Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_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: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 50 of 65
Found at i:9796553 original size:41 final size:41
Alignment explanation
Indices: 9796468--9796646 Score: 159
Period size: 41 Copynumber: 4.3 Consensus size: 41
9796458 ATGTGTAATA
* * * *
9796468 TATTGCGGCGTTTGTGG-TCAAAACGCCGC-CAATTTACCATTC
1 TATTGCGGCGTTT-TGGCT-AAATCGCCGCAAAATTTA-TACTC
* *
9796510 TATTGCGGCGTTTTGGCTCAATCGCCGCAAAATTCATACTC
1 TATTGCGGCGTTTTGGCTAAATCGCCGCAAAATTTATACTC
* * * * *
9796551 TATTGCGGCGTTTGTGG-TAAAAACGCTGC-CAGTTTACCACTC
1 TATTGCGGCGTTT-TGGCT-AAATCGCCGCAAAATTTA-TACTC
*
9796593 TATTGCGGCGTTTTGGCTAAATCGCCGCAAAATTTATAATC
1 TATTGCGGCGTTTTGGCTAAATCGCCGCAAAATTTATACTC
*
9796634 TATTGCAGCGTTT
1 TATTGCGGCGTTT
9796647 GTGATATAAA
Statistics
Matches: 110, Mismatches: 20, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
41 58 0.53
42 52 0.47
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.33
Consensus pattern (41 bp):
TATTGCGGCGTTTTGGCTAAATCGCCGCAAAATTTATACTC
Found at i:9796576 original size:83 final size:83
Alignment explanation
Indices: 9796463--9796687 Score: 315
Period size: 83 Copynumber: 2.7 Consensus size: 83
9796453 ACTATATGTG
* * *
9796463 TAATATATTGCGGCGTTTGTGGTCAAAACGCCGCCAATTTACCATTCTATTGCGGCGTTTTGGCT
1 TAATCTATTGCGGCGTTTGTGGTAAAAACGCCGCCAATTTACCACTCTATTGCGGCGTTTTGGCT
*
9796528 CAATCGCCGCAAAATTCA
66 AAATCGCCGCAAAATTCA
* * *
9796546 TACTCTATTGCGGCGTTTGTGGTAAAAACGCTGCCAGTTTACCACTCTATTGCGGCGTTTTGGCT
1 TAATCTATTGCGGCGTTTGTGGTAAAAACGCCGCCAATTTACCACTCTATTGCGGCGTTTTGGCT
*
9796611 AAATCGCCGCAAAATTTA
66 AAATCGCCGCAAAATTCA
* * * * * * *
9796629 TAATCTATTGCAGCGTTTGTGATATAAACGCCACTAATTTAGCACCCTATTGCGGCGTT
1 TAATCTATTGCGGCGTTTGTGGTAAAAACGCCGCCAATTTACCACTCTATTGCGGCGTT
9796688 GTTCTAAAAA
Statistics
Matches: 124, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
83 124 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.32
Consensus pattern (83 bp):
TAATCTATTGCGGCGTTTGTGGTAAAAACGCCGCCAATTTACCACTCTATTGCGGCGTTTTGGCT
AAATCGCCGCAAAATTCA
Found at i:9797204 original size:16 final size:16
Alignment explanation
Indices: 9797156--9797206 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
9797146 TTTAAAAAAA
* *
9797156 ATAAAAATTTATTTAG
1 ATAAAAAATTATTAAG
* *
9797172 ATTAAAAA-TATAAAAG
1 ATAAAAAATTAT-TAAG
9797188 ATAAAAAATTATTAAG
1 ATAAAAAATTATTAAG
9797204 ATA
1 ATA
9797207 CTCAATACAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
15 3 0.11
16 21 0.78
17 3 0.11
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
ATAAAAAATTATTAAG
Found at i:9797231 original size:24 final size:25
Alignment explanation
Indices: 9797193--9797253 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 25
9797183 AAAAGATAAA
*
9797193 AAATTATT-AAGATACT-CAATACATT
1 AAATTATTAAAAATACTACAA-A-ATT
9797218 AAA-TA-TAAAAATACTACAAAATT
1 AAATTATTAAAAATACTACAAAATT
9797241 AAATTATTAAAAA
1 AAATTATTAAAAA
9797254 ATTAATTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
23 7 0.23
24 12 0.39
25 12 0.39
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (25 bp):
AAATTATTAAAAATACTACAAAATT
Found at i:9812355 original size:3 final size:3
Alignment explanation
Indices: 9812347--9812380 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
9812337 CCCATTCAAA
9812347 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
9812381 TGTGGTCCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:9813305 original size:31 final size:31
Alignment explanation
Indices: 9813270--9813343 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
9813260 AAAAATTAAA
9813270 TGTTTAGGTACTAAAATGGATCAAAACTTAT
1 TGTTTAGGTACTAAAATGGATCAAAACTTAT
* *
9813301 TGTTTAGATACTAAAATGGTTCAAAACTTAT
1 TGTTTAGGTACTAAAATGGATCAAAACTTAT
**
9813332 AATTTAGGTACT
1 TGTTTAGGTACT
9813344 TAATGCATAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (31 bp):
TGTTTAGGTACTAAAATGGATCAAAACTTAT
Found at i:9813596 original size:2 final size:2
Alignment explanation
Indices: 9813591--9813621 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9813581 CAGAAACGTT
9813591 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9813622 TATGCGTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9814394 original size:71 final size:71
Alignment explanation
Indices: 9814316--9814447 Score: 230
Period size: 71 Copynumber: 1.9 Consensus size: 71
9814306 ATAGCAATAT
*
9814316 AAAATAAAAAGTAATAAATTTGAGTTTACAATACAACG-AAGCTCCTAAATCATCCAAATAATAC
1 AAAATAAAAAGTAATAAATTTAAGTTTACAATACAA-GTAAGCTCCTAAATCATCCAAATAATAC
9814380 ACTTATA
65 ACTTATA
*
9814387 AAAATAAAAAGTAATAAATTTAAGTTTACAATACAAGTGAGCTCCTAAATCATCCAAATAA
1 AAAATAAAAAGTAATAAATTTAAGTTTACAATACAAGTAAGCTCCTAAATCATCCAAATAA
9814448 AGCATTGAGT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
70 1 0.02
71 57 0.98
ACGTcount: A:0.52, C:0.14, G:0.08, T:0.27
Consensus pattern (71 bp):
AAAATAAAAAGTAATAAATTTAAGTTTACAATACAAGTAAGCTCCTAAATCATCCAAATAATACA
CTTATA
Found at i:9816175 original size:81 final size:81
Alignment explanation
Indices: 9816080--9816645 Score: 837
Period size: 81 Copynumber: 7.0 Consensus size: 81
9816070 AAATAATCCC
* * * * * * *
9816080 TTATTCTTTTACTCAACAGTGTTTAACCGTACATCTAACTGGCATAGTTAACACATTTCTGTCAA
1 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
9816145 TTGCACAGTTAGGCCA
66 TTGCACAGTTAGGCCA
* * * *
9816161 TTATTATTTTACTCAACAGTATTTAATCGTTCATCTAACTGGAATAATTGACACCTTTCTGCCAA
1 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
*
9816226 TTGCACAATTAGGCCA
66 TTGCACAGTTAGGCCA
* ** *
9816242 TTATTCTTTTACTCAACGGTATTCAACAATTCATCTAACTGGCATAATTGACACTTTTCTGCCAA
1 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
9816307 TTGCACAGTTAGG-CA
66 TTGCACAGTTAGGCCA
*
9816322 TTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACTTTTCTGCCA
1 -TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCC-
9816387 AATTGCACAGTTAGGCCA
64 AATTGCACAGTTAGGCCA
* * *
9816405 TTATTCTTTTACTCAATGGTATTTAACCGTTCATCTAACTGGCATAATTGGCACTTTTCTGCCAA
1 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
9816470 TTGCACAGTTAGGCCA
66 TTGCACAGTTAGGCCA
* *
9816486 TTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTACCAA
1 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
*
9816551 TTTCACAGTTAGGCCA
66 TTGCACAGTTAGGCCA
* * ** * * *
9816567 TTATTCTTTTACTCAACGATATTCAATTGTTCATCTAACTGGCATAATTAACACCTTTCTGTCAT
1 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
9816632 TTGCACAGTTAGGC
66 TTGCACAGTTAGGC
9816646 TTCAAAGGCA
Statistics
Matches: 442, Mismatches: 40, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
80 2 0.00
81 362 0.82
82 76 0.17
83 2 0.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.37
Consensus pattern (81 bp):
TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
TTGCACAGTTAGGCCA
Found at i:9816474 original size:244 final size:243
Alignment explanation
Indices: 9816080--9816645 Score: 873
Period size: 244 Copynumber: 2.3 Consensus size: 243
9816070 AAATAATCCC
* * * *
9816080 TTATTCTTTTACTCAACAGTGTTTAACCGTACATCTAACTGGCATAGTTAACACATTTCTGTCAA
1 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTAACACATTTCTGTCAA
*
9816145 TTGCACAGTTAGGCCATTATTATTTTACTCAACAGTATTTAATCGTTCATCTAACTGGAATAATT
66 TTGCACAGTTAGGCCATTATTATTTTACTCAACAGTATTTAACCGTTCATCTAACTGGAATAATT
9816210 GACACCTTTCTGCCAATTGCACAATTAGGCCATTATTCTTTTACTCAACGGTATTCAACAATTCA
131 GACACCTTTCTGCCAATTGCACAATTAGGCCATTATTCTTTTACTCAACGGTATTCAACAATTCA
* *
9816275 TCTAACTGGCATAATTGACACTTTTCTGCCAATTGCACAGTTAGG-CA
196 TCTAACTGGCATAATTGACACCTTTCTACCAATTGCACAGTTAGGCCA
* * *
9816322 TTTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACTTTTCTGCCA
1 -TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTAACACATTTCTGTC-
* ** *
9816387 AATTGCACAGTTAGGCCATTATTCTTTTACTCAATGGTATTTAACCGTTCATCTAACTGGCATAA
64 AATTGCACAGTTAGGCCATTATTATTTTACTCAACAGTATTTAACCGTTCATCTAACTGGAATAA
* * * * *
9816452 TTGGCACTTTTCTGCCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCATT
129 TTGACACCTTTCTGCCAATTGCACAATTAGGCCATTATTCTTTTACTCAACGGTATTCAACAATT
*
9816517 CATCTAACTGGCATAATTGACACCTTTCTACCAATTTCACAGTTAGGCCA
194 CATCTAACTGGCATAATTGACACCTTTCTACCAATTGCACAGTTAGGCCA
* * ** * *
9816567 TTATTCTTTTACTCAACGATATTCAATTGTTCATCTAACTGGCATAATTAACACCTTTCTGTCAT
1 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTAACACATTTCTGTCAA
9816632 TTGCACAGTTAGGC
66 TTGCACAGTTAGGC
9816646 TTCAAAGGCA
Statistics
Matches: 293, Mismatches: 28, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
243 71 0.24
244 220 0.75
245 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.37
Consensus pattern (243 bp):
TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTAACACATTTCTGTCAA
TTGCACAGTTAGGCCATTATTATTTTACTCAACAGTATTTAACCGTTCATCTAACTGGAATAATT
GACACCTTTCTGCCAATTGCACAATTAGGCCATTATTCTTTTACTCAACGGTATTCAACAATTCA
TCTAACTGGCATAATTGACACCTTTCTACCAATTGCACAGTTAGGCCA
Found at i:9816705 original size:68 final size:68
Alignment explanation
Indices: 9816596--9816851 Score: 386
Period size: 68 Copynumber: 3.8 Consensus size: 68
9816586 TATTCAATTG
* * * *
9816596 TTCATCTAACTGGCATAATTAACACCTTTCTGTCATTTGCACAGTTAGGCTTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
9816661 TCT
66 TCT
* *
9816664 TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCCCAAATGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
9816729 TCT
66 TCT
* * * *
9816732 TTCATATAACTGGCATAAATGACATATTTCTGTTATTTGCACAATTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
* *
9816797 CCC
66 TCT
**
9816800 TTCATCTAACTATCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCT
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCT
9816852 ATAATCGTTT
Statistics
Matches: 168, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 168 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
TCT
Found at i:9817183 original size:55 final size:54
Alignment explanation
Indices: 9817059--9817203 Score: 209
Period size: 55 Copynumber: 2.7 Consensus size: 54
9817049 TCACATCTAT
* **
9817059 TTCCCATACGGAAATTCATACACTTAGTATGAATTTTTCAGTTCGCACCCATGG
1 TTCCCATACAGAAATTCATACACTTAGTATGAATTTTTCAGTTCGCACCCAAAG
* * * *
9817113 TGCCCATACTGAAATTCCTACACTTAGTATGAATTTTTCATTTTCGCACCCAAAG
1 TTCCCATACAGAAATTCATACACTTAGTATGAATTTTTCA-GTTCGCACCCAAAG
*
9817168 TTCCCATACAAAAATTCATACACTTAGTATGAATTT
1 TTCCCATACAGAAATTCATACACTTAGTATGAATTT
9817204 CTTAAATTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
54 37 0.46
55 43 0.54
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (54 bp):
TTCCCATACAGAAATTCATACACTTAGTATGAATTTTTCAGTTCGCACCCAAAG
Found at i:9817733 original size:95 final size:95
Alignment explanation
Indices: 9817548--9817772 Score: 242
Period size: 95 Copynumber: 2.4 Consensus size: 95
9817538 TCTGACTTTA
* * * * *
9817548 TAGTATCGATACTAC-TACCCTAGTATTGATACTTCTATACTATGGTATCGATACCCCCTTCTGG
1 TAGTATCGATAC-ACTTATCATGGTATCGATACTACTATACTATGGTATCGATACCCCCTTCTGG
* * *
9817612 TATCGATACTGATTTTAGGTTTGATGTTCCC
65 TATCGATACCGATTTTAGATTCGATGTTCCC
* ** *
9817643 TAGTATTGATACTGTTA-CTATGGTATCGATACTACTATACTATGGTA-CTGATACCCCTTTAC-
1 TAGTATCGATACACTTATC-ATGGTATCGATACTACTATACTATGGTATC-GATACCCCCTT-CT
* * *
9817705 GGTATCGATACCGATTTTTGATTCGATGTTGCT
63 GGTATCGATACCGATTTTAGATTCGATGTTCCC
*
9817738 TGGTATCGATACACTTATCATGGTATCGATACTAC
1 TAGTATCGATACACTTATCATGGTATCGATACTAC
9817773 CTCTTCGGTA
Statistics
Matches: 107, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
94 2 0.02
95 103 0.96
96 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (95 bp):
TAGTATCGATACACTTATCATGGTATCGATACTACTATACTATGGTATCGATACCCCCTTCTGGT
ATCGATACCGATTTTAGATTCGATGTTCCC
Found at i:9818722 original size:70 final size:70
Alignment explanation
Indices: 9818641--9818780 Score: 217
Period size: 70 Copynumber: 2.0 Consensus size: 70
9818631 TCCATAGCAA
* *
9818641 TATAAAATAAAAAGTAATAAATTTGAGTTTACAATACAACTAAGCTCCTAAATCATCCAAAAAAT
1 TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACGAAGCTCCTAAATCATCCAAAAAAT
9818706 ACACT
66 ACACT
* * * *
9818711 TATAAGATAAAAAGTAATAAATTTAAGTTTACAATACAAGGGAGCTCCTAAATCATCCAAATAAT
1 TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACGAAGCTCCTAAATCATCCAAAAAAT
*
9818776 GCACT
66 ACACT
9818781 GAGTTTAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 63 1.00
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.27
Consensus pattern (70 bp):
TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACGAAGCTCCTAAATCATCCAAAAAAT
ACACT
Found at i:9819519 original size:20 final size:20
Alignment explanation
Indices: 9819494--9819532 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9819484 AATACTGGTA
* *
9819494 CTAACCTCTGGGTATCGATG
1 CTAACCCCTGGATATCGATG
9819514 CTAACCCCTGGATATCGAT
1 CTAACCCCTGGATATCGAT
9819533 ACTACTAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (20 bp):
CTAACCCCTGGATATCGATG
Found at i:9828909 original size:17 final size:17
Alignment explanation
Indices: 9828884--9828920 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
9828874 TATAGATTTT
*
9828884 AATACGATTCCCATAAA
1 AATACGATTCCCAGAAA
*
9828901 AATATGATTCCCAGAAA
1 AATACGATTCCCAGAAA
9828918 AAT
1 AAT
9828921 TCTTGTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.19, G:0.08, T:0.24
Consensus pattern (17 bp):
AATACGATTCCCAGAAA
Found at i:9830366 original size:26 final size:25
Alignment explanation
Indices: 9830330--9830384 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
9830320 AAGTGCTAAG
* *
9830330 ACACATAAGGTTGTGCCCACCATAAT
1 ACACACAAGGTCGTGCCCACCAT-AT
*
9830356 ACACACAAGGTCGTGCCTACCATAT
1 ACACACAAGGTCGTGCCCACCATAT
9830381 ACAC
1 ACAC
9830385 TAAGTTTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.35, C:0.31, G:0.15, T:0.20
Consensus pattern (25 bp):
ACACACAAGGTCGTGCCCACCATAT
Found at i:9831697 original size:26 final size:25
Alignment explanation
Indices: 9831668--9831779 Score: 81
Period size: 26 Copynumber: 4.6 Consensus size: 25
9831658 TTATTTTTTT
9831668 ATTAAATTTAAATTACATATTCTCTA
1 ATTAAATTTAAATTACATATTCT-TA
* ** *
9831694 ATTAAATTTATATTTTAAATT-TTA
1 ATTAAATTTAAATTACATATTCTTA
* * **
9831718 ATTAATTTTAAATT-TATA-AATT-
1 ATTAAATTTAAATTACATATTCTTA
*
9831740 ATTAAATTTAAATTACATAATCTCTA
1 ATTAAATTTAAATTACATATTCT-TA
9831766 ATT-AATTTATAATT
1 ATTAAATTTA-AATT
9831780 TAAATAGTGT
Statistics
Matches: 68, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
22 13 0.19
23 8 0.12
24 15 0.22
25 8 0.12
26 24 0.35
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTAAATTTAAATTACATATTCTTA
Found at i:9831715 original size:7 final size:7
Alignment explanation
Indices: 9831695--9831753 Score: 50
Period size: 7 Copynumber: 8.0 Consensus size: 7
9831685 TATTCTCTAA
9831695 TTAAA-T
1 TTAAATT
*
9831701 TTATATT
1 TTAAATT
9831708 TTAAATT
1 TTAAATT
9831715 TTAATTAATT
1 TT-A--AATT
9831725 TTAAATT
1 TTAAATT
9831732 TATAAATT
1 T-TAAATT
9831740 ATTAAA-T
1 -TTAAATT
9831747 TTAAATT
1 TTAAATT
9831754 ACATAATCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
6 9 0.20
7 16 0.36
8 11 0.25
9 2 0.05
10 6 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAAATT
Found at i:9831812 original size:20 final size:20
Alignment explanation
Indices: 9831770--9831813 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
9831760 TCTCTAATTA
*
9831770 ATTTATAATTTAAATAGTGT
1 ATTTATAATTTAAATACTGT
*
9831790 ATTTA-AATTTAAAATACTTT
1 ATTTATAATTT-AAATACTGT
9831810 ATTT
1 ATTT
9831814 TCTGTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (20 bp):
ATTTATAATTTAAATACTGT
Found at i:9832087 original size:14 final size:14
Alignment explanation
Indices: 9832053--9832094 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
9832043 GTATGTAATT
9832053 TAAATTTAATAAAAAA
1 TAAATTT-AT-AAAAA
*
9832069 TAAATTTATAAACA
1 TAAATTTATAAAAA
9832083 TAAATTTATAAA
1 TAAATTTATAAA
9832095 GTGTTTGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 16 0.64
15 2 0.08
16 7 0.28
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAATTTATAAAAA
Found at i:9832393 original size:24 final size:24
Alignment explanation
Indices: 9832361--9832407 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
9832351 TCCATCCTTT
9832361 CTTCTTAATTTAATAAAACAATTC
1 CTTCTTAATTTAATAAAACAATTC
9832385 CTTCTTAATTTAATAAAACAATT
1 CTTCTTAATTTAATAAAACAATT
9832408 TCATGACCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.43
Consensus pattern (24 bp):
CTTCTTAATTTAATAAAACAATTC
Found at i:9832545 original size:20 final size:19
Alignment explanation
Indices: 9832512--9832581 Score: 77
Period size: 20 Copynumber: 3.6 Consensus size: 19
9832502 TACTGCTCAT
* *
9832512 TACTGTTCACACAGTATCAA
1 TACTATTCATACAGTA-CAA
*
9832532 TATTATTCATACAGTAACAA
1 TACTATTCATACAGT-ACAA
* *
9832552 CACTATTCATACAGTACAG
1 TACTATTCATACAGTACAA
9832571 TACTATTCATA
1 TACTATTCATA
9832582 AAAACATTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 13 0.31
20 28 0.67
21 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (19 bp):
TACTATTCATACAGTACAA
Found at i:9833935 original size:19 final size:19
Alignment explanation
Indices: 9833911--9833956 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
9833901 CTAAATCCCT
*
9833911 TTTCAAAAT-TTATTTTGGC
1 TTTCAAAATCTAATTTT-GC
*
9833930 TTTCAAAATCTAATTTTGT
1 TTTCAAAATCTAATTTTGC
9833949 TTTCAAAA
1 TTTCAAAA
9833957 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.50
Consensus pattern (19 bp):
TTTCAAAATCTAATTTTGC
Found at i:9838151 original size:31 final size:31
Alignment explanation
Indices: 9838114--9838187 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
9838104 AAAAATTAAA
*
9838114 TGTTTAGGTACTAAAATAGATCAAAACTTAT
1 TGTTTAGGTACTAAAACAGATCAAAACTTAT
* *
9838145 TGTTTAGATACTAAAACAGTTCAAAACTTAT
1 TGTTTAGGTACTAAAACAGATCAAAACTTAT
**
9838176 AATTTAGGTACT
1 TGTTTAGGTACT
9838188 TAATGCATAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (31 bp):
TGTTTAGGTACTAAAACAGATCAAAACTTAT
Found at i:9838452 original size:2 final size:2
Alignment explanation
Indices: 9838447--9838475 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9838437 CAGAAACGTT
9838447 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9838476 TATGGGTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9839246 original size:70 final size:70
Alignment explanation
Indices: 9839165--9839304 Score: 217
Period size: 70 Copynumber: 2.0 Consensus size: 70
9839155 TCCATAGCAA
* *
9839165 TATAAAATAAAAAGTAATAAATTTGAGTTTACATTACAACAAAGCTCCTAAATCATCCAAATAAT
1 TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
9839230 ACACT
66 ACACT
* ***
9839235 TATAAGATAAAAAGTAATAAATTTAAGTTTACAATACAAGGGAGCTCCTAAATCATCCAAATAAT
1 TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
*
9839300 GCACT
66 ACACT
9839305 GAGTTTAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 63 1.00
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.28
Consensus pattern (70 bp):
TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
ACACT
Found at i:9840039 original size:20 final size:20
Alignment explanation
Indices: 9840016--9840060 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
9840006 TCAGTATTGG
* *
9840016 TACTAACCTCTGGGTATCGA
1 TACTAACCCCTGGATATCGA
9840036 TACTAACCCCTGGATATCGA
1 TACTAACCCCTGGATATCGA
9840056 TACTA
1 TACTA
9840061 CTAACTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (20 bp):
TACTAACCCCTGGATATCGA
Found at i:9848052 original size:31 final size:31
Alignment explanation
Indices: 9848015--9848088 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
9848005 AAAAATTAAA
*
9848015 TGTTTAGGTACTAAAATAGATCAAAACTTAT
1 TGTTTAGGTACTAAAACAGATCAAAACTTAT
* * *
9848046 TGTTTAGATACTAAAACGGTTCAAAACTTAT
1 TGTTTAGGTACTAAAACAGATCAAAACTTAT
**
9848077 AATTTAGGTACT
1 TGTTTAGGTACT
9848089 TAATGCATAG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (31 bp):
TGTTTAGGTACTAAAACAGATCAAAACTTAT
Found at i:9849136 original size:70 final size:70
Alignment explanation
Indices: 9849055--9849194 Score: 226
Period size: 70 Copynumber: 2.0 Consensus size: 70
9849045 TCCATAGCAA
*
9849055 TATAAAATAAAAAGTAATAAATTTGAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
1 TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
9849120 ACACT
66 ACACT
* ***
9849125 TATAAGATAAAAAGTAATAAATTTAAGTTTACAATACAAGGGAGCTCCTAAATCATCCAAATAAT
1 TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
*
9849190 GCACT
66 ACACT
9849195 GAGTTTAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.27
Consensus pattern (70 bp):
TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
ACACT
Found at i:9849930 original size:20 final size:20
Alignment explanation
Indices: 9849907--9849951 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
9849897 TCAGTATTGG
* **
9849907 TACTAACCTCTGGGTATCGA
1 TACTAACCCCTGGACATCGA
9849927 TACTAACCCCTGGACATCGA
1 TACTAACCCCTGGACATCGA
9849947 TACTA
1 TACTA
9849952 CTAACTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (20 bp):
TACTAACCCCTGGACATCGA
Found at i:9860368 original size:20 final size:20
Alignment explanation
Indices: 9860343--9860386 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
9860333 TCAGTTCAGA
9860343 AACTGCCTAATTTCAACCTT
1 AACTGCCTAATTTCAACCTT
9860363 AACTGCCTAATTTCAACCTT
1 AACTGCCTAATTTCAACCTT
9860383 AACT
1 AACT
9860387 AGTTTCTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.34
Consensus pattern (20 bp):
AACTGCCTAATTTCAACCTT
Found at i:9861427 original size:19 final size:22
Alignment explanation
Indices: 9861371--9861429 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
9861361 GGTACTATGG
9861371 TAGGGGTATCGATACCATAGCA
1 TAGGGGTATCGATACCATAGCA
*
9861393 TAGGGGTATCAATACC-TA-C-
1 TAGGGGTATCGATACCATAGCA
*
9861412 TAGGGGTATCGGTACCAT
1 TAGGGGTATCGATACCAT
9861430 CCGAACATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 14 0.42
20 2 0.06
21 2 0.06
22 15 0.45
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (22 bp):
TAGGGGTATCGATACCATAGCA
Found at i:9864081 original size:21 final size:22
Alignment explanation
Indices: 9864057--9864177 Score: 103
Period size: 21 Copynumber: 5.5 Consensus size: 22
9864047 ACCCGACAGG
*
9864057 GGGTATCGATACCA-T-AAGGGA
1 GGGTATCGATACCATTCAA-AGA
9864078 GGGTATCGATACTCATTCAAAGA
1 GGGTATCGATAC-CATTCAAAGA
*
9864101 GGGTATCGATACCTATTC-AA-T
1 GGGTATCGATACC-ATTCAAAGA
* *
9864122 TGGTATCGATACCTATTCAAAGG
1 GGGTATCGATACC-ATTCAAAGA
9864145 GGGTATCGATACC-TGT-ATAAG-
1 GGGTATCGATACCAT-TCA-AAGA
9864166 GGGTATCGATAC
1 GGGTATCGATAC
9864178 TCTATGCACA
Statistics
Matches: 87, Mismatches: 5, Indels: 16
0.81 0.05 0.15
Matches are distributed among these distances:
21 43 0.49
22 11 0.13
23 31 0.36
24 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.27
Consensus pattern (22 bp):
GGGTATCGATACCATTCAAAGA
Found at i:9864102 original size:23 final size:23
Alignment explanation
Indices: 9864076--9864182 Score: 109
Period size: 21 Copynumber: 4.8 Consensus size: 23
9864066 TACCATAAGG
9864076 GAGGGTATCGATA-CTCATTCAAA
1 GAGGGTATCGATACCT-ATTCAAA
9864099 GAGGGTATCGATACCTATTC-AA
1 GAGGGTATCGATACCTATTCAAA
**
9864121 -TTGGTATCGATACCTATTCAAA
1 GAGGGTATCGATACCTATTCAAA
* *
9864143 GGGGGTATCGATACCT-GT-ATAA
1 GAGGGTATCGATACCTATTCA-AA
9864165 G-GGGTATCGATACTCTAT
1 GAGGGTATCGATAC-CTAT
9864183 GCACAAAATT
Statistics
Matches: 72, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
21 30 0.42
22 10 0.14
23 30 0.42
24 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (23 bp):
GAGGGTATCGATACCTATTCAAA
Found at i:9864171 original size:44 final size:43
Alignment explanation
Indices: 9864054--9864182 Score: 131
Period size: 44 Copynumber: 2.9 Consensus size: 43
9864044 TAAACCCGAC
9864054 AGGGGGTATCGATACC--ATAAGGGAGGGTATCGATA-CTCATTCAA
1 AGGGGGTATCGATACCTTATAA--G-GGGTATCGATACCT-ATTCAA
* **
9864098 AGAGGGTATCGATACC-TATTCAATTGGTATCGATACCTATTCAA
1 AGGGGGTATCGATACCTTA-T-AAGGGGTATCGATACCTATTCAA
9864142 AGGGGGTATCGATACCTGTATAAGGGGTATCGATACTCTAT
1 AGGGGGTATCGATACCT-TATAAGGGGTATCGATAC-CTAT
9864183 GCACAAAATT
Statistics
Matches: 72, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
44 59 0.82
45 8 0.11
46 3 0.04
47 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (43 bp):
AGGGGGTATCGATACCTTATAAGGGGTATCGATACCTATTCAA
Found at i:9869962 original size:22 final size:20
Alignment explanation
Indices: 9869934--9869992 Score: 75
Period size: 22 Copynumber: 2.9 Consensus size: 20
9869924 GTACCTATGG
9869934 TGGGGGTATCGATACCATAGC
1 TGGGGGTATCGATACCATA-C
9869955 ATGGGGGTATCGATACC-TAC
1 -TGGGGGTATCGATACCATAC
* *
9869975 TAGGGGTATCGGTACCAT
1 TGGGGGTATCGATACCAT
9869993 CCGAACATTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.41
20 2 0.06
21 2 0.06
22 16 0.47
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (20 bp):
TGGGGGTATCGATACCATAC
Found at i:9869982 original size:19 final size:22
Alignment explanation
Indices: 9869936--9869992 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 22
9869926 ACCTATGGTG
*
9869936 GGGGTATCGATACCATAGCATG
1 GGGGTATCGATACCATAGCATA
9869958 GGGGTATCGATACC-TA-C-TA
1 GGGGTATCGATACCATAGCATA
*
9869977 GGGGTATCGGTACCAT
1 GGGGTATCGATACCAT
9869993 CCGAACATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 14 0.44
20 2 0.06
21 2 0.06
22 14 0.44
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (22 bp):
GGGGTATCGATACCATAGCATA
Found at i:9870662 original size:26 final size:25
Alignment explanation
Indices: 9870626--9870680 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
9870616 AAGTGCTAAG
* *
9870626 ACACATAAGGTTGTGCCCACCATAAT
1 ACACACAAGGTCGTGCCCACCAT-AT
*
9870652 ACACACAAGGTCGTGCCTACCATAT
1 ACACACAAGGTCGTGCCCACCATAT
9870677 ACAC
1 ACAC
9870681 TAAGTTTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.35, C:0.31, G:0.15, T:0.20
Consensus pattern (25 bp):
ACACACAAGGTCGTGCCCACCATAT
Found at i:9871977 original size:7 final size:7
Alignment explanation
Indices: 9871957--9872015 Score: 50
Period size: 7 Copynumber: 8.0 Consensus size: 7
9871947 TACTTTGTAA
9871957 TTAAA-T
1 TTAAATT
*
9871963 TTATATT
1 TTAAATT
9871970 TTAAATT
1 TTAAATT
9871977 TTAATTAATT
1 TT-A--AATT
9871987 TTAAATT
1 TTAAATT
9871994 TATAAATT
1 T-TAAATT
9872002 ATTAAA-T
1 -TTAAATT
9872009 TTAAATT
1 TTAAATT
9872016 ACATAATCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
6 9 0.20
7 16 0.36
8 11 0.25
9 2 0.05
10 6 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAAATT
Found at i:9871989 original size:24 final size:26
Alignment explanation
Indices: 9871954--9872015 Score: 74
Period size: 24 Copynumber: 2.4 Consensus size: 26
9871944 ACATACTTTG
*
9871954 TAATTAAATTTATATTT-TAAATT-T
1 TAATTAAATTTAAATTTATAAATTAT
*
9871978 TAATTAATTTTAAATTTATAAATTAT
1 TAATTAAATTTAAATTTATAAATTAT
9872004 TAAATTTAAATT
1 T-AA-TTAAATT
9872016 ACATAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 15 0.48
25 6 0.19
26 2 0.06
27 2 0.06
28 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TAATTAAATTTAAATTTATAAATTAT
Found at i:9872031 original size:26 final size:24
Alignment explanation
Indices: 9871930--9872041 Score: 79
Period size: 26 Copynumber: 4.6 Consensus size: 24
9871920 TTATTTTTTT
*
9871930 ATTAAATTTAAATTACATACTTTGTA
1 ATTAAATTTAAATTACATA-ATT-TA
* **
9871956 ATTAAATTTATATTTTA-AATTTTA
1 ATTAAATTTAAATTACATAA-TTTA
* * *
9871980 ATTAATTTTAAATT-TATAAATT-
1 ATTAAATTTAAATTACATAATTTA
9872002 ATTAAATTTAAATTACATAATCTCTA
1 ATTAAATTTAAATTACATAAT-T-TA
9872028 ATT-AATTTATAATT
1 ATTAAATTTA-AATT
9872042 TAAATAGTGT
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
22 13 0.19
23 8 0.12
24 17 0.25
25 10 0.14
26 21 0.30
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (24 bp):
ATTAAATTTAAATTACATAATTTA
Found at i:9872063 original size:72 final size:72
Alignment explanation
Indices: 9871928--9872063 Score: 177
Period size: 72 Copynumber: 1.9 Consensus size: 72
9871918 TTTTATTTTT
* * * * * *
9871928 TTATTAAATTTAAATTACATACTTTGTAATTAAATTTATATTTTAAATTTTAATTAATTTTAAAT
1 TTATTAAATTTAAATTACATAATCTCTAATTAAATTTATAATTTAAATTGTAATTAATATTAAAT
9871993 TTATAAA
66 TTATAAA
*
9872000 TTATTAAATTTAAATTACATAATCTCTAATT-AATTTATAATTTAAATAGTGTATTTAA-ATTAA
1 TTATTAAATTTAAATTACATAATCTCTAATTAAATTTATAATTTAAAT--TGTAATTAATATTAA
9872063 A
64 A
9872064 AATACTTTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
71 15 0.27
72 33 0.60
73 7 0.13
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (72 bp):
TTATTAAATTTAAATTACATAATCTCTAATTAAATTTATAATTTAAATTGTAATTAATATTAAAT
TTATAAA
Found at i:9872769 original size:20 final size:20
Alignment explanation
Indices: 9872741--9872810 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
9872731 TACTGCTCAT
* *
9872741 TACTGTTCACACAGTAACGA
1 TACTATTCATACAGTAACGA
*
9872761 TACTATTCATACAGTAACGG
1 TACTATTCATACAGTAACGA
* *
9872781 CACTATTCATACAGT-ACAA
1 TACTATTCATACAGTAACGA
9872800 TACTATTCATA
1 TACTATTCATA
9872811 AACACATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 12 0.28
20 31 0.72
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (20 bp):
TACTATTCATACAGTAACGA
Found at i:9874166 original size:19 final size:19
Alignment explanation
Indices: 9874142--9874187 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
9874132 CTAAATCCCT
*
9874142 TTTCAAAAT-TTATTTTGGC
1 TTTCAAAATCTAATTTT-GC
*
9874161 TTTCAAAATCTAATTTTGT
1 TTTCAAAATCTAATTTTGC
9874180 TTTCAAAA
1 TTTCAAAA
9874188 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.50
Consensus pattern (19 bp):
TTTCAAAATCTAATTTTGC
Found at i:9875567 original size:20 final size:20
Alignment explanation
Indices: 9875539--9875603 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
9875529 TTCATTATTG
*
9875539 TTCACACAATATCGGTACTA
1 TTCATACAATATCGGTACTA
9875559 TTCATACAATATCGGTACTA
1 TTCATACAATATCGGTACTA
* *
9875579 TTCATACAATA-CAGTTCTA
1 TTCATACAATATCGGTACTA
9875598 TTCATA
1 TTCATA
9875604 AAAACATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 12 0.29
20 30 0.71
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (20 bp):
TTCATACAATATCGGTACTA
Found at i:9883004 original size:53 final size:53
Alignment explanation
Indices: 9882924--9883050 Score: 254
Period size: 53 Copynumber: 2.4 Consensus size: 53
9882914 AATGTTAGGC
9882924 TTTGGCCAATAAGGGGTATTTAGAGAATTAACTTCAGTGTTTATCCTTAAGAG
1 TTTGGCCAATAAGGGGTATTTAGAGAATTAACTTCAGTGTTTATCCTTAAGAG
9882977 TTTGGCCAATAAGGGGTATTTAGAGAATTAACTTCAGTGTTTATCCTTAAGAG
1 TTTGGCCAATAAGGGGTATTTAGAGAATTAACTTCAGTGTTTATCCTTAAGAG
9883030 TTTGGCCAATAAGGGGTATTT
1 TTTGGCCAATAAGGGGTATTT
9883051 GTACAATACC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 74 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (53 bp):
TTTGGCCAATAAGGGGTATTTAGAGAATTAACTTCAGTGTTTATCCTTAAGAG
Found at i:9884217 original size:16 final size:17
Alignment explanation
Indices: 9884192--9884225 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
9884182 ATTACCCTAA
*
9884192 GATGTTAGACTT-TGTT
1 GATGTGAGACTTATGTT
9884208 GATGTGAGACTTATGTT
1 GATGTGAGACTTATGTT
9884225 G
1 G
9884226 CCCATTGTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.21, C:0.06, G:0.29, T:0.44
Consensus pattern (17 bp):
GATGTGAGACTTATGTT
Found at i:9885863 original size:17 final size:17
Alignment explanation
Indices: 9885818--9885863 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
9885808 TTAAAAAAAT
* *
9885818 AAAAATTATT-TAGATT
1 AAAAATTATTAAAGATA
*
9885834 AAAAA-TATAAAAGATA
1 AAAAATTATTAAAGATA
9885850 AAAAATTATTAAAG
1 AAAAATTATTAAAG
9885864 TACTCAATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 3 0.12
16 14 0.58
17 7 0.29
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (17 bp):
AAAAATTATTAAAGATA
Found at i:9885891 original size:24 final size:25
Alignment explanation
Indices: 9885852--9885912 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 25
9885842 AAAAGATAAA
*
9885852 AAATTATT-AAAGTACT-CAATACATT
1 AAATTATTAAAAATACTACAA-A-ATT
9885877 AAA-TA-TAAAAATACTACAAAATT
1 AAATTATTAAAAATACTACAAAATT
9885900 AAATTATTAAAAA
1 AAATTATTAAAAA
9885913 AATTAATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
23 7 0.23
24 12 0.39
25 12 0.39
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (25 bp):
AAATTATTAAAAATACTACAAAATT
Found at i:9886565 original size:28 final size:23
Alignment explanation
Indices: 9886513--9886571 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
9886503 CTTTATTATT
9886513 ATTTAATTTAAATTTTAGTAGTA
1 ATTTAATTTAAATTTTAGTAGTA
9886536 ATTTAATTTAAATTTTAGTAGTA
1 ATTTAATTTAAATTTTAGTAGTA
*
9886559 ATATAA-TTAAATT
1 ATTTAATTTAAATT
9886572 ATATTTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 7 0.20
23 28 0.80
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (23 bp):
ATTTAATTTAAATTTTAGTAGTA
Found at i:9887154 original size:24 final size:24
Alignment explanation
Indices: 9887127--9887183 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
9887117 CGGCACTACC
*
9887127 CAGGCGCAGTCACTTATCACAGCG
1 CAGGCGCAGGCACTTATCACAGCG
9887151 CAGGCGCAGGCACTTATCACAGCG
1 CAGGCGCAGGCACTTATCACAGCG
9887175 CAGGCGCAG
1 CAGGCGCAG
9887184 CCACCGGTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.33, G:0.30, T:0.12
Consensus pattern (24 bp):
CAGGCGCAGGCACTTATCACAGCG
Found at i:9893562 original size:2 final size:2
Alignment explanation
Indices: 9893555--9893587 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9893545 CTCATGACTG
9893555 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9893588 ATTTCTAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9904025 original size:106 final size:106
Alignment explanation
Indices: 9903880--9904523 Score: 878
Period size: 106 Copynumber: 6.0 Consensus size: 106
9903870 GTACTGTTCT
* * * * * *
9903880 GAGTCCAATATCCTCCGCCGTGAAGTTTAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGGAAATGGTTTGTTGACAA
9903945 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC-C
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* * * **
9903985 TGAGTCCAATACCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTTTTTGTTGACA
1 -GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGGAAATGGTTTGTTGACA
* * *
9904050 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGACTC
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* * * * *
9904092 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGGAAATGGTTTGTTGACAA
* * * * * *
9904157 CCAACTGCCCCTTCGCTGTGAAGTTGAGCTTGTGGTGTCTC
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* * * *
9904198 GAGTCTAATATCCTTCGATGTGAAGTTGAAATTGACACTGAAACTGGGAAATGGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGGAAATGGTTTGTTGACAA
**
9904263 CCATACGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* * *
9904304 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGTAATGGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGGAAATGGTTTGTTGACAA
*
9904369 CCAGCCGTCCCTTCCTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* *
9904410 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAATGAAACT-GAAAAGTGGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTC----TGAAACTGGGAAA-TGGTTTGTT
*
9904474 GACAACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTC
61 GACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
9904520 GAGT
1 GAGT
9904524 GGCGTGATAT
Statistics
Matches: 475, Mismatches: 57, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
106 407 0.86
107 1 0.00
109 3 0.01
110 64 0.13
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGGAAATGGTTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
Found at i:9905572 original size:18 final size:18
Alignment explanation
Indices: 9905531--9905573 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
9905521 ACCCACCTTA
* **
9905531 TTTTTTTTCTTTTTTTGT
1 TTTTTTTTCTCTTTTCAT
*
9905549 TCTTTTTTCTCTTTTCAT
1 TTTTTTTTCTCTTTTCAT
9905567 TTTTTTT
1 TTTTTTT
9905574 CAATTTAGGG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (18 bp):
TTTTTTTTCTCTTTTCAT
Found at i:9917751 original size:11 final size:11
Alignment explanation
Indices: 9917737--9917775 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
9917727 TAATAAAATA
9917737 ATAATATTTAT
1 ATAATATTTAT
*
9917748 ATAATATATAT
1 ATAATATTTAT
*
9917759 ATAATA-TAAT
1 ATAATATTTAT
9917769 ATAATAT
1 ATAATAT
9917776 ATAAATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATAATATTTAT
Found at i:9917754 original size:5 final size:5
Alignment explanation
Indices: 9917722--9917784 Score: 58
Period size: 5 Copynumber: 12.4 Consensus size: 5
9917712 TAAAATGTGT
* * *
9917722 TAATT TAATA AAATAA TAATA TTTATA TAATA TATATA TAATA TAATA
1 TAATA TAATA TAAT-A TAATA -TAATA TAATA TA-ATA TAATA TAATA
9917770 TAATA T-ATA -AATA TA
1 TAATA TAATA TAATA TA
9917785 TATGGTCATG
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 6 0.12
5 29 0.60
6 13 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TAATA
Found at i:9917756 original size:2 final size:2
Alignment explanation
Indices: 9917740--9917787 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
9917730 TAAAATAATA
*
9917740 AT AT TT AT AT A- AT AT AT AT AT A- AT AT A- 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
*
9917778 AA AT AT AT AT
1 AT AT AT AT AT
9917788 GGTCATGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
1 4 0.11
2 34 0.89
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:9920224 original size:31 final size:31
Alignment explanation
Indices: 9920187--9920248 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
9920177 AAAAATTAAA
* **
9920187 TGTTTAGGTACTAAAATGGATCAAAACTTAT
1 TGTTTAGATACTAAAACAGATCAAAACTTAT
*
9920218 TGTTTAGATACTAAAACAGTTCAAAACTTAT
1 TGTTTAGATACTAAAACAGATCAAAACTTAT
9920249 AATTTACGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (31 bp):
TGTTTAGATACTAAAACAGATCAAAACTTAT
Found at i:9921317 original size:70 final size:70
Alignment explanation
Indices: 9921235--9921374 Score: 235
Period size: 70 Copynumber: 2.0 Consensus size: 70
9921225 TCCATAGCAA
*
9921235 TATAAAATAAAAAGTAATAAATTTGAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
1 TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
9921300 ACACT
66 ACACT
***
9921305 TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAAGGGAGCTCCTAAATCATCCAAATAAT
1 TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
*
9921370 GCACT
66 ACACT
9921375 GAGTTTAAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.50, C:0.15, G:0.08, T:0.27
Consensus pattern (70 bp):
TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
ACACT
Found at i:9922107 original size:20 final size:21
Alignment explanation
Indices: 9922055--9922107 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
9922045 ACTGTTCATA
9922055 GGTATCGATACTAAGCCCCTC
1 GGTATCGATACTAAGCCCCTC
* * * * *
9922076 AGTATTGGTACTAA-CCTCTG
1 GGTATCGATACTAAGCCCCTC
9922096 GGTATCGATACT
1 GGTATCGATACT
9922108 TGTAACAACC
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (21 bp):
GGTATCGATACTAAGCCCCTC
Found at i:9923067 original size:81 final size:81
Alignment explanation
Indices: 9923029--9923590 Score: 778
Period size: 81 Copynumber: 7.0 Consensus size: 81
9923019 ACTAATCCCC
* * *
9923029 TATTCTTTTACTCAACAGTGTTTAACCGTACATCTAACTGGCATAATTAACACCTTTCTGTCAAT
1 TATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAT
9923094 TGCACAGTTAGGCCAT
66 TGCACAGTTAGGCCAT
*
9923110 TATTCTTTTACTCAACA-TATTTAA-CGTTCATCTAACTGGAATAATTGACACCTTTCTGTCAAT
1 TATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAT
9923173 TGCACAGTTAGGCCAT
66 TGCACAGTTAGGCCAT
* **
9923189 TATTCTTTTACTCAAC-GATATTCAACAATTCATCTAACTGGCATAATTGACACCTTTCT-TCCA
1 TATTCTTTTACTCAACAG-TATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT-CA
9923252 ATTGCACAGTTAGGCCAT
64 ATTGCACAGTTAGGCCAT
* * *
9923270 TATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACTTTTCTGCCAAA
1 TATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTC-AA
**
9923335 TTGCACAGTTAGGTTAT
65 TTGCACAGTTAGGCCAT
* * * * *
9923352 TATTCTTTTACTCAA-AGGTAATTAACTGTTCATCTAACTAGCATAATTGGCACTTTTCT-TCCA
1 TATTCTTTTACTCAACA-GTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT-CA
*
9923415 ATTGCACAATTAGGCCAT
64 ATTGCACAGTTAGGCCAT
* * *
9923433 TATTCTTTTACTCAACGGTATTTAACCATTCATCTAACT-GCATAATTGACACCTTTCTGCCAAT
1 TATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAT
*
9923497 TGCATAGTTAGGCCAT
66 TGCACAGTTAGGCCAT
* * * * * *
9923513 TATTCTTTTACTCAACGGTATTCAATCGTTCATCTAACTAGCATAATTGACACATTTCTGTCATT
1 TATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAT
9923578 TGCACAGTTAGGC
66 TGCACAGTTAGGC
9923591 TTCAAAGGCA
Statistics
Matches: 429, Mismatches: 40, Indels: 24
0.87 0.08 0.05
Matches are distributed among these distances:
79 68 0.16
80 84 0.20
81 205 0.48
82 72 0.17
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (81 bp):
TATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAT
TGCACAGTTAGGCCAT
Found at i:9923398 original size:163 final size:162
Alignment explanation
Indices: 9923029--9923590 Score: 791
Period size: 163 Copynumber: 3.5 Consensus size: 162
9923019 ACTAATCCCC
* * * *
9923029 TATTCTTTTACTCAACAGTGT-TT-AACCGTACATCTAACTGGCATAATTAACACCTTTCTGTCA
1 TATTCTTTTACTCAA-AG-GTATTCAACTGTTCATCTAACTAGCATAATTGACACCTTTCTGTCA
* *
9923092 ATTGCACAGTTAGGCCATTATTCTTTTACTCAAC-ATATTTAA-CGTTCATCTAACTGGAATAAT
64 ATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAAT
*
9923155 TGACACCTTTCTGTCAATTGCACAGTTAGGCCAT
129 TGACACCTTTCTGCCAATTGCACAGTTAGGCCAT
* * ** *
9923189 TATTCTTTTACTCAACGATATTCAACAATTCATCTAACTGGCATAATTGACACCTTTCT-TCCAA
1 TATTCTTTTACTCAAAGGTATTCAACTGTTCATCTAACTAGCATAATTGACACCTTTCTGT-CAA
9923253 TTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATT
65 TTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATT
* **
9923318 GACACTTTTCTGCCAAATTGCACAGTTAGGTTAT
130 GACACCTTTCTGCC-AATTGCACAGTTAGGCCAT
* *
9923352 TATTCTTTTACTCAAAGGTAATT-AACTGTTCATCTAACTAGCATAATTGGCACTTTTCT-TCCA
1 TATTCTTTTACTCAAAGGT-ATTCAACTGTTCATCTAACTAGCATAATTGACACCTTTCTGT-CA
* *
9923415 ATTGCACAATTAGGCCATTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACT-GCATAAT
64 ATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAAT
*
9923479 TGACACCTTTCTGCCAATTGCATAGTTAGGCCAT
129 TGACACCTTTCTGCCAATTGCACAGTTAGGCCAT
* * *
9923513 TATTCTTTTACTCAACGGTATTCAA-TCGTTCATCTAACTAGCATAATTGACACATTTCTGTCAT
1 TATTCTTTTACTCAAAGGTATTCAACT-GTTCATCTAACTAGCATAATTGACACCTTTCTGTCAA
9923577 TTGCACAGTTAGGC
65 TTGCACAGTTAGGC
9923591 TTCAAAGGCA
Statistics
Matches: 362, Mismatches: 30, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
158 1 0.00
159 4 0.01
160 87 0.24
161 88 0.24
162 55 0.15
163 124 0.34
164 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (162 bp):
TATTCTTTTACTCAAAGGTATTCAACTGTTCATCTAACTAGCATAATTGACACCTTTCTGTCAAT
TGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTG
ACACCTTTCTGCCAATTGCACAGTTAGGCCAT
Found at i:9923650 original size:68 final size:68
Alignment explanation
Indices: 9923541--9923796 Score: 413
Period size: 68 Copynumber: 3.8 Consensus size: 68
9923531 TATTCAATCG
* * *
9923541 TTCATCTAACTAGCATAATTGACACATTTCTGTCATTTGCACAGTTAGGCTTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
*
9923606 TCT
66 CCT
* *
9923609 TTCATCTAACTGGCATAAATGGCACATTTCTGTCATTTGCACAGTTAGGCCCCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
9923674 CCT
66 CCT
* * *
9923677 TTCATCTAACTGGCATAAATGATATATTTCTGTCATTTGCACAGTTAGGCCTCAAAGACACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
9923742 CCT
66 CCT
* *
9923745 TTCATCTAACTGACATAAATGACACATTTCTGTCATTTGCACAGTTATGCCT
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCT
9923797 ATAATCGTTT
Statistics
Matches: 173, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 173 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:9924128 original size:55 final size:55
Alignment explanation
Indices: 9924006--9924163 Score: 192
Period size: 55 Copynumber: 2.9 Consensus size: 55
9923996 ACATCTATTT
* * * * ** *
9924006 CCCATACGGAAATTCATACACTTAGTATGAATTTCTCA-GTTCGCACCCATGGTG
1 CCCATACAGAAATTCATACACTTAGTATGAATTTTTCATTTTTGCACCCAAAGTC
* *
9924060 CCCATACTGAAATTCCTACACTTAGTATGAATTTTTCATTTTTGCACCCAAAGTC
1 CCCATACAGAAATTCATACACTTAGTATGAATTTTTCATTTTTGCACCCAAAGTC
* *
9924115 CCCATACAAAAATTCATACACTTAGTATGAATTTGTTAAATTTTTGCAC
1 CCCATACAGAAATTCATACACTTAGTATGAATTT-TT-CATTTTTGCAC
9924164 ACCTAGTGCC
Statistics
Matches: 89, Mismatches: 12, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
54 35 0.39
55 42 0.47
56 2 0.02
57 10 0.11
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (55 bp):
CCCATACAGAAATTCATACACTTAGTATGAATTTTTCATTTTTGCACCCAAAGTC
Found at i:9924679 original size:95 final size:95
Alignment explanation
Indices: 9924493--9924717 Score: 224
Period size: 95 Copynumber: 2.4 Consensus size: 95
9924483 TCTGACTTTA
* * * * * * *
9924493 TAGTATCGATACTAC-TACCCTAGTACCGATACTTCTATACTATGGTATCGATACCCCCTTCTGG
1 TAGTATCGATAC-ACTTATCATGGTATCGATACTACTATACTATGGTACCGATACCCCCTTCTGA
* * **
9924557 TATCGATACTGATTTTAGGTTTGATGTTCCC
65 TATCGATACAGATTTTAGATTCAATGTTCCC
***
9924588 TAGTATCGATATTGTTA-CTATGGTATCGATACTACTATACTATGGTACCGATACCCCCTTAC-G
1 TAGTATCGATACACTTATC-ATGGTATCGATACTACTATACTATGGTACCGATACCCCCTT-CTG
* * *
9924651 ATATCGATACCAG-TTTTTGATTCAATGTTGCT
64 ATATCGATA-CAGATTTTAGATTCAATGTTCCC
*
9924683 TGGTATCGATACACTTATCATGGTATCGATACTAC
1 TAGTATCGATACACTTATCATGGTATCGATACTAC
9924718 CTCTTCGGTA
Statistics
Matches: 105, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
94 1 0.01
95 100 0.95
96 4 0.04
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (95 bp):
TAGTATCGATACACTTATCATGGTATCGATACTACTATACTATGGTACCGATACCCCCTTCTGAT
ATCGATACAGATTTTAGATTCAATGTTCCC
Found at i:9936010 original size:31 final size:31
Alignment explanation
Indices: 9935944--9936015 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
9935934 AAATTAAATG
* **
9935944 TTTAGGTACTAAAATGGATCAAAACTTATTG
1 TTTAGGTACTAAAACGGATCAAAACTTATAA
* *
9935975 TTTAGATACTAAAACGGTTCAAAACTTATAA
1 TTTAGGTACTAAAACGGATCAAAACTTATAA
9936006 TTTAGGTACT
1 TTTAGGTACT
9936016 TAATGCATAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (31 bp):
TTTAGGTACTAAAACGGATCAAAACTTATAA
Found at i:9937063 original size:70 final size:70
Alignment explanation
Indices: 9936981--9937120 Score: 208
Period size: 70 Copynumber: 2.0 Consensus size: 70
9936971 TCCATATCAA
* *
9936981 TATAAAATAAAAAGTAATAAATTTGAGTTTACAATACAACAAAGCTCCTAAATCAACCAAATAAT
1 TATAAAATAAAAAGTAATAAATTTAAGTTTAAAATACAACAAAGCTCCTAAATCAACCAAATAAT
9937046 ACACT
66 ACACT
* *** *
9937051 TATAAGATAAAAAGTAATAAATTTAAGTTTAAAATACAAGGGAGCTCCTAAATCATCCAAATAAT
1 TATAAAATAAAAAGTAATAAATTTAAGTTTAAAATACAACAAAGCTCCTAAATCAACCAAATAAT
*
9937116 GCACT
66 ACACT
9937121 GAGTTTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (70 bp):
TATAAAATAAAAAGTAATAAATTTAAGTTTAAAATACAACAAAGCTCCTAAATCAACCAAATAAT
ACACT
Found at i:9937853 original size:20 final size:20
Alignment explanation
Indices: 9937830--9937874 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
9937820 TCAGTATTGG
* *
9937830 TACTAACCTCTGGGTATCGA
1 TACTAACCCCTGGATATCGA
*
9937850 TACTAACCCCTGGATATGGA
1 TACTAACCCCTGGATATCGA
9937870 TACTA
1 TACTA
9937875 CTAACTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (20 bp):
TACTAACCCCTGGATATCGA
Found at i:9945838 original size:31 final size:31
Alignment explanation
Indices: 9945801--9945874 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
9945791 AAAAATTAAA
*
9945801 TGTTTAGGTACTAAAATGGATCAAAACTTAT
1 TGTTTAGGTACTAAAACGGATCAAAACTTAT
* *
9945832 TGTTTAGATACTAAAACGGTTCAAAACTTAT
1 TGTTTAGGTACTAAAACGGATCAAAACTTAT
**
9945863 AATTTAGGTACT
1 TGTTTAGGTACT
9945875 TAATGCATAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (31 bp):
TGTTTAGGTACTAAAACGGATCAAAACTTAT
Found at i:9946915 original size:70 final size:70
Alignment explanation
Indices: 9946841--9946973 Score: 230
Period size: 70 Copynumber: 1.9 Consensus size: 70
9946831 CAATATAAAA
*
9946841 TAAAAAGTAATAAATTTGAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAATACACTTA
1 TAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAATACACTTA
9946906 TAAGT
66 TAAGT
* * *
9946911 TAAAAAGTAATAAATTTAAGTTTACAATACAAGAGAGCTCCTAAATCATCCAAATAATGCACT
1 TAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAATACACT
9946974 GAGTTTAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 59 1.00
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (70 bp):
TAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAATACACTTA
TAAGT
Found at i:9947708 original size:20 final size:20
Alignment explanation
Indices: 9947685--9947729 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
9947675 TCAGTATTGG
* *
9947685 TACTAACCTCTGGGTATCGA
1 TACTAACCCCTGGATATCGA
9947705 TACTAACCCCTGGATATCGA
1 TACTAACCCCTGGATATCGA
9947725 TACTA
1 TACTA
9947730 CTAACTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (20 bp):
TACTAACCCCTGGATATCGA
Found at i:9955643 original size:31 final size:31
Alignment explanation
Indices: 9955606--9955679 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
9955596 AAAAATTAAA
*
9955606 TGTTTAGGTACTAAAATGGATCAAAACTTAT
1 TGTTTAGGTACTAAAACGGATCAAAACTTAT
* *
9955637 TGTTTAGATACTAAAACGGTTCAAAACTTAT
1 TGTTTAGGTACTAAAACGGATCAAAACTTAT
**
9955668 AATTTAGGTACT
1 TGTTTAGGTACT
9955680 TAATGCATAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (31 bp):
TGTTTAGGTACTAAAACGGATCAAAACTTAT
Found at i:9956712 original size:66 final size:67
Alignment explanation
Indices: 9956636--9956765 Score: 203
Period size: 67 Copynumber: 2.0 Consensus size: 67
9956626 TCCATAGCAA
*
9956636 TATAAAATAAAAAGTAAT-AATTTGAGTTTACAATACACA-A-AGCTCCTAAATCATCCAAATAA
1 TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACA-AGAGAGCTCCTAAATCATCC-AATAA
9956698 TACT
64 TACT
*
9956702 TATAAGATAAAAAGTAATAAATTTAAGTTTACAATACAAGAGAGCTCCTAAATCATCCAATAAT
1 TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAAGAGAGCTCCTAAATCATCCAATAAT
9956766 GCACTGAGTT
Statistics
Matches: 59, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
66 18 0.31
67 25 0.42
68 16 0.27
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.28
Consensus pattern (67 bp):
TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAAGAGAGCTCCTAAATCATCCAATAATA
CT
Found at i:9957504 original size:20 final size:20
Alignment explanation
Indices: 9957455--9957523 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
9957445 TCATTGGTAC
9957455 CGATACTAAGCCCCTCA-ATAT
1 CGATACTAA-CCCCT-AGATAT
* * * * *
9957476 TGGTACTAACCTCTGGGTAT
1 CGATACTAACCCCTAGATAT
9957496 CGATACTAACCCCTAGATAT
1 CGATACTAACCCCTAGATAT
9957516 CGATACTA
1 CGATACTA
9957524 CTAACTTATT
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 30 0.81
21 7 0.19
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (20 bp):
CGATACTAACCCCTAGATAT
Found at i:9966419 original size:17 final size:17
Alignment explanation
Indices: 9966394--9966430 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
9966384 TATAGATTTT
*
9966394 AATACGATTCCCATAAA
1 AATACGATTCCCAGAAA
*
9966411 AATATGATTCCCAGAAA
1 AATACGATTCCCAGAAA
9966428 AAT
1 AAT
9966431 TCTTGTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.19, G:0.08, T:0.24
Consensus pattern (17 bp):
AATACGATTCCCAGAAA
Found at i:9967868 original size:26 final size:25
Alignment explanation
Indices: 9967832--9967886 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 25
9967822 AAGTGCTAAG
*
9967832 ACACATAAGGTTGTGCCCACCATAAT
1 ACACACAAGGTTGTGCCCACCAT-AT
*
9967858 ACACACAAGGTTGTGCCTACCATAT
1 ACACACAAGGTTGTGCCCACCATAT
9967883 ACAC
1 ACAC
9967887 TAAGTTTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.22
Consensus pattern (25 bp):
ACACACAAGGTTGTGCCCACCATAT
Found at i:9969202 original size:7 final size:7
Alignment explanation
Indices: 9969182--9969240 Score: 50
Period size: 7 Copynumber: 8.0 Consensus size: 7
9969172 TACTCTCTAA
9969182 TTAAA-T
1 TTAAATT
*
9969188 TTATATT
1 TTAAATT
9969195 TTAAATT
1 TTAAATT
9969202 TTAATTAATT
1 TT-A--AATT
9969212 TTAAATT
1 TTAAATT
9969219 TATAAATT
1 T-TAAATT
9969227 ATTAAA-T
1 -TTAAATT
9969234 TTAAATT
1 TTAAATT
9969241 ACATAATCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
6 9 0.20
7 16 0.36
8 11 0.25
9 2 0.05
10 6 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAAATT
Found at i:9969299 original size:20 final size:20
Alignment explanation
Indices: 9969257--9969300 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
9969247 TCTCTAATTA
*
9969257 ATTTATAATTTAAATAGTGT
1 ATTTATAATTTAAATACTGT
*
9969277 ATTTA-AATTTAAAATACTTT
1 ATTTATAATTT-AAATACTGT
9969297 ATTT
1 ATTT
9969301 TCTGTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (20 bp):
ATTTATAATTTAAATACTGT
Found at i:9969521 original size:17 final size:17
Alignment explanation
Indices: 9969480--9969521 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
9969470 TATTTCAACT
*
9969480 TTATAATTTAAAACTAA
1 TTATAATTTAAAAATAA
*
9969497 TTAAAATTTAAAATATAA
1 TTATAATTTAAAA-ATAA
9969515 TT-TAATT
1 TTATAATT
9969522 AGAAAGTATG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TTATAATTTAAAAATAA
Found at i:9969569 original size:14 final size:14
Alignment explanation
Indices: 9969536--9969577 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
9969526 AGTATGTAAT
9969536 TTAAATTTAATAAAA
1 TTAAATTT-ATAAAA
* *
9969551 ATAAATTTATAAAC
1 TTAAATTTATAAAA
9969565 TTAAATTTATAAA
1 TTAAATTTATAAA
9969578 GTTTGTGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
TTAAATTTATAAAA
Found at i:9969791 original size:20 final size:20
Alignment explanation
Indices: 9969766--9969805 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
9969756 TGGGGAAAAT
9969766 TACTGTAGCA-GTATCGATAC
1 TACTGTAG-AGGTATCGATAC
9969786 TACTGTAGAGGTATCGATAC
1 TACTGTAGAGGTATCGATAC
9969806 CCATTTTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (20 bp):
TACTGTAGAGGTATCGATAC
Found at i:9969876 original size:20 final size:19
Alignment explanation
Indices: 9969848--9969916 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 19
9969838 TACTGCTCAT
* *
9969848 TACTGTTCACACAGTATCGA
1 TACTATTCATACAGTA-CGA
*
9969868 TACTATTCATACAGTAAAGA
1 TACTATTCATACAGT-ACGA
* *
9969888 CACTATTCATACAGTACAA
1 TACTATTCATACAGTACGA
9969907 TACTATTCAT
1 TACTATTCAT
9969917 GAAAACATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
19 11 0.27
20 29 0.71
21 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.32
Consensus pattern (19 bp):
TACTATTCATACAGTACGA
Found at i:9970935 original size:24 final size:24
Alignment explanation
Indices: 9970908--9970980 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
9970898 CGTTCATTTA
9970908 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
9970932 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * * *
9970956 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
9970980 C
1 C
9970981 ATTCATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 42 0.95
25 2 0.05
ACGTcount: A:0.11, C:0.15, G:0.25, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:9970937 original size:14 final size:14
Alignment explanation
Indices: 9970918--9970973 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
9970908 CGTTCGTGAA
9970918 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
9970932 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
9970946 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
9970956 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
9970970 CGTT
1 CGTT
9970974 TATGTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:9970990 original size:24 final size:23
Alignment explanation
Indices: 9970919--9970993 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
9970909 GTTCGTGAAC
* *
9970919 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
9970943 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
9970967 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCGTTCA-TTAT
9970991 GTT
1 GTT
9970994 TAACCCAATC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.02
24 46 0.98
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTCATTAT
Found at i:9971736 original size:10 final size:10
Alignment explanation
Indices: 9971721--9971779 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
9971711 GGGTCTCCAA
9971721 CGTTTATGTT
1 CGTTTATGTT
9971731 CGTTTATGTT
1 CGTTTATGTT
9971741 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
9971752 ATGTTCGTGTT
1 -CGTTTATGTT
9971763 CGTTTATGTT
1 CGTTTATGTT
9971773 CGTTTAT
1 CGTTTAT
9971780 TTATTAAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
10 28 0.72
11 7 0.18
12 4 0.10
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.58
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:9971752 original size:16 final size:16
Alignment explanation
Indices: 9971727--9971783 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
9971717 CCAACGTTTA
*
9971727 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
9971743 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
9971759 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
9971775 T-TT-ATTTAT
1 TGTTCATTTAT
9971784 TAAATGAACG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
14 5 0.13
15 2 0.05
16 31 0.82
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.60
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:9972476 original size:19 final size:19
Alignment explanation
Indices: 9972452--9972497 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
9972442 CTAAATCCCT
*
9972452 TTTCAAAAT-TTATTTTGGC
1 TTTCAAAATCTAATTTT-GC
*
9972471 TTTCAAAATCTAATTTTGT
1 TTTCAAAATCTAATTTTGC
9972490 TTTCAAAA
1 TTTCAAAA
9972498 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.50
Consensus pattern (19 bp):
TTTCAAAATCTAATTTTGC
Found at i:9973403 original size:33 final size:33
Alignment explanation
Indices: 9973358--9973429 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
9973348 CTTTAAAAAC
* * *
9973358 TCCCTAGTTTTTCATGGGCTAAACTAGAACATT
1 TCCCTAGCTTTTCACGGGATAAACTAGAACATT
* *
9973391 TCCCTAGCTTTTCACGGGATCAACTAGAACTTT
1 TCCCTAGCTTTTCACGGGATAAACTAGAACATT
9973424 TACCCT
1 T-CCCT
9973430 TTACAATGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
33 29 0.88
34 4 0.12
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (33 bp):
TCCCTAGCTTTTCACGGGATAAACTAGAACATT
Found at i:9973929 original size:19 final size:20
Alignment explanation
Indices: 9973869--9973933 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
9973859 TTCATTATTG
* *
9973869 TTCACACAATATCGGTACTA
1 TTCATACAATATCAGTACTA
*
9973889 TTCATACAATATCAGTAATA
1 TTCATACAATATCAGTACTA
* *
9973909 TTCATACAGTA-CAGTTCTA
1 TTCATACAATATCAGTACTA
9973928 TTCATA
1 TTCATA
9973934 AAAACATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 12 0.31
20 27 0.69
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (20 bp):
TTCATACAATATCAGTACTA
Found at i:9976985 original size:21 final size:21
Alignment explanation
Indices: 9976937--9976987 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
9976927 AGATTGATGA
*
9976937 GATGCAAGCCAGCCGAACGTC
1 GATGCATGCCAGCCGAACGTC
9976958 GATGCATGCCAGCCGAACGTC
1 GATGCATGCCAGCCGAACGTC
9976979 GATGCATGC
1 GATGCATGC
9976988 AAATCTTAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.31, G:0.29, T:0.14
Consensus pattern (21 bp):
GATGCATGCCAGCCGAACGTC
Found at i:9978312 original size:2 final size:2
Alignment explanation
Indices: 9978305--9978340 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
9978295 TGTGAAAAGA
9978305 AT AT 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 AT AT
9978341 CTTATATGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9981273 original size:53 final size:53
Alignment explanation
Indices: 9981193--9981319 Score: 254
Period size: 53 Copynumber: 2.4 Consensus size: 53
9981183 AATGTTAGGC
9981193 TTTGGCCAATAAGGGGTATTTAGAGAATTAACTTCAGTGTTTATCCTTAAGAG
1 TTTGGCCAATAAGGGGTATTTAGAGAATTAACTTCAGTGTTTATCCTTAAGAG
9981246 TTTGGCCAATAAGGGGTATTTAGAGAATTAACTTCAGTGTTTATCCTTAAGAG
1 TTTGGCCAATAAGGGGTATTTAGAGAATTAACTTCAGTGTTTATCCTTAAGAG
9981299 TTTGGCCAATAAGGGGTATTT
1 TTTGGCCAATAAGGGGTATTT
9981320 GTACAATACC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 74 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (53 bp):
TTTGGCCAATAAGGGGTATTTAGAGAATTAACTTCAGTGTTTATCCTTAAGAG
Found at i:9982471 original size:16 final size:17
Alignment explanation
Indices: 9982446--9982479 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
9982436 ATTACCCTAA
*
9982446 GATGTTAGACTT-TGTT
1 GATGTGAGACTTATGTT
9982462 GATGTGAGACTTATGTT
1 GATGTGAGACTTATGTT
9982479 G
1 G
9982480 CCCATTGTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.21, C:0.06, G:0.29, T:0.44
Consensus pattern (17 bp):
GATGTGAGACTTATGTT
Found at i:9983967 original size:3 final size:3
Alignment explanation
Indices: 9983961--9983985 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
9983951 TATCATCACA
9983961 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
9983986 GGGGAAGGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:9985772 original size:3 final size:3
Alignment explanation
Indices: 9985764--9985842 Score: 113
Period size: 3 Copynumber: 25.7 Consensus size: 3
9985754 TTTTTCATTC
* *
9985764 TAT TAT TAT TAT TAT TAT TAT TAA AAT TAT TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
*
9985810 TAT TAT TAT TAT TAT ATAA TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA
9985843 AATAATTATA
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
3 63 0.93
4 5 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:9985847 original size:19 final size:19
Alignment explanation
Indices: 9985773--9985848 Score: 100
Period size: 19 Copynumber: 4.1 Consensus size: 19
9985763 CTATTATTAT
*
9985773 TATTATTATTATTAAA-AT
1 TATTATTATTATTAAATAA
** *
9985791 TATTATTATTATTATTTAT
1 TATTATTATTATTAAATAA
*
9985810 TATTATTATTATTATATAA
1 TATTATTATTATTAAATAA
9985829 TATTATTATTATTAAATAA
1 TATTATTATTATTAAATAA
9985848 T
1 T
9985849 TATAAGAACC
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
18 14 0.27
19 38 0.73
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTATTATTATTAAATAA
Found at i:9990384 original size:8 final size:7
Alignment explanation
Indices: 9990360--9990400 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
9990350 TTTTCATACA
9990360 TGCA-TT
1 TGCATTT
9990366 TGCATTT
1 TGCATTT
9990373 TGCATCTT
1 TGCAT-TT
9990381 TGCATTT
1 TGCATTT
*
9990388 T-CATGT
1 TGCATTT
9990394 TGCATTT
1 TGCATTT
9990401 ATGCTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
6 9 0.30
7 14 0.47
8 7 0.23
ACGTcount: A:0.15, C:0.17, G:0.15, T:0.54
Consensus pattern (7 bp):
TGCATTT
Found at i:9992964 original size:24 final size:24
Alignment explanation
Indices: 9992937--9993054 Score: 132
Period size: 24 Copynumber: 4.9 Consensus size: 24
9992927 CATAATTAAC
*
9992937 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCATATCAAAATCCAT
* *
9992961 GTCAAGTAACATAT-AATAATCCAA
1 GTCAAGTATCATATCAA-AATCCAT
*
9992985 GTCAAGTATCATATCAGAATCCAT
1 GTCAAGTATCATATCAAAATCCAT
* *
9993009 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCATATCAAAATCCAT
*
9993033 GTCAAGTATCAGATCAGAAATC
1 GTCAAGTATCATATCA-AAATC
9993055 AAATCGAAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
23 4 0.05
24 71 0.87
25 7 0.09
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCATATCAAAATCCAT
Found at i:9995552 original size:13 final size:13
Alignment explanation
Indices: 9995534--9995563 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
9995524 GCCGGTCAAC
9995534 GGTCAACGGGTCG
1 GGTCAACGGGTCG
9995547 GGTCAACGGGTCG
1 GGTCAACGGGTCG
9995560 GGTC
1 GGTC
9995564 TGGTCGTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:9997676 original size:24 final size:24
Alignment explanation
Indices: 9997666--9997780 Score: 160
Period size: 24 Copynumber: 4.8 Consensus size: 24
9997656 CATAATTCAC
* * *
9997666 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
* * *
9997690 GACAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
9997714 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
9997738 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
9997762 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
9997781 ATCAAATCGA
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 2 0.02
24 77 0.95
25 2 0.02
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:9997797 original size:48 final size:48
Alignment explanation
Indices: 9997647--9997797 Score: 130
Period size: 48 Copynumber: 3.1 Consensus size: 48
9997637 ATATATCAAA
* * * * * * *
9997647 AAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAGGA-CAAG
1 AAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCA-AATC-AG
* **
9997696 TAA-CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCATGTCAG
1 AAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAG
* *
9997743 ATATCAGATCAGAATCCATGTCAAGTATCAGATCAGAAAT-CAAATC-G
1 AAATCAGATCAGAATCCAAGTCAAGTATCAGATCAG-AATCCAAATCAG
9997790 AAAATCAG
1 -AAATCAG
9997798 GTAAAATATT
Statistics
Matches: 83, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
47 4 0.05
48 74 0.89
49 5 0.06
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.22
Consensus pattern (48 bp):
AAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAG
Found at i:9997797 original size:72 final size:71
Alignment explanation
Indices: 9997646--9997797 Score: 155
Period size: 72 Copynumber: 2.1 Consensus size: 71
9997636 GATATATCAA
* * * *
9997646 AAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAGGACAAGTAACAGATCAGAATC
1 AAAATCAGATCAGAATCCACGTCAAGTATCAGATCAAAATCCAGGACAAGTAACAGATCAGAATC
*
9997711 CAAGTC
66 CAAATC
* * * * * *
9997717 AAGTATCAGATCAGAATCCATGTC-AGATATCAGATCAGAATCCATGTCAAGTATCAGATCAGAA
1 AA-AATCAGATCAGAATCCACGTCAAG-TATCAGATCAAAATCCAGGACAAGTAACAGATCAG-A
9997781 AT-CAAATC
63 ATCCAAATC
9997789 GAAAATCAG
1 -AAAATCAG
9997798 GTAAAATATT
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
71 4 0.06
72 56 0.86
73 5 0.08
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.22
Consensus pattern (71 bp):
AAAATCAGATCAGAATCCACGTCAAGTATCAGATCAAAATCCAGGACAAGTAACAGATCAGAATC
CAAATC
Found at i:10000306 original size:18 final size:18
Alignment explanation
Indices: 10000277--10000323 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
10000267 CAACGGTCAA
*
10000277 CGGGTCGTGTCAACGGAT
1 CGGGTCGGGTCAACGGAT
* *
10000295 CTGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGAT
10000313 CGGGTCGGGTC
1 CGGGTCGGGTC
10000324 GTGACCGGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.11, C:0.23, G:0.45, T:0.21
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGAT
Found at i:10002457 original size:24 final size:24
Alignment explanation
Indices: 10002447--10002561 Score: 151
Period size: 24 Copynumber: 4.8 Consensus size: 24
10002437 CATAATTCAC
* * *
10002447 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
* * *
10002471 GACAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
10002495 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
10002519 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
*
10002543 GTCAAGTATCATATCAGAA
1 GTCAAGTATCAGATCAGAA
10002562 ATCAAATCGA
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.03
24 76 0.95
25 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:10002578 original size:48 final size:48
Alignment explanation
Indices: 10002428--10002578 Score: 121
Period size: 48 Copynumber: 3.1 Consensus size: 48
10002418 ATATATCAAA
* * * * * * *
10002428 AAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAGGA-CAAG
1 AAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCA-AATC-AG
* **
10002477 TAA-CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCATGTCAG
1 AAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAG
* * *
10002524 ATATCAGATCAGAATCCATGTCAAGTATCATATCAGAAAT-CAAATC-G
1 AAATCAGATCAGAATCCAAGTCAAGTATCAGATCAG-AATCCAAATCAG
10002571 AAAATCAG
1 -AAATCAG
10002579 GTAAAATATT
Statistics
Matches: 82, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
47 4 0.05
48 73 0.89
49 5 0.06
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (48 bp):
AAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAG
Found at i:10005080 original size:13 final size:13
Alignment explanation
Indices: 10005062--10005091 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
10005052 AACGGTCAAC
10005062 GGTCAACGGGTCG
1 GGTCAACGGGTCG
10005075 GGTCAACGGGTCG
1 GGTCAACGGGTCG
10005088 GGTC
1 GGTC
10005092 GGGTCTTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:10006433 original size:20 final size:20
Alignment explanation
Indices: 10006408--10006447 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
10006398 ATATTATACT
10006408 TGAAAAAAAGCA-AAAAAAGA
1 TGAAAAAAAG-AGAAAAAAGA
10006428 TGAAAAAAAGAGAAAAAAGA
1 TGAAAAAAAGAGAAAAAAGA
10006448 AAAAAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.05
Consensus pattern (20 bp):
TGAAAAAAAGAGAAAAAAGA
Found at i:10006453 original size:20 final size:20
Alignment explanation
Indices: 10006410--10006456 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
10006400 ATTATACTTG
**
10006410 AAAAAAAGCAAAAAAAGATG
1 AAAAAAAGCAAAAAAAGAAA
10006430 AAAAAAAG-AGAAAAAAGAAA
1 AAAAAAAGCA-AAAAAAGAAA
10006450 AAAAAAA
1 AAAAAAA
10006457 CTGAATCAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (20 bp):
AAAAAAAGCAAAAAAAGAAA
Found at i:10006454 original size:9 final size:9
Alignment explanation
Indices: 10006410--10006454 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
10006400 ATTATACTTG
*
10006410 AAAAAAAGC
1 AAAAAAAGA
10006419 AAAAAAAGA
1 AAAAAAAGA
10006428 TGAAAAAAAGA
1 --AAAAAAAGA
*
10006439 GAAAAAAGA
1 AAAAAAAGA
10006448 AAAAAAA
1 AAAAAAA
10006455 AACTGAATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
9 22 0.71
11 9 0.29
ACGTcount: A:0.82, C:0.02, G:0.13, T:0.02
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:10011605 original size:73 final size:73
Alignment explanation
Indices: 10011500--10012087 Score: 1050
Period size: 73 Copynumber: 8.0 Consensus size: 73
10011490 CTATTTCCCA
10011500 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
10011565 CTCAGGGT
66 CTCAGGGT
* * *
10011573 CATCTGTAAGACCTACAGTGCATGATTTTTTCAAGAAGCCTTCGAGAGCTTTTTGATCTTAAACC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
10011638 CTCAGGGT
66 CTCAGGGT
* *
10011646 CATCTGTAAGACCTACAATGCATGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGATCTTAAACC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
10011711 CTCAGGGT
66 CTCAGGGT
* *
10011719 CATCTGTAAGACCTACAGTGCATGTTGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAATCC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
10011784 CTCAGGGT
66 CTCAGGGT
10011792 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
10011857 CTCAGGGT
66 CTCAGGGT
*
10011865 CATCTGTAAGACCTACAGTGCATGATATTTTCAAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTC-AAAAAGCCTTCGGGAGCTTTTTGATCTTAAAC
10011930 CCTCAGGGT
65 CCTCAGGGT
* *
10011939 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
10012004 CTCAGGGT
66 CTCAGGGT
* * *
10012012 CATCCGTAAGCCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCATTTTGATCTTAAACC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
10012077 CTCAGGGT
66 CTCAGGGT
10012085 CAT
1 CAT
10012088 TCATAAGACC
Statistics
Matches: 491, Mismatches: 23, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
73 419 0.85
74 72 0.15
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (73 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
CTCAGGGT
Found at i:10012098 original size:220 final size:219
Alignment explanation
Indices: 10011500--10012087 Score: 1050
Period size: 220 Copynumber: 2.7 Consensus size: 219
10011490 CTATTTCCCA
10011500 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
* * *
10011565 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATTTTTTCAAGAAGCCTTCGAGAGCTTTTTGAT
66 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
*
10011630 CTTAAACCCTCAGGGTCATCTGTAAGACCTACAATGCATGATGTTTTCAAAAAGCCTTCGGGAGA
131 CTTAAACCCTCAGGGTCATCTGTAAGACCTACAATGCATGATATTTTCAAAAAGCCTTCGGGAGA
10011695 TTTTTGATCTTAAACCCTCAGGGT
196 TTTTTGATCTTAAACCCTCAGGGT
* *
10011719 CATCTGTAAGACCTACAGTGCATGTTGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAATCC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
10011784 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
66 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
*
10011849 CTTAAACCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATATTTTCAAAAAAGCCTTCGGGAG
131 CTTAAACCCTCAGGGTCATCTGTAAGACCTACAATGCATGATATTTTC-AAAAAGCCTTCGGGAG
*
10011914 CTTTTTGATCTTAAACCCTCAGGGT
195 ATTTTTGATCTTAAACCCTCAGGGT
* *
10011939 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
* * *
10012004 CTCAGGGTCATCCGTAAGCCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCATTTTGAT
66 CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
10012069 CTTAAACCCTCAGGGTCAT
131 CTTAAACCCTCAGGGTCAT
10012088 TCATAAGACC
Statistics
Matches: 353, Mismatches: 15, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
219 171 0.48
220 182 0.52
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (219 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACC
CTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGAT
CTTAAACCCTCAGGGTCATCTGTAAGACCTACAATGCATGATATTTTCAAAAAGCCTTCGGGAGA
TTTTTGATCTTAAACCCTCAGGGT
Found at i:10012246 original size:3 final size:3
Alignment explanation
Indices: 10012238--10012310 Score: 103
Period size: 3 Copynumber: 23.7 Consensus size: 3
10012228 TTTTTCATTC
10012238 TAT TAT TAT TAT TAT TAT TAT TAAT TAT TAT TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TA-T TAT
*
10012285 TAT TAT TA- TAT ATAA TAT TAT TAT TA
1 TAT TAT TAT TAT -TAT TAT TAT TAT TA
10012311 AATAATTACA
Statistics
Matches: 64, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
2 2 0.03
3 54 0.84
4 8 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:10012267 original size:22 final size:21
Alignment explanation
Indices: 10012238--10012310 Score: 103
Period size: 22 Copynumber: 3.4 Consensus size: 21
10012228 TTTTTCATTC
10012238 TATTATTATTATTATTATTAT
1 TATTATTATTATTATTATTAT
10012259 TAATTATTATTATTATTATTATT
1 T-ATTATTATTATTATTATTA-T
*
10012282 TATTATTATTA-TATATAATAT
1 TATTATTATTATTAT-TATTAT
10012303 TATTATTA
1 TATTATTA
10012311 AATAATTACA
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
21 13 0.27
22 33 0.69
23 2 0.04
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TATTATTATTATTATTATTAT
Found at i:10016414 original size:36 final size:36
Alignment explanation
Indices: 10016292--10016683 Score: 413
Period size: 38 Copynumber: 10.6 Consensus size: 36
10016282 TTATTTTATT
**
10016292 ATATATATATATATTATAG-TTTGCAAATGATTTTTG-AA
1 ATATATATA-ATA-TATAGTTTTG-AAAACA-TTTTGAAA
*
10016330 ATATATATAATATATATAGTTTTGAAAACGGTTTTTGAAAA
1 ATATATAT-A-ATATATAGTTTTGAAAAC--ATTTTG-AAA
* * *
10016371 ATGTATATATTATATAGTTTTGAAATCATTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTGAAA
* *
10016407 ACT-TATATAATATATGGTTTTCAAAAACATTTTG-AA
1 A-TATATATAATATATAGTTTT-GAAAACATTTTGAAA
* *
10016443 A-ATATATAATATATGGTTTTTAAAACATTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTGAAA
10016478 ACT-TATATAATATATAGTTTT-AAAACATTTTGAAAA
1 A-TATATATAATATATAGTTTTGAAAACATTTTG-AAA
* *
10016514 ATATATATAATATATAATTTTGAAAACATTATGAAAAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTG---AAA
* *
10016553 ATATATATAATATATATTTTTTAAAACATTTTGAAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTG-AAA
*
10016590 CATATATATAATATATAGTTTTTAAAACATTTTGAAAA
1 -ATATATATAATATATAGTTTTGAAAACATTTTG-AAA
10016628 TATATATATAATATATAGTTTT-AAAACATTTTGAAA
1 -ATATATATAATATATAGTTTTGAAAACATTTTGAAA
10016664 ATATATATAATATATAGTTT
1 ATATATATAATATATAGTTT
10016684 AAAAATTATT
Statistics
Matches: 316, Mismatches: 20, Indels: 39
0.84 0.05 0.10
Matches are distributed among these distances:
34 11 0.03
35 53 0.17
36 64 0.20
37 41 0.13
38 73 0.23
39 64 0.20
40 1 0.00
41 9 0.03
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTGAAAACATTTTGAAA
Found at i:10018784 original size:33 final size:33
Alignment explanation
Indices: 10018747--10018865 Score: 186
Period size: 33 Copynumber: 3.5 Consensus size: 33
10018737 ATATATATAT
10018747 ATTATA-AGTTTTCAAAATGTTTTAAAAACCATA
1 ATTATATA-TTTTCAAAATGTTTTAAAAACCATA
10018780 ATTATATATTTTCAAAATGTTTTAAAAACCATA
1 ATTATATATTTTCAAAATGTTTTAAAAACCATA
10018813 ATTATATATTTTCAAAATGTTTTTAAAAACCATA
1 ATTATATATTTTCAAAATG-TTTTAAAAACCATA
10018847 TATTATATAAGTTTTCAAA
1 -ATTATAT-A-TTTTCAAA
10018866 TTATTTTTCA
Statistics
Matches: 81, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
33 50 0.62
34 15 0.19
35 7 0.09
36 1 0.01
37 8 0.10
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (33 bp):
ATTATATATTTTCAAAATGTTTTAAAAACCATA
Found at i:10020907 original size:33 final size:34
Alignment explanation
Indices: 10020870--10020936 Score: 111
Period size: 33 Copynumber: 2.0 Consensus size: 34
10020860 ATATATATAT
10020870 ATTATA-AGTTTTCAAAATG-TTTTAAAAACCATA
1 ATTATATA-TTTTCAAAATGTTTTTAAAAACCATA
10020903 ATTATATATTTTCAAAATGTTTTTAAAAACCATA
1 ATTATATATTTTCAAAATGTTTTTAAAAACCATA
10020937 TATTCAGGCG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 17 0.53
34 15 0.47
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (34 bp):
ATTATATATTTTCAAAATGTTTTTAAAAACCATA
Found at i:10024190 original size:37 final size:34
Alignment explanation
Indices: 10024116--10024190 Score: 87
Period size: 37 Copynumber: 2.1 Consensus size: 34
10024106 GTTGTTGTTG
* * *
10024116 TTTTAAAAACCATAGTTATATATTTTCAAAATGT
1 TTTTAAAAACAATAATTATATATTTTCAAAATAT
*
10024150 TTTTAAAAACAATATATTATATAAGTTTTCAAATTAT
1 TTTTAAAAACAATA-ATTATAT-A-TTTTCAAAATAT
10024187 TTTT
1 TTTT
10024191 CAAATTTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 13 0.38
35 6 0.18
36 1 0.03
37 14 0.41
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (34 bp):
TTTTAAAAACAATAATTATATATTTTCAAAATAT
Found at i:10026217 original size:33 final size:33
Alignment explanation
Indices: 10026180--10026338 Score: 257
Period size: 33 Copynumber: 4.7 Consensus size: 33
10026170 ATATATATAT
10026180 ATTATA-AGTTTTCAAAATGTTTTAAAAACCATA
1 ATTATATA-TTTTCAAAATGTTTTAAAAACCATA
*
10026213 ATTATATATTTTCAAAATGTTTTAAAAATCATA
1 ATTATATATTTTCAAAATGTTTTAAAAACCATA
10026246 ATTATATATTTTCAAAATGTTTTTAAAAACCATA
1 ATTATATATTTTCAAAATG-TTTTAAAAACCATA
10026280 TATTATATAAGTTTTCAAAATGTTTTAAAAACCATA
1 -ATTATAT-A-TTTTCAAAATGTTTTAAAAACCATA
10026316 ATTATATATTTTCAAAATGTTTT
1 ATTATATATTTTCAAAATGTTTT
10026339 TCAAATTTCC
Statistics
Matches: 119, Mismatches: 2, Indels: 10
0.91 0.02 0.08
Matches are distributed among these distances:
33 64 0.54
34 15 0.13
35 14 0.12
36 15 0.13
37 11 0.09
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (33 bp):
ATTATATATTTTCAAAATGTTTTAAAAACCATA
Done.