Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007497.1 Hibiscus syriacus cultivar Beakdansim tig00020744_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 114217
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:1813 original size:3 final size:3
Alignment explanation
Indices: 1805--1879 Score: 105
Period size: 3 Copynumber: 25.0 Consensus size: 3
1795 TTAATATATT
* * * *
1805 TAA TAA TAA TAA TAA TAA CAA TGA TAA TAA TAA TAA TAA TGA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1853 TAA TAA TAA TAA TAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1880 ATCAATATGG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1820 original size:21 final size:22
Alignment explanation
Indices: 1796--1879 Score: 93
Period size: 21 Copynumber: 3.9 Consensus size: 22
1786 TATATGCATT
*
1796 TAAT-ATATTTAATAATAATAA
1 TAATAATATATAATAATAATAA
* *
1817 TAATAACA-ATGATAATAATAA
1 TAATAATATATAATAATAATAA
1838 TAATAATGATGATAATAATAATAA
1 TAATAAT-AT-ATAATAATAATAA
*
1862 TAATAA-AAATAATAATAA
1 TAATAATATATAATAATAA
1880 ATCAATATGG
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
21 31 0.58
22 4 0.08
24 18 0.34
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (22 bp):
TAATAATATATAATAATAATAA
Found at i:2402 original size:113 final size:113
Alignment explanation
Indices: 2124--2608 Score: 679
Period size: 113 Copynumber: 4.3 Consensus size: 113
2114 TTGAACAAGC
* *
2124 TGAACTTTCCACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAAC-AAAGGTTGAACAAATTC
1 TGAACTTT-CTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAACAAAAGGTTGAACAAATTC
* *
2188 TTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGACGAGTTCTTCTTATTA
65 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTA
* * * * * * * ** * *
2240 GGAACTCTATCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCT
1 TGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAACAAAAGGTTGAACAAATTCT
*
2305 TCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTA
66 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
2353 TGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCT
1 TGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAACAAAAGGTTGAACAAATTCT
2418 TCTCATTATGAACTT-TCTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
66 TCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * *
2466 TGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGAT-GAATTCAGGCAAAAGGTTGAACAAGTTC
1 TGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA-ACAAAAGGTTGAACAAATTC
*
2530 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTA
65 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
2579 TGAACTTTCTCTGGAAAAACTGATCCATCA
1 TGAACTTTCTCTGGAAAAGCTGATCCATCA
2609 TTATGGATTC
Statistics
Matches: 330, Mismatches: 35, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
112 6 0.02
113 241 0.73
114 1 0.00
115 29 0.09
116 53 0.16
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (113 bp):
TGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAACAAAAGGTTGAACAAATTCT
TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
Found at i:2537 original size:226 final size:226
Alignment explanation
Indices: 2124--2608 Score: 749
Period size: 226 Copynumber: 2.1 Consensus size: 226
2114 TTGAACAAGC
* *
2124 TGAACTTTCCACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAGGTTGAACAAATTCT
1 TGAACTTT-CTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAACAAAGGTTGAACAAATTCT
* *
2189 TCTCATTATGAACTTCTTCTTCCTTCTTTAGATGACGAGTTCTTCTTATTAGGAACTCTATCTGG
65 TCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTAGGAACTCTATCTGG
* * *
2254 CAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACT
128 AAAAGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACT
2319 TCTTCTTCATTCTTCAGATGAGTTCTTCTCATTA
193 TCTTCTTCATTCTTCAGATGAGTTCTTCTCATTA
*
2353 TGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCT
1 TGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAAC-AAAGGTTGAACAAATTCT
* * *
2418 TCTCATTATGAACTT-TCTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGAACTTTCTCTGGA
65 TCTCATTATGAACTTCT-TCTTCCTTCTTCAGATAGAGTTCTTCTCATTAGGAACTCTATCTGGA
* ** *
2481 AAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTT
129 AAAGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
* *
2546 CTTCTTCCTTCTTCAGATGAGTTCTTCTTATTA
194 CTTCTTCATTCTTCAGATGAGTTCTTCTCATTA
*
2579 TGAACTTTCTCTGGAAAAACTGATCCATCA
1 TGAACTTTCTCTGGAAAAGCTGATCCATCA
2609 TTATGGATTC
Statistics
Matches: 236, Mismatches: 18, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
226 144 0.61
228 36 0.15
229 56 0.24
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (226 bp):
TGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAACAAAGGTTGAACAAATTCTT
CTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTAGGAACTCTATCTGGAAA
AGCTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCT
TCTTCATTCTTCAGATGAGTTCTTCTCATTA
Found at i:3484 original size:83 final size:83
Alignment explanation
Indices: 3345--3904 Score: 936
Period size: 83 Copynumber: 6.8 Consensus size: 83
3335 CTGTAGTTCC
*
3345 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAGCACATTCATCTTCT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCT
3410 AAATTCAATGATTGGTTT
66 AAATTCAATGATTGGTTT
*
3428 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATGAGCACATTCATCTTCT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCT
3493 AAATTCAATGATTGGTTCT
66 AAATTCAATGATTGGTT-T
*
3512 GT-CC-AACCAGACCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTC
1 -TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTC
3575 TAAATTCAATGATTGGTTT
65 TAAATTCAATGATTGGTTT
* *
3594 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-GTAAATTCATCTTCT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCT
*
3658 AAATTCAATGATTGGTCCTG
66 AAATTCAATGATTGGT--TT
3678 T-CC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCT
3741 AAATTCAATGATTGGTTCT
66 AAATTCAATGATTGGTT-T
* *
3760 GT-CC-AACCAGACCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGAGCACATTCATCTTC
1 -TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTC
3823 TAAATTCAATGATTGGTTT
65 TAAATTCAATGATTGGTTT
*
3842 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATGAGCACATTCATCTT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTT
3905 GTTCCAGTTA
Statistics
Matches: 450, Mismatches: 16, Indels: 22
0.92 0.03 0.05
Matches are distributed among these distances:
81 3 0.01
82 79 0.18
83 362 0.80
84 5 0.01
85 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (83 bp):
TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCT
AAATTCAATGATTGGTTT
Found at i:3784 original size:248 final size:249
Alignment explanation
Indices: 3345--3904 Score: 1018
Period size: 248 Copynumber: 2.3 Consensus size: 249
3335 CTGTAGTTCC
*
3345 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAGCACATTCATCTTCT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCT
*
3410 AAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTA
66 AAATTCAATGATTGGTTGTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTA
3475 TGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGACCAGATAACTCAAAGAA
131 TGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGACCAGATAACTCAAAGAA
3540 CACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTT
196 CACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTT
* *
3594 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-GTAAATTCATCTTCT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCT
*
3658 AAATTCAATGATTGGTCCTGT-CC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
66 AAATTCAATGATTGGT--TGTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGC
3721 TATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGACCAGATAACTCAAAG
129 TATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGACCAGATAACTCAAAG
*
3786 AACACTTCTAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTT
194 AACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTT
*
3842 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATGAGCACATTCATCTT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTT
3905 GTTCCAGTTA
Statistics
Matches: 299, Mismatches: 9, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
248 236 0.79
249 61 0.20
250 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (249 bp):
TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCT
AAATTCAATGATTGGTTGTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTA
TGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGACCAGATAACTCAAAGAA
CACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTT
Found at i:5063 original size:10 final size:10
Alignment explanation
Indices: 5048--5135 Score: 76
Period size: 10 Copynumber: 8.7 Consensus size: 10
5038 GACCCCCCCC
5048 TTTTCTTCTT
1 TTTTCTTCTT
5058 TTTTC-TCTTT
1 TTTTCTTC-TT
*
5068 TTTTCTTTTT
1 TTTTCTTCTT
5078 TTTTCTT-TCT
1 TTTTCTTCT-T
5088 TTTTCTT-TT
1 TTTTCTTCTT
*
5097 TTTCTTTTCTT
1 TTT-TCTTCTT
5108 TCTTT-TTCTT
1 T-TTTCTTCTT
*
5118 TTCTCTCTCTT
1 TTTTCT-TCTT
5129 TTTTCTT
1 TTTTCTT
5136 TTTCTTCAAG
Statistics
Matches: 66, Mismatches: 4, Indels: 16
0.77 0.05 0.19
Matches are distributed among these distances:
9 9 0.14
10 41 0.62
11 14 0.21
12 2 0.03
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTCTTCTT
Found at i:5071 original size:20 final size:19
Alignment explanation
Indices: 5048--5121 Score: 91
Period size: 18 Copynumber: 3.9 Consensus size: 19
5038 GACCCCCCCC
5048 TTTTCTTCTTTTTTCTCTTT
1 TTTTCTTCTTTTTT-TCTTT
5068 TTTTCTT-TTTTTTTCTTT
1 TTTTCTTCTTTTTTTCTTT
*
5086 CTTT-TTCTTTTTTTCTTT
1 TTTTCTTCTTTTTTTCTTT
5104 TCTTTCTT-TTTCTTTTCT
1 T-TTTCTTCTTT-TTTTCT
5122 CTCTCTTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
17 2 0.04
18 19 0.40
19 12 0.25
20 15 0.31
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTCTTCTTTTTTTCTTT
Found at i:5073 original size:17 final size:17
Alignment explanation
Indices: 5048--5138 Score: 80
Period size: 18 Copynumber: 5.2 Consensus size: 17
5038 GACCCCCCCC
5048 TTTTCTTCTTTTTTCTCTTT
1 TTTTC-TCTTTTTT-TC-TT
*
5068 TTTTCTTTTTTTTTCTT
1 TTTTCTCTTTTTTTCTT
*
5085 TCTTTTTCTTTTTTTC--
1 T-TTTCTCTTTTTTTCTT
5101 TTTTCT-TTCTTTTTCTT
1 TTTTCTCTT-TTTTTCTT
*
5118 TTCTCTCTCTTTTTTCTT
1 TTTTCTCT-TTTTTTCTT
5136 TTT
1 TTT
5139 CTTCAAGCAT
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
14 2 0.03
15 10 0.17
16 1 0.02
17 8 0.14
18 25 0.42
19 8 0.14
20 5 0.08
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTCTCTTTTTTTCTT
Found at i:5139 original size:34 final size:34
Alignment explanation
Indices: 5067--5141 Score: 100
Period size: 33 Copynumber: 2.2 Consensus size: 34
5057 TTTTTCTCTT
* * *
5067 TTTTTCTTTTTTTTTCTTTCTTTTTCTTTTTTTC
1 TTTTTCTTTCTTTTTCTTTCTCTCTCTTTTTTTC
5101 -TTTTCTTTCTTTTTCTTT-TCTCTCTCTTTTTTC
1 TTTTTCTTTCTTTTTCTTTCTCTCTCT-TTTTTTC
5134 TTTTTCTT
1 TTTTTCTT
5142 CAAGCATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 5 0.14
33 24 0.67
34 7 0.19
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (34 bp):
TTTTTCTTTCTTTTTCTTTCTCTCTCTTTTTTTC
Found at i:17949 original size:3 final size:3
Alignment explanation
Indices: 17941--18026 Score: 129
Period size: 3 Copynumber: 29.0 Consensus size: 3
17931 TTAATATATT
* *
17941 TAA TAA TAA TAA TAA TAA TAA CAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
17989 TGA TAA TAA TAA TAA TAA TAA TAA -AA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
18027 ATCAATATGG
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
2 2 0.03
3 73 0.97
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:21887 original size:34 final size:36
Alignment explanation
Indices: 21833--21903 Score: 128
Period size: 34 Copynumber: 2.0 Consensus size: 36
21823 AATTTTAGTA
21833 TCTCATTTACTATATGCGATCACTATATTTGTTGTT
1 TCTCATTTACTATATGCGATCACTATATTTGTTGTT
21869 TCTCATTTA-T-TATGCGATCACTATATTTGTTGTT
1 TCTCATTTACTATATGCGATCACTATATTTGTTGTT
21903 T
1 T
21904 ATCTTCTAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 25 0.71
35 1 0.03
36 9 0.26
ACGTcount: A:0.21, C:0.15, G:0.11, T:0.52
Consensus pattern (36 bp):
TCTCATTTACTATATGCGATCACTATATTTGTTGTT
Found at i:37071 original size:24 final size:24
Alignment explanation
Indices: 37044--37116 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
37034 GTAAACGGAG
*
37044 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
37068 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
37092 AGATCAGAAATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
37116 A
1 A
37117 GGTAATGTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.19
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:37075 original size:12 final size:12
Alignment explanation
Indices: 37048--37117 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
37038 ACGGAGATAT
* *
37048 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
37060 CAGAATTCATAT
1 CAGAATTCAGAA
37072 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
37084 CAGAATCCAGAT
1 CAGAATTCAGAA
*
37096 CAGAAATCAGAA
1 CAGAATTCAGAA
37108 CAGAATTCAG
1 CAGAATTCAG
37118 GTAATGTATC
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 2 0.04
12 41 0.91
13 2 0.04
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:37128 original size:48 final size:47
Alignment explanation
Indices: 37046--37154 Score: 121
Period size: 48 Copynumber: 2.3 Consensus size: 47
37036 AAACGGAGAT
* * * *
37046 ATCAGAAATCAAAACAGAATTCATATCAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAAAAGAATCCA
* * *
37093 GATCAGAAATCAGAACAGAATTCAGGTAATG-TATCATAAAAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGATAA-GATATCAGAAAAGAATCCA
37141 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
37155 TAAAATATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 1 0.02
48 50 0.96
49 1 0.02
ACGTcount: A:0.50, C:0.16, G:0.15, T:0.20
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAAAAGAATCCA
Found at i:37152 original size:24 final size:24
Alignment explanation
Indices: 37047--37154 Score: 80
Period size: 24 Copynumber: 4.5 Consensus size: 24
37037 AACGGAGATA
37047 TCAGAAATCA-AAACAGAATTCATA-
1 TCAGAAATCAGAAA-AGAATTCA-AG
* * *
37071 TCAGATATCAGAACAGAA-TCCAG
1 TCAGAAATCAGAAAAGAATTCAAG
* *
37094 ATCAGAAATCAGAACAGAATTCAGG
1 -TCAGAAATCAGAAAAGAATTCAAG
* * *
37119 TAATG-TATCATAAAAGAATTCAAG
1 TCA-GAAATCAGAAAAGAATTCAAG
37143 TCAGAAATCAGA
1 TCAGAAATCAGA
37155 TAAAATATTT
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
22 1 0.02
23 3 0.05
24 54 0.84
25 6 0.09
ACGTcount: A:0.49, C:0.16, G:0.15, T:0.20
Consensus pattern (24 bp):
TCAGAAATCAGAAAAGAATTCAAG
Found at i:41761 original size:26 final size:26
Alignment explanation
Indices: 41732--41783 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
41722 AATGACGCTC
* *
41732 AATGCGCATCATAAATGTGTGTCATA
1 AATGCGCATCATAAATGCGCGTCATA
**
41758 AATGCGTGTCATAAATGCGCGTCATA
1 AATGCGCATCATAAATGCGCGTCATA
41784 GATTTATGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (26 bp):
AATGCGCATCATAAATGCGCGTCATA
Found at i:41779 original size:15 final size:13
Alignment explanation
Indices: 41740--41783 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
41730 TCAATGCGCA
*
41740 TCATAAATGTGTG
1 TCATAAATGCGTG
41753 TCATAAATGCGTG
1 TCATAAATGCGTG
*
41766 TCATAAATGCGCG
1 TCATAAATGCGTG
41779 TCATA
1 TCATA
41784 GATTTATGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TCATAAATGCGTG
Found at i:46538 original size:30 final size:32
Alignment explanation
Indices: 46502--46564 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
46492 TTATTTCATC
*
46502 ACTAAAT-ATTTT-TTATAACTTTTTACTGTG
1 ACTAAATAATTTTGTTACAACTTTTTACTGTG
* *
46532 ACTAAATAATTTTGTTACAATTTTTTATTGTG
1 ACTAAATAATTTTGTTACAACTTTTTACTGTG
46564 A
1 A
46565 AAGAATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 7 0.25
31 5 0.18
32 16 0.57
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (32 bp):
ACTAAATAATTTTGTTACAACTTTTTACTGTG
Found at i:46610 original size:33 final size:32
Alignment explanation
Indices: 46534--46666 Score: 126
Period size: 33 Copynumber: 4.1 Consensus size: 32
46524 TTACTGTGAC
* *
46534 TAAATAAT-TTTGTTACAATTTTTTATTGTGA
1 TAAATAATATTTGTCACAATTTTTTATTATGA
* * *
46565 AAGAATATTATTTGTCACAATTTTTTATAATGA
1 TA-AATAATATTTGTCACAATTTTTTATTATGA
* * * *
46598 TAAATTAATATTTGTTATAATTTGTTATTTTGA
1 TAAA-TAATATTTGTCACAATTTTTTATTATGA
* *
46631 TTAAATAA-ATTTGTCACAATTTTTCATTTTGA
1 -TAAATAATATTTGTCACAATTTTTTATTATGA
46663 TAAA
1 TAAA
46667 ATATTGGGAC
Statistics
Matches: 82, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
31 5 0.06
32 27 0.33
33 46 0.56
34 4 0.05
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (32 bp):
TAAATAATATTTGTCACAATTTTTTATTATGA
Found at i:46626 original size:66 final size:63
Alignment explanation
Indices: 46534--46654 Score: 154
Period size: 66 Copynumber: 1.9 Consensus size: 63
46524 TTACTGTGAC
* *
46534 TAAATAATTTTGTTACAATTTTTTATTGTGA-AAGAATATTATTTGTCACAATTTTTTATAATGA
1 TAAATAATTTTGTTACAATTTGTTATTGTGATAA-AATA-AATTTGTCACAATTTTTTATAATGA
* * *
46598 TAAATTAATATTTGTTATAATTTGTTATTTTGATTAAATAAATTTGTCACAATTTTT
1 TAAA-TAAT-TTTGTTACAATTTGTTATTGTGATAAAATAAATTTGTCACAATTTTT
46655 CATTTTGATA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
64 4 0.08
65 20 0.41
66 24 0.49
67 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52
Consensus pattern (63 bp):
TAAATAATTTTGTTACAATTTGTTATTGTGATAAAATAAATTTGTCACAATTTTTTATAATGA
Found at i:47184 original size:168 final size:168
Alignment explanation
Indices: 46832--47190 Score: 428
Period size: 168 Copynumber: 2.2 Consensus size: 168
46822 ATTTGTCACA
* * * * * **
46832 ATTTGTTATAAATTGTTATTATGACTGA-ATAAATTTGTCA-AAAGTTTTATTTTGAGAAAATAT
1 ATTTATTATAATTTATTATTATAACT-ATATAAATTAGTCATAATTTTTTATTTTGAGAAAATAT
*
46895 TGTGACAAAATAAATTTAACATAAAATTTTATTTTGACTAAATTTAATATGTTATTTTGACTAAA
65 TGTGACAAAATAAATTTAACATAAAATTTTATTTTAACTAAATTTAATATGTTATTTTGACTAAA
* * *
46960 TAAACTTGTTCTAATTGATTATTGTGAAAAAATATTAAT
130 TAAACTTGATCTAATTGATTAATGTGAAAAAATATGAAT
46999 ATTTATTATAATTTATTATTATAACTATATAAATTAGTCATAATTTTTTATTTTGAGAAAATATT
1 ATTTATTATAATTTATTATTATAACTATATAAATTAGTCATAATTTTTTATTTTGAGAAAATATT
* * * ** * *
47064 TTGACTAAATAAATTTGACATAACTTTTTATTTTAACTAAATTTAATTTGTTATTTTGTCTAAAT
66 GTGACAAAATAAATTTAACATAAAATTTTATTTTAACTAAATTTAATATGTTATTTTGACTAAAT
* * *
47129 AAA-TT-ATCATAATTTG-TTAATGTTACAAAATA-GCAT
131 AAACTTGATC-TAA-TTGATTAATGTGAAAAAATATGAAT
*
47165 -TTTATT-TAAATTTTTTATTATAACTA
1 ATTTATTAT-AATTTATTATTATAACTA
47191 AAATAATTGG
Statistics
Matches: 165, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
164 1 0.01
165 23 0.14
166 5 0.03
167 51 0.31
168 85 0.52
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.48
Consensus pattern (168 bp):
ATTTATTATAATTTATTATTATAACTATATAAATTAGTCATAATTTTTTATTTTGAGAAAATATT
GTGACAAAATAAATTTAACATAAAATTTTATTTTAACTAAATTTAATATGTTATTTTGACTAAAT
AAACTTGATCTAATTGATTAATGTGAAAAAATATGAAT
Found at i:47198 original size:22 final size:23
Alignment explanation
Indices: 47173--47224 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
47163 ATTTTATTTA
*
47173 AATTTTTTATTATAACT-AAAAT
1 AATTTTTTATGATAACTAAAAAT
**
47195 AATTGGTTATGATAACTAAAAAT
1 AATTTTTTATGATAACTAAAAAT
47218 ATATTTT
1 A-ATTTT
47225 AAAACCTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
22 14 0.61
23 6 0.26
24 3 0.13
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (23 bp):
AATTTTTTATGATAACTAAAAAT
Found at i:52079 original size:25 final size:25
Alignment explanation
Indices: 52051--52122 Score: 60
Period size: 25 Copynumber: 3.0 Consensus size: 25
52041 ATTATTTTAA
52051 AAATTTTATTTAATAATAAATATTG
1 AAATTTTATTTAATAATAAATATTG
* * * * *
52076 AAATCTTAGTCTGAT-ATATAT-TTT
1 AAATTTTA-TTTAATAATAAATATTG
*
52100 AAA-TTGATTTAATAATAAATATT
1 AAATTTTATTTAATAATAAATATT
52123 TATGGAACTC
Statistics
Matches: 34, Mismatches: 10, Indels: 7
0.67 0.20 0.14
Matches are distributed among these distances:
22 4 0.12
23 7 0.21
24 7 0.21
25 12 0.35
26 4 0.12
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (25 bp):
AAATTTTATTTAATAATAAATATTG
Found at i:52203 original size:24 final size:23
Alignment explanation
Indices: 52161--52205 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
52151 GTCCAACTTG
*
52161 TAACAAAATTTAAAAATTAAATA
1 TAACAAAAATTAAAAATTAAATA
*
52184 TAACAATAAATTAAATATTAAA
1 TAACAA-AAATTAAAAATTAAA
52206 CAAAATCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (23 bp):
TAACAAAAATTAAAAATTAAATA
Found at i:53198 original size:21 final size:21
Alignment explanation
Indices: 53174--53214 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
53164 TTTAGTTCTT
* *
53174 TTTTAGTATTTTTTATATTTA
1 TTTTAGTATATTTTAAATTTA
*
53195 TTTTTGTATATTTTAAATTT
1 TTTTAGTATATTTTAAATTT
53215 TAAATCTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TTTTAGTATATTTTAAATTTA
Found at i:53877 original size:21 final size:21
Alignment explanation
Indices: 53852--53895 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
53842 TTTAACTGCA
53852 TTTTCACTTTACGTTCAGTAT
1 TTTTCACTTTACGTTCAGTAT
53873 TTTTCACTTTACGTTCAGTAT
1 TTTTCACTTTACGTTCAGTAT
53894 TT
1 TT
53896 GGGTCTCCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.55
Consensus pattern (21 bp):
TTTTCACTTTACGTTCAGTAT
Found at i:56871 original size:2 final size:2
Alignment explanation
Indices: 56825--56861 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
56815 CTTTATGAAT
56825 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56862 TGAATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59328 original size:182 final size:182
Alignment explanation
Indices: 58962--59369 Score: 434
Period size: 182 Copynumber: 2.2 Consensus size: 182
58952 ATATATGCTA
* * *
58962 TCACTATAGTTAAAATTTATAACTACAAATATAATTTGTCACAAAAAACGTGAATATAATTTATT
1 TCACTATAATTAAAATATATAACGACAAATATAATTTGTCACAAAAAACGTGAATATAATTTATT
* * ** * *
59027 TTTTGTGACAATGTTTTTTGTAATAATTATTAACACTTATAGTTACAAAATTTGTCATTATATGA
66 TTTTGTGACAATGTTTTTTGTAACAATAATTAACACTTATAGTTACAAAACATGTCACTATATAA
* *
59092 CTTTTTTTGCGCAAAAAAATATGGAAGAAAATCTTTGTGATAATATACTTTG
131 CTTTTTTTGCACAAAAAAATATGGAAGAAAATCTTTGTGATAATACACTTTG
* * * * * * *
59144 TCACTATAATTAAAACATATAACGACAAATATAATTTTTTTACTAAAAACTTGAATCTCA-TTAT
1 TCACTATAATTAAAATATATAACGACAAATATAA-TTTGTCACAAAAAACGTGAATATAATTTAT
*
59208 TTTTTGTGACAAAT-TTTTTTGTAACAATAATTATA-GCTTATAGTTACAAAACATGTCACTATA
65 TTTTTGTGAC-AATGTTTTTTGTAACAATAATTA-ACACTTATAGTTACAAAACATGTCACTATA
* ** * * * *
59271 TAATTTTGTTTTTTTAC-CAAAAAT-TGG-AGATAATCATTTGTGGCT-ATACATTTTG
128 TAA-CTT-TTTTTGCACAAAAAAATATGGAAGAAAATC-TTTGT-GATAATACACTTTG
** * *
59326 TCACTATAATTAAAATATATAATTACAAACAAAATTTGTCACAA
1 TCACTATAATTAAAATATATAACGACAAATATAATTTGTCACAA
59370 CAAATCTAAT
Statistics
Matches: 185, Mismatches: 34, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
181 14 0.08
182 132 0.71
183 33 0.18
184 6 0.03
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.41
Consensus pattern (182 bp):
TCACTATAATTAAAATATATAACGACAAATATAATTTGTCACAAAAAACGTGAATATAATTTATT
TTTTGTGACAATGTTTTTTGTAACAATAATTAACACTTATAGTTACAAAACATGTCACTATATAA
CTTTTTTTGCACAAAAAAATATGGAAGAAAATCTTTGTGATAATACACTTTG
Found at i:62529 original size:15 final size:15
Alignment explanation
Indices: 62491--62535 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
62481 GTAAATTCAC
*
62491 TTTATCTTT-AAATA
1 TTTATCTTTAAAATT
62505 TTT-T-TTTAAAATT
1 TTTATCTTTAAAATT
*
62518 TTTATCTTTAAAGTT
1 TTTATCTTTAAAATT
62533 TTT
1 TTT
62536 TTGATTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 3 0.12
13 8 0.31
14 4 0.15
15 11 0.42
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.64
Consensus pattern (15 bp):
TTTATCTTTAAAATT
Found at i:68461 original size:22 final size:22
Alignment explanation
Indices: 68433--68486 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
68423 TGGAAAATAA
*
68433 TATAATTTTATTTTAACTAATT
1 TATAATTTTATGTTAACTAATT
* * *
68455 TATAATTATATGTTAAGTCATT
1 TATAATTTTATGTTAACTAATT
*
68477 TAGAATTTTA
1 TATAATTTTA
68487 AATTTTTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.54
Consensus pattern (22 bp):
TATAATTTTATGTTAACTAATT
Found at i:71087 original size:12 final size:12
Alignment explanation
Indices: 71070--71099 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
71060 TGATTGGATT
71070 TGGACCCGTTTC
1 TGGACCCGTTTC
*
71082 TGGACCCGTTTT
1 TGGACCCGTTTC
71094 TGGACC
1 TGGACC
71100 TGGAGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.30, G:0.27, T:0.33
Consensus pattern (12 bp):
TGGACCCGTTTC
Found at i:71141 original size:5 final size:5
Alignment explanation
Indices: 71133--71158 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
71123 AAATTAAATT
71133 AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA A
71159 TAATATGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:71171 original size:19 final size:18
Alignment explanation
Indices: 71108--71188 Score: 55
Period size: 19 Copynumber: 4.6 Consensus size: 18
71098 CCTGGAGAAA
*
71108 AATATATATGAAATTAAATT
1 AATATATAT-AAAATAAA-T
71128 AA-AT-TAATAAAAT-AA-
1 AATATAT-ATAAAATAAAT
*
71143 AATA-AAATAAAATAAAT
1 AATATATATAAAATAAAT
* *
71160 AATATGATATAAACTATAT
1 AATAT-ATATAAAATAAAT
71179 AATATATATA
1 AATATATATA
71189 TTTCAAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
15 9 0.18
16 3 0.06
17 6 0.12
18 10 0.20
19 19 0.39
20 2 0.04
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (18 bp):
AATATATATAAAATAAAT
Found at i:71250 original size:72 final size:69
Alignment explanation
Indices: 71170--71479 Score: 220
Period size: 72 Copynumber: 4.3 Consensus size: 69
71160 AATATGATAT
*
71170 AAACTATATAATATATATATTTCAAAAATATGTTTTAGAAAACTATATATTATACTTAAAAAAAA
1 AAACTATATAATATATATATTTCAAAAA-ATGTTTTA-AAAACTATATATTATA-TTAAAAAAAT
**
71235 GTTTCCA
63 GTTTTAA
* * * * * *
71242 AAACTATATATTACATAGT-TTTC--AAAACGTTTTAAAAA-TATTATATAAGTTTTCAGAAAAA
1 AAACTATATAATATATA-TATTTCAAAAAATGTTTTAAAAACTA-TATATTA-TATT-AAAAAAA
*
71303 TGTTTTTA
62 TGTTTTAA
* * ***
71311 AAACTATATATTATATA-ATTTCACAAAAAATGTTTTTAAAACTATATACTATATATTTTCAAAA
1 AAACTATATAATATATATATTT--CAAAAAATGTTTTAAAAACTATATA-T-TATATTAAAAAAA
71375 TGTTTTAA
62 TGTTTTAA
* * *
71383 AAACTATATAATATATAAACGTTTTC--AAAATGTTTTCAAAACTATATATTATATATATTTTAA
1 AAACTATATAATATATATA---TTTCAAAAAATGTTTTAAAAACTATATATTATAT-TA---AAA
*
71446 AAATATTTTCAA
59 AAATGTTTT-AA
*
71458 AAACTATATAATATATAAATTT
1 AAACTATATAATATATATATTT
71480 TTGAAAATCA
Statistics
Matches: 194, Mismatches: 23, Indels: 42
0.75 0.09 0.16
Matches are distributed among these distances:
67 2 0.01
68 15 0.08
69 35 0.18
70 9 0.05
71 2 0.01
72 87 0.45
73 8 0.04
74 12 0.06
75 21 0.11
76 3 0.02
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (69 bp):
AAACTATATAATATATATATTTCAAAAAATGTTTTAAAAACTATATATTATATTAAAAAAATGTT
TTAA
Found at i:71345 original size:38 final size:36
Alignment explanation
Indices: 71170--71475 Score: 206
Period size: 38 Copynumber: 8.5 Consensus size: 36
71160 AATATGATAT
*
71170 AAACTATATAATATATATATTT-CAAAAATATGTTTTAGA
1 AAACTATATATTATATA-ATTTAC-AAAA-ATGTTTTA-A
* * * **
71209 AAACTATATA-T-TAT-ACTTAAAAAAAAGTTTCCA
1 AAACTATATATTATATAATTTACAAAAATGTTTTAA
* * * *
71242 AAACTATATATTACATAGTTTTC-AAAACGTTTTAA
1 AAACTATATATTATATAATTTACAAAAATGTTTTAA
* * *
71277 AAA-TAT-TA-TATA-AGTTTTCAGAAAAATGTTTTTA
1 AAACTATATATTATATA-ATTT-ACAAAAATGTTTTAA
*
71311 AAACTATATATTATATAATTTCACAAAAAATGTTTTTA
1 AAACTATATATTATATAATTT-AC-AAAAATGTTTTAA
* *
71349 AAACTATATACTATAT-ATTTTC-AAAATGTTTTAA
1 AAACTATATATTATATAATTTACAAAAATGTTTTAA
* * *
71383 AAACTATATAATATATAAACGTTTTC-AAAATGTTTTCA
1 AAACTATATATTATAT-AA--TTTACAAAAATGTTTTAA
* *
71421 AAACTATATATTATATATATTT-TAAAAATATTTTCAA
1 AAACTATATATTATATA-ATTTACAAAAATGTTTT-AA
*
71458 AAACTATATAATATATAA
1 AAACTATATATTATATAA
71476 ATTTTTGAAA
Statistics
Matches: 217, Mismatches: 31, Indels: 41
0.75 0.11 0.14
Matches are distributed among these distances:
31 1 0.00
32 6 0.03
33 13 0.06
34 48 0.22
35 24 0.11
36 19 0.09
37 34 0.16
38 62 0.29
39 10 0.05
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (36 bp):
AAACTATATATTATATAATTTACAAAAATGTTTTAA
Found at i:71494 original size:75 final size:74
Alignment explanation
Indices: 71337--71513 Score: 216
Period size: 74 Copynumber: 2.4 Consensus size: 74
71327 AATTTCACAA
* * * * *
71337 AAAATGTTTTTAAAACTATATA--CTATATATTTTCAAAATGTTTTAAAAACTATATAATATATA
1 AAAATATTTTCAAAACTATATATTATATATATTTTAAAAATATTTTAAAAACTATATAATATATA
71400 AACGTTTTC
66 AACGTTTTC
*
71409 AAAATGTTTTCAAAACTATATATTATATATATTTTAAAAATATTTTCAAAAACTATATAATATAT
1 AAAATATTTTCAAAACTATATATTATATATATTTTAAAAATATTTT-AAAAACTATATAATATAT
* *
71474 AAA-TTTTTG
65 AAACGTTTTC
*
71483 AAAATCATTTTCTGAAAATTATATATTATAT
1 AAAAT-ATTTTC--AAAACTATATATTATAT
71514 TTTGTCAAAA
Statistics
Matches: 91, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
72 21 0.23
74 28 0.31
75 26 0.29
77 16 0.18
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (74 bp):
AAAATATTTTCAAAACTATATATTATATATATTTTAAAAATATTTTAAAAACTATATAATATATA
AACGTTTTC
Found at i:72357 original size:164 final size:165
Alignment explanation
Indices: 72167--73117 Score: 1349
Period size: 165 Copynumber: 5.8 Consensus size: 165
72157 AGGTCTTCGG
* * *
72167 TTGGCAGATAACCCTTCTCAACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTAAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * * *
72232 CGAACTCGAAGGTC-TTTAGTAACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATATG
66 CGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
* *
72296 CCCTCGAAGTTGAGTGTAATCAAACTCGGGGGTCT
131 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCT
* * *
72331 TTGGCAGATAGCCCTTCTCGACTTAAGTTATACTGTAAATGATGTGCCTGGGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * ** *
72396 CGAACTCGAAGGTC-TTTGGTGACATATAACCCTTCTAGCCTTGAGTTATATTGTGAATGATGTG
66 CGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
* * * *
72460 CCCTCCAAGCTGAGAGTAATTGAACTCGAGGGTCT
131 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCT
* *
72495 TTGGCAGATAGCCCTTATCGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
*
72560 CGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAACGATGTG
66 CGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
72625 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCT
131 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCT
*
72660 TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT-GTGCTGAGCGTAG
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC-TTGGAGCTGAGCGTAG
* * *
72724 TCGAACTCAAAGATCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGT
65 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
72789 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCT
130 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCT
72825 TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT-GAGCTGAGCGTAG
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC-TTGGAGCTGAGCGTAG
* * ** * * * * * *
72889 TCGAACTCAAAGGTC-TTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
65 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
* * * * **
72953 G-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
130 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--T
* * * *
72990 GGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTA
1 --TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTA
* *
73055 GTCGAACTCGAAGATCTTTTGGTCACAGATAACCCTTCTAGCC-TGAGTTATGCTGCAAATGAT
64 GTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
73118 TTGTTTTAAA
Statistics
Matches: 707, Mismatches: 72, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
163 27 0.04
164 258 0.36
165 309 0.44
166 4 0.01
167 88 0.12
168 21 0.03
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.29
Consensus pattern (165 bp):
TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCT
Found at i:73048 original size:84 final size:84
Alignment explanation
Indices: 72149--73117 Score: 847
Period size: 84 Copynumber: 11.7 Consensus size: 84
72139 GAATATAATT
* * *
72149 GAACTCGGAGGTCTTCGGTTGGCAGATAACCCTTCTCA-ACTTAAGCTATACTGCAAATGATGTG
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT-AGACTTAAGTTATACTGCAAATGATGTG
*
72213 CCTTGGAGCTAAGCGTAGTC
65 CCTTGGAGCTGAGCGTAGTC
* ** * * * ** *
72233 GAACTCGAAGGTCTTTAG-TAACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATATGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTG-
* * * * *
72297 CCTCGAAGTTGAGTGTAATC
65 CCTTGGAGCTGAGCGTAGTC
* ** * * *
72317 AAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGTTATACTGTAAATGATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGC
*
72378 CTGGGAGCTGAGCGTAGTC
66 CTTGGAGCTGAGCGTAGTC
* * * * * **
72397 GAACTCGAAGGTCTTTGG-TGACATATAACCCTTCTAGCCTTGAGTTATATTGTGAATGATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTG-
*** * * *
72461 CCTCCAAGCTGAGAGTAATT
65 CCTTGGAGCTGAGCGTAGTC
* * * * *
72481 GAACTCGAGGGTC--T--TTGGCAGATAGCCCTTATCGACTTAAGCTATACTGCAAATGATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGC
*
72542 CTTAGAGCTGAGCGTAGTC
66 CTTGGAGCTGAGCGTAGTC
** * * * * *
72561 GAACTCGAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAACGATGTG
1 GAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTG
* * * *
72625 CCCTCGAAGCTGAGTGTAATC
65 -CCTTGGAGCTGAGCGTAGTC
** * * *
72646 GAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGC
*
72707 CGTT-GTGCTGAGCGTAGTC
66 C-TTGGAGCTGAGCGTAGTC
* * ** * * *
72726 GAACTCAAAGATCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTG
1 GAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTG
* * * *
72790 CCCTCGAAGCTGAGTGTAATC
65 -CCTTGGAGCTGAGCGTAGTC
** * * *
72811 GAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGC
72872 CGTT-GAGCTGAGCGTAGTC
66 C-TTGGAGCTGAGCGTAGTC
* * * * *
72891 GAACTCAAAGGTCTTT-GTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGC
72955 CTTGGAGCTGAGCGTAGTC
66 CTTGGAGCTGAGCGTAGTC
* * *
72974 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGTGC
1 GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGC
73039 CTTGGAGCTGAGCGTAGTC
66 CTTGGAGCTGAGCGTAGTC
* ** * * *
73058 GAACTCGAAGATCTTTTGG-TCACAGATAACCCTTCTAG-CCTGAGTTATGCTGCAAATGAT
1 GAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGAT
73118 TTGTTTTAAA
Statistics
Matches: 693, Mismatches: 160, Indels: 65
0.75 0.17 0.07
Matches are distributed among these distances:
80 97 0.14
81 144 0.21
82 9 0.01
83 163 0.24
84 227 0.33
85 53 0.08
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (84 bp):
GAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGC
CTTGGAGCTGAGCGTAGTC
Found at i:75762 original size:20 final size:20
Alignment explanation
Indices: 75738--75783 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
75728 AACAAAATGC
75738 TAATAAATAAAAAATGAATAA
1 TAATAAATAAAAAAT-AATAA
*
75759 -AATATATAAAAAATAATAA
1 TAATAAATAAAAAATAATAA
75778 TAATAA
1 TAATAA
75784 TGAAAGAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (20 bp):
TAATAAATAAAAAATAATAA
Found at i:77157 original size:71 final size:69
Alignment explanation
Indices: 77076--77246 Score: 195
Period size: 71 Copynumber: 2.4 Consensus size: 69
77066 AAAAAATGTT
* * *
77076 TTTTAAAAACTATATTATATATAATTTCACAAAAAATGTTTTTAAAACT-ATA-TACTATATGTT
1 TTTTAAAAACTATATAATATATAATTT--C--AAAATGTTTTCAAAACTAATATTA-TATATATT
* *
77139 TTCAAAATG
61 TTAAAAATA
77148 TTTT-AAAACTATATAATATATAAACGTTTCAAAATGTTTTCAAAACTAATATTATATATATTTT
1 TTTTAAAAACTATATAATATAT-AA--TTTCAAAATGTTTTCAAAACTAATATTATATATATTTT
77212 AAAAATA
63 AAAAATA
77219 TTTTCAAAAACTATATAATATATAATTT
1 TTTT-AAAAACTATATAATATATAATTT
77247 TTGAAAATCA
Statistics
Matches: 87, Mismatches: 5, Indels: 16
0.81 0.05 0.15
Matches are distributed among these distances:
70 19 0.22
71 37 0.43
72 11 0.13
73 17 0.20
74 3 0.03
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (69 bp):
TTTTAAAAACTATATAATATATAATTTCAAAATGTTTTCAAAACTAATATTATATATATTTTAAA
AATA
Found at i:77223 original size:35 final size:38
Alignment explanation
Indices: 77152--77280 Score: 106
Period size: 35 Copynumber: 3.4 Consensus size: 38
77142 AAAATGTTTT
* ** * *
77152 AAAACT-ATATAATATATAAACGTTTCAAAATGTTTTC-
1 AAAACTAATATTATATAT-AATTTTTAAAAATATTTTCA
77189 AAAACTAATATTATATAT-A-TTTTAAAAATATTTTCA
1 AAAACTAATATTATATATAATTTTTAAAAATATTTTCA
* * *
77225 AAAACT-ATATAATATATAATTTTTGAAAATCATTTTCTG
1 AAAACTAATATTATATATAATTTTTAAAAAT-ATTTTC-A
*
77264 AAAATTATATATTATAT
1 AAAACTA-ATATTATAT
77281 TTTGTCAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
35 23 0.31
36 8 0.11
37 15 0.20
38 16 0.21
39 5 0.07
41 8 0.11
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (38 bp):
AAAACTAATATTATATATAATTTTTAAAAATATTTTCA
Found at i:77247 original size:36 final size:35
Alignment explanation
Indices: 77076--77280 Score: 146
Period size: 36 Copynumber: 5.6 Consensus size: 35
77066 AAAAAATGTT
* * * *
77076 TTTTAAAAACTATATTATATATAATTTCACAAAAAATG
1 TTTTCAAAACTATATAATATATAATTT---TAAAAATA
* * * * *
77114 TTTTTAAAACTATATACTATAT-GTTTTCAAAATG
1 TTTTCAAAACTATATAATATATAATTTTAAAAATA
* * *
77148 TTTT-AAAACTATATAATATATAAACGTTTCAAAATG
1 TTTTCAAAACTATATAATATAT-AA-TTTTAAAAATA
*
77184 TTTTCAAAACTA-ATATTATATATATTTTAAAAATA
1 TTTTCAAAACTATATAATATATA-ATTTTAAAAATA
*
77219 TTTTCAAAAACTATATAATATATAATTTTTGAAAATCA
1 TTTTC-AAAACTATATAATATATAA-TTTTAAAAAT-A
* *
77257 TTTTCTGAAAATTATATATTATAT
1 TTTTC--AAAACTATATAATATAT
77281 TTTGTCAAAA
Statistics
Matches: 139, Mismatches: 18, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
33 16 0.12
34 10 0.07
35 14 0.10
36 31 0.22
37 28 0.20
38 25 0.18
39 15 0.11
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.44
Consensus pattern (35 bp):
TTTTCAAAACTATATAATATATAATTTTAAAAATA
Found at i:77649 original size:31 final size:31
Alignment explanation
Indices: 77614--77686 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
77604 AAATATATAT
* *
77614 ATATGGTCACTTTCATTTTTATTTAATTAAG
1 ATATGGTCACTTTCATTTTAATCTAATTAAG
* *
77645 ATATGATCACTTTCGTTTTAATCTAATTAAG
1 ATATGGTCACTTTCATTTTAATCTAATTAAG
*
77676 ATGTGGTCACT
1 ATATGGTCACT
77687 ATGGTTAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (31 bp):
ATATGGTCACTTTCATTTTAATCTAATTAAG
Found at i:77859 original size:118 final size:118
Alignment explanation
Indices: 77639--77878 Score: 432
Period size: 118 Copynumber: 2.0 Consensus size: 118
77629 TTTTTATTTA
77639 ATTAAGATATGATCACTTTCGTTTTAATCTAATTAAGATGTGGTCACTATGGTTAATTGTCGTTA
1 ATTAAGATATGATCACTTTCGTTTTAATCTAATTAAGATGTGGTCACTATGGTTAATTGTCGTTA
77704 AAAGTTAATAAATTAGGTGACGTAGTATTTTGATAATCACAAATTTGGTCTTT
66 AAAGTTAATAAATTAGGTGACGTAGTATTTTGATAATCACAAATTTGGTCTTT
77757 ATTAAGATATGATCAC-TTCGTTTTAATCTAATTAAGATGTGGTCACTATGGGTTAATTGTCGTT
1 ATTAAGATATGATCACTTTCGTTTTAATCTAATTAAGATGTGGTCACTAT-GGTTAATTGTCGTT
77821 AAAA-TTAAT-AATTAGGTGACGTAGTATTTTGATATAATCACAAATTTGGTCTTT
65 AAAAGTTAATAAATTAGGTGACGTAGTATTTTG--ATAATCACAAATTTGGTCTTT
77875 ATTA
1 ATTA
77879 TTTACATTAA
Statistics
Matches: 119, Mismatches: 0, Indels: 6
0.95 0.00 0.05
Matches are distributed among these distances:
116 22 0.18
117 38 0.32
118 59 0.50
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.42
Consensus pattern (118 bp):
ATTAAGATATGATCACTTTCGTTTTAATCTAATTAAGATGTGGTCACTATGGTTAATTGTCGTTA
AAAGTTAATAAATTAGGTGACGTAGTATTTTGATAATCACAAATTTGGTCTTT
Found at i:78110 original size:26 final size:25
Alignment explanation
Indices: 78081--78130 Score: 91
Period size: 26 Copynumber: 2.0 Consensus size: 25
78071 GTCACTTTCT
78081 TTGAAAGAGAATAAAGATGTTCATGG
1 TTGAAAGAGAATAAAGATG-TCATGG
78107 TTGAAAGAGAATAAAGATGTCATG
1 TTGAAAGAGAATAAAGATGTCATG
78131 TGTCATCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.44, C:0.04, G:0.26, T:0.26
Consensus pattern (25 bp):
TTGAAAGAGAATAAAGATGTCATGG
Found at i:78528 original size:31 final size:32
Alignment explanation
Indices: 78484--78573 Score: 130
Period size: 31 Copynumber: 2.8 Consensus size: 32
78474 AATATATTTA
78484 TTAAATATATATTTTATTCTTATTTAAACTTT
1 TTAAATATATATTTTATTCTTATTTAAACTTT
*
78516 TTAAA-ATATATTTTATTATTATTTAAACTTT
1 TTAAATATATATTTTATTCTTATTTAAACTTT
*
78547 TCAAAGTATATATTTTA-TCTTAATTTA
1 TTAAA-TATATATTTTATTCTT-ATTTA
78574 CTAAATATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
31 29 0.56
32 8 0.15
33 15 0.29
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.57
Consensus pattern (32 bp):
TTAAATATATATTTTATTCTTATTTAAACTTT
Found at i:78560 original size:28 final size:28
Alignment explanation
Indices: 78492--78592 Score: 82
Period size: 31 Copynumber: 3.5 Consensus size: 28
78482 TATTAAATAT
* *
78492 ATATTTTATTCTTATTTAAACTTTTTAAA
1 ATATATTATT-TTATTTAAACTTTTCAAA
78521 ATATATTTTATTATTATTTAAACTTTTCAAA
1 ATATA--TTATT-TTATTTAAACTTTTCAAA
* * *
78552 GTATA-TATTTTATCTT-AA-TTTACTAA
1 ATATATTATTTTAT-TTAAACTTTTCAAA
*
78578 ATATATTATATTATT
1 ATATATTATTTTATT
78593 ATTTTAAATT
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
26 11 0.18
27 13 0.22
28 6 0.10
29 4 0.07
31 26 0.43
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.56
Consensus pattern (28 bp):
ATATATTATTTTATTTAAACTTTTCAAA
Found at i:78677 original size:27 final size:27
Alignment explanation
Indices: 78637--78752 Score: 80
Period size: 27 Copynumber: 4.4 Consensus size: 27
78627 ATATTTTCAC
78637 ATAAAATATATTTTTAATTAAAATAAAA
1 ATAAAATAT-TTTTTAATTAAAATAAAA
* * ** *
78665 ATTAAATATTTTTAAATTAAGTTAATA
1 ATAAAATATTTTTTAATTAAAATAAAA
** *
78692 ATAAAATATTTAATAAGTTAATAT-AAA
1 ATAAAATATTTTTTAA-TTAAAATAAAA
* *
78719 A-AATAT-TTTTTTAAATT--AATATAA
1 ATAAAATATTTTTT-AATTAAAATAAAA
78743 ATAAAATATT
1 ATAAAATATT
78753 ATGAACTTAA
Statistics
Matches: 65, Mismatches: 18, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
23 2 0.03
24 3 0.05
25 10 0.15
26 8 0.12
27 29 0.45
28 13 0.20
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (27 bp):
ATAAAATATTTTTTAATTAAAATAAAA
Found at i:78701 original size:53 final size:51
Alignment explanation
Indices: 78637--78752 Score: 119
Period size: 55 Copynumber: 2.2 Consensus size: 51
78627 ATATTTTCAC
**
78637 ATAAAATATATTTTTAA-TTAAAATAAAAATTAAATATTTTTAAATTAAGT-TAATA
1 ATAAAATAT-TTAATAAGTTAAAATAAAAA--AAATATTTTTAAATTAA-TAT-A-A
* * *
78692 ATAAAATATTTAATAAGTTAATATAAAAAATATTTTTTTAAATTAATATAA
1 ATAAAATATTTAATAAGTTAAAATAAAAAAAATATTTTTAAATTAATATAA
78743 ATAAAATATT
1 ATAAAATATT
78753 ATGAACTTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
51 11 0.20
52 2 0.04
53 16 0.30
54 5 0.09
55 20 0.37
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (51 bp):
ATAAAATATTTAATAAGTTAAAATAAAAAAAATATTTTTAAATTAATATAA
Found at i:78709 original size:23 final size:24
Alignment explanation
Indices: 78682--78726 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
78672 ATTTTTAAAT
*
78682 TAAGTTAATA-ATAAAATATTTAA
1 TAAGTTAATATAAAAAATATTTAA
78705 TAAGTTAATATAAAAAATATTT
1 TAAGTTAATATAAAAAATATTT
78727 TTTTAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
TAAGTTAATATAAAAAATATTTAA
Found at i:78717 original size:25 final size:25
Alignment explanation
Indices: 78682--78752 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
78672 ATTTTTAAAT
78682 TAAGTT-A-ATAATAAAATATTTAA
1 TAAGTTAATATAATAAAATATTTAA
**
78705 TAAGTTAATATAA-AAAATATTTTTT
1 TAAGTTAATATAATAAAATA-TTTAA
*
78730 TAAATTAATATAAATAAAATATT
1 TAAGTTAATAT-AATAAAATATT
78753 ATGAACTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 6 0.15
24 7 0.17
25 17 0.43
26 4 0.10
27 6 0.15
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (25 bp):
TAAGTTAATATAATAAAATATTTAA
Found at i:80499 original size:12 final size:12
Alignment explanation
Indices: 80470--80508 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
80460 AATTCTTAAC
80470 ATATTTAA-AAT
1 ATATTTAATAAT
*
80481 ATATTTATTAAT
1 ATATTTAATAAT
*
80493 ATTTTTAATAAT
1 ATATTTAATAAT
80505 ATAT
1 ATAT
80509 ATATATATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 7 0.30
12 16 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
ATATTTAATAAT
Found at i:80518 original size:24 final size:23
Alignment explanation
Indices: 80473--80533 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
80463 TCTTAACATA
*
80473 TTTAAAATATATTTATTAATATT
1 TTTAAAATATATATATTAATATT
80496 TTTAATAATATATATA-TATATATT
1 TTTAA-AATATATATATTA-ATATT
*
80520 ATTAAAATA-ATATA
1 TTTAAAATATATATA
80534 CTCAATTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 5 0.15
23 11 0.32
24 18 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTAAAATATATATATTAATATT
Found at i:80821 original size:29 final size:33
Alignment explanation
Indices: 80758--80826 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 33
80748 GTAATTTATC
**
80758 ATATTTTTATTTTAATAGAATATACTAGAGTTA
1 ATATTTTTATTTTAATAGAATATACTAGAAATA
80791 ATATTTTTA-TTT-ATAGAAT-TA-TAGAAATA
1 ATATTTTTATTTTAATAGAATATACTAGAAATA
80820 ATATTTT
1 ATATTTT
80827 AATAATGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 13 0.38
30 2 0.06
31 7 0.21
32 3 0.09
33 9 0.26
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (33 bp):
ATATTTTTATTTTAATAGAATATACTAGAAATA
Found at i:81019 original size:14 final size:14
Alignment explanation
Indices: 81000--81029 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
80990 TAAACACCAT
81000 AAAACATTTTCCAG
1 AAAACATTTTCCAG
81014 AAAACATTTTCCAG
1 AAAACATTTTCCAG
81028 AA
1 AA
81030 GATGTAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (14 bp):
AAAACATTTTCCAG
Found at i:81310 original size:17 final size:16
Alignment explanation
Indices: 81279--81331 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
81269 ATATCAATTT
81279 AAACTATAATAAAATAA
1 AAAC-ATAATAAAATAA
81296 AAACATAATACAAATAA
1 AAACATAATA-AAATAA
*
81313 AAA-ATAATTATAATAA
1 AAACATAA-TAAAATAA
81329 AAA
1 AAA
81332 TATATATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 18 0.55
17 15 0.45
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.23
Consensus pattern (16 bp):
AAACATAATAAAATAA
Found at i:81980 original size:20 final size:20
Alignment explanation
Indices: 81957--81995 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
81947 CTATTAATTA
81957 AATACTAATTTAAATTTATC
1 AATACTAATTTAAATTTATC
*
81977 AATACTAATTTTAATTTAT
1 AATACTAATTTAAATTTAT
81996 TTAATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (20 bp):
AATACTAATTTAAATTTATC
Found at i:82310 original size:2 final size:2
Alignment explanation
Indices: 82303--82336 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
82293 ATAAATTTTA
82303 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
82337 GTCGACACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84013 original size:11 final size:11
Alignment explanation
Indices: 83997--84022 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
83987 CCATCAGTCG
83997 TCGCGCAGCCA
1 TCGCGCAGCCA
84008 TCGCGCAGCCA
1 TCGCGCAGCCA
84019 TCGC
1 TCGC
84023 CGATGGCTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.46, G:0.27, T:0.12
Consensus pattern (11 bp):
TCGCGCAGCCA
Found at i:85312 original size:176 final size:173
Alignment explanation
Indices: 85097--85436 Score: 425
Period size: 176 Copynumber: 1.9 Consensus size: 173
85087 ACTTCTTATC
* * ***
85097 GGATGAGTTCTTCTCATTATAAACTCTCCACTGGAAATATTGATCCCTCAAGCGAGGTGTTGTTG
1 GGATGAGCTCTTCTCATTATAAACTCTCCACTGGAAATATTGATCCCTCAAGCGAGGCGTCACTG
* * * * *
85162 ATTCAACTCCATATGCGATGAATTGAGCGAT-GTTTGAACAAGTTCTTCTCATTATGAACTTATT
66 ATTCAA----A-ATGCCATGAATCGAGCGATAGGTCGAACAAGCTCTTCTCATTATGAACTTATT
*
85226 ATCCC-TGATCGGATGAGTTATTCTCATTATGAACTCTCACTCTTTTT
126 ATCCCTTGATCGAATGAGTTATTCTCATTATGAACTCTCACTCTTTTT
* * *
85273 GGATGAGCTCTTCTGATTATGAACTCTCTA-TGTGAAATATTGATCCCTCAAGCGAGGCGTCACT
1 GGATGAGCTCTTCTCATTATAAACTCTCCACTG-GAAATATTGATCCCTCAAGCGAGGCGTCACT
* * * *
85337 GATTCAAAATGCCATGAATCGAGTGATAGGTCGAACAAGCTCTTCTTATTATGAACTTCTTCTCC
65 GATTCAAAATGCCATGAATCGAGCGATAGGTCGAACAAGCTCTTCTCATTATGAACTTATTATCC
**
85402 CTTTTTCGAATGAGTTATTCTCATTATGAACTCTC
130 CTTGATCGAATGAGTTATTCTCATTATGAACTCTC
85437 CATTGGAAAT
Statistics
Matches: 141, Mismatches: 20, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
171 16 0.11
172 33 0.23
173 30 0.21
175 2 0.01
176 60 0.43
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (173 bp):
GGATGAGCTCTTCTCATTATAAACTCTCCACTGGAAATATTGATCCCTCAAGCGAGGCGTCACTG
ATTCAAAATGCCATGAATCGAGCGATAGGTCGAACAAGCTCTTCTCATTATGAACTTATTATCCC
TTGATCGAATGAGTTATTCTCATTATGAACTCTCACTCTTTTT
Found at i:85588 original size:139 final size:135
Alignment explanation
Indices: 85274--85592 Score: 363
Period size: 136 Copynumber: 2.3 Consensus size: 135
85264 ACTCTTTTTG
* * * * *
85274 GATGAGCTCTTCTGATTATGAACTCTCTATGTGAAATATTGATCCCTCAAGCGAGGCGTCACTGA
1 GATGAGTTCTTCTCATTATGAACTCTCTATTTGAAATGTTGATTCCTCAAGCGAGGCGTCACTGA
* *
85339 TTCAAAATGCCATGAATCGAGTGATAGGTCGAACAAGCTCTTCTTATTATGAACTTCTTCTCCCT
66 TTCAAAATGCCATGAATCGAGCGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCT
**
85404 TTTTC
131 TCATC
* * * * **
85409 GAATGAGTTATTCTCATTATGAACTCTCCATTGGAAATGTTGATTCCTCAAGCGAGGTGTTGCTG
1 G-ATGAGTTCTTCTCATTATGAACTCTCTATTTGAAATGTTGATTCCTCAAGCGAGGCGTCACTG
** * * * *
85474 ATTCAACTCCATATGTGATTAATCGAGCGA-AGGTTGAACAAGTTCTTCTCATTATGAACTTTTT
65 ATTCAA----A-ATGCCATGAATCGAGCGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTT
85538 CTCCC-TCATC
125 CTCCCTTCATC
*
85548 AGATGAGTTCTTCTCATTATAAACTCTCTATTTGAAATGTTGATT
1 -GATGAGTTCTTCTCATTATGAACTCTCTATTTGAAATGTTGATT
85593 GGTTTACCAT
Statistics
Matches: 152, Mismatches: 25, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
135 1 0.01
136 58 0.38
139 42 0.28
140 37 0.24
141 14 0.09
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36
Consensus pattern (135 bp):
GATGAGTTCTTCTCATTATGAACTCTCTATTTGAAATGTTGATTCCTCAAGCGAGGCGTCACTGA
TTCAAAATGCCATGAATCGAGCGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCT
TCATC
Found at i:86704 original size:42 final size:42
Alignment explanation
Indices: 86562--86694 Score: 126
Period size: 42 Copynumber: 3.2 Consensus size: 42
86552 AGGTCTTATG
* * * * *
86562 GATGGTCCGAATGACTTA-TCATCTTGCTCGAAGGACTTA-T
1 GATGGCCCGAAGGACTTACTCATCATGCTCAAAAGACTTACT
* * * ** *
86602 AGATGACCCGAAGCATTTAAGCATCATGCTCAAAAGGCTTACT
1 -GATGGCCCGAAGGACTTACTCATCATGCTCAAAAGACTTACT
* *
86645 GATGGCCCGTAGGACTTACTCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGACTTACTCATCATGCTCAAAAGACTTACT
86687 GATGGCCC
1 GATGGCCC
86695 AACTGACTTA
Statistics
Matches: 72, Mismatches: 18, Indels: 3
0.77 0.19 0.03
Matches are distributed among these distances:
41 13 0.18
42 58 0.81
43 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (42 bp):
GATGGCCCGAAGGACTTACTCATCATGCTCAAAAGACTTACT
Found at i:86829 original size:84 final size:84
Alignment explanation
Indices: 86710--86913 Score: 293
Period size: 84 Copynumber: 2.4 Consensus size: 84
86700 ACTTATGCTG
* * *
86710 ATTCAAAGTGTTGTGAATCGAGCAGAGGAAATGTTGAAAACATCCTGCCCGAAGGTCTTATGGAT
1 ATTCAAAGTG-TGTGAATCGAGCAAAGGAAATGTTGAAAACACCCTGCCCGAAGGTCTTATGAAT
**
86775 GG-CTCGAATTACTTAAGCCA
65 GGCCT-GAAGGACTTAAGCCA
* *
86795 ATTCGAAGTGTGTGAATCGGGCAAAGGAAATGTTGAAAACACCCTGCCCGAAGGTCTTATGAATG
1 ATTCAAAGTGTGTGAATCGAGCAAAGGAAATGTTGAAAACACCCTGCCCGAAGGTCTTATGAATG
**
86860 GCCTGAAGGACTTAAGCTG
66 GCCTGAAGGACTTAAGCCA
86879 ATTCAAAGTGTGTGAATCGAGCAATAGGAAATGTT
1 ATTCAAAGTGTGTGAATCGAGCAA-AGGAAATGTT
86914 AACCTCTCTG
Statistics
Matches: 106, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
84 85 0.80
85 21 0.20
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.25
Consensus pattern (84 bp):
ATTCAAAGTGTGTGAATCGAGCAAAGGAAATGTTGAAAACACCCTGCCCGAAGGTCTTATGAATG
GCCTGAAGGACTTAAGCCA
Found at i:87143 original size:141 final size:143
Alignment explanation
Indices: 86795--87158 Score: 491
Period size: 144 Copynumber: 2.6 Consensus size: 143
86785 ACTTAAGCCA
* * * * *
86795 ATTCGAAGTG-TGTGAATCGGGCAAAGGAAATGTTGAAAACACCCTGCCCGAAGGTCTTATGAAT
1 ATTCGAAGTGTTGTGAATCGAGAAAAGGAAATGTTGAAAACAACATGCCCGAAGGTCTTATGGAT
* * *
86859 GGCCTGAAGGACTTAAGCTGATTCAAAGTGTGTGAATCGAGCAATAGGAAATGTTAACCTCTCTG
66 GGCCTGAAAGACTTAAGCTGATTCAAAGTGTGTGAATCGAGCAAAAGGAAATGTT-ACCCCTCTG
**
86924 GTGGGGCATTACTG
130 GTAAGGCATTACTG
* * * * ** *
86938 ATACGAAGTGTTGTGAATTGAGAAAAGTAAATGTTGAAAACATCATTACTGAAGGTCTTATGGAT
1 ATTCGAAGTGTTGTGAATCGAGAAAAGGAAATGTTGAAAACAACATGCCCGAAGGTCTTATGGAT
* * *
87003 GGCCCGAAAGACTTAAGCTGATTCGAAGTGTGTGAATTGAGCAAAAGGAAATG-T-CCCCTCTGG
66 GGCCTGAAAGACTTAAGCTGATTCAAAGTGTGTGAATCGAGCAAAAGGAAATGTTACCCCTCTGG
* *
87066 TAAGGCGTTGCTG
131 TAAGGCATTACTG
*
87079 ATTCAAAGTGTTGTGAATCGAGAAAAGGAAATGTTGAAAACAACATGCCCGAAGGTCTTATGGAT
1 ATTCGAAGTGTTGTGAATCGAGAAAAGGAAATGTTGAAAACAACATGCCCGAAGGTCTTATGGAT
87144 GGCCTGAAAGACTTA
66 GGCCTGAAAGACTTA
87159 TCATCTTGCT
Statistics
Matches: 190, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
141 88 0.46
143 10 0.05
144 92 0.48
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.26
Consensus pattern (143 bp):
ATTCGAAGTGTTGTGAATCGAGAAAAGGAAATGTTGAAAACAACATGCCCGAAGGTCTTATGGAT
GGCCTGAAAGACTTAAGCTGATTCAAAGTGTGTGAATCGAGCAAAAGGAAATGTTACCCCTCTGG
TAAGGCATTACTG
Found at i:87192 original size:20 final size:20
Alignment explanation
Indices: 87167--87230 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
87157 TATCATCTTG
87167 CTCGAAAGACTTATAGATGA
1 CTCGAAAGACTTATAGATGA
* * *
87187 CTCGAAGGATTTA-AGCATCA
1 CTCGAAAGACTTATAG-ATGA
*
87207 CGCTCAAAAGACTTATAGATGA
1 --CTCGAAAGACTTATAGATGA
87229 CT
1 CT
87231 TGAAGGATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
19 2 0.06
20 16 0.48
22 13 0.39
23 2 0.06
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (20 bp):
CTCGAAAGACTTATAGATGA
Found at i:87279 original size:42 final size:42
Alignment explanation
Indices: 87166--87263 Score: 178
Period size: 42 Copynumber: 2.3 Consensus size: 42
87156 TTATCATCTT
87166 GCTCGAAAGACTTATAGATGACTCGAAGGATTTAAGCATCAC
1 GCTCGAAAGACTTATAGATGACTCGAAGGATTTAAGCATCAC
* *
87208 GCTCAAAAGACTTATAGATGACTTGAAGGATTTAAGCATCAC
1 GCTCGAAAGACTTATAGATGACTCGAAGGATTTAAGCATCAC
87250 GCTCGAAAGACTTA
1 GCTCGAAAGACTTA
87264 CTGATGGCTC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.24
Consensus pattern (42 bp):
GCTCGAAAGACTTATAGATGACTCGAAGGATTTAAGCATCAC
Found at i:88958 original size:28 final size:27
Alignment explanation
Indices: 88927--89003 Score: 109
Period size: 28 Copynumber: 2.7 Consensus size: 27
88917 TCAGGATGTC
*
88927 TTGGGAATGCAATGTGTTTCAGGTTAAT
1 TTGGGAA-GTAATGTGTTTCAGGTTAAT
88955 TTGGGGAAGTAATGTGTTTCAGGTTAAT
1 TT-GGGAAGTAATGTGTTTCAGGTTAAT
*
88983 TTGGGGAGGTAATGTGTTTCA
1 TT-GGGAAGTAATGTGTTTCA
89004 TGTTGGCTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 41 0.89
29 5 0.11
ACGTcount: A:0.23, C:0.05, G:0.32, T:0.39
Consensus pattern (27 bp):
TTGGGAAGTAATGTGTTTCAGGTTAAT
Found at i:89656 original size:16 final size:16
Alignment explanation
Indices: 89623--89730 Score: 66
Period size: 17 Copynumber: 6.6 Consensus size: 16
89613 TCTATTTTCT
*
89623 TCTTCTTTTTCTTTTTC
1 TCTTCTTTTTC-TCTTC
89640 TCTTCTTTTTCTCTTC
1 TCTTCTTTTTCTCTTC
*
89656 TTTTTCTTCTTT-T-TTC
1 -TCTTCTT-TTTCTCTTC
89672 TC-T-TTTTTCTCTT-
1 TCTTCTTTTTCTCTTC
*
89685 TTTTCTTTTTCCTCTTTTAC
1 TCTTCTTTTT-CTC--TT-C
89705 TCTT-TTTTTCTCTTTC
1 TCTTCTTTTTCTC-TTC
89721 TCTTTCTTTT
1 TC-TTCTTTT
89731 CCTTTCATTC
Statistics
Matches: 73, Mismatches: 5, Indels: 25
0.71 0.05 0.24
Matches are distributed among these distances:
12 3 0.04
13 4 0.05
14 4 0.05
15 6 0.08
16 13 0.18
17 23 0.32
18 12 0.16
19 5 0.07
20 3 0.04
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.75
Consensus pattern (16 bp):
TCTTCTTTTTCTCTTC
Found at i:89663 original size:34 final size:33
Alignment explanation
Indices: 89619--89759 Score: 125
Period size: 34 Copynumber: 4.2 Consensus size: 33
89609 TCTGTCTATT
*
89619 TTCTTCTTCTTTTTCTTTTTCTCTTCTTTTTCTC
1 TTCTTTTTCTTTTTCTTTTTCTCTT-TTTTTCTC
*
89653 TTCTTTTTC-TTCT-TTTTTCTC-TTTTTTCTC
1 TTCTTTTTCTTTTTCTTTTTCTCTTTTTTTCTC
89683 -T-TTTTTCTTTTTCCTCTTTTACTCTTTTTTTCTC
1 TTCTTTTTCTTTTT-CT-TTTT-CTCTTTTTTTCTC
* *
89717 TTTCTCTTTCTTTTCCTTTCATTCT-TTTTTTTGCT-
1 -TTCTTTTTCTTTTTCTTT--TTCTCTTTTTTT-CTC
89752 TTCTTTTT
1 TTCTTTTT
89760 GTGTATTTTT
Statistics
Matches: 89, Mismatches: 6, Indels: 24
0.75 0.05 0.20
Matches are distributed among these distances:
28 6 0.07
29 4 0.04
30 8 0.09
31 2 0.02
32 12 0.13
33 6 0.07
34 24 0.27
35 9 0.10
36 7 0.08
37 11 0.12
ACGTcount: A:0.01, C:0.23, G:0.01, T:0.74
Consensus pattern (33 bp):
TTCTTTTTCTTTTTCTTTTTCTCTTTTTTTCTC
Found at i:89665 original size:9 final size:9
Alignment explanation
Indices: 89622--89725 Score: 80
Period size: 9 Copynumber: 12.0 Consensus size: 9
89612 GTCTATTTTC
89622 TTCTTCTTT
1 TTCTTCTTT
89631 TTCTT-TTT
1 TTCTTCTTT
*
89639 CTCTTCTTTT
1 TTCTTC-TTT
89649 TCTCTTCTTT
1 T-TCTTCTTT
89659 TTCTTC-TT
1 TTCTTCTTT
89667 TT-TTCTCTT
1 TTCTTCT-TT
89676 TT-TTCTCTT
1 TTCTTCT-TT
89685 TT-TTCTTT
1 TTCTTCTTT
*
89693 TTCCTCTTT
1 TTCTTCTTT
*
89702 TAC-TCTTT
1 TTCTTCTTT
*
89710 TT-TTCTCT
1 TTCTTCTTT
89718 TTC-TCTTT
1 TTCTTCTTT
89726 CTTTTCCTTT
Statistics
Matches: 80, Mismatches: 7, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
7 3 0.04
8 31 0.39
9 34 0.43
10 7 0.09
11 5 0.06
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.75
Consensus pattern (9 bp):
TTCTTCTTT
Found at i:89681 original size:30 final size:29
Alignment explanation
Indices: 89634--89694 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
89624 CTTCTTTTTC
89634 TTTTTCTCTTCTTTTTCTCTTCTTTTTCTTCT
1 TTTTTCTC-T-TTTTTCTCTTCTTTTTCTT-T
89666 TTTTTCTCTTTTTTCTC-T-TTTTTCTTT
1 TTTTTCTCTTTTTTCTCTTCTTTTTCTTT
89693 TT
1 TT
89695 CCTCTTTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
27 3 0.10
28 8 0.28
29 1 0.03
30 8 0.28
31 1 0.03
32 8 0.28
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (29 bp):
TTTTTCTCTTTTTTCTCTTCTTTTTCTTT
Found at i:89748 original size:18 final size:16
Alignment explanation
Indices: 89668--89759 Score: 62
Period size: 16 Copynumber: 5.6 Consensus size: 16
89658 TTTCTTCTTT
* *
89668 TTTCTCTTTTTTCTCT
1 TTTCTCTTTTTTTTCC
* ** *
89684 TTTTTCTTTTTCCTCT
1 TTTCTCTTTTTTTTCC
89700 TTTACTC-TTTTTTTCTC
1 TTT-CTCTTTTTTTTC-C
*
89717 TTTCTCTTTCTTTTCC
1 TTTCTCTTTTTTTTCC
*
89733 TTTCATTCTTTTTTTTGC
1 TTTC--TCTTTTTTTTCC
89751 TTTCT-TTTT
1 TTTCTCTTTT
89760 GTGTATTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
15 4 0.06
16 32 0.52
17 12 0.19
18 14 0.23
ACGTcount: A:0.02, C:0.23, G:0.01, T:0.74
Consensus pattern (16 bp):
TTTCTCTTTTTTTTCC
Found at i:91152 original size:20 final size:21
Alignment explanation
Indices: 91090--91152 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 21
91080 TATAGATGCT
*
91090 AATGCAAATATGCACATGC-A
1 AATGCAAATATGCAAATGCAA
** *
91110 AATGCAAATATGGGAATGAAA
1 AATGCAAATATGCAAATGCAA
*
91131 AATGCAAA-ATGTAAATGCAA
1 AATGCAAATATGCAAATGCAA
91151 AA
1 AA
91153 AAGGAATTGA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
20 26 0.74
21 9 0.26
ACGTcount: A:0.52, C:0.11, G:0.17, T:0.19
Consensus pattern (21 bp):
AATGCAAATATGCAAATGCAA
Found at i:96467 original size:44 final size:44
Alignment explanation
Indices: 96419--96666 Score: 286
Period size: 44 Copynumber: 5.6 Consensus size: 44
96409 GGAGTCAGCA
96419 GTAACGGTAAGGACTTACACTTACACATAGCAGAGGAGCCTACG
1 GTAACGGTAAGGACTTACACTTACACATAGCAGAGGAGCCTACG
* * **
96463 GTAACGGTAAGGACTTACACTTGCACGTAGCAGAGGAGCCTGTG
1 GTAACGGTAAGGACTTACACTTACACATAGCAGAGGAGCCTACG
* * *
96507 GTAACGATAAGGACTTA-ACCTTGA-ACGTAACAGAGGAGCCTACG
1 GTAACGGTAAGGACTTACA-CTT-ACACATAGCAGAGGAGCCTACG
* * * *
96551 GTAATGGTAAAGACTTACCCTTGA-ACATAGAAGAGGAGCCTACG
1 GTAACGGTAAGGACTTACACTT-ACACATAGCAGAGGAGCCTACG
* * * * *
96595 GTAACGGTAAGGACTTACCCTTGCACATAGTATAAGAGCCTACG
1 GTAACGGTAAGGACTTACACTTACACATAGCAGAGGAGCCTACG
* *
96639 GTAACGGTAAGGACTTACCCTTGCACAT
1 GTAACGGTAAGGACTTACACTTACACAT
96667 TGCCATCTTG
Statistics
Matches: 178, Mismatches: 22, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
43 1 0.01
44 177 0.99
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (44 bp):
GTAACGGTAAGGACTTACACTTACACATAGCAGAGGAGCCTACG
Found at i:96511 original size:88 final size:88
Alignment explanation
Indices: 96419--96666 Score: 320
Period size: 88 Copynumber: 2.8 Consensus size: 88
96409 GGAGTCAGCA
*
96419 GTAACGGTAAGGACTTACACTTACACATAGCAGAGGAGCCTACGGTAACGGTAAGGACTTACACT
1 GTAACGGTAAGGACTTACACTTACACATAGCAGAGGAGCCTACGGTAACGGTAAGGACTTACCCT
* * **
96484 TGCACGTAGCAGAGGAGCCTGTG
66 TGCACATAGAAGAGGAGCCTACG
* * * * *
96507 GTAACGATAAGGACTTA-ACCTTGA-ACGTAACAGAGGAGCCTACGGTAATGGTAAAGACTTACC
1 GTAACGGTAAGGACTTACA-CTT-ACACATAGCAGAGGAGCCTACGGTAACGGTAAGGACTTACC
*
96570 CTTGAACATAGAAGAGGAGCCTACG
64 CTTGCACATAGAAGAGGAGCCTACG
* * * * *
96595 GTAACGGTAAGGACTTACCCTTGCACATAGTATAAGAGCCTACGGTAACGGTAAGGACTTACCCT
1 GTAACGGTAAGGACTTACACTTACACATAGCAGAGGAGCCTACGGTAACGGTAAGGACTTACCCT
96660 TGCACAT
66 TGCACAT
96667 TGCCATCTTG
Statistics
Matches: 134, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
87 1 0.01
88 132 0.99
89 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (88 bp):
GTAACGGTAAGGACTTACACTTACACATAGCAGAGGAGCCTACGGTAACGGTAAGGACTTACCCT
TGCACATAGAAGAGGAGCCTACG
Found at i:96579 original size:132 final size:132
Alignment explanation
Indices: 96419--96661 Score: 353
Period size: 132 Copynumber: 1.8 Consensus size: 132
96409 GGAGTCAGCA
* *
96419 GTAACGGTAAGGACTTACACTTACACATAGCAGAGGAGCCTACGGTAACGGTAAGGACTTACACT
1 GTAACGGTAAAGACTTACACTTACACATAGAAGAGGAGCCTACGGTAACGGTAAGGACTTACACT
* * **
96484 TGCACGTAGCAGAGGAGCCTGTGGTAACGATAAGGACTTAACCTTGAACGTAACAGAGGAGCCTA
66 TGCACATAGCAGAAGAGCCTACGGTAACGATAAGGACTTAACCTTGAACGTAACAGAGGAGCCTA
96549 CG
131 CG
* * *
96551 GTAATGGTAAAGACTTACCCTTGA-ACATAGAAGAGGAGCCTACGGTAACGGTAAGGACTTACCC
1 GTAACGGTAAAGACTTACACTT-ACACATAGAAGAGGAGCCTACGGTAACGGTAAGGACTTACAC
* * * *
96615 TTGCACATAGTATAAGAGCCTACGGTAACGGTAAGGACTTACCCTTG
65 TTGCACATAGCAGAAGAGCCTACGGTAACGATAAGGACTTAACCTTG
96662 CACATTGCCA
Statistics
Matches: 97, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
132 96 0.99
133 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.21
Consensus pattern (132 bp):
GTAACGGTAAAGACTTACACTTACACATAGAAGAGGAGCCTACGGTAACGGTAAGGACTTACACT
TGCACATAGCAGAAGAGCCTACGGTAACGATAAGGACTTAACCTTGAACGTAACAGAGGAGCCTA
CG
Found at i:98396 original size:50 final size:50
Alignment explanation
Indices: 98341--98444 Score: 131
Period size: 50 Copynumber: 2.1 Consensus size: 50
98331 ATTAAGTGGT
* ** *
98341 TTGATTAATTAAATTGAAACATCAAT-AGTCAAAATGAAA-TTGAGTAATAA
1 TTGATTAACTAAATCAAAACATCAATGA-TCAAAAT-AAAGATGAGTAATAA
*
98391 TTGATTGACTAAATCAAAACATCAATGATCAAAATAAAGATGAGTAATAA
1 TTGATTAACTAAATCAAAACATCAATGATCAAAATAAAGATGAGTAATAA
98441 TTGA
1 TTGA
98445 ATGGTCAAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
49 3 0.06
50 43 0.91
51 1 0.02
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (50 bp):
TTGATTAACTAAATCAAAACATCAATGATCAAAATAAAGATGAGTAATAA
Found at i:100646 original size:19 final size:19
Alignment explanation
Indices: 100590--100654 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
100580 GAAGAGATAT
* * *
100590 AGAAAAAAACATAAAAAAT
1 AGAAAAAAATAGAAAAAAA
100609 AGAAAAAAATAGAAAAAAA
1 AGAAAAAAATAGAAAAAAA
100628 AGAAAAAAA-AGGAAAAAAA
1 AGAAAAAAATA-GAAAAAAA
100647 AGAGAAAA
1 AGA-AAAA
100655 GAAAAAGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
18 1 0.02
19 36 0.88
20 4 0.10
ACGTcount: A:0.82, C:0.02, G:0.12, T:0.05
Consensus pattern (19 bp):
AGAAAAAAATAGAAAAAAA
Found at i:100647 original size:10 final size:9
Alignment explanation
Indices: 100590--100701 Score: 86
Period size: 10 Copynumber: 12.0 Consensus size: 9
100580 GAAGAGATAT
100590 AGAAAAAAA
1 AGAAAAAAA
* *
100599 CATAAAAAAT
1 -AGAAAAAAA
100609 AGAAAAAAA
1 AGAAAAAAA
100618 TAGAAAAAAA
1 -AGAAAAAAA
100628 AGAAAAAAA
1 AGAAAAAAA
100637 AGGAAAAAAA
1 A-GAAAAAAA
*
100647 AG--AGAAA
1 AGAAAAAAA
100654 AGAAAAAGAA
1 AGAAAAA-AA
**
100664 AGAAGGAAA
1 AGAAAAAAA
*
100673 AG-AAAGAA
1 AGAAAAAAA
100681 AGAAAGAAAGA
1 AGAAA-AAA-A
100692 AGAAATAAAA
1 AGAAA-AAAA
100702 TTTATCAAGT
Statistics
Matches: 81, Mismatches: 13, Indels: 16
0.74 0.12 0.15
Matches are distributed among these distances:
7 6 0.07
8 5 0.06
9 26 0.32
10 35 0.43
11 9 0.11
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.04
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:100665 original size:4 final size:4
Alignment explanation
Indices: 100658--100696 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
100648 GAGAAAAGAA
*
100658 AAAG AAAG AAGG AAAAG AAAG AAAG AAAG AAAG -AAG AAA
1 AAAG AAAG AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAA
100697 TAAAATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:101961 original size:57 final size:53
Alignment explanation
Indices: 101839--101980 Score: 155
Period size: 57 Copynumber: 2.6 Consensus size: 53
101829 TAAAAATAAG
* * *
101839 AAGCTAAGCCTAATTTTTAGGGTTTCTTGATG-TTTTCAAATGAGTTTTTAAA
1 AAGCTAAGCCTAATTTTTAGGGTTTCTTAATGATTTTCAAATGAATTTTCAAA
* *
101891 AA-CTAAGCTTAATTTTCAGGGATTTCTTAATGATTATCTCCAAA-GAATTTTCAAGA
1 AAGCTAAGCCTAATTTTTAGGG-TTTCTTAATGATT-T-T-CAAATGAATTTTCAA-A
*
101947 AAGCTAAGCCTAATTTTTAGGGGTTCCTTAATGA
1 AAGCTAAGCCTAATTTTTA-GGGTTTCTTAATGA
101981 CAACTAAGAA
Statistics
Matches: 74, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
51 17 0.23
52 11 0.15
53 2 0.03
54 1 0.01
55 9 0.12
56 7 0.09
57 24 0.32
58 3 0.04
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (53 bp):
AAGCTAAGCCTAATTTTTAGGGTTTCTTAATGATTTTCAAATGAATTTTCAAA
Found at i:102356 original size:42 final size:42
Alignment explanation
Indices: 102291--102384 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
102281 AAGGGTTTTT
* * *
102291 TGATGAGTAATTCCTTCAAGCCA-TCAGTAAGTCTTTCGAGCA
1 TGATGAGTAAGTCATTCAAGCCATTCA-TAAGTCTTTCGACCA
* *
102333 TGATGAGTAAGTCATTCAGGCCATTTATAAGTCTTTCGACCA
1 TGATGAGTAAGTCATTCAAGCCATTCATAAGTCTTTCGACCA
*
102375 AGATGA-TAAG
1 TGATGAGTAAG
102385 ACCTTCGGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 4 0.09
42 39 0.87
43 2 0.04
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (42 bp):
TGATGAGTAAGTCATTCAAGCCATTCATAAGTCTTTCGACCA
Found at i:102365 original size:274 final size:275
Alignment explanation
Indices: 101867--102427 Score: 790
Period size: 274 Copynumber: 2.0 Consensus size: 275
101857 AGGGTTTCTT
101867 GATGTTTTCAAATGAGTTTTTAAAAACTAAGCTTAATTTTCAGGGATTTCTTAATGATTATCTCC
1 GATGTTTTCAAATGAGTTTTTAAAAACTAAGCTTAATTTTCAGGGATTTCTTAATGATTATCTCC
* * *
101932 AAAGAATTTTCAAGAAAGCTAAGCCTAATTTTTAGGGGTTCCTTAATGACAACTAAGAAACTAAG
66 AAAGAATTTTAAAGAAAGCTAAGACTAATTTTTAGGGGTTCCTT-AGGACAACTAAGAAACTAAG
* ** * *
101997 CTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCATTCGGGCCATCAGTTAGTCTTTTGAGCATGA
130 CTTGACTTTCAAGGGTTTCTTGATGAGTAAGTCATTCAAGCCATCAGTAAGTCTTTCGAGCATGA
** * * *
102062 TGCTTAAATCCTCCAGGTCATCTATAAGTCTTTCGAACAAGATGATAAGTCCTTCGGGCCATCCA
195 TGAGTAAATCATCCAGGCCATCTATAAGTCTTTCGAACAAGATGATAAGACCTTCGGGCCATCCA
*
102127 TAAGACCTTCGGGCAG
260 TAAGACCTTCGGGCAC
* * * *
102143 GATGTTCTCAAATGAGTTTTTAGAAACTAAG-TCTGATTTTCAGAGG-TTT-TTTATGATTATCT
1 GATGTTTTCAAATGAGTTTTTAAAAACTAAGCT-TAATTTTCAG-GGATTTCTTAATGATTATCT
* *
102205 CCAAAGAGTTTTTAAAAGGAAGCTAAGACTAATTTTTAGGGGTTCCTT-GGA-AACTAAGAAACT
64 CCAAAGA-ATTTT-AAAGAAAGCTAAGACTAATTTTTAGGGGTTCCTTAGGACAACTAAGAAACT
* * *
102268 AAGCTTGACTTTCAAGGGTTTTTTGATGAGTAATTCCTTCAAGCCATCAGTAAGTCTTTCGAGCA
127 AAGCTTGACTTTCAAGGGTTTCTTGATGAGTAAGTCATTCAAGCCATCAGTAAGTCTTTCGAGCA
* * * * *
102333 TGATGAGTAAGTCATTCAGGCCATTTATAAGTCTTTCGACCAAGATGATAAGACCTTCGGGTCAT
192 TGATGAGTAAATCATCCAGGCCATCTATAAGTCTTTCGAACAAGATGATAAGACCTTCGGGCCAT
102398 CCATAAGACCTTCGGGCAC
257 CCATAAGACCTTCGGGCAC
102417 GATGTTTTCAA
1 GATGTTTTCAA
102428 CATTTTTGGT
Statistics
Matches: 252, Mismatches: 29, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
274 152 0.60
275 22 0.09
276 45 0.18
277 33 0.13
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (275 bp):
GATGTTTTCAAATGAGTTTTTAAAAACTAAGCTTAATTTTCAGGGATTTCTTAATGATTATCTCC
AAAGAATTTTAAAGAAAGCTAAGACTAATTTTTAGGGGTTCCTTAGGACAACTAAGAAACTAAGC
TTGACTTTCAAGGGTTTCTTGATGAGTAAGTCATTCAAGCCATCAGTAAGTCTTTCGAGCATGAT
GAGTAAATCATCCAGGCCATCTATAAGTCTTTCGAACAAGATGATAAGACCTTCGGGCCATCCAT
AAGACCTTCGGGCAC
Found at i:104317 original size:16 final size:16
Alignment explanation
Indices: 104256--104317 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
104246 AATTAGGTCC
*
104256 TTATTTTATGTTTATT
1 TTATTTTATATTTATT
* *
104272 TTATTTTATCATATGTT
1 TTATTTTAT-ATTTATT
*
104289 TTACTTTTTTATTTATT
1 TTA-TTTTATATTTATT
*
104306 TTATTTTCTATT
1 TTATTTTATATT
104318 AAGCTAAATG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
16 17 0.46
17 15 0.41
18 5 0.14
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (16 bp):
TTATTTTATATTTATT
Found at i:108258 original size:18 final size:18
Alignment explanation
Indices: 108235--108273 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
108225 GAAATGTAAA
*
108235 ATTACCAGTGAGAATATG
1 ATTACCAGTGAGAATAAG
* *
108253 ATTACCGGTGGGAATAAG
1 ATTACCAGTGAGAATAAG
108271 ATT
1 ATT
108274 TCTAGGAATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (18 bp):
ATTACCAGTGAGAATAAG
Done.