Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008523.1 Hibiscus syriacus cultivar Beakdansim tig00111392_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: 4657139
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 18
Found at i:476604 original size:34 final size:34
Alignment explanation
Indices: 476561--476629 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
476551 GAATCCTAGC
476561 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
* *
476595 AAAATTCTATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
476629 A
1 A
476630 GTAGGACGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:477485 original size:105 final size:105
Alignment explanation
Indices: 477178--477945 Score: 1134
Period size: 105 Copynumber: 7.3 Consensus size: 105
477168 CATTGTTCCA
* * * * ** * * *
477178 AGTCTAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * *
477243 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** *
477284 AGTCTAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTATTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
477344 AGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
477384 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
477449 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCTTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
477489 AGTCCAATATCCTTCGTTGTGAAGTGGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
477554 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
477594 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
477659 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
477699 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
477764 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
477804 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * * *
477869 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGCCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
477910 AGTGCCATGATATCC-TCCTTCGTGGAGTTGAAATTG
1 AGT-CCA--ATATCCTTCGTT-GTGAAGTTGAAATTG
477946 CAGATGGCCC
Statistics
Matches: 610, Mismatches: 42, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
100 81 0.13
101 1 0.00
102 4 0.01
103 4 0.01
104 3 0.00
105 408 0.67
106 82 0.13
107 3 0.00
108 4 0.01
109 20 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:478668 original size:36 final size:35
Alignment explanation
Indices: 478619--478859 Score: 185
Period size: 36 Copynumber: 6.9 Consensus size: 35
478609 GATTTTGTGT
*
478619 TTCAAGAGTAACTGTCTCAAGATAGACGAAAATTGA
1 TTCAAGAGAAACTGTCTCAAGATAGAC-AAAATTGA
*
478655 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT-A
1 TTCAAGAGAAACTGTCTCAAGATAGACAAAA-TTGA
* ** * *
478690 GTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGT
1 -TT-CAAGAGAAACTGTCTCAAGATAGAC-AAAATTGA
* ** *
478728 TTCAA-AGAAAACATAT-TCAA-AT-----ATTTTGT
1 TTCAAGAG-AAAC-TGTCTCAAGATAGACAAAATTGA
* * *
478757 TTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGATAGAC-AAAATTGA
*
478793 TTCAAGAGAAACTGTCTCAAGATAGACAAAATTTA
1 TTCAAGAGAAACTGTCTCAAGATAGACAAAATTGA
* *
478828 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTCAAGAGAAACTGTCTCAAGATAGACAAAA
478860 CTCTTCTAGT
Statistics
Matches: 169, Mismatches: 19, Indels: 34
0.76 0.09 0.15
Matches are distributed among these distances:
28 2 0.01
29 19 0.11
30 3 0.02
35 12 0.07
36 101 0.60
37 29 0.17
38 3 0.02
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (35 bp):
TTCAAGAGAAACTGTCTCAAGATAGACAAAATTGA
Found at i:479366 original size:18 final size:18
Alignment explanation
Indices: 479339--479374 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
479329 TGATGAATCC
* *
479339 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
479357 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
479375 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:479814 original size:22 final size:22
Alignment explanation
Indices: 479788--479836 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
479778 TTGTGTTTGG
* *
479788 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
479810 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
479832 TCAAA
1 TCAAA
479837 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:479843 original size:22 final size:22
Alignment explanation
Indices: 479800--479843 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
479790 AAAGGTTTGG
* * *
479800 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
479822 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
479844 TGGGGTAGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:480497 original size:23 final size:24
Alignment explanation
Indices: 480471--480520 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
480461 TTGTTCATTC
480471 TTTTTTG-TTCTTGT-TTTTTCCT
1 TTTTTTGCTTCTTGTCTTTTTCCT
* *
480493 TTTTTTGCTTCTTTTCTTTTTTCT
1 TTTTTTGCTTCTTGTCTTTTTCCT
480517 TTTT
1 TTTT
480521 GCCCTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.29
23 6 0.25
24 11 0.46
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (24 bp):
TTTTTTGCTTCTTGTCTTTTTCCT
Found at i:481680 original size:22 final size:20
Alignment explanation
Indices: 481655--481695 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
481645 TTTCATGTTT
481655 ATGAAAATGCTTAAAAATGTAG
1 ATGAAAATGC--AAAAATGTAG
*
481677 ATGAATATGCAAAAATGTA
1 ATGAAAATGCAAAAATGTA
481696 AGAATGCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27
Consensus pattern (20 bp):
ATGAAAATGCAAAAATGTAG
Found at i:485951 original size:21 final size:21
Alignment explanation
Indices: 485925--485964 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
485915 CAGAACCCTA
*
485925 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
485946 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
485965 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:485999 original size:20 final size:20
Alignment explanation
Indices: 485920--486007 Score: 63
Period size: 20 Copynumber: 4.2 Consensus size: 20
485910 TTTAGCAGAA
*
485920 CCCT-AGGGGGGTATCGATT
1 CCCTCAGGGGGGGATCGATT
* *
485939 CCC-CTGTGGGGGGAATCGGTT
1 CCCTCAG-GGGGGG-ATCGATT
* * *
485960 CCCCTTCAAAGGGGGAATCGGTT
1 -CCC-TC-AGGGGGGGATCGATT
485983 CCCTCAGGGGGGGATCGATT
1 CCCTCAGGGGGGGATCGATT
486003 CCCTC
1 CCCTC
486008 TGCACCAAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
19 4 0.08
20 22 0.42
21 8 0.15
22 6 0.11
23 7 0.13
24 6 0.11
ACGTcount: A:0.15, C:0.27, G:0.35, T:0.23
Consensus pattern (20 bp):
CCCTCAGGGGGGGATCGATT
Found at i:489852 original size:22 final size:21
Alignment explanation
Indices: 489810--489849 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
489800 GAGTTTGTTT
*
489810 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
489831 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
489850 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:493169 original size:18 final size:17
Alignment explanation
Indices: 493146--493201 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 17
493136 TTAGATAAAC
493146 AAGGTAAATAAAACAAAT
1 AAGGTAAATAAAA-AAAT
493164 AAGGTAAA-AGGAAAAAAT
1 AAGGTAAATA--AAAAAAT
**
493182 AAAATAAATAAAATAAAT
1 AAGGTAAATAAAA-AAAT
493200 AA
1 AA
493202 ATAAGATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
17 4 0.12
18 24 0.75
19 4 0.12
ACGTcount: A:0.71, C:0.02, G:0.11, T:0.16
Consensus pattern (17 bp):
AAGGTAAATAAAAAAAT
Found at i:493192 original size:9 final size:9
Alignment explanation
Indices: 493178--493211 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
493168 TAAAAGGAAA
493178 AAATAAAAT
1 AAATAAAAT
493187 AAATAAAAT
1 AAATAAAAT
493196 AAAT-AAAT
1 AAATAAAAT
493204 AAGATAAA
1 AA-ATAAA
493212 GGAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:493193 original size:22 final size:22
Alignment explanation
Indices: 493151--493211 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 22
493141 TAAACAAGGT
*
493151 AAATAAA-ACAAATAAGGTAAAAGG
1 AAATAAATA-AAATAA-ATAAAA-G
*
493175 AAA-AAATAAAATAAATAAAAT
1 AAATAAATAAAATAAATAAAAG
*
493196 AAATAAATAAGATAAA
1 AAATAAATAAAATAAA
493212 GGAAAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 3 0.09
22 16 0.50
23 9 0.28
24 4 0.12
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.16
Consensus pattern (22 bp):
AAATAAATAAAATAAATAAAAG
Found at i:493199 original size:13 final size:13
Alignment explanation
Indices: 493177--493211 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
493167 GTAAAAGGAA
493177 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
493191 AAAATAAATAAAT
1 AAAATAAATAAAT
*
493204 AAGATAAA
1 AAAATAAA
493212 GGAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:493710 original size:18 final size:17
Alignment explanation
Indices: 493687--493729 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
493677 ATATATACAT
493687 ATAATAATAATAACATAA
1 ATAATAATAATAA-ATAA
* *
493705 ATAATAAAAATAAATGA
1 ATAATAATAATAAATAA
493722 ATAA-AATA
1 ATAATAATA
493730 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATAA
Found at i:493726 original size:14 final size:13
Alignment explanation
Indices: 493689--493727 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
493679 ATATACATAT
493689 AATAATAATAACATA
1 AATAATAA-AA-ATA
493704 AATAATAAAAATA
1 AATAATAAAAATA
493717 AATGAATAAAA
1 AAT-AATAAAA
493728 TATCCATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (13 bp):
AATAATAAAAATA
Found at i:494185 original size:34 final size:34
Alignment explanation
Indices: 494142--494210 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
494132 GAATCCTAGC
494142 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
* *
494176 AAAATTCTATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
494210 A
1 A
494211 GTAGGACGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:494953 original size:20 final size:19
Alignment explanation
Indices: 494928--494979 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
494918 GCTGCTGGAA
* *
494928 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
494948 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
494967 AACCGGGTTGACC
1 AACCGGTTTGACC
494980 CGACCCGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:494957 original size:10 final size:10
Alignment explanation
Indices: 494928--494977 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
494918 GCTGCTGGAA
494928 AACCGGTTTG
1 AACCGGTTTG
*
494938 -ACCAGTTTTG
1 AACC-GGTTTG
494948 AACCGGTTTG
1 AACCGGTTTG
*
494958 -ACCGGTCTG
1 AACCGGTTTG
*
494967 AACCGGGTTG
1 AACCGGTTTG
494977 A
1 A
494978 CCCGACCCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 11 0.34
10 18 0.56
11 3 0.09
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:494994 original size:14 final size:14
Alignment explanation
Indices: 494975--495002 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
494965 TGAACCGGGT
494975 TGACCCGACCCGAC
1 TGACCCGACCCGAC
494989 TGACCCGACCCGAC
1 TGACCCGACCCGAC
495003 CCGACTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.50, G:0.21, T:0.07
Consensus pattern (14 bp):
TGACCCGACCCGAC
Found at i:495017 original size:17 final size:17
Alignment explanation
Indices: 494973--495031 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
494963 TCTGAACCGG
494973 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
**
494990 GACCCGACCCGACCCGACT
1 G--TTGACCCGACCCGACT
*
495009 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACT
495026 GTTGAC
1 GTTGAC
495032 AGTTGACCGT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 20 0.57
19 15 0.43
ACGTcount: A:0.19, C:0.44, G:0.24, T:0.14
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:495017 original size:22 final size:19
Alignment explanation
Indices: 494976--495025 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 19
494966 GAACCGGGTT
494976 GACCCGACCCGACTGACCC
1 GACCCGACCCGACTGACCC
494995 GACCCGACCCGACTGTTGACCC
1 GACCCGACCCGAC---TGACCC
495017 GACCCGACC
1 GACCCGACC
495026 GTTGACAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.46
22 15 0.54
ACGTcount: A:0.20, C:0.50, G:0.22, T:0.08
Consensus pattern (19 bp):
GACCCGACCCGACTGACCC
Found at i:495989 original size:63 final size:63
Alignment explanation
Indices: 495921--496044 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
495911 CTAATGTGAC
** *
495921 TCTTAGGTAGG-CTCTGTGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTG
1 TCTTAGGTAGGCCTC-ACGGCCCTGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTG
495983 T
63 T
* *
495984 TCTTAGGTAGGCCTCACGGCCCTGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCTCACGGCCCTGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
496045 TCCCTTAGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.02
63 48 0.91
64 4 0.08
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.28
Consensus pattern (63 bp):
TCTTAGGTAGGCCTCACGGCCCTGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:495994 original size:32 final size:31
Alignment explanation
Indices: 495921--496042 Score: 81
Period size: 31 Copynumber: 3.9 Consensus size: 31
495911 CTAATGTGAC
* * *
495921 TCTTAGGTAGGCTCTGTGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
** **
495952 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-CAT
*
495984 TCTTAGGTAGG-CCTCACGGCCCTGAA-ATC-T
1 TCTTAGGTAGGCCCT-GCGGCCCT-AAGATCAT
* *
496014 ATCTTGGGTAGGCTCT-CAGGCCCTAAGAT
1 -TCTTAGGTAGGCCCTGC-GGCCCTAAGAT
496043 GTTCCCTTAG
Statistics
Matches: 71, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
30 4 0.06
31 44 0.62
32 21 0.30
33 2 0.03
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.28
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
Found at i:497846 original size:22 final size:22
Alignment explanation
Indices: 497774--497849 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
497764 ACGGTATTAT
497774 CTACTTAAATATCATTTCATTC
1 CTACTTAAATATCATTTCATTC
* * * * *
497796 TTACATACAT-T-ATTATTATTAT
1 CTACTTAAATATCATT-TCATT-C
497818 CTACTTAAATATCATTTCATTC
1 CTACTTAAATATCATTTCATTC
497840 CTACTTAAAT
1 CTACTTAAAT
497850 TTTAACAATG
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
20 3 0.08
21 5 0.12
22 24 0.60
23 5 0.12
24 3 0.08
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.47
Consensus pattern (22 bp):
CTACTTAAATATCATTTCATTC
Found at i:511605 original size:14 final size:13
Alignment explanation
Indices: 511583--511638 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 13
511573 TAAAACTTTA
*
511583 AACCCTAAACCTT
1 AACCTTAAACCTT
511596 AGACCTTAAA-CTAT
1 A-ACCTTAAACCT-T
*
511610 AACCCTTAAACCCT
1 AA-CCTTAAACCTT
*
511624 AAGCTTAAACCTT
1 AACCTTAAACCTT
511637 AA
1 AA
511639 TTTTAAACCC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 15 0.43
14 19 0.54
15 1 0.03
ACGTcount: A:0.41, C:0.30, G:0.04, T:0.25
Consensus pattern (13 bp):
AACCTTAAACCTT
Found at i:524351 original size:2 final size:2
Alignment explanation
Indices: 524344--524368 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
524334 CTTAATTGAA
524344 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 A
524369 GGGGTACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:524743 original size:258 final size:263
Alignment explanation
Indices: 524282--524765 Score: 666
Period size: 258 Copynumber: 1.8 Consensus size: 263
524272 CCGACCCGAC
* * *
524282 CCGACCCAACCCGAAATAATAAAAAATTATTTTTATTCAATAAAAACATTGACTTAATTGAAATA
1 CCGACCCAACCCGAAATAATAAAAAAATATTTTTATTAAATAAAAACAGTGACTTAATTG-AATA
* * * *
524347 TATATATATATATATATATATAGGGGTACTATTGTAATTATTCTTAAATATATAAGGTAAAATTA
65 TATATATATATATATATATAGAGGGGTACTATTGTAATTATCCCTAAATATAAAAGGTAAAATTA
*
524412 TATATTTTTTGGGTCGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGAATAGCACACT
130 TATATTATTT--GTCGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGAATAGCACACT
*
524477 TAAAAAAAAACCGACCCTACCCAACCAAAATAAAGTTTCACCCGACCCAACCCGAATATATGAAT
193 T-AAAAAAAACCGACCCGACCCAACCAAAATAAAGTTTCACCCGACCCAACCCGAATATATGAAT
524542 TAGAAAT
257 TAGAAAT
* * *
524549 CCGACCCGACCGGAAATAATAAAAAAATATTTTTATTAAATAAAAACAGTGATTTAATTG-A-A-
1 CCGACCCAACCCGAAATAATAAAAAAATATTTTTATTAAATAAAAACAGTGACTTAATTGAATAT
*
524611 A-A-A-A-AT-TATATATAGAGGGGTATTATTGTAATTATCCCTAAATATAAAAGGTAAAATTAT
66 ATATATATATATATATATAGAGGGGTACTATTGTAATTATCCCTAAATATAAAAGGTAAAATTAT
*
524671 ATA-TATTT-TCGGGTCGGGTATTTTTCACCCTAAACCCGAACTCGACCTGACCCGAATATCACA
131 ATATTATTTGTCGGGTCGGGTATTTTTCACCCTAAACCCGAA--C--CC-GACCCGAATAGCACA
* *
524734 CTT-AAAAAAACCGACCCGACCCGACCCAAATA
191 CTTAAAAAAAACCGACCCGACCCAACCAAAATA
524766 TATGAATTAG
Statistics
Matches: 196, Mismatches: 16, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
254 32 0.16
256 1 0.01
257 30 0.15
258 54 0.28
259 19 0.10
260 1 0.01
261 1 0.01
262 1 0.01
263 1 0.01
264 1 0.01
265 1 0.01
267 54 0.28
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (263 bp):
CCGACCCAACCCGAAATAATAAAAAAATATTTTTATTAAATAAAAACAGTGACTTAATTGAATAT
ATATATATATATATATATAGAGGGGTACTATTGTAATTATCCCTAAATATAAAAGGTAAAATTAT
ATATTATTTGTCGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGAATAGCACACTTAA
AAAAAACCGACCCGACCCAACCAAAATAAAGTTTCACCCGACCCAACCCGAATATATGAATTAGA
AAT
Found at i:525029 original size:10 final size:10
Alignment explanation
Indices: 525014--525041 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
525004 GAATTGGATT
525014 CTAATTCCCC
1 CTAATTCCCC
525024 CTAATTCCCC
1 CTAATTCCCC
525034 CTAATTCC
1 CTAATTCC
525042 AAGGGATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.46, G:0.00, T:0.32
Consensus pattern (10 bp):
CTAATTCCCC
Found at i:525467 original size:60 final size:60
Alignment explanation
Indices: 525392--525569 Score: 196
Period size: 60 Copynumber: 3.0 Consensus size: 60
525382 ATATGCCCCA
* * * *
525392 AAACTATGACCCTCATTTTAAATTAATCCATAAACTTTTCAATATTTTAATTTTATCCTC
1 AAACTATGACTCTCATTTTAAATTAATCCATAAACTTTTCAACATTCTAATTTCATCCTC
* * * * *
525452 AAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCTAATTTCATCCTT
1 AAACTATGACTCTCATTTTAAATTAATCCATAAACTTTTCAACATTCTAATTTCATCCTC
* ** * * * *
525512 AAACTATGAATCTC-TTTCTAAATTAATCCCCAAAGTTTTGAATATTCCAATTTCATCC
1 AAACTATGACTCTCATTT-TAAATTAATCCATAAACTTTTCAACATTCTAATTTCATCC
525570 CTAAATTCAT
Statistics
Matches: 100, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
59 2 0.02
60 98 0.98
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (60 bp):
AAACTATGACTCTCATTTTAAATTAATCCATAAACTTTTCAACATTCTAATTTCATCCTC
Found at i:525799 original size:60 final size:60
Alignment explanation
Indices: 525692--525868 Score: 184
Period size: 60 Copynumber: 3.0 Consensus size: 60
525682 GTATATACAT
* *
525692 ATAATTTGGGATGAAATTGGAATGTTCAAAAAGTTTAAGGACCAATTTAGAATGAAAGTC
1 ATAATTTGGGATGAAATTGAAATGTTCAAAAAGTTTAAGGACCAATTTAAAATGAAAGTC
* * * * ***
525752 ATAGTTTGGAGATGAAATTGAAATGTTC-AAAAGTTTGAGGACTAATTTAAAATTATTTTC
1 ATAATTTGG-GATGAAATTGAAATGTTCAAAAAGTTTAAGGACCAATTTAAAATGAAAGTC
* *
525812 ATAATTTAGGGATGAAATTGAAATACTT--AAAAGTTTAA-GATTCAATTTAAAAT-AAAG
1 ATAATTT-GGGATGAAATTGAAAT-GTTCAAAAAGTTTAAGGA-CCAATTTAAAATGAAAG
525869 AACATATTTT
Statistics
Matches: 96, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
59 3 0.03
60 72 0.75
61 21 0.22
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.34
Consensus pattern (60 bp):
ATAATTTGGGATGAAATTGAAATGTTCAAAAAGTTTAAGGACCAATTTAAAATGAAAGTC
Found at i:527767 original size:2 final size:2
Alignment explanation
Indices: 527760--527789 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
527750 GTTTTCTTAA
527760 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
527790 TAACTAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:533452 original size:17 final size:17
Alignment explanation
Indices: 533407--533455 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
533397 ATGATTATTT
* *
533407 AAAAGTATTATATTATA
1 AAAAGTAATATTTTATA
**
533424 ATAATTTAATATTTTATA
1 A-AAAGTAATATTTTATA
533442 AAAAGTAATATTTT
1 AAAAGTAATATTTT
533456 TACACATATT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (17 bp):
AAAAGTAATATTTTATA
Found at i:556963 original size:28 final size:27
Alignment explanation
Indices: 556898--557007 Score: 83
Period size: 25 Copynumber: 4.2 Consensus size: 27
556888 GCACATGTCA
556898 TAATAATAAAATATATTTTTAAAAGTT
1 TAATAATAAAATATATTTTTAAAAGTT
556925 TAGATAA-AAAA-ATATTTTTGAATTAAG-T
1 TA-ATAATAAAATATATTTTT-AA--AAGTT
* *
556953 TAATAATAAAAT-T-TATTTAATAA-AT
1 TAATAATAAAATATATTTTTAA-AAGTT
* *
556978 TAAT-ATAAAAAATGTTTTTAAAAG-T
1 TAATAATAAAATATATTTTTAAAAGTT
557003 TAATA
1 TAATA
557008 TATATATAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 23
0.73 0.03 0.24
Matches are distributed among these distances:
24 6 0.09
25 16 0.23
26 16 0.23
27 16 0.23
28 12 0.17
29 3 0.04
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (27 bp):
TAATAATAAAATATATTTTTAAAAGTT
Found at i:567125 original size:31 final size:31
Alignment explanation
Indices: 567054--567126 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 31
567044 GCCACGTTTC
* * *
567054 ATAATAATAAAATATATATGTAAAAGTTTAG
1 ATAAAAATAAAATATATATGTAAAAGTTAAA
* * *
567085 ATAAGAATAAAATATATATTTTTAAA-TTAAA
1 ATAAAAATAAAATATATA-TGTAAAAGTTAAA
567116 ATAAAAATAAA
1 ATAAAAATAAA
567127 TAATTTTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 30 0.86
32 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.34
Consensus pattern (31 bp):
ATAAAAATAAAATATATATGTAAAAGTTAAA
Found at i:567151 original size:17 final size:17
Alignment explanation
Indices: 567117--567150 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
567107 TAAATTAAAA
567117 TAAAAATAAATAATTTT
1 TAAAAATAAATAATTTT
*
567134 TAAAAATATAT-ATTTT
1 TAAAAATAAATAATTTT
567150 T
1 T
567151 TGAATTAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAAAATAAATAATTTT
Found at i:567193 original size:27 final size:26
Alignment explanation
Indices: 567156--567230 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 26
567146 TTTTTTGAAT
*
567156 TAAGTT-A-ATAATAAAATTTATTTAA
1 TAAGTTAATATAATAAAATTTATGT-A
567181 TAAGTTAATATAA-AAATATTT-TGTA
1 TAAGTTAATATAATAAA-ATTTATGTA
567206 -AAGTTAATATATATAAAATATTATG
1 TAAGTTAATATA-ATAAAAT-TTATG
567231 AATTTAAGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
24 11 0.26
25 10 0.24
26 11 0.26
27 10 0.24
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.43
Consensus pattern (26 bp):
TAAGTTAATATAATAAAATTTATGTA
Found at i:567495 original size:31 final size:31
Alignment explanation
Indices: 567457--567517 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
567447 GTGACTACAT
567457 CTTAATTAAATAAAAACGAAAGTGATCATAA
1 CTTAATTAAATAAAAACGAAAGTGATCATAA
567488 CTTAATTAAATAAAAACGAAAGTGATCATA
1 CTTAATTAAATAAAAACGAAAGTGATCATA
567518 TATTATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (31 bp):
CTTAATTAAATAAAAACGAAAGTGATCATAA
Found at i:567679 original size:2 final size:2
Alignment explanation
Indices: 567672--567721 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
567662 CGTTTCAGTT
567672 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
567714 TA TA TA TA
1 TA TA TA TA
567722 ATTTTGAAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:569729 original size:2 final size:2
Alignment explanation
Indices: 569722--569769 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
569712 CAGTAGAATG
569722 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
569764 TA TA TA
1 TA TA TA
569770 AGGATTCAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:574199 original size:61 final size:59
Alignment explanation
Indices: 574057--574199 Score: 171
Period size: 59 Copynumber: 2.4 Consensus size: 59
574047 TTTAGGACAT
* * * * *
574057 ACTAAATAGTTGGGTGATTATTTTTTAACTTTTAATAGTCGGAAACTCAACAAATCAAC
1 ACTATATAGTTGGGGGATTATTTTATAACTTTTAATAGTCGGAAACTCAAAAAATAAAC
* * *
574116 ACTATATAGTTGAGGGATTATTTTATAATTTTTAATAGTCGAGAAATTCAAAAAATAAATC
1 ACTATATAGTTGGGGGATTATTTTATAACTTTTAATAGTCG-GAAACTCAAAAAATAAA-C
*
574177 A-TCATATAGTTGGGGGACTATTT
1 ACT-ATATAGTTGGGGGATTATTT
574200 GTGTACTTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
59 36 0.51
60 15 0.21
61 20 0.28
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (59 bp):
ACTATATAGTTGGGGGATTATTTTATAACTTTTAATAGTCGGAAACTCAAAAAATAAAC
Found at i:579901 original size:31 final size:30
Alignment explanation
Indices: 579866--579963 Score: 92
Period size: 31 Copynumber: 3.2 Consensus size: 30
579856 GGTCAATTTG
579866 ATATTTTATATAATATTTATGGATTAAATTA
1 ATATTTTATATAA-ATTTATGGATTAAATTA
* * *
579897 ATATTTTATGTAAAGTTTAAGG-TCAAATTA
1 ATATTTTATATAAA-TTTATGGATTAAATTA
* *
579927 ATATTCTATCTAAAATTTAT-GAGTTAAATTA
1 ATATTTTATAT-AAATTTATGGA-TTAAATTA
*
579958 AAATTT
1 ATATTT
579964 AACCATTTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
29 1 0.02
30 21 0.39
31 32 0.59
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (30 bp):
ATATTTTATATAAATTTATGGATTAAATTA
Found at i:583082 original size:78 final size:77
Alignment explanation
Indices: 582876--583103 Score: 306
Period size: 78 Copynumber: 3.0 Consensus size: 77
582866 ATGTTTCTTT
* * * * *
582876 TTATGTATATACCATGAACATGAACATGGTTGTGTGGGATTCCGGTTAATGGCTCATCTGCATAC
1 TTATGCATACACCATGAACATGAACATGGTTGTGTGGGATT-CGGTT-ATGGCTTATATGCATGC
*
582941 TTGGTGGATTGTAC
64 TTGGTGGATTGTTC
582955 TTATGCATACA-C-----CATGAACATGGTTGTGTGGGATTCGGGTTATGGCTTATATGCATGCT
1 TTATGCATACACCATGAACATGAACATGGTTGTGTGGGATTC-GGTTATGGCTTATATGCATGCT
583014 TGGTGGATTGTTC
65 TGGTGGATTGTTC
*
583027 TTATGCATACACCATGAACATGAACATGGTTGTGTGGGATTCGGCTTATGGCTTATGTGCATGCT
1 TTATGCATACACCATGAACATGAACATGGTTGTGTGGGATTCGG-TTATGGCTTATATGCATGCT
*
583092 TGGTTGATTGTT
65 TGGTGGATTGTT
583104 AATCTGTACA
Statistics
Matches: 133, Mismatches: 8, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
72 39 0.29
73 28 0.21
77 2 0.02
78 55 0.41
79 9 0.07
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.37
Consensus pattern (77 bp):
TTATGCATACACCATGAACATGAACATGGTTGTGTGGGATTCGGTTATGGCTTATATGCATGCTT
GGTGGATTGTTC
Found at i:613667 original size:3 final size:3
Alignment explanation
Indices: 613659--613733 Score: 143
Period size: 3 Copynumber: 25.3 Consensus size: 3
613649 CATCTTTAGC
613659 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
613706 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
613734 GCTAAGCAAA
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 69 0.97
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:615871 original size:23 final size:24
Alignment explanation
Indices: 615845--615892 Score: 62
Period size: 27 Copynumber: 1.9 Consensus size: 24
615835 TTAAACGAAA
615845 TTTA-TACTTATAGATAATCATTT
1 TTTATTACTTATAGATAATCATTT
615868 TTTAGTCTTACTTATAGATAATCAT
1 TTTA---TTACTTATAGATAATCAT
615893 GAATAGGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
27 17 0.81
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.50
Consensus pattern (24 bp):
TTTATTACTTATAGATAATCATTT
Found at i:616592 original size:2 final size:2
Alignment explanation
Indices: 616587--616620 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
616577 AAAAATATGA
616587 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
616621 GATTAAAGAA
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:625319 original size:2 final size:2
Alignment explanation
Indices: 625312--625336 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
625302 CAAATAATTA
625312 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 A
625337 ATGATTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:627221 original size:32 final size:32
Alignment explanation
Indices: 627185--627256 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 32
627175 CAAGACAATC
* *
627185 CGAGTAACTTAAACCGCAAGAAACAAATAAAA
1 CGAGTAACTTAAACCACAAGAAACAAAGAAAA
* *
627217 CGAGTAGCTTAAACCACAAGAAACGAAGAAAA
1 CGAGTAACTTAAACCACAAGAAACAAAGAAAA
627249 -GAGTAACT
1 CGAGTAACT
627257 AACCAACCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 7 0.20
32 28 0.80
ACGTcount: A:0.53, C:0.18, G:0.17, T:0.12
Consensus pattern (32 bp):
CGAGTAACTTAAACCACAAGAAACAAAGAAAA
Found at i:632360 original size:33 final size:33
Alignment explanation
Indices: 632313--632378 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
632303 TTTCTATTTA
632313 TTGTCAAGGATCTCTTCTCGTTTGTGGTAATGG
1 TTGTCAAGGATCTCTTCTCGTTTGTGGTAATGG
*
632346 TTGTTAAGGATCTCTTCTCGTTTGTGGTAATGG
1 TTGTCAAGGATCTCTTCTCGTTTGTGGTAATGG
632379 AACTGTTTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.15, C:0.14, G:0.27, T:0.44
Consensus pattern (33 bp):
TTGTCAAGGATCTCTTCTCGTTTGTGGTAATGG
Found at i:638214 original size:51 final size:51
Alignment explanation
Indices: 638137--638236 Score: 164
Period size: 51 Copynumber: 2.0 Consensus size: 51
638127 TCTGCTTTCA
* *
638137 ATGCTTTAACGTATTTAATTGCTCCATCTTTCTTTAATTGCAGTCATTACT
1 ATGCTTCAACATATTTAATTGCTCCATCTTTCTTTAATTGCAGTCATTACT
* *
638188 ATGCTTCAACATATTTGATTGTTCCATCTTTCTTTAATTGCAGTCATTA
1 ATGCTTCAACATATTTAATTGCTCCATCTTTCTTTAATTGCAGTCATTA
638237 TGTAAAGGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.47
Consensus pattern (51 bp):
ATGCTTCAACATATTTAATTGCTCCATCTTTCTTTAATTGCAGTCATTACT
Found at i:641336 original size:47 final size:47
Alignment explanation
Indices: 641276--641369 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
641266 AGAAAGCTAA
641276 TGAGGAACTAAGGTATAAAAAACAACCTGATGCGTCTTAAGAAGTTC
1 TGAGGAACTAAGGTATAAAAAACAACCTGATGCGTCTTAAGAAGTTC
*
641323 TGAGGAACTAAGGTATCAAAAACAACCTGATGCGTCTTAAGAAGTTC
1 TGAGGAACTAAGGTATAAAAAACAACCTGATGCGTCTTAAGAAGTTC
641370 CAATATTGCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.23
Consensus pattern (47 bp):
TGAGGAACTAAGGTATAAAAAACAACCTGATGCGTCTTAAGAAGTTC
Found at i:646395 original size:19 final size:19
Alignment explanation
Indices: 646371--646408 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
646361 CATATACTCA
646371 CCATGCAGACGAGCCATAC
1 CCATGCAGACGAGCCATAC
646390 CCATGCAGACGAGCCATAC
1 CCATGCAGACGAGCCATAC
646409 AAGCCATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.37, G:0.21, T:0.11
Consensus pattern (19 bp):
CCATGCAGACGAGCCATAC
Found at i:646467 original size:32 final size:32
Alignment explanation
Indices: 646423--646493 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
646413 CATATACTCA
* *
646423 CCATGCAGACGAGCCAGCCAACGGAGAGGTCG
1 CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
*
646455 CCATGCAAACGAGCCAGCCAATAGAGAGGTCG
1 CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
646487 CCATGCA
1 CCATGCA
646494 GTCTGGGCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.31, C:0.31, G:0.30, T:0.08
Consensus pattern (32 bp):
CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
Found at i:646764 original size:13 final size:13
Alignment explanation
Indices: 646746--646802 Score: 78
Period size: 13 Copynumber: 4.1 Consensus size: 13
646736 GATGGACGAG
646746 CAACAGCGGCCAC
1 CAACAGCGGCCAC
646759 CAACAGCGGCCACCC
1 CAACAGCGGCCA--C
646774 CAAAGCAGCGGCCAC
1 C-AA-CAGCGGCCAC
646789 CAACAGCGGCCAC
1 CAACAGCGGCCAC
646802 C
1 C
646803 CCAAGCAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
13 23 0.57
14 2 0.05
15 4 0.10
16 2 0.05
17 9 0.22
ACGTcount: A:0.30, C:0.47, G:0.23, T:0.00
Consensus pattern (13 bp):
CAACAGCGGCCAC
Found at i:646785 original size:30 final size:30
Alignment explanation
Indices: 646749--646806 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
646739 GGACGAGCAA
646749 CAGCGGCCACCAACAGCGGCCACCCCAAAG
1 CAGCGGCCACCAACAGCGGCCACCCCAAAG
646779 CAGCGGCCACCAACAGCGGCCACCCCAA
1 CAGCGGCCACCAACAGCGGCCACCCCAA
646807 GCAAATAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.48, G:0.22, T:0.00
Consensus pattern (30 bp):
CAGCGGCCACCAACAGCGGCCACCCCAAAG
Found at i:646860 original size:29 final size:29
Alignment explanation
Indices: 646820--646934 Score: 196
Period size: 29 Copynumber: 4.0 Consensus size: 29
646810 AATAACTTAT
* *
646820 AGGACGCTGGGCGTGCATGGCGTCCT-TA
1 AGGACGCCGGGCGTGCATGGCGACCTATA
646848 TAGGACGCCGGGCGTGCATGGCGACCTATA
1 -AGGACGCCGGGCGTGCATGGCGACCTATA
646878 AGGACGCCGGGCGTGCATGGCGACCTATA
1 AGGACGCCGGGCGTGCATGGCGACCTATA
646907 AGGACGCCGGGCGTGCATGGCGACCTAT
1 AGGACGCCGGGCGTGCATGGCGACCTAT
646935 GTTGCCACTG
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
29 81 0.98
30 2 0.02
ACGTcount: A:0.18, C:0.27, G:0.38, T:0.17
Consensus pattern (29 bp):
AGGACGCCGGGCGTGCATGGCGACCTATA
Found at i:656686 original size:27 final size:25
Alignment explanation
Indices: 656627--656695 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 25
656617 GTATTTTAGA
656627 AAATTTTAATTTTTCTATAAGATAT
1 AAATTTTAATTTTTCTATAAGATAT
*
656652 ATAATTTTAATTTCTTTTAATAA-ATAT
1 A-AATTTTAATTT-TTCT-ATAAGATAT
656679 CAAATTTTTAAATTTTT
1 -AAA-TTTT-AATTTTT
656696 AAATTTTTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
25 1 0.03
26 11 0.30
27 9 0.24
28 11 0.30
29 5 0.14
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.55
Consensus pattern (25 bp):
AAATTTTAATTTTTCTATAAGATAT
Found at i:656703 original size:9 final size:8
Alignment explanation
Indices: 656680--656704 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
656670 AATAAATATC
656680 AAATTTTT
1 AAATTTTT
656688 AAATTTTT
1 AAATTTTT
656696 AAATTTTT
1 AAATTTTT
656704 A
1 A
656705 GGGTAATCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
AAATTTTT
Found at i:658342 original size:13 final size:13
Alignment explanation
Indices: 658324--658348 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
658314 TGGCTTAGAT
658324 GAAAAGAGAGAAA
1 GAAAAGAGAGAAA
658337 GAAAAGAGAGAA
1 GAAAAGAGAGAA
658349 GAAGCGGCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (13 bp):
GAAAAGAGAGAAA
Found at i:660384 original size:17 final size:17
Alignment explanation
Indices: 660362--660401 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
660352 ATGCTGTTGT
660362 TATGCACGATATAATTA
1 TATGCACGATATAATTA
660379 TATGCACGATATAATTA
1 TATGCACGATATAATTA
660396 TATGCA
1 TATGCA
660402 GGGTAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
TATGCACGATATAATTA
Found at i:663692 original size:20 final size:21
Alignment explanation
Indices: 663658--663700 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
663648 CTTCATGGTG
663658 TGCATGGGGGAGATCGGTGCA
1 TGCATGGGGGAGATCGGTGCA
663679 TGCATGGGGG-GATCGGTGCA
1 TGCATGGGGGAGATCGGTGCA
663699 TG
1 TG
663701 GGGAGATCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.16, C:0.14, G:0.49, T:0.21
Consensus pattern (21 bp):
TGCATGGGGGAGATCGGTGCA
Found at i:663700 original size:16 final size:16
Alignment explanation
Indices: 663679--663719 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
663669 GATCGGTGCA
* *
663679 TGCATGGGGGGATCGG
1 TGCATGGGGAGATCAG
663695 TGCATGGGGAGATCAG
1 TGCATGGGGAGATCAG
663711 TGCATGGGG
1 TGCATGGGG
663720 CATGCACGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.17, C:0.12, G:0.51, T:0.20
Consensus pattern (16 bp):
TGCATGGGGAGATCAG
Found at i:668150 original size:49 final size:49
Alignment explanation
Indices: 668097--668432 Score: 550
Period size: 49 Copynumber: 6.9 Consensus size: 49
668087 GGCACCCATC
* *
668097 TATTATTAATATTTAATGATTTGATAATAATGATTAGTAATAATAAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
* *
668146 TATTATTAATTTTTAATGATTTGATAGTAATGAATAGTAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
* *
668195 TATTATTAATTTTTAATGATTTGATAGTAATGATTAATAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
*
668244 TATCATT-ATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
*
668292 TATTATTAAT-TTTTATGATTTGATAGTAATGATTAGTAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
* *
668340 TATCATTAATATTTAATGATTTGATAGTAATGATTAATAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
* *
668389 TATCATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAAT
668433 AATGGAGGGA
Statistics
Matches: 269, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
48 91 0.34
49 178 0.66
ACGTcount: A:0.43, C:0.01, G:0.11, T:0.46
Consensus pattern (49 bp):
TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
Found at i:668302 original size:97 final size:98
Alignment explanation
Indices: 668097--668432 Score: 577
Period size: 97 Copynumber: 3.4 Consensus size: 98
668087 GGCACCCATC
* * * * *
668097 TATTATTAATATTTAATGATTTGATAATAATGATTAGTAATAATAAAATTATTATTAATTTTTAA
1 TATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATCATTAATATTTAA
*
668162 TGATTTGATAGTAATGAATAGTAATAATGAAAT
66 TGATTTGATAGTAATGATTAGTAATAATGAAAT
*
668195 TATTATTAATTTTTAATGATTTGATAGTAATGATTAATAATAATGAAATTATCATT-ATATTTAA
1 TATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATCATTAATATTTAA
668259 TGATTTGATAGTAATGATTAGTAATAATGAAAT
66 TGATTTGATAGTAATGATTAGTAATAATGAAAT
668292 TATTATTAATTTTT-ATGATTTGATAGTAATGATTAGTAATAATGAAATTATCATTAATATTTAA
1 TATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATCATTAATATTTAA
*
668356 TGATTTGATAGTAATGATTAATAATAATGAAAT
66 TGATTTGATAGTAATGATTAGTAATAATGAAAT
*
668389 TATCATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAAT
1 TATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAAT
668433 AATGGAGGGA
Statistics
Matches: 226, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
96 40 0.18
97 106 0.47
98 80 0.35
ACGTcount: A:0.43, C:0.01, G:0.11, T:0.46
Consensus pattern (98 bp):
TATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATCATTAATATTTAA
TGATTTGATAGTAATGATTAGTAATAATGAAAT
Found at i:668356 original size:22 final size:22
Alignment explanation
Indices: 668331--668407 Score: 57
Period size: 22 Copynumber: 3.3 Consensus size: 22
668321 TGATTAGTAA
668331 TAATGAAATTATCATTAATATT
1 TAATGAAATTATCATTAATATT
* * *
668353 TAATGATTTGATAGTAATGATTAATA-A
1 TAATGA----A-A-TTATCATTAATATT
*
668380 TAATGAAATTATCATTAATTTT
1 TAATGAAATTATCATTAATATT
668402 TAATGA
1 TAATGA
668408 TTTGATAGTA
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
21 9 0.22
22 13 0.32
23 1 0.02
26 1 0.02
27 7 0.17
28 10 0.24
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (22 bp):
TAATGAAATTATCATTAATATT
Found at i:668542 original size:12 final size:11
Alignment explanation
Indices: 668521--668563 Score: 68
Period size: 12 Copynumber: 3.7 Consensus size: 11
668511 CATAAAAATG
668521 ATTTAATAATA
1 ATTTAATAATA
668532 ATTTAAATAATA
1 ATTT-AATAATA
668544 ATTTAATAATAA
1 ATTTAATAAT-A
668556 ATTTAATA
1 ATTTAATA
668564 TTTAATGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.33
12 20 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:668547 original size:23 final size:23
Alignment explanation
Indices: 668513--668561 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
668503 CAATTAACCA
*
668513 TAAAAATGATTTAATAAT-AATT
1 TAAAAATAATTTAATAATAAATT
668535 TAAATAATAATTTAATAATAAATT
1 TAAA-AATAATTTAATAATAAATT
668559 TAA
1 TAA
668562 TATTTAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 4 0.17
23 13 0.54
24 7 0.29
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
TAAAAATAATTTAATAATAAATT
Found at i:668628 original size:26 final size:26
Alignment explanation
Indices: 668588--668783 Score: 131
Period size: 26 Copynumber: 7.8 Consensus size: 26
668578 TATTTGATGA
668588 TTTAGTAATGATTTGATAATAATCAT
1 TTTAGTAATGATTTGATAATAATCAT
*
668614 TTTAGTAATGCTTTGATAATAATCA-
1 TTTAGTAATGATTTGATAATAATCAT
*
668639 -TTA-TAATGATTT-AGTAATAATCAA
1 TTTAGTAATGATTTGA-TAATAATCAT
* * * *
668663 TATAATAATGATTTAATAATAATGA-
1 TTTAGTAATGATTTGATAATAATCAT
* * * *
668688 --TAATAATAATTTAATAATAATAAT
1 TTTAGTAATGATTTGATAATAATCAT
** * * * *
668712 GATAATAATGATTTAATAGTAATTA-
1 TTTAGTAATGATTTGATAATAATCAT
*
668737 TTTAGTAATGATTT-ATAATAATGAT
1 TTTAGTAATGATTTGATAATAATCAT
* *
668762 TTAATACTAATGATTTAATAAT
1 TT--TAGTAATGATTTGATAAT
668784 TACTATAATT
Statistics
Matches: 143, Mismatches: 15, Indels: 22
0.79 0.08 0.12
Matches are distributed among these distances:
22 1 0.01
23 38 0.27
24 11 0.08
25 15 0.10
26 61 0.43
27 12 0.08
28 5 0.03
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (26 bp):
TTTAGTAATGATTTGATAATAATCAT
Found at i:668657 original size:49 final size:49
Alignment explanation
Indices: 668593--668783 Score: 188
Period size: 49 Copynumber: 3.8 Consensus size: 49
668583 GATGATTTAG
* * * *
668593 TAATGATTT-GATAATAATCATTTTAGTAATGCTTTGATAATAATCATTA
1 TAATGATTTAG-TAATAATCATTATAATAATGATTTAATAATAATCATTA
* * *
668642 TAATGATTTAGTAATAATCAATATAATAATGATTTAATAATAATGATAA
1 TAATGATTTAGTAATAATCATTATAATAATGATTTAATAATAATCATTA
* * * * * *
668691 TAATAATTTAATAATAATAATGATAATAATGATTTAATAGTAATTATTTA
1 TAATGATTTAGTAATAATCATTATAATAATGATTTAATAATAATCA-TTA
* *
668741 GTAATGATTTA-TAATAATGATTTAATACTAATGATTTAATAAT
1 -TAATGATTTAGTAATAATCA-TT-ATAATAATGATTTAATAAT
668784 TACTATAATT
Statistics
Matches: 117, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
49 79 0.68
50 11 0.09
51 10 0.09
52 17 0.15
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (49 bp):
TAATGATTTAGTAATAATCATTATAATAATGATTTAATAATAATCATTA
Found at i:668670 original size:3 final size:3
Alignment explanation
Indices: 668653--668720 Score: 61
Period size: 3 Copynumber: 23.3 Consensus size: 3
668643 AATGATTTAG
* * *
668653 TAA TAA TCAA T-A TAA TAA TGA T-T TAA TAA TAA TGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
668697 T-T TAA TAA TAA TAA TGA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
668721 GATTTAATAG
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
2 4 0.08
3 45 0.87
4 3 0.06
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:668681 original size:11 final size:11
Alignment explanation
Indices: 668665--668783 Score: 67
Period size: 11 Copynumber: 9.6 Consensus size: 11
668655 ATAATCAATA
668665 TAATAATGATT
1 TAATAATGATT
* *
668676 TAATAATAATGA
1 TAATAATGAT-T
*
668688 TAATAATAATT
1 TAATAATGATT
*
668699 TAATAATAATAAT
1 TAATAATGAT--T
668712 GATAATAATGATT
1 --TAATAATGATT
*
668725 TAATAGTAATTATT
1 T-A-A-TAATGATT
*
668739 TAGTAATGATTT
1 TAATAATGA-TT
668751 ATAATAATGATT
1 -TAATAATGATT
668763 TAATACTAATGATT
1 T-A-A-TAATGATT
668777 TAATAAT
1 TAATAAT
668784 TACTATAATT
Statistics
Matches: 87, Mismatches: 8, Indels: 26
0.72 0.07 0.21
Matches are distributed among these distances:
11 30 0.34
12 17 0.20
13 14 0.16
14 17 0.20
15 9 0.10
ACGTcount: A:0.49, C:0.01, G:0.08, T:0.43
Consensus pattern (11 bp):
TAATAATGATT
Found at i:668702 original size:20 final size:20
Alignment explanation
Indices: 668664--668717 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 20
668654 AATAATCAAT
*
668664 ATAATAATGATTTAATAATAA
1 ATAATAATAATTTAATAAT-A
668685 TGATAATAATAATTTAATAATA
1 --ATAATAATAATTTAATAATA
*
668707 ATAATGATAAT
1 ATAATAATAAT
668718 AATGATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 10 0.34
22 1 0.03
23 18 0.62
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (20 bp):
ATAATAATAATTTAATAATA
Found at i:668944 original size:24 final size:24
Alignment explanation
Indices: 668896--668940 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
668886 GATTTGATAC
*
668896 TAATGATTTACTAATTATTATTAA
1 TAATGATTTACTAATTAATATTAA
*
668920 TAATGATTTA-TTATTAATATT
1 TAATGATTTACTAATTAATATT
668941 TAATTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
TAATGATTTACTAATTAATATTAA
Found at i:668947 original size:17 final size:17
Alignment explanation
Indices: 668907--668948 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
668897 AATGATTTAC
668907 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
668924 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
668941 TAATTATT
1 TAATTATT
668949 TGATACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:671278 original size:30 final size:30
Alignment explanation
Indices: 671244--671346 Score: 115
Period size: 30 Copynumber: 3.4 Consensus size: 30
671234 TTCCTTAAAC
671244 AACTAATAAACTATTCTTTAATATAACGTT-
1 AACTAATAAACTATTCTTTAATATAAC-TTA
671274 AACTAATAAACTATTCTTTAATAT-ACTTA
1 AACTAATAAACTATTCTTTAATATAACTTA
*
671303 AACTAATAAA-TGATT-TTTAATTATAATTTA
1 AACTAATAAACT-ATTCTTTAA-TATAACTTA
* *
671333 CTACTAAAAAACTA
1 -AACTAATAAACTA
671347 ATTAACTAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
28 8 0.12
29 18 0.28
30 28 0.44
31 9 0.14
32 1 0.02
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.40
Consensus pattern (30 bp):
AACTAATAAACTATTCTTTAATATAACTTA
Found at i:671547 original size:21 final size:21
Alignment explanation
Indices: 671523--671562 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
671513 ATTTCTAATG
671523 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
671544 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
671563 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:671694 original size:18 final size:18
Alignment explanation
Indices: 671671--671729 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
671661 TATAACTAAC
671671 TAATAAACTATTTTATTA
1 TAATAAACTATTTTATTA
* *
671689 TAATAAA--ATTTAAACTA
1 TAATAAACTATTT-TATTA
*
671706 CTAATAAACTATTTTTTTA
1 -TAATAAACTATTTTATTA
671725 TAATA
1 TAATA
671730 TAAATTCAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
16 4 0.12
17 3 0.09
18 19 0.59
19 2 0.06
20 4 0.12
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATAAACTATTTTATTA
Found at i:671715 original size:36 final size:38
Alignment explanation
Indices: 671664--671735 Score: 121
Period size: 36 Copynumber: 1.9 Consensus size: 38
671654 TTCTTTATAT
671664 AACTAACTAATAAACTATTTTATTATAATA-AAATTTA
1 AACTAACTAATAAACTATTTTATTATAATATAAATTTA
*
671701 AACT-ACTAATAAACTATTTTTTTATAATATAAATT
1 AACTAACTAATAAACTATTTTATTATAATATAAATT
671736 CAACAACCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
36 24 0.73
37 9 0.27
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (38 bp):
AACTAACTAATAAACTATTTTATTATAATATAAATTTA
Found at i:671789 original size:27 final size:29
Alignment explanation
Indices: 671754--671818 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
671744 AAAATATAAC
*
671754 TTAACTATTTA-ACTAACT-ACAAACTAA
1 TTAATTATTTAGACTAACTAACAAACTAA
*
671781 TTCAA-TA-TTAGACTAACTAACACACTAA
1 TT-AATTATTTAGACTAACTAACAAACTAA
671809 TTAATTATTT
1 TTAATTATTT
671819 TTTTATATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAATTATTTAGACTAACTAACAAACTAA
Found at i:671929 original size:9 final size:9
Alignment explanation
Indices: 671897--671934 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
671887 CTAACAAACT
671897 AATAATTTAA
1 AATAA-TTAA
671907 AATAA-TAA
1 AATAATTAA
*
671915 ACTAATTAA
1 AATAATTAA
671924 AATAATTAA
1 AATAATTAA
671933 AA
1 AA
671935 AAACTTACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 13 0.52
10 5 0.20
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATTAA
Found at i:672332 original size:8 final size:9
Alignment explanation
Indices: 672321--672364 Score: 56
Period size: 8 Copynumber: 5.0 Consensus size: 9
672311 ATGCCATGTT
672321 GCCATGC-C
1 GCCATGCAC
672329 GCCATGCAC
1 GCCATGCAC
*
672338 AGCCATGCAT
1 -GCCATGCAC
672348 GCCATGC-C
1 GCCATGCAC
672356 GCCATGCAC
1 GCCATGCAC
672365 AGCTATACGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 14 0.45
9 9 0.29
10 8 0.26
ACGTcount: A:0.20, C:0.43, G:0.23, T:0.14
Consensus pattern (9 bp):
GCCATGCAC
Found at i:679462 original size:2 final size:2
Alignment explanation
Indices: 679455--679481 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
679445 TATTTTACAT
679455 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 T
679482 GAATAATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:689873 original size:23 final size:23
Alignment explanation
Indices: 689839--689888 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
689829 GCAAGCCCTG
*
689839 ATAAATTGAATTACATTTAAAAT
1 ATAAATTAAATTACATTTAAAAT
*
689862 ATAAATTAAATTACGTTTAAAAT
1 ATAAATTAAATTACATTTAAAAT
689885 ATAA
1 ATAA
689889 TTTTAGGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (23 bp):
ATAAATTAAATTACATTTAAAAT
Found at i:691845 original size:17 final size:17
Alignment explanation
Indices: 691823--691860 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
691813 TATTTAATAG
691823 AAAATACA-AAAAAATCT
1 AAAATACATAAAAAAT-T
*
691840 AAAATATATAAAAAATT
1 AAAATACATAAAAAATT
691857 AAAA
1 AAAA
691861 GTTTTAGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAATACATAAAAAATT
Found at i:693916 original size:12 final size:13
Alignment explanation
Indices: 693899--693927 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
693889 CTTAGTAGCG
693899 AAAATTAAAA-TT
1 AAAATTAAAATTT
693911 AAAATTAAAATTT
1 AAAATTAAAATTT
693924 AAAA
1 AAAA
693928 ATTCAATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:696502 original size:106 final size:106
Alignment explanation
Indices: 696313--698388 Score: 3325
Period size: 105 Copynumber: 19.7 Consensus size: 106
696303 TGAAAGTTAT
* * *
696313 GTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
* *
696378 GTTGACAACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGT
66 GTTGACAACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
696419 GTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAATTGGGAAATTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
696484 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * *
696525 GTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TT
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
*
696589 GTTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * * *
696630 GTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTG-TT
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
696694 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * *
696735 GTTGTCTGGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTGTGAAATTGAGAAA-TGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
*
696799 GTTGACAACCAGCGGTCCATTCGTCGTGAAGTTGAACTTGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
696840 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAAAAATGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
696904 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * *
696945 GTTGTCTGAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
*
697009 GTTGACAACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * * *
697050 GTTGTCTTGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
697114 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * *
697155 GCTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
697220 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
697261 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
* *
697326 ATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
697367 GTTGTCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
697431 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * *
697472 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAAATT-GAAAAATGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
* *
697536 GTTGACAACCAGCGGTTCCTTCGTCGTGAAGTTGAACTTGA
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
697577 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAA-TGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
* *
697641 GTTGACAACCAGCGGTCCTTTCGTCGTGAATTTGAACTTGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * *
697682 GTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
697746 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * *
697787 GCTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
697852 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * * *
697893 GTTGTCTGGAGTCTAATATCCTTCGTTGTGACGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
*
697958 GTTGACAACCAGCGGTTCCTTCGTCGTGAAGTTGAACTTGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * **
697999 ATTGTCTAGAGTCCAATATCCTTC-TCTGTGAAGTTGAAATTGGCTCCAAAATTGGGAAATTGTT
1 GTTGTCTGGAGTCCAATATCCTTCGT-TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTT
*
698063 TGTTGACAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGC
65 TGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * *
698105 GTTGTCTGGAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
*
698170 GTTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTAG-
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT-GC
* * *
698211 GTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
1 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
* *
698276 ATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGC
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * * * *
698317 GTTGTCTTGAGTCCAATATCCTTCGCTT-TGAAGTTGAAATTGACTCTGAAGTTGAGAAGTTGTT
1 GTTGTCTGGAGTCCAATATCCTTCG-TTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTT
698381 TGTTGACA
65 TGTTGACA
698389 GTCAGCTTTT
Statistics
Matches: 1847, Mismatches: 110, Indels: 26
0.93 0.06 0.01
Matches are distributed among these distances:
104 8 0.00
105 974 0.53
106 863 0.47
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
Found at i:697524 original size:632 final size:630
Alignment explanation
Indices: 696313--698388 Score: 3503
Period size: 632 Copynumber: 3.3 Consensus size: 630
696303 TGAAAGTTAT
* *
696313 GTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTT
1 GTTGTCT-GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTT
* * *
696378 GTTGACAACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTT
64 GTTGACAACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTT
* * *
696442 CGTTGTGAAGTTGAAATTGGATCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCG
128 CGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAACCAGCGGTCCCTTCG
* * *
696507 TCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
192 TCGTGAAGTTGAACTTGCGCTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
* *
696572 GAAATTGGGAAGTTG-TTGTTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
257 GAAATTAGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
* *
696636 TTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTG-TTGTTGAC
322 TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGAC
696700 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCGTTGTG
387 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCGTTGTG
* *
696765 AAGTTGAAATTGGCTGTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCATTCGTCGTGAAG
452 AAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
696830 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
517 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
696895 AAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
582 AAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
696944 CGTTGTCTGAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
1 -GTTGTCTG-AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
* *
697009 GTTGACAACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCATTC
64 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTC
697074 GCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTC
129 GCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTC
697139 GTGAAGTTGAACTTGCGCTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
194 GTGAAGTTGAACTTGCGCTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
697204 AATTAGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
259 AATTAGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
697269 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
324 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
697334 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCTTTCGTTGTGAA
389 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCGTTGTGAA
697399 GTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
454 GTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
*
697464 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTGAAA
519 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAAA
*
697529 AATGTTTGTTGACAACCAGCGGTTCCTTCGTCGTGAAGTTGAACTTG
584 AATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
* *
697576 AGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAATGTTT
1 -GTTGTCT-GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
* *
697641 GTTGACAACCAGCGGTCCTTTCGTCGTGAATTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTC
64 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTC
697706 GCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTC
129 GCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTC
697771 GTGAAGTTGAACTTGCGCTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
194 GTGAAGTTGAACTTGCGCTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
697836 AATTAGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
259 AATTAGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
697901 GAGTCTAATATCCTTCGTTGTGACGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
324 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
697966 CCAGCGGTTCCTTCGTCGTGAAGTTGAACTTGCATTGTCTAGAGTCCAATATCCTTC-TCTGTGA
389 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCGT-TGTGA
** * *
698030 AGTTGAAATTGGCTCCAAAATTGGGAAATTGTTTGTTGACAACCAACGGTCCCTTCGTCGTGAAG
453 AGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* * *
698095 TTGAACTTGCGTTGTCTGGAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGG
517 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-G
* * *
698160 GAAATTGTTTGTTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTAG
581 AAAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT-G
* *
698211 GTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
1 GTTGTC-TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTT
* *
698276 ATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTC
64 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTC
* * * *
698341 GCTTTGAAGTTGAAATTGACTCTGAAGTTGAGAAGTTGTTTGTTGACA
129 GCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACA
698389 GTCAGCTTTT
Statistics
Matches: 1368, Mismatches: 64, Indels: 20
0.94 0.04 0.01
Matches are distributed among these distances:
630 105 0.08
631 200 0.15
632 758 0.55
633 95 0.07
634 99 0.07
635 99 0.07
636 12 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (630 bp):
GTTGTCTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGT
TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGC
TGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
GAAGTTGAACTTGCGCTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
TTAGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCGTTGTGAAGT
TGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAA
TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
Found at i:702132 original size:12 final size:13
Alignment explanation
Indices: 702115--702143 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
702105 CTTAGTAGCG
702115 AAAATTAAAA-TT
1 AAAATTAAAATTT
702127 AAAATTAAAATTT
1 AAAATTAAAATTT
702140 AAAA
1 AAAA
702144 ATTCAATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:703898 original size:39 final size:38
Alignment explanation
Indices: 703817--703918 Score: 109
Period size: 39 Copynumber: 2.6 Consensus size: 38
703807 GTAAATAAAT
* *
703817 GTTTTAAAATC-ATATAATATATAATTTCAAAAAATTA
1 GTTTTAAAAACTATATATTATATAATTTCAAAAAATTA
* * *
703854 TTTTTAAAAACTATATATTATATGTATTTC-AAAAATTGG
1 GTTTTAAAAACTATATATTATAT-AATTTCAAAAAATT-A
703893 GTTTTAAAAACTATATTATATATATA
1 GTTTTAAAAACTATA-TAT-TATATA
703919 GATATAGATA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
37 9 0.17
38 17 0.32
39 19 0.36
40 3 0.06
41 5 0.09
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (38 bp):
GTTTTAAAAACTATATATTATATAATTTCAAAAAATTA
Found at i:709000 original size:15 final size:15
Alignment explanation
Indices: 708982--709019 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
708972 TCTGCGGCCC
708982 TCGACTCTGTCACCA
1 TCGACTCTGTCACCA
*
708997 TCGACTCTGTCGCCA
1 TCGACTCTGTCACCA
709012 TCGACTCT
1 TCGACTCT
709020 AACTGCTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.16, C:0.39, G:0.16, T:0.29
Consensus pattern (15 bp):
TCGACTCTGTCACCA
Found at i:712385 original size:65 final size:61
Alignment explanation
Indices: 712304--712440 Score: 211
Period size: 65 Copynumber: 2.2 Consensus size: 61
712294 AACATGTGGC
*
712304 TTTCATTCAACAATTATTTATGATCTATCACATCCGACTTCCTAAAATAAAGGGGACAAACATTG
1 TTTCATTCAACAATTATTTATGATCTATCACATCCGACTACCTAAAATAAA--GG--AAACATTG
* *
712369 TTTCATTCAACGATTATTTCTGATCTATCACATCCGACTACCTAAAATAAAGGAAACATTG
1 TTTCATTCAACAATTATTTATGATCTATCACATCCGACTACCTAAAATAAAGGAAACATTG
712430 TTTCATTCAAC
1 TTTCATTCAAC
712441 TTAGCTTTCT
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
61 19 0.28
63 2 0.03
65 48 0.70
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (61 bp):
TTTCATTCAACAATTATTTATGATCTATCACATCCGACTACCTAAAATAAAGGAAACATTG
Found at i:726448 original size:31 final size:31
Alignment explanation
Indices: 726409--726478 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
726399 CGAGTATTGC
*
726409 TGAA-CTCGACTCG-ACTCGAAAACTCTGAAA
1 TGAAGCTCGACTCGAACTCGAAAAC-CGGAAA
* *
726439 TGAAGCTCGACTCGAACTCGAAATCCGGAAC
1 TGAAGCTCGACTCGAACTCGAAAACCGGAAA
726470 TGAAGCTCG
1 TGAAGCTCG
726479 TGAGCAGCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 4 0.11
31 22 0.63
32 9 0.26
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (31 bp):
TGAAGCTCGACTCGAACTCGAAAACCGGAAA
Found at i:731210 original size:15 final size:16
Alignment explanation
Indices: 731174--731211 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
731164 AGAGCCTCTG
*
731174 AATCATTCAGCGTTTA
1 AATCATTCAGCGCTTA
731190 AATCATTCAGCGCTT-
1 AATCATTCAGCGCTTA
731205 AATCATT
1 AATCATT
731212 TTGAAGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (16 bp):
AATCATTCAGCGCTTA
Found at i:743421 original size:2 final size:2
Alignment explanation
Indices: 743414--743444 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
743404 GATAGTTTTA
743414 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
743445 GTTTAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:743770 original size:2 final size:2
Alignment explanation
Indices: 743763--743790 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
743753 ATGATTTTTA
743763 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
743791 GAACTAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:746340 original size:14 final size:14
Alignment explanation
Indices: 746321--746348 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
746311 AAGTGAAAGA
746321 ATAGTTATATAATT
1 ATAGTTATATAATT
746335 ATAGTTATATAATT
1 ATAGTTATATAATT
746349 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:746412 original size:13 final size:13
Alignment explanation
Indices: 746370--746412 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
746360 TTTTAACCCC
* *
746370 AATTTTATTTTTT
1 AATTATATTATTT
*
746383 AATTATAGTTATAT
1 AATTATA-TTATTT
746397 AATTATATTATTT
1 AATTATATTATTT
746410 AAT
1 AAT
746413 ATGTTTTACC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
AATTATATTATTT
Found at i:761000 original size:15 final size:15
Alignment explanation
Indices: 760980--761010 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
760970 TAGTAAAGGG
760980 ATATATATAAATATT
1 ATATATATAAATATT
*
760995 ATATATATATATATT
1 ATATATATAAATATT
761010 A
1 A
761011 AGTGTCTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATATATAAATATT
Found at i:762819 original size:2 final size:2
Alignment explanation
Indices: 762812--762836 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
762802 TTGATTTCTT
762812 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 T
762837 GAGTTAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:769131 original size:11 final size:11
Alignment explanation
Indices: 769115--769148 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
769105 GAATGTATTC
769115 GTTTAATGTTT
1 GTTTAATGTTT
*
769126 GTTTAATGTTC
1 GTTTAATGTTT
769137 GTTTATATGTTT
1 GTTTA-ATGTTT
769149 AATTTTTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.18, C:0.03, G:0.18, T:0.62
Consensus pattern (11 bp):
GTTTAATGTTT
Found at i:772832 original size:20 final size:21
Alignment explanation
Indices: 772790--772830 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
772780 CCGCCTCTGT
772790 TGCATTTTAGTTTTTTTCCCC
1 TGCATTTTAGTTTTTTTCCCC
772811 TGCATTTTAGTTTTTTTCCC
1 TGCATTTTAGTTTTTTTCCC
772831 TGTGTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.22, G:0.10, T:0.59
Consensus pattern (21 bp):
TGCATTTTAGTTTTTTTCCCC
Found at i:779896 original size:20 final size:20
Alignment explanation
Indices: 779871--779927 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
779861 TGCGATTTTC
*
779871 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
* * *
779891 CAAATTCACAACACAAAAGT
1 CAAATTCGCAACGCGAAAGT
779911 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
779928 CTCCAATTTC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.44, C:0.26, G:0.14, T:0.16
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:780001 original size:20 final size:20
Alignment explanation
Indices: 779939--780001 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
779929 TCCAATTTCA
*
779939 CAACGTGAATAGTAAAATCA
1 CAACGTGAATAGTAAAATCG
*
779959 CAACGTGAATAGTAAAATTG
1 CAACGTGAATAGTAAAATCG
779979 CAACGTGAATAGTAAAATCG
1 CAACGTGAATAGTAAAATCG
779999 CAA
1 CAA
780002 TGAATCTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (20 bp):
CAACGTGAATAGTAAAATCG
Found at i:780454 original size:21 final size:21
Alignment explanation
Indices: 780366--780464 Score: 114
Period size: 21 Copynumber: 4.8 Consensus size: 21
780356 GATTTTCTAA
*
780366 ATTCACGTTACGA-TTTTACT
1 ATTCACGTTGCGATTTTTACT
** *
780386 ATTCATATTGAGA-TTTTACT
1 ATTCACGTTGCGATTTTTACT
*
780406 ATTCACATTGC-ACTTTTTACT
1 ATTCACGTTGCGA-TTTTTACT
780427 ATTCACGTTGCGATTTTTACT
1 ATTCACGTTGCGATTTTTACT
*
780448 ATTCACGCTGCGATTTT
1 ATTCACGTTGCGATTTT
780465 GGAAACTGAA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 25 0.37
21 41 0.60
22 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.46
Consensus pattern (21 bp):
ATTCACGTTGCGATTTTTACT
Found at i:782511 original size:14 final size:15
Alignment explanation
Indices: 782474--782515 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
782464 TGGTTTTCCA
782474 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
782489 GAATTTGAATT-CTG
1 GAAAATGAATTACTG
782503 GAAAATGAATTAC
1 GAAAATGAATTAC
782516 ATTTCTGTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (15 bp):
GAAAATGAATTACTG
Found at i:782521 original size:20 final size:20
Alignment explanation
Indices: 782498--782567 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
782488 GGAATTTGAA
782498 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
782518 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
782538 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
782558 TTCTGGAAAA
1 TTCTGGAAAA
782568 CATCTGAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:782726 original size:11 final size:11
Alignment explanation
Indices: 782712--782759 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
782702 TTAATTACTA
782712 AAATATTATTG
1 AAATATTATTG
782723 AAATA-TA-T-
1 AAATATTATTG
*
782731 AAATAATATTG
1 AAATATTATTG
782742 AAAATATTATTG
1 -AAATATTATTG
782754 AAATAT
1 AAATAT
782760 ATAAATAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
8 5 0.16
9 3 0.09
10 3 0.09
11 11 0.34
12 10 0.31
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (11 bp):
AAATATTATTG
Found at i:782740 original size:19 final size:18
Alignment explanation
Indices: 782712--782748 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
782702 TTAATTACTA
*
782712 AAATATTATTGAAATATAT
1 AAATAATATTGAAA-ATAT
782731 AAATAATATTGAAAATAT
1 AAATAATATTGAAAATAT
782749 TATTGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (18 bp):
AAATAATATTGAAAATAT
Found at i:782930 original size:28 final size:27
Alignment explanation
Indices: 782875--782939 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
782865 TTTACTAAAA
*
782875 TATTATTGAAATATATAAATAATATTAT
1 TATTATT-AAATATATAAAAAATATTAT
782903 TCATTATTAAATATATAAAAAA-ATTTAT
1 T-ATTATTAAATATATAAAAAATA-TTAT
782931 TATATATTA
1 TAT-TATTA
782940 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 3 0.09
28 24 0.73
29 6 0.18
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
TATTATTAAATATATAAAAAATATTAT
Found at i:782965 original size:31 final size:32
Alignment explanation
Indices: 782875--782972 Score: 84
Period size: 31 Copynumber: 3.2 Consensus size: 32
782865 TTTACTAAAA
*
782875 TATTATTGAAATATAT--AAATA-ATATTAT-T
1 TATTATT-AAATATATAAAAAAATATATTATAT
* *
782904 CATTATTAAATATATAAAAAAATTTATTATA-
1 TATTATTAAATATATAAAAAAATATATTATAT
*
782935 TATTATTAAA-ATA-AAAATATAATATCTTATAT
1 TATTATTAAATATATAAAA-A-AATATATTATAT
782967 TATTAT
1 TATTAT
782973 AATATAATTG
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
28 8 0.14
29 10 0.18
30 8 0.14
31 24 0.43
32 6 0.11
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (32 bp):
TATTATTAAATATATAAAAAAATATATTATAT
Found at i:783040 original size:22 final size:22
Alignment explanation
Indices: 782996--783052 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
782986 ATTTTATATA
* *
782996 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
783017 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
783039 ATATTTTAAATATT
1 ATATTATAAATATT
783053 TTGATGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:783041 original size:24 final size:22
Alignment explanation
Indices: 782991--783048 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
782981 TGATTATTTT
*
782991 ATATAATATTAAAAATATAATA
1 ATATATTATTAAAAATATAATA
* *
783013 TTATATTATTATAAATATTAATAA
1 ATATATTATTAAAAATA-TAAT-A
783037 ATATATT-TTAAA
1 ATATATTATTAAA
783049 TATTTTGATG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 14 0.48
23 8 0.28
24 7 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATATTATTAAAAATATAATA
Found at i:783051 original size:52 final size:51
Alignment explanation
Indices: 782932--783052 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 51
782922 AAAATTTATT
**
782932 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAAATATAATA-CTTATATTATTATAATATAATAA
782983 AT-TATTTTATATAATATTAAAAATATAATA-TTATATTATTATAAATATTAATAA
1 ATATA-TTT-TA-AATATTAAAAATATAATACTTATATTATTAT-AATA-TAATAA
783037 ATATATTTTAAATATT
1 ATATATTTTAAATATT
783053 TTGATGAAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 20 0.33
53 7 0.12
54 22 0.37
55 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
ATATATTTTAAATATTAAAAATATAATACTTATATTATTATAATATAATAA
Found at i:783285 original size:42 final size:42
Alignment explanation
Indices: 783226--783345 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
783216 ATGAATTACA
*
783226 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
783268 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
783310 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
783346 TTCGGAGAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.16
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:784888 original size:2 final size:2
Alignment explanation
Indices: 784883--784914 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
784873 TATATATATA
784883 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
784915 ATTCATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:790828 original size:60 final size:60
Alignment explanation
Indices: 790696--790861 Score: 147
Period size: 60 Copynumber: 2.8 Consensus size: 60
790686 AACTATAACT
* * * * * * * **
790696 CTCATTTTAAATTGGTCCTTTAACTTTTAAATATTTTAATTTCATCCCTAAATTATGATT
1 CTCATTCTAAATTAGTCCTTAAACTTTTAAACATTCTAATTTCATCCCTAAACTACGACC
* * * *
790756 CTCATTCCAAATTAGTCCTTAAATTTTTAAACATTCTAATTTTATCCTTAAACTACGACC
1 CTCATTCTAAATTAGTCCTTAAACTTTTAAACATTCTAATTTCATCCCTAAACTACGACC
* ** * * *
790816 CTCTTTCTAAATT--TCCCCAAACTTTTGAATATTCCAATTTCATCCC
1 CTCATTCTAAATTAGTCCTTAAACTTTTAAACATTCTAATTTCATCCC
790862 CAAATTTATC
Statistics
Matches: 83, Mismatches: 23, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
58 25 0.30
60 58 0.70
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.44
Consensus pattern (60 bp):
CTCATTCTAAATTAGTCCTTAAACTTTTAAACATTCTAATTTCATCCCTAAACTACGACC
Found at i:796733 original size:60 final size:61
Alignment explanation
Indices: 796652--796781 Score: 156
Period size: 60 Copynumber: 2.1 Consensus size: 61
796642 TAAACGTTTT
* * * * * *
796652 AATTTTATCCCTAAACTATGACTATGATTCTAAATTAATC-CTCAAAC-CTTTGAACATTTC
1 AATTTCATCCCCAAACAATGACTATCATTATAAATTAATCTCT-AAACTCTTTGAACATTCC
* * *
796712 AATTTCATCCCCAAACAATGACTTTCATTATAAATTGATCTCTAAACTTTTTGAACATTCC
1 AATTTCATCCCCAAACAATGACTATCATTATAAATTAATCTCTAAACTCTTTGAACATTCC
796773 AATTTCATC
1 AATTTCATC
796782 TCAAACTGTA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
60 37 0.63
61 22 0.37
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (61 bp):
AATTTCATCCCCAAACAATGACTATCATTATAAATTAATCTCTAAACTCTTTGAACATTCC
Found at i:797090 original size:60 final size:58
Alignment explanation
Indices: 796910--797092 Score: 161
Period size: 60 Copynumber: 3.1 Consensus size: 58
796900 TTTGGATGAA
* * * * * * *
796910 TTTGGGGATGAAATTGGAATATTCAAAAGTTTGGGGACCAATTTAGGAAGAAAGTCACAG
1 TTTGAGGATGAAATTAGAATATTCAAAAATTT-AGGACCAATTTA-AAAGAGAGTCATAG
* * * * * *
796970 TTTAAGGATGAACTTAAAATGTTCAAAAATTTAAGGACTAATTT-ATAGCATGAGTCATAG
1 TTTGAGGATGAAATTAGAATATTCAAAAATTT-AGGACCAATTTAAAAG-A-GAGTCATAG
* *
797030 TTTGAGGATGAAATTAGAACATTCAAAAATTTAGGAACCAATTTAAAATGAGAGTTATAG
1 TTTGAGGATGAAATTAGAATATTCAAAAATTTAGG-ACCAATTTAAAA-GAGAGTCATAG
797090 TTT
1 TTT
797093 AAGAACATAT
Statistics
Matches: 96, Mismatches: 22, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
58 2 0.02
59 4 0.04
60 86 0.90
61 3 0.03
62 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (58 bp):
TTTGAGGATGAAATTAGAATATTCAAAAATTTAGGACCAATTTAAAAGAGAGTCATAG
Found at i:797641 original size:16 final size:17
Alignment explanation
Indices: 797610--797642 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
797600 AAAATCTCAA
797610 TTTAAACTTCTAAATTT
1 TTTAAACTTCTAAATTT
*
797627 TTTAAA-TTTTAAATTT
1 TTTAAACTTCTAAATTT
797643 CCCCCTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAAACTTCTAAATTT
Done.