Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009637.1 Hibiscus syriacus cultivar Beakdansim tig00117046_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: 867493
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:441728 original size:86 final size:85
Alignment explanation
Indices: 441542--441711 Score: 241
Period size: 85 Copynumber: 2.0 Consensus size: 85
441532 ATATATAACA
* * ** * *
441542 ACATTTTTAGAATAAACGCCGCTAAAGGTCAGATCTATAACGGCATTTTTGGATACAAACGCCGC
1 ACATTTTTGGAACAAACATCGCAAAAGGTCAGATCTATAACGGCATTTTTGGATACAAACGCCAC
441607 AAAAGGTCAGATCTATAGCG
66 AAAAGGTCAGATCTATAGCG
* * *
441627 ATATTTTTGGAACAAACATCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTGGATACAAACGCCA
1 ACATTTTTGGAACAAACATCGCAAAAGGTCAGATCTATAACGGC-ATTTTTGGATACAAACGCCA
*
441692 CAAAAGGTCAGCTCTATAGC
65 CAAAAGGTCAGATCTATAGC
441712 TGCGTTTTTG
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
85 37 0.50
86 37 0.50
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (85 bp):
ACATTTTTGGAACAAACATCGCAAAAGGTCAGATCTATAACGGCATTTTTGGATACAAACGCCAC
AAAAGGTCAGATCTATAGCG
Found at i:446104 original size:40 final size:40
Alignment explanation
Indices: 445769--446104 Score: 153
Period size: 41 Copynumber: 8.2 Consensus size: 40
445759 CGTTTGTAAA
* * *
445769 TAAAAACGCCACTAACGTATGAGTATTTAGCAGTGTTTTGCT
1 TAAAAACGCCACTAAAGTACGAGTATTTAGCAGCG-TTTG-T
* * *
445811 T-AAAACGTCACTAAAATAC--GTATTTAGC-GACATTTGT
1 TAAAAACGCCACTAAAGTACGAGTATTTAGCAG-CGTTTGT
* * * * *
445848 CAAAAA-ACCACTAAAGTACTAG-GTTTAAC-GACGTTTGT
1 TAAAAACGCCACTAAAGTACGAGTATTTAGCAG-CGTTTGT
* * * *
445886 CTAAAAATGCCACTAAAGTACGAGTATTTAACGGCATTTTTGCT
1 -TAAAAACGCCACTAAAGTACGAGTATTTAGCAGC--GTTTG-T
* * *
445930 T-AAAACGCCACTAAAGTACTAATTTTTAGC-GACGTTTGT
1 TAAAAACGCCACTAAAGTACGAGTATTTAGCAG-CGTTTGT
* *
445969 CTAAAAACGCCA-TAATATATGTACCA-TA-TT-GCAGTGTTTGTT
1 -TAAAAACGCCACT-A-A-A-GTACGAGTATTTAGCAGCGTTTG-T
* * * * *
446011 TACAAACACCGCTAAAGTACTTA-TCTTTAGCTGAGCGTTTGT
1 TAAAAACGCCACTAAAGTAC-GAGTATTTAGC--AGCGTTTGT
446053 CATAAAAACGCCACTAAAGTACGAGT-TTTAGCAGCGTTTGT
1 --TAAAAACGCCACTAAAGTACGAGTATTTAGCAGCGTTTGT
446094 TGAAAAACGCC
1 T-AAAAACGCC
446105 GTTAATGTTA
Statistics
Matches: 227, Mismatches: 37, Indels: 62
0.70 0.11 0.19
Matches are distributed among these distances:
37 11 0.05
38 26 0.11
39 20 0.09
40 32 0.14
41 59 0.26
42 34 0.15
43 21 0.09
44 24 0.11
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (40 bp):
TAAAAACGCCACTAAAGTACGAGTATTTAGCAGCGTTTGT
Found at i:446647 original size:29 final size:29
Alignment explanation
Indices: 446613--446670 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
446603 TAAATAATTA
*
446613 ATTCTTATTTTAACGTAAAAATATCTTTT
1 ATTCTTATTTTAACGTAAAAATATATTTT
*
446642 ATTCTTATTTTAACTTAAAAATATATTTT
1 ATTCTTATTTTAACGTAAAAATATATTTT
446671 TTTTTAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (29 bp):
ATTCTTATTTTAACGTAAAAATATATTTT
Found at i:446674 original size:22 final size:24
Alignment explanation
Indices: 446641--446704 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 24
446631 AAATATCTTT
446641 TATTCTTA-TTTTAACTTAAAAATA
1 TATT-TTATTTTTAACTTAAAAATA
*
446665 TATTTT-TTTTTAAC-TACAAATA
1 TATTTTATTTTTAACTTAAAAATA
*
446687 TA-TTTATTTTTATCTTAA
1 TATTTTATTTTTAACTTAA
446705 CTACAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 3 0.09
22 16 0.47
23 11 0.32
24 4 0.12
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (24 bp):
TATTTTATTTTTAACTTAAAAATA
Found at i:446675 original size:23 final size:23
Alignment explanation
Indices: 446649--446704 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
446639 TTTATTCTTA
*
446649 TTTTAACTTAAAAATATATTTTT
1 TTTTAACTTAAAAATATATTTAT
*
446672 TTTTAAC-TACAAATATATTTAT
1 TTTTAACTTAAAAATATATTTAT
*
446694 TTTTATCTTAA
1 TTTTAACTTAA
446705 CTACAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTTAACTTAAAAATATATTTAT
Found at i:446705 original size:27 final size:26
Alignment explanation
Indices: 446641--446727 Score: 92
Period size: 26 Copynumber: 3.4 Consensus size: 26
446631 AAATATCTTT
* *
446641 TATTCTTATTTTAACTTA-AAAATATA
1 TATTTTTATCTTAAC-TACAAAATATA
*
446667 T-TTTTT-T-TTAACTACAAATATATT
1 TATTTTTATCTTAACTACAAA-ATATA
446691 TATTTTTATCTTAACTACAAAATATA
1 TATTTTTATCTTAACTACAAAATATA
*
446717 CATTTTTATCT
1 TATTTTTATCT
446728 CAAATTTAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
22 2 0.04
23 8 0.15
24 6 0.12
25 9 0.17
26 16 0.31
27 11 0.21
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (26 bp):
TATTTTTATCTTAACTACAAAATATA
Found at i:446705 original size:50 final size:52
Alignment explanation
Indices: 446620--446716 Score: 128
Period size: 50 Copynumber: 1.9 Consensus size: 52
446610 TTAATTCTTA
* *
446620 TTTTAACGTAAAAATATCTTTTATTCTTATTTTAACTTA-AAAATATATTTTT
1 TTTTAACGTAAAAATATCATTTATTCTTATCTTAAC-TACAAAATATATTTTT
* *
446672 TTTTAAC-TACAAATAT-ATTTATTTTTATCTTAACTACAAAATATA
1 TTTTAACGTAAAAATATCATTTATTCTTATCTTAACTACAAAATATA
446717 CATTTTTATC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
49 2 0.05
50 23 0.57
51 8 0.20
52 7 0.17
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.51
Consensus pattern (52 bp):
TTTTAACGTAAAAATATCATTTATTCTTATCTTAACTACAAAATATATTTTT
Found at i:450841 original size:19 final size:18
Alignment explanation
Indices: 450798--450843 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
450788 AATGATTTGG
*
450798 TTTTGAAAGCAAACATGA
1 TTTTGAAAACAAACATGA
450816 TTTTGAAAACAAA-ATGAA
1 TTTTGAAAACAAACATG-A
450834 TCTTTGAAAA
1 T-TTTGAAAA
450844 ATGATTAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 3 0.12
18 14 0.56
19 8 0.32
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (18 bp):
TTTTGAAAACAAACATGA
Found at i:452347 original size:3 final size:3
Alignment explanation
Indices: 452339--452444 Score: 117
Period size: 3 Copynumber: 34.7 Consensus size: 3
452329 TTATTTATTA
*
452339 AAT AAT AAT AAT -AT AAT AAT -AT ATAT AAT ATT AAT AAT AAAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT -AAT -AAT
* * * *
452385 ACT AAT AAT AAT AAT AAT AAT AAT ATT AAT AAT GAT AAAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
452431 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
452445 AATGTATAGG
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
2 4 0.05
3 72 0.82
4 12 0.14
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:459925 original size:2 final size:2
Alignment explanation
Indices: 459913--459946 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
459903 CTGAGTTTGC
*
459913 AT AT GT 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
459947 TAGTAGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:463459 original size:22 final size:21
Alignment explanation
Indices: 463431--463491 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
463421 GGGTCTACGC
*
463431 GGTCCTTCGGAACATATACAGA
1 GGTCCTTCGG-ACAAATACAGA
*
463453 GGTCCTTCAGGACAAATACATA
1 GGTCCTTC-GGACAAATACAGA
*
463475 GGTCATTCGAGACAAAT
1 GGTCCTTCG-GACAAAT
463492 TTCACATGCC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.03
22 31 0.91
23 2 0.06
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (21 bp):
GGTCCTTCGGACAAATACAGA
Found at i:464060 original size:21 final size:21
Alignment explanation
Indices: 464036--464107 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
464026 CTGTAGTAGT
464036 ACTGTAACAGTGCATCGGTAC
1 ACTGTAACAGTGCATCGGTAC
* *
464057 ACTGTAGCAGTGCATTGGTAC
1 ACTGTAACAGTGCATCGGTAC
*
464078 ACTGTAGCAGTGCATCGGTAC
1 ACTGTAACAGTGCATCGGTAC
464099 ACTGTAACA
1 ACTGTAACA
464108 CTATTCACGG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (21 bp):
ACTGTAACAGTGCATCGGTAC
Found at i:466030 original size:16 final size:16
Alignment explanation
Indices: 466009--466048 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
465999 ACTATTTACA
466009 TGAATAGTGAATTTCG
1 TGAATAGTGAATTTCG
**
466025 TGAATAGTGAATTTTT
1 TGAATAGTGAATTTCG
466041 TGAATAGT
1 TGAATAGT
466049 AAATATTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.03, G:0.23, T:0.42
Consensus pattern (16 bp):
TGAATAGTGAATTTCG
Found at i:466057 original size:16 final size:16
Alignment explanation
Indices: 466025--466058 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
466015 GTGAATTTCG
* *
466025 TGAATAGTGAATTTTT
1 TGAATAGTAAATATTT
466041 TGAATAGTAAATATTT
1 TGAATAGTAAATATTT
466057 TG
1 TG
466059 TCGGTGATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (16 bp):
TGAATAGTAAATATTT
Found at i:470751 original size:6 final size:6
Alignment explanation
Indices: 470742--470769 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
470732 TCTTTTTCAT
470742 TTCAGA TTCAGA TTCAGA TTCAGA TTCA
1 TTCAGA TTCAGA TTCAGA TTCAGA TTCA
470770 CCTTCGGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (6 bp):
TTCAGA
Found at i:478813 original size:3 final size:3
Alignment explanation
Indices: 478805--478876 Score: 65
Period size: 3 Copynumber: 24.0 Consensus size: 3
478795 TTTTCGTTTG
** * * *
478805 TTA TTA TTA AAA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA ATA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
478852 ATA ATA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA
478877 AATATATATA
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
2 2 0.04
3 52 0.91
4 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:478886 original size:35 final size:36
Alignment explanation
Indices: 478821--478901 Score: 87
Period size: 35 Copynumber: 2.2 Consensus size: 36
478811 TTAAAATTAT
*
478821 TATTATTATTATAAATATTATTATTAATATA-ATA-A
1 TATTATTATTAT-AATATTATTAATAATATATATATA
*
478856 TATTATTATTAT-TTATTATTAAATATATATATATATA
1 TATTATTATTATAATATTATT-AATA-ATATATATATA
478893 TATATATTA
1 TAT-TATTA
478902 CAAAATTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
33 7 0.18
34 3 0.08
35 17 0.44
36 3 0.08
37 4 0.10
38 5 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (36 bp):
TATTATTATTATAATATTATTAATAATATATATATA
Found at i:479972 original size:2 final size:2
Alignment explanation
Indices: 479965--479998 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
479955 GTCATTATCA
479965 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
479999 CTTTATGGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:481572 original size:23 final size:22
Alignment explanation
Indices: 481525--481607 Score: 71
Period size: 23 Copynumber: 3.7 Consensus size: 22
481515 AAATTCATAT
* *
481525 TTTTAATTTTTAATT-CTTTTC
1 TTTTAATTTTTTATTACTTTTA
481546 TTTTAATTTTTTATTACTTATTA
1 TTTTAATTTTTTATTACTT-TTA
* * * *
481569 TTTTTATATATTATTATTTTTTA
1 TTTTAATTTTTTATTA-CTTTTA
481592 TTTT-ATTTATTTATTA
1 TTTTAATTT-TTTATTA
481608 TTCAAGAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
21 14 0.28
22 6 0.12
23 28 0.56
24 2 0.04
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTAATTTTTTATTACTTTTA
Found at i:481574 original size:16 final size:16
Alignment explanation
Indices: 481553--481608 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 16
481543 TTCTTTTAAT
481553 TTTTTAT-TACTTATTA
1 TTTTTATATA-TTATTA
481569 TTTTTATATATTATTA
1 TTTTTATATATTATTA
*
481585 TTTTT-TATTTTATTTA
1 TTTTTATATATTA-TTA
481601 TTTATTAT
1 TTT-TTAT
481609 TCAAGAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
15 6 0.17
16 24 0.69
17 4 0.11
18 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTATATATTATTA
Found at i:483953 original size:8 final size:7
Alignment explanation
Indices: 483929--483969 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
483919 TTTTCATATA
483929 TGCATTT
1 TGCATTT
483936 T-CATTT
1 TGCATTT
483942 TGCATCTT
1 TGCAT-TT
483950 TGCATTT
1 TGCATTT
483957 T-CATTTT
1 TGCA-TTT
483964 TGCATT
1 TGCATT
483970 CATACTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 8 0.27
7 13 0.43
8 9 0.30
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:484030 original size:22 final size:22
Alignment explanation
Indices: 483999--484041 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
483989 TTGAATTGCA
483999 CATTTTGCATTCTTAT-TTTTC
1 CATTTTGCATTCTTATATTTTC
*
484020 CATTTATGCATTTTTATATTTT
1 CATTT-TGCATTCTTATATTTT
484042 TTATTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 10 0.53
23 4 0.21
ACGTcount: A:0.19, C:0.14, G:0.05, T:0.63
Consensus pattern (22 bp):
CATTTTGCATTCTTATATTTTC
Found at i:490595 original size:54 final size:54
Alignment explanation
Indices: 490527--490630 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 54
490517 TGATTGAAAA
* ***
490527 ATCTGAGCATAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTACAAAC
1 ATCTGAGCAGAAGCCACAAAAAAGGATGAATGCACTGTCAAATGTTTTACAAAC
**
490581 ATCTGAGCAGAAGCCACAGGAAAGGATGAATGCACTGTCAAATGTTTTAC
1 ATCTGAGCAGAAGCCACAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
490631 GAACCAGTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.24
Consensus pattern (54 bp):
ATCTGAGCAGAAGCCACAAAAAAGGATGAATGCACTGTCAAATGTTTTACAAAC
Found at i:491848 original size:167 final size:165
Alignment explanation
Indices: 491565--491887 Score: 531
Period size: 167 Copynumber: 1.9 Consensus size: 165
491555 AGAATGAGCA
* *
491565 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAACATAATGAGAAAACGA
1 TTATCTGGAGATTGGGGCATGTTACCCAATCAACAGGTTATTTCAAAAACATAATGAGAAAACGA
* **
491630 TTTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTC
66 TTTCCAAAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTC
*
491695 TTAGTTTTTTTTACTTATTAAACTATTTCCAACAACC
131 TTAG-TTTTTTTACTTAGTAAAC-ATTTCCAACAACC
**
491732 TTATCTGGAGATTGGGGCATGTTACCCAATCAACAGGTTATTT-TGAAACATAATGAGAAAACGA
1 TTATCTGGAGATTGGGGCATGTTACCCAATCAACAGGTTATTTCAAAAACATAATGAGAAAACGA
*
491796 TTTCCAAAGTTTCTCATTCAATCTTTTCTGAAAATGAAATTGTTGAAAAGTAAGAAAATGATTTT
66 TTTCCAAAGTTTCTCATTCAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAACGATTTT
491861 CTTAGTTTTTTTACTTAGTAAACATTT
130 CTTAGTTTTTTTACTTAGTAAACATTT
491888 TCCCTCGAAA
Statistics
Matches: 146, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
165 4 0.03
166 62 0.42
167 80 0.55
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (165 bp):
TTATCTGGAGATTGGGGCATGTTACCCAATCAACAGGTTATTTCAAAAACATAATGAGAAAACGA
TTTCCAAAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTC
TTAGTTTTTTTACTTAGTAAACATTTCCAACAACC
Found at i:491988 original size:73 final size:73
Alignment explanation
Indices: 491886--492116 Score: 399
Period size: 73 Copynumber: 3.2 Consensus size: 73
491876 TAGTAAACAT
* *
491886 TTTCCCTCGAAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTGTCTCGCT
1 TTTCACTCGAAATAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTGTCTCGCT
491951 CGAGACAG
66 CGAGACAG
*
491959 TTTCACTTGAAATAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTGTCTCGCT
1 TTTCACTCGAAATAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTGTCTCGCT
492024 CGAGACAG
66 CGAGACAG
* **
492032 TTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAAGTTGTCTCGCT
1 TTTCACTCGAAATAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTGTCTCGCT
*
492097 TGAGACAG
66 CGAGACAG
492105 TTTCACTCGAAA
1 TTTCACTCGAAA
492117 CATAAATTTT
Statistics
Matches: 150, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 150 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (73 bp):
TTTCACTCGAAATAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTGTCTCGCT
CGAGACAG
Found at i:492118 original size:36 final size:36
Alignment explanation
Indices: 491894--492125 Score: 149
Period size: 36 Copynumber: 6.3 Consensus size: 36
491884 ATTTTCCCTC
* * ** **
491894 GAAACAACAATTTATCTCACTTGAGATTGTTTTTCTT
1 GAAACAA-AATTTGTCTCGCTTGAGACAGTTTCACTT
* * *
491931 AAAACAAACTTTGTCTCGCTCGAGACAGTTTCACTT
1 GAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTT
* * * ** **
491967 GAAATAACAATTTATCTCACTTGAGATTGTTTTTCTT
1 GAAACAA-AATTTGTCTCGCTTGAGACAGTTTCACTT
* * * *
492004 AAAACAAACTTTGTCTCGCTCGAGACAGTTTCACTC
1 GAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTT
* * * * ** **
492040 GAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTT
1 GAAACA-AAATTTGTCTCGCTTGAGACAGTTTCACTT
* * *
492077 AAAACAAAAGTTGTCTCGCTTGAGACAGTTTCACTC
1 GAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTT
492113 GAAACATAAATTT
1 GAAACA-AAATTT
492126 TCATCACTCG
Statistics
Matches: 137, Mismatches: 55, Indels: 6
0.69 0.28 0.03
Matches are distributed among these distances:
36 76 0.55
37 61 0.45
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (36 bp):
GAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTT
Found at i:492230 original size:45 final size:45
Alignment explanation
Indices: 492181--492512 Score: 531
Period size: 45 Copynumber: 7.3 Consensus size: 45
492171 GGGAGCTTTT
492181 TGATGTTTTCAAAACCTACGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTACGGGTCATCTGTAAGCCCTTCAGTGCA
*
492226 TGATGTTTTCAAAACCTACGGGTCATCTATAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTACGGGTCATCTGTAAGCCCTTCAGTGCA
*
492271 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTACGGGTCATCTGTAAGCCCTTCAGTGCA
* ***
492316 TGATGTTTTCAAAACCTACGGGTCATCTATAAG-CCTTCGGGAGCTTTT
1 TGATGTTTTCAAAACCTACGGGTCATCTGTAAGCCCTTC---AG-TGCA
492364 TGATGTTTTCAAAACCTACGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTACGGGTCATCTGTAAGCCCTTCAGTGCA
*
492409 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTACGGGTCATCTGTAAGCCCTTCAGTGCA
* *
492454 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTGCAGTGCA
1 TGATGTTTTCAAAACCTACGGGTCATCTGTAAGCCCTTCAGTGCA
*
492499 TGATGTTTCCAAAA
1 TGATGTTTTCAAAA
492513 AGCCTTCGGG
Statistics
Matches: 267, Mismatches: 15, Indels: 10
0.91 0.05 0.03
Matches are distributed among these distances:
44 5 0.02
45 220 0.82
46 2 0.01
47 2 0.01
48 33 0.12
49 5 0.02
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTACGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:492411 original size:138 final size:134
Alignment explanation
Indices: 492181--492512 Score: 538
Period size: 138 Copynumber: 2.4 Consensus size: 134
492171 GGGAGCTTTT
492181 TGATGTTTTCAAAACCTACGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTACG
1 TGATGTTTTCAAAACCTACGGGTCATCTGTAAG-CCTTCAGTGCATGATGTTTTCAAAACCTACG
492246 GGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCA
65 GGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCA
492311 GTGCA
130 GTGCA
* ***
492316 TGATGTTTTCAAAACCTACGGGTCATCTATAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCT
1 TGATGTTTTCAAAACCTACGGGTCATCTGTAAGCCTTC---AG-TGCATGATGTTTTCAAAACCT
*
492381 ACGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCT
62 ACGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCT
492446 TCAGTGCA
127 TCAGTGCA
* * *
492454 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTGCAGTGCATGATGTTTCCAAAA
1 TGATGTTTTCAAAACCTACGGGTCATCTGTAAG-CCTTCAGTGCATGATGTTTTCAAAA
492513 AGCCTTCGGG
Statistics
Matches: 180, Mismatches: 12, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
134 5 0.03
135 46 0.26
136 2 0.01
137 2 0.01
138 121 0.67
139 4 0.02
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (134 bp):
TGATGTTTTCAAAACCTACGGGTCATCTGTAAGCCTTCAGTGCATGATGTTTTCAAAACCTACGG
GTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAG
TGCA
Found at i:492471 original size:183 final size:183
Alignment explanation
Indices: 492163--492512 Score: 664
Period size: 183 Copynumber: 1.9 Consensus size: 183
492153 TGTTTCCAAA
492163 AAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTACGGGTCATCTGTAAGCCCTTCAGTGCATG
1 AAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTACGGGTCATCTGTAAGCCCTTCAGTGCATG
492228 ATGTTTTCAAAACCTACGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
66 ATGTTTTCAAAACCTACGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
* *
492293 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTACGGGTCATCTAT
131 TCATCTGTAAGCCCTGCAGTGCATGATGTTTCCAAAACCTACGGGTCATCTAT
492346 AAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTACGGGTCATCTGTAAGCCCTTCAGTGCATG
1 AAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTACGGGTCATCTGTAAGCCCTTCAGTGCATG
* *
492411 ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
66 ATGTTTTCAAAACCTACGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
492476 TCATCTGTAAGCCCTGCAGTGCATGATGTTTCCAAAA
131 TCATCTGTAAGCCCTGCAGTGCATGATGTTTCCAAAA
492513 AGCCTTCGGG
Statistics
Matches: 163, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
183 163 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (183 bp):
AAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTACGGGTCATCTGTAAGCCCTTCAGTGCATG
ATGTTTTCAAAACCTACGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
TCATCTGTAAGCCCTGCAGTGCATGATGTTTCCAAAACCTACGGGTCATCTAT
Found at i:492920 original size:76 final size:76
Alignment explanation
Indices: 492454--492886 Score: 821
Period size: 76 Copynumber: 5.7 Consensus size: 76
492444 CTTCAGTGCA
* * *
492454 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTGCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTT
492519 CGGGAGCTTTT
66 CGGGAGCTTTT
492530 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTT
492595 CGGGAGCTTTT
66 CGGGAGCTTTT
*
492606 TGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTT
492671 CGGGAGCTTTT
66 CGGGAGCTTTT
492682 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTT
492747 CGGGAGCTTTT
66 CGGGAGCTTTT
492758 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTT
492823 CGGGAGCTTTT
66 CGGGAGCTTTT
*
492834 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTT
1 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTT
492887 TTAAGACCTC
Statistics
Matches: 351, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 351 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (76 bp):
TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTT
Found at i:493042 original size:3 final size:3
Alignment explanation
Indices: 493034--493135 Score: 64
Period size: 3 Copynumber: 34.3 Consensus size: 3
493024 TTTTCGTTTG
** ** * *
493034 TTA TTA TTA AAA TTA TTA TTA TTA TTA AAA ATA TTA TTA TTA ATA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
493081 ATA ATA ATA TTA TTA TTA ATA -TA ATA ATA ATA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
493126 TTA TTA TTA T
1 TTA TTA TTA T
493136 ATATATATAT
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
2 4 0.05
3 77 0.92
4 3 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (3 bp):
TTA
Found at i:493054 original size:15 final size:16
Alignment explanation
Indices: 493034--493135 Score: 61
Period size: 17 Copynumber: 6.4 Consensus size: 16
493024 TTTTCGTTTG
*
493034 TTATTATTAAAATTATTA
1 TTATTATT-AAA-TAATA
493052 TTATTATTAAA-AATA
1 TTATTATTAAATAATA
493067 TTATTATTAATATAATA
1 TTATTATTAA-ATAATA
* *
493084 ATAATATT--AT--TA
1 TTATTATTAAATAATA
* *
493096 TTAATATAATAATAATA
1 TTATTATTA-AATAATA
* * *
493113 TTATTATTTATTATTA
1 TTATTATTAAATAATA
493129 TTATTAT
1 TTATTAT
493136 ATATATATAT
Statistics
Matches: 67, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
12 8 0.12
14 2 0.03
15 15 0.22
16 13 0.19
17 21 0.31
18 8 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATTATTAAATAATA
Found at i:493093 original size:23 final size:23
Alignment explanation
Indices: 493045--493120 Score: 120
Period size: 23 Copynumber: 3.4 Consensus size: 23
493035 TATTATTAAA
* *
493045 ATTATTATT-AT-TATTAAAAAT
1 ATTATTATTAATATAATAATAAT
493066 ATTATTATTAATATAATAATAAT
1 ATTATTATTAATATAATAATAAT
493089 ATTATTATTAATATAATAATAAT
1 ATTATTATTAATATAATAATAAT
493112 ATTATTATT
1 ATTATTATT
493121 TATTATTATT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
21 9 0.18
22 2 0.04
23 40 0.78
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTATTATTAATATAATAATAAT
Found at i:493150 original size:23 final size:22
Alignment explanation
Indices: 493045--493150 Score: 88
Period size: 20 Copynumber: 5.1 Consensus size: 22
493035 TATTATTAAA
*
493045 ATTATTATTAT-TATTAA-AAAT
1 ATTATTATTATATA-TAATATAT
493066 ATTATTATTA-ATATAATAATAAT
1 ATTATTATTATATATAAT-AT-AT
493089 ATTATTATTA-ATATAATA-AT
1 ATTATTATTATATATAATATAT
* *
493109 AATATTATTAT-T-TATTAT-T
1 ATTATTATTATATATAATATAT
493128 ATTATTA-TATATAT-ATATAT
1 ATTATTATTATATATAATATAT
493148 ATT
1 ATT
493151 GCAAAATTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 19
0.75 0.05 0.20
Matches are distributed among these distances:
18 3 0.04
19 15 0.21
20 20 0.28
21 12 0.17
22 2 0.03
23 19 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTATTATTATATATAATATAT
Found at i:494225 original size:2 final size:2
Alignment explanation
Indices: 494218--494264 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
494208 TCATTATCAG
494218 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
494260 TA TA T
1 TA TA T
494265 TTATGGTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:497362 original size:20 final size:20
Alignment explanation
Indices: 497337--497388 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
497327 ACTTATATGA
497337 AGTATCGATACTCTTGGGCT
1 AGTATCGATACTCTTGGGCT
497357 AGTATCGATACTCTTGGGCT
1 AGTATCGATACTCTTGGGCT
497377 AGTATCGATACT
1 AGTATCGATACT
497389 TTCAGTCAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (20 bp):
AGTATCGATACTCTTGGGCT
Found at i:498902 original size:2 final size:2
Alignment explanation
Indices: 498897--498934 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
498887 ATAATCTATT
498897 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
498935 ATGATAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:500092 original size:46 final size:47
Alignment explanation
Indices: 500028--500128 Score: 132
Period size: 47 Copynumber: 2.2 Consensus size: 47
500018 GGGCAAAACG
* * *
500028 GCCACACAACACTGAAAATG-CCCACGAGGGCAATTGAGGTAGCCTA
1 GCCACACAACACTAAAAATGCCCCACGAGGGAAACTGAGGTAGCCTA
* * * *
500074 GCTACACACCACTAAAAATGCCCCACTAGGGAAACTGAGGTAGCCTC
1 GCCACACAACACTAAAAATGCCCCACGAGGGAAACTGAGGTAGCCTA
500121 GCCACACA
1 GCCACACA
500129 TTAGCATAAC
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
46 17 0.37
47 29 0.63
ACGTcount: A:0.35, C:0.32, G:0.21, T:0.13
Consensus pattern (47 bp):
GCCACACAACACTAAAAATGCCCCACGAGGGAAACTGAGGTAGCCTA
Found at i:500800 original size:12 final size:12
Alignment explanation
Indices: 500783--500852 Score: 77
Period size: 12 Copynumber: 5.8 Consensus size: 12
500773 TATTGGACAA
500783 TATTGATACTGG
1 TATTGATACTGG
*
500795 TATTGATATTGG
1 TATTGATACTGG
*
500807 TATTGATATTGG
1 TATTGATACTGG
* * *
500819 TACTAATACTAG
1 TATTGATACTGG
*
500831 TATTGATACTAG
1 TATTGATACTGG
*
500843 TATCGATACT
1 TATTGATACT
500853 ATAGGAGCAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 50 1.00
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.43
Consensus pattern (12 bp):
TATTGATACTGG
Found at i:508012 original size:26 final size:26
Alignment explanation
Indices: 507981--508035 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 26
507971 CACGTAATAA
507981 AAATGAATTTGAAAAAAATAA-AAAAT
1 AAATGAATTTG-AAAAAATAATAAAAT
508007 AAATGAATTTGAAAAAATAATAAAAT
1 AAATGAATTTGAAAAAATAATAAAAT
508033 AAA
1 AAA
508036 AAATAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 9 0.32
26 19 0.68
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (26 bp):
AAATGAATTTGAAAAAATAATAAAAT
Found at i:509092 original size:19 final size:19
Alignment explanation
Indices: 509065--509112 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
509055 TATTATGGGT
*
509065 TCTTGCTTCATCATCTTCC
1 TCTTTCTTCATCATCTTCC
509084 TCTTTCTTCATCATCTTCC
1 TCTTTCTTCATCATCTTCC
509103 TCTTTCTTCA
1 TCTTTCTTCA
509113 GTAGTTAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.10, C:0.35, G:0.02, T:0.52
Consensus pattern (19 bp):
TCTTTCTTCATCATCTTCC
Found at i:510010 original size:44 final size:44
Alignment explanation
Indices: 509949--510046 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
509939 GGATAATAGT
* * *
509949 AGAAGATGAAGCAAGAACTGATGGTAACTA-CTCAAGAAAAAGGA
1 AGAAGATGAAACAAGAACTCATGATAACTACCT-AAGAAAAAGGA
* *
509993 AGAAGATGAAACAAGAACTCATGATAACTACCTGAGTAAAAGGA
1 AGAAGATGAAACAAGAACTCATGATAACTACCTAAGAAAAAGGA
510037 AGAAGATGAA
1 AGAAGATGAA
510047 GCAACAACCC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 46 0.96
45 2 0.04
ACGTcount: A:0.51, C:0.11, G:0.23, T:0.14
Consensus pattern (44 bp):
AGAAGATGAAACAAGAACTCATGATAACTACCTAAGAAAAAGGA
Found at i:511313 original size:21 final size:21
Alignment explanation
Indices: 511289--511342 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
511279 CAACACAGTT
511289 TCCAAATTCGCAAAGCGATTC
1 TCCAAATTCGCAAAGCGATTC
*
511310 TCCAAATTCGCAAAGCGGTTC
1 TCCAAATTCGCAAAGCGATTC
*
511331 T-CAATTTCGCAA
1 TCCAAATTCGCAA
511343 CGCTAATTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (21 bp):
TCCAAATTCGCAAAGCGATTC
Found at i:511400 original size:20 final size:20
Alignment explanation
Indices: 511375--511413 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
511365 ACACAACTAT
511375 TCGCAACTCAGTTTTCAAAA
1 TCGCAACTCAGTTTTCAAAA
511395 TCGCAACTCAGTTTTCAAA
1 TCGCAACTCAGTTTTCAAA
511414 TTTGTAACGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (20 bp):
TCGCAACTCAGTTTTCAAAA
Found at i:511529 original size:79 final size:78
Alignment explanation
Indices: 511395--511541 Score: 197
Period size: 79 Copynumber: 1.9 Consensus size: 78
511385 GTTTTCAAAA
* * * **
511395 TCGCAACTCAGTTTTCAAATTTGTAACGCGATTCTCCAAATTCGCAACGCTAATTACCGATATAG
1 TCGCAACTCAGTTTTCAAATTCGCAACGCGAATAGCCAAATTCGCAAC-CTAATTACCGATATAG
511460 GTAAACACAACTAT
65 GTAAACACAACTAT
* *
511474 TCGCAACTCAGTTTTCAAATTCGCAACGCGAAATAGCCAATTTTGCAA-CTAAATTACCGATATA
1 TCGCAACTCAGTTTTCAAATTCGCAACGCG-AATAGCCAAATTCGCAACCT-AATTACCGATATA
511538 GGTA
64 GGTA
511542 TACTCGATGG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
78 2 0.03
79 45 0.76
80 12 0.20
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.29
Consensus pattern (78 bp):
TCGCAACTCAGTTTTCAAATTCGCAACGCGAATAGCCAAATTCGCAACCTAATTACCGATATAGG
TAAACACAACTAT
Found at i:516558 original size:15 final size:16
Alignment explanation
Indices: 516530--516561 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
516520 AAAATCTTTC
516530 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
516546 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
516561 T
1 T
516562 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:519910 original size:78 final size:78
Alignment explanation
Indices: 519781--519938 Score: 244
Period size: 78 Copynumber: 2.0 Consensus size: 78
519771 TTTTCTATAT
* * * * * *
519781 TTTTCTTACTTTCTTAAAATACACATTTCTTCTCTTTTTGCCAATAACAACTCTTTTGTGATATA
1 TTTTCTTACATTCTTAAAATACACATTACTTATCTTTTTGCCAACAACAACTATTTTGTGAGATA
519846 CACTCTCTGTGGG
66 CACTCTCTGTGGG
*
519859 TTTTCTTACATTCTTAAAATACATATTACTTATCTTTTTGCCAACAACAACTATTTTGTGAGATA
1 TTTTCTTACATTCTTAAAATACACATTACTTATCTTTTTGCCAACAACAACTATTTTGTGAGATA
*
519924 CATTCTCTGTGGG
66 CACTCTCTGTGGG
519937 TT
1 TT
519939 CGAGATCTGA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.25, C:0.20, G:0.09, T:0.46
Consensus pattern (78 bp):
TTTTCTTACATTCTTAAAATACACATTACTTATCTTTTTGCCAACAACAACTATTTTGTGAGATA
CACTCTCTGTGGG
Found at i:524656 original size:5 final size:5
Alignment explanation
Indices: 524646--524690 Score: 90
Period size: 5 Copynumber: 9.0 Consensus size: 5
524636 CTATTCTCCA
524646 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT
524691 CTCTTTGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:539460 original size:9 final size:11
Alignment explanation
Indices: 539431--539461 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
539421 TAACCTAGGA
539431 AAAAATATATT
1 AAAAATATATT
539442 AAAAATATATT
1 AAAAATATATT
539453 AAAAATATA
1 AAAAATATA
539462 ATTCTTTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAAATATATT
Found at i:539871 original size:44 final size:44
Alignment explanation
Indices: 539804--539909 Score: 167
Period size: 44 Copynumber: 2.4 Consensus size: 44
539794 TGTTAGAACA
*
539804 TTCCAACTTATTCCCTAAGACTATGTTGGAGCTATTAACAACCT
1 TTCCAACTTATTTCCTAAGACTATGTTGGAGCTATTAACAACCT
* * * *
539848 TTCTAACTTATTTCCTAAGACTATGTTGGAGCTATTACCAGCTT
1 TTCCAACTTATTTCCTAAGACTATGTTGGAGCTATTAACAACCT
539892 TTCCAACTTATTTCCTAA
1 TTCCAACTTATTTCCTAA
539910 TTTGATTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (44 bp):
TTCCAACTTATTTCCTAAGACTATGTTGGAGCTATTAACAACCT
Found at i:540597 original size:16 final size:15
Alignment explanation
Indices: 540576--540611 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
540566 TGAAACTAAT
540576 AAAATAAAAAATATAA
1 AAAATAAAAAATA-AA
*
540592 AAAATAATAAATAAA
1 AAAATAAAAAATAAA
540607 AAAAT
1 AAAAT
540612 TAAACTAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAATAAAAAATAAA
Found at i:554346 original size:37 final size:36
Alignment explanation
Indices: 554303--554433 Score: 172
Period size: 37 Copynumber: 3.4 Consensus size: 36
554293 TTTGGAAACC
*
554303 ATATATATAATATATAATTTTTGAAAATATTTTGAA
1 ATATATATAATATATAGTTTTTGAAAATATTTTGAA
*
554339 AGCATATATAATATATAGTTTTTGAAAATATTTTTGAAAAA
1 A-TATATATAATATATAGTTTTTGAAAATA-TTTTG---AA
*
554380 ATATATATAATATATAGTTTTTGCAAATATTTTGAA
1 ATATATATAATATATAGTTTTTGAAAATATTTTGAA
554416 TATATATATATATATATA
1 -ATATATATA-ATATATA
554434 TATATATATA
Statistics
Matches: 84, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
36 3 0.04
37 35 0.42
38 12 0.14
39 5 0.06
40 26 0.31
41 3 0.04
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTTGAAAATATTTTGAA
Found at i:554422 original size:2 final size:2
Alignment explanation
Indices: 554415--554447 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
554405 AATATTTTGA
554415 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
554448 GTTATTGAAA
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:554436 original size:89 final size:88
Alignment explanation
Indices: 554342--554519 Score: 254
Period size: 89 Copynumber: 2.0 Consensus size: 88
554332 TTTTGAAAGC
* * *
554342 ATATATA-ATATATAGTTTTTGAAAATATTTTTGAAAAAATATATATAATATATAGTTTTTGCAA
1 ATATATATATATATAGTTATTGAAAATA-TTTTG--AAAATATATATAATATATAATTTTTGAAA
* *
554406 ATATTTTGAATATATATATATATATAT
63 ACATTTTGAATAAATATATAT-TATAT
554433 ATATATATATATATAGTTATTGAAAATATTTTGAAAATATATATAATATATAATTTTTGAAAACA
1 ATATATATATATATAGTTATTGAAAATATTTTGAAAATATATATAATATATAATTTTTGAAAACA
554498 TTTTG-A-AAATATATATTATAT
66 TTTTGAATAAATATATATTATAT
554519 A
1 A
554520 AAATATTTAT
Statistics
Matches: 81, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
86 6 0.07
87 9 0.11
88 1 0.01
89 34 0.42
91 12 0.15
92 19 0.23
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (88 bp):
ATATATATATATATAGTTATTGAAAATATTTTGAAAATATATATAATATATAATTTTTGAAAACA
TTTTGAATAAATATATATTATAT
Found at i:554461 original size:52 final size:50
Alignment explanation
Indices: 554380--554484 Score: 165
Period size: 52 Copynumber: 2.1 Consensus size: 50
554370 TTTTGAAAAA
* * *
554380 ATATATATAATATATAGTTTTTGCAAATATTTTGAATATATATATATATAT
1 ATATATATAATATATAGTTATTGAAAATATTTTGAAAATATATATA-ATAT
554431 ATATATATATATATATAGTTATTGAAAATATTTTGAAAATATATATAATAT
1 ATATATATA-ATATATAGTTATTGAAAATATTTTGAAAATATATATAATAT
554482 ATA
1 ATA
554485 ATTTTTGAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
51 16 0.32
52 34 0.68
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.47
Consensus pattern (50 bp):
ATATATATAATATATAGTTATTGAAAATATTTTGAAAATATATATAATAT
Found at i:554493 original size:37 final size:37
Alignment explanation
Indices: 554431--554519 Score: 133
Period size: 37 Copynumber: 2.4 Consensus size: 37
554421 ATATATATAT
* *
554431 ATATATATATATATATAGTTATTGAAAATATTTTGAAA
1 ATATATATA-ATATATAATTATTGAAAACATTTTGAAA
*
554469 ATATATATAATATATAATTTTTGAAAACATTTTGAAA
1 ATATATATAATATATAATTATTGAAAACATTTTGAAA
*
554506 ATATATATTATATA
1 ATATATATAATATA
554520 AAATATTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
37 38 0.81
38 9 0.19
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (37 bp):
ATATATATAATATATAATTATTGAAAACATTTTGAAA
Found at i:554550 original size:14 final size:14
Alignment explanation
Indices: 554522--554563 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
554512 ATTATATAAA
*
554522 ATATT-TATGTATT
1 ATATTATATTTATT
554535 ATATTATATTTATT
1 ATATTATATTTATT
554549 ATATTATTATTTATT
1 ATATTA-TATTTATT
554564 TTCTTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 5 0.19
14 13 0.50
15 8 0.31
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (14 bp):
ATATTATATTTATT
Found at i:554555 original size:19 final size:19
Alignment explanation
Indices: 554507--554564 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
554497 ATTTTGAAAA
**
554507 TATATATTATATAAAATATT
1 TATATATTAT-TATTATATT
*
554527 TATGTATTA-TATTATATT
1 TATATATTATTATTATATT
554545 TATTATATTATTATT-TATT
1 TA-TATATTATTATTATATT
554564 T
1 T
554565 TCTTTTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 9 0.28
19 11 0.34
20 12 0.38
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TATATATTATTATTATATT
Found at i:554576 original size:5 final size:5
Alignment explanation
Indices: 554533--554612 Score: 71
Period size: 5 Copynumber: 16.4 Consensus size: 5
554523 TATTTATGTA
* * *
554533 TTATA TTATAT TTATT ATATT ATTA-T TTATT TTCTTT TTATT TT-TT
1 TTATT TTAT-T TTATT TTATT -TTATT TTATT TT-ATT TTATT TTATT
554579 TTATT TTATT TTATT TTA-T TT-TT TT-TT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
554613 GGTCCAAATA
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
4 17 0.27
5 36 0.57
6 10 0.16
ACGTcount: A:0.20, C:0.01, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:554582 original size:24 final size:23
Alignment explanation
Indices: 554555--554612 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
554545 TATTATATTA
*
554555 TTATTTATTTTCTTTTTATTTTTT
1 TTATTTATTTT-ATTTTATTTTTT
554579 TTATTTTATTTTATTTTATTTTTT
1 TTA-TTTATTTTATTTTATTTTTT
554603 TT-TTTATTTT
1 TTATTTATTTT
554613 GGTCCAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 8 0.25
24 16 0.50
25 8 0.25
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (23 bp):
TTATTTATTTTATTTTATTTTTT
Found at i:554592 original size:30 final size:30
Alignment explanation
Indices: 554523--554609 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 30
554513 TTATATAAAA
* *
554523 TATTTATGTATTATATTATATTTATTATATTAT
1 TATTTAT-T-TTAT-TTTTATTTTTTATATTAT
* *
554556 TATTTATTTTCTTTTTATTTTTTTTATT-T
1 TATTTATTTTATTTTTATTTTTTATATTAT
554585 TATTTTATTTTATTTTT-TTTTTTAT
1 TA-TTTATTTTATTTTTATTTTTTAT
554610 TTTGGTCCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
29 10 0.21
30 26 0.55
31 3 0.06
32 1 0.02
33 7 0.15
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.76
Consensus pattern (30 bp):
TATTTATTTTATTTTTATTTTTTATATTAT
Found at i:554597 original size:35 final size:36
Alignment explanation
Indices: 554543--554612 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 36
554533 TTATATTATA
554543 TTTATTATATTATTATTTA-TTTTCTTTTTATTTTT
1 TTTATTATATTATTATTTATTTTTCTTTTTATTTTT
* *
554578 TTTATTTTATT-TTATTTTATTTTTTTTTTTATTTT
1 TTTATTATATTATTA-TTTATTTTTCTTTTTATTTT
554613 GGTCCAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 3 0.10
35 14 0.45
36 14 0.45
ACGTcount: A:0.17, C:0.01, G:0.00, T:0.81
Consensus pattern (36 bp):
TTTATTATATTATTATTTATTTTTCTTTTTATTTTT
Found at i:555789 original size:15 final size:16
Alignment explanation
Indices: 555771--555804 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
555761 TTTATTTTCC
555771 TTTATTTTTTT-ATTT
1 TTTATTTTTTTCATTT
555786 TTTATTTTTTTCATTT
1 TTTATTTTTTTCATTT
555802 TTT
1 TTT
555805 TCTTTGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTATTTTTTTCATTT
Found at i:555806 original size:9 final size:8
Alignment explanation
Indices: 555755--555805 Score: 59
Period size: 9 Copynumber: 6.0 Consensus size: 8
555745 CATTTTATTG
555755 ATTTCTTTT
1 ATTT-TTTT
555764 ATTTTCCTTT
1 ATTTT--TTT
555774 ATTTTTTT
1 ATTTTTTT
555782 A-TTTTTT
1 ATTTTTTT
555789 ATTTTTTT
1 ATTTTTTT
555797 CATTTTTTT
1 -ATTTTTTT
555806 CTTTGTGTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
7 7 0.18
8 11 0.29
9 12 0.32
10 8 0.21
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (8 bp):
ATTTTTTT
Found at i:555909 original size:17 final size:16
Alignment explanation
Indices: 555868--555909 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
555858 TAACGTTGTT
*
555868 TTATTTTTTTATTTAA
1 TTATATTTTTATTTAA
555884 TTA-ACTTTTTATTTACA
1 TTATA-TTTTTATTTA-A
555901 TTATATTTT
1 TTATATTTT
555910 ATTACTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 13 0.59
17 8 0.36
18 1 0.05
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATATTTTTATTTAA
Found at i:564779 original size:33 final size:35
Alignment explanation
Indices: 564712--564780 Score: 97
Period size: 33 Copynumber: 2.0 Consensus size: 35
564702 TCTTTTTTCA
564712 TTTCTTTAGAACTCAATTTTCTTTCATTCAATACT
1 TTTCTTTAGAACTCAATTTTCTTTCATTCAATACT
* * *
564747 TTTCTTTTGAATTCAA-TTT-TTTCATTCTATACT
1 TTTCTTTAGAACTCAATTTTCTTTCATTCAATACT
564780 T
1 T
564781 CGTTTTATCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 14 0.45
34 3 0.10
35 14 0.45
ACGTcount: A:0.23, C:0.17, G:0.03, T:0.57
Consensus pattern (35 bp):
TTTCTTTAGAACTCAATTTTCTTTCATTCAATACT
Found at i:569853 original size:43 final size:41
Alignment explanation
Indices: 569813--570052 Score: 196
Period size: 43 Copynumber: 5.9 Consensus size: 41
569803 TATATATAAG
569813 ATATAATATATAGTTTTTTTATAAA-ATTTTGAAAACATAT-
1 ATATAATATATAGTTTTTTTA-AAATATTTTGAAAACATATA
* * **
569853 ATTTAATATATAGTTTTTTTTTTTAAACGTTTTGAAAACATAT-
1 ATATAATATATAG---TTTTTTTAAAATATTTTGAAAACATATA
*
569896 ATATAATATATAG--TTTTTAAAATATTTTGAAAATATAT-
1 ATATAATATATAGTTTTTTTAAAATATTTTGAAAACATATA
*
569934 ATATATATAATATA-TTGTTTTTGAAAATATTTTGAAAAAATAT-
1 ATATA-AT-ATATAGTT-TTTTT-AAAATATTTTGAAAACATATA
* * * * *
569977 ATATAATATAT-GGTTTTTGAAAACATTTTGGAAATATAT-
1 ATATAATATATAGTTTTTTTAAAATATTTTGAAAACATATA
* * * *
570016 ATATAATATATA-ATCTTTGAAAATATTTTTAAAACAT
1 ATATAATATATAGTTTTTTTAAAATATTTTGAAAACAT
570053 TTTGAAAATA
Statistics
Matches: 168, Mismatches: 20, Indels: 25
0.79 0.09 0.12
Matches are distributed among these distances:
38 26 0.15
39 49 0.29
40 21 0.12
41 5 0.03
42 10 0.06
43 57 0.34
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.47
Consensus pattern (41 bp):
ATATAATATATAGTTTTTTTAAAATATTTTGAAAACATATA
Found at i:569925 original size:81 final size:80
Alignment explanation
Indices: 569813--570027 Score: 254
Period size: 81 Copynumber: 2.6 Consensus size: 80
569803 TATATATAAG
* * * **
569813 ATATAATATATAGTTTTTTTATAAAATTTTGAAAACATATATTTAATATATAGT-TTTTTTTTTT
1 ATATAATATATAG--TTTTTA-AAAATTTTGAAAATATATATATAATATATA-TATTGTTTTTGA
* *
569877 AAACGTTTTGAAAACATAT
62 AAACATTTTGAAAAAATAT
569896 ATATAATATATAGTTTTTAAAATATTTTGAAAATATATATAT-ATATAATATATTGTTTTTGAAA
1 ATATAATATATAGTTTTTAAAA-ATTTTGAAAATATATATATAATAT-ATATATTGTTTTTGAAA
*
569960 ATATTTTGAAAAAATAT
64 ACATTTTGAAAAAATAT
* *
569977 ATATAATATATGGTTTTTGAAAACATTTTGGAAATATATATATAATATATA
1 ATATAATATATAGTTTTT-AAAA-ATTTTGAAAATATATATATAATATATA
570028 ATCTTTGAAA
Statistics
Matches: 116, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
80 8 0.07
81 66 0.57
82 25 0.22
83 17 0.15
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (80 bp):
ATATAATATATAGTTTTTAAAAATTTTGAAAATATATATATAATATATATATTGTTTTTGAAAAC
ATTTTGAAAAAATAT
Found at i:569993 original size:39 final size:39
Alignment explanation
Indices: 569813--570049 Score: 226
Period size: 39 Copynumber: 5.9 Consensus size: 39
569803 TATATATAAG
* *
569813 ATATAATATATAGTTTTTTTATAAA-ATTTTGAAAACATAT
1 ATATAATATATAG-TTTTTGA-AAATATTTTGAAAAAATAT
* ** ** *
569853 ATTTAATATATAGTTTTTTTTTTTAAACGTTTTGAAAACATAT
1 ATATAATATATAG----TTTTTGAAAATATTTTGAAAAAATAT
569896 ATATAATATATAGTTTTT-AAAATATTTTGAAAATATATATAT
1 ATATAATATATAGTTTTTGAAAATATTTTG-AAA-A-A-ATAT
*
569938 ATATAATATATTGTTTTTGAAAATATTTTGAAAAAATAT
1 ATATAATATATAGTTTTTGAAAATATTTTGAAAAAATAT
* * * *
569977 ATATAATATATGGTTTTTGAAAACATTTTGGAAATATAT
1 ATATAATATATAGTTTTTGAAAATATTTTGAAAAAATAT
* * *
570016 ATATAATATATAATCTTTGAAAATATTTTTAAAA
1 ATATAATATATAGTTTTTGAAAATATTTTGAAAA
570050 CATTTTGAAA
Statistics
Matches: 169, Mismatches: 19, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
38 8 0.05
39 75 0.44
40 14 0.08
41 1 0.01
42 27 0.16
43 44 0.26
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (39 bp):
ATATAATATATAGTTTTTGAAAATATTTTGAAAAAATAT
Found at i:570114 original size:15 final size:15
Alignment explanation
Indices: 570094--570132 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
570084 GTAATATATT
570094 TTATTATTTACTATA
1 TTATTATTTACTATA
* *
570109 TTATTATTTATTTTA
1 TTATTATTTACTATA
570124 TTATTATTT
1 TTATTATTT
570133 TATTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
TTATTATTTACTATA
Found at i:570125 original size:5 final size:5
Alignment explanation
Indices: 570115--570171 Score: 73
Period size: 5 Copynumber: 11.6 Consensus size: 5
570105 TATATTATTA
* *
570115 TTTAT TTTAT TATTAT TTTAT TTTAT TTTA- TTTAT TTTCT TTTCT TTT-T
1 TTTAT TTTAT T-TTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
570164 TTTAT TTT
1 TTTAT TTT
570172 GGTCCAAATA
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
4 8 0.17
5 35 0.73
6 5 0.10
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:570129 original size:30 final size:30
Alignment explanation
Indices: 570094--570152 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
570084 GTAATATATT
570094 TTATTA-TTTACTATATTATTATTTATTTTA
1 TTATTATTTTACTATATT-TTATTTATTTTA
* *
570124 TTATTATTTTATTTTATTTTATTTATTTT
1 TTATTATTTTACTATATTTTATTTATTTT
570153 CTTTTCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (30 bp):
TTATTATTTTACTATATTTTATTTATTTTA
Found at i:570142 original size:10 final size:10
Alignment explanation
Indices: 570115--570171 Score: 73
Period size: 9 Copynumber: 5.8 Consensus size: 10
570105 TATATTATTA
570115 TTTATTTTAT
1 TTTATTTTAT
570125 TATTATTTTAT
1 T-TTATTTTAT
570136 TTTATTTTA-
1 TTTATTTTAT
*
570145 TTTATTTTCT
1 TTTATTTTAT
*
570155 TTTCTTTT-T
1 TTTATTTTAT
570164 TTTATTTT
1 TTTATTTT
570172 GGTCCAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
9 16 0.38
10 16 0.38
11 10 0.24
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTATTTTAT
Found at i:570151 original size:19 final size:19
Alignment explanation
Indices: 570115--570171 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
570105 TATATTATTA
570115 TTTATTTTATTATTATTTTAT
1 TTTATTTTA-T-TTATTTTAT
*
570136 TTTATTTTATTTATTTTCT
1 TTTATTTTATTTATTTTAT
* *
570155 TTTCTTTTTTTTATTTT
1 TTTATTTTATTTATTTT
570172 GGTCCAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 23 0.70
20 1 0.03
21 9 0.27
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTATTTTATTTATTTTAT
Found at i:571325 original size:23 final size:23
Alignment explanation
Indices: 571298--571367 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 23
571288 ATCCAACATT
571298 TTATTTATTTCTTTTATTTTCCTA
1 TTATTT-TTTCTTTTATTTTCCTA
* **
571322 -TATTTTTTATTTTTATTTTATTA
1 TTATTTTTT-CTTTTATTTTCCTA
571345 TTATTTTTATTCATTTTATTTTC
1 TTA-TTTT-TTC-TTTTATTTTC
571368 TTTGTGTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
22 3 0.08
23 16 0.44
24 2 0.06
25 4 0.11
26 11 0.31
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (23 bp):
TTATTTTTTCTTTTATTTTCCTA
Found at i:575368 original size:9 final size:9
Alignment explanation
Indices: 575354--575386 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
575344 CATTCGATTG
575354 AGAAAAAGA
1 AGAAAAAGA
575363 AGAAAAAGA
1 AGAAAAAGA
*
575372 A-AGAAAGA
1 AGAAAAAGA
575380 AGAAAAA
1 AGAAAAA
575387 TCACAGCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AGAAAAAGA
Found at i:587397 original size:7 final size:7
Alignment explanation
Indices: 587387--587422 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
587377 TTACATTTTC
587387 ATTCTTT
1 ATTCTTT
587394 ATTCTTT
1 ATTCTTT
587401 ATTCTTT
1 ATTCTTT
587408 ATTCTTT
1 ATTCTTT
587415 ATTCTTT
1 ATTCTTT
587422 A
1 A
587423 CATTCATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (7 bp):
ATTCTTT
Found at i:596996 original size:24 final size:24
Alignment explanation
Indices: 596969--597016 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
596959 GAGTTTCGCA
*
596969 TTTTCT-GTTATATTTTTAAGATGC
1 TTTTCTGGTTAT-TTTGTAAGATGC
*
596993 TTTTTTGGTTATTTTGTAAGATGC
1 TTTTCTGGTTATTTTGTAAGATGC
597017 ATGCATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.19, C:0.06, G:0.17, T:0.58
Consensus pattern (24 bp):
TTTTCTGGTTATTTTGTAAGATGC
Found at i:597854 original size:23 final size:23
Alignment explanation
Indices: 597825--597871 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
597815 GAATTCCTGG
*
597825 GGGGGGGGAGTTCTAACTAAAAT
1 GGGGGGGGAATTCTAACTAAAAT
597848 GGGGGGGGAATTCTAACTAAAAT
1 GGGGGGGGAATTCTAACTAAAAT
597871 G
1 G
597872 AACCTACTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.09, G:0.38, T:0.21
Consensus pattern (23 bp):
GGGGGGGGAATTCTAACTAAAAT
Found at i:601915 original size:32 final size:33
Alignment explanation
Indices: 601864--601925 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
601854 GAATGCTGTA
* * *
601864 ATATTTTTGTTGATCTTTCTTGTCTATGAATGT
1 ATATCTTTCTTGATCTTTCTTGTCCATGAATGT
601897 ATATCTTTCTTGAT-TTTCTTGTCCATGAA
1 ATATCTTTCTTGATCTTTCTTGTCCATGAA
601926 ACAACTACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.54
33 12 0.46
ACGTcount: A:0.19, C:0.13, G:0.13, T:0.55
Consensus pattern (33 bp):
ATATCTTTCTTGATCTTTCTTGTCCATGAATGT
Found at i:604059 original size:18 final size:21
Alignment explanation
Indices: 604013--604059 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
604003 TTTTATATTT
604013 AATTAATGTTTTAGTTTCAAGA
1 AATTAATGTTTTA-TTTCAAGA
*
604035 CATTAATGTTTT-TTT-AA-A
1 AATTAATGTTTTATTTCAAGA
604053 AATTAAT
1 AATTAAT
604060 ATATATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 7 0.30
19 2 0.09
20 3 0.13
22 11 0.48
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (21 bp):
AATTAATGTTTTATTTCAAGA
Found at i:606271 original size:32 final size:32
Alignment explanation
Indices: 606120--606272 Score: 123
Period size: 32 Copynumber: 4.8 Consensus size: 32
606110 AAAATTAAGT
* * * *
606120 ACTAAAATGAAACAAAAAGTTAATAAT-ATGA
1 ACTAAAATGAAATAAAAAGTAAACAATCAGGA
* * ** * *
606151 TGCTAAAATAAAATAAAAAGTAAACTTTTAGGT
1 -ACTAAAATGAAATAAAAAGTAAACAATCAGGA
* **
606184 ACTAAAATGAAATAAAAAGTTAACAATGGGGGTA
1 ACTAAAATGAAATAAAAAGTAAACAAT-CAGG-A
*
606218 A-TAAAATGAAATAAAAAGTAAAC-GTCAGGA
1 ACTAAAATGAAATAAAAAGTAAACAATCAGGA
606248 ACTAAAATGAAATAAAAAAGTAAAC
1 ACTAAAATGAAAT-AAAAAGTAAAC
606273 TCTAGGTGTG
Statistics
Matches: 95, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
30 2 0.02
31 13 0.14
32 54 0.57
33 25 0.26
34 1 0.01
ACGTcount: A:0.58, C:0.07, G:0.14, T:0.22
Consensus pattern (32 bp):
ACTAAAATGAAATAAAAAGTAAACAATCAGGA
Found at i:610307 original size:21 final size:21
Alignment explanation
Indices: 610265--610307 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
610255 TTTCTGGGTT
* * *
610265 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
610286 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
610307 A
1 A
610308 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:610368 original size:66 final size:67
Alignment explanation
Indices: 610265--610436 Score: 231
Period size: 67 Copynumber: 2.6 Consensus size: 67
610255 TTTCTGGGTT
* * *
610265 AGGGGAATCGGTACCCATTCA-AGGGGAACCGATACCCCCTCAACG-AAATGAATTTCCAGAATG
1 AGGGGAATCGGTACCC--CCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATG
610328 CTAG
64 CTAG
* * *
610332 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCT
1 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCT
*
610397 TG
66 AG
* *
610399 AGGGGAATCGATACCCCCAGGGGGGAACCGATTCCCCC
1 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCC
610437 ATGAGAAAAA
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
65 2 0.02
66 22 0.23
67 70 0.74
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.17
Consensus pattern (67 bp):
AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCT
AG
Found at i:610425 original size:20 final size:20
Alignment explanation
Indices: 610400--610437 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
610390 GATTGCTTGA
*
610400 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
610420 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
610438 TGAGAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:610837 original size:30 final size:30
Alignment explanation
Indices: 610803--610861 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
610793 GTTATATGAG
* *
610803 CTATGTGATAAAGGTATGTAAATGATATGT
1 CTATGTGATAAAGGTATGGAAATAATATGT
610833 CTATGTGATAAAGGTATGGAAATAATATG
1 CTATGTGATAAAGGTATGGAAATAATATG
610862 ACTACGCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGGAAATAATATGT
Found at i:611139 original size:23 final size:22
Alignment explanation
Indices: 611075--611142 Score: 118
Period size: 22 Copynumber: 3.0 Consensus size: 22
611065 TTATGGACAT
611075 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
611097 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
*
611119 AATTCTACGGGGTACTTCGGTGC
1 AATTCTAC-GGGCACTTCGGTGC
611142 A
1 A
611143 TTTATACGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 30 0.68
23 14 0.32
ACGTcount: A:0.19, C:0.25, G:0.28, T:0.28
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:617283 original size:66 final size:67
Alignment explanation
Indices: 617179--617350 Score: 222
Period size: 67 Copynumber: 2.6 Consensus size: 67
617169 TTTCTGGGTT
* * * *
617179 AGGGGAATCGGTACCCATTCA-AGGGGAACTGATACCCCCTCAACG-AAATGAATTTCCAGAATG
1 AGGGGAATCGGTACCC--CCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATG
617242 CTAG
64 CTAG
* * *
617246 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCT
1 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCT
*
617311 TG
66 AG
* *
617313 AGGGGAATCGATACCCCCAGGGGGGAACCGATTCCCCC
1 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCC
617351 ATGAGAAAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
65 2 0.02
66 21 0.23
67 70 0.75
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (67 bp):
AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCT
AG
Found at i:617339 original size:20 final size:20
Alignment explanation
Indices: 617314--617351 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
617304 GATTGCTTGA
*
617314 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
617334 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
617352 TGAGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:617748 original size:30 final size:30
Alignment explanation
Indices: 617714--617772 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
617704 GTTATATGAG
* *
617714 CTATGTGATAAAGGTATGTAAATGATATGT
1 CTATGTGATAAAGGTATGGAAATAATATGT
617744 CTATGTGATAAAGGTATGGAAATAATATG
1 CTATGTGATAAAGGTATGGAAATAATATG
617773 ACTACGCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGGAAATAATATGT
Found at i:618046 original size:23 final size:22
Alignment explanation
Indices: 617986--618053 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
617976 TTATGGACAT
617986 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
618008 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
618030 AATTCTACGGGGCACTTCGGTGC
1 AATTCTAC-GGGCACTTCGGTGC
618053 A
1 A
618054 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 30 0.67
23 15 0.33
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.26
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:629555 original size:3 final size:3
Alignment explanation
Indices: 629543--629589 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
629533 AGCTCCCAGT
629543 TTC TTC -TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
629590 CTCCTCCTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:630211 original size:2 final size:2
Alignment explanation
Indices: 630204--630234 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
630194 ACATGCAAAC
630204 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
630235 GTTGTTTTGA
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:635682 original size:18 final size:18
Alignment explanation
Indices: 635656--635700 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
635646 CTTTATATTA
*
635656 TTTAATTAATTATTT-TCT
1 TTTATTTAATT-TTTATCT
635674 TTTATTTAATTTTTATCT
1 TTTATTTAATTTTTATCT
635692 TTTATTTAA
1 TTTATTTAA
635701 AAAAACAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTTAATTTTTATCT
Found at i:635699 original size:22 final size:22
Alignment explanation
Indices: 635647--635699 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
635637 TCACAATCAC
635647 TTTATATTATTTAATTAATTATT
1 TTTAT-TTATTTAATTAATTATT
*
635670 TTCT-TTTATTTAATT-TTTATCT
1 TT-TATTTATTTAATTAATTAT-T
635692 TTTATTTA
1 TTTATTTA
635700 AAAAAACAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 5 0.19
22 17 0.65
23 3 0.12
24 1 0.04
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTATTTATTTAATTAATTATT
Found at i:644893 original size:49 final size:49
Alignment explanation
Indices: 644812--644906 Score: 145
Period size: 49 Copynumber: 1.9 Consensus size: 49
644802 GCCTCCTGAA
* * *
644812 CCGCGCTATACGCTGATTTGGCGTCACGTGGGTATAGCGCGCCCCCGCC
1 CCGCGATATACGCTGATTTGGCGCCACATGGGTATAGCGCGCCCCCGCC
* *
644861 CCGCGATATACGGTGATTTGGCGCCATATGGGTATAGCGCGCCCCC
1 CCGCGATATACGCTGATTTGGCGCCACATGGGTATAGCGCGCCCCC
644907 TGATCCGCGT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.15, C:0.34, G:0.31, T:0.21
Consensus pattern (49 bp):
CCGCGATATACGCTGATTTGGCGCCACATGGGTATAGCGCGCCCCCGCC
Found at i:645025 original size:20 final size:20
Alignment explanation
Indices: 645000--645045 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
644990 CCACATCCCA
*
645000 ATCCTCCCTATAAATACCCT
1 ATCCTCCCTATAAATACCCC
645020 ATCCTCCCTATAAATACCCC
1 ATCCTCCCTATAAATACCCC
645040 ATCCTC
1 ATCCTC
645046 AATCATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.43, G:0.00, T:0.28
Consensus pattern (20 bp):
ATCCTCCCTATAAATACCCC
Found at i:645170 original size:17 final size:18
Alignment explanation
Indices: 645135--645175 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
645125 CTATTATGTA
*
645135 TTTAATTTATTTAATTAT
1 TTTACTTTATTTAATTAT
645153 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAATTAT
645170 TTTACT
1 TTTACT
645176 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTACTTTATTTAATTAT
Found at i:645431 original size:111 final size:111
Alignment explanation
Indices: 645237--645569 Score: 621
Period size: 111 Copynumber: 3.0 Consensus size: 111
645227 TGGAAATCAT
*
645237 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
645302 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
645348 ATATCTCGACACTTTGCTGATACGGTAACATTTTAGCGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
645413 TAATTAGATGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
645459 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
645524 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
645570 TTTTTGTAAT
Statistics
Matches: 215, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 215 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:647440 original size:9 final size:9
Alignment explanation
Indices: 647428--647480 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
647418 ACCTGCTCAA
*
647428 GACGACGAC
1 GACGATGAC
*
647437 GACGATGAT
1 GACGATGAC
* *
647446 GACGACGAT
1 GACGATGAC
**
647455 GACGATGGT
1 GACGATGAC
647464 GACGATGAC
1 GACGATGAC
647473 GACGATGA
1 GACGATGA
647481 TGACAGCAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.32, C:0.19, G:0.36, T:0.13
Consensus pattern (9 bp):
GACGATGAC
Found at i:647451 original size:18 final size:18
Alignment explanation
Indices: 647428--647484 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
647418 ACCTGCTCAA
647428 GACGACGACGACGATGAT
1 GACGACGACGACGATGAT
* *
647446 GACGACGATGACGATGGT
1 GACGACGACGACGATGAT
*
647464 GACGATGACGACGATGAT
1 GACGACGACGACGATGAT
647482 GAC
1 GAC
647485 AGCAAGGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.32, C:0.19, G:0.35, T:0.14
Consensus pattern (18 bp):
GACGACGACGACGATGAT
Found at i:647461 original size:15 final size:15
Alignment explanation
Indices: 647431--647474 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
647421 TGCTCAAGAC
* *
647431 GACGACGACGATGAT
1 GACGACGATGACGAT
647446 GACGACGATGACGAT
1 GACGACGATGACGAT
**
647461 GGTGACGATGACGA
1 GACGACGATGACGA
647475 CGATGATGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.32, C:0.18, G:0.36, T:0.14
Consensus pattern (15 bp):
GACGACGATGACGAT
Found at i:650960 original size:51 final size:50
Alignment explanation
Indices: 650904--651033 Score: 152
Period size: 51 Copynumber: 2.5 Consensus size: 50
650894 ACCCTACGTG
* * * *
650904 GCGTATAGCGCGGAGCAGGGGGCGCGCTATACCCCACGTGTAACCCAGTCA
1 GCGTATAGCGCGGA-CAGGGGGCGCGCTATACCACACGTGGAACCAAATCA
* * *
650955 GCGTATAGCGCGGTACAGGGGGCGCGCTATACTATACGTGGCACCAAATCA
1 GCGTATAGCGCGG-ACAGGGGGCGCGCTATACCACACGTGGAACCAAATCA
* *
651006 GCATATAGCGCGGTTCAGGGGGCGCGCT
1 GCGTATAGCGCGG-ACAGGGGGCGCGCT
651034 TTACTGCTAC
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 68 0.99
52 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.35, T:0.16
Consensus pattern (50 bp):
GCGTATAGCGCGGACAGGGGGCGCGCTATACCACACGTGGAACCAAATCA
Found at i:651684 original size:114 final size:117
Alignment explanation
Indices: 651478--651713 Score: 347
Period size: 114 Copynumber: 2.1 Consensus size: 117
651468 TTAACCTCTT
* * **
651478 AAAA-TTAATTGAGGATATAATTTAAGCACTTATTAAATATAATGGTTATATATAAAGTTTTGTA
1 AAAATTTAATAGAAGATATAATTTAAGCACTTATTAAATATAATGACTATATATAAAGTTTTGTA
*
651542 ACAAAAATCAACTTGATTGTATTTATATTACTTCTAATTATTTTATACTT-G
66 ACAAAAATCAACTTGATTGCATTTATATTACTTCTAATTATTTTATACTTGG
*
651593 AAAATTTAATAGAAGATATAATTTAAGCATTTATT-AA-ATAATGACTATATATAAA-TTTATGT
1 AAAATTTAATAGAAGATATAATTTAAGCACTTATTAAATATAATGACTATATATAAAGTTT-TGT
* * *
651655 AAGAAAAATCAATTTGATTGCATTTATATTAGTTCTAATTATTTTATACTTGG
65 AACAAAAATCAACTTGATTGCATTTATATTACTTCTAATTATTTTATACTTGG
651708 AAAATT
1 AAAATT
651714 CTACAACTCT
Statistics
Matches: 109, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
113 3 0.03
114 66 0.61
115 13 0.12
116 27 0.25
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (117 bp):
AAAATTTAATAGAAGATATAATTTAAGCACTTATTAAATATAATGACTATATATAAAGTTTTGTA
ACAAAAATCAACTTGATTGCATTTATATTACTTCTAATTATTTTATACTTGG
Found at i:651857 original size:21 final size:23
Alignment explanation
Indices: 651813--651860 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
651803 CATATAATTA
*
651813 TAAATTAGTTGAAAATTTAAAGG
1 TAAATTAGTTGAAAATTAAAAGG
*
651836 TAAATTA-TTTAAAA-TAAAAGG
1 TAAATTAGTTGAAAATTAAAAGG
651857 TAAA
1 TAAA
651861 CTATATCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 6 0.26
23 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.33
Consensus pattern (23 bp):
TAAATTAGTTGAAAATTAAAAGG
Found at i:654323 original size:13 final size:13
Alignment explanation
Indices: 654305--654331 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
654295 TTACAGATGC
654305 GCATATGAAGACT
1 GCATATGAAGACT
654318 GCATATGAAGACT
1 GCATATGAAGACT
654331 G
1 G
654332 TTCAACTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:657113 original size:20 final size:20
Alignment explanation
Indices: 657088--657162 Score: 141
Period size: 20 Copynumber: 3.8 Consensus size: 20
657078 ATATTCCCTA
657088 GTAATCTTACATTCCCACTG
1 GTAATCTTACATTCCCACTG
657108 GTAATCTTACATTCCCACTG
1 GTAATCTTACATTCCCACTG
657128 GTAATCTTACATTCCCACTG
1 GTAATCTTACATTCCCACTG
*
657148 ATAATCTTACATTCC
1 GTAATCTTACATTCC
657163 GTGAACCAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.27, C:0.29, G:0.08, T:0.36
Consensus pattern (20 bp):
GTAATCTTACATTCCCACTG
Found at i:658616 original size:21 final size:21
Alignment explanation
Indices: 658590--658645 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
658580 GTTTCCAGAT
*
658590 TCGCAATGCGATTTTGGACTA
1 TCGCAATGCGATTTTCGACTA
**
658611 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGATTTTCGACTA
*
658632 TCGCATTGCGATTT
1 TCGCAATGCGATTT
658646 ACATATTCGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.32
Consensus pattern (21 bp):
TCGCAATGCGATTTTCGACTA
Found at i:658697 original size:21 final size:21
Alignment explanation
Indices: 658606--658700 Score: 83
Period size: 21 Copynumber: 4.6 Consensus size: 21
658596 TGCGATTTTG
* *
658606 GACTATCGCAATGCGA-ACTTC
1 GACTATCGCATTGCGATA-GTC
658627 GACTATCGCATTGCGAT--T-
1 GACTATCGCATTGCGATAGTC
*
658645 TACATATTCGCATTGCGATAGTC
1 GAC-TA-TCGCATTGCGATAGTC
*
658668 GAAGT-TCGCATTGCGATAGTC
1 G-ACTATCGCATTGCGATAGTC
658689 GACTATCGCATT
1 GACTATCGCATT
658701 AGTCCAAAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
18 2 0.03
19 3 0.05
20 14 0.23
21 39 0.64
22 1 0.02
23 1 0.02
24 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (21 bp):
GACTATCGCATTGCGATAGTC
Found at i:658726 original size:21 final size:21
Alignment explanation
Indices: 658652--658735 Score: 79
Period size: 21 Copynumber: 4.2 Consensus size: 21
658642 ATTTACATAT
* **
658652 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAAA
* **
658673 TCGCATTGCGATAGTCGACTA
1 TCGCATTGCGATAGTCCAAAA
658694 TCGCA-T----TAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAA
658710 TCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAA
658731 TCGCA
1 TCGCA
658736 ACGACTGGTG
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
16 12 0.23
17 1 0.02
20 1 0.02
21 38 0.73
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAA
Found at i:659397 original size:12 final size:11
Alignment explanation
Indices: 659365--659400 Score: 56
Period size: 10 Copynumber: 3.3 Consensus size: 11
659355 TCTCGTCTCG
659365 GGTCGGGTCG-
1 GGTCGGGTCGT
659375 GGTCGGGTCGT
1 GGTCGGGTCGT
659386 GGTCGTGGTCGT
1 GGTCG-GGTCGT
659398 GGT
1 GGT
659401 AATACGTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 5 0.21
12 9 0.38
ACGTcount: A:0.00, C:0.17, G:0.56, T:0.28
Consensus pattern (11 bp):
GGTCGGGTCGT
Found at i:659400 original size:6 final size:5
Alignment explanation
Indices: 659362--659396 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
659352 TCGTCTCGTC
659362 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG
659397 TGGTAATACG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.26
Consensus pattern (5 bp):
TCGGG
Found at i:659489 original size:21 final size:21
Alignment explanation
Indices: 659463--659516 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
659453 CAATTTACAT
659463 ATTCGCATTGCGATAGTCCAA
1 ATTCGCATTGCGATAGTCCAA
*
659484 GTTCGCATTGCGATAGTCCAA
1 ATTCGCATTGCGATAGTCCAA
*
659505 AATCGCATTGCG
1 ATTCGCATTGCG
659517 TTTCTGGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (21 bp):
ATTCGCATTGCGATAGTCCAA
Found at i:660895 original size:13 final size:13
Alignment explanation
Indices: 660877--660914 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
660867 ACGGTTCACA
660877 CGCCCCTACGCGC
1 CGCCCCTACGCGC
*
660890 CGCCCCTACGCAC
1 CGCCCCTACGCGC
660903 CGCCCCTACGCG
1 CGCCCCTACGCG
660915 TGGGGAAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.11, C:0.61, G:0.21, T:0.08
Consensus pattern (13 bp):
CGCCCCTACGCGC
Found at i:661007 original size:41 final size:41
Alignment explanation
Indices: 660950--661027 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
660940 AGTTTTGACC
* *
660950 CTTTTGACCGACCCGACCCGGTTCGACCTGACTGCCCAACA
1 CTTTTGACCGACCCGACCCGGTCCGACCCGACTGCCCAACA
660991 CTTTTGACCGACCCGACCCGGTCCGACCCGACTGCCC
1 CTTTTGACCGACCCGACCCGGTCCGACCCGACTGCCC
661028 GACCCGACCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.17, C:0.45, G:0.21, T:0.18
Consensus pattern (41 bp):
CTTTTGACCGACCCGACCCGGTCCGACCCGACTGCCCAACA
Found at i:674421 original size:16 final size:16
Alignment explanation
Indices: 674402--674435 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
674392 AAAAAATTGA
674402 ATATCCGAAAATTCGG
1 ATATCCGAAAATTCGG
* *
674418 ATATCTGAAATTTCGG
1 ATATCCGAAAATTCGG
674434 AT
1 AT
674436 CGAATATCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (16 bp):
ATATCCGAAAATTCGG
Found at i:674613 original size:15 final size:15
Alignment explanation
Indices: 674593--674621 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
674583 TTAAACAAAT
674593 AATAAAATATATTAC
1 AATAAAATATATTAC
674608 AATAAAATATATTA
1 AATAAAATATATTA
674622 AGTAAACAAG
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:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAAAATATATTAC
Found at i:678007 original size:42 final size:42
Alignment explanation
Indices: 677955--678079 Score: 205
Period size: 42 Copynumber: 3.0 Consensus size: 42
677945 CAACTGAATC
*
677955 ATTAGGTGAATTATTGAAATTTCCAATAGGATTATTAGAAGA
1 ATTAGGTGAATCATTGAAATTTCCAATAGGATTATTAGAAGA
* *
677997 ATTAGGTGAATCATTGAAATTTCTAATAGGATTATTAGAAGT
1 ATTAGGTGAATCATTGAAATTTCCAATAGGATTATTAGAAGA
* *
678039 ATTAGGTGAATCATTGGAATTTCCAATCGGATTATTAGAAG
1 ATTAGGTGAATCATTGAAATTTCCAATAGGATTATTAGAAG
678080 GTTTAACCGG
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (42 bp):
ATTAGGTGAATCATTGAAATTTCCAATAGGATTATTAGAAGA
Found at i:678241 original size:28 final size:28
Alignment explanation
Indices: 678208--678266 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
678198 AAATATTTAA
* *
678208 AAGTAATCAATAAAACAAATATAGTAGC
1 AAGTAAACAATAAAACAAATATAATAGC
*
678236 AAGTAAACAATAAAACAGATATAATAGC
1 AAGTAAACAATAAAACAAATATAATAGC
678264 AAG
1 AAG
678267 GAAAGATACA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.59, C:0.10, G:0.12, T:0.19
Consensus pattern (28 bp):
AAGTAAACAATAAAACAAATATAATAGC
Found at i:680117 original size:2 final size:2
Alignment explanation
Indices: 680112--680152 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
680102 TCTCTCTCTC
680112 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
680153 AAGATTTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.