Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008353.1 Hibiscus syriacus cultivar Beakdansim tig00111088_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: 2583621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 10 of 13
Found at i:1972200 original size:20 final size:21
Alignment explanation
Indices: 1972161--1972200 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1972151 TCAATATAAG
*
1972161 GAGAAAAGAAAATTTGAAAAA
1 GAGAAAAGAAAATATGAAAAA
*
1972182 GAGAAAA-AGAATATGAAAA
1 GAGAAAAGAAAATATGAAAA
1972201 TCAAAGATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.12
Consensus pattern (21 bp):
GAGAAAAGAAAATATGAAAAA
Found at i:1972314 original size:3 final size:3
Alignment explanation
Indices: 1972306--1972332 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1972296 TGTAGAATTG
1972306 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1972333 GGACAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1973297 original size:13 final size:13
Alignment explanation
Indices: 1973279--1973312 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1973269 GGCATTGTGA
*
1973279 AAAGAAAATAATG
1 AAAGAAAATAAAG
1973292 AAAGAAAATAAAG
1 AAAGAAAATAAAG
*
1973305 AAATAAAA
1 AAAGAAAA
1973313 GTGGAGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (13 bp):
AAAGAAAATAAAG
Found at i:1975342 original size:3 final size:3
Alignment explanation
Indices: 1975334--1975363 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1975324 TCTTTAAGAT
*
1975334 ATA ATA ATA ATA ATA ATA ATA TTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1975364 TCAATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:1978562 original size:32 final size:32
Alignment explanation
Indices: 1978474--1978562 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
1978464 TTGGTTCGGA
* * ** *
1978474 TCAATACCGGATCAGTTGATTTTTGGGTCGGG
1 TCAATATCGGATCGGTTGATTTTCAGGTCAGG
* *
1978506 TTAATATCGAATCGGTTAGA-TTTCAGGTCAGG
1 TCAATATCGGATCGGTT-GATTTTCAGGTCAGG
1978538 TCAATATCGGATCGGTTGATTTTCA
1 TCAATATCGGATCGGTTGATTTTCA
1978563 ATTTAGGTCA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
31 2 0.04
32 42 0.91
33 2 0.04
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.36
Consensus pattern (32 bp):
TCAATATCGGATCGGTTGATTTTCAGGTCAGG
Found at i:1978571 original size:32 final size:32
Alignment explanation
Indices: 1978508--1978573 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
1978498 GGGTCGGGTT
*
1978508 AATATCGAATCGGTTAGATTTCAGGTCAGGTC
1 AATATCGAATCGGTTAGATTTCAAGTCAGGTC
* * *
1978540 AATATCGGATCGGTT-GATTTTCAATTTAGGTC
1 AATATCGAATCGGTTAGA-TTTCAAGTCAGGTC
1978572 AA
1 AA
1978574 CCTTTAGATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 2 0.07
32 27 0.93
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.35
Consensus pattern (32 bp):
AATATCGAATCGGTTAGATTTCAAGTCAGGTC
Found at i:1979400 original size:16 final size:16
Alignment explanation
Indices: 1979356--1979400 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
1979346 TTCAATTTGG
*
1979356 GTTAA-TTCGGTTCGA
1 GTTAATTTCGGTTCAA
*
1979371 GTTAATTTCAGTTCAA
1 GTTAATTTCGGTTCAA
*
1979387 GTTAATTTTGGTTC
1 GTTAATTTCGGTTC
1979401 GGGTTGCTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 5 0.20
16 20 0.80
ACGTcount: A:0.22, C:0.11, G:0.20, T:0.47
Consensus pattern (16 bp):
GTTAATTTCGGTTCAA
Found at i:1982623 original size:3 final size:3
Alignment explanation
Indices: 1982615--1982653 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
1982605 CAAGGTATCT
*
1982615 TTA TTA TTA TTA CTA TTA TTA TTA TTA TT- TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
1982654 ATATATCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 1 0.03
3 30 0.94
4 1 0.03
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1982657 original size:9 final size:9
Alignment explanation
Indices: 1982619--1982657 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
1982609 GTATCTTTAT
*
1982619 TATTATTAC
1 TATTATTAA
*
1982628 TATTATTAT
1 TATTATTAA
*
1982637 TATTATTTA
1 TATTATTAA
1982646 TATTATTAA
1 TATTATTAA
1982655 TAT
1 TAT
1982658 ATCTTAAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (9 bp):
TATTATTAA
Found at i:1982947 original size:21 final size:20
Alignment explanation
Indices: 1982918--1982956 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1982908 TAAACAGTAA
*
1982918 AAAATAAAACTAAATCAATT
1 AAAATAAAACAAAATCAATT
1982938 AAAATAAAAACAAAATCAA
1 AAAAT-AAAACAAAATCAA
1982957 CTTACCGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (20 bp):
AAAATAAAACAAAATCAATT
Found at i:1986527 original size:18 final size:20
Alignment explanation
Indices: 1986504--1986542 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
1986494 ACACTATTGA
1986504 GAATAATGGA-CATT-CAAT
1 GAATAATGGATCATTCCAAT
1986522 GAATAATGGATCATTCCAAT
1 GAATAATGGATCATTCCAAT
1986542 G
1 G
1986543 TGAACTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 4 0.21
20 5 0.26
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (20 bp):
GAATAATGGATCATTCCAAT
Found at i:1987927 original size:25 final size:24
Alignment explanation
Indices: 1987878--1987968 Score: 107
Period size: 25 Copynumber: 3.8 Consensus size: 24
1987868 AGTAAGGGAC
1987878 AACATTTTTCAAAA--C-TTCATCA
1 AACA-TTTTCAAAATTCTTTCATCA
*
1987900 AACATTTATCAAAATTCTTTCACCA
1 AACATTT-TCAAAATTCTTTCATCA
*
1987925 AACATTTCTCAAAATTCTTTCATAA
1 AACATTT-TCAAAATTCTTTCATCA
1987950 AACATTTTCAAAACTTCTT
1 AACATTTTCAAAA-TTCTT
1987969 CATTACAGTC
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
21 3 0.05
22 10 0.17
24 7 0.12
25 40 0.67
ACGTcount: A:0.40, C:0.22, G:0.00, T:0.38
Consensus pattern (24 bp):
AACATTTTCAAAATTCTTTCATCA
Found at i:1988384 original size:26 final size:26
Alignment explanation
Indices: 1988354--1988405 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1988344 ATTCAAAATA
1988354 ATTGCATTTATGCGTGCACAATTTTT
1 ATTGCATTTATGCGTGCACAATTTTT
1988380 ATTGCATTTATGCGTGCACAATTTTT
1 ATTGCATTTATGCGTGCACAATTTTT
1988406 TACAAACCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (26 bp):
ATTGCATTTATGCGTGCACAATTTTT
Found at i:1998981 original size:17 final size:17
Alignment explanation
Indices: 1998951--1999002 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
1998941 GAGTGAAGAT
* *
1998951 AAAAATGAATATGATAAG
1 AAAAAT-AAAATGATAAA
1998969 AAAAATAAAATGA-AGAA
1 AAAAATAAAATGATA-AA
1998986 AAAAATAATAATGATAA
1 AAAAATAA-AATGATAA
1999003 TAATATATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 1 0.03
17 15 0.52
18 12 0.41
19 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (17 bp):
AAAAATAAAATGATAAA
Found at i:1999079 original size:24 final size:24
Alignment explanation
Indices: 1999052--1999109 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
1999042 GAAAATACAA
1999052 ATAAATAAAACAAATG-TAAAGAAG
1 ATAAATAAAACAAA-GATAAAGAAG
* * *
1999076 ATAAAAAAAATAAAGATAAAGAAT
1 ATAAATAAAACAAAGATAAAGAAG
*
1999100 AAAAATAAAA
1 ATAAATAAAA
1999110 ATGAAATAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.16
Consensus pattern (24 bp):
ATAAATAAAACAAAGATAAAGAAG
Found at i:1999825 original size:37 final size:37
Alignment explanation
Indices: 1999775--1999886 Score: 215
Period size: 37 Copynumber: 3.0 Consensus size: 37
1999765 ATGCTTATAG
1999775 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1999812 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
1999849 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1999886 A
1 A
1999887 ACGTTATATT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 74 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:2001208 original size:110 final size:110
Alignment explanation
Indices: 2001025--2001342 Score: 528
Period size: 110 Copynumber: 2.9 Consensus size: 110
2001015 TTGTGTCGCT
* * *
2001025 TCGAGTTCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
2001090 TGATAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGATAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
*
2001135 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGGAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
*
2001200 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGATAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * *
2001245 TCGAGTCCAATATCATTCGCTGTGAAATTGAAATTGACTCTGAATGAAACTGGAAAGTTATTTGT
1 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* * * *
2001310 TGATAGTCAATCGCTCATTCGCTGTGAACTTGA
66 TGATAGTCAGTCGCCCCTTCGCTGTGAAGTTGA
2001343 AATTGACTCT
Statistics
Matches: 194, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 194 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.35
Consensus pattern (110 bp):
TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
TGATAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
Found at i:2003063 original size:15 final size:14
Alignment explanation
Indices: 2003045--2003091 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
2003035 TTTTCCTTGG
*
2003045 TTTTTGTTTCTCTT
1 TTTTTTTTTCTCTT
2003059 TTTTTATTTTCTC-T
1 TTTTT-TTTTCTCTT
**
2003073 TTGCTTTTTCTCTT
1 TTTTTTTTTCTCTT
2003087 TTTTT
1 TTTTT
2003092 GTTCTGATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
13 7 0.27
14 13 0.50
15 6 0.23
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (14 bp):
TTTTTTTTTCTCTT
Found at i:2003081 original size:32 final size:34
Alignment explanation
Indices: 2003014--2003091 Score: 83
Period size: 32 Copynumber: 2.4 Consensus size: 34
2003004 CATATGTATC
* *
2003014 TTGTCTTCTTTTTTCTTCATTTTTTCCTTGGTTT
1 TTGTCTTCTTTTTTCTTCATTTTCTCCTTGCTTT
*
2003048 TTGT-TTCTCTTTTT-TT-ATTTTCTCTTTGCTTT
1 TTGTCTTCT-TTTTTCTTCATTTTCTCCTTGCTTT
*
2003080 TTCTCTT-TTTTT
1 TTGTCTTCTTTTT
2003092 GTTCTGATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
31 4 0.11
32 17 0.45
33 8 0.21
34 9 0.24
ACGTcount: A:0.03, C:0.17, G:0.06, T:0.74
Consensus pattern (34 bp):
TTGTCTTCTTTTTTCTTCATTTTCTCCTTGCTTT
Found at i:2006309 original size:25 final size:24
Alignment explanation
Indices: 2006268--2006315 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
2006258 AGAAGATAAA
2006268 AAAAATAAAGATAAGGAATAAAAAT
1 AAAAATAAAGATAAGGAA-AAAAAT
*
2006293 AAAAATGAA-ATAGAGGAAAAAAA
1 AAAAATAAAGATA-AGGAAAAAAA
2006316 GGGTAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (24 bp):
AAAAATAAAGATAAGGAAAAAAAT
Found at i:2006331 original size:6 final size:6
Alignment explanation
Indices: 2006321--2006431 Score: 104
Period size: 6 Copynumber: 18.2 Consensus size: 6
2006311 AAAAAGGGTA
*
2006321 AATAAA AATAAAT AA-AAT AGAATAAT AATAAT AATAAT AATAAT AATAAT
1 AATAAT AAT-AAT AATAAT A-A-TAAT AATAAT AATAAT AATAAT AATAAT
* *
2006371 AATAAT AATAAT AATAAT AATAAA AACAAT AAGTAA- AGAGTAAT AA-AAT
1 AATAAT AATAAT AATAAT AATAAT AATAAT AA-TAAT A-A-TAAT AATAAT
*
2006420 AA-AAT AAAAAT A
1 AATAAT AATAAT A
2006432 GAAGGTATAA
Statistics
Matches: 92, Mismatches: 5, Indels: 16
0.81 0.04 0.14
Matches are distributed among these distances:
5 14 0.15
6 60 0.65
7 13 0.14
8 5 0.05
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.25
Consensus pattern (6 bp):
AATAAT
Found at i:2006339 original size:9 final size:9
Alignment explanation
Indices: 2006321--2006431 Score: 104
Period size: 9 Copynumber: 12.1 Consensus size: 9
2006311 AAAAAGGGTA
*
2006321 AATAAAAAT
1 AATAATAAT
2006330 AAATAA-AAT
1 -AATAATAAT
2006339 AGAATAATAAT
1 A-A-TAATAAT
2006350 AATAATAAT
1 AATAATAAT
2006359 AATAATAAT
1 AATAATAAT
2006368 AATAATAAT
1 AATAATAAT
2006377 AATAATAAT
1 AATAATAAT
*
2006386 AATAATAAA
1 AATAATAAT
*
2006395 AACAATAAGT
1 AATAATAA-T
2006405 AA-AGAGTAAT
1 AATA-A-TAAT
2006415 AA-AATAA-
1 AATAATAAT
*
2006422 AATAAAAAT
1 AATAATAAT
2006431 A
1 A
2006432 GAAGGTATAA
Statistics
Matches: 89, Mismatches: 4, Indels: 17
0.81 0.04 0.15
Matches are distributed among these distances:
7 2 0.02
8 8 0.09
9 56 0.63
10 16 0.18
11 7 0.08
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.25
Consensus pattern (9 bp):
AATAATAAT
Found at i:2006349 original size:3 final size:3
Alignment explanation
Indices: 2006341--2006431 Score: 107
Period size: 3 Copynumber: 30.3 Consensus size: 3
2006331 AATAAAATAG
2006341 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
2006389 AAT AAA AAC AAT AAGT AA- AGAGT AAT AA- AAT AA- AAT AAA AAT A
1 AAT AAT AAT AAT AA-T AAT A-A-T AAT AAT AAT AAT AAT AAT AAT A
2006432 GAAGGTATAA
Statistics
Matches: 77, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
2 5 0.06
3 67 0.87
4 4 0.05
5 1 0.01
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:2007142 original size:37 final size:37
Alignment explanation
Indices: 2007092--2007162 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
2007082 TTATGGATCA
2007092 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCC
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCC
*
2007129 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTA
2007163 ACGTTATGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCC
Found at i:2007280 original size:31 final size:31
Alignment explanation
Indices: 2007242--2007329 Score: 140
Period size: 31 Copynumber: 2.8 Consensus size: 31
2007232 GTGTTGACAT
* *
2007242 TTACGTTACCATTTTATTAAGTTTTGATAAC
1 TTACGTTATCGTTTTATTAAGTTTTGATAAC
*
2007273 TTACGTTATCGTTTTATTAAGTTTTGATTAC
1 TTACGTTATCGTTTTATTAAGTTTTGATAAC
*
2007304 TTACATTATCGTTTTATTAAGTTTTG
1 TTACGTTATCGTTTTATTAAGTTTTG
2007330 GTCACTGATT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.25, C:0.10, G:0.11, T:0.53
Consensus pattern (31 bp):
TTACGTTATCGTTTTATTAAGTTTTGATAAC
Found at i:2007452 original size:31 final size:31
Alignment explanation
Indices: 2007417--2007490 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
2007407 TTCAACGCAC
** *
2007417 AAGTGACCAAAACTTAATAAAATGATATCAT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
* ** *
2007448 AAGTGATCAAAGTTTAATAAAACAATAACTT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
2007479 AAGTGACCAAAA
1 AAGTGACCAAAA
2007491 GTGTACAAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.53, C:0.12, G:0.11, T:0.24
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACAATAACAT
Found at i:2007971 original size:17 final size:17
Alignment explanation
Indices: 2007941--2007978 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2007931 TTAAAAAAAG
2007941 GGGGGAGGGACGTCGGC
1 GGGGGAGGGACGTCGGC
* *
2007958 GGGGGTGGGGCGTCGGC
1 GGGGGAGGGACGTCGGC
2007975 GGGG
1 GGGG
2007979 TACGTTGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.05, C:0.16, G:0.71, T:0.08
Consensus pattern (17 bp):
GGGGGAGGGACGTCGGC
Found at i:2009122 original size:28 final size:27
Alignment explanation
Indices: 2009090--2009182 Score: 95
Period size: 28 Copynumber: 3.4 Consensus size: 27
2009080 AGTTTCGATC
2009090 ATAATAAAATATATATTTTAAATTTAA-A
1 ATAATAAAATATAT-TTTTAAA-TTAATA
2009118 ATAATAAAA-ATATTTTTAAATTAATTTA
1 ATAATAAAATATATTTTTAAATTAA--TA
* *
2009146 ATAATAAAATATATTTAATAAGTTAAT-
1 ATAATAAAATATATTT-TTAAATTAATA
2009173 ATAA-AAAATA
1 ATAATAAAATA
2009183 GTTTTAAAGT
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
25 4 0.07
26 13 0.22
27 8 0.14
28 20 0.34
29 6 0.10
30 7 0.12
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (27 bp):
ATAATAAAATATATTTTTAAATTAATA
Found at i:2009141 original size:25 final size:27
Alignment explanation
Indices: 2009090--2009209 Score: 90
Period size: 28 Copynumber: 4.4 Consensus size: 27
2009080 AGTTTCGATC
*
2009090 ATAATAAAATATATATTTTAAATTTAAA
1 ATAATAAAATATAT-TTTTAAAGTTAAA
2009118 ATAATAAAA-ATATTTTTAAA-TTAATTTA
1 ATAATAAAATATATTTTTAAAGTTAA---A
*
2009146 ATAATAAAATATA-TTTAATAAGTT--A
1 ATAATAAAATATATTTTTA-AAGTTAAA
* * *
2009171 AT-ATAAAAAATAGTTTTAAAGTTAAT
1 ATAATAAAATATATTTTTAAAGTTAAA
*
2009197 ATGTATAAAATAT
1 AT-AATAAAATAT
2009210 TATGAATTTA
Statistics
Matches: 76, Mismatches: 5, Indels: 22
0.74 0.05 0.21
Matches are distributed among these distances:
24 14 0.18
25 11 0.14
26 9 0.12
27 4 0.05
28 31 0.41
29 5 0.07
30 2 0.03
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (27 bp):
ATAATAAAATATATTTTTAAAGTTAAA
Found at i:2009148 original size:53 final size:55
Alignment explanation
Indices: 2009091--2009209 Score: 131
Period size: 54 Copynumber: 2.2 Consensus size: 55
2009081 GTTTCGATCA
* * *
2009091 TAATAAAATATATATTTTA-AATTTAAAATAATAAAAATATTTTTAAA-TTAAT-T-
1 TAATAAAATATATATTTAATAAGTTAAAAT-A-AAAAATAGTTTTAAAGTTAATATG
* *
2009144 TAATAATAAAATATATTTAATAAGTTAATATAAAAAATAGTTTTAAAGTTAATATG
1 TAATAA-AATATATATTTAATAAGTTAAAATAAAAAATAGTTTTAAAGTTAATATG
2009200 T-ATAAAATAT
1 TAATAAAATAT
2009210 TATGAATTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
53 20 0.36
54 21 0.38
55 13 0.24
56 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (55 bp):
TAATAAAATATATATTTAATAAGTTAAAATAAAAAATAGTTTTAAAGTTAATATG
Found at i:2009192 original size:24 final size:24
Alignment explanation
Indices: 2009143--2009198 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
2009133 TTAAATTAAT
*
2009143 TTAATAATAAAATATATTTAATAAG
1 TTAAT-ATAAAAAATATTTAATAAG
*
2009168 TTAATATAAAAAATAGTTTTA-AAG
1 TTAATATAAAAAATA-TTTAATAAG
2009192 TTAATAT
1 TTAATAT
2009199 GTATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 19 0.68
25 9 0.32
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (24 bp):
TTAATATAAAAAATATTTAATAAG
Found at i:2009525 original size:33 final size:31
Alignment explanation
Indices: 2009467--2009533 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 31
2009457 TGACTACATC
* * *
2009467 TTAATTAAATAAAAACCAAAGTGACCCTATA
1 TTAATTAAATAAAAACAAAAATGACCATATA
2009498 TTAATTAAATAAAAAAACAAAAATGACCATATA
1 TTAATTAAAT--AAAAACAAAAATGACCATATA
2009531 TTA
1 TTA
2009534 TGAAATCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 10 0.32
33 21 0.68
ACGTcount: A:0.57, C:0.12, G:0.04, T:0.27
Consensus pattern (31 bp):
TTAATTAAATAAAAACAAAAATGACCATATA
Found at i:2019202 original size:28 final size:27
Alignment explanation
Indices: 2019163--2019251 Score: 70
Period size: 28 Copynumber: 3.0 Consensus size: 27
2019153 TTTTTTTATT
2019163 TAAATACCTAAAGTATTTTTTGTCAAAA
1 TAAATA-CTAAAGTATTTTTTGTCAAAA
*
2019191 TAAATACATAAAAGTTATCTTTTGGATCAAAA
1 TAAATAC-T-AAAG-TAT-TTTTTG-TCAAAA
** * *
2019223 TACGTATCTGAAGTATTTTATGTCAAAA
1 TAAATA-CTAAAGTATTTTTTGTCAAAA
2019251 T
1 T
2019252 TGATACCTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
27 1 0.02
28 14 0.29
29 8 0.16
30 6 0.12
31 8 0.16
32 11 0.22
33 1 0.02
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (27 bp):
TAAATACTAAAGTATTTTTTGTCAAAA
Found at i:2019539 original size:18 final size:18
Alignment explanation
Indices: 2019518--2019552 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2019508 GTAAATTTTT
*
2019518 AATTTTTAATAAAATTAA
1 AATTATTAATAAAATTAA
*
2019536 AATTATTAATTAAATTA
1 AATTATTAATAAAATTA
2019553 TAAAAATTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATTATTAATAAAATTAA
Found at i:2025982 original size:25 final size:25
Alignment explanation
Indices: 2025954--2026033 Score: 80
Period size: 25 Copynumber: 3.2 Consensus size: 25
2025944 TATTATGTTT
2025954 ATAAATGTTTATTTGATGTAGAATC
1 ATAAATGTTTATTTGATGTAGAATC
*
2025979 ATAAATCAGATTTATATT-ATGT----TT
1 ATAAAT--G-TTTAT-TTGATGTAGAATC
2026003 ATAAATGTTTATTTGATGTAGAATC
1 ATAAATGTTTATTTGATGTAGAATC
2026028 ATAAAT
1 ATAAAT
2026034 CACATTTAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 18
0.69 0.03 0.28
Matches are distributed among these distances:
20 2 0.05
21 9 0.20
22 1 0.02
24 7 0.16
25 13 0.30
27 1 0.02
28 9 0.20
29 2 0.05
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (25 bp):
ATAAATGTTTATTTGATGTAGAATC
Found at i:2026003 original size:49 final size:49
Alignment explanation
Indices: 2025938--2026041 Score: 199
Period size: 49 Copynumber: 2.1 Consensus size: 49
2025928 TTAATTAAAT
2025938 GATTTATATTATGTTTATAAATGTTTATTTGATGTAGAATCATAAATCA
1 GATTTATATTATGTTTATAAATGTTTATTTGATGTAGAATCATAAATCA
2025987 GATTTATATTATGTTTATAAATGTTTATTTGATGTAGAATCATAAATCA
1 GATTTATATTATGTTTATAAATGTTTATTTGATGTAGAATCATAAATCA
*
2026036 CATTTA
1 GATTTA
2026042 AGAATAATAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 54 1.00
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.47
Consensus pattern (49 bp):
GATTTATATTATGTTTATAAATGTTTATTTGATGTAGAATCATAAATCA
Found at i:2026021 original size:21 final size:22
Alignment explanation
Indices: 2025933--2026014 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 22
2025923 CGAAATTAAT
2025933 TAAATGATTTATATTATGTTTA
1 TAAATGATTTATATTATGTTTA
*
2025955 TAAATG-TTTAT-TTGATGTAGAATCA
1 TAAATGATTTATATT-ATGT----TTA
2025980 TAAATCAGATTTATATTATGTTTA
1 TAAAT--GATTTATATTATGTTTA
2026004 TAAATG-TTTAT
1 TAAATGATTTAT
2026015 TTGATGTAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 19
0.70 0.03 0.27
Matches are distributed among these distances:
20 2 0.04
21 14 0.29
22 7 0.14
24 7 0.14
25 7 0.14
27 1 0.02
28 9 0.18
29 2 0.04
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.50
Consensus pattern (22 bp):
TAAATGATTTATATTATGTTTA
Found at i:2026216 original size:2 final size:2
Alignment explanation
Indices: 2026209--2026247 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2026199 TGATTGACCT
2026209 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2026248 AGAATGATGC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2031772 original size:18 final size:18
Alignment explanation
Indices: 2031749--2031788 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
2031739 ACCCCATTGG
2031749 GGTCTTACATTCGCATGA
1 GGTCTTACATTCGCATGA
2031767 GGTCTTACATTCGCATGA
1 GGTCTTACATTCGCATGA
2031785 GGTC
1 GGTC
2031789 ATAGGAGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.33
Consensus pattern (18 bp):
GGTCTTACATTCGCATGA
Found at i:2033594 original size:7 final size:7
Alignment explanation
Indices: 2033584--2033608 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2033574 AAAATGTTAG
2033584 ATAATAA
1 ATAATAA
2033591 ATAATAA
1 ATAATAA
2033598 ATAATAA
1 ATAATAA
2033605 ATAA
1 ATAA
2033609 ATCCTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAATAA
Found at i:2034708 original size:42 final size:42
Alignment explanation
Indices: 2034661--2034776 Score: 196
Period size: 42 Copynumber: 2.8 Consensus size: 42
2034651 TCCGAAATCT
* * *
2034661 CGTGTTTGTTTCATGTAATTCGTTTTTCGGAAAATGTTTTTC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
*
2034703 CGTGTTTGCTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
2034745 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
2034777 CGTAATTCAT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.16, C:0.17, G:0.20, T:0.47
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
Found at i:2034991 original size:21 final size:20
Alignment explanation
Indices: 2034965--2035011 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
2034955 TAATTATTAA
* *
2034965 AATATTTAAAATATATTTATT
1 AATATTTAAAATA-ATATAAT
*
2034986 AATATTTATAATAATATAAT
1 AATATTTAAAATAATATAAT
2035006 AATATT
1 AATATT
2035012 ATATTTTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATTTAAAATAATATAAT
Found at i:2035011 original size:30 final size:30
Alignment explanation
Indices: 2034977--2035145 Score: 112
Period size: 27 Copynumber: 5.9 Consensus size: 30
2034967 TATTTAAAAT
*
2034977 ATATTTATTAATATTTATAATAATATAATA
1 ATATTTATTTATATTTATAATAATATAATA
* * *
2035007 ATATTATATTTTTAGTT-TAATAATATAATC
1 ATATT-TATTTATATTTATAATAATATAATA
* * * *
2035037 A-A-TTATATTATAATAAT-ATAAGAT-ATT
1 ATATTTAT-TTATATTTATAATAATATAATA
2035064 ATATTT-TTTAT-TTTAATAAT-ATATAATA
1 ATATTTATTTATATTT-ATAATAATATAATA
*
2035092 A-ATTT-TTTATATATT-TAATAAT-GAATA
1 ATATTTATTTATAT-TTATAATAATATAATA
2035119 ATATTTATTTATATATT-TAAATAATAT
1 ATATTTATTTATAT-TTAT-AATAATAT
2035146 TTTAGTAAAG
Statistics
Matches: 109, Mismatches: 15, Indels: 29
0.71 0.10 0.19
Matches are distributed among these distances:
26 1 0.01
27 33 0.30
28 26 0.24
29 17 0.16
30 24 0.22
31 8 0.07
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.52
Consensus pattern (30 bp):
ATATTTATTTATATTTATAATAATATAATA
Found at i:2035110 original size:27 final size:29
Alignment explanation
Indices: 2035080--2035143 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
2035070 TTTATTTTAA
2035080 TAATATAT-AATAA-ATTT-TTTATATATT
1 TAATA-ATGAATAATATTTATTTATATATT
2035107 TAATAATGAATAATATTTATTTATATATT
1 TAATAATGAATAATATTTATTTATATATT
2035136 TAAATAAT
1 T-AATAAT
2035144 ATTTTAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
26 2 0.06
27 10 0.30
28 4 0.12
29 11 0.33
30 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
TAATAATGAATAATATTTATTTATATATT
Found at i:2035319 original size:19 final size:20
Alignment explanation
Indices: 2035287--2035325 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2035277 TAATAAAATT
2035287 ATAAAAAAAATA-TTTAATA
1 ATAAAAAAAATATTTTAATA
* *
2035306 ATAAATAAATTATTTTAATA
1 ATAAAAAAAATATTTTAATA
2035326 TTTTAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAAAAAAAATATTTTAATA
Found at i:2035552 original size:20 final size:20
Alignment explanation
Indices: 2035474--2035543 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
2035464 TTTCCAGATG
*
2035474 TTTTTCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
2035494 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
2035514 TTTTCTAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
2035534 TTTTCCAGAA
1 TTTTCCAGAA
2035544 TTCAAATTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:2035552 original size:40 final size:39
Alignment explanation
Indices: 2035475--2035552 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
2035465 TTCCAGATGT
**
2035475 TTTTCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTCAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
2035514 TTTTCTAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTC-AGAAATGTAATTCATTTTCCAGAAATCAAATTC
2035553 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 5 0.14
40 30 0.86
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (39 bp):
TTTTCAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:2035578 original size:30 final size:30
Alignment explanation
Indices: 2035526--2035607 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
2035516 TTCTAGAAAT
2035526 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
2035555 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
2035585 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
2035608 TTTTCCGGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:2035600 original size:45 final size:44
Alignment explanation
Indices: 2035526--2035613 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 44
2035516 TTCTAGAAAT
**
2035526 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
2035570 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTTCC
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTCC
2035614 GGAAAACCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.34
45 27 0.66
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:2035613 original size:15 final size:15
Alignment explanation
Indices: 2035526--2035607 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
2035516 TTCTAGAAAT
**
2035526 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
2035541 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
2035555 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
2035570 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
2035585 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
2035600 GTAATTCA
1 GTAATTCA
2035608 TTTTCCGGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:2035828 original size:13 final size:14
Alignment explanation
Indices: 2035801--2035851 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
2035791 ATGGGGGCCT
2035801 ATAAAAAATAATTA
1 ATAAAAAATAATTA
*
2035815 ATAAAAAAT-GTTA
1 ATAAAAAATAATTA
* *
2035828 AT-AATAATAATAA
1 ATAAAAAATAATTA
2035841 ATAAATAAATA
1 ATAAA-AAATA
2035852 TAAAAAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
12 5 0.17
13 9 0.31
14 11 0.38
15 4 0.14
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (14 bp):
ATAAAAAATAATTA
Found at i:2036381 original size:84 final size:84
Alignment explanation
Indices: 2036263--2036621 Score: 448
Period size: 84 Copynumber: 4.2 Consensus size: 84
2036253 GAATGAAATA
* * * * * *
2036263 GAACTCGAAAGGTCTCTTGTTGGCAGATAACCCTTATAGCCTTGAGCTATGCTGCAGATAATGTG
1 GAACTCG-AAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATG
* *
2036328 TCTTTGAGCTGAGCGTAGTC
65 CCTTGGAGCTGAGCGTAGTC
* * * * * * *
2036348 GAACTCGAAGGTCTTTTGTTAGCAAATATCCCTTCTTGTCTTGAGTTATGTTGCAAATGATGTGC
1 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGC
2036413 CTTGGAGCTGAGCGTAGTC
66 CTTGGAGCTGAGCGTAGTC
* * * * * * *
2036432 GAACTCAAAGGTCTTTGGTTGGGAGATAACCCTTCTATCCTTGAGTTATACCGTAAATGATATGC
1 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGC
2036497 CTTGGAGCTGAGCGTAGTC
66 CTTGGAGCTGAGCGTAGTC
* * *
2036516 GAACTCGAAGGTCTTTTGGTGGCAGATAGCCCTTCTAGGCTTGAGTTATGCTGCAAATGATATGC
1 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGC
*
2036581 CTTGGAGCTGAGCGTAGTT
66 CTTGGAGCTGAGCGTAGTC
*
2036600 GAACTTCAAAGGTCTTTGTGTT
1 GAAC-TCGAAGGTCTTT-TGTT
2036622 TCAAGAGAAA
Statistics
Matches: 232, Mismatches: 40, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
84 211 0.91
85 18 0.08
86 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (84 bp):
GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGC
CTTGGAGCTGAGCGTAGTC
Found at i:2036655 original size:33 final size:32
Alignment explanation
Indices: 2036604--2036665 Score: 106
Period size: 33 Copynumber: 1.9 Consensus size: 32
2036594 GTAGTTGAAC
2036604 TTCAAAGGTCTTTGTGTTTCAAGAGAAACATT
1 TTCAAAGGTCTTTGTGTTTCAAGAGAAACATT
*
2036636 TTCAAAGGTTTTTTGTGTTTCAAGAGAAAC
1 TTCAAAGG-TCTTTGTGTTTCAAGAGAAAC
2036666 TGTCTTCAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 8 0.29
33 20 0.71
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (32 bp):
TTCAAAGGTCTTTGTGTTTCAAGAGAAACATT
Found at i:2036758 original size:67 final size:66
Alignment explanation
Indices: 2036618--2036962 Score: 218
Period size: 65 Copynumber: 5.0 Consensus size: 66
2036608 AAGGTCTTTG
* ** * * *
2036618 TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTGTGTTTCAAGAGAAACTGTCTTC-AGGGAGGCA
1 TGTTTCAAGAGAAACATATTCAAA-G--AATTGTGTTTCAAGAGAAACTATC-TCAAGAGAGACA
2036682 AAATTT
62 AAA-TT
*
2036688 TGTTTCAAGAGAAACATATTCAAAG-ATTGGTGTTTCAAGAGAAACTATCTCAAGAGAGATAAAA
1 TGTTTCAAGAGAAACATATTCAAAGAATT-GTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA
2036752 CTT
65 -TT
* * * * * * *
2036755 TGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAACTT-AGTTCCAAAAGAAACTGTCTCAAGGG
1 TGTTTCAAGAGAAACATAT-TC-A-A-AG----AA-TTGTGTTTCAAGAGAAACTATCTCAAGAG
*
2036818 AGACGAAATT
57 AGACAAAATT
* *
2036828 TGTTTCAAG-GAAAACATATTCAAAG-ATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
1 TGTTTCAAGAG-AAACATATTCAAAGAATTGTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA
2036891 TT
65 TT
* * * * * *
2036893 TGTTCCAAGGGAAAC-TGTCTCAAGAGAGATAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACATAT-TCAA-AGA-AT----TGTGTTTCAAGAGAAACTATCTCAAGAGAG
2036957 ACAAAA
59 ACAAAA
2036963 CTTAGTTCCA
Statistics
Matches: 222, Mismatches: 29, Indels: 46
0.75 0.10 0.15
Matches are distributed among these distances:
64 4 0.02
65 46 0.21
66 9 0.04
67 46 0.21
68 3 0.01
69 2 0.01
70 27 0.12
71 1 0.00
72 35 0.16
73 17 0.08
74 29 0.13
75 1 0.00
76 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (66 bp):
TGTTTCAAGAGAAACATATTCAAAGAATTGTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAAT
T
Found at i:2036883 original size:102 final size:102
Alignment explanation
Indices: 2036753--2036942 Score: 292
Period size: 101 Copynumber: 1.9 Consensus size: 102
2036743 GAGATAAAAC
* *
2036753 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTAGTTCCAAAAGAAACTGTCTCAAGAG
*
2036818 AGACGAAATTTGTTTCAAG-GAAAACATATTCAAAGAT
65 AGACAAAATTTGTTTCAAGAGAAAACATATTCAAAGAT
* **
2036855 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTGTTCCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTGTCTCAAGAGA
* *
2036920 GATAAAATTTGTTTTAAGAGAAA
66 GACAAAATTTGTTTCAAGAGAAA
2036943 CTGTCTCAAG
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 40 0.51
102 39 0.49
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (102 bp):
TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTGTCTCAAGAGA
GACAAAATTTGTTTCAAGAGAAAACATATTCAAAGAT
Found at i:2036902 original size:36 final size:36
Alignment explanation
Indices: 2036855--2037108 Score: 258
Period size: 36 Copynumber: 7.2 Consensus size: 36
2036845 ATTCAAAGAT
* *
2036855 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
2036891 TTTGTTCCAAGGGAAACTGTCTCAAGAGAGATAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
2036927 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
2036963 CTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACAAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
2037000 TTTGTTT-AATGTA-AAACATAT-T-TA-A-AG----AT
1 TTTGTTTCAA-G-AGAAAC-TGTCTCAAGAGAGACAAAA
*
2037029 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
2037065 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
2037101 CTTTGTTT
1 -TTTGTTT
2037109 TGAGTAAATT
Statistics
Matches: 177, Mismatches: 26, Indels: 29
0.76 0.11 0.12
Matches are distributed among these distances:
28 2 0.01
29 14 0.08
30 3 0.02
31 1 0.01
32 2 0.01
33 2 0.01
35 3 0.02
36 110 0.62
37 40 0.23
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:2036948 original size:174 final size:175
Alignment explanation
Indices: 2036718--2037109 Score: 662
Period size: 174 Copynumber: 2.2 Consensus size: 175
2036708 CAAAGATTGG
* * *
2036718 TGTTTCAAGAGAAACTATCTCAAGAGAGATAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTTGTTTTAAGAGAAACTGTCTCAAGAGAG
*
2036783 ACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAA-GGAAAACATAT
66 ACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTT-AATGGAAAACATAT
2036847 TCAAAGATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
130 TCAAAGATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
* *
2036893 TGTTCCAAGGGAAACTGTCTCAAGAGAGATAAAA-TTTGTTTTAAGAGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTTGTTTTAAGAGAAACTGTCTCAAGAGAG
* *
2036957 ACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACAAAATTTGTTTAATGTAAAACATATT
66 ACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTAATGGAAAACATATT
* *
2037022 TAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
131 CAAAGATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
*
2037067 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTTGTTTT
2037110 GAGTAAATTA
Statistics
Matches: 202, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
173 2 0.01
174 161 0.80
175 39 0.19
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (175 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTTGTTTTAAGAGAAACTGTCTCAAGAGAG
ACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTAATGGAAAACATATT
CAAAGATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
Found at i:2037922 original size:27 final size:27
Alignment explanation
Indices: 2037884--2037938 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2037874 GAGATTGTTA
2037884 TGTTTAAAAATGTTTTTCTCATTTTTC
1 TGTTTAAAAATGTTTTTCTCATTTTTC
2037911 TGTTTAAAAATGTTTTTCTCATTTTTC
1 TGTTTAAAAATGTTTTTCTCATTTTTC
2037938 T
1 T
2037939 TATCTTAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.11, G:0.07, T:0.60
Consensus pattern (27 bp):
TGTTTAAAAATGTTTTTCTCATTTTTC
Found at i:2040177 original size:18 final size:17
Alignment explanation
Indices: 2040156--2040193 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
2040146 AATAATAAAA
2040156 ATGAAAATCCTACCCCAC
1 ATGAAAAT-CTACCCCAC
*
2040174 ATG-ATATCTACCCCAC
1 ATGAAAATCTACCCCAC
2040190 ATGA
1 ATGA
2040194 TTATTATGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
16 12 0.67
17 3 0.17
18 3 0.17
ACGTcount: A:0.37, C:0.34, G:0.08, T:0.21
Consensus pattern (17 bp):
ATGAAAATCTACCCCAC
Found at i:2041224 original size:18 final size:19
Alignment explanation
Indices: 2041201--2041240 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
2041191 AATTAATGGG
*
2041201 AAAATAATAAAATAA-AAT
1 AAAATAAAAAAATAATAAT
2041219 AAAATAAAAAAATAATAAT
1 AAAATAAAAAAATAATAAT
2041238 AAA
1 AAA
2041241 GTGGAGTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (19 bp):
AAAATAAAAAAATAATAAT
Found at i:2043087 original size:18 final size:18
Alignment explanation
Indices: 2043064--2043137 Score: 78
Period size: 18 Copynumber: 3.9 Consensus size: 18
2043054 ACTGAATATT
*
2043064 TGTCCCGAAGGACCACTA
1 TGTCCCAAAGGACCACTA
* *
2043082 TGTCCCAAATGACCTCTGATA
1 TGTCCCAAAGGACCAC---TA
2043103 TGTCCCAAAGGACCACTA
1 TGTCCCAAAGGACCACTA
2043121 TGTCCCGAAA-GACCACT
1 TGTCCC-AAAGGACCACT
2043138 GATAATCCCT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
18 28 0.60
19 3 0.06
21 16 0.34
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:2043107 original size:39 final size:39
Alignment explanation
Indices: 2043064--2043141 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
2043054 ACTGAATATT
* *
2043064 TGTCCCGAAGGACCACTATGTCCC-AAATGACCTCTGATA
1 TGTCCCAAAGGACCACTATGTCCCGAAA-GACCACTGATA
2043103 TGTCCCAAAGGACCACTATGTCCCGAAAGACCACTGATA
1 TGTCCCAAAGGACCACTATGTCCCGAAAGACCACTGATA
2043142 ATCCCTCGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 33 0.92
40 3 0.08
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.21
Consensus pattern (39 bp):
TGTCCCAAAGGACCACTATGTCCCGAAAGACCACTGATA
Found at i:2054599 original size:24 final size:22
Alignment explanation
Indices: 2054549--2054604 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 22
2054539 AATAAAGGTA
2054549 TGCATCGATGCATTCTACAGTG
1 TGCATCGATGCATTCTACAGTG
2054571 T--ATCGATGCATTCCTTA-ACGTG
1 TGCATCGATGCATT-C-TACA-GTG
2054593 TGCATCGATGCA
1 TGCATCGATGCA
2054605 CTACCTGTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 11 0.38
21 2 0.07
22 7 0.24
24 9 0.31
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.32
Consensus pattern (22 bp):
TGCATCGATGCATTCTACAGTG
Found at i:2055682 original size:29 final size:28
Alignment explanation
Indices: 2055650--2055708 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
2055640 TTTTTTAAAA
**
2055650 AAATCTATTTTCGACTCCTGAAATTTTAT
1 AAATCTAAGTTCGACT-CTGAAATTTTAT
* * *
2055679 AAATTTAAGTTCGTCTCTTAAATTTTAT
1 AAATCTAAGTTCGACTCTGAAATTTTAT
2055707 AA
1 AA
2055709 GTTTAAATTC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.46
Consensus pattern (28 bp):
AAATCTAAGTTCGACTCTGAAATTTTAT
Found at i:2058034 original size:20 final size:21
Alignment explanation
Indices: 2057993--2058038 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
2057983 TCTATGTTCC
2057993 TTAAATAATATAATATATATT
1 TTAAATAATATAATATATATT
*
2058014 TGTAAATTATATAAT-TA-ATT
1 T-TAAATAATATAATATATATT
2058034 TTAAA
1 TTAAA
2058039 ATATTCATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 4 0.17
20 4 0.17
21 3 0.13
22 12 0.52
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TTAAATAATATAATATATATT
Found at i:2069310 original size:16 final size:15
Alignment explanation
Indices: 2069289--2069331 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
2069279 AACTTTTATT
2069289 ATTATTTTTTAATAAA
1 ATTATTTTTTAAT-AA
* *
2069305 ATTATTTTTAAATTA
1 ATTATTTTTTAATAA
*
2069320 TTTATTTTTTAA
1 ATTATTTTTTAA
2069332 ATTAAATTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTTTTTAATAA
Found at i:2077229 original size:22 final size:22
Alignment explanation
Indices: 2077201--2077244 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2077191 AAGGAGGGGG
2077201 CTCAGCCGAATTATAATTCAGT
1 CTCAGCCGAATTATAATTCAGT
2077223 CTCAGCCGAATTATAATTCAGT
1 CTCAGCCGAATTATAATTCAGT
2077245 AAAGGGAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (22 bp):
CTCAGCCGAATTATAATTCAGT
Found at i:2091356 original size:19 final size:20
Alignment explanation
Indices: 2091315--2091357 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2091305 AGATATAAAA
*
2091315 TTAATGTTTTTAGGATCTAT
1 TTAATGTTTTTAGCATCTAT
2091335 TTAATG-TTTTAGCA-CTAGT
1 TTAATGTTTTTAGCATCTA-T
2091354 TTAA
1 TTAA
2091358 GGATAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 12 0.57
20 6 0.29
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.51
Consensus pattern (20 bp):
TTAATGTTTTTAGCATCTAT
Found at i:2095042 original size:52 final size:52
Alignment explanation
Indices: 2094986--2095086 Score: 127
Period size: 53 Copynumber: 1.9 Consensus size: 52
2094976 TTATATCTCT
*
2094986 TTCTT-TTTTTTTTCTTTTTG-GT-TCAGTCTCTGTCTCTTCTTTCTGTCTCCTC
1 TTCTTCTTTTTTTTCTTTCTGTGTCTC-GT-TCTGTCTC-TCTTTCTGTCTCCTC
* *
2095038 TTCTTCTTTTTTTTGTTTCTGTGTCTCGTTCTGTCTCTCTTTTTGTCTC
1 TTCTTCTTTTTTTTCTTTCTGTGTCTCGTTCTGTCTCTCTTTCTGTCTC
2095087 GCAGGTGGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
52 16 0.37
53 21 0.49
54 4 0.09
55 2 0.05
ACGTcount: A:0.01, C:0.24, G:0.11, T:0.64
Consensus pattern (52 bp):
TTCTTCTTTTTTTTCTTTCTGTGTCTCGTTCTGTCTCTCTTTCTGTCTCCTC
Found at i:2095069 original size:28 final size:30
Alignment explanation
Indices: 2095025--2095083 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 30
2095015 CTGTCTCTTC
*
2095025 TTTCTGTCTCCTCTTCT-TCT-TTTTTTTG
1 TTTCTGTCTCCTCTTCTGTCTCTCTTTTTG
*
2095053 TTTCTGTGT-CTCGTTCTGTCTCTCTTTTTG
1 TTTCTGTCTCCTC-TTCTGTCTCTCTTTTTG
2095083 T
1 T
2095084 CTCGCAGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 3 0.12
28 12 0.46
29 3 0.12
30 8 0.31
ACGTcount: A:0.00, C:0.24, G:0.12, T:0.64
Consensus pattern (30 bp):
TTTCTGTCTCCTCTTCTGTCTCTCTTTTTG
Found at i:2095459 original size:3 final size:3
Alignment explanation
Indices: 2095451--2095625 Score: 260
Period size: 3 Copynumber: 57.7 Consensus size: 3
2095441 TTATTTATTA
*
2095451 AAT AAT AAT AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT
* **
2095498 ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GCT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
2095546 AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
2095594 GAT AAT AAT AAT ATT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2095626 AATGGATAAA
Statistics
Matches: 154, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
3 148 0.96
4 6 0.04
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:2096094 original size:73 final size:73
Alignment explanation
Indices: 2095974--2096141 Score: 201
Period size: 73 Copynumber: 2.3 Consensus size: 73
2095964 TCTTCAGATG
* ** * * * *
2095974 AGTTCTTCTCATTCATGAACTTTCTTTGGCCATGTTGATACATCAAATGATGAATTTAAACAAAA
1 AGTTCTTCTCATT-ATGAACTTTCTCTGGAAAAGATGATACACCAAATGATGAATTCAAACAAAA
2096039 AGTTGAACA
65 AGTTGAACA
* * *** *
2096048 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATACACCAAATGATGAATTCAAACAAAAA
2096113 GTTGAACA
66 GTTGAACA
*
2096121 AATTCTTCTCATTATGAACTT
1 AGTTCTTCTCATTATGAACTT
2096142 CTTCTTCCTT
Statistics
Matches: 80, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
73 67 0.84
74 13 0.16
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (73 bp):
AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATACACCAAATGATGAATTCAAACAAAAA
GTTGAACA
Found at i:2096332 original size:116 final size:116
Alignment explanation
Indices: 2096048--2096531 Score: 848
Period size: 116 Copynumber: 4.2 Consensus size: 116
2096038 AAGTTGAACA
*
2096048 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCAAAAG
*
2096113 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---G
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACG
2096161 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCAAAAG
2096226 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACG
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACG
2096277 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCAAAAG
2096342 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACG
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACG
* * * *
2096393 AGTTCTTCTCATTATGAACTCTTCCTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAA
1 AGTTCTTCTCATTATGAACT-TT-CTCTGGAAAAG-ATGATCCACCAAATGATGGATTCAGGCAA
* *
2096458 AAAGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGACG
63 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACG
2096512 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
2096532 CTACCTTGCA
Statistics
Matches: 357, Mismatches: 8, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
113 110 0.31
116 137 0.38
117 2 0.01
118 11 0.03
119 97 0.27
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (116 bp):
AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCAAAAG
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACG
Found at i:2097337 original size:52 final size:51
Alignment explanation
Indices: 2097218--2097360 Score: 252
Period size: 52 Copynumber: 2.8 Consensus size: 51
2097208 CCTACCAAAC
2097218 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTTCTGTCTAAT
*
2097268 CAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT-TTCTGTCTAAT
*
2097320 CAGATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
2097361 GGCAAATTCA
Statistics
Matches: 88, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
50 38 0.43
51 1 0.01
52 49 0.56
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (51 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTTCTGTCTAAT
Found at i:2097597 original size:52 final size:52
Alignment explanation
Indices: 2097391--2097596 Score: 342
Period size: 52 Copynumber: 4.0 Consensus size: 52
2097381 TCACTGATTG
**
2097391 GTTCTGTTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
*
2097443 GTTCTGTCCAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
* *
2097495 GTTCTGTCCAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTTT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
*
2097547 GTTCTGAT-TAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 GTTCTG-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
2097597 TGAGCATATT
Statistics
Matches: 147, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
52 146 0.99
53 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (52 bp):
GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
Found at i:2098769 original size:17 final size:14
Alignment explanation
Indices: 2098747--2098788 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
2098737 TTTTCTTCTC
2098747 TTTTTTTCATTTTCTAT
1 TTTTTTTC-TTTT-T-T
2098764 TTTTTTTCTTTTTT
1 TTTTTTTCTTTTTT
2098778 TTTTTTT-TTTT
1 TTTTTTTCTTTT
2098789 CAAGCATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 1 0.04
16 4 0.16
17 8 0.32
ACGTcount: A:0.05, C:0.07, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTCTTTTTT
Found at i:2098770 original size:11 final size:10
Alignment explanation
Indices: 2098756--2098788 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
2098746 CTTTTTTTCA
2098756 TTTTCTATTTT
1 TTTTCT-TTTT
2098767 TTTTCTTTTT
1 TTTTCTTTTT
2098777 TTTT-TTTTT
1 TTTTCTTTTT
2098786 TTT
1 TTT
2098789 CAAGCATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 8 0.36
10 8 0.36
11 6 0.27
ACGTcount: A:0.03, C:0.06, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:2109396 original size:18 final size:17
Alignment explanation
Indices: 2109352--2109398 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
2109342 AAATACTTGC
2109352 AAATAAAAACATATAAAT
1 AAATAAAAA-ATATAAAT
*
2109370 -ATTATAAAAATAATAAAT
1 AAATA-AAAAAT-ATAAAT
2109388 AAATAAAAAAT
1 AAATAAAAAAT
2109399 TTGAAAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
17 5 0.21
18 16 0.67
19 3 0.12
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAAAAAATATAAAT
Found at i:2111051 original size:53 final size:52
Alignment explanation
Indices: 2110994--2111095 Score: 127
Period size: 53 Copynumber: 1.9 Consensus size: 52
2110984 TTATATCTCT
* *
2110994 TTCTTTTTTTTTTTCTTTTTG-GT-TCAGTCTCTGTCTCTTCTTTCTGTCTCCTC
1 TTCTTCTTTTTTTTCTTTCTGTGTCTC-GT-TCTGTCTC-TCTTTCTGTCTCCTC
* *
2111047 TTCTTCTTTTTTTTGTTTCTGTGTCTCGTTCTGTCTCTCTTTTTGTCTC
1 TTCTTCTTTTTTTTCTTTCTGTGTCTCGTTCTGTCTCTCTTTCTGTCTC
2111096 GCAGGTGGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
52 11 0.26
53 26 0.60
54 4 0.09
55 2 0.05
ACGTcount: A:0.01, C:0.24, G:0.11, T:0.65
Consensus pattern (52 bp):
TTCTTCTTTTTTTTCTTTCTGTGTCTCGTTCTGTCTCTCTTTCTGTCTCCTC
Found at i:2111078 original size:28 final size:30
Alignment explanation
Indices: 2111034--2111092 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 30
2111024 CTGTCTCTTC
*
2111034 TTTCTGTCTCCTCTTCT-TCT-TTTTTTTG
1 TTTCTGTCTCCTCTTCTGTCTCTCTTTTTG
*
2111062 TTTCTGTGT-CTCGTTCTGTCTCTCTTTTTG
1 TTTCTGTCTCCTC-TTCTGTCTCTCTTTTTG
2111092 T
1 T
2111093 CTCGCAGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 3 0.12
28 12 0.46
29 3 0.12
30 8 0.31
ACGTcount: A:0.00, C:0.24, G:0.12, T:0.64
Consensus pattern (30 bp):
TTTCTGTCTCCTCTTCTGTCTCTCTTTTTG
Found at i:2111468 original size:3 final size:3
Alignment explanation
Indices: 2111460--2111638 Score: 259
Period size: 3 Copynumber: 58.7 Consensus size: 3
2111450 TTATTTATTA
*
2111460 AAT AAT AAT AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT
* **
2111507 ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GCT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
2111555 AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
2111603 AAT GAT AAT AAT AAAT ATT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AA
2111639 AATGGATAAA
Statistics
Matches: 157, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
3 148 0.94
4 9 0.06
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:2116143 original size:30 final size:29
Alignment explanation
Indices: 2116095--2116167 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 29
2116085 ATGTATTAAT
2116095 TTTAAAAATT-AT-TTTAAATTTTGTACA
1 TTTAAAAATTAATATTTAAATTTTGTACA
2116122 TTTAATAAATTAATATTTAAATTTTGTACA
1 TTTAA-AAATTAATATTTAAATTTTGTACA
2116152 TTTAAAAAATTAATAT
1 TTT-AAAAATTAATAT
2116168 GTTGGTTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
27 5 0.12
28 5 0.12
29 2 0.05
30 28 0.67
31 2 0.05
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (29 bp):
TTTAAAAATTAATATTTAAATTTTGTACA
Found at i:2116154 original size:15 final size:15
Alignment explanation
Indices: 2116107--2116157 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
2116097 TAAAAATTAT
2116107 TTTAAATTTTGTACA
1 TTTAAATTTTGTACA
** * *
2116122 TTTAATAAATT-AATA
1 TTTAA-ATTTTGTACA
2116137 TTTAAATTTTGTACA
1 TTTAAATTTTGTACA
2116152 TTTAAA
1 TTTAAA
2116158 AAATTAATAT
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
14 3 0.12
15 20 0.77
16 3 0.12
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (15 bp):
TTTAAATTTTGTACA
Found at i:2117082 original size:41 final size:40
Alignment explanation
Indices: 2117019--2117138 Score: 152
Period size: 41 Copynumber: 3.0 Consensus size: 40
2117009 CGTTTATACC
* * *
2117019 ACAAACGCCGTAACAGTGTTAATCAATAGTGGCATTTTTA
1 ACAAACGCCATAATAGTTTTAATCAATAGTGGCATTTTTA
*
2117059 GATAAACGCCATAATAGTTTTAATCAATAGTGGCATTTTTTA
1 -ACAAACGCCATAATAGTTTTAATCAATAGTGGCA-TTTTTA
* * *
2117101 ACAAACGCCACAATA-TTGTAATCAATAGTGGCGTTTTT
1 ACAAACGCCATAATAGTTTTAATCAATAGTGGCATTTTT
2117139 TTGTATAAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
39 5 0.07
40 16 0.23
41 43 0.61
42 6 0.09
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (40 bp):
ACAAACGCCATAATAGTTTTAATCAATAGTGGCATTTTTA
Found at i:2118603 original size:41 final size:41
Alignment explanation
Indices: 2118558--2118664 Score: 99
Period size: 41 Copynumber: 2.6 Consensus size: 41
2118548 AAGTTGTACT
**
2118558 TTAGTGGCGTTTTTGACATAAACGCCGCAATAGTGT-GTCCC
1 TTAGTGGCGTTTTTGA-ATAAACGCCGCAATAGAATAGTCCC
* * * * *
2118599 TTAGTGGCATTTTCGTAATAAATGCCGTAATAGAATAGTTCC
1 TTAGTGGCGTTTTTG-AATAAACGCCGCAATAGAATAGTCCC
* *
2118641 TTTGTGGCGTTTTTAATATAAACG
1 TTAGTGGCGTTTTTGA-ATAAACG
2118665 TCGTAATTGT
Statistics
Matches: 51, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
41 29 0.57
42 22 0.43
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (41 bp):
TTAGTGGCGTTTTTGAATAAACGCCGCAATAGAATAGTCCC
Found at i:2125946 original size:21 final size:21
Alignment explanation
Indices: 2125928--2126007 Score: 99
Period size: 21 Copynumber: 3.8 Consensus size: 21
2125918 CAAGGGAAAT
2125928 AGAGAGAGCAGCAGCGGAAGC
1 AGAGAGAGCAGCAGCGGAAGC
**
2125949 AGCTAGAGCAGCAGCGGAAGC
1 AGAGAGAGCAGCAGCGGAAGC
* *
2125970 AGAGAGAGAAGCAGCGGCAGC
1 AGAGAGAGCAGCAGCGGAAGC
*
2125991 ACAGAGAG-AGGCAGCGG
1 AGAGAGAGCA-GCAGCGG
2126008 CAGAACAGAG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 1 0.02
21 50 0.98
ACGTcount: A:0.36, C:0.20, G:0.42, T:0.01
Consensus pattern (21 bp):
AGAGAGAGCAGCAGCGGAAGC
Found at i:2126008 original size:21 final size:21
Alignment explanation
Indices: 2125930--2126022 Score: 98
Period size: 21 Copynumber: 4.4 Consensus size: 21
2125920 AGGGAAATAG
* *
2125930 AGAGAGCAGCAGCGGAAGCAGC
1 AGAGAGAAGCAGCGGCAGCA-C
* * * *
2125952 -TAGAGCAGCAGCGGAAGCAG
1 AGAGAGAAGCAGCGGCAGCAC
2125972 AGAGAGAAGCAGCGGCAGCAC
1 AGAGAGAAGCAGCGGCAGCAC
* *
2125993 AGAGAGAGGCAGCGGCAGAAC
1 AGAGAGAAGCAGCGGCAGCAC
2126014 AGAGAGAAG
1 AGAGAGAAG
2126023 TAATATATCA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.39, C:0.19, G:0.41, T:0.01
Consensus pattern (21 bp):
AGAGAGAAGCAGCGGCAGCAC
Found at i:2126425 original size:43 final size:42
Alignment explanation
Indices: 2126318--2126457 Score: 115
Period size: 43 Copynumber: 3.2 Consensus size: 42
2126308 GTGTTATTTA
** * *
2126318 GCGGCGTTTGTGATAAAAACGCCGCG-AAATCTCAAGACATATTCT
1 GCGGCGTTTGTGAT-AAAACGCCG-GTAAAAAT-AA-ACATCTACT
2126363 GCGGCGTTTGTAGGA-AAAACGCCGGTAAAAATAAACATCTACT
1 GCGGCGTTTGT--GATAAAACGCCGGTAAAAATAAACATCTACT
* * * *
2126406 GCGGCGTTTGTGAATAAAACGCCGCTAAACATCAACGA-CTATT
1 GCGGCGTTTGTG-ATAAAACGCCGGTAAAAATAAAC-ATCTACT
2126449 GCGGCGTTT
1 GCGGCGTTT
2126458 TTATGCCAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 14
0.79 0.08 0.14
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 49 0.60
44 4 0.05
45 24 0.30
47 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (42 bp):
GCGGCGTTTGTGATAAAACGCCGGTAAAAATAAACATCTACT
Found at i:2126797 original size:24 final size:25
Alignment explanation
Indices: 2126765--2126821 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 25
2126755 AACTATTTTT
*
2126765 TTTTAAATAATTTAAT-T-TTGTAGTA
1 TTTT-AATAATTTAATGTATTG-AATA
2126790 TTTTAAT-ATTTAATGTATTGAATA
1 TTTTAATAATTTAATGTATTGAATA
2126814 TTTTAATA
1 TTTTAATA
2126822 CTTGTTAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 7 0.25
24 14 0.50
25 7 0.25
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (25 bp):
TTTTAATAATTTAATGTATTGAATA
Found at i:2126851 original size:6 final size:6
Alignment explanation
Indices: 2126840--2126864 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2126830 TACTATATAT
2126840 TTTAAA TTTAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA T
2126865 AATTTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:2127372 original size:21 final size:20
Alignment explanation
Indices: 2127337--2127395 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
2127327 ATCAATTTAG
*
2127337 CCCTCAAATTATAAACACTAAT
1 CCCT-AAATTATAAAC-CTAAA
* *
2127359 CCCTAAATTCTAAACTTAAAA
1 CCCTAAATTATAAACCT-AAA
2127380 CCCTAAATTATAAACC
1 CCCTAAATTATAAACC
2127396 CTAAGTTAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 1 0.03
21 26 0.84
22 4 0.13
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (20 bp):
CCCTAAATTATAAACCTAAA
Found at i:2127447 original size:21 final size:22
Alignment explanation
Indices: 2127400--2127444 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2127390 TAAACCCTAA
* *
2127400 GTTAGGGTTTAAAGGTTATATG
1 GTTATGGTTTAAAGGTTATAGG
2127422 GTTATGGTTT-AAGGTT-TAGG
1 GTTATGGTTTAAAGGTTATAGG
2127442 GTT
1 GTT
2127445 TATAATTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 6 0.29
22 9 0.43
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.44
Consensus pattern (22 bp):
GTTATGGTTTAAAGGTTATAGG
Found at i:2131711 original size:27 final size:27
Alignment explanation
Indices: 2131673--2131733 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
2131663 CTTAGCCATT
2131673 GCCACCCTTTTATGGCGAAAACTGAAA
1 GCCACCCTTTTATGGCGAAAACTGAAA
2131700 GCCACCCTTTTATGGCGAAAACTGAAA
1 GCCACCCTTTTATGGCGAAAACTGAAA
2131727 GCCACCC
1 GCCACCC
2131734 ATCTGAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (27 bp):
GCCACCCTTTTATGGCGAAAACTGAAA
Found at i:2134241 original size:22 final size:21
Alignment explanation
Indices: 2134205--2134245 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2134195 TTTCTAATTC
*
2134205 ATTATTTTTTAAATAATTAAT
1 ATTATTTTATAAATAATTAAT
2134226 ATTATTCTTATAAATAATTA
1 ATTATT-TTATAAATAATTA
2134246 TTGTTTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTATTTTATAAATAATTAAT
Found at i:2134736 original size:22 final size:22
Alignment explanation
Indices: 2134709--2134768 Score: 120
Period size: 22 Copynumber: 2.7 Consensus size: 22
2134699 AATCACAACT
2134709 AATATTTTATATTTTTTATAAA
1 AATATTTTATATTTTTTATAAA
2134731 AATATTTTATATTTTTTATAAA
1 AATATTTTATATTTTTTATAAA
2134753 AATATTTTATATTTTT
1 AATATTTTATATTTTT
2134769 AACTTAGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
AATATTTTATATTTTTTATAAA
Found at i:2137427 original size:191 final size:193
Alignment explanation
Indices: 2137118--2137523 Score: 529
Period size: 191 Copynumber: 2.1 Consensus size: 193
2137108 TAAATGACGT
* * * *
2137118 TTATACATAACGTCACTTTATAATTGATACTCAATGACAACTAGTTACGTCATTAAATTATATAA
1 TTATGCATAACGTCACTTTATAATTGATACTCAATGACAACTAATTACATCACTAAATTATATAA
2137183 AATTTTGTTATTAATAATTCACATCGTCACGAATAATACATTAAAATCAATCTATATGTGA-AGA
66 AATTTTGTTATTAATAATTCACATCGTCACGAATAATACATTAAAATCAATCTATATGTGACA-A
*
2137247 AAGAGATATTGTCACA-TTTTCAGTGACGTAATATAACATTACCTAATAGTATTATGAATGA-CA
130 AAGAGATATTGTCA-AGTTTTCAGTGACATAATATAACATTACCTAATAGTATTATGAATGATCA
* * **
2137310 CTTATGCATAACGTCATTTTATAACTT-ATATTGC-ATGACAGTTAATTACATCACTAAATTATA
1 -TTATGCATAACGTCACTTTATAA-TTGATACT-CAATGACAACTAATTACATCACTAAATTATA
* * * * *
2137373 TAATA-TTT-TTATTAATAATTTATATCGTCACGAATACTACATTAAAATCAATCTATATGTTAC
63 TAAAATTTTGTTATTAATAATTCACATCGTCACGAATAATACATTAAAATCAATCTATATGTGAC
* ** * * *
2137436 AAAAGAGATATTGTCAAGTTTTTAGTGACATAATATAATGTTATCTAATAGTATTTTGAATGATG
128 AAAAGAGATATTGTCAAGTTTTCAGTGACATAATATAACATTACCTAATAGTATTATGAATGATC
2137501 A
193 A
*
2137502 TTATGCATAACGTCACCTTATA
1 TTATGCATAACGTCACTTTATA
2137524 CAATTTTCTC
Statistics
Matches: 186, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
190 1 0.01
191 124 0.67
192 5 0.03
193 53 0.28
194 3 0.02
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (193 bp):
TTATGCATAACGTCACTTTATAATTGATACTCAATGACAACTAATTACATCACTAAATTATATAA
AATTTTGTTATTAATAATTCACATCGTCACGAATAATACATTAAAATCAATCTATATGTGACAAA
AGAGATATTGTCAAGTTTTCAGTGACATAATATAACATTACCTAATAGTATTATGAATGATCA
Found at i:2140259 original size:14 final size:15
Alignment explanation
Indices: 2140223--2140259 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
2140213 CATTTTTTTT
*
2140223 AAAAGAAAAAGCCAA
1 AAAAAAAAAAGCCAA
2140238 AAATAAAAAAAGCCAA
1 AAA-AAAAAAAGCCAA
2140254 AAAAAA
1 AAAAAA
2140260 TATCCAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.78, C:0.11, G:0.08, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAAGCCAA
Found at i:2142963 original size:25 final size:25
Alignment explanation
Indices: 2142934--2142985 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
2142924 TAAATTCATG
2142934 TCGATATGACGCTTACACTTCATCA
1 TCGATATGACGCTTACACTTCATCA
2142959 TCGATATGACGCTTACACTTCATCA
1 TCGATATGACGCTTACACTTCATCA
2142984 TC
1 TC
2142986 TTAAGTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.33
Consensus pattern (25 bp):
TCGATATGACGCTTACACTTCATCA
Found at i:2149527 original size:29 final size:29
Alignment explanation
Indices: 2149493--2149567 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
2149483 TTTTCAAGAA
*
2149493 AAAAATCATTGGATAACCCAAAAAACCAT
1 AAAAATAATTGGATAACCCAAAAAACCAT
2149522 AAAAATAATTGGATAACCCAAAAAACCAT
1 AAAAATAATTGGATAACCCAAAAAACCAT
2149551 AAAAATAATTGGATAAC
1 AAAAATAATTGGATAAC
2149568 TAAATCAATA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.57, C:0.16, G:0.08, T:0.19
Consensus pattern (29 bp):
AAAAATAATTGGATAACCCAAAAAACCAT
Found at i:2150550 original size:16 final size:17
Alignment explanation
Indices: 2150529--2150562 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2150519 ACTTTATGTG
2150529 ATTC-AAAATATTGTTA
1 ATTCAAAAATATTGTTA
*
2150545 ATTCAAAAATATTTTTA
1 ATTCAAAAATATTGTTA
2150562 A
1 A
2150563 GAAAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (17 bp):
ATTCAAAAATATTGTTA
Found at i:2151883 original size:16 final size:16
Alignment explanation
Indices: 2151859--2151893 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2151849 GATGATTAAA
* *
2151859 TTTATTTTAATTTATT
1 TTTAATTTAATATATT
2151875 TTTAATTTAATATATT
1 TTTAATTTAATATATT
2151891 TTT
1 TTT
2151894 CTCACCAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTAATTTAATATATT
Found at i:2152206 original size:29 final size:29
Alignment explanation
Indices: 2152160--2152233 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
2152150 TTAACTTGTT
*
2152160 AAATATACTTTTATTCTT-TTCCTAATCTAA
1 AAATATA-TTTTAATCTTATT-CTAATCTAA
* *
2152190 AAATATATTTTAATCTTATTTTAATTTAA
1 AAATATATTTTAATCTTATTCTAATCTAA
2152219 AAATATATTTTAATC
1 AAATATATTTTAATC
2152234 CTATCTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 31 0.77
30 9 0.22
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.51
Consensus pattern (29 bp):
AAATATATTTTAATCTTATTCTAATCTAA
Found at i:2152242 original size:29 final size:29
Alignment explanation
Indices: 2152182--2152242 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
2152172 ATTCTTTTCC
* *
2152182 TAATCTAAAAATATATTTTAATCTTATTT
1 TAATCTAAAAATATATTTTAATCCTATCT
*
2152211 TAATTTAAAAATATATTTTAATCCTATCT
1 TAATCTAAAAATATATTTTAATCCTATCT
2152240 TAA
1 TAA
2152243 AAAAATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (29 bp):
TAATCTAAAAATATATTTTAATCCTATCT
Found at i:2153437 original size:17 final size:17
Alignment explanation
Indices: 2153415--2153458 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2153405 ATATAAAAAT
2153415 AAATATTTAAATTTAAA
1 AAATATTTAAATTTAAA
** **
2153432 AAATATAAAAATTTACT
1 AAATATTTAAATTTAAA
2153449 AAATATTTAA
1 AAATATTTAA
2153459 TTAATTAGGG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATATTTAAATTTAAA
Found at i:2155159 original size:19 final size:18
Alignment explanation
Indices: 2155137--2155184 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
2155127 AATAAAAAGT
2155137 TATTAATTTATTATATTAA
1 TATTAATTTATTATATT-A
2155156 TATT-ATTTATT-TATTA
1 TATTAATTTATTATATTA
*
2155172 TTTTAATTT-TTAT
1 TATTAATTTATTAT
2155185 TATTTTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 6 0.23
17 9 0.35
18 7 0.27
19 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTAATTTATTATATTA
Found at i:2155162 original size:22 final size:22
Alignment explanation
Indices: 2155136--2155178 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2155126 GAATAAAAAG
2155136 TTATTAATTTATTATATTAATA
1 TTATTAATTTATTATATTAATA
* *
2155158 TTATTTATTTATTATTTTAAT
1 TTATTAATTTATTATATTAAT
2155179 TTTTATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATTAATTTATTATATTAATA
Found at i:2155590 original size:29 final size:29
Alignment explanation
Indices: 2155557--2155613 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
2155547 ATTAACTCTA
2155557 AAATTCAAGCTTATAGAACTTATCAAGAT
1 AAATTCAAGCTTATAGAACTTATCAAGAT
2155586 AAATTCAAGCTTATAGAACTTATCAAGA
1 AAATTCAAGCTTATAGAACTTATCAAGA
2155614 CATTAGTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (29 bp):
AAATTCAAGCTTATAGAACTTATCAAGAT
Found at i:2155841 original size:14 final size:15
Alignment explanation
Indices: 2155810--2155846 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2155800 ATGAATTAAT
2155810 TAAAA-ATTTAAAAG
1 TAAAATATTTAAAAG
*
2155824 TAAATTATTTAAAA-
1 TAAAATATTTAAAAG
2155838 TAAAATATT
1 TAAAATATT
2155847 AATTACATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
TAAAATATTTAAAAG
Found at i:2156091 original size:15 final size:16
Alignment explanation
Indices: 2156062--2156094 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2156052 ATAATTAATT
*
2156062 TTTTTATAATTTTAAA
1 TTTTTATAATATTAAA
2156078 TTTTTATAA-ATTAAA
1 TTTTTATAATATTAAA
2156093 TT
1 TT
2156095 AATAATGTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTTATAATATTAAA
Found at i:2156151 original size:2 final size:2
Alignment explanation
Indices: 2156144--2156178 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2156134 GAACTTCATA
2156144 AT AT 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 AT AT A
2156179 ACTGTAGGTA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2158870 original size:17 final size:18
Alignment explanation
Indices: 2158842--2158875 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2158832 ATTTGATGTA
2158842 TTTATAAAAATATAATTT
1 TTTATAAAAATATAATTT
2158860 TTTAT-AAAATATAATT
1 TTTATAAAAATATAATT
2158876 ATATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTATAAAAATATAATTT
Found at i:2158885 original size:17 final size:17
Alignment explanation
Indices: 2158847--2158889 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2158837 ATGTATTTAT
* *
2158847 AAAAATATAATTTTTTA
1 AAAAATATAATTATATA
*
2158864 TAAAATATAATTATATA
1 AAAAATATAATTATATA
2158881 AAAAA-ATAA
1 AAAAATATAA
2158890 AATGAACTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAAATATAATTATATA
Found at i:2158977 original size:25 final size:25
Alignment explanation
Indices: 2158943--2158992 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
2158933 TATGTATGTT
2158943 TCTTTATTAAAAAGAGATTCTGAAA
1 TCTTTATTAAAAAGAGATTCTGAAA
2158968 TCTTTATTAAAAAGAGATTCTGAAA
1 TCTTTATTAAAAAGAGATTCTGAAA
2158993 ACTGTTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (25 bp):
TCTTTATTAAAAAGAGATTCTGAAA
Found at i:2159613 original size:52 final size:52
Alignment explanation
Indices: 2159502--2159619 Score: 125
Period size: 52 Copynumber: 2.3 Consensus size: 52
2159492 TATATTTTTG
* * *
2159502 TTATAGTTTAAATTGATATAATTTGTATATAATAATAATTATTTTGAACTTA
1 TTATATTTTAAATTGATATAATTTGTATATAATAATAATTAATTTGAACATA
* * *
2159554 TTTTATTTTAAATTGATATAATTTTTATATAAGTGGA-AATATAATTT-AA-ATA
1 TTATATTTTAAATTGATATAATTTGTATATAA-T-AATAAT-TAATTTGAACATA
*
2159606 TTATATTTTCAATT
1 TTATATTTTAAATT
2159620 TATAACATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
52 43 0.78
53 6 0.11
54 6 0.11
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.52
Consensus pattern (52 bp):
TTATATTTTAAATTGATATAATTTGTATATAATAATAATTAATTTGAACATA
Found at i:2161309 original size:45 final size:45
Alignment explanation
Indices: 2161260--2161358 Score: 114
Period size: 43 Copynumber: 2.2 Consensus size: 45
2161250 CCTTAAACTA
* *
2161260 TAAAAGTAAAAAAAGT-ATGATTGAAAAAATTAGGGTCATCAATTG
1 TAAAAGTAAAAAAAGTGA-GATTAAAAAAATTAGGGGCATCAATTG
* * *
2161305 TAAAAGT--AAAATGTGAGATTAAAAAAATTAGGGGCCTCAATTT
1 TAAAAGTAAAAAAAGTGAGATTAAAAAAATTAGGGGCATCAATTG
*
2161348 TAAAGGTAAAA
1 TAAAAGTAAAA
2161359 GGTAGGGTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
43 35 0.78
44 1 0.02
45 9 0.20
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.26
Consensus pattern (45 bp):
TAAAAGTAAAAAAAGTGAGATTAAAAAAATTAGGGGCATCAATTG
Found at i:2162821 original size:28 final size:28
Alignment explanation
Indices: 2162781--2162835 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
2162771 AAAAGCAAAG
2162781 TCAATTTAAAGTAATTTGGGTTATTTGT
1 TCAATTTAAAGTAATTTGGGTTATTTGT
2162809 TCAATTTAAAGTAATTTGGGTTATTTG
1 TCAATTTAAAGTAATTTGGGTTATTTG
2162836 AACATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (28 bp):
TCAATTTAAAGTAATTTGGGTTATTTGT
Found at i:2162851 original size:28 final size:28
Alignment explanation
Indices: 2162782--2162851 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
2162772 AAAGCAAAGT
* * **
2162782 CAATTTAAAGTAATTTGGGTTATTTGTT
1 CAATATAAAATAATTTGGGTTATTTGAA
* *
2162810 CAATTTAAAGTAATTTGGGTTATTTGAA
1 CAATATAAAATAATTTGGGTTATTTGAA
2162838 C-ATATAAATATAAT
1 CAATATAAA-ATAAT
2162852 ATAATTAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 6 0.16
28 31 0.84
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.44
Consensus pattern (28 bp):
CAATATAAAATAATTTGGGTTATTTGAA
Found at i:2174175 original size:10 final size:10
Alignment explanation
Indices: 2174160--2174198 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
2174150 GACTAACCTT
2174160 TTTTAATTTA
1 TTTTAATTTA
2174170 TTTTAATTTA
1 TTTTAATTTA
* *
2174180 ATAT-ATTTA
1 TTTTAATTTA
2174189 TTTTAATTTA
1 TTTTAATTTA
2174199 AAATTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTAATTTA
Found at i:2181847 original size:32 final size:33
Alignment explanation
Indices: 2181801--2181879 Score: 81
Period size: 32 Copynumber: 2.4 Consensus size: 33
2181791 TTAATAATTC
*
2181801 TAAATAAATAATAATTATATAAAT-ATTATTTTAA
1 TAAA-AAA-AATAATTATATAAATAATTATATTAA
* *
2181835 TAAAAAAAATAA-TATTTATATAATTATATTAA
1 TAAAAAAAATAATTATATAAATAATTATATTAA
* *
2181867 TATAAAATATAAT
1 TAAAAAAAATAAT
2181880 AACTATTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
31 7 0.18
32 24 0.63
33 3 0.08
34 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
TAAAAAAAATAATTATATAAATAATTATATTAA
Found at i:2181881 original size:35 final size:34
Alignment explanation
Indices: 2181802--2181888 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
2181792 TAATAATTCT
*
2181802 AAATAAATAATAATTATATAAATATTATTTTAATAA
1 AAATAAATAAT-ATT-TATAAATATTATATTAATAA
*
2181838 AAA-AAATAATATTTATATA-ATTATATTAATATA
1 AAATAAATAATATTTATAAATATTATATTAATA-A
2181871 AAATATAATAACTATTTA
1 AAATA-AATAA-TATTTA
2181889 AAAAAATACT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
32 11 0.24
33 9 0.20
34 4 0.09
35 12 0.27
36 9 0.20
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (34 bp):
AAATAAATAATATTTATAAATATTATATTAATAA
Done.