Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008123.1 Hibiscus syriacus cultivar Beakdansim tig00110677_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: 770294
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:196360 original size:19 final size:17
Alignment explanation
Indices: 196336--196370 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
196326 TCCTCTCATT
196336 TCTTCTTCCTTCTTCCTTA
1 TCTTCTT-C-TCTTCCTTA
196355 TCTTCTTCTCTTCCTT
1 TCTTCTTCTCTTCCTT
196371 CTCCAAACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.60
Consensus pattern (17 bp):
TCTTCTTCTCTTCCTTA
Found at i:197689 original size:23 final size:23
Alignment explanation
Indices: 197646--197689 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
197636 TCATTATATG
*
197646 GCACTACGGTGCAATTCTACGCA
1 GCACTACGGTGCAATTATACGCA
* *
197669 GCACTTCGGTGCATTTATACG
1 GCACTACGGTGCAATTATACG
197690 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (23 bp):
GCACTACGGTGCAATTATACGCA
Found at i:203256 original size:19 final size:17
Alignment explanation
Indices: 203232--203266 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
203222 TCCTCTCATT
203232 TCTTCTTCCTTCTTCCTTA
1 TCTTCTT-C-TCTTCCTTA
203251 TCTTCTTCTCTTCCTT
1 TCTTCTTCTCTTCCTT
203267 CTCCAAACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.60
Consensus pattern (17 bp):
TCTTCTTCTCTTCCTTA
Found at i:204734 original size:150 final size:150
Alignment explanation
Indices: 204407--204723 Score: 582
Period size: 150 Copynumber: 2.1 Consensus size: 150
204397 GGGTAGAGGG
* * *
204407 TCTACGCGGTCCTTCGGGAGATATGTATATTCTTTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
204472 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
204537 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
204557 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAATACACA
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
204622 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
204687 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
204707 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
204724 TGCATTTATA
Statistics
Matches: 162, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
149 1 0.01
150 161 0.99
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:210410 original size:19 final size:19
Alignment explanation
Indices: 210386--210423 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
210376 GCGATTTTGA
*
210386 AAAATGTGCTGCGATAGTT
1 AAAATGTGCTGCGAGAGTT
*
210405 AAAATGTGTTGCGAGAGTT
1 AAAATGTGCTGCGAGAGTT
210424 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:0.32, C:0.08, G:0.29, T:0.32
Consensus pattern (19 bp):
AAAATGTGCTGCGAGAGTT
Found at i:210937 original size:19 final size:19
Alignment explanation
Indices: 210913--210949 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
210903 TGCGATACTG
* *
210913 GAGATCGCGTTACGATTTA
1 GAGATCGCATTACAATTTA
210932 GAGATCGCATTACAATTT
1 GAGATCGCATTACAATTT
210950 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTACAATTTA
Found at i:222054 original size:24 final size:24
Alignment explanation
Indices: 222023--222071 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
222013 CTAAAATAAC
* *
222023 AAAAAAAGAAATTTTAGGACTAAA
1 AAAAAAAGAAATTTAAGGACCAAA
222047 AAAAAAAGAAATTTAAGGACCAAA
1 AAAAAAAGAAATTTAAGGACCAAA
222071 A
1 A
222072 TAGCAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.16
Consensus pattern (24 bp):
AAAAAAAGAAATTTAAGGACCAAA
Found at i:223769 original size:22 final size:22
Alignment explanation
Indices: 223741--223782 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
223731 AAATGTAAAT
* *
223741 TAATAATAATTAATAAAAATGA
1 TAATAATAATAAAAAAAAATGA
223763 TAATAATAATAAAAAAAAAT
1 TAATAATAATAAAAAAAAAT
223783 TAAAATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
TAATAATAATAAAAAAAAATGA
Found at i:224667 original size:35 final size:36
Alignment explanation
Indices: 224614--224727 Score: 144
Period size: 35 Copynumber: 3.2 Consensus size: 36
224604 TTGTATCTCA
**
224614 GAGAAAAA-TGTCTCAAGCGAGATGAAATTTGTTTT
1 GAGAAAAATTGTCTCAAGCGAGACAAAATTTGTTTT
*
224649 GAGAGAAATTG-CTCAAGCGAGACAAAATTTGTTTT
1 GAGAAAAATTGTCTCAAGCGAGACAAAATTTGTTTT
* *
224684 TAGAAAAATTGTCTCAAGCGAGACAATGA-TTGTTTTT
1 GAGAAAAATTGTCTCAAGCGAGACAA-AATTTG-TTTT
224721 GAGAAAA
1 GAGAAAA
224728 TGATCTCAAG
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
35 38 0.56
36 19 0.28
37 11 0.16
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.30
Consensus pattern (36 bp):
GAGAAAAATTGTCTCAAGCGAGACAAAATTTGTTTT
Found at i:224728 original size:36 final size:34
Alignment explanation
Indices: 224614--224737 Score: 121
Period size: 36 Copynumber: 3.5 Consensus size: 34
224604 TTGTATCTCA
* *
224614 GAGAAAAATGTCTCAAGCGAGATGAAATT-TGTTTT
1 GAGAAAATTGTCTCAAGCGAGA-CAAATTGT-TTTT
224649 GAGAGAAATTG-CTCAAGCGAGACAAAATTTGTTTTT
1 GAGA-AAATTGTCTCAAGCGAGAC-AAA-TTGTTTTT
224685 -AGAAAAATTGTCTCAAGCGAGACAATGATTGTTTTT
1 GAG-AAAATTGTCTCAAGCGAGACAA--ATTGTTTTT
224721 GAGAAAA-TGATCTCAAG
1 GAGAAAATTG-TCTCAAG
224738 TGAAATCAAC
Statistics
Matches: 77, Mismatches: 2, Indels: 19
0.79 0.02 0.19
Matches are distributed among these distances:
35 30 0.39
36 43 0.56
37 4 0.05
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (34 bp):
GAGAAAATTGTCTCAAGCGAGACAAATTGTTTTT
Found at i:224866 original size:104 final size:105
Alignment explanation
Indices: 224730--225038 Score: 387
Period size: 104 Copynumber: 3.0 Consensus size: 105
224720 TGAGAAAATG
* * *
224730 ATCTCAAGTGAAATCAACTTTGTTTAATGTGAAGCAAATTC-AAATTTGTATCTCAAAGGGAAAA
1 ATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAA
*
224794 TGTCTCAAG-AGAGACAAAATATGTTTTGAAAGAAATAATA
66 TGTCTCAAGCA-AGACAAAATATGTTTTGAAAGAAATAACA
* * * * *
224834 ATCTCAAGTGAGATTAATTTTGTTTCAA-GTGAATCAAATTCGAAATTTGTATATCAAAGGAAAA
1 ATCTCAAGTGAGATCAACTTTGTTT-AATGTGAAACAAATTCAAAATTTGTATCTCAAAGG-AAA
* * * *
224898 AATGTCTCAAGCAAGACAAAGTTTGTTTT--AAGAGAA-AGCG
64 AATGTCTCAAGCAAGACAAAATATGTTTTGAAAGA-AATAACA
* * *
224938 ATCTGAAATGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTATATCTCAAAGGAAAAA
1 ATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAA
*
225003 TGTCTCAAGCAAGACGAAATATGTTTTGAAAGAAAT
66 TGTCTCAAGCAAGACAAAATATGTTTTGAAAGAAAT
225039 TGTCTCAAGT
Statistics
Matches: 174, Mismatches: 22, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
103 31 0.18
104 90 0.52
105 25 0.14
106 27 0.16
107 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.30
Consensus pattern (105 bp):
ATCTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAA
TGTCTCAAGCAAGACAAAATATGTTTTGAAAGAAATAACA
Found at i:225079 original size:71 final size:72
Alignment explanation
Indices: 224997--225137 Score: 214
Period size: 71 Copynumber: 2.0 Consensus size: 72
224987 TATCTCAAAG
*
224997 GAAAAATGTCTCAAGCAAGAC-GAAATATGTTTTGAAAGAAATTGTCTCAAGTGAGAC-AAAATT
1 GAAAAATGTCTCAAGCAAGACAG-AATATGTTTTGAAAGAAATTGTCTCAAGCGAGACAAAAATT
225060 TGTTTTTA
65 TGTTTTTA
* * * *
225068 GAAAACTGTCTCAAGCGAGACAGAATTTGTTTTGAGAGAAATTGTCTCAAGCGAGACAAAAATTT
1 GAAAAATGTCTCAAGCAAGACAGAATATGTTTTGAAAGAAATTGTCTCAAGCGAGACAAAAATTT
225133 GTTTT
66 GTTTT
225138 AAAATTCTTA
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 50 0.79
72 13 0.21
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.30
Consensus pattern (72 bp):
GAAAAATGTCTCAAGCAAGACAGAATATGTTTTGAAAGAAATTGTCTCAAGCGAGACAAAAATTT
GTTTTTA
Found at i:225088 original size:35 final size:36
Alignment explanation
Indices: 225003--225137 Score: 182
Period size: 36 Copynumber: 3.8 Consensus size: 36
224993 AAAGGAAAAA
* * * *
225003 TGTCTCAAGCAAGACGAAATATGTTTTGAAAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTGAGAGAAAT
* * *
225039 TGTCTCAAGTGAGACAAAATTTGTTTTTAGA-AAAC
1 TGTCTCAAGCGAGACAAAATTTGTTTTGAGAGAAAT
*
225074 TGTCTCAAGCGAGACAGAATTTGTTTTGAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTGAGAGAAAT
225110 TGTCTCAAGCGAGACAAAAATTTGTTTT
1 TGTCTCAAGCGAGAC-AAAATTTGTTTT
225138 AAAATTCTTA
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
35 31 0.36
36 43 0.51
37 11 0.13
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTGAGAGAAAT
Found at i:225491 original size:14 final size:14
Alignment explanation
Indices: 225459--225549 Score: 89
Period size: 14 Copynumber: 6.6 Consensus size: 14
225449 TGATGTAAAT
225459 TGTATGTATCATATA
1 TGTATGTAT-ATATA
*
225474 TGTATGTATATGTA
1 TGTATGTATATATA
225488 TGTATGTATATATA
1 TGTATGTATATATA
* *
225502 -ATATATATATATA
1 TGTATGTATATATA
* *
225515 TATATATATATATA
1 TGTATGTATATATA
* *
225529 TATATATATATAT-
1 TGTATGTATATATA
225542 TG-ATGTAT
1 TGTATGTAT
225550 GTTTTTATCA
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
12 5 0.07
13 12 0.17
14 43 0.62
15 9 0.13
ACGTcount: A:0.40, C:0.01, G:0.10, T:0.49
Consensus pattern (14 bp):
TGTATGTATATATA
Found at i:225501 original size:2 final size:2
Alignment explanation
Indices: 225469--225541 Score: 94
Period size: 2 Copynumber: 37.0 Consensus size: 2
225459 TGTATGTATC
* * * * *
225469 AT AT AT GT AT GT AT AT GT AT GT AT GT AT AT AT A- 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
225510 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
225542 TGATGTATGT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (2 bp):
AT
Found at i:229549 original size:333 final size:333
Alignment explanation
Indices: 228944--229610 Score: 1318
Period size: 333 Copynumber: 2.0 Consensus size: 333
228934 GAATATTGCA
228944 CGATCTTCGAGCTCACTGCTTTGTCTCGGATCTTTGTATTTGGAACTAATACCCCCAATACTCTA
1 CGATCTTCGAGCTCACTGCTTTGTCTCGGATCTTTGTATTTGGAACTAATACCCCCAATACTCTA
229009 TAAACTAACTCTGTTAATGCCTCGATAATACTGAAATTAGTGCGTCACTCTTGGTAGTTATCGTT
66 TAAACTAACTCTGTTAATGCCTCGATAATACTGAAATTAGTGCGTCACTCTTGGTAGTTATCGTT
229074 GGAACAATCGTAGATAAGAATCTACCACTGGATTACTCATCGGATCTATAGATCACCTTTCCAAT
131 GGAACAATCGTAGATAAGAATCTACCACTGGATTACTCATCGGATCTATAGATCACCTTTCCAAT
229139 CTCGAATATTACATGATCTTTGATCAAATCTCATTTTGGGTACTCTGAACTCCTTTTAGCCTTCA
196 CTCGAATATTACATGATCTTTGATCAAATCTCATTTTGGGTACTCTGAACTCCTTTTAGCCTTCA
229204 ATGCATGTCTGTATATGAGACTGCTTGATTGAAAACTTTTACCTCTTC-TGTGAAGATTTTCTAT
261 ATGCATGTCTGTATATGAGACTGCTTGATTGAAAACTTTTACCTCTTCTTGTGAAGATTTTCTAT
229268 CGAATATC
326 CGAATATC
229276 CGATCTTCGAGCTCACTGCTTTGTCTCGGATCTTTGTATTTGGAACTAATACCCCCAATACTCTA
1 CGATCTTCGAGCTCACTGCTTTGTCTCGGATCTTTGTATTTGGAACTAATACCCCCAATACTCTA
229341 TAAACTAACTCTGTTAATGCCTCGATAATACTGAAATTAGTGCGTCACTCTTTGGTAGTTATCGT
66 TAAACTAACTCTGTTAATGCCTCGATAATACTGAAATTAGTGCGTCACTC-TTGGTAGTTATCGT
229406 TGGAACAATCGTAGATAAGAATCTACCACTGGATTACTCATCGGATCTATAGATCACCTTTCCAA
130 TGGAACAATCGTAGATAAGAATCTACCACTGGATTACTCATCGGATCTATAGATCACCTTTCCAA
229471 TCTCGAATATTACATGATCTTTGATCAAATCTCATTTTGGGTACTCTGAACTCCTTTTAGCCTTC
195 TCTCGAATATTACATGATCTTTGATCAAATCTCATTTTGGGTACTCTGAACTCCTTTTAGCCTTC
229536 AATGCATGTCTGTATATGAGACTGCTTGATTGAAAACTTTTACCTCTTCTTGTGAAGATTTTCTA
260 AATGCATGTCTGTATATGAGACTGCTTGATTGAAAACTTTTACCTCTTCTTGTGAAGATTTTCTA
229601 TCGAATATC
325 TCGAATATC
229610 C
1 C
229611 TCTTGTGGAT
Statistics
Matches: 333, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
332 115 0.35
333 193 0.58
334 25 0.08
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (333 bp):
CGATCTTCGAGCTCACTGCTTTGTCTCGGATCTTTGTATTTGGAACTAATACCCCCAATACTCTA
TAAACTAACTCTGTTAATGCCTCGATAATACTGAAATTAGTGCGTCACTCTTGGTAGTTATCGTT
GGAACAATCGTAGATAAGAATCTACCACTGGATTACTCATCGGATCTATAGATCACCTTTCCAAT
CTCGAATATTACATGATCTTTGATCAAATCTCATTTTGGGTACTCTGAACTCCTTTTAGCCTTCA
ATGCATGTCTGTATATGAGACTGCTTGATTGAAAACTTTTACCTCTTCTTGTGAAGATTTTCTAT
CGAATATC
Found at i:231098 original size:22 final size:22
Alignment explanation
Indices: 231071--231112 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
231061 GGAGATAGAC
231071 GGATTTCGTCGGAGATGGGGAT
1 GGATTTCGTCGGAGATGGGGAT
231093 GGATTTCGTCGGAGATGGGG
1 GGATTTCGTCGGAGATGGGG
231113 GCAGATGTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.17, C:0.10, G:0.48, T:0.26
Consensus pattern (22 bp):
GGATTTCGTCGGAGATGGGGAT
Found at i:231271 original size:20 final size:20
Alignment explanation
Indices: 231246--231375 Score: 77
Period size: 20 Copynumber: 6.4 Consensus size: 20
231236 GCGTAAAAAC
231246 ATTTGACTTTTGCGTTGCGA
1 ATTTGACTTTTGCGTTGCGA
* * *
231266 ATTTGACTATCGCGTTACGA
1 ATTTGACTTTTGCGTTGCGA
* * * *
231286 ATTTAACCTCTCTGTGTCGCG-
1 ATTTGA-CT-TTTGCGTTGCGA
* *
231307 ATTT-ACAAATTCGCGTTGCGA
1 ATTTGAC--TTTTGCGTTGCGA
*
231328 ATTTGACTTTT-CTGTTGAGA
1 ATTTGACTTTTGC-GTTGCGA
* * *
231348 ATTTGACTATAGCGTTGTGA
1 ATTTGACTTTTGCGTTGCGA
231368 ATTTGACT
1 ATTTGACT
231376 ATCGCATTGC
Statistics
Matches: 81, Mismatches: 21, Indels: 16
0.69 0.18 0.14
Matches are distributed among these distances:
19 2 0.02
20 61 0.75
21 11 0.14
22 7 0.09
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.41
Consensus pattern (20 bp):
ATTTGACTTTTGCGTTGCGA
Found at i:231444 original size:20 final size:20
Alignment explanation
Indices: 231397--231463 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
231387 ATAGTCAAAT
231397 TCGCGTTGCGAAATTGGA-A
1 TCGCGTTGCGAAATTGGAGA
* * *
231416 ACTGGGTTGCGAAATTGGAGT
1 TC-GCGTTGCGAAATTGGAGA
*
231437 TCGCGTTGCG-AATTTGAGA
1 TCGCGTTGCGAAATTGGAGA
231456 TCGCGTTG
1 TCGCGTTG
231464 TGAATTTGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 16 0.41
20 22 0.56
21 1 0.03
ACGTcount: A:0.21, C:0.15, G:0.34, T:0.30
Consensus pattern (20 bp):
TCGCGTTGCGAAATTGGAGA
Found at i:231459 original size:19 final size:19
Alignment explanation
Indices: 231421--231471 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
231411 TGGAAACTGG
* *
231421 GTTGCGAAATTGGAGTTCGC
1 GTTGCG-AATTTGAGATCGC
231441 GTTGCGAATTTGAGATCGC
1 GTTGCGAATTTGAGATCGC
*
231460 GTTGTGAATTTG
1 GTTGCGAATTTG
231472 TTGGTCATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.20, C:0.12, G:0.33, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTTGAGATCGC
Found at i:234544 original size:16 final size:17
Alignment explanation
Indices: 234510--234547 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
234500 AATCTATTTG
234510 TTATTTCAATTTTTATT
1 TTATTTCAATTTTTATT
*
234527 TTATTTGAATTTTT-TT
1 TTATTTCAATTTTTATT
234543 TTATT
1 TTATT
234548 GGGAAAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (17 bp):
TTATTTCAATTTTTATT
Found at i:237586 original size:31 final size:31
Alignment explanation
Indices: 237548--237665 Score: 166
Period size: 31 Copynumber: 3.8 Consensus size: 31
237538 ACTTAATATG
* *
237548 TTTAGTACTTAAACTATT-AATTTTAGACCGT
1 TTTAGTACCTAAACT-TTCAATTTTAGTCCGT
**
237579 TTTAGTACCTAAACTTTCAATTTTAGTCTAT
1 TTTAGTACCTAAACTTTCAATTTTAGTCCGT
*
237610 TTTAGTACCTAAAATTTTCAATTTTAGTCCGT
1 TTTAGTACCT-AAACTTTCAATTTTAGTCCGT
237642 TTTAGTACCTAAACTTTCAATTTT
1 TTTAGTACCTAAACTTTCAATTTT
237666 TTTAAAACTT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
30 2 0.03
31 47 0.61
32 28 0.36
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.47
Consensus pattern (31 bp):
TTTAGTACCTAAACTTTCAATTTTAGTCCGT
Found at i:237636 original size:63 final size:62
Alignment explanation
Indices: 237548--237665 Score: 191
Period size: 63 Copynumber: 1.9 Consensus size: 62
237538 ACTTAATATG
* *
237548 TTTAGTACTTAAACTATTAATTTTAGACCGTTTTAGTACCTAAACTTTCAATTTTAGTCTAT
1 TTTAGTACCTAAAATATTAATTTTAGACCGTTTTAGTACCTAAACTTTCAATTTTAGTCTAT
* *
237610 TTTAGTACCTAAAATTTTCAATTTTAGTCCGTTTTAGTACCTAAACTTTCAATTTT
1 TTTAGTACCTAAAATATT-AATTTTAGACCGTTTTAGTACCTAAACTTTCAATTTT
237666 TTTAAAACTT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
62 15 0.29
63 36 0.71
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.47
Consensus pattern (62 bp):
TTTAGTACCTAAAATATTAATTTTAGACCGTTTTAGTACCTAAACTTTCAATTTTAGTCTAT
Found at i:237997 original size:32 final size:32
Alignment explanation
Indices: 237935--238017 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
237925 GATTACACTT
* *
237935 TTTTATCCCTCAACTTTTATTATACATTTTT-A
1 TTTTATCACTCAA-TTTTTTTATACATTTTTAA
* *
237967 TTTTATCACTCATTTTTTTTATATAGTTTTTAA
1 TTTTATCACTCAATTTTTTTATACA-TTTTTAA
* *
238000 TTTGATTACTCAATTTTT
1 TTTTATCACTCAATTTTT
238018 AAATTACTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
31 10 0.24
32 16 0.38
33 16 0.38
ACGTcount: A:0.24, C:0.13, G:0.02, T:0.60
Consensus pattern (32 bp):
TTTTATCACTCAATTTTTTTATACATTTTTAA
Found at i:238017 original size:33 final size:31
Alignment explanation
Indices: 237943--238017 Score: 78
Period size: 33 Copynumber: 2.3 Consensus size: 31
237933 TTTTTTATCC
* *
237943 CTCAACTTTTATTATACATTTTTATTTTATCA
1 CTCAA-TTTTTTTATACATTTTTATTTGATCA
* * *
237975 CTCATTTTTTTTATATAGTTTTTAATTTGATTA
1 CTCAATTTTTTTATACA-TTTTT-ATTTGATCA
238008 CTCAATTTTT
1 CTCAATTTTT
238018 AAATTACTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
31 10 0.29
32 9 0.26
33 16 0.46
ACGTcount: A:0.25, C:0.12, G:0.03, T:0.60
Consensus pattern (31 bp):
CTCAATTTTTTTATACATTTTTATTTGATCA
Found at i:238495 original size:13 final size:13
Alignment explanation
Indices: 238474--238533 Score: 79
Period size: 13 Copynumber: 4.8 Consensus size: 13
238464 ATTTTATTAG
238474 TATTTTATTTAAT
1 TATTTTATTTAAT
* *
238487 TATTGTA-TTATT
1 TATTTTATTTAAT
*
238499 TA-ATTATTTAAT
1 TATTTTATTTAAT
238511 TATTTTATTTAAT
1 TATTTTATTTAAT
238524 TATTTTATTT
1 TATTTTATTT
238534 TTTTACAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 2 0.05
12 12 0.31
13 25 0.64
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:238496 original size:8 final size:8
Alignment explanation
Indices: 238478--238528 Score: 65
Period size: 8 Copynumber: 6.8 Consensus size: 8
238468 TATTAGTATT
238478 TTATTTAA
1 TTATTTAA
238486 TTATTGT-A
1 TTATT-TAA
238494 TTATTTAA
1 TTATTTAA
238502 TTATTTAA
1 TTATTTAA
238510 TTA-TT--
1 TTATTTAA
238515 TTATTTAA
1 TTATTTAA
238523 TTATTT
1 TTATTT
238529 TATTTTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
5 3 0.08
6 2 0.05
7 3 0.08
8 29 0.76
9 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (8 bp):
TTATTTAA
Found at i:238803 original size:8 final size:8
Alignment explanation
Indices: 238785--238837 Score: 60
Period size: 8 Copynumber: 7.1 Consensus size: 8
238775 TTTATAACTG
238785 TAAAA-AA
1 TAAAATAA
238792 TAAAATAA
1 TAAAATAA
238800 T--AA-AA
1 TAAAATAA
238805 TAAAATAA
1 TAAAATAA
*
238813 TAAAAAAA
1 TAAAATAA
*
238821 TTAAATAA
1 TAAAATAA
238829 TAAAATAA
1 TAAAATAA
238837 T
1 T
238838 TAATACAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
5 3 0.08
6 2 0.05
7 7 0.18
8 26 0.68
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
TAAAATAA
Found at i:238804 original size:13 final size:13
Alignment explanation
Indices: 238788--238837 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
238778 ATAACTGTAA
238788 AAAATAAAATAAT
1 AAAATAAAATAAT
238801 AAAATAAAATAAT
1 AAAATAAAATAAT
*
238814 AAAA-AAATTAA-
1 AAAATAAAATAAT
*
238825 ATAATAAAATAAT
1 AAAATAAAATAAT
238838 TAATACAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 3 0.09
12 12 0.38
13 17 0.53
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:242943 original size:37 final size:37
Alignment explanation
Indices: 242867--242943 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
242857 TTTTTATGTT
*
242867 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
242904 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
242941 TTT
1 TTT
242944 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:242965 original size:17 final size:17
Alignment explanation
Indices: 242921--242966 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
242911 TTTTAAAGAA
*
242921 AATATATAAATATTTTAC
1 AATATAT-AATATTATAC
* *
242939 AATTTGTAATATTATAC
1 AATATATAATATTATAC
242956 AATATATAATA
1 AATATATAATA
242967 AGGACAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (17 bp):
AATATATAATATTATAC
Found at i:248698 original size:21 final size:21
Alignment explanation
Indices: 248673--248728 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
248663 ACCTTACGGT
248673 GGTGGCATCTGAAATGGTTGC
1 GGTGGCATCTGAAATGGTTGC
248694 GGTGGCATCTGAAATGGTTGC
1 GGTGGCATCTGAAATGGTTGC
*
248715 GGTGTCATCTGAAA
1 GGTGGCATCTGAAA
248729 CAACTGCGAT
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:0.14, G:0.36, T:0.29
Consensus pattern (21 bp):
GGTGGCATCTGAAATGGTTGC
Found at i:250569 original size:36 final size:36
Alignment explanation
Indices: 250518--250589 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
250508 GAGCTATGCA
* *
250518 CACAAAGATCATGTTATATTAATACCAAAAGTATTC
1 CACAAAGATCATGTTAGATTAATACCAAAAGCATTC
* *
250554 CACAAAGATCCTGTTAGATTGATACCAAAAGCATTC
1 CACAAAGATCATGTTAGATTAATACCAAAAGCATTC
250590 TACGGTAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (36 bp):
CACAAAGATCATGTTAGATTAATACCAAAAGCATTC
Found at i:261697 original size:21 final size:21
Alignment explanation
Indices: 261668--261708 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
261658 AAGGGAGAAG
*
261668 AAAATGATAGAAAGTAAAAGT
1 AAAAAGATAGAAAGTAAAAGT
*
261689 AAAAAGATAGAAAGTGAAAG
1 AAAAAGATAGAAAGTAAAAG
261709 GTGAAAACGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (21 bp):
AAAAAGATAGAAAGTAAAAGT
Found at i:261959 original size:19 final size:19
Alignment explanation
Indices: 261935--261971 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
261925 CTTGCAAAAA
261935 TAAAATGAAAATGATTAAT
1 TAAAATGAAAATGATTAAT
*
261954 TAAAATGAAAATTATTAA
1 TAAAATGAAAATGATTAA
261972 AAATAAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (19 bp):
TAAAATGAAAATGATTAAT
Found at i:269458 original size:20 final size:20
Alignment explanation
Indices: 269421--269463 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
269411 AATCCACCAC
269421 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGCTTCTAA
* * *
269441 ATGCATCTATATGGTTCTAA
1 ATGCAACTAAATGCTTCTAA
269461 ATG
1 ATG
269464 GGCCTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (20 bp):
ATGCAACTAAATGCTTCTAA
Found at i:270140 original size:36 final size:36
Alignment explanation
Indices: 269934--270119 Score: 201
Period size: 37 Copynumber: 5.1 Consensus size: 36
269924 GAATGTTTTC
269934 AAACAGAAATTTATCTCACTTGAGATTGTTTTTCTTA
1 AAACA-AAATTTATCTCACTTGAGATTGTTTTTCTTA
* * ** ** **
269971 AAACAAAATTTGTCTCGCTTGAGACAGTTTCACTCG
1 AAACAAAATTTATCTCACTTGAGATTGTTTTTCTTA
270007 AAACAGAAATTTATCTCACTTGAGATTGTTTTTCTTA
1 AAACA-AAATTTATCTCACTTGAGATTGTTTTTCTTA
* ** ** **
270044 AAACAAAATTTATCTCGCTTGAGACAGTTTCACTCG
1 AAACAAAATTTATCTCACTTGAGATTGTTTTTCTTA
*
270080 AAAGAATAATTTATCTCACTTGAGATTGTTTTTCTTA
1 AAACAA-AATTTATCTCACTTGAGATTGTTTTTCTTA
270117 AAA
1 AAA
270120 TAAGATTCGT
Statistics
Matches: 116, Mismatches: 31, Indels: 4
0.77 0.21 0.03
Matches are distributed among these distances:
36 57 0.49
37 59 0.51
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (36 bp):
AAACAAAATTTATCTCACTTGAGATTGTTTTTCTTA
Found at i:270172 original size:73 final size:73
Alignment explanation
Indices: 269934--270164 Score: 392
Period size: 73 Copynumber: 3.2 Consensus size: 73
269924 GAATGTTTTC
269934 AAACAGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGT
1 AAACAGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGT
269999 TTCACTCG
66 TTCACTCG
*
270007 AAACAGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTATCTCGCTTGAGACAGT
1 AAACAGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGT
270072 TTCACTCG
66 TTCACTCG
* * * *
270080 AAAGA-ATAATTTATCTCACTTGAGATTGTTTTTCTTAAAATAAGATTCGTCTCGCTTGAGACAG
1 AAACAGA-AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAG
*
270144 TTTCACTAG
65 TTTCACTCG
270153 AAACAGAAATTT
1 AAACAGAAATTT
270165 CCATCACTCG
Statistics
Matches: 148, Mismatches: 8, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
72 1 0.01
73 146 0.99
74 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.37
Consensus pattern (73 bp):
AAACAGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGT
TTCACTCG
Found at i:270398 original size:123 final size:123
Alignment explanation
Indices: 270201--270635 Score: 683
Period size: 123 Copynumber: 3.5 Consensus size: 123
270191 AGAAATAGTC
*
270201 CATAATGAGAAGAACTCATATGAAGATGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCT
1 CATAATGAGAAGAACTCATATGAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCT
* * *
270266 TTTGCTCGATTCTATCACAGAATGAGATATACCAGCATCAACATTTTCAGAGGAAGTT
66 TTTGCTCGATTCTATCACAGAAGGAGATAGATCAGCATCAACATTTTCAGAGGAAGTT
* * *
270324 CATAACGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCAAAATGAGAAGAACTTGTTCAACCT
1 CATAATGAGAAGAACTCATATGAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCT
* *
270389 TTTGCTCGATTCTATCACAAAAGGAGATAGATCAGCATCAACATTTCCAGAGGAAGTT
66 TTTGCTCGATTCTATCACAGAAGGAGATAGATCAGCATCAACATTTTCAGAGGAAGTT
* *
270447 CATAATGAGAATAACTCATATGAAGAGGAAGAAAAAGTTCATAATAAGAAGAACTTGTTCAACCT
1 CATAATGAGAAGAACTCATATGAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCT
* * *
270512 TTTGCTCGATTCTATCACAGAAGGAGATAGATCAACATCAAC-GTTTCTAGATGAAGTT
66 TTTGCTCGATTCTATCACAGAAGGAGATAGATCAGCATCAACATTTTC-AGAGGAAGTT
* * * * *
270570 CATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATTATGAGAAGAAATTGTTCGACCT
1 CATAATGAGAAGAACTCATATGAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCT
270635 T
66 T
270636 AGCTTGATTC
Statistics
Matches: 285, Mismatches: 26, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
122 3 0.01
123 282 0.99
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.25
Consensus pattern (123 bp):
CATAATGAGAAGAACTCATATGAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCT
TTTGCTCGATTCTATCACAGAAGGAGATAGATCAGCATCAACATTTTCAGAGGAAGTT
Found at i:270768 original size:20 final size:20
Alignment explanation
Indices: 270706--270769 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 20
270696 TTCAGAGGAA
270706 GTTCATAATGAGAAGAACTCAT
1 GTTCATAATGAGAAGAACT--T
* *
270728 -TTGAAAATGAAGAAGAA---
1 GTTCATAATG-AGAAGAACTT
270745 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
270765 GTTCA
1 GTTCA
270770 ACCTTGCCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
17 7 0.21
18 7 0.21
20 5 0.15
21 7 0.21
22 7 0.21
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:270800 original size:139 final size:137
Alignment explanation
Indices: 270555--270881 Score: 410
Period size: 139 Copynumber: 2.4 Consensus size: 137
270545 AACATCAACG
* * *
270555 TTTCTAGATGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATTATGAGAA
1 TTTC-AGAGGAAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAA
* * * *
270620 GAAATTGTTCGACCTTAGCTTGATTCATCATCTATGGAGTTGAATGAAAGAAGAACCTCACTT-G
65 GAAATTGTTCAACCTTAGCTTAATTCATCATCTATGAAGTTGAATCAAAG-A-AACCTC-CTTCG
*
270684 AGGATCAATAT
127 AGGATCAACAT
* *
270695 TTTCAGAGGAAGTTCATAATGAGAAGAACTCATTTGAAAATGAAGAAGAAGTTCATAATGAGAAG
1 TTTCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAG
* * * *
270760 AACTTGTTCAACCTT-GCCTTAATTCATCA-CATATGAAGTTGAATCAATGACACCTCTTTCGAG
66 AAATTGTTCAACCTTAG-CTTAATTCATCATC-TATGAAGTTGAATCAAAGAAACCTCCTTCGAG
*
270823 GATCAGCAT
129 GATCAACAT
* *
270832 TTCCAGAAGG-AGTTCATAATGAGAAGAACTCATCTGACAAGGAAGAAGAA
1 TTTCAG-AGGAAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAA
270882 CTTGTTCAAT
Statistics
Matches: 164, Mismatches: 19, Indels: 11
0.85 0.10 0.06
Matches are distributed among these distances:
136 2 0.01
137 57 0.35
138 6 0.04
139 95 0.58
140 4 0.02
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (137 bp):
TTTCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAG
AAATTGTTCAACCTTAGCTTAATTCATCATCTATGAAGTTGAATCAAAGAAACCTCCTTCGAGGA
TCAACAT
Found at i:272363 original size:20 final size:21
Alignment explanation
Indices: 272316--272378 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 21
272306 ATTTTAGCTC
*
272316 TTTACTTTATATTTTAATTTA
1 TTTAATTTATATTTTAATTTA
** *
272337 TGCAATTTAT-TTTTTATTTA
1 TTTAATTTATATTTTAATTTA
*
272357 TTTAATTTCATTACTTTAATTT
1 TTTAATTT-A-TATTTTAATTT
272379 TCTATTTTTG
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
20 15 0.48
21 8 0.26
22 1 0.03
23 7 0.23
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTAATTTATATTTTAATTTA
Found at i:275457 original size:16 final size:16
Alignment explanation
Indices: 275436--275471 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
275426 TTCTTGGAAT
275436 TTTTAAATTTTTTAAA
1 TTTTAAATTTTTTAAA
* *
275452 TTTTAATTTTTTTATA
1 TTTTAAATTTTTTAAA
275468 TTTT
1 TTTT
275472 TTACTGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTAAATTTTTTAAA
Found at i:278117 original size:33 final size:32
Alignment explanation
Indices: 278078--278156 Score: 128
Period size: 30 Copynumber: 2.5 Consensus size: 32
278068 TTTTTTACCG
278078 AAAATATTAATATTTTTTTATAAAGTATTATTT
1 AAAATATT-ATATTTTTTTATAAAGTATTATTT
278111 AAAATA-T-TATTTTTTTATAAAGTATTATTT
1 AAAATATTATATTTTTTTATAAAGTATTATTT
278141 AAAATATTAT-TTTTTT
1 AAAATATTATATTTTTT
278157 ATCAAAAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
30 29 0.66
31 7 0.16
32 2 0.05
33 6 0.14
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (32 bp):
AAAATATTATATTTTTTTATAAAGTATTATTT
Found at i:278121 original size:15 final size:15
Alignment explanation
Indices: 278103--278151 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
278093 TTTTATAAAG
278103 TATTATTTAAAATAT
1 TATTATTTAAAATAT
* * *
278118 TATTTTTTTATAA-AG
1 TA-TTATTTAAAATAT
278133 TATTATTTAAAATAT
1 TATTATTTAAAATAT
278148 TATT
1 TATT
278152 TTTTTATCAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 8 0.31
15 10 0.38
16 8 0.31
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
TATTATTTAAAATAT
Found at i:278124 original size:30 final size:30
Alignment explanation
Indices: 278088--278158 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
278078 AAAATATTAA
278088 TATTTTTTTATAAAGTATTATTTAAAATAT
1 TATTTTTTTATAAAGTATTATTTAAAATAT
278118 TATTTTTTTATAAAGTATTATTTAAAATAT
1 TATTTTTTTATAAAGTATTATTTAAAATAT
278148 TATTTTTTTAT
1 TATTTTTTTAT
278159 CAAAAATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (30 bp):
TATTTTTTTATAAAGTATTATTTAAAATAT
Found at i:278136 original size:18 final size:18
Alignment explanation
Indices: 278088--278140 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
278078 AAAATATTAA
278088 TATTTTTTTATAAAGTAT
1 TATTTTTTTATAAAGTAT
278106 TA----TTTA-AAA-TAT
1 TATTTTTTTATAAAGTAT
278118 TATTTTTTTATAAAGTAT
1 TATTTTTTTATAAAGTAT
278136 TATTT
1 TATTT
278141 AAAATATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
12 5 0.17
13 3 0.10
14 4 0.14
16 4 0.14
17 3 0.10
18 10 0.34
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (18 bp):
TATTTTTTTATAAAGTAT
Found at i:278985 original size:112 final size:112
Alignment explanation
Indices: 278751--279031 Score: 307
Period size: 112 Copynumber: 2.5 Consensus size: 112
278741 TCATATTTAC
* * *
278751 CTAAACTATCAATTTTGATCCATTTTAATATCTAAACTTTTAATTGTTTTTCAAAA-CATACCTA
1 CTAAACTATCAATTTTGATCCGTTTT-ATATCTAAA-TTTTCATT-TTTTTCAAAATCATACCAA
** * * * * *
278815 ATGTTTAATTTTTTTAGTATTCCGCTGCTAAAAACTTCCGTTTTTAGTAT
63 ACATTTAATTTTTATAGTATCCCACCGCTAAAAACTTCCGCTTTTAGTAT
* *
278865 CTAAACTATCAATTTTGATCCGTTTTAGTATTTAAAATTTCA-TTTTTTCAAAATCATACCAAAC
1 CTAAACTATCAATTTTGATCCGTTTTA-TATCTAAATTTTCATTTTTTTCAAAATCATACCAAAC
* * * *
278929 ATTTAGTTTTTATAGTA-CCCACCGCTAAAAACTTCATGCTTTTATTGT
65 ATTTAATTTTTATAGTATCCCACCGCTAAAAACTTC-CGCTTTTAGTAT
* * * *
278977 CTAAACTATTAGTTTTGACCCGTTTTATCACCTAAATTTTCATTTTTTTCAAAAT
1 CTAAACTATCAATTTTGATCCGTTTTAT-ATCTAAATTTTCATTTTTTTCAAAAT
279032 TTGATGTTAA
Statistics
Matches: 140, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
111 26 0.19
112 65 0.46
113 17 0.12
114 32 0.23
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (112 bp):
CTAAACTATCAATTTTGATCCGTTTTATATCTAAATTTTCATTTTTTTCAAAATCATACCAAACA
TTTAATTTTTATAGTATCCCACCGCTAAAAACTTCCGCTTTTAGTAT
Found at i:281994 original size:18 final size:16
Alignment explanation
Indices: 281953--281995 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
281943 TTTATAATTC
*
281953 TTTTAAAAATATTATG
1 TTTTAAAAATATTATA
*
281969 TTTGAAAAATTAATTATA
1 TTTTAAAAA-T-ATTATA
281987 TTTTAAAAA
1 TTTTAAAAA
281996 AATCATCGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
17 1 0.05
18 13 0.59
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (16 bp):
TTTTAAAAATATTATA
Found at i:286617 original size:34 final size:34
Alignment explanation
Indices: 286574--286641 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
286564 TCCTCCAGGA
*
286574 GGGGTCATAAAACTC-TGTGAC-GATGGCGGCGGCG
1 GGGGTCATAAAAC-CAGGTGACAG-TGGCGGCGGCG
286608 GGGGTCATAAAACCAGGTGACAGTGGCGGCGGCG
1 GGGGTCATAAAACCAGGTGACAGTGGCGGCGGCG
286642 ACATCGGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 1 0.03
34 29 0.94
35 1 0.03
ACGTcount: A:0.22, C:0.21, G:0.43, T:0.15
Consensus pattern (34 bp):
GGGGTCATAAAACCAGGTGACAGTGGCGGCGGCG
Found at i:288434 original size:17 final size:16
Alignment explanation
Indices: 288408--288453 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
288398 AAGCAAATAT
288408 AATATTAAATAATTTA
1 AATATTAAATAATTTA
*
288424 AATACTTAAATAAATTA
1 AATA-TTAAATAATTTA
*
288441 AATATAAAATAAT
1 AATATTAAATAAT
288454 AAATATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
AATATTAAATAATTTA
Found at i:290559 original size:11 final size:11
Alignment explanation
Indices: 290543--290584 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
290533 GAATTTTAAA
290543 ATTATAAAATT
1 ATTATAAAATT
290554 ATTATAAAATT
1 ATTATAAAATT
**
290565 -TTATTGAATT
1 ATTATAAAATT
*
290575 ATTACAAAAT
1 ATTATAAAAT
290585 GATCATTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (11 bp):
ATTATAAAATT
Found at i:294020 original size:18 final size:18
Alignment explanation
Indices: 293981--294014 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
293971 AGGATGAAAA
*
293981 ATAACATATATTAATATC
1 ATAACATATATAAATATC
293999 ATAACAT-TATAAATAT
1 ATAACATATATAAATAT
294015 TTATAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAACATATATAAATATC
Found at i:294391 original size:15 final size:15
Alignment explanation
Indices: 294371--294403 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
294361 TATTATTTGA
294371 TGCTTTTGGACAGCT
1 TGCTTTTGGACAGCT
294386 TGCTTTTGGACAGCT
1 TGCTTTTGGACAGCT
294401 TGC
1 TGC
294404 CATGCTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.21, G:0.27, T:0.39
Consensus pattern (15 bp):
TGCTTTTGGACAGCT
Found at i:296715 original size:64 final size:65
Alignment explanation
Indices: 296645--296770 Score: 191
Period size: 64 Copynumber: 2.0 Consensus size: 65
296635 TAGACCCTTA
* *
296645 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGACTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCAGAGTGCATCGATGCATGACTG
* * **
296709 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAACATCCTTAGTGCATCGATGCATGA
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCAGAGTGCATCGATGCATGA
296771 AATACATTCG
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
64 28 0.51
65 27 0.49
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCAGAGTGCATCGATGCATGACTG
Found at i:296814 original size:45 final size:45
Alignment explanation
Indices: 296707--296814 Score: 121
Period size: 46 Copynumber: 2.4 Consensus size: 45
296697 GATGCATGAC
* * *
296707 TGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAACATCCT
1 TGGTGCATCGATGCATGAAATACATTCGATG-TTTCATAACATCCA
* * *
296753 TAGTGCATCGATGCATGAAATACATTCGATG-TTCAATTTA-ATTCA
1 TGGTGCATCGATGCATGAAATACATTCGATGTTTC-A-TAACATCCA
296798 TGGTGCATCGATGCATG
1 TGGTGCATCGATGCATG
296815 GATCGGTGCA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
44 3 0.06
45 20 0.38
46 30 0.57
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (45 bp):
TGGTGCATCGATGCATGAAATACATTCGATGTTTCATAACATCCA
Found at i:308252 original size:18 final size:16
Alignment explanation
Indices: 308211--308253 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
308201 TTTATAATTC
*
308211 TTTTAAAAATATTATG
1 TTTTAAAAATATTATA
*
308227 TTTAAAAAATTAATTATA
1 TTTTAAAAA-T-ATTATA
308245 TTTTAAAAA
1 TTTTAAAAA
308254 AAATCATCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
17 1 0.05
18 13 0.59
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
TTTTAAAAATATTATA
Found at i:308614 original size:41 final size:41
Alignment explanation
Indices: 308532--308614 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 41
308522 ACGTAGGGTA
* * * *
308532 ATAGCGCGGGGCAGGGGCCGCGTCTTACCTTTCAATTATAT
1 ATAGCGCGGGGAAGGGACCGCATCTTACCTTTCAATAATAT
* *
308573 ATAGCGCGGGGAAGGGATCGCATCTTAGCTTT-AACTAATAT
1 ATAGCGCGGGGAAGGGACCGCATCTTACCTTTCAA-TAATAT
308614 A
1 A
308615 ATTATATAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
40 2 0.06
41 33 0.94
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (41 bp):
ATAGCGCGGGGAAGGGACCGCATCTTACCTTTCAATAATAT
Found at i:312586 original size:15 final size:15
Alignment explanation
Indices: 312566--312596 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
312556 CTCGCTGTCA
312566 TCATCGTCGTCGTCG
1 TCATCGTCGTCGTCG
312581 TCATCGTCGTCGTCG
1 TCATCGTCGTCGTCG
312596 T
1 T
312597 GAGTAGCTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.32, G:0.26, T:0.35
Consensus pattern (15 bp):
TCATCGTCGTCGTCG
Found at i:314453 original size:17 final size:16
Alignment explanation
Indices: 314427--314472 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
314417 AATTAAATAC
314427 AATATTAAATAATTTA
1 AATATTAAATAATTTA
*
314443 AATACTTAAATAAATTA
1 AATA-TTAAATAATTTA
*
314460 AATATAAAATAAT
1 AATATTAAATAAT
314473 AAATATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
AATATTAAATAATTTA
Found at i:317321 original size:11 final size:11
Alignment explanation
Indices: 317305--317346 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
317295 GAATTTTAAA
317305 ATTATAAAATT
1 ATTATAAAATT
317316 ATTATAAAATT
1 ATTATAAAATT
**
317327 -TTATTGAATT
1 ATTATAAAATT
*
317337 ATTACAAAAT
1 ATTATAAAAT
317347 GATCATTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (11 bp):
ATTATAAAATT
Found at i:317624 original size:21 final size:21
Alignment explanation
Indices: 317593--317641 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
317583 ATTATGTTTC
*
317593 AAACTCTTCATTTTTTTATTA
1 AAACTTTTCATTTTTTTATTA
*
317614 AACCTTTTCATTTTTTTATTA
1 AAACTTTTCATTTTTTTATTA
317635 AAACTTT
1 AAACTTT
317642 AATGGTAGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (21 bp):
AAACTTTTCATTTTTTTATTA
Found at i:319338 original size:25 final size:25
Alignment explanation
Indices: 319310--319358 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
319300 AAAACAATAT
*
319310 AAAGAAATATATATATTTATATGAA
1 AAAGAAATATATATATATATATGAA
*
319335 AAAGAAATATATATGTATATATGA
1 AAAGAAATATATATATATATATGA
319359 TTTAATTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (25 bp):
AAAGAAATATATATATATATATGAA
Found at i:332236 original size:25 final size:25
Alignment explanation
Indices: 332202--332265 Score: 110
Period size: 25 Copynumber: 2.6 Consensus size: 25
332192 AGCAGGCGGT
332202 GGCTGCTTGAAATTCAAAGGTGGGG
1 GGCTGCTTGAAATTCAAAGGTGGGG
332227 GGCTGCTTGAAATTCAAAGGTGGGG
1 GGCTGCTTGAAATTCAAAGGTGGGG
* *
332252 GCCTGCTTTAAATT
1 GGCTGCTTGAAATT
332266 TCAATGTTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.23, C:0.14, G:0.34, T:0.28
Consensus pattern (25 bp):
GGCTGCTTGAAATTCAAAGGTGGGG
Found at i:338301 original size:13 final size:12
Alignment explanation
Indices: 338276--338310 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
338266 GATGAATACA
*
338276 TTAATTAATTTT
1 TTAATTAAATTT
338288 TTAATTTAAATTT
1 TTAA-TTAAATTT
338301 TTAATTAAAT
1 TTAATTAAAT
338311 GCAAAAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTAATTAAATTT
Found at i:339913 original size:39 final size:38
Alignment explanation
Indices: 339863--340038 Score: 169
Period size: 39 Copynumber: 4.4 Consensus size: 38
339853 TATATATATA
* *
339863 ATATATA-ATATATATTTTTTTAATAAAATTTTGAATATATAT
1 ATATATATATATATAGTTTTTGAA-AAAATTTTG-A-A-A-AT
* *
339905 ATATATATATAATATAGTTTTTTTAAAAAACATTTTGAAAAC
1 ATATATATAT-ATATAG--TTTTTGAAAAA-ATTTTGAAAAT
* * *
339947 ATATATA-ATATATAGTTTTTGAAAACATTTTAAAAAC
1 ATATATATATATATAGTTTTTGAAAAAATTTTGAAAAT
*
339984 ATATATATAATATATAGTTTTTGAAAATATTTTGAAAAT
1 ATATATAT-ATATATAGTTTTTGAAAAAATTTTGAAAAT
340023 ATATATAT-TATATAGT
1 ATATATATATATATAGT
340039 ATAACATTAT
Statistics
Matches: 118, Mismatches: 9, Indels: 19
0.81 0.06 0.13
Matches are distributed among these distances:
37 25 0.21
38 9 0.08
39 35 0.30
40 6 0.05
41 2 0.02
42 15 0.13
43 3 0.03
44 6 0.05
45 4 0.03
46 13 0.11
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (38 bp):
ATATATATATATATAGTTTTTGAAAAAATTTTGAAAAT
Found at i:339928 original size:46 final size:45
Alignment explanation
Indices: 339852--339960 Score: 157
Period size: 45 Copynumber: 2.4 Consensus size: 45
339842 TCTATTTAGC
*
339852 ATATATATATAATATATAATATATATTTTTTTAATAAA-ATTTTGA
1 ATATATATATAATATATAATATA-ATTTTTTTAAAAAACATTTTGA
*
339897 ATATATATATATATATATAATATAGTTTTTTTAAAAAACATTTTGA
1 ATATATATATA-ATATATAATATAATTTTTTTAAAAAACATTTTGA
* *
339943 AAACATATATAATATATA
1 ATATATATATAATATATA
339961 GTTTTTGAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
45 30 0.52
46 28 0.48
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.47
Consensus pattern (45 bp):
ATATATATATAATATATAATATAATTTTTTTAAAAAACATTTTGA
Found at i:341231 original size:21 final size:20
Alignment explanation
Indices: 341199--341250 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
341189 AATTGTTCTT
*
341199 TTTTAAT-TTTTTTATTTTTA
1 TTTTAATATTTTTT-TCTTTA
341219 TTTTAATAATTTTTTTCTTTA
1 TTTTAAT-ATTTTTTTCTTTA
341240 -TTT-ATATTTTT
1 TTTTAATATTTTT
341251 CAATTGATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 6 0.21
19 2 0.07
20 10 0.34
21 5 0.17
22 6 0.21
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTAATATTTTTTTCTTTA
Found at i:342106 original size:40 final size:38
Alignment explanation
Indices: 341994--342122 Score: 98
Period size: 40 Copynumber: 3.2 Consensus size: 38
341984 AACTATATAA
** * *
341994 CATATATTATATTTTCAAAAACTATATGTTTTCAAAAAT
1 CATATATTATATTTTTTAAAACTATATATTTTC-AAAAC
* * * *
342033 TATTTATATTATATATGTTTAAAA-AAAACTATTTTCAAAAGC
1 CA--TATATTATAT-TTTTTAAAACTATA-TATTTTCAAAA-C
342075 CATATATTATATGTTTTTAAAACTATATATTTTCGAAAAC
1 CATATATTATAT-TTTTTAAAACTATATATTTTC-AAAAC
*
342115 TATATATT
1 CATATATT
342123 TTCAAAACCA
Statistics
Matches: 69, Mismatches: 14, Indels: 13
0.72 0.15 0.14
Matches are distributed among these distances:
39 1 0.01
40 33 0.48
41 22 0.32
42 13 0.19
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.45
Consensus pattern (38 bp):
CATATATTATATTTTTTAAAACTATATATTTTCAAAAC
Found at i:342115 original size:17 final size:16
Alignment explanation
Indices: 342082--342138 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
342072 AGCCATATAT
* *
342082 TATATGTTTTTAAAAC
1 TATATATTTTCAAAAC
342098 TATATATTTTCGAAAAC
1 TATATATTTTC-AAAAC
342115 TATATATTTTCAAAAC
1 TATATATTTTCAAAAC
*
342131 CATATATT
1 TATATATT
342139 ATATACATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 21 0.57
17 16 0.43
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.46
Consensus pattern (16 bp):
TATATATTTTCAAAAC
Found at i:344938 original size:2 final size:2
Alignment explanation
Indices: 344931--344961 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
344921 TAAAATAGGG
344931 AT AT 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 AT AT A
344962 CATGATGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:348020 original size:23 final size:21
Alignment explanation
Indices: 347968--348029 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
347958 TTTTGATGCA
*
347968 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
347988 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
348009 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
348030 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:354534 original size:33 final size:34
Alignment explanation
Indices: 354497--354563 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
354487 TTCAACCCTT
* * *
354497 GGCTGAAAATTAACATGGAA-TATATGATTATTA
1 GGCTGAAAAGTAACATGAAATTATATGATAATTA
**
354530 GGCTGAAGGGTAACATGAAATTATATGATAATTA
1 GGCTGAAAAGTAACATGAAATTATATGATAATTA
354564 TACTATATAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (34 bp):
GGCTGAAAAGTAACATGAAATTATATGATAATTA
Found at i:359058 original size:44 final size:42
Alignment explanation
Indices: 358977--359153 Score: 160
Period size: 42 Copynumber: 4.0 Consensus size: 42
358967 TTAAAAGGAG
358977 AAGACAAAGCCATGGAA-TTAATAATTAAAGCACTATGGAAT
1 AAGACAAAGCCATGGAATTTAATAATTAAAGCACTATGGAAT
* *
359018 AAAGACAATGCCATGGAATTTCAATAATTAAAGCATTATGGAAT
1 -AAGACAAAGCCATGGAATTT-AATAATTAAAGCACTATGGAAT
* * * *
359062 ATGACAAAGCTATAGAATTTAATAATTAACA-AACTATGGAACAAGT
1 AAGACAAAGCCATGGAATTTAATAATTAA-AGCACTATGG---AA-T
* * *
359108 CAACAAGATAAAGCCATGGGATTTAATAATTAAATCACTATGGAAT
1 ----AAGACAAAGCCATGGAATTTAATAATTAAAGCACTATGGAAT
359154 TTGAAACTTT
Statistics
Matches: 109, Mismatches: 14, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
42 31 0.28
43 19 0.17
44 21 0.19
45 2 0.02
46 2 0.02
47 2 0.02
49 1 0.01
50 31 0.28
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.25
Consensus pattern (42 bp):
AAGACAAAGCCATGGAATTTAATAATTAAAGCACTATGGAAT
Found at i:361585 original size:256 final size:254
Alignment explanation
Indices: 361061--361721 Score: 866
Period size: 256 Copynumber: 2.6 Consensus size: 254
361051 AGTTGTATAG
* *
361061 GGCCCCTTCGTCGTGAAGTTGAGCCTTGGAATTGGACATCCTTCGTCATGAAGTTGAAATCCAAT
1 GGCCCCTTCGTCGTGAAGTTGAGCCTT-GAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA-
*** * * * * *
361126 GTAAGTTACGCTGTTTCGAGGCCAATATCCTCCGTTGTGAAGTTGAAATTGACTTTGAAACTTGG
64 GTAAGTTATATTGTTTCGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAAC-TGG
* * * * * * *
361191 -AA--GTTTGTTGACAGACACTCTTTCTTTGAGTTGGATATATTTCGTCGTGAAGTTGAAATCCA
128 AAATTATTTGTTGACAGACAGTCATTCTTTGAATTGGATATACTTCATAGTGAAGTTGAAATCCA
** * * * *
361253 AACTAGAGATGGATGTTGCTTGTGTGCATGATTCCCTTCGTCGTGAAGTTGAAACTGCGGGT
193 AACTAGAGATGGATAATGCTTATATGCACGATTCCCTTCGTCGTGAAGTTGAAAATGCGGGT
* *
361315 GGCCCCTTCGTCGTGAAGTTGAGCC-TGAAATTGGATATCCTTCGCCGTGAAGTTGAAATTCAAG
1 GGCCCCTTCGTCGTGAAGTTGAGCCTTG-AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAG
* * *
361379 TAAGTTGTATTGTTCCGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGAA
65 TAAGTTATATTGTTTCGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACTGG-A
* *
361444 AATTATTTGTTGACAGCCAGTCATTCTTTGAATTGGATATCCTTCATAGTGAAGTTGAAATCCAA
129 AATTATTTGTTGACAGACAGTCATTCTTTGAATTGGATATACTTCATAGTGAAGTTGAAATCCAA
*
361509 ATCTGGAGATGGATAATGCTTATATGCACGATTCCCTTCGTCGTGAAGTT-AAAAT-CGTGGAT
194 A-CTAGAGATGGATAATGCTTATATGCACGATTCCCTTCGTCGTGAAGTTGAAAATGCG-GG-T
* *
361571 GGCCCCTCCGTCGTGAAGTTGAGCCTTGAATTGGATATCCTTTGTCGTGAAGTTGAAATCCAAGT
1 GGCCCCTTCGTCGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGT
* * *
361636 AAGTTTTATTGTTTCGAGTCTAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGGAACTAGGAA
66 AAGTTATATTGTTTCGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACT-GGAA
*
361701 ATTATTTGTTGACAGTCAGTC
130 ATTATTTGTTGACAGACAGTC
361722 GCCCCTTCGC
Statistics
Matches: 356, Mismatches: 41, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
251 3 0.01
252 51 0.14
253 34 0.10
254 27 0.08
255 59 0.17
256 178 0.50
257 4 0.01
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (254 bp):
GGCCCCTTCGTCGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGT
AAGTTATATTGTTTCGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACTGGAAA
TTATTTGTTGACAGACAGTCATTCTTTGAATTGGATATACTTCATAGTGAAGTTGAAATCCAAAC
TAGAGATGGATAATGCTTATATGCACGATTCCCTTCGTCGTGAAGTTGAAAATGCGGGT
Found at i:361738 original size:63 final size:65
Alignment explanation
Indices: 361662--361809 Score: 178
Period size: 67 Copynumber: 2.3 Consensus size: 65
361652 AGTCTAATAT
* * * *
361662 CCTTCGTCGTGAAGTTGAAATTGGCTCT-G-GAA-CTAGGAAA-TTATTTGTTGACAGTCAGTCG
1 CCTTCGT-GTGAAGTTGAAATTGACTCTAGCGAATCT-GAAAAGTTACTTGTTGACAATCAGTCG
361723 CC
64 CC
*
361725 CCTTCGCTGTGAAGTTGAAATTGACTCTGAGCGAATCTGAAAAGTTACTTGTTGACAATCAGTGG
1 CCTTCG-TGTGAAGTTGAAATTGACTCT-AGCGAATCTGAAAAGTTACTTGTTGACAATCAGTCG
361790 CC
64 CC
361792 CCTTCGTTGTGAAGTTGA
1 CCTTCG-TGTGAAGTTGA
361810 GCTTGTGTTG
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
63 25 0.34
64 1 0.01
65 1 0.01
66 7 0.10
67 39 0.53
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (65 bp):
CCTTCGTGTGAAGTTGAAATTGACTCTAGCGAATCTGAAAAGTTACTTGTTGACAATCAGTCGCC
Found at i:361918 original size:110 final size:110
Alignment explanation
Indices: 361725--361922 Score: 306
Period size: 110 Copynumber: 1.8 Consensus size: 110
361715 GTCAGTCGCC
* * * * *
361725 CCTTCGCTGTGAAGTTGAAATTGACTCTGAGCGAATCTGAAAAGTTACTTGTTGACAATCAGTGG
1 CCTTCGCTGTGAAGTTGAAATTGACTCTAAACGAAACTGAAAAGTTACTTGTTGACAACCAGTCG
361790 CCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATAT
66 CCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATAT
* * * **
361835 CCTTCGCTGTGAAGTTGAAATTGGCTCTAAATGAAACTGAGAAGTTGTTTGTTGACAACCAGTCG
1 CCTTCGCTGTGAAGTTGAAATTGACTCTAAACGAAACTGAAAAGTTACTTGTTGACAACCAGTCG
361900 CCCCTTCGTTGTGAAGTTGAGCT
66 CCCCTTCGTTGTGAAGTTGAGCT
361923 ACCACCATCA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
110 78 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (110 bp):
CCTTCGCTGTGAAGTTGAAATTGACTCTAAACGAAACTGAAAAGTTACTTGTTGACAACCAGTCG
CCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATAT
Found at i:365907 original size:44 final size:42
Alignment explanation
Indices: 365826--366002 Score: 160
Period size: 42 Copynumber: 4.0 Consensus size: 42
365816 TTAAAAGGAG
365826 AAGACAAAGCCATGGAA-TTAATAATTAAAGCACTATGGAAT
1 AAGACAAAGCCATGGAATTTAATAATTAAAGCACTATGGAAT
* *
365867 AAAGACAATGCCATGGAATTTCAATAATTAAAGCATTATGGAAT
1 -AAGACAAAGCCATGGAATTT-AATAATTAAAGCACTATGGAAT
* * * *
365911 ATGACAAAGCTATAGAATTTAATAATTAACA-AACTATGGAACAAGT
1 AAGACAAAGCCATGGAATTTAATAATTAA-AGCACTATGG---AA-T
* * *
365957 CAACAAGATAAAGCCATGGGATTTAATAATTAAATCACTATGGAAT
1 ----AAGACAAAGCCATGGAATTTAATAATTAAAGCACTATGGAAT
366003 TTGAAACTTT
Statistics
Matches: 109, Mismatches: 14, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
42 31 0.28
43 19 0.17
44 21 0.19
45 2 0.02
46 2 0.02
47 2 0.02
49 1 0.01
50 31 0.28
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.25
Consensus pattern (42 bp):
AAGACAAAGCCATGGAATTTAATAATTAAAGCACTATGGAAT
Found at i:367786 original size:29 final size:29
Alignment explanation
Indices: 367747--367831 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
367737 ACCCAACCCA
* * *
367747 TAGGTCTCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCGGCGACCTAC
* * *
367776 TAGGTCGCCATGCACTCCGGGCGACCAAG
1 TAGGTCGCCATGCACTCCCGGCGACCTAC
* *
367805 GAGGTCGCCATGCACGCCCGGCGACCT
1 TAGGTCGCCATGCACTCCCGGCGACCT
367832 TGTCTCCTTG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.18, C:0.40, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCGGCGACCTAC
Found at i:368020 original size:29 final size:29
Alignment explanation
Indices: 367974--368060 Score: 102
Period size: 29 Copynumber: 3.0 Consensus size: 29
367964 GGGTTAAAAG
* * *
367974 CTTGGTCGACGGGCGTGCATGGCGACCTC
1 CTTGGTCGCCGGGAGTGCATGGCGACCTA
*
368003 CTTGGTCGCCCGGAGTGCATGGCGACCTA
1 CTTGGTCGCCGGGAGTGCATGGCGACCTA
*** *
368032 GGAGGTCGCTGGGAGTGCATGGCGACCTA
1 CTTGGTCGCCGGGAGTGCATGGCGACCTA
368061 TGGGTTGGGT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.14, C:0.28, G:0.39, T:0.20
Consensus pattern (29 bp):
CTTGGTCGCCGGGAGTGCATGGCGACCTA
Found at i:373946 original size:13 final size:13
Alignment explanation
Indices: 373928--373958 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
373918 ATTAGATGAT
373928 TGAAGCCCAAGTC
1 TGAAGCCCAAGTC
373941 TGAAGCCCAAGTC
1 TGAAGCCCAAGTC
373954 TGAAG
1 TGAAG
373959 TCATTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.16
Consensus pattern (13 bp):
TGAAGCCCAAGTC
Found at i:376649 original size:20 final size:19
Alignment explanation
Indices: 376617--376663 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
376607 GATTATTTTC
*
376617 ATTTATATTTTGCCAATGT
1 ATTTATATCTTGCCAATGT
*
376636 ATTTCATATCTTGCCAATAT
1 ATTT-ATATCTTGCCAATGT
*
376656 ATATATAT
1 ATTTATAT
376664 AATATTCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.49
Consensus pattern (19 bp):
ATTTATATCTTGCCAATGT
Found at i:378161 original size:2 final size:2
Alignment explanation
Indices: 378154--378236 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
378144 TATTTCAAAT
378154 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
378196 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
378237 CAATTAAAAG
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:391647 original size:23 final size:23
Alignment explanation
Indices: 391616--391704 Score: 70
Period size: 23 Copynumber: 3.9 Consensus size: 23
391606 CACCACAGCT
* *
391616 CATATAAATGCACCAAAGTGTCG
1 CATAGAAATGCACCGAAGTGTCG
* * * *
391639 CATAGAAATGTACCGTAGTGCCA
1 CATAGAAATGCACCGAAGTGTCG
* * *
391662 CGTATAATTGCACCGAAGTGTCG
1 CATAGAAATGCACCGAAGTGTCG
** *
391685 TGTAGAAATGCACCGTAGTG
1 CATAGAAATGCACCGAAGTG
391705 CCATATAATG
Statistics
Matches: 49, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (23 bp):
CATAGAAATGCACCGAAGTGTCG
Found at i:391674 original size:46 final size:46
Alignment explanation
Indices: 391618--391707 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
391608 CCACAGCTCA
*
391618 TATAAATGCACCAAAGTGTCGCATAGAAATGTACCGTAGTGCCACG
1 TATAAATGCACCAAAGTGTCGCATAGAAATGCACCGTAGTGCCACG
* * **
391664 TATAATTGCACCGAAGTGTCGTGTAGAAATGCACCGTAGTGCCA
1 TATAAATGCACCAAAGTGTCGCATAGAAATGCACCGTAGTGCCA
391708 TATAATGTCC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (46 bp):
TATAAATGCACCAAAGTGTCGCATAGAAATGCACCGTAGTGCCACG
Found at i:393687 original size:12 final size:12
Alignment explanation
Indices: 393670--393694 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
393660 CCTTGATAAG
393670 TCAAATTTAACT
1 TCAAATTTAACT
393682 TCAAATTTAACT
1 TCAAATTTAACT
393694 T
1 T
393695 ATCAACTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (12 bp):
TCAAATTTAACT
Found at i:395875 original size:23 final size:23
Alignment explanation
Indices: 395841--395923 Score: 103
Period size: 23 Copynumber: 3.6 Consensus size: 23
395831 CTCGTATAAT
*
395841 TGCACCGAAGTGCCGCATAGAAA
1 TGCACCGTAGTGCCGCATAGAAA
* * * *
395864 TGCACTGTAGTGCCACCTAGAAT
1 TGCACCGTAGTGCCGCATAGAAA
* *
395887 TGCACCGAAGTGCCGCGTAGAAA
1 TGCACCGTAGTGCCGCATAGAAA
395910 TGCACCGTAGTGCC
1 TGCACCGTAGTGCC
395924 ATATAATGTC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.18
Consensus pattern (23 bp):
TGCACCGTAGTGCCGCATAGAAA
Found at i:397571 original size:19 final size:19
Alignment explanation
Indices: 397547--397595 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
397537 TTAAGGGGTG
*
397547 CATCGATGCACTTCCTGTA
1 CATCGATACACTTCCTGTA
*
397566 CATCGATACACTTCCTGTG
1 CATCGATACACTTCCTGTA
397585 CATCGATACAC
1 CATCGATACAC
397596 ACTGAACAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.29
Consensus pattern (19 bp):
CATCGATACACTTCCTGTA
Found at i:397919 original size:12 final size:12
Alignment explanation
Indices: 397902--397926 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
397892 CCTTGATAAG
397902 TCAAATTTAACT
1 TCAAATTTAACT
397914 TCAAATTTAACT
1 TCAAATTTAACT
397926 T
1 T
397927 ATCAACTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (12 bp):
TCAAATTTAACT
Found at i:409466 original size:19 final size:20
Alignment explanation
Indices: 409424--409466 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
409414 TTTTCCTAAT
*
409424 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACATAAA
409444 TCGCAACGCGAATACAT-AA
1 TCGCAACGCGAATACATAAA
409463 TCGC
1 TCGC
409467 GTTGCGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.37, C:0.28, G:0.19, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGAATACATAAA
Found at i:410398 original size:24 final size:24
Alignment explanation
Indices: 410347--410400 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
410337 GTATTCGAAA
*
410347 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
410371 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
410395 TTTGAT
1 TTTGAT
410401 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:412977 original size:19 final size:19
Alignment explanation
Indices: 412955--413122 Score: 131
Period size: 19 Copynumber: 9.3 Consensus size: 19
412945 GAATCGTAAT
412955 GCGAAATGAAAATCGCAAC
1 GCGAAATGAAAATCGCAAC
* *
412974 GCGAATATGAATATCACAAC
1 GCGAA-ATGAAAATCGCAAC
** *
412994 GCGGAAATGACTATCGCAAT
1 GC-GAAATGAAAATCGCAAC
* *
413014 GTGAAATGAAAATCCCAA-
1 GCGAAATGAAAATCGCAAC
* *
413032 -CG--A-GAGAATCGCAAT
1 GCGAAATGAAAATCGCAAC
*
413047 GCGAAATGAAAATCGCAAT
1 GCGAAATGAAAATCGCAAC
413066 GCGAAATGAAAATCGCAA-
1 GCGAAATGAAAATCGCAAC
* *
413084 -CG--A-GGAAATCGCAAA
1 GCGAAATGAAAATCGCAAC
*
413099 GCGAAATGAAAATCACAAC
1 GCGAAATGAAAATCGCAAC
413118 GCGAA
1 GCGAA
413123 TTTAGTTTCG
Statistics
Matches: 120, Mismatches: 17, Indels: 24
0.75 0.11 0.15
Matches are distributed among these distances:
14 19 0.16
15 2 0.02
16 4 0.03
17 3 0.03
18 2 0.02
19 61 0.51
20 26 0.22
21 3 0.03
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (19 bp):
GCGAAATGAAAATCGCAAC
Found at i:413062 original size:52 final size:52
Alignment explanation
Indices: 412997--413122 Score: 173
Period size: 52 Copynumber: 2.4 Consensus size: 52
412987 TCACAACGCG
** * *
412997 GAAATGACTATCGCAATGTGAAATGAAAATCCCAACGA-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGAAATGAAAATCCCAACGAGGA-AATCGCAAAGC
*
413049 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGGAAATCGCAAAGC
1 GAAATGAAAATCGCAATGCGAAATGAAAATCCCAACGAGGAAATCGCAAAGC
* *
413101 GAAATGAAAATCACAACGCGAA
1 GAAATGAAAATCGCAATGCGAA
413123 TTTAGTTTCG
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
52 64 0.97
53 2 0.03
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.13
Consensus pattern (52 bp):
GAAATGAAAATCGCAATGCGAAATGAAAATCCCAACGAGGAAATCGCAAAGC
Found at i:413103 original size:33 final size:33
Alignment explanation
Indices: 413056--413118 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
413046 TGCGAAATGA
* *
413056 AAATCGCAATGCGAAATGAAAATCGCAACGAGG
1 AAATCGCAAAGCGAAATGAAAATCACAACGAGG
413089 AAATCGCAAAGCGAAATGAAAATCACAACG
1 AAATCGCAAAGCGAAATGAAAATCACAACG
413119 CGAATTTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.49, C:0.19, G:0.21, T:0.11
Consensus pattern (33 bp):
AAATCGCAAAGCGAAATGAAAATCACAACGAGG
Found at i:413140 original size:19 final size:19
Alignment explanation
Indices: 413118--413192 Score: 65
Period size: 19 Copynumber: 4.2 Consensus size: 19
413108 AAATCACAAC
413118 GCGAATTT-AGTTTCGCATT
1 GCGAATTTCA-TTTCGCATT
*
413137 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCATT
413156 GCG-A-TTC-TCTT-G--TT
1 GCGAATTTCAT-TTCGCATT
*
413170 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCATT
413189 GCGA
1 GCGA
413193 TAATCATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
14 5 0.11
16 7 0.16
17 7 0.16
19 25 0.56
20 1 0.02
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.44
Consensus pattern (19 bp):
GCGAATTTCATTTCGCATT
Found at i:413201 original size:19 final size:19
Alignment explanation
Indices: 413128--413193 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
413118 GCGAATTTAG
413128 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
413147 TTTCGCATTGCGATTCTC-
1 TTTCGCATTGCGATTTTCA
413165 -TT-G--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
413180 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
413194 AATCATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
14 10 0.25
16 3 0.08
17 3 0.08
19 24 0.60
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:413319 original size:14 final size:14
Alignment explanation
Indices: 413300--413336 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
413290 CATCAATTAA
413300 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
413314 ACAAATCATCTTTT
1 ACAAATCAACTTTT
413328 ACAAATCAA
1 ACAAATCAA
413337 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:415259 original size:14 final size:14
Alignment explanation
Indices: 415237--415325 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
415227 AACACGAAAT
*
415237 GAATTGCAACGAGA
1 GAATCGCAACGAGA
415251 GAATCGCAACGCGAAATGA
1 GAATCGCAA--CG--A-GA
*
415270 AAATCGCAACGAGA
1 GAATCGCAACGAGA
415284 GAATCGCAACGCGAAATGA
1 GAATCGCAA--CG--A-GA
*
415303 AAATCGCAACGAGA
1 GAATCGCAACGAGA
415317 GAATCGCAA
1 GAATCGCAA
415326 TGCGAAATGA
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
14 28 0.47
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 20 0.33
ACGTcount: A:0.45, C:0.20, G:0.25, T:0.10
Consensus pattern (14 bp):
GAATCGCAACGAGA
Found at i:415276 original size:19 final size:19
Alignment explanation
Indices: 415252--415349 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
415242 GCAACGAGAG
415252 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
415271 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
415285 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
415304 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
415318 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
415337 AATTGCAACGCGA
1 AATCGCAACGCGA
415350 TTATAGTTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:415284 original size:33 final size:33
Alignment explanation
Indices: 415222--415346 Score: 200
Period size: 33 Copynumber: 3.8 Consensus size: 33
415212 AAAAATGACT
* *
415222 ATCGCAACACGAAATG--AATTGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
415253 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
415286 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
415319 ATCGCAATGCGAAATGAAAATTGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
415347 CGATTATAGT
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 15 0.17
33 73 0.83
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:415368 original size:19 final size:17
Alignment explanation
Indices: 415346--415468 Score: 66
Period size: 19 Copynumber: 7.3 Consensus size: 17
415336 AAATTGCAAC
415346 GCGATTATAGTTTCGCGTT
1 GCGATT-TA-TTTCGCGTT
415365 GCGATTT-TTT--CGTT
1 GCGATTTATTTCGCGTT
415379 GCGATTTTCATTTCGCGTT
1 GCGA-TTT-ATTTCGCGTT
* *
415398 GCGA--T-TCTCTCGTT
1 GCGATTTATTTCGCGTT
*
415412 GCGATTTTCATTTTGCGTT
1 GCGA-TTT-ATTTCGCGTT
* *
415431 GCGA--T-TCTCTCGTT
1 GCGATTTATTTCGCGTT
415445 GCGATTTTCATTTCGCGTT
1 GCGA-TTT-ATTTCGCGTT
415464 GCGAT
1 GCGAT
415469 AGTCATTTTT
Statistics
Matches: 79, Mismatches: 10, Indels: 31
0.66 0.08 0.26
Matches are distributed among these distances:
14 29 0.37
15 3 0.04
16 5 0.06
17 5 0.06
18 2 0.03
19 35 0.44
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
GCGATTTATTTCGCGTT
Found at i:415378 original size:14 final size:14
Alignment explanation
Indices: 415361--415452 Score: 58
Period size: 14 Copynumber: 5.9 Consensus size: 14
415351 TATAGTTTCG
415361 CGTTGCGATTTTTT
1 CGTTGCGATTTTTT
415375 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TTT
* *
415392 CGCGTTGCGATTCTCT
1 --CGTTGCGATTTTTT
415408 CGTTGCGATTTTCATTTT
1 CGTTGCGA--TT--TTTT
* *
415426 GCGTTGCGATTCTCT
1 -CGTTGCGATTTTTT
415441 CGTTGCGATTTT
1 CGTTGCGATTTT
415453 CATTTCGCGT
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 27 0.44
15 5 0.08
16 4 0.07
17 5 0.08
18 4 0.07
19 16 0.26
ACGTcount: A:0.09, C:0.21, G:0.22, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:415393 original size:33 final size:33
Alignment explanation
Indices: 415356--415468 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
415346 GCGATTATAG
* *
415356 TTTCGCGTTGCGATTTTTTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
415389 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
*
415422 TTTTGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
415455 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
415469 AGTCATTTTT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.09, C:0.21, G:0.22, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:415702 original size:94 final size:93
Alignment explanation
Indices: 415556--415829 Score: 381
Period size: 94 Copynumber: 3.1 Consensus size: 93
415546 ATGGATTGCA
* *
415556 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
* *
415621 TAGCAGAATTGACAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAATAAAT
*
415649 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAAT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
415714 TTAGCAGAATTGGTAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAATAAAT
* *
415743 TTACTTCAA-C------C---A-AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAATAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
*
415797 TAGCAGTATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAATAAAT
415825 TTACT
1 TTACT
415830 AAGCAATCTA
Statistics
Matches: 169, Mismatches: 11, Indels: 13
0.88 0.06 0.07
Matches are distributed among these distances:
82 70 0.41
83 1 0.01
86 1 0.01
92 1 0.01
93 9 0.05
94 87 0.51
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAATAAAT
Found at i:415814 original size:82 final size:82
Alignment explanation
Indices: 415673--415829 Score: 269
Period size: 82 Copynumber: 1.9 Consensus size: 82
415663 AAGACAAAAC
* *
415673 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAATTTAGCAGAATTGGTAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAATTTAGCAGAATTGGCAGCAACCGAA
415738 TAAATTTACTTCAACCA
66 TAAATTTACTTCAACCA
* * *
415755 AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAATAGTTTAGCAGTATTGGCAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAATTTAGCAGAATTGGCAGCAACCGAA
415820 TAAATTTACT
66 TAAATTTACT
415830 AAGCAATCTA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 70 1.00
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.25
Consensus pattern (82 bp):
AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAATTTAGCAGAATTGGCAGCAACCGAA
TAAATTTACTTCAACCA
Found at i:417558 original size:20 final size:20
Alignment explanation
Indices: 417533--417588 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
417523 TGAAATGAAA
*
417533 ATCGCAACGAGAGAATTACT
1 ATCGCAACGAGAGAATGACT
*
417553 ATCGCAACGCG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
417573 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
417589 CGCAACGCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:417592 original size:14 final size:14
Alignment explanation
Indices: 417573--417628 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
417563 GGAAATGACT
417573 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
417587 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
417606 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
417620 ATCGCAACG
1 ATCGCAACG
417629 CGAAATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:417610 original size:19 final size:19
Alignment explanation
Indices: 417524--417669 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
417514 TCTTTTGGTT
*
417524 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* **
417543 GAGAATTACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
417563 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
417581 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
417597 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
417614 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
417630 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
417649 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
417668 GA
1 GA
417670 TTTTGGTTTC
Statistics
Matches: 102, Mismatches: 13, Indels: 24
0.73 0.09 0.17
Matches are distributed among these distances:
14 19 0.19
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 43 0.42
20 26 0.25
21 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:417610 original size:33 final size:33
Alignment explanation
Indices: 417524--417647 Score: 158
Period size: 33 Copynumber: 3.5 Consensus size: 33
417514 TCTTTTGGTT
417524 GAAATGAAAATCGCAACGAGAGAATTACTATCGCAACGC
1 GAAATGAAAATCGCAACGAGAG----A--ATCGCAACGC
**
417563 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
417597 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
417630 GAAATTAAAATCGCAACG
1 GAAATGAAAATCGCAACG
417648 CGAAATGAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
33 48 0.61
34 10 0.13
36 1 0.01
40 20 0.25
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.13
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:417687 original size:19 final size:19
Alignment explanation
Indices: 417665--417786 Score: 74
Period size: 20 Copynumber: 6.5 Consensus size: 19
417655 AAAATCGCAA
** *
417665 TGCGATTTTGGTTTCGTGT
1 TGCGATTTTCATTTCGCGT
417684 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
417703 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
*
417717 TGCGATTTTCATTTCTCTCGT
1 TGCGATTTTCA-TT-TCGCGT
** **
417738 TGCGATAGTCATTTTCATGT
1 TGCGATTTTCA-TTTCGCGT
**
417758 TGCGATTTTCATTTTCATGT
1 TGCGATTTTCA-TTTCGCGT
417778 TGCGATTTT
1 TGCGATTTT
417787 AAGTTTAGAA
Statistics
Matches: 86, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
14 10 0.12
16 3 0.03
17 3 0.03
19 21 0.24
20 31 0.36
21 18 0.21
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:417784 original size:20 final size:20
Alignment explanation
Indices: 417715--417786 Score: 101
Period size: 20 Copynumber: 3.5 Consensus size: 20
417705 CGATTCTCTC
417715 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
**
417735 CGTTGCGATAGTCATTTTCAT
1 -GTTGCGATTTTCATTTTCAT
417756 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
417776 GTTGCGATTTT
1 GTTGCGATTTT
417787 AAGTTTAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
20 31 0.67
21 15 0.33
ACGTcount: A:0.14, C:0.17, G:0.18, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:418369 original size:20 final size:20
Alignment explanation
Indices: 418344--418557 Score: 243
Period size: 20 Copynumber: 10.6 Consensus size: 20
418334 CTTTAAAAAT
418344 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
418364 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
418384 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
418405 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
418425 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
418445 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
418465 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
418485 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
418505 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
418526 TGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
418547 CTCGTTGCGAT
1 CGCGTTGCGAT
418558 AGTCAGAATC
Statistics
Matches: 162, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
20 109 0.67
21 53 0.33
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:418430 original size:40 final size:41
Alignment explanation
Indices: 418346--418557 Score: 347
Period size: 41 Copynumber: 5.2 Consensus size: 41
418336 TTAAAAATCG
*
418346 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
418387 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
418427 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
418467 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
418508 CGTTGCGATTTACGGATATGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
418549 CGTTGCGAT
1 CGTTGCGAT
418558 AGTCAGAATC
Statistics
Matches: 160, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 76 0.47
41 84 0.52
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:418575 original size:41 final size:42
Alignment explanation
Indices: 418346--418618 Score: 291
Period size: 40 Copynumber: 6.7 Consensus size: 42
418336 TTAAAAATCG
* *
418346 CGTTGCGATTTAC-GGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACAGAATACGCGTTGCGATTTTACGTATTCT
* *
418387 CGTTGCGATTTAC-GGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACAGAATACGCGTTGCGATTTTACGTATTCT
418427 CGTTGCGATTTACAG-ATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACAGAATACGCGTTGCGATTTTACGTATTCT
* *
418467 CGTTGCGATTTAC-GGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACAGAATACGCGTTGCGATTTTACGTATTCT
* * * *
418508 CGTTGCGATTTAC-GGATATGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACAGAATACGCGTTGCGATTTTACGTATTCT
* * * *
418549 CGTTGCGATAGT-CAGAAT-CGCATTGCGATTTATA--TGTTCC
1 CGTTGCGAT-TTACAGAATACGCGTTGCGATTT-TACGTATTCT
* * *
418589 CGTTGCGATTTTCA-TATTCGCGTTGCGATT
1 CGTTGCGATTTACAGAATACGCGTTGCGATT
418619 CTGGAAAATC
Statistics
Matches: 205, Mismatches: 19, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
39 4 0.02
40 98 0.48
41 97 0.47
42 6 0.03
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (42 bp):
CGTTGCGATTTACAGAATACGCGTTGCGATTTTACGTATTCT
Found at i:418594 original size:20 final size:20
Alignment explanation
Indices: 418571--418618 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
418561 CAGAATCGCA
*
418571 TTGCGATTTAT-ATGTTCCCG
1 TTGCGATTT-TCATATTCCCG
*
418591 TTGCGATTTTCATATTCGCG
1 TTGCGATTTTCATATTCCCG
418611 TTGCGATT
1 TTGCGATT
418619 CTGGAAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTCATATTCCCG
Found at i:418612 original size:81 final size:81
Alignment explanation
Indices: 418346--418618 Score: 329
Period size: 81 Copynumber: 3.4 Consensus size: 81
418336 TTAAAAATCG
* *
418346 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCATT
**
418411 GCGATTTACGTATTCT
66 GCGATTTATATATTCT
*
418427 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCGTT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCATT
*
418491 GCGATTT-TACGTATTGT
66 GCGATTTATA--TATTCT
* * * * * *
418508 CGTTGCGATTTACGGATATGCGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-ATCGCA
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGAT-TTACGGATA-CGCA
* *
418571 TTGCGATTTATATGTTCC
64 TTGCGATTTATATATTCT
* * *
418589 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACAGATACGCGTTGCGATT
418619 CTGGAAAATC
Statistics
Matches: 165, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
80 41 0.25
81 87 0.53
82 34 0.21
83 3 0.02
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (81 bp):
CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCATT
GCGATTTATATATTCT
Found at i:418717 original size:20 final size:19
Alignment explanation
Indices: 418668--418721 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
418658 ATTCTTCACA
418668 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
418687 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
418708 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
418722 TTTATTTCGA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:418975 original size:126 final size:126
Alignment explanation
Indices: 418787--419036 Score: 491
Period size: 126 Copynumber: 2.0 Consensus size: 126
418777 TAAAATCGTA
418787 TATTATAAGGCATTTTTGGTCACTGAGGCGATTTTCTCTAATTTTTATTAGTAACTTTAAAGTGG
1 TATTATAAGGCATTTTTGGTCACTGAGGCGATTTTCTCTAATTTTTATTAGTAACTTTAAAGTGG
418852 ATGAATTGGTTTGACACGTGTATAATTTTTATATTGTATGTATTCTTCCATAATATCTAGG
66 ATGAATTGGTTTGACACGTGTATAATTTTTATATTGTATGTATTCTTCCATAATATCTAGG
*
418913 TATTATAAGGCATTTTTGGTCACTGAGGCTATTTTCTCTAATTTTTATTAGTAACTTTAAAGTGG
1 TATTATAAGGCATTTTTGGTCACTGAGGCGATTTTCTCTAATTTTTATTAGTAACTTTAAAGTGG
418978 ATGAATTGGTTTGACACGTGTATAATTTTTATATTGTATGTATTCTTCCATAATATCTA
66 ATGAATTGGTTTGACACGTGTATAATTTTTATATTGTATGTATTCTTCCATAATATCTA
419037 TGTTCCTCCA
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 123 1.00
ACGTcount: A:0.27, C:0.10, G:0.16, T:0.46
Consensus pattern (126 bp):
TATTATAAGGCATTTTTGGTCACTGAGGCGATTTTCTCTAATTTTTATTAGTAACTTTAAAGTGG
ATGAATTGGTTTGACACGTGTATAATTTTTATATTGTATGTATTCTTCCATAATATCTAGG
Found at i:421138 original size:18 final size:18
Alignment explanation
Indices: 421115--421159 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
421105 TGGAAAAGTT
421115 ATGTAAGAGTTGGAAATG
1 ATGTAAGAGTTGGAAATG
421133 ATGTAAGAGTTGGAAATG
1 ATGTAAGAGTTGGAAATG
421151 ATGTAAGAG
1 ATGTAAGAG
421160 GTATTCTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.27
Consensus pattern (18 bp):
ATGTAAGAGTTGGAAATG
Found at i:422551 original size:22 final size:22
Alignment explanation
Indices: 422526--422570 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
422516 ATCATTTTTT
422526 ATTATATATGATGTTTATCATG
1 ATTATATATGATGTTTATCATG
*
422548 ATTATATATGATGTTTATTATG
1 ATTATATATGATGTTTATCATG
422570 A
1 A
422571 ATGATATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.51
Consensus pattern (22 bp):
ATTATATATGATGTTTATCATG
Done.