Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001444.1 Hibiscus syriacus cultivar Beakdansim tig00002793_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: 2564052
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 12
Found at i:1773651 original size:16 final size:16
Alignment explanation
Indices: 1773630--1773662 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1773620 GTTACTTATG
1773630 TAAAAATATAATAAAT
1 TAAAAATATAATAAAT
*
1773646 TAAAAATATAATTAAT
1 TAAAAATATAATAAAT
1773662 T
1 T
1773663 TATTAACGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAAAATATAATAAAT
Found at i:1775887 original size:20 final size:20
Alignment explanation
Indices: 1775862--1775900 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1775852 TTATAGTATT
1775862 CAAATGATAGGACAAATATA
1 CAAATGATAGGACAAATATA
*
1775882 CAAATGATATGACAAATAT
1 CAAATGATAGGACAAATAT
1775901 GAGGAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.23
Consensus pattern (20 bp):
CAAATGATAGGACAAATATA
Found at i:1779540 original size:18 final size:18
Alignment explanation
Indices: 1779496--1779540 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1779486 TTGTCATTAT
*
1779496 CATCAATAGCGTCACTAG
1 CATCAATATCGTCACTAG
1779514 CATCAATATCGTCACTAG
1 CATCAATATCGTCACTAG
1779532 CATCAATAT
1 CATCAATAT
1779541 TGATATCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.27
Consensus pattern (18 bp):
CATCAATATCGTCACTAG
Found at i:1783172 original size:20 final size:20
Alignment explanation
Indices: 1783147--1783194 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
1783137 TTTGTTTACT
1783147 GTTGAATGTAACCATTCAAC
1 GTTGAATGTAACCATTCAAC
1783167 GTTGAATGTAACCATTCAAC
1 GTTGAATGTAACCATTCAAC
1783187 GTTGAATG
1 GTTGAATG
1783195 CTGAACCGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (20 bp):
GTTGAATGTAACCATTCAAC
Found at i:1783263 original size:23 final size:23
Alignment explanation
Indices: 1783233--1783286 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
1783223 ATTCTCACAT
1783233 CTGAATGAAACAACAAAACACTG
1 CTGAATGAAACAACAAAACACTG
1783256 CTGAATGAAACAACAAAACACTG
1 CTGAATGAAACAACAAAACACTG
*
1783279 ATGAATGA
1 CTGAATGA
1783287 TTCAGTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.52, C:0.19, G:0.15, T:0.15
Consensus pattern (23 bp):
CTGAATGAAACAACAAAACACTG
Found at i:1786292 original size:27 final size:27
Alignment explanation
Indices: 1786262--1786319 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
1786252 TGAATAGTGT
1786262 CTAAATTTTTTTGAATCATCCGGATGC
1 CTAAATTTTTTTGAATCATCCGGATGC
*
1786289 CTAATTTTTTTTGAATCATCCGGATGC
1 CTAAATTTTTTTGAATCATCCGGATGC
1786316 CTAA
1 CTAA
1786320 CGGTGACAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (27 bp):
CTAAATTTTTTTGAATCATCCGGATGC
Found at i:1786440 original size:20 final size:20
Alignment explanation
Indices: 1786417--1786456 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1786407 TTGAAATTTT
* *
1786417 TATTTTTATTTTTATAAAAA
1 TATTATTATATTTATAAAAA
1786437 TATTATTATATTTATAAAAA
1 TATTATTATATTTATAAAAA
1786457 AACTTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTATTATATTTATAAAAA
Found at i:1791211 original size:266 final size:265
Alignment explanation
Indices: 1790738--1791225 Score: 746
Period size: 266 Copynumber: 1.8 Consensus size: 265
1790728 CAATTTTTTG
* * * * *
1790738 AAAGTAATCTGTATACGTTAGAATGAACTTGACCAATCTTACGTCTCTGTTCAAGATAAGAATTG
1 AAAGTAATATGTAAACATTAGAATGAACCTGACCAATCTTACGTCTCTATTCAAGATAAGAATTG
* * * * * *
1790803 GGCATGAGTTATACAATGCATCTGGATGATTTGAGAGCCAGATTCATCTGTTTAATTCAGCAGTT
66 GCCATGAGTTATACAATGCATCTGGACGATTTGAGAGCCAGATTCATATGTTTAATTAAACACTT
* * *
1790868 TCAGTTGTTTAAAGATAGCAGTTACACATAGTTAATTTCGGGAAATAAAATCATATTTATTTATG
131 TCAGTTGTTTAAAGATAGCAGTTACACAGAGTTAATTTCGGGAAATAAAATCAGATTTATTTATA
*
1790933 ATTTGTGTTGGACGAAAATGGCCCTATTTGCAGAGAGTAACAACTATTTAATTAGCTATATTGAT
196 AGTTGTGTTGGACGAAAATGGCCCTATTTGCAGAGAGTAACAACTATTTAATTAGCTATATTGAT
1790998 TTCTA
261 TTCTA
* * *
1791003 AAAGTAATATGTAAACATTAGAATGAACCTGACCAATTTTACGTCTCTATTGAAGATAATAATTG
1 AAAGTAATATGTAAACATTAGAATGAACCTGACCAATCTTACGTCTCTATTCAAGATAAGAATTG
* *
1791068 AGCCTGTGAGTTATACAATGTATC-GGACGATTTGAGAGCCAGATTCATATGTTTAATTAAACAA
66 -GCC-ATGAGTTATACAATGCATCTGGACGATTTGAGAGCCAGATTCATATGTTTAATTAAAC-A
*
1791132 CTTT-ATTTGTTTAAAGATAGCAGTTACACAGAGTTAATTTCGGGAAATAAAATCAGATTTATTT
128 CTTTCAGTTGTTTAAAGATAGCAGTTACACAGAGTTAATTTCGGGAAATAAAATCAGATTTATTT
1791196 ATAAGTTGTGTTGGACGAAAATGGCCCTAT
193 ATAAGTTGTGTTGGACGAAAATGGCCCTAT
1791226 ATCTAGCCTA
Statistics
Matches: 199, Mismatches: 21, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
265 57 0.29
266 121 0.61
267 21 0.11
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (265 bp):
AAAGTAATATGTAAACATTAGAATGAACCTGACCAATCTTACGTCTCTATTCAAGATAAGAATTG
GCCATGAGTTATACAATGCATCTGGACGATTTGAGAGCCAGATTCATATGTTTAATTAAACACTT
TCAGTTGTTTAAAGATAGCAGTTACACAGAGTTAATTTCGGGAAATAAAATCAGATTTATTTATA
AGTTGTGTTGGACGAAAATGGCCCTATTTGCAGAGAGTAACAACTATTTAATTAGCTATATTGAT
TTCTA
Found at i:1792955 original size:24 final size:24
Alignment explanation
Indices: 1792923--1792970 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1792913 TAGAAACTCA
1792923 ACTTAATGAGAATAAAGCTACCAC
1 ACTTAATGAGAATAAAGCTACCAC
1792947 ACTTAATGAGAATAAAGCTACCAC
1 ACTTAATGAGAATAAAGCTACCAC
1792971 TTCCACTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.21, G:0.12, T:0.21
Consensus pattern (24 bp):
ACTTAATGAGAATAAAGCTACCAC
Found at i:1798129 original size:21 final size:22
Alignment explanation
Indices: 1798093--1798146 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
1798083 CAGAACTCGT
* *
1798093 GGGGGTATCGATTCCC-T-AAA
1 GGGGGAATCGAGTCCCATCAAA
1798113 GGAGGGAATCGAGTCCCATTCAAA
1 GG-GGGAATCGAGTCCCA-TCAAA
1798137 GGGGGAATCG
1 GGGGGAATCG
1798147 GTTCCTCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 2 0.07
21 12 0.43
23 9 0.32
24 5 0.18
ACGTcount: A:0.28, C:0.19, G:0.35, T:0.19
Consensus pattern (22 bp):
GGGGGAATCGAGTCCCATCAAA
Found at i:1798157 original size:23 final size:23
Alignment explanation
Indices: 1798110--1798175 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 23
1798100 TCGATTCCCT
1798110 AAAGGAGGGAATCGAG-TCCCATTC
1 AAAGG-GGGAATCG-GTTCCCATTC
1798134 AAAGGGGGAATCGGTTCCTC-TTC
1 AAAGGGGGAATCGGTTCC-CATTC
* * *
1798157 AAGGGGGGTATCGATTCCC
1 AAAGGGGGAATCGGTTCCC
1798176 TCTGCACTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
22 2 0.05
23 29 0.78
24 6 0.16
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.21
Consensus pattern (23 bp):
AAAGGGGGAATCGGTTCCCATTC
Found at i:1799618 original size:19 final size:19
Alignment explanation
Indices: 1799590--1799627 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1799580 GTGATTTTGA
* *
1799590 AAAATGTGTTGCGATAGTT
1 AAAATATGTTGCGAGAGTT
1799609 AAAATATGTTGCGAGAGTT
1 AAAATATGTTGCGAGAGTT
1799628 TGAAAAACGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.34
Consensus pattern (19 bp):
AAAATATGTTGCGAGAGTT
Found at i:1799640 original size:22 final size:21
Alignment explanation
Indices: 1799585--1799641 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 21
1799575 GCAATGTGAT
*
1799585 TTTGAAAAATGTGTTGCGATAG
1 TTTGAAAAA-GTGTTGCGAGAG
1799607 -TT-AAAATA-TGTTGCGAGAG
1 TTTGAAAA-AGTGTTGCGAGAG
1799626 TTTGAAAAACGTGTTG
1 TTTGAAAAA-GTGTTG
1799642 TTGCAATAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
19 10 0.34
20 7 0.24
21 7 0.24
22 5 0.17
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (21 bp):
TTTGAAAAAGTGTTGCGAGAG
Found at i:1799664 original size:19 final size:19
Alignment explanation
Indices: 1799640--1799676 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1799630 AAAAACGTGT
1799640 TGTTGCAATAGTGAAAAAG
1 TGTTGCAATAGTGAAAAAG
1799659 TGTTGCAATAGTGAAAAA
1 TGTTGCAATAGTGAAAAA
1799677 TCCAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.27
Consensus pattern (19 bp):
TGTTGCAATAGTGAAAAAG
Found at i:1800168 original size:41 final size:41
Alignment explanation
Indices: 1800122--1800213 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 41
1800112 ATCACGTTGT
* *
1800122 ATTGCAATTTTGTATTATCGCATTGCGATAGTCAGAATCGC
1 ATTGCAATTTTGTATTATCACATTACGATAGTCAGAATCGC
* * *
1800163 GTTGCAATTTTGTATTATCACGTTACGATAGTTAGAATCGC
1 ATTGCAATTTTGTATTATCACATTACGATAGTCAGAATCGC
*
1800204 ATTGCGATTT
1 ATTGCAATTT
1800214 ACATAGGTCG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (41 bp):
ATTGCAATTTTGTATTATCACATTACGATAGTCAGAATCGC
Found at i:1800350 original size:21 final size:21
Alignment explanation
Indices: 1800324--1800374 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1800314 ATTTTCCAAA
1800324 ATCGCAACGCAAACTTGGACT
1 ATCGCAACGCAAACTTGGACT
**
1800345 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCAAACTTGGACT
*
1800366 ATTGCAACG
1 ATCGCAACG
1800375 AATTTGGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCAAACTTGGACT
Found at i:1800440 original size:46 final size:46
Alignment explanation
Indices: 1800388--1800481 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
1800378 TTGGAAAATC
*
1800388 GCATTGCGATTTTGTATTATCGCATTGCAATAGTCAGAATCGCGTT
1 GCATTGCGATTTTGTATTATCGCATTACAATAGTCAGAATCGCGTT
* *
1800434 GCATTGCGATTTTGTATTATCGCGTTACGATAGTCAGAATCGCGTT
1 GCATTGCGATTTTGTATTATCGCATTACAATAGTCAGAATCGCGTT
1800480 GC
1 GC
1800482 GATTTACATA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.36
Consensus pattern (46 bp):
GCATTGCGATTTTGTATTATCGCATTACAATAGTCAGAATCGCGTT
Found at i:1800516 original size:20 final size:20
Alignment explanation
Indices: 1800461--1800523 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
1800451 TATCGCGTTA
* *
1800461 CGATAGTCAGAATCGCGTTG
1 CGATAGTCAAAATCGCATTG
* * *
1800481 CGAT-TTACATATTCGCATTG
1 CGATAGT-CAAAATCGCATTG
1800501 CGATAGTCAAAATCGCATTG
1 CGATAGTCAAAATCGCATTG
1800521 CGA
1 CGA
1800524 ATCTGGAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (20 bp):
CGATAGTCAAAATCGCATTG
Found at i:1800533 original size:20 final size:21
Alignment explanation
Indices: 1800493--1800563 Score: 51
Period size: 20 Copynumber: 3.5 Consensus size: 21
1800483 ATTTACATAT
* **
1800493 TCGCATTGCG-ATAGTCAAAA
1 TCGCATTGCGAATACTGGAAA
1800513 TCGCATTGCGAAT-CTGGAAA
1 TCGCATTGCGAATACTGGAAA
* *
1800533 TTG-ATTTGCG-ATACTGGAGA
1 TCGCA-TTGCGAATACTGGAAA
*
1800553 TCGCGTTGCGA
1 TCGCATTGCGA
1800564 TTTAGAGATC
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
19 3 0.08
20 34 0.87
21 2 0.05
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGAATACTGGAAA
Found at i:1805347 original size:21 final size:21
Alignment explanation
Indices: 1805307--1805361 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1805297 GATTCTTGAA
1805307 AATCGCAATGCGATAGTACA-
1 AATCGCAATGCGATAGTACAG
* **
1805327 AATTCGCATTGCGATTTTACAG
1 AA-TCGCAATGCGATAGTACAG
*
1805349 AATCGCAACGCGA
1 AATCGCAATGCGA
1805362 ATATGAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (21 bp):
AATCGCAATGCGATAGTACAG
Found at i:1805443 original size:20 final size:20
Alignment explanation
Indices: 1805349--1805512 Score: 206
Period size: 20 Copynumber: 8.2 Consensus size: 20
1805339 GATTTTACAG
* ** *
1805349 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1805369 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1805389 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1805409 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1805429 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1805449 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1805469 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1805489 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1805509 AATC
1 AATC
1805513 TGTAAATCGC
Statistics
Matches: 127, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
19 2 0.02
20 123 0.97
21 2 0.02
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1805518 original size:28 final size:28
Alignment explanation
Indices: 1805486--1805540 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1805476 ACGCGTATCC
1805486 GTAAATCGCAACGATAATCCGTAAATCT
1 GTAAATCGCAACGATAATCCGTAAATCT
1805514 GTAAATCGCAACGATAATCCGTAAATC
1 GTAAATCGCAACGATAATCCGTAAATC
1805541 GCAACGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.24
Consensus pattern (28 bp):
GTAAATCGCAACGATAATCCGTAAATCT
Found at i:1805537 original size:20 final size:20
Alignment explanation
Indices: 1805509--1805565 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
1805499 ATAATCCGTA
*
1805509 AATCTGTAAATCGCAACGAT
1 AATCTGTAAATCGCAACGAG
*
1805529 AATCCGTAAATCGCAACGAG
1 AATCTGTAAATCGCAACGAG
*
1805549 AATCTGTAAATCACAAC
1 AATCTGTAAATCGCAAC
1805566 ACTGAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.21
Consensus pattern (20 bp):
AATCTGTAAATCGCAACGAG
Found at i:1808620 original size:19 final size:19
Alignment explanation
Indices: 1808551--1808718 Score: 159
Period size: 19 Copynumber: 9.5 Consensus size: 19
1808541 GCAAAGAGAG
1808551 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1808570 ATCCCAA--C---ATGAAAA
1 ATCGCAATGCGAAATG-AAA
1808585 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
*
1808605 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1808624 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1808638 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1808658 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1808677 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
1808691 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1808710 ATCGCAATG
1 ATCGCAATG
1808719 AGATTTTGGT
Statistics
Matches: 122, Mismatches: 9, Indels: 36
0.73 0.05 0.22
Matches are distributed among these distances:
14 23 0.19
15 11 0.09
16 3 0.02
17 6 0.05
18 1 0.01
19 50 0.41
20 25 0.20
21 3 0.02
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1808657 original size:53 final size:53
Alignment explanation
Indices: 1808551--1808718 Score: 268
Period size: 53 Copynumber: 3.2 Consensus size: 53
1808541 GCAAAGAGAG
* *
1808551 ATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAAATCGCAATGCGGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGA-G-AGAATCGCAATGCGGAAATGAAA
*
1808605 ATCGCAATGTGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAA
*
1808658 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAACGC-GAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAA
1808710 ATCGCAATG
1 ATCGCAATG
1808719 AGATTTTGGT
Statistics
Matches: 108, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
52 18 0.17
53 63 0.58
54 26 0.24
55 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAA
Found at i:1808703 original size:33 final size:34
Alignment explanation
Indices: 1808551--1808716 Score: 135
Period size: 33 Copynumber: 4.8 Consensus size: 34
1808541 GCAAAGAGAG
* *
1808551 ATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGATG-AAA
* *
1808585 ATCGCAATGCGGAAATGAAAATCGCAATGTGAAATGAAA
1 ATCGCAACGC-GAAATGAAAATCGCAA--CG--ATGAAA
* * *
1808624 ATCGCAACGAGAGAATCG-CAATGCGGAA--ATGAAA
1 ATCGCAACGCGA-AAT-GAAAAT-CGCAACGATGAAA
* *
1808658 ATCGCAATGCGAAATGAAAATCGCAACGA-GAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGATGAAA
1808691 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
1808717 TGAGATTTTG
Statistics
Matches: 108, Mismatches: 12, Indels: 25
0.74 0.08 0.17
Matches are distributed among these distances:
32 5 0.05
33 34 0.31
34 27 0.25
35 15 0.14
38 2 0.02
39 17 0.16
40 8 0.07
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
ATCGCAACGCGAAATGAAAATCGCAACGATGAAA
Found at i:1808742 original size:19 final size:18
Alignment explanation
Indices: 1808720--1808808 Score: 77
Period size: 19 Copynumber: 5.2 Consensus size: 18
1808710 ATCGCAATGA
1808720 GATTTTGGTTTCGCGTTGC
1 GATTTT-GTTTCGCGTTGC
1808739 GATTTTG--T--CGTTGC
1 GATTTTGTTTCGCGTTGC
1808753 GATTTTGGTTTCGCGTTGC
1 GATTTT-GTTTCGCGTTGC
*
1808772 GATTCT-TTT---GTTGC
1 GATTTTGTTTCGCGTTGC
*
1808786 GATTTTCATTTCGCGTTGC
1 GATTTT-GTTTCGCGTTGC
1808805 GATT
1 GATT
1808809 CTCTCGTTGC
Statistics
Matches: 58, Mismatches: 2, Indels: 20
0.73 0.03 0.25
Matches are distributed among these distances:
14 22 0.38
15 1 0.02
16 4 0.07
17 4 0.07
18 1 0.02
19 26 0.45
ACGTcount: A:0.08, C:0.16, G:0.27, T:0.49
Consensus pattern (18 bp):
GATTTTGTTTCGCGTTGC
Found at i:1808752 original size:14 final size:14
Alignment explanation
Indices: 1808733--1808759 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1808723 TTTGGTTTCG
1808733 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
1808747 CGTTGCGATTTTG
1 CGTTGCGATTTTG
1808760 GTTTCGCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1808762 original size:33 final size:32
Alignment explanation
Indices: 1808720--1808824 Score: 147
Period size: 33 Copynumber: 3.2 Consensus size: 32
1808710 ATCGCAATGA
1808720 GATTTTGGTTTCGCGTTGCGATTTTGTCGTTGC
1 GATTTTGGTTTCGCGTTGCGATTTT-TCGTTGC
*
1808753 GATTTTGGTTTCGCGTTGCGATTCTTTTGTTGC
1 GATTTTGGTTTCGCGTTGCGATT-TTTCGTTGC
** *
1808786 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
1 GATTTTGGTTTCGCGTTGCGATT-TTTCGTTGC
1808819 GATTTT
1 GATTTT
1808825 AAGTTTCGTG
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 64 0.97
34 2 0.03
ACGTcount: A:0.08, C:0.17, G:0.26, T:0.50
Consensus pattern (32 bp):
GATTTTGGTTTCGCGTTGCGATTTTTCGTTGC
Found at i:1809077 original size:93 final size:93
Alignment explanation
Indices: 1808888--1809167 Score: 514
Period size: 93 Copynumber: 3.1 Consensus size: 93
1808878 ATGGATTGCA
*
1808888 TTAC-TTCAACCAAAAGACAAAACAAAGTCAAATACTATTTCACAGTGTT--A-AATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1808949 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1808977 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1809042 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1809070 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1809135 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1809163 TTACT
1 TTACT
1809168 AAGCAATCTA
Statistics
Matches: 185, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
89 4 0.02
90 44 0.24
92 1 0.01
93 136 0.74
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.23
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1810872 original size:20 final size:20
Alignment explanation
Indices: 1810840--1810935 Score: 91
Period size: 19 Copynumber: 5.2 Consensus size: 20
1810830 TTTTGGTTGA
1810840 AATG-AAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
1810859 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1810879 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
1810898 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
1810913 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1810933 AAT
1 AAT
1810936 CGCAACGCGA
Statistics
Matches: 61, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
14 9 0.15
16 4 0.07
17 2 0.03
19 19 0.31
20 15 0.25
21 12 0.20
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1810891 original size:21 final size:21
Alignment explanation
Indices: 1810838--1810901 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
1810828 TCTTTTGGTT
1810838 GAAATG-AAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
1810858 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1810878 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1810899 GAA
1 GAA
1810902 TCGCAACGCG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
19 4 0.11
20 13 0.36
21 19 0.53
ACGTcount: A:0.47, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:1810893 original size:41 final size:35
Alignment explanation
Indices: 1810838--1810959 Score: 137
Period size: 33 Copynumber: 3.5 Consensus size: 35
1810828 TCTTTTGGTT
1810838 GAAATG-AAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAGAAT-A---TCGCAAC--GA
*
1810878 GAAATGAAAATCGCAACGAGAG-A-ATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATATCGCAACGA
*
1810911 GAAATGAAAATCGCAACGAGAG-A-ATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATATCGCAACGA
1810944 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1810960 TGCGATTTGG
Statistics
Matches: 80, Mismatches: 1, Indels: 9
0.89 0.01 0.10
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 7 0.09
41 15 0.19
ACGTcount: A:0.46, C:0.19, G:0.25, T:0.11
Consensus pattern (35 bp):
GAAATGAAAATCGCAACGAGAGAATATCGCAACGA
Found at i:1810905 original size:14 final size:14
Alignment explanation
Indices: 1810886--1810942 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1810876 GAGAAATGAA
1810886 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1810900 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1810919 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1810933 AATCGCAACG
1 AATCGCAACG
1810943 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1810918 original size:33 final size:33
Alignment explanation
Indices: 1810878--1810959 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
1810868 CGCAACGAGA
1810878 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1810911 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1810944 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1810960 TGCGATTTGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.48, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1810924 original size:19 final size:19
Alignment explanation
Indices: 1810838--1810964 Score: 78
Period size: 19 Copynumber: 7.1 Consensus size: 19
1810828 TCTTTTGGTT
*
1810838 GAAATG-AAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*** *
1810856 GAGAATGACTGTCGCAACGAGA
1 GA-AATGAAAATCGCAAC--GC
1810878 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1810895 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1810911 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1810928 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1810944 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1810963 GA
1 GA
1810965 TTTGGTTTCG
Statistics
Matches: 83, Mismatches: 12, Indels: 27
0.68 0.10 0.22
Matches are distributed among these distances:
14 20 0.24
15 2 0.02
16 4 0.05
17 3 0.04
18 4 0.05
19 28 0.34
20 7 0.08
21 11 0.13
22 4 0.05
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1810994 original size:14 final size:14
Alignment explanation
Indices: 1810975--1811031 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1810965 TTTGGTTTCG
1810975 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1810989 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1811008 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1811022 CGTTGCGATT
1 CGTTGCGATT
1811032 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1811010 original size:33 final size:33
Alignment explanation
Indices: 1810970--1811039 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
1810960 TGCGATTTGG
1810970 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1811003 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1811036 TTTC
1 TTTC
1811040 TCTCGTTGCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.09, C:0.24, G:0.20, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:1811042 original size:21 final size:21
Alignment explanation
Indices: 1811016--1811091 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1811006 CGCGTTGCGA
1811016 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1811037 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1811057 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
1811078 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
1811092 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1811072 original size:41 final size:41
Alignment explanation
Indices: 1811015--1811092 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1811005 TCGCGTTGCG
*
1811015 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
1811056 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1811093 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:1811222 original size:33 final size:33
Alignment explanation
Indices: 1811171--1811241 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
1811161 AATACTAACT
*
1811171 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
* * *
1811204 TGAAAATCGTAACAAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
1811237 TGAAA
1 TGAAA
1811242 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.15, G:0.23, T:0.13
Consensus pattern (33 bp):
TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
Found at i:1811643 original size:20 final size:20
Alignment explanation
Indices: 1811618--1811810 Score: 228
Period size: 20 Copynumber: 9.6 Consensus size: 20
1811608 CTTTAAAAAT
1811618 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1811638 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
1811658 TGTCGTTGTGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
1811679 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1811699 CACATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
1811719 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1811739 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1811759 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1811779 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1811799 CGCGTTGCGATT
1 CGCGTTGCGATT
1811811 CTGTAAAATC
Statistics
Matches: 148, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
20 131 0.89
21 17 0.11
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1811828 original size:21 final size:20
Alignment explanation
Indices: 1811804--1811853 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
1811794 ATATTCGCGT
1811804 TGCGATTCTGTAAAATCGCAA
1 TGCGATT-TGTAAAATCGCAA
** *
1811825 TGCGAATTTGTACTATCGCAT
1 TGCG-ATTTGTAAAATCGCAA
1811846 TGCGATTT
1 TGCGATTT
1811854 TCAAGAATCG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 4 0.16
21 18 0.72
22 3 0.12
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (20 bp):
TGCGATTTGTAAAATCGCAA
Found at i:1813019 original size:65 final size:64
Alignment explanation
Indices: 1812820--1813029 Score: 232
Period size: 65 Copynumber: 3.2 Consensus size: 64
1812810 TGCACTAAGA
* * ** *
1812820 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATGCATGGATG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGATT
* *
1812884 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGGTGCATGG-
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGGA
1812946 TAT
63 T-T
* *
1812949 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCATGGATT
*
1813013 GATGCATCAATGCATCA
1 G-TGCATCGATGCATCA
1813030 CTTTGATAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 53 0.43
65 62 0.50
67 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGATT
Found at i:1817392 original size:22 final size:21
Alignment explanation
Indices: 1817350--1817389 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1817340 GAGTTTATTT
*
1817350 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1817371 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1817390 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1819411 original size:19 final size:19
Alignment explanation
Indices: 1819372--1819411 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1819362 AAAATCCTCA
* **
1819372 GTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATGAAAT
1819391 GTGCATCGATGCATGAAAT
1 GTGCATCGATGCATGAAAT
1819410 GT
1 GT
1819412 ATTCGATGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.30
Consensus pattern (19 bp):
GTGCATCGATGCATGAAAT
Found at i:1819463 original size:65 final size:63
Alignment explanation
Indices: 1819306--1819471 Score: 176
Period size: 65 Copynumber: 2.6 Consensus size: 63
1819296 AAATAGCCAG
*
1819306 AGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTC
1 AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTC
* * * **
1819371 AGTGCATCGGTGCATGGTAT-GTGCATCGATGCATGAAATGTATTCGATG-TTCAATTTAAT-TC
1 AGTGCATCGATGCATGGT-TGGTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTC
* *
1819433 ATGGTGCATCGATGCATGGATTGGTACATCGGTGCATCA
1 A--GTGCATCGATGCATGG-TTGGTGCATCGATGCATCA
1819472 CTTTGATAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 21 0.25
65 57 0.67
66 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (63 bp):
AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTC
Found at i:1821105 original size:2 final size:2
Alignment explanation
Indices: 1821100--1821124 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1821090 TATACTTTTG
1821100 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1821125 CTTACACGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1825422 original size:8 final size:8
Alignment explanation
Indices: 1825388--1825440 Score: 65
Period size: 8 Copynumber: 6.6 Consensus size: 8
1825378 CTTTTTATAC
*
1825388 ATTATAAT
1 ATTATAGT
1825396 ATATATA-T
1 AT-TATAGT
1825404 ATATATA-T
1 AT-TATAGT
1825412 ATTATAGT
1 ATTATAGT
1825420 ATTATAGT
1 ATTATAGT
1825428 ATTATAGT
1 ATTATAGT
1825436 ATTAT
1 ATTAT
1825441 TATTATTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
7 4 0.09
8 35 0.81
9 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (8 bp):
ATTATAGT
Found at i:1825430 original size:16 final size:15
Alignment explanation
Indices: 1825388--1825459 Score: 71
Period size: 16 Copynumber: 4.8 Consensus size: 15
1825378 CTTTTTATAC
1825388 ATTATAATATATATA-T
1 ATTAT-ATAT-TATAGT
1825404 ATATATATATTATAGT
1 AT-TATATATTATAGT
1825420 ATTATAGTATTATAGT
1 ATTATA-TATTATAGT
1825436 ATTAT-TATTAT--T
1 ATTATATATTATAGT
*
1825448 ATTATTTATTAT
1 ATTATATATTAT
1825460 TTTATTTTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
12 6 0.12
13 6 0.12
14 6 0.12
15 8 0.15
16 23 0.44
17 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (15 bp):
ATTATATATTATAGT
Found at i:1828632 original size:21 final size:21
Alignment explanation
Indices: 1828607--1828646 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1828597 ATACTTTGCA
1828607 TTTTATATATTTCATGTTTAT
1 TTTTATATATTTCATGTTTAT
*
1828628 TTTTATATTTTTCATGTTT
1 TTTTATATATTTCATGTTT
1828647 TTACATTCGT
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:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTTATATATTTCATGTTTAT
Found at i:1829884 original size:21 final size:21
Alignment explanation
Indices: 1829858--1829902 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1829848 GATTTCTGGG
* *
1829858 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1829879 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1829900 CAA
1 CAA
1829903 ACGACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1830506 original size:18 final size:18
Alignment explanation
Indices: 1830483--1830517 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1830473 CTAGGAGATT
1830483 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1830501 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1830518 TTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1830603 original size:21 final size:22
Alignment explanation
Indices: 1830574--1830624 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
1830564 GTTGTATGAT
1830574 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
1830595 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
*
1830617 AAAAAATT
1 AGAAAATT
1830625 GAATTAAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:1831965 original size:149 final size:149
Alignment explanation
Indices: 1831502--1831954 Score: 852
Period size: 149 Copynumber: 3.0 Consensus size: 149
1831492 GAGTCGAGGG
*
1831502 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1831567 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
1831632 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1831651 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
*
1831716 ACTTGATCCCTAGCATATGCATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
1831781 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
1831800 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* *
1831865 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
*
1831930 TATGGCACTACGGTGTAAT
131 TATGGCACTACGGTGCAAT
1831949 TCTACG
1 TCTACG
1831955 GGGCACTTCG
Statistics
Matches: 297, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 297 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:1831977 original size:23 final size:23
Alignment explanation
Indices: 1831933--1831977 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1831923 ATCATTATAT
* *
1831933 GGCACTACGGTGTAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
1831956 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1831978 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:1835136 original size:21 final size:21
Alignment explanation
Indices: 1835110--1835154 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1835100 GATTTCTGGG
* *
1835110 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1835131 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1835152 CAA
1 CAA
1835155 ACGACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1835758 original size:18 final size:18
Alignment explanation
Indices: 1835735--1835769 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1835725 CTAGGAGATT
1835735 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1835753 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1835770 TTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1835855 original size:21 final size:22
Alignment explanation
Indices: 1835826--1835876 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
1835816 GTTGTATGAT
1835826 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
1835847 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
*
1835869 AAAAAATT
1 AGAAAATT
1835877 GAATTAAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:1837221 original size:149 final size:149
Alignment explanation
Indices: 1836758--1837210 Score: 852
Period size: 149 Copynumber: 3.0 Consensus size: 149
1836748 GAGTCGAGGG
*
1836758 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1836823 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
1836888 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1836907 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1836972 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
1837037 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
1837056 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAATATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* *
1837121 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
*
1837186 TATGGCACTACGGTGTAAT
131 TATGGCACTACGGTGCAAT
1837205 TCTACG
1 TCTACG
1837211 GGGCACTTCG
Statistics
Matches: 298, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 298 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:1837233 original size:23 final size:23
Alignment explanation
Indices: 1837189--1837233 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1837179 ATCATTATAT
* *
1837189 GGCACTACGGTGTAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
1837212 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1837234 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:1844561 original size:8 final size:7
Alignment explanation
Indices: 1844544--1844592 Score: 64
Period size: 7 Copynumber: 6.9 Consensus size: 7
1844534 ACCCTAAATT
1844544 GAAAAAA
1 GAAAAAA
1844551 GAAAAAGA
1 GAAAAA-A
1844559 GAAAAAA
1 GAAAAAA
1844566 GAACAAAA
1 GAA-AAAA
1844574 G-AAAAA
1 GAAAAAA
*
1844580 GAGAAAA
1 GAAAAAA
1844587 GAAAAA
1 GAAAAA
1844593 TAAGGTGGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
6 5 0.14
7 20 0.54
8 12 0.32
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:1844564 original size:15 final size:14
Alignment explanation
Indices: 1844544--1844592 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
1844534 ACCCTAAATT
1844544 GAAAAAAGAAAAAGA
1 GAAAAAAGAAAAA-A
1844559 GAAAAAAGAACAAAA
1 GAAAAAAGAA-AAAA
*
1844574 G-AAAAAGAGAAAA
1 GAAAAAAGAAAAAA
1844587 GAAAAA
1 GAAAAA
1844593 TAAGGTGGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
13 5 0.16
14 11 0.35
15 12 0.39
16 3 0.10
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (14 bp):
GAAAAAAGAAAAAA
Found at i:1844566 original size:9 final size:8
Alignment explanation
Indices: 1844545--1844586 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
1844535 CCCTAAATTG
1844545 AAAAAAGA
1 AAAAAAGA
*
1844553 AAAAGAG-
1 AAAAAAGA
1844560 AAAAAAGA
1 AAAAAAGA
*
1844568 ACAAAAGA
1 AAAAAAGA
*
1844576 AAAAGAGA
1 AAAAAAGA
1844584 AAA
1 AAA
1844587 GAAAAATAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:1845223 original size:14 final size:14
Alignment explanation
Indices: 1845204--1845230 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1845194 GATCAGAGCT
1845204 TCAAGATTCCAGAA
1 TCAAGATTCCAGAA
1845218 TCAAGATTCCAGA
1 TCAAGATTCCAGA
1845231 CAGGCAACCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAA
Found at i:1847912 original size:2 final size:2
Alignment explanation
Indices: 1847901--1847929 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1847891 CTACAAGCTA
1847901 AT AT -T 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
1847930 TATCCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1847995 original size:15 final size:15
Alignment explanation
Indices: 1847946--1847995 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
1847936 TTTTCCCTCG
* * *
1847946 TTTTGTTTATTTTAC
1 TTTTATTTAATTTAT
*
1847961 TTTTACTTTTATTTAT
1 TTTTA-TTTAATTTAT
1847977 TTTTATTTAATTTAT
1 TTTTATTTAATTTAT
1847992 TTTT
1 TTTT
1847996 TGTATGTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTTATTTAATTTAT
Found at i:1849140 original size:17 final size:18
Alignment explanation
Indices: 1849099--1849145 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1849089 TGTTTATGAG
*
1849099 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTCAA
1849117 GGAATTGGAATCTGTCAA
1 GGAATTGGAATCTGTCAA
1849135 -GAATTGGAATC
1 GGAATTGGAATC
1849146 CAATTCCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTCAA
Found at i:1853497 original size:48 final size:49
Alignment explanation
Indices: 1853385--1853506 Score: 201
Period size: 49 Copynumber: 2.5 Consensus size: 49
1853375 AAAAATATTT
*
1853385 AGTCCCAAATGGTTCATCCGAATACCATTTGATATGAAAACAATAACCA
1 AGTCCCAAATGGTTCATCCGAATCCCATTTGATATGAAAACAATAACCA
* *
1853434 AGTCCCAAATGGTTCATCCGAATCCCATTTGATATG-AAAGAATAACTA
1 AGTCCCAAATGGTTCATCCGAATCCCATTTGATATGAAAACAATAACCA
*
1853482 AGTCCCAAATGGTTCATCCAAATCC
1 AGTCCCAAATGGTTCATCCGAATCC
1853507 GACAGTTGGA
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
48 34 0.49
49 35 0.51
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (49 bp):
AGTCCCAAATGGTTCATCCGAATCCCATTTGATATGAAAACAATAACCA
Found at i:1856050 original size:38 final size:38
Alignment explanation
Indices: 1855995--1856077 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 38
1855985 TTTATTTTGT
1855995 TCGGGTC-GGGTTTTTTAAGTGCGATATTCGGGTCGAG
1 TCGGGTCGGGGTTTTTTAAGTGCGATATTCGGGTCGAG
* * *
1856032 TCGTGTCGGGGTTTTTTAAGTGTGATATTCGGGTCGGG
1 TCGGGTCGGGGTTTTTTAAGTGCGATATTCGGGTCGAG
1856070 TCGGGTCG
1 TCGGGTCG
1856078 TGTTTAGGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 6 0.15
38 35 0.85
ACGTcount: A:0.11, C:0.13, G:0.40, T:0.36
Consensus pattern (38 bp):
TCGGGTCGGGGTTTTTTAAGTGCGATATTCGGGTCGAG
Found at i:1856692 original size:18 final size:17
Alignment explanation
Indices: 1856651--1856695 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
1856641 TATGAAATTG
*
1856651 GATTCAAATTCTTGACA
1 GATTCCAATTCTTGACA
* *
1856668 TATTCCAATTCCTTTACA
1 GATTCCAATT-CTTGACA
1856686 GATTCCAATT
1 GATTCCAATT
1856696 TCCTCATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (17 bp):
GATTCCAATTCTTGACA
Found at i:1857034 original size:31 final size:31
Alignment explanation
Indices: 1856996--1857054 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
1856986 TCAAAAAATA
1856996 ATAATTTAGGAAGCTATTCGTGAAATACGCT
1 ATAATTTAGGAAGCTATTCGTGAAATACGCT
1857027 ATAATTTAGGAAGCTATTCGTGAAATAC
1 ATAATTTAGGAAGCTATTCGTGAAATAC
1857055 CTAAAGTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (31 bp):
ATAATTTAGGAAGCTATTCGTGAAATACGCT
Found at i:1858043 original size:34 final size:34
Alignment explanation
Indices: 1857999--1858083 Score: 116
Period size: 34 Copynumber: 2.5 Consensus size: 34
1857989 TGTTTGTTAA
* ** *
1857999 AAAATGTTGCTCGACTCTTCTTGTTAAACTCGTT
1 AAAATTTTGCTCGACTCTAATCGTTAAACTCGTT
*
1858033 AAAATTTTGCTCAACTCTAATCGTTAAACTCGTT
1 AAAATTTTGCTCGACTCTAATCGTTAAACTCGTT
*
1858067 AAAATTTTACTCGACTC
1 AAAATTTTGCTCGACTC
1858084 ATGCTCGTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (34 bp):
AAAATTTTGCTCGACTCTAATCGTTAAACTCGTT
Found at i:1861437 original size:3 final size:3
Alignment explanation
Indices: 1861431--1861468 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1861421 TATAGTTAGA
1861431 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1861469 CGATAATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1862007 original size:133 final size:133
Alignment explanation
Indices: 1861688--1862128 Score: 526
Period size: 133 Copynumber: 3.3 Consensus size: 133
1861678 GGTGACTCAG
* * *
1861688 CTCCTACGTGATAAGGATATCTGGTCAGGGGATGACACTGCTCATATGTGATGAAGAGTTTTTGG
1 CTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACAC-GCTCATATGTGATGAAGAG-TTTTGG
* ** ** *
1861753 CCATCTTTAGGAATAGTGATAACTCGGTTCCTATATGATGAGGACGGGTGATTATCTAGGGGTGA
64 CCATCTTTAGGAATGGTGATAACTCGGTTCCTACGTGATGAGGACGACTGGTTATCTAGGGGTGA
*
1861818 CACGA
129 CATGA
* *
1861823 CTCCTACGTGATGAGGAGATCTGGTCGGAGGATGTCACGGCTCATATGTGATGAAGAGTTTTGGC
1 CTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACAC-GCTCATATGTGATGAAGAGTTTTGGC
* *
1861888 CATCTTTAGGAAGGGTGATAACTCAGTTCCTACGTGATGAGGACGACTGGTTATC-AGGGGTGAC
65 CATCTTTAGGAATGGTGATAACTCGGTTCCTACGTGATGAGGACGACTGGTTATCTAGGGGTGAC
1861952 ATGA
130 ATGA
* * * * * *
1861956 CTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGAGACGACTCATACGTGATGAAGGGTTCTGAC
1 CTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACG-CTCATATGTGATGAAGAGTTTTGGC
* * * * * * * *
1862021 CATATTTAAGAATGGCGATAGCACGGTTCTTACGCGATGAGGACGACTGGTTATCTAGGGGTAAC
65 CATCTTTAGGAATGGTGATAACTCGGTTCCTACGTGATGAGGACGACTGGTTATCTAGGGGTGAC
1862086 ATTG-
130 A-TGA
* * * * *
1862090 CTCCTACATGATGAAGAGGTATGGTCGGTGGATGACACG
1 CTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACG
1862129 GTTCCTACGC
Statistics
Matches: 265, Mismatches: 38, Indels: 7
0.85 0.12 0.02
Matches are distributed among these distances:
132 1 0.00
133 113 0.43
134 97 0.37
135 54 0.20
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.27
Consensus pattern (133 bp):
CTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGCTCATATGTGATGAAGAGTTTTGGCC
ATCTTTAGGAATGGTGATAACTCGGTTCCTACGTGATGAGGACGACTGGTTATCTAGGGGTGACA
TGA
Found at i:1862428 original size:65 final size:65
Alignment explanation
Indices: 1862281--1862412 Score: 221
Period size: 65 Copynumber: 2.0 Consensus size: 65
1862271 AATTTATTTC
* * *
1862281 CAAA-GAAACATACTCAAATATTTTTCTCAAAAGAAATTGTCTCAAGAGAGACAAAACTTTGTTT
1 CAAAGGAAACAAACTCAAAGATTGTTCTCAAAAGAAATTGTCTCAAGAGAGACAAAACTTTGTTT
*
1862345 CAAAGGAAACAAACTCAAAGATTGTTCTCAAAAGAAATTGTCTCAAGAGAGCCAAAACTTTGTTT
1 CAAAGGAAACAAACTCAAAGATTGTTCTCAAAAGAAATTGTCTCAAGAGAGACAAAACTTTGTTT
1862410 CAA
1 CAA
1862413 GATTTTGTGT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
64 4 0.06
65 59 0.94
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.27
Consensus pattern (65 bp):
CAAAGGAAACAAACTCAAAGATTGTTCTCAAAAGAAATTGTCTCAAGAGAGACAAAACTTTGTTT
Found at i:1862860 original size:32 final size:33
Alignment explanation
Indices: 1862824--1862885 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
1862814 TCCCCAAAGG
*
1862824 TGCCCCAATATTCGATG-TGATTGCTTCAAATA
1 TGCCCCAATATTCAATGTTGATTGCTTCAAATA
* *
1862856 TGCCCCAATATTTAATGTTGATTGTTTCAA
1 TGCCCCAATATTCAATGTTGATTGCTTCAA
1862886 CATTGATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 15 0.58
33 11 0.42
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (33 bp):
TGCCCCAATATTCAATGTTGATTGCTTCAAATA
Found at i:1863940 original size:23 final size:22
Alignment explanation
Indices: 1863910--1863988 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 22
1863900 CTTATTGTCC
1863910 TCTT-TTTTCTTCGCTTATTTTT
1 TCTTATTTTCTTCGCTT-TTTTT
* * *
1863932 TGTTATTTTCTTTGCTTTTTTA
1 TCTTATTTTCTTCGCTTTTTTT
*
1863954 TCTTATTTT-TTCTCTTTGTTTTT
1 TCTTATTTTCTTCGC-TT-TTTTT
*
1863977 TCTTTTTTTCTT
1 TCTTATTTTCTT
1863989 TTTCTTTGAT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
21 3 0.07
22 17 0.38
23 23 0.51
24 2 0.04
ACGTcount: A:0.05, C:0.14, G:0.05, T:0.76
Consensus pattern (22 bp):
TCTTATTTTCTTCGCTTTTTTT
Found at i:1863952 original size:12 final size:12
Alignment explanation
Indices: 1863911--1864060 Score: 75
Period size: 12 Copynumber: 12.6 Consensus size: 12
1863901 TTATTGTCCT
*
1863911 CTTTTTTCTTCG
1 CTTTTTTCTTTG
*
1863923 CTTATTT-TTTG
1 CTTTTTTCTTTG
1863934 -TTATTTTCTTTG
1 CTT-TTTTCTTTG
* *
1863946 CTTTTTTATCTTA
1 CTTTTTTCT-TTG
*
1863959 TTTTTTCTCTTTG
1 CTTTTT-TCTTTG
*
1863972 -TTTTTTCTTTTT
1 CTTTTTTC-TTTG
*
1863984 TTCTTTTTCTTTG
1 CT-TTTTTCTTTG
* *
1863997 ATTTTCTCTTTG
1 CTTTTTTCTTTG
*
1864009 -TTTCTTTCTCT-
1 CTTT-TTTCTTTG
1864020 CTTTTTTCTTTG
1 CTTTTTTCTTTG
1864032 -TTTTCTT-TTT-
1 CTTTT-TTCTTTG
1864042 CTTTTGTT-TTTG
1 CTTTT-TTCTTTG
1864054 CTTTTTT
1 CTTTTTT
1864061 TTTTACTCTT
Statistics
Matches: 108, Mismatches: 16, Indels: 29
0.71 0.10 0.19
Matches are distributed among these distances:
10 2 0.02
11 35 0.32
12 47 0.44
13 16 0.15
14 8 0.07
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (12 bp):
CTTTTTTCTTTG
Found at i:1863990 original size:26 final size:26
Alignment explanation
Indices: 1863961--1864070 Score: 106
Period size: 26 Copynumber: 4.3 Consensus size: 26
1863951 TTATCTTATT
1863961 TTTTCTCTTTGTTTTTTCTTTTTTTC
1 TTTTCTCTTTGTTTTTTCTTTTTTTC
* *
1863987 TTTT-TCTTTGATTTTCTCTTTGTTTC
1 TTTTCTCTTTG-TTTTTTCTTTTTTTC
*
1864013 -TTTCTC--TCTTTTTTCTTTGTTTTC
1 TTTTCTCTTTGTTTTTTCTTT-TTTTC
*
1864037 TTTT-TCTTTTGTTTTTGCTTTTTTT-
1 TTTTCTC-TTTGTTTTTTCTTTTTTTC
*
1864062 TTTACTCTT
1 TTTTCTCTT
1864071 CTACCTACTT
Statistics
Matches: 68, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
23 9 0.13
24 7 0.10
25 17 0.25
26 25 0.37
27 10 0.15
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.77
Consensus pattern (26 bp):
TTTTCTCTTTGTTTTTTCTTTTTTTC
Found at i:1863993 original size:51 final size:50
Alignment explanation
Indices: 1863937--1864045 Score: 132
Period size: 51 Copynumber: 2.2 Consensus size: 50
1863927 TTTTTTGTTA
* * *
1863937 TTTTCTTTGCTTTTTTATCTTATTT-TTTCTCTTTGTTTTTTCTTT-TTTTCT
1 TTTTCTTTGATTTTCTAT-TTATTTCTTTCTC--TCTTTTTTCTTTGTTTTCT
* *
1863988 TTTTCTTTGATTTTCTCTTTGTTTCTTTCTCTCTTTTTTCTTTGTTTTCT
1 TTTTCTTTGATTTTCTATTTATTTCTTTCTCTCTTTTTTCTTTGTTTTCT
1864038 TTTTCTTT
1 TTTTCTTT
1864046 TGTTTTTGCT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
49 11 0.22
50 19 0.37
51 21 0.41
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.77
Consensus pattern (50 bp):
TTTTCTTTGATTTTCTATTTATTTCTTTCTCTCTTTTTTCTTTGTTTTCT
Found at i:1864001 original size:16 final size:15
Alignment explanation
Indices: 1863973--1864051 Score: 70
Period size: 16 Copynumber: 4.9 Consensus size: 15
1863963 TTCTCTTTGT
1863973 TTTTTCTTT-TTTTC
1 TTTTTCTTTGTTTTC
1863987 TTTTTCTTTGATTTTC
1 TTTTTCTTTG-TTTTC
* * *
1864003 TCTTTGTTTCTTTCTCTC
1 TTTTTCTTT-GTT-T-TC
1864021 TTTTTTCTTTGTTTTC
1 -TTTTTCTTTGTTTTC
1864037 TTTTTCTTTTGTTTT
1 TTTTTC-TTTGTTTT
1864052 TGCTTTTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
14 9 0.17
15 6 0.12
16 24 0.46
17 2 0.04
18 4 0.08
19 7 0.13
ACGTcount: A:0.01, C:0.15, G:0.05, T:0.78
Consensus pattern (15 bp):
TTTTTCTTTGTTTTC
Found at i:1866872 original size:36 final size:36
Alignment explanation
Indices: 1866822--1866918 Score: 106
Period size: 36 Copynumber: 2.7 Consensus size: 36
1866812 AAAGTTTGCA
* * * *
1866822 TCAATTCGAGTCGAACGGAGGGAAGCATT-GACATTT
1 TCAATTCAAATCGAACGGAAGGAAGCATTCG-CACTT
*
1866858 TCAATTCAAATCGAACGGAATGAAGCATTCGCACTT
1 TCAATTCAAATCGAACGGAAGGAAGCATTCGCACTT
* * *
1866894 CCGATTCAAATCGAACGGAATGAAG
1 TCAATTCAAATCGAACGGAAGGAAG
1866919 TATCGGCACT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
36 52 0.98
37 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (36 bp):
TCAATTCAAATCGAACGGAAGGAAGCATTCGCACTT
Found at i:1866928 original size:36 final size:36
Alignment explanation
Indices: 1866861--1866959 Score: 146
Period size: 36 Copynumber: 2.8 Consensus size: 36
1866851 GACATTTTCA
1866861 ATTCAAATCGAACGGAATGAAGCATTC-GCACTTCCG
1 ATTCAAATCGAACGGAATGAAGCA-TCGGCACTTCCG
*
1866897 ATTCAAATCGAACGGAATGAAGTATCGGCACTTCCG
1 ATTCAAATCGAACGGAATGAAGCATCGGCACTTCCG
* * *
1866933 GTTCAAGTCGAACAGAATGAAGCATCG
1 ATTCAAATCGAACGGAATGAAGCATCG
1866960 ATGTACACCC
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 2 0.04
36 55 0.96
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.21
Consensus pattern (36 bp):
ATTCAAATCGAACGGAATGAAGCATCGGCACTTCCG
Found at i:1868030 original size:2 final size:2
Alignment explanation
Indices: 1868025--1868091 Score: 109
Period size: 2 Copynumber: 33.0 Consensus size: 2
1868015 TTATATAAAC
1868025 AT AT AT CAT AT AT -T CAT 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
1868068 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
1868092 CCGCAAACAC
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 58 0.94
3 3 0.05
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1872174 original size:23 final size:24
Alignment explanation
Indices: 1872132--1872184 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
1872122 CCACTAGGGG
*
1872132 CTATGAAATTTGTCCTGAAGGACCA
1 CTATGAAA-TTGTCCAGAAGGACCA
1872157 CTATGAAA-TGTCCAGAAGGACCA
1 CTATGAAATTGTCCAGAAGGACCA
1872180 CTATG
1 CTATG
1872185 TGTCGAAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 19 0.70
25 8 0.30
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (24 bp):
CTATGAAATTGTCCAGAAGGACCA
Found at i:1872192 original size:18 final size:21
Alignment explanation
Indices: 1872142--1872199 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 21
1872132 CTATGAAATT
*
1872142 TGTCCTGAAGGACCACTATGAAA
1 TGTCCAGAAGGACCACTATG--A
1872165 TGTCCAGAAGGACCACTATG-
1 TGTCCAGAAGGACCACTATGA
1872185 TGT-C-GAAGGACCACT
1 TGTCCAGAAGGACCACT
1872200 GTGTCCCGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 11 0.32
19 1 0.03
20 3 0.09
23 19 0.56
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (21 bp):
TGTCCAGAAGGACCACTATGA
Found at i:1872209 original size:18 final size:18
Alignment explanation
Indices: 1872164--1872212 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1872154 CCACTATGAA
*
1872164 ATGTCCAGAAGGACCACT
1 ATGTCCCGAAGGACCACT
**
1872182 ATGTGTCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
*
1872200 GTGTCCCGAAGGA
1 ATGTCCCGAAGGA
1872213 TCGCATATAC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.29, C:0.24, G:0.29, T:0.18
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:1873962 original size:36 final size:36
Alignment explanation
Indices: 1873877--1873962 Score: 136
Period size: 36 Copynumber: 2.4 Consensus size: 36
1873867 GGCACTTCCA
* *
1873877 ATTCAAATCGAACAGAAGGAAGCATCAACACTTTCG
1 ATTCAAATCAAACGGAAGGAAGCATCAACACTTTCG
*
1873913 ATTCAAATCAAACGGAAGGAAGCATCGACACTTTCG
1 ATTCAAATCAAACGGAAGGAAGCATCAACACTTTCG
*
1873949 ATTCAAATTAAACG
1 ATTCAAATCAAACG
1873963 AATGGTTTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (36 bp):
ATTCAAATCAAACGGAAGGAAGCATCAACACTTTCG
Found at i:1877285 original size:3 final size:3
Alignment explanation
Indices: 1877279--1877304 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1877269 TATAATTAGA
1877279 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1877305 CAACAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1877550 original size:4 final size:4
Alignment explanation
Indices: 1877541--1877567 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1877531 AGAAAGCCTT
1877541 GAAA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAA
1877568 GGAGAACCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:1878031 original size:52 final size:52
Alignment explanation
Indices: 1877969--1878072 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
1877959 ACTACTTTAA
*
1877969 ACAATTAATTGAATAACATAGAAAAATGAATAAACTTTTTCTAATATTAGTT
1 ACAATTAATTGAATAACATAGAAAAATGAATAAACTTTTTCGAATATTAGTT
* *
1878021 ACAATTAATTGAATATCATAGAAAAATGATTAAACTTTTTCGAATATTAGTT
1 ACAATTAATTGAATAACATAGAAAAATGAATAAACTTTTTCGAATATTAGTT
1878073 TTGTTGTTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.38
Consensus pattern (52 bp):
ACAATTAATTGAATAACATAGAAAAATGAATAAACTTTTTCGAATATTAGTT
Found at i:1878644 original size:53 final size:51
Alignment explanation
Indices: 1878542--1878738 Score: 180
Period size: 53 Copynumber: 4.0 Consensus size: 51
1878532 CCTCAATTAT
** * *
1878542 AAAAGTAGAAATTGAGATTGAAAAAACTTAGGGGTCTCAATTGTAAAAGTAG
1 AAAAGTAGAAAGAGAGATTGAAAAAACTTAAGGGTCTCAATTAT-AAAGTAG
* *
1878594 AAAAGGTAGAAAGAGAGATTGAAAAAAACTTAAGGGTATCAATTATAAAGT-T
1 AAAA-GTAGAAAGAGAGATTG-AAAAAACTTAAGGGTCTCAATTATAAAGTAG
*
1878646 AAAAGT-----GA-A-ATTG-AAAAA-TTAGGGGTCTCAATTATAAAGGTAG
1 AAAAGTAGAAAGAGAGATTGAAAAAACTTAAGGGTCTCAATTATAAA-GTAG
* * * *
1878689 AAAACGTAGAAAGTGAGATTGAAAAAACTTAAGAGCCTCAATAATAAAGT
1 AAAA-GTAGAAAGAGAGATTGAAAAAACTTAAGGGTCTCAATTATAAAGT
1878739 TAAAAAATTG
Statistics
Matches: 117, Mismatches: 14, Indels: 28
0.74 0.09 0.18
Matches are distributed among these distances:
41 18 0.15
42 7 0.06
43 4 0.03
44 6 0.05
45 1 0.01
46 2 0.02
49 1 0.01
50 1 0.01
51 6 0.05
52 15 0.13
53 35 0.30
54 21 0.18
ACGTcount: A:0.49, C:0.06, G:0.21, T:0.23
Consensus pattern (51 bp):
AAAAGTAGAAAGAGAGATTGAAAAAACTTAAGGGTCTCAATTATAAAGTAG
Found at i:1878690 original size:95 final size:94
Alignment explanation
Indices: 1878525--1878787 Score: 314
Period size: 95 Copynumber: 2.7 Consensus size: 94
1878515 TAAAAAAGTG
* * *
1878525 TTAAGAGCCTCAATTATAAAAG-TAGAAATTGAGATTGAAAAAACTTAGGGGTCTCAATTGTAAA
1 TTAAGAGCATCAATTAT-AAAGTTA-AAATTGAAATTG-AAAAA-TTAGGGGTCTCAATTATAAA
* *
1878589 AGTAGAAAAGGTAGAAAGAGAGATTGAAAAAAAC
62 GGTAGAAAACGTAGAAAGAGAGATTG-AAAAAAC
* * *
1878623 TTAAGGGTATCAATTATAAAGTTAAAAGTGAAATTGAAAAATTAGGGGTCTCAATTATAAAGGTA
1 TTAAGAGCATCAATTATAAAGTTAAAATTGAAATTGAAAAATTAGGGGTCTCAATTATAAAGGTA
*
1878688 GAAAACGTAGAAAGTGAGATTGAAAAAAC
66 GAAAACGTAGAAAGAGAGATTGAAAAAAC
* * * * *
1878717 TTAAGAGCCTCAATAATAAAGTTAAAAAATTG-AATTAAAAAATTAGGGGTTTTAATTATAAAGG
1 TTAAGAGCATCAATTATAAAGTT--AAAATTGAAATTGAAAAATTAGGGGTCTCAATTATAAAGG
*
1878781 TAAAAAA
64 TAGAAAA
1878788 AGGGATTGAA
Statistics
Matches: 144, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
94 26 0.18
95 77 0.53
96 11 0.08
97 14 0.10
98 16 0.11
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.25
Consensus pattern (94 bp):
TTAAGAGCATCAATTATAAAGTTAAAATTGAAATTGAAAAATTAGGGGTCTCAATTATAAAGGTA
GAAAACGTAGAAAGAGAGATTGAAAAAAC
Found at i:1878801 original size:44 final size:44
Alignment explanation
Indices: 1878703--1878888 Score: 141
Period size: 44 Copynumber: 4.3 Consensus size: 44
1878693 CGTAGAAAGT
* * * * * *
1878703 GAGATTGAAAAAACTTA-AGAGCCTCAATAATAAAGTTAAAAAATT
1 GAGATTGAAAAAAATTAGGGA-CTTCAATTATAAAGGTAAAAAA-A
** *
1878748 GA-ATT--AAAAAATTAGGGGTTTTAATTATAAAGGTAAAAAAA
1 GAGATTGAAAAAAATTAGGGACTTCAATTATAAAGGTAAAAAAA
* * * **
1878789 GGGATTGAAAAAAATTAGAGACTTCAATTATAAAGATAAAAAGT
1 GAGATTGAAAAAAATTAGGGACTTCAATTATAAAGGTAAAAAAA
* * *
1878833 GAGATTGAATAATACTA-GGACTTCAATTATAAAGGTAAAAAATA
1 GAGATTGAAAAAAATTAGGGACTTCAATTATAAAGGTAAAAAA-A
*
1878877 -AGATTTAAAAAA
1 GAGATTGAAAAAA
1878889 TAAGGACCTA
Statistics
Matches: 108, Mismatches: 28, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
41 1 0.01
42 28 0.26
43 32 0.30
44 45 0.42
45 2 0.02
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (44 bp):
GAGATTGAAAAAAATTAGGGACTTCAATTATAAAGGTAAAAAAA
Found at i:1879493 original size:186 final size:189
Alignment explanation
Indices: 1879181--1879575 Score: 478
Period size: 186 Copynumber: 2.1 Consensus size: 189
1879171 TCACATAATA
* * *
1879181 AGTTGCGTCGAAAATGTTATTAGAGTTAAAAGCTGATAGAGCCTTTTAAGTTCCTACGATAATAC
1 AGTTGCGCCTAAAATGTTATCAGAGTTAAAAGCTGATAGAGCCTTTTAAGTTCCTACGATAATAC
* * * * ** *
1879246 AATAGGTAAAAAAACTGAAAGTGTTATGAACATATATAATAAATATGGTTTCATTCAATAATGTC
66 AATAAGTAAAAAAACTGAAAATGTCATGAACATATATAATAAATATGGTTGCACCCAATAATGTA
* * * * * *
1879311 TTGCTTCAGTAAGGAAGTATGTTGTAATCTAGAATATTAATATGTTT-AATAATAAAAT-
131 TTACTTCAGTAAAGAAGTAAGTTGCAATATAGAATATTAATAT-TTTAAAAAATAAAATG
* * * * *
1879369 AGGTTGTGCCTAAAATGTTATCAGAGTTAAAAG-TGATAGAGCCTTTTAATTTTCTATGATATGT
1 A-GTTGCGCCTAAAATGTTATCAGAGTTAAAAGCTGATAGAGCCTTTTAAGTTCCTACGATA-AT
*
1879433 A-AATAAGT-TAAAAA-TGAAAATGTCATGAACATATATAATAAATATGGTTGCACCCAATAATG
64 ACAATAAGTAAAAAAACTGAAAATGTCATGAACATATATAATAAATATGGTTGCACCCAATAATG
* * * *
1879495 TATTATTTCAGTAAAGAAGTAAGTTGCAATATGGATTCTTAATATTTTAAAAAATAAAATG
129 TATTACTTCAGTAAAGAAGTAAGTTGCAATATAGAATATTAATATTTTAAAAAATAAAATG
*
1879556 AGTTGCGTCTAAAATGTTAT
1 AGTTGCGCCTAAAATGTTAT
1879576 TAAAGTTTAA
Statistics
Matches: 175, Mismatches: 28, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
185 3 0.02
186 105 0.60
187 6 0.03
188 32 0.18
189 29 0.17
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (189 bp):
AGTTGCGCCTAAAATGTTATCAGAGTTAAAAGCTGATAGAGCCTTTTAAGTTCCTACGATAATAC
AATAAGTAAAAAAACTGAAAATGTCATGAACATATATAATAAATATGGTTGCACCCAATAATGTA
TTACTTCAGTAAAGAAGTAAGTTGCAATATAGAATATTAATATTTTAAAAAATAAAATG
Found at i:1881290 original size:23 final size:22
Alignment explanation
Indices: 1881264--1881314 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 22
1881254 ACCGGTCACA
1881264 ACCCGACCCGACATGAACCGTT
1 ACCCGACCCGACATGAACCGTT
1881286 ----GACCCGACATGAACCGTT
1 ACCCGACCCGACATGAACCGTT
1881304 GACCCGACCCG
1 -ACCCGACCCG
1881315 TTGACCGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
18 18 0.75
23 6 0.25
ACGTcount: A:0.25, C:0.41, G:0.22, T:0.12
Consensus pattern (22 bp):
ACCCGACCCGACATGAACCGTT
Found at i:1881291 original size:18 final size:18
Alignment explanation
Indices: 1881268--1881311 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
1881258 GTCACAACCC
1881268 GACCCGACATGAACCGTT
1 GACCCGACATGAACCGTT
1881286 GACCCGACATGAACCGTT
1 GACCCGACATGAACCGTT
1881304 GACCCGAC
1 GACCCGAC
1881312 CCGTTGACCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.27, C:0.36, G:0.23, T:0.14
Consensus pattern (18 bp):
GACCCGACATGAACCGTT
Found at i:1883844 original size:24 final size:24
Alignment explanation
Indices: 1883817--1883903 Score: 102
Period size: 24 Copynumber: 3.6 Consensus size: 24
1883807 TTTCCGACTA
*
1883817 GAATTCTGTTATGATATATGACCT
1 GAATTCTGTTATGATATATGATCT
* * * *
1883841 GAATTATGTTATGATTTCTGATAT
1 GAATTCTGTTATGATATATGATCT
* *
1883865 GGATTCTGTTATGATATATGTTCT
1 GAATTCTGTTATGATATATGATCT
*
1883889 GAATTCTGTTTTGAT
1 GAATTCTGTTATGAT
1883904 TTCTGATATC
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.48
Consensus pattern (24 bp):
GAATTCTGTTATGATATATGATCT
Found at i:1883865 original size:12 final size:12
Alignment explanation
Indices: 1883847--1883908 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
1883837 ACCTGAATTA
1883847 TGTTATGATTTC
1 TGTTATGATTTC
*
1883859 TGATATGGA-TTC
1 TGTTAT-GATTTC
* *
1883871 TGTTATGATATA
1 TGTTATGATTTC
* *
1883883 TGTTCTGAATTC
1 TGTTATGATTTC
*
1883895 TGTTTTGATTTC
1 TGTTATGATTTC
1883907 TG
1 TG
1883909 ATATCTCCGT
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
11 2 0.05
12 34 0.89
13 2 0.05
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.53
Consensus pattern (12 bp):
TGTTATGATTTC
Found at i:1883875 original size:48 final size:48
Alignment explanation
Indices: 1883819--1883912 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
1883809 TCCGACTAGA
1883819 ATTCTGTTATGATATATGACCTGAATTATGTTATGATTTCTGATATGG
1 ATTCTGTTATGATATATGACCTGAATTATGTTATGATTTCTGATATGG
** * *
1883867 ATTCTGTTATGATATATGTTCTGAATTCTGTTTTGATTTCTGATAT
1 ATTCTGTTATGATATATGACCTGAATTATGTTATGATTTCTGATAT
1883913 CTCCGTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.24, C:0.09, G:0.17, T:0.50
Consensus pattern (48 bp):
ATTCTGTTATGATATATGACCTGAATTATGTTATGATTTCTGATATGG
Found at i:1884077 original size:2 final size:2
Alignment explanation
Indices: 1884070--1884096 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1884060 GGGATGGGGG
1884070 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1884097 GTTTTAAAAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1891300 original size:16 final size:16
Alignment explanation
Indices: 1891279--1891321 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
1891269 AATTGCTTTT
1891279 CATAACTGATTTTAGC
1 CATAACTGATTTTAGC
1891295 CATAACTGATTTTAGC
1 CATAACTGATTTTAGC
1891311 CATAACTGATT
1 CATAACTGATT
1891322 ATTATAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (16 bp):
CATAACTGATTTTAGC
Found at i:1891365 original size:19 final size:19
Alignment explanation
Indices: 1891341--1891394 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
1891331 ATCTATTATG
*
1891341 TACAACCAATAATGTTCTC
1 TACAACCAATAATGTTCTA
*
1891360 TACAACCCAAT-ATTTTCTA
1 TACAA-CCAATAATGTTCTA
* *
1891379 TTCAACCTATAATGTT
1 TACAACCAATAATGTT
1891395 ACATTGCACT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 4 0.14
19 19 0.68
20 5 0.18
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (19 bp):
TACAACCAATAATGTTCTA
Found at i:1892630 original size:18 final size:18
Alignment explanation
Indices: 1892570--1892630 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 18
1892560 GAAACGATGA
*
1892570 GAGCACCGAGCAATGAGT
1 GAGCACCGAGCAGTGAGT
* *
1892588 GAGCACCTGACCGGTAGATATGT
1 GAGCACC-GAGCAGT-G--A-GT
1892611 GAGCACCGAGCAGTGAGT
1 GAGCACCGAGCAGTGAGT
1892629 GA
1 GA
1892631 TCGTCTGGCG
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
18 11 0.33
19 5 0.15
20 1 0.03
21 1 0.03
22 6 0.18
23 9 0.27
ACGTcount: A:0.30, C:0.21, G:0.34, T:0.15
Consensus pattern (18 bp):
GAGCACCGAGCAGTGAGT
Found at i:1893755 original size:2 final size:2
Alignment explanation
Indices: 1893748--1893776 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1893738 TATGTATAAA
1893748 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1893777 TTATAATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1897805 original size:23 final size:22
Alignment explanation
Indices: 1897763--1897820 Score: 80
Period size: 23 Copynumber: 2.6 Consensus size: 22
1897753 GTTCGTGTGG
* *
1897763 TTTAATTTTAATTATTTAATAT
1 TTTATTTTTAATTATCTAATAT
1897785 TTTATTTTTGAATTATCTAATAT
1 TTTATTTTT-AATTATCTAATAT
*
1897808 TATATTTTTAATT
1 TTTATTTTTAATT
1897821 TATTTTAGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 12 0.38
23 20 0.62
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTATTTTTAATTATCTAATAT
Found at i:1902626 original size:50 final size:50
Alignment explanation
Indices: 1902572--1902681 Score: 132
Period size: 50 Copynumber: 2.2 Consensus size: 50
1902562 TTAGCAGAAA
* * * * * *
1902572 AGCGCGCCCCCTG-CACTGCGCTATATGTTGATTTGACGTCACGTGGGTAT
1 AGCGCGCCCCCTGTC-CCGCGATATACGGTGATCTGACGCCACGTGGGTAT
*
1902622 AGCGCGCCCCCTGTCCCGCGATATACGGTGATCTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGTCCCGCGATATACGGTGATCTGACGCCACGTGGGTAT
*
1902672 AGCGCTCCCC
1 AGCGCGCCCC
1902682 TGATCCGTGC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
50 50 0.98
51 1 0.02
ACGTcount: A:0.15, C:0.34, G:0.29, T:0.23
Consensus pattern (50 bp):
AGCGCGCCCCCTGTCCCGCGATATACGGTGATCTGACGCCACGTGGGTAT
Found at i:1904430 original size:35 final size:34
Alignment explanation
Indices: 1904345--1904431 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
1904335 ATTTGATATT
*
1904345 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
1904379 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
1904417 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
1904432 ACTAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:1904662 original size:6 final size:6
Alignment explanation
Indices: 1904646--1904699 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
1904636 ACTCCTCGCT
* * *
1904646 GTCATC ATCATC GTCATC GTCGTT GTCA-C --CATC GTCATC GTCATC
1 GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC
*
1904691 GTCGTC GTC
1 GTCATC GTC
1904700 CTGAACAGGT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
3 2 0.05
4 1 0.03
6 35 0.92
ACGTcount: A:0.15, C:0.33, G:0.19, T:0.33
Consensus pattern (6 bp):
GTCATC
Found at i:1905073 original size:18 final size:18
Alignment explanation
Indices: 1905050--1905084 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1905040 GGCGATGGCG
1905050 GCATCATATATGGTTGTA
1 GCATCATATATGGTTGTA
1905068 GCATCATATATGGTTGT
1 GCATCATATATGGTTGT
1905085 GGTGGCTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (18 bp):
GCATCATATATGGTTGTA
Found at i:1906625 original size:111 final size:111
Alignment explanation
Indices: 1906488--1906709 Score: 399
Period size: 111 Copynumber: 2.0 Consensus size: 111
1906478 ATTACAAAAA
* *
1906488 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* * *
1906553 AATTAAAACGTTAAAATGTTATCGTATTAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
1906599 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1906664 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
1906710 ATGATTTCCA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:1906847 original size:12 final size:10
Alignment explanation
Indices: 1906833--1906873 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
1906823 ACCTTAAAAA
*
1906833 GAGAGTATTT
1 GAGAGAATTT
1906843 GAGAGAAATTT
1 GAGAG-AATTT
1906854 -AGAGAATTT
1 GAGAGAATTT
1906863 GAGAGAATTT
1 GAGAGAATTT
1906873 G
1 G
1906874 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:1908741 original size:22 final size:23
Alignment explanation
Indices: 1908716--1908758 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1908706 TTTGAAAGTA
* *
1908716 TATAGTATAT-GTTTTGAAAACG
1 TATAATATATGGTTTCGAAAACG
1908738 TATAATATATGGTTTCGAAAA
1 TATAATATATGGTTTCGAAAA
1908759 TATTTTTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.40
Consensus pattern (23 bp):
TATAATATATGGTTTCGAAAACG
Found at i:1908814 original size:35 final size:35
Alignment explanation
Indices: 1908722--1909045 Score: 389
Period size: 35 Copynumber: 9.0 Consensus size: 35
1908712 AGTATATAGT
* * **
1908722 ATATGTTTTGAAAACGTATAATATATGGTTTCGAAA
1 ATAT-TTTTGAAAACATATAATATATAGTTTTTAAA
*
1908758 ATATTTTTTGGAAAACATATAATATATAGTTTTTGAA
1 ATA-TTTTT-GAAAACATATAATATATAGTTTTTAAA
* *
1908795 ATATCTTTGAAAACATATAATATATAGTTTTCAAA
1 ATATTTTTGAAAACATATAATATATAGTTTTTAAA
* *
1908830 ATATCTTTGAAAACATATTATATATAGTTTTTTTTAAAA
1 ATATTTTTGAAAACATATAATATATAG---TTTTT-AAA
* *
1908869 ATATTTTTGAAAACGTATAATATATAGTTTTCAAA
1 ATATTTTTGAAAACATATAATATATAGTTTTTAAA
* * *
1908904 CTATCTTTGAAAACATATAATATATAGTTTTAAAAAA
1 ATATTTTTGAAAACATATAATATATAGTTTT--TAAA
* *
1908941 ATATTTTTGGAAAACGTATAATATATA-TATTTTTAA
1 ATATTTTT-GAAAACATATAATATATAGT-TTTTAAA
*
1908977 ATATTTTTGAAAACATATAGTATATAGTTTTTAAA
1 ATATTTTTGAAAACATATAATATATAGTTTTTAAA
1909012 ATATTTTTGAAAACATATAATATATAGTTTTTAA
1 ATATTTTTGAAAACATATAATATATAGTTTTTAA
1909046 TGGTTTTTAT
Statistics
Matches: 250, Mismatches: 27, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
35 137 0.55
36 26 0.10
37 36 0.14
38 24 0.10
39 27 0.11
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (35 bp):
ATATTTTTGAAAACATATAATATATAGTTTTTAAA
Found at i:1908889 original size:74 final size:70
Alignment explanation
Indices: 1908722--1909042 Score: 403
Period size: 73 Copynumber: 4.4 Consensus size: 70
1908712 AGTATATAGT
* *
1908722 ATATGTTTTGAAAACGTATAATATAT-GGTTTCGAAAATATTTTTTGGAAAACATATAATATATA
1 ATAT-TTTTGAAAACGTATAATATATAGTTTTC-AAAATA-TCTTT-GAAAACATATAATATATA
*
1908786 GTTTTTGAA
62 GTTTTTAAA
* * *
1908795 ATATCTTTGAAAACATATAATATATAGTTTTCAAAATATCTTTGAAAACATATTATATATAGTTT
1 ATATTTTTGAAAACGTATAATATATAGTTTTCAAAATATCTTTGAAAACATATAATATATAG---
1908860 TTTTTAAAA
63 TTTTT-AAA
*
1908869 ATATTTTTGAAAACGTATAATATATAGTTTTCAAACTATCTTTGAAAACATATAATATATAGTTT
1 ATATTTTTGAAAACGTATAATATATAGTTTTCAAAATATCTTTGAAAACATATAATATATAGTTT
*
1908934 TAAAAAA
66 T--TAAA
** * *
1908941 ATATTTTTGGAAAACGTATAATATATA-TATTTTTAAATATTTTTGAAAACATATAGTATATAGT
1 ATATTTTT-GAAAACGTATAATATATAGT-TTTCAAAATATCTTTGAAAACATATAATATATAGT
1909005 TTTTAAA
64 TTTTAAA
*
1909012 ATATTTTTGAAAACATATAATATATAGTTTT
1 ATATTTTTGAAAACGTATAATATATAGTTTT
1909043 TAATGGTTTT
Statistics
Matches: 220, Mismatches: 18, Indels: 23
0.84 0.07 0.09
Matches are distributed among these distances:
70 38 0.17
71 20 0.09
72 37 0.17
73 65 0.30
74 60 0.27
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (70 bp):
ATATTTTTGAAAACGTATAATATATAGTTTTCAAAATATCTTTGAAAACATATAATATATAGTTT
TTAAA
Found at i:1910496 original size:59 final size:59
Alignment explanation
Indices: 1910398--1910654 Score: 313
Period size: 59 Copynumber: 4.4 Consensus size: 59
1910388 ATTAATTATT
*
1910398 AATG-TAAGAAATTCATACTAACTGTATAAATTTCCGTATAGGGCACTTTATGCGCTAA
1 AATGTTAAGAAATTCATACTAAGTGTATAAATTTCCGTATAGGGCACTTTATGCGCTAA
* * * *
1910456 AATGTTAAGAAATTCATACTAAGTATATGAATTTCTGTATAGGGCACTTTATCCGCTAA
1 AATGTTAAGAAATTCATACTAAGTGTATAAATTTCCGTATAGGGCACTTTATGCGCTAA
* * * *
1910515 AATGCTAAGAAATTCATACTAAGTGTATAAATTTCCGTATTGGGCACTTTGTGTGCT-A
1 AATGTTAAGAAATTCATACTAAGTGTATAAATTTCCGTATAGGGCACTTTATGCGCTAA
* * * * * ** * *
1910573 AATGATAAGAAATTCATACTAAGTTTATGAATTTCCGTAT-GGGAAATACATGTGTATAA
1 AATGTTAAGAAATTCATACTAAGTGTATAAATTTCCGTATAGGGCACTTTATGCG-CTAA
*
1910632 AATGTTAAGAAATTCATAATAAG
1 AATGTTAAGAAATTCATACTAAG
1910655 GAAATGGCTT
Statistics
Matches: 172, Mismatches: 24, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
57 9 0.05
58 43 0.25
59 120 0.70
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.34
Consensus pattern (59 bp):
AATGTTAAGAAATTCATACTAAGTGTATAAATTTCCGTATAGGGCACTTTATGCGCTAA
Found at i:1910644 original size:117 final size:117
Alignment explanation
Indices: 1910398--1910654 Score: 338
Period size: 117 Copynumber: 2.2 Consensus size: 117
1910388 ATTAATTATT
* *
1910398 AATGTAAGAAATTCATACTAACTGTATAAATTTCCGTATAGGGCACTTTATGCGCTAAAATGTTA
1 AATGTAAGAAATTCATACTAAGTGTATAAATTTCCGTATAGGGCACTTTATGCGCTAAAATGATA
* * * ** *
1910463 AGAAATTCATACTAAGTATATGAATTTCTGTATAGGGCACTTTATCCGCTAA
66 AGAAATTCATACTAAGTATATGAATTTCCGTATAGGGAAATACATCCGATAA
* * *
1910515 AATGCTAAGAAATTCATACTAAGTGTATAAATTTCCGTATTGGGCACTTTGTGTGCT-AAATGAT
1 AATG-TAAGAAATTCATACTAAGTGTATAAATTTCCGTATAGGGCACTTTATGCGCTAAAATGAT
* **
1910579 AAGAAATTCATACTAAGTTTATGAATTTCCGTAT-GGGAAATACATGTGTATAA
65 AAGAAATTCATACTAAGTATATGAATTTCCGTATAGGGAAATACATCCG-ATAA
*
1910632 AATGTTAAGAAATTCATAATAAG
1 AATG-TAAGAAATTCATACTAAG
1910655 GAAATGGCTT
Statistics
Matches: 122, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
116 8 0.07
117 66 0.54
118 48 0.39
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.34
Consensus pattern (117 bp):
AATGTAAGAAATTCATACTAAGTGTATAAATTTCCGTATAGGGCACTTTATGCGCTAAAATGATA
AGAAATTCATACTAAGTATATGAATTTCCGTATAGGGAAATACATCCGATAA
Found at i:1911076 original size:68 final size:68
Alignment explanation
Indices: 1910964--1911097 Score: 189
Period size: 68 Copynumber: 2.0 Consensus size: 68
1910954 TATTAAAGGT
* * * *
1910964 CTAACTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAATTAGATGAAAGGCTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAAATAGATGAAAGGCTAAGTACCGTTGA
1911029 GGC
66 GGC
* * *
1911032 CTAACTGTGCATTTGATAGAAAGGTGTCAATTATG-CAAGATAGATGAATGGTTAAGTACCGTTG
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAA-ATAGATGAAAGGCTAAGTACCGTTG
1911096 AG
65 AG
1911098 TAAAAGAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
67 3 0.05
68 55 0.95
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.29
Consensus pattern (68 bp):
CTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAAATAGATGAAAGGCTAAGTACCGTTGA
GGC
Found at i:1911220 original size:68 final size:68
Alignment explanation
Indices: 1911111--1911431 Score: 455
Period size: 68 Copynumber: 4.7 Consensus size: 68
1911101 AAGAATAATA
* * * ** *
1911111 GCCTAGCTATGCATTTGACAAAAATATGTCAATCATGCCAGTTAGATGAAAGGCTAAGTG-CATT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGTC-TT
1911175 TGAG
65 TGAG
* * * * *
1911179 GCCTAATTGTGCATTTGATAGAAAGATGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGTCTTT
1911244 GAG
66 GAG
* *
1911247 GCCTAACTGTGTATTTGACAGAAAGGTGTCAATTATGCCAATTAGATGAAAGGCTAAGTGTCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGTCTTT
*
1911312 AAG
66 GAG
* *
1911315 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTAAGCCAGTTAGATGAAAGACTAAGTGTCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGTCTTT
1911380 GAG
66 GAG
* * *
1911383 GCATAACTGTGTATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGA
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGA
1911432 GCGGTTACGT
Statistics
Matches: 229, Mismatches: 23, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
68 228 1.00
69 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (68 bp):
GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGTCTTT
GAG
Done.