Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 36 of 54
Found at i:8636430 original size:118 final size:118
Alignment explanation
Indices: 8636282--8636494 Score: 318
Period size: 118 Copynumber: 1.8 Consensus size: 118
8636272 CAGTGCTATC
* * * * *
8636282 ATCATAATCAGAATATATAAGCACACACAATGCTATTATATCAAAATCATAATGTGCACACAAAG
1 ATCAAAATCAGAACATATAAACACACACAATGCTATCATATCAAAATCATAATATGCACACAAAG
* * *
8636347 TGCAATCAGATCAGAATATATATACTAGTGCACCCACTAATACACCACAATAT
66 AGCAATCACATCAAAATATATATACTAGTGCACCCACTAATACACCACAATAT
* * * *
8636400 ATCAAAATCGGAACATATAAACACACACAATGCTATCATATCAGAATCGTAATATGTACACAAAG
1 ATCAAAATCAGAACATATAAACACACACAATGCTATCATATCAAAATCATAATATGCACACAAAG
8636465 AGCAATCACATCAAAATATATATACTAGTG
66 AGCAATCACATCAAAATATATATACTAGTG
8636495 TACCTTCAGG
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
118 83 1.00
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (118 bp):
ATCAAAATCAGAACATATAAACACACACAATGCTATCATATCAAAATCATAATATGCACACAAAG
AGCAATCACATCAAAATATATATACTAGTGCACCCACTAATACACCACAATAT
Found at i:8639003 original size:2 final size:2
Alignment explanation
Indices: 8638998--8639076 Score: 142
Period size: 2 Copynumber: 40.0 Consensus size: 2
8638988 TTACTCACAC
8638998 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
8639039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8639077 TACACATTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 73 0.99
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8646554 original size:15 final size:16
Alignment explanation
Indices: 8646529--8646565 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
8646519 AGGAAAAGCA
*
8646529 AAAACAAACAATAATT
1 AAAACAAACAATAACT
8646545 AAAA-AAACAATAACT
1 AAAACAAACAATAACT
8646560 AAAACA
1 AAAACA
8646566 TGAAAAAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.73, C:0.14, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAACAAACAATAACT
Found at i:8653520 original size:20 final size:21
Alignment explanation
Indices: 8653484--8653522 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
8653474 TTACTTGAGG
*
8653484 GGTATCGATACCCCTGCTATA
1 GGTACCGATACCCCTGCTATA
8653505 GGTACCGATA-CCCTGCTA
1 GGTACCGATACCCCTGCTA
8653523 CAATACTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.26
Consensus pattern (21 bp):
GGTACCGATACCCCTGCTATA
Found at i:8654381 original size:29 final size:29
Alignment explanation
Indices: 8654321--8654381 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
8654311 TGAATATGTC
* * **
8654321 CCGAAAGACCTATGGGTTGTCCATATTCA
1 CCGAAAGACCTATGAGTTGTCCAGAAGCA
* *
8654350 CCGAAAGACCTATGAGTTGTCCCGAAGGA
1 CCGAAAGACCTATGAGTTGTCCAGAAGCA
8654379 CCG
1 CCG
8654382 CGTAGACCCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.21
Consensus pattern (29 bp):
CCGAAAGACCTATGAGTTGTCCAGAAGCA
Found at i:8661578 original size:39 final size:39
Alignment explanation
Indices: 8661504--8661594 Score: 110
Period size: 39 Copynumber: 2.3 Consensus size: 39
8661494 TCTATGACTT
* * * * *
8661504 GTAAGACCTTAACACATGCTTATCTGCTTTGTGCTCAGG
1 GTAAGTCCTTACCACATGCTCATCTACTTTATGCTCAGG
* *
8661543 TTAAGTCCTTACCACATGCTCCTCTACTTTATGCTCAGG
1 GTAAGTCCTTACCACATGCTCATCTACTTTATGCTCAGG
*
8661582 GTAAGTTCTTACC
1 GTAAGTCCTTACC
8661595 GTAGGTCCTT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.35
Consensus pattern (39 bp):
GTAAGTCCTTACCACATGCTCATCTACTTTATGCTCAGG
Found at i:8668280 original size:39 final size:39
Alignment explanation
Indices: 8668219--8668307 Score: 124
Period size: 39 Copynumber: 2.3 Consensus size: 39
8668209 ACTTGTAAGA
* * * *
8668219 CCTTACCGCAAGCTCGTCTGCTTTGTGCTCAAGGTAAAT
1 CCTTACCGTAGGCTCCTATGCTTTGTGCTCAAGGTAAAT
* *
8668258 CCTTACCGTAGGCTCCTATGCTTTGTGCTCAGGGTAAGT
1 CCTTACCGTAGGCTCCTATGCTTTGTGCTCAAGGTAAAT
8668297 CCTTACCGTAG
1 CCTTACCGTAG
8668308 ATACTTATGC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.18, C:0.28, G:0.22, T:0.31
Consensus pattern (39 bp):
CCTTACCGTAGGCTCCTATGCTTTGTGCTCAAGGTAAAT
Found at i:8669518 original size:23 final size:23
Alignment explanation
Indices: 8669492--8669535 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
8669482 CTTTATTTAT
8669492 GCATTCAAGGTAATCTTATCAAG
1 GCATTCAAGGTAATCTTATCAAG
* *
8669515 GCATTCAAGGTATTTTTATCA
1 GCATTCAAGGTAATCTTATCA
8669536 TCCCATCGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (23 bp):
GCATTCAAGGTAATCTTATCAAG
Found at i:8670472 original size:13 final size:13
Alignment explanation
Indices: 8670454--8670521 Score: 100
Period size: 13 Copynumber: 5.2 Consensus size: 13
8670444 TGCGTCATAA
*
8670454 ATTTATGACGCAC
1 ATTTATGACGCGC
*
8670467 ATTTATGACACGC
1 ATTTATGACGCGC
*
8670480 ATTTATGACACGC
1 ATTTATGACGCGC
8670493 ATTTATGACGCGC
1 ATTTATGACGCGC
*
8670506 ATTTATGACGCTC
1 ATTTATGACGCGC
8670519 ATT
1 ATT
8670522 GCGCGTCATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 51 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:8684673 original size:15 final size:15
Alignment explanation
Indices: 8684636--8684677 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
8684626 AAGGGTGTTT
*
8684636 GAATG-AAATAAAAA
1 GAATGAAAATGAAAA
*
8684650 GAGTGGAAAATGAAAA
1 GAAT-GAAAATGAAAA
8684666 GAATGAAAATGA
1 GAATGAAAATGA
8684678 GAGAGTGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 3 0.13
15 9 0.39
16 11 0.48
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (15 bp):
GAATGAAAATGAAAA
Found at i:8684688 original size:15 final size:16
Alignment explanation
Indices: 8684641--8684689 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 16
8684631 TGTTTGAATG
*
8684641 AAATAAAAAGAGTGGA
1 AAATGAAAAGAGTGGA
*
8684657 AAATGAAAAGAAT-GA
1 AAATGAAAAGAGTGGA
*
8684672 AAATG-AGAGAGTGGA
1 AAATGAAAAGAGTGGA
8684687 AAA
1 AAA
8684690 AGGAAATGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 5 0.18
15 12 0.43
16 11 0.39
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.12
Consensus pattern (16 bp):
AAATGAAAAGAGTGGA
Found at i:8686063 original size:17 final size:17
Alignment explanation
Indices: 8686032--8686074 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
8686022 GATCATTCAA
8686032 TAAAGCTAGTCCATTAAT
1 TAAA-CTAGTCCATTAAT
*
8686050 TAAACTAGTTCATTAAT
1 TAAACTAGTCCATTAAT
8686067 TAAACTAG
1 TAAACTAG
8686075 CTACTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (17 bp):
TAAACTAGTCCATTAAT
Found at i:8692457 original size:15 final size:15
Alignment explanation
Indices: 8692437--8692465 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
8692427 CCCTCAATTC
8692437 TTTGTTCCCTAATGT
1 TTTGTTCCCTAATGT
8692452 TTTGTTCCCTAATG
1 TTTGTTCCCTAATG
8692466 CACATACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.52
Consensus pattern (15 bp):
TTTGTTCCCTAATGT
Found at i:8695648 original size:24 final size:25
Alignment explanation
Indices: 8695615--8695681 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 25
8695605 CACTGTATGG
*
8695615 AAGTGCCTTAGCACTGATAT-ACTA
1 AAGTACCTTAGCACTGATATCACTA
* * *
8695639 AAGTATCTTAGCATTGAT-TCACTC
1 AAGTACCTTAGCACTGATATCACTA
*
8695663 AAGTGCCTTAGCACT-ATAT
1 AAGTACCTTAGCACTGATAT
8695682 GGAGCATATC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
23 3 0.09
24 31 0.91
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (25 bp):
AAGTACCTTAGCACTGATATCACTA
Found at i:8701621 original size:16 final size:16
Alignment explanation
Indices: 8701602--8701644 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
8701592 ATTTGTATGT
* *
8701602 ATATATATATAATTTC
1 ATATATATATAAATAC
**
8701618 ATATACCTATAAATAC
1 ATATATATATAAATAC
8701634 ATATATATATA
1 ATATATATATA
8701645 TATATATATG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATATATATAAATAC
Found at i:8702195 original size:56 final size:56
Alignment explanation
Indices: 8702007--8702867 Score: 941
Period size: 56 Copynumber: 15.5 Consensus size: 56
8701997 TTTTTTTAGA
* * *
8702007 AAACGGGTCTGCTCCCTCTTCTTTCAAGG-AGTATAGGACTCG-AACAATCTT-GGAC
1 AAACGTGTCTGCTCCCTCTTCTTTC-AGGAAGTATAGGACTTGAAACAATCTTCAG-C
* * * * *
8702062 AAAAGTGT-TCGATCCCTCTTCTTTCAGGAAGTATAGGAATCG-AACAATCTTCAAC
1 AAACGTGTCT-GCTCCCTCTTCTTTCAGGAAGTATAGGACTTGAAACAATCTTCAGC
* * * * *
8702117 AAACGTGACCGCTCCCTTTTCTTTTAGGAAGTATAGGATTTGAAACAATCTTCAGC
1 AAACGTGTCTGCTCCCTCTTCTTTCAGGAAGTATAGGACTTGAAACAATCTTCAGC
* * * * * **
8702173 AAATGTGTCTTCTCCTTCTTCTTTCAAGG-AGTATAGGAATCG-AACAATCTTCAAA
1 AAACGTGTCTGCTCCCTCTTCTTTC-AGGAAGTATAGGACTTGAAACAATCTTCAGC
*
8702228 AAACGTGTCCGCTCCCTCTTCTTTCAGGAAGTATAGGACTTGAAACAATCTTCAAG-
1 AAACGTGTCTGCTCCCTCTTCTTTCAGGAAGTATAGGACTTGAAACAATCTTC-AGC
* * *
8702284 AAACGTGTTTTCTCCCTCTTCTTTCAGGTAGTATAGGACTTGAAACAATCTTCAGC
1 AAACGTGTCTGCTCCCTCTTCTTTCAGGAAGTATAGGACTTGAAACAATCTTCAGC
* *
8702340 AAACGTGTCTGCTCCCTCTTCTTTCAGAAAGTATAGGACTTGAAACAATCTTCAAC
1 AAACGTGTCTGCTCCCTCTTCTTTCAGGAAGTATAGGACTTGAAACAATCTTCAGC
* * *
8702396 AAACGTGT-TCGCTCCTTCTTCTTTCAAGG-AGTATAGGAATCG-AACAATCTTCAGC
1 AAACGTGTCT-GCTCCCTCTTCTTTC-AGGAAGTATAGGACTTGAAACAATCTTCAGC
** * *
8702451 AAATATGT-TCGCTCCCTCTTCTTTTAGGAAGTATAGGA-TTGTAAACAATCTTTTA-C
1 AAACGTGTCT-GCTCCCTCTTCTTTCAGGAAGTATAGGACTTG-AAACAATC-TTCAGC
** * * *
8702507 AAACGTGTCCACTTCCTCTTCTTTCAGAAAGTATAGGACTTGAAACAATCTTTAGC
1 AAACGTGTCTGCTCCCTCTTCTTTCAGGAAGTATAGGACTTGAAACAATCTTCAGC
* * *
8702563 AAACGTGTCTGCTCCCTCTTCTTTTATGAAGTATAGAACTTGAAACAATCTTCAGC
1 AAACGTGTCTGCTCCCTCTTCTTTCAGGAAGTATAGGACTTGAAACAATCTTCAGC
** * *
8702619 AAACGTGTCCACTCCCTCTTATTTCAGGAAGTATAGGACTTGAAATAATCTTCAGC
1 AAACGTGTCTGCTCCCTCTTCTTTCAGGAAGTATAGGACTTGAAACAATCTTCAGC
* * *
8702675 AAACGTGTCTGCT-CC-CATCTTTCAGTAAGTATAGGACTTGAAACAATCTTCAAC
1 AAACGTGTCTGCTCCCTCTTCTTTCAGGAAGTATAGGACTTGAAACAATCTTCAGC
* * * * *
8702729 AAACATGCCCGCTCTCTCTTCTTTC-GCGAAGTATAGGACTTGAAACAATCTTCAAC
1 AAACGTGTCTGCTCCCTCTTCTTTCAG-GAAGTATAGGACTTGAAACAATCTTCAGC
* * * * **
8702785 AAACGTGTCCGCTCCTTCCTCTTTCAAGG-AGTATAGGAC-TCAAACAATCTTTGGC
1 AAACGTGTCTGCTCCCTCTTCTTTC-AGGAAGTATAGGACTTGAAACAATCTTCAGC
*
8702840 AAACGGGTCTGCTCCCTCTTCTTTCAGG
1 AAACGTGTCTGCTCCCTCTTCTTTCAGG
8702868 GATGATCAGA
Statistics
Matches: 681, Mismatches: 101, Indels: 49
0.82 0.12 0.06
Matches are distributed among these distances:
54 59 0.09
55 204 0.30
56 404 0.59
57 13 0.02
58 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (56 bp):
AAACGTGTCTGCTCCCTCTTCTTTCAGGAAGTATAGGACTTGAAACAATCTTCAGC
Found at i:8702413 original size:223 final size:223
Alignment explanation
Indices: 8702004--8702844 Score: 977
Period size: 223 Copynumber: 3.8 Consensus size: 223
8701994 AATTTTTTTT
* * * ** *
8702004 AGAAAACGGGTCTGCTCCCTCTTCTTTCAAGG-AGTATAGGACTCG-AACAATCTTGGACAAAAG
1 AGAAAACGTGTCCGCTCCCTCTTCTTTC-AGGAAGTATAGGACTTGAAACAATCTTCAACAAACG
* * * * *
8702067 TGTTCGATCCCTCTTCTTTCAGGAAGTATAGGAATCG-AACAATCTTCAACAAACGTGACCGCTC
65 TGTCCGCTCCCTCTTCTTTCAGGAAGTATAGGACTTGAAACAATCTTCAACAAACGTGTCCGCTC
* * * * * *
8702131 CCTTTTCTTTTAGGAAGTATAGGATTTGAAACAATCTTCAGCAAATGTG-TCTTCTCCTTCTTCT
130 CCTCTTCTTTCAGAAAGTATAGGACTTGAAACAATCTTCAGCAAACGTGTTC-ACTCCTTCTTCT
8702195 TTCAAGGAGTATAGGAATCGAACAATCTTC
194 TTCAAGGAGTATAGGAATCGAACAATCTTC
* *
8702225 AAAAAACGTGTCCGCTCCCTCTTCTTTCAGGAAGTATAGGACTTGAAACAATCTTCAAGAAACGT
1 AGAAAACGTGTCCGCTCCCTCTTCTTTCAGGAAGTATAGGACTTGAAACAATCTTCAACAAACGT
*** * * *
8702290 GTTTTCTCCCTCTTCTTTCAGGTAGTATAGGACTTGAAACAATCTTCAGCAAACGTGTCTGCTCC
66 GTCCGCTCCCTCTTCTTTCAGGAAGTATAGGACTTGAAACAATCTTCAACAAACGTGTCCGCTCC
* *
8702355 CTCTTCTTTCAGAAAGTATAGGACTTGAAACAATCTTCAACAAACGTGTTCGCTCCTTCTTCTTT
131 CTCTTCTTTCAGAAAGTATAGGACTTGAAACAATCTTCAGCAAACGTGTTCACTCCTTCTTCTTT
8702420 CAAGGAGTATAGGAATCGAACAATCTTC
196 CAAGGAGTATAGGAATCGAACAATCTTC
* ** * * **
8702448 AGCAAATATGTTCGCTCCCTCTTCTTTTAGGAAGTATAGGA-TTGTAAACAATCTTTTACAAACG
1 AGAAAACGTGTCCGCTCCCTCTTCTTTCAGGAAGTATAGGACTTG-AAACAATCTTCAACAAACG
* * * * * *
8702512 TGTCCACTTCCTCTTCTTTCAGAAAGTATAGGACTTGAAACAATCTTTAGCAAACGTGTCTGCTC
65 TGTCCGCTCCCTCTTCTTTCAGGAAGTATAGGACTTGAAACAATCTTCAACAAACGTGTCCGCTC
* * * * *
8702577 CCTCTTCTTTTATG-AAGTATAGAACTTGAAACAATCTTCAGCAAACGTGTCCACTCCCTCTTAT
130 CCTCTTCTTTCA-GAAAGTATAGGACTTGAAACAATCTTCAGCAAACGTGTTCACTCCTTCTTCT
* * *
8702641 TTC-AGGAAGTATAGGACTTGAAATAATCTTC
194 TTCAAGG-AGTATAGGAATCG-AACAATCTTC
* * * * *
8702672 AGCAAACGTGTCTGCT-CC-CATCTTTCAGTAAGTATAGGACTTGAAACAATCTTCAACAAACAT
1 AGAAAACGTGTCCGCTCCCTCTTCTTTCAGGAAGTATAGGACTTGAAACAATCTTCAACAAACGT
* *
8702735 GCCCGCTCTCTCTTCTTTC-GCGAAGTATAGGACTTGAAACAATCTTCAACAAACGTGTCCGCTC
66 GTCCGCTCCCTCTTCTTTCAG-GAAGTATAGGACTTGAAACAATCTTCAACAAACGTGTCCGCTC
* * * * **
8702799 CTTCCTCTTTCA-AGGAGTATAGGAC-TCAAACAATCTTTGGCAAACG
130 CCTCTTCTTTCAGA-AAGTATAGGACTTGAAACAATCTTCAGCAAACG
8702845 GGTCTGCTCC
Statistics
Matches: 532, Mismatches: 76, Indels: 24
0.84 0.12 0.04
Matches are distributed among these distances:
220 3 0.01
221 56 0.11
222 158 0.30
223 291 0.55
224 24 0.05
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (223 bp):
AGAAAACGTGTCCGCTCCCTCTTCTTTCAGGAAGTATAGGACTTGAAACAATCTTCAACAAACGT
GTCCGCTCCCTCTTCTTTCAGGAAGTATAGGACTTGAAACAATCTTCAACAAACGTGTCCGCTCC
CTCTTCTTTCAGAAAGTATAGGACTTGAAACAATCTTCAGCAAACGTGTTCACTCCTTCTTCTTT
CAAGGAGTATAGGAATCGAACAATCTTC
Found at i:8702954 original size:34 final size:35
Alignment explanation
Indices: 8702884--8702968 Score: 118
Period size: 34 Copynumber: 2.4 Consensus size: 35
8702874 CAGACTCAAT
* *
8702884 ATTAATTTGCTTCACTACTCTTTTGTGAAGGCTTAAG
1 ATTAATTTGCTTCACTACTC--TAGTGAAGGATTAAG
8702921 ATTAATTTGCTTCACTACTC-AGTGAAGGATTAAG
1 ATTAATTTGCTTCACTACTCTAGTGAAGGATTAAG
*
8702955 ATTAATTTGTTTCA
1 ATTAATTTGCTTCA
8702969 AAAGTCAAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
34 25 0.56
37 20 0.44
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.42
Consensus pattern (35 bp):
ATTAATTTGCTTCACTACTCTAGTGAAGGATTAAG
Found at i:8704242 original size:8 final size:8
Alignment explanation
Indices: 8704231--8704292 Score: 74
Period size: 8 Copynumber: 7.8 Consensus size: 8
8704221 CTTTTTATTT
8704231 TTTTTTCA
1 TTTTTTCA
8704239 TTTTTTCA
1 TTTTTTCA
*
8704247 TTTTTTCCT
1 TTTTTT-CA
8704256 TTTTTTCA
1 TTTTTTCA
*
8704264 TTTTCGTC-
1 TTTT-TTCA
8704272 TTTTTTCA
1 TTTTTTCA
8704280 TTTTTT-A
1 TTTTTTCA
8704287 TTTTTT
1 TTTTTT
8704293 TCTCTTCTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
7 9 0.19
8 29 0.62
9 9 0.19
ACGTcount: A:0.08, C:0.13, G:0.02, T:0.77
Consensus pattern (8 bp):
TTTTTTCA
Found at i:8704250 original size:25 final size:26
Alignment explanation
Indices: 8704222--8704285 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
8704212 TAAACCCCCC
*
8704222 TTTTTATTTTTTTTTCATTTT-TTCA
1 TTTTTATTTTTTTTTCATTTTCGTCA
* *
8704247 TTTTT-TCCTTTTTTTCATTTTCGTCT
1 TTTTTAT-TTTTTTTTCATTTTCGTCA
8704273 TTTTTCATTTTTT
1 TTTTT-ATTTTTT
8704286 ATTTTTTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
24 1 0.03
25 18 0.58
26 7 0.23
27 4 0.13
28 1 0.03
ACGTcount: A:0.08, C:0.12, G:0.02, T:0.78
Consensus pattern (26 bp):
TTTTTATTTTTTTTTCATTTTCGTCA
Found at i:8704298 original size:25 final size:24
Alignment explanation
Indices: 8704222--8704306 Score: 66
Period size: 25 Copynumber: 3.4 Consensus size: 24
8704212 TAAACCCCCC
*
8704222 TTTTT-ATTTTTTTTTCATTTTTTCAT
1 TTTTTCATTTTTTTTT--TTTTCTC-T
* **
8704248 TTTTTCCTTTTTTTCATTTTCGTCT
1 TTTTTCATTTTTTTTTTTTTC-TCT
8704273 TTTTTCATTTTTTATTTTTTTCTC-
1 TTTTTCATTTTTT-TTTTTTTCTCT
*
8704297 TTCTTCATTT
1 TTTTTCATTT
8704307 CTTCTTTAGG
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
24 9 0.19
25 19 0.40
26 13 0.27
27 7 0.15
ACGTcount: A:0.08, C:0.14, G:0.01, T:0.76
Consensus pattern (24 bp):
TTTTTCATTTTTTTTTTTTTCTCT
Found at i:8717746 original size:101 final size:101
Alignment explanation
Indices: 8717571--8717772 Score: 404
Period size: 101 Copynumber: 2.0 Consensus size: 101
8717561 TTTAAAAAAC
8717571 CCTAAAGTTGTTATCATCCATCTAAGTCATTAGATGGAAAACTCCAAATCTGACGGTTCTTTTAT
1 CCTAAAGTTGTTATCATCCATCTAAGTCATTAGATGGAAAACTCCAAATCTGACGGTTCTTTTAT
8717636 TGTGGCGCTGGGAGCTGGTGACAAATAACCCTAGTG
66 TGTGGCGCTGGGAGCTGGTGACAAATAACCCTAGTG
8717672 CCTAAAGTTGTTATCATCCATCTAAGTCATTAGATGGAAAACTCCAAATCTGACGGTTCTTTTAT
1 CCTAAAGTTGTTATCATCCATCTAAGTCATTAGATGGAAAACTCCAAATCTGACGGTTCTTTTAT
8717737 TGTGGCGCTGGGAGCTGGTGACAAATAACCCTAGTG
66 TGTGGCGCTGGGAGCTGGTGACAAATAACCCTAGTG
8717773 GTCCTCGCGT
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.31
Consensus pattern (101 bp):
CCTAAAGTTGTTATCATCCATCTAAGTCATTAGATGGAAAACTCCAAATCTGACGGTTCTTTTAT
TGTGGCGCTGGGAGCTGGTGACAAATAACCCTAGTG
Found at i:8721067 original size:17 final size:18
Alignment explanation
Indices: 8721035--8721068 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
8721025 TATACGGGTG
*
8721035 TTTTATTTCTTTTCTTCA
1 TTTTATTTCCTTTCTTCA
8721053 TTTTA-TTCCTTTCTTC
1 TTTTATTTCCTTTCTTC
8721069 CTCCTCCCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATTTCCTTTCTTCA
Found at i:8724169 original size:105 final size:105
Alignment explanation
Indices: 8723948--8724991 Score: 1656
Period size: 105 Copynumber: 9.9 Consensus size: 105
8723938 TTAAACAAGT
* * *
8723948 TCTTCTCATTACGAACTTCTTATTCTTTTATCGGATGAGTTCTTCTCATTATGAACTCTTCTGGA
1 TCTTCTCATTACGAAC--CTT-CTCCTTTA--GGACGAGTTCTTCTCATTATGAACTCTTCTGGA
* * * **
8724013 AATGTCGATTCACCTCCTTCTGGGGTCAATTTGAAAGGAACAGGC
61 AATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
* *
8724058 TCTTCTCATTATGAACCTTCTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
* * ***
8724123 TGGTTCACCTCCTTCTGCGATGGATTTGAAATGAACATAT
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
* * * *
8724163 TATTCTCATTATGAACCTTCTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATAT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
8724228 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
*
8724268 TCTTCTCATTACGAACCTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
*
8724333 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAAGC
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
*
8724373 TCTTCTCATTACGAAACTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
*
8724438 TGGTTCACCTCCTTCTGCAGTGGATTTGAAAGGAACAGGC
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
8724478 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
* * *
8724543 TGGGTCACCTCCTTCTGTGGTGGATTTGAAAGGAACAAGC
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
*
8724583 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATAT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
* *
8724648 TAGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAAAAGGC
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
* *
8724688 TCTTCTCATTACGAACATTCTCCTTTTGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
* * * * *
8724753 TGGGTCACCTCCTTCTGTGGTGGATTTGAAAGAAACAAGT
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
*
8724793 TCTTCTCATTACGAACCTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
* * *
8724858 TGGATCACCTCCTTCTGTGGTGGATTTGAAAGGAACATGC
66 TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
*
8724898 TCTTCTCATTACGAACCTTCTCTTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
1 TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
* *
8724963 TGGGTCACCTCCTTCTGTGGTGGATTTGA
66 TGGTTCACCTCCTTCTGCGGTGGATTTGA
8724992 TTGTTGTTGA
Statistics
Matches: 871, Mismatches: 63, Indels: 5
0.93 0.07 0.01
Matches are distributed among these distances:
105 847 0.97
107 6 0.01
108 3 0.00
110 15 0.02
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.37
Consensus pattern (105 bp):
TCTTCTCATTACGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT
TGGTTCACCTCCTTCTGCGGTGGATTTGAAAGGAACAGGC
Found at i:8725925 original size:8 final size:8
Alignment explanation
Indices: 8725914--8726012 Score: 105
Period size: 8 Copynumber: 12.0 Consensus size: 8
8725904 TTCTTTTTTC
8725914 TTTTCATT
1 TTTTCATT
8725922 TTTTCATTT
1 TTTTCA-TT
8725931 TTTTCATT
1 TTTTCATT
8725939 TTTTCATTTT
1 TTTTCA--TT
8725949 TTTTCATTTT
1 TTTTCA--TT
8725959 TTTTCATT
1 TTTTCATT
8725967 TTTTCATT
1 TTTTCATT
8725975 TTTT--TT
1 TTTTCATT
*
8725981 ATTTT-TTT
1 -TTTTCATT
*
8725989 TTTTCACT
1 TTTTCATT
8725997 TTTTCATT
1 TTTTCATT
8726005 TTTTCATT
1 TTTTCATT
8726013 CATTCTCTTT
Statistics
Matches: 82, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
6 2 0.02
7 8 0.10
8 46 0.56
9 8 0.10
10 18 0.22
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTCATT
Found at i:8725940 original size:28 final size:26
Alignment explanation
Indices: 8725915--8726012 Score: 102
Period size: 28 Copynumber: 3.9 Consensus size: 26
8725905 TCTTTTTTCT
8725915 TTTCATTTTTTCATTTTTTTCA-TTT
1 TTTCATTTTTTCATTTTTTTCATTTT
8725940 TTTCATTTTTTTTCATTTTTTTTCA-TTT
1 TTTCA--TTTTTTCA-TTTTTTTCATTTT
*
8725968 TTTCATTTTTT--TTATTTT--TTTT
1 TTTCATTTTTTCATTTTTTTCATTTT
*
8725990 TTTCACTTTTTCA-TTTTTTCATT
1 TTTCATTTTTTCATTTTTTTCATT
8726013 CATTCTCTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
22 13 0.21
23 11 0.18
25 7 0.11
26 6 0.10
27 8 0.13
28 17 0.27
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTCATTTTTTCATTTTTTTCATTTT
Found at i:8725949 original size:38 final size:36
Alignment explanation
Indices: 8725901--8726030 Score: 133
Period size: 37 Copynumber: 3.5 Consensus size: 36
8725891 CGAACCCTCC
8725901 TTTTTC-TTTTTTCTTTTCATTTTTTCATTTTTTTCAT
1 TTTTTCATTTTTT-TTTTCATTTTTTCA-TTTTTTCAT
8725938 TTTTTCA--TTTTTTTTCATTTTTTTTCATTTTTTCATT
1 TTTTTCATTTTTTTTTTCA--TTTTTTCATTTTTTCA-T
* *
8725975 TTTTTTATTTTTTTTTTTCACTTTTTCATTTTTTCAT
1 TTTTTCA-TTTTTTTTTTCATTTTTTCATTTTTTCAT
**
8726012 TCATTC-TCTTTTTTTTTCA
1 TTTTTCAT-TTTTTTTTTCA
8726031 AGCATAGTAC
Statistics
Matches: 80, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
35 7 0.09
36 23 0.29
37 25 0.31
38 15 0.19
40 10 0.12
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (36 bp):
TTTTTCATTTTTTTTTTCATTTTTTCATTTTTTCAT
Found at i:8725950 original size:45 final size:44
Alignment explanation
Indices: 8725901--8725987 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 44
8725891 CGAACCCTCC
*
8725901 TTTTTCTTT-TTTCTTTTCATTTTTTCATTTTTTTCATTTTTTCA
1 TTTTT-TTTATTTTTTTTCATTTTTTCATTTTTTTCATTTTTTCA
*
8725945 TTTTTTTTCATTTTTTTTCATTTTTTCATTTTTTTTATTTTTT
1 TTTTTTTT-ATTTTTTTTCATTTTTTCATTTTTTTCATTTTTT
8725988 TTTTTCACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
43 3 0.08
44 5 0.13
45 31 0.79
ACGTcount: A:0.09, C:0.10, G:0.00, T:0.80
Consensus pattern (44 bp):
TTTTTTTTATTTTTTTTCATTTTTTCATTTTTTTCATTTTTTCA
Found at i:8725990 original size:10 final size:10
Alignment explanation
Indices: 8725920--8725989 Score: 98
Period size: 10 Copynumber: 7.6 Consensus size: 10
8725910 TTTCTTTTCA
8725920 TTTTTTCA-T
1 TTTTTTCATT
8725929 TTTTTTCA--
1 TTTTTTCATT
8725937 TTTTTTCATT
1 TTTTTTCATT
8725947 TTTTTTCATT
1 TTTTTTCATT
8725957 TTTTTTCA--
1 TTTTTTCATT
8725965 TTTTTTCATT
1 TTTTTTCATT
8725975 TTTTTT-ATT
1 TTTTTTCATT
8725984 TTTTTT
1 TTTTTT
8725990 TTTCACTTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
8 16 0.28
9 17 0.30
10 24 0.42
ACGTcount: A:0.10, C:0.09, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTTCATT
Found at i:8728444 original size:61 final size:61
Alignment explanation
Indices: 8728370--8728493 Score: 239
Period size: 61 Copynumber: 2.0 Consensus size: 61
8728360 AATTGCAAAA
*
8728370 TGAATCGAGATATATAATTTAACCTTCCCAGAAAACCTCGAACTTCTTTTTGTGTACGAGG
1 TGAATCGAGATATATAATTTAACCTTCCCAAAAAACCTCGAACTTCTTTTTGTGTACGAGG
8728431 TGAATCGAGATATATAATTTAACCTTCCCAAAAAACCTCGAACTTCTTTTTGTGTACGAGG
1 TGAATCGAGATATATAATTTAACCTTCCCAAAAAACCTCGAACTTCTTTTTGTGTACGAGG
8728492 TG
1 TG
8728494 GCGGAAGATC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (61 bp):
TGAATCGAGATATATAATTTAACCTTCCCAAAAAACCTCGAACTTCTTTTTGTGTACGAGG
Found at i:8731898 original size:164 final size:164
Alignment explanation
Indices: 8731627--8731954 Score: 656
Period size: 164 Copynumber: 2.0 Consensus size: 164
8731617 GTTTAGGATC
8731627 TTATTGAACCATACCGACATGATAAAGTTGTTGGAACACCCAAATGAAGGGAGATTTGATTTCAT
1 TTATTGAACCATACCGACATGATAAAGTTGTTGGAACACCCAAATGAAGGGAGATTTGATTTCAT
8731692 CAACATCTATCTTCGTTTTTTTCCTATTCTCCTCATGGACTGCGTTCACACCTTTACCTCCATGA
66 CAACATCTATCTTCGTTTTTTTCCTATTCTCCTCATGGACTGCGTTCACACCTTTACCTCCATGA
8731757 TTCGGTAGTGGGTGTGTCGATACATCAGGTGAAT
131 TTCGGTAGTGGGTGTGTCGATACATCAGGTGAAT
8731791 TTATTGAACCATACCGACATGATAAAGTTGTTGGAACACCCAAATGAAGGGAGATTTGATTTCAT
1 TTATTGAACCATACCGACATGATAAAGTTGTTGGAACACCCAAATGAAGGGAGATTTGATTTCAT
8731856 CAACATCTATCTTCGTTTTTTTCCTATTCTCCTCATGGACTGCGTTCACACCTTTACCTCCATGA
66 CAACATCTATCTTCGTTTTTTTCCTATTCTCCTCATGGACTGCGTTCACACCTTTACCTCCATGA
8731921 TTCGGTAGTGGGTGTGTCGATACATCAGGTGAAT
131 TTCGGTAGTGGGTGTGTCGATACATCAGGTGAAT
8731955 CAAATTGCAA
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
164 164 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (164 bp):
TTATTGAACCATACCGACATGATAAAGTTGTTGGAACACCCAAATGAAGGGAGATTTGATTTCAT
CAACATCTATCTTCGTTTTTTTCCTATTCTCCTCATGGACTGCGTTCACACCTTTACCTCCATGA
TTCGGTAGTGGGTGTGTCGATACATCAGGTGAAT
Found at i:8746259 original size:15 final size:15
Alignment explanation
Indices: 8746239--8746268 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
8746229 TTAATTATCC
8746239 ACGCTATTCTAAAAA
1 ACGCTATTCTAAAAA
8746254 ACGCTATTCTAAAAA
1 ACGCTATTCTAAAAA
8746269 TGAGAGCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (15 bp):
ACGCTATTCTAAAAA
Found at i:8747273 original size:12 final size:12
Alignment explanation
Indices: 8747256--8747284 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
8747246 GAGGAGGAGG
8747256 AGAAGAGGAAGA
1 AGAAGAGGAAGA
8747268 AGAAGAGGAAGA
1 AGAAGAGGAAGA
8747280 AGAAG
1 AGAAG
8747285 GGGGTTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (12 bp):
AGAAGAGGAAGA
Found at i:8747966 original size:3 final size:3
Alignment explanation
Indices: 8747954--8747983 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
8747944 TTATTATAAA
8747954 ATT ATAT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT AT
8747984 AAATAAACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:8748176 original size:17 final size:17
Alignment explanation
Indices: 8748154--8748206 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
8748144 ATTGCCGCCA
8748154 CTGCCACCTCCTGCATT
1 CTGCCACCTCCTGCATT
*
8748171 CTGCCA-CTAC--CA--
1 CTGCCACCTCCTGCATT
*
8748183 CTGCCACCTCTTGCATT
1 CTGCCACCTCCTGCATT
8748200 CTGCCAC
1 CTGCCAC
8748207 TACCACTGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 10
0.68 0.07 0.24
Matches are distributed among these distances:
12 6 0.21
13 2 0.07
14 2 0.07
15 2 0.07
16 3 0.11
17 13 0.46
ACGTcount: A:0.15, C:0.47, G:0.11, T:0.26
Consensus pattern (17 bp):
CTGCCACCTCCTGCATT
Found at i:8748185 original size:29 final size:29
Alignment explanation
Indices: 8748151--8748218 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
8748141 GCTATTGCCG
8748151 CCACTGCCACCTCCTGCATTCTGCCACTA
1 CCACTGCCACCTCCTGCATTCTGCCACTA
*
8748180 CCACTGCCACCTCTTGCATTCTGCCACTA
1 CCACTGCCACCTCCTGCATTCTGCCACTA
8748209 CCACTGCCAC
1 CCACTGCCAC
8748219 AAGGGATAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.18, C:0.49, G:0.10, T:0.24
Consensus pattern (29 bp):
CCACTGCCACCTCCTGCATTCTGCCACTA
Found at i:8749257 original size:25 final size:26
Alignment explanation
Indices: 8749229--8749284 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 26
8749219 TTTTTGGTTG
** *
8749229 TTTTTACTATTTTTATTATTTGTT-A
1 TTTTTACTAAGTTTATTATTAGTTAA
* *
8749254 TTTTAATTAAGTTTATTATTAGTTAA
1 TTTTTACTAAGTTTATTATTAGTTAA
8749280 TTTTT
1 TTTTT
8749285 TTCATAATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (26 bp):
TTTTTACTAAGTTTATTATTAGTTAA
Found at i:8752699 original size:22 final size:22
Alignment explanation
Indices: 8752669--8752720 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
8752659 GACAAATAAA
*
8752669 AAAATTAAAAATAGTAA-AAACAT
1 AAAA-TAAAAATA-AAACAAACAT
*
8752692 AGAATAAAAATAAAACAAACAT
1 AAAATAAAAATAAAACAAACAT
8752714 AAAATAA
1 AAAATAA
8752721 GGACCTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 20 0.80
23 3 0.12
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.17
Consensus pattern (22 bp):
AAAATAAAAATAAAACAAACAT
Found at i:8752935 original size:5 final size:5
Alignment explanation
Indices: 8752900--8752931 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
8752890 AAATAGTGAT
*
8752900 TAAAA TAAAA TAAAA TAAAA TAAAA TAGAA TA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA
8752932 GAATGATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:8754289 original size:61 final size:61
Alignment explanation
Indices: 8754219--8754362 Score: 216
Period size: 61 Copynumber: 2.4 Consensus size: 61
8754209 CGAGTGAGGT
* * *
8754219 GTTGTTGATTCGAAATGTTGTGTGAATTGAGCAAAAGAAATGCCATCCCTTTTGGTGGGGC
1 GTTGTTGATTCGAAATGTTGTGTGAATTGAGAAAAAGAAATGCCATCCCCTCTGGTGGGGC
* **
8754280 GTTGTTGATTCAAAATGTTGTGTGAATTGAGAAAAAGAAATGTTATCCCCTCTGGTGGGGC
1 GTTGTTGATTCGAAATGTTGTGTGAATTGAGAAAAAGAAATGCCATCCCCTCTGGTGGGGC
* *
8754341 GTTGATGATTCGAAGTGTTGTG
1 GTTGTTGATTCGAAATGTTGTG
8754363 AATTAAGCAA
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 74 1.00
ACGTcount: A:0.25, C:0.11, G:0.30, T:0.34
Consensus pattern (61 bp):
GTTGTTGATTCGAAATGTTGTGTGAATTGAGAAAAAGAAATGCCATCCCCTCTGGTGGGGC
Found at i:8754651 original size:42 final size:41
Alignment explanation
Indices: 8754545--8754651 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 41
8754535 GGTCTTATGG
* * *
8754545 ATGGCCCGTAGGACTTATCATCTTGCTCAAAAGACTTATAT
1 ATGGCCCGAAGGATTTATCATCATGCTCAAAAGACTTATAT
* * * *
8754586 ATGACCCGAAGTATTTAAGCATCATGCTCGAAAGACTTACTA-
1 ATGGCCCGAAGGATTT-ATCATCATGCTCAAAAGACTTA-TAT
8754628 ATGGCCCGAAGGATTTACTCATCA
1 ATGGCCCGAAGGATTTA-TCATCA
8754652 AGAAACCCTT
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
41 13 0.25
42 38 0.72
43 2 0.04
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (41 bp):
ATGGCCCGAAGGATTTATCATCATGCTCAAAAGACTTATAT
Found at i:8754736 original size:38 final size:38
Alignment explanation
Indices: 8754684--8754836 Score: 216
Period size: 38 Copynumber: 4.0 Consensus size: 38
8754674 TAGTTTCTTA
* *
8754684 AAATCTTTTATTTCGAGCGAAACTATCTCAAGCGAGAT
1 AAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGAT
* *
8754722 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGTGAGAT
1 AAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGAT
* * *
8754760 AAATCTTCTTTTTCAAGTGAAACTATCTCAAACGAGAT
1 AAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGAT
* *
8754798 AAAGTCTTCTATTTCGAGTAAAACTATCTCAAGTGAGAT
1 AAA-TCTTCTATTTCGAGTGAAACTATCTCAAGCGAGAT
8754837 GTTGATCCCT
Statistics
Matches: 101, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
38 71 0.70
39 30 0.30
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (38 bp):
AAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGAT
Found at i:8755257 original size:52 final size:57
Alignment explanation
Indices: 8755141--8755337 Score: 185
Period size: 52 Copynumber: 3.5 Consensus size: 57
8755131 TTTTCAGTTG
* * * * *
8755141 TCATAAAGAAACCCTTAAAAATTAGGATTAGCTTCTTTTAAAAATTCTTTTGAGATAA
1 TCATCAAGAAACCCCTAAAAATTAGGATTAGC-TCTTCTAAAAACTCATTTGAGATAA
**
8755199 TCATCAAGAAACCCCTGGAAATTAGGATTAG-T-TTCTAAAAACTCATTTGA-A-AA
1 TCATCAAGAAACCCCTAAAAATTAGGATTAGCTCTTCTAAAAACTCATTTGAGATAA
* * * * *
8755252 -CATCAAGAAACCCCTAAAAATTAGGCTT--CTTCTTTTAAAAATTCA-TTGAAAATCA
1 TCATCAAGAAACCCCTAAAAATTAGGATTAGC-TCTTCTAAAAACTCATTTG-AGATAA
* *
8755307 TCATCAAGAAACCCCTAAAAATCAGGCTTAG
1 TCATCAAGAAACCCCTAAAAATTAGGATTAG
8755338 TTTCTTTAAA
Statistics
Matches: 116, Mismatches: 14, Indels: 18
0.78 0.09 0.12
Matches are distributed among these distances:
52 29 0.25
53 14 0.12
54 2 0.02
55 16 0.14
56 28 0.24
58 27 0.23
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.30
Consensus pattern (57 bp):
TCATCAAGAAACCCCTAAAAATTAGGATTAGCTCTTCTAAAAACTCATTTGAGATAA
Found at i:8755316 original size:108 final size:109
Alignment explanation
Indices: 8755146--8755342 Score: 281
Period size: 108 Copynumber: 1.8 Consensus size: 109
8755136 AGTTGTCATA
* * *
8755146 AAGAAACCCTTAAAAATTAGGATTAGCTTCTTTTAAAAATTCTTTTGAGATAATCATCAAGAAAC
1 AAGAAACCCCTAAAAATTAGGATTA-CTTCTTTTAAAAATTCTATTGAAATAATCATCAAGAAAC
** *
8755211 CCCTGGAAATTAGGATTAGTTTCTAAAAACTCATTTGAAAACATC
65 CCCTAAAAATCAGGATTAGTTTCTAAAAACTCATTTGAAAACATC
* *
8755256 AAGAAACCCCTAAAAATTAGGCTT-CTTCTTTTAAAAATTC-ATTGAAAATCATCATCAAGAAAC
1 AAGAAACCCCTAAAAATTAGGATTACTTCTTTTAAAAATTCTATTG-AAATAATCATCAAGAAAC
*
8755319 CCCTAAAAATCAGGCTTAGTTTCT
65 CCCTAAAAATCAGGATTAGTTTCT
8755343 TTAAAAATTC
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 3 0.04
108 52 0.68
110 22 0.29
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.31
Consensus pattern (109 bp):
AAGAAACCCCTAAAAATTAGGATTACTTCTTTTAAAAATTCTATTGAAATAATCATCAAGAAACC
CCTAAAAATCAGGATTAGTTTCTAAAAACTCATTTGAAAACATC
Found at i:8757609 original size:2 final size:2
Alignment explanation
Indices: 8757602--8757633 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8757592 AACAAAAGGG
8757602 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8757634 TTGAAAGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8775389 original size:60 final size:60
Alignment explanation
Indices: 8775290--8775776 Score: 670
Period size: 60 Copynumber: 8.1 Consensus size: 60
8775280 AAATATATTG
* * * * * * *
8775290 TTTTCCTCTAGCTTGCATAAGTGGTACCTTTCTTCCAAAATGCACCATTACGCATTTAAC
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACCGTTAGGCATTTAAC
* * * *
8775350 TTTTCATCTAAC-TGTCATTAGTGGTACATTTCTATCAAAATGCACTGTTAGGCATTTAAC
1 TTTTCATCTAACTTG-CATTAGTGGCACCTTTCTACCAAAATGCACCGTTAGGCATTTAAC
* * *
8775410 TTTTCATCTAACTTGAATTAGTGGCACCTTTCTGCCAAAATGCACCGTTAGCCATTTAAC
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACCGTTAGGCATTTAAC
* *
8775470 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACTGTTAGGCATTTAAC
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACCGTTAGGCATTTAAC
* *
8775530 TTTTCATCTAACTTGCATTAGTGGCACCTTTTTACCAAAATGCACAGTTAGGCATTTAAC
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACCGTTAGGCATTTAAC
* * * * * *
8775590 TTTTTATCTAACTTGCATTAGAGGTAACTTTCTGCCAAAATGCACCATTAGGCATTTAAC
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACCGTTAGGCATTTAAC
* ** *
8775650 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTACCAAAATTCATTGTTAGGTATTTAAC
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACCGTTAGGCATTTAAC
* * * *
8775710 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACAGTTAGGAATTTGAT
1 TTTTCATCTAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACCGTTAGGCATTTAAC
8775770 TTTTCAT
1 TTTTCAT
8775777 TTTAGAGCAG
Statistics
Matches: 379, Mismatches: 46, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
59 2 0.01
60 375 0.99
61 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (60 bp):
TTTTCATCTAACTTGCATTAGTGGCACCTTTCTACCAAAATGCACCGTTAGGCATTTAAC
Found at i:8779360 original size:19 final size:19
Alignment explanation
Indices: 8779319--8779361 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
8779309 GGTCAACTCT
**
8779319 AGTCAAAGTCAACAGGTTG
1 AGTCAAAGTCAACAGGTCA
8779338 AGTCAAAGTCAAC-GTGTCA
1 AGTCAAAGTCAACAG-GTCA
8779357 AGTCA
1 AGTCA
8779362 GGTTGACTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (19 bp):
AGTCAAAGTCAACAGGTCA
Found at i:8779383 original size:15 final size:15
Alignment explanation
Indices: 8779363--8779413 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
8779353 GTCAAGTCAG
8779363 GTTGACTCTGTTCGA
1 GTTGACTCTGTTCGA
** *
8779378 GTTGACTC--AACGG
1 GTTGACTCTGTTCGA
8779391 GTTGACTCTGTTCGA
1 GTTGACTCTGTTCGA
8779406 GTTGACTC
1 GTTGACTC
8779414 AACGGGTTGA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
13 10 0.36
15 18 0.64
ACGTcount: A:0.16, C:0.22, G:0.27, T:0.35
Consensus pattern (15 bp):
GTTGACTCTGTTCGA
Found at i:8779396 original size:13 final size:13
Alignment explanation
Indices: 8779375--8779463 Score: 101
Period size: 13 Copynumber: 6.8 Consensus size: 13
8779365 TGACTCTGTT
8779375 CGAGTTGACTCAA
1 CGAGTTGACTCAA
* **
8779388 CGGGTTGACTCTGTT
1 CGAGTTGACTC--AA
8779403 CGAGTTGACTCAA
1 CGAGTTGACTCAA
*
8779416 CGGGTTGACTC-A
1 CGAGTTGACTCAA
8779428 CGAGTTGACTCAA
1 CGAGTTGACTCAA
*
8779441 CGGGTTGACTC-A
1 CGAGTTGACTCAA
8779453 CGAGTTGACTC
1 CGAGTTGACTC
8779464 GACTGACTCA
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
12 22 0.35
13 31 0.49
15 10 0.16
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (13 bp):
CGAGTTGACTCAA
Found at i:8779402 original size:28 final size:28
Alignment explanation
Indices: 8779362--8779451 Score: 150
Period size: 28 Copynumber: 3.3 Consensus size: 28
8779352 TGTCAAGTCA
8779362 GGTTGACTCTGTTCGAGTTGACTCAACG
1 GGTTGACTCTGTTCGAGTTGACTCAACG
8779390 GGTTGACTCTGTTCGAGTTGACTCAACG
1 GGTTGACTCTGTTCGAGTTGACTCAACG
*
8779418 GGTTGACTC---ACGAGTTGACTCAACG
1 GGTTGACTCTGTTCGAGTTGACTCAACG
8779443 GGTTGACTC
1 GGTTGACTC
8779452 ACGAGTTGAC
Statistics
Matches: 61, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
25 24 0.39
28 37 0.61
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (28 bp):
GGTTGACTCTGTTCGAGTTGACTCAACG
Found at i:8779437 original size:25 final size:25
Alignment explanation
Indices: 8779375--8779463 Score: 142
Period size: 25 Copynumber: 3.4 Consensus size: 25
8779365 TGACTCTGTT
*
8779375 CGAGTTGACTCAACGGGTTGACTCTGTT
1 CGAGTTGACTCAACGGGTTGACTC---A
8779403 CGAGTTGACTCAACGGGTTGACTCA
1 CGAGTTGACTCAACGGGTTGACTCA
8779428 CGAGTTGACTCAACGGGTTGACTCA
1 CGAGTTGACTCAACGGGTTGACTCA
8779453 CGAGTTGACTC
1 CGAGTTGACTC
8779464 GACTGACTCA
Statistics
Matches: 60, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
25 36 0.60
28 24 0.40
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (25 bp):
CGAGTTGACTCAACGGGTTGACTCA
Found at i:8783791 original size:31 final size:31
Alignment explanation
Indices: 8783753--8783877 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
8783743 CCCAAAGGAC
* * *
8783753 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
8783784 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
8783815 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
8783846 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
8783877 C
1 C
8783878 CCTCGACCCT
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:8788280 original size:31 final size:31
Alignment explanation
Indices: 8788257--8788366 Score: 193
Period size: 31 Copynumber: 3.5 Consensus size: 31
8788247 CATAGATTCT
* *
8788257 GAAGAACCTAGGTAATCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
8788288 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
8788319 GAAGAACATAGGTAAACAGTCCATATGTTCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
8788350 GAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
8788367 CCTCGACCCT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:8795967 original size:5 final size:5
Alignment explanation
Indices: 8795946--8796123 Score: 247
Period size: 5 Copynumber: 35.2 Consensus size: 5
8795936 ATAGAAACAA
8795946 ATAA- ATAAT ATTAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT A-TAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
8795996 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* * *
8796046 ATAAT ATAAT ATAAT ATAAT A-AAT CTAAA ATAAT AATAAT ACTATAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT A-TA-AT
8796093 ATAAT ATATAT ATATAT ATAAT A-AAT A-AAT A
1 ATAAT ATA-AT ATA-AT ATAAT ATAAT ATAAT A
8796124 ATATATACAC
Statistics
Matches: 161, Mismatches: 6, Indels: 14
0.89 0.03 0.08
Matches are distributed among these distances:
4 15 0.09
5 119 0.74
6 25 0.16
7 2 0.01
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:8796083 original size:17 final size:18
Alignment explanation
Indices: 8795946--8796130 Score: 76
Period size: 18 Copynumber: 10.2 Consensus size: 18
8795936 ATAGAAACAA
*
8795946 ATAAATAATATTAATA-T
1 ATAAATAATAATAATACT
*
8795963 AATATAAT-ATAAT-ATAAT
1 -ATA-AATAATAATAATACT
8795981 ATAATATAAT-ATAATA-T
1 ATAA-ATAATAATAATACT
*
8795998 AATATAAT-ATAAT-ATAAT
1 -ATA-AATAATAATAATACT
8796016 ATAATATAAT-ATAATA-T
1 ATAA-ATAATAATAATACT
*
8796033 AATATAAT-ATAAT-ATAAT
1 -ATA-AATAATAATAATACT
8796051 ATAATATAAT-ATAATAAATCT
1 ATAA-ATAATAATAAT--A-CT
8796072 A-AAATAATAATAATACT
1 ATAAATAATAATAATACT
8796089 ATAAATAATATATATATA-T
1 ATAAATAATA-ATA-ATACT
8796108 ATATAATAAATAAATAATA-T
1 ATA-AAT-AAT-AATAATACT
8796128 ATA
1 ATA
8796131 CACTATATTT
Statistics
Matches: 136, Mismatches: 2, Indels: 56
0.70 0.01 0.29
Matches are distributed among these distances:
16 3 0.02
17 39 0.29
18 47 0.35
19 17 0.12
20 21 0.15
21 8 0.06
22 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAATAATAATAATACT
Found at i:8796178 original size:29 final size:29
Alignment explanation
Indices: 8796124--8796179 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
8796114 TAAATAAATA
*
8796124 ATATATACACTATATTTATTTTAAAAACT
1 ATATATACACTATATTAATTTTAAAAACT
8796153 ATATA-ACA-TATATTAAATTTTCAAAAA
1 ATATATACACTATATT-AATTTT-AAAAA
8796180 AAATAATATG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 6 0.25
28 8 0.33
29 10 0.42
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (29 bp):
ATATATACACTATATTAATTTTAAAAACT
Found at i:8796277 original size:16 final size:16
Alignment explanation
Indices: 8796252--8796282 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8796242 CCATATATAT
*
8796252 TATATTTTTTCAAAAC
1 TATATATTTTCAAAAC
8796268 TATATATTTTCAAAA
1 TATATATTTTCAAAA
8796283 ATTACATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
TATATATTTTCAAAAC
Found at i:8797997 original size:23 final size:24
Alignment explanation
Indices: 8797970--8798014 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
8797960 ACTCCCTTTT
8797970 TTTC-TTTTGCTCTTTTTTTTTAA
1 TTTCTTTTTGCTCTTTTTTTTTAA
*
8797993 TTTCTTTTTTCTCTTTTTTTTT
1 TTTCTTTTTGCTCTTTTTTTTT
8798015 GAGTTGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.80
Consensus pattern (24 bp):
TTTCTTTTTGCTCTTTTTTTTTAA
Found at i:8815804 original size:54 final size:54
Alignment explanation
Indices: 8815729--8816178 Score: 580
Period size: 54 Copynumber: 8.3 Consensus size: 54
8815719 TACCGAATGA
* * *
8815729 GCACTATGTGTGGAACGTAAGAAATTCATAATAAGTTTATGAATTTTCGAATTG
1 GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTG
*
8815783 GCACTATGTGTGCAACCTAAGAAATTCATTATAAGTTTATGAATTTTCGTATTG
1 GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTG
8815837 GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAA-TTTCTGTATTG
1 GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTC-GTATTG
* * *
8815891 GCACTATGTGTGTAACCAAAGAAAATCATAATAAGTTTATGAATTTTCGTATTG
1 GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTG
* * * *
8815945 TCACTATGTGTACAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTG
1 GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTG
* *
8815999 GCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTTTGTATTG
1 GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTG
** * * * * * *
8816053 GCACTATAAGTACAACCCCCATGAAACTCATAATGAGTTTATGAA-TTTCATTATTG
1 GCACTATGTGTGCAA--CCTAAGAAATTCATAATAAGTTTATGAATTTTC-GTATTG
* * * * * * *
8816109 GCACTATGTATGCAACCTCATGTACTTCATAATGAGTTTATGAATTATCGTATCG
1 GCACTATGTGTGCAACCT-AAGAAATTCATAATAAGTTTATGAATTTTCGTATTG
*
8816164 GCACTAAGTGTGCAA
1 GCACTATGTGTGCAA
8816179 AAACCATGGA
Statistics
Matches: 349, Mismatches: 40, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
53 4 0.01
54 255 0.73
55 46 0.13
56 44 0.13
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (54 bp):
GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTG
Found at i:8822420 original size:5 final size:5
Alignment explanation
Indices: 8822377--8822401 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
8822367 GTTAAACAAT
8822377 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
8822402 GATCATGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:8823520 original size:24 final size:24
Alignment explanation
Indices: 8823493--8823544 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
8823483 CTTCCTTTGA
8823493 TGGGCTCCCATCGGGTTTGCTTGC
1 TGGGCTCCCATCGGGTTTGCTTGC
8823517 TGGGCTCCCATCGGGTTTGCTTGC
1 TGGGCTCCCATCGGGTTTGCTTGC
8823541 TGGG
1 TGGG
8823545 TCAGGCTTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.04, C:0.27, G:0.37, T:0.33
Consensus pattern (24 bp):
TGGGCTCCCATCGGGTTTGCTTGC
Found at i:8823709 original size:21 final size:21
Alignment explanation
Indices: 8823638--8823791 Score: 76
Period size: 21 Copynumber: 7.4 Consensus size: 21
8823628 AAAATAATAT
*
8823638 TAATAATAATATAATGTACTATA
1 TAAT-ATAAGATAA-GTACTATA
*
8823661 TAATAAATAGATAAGTACTATA
1 TAATATA-AGATAAGTACTATA
8823683 -ACATATAAGATAAGTA-TATA
1 TA-ATATAAGATAAGTACTATA
*
8823703 CTAATATAATATAA-TA-TA-A
1 -TAATATAAGATAAGTACTATA
* * *
8823722 TACTATAATAATAA-TAATATA
1 TAATATAA-GATAAGTACTATA
8823743 TAATATATAG-TATA-TA-TATA
1 TAATATA-AGATA-AGTACTATA
* * *
8823763 TACTATAATATATA-TAATATA
1 TAATATAAGATA-AGTACTATA
8823784 TAATATAA
1 TAATATAA
8823792 TAAGATGTAA
Statistics
Matches: 109, Mismatches: 11, Indels: 24
0.76 0.08 0.17
Matches are distributed among these distances:
18 7 0.06
19 8 0.07
20 28 0.26
21 41 0.38
22 16 0.15
23 9 0.08
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (21 bp):
TAATATAAGATAAGTACTATA
Found at i:8823712 original size:5 final size:5
Alignment explanation
Indices: 8823685--8823882 Score: 93
Period size: 5 Copynumber: 40.0 Consensus size: 5
8823675 GTACTATAAC
* *
8823685 ATATA AGATA AGTAT- ATACTA ATATA ATATA ATAT- A-ATA CTATA ATAATA
1 ATATA ATATA A-TATA ATA-TA ATATA ATATA ATATA ATATA ATATA AT-ATA
*
8823735 ATA-A TATATA ATAT- ATAGT- ATATA TATATA CTATA ATAT- ATATAA
1 ATATA -ATATA ATATA ATA-TA ATATA -ATATA ATATA ATATA ATAT-A
* * *
8823780 TATATA ATATA ATA-A GATGTA ATA-A ATAT- ATTTA CTATA ATAT- ATA-A
1 -ATATA ATATA ATATA -ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* *
8823827 TATATA ATAT- A-ATA CTATA ATAATA ATATA CTATATA ATACA ATAT-
1 -ATATA ATATA ATATA ATATA AT-ATA ATATA --ATATA ATATA ATATA
*
8823873 ATATA CTATA
1 ATATA ATATA
8823883 TACCATAATA
Statistics
Matches: 149, Mismatches: 17, Indels: 54
0.68 0.08 0.25
Matches are distributed among these distances:
3 4 0.03
4 28 0.19
5 84 0.56
6 24 0.16
7 9 0.06
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:8823792 original size:21 final size:21
Alignment explanation
Indices: 8823631--8823896 Score: 127
Period size: 23 Copynumber: 12.0 Consensus size: 21
8823621 AAACCAAAAA
8823631 ATAATAT-TAATAATAATATAAT
1 ATAATATATAAT-ATAATAT-AT
* * *
8823653 GTACTATATAATA-AATAGAT
1 ATAATATATAATATAATATAT
* *
8823673 A-AGTACTATAACATATAAGATA-
1 ATAATA-TAT-A-ATATAATATAT
8823695 AGT-ATATACTAATATAATATAAT
1 A-TAATATA-TAATATAATAT-AT
8823718 ATAATACTATAATAATAATAATAT
1 ATAATA-TATAAT-ATAAT-ATAT
*
8823742 ATAATATATAGTAT-ATATAT
1 ATAATATATAATATAATATAT
*
8823762 AT-A-CTATAATATATATAATAT
1 ATAATATATAATATA-AT-ATAT
* *
8823783 ATAATATAATAAGATGTAATAAAT
1 ATAATAT-AT-A-ATATAATATAT
*
8823807 ATATTTACTATAATAT-ATAATAT
1 ATA-ATA-TATAATATAAT-ATAT
*
8823830 ATAATATAATACTATAATAATAAT
1 ATAATAT-ATAATATAAT-AT-AT
* *
8823854 ATACTATATAATACAATATAT
1 ATAATATATAATATAATATAT
* **
8823875 ATACTATATACCATAATATAT
1 ATAATATATAATATAATATAT
8823896 A
1 A
8823897 CTATTACAGA
Statistics
Matches: 190, Mismatches: 26, Indels: 57
0.70 0.10 0.21
Matches are distributed among these distances:
18 7 0.04
19 4 0.02
20 13 0.07
21 43 0.23
22 30 0.16
23 47 0.25
24 32 0.17
25 9 0.05
26 5 0.03
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (21 bp):
ATAATATATAATATAATATAT
Found at i:8823885 original size:7 final size:7
Alignment explanation
Indices: 8823711--8823884 Score: 122
Period size: 7 Copynumber: 23.7 Consensus size: 7
8823701 TACTAATATA
8823711 ATATAAT
1 ATATAAT
*
8823718 ATAATACT
1 AT-ATAAT
8823726 ATAATAAT
1 AT-ATAAT
8823734 A-ATAAT
1 ATATAAT
8823740 ATATAAT
1 ATATAAT
*
8823747 ATATAGT
1 ATATAAT
8823754 ATAT-AT
1 ATATAAT
*
8823760 ATATACT
1 ATATAAT
8823767 ATA-ATAT
1 ATATA-AT
8823774 ATATAAT
1 ATATAAT
8823781 ATATAAT
1 ATATAAT
*
8823788 ATAATAAG
1 AT-ATAAT
*
8823796 ATGTAAT
1 ATATAAT
*
8823803 AAATATATTT
1 --ATATA-AT
8823813 ACTATAAT
1 A-TATAAT
8823821 ATATAAT
1 ATATAAT
8823828 ATATAAT
1 ATATAAT
*
8823835 ATAATACT
1 AT-ATAAT
8823843 ATAATAAT
1 AT-ATAAT
*
8823851 AATATACT
1 -ATATAAT
8823859 ATATAAT
1 ATATAAT
*
8823866 ACA-ATAT
1 ATATA-AT
*
8823873 ATATACT
1 ATATAAT
8823880 ATATA
1 ATATA
8823885 CCATAATATA
Statistics
Matches: 134, Mismatches: 19, Indels: 28
0.74 0.10 0.15
Matches are distributed among these distances:
6 13 0.10
7 72 0.54
8 38 0.28
9 10 0.07
10 1 0.01
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (7 bp):
ATATAAT
Found at i:8823894 original size:38 final size:33
Alignment explanation
Indices: 8823706--8823875 Score: 74
Period size: 34 Copynumber: 5.2 Consensus size: 33
8823696 GTATATACTA
8823706 ATATAATAT--AATATAATACTATAATAATAATAAT
1 ATATAATATACAATATAATAC--T-ATAATAATAAT
* *
8823740 ATATAATATATAGTATATATA-TATACTATAAT-AT
1 ATATAATATACAATATA-ATACTATA--ATAATAAT
* * *
8823774 ATATAATATATAATATAATAAGATGTAATAA-ATAT
1 ATATAATATACAATATAAT-A-CTATAATAATA-AT
* *
8823809 ATTTACTATA-ATATATAATA-TATAAT-ATAAT
1 ATATAATATACA-ATATAATACTATAATAATAAT
* * *
8823840 ACTATAATA-ATAATATACTA-TATAAT-ACAAT
1 A-TATAATATACAATATAATACTATAATAATAAT
8823871 ATATA
1 ATATA
8823876 TACTATATAC
Statistics
Matches: 112, Mismatches: 10, Indels: 32
0.73 0.06 0.21
Matches are distributed among these distances:
30 4 0.04
31 23 0.21
32 12 0.11
33 5 0.04
34 35 0.31
35 22 0.20
36 8 0.07
37 3 0.03
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (33 bp):
ATATAATATACAATATAATACTATAATAATAAT
Found at i:8824135 original size:16 final size:15
Alignment explanation
Indices: 8824094--8824135 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
8824084 ATATAATTCG
8824094 GAGAGATAAAAAGAA
1 GAGAGATAAAAAGAA
8824109 GAAGAGA-AAAAAGATA
1 G-AGAGATAAAAAGA-A
*
8824125 GAGAAATAAAA
1 GAGAGATAAAA
8824136 GAAATCGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07
Consensus pattern (15 bp):
GAGAGATAAAAAGAA
Found at i:8824960 original size:5 final size:5
Alignment explanation
Indices: 8824952--8825087 Score: 272
Period size: 5 Copynumber: 27.2 Consensus size: 5
8824942 AACATAAACA
8824952 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
8825002 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
8825052 ATATT ATATT ATATT ATATT ATATT ATATT ATATT A
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT A
8825088 AAAATTTTAA
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 131 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:8825540 original size:5 final size:5
Alignment explanation
Indices: 8825462--8825534 Score: 146
Period size: 5 Copynumber: 14.6 Consensus size: 5
8825452 ATGCACGTGG
8825462 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
8825512 TATTA TATTA TATTA TATTA TAT
1 TATTA TATTA TATTA TATTA TAT
8825535 ATTATAATAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 68 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:8825858 original size:455 final size:453
Alignment explanation
Indices: 8825008--8825918 Score: 1734
Period size: 455 Copynumber: 2.0 Consensus size: 453
8824998 TATTATATTA
8825008 TATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTA
1 TATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTA
* *
8825073 TATTATATTATATTAAAAATTTTAAAAAAAATACATGTTTTTAACTTGGTTTTGCGATTAAGTAT
66 TATTATATTATATAAAAAATTTAAAAAAAAATACATGTTTTTAACTTGGTTTTGCGATTAAGTAT
*
8825138 GGGATTTTCAATCTCAAAAGGTGAAGTTCAAGTTCGTGATTTGTATTTTTTTTTTTAATCTCATC
131 GGGATTTTCAATCTCAAAAGGTGAAGTTCAAGTTCGTGATTTGCA-TTTTTTTTTTAATCTCATC
8825203 TTTTCAATGAAATGATAATATGTATCGTATCATTGGATGAAAAAAATAAAATTAATTTGATAAAA
195 TTTTCAATGAAATGATAATATGTATCGTATCATTGGATGAAAAAAATAAAATTAATTTGATAAAA
*
8825268 AATTTACTCACGTTATATAGAGAAAATGTGAGATGGGTGATTTTTATTGGTTGAGAGTTGAGACT
260 AATTTACTCACGTGATATAGAGAAAATGTGAGATGGGTGATTTTTATTGGTTGAGAGTTGAGACT
*
8825333 ATGAATGATGTGGTGAACAAGGTTCATGTAATAATTTTTCTTGCGTTGGACATGTGACCTGTGAC
325 ATGAATGATGTGGTGAACAAGGTTCATGTAATAATTTTTCTTGCGTTGGACATGTGACCTATGAC
8825398 ACGTGACATGTCATCCCTTTATATATATATGATATGTACCATATCATGACTTATATGCACGTGG
390 ACGTGACATGTCATCCCTTTATATATATATGATATGTACCATATCATGACTTATATGCACGTGG
8825462 TATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTA
1 TATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTA
8825527 TATTATATATTATAATAAAAAATTTAAAAAAAAATACATGTTTTTAACTTGGTTTTGCGATTAAG
66 TA-T-TATATTAT-ATAAAAAATTTAAAAAAAAATACATGTTTTTAACTTGGTTTTGCGATTAAG
8825592 TATGGGATTTTCAATCTCAAAAGGTGAAGTTCAAGTTCGTGATTTGCA-TTTTTTTTTAATCTCA
128 TATGGGATTTTCAATCTCAAAAGGTGAAGTTCAAGTTCGTGATTTGCATTTTTTTTTTAATCTCA
8825656 TCTTTTCAATGAAATGATAATATGTATCGTATCATTGGATGAAAAAAATAAAATTAATTTGATAA
193 TCTTTTCAATGAAATGATAATATGTATCGTATCATTGGATGAAAAAAATAAAATTAATTTGATAA
8825721 AAAATTTACTCACGTGATATAGAGAAAATGTGAGATGGGTGATTTTTATTGGTTGAGAGTTGAGA
258 AAAATTTACTCACGTGATATAGAGAAAATGTGAGATGGGTGATTTTTATTGGTTGAGAGTTGAGA
8825786 CTATGAATGATGTGGTGAACAAGGTTCATGTAATAATTTTTCTTGCGTTGGACATGTGACCTATG
323 CTATGAATGATGTGGTGAACAAGGTTCATGTAATAATTTTTCTTGCGTTGGACATGTGACCTATG
8825851 ACACGTGACATGTCATCCCTTTATATATATATGATATGTACCATATCATGACTTATATGCACGTG
388 ACACGTGACATGTCATCCCTTTATATATATATGATATGTACCATATCATGACTTATATGCACGTG
8825916 G
453 G
8825917 TA
1 TA
8825919 GTCTCAAGTT
Statistics
Matches: 449, Mismatches: 5, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
454 67 0.15
455 278 0.62
456 8 0.02
457 96 0.21
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (453 bp):
TATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTA
TATTATATTATATAAAAAATTTAAAAAAAAATACATGTTTTTAACTTGGTTTTGCGATTAAGTAT
GGGATTTTCAATCTCAAAAGGTGAAGTTCAAGTTCGTGATTTGCATTTTTTTTTTAATCTCATCT
TTTCAATGAAATGATAATATGTATCGTATCATTGGATGAAAAAAATAAAATTAATTTGATAAAAA
ATTTACTCACGTGATATAGAGAAAATGTGAGATGGGTGATTTTTATTGGTTGAGAGTTGAGACTA
TGAATGATGTGGTGAACAAGGTTCATGTAATAATTTTTCTTGCGTTGGACATGTGACCTATGACA
CGTGACATGTCATCCCTTTATATATATATGATATGTACCATATCATGACTTATATGCACGTGG
Found at i:8826146 original size:4 final size:4
Alignment explanation
Indices: 8826139--8826176 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
8826129 AGTTAGATAG
*
8826139 AGTT AGTT AGTT AGTT AGTT AGTT AGGT A-TT A-TT AGTT
1 AGTT AGTT AGTT AGTT AGTT AGTT AGTT AGTT AGTT AGTT
8826177 TGTGTATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 5 0.16
4 26 0.84
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
AGTT
Found at i:8829495 original size:2 final size:2
Alignment explanation
Indices: 8829488--8829517 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
8829478 TCCGGAAAAC
*
8829488 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8829518 TATTCAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8833115 original size:14 final size:13
Alignment explanation
Indices: 8833090--8833114 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8833080 ATTTACAATA
8833090 AAAATAAAAAAAC
1 AAAATAAAAAAAC
8833103 AAAATAAAAAAA
1 AAAATAAAAAAA
8833115 ATTTAAACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.04, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAATAAAAAAAC
Found at i:8833755 original size:327 final size:316
Alignment explanation
Indices: 8833049--8833784 Score: 845
Period size: 327 Copynumber: 2.3 Consensus size: 316
8833039 AAAAATTTGT
* *
8833049 TAAATCAAAATAAATAGTCTAATTAATTTATATTTACAATAAAAATAAAAAAACAAAATAAAAAA
1 TAAATCAAAATAAATAGTCTAATTAATTTATATTTACAATAAAAAT-AAAAAACAAAA-CAATAA
* ** *
8833114 AATTTAAACTAAACTTACCAAACCACTCAAATACAATTTAATATGTAAAATCGAGATAAATACTT
64 AATTTAAACTAAACTTACCAAACCACTAAAATACAATTTAATATGTAAAATAAAAATAAATACTT
* * *
8833179 CAATAATTTATATTACTCAATAAAAAAAATTAAACTAAACTTACCAAACAACTCAAATATAACTT
129 CAATAATTTATATTACTAAAAAAAAAAAATTAAACTAAACTTACCAAACAACTCAAATACAACTT
* * *
8833244 AATATGTAAAATCATAATAAATAGTCTAATAATTATAATTTAAATTAAAAACAAATATTAGACTA
194 AATATGTAAAATCAAAATAAATAGTCTAATAATTATAATTTAAATTAAAAACAAAAATTACACTA
* * * *
8833309 AAAATTACACGAAATTTTTAAATTAACTTGCCAAACCACTCGAATATAGTTTAATCTG
259 AAAATTACACGAAATATTTAAATTAACTTACCAAACCACTAGAATACAGTTTAATCTG
* * * * * *
8833367 TGAAATCAAAACAAATAGACTAATTAATTTATTTTTACAATAAAAACACAAAATAAAACAATAAA
1 T-AAATCAAAATAAATAGTCTAATTAATTTATATTTACAATAAAAATAAAAAACAAAACAATAAA
* * * * * *
8833432 TTTTAAACTAAACTTACCAAGCTACTAAAATACGATTTAATATGTAAAATAAAAATAATTA-GTC
65 ATTTAAACTAAACTTACCAAACCACTAAAATACAATTTAATATGTAAAATAAAAATAAATACTTC
* * ***
8833496 TGATAATTTATATTACTAAAAAAATTAATGTAATAATTTAAACTACACTTACCAAGTTTTACTCA
130 -AATAATTTATATTACT-AAAAAA--AA---AA-AA-TTAAACTAAACTTACCAA--ACAACTCA
* * *
8833561 AATACAACTTAATATGTAAAATTAAAATAAATA-TCCTAATAATTATAATTTAAGTTAATAACAA
184 AATACAACTTAATATGTAAAATCAAAATAAATAGT-CTAATAATTATAATTTAAATTAAAAACAA
* * *
8833625 AAATTACACTAAAAATTACATGAAA-ATTTAAATTAAACTTACTAAGCCACTAGAATACAGTTTA
248 AAATTACACTAAAAATTACACGAAATATTTAAATT-AACTTACCAAACCACTAGAATACAGTTTA
8833689 ATCTG
312 ATCTG
* *
8833694 TAAATTCAAAATAAATCA-TCTAATTAATTTATATTT-CAAATAAAAATTAAATAA-GAAACAAT
1 TAAA-TCAAAATAAAT-AGTCTAATTAATTTATATTTAC-AATAAAAA-TAAAAAACAAAACAAT
* * * *
8833756 AAAATTTACACTAAATTTATCAAATCACT
62 AAAATTTAAACTAAACTTACCAAACCACT
8833785 TACTAAAGCA
Statistics
Matches: 347, Mismatches: 53, Indels: 27
0.81 0.12 0.06
Matches are distributed among these distances:
316 2 0.01
317 72 0.21
318 14 0.04
319 41 0.12
320 2 0.01
323 2 0.01
324 2 0.01
325 17 0.05
326 13 0.04
327 177 0.51
328 5 0.01
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.32
Consensus pattern (316 bp):
TAAATCAAAATAAATAGTCTAATTAATTTATATTTACAATAAAAATAAAAAACAAAACAATAAAA
TTTAAACTAAACTTACCAAACCACTAAAATACAATTTAATATGTAAAATAAAAATAAATACTTCA
ATAATTTATATTACTAAAAAAAAAAAATTAAACTAAACTTACCAAACAACTCAAATACAACTTAA
TATGTAAAATCAAAATAAATAGTCTAATAATTATAATTTAAATTAAAAACAAAAATTACACTAAA
AATTACACGAAATATTTAAATTAACTTACCAAACCACTAGAATACAGTTTAATCTG
Found at i:8834140 original size:38 final size:37
Alignment explanation
Indices: 8834093--8834201 Score: 123
Period size: 38 Copynumber: 2.9 Consensus size: 37
8834083 GTCCTCTGCC
*
8834093 TTGCCTGAAGACGCCGCGTGTTCCCGAAGTCTTCATT
1 TTGCCTGAAGACGCCGAGTGTTCCCGAAGTCTTCATT
* * *
8834130 TATGCTTGAAGACGCCAAGTGATCCCGGAGAGT-TTCATT
1 T-TGCCTGAAGACGCCGAGTGTTCCC-GA-AGTCTTCATT
*
8834169 TTGCCTGAAGACGCCGAGAT-TTCCTGAAGTCTT
1 TTGCCTGAAGACGCCGAG-TGTTCCCGAAGTCTT
8834202 TAGGCTTGTA
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
36 3 0.05
37 5 0.08
38 38 0.64
39 10 0.17
40 3 0.05
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (37 bp):
TTGCCTGAAGACGCCGAGTGTTCCCGAAGTCTTCATT
Found at i:8835336 original size:21 final size:21
Alignment explanation
Indices: 8835310--8835362 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
8835300 TCGGATTTCA
8835310 ATCCGATCCGGATCGGTTTTT
1 ATCCGATCCGGATCGGTTTTT
8835331 ATCCGATCCGGATCGGTTTTT
1 ATCCGATCCGGATCGGTTTTT
8835352 ATCCGATCCGG
1 ATCCGATCCGG
8835363 TTTTTTCCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.15, C:0.26, G:0.25, T:0.34
Consensus pattern (21 bp):
ATCCGATCCGGATCGGTTTTT
Found at i:8835476 original size:15 final size:15
Alignment explanation
Indices: 8835458--8835513 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
8835448 TAACCGGTTT
8835458 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
8835473 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
8835490 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
8835505 CGATTTTAA
1 CGGTTTTAA
8835514 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:8835486 original size:17 final size:17
Alignment explanation
Indices: 8835461--8835511 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
8835451 CCGGTTTCGG
8835461 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
8835478 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
8835493 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
8835510 TT
1 TT
8835512 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:8835931 original size:13 final size:13
Alignment explanation
Indices: 8835910--8835964 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
8835900 AAGTTCGATA
*
8835910 AATTCAAATACTT
1 AATTGAAATACTT
8835923 AATTGAAATACTT
1 AATTGAAATACTT
* *
8835936 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
8835950 AATTGAAATACTT
1 AATTGAAATACTT
8835963 AA
1 AA
8835965 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:8836046 original size:32 final size:33
Alignment explanation
Indices: 8835950--8836048 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
8835940 AACTCAACAT
* * *
8835950 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
8835983 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
8836016 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
8836048 A
1 A
8836049 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:8836067 original size:21 final size:21
Alignment explanation
Indices: 8836043--8836082 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
8836033 ACTTCAAGTT
8836043 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
8836064 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
8836083 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:8843216 original size:33 final size:34
Alignment explanation
Indices: 8843179--8843247 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
8843169 AAAAATATAT
*
8843179 ATATTATGAGGTATA-TTAT-TTTTTCAATTTAAA
1 ATATTATG-GGTATATTTATATTTTGCAATTTAAA
*
8843212 ATATTATGTGTATATTTATATTTTGCAATTTAAA
1 ATATTATGGGTATATTTATATTTTGCAATTTAAA
8843246 AT
1 AT
8843248 CATGTATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 5 0.16
33 12 0.38
34 15 0.47
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (34 bp):
ATATTATGGGTATATTTATATTTTGCAATTTAAA
Found at i:8843657 original size:17 final size:16
Alignment explanation
Indices: 8843635--8843671 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
8843625 GAACGGTTAA
8843635 AATTAAGACATTTTCTT
1 AATTAA-ACATTTTCTT
*
8843652 AATTAAATATTTTCTT
1 AATTAAACATTTTCTT
8843668 AATT
1 AATT
8843672 TGATATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (16 bp):
AATTAAACATTTTCTT
Found at i:8853340 original size:31 final size:30
Alignment explanation
Indices: 8853294--8853373 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
8853284 TTCGATAATA
*
8853294 TAATAATTATTTTATAGT-ATTTAGATAAATT
1 TAATAA-TATTTTATAATCATTTA-ATAAATT
* *
8853325 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATCATTTAATAAATT
8853356 TAATAAGTATTTTATAAT
1 TAATAA-TATTTTATAAT
8853374 TTTTCAGACT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
30 1 0.02
31 36 0.86
32 5 0.12
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (30 bp):
TAATAATATTTTATAATCATTTAATAAATT
Found at i:8853351 original size:19 final size:20
Alignment explanation
Indices: 8853327--8853376 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
8853317 GATAAATTTA
*
8853327 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
8853346 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
8853367 TT-ATAATTTT
1 TTAATAATTTT
8853377 TCAGACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:8854141 original size:31 final size:31
Alignment explanation
Indices: 8854106--8854192 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
8854096 TCAATAAAGT
*
8854106 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATACTTATTAAATGTA
* *
8854137 TTAAAAGATTATAAAAT-CATTAATAAATGTA
1 TTAAAAAATTATAAAATAC-TTATTAAATGTA
* * *
8854168 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAATACTTATTA
8854193 TATTATCAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.96
32 1 0.02
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (31 bp):
TTAAAAAATTATAAAATACTTATTAAATGTA
Found at i:8855064 original size:14 final size:14
Alignment explanation
Indices: 8855045--8855078 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
8855035 CGTGGGTAAA
8855045 CGCGCTCCCTGAAG
1 CGCGCTCCCTGAAG
8855059 CGCGCTCCCTGAAG
1 CGCGCTCCCTGAAG
8855073 CGCGCT
1 CGCGCT
8855079 TTATACTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.12, C:0.44, G:0.29, T:0.15
Consensus pattern (14 bp):
CGCGCTCCCTGAAG
Found at i:8857718 original size:34 final size:36
Alignment explanation
Indices: 8857680--8857754 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 36
8857670 TTATTTCATT
8857680 AATTTGGTTGGA-TTTATT-TTAAT-TCATTTT-GTTA
1 AATTTGGTTGGACTTT-TTGTTAATGT-ATTTTGGTTA
8857714 AATTT-GTTGGACTTTTTGTTAATGTATTTTGGTTA
1 AATTTGGTTGGACTTTTTGTTAATGTATTTTGGTTA
*
8857749 ATTTTG
1 AATTTG
8857755 TTTATTACTA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
33 8 0.23
34 18 0.51
35 9 0.26
ACGTcount: A:0.21, C:0.03, G:0.17, T:0.59
Consensus pattern (36 bp):
AATTTGGTTGGACTTTTTGTTAATGTATTTTGGTTA
Found at i:8861398 original size:491 final size:491
Alignment explanation
Indices: 8860453--8861434 Score: 1626
Period size: 491 Copynumber: 2.0 Consensus size: 491
8860443 TGCGATGTTT
* * *
8860453 CCATACAGATTATTCGTGGACCTACCTCGGTACATATCGTAAAGAGTTGTGGATGAATGTCTCCC
1 CCATACAGATTATTCGTAGACCCACCTCGGTACATATCGTAAAGAGTTGCGGATGAATGTCTCCC
* * *
8860518 CATTAAAGTTGATGTGACGGCACCATGATGCAAATTTCCCATTATGGCATTAAAATCATTACGCA
66 CATTAAAGTTGATGTGACGGCACCATGATGCAAATTTCCCATAATGACATTAAAATCATTACACA
* * *
8860583 TTACTGTAGTCGGGTTGTTAACTTGATTAACTTGTTCAGCCAGCCCATAGTGGGAGCTTAATGAC
131 TTACTGTAGTCGGGCTGTCAACTTGATCAACTTGTTCAGCCAGCCCATAGTGGGAGCTTAATGAC
* *
8860648 TGACCCCGAACAGCACGCACTTGAACAAACCTTGCATACATCTCAATATCGTCGTCTGAATAATT
196 TGACCCCGAACAACACGCACTTGAACAAACCTTGCATACATCTCAATATCGACGTCTGAATAATT
*
8860713 ACATTGAGAATCAACCATCATTTTAACATTATAATTGTTCGATAGTTCAAACGATGTATAAGTTA
261 ACATTGAGAATCAACCATCATTTTAACATCATAATTGTTCGATAGTTCAAACGATGTATAAGTTA
* *
8860778 ATGGCAACAATGATGTTGGAAATCTGTACTGCAACGACGACATTCTTCTACTACTTTCAACATGA
326 ATGGCAACAATGATGTTGGAAATCTATACTGCAACGACGACATTCTTCTACTACTTCCAACATGA
* *
8860843 ACCTTCCTCGAAATCTTCGTTATCATCTCCTCAAGAGTTATGTTTCTCTTGAATGATATTTTAAC
391 ACCTTCCTCGAAATCTTCGTTATCATCTCCTCAAGAGTTATATTTCTCTTGAATAATATTTTAAC
* *
8860908 ACGCTCATTTGATACAAAAACAACGTCGGTTTCATC
456 ACGCTCATTTGATACAAAAACAACGCCAGTTTCATC
* * *
8860944 CCATACGGATTGTTCGTAGACCCACCTCGGTACATATTGTAAAGAGTTGCGGATGAATGTCTCCC
1 CCATACAGATTATTCGTAGACCCACCTCGGTACATATCGTAAAGAGTTGCGGATGAATGTCTCCC
* ** *
8861009 CATTGAAGTTGATGTGACGGCACCATGATGCGGATTTCCCATAATGACATTAAAATCATTACACT
66 CATTAAAGTTGATGTGACGGCACCATGATGCAAATTTCCCATAATGACATTAAAATCATTACACA
*
8861074 TTACTGTAGTCGGGCTGTCAACTTGATCAACTTGTTCAGCCAGCCCGTAGTGGGAGCTTAATGAC
131 TTACTGTAGTCGGGCTGTCAACTTGATCAACTTGTTCAGCCAGCCCATAGTGGGAGCTTAATGAC
* *
8861139 TGAGCCCGAACAACACGCACTTGAACAAACTTTGCATACATCTCAATATCGACGTCTGAATAATT
196 TGACCCCGAACAACACGCACTTGAACAAACCTTGCATACATCTCAATATCGACGTCTGAATAATT
* * * *
8861204 ACATTGAGAATCAGCCATCATTTTAACATCATCATTGTTTGATAGTTCGAAC-ACTGTATAAGTT
261 ACATTGAGAATCAACCATCATTTTAACATCATAATTGTTCGATAGTTCAAACGA-TGTATAAGTT
8861268 AATGGCAACAATGATGTTGGAAATCTATACTGCAACGACGACATTCTTCTACTACTTCCAACATG
325 AATGGCAACAATGATGTTGGAAATCTATACTGCAACGACGACATTCTTCTACTACTTCCAACATG
8861333 AACCTTCC-CTGAAATCTTCGTTATCATCTCCTCAAGAGTTATATTTCTCTTGAATAATATTTTA
390 AACCTTCCTC-GAAATCTTCGTTATCATCTCCTCAAGAGTTATATTTCTCTTGAATAATATTTTA
* *
8861397 ACACGCTCATTTGATACGAAACCAACGCCAGTTTCATC
454 ACACGCTCATTTGATACAAAAACAACGCCAGTTTCATC
8861435 TTCTCGAATT
Statistics
Matches: 455, Mismatches: 34, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
490 2 0.00
491 453 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (491 bp):
CCATACAGATTATTCGTAGACCCACCTCGGTACATATCGTAAAGAGTTGCGGATGAATGTCTCCC
CATTAAAGTTGATGTGACGGCACCATGATGCAAATTTCCCATAATGACATTAAAATCATTACACA
TTACTGTAGTCGGGCTGTCAACTTGATCAACTTGTTCAGCCAGCCCATAGTGGGAGCTTAATGAC
TGACCCCGAACAACACGCACTTGAACAAACCTTGCATACATCTCAATATCGACGTCTGAATAATT
ACATTGAGAATCAACCATCATTTTAACATCATAATTGTTCGATAGTTCAAACGATGTATAAGTTA
ATGGCAACAATGATGTTGGAAATCTATACTGCAACGACGACATTCTTCTACTACTTCCAACATGA
ACCTTCCTCGAAATCTTCGTTATCATCTCCTCAAGAGTTATATTTCTCTTGAATAATATTTTAAC
ACGCTCATTTGATACAAAAACAACGCCAGTTTCATC
Found at i:8868227 original size:2 final size:2
Alignment explanation
Indices: 8868220--8868248 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
8868210 TCAATCTACA
8868220 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8868249 TTACGAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8868447 original size:13 final size:13
Alignment explanation
Indices: 8868401--8868449 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
8868391 TCAATGACGC
*
8868401 GCGCCTCATAAAT
1 GCGCGTCATAAAT
* *
8868414 GTGAGTCATAAAT
1 GCGCGTCATAAAT
**
8868427 GCATGTCATAAAT
1 GCGCGTCATAAAT
8868440 GCGCGTCATA
1 GCGCGTCATA
8868450 GATTTATGAC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (13 bp):
GCGCGTCATAAAT
Found at i:8876654 original size:30 final size:31
Alignment explanation
Indices: 8876610--8876667 Score: 66
Period size: 30 Copynumber: 1.9 Consensus size: 31
8876600 TTGAAGACTT
* *
8876610 ATTAATTTAAAAAATT-AAA-AATGTATTTAA
1 ATTAAATTAAAAAATATAAACAAT-TATTTAA
*
8876640 ATTAAATTATAAAATATAAACAATTATT
1 ATTAAATTAAAAAATATAAACAATTATT
8876668 AAGATATTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
30 13 0.57
31 7 0.30
32 3 0.13
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (31 bp):
ATTAAATTAAAAAATATAAACAATTATTTAA
Found at i:8876907 original size:16 final size:16
Alignment explanation
Indices: 8876872--8876912 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
8876862 GTTTACTTCA
*
8876872 GAATGATT-AAACGTT
1 GAATGATTCAAACGCT
*
8876887 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
8876903 GAATGATTCA
1 GAATGATTCA
8876913 GAGGTTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.32
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:8877082 original size:14 final size:14
Alignment explanation
Indices: 8877063--8877094 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
8877053 AAACGCGCTA
8877063 AATGCTGAACGTTG
1 AATGCTGAACGTTG
8877077 AATGCTGAACGTTG
1 AATGCTGAACGTTG
8877091 AATG
1 AATG
8877095 GTTCCATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.28
Consensus pattern (14 bp):
AATGCTGAACGTTG
Found at i:8885837 original size:16 final size:16
Alignment explanation
Indices: 8885816--8885848 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
8885806 TAATAAATAA
8885816 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
8885832 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
8885848 A
1 A
8885849 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:8885933 original size:10 final size:10
Alignment explanation
Indices: 8885914--8885962 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
8885904 CATTTAATAA
*
8885914 ATAAATGAAC
1 ATAAACGAAC
8885924 ATAAACGAAC
1 ATAAACGAAC
*
8885934 ACGAACACGAAC
1 A-TAA-ACGAAC
*
8885946 ATAAACAAAC
1 ATAAACGAAC
8885956 ATAAACG
1 ATAAACG
8885963 TTGGAGATCC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
10 21 0.66
11 4 0.12
12 7 0.22
ACGTcount: A:0.59, C:0.20, G:0.10, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:8886568 original size:24 final size:24
Alignment explanation
Indices: 8886516--8886568 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
8886506 AAACAAAAAT
* *
8886516 GAACGAACATAACCGAATGAACAT
1 GAACGAACATAACCGAACGAACAC
* **
8886540 AAACGAACATAACCGAACGTTCAC
1 GAACGAACATAACCGAACGAACAC
8886564 GAACG
1 GAACG
8886569 TAAATGAACG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (24 bp):
GAACGAACATAACCGAACGAACAC
Found at i:8887923 original size:188 final size:187
Alignment explanation
Indices: 8887607--8887979 Score: 737
Period size: 188 Copynumber: 2.0 Consensus size: 187
8887597 CAATGGGCCC
8887607 ACCATTTAACCCAAATATGTAACCCTAAACCCTAGCCGCCATCATCCACCACCGTTGGATCTGGC
1 ACCATTTAACCCAAATATGTAACCCTAAACCCTAGCCGCCATCATCCACCACCGTTGGATCTGGC
8887672 ATGATCCAACGGTCCAAGAGCTTCCAGATGCAAACCCTAGGGTATCATACCCTAGGGCCACGCGG
66 ATGATCCAACGGTCCAAGAGCTTCCAGATGCAAACCCTAGGGTATCATACCCTAGGGCCACGCGG
8887737 CCACCGCAGCTGCTCTCGCCGTCTCCACCGCTGCCACGTCCCAACCGAAGGCTCCCA
131 CCACCGCAGCTGCTCTCGCCGTCTCCACCGCTGCCACGTCCCAACCGAAGGCTCCCA
8887794 ACCATTTAACCCAAATATGTAACCCTAAACCCTAGCCGCCATCATCCATCCACCGTTGGATCTGG
1 ACCATTTAACCCAAATATGTAACCCTAAACCCTAGCCGCCATCATCCA-CCACCGTTGGATCTGG
8887859 CATGATCCAACGGTCCAAGAGCTTCCAGATGCAAACCCTAGGGTATCATACCCTAGGGCCACGCG
65 CATGATCCAACGGTCCAAGAGCTTCCAGATGCAAACCCTAGGGTATCATACCCTAGGGCCACGCG
8887924 GCCACCGCAGCTGCTCTCGCCGTCTCCACCGCTGCCACGTCCCAACCGAAGGCTCC
130 GCCACCGCAGCTGCTCTCGCCGTCTCCACCGCTGCCACGTCCCAACCGAAGGCTCC
8887980 AGAAGCTCCA
Statistics
Matches: 185, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
187 48 0.26
188 137 0.74
ACGTcount: A:0.24, C:0.39, G:0.19, T:0.18
Consensus pattern (187 bp):
ACCATTTAACCCAAATATGTAACCCTAAACCCTAGCCGCCATCATCCACCACCGTTGGATCTGGC
ATGATCCAACGGTCCAAGAGCTTCCAGATGCAAACCCTAGGGTATCATACCCTAGGGCCACGCGG
CCACCGCAGCTGCTCTCGCCGTCTCCACCGCTGCCACGTCCCAACCGAAGGCTCCCA
Found at i:8888259 original size:15 final size:15
Alignment explanation
Indices: 8888239--8888280 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
8888229 ACAACACAAC
8888239 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
8888254 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
8888269 AAAGAAGAGAAA
1 AAAGAAAAGAAA
8888281 CTTACTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:8888264 original size:20 final size:20
Alignment explanation
Indices: 8888239--8888280 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
8888229 ACAACACAAC
*
8888239 AAAGAAACAGAAAAGAA-AGA
1 AAAGAAAAAG-AAAGAAGAGA
8888259 AAAGAAAAAGAAAGAAGAGA
1 AAAGAAAAAGAAAGAAGAGA
8888279 AA
1 AA
8888281 CTTACTCTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAAGAGA
Found at i:8889114 original size:14 final size:15
Alignment explanation
Indices: 8889088--8889137 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
8889078 CTAGTTGTAT
8889088 TTTTATTGTTTTA-A
1 TTTTATTGTTTTATA
8889102 TTTTACTTG-TTTATA
1 TTTTA-TTGTTTTATA
* *
8889117 TTTT-TTATTTTATT
1 TTTTATTGTTTTATA
8889131 TTTTATT
1 TTTTATT
8889138 TTTATGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
13 2 0.07
14 18 0.60
15 10 0.33
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (15 bp):
TTTTATTGTTTTATA
Found at i:8889114 original size:22 final size:20
Alignment explanation
Indices: 8889085--8889140 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 20
8889075 GTTCTAGTTG
8889085 TATT-TTTATTGTTTTAATTT
1 TATTGTTTATT-TTTTAATTT
*
8889105 TACTTGTTTATATTTTTTATTT
1 TA-TTGTTTAT-TTTTTAATTT
*
8889127 TATTTTTTATTTTT
1 TATTGTTTATTTTT
8889141 ATGTATTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 6 0.19
21 9 0.29
22 15 0.48
23 1 0.03
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.77
Consensus pattern (20 bp):
TATTGTTTATTTTTTAATTT
Found at i:8889142 original size:13 final size:12
Alignment explanation
Indices: 8889115--8889139 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8889105 TACTTGTTTA
8889115 TATTTTTTATTT
1 TATTTTTTATTT
8889127 TATTTTTTATTT
1 TATTTTTTATTT
8889139 T
1 T
8889140 TATGTATTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TATTTTTTATTT
Found at i:8900484 original size:15 final size:15
Alignment explanation
Indices: 8900451--8900528 Score: 75
Period size: 15 Copynumber: 5.0 Consensus size: 15
8900441 GCTTGAAGAA
*
8900451 AAAAGAAAAAAGAAAG
1 AAAAGAAAAAA-AAGG
8900467 AAAAGAAAAAAAAGG
1 AAAAGAAAAAAAAGG
* *
8900482 AAAAGAAAAAAATTGA
1 AAAAGAAAAAAA-AGG
* *
8900498 AAAATGAAAAAAGAGA
1 AAAA-GAAAAAAAAGG
*
8900514 AAAAGAAGAAAAAGG
1 AAAAGAAAAAAAAGG
8900529 GGGGGTCAAG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
15 23 0.44
16 22 0.42
17 7 0.13
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (15 bp):
AAAAGAAAAAAAAGG
Found at i:8900881 original size:18 final size:18
Alignment explanation
Indices: 8900856--8900895 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
8900846 TTCAAGTTCA
*
8900856 ATTTTTTGAAATTCAATTT
1 ATTTTTGGAAATTC-ATTT
8900875 ATTTTTGGAAATTCATTT
1 ATTTTTGGAAATTCATTT
8900893 ATT
1 ATT
8900896 ATTCTATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (18 bp):
ATTTTTGGAAATTCATTT
Found at i:8901790 original size:83 final size:83
Alignment explanation
Indices: 8901655--8901978 Score: 548
Period size: 83 Copynumber: 4.0 Consensus size: 83
8901645 ACATTAGCTG
*
8901655 GAAAGATG-A-ATG-TCATAGCATC-TCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
8901716 AAACCAATCATTGAATTT
66 AAACCAATCATTGAATTT
* *
8901734 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTGTGAGTTATCTGATCTGGTTTGGCA
1 GAAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
*
8901799 GAACCAATCATTGAATTT
66 AAACCAATCATTGAATTT
* *
8901817 GGAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
8901882 AAACCAATCATTGAATTT
66 AAACCAATCATTGAATTT
*
8901900 GGAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
1 GAAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
*
8901965 GAACCAATCATTGA
66 AAACCAATCATTGA
8901979 TGGTTTGGTA
Statistics
Matches: 230, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
79 8 0.03
80 1 0.00
81 2 0.01
82 10 0.04
83 209 0.91
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (83 bp):
GAAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
AAACCAATCATTGAATTT
Found at i:8901983 original size:24 final size:24
Alignment explanation
Indices: 8901955--8902002 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
8901945 TTATCTGATC
*
8901955 TGGTTTGGCAGAACCAATCATTGA
1 TGGTTTGGCAAAACCAATCATTGA
*
8901979 TGGTTTGGTAAAACCAATCATTGA
1 TGGTTTGGCAAAACCAATCATTGA
8902003 ATTTGAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (24 bp):
TGGTTTGGCAAAACCAATCATTGA
Found at i:8902060 original size:108 final size:107
Alignment explanation
Indices: 8901872--8902070 Score: 353
Period size: 108 Copynumber: 1.9 Consensus size: 107
8901862 TTATCTGATC
* * *
8901872 TGGTTTGGTAAAACCAATCATTGAATTTGGAAGATGAATATGCTCATAGCATCTTCTGGAAGTGT
1 TGGTTTGGTAAAACCAATCATTGAATTTGAAAGACGAATATGCCCATAGCATCTTCTGGAAGTGT
8901937 TCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGA
66 TCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGA
*
8901979 TGGTTTGGTAAAACCAATCATTGAATTTGAAAGACGAATGTGCCCAATAGCATCTTCTGGAAGTG
1 TGGTTTGGTAAAACCAATCATTGAATTTGAAAGACGAATATGCCC-ATAGCATCTTCTGGAAGTG
8902044 TTCTTTGAGTTATCTGATCTGGTTTGG
65 TTCTTTGAGTTATCTGATCTGGTTTGG
8902071 TATGAACCCC
Statistics
Matches: 87, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
107 41 0.47
108 46 0.53
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (107 bp):
TGGTTTGGTAAAACCAATCATTGAATTTGAAAGACGAATATGCCCATAGCATCTTCTGGAAGTGT
TCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGA
Found at i:8902134 original size:200 final size:190
Alignment explanation
Indices: 8901789--8902156 Score: 565
Period size: 200 Copynumber: 1.9 Consensus size: 190
8901779 TTATCTGATC
* * * *
8901789 TGGTTTGGCAGAACCAATCATTGAATTTGGAAGATGAATATGCTCATAGCATCTTCTGGAAGTGT
1 TGGTTTGGCAAAACCAATCATTGAATTTGAAAGACGAATATGCCCATAGCATCTTCTGGAAGTGT
* *
8901854 TCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGGAAGATGAATATGCTCAT
66 TCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAAGTTGAAAGATGAATATGCTCAT
8901919 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGA
131 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGA
* *
8901979 TGGTTTGGTAAAACCAATCATTGAATTTGAAAGACGAATGTGCCCAATAGCATCTTCTGGAAGTG
1 TGGTTTGGCAAAACCAATCATTGAATTTGAAAGACGAATATGCCC-ATAGCATCTTCTGGAAGTG
8902044 TTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAACCAATCATTGAAGTTGAAAGATGA
65 TTCTTTGAGTTATCTGATCTGGTTTGG--T-------AAAACCAATCATTGAAGTTGAAAGATGA
*
8902109 ATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
121 ATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
8902157 ATTCAGTAGG
Statistics
Matches: 159, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
190 39 0.25
191 46 0.29
193 1 0.01
200 73 0.46
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (190 bp):
TGGTTTGGCAAAACCAATCATTGAATTTGAAAGACGAATATGCCCATAGCATCTTCTGGAAGTGT
TCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAAGTTGAAAGATGAATATGCTCAT
AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGA
Found at i:8902146 original size:92 final size:92
Alignment explanation
Indices: 8901988--8902201 Score: 304
Period size: 92 Copynumber: 2.3 Consensus size: 92
8901978 ATGGTTTGGT
*
8901988 AAAACCAATCATTGAATTTGAAAGACGAATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
1 AAAACCAATCATTGAA-TTGAAAGATGAATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
* ** *
8902053 TTATCTGATCTGGTTTGGTATGAACCCC
65 TTATCTGATCTGATTCAGTAGGAACCCC
* *
8902081 AAAACCAATCATTGAAGTTGAAAGATGAATTTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAG
1 AAAACCAATCATTGAA-TTGAAAGATGAATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
8902145 TTATCTGATCTGATTCAGTAGGAACCCC
65 TTATCTGATCTGATTCAGTAGGAACCCC
* * *
8902173 AGAACCGATCGTTGGAATTGAAAGATGAA
1 AAAACCAATCATT-GAATTGAAAGATGAA
8902202 CTGCATGATC
Statistics
Matches: 109, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
92 74 0.68
93 35 0.32
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (92 bp):
AAAACCAATCATTGAATTGAAAGATGAATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
TATCTGATCTGATTCAGTAGGAACCCC
Found at i:8903068 original size:113 final size:112
Alignment explanation
Indices: 8902880--8903729 Score: 932
Period size: 113 Copynumber: 7.5 Consensus size: 112
8902870 GCAAAGATTC
* * * *
8902880 AAATCCATCATTCGATGGATCAACATTGT-CAGGTCGAGTTCATAATAAGAAGAACTCATCTGAA
1 AAATTCATCATT-GATGGATTAAC-TTTTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAA
* *
8902944 GAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAA-CTTTTCGCTT
64 GAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GCTT
* * * * * *
8902993 GAATTCATCATTCGATAGATCAACATTGCCAGGTCGAGTTCATAATGAGAATAACTCATCTGAAG
1 AAATTCATCATT-GATGGATTAACTTTTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
8903058 AAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATCTTTTGCTC
65 AAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * **
8903106 AAATCCATCATTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATTCATCA-TTGATGGATTAACTTTTCCAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAA
* * *
8903170 GAAGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
64 GAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * *
8903219 AAATTCATCATATGATGGATTAACATTGCCAGGTAGAGTTCATAAAGAGAAGAACTCGTCATCTG
1 AAATTCATCAT-TGATGGATTAACTTTTCCAGGTCGAGTTCATAATGAGAAGAA--C-TCATCTG
* *
8903284 AAG-AAGAA-TA-AA-TTCATAATGAGAAGAATTTGTTCAACTTTTTGCTT
62 AAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * *
8903331 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCGTCTGAAG
1 AAATTCATCA-TTGATGGATTAACTTTTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
8903396 AAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 AAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* *
8903444 AAA-TCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATTC-ATCA-TTGATGGATTAACTTTTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAA
* * *
8903508 G-AAGGATAAGAAGTTCATAATGAGAAGAATTTGTTCAACCCTTTTGCTC
64 GAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CCTTTTGCTT
* ** * *
8903557 AAA-TCTATCACTTGATAGATTAGTTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAA
1 AAATTC-ATCA-TTGATGGATTAACTTTTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAA
* * * ** *
8903621 GAAGGATGAAGAAGTTCATAATGAAAAGAATTTGTTCAGATTTTTTGCTC
64 GAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA-ACCTTTTGCTT
* * * * *
8903671 AAATCCATCACTTGATGGGTCAATTTTTCCAGAG--AAGTTCATAATGAGAAGAACTCATC
1 AAATTCATCA-TTGATGGATTAACTTTTCCAG-GTCGAGTTCATAATGAGAAGAACTCATC
8903730 AAGAGCTTAT
Statistics
Matches: 641, Mismatches: 76, Indels: 40
0.85 0.10 0.05
Matches are distributed among these distances:
109 9 0.01
110 4 0.01
111 1 0.00
112 117 0.18
113 420 0.66
114 73 0.11
115 7 0.01
116 10 0.02
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (112 bp):
AAATTCATCATTGATGGATTAACTTTTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
AAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
Found at i:8903598 original size:338 final size:336
Alignment explanation
Indices: 8902878--8903729 Score: 1051
Period size: 338 Copynumber: 2.5 Consensus size: 336
8902868 TAGCAAAGAT
* * * *
8902878 TCAAATCCATCAT-TCGATGGATCAACATTGTCAGGTCGAGTTCATAATAAGAAGAACTCATCTG
1 TCAAATTCATCATAT-GATAGATTAACATTGCCAGGTCGAGTTCATAATAAGAAGAACTCATCTG
* * * * * *
8902942 AAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACTTTTCGCTTGAATTCATCA-TTC
65 AAG-AAGAA-TAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTAAATCCATCACTT-
* * * *
8903006 GATAGATCAA-CATTGCCAGGTCGAGTTCATAATGAGAATAACTCATCTGAAGAAAGAAGAAGAA
127 GATGGAT-AATCTTTTCCA-GTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAA
* *
8903070 ATTCATAATGAGAAGAATTTGTTCAATCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTC
190 ATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTC
*
8903135 CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAA
255 CAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
*
8903200 TTTGTTCAACCTTTTGT
320 TTTGTTCAACCTTTTGC
* * *
8903217 TTAAATTCATCATATGATGGATTAACATTGCCAGGTAGAGTTCATAA-AGAGAAGAACTCGTCAT
1 TCAAATTCATCATATGATAGATTAACATTGCCAGGTCGAGTTCATAATA-AGAAGAA--C-TCAT
8903281 CTGAAGAAGAATA-AA-TTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTAAATCCATCACTT
62 CTGAAGAAGAATAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTAAATCCATCACTT
* * * * *
8903344 GATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCGTCTGAAGAAGGATGAAGAAG
127 GATGGATAATCTTTTCCAG-TCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAA
* * *
8903409 TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTATCTTTTCC
191 TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCC
**** *
8903474 AGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-ATAAGAAGTTCATAATGAGAAGAAT
256 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
8903538 TTGTTCAACCCTTTTGC
321 TTGTTCAA-CCTTTTGC
*** * *
8903555 TCAAA-TCTATCACT-TGATAGATTAGTTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCT
1 TCAAATTC-ATCA-TATGATAGATTAACATTGCCAGGTCGAGTTCATAATAAGAAGAACTCATCT
* * * *
8903618 GAAGAAGGATGAAGAAGTTCATAATGAAAAGAATTTGTTCAGATTTTTTGCTCAAATCCATCACT
64 GAAGAAGAAT--AGAAGTTCATAATGAGAAGAATTTGTTCA-ACTTTTTGCTTAAATCCATCACT
* *
8903683 TGATGGGTCAAT-TTTTCCAG-AGAAGTTCATAATGAGAAGAACTCATC
126 TGATGGAT-AATCTTTTCCAGTCG-AGTTCATAATGAGAAGAACTCATC
8903730 AAGAGCTTAT
Statistics
Matches: 446, Mismatches: 48, Indels: 38
0.84 0.09 0.07
Matches are distributed among these distances:
335 15 0.03
336 1 0.00
337 36 0.08
338 239 0.54
339 99 0.22
340 38 0.09
341 8 0.02
342 10 0.02
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (336 bp):
TCAAATTCATCATATGATAGATTAACATTGCCAGGTCGAGTTCATAATAAGAAGAACTCATCTGA
AGAAGAATAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTAAATCCATCACTTGATG
GATAATCTTTTCCAGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCAT
AATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGA
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
CAACCTTTTGC
Found at i:8903658 original size:226 final size:223
Alignment explanation
Indices: 8902913--8903729 Score: 1027
Period size: 226 Copynumber: 3.6 Consensus size: 223
8902903 CATTGTCAGG
* *
8902913 TCGAGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTG
1 TCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
* ** * * *
8902978 TTTAA-CTTTTCGCTTGAATTCATCATTCGATAGATCAACATTGCCAGGTCGAGTTCATAATGAG
66 TTCAACCTTTT-GCTCAAATTCATCATT-GATGGATTAACATTGCCAGGTAGAGTTCATAATGAG
* * *
8903042 AATAACTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATCTTTTGCTCA
129 AAGAACTCATCTGAAG-AAGAATAAG-AATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCA
* * * *
8903107 AATCCATCATTTGATGGATCAGCTTTTCCAGA
192 AATCCATCACTTGATGGATTAGTTTTTCCAGT
*** * *
8903139 GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAATTTG
1 TCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
* * *
8903204 TTCAACCTTTTGTTTAAATTCATCATATGATGGATTAACATTGCCAGGTAGAGTTCATAAAGAGA
66 TTCAACCTTTTGCTCAAATTCATCAT-TGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGA
* *
8903269 AGAACTCGTCATCTGAAGAAGAAT-A-AATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTA
130 AGAA--C-TCATCTGAAGAAGAATAAGAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCA
8903332 AATCCATCACTTGATGGATTA-TCTTTTCCAGT
192 AATCCATCACTTGATGGATTAGT-TTTTCCAGT
* * *
8903364 TCGAGTTCATAATGAGAAGAACTCGTCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTG
1 TCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
* * * * *
8903429 TTCAACCTTTTGCTCAAA-TCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAG
66 TTCAACCTTTTGCTCAAATTC-ATCA-TTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAG
*
8903493 AAGAACTCATCTGAAGAAGGATAAGAAGTTCATAATGAGAAGAATTTGTTCAACCCTTTTGCTCA
129 AAGAACTCATCTGAAGAAGAATAAGAA-TTCATAATGAGAAGAATTTGTTCAA-CCTTTTGCTCA
* *
8903558 AATCTATCACTTGATAGATTAGTTTTTCCAGT
192 AATCCATCACTTGATGGATTAGTTTTTCCAGT
* *
8903590 TCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGATGAAGAAGTTCATAATGAAAAGAATTTG
1 TCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
** * * * ** *
8903655 TTCAGATTTTTTGCTCAAATCCATCACTTGATGGGTCAATTTTTCCA-G-AGAAGTTCATAATGA
66 TTCA-ACCTTTTGCTCAAATTCATCA-TTGATGGATTAACATTGCCAGGTAG-AGTTCATAATGA
8903718 GAAGAACTCATC
128 GAAGAACTCATC
8903730 AAGAGCTTAT
Statistics
Matches: 521, Mismatches: 54, Indels: 32
0.86 0.09 0.05
Matches are distributed among these distances:
222 15 0.03
223 2 0.00
224 4 0.01
225 203 0.39
226 239 0.46
227 41 0.08
228 7 0.01
229 10 0.02
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (223 bp):
TCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
TTCAACCTTTTGCTCAAATTCATCATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAA
GAACTCATCTGAAGAAGAATAAGAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
CATCACTTGATGGATTAGTTTTTCCAGT
Found at i:8904047 original size:11 final size:10
Alignment explanation
Indices: 8904007--8904044 Score: 51
Period size: 9 Copynumber: 3.7 Consensus size: 10
8903997 TAATTATTAT
8904007 TATTAAAT-A
1 TATTAAATAA
8904016 TATTAAATACA
1 TATTAAATA-A
8904027 TATATAAATAA
1 TAT-TAAATAA
8904038 TATTAAA
1 TATTAAA
8904045 ATATATACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.31
10 4 0.15
11 8 0.31
12 6 0.23
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (10 bp):
TATTAAATAA
Found at i:8904557 original size:15 final size:15
Alignment explanation
Indices: 8904537--8904578 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
8904527 ACAACACAGC
8904537 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
8904552 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
8904567 AAAGAAGAGAAA
1 AAAGAAAAGAAA
8904579 CTTACTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:8904562 original size:20 final size:20
Alignment explanation
Indices: 8904537--8904578 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
8904527 ACAACACAGC
*
8904537 AAAGAAACAGAAAAGAA-AGA
1 AAAGAAAAAG-AAAGAAGAGA
8904557 AAAGAAAAAGAAAGAAGAGA
1 AAAGAAAAAGAAAGAAGAGA
8904577 AA
1 AA
8904579 CTTACTCTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAAGAGA
Found at i:8905441 original size:13 final size:12
Alignment explanation
Indices: 8905414--8905438 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8905404 TACATGTTTA
8905414 TATTTTTTATTT
1 TATTTTTTATTT
8905426 TATTTTTTATTT
1 TATTTTTTATTT
8905438 T
1 T
8905439 TATGTATTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TATTTTTTATTT
Found at i:8906632 original size:19 final size:19
Alignment explanation
Indices: 8906590--8906633 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
8906580 TGAATGGATG
**
8906590 CAACTTTAAACCAATGATG
1 CAACTTTAAACCAATGACA
*
8906609 CAACTTTAAACCAGTGACA
1 CAACTTTAAACCAATGACA
*
8906628 TAACTT
1 CAACTT
8906634 ATTATTAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.27
Consensus pattern (19 bp):
CAACTTTAAACCAATGACA
Found at i:8908669 original size:20 final size:19
Alignment explanation
Indices: 8908644--8908696 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
8908634 TGATTCAATC
* *
8908644 AGTATCGATACCGAAGGAGG
1 AGTATCGATACCAAAGG-GA
8908664 AGTATCGATACCAAAGGGA
1 AGTATCGATACCAAAGGGA
8908683 AGGTATCGATACCA
1 A-GTATCGATACCA
8908697 TTTTGAAACC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.17
Consensus pattern (19 bp):
AGTATCGATACCAAAGGGA
Found at i:8909622 original size:219 final size:220
Alignment explanation
Indices: 8909241--8909708 Score: 694
Period size: 219 Copynumber: 2.1 Consensus size: 220
8909231 TATATTCCAT
* *
8909241 GGAATTCATCAT-GAGTTGATGAATAACCATTTCGACACTAAGTGTGCATTTCACGGAATTCATC
1 GGAATTCATCATGGAGTGGATGAATAACCATTTCGACACTAAGTGTACATTTCACGGAATTCATC
*
8909305 ATGGGTTGATGAATCACCGTACAAGCACTTTGTGTGAAAATCCACAGAATTCATCATGGGTTGAT
66 ATGGGTTGATGAATCACCGTACAAGCACTTTGTGTGAAAATCCACAGAATTCATCATGGGTTAAT
* *
8909370 GAATCACCGTACAAACACTATGGGTGCAAATCCACATAATTCATCATGGGTTGATGAATAATCGT
131 GAATCACCGTACAAACACTATGAGTGCAAATCCACATAATTCATCATGGGTTGATGAATAACCGT
**
8909435 ACATGCACTTTGTGTGCAAATACAC
196 ACAAACACTTTGTGTGCAAATACAC
*
8909460 GGAATTCATCATGGA-TGGATGAATAACCGTTTC-AGCACTAAGTGTACATTTCACGGAATTCAT
1 GGAATTCATCATGGAGTGGATGAATAACCATTTCGA-CACTAAGTGTACATTTCACGGAATTCAT
* * * *
8909523 CATGGGTTGATGAATCACTGTACATGCACTTTGTGTGCAAATCCAC-GTAATTTATCATGGGTTA
65 CATGGGTTGATGAATCACCGTACAAGCACTTTGTGTGAAAATCCACAG-AATTCATCATGGGTTA
* * * *
8909587 ATGAATCACCGTACAAACACTTTGAGTGTAAATCCACGTAATTCATCATGGGTTGATGAATCACC
129 ATGAATCACCGTACAAACACTATGAGTGCAAATCCACATAATTCATCATGGGTTGATGAATAACC
* *
8909652 GTACAAACACTTTGTGTGCAAATCCAT
194 GTACAAACACTTTGTGTGCAAATACAC
** *
8909679 GGAATTCATCAT-GAGTTAATGAATCACCAT
1 GGAATTCATCATGGAGTGGATGAATAACCAT
8909709 ACAAACACTA
Statistics
Matches: 223, Mismatches: 22, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
218 4 0.02
219 217 0.97
220 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (220 bp):
GGAATTCATCATGGAGTGGATGAATAACCATTTCGACACTAAGTGTACATTTCACGGAATTCATC
ATGGGTTGATGAATCACCGTACAAGCACTTTGTGTGAAAATCCACAGAATTCATCATGGGTTAAT
GAATCACCGTACAAACACTATGAGTGCAAATCCACATAATTCATCATGGGTTGATGAATAACCGT
ACAAACACTTTGTGTGCAAATACAC
Done.