 ATTCCGAAGA
Statistics
Matches: 74, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
39 6 0.08
40 66 0.89
41 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (39 bp):
TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGTTA
Found at i:122406 original size:40 final size:39
Alignment explanation
Indices: 122330--122424 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 39
122320 CCATCTCCGA
* * *
122330 CCAACCCAACACACC-ATATGGGGATAGAATCGACCCAC
1 CCAACCCTACACACCAATATGCGGATAGAATCAACCCAC
* *
122368 CCAACCCTACACACCAAGTATGCGGATATAATCAACCCAT
1 CCAACCCTACACACCAA-TATGCGGATAGAATCAACCCAC
*
122408 CCAACCCTACAGACCAA
1 CCAACCCTACACACCAA
122425 AAGGTACCGT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
38 14 0.29
39 1 0.02
40 34 0.69
ACGTcount: A:0.38, C:0.38, G:0.12, T:0.13
Consensus pattern (39 bp):
CCAACCCTACACACCAATATGCGGATAGAATCAACCCAC
Found at i:133619 original size:40 final size:38
Alignment explanation
Indices: 133534--133629 Score: 113
Period size: 40 Copynumber: 2.5 Consensus size: 38
133524 AGCATCTTCG
* * *
133534 ACCAACCCAACACACC-ATGTGGGGATAGAATCGACCC
1 ACCAACCCTACACACCAATATGGGGATAGAATCAACCC
* *
133571 ACCAAACCCTACACACCAAGTATGGGGATATAATCAACTC
1 ACC-AACCCTACACACCAA-TATGGGGATAGAATCAACCC
133611 ATCCAACCCTACACACCAA
1 A-CCAACCCTACACACCAA
133630 AAGGTACCGT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
37 3 0.06
38 12 0.24
39 1 0.02
40 32 0.64
41 2 0.04
ACGTcount: A:0.39, C:0.35, G:0.12, T:0.14
Consensus pattern (38 bp):
ACCAACCCTACACACCAATATGGGGATAGAATCAACCC
Found at i:134666 original size:13 final size:13
Alignment explanation
Indices: 134648--134672 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
134638 ACGGGAAATC
134648 AAAGGAGAAGAAA
1 AAAGGAGAAGAAA
134661 AAAGGAGAAGAA
1 AAAGGAGAAGAA
134673 GGAAAAAGAA
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (13 bp):
AAAGGAGAAGAAA
Found at i:136543 original size:85 final size:85
Alignment explanation
Indices: 136397--136575 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
136387 GGCCGGCCAT
*
136397 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
136462 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
136482 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
136547 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
136567 GAGCATGGG
1 GAGCATGGG
136576 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.39, C:0.08, G:0.27, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAATGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:138489 original size:47 final size:47
Alignment explanation
Indices: 138341--138669 Score: 532
Period size: 47 Copynumber: 6.9 Consensus size: 47
138331 NNNNNNNNNN
*
138341 AATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCTT
1 AATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCT
*
138390 AATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCTT
1 AATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCT
138439 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
1 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
138486 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
1 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
138533 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
1 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
* * *
138580 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCG
1 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
* * * * *
138627 AGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
138670 TCCCGAAGGG
Statistics
Matches: 269, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
47 192 0.71
49 77 0.29
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
Found at i:138844 original size:37 final size:37
Alignment explanation
Indices: 138788--138866 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
138778 CCGAGCTCTA
* * *
138788 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
138825 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
138862 AAGAC
1 AAGAC
138867 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:152112 original size:43 final size:42
Alignment explanation
Indices: 152037--152154 Score: 132
Period size: 43 Copynumber: 2.7 Consensus size: 42
152027 AACACATATC
* *
152037 GTACAATGCCAATGTCCCAGAC-GTGGTCTTACATGTAATCACAA
1 GTACGATGCC-ATGTCCCAGACAG-GGTTTTACATG-AATCACAA
152081 GT-CGATGCCACTGTCCCAGACAGGGTTTTACATGAATCACAA
1 GTACGATGCCA-TGTCCCAGACAGGGTTTTACATGAATCACAA
* * *
152123 TTATGATGCCGATGTCCCAGACATGGTTTTAC
1 GTACGATGCC-ATGTCCCAGACAGGGTTTTAC
152155 TCGAAATCAC
Statistics
Matches: 65, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
42 10 0.15
43 51 0.78
44 4 0.06
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (42 bp):
GTACGATGCCATGTCCCAGACAGGGTTTTACATGAATCACAA
Found at i:152175 original size:43 final size:41
Alignment explanation
Indices: 152040--152176 Score: 127
Period size: 43 Copynumber: 3.2 Consensus size: 41
152030 ACATATCGTA
* *
152040 CAATGCCAATGTCCCAGACGTGGTCTTACATGTAATCACA-AGT
1 CAATGCC-ATGTCCCAGACATGGTTTTACATG-AATCACATA-T
* *
152083 CGATGCCACTGTCCCAGACAGGGTTTTACATGAATCACAATTAT
1 CAATGCCA-TGTCCCAGACATGGTTTTACATGAATCAC-A-TAT
*
152127 -GATGCCGATGTCCCAGACATGGTTTTAC-TCGAAATCACATAT
1 CAATGCC-ATGTCCCAGACATGGTTTTACAT-G-AATCACATAT
152169 CAATGCCA
1 CAATGCCA
152177 ACATCCCAGA
Statistics
Matches: 80, Mismatches: 6, Indels: 17
0.78 0.06 0.17
Matches are distributed among these distances:
42 12 0.15
43 59 0.74
44 8 0.10
45 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (41 bp):
CAATGCCATGTCCCAGACATGGTTTTACATGAATCACATAT
Found at i:155569 original size:55 final size:54
Alignment explanation
Indices: 155427--155634 Score: 246
Period size: 55 Copynumber: 3.8 Consensus size: 54
155417 ATCCTTTTGA
* *
155427 AACTTACCATTGCCATGTCTTGGCATGGTCTTACATG-GTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGGCATGGTCTTACATGAG-ATCCTTGCCTTATAG
* *
155480 AACTCACAAATGCCATGCCTTGGCATGGTCTTACATGAGA-CCTTTGCCTTATAG
1 AACTTACCAATGCCATGCCTTGGCATGGTCTTACATGAGATCC-TTGCCTTATAG
* * * * *
155534 TAACTTATCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGA-
1 -AACTTACCAATGCCATGCCTTGGCATGGTCTTACATGAGATCCTTGCCTTATAG
155588 AACCTTACCAATTGCCATGCCTTGGCATGGTCTTACATG-GTATCCTT
1 AA-CTTACCAA-TGCCATGCCTTGGCATGGTCTTACATGAG-ATCCTT
155635 AAACCCTAAT
Statistics
Matches: 132, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
52 2 0.02
53 45 0.34
54 9 0.07
55 74 0.56
56 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGGCATGGTCTTACATGAGATCCTTGCCTTATAG
Found at i:155571 original size:108 final size:110
Alignment explanation
Indices: 155427--155626 Score: 316
Period size: 108 Copynumber: 1.8 Consensus size: 110
155417 ATCCTTTTGA
* * *
155427 AACTTACCATTGCCATGTCTTGGCATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCA-CAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
155489 ATGCCATGCCTTGGCATGGTCTTACATGAGACCTTTGCCTTATAGT
65 ATGCCATGCCTTGGCATGGTCTTACATGAGACCTTTGCCTTATAGT
* * *
155535 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAA
155600 TGCCATGCCTTGGCATGGTCTTACATG
66 TGCCATGCCTTGGCATGGTCTTACATG
155627 GTATCCTTAA
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
107 1 0.01
108 49 0.59
109 3 0.04
110 30 0.36
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAA
TGCCATGCCTTGGCATGGTCTTACATGAGACCTTTGCCTTATAGT
Found at i:157901 original size:31 final size:31
Alignment explanation
Indices: 157863--157922 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
157853 TTCATATTTC
157863 ATATTTCATAACACTGGGCCGAAGCCTTTTT
1 ATATTTCATAACACTGGGCCGAAGCCTTTTT
**
157894 ATATTTCATATTACTGGGCCGAAGCCTTT
1 ATATTTCATAACACTGGGCCGAAGCCTTT
157923 ACTGTAAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (31 bp):
ATATTTCATAACACTGGGCCGAAGCCTTTTT
Found at i:158064 original size:24 final size:24
Alignment explanation
Indices: 157991--158102 Score: 147
Period size: 24 Copynumber: 4.7 Consensus size: 24
157981 GCTTTATCAT
*
157991 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
158016 ATAACTGGGGCA-AAGTCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
158039 ATAACTAGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
**
158063 ATAACTGGGGCATAATACCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
158087 ATAACTGGGGCATAAG
1 ATAACTGGGGCATAAG
158103 TTCTTTTACA
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
23 17 0.22
24 52 0.68
25 8 0.10
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:158108 original size:24 final size:24
Alignment explanation
Indices: 158010--158110 Score: 152
Period size: 24 Copynumber: 4.2 Consensus size: 24
158000 GGCCTAGCCT
158010 CTTTTAATAACTGGGGCA-AAGTC
1 CTTTTAATAACTGGGGCATAAGTC
* *
158033 CTTTTAATAACTAGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGTC
158057 CTTTTAATAACTGGGGCATAA-TAC
1 CTTTTAATAACTGGGGCATAAGT-C
*
158081 CTTTTAATAACTGGGGCATAAGTT
1 CTTTTAATAACTGGGGCATAAGTC
158105 CTTTTA
1 CTTTTA
158111 CACTTCCTCC
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
23 17 0.24
24 52 0.74
25 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (24 bp):
CTTTTAATAACTGGGGCATAAGTC
Found at i:158204 original size:20 final size:20
Alignment explanation
Indices: 158161--158205 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
158151 ATGAATACAT
**
158161 CATGTGCATAGCATACATGT
1 CATGTGCATAGCATACATAC
**
158181 CATGTGCATATTATACATAC
1 CATGTGCATAGCATACATAC
158201 CATGT
1 CATGT
158206 TTACTAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (20 bp):
CATGTGCATAGCATACATAC
Found at i:160516 original size:22 final size:22
Alignment explanation
Indices: 160465--160530 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
160455 GGTATTTGGG
* *
160465 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
160486 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
160508 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
160531 TCAAAAGGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:163276 original size:20 final size:20
Alignment explanation
Indices: 163251--163288 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
163241 CAATCACTTC
*
163251 TTTTTTTT-AATTCTGAATT
1 TTTTTTTTCAATACTGAATT
163270 TTTTTTTTCAATACTGAAT
1 TTTTTTTTCAATACTGAAT
163289 ACACAAAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTTTTTCAATACTGAATT
Done.