Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001174.1 Hibiscus syriacus cultivar Beakdansim tig00002338_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: 2182627
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:1662201 original size:21 final size:21
Alignment explanation
Indices: 1662136--1662204 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
1662126 GTGAATCGGG
*
1662136 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1662156 CTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA
1662177 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1662198 CTCTTGA
1 CTCTTGA
1662205 GGAATGATAG
Statistics
Matches: 35, Mismatches: 13, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
20 11 0.31
21 24 0.69
ACGTcount: A:0.20, C:0.19, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1662220 original size:42 final size:41
Alignment explanation
Indices: 1662136--1662257 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 41
1662126 GTGAATCGGG
* * * * *
1662136 CTCTTGAATGGTGGGA-GGGACTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGACTCTT-GAGGATGATAGGGGC
1662177 CTCTTGAACGGTGGGAGGGGACTCTTGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTTGAGG-ATGATAGGGGC
* * * *
1662219 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTTGA-GGATGATAGG
1662258 CGTCGGGCTT
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
41 17 0.25
42 50 0.72
43 2 0.03
ACGTcount: A:0.23, C:0.16, G:0.37, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTTGAGGATGATAGGGGC
Found at i:1664246 original size:20 final size:19
Alignment explanation
Indices: 1664215--1664379 Score: 71
Period size: 19 Copynumber: 8.9 Consensus size: 19
1664205 TCTTTTGGTT
1664215 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* * *
1664234 GATAATGAGAATCGCAATGC
1 GA-AATGAAAATCGCAACGA
**
1664254 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1664273 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
1664287 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * *
1664303 -CCA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
* *
1664320 GAAATGAAAAGCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
* *
1664340 GAAATAAAAAATCGCAACGC
1 GAAAT-GAAAATCGCAACGA
1664360 GAAATATGAAAATCGCAACG
1 G-AA-ATGAAAATCGCAACG
1664380 CCAATGCGAT
Statistics
Matches: 109, Mismatches: 22, Indels: 28
0.69 0.14 0.18
Matches are distributed among these distances:
14 17 0.16
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 29 0.27
20 28 0.26
21 23 0.21
22 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1664282 original size:33 final size:33
Alignment explanation
Indices: 1664240--1664326 Score: 138
Period size: 33 Copynumber: 2.6 Consensus size: 33
1664230 ACGAGATAAT
* *
1664240 GAGAATCGCAATGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
*
1664273 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
*
1664306 GACAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
1664327 AAAGCGCAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.13
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:1664355 original size:21 final size:20
Alignment explanation
Indices: 1664309--1664380 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 20
1664299 GCGACCAGAC
1664309 AATCGCAACGCGAAAT-GAA
1 AATCGCAACGCGAAATAGAA
* *
1664328 AAGCGCAACCGCGAAATAAAA
1 AATCGCAA-CGCGAAATAGAA
1664349 AATCGCAACGCGAAATATGAA
1 AATCGCAACGCGAAATA-GAA
1664370 AATCGCAACGC
1 AATCGCAACGC
1664381 CAATGCGATT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 7 0.15
20 17 0.37
21 22 0.48
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (20 bp):
AATCGCAACGCGAAATAGAA
Found at i:1664407 original size:18 final size:18
Alignment explanation
Indices: 1664384--1664428 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
1664374 GCAACGCCAA
*
1664384 TGCGATTTGGTTTCGCGT
1 TGCGATTTGATTTCGCGT
*
1664402 TGCGATTTTTTATTTCGCGT
1 TGCGA--TTTGATTTCGCGT
1664422 TGCGATT
1 TGCGATT
1664429 CTCGTTGCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (18 bp):
TGCGATTTGATTTCGCGT
Found at i:1665067 original size:20 final size:20
Alignment explanation
Indices: 1664987--1665067 Score: 83
Period size: 20 Copynumber: 4.0 Consensus size: 20
1664977 GCGTTGCAAA
* * *
1664987 AGTCAGAATCGCGTTGCGAA
1 AGTCAGTATCGCATTGCGAT
*
1665007 AGTCAGTATCTCATTGCGATTT
1 AGTCAGTATCGCATTGCGA--T
* *
1665029 TGT-ATTATCGCATTGCGAT
1 AGTCAGTATCGCATTGCGAT
1665048 AGTCAGTATCGCATTGCGAT
1 AGTCAGTATCGCATTGCGAT
1665068 TTTCCCAATT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
19 3 0.06
20 31 0.63
21 13 0.27
22 2 0.04
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (20 bp):
AGTCAGTATCGCATTGCGAT
Found at i:1665086 original size:41 final size:41
Alignment explanation
Indices: 1664994--1665088 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
1664984 AAAAGTCAGA
* * ** *
1664994 ATCGCGTTGCGAAAGTCAGTATCTCATTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
*
1665035 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CCAAT
1665077 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1665089 TTACTTATTC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
41 44 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:1665178 original size:21 final size:21
Alignment explanation
Indices: 1665138--1665178 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1665128 ATTGTATACC
**
1665138 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1665159 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1665179 GCGAATTTGC
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:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1665324 original size:3 final size:3
Alignment explanation
Indices: 1665316--1665346 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1665306 TTATTTTCTC
*
1665316 TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1665347 TAAAAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1666686 original size:19 final size:20
Alignment explanation
Indices: 1666664--1666702 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1666654 GGATATTATA
1666664 ATAAAATA-AATTAAAAAAT
1 ATAAAATAGAATTAAAAAAT
* *
1666683 ATAAACTAGGATTAAAAAAT
1 ATAAAATAGAATTAAAAAAT
1666703 TAATTATTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (20 bp):
ATAAAATAGAATTAAAAAAT
Found at i:1667366 original size:20 final size:20
Alignment explanation
Indices: 1667320--1667366 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1667310 TTTCTGTGTA
*
1667320 TTTTTCTCTCTTTCTCTGTT
1 TTTTTCTCTCTGTCTCTGTT
* * *
1667340 CTGTTCTCTCTGTCTCTTTT
1 TTTTTCTCTCTGTCTCTGTT
1667360 TTTTTCT
1 TTTTTCT
1667367 TTTTTTCAGG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.00, C:0.26, G:0.06, T:0.68
Consensus pattern (20 bp):
TTTTTCTCTCTGTCTCTGTT
Found at i:1667569 original size:17 final size:16
Alignment explanation
Indices: 1667531--1667584 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
1667521 GGGAGTGGCA
1667531 GCGG-TGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
1667546 GCGGCTGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
1667562 GCCGGCTGGAGGCAGAG
1 G-CGGCTGGAGGCAGAG
1667579 GCGGCT
1 GCGGCT
1667585 AGGGATTAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
15 4 0.11
16 17 0.46
17 16 0.43
ACGTcount: A:0.17, C:0.20, G:0.56, T:0.07
Consensus pattern (16 bp):
GCGGCTGGAGGCAGAG
Found at i:1667708 original size:3 final size:3
Alignment explanation
Indices: 1667700--1667747 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
1667690 TTAATATATT
*
1667700 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA T-A TAA T-A TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
1667744 TAA T
1 TAA T
1667748 CAATTAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.82
4 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1668510 original size:107 final size:110
Alignment explanation
Indices: 1668064--1668608 Score: 552
Period size: 107 Copynumber: 5.0 Consensus size: 110
1668054 ATAGAATTAT
* *
1668064 GCAAAA-GTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTCTCAT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAA-TTCTTCTTCCTTCTTCAGATGAGTTTCTCAT
* * *
1668128 TATGAAC-TTCTCTGGAAAAACTGCTCCATCAAGTGATGGATTTGA
65 TATGAACTTTCTCTGGAAAATCTGATCCATCAAATGATGGATTTGA
* * *
1668173 GCAAAAGGTTGAA-AAATTCTTCTTATTATGAA--CTTCTTCCTTCTTTAGATGACGAGTTCTTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAATTCTTCTTCCTTCTTCAGAT---GAG-T-TTC
* * * * **
1668235 TCATTATG-ACTCTAC-CTGG-CAATGTTGATCCATCAAATGATGAATTCAA
61 TCATTATGAACT-TTCTCTGGAAAAT-CTGATCCATCAAATGATGGATTTGA
* *
1668284 ACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAA-TTCTTCTTCCTTCTTCAGATGAG-T-TTCTC
** * * * *
1668349 ATTATGAACTTTCTCTGGAAAAGATGATCCATCAATTGA-CGAATTCA
63 ATTATGAACTTTCTCTGGAAAATCTGATCCATCAAATGATGGATTTGA
* * *
1668396 TGTAAAAGGTTGAACAAGTTTTTCTCATTA-GAATTCTTCTTCCTTCTTCAG-TGAG-ATCTCAT
1 -GCAAAAGGTTGAACAAGTTCTTCTCATTATGAATTCTTCTTCCTTCTTCAGATGAGTTTCTCAT
*
1668458 TATGAACTTTTTCTGGAAAATCTGATCCATCAAATGATGGATTTGA
65 TATGAACTTTCTCTGGAAAATCTGATCCATCAAATGATGGATTTGA
* * *
1668504 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAA--CTTTTTCCTTCCTTCAGATGAGTTTTTCA-
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAATTCTTCTTCCTT-CTTCAGATGAGTTTCTCAT
**
1668566 TATAGAAC-TT-TCTGGAATGT-TGAT-CATCAAATGATGGATTTGA
65 TAT-GAACTTTCTCTGGAAAATCTGATCCATCAAATGATGGATTTGA
1668609 ATCTTTGCTA
Statistics
Matches: 368, Mismatches: 45, Indels: 50
0.79 0.10 0.11
Matches are distributed among these distances:
105 19 0.05
106 30 0.08
107 79 0.21
108 17 0.05
109 36 0.10
110 15 0.04
111 63 0.17
112 44 0.12
113 46 0.12
114 2 0.01
115 17 0.05
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (110 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAATTCTTCTTCCTTCTTCAGATGAGTTTCTCATT
ATGAACTTTCTCTGGAAAATCTGATCCATCAAATGATGGATTTGA
Found at i:1668532 original size:220 final size:218
Alignment explanation
Indices: 1668064--1668578 Score: 590
Period size: 220 Copynumber: 2.4 Consensus size: 218
1668054 ATAGAATTAT
* *
1668064 GCAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAG-TTTCTCAT
1 GCAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTCTCAT
* * * *
1668128 TATGAAC-TTCTCTGGAAAAACTGCTCCATCAAGTGATGGATTTGAGCAAAAGGTTGAAAAATTC
66 TATGAACTTTCTCTGGAAAAACTGATCCATCAAGTGATCGAATTCAGCAAAAGGTTGAAAAATTC
* * *
1668192 TTCTTATTATGAACTTCTTCCTTCTTTAGATGACGAGTTCTTCTCATTATGACTCTACCTGGCAA
131 TTCTCATTATGAACTTCTTCCTTCTTCAGATGACGA----TTCTCATTATGACTCTACCTGGAAA
*
1668257 TGTTGATCCATCAAATGATGAATTCAA
192 TGCTGATCCATCAAATGATGAATTCAA
*
1668284 ACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GC-AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT-TTCTC
* *
1668349 ATTATGAACTTTCTCTGGAAAAGA-TGATCCATCAATTGA-CGAATTCATGTAAAAGGTTGAACA
64 ATTATGAACTTTCTCTGGAAAA-ACTGATCCATCAAGTGATCGAATTCA-GCAAAAGGTTGAA-A
* * * **
1668412 AGTTTTTCTCATTA-GAATTCTTCTTCCTTCTTCAG-TGA-GA-TCTCATTATGAACTTTTTCTG
126 AATTCTTCTCATTATGAA--CTTCTTCCTTCTTCAGATGACGATTCTCATTATG-ACTCTACCTG
* **
1668473 GAAAAT-CTGATCCATCAAATGATGGATTTGA
188 G-AAATGCTGATCCATCAAATGATGAATTCAA
*
1668504 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC-T-TT-TTCCTTCCTTCAGATGAGTTTT-TC
1 GCAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTT-CTTCAGATGAGTTTTCTC
1668565 A-TATAGAACTTTCT
64 ATTAT-GAACTTTCT
1668579 GGAATGTTGA
Statistics
Matches: 258, Mismatches: 23, Indels: 32
0.82 0.07 0.10
Matches are distributed among these distances:
215 3 0.01
216 12 0.05
217 8 0.03
218 15 0.06
219 15 0.06
220 57 0.22
221 55 0.21
222 1 0.00
223 19 0.07
224 42 0.16
225 16 0.06
226 15 0.06
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (218 bp):
GCAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTCTCAT
TATGAACTTTCTCTGGAAAAACTGATCCATCAAGTGATCGAATTCAGCAAAAGGTTGAAAAATTC
TTCTCATTATGAACTTCTTCCTTCTTCAGATGACGATTCTCATTATGACTCTACCTGGAAATGCT
GATCCATCAAATGATGAATTCAA
Found at i:1669552 original size:83 final size:82
Alignment explanation
Indices: 1669395--1669559 Score: 312
Period size: 83 Copynumber: 2.0 Consensus size: 82
1669385 TCTACTATGA
*
1669395 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAACCAGATCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAACCAGATCAGATAACTCAAAGAACACT
1669460 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
1669477 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCC-AACCAGATCAGATAACTCAAAGAACAC
1669542 TTCCAGAAGATGCTATTG
65 TTCCAGAAGATGCTATTG
1669560 AGTCTCCTTA
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
82 36 0.44
83 45 0.56
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (82 bp):
GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAACCAGATCAGATAACTCAAAGAACACT
TCCAGAAGATGCTATTG
Found at i:1669687 original size:77 final size:84
Alignment explanation
Indices: 1669590--1669749 Score: 253
Period size: 79 Copynumber: 2.0 Consensus size: 84
1669580 GAGTAAATCT
* *
1669590 CAAATTCAAATGATTGGTTCTGCC-AACCAGAT-AGATAACTCAAAGAACACTTCCAG-A-A-G-
1 CAAATTCAAATGATTAGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
1669649 TATTGGCAAATTCATCTTC
66 TATTGGCAAATTCATCTTC
1669668 CAAATTC-AATGATTAGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
1 CAAATTCAAATGATTAGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
1669732 TATTGGCAAATTCATCTT
66 TATTGGCAAATTCATCTT
1669750 ATTCCAGTTA
Statistics
Matches: 74, Mismatches: 2, Indels: 7
0.89 0.02 0.08
Matches are distributed among these distances:
77 14 0.19
78 15 0.20
79 24 0.32
80 1 0.01
81 1 0.01
82 1 0.01
83 18 0.24
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (84 bp):
CAAATTCAAATGATTAGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
TATTGGCAAATTCATCTTC
Found at i:1669710 original size:177 final size:185
Alignment explanation
Indices: 1669316--1669736 Score: 691
Period size: 177 Copynumber: 2.3 Consensus size: 185
1669306 GATTGGTTTG
1669316 TAGTTCTTACCAAACCAGATCA-ATAACTCAAAGAACAACTTCCAGAAGATGCTATTGAGTCTCC
1 TAGTTC-TACCAAACCAGATCAGATAACTCAAAGAAC-ACTTCCAGAAGATGCTATTGAGTCTCC
1669380 TTATTTCTACTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAACCAGATCAGAT
64 TTATTTCTACTATGAGCAAA-T-ATCTTCTAAATTCAATGATTGGTTCTGCCAACCAGATCAGAT
1669445 AACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGAT
127 AACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGAT
* *
1669504 TGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTT
1 TAGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTT
* *
1669569 ATTTTTACTATGAG-TAA-ATC-TC-AAATTCAAATGATTGGTTCTGCCAACCAGAT-AGATAAC
66 ATTTCTACTATGAGCAAATATCTTCTAAATTC-AATGATTGGTTCTGCCAACCAGATCAGATAAC
1669629 TCAAAGAACACTTCCAG-A-A-G-TATTGGCAAATTCATCTTCCAAATTCAATGAT
130 TCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGAT
1669681 TAGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
1 TAGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
1669737 GCAAATTCAT
Statistics
Matches: 225, Mismatches: 6, Indels: 15
0.91 0.02 0.06
Matches are distributed among these distances:
177 86 0.38
178 1 0.00
179 1 0.00
180 1 0.00
181 30 0.13
182 26 0.12
183 3 0.01
186 2 0.01
187 56 0.25
188 19 0.08
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (185 bp):
TAGTTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTT
ATTTCTACTATGAGCAAATATCTTCTAAATTCAATGATTGGTTCTGCCAACCAGATCAGATAACT
CAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGAT
Found at i:1681784 original size:17 final size:18
Alignment explanation
Indices: 1681748--1681798 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
1681738 AAATACTAGC
*
1681748 AAATAAA-ACAAAACATAT
1 AAATAAATATAAAA-ATAT
*
1681766 AAAT-ATTATAAAAATAT
1 AAATAAATATAAAAATAT
*
1681783 AAGTAAATATAAAAAT
1 AAATAAATATAAAAAT
1681799 TTTAAAAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 8 0.30
18 19 0.70
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (18 bp):
AAATAAATATAAAAATAT
Found at i:1683686 original size:16 final size:16
Alignment explanation
Indices: 1683661--1683709 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
1683651 GGACGTGGCA
1683661 GCGG-TGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
1683676 GCGGCTGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
1683692 GCGGCTGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
1683708 GC
1 GC
1683710 AGCTAGGGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 4 0.12
16 29 0.88
ACGTcount: A:0.18, C:0.18, G:0.57, T:0.06
Consensus pattern (16 bp):
GCGGCTGGAGGCAGAG
Found at i:1683832 original size:9 final size:10
Alignment explanation
Indices: 1683799--1683837 Score: 53
Period size: 9 Copynumber: 3.8 Consensus size: 10
1683789 TGGGCTTGTA
1683799 ATTTAATATT
1 ATTTAATATT
1683809 ATTTATATATGT
1 ATTTA-ATAT-T
1683821 ATTTAATA-T
1 ATTTAATATT
1683830 ATTTAATA
1 ATTTAATA
1683838 ATAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.33
10 5 0.19
11 7 0.26
12 6 0.22
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:1683841 original size:3 final size:3
Alignment explanation
Indices: 1683833--1683896 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
1683823 TTAATATATT
* *
1683833 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1683881 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
1683897 CAATTAATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1688133 original size:702 final size:700
Alignment explanation
Indices: 1686680--1688088 Score: 2036
Period size: 702 Copynumber: 2.0 Consensus size: 700
1686670 TCGAGGTATA
* * * ** * * *
1686680 TAAAGAATCGAACATCCTTATTCTCATTAAAGATTGGTAAAATAAATAATTAATTATACTTGCTT
1 TAAATAATCGAACATCCATATGCAAATTAAATATTGGTAAAATAATTAATTAATTATACTTGCTG
* * *
1686745 GATATATGCTTTTAATTTGCTTTATTTTTGCATGTGTTTTTAATGGGTTTTCAAAATAATATCAA
66 GATATATGCTTTTAATTTGCTTTATTTTTGAATGTGTTTTCAATGGGTTTTCAAAATAATAACAA
* * * *
1686810 TCGAATCGATATTGAGAATAGTGATAACTCTTCATTTTGATTGGAGTAATAAACGATTTCTTTAA
131 TCGAATCAATATTGAGAATAGTGATAACTCTTCATTTCGATTGGAGTAATAAACGACTGCTTTAA
* * * **
1686875 GGCATGAGAGGTCATTTATTCTTGATTGGAAATAATTAGATATTATCGTTTTCACTTGAATCAAT
196 GGCATGAGAGGTCATTTATTCTCGATTGAAAATAAGTAGATATTATCGTTTTCACTCAAATCAAT
*
1686940 ATTGAATTTTGAGACAAAATAGTGACATCTCTTTATTTCAATTAGGGAAATAAATGACTAGTTTA
261 ATTGAATTTTGAGACAAAATAGTGACATCTCTTCATTTCAATTAGGGAAATAAATGACTAGTTTA
* * * * * *
1687005 AGGCATGAATGGTTTTTTATTCTCAATTGAAAATAATTAGATATTATCTTTTTCTCTTTTAAAAT
326 AGGCATGAAAGGTTATTTAGTATCAATTGAAAATAATTAGATATTATCGTTTTCTCTCTTAAAAT
* *
1687070 TATTTTAGGTGTTGTTATTTTGAATTAATAATGAACTTTGGAATAGAATTTTAGTATTTCTTTAT
391 TATTTTAGGTGTTGTAATTTTGAATTAATAATGAACTTTGGAATAGAATTTTAATATTTCTTTAT
* *
1687135 TTCGATTGGAGTAAGAATCGATTACTTTAAGGTATGAGAGGTTGATTATTCTCAATAGGAAATAA
456 TTCGATTGGAGTAAGAATCAATTACTATAAGGTATGAGAGGTTGATTATTCTCAATAGGAAATAA
*
1687200 TTAAATATTATTATGCTTCGTCCTAAAATTAAAAAAAAATTATTTGTAAGGGATCTTAAATTAAA
521 TTAAATATTATTATGCTTCATCCTAAAATTAAAAAAAAATTATTTGTAAGGGATCTTAAATTAAA
* * *
1687265 TTAGACTTGAATTCTTAAATTTCATTGCAAAGACAATTAATTAATCGACTAGGTACCGATTTAGG
586 TTAAACTCGAATTCTTAAATTTCATTGCAAAGACAACTAATTAATCGACTAGGTACCGATTTAGG
*
1687330 GCGCTGTGGGGATGCTAACCCTTCCCCACACGTAACCGACTCTCGAGGTATT
651 GCGCTGTGGGGATGCTAACCCTTCCCCACACGTAACCGACTCTCGA-G-ACT
* * ** *
1687382 TAAATAATCGAACATCCTTATTCTCATTAAATATTGGTAAAATAATTAATTAATTATATTTGCTG
1 TAAATAATCGAACATCCATATGCAAATTAAATATTGGTAAAATAATTAATTAATTATACTTGCTG
*
1687447 GATATATGCTTTTAATTTGCTTTATTTTTTAATGTGTTTTCCAATGGGTTTTCAAAATAATAACA
66 GATATATGCTTTTAATTTGCTTTATTTTTGAATGTGTTTT-CAATGGGTTTTCAAAATAATAACA
* * * * *
1687512 CTTGAATCAATATTGAGAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAA-TACTGCTTTT
130 ATCGAATCAATATTGAGAATAGTGATAACTCTTCATTTCGATTGGAGTAATAAACGACTGCTTTA
* *
1687576 AGGCATGAGAGGTCATTTATTCTCGATTGAAAATCAGTATATATTATCGTTTTCACTCAAATCAA
195 AGGCATGAGAGGTCATTTATTCTCGATTGAAAATAAGTAGATATTATCGTTTTCACTCAAATCAA
* ** * * * * * * *
1687641 TATTGAATTTTGATATGAAATAGTGATATTTCTTCATTTCATTTGGGGTAATAAATG-GTTGTTT
260 TATTGAATTTTGAGACAAAATAGTGACATCTCTTCATTTCAATTAGGGAAATAAATGACTAG-TT
* *
1687705 TAAGGCATGAAAGGTTATTTAGTATCTATTGGAAATAATTAGATATTATCGTTTTCTCTCTTAAA
324 TAAGGCATGAAAGGTTATTTAGTATCAATTGAAAATAATTAGATATTATCGTTTTCTCTCTTAAA
* *
1687770 ATTATTTTTGGATGTTGTAATTTTGAATTAATAATGAACTTTGGAGTAGAATTTTAATATTTCTT
389 ATTATTTTAGG-TGTTGTAATTTTGAATTAATAATGAACTTTGGAATAGAATTTTAATATTTCTT
* **
1687835 TATTT-GTATTGGAGTAAGAATCAATTACTATAAGGTATGAGAGGTTGATTCTTCTTGATAGGAA
453 TATTTCG-ATTGGAGTAAGAATCAATTACTATAAGGTATGAGAGGTTGATTATTCTCAATAGGAA
* * * *
1687899 ATAATTAAATATTATTCTGCTTCATCCTAAAATTTTAAAAAATATTATTTGTAGGGGATCTTAAA
517 ATAATTAAATATTATTATGCTTCATCCTAAAA-TTAAAAAAAAATTATTTGTAAGGGATCTTAAA
* *
1687964 TTAAATTAAACTCGAATTCTTAAATTTCATTGCAAAGACAACTAATTAATTGACTAGGTACCGTT
581 TTAAATTAAACTCGAATTCTTAAATTTCATTGCAAAGACAACTAATTAATCGACTAGGTACCGAT
* *
1688029 TTAGGGCGCTGTGGGGGTGCTAATTCCTTCCCCACACGTAACCGACTC-CTGA-ACT
646 TTAGGGCGCTGTGGGGATGCTAA-CCCTTCCCCACACGTAACCGACTCTC-GAGACT
1688084 TAAAT
1 TAAAT
1688089 TTTGATAACG
Statistics
Matches: 634, Mismatches: 66, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
701 2 0.00
702 287 0.45
703 208 0.33
704 112 0.18
705 25 0.04
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.40
Consensus pattern (700 bp):
TAAATAATCGAACATCCATATGCAAATTAAATATTGGTAAAATAATTAATTAATTATACTTGCTG
GATATATGCTTTTAATTTGCTTTATTTTTGAATGTGTTTTCAATGGGTTTTCAAAATAATAACAA
TCGAATCAATATTGAGAATAGTGATAACTCTTCATTTCGATTGGAGTAATAAACGACTGCTTTAA
GGCATGAGAGGTCATTTATTCTCGATTGAAAATAAGTAGATATTATCGTTTTCACTCAAATCAAT
ATTGAATTTTGAGACAAAATAGTGACATCTCTTCATTTCAATTAGGGAAATAAATGACTAGTTTA
AGGCATGAAAGGTTATTTAGTATCAATTGAAAATAATTAGATATTATCGTTTTCTCTCTTAAAAT
TATTTTAGGTGTTGTAATTTTGAATTAATAATGAACTTTGGAATAGAATTTTAATATTTCTTTAT
TTCGATTGGAGTAAGAATCAATTACTATAAGGTATGAGAGGTTGATTATTCTCAATAGGAAATAA
TTAAATATTATTATGCTTCATCCTAAAATTAAAAAAAAATTATTTGTAAGGGATCTTAAATTAAA
TTAAACTCGAATTCTTAAATTTCATTGCAAAGACAACTAATTAATCGACTAGGTACCGATTTAGG
GCGCTGTGGGGATGCTAACCCTTCCCCACACGTAACCGACTCTCGAGACT
Found at i:1695575 original size:135 final size:134
Alignment explanation
Indices: 1695418--1696534 Score: 1305
Period size: 135 Copynumber: 8.3 Consensus size: 134
1695408 ACGAATCAAA
* * * * * * *
1695418 CTCGATTCAATCTTCTCTGAAGAACAGCGGAATAAATCAAGATTTCCATATATGATTTCCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
* * * * * **
1695483 AGAAACAGAGGAACATATCCCTATTTTTTCCAGATTTGTTATTCATTGAGTAGCAGTGGAACAAG
66 AGAAGCAGAGGAACAAATCCCT-CTCTTTCCAGATTTGATATTCCCTGAGTAGCAGTGGAACAAG
*
1695548 TTTAC
130 TCTAC
* * * *
1695553 CTCGATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACATTTCCGGATTTTATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
* * **
1695618 AGAAGCAGCGGAACAAATCCCCTCTCTTTCCAGATTTGATATTCCCT-AATAATAGTGGAACAAG
66 AGAAGCAGAGGAACAAAT-CCCTCTCTTTCCAGATTTGATATTCCCTGAGTAGCAGTGGAACAAG
1695682 TCTAC
130 TCTAC
* * * * * * *
1695687 CTAGATTCAATATTCCTTGAAGAACAGTGTAATGAATCAACAATTCCATATTTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
* * * * *
1695752 ATAAGCA-ATGGAATAAATCCCCTCTCTTTCCATATTTGATCTTCCCTAAGTAGCAGTGGAACAA
66 AGAAGCAGA-GGAACAAAT-CCCTCTCTTTCCAGATTTGATATTCCCTGAGTAGCAGTGGAACAA
1695816 GTCTAC
129 GTCTAC
* * * *
1695822 CTCGATTCAATCTTCCCTGAAGAACAGTGTAATGAATCAACATTTCTAGATCTGATTTTACCTTA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
** * * *
1695887 AGAAG-ATGCCGAACAAATTTCCC-CTCTTTCTAGATTTGATCTTCCCTGAGTAGTAGTGGAACA
66 AGAAGCA-GAGGAACAAA--TCCCTCTCTTTCCAGATTTGATATTCCCTGAGTAGCAGTGGAACA
*
1695950 ATTCTAC
128 AGTCTAC
* *
1695957 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTTCATATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
* * * * *
1696022 AGAAGTA-ATGAAACAGATCCCATCTCTTTCCAGATTTGATATTCCATGAGTAGCAGTGAAACAA
66 AGAAGCAGA-GGAACAAATCCC-TCTCTTTCCAGATTTGATATTCCCTGAGTAGCAGTGGAACAA
1696086 GTCTAC
129 GTCTAC
* *
1696092 CTCGATTCAATCTTCCCTGAAGAACAGTTGAATGAATCAACATTTTCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
** * * * * *
1696157 AGAAGTTGTGGAACAGATCCCCTCTCTTTCCAGATTTGATTTTCTCTGGGTAGCAGTGGAACAAG
66 AGAAGCAGAGGAACAAAT-CCCTCTCTTTCCAGATTTGATATTCCCTGAGTAGCAGTGGAACAAG
1696222 TCTAC
130 TCTAC
* * * *
1696227 CTAGATTTAATCTTCCCTGAAGAATAGTGGAATGAATCAACATTTCTAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
* ** * * *
1696292 AGAAGCAGTGGAACAAATCTTATCTCTTTCCAAATTTGATCTTCCCTGAGTAGCAGTGGAATAAG
66 AGAAGCAGAGGAACAAATC-CCTCTCTTTCCAGATTTGATATTCCCTGAGTAGCAGTGGAACAAG
1696357 TCTAC
130 TCTAC
* *
1696362 CTCGATCCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTAATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
* * * * * * * *
1696427 AGAAACAGCA-GAATAGATCCCTCT-TTTTCAAATTTGATCA-TCCCTAAGGAACAGTGGAACAA
66 AGAAGCAG-AGGAACAAATCCCTCTCTTTCCAGATTTGAT-ATTCCCTGAGTAGCAGTGGAACAA
*
1696489 ATCTAC
129 GTCTAC
* *
1696495 CTCGATTTAATCTTCCCTTAAGAACAGTGGAATGAATCAA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAA
1696535 TGTTTCTCGA
Statistics
Matches: 847, Mismatches: 119, Indels: 34
0.85 0.12 0.03
Matches are distributed among these distances:
133 77 0.09
134 122 0.14
135 636 0.75
136 11 0.01
137 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (134 bp):
CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
AGAAGCAGAGGAACAAATCCCTCTCTTTCCAGATTTGATATTCCCTGAGTAGCAGTGGAACAAGT
CTAC
Found at i:1696430 original size:45 final size:45
Alignment explanation
Indices: 1696229--1696430 Score: 128
Period size: 45 Copynumber: 4.5 Consensus size: 45
1696219 AAGTCTACCT
* * * *
1696229 AGATTTAATCTTCCCTGAAGAATAGTGGAATGAATCAACATTTCT
1 AGATCTAATCTTCCCTCAAGAACAGTGGAATGAATCAACATTTCC
* * ** * *
1696274 AGATCTGATTTTCCCTCAAGAAGCAGTGGAACAAATCTTATCTCTTTCC
1 AGATCTAATCTTCCCTCAAGAA-CAGTGGAATGAATC--AAC-ATTTCC
* * * * * * *
1696323 AAATTTGATCTTCCCT-GAGTAGCAGTGGAAT-AAGTCTAC--CT-C
1 AGATCTAATCTTCCCTCAAG-AACAGTGGAATGAA-TCAACATTTCC
* *
1696365 -GATCCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCC
1 AGATCTAATCTTCCCTCAAGAACAGTGGAATGAATCAACATTTCC
*
1696409 AGATCTAATTTTCCCTCAAGAA
1 AGATCTAATCTTCCCTCAAGAA
1696431 ACAGCAGAAT
Statistics
Matches: 115, Mismatches: 30, Indels: 24
0.68 0.18 0.14
Matches are distributed among these distances:
41 25 0.22
42 5 0.04
43 2 0.02
44 1 0.01
45 36 0.31
46 12 0.10
47 2 0.02
48 14 0.12
49 18 0.16
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (45 bp):
AGATCTAATCTTCCCTCAAGAACAGTGGAATGAATCAACATTTCC
Found at i:1696747 original size:13 final size:13
Alignment explanation
Indices: 1696710--1696747 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1696700 CCTGATGTTT
*
1696710 TTATTATTATTAA
1 TTATTATTATTTA
*
1696723 TTATAATTATTTA
1 TTATTATTATTTA
1696736 TTATTATTATTT
1 TTATTATTATTT
1696748 TTTAGGCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTATTATTTA
Found at i:1698498 original size:22 final size:22
Alignment explanation
Indices: 1698473--1698533 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
1698463 GTGGAATTTT
1698473 TCCCGAAGGACCTATGTATATG
1 TCCCGAAGGACCTATGTATATG
* * *
1698495 TCCCGAATGACCTCTGTATTTG
1 TCCCGAAGGACCTATGTATATG
1698517 TCCCGAAGGACCTATGT
1 TCCCGAAGGACCTATGT
1698534 GTAACCCTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (22 bp):
TCCCGAAGGACCTATGTATATG
Found at i:1702496 original size:32 final size:34
Alignment explanation
Indices: 1702460--1702530 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
1702450 CCTTACAAAC
*
1702460 TCCCTAG-TTTTTC-CGGG-TTAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGATT-AACTAGAACCTT
*
1702492 TCCCTAGCTTTTACACGGGATTATCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATTAACTAGAACCTT
1702526 TCCCT
1 TCCCT
1702531 TTTATAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 20 0.59
35 2 0.06
ACGTcount: A:0.21, C:0.28, G:0.14, T:0.37
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATTAACTAGAACCTT
Found at i:1702768 original size:20 final size:22
Alignment explanation
Indices: 1702743--1702782 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1702733 TGTTGTATAT
1702743 AGTCG-TTGGGGATG-TTTTGG
1 AGTCGTTTGGGGATGATTTTGG
1702763 AGTCGTTTGGGGATGATTTT
1 AGTCGTTTGGGGATGATTTT
1702783 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.05, G:0.40, T:0.42
Consensus pattern (22 bp):
AGTCGTTTGGGGATGATTTTGG
Found at i:1702925 original size:20 final size:20
Alignment explanation
Indices: 1702902--1702968 Score: 98
Period size: 20 Copynumber: 3.3 Consensus size: 20
1702892 TCGTGCATGC
1702902 ATGCACAGCAGGATGCATCG
1 ATGCACAGCAGGATGCATCG
**
1702922 ATGCACAGCCTTGATGCATCG
1 ATGCACAG-CAGGATGCATCG
*
1702943 ATGCACAGAAGGATGCATCG
1 ATGCACAGCAGGATGCATCG
1702963 ATGCAC
1 ATGCAC
1702969 TAATTGCATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
20 23 0.56
21 18 0.44
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (20 bp):
ATGCACAGCAGGATGCATCG
Found at i:1702931 original size:41 final size:41
Alignment explanation
Indices: 1702886--1702968 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 41
1702876 CTAGTCGTTG
*
1702886 CAGCCTTCG-TGCAT-GCATGCACAGCAGGATGCATCGATGCA
1 CAGCCTT-GATGCATCG-ATGCACAGAAGGATGCATCGATGCA
1702927 CAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
1702968 C
1 C
1702969 TAATTGCATT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
40 1 0.03
41 37 0.95
42 1 0.03
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.19
Consensus pattern (41 bp):
CAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
Found at i:1703016 original size:21 final size:21
Alignment explanation
Indices: 1702990--1703045 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1702980 GGTGTTTGAG
1702990 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
*
1703011 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCAGGGA
1703032 TGCATGGATGCACT
1 TGCATGGATGCACT
1703046 TTGACACCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.21, C:0.20, G:0.38, T:0.21
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:1703148 original size:29 final size:29
Alignment explanation
Indices: 1703126--1703183 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
1703116 AAACTTTGAA
1703126 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
*
1703155 TAAATTCAATTCAAGTCTAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
1703184 TGCCTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 13 0.50
31 2 0.08
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:1703177 original size:30 final size:30
Alignment explanation
Indices: 1703126--1703185 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
1703116 AAACTTTGAA
1703126 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
*
1703155 TAAATTCAATTCAAGTCTAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
1703186 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:1704455 original size:19 final size:20
Alignment explanation
Indices: 1704412--1704459 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1704402 TCTAAATCCT
*
1704412 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1704432 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1704451 TTTTCAAAA
1 TTTTCAAAA
1704460 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1705790 original size:41 final size:41
Alignment explanation
Indices: 1705745--1705825 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
1705735 TAGCCGTTGC
* * *
1705745 AGCCTTCG-TGCATGGATTCACAGCAGGATGCATCGATGCAT
1 AGCCTT-GATGCATCGATGCACAGAAGGATGCATCGATGCAT
*
1705786 AGCCTTGATGCATCGATGCACAGAAGGATTCATCGATGCA
1 AGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
1705826 CTAATTGCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 1 0.03
41 34 0.97
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.23
Consensus pattern (41 bp):
AGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCAT
Found at i:1705869 original size:13 final size:13
Alignment explanation
Indices: 1705848--1705906 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
1705838 AGTTTTTGAG
*
1705848 TGCATGGATGCAC
1 TGCAGGGATGCAC
1705861 TGCAGGGATGCA-
1 TGCAGGGATGCAC
1705873 T----GGATGCAC
1 TGCAGGGATGCAC
*
1705882 TGCAGGGGTGCAC
1 TGCAGGGATGCAC
*
1705895 TGCAGGGGTGCA
1 TGCAGGGATGCA
1705907 TGGATGCACT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 7 0.18
9 1 0.03
12 1 0.03
13 30 0.77
ACGTcount: A:0.20, C:0.20, G:0.41, T:0.19
Consensus pattern (13 bp):
TGCAGGGATGCAC
Found at i:1705874 original size:21 final size:21
Alignment explanation
Indices: 1705848--1705893 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1705838 AGTTTTTGAG
1705848 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
*
1705869 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCAGGGA
1705890 TGCA
1 TGCA
1705894 CTGCAGGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.39, T:0.20
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:1706017 original size:29 final size:29
Alignment explanation
Indices: 1705985--1706047 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
1705975 GAAACCTTTT
1705985 AAAACTTTGAATAAATTCAATT-AAGTCCAAA
1 AAAACTTTG--TAAATTCAATTCAAGTCC-AA
*
1706016 AAAATTTTGTAAATTCAATTCAAGTCCAA
1 AAAACTTTGTAAATTCAATTCAAGTCCAA
1706045 AAA
1 AAA
1706048 CCATTTTGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 16 0.53
30 6 0.20
31 8 0.27
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (29 bp):
AAAACTTTGTAAATTCAATTCAAGTCCAA
Found at i:1708499 original size:3 final size:3
Alignment explanation
Indices: 1708491--1708584 Score: 188
Period size: 3 Copynumber: 31.3 Consensus size: 3
1708481 CCGATCCCTT
1708491 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1708539 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1708585 GATCATGATC
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 91 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1708642 original size:40 final size:41
Alignment explanation
Indices: 1708598--1708677 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 41
1708588 CATGATCATG
1708598 ATCATCATCATTAATTATTATTTG-TTATTTACATTATTAT
1 ATCATCATCATTAATTATTATTTGTTTATTTACATTATTAT
1708638 ATCATCATCATTAATTATTATTTGTTTATTTACATTATTA
1 ATCATCATCATTAATTATTATTTGTTTATTTACATTATTA
1708678 CTAATCAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
40 24 0.62
41 15 0.38
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.55
Consensus pattern (41 bp):
ATCATCATCATTAATTATTATTTGTTTATTTACATTATTAT
Found at i:1716148 original size:23 final size:23
Alignment explanation
Indices: 1716086--1716173 Score: 94
Period size: 23 Copynumber: 3.9 Consensus size: 23
1716076 CAGCTCGTAA
1716086 TTTGCACCGAAGTGCCACATA--
1 TTTGCACCGAAGTGCCACATAGG
* *
1716107 TTTGTC-CC-AAATGAACACATAGG
1 TTTG-CACCGAAGTG-CCACATAGG
*
1716130 TTTGCACTGAAGTGCCACATAGG
1 TTTGCACCGAAGTGCCACATAGG
*
1716153 TTTGCACCGAAGTGCGACATA
1 TTTGCACCGAAGTGCCACATA
1716174 TTTGTTCCGA
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
20 4 0.07
21 12 0.22
22 2 0.04
23 32 0.59
24 4 0.07
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.25
Consensus pattern (23 bp):
TTTGCACCGAAGTGCCACATAGG
Found at i:1716417 original size:14 final size:14
Alignment explanation
Indices: 1716400--1716429 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1716390 ATAATCATAA
*
1716400 AATATAACTTGTAT
1 AATATAACTTGAAT
1716414 AATATAACTTGAAT
1 AATATAACTTGAAT
1716428 AA
1 AA
1716430 AACATTGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (14 bp):
AATATAACTTGAAT
Found at i:1722096 original size:23 final size:23
Alignment explanation
Indices: 1722028--1722096 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
1722018 TAATTAATAA
* * *
1722028 GATGTGAATATTATGCATTAATA
1 GATGAGAATAATATGCATTAATG
** * *
1722051 GACAAGTATACTATGCATTAATG
1 GATGAGAATAATATGCATTAATG
1722074 GATGAGAATAATATGCATTAATG
1 GATGAGAATAATATGCATTAATG
1722097 ATTCCTTAAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (23 bp):
GATGAGAATAATATGCATTAATG
Found at i:1734321 original size:19 final size:19
Alignment explanation
Indices: 1734297--1734364 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 19
1734287 CGACAAATAC
1734297 ACCAAATTAACATACTAAA
1 ACCAAATTAACATACTAAA
* * *
1734316 ACCAAAGTAACAATCCAAAAA
1 ACCAAATTAAC-ATAC-TAAA
*
1734337 TCCACCAAATTAACATATTAAA
1 ---ACCAAATTAACATACTAAA
1734359 ACCAAA
1 ACCAAA
1734365 GAACTTAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
19 16 0.43
20 3 0.08
21 3 0.08
22 3 0.08
23 2 0.05
24 10 0.27
ACGTcount: A:0.57, C:0.24, G:0.01, T:0.18
Consensus pattern (19 bp):
ACCAAATTAACATACTAAA
Found at i:1734329 original size:43 final size:43
Alignment explanation
Indices: 1734282--1734365 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
1734272 TTCCAAACTC
* *
1734282 ACAATCGACAAATACACCAAATTAACATACTAAAACCAAAGTA
1 ACAATCCAAAAATACACCAAATTAACATACTAAAACCAAAGTA
* *
1734325 ACAATCCAAAAATCCACCAAATTAACATATTAAAACCAAAG
1 ACAATCCAAAAATACACCAAATTAACATACTAAAACCAAAG
1734366 AACTTAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.56, C:0.24, G:0.04, T:0.17
Consensus pattern (43 bp):
ACAATCCAAAAATACACCAAATTAACATACTAAAACCAAAGTA
Found at i:1734496 original size:28 final size:28
Alignment explanation
Indices: 1734464--1734523 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
1734454 TCACAATCGA
*
1734464 CAAATACACCAAATTAACATATTAAAAC
1 CAAATACACCAAACTAACATATTAAAAC
*
1734492 CAAATCCACCAAACTAACATATTAAAAC
1 CAAATACACCAAACTAACATATTAAAAC
1734520 CAAA
1 CAAA
1734524 GTAACAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.57, C:0.25, G:0.00, T:0.18
Consensus pattern (28 bp):
CAAATACACCAAACTAACATATTAAAAC
Found at i:1734806 original size:17 final size:17
Alignment explanation
Indices: 1734784--1734817 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1734774 GAATAATATA
1734784 GAACTAAATCAATTAAT
1 GAACTAAATCAATTAAT
1734801 GAACTAAATCAATTAAT
1 GAACTAAATCAATTAAT
1734818 ATGCTTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (17 bp):
GAACTAAATCAATTAAT
Found at i:1737580 original size:7 final size:7
Alignment explanation
Indices: 1737568--1737595 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1737558 GATTTGTGGT
1737568 TTTGAGA
1 TTTGAGA
1737575 TTTGAGA
1 TTTGAGA
1737582 TTTGAGA
1 TTTGAGA
1737589 TTTGAGA
1 TTTGAGA
1737596 GAAAAGAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (7 bp):
TTTGAGA
Found at i:1750163 original size:16 final size:17
Alignment explanation
Indices: 1750137--1750169 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1750127 AACGATATAC
1750137 GTGATTACATGTAATAT
1 GTGATTACATGTAATAT
*
1750154 GTGA-TACATGTTATAT
1 GTGATTACATGTAATAT
1750170 CATGATATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.42
Consensus pattern (17 bp):
GTGATTACATGTAATAT
Found at i:1751169 original size:23 final size:23
Alignment explanation
Indices: 1751115--1751174 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1751105 CACCACAACT
*
1751115 CATATAATTGCACCGAAGTCCCA
1 CATAGAATTGCACCGAAGTCCCA
* * * *
1751138 CATATAATTGCACCGGAGTGCCG
1 CATAGAATTGCACCGAAGTCCCA
*
1751161 CGTAGAATTGCACC
1 CATAGAATTGCACC
1751175 ATAGTGCCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (23 bp):
CATAGAATTGCACCGAAGTCCCA
Found at i:1751373 original size:105 final size:103
Alignment explanation
Indices: 1751199--1751418 Score: 359
Period size: 105 Copynumber: 2.1 Consensus size: 103
1751189 TAATGTCCAT
* * *
1751199 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
1751264 GACTTCACACATGTTCCAAAGAATATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAG-A-ATACATATATATCCCG
* *
1751304 AATGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1751369 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
*
1751407 AAGGACAACATA
1 AAGGACCACATA
1751419 GACCCTCGAC
Statistics
Matches: 107, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
103 25 0.23
104 1 0.01
105 81 0.76
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATATCCCG
Found at i:1752273 original size:18 final size:19
Alignment explanation
Indices: 1752226--1752273 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1752216 TATTACTGGG
1752226 ATGCATCGATGCACTACTT
1 ATGCATCGATGCACTACTT
*
1752245 ATACATCGATGCACTA-TT
1 ATGCATCGATGCACTACTT
1752263 -TGCATTCGATG
1 ATGCA-TCGATG
1752274 TATTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 3 0.12
18 8 0.31
19 15 0.58
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (19 bp):
ATGCATCGATGCACTACTT
Found at i:1756886 original size:23 final size:23
Alignment explanation
Indices: 1756860--1756937 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
1756850 CACCACAGCT
1756860 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * *
1756883 CATATAATTGCACCGGAGTACCG
1 CATATAATTGCACCGAAGTGCCA
* * *
1756906 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
1756929 TATAATAAT
1 CAT-ATAAT
1756938 GTCCATAAGG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 39 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:1757115 original size:103 final size:103
Alignment explanation
Indices: 1756944--1757162 Score: 377
Period size: 103 Copynumber: 2.1 Consensus size: 103
1756934 TAATGTCCAT
*
1756944 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGTATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAGGTATCAAGTATGTGTCTCACCA
*
1757009 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
* *
1757047 AAGGACCACATATCATTCCTTAATAATCATATACATATGCCAAGG-ATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATAT-ACAAGGTATCAAGTATGTGTCTCACC
*
1757111 AGACTTCACACATGTTCCAAAGAATACATATATATCCTG
65 AGACTTCACACATGTTCCAAAGAATACATATATATCCCG
1757150 AAGGACCACATAT
1 AAGGACCACATAT
1757163 ACCCTCGACT
Statistics
Matches: 110, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
103 106 0.96
104 4 0.04
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAGGTATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATATCCCG
Found at i:1759019 original size:31 final size:31
Alignment explanation
Indices: 1758981--1759134 Score: 236
Period size: 31 Copynumber: 5.0 Consensus size: 31
1758971 GAGTCGAGGG
1758981 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGA
* *
1759012 TTACCTATGTTTTTCGGGACATATGGATTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGA
*
1759043 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGA
* * *
1759074 TTACCTATGTGCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGA
* *
1759105 TTACCTAGGTTCTTCGGGACTTATGGACTG
1 TTACCTATGTTCTTCGGGACATATGGACTG
1759135 GTCCTTCGGG
Statistics
Matches: 112, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 112 1.00
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGA
Found at i:1759754 original size:21 final size:21
Alignment explanation
Indices: 1759696--1759768 Score: 101
Period size: 21 Copynumber: 3.4 Consensus size: 21
1759686 GGGAGAAATT
* *
1759696 ACTGTAGCAAGGTATCAGTAC
1 ACTGTAGCAGGGTATCGGTAC
1759717 ACTGTAGCAGGGTATCGGTAC
1 ACTGTAGCAGGGTATCGGTAC
*
1759738 ACTGTAGCAGGGTATCGATAC
1 ACTGTAGCAGGGTATCGGTAC
*
1759759 CCTTGTAGCA
1 AC-TGTAGCA
1759769 TTCATGAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
21 40 0.85
22 7 0.15
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAGGGTATCGGTAC
Found at i:1759914 original size:39 final size:39
Alignment explanation
Indices: 1759856--1759939 Score: 150
Period size: 39 Copynumber: 2.2 Consensus size: 39
1759846 TATATTATCG
*
1759856 TATTTTCTTAATATTAGTAAAAGATTTAAAATTGTTCAC
1 TATTTTCTTAATATCAGTAAAAGATTTAAAATTGTTCAC
*
1759895 TATTTTCTTAATATCAGTAAAATATTTAAAATTGTTCAC
1 TATTTTCTTAATATCAGTAAAAGATTTAAAATTGTTCAC
1759934 TATTTT
1 TATTTT
1759940 GTACAAGTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (39 bp):
TATTTTCTTAATATCAGTAAAAGATTTAAAATTGTTCAC
Found at i:1762398 original size:70 final size:69
Alignment explanation
Indices: 1762313--1762491 Score: 232
Period size: 70 Copynumber: 2.6 Consensus size: 69
1762303 TCTAAATTTA
* * **** *
1762313 AAAAAATATTTATTATCTCTTTAAATTAAATATTAGTGGGACAATTATATCCTTTTAAATATTTC
1 AAAAGATATTTATTATCTCTTTAAATTGAATATTA-AAAAACAATTATATCATTTTAAATATTTC
1762378 AAATT
65 AAATT
* *
1762383 AAAAGATATTTATTATCTCTTTAAATGTGAATATTAAAAAATAATTATATCATTTTGAATATTTC
1 AAAAGATATTTATTATCTCTTTAAAT-TGAATATTAAAAAACAATTATATCATTTTAAATATTTC
1762448 AAATT
65 AAATT
* *
1762453 AAAAGATATTTATTATATATTTAAATTTGAATATTAAAA
1 AAAAGATATTTATTATCTCTTTAAA-TTGAATATTAAAA
1762492 GGATATCTAT
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
70 87 0.91
71 9 0.09
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.44
Consensus pattern (69 bp):
AAAAGATATTTATTATCTCTTTAAATTGAATATTAAAAAACAATTATATCATTTTAAATATTTCA
AATT
Found at i:1762421 original size:35 final size:34
Alignment explanation
Indices: 1762380--1762502 Score: 124
Period size: 35 Copynumber: 3.5 Consensus size: 34
1762370 AATATTTCAA
*
1762380 ATTAAAAGATATTTATTATCTCTTTAAATGTGAAT
1 ATTAAAAGATATTTATTATCT-TTTAAATTTGAAT
* * *
1762415 ATTAAAAAATAATTA-TATCATTTTGAATATTTCAA-
1 ATTAAAAGATATTTATTATC-TTTT-AA-ATTTGAAT
*
1762450 ATTAAAAGATATTTATTATATATTTAAATTTGAAT
1 ATTAAAAGATATTTATTATCT-TTTAAATTTGAAT
*
1762485 ATTAAAAGGATATCTATT
1 ATTAAAA-GATATTTATT
1762503 TTGAGTAAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 13
0.77 0.10 0.14
Matches are distributed among these distances:
34 13 0.18
35 39 0.54
36 20 0.28
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (34 bp):
ATTAAAAGATATTTATTATCTTTTAAATTTGAAT
Found at i:1764175 original size:191 final size:191
Alignment explanation
Indices: 1763851--1764229 Score: 742
Period size: 191 Copynumber: 2.0 Consensus size: 191
1763841 TATGTGAGTA
1763851 ATATAATGAAGTATTTATTAAAAGATTTTCAACCATTTGATAATGGTCGTTTTTTGTATACACTA
1 ATATAATGAAGTATTTATTAAAAGATTTTCAACCATTTGATAATGGTCGTTTTTTGTATACACTA
1763916 TATTTGAACCCAAAACATTAAGAAATTATAATAAATCTTTTACCTATTAAGGTTGCTAGTTTCAT
66 TATTTGAACCCAAAACATTAAGAAATTATAATAAATCTTTTACCTATTAAGGTTGCTAGTTTCAT
1763981 ACATGAACATATGAATGATAAAGTTAGTAGAAAATGAAATGCGGTAATGAATAATTCCAGT
131 ACATGAACATATGAATGATAAAGTTAGTAGAAAATGAAATGCGGTAATGAATAATTCCAGT
1764042 ATATAATGAAGTATTTATTAAAAGATTTTCAACCATTTGATAATGGTCGTTTTTTGTATACACTA
1 ATATAATGAAGTATTTATTAAAAGATTTTCAACCATTTGATAATGGTCGTTTTTTGTATACACTA
1764107 TATTTGAACCCAAAACATTAAGAAATTATAATAAATCTTTTACCTATTAAGGTTGCTTAG-TTCA
66 TATTTGAACCCAAAACATTAAGAAATTATAATAAATCTTTTACCTATTAAGGTTGC-TAGTTTCA
1764171 TACATGAACATATGAATGATAAAGTTAGTAGAAAATGAAATGCGGTAATGAATAATTCC
130 TACATGAACATATGAATGATAAAGTTAGTAGAAAATGAAATGCGGTAATGAATAATTCC
1764230 CTATAGATAA
Statistics
Matches: 187, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
191 184 0.98
192 3 0.02
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (191 bp):
ATATAATGAAGTATTTATTAAAAGATTTTCAACCATTTGATAATGGTCGTTTTTTGTATACACTA
TATTTGAACCCAAAACATTAAGAAATTATAATAAATCTTTTACCTATTAAGGTTGCTAGTTTCAT
ACATGAACATATGAATGATAAAGTTAGTAGAAAATGAAATGCGGTAATGAATAATTCCAGT
Found at i:1768418 original size:20 final size:20
Alignment explanation
Indices: 1768393--1768431 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1768383 ACTGAAATAT
* *
1768393 TACTTAATTTTTATTTTAGC
1 TACTTAACTATTATTTTAGC
1768413 TACTTAACTATTATTTTAG
1 TACTTAACTATTATTTTAG
1768432 GTTCTAATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.56
Consensus pattern (20 bp):
TACTTAACTATTATTTTAGC
Found at i:1769368 original size:18 final size:19
Alignment explanation
Indices: 1769337--1769372 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1769327 TATTTTGTTC
1769337 TATTTTGATATTTAAATTT
1 TATTTTGATATTTAAATTT
*
1769356 TATTTT-ATTTTTAAATT
1 TATTTTGATATTTAAATT
1769373 ATATCTAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
TATTTTGATATTTAAATTT
Found at i:1769717 original size:24 final size:25
Alignment explanation
Indices: 1769676--1769726 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 25
1769666 AATATTTATG
1769676 TATTACATATAATAAAAA-ATATAA
1 TATTACATATAATAAAAATATATAA
* * * *
1769700 TATTATATATATTTAAAATATTTAA
1 TATTACATATAATAAAAATATATAA
1769725 TA
1 TA
1769727 CGATGAACTC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TATTACATATAATAAAAATATATAA
Found at i:1781412 original size:127 final size:126
Alignment explanation
Indices: 1781235--1781472 Score: 390
Period size: 127 Copynumber: 1.9 Consensus size: 126
1781225 TTATATAAGT
* *
1781235 TATAAGATTTCGAAGATATAAAATTGTTAAATTTAAAATTAAATAGGACTCTAATTAATTTAATT
1 TATAAGATTTCGAAGAGATAAAATTGTTAAATTTAAAATTAAATAAGACTCTAATTAATTTAATT
1781300 TTGATTAAATAGAATTATAATTATAATTGAAA-TTAATAAAATTATATTTTTTTTCTCTTAG
66 TTGATTAAATAGAATTATAATTA-AATTGAAATTTAATAAAATTATATTTTTTTTCTCTTAG
*
1781361 TATAAGATATT-GAAGAGATAAGATTAGTTAAATTTAAAATTAAATAAGACTCTAATTAATTTAA
1 TATAAGAT-TTCGAAGAGATAAAATT-GTTAAATTTAAAATTAAATAAGACTCTAATTAATTTAA
* *
1781425 TTTTGATTCAATAGAATTATAATTAAATTTAAATTTAATAAAATTATA
64 TTTTGATTAAATAGAATTATAATTAAATTGAAATTTAATAAAATTATA
1781473 AAAAAATATC
Statistics
Matches: 104, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
126 27 0.26
127 77 0.74
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.42
Consensus pattern (126 bp):
TATAAGATTTCGAAGAGATAAAATTGTTAAATTTAAAATTAAATAAGACTCTAATTAATTTAATT
TTGATTAAATAGAATTATAATTAAATTGAAATTTAATAAAATTATATTTTTTTTCTCTTAG
Found at i:1782109 original size:232 final size:233
Alignment explanation
Indices: 1781698--1782140 Score: 642
Period size: 232 Copynumber: 1.9 Consensus size: 233
1781688 TTTCATAACA
*
1781698 TACACAATATAAAATTCTTTAGTTTTACACAAATTTAGAATCGTTGAATGAGTAAAAATATATGG
1 TACACAATATAAAATTCTTTAGTTTTACACAAATTTAGAATCGTTGAATGAGTAAAAATAGATGG
* * * * *
1781763 TTGAGATTGACTCATTGTTTATTTTCTTCTATTGAGTATCTTCTCATTTTCTAATGTTAATCTCA
66 TTGAGATTGACTCATTGTTTATTTTCATCTAGTGAATATCATCTCATTTCCTAATGTTAATCTCA
* * * *
1781828 GCTATCTATTTTCTCTCATCCAATGGTCCTAAATCTGTGTAAGACTAAAAGAATTTTA-CATTGT
131 GCCATCTATTTTCTCTCATCCAACGATCCTAAATCTGTGTAAAACTAAAA-AATTTTATCATTGT
*
1781892 GT-AACATGATCCTATCCCTGTATGGGTTAGGATCCACT
195 GTAAACATGATCATATCCCTGTATGGGTTAGGATCCACT
* * * *
1781930 TACACAATGTAAAATTCTTTAGTTTTACACAGATTTAGAATCGTTGGATGAGTGAAAATAGATGG
1 TACACAATATAAAATTCTTTAGTTTTACACAAATTTAGAATCGTTGAATGAGTAAAAATAGATGG
* * *
1781995 TTGAGATTGACTCATTGTTTTTTTTTCATCTAGTGAATATCATCTCATTTCCTACTGTTAATTTC
66 TTGAGATTGACTCATTG-TTTATTTTCATCTAGTGAATATCATCTCATTTCCTAATGTTAATCTC
** *
1782060 AGCCATCTATTTT-TACTTTTCCAACGATCC-AAATCTGTGTAAAACTAAAAAGTTTTATCATTG
130 AGCCATCTATTTTCT-CTCATCCAACGATCCTAAATCTGTGTAAAACTAAAAAATTTTATCATTG
1782123 TGTAAACATGATCATATC
194 TGTAAACATGATCATATC
1782141 ATTATATATA
Statistics
Matches: 186, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
231 6 0.03
232 105 0.56
233 75 0.40
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (233 bp):
TACACAATATAAAATTCTTTAGTTTTACACAAATTTAGAATCGTTGAATGAGTAAAAATAGATGG
TTGAGATTGACTCATTGTTTATTTTCATCTAGTGAATATCATCTCATTTCCTAATGTTAATCTCA
GCCATCTATTTTCTCTCATCCAACGATCCTAAATCTGTGTAAAACTAAAAAATTTTATCATTGTG
TAAACATGATCATATCCCTGTATGGGTTAGGATCCACT
Found at i:1800493 original size:23 final size:23
Alignment explanation
Indices: 1800460--1800532 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1800450 CAGCTCGTAT
*
1800460 AAATGCACCGAAGTACCATGTAG
1 AAATGCACCGAAGTGCCATGTAG
* **
1800483 AATTGCACCGAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCATGTAG
* *
1800506 AAATACACCGAAGTGCCATATA-
1 AAATGCACCGAAGTGCCATGTAG
1800528 AAATG
1 AAATG
1800533 TTTATAAGGA
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
22 4 0.10
23 36 0.90
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCATGTAG
Found at i:1800589 original size:21 final size:20
Alignment explanation
Indices: 1800574--1800628 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
1800564 AACCATATAC
*
1800574 ATATTCCAAAGGACCAA-AT
1 ATATTCCAAAGGACCAATAA
*
1800593 ATGTGTCTCAAAGGACCACATAA
1 ATAT-TC-CAAAGGACCA-ATAA
1800616 ATATTCCAAAGGA
1 ATATTCCAAAGGA
1800629 TTACATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 3 0.10
20 2 0.07
21 17 0.59
22 3 0.10
23 4 0.14
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.22
Consensus pattern (20 bp):
ATATTCCAAAGGACCAATAA
Found at i:1800649 original size:42 final size:42
Alignment explanation
Indices: 1800565--1800656 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 42
1800555 CTCCTTAAAA
* * * *
1800565 ACCATATACATATTCCAAAGGACCAAATATGTGTCTCAAAGG
1 ACCACATAAATATTCCAAAGGACCAAATATATGTCCCAAAGG
** * *
1800607 ACCACATAAATATTCCAAAGGATTACATATATGTCCCGAAGG
1 ACCACATAAATATTCCAAAGGACCAAATATATGTCCCAAAGG
*
1800649 ACCGCATA
1 ACCACATA
1800657 GACCATCGAC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (42 bp):
ACCACATAAATATTCCAAAGGACCAAATATATGTCCCAAAGG
Found at i:1803345 original size:55 final size:55
Alignment explanation
Indices: 1803261--1803406 Score: 186
Period size: 55 Copynumber: 2.7 Consensus size: 55
1803251 TGTATGAGTG
* * * * *
1803261 TGTATCGGTACACTAAGGAGTGTATCGATACACTTATAAA-ATCTAATGCCATTTA
1 TGTATCGGTACACTGAGGAGTGTATCGATACACTCA-AAACATCGAAAGCAATTTA
* * *
1803316 TGTATTGGTACATTGAGGAGTGTATCGATACACTCAAAACATCGAAAGCAATTTG
1 TGTATCGGTACACTGAGGAGTGTATCGATACACTCAAAACATCGAAAGCAATTTA
* *
1803371 TGTATCGGCACACTGAGGAGTGTATCGATACCCTCA
1 TGTATCGGTACACTGAGGAGTGTATCGATACACTCA
1803407 TTATGAAATG
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
54 3 0.04
55 75 0.96
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (55 bp):
TGTATCGGTACACTGAGGAGTGTATCGATACACTCAAAACATCGAAAGCAATTTA
Found at i:1804548 original size:19 final size:19
Alignment explanation
Indices: 1804524--1804575 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
1804514 GAATGCAATT
*
1804524 AGTGCATCGATGCATAGGG
1 AGTGCATCGATGCATAAGG
1804543 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
1804562 AGTGCATCGATGCA
1 AGTGCATCGATGCA
1804576 CCTTTTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.29, C:0.17, G:0.33, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:1804955 original size:2 final size:2
Alignment explanation
Indices: 1804948--1804995 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1804938 ATGTACATGC
1804948 AT AT AT AT 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 AT AT AT AT
1804990 AT AT AT
1 AT AT AT
1804996 GTTAATGTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1805264 original size:18 final size:18
Alignment explanation
Indices: 1805241--1805313 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
1805231 AGGGATTATC
1805241 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* * *
1805259 AGTGGTTCTTCAGAACAAT
1 AGTGGTCCTTCGGGAC-AT
*
1805278 CAGTGGTCTTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
1805297 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
1805314 AATATTCAGT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
18 29 0.64
19 4 0.09
20 12 0.27
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1806090 original size:22 final size:23
Alignment explanation
Indices: 1806032--1806082 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
1806022 CGGGACAAAT
1806032 ATGTGGCACTTCGGTGCAACTCC
1 ATGTGGCACTTCGGTGCAACTCC
*
1806055 ATGTGGCACTTCGGTGCAA-TCT
1 ATGTGGCACTTCGGTGCAACTCC
1806077 ATGTGG
1 ATGTGG
1806083 TCTTTCGGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (23 bp):
ATGTGGCACTTCGGTGCAACTCC
Found at i:1812293 original size:55 final size:55
Alignment explanation
Indices: 1812204--1812345 Score: 180
Period size: 55 Copynumber: 2.6 Consensus size: 55
1812194 TGTATGAGTG
* * *
1812204 TGTATCGGTACACT-AAGAGTGTATCGATACACTCATAACATCGAATGTC-ATTTA
1 TGTATCGGTACACTGAGGAGTGTATCGATACACTCAAAACATCGAAAG-CAATTTA
* * ** *
1812258 TGTATCGGTACATTGAGGAGTGTATTGATTTACTCAAAACATCGAAAGCAATTTG
1 TGTATCGGTACACTGAGGAGTGTATCGATACACTCAAAACATCGAAAGCAATTTA
*
1812313 TGTATCGGTACACTGAGGAGTGTATCAATACAC
1 TGTATCGGTACACTGAGGAGTGTATCGATACAC
1812346 ACTGTTATGA
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
54 14 0.19
55 59 0.81
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (55 bp):
TGTATCGGTACACTGAGGAGTGTATCGATACACTCAAAACATCGAAAGCAATTTA
Found at i:1812890 original size:21 final size:21
Alignment explanation
Indices: 1812861--1812910 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1812851 AGTCGAGGGT
* *
1812861 TTATTTGGTCCTTCAGGACAA
1 TTATGTGGTCCTCCAGGACAA
*
1812882 TTATGTGGTCCTCCGGGACAA
1 TTATGTGGTCCTCCAGGACAA
*
1812903 ATATGTGG
1 TTATGTGG
1812911 CACTTCGGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (21 bp):
TTATGTGGTCCTCCAGGACAA
Found at i:1818617 original size:23 final size:23
Alignment explanation
Indices: 1818591--1818651 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
1818581 CTCGTATAAA
*
1818591 TGCACCGAAGTGTCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
1818614 TGCACCGAAGTGCCGCGTAGAAA
1 TGCACCGAAGTGCCACGTAGAAT
**
1818637 TGGGCCGAAGTGCCA
1 TGCACCGAAGTGCCA
1818652 TATAAAATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.28, C:0.25, G:0.31, T:0.16
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1820458 original size:11 final size:10
Alignment explanation
Indices: 1820441--1820487 Score: 62
Period size: 9 Copynumber: 4.9 Consensus size: 10
1820431 ATTTTTTTTT
*
1820441 CAAAAAAAGG
1 CAAAAAAAAG
1820451 CAAAAAAAA-
1 CAAAAAAAAG
1820460 CAAAAAAAAG
1 CAAAAAAAAG
*
1820470 CCAAAAAAA-
1 CAAAAAAAAG
1820479 CAAAAAAAA
1 CAAAAAAAA
1820488 AAGCCAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
9 17 0.52
10 16 0.48
ACGTcount: A:0.81, C:0.13, G:0.06, T:0.00
Consensus pattern (10 bp):
CAAAAAAAAG
Found at i:1820467 original size:20 final size:21
Alignment explanation
Indices: 1820443--1820498 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
1820433 TTTTTTTTCA
* *
1820443 AAAAAAGGCAAAAAAA-ACAA
1 AAAAAAGCCAAAAAAACAAAA
1820463 AAAAAAGCCAAAAAAACAAAA
1 AAAAAAGCCAAAAAAACAAAA
1820484 AAAAAAGCCAAAAAA
1 AAAAAAGCCAAAAAA
1820499 GCCAAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.80, C:0.12, G:0.07, T:0.00
Consensus pattern (21 bp):
AAAAAAGCCAAAAAAACAAAA
Found at i:1820477 original size:30 final size:28
Alignment explanation
Indices: 1820441--1820505 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 28
1820431 ATTTTTTTTT
1820441 CAAAAAAAGGCAAAAAAAACAA-AAAAAAGC
1 CAAAAAAA--CAAAAAAAA-AACAAAAAAGC
1820471 CAAAAAAACAAAAAAAAAAGCCAAAAAAGC
1 CAAAAAAACAAAAAAAAAA--CAAAAAAGC
1820501 CAAAA
1 CAAAA
1820506 TTTCAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
27 2 0.06
28 9 0.28
30 21 0.66
ACGTcount: A:0.77, C:0.15, G:0.08, T:0.00
Consensus pattern (28 bp):
CAAAAAAACAAAAAAAAAACAAAAAAGC
Found at i:1820505 original size:19 final size:19
Alignment explanation
Indices: 1820441--1820498 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
1820431 ATTTTTTTTT
* *
1820441 CAAAAAAAGGCAAAAAAAA
1 CAAAAAAAAGCCAAAAAAA
1820460 CAAAAAAAAGCCAAAAAAA
1 CAAAAAAAAGCCAAAAAAA
1820479 CAAAAAAAAAAGCCAAAAAA
1 C--AAAAAAAAGCCAAAAAA
1820499 GCCAAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 18 0.51
21 17 0.49
ACGTcount: A:0.79, C:0.14, G:0.07, T:0.00
Consensus pattern (19 bp):
CAAAAAAAAGCCAAAAAAA
Found at i:1820505 original size:21 final size:21
Alignment explanation
Indices: 1820442--1820505 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
1820432 TTTTTTTTTC
* *
1820442 AAAAAAAGGCAAAAAAAAC-A
1 AAAAAAAGCCAAAAAAACCAA
*
1820462 AAAAAAAGCCAAAAAAACAAA
1 AAAAAAAGCCAAAAAAACCAA
*
1820483 AAAAAAAGCCAAAAAAGCCAA
1 AAAAAAAGCCAAAAAAACCAA
1820504 AA
1 AA
1820506 TTTCAAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
20 16 0.42
21 22 0.58
ACGTcount: A:0.78, C:0.14, G:0.08, T:0.00
Consensus pattern (21 bp):
AAAAAAAGCCAAAAAAACCAA
Found at i:1824177 original size:21 final size:23
Alignment explanation
Indices: 1824128--1824177 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
1824118 GGTACAGTAC
*
1824128 CGATAATTCCTTTATAATGGTAT
1 CGATACTTCCTTTATAATGGTAT
1824151 CGATACTTCCTTTAT-ATGGTA-
1 CGATACTTCCTTTATAATGGTAT
1824172 CGATAC
1 CGATAC
1824178 CCTCCTTGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 6 0.23
22 6 0.23
23 14 0.54
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (23 bp):
CGATACTTCCTTTATAATGGTAT
Found at i:1824183 original size:22 final size:23
Alignment explanation
Indices: 1824135--1824184 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
1824125 TACCGATAAT
*
1824135 TCCTTTATAATGGTATCGATACT
1 TCCTTTATAATGGTATCGATACC
1824158 TCCTTTAT-ATGGTA-CGATACCC
1 TCCTTTATAATGGTATCGATA-CC
1824180 TCCTT
1 TCCTT
1824185 GAGTAGGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 5 0.20
22 12 0.48
23 8 0.32
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (23 bp):
TCCTTTATAATGGTATCGATACC
Found at i:1824863 original size:23 final size:23
Alignment explanation
Indices: 1824808--1824863 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
1824798 CCAAGGTACA
*
1824808 GTACCGATAATTCCTTTATAATG
1 GTACCGATACTTCCTTTATAATG
1824831 GTACCGATACTTCCTTTATAATG
1 GTACCGATACTTCCTTTATAATG
1824854 GTACCGATAC
1 GTACCGATAC
1824864 CCTCCTTGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (23 bp):
GTACCGATACTTCCTTTATAATG
Found at i:1825972 original size:22 final size:23
Alignment explanation
Indices: 1825947--1825990 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1825937 TATATATATC
*
1825947 ATAATTTA-TAAAATAAT-AAAAT
1 ATAAATTATTAAAA-AATCAAAAT
1825969 ATAAATTATTAAAAAATCAAAA
1 ATAAATTATTAAAAAATCAAAA
1825991 ACATTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
ATAAATTATTAAAAAATCAAAAT
Found at i:1827408 original size:27 final size:30
Alignment explanation
Indices: 1827349--1827406 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1827339 TAAAATAAAG
*
1827349 TAAAAATAAAATAATTTTTTATATTTTATT
1 TAAAAATAAAATAATTATTTATATTTTATT
*
1827379 TAAAAATATAAT-ATTATTTAT-TTTTATT
1 TAAAAATAAAATAATTATTTATATTTTATT
1827407 AATTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 7 0.27
29 8 0.31
30 11 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TAAAAATAAAATAATTATTTATATTTTATT
Found at i:1838539 original size:58 final size:56
Alignment explanation
Indices: 1838450--1838560 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 56
1838440 GTTTGGACGG
* *
1838450 TAACCGTTGCTTTTAATAGTAAATCACATCGAAGTATAAATATTTGTGGTGTTTGAAT
1 TAACCGTTGCTTTAAATAGTAAATCAAATCGAAGTATAAATA--TGTGGTGTTTGAAT
*
1838508 TAACTGTTGCTTTAAATAGT-AATCCAAATCGAAGTATAAATATGTGGTGTTTG
1 TAACCGTTGCTTTAAATAGTAAAT-CAAATCGAAGTATAAATATGTGGTGTTTG
1838561 TACTTCTTAC
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
56 11 0.22
57 3 0.06
58 35 0.71
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (56 bp):
TAACCGTTGCTTTAAATAGTAAATCAAATCGAAGTATAAATATGTGGTGTTTGAAT
Found at i:1839158 original size:152 final size:153
Alignment explanation
Indices: 1838875--1839182 Score: 609
Period size: 152 Copynumber: 2.0 Consensus size: 153
1838865 CATGTTAGTT
1838875 TTCTCTCCCTCTATGCCTACTTTTGATAGTGTCAAACTCCAGAAACATTGATGTCATTTTTTTTG
1 TTCTCTCCCTCTATGCCTACTTTTGATAGTGTCAAACTCCAGAAACATTGATGTCATTTTTTTTG
1838940 ATTAGTTGCTGGATATGCCAAAACAAAGCTTATATCAAGCAGCAGAGGATTCGGCAGTATTTTGC
66 ATTAGTTGCTGGATATGCCAAAACAAAGCTTATATCAAGCAGCAGAGGATTCGGCAGTATTTTGC
1839005 ACCATTTAAGCCACTTATACGGA
131 ACCATTTAAGCCACTTATACGGA
1839028 TTCTCT-CCTCTATGCCTACTTTTGATAGTGTCAAACTCCAGAAACATTGATGTCATTTTTTTTG
1 TTCTCTCCCTCTATGCCTACTTTTGATAGTGTCAAACTCCAGAAACATTGATGTCATTTTTTTTG
1839092 ATTAGTTGCTGGATATGCCAAAACAAAGCTTATATCAAGCAGCAGAGGATTCGGCAGTATTTTGC
66 ATTAGTTGCTGGATATGCCAAAACAAAGCTTATATCAAGCAGCAGAGGATTCGGCAGTATTTTGC
1839157 ACCATTTAAGCCACTTATACGGA
131 ACCATTTAAGCCACTTATACGGA
1839180 TTC
1 TTC
1839183 CTTATTATTC
Statistics
Matches: 155, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
152 149 0.96
153 6 0.04
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (153 bp):
TTCTCTCCCTCTATGCCTACTTTTGATAGTGTCAAACTCCAGAAACATTGATGTCATTTTTTTTG
ATTAGTTGCTGGATATGCCAAAACAAAGCTTATATCAAGCAGCAGAGGATTCGGCAGTATTTTGC
ACCATTTAAGCCACTTATACGGA
Found at i:1849809 original size:15 final size:15
Alignment explanation
Indices: 1849791--1849846 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
1849781 TAACCGGTTT
1849791 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
1849806 CGGTTTTTTAAAAAAAC
1 CGG--TTTTAAAAAAAC
* *
1849823 CGGTTATAAAAAAAT
1 CGGTTTTAAAAAAAC
*
1849838 CGATTTTAA
1 CGGTTTTAA
1849847 TATTCCAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
15 20 0.57
17 15 0.43
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:1849816 original size:17 final size:17
Alignment explanation
Indices: 1849794--1849827 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1849784 CCGGTTTCGG
1849794 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
1849811 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
1849828 ATAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:1849835 original size:17 final size:17
Alignment explanation
Indices: 1849798--1849836 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1849788 TTTCGGTTTT
* **
1849798 AAAAAAACCGGTTTTTT
1 AAAAAAACCGGTTATAA
1849815 AAAAAAACCGGTTATAA
1 AAAAAAACCGGTTATAA
1849832 AAAAA
1 AAAAA
1849837 TCGATTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.23
Consensus pattern (17 bp):
AAAAAAACCGGTTATAA
Found at i:1850064 original size:21 final size:21
Alignment explanation
Indices: 1850012--1850068 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
1850002 TTTTACACTT
1850012 AGGGAACCGATTCCCTATGAG
1 AGGGAACCGATTCCCTATGAG
* * *
1850033 AGGAAATCGATTCTCTATGAG
1 AGGGAACCGATTCCCTATGAG
*
1850054 AGGGTACCGATTCCC
1 AGGGAACCGATTCCC
1850069 CCACGCTCCA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (21 bp):
AGGGAACCGATTCCCTATGAG
Found at i:1850285 original size:13 final size:13
Alignment explanation
Indices: 1850264--1850318 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1850254 AAGTTCGATA
*
1850264 AATTCAAATACTT
1 AATTGAAATACTT
1850277 AATTGAAATACTT
1 AATTGAAATACTT
* *
1850290 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
1850304 AATTGAAATACTT
1 AATTGAAATACTT
1850317 AA
1 AA
1850319 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:1850400 original size:32 final size:33
Alignment explanation
Indices: 1850304--1850402 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1850294 AACTCAACAT
* * *
1850304 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1850337 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1850370 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1850402 A
1 A
1850403 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:1850421 original size:21 final size:21
Alignment explanation
Indices: 1850397--1850436 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1850387 ACTTCAAGTT
1850397 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
1850418 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
1850437 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:1852738 original size:24 final size:25
Alignment explanation
Indices: 1852711--1852764 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
1852701 TTAAACCCAG
* *
1852711 ACCGGTTTTTTTTTCCGG-ATAAAA
1 ACCGGTTTTTTTATCCGGTAAAAAA
1852735 ACCGG-TTTTTTATCCGGTAAAAAA
1 ACCGGTTTTTTTATCCGGTAAAAAA
1852759 ACCGGT
1 ACCGGT
1852765 CTAGGTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (25 bp):
ACCGGTTTTTTTATCCGGTAAAAAA
Found at i:1853617 original size:23 final size:22
Alignment explanation
Indices: 1853574--1853645 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 22
1853564 TCTACTTTTT
*
1853574 TTTTCCATTTAGGTGTCTACACTC
1 TTTT-CATTTAAGTGT-TACACTC
1853598 TTTTCATTTAAGTGATTACACTC
1 TTTTCATTTAAGTG-TTACACTC
*
1853621 TTTTCATTTAAGTGCCTACACTC
1 TTTTCATTTAAGTG-TTACACTC
1853644 TT
1 TT
1853646 GTTGGTTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
23 39 0.89
24 5 0.11
ACGTcount: A:0.21, C:0.22, G:0.10, T:0.47
Consensus pattern (22 bp):
TTTTCATTTAAGTGTTACACTC
Found at i:1870030 original size:48 final size:48
Alignment explanation
Indices: 1869975--1870070 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
1869965 GCTGATGACT
1869975 CCGAAGAATGTCAATGCATTTTCAAAATGAACTTATTGATTGAAGAGG
1 CCGAAGAATGTCAATGCATTTTCAAAATGAACTTATTGATTGAAGAGG
1870023 CCGAAGAATGTCAATGCATTTTCAAAATGAACTTATTGATTGAAGAGG
1 CCGAAGAATGTCAATGCATTTTCAAAATGAACTTATTGATTGAAGAGG
1870071 AAAGTGAACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (48 bp):
CCGAAGAATGTCAATGCATTTTCAAAATGAACTTATTGATTGAAGAGG
Found at i:1870994 original size:109 final size:109
Alignment explanation
Indices: 1870855--1871073 Score: 438
Period size: 109 Copynumber: 2.0 Consensus size: 109
1870845 TTGGTAATTT
1870855 GGAAAAAGTTCTTAAAAGATGAGATGAGGATGGCTTGGTTTTGAAATGGGAGAAATGTCACTTGA
1 GGAAAAAGTTCTTAAAAGATGAGATGAGGATGGCTTGGTTTTGAAATGGGAGAAATGTCACTTGA
1870920 TAGTGATTGAGGCATTATATTAGGGCACAAGATATCCCATAAGG
66 TAGTGATTGAGGCATTATATTAGGGCACAAGATATCCCATAAGG
1870964 GGAAAAAGTTCTTAAAAGATGAGATGAGGATGGCTTGGTTTTGAAATGGGAGAAATGTCACTTGA
1 GGAAAAAGTTCTTAAAAGATGAGATGAGGATGGCTTGGTTTTGAAATGGGAGAAATGTCACTTGA
1871029 TAGTGATTGAGGCATTATATTAGGGCACAAGATATCCCATAAGG
66 TAGTGATTGAGGCATTATATTAGGGCACAAGATATCCCATAAGG
1871073 G
1 G
1871074 CATTGTGGTG
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 110 1.00
ACGTcount: A:0.35, C:0.09, G:0.29, T:0.27
Consensus pattern (109 bp):
GGAAAAAGTTCTTAAAAGATGAGATGAGGATGGCTTGGTTTTGAAATGGGAGAAATGTCACTTGA
TAGTGATTGAGGCATTATATTAGGGCACAAGATATCCCATAAGG
Found at i:1878205 original size:23 final size:23
Alignment explanation
Indices: 1878139--1878205 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
1878129 TAATGAAAAA
*
1878139 TAATGTAATTAAT-ATTTTA-TTT
1 TAAT-TAATTTATAATTTTATTTT
*
1878161 TAAATAA-TT-TAATTTTAGATTTT
1 TAATTAATTTATAATTTT--ATTTT
1878184 TAATTAATTTATAATTTTATTT
1 TAATTAATTTATAATTTTATTT
1878206 CGAGTCCTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
19 1 0.03
20 6 0.17
21 3 0.08
22 4 0.11
23 13 0.36
24 2 0.06
25 7 0.19
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (23 bp):
TAATTAATTTATAATTTTATTTT
Found at i:1878551 original size:169 final size:167
Alignment explanation
Indices: 1878232--1878781 Score: 608
Period size: 169 Copynumber: 3.3 Consensus size: 167
1878222 AACCCCTGGC
* *
1878232 ATGTTTGATGGGATGAGACAATATGACATGGCATAGATTCTCTAAAAAAGTTGAAAGCGCTTCTT
1 ATGTTTGATGGGATGAGACAATATGACATGGCATAGATTCTCTGAAAAAGTTGAAAGCGCTTATT
** * * * * *
1878297 GTGGGACT-CGTCTTCCCTTTTTGTCAGAGTTCCTCTGCATGCTTTAGTTAATAATAGGCAAAAA
66 GTGGGA-TGCACCTTCCCTTTTCGTTAGAGTTCCTATGCATTCTTCA-TTAATAATAGGCAAAAA
* * *
1878361 TGATGTTCCCAGCCGGGGAACTATTCACGCCAACCCCTAGT
129 TGATGTTCACAGTC-GGGAACTATTCAC-CCAACCCCTAAT
* * * * *
1878402 ATGTTTGATGGGATAAGACAGTATGACATGGTAGAGATTCTCTGAAAAAGTTGAAAGTGCTT-TT
1 ATGTTTGATGGGATGAGACAATATGACATGGCATAGATTCTCTGAAAAAGTTGAAAGCGCTTATT
* *
1878466 GTGGGATGCACCTTCCCTTTTCGTTAGAGTTCCTATGCATTCTTCGATTAATAATAGGTAGAAAT
66 GTGGGATGCACCTTCCCTTTTCGTTAGAGTTCCTATGCATTCTTC-ATTAATAATAGGCAAAAAT
** * *
1878531 GATGTTCTGAGTCAGGGAACTATTCACCTAAACCCTAAT
130 GATGTTCACAGTC-GGGAACTATTCACCCAACCCCTAAT
* * * * * *
1878570 ATGTTTGATGGGATGAGACAAAATGACATGACATATATTCTCAGAAAAAGTTAAAAGCGATTATT
1 ATGTTTGATGGGATGAGACAATATGACATGGCATAGATTCTCTGAAAAAGTTGAAAGCGCTTATT
* * * * * *
1878635 GTGGGAAGCACCTTCCTTTTTC-TTCTGAGTTTCTTTAG-ATTCTTCATTAAATAATAGGCATAA
66 GTGGGATGCACCTTCCCTTTTCGTT-AGAGTTCCTAT-GCATTCTTCATT-AATAATAGGCAAAA
*
1878698 ATGATGTTCACAGTCGAGGAACTATTCACCTAAACCCCTAAT
128 ATGATGTTCACAGTCG-GGAACTATTCACC-CAACCCCTAAT
* *
1878740 ATGTTTGATGGGATGATA-AAGTATGACATGG-AAAGATTCTCT
1 ATGTTTGATGGGATGAGACAA-TATGACATGGCATAGATTCTCT
1878782 TATCACATCA
Statistics
Matches: 321, Mismatches: 50, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
168 67 0.21
169 162 0.50
170 92 0.29
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (167 bp):
ATGTTTGATGGGATGAGACAATATGACATGGCATAGATTCTCTGAAAAAGTTGAAAGCGCTTATT
GTGGGATGCACCTTCCCTTTTCGTTAGAGTTCCTATGCATTCTTCATTAATAATAGGCAAAAATG
ATGTTCACAGTCGGGAACTATTCACCCAACCCCTAAT
Found at i:1879684 original size:12 final size:12
Alignment explanation
Indices: 1879647--1879715 Score: 68
Period size: 12 Copynumber: 5.8 Consensus size: 12
1879637 TTAATGTAAA
*
1879647 ATTT-AATTTGA
1 ATTTGAATTTGG
*
1879658 ATATGAATTTGG
1 ATTTGAATTTGG
*
1879670 ATTTGAATTTAG
1 ATTTGAATTTGG
*
1879682 ATTTGGATTTGG
1 ATTTGAATTTGG
* *
1879694 ATTTCAATTTGC
1 ATTTGAATTTGG
*
1879706 ATTTAAATTT
1 ATTTGAATTT
1879716 TATTTTGGGT
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
11 3 0.06
12 44 0.94
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.51
Consensus pattern (12 bp):
ATTTGAATTTGG
Found at i:1879703 original size:18 final size:17
Alignment explanation
Indices: 1879652--1879720 Score: 66
Period size: 18 Copynumber: 3.9 Consensus size: 17
1879642 GTAAAATTTA
*
1879652 ATTTGAATATGAATTTGG
1 ATTTGAAT-TTAATTTGG
1879670 ATTTGAATTTAGATTTGG
1 ATTTGAATTTA-ATTTGG
* *
1879688 ATTTGGATTTCAATTTGC
1 ATTTGAATTT-AATTTGG
* *
1879706 ATTTAAATTTTATTT
1 ATTTGAATTTAATTT
1879721 TGGGTAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
17 6 0.14
18 36 0.84
19 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.52
Consensus pattern (17 bp):
ATTTGAATTTAATTTGG
Found at i:1879709 original size:6 final size:6
Alignment explanation
Indices: 1879664--1879697 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1879654 TTGAATATGA
* *
1879664 ATTTGG ATTTGA ATTTAG ATTTGG ATTTGG ATTT
1 ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG ATTT
1879698 CAATTTGCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (6 bp):
ATTTGG
Found at i:1886297 original size:20 final size:20
Alignment explanation
Indices: 1886268--1886320 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
1886258 CGCCTTGAAT
1886268 ATGCATCGATGCACAAGGCC
1 ATGCATCGATGCACAAGGCC
*
1886288 ATGTATCGATGCACAAGGCC
1 ATGCATCGATGCACAAGGCC
1886308 ATGCATCGATGCA
1 ATGCATCGATGCA
1886321 TCCGTCGGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (20 bp):
ATGCATCGATGCACAAGGCC
Found at i:1889093 original size:19 final size:19
Alignment explanation
Indices: 1889069--1889151 Score: 148
Period size: 19 Copynumber: 4.4 Consensus size: 19
1889059 GCATTTGATA
1889069 CATCGATGCACATAACATG
1 CATCGATGCACATAACATG
1889088 CATCGATGCACATAACATG
1 CATCGATGCACATAACATG
*
1889107 CATCAATGCACATAACATG
1 CATCGATGCACATAACATG
*
1889126 CATAGATGCACATAACATG
1 CATCGATGCACATAACATG
1889145 CATCGAT
1 CATCGAT
1889152 ACACTCAGGC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 60 1.00
ACGTcount: A:0.39, C:0.25, G:0.14, T:0.22
Consensus pattern (19 bp):
CATCGATGCACATAACATG
Found at i:1890445 original size:5 final size:5
Alignment explanation
Indices: 1890435--1890459 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1890425 TTAATGCTTC
1890435 TAATG TAATG TAATG TAATG TAATG
1 TAATG TAATG TAATG TAATG TAATG
1890460 CTTGTAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
TAATG
Found at i:1890543 original size:5 final size:5
Alignment explanation
Indices: 1890533--1890578 Score: 56
Period size: 5 Copynumber: 9.2 Consensus size: 5
1890523 TTAATGCTTC
* * **
1890533 TAATG TAATG TAATG TACTC TAATG TCGTG TAATG TAATG TAATG T
1 TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG T
1890579 TGTGTACTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.41
Consensus pattern (5 bp):
TAATG
Found at i:1890576 original size:20 final size:20
Alignment explanation
Indices: 1890531--1890584 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1890521 AGTTAATGCT
** *
1890531 TCTAATGTAATGTAATGTAC
1 TCTAATGTCGTGTAATGTAA
1890551 TCTAATGTCGTGTAATGTAA
1 TCTAATGTCGTGTAATGTAA
* *
1890571 TGTAATGTTGTGTA
1 TCTAATGTCGTGTA
1890585 CTATTCGAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (20 bp):
TCTAATGTCGTGTAATGTAA
Found at i:1890584 original size:10 final size:10
Alignment explanation
Indices: 1890533--1890584 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
1890523 TTAATGCTTC
*
1890533 TAATGTAATG
1 TAATGTAGTG
* *
1890543 TAATGTACTC
1 TAATGTAGTG
*
1890553 TAATGTCGTG
1 TAATGTAGTG
*
1890563 TAATGTAATG
1 TAATGTAGTG
*
1890573 TAATGTTGTG
1 TAATGTAGTG
1890583 TA
1 TA
1890585 CTATTCGAGT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.42
Consensus pattern (10 bp):
TAATGTAGTG
Found at i:1892804 original size:20 final size:21
Alignment explanation
Indices: 1892781--1892828 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 21
1892771 TCATTTCCCT
1892781 AATTAAAATAACAT-TCCACA
1 AATTAAAATAACATATCCACA
* *
1892801 AATT--AATAACATATTCATA
1 AATTAAAATAACATATCCACA
1892820 AATTAAAAT
1 AATTAAAAT
1892829 TAATACAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 8 0.35
19 8 0.35
20 4 0.17
21 3 0.13
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (21 bp):
AATTAAAATAACATATCCACA
Found at i:1892839 original size:25 final size:25
Alignment explanation
Indices: 1892800--1892895 Score: 81
Period size: 25 Copynumber: 3.9 Consensus size: 25
1892790 AACATTCCAC
* *
1892800 AAATTAATAACATATTCATAAATTA
1 AAATTAATAACATATTAAAAAATTA
1892825 AAATTAAT-ACAATATTAAAAAATT-
1 AAATTAATAAC-ATATTAAAAAATTA
* * * *
1892849 ACATTATTTA-TTATTAAAAATATTA
1 AAATTAATAACATATTAAAAA-ATTA
* *
1892874 CAATTAATAAAATATTAAAAAA
1 AAATTAATAACATATTAAAAAA
1892896 CAATTAAAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
23 9 0.16
24 11 0.20
25 27 0.48
26 9 0.16
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.36
Consensus pattern (25 bp):
AAATTAATAACATATTAAAAAATTA
Found at i:1892843 original size:17 final size:17
Alignment explanation
Indices: 1892821--1892893 Score: 55
Period size: 17 Copynumber: 4.4 Consensus size: 17
1892811 ATATTCATAA
1892821 ATTAAAATTAATACAAT
1 ATTAAAATTAATACAAT
*
1892838 ATTAAAA--AATTACATT
1 ATTAAAATTAA-TACAAT
**
1892854 ATTTATTATTAA-A-AAT
1 A-TTAAAATTAATACAAT
* *
1892870 ATTACAATTAATAAAAT
1 ATTAAAATTAATACAAT
1892887 ATTAAAA
1 ATTAAAA
1892894 AACAATTAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
15 10 0.23
16 10 0.23
17 21 0.49
19 2 0.05
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTAAAATTAATACAAT
Found at i:1893055 original size:2 final size:2
Alignment explanation
Indices: 1893048--1893074 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1893038 AGTCTATTTA
1893048 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1893075 ATAATTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1894331 original size:14 final size:15
Alignment explanation
Indices: 1894313--1894345 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1894303 CCTAAATTAT
1894313 TTTTTACATA-AAATA
1 TTTTTA-ATATAAATA
1894328 TTTTTAATATAAATA
1 TTTTTAATATAAATA
1894343 TTT
1 TTT
1894346 AATAAACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTTAATATAAATA
Found at i:1894956 original size:13 final size:13
Alignment explanation
Indices: 1894940--1894974 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1894930 AATTTTTTAT
1894940 ATAAAATTATAAA
1 ATAAAATTATAAA
1894953 ATAAAATTAT-AA
1 ATAAAATTATAAA
1894965 A-AAAATTATA
1 ATAAAATTATA
1894975 TATTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.38
12 3 0.14
13 10 0.48
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAAATTATAAA
Found at i:1896418 original size:2 final size:2
Alignment explanation
Indices: 1896411--1896438 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1896401 TTTGAATTTG
1896411 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
1896439 TAATATTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1896636 original size:37 final size:37
Alignment explanation
Indices: 1896504--1896637 Score: 146
Period size: 38 Copynumber: 3.6 Consensus size: 37
1896494 ATGATAATAT
* * * **
1896504 TATATTATTTAAGGATTTATATTCAATTGAAATTTGAA
1 TATATTATTTATGAATTTATATT-TATTGAAATAAGAA
* *
1896542 TATGTTATTTACGAATTTATATTCTATTGAAATAAGAA
1 TATATTATTTATGAATTTATATT-TATTGAAATAAGAA
*
1896580 TATATTATTTAT-AATTTTATATTTGATT-AAATAAAAA
1 TATATTATTTATGAA-TTTATATTT-ATTGAAATAAGAA
1896617 TATATTATTTATGAATTTATA
1 TATATTATTTATGAATTTATA
1896638 AAATATAAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
37 29 0.35
38 55 0.65
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (37 bp):
TATATTATTTATGAATTTATATTTATTGAAATAAGAA
Done.