Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008724.1 Hibiscus syriacus cultivar Beakdansim tig00111783_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: 5289199
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 23
Found at i:2221447 original size:118 final size:117
Alignment explanation
Indices: 2221237--2222043 Score: 1159
Period size: 118 Copynumber: 6.9 Consensus size: 117
2221227 AGAAAAAATA
* * *
2221237 ATCTCAAGTGAGAT-AAATATTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAAATATTCTG
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTCTG
* *
2221301 TTTCGAGTGAAACTATCTCAAGCTAGATAAAATCTTATGTTTCGGGTGAAACT
65 TTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGTGAAACT
* * *
2221354 ATCTCAAGCGAGATAAAAATCTTATGTTTCGAGTGAAAGTATCTCAAGCGAGATAAAATCTTTTG
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTG
* * * * * *
2221419 TTTCGAGTGAAAGTATCTAAAGCGAGATAAAATCTTCTGTTTTGACTGCAACT
65 TTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGTGAAACT
* * *
2221472 ATCTCAAGCGAGATAAAAATATTTTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTC
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTG
*
2221537 TTTCGAGTGAAACTATCTCAAGAGAGATAAAAATCTTATGTTTCGAGTGAAACT
65 TTTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTATGTTTCGAGTGAAACT
* *
2221591 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGGGATAAAATATTCTGT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGT
*
2221656 TTCGAGTGAAACTATCTCAAGCGAGATAAAAATCTTATGTTTCAAGTGAAACT
66 TTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTATGTTTCGAGTGAAACT
* * * *
2221709 ATCTTAAGCAAGATAAAATCTTCTATTTCGAGTGAAACTATCTCAAGCCAGATAAAATCTTCTGT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGT
* *
2221774 TTCGAGTGAAACTATCTCAAGCGAGAT-AGATCTTCTGTTTCGAGTGAAACT
66 TTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGTGAAACT
* ** * * * * *
2221825 ATCTTAATTGAGATAAAAATCTTTTGTTTTGAGTGAAATTATCTCAAGCGAGATAAAATCTTTTA
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTG
* *
2221890 TTTCGAGTAAAACTATCTCAAGCGAGATAAAAATCTTCTGTTTCGAGTGAAACT
65 TTTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTATGTTTCGAGTGAAACT
* * * *
2221944 ATCTCAAGCGAGATAAAATCTTCTGTTTTGAGTGAAATTATCTCAAGTGAGATAAAATCTTATGT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGT
*
2222009 TTCAAGTGAAACTATCTCAAGCGAGATAAAATCTT
66 TTCGAGTGAAACTATCTCAAGCGAGATAAAATCTT
2222044 GTTTTAAAAA
Statistics
Matches: 621, Mismatches: 63, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
116 32 0.05
117 91 0.15
118 394 0.63
119 104 0.17
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (117 bp):
ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGT
TTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGTGAAACT
Found at i:2221915 original size:19 final size:20
Alignment explanation
Indices: 2221893--2221961 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
2221883 TCTTTTATTT
2221893 CGAG-TAAAACTATCTCAAG
1 CGAGATAAAACTATCTCAAG
****
2221912 CGAGATAAAAATCT-TCTGTTT
1 CGAGAT-AAAA-CTATCTCAAG
*
2221933 CGAG-TGAAACTATCTCAAG
1 CGAGATAAAACTATCTCAAG
2221952 CGAGATAAAA
1 CGAGATAAAA
2221962 TCTTCTGTTT
Statistics
Matches: 35, Mismatches: 10, Indels: 9
0.65 0.19 0.17
Matches are distributed among these distances:
18 2 0.06
19 14 0.40
20 6 0.17
21 11 0.31
22 2 0.06
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (20 bp):
CGAGATAAAACTATCTCAAG
Found at i:2222142 original size:76 final size:76
Alignment explanation
Indices: 2222008--2222212 Score: 283
Period size: 76 Copynumber: 2.7 Consensus size: 76
2221998 AAATCTTATG
* * * *
2222008 TTTCAAGT-GAAACTATCTCAAGCGAGATAAAATCTTGTTTT---AAAAACAATCTTGAGTGAAA
1 TTTCAAGTAAAAACTGTCTCAAGCGAGA-CAAATCTCGTTTTAAGAAAAACAATCTTGAGTGAAA
2222069 TGAAATGTCTTC
65 TGAAATGTCTTC
** *
2222081 TTTTGAGTAAAAACTGTCTCAAGCGAGACAAATCTCGTTTTAAGAAAAACTATCTTGAGTGAAAT
1 TTTCAAGTAAAAACTGTCTCAAGCGAGACAAATCTCGTTTTAAGAAAAACAATCTTGAGTGAAAT
2222146 GAAATGTCTTC
66 GAAATGTCTTC
* *
2222157 TTTCAAGTAAAAACTGTCTCAAGTGAGACAAATCTGGTTTTAAAGAAAAACAATCT
1 TTTCAAGTAAAAACTGTCTCAAGCGAGACAAATCTCGTTTT-AAGAAAAACAATCT
2222213 CAAGTAAGAT
Statistics
Matches: 115, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
73 17 0.15
74 17 0.15
76 68 0.59
77 13 0.11
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (76 bp):
TTTCAAGTAAAAACTGTCTCAAGCGAGACAAATCTCGTTTTAAGAAAAACAATCTTGAGTGAAAT
GAAATGTCTTC
Found at i:2222182 original size:40 final size:39
Alignment explanation
Indices: 2222062--2222182 Score: 122
Period size: 40 Copynumber: 3.1 Consensus size: 39
2222052 AACAATCTTG
*
2222062 AGTGAAATGAAATGTCTTCTTTTGAGTAAAAACTGTCTCA
1 AGTGAAATGAAATGTCTTC-TTTAAGTAAAAACTGTCTCA
* * * * * * **
2222102 AGCGAGA-CAAATCTCGT-TTTAAG-AAAAACTATCTTG
1 AGTGAAATGAAATGTCTTCTTTAAGTAAAAACTGTCTCA
2222138 AGTGAAATGAAATGTCTTCTTTCAAGTAAAAACTGTCTCA
1 AGTGAAATGAAATGTCTTCTTT-AAGTAAAAACTGTCTCA
2222178 AGTGA
1 AGTGA
2222183 GACAAATCTG
Statistics
Matches: 60, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
36 15 0.25
37 12 0.20
38 3 0.05
39 10 0.17
40 20 0.33
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (39 bp):
AGTGAAATGAAATGTCTTCTTTAAGTAAAAACTGTCTCA
Found at i:2222214 original size:37 final size:36
Alignment explanation
Indices: 2222089--2222226 Score: 114
Period size: 37 Copynumber: 3.7 Consensus size: 36
2222079 TCTTTTGAGT
* *
2222089 AAAAACTGTCTCAAGCGAGACAAATCTCGTTTTAAG
1 AAAAACTATCTCAAGTGAGACAAATCTCGTTTTAAG
** * * * *
2222125 AAAAACTATCTTGAGTGAAATGAAATGTCTTCTTTCAAG
1 AAAAACTATCTCAAGTGAGA-CAAATCTCGT-TTT-AAG
* *
2222164 TAAAAACTGTCTCAAGTGAGACAAATCTGGTTTTAAAG
1 -AAAAACTATCTCAAGTGAGACAAATCTCGTTTT-AAG
* * *
2222202 AAAAACAATCTCAAGTAAGATAAAT
1 AAAAACTATCTCAAGTGAGACAAAT
2222227 TTTCTGTATT
Statistics
Matches: 77, Mismatches: 21, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
36 15 0.19
37 28 0.36
38 9 0.12
39 9 0.12
40 16 0.21
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (36 bp):
AAAAACTATCTCAAGTGAGACAAATCTCGTTTTAAG
Found at i:2229690 original size:13 final size:13
Alignment explanation
Indices: 2229674--2229702 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2229664 TGTTTGTGTT
2229674 TTTTTTTTCTTTA
1 TTTTTTTTCTTTA
2229687 TTTTTTTTCTTTA
1 TTTTTTTTCTTTA
2229700 TTT
1 TTT
2229703 ACTTTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTTCTTTA
Found at i:2229694 original size:17 final size:18
Alignment explanation
Indices: 2229672--2229708 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
2229662 AGTGTTTGTG
*
2229672 TTTTTTT-TTTCTTTA-T
1 TTTTTTTCTTTATTTACT
2229688 TTTTTTTCTTTATTTACT
1 TTTTTTTCTTTATTTACT
2229706 TTT
1 TTT
2229709 AATATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 7 0.39
18 4 0.22
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTTTCTTTATTTACT
Found at i:2234558 original size:55 final size:55
Alignment explanation
Indices: 2234487--2235037 Score: 773
Period size: 55 Copynumber: 10.1 Consensus size: 55
2234477 TATATGTTGC
* **
2234487 AATTTTTGTATTGGCACTATGTGCACAACCCCACGAAATTCATAATGAGTTTATG
1 AATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
* * *
2234542 AATTTTCGTATTGGCACTATGTGTGCAACACCATGAAATTCATAAAGAGTTTATG
1 AATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
* * * *
2234597 AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAAATTTATAATGATTTTATG
1 AATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
* *
2234652 AATTTCCATATTGGCACTATGTGTGCAA-CCCACGAAATTCATAATGAGTTTATG
1 AATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
* * *
2234706 AAATTTCGTATTGGCACTATGTGTGCAACCCCATGAAATTCATAATGCGTTTATG
1 AATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
* * * * * * *
2234761 AATTTTTGTATTGGCACTATATGCGTAACCCCATGAAATTCATAACGAGTTTAAG
1 AATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
2234816 AATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
1 AATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
* * * *
2234871 AATTTTCATATTCGCACTAGGTGTGCAACCCCACAAAATTCATAATGAGTTTATG
1 AATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
* * *
2234926 AATTTTTGTATTGGCACTATGTGTGCAACCCCATGAAATGCATAATGAGTTTATG
1 AATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
* * * * * *
2234981 AATTTCCGTATTGGCACTATGTGTGCAA-CCTACGTAATTCACAAAGAGTTTGTG
1 AATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
2235035 AAT
1 AAT
2235038 GACCATATGG
Statistics
Matches: 438, Mismatches: 57, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
54 70 0.16
55 368 0.84
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (55 bp):
AATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
Found at i:2235640 original size:2 final size:2
Alignment explanation
Indices: 2235633--2235661 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2235623 GACGTGTTTA
2235633 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 A
2235662 ATTGAAGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2239710 original size:55 final size:55
Alignment explanation
Indices: 2239634--2239965 Score: 488
Period size: 55 Copynumber: 6.1 Consensus size: 55
2239624 TATATGTTGC
* *
2239634 AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATG
1 AATTTACGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
* *
2239689 AATTTACGTATTGGCATTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATG
1 AATTTACGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
* * * *
2239744 AATTTCCATATTGGCACTATGTATGCAACCCCACGAAATTCCTAATGAGTTTATG
1 AATTTACGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
*
2239799 AATATT-CGTATTGGCACTATGTGTGCAACCCCACGAAATTTATAATGAGTTTATG
1 AAT-TTACGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
* *
2239854 AATTTACGTATTGGCACTATATGTGCAACCCCATGAAATTCATAATGAGTTTATG
1 AATTTACGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
** * * * *
2239909 AATTTTTGTATTGGCACTATGTGTGCAA-CCTACGTAATTCACAATGAGTTTGTG
1 AATTTACGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
2239963 AAT
1 AAT
2239966 GACTGTATCG
Statistics
Matches: 252, Mismatches: 23, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
54 26 0.10
55 224 0.89
56 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (55 bp):
AATTTACGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
Found at i:2244421 original size:13 final size:13
Alignment explanation
Indices: 2244391--2244435 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
2244381 CATGATTTTA
*
2244391 TTATATGT-GATG
1 TTATATGTATATG
*
2244403 TGATATGTATATG
1 TTATATGTATATG
*
2244416 TTATATATATATG
1 TTATATGTATATG
2244429 TTATATG
1 TTATATG
2244436 ATGATGATCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 7 0.26
13 20 0.74
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (13 bp):
TTATATGTATATG
Found at i:2244804 original size:24 final size:24
Alignment explanation
Indices: 2244771--2244871 Score: 114
Period size: 24 Copynumber: 4.2 Consensus size: 24
2244761 GAGTCGAGGG
* *
2244771 TTCTACGCGATCCTTCGGGGACAAA
1 TTCTATGCGATCCTTC-GAGACAAA
*
2244796 -TCTATGCGATCCTTCGAGATAAA
1 TTCTATGCGATCCTTCGAGACAAA
* * * *
2244819 TTCTATGTGGTCCTTCGGGATAAA
1 TTCTATGCGATCCTTCGAGACAAA
*
2244843 TTCTATGCGGTCCTTCGAGACAAA
1 TTCTATGCGATCCTTCGAGACAAA
2244867 TTCTA
1 TTCTA
2244872 CGTGGTACTT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
23 6 0.09
24 60 0.91
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.32
Consensus pattern (24 bp):
TTCTATGCGATCCTTCGAGACAAA
Found at i:2244833 original size:48 final size:48
Alignment explanation
Indices: 2244771--2244877 Score: 144
Period size: 48 Copynumber: 2.2 Consensus size: 48
2244761 GAGTCGAGGG
* * *
2244771 TTCTACGCGATCCTTCGGGGACAAA-TCTATGCGATCCTTCGAGATAAA
1 TTCTACGTGGTCCTTC-GGGACAAATTCTATGCGATCCTTCGAGACAAA
* * *
2244819 TTCTATGTGGTCCTTCGGGATAAATTCTATGCGGTCCTTCGAGACAAA
1 TTCTACGTGGTCCTTCGGGACAAATTCTATGCGATCCTTCGAGACAAA
2244867 TTCTACGTGGT
1 TTCTACGTGGT
2244878 ACTTTGGTGC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
47 7 0.14
48 44 0.86
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.32
Consensus pattern (48 bp):
TTCTACGTGGTCCTTCGGGACAAATTCTATGCGATCCTTCGAGACAAA
Found at i:2246074 original size:50 final size:50
Alignment explanation
Indices: 2245999--2246098 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
2245989 TGGGGACCTT
2245999 CACCTCTCAATTCAAACGGTAGGAAGGTTTAAAGCACCACCGGGAACGTC
1 CACCTCTCAATTCAAACGGTAGGAAGGTTTAAAGCACCACCGGGAACGTC
2246049 CACCTCTCAATTCAAACGGTAGGAAGGTTTAAAGCACCACCGGGAACGTC
1 CACCTCTCAATTCAAACGGTAGGAAGGTTTAAAGCACCACCGGGAACGTC
2246099 ATACCTCAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.18
Consensus pattern (50 bp):
CACCTCTCAATTCAAACGGTAGGAAGGTTTAAAGCACCACCGGGAACGTC
Found at i:2246997 original size:22 final size:22
Alignment explanation
Indices: 2246968--2247015 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2246958 ATTCTTCTTA
* *
2246968 TTTAATTTACTAACTTTGTTTAT
1 TTTATTTTACTAA-TTTATTTAT
*
2246991 TTTATTTTCCTAATTTATTTAT
1 TTTATTTTACTAATTTATTTAT
2247013 TTT
1 TTT
2247016 CCCTTTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTATTTTACTAATTTATTTAT
Found at i:2247947 original size:18 final size:18
Alignment explanation
Indices: 2247918--2247982 Score: 112
Period size: 18 Copynumber: 3.6 Consensus size: 18
2247908 CTTTGCATCC
2247918 ATAATGATTTCTAAATTAA
1 ATAAT-ATTTCTAAATTAA
2247937 ATAATATTTCTAAATTAA
1 ATAATATTTCTAAATTAA
*
2247955 ATAATATTTCGAAATTAA
1 ATAATATTTCTAAATTAA
2247973 ATAATATTTC
1 ATAATATTTC
2247983 AAACTCCAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
18 40 0.89
19 5 0.11
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (18 bp):
ATAATATTTCTAAATTAA
Found at i:2251307 original size:45 final size:45
Alignment explanation
Indices: 2251235--2251328 Score: 113
Period size: 45 Copynumber: 2.1 Consensus size: 45
2251225 TATTTCATTC
*
2251235 AAAAAATAAATTTAAATAATAATTATTAATT-TATTAATAAATGAT
1 AAAAAATAAATTTAAATAATAATTATT-ATTCTATTAATAAATAAT
* *
2251280 AAAAAATAATAATTTAATTAAT-A-TATTATTCTTTTAATAAATAAT
1 AAAAAAT-A-AATTTAAATAATAATTATTATTCTATTAATAAATAAT
2251325 AAAA
1 AAAA
2251329 TATTATTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
44 3 0.07
45 27 0.63
46 2 0.05
47 11 0.26
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (45 bp):
AAAAAATAAATTTAAATAATAATTATTATTCTATTAATAAATAAT
Found at i:2251355 original size:18 final size:18
Alignment explanation
Indices: 2251292--2251356 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 18
2251282 AAAATAATAA
*
2251292 TTTAATTAATATATTATTCT
1 TTTAATTAATA-A-TATTAT
* *
2251312 TTTAATAAATAATAAAATAT
1 TTTAATTAATAAT--ATTAT
2251332 TATTAATTAATAATATTAT
1 T-TTAATTAATAATATTAT
2251351 TTTAAT
1 TTTAAT
2251357 ACAAAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
18 6 0.16
19 6 0.16
20 14 0.38
21 11 0.30
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTAATTAATAATATTAT
Found at i:2252401 original size:22 final size:24
Alignment explanation
Indices: 2252376--2252420 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2252366 AGAAAAAATA
*
2252376 AATAAA-A-ATAATATTTCTAAAG
1 AATAAATATATAATATATCTAAAG
2252398 AATAAATATATAATATATCTAAA
1 AATAAATATATAATATATCTAAA
2252421 TTTAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 1 0.05
24 13 0.65
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (24 bp):
AATAAATATATAATATATCTAAAG
Found at i:2270181 original size:15 final size:16
Alignment explanation
Indices: 2270154--2270184 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2270144 ATTTTTATAT
2270154 TTTTATTATTTAAATA
1 TTTTATTATTTAAATA
2270170 TTTTATTA-TTAAATA
1 TTTTATTATTTAAATA
2270185 ACATGTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTATTATTTAAATA
Found at i:2272541 original size:27 final size:27
Alignment explanation
Indices: 2272511--2272563 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
2272501 TAGTTTCAAA
2272511 AAATAAAAATTATTATTTATTTATTTC
1 AAATAAAAATTATTATTTATTTATTTC
2272538 AAATAAAAATTATTATTTATTTATTT
1 AAATAAAAATTATTATTTATTTATTT
2272564 ATATCGAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
AAATAAAAATTATTATTTATTTATTTC
Found at i:2276090 original size:23 final size:23
Alignment explanation
Indices: 2276063--2276132 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
2276053 GAGTTGAGGG
* *
2276063 TTCTATGCGGTCCTTCAAGACAA
1 TTCTACGCGGTCCTTCAGGACAA
* * * *
2276086 TTCTACGTGGTCCTTCGGGATAT
1 TTCTACGCGGTCCTTCAGGACAA
2276109 TTCTACGCGGTCCTTCAGGACAA
1 TTCTACGCGGTCCTTCAGGACAA
2276132 T
1 T
2276133 ATTATGTGGT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCAGGACAA
Found at i:2276142 original size:46 final size:46
Alignment explanation
Indices: 2276063--2276161 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 46
2276053 GAGTTGAGGG
* *
2276063 TTCTATGCGGTCCTTCAAGACAATTCTACGTGGTCCTTCGGGATAT
1 TTCTACGCGGTCCTTCAAGACAATTCTACGTGGTCCTTCGGGACAT
* * * *
2276109 TTCTACGCGGTCCTTCAGGACAATAT-TATGTGGTCTTTTGGGACAT
1 TTCTACGCGGTCCTTCAAGACAAT-TCTACGTGGTCCTTCGGGACAT
*
2276155 TTATACG
1 TTCTACG
2276162 TTTCACTTCG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.36
Consensus pattern (46 bp):
TTCTACGCGGTCCTTCAAGACAATTCTACGTGGTCCTTCGGGACAT
Found at i:2276185 original size:24 final size:22
Alignment explanation
Indices: 2276165--2276233 Score: 84
Period size: 24 Copynumber: 3.0 Consensus size: 22
2276155 TTATACGTTT
*
2276165 CACTTCGGTGCAATTTCTACGCGG
1 CACTTCGGTGCAATTTATA--CGG
*
2276189 CACTTTGGTGCAATTTCCATACGG
1 CACTTCGGTGCAATTT--ATACGG
2276213 CACTTCGGTGCAATTTATACG
1 CACTTCGGTGCAATTTATACG
2276234 AGTTGTGGTG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
22 5 0.12
24 33 0.82
26 2 0.05
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (22 bp):
CACTTCGGTGCAATTTATACGG
Found at i:2276448 original size:27 final size:23
Alignment explanation
Indices: 2276394--2276449 Score: 58
Period size: 27 Copynumber: 2.3 Consensus size: 23
2276384 ATGATATGTA
2276394 TATATGTATGCATATATGTTTTT
1 TATATGTATGCATATATGTTTTT
* *
2276417 GATATGTGATGTATTATATGGTTTCTT
1 TATATGT-ATGCA-TATAT-GTTT-TT
2276444 TATATG
1 TATATG
2276450 ATTTTATGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 6 0.23
24 4 0.15
25 5 0.19
26 4 0.15
27 7 0.27
ACGTcount: A:0.25, C:0.04, G:0.18, T:0.54
Consensus pattern (23 bp):
TATATGTATGCATATATGTTTTT
Found at i:2276974 original size:15 final size:15
Alignment explanation
Indices: 2276956--2277025 Score: 59
Period size: 15 Copynumber: 4.7 Consensus size: 15
2276946 TAATTATGTA
2276956 ATTGTATTTTATGGT
1 ATTGTATTTTATGGT
* * *
2276971 ATTGAAATTTATGTT
1 ATTGTATTTTATGGT
* * * *
2276986 ATTTTAATTTCTAGT
1 ATTGTATTTTATGGT
* *
2277001 ATTATATTTTATGTT
1 ATTGTATTTTATGGT
2277016 ATTGTATTTT
1 ATTGTATTTT
2277026 TGGACCATTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.26, C:0.01, G:0.11, T:0.61
Consensus pattern (15 bp):
ATTGTATTTTATGGT
Found at i:2283569 original size:31 final size:32
Alignment explanation
Indices: 2283534--2283649 Score: 101
Period size: 32 Copynumber: 3.7 Consensus size: 32
2283524 AGTACCTTAT
* * * *
2283534 GGCCTTAGAGTCTGCCCAAGGAA-TACCTTGG
1 GGCCTCAGAGCCTACCCAAGGAAGCACCTTGG
* *
2283565 GGCCTCAAAGCCTACCCAAGGAAGCATCTTGG
1 GGCCTCAGAGCCTACCCAAGGAAGCACCTTGG
* * * *
2283597 GGCCTGAGAGCCTATCCAAAGGAA-CATCTCGG
1 GGCCTCAGAGCCTA-CCCAAGGAAGCACCTTGG
* *
2283629 GTCCTAAGAGCCTACCCAAGG
1 GGCCTCAGAGCCTACCCAAGG
2283650 GTTACCCTAG
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
31 25 0.36
32 37 0.53
33 8 0.11
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (32 bp):
GGCCTCAGAGCCTACCCAAGGAAGCACCTTGG
Found at i:2283600 original size:32 final size:30
Alignment explanation
Indices: 2283548--2283649 Score: 105
Period size: 32 Copynumber: 3.2 Consensus size: 30
2283538 TTAGAGTCTG
* *
2283548 CCCAAGGAATACCTTGGGGCCTCAAAGCCTA
1 CCCAAGGAACATCTTGGGGCCT-AAAGCCTA
*
2283579 CCCAAGGAAGCATCTTGGGGCCTGAGAGCCTA
1 CCCAAGGAA-CATCTTGGGGCCT-AAAGCCTA
* * *
2283611 TCCAAAGGAACATCTCGGGTCCTAAGAGCCTA
1 -CCCAAGGAACATCTTGGGGCCTAA-AGCCTA
2283643 CCCAAGG
1 CCCAAGG
2283650 GTTACCCTAG
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
31 16 0.27
32 35 0.59
33 8 0.14
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.16
Consensus pattern (30 bp):
CCCAAGGAACATCTTGGGGCCTAAAGCCTA
Found at i:2286723 original size:21 final size:21
Alignment explanation
Indices: 2286697--2286755 Score: 102
Period size: 21 Copynumber: 2.8 Consensus size: 21
2286687 ATTTTGAATG
2286697 GGAGTATCGATACTTCCAAGA
1 GGAGTATCGATACTTCCAAGA
2286718 GGAGTATCGATACTTCCAAGA
1 GGAGTATCGATACTTCCAAGA
2286739 GGAGTATC-AGTACTTCC
1 GGAGTATCGA-TACTTCC
2286756 CCTGTAGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 1 0.03
21 36 0.97
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (21 bp):
GGAGTATCGATACTTCCAAGA
Found at i:2287862 original size:22 final size:22
Alignment explanation
Indices: 2287803--2287865 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
2287793 GAGCTAAGGT
* * *
2287803 ACTTTAGTATCACTGCGAATGC
1 ACTTTAGTACCAATGCTAATGC
* *
2287825 ACTTTTGTATCC-ATGCTTATGC
1 ACTTTAGTA-CCAATGCTAATGC
2287847 ACTTTAGTACCAATGCTAA
1 ACTTTAGTACCAATGCTAA
2287866 GACACTTCTG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
21 2 0.06
22 29 0.91
23 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (22 bp):
ACTTTAGTACCAATGCTAATGC
Found at i:2288948 original size:200 final size:195
Alignment explanation
Indices: 2288620--2289293 Score: 709
Period size: 200 Copynumber: 3.5 Consensus size: 195
2288610 TTTAGATCAC
* * * * * * * *
2288620 TTACAATATCTCGTATGTGCCGATACTAGCCTCAATTGAAATAT-AAGTATCAATACTATGCCTC
1 TTACAATATCTCATATGTGTCGATATTAGACTCAACTGAAAGATAAAGT-CCAATACTACGCCTC
** * * * *
2288684 TAATCTTATAAATTACAAAAAATTTCAGATTAGCTACCCGAAAATAGCCCTCGAATAAGCCTATC
65 TAATCTTATAAATTACAAAATTTTTCAGATTAACTACCCAAAAATACCCCTCGAATATGCCTATC
*
2288749 AAACCATTTTAGCTTCTTCTTCATTCACAAAATCAAGCTTTGGAAGCGTATTTAACGCGATTTTT
130 AAACCATTTTAGCTT-TTCTTCATGCACAAAA-CAAGCTTT--AA-CGTA-TTAACGCGATTTTT
2288814 ACCCCAT
189 ACCCCAT
* * * * *
2288821 TTACAATGTTTCATATATGT-GATATTAGACTCAAGTGAAAGAT-AAGTCGCAATACTATGCCTC
1 TTACAATATCTCATATGTGTCGATATTAGACTCAACTGAAAGATAAAGTC-CAATACTACGCCTC
*
2288884 GAATCTTATAAATTACAAAAGTTTTTCAGATTAACTA-CCAAAAATACCCCTCGAATATGCCTAT
65 TAATCTTATAAATTACAAAA-TTTTTCAGATTAACTACCCAAAAATACCCCTCGAATATGCCTAT
*
2288948 CAAACTATTTTAGCTTTTTCTTCATGCACAAAACAAGCTTT-A-G----AAC-C-A-TTTT-CCC
129 CAAACCATTTTAGC-TTTTCTTCATGCACAAAACAAGCTTTAACGTATTAACGCGATTTTTACCC
*
2289003 CAC
193 CAT
* * * * *
2289006 TTA-AGATATCTCATATGTGTCGATATTGGCCTCAACTGAAAGATAAATTCTAATATTACGCCTC
1 TTACA-ATATCTCATATGTGTCGATATTAGACTCAACTGAAAGATAAAGTCCAATACTACGCCTC
* * * *
2289070 TAATCTTATAAATTATGAAAA-TTTTCAGATTAACTACCCAAAAATACCCCTCAAATATACATAT
65 TAATCTTATAAATTA-CAAAATTTTTCAGATTAACTACCCAAAAATACCCCTCGAATATGCCTAT
* *
2289134 CAAACCATTTTAGATTTTCTTCATGCACAAAACAAGCTTTAAAAC-TAATATCAATGCGATTTTT
129 CAAACCATTTTAGCTTTTCTTCATGCACAAAACAAGCTTT--AACGT-AT-T-AACGCGATTTTT
2289198 ACCCCAT
189 ACCCCAT
* * * *
2289205 TTACAATATCTCGTATGTGTCGATATT-GACCTCAACTGAAAGATAAATTCCAATAATACGCATC
1 TTACAATATCTCATATGTGTCGATATTAGA-CTCAACTGAAAGATAAAGTCCAATACTACGCCTC
*
2289269 TAATCTTATAAATTACGAAATTTTT
65 TAATCTTATAAATTACAAAATTTTT
2289294 TAAATTAAGT
Statistics
Matches: 401, Mismatches: 46, Indels: 54
0.80 0.09 0.11
Matches are distributed among these distances:
184 1 0.00
185 61 0.15
186 85 0.21
187 9 0.02
188 2 0.00
189 3 0.01
194 1 0.00
195 2 0.00
196 2 0.00
197 1 0.00
198 8 0.02
199 87 0.22
200 109 0.27
201 30 0.07
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (195 bp):
TTACAATATCTCATATGTGTCGATATTAGACTCAACTGAAAGATAAAGTCCAATACTACGCCTCT
AATCTTATAAATTACAAAATTTTTCAGATTAACTACCCAAAAATACCCCTCGAATATGCCTATCA
AACCATTTTAGCTTTTCTTCATGCACAAAACAAGCTTTAACGTATTAACGCGATTTTTACCCCAT
Found at i:2289363 original size:386 final size:386
Alignment explanation
Indices: 2288617--2289365 Score: 849
Period size: 386 Copynumber: 1.9 Consensus size: 386
2288607 ATTTTTAGAT
* * * * *
2288617 CACTTACAATATCTCGTATGTGCCGATACTAGCCTCAATTGAAATATAAGTATCAATACTATGCC
1 CACTTACAATATCTCATATGTGCCGATACTAGCCTCAACTGAAAGATAAATATCAATACTACGCC
* * * * *
2288682 TCTAATCTTATAAATTACAAAAAATTTCAGATTAGCTACCCGAAAATAGCCCTCGAATAAGCCTA
66 TCTAATCTTATAAATTACAAAAAATTTCAGATTAACTACCCAAAAATACCCCTCAAATAAGCATA
* * * * *
2288747 TCAAACCATTTTAGCTTCTTCTTCATTCACAAAATCAAGCTTTGGAAGCGTATTTAACGCGATTT
131 TCAAACCATTTTAGATTCTTCTTCATGCACAAAATCAAGCTTTGAAAACGTATTCAACGCGATTT
* * * *
2288812 TTACCCCATTTACAATGTTTCATATATGTGATATTAGACTCAAGTGAAAGATAAGTCGCAATACT
196 TTACCCCATTTACAATATCTCATATATGTGATATTAGACTCAACTGAAAGATAAGTCGCAATAAT
* * * *
2288877 ATGCCTCGAATCTTATAAATTACAAAAGTTTTTCAGATTAACTACCAAAAATACCCCTCGAATAT
261 ACGCATCGAATCTTATAAATTACAAAAGTTTTTCAAATTAACTACCAAAAATACCCCTCGAACAT
* * *** **
2288942 GCCTATCAAACTATTTTAGCTTTTTCTTCATGCACAAAACAAGCTTTAGAACCATTTTCCC
326 GCCTATCAAACTATTGTAGATTGGGCTAAATGCACAAAACAAGCTTTAGAACCATTTTCCC
* * * *
2289003 CACTTA-AGATATCTCATATGTGTCGATATTGGCCTCAACTGAAAGATAAAT-TCTAATATTACG
1 CACTTACA-ATATCTCATATGTGCCGATACTAGCCTCAACTGAAAGATAAATATC-AATACTACG
** *
2289066 CCTCTAATCTTATAAATTATGAAAATTTTCAGATTAACTACCCAAAAATACCCCTCAAATATA-C
64 CCTCTAATCTTATAAATTACAAAAAATTTCAGATTAACTACCCAAAAATACCCCTCAAATA-AGC
*
2289130 ATATCAAACCATTTTAGATT-TTCTTCATGCACAAAA-CAAGCTTT-AAAAC-TAATATCAATGC
128 ATATCAAACCATTTTAGATTCTTCTTCATGCACAAAATCAAGCTTTGAAAACGT-AT-TCAACGC
* * *
2289191 GATTTTTACCCCATTTACAATATCTCGTATGTGTCGATATT-GACCTCAACTGAAAGATAAATTC
191 GATTTTTACCCCATTTACAATATCTCATATATGT-GATATTAGA-CTCAACTGAAAGAT-AAGTC
* * * * * **
2289255 -CAATAATACGCATCTAATCTTATAAATTACGAAA-TTTTTTAAATTAAGTACCTAAATATACTT
253 GCAATAATACGCATCGAATCTTATAAATTACAAAAGTTTTTCAAATTAACTACC-AAAAATACCC
*
2289318 CTTGAACATGCCTAT-AAAC-ACTTGTA-ATGTGGGCTGAAAATGCACAAA
317 CTCGAACATGCCTATCAAACTA-TTGTAGAT-TGGGCT--AAATGCACAAA
2289366 CCTCGCGTTC
Statistics
Matches: 301, Mismatches: 49, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
382 1 0.00
383 7 0.02
384 71 0.24
385 86 0.29
386 135 0.45
387 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (386 bp):
CACTTACAATATCTCATATGTGCCGATACTAGCCTCAACTGAAAGATAAATATCAATACTACGCC
TCTAATCTTATAAATTACAAAAAATTTCAGATTAACTACCCAAAAATACCCCTCAAATAAGCATA
TCAAACCATTTTAGATTCTTCTTCATGCACAAAATCAAGCTTTGAAAACGTATTCAACGCGATTT
TTACCCCATTTACAATATCTCATATATGTGATATTAGACTCAACTGAAAGATAAGTCGCAATAAT
ACGCATCGAATCTTATAAATTACAAAAGTTTTTCAAATTAACTACCAAAAATACCCCTCGAACAT
GCCTATCAAACTATTGTAGATTGGGCTAAATGCACAAAACAAGCTTTAGAACCATTTTCCC
Found at i:2305171 original size:31 final size:30
Alignment explanation
Indices: 2305125--2305185 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
2305115 AATTTATTTA
2305125 ATATATTTTATTAAATTAATAA-AATATTAT
1 ATATATTTTATTAAATTAATAATAA-ATTAT
*
2305155 ATATTTTTATATTAAATTAATAATAAATTAT
1 ATATATTT-TATTAAATTAATAATAAATTAT
2305186 TTAAATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.25
31 19 0.68
32 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
ATATATTTTATTAAATTAATAATAAATTAT
Found at i:2305300 original size:27 final size:27
Alignment explanation
Indices: 2305244--2305329 Score: 75
Period size: 29 Copynumber: 3.1 Consensus size: 27
2305234 TGGTAAATAT
* * *
2305244 AAAATATATATTT-TTACATTAAAATAA
1 AAAATATATATTTAATAAATTAAAA-CA
*
2305271 AAAATATATATTTAATAAATTAAGACA
1 AAAATATATATTTAATAAATTAAAACA
* * *
2305298 AAAGTAAAAATATTTAATAAGTTAAAACA
1 AAA--ATATATATTTAATAAATTAAAACA
2305327 AAA
1 AAA
2305330 GTAAATAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
27 17 0.35
28 8 0.17
29 23 0.48
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (27 bp):
AAAATATATATTTAATAAATTAAAACA
Found at i:2305315 original size:29 final size:29
Alignment explanation
Indices: 2305278--2305334 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
2305268 TAAAAAATAT
*
2305278 ATATTTAATAAATTAAGACAAAAGTAAAA
1 ATATTTAATAAATTAAAACAAAAGTAAAA
*
2305307 ATATTTAATAAGTTAAAACAAAAGTAAA
1 ATATTTAATAAATTAAAACAAAAGTAAA
2305335 TAAATAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (29 bp):
ATATTTAATAAATTAAAACAAAAGTAAAA
Found at i:2306152 original size:3 final size:3
Alignment explanation
Indices: 2306144--2306231 Score: 151
Period size: 3 Copynumber: 29.7 Consensus size: 3
2306134 TTTTTATCCA
* *
2306144 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2306192 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2306232 AATATATTAA
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
2 2 0.03
3 78 0.98
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2306707 original size:19 final size:20
Alignment explanation
Indices: 2306683--2306722 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
2306673 ACACAGAAAC
*
2306683 CAGAGACAGAAAAAAA-AAA
1 CAGAGAAAGAAAAAAATAAA
2306702 CAGAGAAAGAAAAAAATAAA
1 CAGAGAAAGAAAAAAATAAA
2306722 C
1 C
2306723 TATACCAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.72, C:0.10, G:0.15, T:0.03
Consensus pattern (20 bp):
CAGAGAAAGAAAAAAATAAA
Found at i:2308238 original size:18 final size:16
Alignment explanation
Indices: 2308217--2308260 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
2308207 TAATTCTTTC
2308217 TTTTTATTTATTTATTA
1 TTTTTATTTATTTA-TA
*
2308234 TTTTTATAATATTTATA
1 TTTTTAT-TTATTTATA
2308251 TGTTTTATTT
1 T-TTTTATTT
2308261 GCAAGTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTTTATTTATTTATA
Found at i:2318907 original size:16 final size:16
Alignment explanation
Indices: 2318886--2318917 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2318876 GCTTGAAAAA
2318886 AAAAAAAAAAAAAGGG
1 AAAAAAAAAAAAAGGG
*
2318902 AAAAAAGAAAAAAGGG
1 AAAAAAAAAAAAAGGG
2318918 GGGTCAAGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAGGG
Found at i:2319260 original size:16 final size:16
Alignment explanation
Indices: 2319232--2319268 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2319222 CAATTATATC
2319232 TATTTCAAGTTCAATT
1 TATTTCAAGTTCAATT
2319248 TATTT-AAGATTCAATT
1 TATTTCAAG-TTCAATT
2319264 TATTT
1 TATTT
2319269 TTAGAAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.54
Consensus pattern (16 bp):
TATTTCAAGTTCAATT
Found at i:2319994 original size:52 final size:52
Alignment explanation
Indices: 2319883--2320152 Score: 443
Period size: 52 Copynumber: 5.2 Consensus size: 52
2319873 ATGGAAAAGC
*
2319883 ATCAGAACATAGCATCTTCTGGAAGTGTTTCTTTGAGTTATCTGATTTGGTTGG
1 ATCAGAACATAGCATCTTCTGGAAGTG-TTCTTTGAGTTATCTGATCTGGTT-G
*
2319937 A-CAGAACATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTG
1 ATCAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTG
* *
2319988 ATCAGAACATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTG
1 ATCAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTG
*
2320040 ATCAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTG
1 ATCAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTG
*
2320092 ATCAGAACATAGCATCTTCTGGAAGTGTTTCTTTGAGTTATCTGATCTGGTTT
1 ATCAGAACATAGCATCTTCTGGAAGTG-TTCTTTGAGTTATCTGATCTGGTTG
*
2320145 AGCAGAAC
1 ATCAGAAC
2320153 CAATCATTGA
Statistics
Matches: 205, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
51 2 0.01
52 148 0.72
53 54 0.26
54 1 0.00
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.39
Consensus pattern (52 bp):
ATCAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTG
Found at i:2321010 original size:113 final size:113
Alignment explanation
Indices: 2320812--2321371 Score: 913
Period size: 113 Copynumber: 4.9 Consensus size: 113
2320802 CAAAGATTCA
*
2320812 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCGGAAGA
1 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
2320877 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
2320925 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
2320990 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
2321038 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
2321103 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * * * * *
2321151 AATCCATCATTTGATGGATCAACATTACCAGAGAAGGTTCATAATGAAAAGAACTCATCTGATGA
1 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *** *
2321216 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTA
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * * * *
2321264 AATTCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATGAATGAAAAGAACTCATCTGAAG
1 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAG
**
2321329 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
2321372 GTTTGATATT
Statistics
Matches: 426, Mismatches: 20, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
113 364 0.85
114 62 0.15
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:2321674 original size:3 final size:3
Alignment explanation
Indices: 2321666--2321762 Score: 151
Period size: 3 Copynumber: 32.7 Consensus size: 3
2321656 TTTTTATCCA
* * *
2321666 TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2321714 TAT TAT TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2321761 TA
1 TA
2321763 AATATATTAA
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
2 2 0.02
3 83 0.98
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2322238 original size:19 final size:20
Alignment explanation
Indices: 2322214--2322253 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
2322204 ACACAGAAAC
*
2322214 CAGAGACAGAAAAAAA-AAA
1 CAGAGAAAGAAAAAAATAAA
2322233 CAGAGAAAGAAAAAAATAAA
1 CAGAGAAAGAAAAAAATAAA
2322253 C
1 C
2322254 TATACCAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.72, C:0.10, G:0.15, T:0.03
Consensus pattern (20 bp):
CAGAGAAAGAAAAAAATAAA
Found at i:2327504 original size:19 final size:19
Alignment explanation
Indices: 2327480--2327518 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2327470 TCCAATGTTC
*
2327480 AATTCAACGCAAAATTAAA
1 AATTCAACGAAAAATTAAA
*
2327499 AATTCATCGAAAAATTAAA
1 AATTCAACGAAAAATTAAA
2327518 A
1 A
2327519 CAATCAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.13, G:0.05, T:0.23
Consensus pattern (19 bp):
AATTCAACGAAAAATTAAA
Found at i:2331859 original size:21 final size:19
Alignment explanation
Indices: 2331817--2331860 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
2331807 ACATGATTAA
* *
2331817 CTTTGCACATCGAATGATT
1 CTTTGCACATAGAATAATT
2331836 CTTTGCACAATAGAAGTAATT
1 CTTTGCAC-ATAGAA-TAATT
2331857 CTTT
1 CTTT
2331861 TTCTATCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 5 0.24
21 8 0.38
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (19 bp):
CTTTGCACATAGAATAATT
Found at i:2334208 original size:21 final size:21
Alignment explanation
Indices: 2334166--2334216 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2334156 TCGGCTTATT
* *
2334166 AATTTTTCCTGGGAAGTAACC
1 AATTTCTCCTGGGAAATAACC
* *
2334187 AATTTCTCTTGGGAAATCACC
1 AATTTCTCCTGGGAAATAACC
*
2334208 AACTTCTCC
1 AATTTCTCC
2334217 ATCATCGCCT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (21 bp):
AATTTCTCCTGGGAAATAACC
Found at i:2340788 original size:108 final size:108
Alignment explanation
Indices: 2340583--2340795 Score: 266
Period size: 108 Copynumber: 2.0 Consensus size: 108
2340573 CAACTTAATA
** * * * * * *
2340583 AATTCATAATAAGTTTATGAATTTCTGTATTGGCACTATGTGTGCACCCCACGTAACTCATAATG
1 AATTCATAATAAGTTTATGAAGATCTGTATCGACAATAAGTGTGCAACCCACGAAACTCATAATG
* * * *
2340648 AGTTTGTGAATTACTGTATCGACACTAAGTGTGCAACCCACTG
66 AGCTTATGAATGACCGTATCGACACTAAGTGTGCAACCCACTG
*
2340691 AATTCATAATAAGTTTATGAACGATC-GTATCGACAATAAGTGTGCAACCCACGAAATTCATAAT
1 AATTCATAATAAGTTTATGAA-GATCTGTATCGACAATAAGTGTGCAACCCACGAAACTCATAAT
* * *
2340755 GAGCTTATGAATGACCGTATCGATACTACGTGTGCACCCCA
65 GAGCTTATGAATGACCGTATCGACACTAAGTGTGCAACCCA
2340796 AAGAACTTAT
Statistics
Matches: 88, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
108 86 0.98
109 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30
Consensus pattern (108 bp):
AATTCATAATAAGTTTATGAAGATCTGTATCGACAATAAGTGTGCAACCCACGAAACTCATAATG
AGCTTATGAATGACCGTATCGACACTAAGTGTGCAACCCACTG
Found at i:2340790 original size:54 final size:54
Alignment explanation
Indices: 2340184--2340766 Score: 738
Period size: 54 Copynumber: 10.8 Consensus size: 54
2340174 TATCGAATGA
* * *
2340184 CACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCTTATTGG
1 CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGG
* * *
2340238 CACTGTGTGTGCAACTTATGAAATTCATAATAAGTTTATGAATTTCCGTATTGG
1 CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGG
2340292 CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGG
1 CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGG
* *
2340346 CACTATGTGTGCAACCTAAGAAATTTATAATAAGTTTATGAATTTCCGCATTGG
1 CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGG
* * * *
2340400 CACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATAAATTTTCGTATTGG
1 CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGG
2340454 CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGG
1 CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGG
* * * * *
2340508 CACTATGTGTGCAACTTAAGAAATTCATGATAAGGTTATAAATTTTCGTATTGG
1 CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGG
* * *
2340562 CACTATGTGTGCAACTTAATAAATTCATAATAAGTTTATGAATTTCTGTATTGG
1 CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGG
* * * * * * * * * * *
2340616 CACTATGTGTGCACCCCACGTAACTCATAATGAGTTTGTGAATTACTGTATCGA
1 CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGG
* * * ** * *
2340670 CACTAAGTGTGCAACCCACTG-AATTCATAATAAGTTTATGAACGAT-CGTATCGA
1 CACTATGTGTGCAACCTA-AGAAATTCATAATAAGTTTATGAA-TTTCCGTATTGG
* * * * * *
2340724 CAATAAGTGTGCAACCCACGAAATTCATAATGAGCTTATGAAT
1 CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAT
2340767 GACCGTATCG
Statistics
Matches: 469, Mismatches: 57, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
53 1 0.00
54 467 1.00
55 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (54 bp):
CACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGG
Found at i:2345880 original size:2 final size:2
Alignment explanation
Indices: 2345875--2345907 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
2345865 AAAAAATGAT
2345875 TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
2345908 AGTGTCAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2348534 original size:14 final size:13
Alignment explanation
Indices: 2348506--2348566 Score: 52
Period size: 14 Copynumber: 4.5 Consensus size: 13
2348496 TTTGCATACA
*
2348506 TGCACTTTGCACTT
1 TGCA-TTTGCACAT
*
2348520 TGCATTTGCATCTT
1 TGCATTTGCA-CAT
*
2348534 TGCATTT-TACAT
1 TGCATTTGCACAT
2348546 TGTCATTTGCATCAT
1 TG-CATTTGCA-CAT
2348561 TGCATT
1 TGCATT
2348567 CATACGTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 4 0.10
13 12 0.30
14 19 0.47
15 5 0.12
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.48
Consensus pattern (13 bp):
TGCATTTGCACAT
Found at i:2348536 original size:21 final size:20
Alignment explanation
Indices: 2348506--2348546 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2348496 TTTGCATACA
*
2348506 TGCACTTTGCACTTTGCATT
1 TGCACTTTGCACTTTACATT
*
2348526 TGCATCTTTGCATTTTACATT
1 TGCA-CTTTGCACTTTACATT
2348547 GTCATTTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.17, C:0.22, G:0.12, T:0.49
Consensus pattern (20 bp):
TGCACTTTGCACTTTACATT
Found at i:2351738 original size:19 final size:19
Alignment explanation
Indices: 2351714--2351751 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2351704 TTTTTTCTCA
*
2351714 CCTACCACCCTCCTCCTCC
1 CCTACCACCATCCTCCTCC
2351733 CCTACCACCATCCTCCTCC
1 CCTACCACCATCCTCCTCC
2351752 TCCCCTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.66, G:0.00, T:0.21
Consensus pattern (19 bp):
CCTACCACCATCCTCCTCC
Found at i:2351742 original size:22 final size:22
Alignment explanation
Indices: 2351717--2351758 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2351707 TTTCTCACCT
2351717 ACCACCCTCCTCCTCCCCTACC
1 ACCACCCTCCTCCTCCCCTACC
*
2351739 ACCATCCTCCTCCTCCCCTA
1 ACCACCCTCCTCCTCCCCTA
2351759 TATAAACCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.64, G:0.00, T:0.21
Consensus pattern (22 bp):
ACCACCCTCCTCCTCCCCTACC
Found at i:2351971 original size:30 final size:30
Alignment explanation
Indices: 2351908--2351999 Score: 84
Period size: 30 Copynumber: 3.1 Consensus size: 30
2351898 ATAGTTGTTA
* *
2351908 TATTTTTTATTAATATAAT-TATATA-AATGT
1 TATTTTTTATTAAAATAATATTTATATAA--T
2351938 TATTTTTTATTAAAATAATATTTATATAAT
1 TATTTTTTATTAAAATAATATTTATATAAT
* * * *
2351968 TATTGTTTATTTAAAT-TTATTAAT-TAAT
1 TATTTTTTATTAAAATAATATTTATATAAT
2351996 TATT
1 TATT
2352000 ATTTGTGCTA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
28 8 0.15
29 6 0.11
30 33 0.61
31 5 0.09
32 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (30 bp):
TATTTTTTATTAAAATAATATTTATATAAT
Found at i:2352001 original size:24 final size:25
Alignment explanation
Indices: 2351957--2352003 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
2351947 TTAAAATAAT
*
2351957 ATTTATATAATTATTGTTTATTTAA
1 ATTTATATAATTATTGATTATTTAA
2351982 ATTTAT-TAATTAATT-ATTATTT
1 ATTTATATAATT-ATTGATTATTT
2352004 GTGCTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
ATTTATATAATTATTGATTATTTAA
Found at i:2353806 original size:42 final size:42
Alignment explanation
Indices: 2353707--2353814 Score: 119
Period size: 42 Copynumber: 2.5 Consensus size: 42
2353697 ATGATGCCAC
* **
2353707 AGGGATACATGCCCAGCCCTTCAGTTCAGATGCCATCTCCGTA
1 AGGG-TACATGCCTAGCCCACCAGTTCAGATGCCATCTCCGTA
* * *
2353750 AGGGTATATGCCTAGCCCACCAGTTCATATGCCATCTCCG-C
1 AGGGTACATGCCTAGCCCACCAGTTCAGATGCCATCTCCGTA
* *
2353791 AGGGTTACATTCCTAGCCCGCCAG
1 AGGG-TACATGCCTAGCCCACCAG
2353815 GTTACATGCC
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
41 4 0.07
42 47 0.85
43 4 0.07
ACGTcount: A:0.22, C:0.33, G:0.21, T:0.23
Consensus pattern (42 bp):
AGGGTACATGCCTAGCCCACCAGTTCAGATGCCATCTCCGTA
Found at i:2355295 original size:137 final size:137
Alignment explanation
Indices: 2354892--2355797 Score: 1235
Period size: 138 Copynumber: 6.6 Consensus size: 137
2354882 TTGCGTCTCC
* * *
2354892 GGACATGACTCATAAAATAGGGCAATTATAACATATTCTCTGACATAATAAT-GAATGGCGCCCC
1 GGACATGACTCACATAATAGGGCAATTATAACATATTCTCTGACAAAATAATGGAA-GGCG-CCC
* * * * * * *
2354956 CCCTGAAACGCGCTTTCACCAATTTGATGTGTCCCTTCAAACATGATAGGTATTGACATGAATAA
64 CCCTGAAACGCGCCTTCACCACTTTGTTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAG
*
2355021 AGCCCCGGG
129 TGCCCCGGG
* * * *
2355030 GGACATGACTTACACAATAGGGCAATTATAATATATTCTCTGACAAAATAATGGAAGACGCACCC
1 GGACATGACTCACATAATAGGGCAATTATAACATATTCTCTGACAAAATAATGGAAGGCGC-CCC
* * * *
2355095 CCTAAAACGCTCCTTCACCACTTTGATGCGTCCCCACAAACATGATAGGTACTGACATGAATAGT
65 CCTGAAACGCGCCTTCACCACTTTGTTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGT
2355160 GCCCCGGG
130 GCCCCGGG
*
2355168 GGACATGACTCACATAATAGGGCAATTATAAGATATTCTCTGACAAAATAATGGAAGGCGCCCCC
1 GGACATGACTCACATAATAGGGCAATTATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCC
* *
2355233 CTGAAACGCGCCTTCACCACTTTGTTACGTCCCCTCAAACATGATAGGTACTGATATGAATAGTG
66 CTGAAACGCGCCTTCACCACTTTGTTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTG
*
2355298 CCCGGGG
131 CCCCGGG
** * * * *
2355305 GGACATGACTCACATAATAGGAAAATTATAACATATTATCTAACAAAATAATAGAAGGCG--CCT
1 GGACATGACTCACATAATAGGGCAATTATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCC
* * * *
2355368 CTGAAACACGCATTCACCACTTTGCTACGTCCCCTCAAACATGATAGGTACTGACATGAATAGTG
66 CTGAAACGCGCCTTCACCACTTTGTTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTG
2355433 CCCCCGGG
131 -CCCCGGG
* * *
2355441 GGACATGAATCACATTATAGGGAAATTATAACATATTCTCTGACAAAATAATGGAAGGCG-CCCC
1 GGACATGACTCACATAATAGGGCAATTATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCC
* *
2355505 CTAAAACGCGCCTTCACCACTTTGTTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTA
66 CTGAAACGCGCCTTCACCACTTTGTTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTG
2355570 CCCCGGG
131 CCCCGGG
* * * * *
2355577 GGACATGACTCACATAATAGGACAATTATAACATATTCTCTGATAAAATAATGAAAGGTGTGCCC
1 GGACATGACTCACATAATAGGGCAATTATAACATATTCTCTGACAAAATAATGGAAGGCG-CCCC
* * *
2355642 CCTGAAATGCGCTTTCACCACTTTGTTGCGTCCCCTCGAACATGATAGGTACTGACATGAATAGT
65 CCTGAAACGCGCCTTCACCACTTTGTTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGT
**
2355707 GCCCCCAG
130 GCCCCGGG
* * ** * * *
2355715 GGTCATGAATGGCATAATAGGTCAATTATAACATATTCTCTGAGAAAATAATGGAAGGTGCGCCC
1 GGACATGACTCACATAATAGGGCAATTATAACATATTCTCTGACAAAATAATGGAAGGCGC-CCC
2355780 CCTGAAACGCGCCTTCAC
65 CCTGAAACGCGCCTTCAC
2355798 ATGAATAGTA
Statistics
Matches: 685, Mismatches: 76, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
135 63 0.09
136 120 0.18
137 185 0.27
138 314 0.46
139 3 0.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (137 bp):
GGACATGACTCACATAATAGGGCAATTATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCC
CTGAAACGCGCCTTCACCACTTTGTTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTG
CCCCGGG
Found at i:2361534 original size:14 final size:15
Alignment explanation
Indices: 2361503--2361535 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2361493 TTAATCATGA
2361503 TATTGTTCATGATAT
1 TATTGTTCATGATAT
*
2361518 TATTGTT-ATGGTAT
1 TATTGTTCATGATAT
2361532 TATT
1 TATT
2361536 ACCATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.58
Consensus pattern (15 bp):
TATTGTTCATGATAT
Found at i:2361870 original size:46 final size:45
Alignment explanation
Indices: 2361732--2361896 Score: 192
Period size: 45 Copynumber: 3.6 Consensus size: 45
2361722 TAATTTAAGG
* *
2361732 CTTTTGATTATT-GAGTTGTTAAAAGTAAAATCAAAGGATTAGTTC
1 CTTTTGATTATTGGA-TTGTGAAAATTAAAATCAAAGGATTAGTTC
** *
2361777 CTTTTGATTATTGTG-TTGCCAAAAATAAAATCAAAGGATTAGTTC
1 CTTTTGATTATTG-GATTGTGAAAATTAAAATCAAAGGATTAGTTC
* **
2361822 CTTTCGATTATTGGATTGTGAAAATTAAAAATCAATTGATTAGTTC
1 CTTTTGATTATTGGATTGTGAAAATT-AAAATCAAAGGATTAGTTC
*
2361868 CTTTTGATTATTGGGTTG-GTAAAATTAAA
1 CTTTTGATTATTGGATTGTG-AAAATTAAA
2361897 GGATTAATTC
Statistics
Matches: 104, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
44 1 0.01
45 63 0.61
46 39 0.38
47 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.41
Consensus pattern (45 bp):
CTTTTGATTATTGGATTGTGAAAATTAAAATCAAAGGATTAGTTC
Found at i:2362117 original size:58 final size:59
Alignment explanation
Indices: 2362035--2362149 Score: 162
Period size: 58 Copynumber: 2.0 Consensus size: 59
2362025 TCATCATTAG
* * *
2362035 AATATTGCGTTGATTCTAACTTTGTAAGGAAAAT-AGATTGTTGAATTTATTTCCTTGGA
1 AATATTGCGATGATTCTAACTTTGTAAGAAAAATAAG-TTGTCGAATTTATTTCCTTGGA
* *
2362094 AATATTGC-ATGATTTTAACTTTGTAAGAAAAATAAGTTGTCGAATTTATTTTCTTG
1 AATATTGCGATGATTCTAACTTTGTAAGAAAAATAAGTTGTCGAATTTATTTCCTTG
2362150 AGAATCGTGG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 40 0.80
59 10 0.20
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (59 bp):
AATATTGCGATGATTCTAACTTTGTAAGAAAAATAAGTTGTCGAATTTATTTCCTTGGA
Found at i:2362164 original size:58 final size:58
Alignment explanation
Indices: 2362045--2362168 Score: 153
Period size: 58 Copynumber: 2.1 Consensus size: 58
2362035 AATATTGCGT
* * *
2362045 TGATTCTAACTTTGTAAGGAAAATAGATTGTTGAATTTATTTCCTTGGAAATATTGCA
1 TGATTCTAACTTTGTAAGAAAAATAGATTGTCGAATTTATTTCCTTGGAAATAGTGCA
* * * *
2362103 TGATTTTAACTTTGTAAGAAAAATA-AGTTGTCGAATTTATTTTCTT-GAGAATCGTGGA
1 TGATTCTAACTTTGTAAGAAAAATAGA-TTGTCGAATTTATTTCCTTGGA-AATAGTGCA
2362161 TGATTCTA
1 TGATTCTA
2362169 TCCTTTAGAA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
57 3 0.05
58 53 0.95
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (58 bp):
TGATTCTAACTTTGTAAGAAAAATAGATTGTCGAATTTATTTCCTTGGAAATAGTGCA
Found at i:2362198 original size:58 final size:56
Alignment explanation
Indices: 2362136--2362333 Score: 229
Period size: 58 Copynumber: 3.5 Consensus size: 56
2362126 TAAGTTGTCG
* ** * *
2362136 AATTTATTTTCTTGAGAATCGTGGATGATTCTATCCTTTAGAAAGAAAGAAATTGTTA
1 AATTTATTTTCTTGAGAATCTTAAATGATTCTAT-TTTTA-AAAGAAATAAATTGTTA
* * *
2362194 AATTT-TGTT-TTGAGAATCTTAAATGATTTTATTTTGTAAAAGTTAATAAATTGTTA
1 AATTTATTTTCTTGAGAATCTTAAATGATTCTATTTT-TAAAAG-AAATAAATTGTTA
*
2362250 AATTTATTTTCTTGAGAATCTTAAATGATTCTATTTTGTTAAAGGAAATAAATTGTTA
1 AATTTATTTTCTTGAGAATCTTAAATGATTCTA-TTT-TTAAAAGAAATAAATTGTTA
* *
2362308 AATTTATTTTCTTGGGAATTTTAAAT
1 AATTTATTTTCTTGAGAATCTTAAAT
2362334 AAAGAAATCA
Statistics
Matches: 120, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
55 6 0.05
56 37 0.31
57 6 0.05
58 62 0.52
59 8 0.07
60 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (56 bp):
AATTTATTTTCTTGAGAATCTTAAATGATTCTATTTTTAAAAGAAATAAATTGTTA
Found at i:2362485 original size:38 final size:38
Alignment explanation
Indices: 2362372--2362491 Score: 186
Period size: 38 Copynumber: 3.1 Consensus size: 38
2362362 TTATATGATT
2362372 CTATTTTGAAAAGAAAATAAATCGTTAGATTTATTTTTC
1 CTATTTTGAAAAGAAAATAAATCGTTAGATTTA-TTTTC
* *
2362411 CTATTTTGTAAAATAAAATAAATCGTTAGATATATTTTC
1 CTATTTTG-AAAAGAAAATAAATCGTTAGATTTATTTTC
* *
2362450 CTATTTTGAAAAGAAAATAAATCGGTAAATTTATTTTC
1 CTATTTTGAAAAGAAAATAAATCGTTAGATTTATTTTC
2362488 CTAT
1 CTAT
2362492 GAATCTTGTA
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
38 30 0.41
39 21 0.28
40 23 0.31
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.42
Consensus pattern (38 bp):
CTATTTTGAAAAGAAAATAAATCGTTAGATTTATTTTC
Found at i:2362543 original size:96 final size:96
Alignment explanation
Indices: 2362417--2362681 Score: 365
Period size: 96 Copynumber: 2.8 Consensus size: 96
2362407 TTTCCTATTT
* * *
2362417 TGTAAAATAAAATAAATCGTT-AGATATATTTTCCTATTTTGAAAAGAAAATAAATCGGTAAATT
1 TGTAAAAGAAAATAAATCGTTGA-ATTTATTTTCCTATTTTGAAAAGAAAATAAATCGATAAATT
* *
2362481 TATTTTCCTATGAATCTTGTATGATTCTGAAA
65 TATTTTCCTAAGAATCTTATATGATTCTGAAA
* *
2362513 TGTAAAAGGAAATAAATCGTTGAATTTATTTTCCTATTTTGAAAAGAAAATAAATTGATAAATTT
1 TGTAAAAGAAAATAAATCGTTGAATTTATTTTCCTATTTTGAAAAGAAAATAAATCGATAAATTT
* **
2362578 ATTTTCCTAAGAATTTTATATGATTCTGATT
66 ATTTTCCTAAGAATCTTATATGATTCTGAAA
* *
2362609 TATAAAAGAAAATAAATCGTTTG-GTTTATTTTCCTATTTTGAAAAGAAAATAAATC-ATAGAAT
1 TGTAAAAGAAAATAAATCG-TTGAATTTATTTTCCTATTTTGAAAAGAAAATAAATCGATA-AAT
*
2362672 TTAGTTTCCT
64 TTATTTTCCT
2362682 GGTTTATAAA
Statistics
Matches: 151, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
95 3 0.02
96 144 0.95
97 4 0.03
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (96 bp):
TGTAAAAGAAAATAAATCGTTGAATTTATTTTCCTATTTTGAAAAGAAAATAAATCGATAAATTT
ATTTTCCTAAGAATCTTATATGATTCTGAAA
Found at i:2362713 original size:39 final size:38
Alignment explanation
Indices: 2362606--2362746 Score: 135
Period size: 39 Copynumber: 3.6 Consensus size: 38
2362596 TATGATTCTG
2362606 ATTTATAAAAGAAAATAAATCGTTTGG-TTTATTTTCCT
1 ATTTATAAAAGAAAATAAATCG-TTGGATTTATTTTCCT
* * * *
2362644 ATTT-TGAAAAGAAAATAAATCATAGAATTTAGTTTCCT
1 ATTTAT-AAAAGAAAATAAATCGTTGGATTTATTTTCCT
* * *
2362682 GGTTTATAAAAGGAAATAAATTGTTGGATTTATTTTCCT
1 -ATTTATAAAAGAAAATAAATCGTTGGATTTATTTTCCT
*
2362721 ACTTTGTAGAAATG-AAATAAATCGTT
1 A-TTTATA-AAA-GAAAATAAATCGTT
2362747 AAAAATGAAA
Statistics
Matches: 82, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
37 3 0.04
38 29 0.35
39 34 0.41
40 15 0.18
41 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.40
Consensus pattern (38 bp):
ATTTATAAAAGAAAATAAATCGTTGGATTTATTTTCCT
Found at i:2362761 original size:59 final size:58
Alignment explanation
Indices: 2362689--2362802 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 58
2362679 CCTGGTTTAT
* * *
2362689 AAAAGGAAATAAATTGTTGGATTTATTTTCCTACTTTGTAGAAATGAAATAAATCGTTA
1 AAAAGGAAATAAATAGTTGGATTTAGTTTCCTACTTTGTA-AAAGGAAATAAATCGTTA
* *
2362748 AAAATGAAATAAATAGTTGGATTTAGTTTCCTATTTTGTAAAAGGAAATAAATCG
1 AAAAGGAAATAAATAGTTGGATTTAGTTTCCTACTTTGTAAAAGGAAATAAATCG
2362803 AAACAAATCA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
58 14 0.28
59 36 0.72
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (58 bp):
AAAAGGAAATAAATAGTTGGATTTAGTTTCCTACTTTGTAAAAGGAAATAAATCGTTA
Found at i:2362884 original size:40 final size:40
Alignment explanation
Indices: 2362817--2362904 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
2362807 AAATCATTTT
* * **
2362817 ATTTA-TTTTCTTGTTTTGTGAAAGGAAATAAATCGTTGG
1 ATTTATTTTTATTGTTTTGTAAAAGGAAATAAATCGTCAG
*
2362856 ATTTATTTTTATTTTTTTGTAAAAGGAAATAAATCGTCAG
1 ATTTATTTTTATTGTTTTGTAAAAGGAAATAAATCGTCAG
2362896 ATTTATTTT
1 ATTTATTTT
2362905 CCTATTTTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 5 0.12
40 38 0.88
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.50
Consensus pattern (40 bp):
ATTTATTTTTATTGTTTTGTAAAAGGAAATAAATCGTCAG
Found at i:2362929 original size:39 final size:38
Alignment explanation
Indices: 2362817--2362926 Score: 123
Period size: 40 Copynumber: 2.8 Consensus size: 38
2362807 AAATCATTTT
* **
2362817 ATTTATTTTCTTGTTTTGTGAAAGGAAATAAATCGTTGG
1 ATTTATTTTCTTATTTTGT-AAAGGAAATAAATCGTCAG
* *
2362856 ATTTATTTTTATTTTTTTGTAAAAGGAAATAAATCGTCAG
1 ATTTA-TTTTCTTATTTTGT-AAAGGAAATAAATCGTCAG
*
2362896 ATTTATTTTCCTATTTTGTAAATGG-AATAAA
1 ATTTATTTTCTTATTTTGTAAA-GGAAATAAA
2362927 ATCATTGATT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
38 9 0.15
39 18 0.30
40 34 0.56
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (38 bp):
ATTTATTTTCTTATTTTGTAAAGGAAATAAATCGTCAG
Found at i:2363782 original size:21 final size:21
Alignment explanation
Indices: 2363752--2363809 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
2363742 AAATAGAATT
*
2363752 TGTCCCAAAGGACCACATATA
1 TGTCCCAAAGGACCACATAGA
*
2363773 TGTCCTAAAGGACCACATAGA
1 TGTCCCAAAGGACCACATAGA
*
2363794 TGTCCCGAAGGACCAC
1 TGTCCCAAAGGACCAC
2363810 TCCTTAAGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.17
Consensus pattern (21 bp):
TGTCCCAAAGGACCACATAGA
Found at i:2363889 original size:21 final size:21
Alignment explanation
Indices: 2363815--2363910 Score: 59
Period size: 21 Copynumber: 4.6 Consensus size: 21
2363805 ACCACTCCTT
* *
2363815 AAGGATCACATATATATTCCA
1 AAGGACCACATATATGTTCCA
* * * *
2363836 AAGGACCAAATATGTGTCCCG
1 AAGGACCACATATATGTTCCA
* **
2363857 AAGAACTGCATATATGTTCCA
1 AAGGACCACATATATGTTCCA
** * *
2363878 AAGGATTACATATAT-ATCCTG
1 AAGGACCACATATATGTTCC-A
2363899 AAGGACCACATA
1 AAGGACCACATA
2363911 GAACCCTCGA
Statistics
Matches: 54, Mismatches: 20, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
20 3 0.06
21 51 0.94
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.25
Consensus pattern (21 bp):
AAGGACCACATATATGTTCCA
Found at i:2364243 original size:14 final size:15
Alignment explanation
Indices: 2364224--2364253 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2364214 TATATCATGG
2364224 TCATATAG-CATGTA
1 TCATATAGACATGTA
2364238 TCATATAGACATGTA
1 TCATATAGACATGTA
2364253 T
1 T
2364254 TCTCATGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (15 bp):
TCATATAGACATGTA
Found at i:2364759 original size:20 final size:18
Alignment explanation
Indices: 2364734--2364786 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 18
2364724 TTATTTCAAA
2364734 ATGGTATCGATACTTACCTC
1 ATGGTATCGATAC-TACC-C
*
2364754 ATGGTATTGATACTACCC
1 ATGGTATCGATACTACCC
2364772 ATTAGGTATCGATAC
1 A-T-GGTATCGATAC
2364787 CCCTTGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 2 0.07
19 5 0.17
20 22 0.76
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (18 bp):
ATGGTATCGATACTACCC
Found at i:2367956 original size:20 final size:21
Alignment explanation
Indices: 2367927--2367979 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
2367917 ATAATTTGTC
* *
2367927 CCGAAAGACCACATATATG-T
1 CCGAATGACCACATAGATGTT
2367947 CCGAATGACCACATAGATGTT
1 CCGAATGACCACATAGATGTT
2367968 CCGAATGACCAC
1 CCGAATGACCAC
2367980 TCCTTAAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (21 bp):
CCGAATGACCACATAGATGTT
Found at i:2368079 original size:21 final size:21
Alignment explanation
Indices: 2367985--2368080 Score: 66
Period size: 21 Copynumber: 4.6 Consensus size: 21
2367975 ACCACTCCTT
* **
2367985 AAGGATCACATATATATTACA
1 AAGGACCACATATATATCCCA
* * * **
2368006 AAGGACCAAATATGTGTCCTG
1 AAGGACCACATATATATCCCA
* * * *
2368027 AAGAACCGCATATATGTTCCA
1 AAGGACCACATATATATCCCA
**
2368048 AAGGATTACATATATATCCCA
1 AAGGACCACATATATATCCCA
2368069 AAGGACCACATA
1 AAGGACCACATA
2368081 GAACCCTCGA
Statistics
Matches: 52, Mismatches: 23, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.24
Consensus pattern (21 bp):
AAGGACCACATATATATCCCA
Found at i:2368848 original size:23 final size:20
Alignment explanation
Indices: 2368798--2368851 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
2368788 ACTTTGAGTA
*
2368798 ATATCGATACCCCATGTATG
1 ATATCGATACCCCATCTATG
* *
2368818 GTACCGATACTTCCCTATCTATG
1 ATATCGATAC--CCC-ATCTATG
2368841 ATATCGATACC
1 ATATCGATACC
2368852 AAACCTGGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
20 8 0.31
21 1 0.04
22 3 0.12
23 14 0.54
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (20 bp):
ATATCGATACCCCATCTATG
Found at i:2372157 original size:12 final size:12
Alignment explanation
Indices: 2372122--2372159 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
2372112 ATGTTAAGTT
2372122 AAACACAATTCAA
1 AAAC-CAATTCAA
*
2372135 AAA-CAACTCAA
1 AAACCAATTCAA
2372146 AAACCAATTCAA
1 AAACCAATTCAA
2372158 AA
1 AA
2372160 GAATTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 10 0.45
12 9 0.41
13 3 0.14
ACGTcount: A:0.63, C:0.24, G:0.00, T:0.13
Consensus pattern (12 bp):
AAACCAATTCAA
Found at i:2373262 original size:3 final size:3
Alignment explanation
Indices: 2373254--2373301 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
2373244 TGTCTGAGTT
* *
2373254 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA ATA ATA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2373300 TT
1 TT
2373302 TTTACATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2374191 original size:2 final size:2
Alignment explanation
Indices: 2374184--2374225 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2374174 TGTATGTTGG
2374184 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
2374226 TGGATGCCAA
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:2377701 original size:115 final size:113
Alignment explanation
Indices: 2377499--2377738 Score: 426
Period size: 115 Copynumber: 2.1 Consensus size: 113
2377489 GTAACTTACC
* * *
2377499 TTTTTTAATAAATTCGAGATCAATATTGATCATTAAAAACAAAGACATGTGAAAAGAGGATCTTA
1 TTTTTTTATAAATTCGAGAACAATATTGATCATTAAAAACAAAGACACGTGAAAAGAGGATCTTA
*
2377564 TGTTTATTTAGATGATTGTGAAATTTAAAATATTAAATAATAATTCAT
66 TGTTTATTTAGATGATTGTGAAATTTAAAATAATAAATAATAATTCAT
2377612 ATTTTTTTAGTAAATTCGAGAACAATATTGATCATTAAAAACAAAGACACGTGAAAAGAGGATCT
1 -TTTTTTTA-TAAATTCGAGAACAATATTGATCATTAAAAACAAAGACACGTGAAAAGAGGATCT
2377677 TATGTTTATTTAGATGATTGTGAAATTTAAAATAATAAATAATAATTCAT
64 TATGTTTATTTAGATGATTGTGAAATTTAAAATAATAAATAATAATTCAT
2377727 TTTTTTTATAAA
1 TTTTTTTATAAA
2377739 CGCATACGAA
Statistics
Matches: 121, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
113 4 0.03
114 15 0.12
115 102 0.84
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.38
Consensus pattern (113 bp):
TTTTTTTATAAATTCGAGAACAATATTGATCATTAAAAACAAAGACACGTGAAAAGAGGATCTTA
TGTTTATTTAGATGATTGTGAAATTTAAAATAATAAATAATAATTCAT
Found at i:2385452 original size:182 final size:180
Alignment explanation
Indices: 2385139--2385797 Score: 903
Period size: 182 Copynumber: 3.7 Consensus size: 180
2385129 GATACAAATA
* * * * *
2385139 AAAAATGTATCGATCCATAGCAATATAACAGATAAAAATATAACAAAACCAGTCTCGAAATGATC
1 AAAAATGTATCGATCCATAACAATATAACAGATAAAAATATGATAAAACCGGTCTCAAAATGA-C
* * *
2385204 -AAACCGGTAAAGCGCTACCGTATATGTTGAAAGTGTCGATACTTTATTATAAGCATCGACACTT
65 AAAACCGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGACACTT
* *
2385268 TTGGAATTTAAAAGAAAATCAGTAATAGCGCCTACAAAGTATTGATACTTTAT
130 TTGGAATTTAAAAGAAAA-CAGTAATAGCGCCTA-AAAGTGTCGATACTTTAT
*
2385321 AAAAATGTATCGATCCATAACAATATAACATG-TAAAAATATGATAAAATCGGTCTCAAAATGAC
1 AAAAATGTATCGATCCATAACAATATAACA-GATAAAAATATGATAAAACCGGTCTCAAAATGAC
* *
2385385 AAAACCGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATATTTTATTATAAGTATCGAAACTT
65 AAAACCGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGACACTT
*
2385450 TTGGAATTTAAAAGACAAGCAGTAATAGCG------AGTGTCGATACTTTAT
130 TTGGAATTTAAAAGA-AAACAGTAATAGCGCCTAAAAGTGTCGATACTTTAT
* ** *
2385496 AAAAACGTATTAAT-CATTAACAATATAACATG-TAAAAATATGATAAAACTGGTCTCAAAATGA
1 AAAAATGTATCGATCCA-TAACAATATAACA-GATAAAAATATGATAAAACCGGTCTCAAAATGA
* * * *
2385559 CAAAACCGCTAAAGTGCTACCGGATATGTTGAAAGTGTCGATATTTTATTATGAGTATCGACACT
64 CAAAACCGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGACACT
2385624 TTTGGAATTTAAAAGACAAACAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
129 TTTGGAATTTAAAAGA-AAACAGTAATAGCGCCTA-AAAGTGTCGATACTTTAT
* * *
2385678 AAAAATGTATCGATCCATAACAATATAATAGATAAAAATATGACAAAAACCGGTCTCGAAATGAC
1 AAAAATGTATCGATCCATAACAATATAACAGATAAAAATATGA-TAAAACCGGTCTCAAAATGAC
2385743 AAAACCGGTAAAGTA-CTACCGGATATGTTGAAAGTGTCGATACTTTA--ATAAGTAT
65 AAAACCGGTAAAG-AGCTACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGTAT
2385798 GCGTAATAAA
Statistics
Matches: 427, Mismatches: 35, Indels: 31
0.87 0.07 0.06
Matches are distributed among these distances:
174 2 0.00
175 160 0.37
181 9 0.02
182 190 0.44
183 66 0.15
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (180 bp):
AAAAATGTATCGATCCATAACAATATAACAGATAAAAATATGATAAAACCGGTCTCAAAATGACA
AAACCGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGACACTTT
TGGAATTTAAAAGAAAACAGTAATAGCGCCTAAAAGTGTCGATACTTTAT
Found at i:2391001 original size:200 final size:200
Alignment explanation
Indices: 2390472--2391008 Score: 799
Period size: 200 Copynumber: 2.7 Consensus size: 200
2390462 AACAGATGTA
* * **
2390472 TCGAAACAGTTATAAAAAGTATCGATCTGAAAAACATCGAAACCCATAATTATAATGTAATAGGT
1 TCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGT
* * *
2390537 AATTTTTCAATGTAATCAA-TATAAATATACCGGTTTTATGAGAGAATAAGT-ATACTTAATATA
66 AATTTTTCAATGTAA-CAAGTATAAATATACCGGTTTTATGAGAGAATAGGTCA-ACATAATGTA
*
2390600 TCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAAGGTGCACACA
129 TCGACACTTGTGGAATTTGTATCGATACTTTTTGTCCAGAATGAATGCCCAAAAAGGTGCACACA
2390665 TAAAGTG
194 TAAAGTG
* *
2390672 TCGATACATTTATAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATGATGTAATAGGT
1 TCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGT
** * * *
2390737 AATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTATATTATGTATC
66 AATTTTTCAATGTAACAAGTATAAATATACCGGTTTTATGAGAGAATAGGTCAACATAATGTATC
* *
2390802 GACACTTGTGGAATTTGTATCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGTGCACGCATA
131 GACACTTGTGGAATTTGTATCGATACTTTTTGTCCAGAATGAATGCCCAAAAAGGTGCACACATA
2390867 AAGTG
196 AAGTG
* *
2390872 TCGATATATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGT
1 TCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGT
* * * * * * **
2390937 AAATTTTCAATGTAACAAGTATAAATATATCGGTTTAATTAAAAAAGCGGTCAACATAATGTATC
66 AATTTTTCAATGTAACAAGTATAAATATACCGGTTTTATGAGAGAATAGGTCAACATAATGTATC
2391002 GACACTT
131 GACACTT
2391009 TTTTAAATTT
Statistics
Matches: 301, Mismatches: 34, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
199 1 0.00
200 300 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (200 bp):
TCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGT
AATTTTTCAATGTAACAAGTATAAATATACCGGTTTTATGAGAGAATAGGTCAACATAATGTATC
GACACTTGTGGAATTTGTATCGATACTTTTTGTCCAGAATGAATGCCCAAAAAGGTGCACACATA
AAGTG
Found at i:2391344 original size:15 final size:15
Alignment explanation
Indices: 2391324--2391373 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
2391314 GTCTTTCTCA
2391324 AAGCTCTTCTCAACC
1 AAGCTCTTCTCAACC
2391339 AAGCTCTTCTCAACGAC
1 AAGCTCTTCTCAAC--C
*
2391356 AACCTCCTTCTCAACC
1 AAGCT-CTTCTCAACC
2391372 AA
1 AA
2391374 TTACTTCTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 14 0.45
16 3 0.10
17 5 0.16
18 9 0.29
ACGTcount: A:0.30, C:0.40, G:0.06, T:0.24
Consensus pattern (15 bp):
AAGCTCTTCTCAACC
Found at i:2395391 original size:15 final size:15
Alignment explanation
Indices: 2395371--2395400 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2395361 ATGTATCGAC
*
2395371 ACATAAAGTTTCCAA
1 ACATAAAGCTTCCAA
2395386 ACATAAAGCTTCCAA
1 ACATAAAGCTTCCAA
2395401 CAAAGTGTCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.23, G:0.07, T:0.23
Consensus pattern (15 bp):
ACATAAAGCTTCCAA
Found at i:2395606 original size:106 final size:106
Alignment explanation
Indices: 2395402--2395594 Score: 255
Period size: 106 Copynumber: 1.8 Consensus size: 106
2395392 AGCTTCCAAC
* * * * *
2395402 AAAGTGTCGATACATTTATTAAAAGTATCGATCCTAAAAACATCGAAACATATTATTATAAAGTA
1 AAAGTGTCGATACATATATTAAAAGTATCAATCCCAAAAACATCGAAACAGATAATTATAAAGTA
* ** * *
2395467 ATAGGTAAAATATACCGGTTTAATAAGAGAATATGTAAACA
66 ATAAGTAAAATATACCAATGTAACAAGAGAATATGTAAACA
*
2395508 AAAGTGTCGATACATATATTAAAAGTATCAATCCCAAAAACATCGAAACAGATAATTATAATGTA
1 AAAGTGTCGATACATATATTAAAAGTATCAATCCCAAAAACATCGAAACAGATAATTATAAAGTA
* *
2395573 ATAAGT-GAAT-TTCCAATGTAAC
66 ATAAGTAAAATATACCAATGTAAC
2395595 CGGTAGAAAT
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
104 7 0.09
105 3 0.04
106 64 0.86
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (106 bp):
AAAGTGTCGATACATATATTAAAAGTATCAATCCCAAAAACATCGAAACAGATAATTATAAAGTA
ATAAGTAAAATATACCAATGTAACAAGAGAATATGTAAACA
Found at i:2395876 original size:200 final size:199
Alignment explanation
Indices: 2395508--2396470 Score: 1414
Period size: 200 Copynumber: 4.8 Consensus size: 199
2395498 TATGTAAACA
* *
2395508 AAAGTGTCGATACATATATTAAAAGTATCAATCCCAAAAACATCGAAACAGATAATTATAATGTA
1 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
* *
2395573 ATAAGTGAATTTCCAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTCTACATAAT
66 ATAGGTAAATTTCCAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTCTACATAAT
*
2395638 GTATCGACACTTTTTAAATTTGTGTCGATACTTTTTTGTCCAGAATGAATATCAAACGGGGTGCA
131 GTATCGACACTTTTTAAATTTGTGTCGATAC-TTTTTGTCCAGAATGAATACCAAACGGGGTGCA
2395703 CGCAT
195 CGCAT
* *
2395708 AAAGTGTCGATGCATTTATTAAAAGTATCGATCCCAAAAACATCGAAACATATAATTATAATGTA
1 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
* *
2395773 ATAGGTAAATTTCCAATGTAACCGGGTAGAAATATACTGGTTAATTAGAAAACAGGTCTACATAA
66 ATAGGTAAATTTCCAATGTAACC-GGTAGAAATATACCGGTTAATTAGAAAATAGGTCTACATAA
* * *
2395838 TGTATCGACACTTTTTAAATTTGTGTCTATACTTTTTGTCCAGAATGAATGCCAAATGGGGTGCA
130 TGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATACCAAACGGGGTGCA
2395903 CGCAT
195 CGCAT
*
2395908 AAAGTGTCGATACATTTATCAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
1 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
* * * * * **
2395973 ATAGGTAAATTTTCAATGTAACTGGTAGATATATACCGGTTTAATTAGAAAAGAAGTAAACATAA
66 ATAGGTAAATTTCCAATGTAACCGGTAGAAATATACCGG-TTAATTAGAAAATAGGTCTACATAA
* * * * *
2396038 TGTATTGACACTTTTTAAA-GTGTGTCGATACTTTTTGTTCAGAATGAATACCCAACCGAGGTGC
130 TGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATA-CCAAACGGGGTGC
2396102 ACGCAT
194 ACGCAT
* * * *
2396108 AAAGTGTTGATACATTTATTAAAAGTAACGATCCTAAAAACATCGAAACATATAATTATAATGTA
1 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
* * *
2396173 ATAGGTAAAATTCCAATGTAACTGATAGAAATATACCGGTTAATTAGAAAATAGGTCTACATAAT
66 ATAGGTAAATTTCCAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTCTACATAAT
* * *
2396238 GTATTGACACTTTTTAAATTTTTGTCGATACTTTTTGTCCAGAATGAATGCCAAA-GGGGTGCAC
131 GTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATACCAAACGGGGTGCAC
2396302 GCAT
196 GCAT
* * * *
2396306 AAAGTATTGATACA-TT-TTAAAATGTATCGATCCCAAAAACATCGAAACCGATAATTACAATGT
1 AAAGTGTCGATACATTTATTAAAA-GTATCGATCCCAAAAACATCGAAACAGATAATTATAATGT
** * * * *
2396369 AATAGGTAAATTAACAATGTAACCGGTACAAATTTACCGGTTTTATGAGAAAATAGGTCTACATA
65 AATAGGTAAATTTCCAATGTAACCGGTAGAAATATACCGG-TTAATTAGAAAATAGGTCTACATA
* *
2396434 ATGTATCGACACTTTTTAAAATTGTATCGAT-CTTTTT
129 ATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTT
2396471 TTTTAAAGTA
Statistics
Matches: 688, Mismatches: 69, Indels: 15
0.89 0.09 0.02
Matches are distributed among these distances:
196 6 0.01
197 76 0.11
198 74 0.11
199 85 0.12
200 377 0.55
201 70 0.10
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (199 bp):
AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
ATAGGTAAATTTCCAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTCTACATAAT
GTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATACCAAACGGGGTGCAC
GCAT
Found at i:2396396 original size:20 final size:19
Alignment explanation
Indices: 2396358--2396396 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2396348 CGAAACCGAT
*
2396358 AATTACAATGTAATAGGTA
1 AATTACAATGTAACAGGTA
*
2396377 AATTAACAATGTAACCGGTA
1 AATT-ACAATGTAACAGGTA
2396397 CAAATTTACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.28
Consensus pattern (19 bp):
AATTACAATGTAACAGGTA
Found at i:2398008 original size:19 final size:19
Alignment explanation
Indices: 2397984--2398050 Score: 116
Period size: 19 Copynumber: 3.5 Consensus size: 19
2397974 ATATAGGGGA
* *
2397984 AATTTTGTATACGATTCAT
1 AATTTTGTATACAATTTAT
2398003 AATTTTGTATACAATTTAT
1 AATTTTGTATACAATTTAT
2398022 AATTTTGTATACAATTTAT
1 AATTTTGTATACAATTTAT
2398041 AATTTTGTAT
1 AATTTTGTAT
2398051 GTGAATGTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.34, C:0.06, G:0.07, T:0.52
Consensus pattern (19 bp):
AATTTTGTATACAATTTAT
Found at i:2400894 original size:16 final size:16
Alignment explanation
Indices: 2400873--2400903 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2400863 AAATATACAG
2400873 GTTAATTAGAAAACAT
1 GTTAATTAGAAAACAT
2400889 GTTAATTAGAAAACA
1 GTTAATTAGAAAACA
2400904 GGTCAACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (16 bp):
GTTAATTAGAAAACAT
Found at i:2401252 original size:199 final size:196
Alignment explanation
Indices: 2400896--2401510 Score: 686
Period size: 199 Copynumber: 3.1 Consensus size: 196
2400886 CATGTTAATT
* * * ** * * *
2400896 AGAAAACAGGTCAACATAATGTATCAAAACTTGTGGAATTTGTGTCGAGACTTATGTCCAGAATG
1 AGAAAATAGGTCAACATAATGTATCGACACTT-TTTAAATTGTGTCGATACTTTTGTCCAGAATG
** * * * *
2400961 AAT-TCCCAAACGGGGTGCACGCGTAAAGTGTTGATACATTTATTAAAATTATCTATCCAAAAAA
65 AATGT--CAAACGAAGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCAATCCAAAAAA
** **
2401025 CATCAAAAATGATAATTATAATGTAATAGGTAAATTTACTGTGTAACCGTATAAATATACCGGTT
128 CATC-AAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGTATAAATATACCGGTT
2401090 TTATG
192 TTATG
*
2401095 AGAGAATAGGTCAACATAATGTATCGACACTTTTTAAACTTGTGTCGATACATTTTGTCCAGAAT
1 AGAAAATAGGTCAACATAATGTATCGACACTTTTTAAA-TTGTGTCGATAC-TTTTGTCCAGAAT
* *
2401160 GAATGTCAAACGAAGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAAC
64 GAATGTCAAACGAAGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCAATCCAAAAAAC
* * * * *
2401225 ATCACAACCGATAATTACAAAGTAATAGGTAAATTTACAATGTACCCGGTAGAAATATATCGGTT
129 ATCA-AACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACC-GTATAAATATACCGGTT
2401290 TTATG
192 TTATG
* *
2401295 AGAAAATAAGTCTACATAATGTATCGACACTTTTTAAGATTGTGTCGATACGTTTT-TCCAGAAT
1 AGAAAATAGGTCAACATAATGTATCGACACTTTTTAA-ATTGTGTCGATAC-TTTTGTCCAGAAT
* * * * **
2401359 GAATG-CCAAC-AAGGTGCATGAATAAAGTGTCGATACATTTA--AAATTGTATCAATCCGGAAA
64 GAATGTCAAACGAA-GTGCACGCATAAAGTGTCGATACATTTATTAAA-AGTATCAATCCAAAAA
* * *
2401420 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTGCAATGTTACCGATATAAATATACTGG
127 ACATC-AAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCG-TATAAATATACCGG
*
2401485 -TTTAGTT
190 TTTTA-TG
* *
2401492 AAAAAATAGGTCAATATAA
1 AGAAAATAGGTCAACATAA
2401511 GCGCTATCTA
Statistics
Matches: 356, Mismatches: 49, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
196 8 0.02
197 83 0.23
198 35 0.10
199 142 0.40
200 86 0.24
201 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (196 bp):
AGAAAATAGGTCAACATAATGTATCGACACTTTTTAAATTGTGTCGATACTTTTGTCCAGAATGA
ATGTCAAACGAAGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCAATCCAAAAAACAT
CAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGTATAAATATACCGGTTTTAT
G
Found at i:2401594 original size:64 final size:64
Alignment explanation
Indices: 2401525--2401644 Score: 213
Period size: 64 Copynumber: 1.9 Consensus size: 64
2401515 TATCTATTAC
* * *
2401525 ATTATATAAGCGCTGCCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGCCTATTTT
1 ATTATATAAGCGCTACCTAATATGTTATTATAATTGATAATATTTCCGGTTAAATGCCTATTTT
2401589 ATTATATAAGCGCTACCTAATATGTTATTATAATTGATAATATTTCCGGTTAAATG
1 ATTATATAAGCGCTACCTAATATGTTATTATAATTGATAATATTTCCGGTTAAATG
2401645 ATATAACATA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.42
Consensus pattern (64 bp):
ATTATATAAGCGCTACCTAATATGTTATTATAATTGATAATATTTCCGGTTAAATGCCTATTTT
Found at i:2402071 original size:10 final size:10
Alignment explanation
Indices: 2402056--2402087 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
2402046 TAATTTAGAA
2402056 ACTCGATCCG
1 ACTCGATCCG
2402066 ACTCGATCCG
1 ACTCGATCCG
2402076 ACTCGATCCG
1 ACTCGATCCG
2402086 AC
1 AC
2402088 CCGAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.22, C:0.41, G:0.19, T:0.19
Consensus pattern (10 bp):
ACTCGATCCG
Found at i:2406112 original size:3 final size:3
Alignment explanation
Indices: 2406104--2406144 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2406094 TAAAATATTT
2406104 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2406145 GTAAGATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2410902 original size:27 final size:27
Alignment explanation
Indices: 2410864--2410933 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
2410854 CTTAAGGAGT
* *
2410864 GGTCCTTCGGGACAAATATAGTACATA
1 GGTCCTTCGGGACAAATACAATACATA
2410891 GGTCCTTCGGGACAAATACAATACATA
1 GGTCCTTCGGGACAAATACAATACATA
*
2410918 GGTCATTCGGGACAAA
1 GGTCCTTCGGGACAAA
2410934 ATTCATATGC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (27 bp):
GGTCCTTCGGGACAAATACAATACATA
Found at i:2423130 original size:20 final size:20
Alignment explanation
Indices: 2423105--2423148 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
2423095 ATATGAATCA
2423105 AATGAA-TAATATCGATACT
1 AATGAAGTAATATCGATACT
* *
2423124 GAATGAAGTAGTATTGATACT
1 -AATGAAGTAATATCGATACT
2423145 AATG
1 AATG
2423149 TGGAGGTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (20 bp):
AATGAAGTAATATCGATACT
Found at i:2423655 original size:15 final size:15
Alignment explanation
Indices: 2423635--2423704 Score: 104
Period size: 15 Copynumber: 4.7 Consensus size: 15
2423625 ATTTTATTAG
*
2423635 TATGTGAATATGTTA
1 TATGTGAATATGTTC
2423650 TATGTGAATATGTTC
1 TATGTGAATATGTTC
* *
2423665 TATGTGAAAATGTTT
1 TATGTGAATATGTTC
*
2423680 TATGTGAATGTGTTC
1 TATGTGAATATGTTC
2423695 TATGTGAATA
1 TATGTGAATA
2423705 AATGATACTG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 48 1.00
ACGTcount: A:0.30, C:0.03, G:0.21, T:0.46
Consensus pattern (15 bp):
TATGTGAATATGTTC
Found at i:2423892 original size:24 final size:24
Alignment explanation
Indices: 2423828--2423884 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
2423818 CTTTCGGGAT
2423828 AATTCTATGTGGAACTTCGGTGCA
1 AATTCTATGTGGAACTTCGGTGCA
* *
2423852 TATTCTATGT-GACACTTCGGTGTA
1 AATTCTATGTGGA-ACTTCGGTGCA
2423876 AATTCTATG
1 AATTCTATG
2423885 CGGTACTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 2 0.07
24 27 0.93
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.39
Consensus pattern (24 bp):
AATTCTATGTGGAACTTCGGTGCA
Found at i:2424643 original size:18 final size:18
Alignment explanation
Indices: 2424620--2424659 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
2424610 TGTATTCTCT
2424620 TACACATACATTGGGCTA
1 TACACATACATTGGGCTA
2424638 TACACATACATTGGGCTA
1 TACACATACATTGGGCTA
2424656 TACA
1 TACA
2424660 AATAAATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (18 bp):
TACACATACATTGGGCTA
Found at i:2435529 original size:315 final size:315
Alignment explanation
Indices: 2434957--2435584 Score: 985
Period size: 315 Copynumber: 2.0 Consensus size: 315
2434947 CTCTCAAACC
2434957 TACTGGGATAAATTTTCAATTGCGCTTTTCTCTTAATCCACCCAGCCGATTTCAAATCTATCTTC
1 TACTGGGATAAATTTTCAATTGCGCTTTTCTCTTAATCCACCCAGCCGATTTCAAATCTATCTTC
* * * *
2435022 ACCATTTTTCTTATCTTTTCCTCCTCTTCTTAACGAGCCTTCATCCATCAAGATCAAACCACAAC
66 ACCATCTTTCTTATCTTTTCATCCTCTTCCTAACGAGCCTTCATCCATCAAGATCAAACCAAAAC
* * * * * *
2435087 ACATTGGGTGCCTATTACCAGGGATGATAACAACTAAAGCCCTCTTAAAACCCTAATCTTTACTG
131 ACATTGGGTGCCTATTACAAAGGAAGATAACAACTAAAGCCCTCCTAAAACCCTAATATTTACCG
2435152 CAAACACCTAAACCTCCATTCAAGACCATTCATTTTTTCATCGAGTCTAGAGCCTTCTTAGGTTT
196 CAAACACCTAAACCTCCATTCAAGACCATTCATTTTTTCATCGAGTCTAGAGCCTTCTTAGGTTT
* * *
2435217 GTTCCCTCGATAAGA-TACTGTTCACATCATATGCTT-CTGCTTCTCTATCAATTAG
261 -TTCCCTCGATAAGAGAACCGTTCAAATCATATG-TTGCTGCTTCTCTATCAATTAG
* *
2435272 TACTGGGATAAATTTTCAATTGCGCTTTTCTCTTAATCCACCCATCCGATTTCAAATTTATCTTC
1 TACTGGGATAAATTTTCAATTGCGCTTTTCTCTTAATCCACCCAGCCGATTTCAAATCTATCTTC
*
2435337 ACCATCTTTCTTATCTTTTCATCCTCTTCCTAACGAGCCATT-ATCCATCAATATCAAACCAAAA
66 ACCATCTTTCTTATCTTTTCATCCTCTTCCTAACGAGCC-TTCATCCATCAAGATCAAACCAAAA
* *
2435401 CACATTGGGTGCCTATTACAAAGGAAGATAACAACTAAAGTCCTCCTAAAACCCTAATATTTGCC
130 CACATTGGGTGCCTATTACAAAGGAAGATAACAACTAAAGCCCTCCTAAAACCCTAATATTTACC
* * *
2435466 GCCACCACCT-AACCTCCATTCAAGACCATTCATTTTTTTCATCGAGTCTATAGCCTTCTTAGGT
195 GCAAACACCTAAACCTCCATTCAAGACCATTCA-TTTTTTCATCGAGTCTAGAGCCTTCTTAGGT
* *
2435530 TTTTCCCTCGATAAGAGAACCGTTCAAATCATATGTTGTTGCTTCTCTATTAATT
259 TTTTCCCTCGATAAGAGAACCGTTCAAATCATATGTTGCTGCTTCTCTATCAATT
2435585 GGTATCAGAC
Statistics
Matches: 286, Mismatches: 23, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
314 38 0.13
315 246 0.86
316 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.35
Consensus pattern (315 bp):
TACTGGGATAAATTTTCAATTGCGCTTTTCTCTTAATCCACCCAGCCGATTTCAAATCTATCTTC
ACCATCTTTCTTATCTTTTCATCCTCTTCCTAACGAGCCTTCATCCATCAAGATCAAACCAAAAC
ACATTGGGTGCCTATTACAAAGGAAGATAACAACTAAAGCCCTCCTAAAACCCTAATATTTACCG
CAAACACCTAAACCTCCATTCAAGACCATTCATTTTTTCATCGAGTCTAGAGCCTTCTTAGGTTT
TTCCCTCGATAAGAGAACCGTTCAAATCATATGTTGCTGCTTCTCTATCAATTAG
Found at i:2439807 original size:21 final size:21
Alignment explanation
Indices: 2439777--2439852 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
2439767 TATCCCGTAT
*
2439777 GACCACATATATGTTCCAAAG
1 GACCAAATATATGTTCCAAAG
* * *
2439798 GACCAAATATATATCCCTAAG
1 GACCAAATATATGTTCCAAAG
2439819 GA-CAACATATATGTTCCAAAG
1 GACCAA-ATATATGTTCCAAAG
* *
2439840 GATCACATATATG
1 GACCAAATATATG
2439853 CCCCGAAGGA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 3 0.07
21 40 0.89
22 2 0.04
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (21 bp):
GACCAAATATATGTTCCAAAG
Found at i:2439861 original size:21 final size:21
Alignment explanation
Indices: 2439780--2439862 Score: 60
Period size: 21 Copynumber: 4.0 Consensus size: 21
2439770 CCCGTATGAC
** *
2439780 CACATATATGTTCCAAAGGAC
1 CACATATATGCCCCAAAGGAT
* ** *
2439801 CAAATATATATCCCTAAGGA-
1 CACATATATGCCCCAAAGGAT
**
2439821 CAACATATATGTTCCAAAGGAT
1 C-ACATATATGCCCCAAAGGAT
*
2439843 CACATATATGCCCCGAAGGA
1 CACATATATGCCCCAAAGGA
2439863 CACCGTAGAA
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
20 1 0.02
21 47 0.96
22 1 0.02
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (21 bp):
CACATATATGCCCCAAAGGAT
Found at i:2439862 original size:42 final size:42
Alignment explanation
Indices: 2439781--2439864 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
2439771 CCGTATGACC
* *
2439781 ACATATATGTTCCAAAGGACCAAATATATATCCCTAAGGACA
1 ACATATATGTTCCAAAGGACCAAATATATACCCCGAAGGACA
* * *
2439823 ACATATATGTTCCAAAGGATCACATATATGCCCCGAAGGACA
1 ACATATATGTTCCAAAGGACCAAATATATACCCCGAAGGACA
2439865 CCGTAGAACC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (42 bp):
ACATATATGTTCCAAAGGACCAAATATATACCCCGAAGGACA
Found at i:2456085 original size:21 final size:21
Alignment explanation
Indices: 2456059--2456102 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2456049 CAACAAGTTC
2456059 TTTGTAGTTGCCAT-AATATCT
1 TTTGTAGTTGCCATGAA-ATCT
*
2456080 TTTGTAGTTGGCATGAAATCT
1 TTTGTAGTTGCCATGAAATCT
2456101 TT
1 TT
2456103 AAAGCATCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.23, C:0.11, G:0.18, T:0.48
Consensus pattern (21 bp):
TTTGTAGTTGCCATGAAATCT
Found at i:2456697 original size:15 final size:15
Alignment explanation
Indices: 2456677--2456713 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
2456667 TTGTTTTCAT
2456677 CTCTTCTCATTTTCC
1 CTCTTCTCATTTTCC
*
2456692 CTCTTCTCATTTTGC
1 CTCTTCTCATTTTCC
2456707 CTCTTCT
1 CTCTTCT
2456714 TTCTTCTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.38, G:0.03, T:0.54
Consensus pattern (15 bp):
CTCTTCTCATTTTCC
Found at i:2458666 original size:20 final size:20
Alignment explanation
Indices: 2458643--2458691 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2458633 TGACCTTTCA
*
2458643 GTATCGTTACTCAACCT-CTG
1 GTATCGATA-TCAACCTGCTG
2458663 GTATCGATATCAACCTGCTG
1 GTATCGATATCAACCTGCTG
2458683 GTATCGATA
1 GTATCGATA
2458692 CCCTCAACTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (20 bp):
GTATCGATATCAACCTGCTG
Found at i:2462803 original size:79 final size:79
Alignment explanation
Indices: 2462713--2463212 Score: 743
Period size: 79 Copynumber: 6.3 Consensus size: 79
2462703 TTTAAACTTT
*
2462713 GGCATCCTTTCATGCCAATAATGCACCCATATGAATTATTCTTTTATGTCGATAATGTACCCATA
1 GGCATCCTTTCATGCCAATAATGCACCCATATGAATTATTCTTTTATGCCGATAATGTACCCATA
2462778 TACATTTCAGCTAA
66 TACATTTCAGCTAA
* *
2462792 GGCATCATTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCCGATAATGTACCCATA
1 GGCATCCTTTCATGCCAATAATGCACCCATATGAATTATTCTTTTATGCCGATAATGTACCCATA
* *
2462857 TATATTTCAGCTAT
66 TACATTTCAGCTAA
* *
2462871 GGCATCCTTTCATGCCAATAATGCACCCATATGAATTATTTTTTTATGTCGATAATGTACCCATA
1 GGCATCCTTTCATGCCAATAATGCACCCATATGAATTATTCTTTTATGCCGATAATGTACCCATA
2462936 TACATTTCAGCTAA
66 TACATTTCAGCTAA
* * ** *
2462950 GACATCCTTTCATGCCAATAATGCACCTATATGCTTTATTCTTTTATGCCGATAATATACCCATA
1 GGCATCCTTTCATGCCAATAATGCACCCATATGAATTATTCTTTTATGCCGATAATGTACCCATA
* *
2463015 TATATTTAAGCTAA
66 TACATTTCAGCTAA
* * * *
2463029 GGCATCATTTCATGCCAATAATGCACCTATAT-ACTTTATTCTTTTATGCCGATAATGTACTCAT
1 GGCATCCTTTCATGCCAATAATGCACCCATATGA-ATTATTCTTTTATGCCGATAATGTACCCAT
2463093 ATACATTTC-GACTAA
65 ATACATTTCAG-CTAA
** **
2463108 GGTGTCCTTTCATGCCAATAATGCACCCATATTCATTATTCTTTTATGCCGATAATGTACCCATA
1 GGCATCCTTTCATGCCAATAATGCACCCATATGAATTATTCTTTTATGCCGATAATGTACCCATA
*
2463173 TACATTTTAGCTAA
66 TACATTTCAGCTAA
**
2463187 GGCATCCTTTCATAACAATAATGCAC
1 GGCATCCTTTCATGCCAATAATGCAC
2463213 ACAAAGTGCC
Statistics
Matches: 378, Mismatches: 39, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
78 1 0.00
79 376 0.99
80 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (79 bp):
GGCATCCTTTCATGCCAATAATGCACCCATATGAATTATTCTTTTATGCCGATAATGTACCCATA
TACATTTCAGCTAA
Found at i:2463163 original size:34 final size:34
Alignment explanation
Indices: 2463114--2463178 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
2463104 CTAAGGTGTC
*
2463114 CTTTCATGCCAATAATGCACCCATATTCATTATT
1 CTTTCATGCCAATAATGCACCCATATACATTATT
* * *
2463148 CTTTTATGCCGATAATGTACCCATATACATT
1 CTTTCATGCCAATAATGCACCCATATACATT
2463179 TTAGCTAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (34 bp):
CTTTCATGCCAATAATGCACCCATATACATTATT
Found at i:2469896 original size:19 final size:19
Alignment explanation
Indices: 2469872--2469945 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 19
2469862 ATACAAAAAT
*
2469872 GGTATCGATACCATAATAG
1 GGTATCGATACCATAGTAG
2469891 GGTATC-AGTACCATAGTAG
1 GGTATCGA-TACCATAGTAG
* *
2469910 GGTAATATTGATACCATGGTAAG
1 GG---TATCGATACCATAGT-AG
2469933 GGTATCGATACCA
1 GGTATCGATACCA
2469946 GGCAACATTG
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
18 1 0.02
19 18 0.40
20 10 0.22
22 11 0.24
23 5 0.11
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (19 bp):
GGTATCGATACCATAGTAG
Found at i:2470713 original size:46 final size:46
Alignment explanation
Indices: 2470439--2470695 Score: 390
Period size: 46 Copynumber: 5.6 Consensus size: 46
2470429 TAATTAAAAT
2470439 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
*
2470485 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATACATTAAG
1 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
* * * * *
2470531 GCATGAAAAGATGATATAGTTAAAATGCATGAAATGATACATTAAG
1 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
*
2470577 GCATGAAAGGATGCCATAATTAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
* * *
2470623 GCATGAAATGATGCCATAATTAAAATGCATGAAAGAATGCATTAAG
1 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
* *
2470669 TCATGAAAGGAT-ACCATAATTTAAATG
1 GCATGAAAGGATGA-CATAATTAAAATG
2470696 TATAAATTGA
Statistics
Matches: 193, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
46 193 1.00
ACGTcount: A:0.46, C:0.09, G:0.21, T:0.24
Consensus pattern (46 bp):
GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
Found at i:2476867 original size:20 final size:20
Alignment explanation
Indices: 2476842--2476891 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2476832 TAGTAATCAA
2476842 TATCGATACCAAAGGGGAA-G
1 TATCGATACCAAA-GGGAAGG
*
2476862 TATCGATACCGAAGGGAAGG
1 TATCGATACCAAAGGGAAGG
*
2476882 TATCAATACC
1 TATCGATACC
2476892 TTTTCAGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (20 bp):
TATCGATACCAAAGGGAAGG
Found at i:2477535 original size:20 final size:20
Alignment explanation
Indices: 2477508--2477723 Score: 81
Period size: 20 Copynumber: 9.6 Consensus size: 20
2477498 TAATTAAAAT
2477508 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
2477528 GTATGAAAGGATGACATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
2477554 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* ** *
2477574 GCATGAAAATATGATATAATTAAAAT
1 GCATG--AA-AGGAT-GCATT--AAG
* * *
2477600 CCATGAAATGATACATTAAG
1 GCATGAAAGGATGCATTAAG
*
2477620 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
*
2477646 GCATGAAAGGATACATTAAG
1 GCATGAAAGGATGCATTAAG
* *
2477666 GCATGAAATGATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
*
2477692 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
2477712 TCATGAAAGGAT
1 GCATGAAAGGAT
2477724 ACCATAATTT
Statistics
Matches: 148, Mismatches: 24, Indels: 48
0.67 0.11 0.22
Matches are distributed among these distances:
20 56 0.38
21 3 0.02
22 14 0.09
23 9 0.06
24 14 0.09
25 3 0.02
26 49 0.33
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.25
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:2477543 original size:46 final size:46
Alignment explanation
Indices: 2477482--2477756 Score: 374
Period size: 46 Copynumber: 6.0 Consensus size: 46
2477472 TAATTAAAAT
2477482 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
*
2477528 GTATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
** * * * *
2477574 GCATGAAAATATGATATAATTAAAATCCATGAAATGATACATTAAG
1 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
* *
2477620 GCATGAAAGGATGCCATAATTAAAATGCATGAAAGGATACATTAAG
1 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
* * *
2477666 GCATGAAATGATGCCATAATTAAAATGCATGAAATGATGCATTAAG
1 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
* * * *
2477712 TCATGAAAGGAT-ACCATAATTTAAATGTAT-AAATGGATGTATTAA
1 GCATGAAAGGATGA-CATAATTAAAATGCATGAAA-GGATGCATTAA
2477757 TATGTGAAAA
Statistics
Matches: 203, Mismatches: 24, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
45 3 0.01
46 200 0.99
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.26
Consensus pattern (46 bp):
GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
Found at i:2483038 original size:24 final size:24
Alignment explanation
Indices: 2483005--2483056 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2482995 TAGAGTATCG
* * *
2483005 ATACTCATATCAACACCCGCATCA
1 ATACTAATATCAACACCCACACCA
*
2483029 ATACTAATATCAATACCCACACCA
1 ATACTAATATCAACACCCACACCA
2483053 ATAC
1 ATAC
2483057 CAGCATCAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.35, G:0.02, T:0.21
Consensus pattern (24 bp):
ATACTAATATCAACACCCACACCA
Found at i:2487131 original size:15 final size:16
Alignment explanation
Indices: 2487108--2487154 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
2487098 CTAGGTTTAG
*
2487108 TAATCGATTTTT-ATT
1 TAATTGATTTTTAATT
2487123 TAATTGATTTTTTAATT
1 TAATTGA-TTTTTAATT
*
2487140 AAATTGA-TTTTAATT
1 TAATTGATTTTTAATT
2487155 AATAAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 14 0.50
16 5 0.18
17 9 0.32
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (16 bp):
TAATTGATTTTTAATT
Found at i:2487136 original size:16 final size:17
Alignment explanation
Indices: 2487115--2487150 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2487105 TAGTAATCGA
*
2487115 TTTTT-ATTTAATTGAT
1 TTTTTAATTAAATTGAT
2487131 TTTTTAATTAAATTGAT
1 TTTTTAATTAAATTGAT
2487148 TTT
1 TTT
2487151 AATTAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTTAATTAAATTGAT
Found at i:2487155 original size:15 final size:15
Alignment explanation
Indices: 2487113--2487156 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
2487103 TTTAGTAATC
* *
2487113 GATTTTTATTTAATT
1 GATTTTAATTAAATT
2487128 GATTTTTTAATTAAATT
1 GA--TTTTAATTAAATT
2487145 GATTTTAATTAA
1 GATTTTAATTAA
2487157 TAAAAATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 12 0.48
17 13 0.52
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (15 bp):
GATTTTAATTAAATT
Found at i:2487279 original size:6 final size:6
Alignment explanation
Indices: 2487270--2487298 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2487260 TCGACTCGGA
2487270 CTCGAG CTCGAG CTCGAG CTCGA- CTCGAG
1 CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG
2487299 ATCTTAACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.17, C:0.34, G:0.31, T:0.17
Consensus pattern (6 bp):
CTCGAG
Found at i:2487285 original size:12 final size:11
Alignment explanation
Indices: 2487257--2487298 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
2487247 GGATCGAATG
2487257 GACTCGA-CTC
1 GACTCGAGCTC
2487267 GGACTCGAGCTC
1 -GACTCGAGCTC
2487279 GAGCTCGAGCTC
1 GA-CTCGAGCTC
2487291 GACTCGAG
1 GACTCGAG
2487299 ATCTTAACGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 15 0.52
12 14 0.48
ACGTcount: A:0.19, C:0.33, G:0.31, T:0.17
Consensus pattern (11 bp):
GACTCGAGCTC
Found at i:2491048 original size:18 final size:17
Alignment explanation
Indices: 2491016--2491050 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2491006 TTCAAATGTT
2491016 AATCTAAATTAAAACTA
1 AATCTAAATTAAAACTA
*
2491033 AATCTATAATTTAAACTA
1 AATCTA-AATTAAAACTA
2491051 TGAATCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (17 bp):
AATCTAAATTAAAACTA
Found at i:2491100 original size:11 final size:11
Alignment explanation
Indices: 2491083--2491158 Score: 64
Period size: 11 Copynumber: 6.5 Consensus size: 11
2491073 AACTTAACAT
2491083 TAAAAAAATAAA
1 TAAAAAAA-AAA
*
2491095 -AAAAAAACAA
1 TAAAAAAAAAA
*
2491105 TAATAAAAAAA
1 TAAAAAAAAAA
2491116 TAAGTAAAAAAAA
1 TAA--AAAAAAAA
2491129 GTAAAAAAACAACA
1 -TAAAAAAA-AA-A
*
2491143 TAAAATAAAAA
1 TAAAAAAAAAA
2491154 TAAAA
1 TAAAA
2491159 TAAACATGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
10 2 0.04
11 24 0.45
12 7 0.13
13 16 0.30
14 4 0.08
ACGTcount: A:0.80, C:0.04, G:0.03, T:0.13
Consensus pattern (11 bp):
TAAAAAAAAAA
Done.