Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005606.1 Hibiscus syriacus cultivar Beakdansim tig00013040_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: 3509357
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 11
Found at i:2828960 original size:13 final size:13
Alignment explanation
Indices: 2828944--2828979 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2828934 ATTTTATTCC
*
2828944 TTTATTTTTTTAA
1 TTTATTTCTTTAA
2828957 TTTATTTCTTTAA
1 TTTATTTCTTTAA
*
2828970 TTCATTTCTT
1 TTTATTTCTT
2828980 ATTTCATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTTCTTTAA
Found at i:2828983 original size:20 final size:20
Alignment explanation
Indices: 2828958--2828999 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2828948 TTTTTTTAAT
2828958 TTATTTC-TTTAATTCATTTC
1 TTATTTCATTTAATTC-TTTC
2828978 TTATTTCATTTAATTCTTTC
1 TTATTTCATTTAATTCTTTC
2828998 TT
1 TT
2829000 CCATTACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTCATTTAATTCTTTC
Found at i:2832210 original size:90 final size:88
Alignment explanation
Indices: 2832057--2832230 Score: 303
Period size: 90 Copynumber: 2.0 Consensus size: 88
2832047 CCTAACACAC
2832057 CCTTTTATAGCCAAGTTACCATAATCATATTAGGATTTTATTATTTCAAATTAATTAAATATATA
1 CCTTTTATAGCCAAGTTACCATAATCATATTAGGATTTTATTATTTCAAATTAATTAAATATATA
*
2832122 TTTAATTAATTAGAATTTAATAAT
66 TTTAATTAATT-GAAATTAATAAT
* *
2832146 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATATAT
1 CCTTTTATAGCCAAGTTACCATAATCATATTA-GGATTTTATTATTTCAAATTAATTAAATATAT
2832211 ATTTAATTAATTGAAATTAA
65 ATTTAATTAATTGAAATTAA
2832231 ATATTTGGGA
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
89 37 0.46
90 44 0.54
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.45
Consensus pattern (88 bp):
CCTTTTATAGCCAAGTTACCATAATCATATTAGGATTTTATTATTTCAAATTAATTAAATATATA
TTTAATTAATTGAAATTAATAAT
Found at i:2832220 original size:20 final size:21
Alignment explanation
Indices: 2832195--2832264 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
2832185 TATTATTTCA
2832195 AATTAATT-AAATATATATTT
1 AATTAATTAAAATATATATTT
* *
2832215 AATTAATTGAAATTAAATATTT
1 AATTAATT-AAAATATATATTT
* *
2832237 GGGATT-ATTAAAACATATATTT
1 --AATTAATTAAAATATATATTT
2832259 AATTAA
1 AATTAA
2832265 CTCTAGATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 11 0.29
21 1 0.03
22 20 0.53
23 3 0.08
24 3 0.08
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (21 bp):
AATTAATTAAAATATATATTT
Found at i:2837311 original size:44 final size:44
Alignment explanation
Indices: 2837262--2837655 Score: 463
Period size: 44 Copynumber: 9.0 Consensus size: 44
2837252 CTGCTCTAAA
* * * *
2837262 ATAAATGAAAATGCATAACAATGCCTTATTGGTAGAAATGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* * *
2837306 ATAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGATGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* *
2837350 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTACC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
*
2837394 ATAAATGAAAATGC---ACGGTGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* * * * *
2837435 ATAAATGAAAATGTACAACGGTGCATTACTGGTAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* * ** * *
2837479 ATAAATTAAAATACATAACGATTTATTATTGGCAGAAAAGAGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
*
2837523 ATAAATGAAAATACATAACGATGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* * * * * *
2837567 ATAAATGAAAAATACAAAACAATGCATTATTGG-AAAAAAGTGAC
1 ATAAATG-AAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
* * * *
2837611 ATAAATAAAAATGCATAACGATACATTACTGGCATAAAGGTGCC
1 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
2837655 A
1 A
2837656 CTCATGGTAT
Statistics
Matches: 301, Mismatches: 44, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
41 39 0.13
43 20 0.07
44 219 0.73
45 23 0.08
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.24
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
Found at i:2837525 original size:129 final size:130
Alignment explanation
Indices: 2837262--2837644 Score: 412
Period size: 129 Copynumber: 2.9 Consensus size: 130
2837252 CTGCTCTAAA
* * * * * * *
2837262 ATAAATGAAAATGCATAACAATGCCTTATTGGTAGAAATGTGCCATAAATGAAAATGCATAATGG
1 ATAAATGAAAAT--ACAACGATGCATTATTGGCAGAAAGGTGCCATAAATGAAAATGCACAACGG
* * * *
2837327 TGCATTATTGGCAGAAAGATGCCATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTA
64 TGCATTACTGGCAGAAAGATGCCATAAATGAAAATACATAACGATGCATTATTGGCAGAAAAGTA
2837392 CC
129 CC
* * *
2837394 ATAAATGAAAATGC-ACGGTGCATTATTGGCAGAAAGGTGCCATAAATGAAAATGTACAACGGTG
1 ATAAATGAAAATACAACGATGCATTATTGGCAGAAAGGTGCCATAAATGAAAATGCACAACGGTG
* * * **
2837458 CATTACTGGTAGAAAGGTGCCATAAATTAAAATACATAACGATTTATTATTGGCAGAAAAG-AGC
66 CATTACTGGCAGAAAGATGCCATAAATGAAAATACATAACGATGCATTATTGGCAGAAAAGTA-C
2837522 C
130 C
* * *
2837523 ATAAATGAAAATACATAACGATGCATTATTGGCAGAAAGGTGCCATAAATGAAAAATACAAAACA
1 ATAAATGAAAATAC--AACGATGCATTATTGGCAGAAAGGTGCCATAAATG-AAAATGCACAACG
* * * * * * * * *
2837588 ATGCATTATTGGAAAAAAG-TGACATAAATAAAAATGCATAACGATACATTACTGGCA
63 GTGCATTACTGGCAGAAAGATGCCATAAATGAAAATACATAACGATGCATTATTGGCA
2837645 TAAAGGTGCC
Statistics
Matches: 211, Mismatches: 35, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
128 1 0.00
129 109 0.52
132 77 0.36
133 24 0.11
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.24
Consensus pattern (130 bp):
ATAAATGAAAATACAACGATGCATTATTGGCAGAAAGGTGCCATAAATGAAAATGCACAACGGTG
CATTACTGGCAGAAAGATGCCATAAATGAAAATACATAACGATGCATTATTGGCAGAAAAGTACC
Found at i:2837551 original size:173 final size:173
Alignment explanation
Indices: 2837262--2837655 Score: 477
Period size: 173 Copynumber: 2.3 Consensus size: 173
2837252 CTGCTCTAAA
* * * * * * *
2837262 ATAAATGAAAATGCATAACAATGCCTTATTGGTAGAAATGTGCCATAAATGAAAATGCATAATGG
1 ATAAATGAAAATGCACAACAATGCATTACTGGTAGAAAGGTGCCATAAATGAAAATACATAACGA
* *
2837327 TGCATTATTGGCAGAAAGATGCCATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTA
66 TGCATTATTGGCAGAAAGATGCCATAAATGAAAATACATAACGATGCATTATTGGCAGAAAGGTA
2837392 CCATAAATGAAAATGCACGGTGCATTATTGGCAGAAAGGTGCC
131 CCATAAATGAAAATGCACGGTGCATTATTGGCAGAAAGGTGCC
* ** *
2837435 ATAAATGAAAATGTACAACGGTGCATTACTGGTAGAAAGGTGCCATAAATTAAAATACATAACGA
1 ATAAATGAAAATGCACAACAATGCATTACTGGTAGAAAGGTGCCATAAATGAAAATACATAACGA
**
2837500 TTTATTATTGGCAGAAAAGA-GCCATAAATGAAAATACATAACGATGCATTATTGGCAGAAAGGT
66 TGCATTATTGGCAG-AAAGATGCCATAAATGAAAATACATAACGATGCATTATTGGCAGAAAGGT
* * ** * * *
2837564 GCCATAAATGAAAAATACAAAACAATGCATTATTGG-AAAAAAGTGAC
130 ACCATAAATG-AAAATGC---ACGGTGCATTATTGGCAGAAAGGTGCC
* * * * * *
2837611 ATAAATAAAAATGCATAACGATACATTACTGGCATAAAGGTGCCA
1 ATAAATGAAAATGCACAACAATGCATTACTGGTAGAAAGGTGCCA
2837656 CTCATGGTAT
Statistics
Matches: 187, Mismatches: 29, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
173 117 0.63
174 11 0.06
176 46 0.25
177 13 0.07
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.24
Consensus pattern (173 bp):
ATAAATGAAAATGCACAACAATGCATTACTGGTAGAAAGGTGCCATAAATGAAAATACATAACGA
TGCATTATTGGCAGAAAGATGCCATAAATGAAAATACATAACGATGCATTATTGGCAGAAAGGTA
CCATAAATGAAAATGCACGGTGCATTATTGGCAGAAAGGTGCC
Found at i:2839988 original size:20 final size:21
Alignment explanation
Indices: 2839963--2840005 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2839953 TGTATAAAGT
2839963 CTATGAGCTAATAAAA-ATGC
1 CTATGAGCTAATAAAATATGC
**
2839983 CTATGATTTAATAAAATATGC
1 CTATGAGCTAATAAAATATGC
2840004 CT
1 CT
2840006 TAATGTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.33
Consensus pattern (21 bp):
CTATGAGCTAATAAAATATGC
Found at i:2842817 original size:23 final size:24
Alignment explanation
Indices: 2842764--2842814 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2842754 ATTATTTGTT
* * *
2842764 TTTTTTTCTTTTTGAGTGCTGGAA
1 TTTTCTTCTTTTGGAGTGCTGCAA
*
2842788 TTTTCTTCTTTTGGAGTGCTTCAA
1 TTTTCTTCTTTTGGAGTGCTGCAA
2842812 TTT
1 TTT
2842815 CTTTGATGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.59
Consensus pattern (24 bp):
TTTTCTTCTTTTGGAGTGCTGCAA
Found at i:2849787 original size:33 final size:33
Alignment explanation
Indices: 2849750--2849822 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
2849740 GATATCCTTC
2849750 TATTTTTAAAAAAAATCAATATGACCCTCATGT
1 TATTTTTAAAAAAAATCAATATGACCCTCATGT
*
2849783 TATTTTTAAAAAAAATCAATCTGACCCTCATGT
1 TATTTTTAAAAAAAATCAATATGACCCTCATGT
2849816 TATTTTT
1 TATTTTT
2849823 CTCTCAATGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.41
Consensus pattern (33 bp):
TATTTTTAAAAAAAATCAATATGACCCTCATGT
Found at i:2858529 original size:21 final size:18
Alignment explanation
Indices: 2858484--2858528 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
2858474 GTAATGGAAT
2858484 AATGATGATATGGACGTG
1 AATGATGATATGGACGTG
2858502 AATGATGATATGGACGTG
1 AATGATGATATGGACGTG
*
2858520 AATGGTGAT
1 AATGATGAT
2858529 GGAAGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.33, T:0.29
Consensus pattern (18 bp):
AATGATGATATGGACGTG
Found at i:2865792 original size:15 final size:15
Alignment explanation
Indices: 2865772--2865814 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
2865762 ATATGATCTT
*
2865772 TCATATTCATTTTCA
1 TCATATTCATTCTCA
2865787 TCATATTCATTCTCA
1 TCATATTCATTCTCA
2865802 TCATATTCATTCT
1 TCATATTCATTCT
2865815 ACTTCCCTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (15 bp):
TCATATTCATTCTCA
Found at i:2870375 original size:21 final size:21
Alignment explanation
Indices: 2870351--2870390 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2870341 AAAAAGAAAG
2870351 AAAAGACAAAAAAGAAGAAGA
1 AAAAGACAAAAAAGAAGAAGA
** *
2870372 AAAATTCAGAAAAGAAGAA
1 AAAAGACAAAAAAGAAGAA
2870391 AAAGAATAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.72, C:0.05, G:0.17, T:0.05
Consensus pattern (21 bp):
AAAAGACAAAAAAGAAGAAGA
Found at i:2870389 original size:24 final size:24
Alignment explanation
Indices: 2870358--2870411 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
2870348 AAGAAAAGAC
*
2870358 AAAA-AAGAAGAAGAA-AAATTCA
1 AAAAGAAGAAAAAGAATAAATTCA
*
2870380 GAAAAGAAGAAAAAGAATAATTTCA
1 -AAAAGAAGAAAAAGAATAAATTCA
2870405 AAAAGAA
1 AAAAGAA
2870412 AGCAAAGCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 4 0.15
24 17 0.63
25 6 0.22
ACGTcount: A:0.70, C:0.04, G:0.15, T:0.11
Consensus pattern (24 bp):
AAAAGAAGAAAAAGAATAAATTCA
Found at i:2875743 original size:26 final size:26
Alignment explanation
Indices: 2875707--2875770 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
2875697 GGGGGCCGAA
*
2875707 CATACAATGAAACATTCCTCCAATTT
1 CATACAATGAAACATTCCTCCAAATT
2875733 CATACAATGAAACATTCCTCCAAATT
1 CATACAATGAAACATTCCTCCAAATT
* *
2875759 CATGCAAGGAAA
1 CATACAATGAAA
2875771 TGAACCAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.25
Consensus pattern (26 bp):
CATACAATGAAACATTCCTCCAAATT
Found at i:2876335 original size:2 final size:2
Alignment explanation
Indices: 2876328--2876354 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2876318 ATCACCAACT
2876328 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
2876355 TCCGCTACCA
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:2892028 original size:15 final size:16
Alignment explanation
Indices: 2892000--2892029 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2891990 AAATATGAAC
2892000 TAAGAAATGGAAATGA
1 TAAGAAATGGAAATGA
2892016 TAAGAAA-GGAAATG
1 TAAGAAATGGAAATG
2892030 GCAAGAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.17
Consensus pattern (16 bp):
TAAGAAATGGAAATGA
Found at i:2892035 original size:15 final size:16
Alignment explanation
Indices: 2892001--2892038 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2891991 AATATGAACT
*
2892001 AAGAAATGGAAATGAT
1 AAGAAATGGAAATGAC
*
2892017 AAGAAA-GGAAATGGC
1 AAGAAATGGAAATGAC
2892032 AAGAAAT
1 AAGAAAT
2892039 CATATCAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.58, C:0.03, G:0.26, T:0.13
Consensus pattern (16 bp):
AAGAAATGGAAATGAC
Found at i:2900063 original size:12 final size:12
Alignment explanation
Indices: 2900046--2900088 Score: 86
Period size: 12 Copynumber: 3.6 Consensus size: 12
2900036 TGAAGATAAC
2900046 TTACAACTCAAG
1 TTACAACTCAAG
2900058 TTACAACTCAAG
1 TTACAACTCAAG
2900070 TTACAACTCAAG
1 TTACAACTCAAG
2900082 TTACAAC
1 TTACAAC
2900089 ACTTACTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.26
Consensus pattern (12 bp):
TTACAACTCAAG
Found at i:2900235 original size:23 final size:25
Alignment explanation
Indices: 2900191--2900236 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
2900181 TTGCAACTTT
2900191 TTCTTCTCTTTTCTTTTGCTTTCGA
1 TTCTTCTCTTTTCTTTTGCTTTCGA
2900216 TTCTTCT-TTTTCTTTT-CTTTC
1 TTCTTCTCTTTTCTTTTGCTTTC
2900237 TTTTGCACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 5 0.24
24 9 0.43
25 7 0.33
ACGTcount: A:0.02, C:0.24, G:0.04, T:0.70
Consensus pattern (25 bp):
TTCTTCTCTTTTCTTTTGCTTTCGA
Found at i:2900522 original size:16 final size:16
Alignment explanation
Indices: 2900478--2900542 Score: 55
Period size: 16 Copynumber: 4.0 Consensus size: 16
2900468 TAAAAGAAAT
*
2900478 AAATGATTA-AAATGGA
1 AAATGATAAGAAAT-GA
2900494 AAATGAAATAAGAAATGA
1 AAATG--ATAAGAAATGA
*
2900512 AAATGATAAGAAA-GG
1 AAATGATAAGAAATGA
2900527 AAATGGA-AAGAAATGA
1 AAAT-GATAAGAAATGA
2900543 TATCAAAGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
15 11 0.27
16 16 0.39
18 10 0.24
19 4 0.10
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.17
Consensus pattern (16 bp):
AAATGATAAGAAATGA
Found at i:2900712 original size:13 final size:13
Alignment explanation
Indices: 2900694--2900733 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
2900684 ATATGGGCGT
2900694 GAATGGTGATGGA
1 GAATGGTGATGGA
*
2900707 GAATGGTGATTGAA
1 GAATGGTGA-TGGA
*
2900721 AAATGGTGATGGA
1 GAATGGTGATGGA
2900734 AATAGTATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.35, C:0.00, G:0.40, T:0.25
Consensus pattern (13 bp):
GAATGGTGATGGA
Found at i:2906386 original size:43 final size:46
Alignment explanation
Indices: 2906291--2906396 Score: 130
Period size: 50 Copynumber: 2.3 Consensus size: 46
2906281 AGGATTAGAT
*
2906291 TTATTATTTTATTAGGAATTAATGATTAGTTAAAACGTTATTTTTAGTTA
1 TTATTATTTTATTAGGAATTAATG--TAGTTAAAAC--TATGTTTAGTTA
2906341 TTATTATTTTATTAGGAATT-A-G-AGTTAAAAC-ATGTTTAGTTTA
1 TTATTATTTTATTAGGAATTAATGTAGTTAAAACTATGTTTAG-TTA
2906384 TTATTATTTTATT
1 TTATTATTTTATT
2906397 CATTAGTTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
42 7 0.13
43 16 0.30
45 9 0.17
48 1 0.02
49 1 0.02
50 20 0.37
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.54
Consensus pattern (46 bp):
TTATTATTTTATTAGGAATTAATGTAGTTAAAACTATGTTTAGTTA
Found at i:2910194 original size:16 final size:16
Alignment explanation
Indices: 2910170--2910203 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2910160 AGGGAAATTG
2910170 AGGGGCATGACCGAAT
1 AGGGGCATGACCGAAT
* *
2910186 AGGGTCATGGCCGAAT
1 AGGGGCATGACCGAAT
2910202 AG
1 AG
2910204 AGACATGGTG
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:0.29, C:0.18, G:0.38, T:0.15
Consensus pattern (16 bp):
AGGGGCATGACCGAAT
Found at i:2914364 original size:24 final size:25
Alignment explanation
Indices: 2914318--2914372 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
2914308 ACAGTTATGC
*
2914318 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
2914342 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
2914367 CA-TTGA
1 CACTTGA
2914373 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:2919385 original size:15 final size:15
Alignment explanation
Indices: 2919365--2919394 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2919355 GCAAATAATA
2919365 ATGAGAAGGGTGGCT
1 ATGAGAAGGGTGGCT
2919380 ATGAGAAGGGTGGCT
1 ATGAGAAGGGTGGCT
2919395 TAGAAACAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.47, T:0.20
Consensus pattern (15 bp):
ATGAGAAGGGTGGCT
Found at i:2919602 original size:23 final size:24
Alignment explanation
Indices: 2919549--2919599 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2919539 ATTCTTTGCT
* *
2919549 TTTTCTTCTTTTTGAGTGATGGAA
1 TTTTCTTCTTTTGGAGTGATGCAA
* *
2919573 TTTTCTTCTTTTGGAGTGCTTCAA
1 TTTTCTTCTTTTGGAGTGATGCAA
2919597 TTT
1 TTT
2919600 CTTTGCTGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.14, C:0.12, G:0.18, T:0.57
Consensus pattern (24 bp):
TTTTCTTCTTTTGGAGTGATGCAA
Found at i:2930673 original size:43 final size:46
Alignment explanation
Indices: 2930568--2930674 Score: 123
Period size: 50 Copynumber: 2.3 Consensus size: 46
2930558 TAGGATTAGA
*
2930568 TTTATTATTTTATTAGGAATTAAGGATGAGTTAAAACATTAATTTTAGTT
1 TTTATTATTTTATTAGGAATT-A--ATGAGTTAAAACATT-AGTTTAGTT
*
2930618 ATTATTATTTTATTAGGAATT-A-GAGTTAAAACA-T-GTTTAGTTT
1 TTTATTATTTTATTAGGAATTAATGAGTTAAAACATTAGTTTAG-TT
2930661 TTTATTATTTTATT
1 TTTATTATTTTATT
2930675 CATCAGTTAT
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
42 5 0.09
43 15 0.28
44 1 0.02
45 11 0.21
46 1 0.02
50 20 0.38
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (46 bp):
TTTATTATTTTATTAGGAATTAATGAGTTAAAACATTAGTTTAGTT
Found at i:2931112 original size:22 final size:22
Alignment explanation
Indices: 2931070--2931112 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2931060 TAAGTTCTTT
* *
2931070 ATCTTTTTTTTATCTTATTTTA
1 ATCTTTTTCTTACCTTATTTTA
2931092 ATCTTGTTTCTTACCTT-TTTT
1 ATCTT-TTTCTTACCTTATTTT
2931113 CCAGAACCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.70
Consensus pattern (22 bp):
ATCTTTTTCTTACCTTATTTTA
Found at i:2936008 original size:11 final size:12
Alignment explanation
Indices: 2935990--2936020 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2935980 CTATTTTTTT
2935990 CAAAAAAAAAGC
1 CAAAAAAAAAGC
2936002 CAAAAAAAAAGC
1 CAAAAAAAAAGC
2936014 CAAAAAA
1 CAAAAAA
2936021 GCCAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.77, C:0.16, G:0.06, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAGC
Found at i:2941261 original size:2 final size:2
Alignment explanation
Indices: 2941254--2941289 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2941244 TGGTAGCGGA
2941254 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2941290 GTAAGTTGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2943390 original size:16 final size:16
Alignment explanation
Indices: 2943369--2943411 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
2943359 AGAGATGTCT
*
2943369 AGTGGAGATAAAACCA
1 AGTGGAGACAAAACCA
*
2943385 AGTGGAGACAAAGCCA
1 AGTGGAGACAAAACCA
2943401 AGTGGAGACAA
1 AGTGGAGACAA
2943412 GGAATCTTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.47, C:0.14, G:0.30, T:0.09
Consensus pattern (16 bp):
AGTGGAGACAAAACCA
Found at i:2946923 original size:16 final size:16
Alignment explanation
Indices: 2946901--2946944 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
2946891 AGAGATGTCT
2946901 AGTGGAGACAAAACCA
1 AGTGGAGACAAAACCA
* *
2946917 TGTGGAGACAAAGCCA
1 AGTGGAGACAAAACCA
2946933 AGTGGAGACAAA
1 AGTGGAGACAAA
2946945 CAATCTTCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.45, C:0.16, G:0.30, T:0.09
Consensus pattern (16 bp):
AGTGGAGACAAAACCA
Found at i:2949840 original size:16 final size:16
Alignment explanation
Indices: 2949819--2949861 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
2949809 AGAGATGTCT
*
2949819 AGTGGAGACAAAACCA
1 AGTGGAGACAAAACAA
*
2949835 AGTGGAGACAAAGCAA
1 AGTGGAGACAAAACAA
2949851 AGTGGAGACAA
1 AGTGGAGACAA
2949862 GCAATCTTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.30, T:0.07
Consensus pattern (16 bp):
AGTGGAGACAAAACAA
Found at i:2955045 original size:9 final size:9
Alignment explanation
Indices: 2955009--2955048 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
2954999 AATTTGATCC
2955009 CTTTCATTT
1 CTTTCATTT
2955018 CTTATCATTT
1 CTT-TCATTT
2955028 CATTT-ATTT
1 C-TTTCATTT
2955037 CTTTCATTT
1 CTTTCATTT
2955046 CTT
1 CTT
2955049 ATTTCATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 3 0.11
9 15 0.54
10 8 0.29
11 2 0.07
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.65
Consensus pattern (9 bp):
CTTTCATTT
Found at i:2956717 original size:21 final size:21
Alignment explanation
Indices: 2956691--2956732 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2956681 AAATTCACTC
2956691 CCACTCGCATTTCACTTGGGA
1 CCACTCGCATTTCACTTGGGA
2956712 CCACTCGCATTTCACTTGGGA
1 CCACTCGCATTTCACTTGGGA
2956733 TGACTTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.19, T:0.29
Consensus pattern (21 bp):
CCACTCGCATTTCACTTGGGA
Found at i:2958616 original size:2 final size:2
Alignment explanation
Indices: 2958609--2958645 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2958599 TCATAATAAC
2958609 TA TA TA TA -A TA T- 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 TA TA TA TA T
2958646 GAAAATAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2961615 original size:27 final size:28
Alignment explanation
Indices: 2961567--2961633 Score: 93
Period size: 27 Copynumber: 2.4 Consensus size: 28
2961557 TGAAATTCTA
2961567 TTCTTT-TTCTTTTCTTCTTTTTTGAATT
1 TTCTTTCTT-TTTTCTTCTTTTTTGAATT
**
2961595 TTCTTTCTTTTTTCTTC-TTTTTGTCTT
1 TTCTTTCTTTTTTCTTCTTTTTTGAATT
2961622 TTCTTTCTTTTT
1 TTCTTTCTTTTT
2961634 GTACTCCAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 20 0.56
28 14 0.39
29 2 0.06
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (28 bp):
TTCTTTCTTTTTTCTTCTTTTTTGAATT
Found at i:2961623 original size:17 final size:17
Alignment explanation
Indices: 2961604--2961635 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2961594 TTTCTTTCTT
2961604 TTTTC-TTCTTTTTGTC
1 TTTTCTTTCTTTTTGTC
2961620 TTTTCTTTCTTTTTGT
1 TTTTCTTTCTTTTTGT
2961636 ACTCCAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (17 bp):
TTTTCTTTCTTTTTGTC
Found at i:2961633 original size:28 final size:29
Alignment explanation
Indices: 2961567--2961633 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 29
2961557 TGAAATTCTA
*
2961567 TTCTTT-TTCTTTTCTTCTTTTTTGAATT
1 TTCTTTCTTTTTTTCTTCTTTTTTGAATT
**
2961595 TTCTTTC-TTTTTTCTTC-TTTTTGTCTT
1 TTCTTTCTTTTTTTCTTCTTTTTTGAATT
2961622 TTCTTTCTTTTT
1 TTCTTTCTTTTT
2961634 GTACTCCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 15 0.44
28 19 0.56
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (29 bp):
TTCTTTCTTTTTTTCTTCTTTTTTGAATT
Found at i:2964741 original size:2 final size:2
Alignment explanation
Indices: 2964734--2964775 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2964724 ACTATAGATA
2964734 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2964776 GAAAATAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2966080 original size:17 final size:17
Alignment explanation
Indices: 2966058--2966090 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2966048 TAAGAGTTAA
2966058 TTTAA-TAATTGAACTAG
1 TTTAATTAA-TGAACTAG
2966075 TTTAATTAATGAACTA
1 TTTAATTAATGAACTA
2966091 CTTCCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (17 bp):
TTTAATTAATGAACTAG
Found at i:2970737 original size:8 final size:7
Alignment explanation
Indices: 2970711--2970736 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2970701 AAGAAAAAAG
2970711 AAAAATA
1 AAAAATA
2970718 AAAAATA
1 AAAAATA
2970725 AAAAATA
1 AAAAATA
2970732 AAAAA
1 AAAAA
2970737 AGAAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:2970742 original size:14 final size:14
Alignment explanation
Indices: 2970704--2970742 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
2970694 TAACAAGAAG
2970704 AAAAAAGAAAAATA
1 AAAAAAGAAAAATA
2970718 AAAAATA-AAAAATA
1 AAAAA-AGAAAAATA
2970732 AAAAAAGAAAA
1 AAAAAAGAAAA
2970743 GAAAAGACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.87, C:0.00, G:0.05, T:0.08
Consensus pattern (14 bp):
AAAAAAGAAAAATA
Found at i:2970819 original size:22 final size:21
Alignment explanation
Indices: 2970771--2970820 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
2970761 AATTTGGAGT
2970771 GCAAAAGAAAGAAAAAGAATAA
1 GCAAAAGAAAGAAAAAG-ATAA
*
2970793 TCAAAAGCAAAGAAAAAG-TGAA
1 GCAAAAG-AAAGAAAAAGAT-AA
2970815 GCAAAA
1 GCAAAA
2970821 TTGCAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 1 0.04
22 13 0.54
23 10 0.42
ACGTcount: A:0.68, C:0.08, G:0.18, T:0.06
Consensus pattern (21 bp):
GCAAAAGAAAGAAAAAGATAA
Found at i:2980456 original size:24 final size:25
Alignment explanation
Indices: 2980404--2980457 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
2980394 AATTTTTCAT
* * *
2980404 TCAAAGGACGTGTCCTTTAGAGGAC
1 TCAATGGACGTGACCTATAGAGGAC
2980429 -CAATGGACGTGACCTAT-GAGGAC
1 TCAATGGACGTGACCTATAGAGGAC
2980452 TCAATG
1 TCAATG
2980458 ATCATGCCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (25 bp):
TCAATGGACGTGACCTATAGAGGAC
Found at i:2986165 original size:10 final size:11
Alignment explanation
Indices: 2986146--2986175 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
2986136 TTACACCTCC
2986146 TTTTGTTTTTT
1 TTTTGTTTTTT
2986157 TTTTGTTTTTT
1 TTTTGTTTTTT
2986168 TTTATGTT
1 TTT-TGTT
2986176 GTACGTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.87
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:2987901 original size:101 final size:101
Alignment explanation
Indices: 2987726--2987927 Score: 404
Period size: 101 Copynumber: 2.0 Consensus size: 101
2987716 CGTATAGCTC
2987726 AAATCTTCAGCTCATTCCATCTATGAGCTCACGGGTTTCCAGACAACTTTTCACCAATTATTCCT
1 AAATCTTCAGCTCATTCCATCTATGAGCTCACGGGTTTCCAGACAACTTTTCACCAATTATTCCT
2987791 TGTGCTTTCTTAAATGTCCCCATGTAAGTTTCCTTT
66 TGTGCTTTCTTAAATGTCCCCATGTAAGTTTCCTTT
2987827 AAATCTTCAGCTCATTCCATCTATGAGCTCACGGGTTTCCAGACAACTTTTCACCAATTATTCCT
1 AAATCTTCAGCTCATTCCATCTATGAGCTCACGGGTTTCCAGACAACTTTTCACCAATTATTCCT
2987892 TGTGCTTTCTTAAATGTCCCCATGTAAGTTTCCTTT
66 TGTGCTTTCTTAAATGTCCCCATGTAAGTTTCCTTT
2987928 CCTTTGCTTT
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.39
Consensus pattern (101 bp):
AAATCTTCAGCTCATTCCATCTATGAGCTCACGGGTTTCCAGACAACTTTTCACCAATTATTCCT
TGTGCTTTCTTAAATGTCCCCATGTAAGTTTCCTTT
Found at i:2992010 original size:19 final size:18
Alignment explanation
Indices: 2991988--2992034 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
2991978 GCATCATATG
2991988 ATAATGAATAAATATTATT
1 ATAATGAATAAATATTA-T
*
2992007 ATAAT-AACTATATATTAT
1 ATAATGAA-TAAATATTAT
*
2992025 AGAATGAATA
1 ATAATGAATA
2992035 TCAATCAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.38
Consensus pattern (18 bp):
ATAATGAATAAATATTAT
Found at i:3002829 original size:90 final size:88
Alignment explanation
Indices: 3002677--3002846 Score: 286
Period size: 90 Copynumber: 1.9 Consensus size: 88
3002667 ACACACCTTT
*
3002677 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTAAAATTAATTAAATCTATATTTA
*
3002742 ATTAATTAGAATTTAATAATCCTC
66 ATTAATT-GAAATTAATAATCCTC
* *
3002766 TTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTAAAATTAATTAAATTTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTAAAATTAATTAAATCTATATTT
3002831 AATTAATTGAAATTAA
65 AATTAATTGAAATTAA
3002847 ATATTTGGAT
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
89 37 0.49
90 39 0.51
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (88 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTAAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAATAATCCTC
Found at i:3002834 original size:20 final size:21
Alignment explanation
Indices: 3002811--3002879 Score: 70
Period size: 22 Copynumber: 3.3 Consensus size: 21
3002801 TATTATTTAA
3002811 AATTAATT-AAATTTATATTT
1 AATTAATTAAAATTTATATTT
* *
3002831 AATTAATTGAAATTAAATATTT
1 AATTAATTAAAATT-TATATTT
* *
3002853 GGATT-ATTAAAATATATATTT
1 -AATTAATTAAAATTTATATTT
3002874 AATTAA
1 AATTAA
3002880 CTCTAGATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
20 11 0.28
21 12 0.31
22 13 0.33
23 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (21 bp):
AATTAATTAAAATTTATATTT
Found at i:3019180 original size:15 final size:15
Alignment explanation
Indices: 3019160--3019192 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3019150 TGCTCTTGTT
3019160 GAAGAATCAAACCTA
1 GAAGAATCAAACCTA
3019175 GAAGAATCAAACCTA
1 GAAGAATCAAACCTA
3019190 GAA
1 GAA
3019193 AGCTCTAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.55, C:0.18, G:0.15, T:0.12
Consensus pattern (15 bp):
GAAGAATCAAACCTA
Found at i:3026229 original size:21 final size:20
Alignment explanation
Indices: 3026192--3026237 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
3026182 GGAGTTCTAC
3026192 CTTACTTTATCTTATAT-TTA
1 CTTA-TTTATCTTATATATTA
3026212 CTTATTTATGCTGTATATATTA
1 CTTATTTAT-CT-TATATATTA
3026234 -TTAT
1 CTTAT
3026238 GAGCATACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 5 0.22
20 6 0.26
21 9 0.39
22 3 0.13
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.59
Consensus pattern (20 bp):
CTTATTTATCTTATATATTA
Found at i:3027264 original size:19 final size:20
Alignment explanation
Indices: 3027240--3027282 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3027230 AGCATTTATC
*
3027240 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
3027259 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
3027279 TTCA
1 TTCA
3027283 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:3031630 original size:21 final size:21
Alignment explanation
Indices: 3031591--3031630 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3031581 ATGCATTCTT
* * *
3031591 ATTAGCTCATAGACTTTATAC
1 ATTAGCTCACACACATTATAC
3031612 ATTAGCTCACACACATTAT
1 ATTAGCTCACACACATTAT
3031631 GAGATGATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (21 bp):
ATTAGCTCACACACATTATAC
Found at i:3043262 original size:23 final size:26
Alignment explanation
Indices: 3043234--3043285 Score: 83
Period size: 24 Copynumber: 2.1 Consensus size: 26
3043224 TTCAGCAAAG
3043234 AAATTG-AAGCACTC-AAAA-GAAGA
1 AAATTGCAAGCACTCAAAAAGGAAGA
3043257 AAATTGCAAGCACTCAAAAAGGAAGA
1 AAATTGCAAGCACTCAAAAAGGAAGA
3043283 AAA
1 AAA
3043286 GAAAAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 6 0.23
24 8 0.31
25 4 0.15
26 8 0.31
ACGTcount: A:0.58, C:0.13, G:0.17, T:0.12
Consensus pattern (26 bp):
AAATTGCAAGCACTCAAAAAGGAAGA
Found at i:3049608 original size:140 final size:139
Alignment explanation
Indices: 3049374--3049652 Score: 452
Period size: 140 Copynumber: 2.0 Consensus size: 139
3049364 TCAATCTAAG
* *
3049374 GGAGTTCTACTGTACTTTATCTTATATTTACTCATTTATGTAGTATGTATTATTTTGAGAAGACA
1 GGAGTTCTACTGTAATTTATCTTATATTTACTCATTTATGTAGCATGTATTATTTTGAGAAGACA
* *
3049439 TTTGCATATTAGAATATACTTAATTTATCATAACATGTGCACTCATTCTATGGTTTGCATCATTG
66 TTTGCATATTAGAATATACTTAATTTATCATAACATGTGCACTCATTCT-TGATTTGCATCATTA
3049504 ATGATATTCA
130 ATGATATTCA
* *
3049514 GGAGTTCTACCT-TAATTTATCTTATATTTACTCATTTATGTAGCATGTATTATTTTGAGCATAC
1 GGAGTTCTA-CTGTAATTTATCTTATATTTACTCATTTATGTAGCATGTATTATTTTGAGAAGAC
* * *
3049578 ATTTGCATATTAGAATATACTTGATTTATCATAACATGTGCATTCATTCTTTATTTGCATCATTA
65 ATTTGCATATTAGAATATACTTAATTTATCATAACATGTGCACTCATTCTTGATTTGCATCATTA
3049643 ATGATATTCA
130 ATGATATTCA
3049653 TACATATACT
Statistics
Matches: 129, Mismatches: 9, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
139 22 0.17
140 105 0.81
141 2 0.02
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.45
Consensus pattern (139 bp):
GGAGTTCTACTGTAATTTATCTTATATTTACTCATTTATGTAGCATGTATTATTTTGAGAAGACA
TTTGCATATTAGAATATACTTAATTTATCATAACATGTGCACTCATTCTTGATTTGCATCATTAA
TGATATTCA
Found at i:3051144 original size:21 final size:20
Alignment explanation
Indices: 3051111--3051151 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
3051101 AACATTACTA
3051111 TCCATTTCATTTCATTTCTT
1 TCCATTTCATTTCATTTCTT
*
3051131 TCCATTTCCATTTCCTTTCTT
1 TCCATTT-CATTTCATTTCTT
3051152 AATTATCCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.12, C:0.29, G:0.00, T:0.59
Consensus pattern (20 bp):
TCCATTTCATTTCATTTCTT
Found at i:3051585 original size:16 final size:16
Alignment explanation
Indices: 3051564--3051600 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
3051554 GTAAGTTATC
*
3051564 TTCATTTTCTTACTAT
1 TTCATTTCCTTACTAT
*
3051580 TTCATTTCCTTATTAT
1 TTCATTTCCTTACTAT
3051596 TTCAT
1 TTCAT
3051601 CTTTTCTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (16 bp):
TTCATTTCCTTACTAT
Found at i:3059416 original size:10 final size:9
Alignment explanation
Indices: 3059402--3059453 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 9
3059392 GTAAAAAGAA
3059402 AAAAAAAAG
1 AAAAAAAAG
*
3059411 ACAAAATAAG
1 A-AAAAAAAG
**
3059421 AAAAAAATT
1 AAAAAAAAG
3059430 AAAAAAGAAG
1 AAAAAA-AAG
3059440 AAAAGAAAAG
1 AAAA-AAAAG
3059450 AAAA
1 AAAA
3059454 GAAATATTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
9 12 0.35
10 20 0.59
11 2 0.06
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.06
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:3059453 original size:19 final size:18
Alignment explanation
Indices: 3059394--3059453 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
3059384 ATTGGAGTGT
3059394 AAAAAGAA-AAAAAAAAG
1 AAAAAGAAGAAAAAAAAG
*
3059411 ACAAAATAAGAAAAAAATTA-
1 A-AAAAGAAGAAAAAAA--AG
3059431 AAAAAGAAGAAAAGAAAAG
1 AAAAAGAAGAAAA-AAAAG
3059450 AAAA
1 AAAA
3059454 GAAATATTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
17 1 0.03
18 7 0.20
19 22 0.63
20 4 0.11
21 1 0.03
ACGTcount: A:0.82, C:0.02, G:0.12, T:0.05
Consensus pattern (18 bp):
AAAAAGAAGAAAAAAAAG
Found at i:3065308 original size:24 final size:24
Alignment explanation
Indices: 3065281--3065326 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
3065271 CCTCAATGAT
*
3065281 CACAACTTGTGGTACTTCAAGTAA
1 CACAACTTGTGGAACTTCAAGTAA
* * *
3065305 CACATCTTTTTGAACTTCAAGT
1 CACAACTTGTGGAACTTCAAGT
3065327 GGCATAATTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (24 bp):
CACAACTTGTGGAACTTCAAGTAA
Found at i:3071455 original size:16 final size:17
Alignment explanation
Indices: 3071436--3071470 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
3071426 CAAAGCACTC
3071436 AAAAAG-GAAGAAAAAG
1 AAAAAGAGAAGAAAAAG
3071452 -AAAAGAGAAGAAAAAG
1 AAAAAGAGAAGAAAAAG
3071468 AAA
1 AAA
3071471 TAAAGTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.29
16 10 0.59
17 2 0.12
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAAAAGAGAAGAAAAAG
Found at i:3071570 original size:15 final size:15
Alignment explanation
Indices: 3071550--3071585 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3071540 TGATAGAAGG
3071550 TTGTAAAGTGACTTT
1 TTGTAAAGTGACTTT
*
3071565 TTGTAAAGTGAGTTT
1 TTGTAAAGTGACTTT
*
3071580 GTGTAA
1 TTGTAA
3071586 GTAAACCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.03, G:0.25, T:0.44
Consensus pattern (15 bp):
TTGTAAAGTGACTTT
Found at i:3080455 original size:15 final size:15
Alignment explanation
Indices: 3080437--3080484 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 15
3080427 TTTTTTGAAA
3080437 TTTTGGCTTTTTTGT
1 TTTTGGCTTTTTTGT
*
3080452 TTTT-G-TTTTTTTT
1 TTTTGGCTTTTTTGT
*
3080465 TTTTGTCTTTTTTTGT
1 TTTTGGC-TTTTTTGT
3080481 TTTT
1 TTTT
3080485 TTTAAATAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 11 0.41
14 1 0.04
15 4 0.15
16 11 0.41
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.83
Consensus pattern (15 bp):
TTTTGGCTTTTTTGT
Found at i:3080466 original size:19 final size:20
Alignment explanation
Indices: 3080444--3080487 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
3080434 AAATTTTGGC
3080444 TTTTTTGT-TTTTGTTT-TTT
1 TTTTTTGTCTTTT-TTTGTTT
3080463 TTTTTTGTCTTTTTTTGTTT
1 TTTTTTGTCTTTTTTTGTTT
3080483 TTTTT
1 TTTTT
3080488 AAATAGCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (20 bp):
TTTTTTGTCTTTTTTTGTTT
Found at i:3082998 original size:12 final size:13
Alignment explanation
Indices: 3082974--3083006 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3082964 ATCCTTATTC
3082974 TTTCATTTCATCA
1 TTTCATTTCATCA
*
3082987 TTT-ATTTTATCA
1 TTTCATTTCATCA
3082999 TTTCATTT
1 TTTCATTT
3083007 ATCCATTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTCATTTCATCA
Found at i:3083274 original size:13 final size:12
Alignment explanation
Indices: 3083258--3083317 Score: 66
Period size: 13 Copynumber: 4.7 Consensus size: 12
3083248 ATTGGAGTGC
*
3083258 AAAAAGAAAGAA
1 AAAAAAAAAGAA
3083270 AAAAACAAAAGAA
1 AAAAA-AAAAGAA
3083283 GAAAAAAAAAGAA
1 -AAAAAAAAAGAA
*
3083296 GAAAAGAAAAGAA
1 -AAAAAAAAAGAA
3083309 AAAGAAAAA
1 AAA-AAAAA
3083318 TTCAAAAAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
12 8 0.19
13 29 0.69
14 5 0.12
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:3083286 original size:16 final size:15
Alignment explanation
Indices: 3083258--3083317 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 15
3083248 ATTGGAGTGC
3083258 AAAAAGAAAGAAAAAA
1 AAAAAG-AAGAAAAAA
3083274 ACAAAAGAAG--AAAA
1 A-AAAAGAAGAAAAAA
3083288 AAAAAGAAGAAAAGAA
1 AAAAAGAAGAAAA-AA
3083304 AAGAAA-AAGAAAAA
1 AA-AAAGAAGAAAAA
3083318 TTCAAAAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
13 8 0.21
14 5 0.13
15 3 0.08
16 15 0.38
17 8 0.21
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAGAAGAAAAAA
Found at i:3083287 original size:26 final size:26
Alignment explanation
Indices: 3083258--3083317 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
3083248 ATTGGAGTGC
*
3083258 AAAAAGAAAGAAAAAAACAAAAGAAG
1 AAAAAAAAAGAAAAAAACAAAAGAAG
* *
3083284 AAAAAAAAAGAAGAAAAGAAAAGAA-
1 AAAAAAAAAGAAAAAAACAAAAGAAG
*
3083309 AAAGAAAAA
1 AAAAAAAAA
3083318 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 8 0.27
26 22 0.73
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (26 bp):
AAAAAAAAAGAAAAAAACAAAAGAAG
Found at i:3101963 original size:23 final size:23
Alignment explanation
Indices: 3101932--3101990 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
3101922 CTTTTTGAAA
*
3101932 TTCTATTCTTTTTCTTTTCTTCTT
1 TTCT-TTCTTTTTCTTTTCTTCAT
* * *
3101956 TTTTTTCTTCTTCTTTTTTTCAT
1 TTCTTTCTTTTTCTTTTCTTCAT
3101979 TTCTTTCTTTTT
1 TTCTTTCTTTTT
3101991 GTACTCCAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
23 26 0.90
24 3 0.10
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (23 bp):
TTCTTTCTTTTTCTTTTCTTCAT
Found at i:3101966 original size:15 final size:14
Alignment explanation
Indices: 3101937--3101990 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
3101927 TGAAATTCTA
*
3101937 TTCTTTTTCTTTTC
1 TTCTTTTTTTTTTC
3101951 TTCTTTTTTTTCTTC
1 TTCTTTTTTTT-TTC
3101966 TTCTTTTTTTCATTTC
1 TTCTTTTTTT--TTTC
3101982 TTTCTTTTT
1 -TTCTTTTT
3101991 GTACTCCAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
14 10 0.29
15 13 0.37
16 3 0.09
17 9 0.26
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.80
Consensus pattern (14 bp):
TTCTTTTTTTTTTC
Found at i:3115294 original size:23 final size:24
Alignment explanation
Indices: 3115245--3115297 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
3115235 TTCTTTGCTT
* *
3115245 TTTC-TTCTTTTGAGTGCTGGATT
1 TTTCTTTCTTTTGAGTGCTGCATC
*
3115268 TTTCTTTCTTTTGAGTGCTTCA-C
1 TTTCTTTCTTTTGAGTGCTGCATC
3115291 TTTCTTT
1 TTTCTTT
3115298 TCTGATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.08, C:0.17, G:0.15, T:0.60
Consensus pattern (24 bp):
TTTCTTTCTTTTGAGTGCTGCATC
Found at i:3125671 original size:15 final size:15
Alignment explanation
Indices: 3125648--3125686 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3125638 GTACTTCAAC
3125648 TTTCCTTTCCTTTCT
1 TTTCCTTTCCTTTCT
* *
3125663 TTTCTTTTCTTTTCT
1 TTTCCTTTCCTTTCT
3125678 TCTTCCTTT
1 T-TTCCTTT
3125687 TGAGTGCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTCCTTTCCTTTCT
Found at i:3125712 original size:24 final size:25
Alignment explanation
Indices: 3125677--3125725 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
3125667 TTTTCTTTTC
*
3125677 TTCTTCCTTTTGAGTGCTTGAATTT
1 TTCTTCCTTTTGAGTGCTTCAATTT
3125702 TTCTT-CTTTTGAGTGCTTCAATTT
1 TTCTTCCTTTTGAGTGCTTCAATTT
3125726 CTTTACTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.12, C:0.16, G:0.14, T:0.57
Consensus pattern (25 bp):
TTCTTCCTTTTGAGTGCTTCAATTT
Found at i:3132014 original size:19 final size:20
Alignment explanation
Indices: 3131986--3132023 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3131976 TATTTAAATT
*
3131986 AATTATAAACTTTT-TTTTG
1 AATTAAAAACTTTTATTTTG
3132005 AATTAAAAACTTTTATTTT
1 AATTAAAAACTTTTATTTT
3132024 TTATATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (20 bp):
AATTAAAAACTTTTATTTTG
Found at i:3137024 original size:17 final size:17
Alignment explanation
Indices: 3137004--3137036 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3136994 ATGAGTTAGA
3137004 TTAATAAATGAACTAGT
1 TTAATAAATGAACTAGT
*
3137021 TTAATTAATGAACTAG
1 TTAATAAATGAACTAG
3137037 ATACATGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (17 bp):
TTAATAAATGAACTAGT
Found at i:3137484 original size:23 final size:23
Alignment explanation
Indices: 3137458--3137502 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3137448 GCTTAGTAGT
3137458 TATTTTAAGTGA-ATATGAAAGGC
1 TATTTTAA-TGATATATGAAAGGC
*
3137481 TATTTTTATGATATATGAAAGG
1 TATTTTAATGATATATGAAAGG
3137503 TTATGGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.38, C:0.02, G:0.20, T:0.40
Consensus pattern (23 bp):
TATTTTAATGATATATGAAAGGC
Found at i:3149584 original size:20 final size:20
Alignment explanation
Indices: 3149559--3149601 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
3149549 TAAATGATTA
3149559 AAATGGAAAT-ATGAAAAAAG
1 AAATGGAAATGAT-AAAAAAG
*
3149579 AAATGGAAATGATAAGAAAG
1 AAATGGAAATGATAAAAAAG
3149599 AAA
1 AAA
3149602 ATAGCAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.14
Consensus pattern (20 bp):
AAATGGAAATGATAAAAAAG
Found at i:3152829 original size:24 final size:24
Alignment explanation
Indices: 3152802--3152854 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
3152792 AATCAGCCAT
* *
3152802 GAAAAGTCAAGCACTCCAAAATAA
1 GAAAAGTCAAGCACTCAAAAAGAA
3152826 GAAAAGTCAAGCACTCAAAAAGAA
1 GAAAAGTCAAGCACTCAAAAAGAA
3152850 GAAAA
1 GAAAA
3152855 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.58, C:0.17, G:0.15, T:0.09
Consensus pattern (24 bp):
GAAAAGTCAAGCACTCAAAAAGAA
Found at i:3153046 original size:34 final size:34
Alignment explanation
Indices: 3152971--3153046 Score: 118
Period size: 34 Copynumber: 2.2 Consensus size: 34
3152961 TGTGTAAGTA
3152971 ACCCTTTCTGTTCTATTCTTTCTATTTCTAAGAC
1 ACCCTTTCTGTTCTATTCTTTCTATTTCTAAGAC
* *
3153005 ACTCTTTCTGTTCTCTTCTTTCTATTTCTAAG-C
1 ACCCTTTCTGTTCTATTCTTTCTATTTCTAAGAC
3153038 TACCCTTTC
1 -ACCCTTTC
3153047 ATTATATTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 1 0.03
34 37 0.97
ACGTcount: A:0.14, C:0.29, G:0.05, T:0.51
Consensus pattern (34 bp):
ACCCTTTCTGTTCTATTCTTTCTATTTCTAAGAC
Found at i:3159115 original size:20 final size:19
Alignment explanation
Indices: 3159078--3159115 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
3159068 TTGAAATCAC
3159078 TAAAAAAAAGGAAGAAAAA
1 TAAAAAAAAGGAAGAAAAA
3159097 TAAAATAAAA-GAAGAAAAA
1 TAAAA-AAAAGGAAGAAAAA
3159116 GAAAGAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (19 bp):
TAAAAAAAAGGAAGAAAAA
Found at i:3160533 original size:258 final size:254
Alignment explanation
Indices: 3160048--3160559 Score: 940
Period size: 258 Copynumber: 2.0 Consensus size: 254
3160038 TTTCTTTATA
3160048 CCATAGTTATGATAATAGCTTACATACATTATATTTATAGTTATGATGATGATATTATGAATGTA
1 CCATAGTTATGATAATAGCTTACATACATTATATTTATAGTTATGATGATGATATTATGAATGTA
3160113 TGAGTTATTATTATGAACCCAACATATTTATATATTATATCTATTACTTAGCTTATAAATGCTTT
66 TGAGTTATTATTATGAACCCAACATATTTATATATTATATCTATTACTTAGCTTATAAATGCTTT
3160178 ATTTTATAGGAACATGTTCGGCCACATCATGGGAGCGTGACTTAAAGCTAGTATTAGAGTCAATG
131 ATTTTATAGGAACATGTTCGGCCACATCATGGGAGCGTGACTTAAAGCTAGTATTAGAGTCAATG
3160243 AGCTAAGGAAACTTGACTAGGACAACTCCGGGACAGCTCAAGGACATTTTGAGACAAAG
196 AGCTAAGGAAACTTGACTAGGACAACTCCGGGACAGCTCAAGGACATTTTGAGACAAAG
3160302 CCATAGTTATGATAATAGCTTACATACATTATATTTATAGTTATGATGATGATATTATGAATGTA
1 CCATAGTTATGATAATAGCTTACATACATTATATTTATAGTTATGATGATGATATTATGAATGTA
3160367 TGAAGTTATTATTATGAA-CC-ACATATTTATATATATTTATATCTTATATTACTTAGCTTATAA
66 TG-AGTTATTATTATGAACCCAACATA-TT-TATATA-TTATATC---TATTACTTAGCTTATAA
3160430 ATGCTTTATTTTATAGGAACATGTTCGGCCACATCATGGGAGC-TGACTTAAAGCTAGTATTAGA
124 ATGCTTTATTTTATAGGAACATGTTCGGCCACATCATGGGAGCGTGACTTAAAGCTAGTATTAGA
3160494 GTCAATGAGCTAAGGAAACTTGACTAGGACAACTCCGGGACAGCTCAAGGACATTTTGAGACAAA
189 GTCAATGAGCTAAGGAAACTTGACTAGGACAACTCCGGGACAGCTCAAGGACATTTTGAGACAAA
3160559 G
254 G
3160560 TTACCAGTTG
Statistics
Matches: 251, Mismatches: 0, Indels: 10
0.96 0.00 0.04
Matches are distributed among these distances:
253 5 0.02
254 71 0.28
255 21 0.08
256 7 0.03
258 87 0.35
259 60 0.24
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Consensus pattern (254 bp):
CCATAGTTATGATAATAGCTTACATACATTATATTTATAGTTATGATGATGATATTATGAATGTA
TGAGTTATTATTATGAACCCAACATATTTATATATTATATCTATTACTTAGCTTATAAATGCTTT
ATTTTATAGGAACATGTTCGGCCACATCATGGGAGCGTGACTTAAAGCTAGTATTAGAGTCAATG
AGCTAAGGAAACTTGACTAGGACAACTCCGGGACAGCTCAAGGACATTTTGAGACAAAG
Found at i:3167247 original size:24 final size:23
Alignment explanation
Indices: 3167200--3167247 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
3167190 AAGAAATCAC
**
3167200 AGCACTCAAAAGAAGAAATTGAA
1 AGCACTCAAAAGAAGAAAAAGAA
3167223 AGCACTCAAAAAGAAGAAAAAGAA
1 AGCACTC-AAAAGAAGAAAAAGAA
3167247 A
1 A
3167248 AGAAAGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.62, C:0.12, G:0.17, T:0.08
Consensus pattern (23 bp):
AGCACTCAAAAGAAGAAAAAGAA
Found at i:3173611 original size:22 final size:24
Alignment explanation
Indices: 3173564--3173615 Score: 81
Period size: 22 Copynumber: 2.2 Consensus size: 24
3173554 TTCTTTTCTT
3173564 TTTCTTCTTTTTGAGTACTTTCAA
1 TTTCTTCTTTTTGAGTACTTTCAA
*
3173588 TTTCTTC-TTTTGAGTGC-TTCAA
1 TTTCTTCTTTTTGAGTACTTTCAA
3173610 TTTCTT
1 TTTCTT
3173616 TTATGGATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 11 0.41
23 9 0.33
24 7 0.26
ACGTcount: A:0.13, C:0.17, G:0.10, T:0.60
Consensus pattern (24 bp):
TTTCTTCTTTTTGAGTACTTTCAA
Found at i:3176099 original size:22 final size:21
Alignment explanation
Indices: 3176062--3176103 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
3176052 CCATCTTTAT
3176062 TTCATCATCAACACCATCAAC
1 TTCATCATCAACACCATCAAC
*
3176083 TTCATCCATCAAGACCATCAA
1 TTCAT-CATCAACACCATCAA
3176104 TTCTGCAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.38, C:0.36, G:0.02, T:0.24
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:3179078 original size:19 final size:20
Alignment explanation
Indices: 3179031--3179081 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
3179021 AAAATCCCTT
**
3179031 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
3179051 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
3179070 TGAAGATACATG
1 TGAAAATACATG
3179082 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:3184102 original size:29 final size:29
Alignment explanation
Indices: 3184068--3184123 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
3184058 AATGATTAAG
3184068 CATGCTTCCATTTCATGAATGTATTGATT
1 CATGCTTCCATTTCATGAATGTATTGATT
3184097 CATGCTTCCATTTCATGAATGTATTGA
1 CATGCTTCCATTTCATGAATGTATTGA
3184124 ATGATATAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (29 bp):
CATGCTTCCATTTCATGAATGTATTGATT
Found at i:3184968 original size:165 final size:167
Alignment explanation
Indices: 3184696--3185027 Score: 650
Period size: 165 Copynumber: 2.0 Consensus size: 167
3184686 TGAAATAATC
3184696 TTCAATGCTCCGATTTCATTGTTTAAGATTTTGAAGCTTGTGATAAATATCACGGTGATAGTGAG
1 TTCAATGCTCCGATTTCATTGTTTAAGATTTTGAAGCTTGTGATAAATATCACGGTGATAGTGAG
3184761 TAGGCACGAACCTTTTCCTCATAATGGCCTTCATTTCTTCATAAGTATTGATTGGTCGTTCACCA
66 TAGGCACGAACCTTTTCCTCATAATGGCCTTCATTTCTTCATAAGTATTGATTGGTCGTTCACCA
3184826 TTTCTTCTTCTCGAAC-T-CTAATTGGTCCCACCAAA
131 TTTCTTCTTCTCGAACTTACTAATTGGTCCCACCAAA
3184861 TTCAATGCTCCGATTTCATTGTTTAAGATTTTGAAGCTTGTGATAAATATCACGGTGATAGTGAG
1 TTCAATGCTCCGATTTCATTGTTTAAGATTTTGAAGCTTGTGATAAATATCACGGTGATAGTGAG
3184926 TAGGCACGAACCTTTTCCTCATAATGGCCTTCATTTCTTCATAAGTATTGATTGGTCGTTCACCA
66 TAGGCACGAACCTTTTCCTCATAATGGCCTTCATTTCTTCATAAGTATTGATTGGTCGTTCACCA
3184991 TTTCTTCTTCTCGAACTTACTAATTGGTCCCACCAAA
131 TTTCTTCTTCTCGAACTTACTAATTGGTCCCACCAAA
3185028 CATTGGCGTA
Statistics
Matches: 165, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
165 146 0.88
166 1 0.01
167 18 0.11
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (167 bp):
TTCAATGCTCCGATTTCATTGTTTAAGATTTTGAAGCTTGTGATAAATATCACGGTGATAGTGAG
TAGGCACGAACCTTTTCCTCATAATGGCCTTCATTTCTTCATAAGTATTGATTGGTCGTTCACCA
TTTCTTCTTCTCGAACTTACTAATTGGTCCCACCAAA
Found at i:3185685 original size:21 final size:21
Alignment explanation
Indices: 3185625--3185676 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
3185615 AAGGAAGATT
3185625 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAGATAAGG
3185646 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAGATAAGG
3185667 AATGAAATGA
1 AATGAAATGA
3185677 AATAAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.58, C:0.00, G:0.23, T:0.19
Consensus pattern (21 bp):
AATGAAATGATAAAGATAAGG
Found at i:3185734 original size:22 final size:21
Alignment explanation
Indices: 3185708--3185748 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3185698 GCTACAGAAT
3185708 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
3185730 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
3185749 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:3194040 original size:5 final size:5
Alignment explanation
Indices: 3194030--3194080 Score: 59
Period size: 5 Copynumber: 9.8 Consensus size: 5
3194020 CTTTTTGAAA
*
3194030 TTTTC TTTTC TTTTC TTTAC TTTTTC TTCTT- TTTATC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC -TTTTC TT-TTC TTT-TC TTTTC TTTTC
3194077 TTTT
1 TTTT
3194081 TGCACTCCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 1 0.03
5 30 0.75
6 9 0.22
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:3194054 original size:16 final size:16
Alignment explanation
Indices: 3194033--3194079 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
3194023 TTTGAAATTT
3194033 TCTTTTCTTTTCTTTA
1 TCTTTTCTTTTCTTTA
3194049 -CTTTTTCTTCTT-TTTA
1 TC-TTTTCTT-TTCTTTA
3194065 TCTTTTCTTTTCTTT
1 TCTTTTCTTTTCTTT
3194080 TTGCACTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
15 3 0.11
16 21 0.78
17 3 0.11
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (16 bp):
TCTTTTCTTTTCTTTA
Found at i:3194370 original size:21 final size:21
Alignment explanation
Indices: 3194331--3194370 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3194321 AAGGAAGATT
*
3194331 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
3194352 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
3194371 AGGATAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:3194421 original size:22 final size:21
Alignment explanation
Indices: 3194393--3194433 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3194383 GATACAGAAC
3194393 TGATGGTCTTGATGGATGAATA
1 TGATGGTCTTGAT-GATGAATA
*
3194415 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
3194434 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.34, T:0.37
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAATA
Found at i:3210460 original size:21 final size:21
Alignment explanation
Indices: 3210421--3210460 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3210411 AAGGAAGATT
*
3210421 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
3210442 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
3210461 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:3212815 original size:19 final size:20
Alignment explanation
Indices: 3212791--3212833 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3212781 AGCATTTATC
*
3212791 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
3212810 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
3212830 TTCA
1 TTCA
3212834 AAGGGTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:3214079 original size:25 final size:25
Alignment explanation
Indices: 3214051--3214102 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
3214041 TAAGCGAAAA
3214051 AAAGCAAATGAGAGGGTGAGTTCAG
1 AAAGCAAATGAGAGGGTGAGTTCAG
3214076 AAAGCAAATGAGAGGGTGAGTTCAG
1 AAAGCAAATGAGAGGGTGAGTTCAG
3214101 AA
1 AA
3214103 GGGGGATCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.35, T:0.15
Consensus pattern (25 bp):
AAAGCAAATGAGAGGGTGAGTTCAG
Found at i:3214914 original size:24 final size:24
Alignment explanation
Indices: 3214887--3214940 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
3214877 GAATGATGGT
3214887 TTTTGGAGAACTAAA-AGATGTGAC
1 TTTTGGAGAAC-AAATAGATGTGAC
** * *
3214911 TTTTAAAGAACAAATAGTTGTTAC
1 TTTTGGAGAACAAATAGATGTGAC
3214935 TTTTGG
1 TTTTGG
3214941 TGATCAACGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.37
Consensus pattern (24 bp):
TTTTGGAGAACAAATAGATGTGAC
Found at i:3218433 original size:13 final size:13
Alignment explanation
Indices: 3218415--3218441 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3218405 CTCTATCCTT
3218415 TCTTATTCTTTCA
1 TCTTATTCTTTCA
3218428 TCTTATTCTTTCA
1 TCTTATTCTTTCA
3218441 T
1 T
3218442 TACTATATAT
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:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (13 bp):
TCTTATTCTTTCA
Found at i:3218765 original size:20 final size:21
Alignment explanation
Indices: 3218717--3218765 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
3218707 GTGCAAAAAG
*
3218717 AAAGAAAAAGACAAAAGAAGGA
1 AAAG-AAAACACAAAAGAAGGA
*
3218739 AAA-AAAACACAAAAGGA-GA
1 AAAGAAAACACAAAAGAAGGA
3218758 AAAGAAAA
1 AAAGAAAA
3218766 GAAAAATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 5 0.21
20 16 0.67
22 3 0.12
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (21 bp):
AAAGAAAACACAAAAGAAGGA
Found at i:3222912 original size:17 final size:16
Alignment explanation
Indices: 3222877--3222919 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3222867 TATCCTTTCT
* *
3222877 TTATTTCATTTTATTC
1 TTATTTTATTTCATTC
3222893 TTATTTTATTTCATTAC
1 TTATTTTATTTCATT-C
*
3222910 TTATATTATT
1 TTATTTTATT
3222920 ATTCCCTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTTTATTTCATTC
Found at i:3224381 original size:27 final size:27
Alignment explanation
Indices: 3224351--3224402 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
3224341 ACTATGAATA
3224351 AATATGCATTGAATGAGTTATATAATG
1 AATATGCATTGAATGAGTTATATAATG
3224378 AATATGCATTGAATGAGTTATATAA
1 AATATGCATTGAATGAGTTATATAA
3224403 AGATGTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.37
Consensus pattern (27 bp):
AATATGCATTGAATGAGTTATATAATG
Found at i:3230338 original size:19 final size:20
Alignment explanation
Indices: 3230314--3230356 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3230304 AGCATTTATG
*
3230314 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
3230333 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
3230353 TTCA
1 TTCA
3230357 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:3233208 original size:14 final size:14
Alignment explanation
Indices: 3233189--3233230 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
3233179 TATGATACTA
3233189 TTTCCATCACCATC
1 TTTCCATCACCATC
3233203 TTTCCATCACCATC
1 TTTCCATCACCATC
3233217 TTTCCATCACCATC
1 TTTCCATCACCATC
3233231 CTTGATGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.21, C:0.43, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:3234113 original size:110 final size:110
Alignment explanation
Indices: 3233920--3234139 Score: 440
Period size: 110 Copynumber: 2.0 Consensus size: 110
3233910 ACCTTTGTTT
3233920 TGTTATTATATTTTCCACTTAATCAAGCAAAGAAGAAGGCAAACTCACACCACATACAATAGAAC
1 TGTTATTATATTTTCCACTTAATCAAGCAAAGAAGAAGGCAAACTCACACCACATACAATAGAAC
3233985 TTAAGGACAGCCCATGTGCGTGAGAGAACAAGGCACTACAAACAG
66 TTAAGGACAGCCCATGTGCGTGAGAGAACAAGGCACTACAAACAG
3234030 TGTTATTATATTTTCCACTTAATCAAGCAAAGAAGAAGGCAAACTCACACCACATACAATAGAAC
1 TGTTATTATATTTTCCACTTAATCAAGCAAAGAAGAAGGCAAACTCACACCACATACAATAGAAC
3234095 TTAAGGACAGCCCATGTGCGTGAGAGAACAAGGCACTACAAACAG
66 TTAAGGACAGCCCATGTGCGTGAGAGAACAAGGCACTACAAACAG
3234140 CCATTGTGCT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 110 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (110 bp):
TGTTATTATATTTTCCACTTAATCAAGCAAAGAAGAAGGCAAACTCACACCACATACAATAGAAC
TTAAGGACAGCCCATGTGCGTGAGAGAACAAGGCACTACAAACAG
Found at i:3235789 original size:10 final size:10
Alignment explanation
Indices: 3235774--3235799 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3235764 ACTCAAACAG
3235774 AAGAAAAGGA
1 AAGAAAAGGA
3235784 AAGAAAAGGA
1 AAGAAAAGGA
3235794 AAGAAA
1 AAGAAA
3235800 GAAAGTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (10 bp):
AAGAAAAGGA
Found at i:3235897 original size:30 final size:31
Alignment explanation
Indices: 3235837--3235898 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
3235827 TCATCACCAA
3235837 GCCATTCAAGTAAGTCTTTTAGATTGATTAT
1 GCCATTCAAGTAAGTCTTTTAGATTGATTAT
3235868 GCCATTCAAGTAAGTCTTTTAGA-TGATTAT
1 GCCATTCAAGTAAGTCTTTTAGATTGATTAT
3235898 G
1 G
3235899 GTGATAGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (31 bp):
GCCATTCAAGTAAGTCTTTTAGATTGATTAT
Found at i:3239061 original size:91 final size:91
Alignment explanation
Indices: 3238810--3239082 Score: 404
Period size: 90 Copynumber: 3.0 Consensus size: 91
3238800 CCTAGAACAC
** * * * * *
3238810 CCATGTGCCTTGCATATGACCATACCCCATGTGCCTTTCATGTGGATCATTTAGGCGCCAAGATA
1 CCATGTGTTTTGCATGTGATCATCCCCCATGTGCCTTACATGTGGATCATTTAGGCGCCAAGATG
* *
3238875 AAGAGTTCTCTCCCTATTCAGACAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
*
3238901 CCATGTGTTTTGCATGTGATCA-CCCCCATGTGCCTTACATGTGGATCATTTAGGTGCCAAGATG
1 CCATGTGTTTTGCATGTGATCATCCCCCATGTGCCTTACATGTGGATCATTTAGGCGCCAAGATG
*
3238965 AAGAGTTGTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
* * *
3238991 CCATGTGTTTTGCATGTGATCATCCCCCATGTGCCTTGCATGTGGTTCATTTAGGCACCAAGATG
1 CCATGTGTTTTGCATGTGATCATCCCCCATGTGCCTTACATGTGGATCATTTAGGCGCCAAGATG
*
3239056 AAGAGTTCTCTCCCTATTCGGCAAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
3239082 C
1 C
3239083 ATCAACTACC
Statistics
Matches: 164, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
90 83 0.51
91 81 0.49
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.30
Consensus pattern (91 bp):
CCATGTGTTTTGCATGTGATCATCCCCCATGTGCCTTACATGTGGATCATTTAGGCGCCAAGATG
AAGAGTTCTCTCCCTATTCGGCCAAG
Found at i:3242386 original size:11 final size:13
Alignment explanation
Indices: 3242352--3242383 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3242342 TTTGGCCAAA
3242352 GTTGAAAAGGTAT
1 GTTGAAAAGGTAT
3242365 GTTGAAAAGGTAT
1 GTTGAAAAGGTAT
3242378 G-TGAAA
1 GTTGAAA
3242384 GGTGTCTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (13 bp):
GTTGAAAAGGTAT
Found at i:3246391 original size:22 final size:23
Alignment explanation
Indices: 3246363--3246406 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3246353 AAATCCATCA
*
3246363 AAGAAA-TCACAACACTCAAAAG
1 AAGAAATTCAAAACACTCAAAAG
*
3246385 AAGAAATTGAAAACACTCAAAA
1 AAGAAATTCAAAACACTCAAAA
3246407 AGATGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.61, C:0.18, G:0.09, T:0.11
Consensus pattern (23 bp):
AAGAAATTCAAAACACTCAAAAG
Found at i:3246420 original size:24 final size:23
Alignment explanation
Indices: 3246373--3246421 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
3246363 AAGAAATCAC
**
3246373 AACACTCAAAAGAAGAAATTGAA
1 AACACTCAAAAGAAGAAAAAGAA
*
3246396 AACACTCAAAAAGATGAAAAAGAA
1 AACACTC-AAAAGAAGAAAAAGAA
3246420 AA
1 AA
3246422 GAAAGAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.65, C:0.12, G:0.12, T:0.10
Consensus pattern (23 bp):
AACACTCAAAAGAAGAAAAAGAA
Found at i:3248090 original size:22 final size:21
Alignment explanation
Indices: 3248064--3248104 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3248054 GCTACGGAAA
3248064 TGATGGTCTTGATGGATGAAGT
1 TGATGGTCTTGAT-GATGAAGT
*
3248086 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
3248105 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.24, C:0.02, G:0.37, T:0.37
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGT
Found at i:3248831 original size:23 final size:23
Alignment explanation
Indices: 3248786--3248831 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3248776 TTATAACTAT
*
3248786 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
3248809 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
3248832 TATATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:3250475 original size:17 final size:18
Alignment explanation
Indices: 3250455--3250505 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
3250445 AATTGGAGTG
*
3250455 CAAAAAGAAAGAAAATA-
1 CAAAAAGAAAGAAAAAAT
3250472 CAAAAAGAAGAGAAAAAAT
1 CAAAAAGAA-AGAAAAAAT
3250491 CAGAAAAG-AAGAAAA
1 CA-AAAAGAAAGAAAA
3250506 GAAAAGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 9 0.30
18 13 0.43
19 3 0.10
20 5 0.17
ACGTcount: A:0.75, C:0.06, G:0.16, T:0.04
Consensus pattern (18 bp):
CAAAAAGAAAGAAAAAAT
Found at i:3250489 original size:20 final size:17
Alignment explanation
Indices: 3250455--3250502 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 17
3250445 AATTGGAGTG
3250455 CAAAAAGAA-AGAAAAT
1 CAAAAAGAAGAGAAAAT
3250471 ACAAAAAGAAGAGAAAAAAT
1 -CAAAAAGAAGAG--AAAAT
3250491 CAGAAAAGAAGA
1 CA-AAAAGAAGA
3250503 AAAGAAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.33
18 2 0.07
19 2 0.07
20 14 0.52
ACGTcount: A:0.73, C:0.06, G:0.17, T:0.04
Consensus pattern (17 bp):
CAAAAAGAAGAGAAAAT
Found at i:3253454 original size:23 final size:23
Alignment explanation
Indices: 3253409--3253454 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3253399 TTATACCTAT
*
3253409 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
3253432 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
3253455 TATATTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:3254802 original size:24 final size:24
Alignment explanation
Indices: 3254768--3254826 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
3254758 TCATCCTTTC
3254768 TTTA-TTTCATTTCATTCTTATTA
1 TTTATTTTCATTTCATTCTTATTA
3254791 TTTATTTTCATTTCATTCTTATTA
1 TTTATTTTCATTTCATTCTTATTA
3254815 TTTATTTTCATT
1 TTTATTTTCATT
3254827 ACTTATATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 4 0.11
24 31 0.89
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTATTTTCATTTCATTCTTATTA
Found at i:3254840 original size:28 final size:24
Alignment explanation
Indices: 3254768--3254840 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 24
3254758 TCATCCTTTC
*
3254768 TTTA-TTTCATTTCATTCTTATTA
1 TTTATTTTCATTTCATTATTATTA
*
3254791 TTTATTTTCATTTCATTCTTATTA
1 TTTATTTTCATTTCATTATTATTA
* *
3254815 TTTATTTTCATTACTTATATTATTA
1 TTTATTTTCATTTCAT-TATTATTA
3254840 T
1 T
3254841 CCCCTTTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 4 0.09
24 33 0.73
25 8 0.18
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTATTTTCATTTCATTATTATTA
Found at i:3259533 original size:17 final size:17
Alignment explanation
Indices: 3259505--3259547 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3259495 TCTTGGCTTG
*
3259505 TTTTCTCTTTTTGATTT
1 TTTTCTTTTTTTGATTT
**
3259522 TTTTCTTTTTTTTCTTT
1 TTTTCTTTTTTTGATTT
*
3259539 TATTCTTTT
1 TTTTCTTTT
3259548 CTGAATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (17 bp):
TTTTCTTTTTTTGATTT
Done.