Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008029.1 Hibiscus syriacus cultivar Beakdansim tig00110505_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: 3983240
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 18
Found at i:2008248 original size:21 final size:21
Alignment explanation
Indices: 2008182--2008248 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2008172 GTGAATCGGG
*
2008182 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2008202 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2008224 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2008245 CTCT
1 CTCT
2008249 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2008267 original size:42 final size:41
Alignment explanation
Indices: 2008182--2008304 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
2008172 GTGAATCGGG
* * * * *
2008182 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
2008224 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
2008266 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
2008305 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:2009452 original size:21 final size:22
Alignment explanation
Indices: 2009410--2009452 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2009400 AATAACAAAC
*
2009410 ATTAGTAATTGTTAAATAATTA
1 ATTAGTAATTGTTAAAAAATTA
2009432 ATTA-TAATT-TTAAAAACATTA
1 ATTAGTAATTGTTAAAAA-ATTA
2009453 TATAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
ATTAGTAATTGTTAAAAAATTA
Found at i:2010350 original size:20 final size:19
Alignment explanation
Indices: 2010305--2010426 Score: 57
Period size: 20 Copynumber: 6.8 Consensus size: 19
2010295 TCTTTTGGTT
2010305 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* * *
2010324 GATAATGAGAATTGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
2010345 GAAATGACTATCGCAATGA
1 GAAATGAAAATCGCAACGA
*
2010364 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
2010378 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
2010397 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
2010411 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2010427 TGCGATTTTG
Statistics
Matches: 74, Mismatches: 17, Indels: 24
0.64 0.15 0.21
Matches are distributed among these distances:
14 18 0.24
16 4 0.05
17 4 0.05
19 20 0.27
20 26 0.35
21 2 0.03
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:2010387 original size:33 final size:33
Alignment explanation
Indices: 2010330--2010428 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
2010320 ACGAGATAAT
*
2010330 GAGAATTGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAATGA
* *
2010364 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAATGA
**
2010397 GAGAATCGCAACGCGAAATGAAAATCGCAATG
1 GAGAATCGCAACGCGAAATGACTATCGCAATG
2010429 CGATTTTGGT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 45 0.78
34 13 0.22
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.14
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAATGA
Found at i:2010460 original size:19 final size:19
Alignment explanation
Indices: 2010427--2010493 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
2010417 AAAATCGCAA
**
2010427 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
2010446 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
** *
2010465 TGCGATAGTTATTTCCGCTT
1 TGCGATTTTTATTT-CGCGT
2010485 TGCGATTTT
1 TGCGATTTT
2010494 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:2011109 original size:20 final size:20
Alignment explanation
Indices: 2011016--2011109 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
2011006 CGCTAAGTAA
*
2011016 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
2011036 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
2011056 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
2011077 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
2011097 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
2011110 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:2011128 original size:41 final size:41
Alignment explanation
Indices: 2011037--2011171 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
2011027 AAAGTCAGTA
* * * ** *
2011037 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
2011077 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
2011119 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
2011160 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2011172 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:2011142 original size:20 final size:20
Alignment explanation
Indices: 2011098--2011190 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
2011088 ATAGTCAGTA
* **
2011098 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
2011119 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
2011139 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
2011160 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
2011180 TCGCATTGCGA
1 TCGCATTGCGA
2011191 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:2011172 original size:41 final size:41
Alignment explanation
Indices: 2011098--2011193 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
2011088 ATAGTCAGTA
*
2011098 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
2011139 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
2011180 TCGCATTGCGAATT
1 TCGCATTGCGAATT
2011194 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:2012622 original size:14 final size:14
Alignment explanation
Indices: 2012605--2012650 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
2012595 AATGAACATA
2012605 AACGAACATAACCG
1 AACGAACATAACCG
* *
2012619 AACGAATATAACTG
1 AACGAACATAACCG
2012633 AACGAACATAACCG
1 AACGAACATAACCG
2012647 AACG
1 AACG
2012651 TTCACGAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.50, C:0.24, G:0.15, T:0.11
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:2022520 original size:2 final size:2
Alignment explanation
Indices: 2022515--2022545 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2022505 ATGTTGTACA
2022515 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
2022546 AACATAAAAG
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:2022869 original size:21 final size:21
Alignment explanation
Indices: 2022732--2022872 Score: 77
Period size: 21 Copynumber: 6.6 Consensus size: 21
2022722 TTCTAGGCGA
*
2022732 TCCTTCGGGACATATATGTGA
1 TCCTTCGGGACATATATGTGG
* *
2022753 TCCTT-GGGAACTTATATGTGA
1 TCCTTCGGG-ACATATATGTGG
** * * * *
2022774 TCCTTCATGATATATGTTTTG
1 TCCTTCGGGACATATATGTGG
** *
2022795 TCCTTTAGAACATATATGTGG
1 TCCTTCGGGACATATATGTGG
* * * *
2022816 TCCTACGGGATAATTCTTTGTGG
1 TCCTTCGGGA-CA-TATATGTGG
**
2022839 TTATTCGGGACATATATGTGG
1 TCCTTCGGGACATATATGTGG
*
2022860 TCCTTTGGGACAT
1 TCCTTCGGGACAT
2022873 TCTATATGGC
Statistics
Matches: 84, Mismatches: 32, Indels: 8
0.68 0.26 0.06
Matches are distributed among these distances:
20 3 0.04
21 64 0.76
22 3 0.04
23 14 0.17
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.40
Consensus pattern (21 bp):
TCCTTCGGGACATATATGTGG
Found at i:2023134 original size:2 final size:2
Alignment explanation
Indices: 2023127--2023177 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2023117 TCATTTTTAT
2023127 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
2023169 TA TA TA TA T
1 TA TA TA TA T
2023178 GCCCAACTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2029481 original size:22 final size:22
Alignment explanation
Indices: 2029455--2029498 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2029445 AAAATATGGT
* *
2029455 ATGAACAATATCGTGAATAGTA
1 ATGAACAATATCATGAACAGTA
2029477 ATGAACAATATCATGAACAGTA
1 ATGAACAATATCATGAACAGTA
2029499 GTGAGCAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (22 bp):
ATGAACAATATCATGAACAGTA
Found at i:2029616 original size:22 final size:22
Alignment explanation
Indices: 2029591--2029633 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2029581 TACAGTGTCA
*
2029591 CTACAATGCTGCTACAATACCG
1 CTACAATACTGCTACAATACCG
* *
2029613 CTACAGTACTGCTACAGTACC
1 CTACAATACTGCTACAATACC
2029634 TCAGCAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.33, G:0.14, T:0.23
Consensus pattern (22 bp):
CTACAATACTGCTACAATACCG
Found at i:2029629 original size:11 final size:11
Alignment explanation
Indices: 2029599--2029632 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2029589 CACTACAATG
*
2029599 CTGCTACAATA
1 CTGCTACAGTA
*
2029610 CCGCTACAGTA
1 CTGCTACAGTA
2029621 CTGCTACAGTA
1 CTGCTACAGTA
2029632 C
1 C
2029633 CTCAGCAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.32, G:0.15, T:0.24
Consensus pattern (11 bp):
CTGCTACAGTA
Found at i:2030402 original size:31 final size:31
Alignment explanation
Indices: 2030348--2030507 Score: 119
Period size: 32 Copynumber: 5.1 Consensus size: 31
2030338 GAACCTCGAC
* *
2030348 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* **
2030379 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* * * * *
2030410 TATTGTCTATATGTCTC-AAAAGACATAGGTA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGTA
* *
2030441 ATTCTGTCCATATGTCTCGAA-AGACATAGGTA
1 A-ACTGTCCATATGTCCCGAAGA-ACATAGGTA
* * *
2030473 ATTA-TGTCCATATTTTCCGTAGAACATAGGTA
1 A--ACTGTCCATATGTCCCGAAGAACATAGGTA
2030505 AAC
1 AAC
2030508 CCTCGACTCT
Statistics
Matches: 102, Mismatches: 21, Indels: 12
0.76 0.16 0.09
Matches are distributed among these distances:
30 3 0.03
31 47 0.46
32 48 0.47
33 4 0.04
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:2030505 original size:32 final size:32
Alignment explanation
Indices: 2030401--2030485 Score: 120
Period size: 32 Copynumber: 2.7 Consensus size: 32
2030391 GTTCCTTAGA
* *
2030401 ACATAGGT-A-TATTGTCTATATGTCTCAAAAG
1 ACATAGGTAATTA-TGTCCATATGTCTCGAAAG
*
2030432 ACATAGGTAATTCTGTCCATATGTCTCGAAAG
1 ACATAGGTAATTATGTCCATATGTCTCGAAAG
2030464 ACATAGGTAATTATGTCCATAT
1 ACATAGGTAATTATGTCCATAT
2030486 TTTCCGTAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
31 8 0.17
32 39 0.81
33 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (32 bp):
ACATAGGTAATTATGTCCATATGTCTCGAAAG
Found at i:2032633 original size:42 final size:44
Alignment explanation
Indices: 2032564--2032714 Score: 136
Period size: 42 Copynumber: 3.5 Consensus size: 44
2032554 GGTTCTACGC
* * *
2032564 GGTCCTTCGGGAC-A-TATATGTGATCCTTGGGAACTTATATGT
1 GGTCCTTCGGGACAATTCTTTGTGATCCTTGGGAACATATATGT
* * * ** *
2032606 GATCCTTCGGGA-TATATGTTT-TG-TCCTTTTGAACATATATAT
1 GGTCCTTCGGGACAAT-TCTTTGTGATCCTTGGGAACATATATGT
*
2032648 GGTCCTACGGGACAATTCTTTGTGATCCTTTGGG-ACATATATGT
1 GGTCCTTCGGGACAATTCTTTGTGATCC-TTGGGAACATATATGT
*
2032692 GGTCCTTCGGGAC-ATTCTATGTG
1 GGTCCTTCGGGACAATTCTTTGTG
2032715 TCACTTCGAT
Statistics
Matches: 86, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
42 41 0.48
43 15 0.17
44 27 0.31
45 3 0.03
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (44 bp):
GGTCCTTCGGGACAATTCTTTGTGATCCTTGGGAACATATATGT
Found at i:2032697 original size:21 final size:21
Alignment explanation
Indices: 2032564--2032706 Score: 108
Period size: 21 Copynumber: 6.7 Consensus size: 21
2032554 GGTTCTACGC
2032564 GGTCCTTCGGGACATATATGT
1 GGTCCTTCGGGACATATATGT
* *
2032585 GATCCTT-GGGAACTTATATGT
1 GGTCCTTCGGG-ACATATATGT
* * * *
2032606 GATCCTTCGGGATATATGTTT
1 GGTCCTTCGGGACATATATGT
* ** * *
2032627 TGTCCTTTTGAACATATATAT
1 GGTCCTTCGGGACATATATGT
* * *
2032648 GGTCCTACGGGACAATTCTTTGT
1 GGTCCTTCGGGAC-A-TATATGT
* *
2032671 GATCCTTTGGGACATATATGT
1 GGTCCTTCGGGACATATATGT
2032692 GGTCCTTCGGGACAT
1 GGTCCTTCGGGACAT
2032707 TCTATGTGTC
Statistics
Matches: 89, Mismatches: 29, Indels: 8
0.71 0.23 0.06
Matches are distributed among these distances:
20 3 0.03
21 67 0.75
22 5 0.06
23 14 0.16
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (21 bp):
GGTCCTTCGGGACATATATGT
Found at i:2032721 original size:22 final size:21
Alignment explanation
Indices: 2032565--2032722 Score: 76
Period size: 21 Copynumber: 7.4 Consensus size: 21
2032555 GTTCTACGCG
*
2032565 GTCCTTCGGGACA-TATATGT
1 GTCCTTCGGGACATTCTATGT
*
2032585 GATCCTT-GGGA-ACTTATATGT
1 G-TCCTTCGGGACA-TTCTATGT
* * *
2032606 GATCCTTCGGGATATATGT-TTT
1 G-TCCTTCGGGACAT-TCTATGT
** * *
2032628 GTCCTTTTGAACATATATATG-
1 GTCCTTCGGGACAT-TCTATGT
* *
2032649 GTCCTACGGGACAATTCTTTGT
1 GTCCTTCGGGAC-ATTCTATGT
* *
2032671 GATCCTTTGGGACA-TATATGT
1 G-TCCTTCGGGACATTCTATGT
2032692 GGTCCTTCGGGACATTCTATGT
1 -GTCCTTCGGGACATTCTATGT
2032714 GTCACTTCG
1 GTC-CTTCG
2032723 ATGCATATTC
Statistics
Matches: 105, Mismatches: 20, Indels: 24
0.70 0.13 0.16
Matches are distributed among these distances:
19 1 0.01
20 5 0.05
21 62 0.59
22 25 0.24
23 12 0.11
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (21 bp):
GTCCTTCGGGACATTCTATGT
Found at i:2032736 original size:24 final size:24
Alignment explanation
Indices: 2032705--2032752 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2032695 CCTTCGGGAC
* *
2032705 ATTCTATGTGTCACTTCGATGCAT
1 ATTCTATGCGGCACTTCGATGCAT
*
2032729 ATTCTATGCGGCACTTCGGTGCAT
1 ATTCTATGCGGCACTTCGATGCAT
2032753 TTTAGACGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.38
Consensus pattern (24 bp):
ATTCTATGCGGCACTTCGATGCAT
Found at i:2035165 original size:33 final size:32
Alignment explanation
Indices: 2035102--2035173 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 32
2035092 TACATTTATC
* *
2035102 TGAGTCACCAAAGTCATACCATTACATCTCTT
1 TGAGGCACCAAAATCATACCATTACATCTCTT
* *
2035134 TGAGGCACTCAAAATCATACCCTTACCTCTCTT
1 TGAGGCAC-CAAAATCATACCATTACATCTCTT
2035167 TGAGGCA
1 TGAGGCA
2035174 ATAAAGTCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
32 7 0.20
33 28 0.80
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (32 bp):
TGAGGCACCAAAATCATACCATTACATCTCTT
Found at i:2035400 original size:18 final size:18
Alignment explanation
Indices: 2035377--2035417 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
2035367 GAAGAAGAAG
2035377 AAATAAAGGGAATGATTT
1 AAATAAAGGGAATGATTT
2035395 AAATAAAGGGAATGATTT
1 AAATAAAGGGAATGATTT
2035413 AAATA
1 AAATA
2035418 CTTATATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.27
Consensus pattern (18 bp):
AAATAAAGGGAATGATTT
Found at i:2037527 original size:23 final size:23
Alignment explanation
Indices: 2037501--2037549 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2037491 ATAAAGAACC
*
2037501 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
2037524 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
2037547 AAA
1 AAA
2037550 CCAACACCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:2040790 original size:20 final size:20
Alignment explanation
Indices: 2040754--2040795 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
2040744 GATAAAAAGT
*
2040754 AAAAGTTAAAAATGAAATAG
1 AAAAGTTAAAAATGAAAGAG
*
2040774 AAAAGTTAAGGAA-GAAAGAG
1 AAAAGTTAA-AAATGAAAGAG
2040794 AA
1 AA
2040796 GAAAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.14
Consensus pattern (20 bp):
AAAAGTTAAAAATGAAAGAG
Found at i:2045099 original size:21 final size:21
Alignment explanation
Indices: 2045058--2045099 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2045048 CGAGCTATGG
* *
2045058 CTTTGAAGTAAGGCGCCTTGA
1 CTTTGAAGTAAAGCGCATTGA
*
2045079 CTTTGAAGTAAAGCTCATTGA
1 CTTTGAAGTAAAGCGCATTGA
2045100 TTCTTAATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (21 bp):
CTTTGAAGTAAAGCGCATTGA
Found at i:2047423 original size:23 final size:23
Alignment explanation
Indices: 2047397--2047445 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2047387 ATAAAGAACC
*
2047397 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
2047420 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
2047443 AAA
1 AAA
2047446 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:2050345 original size:2 final size:2
Alignment explanation
Indices: 2050338--2050365 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2050328 ATTTACATGC
2050338 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
2050366 TAATGTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2050646 original size:18 final size:18
Alignment explanation
Indices: 2050623--2050657 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2050613 AGGGATTAAC
*
2050623 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
2050641 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
2050658 AATATTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:2056770 original size:21 final size:21
Alignment explanation
Indices: 2056746--2056794 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
2056736 CATTTCGCTT
2056746 TTGCGATAGTTGGAAATCACG
1 TTGCGATAGTTGGAAATCACG
*
2056767 TTGCGATAGTTGGAAATCGCG
1 TTGCGATAGTTGGAAATCACG
2056788 TTGCGAT
1 TTGCGAT
2056795 GGTCTACAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGCGATAGTTGGAAATCACG
Found at i:2056896 original size:20 final size:20
Alignment explanation
Indices: 2056868--2056959 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
2056858 TGGTAAAATT
*
2056868 GCAATGCGATACTGACTATC
1 GCAACGCGATACTGACTATC
* *
2056888 GCAACGCGATAAT-ACAAAATC
1 GCAACGCGATACTGAC--TATC
*
2056909 GCAACGCGATACTGACTTTC
1 GCAACGCGATACTGACTATC
* * *
2056929 GTAACGCGATTCTGACTTTC
1 GCAACGCGATACTGACTATC
*
2056949 GCAACGAGATA
1 GCAACGCGATA
2056960 ATACAGAATC
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
19 2 0.03
20 39 0.67
21 15 0.26
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.23
Consensus pattern (20 bp):
GCAACGCGATACTGACTATC
Found at i:2057132 original size:12 final size:12
Alignment explanation
Indices: 2057113--2057146 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2057103 CTCTCTGGCG
2057113 ACATCCGTTCCT
1 ACATCCGTTCCT
*
2057125 ATATCCGTTCCT
1 ACATCCGTTCCT
2057137 ACATCC-TTCC
1 ACATCCGTTCC
2057147 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:2057320 original size:20 final size:20
Alignment explanation
Indices: 2057295--2057412 Score: 182
Period size: 20 Copynumber: 5.9 Consensus size: 20
2057285 ATTCATTTGA
*
2057295 CTATCGCAATGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
2057315 CTATCGTAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
2057335 CTATCGCAACACAAAAATGG
1 CTATCGCAACGCGAAAATGG
2057355 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
2057375 CTATCGCAACACGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
2057395 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
2057413 CGCAATGCGA
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 88 1.00
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:2057472 original size:19 final size:19
Alignment explanation
Indices: 2057431--2057495 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
2057421 GAAATGAAAA
2057431 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
2057447 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2057464 TCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
2057483 TCGCATTGCGATT
1 TCGCATTGCGATT
2057496 CTCTCGTTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
14 11 0.26
16 3 0.07
17 3 0.07
19 26 0.60
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2057654 original size:14 final size:14
Alignment explanation
Indices: 2057635--2057671 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2057625 CATCAATTAA
2057635 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2057649 ACAAATCATCTTTT
1 ACAAATCAACATTT
2057663 ACAAATCAA
1 ACAAATCAA
2057672 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2059138 original size:21 final size:20
Alignment explanation
Indices: 2059114--2059172 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
2059104 AACGGTGGGG
2059114 GGGGACTCTTGAGGGA-GGATA
1 GGGGACTCTTGAGGGATGG--A
* **
2059135 GGGGCCTCTTGAACGATTGGA
1 GGGGACTCTTGAGGGA-TGGA
2059156 GGGGACTCTTGAGGGAT
1 GGGGACTCTTGAGGGAT
2059173 AACAGGTGAG
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 1 0.03
21 27 0.90
23 2 0.07
ACGTcount: A:0.20, C:0.14, G:0.44, T:0.22
Consensus pattern (20 bp):
GGGGACTCTTGAGGGATGGA
Found at i:2059565 original size:20 final size:19
Alignment explanation
Indices: 2059542--2059607 Score: 78
Period size: 20 Copynumber: 3.4 Consensus size: 19
2059532 AACATAAAAC
2059542 CGCAACGCGAAAATGACTAT
1 CGCAACGCG-AAATGACTAT
*
2059562 CGCAACGCGGAAATGGCTAT
1 CGCAACGC-GAAATGACTAT
* **
2059582 CGCAATGCGAAATGAAAAT
1 CGCAACGCGAAATGACTAT
2059601 CGCAACG
1 CGCAACG
2059608 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
19 14 0.36
20 24 0.62
21 1 0.03
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.14
Consensus pattern (19 bp):
CGCAACGCGAAATGACTAT
Found at i:2059641 original size:18 final size:18
Alignment explanation
Indices: 2059614--2059676 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
2059604 AACGACAAAA
*
2059614 TCGCAATGCGATTTCATT
1 TCGCATTGCGATTTCATT
*
2059632 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
2059648 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
2059665 TCGCATTGCGAT
1 TCGCATTGCGAT
2059677 AGCCATTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 4 0.11
17 4 0.11
18 14 0.38
19 6 0.16
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.43
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:2059695 original size:20 final size:19
Alignment explanation
Indices: 2059661--2059715 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
2059651 TTGCGATTTT
*
2059661 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
2059680 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
2059700 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
2059716 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:2060223 original size:18 final size:18
Alignment explanation
Indices: 2060197--2060241 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2060187 GTCGATCAGA
*
2060197 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
2060215 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
2060233 TGATGGCTC
1 TGATGGCTC
2060242 CCAAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:2061609 original size:20 final size:20
Alignment explanation
Indices: 2061561--2061619 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2061551 AATAGCTTCT
** *
2061561 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
2061581 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
2061601 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
2061620 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:2062139 original size:20 final size:20
Alignment explanation
Indices: 2062114--2062165 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2062104 ATTATGTATT
2062114 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
* *
2062134 ATCGCGTTGTGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
2062154 ATCTCGTTGCGA
1 ATCGCGTTGCGA
2062166 TTTTGTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:2062199 original size:20 final size:20
Alignment explanation
Indices: 2062174--2062227 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2062164 GATTTTGTAT
2062174 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
2062194 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
2062214 TATCGCATTGCGAT
1 TATCGCATTGCGAT
2062228 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:2062199 original size:61 final size:61
Alignment explanation
Indices: 2062093--2062230 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
2062083 CGATTAGAAA
* * * * *
2062093 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGTGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
2062154 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
2062215 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
2062231 CCCAATTCAC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:2062773 original size:18 final size:17
Alignment explanation
Indices: 2062750--2062793 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2062740 AACAGTGGTC
2062750 CTTCGGGACATAGCGGT
1 CTTCGGGACATAGCGGT
*
2062767 GCTTCGGGACATAGTGGT
1 -CTTCGGGACATAGCGGT
2062785 CATTCGGGA
1 C-TTCGGGA
2062794 TAAATATTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.18, C:0.20, G:0.36, T:0.25
Consensus pattern (17 bp):
CTTCGGGACATAGCGGT
Found at i:2064776 original size:42 final size:41
Alignment explanation
Indices: 2064730--2064809 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
2064720 GCCCTCGGTA
* * *
2064730 AGTCTTTTGAGCATGATGATTAAATCCTTCGGGTAATCTGTC
1 AGTCTTTCGAGCAAGATGA-TAAATCATTCGGGTAATCTGTC
*
2064772 AGTCTTTCGAGCAAGATGATAAATCATTCGGGTCATCT
1 AGTCTTTCGAGCAAGATGATAAATCATTCGGGTAATCT
2064810 ATAAGACCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
41 17 0.50
42 17 0.50
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35
Consensus pattern (41 bp):
AGTCTTTCGAGCAAGATGATAAATCATTCGGGTAATCTGTC
Found at i:2064780 original size:258 final size:259
Alignment explanation
Indices: 2064320--2065553 Score: 1794
Period size: 259 Copynumber: 4.8 Consensus size: 259
2064310 AAGTTGTCTT
* *
2064320 TATGATAATTTAAAAAATGA-AAAACGAATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATG
1 TATGATAATTTGAAAAATGAGAAAGCG-ATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATG
* *
2064384 AAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTATTACCTAGTAAACTATTTCCAAAATTA
65 AAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
* *
2064449 GTAAGT-CTTACGGGCTATCAGTAAGTCTTTCCAGCATGATGATTAAATCCTTCGGGTTATCTGT
130 GTAAGTCCTT-CGGGCTATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGT
* * * *
2064513 CAGTCTTTCGAGCAAGATGATAATTCCTTCAGACCATCTATAAGACCTTTGGGCAAGATGTTTTC
194 CAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCAAGATGCTTTC
2064578 A
259 A
*
2064579 TGTGATAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGA
1 TATGATAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGA
* *
2064644 AA-TTTTGAAAAGCAAGAAAGTAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGG
66 AATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGG
** * * *
2064708 TAAGTCCTTCGGGCCCTCGGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGTAATCTGTCA
131 TAAGTCCTTCGGGCTATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCA
* * * *
2064773 GTCTTTCGAGCAAGATGATAAATCATTCGGGTCATCTATAAGACCTTTGGGCAAGATGTTTTCA
196 GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCAAGATGCTTTCA
* * *
2064837 TGTGATAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTATTATTTTCAAAAAACT-
1 TATGATAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAA-TG
* * * *
2064901 AAATTTTTGAAAAGTAATAAAGCGATTTCCAAAGTTTCTTACCTAATAAACTATTTCCAAAAGTG
65 AAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
* ** * *
2064966 GTAAGTCATTCTAGCTATCAGTAAGTCTTTCGAGCATGACGATTAAATCCTTTGGGTCATCTGTC
130 GTAAGTCCTTCGGGCTATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTC
* * * *
2065031 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATTTATAAAACCTTCGGTCAAGATGCTTTCA
195 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCAAGATGCTTTCA
* *
2065096 TATGATAATTTGAAAAACGAGAAAGCGATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGA
1 TATGATAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGA
* *
2065161 AATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAATTATTTCCGAAATTGG
66 AATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGG
* * * * * * * *
2065226 TAAATCCCTC-GACTATCAATAAGCCTTTCGAGCATGATGATTAAATCCTTTGGGTCATCTTTTA
131 TAAGTCCTTCGGGCTATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCA
* * * *
2065290 GTCTTTCGAGCTAGATAATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCACGATGCTCTCA
196 GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCAAGATGCTTTCA
* *
2065354 TATGATAATTTGAAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAGTATATTCAGAAAAATG
1 TATGATAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTTTCAG-AAAATG
* * * * *
2065419 AAATTTTTGATAAGTAAGAAAGCGATTTCAAAAGTTTCTTACCTAGTAAACTATTTCCAAAAATA
65 AAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
* * * * * *
2065484 GTAAGTTCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGATTAGATTCTTCGGGTCATCTTTC
130 GTAAGTCCTTCGGGCTATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTC
2065549 AGTCT
195 AGTCT
2065554 CACTTGAGAC
Statistics
Matches: 873, Mismatches: 95, Indels: 13
0.89 0.10 0.01
Matches are distributed among these distances:
258 393 0.45
259 426 0.49
260 54 0.06
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (259 bp):
TATGATAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGA
AATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGG
TAAGTCCTTCGGGCTATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCA
GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCAAGATGCTTTCA
Found at i:2065295 original size:517 final size:516
Alignment explanation
Indices: 2064320--2065553 Score: 1817
Period size: 517 Copynumber: 2.4 Consensus size: 516
2064310 AAGTTGTCTT
* * *
2064320 TATGATAATTTAAAAAATGA-AAAACGAATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATG
1 TATGATAATTTGAAAAATGAGAAAGCG-ATTTTCAAAGTTTCTCATTTAGTATTTTCAAAAAATG
* * *
2064384 AAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTATTACCTAGTAAACTATTTCCAAAATTA
65 AAATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAATA
* *
2064449 GTAAGTCTTACGGGCTATCAGTAAGTCTTTCCAGCATGATGATTAAATCCTTCGGGTTATCTGTC
130 GTAAGTCTT-CGGGCTATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTC
* * * *
2064514 AGTCTTTCGAGCAAGATGATAATTCCTTCAGACCATCTATAAGACCTTTGGGCAAGATGTTTTCA
194 AGTCTTTCGAGCAAGATGATAAGTCCTTCAGACCATCTATAAAACCTTCGGGCAAGATGCTTTCA
* * *
2064579 TGTGATAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATGA
259 TATGATAATTTGAAAAACGAGAAAGCGATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGA
2064644 AATTTTGAAAAGCAAGAAAGTAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGT
324 AATTTTGAAAAGCAAGAAAGTAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGT
* * * * ** * *
2064709 AAGTCCTTCGGGCCCTCGGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGTAATCTGTCAG
389 AAATCCCTCGGACCATCAATAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTAATCTGTCAG
* * * *
2064774 TCTTTCGAGCAAGATGATAAATCATTCGGGTCATCTATAAGACCTTTGGGCAAGATGTTTTCA
454 TCTTTCGAGCAAGATAATAAATCATTCGGGCCATCTATAAGACCTTTGGGCAAGATGCTCTCA
* *
2064837 TGTGATAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTATTATTTTCAAAAAACT-
1 TATGATAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTTTCAAAAAA-TG
* * * *
2064901 AAATTTTTGAAAAGTAATAAAGCGATTTCCAAAGTTTCTTACCTAATAAACTATTTCCAAAAGTG
65 AAATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAATA
** * *
2064966 GTAAGTCATTCTAGCTATCAGTAAGTCTTTCGAGCATGACGATTAAATCCTTTGGGTCATCTGTC
130 GTAAGTC-TTCGGGCTATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTC
* * * *
2065031 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATTTATAAAACCTTCGGTCAAGATGCTTTCA
194 AGTCTTTCGAGCAAGATGATAAGTCCTTCAGACCATCTATAAAACCTTCGGGCAAGATGCTTTCA
2065096 TATGATAATTTGAAAAACGAGAAAGCGATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGA
259 TATGATAATTTGAAAAACGAGAAAGCGATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGA
* * * *
2065161 AATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAATTATTTCCGAAATTGG
324 AA-TTTTGAAAAGCAAGAAAGTAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGG
* * * * *
2065226 TAAATCCCTC-GACTATCAATAAGCCTTTCGAGCATGATGATTAAATCCTTTGGGTCATCTTTTA
388 TAAATCCCTCGGACCATCAATAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTAATCTGTCA
* * * *
2065290 GTCTTTCGAGCTAGATAATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCACGATGCTCTCA
453 GTCTTTCGAGCAAGATAATAAATCATTCGGGCCATCTATAAGACCTTTGGGCAAGATGCTCTCA
* *
2065354 TATGATAATTTGAAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAGTATATTCAGAAAAATG
1 TATGATAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTTTCA-AAAAATG
* *
2065419 AAATTTTTGATAAGTAAGAAAGCGATTTCAAAAGTTTCTTACCTAGTAAACTATTTCCAAAAATA
65 AAATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAATA
* * * * *
2065484 GTAAGTTCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGATTAGATTCTTCGGGTCATCTTTC
130 GTAAG-TCTTCGGGCTATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTC
2065549 AGTCT
194 AGTCT
2065554 CACTTGAGAC
Statistics
Matches: 638, Mismatches: 72, Indels: 13
0.88 0.10 0.02
Matches are distributed among these distances:
517 440 0.69
518 196 0.31
519 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (516 bp):
TATGATAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTTTCAAAAAATGA
AATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAATAG
TAAGTCTTCGGGCTATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAG
TCTTTCGAGCAAGATGATAAGTCCTTCAGACCATCTATAAAACCTTCGGGCAAGATGCTTTCATA
TGATAATTTGAAAAACGAGAAAGCGATTTTCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAA
TTTTGAAAAGCAAGAAAGTAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAA
ATCCCTCGGACCATCAATAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTAATCTGTCAGTC
TTTCGAGCAAGATAATAAATCATTCGGGCCATCTATAAGACCTTTGGGCAAGATGCTCTCA
Found at i:2067685 original size:17 final size:17
Alignment explanation
Indices: 2067663--2067701 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
2067653 TGAATCAAAT
2067663 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
2067680 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
2067697 -AATTA
1 TAATTA
2067702 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:2073585 original size:31 final size:30
Alignment explanation
Indices: 2073491--2073585 Score: 70
Period size: 31 Copynumber: 3.1 Consensus size: 30
2073481 GTATTAAATG
* *
2073491 TCCTTAAATCATGAT-TCACATTCTAAATTAG
1 TCCTTAAATTATGATAT--CATTCTAAATTAA
* * * * *
2073522 TCCCTAAACTT-TGAAAT-ATTTTAATTTCA
1 TCCTTAAA-TTATGATATCATTCTAAATTAA
2073551 TCCTTAAATTATGACTATCATTCTAAATTAA
1 TCCTTAAATTATGA-TATCATTCTAAATTAA
2073582 TCCT
1 TCCT
2073586 CAAACTTTTG
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
28 2 0.04
29 18 0.38
30 2 0.04
31 23 0.49
32 2 0.04
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (30 bp):
TCCTTAAATTATGATATCATTCTAAATTAA
Found at i:2073591 original size:60 final size:58
Alignment explanation
Indices: 2073491--2073674 Score: 167
Period size: 60 Copynumber: 3.1 Consensus size: 58
2073481 GTATTAAATG
* * * * *
2073491 TCCTTAAATCATGATTCA-CATTCTAAATTAGTCCCTAAACTTTGAAATATTTTAATTTCA
1 TCCTTAAATTATGACT-ATCATTCTAAATTAGTCCC-AAACTTTG-AACATTTCAATTCCA
*
2073551 TCCTTAAATTATGACTATCATTCTAAATTAATCCTCAAACTTTTGAACATTTCAATTCCA
1 TCCTTAAATTATGACTATCATTCTAAATTAGTCC-CAAAC-TTTGAACATTTCAATTCCA
* * * *
2073611 TACC-CAAACTATGACCT-TCATTCTAAACTAGTCCCCAAACTTTTTGAACATTTCAATTTCA
1 T-CCTTAAATTATGA-CTATCATTCTAAATTAGT-CCCAAAC--TTTGAACATTTCAATTCCA
2073672 TCC
1 TCC
2073675 AAACTATATG
Statistics
Matches: 106, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
59 1 0.01
60 74 0.70
61 31 0.29
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (58 bp):
TCCTTAAATTATGACTATCATTCTAAATTAGTCCCAAACTTTGAACATTTCAATTCCA
Found at i:2074808 original size:2 final size:2
Alignment explanation
Indices: 2074803--2074839 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2074793 TTTTTTAATT
2074803 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2074840 TTAATTCACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2075339 original size:3 final size:3
Alignment explanation
Indices: 2075333--2075363 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2075323 CTGTATTATT
*
2075333 ATA ATA ATA ATA ATA ATA AAA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2075364 CATTTGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:2075596 original size:2 final size:2
Alignment explanation
Indices: 2075589--2075616 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2075579 TGAAGGGGGC
2075589 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2075617 CTCCATTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2083967 original size:45 final size:45
Alignment explanation
Indices: 2083902--2084078 Score: 293
Period size: 45 Copynumber: 3.9 Consensus size: 45
2083892 GAAACAATTT
*
2083902 CTTTTTCACCATCCTCGACCCCAGCTTCTTCAATGGTGAAGGTTG
1 CTTTCTCACCATCCTCGACCCCAGCTTCTTCAATGGTGAAGGTTG
* *
2083947 CTTTCTCAGCATCCTTGACCCCAGCTTCTTCAATGGTGAAGGTTG
1 CTTTCTCACCATCCTCGACCCCAGCTTCTTCAATGGTGAAGGTTG
*
2083992 CTTTCTCAGCATCCTCGACCCCAGCTTCTTCAATGGTGAAGGTTG
1 CTTTCTCACCATCCTCGACCCCAGCTTCTTCAATGGTGAAGGTTG
*
2084037 CTTT-TGCACCATCCTCAACCCCAGCTTCTTCAATGGTGAAGG
1 CTTTCT-CACCATCCTCGACCCCAGCTTCTTCAATGGTGAAGG
2084079 CAGTATCTAA
Statistics
Matches: 125, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
44 1 0.01
45 124 0.99
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.32
Consensus pattern (45 bp):
CTTTCTCACCATCCTCGACCCCAGCTTCTTCAATGGTGAAGGTTG
Found at i:2091869 original size:120 final size:119
Alignment explanation
Indices: 2091623--2091944 Score: 344
Period size: 120 Copynumber: 2.7 Consensus size: 119
2091613 AGGTGCATTA
* * * *
2091623 AACTATGATCCTCTGCAGCAAGACTTT-TATCCTCTTTAACTTCCATTTTGTCACTTTCCAGATA
1 AACTCTGATCCTCTACAGCAAGA-TTTGTATCCTCTTTAACTTCCATTTTATCACTTTCCCGATA
* * * * * ***
2091687 CCTAACTCCTGAACTGGTCCAGCAGCAGTCATGTTGGTATCTTCTATGTGCATTT
65 ACTAACTCCTGAACTGGTCCAGCAACAATCATGTTGGTATCTTCTAAGTGAAAGG
* *
2091742 AACTCTGATCCTCTACAGCAAGATTTGTGTCCTCTTTAACTTTCATTTT-TCCACTTTCCCGAAT
1 AACTCTGATCCTCTACAGCAAGATTTGTATCCTCTTTAACTTCCATTTTAT-CACTTTCCCG-AT
* *
2091806 AAGTAACTCCTGAACTGAG-CCAGCAACAATTATGTTGGTATCTTCTAAGTGAAAGG
64 AACTAACTCCTGAACTG-GTCCAGCAACAATCATGTTGGTATCTTCTAAGTGAAAGG
* ** * * * *
2091862 AACTCTGATCCTTTTGAGCAGGACTTGTAACCTCTTTAACATCCATTTTATCACTTTCCCGGATA
1 AACTCTGATCCTCTACAGCAAGATTTGTATCCTCTTTAACTTCCATTTTATCACTTTCCC-GATA
* * *
2091927 ACTACCTTCTGAAATGGT
65 ACTAACTCCTGAACTGGT
2091945 TCGGTTGCAG
Statistics
Matches: 168, Mismatches: 28, Indels: 13
0.80 0.13 0.06
Matches are distributed among these distances:
118 4 0.02
119 51 0.30
120 110 0.65
121 3 0.02
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (119 bp):
AACTCTGATCCTCTACAGCAAGATTTGTATCCTCTTTAACTTCCATTTTATCACTTTCCCGATAA
CTAACTCCTGAACTGGTCCAGCAACAATCATGTTGGTATCTTCTAAGTGAAAGG
Found at i:2092843 original size:35 final size:36
Alignment explanation
Indices: 2092772--2092843 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
2092762 AAGGAATTCA
*
2092772 AAGGGTACCGATACCTTGAAGAACAGTATCGGTACC
1 AAGGGTACCGATACCTTGAAGAACAGTATCGATACC
* * **
2092808 AAGGGTACTGATACCTT-AAGGATGGTATCGATACC
1 AAGGGTACCGATACCTTGAAGAACAGTATCGATACC
2092843 A
1 A
2092844 CTTTTGAACG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
35 15 0.48
36 16 0.52
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.22
Consensus pattern (36 bp):
AAGGGTACCGATACCTTGAAGAACAGTATCGATACC
Found at i:2093416 original size:22 final size:21
Alignment explanation
Indices: 2093391--2093437 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2093381 AGTGAATTGT
* *
2093391 ATGTTTATATGAGAAGTGAGTA
1 ATGTGTATATGA-AAATGAGTA
*
2093413 ATGTGTATATGAAAATGTGTA
1 ATGTGTATATGAAAATGAGTA
2093434 ATGT
1 ATGT
2093438 AATCATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.36, C:0.00, G:0.26, T:0.38
Consensus pattern (21 bp):
ATGTGTATATGAAAATGAGTA
Found at i:2105998 original size:36 final size:35
Alignment explanation
Indices: 2105950--2106022 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
2105940 GGAAGAAATT
2105950 CAAGAGTACCGATACCTTGAAGAACAGTATCGATAC
1 CAAGAGTACCGATA-CTTGAAGAACAGTATCGATAC
* * * **
2105986 CAAGGGTACCGATACTTTAAGGAGGGTATCGATAC
1 CAAGAGTACCGATACTTGAAGAACAGTATCGATAC
2106021 CA
1 CA
2106023 CTTTTGAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
35 19 0.59
36 13 0.41
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21
Consensus pattern (35 bp):
CAAGAGTACCGATACTTGAAGAACAGTATCGATAC
Found at i:2109039 original size:104 final size:105
Alignment explanation
Indices: 2108851--2109060 Score: 413
Period size: 104 Copynumber: 2.0 Consensus size: 105
2108841 GTGAATGATG
2108851 GAATCCATTAGTAAATGCGATATTAGTATTGTTAGCAAAGAAGTTACTGCTTGAGGGATGTCAGG
1 GAATCCATTAGTAAATGCGATATTAGTATTGTTAGCAAAGAAGTTACTGCTTGAGGGATGTCAGG
2108916 GGTTCATTACTAATGTGTTGGATGTTAGAGCTAAAGAGAA
66 GGTTCATTACTAATGTGTTGGATGTTAGAGCTAAAGAGAA
2108956 GAATCCA-TAGTAAATGCGATATTAGTATTGTTAGCAAAGAAGTTACTGCTTGAGGGATGTCAGG
1 GAATCCATTAGTAAATGCGATATTAGTATTGTTAGCAAAGAAGTTACTGCTTGAGGGATGTCAGG
2109020 GGTTCATTACTAATGTGTTGGATGTTAGAGCTAAAGAGAA
66 GGTTCATTACTAATGTGTTGGATGTTAGAGCTAAAGAGAA
2109060 G
1 G
2109061 GGGATTGAAG
Statistics
Matches: 105, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
104 98 0.93
105 7 0.07
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.31
Consensus pattern (105 bp):
GAATCCATTAGTAAATGCGATATTAGTATTGTTAGCAAAGAAGTTACTGCTTGAGGGATGTCAGG
GGTTCATTACTAATGTGTTGGATGTTAGAGCTAAAGAGAA
Found at i:2114540 original size:21 final size:23
Alignment explanation
Indices: 2114465--2114525 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
2114455 TAGTCCCGAC
* * *
2114465 AGGGGGTATCGGTAC-C-CTCAT
1 AGGGGGTATCGATACACATTCAA
*
2114486 AGGTGGTATCGATACACATTCAA
1 AGGGGGTATCGATACACATTCAA
2114509 AGGGGGTATCGATACAC
1 AGGGGGTATCGATACAC
2114526 GTTGAAGGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 13 0.39
22 1 0.03
23 19 0.58
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (23 bp):
AGGGGGTATCGATACACATTCAA
Found at i:2117673 original size:432 final size:432
Alignment explanation
Indices: 2116870--2117740 Score: 1679
Period size: 432 Copynumber: 2.0 Consensus size: 432
2116860 TGGCCTAATC
2116870 ATTACTCGGTTTATAACATAACAAGCGGTATTTGTGGCTTTTGCCCAAAAATATTTTGGCAAATT
1 ATTACTCGGTTTATAACATAACAAGCGGTATTTGTGGCTTTTGCCCAAAAATATTTTGGCAAATT
2116935 ATTTTCACAAAGCATGGTTCTAACCATTTCTTCTAAAGTTCAATTTTTCCTCTCAACAACTCTAT
66 ATTTTCACAAAGCATGGTTCTAACCATTTCTTCTAAAGTTCAATTTTTCCTCTCAACAACTCTAT
2117000 TTTGTTGAGGGGTTCTCGGAGCTAAAAAATTATGACTAATACCATTAGAATTACAAAAATCAGTA
131 TTTGTTGAGGGGTTCTCGGAGCTAAAAAATTATGACTAATACCATTAGAATTACAAAAATCAGTA
*
2117065 AATCCAAGATTTTCAAATTCAGTACCATGATCACTCCTAGCACTAGTTATGGAGTAACCTTTTTC
196 AATCCAAGATTTTCAAATTCAGTACCATGATCACTCCTAGCACTAGTTATGGAGTAAACTTTTTC
2117130 ATTTTGGATTACTTTTGAAAACGTGATGAATTTTTATAATGCTTCATCTTTAGTACTTAAAAATA
261 ATTTTGGATTACTTTTGAAAACGTGATGAATTTTTATAATGCTTCATCTTTAGTACTTAAAAATA
2117195 GAACCCAAGTATATCTAGAATAGTCATCTATCAATACAAAGTAATATTGTTTTCCACCCAAGCTA
326 GAACCCAAGTATATCTAGAATAGTCATCTATCAATACAAAGTAATATTGTTTTCCACCCAAGCTA
2117260 ATAGTTCTAATTGGCTCAAAAAGATCTATATGGATCAATTGT
391 ATAGTTCTAATTGGCTCAAAAAGATCTATATGGATCAATTGT
2117302 ATTACTCGGTTTATAACATAACAAGCGGTATTTGTGGCTTTTGCCCAAAAATATTTTGGCAAATT
1 ATTACTCGGTTTATAACATAACAAGCGGTATTTGTGGCTTTTGCCCAAAAATATTTTGGCAAATT
* * *
2117367 GTTTTCACAAAGCATTGTTCTAACCATTTCTTCTAAAGTTCGATTTTTCCTCTCAACAACTCTAT
66 ATTTTCACAAAGCATGGTTCTAACCATTTCTTCTAAAGTTCAATTTTTCCTCTCAACAACTCTAT
*
2117432 TTTGTTGAGGGGTTCTCGGAGCTAAAAAATTATGACTAATACCATTAGAATTATAAAAATCAGTA
131 TTTGTTGAGGGGTTCTCGGAGCTAAAAAATTATGACTAATACCATTAGAATTACAAAAATCAGTA
2117497 AATCCAAGATTTTCAAATTCAGTACCATGATCACTCCTAGCACTAGTTATGGAGTAAACTTTTTC
196 AATCCAAGATTTTCAAATTCAGTACCATGATCACTCCTAGCACTAGTTATGGAGTAAACTTTTTC
2117562 ATTTTGGATTACTTTTGAAAACGTGATGAATTTTTATAATGCTTCATCTTTAGTACTTAAAAATA
261 ATTTTGGATTACTTTTGAAAACGTGATGAATTTTTATAATGCTTCATCTTTAGTACTTAAAAATA
*
2117627 GAACCCAAGTATATCTATAATAGTCATCTATCAATACAAAGTAATATTGTTTTCCACCCAAGCTA
326 GAACCCAAGTATATCTAGAATAGTCATCTATCAATACAAAGTAATATTGTTTTCCACCCAAGCTA
2117692 ATAGTTCTAATTGGCTCAAAAAGATCTATATGGATCAATTGT
391 ATAGTTCTAATTGGCTCAAAAAGATCTATATGGATCAATTGT
*
2117734 AATACTC
1 ATTACTC
2117741 TACTAGTTGA
Statistics
Matches: 432, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
432 432 1.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (432 bp):
ATTACTCGGTTTATAACATAACAAGCGGTATTTGTGGCTTTTGCCCAAAAATATTTTGGCAAATT
ATTTTCACAAAGCATGGTTCTAACCATTTCTTCTAAAGTTCAATTTTTCCTCTCAACAACTCTAT
TTTGTTGAGGGGTTCTCGGAGCTAAAAAATTATGACTAATACCATTAGAATTACAAAAATCAGTA
AATCCAAGATTTTCAAATTCAGTACCATGATCACTCCTAGCACTAGTTATGGAGTAAACTTTTTC
ATTTTGGATTACTTTTGAAAACGTGATGAATTTTTATAATGCTTCATCTTTAGTACTTAAAAATA
GAACCCAAGTATATCTAGAATAGTCATCTATCAATACAAAGTAATATTGTTTTCCACCCAAGCTA
ATAGTTCTAATTGGCTCAAAAAGATCTATATGGATCAATTGT
Found at i:2120196 original size:16 final size:16
Alignment explanation
Indices: 2120177--2120215 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
2120167 ACCTTAGCTA
* *
2120177 TCCACATTAAGGATTT
1 TCCACAATAAGCATTT
2120193 TCCACAATAAGCATTT
1 TCCACAATAAGCATTT
2120209 TCCACAA
1 TCCACAA
2120216 ATTCACTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.31
Consensus pattern (16 bp):
TCCACAATAAGCATTT
Found at i:2129333 original size:37 final size:38
Alignment explanation
Indices: 2129278--2129349 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 38
2129268 AAATCGACGG
*
2129278 TTTGAACTCAAATGTTC-AAGGGCCAGTTCTGGCGCGA
1 TTTGAACTCAAATGTTCAAACGGCCAGTTCTGGCGCGA
* * *
2129315 TTTGAATTCAAATTTTCAAACGGCCAGTTTTGGCG
1 TTTGAACTCAAATGTTCAAACGGCCAGTTCTGGCG
2129350 ATTCTTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 15 0.50
38 15 0.50
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (38 bp):
TTTGAACTCAAATGTTCAAACGGCCAGTTCTGGCGCGA
Found at i:2130245 original size:2 final size:2
Alignment explanation
Indices: 2130238--2130272 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2130228 GTATATGAAC
2130238 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 T
2130273 GGGTGAGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2136809 original size:32 final size:32
Alignment explanation
Indices: 2136712--2136851 Score: 160
Period size: 32 Copynumber: 4.4 Consensus size: 32
2136702 ATATGTCCTA
* *
2136712 AAGAACATAGGTAATC-TATCCATATGTTCCG
1 AAGAACATAGGTAATCATGTCTATATGTTCCG
* * * *
2136743 AAGAACATAGATAA--ATTGACCATATGTCCCG
1 AAGAACATAGGTAATCA-TGTCTATATGTTCCG
* * * *
2136774 AAGAATATAGGTAATTATGTTTATATGTTCTG
1 AAGAACATAGGTAATCATGTCTATATGTTCCG
2136806 AAGAACATAGGTAATCATGTCTATATGTTCCG
1 AAGAACATAGGTAATCATGTCTATATGTTCCG
2136838 AAGAACATAGGTAA
1 AAGAACATAGGTAA
2136852 CCCTTGACTC
Statistics
Matches: 90, Mismatches: 15, Indels: 7
0.80 0.13 0.06
Matches are distributed among these distances:
31 37 0.41
32 52 0.58
33 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30
Consensus pattern (32 bp):
AAGAACATAGGTAATCATGTCTATATGTTCCG
Found at i:2138142 original size:20 final size:20
Alignment explanation
Indices: 2138117--2138154 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2138107 CACATGTTAA
*
2138117 AGAATGCATCGATACACTGT
1 AGAATGCACCGATACACTGT
*
2138137 AGAATGCACCGATGCACT
1 AGAATGCACCGATACACT
2138155 TCAAGGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (20 bp):
AGAATGCACCGATACACTGT
Found at i:2138621 original size:25 final size:25
Alignment explanation
Indices: 2138593--2138654 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
2138583 ACACTTGTGA
2138593 TATATGTG-ATAT-TAATATAAGTAAT
1 TATATG-GAATATGTAATATAAGT-AT
*
2138618 TATA-GGAATCTGTAATATAAGTAT
1 TATATGGAATATGTAATATAAGTAT
2138642 TATAT-GAA-ATGTA
1 TATATGGAATATGTA
2138655 GCTATGTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
23 5 0.16
24 13 0.41
25 14 0.44
ACGTcount: A:0.44, C:0.02, G:0.15, T:0.40
Consensus pattern (25 bp):
TATATGGAATATGTAATATAAGTAT
Found at i:2139102 original size:31 final size:31
Alignment explanation
Indices: 2138994--2139102 Score: 130
Period size: 31 Copynumber: 3.5 Consensus size: 31
2138984 AGAGTCGAGG
2138994 GTTTACCTATGTTCTATGGAACATATGGACA
1 GTTTACCTATGTTCTATGGAACATATGGACA
* * *
2139025 GAATTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTATGGA-ACATATGGACA
* * *
2139057 GTATACCTATGTTCTAAGGAACATATGAACA
1 GTTTACCTATGTTCTATGGAACATATGGACA
*
2139088 GTTTACCTAGGTTCT
1 GTTTACCTATGTTCT
2139103 TCAGGACCTA
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
31 38 0.59
32 26 0.41
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTATGGAACATATGGACA
Found at i:2139120 original size:31 final size:31
Alignment explanation
Indices: 2138994--2139121 Score: 107
Period size: 31 Copynumber: 4.1 Consensus size: 31
2138984 AGAGTCGAGG
* *
2138994 GTTTACCTATGTTCTATGGAACATATGGACA
1 GTTTACCTAGGTTCTAAGGAACATATGGACA
* * ***
2139025 GAATTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTAGGTTCTAAGGA-ACATATGGACA
* * *
2139057 GTATACCTATGTTCTAAGGAACATATGAACA
1 GTTTACCTAGGTTCTAAGGAACATATGGACA
* *
2139088 GTTTACCTAGGTTCTTCAGG-ACCTATGGACA
1 GTTTACCTAGGTTC-TAAGGAACATATGGACA
2139119 GTT
1 GTT
2139122 GTCGAGGTTC
Statistics
Matches: 79, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
31 49 0.62
32 30 0.38
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (31 bp):
GTTTACCTAGGTTCTAAGGAACATATGGACA
Found at i:2142936 original size:25 final size:25
Alignment explanation
Indices: 2142908--2142962 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
2142898 ACACTTGTGA
2142908 TATATGTG-ATAT-TAATATAAGTAAT
1 TATATG-GAATATGTAATATAAGT-AT
*
2142933 TATA-GGAATATGTAATATAAGTGT
1 TATATGGAATATGTAATATAAGTAT
2142957 TATATG
1 TATATG
2142963 AAATGTGACT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 1 0.04
24 10 0.38
25 15 0.58
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (25 bp):
TATATGGAATATGTAATATAAGTAT
Found at i:2143005 original size:19 final size:19
Alignment explanation
Indices: 2142963--2143005 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2142953 GTGTTATATG
*
2142963 AAATGTGACTATGTGATAT
1 AAATGTGACTATGTGACAT
*
2142982 GAATGTGA-TATGTGAACAT
1 AAATGTGACTATGTG-ACAT
2143001 AAATG
1 AAATG
2143006 ACTAATCGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.33
Consensus pattern (19 bp):
AAATGTGACTATGTGACAT
Found at i:2143248 original size:31 final size:31
Alignment explanation
Indices: 2143157--2143267 Score: 109
Period size: 31 Copynumber: 3.5 Consensus size: 31
2143147 TTATACATAC
*
2143157 GGAACATATGGACAGAATTACCTATG-TCTTT
1 GGAACATATGGACAG-TTTACCTATGTTCTTT
* * **
2143188 CGAGACATATGGACA-TTATGCCTATGTTCTAA
1 GGA-ACATATGGACAGTT-TACCTATGTTCTTT
*
2143220 GGAACATATGGACAGTTTACCTAGGTTCTTT
1 GGAACATATGGACAGTTTACCTATGTTCTTT
* *
2143251 GGGACCTATGGACAGTT
1 GGAACATATGGACAGTT
2143268 GTCGAGGTTC
Statistics
Matches: 64, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
30 1 0.02
31 45 0.70
32 18 0.28
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.32
Consensus pattern (31 bp):
GGAACATATGGACAGTTTACCTATGTTCTTT
Found at i:2145935 original size:19 final size:21
Alignment explanation
Indices: 2145911--2145956 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
2145901 AACCGACTGA
2145911 GAACCGG-T-AAAACCGGGGT
1 GAACCGGCTAAAAACCGGGGT
*
2145930 GAACCGGCTAAAAACCGGTGT
1 GAACCGGCTAAAAACCGGGGT
2145951 GAACCG
1 GAACCG
2145957 CCGGTTCTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.29
20 1 0.04
21 16 0.67
ACGTcount: A:0.33, C:0.24, G:0.33, T:0.11
Consensus pattern (21 bp):
GAACCGGCTAAAAACCGGGGT
Found at i:2147311 original size:20 final size:21
Alignment explanation
Indices: 2147288--2147326 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2147278 ATACGTGAAT
2147288 ATTGGTTAATT-ACTTTTAAA
1 ATTGGTTAATTGACTTTTAAA
2147308 ATTGGTTAATTGACTTTTA
1 ATTGGTTAATTGACTTTTA
2147327 GATTTTAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51
Consensus pattern (21 bp):
ATTGGTTAATTGACTTTTAAA
Found at i:2149993 original size:14 final size:14
Alignment explanation
Indices: 2149974--2150019 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
2149964 AGCAACTCGA
*
2149974 AAAATTAATATATT
1 AAAATTAATTTATT
*
2149988 AAAATTTTAATTTTTT
1 AAAA--TTAATTTATT
2150004 AAAATTAATTTATT
1 AAAATTAATTTATT
2150018 AA
1 AA
2150020 TAATATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 15 0.56
16 12 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAAATTAATTTATT
Found at i:2150010 original size:30 final size:31
Alignment explanation
Indices: 2149974--2150033 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
2149964 AGCAACTCGA
* *
2149974 AAAATTAATATATTAA-AATTTTAATTTTTT
1 AAAATTAATATATTAATAATATTAAATTTTT
*
2150004 AAAATTAATTTATTAATAATATTAAATTTT
1 AAAATTAATATATTAATAATATTAAATTTT
2150034 GTATTTTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
AAAATTAATATATTAATAATATTAAATTTTT
Found at i:2154959 original size:29 final size:29
Alignment explanation
Indices: 2154926--2154985 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
2154916 CCAAATTTTG
*
2154926 TTTAGTAA-AAAAATGTAAGTTTTGAAAAA
1 TTTAGTAACAAAAATG-AAATTTTGAAAAA
*
2154955 TTTAGTAACTAAAATGAAATTTTGAAAAA
1 TTTAGTAACAAAAATGAAATTTTGAAAAA
2154984 TT
1 TT
2154986 GAAGGGTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 22 0.79
30 6 0.21
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.37
Consensus pattern (29 bp):
TTTAGTAACAAAAATGAAATTTTGAAAAA
Found at i:2165895 original size:20 final size:19
Alignment explanation
Indices: 2165863--2165900 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2165853 AAATAAAATA
*
2165863 AAACAAAATAAAAATAAAG
1 AAACAAAAGAAAAATAAAG
2165882 AAACGAAAAGAAAAATAAA
1 AAAC-AAAAGAAAAATAAA
2165901 TAAATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.79, C:0.05, G:0.08, T:0.08
Consensus pattern (19 bp):
AAACAAAAGAAAAATAAAG
Found at i:2166058 original size:20 final size:19
Alignment explanation
Indices: 2166021--2166070 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 19
2166011 CAAGAGAAAA
2166021 AAATAAAATAAAATTAGAT
1 AAATAAAATAAAATTAGAT
*
2166040 AAATAAAATATATATTAGAT
1 AAATAAAATA-AAATTAGAT
*
2166060 AAACAAAATAA
1 AAATAAAATAA
2166071 TAAGATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (19 bp):
AAATAAAATAAAATTAGAT
Found at i:2179675 original size:5 final size:5
Alignment explanation
Indices: 2179665--2179784 Score: 68
Period size: 5 Copynumber: 23.0 Consensus size: 5
2179655 AATATAGAAG
* * *
2179665 ATAAA ATAAA AT-AA ATAAA AGAAA GACAAA GAAAAGA ATAATA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA -ATAAA -ATAA-A ATAA-A ATAAA
* **
2179713 ATAAA GATAACA AGT-AA ATAAA ACAAA ATAAA A-ATAA ATAAA CGAAA
1 ATAAA -ATAA-A A-TAAA ATAAA ATAAA ATAAA ATA-AA ATAAA ATAAA
*
2179760 AGAAA A-ATAA ATAAA ATAAA ATAAA
1 ATAAA ATA-AA ATAAA ATAAA ATAAA
2179785 CGACATAAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
4 7 0.07
5 60 0.64
6 24 0.26
7 3 0.03
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (5 bp):
ATAAA
Found at i:2179682 original size:14 final size:14
Alignment explanation
Indices: 2179665--2179837 Score: 72
Period size: 14 Copynumber: 11.9 Consensus size: 14
2179655 AATATAGAAG
2179665 ATAAAATAAAATAA
1 ATAAAATAAAATAA
* *
2179679 ATAAAAGAAAGACAA
1 ATAAAATAAA-ATAA
* *
2179694 AGAAAAGAATAAT-A
1 ATAAAATAA-AATAA
2179708 ATAAAATAAAGATAA
1 ATAAAATAAA-ATAA
*
2179723 CA-AGTAAATAAAACAAA
1 -ATA--AAATAAAA-TAA
2179740 ATAAAA-ATAAATAA
1 ATAAAATA-AAATAA
* *
2179754 ACGAAAAGAAAAATAA
1 A-TAAAA-TAAAATAA
2179770 ATAAAATAAAATAA
1 ATAAAATAAAATAA
** *
2179784 ACGACATAAAAATAA
1 ATAAAAT-AAAATAA
* *
2179799 AT-AAATGAAGTAA
1 ATAAAATAAAATAA
2179812 A-AAAA-ACAAATGAA
1 ATAAAATA-AAAT-AA
2179826 AT-AAATAAAATA
1 ATAAAATAAAATA
2179838 CTGGAAAATA
Statistics
Matches: 120, Mismatches: 20, Indels: 39
0.67 0.11 0.22
Matches are distributed among these distances:
13 14 0.12
14 47 0.39
15 37 0.31
16 11 0.09
17 11 0.09
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (14 bp):
ATAAAATAAAATAA
Found at i:2179743 original size:10 final size:9
Alignment explanation
Indices: 2179667--2179837 Score: 63
Period size: 10 Copynumber: 17.7 Consensus size: 9
2179657 TATAGAAGAT
2179667 AAAATAAAA
1 AAAATAAAA
*
2179676 TAAATAAAA
1 AAAATAAAA
* *
2179685 GAAAGACAAAG
1 -AAA-ATAAAA
* *
2179696 AAAAGAATA
1 AAAATAAAA
*
2179705 ATAATAAAA
1 AAAATAAAA
2179714 TAAAGATAACAA
1 -AAA-ATAA-AA
*
2179726 GTAAATAAAA
1 -AAAATAAAA
2179736 CAAAATAAAA
1 -AAAATAAAA
*
2179746 ATAAATAAACG
1 A-AAATAAA-A
*
2179757 AAAAGAAAA
1 AAAATAAAA
2179766 ATAAATAAAA
1 A-AAATAAAA
*
2179776 TAAAATAAAC
1 -AAAATAAAA
* *
2179786 GACATAAAA
1 AAAATAAAA
*
2179795 ATAAATAAAT
1 A-AAATAAAA
* *
2179805 GAAGTAAAA
1 AAAATAAAA
* *
2179814 AAAACAAAT
1 AAAATAAAA
* *
2179823 GAAATAAAT
1 AAAATAAAA
2179832 AAAATA
1 AAAATA
2179838 CTGGAAAATA
Statistics
Matches: 116, Mismatches: 36, Indels: 20
0.67 0.21 0.12
Matches are distributed among these distances:
9 48 0.41
10 50 0.43
11 14 0.12
12 4 0.03
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (9 bp):
AAAATAAAA
Found at i:2179752 original size:20 final size:20
Alignment explanation
Indices: 2179707--2179784 Score: 86
Period size: 20 Copynumber: 3.8 Consensus size: 20
2179697 AAAGAATAAT
* *
2179707 AATAAAATAAAGATAACAAGTA
1 AATAAAACAAA-ATAA-AAATA
2179729 AATAAAACAAAATAAAAATA
1 AATAAAACAAAATAAAAATA
*
2179749 AAT-AAACGAAAAGAAAAATA
1 AATAAAAC-AAAATAAAAATA
*
2179769 AATAAAATAAAATAAA
1 AATAAAACAAAATAAA
2179785 CGACATAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
19 4 0.08
20 28 0.57
21 7 0.14
22 10 0.20
ACGTcount: A:0.76, C:0.04, G:0.05, T:0.15
Consensus pattern (20 bp):
AATAAAACAAAATAAAAATA
Found at i:2179774 original size:30 final size:30
Alignment explanation
Indices: 2179738--2179803 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 30
2179728 AAATAAAACA
2179738 AAATAAAAAT-AAATAAACGAAAAGAAAAAT
1 AAATAAAAATAAAATAAACG-AAAGAAAAAT
* *
2179768 AAAT-AAAATAAAATAAACGACATAAAAAT
1 AAATAAAAATAAAATAAACGAAAGAAAAAT
2179797 AAATAAA
1 AAATAAA
2179804 TGAAGTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 17 0.53
30 15 0.47
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.15
Consensus pattern (30 bp):
AAATAAAAATAAAATAAACGAAAGAAAAAT
Found at i:2179779 original size:29 final size:30
Alignment explanation
Indices: 2179672--2179837 Score: 103
Period size: 30 Copynumber: 5.5 Consensus size: 30
2179662 AAGATAAAAT
* *
2179672 AAAATAAATAAAAGAAAGA-CAAAGAAAAGA
1 AAAATAAATAAAATAAA-ATAAAAGAAAAGA
* * *
2179702 ATAAT-AATAAAATAAAGATAACAAGTAAATA
1 AAAATAAATAAAATAAA-ATAA-AAGAAAAGA
*
2179733 AAACA-AAATAAAA-ATAAATAAACGAAAAGA
1 AAA-ATAAATAAAATA-AAATAAAAGAAAAGA
* * *
2179763 AAAATAAATAAAATAAAATAAACG-ACATA
1 AAAATAAATAAAATAAAATAAAAGAAAAGA
* * *
2179792 AAAATAAAT-AAATGAAGTAAAA-AAAACAA
1 AAAATAAATAAAATAAAATAAAAGAAAA-GA
2179821 ATGAAATAAATAAAATA
1 A--AAATAAATAAAATA
2179838 CTGGAAAATA
Statistics
Matches: 107, Mismatches: 17, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
28 12 0.11
29 27 0.25
30 31 0.29
31 23 0.21
32 14 0.13
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.15
Consensus pattern (30 bp):
AAAATAAATAAAATAAAATAAAAGAAAAGA
Found at i:2179794 original size:19 final size:17
Alignment explanation
Indices: 2179739--2179837 Score: 71
Period size: 18 Copynumber: 5.8 Consensus size: 17
2179729 AATAAAACAA
*
2179739 AATAAAAATAAATAAACG
1 AATAAAAA-AAATAAATG
*
2179757 AA-AAGAAAAATAAAT-
1 AATAAAAAAAATAAATG
* *
2179772 -A-AAATAAAATAAACG
1 AATAAAAAAAATAAATG
2179787 ACATAAAAATAAATAAATG
1 A-ATAAAAA-AAATAAATG
*
2179806 AAGTAAAAAAAACAAATG
1 AA-TAAAAAAAATAAATG
*
2179824 AAATAAATAAAATA
1 -AATAAAAAAAATA
2179838 CTGGAAAATA
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
14 11 0.17
16 7 0.11
17 5 0.08
18 24 0.38
19 17 0.27
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.16
Consensus pattern (17 bp):
AATAAAAAAAATAAATG
Found at i:2179822 original size:18 final size:18
Alignment explanation
Indices: 2179764--2179835 Score: 65
Period size: 19 Copynumber: 3.9 Consensus size: 18
2179754 ACGAAAAGAA
*
2179764 AAAT-AAATAAAATAAAAT
1 AAATGAAATAAAA-AAAAC
* * *
2179782 AAACGACATAAAAATAAAT
1 AAATGAAATAAAAA-AAAC
*
2179801 AAATGAAGTAAAAAAAAC
1 AAATGAAATAAAAAAAAC
2179819 AAATGAAATAAATAAAA
1 AAATGAAATAAA-AAAA
2179836 TACTGGAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
18 18 0.41
19 26 0.59
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.17
Consensus pattern (18 bp):
AAATGAAATAAAAAAAAC
Found at i:2179822 original size:22 final size:22
Alignment explanation
Indices: 2179791--2179835 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2179781 TAAACGACAT
* *
2179791 AAAAATAAAT-AAATGAAGTAAA
1 AAAAACAAATGAAAT-AAATAAA
2179813 AAAAACAAATGAAATAAATAAA
1 AAAAACAAATGAAATAAATAAA
2179835 A
1 A
2179836 TACTGGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.16
Consensus pattern (22 bp):
AAAAACAAATGAAATAAATAAA
Found at i:2179931 original size:20 final size:19
Alignment explanation
Indices: 2179897--2179978 Score: 62
Period size: 20 Copynumber: 4.3 Consensus size: 19
2179887 TGCAAGAAAA
* *
2179897 AAAATAAAATTAGATAAAT
1 AAAATAATATAAGATAAAT
*
2179916 AAAATAGATATAAGATAAAC
1 AAAATA-ATATAAGATAAAT
*
2179936 AAAAT-A-ATAAGATATAT
1 AAAATAATATAAGATAAAT
* *
2179953 ATAAA-AATAATAATATTAAT
1 A-AAATAAT-ATAAGATAAAT
2179973 AAAATA
1 AAAATA
2179979 GATAAAGGGA
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
17 10 0.20
18 5 0.10
19 9 0.18
20 25 0.51
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (19 bp):
AAAATAATATAAGATAAAT
Found at i:2179956 original size:23 final size:24
Alignment explanation
Indices: 2179912--2179968 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
2179902 AAAATTAGAT
*
2179912 AAATAAAATAGATATAAGATAAACA
1 AAATAATATAGATATAAGATAAA-A
*
2179937 AAATAATA-AGATAT-ATATAAAA
1 AAATAATATAGATATAAGATAAAA
2179959 ATAATAATAT
1 A-AATAATAT
2179969 TAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 2 0.07
23 13 0.46
24 6 0.21
25 7 0.25
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (24 bp):
AAATAATATAGATATAAGATAAAA
Found at i:2180070 original size:2 final size:2
Alignment explanation
Indices: 2180063--2180091 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2180053 AAATGAATGA
2180063 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 A
2180092 ATAAAACTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2184542 original size:56 final size:56
Alignment explanation
Indices: 2184456--2184567 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
2184446 GCCACATCAT
*
2184456 CTCCTCCATTAATATTTAACGGCAGGTGGCTTGATTGACAAGATTTAAATAGTTAG
1 CTCCTCCATTAATATTTAACGGCAGGTGGCTTGATTGACAAAATTTAAATAGTTAG
2184512 CTCCTCCATTAATATTTAACGGCAGGTGGCTTGATTGACAAAATTTAAATAGTTAG
1 CTCCTCCATTAATATTTAACGGCAGGTGGCTTGATTGACAAAATTTAAATAGTTAG
2184568 GTGACCGGAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (56 bp):
CTCCTCCATTAATATTTAACGGCAGGTGGCTTGATTGACAAAATTTAAATAGTTAG
Found at i:2184747 original size:22 final size:22
Alignment explanation
Indices: 2184706--2184747 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2184696 GATCTTTAAC
*
2184706 TACTTTATAATTATATGTTTAG
1 TACTTTATAATTATACGTTTAG
2184728 TACTTTATAATT-TAACGTTT
1 TACTTTATAATTAT-ACGTTT
2184748 TATTAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (22 bp):
TACTTTATAATTATACGTTTAG
Found at i:2185852 original size:18 final size:20
Alignment explanation
Indices: 2185821--2185858 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2185811 TTAGTTAGTG
2185821 AAAATAATATTTTTA-ATAA
1 AAAATAATATTTTTAGATAA
2185840 AAAATAATA-TTTTAGATAA
1 AAAATAATATTTTTAGATAA
2185859 CATTTTATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
AAAATAATATTTTTAGATAA
Found at i:2190792 original size:44 final size:44
Alignment explanation
Indices: 2190729--2190852 Score: 203
Period size: 44 Copynumber: 2.8 Consensus size: 44
2190719 ACAGATGAAC
*
2190729 ATTGTTAATTATGAATATCATTAAATTAGTTTATAAAATATTAA
1 ATTGTTAATTATGAATATCATTAAATTAATTTATAAAATATTAA
*
2190773 ATTGTTAATTATGAATATCATTAAATTAATGTATAAAATATTAA
1 ATTGTTAATTATGAATATCATTAAATTAATTTATAAAATATTAA
* * *
2190817 ATCGTTAATTATAAATATTATTAAATTAATTTATAA
1 ATTGTTAATTATGAATATCATTAAATTAATTTATAA
2190853 TTATAAATTT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 74 1.00
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (44 bp):
ATTGTTAATTATGAATATCATTAAATTAATTTATAAAATATTAA
Found at i:2190801 original size:21 final size:19
Alignment explanation
Indices: 2190733--2190861 Score: 82
Period size: 21 Copynumber: 6.1 Consensus size: 19
2190723 ATGAACATTG
2190733 TTAATTATGAATATCATTAAA
1 TTAATTAT-AATAT-ATTAAA
* *
2190754 TTAGTTTATAAAATATTAAA
1 TTA-ATTATAATATATTAAA
2190774 TTGTTAATTATGAATATCATTAAA
1 ---TTAATTAT-AATAT-ATTAAA
*
2190798 TTAATGTATAAAATATTAAA
1 TTAAT-TATAATATATTAAA
2190818 TCGTTAATTATAAATATTATTAAA
1 ---TTAATTAT-AATA-TATTAAA
2190842 TTAATTTATAAT-TA-TAAA
1 TTAA-TTATAATATATTAAA
2190860 TT
1 TT
2190862 TAATATTTTA
Statistics
Matches: 89, Mismatches: 6, Indels: 29
0.72 0.05 0.23
Matches are distributed among these distances:
18 6 0.07
19 2 0.02
20 12 0.13
21 23 0.26
22 18 0.20
23 15 0.17
24 13 0.15
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (19 bp):
TTAATTATAATATATTAAA
Found at i:2190878 original size:15 final size:15
Alignment explanation
Indices: 2190853--2190896 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
2190843 TAATTTATAA
2190853 TTATAAATTTAATATT
1 TTAT-AATTTAATATT
2190869 TTATAATTTAATATT
1 TTATAATTTAATATT
*
2190884 TTATAAATTAATA
1 TTATAATTTAATA
2190897 ATATTTATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
15 23 0.85
16 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATAATTTAATATT
Found at i:2191441 original size:26 final size:26
Alignment explanation
Indices: 2191411--2191467 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
2191401 AATAAATTCA
*
2191411 TTTTAT-ATA-AAATATAATTTTATTAT
1 TTTTATCATATAAAT-TAA-TTTACTAT
*
2191437 TTTTATCATATTAATTAATTTACTAT
1 TTTTATCATATAAATTAATTTACTAT
2191463 TTTTA
1 TTTTA
2191468 GCTAGTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 18 0.67
27 6 0.22
28 3 0.11
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTTATCATATAAATTAATTTACTAT
Found at i:2191713 original size:14 final size:14
Alignment explanation
Indices: 2191694--2191725 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2191684 TGTTTCATGT
*
2191694 AAAATATTTTTTGA
1 AAAATATTTTCTGA
2191708 AAAATATTTTCTGA
1 AAAATATTTTCTGA
2191722 AAAA
1 AAAA
2191726 CGTTTTCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (14 bp):
AAAATATTTTCTGA
Found at i:2193970 original size:43 final size:43
Alignment explanation
Indices: 2193904--2194171 Score: 160
Period size: 43 Copynumber: 6.3 Consensus size: 43
2193894 AATTAGCGAC
2193904 GTTTGTAT-AAAAAAATGCCGCTATAGATATGACATTTTACGGA
1 GTTTGT-TCAAAAAAATGCCGCTATAGATATGACATTTTACGGA
** * * *
2193947 GTTTGTTCAAAAAAATGTTGCTATAGATATGACCTTTTGCGGC
1 GTTTGTTCAAAAAAATGCCGCTATAGATATGACATTTTACGGA
* * *
2193990 GTTTGTTC-CAAAAATGCCGCTATAG--ATGACTTTTTTC-GA
1 GTTTGTTCAAAAAAATGCCGCTATAGATATGACATTTTACGGA
* * * * * *
2194029 CGTTTGTTACAAAAACA--CAGCTATAGATATGACCTTTTGCTGC
1 -GTTTGTT-CAAAAAAATGCCGCTATAGATATGACATTTTACGGA
* * * * * **
2194072 GTTTGTTC-CAAAAACGCCGCAAAAGATCTCGATGTTTTAC-GA
1 GTTTGTTCAAAAAAATGCCGCTATAGATAT-GACATTTTACGGA
* * * * * *
2194114 CATTTGTTC-CAAAAATGTCGCTATAGATATCGACTTTTTGCGGC
1 -GTTTGTTCAAAAAAATGCCGCTATAGATAT-GACATTTTACGGA
*
2194158 GTTTGTTCCAAAAA
1 GTTTGTTCAAAAAA
2194172 CGCCGTGAAC
Statistics
Matches: 173, Mismatches: 39, Indels: 25
0.73 0.16 0.11
Matches are distributed among these distances:
39 1 0.01
40 29 0.17
41 2 0.01
42 46 0.27
43 90 0.52
44 5 0.03
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (43 bp):
GTTTGTTCAAAAAAATGCCGCTATAGATATGACATTTTACGGA
Found at i:2194012 original size:85 final size:85
Alignment explanation
Indices: 2193914--2194176 Score: 295
Period size: 82 Copynumber: 3.1 Consensus size: 85
2193904 GTTTGTATAA
* *
2193914 AAAAATGCCGCTATAGATATGACATTTTACGGA-GTTTGTTCAAAAAAATGTTGCTATAGATATG
1 AAAAACGCCGCTATAGATATGACATTTTAC-GACGTTTGTTCAAAAAAATGTAGCTATAGATATG
2193978 ACCTTTTGCGGCGTTTGTTCC
65 ACCTTTTGCGGCGTTTGTTCC
* * * * *
2193999 AAAAATGCCGCTATAG--ATGACTTTTTTCGACGTTTGTTACAAAAACA--CAGCTATAGATATG
1 AAAAACGCCGCTATAGATATGACATTTTACGACGTTTGTT-CAAAAAAATGTAGCTATAGATATG
*
2194060 ACCTTTTGCTGCGTTTGTTCC
65 ACCTTTTGCGGCGTTTGTTCC
* * * ** * * *
2194081 AAAAACGCCGCAAAAGATCTCGATGTTTTACGACATTTGTTC-CAAAAATGTCGCTATAGATATC
1 AAAAACGCCGCTATAGATAT-GACATTTTACGACGTTTGTTCAAAAAAATGTAGCTATAGATAT-
*
2194145 GACTTTTTGCGGCGTTTGTTCC
64 GACCTTTTGCGGCGTTTGTTCC
2194167 AAAAACGCCG
1 AAAAACGCCG
2194177 TGAACTTTGG
Statistics
Matches: 150, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
82 47 0.31
83 21 0.14
84 9 0.06
85 43 0.29
86 30 0.20
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (85 bp):
AAAAACGCCGCTATAGATATGACATTTTACGACGTTTGTTCAAAAAAATGTAGCTATAGATATGA
CCTTTTGCGGCGTTTGTTCC
Found at i:2200522 original size:31 final size:31
Alignment explanation
Indices: 2200484--2200611 Score: 109
Period size: 31 Copynumber: 4.1 Consensus size: 31
2200474 GAACCTCAGC
* *
2200484 AACTGTTCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTTCATATGTCCCGAAGAACATAGGTA
* **
2200515 AACTGTTCATATGTTCCTTAGAACATAGGTA
1 AACTGTTCATATGTCCCGAAGAACATAGGTA
* *
2200546 TACTGTCCATATGTCCCGAA-AGACATAGGTA
1 AACTGTTCATATGTCCCGAAGA-ACATAGGTA
* * *
2200577 ATTA-TGTACATATGTTCC-ATAGAACATATGTA
1 A--ACTGTTCATATGTCCCGA-AGAACATAGGTA
2200609 AAC
1 AAC
2200612 CCTCGACTCT
Statistics
Matches: 77, Mismatches: 14, Indels: 12
0.75 0.14 0.12
Matches are distributed among these distances:
30 2 0.03
31 51 0.66
32 22 0.29
33 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (31 bp):
AACTGTTCATATGTCCCGAAGAACATAGGTA
Found at i:2201423 original size:31 final size:29
Alignment explanation
Indices: 2201387--2201454 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 29
2201377 AACCATTTAC
2201387 AACTTTTCAAAAAATTAT-GAATGGGTCCCCT
1 AACTTTTC-AAAAATTATAGAAT-GGT-CCCT
*
2201418 AACTTTTCAAAATTTATAGAATGGTCCCT
1 AACTTTTCAAAAATTATAGAATGGTCCCT
*
2201447 AAATTTTC
1 AACTTTTC
2201455 TAAAGCTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 11 0.32
30 11 0.32
31 12 0.35
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (29 bp):
AACTTTTCAAAAATTATAGAATGGTCCCT
Found at i:2202956 original size:17 final size:17
Alignment explanation
Indices: 2202911--2202956 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
2202901 ATTTATCATA
*
2202911 CTTAACCCTTTAATTTC
1 CTTATCCCTTTAATTTC
* * *
2202928 CTTTTTCATTTAATTTC
1 CTTATCCCTTTAATTTC
2202945 CTTATCCCTTTA
1 CTTATCCCTTTA
2202957 CTTATCCACA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.20, C:0.26, G:0.00, T:0.54
Consensus pattern (17 bp):
CTTATCCCTTTAATTTC
Found at i:2204964 original size:32 final size:31
Alignment explanation
Indices: 2204814--2204969 Score: 127
Period size: 32 Copynumber: 4.9 Consensus size: 31
2204804 ACCTCAGCAA
* * *
2204814 CTGTCCATAGGTCCCGAAGAACCTAGGTAAAT
1 CTGTCCATATGTCCCG-AGAACATAGGTAATT
** *
2204846 -TGTCCATATGTTCCTTAGAACATAGGT-ATA
1 CTGTCCATATG-TCCCGAGAACATAGGTAATT
* * *
2204876 ATGTCCATATGTCCCGAAAGACATACGTAATT
1 CTGTCCATATGTCCCGAGA-ACATAGGTAATT
* * *
2204908 CTGTTCATATATCCCGAAAGACATAGGTAATT
1 CTGTCCATATGTCCCGAGA-ACATAGGTAATT
* *
2204940 CTGTCCATATGTTCCGTAGAACATATGTAA
1 CTGTCCATATGTCCCG-AGAACATAGGTAA
2204970 ACCCTCGACT
Statistics
Matches: 99, Mismatches: 20, Indels: 10
0.77 0.16 0.08
Matches are distributed among these distances:
30 6 0.06
31 36 0.36
32 55 0.56
33 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (31 bp):
CTGTCCATATGTCCCGAGAACATAGGTAATT
Found at i:2210548 original size:18 final size:18
Alignment explanation
Indices: 2210525--2210576 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
2210515 ATATAACACA
2210525 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
* *
2210543 TATGTCCCAAAGCACCAC
1 TATGTCCCGAAGGACCAC
* *
2210561 TATATCCCGAAAGACC
1 TATGTCCCGAAGGACC
2210577 GCGTAGACCC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.33, C:0.35, G:0.15, T:0.17
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:2211403 original size:24 final size:20
Alignment explanation
Indices: 2211350--2211407 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
2211340 TTCCCCTTGA
*
2211350 AGTGCATTGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
2211370 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
2211393 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
2211408 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:2211466 original size:65 final size:63
Alignment explanation
Indices: 2211395--2211533 Score: 183
Period size: 65 Copynumber: 2.2 Consensus size: 63
2211385 TCTTTAACAT
*
2211395 GTGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTCGATGTTTTCATT-TTTAAAG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGATG-TTTC-TTCTTTAAAG
*
2211458 G
63 A
* * *
2211459 GATGCATCGATGCACTCCTCATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCTTCTTTAAAGA
2211523 GTGCATCGATG
1 GTGCATCGATG
2211534 TCGATACACC
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
63 12 0.18
64 15 0.22
65 40 0.60
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCTTCTTTAAAGA
Found at i:2214526 original size:49 final size:46
Alignment explanation
Indices: 2214464--2214624 Score: 171
Period size: 49 Copynumber: 3.6 Consensus size: 46
2214454 GCGTAGAATT
2214464 TGTCCCGAAGGACCACGTAGATGTCCCAAAGGACTACATATAACACATA
1 TGTCCCGAAGGACCAC-T--ATGTCCCAAAGGACTACATATAACACATA
* *
2214513 TGTCTCGAAGGACCACTATGTCCCAAATG---AC------CAC-TA
1 TGTCCCGAAGGACCACTATGTCCCAAAGGACTACATATAACACATA
*
2214549 TGTCCCGAAGGACCGCGTAGATGTCCCAAAGGACTACATATAACACATA
1 TGTCCCGAAGGACCAC-T--ATGTCCCAAAGGACTACATATAACACATA
2214598 TGTCCCGAAGGACCACTATGTCCCAAA
1 TGTCCCGAAGGACCACTATGTCCCAAA
2214625 TGACCACTAT
Statistics
Matches: 93, Mismatches: 6, Indels: 29
0.73 0.05 0.23
Matches are distributed among these distances:
36 16 0.17
37 4 0.04
39 11 0.12
42 2 0.02
43 2 0.02
46 21 0.23
48 5 0.05
49 32 0.34
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.19
Consensus pattern (46 bp):
TGTCCCGAAGGACCACTATGTCCCAAAGGACTACATATAACACATA
Found at i:2214534 original size:18 final size:18
Alignment explanation
Indices: 2214511--2214649 Score: 105
Period size: 18 Copynumber: 8.0 Consensus size: 18
2214501 ATATAACACA
*
2214511 TATGTCTCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
* *
2214529 TATGTCCCAAATGACCAC
1 TATGTCCCGAAGGACCAC
*
2214547 TATGTCCCGAAGGACCGC
1 TATGTCCCGAAGGACCAC
* *
2214565 GTAGATGTCCCAAAGGACTAC
1 -T--ATGTCCCGAAGGACCAC
* *
2214586 -ATAT----AA-CA-CA-
1 TATGTCCCGAAGGACCAC
2214596 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
* *
2214614 TATGTCCCAAATGACCAC
1 TATGTCCCGAAGGACCAC
2214632 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
2214650 GTAGACCCTC
Statistics
Matches: 92, Mismatches: 18, Indels: 22
0.70 0.14 0.17
Matches are distributed among these distances:
11 4 0.04
12 1 0.01
13 2 0.02
15 2 0.02
16 1 0.01
17 5 0.05
18 62 0.67
19 1 0.01
21 14 0.15
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:2214558 original size:36 final size:36
Alignment explanation
Indices: 2214511--2214649 Score: 134
Period size: 36 Copynumber: 3.5 Consensus size: 36
2214501 ATATAACACA
*
2214511 TATGTCTCGAAGGACCACTATGTCCCAAATGACCAC
1 TATGTCCCGAAGGACCACTATGTCCCAAATGACCAC
* *
2214547 TATGTCCCGAAGGACCGCGTAGATGTCCCAAAGGACTACATATAACAC
1 TATGTCCCGAAGGACCAC-T--ATGTCCCAAATG---AC------CAC
2214595 ATATGTCCCGAAGGACCACTATGTCCCAAATGACCAC
1 -TATGTCCCGAAGGACCACTATGTCCCAAATGACCAC
2214632 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
2214650 GTAGACCCTC
Statistics
Matches: 85, Mismatches: 5, Indels: 26
0.73 0.04 0.22
Matches are distributed among these distances:
36 34 0.40
37 4 0.05
39 11 0.13
42 2 0.02
43 2 0.02
46 11 0.13
48 4 0.05
49 17 0.20
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (36 bp):
TATGTCCCGAAGGACCACTATGTCCCAAATGACCAC
Found at i:2214607 original size:85 final size:85
Alignment explanation
Indices: 2214464--2214654 Score: 364
Period size: 85 Copynumber: 2.2 Consensus size: 85
2214454 GCGTAGAATT
*
2214464 TGTCCCGAAGGACCACGTAGATGTCCCAAAGGACTACATATAACACATATGTCTCGAAGGACCAC
1 TGTCCCGAAGGACCACGTAGATGTCCCAAAGGACTACATATAACACATATGTCCCGAAGGACCAC
2214529 TATGTCCCAAATGACCACTA
66 TATGTCCCAAATGACCACTA
*
2214549 TGTCCCGAAGGACCGCGTAGATGTCCCAAAGGACTACATATAACACATATGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCACGTAGATGTCCCAAAGGACTACATATAACACATATGTCCCGAAGGACCAC
2214614 TATGTCCCAAATGACCACTA
66 TATGTCCCAAATGACCACTA
2214634 TGTCCCGAAGGACCACGTAGA
1 TGTCCCGAAGGACCACGTAGA
2214655 CCCTCGACTC
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 103 1.00
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (85 bp):
TGTCCCGAAGGACCACGTAGATGTCCCAAAGGACTACATATAACACATATGTCCCGAAGGACCAC
TATGTCCCAAATGACCACTA
Found at i:2215443 original size:20 final size:22
Alignment explanation
Indices: 2215418--2215475 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
2215408 TTCCCCTTGA
2215418 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
*
2215438 AGTGCATCGATACATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
2215461 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
2215476 CTACCCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:2215537 original size:65 final size:63
Alignment explanation
Indices: 2215463--2215604 Score: 173
Period size: 65 Copynumber: 2.2 Consensus size: 63
2215453 TCTTTAACAT
* *
2215463 GTGCATCGATGCACTACC-CATGCATCGAT-ACACAAATTACCTTTGATGTTTTCATT-TTTAAA
1 GTGCATCGATGCACT-CCTCATGCATCGATGA-ACAAATTACATTCGATG-TTTC-TTCTTTAAA
2215525 GA
62 GA
* * *
2215527 GATGCATCGATGCACTCCTTATGCATCGATGAACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATGAACAAATTACATTCGATGTTTCTTCTTTAAAGA
2215591 GTGCATCGATGCAC
1 GTGCATCGATGCAC
2215605 ATTCAATGTG
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
63 15 0.22
64 16 0.23
65 37 0.54
66 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATGAACAAATTACATTCGATGTTTCTTCTTTAAAGA
Found at i:2218013 original size:21 final size:23
Alignment explanation
Indices: 2217973--2218022 Score: 86
Period size: 21 Copynumber: 2.3 Consensus size: 23
2217963 GCTGACCTGA
2217973 CTTGTACCTTAACAATCCATAAG
1 CTTGTACCTTAACAATCCATAAG
2217996 CTTGTA-CTTAAC-ATCCATAAG
1 CTTGTACCTTAACAATCCATAAG
2218017 CTTGTA
1 CTTGTA
2218023 AGAACTTGCG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 15 0.56
22 6 0.22
23 6 0.22
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (23 bp):
CTTGTACCTTAACAATCCATAAG
Found at i:2218613 original size:18 final size:18
Alignment explanation
Indices: 2218590--2218641 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
2218580 ATATAACACA
2218590 TATGTCCCGAAGAACCAC
1 TATGTCCCGAAGAACCAC
*
2218608 TATGTCCCAAATG-ACCAC
1 TATGTCCCGAA-GAACCAC
2218626 TATGTCCCGAAGAACC
1 TATGTCCCGAAGAACC
2218642 GCATAGACCC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 1 0.03
18 28 0.93
19 1 0.03
ACGTcount: A:0.33, C:0.33, G:0.15, T:0.19
Consensus pattern (18 bp):
TATGTCCCGAAGAACCAC
Found at i:2219441 original size:20 final size:22
Alignment explanation
Indices: 2219416--2219475 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 22
2219406 TTCCCCTTGA
2219416 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
*
2219436 AGTGCATCGATGAATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
2219459 ATGTGCATCGATGCATT
1 A-GTGCATCGATGCATT
2219476 ACCCATGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.47
22 1 0.03
23 3 0.09
24 14 0.41
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Done.