Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001486.1 Hibiscus syriacus cultivar Beakdansim tig00002889_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: 112789
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:6282 original size:68 final size:68
Alignment explanation
Indices: 6173--6307 Score: 261
Period size: 68 Copynumber: 2.0 Consensus size: 68
6163 TACGCCGAAC
*
6173 AGTTTGTGTGCGTTCTGGAAAATTTTGGTTTGGTCGGCCGGGAAATACGGAGCGAGGAGACATTC
1 AGTTTGTGTGCGTTCTGGAAAACTTTGGTTTGGTCGGCCGGGAAATACGGAGCGAGGAGACATTC
6238 GGG
66 GGG
6241 AGTTTGTGTGCGTTCTGGAAAACTTTGGTTTGGTCGGCCGGGAAATACGGAGCGAGGAGACATTC
1 AGTTTGTGTGCGTTCTGGAAAACTTTGGTTTGGTCGGCCGGGAAATACGGAGCGAGGAGACATTC
6306 GG
66 GG
6308 AGATGCACTT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.21, C:0.14, G:0.38, T:0.27
Consensus pattern (68 bp):
AGTTTGTGTGCGTTCTGGAAAACTTTGGTTTGGTCGGCCGGGAAATACGGAGCGAGGAGACATTC
GGG
Found at i:22486 original size:20 final size:20
Alignment explanation
Indices: 22450--22491 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
22440 TTTAATATAG
*
22450 AACAAATGGGTTCCATATGA
1 AACAAATGGATTCCATATGA
*
22470 AACAAATGGATTTCATATGA
1 AACAAATGGATTCCATATGA
22490 AA
1 AA
22492 AACCCAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (20 bp):
AACAAATGGATTCCATATGA
Found at i:26828 original size:17 final size:17
Alignment explanation
Indices: 26808--26854 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
26798 TTATAATCCT
*
26808 ATTATTTCAAAATTATA
1 ATTATTTAAAAATTATA
* *
26825 ATTATATAAAAAATATA
1 ATTATTTAAAAATTATA
*
26842 TTTATTTAAAAAT
1 ATTATTTAAAAAT
26855 ATCAGAAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTATTTAAAAATTATA
Found at i:28497 original size:3 final size:3
Alignment explanation
Indices: 28491--28565 Score: 89
Period size: 3 Copynumber: 25.0 Consensus size: 3
28481 TATTATTTTT
* *
28491 TAA TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* * *
28536 TAA TAA TAA TTA TTA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28566 AAATGGGTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.03
3 57 0.92
4 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:28920 original size:124 final size:121
Alignment explanation
Indices: 28704--28995 Score: 369
Period size: 124 Copynumber: 2.4 Consensus size: 121
28694 GTTGAATAAA
* * *
28704 TTCTTCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGTTGG---GGATGATGTTGAC
1 TTCTT-TCTTT-TTCAGATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAAGGATGATGCTAAC
* * *
28766 CTATTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTC
63 CTATCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAA---C
* * * *
28828 TTCTTTCTTTTTTAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAGGTTGATGCTAATCTA
1 TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACCTA
* * *
28893 TCTGCTTCTGTGATAGAATTATGCAAAAGGTTGAATAAGCTCTTCTCATTGTGAAC
66 TCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAAC
*
28949 TT-TTTCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAA
1 TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
28996 AACTGATCCA
Statistics
Matches: 149, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
119 11 0.07
120 31 0.21
121 6 0.04
122 30 0.20
123 5 0.03
124 66 0.44
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.43
Consensus pattern (121 bp):
TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACCTA
TCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAAC
Found at i:29195 original size:114 final size:115
Alignment explanation
Indices: 28915--29707 Score: 1007
Period size: 114 Copynumber: 7.0 Consensus size: 115
28905 ATAGAATTAT
* ** *
28915 GCAAAAGGTTGAATAAGCTCTTCTCATTGTGAAC-T-TT-TT-CTTCTTC--A-GATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
** *
28973 CTCATTATGAACTTCT-CTGGAAAAACTGATCCATCAAGTGATGGATTTGA
66 CTCATTATGAAC-TCTACTGGAAATGCTGATCCATCAATTGATGGATTTGA
*
29023 GCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
* * * * * **
29088 CTCATTATGAACTCTACATGGCAATGTTAATCCATCAAATGATGAATTCAA
66 CTCATTATGAACTCTAC-TGGAAATGCTGATCCATCAATTGATGGATTTGA
* *
29139 ACAAAAGGTTGAACAAATTC-T-TCATTATGAATTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
** * * **
29202 CTCATTATGAACTTTCT-CTGGAAAAACTGATCCATCAAATGATGAATTCAA
66 CTCATTATGAAC--TCTACTGGAAATGCTGATCCATCAATTGATGGATTTGA
*
29253 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
* * ** *
29315 CTCATTATGAACTTTATTTGGAAAAAACTGATCCATCAAGTGATGGATTTGA
66 CTCATTATGAACTCTA-CTGG-AAATGCTGATCCATCAATTGATGGATTTGA
* *
29367 GCAAAAAGTTGAACAAATTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
* *
29428 CTCATTATGAACTCTACATGGCAATGTTGATCCATCAATTGATGGATTTGA
66 CTCATTATGAACTCTAC-TGGAAATGCTGATCCATCAATTGATGGATTTGA
*
29479 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTTTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
* * * *
29541 CTTATTATGAACTCGAACTGGTAATGTTGATCCATCAATTGATGGATTTGA
66 CTCATTATGAACTC-TACTGGAAATGCTGATCCATCAATTGATGGATTTGA
29592 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
*
29657 CTCATTATGAACTCTATCTGGTAATGCTGATCCATCAATTGATGGATTTGA
66 CTCATTATGAACTCTA-CTGGAAATGCTGATCCATCAATTGATGGATTTGA
29708 ATCTTTGCTA
Statistics
Matches: 607, Mismatches: 49, Indels: 50
0.86 0.07 0.07
Matches are distributed among these distances:
108 29 0.05
109 1 0.00
110 9 0.01
111 9 0.01
112 66 0.11
113 158 0.26
114 167 0.28
115 34 0.06
116 134 0.22
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (115 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
CTCATTATGAACTCTACTGGAAATGCTGATCCATCAATTGATGGATTTGA
Found at i:29503 original size:226 final size:227
Alignment explanation
Indices: 28915--29707 Score: 1034
Period size: 226 Copynumber: 3.5 Consensus size: 227
28905 ATAGAATTAT
* ** * *
28915 GCAAAAGGTTGAATAAGCTCTTCTCATTGTGAA--CTT-TTTCTTCTTC--A-GATGAGTTCTTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
* *
28974 TCATTATGAACTTCTCTGGAAAAACTGATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAA
66 TCATTATGAACTTCTCTGGAAAAACTGATCCATCAATTGATGGATTTGAGCAAAAGGTTGAACAA
29039 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTA
131 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTCTCATTATGAACTCTA
* * * * **
29104 CATGGCAATGTTAATCCATCAAATGATGAATTCAA
193 AATGGAAATGTTGATCCATCAAATGATGGATTTGA
*
29139 ACAAAAGGTTGAACAAATTC-T-TCATTATGAATTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTCCTTCTTCAGATGATGAGTTCTT
* * ** *
29202 CTCATTATGAACTTTCTCTGGAAAAACTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAAC
65 CTCATTATGAAC-TTCTCTGGAAAAACTGATCCATCAATTGATGGATTTGAGCAAAAGGTTGAAC
* *
29267 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAT
129 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAA
* *** *
29332 TTGGAAAAAACTGATCCATCAAGTGATGGATTTGA
194 ATGG-AAATGTTGATCCATCAAATGATGGATTTGA
* *
29367 GCAAAAAGTTGAACAAATTCTTCTCATTATGAA-T-TTCTT-CTTCTTCAGATGACGAGTTCTTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
* ***
29429 TCATTATGAAC-TCTACATGGCAATGTTGATCCATCAATTGATGGATTTGAGCAAAAGGTTGAAC
66 TCATTATGAACTTCT-C-TGGAAAAACTGATCCATCAATTGATGGATTTGAGCAAAAGGTTGAAC
* * *
29493 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTTATTATGAACTCGAA
129 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAA
* * *
29558 CTGGTAATGTTGATCCATCAATTGATGGATTTGA
194 ATGGAAATGTTGATCCATCAAATGATGGATTTGA
29592 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTCCTTCTTCAGATGATGAGTTCTT
* * **
29657 CTCATTATGAACTCTATCTGGTAATGCTGATCCATCAATTGATGGATTTGA
65 CTCATTATGAACT-TCTCTGGAAAAACTGATCCATCAATTGATGGATTTGA
29708 ATCTTTGCTA
Statistics
Matches: 498, Mismatches: 52, Indels: 33
0.85 0.09 0.06
Matches are distributed among these distances:
222 9 0.02
223 1 0.00
224 19 0.04
225 61 0.12
226 143 0.29
227 35 0.07
228 47 0.09
229 88 0.18
230 93 0.19
231 2 0.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (227 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
TCATTATGAACTTCTCTGGAAAAACTGATCCATCAATTGATGGATTTGAGCAAAAGGTTGAACAA
ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAAAT
GGAAATGTTGATCCATCAAATGATGGATTTGA
Found at i:30631 original size:93 final size:92
Alignment explanation
Indices: 30393--31043 Score: 854
Period size: 93 Copynumber: 7.0 Consensus size: 92
30383 GATCATGCAG
* * * *
30393 TTCATCTT-TTAATTCCAATGATTGG-TTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAA
1 TTCATCTTCTAAATT-CAATGATTGGTTTTTG-GGTTCATACCAAACCAGATCAGATAACTCAAA
*
30456 GAACACTTCCAGAAGATGCTATTGAGTCTC-
64 GAACACTTCCAGAAGATGCTA-TGAG-CACA
* * *
30486 TTTAT-TTC-AAATTCAATGATTGGTTTTCGGGGTTCATATCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTCTAAATTCAATGATTGGTTTT-TGGGTTCATACCAAACCAGATCAGATAACTCAAAG
*
30549 AACACTTCCAGAAGATGTTATGAGCACA
65 AACACTTCCAGAAGATGCTATGAGCACA
30577 TTCATCTTCTAAATTCAATGATTGGTTTTTGGGATTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTCTAAATTCAATGATTGGTTTTTGGG-TTCATACCAAACCAGATCAGATAACTCAAAG
* ** *
30642 AACATTTTAAGAAGATGCTATGAGCACG
65 AACACTTCCAGAAGATGCTATGAGCACA
* *
30670 TTCATCTTCCAAATTCAATGATTAGTTTTTTGTGGTTCATACCAAACCAGATCAGATAACTCAAA
1 TTCATCTTCTAAATTCAATGATT-GGTTTTTG-GGTTCATACCAAACCAGATCAGATAACTCAAA
*
30735 GAACACTTCCAGAAGATGTTATGAGCACA
64 GAACACTTCCAGAAGATGCTATGAGCACA
* *
30764 TTCATCTT-TCAAATCCAATAATTGGTTTTTGGGATTCATACCAAACCAGATCAGATAACTCAAA
1 TTCATCTTCT-AAATTCAATGATTGGTTTTTGGG-TTCATACCAAACCAGATCAGATAACTCAAA
30828 GAACACTTCCAGAAGATGCTATGAGCACA
64 GAACACTTCCAGAAGATGCTATGAGCACA
* *
30857 TTCATCTT-TCAAATCCAATAATTGGTTTTTTGTGGTTCATACCAAACCAGATCAGATAACTCAA
1 TTCATCTTCT-AAATTCAATGATTGG-TTTTTG-GGTTCATACCAAACCAGATCAGATAACTCAA
* *
30921 AGAACACTTCCAGAAGATGCTATTAGGTCTC-
63 AGAACACTTCCAGAAGATGCTATGA-G-CACA
* * * *
30952 TTTAT-TTC-AAATCCAATGATTGGTTTTCGGGGTTCATATCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTCTAAATTCAATGATTGGTTTT-TGGGTTCATACCAAACCAGATCAGATAACTCAAAG
31015 AACACTTCCAGAAGATGCTATGAGCACA
65 AACACTTCCAGAAGATGCTATGAGCACA
31043 T
1 T
31044 GGCACTTGTT
Statistics
Matches: 503, Mismatches: 37, Indels: 38
0.87 0.06 0.07
Matches are distributed among these distances:
90 4 0.01
91 20 0.04
92 123 0.24
93 204 0.41
94 141 0.28
95 9 0.02
96 2 0.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (92 bp):
TTCATCTTCTAAATTCAATGATTGGTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATGAGCACA
Found at i:30741 original size:187 final size:183
Alignment explanation
Indices: 30393--31041 Score: 912
Period size: 187 Copynumber: 3.5 Consensus size: 183
30383 GATCATGCAG
* * * *
30393 TTCATCTTTTAATTCCAATGATTGG-TTCTGTGG-TTCCTACCGAACCAGATCAGATAACTCAAA
1 TTCATC-TTTAAATCCAATGATTGGTTTTTG-GGATTCATACCAAACCAGATCAGATAACTCAAA
* * * * *
30456 GAACACTTCCAGAAGATGCTATTGAGTCTCTTTAT-TTCAAATTCAATGATTGGTTTTCGGGGTT
64 GAACACTTCCAGAAGATGCTA-TGAG-CACTTCATCTTCAAATTCAATGATTGTTTTTTGTGGTT
*
30520 CATATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAGCACA
127 CATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAGCACA
*
30577 TTCATCTTCTAAATTCAATGATTGGTTTTTGGGATTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTT-TAAATCCAATGATTGGTTTTTGGGATTCATACCAAACCAGATCAGATAACTCAAAG
* **
30642 AACATTTTAAGAAGATGCTATGAGCACGTTCATCTTCCAAATTCAATGATTAGTTTTTTGTGGTT
65 AACACTTCCAGAAGATGCTATGAGCAC-TTCATCTT-CAAATTCAATGATT-GTTTTTTGTGGTT
30707 CATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAGCACA
127 CATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAGCACA
*
30764 TTCATCTTTCAAATCCAATAATTGGTTTTTGGGATTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTT-AAATCCAATGATTGGTTTTTGGGATTCATACCAAACCAGATCAGATAACTCAAAG
* *
30829 AACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATCCAATAATTGGTTTTTTGTGGTT
65 AACACTTCCAGAAGATGCTATGAGCAC-TTCATC-TTCAAATTCAATGATT-GTTTTTTGTGGTT
* * *
30894 CATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGGTCTC-
127 CATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGA-G-CACA
* * * * *
30952 TTTAT-TTCAAATCCAATGATTGGTTTTCGGGGTTCATATCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTAAATCCAATGATTGGTTTTTGGGATTCATACCAAACCAGATCAGATAACTCAAAGA
31016 ACACTTCCAGAAGATGCTATGAGCAC
66 ACACTTCCAGAAGATGCTATGAGCAC
31042 ATGGCACTTG
Statistics
Matches: 422, Mismatches: 32, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
183 4 0.01
184 30 0.07
185 52 0.12
186 93 0.22
187 234 0.55
188 7 0.02
189 2 0.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (183 bp):
TTCATCTTTAAATCCAATGATTGGTTTTTGGGATTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATGAGCACTTCATCTTCAAATTCAATGATTGTTTTTTGTGGTTCATA
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAGCACA
Found at i:32053 original size:11 final size:11
Alignment explanation
Indices: 32037--32069 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
32027 TTAACCCCCC
32037 TTTTTTTCTTT
1 TTTTTTTCTTT
32048 TTTTTTTCTTT
1 TTTTTTTCTTT
32059 TTTCTTTTCTT
1 TTT-TTTTCTT
32070 GAAGCATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:32054 original size:12 final size:12
Alignment explanation
Indices: 32037--32069 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
32027 TTAACCCCCC
32037 TTTTTTTC-TTT
1 TTTTTTTCTTTT
32048 TTTTTTTCTTTT
1 TTTTTTTCTTTT
*
32060 TTCTTTTCTT
1 TTTTTTTCTT
32070 GAAGCATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTTTTCTTTT
Found at i:38759 original size:15 final size:15
Alignment explanation
Indices: 38736--38767 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
38726 TGCAATGAAT
38736 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
38751 AATGCATGTATGCAA
1 AATGAATGTATGCAA
38766 AA
1 AA
38768 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:42585 original size:17 final size:17
Alignment explanation
Indices: 42565--42611 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
42555 TTATAATCCT
*
42565 ATTATTTCAAAATTATA
1 ATTATTTAAAAATTATA
* *
42582 ATTATATAAAAAATATA
1 ATTATTTAAAAATTATA
*
42599 TTTATTTAAAAAT
1 ATTATTTAAAAAT
42612 ATCATAAAAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTATTTAAAAATTATA
Found at i:44243 original size:3 final size:3
Alignment explanation
Indices: 44237--44299 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
44227 ATTAATTTTT
*
44237 TAA TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* *
44282 TTA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
44300 AAATGGGTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:45563 original size:2 final size:2
Alignment explanation
Indices: 45556--45587 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
45546 GATTATTATC
45556 AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
45588 AAATGATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:46655 original size:2 final size:2
Alignment explanation
Indices: 46648--46803 Score: 285
Period size: 2 Copynumber: 78.0 Consensus size: 2
46638 GTTATGCATC
* *
46648 GT GT GT GT GT GT GT AT GT AT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
46690 GT GT GT GT GT GT GT GT CT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
46732 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
46774 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
46804 ATGTATGTAT
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 148 1.00
ACGTcount: A:0.01, C:0.01, G:0.48, T:0.50
Consensus pattern (2 bp):
GT
Found at i:46808 original size:4 final size:4
Alignment explanation
Indices: 46801--47111 Score: 599
Period size: 4 Copynumber: 78.2 Consensus size: 4
46791 TGTGTGTGTG
46801 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
46849 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
46897 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
46945 TGTA TGTA --TA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
46991 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTG TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
47039 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
47087 TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
47112 TCTGCTTGCT
Statistics
Matches: 303, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
2 2 0.01
4 301 0.99
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:56572 original size:87 final size:87
Alignment explanation
Indices: 56467--56642 Score: 343
Period size: 87 Copynumber: 2.0 Consensus size: 87
56457 AACTAAAAAA
56467 TATTATTACAATTATTCTTAATTATATAAATCATAATTATAATATTATATTAGGTCGAATAAGAT
1 TATTATTACAATTATTCTTAATTATATAAATCATAATTATAATATTATATTAGGTCGAATAAGAT
56532 GTTTTTATAATAAATCTGAATT
66 GTTTTTATAATAAATCTGAATT
*
56554 TATTATTACAATTGTTCTTAATTATATAAATCATAATTATAATATTATATTAGGTCGAATAAGAT
1 TATTATTACAATTATTCTTAATTATATAAATCATAATTATAATATTATATTAGGTCGAATAAGAT
56619 GTTTTTATAATAAATCTGAATT
66 GTTTTTATAATAAATCTGAATT
56641 TA
1 TA
56643 ACTCAACTAC
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (87 bp):
TATTATTACAATTATTCTTAATTATATAAATCATAATTATAATATTATATTAGGTCGAATAAGAT
GTTTTTATAATAAATCTGAATT
Found at i:59672 original size:18 final size:16
Alignment explanation
Indices: 59645--59678 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
59635 TATATTCATC
59645 TTTTTTTTATATTATAT
1 TTTTTTTTATA-TATAT
59662 TTTTTTATTATATATAT
1 TTTTTT-TTATATATAT
59679 CTTATATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTTTATATATAT
Found at i:59698 original size:14 final size:14
Alignment explanation
Indices: 59689--59724 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
59679 CTTATATCAT
59689 TGTATATATATATA
1 TGTATATATATATA
59703 TGTATAGATATATATA
1 TGTAT--ATATATATA
59719 TGTATA
1 TGTATA
59725 GATGTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.30
16 14 0.70
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (14 bp):
TGTATATATATATA
Found at i:59713 original size:16 final size:16
Alignment explanation
Indices: 59694--59727 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
59684 ATCATTGTAT
59694 ATATATATATGTATAG
1 ATATATATATGTATAG
59710 ATATATATATGTATAG
1 ATATATATATGTATAG
59726 AT
1 AT
59728 GTATTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (16 bp):
ATATATATATGTATAG
Found at i:60062 original size:164 final size:164
Alignment explanation
Indices: 59791--60121 Score: 653
Period size: 164 Copynumber: 2.0 Consensus size: 164
59781 TTATGATTCG
*
59791 TCTCAATTGTAAAACCGTGAAAGGGGCAATATTTTCAAAACTTCTGATTAAACATTTTTCGAAAC
1 TCTCAATTGTAAAACCGTGAAAGGGGCAATATTTTCAAAACTTATGATTAAACATTTTTCGAAAC
59856 TCTTTTAATTGATATTTTCAGAATTTTGAAAATAAAAGAGAAACATTTTTTCAAACAAGACAATC
66 TCTTTTAATTGATATTTTCAGAATTTTGAAAATAAAAGAGAAACATTTTTTCAAACAAGACAATC
59921 TCTCTAAAGTGGATCTTGGTAAATGACATATGGC
131 TCTCTAAAGTGGATCTTGGTAAATGACATATGGC
59955 TCTCAATTGTAAAACCGTGAAAGGGGCAATATTTTCAAAACTTATGATTAAACATTTTTCGAAAC
1 TCTCAATTGTAAAACCGTGAAAGGGGCAATATTTTCAAAACTTATGATTAAACATTTTTCGAAAC
60020 TCTTTTAATTGATATTTTCAGAATTTTGAAAATAAAAGAGAAACATTTTTTCAAACAAGACAATC
66 TCTTTTAATTGATATTTTCAGAATTTTGAAAATAAAAGAGAAACATTTTTTCAAACAAGACAATC
60085 TCTCTAAAGTGGATCTTGGTAAATGACATATGGC
131 TCTCTAAAGTGGATCTTGGTAAATGACATATGGC
60119 TCT
1 TCT
60122 TAGACAGTAA
Statistics
Matches: 166, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
164 166 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (164 bp):
TCTCAATTGTAAAACCGTGAAAGGGGCAATATTTTCAAAACTTATGATTAAACATTTTTCGAAAC
TCTTTTAATTGATATTTTCAGAATTTTGAAAATAAAAGAGAAACATTTTTTCAAACAAGACAATC
TCTCTAAAGTGGATCTTGGTAAATGACATATGGC
Found at i:60650 original size:37 final size:37
Alignment explanation
Indices: 60598--60976 Score: 167
Period size: 36 Copynumber: 11.1 Consensus size: 37
60588 TAAAAAGAAT
*
60598 ATTTTATCTCACTTGAGATAGTTTCCCTTGAAACAAA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
* * * *
60635 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
* **
60672 A----A---CA-TTGAAAACA-TTTCCCTTGAAA-TGA
1 ATTTTATCTCACTTG-AGACAGTTTCCCTTGAAACAAA
* * *
60700 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
* * * ** *
60737 A-TTTACCTCCCTTGAGATAGTTTTTCTTGAAACATA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
*
60773 A----A---CA-TTGAAAACA-TTTCCCTTGAAAC-AA
1 ATTTTATCTCACTTG-AGACAGTTTCCCTTGAAACAAA
* *
60801 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
* ***
60837 A--TTA--T---TTGA-ATATGTTTTATTTGAAAC-AA
1 ATTTTATCTCACTTGAGACA-GTTTCCCTTGAAACAAA
* * * ** * *
60866 ATTTCATCTCCCTTAAGACAGTTTCTTTTGGAACTAA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
* * *
60903 A-TTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
** *
60938 ATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
60975 AT
1 AT
60977 CTTTGAATTT
Statistics
Matches: 258, Mismatches: 51, Indels: 66
0.69 0.14 0.18
Matches are distributed among these distances:
28 6 0.02
29 46 0.18
30 9 0.03
31 2 0.01
32 1 0.00
33 2 0.01
34 2 0.01
35 12 0.05
36 134 0.52
37 44 0.17
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (37 bp):
ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
Found at i:60779 original size:101 final size:102
Alignment explanation
Indices: 60598--60837 Score: 392
Period size: 101 Copynumber: 2.4 Consensus size: 102
60588 TAAAAAGAAT
* * **
60598 ATTTTATCTCACTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTACCTCCCTTGAGACAGTTTCTCT
**
60663 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
* *
60700 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA-TTTACCTCCCTTGAGATAGTTTTTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTACCTCCCTTGAGACAGTTTCTCT
60764 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
*
60801 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA
60838 TTATTTGAAT
Statistics
Matches: 129, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
101 93 0.72
102 36 0.28
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (102 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTACCTCCCTTGAGACAGTTTCTCT
TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
Found at i:60833 original size:36 final size:36
Alignment explanation
Indices: 60786--60974 Score: 180
Period size: 36 Copynumber: 5.4 Consensus size: 36
60776 ATTGAAAACA
*
60786 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* *
60822 TTTCCCTTGAAACAAA-----T-TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
*** * * *
60851 TTTTATTTGAAACAAATTTCATCTCCCTTAAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
** *
60887 TTTCTTTTGGAACTAAATTT-GTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
*
60923 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
60959 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
60975 ATCTTTGAAT
Statistics
Matches: 124, Mismatches: 18, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
28 2 0.02
29 18 0.15
30 2 0.02
31 1 0.01
34 1 0.01
35 7 0.06
36 85 0.69
37 8 0.06
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:60846 original size:65 final size:65
Alignment explanation
Indices: 60721--61103 Score: 268
Period size: 65 Copynumber: 5.8 Consensus size: 65
60711 CTTGAGATAG
* ** * * * *
60721 TTTCCCTTGAAACAAAATTTACCTCCCTTGAGATAGTTTTTCTTGAAACATAAACA-TTGAAAAC
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-AAATATTTGAATAC
60785 A
65 A
* * * **
60786 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTATTTGAATATG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATATTTGAATACA
*** ** * * * * *
60851 TTTTATTTGAAACAAATTTCATCTCCCTTAAGACAGTTTCTTTTGGAACTAAATTTGTCTCTCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAA-----ATAT-TT
*
60916 G-AGACA
59 GAATACA
* * * * * **
60922 GTTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTT
1 -TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATATTTGAATAC
60987 A
65 A
* * * * * ** **
60988 TTTCCCCTAAAATAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAATCTTCAAATTTA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATATTTGAATACA
* * * *
61053 TTTCCCTTAAAACAAAATTTTGTTTCCCTTGAGACCGTTT-TCATGAAACAA
1 TTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
61104 CAAGATTGTT
Statistics
Matches: 251, Mismatches: 56, Indels: 22
0.76 0.17 0.07
Matches are distributed among these distances:
64 3 0.01
65 166 0.66
66 32 0.13
71 7 0.03
72 43 0.17
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (65 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATATTTGAATACA
Found at i:60919 original size:166 final size:167
Alignment explanation
Indices: 60619--60936 Score: 379
Period size: 166 Copynumber: 1.9 Consensus size: 167
60609 CTTGAGATAG
*
60619 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTGAAAAC
* ** ** * * *
60684 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTACCTCCCT
66 ATTTCACTTGAAACAAATTTCATCTCCCTTAAGACAGTTTCCCTTGAAACAAAATTTACCTCCCT
* *
60749 TGAGATAGTTTTTCTTGAAACATAAACATTGAAAACA
131 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* ** *
60786 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AATTATTTGAATA
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAACA-TTGAAAA
** * * ** * * ** *
60849 TGTTTTATTTGAAACAAATTTCATCTCCCTTAAGACAGTTTCTTTTGGAACTAAATTTGTCTCTC
65 CATTTCACTTGAAACAAATTTCATCTCCCTTAAGACAGTTTCCCTTGAAACAAAATTTACCTCCC
60914 TTGAGACAGTTTCTCTTGAAACA
130 TTGAGACAGTTTCTCTTGAAACA
60937 AATTTCGTCT
Statistics
Matches: 124, Mismatches: 26, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
165 3 0.02
166 108 0.87
167 13 0.10
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (167 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTGAAAAC
ATTTCACTTGAAACAAATTTCATCTCCCTTAAGACAGTTTCCCTTGAAACAAAATTTACCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:61068 original size:202 final size:202
Alignment explanation
Indices: 60702--61068 Score: 454
Period size: 202 Copynumber: 1.8 Consensus size: 202
60692 TGAAATGAAT
* * **
60702 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTACCTCCCTTGAGATAGTTTTTCTTGA
1 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTACCTCCCTTGAGACAGTTTCCCTTGA
* * *
60767 AACATAAACATTGAAAACATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
66 AACATAAACATTGAAAACATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGA
** * * * *
60832 AACAAATTATTTGAATATGTTTTATTTGAAACAAATTTCATCTCCCTTAAGACAGTTTCTTTTGG
131 AACAAATTATTCAAATATATTTCACTTAAAACAAATTTCATCTCCCTTAAGACAGTTTCTTTTGG
60897 AACTAAA
196 AACTAAA
* *
60904 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAATTT-CGTCTCTCTTGAGACAGTTTCCCTT
1 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTAC--CTCCCTTGAGACAGTTTCCCTT
* *** * *
60967 GAAACA-AAATCTTTGAATTTATTTCCCCTAAAATAAATTTTGTCTCCCTTGAGACAGTTTCTCT
64 GAAACATAAA-CATTGAAAACATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCT
* * *
61031 TGAAACACAA-TCTTCAAATTTATTTCCCTTAAAACAAA
128 TGAAACA-AATTATTCAAATATATTTCACTTAAAACAAA
61069 ATTTTGTTTC
Statistics
Matches: 137, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
200 1 0.01
201 9 0.07
202 125 0.91
203 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.39
Consensus pattern (202 bp):
TTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTACCTCCCTTGAGACAGTTTCCCTTGA
AACATAAACATTGAAAACATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGA
AACAAATTATTCAAATATATTTCACTTAAAACAAATTTCATCTCCCTTAAGACAGTTTCTTTTGG
AACTAAA
Found at i:69541 original size:14 final size:14
Alignment explanation
Indices: 69515--69554 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
69505 AAATTAATTA
69515 ATTAATAAATTATAT
1 ATTAAT-AATTATAT
69530 ATTAATAATTATAT
1 ATTAATAATTATAT
* *
69544 TTTAAAAATTA
1 ATTAATAATTA
69555 ATCATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTAATAATTATAT
Found at i:70398 original size:3 final size:3
Alignment explanation
Indices: 70390--70419 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
70380 ATCATAATTA
70390 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
70420 TTACCTAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:72262 original size:87 final size:87
Alignment explanation
Indices: 72157--72332 Score: 343
Period size: 87 Copynumber: 2.0 Consensus size: 87
72147 AACTAAAAAA
72157 TATTATTACAATTATTCTTAATTATATAAATCATAATTATAATATTATATTAGGTCGAATAAGAT
1 TATTATTACAATTATTCTTAATTATATAAATCATAATTATAATATTATATTAGGTCGAATAAGAT
72222 GTTTTTATAATAAATCTGAATT
66 GTTTTTATAATAAATCTGAATT
*
72244 TATTATTACAATTGTTCTTAATTATATAAATCATAATTATAATATTATATTAGGTCGAATAAGAT
1 TATTATTACAATTATTCTTAATTATATAAATCATAATTATAATATTATATTAGGTCGAATAAGAT
72309 GTTTTTATAATAAATCTGAATT
66 GTTTTTATAATAAATCTGAATT
72331 TA
1 TA
72333 ACTCAACTAC
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (87 bp):
TATTATTACAATTATTCTTAATTATATAAATCATAATTATAATATTATATTAGGTCGAATAAGAT
GTTTTTATAATAAATCTGAATT
Found at i:72545 original size:16 final size:17
Alignment explanation
Indices: 72516--72557 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
72506 CGATTATATA
*
72516 TATATATATAATATT-T
1 TATATATTTAATATTAT
*
72532 TATATATTTTATATTAAT
1 TATATATTTAATATT-AT
72550 TATATATT
1 TATATATT
72558 ACAAACCCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 13 0.59
18 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATATTTAATATTAT
Found at i:75358 original size:16 final size:16
Alignment explanation
Indices: 75327--75370 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 16
75317 ATTTAGTTAC
*
75327 TATATTCATCTTTTTTT
1 TATATT-ATATTTTTTT
75344 TATATTATATTTTTTT
1 TATATTATATTTTTTT
75360 TATATATATAT
1 TATAT-TATAT
75371 CATTGTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (16 bp):
TATATTATATTTTTTT
Found at i:75394 original size:14 final size:14
Alignment explanation
Indices: 75377--75406 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
75367 ATATCATTGT
75377 ATATATATGTATAG
1 ATATATATGTATAG
75391 ATATATATGTATAG
1 ATATATATGTATAG
75405 AT
1 AT
75407 GTATTAATTT
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:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (14 bp):
ATATATATGTATAG
Found at i:77475 original size:27 final size:27
Alignment explanation
Indices: 77436--77497 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 27
77426 ATCAGAACAA
*
77436 AAAGAGAAAA-AAAAAGA-AAAAAAGC
1 AAAGAGAAAATAAAAAGATAAAAAAAC
77461 AAAGAGAAAATAAAAAGATAAAAAAAC
1 AAAGAGAAAATAAAAAGATAAAAAAAC
77488 AAAG-GAAAAT
1 AAAGAGAAAAT
77498 TGAAGAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 10 0.29
26 13 0.38
27 11 0.32
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (27 bp):
AAAGAGAAAATAAAAAGATAAAAAAAC
Found at i:78635 original size:164 final size:164
Alignment explanation
Indices: 78364--78694 Score: 653
Period size: 164 Copynumber: 2.0 Consensus size: 164
78354 TTATGATTCG
*
78364 TCTCAATTGTAAAACCGTGAAAGGGGCAATATTTTCAAAACTTCTGATTAAACATTTTTCGAAAC
1 TCTCAATTGTAAAACCGTGAAAGGGGCAATATTTTCAAAACTTATGATTAAACATTTTTCGAAAC
78429 TCTTTTAATTGATATTTTCAGAATTTTGAAAATAAAAGAGAAACATTTTTTCAAACAAGACAATC
66 TCTTTTAATTGATATTTTCAGAATTTTGAAAATAAAAGAGAAACATTTTTTCAAACAAGACAATC
78494 TCTCTAAAGTGGATCTTGGTAAATGACATATGGC
131 TCTCTAAAGTGGATCTTGGTAAATGACATATGGC
78528 TCTCAATTGTAAAACCGTGAAAGGGGCAATATTTTCAAAACTTATGATTAAACATTTTTCGAAAC
1 TCTCAATTGTAAAACCGTGAAAGGGGCAATATTTTCAAAACTTATGATTAAACATTTTTCGAAAC
78593 TCTTTTAATTGATATTTTCAGAATTTTGAAAATAAAAGAGAAACATTTTTTCAAACAAGACAATC
66 TCTTTTAATTGATATTTTCAGAATTTTGAAAATAAAAGAGAAACATTTTTTCAAACAAGACAATC
78658 TCTCTAAAGTGGATCTTGGTAAATGACATATGGC
131 TCTCTAAAGTGGATCTTGGTAAATGACATATGGC
78692 TCT
1 TCT
78695 TAGACAGTAA
Statistics
Matches: 166, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
164 166 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (164 bp):
TCTCAATTGTAAAACCGTGAAAGGGGCAATATTTTCAAAACTTATGATTAAACATTTTTCGAAAC
TCTTTTAATTGATATTTTCAGAATTTTGAAAATAAAAGAGAAACATTTTTTCAAACAAGACAATC
TCTCTAAAGTGGATCTTGGTAAATGACATATGGC
Found at i:79224 original size:37 final size:37
Alignment explanation
Indices: 79172--79552 Score: 185
Period size: 37 Copynumber: 11.1 Consensus size: 37
79162 TAAAAAGAAT
*
79172 ATTTTATCTCACTTGAGATAGTTTCCCTTGAAACAAA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
* * * *
79209 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
* **
79246 A----A---CA-TTGAAAACA-TTTCCCTTGAAA-TGA
1 ATTTTATCTCACTTG-AGACAGTTTCCCTTGAAACAAA
* * *
79274 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
* * * ** *
79311 ATTTTACCTCCCTTGAGATAGTTTTTCTTGAAACATA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
*
79348 A----A---CA-TTGAAAACA-TTTCCCTTGAAAC-AA
1 ATTTTATCTCACTTG-AGACAGTTTCCCTTGAAACAAA
* *
79376 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
* ***
79412 A--TTA--T---TTGA-ATATGTTTTATTTGAAAC-AA
1 ATTTTATCTCACTTGAGACA-GTTTCCCTTGAAACAAA
* * * ** * *
79441 ATTTCATCTCCCTTAAGACAGTTTCTTTTGGAACTAA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
* * *
79478 ATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
** *
79514 ATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
79551 AT
1 AT
79553 CTTTGAATTT
Statistics
Matches: 261, Mismatches: 51, Indels: 64
0.69 0.14 0.17
Matches are distributed among these distances:
28 6 0.02
29 46 0.18
30 9 0.03
31 2 0.01
32 1 0.00
33 2 0.01
34 2 0.01
35 9 0.03
36 82 0.31
37 102 0.39
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (37 bp):
ATTTTATCTCACTTGAGACAGTTTCCCTTGAAACAAA
Found at i:79300 original size:102 final size:102
Alignment explanation
Indices: 79172--79412 Score: 401
Period size: 102 Copynumber: 2.4 Consensus size: 102
79162 TAAAAAGAAT
* * **
79172 ATTTTATCTCACTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTACCTCCCTTGAGACAGTTTCTCT
**
79237 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
* *
79274 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTACCTCCCTTGAGATAGTTTTTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTACCTCCCTTGAGACAGTTTCTCT
79339 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
*
79376 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA
79413 TTATTTGAAT
Statistics
Matches: 130, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 130 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (102 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTACCTCCCTTGAGACAGTTTCTCT
TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
Found at i:79406 original size:65 final size:64
Alignment explanation
Indices: 79295--79679 Score: 236
Period size: 65 Copynumber: 5.8 Consensus size: 64
79285 CTTGAGATAG
** * * *
79295 TTTCCCTTGAAACAAAATTTTACCTCCCTTGAGATAGTTTTTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-AAACATTGAAAAT
79360 A
64 A
* * ** * *
79361 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTATTTGAATATG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAACA-TTGAAAATA
*** ** * * * * *
79426 TTTTATTTGAAACAAATTTCATCTCCCTTAAGACAGTTTCTTTTGGAACTAAATTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAA-------AC-AT
* *
79491 TGAGACA-G
57 TGA-AAATA
* * * * * **
79499 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAA-CATTGAAAATA
* * * * * *
79564 TTTCCCCTAAAATAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAATC-TTCAAATTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-AAACATTGAAA-AT
79628 A
64 A
* * * *
79629 TTTCCCTTAAAACAAAATTTTGTTTCCCTTGAGACCGTTT-TCATGAAACAA
1 TTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
79680 CAAGATTGTT
Statistics
Matches: 250, Mismatches: 53, Indels: 34
0.74 0.16 0.10
Matches are distributed among these distances:
64 9 0.04
65 147 0.59
66 43 0.17
72 3 0.01
73 46 0.18
74 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (64 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAACATTGAAAATA
Found at i:79408 original size:36 final size:36
Alignment explanation
Indices: 79361--79550 Score: 180
Period size: 36 Copynumber: 5.4 Consensus size: 36
79351 ATTGAAAACA
*
79361 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* *
79397 TTTCCCTTGAAACAAA-----T-TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
*** * * *
79426 TTTTATTTGAAACAAATTTCATCTCCCTTAAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
** * *
79462 TTTCTTTTGGAACTAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
*
79499 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
79535 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
79551 ATCTTTGAAT
Statistics
Matches: 124, Mismatches: 20, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.02
29 18 0.15
30 2 0.02
31 1 0.01
34 1 0.01
35 1 0.01
36 67 0.54
37 32 0.26
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:79482 original size:167 final size:168
Alignment explanation
Indices: 79193--79512 Score: 383
Period size: 167 Copynumber: 1.9 Consensus size: 168
79183 CTTGAGATAG
*
79193 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTGAAAAC
* ** ** * * *
79258 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTACCTCCC
66 ATTTCACTTGAAACAAATTTCATCTCCCTTAAGACAGTTTCCCTTGAAACAAAATTTTACCTCCC
* *
79323 TTGAGATAGTTTTTCTTGAAACATAAACATTGAAAACA
131 TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* ** *
79361 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AATTATTTGAATA
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAACA-TTGAAAA
** * * ** * * ** *
79424 TGTTTTATTTGAAACAAATTTCATCTCCCTTAAGACAGTTTCTTTTGGAACTAAATTTTGTCTCT
65 CATTTCACTTGAAACAAATTTCATCTCCCTTAAGACAGTTTCCCTTGAAACAAAATTTTACCTCC
79489 CTTGAGACAGTTTCTCTTGAAACA
130 CTTGAGACAGTTTCTCTTGAAACA
79513 AATTTCGTCT
Statistics
Matches: 125, Mismatches: 26, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
166 3 0.02
167 109 0.87
168 13 0.10
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.39
Consensus pattern (168 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTGAAAAC
ATTTCACTTGAAACAAATTTCATCTCCCTTAAGACAGTTTCCCTTGAAACAAAATTTTACCTCCC
TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:79644 original size:203 final size:204
Alignment explanation
Indices: 79273--79644 Score: 462
Period size: 203 Copynumber: 1.8 Consensus size: 204
79263 CCTTGAAATG
* * * **
79273 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTACCTCCCTTGAGATAGTTTTTC
1 AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTCACCTCCCTTGAGACAGTTTCCC
* * *
79338 TTGAAACATAAACATTGAAAACATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCC
66 TTGAAACATAAACATTGAAAACATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCC
** * * * *
79403 TTGAAACAAATTATTTGAATATGTTTTATTTGAAACAAATTTCATCTCCCTTAAGACAGTTTCTT
131 TTGAAACAAATTATTCAAATATATTTCACTTAAAACAAATTTCATCTCCCTTAAGACAGTTTCTT
79468 TTGGAACTA
196 TTGGAACTA
* ** *
79477 AATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTCTCTTGAGACAGTTTCCC
1 AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTCACCTCCCTTGAGACAGTTTCCC
* *** * *
79541 TTGAAACA-AAATCTTTGAATTTATTTCCCCTAAAATAAATTTTGTCTCCCTTGAGACAGTTTCT
66 TTGAAACATAAA-CATTGAAAACATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCC
* * *
79605 CTTGAAACACAA-TCTTCAAATTTATTTCCCTTAAAACAAA
130 CTTGAAACA-AATTATTCAAATATATTTCACTTAAAACAAA
79645 ATTTTGTTTC
Statistics
Matches: 139, Mismatches: 27, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
202 3 0.02
203 101 0.73
204 35 0.25
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (204 bp):
AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTCACCTCCCTTGAGACAGTTTCCC
TTGAAACATAAACATTGAAAACATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCC
TTGAAACAAATTATTCAAATATATTTCACTTAAAACAAATTTCATCTCCCTTAAGACAGTTTCTT
TTGGAACTA
Found at i:88088 original size:14 final size:14
Alignment explanation
Indices: 88062--88101 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
88052 AAATTAATTA
88062 ATTAATAAATTATAT
1 ATTAAT-AATTATAT
88077 ATTAATAATTATAT
1 ATTAATAATTATAT
* *
88091 TTTAAAAATTA
1 ATTAATAATTA
88102 ATCATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTAATAATTATAT
Found at i:88947 original size:3 final size:3
Alignment explanation
Indices: 88939--88971 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
88929 ATCATAATTA
88939 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
88972 TTACCTAGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:93507 original size:132 final size:132
Alignment explanation
Indices: 93315--93558 Score: 290
Period size: 132 Copynumber: 1.8 Consensus size: 132
93305 AGAAATAGCG
* * ** ** *
93315 CAGCTGAGAAGATGAACAAAGAGACGGACTTGAAAATAAATAATTCGGCAGAAAAGATGAAAAAA
1 CAGCTGAGAAGAAGAACAAAGAGACGCACTTGAAAATAAATAAAGCACCAGAAAACATGAAAAAA
* ** * ** * *
93380 GAGACAGCCGTGATGGTAAATAGCTCGGCTGAGAAGATGAGAGAAGAAACTGCTACAACAAATGG
66 GAGACAGCCATGACAGTAAACAGCTCAACAGAGAAGATGAGACAAGAAACTGCTACAACAAATGG
93445 CT
131 CT
* * * * * *
93447 CAGCTGAGAAGAAGAAGAAAGAGACGCCCTTGACAATAAATAAAGCACCTGAGAACATGAAGAAA
1 CAGCTGAGAAGAAGAACAAAGAGACGCACTTGAAAATAAATAAAGCACCAGAAAACATGAAAAAA
*
93512 GAGATAGCCATGACAGTAAACAGCTCAACAGAGAAGATGAGACAAGA
66 GAGACAGCCATGACAGTAAACAGCTCAACAGAGAAGATGAGACAAGA
93559 GACAGATACA
Statistics
Matches: 90, Mismatches: 22, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
132 90 1.00
ACGTcount: A:0.46, C:0.15, G:0.25, T:0.13
Consensus pattern (132 bp):
CAGCTGAGAAGAAGAACAAAGAGACGCACTTGAAAATAAATAAAGCACCAGAAAACATGAAAAAA
GAGACAGCCATGACAGTAAACAGCTCAACAGAGAAGATGAGACAAGAAACTGCTACAACAAATGG
CT
Found at i:93546 original size:45 final size:44
Alignment explanation
Indices: 93497--93908 Score: 258
Period size: 45 Copynumber: 9.4 Consensus size: 44
93487 TAAAGCACCT
* * *
93497 GAGAACATGAAGAAAGAGATAGCCATGACAGTAAACAGCTCAACA
1 GAGAAGATGAAGAAAGAGATAG-CATGACAGTAAATAGCTCAGCA
* * **
93542 GAGAAGATG-AGACAAGAGACAG-AT-ACAGTAAATAGCACAGTT
1 GAGAAGATGAAGA-AAGAGATAGCATGACAGTAAATAGCTCAGCA
** *
93584 GAGAAGAT---GAAAGAGAGGGCGTTGACAGTAAATAGCTCAGCA
1 GAGAAGATGAAGAAAGAGATAGC-ATGACAGTAAATAGCTCAGCA
* * * * * * *
93626 GAGAAGATGAAGAAAGAGATTGCTGTGAAAGTGAATGGCTTAGCT
1 GAGAAGATGAAGAAAGAGATAGC-ATGACAGTAAATAGCTCAGCA
* * *
93671 GAGAAGAT---GAAAGAGATGGCATTGACAGTGAATAGCTCAGCG
1 GAGAAGATGAAGAAAGAGATAGCA-TGACAGTAAATAGCTCAGCA
* * * * * * *
93713 GAGAAGGTGGAA-AAAGAGATTGCTGTGAAAGTGAATGGCTCAGCT
1 GAGAAGAT-GAAGAAAGAGATAGC-ATGACAGTAAATAGCTCAGCA
93758 GAGAAGAT---GAAAGAGATAGCATTGACAGTAAATAGCTCAGCA
1 GAGAAGATGAAGAAAGAGATAGCA-TGACAGTAAATAGCTCAGCA
* * * * * * *
93800 GAGAAGGTGAAGAAAGAGATTGCTGTGAAAGTGAATGGCTCAGCT
1 GAGAAGATGAAGAAAGAGATAGC-ATGACAGTAAATAGCTCAGCA
** * * * *
93845 GAGAAGGGGAAGAAAGAGATAGCTGTGGA-AGTGAATGGCTCAGCT
1 GAGAAGATGAAGAAAGAGATAGC-AT-GACAGTAAATAGCTCAGCA
*
93890 GAGAAGATGAAAAAAGAGA
1 GAGAAGATGAAGAAAGAGA
93909 CAACTTTGGC
Statistics
Matches: 294, Mismatches: 53, Indels: 40
0.76 0.14 0.10
Matches are distributed among these distances:
39 7 0.02
40 2 0.01
41 1 0.00
42 111 0.38
43 2 0.01
44 3 0.01
45 166 0.56
46 2 0.01
ACGTcount: A:0.42, C:0.10, G:0.32, T:0.16
Consensus pattern (44 bp):
GAGAAGATGAAGAAAGAGATAGCATGACAGTAAATAGCTCAGCA
Found at i:93699 original size:87 final size:87
Alignment explanation
Indices: 93508--93908 Score: 460
Period size: 87 Copynumber: 4.6 Consensus size: 87
93498 AGAACATGAA
* * *
93508 GAAAGAGATAGCCA-TGACAGTAAACAGCTCAACAGAGAAGATG-AGACAAGAGA---CAGAT-A
1 GAAAGAGATAG-CATTGACAGTAAATAGCTCAGCAGAGAAGATGAAGA-AAGAGATTGCTG-TGA
* * * * *
93567 CAGTAAATAGCACAGTTGAGAAGAT
63 AAGTGAATGGCTCAGCTGAGAAGAT
** *
93592 GAAAGAGAGGGCGTTGACAGTAAATAGCTCAGCAGAGAAGATGAAGAAAGAGATTGCTGTGAAAG
1 GAAAGAGATAGCATTGACAGTAAATAGCTCAGCAGAGAAGATGAAGAAAGAGATTGCTGTGAAAG
*
93657 TGAATGGCTTAGCTGAGAAGAT
66 TGAATGGCTCAGCTGAGAAGAT
* * * *
93679 GAAAGAGATGGCATTGACAGTGAATAGCTCAGCGGAGAAGGTGGAA-AAAGAGATTGCTGTGAAA
1 GAAAGAGATAGCATTGACAGTAAATAGCTCAGCAGAGAAGAT-GAAGAAAGAGATTGCTGTGAAA
93743 GTGAATGGCTCAGCTGAGAAGAT
65 GTGAATGGCTCAGCTGAGAAGAT
*
93766 GAAAGAGATAGCATTGACAGTAAATAGCTCAGCAGAGAAGGTGAAGAAAGAGATTGCTGTGAAAG
1 GAAAGAGATAGCATTGACAGTAAATAGCTCAGCAGAGAAGATGAAGAAAGAGATTGCTGTGAAAG
*
93831 TGAATGGCTCAGCTGAGAAGGGGAA
66 TGAATGGCTCAGCTGAGAA---GAT
* * * *
93856 GAAAGAGATAGC-TGTGGA-AGTGAATGGCTCAGCTGAGAAGATGAAAAAAGAGA
1 GAAAGAGATAGCAT-T-GACAGTAAATAGCTCAGCAGAGAAGATGAAGAAAGAGA
93909 CAACTTTGGC
Statistics
Matches: 277, Mismatches: 27, Indels: 20
0.85 0.08 0.06
Matches are distributed among these distances:
83 1 0.00
84 42 0.15
85 3 0.01
86 4 0.01
87 176 0.64
88 3 0.01
89 1 0.00
90 45 0.16
91 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.32, T:0.16
Consensus pattern (87 bp):
GAAAGAGATAGCATTGACAGTAAATAGCTCAGCAGAGAAGATGAAGAAAGAGATTGCTGTGAAAG
TGAATGGCTCAGCTGAGAAGAT
Found at i:98736 original size:55 final size:55
Alignment explanation
Indices: 98640--98837 Score: 272
Period size: 56 Copynumber: 3.6 Consensus size: 55
98630 CCCTATGTTC
* * * * *
98640 TAGATATATTCGATTACGAGACTCTTATTTTTATGCTTCTTATTGGCAACAACTGA
1 TAGATATATTCGATTTCG-GGCTCCTATTTTTATGCTTCTTAATGACAACAACTGA
*
98696 TAGATATATTCGATTTCGGGCTCCTATTTTTATGCCTCTTAATGACAACAACTGA
1 TAGATATATTCGATTTCGGGCTCCTATTTTTATGCTTCTTAATGACAACAACTGA
* * *
98751 TAGATATACTCGATTTCGGGATCCCTATTTTTATGCTTATTAATGACAACAACTGA
1 TAGATATATTCGATTTCGGGCT-CCTATTTTTATGCTTCTTAATGACAACAACTGA
*
98807 TAAATATATTCGATTTCGGGC-CTCTATTTTT
1 TAGATATATTCGATTTCGGGCTC-CTATTTTT
98838 GAGGCCCTGC
Statistics
Matches: 127, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
54 1 0.01
55 60 0.47
56 66 0.52
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (55 bp):
TAGATATATTCGATTTCGGGCTCCTATTTTTATGCTTCTTAATGACAACAACTGA
Done.